[med-svn] [ncbi-blast+] 01/04: Imported Upstream version 2.3.0
Andreas Tille
tille at debian.org
Tue Apr 12 14:08:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ncbi-blast+.
commit 35cc89086e8448b35b6cb59f82bc35cb6f9240b3
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 12 14:52:30 2016 +0200
Imported Upstream version 2.3.0
---
c++/compilers/cygwin/build.sh | 6 +-
c++/compilers/msvc1000_prj/check.sh | 202 +-
.../msvc1000_prj/dll/third_party_dll_install.mak | 8 +-
.../static/build/corelib/xncbi.lib.vcxproj | 6 +
.../static/third_party_static_install.mak | 8 +-
.../msvc1000_prj/third_party_install.meta.mk | 18 +-
.../msvc900_prj/dll/third_party_dll_install.mak | 8 +-
.../static/third_party_static_install.mak | 8 +-
.../msvc900_prj/third_party_install.meta.mk | 18 +-
c++/compilers/unix/GCC.sh | 4 +-
c++/compilers/unix/ICC.sh | 2 +-
.../vs2012/dll/third_party_dll_install.mak | 8 +-
.../vs2012/static/third_party_static_install.mak | 8 +-
c++/compilers/vs2012/third_party_install.meta.mk | 18 +-
c++/compilers/vs2013/check.sh | 203 +-
c++/compilers/vs2013/configure.bat | 11 +-
.../gbench/gbench_install/gbench-install.vcxproj | 72 +-
.../vs2013/dll/third_party_dll_install.mak | 8 +-
.../vs2013/dll/third_party_msvcdll_install.vcxproj | 144 +-
c++/compilers/vs2013/make.bat | 7 +-
.../vs2013/static/build/corelib/xncbi.lib.vcxproj | 6 +
.../static/third_party_msvcstatic_install.vcxproj | 144 +-
.../vs2013/static/third_party_static_install.mak | 8 +-
c++/compilers/vs2013/third_party_install.meta.mk | 18 +-
c++/compilers/xCode/Application.applescript | 4 +-
c++/compilers/xcode30_prj/configure | 16 +-
c++/compilers/xcode30_prj/datatool.sh | 7 +-
c++/compilers/xcode30_prj/ptb.sh | 18 +-
.../UtilityProjects/PTB.xcodeproj/project.pbxproj | 16350 ++-
c++/compilers/xcode30_prj/xcodebuild.sh | 24 +
c++/include/algo/blast/api/bl2seq.hpp | 16 +-
.../algo/blast/api/blast_advprot_options.hpp | 4 +-
c++/include/algo/blast/api/blast_options.hpp | 2 +-
.../algo/blast/api/blast_options_builder.hpp | 10 +-
.../algo/blast/api/blast_options_handle.hpp | 4 +-
c++/include/algo/blast/api/blast_prot_options.hpp | 5 +-
c++/include/algo/blast/api/local_db_adapter.hpp | 12 +-
c++/include/algo/blast/api/psiblast_options.hpp | 4 +-
c++/include/algo/blast/api/remote_blast.hpp | 15 +-
c++/include/algo/blast/api/search_strategy.hpp | 5 +-
c++/include/algo/blast/api/seqsrc_multiseq.hpp | 6 +-
c++/include/algo/blast/api/tblastn_options.hpp | 3 +-
c++/include/algo/blast/api/traceback_stage.hpp | 5 +-
c++/include/algo/blast/api/uniform_search.hpp | 4 +-
c++/include/algo/blast/blastinput/blast_args.hpp | 44 +-
.../algo/blast/blastinput/blast_input_aux.hpp | 12 +-
.../algo/blast/blastinput/cmdline_flags.hpp | 7 +-
.../algo/blast/blastinput/deltablast_args.hpp | 5 +-
.../algo/blast/blastinput/psiblast_args.hpp | 6 +-
c++/include/algo/blast/core/blast_hits.h | 2 +-
c++/include/algo/blast/core/blast_message.h | 2 +-
c++/include/algo/blast/core/blast_options.h | 2 +-
c++/include/algo/blast/core/blast_stat.h | 2 +-
c++/include/algo/blast/format/blast_format.hpp | 23 +-
c++/include/algo/blast/format/blastfmtutil.hpp | 10 +-
c++/include/algo/blast/format/blastxml2_format.hpp | 8 +-
c++/include/algo/blast/format/data4xml2format.hpp | 4 +-
.../blast/format/sam.hpp} | 54 +-
c++/include/algo/dustmask/symdust.hpp | 17 +-
c++/include/algo/winmask/seq_masker.hpp | 6 +-
c++/include/algo/winmask/seq_masker_istat.hpp | 49 +-
.../algo/winmask/seq_masker_istat_ascii.hpp | 6 +-
c++/include/algo/winmask/seq_masker_istat_bin.hpp | 6 +-
.../algo/winmask/seq_masker_istat_factory.hpp | 23 +-
.../algo/winmask/seq_masker_istat_oascii.hpp | 6 +-
.../algo/winmask/seq_masker_istat_obinary.hpp | 6 +-
c++/include/algo/winmask/seq_masker_ostat.hpp | 65 +-
.../algo/winmask/seq_masker_ostat_ascii.hpp | 38 +-
c++/include/algo/winmask/seq_masker_ostat_bin.hpp | 42 +-
c++/include/algo/winmask/seq_masker_ostat_opt.hpp | 24 +-
.../algo/winmask/seq_masker_ostat_opt_ascii.hpp | 10 +-
.../algo/winmask/seq_masker_ostat_opt_bin.hpp | 10 +-
.../winmask/seq_masker_version.hpp} | 54 +-
c++/include/algo/winmask/seq_masker_window.hpp | 7 +-
c++/include/cgi/cgi_exception.hpp | 2 +-
c++/include/cgi/error_codes.hpp | 4 +-
c++/include/cgi/ncbicgi.hpp | 2 +-
c++/include/cgi/ncbicgir.hpp | 21 +-
c++/include/cgi/user_agent.hpp | 2 +-
c++/include/common/config/ncbiconf_msvc.h | 5 +-
c++/include/common/config/ncbiconf_xcode.h | 13 +-
c++/include/common/metamodules_doxygen.h | 8 +-
c++/include/common/ncbi_export.h | 3 +-
c++/include/common/ncbi_package_ver.h | 4 +-
c++/include/common/ncbi_source_ver.h | 6 +-
c++/include/common/ncbiconf_impl.h | 19 +-
c++/include/common/test_assert_impl.h | 4 +-
c++/include/connect/error_codes.hpp | 7 +-
c++/include/connect/impl/server_connection.hpp | 4 +-
c++/include/connect/ncbi_buffer.h | 10 +-
c++/include/connect/ncbi_conn_reader_writer.hpp | 20 +-
c++/include/connect/ncbi_conn_stream.hpp | 118 +-
c++/include/connect/ncbi_connection.h | 32 +-
c++/include/connect/ncbi_connutil.h | 129 +-
c++/include/connect/ncbi_http_connector.h | 28 +-
c++/include/connect/ncbi_http_session.hpp | 97 +-
c++/include/connect/ncbi_namedpipe.hpp | 2 +-
c++/include/connect/ncbi_namedpipe_connector.hpp | 9 +-
c++/include/connect/ncbi_pipe.hpp | 7 +-
c++/include/connect/ncbi_pipe_connector.hpp | 9 +-
c++/include/connect/ncbi_sendmail.h | 36 +-
c++/include/connect/ncbi_server_info.h | 60 +-
c++/include/connect/ncbi_service.h | 4 +-
c++/include/connect/ncbi_service_connector.h | 17 +-
c++/include/connect/ncbi_socket.h | 35 +-
c++/include/connect/ncbi_socket.hpp | 10 +-
c++/include/connect/ncbi_types.h | 6 +-
c++/include/connect/ncbi_util.h | 4 +-
c++/include/connect/services/clparser.hpp | 5 +-
c++/include/connect/services/compound_id.hpp | 5 +-
c++/include/connect/services/grid_client.hpp | 3 +-
c++/include/connect/services/grid_globals.hpp | 2 +-
c++/include/connect/services/grid_worker.hpp | 20 +-
c++/include/connect/services/grid_worker_app.hpp | 4 +-
c++/include/connect/services/named_parameters.hpp | 2 +-
c++/include/connect/services/netcache_admin.hpp | 2 +-
c++/include/connect/services/netcache_api.hpp | 40 +-
c++/include/connect/services/netcomponent.hpp | 6 +-
c++/include/connect/services/neticache_client.hpp | 8 +-
c++/include/connect/services/netschedule_api.hpp | 80 +-
c++/include/connect/services/netservice_api.hpp | 17 +-
c++/include/connect/services/netstorage.hpp | 69 +-
c++/include/connect/services/netstorage_impl.hpp | 269 +-
c++/include/connect/services/srv_connections.hpp | 43 +-
c++/include/connect/threaded_server.hpp | 3 +-
c++/include/corelib/env_reg.hpp | 4 +-
c++/include/corelib/error_codes.hpp | 9 +-
c++/include/corelib/expr.hpp | 4 +-
c++/include/corelib/guard.hpp | 33 +-
c++/include/corelib/hash_impl/stlp_defs.hpp | 2 +-
.../corelib/impl/listener_stack.hpp} | 65 +-
c++/include/corelib/impl/ncbi_atomic_defs.h | 31 +-
c++/include/corelib/impl/ncbi_panfs.h | 2 +-
c++/include/corelib/impl/ncbi_param_impl.hpp | 3 +-
c++/include/corelib/impl/rwstreambuf.hpp | 46 +-
c++/include/corelib/impl/stringutf8_deprecated.hpp | 28 +-
c++/include/corelib/impl/stringutf8_deprecated.inl | 30 +-
c++/include/corelib/metareg.hpp | 4 +-
c++/include/corelib/ncbi_autoinit.hpp | 23 +-
c++/include/corelib/ncbi_config.hpp | 5 +-
c++/include/corelib/ncbi_cookies.hpp | 4 +-
c++/include/corelib/ncbi_limits.hpp | 10 +-
c++/include/corelib/ncbi_message.hpp | 309 +
c++/include/corelib/ncbi_os_mswin.hpp | 23 +-
c++/include/corelib/ncbi_param.hpp | 2 +-
c++/include/corelib/ncbi_process.hpp | 69 +-
c++/include/corelib/ncbi_url.hpp | 2 +-
c++/include/corelib/ncbiapp.hpp | 2 +-
c++/include/corelib/ncbiargs.hpp | 63 +-
c++/include/corelib/ncbicntr.hpp | 7 +-
c++/include/corelib/ncbictype.hpp | 81 +
c++/include/corelib/ncbidbg.hpp | 59 +-
c++/include/corelib/ncbidiag.hpp | 218 +-
c++/include/corelib/ncbidiag.inl | 14 +-
c++/include/corelib/ncbienv.hpp | 15 +-
c++/include/corelib/ncbierror.hpp | 3 +-
c++/include/corelib/ncbiexpt.hpp | 103 +-
c++/include/corelib/ncbifile.hpp | 2 +-
c++/include/corelib/ncbifloat.h | 26 +-
c++/include/corelib/ncbimisc.hpp | 364 +-
c++/include/corelib/ncbimtx.hpp | 2 +-
c++/include/corelib/ncbimtx.inl | 14 +-
c++/include/corelib/ncbiobj.hpp | 94 +-
c++/include/corelib/ncbireg.hpp | 2 +-
c++/include/corelib/ncbistl.hpp | 2 +-
c++/include/corelib/ncbistr.hpp | 300 +-
c++/include/corelib/ncbistre.hpp | 7 +-
c++/include/corelib/ncbithr.hpp | 6 +-
c++/include/corelib/ncbitime.hpp | 451 +-
c++/include/corelib/perf_log.hpp | 133 +-
c++/include/corelib/plugin_manager.hpp | 10 +-
c++/include/corelib/reader_writer.hpp | 16 +-
c++/include/corelib/request_ctx.hpp | 72 +-
c++/include/corelib/request_status.hpp | 2 +-
c++/include/corelib/resource_info.hpp | 2 +-
c++/include/corelib/stream_utils.hpp | 47 +-
c++/include/corelib/tempstr.hpp | 225 +-
c++/include/corelib/test_boost.hpp | 16 +-
c++/include/dbapi/dbapi.hpp | 2 +-
c++/include/dbapi/driver/dbapi_conn_factory.hpp | 10 +-
.../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +-
.../dbapi/driver/impl/dbapi_impl_connection.hpp | 17 +-
.../dbapi/driver/impl/dbapi_impl_context.hpp | 28 +-
c++/include/dbapi/driver/interfaces.hpp | 13 +-
c++/include/dbapi/driver/public.hpp | 10 +-
c++/include/dbapi/error_codes.hpp | 4 +-
c++/include/dbapi/variant.hpp | 5 +-
c++/include/html/htmlhelper.hpp | 4 +-
c++/include/ncbi_pch.hpp | 2 +-
c++/include/ncbi_source_ver.h | 2 +-
c++/include/ncbiconf.h | 2 +-
c++/include/objects/biblio/Auth_list.hpp | 2 +-
c++/include/objects/blast/names.hpp | 2 +-
c++/include/objects/blastdb/defline_extra.hpp | 5 +-
c++/include/objects/general/Dbtag.hpp | 2 +-
c++/include/objects/general/Object_id.hpp | 80 +-
c++/include/objects/general/User_object.hpp | 8 +-
.../genomecoll/GCClient_GetAssemblyReques.hpp | 5 +-
c++/include/objects/genomecoll/GC_Assembly.hpp | 2 +-
c++/include/objects/genomecoll/GC_Sequence.hpp | 13 +-
.../objects/genomecoll/cached_assembly.hpp} | 38 +-
.../objects/genomecoll/genomic_collections_cli.hpp | 40 +-
c++/include/objects/macro/Search_func.hpp | 4 +-
c++/include/objects/macro/String_constraint.hpp | 12 +-
c++/include/objects/macro/Suspect_rule_set.hpp | 6 +-
c++/include/objects/macro/Word_substitution.hpp | 2 +-
c++/include/objects/misc/error_codes.hpp | 6 +-
c++/include/objects/pub/Pub.hpp | 2 +-
c++/include/objects/pub/Pub_equiv.hpp | 2 +-
c++/include/objects/seq/Bioseq.hpp | 2 +-
c++/include/objects/seq/Seq_descr.hpp | 2 +-
c++/include/objects/seq/annot_mapper_exception.hpp | 2 +-
c++/include/objects/seq/seq_align_mapper_base.hpp | 18 +-
c++/include/objects/seq/seq_id_handle.hpp | 6 +-
c++/include/objects/seq/seq_loc_mapper_base.hpp | 146 +-
c++/include/objects/seqalign/Dense_diag.hpp | 4 +-
c++/include/objects/seqfeat/BioSource.hpp | 2 +-
c++/include/objects/seqfeat/Gb_qual.hpp | 7 +-
c++/include/objects/seqfeat/Gene_ref.hpp | 4 +-
c++/include/objects/seqfeat/ISeq_feat.hpp | 2 +-
c++/include/objects/seqfeat/OrgMod.hpp | 2 +-
c++/include/objects/seqfeat/OrgName.hpp | 23 +-
c++/include/objects/seqfeat/Org_ref.hpp | 2 +-
c++/include/objects/seqfeat/PCRPrimerSeq.hpp | 2 +-
c++/include/objects/seqfeat/RNA_ref.hpp | 5 +-
c++/include/objects/seqfeat/SeqFeatData.hpp | 9 +-
c++/include/objects/seqfeat/Seq_feat.hpp | 22 +-
c++/include/objects/seqfeat/SubSource.hpp | 6 +-
c++/include/objects/seqloc/Seq_id.hpp | 23 +-
c++/include/objects/seqloc/Seq_loc.hpp | 454 +-
.../objects/seqtable/Scaled_int_multi_data.hpp | 9 +-
.../objects/seqtable/Scaled_real_multi_data.hpp | 4 +-
c++/include/objects/seqtable/SeqTable_column.hpp | 43 +-
.../objects/seqtable/SeqTable_multi_data.hpp | 100 +-
.../objects/seqtable/SeqTable_single_data.hpp | 119 +
c++/include/objects/seqtable/Seq_table.hpp | 5 +-
c++/include/objects/seqtable/impl/delta_cache.hpp | 65 +-
.../objects/seqtable/seq_table_exception.hpp | 4 +-
.../Auth_list.hpp => taxon1/Taxon2_data.hpp} | 63 +-
.../taxon3/{taxon3.hpp => cached_taxon3.hpp} | 58 +-
.../objects/taxon3/{taxon3.hpp => itaxon3.hpp} | 40 +-
c++/include/objects/taxon3/taxon3.hpp | 18 +-
c++/include/objects/trackmgr/gridrpcclient.hpp | 284 +-
c++/include/objects/valerr/ValidErrItem.hpp | 5 +-
c++/include/objects/valerr/ValidError.hpp | 2 +-
c++/include/objmgr/bioseq_handle.hpp | 2 +-
c++/include/objmgr/bioseq_set_handle.hpp | 2 +-
c++/include/objmgr/data_loader.hpp | 9 +-
c++/include/objmgr/gc_assembly_parser.hpp | 10 +-
c++/include/objmgr/graph_ci.hpp | 5 +-
c++/include/objmgr/impl/annot_collector.hpp | 2 +-
c++/include/objmgr/impl/annot_type_index.hpp | 49 +-
c++/include/objmgr/impl/bioseq_base_info.hpp | 2 +-
c++/include/objmgr/impl/data_source.hpp | 21 +-
c++/include/objmgr/impl/handle_range_map.hpp | 10 +-
c++/include/objmgr/impl/scope_impl.hpp | 33 +-
c++/include/objmgr/impl/scope_info.hpp | 17 +-
c++/include/objmgr/impl/seq_annot_info.hpp | 2 +-
c++/include/objmgr/impl/seq_table_info.hpp | 40 +-
c++/include/objmgr/impl/seq_table_setter.hpp | 4 +-
c++/include/objmgr/impl/seq_table_setters.hpp | 8 +-
c++/include/objmgr/impl/snp_annot_info.hpp | 3 +-
c++/include/objmgr/impl/synonyms.hpp | 6 +-
c++/include/objmgr/impl/tse_assigner.hpp | 6 +-
c++/include/objmgr/impl/tse_info.hpp | 4 +-
c++/include/objmgr/impl/tse_split_info.hpp | 9 +-
c++/include/objmgr/object_manager.hpp | 21 +-
c++/include/objmgr/objmgr_exception.hpp | 5 +-
c++/include/objmgr/scope.hpp | 11 +-
c++/include/objmgr/seq_entry_ci.hpp | 7 +-
c++/include/objmgr/seq_feat_handle.hpp | 2 +-
c++/include/objmgr/seq_loc_mapper.hpp | 6 +-
c++/include/objmgr/table_field.hpp | 101 +-
c++/include/objmgr/util/create_defline.hpp | 21 +-
c++/include/objmgr/util/feature.hpp | 63 +-
c++/include/objmgr/util/obj_sniff.hpp | 2 +-
.../utils.hpp => include/objmgr/util/objutil.hpp} | 15 +-
c++/include/objmgr/util/seq_loc_util.hpp | 49 +-
c++/include/objmgr/util/sequence.hpp | 8 +-
.../objtools/align_format/align_format_util.hpp | 35 +-
c++/include/objtools/align_format/format_flags.hpp | 31 +-
.../objtools/align_format/seqalignfilter.hpp | 4 +-
c++/include/objtools/align_format/tabular.hpp | 7 +-
c++/include/objtools/alnmgr/aln_converters.hpp | 84 +-
c++/include/objtools/alnmgr/seqids_extractor.hpp | 2 +-
.../blast/blastdb_format/blastdb_seqid.hpp | 8 +-
.../blast/seqdb_reader/impl/seqdbatlas.hpp | 720 +-
.../blast/seqdb_reader/impl/seqdbgeneral.hpp | 5 +-
.../objtools/blast/seqdb_reader/impl/seqdbisam.hpp | 441 +-
.../objtools/blast/seqdb_reader/impl/seqdbvol.hpp | 352 +-
c++/include/objtools/blast/seqdb_reader/seqdb.hpp | 66 +-
.../objtools/blast/seqdb_reader/seqdbcommon.hpp | 487 +-
.../objtools/blast/seqdb_reader/seqdbexpert.hpp | 44 +-
.../objtools/blast/seqdb_writer/build_db.hpp | 126 +-
.../blast/seqdb_writer/multisource_util.hpp | 44 +-
.../objtools/blast/seqdb_writer/writedb.hpp | 178 +-
.../objtools/blast/seqdb_writer/writedb_files.hpp | 127 +-
.../objtools/blast/services/blast_services.hpp | 2 +-
c++/include/objtools/cleanup/cleanup.hpp | 112 +-
c++/include/objtools/cleanup/cleanup_change.hpp | 3 +-
c++/include/objtools/cleanup/newcleanup.hpp | 2 +-
.../data_loaders/blastdb/blastdb_adapter.hpp | 4 +-
.../data_loaders/genbank/cache/reader_cache.hpp | 6 +-
.../data_loaders/genbank/cache/writer_cache.hpp | 9 +-
.../objtools/data_loaders/genbank/gbloader.hpp | 16 +-
.../data_loaders/genbank/gbloader_params.h | 4 +-
.../data_loaders/genbank/id1/reader_id1.hpp | 6 +-
.../data_loaders/genbank/impl/dispatcher.hpp | 7 +-
.../data_loaders/genbank/impl/info_cache.hpp | 2 +-
.../data_loaders/genbank/impl/processor.hpp | 51 +-
.../data_loaders/genbank/impl/processors.hpp | 2 +-
.../data_loaders/genbank/impl/reader_id2_base.hpp | 21 +-
.../data_loaders/genbank/impl/request_result.hpp | 61 +-
.../data_loaders/genbank/impl/statistics.hpp | 3 +-
.../objtools/data_loaders/genbank/reader.hpp | 10 +-
.../objtools/data_loaders/genbank/writer.hpp | 4 +-
c++/include/objtools/data_loaders/loaders.hpp | 2 +-
c++/include/objtools/edit/apply_object.hpp | 2 +-
c++/include/objtools/edit/autodef.hpp | 140 +-
.../objtools/edit/autodef_feature_clause.hpp | 68 +-
.../objtools/edit/autodef_feature_clause_base.hpp | 77 +-
c++/include/objtools/edit/autodef_mod_combo.hpp | 71 +-
c++/include/objtools/edit/autodef_options.hpp | 262 +
.../objtools/edit/capitalization_string.hpp | 2 +-
c++/include/objtools/edit/cds_fix.hpp | 3 +-
c++/include/objtools/edit/dblink_field.hpp | 2 +-
c++/include/objtools/edit/feattable_edit.hpp | 36 +-
c++/include/objtools/edit/field_handler.hpp | 2 +-
c++/include/objtools/edit/gaps_edit.hpp | 17 +-
c++/include/objtools/edit/loc_edit.hpp | 2 +-
c++/include/objtools/edit/parse_text_options.hpp | 128 +
c++/include/objtools/edit/remote_updater.hpp | 10 +-
c++/include/objtools/edit/rna_edit.hpp | 9 +-
c++/include/objtools/edit/seq_entry_edit.hpp | 8 +-
c++/include/objtools/edit/source_edit.hpp | 8 +-
c++/include/objtools/error_codes.hpp | 2 +-
c++/include/objtools/format/cigar_formatter.hpp | 8 +-
c++/include/objtools/format/context.hpp | 7 +-
c++/include/objtools/format/flat_file_config.hpp | 165 +-
.../objtools/format/flat_file_generator.hpp | 7 +-
c++/include/objtools/format/gather_items.hpp | 7 +-
c++/include/objtools/format/genbank_formatter.hpp | 6 +-
c++/include/objtools/format/items/comment_item.hpp | 3 +-
c++/include/objtools/format/items/feature_item.hpp | 12 +-
.../objtools/format/items/flat_qual_slots.hpp | 2 +-
c++/include/objtools/format/items/qualifiers.hpp | 90 +-
c++/include/objtools/format/sam_formatter.hpp | 83 +-
c++/include/objtools/readers/agp_util.hpp | 31 +-
.../objtools/readers/agp_validate_reader.hpp | 28 +-
c++/include/objtools/readers/bed_reader.hpp | 28 +-
c++/include/objtools/readers/cigar.hpp | 6 +-
c++/include/objtools/readers/error_container.hpp | 4 +-
c++/include/objtools/readers/fasta.hpp | 50 +-
c++/include/objtools/readers/gff2_data.hpp | 44 +-
c++/include/objtools/readers/gff2_reader.hpp | 50 +-
c++/include/objtools/readers/gff3_reader.hpp | 20 +-
c++/include/objtools/readers/gff_reader.hpp | 8 +-
c++/include/objtools/readers/gtf_reader.hpp | 8 +-
c++/include/objtools/readers/gvf_reader.hpp | 12 +-
c++/include/objtools/readers/idmapper.hpp | 19 +-
c++/include/objtools/readers/line_error.hpp | 49 +-
c++/include/objtools/readers/message_listener.hpp | 63 +-
c++/include/objtools/readers/microarray_reader.hpp | 10 +-
c++/include/objtools/readers/read_util.hpp | 2 +-
c++/include/objtools/readers/reader_base.hpp | 52 +-
c++/include/objtools/readers/readfeat.hpp | 22 +-
c++/include/objtools/readers/rm_reader.hpp | 20 +-
c++/include/objtools/readers/source_mod_parser.hpp | 2 +-
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c++/src/objtools/align_format/showdefline.cpp | 54 +-
c++/src/objtools/align_format/tabular.cpp | 40 +-
.../unit_test/Makefile.align_format_unit_test.app | 4 +-
.../unit_test/align_format_unit_test.ini | 5 +
.../unit_test/aln_printer_unit_test.cpp | 157 +-
.../unit_test/data/in_showalign_use_this_gi.asn | 985 +
.../align_format/unit_test/data/protein.fa | 862 +
.../unit_test/data/tabular_seqalignset_2.asn | 303 +-
.../align_format/unit_test/showalign_unit_test.cpp | 44 +-
.../unit_test/showdefline_unit_test.cpp | 6 +-
.../unit_test/tabularinof_unit_test.cpp | 81 +-
c++/src/objtools/alnmgr/Makefile.alnmgr.lib | 4 +-
c++/src/objtools/alnmgr/aln_builders.cpp | 3 +-
c++/src/objtools/alnmgr/alnmap.cpp | 4 +-
c++/src/objtools/alnmgr/alnmerger.cpp | 2 +-
c++/src/objtools/alnmgr/alntext.cpp | 6 +-
c++/src/objtools/alnmgr/score_builder_base.cpp | 32 +-
.../blast/blastdb_format/blastdb_dataextract.cpp | 46 +-
.../objtools/blast/blastdb_format/seq_writer.cpp | 4 +-
.../objtools/blast/seqdb_reader/Makefile.seqdb.lib | 3 +-
.../blast/seqdb_reader/demo/seqdb_demo.cpp | 4 +-
c++/src/objtools/blast/seqdb_reader/seqdb.cpp | 112 +-
c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp | 27 +-
.../objtools/blast/seqdb_reader/seqdbcommon.cpp | 134 +-
.../objtools/blast/seqdb_reader/seqdbexpert.cpp | 10 +-
.../objtools/blast/seqdb_reader/seqdbgilistset.cpp | 140 +-
.../objtools/blast/seqdb_reader/seqdbgimask.cpp | 58 +-
.../objtools/blast/seqdb_reader/seqdbgimask.hpp | 52 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp | 71 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 25 +-
c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp | 688 +-
c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp | 1095 +-
.../blast/seqdb_reader/test/seqdb_perf.cpp | 62 +-
.../objtools/blast/seqdb_writer/build-alias-index | 2 +-
c++/src/objtools/blast/seqdb_writer/build_db.cpp | 520 +-
.../blast/seqdb_writer/multisource_util.cpp | 56 +-
.../seqdb_writer/unit_test/criteria_unit_test.cpp | 4 +-
.../seqdb_writer/unit_test/writedb_unit_test.cpp | 879 +-
c++/src/objtools/blast/seqdb_writer/writedb.cpp | 56 +-
.../objtools/blast/seqdb_writer/writedb_files.cpp | 69 +-
.../objtools/blast/seqdb_writer/writedb_gimask.cpp | 58 +-
.../objtools/blast/seqdb_writer/writedb_gimask.hpp | 64 +-
.../objtools/blast/seqdb_writer/writedb_impl.cpp | 529 +-
.../objtools/blast/seqdb_writer/writedb_impl.hpp | 182 +-
.../objtools/blast/seqdb_writer/writedb_isam.cpp | 232 +-
.../objtools/blast/seqdb_writer/writedb_volume.cpp | 134 +-
.../objtools/blast/seqdb_writer/writedb_volume.hpp | 82 +-
.../blast/services/Makefile.blast_services.lib | 4 +-
c++/src/objtools/blast/services/blast_services.cpp | 2 +-
c++/src/objtools/cleanup/autogenerated_cleanup.cpp | 1839 +-
c++/src/objtools/cleanup/autogenerated_cleanup.hpp | 183 +-
c++/src/objtools/cleanup/autogenerated_cleanup.sh | 4 +
c++/src/objtools/cleanup/autogenerated_cleanup.txt | 78 +-
.../cleanup/autogenerated_extended_cleanup.cpp | 185 +-
.../cleanup/autogenerated_extended_cleanup.hpp | 26 +-
.../cleanup/autogenerated_extended_cleanup.sh | 4 +
.../cleanup/autogenerated_extended_cleanup.txt | 48 +
c++/src/objtools/cleanup/cleanup.cpp | 776 +-
c++/src/objtools/cleanup/cleanup_utils.cpp | 371 +-
c++/src/objtools/cleanup/cleanup_utils.hpp | 35 +-
c++/src/objtools/cleanup/newcleanupp.cpp | 2644 +-
c++/src/objtools/cleanup/newcleanupp.hpp | 41 +-
c++/src/objtools/data_loaders/Makefile.in | 4 +-
.../blastdb/Makefile.ncbi_xloader_blastdb.lib | 4 +-
.../blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 4 +-
.../objtools/data_loaders/blastdb/bdbloader.cpp | 8 +-
.../data_loaders/blastdb/bdbloader_rmt.cpp | 8 +-
.../data_loaders/blastdb/cached_sequence.cpp | 40 +-
.../data_loaders/blastdb/local_blastdb_adapter.cpp | 10 +-
.../data_loaders/blastdb/local_blastdb_adapter.hpp | 4 +-
.../blastdb/remote_blastdb_adapter.cpp | 6 +-
.../blastdb/remote_blastdb_adapter.hpp | 4 +-
.../data_loaders/genbank/Makefile.ncbi_xreader.lib | 5 +-
.../data_loaders/genbank/cache/reader_cache.cpp | 79 +-
.../data_loaders/genbank/cache/writer_cache.cpp | 22 +-
.../objtools/data_loaders/genbank/dispatcher.cpp | 122 +-
c++/src/objtools/data_loaders/genbank/gbloader.cpp | 68 +-
.../data_loaders/genbank/id1/reader_id1.cpp | 48 +-
.../objtools/data_loaders/genbank/processors.cpp | 207 +-
c++/src/objtools/data_loaders/genbank/reader.cpp | 64 +-
.../data_loaders/genbank/reader_id2_base.cpp | 301 +-
.../data_loaders/genbank/reader_service.cpp | 2 +-
.../objtools/data_loaders/genbank/reader_snp.cpp | 57 +-
.../data_loaders/genbank/request_result.cpp | 236 +-
c++/src/objtools/data_loaders/genbank/seqref.cpp | 4 +-
c++/src/objtools/edit/Makefile.edit.lib | 10 +-
c++/src/objtools/edit/apply_object.cpp | 2 +-
c++/src/objtools/edit/autodef.cpp | 517 +-
.../objtools/edit/autodef_available_modifier.cpp | 2 +-
c++/src/objtools/edit/autodef_feature_clause.cpp | 579 +-
.../objtools/edit/autodef_feature_clause_base.cpp | 482 +-
c++/src/objtools/edit/autodef_mod_combo.cpp | 326 +-
c++/src/objtools/edit/autodef_options.cpp | 439 +
c++/src/objtools/edit/capitalization_string.cpp | 2 +-
c++/src/objtools/edit/cds_fix.cpp | 127 +-
c++/src/objtools/edit/dblink_field.cpp | 2 +-
c++/src/objtools/edit/feattable_edit.cpp | 399 +-
c++/src/objtools/edit/field_handler.cpp | 23 +-
c++/src/objtools/edit/gaps_edit.cpp | 44 +-
c++/src/objtools/edit/gene_utils.cpp | 2 +-
c++/src/objtools/edit/link_cds_mrna.cpp | 9 +-
c++/src/objtools/edit/loc_edit.cpp | 6 +-
c++/src/objtools/edit/parse_text_options.cpp | 247 +
c++/src/objtools/edit/remote_updater.cpp | 12 +-
c++/src/objtools/edit/rna_edit.cpp | 2 +-
c++/src/objtools/edit/seq_entry_edit.cpp | 81 +-
c++/src/objtools/edit/seqid_guesser.cpp | 22 +-
c++/src/objtools/edit/source_edit.cpp | 2 +-
c++/src/objtools/edit/string_constraint.cpp | 2 +-
c++/src/objtools/format/Makefile.xformat.lib | 10 +-
c++/src/objtools/format/accession_item.cpp | 4 +-
c++/src/objtools/format/cigar_formatter.cpp | 36 +-
c++/src/objtools/format/comment_item.cpp | 176 +-
c++/src/objtools/format/context.cpp | 12 +-
c++/src/objtools/format/ctrl_items.cpp | 4 +-
c++/src/objtools/format/dbsource_item.cpp | 8 +-
c++/src/objtools/format/defline_item.cpp | 7 +-
c++/src/objtools/format/embl_formatter.cpp | 4 +-
c++/src/objtools/format/feature_item.cpp | 155 +-
c++/src/objtools/format/flat_file_config.cpp | 26 +-
c++/src/objtools/format/flat_file_generator.cpp | 11 +-
c++/src/objtools/format/flat_qual_slots.cpp | 2 +-
c++/src/objtools/format/flat_seqloc.cpp | 4 +-
c++/src/objtools/format/gather_items.cpp | 157 +-
c++/src/objtools/format/gbseq_formatter.cpp | 6 +-
c++/src/objtools/format/genbank_formatter.cpp | 336 +-
c++/src/objtools/format/gene_finder.cpp | 83 +-
c++/src/objtools/format/genome_project_item.cpp | 24 +-
c++/src/objtools/format/gff_gather.cpp | 4 +-
c++/src/objtools/format/inst_info_map.cpp | 2 +-
c++/src/objtools/format/item_formatter.cpp | 20 +-
c++/src/objtools/format/keywords_item.cpp | 11 +-
c++/src/objtools/format/locus_item.cpp | 6 +-
c++/src/objtools/format/primary_item.cpp | 4 +-
c++/src/objtools/format/qualifiers.cpp | 289 +-
c++/src/objtools/format/reference_item.cpp | 10 +-
c++/src/objtools/format/sam_formatter.cpp | 190 +-
c++/src/objtools/format/source_item.cpp | 4 +-
c++/src/objtools/readers/Makefile.xobjread.lib | 6 +-
c++/src/objtools/readers/agp_util.cpp | 78 +-
c++/src/objtools/readers/agp_validate_reader.cpp | 142 +-
c++/src/objtools/readers/bed_reader.cpp | 63 +-
c++/src/objtools/readers/cigar.cpp | 3 +-
c++/src/objtools/readers/fasta.cpp | 69 +-
c++/src/objtools/readers/format_guess_ex.cpp | 30 +-
c++/src/objtools/readers/gff2_data.cpp | 370 +-
c++/src/objtools/readers/gff2_reader.cpp | 204 +-
c++/src/objtools/readers/gff3_reader.cpp | 74 +-
c++/src/objtools/readers/gff_reader.cpp | 4 +-
c++/src/objtools/readers/gtf_reader.cpp | 16 +-
c++/src/objtools/readers/gvf_reader.cpp | 12 +-
c++/src/objtools/readers/idmapper.cpp | 6 +-
c++/src/objtools/readers/idmapper_builtin.cpp | 4 +-
c++/src/objtools/readers/idmapper_config.cpp | 6 +-
c++/src/objtools/readers/microarray_reader.cpp | 14 +-
c++/src/objtools/readers/read_util.cpp | 8 +-
c++/src/objtools/readers/reader_base.cpp | 54 +-
c++/src/objtools/readers/reader_data.cpp | 2 +-
c++/src/objtools/readers/reader_data.hpp | 2 +-
c++/src/objtools/readers/readfeat.cpp | 83 +-
c++/src/objtools/readers/rm_reader.cpp | 6 +-
c++/src/objtools/readers/source_mod_parser.cpp | 109 +-
c++/src/objtools/readers/ucscregion_reader.cpp | 8 +-
c++/src/objtools/readers/vcf_reader.cpp | 111 +-
c++/src/objtools/readers/wiggle_reader.cpp | 44 +-
c++/src/serial/Makefile.serial.lib | 6 +-
c++/src/serial/choice.cpp | 76 +-
c++/src/serial/continfo.cpp | 19 +-
c++/src/serial/datatool/aparser.cpp | 11 +-
c++/src/serial/datatool/aparser.hpp | 4 +-
c++/src/serial/datatool/blocktype.cpp | 7 +-
c++/src/serial/datatool/choicestr.cpp | 22 +-
c++/src/serial/datatool/choicestr.hpp | 8 +-
c++/src/serial/datatool/choicetype.cpp | 7 +-
c++/src/serial/datatool/classstr.cpp | 20 +-
c++/src/serial/datatool/classstr.hpp | 11 +-
c++/src/serial/datatool/datatool.cpp | 11 +-
c++/src/serial/datatool/datatool.hpp | 3 +-
c++/src/serial/datatool/dtdparser.cpp | 45 +-
c++/src/serial/datatool/enumstr.cpp | 16 +-
c++/src/serial/datatool/enumtype.cpp | 18 +-
c++/src/serial/datatool/enumtype.hpp | 26 +-
c++/src/serial/datatool/generate.cpp | 6 +-
c++/src/serial/datatool/parser.cpp | 41 +-
c++/src/serial/datatool/parser.hpp | 8 +-
c++/src/serial/datatool/srcutil.cpp | 16 +-
.../serial/datatool/traversal_code_generator.cpp | 2 +-
c++/src/serial/datatool/type.cpp | 7 +-
c++/src/serial/datatool/unitype.cpp | 6 +-
c++/src/serial/datatool/wsdlparser.cpp | 4 +-
c++/src/serial/datatool/xsdlexer.cpp | 18 +-
c++/src/serial/datatool/xsdparser.cpp | 23 +-
c++/src/serial/enumerated.cpp | 38 +-
c++/src/serial/exception.cpp | 14 +-
c++/src/serial/item.cpp | 14 +-
c++/src/serial/member.cpp | 11 +-
c++/src/serial/memberlist.cpp | 16 +-
c++/src/serial/objistr.cpp | 2 +-
c++/src/serial/objistrasn.cpp | 8 +-
c++/src/serial/objistrasnb.cpp | 19 +-
c++/src/serial/objistrjson.cpp | 55 +-
c++/src/serial/objistrxml.cpp | 36 +-
c++/src/serial/objlist.cpp | 4 +-
c++/src/serial/objostr.cpp | 92 +-
c++/src/serial/objostrasn.cpp | 42 +-
c++/src/serial/objostrasnb.cpp | 40 +-
c++/src/serial/objostrjson.cpp | 43 +-
c++/src/serial/objostrxml.cpp | 64 +-
c++/src/serial/objstack.cpp | 17 +-
c++/src/serial/pack_string.cpp | 4 +-
c++/src/serial/pathhook.cpp | 5 +-
c++/src/serial/rpcbase.cpp | 335 +
c++/src/util/Makefile.util.lib | 4 +-
c++/src/util/checksum.cpp | 1052 +-
c++/src/util/compress/api/archive_zip.cpp | 22 +-
c++/src/util/compress/api/archive_zip.hpp | 8 +-
c++/src/util/compress/api/miniz/miniz.c | 414 +-
c++/src/util/compress/api/miniz/tinfl.c | 82 +-
c++/src/util/compress/api/tar.cpp | 57 +-
c++/src/util/compress/api/zlib.cpp | 4 +-
c++/src/util/compress/zlib/ChangeLog | 2 +-
c++/src/util/compress/zlib/Makefile.zlib.lib | 2 +-
c++/src/util/compress/zlib/adler32.c | 2 +-
c++/src/util/compress/zlib/compress.c | 2 +-
c++/src/util/compress/zlib/crc32.c | 2 +-
c++/src/util/compress/zlib/deflate.c | 2 +-
c++/src/util/compress/zlib/deflate.h | 2 +-
c++/src/util/compress/zlib/trees.c | 2 +-
c++/src/util/compress/zlib/uncompr.c | 2 +-
c++/src/util/compress/zlib/zutil.c | 2 +-
c++/src/util/crc32tables.c | 1598 +
c++/src/util/creaders/alnread.c | 109 +-
c++/src/util/dictionary_util.cpp | 29 +-
c++/src/util/distribution.cpp | 2 +-
c++/src/util/format_guess.cpp | 68 +-
c++/src/util/md5.cpp | 8 +-
c++/src/util/random_gen.cpp | 26 +-
c++/src/util/rangelist.cpp | 2 +-
c++/src/util/regexp/pcretest.c | 2 +-
c++/src/util/regexp/test_pcre.sh | 2 +-
c++/src/util/retry_ctx.cpp | 165 +
c++/src/util/sequtil/Makefile.sequtil.lib | 4 +-
c++/src/util/sequtil/sequtil_convert.cpp | 2 +-
c++/src/util/sequtil/sequtil_convert_imp.cpp | 2 +-
c++/src/util/strbuffer.cpp | 58 +-
c++/src/util/strsearch.cpp | 26 +-
c++/src/util/tables/raw_scoremat.c | 2 +-
c++/src/util/tables/sm_identity.c | 2 +-
c++/src/util/thread_pool_old.cpp | 2 +-
c++/src/util/unicode.cpp | 13 +-
c++/src/util/util_misc.cpp | 6 +-
c++/src/util/xregexp/Makefile.in | 4 +-
c++/src/util/xregexp/Makefile.xregexp.lib | 8 +-
.../xregexp/Makefile.xregexp_template_tester.lib | 14 +
c++/src/util/xregexp/regexp_template_tester.cpp | 710 +
1369 files changed, 117146 insertions(+), 78388 deletions(-)
diff --git a/c++/compilers/cygwin/build.sh b/c++/compilers/cygwin/build.sh
index e133796..811deae 100644
--- a/c++/compilers/cygwin/build.sh
+++ b/c++/compilers/cygwin/build.sh
@@ -1,5 +1,5 @@
#! /bin/sh
-# $Id: build.sh 467527 2015-05-14 11:34:48Z ivanov $
+# $Id: build.sh 466738 2015-05-06 11:20:57Z ivanov $
# Author: Vladimir Ivanov (ivanov at ncbi.nlm.nih.gov)
#
# Build C++ Toolkit using Cygwin
@@ -14,8 +14,8 @@ arch=${2}
########### Global variables
-cmd_Debug='--with-debug --without-mt --without-dll'
-cmd_DebugMT='--with-debug --with-mt --without-dll'
+cmd_Debug='--with-debug --without-mt --without-dll CFLAGS=-g0 CXXFLAGS=-g0'
+cmd_DebugMT='--with-debug --with-mt --without-dll CFLAGS=-g0 CXXFLAGS=-g0'
##cmd_DebugDLL='--with-debug --with-mt --with-dll'
cmd_Release='--without-debug --without-mt --without-dll'
cmd_ReleaseMT='--without-debug --with-mt --without-dll'
diff --git a/c++/compilers/msvc1000_prj/check.sh b/c++/compilers/msvc1000_prj/check.sh
index f816810..fe8a58c 100644
--- a/c++/compilers/msvc1000_prj/check.sh
+++ b/c++/compilers/msvc1000_prj/check.sh
@@ -1,5 +1,5 @@
#! /bin/sh
-# $Id: check.sh 417079 2013-11-04 16:46:24Z ivanov $
+# $Id: check.sh 471331 2015-06-25 15:57:14Z ivanov $
# Author: Vladimir Ivanov (ivanov at ncbi.nlm.nih.gov)
#
# Check C++ Toolkit in all previously built configurations
@@ -12,20 +12,44 @@
# For 'concat_cfg' -- use 'run', 'concat' and 'concat_err' commands first.
+
########### Arguments
script="$0"
method="$1"
+# Maximum number of parallel running test configurations
+max_tasks=2
+# Sleep timeout between checks on finished 'run' tasks (seconds)
+sleeptime=60
+
########## Functions
-error()
+Error()
{
echo "[`basename $script`] ERROR: $1"
exit 1
}
+ParseConfig()
+{
+ if [ -z "$1" ] ; then
+ Error "Unknown configuration name"
+ fi
+ x_tree=`echo $1 | sed -e 's/,.*$//'`
+ x_sol=`echo $1 | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
+ x_cfg=`echo $1 | sed -e 's/^.*,//'`
+}
+
+CopyConfigLogs()
+{
+ cat ${tasks_dir[$1]}/check.sh.log >> $res_log
+ cat ${tasks_dir[$1]}/check.sh.log >> \
+ $build_dir/check.sh.${tasks_tree[$1]}_${tasks_cfg[$1]}.log
+}
+
+
########## Main
@@ -37,9 +61,9 @@ build_dir=`(cd "$build_dir"; pwd)`
timer="date +'%H:%M'"
if [ ! -d $build_dir ] ; then
- error "Build directory $build_dir not found"
+ Error "Build directory $build_dir not found"
fi
-cd $build_dir || error "Cannot change directory"
+cd $build_dir || Error "Cannot change directory"
res_log="$build_dir/check.sh.log"
res_concat="$build_dir/check.sh.out"
@@ -47,10 +71,11 @@ res_concat_err="$build_dir/check.sh.out_err"
cfgs="`cat cfgs.log`"
if [ -z "$cfgs" ] ; then
- error "Build some configurations first"
+ Error "Build some configurations first"
fi
-# Initialization
+
+# --- Initialization
case "$method" in
run )
@@ -58,7 +83,17 @@ case "$method" in
rm -f "$build_dir/check.sh.*.log" > /dev/null 2>&1
# Init checks
$build_dir/../../scripts/common/check/check_make_win_cfg.sh init || \
- error "Check initialization failed"
+ Error "Check initialization failed"
+ # Init task list
+ i=0
+ while [ $i -lt $max_tasks ] ; do
+ tasks_name[$i]=""
+ tasks_tree[$i]=""
+ tasks_cfg[$i]=""
+ tasks_dir[$i]=""
+ tasks_start[$i]=""
+ i=`expr $i + 1`
+ done
;;
clean )
# not implemented, 'clean' method is not used on Windows
@@ -71,50 +106,103 @@ case "$method" in
egrep 'ERR \[|TO -' $res_log > $res_concat_err
;;
concat_cfg )
- #rm -f "$build_dir/check.sh.*.out" > /dev/null 2>&1
rm -f "$build_dir/check.sh.*.out_err" > /dev/null 2>&1
;;
load_to_db )
;;
* )
- error "Invalid method name"
+ Error "Invalid method name"
;;
esac
-# Run checks for each previously built configuration
+
+# --- Run checks for each previously built configuration
+
for cfg in $cfgs ; do
- if [ -z "$cfg" ] ; then
- error "Unknown configuration name"
- fi
- x_tree=`echo $cfg | sed -e 's/,.*$//'`
- x_sol=`echo $cfg | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
- x_cfg=`echo $cfg | sed -e 's/^.*,//'`
- start=`eval $timer`
- echo $start
- echo CHECK_$method: $x_tree/$x_sol/$x_cfg
+ ParseConfig $cfg
cd $build_dir
+
+ check_name=$x_tree/$x_sol/$x_cfg
check_dir="$x_tree/build/${x_sol}.check/$x_cfg"
if [ ! -d "$check_dir" ] ; then
- error "Check directory \"$check_dir\" not found"
+ Error "Check directory \"$check_dir\" not found"
fi
- if test "$method" != "run"; then
- test -x "$check_dir/check.sh" || error "Run checks first. $check_dir/check.sh not found."
+
+ # Special processing for 'run' to allow parallel test runs
+
+ if [ "$method" = "run" ]; then
+
+ while true; do
+ i=0
+ idx=999
+
+ while [ $i -lt $max_tasks ]; do
+ # Find first free slot
+ if [ -z "${tasks_name[$i]}" ]; then
+ idx=$i
+ break
+ fi
+ # Check on finished tasks
+ if [ -f "${tasks_dir[$i]}/check.success" ]; then
+ idx=$i
+ fi
+ if [ -f "${tasks_dir[$i]}/check.failed" ]; then
+ idx=$i
+ errcode=1
+ fi
+ if [ $idx -lt $max_tasks ]; then
+ CopyConfigLogs $idx
+ echo `eval $timer`
+ echo CHECK_$method: finished: ${tasks_name[$idx]} \(${tasks_start[idx]} - `eval $timer`\)
+ tasks_name[$idx]=""
+ break
+ fi
+ i=`expr $i + 1`
+ done
+
+ if [ $idx -lt $max_tasks ]; then
+ # Run tests for current configuration $cfg
+ tasks_name[$idx]="$x_tree/$x_sol/$x_cfg"
+ tasks_tree[$idx]="$x_tree"
+ tasks_cfg[$idx]="$x_cfg"
+ tasks_dir[$idx]="$check_dir"
+ tasks_start[$idx]=`eval $timer`
+
+ echo ${tasks_start[$idx]}
+ echo CHECK_$method: started : ${tasks_name[$idx]}
+ rm ${tasks_dir[$idx]}/check.success ${tasks_dir[$idx]}/check.failed >/dev/null 2>&1
+
+ ../../scripts/common/check/check_make_win_cfg.sh create "$x_sol" "$x_tree" "$x_cfg" || \
+ Error "Creating check script for \"$check_dir\" failed"
+ test -x "${tasks_dir[$idx]}/check.sh" || \
+ Error "Cannot find $check_dir/check.sh"
+
+ ${tasks_dir[$idx]}/check.sh run >/dev/null 2>&1 &
+
+ # Move to next configuration
+ break
+ else
+ # All slots busy -- waiting
+ sleep $sleeptime
+ fi
+ done
+
+ continue
fi
- # Action
-
+
+ # All actions except 'run'
+
+ test -x "$check_dir/check.sh" || \
+ Error "Run checks first. $check_dir/check.sh not found."
+
+ echo `eval $timer`
+ echo CHECK_$method: $check_name
+
case "$method" in
- run )
- ../../scripts/common/check/check_make_win_cfg.sh create "$x_sol" "$x_tree" "$x_cfg" || \
- error "Creating check script for \"$check_dir\" failed"
- $check_dir/check.sh run || errcode=$?
- cat $check_dir/check.sh.log >> $res_log
- cat $check_dir/check.sh.log >> $build_dir/check.sh.${x_tree}_${x_cfg}.log
- echo "Check time: $start - `eval $timer`"
- ;;
concat )
$check_dir/check.sh concat
cat $check_dir/check.sh.out >> $res_concat
@@ -126,7 +214,8 @@ for cfg in $cfgs ; do
concat_cfg )
# Copy log entries
egrep 'ERR \[|TO -' $check_dir/check.sh.log >> $build_dir/check.sh.${x_tree}_${x_cfg}.out_err
- # see below copying of failed tests outputs
+ # See below for copying of failed tests outputs,
+ # it should be printed after log entries for all configurations.
;;
load_to_db )
$check_dir/check.sh load_to_db
@@ -134,14 +223,51 @@ for cfg in $cfgs ; do
esac
done
-if test "$method" = "concat_cfg"; then
+
+# --- Waiting unfinished tasks for 'run'
+
+if [ "$method" = "run" ]; then
+ while true; do
+ i=0
+ idx=999
+ active=false
+
+ while [ $i -lt $max_tasks ]; do
+ if [ -n "${tasks_name[$i]}" ]; then
+ # Check on finished tasks
+ if [ -f "${tasks_dir[$i]}/check.success" ]; then
+ idx=$i
+ fi
+ if [ -f "${tasks_dir[$i]}/check.failed" ]; then
+ idx=$i
+ errcode=1
+ fi
+ if [ $idx -lt $max_tasks ]; then
+ CopyConfigLogs $idx
+ echo `eval $timer`
+ echo CHECK_$method: finished: ${tasks_name[$idx]} \(${tasks_start[$idx]} - `eval $timer`\)
+ tasks_name[$idx]=""
+ idx=999
+ else
+ active=true
+ fi
+ fi
+ i=`expr $i + 1`
+ done
+
+ if $active; then
+ sleep $sleeptime
+ else
+ break
+ fi
+ done
+fi
+
+if [ "$method" = "concat_cfg" ]; then
for cfg in $cfgs ; do
- x_tree=`echo $cfg | sed -e 's/,.*$//'`
- x_sol=`echo $cfg | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
- x_cfg=`echo $cfg | sed -e 's/^.*,//'`
+ ParseConfig $cfg
cd $build_dir
check_dir="$x_tree/build/${x_sol}.check/$x_cfg"
- #cat $check_dir/check.sh.out >> $build_dir/check.sh.${x_tree}_${x_cfg}.out
cat $check_dir/check.sh.out_err >> $build_dir/check.sh.${x_tree}_${x_cfg}.out_err
done
fi
diff --git a/c++/compilers/msvc1000_prj/dll/third_party_dll_install.mak b/c++/compilers/msvc1000_prj/dll/third_party_dll_install.mak
index f838f48..61fc53f 100644
--- a/c++/compilers/msvc1000_prj/dll/third_party_dll_install.mak
+++ b/c++/compilers/msvc1000_prj/dll/third_party_dll_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_dll_install.mak 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_dll_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/msvc1000_prj/static/build/corelib/xncbi.lib.vcxproj b/c++/compilers/msvc1000_prj/static/build/corelib/xncbi.lib.vcxproj
index 852da1f..7e5817c 100644
--- a/c++/compilers/msvc1000_prj/static/build/corelib/xncbi.lib.vcxproj
+++ b/c++/compilers/msvc1000_prj/static/build/corelib/xncbi.lib.vcxproj
@@ -370,6 +370,12 @@
<PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ncbi_pch.hpp</PrecompiledHeaderFile>
</ClCompile>
+ <ClCompile Include="..\..\..\..\..\src\corelib\guard.cpp">
+ <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ncbi_pch.hpp</PrecompiledHeaderFile>
+ <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ncbi_pch.hpp</PrecompiledHeaderFile>
+ </ClCompile>
<ClCompile Include="..\..\..\..\..\src\corelib\ncbierror.cpp">
<PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ncbi_pch.hpp</PrecompiledHeaderFile>
diff --git a/c++/compilers/msvc1000_prj/static/third_party_static_install.mak b/c++/compilers/msvc1000_prj/static/third_party_static_install.mak
index 404fbd2..c8794e2 100644
--- a/c++/compilers/msvc1000_prj/static/third_party_static_install.mak
+++ b/c++/compilers/msvc1000_prj/static/third_party_static_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_static_install.mak 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_static_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/msvc1000_prj/third_party_install.meta.mk b/c++/compilers/msvc1000_prj/third_party_install.meta.mk
index 3c6f125..3752e7d 100644
--- a/c++/compilers/msvc1000_prj/third_party_install.meta.mk
+++ b/c++/compilers/msvc1000_prj/third_party_install.meta.mk
@@ -1,4 +1,4 @@
-# $Id: third_party_install.meta.mk 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_install.meta.mk 468588 2015-05-26 17:46:51Z ucko $
#################################################################
#
@@ -123,6 +123,8 @@ LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(INTDIR)
LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(ALTDIR)
!ENDIF
+VDB_SRC = $(VDB_BINPATH)
+
#################################################################
@@ -292,6 +294,20 @@ install_libxslt : $(LIBXSLT_SRC).libxslt_install
clean_libxslt : $(LIBXSLT_SRC).libxslt_clean
+VDB_ORIG = $(INSTALL_BINPATH)\ncbi-vdb-md.dll
+VDB_COPY = $(INSTALL_BINPATH)\ncbi-vdb-dll-md.dll
+$(VDB_SRC).vdb_install :
+ @echo ---- & echo Copying VDB DLLs & $(INSTALL_CMD)
+# The trailing * suppresses a spurious prompt, per
+# http://stackoverflow.com/a/26034267/1231
+ @if exist "$(VDB_ORIG)" xcopy /Y /D /F "$(VDB_ORIG)" "$(VDB_COPY)"*
+$(VDB_SRC).vdb_clean :
+ @echo ---- & echo Deleting VDB DLLs & $(CLEAN_CMD)
+ @if exist "$(VDB_COPY)" ( echo $(VDB_COPY) & del /f "$(VDB_COPY)" )
+install_vdb : $(VDB_SRC).vdb_install
+clean_vdb : $(VDB_SRC).vdb_clean
+
+
# -----------------------------------------
# MSVC RT DLLs are not included into 'all'
diff --git a/c++/compilers/msvc900_prj/dll/third_party_dll_install.mak b/c++/compilers/msvc900_prj/dll/third_party_dll_install.mak
index f838f48..61fc53f 100644
--- a/c++/compilers/msvc900_prj/dll/third_party_dll_install.mak
+++ b/c++/compilers/msvc900_prj/dll/third_party_dll_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_dll_install.mak 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_dll_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/msvc900_prj/static/third_party_static_install.mak b/c++/compilers/msvc900_prj/static/third_party_static_install.mak
index 404fbd2..c8794e2 100644
--- a/c++/compilers/msvc900_prj/static/third_party_static_install.mak
+++ b/c++/compilers/msvc900_prj/static/third_party_static_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_static_install.mak 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_static_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/msvc900_prj/third_party_install.meta.mk b/c++/compilers/msvc900_prj/third_party_install.meta.mk
index 3c6f125..3752e7d 100644
--- a/c++/compilers/msvc900_prj/third_party_install.meta.mk
+++ b/c++/compilers/msvc900_prj/third_party_install.meta.mk
@@ -1,4 +1,4 @@
-# $Id: third_party_install.meta.mk 381093 2012-11-19 16:57:46Z ivanov $
+# $Id: third_party_install.meta.mk 468588 2015-05-26 17:46:51Z ucko $
#################################################################
#
@@ -123,6 +123,8 @@ LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(INTDIR)
LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(ALTDIR)
!ENDIF
+VDB_SRC = $(VDB_BINPATH)
+
#################################################################
@@ -292,6 +294,20 @@ install_libxslt : $(LIBXSLT_SRC).libxslt_install
clean_libxslt : $(LIBXSLT_SRC).libxslt_clean
+VDB_ORIG = $(INSTALL_BINPATH)\ncbi-vdb-md.dll
+VDB_COPY = $(INSTALL_BINPATH)\ncbi-vdb-dll-md.dll
+$(VDB_SRC).vdb_install :
+ @echo ---- & echo Copying VDB DLLs & $(INSTALL_CMD)
+# The trailing * suppresses a spurious prompt, per
+# http://stackoverflow.com/a/26034267/1231
+ @if exist "$(VDB_ORIG)" xcopy /Y /D /F "$(VDB_ORIG)" "$(VDB_COPY)"*
+$(VDB_SRC).vdb_clean :
+ @echo ---- & echo Deleting VDB DLLs & $(CLEAN_CMD)
+ @if exist "$(VDB_COPY)" ( echo $(VDB_COPY) & del /f "$(VDB_COPY)" )
+install_vdb : $(VDB_SRC).vdb_install
+clean_vdb : $(VDB_SRC).vdb_clean
+
+
# -----------------------------------------
# MSVC RT DLLs are not included into 'all'
diff --git a/c++/compilers/unix/GCC.sh b/c++/compilers/unix/GCC.sh
index 12ca013..45fedef 100755
--- a/c++/compilers/unix/GCC.sh
+++ b/c++/compilers/unix/GCC.sh
@@ -3,7 +3,7 @@
# Setup the local working environment for the "configure" script
# Compiler: GCC
#
-# $Revision: 449296 $ // by Denis Vakatov, NCBI (vakatov at ncbi.nlm.nih.gov)
+# $Revision: 466369 $ // by Denis Vakatov, NCBI (vakatov at ncbi.nlm.nih.gov)
#############################################################################
@@ -45,7 +45,7 @@ case "$1" in
elif llvm-$CXX-$1 -dumpversion >/dev/null 2>&1; then
CXX="llvm-$CXX-$1"
CC="llvm-$CC-$1"
- elif "`$CXX -V$1 -dumpversion 2>/dev/null`" = "$1"; then
+ elif test "`$CXX -V$1 -dumpversion 2>/dev/null`" = "$1"; then
CXX="$CXX -V$1"
CC="$CC -V$1"
elif test "`$CXX -dumpversion 2>/dev/null`" \!= "$1"; then
diff --git a/c++/compilers/unix/ICC.sh b/c++/compilers/unix/ICC.sh
index 6f07544..d9ddafe 100755
--- a/c++/compilers/unix/ICC.sh
+++ b/c++/compilers/unix/ICC.sh
@@ -5,7 +5,7 @@
# OS: Linux
# Processor: Intel X86(-64)
#
-# $Revision: 441500 $ // Dmitriy Beloslyudtsev, NCBI (beloslyu at ncbi.nlm.nih.gov)
+# $Revision: 441489 $ // Dmitriy Beloslyudtsev, NCBI (beloslyu at ncbi.nlm.nih.gov)
#############################################################################
diff --git a/c++/compilers/vs2012/dll/third_party_dll_install.mak b/c++/compilers/vs2012/dll/third_party_dll_install.mak
index d7beb08..61fc53f 100644
--- a/c++/compilers/vs2012/dll/third_party_dll_install.mak
+++ b/c++/compilers/vs2012/dll/third_party_dll_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_dll_install.mak 407441 2013-07-22 13:01:08Z gouriano $
+# $Id: third_party_dll_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/vs2012/static/third_party_static_install.mak b/c++/compilers/vs2012/static/third_party_static_install.mak
index 43b850f..c8794e2 100644
--- a/c++/compilers/vs2012/static/third_party_static_install.mak
+++ b/c++/compilers/vs2012/static/third_party_static_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_static_install.mak 407452 2013-07-22 13:13:25Z gouriano $
+# $Id: third_party_static_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/vs2012/third_party_install.meta.mk b/c++/compilers/vs2012/third_party_install.meta.mk
index ae94c19..3752e7d 100644
--- a/c++/compilers/vs2012/third_party_install.meta.mk
+++ b/c++/compilers/vs2012/third_party_install.meta.mk
@@ -1,4 +1,4 @@
-# $Id: third_party_install.meta.mk 407440 2013-07-22 13:00:11Z gouriano $
+# $Id: third_party_install.meta.mk 468588 2015-05-26 17:46:51Z ucko $
#################################################################
#
@@ -123,6 +123,8 @@ LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(INTDIR)
LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(ALTDIR)
!ENDIF
+VDB_SRC = $(VDB_BINPATH)
+
#################################################################
@@ -292,6 +294,20 @@ install_libxslt : $(LIBXSLT_SRC).libxslt_install
clean_libxslt : $(LIBXSLT_SRC).libxslt_clean
+VDB_ORIG = $(INSTALL_BINPATH)\ncbi-vdb-md.dll
+VDB_COPY = $(INSTALL_BINPATH)\ncbi-vdb-dll-md.dll
+$(VDB_SRC).vdb_install :
+ @echo ---- & echo Copying VDB DLLs & $(INSTALL_CMD)
+# The trailing * suppresses a spurious prompt, per
+# http://stackoverflow.com/a/26034267/1231
+ @if exist "$(VDB_ORIG)" xcopy /Y /D /F "$(VDB_ORIG)" "$(VDB_COPY)"*
+$(VDB_SRC).vdb_clean :
+ @echo ---- & echo Deleting VDB DLLs & $(CLEAN_CMD)
+ @if exist "$(VDB_COPY)" ( echo $(VDB_COPY) & del /f "$(VDB_COPY)" )
+install_vdb : $(VDB_SRC).vdb_install
+clean_vdb : $(VDB_SRC).vdb_clean
+
+
# -----------------------------------------
# MSVC RT DLLs are not included into 'all'
diff --git a/c++/compilers/vs2013/check.sh b/c++/compilers/vs2013/check.sh
index 2936b79..be6bf90 100644
--- a/c++/compilers/vs2013/check.sh
+++ b/c++/compilers/vs2013/check.sh
@@ -1,5 +1,5 @@
#! /bin/sh
-# $Id: check.sh 430635 2014-03-27 17:34:42Z gouriano $
+# $Id: check.sh 473888 2015-07-23 12:02:15Z ivanov $
# Author: Vladimir Ivanov (ivanov at ncbi.nlm.nih.gov)
#
# Check C++ Toolkit in all previously built configurations
@@ -12,20 +12,44 @@
# For 'concat_cfg' -- use 'run', 'concat' and 'concat_err' commands first.
+
########### Arguments
script="$0"
method="$1"
+# Maximum number of parallel running test configurations
+max_tasks=2
+# Sleep timeout between checks on finished 'run' tasks (seconds)
+sleeptime=60
+
########## Functions
-error()
+Error()
{
echo "[`basename $script`] ERROR: $1"
exit 1
}
+ParseConfig()
+{
+ if [ -z "$1" ] ; then
+ Error "Unknown configuration name"
+ fi
+ x_tree=`echo $1 | sed -e 's/,.*$//'`
+ x_sol=`echo $1 | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
+ x_cfg=`echo $1 | sed -e 's/^.*,//'`
+}
+
+CopyConfigLogs()
+{
+ cat ${tasks_dir[$1]}/check.sh.log >> $res_log
+ cat ${tasks_dir[$1]}/check.sh.log >> \
+ $build_dir/check.sh.${tasks_tree[$1]}_${tasks_cfg[$1]}.log
+}
+
+
########## Main
@@ -37,9 +61,9 @@ build_dir=`(cd "$build_dir"; pwd)`
timer="date +'%H:%M'"
if [ ! -d $build_dir ] ; then
- error "Build directory $build_dir not found"
+ Error "Build directory $build_dir not found"
fi
-cd $build_dir || error "Cannot change directory"
+cd $build_dir || Error "Cannot change directory"
res_log="$build_dir/check.sh.log"
res_concat="$build_dir/check.sh.out"
@@ -47,10 +71,11 @@ res_concat_err="$build_dir/check.sh.out_err"
cfgs="`cat cfgs.log`"
if [ -z "$cfgs" ] ; then
- error "Build some configurations first"
+ Error "Build some configurations first"
fi
-# Initialization
+
+# --- Initialization
case "$method" in
run )
@@ -58,7 +83,17 @@ case "$method" in
rm -f "$build_dir/check.sh.*.log" > /dev/null 2>&1
# Init checks
$build_dir/../../scripts/common/check/check_make_win_cfg.sh init || \
- error "Check initialization failed"
+ Error "Check initialization failed"
+ # Init task list
+ i=0
+ while [ $i -lt $max_tasks ] ; do
+ tasks_name[$i]=""
+ tasks_tree[$i]=""
+ tasks_cfg[$i]=""
+ tasks_dir[$i]=""
+ tasks_start[$i]=""
+ i=`expr $i + 1`
+ done
;;
clean )
# not implemented, 'clean' method is not used on Windows
@@ -71,50 +106,104 @@ case "$method" in
egrep 'ERR \[|TO -' $res_log > $res_concat_err
;;
concat_cfg )
- #rm -f "$build_dir/check.sh.*.out" > /dev/null 2>&1
rm -f "$build_dir/check.sh.*.out_err" > /dev/null 2>&1
;;
load_to_db )
+ rm -f "$build_dir/test_stat_load.log" > /dev/null 2>&1
;;
* )
- error "Invalid method name"
+ Error "Invalid method name"
;;
esac
-# Run checks for each previously built configuration
+
+# --- Run checks for each previously built configuration
+
for cfg in $cfgs ; do
- if [ -z "$cfg" ] ; then
- error "Unknown configuration name"
- fi
- x_tree=`echo $cfg | sed -e 's/,.*$//'`
- x_sol=`echo $cfg | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
- x_cfg=`echo $cfg | sed -e 's/^.*,//'`
- start=`eval $timer`
- echo $start
- echo CHECK_$method: $x_tree/$x_sol/$x_cfg
+ ParseConfig $cfg
cd $build_dir
+
+ check_name=$x_tree/$x_sol/$x_cfg
check_dir="$x_tree/build/${x_sol}.check/$x_cfg"
if [ ! -d "$check_dir" ] ; then
- error "Check directory \"$check_dir\" not found"
+ Error "Check directory \"$check_dir\" not found"
fi
- if test "$method" != "run"; then
- test -x "$check_dir/check.sh" || error "Run checks first. $check_dir/check.sh not found."
+
+ # Special processing for 'run' to allow parallel test runs
+
+ if [ "$method" = "run" ]; then
+
+ while true; do
+ i=0
+ idx=999
+
+ while [ $i -lt $max_tasks ]; do
+ # Find first free slot
+ if [ -z "${tasks_name[$i]}" ]; then
+ idx=$i
+ break
+ fi
+ # Check on finished tasks
+ if [ -f "${tasks_dir[$i]}/check.success" ]; then
+ idx=$i
+ fi
+ if [ -f "${tasks_dir[$i]}/check.failed" ]; then
+ idx=$i
+ errcode=1
+ fi
+ if [ $idx -lt $max_tasks ]; then
+ CopyConfigLogs $idx
+ echo `eval $timer`
+ echo CHECK_$method: finished: ${tasks_name[$idx]} \(${tasks_start[idx]} - `eval $timer`\)
+ tasks_name[$idx]=""
+ break
+ fi
+ i=`expr $i + 1`
+ done
+
+ if [ $idx -lt $max_tasks ]; then
+ # Run tests for current configuration $cfg
+ tasks_name[$idx]="$x_tree/$x_sol/$x_cfg"
+ tasks_tree[$idx]="$x_tree"
+ tasks_cfg[$idx]="$x_cfg"
+ tasks_dir[$idx]="$check_dir"
+ tasks_start[$idx]=`eval $timer`
+
+ echo ${tasks_start[$idx]}
+ echo CHECK_$method: started : ${tasks_name[$idx]}
+ rm ${tasks_dir[$idx]}/check.success ${tasks_dir[$idx]}/check.failed >/dev/null 2>&1
+
+ ../../scripts/common/check/check_make_win_cfg.sh create "$x_sol" "$x_tree" "$x_cfg" || \
+ Error "Creating check script for \"$check_dir\" failed"
+ test -x "${tasks_dir[$idx]}/check.sh" || \
+ Error "Cannot find $check_dir/check.sh"
+
+ ${tasks_dir[$idx]}/check.sh run >/dev/null 2>&1 &
+
+ # Move to next configuration
+ break
+ else
+ # All slots busy -- waiting
+ sleep $sleeptime
+ fi
+ done
+
+ continue
fi
- # Action
-
+
+ # All actions except 'run'
+
+ test -x "$check_dir/check.sh" || \
+ Error "Run checks first. $check_dir/check.sh not found."
+
+ echo `eval $timer`
+ echo CHECK_$method: $check_name
+
case "$method" in
- run )
- ../../scripts/common/check/check_make_win_cfg.sh create "$x_sol" "$x_tree" "$x_cfg" || \
- error "Creating check script for \"$check_dir\" failed"
- $check_dir/check.sh run || errcode=$?
- cat $check_dir/check.sh.log >> $res_log
- cat $check_dir/check.sh.log >> $build_dir/check.sh.${x_tree}_${x_cfg}.log
- echo "Check time: $start - `eval $timer`"
- ;;
concat )
$check_dir/check.sh concat
cat $check_dir/check.sh.out >> $res_concat
@@ -126,7 +215,8 @@ for cfg in $cfgs ; do
concat_cfg )
# Copy log entries
egrep 'ERR \[|TO -' $check_dir/check.sh.log >> $build_dir/check.sh.${x_tree}_${x_cfg}.out_err
- # see below copying of failed tests outputs
+ # See below for copying of failed tests outputs,
+ # it should be printed after log entries for all configurations.
;;
load_to_db )
$check_dir/check.sh load_to_db
@@ -134,14 +224,51 @@ for cfg in $cfgs ; do
esac
done
-if test "$method" = "concat_cfg"; then
+
+# --- Waiting unfinished tasks for 'run'
+
+if [ "$method" = "run" ]; then
+ while true; do
+ i=0
+ idx=999
+ active=false
+
+ while [ $i -lt $max_tasks ]; do
+ if [ -n "${tasks_name[$i]}" ]; then
+ # Check on finished tasks
+ if [ -f "${tasks_dir[$i]}/check.success" ]; then
+ idx=$i
+ fi
+ if [ -f "${tasks_dir[$i]}/check.failed" ]; then
+ idx=$i
+ errcode=1
+ fi
+ if [ $idx -lt $max_tasks ]; then
+ CopyConfigLogs $idx
+ echo `eval $timer`
+ echo CHECK_$method: finished: ${tasks_name[$idx]} \(${tasks_start[$idx]} - `eval $timer`\)
+ tasks_name[$idx]=""
+ idx=999
+ else
+ active=true
+ fi
+ fi
+ i=`expr $i + 1`
+ done
+
+ if $active; then
+ sleep $sleeptime
+ else
+ break
+ fi
+ done
+fi
+
+if [ "$method" = "concat_cfg" ]; then
for cfg in $cfgs ; do
- x_tree=`echo $cfg | sed -e 's/,.*$//'`
- x_sol=`echo $cfg | sed -e 's/^[^,]*,//' -e 's/,.*$//' -e 's/\.sln//' -e 's|\\\|/|g'`
- x_cfg=`echo $cfg | sed -e 's/^.*,//'`
+ ParseConfig $cfg
cd $build_dir
check_dir="$x_tree/build/${x_sol}.check/$x_cfg"
- #cat $check_dir/check.sh.out >> $build_dir/check.sh.${x_tree}_${x_cfg}.out
cat $check_dir/check.sh.out_err >> $build_dir/check.sh.${x_tree}_${x_cfg}.out_err
done
fi
diff --git a/c++/compilers/vs2013/configure.bat b/c++/compilers/vs2013/configure.bat
index 7289967..9354ee8 100644
--- a/c++/compilers/vs2013/configure.bat
+++ b/c++/compilers/vs2013/configure.bat
@@ -1,5 +1,5 @@
@echo off
-REM $Id: configure.bat 430635 2014-03-27 17:34:42Z gouriano $
+REM $Id: configure.bat 449189 2014-10-14 14:54:57Z gouriano $
REM ===========================================================================
REM
REM PUBLIC DOMAIN NOTICE
@@ -43,7 +43,6 @@ set use_dll=no
set use_64=no
set use_staticstd=no
set use_arch=Win32
-set use_ide=1100
set use_flags=
set help_req=no
set srcroot=../..
@@ -287,14 +286,6 @@ if "%help_req%"=="yes" (
)
REM --------------------------------------------------------------------------------
-REM identify target MSVC version (based on the script location msvcNNN_prj)
-
-for /f "delims=" %%a in ('echo %script_dir%') do (set msvc_ver=%%~na)
-set msvc_ver=%msvc_ver:msvc=%
-set msvc_ver=%msvc_ver:_prj=%
-if not "%msvc_ver%"=="" (set use_ide=%msvc_ver%)
-
-REM --------------------------------------------------------------------------------
REM target architecture, solution path, configuration and flags
if "%use_64%"=="yes" (
diff --git a/c++/compilers/vs2013/dll/build/gbench/gbench_install/gbench-install.vcxproj b/c++/compilers/vs2013/dll/build/gbench/gbench_install/gbench-install.vcxproj
index 6ad2236..f6d4f17 100644
--- a/c++/compilers/vs2013/dll/build/gbench/gbench_install/gbench-install.vcxproj
+++ b/c++/compilers/vs2013/dll/build/gbench/gbench_install/gbench-install.vcxproj
@@ -136,75 +136,75 @@
<_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">Unicode_DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">Unicode_DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">Unicode_DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">Unicode_DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">Unicode_ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">Unicode_ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">Unicode_ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">Unicode_ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">VTune_DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">VTune_DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">VTune_DebugDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">VTune_DebugDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">VTune_ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">VTune_ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">VTune_ReleaseDLL\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">VTune_ReleaseDLL\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="msvc11.64\11"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak all IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f ..\..\..\..\..\..\src\app\gbench\gbench_install\gbench_install.win32.mak clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">gbench-install.exe</NMakeOutput>
</PropertyGroup>
<ItemDefinitionGroup>
diff --git a/c++/compilers/vs2013/dll/third_party_dll_install.mak b/c++/compilers/vs2013/dll/third_party_dll_install.mak
index cbbe755..61fc53f 100644
--- a/c++/compilers/vs2013/dll/third_party_dll_install.mak
+++ b/c++/compilers/vs2013/dll/third_party_dll_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_dll_install.mak 430636 2014-03-27 17:37:44Z gouriano $
+# $Id: third_party_dll_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/vs2013/dll/third_party_msvcdll_install.vcxproj b/c++/compilers/vs2013/dll/third_party_msvcdll_install.vcxproj
index 8757200..3b9d640 100644
--- a/c++/compilers/vs2013/dll/third_party_msvcdll_install.vcxproj
+++ b/c++/compilers/vs2013/dll/third_party_msvcdll_install.vcxproj
@@ -279,147 +279,147 @@
<_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_dll_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
</PropertyGroup>
<ItemDefinitionGroup>
diff --git a/c++/compilers/vs2013/make.bat b/c++/compilers/vs2013/make.bat
index caa99e8..9a59b37 100644
--- a/c++/compilers/vs2013/make.bat
+++ b/c++/compilers/vs2013/make.bat
@@ -1,5 +1,5 @@
@ECHO OFF
-REM $Id: make.bat 467528 2015-05-14 11:35:20Z ivanov $
+REM $Id: make.bat 485601 2015-11-24 13:12:30Z ivanov $
REM ===========================================================================
REM
REM PUBLIC DOMAIN NOTICE
@@ -52,8 +52,6 @@ rem Always configure with additional Unicode configurations
if _%SRV_NAME% == _ set SRV_NAME=%COMPUTERNAME%
call msvcvars.bat > NUL
-set archw=Win32
-if _%arch%_ == _64_ set archw=x64
rem --- Required parameters
@@ -63,6 +61,9 @@ set solution=%~2
set libdll=%~3
set arch=%~4
+set archw=Win32
+if _%arch%_ == _64_ set archw=x64
+
shift
shift
shift
diff --git a/c++/compilers/vs2013/static/build/corelib/xncbi.lib.vcxproj b/c++/compilers/vs2013/static/build/corelib/xncbi.lib.vcxproj
index d3b2309..e044fbb 100644
--- a/c++/compilers/vs2013/static/build/corelib/xncbi.lib.vcxproj
+++ b/c++/compilers/vs2013/static/build/corelib/xncbi.lib.vcxproj
@@ -372,6 +372,12 @@
<PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ncbi_pch.hpp</PrecompiledHeaderFile>
</ClCompile>
+ <ClCompile Include="..\..\..\..\..\src\corelib\guard.cpp">
+ <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ncbi_pch.hpp</PrecompiledHeaderFile>
+ <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">ncbi_pch.hpp</PrecompiledHeaderFile>
+ </ClCompile>
<ClCompile Include="..\..\..\..\..\src\corelib\ncbierror.cpp">
<PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">NCBI_USE_PCH;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<PrecompiledHeaderFile Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">ncbi_pch.hpp</PrecompiledHeaderFile>
diff --git a/c++/compilers/vs2013/static/third_party_msvcstatic_install.vcxproj b/c++/compilers/vs2013/static/third_party_msvcstatic_install.vcxproj
index 41cc27a..3f90659 100644
--- a/c++/compilers/vs2013/static/third_party_msvcstatic_install.vcxproj
+++ b/c++/compilers/vs2013/static/third_party_msvcstatic_install.vcxproj
@@ -279,147 +279,147 @@
<_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Unicode_ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugMT|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|Win32'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_DebugDLL|x64'">gbench-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseMT|x64'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|Win32'">dlls-install.exe</NMakeOutput>
<OutDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">$(Configuration)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">$(Configuration)\</IntDir>
- <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeBuildCommandLine>
- <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeReBuildCommandLine>
- <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2012.64"</NMakeCleanCommandLine>
+ <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_install IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeBuildCommandLine>
+ <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_rebuild IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeReBuildCommandLine>
+ <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">call "$(ProjectDir)..\msvcvars.bat" & nmake -f "$(ProjectDir)\third_party_static_install.mak" msvc_clean IntDir=$(IntDir) MSVC_SRC="vs2013.64"</NMakeCleanCommandLine>
<NMakeOutput Condition="'$(Configuration)|$(Platform)'=='VTune_ReleaseDLL|x64'">dlls-install.exe</NMakeOutput>
</PropertyGroup>
<ItemDefinitionGroup>
diff --git a/c++/compilers/vs2013/static/third_party_static_install.mak b/c++/compilers/vs2013/static/third_party_static_install.mak
index 759ed99..c8794e2 100644
--- a/c++/compilers/vs2013/static/third_party_static_install.mak
+++ b/c++/compilers/vs2013/static/third_party_static_install.mak
@@ -1,4 +1,4 @@
-# $Id: third_party_static_install.mak 430646 2014-03-27 17:52:59Z gouriano $
+# $Id: third_party_static_install.mak 463528 2015-03-30 14:10:31Z ucko $
#################################################################
@@ -30,7 +30,8 @@ THIRD_PARTY_LIBS = \
install_xalan \
install_xerces \
install_libxml \
- install_libxslt
+ install_libxslt \
+ install_vdb
CLEAN_THIRD_PARTY_LIBS = \
clean_berkeleydb \
@@ -48,7 +49,8 @@ CLEAN_THIRD_PARTY_LIBS = \
clean_xalan \
clean_xerces \
clean_libxml \
- clean_libxslt
+ clean_libxslt \
+ clean_vdb
all : dirs $(THIRD_PARTY_LIBS)
diff --git a/c++/compilers/vs2013/third_party_install.meta.mk b/c++/compilers/vs2013/third_party_install.meta.mk
index cdb1448..3752e7d 100644
--- a/c++/compilers/vs2013/third_party_install.meta.mk
+++ b/c++/compilers/vs2013/third_party_install.meta.mk
@@ -1,4 +1,4 @@
-# $Id: third_party_install.meta.mk 430635 2014-03-27 17:34:42Z gouriano $
+# $Id: third_party_install.meta.mk 468588 2015-05-26 17:46:51Z ucko $
#################################################################
#
@@ -123,6 +123,8 @@ LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(INTDIR)
LIBXSLT_SRC = $(LIBXSLT_BINPATH)\$(ALTDIR)
!ENDIF
+VDB_SRC = $(VDB_BINPATH)
+
#################################################################
@@ -292,6 +294,20 @@ install_libxslt : $(LIBXSLT_SRC).libxslt_install
clean_libxslt : $(LIBXSLT_SRC).libxslt_clean
+VDB_ORIG = $(INSTALL_BINPATH)\ncbi-vdb-md.dll
+VDB_COPY = $(INSTALL_BINPATH)\ncbi-vdb-dll-md.dll
+$(VDB_SRC).vdb_install :
+ @echo ---- & echo Copying VDB DLLs & $(INSTALL_CMD)
+# The trailing * suppresses a spurious prompt, per
+# http://stackoverflow.com/a/26034267/1231
+ @if exist "$(VDB_ORIG)" xcopy /Y /D /F "$(VDB_ORIG)" "$(VDB_COPY)"*
+$(VDB_SRC).vdb_clean :
+ @echo ---- & echo Deleting VDB DLLs & $(CLEAN_CMD)
+ @if exist "$(VDB_COPY)" ( echo $(VDB_COPY) & del /f "$(VDB_COPY)" )
+install_vdb : $(VDB_SRC).vdb_install
+clean_vdb : $(VDB_SRC).vdb_clean
+
+
# -----------------------------------------
# MSVC RT DLLs are not included into 'all'
diff --git a/c++/compilers/xCode/Application.applescript b/c++/compilers/xCode/Application.applescript
index 64e5499..8416e4c 100644
--- a/c++/compilers/xCode/Application.applescript
+++ b/c++/compilers/xCode/Application.applescript
@@ -1,4 +1,4 @@
-(* $Id: Application.applescript 281982 2011-05-09 15:34:15Z mcelhany $
+(* $Id: Application.applescript 449199 2014-10-14 16:10:59Z serovav $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -217,7 +217,7 @@ on clicked theObject
(* Help button pressed *)
if theObject is equal to button "helpButton" then
- open location "http://www.ncbi.nlm.nih.gov/books/NBK7160/"
+ open location "http://www.ncbi.nlm.nih.gov/toolkit/doc/book/"
end if
(* Handle Paths *)
diff --git a/c++/compilers/xcode30_prj/configure b/c++/compilers/xcode30_prj/configure
index e02d686..1e467fc 100755
--- a/c++/compilers/xcode30_prj/configure
+++ b/c++/compilers/xcode30_prj/configure
@@ -1,6 +1,6 @@
#!/bin/sh
-# $Id: configure 381201 2012-11-20 14:30:39Z ucko $
+# $Id: configure 470941 2015-06-22 02:15:08Z ucko $
# Author: Andrei Gourianov, NCBI (gouriano at ncbi.nlm.nih.gov)
#-----------------------------------------------------------------------------
@@ -294,7 +294,11 @@ if test -z "$use_arch"; then
use_arch="ppc i386"
fi
else
- use_arch="$arch"
+ if test "$use_64" == "yes"; then
+ use_arch="x86_64"
+ else
+ use_arch="i386"
+ fi
fi
fi
PTB_PLATFORM="$use_arch"
@@ -348,7 +352,7 @@ test -e "$srcroot/$use_projectlst" || Error "$use_projectlst not found"
export PTB_PLATFORM
export PTB_FLAGS
-export PTB_PATH=./static/bin/ReleaseDLL
+export PTB_PATH=./static/UtilityProjects/bin/ReleaseDLL
export SLN_PATH=$sln_path/$sln_name
export TREE_ROOT=$srcroot
export BUILD_TREE_ROOT=.
@@ -356,6 +360,12 @@ export PTB_PROJECT_REQ="$use_projectlst"
export PTB_SAVED_CFG_REQ="$use_savedcfg"
./ptb.sh
+datatool=static/bin/ReleaseDLL/datatool
+if test -x "$PTB_PATH"/datatool &&
+ test \! -x $datatool -o "$PTB_PATH"/datatool -nt $datatool; then
+ mkdir -p `dirname $datatool`
+ cp "$PTB_PATH"/datatool $datatool
+fi
if test $? -ne 0; then
echo "ERROR: Configuration failed" 1>&2
cd "$initial_dir"
diff --git a/c++/compilers/xcode30_prj/datatool.sh b/c++/compilers/xcode30_prj/datatool.sh
index 256bb48..bc9f5f0 100755
--- a/c++/compilers/xcode30_prj/datatool.sh
+++ b/c++/compilers/xcode30_prj/datatool.sh
@@ -1,5 +1,5 @@
#!/bin/sh
-# $Id: datatool.sh 193249 2010-06-02 15:29:25Z gouriano $
+# $Id: datatool.sh 472266 2015-07-08 17:20:47Z ivanov $
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
@@ -91,9 +91,10 @@ fi
if test ! -x "$DATATOOL_EXE"; then
echo "=============================================================================="
echo Building $DT locally, please wait
- echo "xcodebuild -project $PTB_SLN -target $DT -configuration ReleaseDLL"
+ cmd="`dirname $0`/xcodebuild.sh -project $PTB_SLN -target $DT -configuration ReleaseDLL"
+ echo "$cmd"
echo "=============================================================================="
- xcodebuild -project $PTB_SLN -target $DT -configuration ReleaseDLL
+ $cmd
else
echo "=============================================================================="
echo "Using PREBUILT $DT at $DATATOOL_EXE"
diff --git a/c++/compilers/xcode30_prj/ptb.sh b/c++/compilers/xcode30_prj/ptb.sh
index d9d7944..de829e8 100755
--- a/c++/compilers/xcode30_prj/ptb.sh
+++ b/c++/compilers/xcode30_prj/ptb.sh
@@ -1,5 +1,5 @@
#!/bin/sh
-# $Id: ptb.sh 433131 2014-04-23 00:33:23Z ucko $
+# $Id: ptb.sh 472266 2015-07-08 17:20:47Z ivanov $
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
@@ -162,21 +162,7 @@ test -z "$PTB_PROJECT" && PTB_PROJECT=${PTB_PROJECT_REQ}
if test ! -x "$PTB_EXE"; then
echo "=============================================================================="
echo Building project tree builder locally, please wait
- cmd="xcodebuild -project $PTB_SLN -target $ptbname -configuration ReleaseDLL"
- case "`uname -r`" in
- ?.* | 1[01].* ) # Mac OS X 10.7.x or older
- for v in 10.5 10.6 10.7; do
- sdk=/Developer/SDKs/MacOSX$v.sdk
- [ -d "$sdk" ] && break
- done
- ;;
- * )
- sdk=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk
- ;;
- esac
- if [ -d "$sdk" ]; then
- cmd="$cmd -sdk $sdk"
- fi
+ cmd="`dirname $0`/xcodebuild.sh -project $PTB_SLN -target $ptbname -configuration ReleaseDLL"
echo "$cmd"
echo "=============================================================================="
$cmd
diff --git a/c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj b/c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj
index 14161c9..e4747eb 100644
--- a/c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj
+++ b/c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj
@@ -57,12 +57,12 @@
<string>dwarf-with-dsym</string>
<key>GCC_DEBUGGING_SYMBOLS</key>
<string>default</string>
- <key>SDKROOT</key>
- <string></string>
<key>FRAMEWORK_SEARCH_PATHS</key>
<string>/System/Library/Frameworks/CoreServices.framework/Frameworks</string>
<key>USE_HEADERMAP</key>
<string>NO</string>
+ <key>OTHER_CPLUSPLUSFLAGS</key>
+ <string>-std=gnu++11 -stdlib=libc++ -Wno-deprecated-register</string>
<key>DEAD_CODE_STRIPPING</key>
<string>NO</string>
<key>PREBINDING</key>
@@ -106,12 +106,12 @@
<string>dwarf-with-dsym</string>
<key>GCC_DEBUGGING_SYMBOLS</key>
<string>default</string>
- <key>SDKROOT</key>
- <string></string>
<key>FRAMEWORK_SEARCH_PATHS</key>
<string>/System/Library/Frameworks/CoreServices.framework/Frameworks</string>
<key>USE_HEADERMAP</key>
<string>NO</string>
+ <key>OTHER_CPLUSPLUSFLAGS</key>
+ <string>-std=gnu++11 -stdlib=libc++ -Wno-deprecated-register</string>
<key>DEAD_CODE_STRIPPING</key>
<string>NO</string>
<key>PREBINDING</key>
@@ -149,12 +149,12 @@
<string>YES</string>
<key>GCC_GENERATE_DEBUGGING_SYMBOLS</key>
<string>NO</string>
- <key>SDKROOT</key>
- <string></string>
<key>FRAMEWORK_SEARCH_PATHS</key>
<string>/System/Library/Frameworks/CoreServices.framework/Frameworks</string>
<key>USE_HEADERMAP</key>
<string>NO</string>
+ <key>OTHER_CPLUSPLUSFLAGS</key>
+ <string>-std=gnu++11 -stdlib=libc++ -Wno-deprecated-register</string>
<key>DEAD_CODE_STRIPPING</key>
<string>NO</string>
<key>PREBINDING</key>
@@ -192,12 +192,12 @@
<string>YES</string>
<key>GCC_GENERATE_DEBUGGING_SYMBOLS</key>
<string>NO</string>
- <key>SDKROOT</key>
- <string></string>
<key>FRAMEWORK_SEARCH_PATHS</key>
<string>/System/Library/Frameworks/CoreServices.framework/Frameworks</string>
<key>USE_HEADERMAP</key>
<string>NO</string>
+ <key>OTHER_CPLUSPLUSFLAGS</key>
+ <string>-std=gnu++11 -stdlib=libc++ -Wno-deprecated-register</string>
<key>DEAD_CODE_STRIPPING</key>
<string>NO</string>
<key>PREBINDING</key>
@@ -221,27 +221,34 @@
<key>isa</key>
<string>PBXProject</string>
<key>mainGroup</key>
- <string>ABCDABCDABCDABCD00000396</string>
+ <string>ABCDABCDABCDABCD00000584</string>
<key>productRefGroup</key>
- <string>ABCDABCDABCDABCD00000397</string>
+ <string>ABCDABCDABCDABCD00000585</string>
<key>projectDirPath</key>
<string></string>
<key>projectRoot</key>
<string></string>
<key>targets</key>
<array>
- <string>ABCDABCDABCDABCD000003B2</string>
- <string>ABCDABCDABCDABCD000003AC</string>
- <string>ABCDABCDABCDABCD000003A6</string>
- <string>ABCDABCDABCDABCD0000039F</string>
- <string>ABCDABCDABCDABCD00000398</string>
- <string>ABCDABCDABCDABCD00000095</string>
- <string>ABCDABCDABCDABCD0000011B</string>
- <string>ABCDABCDABCDABCD0000015D</string>
- <string>ABCDABCDABCDABCD0000021F</string>
- <string>ABCDABCDABCDABCD00000235</string>
- <string>ABCDABCDABCDABCD000002F8</string>
- <string>ABCDABCDABCDABCD0000038F</string>
+ <string>ABCDABCDABCDABCD000005A8</string>
+ <string>ABCDABCDABCDABCD000005A2</string>
+ <string>ABCDABCDABCDABCD0000059C</string>
+ <string>ABCDABCDABCDABCD00000595</string>
+ <string>ABCDABCDABCDABCD0000058E</string>
+ <string>ABCDABCDABCDABCD00000586</string>
+ <string>ABCDABCDABCDABCD00000029</string>
+ <string>ABCDABCDABCDABCD000000C9</string>
+ <string>ABCDABCDABCDABCD00000155</string>
+ <string>ABCDABCDABCDABCD00000196</string>
+ <string>ABCDABCDABCDABCD0000020D</string>
+ <string>ABCDABCDABCDABCD00000282</string>
+ <string>ABCDABCDABCDABCD0000029E</string>
+ <string>ABCDABCDABCDABCD0000030A</string>
+ <string>ABCDABCDABCDABCD000003ED</string>
+ <string>ABCDABCDABCDABCD00000403</string>
+ <string>ABCDABCDABCDABCD00000415</string>
+ <string>ABCDABCDABCDABCD000004D9</string>
+ <string>ABCDABCDABCDABCD0000057D</string>
</array>
</dict>
<key>ABCDABCDABCDABCD00000007</key>
@@ -249,4610 +256,4275 @@
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD0000015D</string>
+ <string>ABCDABCDABCDABCD00000196</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD00000121</string>
+ <string>ABCDABCDABCDABCD0000015B</string>
</dict>
<key>ABCDABCDABCDABCD00000008</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD0000021F</string>
+ <string>ABCDABCDABCDABCD0000020D</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD00000163</string>
+ <string>ABCDABCDABCDABCD0000019C</string>
</dict>
<key>ABCDABCDABCDABCD00000009</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD00000235</string>
+ <string>ABCDABCDABCDABCD00000282</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD00000225</string>
+ <string>ABCDABCDABCDABCD00000213</string>
</dict>
<key>ABCDABCDABCDABCD0000000A</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD000002F8</string>
+ <string>ABCDABCDABCDABCD0000030A</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD0000023B</string>
+ <string>ABCDABCDABCDABCD000002A4</string>
</dict>
<key>ABCDABCDABCDABCD0000000B</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD0000038F</string>
+ <string>ABCDABCDABCDABCD000003ED</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD000002FE</string>
+ <string>ABCDABCDABCDABCD00000310</string>
</dict>
<key>ABCDABCDABCDABCD0000000C</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD00000095</string>
+ <string>ABCDABCDABCDABCD00000403</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD0000000E</string>
+ <string>ABCDABCDABCDABCD000003F3</string>
</dict>
<key>ABCDABCDABCDABCD0000000D</key>
<dict>
<key>isa</key>
<string>PBXTargetDependency</string>
<key>target</key>
- <string>ABCDABCDABCDABCD0000011B</string>
+ <string>ABCDABCDABCDABCD00000415</string>
<key>targetProxy</key>
- <string>ABCDABCDABCDABCD0000009B</string>
+ <string>ABCDABCDABCDABCD00000409</string>
</dict>
<key>ABCDABCDABCDABCD0000000E</key>
<dict>
- <key>containerPortal</key>
- <string>ABCDABCDABCDABCD00000006</string>
<key>isa</key>
- <string>PBXContainerItemProxy</string>
- <key>proxyType</key>
- <string>1</string>
- <key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD00000095</string>
- <key>remoteInfo</key>
- <string>datatool</string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD000004D9</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD0000041B</string>
</dict>
<key>ABCDABCDABCDABCD0000000F</key>
<dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000013</string>
- <string>ABCDABCDABCDABCD00000015</string>
- <string>ABCDABCDABCDABCD00000017</string>
- <string>ABCDABCDABCDABCD00000019</string>
- <string>ABCDABCDABCDABCD0000001B</string>
- <string>ABCDABCDABCDABCD0000001D</string>
- <string>ABCDABCDABCDABCD0000001F</string>
- <string>ABCDABCDABCDABCD00000021</string>
- <string>ABCDABCDABCDABCD00000023</string>
- <string>ABCDABCDABCDABCD00000025</string>
- <string>ABCDABCDABCDABCD00000027</string>
- <string>ABCDABCDABCDABCD00000029</string>
- <string>ABCDABCDABCDABCD0000002B</string>
- <string>ABCDABCDABCDABCD0000002D</string>
- <string>ABCDABCDABCDABCD0000002F</string>
- <string>ABCDABCDABCDABCD00000031</string>
- <string>ABCDABCDABCDABCD00000033</string>
- <string>ABCDABCDABCDABCD00000035</string>
- <string>ABCDABCDABCDABCD00000037</string>
- <string>ABCDABCDABCDABCD00000039</string>
- <string>ABCDABCDABCDABCD0000003B</string>
- <string>ABCDABCDABCDABCD0000003D</string>
- <string>ABCDABCDABCDABCD0000003F</string>
- <string>ABCDABCDABCDABCD00000041</string>
- <string>ABCDABCDABCDABCD00000043</string>
- <string>ABCDABCDABCDABCD00000045</string>
- <string>ABCDABCDABCDABCD00000047</string>
- <string>ABCDABCDABCDABCD00000049</string>
- <string>ABCDABCDABCDABCD0000004B</string>
- <string>ABCDABCDABCDABCD0000004D</string>
- <string>ABCDABCDABCDABCD0000004F</string>
- <string>ABCDABCDABCDABCD00000051</string>
- <string>ABCDABCDABCDABCD00000053</string>
- <string>ABCDABCDABCDABCD00000055</string>
- <string>ABCDABCDABCDABCD00000057</string>
- <string>ABCDABCDABCDABCD00000059</string>
- <string>ABCDABCDABCDABCD0000005B</string>
- <string>ABCDABCDABCDABCD0000005D</string>
- <string>ABCDABCDABCDABCD0000005F</string>
- <string>ABCDABCDABCDABCD00000061</string>
- <string>ABCDABCDABCDABCD00000063</string>
- <string>ABCDABCDABCDABCD00000065</string>
- <string>ABCDABCDABCDABCD00001065</string>
- <string>ABCDABCDABCDABCD00001165</string>
- <string>ABCDABCDABCDABCD00001265</string>
- <string>ABCDABCDABCDABCD00001365</string>
- <string>ABCDABCDABCDABCD00001465</string>
- </array>
<key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>Source Files</string>
- <key>sourceTree</key>
- <string><group></string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD0000057D</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD000004DF</string>
</dict>
<key>ABCDABCDABCDABCD00000010</key>
<dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000067</string>
- <string>ABCDABCDABCDABCD00000068</string>
- <string>ABCDABCDABCDABCD00000069</string>
- <string>ABCDABCDABCDABCD0000006A</string>
- <string>ABCDABCDABCDABCD0000006B</string>
- <string>ABCDABCDABCDABCD0000006C</string>
- <string>ABCDABCDABCDABCD0000006D</string>
- <string>ABCDABCDABCDABCD0000006E</string>
- <string>ABCDABCDABCDABCD0000006F</string>
- <string>ABCDABCDABCDABCD00000070</string>
- <string>ABCDABCDABCDABCD00000071</string>
- <string>ABCDABCDABCDABCD00000072</string>
- <string>ABCDABCDABCDABCD00000073</string>
- <string>ABCDABCDABCDABCD00000074</string>
- <string>ABCDABCDABCDABCD00000075</string>
- <string>ABCDABCDABCDABCD00000076</string>
- <string>ABCDABCDABCDABCD00000077</string>
- <string>ABCDABCDABCDABCD00000078</string>
- <string>ABCDABCDABCDABCD00000079</string>
- <string>ABCDABCDABCDABCD0000007A</string>
- <string>ABCDABCDABCDABCD0000007B</string>
- <string>ABCDABCDABCDABCD0000007C</string>
- <string>ABCDABCDABCDABCD0000007D</string>
- <string>ABCDABCDABCDABCD0000007E</string>
- <string>ABCDABCDABCDABCD0000007F</string>
- <string>ABCDABCDABCDABCD00000080</string>
- <string>ABCDABCDABCDABCD00000081</string>
- <string>ABCDABCDABCDABCD00000082</string>
- <string>ABCDABCDABCDABCD00000083</string>
- <string>ABCDABCDABCDABCD00000084</string>
- <string>ABCDABCDABCDABCD00000085</string>
- <string>ABCDABCDABCDABCD00000086</string>
- <string>ABCDABCDABCDABCD00000087</string>
- <string>ABCDABCDABCDABCD00000088</string>
- <string>ABCDABCDABCDABCD00000089</string>
- <string>ABCDABCDABCDABCD0000008A</string>
- <string>ABCDABCDABCDABCD0000008B</string>
- <string>ABCDABCDABCDABCD0000008C</string>
- <string>ABCDABCDABCDABCD0000008D</string>
- <string>ABCDABCDABCDABCD0000008E</string>
- <string>ABCDABCDABCDABCD0000008F</string>
- <string>ABCDABCDABCDABCD00000090</string>
- <string>ABCDABCDABCDABCD00000091</string>
- <string>ABCDABCDABCDABCD00000092</string>
- </array>
<key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>Header Files</string>
- <key>sourceTree</key>
- <string><group></string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD000000C9</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD0000002F</string>
</dict>
- <key>ABCDABCDABCDABCD00000012</key>
+ <key>ABCDABCDABCDABCD00000011</key>
<dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD0000000F</string>
- <string>ABCDABCDABCDABCD00000010</string>
- </array>
<key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>datatool</string>
- <key>sourceTree</key>
- <string><group></string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD00000155</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD000000CF</string>
</dict>
- <key>ABCDABCDABCDABCD00000013</key>
+ <key>ABCDABCDABCDABCD00000012</key>
<dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>alexer.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/alexer.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD0000029E</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD00000288</string>
</dict>
- <key>ABCDABCDABCDABCD00000014</key>
+ <key>ABCDABCDABCDABCD00000013</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000013</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD00000029</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD00000021</string>
</dict>
<key>ABCDABCDABCDABCD00000015</key>
<dict>
+ <key>explicitFileType</key>
+ <string>compiled.mach-o.executable</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>aliasstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/aliasstr.cpp</string>
+ <string>datatool</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD00000016</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000015</string>
+ <key>explicitFileType</key>
+ <string>compiled.mach-o.executable</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXFileReference</string>
+ <key>path</key>
+ <string>project_tree_builder</string>
+ <key>sourceTree</key>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD00000017</key>
<dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>aparser.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/aparser.cpp</string>
+ <string>libregexp_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD00000018</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000017</string>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXFileReference</string>
+ <key>path</key>
+ <string>libtest_boost_bootstrap.a</string>
+ <key>sourceTree</key>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD00000019</key>
<dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>blocktype.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/blocktype.cpp</string>
+ <string>libtest_mt_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001A</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000019</string>
+ <key>explicitFileType</key>
+ <string>compiled.mach-o.executable</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXFileReference</string>
+ <key>path</key>
+ <string>test_pcre</string>
+ <key>sourceTree</key>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001B</key>
<dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>choiceptrstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/choiceptrstr.cpp</string>
+ <string>libxcser_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001C</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000001B</string>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXFileReference</string>
+ <key>path</key>
+ <string>libxncbi_bootstrap.a</string>
+ <key>sourceTree</key>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001D</key>
<dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>choicestr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/choicestr.cpp</string>
+ <string>libxregexp_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001E</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000001D</string>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXFileReference</string>
+ <key>path</key>
+ <string>libxregexp_template_tester_bootstrap.a</string>
+ <key>sourceTree</key>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD0000001F</key>
<dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>choicetype.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/choicetype.cpp</string>
+ <string>libxser_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
<key>ABCDABCDABCDABCD00000020</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000001F</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000021</key>
- <dict>
+ <key>explicitFileType</key>
+ <string>archive.ar</string>
+ <key>includeInIndex</key>
+ <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>classstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/classstr.cpp</string>
+ <string>libxutil_bootstrap.a</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>BUILT_PRODUCTS_DIR</string>
</dict>
- <key>ABCDABCDABCDABCD00000022</key>
+ <key>ABCDABCDABCDABCD00000021</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000021</string>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD00000029</string>
+ <key>remoteInfo</key>
+ <string>_generate_all_objects</string>
</dict>
- <key>ABCDABCDABCDABCD00000023</key>
+ <key>ABCDABCDABCDABCD00000024</key>
<dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000026</string>
+ <string>ABCDABCDABCDABCD00000027</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>PBXGroup</string>
<key>name</key>
- <string>code.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/code.cpp</string>
+ <string>Datatool Files</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000024</key>
+ <key>ABCDABCDABCDABCD00000025</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000023</string>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000024</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>_generate_all_objects</string>
+ <key>sourceTree</key>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000025</key>
+ <key>ABCDABCDABCDABCD00000026</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>text</string>
<key>name</key>
- <string>comments.cpp</string>
+ <string>msvc71_project.dtd</string>
<key>path</key>
- <string>../../../../src/serial/datatool/comments.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000026</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000025</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
<key>ABCDABCDABCDABCD00000027</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>text.xml</string>
<key>name</key>
- <string>datatool.cpp</string>
+ <string>property_list.xsd</string>
<key>path</key>
- <string>../../../../src/serial/datatool/datatool.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
<key>ABCDABCDABCDABCD00000028</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000027</string>
+ <key>files</key>
+ <array></array>
+ <key>inputPaths</key>
+ <array>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.def</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.def</string>
+ </array>
+ <key>outputPaths</key>
+ <array>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.files</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project__.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project___.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.files</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list__.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list___.cpp</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXShellScriptBuildPhase</string>
+ <key>shellPath</key>
+ <string>/bin/sh</string>
+ <key>shellScript</key>
+ <string>export PTB_PLATFORM="$ARCHS"
export DATATOOL_PATH=bin/ReleaseDLL
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
"$BUILD_TREE_ROOT/datatool.sh" -oex "" -oA -odi -ocvs -pch ncbi_pch.hpp -m build-system/project_tree_builder/msvc71_project.dtd -oc msvc71_project -od ../../../../src/build-system/project_tree_builder/msvc71_project.def -or build-system/project_tree_builder/ -oR ../../../../
"$BUILD_TREE_ROOT/data [...]
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
<key>ABCDABCDABCDABCD00000029</key>
<dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD0000002A</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000028</string>
+ </array>
+ <key>dependencies</key>
+ <array></array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>PBXAggregateTarget</string>
<key>name</key>
- <string>dtdaux.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/dtdaux.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>_generate_all_objects</string>
+ <key>productName</key>
+ <string>_generate_all_objects</string>
</dict>
<key>ABCDABCDABCDABCD0000002A</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000029</string>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000002B</string>
+ <string>ABCDABCDABCDABCD0000002C</string>
+ <string>ABCDABCDABCDABCD0000002D</string>
+ <string>ABCDABCDABCDABCD0000002E</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCConfigurationList</string>
</dict>
<key>ABCDABCDABCDABCD0000002B</key>
<dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_generate_all_objects</string>
+ </dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>XCBuildConfiguration</string>
<key>name</key>
- <string>dtdlexer.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/dtdlexer.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>DebugDLL</string>
</dict>
<key>ABCDABCDABCDABCD0000002C</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000002B</string>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_generate_all_objects</string>
+ </dict>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugMT</string>
</dict>
<key>ABCDABCDABCDABCD0000002D</key>
<dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_generate_all_objects</string>
+ </dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>XCBuildConfiguration</string>
<key>name</key>
- <string>dtdparser.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/dtdparser.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>ReleaseDLL</string>
</dict>
<key>ABCDABCDABCDABCD0000002E</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000002D</string>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_generate_all_objects</string>
+ </dict>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseMT</string>
</dict>
<key>ABCDABCDABCDABCD0000002F</key>
<dict>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>enumstr.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/enumstr.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD000000C9</string>
+ <key>remoteInfo</key>
+ <string>datatool</string>
</dict>
<key>ABCDABCDABCDABCD00000030</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000002F</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000031</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>enumtype.cpp</string>
- <key>path</key>
- <string>../../../../src/serial/datatool/enumtype.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000032</key>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000034</string>
+ <string>ABCDABCDABCDABCD00000036</string>
+ <string>ABCDABCDABCDABCD00000038</string>
+ <string>ABCDABCDABCDABCD0000003A</string>
+ <string>ABCDABCDABCDABCD0000003C</string>
+ <string>ABCDABCDABCDABCD0000003E</string>
+ <string>ABCDABCDABCDABCD00000040</string>
+ <string>ABCDABCDABCDABCD00000042</string>
+ <string>ABCDABCDABCDABCD00000044</string>
+ <string>ABCDABCDABCDABCD00000046</string>
+ <string>ABCDABCDABCDABCD00000048</string>
+ <string>ABCDABCDABCDABCD0000004A</string>
+ <string>ABCDABCDABCDABCD0000004C</string>
+ <string>ABCDABCDABCDABCD0000004E</string>
+ <string>ABCDABCDABCDABCD00000050</string>
+ <string>ABCDABCDABCDABCD00000052</string>
+ <string>ABCDABCDABCDABCD00000054</string>
+ <string>ABCDABCDABCDABCD00000056</string>
+ <string>ABCDABCDABCDABCD00000058</string>
+ <string>ABCDABCDABCDABCD0000005A</string>
+ <string>ABCDABCDABCDABCD0000005C</string>
+ <string>ABCDABCDABCDABCD0000005E</string>
+ <string>ABCDABCDABCDABCD00000060</string>
+ <string>ABCDABCDABCDABCD00000062</string>
+ <string>ABCDABCDABCDABCD00000064</string>
+ <string>ABCDABCDABCDABCD00000066</string>
+ <string>ABCDABCDABCDABCD00000068</string>
+ <string>ABCDABCDABCDABCD0000006A</string>
+ <string>ABCDABCDABCDABCD0000006C</string>
+ <string>ABCDABCDABCDABCD0000006E</string>
+ <string>ABCDABCDABCDABCD00000070</string>
+ <string>ABCDABCDABCDABCD00000072</string>
+ <string>ABCDABCDABCDABCD00000074</string>
+ <string>ABCDABCDABCDABCD00000076</string>
+ <string>ABCDABCDABCDABCD00000078</string>
+ <string>ABCDABCDABCDABCD0000007A</string>
+ <string>ABCDABCDABCDABCD0000007C</string>
+ <string>ABCDABCDABCDABCD0000007E</string>
+ <string>ABCDABCDABCDABCD00000080</string>
+ <string>ABCDABCDABCDABCD00000082</string>
+ <string>ABCDABCDABCDABCD00000084</string>
+ <string>ABCDABCDABCDABCD00000086</string>
+ <string>ABCDABCDABCDABCD00000088</string>
+ <string>ABCDABCDABCDABCD0000008A</string>
+ <string>ABCDABCDABCDABCD0000008C</string>
+ <string>ABCDABCDABCDABCD0000008E</string>
+ <string>ABCDABCDABCDABCD00000090</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Source Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000031</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000031</string>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000092</string>
+ <string>ABCDABCDABCDABCD00000093</string>
+ <string>ABCDABCDABCDABCD00000094</string>
+ <string>ABCDABCDABCDABCD00000095</string>
+ <string>ABCDABCDABCDABCD00000096</string>
+ <string>ABCDABCDABCDABCD00000097</string>
+ <string>ABCDABCDABCDABCD00000098</string>
+ <string>ABCDABCDABCDABCD00000099</string>
+ <string>ABCDABCDABCDABCD0000009A</string>
+ <string>ABCDABCDABCDABCD0000009B</string>
+ <string>ABCDABCDABCDABCD0000009C</string>
+ <string>ABCDABCDABCDABCD0000009D</string>
+ <string>ABCDABCDABCDABCD0000009E</string>
+ <string>ABCDABCDABCDABCD0000009F</string>
+ <string>ABCDABCDABCDABCD000000A0</string>
+ <string>ABCDABCDABCDABCD000000A1</string>
+ <string>ABCDABCDABCDABCD000000A2</string>
+ <string>ABCDABCDABCDABCD000000A3</string>
+ <string>ABCDABCDABCDABCD000000A4</string>
+ <string>ABCDABCDABCDABCD000000A5</string>
+ <string>ABCDABCDABCDABCD000000A6</string>
+ <string>ABCDABCDABCDABCD000000A7</string>
+ <string>ABCDABCDABCDABCD000000A8</string>
+ <string>ABCDABCDABCDABCD000000A9</string>
+ <string>ABCDABCDABCDABCD000000AA</string>
+ <string>ABCDABCDABCDABCD000000AB</string>
+ <string>ABCDABCDABCDABCD000000AC</string>
+ <string>ABCDABCDABCDABCD000000AD</string>
+ <string>ABCDABCDABCDABCD000000AE</string>
+ <string>ABCDABCDABCDABCD000000AF</string>
+ <string>ABCDABCDABCDABCD000000B0</string>
+ <string>ABCDABCDABCDABCD000000B1</string>
+ <string>ABCDABCDABCDABCD000000B2</string>
+ <string>ABCDABCDABCDABCD000000B3</string>
+ <string>ABCDABCDABCDABCD000000B4</string>
+ <string>ABCDABCDABCDABCD000000B5</string>
+ <string>ABCDABCDABCDABCD000000B6</string>
+ <string>ABCDABCDABCDABCD000000B7</string>
+ <string>ABCDABCDABCDABCD000000B8</string>
+ <string>ABCDABCDABCDABCD000000B9</string>
+ <string>ABCDABCDABCDABCD000000BA</string>
+ <string>ABCDABCDABCDABCD000000BB</string>
+ <string>ABCDABCDABCDABCD000000BC</string>
+ <string>ABCDABCDABCDABCD000000BD</string>
+ <string>ABCDABCDABCDABCD000000BE</string>
+ <string>ABCDABCDABCDABCD000000BF</string>
+ <string>ABCDABCDABCDABCD000000C0</string>
+ <string>ABCDABCDABCDABCD000000C1</string>
+ <string>ABCDABCDABCDABCD000000C2</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Header Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
</dict>
<key>ABCDABCDABCDABCD00000033</key>
<dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000030</string>
+ <string>ABCDABCDABCDABCD00000031</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>datatool</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000034</key>
+ <dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>exceptions.cpp</string>
+ <string>alexer.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/exceptions.cpp</string>
+ <string>../../../../src/serial/datatool/alexer.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000034</key>
+ <key>ABCDABCDABCDABCD00000035</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000033</string>
+ <string>ABCDABCDABCDABCD00000034</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000035</key>
+ <key>ABCDABCDABCDABCD00000036</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>filecode.cpp</string>
+ <string>aliasstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/filecode.cpp</string>
+ <string>../../../../src/serial/datatool/aliasstr.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000036</key>
+ <key>ABCDABCDABCDABCD00000037</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000035</string>
+ <string>ABCDABCDABCDABCD00000036</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000037</key>
+ <key>ABCDABCDABCDABCD00000038</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>fileutil.cpp</string>
+ <string>aparser.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/fileutil.cpp</string>
+ <string>../../../../src/serial/datatool/aparser.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000038</key>
+ <key>ABCDABCDABCDABCD00000039</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000037</string>
+ <string>ABCDABCDABCDABCD00000038</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000039</key>
+ <key>ABCDABCDABCDABCD0000003A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>generate.cpp</string>
+ <string>blocktype.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/generate.cpp</string>
+ <string>../../../../src/serial/datatool/blocktype.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000003A</key>
+ <key>ABCDABCDABCDABCD0000003B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000039</string>
+ <string>ABCDABCDABCDABCD0000003A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000003B</key>
+ <key>ABCDABCDABCDABCD0000003C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>lexer.cpp</string>
+ <string>choiceptrstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/lexer.cpp</string>
+ <string>../../../../src/serial/datatool/choiceptrstr.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000003C</key>
+ <key>ABCDABCDABCDABCD0000003D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000003B</string>
+ <string>ABCDABCDABCDABCD0000003C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000003D</key>
+ <key>ABCDABCDABCDABCD0000003E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>mcontainer.cpp</string>
+ <string>choicestr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/mcontainer.cpp</string>
+ <string>../../../../src/serial/datatool/choicestr.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000003E</key>
+ <key>ABCDABCDABCDABCD0000003F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000003D</string>
+ <string>ABCDABCDABCDABCD0000003E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000003F</key>
+ <key>ABCDABCDABCDABCD00000040</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>module.cpp</string>
+ <string>choicetype.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/module.cpp</string>
+ <string>../../../../src/serial/datatool/choicetype.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000040</key>
+ <key>ABCDABCDABCDABCD00000041</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000003F</string>
+ <string>ABCDABCDABCDABCD00000040</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000041</key>
+ <key>ABCDABCDABCDABCD00000042</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>moduleset.cpp</string>
+ <string>classstr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/moduleset.cpp</string>
+ <string>../../../../src/serial/datatool/classstr.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000042</key>
+ <key>ABCDABCDABCDABCD00000043</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000041</string>
+ <string>ABCDABCDABCDABCD00000042</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000043</key>
+ <key>ABCDABCDABCDABCD00000044</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>namespace.cpp</string>
+ <string>code.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/namespace.cpp</string>
+ <string>../../../../src/serial/datatool/code.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000044</key>
+ <key>ABCDABCDABCDABCD00000045</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000043</string>
+ <string>ABCDABCDABCDABCD00000044</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000045</key>
+ <key>ABCDABCDABCDABCD00000046</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>parser.cpp</string>
+ <string>comments.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/parser.cpp</string>
+ <string>../../../../src/serial/datatool/comments.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000046</key>
+ <key>ABCDABCDABCDABCD00000047</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000045</string>
+ <string>ABCDABCDABCDABCD00000046</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000047</key>
+ <key>ABCDABCDABCDABCD00000048</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>ptrstr.cpp</string>
+ <string>datatool.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/ptrstr.cpp</string>
+ <string>../../../../src/serial/datatool/datatool.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000048</key>
+ <key>ABCDABCDABCDABCD00000049</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000047</string>
+ <string>ABCDABCDABCDABCD00000048</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000049</key>
+ <key>ABCDABCDABCDABCD0000004A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>reftype.cpp</string>
+ <string>dtdaux.cpp</string>
<key>path</key>
- <string>../../../../src/serial/datatool/reftype.cpp</string>
+ <string>../../../../src/serial/datatool/dtdaux.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000004A</key>
+ <key>ABCDABCDABCDABCD0000004B</key>
<dict>
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+ <key>ABCDABCDABCDABCD000000B8</key>
<dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD0000009C</string>
- <string>ABCDABCDABCDABCD0000009D</string>
- <string>ABCDABCDABCDABCD0000009E</string>
- </array>
<key>isa</key>
- <string>PBXGroup</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>project_tree_builder</string>
+ <string>traversal_node.hpp</string>
+ <key>path</key>
+ <string>../../../../src/serial/datatool/traversal_node.hpp</string>
<key>sourceTree</key>
- <string><group></string>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A0</key>
+ <key>ABCDABCDABCDABCD000000B9</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>configurable_file.cpp</string>
+ <string>traversal_pattern_match_callback.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/configurable_file.cpp</string>
+ <string>../../../../src/serial/datatool/traversal_pattern_match_callback.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A1</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000A0</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000A2</key>
+ <key>ABCDABCDABCDABCD000000BA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>file_contents.cpp</string>
+ <string>traversal_spec_file_parser.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/file_contents.cpp</string>
+ <string>../../../../src/serial/datatool/traversal_spec_file_parser.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A3</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000A2</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000A4</key>
+ <key>ABCDABCDABCDABCD000000BB</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>mac_prj_generator.cpp</string>
+ <string>type.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/mac_prj_generator.cpp</string>
+ <string>../../../../src/serial/datatool/type.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A5</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000A4</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000A6</key>
+ <key>ABCDABCDABCDABCD000000BC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_configure.cpp</string>
+ <string>typestr.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_configure.cpp</string>
+ <string>../../../../src/serial/datatool/typestr.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A7</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000A6</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000A8</key>
+ <key>ABCDABCDABCDABCD000000BD</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_configure_prj_generator.cpp</string>
+ <string>unitype.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_configure_prj_generator.cpp</string>
+ <string>../../../../src/serial/datatool/unitype.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000A9</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000A8</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000AA</key>
+ <key>ABCDABCDABCDABCD000000BE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_dlls_info.cpp</string>
+ <string>value.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info.cpp</string>
+ <string>../../../../src/serial/datatool/value.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000AB</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000AA</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000AC</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>msvc_makefile.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_makefile.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000AD</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000AC</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000AE</key>
+ <key>ABCDABCDABCDABCD000000BF</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_masterproject_generator.cpp</string>
+ <string>wsdllexer.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_masterproject_generator.cpp</string>
+ <string>../../../../src/serial/datatool/wsdllexer.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000AF</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000AE</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000B0</key>
+ <key>ABCDABCDABCDABCD000000C0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_files_collector.cpp</string>
+ <string>wsdlparser.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_files_collector.cpp</string>
+ <string>../../../../src/serial/datatool/wsdlparser.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000B1</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000B0</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000B2</key>
+ <key>ABCDABCDABCDABCD000000C1</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_generator.cpp</string>
+ <string>xsdlexer.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_generator.cpp</string>
+ <string>../../../../src/serial/datatool/xsdlexer.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000B3</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000B2</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD000000B4</key>
+ <key>ABCDABCDABCDABCD000000C2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_utils.cpp</string>
+ <string>xsdparser.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_utils.cpp</string>
+ <string>../../../../src/serial/datatool/xsdparser.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000B5</key>
+ <key>ABCDABCDABCDABCD000000C3</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000B4</string>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000035</string>
+ <string>ABCDABCDABCDABCD00000037</string>
+ <string>ABCDABCDABCDABCD00000039</string>
+ <string>ABCDABCDABCDABCD0000003B</string>
+ <string>ABCDABCDABCDABCD0000003D</string>
+ <string>ABCDABCDABCDABCD0000003F</string>
+ <string>ABCDABCDABCDABCD00000041</string>
+ <string>ABCDABCDABCDABCD00000043</string>
+ <string>ABCDABCDABCDABCD00000045</string>
+ <string>ABCDABCDABCDABCD00000047</string>
+ <string>ABCDABCDABCDABCD00000049</string>
+ <string>ABCDABCDABCDABCD0000004B</string>
+ <string>ABCDABCDABCDABCD0000004D</string>
+ <string>ABCDABCDABCDABCD0000004F</string>
+ <string>ABCDABCDABCDABCD00000051</string>
+ <string>ABCDABCDABCDABCD00000053</string>
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+ <string>ABCDABCDABCDABCD00000057</string>
+ <string>ABCDABCDABCDABCD00000059</string>
+ <string>ABCDABCDABCDABCD0000005B</string>
+ <string>ABCDABCDABCDABCD0000005D</string>
+ <string>ABCDABCDABCDABCD0000005F</string>
+ <string>ABCDABCDABCDABCD00000061</string>
+ <string>ABCDABCDABCDABCD00000063</string>
+ <string>ABCDABCDABCDABCD00000065</string>
+ <string>ABCDABCDABCDABCD00000067</string>
+ <string>ABCDABCDABCDABCD00000069</string>
+ <string>ABCDABCDABCDABCD0000006B</string>
+ <string>ABCDABCDABCDABCD0000006D</string>
+ <string>ABCDABCDABCDABCD0000006F</string>
+ <string>ABCDABCDABCDABCD00000071</string>
+ <string>ABCDABCDABCDABCD00000073</string>
+ <string>ABCDABCDABCDABCD00000075</string>
+ <string>ABCDABCDABCDABCD00000077</string>
+ <string>ABCDABCDABCDABCD00000079</string>
+ <string>ABCDABCDABCDABCD0000007B</string>
+ <string>ABCDABCDABCDABCD0000007D</string>
+ <string>ABCDABCDABCDABCD0000007F</string>
+ <string>ABCDABCDABCDABCD00000081</string>
+ <string>ABCDABCDABCDABCD00000083</string>
+ <string>ABCDABCDABCDABCD00000085</string>
+ <string>ABCDABCDABCDABCD00000087</string>
+ <string>ABCDABCDABCDABCD00000089</string>
+ <string>ABCDABCDABCDABCD0000008B</string>
+ <string>ABCDABCDABCDABCD0000008D</string>
+ <string>ABCDABCDABCDABCD0000008F</string>
+ <string>ABCDABCDABCDABCD00000091</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXSourcesBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD000000B6</key>
+ <key>ABCDABCDABCDABCD000000C4</key>
<dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000C5</string>
+ <string>ABCDABCDABCDABCD000000C6</string>
+ <string>ABCDABCDABCDABCD000000C7</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>msvc_project_context.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_project_context.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXFrameworksBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD000000B7</key>
+ <key>ABCDABCDABCDABCD000000C5</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000B6</string>
+ <string>ABCDABCDABCDABCD0000001C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000B8</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>msvc_site.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_site.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000B9</key>
+ <key>ABCDABCDABCDABCD000000C6</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000B8</string>
+ <string>ABCDABCDABCDABCD0000001F</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000BA</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>msvc_sln_generator.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_sln_generator.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000BB</key>
+ <key>ABCDABCDABCDABCD000000C7</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000BA</string>
+ <string>ABCDABCDABCDABCD00000020</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000BC</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>prj_file_collector.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/prj_file_collector.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000BD</key>
+ <key>ABCDABCDABCDABCD000000C8</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000BC</string>
+ <key>files</key>
+ <array></array>
+ <key>inputPaths</key>
+ <array>
+ <string>$(TARGET_BUILD_DIR)/$(TARGET_NAME)</string>
+ </array>
+ <key>outputPaths</key>
+ <array></array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXShellScriptBuildPhase</string>
+ <key>shellPath</key>
+ <string>/bin/sh</string>
+ <key>shellScript</key>
+ <string>export BUILD_TREE_ROOT=../..
export BUILD_TREE_BIN=bin/${CONFIGURATION}
"$BUILD_TREE_ROOT/copybin.sh"</string>
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
- <key>ABCDABCDABCDABCD000000BE</key>
+ <key>ABCDABCDABCDABCD000000C9</key>
<dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD000000CA</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000C3</string>
+ <string>ABCDABCDABCDABCD000000C4</string>
+ <string>ABCDABCDABCDABCD000000C8</string>
+ </array>
+ <key>dependencies</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000000B</string>
+ <string>ABCDABCDABCDABCD0000000E</string>
+ <string>ABCDABCDABCDABCD0000000F</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>PBXNativeTarget</string>
<key>name</key>
- <string>proj_builder_app.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_builder_app.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>datatool</string>
+ <key>productName</key>
+ <string>datatool</string>
+ <key>productReference</key>
+ <string>ABCDABCDABCDABCD00000015</string>
+ <key>productType</key>
+ <string>com.apple.product-type.tool</string>
</dict>
- <key>ABCDABCDABCDABCD000000BF</key>
+ <key>ABCDABCDABCDABCD000000CA</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000BE</string>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000CB</string>
+ <string>ABCDABCDABCDABCD000000CC</string>
+ <string>ABCDABCDABCDABCD000000CD</string>
+ <string>ABCDABCDABCDABCD000000CE</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000000C0</key>
+ <key>ABCDABCDABCDABCD000000CB</key>
<dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>datatool</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>proj_datatool_generated_src.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_datatool_generated_src.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000C1</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000C0</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000000C2</key>
+ <key>ABCDABCDABCDABCD000000CC</key>
<dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>datatool</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>XCBuildConfiguration</string>
<key>name</key>
- <string>proj_item.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_item.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000000C3</key>
+ <key>ABCDABCDABCDABCD000000CD</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000C2</string>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>datatool</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000000C4</key>
+ <key>ABCDABCDABCDABCD000000CE</key>
<dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>datatool</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>XCBuildConfiguration</string>
<key>name</key>
- <string>proj_projects.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_projects.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD000000C5</key>
+ <key>ABCDABCDABCDABCD000000CF</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000C4</string>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD00000155</string>
+ <key>remoteInfo</key>
+ <string>project_tree_builder</string>
</dict>
- <key>ABCDABCDABCDABCD000000C6</key>
+ <key>ABCDABCDABCDABCD000000D0</key>
<dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000D4</string>
+ <string>ABCDABCDABCDABCD000000D6</string>
+ <string>ABCDABCDABCDABCD000000D8</string>
+ <string>ABCDABCDABCDABCD000000DA</string>
+ <string>ABCDABCDABCDABCD000000DC</string>
+ <string>ABCDABCDABCDABCD000000DE</string>
+ <string>ABCDABCDABCDABCD000000E0</string>
+ <string>ABCDABCDABCDABCD000000E2</string>
+ <string>ABCDABCDABCDABCD000000E4</string>
+ <string>ABCDABCDABCDABCD000000E6</string>
+ <string>ABCDABCDABCDABCD000000E8</string>
+ <string>ABCDABCDABCDABCD000000EA</string>
+ <string>ABCDABCDABCDABCD000000EC</string>
+ <string>ABCDABCDABCDABCD000000EE</string>
+ <string>ABCDABCDABCDABCD000000F0</string>
+ <string>ABCDABCDABCDABCD000000F2</string>
+ <string>ABCDABCDABCDABCD000000F4</string>
+ <string>ABCDABCDABCDABCD000000F6</string>
+ <string>ABCDABCDABCDABCD000000F8</string>
+ <string>ABCDABCDABCDABCD000000FA</string>
+ <string>ABCDABCDABCDABCD000000FC</string>
+ <string>ABCDABCDABCDABCD000000FE</string>
+ <string>ABCDABCDABCDABCD00000100</string>
+ <string>ABCDABCDABCDABCD00000102</string>
+ <string>ABCDABCDABCDABCD00000104</string>
+ <string>ABCDABCDABCDABCD00000106</string>
+ <string>ABCDABCDABCDABCD00000108</string>
+ <string>ABCDABCDABCDABCD0000010A</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
+ <string>PBXGroup</string>
<key>name</key>
- <string>proj_src_resolver.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_src_resolver.cpp</string>
+ <string>Source Files</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000000C7</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000C6</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD000000C8</key>
+ <key>ABCDABCDABCDABCD000000D1</key>
<dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>proj_tree.cpp</string>
- <key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_tree.cpp</string>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000010C</string>
+ <string>ABCDABCDABCDABCD0000010D</string>
+ <string>ABCDABCDABCDABCD0000010E</string>
+ <string>ABCDABCDABCDABCD0000010F</string>
+ <string>ABCDABCDABCDABCD00000110</string>
+ <string>ABCDABCDABCDABCD00000111</string>
+ <string>ABCDABCDABCDABCD00000112</string>
+ <string>ABCDABCDABCDABCD00000113</string>
+ <string>ABCDABCDABCDABCD00000114</string>
+ <string>ABCDABCDABCDABCD00000115</string>
+ <string>ABCDABCDABCDABCD00000116</string>
+ <string>ABCDABCDABCDABCD00000117</string>
+ <string>ABCDABCDABCDABCD00000118</string>
+ <string>ABCDABCDABCDABCD00000119</string>
+ <string>ABCDABCDABCDABCD0000011A</string>
+ <string>ABCDABCDABCDABCD0000011B</string>
+ <string>ABCDABCDABCDABCD0000011C</string>
+ <string>ABCDABCDABCDABCD0000011D</string>
+ <string>ABCDABCDABCDABCD0000011E</string>
+ <string>ABCDABCDABCDABCD0000011F</string>
+ <string>ABCDABCDABCDABCD00000120</string>
+ <string>ABCDABCDABCDABCD00000121</string>
+ <string>ABCDABCDABCDABCD00000122</string>
+ <string>ABCDABCDABCDABCD00000123</string>
+ <string>ABCDABCDABCDABCD00000124</string>
+ <string>ABCDABCDABCDABCD00000125</string>
+ <string>ABCDABCDABCDABCD00000126</string>
+ <string>ABCDABCDABCDABCD00000127</string>
+ <string>ABCDABCDABCDABCD00000128</string>
+ <string>ABCDABCDABCDABCD00000129</string>
+ <string>ABCDABCDABCDABCD0000012A</string>
+ <string>ABCDABCDABCDABCD0000012B</string>
+ <string>ABCDABCDABCDABCD0000012C</string>
+ <string>ABCDABCDABCDABCD0000012D</string>
+ <string>ABCDABCDABCDABCD0000012E</string>
+ <string>ABCDABCDABCDABCD0000012F</string>
+ <string>ABCDABCDABCDABCD00000130</string>
+ <string>ABCDABCDABCDABCD00000131</string>
+ <string>ABCDABCDABCDABCD00000132</string>
+ <string>ABCDABCDABCDABCD00000133</string>
+ <string>ABCDABCDABCDABCD00000134</string>
+ <string>ABCDABCDABCDABCD00000135</string>
+ <string>ABCDABCDABCDABCD00000136</string>
+ <string>ABCDABCDABCDABCD00000137</string>
+ <string>ABCDABCDABCDABCD00000138</string>
+ <string>ABCDABCDABCDABCD00000139</string>
+ <string>ABCDABCDABCDABCD0000013A</string>
+ <string>ABCDABCDABCDABCD0000013B</string>
+ <string>ABCDABCDABCDABCD0000013C</string>
+ <string>ABCDABCDABCDABCD0000013D</string>
+ <string>ABCDABCDABCDABCD0000013E</string>
+ <string>ABCDABCDABCDABCD0000013F</string>
+ <string>ABCDABCDABCDABCD00000140</string>
+ <string>ABCDABCDABCDABCD00000141</string>
+ <string>ABCDABCDABCDABCD00000142</string>
+ <string>ABCDABCDABCDABCD00000143</string>
+ <string>ABCDABCDABCDABCD00000144</string>
+ <string>ABCDABCDABCDABCD00000145</string>
+ <string>ABCDABCDABCDABCD00000146</string>
+ <string>ABCDABCDABCDABCD00000147</string>
+ <string>ABCDABCDABCDABCD00000148</string>
+ <string>ABCDABCDABCDABCD00000149</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Header Files</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD000000C9</key>
+ <key>ABCDABCDABCDABCD000000D2</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD000000C8</string>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000014A</string>
+ <string>ABCDABCDABCDABCD0000014B</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Datatool Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD000000CA</key>
+ <key>ABCDABCDABCDABCD000000D3</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000D0</string>
+ <string>ABCDABCDABCDABCD000000D1</string>
+ <string>ABCDABCDABCDABCD000000D2</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>project_tree_builder</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000D4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>proj_tree_builder.cpp</string>
+ <string>configurable_file.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_tree_builder.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/configurable_file.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000CB</key>
+ <key>ABCDABCDABCDABCD000000D5</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000CA</string>
+ <string>ABCDABCDABCDABCD000000D4</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000CC</key>
+ <key>ABCDABCDABCDABCD000000D6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>proj_utils.cpp</string>
+ <string>file_contents.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_utils.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/file_contents.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000CD</key>
+ <key>ABCDABCDABCDABCD000000D7</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000CC</string>
+ <string>ABCDABCDABCDABCD000000D6</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000CE</key>
+ <key>ABCDABCDABCDABCD000000D8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>property_list__.cpp</string>
+ <string>mac_prj_generator.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/property_list__.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/mac_prj_generator.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000CF</key>
+ <key>ABCDABCDABCDABCD000000D9</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000CE</string>
+ <string>ABCDABCDABCDABCD000000D8</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000D0</key>
+ <key>ABCDABCDABCDABCD000000DA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>property_list___.cpp</string>
+ <string>msvc_configure.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/property_list___.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_configure.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000D1</key>
+ <key>ABCDABCDABCDABCD000000DB</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000D0</string>
+ <string>ABCDABCDABCDABCD000000DA</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000D2</key>
+ <key>ABCDABCDABCDABCD000000DC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>ptb_gui.cpp</string>
+ <string>msvc_configure_prj_generator.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/ptb_gui.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_configure_prj_generator.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000D3</key>
+ <key>ABCDABCDABCDABCD000000DD</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000D2</string>
+ <string>ABCDABCDABCDABCD000000DC</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000D4</key>
+ <key>ABCDABCDABCDABCD000000DE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>ptb_registry.cpp</string>
+ <string>msvc_dlls_info.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/ptb_registry.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000D5</key>
+ <key>ABCDABCDABCDABCD000000DF</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000D4</string>
+ <string>ABCDABCDABCDABCD000000DE</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000D6</key>
+ <key>ABCDABCDABCDABCD000000E0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>resolver.cpp</string>
+ <string>msvc_makefile.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/resolver.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_makefile.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000D7</key>
+ <key>ABCDABCDABCDABCD000000E1</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD000000D6</string>
+ <string>ABCDABCDABCDABCD000000E0</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD000000D8</key>
+ <key>ABCDABCDABCDABCD000000E2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Array.hpp</string>
+ <string>msvc_masterproject_generator.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Array.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_masterproject_generator.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000D9</key>
+ <key>ABCDABCDABCDABCD000000E3</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000E2</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000E4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Array_.hpp</string>
+ <string>msvc_prj_files_collector.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Array_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_files_collector.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DA</key>
+ <key>ABCDABCDABCDABCD000000E5</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000E4</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000E6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>configurable_file.hpp</string>
+ <string>msvc_prj_generator.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/configurable_file.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_generator.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DB</key>
+ <key>ABCDABCDABCDABCD000000E7</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000E6</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000E8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Configuration.hpp</string>
+ <string>msvc_prj_utils.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Configuration.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_utils.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DC</key>
+ <key>ABCDABCDABCDABCD000000E9</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000E8</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000EA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Configuration_.hpp</string>
+ <string>msvc_project_context.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Configuration_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_project_context.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DD</key>
+ <key>ABCDABCDABCDABCD000000EB</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000EA</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000EC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Configurations.hpp</string>
+ <string>msvc_site.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Configurations.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_site.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DE</key>
+ <key>ABCDABCDABCDABCD000000ED</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000EC</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000EE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Configurations_.hpp</string>
+ <string>msvc_sln_generator.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Configurations_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_sln_generator.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000DF</key>
+ <key>ABCDABCDABCDABCD000000EF</key>
<dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000EE</string>
<key>isa</key>
- <string>PBXFileReference</string>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000F0</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Dict.hpp</string>
+ <string>prj_file_collector.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Dict.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/prj_file_collector.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E0</key>
+ <key>ABCDABCDABCDABCD000000F1</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000F0</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Dict_.hpp</string>
+ <string>proj_builder_app.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Dict_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_builder_app.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E1</key>
+ <key>ABCDABCDABCDABCD000000F3</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000F2</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000F4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>File.hpp</string>
+ <string>proj_datatool_generated_src.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/File.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_datatool_generated_src.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E2</key>
+ <key>ABCDABCDABCDABCD000000F5</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000F4</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000F6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>File_.hpp</string>
+ <string>proj_item.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/File_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_item.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E3</key>
+ <key>ABCDABCDABCDABCD000000F7</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000F6</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000F8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>file_contents.hpp</string>
+ <string>proj_projects.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/file_contents.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_projects.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E4</key>
+ <key>ABCDABCDABCDABCD000000F9</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000F8</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000FA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>FileConfiguration.hpp</string>
+ <string>proj_src_resolver.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/FileConfiguration.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_src_resolver.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E5</key>
+ <key>ABCDABCDABCDABCD000000FB</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000FA</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000000FC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>FileConfiguration_.hpp</string>
+ <string>proj_tree.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/FileConfiguration_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_tree.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E6</key>
+ <key>ABCDABCDABCDABCD000000FD</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000FC</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD000000FE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Files.hpp</string>
+ <string>proj_tree_builder.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Files.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_tree_builder.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E7</key>
+ <key>ABCDABCDABCDABCD000000FF</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000000FE</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD00000100</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Files_.hpp</string>
+ <string>proj_utils.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Files_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_utils.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E8</key>
+ <key>ABCDABCDABCDABCD00000101</key>
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+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000100</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD00000102</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Filter.hpp</string>
+ <string>property_list__.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Filter.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list__.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000E9</key>
+ <key>ABCDABCDABCDABCD00000103</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000102</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD00000104</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>Filter_.hpp</string>
+ <string>property_list___.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Filter_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list___.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000EA</key>
+ <key>ABCDABCDABCDABCD00000105</key>
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+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000104</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>mac_prj_generator.hpp</string>
+ <string>ptb_gui.cpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/mac_prj_generator.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/ptb_gui.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000EB</key>
+ <key>ABCDABCDABCDABCD00000107</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000106</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD00000108</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>msvc71_project__.hpp</string>
+ <string>ptb_registry.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/msvc71_project__.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/ptb_registry.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000EC</key>
+ <key>ABCDABCDABCDABCD00000109</key>
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+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000108</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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+ <key>ABCDABCDABCDABCD0000010A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>msvc71_project_module.hpp</string>
+ <string>resolver.cpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/msvc71_project_module.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/resolver.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000ED</key>
+ <key>ABCDABCDABCDABCD0000010B</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000010A</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_configure.hpp</string>
+ <string>Array.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_configure.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Array.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000EE</key>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_configure_prj_generator.hpp</string>
+ <string>Array_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_configure_prj_generator.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Array_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000EF</key>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_dlls_info.hpp</string>
+ <string>configurable_file.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/configurable_file.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_dlls_info_utils.hpp</string>
+ <string>Configuration.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info_utils.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Configuration.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_makefile.hpp</string>
+ <string>Configuration_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_makefile.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Configuration_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000F2</key>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_masterproject_generator.hpp</string>
+ <string>Configurations.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_masterproject_generator.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Configurations.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000F3</key>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_defines.hpp</string>
+ <string>Configurations_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_defines.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Configurations_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_files_collector.hpp</string>
+ <string>Dict.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_files_collector.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Dict.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_generator.hpp</string>
+ <string>Dict_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_generator.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Dict_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_prj_utils.hpp</string>
+ <string>File.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_prj_utils.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/File.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000F7</key>
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<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_project_context.hpp</string>
+ <string>File_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_project_context.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/File_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000F8</key>
+ <key>ABCDABCDABCDABCD00000117</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_site.hpp</string>
+ <string>file_contents.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_site.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/file_contents.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000F9</key>
+ <key>ABCDABCDABCDABCD00000118</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_sln_generator.hpp</string>
+ <string>FileConfiguration.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_sln_generator.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/FileConfiguration.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FA</key>
+ <key>ABCDABCDABCDABCD00000119</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_tools_implement.hpp</string>
+ <string>FileConfiguration_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_tools_implement.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/FileConfiguration_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FB</key>
+ <key>ABCDABCDABCDABCD0000011A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc_traits.hpp</string>
+ <string>Files.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc_traits.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Files.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FC</key>
+ <key>ABCDABCDABCDABCD0000011B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Platform.hpp</string>
+ <string>Files_.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Platform.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Files_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FD</key>
+ <key>ABCDABCDABCDABCD0000011C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Platform_.hpp</string>
+ <string>Filter.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Platform_.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Filter.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FE</key>
+ <key>ABCDABCDABCDABCD0000011D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Platforms.hpp</string>
+ <string>Filter_.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Platforms.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Filter_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000000FF</key>
+ <key>ABCDABCDABCDABCD0000011E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Platforms_.hpp</string>
+ <string>mac_prj_generator.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Platforms_.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/mac_prj_generator.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000100</key>
+ <key>ABCDABCDABCDABCD0000011F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Plist.hpp</string>
+ <string>msvc71_project__.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Plist.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/msvc71_project__.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000101</key>
+ <key>ABCDABCDABCDABCD00000120</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Plist_.hpp</string>
+ <string>msvc71_project_module.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Plist_.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/msvc71_project_module.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000102</key>
+ <key>ABCDABCDABCDABCD00000121</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>prj_file_collector.hpp</string>
+ <string>msvc_configure.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/prj_file_collector.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_configure.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000103</key>
+ <key>ABCDABCDABCDABCD00000122</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_builder_app.hpp</string>
+ <string>msvc_configure_prj_generator.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_builder_app.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_configure_prj_generator.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000104</key>
+ <key>ABCDABCDABCDABCD00000123</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_datatool_generated_src.hpp</string>
+ <string>msvc_dlls_info.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_datatool_generated_src.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000105</key>
+ <key>ABCDABCDABCDABCD00000124</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_item.hpp</string>
+ <string>msvc_dlls_info_utils.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_item.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_dlls_info_utils.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000106</key>
+ <key>ABCDABCDABCDABCD00000125</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_projects.hpp</string>
+ <string>msvc_makefile.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_projects.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_makefile.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000107</key>
+ <key>ABCDABCDABCDABCD00000126</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_src_resolver.hpp</string>
+ <string>msvc_masterproject_generator.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_src_resolver.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_masterproject_generator.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000108</key>
+ <key>ABCDABCDABCDABCD00000127</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_tree.hpp</string>
+ <string>msvc_prj_defines.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_tree.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_defines.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000109</key>
+ <key>ABCDABCDABCDABCD00000128</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_tree_builder.hpp</string>
+ <string>msvc_prj_files_collector.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_tree_builder.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_files_collector.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010A</key>
+ <key>ABCDABCDABCDABCD00000129</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>proj_utils.hpp</string>
+ <string>msvc_prj_generator.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/proj_utils.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_generator.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010B</key>
+ <key>ABCDABCDABCDABCD0000012A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>property_list__.hpp</string>
+ <string>msvc_prj_utils.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/property_list__.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_prj_utils.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010C</key>
+ <key>ABCDABCDABCDABCD0000012B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>property_list_module.hpp</string>
+ <string>msvc_project_context.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/property_list_module.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_project_context.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010D</key>
+ <key>ABCDABCDABCDABCD0000012C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>ptb_err_codes.hpp</string>
+ <string>msvc_site.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/ptb_err_codes.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_site.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010E</key>
+ <key>ABCDABCDABCDABCD0000012D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>ptb_gui.h</string>
+ <string>msvc_sln_generator.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/ptb_gui.h</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_sln_generator.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000010F</key>
+ <key>ABCDABCDABCDABCD0000012E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>ptb_registry.hpp</string>
+ <string>msvc_tools_implement.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/ptb_registry.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_tools_implement.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000110</key>
+ <key>ABCDABCDABCDABCD0000012F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>resolver.hpp</string>
+ <string>msvc_traits.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/resolver.hpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc_traits.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000111</key>
+ <key>ABCDABCDABCDABCD00000130</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>stl_msvc_usage.hpp</string>
+ <string>Platform.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/stl_msvc_usage.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Platform.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000112</key>
+ <key>ABCDABCDABCDABCD00000131</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Tool.hpp</string>
+ <string>Platform_.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Tool.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Platform_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000113</key>
+ <key>ABCDABCDABCDABCD00000132</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>Tool_.hpp</string>
+ <string>Platforms.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/Tool_.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Platforms.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000114</key>
+ <key>ABCDABCDABCDABCD00000133</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>VisualStudioProject.hpp</string>
+ <string>Platforms_.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/VisualStudioProject.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Platforms_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000115</key>
+ <key>ABCDABCDABCDABCD00000134</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>VisualStudioProject_.hpp</string>
+ <string>Plist.hpp</string>
<key>path</key>
- <string>../../../../include/build-system/project_tree_builder/VisualStudioProject_.hpp</string>
+ <string>../../../../include/build-system/project_tree_builder/Plist.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000116</key>
+ <key>ABCDABCDABCDABCD00000135</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>text</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>msvc71_project.dtd</string>
+ <string>Plist_.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
+ <string>../../../../include/build-system/project_tree_builder/Plist_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000117</key>
+ <key>ABCDABCDABCDABCD00000136</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>text.xml</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>property_list.xsd</string>
+ <string>prj_file_collector.hpp</string>
<key>path</key>
- <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
+ <string>../../../../src/build-system/project_tree_builder/prj_file_collector.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000118</key>
+ <key>ABCDABCDABCDABCD00000137</key>
<dict>
- <key>files</key>
- <array></array>
- <key>inputPaths</key>
- <array>
- <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
- <string>../../../../src/build-system/project_tree_builder/msvc71_project.def</string>
- <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
- <string>../../../../src/build-system/project_tree_builder/property_list.def</string>
- </array>
- <key>outputPaths</key>
- <array>
- <string>../../../../src/build-system/project_tree_builder/msvc71_project.files</string>
- <string>../../../../src/build-system/project_tree_builder/property_list.files</string>
- </array>
<key>isa</key>
- <string>PBXShellScriptBuildPhase</string>
- <key>shellPath</key>
- <string>/bin/sh</string>
- <key>shellScript</key>
- <string>echo Using datatool to create a C++ objects from msvc71_project.dtd
../bin/$CONFIGURATION/datatool -oex "" -oA -odi -ocvs -pch ncbi_pch.hpp -m build-system/project_tree_builder/msvc71_project.dtd -oc msvc71_project -od ../../../../src/build-system/project_tree_builder/msvc71_project.def -or build-system/project_tree_builder/ -oR ../../../../
echo Using datatool to create a C++ objects from property_list.xsd
../bin/$CONFIGURATION/datatool -oex "& [...]
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>proj_builder_app.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_builder_app.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000119</key>
+ <key>ABCDABCDABCDABCD00000138</key>
<dict>
- <key>files</key>
- <array>
- <string>ABCDABCDABCDABCD000000A1</string>
- <string>ABCDABCDABCDABCD000000A3</string>
- <string>ABCDABCDABCDABCD000000A5</string>
- <string>ABCDABCDABCDABCD000000A7</string>
- <string>ABCDABCDABCDABCD000000A9</string>
- <string>ABCDABCDABCDABCD000000AB</string>
- <string>ABCDABCDABCDABCD000000AD</string>
- <string>ABCDABCDABCDABCD000000AF</string>
- <string>ABCDABCDABCDABCD000000B1</string>
- <string>ABCDABCDABCDABCD000000B3</string>
- <string>ABCDABCDABCDABCD000000B5</string>
- <string>ABCDABCDABCDABCD000000B7</string>
- <string>ABCDABCDABCDABCD000000B9</string>
- <string>ABCDABCDABCDABCD000000BB</string>
- <string>ABCDABCDABCDABCD000000BD</string>
- <string>ABCDABCDABCDABCD000000BF</string>
- <string>ABCDABCDABCDABCD000000C1</string>
- <string>ABCDABCDABCDABCD000000C3</string>
- <string>ABCDABCDABCDABCD000000C5</string>
- <string>ABCDABCDABCDABCD000000C7</string>
- <string>ABCDABCDABCDABCD000000C9</string>
- <string>ABCDABCDABCDABCD000000CB</string>
- <string>ABCDABCDABCDABCD000000CD</string>
- <string>ABCDABCDABCDABCD000000CF</string>
- <string>ABCDABCDABCDABCD000000D1</string>
- <string>ABCDABCDABCDABCD000000D3</string>
- <string>ABCDABCDABCDABCD000000D5</string>
- <string>ABCDABCDABCDABCD000000D7</string>
- </array>
<key>isa</key>
- <string>PBXSourcesBuildPhase</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>proj_datatool_generated_src.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_datatool_generated_src.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011A</key>
+ <key>ABCDABCDABCDABCD00000139</key>
<dict>
- <key>explicitFileType</key>
- <string>compiled.mach-o.executable</string>
- <key>includeInIndex</key>
- <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>proj_item.hpp</string>
<key>path</key>
- <string>project_tree_builder</string>
+ <string>../../../../src/build-system/project_tree_builder/proj_item.hpp</string>
<key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011B</key>
+ <key>ABCDABCDABCDABCD0000013A</key>
<dict>
- <key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD0000011C</string>
- <key>buildPhases</key>
- <array>
- <string>ABCDABCDABCDABCD00000118</string>
- <string>ABCDABCDABCDABCD00000119</string>
- </array>
- <key>dependencies</key>
- <array>
- <string>ABCDABCDABCDABCD00000007</string>
- <string>ABCDABCDABCDABCD00000008</string>
- <string>ABCDABCDABCDABCD00000009</string>
- <string>ABCDABCDABCDABCD0000000A</string>
- <string>ABCDABCDABCDABCD0000000B</string>
- <string>ABCDABCDABCDABCD0000000C</string>
- </array>
<key>isa</key>
- <string>PBXNativeTarget</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>project_tree_builder</string>
- <key>productName</key>
- <string>project_tree_builder</string>
- <key>productReference</key>
- <string>ABCDABCDABCDABCD0000011A</string>
- <key>productType</key>
- <string>com.apple.product-type.tool</string>
+ <string>proj_projects.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_projects.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011C</key>
+ <key>ABCDABCDABCDABCD0000013B</key>
<dict>
- <key>buildConfigurations</key>
- <array>
- <string>ABCDABCDABCDABCD0000011D</string>
- <string>ABCDABCDABCDABCD0000011E</string>
- <string>ABCDABCDABCDABCD0000011F</string>
- <string>ABCDABCDABCDABCD00000120</string>
- </array>
- <key>defaultConfigurationIsVisible</key>
- <string>0</string>
- <key>defaultConfigurationName</key>
- <string>ReleaseDLL</string>
<key>isa</key>
- <string>XCConfigurationList</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>proj_src_resolver.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_src_resolver.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011D</key>
+ <key>ABCDABCDABCDABCD0000013C</key>
<dict>
- <key>buildSettings</key>
- <dict>
- <key>CONFIGURATION_BUILD_DIR</key>
- <string>../bin/$(CONFIGURATION)</string>
- <key>CONFIGURATION_TEMP_DIR</key>
- <string>$(OBJROOT)/$(CONFIGURATION)</string>
- <key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../bin/$(CONFIGURATION)</string>
- <key>OBJROOT</key>
- <string>../build</string>
- <key>LIBRARY_SEARCH_PATHS</key>
- <array>
- <string>../lib/$(CONFIGURATION)</string>
- </array>
- <key>MACH_O_TYPE</key>
- <string>mh_execute</string>
- <key>OTHER_LDFLAGS</key>
- <string> -lxregexp -lregexp -lxncbi -lxser -lxutil -framework CoreServices</string>
- <key>HEADER_SEARCH_PATHS</key>
- <array>
- <string>../inc/$(CONFIGURATION)</string>
- <string>../../../../include</string>
- <string>../../../../include/internal</string>
- <string>/sw/include</string>
- </array>
- <key>PRODUCT_NAME</key>
- <string>project_tree_builder</string>
- <key>GCC_PREPROCESSOR_DEFINITIONS</key>
- <array>
- <string>NCBI_XCODE_BUILD</string>
- <string>_DEBUG</string>
- <string>_MT</string>
- </array>
- <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
- <string>YES</string>
- <key>GCC_PREFIX_HEADER</key>
- <string>../../../../include/ncbi_pch.hpp</string>
- </dict>
<key>isa</key>
- <string>XCBuildConfiguration</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>DebugDLL</string>
+ <string>proj_tree.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_tree.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011E</key>
+ <key>ABCDABCDABCDABCD0000013D</key>
<dict>
- <key>buildSettings</key>
- <dict>
- <key>CONFIGURATION_BUILD_DIR</key>
- <string>../bin/$(CONFIGURATION)</string>
- <key>CONFIGURATION_TEMP_DIR</key>
- <string>$(OBJROOT)/$(CONFIGURATION)</string>
- <key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../bin/$(CONFIGURATION)</string>
- <key>OBJROOT</key>
- <string>../build</string>
- <key>LIBRARY_SEARCH_PATHS</key>
- <array>
- <string>../lib/$(CONFIGURATION)</string>
- </array>
- <key>MACH_O_TYPE</key>
- <string>mh_execute</string>
- <key>OTHER_LDFLAGS</key>
- <string> -lxregexp -lregexp -lxncbi -lxser -lxutil -framework CoreServices</string>
- <key>HEADER_SEARCH_PATHS</key>
- <array>
- <string>../inc/$(CONFIGURATION)</string>
- <string>../../../../include</string>
- <string>../../../../include/internal</string>
- <string>/sw/include</string>
- </array>
- <key>PRODUCT_NAME</key>
- <string>project_tree_builder</string>
- <key>GCC_PREPROCESSOR_DEFINITIONS</key>
- <array>
- <string>NCBI_XCODE_BUILD</string>
- <string>_DEBUG</string>
- <string>_MT</string>
- </array>
- <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
- <string>YES</string>
- <key>GCC_PREFIX_HEADER</key>
- <string>../../../../include/ncbi_pch.hpp</string>
- </dict>
<key>isa</key>
- <string>XCBuildConfiguration</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>DebugMT</string>
+ <string>proj_tree_builder.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_tree_builder.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000011F</key>
+ <key>ABCDABCDABCDABCD0000013E</key>
<dict>
- <key>buildSettings</key>
- <dict>
- <key>CONFIGURATION_BUILD_DIR</key>
- <string>../bin/$(CONFIGURATION)</string>
- <key>CONFIGURATION_TEMP_DIR</key>
- <string>$(OBJROOT)/$(CONFIGURATION)</string>
- <key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../bin/$(CONFIGURATION)</string>
- <key>OBJROOT</key>
- <string>../build</string>
- <key>LIBRARY_SEARCH_PATHS</key>
- <array>
- <string>../lib/$(CONFIGURATION)</string>
- </array>
- <key>MACH_O_TYPE</key>
- <string>mh_execute</string>
- <key>OTHER_LDFLAGS</key>
- <string> -lxregexp -lregexp -lxncbi -lxser -lxutil -framework CoreServices</string>
- <key>HEADER_SEARCH_PATHS</key>
- <array>
- <string>../inc/$(CONFIGURATION)</string>
- <string>../../../../include</string>
- <string>../../../../include/internal</string>
- <string>/sw/include</string>
- </array>
- <key>PRODUCT_NAME</key>
- <string>project_tree_builder</string>
- <key>GCC_PREPROCESSOR_DEFINITIONS</key>
- <array>
- <string>NCBI_XCODE_BUILD</string>
- <string>NDEBUG</string>
- <string>_MT</string>
- </array>
- <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
- <string>YES</string>
- <key>GCC_PREFIX_HEADER</key>
- <string>../../../../include/ncbi_pch.hpp</string>
- </dict>
<key>isa</key>
- <string>XCBuildConfiguration</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>ReleaseDLL</string>
+ <string>proj_utils.hpp</string>
+ <key>path</key>
+ <string>../../../../src/build-system/project_tree_builder/proj_utils.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000120</key>
+ <key>ABCDABCDABCDABCD0000013F</key>
<dict>
- <key>buildSettings</key>
- <dict>
- <key>CONFIGURATION_BUILD_DIR</key>
- <string>../bin/$(CONFIGURATION)</string>
- <key>CONFIGURATION_TEMP_DIR</key>
- <string>$(OBJROOT)/$(CONFIGURATION)</string>
- <key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../bin/$(CONFIGURATION)</string>
- <key>OBJROOT</key>
- <string>../build</string>
- <key>LIBRARY_SEARCH_PATHS</key>
- <array>
- <string>../lib/$(CONFIGURATION)</string>
- </array>
- <key>MACH_O_TYPE</key>
- <string>mh_execute</string>
- <key>OTHER_LDFLAGS</key>
- <string> -lxregexp -lregexp -lxncbi -lxser -lxutil -framework CoreServices</string>
- <key>HEADER_SEARCH_PATHS</key>
- <array>
- <string>../inc/$(CONFIGURATION)</string>
- <string>../../../../include</string>
- <string>../../../../include/internal</string>
- <string>/sw/include</string>
- </array>
- <key>PRODUCT_NAME</key>
- <string>project_tree_builder</string>
- <key>GCC_PREPROCESSOR_DEFINITIONS</key>
- <array>
- <string>NCBI_XCODE_BUILD</string>
- <string>NDEBUG</string>
- <string>_MT</string>
- </array>
- <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
- <string>YES</string>
- <key>GCC_PREFIX_HEADER</key>
- <string>../../../../include/ncbi_pch.hpp</string>
- </dict>
<key>isa</key>
- <string>XCBuildConfiguration</string>
- <key>name</key>
- <string>ReleaseMT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000121</key>
- <dict>
- <key>containerPortal</key>
- <string>ABCDABCDABCDABCD00000006</string>
- <key>isa</key>
- <string>PBXContainerItemProxy</string>
- <key>proxyType</key>
- <string>1</string>
- <key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD0000015D</string>
- <key>remoteInfo</key>
- <string>regexp</string>
- </dict>
- <key>ABCDABCDABCDABCD00000122</key>
- <dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000126</string>
- <string>ABCDABCDABCDABCD00000128</string>
- <string>ABCDABCDABCDABCD0000012A</string>
- <string>ABCDABCDABCDABCD0000012C</string>
- <string>ABCDABCDABCDABCD0000012E</string>
- <string>ABCDABCDABCDABCD00000130</string>
- <string>ABCDABCDABCDABCD00000132</string>
- <string>ABCDABCDABCDABCD00000134</string>
- <string>ABCDABCDABCDABCD00000136</string>
- <string>ABCDABCDABCDABCD00000138</string>
- <string>ABCDABCDABCDABCD0000013A</string>
- <string>ABCDABCDABCDABCD0000013C</string>
- <string>ABCDABCDABCDABCD0000013E</string>
- <string>ABCDABCDABCDABCD00000140</string>
- <string>ABCDABCDABCDABCD00000142</string>
- <string>ABCDABCDABCDABCD00000144</string>
- <string>ABCDABCDABCDABCD00000146</string>
- <string>ABCDABCDABCDABCD00000148</string>
- <string>ABCDABCDABCDABCD0000014A</string>
- <string>ABCDABCDABCDABCD0000014C</string>
- <string>ABCDABCDABCDABCD0000014E</string>
- </array>
- <key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>Source Files</string>
- <key>sourceTree</key>
- <string><group></string>
- </dict>
- <key>ABCDABCDABCDABCD00000123</key>
- <dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000150</string>
- <string>ABCDABCDABCDABCD00000151</string>
- <string>ABCDABCDABCDABCD00000152</string>
- <string>ABCDABCDABCDABCD00000153</string>
- <string>ABCDABCDABCDABCD00000154</string>
- <string>ABCDABCDABCDABCD00000155</string>
- <string>ABCDABCDABCDABCD00000156</string>
- <string>ABCDABCDABCDABCD00000157</string>
- <string>ABCDABCDABCDABCD00000158</string>
- <string>ABCDABCDABCDABCD00000159</string>
- <string>ABCDABCDABCDABCD0000015A</string>
- </array>
- <key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>Header Files</string>
- <key>sourceTree</key>
- <string><group></string>
- </dict>
- <key>ABCDABCDABCDABCD00000125</key>
- <dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000122</string>
- <string>ABCDABCDABCDABCD00000123</string>
- </array>
- <key>isa</key>
- <string>PBXGroup</string>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>regexp</string>
+ <string>property_list__.hpp</string>
+ <key>path</key>
+ <string>../../../../include/build-system/project_tree_builder/property_list__.hpp</string>
<key>sourceTree</key>
- <string><group></string>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000126</key>
+ <key>ABCDABCDABCDABCD00000140</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_chartables.c</string>
+ <string>property_list_module.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_chartables.c</string>
+ <string>../../../../include/build-system/project_tree_builder/property_list_module.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000127</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000126</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000128</key>
+ <key>ABCDABCDABCDABCD00000141</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_compile.c</string>
+ <string>ptb_err_codes.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_compile.c</string>
+ <string>../../../../src/build-system/project_tree_builder/ptb_err_codes.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000129</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000128</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000012A</key>
+ <key>ABCDABCDABCDABCD00000142</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.c.h</string>
<key>name</key>
- <string>pcre_config.c</string>
+ <string>ptb_gui.h</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_config.c</string>
+ <string>../../../../src/build-system/project_tree_builder/ptb_gui.h</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000012B</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000012A</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000012C</key>
+ <key>ABCDABCDABCDABCD00000143</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_dfa_exec.c</string>
+ <string>ptb_registry.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_dfa_exec.c</string>
+ <string>../../../../src/build-system/project_tree_builder/ptb_registry.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000012D</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000012C</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000012E</key>
+ <key>ABCDABCDABCDABCD00000144</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_exec.c</string>
+ <string>resolver.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_exec.c</string>
+ <string>../../../../src/build-system/project_tree_builder/resolver.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000012F</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000012E</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000130</key>
+ <key>ABCDABCDABCDABCD00000145</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_fullinfo.c</string>
+ <string>stl_msvc_usage.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_fullinfo.c</string>
+ <string>../../../../src/build-system/project_tree_builder/stl_msvc_usage.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000131</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000130</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000132</key>
+ <key>ABCDABCDABCDABCD00000146</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_get.c</string>
+ <string>Tool.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_get.c</string>
+ <string>../../../../include/build-system/project_tree_builder/Tool.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000133</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000132</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000134</key>
+ <key>ABCDABCDABCDABCD00000147</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_globals.c</string>
+ <string>Tool_.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_globals.c</string>
+ <string>../../../../include/build-system/project_tree_builder/Tool_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000135</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000134</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000136</key>
+ <key>ABCDABCDABCDABCD00000148</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_info.c</string>
+ <string>VisualStudioProject.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_info.c</string>
+ <string>../../../../include/build-system/project_tree_builder/VisualStudioProject.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000137</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000136</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000138</key>
+ <key>ABCDABCDABCDABCD00000149</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>sourcecode.cpp.h</string>
<key>name</key>
- <string>pcre_maketables.c</string>
+ <string>VisualStudioProject_.hpp</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_maketables.c</string>
+ <string>../../../../include/build-system/project_tree_builder/VisualStudioProject_.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000139</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000138</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000013A</key>
+ <key>ABCDABCDABCDABCD0000014A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>text</string>
<key>name</key>
- <string>pcre_newline.c</string>
+ <string>msvc71_project.dtd</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_newline.c</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000013B</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000013A</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000013C</key>
+ <key>ABCDABCDABCDABCD0000014B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>text.xml</string>
<key>name</key>
- <string>pcre_ord2utf8.c</string>
+ <string>property_list.xsd</string>
<key>path</key>
- <string>../../../../src/util/regexp/pcre_ord2utf8.c</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000013D</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000013C</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000013E</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_refcount.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_refcount.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000013F</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000013E</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD00000140</key>
+ <key>ABCDABCDABCDABCD0000014C</key>
<dict>
+ <key>files</key>
+ <array></array>
+ <key>inputPaths</key>
+ <array>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.dtd</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.def</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.xsd</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.def</string>
+ </array>
+ <key>outputPaths</key>
+ <array>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project.files</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project__.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/msvc71_project___.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list.files</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list__.cpp</string>
+ <string>../../../../src/build-system/project_tree_builder/property_list___.cpp</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_study.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_study.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXShellScriptBuildPhase</string>
+ <key>shellPath</key>
+ <string>/bin/sh</string>
+ <key>shellScript</key>
+ <string>export PTB_PLATFORM="$ARCHS"
export DATATOOL_PATH=bin/ReleaseDLL
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
"$BUILD_TREE_ROOT/datatool.sh" -oex "" -oA -odi -ocvs -pch ncbi_pch.hpp -m build-system/project_tree_builder/msvc71_project.dtd -oc msvc71_project -od ../../../../src/build-system/project_tree_builder/msvc71_project.def -or build-system/project_tree_builder/ -oR ../../../../
"$BUILD_TREE_ROOT/data [...]
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
- <key>ABCDABCDABCDABCD00000141</key>
+ <key>ABCDABCDABCDABCD0000014D</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD00000140</string>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD000000D5</string>
+ <string>ABCDABCDABCDABCD000000D7</string>
+ <string>ABCDABCDABCDABCD000000D9</string>
+ <string>ABCDABCDABCDABCD000000DB</string>
+ <string>ABCDABCDABCDABCD000000DD</string>
+ <string>ABCDABCDABCDABCD000000DF</string>
+ <string>ABCDABCDABCDABCD000000E1</string>
+ <string>ABCDABCDABCDABCD000000E3</string>
+ <string>ABCDABCDABCDABCD000000E5</string>
+ <string>ABCDABCDABCDABCD000000E7</string>
+ <string>ABCDABCDABCDABCD000000E9</string>
+ <string>ABCDABCDABCDABCD000000EB</string>
+ <string>ABCDABCDABCDABCD000000ED</string>
+ <string>ABCDABCDABCDABCD000000EF</string>
+ <string>ABCDABCDABCDABCD000000F1</string>
+ <string>ABCDABCDABCDABCD000000F3</string>
+ <string>ABCDABCDABCDABCD000000F5</string>
+ <string>ABCDABCDABCDABCD000000F7</string>
+ <string>ABCDABCDABCDABCD000000F9</string>
+ <string>ABCDABCDABCDABCD000000FB</string>
+ <string>ABCDABCDABCDABCD000000FD</string>
+ <string>ABCDABCDABCDABCD000000FF</string>
+ <string>ABCDABCDABCDABCD00000101</string>
+ <string>ABCDABCDABCDABCD00000103</string>
+ <string>ABCDABCDABCDABCD00000105</string>
+ <string>ABCDABCDABCDABCD00000107</string>
+ <string>ABCDABCDABCDABCD00000109</string>
+ <string>ABCDABCDABCDABCD0000010B</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXSourcesBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD00000142</key>
+ <key>ABCDABCDABCDABCD0000014E</key>
<dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000014F</string>
+ <string>ABCDABCDABCDABCD00000150</string>
+ <string>ABCDABCDABCDABCD00000151</string>
+ <string>ABCDABCDABCDABCD00000152</string>
+ <string>ABCDABCDABCDABCD00000153</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_tables.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_tables.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXFrameworksBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD00000143</key>
+ <key>ABCDABCDABCDABCD0000014F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000142</string>
+ <string>ABCDABCDABCDABCD00000017</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000144</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_try_flipped.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_try_flipped.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000145</key>
+ <key>ABCDABCDABCDABCD00000150</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000144</string>
+ <string>ABCDABCDABCDABCD0000001C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000146</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_ucd.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_ucd.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000147</key>
+ <key>ABCDABCDABCDABCD00000151</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000146</string>
+ <string>ABCDABCDABCDABCD0000001D</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000148</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_valid_utf8.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_valid_utf8.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000149</key>
+ <key>ABCDABCDABCDABCD00000152</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000148</string>
+ <string>ABCDABCDABCDABCD0000001F</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000014A</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_version.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_version.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000014B</key>
+ <key>ABCDABCDABCDABCD00000153</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000014A</string>
+ <string>ABCDABCDABCDABCD00000020</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000014C</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
- <key>name</key>
- <string>pcre_xclass.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_xclass.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000014D</key>
+ <key>ABCDABCDABCDABCD00000154</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000014C</string>
+ <key>files</key>
+ <array></array>
+ <key>inputPaths</key>
+ <array>
+ <string>$(TARGET_BUILD_DIR)/$(TARGET_NAME)</string>
+ </array>
+ <key>outputPaths</key>
+ <array></array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXShellScriptBuildPhase</string>
+ <key>shellPath</key>
+ <string>/bin/sh</string>
+ <key>shellScript</key>
+ <string>export BUILD_TREE_ROOT=../..
export BUILD_TREE_BIN=bin/${CONFIGURATION}
"$BUILD_TREE_ROOT/copybin.sh"</string>
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
- <key>ABCDABCDABCDABCD0000014E</key>
+ <key>ABCDABCDABCDABCD00000155</key>
<dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD00000156</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000014C</string>
+ <string>ABCDABCDABCDABCD0000014D</string>
+ <string>ABCDABCDABCDABCD0000014E</string>
+ <string>ABCDABCDABCDABCD00000154</string>
+ </array>
+ <key>dependencies</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000007</string>
+ <string>ABCDABCDABCDABCD0000000B</string>
+ <string>ABCDABCDABCDABCD0000000C</string>
+ <string>ABCDABCDABCDABCD0000000E</string>
+ <string>ABCDABCDABCDABCD0000000F</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.c</string>
+ <string>PBXNativeTarget</string>
<key>name</key>
- <string>pcreposix.c</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcreposix.c</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>project_tree_builder</string>
+ <key>productName</key>
+ <string>project_tree_builder</string>
+ <key>productReference</key>
+ <string>ABCDABCDABCDABCD00000016</string>
+ <key>productType</key>
+ <string>com.apple.product-type.tool</string>
</dict>
- <key>ABCDABCDABCDABCD0000014F</key>
+ <key>ABCDABCDABCDABCD00000156</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000014E</string>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000157</string>
+ <string>ABCDABCDABCDABCD00000158</string>
+ <string>ABCDABCDABCDABCD00000159</string>
+ <string>ABCDABCDABCDABCD0000015A</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD00000150</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>config.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/config.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000151</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcre.h</string>
- <key>path</key>
- <string>../../../../include/util/regexp/pcre.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000152</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcre_internal.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_internal.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000153</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcre_scanner.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcre_scanner.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000154</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcrecpp.h</string>
- <key>path</key>
- <string>../../../../include/util/regexp/pcrecpp.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000155</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcrecpp.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcrecpp.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000156</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcrecpp_internal.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcrecpp_internal.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000157</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcrecpparg.h</string>
- <key>path</key>
- <string>../../../../include/util/regexp/pcrecpparg.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000158</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcreposix.h</string>
- <key>path</key>
- <string>../../../../include/util/regexp/pcreposix.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000159</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>pcreposix.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/pcreposix.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015A</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.c.h</string>
- <key>name</key>
- <string>ucp.h</string>
- <key>path</key>
- <string>../../../../src/util/regexp/ucp.h</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015B</key>
- <dict>
- <key>files</key>
- <array>
- <string>ABCDABCDABCDABCD00000127</string>
- <string>ABCDABCDABCDABCD00000129</string>
- <string>ABCDABCDABCDABCD0000012B</string>
- <string>ABCDABCDABCDABCD0000012D</string>
- <string>ABCDABCDABCDABCD0000012F</string>
- <string>ABCDABCDABCDABCD00000131</string>
- <string>ABCDABCDABCDABCD00000133</string>
- <string>ABCDABCDABCDABCD00000135</string>
- <string>ABCDABCDABCDABCD00000137</string>
- <string>ABCDABCDABCDABCD00000139</string>
- <string>ABCDABCDABCDABCD0000013B</string>
- <string>ABCDABCDABCDABCD0000013D</string>
- <string>ABCDABCDABCDABCD0000013F</string>
- <string>ABCDABCDABCDABCD00000141</string>
- <string>ABCDABCDABCDABCD00000143</string>
- <string>ABCDABCDABCDABCD00000145</string>
- <string>ABCDABCDABCDABCD00000147</string>
- <string>ABCDABCDABCDABCD00000149</string>
- <string>ABCDABCDABCDABCD0000014B</string>
- <string>ABCDABCDABCDABCD0000014D</string>
- <string>ABCDABCDABCDABCD0000014F</string>
- </array>
- <key>isa</key>
- <string>PBXSourcesBuildPhase</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015C</key>
- <dict>
- <key>explicitFileType</key>
- <string>archive.ar</string>
- <key>includeInIndex</key>
- <string>0</string>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>path</key>
- <string>libregexp.a</string>
- <key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015D</key>
- <dict>
- <key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD0000015E</string>
- <key>buildPhases</key>
- <array>
- <string>ABCDABCDABCDABCD0000015B</string>
- </array>
- <key>dependencies</key>
- <array></array>
- <key>isa</key>
- <string>PBXNativeTarget</string>
- <key>name</key>
- <string>regexp</string>
- <key>productName</key>
- <string>regexp</string>
- <key>productReference</key>
- <string>ABCDABCDABCDABCD0000015C</string>
- <key>productType</key>
- <string>com.apple.product-type.library.static</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015E</key>
- <dict>
- <key>buildConfigurations</key>
- <array>
- <string>ABCDABCDABCDABCD0000015F</string>
- <string>ABCDABCDABCDABCD00000160</string>
- <string>ABCDABCDABCDABCD00000161</string>
- <string>ABCDABCDABCDABCD00000162</string>
- </array>
- <key>defaultConfigurationIsVisible</key>
- <string>0</string>
- <key>defaultConfigurationName</key>
- <string>ReleaseDLL</string>
- <key>isa</key>
- <string>XCConfigurationList</string>
- </dict>
- <key>ABCDABCDABCDABCD0000015F</key>
+ <key>ABCDABCDABCDABCD00000157</key>
<dict>
<key>buildSettings</key>
<dict>
- <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
- <string>YES</string>
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
<key>MACH_O_TYPE</key>
- <string>staticlib</string>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>project_tree_builder</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>regexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
- <string>HAVE_CONFIG_H</string>
<string>NCBI_XCODE_BUILD</string>
<string>_DEBUG</string>
<string>_MT</string>
@@ -4867,39 +4539,40 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000160</key>
+ <key>ABCDABCDABCDABCD00000158</key>
<dict>
<key>buildSettings</key>
<dict>
- <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
- <string>YES</string>
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
<key>MACH_O_TYPE</key>
- <string>staticlib</string>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>project_tree_builder</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>regexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
- <string>HAVE_CONFIG_H</string>
<string>NCBI_XCODE_BUILD</string>
<string>_DEBUG</string>
<string>_MT</string>
@@ -4914,39 +4587,40 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000161</key>
+ <key>ABCDABCDABCDABCD00000159</key>
<dict>
<key>buildSettings</key>
<dict>
- <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
- <string>YES</string>
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
<key>MACH_O_TYPE</key>
- <string>staticlib</string>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>project_tree_builder</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>regexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
- <string>HAVE_CONFIG_H</string>
<string>NCBI_XCODE_BUILD</string>
<string>NDEBUG</string>
<string>_MT</string>
@@ -4961,39 +4635,40 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000162</key>
+ <key>ABCDABCDABCDABCD0000015A</key>
<dict>
<key>buildSettings</key>
<dict>
- <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
- <string>YES</string>
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
<key>MACH_O_TYPE</key>
- <string>staticlib</string>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>project_tree_builder</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>regexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
- <string>HAVE_CONFIG_H</string>
<string>NCBI_XCODE_BUILD</string>
<string>NDEBUG</string>
<string>_MT</string>
@@ -5008,7 +4683,7 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000163</key>
+ <key>ABCDABCDABCDABCD0000015B</key>
<dict>
<key>containerPortal</key>
<string>ABCDABCDABCDABCD00000006</string>
@@ -5017,19 +4692,22 @@
<key>proxyType</key>
<string>1</string>
<key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD0000021F</string>
+ <string>ABCDABCDABCDABCD00000196</string>
<key>remoteInfo</key>
- <string>xncbi</string>
+ <string>regexp</string>
</dict>
- <key>ABCDABCDABCDABCD00000164</key>
+ <key>ABCDABCDABCDABCD0000015C</key>
<dict>
<key>children</key>
<array>
+ <string>ABCDABCDABCDABCD00000160</string>
+ <string>ABCDABCDABCDABCD00000162</string>
+ <string>ABCDABCDABCDABCD00000164</string>
+ <string>ABCDABCDABCDABCD00000166</string>
<string>ABCDABCDABCDABCD00000168</string>
<string>ABCDABCDABCDABCD0000016A</string>
<string>ABCDABCDABCDABCD0000016C</string>
<string>ABCDABCDABCDABCD0000016E</string>
- <string>BBCDABCDABCDABCD0000016E</string>
<string>ABCDABCDABCDABCD00000170</string>
<string>ABCDABCDABCDABCD00000172</string>
<string>ABCDABCDABCDABCD00000174</string>
@@ -5043,2542 +4721,9625 @@
<string>ABCDABCDABCDABCD00000184</string>
<string>ABCDABCDABCDABCD00000186</string>
<string>ABCDABCDABCDABCD00000188</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Source Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000015D</key>
+ <dict>
+ <key>children</key>
+ <array>
<string>ABCDABCDABCDABCD0000018A</string>
+ <string>ABCDABCDABCDABCD0000018B</string>
<string>ABCDABCDABCDABCD0000018C</string>
+ <string>ABCDABCDABCDABCD0000018D</string>
<string>ABCDABCDABCDABCD0000018E</string>
+ <string>ABCDABCDABCDABCD0000018F</string>
<string>ABCDABCDABCDABCD00000190</string>
+ <string>ABCDABCDABCDABCD00000191</string>
<string>ABCDABCDABCDABCD00000192</string>
+ <string>ABCDABCDABCDABCD00000193</string>
<string>ABCDABCDABCDABCD00000194</string>
- <string>ABCDABCDABCDABCD00000196</string>
- <string>ABCDABCDABCDABCD00000198</string>
- <string>ABCDABCDABCDABCD0000019A</string>
- <string>ABCDABCDABCDABCD0000019C</string>
- <string>ABCDABCDABCDABCD0000019E</string>
- <string>ABCDABCDABCDABCD000001A0</string>
- <string>ABCDABCDABCDABCD000001A2</string>
- <string>ABCDABCDABCDABCD000001A4</string>
- <string>ABCDABCDABCDABCD000001A6</string>
- <string>ABCDABCDABCDABCD000001A8</string>
- <string>ABCDABCDABCDABCD000001AA</string>
- <string>ABCDABCDABCDABCD000001AC</string>
- <string>ABCDABCDABCDABCD000001AE</string>
- <string>ABCDABCDABCDABCD000001B0</string>
- <string>ABCDABCDABCDABCD000001B2</string>
- <string>ABCDABCDABCDABCD000001B4</string>
- <string>ABCDABCDABCDABCD000001B6</string>
- <string>ABCDABCDABCDABCD000001B8</string>
- <string>ABCDABCDABCDABCD000001BA</string>
- <string>ABCDABCDABCDABCD000001BC</string>
- <string>ABCDABCDABCDABCD000001BE</string>
- <string>ABCDABCDABCDABCD000001C0</string>
- <string>CBCDABCDABCDABCD00000001</string>
- <string>CBCDABCDABCDABCD00000003</string>
- <string>CBCDABCDABCDABCD00000005</string>
- <string>CBCDABCDABCDABCD00000007</string>
- <string>CBCDABCDABCDABCD00000009</string>
- <string>CBCDABCDABCDABCD0000000B</string>
- <string>CBCDABCDABCDABCD0000000D</string>
- <string>CBCDABCDABCDABCD0000000F</string>
- <string>CBCDABCDABCDABCD00000011</string>
</array>
<key>isa</key>
- <string>PBXGroup</string>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Header Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000015F</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000015C</string>
+ <string>ABCDABCDABCDABCD0000015D</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>regexp</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000160</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_chartables.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_chartables.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000161</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000160</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000162</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_compile.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_compile.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000163</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000162</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000164</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_config.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_config.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000165</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000164</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000166</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_dfa_exec.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_dfa_exec.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000167</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000166</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000168</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_exec.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_exec.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000169</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000168</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016A</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_fullinfo.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_fullinfo.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016B</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000016A</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016C</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_get.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_get.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016D</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000016C</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016E</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_globals.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_globals.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000016F</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000016E</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000170</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_info.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_info.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000171</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000170</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000172</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_maketables.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_maketables.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000173</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000172</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000174</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_newline.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_newline.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000175</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000174</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000176</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_ord2utf8.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_ord2utf8.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000177</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000176</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000178</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_refcount.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_refcount.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000179</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000178</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017A</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_study.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_study.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017B</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000017A</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017C</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_tables.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_tables.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017D</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000017C</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017E</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_try_flipped.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_try_flipped.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000017F</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000017E</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000180</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_ucd.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_ucd.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000181</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000180</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000182</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_valid_utf8.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_valid_utf8.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000183</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000182</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000184</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_version.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_version.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000185</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000184</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000186</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcre_xclass.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_xclass.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000187</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000186</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000188</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcreposix.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcreposix.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000189</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000188</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018A</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>config.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/config.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018B</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcre.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018C</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre_internal.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_internal.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018D</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre_scanner.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_scanner.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018E</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcrecpp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000018F</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcrecpp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000190</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp_internal.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcrecpp_internal.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000191</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpparg.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcrecpparg.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000192</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcreposix.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcreposix.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000193</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcreposix.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcreposix.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000194</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>ucp.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/ucp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000195</key>
+ <dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000161</string>
+ <string>ABCDABCDABCDABCD00000163</string>
+ <string>ABCDABCDABCDABCD00000165</string>
+ <string>ABCDABCDABCDABCD00000167</string>
+ <string>ABCDABCDABCDABCD00000169</string>
+ <string>ABCDABCDABCDABCD0000016B</string>
+ <string>ABCDABCDABCDABCD0000016D</string>
+ <string>ABCDABCDABCDABCD0000016F</string>
+ <string>ABCDABCDABCDABCD00000171</string>
+ <string>ABCDABCDABCDABCD00000173</string>
+ <string>ABCDABCDABCDABCD00000175</string>
+ <string>ABCDABCDABCDABCD00000177</string>
+ <string>ABCDABCDABCDABCD00000179</string>
+ <string>ABCDABCDABCDABCD0000017B</string>
+ <string>ABCDABCDABCDABCD0000017D</string>
+ <string>ABCDABCDABCDABCD0000017F</string>
+ <string>ABCDABCDABCDABCD00000181</string>
+ <string>ABCDABCDABCDABCD00000183</string>
+ <string>ABCDABCDABCDABCD00000185</string>
+ <string>ABCDABCDABCDABCD00000187</string>
+ <string>ABCDABCDABCDABCD00000189</string>
+ </array>
+ <key>isa</key>
+ <string>PBXSourcesBuildPhase</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000196</key>
+ <dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD00000197</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000195</string>
+ </array>
+ <key>dependencies</key>
+ <array></array>
+ <key>isa</key>
+ <string>PBXNativeTarget</string>
+ <key>name</key>
+ <string>regexp</string>
+ <key>productName</key>
+ <string>regexp</string>
+ <key>productReference</key>
+ <string>ABCDABCDABCDABCD00000017</string>
+ <key>productType</key>
+ <string>com.apple.product-type.library.static</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000197</key>
+ <dict>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000198</string>
+ <string>ABCDABCDABCDABCD00000199</string>
+ <string>ABCDABCDABCDABCD0000019A</string>
+ <string>ABCDABCDABCDABCD0000019B</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
+ <key>isa</key>
+ <string>XCConfigurationList</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000198</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>regexp</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000199</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>regexp</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000019A</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>regexp</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000019B</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>regexp</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000019C</key>
+ <dict>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
+ <key>isa</key>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD0000020D</string>
+ <key>remoteInfo</key>
+ <string>test_boost</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000019D</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD000001A1</string>
+ <string>ABCDABCDABCDABCD000001A3</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Source Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000019E</key>
+ <dict>
+ <key>children</key>
+ <array>
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+ <string>ABCDABCDABCDABCD000001B0</string>
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+ <string>ABCDABCDABCDABCD000001BB</string>
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+ <string>test_boost.hpp</string>
+ <key>path</key>
+ <string>../../../../include/corelib/test_boost.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000027F</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>test_mt.hpp</string>
+ <key>path</key>
+ <string>../../../../include/corelib/test_mt.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000280</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>version.hpp</string>
+ <key>path</key>
+ <string>../../../../include/corelib/version.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000281</key>
+ <dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000219</string>
+ </array>
+ <key>isa</key>
+ <string>PBXSourcesBuildPhase</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000282</key>
+ <dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD00000283</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000281</string>
+ </array>
+ <key>dependencies</key>
+ <array></array>
+ <key>isa</key>
+ <string>PBXNativeTarget</string>
+ <key>name</key>
+ <string>test_mt</string>
+ <key>productName</key>
+ <string>test_mt</string>
+ <key>productReference</key>
+ <string>ABCDABCDABCDABCD00000019</string>
+ <key>productType</key>
+ <string>com.apple.product-type.library.static</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000283</key>
+ <dict>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000284</string>
+ <string>ABCDABCDABCDABCD00000285</string>
+ <string>ABCDABCDABCDABCD00000286</string>
+ <string>ABCDABCDABCDABCD00000287</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
+ <key>isa</key>
+ <string>XCConfigurationList</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000284</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_mt</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000285</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_mt</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000286</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_mt</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000287</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_ENABLE_SYMBOL_SEPARATION</key>
+ <string>YES</string>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>MACH_O_TYPE</key>
+ <string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_mt</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>NDEBUG</string>
+ <string>_MT</string>
+ </array>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000288</key>
+ <dict>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
+ <key>isa</key>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD0000029E</string>
+ <key>remoteInfo</key>
+ <string>test_pcre</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000289</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000028D</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Source Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000028A</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000028F</string>
+ <string>ABCDABCDABCDABCD00000290</string>
+ <string>ABCDABCDABCDABCD00000291</string>
+ <string>ABCDABCDABCDABCD00000292</string>
+ <string>ABCDABCDABCDABCD00000293</string>
+ <string>ABCDABCDABCDABCD00000294</string>
+ <string>ABCDABCDABCDABCD00000295</string>
+ <string>ABCDABCDABCDABCD00000296</string>
+ <string>ABCDABCDABCDABCD00000297</string>
+ <string>ABCDABCDABCDABCD00000298</string>
+ <string>ABCDABCDABCDABCD00000299</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>Header Files</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000028C</key>
+ <dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000289</string>
+ <string>ABCDABCDABCDABCD0000028A</string>
+ </array>
+ <key>isa</key>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>test_pcre</string>
+ <key>sourceTree</key>
+ <string><group></string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000028D</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.c</string>
+ <key>name</key>
+ <string>pcretest.c</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcretest.c</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000028E</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000028D</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000028F</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>config.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/config.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000290</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcre.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000291</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre_internal.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_internal.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000292</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcre_scanner.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcre_scanner.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000293</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcrecpp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000294</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcrecpp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000295</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpp_internal.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcrecpp_internal.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000296</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcrecpparg.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcrecpparg.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000297</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcreposix.h</string>
+ <key>path</key>
+ <string>../../../../include/util/regexp/pcreposix.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000298</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>pcreposix.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/pcreposix.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000299</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.c.h</string>
+ <key>name</key>
+ <string>ucp.h</string>
+ <key>path</key>
+ <string>../../../../src/util/regexp/ucp.h</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029A</key>
+ <dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000028E</string>
+ </array>
+ <key>isa</key>
+ <string>PBXSourcesBuildPhase</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029B</key>
+ <dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000029C</string>
+ </array>
+ <key>isa</key>
+ <string>PBXFrameworksBuildPhase</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029C</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000017</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029D</key>
+ <dict>
+ <key>files</key>
+ <array></array>
+ <key>inputPaths</key>
+ <array>
+ <string>$(TARGET_BUILD_DIR)/$(TARGET_NAME)</string>
+ </array>
+ <key>outputPaths</key>
+ <array></array>
+ <key>isa</key>
+ <string>PBXShellScriptBuildPhase</string>
+ <key>shellPath</key>
+ <string>/bin/sh</string>
+ <key>shellScript</key>
+ <string>export BUILD_TREE_ROOT=../..
export BUILD_TREE_BIN=bin/${CONFIGURATION}
"$BUILD_TREE_ROOT/copybin.sh"</string>
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029E</key>
+ <dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD0000029F</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000029A</string>
+ <string>ABCDABCDABCDABCD0000029B</string>
+ <string>ABCDABCDABCDABCD0000029D</string>
+ </array>
+ <key>dependencies</key>
+ <array>
+ <string>ABCDABCDABCDABCD00000007</string>
+ </array>
+ <key>isa</key>
+ <string>PBXNativeTarget</string>
+ <key>name</key>
+ <string>test_pcre</string>
+ <key>productName</key>
+ <string>test_pcre</string>
+ <key>productReference</key>
+ <string>ABCDABCDABCDABCD0000001A</string>
+ <key>productType</key>
+ <string>com.apple.product-type.tool</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000029F</key>
+ <dict>
+ <key>buildConfigurations</key>
+ <array>
+ <string>ABCDABCDABCDABCD000002A0</string>
+ <string>ABCDABCDABCDABCD000002A1</string>
+ <string>ABCDABCDABCDABCD000002A2</string>
+ <string>ABCDABCDABCDABCD000002A3</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
+ <key>isa</key>
+ <string>XCConfigurationList</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000002A0</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_pcre</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ <string>../../../../src/util</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000002A1</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
+ <string>NO</string>
+ <key>CONFIGURATION_BUILD_DIR</key>
+ <string>lib/$(CONFIGURATION)</string>
+ <key>CONFIGURATION_TEMP_DIR</key>
+ <string>$(OBJROOT)/$(CONFIGURATION)</string>
+ <key>INSTALL_PATH</key>
+ <string>$(PROJECT_DIR)/bin/$(CONFIGURATION)</string>
+ <key>OBJROOT</key>
+ <string>build</string>
+ <key>LIBRARY_SEARCH_PATHS</key>
+ <array>
+ <string>lib/$(CONFIGURATION)</string>
+ </array>
+ <key>MACH_O_TYPE</key>
+ <string>mh_execute</string>
+ <key>OTHER_LDFLAGS</key>
+ <string> -stdlib=libc++ -framework CoreServices</string>
+ <key>PRODUCT_NAME</key>
+ <string>test_pcre</string>
+ <key>HEADER_SEARCH_PATHS</key>
+ <array>
+ <string>inc/$(CONFIGURATION)</string>
+ <string>../../../../include</string>
+ <string>../../../../include/internal</string>
+ <string>../../../../include/util/regexp</string>
+ <string>../../../../src/util</string>
+ </array>
+ <key>GCC_PREPROCESSOR_DEFINITIONS</key>
+ <array>
+ <string>HAVE_CONFIG_H</string>
+ <string>NCBI_XCODE_BUILD</string>
+ <string>_DEBUG</string>
+ <string>_MT</string>
+ </array>
+ <key>GCC_PRECOMPILE_PREFIX_HEADER</key>
+ <string>YES</string>
+ <key>GCC_PREFIX_HEADER</key>
+ <string>../../../../include/ncbi_pch.hpp</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000002A2</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
+ <string>NO</string>
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<key>sourceTree</key>
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<key>path</key>
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<key>sourceTree</key>
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<key>sourceTree</key>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
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<key>isa</key>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
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<key>name</key>
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<key>path</key>
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<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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- <key>path</key>
- <string>../../../../include/corelib/ncbiutil.hpp</string>
- <key>sourceTree</key>
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- <key>path</key>
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+ <key>INSTALL_PATH</key>
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- <key>path</key>
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- <key>path</key>
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<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000212</key>
+ <key>ABCDABCDABCDABCD000003F7</key>
<dict>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD000003F4</string>
+ <string>ABCDABCDABCDABCD000003F5</string>
+ </array>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>PBXGroup</string>
<key>name</key>
- <string>request_status.hpp</string>
- <key>path</key>
- <string>../../../../include/corelib/request_status.hpp</string>
+ <string>xregexp</string>
<key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000213</key>
+ <key>ABCDABCDABCDABCD000003F8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>resource_info.hpp</string>
+ <string>arg_regexp.cpp</string>
<key>path</key>
- <string>../../../../include/corelib/resource_info.hpp</string>
+ <string>../../../../src/util/xregexp/arg_regexp.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000214</key>
+ <key>ABCDABCDABCDABCD000003F9</key>
<dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000003F8</string>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
- <key>name</key>
- <string>rwstream.hpp</string>
- <key>path</key>
- <string>../../../../include/corelib/rwstream.hpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000215</key>
+ <key>ABCDABCDABCDABCD000003FA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>rwstreambuf.hpp</string>
+ <string>mask_regexp.cpp</string>
<key>path</key>
- <string>../../../../include/corelib/impl/rwstreambuf.hpp</string>
+ <string>../../../../src/util/xregexp/mask_regexp.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000216</key>
+ <key>ABCDABCDABCDABCD000003FB</key>
<dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000003FA</string>
<key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
- <key>name</key>
- <string>stream_utils.hpp</string>
- <key>path</key>
- <string>../../../../include/corelib/stream_utils.hpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
+ <string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000217</key>
+ <key>ABCDABCDABCDABCD000003FC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
+ <string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>syslog.hpp</string>
+ <string>regexp.cpp</string>
<key>path</key>
- <string>../../../../include/corelib/syslog.hpp</string>
+ <string>../../../../src/util/xregexp/regexp.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000218</key>
+ <key>ABCDABCDABCDABCD000003FD</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000003FC</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000003FE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>tempstr.hpp</string>
+ <string>arg_regexp.hpp</string>
<key>path</key>
- <string>../../../../include/corelib/tempstr.hpp</string>
+ <string>../../../../include/util/xregexp/arg_regexp.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000219</key>
+ <key>ABCDABCDABCDABCD000003FF</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>test_boost.hpp</string>
+ <string>mask_regexp.hpp</string>
<key>path</key>
- <string>../../../../include/corelib/test_boost.hpp</string>
+ <string>../../../../include/util/xregexp/mask_regexp.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000021A</key>
+ <key>ABCDABCDABCDABCD00000400</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>test_mt.hpp</string>
+ <string>regexp.hpp</string>
<key>path</key>
- <string>../../../../include/corelib/test_mt.hpp</string>
+ <string>../../../../include/util/xregexp/regexp.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000021B</key>
+ <key>ABCDABCDABCDABCD00000401</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>version.hpp</string>
+ <string>regexp_template_tester.hpp</string>
<key>path</key>
- <string>../../../../include/corelib/version.hpp</string>
+ <string>../../../../include/util/xregexp/regexp_template_tester.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000021D</key>
+ <key>ABCDABCDABCDABCD00000402</key>
<dict>
<key>files</key>
<array>
- <string>ABCDABCDABCDABCD00000169</string>
- <string>ABCDABCDABCDABCD0000016B</string>
- <string>ABCDABCDABCDABCD0000016D</string>
- <string>ABCDABCDABCDABCD0000016F</string>
- <string>BBCDABCDABCDABCD0000016F</string>
- <string>ABCDABCDABCDABCD00000171</string>
- <string>ABCDABCDABCDABCD00000173</string>
- <string>ABCDABCDABCDABCD00000175</string>
- <string>ABCDABCDABCDABCD00000177</string>
- <string>ABCDABCDABCDABCD00000179</string>
- <string>ABCDABCDABCDABCD0000017B</string>
- <string>ABCDABCDABCDABCD0000017D</string>
- <string>ABCDABCDABCDABCD0000017F</string>
- <string>ABCDABCDABCDABCD00000181</string>
- <string>ABCDABCDABCDABCD00000183</string>
- <string>ABCDABCDABCDABCD00000185</string>
- <string>ABCDABCDABCDABCD00000187</string>
- <string>ABCDABCDABCDABCD00000189</string>
- <string>ABCDABCDABCDABCD0000018B</string>
- <string>ABCDABCDABCDABCD0000018D</string>
- <string>ABCDABCDABCDABCD0000018F</string>
- <string>ABCDABCDABCDABCD00000191</string>
- <string>ABCDABCDABCDABCD00000193</string>
- <string>ABCDABCDABCDABCD00000195</string>
- <string>ABCDABCDABCDABCD00000197</string>
- <string>ABCDABCDABCDABCD00000199</string>
- <string>ABCDABCDABCDABCD0000019B</string>
- <string>ABCDABCDABCDABCD0000019D</string>
- <string>ABCDABCDABCDABCD0000019F</string>
- <string>ABCDABCDABCDABCD000001A1</string>
- <string>ABCDABCDABCDABCD000001A3</string>
- <string>ABCDABCDABCDABCD000001A5</string>
- <string>ABCDABCDABCDABCD000001A7</string>
- <string>ABCDABCDABCDABCD000001A9</string>
- <string>ABCDABCDABCDABCD000001AB</string>
- <string>ABCDABCDABCDABCD000001AD</string>
- <string>ABCDABCDABCDABCD000001AF</string>
- <string>ABCDABCDABCDABCD000001B1</string>
- <string>ABCDABCDABCDABCD000001B3</string>
- <string>ABCDABCDABCDABCD000001B5</string>
- <string>ABCDABCDABCDABCD000001B7</string>
- <string>ABCDABCDABCDABCD000001B9</string>
- <string>ABCDABCDABCDABCD000001BB</string>
- <string>ABCDABCDABCDABCD000001BD</string>
- <string>ABCDABCDABCDABCD000001BF</string>
- <string>ABCDABCDABCDABCD000001C1</string>
- <string>CBCDABCDABCDABCD00000002</string>
- <string>CBCDABCDABCDABCD00000004</string>
- <string>CBCDABCDABCDABCD00000006</string>
- <string>CBCDABCDABCDABCD00000008</string>
- <string>CBCDABCDABCDABCD0000000A</string>
- <string>CBCDABCDABCDABCD0000000C</string>
- <string>CBCDABCDABCDABCD0000000E</string>
- <string>CBCDABCDABCDABCD00000010</string>
- <string>CBCDABCDABCDABCD00000012</string>
+ <string>ABCDABCDABCDABCD000003F9</string>
+ <string>ABCDABCDABCDABCD000003FB</string>
+ <string>ABCDABCDABCDABCD000003FD</string>
</array>
<key>isa</key>
<string>PBXSourcesBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD0000021E</key>
- <dict>
- <key>explicitFileType</key>
- <string>archive.ar</string>
- <key>includeInIndex</key>
- <string>0</string>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>path</key>
- <string>libxncbi.a</string>
- <key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
- </dict>
- <key>ABCDABCDABCDABCD0000021F</key>
+ <key>ABCDABCDABCDABCD00000403</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD00000220</string>
+ <string>ABCDABCDABCDABCD00000404</string>
<key>buildPhases</key>
<array>
- <string>ABCDABCDABCDABCD0000021D</string>
+ <string>ABCDABCDABCDABCD00000402</string>
</array>
<key>dependencies</key>
<array></array>
<key>isa</key>
<string>PBXNativeTarget</string>
<key>name</key>
- <string>xncbi</string>
+ <string>xregexp</string>
<key>productName</key>
- <string>xncbi</string>
+ <string>xregexp</string>
<key>productReference</key>
- <string>ABCDABCDABCDABCD0000021E</string>
+ <string>ABCDABCDABCDABCD0000001D</string>
<key>productType</key>
<string>com.apple.product-type.library.static</string>
</dict>
- <key>ABCDABCDABCDABCD00000220</key>
+ <key>ABCDABCDABCDABCD00000404</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD00000221</string>
- <string>ABCDABCDABCDABCD00000222</string>
- <string>ABCDABCDABCDABCD00000223</string>
- <string>ABCDABCDABCDABCD00000224</string>
+ <string>ABCDABCDABCDABCD00000405</string>
+ <string>ABCDABCDABCDABCD00000406</string>
+ <string>ABCDABCDABCDABCD00000407</string>
+ <string>ABCDABCDABCDABCD00000408</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -7587,7 +14348,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD00000221</key>
+ <key>ABCDABCDABCDABCD00000405</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -7596,26 +14357,26 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
+ <string>../../../../include/util/regexp</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xncbi</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -7632,7 +14393,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000222</key>
+ <key>ABCDABCDABCDABCD00000406</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -7641,26 +14402,26 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
+ <string>../../../../include/util/regexp</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xncbi</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -7677,7 +14438,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000223</key>
+ <key>ABCDABCDABCDABCD00000407</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -7686,26 +14447,26 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
+ <string>../../../../include/util/regexp</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xncbi</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -7722,7 +14483,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000224</key>
+ <key>ABCDABCDABCDABCD00000408</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -7731,26 +14492,26 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
+ <string>../../../../include/util/regexp</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xncbi</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -7767,7 +14528,7 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000225</key>
+ <key>ABCDABCDABCDABCD00000409</key>
<dict>
<key>containerPortal</key>
<string>ABCDABCDABCDABCD00000006</string>
@@ -7776,17 +14537,15 @@
<key>proxyType</key>
<string>1</string>
<key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD00000235</string>
+ <string>ABCDABCDABCDABCD00000415</string>
<key>remoteInfo</key>
- <string>xregexp</string>
+ <string>xregexp_template_tester</string>
</dict>
- <key>ABCDABCDABCDABCD00000226</key>
+ <key>ABCDABCDABCDABCD0000040A</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD0000022A</string>
- <string>ABCDABCDABCDABCD0000022C</string>
- <string>ABCDABCDABCDABCD0000022E</string>
+ <string>ABCDABCDABCDABCD0000040E</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -7795,13 +14554,14 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000227</key>
+ <key>ABCDABCDABCDABCD0000040B</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000230</string>
- <string>ABCDABCDABCDABCD00000231</string>
- <string>ABCDABCDABCDABCD00000232</string>
+ <string>ABCDABCDABCDABCD00000410</string>
+ <string>ABCDABCDABCDABCD00000411</string>
+ <string>ABCDABCDABCDABCD00000412</string>
+ <string>ABCDABCDABCDABCD00000413</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -7810,81 +14570,41 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000229</key>
- <dict>
- <key>children</key>
- <array>
- <string>ABCDABCDABCDABCD00000226</string>
- <string>ABCDABCDABCDABCD00000227</string>
- </array>
- <key>isa</key>
- <string>PBXGroup</string>
- <key>name</key>
- <string>xregexp</string>
- <key>sourceTree</key>
- <string><group></string>
- </dict>
- <key>ABCDABCDABCDABCD0000022A</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>arg_regexp.cpp</string>
- <key>path</key>
- <string>../../../../src/util/xregexp/arg_regexp.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000022B</key>
- <dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000022A</string>
- <key>isa</key>
- <string>PBXBuildFile</string>
- </dict>
- <key>ABCDABCDABCDABCD0000022C</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.cpp</string>
- <key>name</key>
- <string>mask_regexp.cpp</string>
- <key>path</key>
- <string>../../../../src/util/xregexp/mask_regexp.cpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000022D</key>
+ <key>ABCDABCDABCDABCD0000040D</key>
<dict>
- <key>fileRef</key>
- <string>ABCDABCDABCDABCD0000022C</string>
+ <key>children</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000040A</string>
+ <string>ABCDABCDABCDABCD0000040B</string>
+ </array>
<key>isa</key>
- <string>PBXBuildFile</string>
+ <string>PBXGroup</string>
+ <key>name</key>
+ <string>xregexp_template_tester</string>
+ <key>sourceTree</key>
+ <string><group></string>
</dict>
- <key>ABCDABCDABCDABCD0000022E</key>
+ <key>ABCDABCDABCDABCD0000040E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>regexp.cpp</string>
+ <string>regexp_template_tester.cpp</string>
<key>path</key>
- <string>../../../../src/util/xregexp/regexp.cpp</string>
+ <string>../../../../src/util/xregexp/regexp_template_tester.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000022F</key>
+ <key>ABCDABCDABCDABCD0000040F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000022E</string>
+ <string>ABCDABCDABCDABCD0000040E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000230</key>
+ <key>ABCDABCDABCDABCD00000410</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -7897,7 +14617,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000231</key>
+ <key>ABCDABCDABCDABCD00000411</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -7910,7 +14630,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000232</key>
+ <key>ABCDABCDABCDABCD00000412</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -7923,59 +14643,57 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000233</key>
+ <key>ABCDABCDABCDABCD00000413</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>regexp_template_tester.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/xregexp/regexp_template_tester.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000414</key>
<dict>
<key>files</key>
<array>
- <string>ABCDABCDABCDABCD0000022B</string>
- <string>ABCDABCDABCDABCD0000022D</string>
- <string>ABCDABCDABCDABCD0000022F</string>
+ <string>ABCDABCDABCDABCD0000040F</string>
</array>
<key>isa</key>
<string>PBXSourcesBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD00000234</key>
- <dict>
- <key>explicitFileType</key>
- <string>archive.ar</string>
- <key>includeInIndex</key>
- <string>0</string>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>path</key>
- <string>libxregexp.a</string>
- <key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
- </dict>
- <key>ABCDABCDABCDABCD00000235</key>
+ <key>ABCDABCDABCDABCD00000415</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD00000236</string>
+ <string>ABCDABCDABCDABCD00000416</string>
<key>buildPhases</key>
<array>
- <string>ABCDABCDABCDABCD00000233</string>
+ <string>ABCDABCDABCDABCD00000414</string>
</array>
<key>dependencies</key>
<array></array>
<key>isa</key>
<string>PBXNativeTarget</string>
<key>name</key>
- <string>xregexp</string>
+ <string>xregexp_template_tester</string>
<key>productName</key>
- <string>xregexp</string>
+ <string>xregexp_template_tester</string>
<key>productReference</key>
- <string>ABCDABCDABCDABCD00000234</string>
+ <string>ABCDABCDABCDABCD0000001E</string>
<key>productType</key>
<string>com.apple.product-type.library.static</string>
</dict>
- <key>ABCDABCDABCDABCD00000236</key>
+ <key>ABCDABCDABCDABCD00000416</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD00000237</string>
- <string>ABCDABCDABCDABCD00000238</string>
- <string>ABCDABCDABCDABCD00000239</string>
- <string>ABCDABCDABCDABCD0000023A</string>
+ <string>ABCDABCDABCDABCD00000417</string>
+ <string>ABCDABCDABCDABCD00000418</string>
+ <string>ABCDABCDABCDABCD00000419</string>
+ <string>ABCDABCDABCDABCD0000041A</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -7984,7 +14702,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD00000237</key>
+ <key>ABCDABCDABCDABCD00000417</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -7993,27 +14711,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp_template_tester</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xregexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -8030,7 +14746,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000238</key>
+ <key>ABCDABCDABCDABCD00000418</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -8039,27 +14755,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp_template_tester</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xregexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -8076,7 +14790,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000239</key>
+ <key>ABCDABCDABCDABCD00000419</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -8085,27 +14799,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp_template_tester</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xregexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -8122,7 +14834,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD0000023A</key>
+ <key>ABCDABCDABCDABCD0000041A</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -8131,27 +14843,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xregexp_template_tester</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>../../../../include/util/regexp</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xregexp</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -8168,7 +14878,7 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD0000023B</key>
+ <key>ABCDABCDABCDABCD0000041B</key>
<dict>
<key>containerPortal</key>
<string>ABCDABCDABCDABCD00000006</string>
@@ -8177,60 +14887,60 @@
<key>proxyType</key>
<string>1</string>
<key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD000002F8</string>
+ <string>ABCDABCDABCDABCD000004D9</string>
<key>remoteInfo</key>
<string>xser</string>
</dict>
- <key>ABCDABCDABCDABCD0000023C</key>
+ <key>ABCDABCDABCDABCD0000041C</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000240</string>
- <string>ABCDABCDABCDABCD00000242</string>
- <string>ABCDABCDABCDABCD00000244</string>
- <string>ABCDABCDABCDABCD00000246</string>
- <string>ABCDABCDABCDABCD00000248</string>
- <string>ABCDABCDABCDABCD0000024A</string>
- <string>ABCDABCDABCDABCD0000024C</string>
- <string>ABCDABCDABCDABCD0000024E</string>
- <string>ABCDABCDABCDABCD00000250</string>
- <string>ABCDABCDABCDABCD00000252</string>
- <string>ABCDABCDABCDABCD00000254</string>
- <string>ABCDABCDABCDABCD00000256</string>
- <string>ABCDABCDABCDABCD00000258</string>
- <string>ABCDABCDABCDABCD0000025A</string>
- <string>ABCDABCDABCDABCD0000025C</string>
- <string>ABCDABCDABCDABCD0000025E</string>
- <string>ABCDABCDABCDABCD00000260</string>
- <string>ABCDABCDABCDABCD00000262</string>
- <string>ABCDABCDABCDABCD00000264</string>
- <string>ABCDABCDABCDABCD00000266</string>
- <string>ABCDABCDABCDABCD00000268</string>
- <string>ABCDABCDABCDABCD0000026A</string>
- <string>ABCDABCDABCDABCD0000026C</string>
- <string>ABCDABCDABCDABCD0000026E</string>
- <string>ABCDABCDABCDABCD00000270</string>
- <string>ABCDABCDABCDABCD00000272</string>
- <string>ABCDABCDABCDABCD00000274</string>
- <string>ABCDABCDABCDABCD00000276</string>
- <string>ABCDABCDABCDABCD00000278</string>
- <string>ABCDABCDABCDABCD0000027A</string>
- <string>ABCDABCDABCDABCD0000027C</string>
- <string>BBCDABCDABCDABCD0000027C</string>
- <string>ABCDABCDABCDABCD0000027E</string>
- <string>ABCDABCDABCDABCD00000280</string>
- <string>ABCDABCDABCDABCD00000282</string>
- <string>ABCDABCDABCDABCD00000284</string>
- <string>ABCDABCDABCDABCD00000286</string>
- <string>ABCDABCDABCDABCD00000288</string>
- <string>ABCDABCDABCDABCD0000028A</string>
- <string>ABCDABCDABCDABCD0000028C</string>
- <string>ABCDABCDABCDABCD0000028E</string>
- <string>ABCDABCDABCDABCD00000290</string>
- <string>ABCDABCDABCDABCD00000292</string>
- <string>ABCDABCDABCDABCD00000294</string>
- <string>ABCDABCDABCDABCD00000296</string>
- <string>ABCDABCDABCDABCD00000298</string>
+ <string>ABCDABCDABCDABCD00000420</string>
+ <string>ABCDABCDABCDABCD00000422</string>
+ <string>ABCDABCDABCDABCD00000424</string>
+ <string>ABCDABCDABCDABCD00000426</string>
+ <string>ABCDABCDABCDABCD00000428</string>
+ <string>ABCDABCDABCDABCD0000042A</string>
+ <string>ABCDABCDABCDABCD0000042C</string>
+ <string>ABCDABCDABCDABCD0000042E</string>
+ <string>ABCDABCDABCDABCD00000430</string>
+ <string>ABCDABCDABCDABCD00000432</string>
+ <string>ABCDABCDABCDABCD00000434</string>
+ <string>ABCDABCDABCDABCD00000436</string>
+ <string>ABCDABCDABCDABCD00000438</string>
+ <string>ABCDABCDABCDABCD0000043A</string>
+ <string>ABCDABCDABCDABCD0000043C</string>
+ <string>ABCDABCDABCDABCD0000043E</string>
+ <string>ABCDABCDABCDABCD00000440</string>
+ <string>ABCDABCDABCDABCD00000442</string>
+ <string>ABCDABCDABCDABCD00000444</string>
+ <string>ABCDABCDABCDABCD00000446</string>
+ <string>ABCDABCDABCDABCD00000448</string>
+ <string>ABCDABCDABCDABCD0000044A</string>
+ <string>ABCDABCDABCDABCD0000044C</string>
+ <string>ABCDABCDABCDABCD0000044E</string>
+ <string>ABCDABCDABCDABCD00000450</string>
+ <string>ABCDABCDABCDABCD00000452</string>
+ <string>ABCDABCDABCDABCD00000454</string>
+ <string>ABCDABCDABCDABCD00000456</string>
+ <string>ABCDABCDABCDABCD00000458</string>
+ <string>ABCDABCDABCDABCD0000045A</string>
+ <string>ABCDABCDABCDABCD0000045C</string>
+ <string>ABCDABCDABCDABCD0000045E</string>
+ <string>ABCDABCDABCDABCD00000460</string>
+ <string>ABCDABCDABCDABCD00000462</string>
+ <string>ABCDABCDABCDABCD00000464</string>
+ <string>ABCDABCDABCDABCD00000466</string>
+ <string>ABCDABCDABCDABCD00000468</string>
+ <string>ABCDABCDABCDABCD0000046A</string>
+ <string>ABCDABCDABCDABCD0000046C</string>
+ <string>ABCDABCDABCDABCD0000046E</string>
+ <string>ABCDABCDABCDABCD00000470</string>
+ <string>ABCDABCDABCDABCD00000472</string>
+ <string>ABCDABCDABCDABCD00000474</string>
+ <string>ABCDABCDABCDABCD00000476</string>
+ <string>ABCDABCDABCDABCD00000478</string>
+ <string>ABCDABCDABCDABCD0000047A</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -8239,102 +14949,102 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD0000023D</key>
+ <key>ABCDABCDABCDABCD0000041D</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD0000029A</string>
- <string>ABCDABCDABCDABCD0000029B</string>
- <string>ABCDABCDABCDABCD0000029C</string>
- <string>ABCDABCDABCDABCD0000029D</string>
- <string>ABCDABCDABCDABCD0000029E</string>
- <string>ABCDABCDABCDABCD0000029F</string>
- <string>ABCDABCDABCDABCD000002A0</string>
- <string>ABCDABCDABCDABCD000002A1</string>
- <string>ABCDABCDABCDABCD000002A2</string>
- <string>ABCDABCDABCDABCD000002A3</string>
- <string>ABCDABCDABCDABCD000002A4</string>
- <string>ABCDABCDABCDABCD000002A5</string>
- <string>ABCDABCDABCDABCD000002A6</string>
- <string>ABCDABCDABCDABCD000002A7</string>
- <string>ABCDABCDABCDABCD000002A8</string>
- <string>ABCDABCDABCDABCD000002A9</string>
- <string>ABCDABCDABCDABCD000002AA</string>
- <string>ABCDABCDABCDABCD000002AB</string>
- <string>ABCDABCDABCDABCD000002AC</string>
- <string>ABCDABCDABCDABCD000002AD</string>
- <string>ABCDABCDABCDABCD000002AE</string>
- <string>ABCDABCDABCDABCD000002AF</string>
- <string>ABCDABCDABCDABCD000002B0</string>
- <string>ABCDABCDABCDABCD000002B1</string>
- <string>ABCDABCDABCDABCD000002B2</string>
- <string>ABCDABCDABCDABCD000002B3</string>
- <string>ABCDABCDABCDABCD000002B4</string>
- <string>ABCDABCDABCDABCD000002B5</string>
- <string>ABCDABCDABCDABCD000002B6</string>
- <string>ABCDABCDABCDABCD000002B7</string>
- <string>ABCDABCDABCDABCD000002B8</string>
- <string>ABCDABCDABCDABCD000002B9</string>
- <string>ABCDABCDABCDABCD000002BA</string>
- <string>ABCDABCDABCDABCD000002BB</string>
- <string>ABCDABCDABCDABCD000002BC</string>
- <string>ABCDABCDABCDABCD000002BD</string>
- <string>ABCDABCDABCDABCD000002BE</string>
- <string>ABCDABCDABCDABCD000002BF</string>
- <string>ABCDABCDABCDABCD000002C0</string>
- <string>ABCDABCDABCDABCD000002C1</string>
- <string>ABCDABCDABCDABCD000002C2</string>
- <string>ABCDABCDABCDABCD000002C3</string>
- <string>ABCDABCDABCDABCD000002C4</string>
- <string>ABCDABCDABCDABCD000002C5</string>
- <string>ABCDABCDABCDABCD000002C6</string>
- <string>ABCDABCDABCDABCD000002C7</string>
- <string>ABCDABCDABCDABCD000002C8</string>
- <string>ABCDABCDABCDABCD000002C9</string>
- <string>ABCDABCDABCDABCD000002CA</string>
- <string>ABCDABCDABCDABCD000002CB</string>
- <string>ABCDABCDABCDABCD000002CC</string>
- <string>ABCDABCDABCDABCD000002CD</string>
- <string>ABCDABCDABCDABCD000002CE</string>
- <string>ABCDABCDABCDABCD000002CF</string>
- <string>ABCDABCDABCDABCD000002D0</string>
- <string>ABCDABCDABCDABCD000002D1</string>
- <string>ABCDABCDABCDABCD000002D2</string>
- <string>ABCDABCDABCDABCD000002D3</string>
- <string>ABCDABCDABCDABCD000002D4</string>
- <string>ABCDABCDABCDABCD000002D5</string>
- <string>ABCDABCDABCDABCD000002D6</string>
- <string>ABCDABCDABCDABCD000002D7</string>
- <string>ABCDABCDABCDABCD000002D8</string>
- <string>ABCDABCDABCDABCD000002D9</string>
- <string>ABCDABCDABCDABCD000002DA</string>
- <string>ABCDABCDABCDABCD000002DB</string>
- <string>ABCDABCDABCDABCD000002DC</string>
- <string>ABCDABCDABCDABCD000002DD</string>
- <string>ABCDABCDABCDABCD000002DE</string>
- <string>ABCDABCDABCDABCD000002DF</string>
- <string>ABCDABCDABCDABCD000002E0</string>
- <string>ABCDABCDABCDABCD000002E1</string>
- <string>ABCDABCDABCDABCD000002E2</string>
- <string>ABCDABCDABCDABCD000002E3</string>
- <string>ABCDABCDABCDABCD000002E4</string>
- <string>ABCDABCDABCDABCD000002E5</string>
- <string>ABCDABCDABCDABCD000002E6</string>
- <string>ABCDABCDABCDABCD000002E7</string>
- <string>ABCDABCDABCDABCD000002E8</string>
- <string>ABCDABCDABCDABCD000002E9</string>
- <string>ABCDABCDABCDABCD000002EA</string>
- <string>ABCDABCDABCDABCD000002EB</string>
- <string>ABCDABCDABCDABCD000002EC</string>
- <string>ABCDABCDABCDABCD000002ED</string>
- <string>ABCDABCDABCDABCD000002EE</string>
- <string>ABCDABCDABCDABCD000002EF</string>
- <string>ABCDABCDABCDABCD000002F0</string>
- <string>ABCDABCDABCDABCD000002F1</string>
- <string>ABCDABCDABCDABCD000002F2</string>
- <string>ABCDABCDABCDABCD000002F3</string>
- <string>ABCDABCDABCDABCD000002F4</string>
- <string>ABCDABCDABCDABCD000002F5</string>
+ <string>ABCDABCDABCDABCD0000047C</string>
+ <string>ABCDABCDABCDABCD0000047D</string>
+ <string>ABCDABCDABCDABCD0000047E</string>
+ <string>ABCDABCDABCDABCD0000047F</string>
+ <string>ABCDABCDABCDABCD00000480</string>
+ <string>ABCDABCDABCDABCD00000481</string>
+ <string>ABCDABCDABCDABCD00000482</string>
+ <string>ABCDABCDABCDABCD00000483</string>
+ <string>ABCDABCDABCDABCD00000484</string>
+ <string>ABCDABCDABCDABCD00000485</string>
+ <string>ABCDABCDABCDABCD00000486</string>
+ <string>ABCDABCDABCDABCD00000487</string>
+ <string>ABCDABCDABCDABCD00000488</string>
+ <string>ABCDABCDABCDABCD00000489</string>
+ <string>ABCDABCDABCDABCD0000048A</string>
+ <string>ABCDABCDABCDABCD0000048B</string>
+ <string>ABCDABCDABCDABCD0000048C</string>
+ <string>ABCDABCDABCDABCD0000048D</string>
+ <string>ABCDABCDABCDABCD0000048E</string>
+ <string>ABCDABCDABCDABCD0000048F</string>
+ <string>ABCDABCDABCDABCD00000490</string>
+ <string>ABCDABCDABCDABCD00000491</string>
+ <string>ABCDABCDABCDABCD00000492</string>
+ <string>ABCDABCDABCDABCD00000493</string>
+ <string>ABCDABCDABCDABCD00000494</string>
+ <string>ABCDABCDABCDABCD00000495</string>
+ <string>ABCDABCDABCDABCD00000496</string>
+ <string>ABCDABCDABCDABCD00000497</string>
+ <string>ABCDABCDABCDABCD00000498</string>
+ <string>ABCDABCDABCDABCD00000499</string>
+ <string>ABCDABCDABCDABCD0000049A</string>
+ <string>ABCDABCDABCDABCD0000049B</string>
+ <string>ABCDABCDABCDABCD0000049C</string>
+ <string>ABCDABCDABCDABCD0000049D</string>
+ <string>ABCDABCDABCDABCD0000049E</string>
+ <string>ABCDABCDABCDABCD0000049F</string>
+ <string>ABCDABCDABCDABCD000004A0</string>
+ <string>ABCDABCDABCDABCD000004A1</string>
+ <string>ABCDABCDABCDABCD000004A2</string>
+ <string>ABCDABCDABCDABCD000004A3</string>
+ <string>ABCDABCDABCDABCD000004A4</string>
+ <string>ABCDABCDABCDABCD000004A5</string>
+ <string>ABCDABCDABCDABCD000004A6</string>
+ <string>ABCDABCDABCDABCD000004A7</string>
+ <string>ABCDABCDABCDABCD000004A8</string>
+ <string>ABCDABCDABCDABCD000004A9</string>
+ <string>ABCDABCDABCDABCD000004AA</string>
+ <string>ABCDABCDABCDABCD000004AB</string>
+ <string>ABCDABCDABCDABCD000004AC</string>
+ <string>ABCDABCDABCDABCD000004AD</string>
+ <string>ABCDABCDABCDABCD000004AE</string>
+ <string>ABCDABCDABCDABCD000004AF</string>
+ <string>ABCDABCDABCDABCD000004B0</string>
+ <string>ABCDABCDABCDABCD000004B1</string>
+ <string>ABCDABCDABCDABCD000004B2</string>
+ <string>ABCDABCDABCDABCD000004B3</string>
+ <string>ABCDABCDABCDABCD000004B4</string>
+ <string>ABCDABCDABCDABCD000004B5</string>
+ <string>ABCDABCDABCDABCD000004B6</string>
+ <string>ABCDABCDABCDABCD000004B7</string>
+ <string>ABCDABCDABCDABCD000004B8</string>
+ <string>ABCDABCDABCDABCD000004B9</string>
+ <string>ABCDABCDABCDABCD000004BA</string>
+ <string>ABCDABCDABCDABCD000004BB</string>
+ <string>ABCDABCDABCDABCD000004BC</string>
+ <string>ABCDABCDABCDABCD000004BD</string>
+ <string>ABCDABCDABCDABCD000004BE</string>
+ <string>ABCDABCDABCDABCD000004BF</string>
+ <string>ABCDABCDABCDABCD000004C0</string>
+ <string>ABCDABCDABCDABCD000004C1</string>
+ <string>ABCDABCDABCDABCD000004C2</string>
+ <string>ABCDABCDABCDABCD000004C3</string>
+ <string>ABCDABCDABCDABCD000004C4</string>
+ <string>ABCDABCDABCDABCD000004C5</string>
+ <string>ABCDABCDABCDABCD000004C6</string>
+ <string>ABCDABCDABCDABCD000004C7</string>
+ <string>ABCDABCDABCDABCD000004C8</string>
+ <string>ABCDABCDABCDABCD000004C9</string>
+ <string>ABCDABCDABCDABCD000004CA</string>
+ <string>ABCDABCDABCDABCD000004CB</string>
+ <string>ABCDABCDABCDABCD000004CC</string>
+ <string>ABCDABCDABCDABCD000004CD</string>
+ <string>ABCDABCDABCDABCD000004CE</string>
+ <string>ABCDABCDABCDABCD000004CF</string>
+ <string>ABCDABCDABCDABCD000004D0</string>
+ <string>ABCDABCDABCDABCD000004D1</string>
+ <string>ABCDABCDABCDABCD000004D2</string>
+ <string>ABCDABCDABCDABCD000004D3</string>
+ <string>ABCDABCDABCDABCD000004D4</string>
+ <string>ABCDABCDABCDABCD000004D5</string>
+ <string>ABCDABCDABCDABCD000004D6</string>
+ <string>ABCDABCDABCDABCD000004D7</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -8343,12 +15053,12 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD0000023F</key>
+ <key>ABCDABCDABCDABCD0000041F</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD0000023C</string>
- <string>ABCDABCDABCDABCD0000023D</string>
+ <string>ABCDABCDABCDABCD0000041C</string>
+ <string>ABCDABCDABCDABCD0000041D</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -8357,7 +15067,7 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000240</key>
+ <key>ABCDABCDABCDABCD00000420</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8370,14 +15080,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000241</key>
+ <key>ABCDABCDABCDABCD00000421</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000240</string>
+ <string>ABCDABCDABCDABCD00000420</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000242</key>
+ <key>ABCDABCDABCDABCD00000422</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8390,14 +15100,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000243</key>
+ <key>ABCDABCDABCDABCD00000423</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000242</string>
+ <string>ABCDABCDABCDABCD00000422</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000244</key>
+ <key>ABCDABCDABCDABCD00000424</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8410,14 +15120,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000245</key>
+ <key>ABCDABCDABCDABCD00000425</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000244</string>
+ <string>ABCDABCDABCDABCD00000424</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000246</key>
+ <key>ABCDABCDABCDABCD00000426</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8430,14 +15140,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000247</key>
+ <key>ABCDABCDABCDABCD00000427</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000246</string>
+ <string>ABCDABCDABCDABCD00000426</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000248</key>
+ <key>ABCDABCDABCDABCD00000428</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8450,14 +15160,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000249</key>
+ <key>ABCDABCDABCDABCD00000429</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000248</string>
+ <string>ABCDABCDABCDABCD00000428</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000024A</key>
+ <key>ABCDABCDABCDABCD0000042A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8470,14 +15180,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000024B</key>
+ <key>ABCDABCDABCDABCD0000042B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000024A</string>
+ <string>ABCDABCDABCDABCD0000042A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000024C</key>
+ <key>ABCDABCDABCDABCD0000042C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8490,14 +15200,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000024D</key>
+ <key>ABCDABCDABCDABCD0000042D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000024C</string>
+ <string>ABCDABCDABCDABCD0000042C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000024E</key>
+ <key>ABCDABCDABCDABCD0000042E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8510,14 +15220,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000024F</key>
+ <key>ABCDABCDABCDABCD0000042F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000024E</string>
+ <string>ABCDABCDABCDABCD0000042E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000250</key>
+ <key>ABCDABCDABCDABCD00000430</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8530,14 +15240,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000251</key>
+ <key>ABCDABCDABCDABCD00000431</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000250</string>
+ <string>ABCDABCDABCDABCD00000430</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000252</key>
+ <key>ABCDABCDABCDABCD00000432</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8550,14 +15260,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000253</key>
+ <key>ABCDABCDABCDABCD00000433</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000252</string>
+ <string>ABCDABCDABCDABCD00000432</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000254</key>
+ <key>ABCDABCDABCDABCD00000434</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8570,14 +15280,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000255</key>
+ <key>ABCDABCDABCDABCD00000435</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000254</string>
+ <string>ABCDABCDABCDABCD00000434</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000256</key>
+ <key>ABCDABCDABCDABCD00000436</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8590,14 +15300,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000257</key>
+ <key>ABCDABCDABCDABCD00000437</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000256</string>
+ <string>ABCDABCDABCDABCD00000436</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000258</key>
+ <key>ABCDABCDABCDABCD00000438</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8610,14 +15320,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000259</key>
+ <key>ABCDABCDABCDABCD00000439</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000258</string>
+ <string>ABCDABCDABCDABCD00000438</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000025A</key>
+ <key>ABCDABCDABCDABCD0000043A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8630,14 +15340,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000025B</key>
+ <key>ABCDABCDABCDABCD0000043B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000025A</string>
+ <string>ABCDABCDABCDABCD0000043A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000025C</key>
+ <key>ABCDABCDABCDABCD0000043C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8650,14 +15360,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000025D</key>
+ <key>ABCDABCDABCDABCD0000043D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000025C</string>
+ <string>ABCDABCDABCDABCD0000043C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000025E</key>
+ <key>ABCDABCDABCDABCD0000043E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8670,14 +15380,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000025F</key>
+ <key>ABCDABCDABCDABCD0000043F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000025E</string>
+ <string>ABCDABCDABCDABCD0000043E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000260</key>
+ <key>ABCDABCDABCDABCD00000440</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8690,14 +15400,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000261</key>
+ <key>ABCDABCDABCDABCD00000441</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000260</string>
+ <string>ABCDABCDABCDABCD00000440</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000262</key>
+ <key>ABCDABCDABCDABCD00000442</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8710,14 +15420,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000263</key>
+ <key>ABCDABCDABCDABCD00000443</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000262</string>
+ <string>ABCDABCDABCDABCD00000442</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000264</key>
+ <key>ABCDABCDABCDABCD00000444</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8730,14 +15440,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000265</key>
+ <key>ABCDABCDABCDABCD00000445</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000264</string>
+ <string>ABCDABCDABCDABCD00000444</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000266</key>
+ <key>ABCDABCDABCDABCD00000446</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8750,14 +15460,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000267</key>
+ <key>ABCDABCDABCDABCD00000447</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000266</string>
+ <string>ABCDABCDABCDABCD00000446</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000268</key>
+ <key>ABCDABCDABCDABCD00000448</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8770,14 +15480,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000269</key>
+ <key>ABCDABCDABCDABCD00000449</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000268</string>
+ <string>ABCDABCDABCDABCD00000448</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000026A</key>
+ <key>ABCDABCDABCDABCD0000044A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8790,14 +15500,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000026B</key>
+ <key>ABCDABCDABCDABCD0000044B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000026A</string>
+ <string>ABCDABCDABCDABCD0000044A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000026C</key>
+ <key>ABCDABCDABCDABCD0000044C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8810,14 +15520,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000026D</key>
+ <key>ABCDABCDABCDABCD0000044D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000026C</string>
+ <string>ABCDABCDABCDABCD0000044C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000026E</key>
+ <key>ABCDABCDABCDABCD0000044E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8830,14 +15540,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000026F</key>
+ <key>ABCDABCDABCDABCD0000044F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000026E</string>
+ <string>ABCDABCDABCDABCD0000044E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000270</key>
+ <key>ABCDABCDABCDABCD00000450</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -8850,154 +15560,154 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000271</key>
+ <key>ABCDABCDABCDABCD00000451</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000270</string>
+ <string>ABCDABCDABCDABCD00000450</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000272</key>
+ <key>ABCDABCDABCDABCD00000452</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objistrxml.cpp</string>
+ <string>objistrjson.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objistrxml.cpp</string>
+ <string>../../../../src/serial/objistrjson.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000273</key>
+ <key>ABCDABCDABCDABCD00000453</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000272</string>
+ <string>ABCDABCDABCDABCD00000452</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000274</key>
+ <key>ABCDABCDABCDABCD00000454</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objlist.cpp</string>
+ <string>objistrxml.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objlist.cpp</string>
+ <string>../../../../src/serial/objistrxml.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000275</key>
+ <key>ABCDABCDABCDABCD00000455</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000274</string>
+ <string>ABCDABCDABCDABCD00000454</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000276</key>
+ <key>ABCDABCDABCDABCD00000456</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objostr.cpp</string>
+ <string>objlist.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objostr.cpp</string>
+ <string>../../../../src/serial/objlist.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000277</key>
+ <key>ABCDABCDABCDABCD00000457</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000276</string>
+ <string>ABCDABCDABCDABCD00000456</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000278</key>
+ <key>ABCDABCDABCDABCD00000458</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objostrasn.cpp</string>
+ <string>objostr.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objostrasn.cpp</string>
+ <string>../../../../src/serial/objostr.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000279</key>
+ <key>ABCDABCDABCDABCD00000459</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000278</string>
+ <string>ABCDABCDABCDABCD00000458</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000027A</key>
+ <key>ABCDABCDABCDABCD0000045A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objostrasnb.cpp</string>
+ <string>objostrasn.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objostrasnb.cpp</string>
+ <string>../../../../src/serial/objostrasn.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000027B</key>
+ <key>ABCDABCDABCDABCD0000045B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000027A</string>
+ <string>ABCDABCDABCDABCD0000045A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000027C</key>
+ <key>ABCDABCDABCDABCD0000045C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objostrjson.cpp</string>
+ <string>objostrasnb.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objostrjson.cpp</string>
+ <string>../../../../src/serial/objostrasnb.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000027D</key>
+ <key>ABCDABCDABCDABCD0000045D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000027C</string>
+ <string>ABCDABCDABCDABCD0000045C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>BBCDABCDABCDABCD0000027C</key>
+ <key>ABCDABCDABCDABCD0000045E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>objistrjson.cpp</string>
+ <string>objostrjson.cpp</string>
<key>path</key>
- <string>../../../../src/serial/objistrjson.cpp</string>
+ <string>../../../../src/serial/objostrjson.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>BBCDABCDABCDABCD0000027D</key>
+ <key>ABCDABCDABCDABCD0000045F</key>
<dict>
<key>fileRef</key>
- <string>BBCDABCDABCDABCD0000027C</string>
+ <string>ABCDABCDABCDABCD0000045E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000027E</key>
+ <key>ABCDABCDABCDABCD00000460</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9010,14 +15720,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000027F</key>
+ <key>ABCDABCDABCDABCD00000461</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000027E</string>
+ <string>ABCDABCDABCDABCD00000460</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000280</key>
+ <key>ABCDABCDABCDABCD00000462</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9030,14 +15740,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000281</key>
+ <key>ABCDABCDABCDABCD00000463</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000280</string>
+ <string>ABCDABCDABCDABCD00000462</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000282</key>
+ <key>ABCDABCDABCDABCD00000464</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9050,14 +15760,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000283</key>
+ <key>ABCDABCDABCDABCD00000465</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000282</string>
+ <string>ABCDABCDABCDABCD00000464</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000284</key>
+ <key>ABCDABCDABCDABCD00000466</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9070,14 +15780,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000285</key>
+ <key>ABCDABCDABCDABCD00000467</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000284</string>
+ <string>ABCDABCDABCDABCD00000466</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000286</key>
+ <key>ABCDABCDABCDABCD00000468</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9090,14 +15800,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000287</key>
+ <key>ABCDABCDABCDABCD00000469</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000286</string>
+ <string>ABCDABCDABCDABCD00000468</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000288</key>
+ <key>ABCDABCDABCDABCD0000046A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9110,14 +15820,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000289</key>
+ <key>ABCDABCDABCDABCD0000046B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000288</string>
+ <string>ABCDABCDABCDABCD0000046A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000028A</key>
+ <key>ABCDABCDABCDABCD0000046C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9130,14 +15840,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000028B</key>
+ <key>ABCDABCDABCDABCD0000046D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000028A</string>
+ <string>ABCDABCDABCDABCD0000046C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000028C</key>
+ <key>ABCDABCDABCDABCD0000046E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9150,14 +15860,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000028D</key>
+ <key>ABCDABCDABCDABCD0000046F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000028C</string>
+ <string>ABCDABCDABCDABCD0000046E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000028E</key>
+ <key>ABCDABCDABCDABCD00000470</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9170,14 +15880,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000028F</key>
+ <key>ABCDABCDABCDABCD00000471</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000028E</string>
+ <string>ABCDABCDABCDABCD00000470</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000472</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9190,14 +15900,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000291</key>
+ <key>ABCDABCDABCDABCD00000473</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000290</string>
+ <string>ABCDABCDABCDABCD00000472</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000292</key>
+ <key>ABCDABCDABCDABCD00000474</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9210,14 +15920,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000293</key>
+ <key>ABCDABCDABCDABCD00000475</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000292</string>
+ <string>ABCDABCDABCDABCD00000474</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000294</key>
+ <key>ABCDABCDABCDABCD00000476</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9230,14 +15940,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000477</key>
<dict>
<key>fileRef</key>
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+ <string>ABCDABCDABCDABCD00000476</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000478</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9250,14 +15960,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000479</key>
<dict>
<key>fileRef</key>
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+ <string>ABCDABCDABCDABCD00000478</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000298</key>
+ <key>ABCDABCDABCDABCD0000047A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9270,14 +15980,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000299</key>
+ <key>ABCDABCDABCDABCD0000047B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000298</string>
+ <string>ABCDABCDABCDABCD0000047A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000029A</key>
+ <key>ABCDABCDABCDABCD0000047C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9290,7 +16000,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000029B</key>
+ <key>ABCDABCDABCDABCD0000047D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9303,7 +16013,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000029C</key>
+ <key>ABCDABCDABCDABCD0000047E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9316,7 +16026,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000029D</key>
+ <key>ABCDABCDABCDABCD0000047F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9329,7 +16039,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000029E</key>
+ <key>ABCDABCDABCDABCD00000480</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9342,7 +16052,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000029F</key>
+ <key>ABCDABCDABCDABCD00000481</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9355,7 +16065,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A0</key>
+ <key>ABCDABCDABCDABCD00000482</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9368,7 +16078,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A1</key>
+ <key>ABCDABCDABCDABCD00000483</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9381,7 +16091,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A2</key>
+ <key>ABCDABCDABCDABCD00000484</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9394,7 +16104,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A3</key>
+ <key>ABCDABCDABCDABCD00000485</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9407,7 +16117,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A4</key>
+ <key>ABCDABCDABCDABCD00000486</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9420,7 +16130,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A5</key>
+ <key>ABCDABCDABCDABCD00000487</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9433,7 +16143,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002A6</key>
+ <key>ABCDABCDABCDABCD00000488</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9446,20 +16156,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
- <key>name</key>
- <string>Copy of stltypes.hpp</string>
- <key>path</key>
- <string>../../../../include/serial/impl/Copy of stltypes.hpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD000002A8</key>
+ <key>ABCDABCDABCDABCD00000489</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9472,7 +16169,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD0000048A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9485,7 +16182,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002AA</key>
+ <key>ABCDABCDABCDABCD0000048B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9498,7 +16195,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD0000048C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9511,7 +16208,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD0000048D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9524,7 +16221,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD0000048E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9537,7 +16234,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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- <key>ABCDABCDABCDABCD000002AE</key>
+ <key>ABCDABCDABCDABCD0000048F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9550,7 +16247,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000490</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9563,7 +16260,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000491</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9576,7 +16273,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000492</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9589,7 +16286,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000493</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9602,7 +16299,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
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+ <key>ABCDABCDABCDABCD00000494</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9615,7 +16312,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002B4</key>
+ <key>ABCDABCDABCDABCD00000495</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9628,7 +16325,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000496</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9641,7 +16338,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000497</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9654,7 +16351,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000498</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9667,7 +16364,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD00000499</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9680,7 +16377,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
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+ <key>ABCDABCDABCDABCD0000049A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9693,7 +16390,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BA</key>
+ <key>ABCDABCDABCDABCD0000049B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9706,7 +16403,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BB</key>
+ <key>ABCDABCDABCDABCD0000049C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9719,7 +16416,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BC</key>
+ <key>ABCDABCDABCDABCD0000049D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9732,7 +16429,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BD</key>
+ <key>ABCDABCDABCDABCD0000049E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9745,7 +16442,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BE</key>
+ <key>ABCDABCDABCDABCD0000049F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9758,7 +16455,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002BF</key>
+ <key>ABCDABCDABCDABCD000004A0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9771,7 +16468,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C0</key>
+ <key>ABCDABCDABCDABCD000004A1</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9784,7 +16481,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C1</key>
+ <key>ABCDABCDABCDABCD000004A2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9797,7 +16494,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C2</key>
+ <key>ABCDABCDABCDABCD000004A3</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9810,7 +16507,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C3</key>
+ <key>ABCDABCDABCDABCD000004A4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9823,7 +16520,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C4</key>
+ <key>ABCDABCDABCDABCD000004A5</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9836,7 +16533,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C5</key>
+ <key>ABCDABCDABCDABCD000004A6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9849,7 +16546,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C6</key>
+ <key>ABCDABCDABCDABCD000004A7</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9862,7 +16559,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C7</key>
+ <key>ABCDABCDABCDABCD000004A8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9875,7 +16572,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C8</key>
+ <key>ABCDABCDABCDABCD000004A9</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9888,7 +16585,20 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002C9</key>
+ <key>ABCDABCDABCDABCD000004AA</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>objistrjson.hpp</string>
+ <key>path</key>
+ <string>../../../../include/serial/objistrjson.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000004AB</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9901,7 +16611,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CA</key>
+ <key>ABCDABCDABCDABCD000004AC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9914,7 +16624,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CB</key>
+ <key>ABCDABCDABCDABCD000004AD</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9927,7 +16637,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CC</key>
+ <key>ABCDABCDABCDABCD000004AE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9940,7 +16650,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CD</key>
+ <key>ABCDABCDABCDABCD000004AF</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9953,7 +16663,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CE</key>
+ <key>ABCDABCDABCDABCD000004B0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9966,7 +16676,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002CF</key>
+ <key>ABCDABCDABCDABCD000004B1</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9979,7 +16689,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D0</key>
+ <key>ABCDABCDABCDABCD000004B2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -9992,7 +16702,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D1</key>
+ <key>ABCDABCDABCDABCD000004B3</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10005,7 +16715,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D2</key>
+ <key>ABCDABCDABCDABCD000004B4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10018,7 +16728,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D3</key>
+ <key>ABCDABCDABCDABCD000004B5</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10031,7 +16741,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D4</key>
+ <key>ABCDABCDABCDABCD000004B6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10044,7 +16754,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D5</key>
+ <key>ABCDABCDABCDABCD000004B7</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10057,7 +16767,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D6</key>
+ <key>ABCDABCDABCDABCD000004B8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10070,7 +16780,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D7</key>
+ <key>ABCDABCDABCDABCD000004B9</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10083,7 +16793,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D8</key>
+ <key>ABCDABCDABCDABCD000004BA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10096,7 +16806,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002D9</key>
+ <key>ABCDABCDABCDABCD000004BB</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10109,7 +16819,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DA</key>
+ <key>ABCDABCDABCDABCD000004BC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10122,7 +16832,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DB</key>
+ <key>ABCDABCDABCDABCD000004BD</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10135,7 +16845,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DC</key>
+ <key>ABCDABCDABCDABCD000004BE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10148,7 +16858,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DD</key>
+ <key>ABCDABCDABCDABCD000004BF</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10161,7 +16871,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DE</key>
+ <key>ABCDABCDABCDABCD000004C0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10174,7 +16884,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002DF</key>
+ <key>ABCDABCDABCDABCD000004C1</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10187,7 +16897,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E0</key>
+ <key>ABCDABCDABCDABCD000004C2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10200,7 +16910,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E1</key>
+ <key>ABCDABCDABCDABCD000004C3</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10213,7 +16923,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E2</key>
+ <key>ABCDABCDABCDABCD000004C4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10226,7 +16936,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E3</key>
+ <key>ABCDABCDABCDABCD000004C5</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10239,7 +16949,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E4</key>
+ <key>ABCDABCDABCDABCD000004C6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10252,7 +16962,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E5</key>
+ <key>ABCDABCDABCDABCD000004C7</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10265,7 +16975,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E6</key>
+ <key>ABCDABCDABCDABCD000004C8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10278,7 +16988,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E7</key>
+ <key>ABCDABCDABCDABCD000004C9</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10291,7 +17001,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E8</key>
+ <key>ABCDABCDABCDABCD000004CA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10304,7 +17014,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002E9</key>
+ <key>ABCDABCDABCDABCD000004CB</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10317,7 +17027,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002EA</key>
+ <key>ABCDABCDABCDABCD000004CC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10330,7 +17040,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002EB</key>
+ <key>ABCDABCDABCDABCD000004CD</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10343,7 +17053,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002EC</key>
+ <key>ABCDABCDABCDABCD000004CE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10356,7 +17066,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002ED</key>
+ <key>ABCDABCDABCDABCD000004CF</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10369,7 +17079,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002EE</key>
+ <key>ABCDABCDABCDABCD000004D0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10382,7 +17092,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002EF</key>
+ <key>ABCDABCDABCDABCD000004D1</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10395,7 +17105,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F0</key>
+ <key>ABCDABCDABCDABCD000004D2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10408,7 +17118,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F1</key>
+ <key>ABCDABCDABCDABCD000004D3</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10421,7 +17131,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F2</key>
+ <key>ABCDABCDABCDABCD000004D4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10434,7 +17144,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F3</key>
+ <key>ABCDABCDABCDABCD000004D5</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10447,7 +17157,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F4</key>
+ <key>ABCDABCDABCDABCD000004D6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10460,7 +17170,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F5</key>
+ <key>ABCDABCDABCDABCD000004D7</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10473,80 +17183,67 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD000002F6</key>
+ <key>ABCDABCDABCDABCD000004D8</key>
<dict>
<key>files</key>
<array>
- <string>ABCDABCDABCDABCD00000241</string>
- <string>ABCDABCDABCDABCD00000243</string>
- <string>ABCDABCDABCDABCD00000245</string>
- <string>ABCDABCDABCDABCD00000247</string>
- <string>ABCDABCDABCDABCD00000249</string>
- <string>ABCDABCDABCDABCD0000024B</string>
- <string>ABCDABCDABCDABCD0000024D</string>
- <string>ABCDABCDABCDABCD0000024F</string>
- <string>ABCDABCDABCDABCD00000251</string>
- <string>ABCDABCDABCDABCD00000253</string>
- <string>ABCDABCDABCDABCD00000255</string>
- <string>ABCDABCDABCDABCD00000257</string>
- <string>ABCDABCDABCDABCD00000259</string>
- <string>ABCDABCDABCDABCD0000025B</string>
- <string>ABCDABCDABCDABCD0000025D</string>
- <string>ABCDABCDABCDABCD0000025F</string>
- <string>ABCDABCDABCDABCD00000261</string>
- <string>ABCDABCDABCDABCD00000263</string>
- <string>ABCDABCDABCDABCD00000265</string>
- <string>ABCDABCDABCDABCD00000267</string>
- <string>ABCDABCDABCDABCD00000269</string>
- <string>ABCDABCDABCDABCD0000026B</string>
- <string>ABCDABCDABCDABCD0000026D</string>
- <string>ABCDABCDABCDABCD0000026F</string>
- <string>ABCDABCDABCDABCD00000271</string>
- <string>ABCDABCDABCDABCD00000273</string>
- <string>ABCDABCDABCDABCD00000275</string>
- <string>ABCDABCDABCDABCD00000277</string>
- <string>ABCDABCDABCDABCD00000279</string>
- <string>ABCDABCDABCDABCD0000027B</string>
- <string>ABCDABCDABCDABCD0000027D</string>
- <string>BBCDABCDABCDABCD0000027D</string>
- <string>ABCDABCDABCDABCD0000027F</string>
- <string>ABCDABCDABCDABCD00000281</string>
- <string>ABCDABCDABCDABCD00000283</string>
- <string>ABCDABCDABCDABCD00000285</string>
- <string>ABCDABCDABCDABCD00000287</string>
- <string>ABCDABCDABCDABCD00000289</string>
- <string>ABCDABCDABCDABCD0000028B</string>
- <string>ABCDABCDABCDABCD0000028D</string>
- <string>ABCDABCDABCDABCD0000028F</string>
- <string>ABCDABCDABCDABCD00000291</string>
- <string>ABCDABCDABCDABCD00000293</string>
- <string>ABCDABCDABCDABCD00000295</string>
- <string>ABCDABCDABCDABCD00000297</string>
- <string>ABCDABCDABCDABCD00000299</string>
+ <string>ABCDABCDABCDABCD00000421</string>
+ <string>ABCDABCDABCDABCD00000423</string>
+ <string>ABCDABCDABCDABCD00000425</string>
+ <string>ABCDABCDABCDABCD00000427</string>
+ <string>ABCDABCDABCDABCD00000429</string>
+ <string>ABCDABCDABCDABCD0000042B</string>
+ <string>ABCDABCDABCDABCD0000042D</string>
+ <string>ABCDABCDABCDABCD0000042F</string>
+ <string>ABCDABCDABCDABCD00000431</string>
+ <string>ABCDABCDABCDABCD00000433</string>
+ <string>ABCDABCDABCDABCD00000435</string>
+ <string>ABCDABCDABCDABCD00000437</string>
+ <string>ABCDABCDABCDABCD00000439</string>
+ <string>ABCDABCDABCDABCD0000043B</string>
+ <string>ABCDABCDABCDABCD0000043D</string>
+ <string>ABCDABCDABCDABCD0000043F</string>
+ <string>ABCDABCDABCDABCD00000441</string>
+ <string>ABCDABCDABCDABCD00000443</string>
+ <string>ABCDABCDABCDABCD00000445</string>
+ <string>ABCDABCDABCDABCD00000447</string>
+ <string>ABCDABCDABCDABCD00000449</string>
+ <string>ABCDABCDABCDABCD0000044B</string>
+ <string>ABCDABCDABCDABCD0000044D</string>
+ <string>ABCDABCDABCDABCD0000044F</string>
+ <string>ABCDABCDABCDABCD00000451</string>
+ <string>ABCDABCDABCDABCD00000453</string>
+ <string>ABCDABCDABCDABCD00000455</string>
+ <string>ABCDABCDABCDABCD00000457</string>
+ <string>ABCDABCDABCDABCD00000459</string>
+ <string>ABCDABCDABCDABCD0000045B</string>
+ <string>ABCDABCDABCDABCD0000045D</string>
+ <string>ABCDABCDABCDABCD0000045F</string>
+ <string>ABCDABCDABCDABCD00000461</string>
+ <string>ABCDABCDABCDABCD00000463</string>
+ <string>ABCDABCDABCDABCD00000465</string>
+ <string>ABCDABCDABCDABCD00000467</string>
+ <string>ABCDABCDABCDABCD00000469</string>
+ <string>ABCDABCDABCDABCD0000046B</string>
+ <string>ABCDABCDABCDABCD0000046D</string>
+ <string>ABCDABCDABCDABCD0000046F</string>
+ <string>ABCDABCDABCDABCD00000471</string>
+ <string>ABCDABCDABCDABCD00000473</string>
+ <string>ABCDABCDABCDABCD00000475</string>
+ <string>ABCDABCDABCDABCD00000477</string>
+ <string>ABCDABCDABCDABCD00000479</string>
+ <string>ABCDABCDABCDABCD0000047B</string>
</array>
<key>isa</key>
<string>PBXSourcesBuildPhase</string>
</dict>
- <key>ABCDABCDABCDABCD000002F7</key>
- <dict>
- <key>explicitFileType</key>
- <string>archive.ar</string>
- <key>includeInIndex</key>
- <string>0</string>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>path</key>
- <string>libxser.a</string>
- <key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
- </dict>
- <key>ABCDABCDABCDABCD000002F8</key>
+ <key>ABCDABCDABCDABCD000004D9</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD000002F9</string>
+ <string>ABCDABCDABCDABCD000004DA</string>
<key>buildPhases</key>
<array>
- <string>ABCDABCDABCDABCD000002F6</string>
+ <string>ABCDABCDABCDABCD000004D8</string>
</array>
<key>dependencies</key>
<array></array>
@@ -10557,18 +17254,18 @@
<key>productName</key>
<string>xser</string>
<key>productReference</key>
- <string>ABCDABCDABCDABCD000002F7</string>
+ <string>ABCDABCDABCDABCD0000001F</string>
<key>productType</key>
<string>com.apple.product-type.library.static</string>
</dict>
- <key>ABCDABCDABCDABCD000002F9</key>
+ <key>ABCDABCDABCDABCD000004DA</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD000002FA</string>
- <string>ABCDABCDABCDABCD000002FB</string>
- <string>ABCDABCDABCDABCD000002FC</string>
- <string>ABCDABCDABCDABCD000002FD</string>
+ <string>ABCDABCDABCDABCD000004DB</string>
+ <string>ABCDABCDABCDABCD000004DC</string>
+ <string>ABCDABCDABCDABCD000004DD</string>
+ <string>ABCDABCDABCDABCD000004DE</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -10577,7 +17274,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000002FA</key>
+ <key>ABCDABCDABCDABCD000004DB</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -10586,26 +17283,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xser</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xser</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -10622,7 +17318,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000002FB</key>
+ <key>ABCDABCDABCDABCD000004DC</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -10631,26 +17327,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xser</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xser</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -10667,7 +17362,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000002FC</key>
+ <key>ABCDABCDABCDABCD000004DD</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -10676,26 +17371,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xser</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xser</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -10712,7 +17406,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000002FD</key>
+ <key>ABCDABCDABCDABCD000004DE</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -10721,26 +17415,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xser</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xser</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -10757,7 +17450,7 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD000002FE</key>
+ <key>ABCDABCDABCDABCD000004DF</key>
<dict>
<key>containerPortal</key>
<string>ABCDABCDABCDABCD00000006</string>
@@ -10766,48 +17459,52 @@
<key>proxyType</key>
<string>1</string>
<key>remoteGlobalIDString</key>
- <string>ABCDABCDABCDABCD0000038F</string>
+ <string>ABCDABCDABCDABCD0000057D</string>
<key>remoteInfo</key>
<string>xutil</string>
</dict>
- <key>ABCDABCDABCDABCD000002FF</key>
+ <key>ABCDABCDABCDABCD000004E0</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000303</string>
- <string>ABCDABCDABCDABCD00000305</string>
- <string>ABCDABCDABCDABCD00000307</string>
- <string>ABCDABCDABCDABCD00000309</string>
- <string>ABCDABCDABCDABCD0000030B</string>
- <string>ABCDABCDABCDABCD0000030D</string>
- <string>ABCDABCDABCDABCD0000030F</string>
- <string>ABCDABCDABCDABCD00000311</string>
- <string>ABCDABCDABCDABCD00000313</string>
- <string>ABCDABCDABCDABCD00000315</string>
- <string>ABCDABCDABCDABCD00000317</string>
- <string>ABCDABCDABCDABCD00000319</string>
- <string>ABCDABCDABCDABCD0000031B</string>
- <string>ABCDABCDABCDABCD0000031D</string>
- <string>ABCDABCDABCDABCD0000031F</string>
- <string>ABCDABCDABCDABCD00000321</string>
- <string>ABCDABCDABCDABCD00000323</string>
- <string>ABCDABCDABCDABCD00000325</string>
- <string>ABCDABCDABCDABCD00000327</string>
- <string>ABCDABCDABCDABCD00000329</string>
- <string>ABCDABCDABCDABCD0000032B</string>
- <string>ABCDABCDABCDABCD0000032D</string>
- <string>ABCDABCDABCDABCD0000032F</string>
- <string>ABCDABCDABCDABCD00000331</string>
- <string>ABCDABCDABCDABCD00000333</string>
- <string>ABCDABCDABCDABCD00000335</string>
- <string>ABCDABCDABCDABCD00000337</string>
- <string>ABCDABCDABCDABCD00000339</string>
- <string>ABCDABCDABCDABCD0000033B</string>
- <string>ABCDABCDABCDABCD0000033D</string>
- <string>ABCDABCDABCDABCD0000033F</string>
- <string>ABCDABCDABCDABCD00000341</string>
- <string>ABCDABCDABCDABCD00000343</string>
- <string>ABCDABCDABCDABCD00000345</string>
+ <string>ABCDABCDABCDABCD000004E4</string>
+ <string>ABCDABCDABCDABCD000004E6</string>
+ <string>ABCDABCDABCDABCD000004E8</string>
+ <string>ABCDABCDABCDABCD000004EA</string>
+ <string>ABCDABCDABCDABCD000004EC</string>
+ <string>ABCDABCDABCDABCD000004EE</string>
+ <string>ABCDABCDABCDABCD000004F0</string>
+ <string>ABCDABCDABCDABCD000004F2</string>
+ <string>ABCDABCDABCDABCD000004F4</string>
+ <string>ABCDABCDABCDABCD000004F6</string>
+ <string>ABCDABCDABCDABCD000004F8</string>
+ <string>ABCDABCDABCDABCD000004FA</string>
+ <string>ABCDABCDABCDABCD000004FC</string>
+ <string>ABCDABCDABCDABCD000004FE</string>
+ <string>ABCDABCDABCDABCD00000500</string>
+ <string>ABCDABCDABCDABCD00000502</string>
+ <string>ABCDABCDABCDABCD00000504</string>
+ <string>ABCDABCDABCDABCD00000506</string>
+ <string>ABCDABCDABCDABCD00000508</string>
+ <string>ABCDABCDABCDABCD0000050A</string>
+ <string>ABCDABCDABCDABCD0000050C</string>
+ <string>ABCDABCDABCDABCD0000050E</string>
+ <string>ABCDABCDABCDABCD00000510</string>
+ <string>ABCDABCDABCDABCD00000512</string>
+ <string>ABCDABCDABCDABCD00000514</string>
+ <string>ABCDABCDABCDABCD00000516</string>
+ <string>ABCDABCDABCDABCD00000518</string>
+ <string>ABCDABCDABCDABCD0000051A</string>
+ <string>ABCDABCDABCDABCD0000051C</string>
+ <string>ABCDABCDABCDABCD0000051E</string>
+ <string>ABCDABCDABCDABCD00000520</string>
+ <string>ABCDABCDABCDABCD00000522</string>
+ <string>ABCDABCDABCDABCD00000524</string>
+ <string>ABCDABCDABCDABCD00000526</string>
+ <string>ABCDABCDABCDABCD00000528</string>
+ <string>ABCDABCDABCDABCD0000052A</string>
+ <string>ABCDABCDABCDABCD0000052C</string>
+ <string>ABCDABCDABCDABCD0000052E</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -10816,80 +17513,86 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000300</key>
+ <key>ABCDABCDABCDABCD000004E1</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000347</string>
- <string>ABCDABCDABCDABCD00000348</string>
- <string>ABCDABCDABCDABCD00000349</string>
- <string>ABCDABCDABCDABCD0000034A</string>
- <string>ABCDABCDABCDABCD0000034B</string>
- <string>ABCDABCDABCDABCD0000034C</string>
- <string>ABCDABCDABCDABCD0000034D</string>
- <string>ABCDABCDABCDABCD0000034E</string>
- <string>ABCDABCDABCDABCD0000034F</string>
- <string>ABCDABCDABCDABCD00000350</string>
- <string>ABCDABCDABCDABCD00000351</string>
- <string>ABCDABCDABCDABCD00000352</string>
- <string>ABCDABCDABCDABCD00000353</string>
- <string>ABCDABCDABCDABCD00000354</string>
- <string>ABCDABCDABCDABCD00000355</string>
- <string>ABCDABCDABCDABCD00000356</string>
- <string>ABCDABCDABCDABCD00000357</string>
- <string>ABCDABCDABCDABCD00000358</string>
- <string>ABCDABCDABCDABCD00000359</string>
- <string>ABCDABCDABCDABCD0000035A</string>
- <string>ABCDABCDABCDABCD0000035B</string>
- <string>ABCDABCDABCDABCD0000035C</string>
- <string>ABCDABCDABCDABCD0000035D</string>
- <string>ABCDABCDABCDABCD0000035E</string>
- <string>ABCDABCDABCDABCD0000035F</string>
- <string>ABCDABCDABCDABCD00000360</string>
- <string>ABCDABCDABCDABCD00000361</string>
- <string>ABCDABCDABCDABCD00000362</string>
- <string>ABCDABCDABCDABCD00000363</string>
- <string>ABCDABCDABCDABCD00000364</string>
- <string>ABCDABCDABCDABCD00000365</string>
- <string>ABCDABCDABCDABCD00000366</string>
- <string>ABCDABCDABCDABCD00000367</string>
- <string>ABCDABCDABCDABCD00000368</string>
- <string>ABCDABCDABCDABCD00000369</string>
- <string>ABCDABCDABCDABCD0000036A</string>
- <string>ABCDABCDABCDABCD0000036B</string>
- <string>ABCDABCDABCDABCD0000036C</string>
- <string>ABCDABCDABCDABCD0000036D</string>
- <string>ABCDABCDABCDABCD0000036E</string>
- <string>ABCDABCDABCDABCD0000036F</string>
- <string>ABCDABCDABCDABCD00000370</string>
- <string>ABCDABCDABCDABCD00000371</string>
- <string>ABCDABCDABCDABCD00000372</string>
- <string>ABCDABCDABCDABCD00000373</string>
- <string>ABCDABCDABCDABCD00000374</string>
- <string>ABCDABCDABCDABCD00000375</string>
- <string>ABCDABCDABCDABCD00000376</string>
- <string>ABCDABCDABCDABCD00000377</string>
- <string>ABCDABCDABCDABCD00000378</string>
- <string>ABCDABCDABCDABCD00000379</string>
- <string>ABCDABCDABCDABCD0000037A</string>
- <string>ABCDABCDABCDABCD0000037B</string>
- <string>ABCDABCDABCDABCD0000037C</string>
- <string>ABCDABCDABCDABCD0000037D</string>
- <string>ABCDABCDABCDABCD0000037E</string>
- <string>ABCDABCDABCDABCD0000037F</string>
- <string>ABCDABCDABCDABCD00000380</string>
- <string>ABCDABCDABCDABCD00000381</string>
- <string>ABCDABCDABCDABCD00000382</string>
- <string>ABCDABCDABCDABCD00000383</string>
- <string>ABCDABCDABCDABCD00000384</string>
- <string>ABCDABCDABCDABCD00000385</string>
- <string>ABCDABCDABCDABCD00000386</string>
- <string>ABCDABCDABCDABCD00000387</string>
- <string>ABCDABCDABCDABCD00000388</string>
- <string>ABCDABCDABCDABCD00000389</string>
- <string>ABCDABCDABCDABCD0000038A</string>
- <string>ABCDABCDABCDABCD0000038B</string>
- <string>ABCDABCDABCDABCD0000038C</string>
+ <string>ABCDABCDABCDABCD00000530</string>
+ <string>ABCDABCDABCDABCD00000531</string>
+ <string>ABCDABCDABCDABCD00000532</string>
+ <string>ABCDABCDABCDABCD00000533</string>
+ <string>ABCDABCDABCDABCD00000534</string>
+ <string>ABCDABCDABCDABCD00000535</string>
+ <string>ABCDABCDABCDABCD00000536</string>
+ <string>ABCDABCDABCDABCD00000537</string>
+ <string>ABCDABCDABCDABCD00000538</string>
+ <string>ABCDABCDABCDABCD00000539</string>
+ <string>ABCDABCDABCDABCD0000053A</string>
+ <string>ABCDABCDABCDABCD0000053B</string>
+ <string>ABCDABCDABCDABCD0000053C</string>
+ <string>ABCDABCDABCDABCD0000053D</string>
+ <string>ABCDABCDABCDABCD0000053E</string>
+ <string>ABCDABCDABCDABCD0000053F</string>
+ <string>ABCDABCDABCDABCD00000540</string>
+ <string>ABCDABCDABCDABCD00000541</string>
+ <string>ABCDABCDABCDABCD00000542</string>
+ <string>ABCDABCDABCDABCD00000543</string>
+ <string>ABCDABCDABCDABCD00000544</string>
+ <string>ABCDABCDABCDABCD00000545</string>
+ <string>ABCDABCDABCDABCD00000546</string>
+ <string>ABCDABCDABCDABCD00000547</string>
+ <string>ABCDABCDABCDABCD00000548</string>
+ <string>ABCDABCDABCDABCD00000549</string>
+ <string>ABCDABCDABCDABCD0000054A</string>
+ <string>ABCDABCDABCDABCD0000054B</string>
+ <string>ABCDABCDABCDABCD0000054C</string>
+ <string>ABCDABCDABCDABCD0000054D</string>
+ <string>ABCDABCDABCDABCD0000054E</string>
+ <string>ABCDABCDABCDABCD0000054F</string>
+ <string>ABCDABCDABCDABCD00000550</string>
+ <string>ABCDABCDABCDABCD00000551</string>
+ <string>ABCDABCDABCDABCD00000552</string>
+ <string>ABCDABCDABCDABCD00000553</string>
+ <string>ABCDABCDABCDABCD00000554</string>
+ <string>ABCDABCDABCDABCD00000555</string>
+ <string>ABCDABCDABCDABCD00000556</string>
+ <string>ABCDABCDABCDABCD00000557</string>
+ <string>ABCDABCDABCDABCD00000558</string>
+ <string>ABCDABCDABCDABCD00000559</string>
+ <string>ABCDABCDABCDABCD0000055A</string>
+ <string>ABCDABCDABCDABCD0000055B</string>
+ <string>ABCDABCDABCDABCD0000055C</string>
+ <string>ABCDABCDABCDABCD0000055D</string>
+ <string>ABCDABCDABCDABCD0000055E</string>
+ <string>ABCDABCDABCDABCD0000055F</string>
+ <string>ABCDABCDABCDABCD00000560</string>
+ <string>ABCDABCDABCDABCD00000561</string>
+ <string>ABCDABCDABCDABCD00000562</string>
+ <string>ABCDABCDABCDABCD00000563</string>
+ <string>ABCDABCDABCDABCD00000564</string>
+ <string>ABCDABCDABCDABCD00000565</string>
+ <string>ABCDABCDABCDABCD00000566</string>
+ <string>ABCDABCDABCDABCD00000567</string>
+ <string>ABCDABCDABCDABCD00000568</string>
+ <string>ABCDABCDABCDABCD00000569</string>
+ <string>ABCDABCDABCDABCD0000056A</string>
+ <string>ABCDABCDABCDABCD0000056B</string>
+ <string>ABCDABCDABCDABCD0000056C</string>
+ <string>ABCDABCDABCDABCD0000056D</string>
+ <string>ABCDABCDABCDABCD0000056E</string>
+ <string>ABCDABCDABCDABCD0000056F</string>
+ <string>ABCDABCDABCDABCD00000570</string>
+ <string>ABCDABCDABCDABCD00000571</string>
+ <string>ABCDABCDABCDABCD00000572</string>
+ <string>ABCDABCDABCDABCD00000573</string>
+ <string>ABCDABCDABCDABCD00000574</string>
+ <string>ABCDABCDABCDABCD00000575</string>
+ <string>ABCDABCDABCDABCD00000576</string>
+ <string>ABCDABCDABCDABCD00000577</string>
+ <string>ABCDABCDABCDABCD00000578</string>
+ <string>ABCDABCDABCDABCD00000579</string>
+ <string>ABCDABCDABCDABCD0000057A</string>
+ <string>ABCDABCDABCDABCD0000057B</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -10898,12 +17601,12 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000302</key>
+ <key>ABCDABCDABCDABCD000004E3</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD000002FF</string>
- <string>ABCDABCDABCDABCD00000300</string>
+ <string>ABCDABCDABCDABCD000004E0</string>
+ <string>ABCDABCDABCDABCD000004E1</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -10912,7 +17615,7 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000303</key>
+ <key>ABCDABCDABCDABCD000004E4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10925,14 +17628,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000304</key>
+ <key>ABCDABCDABCDABCD000004E5</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000303</string>
+ <string>ABCDABCDABCDABCD000004E4</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000305</key>
+ <key>ABCDABCDABCDABCD000004E6</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10945,14 +17648,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000306</key>
+ <key>ABCDABCDABCDABCD000004E7</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000305</string>
+ <string>ABCDABCDABCDABCD000004E6</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000307</key>
+ <key>ABCDABCDABCDABCD000004E8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10965,14 +17668,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000308</key>
+ <key>ABCDABCDABCDABCD000004E9</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000307</string>
+ <string>ABCDABCDABCDABCD000004E8</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000309</key>
+ <key>ABCDABCDABCDABCD000004EA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -10985,14 +17688,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000030A</key>
+ <key>ABCDABCDABCDABCD000004EB</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000309</string>
+ <string>ABCDABCDABCDABCD000004EA</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000030B</key>
+ <key>ABCDABCDABCDABCD000004EC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11005,14 +17708,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000030C</key>
+ <key>ABCDABCDABCDABCD000004ED</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000030B</string>
+ <string>ABCDABCDABCDABCD000004EC</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000030D</key>
+ <key>ABCDABCDABCDABCD000004EE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11025,14 +17728,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000030E</key>
+ <key>ABCDABCDABCDABCD000004EF</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000030D</string>
+ <string>ABCDABCDABCDABCD000004EE</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000030F</key>
+ <key>ABCDABCDABCDABCD000004F0</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11045,14 +17748,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000310</key>
+ <key>ABCDABCDABCDABCD000004F1</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000030F</string>
+ <string>ABCDABCDABCDABCD000004F0</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000311</key>
+ <key>ABCDABCDABCDABCD000004F2</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11065,14 +17768,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000312</key>
+ <key>ABCDABCDABCDABCD000004F3</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000311</string>
+ <string>ABCDABCDABCDABCD000004F2</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000313</key>
+ <key>ABCDABCDABCDABCD000004F4</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11085,14 +17788,34 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000314</key>
+ <key>ABCDABCDABCDABCD000004F5</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000313</string>
+ <string>ABCDABCDABCDABCD000004F4</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000315</key>
+ <key>ABCDABCDABCDABCD000004F6</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.cpp</string>
+ <key>name</key>
+ <string>histogram_binning.cpp</string>
+ <key>path</key>
+ <string>../../../../src/util/histogram_binning.cpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000004F7</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD000004F6</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD000004F8</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11105,14 +17828,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000316</key>
+ <key>ABCDABCDABCDABCD000004F9</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000315</string>
+ <string>ABCDABCDABCDABCD000004F8</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000317</key>
+ <key>ABCDABCDABCDABCD000004FA</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11125,14 +17848,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000318</key>
+ <key>ABCDABCDABCDABCD000004FB</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000317</string>
+ <string>ABCDABCDABCDABCD000004FA</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000319</key>
+ <key>ABCDABCDABCDABCD000004FC</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11145,14 +17868,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000031A</key>
+ <key>ABCDABCDABCDABCD000004FD</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000319</string>
+ <string>ABCDABCDABCDABCD000004FC</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000031B</key>
+ <key>ABCDABCDABCDABCD000004FE</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11165,14 +17888,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000031C</key>
+ <key>ABCDABCDABCDABCD000004FF</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000031B</string>
+ <string>ABCDABCDABCDABCD000004FE</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000031D</key>
+ <key>ABCDABCDABCDABCD00000500</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11185,14 +17908,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000031E</key>
+ <key>ABCDABCDABCDABCD00000501</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000031D</string>
+ <string>ABCDABCDABCDABCD00000500</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000031F</key>
+ <key>ABCDABCDABCDABCD00000502</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11205,14 +17928,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000320</key>
+ <key>ABCDABCDABCDABCD00000503</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000031F</string>
+ <string>ABCDABCDABCDABCD00000502</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000321</key>
+ <key>ABCDABCDABCDABCD00000504</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11225,14 +17948,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000322</key>
+ <key>ABCDABCDABCDABCD00000505</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000321</string>
+ <string>ABCDABCDABCDABCD00000504</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000323</key>
+ <key>ABCDABCDABCDABCD00000506</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11245,14 +17968,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000324</key>
+ <key>ABCDABCDABCDABCD00000507</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000323</string>
+ <string>ABCDABCDABCDABCD00000506</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000325</key>
+ <key>ABCDABCDABCDABCD00000508</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11265,14 +17988,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000326</key>
+ <key>ABCDABCDABCDABCD00000509</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000325</string>
+ <string>ABCDABCDABCDABCD00000508</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000327</key>
+ <key>ABCDABCDABCDABCD0000050A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11285,14 +18008,34 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000328</key>
+ <key>ABCDABCDABCDABCD0000050B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000327</string>
+ <string>ABCDABCDABCDABCD0000050A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000329</key>
+ <key>ABCDABCDABCDABCD0000050C</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.cpp</string>
+ <key>name</key>
+ <string>rangelist.cpp</string>
+ <key>path</key>
+ <string>../../../../src/util/rangelist.cpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000050D</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD0000050C</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000050E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11305,14 +18048,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000032A</key>
+ <key>ABCDABCDABCDABCD0000050F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000329</string>
+ <string>ABCDABCDABCDABCD0000050E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000032B</key>
+ <key>ABCDABCDABCDABCD00000510</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11325,14 +18068,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000032C</key>
+ <key>ABCDABCDABCDABCD00000511</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000032B</string>
+ <string>ABCDABCDABCDABCD00000510</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000032D</key>
+ <key>ABCDABCDABCDABCD00000512</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11345,54 +18088,94 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000032E</key>
+ <key>ABCDABCDABCDABCD00000513</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000032D</string>
+ <string>ABCDABCDABCDABCD00000512</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000032F</key>
+ <key>ABCDABCDABCDABCD00000514</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.cpp</string>
+ <key>name</key>
+ <string>static_set.cpp</string>
+ <key>path</key>
+ <string>../../../../src/util/static_set.cpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000515</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000514</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000516</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.cpp</string>
+ <key>name</key>
+ <string>strbuffer.cpp</string>
+ <key>path</key>
+ <string>../../../../src/util/strbuffer.cpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000517</key>
+ <dict>
+ <key>fileRef</key>
+ <string>ABCDABCDABCDABCD00000516</string>
+ <key>isa</key>
+ <string>PBXBuildFile</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000518</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>strbuffer.cpp</string>
+ <string>strsearch.cpp</string>
<key>path</key>
- <string>../../../../src/util/strbuffer.cpp</string>
+ <string>../../../../src/util/strsearch.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000330</key>
+ <key>ABCDABCDABCDABCD00000519</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000032F</string>
+ <string>ABCDABCDABCDABCD00000518</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000331</key>
+ <key>ABCDABCDABCDABCD0000051A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.cpp</string>
<key>name</key>
- <string>strsearch.cpp</string>
+ <string>table_printer.cpp</string>
<key>path</key>
- <string>../../../../src/util/strsearch.cpp</string>
+ <string>../../../../src/util/table_printer.cpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000332</key>
+ <key>ABCDABCDABCDABCD0000051B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000331</string>
+ <string>ABCDABCDABCDABCD0000051A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000333</key>
+ <key>ABCDABCDABCDABCD0000051C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11405,14 +18188,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000334</key>
+ <key>ABCDABCDABCDABCD0000051D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000333</string>
+ <string>ABCDABCDABCDABCD0000051C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000335</key>
+ <key>ABCDABCDABCDABCD0000051E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11425,14 +18208,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000336</key>
+ <key>ABCDABCDABCDABCD0000051F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000335</string>
+ <string>ABCDABCDABCDABCD0000051E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000337</key>
+ <key>ABCDABCDABCDABCD00000520</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11445,14 +18228,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000338</key>
+ <key>ABCDABCDABCDABCD00000521</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000337</string>
+ <string>ABCDABCDABCDABCD00000520</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000339</key>
+ <key>ABCDABCDABCDABCD00000522</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11465,14 +18248,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000033A</key>
+ <key>ABCDABCDABCDABCD00000523</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000339</string>
+ <string>ABCDABCDABCDABCD00000522</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000033B</key>
+ <key>ABCDABCDABCDABCD00000524</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11485,14 +18268,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000033C</key>
+ <key>ABCDABCDABCDABCD00000525</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000033B</string>
+ <string>ABCDABCDABCDABCD00000524</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000033D</key>
+ <key>ABCDABCDABCDABCD00000526</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11505,14 +18288,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000033E</key>
+ <key>ABCDABCDABCDABCD00000527</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000033D</string>
+ <string>ABCDABCDABCDABCD00000526</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD0000033F</key>
+ <key>ABCDABCDABCDABCD00000528</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11525,14 +18308,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000340</key>
+ <key>ABCDABCDABCDABCD00000529</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD0000033F</string>
+ <string>ABCDABCDABCDABCD00000528</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000341</key>
+ <key>ABCDABCDABCDABCD0000052A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11545,14 +18328,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000342</key>
+ <key>ABCDABCDABCDABCD0000052B</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000341</string>
+ <string>ABCDABCDABCDABCD0000052A</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000343</key>
+ <key>ABCDABCDABCDABCD0000052C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11565,14 +18348,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000344</key>
+ <key>ABCDABCDABCDABCD0000052D</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000343</string>
+ <string>ABCDABCDABCDABCD0000052C</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000345</key>
+ <key>ABCDABCDABCDABCD0000052E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11585,14 +18368,14 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000346</key>
+ <key>ABCDABCDABCDABCD0000052F</key>
<dict>
<key>fileRef</key>
- <string>ABCDABCDABCDABCD00000345</string>
+ <string>ABCDABCDABCDABCD0000052E</string>
<key>isa</key>
<string>PBXBuildFile</string>
</dict>
- <key>ABCDABCDABCDABCD00000347</key>
+ <key>ABCDABCDABCDABCD00000530</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11605,7 +18388,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000348</key>
+ <key>ABCDABCDABCDABCD00000531</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11618,7 +18401,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000349</key>
+ <key>ABCDABCDABCDABCD00000532</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11631,7 +18414,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034A</key>
+ <key>ABCDABCDABCDABCD00000533</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11644,7 +18427,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034B</key>
+ <key>ABCDABCDABCDABCD00000534</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11657,46 +18440,46 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034C</key>
+ <key>ABCDABCDABCDABCD00000535</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>bytesrc.hpp</string>
+ <string>buffer_writer.hpp</string>
<key>path</key>
- <string>../../../../include/util/bytesrc.hpp</string>
+ <string>../../../../include/util/buffer_writer.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034D</key>
+ <key>ABCDABCDABCDABCD00000536</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>checksum.hpp</string>
+ <string>bytesrc.hpp</string>
<key>path</key>
- <string>../../../../include/util/checksum.hpp</string>
+ <string>../../../../include/util/bytesrc.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034E</key>
+ <key>ABCDABCDABCDABCD00000537</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
<key>lastKnownFileType</key>
<string>sourcecode.cpp.h</string>
<key>name</key>
- <string>checksum.inl</string>
+ <string>checksum.hpp</string>
<key>path</key>
- <string>../../../../include/util/checksum.inl</string>
+ <string>../../../../include/util/checksum.hpp</string>
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000034F</key>
+ <key>ABCDABCDABCDABCD00000538</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11709,7 +18492,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000350</key>
+ <key>ABCDABCDABCDABCD00000539</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11722,7 +18505,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000351</key>
+ <key>ABCDABCDABCDABCD0000053A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11735,7 +18518,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000352</key>
+ <key>ABCDABCDABCDABCD0000053B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11748,7 +18531,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000353</key>
+ <key>ABCDABCDABCDABCD0000053C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11761,7 +18544,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000354</key>
+ <key>ABCDABCDABCDABCD0000053D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11774,7 +18557,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000355</key>
+ <key>ABCDABCDABCDABCD0000053E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11787,7 +18570,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000356</key>
+ <key>ABCDABCDABCDABCD0000053F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11800,7 +18583,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000357</key>
+ <key>ABCDABCDABCDABCD00000540</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11813,7 +18596,33 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000358</key>
+ <key>ABCDABCDABCDABCD00000541</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>histogram_binning.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/histogram_binning.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000542</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>icanceled.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/icanceled.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000543</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11826,7 +18635,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000359</key>
+ <key>ABCDABCDABCDABCD00000544</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11839,7 +18648,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035A</key>
+ <key>ABCDABCDABCDABCD00000545</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11852,7 +18661,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035B</key>
+ <key>ABCDABCDABCDABCD00000546</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11865,7 +18674,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035C</key>
+ <key>ABCDABCDABCDABCD00000547</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11878,7 +18687,20 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035D</key>
+ <key>ABCDABCDABCDABCD00000548</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>limited_size_map.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/limited_size_map.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000549</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11891,7 +18713,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035E</key>
+ <key>ABCDABCDABCDABCD0000054A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11904,7 +18726,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000035F</key>
+ <key>ABCDABCDABCDABCD0000054B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11917,7 +18739,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000360</key>
+ <key>ABCDABCDABCDABCD0000054C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11930,7 +18752,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000361</key>
+ <key>ABCDABCDABCDABCD0000054D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11943,7 +18765,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000362</key>
+ <key>ABCDABCDABCDABCD0000054E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11956,7 +18778,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000363</key>
+ <key>ABCDABCDABCDABCD0000054F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11969,7 +18791,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000364</key>
+ <key>ABCDABCDABCDABCD00000550</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11982,7 +18804,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000365</key>
+ <key>ABCDABCDABCDABCD00000551</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -11995,7 +18817,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000366</key>
+ <key>ABCDABCDABCDABCD00000552</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12008,7 +18830,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000367</key>
+ <key>ABCDABCDABCDABCD00000553</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12021,7 +18843,20 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000368</key>
+ <key>ABCDABCDABCDABCD00000554</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>ncbi_url.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/ncbi_url.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000555</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12034,7 +18869,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000369</key>
+ <key>ABCDABCDABCDABCD00000556</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12047,7 +18882,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036A</key>
+ <key>ABCDABCDABCDABCD00000557</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12060,7 +18895,20 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036B</key>
+ <key>ABCDABCDABCDABCD00000558</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>rangelist.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/rangelist.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000559</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12073,7 +18921,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036C</key>
+ <key>ABCDABCDABCDABCD0000055A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12086,7 +18934,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036D</key>
+ <key>ABCDABCDABCDABCD0000055B</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12099,7 +18947,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036E</key>
+ <key>ABCDABCDABCDABCD0000055C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12112,7 +18960,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000036F</key>
+ <key>ABCDABCDABCDABCD0000055D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12125,7 +18973,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000370</key>
+ <key>ABCDABCDABCDABCD0000055E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12138,7 +18986,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000371</key>
+ <key>ABCDABCDABCDABCD0000055F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12151,20 +18999,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000372</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
- <key>name</key>
- <string>rwstream.hpp</string>
- <key>path</key>
- <string>../../../../include/util/rwstream.hpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD00000373</key>
+ <key>ABCDABCDABCDABCD00000560</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12177,7 +19012,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000374</key>
+ <key>ABCDABCDABCDABCD00000561</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12190,7 +19025,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000375</key>
+ <key>ABCDABCDABCDABCD00000562</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12203,7 +19038,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000376</key>
+ <key>ABCDABCDABCDABCD00000563</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12216,7 +19051,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000377</key>
+ <key>ABCDABCDABCDABCD00000564</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12229,7 +19064,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000378</key>
+ <key>ABCDABCDABCDABCD00000565</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12242,7 +19077,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000379</key>
+ <key>ABCDABCDABCDABCD00000566</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12255,7 +19090,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037A</key>
+ <key>ABCDABCDABCDABCD00000567</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12268,7 +19103,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037B</key>
+ <key>ABCDABCDABCDABCD00000568</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12281,7 +19116,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037C</key>
+ <key>ABCDABCDABCDABCD00000569</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12294,7 +19129,33 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037D</key>
+ <key>ABCDABCDABCDABCD0000056A</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>table_printer.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/table_printer.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000056B</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>text_joiner.hpp</string>
+ <key>path</key>
+ <string>../../../../include/util/text_joiner.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000056C</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12307,7 +19168,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037E</key>
+ <key>ABCDABCDABCDABCD0000056D</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12320,7 +19181,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000037F</key>
+ <key>ABCDABCDABCDABCD0000056E</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12333,7 +19194,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000380</key>
+ <key>ABCDABCDABCDABCD0000056F</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12346,7 +19207,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000381</key>
+ <key>ABCDABCDABCDABCD00000570</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12359,7 +19220,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000382</key>
+ <key>ABCDABCDABCDABCD00000571</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12372,7 +19233,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000383</key>
+ <key>ABCDABCDABCDABCD00000572</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12385,7 +19246,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000384</key>
+ <key>ABCDABCDABCDABCD00000573</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12398,7 +19259,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000385</key>
+ <key>ABCDABCDABCDABCD00000574</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12411,7 +19272,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000386</key>
+ <key>ABCDABCDABCDABCD00000575</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12424,7 +19285,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000387</key>
+ <key>ABCDABCDABCDABCD00000576</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12437,7 +19298,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000388</key>
+ <key>ABCDABCDABCDABCD00000577</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12450,7 +19311,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD00000389</key>
+ <key>ABCDABCDABCDABCD00000578</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12463,7 +19324,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000038A</key>
+ <key>ABCDABCDABCDABCD00000579</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12476,7 +19337,7 @@
<key>sourceTree</key>
<string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000038B</key>
+ <key>ABCDABCDABCDABCD0000057A</key>
<dict>
<key>isa</key>
<string>PBXFileReference</string>
@@ -12485,85 +19346,76 @@
<key>name</key>
<string>weakmap.hpp</string>
<key>path</key>
- <string>../../../../include/util/weakmap.hpp</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000038C</key>
- <dict>
- <key>isa</key>
- <string>PBXFileReference</string>
- <key>lastKnownFileType</key>
- <string>sourcecode.cpp.h</string>
- <key>name</key>
- <string>weakmap.inl</string>
- <key>path</key>
- <string>../../../../include/util/weakmap.inl</string>
- <key>sourceTree</key>
- <string>SOURCE_ROOT</string>
- </dict>
- <key>ABCDABCDABCDABCD0000038D</key>
- <dict>
- <key>files</key>
- <array>
- <string>ABCDABCDABCDABCD00000304</string>
- <string>ABCDABCDABCDABCD00000306</string>
- <string>ABCDABCDABCDABCD00000308</string>
- <string>ABCDABCDABCDABCD0000030A</string>
- <string>ABCDABCDABCDABCD0000030C</string>
- <string>ABCDABCDABCDABCD0000030E</string>
- <string>ABCDABCDABCDABCD00000310</string>
- <string>ABCDABCDABCDABCD00000312</string>
- <string>ABCDABCDABCDABCD00000314</string>
- <string>ABCDABCDABCDABCD00000316</string>
- <string>ABCDABCDABCDABCD00000318</string>
- <string>ABCDABCDABCDABCD0000031A</string>
- <string>ABCDABCDABCDABCD0000031C</string>
- <string>ABCDABCDABCDABCD0000031E</string>
- <string>ABCDABCDABCDABCD00000320</string>
- <string>ABCDABCDABCDABCD00000322</string>
- <string>ABCDABCDABCDABCD00000324</string>
- <string>ABCDABCDABCDABCD00000326</string>
- <string>ABCDABCDABCDABCD00000328</string>
- <string>ABCDABCDABCDABCD0000032A</string>
- <string>ABCDABCDABCDABCD0000032C</string>
- <string>ABCDABCDABCDABCD0000032E</string>
- <string>ABCDABCDABCDABCD00000330</string>
- <string>ABCDABCDABCDABCD00000332</string>
- <string>ABCDABCDABCDABCD00000334</string>
- <string>ABCDABCDABCDABCD00000336</string>
- <string>ABCDABCDABCDABCD00000338</string>
- <string>ABCDABCDABCDABCD0000033A</string>
- <string>ABCDABCDABCDABCD0000033C</string>
- <string>ABCDABCDABCDABCD0000033E</string>
- <string>ABCDABCDABCDABCD00000340</string>
- <string>ABCDABCDABCDABCD00000342</string>
- <string>ABCDABCDABCDABCD00000344</string>
- <string>ABCDABCDABCDABCD00000346</string>
- </array>
- <key>isa</key>
- <string>PBXSourcesBuildPhase</string>
+ <string>../../../../include/util/weakmap.hpp</string>
+ <key>sourceTree</key>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000038E</key>
+ <key>ABCDABCDABCDABCD0000057B</key>
<dict>
- <key>explicitFileType</key>
- <string>archive.ar</string>
- <key>includeInIndex</key>
- <string>0</string>
<key>isa</key>
<string>PBXFileReference</string>
+ <key>lastKnownFileType</key>
+ <string>sourcecode.cpp.h</string>
+ <key>name</key>
+ <string>weakmap.inl</string>
<key>path</key>
- <string>libxutil.a</string>
+ <string>../../../../include/util/weakmap.inl</string>
<key>sourceTree</key>
- <string>BUILT_PRODUCTS_DIR</string>
+ <string>SOURCE_ROOT</string>
</dict>
- <key>ABCDABCDABCDABCD0000038F</key>
+ <key>ABCDABCDABCDABCD0000057C</key>
+ <dict>
+ <key>files</key>
+ <array>
+ <string>ABCDABCDABCDABCD000004E5</string>
+ <string>ABCDABCDABCDABCD000004E7</string>
+ <string>ABCDABCDABCDABCD000004E9</string>
+ <string>ABCDABCDABCDABCD000004EB</string>
+ <string>ABCDABCDABCDABCD000004ED</string>
+ <string>ABCDABCDABCDABCD000004EF</string>
+ <string>ABCDABCDABCDABCD000004F1</string>
+ <string>ABCDABCDABCDABCD000004F3</string>
+ <string>ABCDABCDABCDABCD000004F5</string>
+ <string>ABCDABCDABCDABCD000004F7</string>
+ <string>ABCDABCDABCDABCD000004F9</string>
+ <string>ABCDABCDABCDABCD000004FB</string>
+ <string>ABCDABCDABCDABCD000004FD</string>
+ <string>ABCDABCDABCDABCD000004FF</string>
+ <string>ABCDABCDABCDABCD00000501</string>
+ <string>ABCDABCDABCDABCD00000503</string>
+ <string>ABCDABCDABCDABCD00000505</string>
+ <string>ABCDABCDABCDABCD00000507</string>
+ <string>ABCDABCDABCDABCD00000509</string>
+ <string>ABCDABCDABCDABCD0000050B</string>
+ <string>ABCDABCDABCDABCD0000050D</string>
+ <string>ABCDABCDABCDABCD0000050F</string>
+ <string>ABCDABCDABCDABCD00000511</string>
+ <string>ABCDABCDABCDABCD00000513</string>
+ <string>ABCDABCDABCDABCD00000515</string>
+ <string>ABCDABCDABCDABCD00000517</string>
+ <string>ABCDABCDABCDABCD00000519</string>
+ <string>ABCDABCDABCDABCD0000051B</string>
+ <string>ABCDABCDABCDABCD0000051D</string>
+ <string>ABCDABCDABCDABCD0000051F</string>
+ <string>ABCDABCDABCDABCD00000521</string>
+ <string>ABCDABCDABCDABCD00000523</string>
+ <string>ABCDABCDABCDABCD00000525</string>
+ <string>ABCDABCDABCDABCD00000527</string>
+ <string>ABCDABCDABCDABCD00000529</string>
+ <string>ABCDABCDABCDABCD0000052B</string>
+ <string>ABCDABCDABCDABCD0000052D</string>
+ <string>ABCDABCDABCDABCD0000052F</string>
+ </array>
+ <key>isa</key>
+ <string>PBXSourcesBuildPhase</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000057D</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD00000390</string>
+ <string>ABCDABCDABCDABCD0000057E</string>
<key>buildPhases</key>
<array>
- <string>ABCDABCDABCDABCD0000038D</string>
+ <string>ABCDABCDABCDABCD0000057C</string>
</array>
<key>dependencies</key>
<array></array>
@@ -12574,18 +19426,18 @@
<key>productName</key>
<string>xutil</string>
<key>productReference</key>
- <string>ABCDABCDABCDABCD0000038E</string>
+ <string>ABCDABCDABCDABCD00000020</string>
<key>productType</key>
<string>com.apple.product-type.library.static</string>
</dict>
- <key>ABCDABCDABCDABCD00000390</key>
+ <key>ABCDABCDABCDABCD0000057E</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD00000391</string>
- <string>ABCDABCDABCDABCD00000392</string>
- <string>ABCDABCDABCDABCD00000393</string>
- <string>ABCDABCDABCDABCD00000394</string>
+ <string>ABCDABCDABCDABCD0000057F</string>
+ <string>ABCDABCDABCDABCD00000580</string>
+ <string>ABCDABCDABCDABCD00000581</string>
+ <string>ABCDABCDABCDABCD00000582</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -12594,7 +19446,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD00000391</key>
+ <key>ABCDABCDABCDABCD0000057F</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12603,26 +19455,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xutil</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xutil</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -12639,7 +19490,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000392</key>
+ <key>ABCDABCDABCDABCD00000580</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12648,26 +19499,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xutil</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xutil</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -12684,7 +19534,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000393</key>
+ <key>ABCDABCDABCDABCD00000581</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12693,26 +19543,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xutil</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xutil</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -12729,7 +19578,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD00000394</key>
+ <key>ABCDABCDABCDABCD00000582</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12738,26 +19587,25 @@
<key>GCC_INLINES_ARE_PRIVATE_EXTERN</key>
<string>NO</string>
<key>GCC_SYMBOLS_PRIVATE_EXTERN</key>
- <string>YES</string>
+ <string>NO</string>
<key>CONFIGURATION_BUILD_DIR</key>
- <string>../lib/$(CONFIGURATION)</string>
+ <string>lib/$(CONFIGURATION)</string>
<key>CONFIGURATION_TEMP_DIR</key>
<string>$(OBJROOT)/$(CONFIGURATION)</string>
<key>INSTALL_PATH</key>
- <string>$(PROJECT_DIR)/../lib/$(CONFIGURATION)</string>
+ <string>$(PROJECT_DIR)/lib/$(CONFIGURATION)</string>
<key>OBJROOT</key>
- <string>../build</string>
+ <string>build</string>
<key>MACH_O_TYPE</key>
<string>staticlib</string>
+ <key>PRODUCT_NAME</key>
+ <string>xutil</string>
<key>HEADER_SEARCH_PATHS</key>
<array>
- <string>../inc/$(CONFIGURATION)</string>
+ <string>inc/$(CONFIGURATION)</string>
<string>../../../../include</string>
<string>../../../../include/internal</string>
- <string>/sw/include</string>
</array>
- <key>PRODUCT_NAME</key>
- <string>xutil</string>
<key>GCC_PREPROCESSOR_DEFINITIONS</key>
<array>
<string>NCBI_XCODE_BUILD</string>
@@ -12774,17 +19622,23 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD00000395</key>
+ <key>ABCDABCDABCDABCD00000583</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000012</string>
- <string>ABCDABCDABCDABCD0000009F</string>
- <string>ABCDABCDABCDABCD00000125</string>
- <string>ABCDABCDABCDABCD00000167</string>
- <string>ABCDABCDABCDABCD00000229</string>
- <string>ABCDABCDABCDABCD0000023F</string>
- <string>ABCDABCDABCDABCD00000302</string>
+ <string>ABCDABCDABCDABCD00000025</string>
+ <string>ABCDABCDABCDABCD00000033</string>
+ <string>ABCDABCDABCDABCD000000D3</string>
+ <string>ABCDABCDABCDABCD0000015F</string>
+ <string>ABCDABCDABCDABCD000001A0</string>
+ <string>ABCDABCDABCDABCD00000217</string>
+ <string>ABCDABCDABCDABCD0000028C</string>
+ <string>ABCDABCDABCDABCD000002A8</string>
+ <string>ABCDABCDABCDABCD00000314</string>
+ <string>ABCDABCDABCDABCD000003F7</string>
+ <string>ABCDABCDABCDABCD0000040D</string>
+ <string>ABCDABCDABCDABCD0000041F</string>
+ <string>ABCDABCDABCDABCD000004E3</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -12793,12 +19647,12 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000396</key>
+ <key>ABCDABCDABCDABCD00000584</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000395</string>
- <string>ABCDABCDABCDABCD00000397</string>
+ <string>ABCDABCDABCDABCD00000583</string>
+ <string>ABCDABCDABCDABCD00000585</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -12807,17 +19661,22 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000397</key>
+ <key>ABCDABCDABCDABCD00000585</key>
<dict>
<key>children</key>
<array>
- <string>ABCDABCDABCDABCD00000094</string>
- <string>ABCDABCDABCDABCD0000011A</string>
- <string>ABCDABCDABCDABCD0000015C</string>
- <string>ABCDABCDABCDABCD0000021E</string>
- <string>ABCDABCDABCDABCD00000234</string>
- <string>ABCDABCDABCDABCD000002F7</string>
- <string>ABCDABCDABCDABCD0000038E</string>
+ <string>ABCDABCDABCDABCD00000015</string>
+ <string>ABCDABCDABCDABCD00000016</string>
+ <string>ABCDABCDABCDABCD00000017</string>
+ <string>ABCDABCDABCDABCD00000018</string>
+ <string>ABCDABCDABCDABCD00000019</string>
+ <string>ABCDABCDABCDABCD0000001A</string>
+ <string>ABCDABCDABCDABCD0000001B</string>
+ <string>ABCDABCDABCDABCD0000001C</string>
+ <string>ABCDABCDABCDABCD0000001D</string>
+ <string>ABCDABCDABCDABCD0000001E</string>
+ <string>ABCDABCDABCDABCD0000001F</string>
+ <string>ABCDABCDABCDABCD00000020</string>
</array>
<key>isa</key>
<string>PBXGroup</string>
@@ -12826,16 +19685,125 @@
<key>sourceTree</key>
<string><group></string>
</dict>
- <key>ABCDABCDABCDABCD00000398</key>
+ <key>ABCDABCDABCDABCD00000586</key>
<dict>
+ <key>buildArgumentsString</key>
+ <string>$(PROJECT_DIR)/../precfg.sh</string>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD0000039A</string>
+ <string>ABCDABCDABCDABCD00000587</string>
<key>buildPhases</key>
+ <array></array>
+ <key>buildToolPath</key>
+ <string>/bin/sh</string>
+ <key>dependencies</key>
+ <array></array>
+ <key>isa</key>
+ <string>PBXLegacyTarget</string>
+ <key>name</key>
+ <string>_pre_CONFIGURE</string>
+ <key>passBuildSettingsInEnvironment</key>
+ <string>1</string>
+ <key>productName</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000587</key>
+ <dict>
+ <key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD00000399</string>
+ <string>ABCDABCDABCDABCD00000588</string>
+ <string>ABCDABCDABCDABCD00000589</string>
+ <string>ABCDABCDABCDABCD0000058A</string>
+ <string>ABCDABCDABCDABCD0000058B</string>
+ </array>
+ <key>defaultConfigurationIsVisible</key>
+ <string>0</string>
+ <key>defaultConfigurationName</key>
+ <string>ReleaseDLL</string>
+ <key>isa</key>
+ <string>XCConfigurationList</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000588</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD00000589</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>DebugMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000058A</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseDLL</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000058B</key>
+ <dict>
+ <key>buildSettings</key>
+ <dict>
+ <key>PRODUCT_NAME</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>isa</key>
+ <string>XCBuildConfiguration</string>
+ <key>name</key>
+ <string>ReleaseMT</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000058C</key>
+ <dict>
+ <key>isa</key>
+ <string>PBXTargetDependency</string>
+ <key>target</key>
+ <string>ABCDABCDABCDABCD00000586</string>
+ <key>targetProxy</key>
+ <string>ABCDABCDABCDABCD0000058D</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000058D</key>
+ <dict>
+ <key>containerPortal</key>
+ <string>ABCDABCDABCDABCD00000006</string>
+ <key>isa</key>
+ <string>PBXContainerItemProxy</string>
+ <key>proxyType</key>
+ <string>1</string>
+ <key>remoteGlobalIDString</key>
+ <string>ABCDABCDABCDABCD00000586</string>
+ <key>remoteInfo</key>
+ <string>_pre_CONFIGURE</string>
+ </dict>
+ <key>ABCDABCDABCDABCD0000058E</key>
+ <dict>
+ <key>buildConfigurationList</key>
+ <string>ABCDABCDABCDABCD00000590</string>
+ <key>buildPhases</key>
+ <array>
+ <string>ABCDABCDABCDABCD0000058F</string>
</array>
<key>dependencies</key>
- <array></array>
+ <array>
+ <string>ABCDABCDABCDABCD0000058C</string>
+ </array>
<key>isa</key>
<string>PBXAggregateTarget</string>
<key>name</key>
@@ -12843,7 +19811,7 @@
<key>productName</key>
<string>CONFIGURE_DIALOG</string>
</dict>
- <key>ABCDABCDABCDABCD00000399</key>
+ <key>ABCDABCDABCDABCD0000058F</key>
<dict>
<key>files</key>
<array></array>
@@ -12856,16 +19824,18 @@
<key>shellPath</key>
<string>/bin/sh</string>
<key>shellScript</key>
- <string>export PTB_PLATFORM="$ARCHS"
export PTB_PATH=../../static/bin/ReleaseDLL
export SLN_PATH=../PTB
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
../UtilityProjects/configure_gui_PTB.sh</string>
+ <string>export PTB_PLATFORM="$ARCHS"
export PTB_PATH=../../static/bin/ReleaseDLL
export SLN_PATH="$PROJECT_NAME"
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
UtilityProjects/configure_gui_PTB.sh</string>
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
- <key>ABCDABCDABCDABCD0000039A</key>
+ <key>ABCDABCDABCDABCD00000590</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD0000039B</string>
- <string>ABCDABCDABCDABCD0000039C</string>
- <string>ABCDABCDABCDABCD0000039D</string>
- <string>ABCDABCDABCDABCD0000039E</string>
+ <string>ABCDABCDABCDABCD00000591</string>
+ <string>ABCDABCDABCDABCD00000592</string>
+ <string>ABCDABCDABCDABCD00000593</string>
+ <string>ABCDABCDABCDABCD00000594</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -12874,7 +19844,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD0000039B</key>
+ <key>ABCDABCDABCDABCD00000591</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12886,7 +19856,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD0000039C</key>
+ <key>ABCDABCDABCDABCD00000592</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12898,7 +19868,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD0000039D</key>
+ <key>ABCDABCDABCDABCD00000593</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12910,7 +19880,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD0000039E</key>
+ <key>ABCDABCDABCDABCD00000594</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12922,16 +19892,18 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD0000039F</key>
+ <key>ABCDABCDABCDABCD00000595</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD000003A1</string>
+ <string>ABCDABCDABCDABCD00000597</string>
<key>buildPhases</key>
<array>
- <string>ABCDABCDABCDABCD000003A0</string>
+ <string>ABCDABCDABCDABCD00000596</string>
</array>
<key>dependencies</key>
- <array></array>
+ <array>
+ <string>ABCDABCDABCDABCD0000058C</string>
+ </array>
<key>isa</key>
<string>PBXAggregateTarget</string>
<key>name</key>
@@ -12939,7 +19911,7 @@
<key>productName</key>
<string>CONFIGURE</string>
</dict>
- <key>ABCDABCDABCDABCD000003A0</key>
+ <key>ABCDABCDABCDABCD00000596</key>
<dict>
<key>files</key>
<array></array>
@@ -12952,16 +19924,18 @@
<key>shellPath</key>
<string>/bin/sh</string>
<key>shellScript</key>
- <string>export PTB_PLATFORM="$ARCHS"
export PTB_PATH=../../static/bin/ReleaseDLL
export SLN_PATH=../PTB
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
../UtilityProjects/configure_PTB.sh</string>
+ <string>export PTB_PLATFORM="$ARCHS"
export PTB_PATH=../../static/bin/ReleaseDLL
export SLN_PATH="$PROJECT_NAME"
export TREE_ROOT=../../../..
export BUILD_TREE_ROOT=../..
UtilityProjects/configure_PTB.sh</string>
+ <key>showEnvVarsInLog</key>
+ <string>0</string>
</dict>
- <key>ABCDABCDABCDABCD000003A1</key>
+ <key>ABCDABCDABCDABCD00000597</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD000003A2</string>
- <string>ABCDABCDABCDABCD000003A3</string>
- <string>ABCDABCDABCDABCD000003A4</string>
- <string>ABCDABCDABCDABCD000003A5</string>
+ <string>ABCDABCDABCDABCD00000598</string>
+ <string>ABCDABCDABCDABCD00000599</string>
+ <string>ABCDABCDABCDABCD0000059A</string>
+ <string>ABCDABCDABCDABCD0000059B</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -12970,7 +19944,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000003A2</key>
+ <key>ABCDABCDABCDABCD00000598</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12982,7 +19956,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003A3</key>
+ <key>ABCDABCDABCDABCD00000599</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -12994,7 +19968,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003A4</key>
+ <key>ABCDABCDABCDABCD0000059A</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -13006,7 +19980,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003A5</key>
+ <key>ABCDABCDABCDABCD0000059B</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -13018,37 +19992,34 @@
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003A6</key>
+ <key>ABCDABCDABCDABCD0000059C</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD000003A7</string>
+ <string>ABCDABCDABCDABCD0000059D</string>
<key>buildPhases</key>
<array></array>
<key>comments</key>
- <string>5 targets</string>
+ <string>2 targets</string>
<key>dependencies</key>
<array>
- <string>ABCDABCDABCDABCD00000007</string>
- <string>ABCDABCDABCDABCD00000008</string>
- <string>ABCDABCDABCDABCD00000009</string>
- <string>ABCDABCDABCDABCD0000000A</string>
- <string>ABCDABCDABCDABCD0000000B</string>
+ <string>ABCDABCDABCDABCD00000011</string>
+ <string>ABCDABCDABCDABCD00000013</string>
</array>
<key>isa</key>
<string>PBXAggregateTarget</string>
<key>name</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
<key>productName</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
</dict>
- <key>ABCDABCDABCDABCD000003A7</key>
+ <key>ABCDABCDABCDABCD0000059D</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD000003A8</string>
- <string>ABCDABCDABCDABCD000003A9</string>
- <string>ABCDABCDABCDABCD000003AA</string>
- <string>ABCDABCDABCDABCD000003AB</string>
+ <string>ABCDABCDABCDABCD0000059E</string>
+ <string>ABCDABCDABCDABCD0000059F</string>
+ <string>ABCDABCDABCDABCD000005A0</string>
+ <string>ABCDABCDABCDABCD000005A1</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -13057,82 +20028,89 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000003A8</key>
+ <key>ABCDABCDABCDABCD0000059E</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003A9</key>
+ <key>ABCDABCDABCDABCD0000059F</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003AA</key>
+ <key>ABCDABCDABCDABCD000005A0</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003AB</key>
+ <key>ABCDABCDABCDABCD000005A1</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_LIBS</string>
+ <string>DATASPEC_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003AC</key>
+ <key>ABCDABCDABCDABCD000005A2</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD000003AD</string>
+ <string>ABCDABCDABCDABCD000005A3</string>
<key>buildPhases</key>
<array></array>
<key>comments</key>
- <string>2 targets</string>
+ <string>9 targets</string>
<key>dependencies</key>
<array>
+ <string>ABCDABCDABCDABCD00000007</string>
+ <string>ABCDABCDABCDABCD00000008</string>
+ <string>ABCDABCDABCDABCD00000009</string>
+ <string>ABCDABCDABCDABCD0000000A</string>
+ <string>ABCDABCDABCDABCD0000000B</string>
<string>ABCDABCDABCDABCD0000000C</string>
<string>ABCDABCDABCDABCD0000000D</string>
+ <string>ABCDABCDABCDABCD0000000E</string>
+ <string>ABCDABCDABCDABCD0000000F</string>
</array>
<key>isa</key>
<string>PBXAggregateTarget</string>
<key>name</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
<key>productName</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
</dict>
- <key>ABCDABCDABCDABCD000003AD</key>
+ <key>ABCDABCDABCDABCD000005A3</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD000003AE</string>
- <string>ABCDABCDABCDABCD000003AF</string>
- <string>ABCDABCDABCDABCD000003B0</string>
- <string>ABCDABCDABCDABCD000003B1</string>
+ <string>ABCDABCDABCDABCD000005A4</string>
+ <string>ABCDABCDABCDABCD000005A5</string>
+ <string>ABCDABCDABCDABCD000005A6</string>
+ <string>ABCDABCDABCDABCD000005A7</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -13141,62 +20119,62 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000003AE</key>
+ <key>ABCDABCDABCDABCD000005A4</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003AF</key>
+ <key>ABCDABCDABCDABCD000005A5</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003B0</key>
+ <key>ABCDABCDABCDABCD000005A6</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003B1</key>
+ <key>ABCDABCDABCDABCD000005A7</key>
<dict>
<key>buildSettings</key>
<dict>
<key>PRODUCT_NAME</key>
- <string>BUILD_APPS</string>
+ <string>LIBS_ALL</string>
</dict>
<key>isa</key>
<string>XCBuildConfiguration</string>
<key>name</key>
<string>ReleaseMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003B2</key>
+ <key>ABCDABCDABCDABCD000005A8</key>
<dict>
<key>buildConfigurationList</key>
- <string>ABCDABCDABCDABCD000003B3</string>
+ <string>ABCDABCDABCDABCD000005A9</string>
<key>buildPhases</key>
<array></array>
<key>comments</key>
- <string>7 targets</string>
+ <string>13 targets</string>
<key>dependencies</key>
<array>
<string>ABCDABCDABCDABCD00000007</string>
@@ -13206,6 +20184,12 @@
<string>ABCDABCDABCDABCD0000000B</string>
<string>ABCDABCDABCDABCD0000000C</string>
<string>ABCDABCDABCDABCD0000000D</string>
+ <string>ABCDABCDABCDABCD0000000E</string>
+ <string>ABCDABCDABCDABCD0000000F</string>
+ <string>ABCDABCDABCDABCD00000010</string>
+ <string>ABCDABCDABCDABCD00000011</string>
+ <string>ABCDABCDABCDABCD00000012</string>
+ <string>ABCDABCDABCDABCD00000013</string>
</array>
<key>isa</key>
<string>PBXAggregateTarget</string>
@@ -13214,14 +20198,14 @@
<key>productName</key>
<string>BUILD_ALL</string>
</dict>
- <key>ABCDABCDABCDABCD000003B3</key>
+ <key>ABCDABCDABCDABCD000005A9</key>
<dict>
<key>buildConfigurations</key>
<array>
- <string>ABCDABCDABCDABCD000003B4</string>
- <string>ABCDABCDABCDABCD000003B5</string>
- <string>ABCDABCDABCDABCD000003B6</string>
- <string>ABCDABCDABCDABCD000003B7</string>
+ <string>ABCDABCDABCDABCD000005AA</string>
+ <string>ABCDABCDABCDABCD000005AB</string>
+ <string>ABCDABCDABCDABCD000005AC</string>
+ <string>ABCDABCDABCDABCD000005AD</string>
</array>
<key>defaultConfigurationIsVisible</key>
<string>0</string>
@@ -13230,7 +20214,7 @@
<key>isa</key>
<string>XCConfigurationList</string>
</dict>
- <key>ABCDABCDABCDABCD000003B4</key>
+ <key>ABCDABCDABCDABCD000005AA</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -13242,7 +20226,7 @@
<key>name</key>
<string>DebugDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003B5</key>
+ <key>ABCDABCDABCDABCD000005AB</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -13254,7 +20238,7 @@
<key>name</key>
<string>DebugMT</string>
</dict>
- <key>ABCDABCDABCDABCD000003B6</key>
+ <key>ABCDABCDABCDABCD000005AC</key>
<dict>
<key>buildSettings</key>
<dict>
@@ -13266,7 +20250,7 @@
<key>name</key>
<string>ReleaseDLL</string>
</dict>
- <key>ABCDABCDABCDABCD000003B7</key>
+ <key>ABCDABCDABCDABCD000005AD</key>
<dict>
<key>buildSettings</key>
<dict>
diff --git a/c++/compilers/xcode30_prj/xcodebuild.sh b/c++/compilers/xcode30_prj/xcodebuild.sh
new file mode 100755
index 0000000..dda44c0
--- /dev/null
+++ b/c++/compilers/xcode30_prj/xcodebuild.sh
@@ -0,0 +1,24 @@
+#!/bin/sh
+# $Id: xcodebuild.sh 472266 2015-07-08 17:20:47Z ivanov $
+# Simple wrapper for xcodebuild that favors older SDK versions so as
+# to yield more portable binaries.
+
+cmd=xcodebuild
+case "`uname -r`" in
+ ?.* | 1[01].* ) # Mac OS X 10.7.x or older
+ for v in 10.5 10.6 10.7; do
+ sdk=/Developer/SDKs/MacOSX$v.sdk
+ [ -d "$sdk" ] && break
+ done
+ ;;
+ * )
+ for v in 10.8 10.9 10.10; do
+ sdk=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX$v.sdk
+ [ -d "$sdk" ] && break
+ done
+ ;;
+esac
+if [ -d "$sdk" ]; then
+ cmd="$cmd -sdk $sdk"
+fi
+exec $cmd "$@"
diff --git a/c++/include/algo/blast/api/bl2seq.hpp b/c++/include/algo/blast/api/bl2seq.hpp
index c55c5cd..d7ce49b 100644
--- a/c++/include/algo/blast/api/bl2seq.hpp
+++ b/c++/include/algo/blast/api/bl2seq.hpp
@@ -1,4 +1,4 @@
-/* $Id: bl2seq.hpp 303807 2011-06-13 18:22:23Z camacho $
+/* $Id: bl2seq.hpp 478803 2015-09-14 15:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,11 +63,14 @@ public:
/// Constructor to compare query against all subject sequences with
/// default options
- CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects, EProgram p);
+ /// @param dbscan_mode Database search mode (as opposed to pairwise)
+ CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects, EProgram p,
+ bool dbscan_mode=false);
/// Constructor to allow query concatenation with default options
+ /// @param dbscan_mode Database search mode (as opposed to pairwise)
CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects,
- EProgram p);
+ EProgram p, bool dbscan_mode=false);
/// Constructor to compare 2 sequences with specified options
CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject,
@@ -75,12 +78,14 @@ public:
/// Constructor to compare query against all subject sequences with
/// specified options
+ /// @param dbscan_mode Database search mode (as opposed to pairwise)
CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects,
- CBlastOptionsHandle& opts);
+ CBlastOptionsHandle& opts, bool dbscan_mode=false);
/// Constructor to allow query concatenation with specified options
+ /// @param dbscan_mode Database search mode (as opposed to pairwise)
CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects,
- CBlastOptionsHandle& opts);
+ CBlastOptionsHandle& opts, bool dbscan_mode=false);
/// Destructor
virtual ~CBl2Seq();
@@ -177,6 +182,7 @@ private:
TSeqLocVector m_tSubjects; ///< sequence(s) to BLAST against
CRef<CBlastOptionsHandle> m_OptsHandle; ///< Blast options
CRef<CLocalBlast> m_Blast; ///< The actual BLAST instance
+ bool m_DbScanMode; ///< Scan like a databsase (as opposed to pairwise)
/// Common initialization code for all c-tors
void x_Init(const TSeqLocVector& queries, const TSeqLocVector& subjs);
diff --git a/c++/include/algo/blast/api/blast_advprot_options.hpp b/c++/include/algo/blast/api/blast_advprot_options.hpp
index 53bf77d..2c9383d 100644
--- a/c++/include/algo/blast/api/blast_advprot_options.hpp
+++ b/c++/include/algo/blast/api/blast_advprot_options.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___ADVPROT_OPTIONS__HPP
#define ALGO_BLAST_API___ADVPROT_OPTIONS__HPP
-/* $Id: blast_advprot_options.hpp 431056 2014-04-01 15:13:51Z camacho $
+/* $Id: blast_advprot_options.hpp 474219 2015-07-27 17:07:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,6 +61,8 @@ public:
/// Creates object with default options set
CBlastAdvancedProteinOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
+ CBlastAdvancedProteinOptionsHandle(CRef<CBlastOptions> opt):CBlastProteinOptionsHandle(opt){}
+
/******************* Gapped extension options *******************/
/// Returns this mode, which mostly specifies whether composition of db
diff --git a/c++/include/algo/blast/api/blast_options.hpp b/c++/include/algo/blast/api/blast_options.hpp
index c3ef63c..12943c8 100644
--- a/c++/include/algo/blast/api/blast_options.hpp
+++ b/c++/include/algo/blast/api/blast_options.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_options.hpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_options.hpp 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/algo/blast/api/blast_options_builder.hpp b/c++/include/algo/blast/api/blast_options_builder.hpp
index ae0cf4c..0a96ffd 100644
--- a/c++/include/algo/blast/api/blast_options_builder.hpp
+++ b/c++/include/algo/blast/api/blast_options_builder.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___BLAST_OPTIONS_BUILDER__HPP
#define ALGO_BLAST_API___BLAST_OPTIONS_BUILDER__HPP
-/* $Id: blast_options_builder.hpp 421717 2013-12-13 16:07:22Z boratyng $
+/* $Id: blast_options_builder.hpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -111,13 +111,13 @@ public:
bool HaveGiList();
/// Get the GI list.
- list<int> GetGiList();
+ list<TGi> GetGiList();
/// Check whether a negative GI list is specified.
bool HaveNegativeGiList();
/// Get the negative GI list.
- list<int> GetNegativeGiList();
+ list<TGi> GetNegativeGiList();
/// Check whether a database filtering algorithm ID is specified
bool HasDbFilteringAlgorithmId();
@@ -282,10 +282,10 @@ private:
SOptional<int> m_FinalDbSeq;
/// The GI list (or none).
- SOptional< list<int> > m_GiList;
+ SOptional< list<TGi> > m_GiList;
/// The negative GI list (or none).
- SOptional< list<int> > m_NegativeGiList;
+ SOptional< list<TGi> > m_NegativeGiList;
/// The GI list (or none).
SOptional<int> m_DbFilteringAlgorithmId;
diff --git a/c++/include/algo/blast/api/blast_options_handle.hpp b/c++/include/algo/blast/api/blast_options_handle.hpp
index ed6ec10..a746b90 100644
--- a/c++/include/algo/blast/api/blast_options_handle.hpp
+++ b/c++/include/algo/blast/api/blast_options_handle.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___BLAST_OPTIONS_HANDLE__HPP
#define ALGO_BLAST_API___BLAST_OPTIONS_HANDLE__HPP
-/* $Id: blast_options_handle.hpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_options_handle.hpp 474219 2015-07-27 17:07:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -323,7 +323,7 @@ public:
m_Opts->SetEffectiveSearchSpace(eff);
}
-protected:
+protected:
/// Create Options Handle from Existing CBlastOptions Object
CBlastOptionsHandle(CRef<CBlastOptions> opt);
diff --git a/c++/include/algo/blast/api/blast_prot_options.hpp b/c++/include/algo/blast/api/blast_prot_options.hpp
index d36a76d..5e27b4c 100644
--- a/c++/include/algo/blast/api/blast_prot_options.hpp
+++ b/c++/include/algo/blast/api/blast_prot_options.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___BLAST_PROT_OPTIONS__HPP
#define ALGO_BLAST_API___BLAST_PROT_OPTIONS__HPP
-/* $Id: blast_prot_options.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: blast_prot_options.hpp 474219 2015-07-27 17:07:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,6 +58,9 @@ public:
/// Creates object with default options set
CBlastProteinOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
+ /// Create Options Handle from Existing CBlastOptions Object
+ CBlastProteinOptionsHandle(CRef<CBlastOptions> opt):CBlastOptionsHandle(opt) {}
+
/******************* Lookup table options ***********************/
/// Returns WordThreshold
double GetWordThreshold() const { return m_Opts->GetWordThreshold(); }
diff --git a/c++/include/algo/blast/api/local_db_adapter.hpp b/c++/include/algo/blast/api/local_db_adapter.hpp
index 0a8bd78..54d9830 100644
--- a/c++/include/algo/blast/api/local_db_adapter.hpp
+++ b/c++/include/algo/blast/api/local_db_adapter.hpp
@@ -1,4 +1,4 @@
-/* $Id: local_db_adapter.hpp 403214 2013-06-13 13:25:50Z fongah2 $
+/* $Id: local_db_adapter.hpp 478802 2015-09-14 15:44:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -69,8 +69,10 @@ public:
/// Set of sequences which should be used as subjects
/// @param opts_handle
/// Options to be used (needed to create the ILocalQueryData)
+ /// @param dbscan_mode Database search mode (as opposed to pairwise)
CLocalDbAdapter(CRef<IQueryFactory> subject_sequences,
- CConstRef<CBlastOptionsHandle> opts_handle);
+ CConstRef<CBlastOptionsHandle> opts_handle,
+ bool dbscan_mode=false);
/// Constructor taking custom BlastSeqSrc and IBlastSeqInfoSrc objects
/// @param seqSrc
@@ -121,6 +123,9 @@ public:
/// Returns true if this object represents a BLAST database
bool IsBlastDb() const { return m_DbName != kEmptyStr; }
+ /// Returns true if this is not a database but is database scanning mode
+ bool IsDbScanMode() const { return m_DbScanMode; }
+
private:
/// Pointer to the BlastSeqSrc this object owns and manages
BlastSeqSrc* m_SeqSrc;
@@ -144,6 +149,9 @@ private:
/// This is initialized ONLY if this object represents a BLAST database
const string m_DbName;
+
+ /// Specifies that bl2seq search run in database scan mode (not pairwise)
+ bool m_DbScanMode;
/// Prohibit copy-constructor
CLocalDbAdapter(const CLocalDbAdapter&);
diff --git a/c++/include/algo/blast/api/psiblast_options.hpp b/c++/include/algo/blast/api/psiblast_options.hpp
index ab47d84..d77baeb 100644
--- a/c++/include/algo/blast/api/psiblast_options.hpp
+++ b/c++/include/algo/blast/api/psiblast_options.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___PSIBLAST_OPTIONS__HPP
#define ALGO_BLAST_API___PSIBLAST_OPTIONS__HPP
-/* $Id: psiblast_options.hpp 162130 2009-06-03 13:44:30Z camacho $
+/* $Id: psiblast_options.hpp 474219 2015-07-27 17:07:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,8 @@ public:
/// Creates object with default options set
CPSIBlastOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
+
+ CPSIBlastOptionsHandle(CRef<CBlastOptions> opt):CBlastAdvancedProteinOptionsHandle(opt) {}
/// Destructor
~CPSIBlastOptionsHandle() {}
diff --git a/c++/include/algo/blast/api/remote_blast.hpp b/c++/include/algo/blast/api/remote_blast.hpp
index 4f5004e..23f24d8 100644
--- a/c++/include/algo/blast/api/remote_blast.hpp
+++ b/c++/include/algo/blast/api/remote_blast.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___REMOTE_BLAST__HPP
#define ALGO_BLAST_API___REMOTE_BLAST__HPP
-/* $Id: remote_blast.hpp 413750 2013-09-17 21:40:25Z camacho $
+/* $Id: remote_blast.hpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -134,12 +134,12 @@ public:
/// This restricts the subject database to this list of GIs (this is not
/// supported yet on the server end).
/// @param gi_list list of GIs to restrict the search to [in]
- void SetGIList(const list<Int4> & gi_list);
+ void SetGIList(const list<TGi> & gi_list);
/// This excludes the provided GIs from the subject database (this is not
/// supported yet on the server end).
/// @param gi_list list of GIs to exclude [in]
- void SetNegativeGIList(const list<Int4> & gi_list);
+ void SetNegativeGIList(const list<TGi> & gi_list);
/// Sets the filtering algorithm ID to be applied to the BLAST database
/// (not supported by server yet)
@@ -588,6 +588,11 @@ private:
/// @param value Pointer to list of integers to use.
void x_SetOneParam(objects::CBlast4Field & field, const list<int> * value);
+ /// Set a list of 8 byte integers.
+ /// @param field CBlast4Field object corresponding to option.
+ /// @param value Pointer to list of integers to use.
+ void x_SetOneParam(objects::CBlast4Field & field, const list<Int8> * value);
+
/// Set a string parameter.
/// @param field CBlast4Field object corresponding to option.
/// @param value Pointer to pointer to null delimited string.
@@ -802,10 +807,10 @@ private:
string m_FinalDbSeq;
/// GI list.
- list<Int4> m_GiList;
+ list<TGi> m_GiList;
/// Negative GI list.
- list<Int4> m_NegativeGiList;
+ list<TGi> m_NegativeGiList;
/// filtering algorithm to use in the database
int m_DbFilteringAlgorithmId;
diff --git a/c++/include/algo/blast/api/search_strategy.hpp b/c++/include/algo/blast/api/search_strategy.hpp
index 1f64606..9ac6ddb 100644
--- a/c++/include/algo/blast/api/search_strategy.hpp
+++ b/c++/include/algo/blast/api/search_strategy.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___SEARCH_STRATEGY__HPP
#define ALGO_BLAST_API___SEARCH_STRATEGY__HPP
-/* $Id: search_strategy.hpp 421717 2013-12-13 16:07:22Z boratyng $
+/* $Id: search_strategy.hpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -244,7 +244,8 @@ private:
const int int_value);
void x_AddParameterToProgramOptions(objects::CBlast4Field & field,
const vector<int> & int_list);
-
+ void x_AddParameterToProgramOptions(objects::CBlast4Field & field,
+ const vector<Int8> & int_list);
void x_AddParameterToProgramOptions(objects::CBlast4Field & field,
const string & str);
diff --git a/c++/include/algo/blast/api/seqsrc_multiseq.hpp b/c++/include/algo/blast/api/seqsrc_multiseq.hpp
index 793935e..3d07be5 100644
--- a/c++/include/algo/blast/api/seqsrc_multiseq.hpp
+++ b/c++/include/algo/blast/api/seqsrc_multiseq.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___SEQSRC_MULTISEQ__HPP
#define ALGO_BLAST_API___SEQSRC_MULTISEQ__HPP
-/* $Id: seqsrc_multiseq.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: seqsrc_multiseq.hpp 478802 2015-09-14 15:44:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,10 +50,12 @@ BEGIN_SCOPE(blast)
/** Initialize the sequence source structure.
* @param seq_vector Vector of sequence locations [in]
* @param program Type of BLAST to be performed [in]
+ * @param dbscanmode Database search mode (not pairwise) [in]
*/
NCBI_XBLAST_EXPORT BlastSeqSrc*
MultiSeqBlastSeqSrcInit(TSeqLocVector& seq_vector,
- EBlastProgramType program);
+ EBlastProgramType program,
+ bool dbscan_mode=false);
END_SCOPE(blast)
END_NCBI_SCOPE
diff --git a/c++/include/algo/blast/api/tblastn_options.hpp b/c++/include/algo/blast/api/tblastn_options.hpp
index 68920c2..4576635 100644
--- a/c++/include/algo/blast/api/tblastn_options.hpp
+++ b/c++/include/algo/blast/api/tblastn_options.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___TBLASTN_OPTIONS__HPP
#define ALGO_BLAST_API___TBLASTN_OPTIONS__HPP
-/* $Id: tblastn_options.hpp 431056 2014-04-01 15:13:51Z camacho $
+/* $Id: tblastn_options.hpp 474219 2015-07-27 17:07:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,7 @@ public:
/// Creates object with default options set
CTBlastnOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
+ CTBlastnOptionsHandle(CRef<CBlastOptions> opt):CBlastAdvancedProteinOptionsHandle(opt) {}
~CTBlastnOptionsHandle() {}
/************************ Scoring options ************************/
diff --git a/c++/include/algo/blast/api/traceback_stage.hpp b/c++/include/algo/blast/api/traceback_stage.hpp
index c24b1ae..c0c6196 100644
--- a/c++/include/algo/blast/api/traceback_stage.hpp
+++ b/c++/include/algo/blast/api/traceback_stage.hpp
@@ -1,4 +1,4 @@
-/* $Id: traceback_stage.hpp 419225 2013-11-22 17:08:29Z camacho $
+/* $Id: traceback_stage.hpp 457458 2015-01-23 12:27:33Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -78,6 +78,9 @@ public:
/// Run the traceback search.
CRef<CSearchResultSet> Run();
+ /// Runs the traceback but only returns the HSP's and not the Seq-Align.
+ BlastHSPResults* RunSimple();
+
/// Specifies how the Seq-align-set returned as part of the
/// results is formatted.
void SetResultType(EResultType type);
diff --git a/c++/include/algo/blast/api/uniform_search.hpp b/c++/include/algo/blast/api/uniform_search.hpp
index 58e7ef8..40b449d 100644
--- a/c++/include/algo/blast/api/uniform_search.hpp
+++ b/c++/include/algo/blast/api/uniform_search.hpp
@@ -1,4 +1,4 @@
-/* $Id: uniform_search.hpp 403214 2013-06-13 13:25:50Z fongah2 $
+/* $Id: uniform_search.hpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -109,7 +109,7 @@ public:
class NCBI_XBLAST_EXPORT CSearchDatabase : public CObject {
public:
/// Define a list of gis
- typedef vector<int> TGiList;
+ typedef vector<TGi> TGiList;
/// Molecule of the BLAST database
enum EMoleculeType {
diff --git a/c++/include/algo/blast/blastinput/blast_args.hpp b/c++/include/algo/blast/blastinput/blast_args.hpp
index 96d0f34..d84202c 100644
--- a/c++/include/algo/blast/blastinput/blast_args.hpp
+++ b/c++/include/algo/blast/blastinput/blast_args.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_args.hpp 457395 2015-01-22 18:07:29Z ivanov $
+/* $Id: blast_args.hpp 485060 2015-11-18 16:07:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -512,7 +512,8 @@ public:
bool is_deltablast = false)
: m_DbTarget(db_target), m_NumIterations(1),
m_CheckPointOutput(0), m_AsciiMatrixOutput(0),
- m_IsDeltaBlast(is_deltablast)
+ m_IsDeltaBlast(is_deltablast),
+ m_SaveLastPssm(false)
{};
/// Our virtual destructor
@@ -562,6 +563,16 @@ public:
m_Pssm = pssm;
}
+ /// Should the PSSM after the last database search be saved
+ bool GetSaveLastPssm(void) const {
+ return m_SaveLastPssm;
+ }
+
+ /// Set the on/off switch for saving PSSM after the last database search
+ void SetSaveLastPssm(bool b) {
+ m_SaveLastPssm = b;
+ }
+
private:
/// Molecule of the database
ETargetDatabase m_DbTarget;
@@ -577,6 +588,9 @@ private:
/// Are the aruments set up for Delta Blast
bool m_IsDeltaBlast;
+ /// Save PSSM after the last database search
+ bool m_SaveLastPssm;
+
/// Prohibit copy constructor
CPsiBlastArgs(const CPsiBlastArgs& rhs);
/// Prohibit assignment operator
@@ -855,24 +869,38 @@ public:
eArchiveFormat,
/// JSON seq-align
eJsonSeqalign,
- /// JSON output
+ /// JSON XInclude
eJson,
- /// XML2 output
+ /// XML2 XInclude
eXml2,
+ /// JSON2 single file
+ eJson_S,
+ /// XML2 single file
+ eXml2_S,
/// SAM format
eSAM,
/// Sentinel value for error checking
eEndValue
};
+ enum EFormatFlags {
+ eDefaultFlag = 0,
+ // Set if VDB
+ eIsVDB = 0x01,
+ // Set if SAM format is supported
+ eIsSAM = 0x02,
+ // Set if both VDB and SAM is true
+ eIsVDB_SAM = eIsVDB | eIsSAM
+ };
/// Default constructor
- CFormattingArgs(bool isIgblast = false)
+ CFormattingArgs(bool isIgblast = false, EFormatFlags flag = eDefaultFlag)
: m_OutputFormat(ePairwise), m_ShowGis(false),
m_NumDescriptions(0), m_NumAlignments(0),
m_DfltNumDescriptions(0), m_DfltNumAlignments(0),
m_Html(false),
m_IsIgBlast(isIgblast),
- m_LineLength(align_format::kDfltLineLength)
+ m_LineLength(align_format::kDfltLineLength),
+ m_FormatFlags(flag)
{
if (m_IsIgBlast) {
m_DfltNumAlignments = m_DfltNumDescriptions = 10;
@@ -915,6 +943,8 @@ public:
m_OutputFormat == eAsnBinary ||
m_OutputFormat == eXml2 ||
m_OutputFormat == eJson ||
+ m_OutputFormat == eXml2_S ||
+ m_OutputFormat == eJson_S ||
m_OutputFormat == eJsonSeqalign ||
m_OutputFormat == eSAM;
}
@@ -961,6 +991,8 @@ private:
string m_CustomOutputFormatSpec;
size_t m_LineLength;
+ EFormatFlags m_FormatFlags;
+
};
/// Argument class to collect multi-threaded arguments
diff --git a/c++/include/algo/blast/blastinput/blast_input_aux.hpp b/c++/include/algo/blast/blastinput/blast_input_aux.hpp
index 6941e92..27890a7 100644
--- a/c++/include/algo/blast/blastinput/blast_input_aux.hpp
+++ b/c++/include/algo/blast/blastinput/blast_input_aux.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_input_aux.hpp 429443 2014-03-14 14:31:27Z fongah2 $
+/* $Id: blast_input_aux.hpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,8 +48,11 @@ class NCBI_BLASTINPUT_EXPORT CAutoOutputFileReset : public CObject
public:
/// Constructor
/// @param file_name name of the output file [in]
- CAutoOutputFileReset(const string& file_name)
- : m_FileName(file_name), m_FileStream(0) {}
+ /// @param use_version if true, new files will be saved with versions
+ /// added to the file name
+ CAutoOutputFileReset(const string& file_name, bool use_versions = false)
+ : m_FileName(file_name), m_FileStream(0),
+ m_Version(use_versions ? 1 : 0) {}
/// Retrieve the newly opened stream, caller doesn't own the return value
CNcbiOstream* GetStream();
@@ -60,6 +63,9 @@ private:
/// The output stream
auto_ptr<CNcbiOstream> m_FileStream;
+ /// File version if larger than zero
+ int m_Version;
+
/// Prohibit copy constructor
CAutoOutputFileReset(const CAutoOutputFileReset& rhs);
/// Prohibit assignment operator
diff --git a/c++/include/algo/blast/blastinput/cmdline_flags.hpp b/c++/include/algo/blast/blastinput/cmdline_flags.hpp
index fa24a3b..dfa0480 100644
--- a/c++/include/algo/blast/blastinput/cmdline_flags.hpp
+++ b/c++/include/algo/blast/blastinput/cmdline_flags.hpp
@@ -1,4 +1,4 @@
-/* $Id: cmdline_flags.hpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: cmdline_flags.hpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -272,6 +272,11 @@ NCBI_BLASTINPUT_EXPORT extern const string kArgPSIPseudocount;
/// Argument to specify the evalue inclusion threshold for considering
/// aligned sequences for PSSM constructions
NCBI_BLASTINPUT_EXPORT extern const string kArgPSIInclusionEThreshold;
+/// Argument to specify whether the PSSM after the last psiblast database
+/// search should be saved
+NCBI_BLASTINPUT_EXPORT extern const string kArgSaveLastPssm;
+/// Argument to specify whether to save PSSM after each psiblast iteration
+NCBI_BLASTINPUT_EXPORT extern const string kArgSaveAllPssms;
/// Argument to specify the germline subject file for igblast
NCBI_BLASTINPUT_EXPORT extern const string kArgGLSubject;
diff --git a/c++/include/algo/blast/blastinput/deltablast_args.hpp b/c++/include/algo/blast/blastinput/deltablast_args.hpp
index a1b5349..acd71d6 100644
--- a/c++/include/algo/blast/blastinput/deltablast_args.hpp
+++ b/c++/include/algo/blast/blastinput/deltablast_args.hpp
@@ -1,4 +1,4 @@
-/* $Id: deltablast_args.hpp 347205 2011-12-14 20:08:44Z boratyng $
+/* $Id: deltablast_args.hpp 483793 2015-11-04 11:13:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -79,6 +79,9 @@ public:
/// Get query batch size
virtual int GetQueryBatchSize(void) const;
+ /// Should PSSM after last database search be saved
+ bool GetSaveLastPssm(void) const;
+
protected:
/// Create the options handle based on the command line arguments
/// @param locality whether the search will be executed locally or remotely
diff --git a/c++/include/algo/blast/blastinput/psiblast_args.hpp b/c++/include/algo/blast/blastinput/psiblast_args.hpp
index 3883af6..451bda0 100644
--- a/c++/include/algo/blast/blastinput/psiblast_args.hpp
+++ b/c++/include/algo/blast/blastinput/psiblast_args.hpp
@@ -1,4 +1,4 @@
-/* $Id: psiblast_args.hpp 334322 2011-09-06 14:50:26Z fongah2 $
+/* $Id: psiblast_args.hpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -74,6 +74,10 @@ public:
bool SaveAsciiPssm() const;
/// Retrieve the stream to write the ASCII PSSM
CNcbiOstream* GetAsciiPssmStream();
+
+ /// Should the PSSM after the last database search be saved
+ bool GetSaveLastPssm() const;
+
protected:
/// Create the options handle based on the command line arguments
/// @param locality whether the search will be executed locally or remotely
diff --git a/c++/include/algo/blast/core/blast_hits.h b/c++/include/algo/blast/core/blast_hits.h
index 03b1d47..b227fff 100644
--- a/c++/include/algo/blast/core/blast_hits.h
+++ b/c++/include/algo/blast/core/blast_hits.h
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.h 458751 2015-02-09 19:42:06Z ivanov $
+/* $Id: blast_hits.h 458579 2015-02-06 15:12:03Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/algo/blast/core/blast_message.h b/c++/include/algo/blast/core/blast_message.h
index 05ca0d8..c16545e 100644
--- a/c++/include/algo/blast/core/blast_message.h
+++ b/c++/include/algo/blast/core/blast_message.h
@@ -1,4 +1,4 @@
-/* $Id: blast_message.h 444369 2014-08-25 11:42:15Z ivanov $
+/* $Id: blast_message.h 442874 2014-08-07 19:26:31Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/algo/blast/core/blast_options.h b/c++/include/algo/blast/core/blast_options.h
index f929c39..bec10f3 100644
--- a/c++/include/algo/blast/core/blast_options.h
+++ b/c++/include/algo/blast/core/blast_options.h
@@ -1,4 +1,4 @@
-/* $Id: blast_options.h 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_options.h 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/algo/blast/core/blast_stat.h b/c++/include/algo/blast/core/blast_stat.h
index 1641653..84f4a16 100644
--- a/c++/include/algo/blast/core/blast_stat.h
+++ b/c++/include/algo/blast/core/blast_stat.h
@@ -1,4 +1,4 @@
-/* $Id: blast_stat.h 459037 2015-02-12 17:28:20Z ivanov $
+/* $Id: blast_stat.h 458581 2015-02-06 15:18:12Z boratyng $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/algo/blast/format/blast_format.hpp b/c++/include/algo/blast/format/blast_format.hpp
index 952de9c..0142ae1 100644
--- a/c++/include/algo/blast/format/blast_format.hpp
+++ b/c++/include/algo/blast/format/blast_format.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_format.hpp 457395 2015-01-22 18:07:29Z ivanov $
+/* $Id: blast_format.hpp 481977 2015-10-19 17:00:20Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -52,7 +52,7 @@ Author: Jason Papadopoulos
#include <algo/blast/blastinput/blast_args.hpp>
#include <algo/blast/api/local_db_adapter.hpp>
#include <algo/blast/api/blast_seqinfosrc.hpp>
-#include <objtools/format/sam_formatter.hpp>
+#include <algo/blast/format/sam.hpp>
BEGIN_NCBI_SCOPE
@@ -105,6 +105,8 @@ public:
/// tabular/comma-separated value output format. An empty string implies to
/// use the default value when applicable. [in]
/// @param domain_db_adapter Domain database for Delta-blast [in]
+ /// @param cmdline Actual command-line for SAM [in]
+ /// @param subjectTag Identifier for set of subjects [in]
CBlastFormat(const blast::CBlastOptions& opts,
blast::CLocalDbAdapter& db_adapter,
blast::CFormattingArgs::EOutputFormat format_type,
@@ -124,7 +126,9 @@ public:
bool is_megablast = false,
bool is_indexed = false,
const blast::CIgBlastOptions * ig_opts = NULL,
- const blast::CLocalDbAdapter* domain_db_adapter = NULL);
+ const blast::CLocalDbAdapter* domain_db_adapter = NULL,
+ const string & cmdline = kEmptyStr,
+ const string& subjectTag = kEmptyStr);
/// Constructor
/// @param opts BLAST options used in the search [in]
@@ -164,7 +168,8 @@ public:
bool is_html = false,
bool is_remote_search = false,
const string& custom_output_format = kEmptyStr,
- bool is_vdb = false);
+ bool is_vdb = false,
+ const string & cmdline = kEmptyStr);
/// Class destructor
~CBlastFormat();
@@ -295,6 +300,10 @@ private:
CRef<CScope> m_Scope;
/** True if we are formatting for BLAST2Sequences */
bool m_IsBl2Seq;
+ /// True if it is m_IsBl2Seq in dbscan mode
+ bool m_IsDbScan;
+ /// Tag for subject sequences (e.g., name of input file)
+ string m_SubjectTag;
/// True if this object is formatting the results of a remote search
bool m_IsRemoteSearch;
/// Used to count number of searches formatted.
@@ -348,7 +357,9 @@ private:
IOS_BASE::iostate m_OrigExceptionMask;
/// Pointer to the SAM formatting object
- auto_ptr<CSAM_Formatter> m_SamFormatter;
+ auto_ptr<CBlast_SAM_Formatter> m_SamFormatter;
+
+ string m_Cmdline;
/// Output the ancillary data for one query that was searched
/// @param summary The ancillary data to report [in]
@@ -439,6 +450,8 @@ private:
void x_GenerateXML2MasterFile(void);
void x_GenerateJSONMasterFile(void);
void x_WriteXML2(CCmdLineBlastXML2ReportData & report_data);
+
+ void x_InitSAMFormatter();
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/blast/format/blastfmtutil.hpp b/c++/include/algo/blast/format/blastfmtutil.hpp
index 1b9ea06..d776781 100644
--- a/c++/include/algo/blast/format/blastfmtutil.hpp
+++ b/c++/include/algo/blast/format/blastfmtutil.hpp
@@ -1,4 +1,4 @@
-/* $Id: blastfmtutil.hpp 446084 2014-09-11 11:52:44Z ivanov $
+/* $Id: blastfmtutil.hpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -177,9 +177,15 @@ public:
*
*/
+ enum ESubjectScores {
+ eNoQuerySubjCov = 0,
+ eQueryCovPerSubj = 0x01,
+ eQueryCovPerUniqSubj = 0x02,
+ eBothQuerySubjCov = eQueryCovPerSubj | eQueryCovPerUniqSubj
+ };
static void InsertSubjectScores (objects::CSeq_align_set & org_align_set,
const objects::CBioseq_Handle & query_handle,
- TSeqRange query_range = TSeqRange());
+ TSeqRange query_range = TSeqRange(), ESubjectScores score_type=eQueryCovPerSubj);
};
diff --git a/c++/include/algo/blast/format/blastxml2_format.hpp b/c++/include/algo/blast/format/blastxml2_format.hpp
index bf1de5e..322c690 100644
--- a/c++/include/algo/blast/format/blastxml2_format.hpp
+++ b/c++/include/algo/blast/format/blastxml2_format.hpp
@@ -1,4 +1,4 @@
-/* $Id: blastxml2_format.hpp 465307 2015-04-20 16:56:07Z ivanov $
+/* $Id: blastxml2_format.hpp 482725 2015-10-26 16:29:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -135,6 +135,9 @@ NCBI_XBLASTFORMAT_EXPORT
void BlastXML2_FormatReport(const IBlastXML2ReportData* data, string file_name);
NCBI_XBLASTFORMAT_EXPORT
+void BlastXML2_PrintHeader(CNcbiOstream *out_stream);
+
+NCBI_XBLASTFORMAT_EXPORT
void BlastXML2_FormatError( int exit_code,
string err_msg,
CNcbiOstream *out_stream);
@@ -147,6 +150,9 @@ NCBI_XBLASTFORMAT_EXPORT
void
BlastJSON_FormatReport(const IBlastXML2ReportData* data, CNcbiOstream *out_stream );
+NCBI_XBLASTFORMAT_EXPORT
+void
+BlastJSON_PrintHeader(CNcbiOstream *out_stream);
/* @} */
END_NCBI_SCOPE
diff --git a/c++/include/algo/blast/format/data4xml2format.hpp b/c++/include/algo/blast/format/data4xml2format.hpp
index 96371b0..5c7e588 100644
--- a/c++/include/algo/blast/format/data4xml2format.hpp
+++ b/c++/include/algo/blast/format/data4xml2format.hpp
@@ -1,4 +1,4 @@
-/* $Id: data4xml2format.hpp 465307 2015-04-20 16:56:07Z ivanov $
+/* $Id: data4xml2format.hpp 482740 2015-10-26 16:34:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -231,7 +231,7 @@ private:
static const unsigned int kMatrixCols = 28;
/// Score matrix used to determine neighboring protein residues
- int *m_Matrix[kMatrixCols];
+ CBlastFormattingMatrix * m_Matrix;
list<string> m_SubjectIds;
diff --git a/c++/include/objects/seqtable/seq_table_exception.hpp b/c++/include/algo/blast/format/sam.hpp
similarity index 58%
copy from c++/include/objects/seqtable/seq_table_exception.hpp
copy to c++/include/algo/blast/format/sam.hpp
index 233e43f..93dd6cc 100644
--- a/c++/include/objects/seqtable/seq_table_exception.hpp
+++ b/c++/include/algo/blast/format/sam.hpp
@@ -1,7 +1,4 @@
-#ifndef SEQ_TABLE_EXCEPTION__HPP
-#define SEQ_TABLE_EXCEPTION__HPP
-
-/* $Id: seq_table_exception.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -9,7 +6,7 @@
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
-* the author's official duties as a United States Government employee and
+* the author's offical duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
@@ -26,44 +23,39 @@
*
* ===========================================================================
*
-* Author: Eugene Vasilchenko
-*
-* File Description:
-* Exception class for Seq-table objects
+* Author: Amelia Fong
*
+* ===========================================================================
*/
-#include <corelib/ncbiexpt.hpp>
+/// @file: sam.hpp
+/// Formatting of pairwise sequence alignments in SAM form.
+#ifndef ALGO_BLAST_FORMAT___SAM_HPP
+#define ALGO_BLAST_FORMAT___SAM_HPP
+
+#include <objtools/format/sam_formatter.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
-
-/** @addtogroup ObjectManagerCore
- *
- * @{
- */
-
-
-/// Seq-loc and seq-align mapper exceptions
-class NCBI_SEQ_EXPORT CSeqTableException : public CException
+class NCBI_XBLASTFORMAT_EXPORT CBlast_SAM_Formatter : public CSAM_Formatter
{
public:
- enum EErrCode {
- eColumnNotFound, ///< Requested column is missing
- eRowNotFound, ///< Requested row is missing
- eIncompatibleRowType, ///< Data cannot be converted to asked type
- eOtherError
- };
- virtual const char* GetErrCodeString(void) const;
- NCBI_EXCEPTION_DEFAULT(CSeqTableException, CException);
-};
+ CBlast_SAM_Formatter (CNcbiOstream& out,
+ CScope& scope,
+ const string & custom_spec,
+ const CSAM_Formatter::SProgramInfo & info);
+ void Print(const CSeq_align_set & aln);
-/* @} */
+private :
+ void x_ProcessCustomSpec(const string & custom_spec, const CSAM_Formatter::SProgramInfo & info);
+ void x_Print(const CSeq_align_set & aln);
+ unsigned int m_refRow;
+
+};
END_SCOPE(objects)
END_NCBI_SCOPE
-
-#endif // SEQ_TABLE_EXCEPTION__HPP
+#endif /* ALGo_BLAST_FORMAT___SAM_HPP */
diff --git a/c++/include/algo/dustmask/symdust.hpp b/c++/include/algo/dustmask/symdust.hpp
index fc23b7c..158164b 100644
--- a/c++/include/algo/dustmask/symdust.hpp
+++ b/c++/include/algo/dustmask/symdust.hpp
@@ -1,4 +1,4 @@
-/* $Id: symdust.hpp 416745 2013-10-30 21:04:30Z morgulis $
+/* $Id: symdust.hpp 464803 2015-04-14 16:29:37Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,6 +33,14 @@
#ifndef C_SYM_DUST_MASKER_HPP
#define C_SYM_DUST_MASKER_HPP
+#include <corelib/ncbitype.h>
+#include <corelib/ncbistr.hpp>
+#include <corelib/ncbiobj.hpp>
+
+#include <objects/seqloc/Seq_loc.hpp>
+#include <objects/seqloc/Packed_seqint.hpp>
+#include <objmgr/seq_vector.hpp>
+
#include <iostream>
#include <vector>
#include <algorithm>
@@ -41,13 +49,6 @@
#include <deque>
#include <list>
-#include <corelib/ncbitype.h>
-#include <corelib/ncbistr.hpp>
-#include <corelib/ncbiobj.hpp>
-
-#include <objects/seqloc/Seq_loc.hpp>
-#include <objects/seqloc/Packed_seqint.hpp>
-#include <objmgr/seq_vector.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker.hpp b/c++/include/algo/winmask/seq_masker.hpp
index 87c34be..946694f 100644
--- a/c++/include/algo/winmask/seq_masker.hpp
+++ b/c++/include/algo/winmask/seq_masker.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker.hpp 428457 2014-03-04 17:08:04Z morgulis $
+/* $Id: seq_masker.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,7 @@
#include <algo/winmask/seq_masker_window.hpp>
#include <algo/winmask/seq_masker_istat.hpp>
+#include <algo/winmask/seq_masker_version.hpp>
BEGIN_NCBI_SCOPE
@@ -52,6 +53,9 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMasker
{
public:
+ /// Version of window masking algorithm.
+ static CSeqMaskerVersion AlgoVersion;
+
/**
**\brief Type representing a masked interval within a sequence.
**
diff --git a/c++/include/algo/winmask/seq_masker_istat.hpp b/c++/include/algo/winmask/seq_masker_istat.hpp
index 7db411d..c33bdf6 100644
--- a/c++/include/algo/winmask/seq_masker_istat.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_istat.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,8 +36,13 @@
#include <corelib/ncbitype.h>
#include <corelib/ncbistr.hpp>
#include <corelib/ncbiobj.hpp>
+#include <corelib/version.hpp>
#include <algo/winmask/seq_masker_window.hpp>
+#include <algo/winmask/seq_masker_version.hpp>
+#include <algo/winmask/seq_masker_ostat.hpp>
+
+#include <memory>
BEGIN_NCBI_SCOPE
@@ -97,7 +102,8 @@ public:
min_count( arg_min_count ),
use_min_count( arg_use_min_count ),
ambig_unit( 0 ),
- opt_data_( 0, 0 )
+ opt_data_( 0, 0 ),
+ fmt_gen_algo_ver( CSeqMaskerOstat::StatAlgoVersion )
{ total_ = 0; }
/**
@@ -149,6 +155,16 @@ public:
const optimization_data * get_optimization_data() const
{ return opt_data_.cba_ == 0 ? 0 : &opt_data_; }
+ /** Return the version of the algorithm used to generate counts */
+ CSeqMaskerVersion const & GetStatAlgoVersion() const {
+ return fmt_gen_algo_ver;
+ }
+
+ /** Set the version of the algorithm used to generate counts */
+ void SetStatAlgoVersion( CSeqMaskerVersion const & v ) {
+ fmt_gen_algo_ver = v;
+ }
+
mutable Uint8 total_;
protected:
@@ -268,6 +284,14 @@ public:
/**\brief Return the metadata string. */
string const & GetMetaData() const { return metadata; }
+ /**\brief Return the encoding of the source statistics file. */
+ string const & GetFmtEncoding() const { return fmt_encoding; }
+
+ /**\brief Return the format version of the source statistics file. */
+ CComponentVersionInfo const * GetFmtVersion() const {
+ return fmt_version.get();
+ }
+
protected:
/**
**\brief Set the count value for units with actual counts
@@ -303,9 +327,23 @@ protected:
void set_optimization_data( const optimization_data & opt_data )
{ opt_data_ = opt_data; }
+public:
+
/** Set metadata string. */
void SetMetaData( string const & md ) { metadata = md; }
+protected:
+
+ /** Set the statistics file format encoding. */
+ void SetFmtEncoding( string const & e ) { fmt_encoding = e; }
+
+ /** Set the statistics file format version. */
+ void SetFmtVersion( string const & name,
+ int major, int minor, int patch ) {
+ fmt_version.reset(
+ new CComponentVersionInfo( name, major, minor, patch ) );
+ }
+
private:
/**\name Provide reference semantics for CSeqMaskerOstat. */
@@ -323,10 +361,17 @@ private:
Uint1 unit_size; /**<\internal The unit size. */
string metadata; /**<\internal Metadata string. */
+ string fmt_encoding; /**<\internal Encoding of the stats file from which the data was read. */
+
+ /** Format version of the statistics file from which the data was read. */
+ std::auto_ptr< CComponentVersionInfo > fmt_version;
CSeqMaskerWindow::TUnit ambig_unit; /**<\internal Unit value to represent ambiguities. */
optimization_data opt_data_; /**<\internal Optimization parameters. */
+
+ /** version of the algorithm used to generate counts */
+ CSeqMaskerVersion fmt_gen_algo_ver;
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker_istat_ascii.hpp b/c++/include/algo/winmask/seq_masker_istat_ascii.hpp
index 38a1d1d..0633581 100644
--- a/c++/include/algo/winmask/seq_masker_istat_ascii.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat_ascii.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_ascii.hpp 122478 2008-03-19 19:14:23Z morgulis $
+/* $Id: seq_masker_istat_ascii.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -87,6 +87,7 @@ public:
**\param arg_use_max_count value to use for units with count > T_high
**\param arg_min_count T_low
**\param arg_use_min_count value to use for units with count < T_low
+ **\param start_line skip this many lines in the beginning
**/
explicit CSeqMaskerIstatAscii( const string & name,
Uint4 arg_threshold,
@@ -94,7 +95,8 @@ public:
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count );
+ Uint4 arg_use_min_count,
+ Uint4 start_line = 0 );
/**
**\brief Object destructor.
diff --git a/c++/include/algo/winmask/seq_masker_istat_bin.hpp b/c++/include/algo/winmask/seq_masker_istat_bin.hpp
index efc38ae..899ad60 100644
--- a/c++/include/algo/winmask/seq_masker_istat_bin.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat_bin.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_bin.hpp 122478 2008-03-19 19:14:23Z morgulis $
+/* $Id: seq_masker_istat_bin.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,6 +80,7 @@ public:
**\param arg_use_max_count value to use for units with count > T_high
**\param arg_min_count T_low
**\param arg_use_min_count value to use for units with count < T_low
+ **\param skip skip this many bytes in the beginning
**/
explicit CSeqMaskerIstatBin( const string & name,
Uint4 arg_threshold,
@@ -87,7 +88,8 @@ public:
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count );
+ Uint4 arg_use_min_count,
+ Uint4 skip = 0 );
/**
**\brief Object destructor.
diff --git a/c++/include/algo/winmask/seq_masker_istat_factory.hpp b/c++/include/algo/winmask/seq_masker_istat_factory.hpp
index 155da65..45f66f8 100644
--- a/c++/include/algo/winmask/seq_masker_istat_factory.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat_factory.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_factory.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: seq_masker_istat_factory.hpp 463278 2015-03-26 14:15:38Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,6 +51,16 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerIstatFactory
{
public:
+ /// Counts statistics formats.
+ ///
+ enum EStatType {
+ eAscii,
+ eBinary,
+ eOAscii,
+ eOBinary,
+ eUnknown
+ };
+
/**
**\brief Exceptions that CSeqMaskerIstatFactory might throw.
**/
@@ -75,6 +85,10 @@ public:
};
+ /// Return the format of the counts statistics file.
+ ///
+ static EStatType DiscoverStatType( string const & name );
+
/**
**\brief Create a unit counts container from a file.
**
@@ -100,6 +114,13 @@ public:
bool use_ba );
private:
+
+ /// Return the format of the counts statistics file. At the same time
+ /// return the number of metadata lines (for text formats) and size
+ /// of metadata in bytes (for binary formats).
+ ///
+ static EStatType DiscoverStatType(
+ string const & name, vector< string > & md, size_t & skip );
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker_istat_oascii.hpp b/c++/include/algo/winmask/seq_masker_istat_oascii.hpp
index 615dcb7..d861f47 100644
--- a/c++/include/algo/winmask/seq_masker_istat_oascii.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat_oascii.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_oascii.hpp 122478 2008-03-19 19:14:23Z morgulis $
+/* $Id: seq_masker_istat_oascii.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -88,6 +88,7 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerIstatOAscii
**\param arg_use_max_count value to use for units with count > T_high
**\param arg_min_count T_low
**\param arg_use_min_count value to use for units with count < T_low
+ **\param start_line number of initial lines to skip
**/
explicit CSeqMaskerIstatOAscii( const string & name,
Uint4 arg_threshold,
@@ -95,7 +96,8 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerIstatOAscii
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count );
+ Uint4 arg_use_min_count,
+ Uint4 start_line = 0 );
/**
**\brief Object destructor.
diff --git a/c++/include/algo/winmask/seq_masker_istat_obinary.hpp b/c++/include/algo/winmask/seq_masker_istat_obinary.hpp
index d3dd21f..c925f50 100644
--- a/c++/include/algo/winmask/seq_masker_istat_obinary.hpp
+++ b/c++/include/algo/winmask/seq_masker_istat_obinary.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_obinary.hpp 122478 2008-03-19 19:14:23Z morgulis $
+/* $Id: seq_masker_istat_obinary.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -89,6 +89,7 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerIstatOBinary
**\param arg_min_count T_low
**\param arg_use_min_count value to use for units with count < T_low
**\param arg_use_ba use bit array optimization if available
+ **\param skip skip this many bytes in the beginning
**/
explicit CSeqMaskerIstatOBinary( const string & name,
Uint4 arg_threshold,
@@ -97,7 +98,8 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerIstatOBinary
Uint4 arg_use_max_count,
Uint4 arg_min_count,
Uint4 arg_use_min_count,
- bool arg_use_ba );
+ bool arg_use_ba,
+ Uint4 skip = 0 );
/**
**\brief Object destructor.
diff --git a/c++/include/algo/winmask/seq_masker_ostat.hpp b/c++/include/algo/winmask/seq_masker_ostat.hpp
index 6ba3355..d9f352b 100644
--- a/c++/include/algo/winmask/seq_masker_ostat.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,8 @@
#include <corelib/ncbistr.hpp>
#include <corelib/ncbiargs.hpp>
+#include <algo/winmask/seq_masker_version.hpp>
+
BEGIN_NCBI_SCOPE
/**
@@ -48,6 +50,11 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerOstat : public CObject
{
public:
+ static char const * STAT_ALGO_COMPONENT_NAME;
+
+ /// Version of the statistics generation algorithm.
+ static CSeqMaskerVersion StatAlgoVersion;
+
/**
**\brief Exceptions that CSeqMaskerOstat can throw.
**/
@@ -74,9 +81,7 @@ public:
**\param os C++ stream that should be used to save the unit counts data
**/
explicit CSeqMaskerOstat(
- CNcbiOstream & os, bool alloc, string const & metadata )
- : out_stream( os ), alloc( alloc ), metadata( metadata ), state( start )
- {}
+ CNcbiOstream & os, bool alloc, string const & metadata );
/**
**\brief Trivial object destructor.
@@ -125,31 +130,45 @@ public:
void setParam( const string & name, Uint4 value );
/**
- **\brief Create a blank line in the unit counts file.
- **
- ** It is possible that this method is NOP for some unit counts
- ** formats.
- **/
- void setBlank() { doSetBlank(); }
-
- /**
**\brief Perform any final tasks required to generate unit
** counts in the particular format.
**/
void finalize();
+ /** Set the counts generation algorithm version explicitly
+ (needed for convertions).
+ */
+ void SetStatAlgoVersion( CSeqMaskerVersion const & v ) {
+ fmt_gen_algo_ver = v;
+ }
+
+ /** Get actual counts format version. */
+ virtual CSeqMaskerVersion const & GetStatFmtVersion() const = 0;
+
protected:
+ /** Algorithm parameter names. */
+ static const char * PARAMS[];
+
/**\name Methods used to delegate functionality to derived classes */
/**@{*/
- virtual void doSetUnitSize( Uint4 us ) = 0;
+ virtual void doSetUnitSize( Uint4 us ) { unit_size = (Uint1)us; }
virtual void doSetUnitCount( Uint4 unit, Uint4 count ) = 0;
- virtual void doSetComment( const string & msg ) = 0;
- virtual void doSetParam( const string & name, Uint4 value ) = 0;
- virtual void doSetBlank() = 0;
+ virtual void doSetComment( const string & msg ) {}
+ virtual void doSetParam( const string & name, Uint4 value );
+ // virtual void doSetBlank() {}
virtual void doFinalize() {}
/**@}*/
+ /// Format algorithm parameters into a string.
+ string FormatParameters() const;
+
+ /// Combine version data and metadata into a single string.
+ string FormatMetaData() const;
+
+ /// Write metadata in binary format.
+ void WriteBinMetaData( std::ostream & os ) const;
+
/**
**\brief Refers to the C++ stream that should be used to write
** out the unit counts data.
@@ -162,6 +181,20 @@ protected:
/** metadata string */
string metadata;
+ /** unit size */
+ Uint1 unit_size;
+
+ /**\internal
+ **\brief Parameter values.
+ **/
+ vector< Uint4 > pvalues;
+
+ /** Unit counts */
+ vector< pair< Uint4, Uint4 > > counts;
+
+ /** version of the algorithm used to generate counts */
+ CSeqMaskerVersion fmt_gen_algo_ver;
+
private:
/**\name Provide reference semantics for the class */
diff --git a/c++/include/algo/winmask/seq_masker_ostat_ascii.hpp b/c++/include/algo/winmask/seq_masker_ostat_ascii.hpp
index bebaf8a..b6a41fa 100644
--- a/c++/include/algo/winmask/seq_masker_ostat_ascii.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat_ascii.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_ascii.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_ascii.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
#define C_WIN_MASK_USTAT_ASCII_H
#include <string>
+#include <vector>
#include <corelib/ncbistre.hpp>
@@ -49,6 +50,9 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerOstatAscii : public CSeqMaskerOstat
{
public:
+ /// Format version.
+ static CSeqMaskerVersion FormatVersion;
+
/**
**\brief Exceptions that CSeqMaskerOstatAscii might throw.
**/
@@ -89,13 +93,12 @@ public:
**/
virtual ~CSeqMaskerOstatAscii();
-protected:
+ /** Get actual counts format version. */
+ virtual CSeqMaskerVersion const & GetStatFmtVersion() const {
+ return FormatVersion;
+ }
- /**
- **\brief Output a line containing the unit size.
- **\param us the value of the unit size
- **/
- virtual void doSetUnitSize( Uint4 us );
+protected:
/**
**\brief Output a line with information about the given unit count.
@@ -117,21 +120,14 @@ protected:
virtual void doSetComment( const string & msg );
/**
- **\brief Output a line with information about the given parameter value.
- **
- ** The line starts with '>' and contains 2 words: the name of the
- ** parameter and the decimal integer value of the parameter.
- ** This method should be called after all unit counts are reported.
- **
- **\param name the parameter name
- **\param value the parameter value
- **/
- virtual void doSetParam( const string & name, Uint4 value );
+ **\brief Write data to output file.
+ **/
+ virtual void doFinalize();
- /**
- **\brief Create a blank line in the output file.
- **/
- virtual void doSetBlank();
+private:
+
+ /** Set of comments to print in the end of the stats file. */
+ std::vector< std::string > comments;
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker_ostat_bin.hpp b/c++/include/algo/winmask/seq_masker_ostat_bin.hpp
index 98891e2..a833fd2 100644
--- a/c++/include/algo/winmask/seq_masker_ostat_bin.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat_bin.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_bin.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_bin.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -47,6 +47,9 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerOstatBin : public CSeqMaskerOstat
{
public:
+ /// Format version.
+ static CSeqMaskerVersion FormatVersion;
+
/**
**\brief Object constructor.
**\param name the name of the output file stream
@@ -65,23 +68,12 @@ public:
**/
virtual ~CSeqMaskerOstatBin();
-protected:
-
- /**
- **\brief Noop - comments are not available in the binary format.
- **/
- virtual void doSetComment( const string & msg ) {}
-
- /**
- **\brief Noop - blank lines do not make sense in the binary format.
- **/
- virtual void doSetBlank() {}
+ /** Get actual counts format version. */
+ virtual CSeqMaskerVersion const & GetStatFmtVersion() const {
+ return FormatVersion;
+ }
- /**
- **\brief Write the unit size value to the binary output.
- **\param us the unit size
- **/
- virtual void doSetUnitSize( Uint4 us );
+protected:
/**
**\brief Write count information for the unit to the binary output.
@@ -92,14 +84,9 @@ protected:
virtual void doSetUnitCount( Uint4 unit, Uint4 count );
/**
- **\brief Write a parameter value to the binary output.
- **
- ** Only recognized parameters will be written.
- **
- **\param name the parameter name
- **\param value the parameter value
- **/
- virtual void doSetParam( const string & name, Uint4 value );
+ **\brief Write data to output file.
+ **/
+ virtual void doFinalize();
private:
@@ -108,11 +95,6 @@ private:
**\param word a 32 bit value
**/
void write_word( Uint4 word );
-
- /**\internal
- **\brief Parameter values.
- **/
- vector< Uint4 > pvalues;
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker_ostat_opt.hpp b/c++/include/algo/winmask/seq_masker_ostat_opt.hpp
index 5e7f03b..a344d44 100644
--- a/c++/include/algo/winmask/seq_masker_ostat_opt.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat_opt.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -142,26 +142,6 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerOstatOpt : public CSeqMaskerOstat
virtual void doSetUnitCount( Uint4 unit, Uint4 count );
/**
- **\brief Noop.
- **/
- virtual void doSetComment( const string & msg ) {}
-
- /**
- **\brief Set a parameter value.
- **
- ** Only recognized parameters will be accepted.
- **
- **\param name the parameter name
- **\param value the parameter value
- **/
- virtual void doSetParam( const string & name, Uint4 value );
-
- /**
- **\brief Noop.
- **/
- virtual void doSetBlank() {}
-
- /**
**\brief Generate a hash function and dump the optimized unit counts
** data to the output stream.
**/
@@ -195,8 +175,6 @@ class NCBI_XALGOWINMASK_EXPORT CSeqMaskerOstatOpt : public CSeqMaskerOstat
vector< Uint4 > units; /**<\internal Array of units with counts >= T_low. */
vector< Uint2 > counts; /**<\internal Array of corresponding counts. */
-
- vector< Uint4 > pvalues; /**<\internal Array of threshold parameters. */
};
END_NCBI_SCOPE
diff --git a/c++/include/algo/winmask/seq_masker_ostat_opt_ascii.hpp b/c++/include/algo/winmask/seq_masker_ostat_opt_ascii.hpp
index 053d47c..9942ef2 100644
--- a/c++/include/algo/winmask/seq_masker_ostat_opt_ascii.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat_opt_ascii.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt_ascii.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt_ascii.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,6 +46,9 @@ CSeqMaskerOstatOptAscii : public CSeqMaskerOstatOpt
{
public:
+ /// Format version.
+ static CSeqMaskerVersion FormatVersion;
+
/**
**\brief Object constructor.
**\param name output file name
@@ -69,6 +72,11 @@ CSeqMaskerOstatOptAscii : public CSeqMaskerOstatOpt
**/
virtual ~CSeqMaskerOstatOptAscii() {}
+ /** Get actual counts format version. */
+ virtual CSeqMaskerVersion const & GetStatFmtVersion() const {
+ return FormatVersion;
+ }
+
protected:
/**
diff --git a/c++/include/algo/winmask/seq_masker_ostat_opt_bin.hpp b/c++/include/algo/winmask/seq_masker_ostat_opt_bin.hpp
index 778373e..6e93289 100644
--- a/c++/include/algo/winmask/seq_masker_ostat_opt_bin.hpp
+++ b/c++/include/algo/winmask/seq_masker_ostat_opt_bin.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt_bin.hpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt_bin.hpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,6 +45,9 @@ class NCBI_XALGOWINMASK_EXPORT
CSeqMaskerOstatOptBin : public CSeqMaskerOstatOpt
{
public:
+
+ /// Format version.
+ static CSeqMaskerVersion FormatVersion;
/**
**\brief Object constructor.
@@ -73,6 +76,11 @@ CSeqMaskerOstatOptBin : public CSeqMaskerOstatOpt
**/
virtual ~CSeqMaskerOstatOptBin() {}
+ /** Get actual counts format version. */
+ virtual CSeqMaskerVersion const & GetStatFmtVersion() const {
+ return FormatVersion;
+ }
+
protected:
/**
diff --git a/c++/include/cgi/error_codes.hpp b/c++/include/algo/winmask/seq_masker_version.hpp
similarity index 52%
copy from c++/include/cgi/error_codes.hpp
copy to c++/include/algo/winmask/seq_masker_version.hpp
index dd17eb8..a1ed1f7 100644
--- a/c++/include/cgi/error_codes.hpp
+++ b/c++/include/algo/winmask/seq_masker_version.hpp
@@ -1,7 +1,4 @@
-#ifndef CGI___ERROR_CODES__HPP
-#define CGI___ERROR_CODES__HPP
-
-/* $Id: error_codes.hpp 426474 2014-02-10 19:37:46Z grichenk $
+/* $Id: seq_masker_version.hpp 462582 2015-03-19 16:28:00Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,29 +23,54 @@
*
* ===========================================================================
*
- * Authors: Pavel Ivanov
+ * Authors: Aleksandr Morgulis
*
*/
-/// @file error_codes.hpp
-/// Definition of all error codes used in cgi (xcgi.lib).
-///
-
+#ifndef C_WIN_MASK_VERSION_HPP
+#define C_WIN_MASK_VERSION_HPP
-#include <corelib/ncbidiag.hpp>
+#include <corelib/version.hpp>
+#include <string>
+#include <sstream>
BEGIN_NCBI_SCOPE
+//------------------------------------------------------------------------------
+class CSeqMaskerVersion : public CComponentVersionInfo {
+public:
+
+ CSeqMaskerVersion( std::string const & component_name,
+ int ver_major, int ver_minor, int patch_level,
+ std::string const & ver_pfx = "" )
+ : CComponentVersionInfo(
+ component_name, ver_major, ver_minor, patch_level ),
+ ver_pfx_( ver_pfx )
+ {}
+
+ CSeqMaskerVersion( CSeqMaskerVersion const & src )
+ : CComponentVersionInfo( src ), ver_pfx_( src.ver_pfx_ )
+ {}
+
+ CSeqMaskerVersion & operator=( CSeqMaskerVersion const & src ) {
+ CComponentVersionInfo::operator=( src );
+ ver_pfx_ = src.ver_pfx_;
+ return *this;
+ }
+
+ virtual std::string Print() const {
+ std::ostringstream os;
+ os << GetComponentName() << ':' << ver_pfx_ << CVersionInfo::Print();
+ return os.str();
+ }
-NCBI_DEFINE_ERRCODE_X(Cgi_API, 501, 10);
-NCBI_DEFINE_ERRCODE_X(Cgi_Application, 502, 14);
-NCBI_DEFINE_ERRCODE_X(Cgi_Response, 503, 4);
-NCBI_DEFINE_ERRCODE_X(Cgi_Resourse, 504, 1);
-NCBI_DEFINE_ERRCODE_X(Cgi_Fast, 505, 9);
+private:
+ std::string ver_pfx_;
+};
END_NCBI_SCOPE
+#endif
-#endif /* CGI___ERROR_CODES__HPP */
diff --git a/c++/include/algo/winmask/seq_masker_window.hpp b/c++/include/algo/winmask/seq_masker_window.hpp
index 933ac04..68911c3 100644
--- a/c++/include/algo/winmask/seq_masker_window.hpp
+++ b/c++/include/algo/winmask/seq_masker_window.hpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_window.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: seq_masker_window.hpp 464804 2015-04-14 16:29:37Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,11 +33,12 @@
#ifndef C_SEQ_MASKER_WINDOW_H
#define C_SEQ_MASKER_WINDOW_H
-#include <vector>
-
#include <corelib/ncbiobj.hpp>
#include <objmgr/seq_vector.hpp>
+#include <vector>
+
+
BEGIN_NCBI_SCOPE
diff --git a/c++/include/cgi/cgi_exception.hpp b/c++/include/cgi/cgi_exception.hpp
index 8d9b90d..c0ed6b5 100644
--- a/c++/include/cgi/cgi_exception.hpp
+++ b/c++/include/cgi/cgi_exception.hpp
@@ -1,7 +1,7 @@
#ifndef CGI___CGI_EXCEPTION__HPP
#define CGI___CGI_EXCEPTION__HPP
-/* $Id: cgi_exception.hpp 446390 2014-09-15 17:56:49Z ivanov $
+/* $Id: cgi_exception.hpp 441525 2014-07-24 16:55:45Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/cgi/error_codes.hpp b/c++/include/cgi/error_codes.hpp
index dd17eb8..fd235c2 100644
--- a/c++/include/cgi/error_codes.hpp
+++ b/c++/include/cgi/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef CGI___ERROR_CODES__HPP
#define CGI___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 426474 2014-02-10 19:37:46Z grichenk $
+/* $Id: error_codes.hpp 460217 2015-02-25 18:00:11Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -43,7 +43,7 @@ BEGIN_NCBI_SCOPE
NCBI_DEFINE_ERRCODE_X(Cgi_API, 501, 10);
NCBI_DEFINE_ERRCODE_X(Cgi_Application, 502, 14);
-NCBI_DEFINE_ERRCODE_X(Cgi_Response, 503, 4);
+NCBI_DEFINE_ERRCODE_X(Cgi_Response, 503, 5);
NCBI_DEFINE_ERRCODE_X(Cgi_Resourse, 504, 1);
NCBI_DEFINE_ERRCODE_X(Cgi_Fast, 505, 9);
diff --git a/c++/include/cgi/ncbicgi.hpp b/c++/include/cgi/ncbicgi.hpp
index 1449a47..355e99b 100644
--- a/c++/include/cgi/ncbicgi.hpp
+++ b/c++/include/cgi/ncbicgi.hpp
@@ -1,7 +1,7 @@
#ifndef CGI___NCBICGI__HPP
#define CGI___NCBICGI__HPP
-/* $Id: ncbicgi.hpp 443818 2014-08-19 18:05:44Z ivanov $
+/* $Id: ncbicgi.hpp 443709 2014-08-18 18:58:59Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/cgi/ncbicgir.hpp b/c++/include/cgi/ncbicgir.hpp
index 49d3a9c..13f1344 100644
--- a/c++/include/cgi/ncbicgir.hpp
+++ b/c++/include/cgi/ncbicgir.hpp
@@ -1,7 +1,7 @@
#ifndef CGI___NCBICGIR__HPP
#define CGI___NCBICGIR__HPP
-/* $Id: ncbicgir.hpp 433624 2014-04-28 15:39:19Z grichenk $
+/* $Id: ncbicgir.hpp 483517 2015-11-02 14:43:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,6 +35,7 @@
#include <cgi/ncbicgi.hpp>
#include <corelib/ncbitime.hpp>
+#include <util/retry_ctx.hpp>
#include <map>
@@ -144,6 +145,15 @@ public:
CNcbiOstream& WriteHeader(void) const;
CNcbiOstream& WriteHeader(CNcbiOstream& os) const;
bool IsHeaderWritten() const;
+ /// Define if WriteHeader() must be called or can be skipped.
+ /// @param require
+ /// true - report (to application log) if WriteHeader has not
+ /// been called by the end of ProcessRequest();
+ /// false - allow to skip WriteHeader call (e.g when the user
+ /// writes custom HTTP header directly to the output
+ /// stream).
+ /// The default setting is 'true'.
+ void RequireWriteHeader(bool require);
void SetTrackingCookie(const string& name, const string& value,
const string& domain, const string& path,
@@ -195,6 +205,9 @@ public:
/// Do not call it directly from the user code!
void Finalize(void) const;
+ /// Set retry headers from the context.
+ void SetRetryContext(const CRetryContext& ctx);
+
public:
void x_SetSession(const CCgiSession& session);
@@ -226,6 +239,7 @@ protected:
CNcbiOstream* m_Output; // Default output stream
int m_OutputFD; // Output file descriptor, if available
mutable bool m_HeaderWritten; // Did we already complete the header?
+ bool m_RequireWriteHeader; // Check if WriteHeader was called?
CNcbiOstream::iostate m_OutputExpt; // Original output exceptions
CCgiRequest::ERequestMethod m_RequestMethod; // Request method from CCgiRequest
@@ -342,6 +356,11 @@ inline CNcbiOstream& CCgiResponse::WriteHeader(void) const
return WriteHeader(out());
}
+inline void CCgiResponse::RequireWriteHeader(bool require)
+{
+ m_RequireWriteHeader = require;
+}
+
inline bool CCgiResponse::IsHeaderWritten(void) const
{
return m_HeaderWritten;
diff --git a/c++/include/cgi/user_agent.hpp b/c++/include/cgi/user_agent.hpp
index ae6ec7d..aee40b1 100644
--- a/c++/include/cgi/user_agent.hpp
+++ b/c++/include/cgi/user_agent.hpp
@@ -1,7 +1,7 @@
#ifndef CGI___USER_AGENT__HPP
#define CGI___USER_AGENT__HPP
-/* $Id: user_agent.hpp 466744 2015-05-06 12:24:35Z ivanov $
+/* $Id: user_agent.hpp 466541 2015-05-04 14:38:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/common/config/ncbiconf_msvc.h b/c++/include/common/config/ncbiconf_msvc.h
index c82d1b2..0a40159 100644
--- a/c++/include/common/config/ncbiconf_msvc.h
+++ b/c++/include/common/config/ncbiconf_msvc.h
@@ -1,4 +1,4 @@
-/* $Id: ncbiconf_msvc.h 436002 2014-05-22 15:12:14Z ivanov $
+/* $Id: ncbiconf_msvc.h 457074 2015-01-20 16:19:10Z ucko $
* By Denis Vakatov, NCBI (vakatov at ncbi.nlm.nih.gov)
*
* MS-Win 32/64, MSVC++ 6.0/.NET
@@ -72,9 +72,12 @@
#define NCBI_DEPRECATED __declspec(deprecated)
#define NCBI_NORETURN __declspec(noreturn)
#define NCBI_FORCEINLINE __forceinline
+#define NCBI_PACKED_ENUM_TYPE(type) : type
+#define NCBI_PACKED_ENUM_END()
#define NCBI_RESTRICT_C
#define NCBI_RESTRICT_CXX
#define NCBI_TLS_VAR __declspec(thread)
+#define NCBI_WARN_UNUSED_RESULT _Check_return_
#ifdef _WIN64
# define HOST "i386-pc-win64"
diff --git a/c++/include/common/config/ncbiconf_xcode.h b/c++/include/common/config/ncbiconf_xcode.h
index ce6187a..65e171a 100644
--- a/c++/include/common/config/ncbiconf_xcode.h
+++ b/c++/include/common/config/ncbiconf_xcode.h
@@ -1,4 +1,4 @@
-/* $Id: ncbiconf_xcode.h 434182 2014-05-05 14:23:49Z ucko $
+/* $Id: ncbiconf_xcode.h 457074 2015-01-20 16:19:10Z ucko $
* By Vlad Lebedev, NCBI (lebedev at ncbi.nlm.nih.gov)
*
* Mac OS X - xCode Build
@@ -150,6 +150,9 @@
/* Define to 1 if the preprocessor supports C99-style variadic macros. */
#define HAVE_CPP_STD_VARARGS 1
+/* Define to 1 if you have the <cpuid.h> header file. */
+/* #undef HAVE_CPUID_H */
+
/* Define to 1 if you have the <dlfcn.h> header file. */
#define HAVE_DLFCN_H 1
@@ -638,6 +641,10 @@
/* Define to 1 if `string::compare()' is non-standard. */
/* #undef NCBI_OBSOLETE_STR_COMPARE */
+/* Define to whatever syntax, if any, your compiler supports for marking types
+ as packed to save memory. */
+#define NCBI_PACKED __attribute__((packed))
+
/* Define to whatever syntax, if any, your C compiler supports for marking
pointers as restricted in the C99 sense. */
#define NCBI_RESTRICT_C __restrict__
@@ -661,6 +668,10 @@
/* Define to 1 if prototypes can use exception specifications. */
#define NCBI_USE_THROW_SPEC 1
+/* Define to whatever syntax, if any, your compiler supports for marking
+ functions whose (status) result is important to check. */
+#define NCBI_WARN_UNUSED_RESULT __attribute__ ((warn_unused_result))
+
/* Define to 1 if the BSD-style netdb interface is reentrant. */
/* #undef NETDB_REENTRANT */
diff --git a/c++/include/common/metamodules_doxygen.h b/c++/include/common/metamodules_doxygen.h
index 940224d..464ce91 100644
--- a/c++/include/common/metamodules_doxygen.h
+++ b/c++/include/common/metamodules_doxygen.h
@@ -1,4 +1,4 @@
-/* $Id: metamodules_doxygen.h 119500 2008-02-11 02:52:52Z vakatov $
+/* $Id: metamodules_doxygen.h 441216 2014-07-22 14:12:16Z rudnev $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -790,6 +790,12 @@
* Genome Workbench application and support classes
*/
+/** @defgroup GUI_MACRO_SCRIPTS_UTIL Macro language classes
+ * @ingroup GUI
+ *
+ */
+
+
/* ========================================================================= */
diff --git a/c++/include/common/ncbi_export.h b/c++/include/common/ncbi_export.h
index 6b21d49..40c84ef 100644
--- a/c++/include/common/ncbi_export.h
+++ b/c++/include/common/ncbi_export.h
@@ -1,7 +1,7 @@
#ifndef COMMON___NCBI_EXPORT__H
#define COMMON___NCBI_EXPORT__H
-/* $Id: ncbi_export.h 464001 2015-04-02 20:13:29Z ucko $
+/* $Id: ncbi_export.h 461904 2015-03-13 15:31:15Z kachalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -154,6 +154,7 @@
# define NCBI_VALERR_EXPORTS
# define NCBI_VALID_EXPORTS
# define NCBI_BLASTDB_FORMAT_EXPORTS
+# define NCBI_DISCREPANCY_REPORT_EXPORTS
#endif
diff --git a/c++/include/common/ncbi_package_ver.h b/c++/include/common/ncbi_package_ver.h
index 554f9c3..c5a4d4c 100644
--- a/c++/include/common/ncbi_package_ver.h
+++ b/c++/include/common/ncbi_package_ver.h
@@ -7,8 +7,8 @@
#define NCBI_PACKAGE 1
#define NCBI_PACKAGE_NAME "blast"
#define NCBI_PACKAGE_VERSION_MAJOR 2
-#define NCBI_PACKAGE_VERSION_MINOR 2
-#define NCBI_PACKAGE_VERSION_PATCH 31
+#define NCBI_PACKAGE_VERSION_MINOR 3
+#define NCBI_PACKAGE_VERSION_PATCH 0
#define NCBI_PACKAGE_CONFIG ""
#define NCBI_PACKAGE_VERSION_STRINGIFY(x) #x
diff --git a/c++/include/common/ncbi_source_ver.h b/c++/include/common/ncbi_source_ver.h
index 82df691..ecf53ff 100644
--- a/c++/include/common/ncbi_source_ver.h
+++ b/c++/include/common/ncbi_source_ver.h
@@ -1,4 +1,4 @@
-/* $Id: ncbi_source_ver.h 460595 2015-02-28 05:09:57Z ucko $
+/* $Id: ncbi_source_ver.h 472591 2015-07-11 04:03:06Z syncbot $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -24,5 +24,5 @@
* ===========================================================================
*/
-#define NCBI_PRODUCTION_VER 20150221
-#define NCBI_DEVELOPMENT_VER 20140721
+#define NCBI_PRODUCTION_VER 20150711
+#define NCBI_DEVELOPMENT_VER 20150604
diff --git a/c++/include/common/ncbiconf_impl.h b/c++/include/common/ncbiconf_impl.h
index 6d7cbfa..954f54b 100644
--- a/c++/include/common/ncbiconf_impl.h
+++ b/c++/include/common/ncbiconf_impl.h
@@ -1,7 +1,7 @@
#ifndef COMMON___NCBICONF_IMPL__H
#define COMMON___NCBICONF_IMPL__H
-/* $Id: ncbiconf_impl.h 430560 2014-03-26 21:36:15Z ucko $
+/* $Id: ncbiconf_impl.h 457074 2015-01-20 16:19:10Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -110,6 +110,23 @@
# endif
#endif
+/* Definition of packed enum type, to save some memory */
+/* enum EMyEnum NCBI_PACKED_ENUM_TYPE(Type) { ... } NCBI_PACKED_ENUM_END(); */
+#ifndef NCBI_PACKED_ENUM_TYPE
+# define NCBI_PACKED_ENUM_TYPE(type)
+#endif
+#ifndef NCBI_PACKED_ENUM_END
+# ifdef NCBI_PACKED
+# define NCBI_PACKED_ENUM_END() NCBI_PACKED
+# else
+# define NCBI_PACKED_ENUM_END()
+# endif
+#endif
+
+#ifndef NCBI_WARN_UNUSED_RESULT
+# define NCBI_WARN_UNUSED_RESULT
+#endif
+
#ifdef __cplusplus
# if __cplusplus >= 201103L || defined(__GXX_EXPERIMENTAL_CXX0X__) \
|| defined(__GXX_EXPERIMENTAL_CPP0X__)
diff --git a/c++/include/common/test_assert_impl.h b/c++/include/common/test_assert_impl.h
index 2ecde59..97052f3 100644
--- a/c++/include/common/test_assert_impl.h
+++ b/c++/include/common/test_assert_impl.h
@@ -1,7 +1,7 @@
#ifndef COMMON__TEST_ASSERT_IMPL__H
#define COMMON__TEST_ASSERT_IMPL__H
-/* $Id: test_assert_impl.h 421371 2013-12-11 19:23:19Z gouriano $
+/* $Id: test_assert_impl.h 463634 2015-03-31 14:35:18Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -150,7 +150,7 @@ static int (*_SDPM)(void) = _SuppressDiagPopupMessages;
#ifdef _TROUBLE
# undef _TROUBLE
#endif
-#define _TROUBLE assert(0)
+#define _TROUBLE do { assert(0); abort(); } while (0)
/* Often, both _DEBUG_ARG and _ASSERT are used together
Once we redefine one, we should redefine another as well
diff --git a/c++/include/connect/error_codes.hpp b/c++/include/connect/error_codes.hpp
index 858a655..00e73e9 100644
--- a/c++/include/connect/error_codes.hpp
+++ b/c++/include/connect/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___ERROR_CODES__HPP
#define CONNECT___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 354749 2012-02-29 17:24:19Z ivanovp $
+/* $Id: error_codes.hpp 451390 2014-11-06 15:25:51Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -41,13 +41,12 @@
BEGIN_NCBI_SCOPE
-// Here are only error codes used in C++ sources. For error codes used in
-// C sources see src/connect/ncbi_priv.h.
+// Here are only error codes used in C++ sources.
+// For error codes used in C sources see src/connect/ncbi_priv.h.
NCBI_DEFINE_ERRCODE_X(Connect_Stream, 315, 10);
NCBI_DEFINE_ERRCODE_X(Connect_Pipe, 316, 16);
NCBI_DEFINE_ERRCODE_X(Connect_ThrServer, 317, 11);
NCBI_DEFINE_ERRCODE_X(Connect_Core, 318, 8);
-// Caution: src/connect/ncbi_priv.h contains greater error codes
END_NCBI_SCOPE
diff --git a/c++/include/connect/impl/server_connection.hpp b/c++/include/connect/impl/server_connection.hpp
index e2ddd4f..a8920d6 100644
--- a/c++/include/connect/impl/server_connection.hpp
+++ b/c++/include/connect/impl/server_connection.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___SERVER_CONNECTION__HPP
#define CONNECT___SERVER_CONNECTION__HPP
-/* $Id: server_connection.hpp 355488 2012-03-06 17:12:11Z kazimird $
+/* $Id: server_connection.hpp 462064 2015-03-16 14:27:31Z satskyse $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
/// Internal header for threaded server connections.
#include <connect/server.hpp>
+#include <string>
/** @addtogroup ThreadedServer
@@ -54,6 +55,7 @@ enum EServerConnType {
ePreClosedSocket,
eClosedSocket
};
+std::string g_ServerConnTypeToString(enum EServerConnType conn_type);
class CServer_ConnectionPool;
diff --git a/c++/include/connect/ncbi_buffer.h b/c++/include/connect/ncbi_buffer.h
index 819b605..8ecea35 100644
--- a/c++/include/connect/ncbi_buffer.h
+++ b/c++/include/connect/ncbi_buffer.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_BUFFER__H
#define CONNECT___NCBI_BUFFER__H
-/* $Id: ncbi_buffer.h 440949 2014-07-18 14:00:05Z lavr $
+/* $Id: ncbi_buffer.h 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
* Author: Denis Vakatov, Anton Lavrentiev
*
* File Description:
- * Memory-resident FIFO storage area (to be used e.g. in I/O buffering)
+ * Memory-resident storage area (to be used e.g. in I/O buffering)
*
* Handle: BUF
*
@@ -39,7 +39,7 @@
* BUF_Prepend[Ex]
* BUF_Append[Ex]
* BUF_Write
- * BUF_PushBack
+ * BUF_Pushback
* BUF_Peek
* BUF_PeekAt
* BUF_PeekAtCB
@@ -159,12 +159,14 @@ extern NCBI_XCONNECT_EXPORT /*bool*/int BUF_Write
);
+#define BUF_PushBack BUF_Pushback
+
/*!
* Write the data to the very beginning of "*pBuf" (to be read first).
* On error (failed memory allocation), return zero value.
* NOTE: if "*pBuf" == NULL then create it.
*/
-extern NCBI_XCONNECT_EXPORT /*bool*/int BUF_PushBack
+extern NCBI_XCONNECT_EXPORT /*bool*/int BUF_Pushback
(BUF* pBuf,
const void* data,
size_t size
diff --git a/c++/include/connect/ncbi_conn_reader_writer.hpp b/c++/include/connect/ncbi_conn_reader_writer.hpp
index dcfd865..379810b 100644
--- a/c++/include/connect/ncbi_conn_reader_writer.hpp
+++ b/c++/include/connect/ncbi_conn_reader_writer.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONN_READER_WRITER__HPP
#define CONNECT___NCBI_CONN_READER_WRITER__HPP
-/* $Id: ncbi_conn_reader_writer.hpp 341365 2011-10-19 14:10:03Z lavr $
+/* $Id: ncbi_conn_reader_writer.hpp 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -52,7 +52,6 @@ class NCBI_XCONNECT_EXPORT CSocketReaderWriter : public IReaderWriter,
{
public:
CSocketReaderWriter(CSocket* sock, EOwnership if_to_own = eNoOwnership);
- virtual ~CSocketReaderWriter();
virtual ERW_Result Read(void* buf,
size_t count,
@@ -60,6 +59,8 @@ public:
virtual ERW_Result PendingCount(size_t* count);
+ virtual ERW_Result Pushback(const void* buf, size_t count, void* del_ptr);
+
virtual ERW_Result Write(const void* buf,
size_t count,
size_t* bytes_written = 0);
@@ -71,10 +72,9 @@ public:
ERW_Result SetTimeout(EIO_Event event, const STimeout* timeout);
protected:
- ERW_Result x_Result(EIO_Status status);
+ ERW_Result x_Result(EIO_Status status);
- CSocket* m_Sock;
- EOwnership m_IsOwned;
+ AutoPtr<CSocket> m_Sock;
private:
CSocketReaderWriter(const CSocketReaderWriter&);
@@ -85,16 +85,8 @@ private:
inline CSocketReaderWriter::CSocketReaderWriter(CSocket* sock,
EOwnership if_to_own)
- : m_Sock(sock), m_IsOwned(if_to_own)
-{
-}
-
-
-inline CSocketReaderWriter::~CSocketReaderWriter()
+ : m_Sock(sock, if_to_own)
{
- if (m_IsOwned) {
- delete m_Sock;
- }
}
diff --git a/c++/include/connect/ncbi_conn_stream.hpp b/c++/include/connect/ncbi_conn_stream.hpp
index bfdedc7..3ced550 100644
--- a/c++/include/connect/ncbi_conn_stream.hpp
+++ b/c++/include/connect/ncbi_conn_stream.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONN_STREAM__HPP
#define CONNECT___NCBI_CONN_STREAM__HPP
-/* $Id: ncbi_conn_stream.hpp 450563 2014-10-28 15:19:24Z ivanov $
+/* $Id: ncbi_conn_stream.hpp 464976 2015-04-15 18:27:40Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -106,11 +106,11 @@ const size_t kConn_DefaultBufSize = 4096;
/// (default), which means that any input attempt first flushes any pending
/// output from the internal buffers.
///
-/// @note CConn_IOStream implementation utilizes the eCONN_OnClose callback
+/// @note CConn_IOStream implementation utilizes some connection callbacks
/// on the underlying CONN object. Care must be taken when intercepting
-/// the callback using the native CONN API.
+/// the callbacks using the native CONN API.
/// @sa
-/// CONN_SetCallback, eCONN_OnClose
+/// CONN_SetCallback
class NCBI_XCONNECT_EXPORT CConn_IOStream : public CNcbiIostream,
virtual protected CConnIniter
@@ -248,7 +248,7 @@ private:
CConn_Streambuf* m_CSb;
// Cancellation
- SCONN_Callback m_CB[3];
+ SCONN_Callback m_CB[4];
CConstIRef<ICanceled> m_Canceled;
static EIO_Status x_IsCanceled(CONN conn, TCONN_Callback type, void* data);
@@ -339,7 +339,7 @@ inline CConn_IOStream& operator<< (CConn_IOStream& os,
/// More details on that: <connect/ncbi_socket_connector.h>.
///
/// @sa
-/// SOCK_Create
+/// SOCK_CreateConnector, SOCK_Create
///
class NCBI_XCONNECT_EXPORT CConn_SocketStream : public CConn_IOStream
@@ -471,6 +471,15 @@ public:
+/// Helper class to fetch HTTP status code and text
+struct SHTTP_StatusData {
+ int code;
+ string text;
+ SHTTP_StatusData(void) : code(0), text(kEmptyStr) { }
+};
+
+
+
/////////////////////////////////////////////////////////////////////////////
///
/// This stream exchanges data with an HTTP server located at the URL:
@@ -498,6 +507,9 @@ public:
/// kDefaultTimeout, it overrides a value supplied by the HTTP connector
/// (the latter value is kept at SConnNetInfo::timeout).
///
+/// @sa
+/// HTTP_CreateConnector
+///
class NCBI_XCONNECT_EXPORT CConn_HttpStream : public CConn_IOStream
{
@@ -522,6 +534,15 @@ public:
CConn_HttpStream
(const string& url,
+ EReqMethod method,
+ const string& user_header = kEmptyStr,
+ THTTP_Flags flags = fHTTP_AutoReconnect,
+ const STimeout* timeout = kDefaultTimeout,
+ size_t buf_size = kConn_DefaultBufSize
+ );
+
+ CConn_HttpStream
+ (const string& url,
const SConnNetInfo* net_info,
const string& user_header = kEmptyStr,
FHTTP_ParseHeader parse_header = 0,
@@ -545,32 +566,34 @@ public:
size_t buf_size = kConn_DefaultBufSize
);
+ /// Flush the stream and fetch the response (w/o extracting any user data)
+ EIO_Status Fetch(const STimeout* timeout = kDefaultTimeout);
+
/// Get the last seen HTTP status code
- int GetStatusCode(void) const { return m_Code; }
+ int GetStatusCode(void) const { return m_StatusData.code; }
/// Get the last seen HTTP status text
- const string& GetStatusText(void) const { return m_Text; }
+ const string& GetStatusText(void) const { return m_StatusData.text; }
protected:
// Chained callbacks
- FHTTP_ParseHeader m_UserParseHeader;
void* m_UserData;
FHTTP_Adjust m_UserAdjust;
FHTTP_Cleanup m_UserCleanup;
+ FHTTP_ParseHeader m_UserParseHeader;
// HTTP status & text seen last
- int m_Code;
- string m_Text;
+ SHTTP_StatusData m_StatusData;
private:
// Interceptors
- static EHTTP_HeaderParse x_ParseHeader(const char* header,
- void* data,
- int code);
static int/*bool*/ x_Adjust (SConnNetInfo* net_info,
void* data,
unsigned int count);
static void x_Cleanup (void* data);
+ static EHTTP_HeaderParse x_ParseHeader(const char* header,
+ void* data,
+ int code);
};
@@ -589,6 +612,9 @@ private:
/// kDefaultTimeout, it overrides the value supplied by an underlying connector
/// (the latter value is kept in SConnNetInfo::timeout).
///
+/// @sa
+/// SERVICE_CreateConnector
+///
class NCBI_XCONNECT_EXPORT CConn_ServiceStream : public CConn_IOStream
{
@@ -597,7 +623,7 @@ public:
(const string& service,
TSERV_Type types = fSERV_Any,
const SConnNetInfo* net_info = 0,
- const SSERVICE_Extra* params = 0,
+ const SSERVICE_Extra* extra = 0,
const STimeout* timeout = kDefaultTimeout,
size_t buf_size = kConn_DefaultBufSize);
@@ -605,9 +631,45 @@ public:
(const string& service,
const string& user_header,
TSERV_Type types = fSERV_Any,
- const SSERVICE_Extra* params = 0,
+ const SSERVICE_Extra* extra = 0,
const STimeout* timeout = kDefaultTimeout,
size_t buf_size = kConn_DefaultBufSize);
+
+ /// Flush the stream and fetch the response (w/o extracting any user data)
+ EIO_Status Fetch(const STimeout* timeout = kDefaultTimeout);
+
+ /// Get the last seen HTTP status code, if available
+ int GetStatusCode(void) const { return m_CBData.status.code; }
+
+ /// Get the last seen HTTP status text, if available
+ const string& GetStatusText(void) const { return m_CBData.status.text; }
+
+ /// Get underlying SOCK, if available after Fetch()
+ SOCK GetSOCK(void);
+
+public:
+ /// Helper class
+ struct SSERVICE_CBData {
+ SSERVICE_Extra extra;
+ SHTTP_StatusData status;
+ };
+
+protected:
+ // Chained callbacks
+ SSERVICE_CBData m_CBData;
+
+private:
+ // Interceptors
+ static void x_Reset (void* data);
+ static int/*bool*/ x_Adjust (SConnNetInfo* net_info,
+ void* data,
+ unsigned int count);
+ static void x_Cleanup (void* data);
+ static EHTTP_HeaderParse x_ParseHeader(const char* header,
+ void* data,
+ int code);
+ static const SSERV_Info* x_GetNextInfo(void* data,
+ SERV_ITER iter);
};
@@ -616,6 +678,9 @@ public:
///
/// In-memory stream (a la strstream or stringstream)
///
+/// @sa
+/// MEMORY_CreateConnector
+///
class NCBI_XCONNECT_EXPORT CConn_MemoryStream : public CConn_IOStream
{
@@ -667,11 +732,14 @@ protected:
///
/// CConn_PipeStream for command piping
///
-/// @note Use caution when operating on the underlying pipe while it's being in
-/// use as it may cause undefined behavior.
+/// @note Exercise caution when operating on the underlying pipe while it's
+/// being in use as it may cause undefined behavior.
+///
+/// Provided "timeout" is set at the connection level if different from
+/// kDefaultTimeout (which is infinite for this class be default).
///
/// @sa
-/// CPipe
+/// PIPE_CreateConnector, CPipe
///
class NCBI_XCONNECT_EXPORT CConn_PipeStream : public CConn_IOStream
@@ -705,8 +773,11 @@ protected:
///
/// CConn_NamedPipeStream for inter-process communication
///
+/// Provided "timeout" is set at the connection level if different from
+/// kDefaultTimeout (which is infinite for this class be default).
+///
/// @sa
-/// CNamedPipe
+/// NAMEDPIPE_CreateConnector, CNamedPipe
///
class NCBI_XCONNECT_EXPORT CConn_NamedPipeStream : public CConn_IOStream
@@ -729,6 +800,13 @@ public:
/// See <connect/ncbi_ftp_connector.h> for detailed explanations
/// of supported features.
///
+/// Provided "timeout" is set at the connection level, and if different from
+/// kDefaultTimeout, it overrides a value supplied by the FTP connector
+/// (the latter value is kept at SConnNetInfo::timeout).
+///
+/// @sa
+/// FTP_CreateConnector
+///
class NCBI_XCONNECT_EXPORT CConn_FtpStream : public CConn_IOStream
{
diff --git a/c++/include/connect/ncbi_connection.h b/c++/include/connect/ncbi_connection.h
index 54636ac..7174839 100644
--- a/c++/include/connect/ncbi_connection.h
+++ b/c++/include/connect/ncbi_connection.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONNECTION__H
#define CONNECT___NCBI_CONNECTION__H
-/* $Id: ncbi_connection.h 424624 2014-01-17 18:22:57Z lavr $
+/* $Id: ncbi_connection.h 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -221,7 +221,7 @@ extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Write
);
-/** Push back "size" bytes from the buffer "buf" into connection.
+/** Push "size" bytes from the buffer "buf" back into connection.
* Return eIO_Success on success, other code on error.
* @note The data pushed back may not necessarily be the same as previously
* obtained from the connection.
@@ -231,7 +231,7 @@ extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Write
* @sa
* CONN_Read, CONN_Write
*/
-extern NCBI_XCONNECT_EXPORT EIO_Status CONN_PushBack
+extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Pushback
(CONN conn, /**< [in] connection handle */
const void* buf, /**< [in] pointer to the data being pushed back */
size_t size /**< [in] # of bytes to push back */
@@ -339,16 +339,17 @@ extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Close
/** Set user callback function to be invoked upon an event specified by the
- * callback type. Note that the callback function is always called prior
+ * callback type. Note that the callback function gets always called prior
* to the event to happen, e.g. the eCONN_OnClose callback is called when
* the connection is about to close, but has not yet been closed.
* @par
- * The callback function is supplied with 3 arguments: the connection handle,
+ * The callback function is supplied with 3 arguments: the connection handle,
* a type of event (except for eCONN_OnTimeout), and a user data (specified
* when the callback was set).
- * When eCONN_OnTimeout callback occurs, the callback type eCONN_OnTimeout
- * gets OR'ed with I/O direction, which timed out (eIO_Read, eIO_Write, or
- * both when flushing), then passed in as the type argument.
+ * When eCONN_OnTimeout callback occurs, the callback type eCONN_OnTimeout gets
+ * OR'ed with I/O direction, which has timed out: eIO_Open (when opening),
+ * eIO_Read, eIO_Write, or both (when flushing), then passed in the "type"
+ * argument.
* @par
* CONN_SetCallback() stores previous callback in "old_cb" (if it is not NULL).
* @par
@@ -356,8 +357,8 @@ extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Close
* or the connection becomes closed.
* @par
* This also means that if a callback is intercepted and then relayed to an old
- * handler, the interceptor may not assume the callback remains set, and must
- * reinstate itself upon each upcall of the old handler (in general).
+ * handler, the interceptor may not always assume the callback remains set, and
+ * so in general must reinstate itself upon each upcall of the old handler.
* @par
* Normally, callback would return eIO_Success and let the operation continue;
* non-eIO_Success return value causes it to be returned to the caller level
@@ -368,8 +369,10 @@ extern NCBI_XCONNECT_EXPORT EIO_Status CONN_Close
* fail with eIO_Interrupt.
* @note non-eIO_Success from an eCONN_OnClose callback cannot postpone the
* connection closure (but the error code is still passed through to the user).
- * @note by returning eIO_Success, eCONN_OnTimeout can restart the I/O that
- * has timed out.
+ * @note by returning eIO_Success, eCONN_OnTimeout restarts the I/O that
+ * has timed out (except for open).
+ * @note eCONN_OnTimeout for connection open is only called if eCONN_OnOpen
+ * was also set for that connection.
* @sa
* CONN_Read, CONN_Write, CONN_Close
*/
@@ -378,9 +381,10 @@ typedef enum {
eCONN_OnRead = 1, /**< Read from connector is about to occur */
eCONN_OnWrite = 2, /**< Write to connector is about to occur */
eCONN_OnFlush = 3, /**< About to be flushed (NB: == eIO_ReadWrite) */
- eCONN_OnTimeout = 4 /**< Connector I/O has timed out */
+ eCONN_OnTimeout = 4, /**< Connector I/O has timed out */
+ eCONN_OnOpen = 8 /**< Call prior to open (NB: "conn" still closed) */
} ECONN_Callback;
-#define CONN_N_CALLBACKS 5
+#define CONN_N_CALLBACKS 6
typedef unsigned int TCONN_Callback; /* Bitwise ECONN_Callback for time-out */
diff --git a/c++/include/connect/ncbi_connutil.h b/c++/include/connect/ncbi_connutil.h
index 47701b4..9ab4a94 100644
--- a/c++/include/connect/ncbi_connutil.h
+++ b/c++/include/connect/ncbi_connutil.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONNUTIL__H
#define CONNECT___NCBI_CONNUTIL__H
-/* $Id: ncbi_connutil.h 425982 2014-02-05 03:50:14Z lavr $
+/* $Id: ncbi_connutil.h 464990 2015-04-15 19:48:15Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,7 @@
* ConnNetInfo_Print()
* ConnNetInfo_Destroy()
* ConnNetInfo_Log()
+ * ConnNetInfo_URL()
* ConnNetInfo_ParseURL()
* ConnNetInfo_SetTimeout()
* ConnNetInfo_SetUserHeader()
@@ -168,7 +169,9 @@ typedef struct { /* NCBI_FAKE_WARNING: ICC */
unsigned stateless:1; /* to connect in HTTP-like fashion only*/
unsigned lb_disable:1; /* to disable local load-balancing */
EBDebugPrintout debug_printout:2; /* switch to printout some debug info */
+ unsigned http_push_auth:1; /* push authorize tags even w/o 401/407*/
unsigned http_proxy_leak:1;/* non-zero when can fallback to direct*/
+ unsigned reserved:15; /* MBZ */
char user[64]; /* username (if specified) */
char pass[64]; /* password (if any) */
char host[256]; /* host to connect to */
@@ -179,7 +182,6 @@ typedef struct { /* NCBI_FAKE_WARNING: ICC */
unsigned short http_proxy_port; /* port # of HTTP proxy server */
char http_proxy_user[64]; /* http proxy username (if req'd) */
char http_proxy_pass[64]; /* http proxy password */
- char proxy_host[256]; /* CERN-like (non-transp) f/w proxy srv*/
unsigned short max_try; /* max. # of attempts to connect (>= 1)*/
const STimeout* timeout; /* ptr to I/O timeout(infinite if NULL)*/
const char* http_user_header; /* user header to add to HTTP request */
@@ -232,6 +234,9 @@ typedef struct { /* NCBI_FAKE_WARNING: ICC */
#define REG_CONN_HTTP_PROXY_LEAK "HTTP_PROXY_LEAK"
#define DEF_CONN_HTTP_PROXY_LEAK ""
+#define REG_CONN_HTTP_PUSH_AUTH "HTTP_PUSH_AUTH"
+#define DEF_CONN_HTTP_PUSH_AUTH ""
+
#define REG_CONN_PROXY_HOST "PROXY_HOST"
#define DEF_CONN_PROXY_HOST ""
@@ -314,16 +319,18 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ ConnNetInfo_Boolean
* -- INFO FIELD -- ----- NAME ----- ---------- REMARKS/EXAMPLES ---------
* client_host local host name assigned automatically
* req_method REQ_METHOD
+ * user USER
+ * pass PASS
* host HOST
* port PORT
* path PATH
* args ARGS
- * http_proxy_host HTTP_PROXY_HOST if NULL http_proxy_port is set 0
+ * http_proxy_host HTTP_PROXY_HOST if empty http_proxy_port is set 0
* http_proxy_port HTTP_PROXY_PORT no HTTP proxy if 0
* http_proxy_user HTTP_PROXY_USER
* http_proxy_pass HTTP_PROXY_PASS
- * http_proxy_must HTTP_PROXY_MUST for non-HTTP CONNECT links only
- * proxy_host PROXY_HOST
+ * http_proxy_leak HTTP_PROXY_LEAK 1 means to also re-try w/o the proxy
+ * http_push_auth HTTP_PUSH_AUTH Send credentials pre-emptively
* timeout TIMEOUT "<sec>.<usec>": "3.00005", "infinite"
* max_try MAX_TRY
* firewall FIREWALL
@@ -390,7 +397,7 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ ConnNetInfo_DeleteArg
);
/* delete all arguments specified in "args" from the list in "info" */
-extern NCBI_XCONNECT_EXPORT void ConnNetInfo_DeleteAllArgs
+extern NCBI_XCONNECT_EXPORT void ConnNetInfo_DeleteAllArgs
(SConnNetInfo* info,
const char* args
);
@@ -463,7 +470,7 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ ConnNetInfo_ExtendUserHeader
/* Delete entries from current user header, if their tags match those
* passed in "header" (regardless of the values, if any, in the latter).
*/
-extern NCBI_XCONNECT_EXPORT void ConnNetInfo_DeleteUserHeader
+extern NCBI_XCONNECT_EXPORT void ConnNetInfo_DeleteUserHeader
(SConnNetInfo* info,
const char* header
);
@@ -494,7 +501,7 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ ConnNetInfo_SetupStandardArgs
/* Log the contents of "*info" into specified "log" with severity "sev".
*/
-extern NCBI_XCONNECT_EXPORT void ConnNetInfo_Log
+extern NCBI_XCONNECT_EXPORT void ConnNetInfo_Log
(const SConnNetInfo* info,
ELOG_Level sev,
LOG log
@@ -506,7 +513,7 @@ extern NCBI_XCONNECT_EXPORT void ConnNetInfo_Log
* Returned string must be free()'d when no longer necessary.
* Return NULL on error.
*/
-extern NCBI_XCONNECT_EXPORT char* ConnNetInfo_URL
+extern NCBI_XCONNECT_EXPORT char* ConnNetInfo_URL
(const SConnNetInfo* info
);
@@ -535,50 +542,53 @@ extern NCBI_XCONNECT_EXPORT void ConnNetInfo_Destroy(SConnNetInfo* info);
* @sa
* HTTP_CreateConnector, CConn_HttpStream
*
- * Hit URL "http[s]://host[:port]/path?args" with the following request
+ * Hit URL "http[s]://host[:port]/path[?args]" with the following request
* (argument substitution is shown as enclosed in angle brackets (not present
* in the actual request), and all optional parts shown in square brackets):
*
- * {CONNECT|POST|GET} <path>[?<args>] HTTP/1.0\r\n
- * [Host: host[:port]\r\n]
+ * METHOD <path>[?<args>] HTTP/1.x\r\n
* [Content-Length: <content_length>\r\n]
- * [<user_header>]
- *
- * Request method "eReqMethod_Any" selects an appropriate method depending on
- * the value of "content_length": results in GET when no content is expected
- * ("content_length"==0), and POST when "content_length" provided non-zero.
- *
- * For GET/POST(or ANY) methods the call attempts to provide a "Host:" HTTP
- * tag using information from the "host" and "port" parameters if the tag is
- * not present within "user_header" (notwithstanding below, the port part of
- * the tag does not get added for non-specified "port" passed as 0). Note
- * that the result of the above said auto-magic can be incorrect for HTTP
- * retrievals through a proxy server (since the built tag would correspond
- * to the proxy connection point, not the actual resource as it should have),
- * which is why the "Host:" tag courtesy is to be discontinued in the future.
+ * [<user_header>\r\n]\r\n
*
* If "port" is not specified (0) it will be assigned automatically to a
* well-known standard value depending on the "fSOCK_Secure" bit in the "flags"
* parameter, when connecting to an HTTP server.
*
- * The "content_length" must specify the exact(!) amount of data that is going
- * to POST (or be sent with CONNECT request) to the HTTP server (0 if none).
- * The "Content-Length" header gets always added in all POST requests, yet it
- * is always omitted in all other requests.
+ * A protocol version "1.x" is selected by the "req_method"'s value, and
+ * can be either 1.0 or 1.1. METHOD can be any of those of EReqMethod.
+ *
+ * @note Unlike deprecated URL_Connect(), this call never encodes any "args",
+ * and never auto-inserts any "Host:" tag into the headers (unless provided by
+ * the "user_header" argument).
+ *
+ * Request method "eReqMethod_Any" selects an appropriate method depending on
+ * the value of "content_length": results in GET when no content is expected
+ * ("content_length"==0), and POST when "content_length" provided non-zero.
+ *
+ * The "content_length" parameter must specify the exact(!) amount of data
+ * that is going to be sent (0 if none) to HTTP server. The "Content-Length"
+ * header gets always added to all legal requests (but GET / HEAD / CONNECT),
+ * whether or not the data payload has any defined protocol semantics
+ * (e.g. for DELETE / TRACE / OPTIONS).
*
- * If string "user_header" is not NULL/empty, then it *must* be terminated with
- * a single(!) '\r\n'.
+ * Alternatively, "content_length" can specify the amount of initial data to be
+ * sent with a CONNECT request into the established tunnel, and held by the
+ * "args" parameter (although, no header tag will get added to the HTTP header
+ * in that case, see below).
+ *
+ * If the string "user_header" is not NULL/empty, it will be stripped off any
+ * surrounding white space (including "\r\n"), then get added to the HTTP
+ * header, followed by the header termination sequence of "\r\n\r\n".
+ * @note that any interior whitespace in "user_header" is not analyzed/guarded.
*
* The "cred" parameter is only used to pass additional connection credentials
* for secure connections, and is ignored otherwise.
*
- * @note Unlike deprecated URL_Connect(), this call never encodes any "args".
- *
- * If the request method is "eReqMethod_Connect", then the connection is
+ * If the request method contains "eReqMethod_Connect", then the connection is
* assumed to be tunneled via a proxy, so "path" must specify a "host:port"
* pair to connect to; "content_length" can provide initial size of the data
* been tunneled, in which case "args" must be a pointer to such data, but no
- * "Content-Length" header tag gets added.
+ * "Content-Length:" header tag will get added.
*
* If "*sock" is non-NULL, the call _does not_ create a new socket, but builds
* an HTTP(S) data stream on top of the passed socket. Regardless of the
@@ -590,12 +600,12 @@ extern NCBI_XCONNECT_EXPORT void ConnNetInfo_Destroy(SConnNetInfo* info);
* On success, return eIO_Success and non-NULL handle of a socket via the last
* parameter.
*
- * ATTENTION: due to the very essence of the HTTP/1.0 connection, you may
+ * ATTENTION: due to the very essence of the HTTP/1.x connection, you may
* perform only one { WRITE, ..., WRITE, READ, ..., READ } cycle,
- * if doing either a GET or a POST.
+ * if using non-CONNECT request methods.
*
- * The returned socket must be exipicitly closed by "SOCK_Close()" when
- * no longer needed.
+ * The returned socket must be exipicitly closed by "SOCK_Close()" when no
+ * longer needed.
*
* NOTE: The returned socket may not be immediately readable/writeable if
* either open or read/write timeouts were passed as {0,0}, meaning that
@@ -612,10 +622,10 @@ extern NCBI_XCONNECT_EXPORT EIO_Status URL_ConnectEx
const char* path, /* must be provided */
const char* args, /* may be NULL or empty */
TReqMethod req_method, /* ANY selects method by "content_length" */
- size_t content_length,
+ size_t content_length, /* may not be used with HEAD or GET */
const STimeout* o_timeout, /* timeout for an OPEN stage */
const STimeout* rw_timeout, /* timeout for READ and WRITE */
- const char* user_header,
+ const char* user_header, /* should include "Host:" in most cases */
NCBI_CRED cred, /* connection credentials, if any */
TSOCK_Flags flags, /* additional socket requirements */
SOCK* sock /* returned socket (on eIO_Success only) */
@@ -623,8 +633,26 @@ extern NCBI_XCONNECT_EXPORT EIO_Status URL_ConnectEx
/* Equivalent to the above except that it returns a non-NULL socket handle
* on success, and NULL on error without providing a reason for the failure.
+ *
+ * @note Only HTTP/1.0 methods can be used with this call. For HTTP/1.1
+ * see URL_ConnectEx().
+ *
+ * For GET/POST(or ANY) methods the call attempts to provide a "Host:" HTTP tag
+ * using information from the "host" and "port" parameters if such a tag is not
+ * found within "user_header" (notwithstanding below, the port part of the tag
+ * does not get added for non-specified "port" passed as 0). Note that the
+ * result of the above-said auto-magic can be incorrect for HTTP retrievals
+ * through a proxy server (since the built tag would correspond to the proxy
+ * connection point, but not the actual server as it should have):
+ *
+ * Host: host[:port]\r\n
+ *
* @note DO NOT USE THIS CALL!
+ *
* CAUTION: If requested, "args" can get encoded but will do that as a whole!
+ *
+ * @sa
+ * URL_ConnectEx
*/
#ifndef NCBI_DEPRECATED
# define NCBI_CONNUTIL_DEPRECATED
@@ -637,21 +665,24 @@ extern NCBI_XCONNECT_EXPORT NCBI_CONNUTIL_DEPRECATED SOCK URL_Connect
const char* path, /* must be provided */
const char* args, /* may be NULL or empty */
EReqMethod req_method, /* ANY selects method by "content_length" */
- size_t content_length,
+ size_t content_length, /* may not be used with HEAD or GET */
const STimeout* o_timeout, /* timeout for an OPEN stage */
const STimeout* rw_timeout, /* timeout for READ and WRITE */
- const char* user_header,
+ const char* user_header, /* may get auto-extended with a "Host" tag */
int/*bool*/ encode_args, /* URL-encode "args" entirely (CAUTION!) */
TSOCK_Flags flags /* additional socket requirements */
);
-/* Discard all input data before(and including) the first occurrence of
- * "pattern". If "discard" is not NULL then add the discarded data(including
+/* Discard all input data before (and including) the first occurrence of a
+ * "pattern". If "discard" is not NULL then add the stripped data (including
* the "pattern") to it. If "n_discarded" is not NULL then "*n_discarded"
- * will return the number of discarded bytes. If there was some excess read,
- * push it back to the original source.
- * NOTE: "pattern" == NULL causes stripping to the EOF.
+ * will return the number of actually stripped bytes. If there was some excess
+ * read, push it back to the original source (and not count as discarded).
+ * NOTE: If "pattern_size" == 0, then "pattern" is ignored (assumed to be NULL)
+ * and the stripping continues until EOF; if "pattern" is NULL and
+ * "pattern_size" is not 0, then exactly "pattern_size" bytes will have
+ * attempted to be stripped (unless an I/O error occurs prematurely).
*/
extern NCBI_XCONNECT_EXPORT EIO_Status CONN_StripToPattern
(CONN conn,
diff --git a/c++/include/connect/ncbi_http_connector.h b/c++/include/connect/ncbi_http_connector.h
index 3ef0071..d0ad7fb 100644
--- a/c++/include/connect/ncbi_http_connector.h
+++ b/c++/include/connect/ncbi_http_connector.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___HTTP_CONNECTOR__H
#define CONNECT___HTTP_CONNECTOR__H
-/* $Id: ncbi_http_connector.h 457999 2015-01-29 19:41:58Z kazimird $
+/* $Id: ncbi_http_connector.h 468400 2015-05-22 15:00:30Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -73,15 +73,15 @@ extern "C" {
* any server error, which then is made available for reading as well)
* *NOTE* this flag disables automatic authorization and redirection.
*
- * @var fHTTP_UrlDecodeInput
+ * @var fHCC_UrlDecodeInput
* Assume the response body as single-part, URL-encoded; perform the
- * URL-decoding on read, and deliver decoded data to the user.
+ * URL-decoding on read, and deliver decoded data to the user. Obsolete.
*
* @var fHTTP_NoUpread
* Do *not* do internal reading into temporary buffer while sending data
- * to HTTP server; by default any send operation tries to extract data
- * as they are coming back from the server in order to prevent stalling
- * due to data clogging the connection.
+ * to HTTP server; by default any send operation tries to fetch data as
+ * they are coming back from the server in order to prevent stalling due
+ * to data clogging the connection.
*
* @var fHTTP_DropUnread
* Do not collect incoming data in "Read" mode before switching into
@@ -100,7 +100,7 @@ extern "C" {
* this flag allows such redirects (when encountered) to be honored.
*
* @note
- * URL encoding/decoding (in the "fHTTP_Url*" cases and "net_info->args")
+ * URL encoding/decoding (in the "fHCC_Url*" cases and "net_info->args")
* is performed by URL_Encode() and URL_Decode() -- see "ncbi_connutil.[ch]".
*
* @sa
@@ -110,10 +110,10 @@ enum EHTTP_Flag {
fHTTP_AutoReconnect = 0x1, /**< See HTTP_CreateConnectorEx() */
fHTTP_Flushable = 0x2, /**< Connector will really flush on Flush()*/
fHTTP_KeepHeader = 0x4, /**< Keep HTTP header (see limitations) */
- /*fHTTP_UrlEncodeArgs = 0x8, URL-encode "info->args" (w/o fragment)*/
- fHTTP_UrlDecodeInput = 0x10, /**< URL-decode response body */
- fHTTP_UrlEncodeOutput = 0x20, /**< URL-encode all output data */
- fHTTP_UrlCodec = 0x30, /**< fHTTP_UrlDecodeInput | ...EncodeOutput*/
+ /*fHTTP_UrlEncodeArgs = 0x8, URL-encode "info->args" (w/o fragment)
+ fHTTP_UrlDecodeInput = 0x10, URL-decode response body
+ fHTTP_UrlEncodeOutput = 0x20, URL-encode all output data
+ fHTTP_UrlCodec = 0x30, fHTTP_UrlDecodeInput | ...EncodeOutput*/
fHTTP_NoUpread = 0x40, /**< Do not use SOCK_SetReadOnWrite() */
fHTTP_DropUnread = 0x80, /**< Each microsession drops unread data */
fHTTP_NoAutoRetry = 0x100,/**< No auto-retries allowed */
@@ -129,10 +129,10 @@ typedef enum {
fHCC_AutoReconnect = fHTTP_AutoReconnect,
fHCC_SureFlush = fHTTP_Flushable,
fHCC_KeepHeader = fHTTP_KeepHeader,
- fHCC_UrlDecodeInput = fHTTP_UrlDecodeInput,
- fHCC_UrlEncodeOutput = fHTTP_UrlEncodeOutput,
- fHCC_UrlCodec = fHTTP_UrlCodec,
fHCC_UrlEncodeArgs = 0x8, /**< NB: Error-prone semantics, do not use!*/
+ fHCC_UrlDecodeInput = 0x10, /**< Obsolete, may not work, do not use! */
+ fHCC_UrlEncodeOutput = 0x20, /**< Obsolete, may not work, do not use! */
+ fHCC_UrlCodec = 0x30, /**< fHCC_UrlDecodeInput | ...EncodeOutput */
fHCC_DropUnread = fHTTP_DropUnread,
fHCC_NoUpread = fHTTP_NoUpread,
fHCC_Flushable = fHTTP_Flushable,
diff --git a/c++/include/connect/ncbi_http_session.hpp b/c++/include/connect/ncbi_http_session.hpp
index 7604048..5bb0a62 100644
--- a/c++/include/connect/ncbi_http_session.hpp
+++ b/c++/include/connect/ncbi_http_session.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_HTTP_SESSION__HPP
#define CONNECT___NCBI_HTTP_SESSION__HPP
-/* $Id: ncbi_http_session.hpp 441068 2014-07-19 17:16:33Z lavr $
+/* $Id: ncbi_http_session.hpp 465171 2015-04-17 15:05:33Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,11 +34,7 @@
*
*/
-#include <corelib/ncbistd.hpp>
-#include <corelib/ncbitime.hpp>
-#include <corelib/ncbi_url.hpp>
#include <corelib/ncbi_cookies.hpp>
-#include <connect/connect_export.h>
#include <connect/ncbi_conn_stream.hpp>
@@ -51,12 +47,66 @@
BEGIN_NCBI_SCOPE
+// Forward declarations for shortcut functions.
+class CHttpResponse;
+class CHttpHeaders;
+
+
+// Default retries value.
+struct SGetHttpDefaultRetries
+{
+ unsigned short operator()(void) const;
+};
+
+/// Nullable retries for CHttpRequest
+typedef CNullable<unsigned short, SGetHttpDefaultRetries> THttpRetries;
+
+
+/// Shortcut for GET request. Each request uses a separate session,
+/// no data like cookies is shared between multiple requests.
+/// @sa CHttpSession::Get()
+NCBI_XCONNECT_EXPORT
+CHttpResponse g_HttpGet(const CUrl& url,
+ const CTimeout& timeout = CTimeout(CTimeout::eDefault),
+ THttpRetries retries = null);
+
+/// Shortcut for GET request with custom headers. Each request uses a separate
+/// session, no data like cookies is shared between multiple requests.
+/// @sa CHttpSession::Get()
+NCBI_XCONNECT_EXPORT
+CHttpResponse g_HttpGet(const CUrl& url,
+ const CHttpHeaders& headers,
+ const CTimeout& timeout = CTimeout(CTimeout::eDefault),
+ THttpRetries retries = null);
+
+/// Shortcut for POST request. Each request uses a separate session,
+/// no data like cookies is shared between multiple requests.
+/// @sa CHttpSession::Post()
+NCBI_XCONNECT_EXPORT
+CHttpResponse g_HttpPost(const CUrl& url,
+ CTempString data,
+ CTempString content_type = kEmptyStr,
+ const CTimeout& timeout = CTimeout(CTimeout::eDefault),
+ THttpRetries retries = null);
+
+/// Shortcut for POST request with custom headers. Each request uses a separate
+/// session, no data like cookies is shared between multiple requests.
+/// @sa CHttpSession::Post()
+NCBI_XCONNECT_EXPORT
+CHttpResponse g_HttpPost(const CUrl& url,
+ const CHttpHeaders& headers,
+ CTempString data,
+ CTempString content_type = kEmptyStr,
+ const CTimeout& timeout = CTimeout(CTimeout::eDefault),
+ THttpRetries retries = null);
+
class CHttpSession;
class NCBI_XCONNECT_EXPORT CHttpHeaders : public CObject
{
public:
+ /// Create empty headers list.
CHttpHeaders(void) {}
/// Some standard HTTP headers.
@@ -155,7 +205,7 @@ private:
public:
/// Parse headers from the string (usually provided by a stream callback).
/// The new headers are added to the existing ones.
- void ParseHttpHeader(const char* header);
+ void ParseHttpHeader(const CTempString& headers);
/// Get all headers as a single string as required by CConn_HttpStream.
/// Each header line is terminated by a single HTTP_EOL.
@@ -202,6 +252,8 @@ public:
/// @param value
/// Value for the input. If the form content type is eFormUrlEncoded,
/// the value will be URL encoded properly. Otherwise the value is sent as-is.
+ /// URL-encoded form data allows only one value per entry, otherwise
+ /// exception will be thrown when sending the data.
/// @param content_type
/// Content type for the entry used if the form content type is
/// eMultipartFormData. If not set, the protocol assumes 'text/plain'
@@ -345,13 +397,12 @@ private:
CHttpStreamRef(void) {}
virtual ~CHttpStreamRef(void) {}
bool IsInitialized(void) const { return m_ConnStream.get() ? true : false; }
- CConn_HttpStream& GetConnStream(void) const { return *m_ConnStream; }
- void SetConnStream(CConn_HttpStream* stream) { m_ConnStream.reset(stream); }
+ CConn_IOStream& GetConnStream(void) const { return *m_ConnStream; }
+ void SetConnStream(CConn_IOStream* stream) { m_ConnStream.reset(stream); }
private:
CHttpStreamRef(const CHttpStreamRef&);
CHttpStreamRef& operator=(const CHttpStreamRef&);
- // SConnNetInfo must be stored here to be destroyed using proper function.
- auto_ptr<CConn_HttpStream> m_ConnStream;
+ auto_ptr<CConn_IOStream> m_ConnStream;
};
CHttpResponse(CHttpSession& session, const CUrl& url, CHttpStreamRef& stream);
@@ -370,13 +421,6 @@ private:
};
-struct SGetHttpDefaultRetries
-{
- unsigned short operator()(void) const;
-};
-
-typedef CNullable<unsigned short, SGetHttpDefaultRetries> THttpRetries;
-
/// HTTP request
class NCBI_XCONNECT_EXPORT CHttpRequest
{
@@ -531,25 +575,6 @@ private:
};
-/// Shortcut for GET request. Each request uses a separate session,
-/// no data like cookies is shared between multiple requests.
-/// @sa CHttpSession::Get()
-NCBI_XCONNECT_EXPORT
-CHttpResponse g_HttpGet(const CUrl& url,
- const CTimeout& timeout = CTimeout(CTimeout::eDefault),
- THttpRetries retries = null);
-
-/// Shortcut for POST request. Each request uses a separate session,
-/// no data like cookies is shared between multiple requests.
-/// @sa CHttpSession::Post()
-NCBI_XCONNECT_EXPORT
-CHttpResponse g_HttpPost(const CUrl& url,
- CTempString data,
- CTempString content_type = kEmptyStr,
- const CTimeout& timeout = CTimeout(CTimeout::eDefault),
- THttpRetries retries = null);
-
-
/////////////////////////////////////////////////////////////////////////////
///
/// CHttpSessionException --
diff --git a/c++/include/connect/ncbi_namedpipe.hpp b/c++/include/connect/ncbi_namedpipe.hpp
index 3347164..cf6de52 100644
--- a/c++/include/connect/ncbi_namedpipe.hpp
+++ b/c++/include/connect/ncbi_namedpipe.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_NAMEDPIPE__HPP
#define CONNECT___NCBI_NAMEDPIPE__HPP
-/* $Id: ncbi_namedpipe.hpp 450563 2014-10-28 15:19:24Z ivanov $
+/* $Id: ncbi_namedpipe.hpp 445730 2014-09-08 13:17:51Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/connect/ncbi_namedpipe_connector.hpp b/c++/include/connect/ncbi_namedpipe_connector.hpp
index a4646c5..705210f 100644
--- a/c++/include/connect/ncbi_namedpipe_connector.hpp
+++ b/c++/include/connect/ncbi_namedpipe_connector.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_NAMEDPIPE_CONNECTOR__HPP
#define CONNECT___NCBI_NAMEDPIPE_CONNECTOR__HPP
-/* $Id: ncbi_namedpipe_connector.hpp 355977 2012-03-09 17:47:12Z lavr $
+/* $Id: ncbi_namedpipe_connector.hpp 447122 2014-09-22 18:33:27Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -52,18 +52,13 @@
BEGIN_NCBI_SCOPE
-/* Create new CONNECTOR structure to handle a data transfer between two
- * processes over named pipe. Return NULL on error.
- *
- */
-
/// Create CNamedPipe-based CONNECTOR.
///
/// Create new CONNECTOR structure to handle a data transfer between two
/// process over nemed pipe. Return NULL on error.
extern NCBI_XCONNECT_EXPORT CONNECTOR NAMEDPIPE_CreateConnector
(const string& pipename,
- size_t pipebufsize = 0 /** use default */
+ size_t pipesize = 0/**< use default */
);
diff --git a/c++/include/connect/ncbi_pipe.hpp b/c++/include/connect/ncbi_pipe.hpp
index 454dadc..0d85f02 100644
--- a/c++/include/connect/ncbi_pipe.hpp
+++ b/c++/include/connect/ncbi_pipe.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_PIPE__HPP
#define CONNECT___NCBI_PIPE__HPP
-/* $Id: ncbi_pipe.hpp 450563 2014-10-28 15:19:24Z ivanov $
+/* $Id: ncbi_pipe.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,10 +39,8 @@
///
/// Implemented for: UNIX, MS-Windows
-#include <corelib/ncbistre.hpp>
#include <corelib/ncbi_process.hpp>
#include <connect/ncbi_core_cxx.hpp>
-#include <vector>
#if !defined(NCBI_OS_MSWIN) && !defined(NCBI_OS_UNIX)
# error "Class CPipe is only supported on Windows and Unix"
@@ -395,7 +393,8 @@ public:
/// after the Watch() method has returned.
enum EAction {
eContinue, ///< Continue running
- eStop ///< Kill the child process and exit
+ eStop, ///< Kill the child process and exit
+ eExit ///< Exit without waiting for the child process
};
virtual ~IProcessWatcher();
diff --git a/c++/include/connect/ncbi_pipe_connector.hpp b/c++/include/connect/ncbi_pipe_connector.hpp
index 4f45683..270e052 100644
--- a/c++/include/connect/ncbi_pipe_connector.hpp
+++ b/c++/include/connect/ncbi_pipe_connector.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_PIPE_CONNECTOR__HPP
#define CONNECT___NCBI_PIPE_CONNECTOR__HPP
-/* $Id: ncbi_pipe_connector.hpp 337342 2011-09-11 01:13:46Z lavr $
+/* $Id: ncbi_pipe_connector.hpp 447122 2014-09-22 18:33:27Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,9 +59,10 @@ BEGIN_NCBI_SCOPE
extern NCBI_XCONNECT_EXPORT CONNECTOR PIPE_CreateConnector
(const string& cmd,
const vector<string>& args,
- CPipe::TCreateFlags create_flags = 0,
- CPipe* pipe = 0,
- EOwnership own_pipe = eTakeOwnership
+ CPipe::TCreateFlags flags = 0,
+ CPipe* pipe = 0,
+ EOwnership own_pipe = eTakeOwnership, /**< only if "pipe" given */
+ size_t pipe_size = 0 /**< use default */
);
diff --git a/c++/include/connect/ncbi_sendmail.h b/c++/include/connect/ncbi_sendmail.h
index 903bc0f..0a06a57 100644
--- a/c++/include/connect/ncbi_sendmail.h
+++ b/c++/include/connect/ncbi_sendmail.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SENDMAIL__H
#define CONNECT___NCBI_SENDMAIL__H
-/* $Id: ncbi_sendmail.h 403426 2013-06-14 15:40:06Z lavr $
+/* $Id: ncbi_sendmail.h 455154 2014-12-23 16:33:41Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,8 +56,8 @@ enum ESendMailOption {
fSendMail_LogOff = eOff, /**< fSOCK_LogDefault */
fSendMail_NoMxHeader = (1 << 4), /**< Don't add standard mail header,
just use what user provided */
- fSendMail_Old822Headers = (1 << 6), /**< Do not form "Date:" and "From:"
- but let them be defaulted */
+ fSendMail_Old822Headers = (1 << 6), /**< Form "Date:" and "From:" hdrs
+ (usually they are defaulted) */
fSendMail_StripNonFQDNHost = (1 << 8), /**< Strip host part off the "from"
field if it does not look like
an FQDN (i.e. does not have at
@@ -86,14 +86,14 @@ typedef struct {
/** Initialize SSendMailInfo structure, setting:
* 'cc', 'bcc', 'header' to NULL (means no recipients/additional headers);
- * 'from' filled out using either the provided (non-empty) user name
- * or the name of the current user if discovered, 'anonymous'
- * otherwise, and host in the form: username at hostname; may be later
- * reset by the application to "" for sending no-return messages
- * (aka MAILER-DAEMON messages);
+ * 'from' filled out with a return address using either the provided
+ * (non-empty) user name or the name of the current user if
+ * discoverable ("anonymous" otherwise), and the host, in the form:
+ * "username at hostname"; that may later be reset by the application
+ * to "" for sending no-return messages (aka MAILER-DAEMON messages);
* 'mx_*' filled out in accordance with some hard-coded defaults, which are
- * very NCBI-specific; an outside application is likely to choose and
- * use different values (at least for mx_host).
+ * rather NCBI-specific; an outside application is likely to choose
+ * and use different values (at least for 'mx_host').
* The mx_... fields can be configured via the registry file at
* [CONN]MX_HOST, [CONN]MX_PORT, and [CONN]MX_TIMEOUT, as well as
* through their process environment equivalents (which have higher
@@ -105,16 +105,16 @@ typedef struct {
* A pointer to the structure to initialize
* @param from
* Return address pattern to use in 'info->from' as the following:
- * * "user at host" or "user" is copied verbatim;
+ * * "user at host" or "user" is copied verbatim (as-is);
* * "user@" is appended with the local host name;
- * * "@host" is prepended with the user name according to the "user" argument;
- * * "@" is replaced with an empty string (no-return message);
+ * * "@host" is prepended with the user name according to the 'user' argument;
+ * * "@" is replaced with an empty string (for no-return messages);
* * "" or NULL cause to generate both the user and the host parts.
* @param user
- * Which username to use when auto-generating (otherwise ignored)
+ * Which username to use when auto-generating (ignored otherwise)
* @return
* Return value equals the argument 'info' passed in.
- * @note It is allowed to pre-fill "'info->from' (of the 'info' being inited)
+ * @note It is allowed to pre-fill 'info->from' (of the 'info' being inited)
* with one of the above patterns, and pass it as the 'from' parameter.
* @note Unlike the username part of the return address, the hostname part is
* never truncated but dropped altogether if it does not fit.
@@ -153,9 +153,9 @@ extern NCBI_XCONNECT_EXPORT SSendMailInfo* SendMailInfo_InitEx
* SendMailInfo_InitEx, CORE_SendMailEx
*/
extern NCBI_XCONNECT_EXPORT const char* CORE_SendMail
-(const char* to,
- const char* subject,
- const char* body
+(const char* to,
+ const char* subject,
+ const char* body
);
/** Send a message as in CORE_SendMail() but by explicitly specifying all
diff --git a/c++/include/connect/ncbi_server_info.h b/c++/include/connect/ncbi_server_info.h
index 1f11828..05a15c5 100644
--- a/c++/include/connect/ncbi_server_info.h
+++ b/c++/include/connect/ncbi_server_info.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SERVER_INFO__H
#define CONNECT___NCBI_SERVER_INFO__H
-/* $Id: ncbi_server_info.h 430180 2014-03-24 17:35:34Z lavr $
+/* $Id: ncbi_server_info.h 451391 2014-11-06 15:31:05Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -72,23 +72,36 @@ typedef enum {
} ESERV_Type;
-/* Algos to specify an algorithm for selecting the most preferred server from
+/* Flag to specify an algorithm for selecting the most preferred server from
* a set of available servers (NB: binary properties of the enumerated values
* may be in use!). Should have been named ESERV_Algo, but since it's now
* adding the "Inter" feature (also misplaced, and to be moved away to the part
* of "locl" area, the mis-name is still retained.
*/
typedef enum {
- eSERV_Regular = 0, /* Server either tied up to lavg or static */
- eSERV_Blast = 1, /* Server is tied up to an instant host load */
- eSERV_RegularInter = 2, /* Regular server shared between LBSM domains */
- eSERV_BlastInter = 3, /* ... same for Blast-type server */
+ eSERV_Regular = 0, /* Server either tied up to lavg or static */
+ eSERV_Blast = 1, /* Server is tied up to an instant host load */
+ eSERV_RegularInter = 2, /* Regular server shared between LBSM zones */
+ eSERV_BlastInter = 3, /* ... same for Blast-type server */
/* compatibility only, deprecated */
fSERV_Regular = eSERV_Regular,
fSERV_Blast = eSERV_Blast
} ESERV_Flag;
+typedef enum {
+ fSERV_Stateful = 1,
+ fSERV_Secure = 2
+} ESERV_Mode;
+
+
+typedef enum {
+ fSERV_Local = 1,
+ fSERV_Private = 2,
+ fSERV_SiteMask = 0xF0
+} ESERV_Site;
+
+
/* Verbal representation of a server type (no internal spaces allowed)
*/
extern NCBI_XCONNECT_EXPORT const char* SERV_TypeStr
@@ -149,8 +162,8 @@ typedef struct {
ESERV_Type type; /* type of server */
unsigned int host; /* host the server running on, network b.o. */
unsigned short port; /* port the server running on, host b.o. */
- unsigned char/*bool*/ sful; /* true for stateful-only server (default=no)*/
- unsigned char/*bool*/ locl; /* true for local (LBSMD-only) server(def=no)*/
+ unsigned char mode; /* connection mode (stateful, secure, etc) */
+ unsigned char site; /* site info (LSB: local, private; MSB: @#) */
TNCBI_Time time; /* relaxation period / expiration time */
double coef; /* bonus coefficient for server run locally */
double rate; /* rate of the server */
@@ -158,8 +171,7 @@ typedef struct {
EMIME_SubType mime_s; /* subtype, */
EMIME_Encoding mime_e; /* and encoding for content-type */
ESERV_Flag flag; /* rate algorithm for the server (NB: algo!) */
- unsigned char reserved[14]; /* zeroed reserved area - do not use! */
- unsigned short quorum; /* quorum required to override this entry */
+ unsigned char reserved[16]; /* zeroed reserved area - do not use! */
USERV_Info u; /* server type-specific data/params */
} SSERV_Info;
@@ -217,7 +229,7 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
*
* Server-specific parameters:
*
- * Standalone servers: None
+ * STANDALONE servers: None
* Servers of this type do not take any arguments.
*
* NCBID servers: Arguments to CGI in addition to specified by application.
@@ -259,7 +271,7 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
* of locally run servers).
* Negative value denotes that locally run server should be taken
* in the first place, regardless of its rate, if that rate
- * is as large as the percent (expressed by the absolute value
+ * is as large as the percentage (expressed by the absolute value
* of this coefficient) of the average rate coefficient of other
* servers for the same service. In other words, -5 instructs to
* ignore locally run server only if its rate is less than 5% of
@@ -291,16 +303,6 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
* 'P=no' in verbal representation resulted from SERV_WriteInfo().
* This tag is not allowed in DNS server specifications.
*
- * Quorum:
- * Q=integer [0 = default]
- * specifies how many dynamic service entries have to be defined
- * by respective hosts in order for this entry to be INACTIVE.
- * Note that value 0 disables the quorum and the entry becomes
- * effective immediately. The quorum flag is to create a standby
- * configuration, which is to be activated in case of either server
- * or network malfunction. Use of this flag is not encouraged.
- * Only static and non-FIREWALL server specs can have this tag.
- *
* Reachability base rate:
* R=double [0.0 = default]
* specifies availability rate for the server, expressed as
@@ -321,9 +323,9 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
* Values less than 0.01 define standby server entries, which are
* used by the clients only if there are no working entries with a
* higher initial rate available. Standby entries are not governed
- * by the host load but servers are used up according to the values
- * of rates in descending order (for same-rate entries, an entry is
- * taken at random).
+ * by the host load but are used up according to the values of rates
+ * in descending order (for same-rate entries, an entry is taken at
+ * random).
*
* Stateful server:
* S=no (default)
@@ -332,6 +334,12 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
* bearing, dedicated socket (stateful) connections.
* This tag is not allowed for HTTP* and DNS servers.
*
+ * Secure connection:
+ * $=no (default)
+ * $=yes
+ * indicates that connection to the server must be made over a secure
+ * protocol (HTTPS or SSL).
+ *
* Validity period:
* T=integer [0 = default]
* specifies the time in seconds that this server entry is valid for
@@ -340,7 +348,7 @@ extern NCBI_XCONNECT_EXPORT char* SERV_WriteInfo
*
*
* Note that optional arguments can be omitted along with all preceding
- * optional arguments, that is the following 2 server specifications are
+ * optional arguments; that is, the following 2 server specifications are
* both valid:
*
* NCBID ''
diff --git a/c++/include/connect/ncbi_service.h b/c++/include/connect/ncbi_service.h
index f4ebf34..d367094 100644
--- a/c++/include/connect/ncbi_service.h
+++ b/c++/include/connect/ncbi_service.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SERVICE__H
#define CONNECT___NCBI_SERVICE__H
-/* $Id: ncbi_service.h 440975 2014-07-18 16:15:14Z lavr $
+/* $Id: ncbi_service.h 451379 2014-11-06 15:07:53Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -79,7 +79,7 @@ enum ESERV_TypeSpecial {
fSERV_Any = 0,
fSERV_All = 0x0000FFFF,
fSERV_Stateless = 0x00100000, /**< Stateless servers only */
- fSERV_Reserved = 0x00200000, /**< Reserved, MBZ */
+ fSERV_Reserved = 0x00400000,
fSERV_ReverseDns = 0x00800000, /**< LB-DNS translation */
/* The following allow to get currently inactive service instances */
fSERV_IncludeDown = 0x08000000,
diff --git a/c++/include/connect/ncbi_service_connector.h b/c++/include/connect/ncbi_service_connector.h
index 8c1933d..223380d 100644
--- a/c++/include/connect/ncbi_service_connector.h
+++ b/c++/include/connect/ncbi_service_connector.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SERVICE_CONNECTOR__H
#define CONNECT___NCBI_SERVICE_CONNECTOR__H
-/* $Id: ncbi_service_connector.h 354443 2012-02-27 15:07:20Z lavr $
+/* $Id: ncbi_service_connector.h 464976 2015-04-15 18:27:40Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,17 +51,18 @@ extern "C" {
#endif
-typedef void (*FSERVICE_ResetData) (void* data);
-typedef void (*FSERVICE_CleanupData)(void* data);
+typedef void (*FSERVICE_Reset) (void* data);
+typedef void (*FSERVICE_Cleanup) (void* data);
typedef const SSERV_Info* (*FSERVICE_GetNextInfo)(void* data, SERV_ITER iter);
typedef struct {
void* data; /* User-supplied callback data */
- FSERVICE_ResetData reset; /* Called prior to each iter reset */
- FSERVICE_CleanupData cleanup; /* Called prior to connector close */
- FSERVICE_GetNextInfo get_next_info; /* Called to get conn point */
- FHTTP_ParseHeader parse_header; /* Called if data source is HTTP */
+ FSERVICE_Reset reset; /* Called prior to each iter reset */
+ FHTTP_Adjust adjust; /* Called when data source is HTTP(S)*/
+ FSERVICE_Cleanup cleanup; /* Called prior to connector destroy */
+ FHTTP_ParseHeader parse_header; /* Called when data source is HTTP(S)*/
+ FSERVICE_GetNextInfo get_next_info; /* Called to get connection point */
THTTP_Flags flags; /* fHTTP_Flushable|fHTTP_NoAutoRetry */
} SSERVICE_Extra;
@@ -70,7 +71,7 @@ extern NCBI_XCONNECT_EXPORT CONNECTOR SERVICE_CreateConnectorEx
(const char* service,
TSERV_Type types,
const SConnNetInfo* net_info,
- const SSERVICE_Extra* params
+ const SSERVICE_Extra* extra
);
#define SERVICE_CreateConnector(service) \
diff --git a/c++/include/connect/ncbi_socket.h b/c++/include/connect/ncbi_socket.h
index 7a9b453..b27c371 100644
--- a/c++/include/connect/ncbi_socket.h
+++ b/c++/include/connect/ncbi_socket.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SOCKET__H
#define CONNECT___NCBI_SOCKET__H
-/* $Id: ncbi_socket.h 426322 2014-02-07 17:27:10Z lavr $
+/* $Id: ncbi_socket.h 464049 2015-04-03 14:32:14Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -74,7 +74,7 @@
* SOCK_GetTimeout
* SOCK_Read (including "peek" and "persistent read")
* SOCK_ReadLine
- * SOCK_PushBack
+ * SOCK_Pushback
* SOCK_Status
* SOCK_Write
* SOCK_Abort
@@ -636,9 +636,9 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Create
* When a socket gets created on top of a "SOCK" handle, the original SOCK gets
* always emptied (the underlying OS handle removed from it) upon the call
* returns: either the handle gets migrated to the new socket just created,
- * or it gets closed unconditionally of the fSOCK_KeepOnClose flag in the
+ * or it gets closed unconditionally by the fSOCK_KeepOnClose flag in the
* original socket. In either case, the original SOCK will still need
- * SOCK_Close() in the caller's code to free up the memory it occupies.
+ * SOCK_Destroy() in the caller's code to free up the memory it occupies.
* Any secure session that may have existed in the original SOCK will have
* been terminated (and new session may have been initiated in the new SOCK --
* at this time the old session is not allowed to "migrate").
@@ -961,10 +961,11 @@ extern NCBI_XCONNECT_EXPORT const STimeout* SOCK_GetTimeout
* then return eIO_Timeout.
*
* Both eIO_ReadPlain and eIO_ReadPeek return eIO_Success iff some data have
- * been read (perhaps within the time allowance specified by eIO_Read timeout).
- * Both mothods return any other code when no data at all were available.
- * eIO_ReadPersist differs from the other two methods as it can return an
- * error condition even if some data were actually obtained from the socket.
+ * been actually read (within the time allotted by the eIO_Read timeout).
+ * Both methods return any other code when no data at all were available.
+ * In that respect, eIO_ReadPersist differs from the other two methods as it
+ * can return an error condition even if some (but not all) data were actually
+ * obtained from the socket.
*
* Hence, as the *rule of thumb*, an application should always check the number
* of read bytes BEFORE checking the return status, which merely advises as to
@@ -976,13 +977,13 @@ extern NCBI_XCONNECT_EXPORT const STimeout* SOCK_GetTimeout
* eIO_Read[Persist] -- discard up to "size" bytes from internal buffer
* and socket (check "*n_read" to know how many).
*
- * @note "Read" and "peek" methods differ: if "read" is
- * performed and not enough but only some data available immediately
- * from the internal buffer, then the call still completes with
- * eIO_Success status. For "peek", if not all requested data were
- * available, the real I/O occurs to pick up additional data (if any)
- * from the system. Keep this difference in mind when programming
- * loops that heavily use "peek"s without "read"s.
+ * @note "Read" and "peek" methods differ: when "read" is performed and not
+ * enough but only some data are available immediately from the internal
+ * buffer, then the call still completes with the eIO_Success status.
+ * For "peek", if not all requested data were available right away, the
+ * real I/O occurs to try to pick up additional data from the system.
+ * Keep this difference in mind when programming loops that heavily use
+ * "peek"s without "read"s.
* @note If on input "size" == 0, then "*n_read" is set to 0,
* and the return value can be either of eIO_Success, eIO_Closed or
* eIO_Unknown depending on connection status of the socket.
@@ -1037,6 +1038,8 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_ReadLine
);
+#define SOCK_PushBack SOCK_Pushback
+
/** Push the specified data back to the socket input queue (in the socket's
* internal read buffer). These can be any data, not necessarily the data
* previously read from the socket.
@@ -1047,7 +1050,7 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_ReadLine
* @param size
* [in] # of bytes (starting at "buf") to push back
*/
-extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_PushBack
+extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Pushback
(SOCK sock,
const void* buf,
size_t size
diff --git a/c++/include/connect/ncbi_socket.hpp b/c++/include/connect/ncbi_socket.hpp
index aac3290..c9550ef 100644
--- a/c++/include/connect/ncbi_socket.hpp
+++ b/c++/include/connect/ncbi_socket.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SOCKET__HPP
#define CONNECT___NCBI_SOCKET__HPP
-/* $Id: ncbi_socket.hpp 424666 2014-01-17 22:01:17Z lavr $
+/* $Id: ncbi_socket.hpp 463901 2015-04-02 00:32:02Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -295,8 +295,8 @@ public:
/// @param size
///
/// @sa
- /// SOCK_PushBack
- EIO_Status PushBack(const void* buf,
+ /// SOCK_Pushback
+ EIO_Status Pushback(const void* buf,
size_t size);
/// Write to socket.
@@ -869,9 +869,9 @@ inline EIO_Status CSocket::ReadLine(char* buf, size_t size, size_t* n_read)
}
-inline EIO_Status CSocket::PushBack(const void* buf, size_t size)
+inline EIO_Status CSocket::Pushback(const void* buf, size_t size)
{
- return m_Socket ? SOCK_PushBack(m_Socket, buf, size) : eIO_Closed;
+ return m_Socket ? SOCK_Pushback(m_Socket, buf, size) : eIO_Closed;
}
diff --git a/c++/include/connect/ncbi_types.h b/c++/include/connect/ncbi_types.h
index ea6d4ed..80e4853 100644
--- a/c++/include/connect/ncbi_types.h
+++ b/c++/include/connect/ncbi_types.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_TYPES__H
#define CONNECT___NCBI_TYPES__H
-/* $Id: ncbi_types.h 437570 2014-06-06 17:54:54Z lavr $
+/* $Id: ncbi_types.h 445734 2014-09-08 13:43:28Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -78,8 +78,8 @@ typedef struct STimeoutTag {
unsigned int usec; /**< microseconds (modulo 1,000,000) */
} STimeout;
-#define kDefaultTimeout ((const STimeout*)(-1))
-#define kInfiniteTimeout ((const STimeout*)( 0))
+#define kDefaultTimeout ((const STimeout*)(-1))
+#define kInfiniteTimeout ((const STimeout*)( 0))
extern NCBI_XCONNECT_EXPORT unsigned long NcbiTimeoutToMs
diff --git a/c++/include/connect/ncbi_util.h b/c++/include/connect/ncbi_util.h
index 5930c3e..7fd08e3 100644
--- a/c++/include/connect/ncbi_util.h
+++ b/c++/include/connect/ncbi_util.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_UTIL__H
#define CONNECT___NCBI_UTIL__H
-/* $Id: ncbi_util.h 449177 2014-10-14 13:58:55Z ivanov $
+/* $Id: ncbi_util.h 459572 2015-02-19 18:21:38Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -596,7 +596,7 @@ extern NCBI_XCONNECT_EXPORT char* UTIL_NcbiLocalHostName
/** Calculate size of buffer needed to store printable representation of the
* block of data of the specified size (or, if size is 0, strlen(data)).
- * NOTE: The calculated size does not include terminating '\0'.
+ * NOTE: The calculated size does not account for a terminating '\0'.
* @param data
* Block of data (NULL causes 0 to return regardless of "size")
* @param size
diff --git a/c++/include/connect/services/clparser.hpp b/c++/include/connect/services/clparser.hpp
index 885c9ad..5298ffe 100644
--- a/c++/include/connect/services/clparser.hpp
+++ b/c++/include/connect/services/clparser.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__CLI__HPP
#define CONNECT_SERVICES__CLI__HPP
-/* $Id: clparser.hpp 365230 2012-06-04 18:34:24Z kazimird $
+/* $Id: clparser.hpp 461660 2015-03-11 18:47:49Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -85,7 +85,8 @@ class NCBI_XCONNECT_EXPORT CCommandLineParser
void AddAssociation(int cmd_id, int opt_id);
- /// Parse the command line.
+ /// Parse the command line. Print program version or the help screen
+ /// if requested by the command line arguments.
/// @return One of the command identifiers or -1 if the requested
/// command is either help or version command, in which
/// case it has been already processed by this method, and
diff --git a/c++/include/connect/services/compound_id.hpp b/c++/include/connect/services/compound_id.hpp
index c3f8d2a..9429ed9 100644
--- a/c++/include/connect/services/compound_id.hpp
+++ b/c++/include/connect/services/compound_id.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__COMPOUND_ID__HPP
#define CONNECT_SERVICES__COMPOUND_ID__HPP
-/* $Id: compound_id.hpp 431243 2014-04-02 15:31:07Z kazimird $
+/* $Id: compound_id.hpp 458824 2015-02-10 17:42:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,6 +51,7 @@ enum ECompoundIDClass {
eCIC_GenericID,
eCIC_NetCacheBlobKey,
eCIC_NetScheduleJobKey,
+ eCIC_NetStorageObjectLocV1, ///< Old version of NetStorageObjectLoc
eCIC_NetStorageObjectLoc,
eCIC_NumberOfClasses
@@ -303,7 +304,7 @@ class NCBI_XCONNECT_EXPORT CCompoundID
///
class NCBI_XCONNECT_EXPORT CCompoundIDPool
{
- NCBI_NET_COMPONENT_WITH_DEFAULT_CTOR(CompoundIDPool);
+ NCBI_NET_COMPONENT_IMPL(CompoundIDPool);
/// Construct a new pool of CompoundID objects.
CCompoundIDPool();
diff --git a/c++/include/connect/services/grid_client.hpp b/c++/include/connect/services/grid_client.hpp
index 967175d..abffe55 100644
--- a/c++/include/connect/services/grid_client.hpp
+++ b/c++/include/connect/services/grid_client.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES_GRID__GRID_CLIENT__HPP
#define CONNECT_SERVICES_GRID__GRID_CLIENT__HPP
-/* $Id: grid_client.hpp 373582 2012-08-30 18:29:40Z kazimird $
+/* $Id: grid_client.hpp 470125 2015-06-11 14:18:05Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -296,6 +296,7 @@ private:
void x_ProlongBlobLifetime(const string& blob_key, unsigned ttl);
bool x_ProlongJobFieldLifetime(const string& job_field, unsigned ttl);
void x_RenewAllJobBlobs(time_t job_exptime);
+ bool x_CleanUpAllJobBlobs(CNetScheduleAPI::EJobStatus status);
void x_GetJobDetails();
size_t m_BlobSize;
diff --git a/c++/include/connect/services/grid_globals.hpp b/c++/include/connect/services/grid_globals.hpp
index d66c831..4ee4261 100644
--- a/c++/include/connect/services/grid_globals.hpp
+++ b/c++/include/connect/services/grid_globals.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___GRID_GLOBALS__HPP
#define CONNECT_SERVICES___GRID_GLOBALS__HPP
-/* $Id: grid_globals.hpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: grid_globals.hpp 443514 2014-08-14 21:35:38Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/connect/services/grid_worker.hpp b/c++/include/connect/services/grid_worker.hpp
index ca5fee8..bf3a0b2 100644
--- a/c++/include/connect/services/grid_worker.hpp
+++ b/c++/include/connect/services/grid_worker.hpp
@@ -2,7 +2,7 @@
#define CONNECT_SERVICES__GRID_WORKER_HPP
-/* $Id: grid_worker.hpp 452162 2014-11-17 15:23:48Z ivanov $
+/* $Id: grid_worker.hpp 455687 2015-01-02 17:47:12Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -340,19 +340,19 @@ class NCBI_XCONNECT_EXPORT CWorkerNodeJobContext
unsigned int GetJobNumber() const;
enum ECommitStatus {
- eDone,
- eFailure,
- eReturn,
- eRescheduled,
- eNotCommitted,
- eCanceled
+ eCS_Done,
+ eCS_Failure,
+ eCS_Return,
+ eCS_Reschedule,
+ eCS_NotCommitted,
+ eCS_JobIsLost
};
bool IsJobCommitted() const;
ECommitStatus GetCommitStatus() const;
static const char* GetCommitStatusDescription(ECommitStatus commit_status);
- bool IsCanceled() const;
+ bool IsJobLost() const;
IWorkerNodeCleanupEventSource* GetCleanupEventSource();
@@ -648,7 +648,7 @@ class NCBI_XCONNECT_EXPORT CGridWorkerNodeException : public CException
public:
enum EErrCode {
ePortBusy,
- eJobIsCanceled,
+ eJobIsLost,
eJobFactoryIsNotSet,
eExclusiveModeIsAlreadySet
};
@@ -658,7 +658,7 @@ public:
switch (GetErrCode())
{
case ePortBusy: return "ePortBusy";
- case eJobIsCanceled: return "eJobIsCanceled";
+ case eJobIsLost: return "eJobIsLost";
case eJobFactoryIsNotSet: return "eJobFactoryIsNotSet";
case eExclusiveModeIsAlreadySet: return "eExclusiveModeIsAlreadySet";
default: return CException::GetErrCodeString();
diff --git a/c++/include/connect/services/grid_worker_app.hpp b/c++/include/connect/services/grid_worker_app.hpp
index b0c7dde..7b8a1e0 100644
--- a/c++/include/connect/services/grid_worker_app.hpp
+++ b/c++/include/connect/services/grid_worker_app.hpp
@@ -2,7 +2,7 @@
#define CONNECT_SERVICES__GRID_WORKER_APP_HPP
-/* $Id: grid_worker_app.hpp 447462 2014-09-25 20:48:45Z kazimird $
+/* $Id: grid_worker_app.hpp 469237 2015-06-02 18:26:13Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -90,7 +90,7 @@ public:
/// if the worker node cannot be launched at this time.
/// The method is called from the Init() method of the
/// worker node application prior to daemonizing.
- virtual void OnInit(CNcbiApplication* app);
+ virtual void OnInit(CNcbiApplication*) {}
/// Notify that CGridWorkerNode::Run() is about to be executed.
/// This method can be overridden to implement worker node-
diff --git a/c++/include/connect/services/named_parameters.hpp b/c++/include/connect/services/named_parameters.hpp
index 9392dac..79b376c 100644
--- a/c++/include/connect/services/named_parameters.hpp
+++ b/c++/include/connect/services/named_parameters.hpp
@@ -1,4 +1,4 @@
-/* $Id: named_parameters.hpp 451452 2014-11-06 19:29:21Z ivanov $
+/* $Id: named_parameters.hpp 445235 2014-09-02 20:02:06Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/connect/services/netcache_admin.hpp b/c++/include/connect/services/netcache_admin.hpp
index f1fe5d6..ea821d6 100644
--- a/c++/include/connect/services/netcache_admin.hpp
+++ b/c++/include/connect/services/netcache_admin.hpp
@@ -1,7 +1,7 @@
#ifndef CONN___NETCACHE_ADMIN__HPP
#define CONN___NETCACHE_ADMIN__HPP
-/* $Id: netcache_admin.hpp 450571 2014-10-28 15:21:52Z ivanov $
+/* $Id: netcache_admin.hpp 450470 2014-10-27 18:24:02Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/connect/services/netcache_api.hpp b/c++/include/connect/services/netcache_api.hpp
index 55d9a98..c9e0a57 100644
--- a/c++/include/connect/services/netcache_api.hpp
+++ b/c++/include/connect/services/netcache_api.hpp
@@ -1,7 +1,7 @@
#ifndef CONN___NETCACHE_API__HPP
#define CONN___NETCACHE_API__HPP
-/* $Id: netcache_api.hpp 458672 2015-02-09 11:57:13Z kazimird $
+/* $Id: netcache_api.hpp 458433 2015-02-04 21:48:50Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -90,6 +90,11 @@ BEGIN_NCBI_SCOPE
/// @see CNetCacheAPI::TServerToUse
#define nc_server_to_use CNetCacheAPI::TServerToUse()
+/// Pointer to a variable for saving the CNetServer that was last used.
+/// Works only with (some of) CNetICacheClient methods.
+/// @see CNetCacheAPI::TServerLastUsedPtr
+#define nc_server_last_used CNetCacheAPI::TServerLastUsedPtr()
+
/// Do not read the blob if its age is greater than the specified value.
/// @see CNetCacheAPI::TMaxBlobAge
#define nc_max_age CNetCacheAPI::TMaxBlobAge()
@@ -103,10 +108,10 @@ BEGIN_NCBI_SCOPE
/// @see CNetCacheAPI::TUseCompoundID
#define nc_use_compound_id CNetCacheAPI::TUseCompoundID()
-/// Whether to run a request through all NetCache servers in the
-/// ICache service in an attempt to find the blob.
-/// @see CNetCacheAPI::TTryAllServers
-#define nc_try_all_servers CNetCacheAPI::TTryAllServers()
+/// When looking for an ICache blob, use only the most likely server
+/// to hold the blob; do not query other servers.
+/// @see CNetCacheAPI::TSingleServer
+#define nc_single_server CNetCacheAPI::TSingleServer()
/// In ICache mode, override the name of the cache specified
/// in the CNetICacheClient constructor.
@@ -212,10 +217,11 @@ class NCBI_XCONNECT_EXPORT CNetCacheAPI
eNPT_ServerCheckHint,
eNPT_Password,
eNPT_ServerToUse,
+ eNPT_ServerLastUsedPtr,
eNPT_MaxBlobAge,
eNPT_ActualBlobAgePtr,
eNPT_UseCompoundID,
- eNPT_TryAllServers,
+ eNPT_SingleServer,
eNPT_CacheName,
};
@@ -534,6 +540,16 @@ class NCBI_XCONNECT_EXPORT CNetCacheAPI
typedef CNamedParameter<CNetServer::TInstance,
eNPT_ServerToUse> TServerToUse;
+ /// Named parameter type to supply a pointer to a variable for saving
+ /// the CNetServer object that was last used. This parameter works
+ /// only with (some of) CNetICacheClient methods.
+ /// This type of parameter can be defined through the nc_server_last_used
+ /// macro substitution, for example:
+ /// nc_server_last_used = &netserver_object
+ /// @see nc_server_last_used
+ typedef CNamedParameter<CNetServer*,
+ eNPT_ServerLastUsedPtr> TServerLastUsedPtr;
+
/// Named parameter type to specify that the blob should not be read
/// if its age in seconds is greater than the specified value.
/// This type of parameter can be defined through the nc_max_age
@@ -558,13 +574,13 @@ class NCBI_XCONNECT_EXPORT CNetCacheAPI
/// @see nc_use_compound_id
typedef CNamedParameter<bool, eNPT_UseCompoundID> TUseCompoundID;
- /// Named parameter type to define whether to run a request through all
- /// NetCache servers in the ICache service in an attempt to find the blob.
+ /// Named parameter type to define whether to use only the most
+ /// likely server when looking for an ICache blob.
/// This type of parameter can be defined through the
- /// nc_try_all_servers macro substitution, for example:
- /// nc_try_all_servers = true
- /// @see nc_try_all_servers
- typedef CNamedParameter<bool, eNPT_TryAllServers> TTryAllServers;
+ /// nc_single_server macro substitution, for example:
+ /// nc_single_server = true
+ /// @see nc_single_server
+ typedef CNamedParameter<bool, eNPT_SingleServer> TSingleServer;
/// In ICache mode, override the name of the cache specified
/// in the CNetICacheClient constructor.
diff --git a/c++/include/connect/services/netcomponent.hpp b/c++/include/connect/services/netcomponent.hpp
index f70456a..7f47535 100644
--- a/c++/include/connect/services/netcomponent.hpp
+++ b/c++/include/connect/services/netcomponent.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__NET_OBJECT_HPP
#define CONNECT_SERVICES__NET_OBJECT_HPP
-/* $Id: netcomponent.hpp 353379 2012-02-15 16:24:52Z kazimird $
+/* $Id: netcomponent.hpp 458824 2015-02-10 17:42:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -74,7 +74,7 @@ public:
};
-#define NCBI_NET_COMPONENT_WITH_DEFAULT_CTOR(component) \
+#define NCBI_NET_COMPONENT_IMPL(component) \
protected: \
CRef<S##component##Impl, \
CNetComponentCounterLocker<S##component##Impl> > m_Impl; \
@@ -91,7 +91,7 @@ public:
C##component(EVoid /* create_void */) {}
#define NCBI_NET_COMPONENT(component) \
- NCBI_NET_COMPONENT_WITH_DEFAULT_CTOR(component) \
+ NCBI_NET_COMPONENT_IMPL(component) \
C##component() {}
END_NCBI_SCOPE
diff --git a/c++/include/connect/services/neticache_client.hpp b/c++/include/connect/services/neticache_client.hpp
index 424f778..b5bb9bc 100644
--- a/c++/include/connect/services/neticache_client.hpp
+++ b/c++/include/connect/services/neticache_client.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___NETICACHE_CLIENT__HPP
#define CONNECT_SERVICES___NETICACHE_CLIENT__HPP
-/* $Id: neticache_client.hpp 447467 2014-09-25 20:55:03Z kazimird $
+/* $Id: neticache_client.hpp 458824 2015-02-10 17:42:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -66,7 +66,7 @@ struct SNetICacheClientImpl;
///
class NCBI_NET_CACHE_EXPORT CNetICacheClient : public ICache
{
- NCBI_NET_COMPONENT_WITH_DEFAULT_CTOR(NetICacheClient);
+ NCBI_NET_COMPONENT_IMPL(NetICacheClient);
/// Defines how this object must be initialized.
enum EAppRegistry {
@@ -317,10 +317,6 @@ class NCBI_NET_CACHE_EXPORT CNetICacheClient : public ICache
/// Print meta information about the specified blob.
void PrintBlobInfo(const string& key, int version, const string& subkey);
- /// Return the server that this object is
- /// currently using for blob access.
- CNetServer GetCurrentServer();
-
CNetService GetService();
/// This method is for use by the grid_cli utility only.
diff --git a/c++/include/connect/services/netschedule_api.hpp b/c++/include/connect/services/netschedule_api.hpp
index c244890..d36fb5a 100644
--- a/c++/include/connect/services/netschedule_api.hpp
+++ b/c++/include/connect/services/netschedule_api.hpp
@@ -1,7 +1,7 @@
#ifndef CONN___NETSCHEDULE_API__HPP
#define CONN___NETSCHEDULE_API__HPP
-/* $Id: netschedule_api.hpp 451458 2014-11-06 19:31:25Z ivanov $
+/* $Id: netschedule_api.hpp 470759 2015-06-18 17:19:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -225,7 +225,14 @@ class NCBI_XCONNECT_EXPORT CNetScheduleAPI
CNetScheduleExecutor GetExecutor();
/// Create an instance of CNetScheduleJobReader.
- CNetScheduleJobReader GetJobReader();
+ ///
+ /// @param group
+ /// Restrict job retrieval to the specified job group name.
+ /// @param affinity
+ /// Restrict job retrieval to the specified affinity.
+ ///
+ CNetScheduleJobReader GetJobReader(const string& group = kEmptyStr,
+ const string& affinity = kEmptyStr);
CNetScheduleAdmin GetAdmin();
@@ -330,7 +337,7 @@ class NCBI_XCONNECT_EXPORT CNetScheduleAPI
///
struct CNetScheduleJob
{
- CNetScheduleJob(const string& _input = kEmptyStr,
+ explicit CNetScheduleJob(const string& _input = kEmptyStr,
const string& _affinity = kEmptyStr,
CNetScheduleAPI::TJobMask _mask = CNetScheduleAPI::eEmptyMask) :
input(_input),
@@ -355,6 +362,7 @@ struct CNetScheduleJob
progress_msg.erase();
group.erase();
auth_token.erase();
+ server = NULL;
}
// input parameters
@@ -383,6 +391,9 @@ struct CNetScheduleJob
string group;
string auth_token;
+
+ /// The server the job belongs to.
+ CNetServer server;
};
struct SNetScheduleSubmitterImpl;
@@ -727,17 +738,29 @@ class NCBI_XCONNECT_EXPORT CNetScheduleExecutor
/// cannot be found (job record has expired).
///
CNetScheduleAPI::EJobStatus GetJobStatus(
- const string& job_key,
+ const CNetScheduleJob& job,
time_t* job_exptime = NULL,
ENetScheduleQueuePauseMode* pause_mode = NULL);
- /// Switch the job back to the "Pending" status. It will be
+ NCBI_DEPRECATED
+ CNetScheduleAPI::EJobStatus GetJobStatus(
+ const string& job_key,
+ time_t* job_exptime = NULL,
+ ENetScheduleQueuePauseMode* pause_mode = NULL)
+ {
+ CNetScheduleJob job;
+ job.job_id = job_key;
+ return GetJobStatus(job, job_exptime, pause_mode);
+ }
+
+ /// Switch the job back to the "Pending" status so that it can be
/// run again on a different worker node.
///
- /// Node may decide to return the job if it cannot process it right
- /// now (does not have resources, being asked to shutdown, etc.)
+ /// The node may decide to return the job if it cannot be processed
+ /// at the moment (not enough resources, the node is shutting down,
+ /// etc.)
///
- void ReturnJob(const string& job_key, const string& auth_token);
+ void ReturnJob(const CNetScheduleJob& job);
/// Increment job execution timeout
///
@@ -749,7 +772,7 @@ class NCBI_XCONNECT_EXPORT CNetScheduleExecutor
/// @param runtime_inc
/// Estimated time in seconds(from the current moment) to
/// finish the job.
- void JobDelayExpiration(const string& job_key, unsigned runtime_inc);
+ void JobDelayExpiration(const CNetScheduleJob& job, unsigned runtime_inc);
/// Retrieve queue parameters from the server.
const CNetScheduleAPI::SServerParams& GetServerParams();
@@ -790,20 +813,24 @@ class NCBI_XCONNECT_EXPORT CNetScheduleJobReader
{
NCBI_NET_COMPONENT(NetScheduleJobReader);
- /// Restrict job retrieval to the specified job group name.
+ /// @deprecated
+ /// Use GetJobReader(group, ...) instead.
///
+ NCBI_DEPRECATED
void SetJobGroup(const string& group_name);
- /// Restrict job retrieval to the specified affinity.
+ /// @deprecated
+ /// Use GetJobReader(..., affinity) instead.
///
+ NCBI_DEPRECATED
void SetAffinity(const string& affinity);
/// Possible outcomes of ReadNextJob() calls.
enum EReadNextJobResult {
eRNJ_JobReady, ///< A job is returned.
- eRNJ_Timeout, ///< Operation has timed out.
- eRNJ_NoMoreJobs, ///< There are no more jobs matching
- ///< the requested criteria on the server.
+ eRNJ_NotReady, ///< No matching jobs are ready for reading.
+ eRNJ_Timeout = eRNJ_NotReady,
+ eRNJ_NoMoreJobs, ///< No matching jobs.
eRNJ_Interrupt, ///< ReadNextJob() has been interrupted.
};
@@ -824,12 +851,9 @@ class NCBI_XCONNECT_EXPORT CNetScheduleJobReader
/// @param timeout Timeout to wait for job completion.
/// If NULL, the method returns immediately.
///
- /// @return True if a completed job is returned. False if there
- /// are no more jobs matching the specified criteria.
- ///
EReadNextJobResult ReadNextJob(CNetScheduleJob* job,
CNetScheduleAPI::EJobStatus* job_status,
- CTimeout* timeout = NULL);
+ const CTimeout* timeout = NULL);
/// Abort waiting for a completed job in the above method.
/// Can be called from a signal handler or a parallel thread.
@@ -1033,6 +1057,7 @@ public:
CNetScheduleAPI::EJobStatus* job_status,
int* last_event_index = NULL);
+ // This method requires calling SubmitJob prior with wait_time set
CNetScheduleAPI::EJobStatus WaitForJobCompletion(CNetScheduleJob& job,
CDeadline& deadline, CNetScheduleAPI ns_api);
@@ -1042,13 +1067,26 @@ public:
CNetScheduleAPI::EJobStatus* job_status,
int* last_event_index);
+ enum EJobStatusMask {
+ fJSM_Pending = 1 << CNetScheduleAPI::ePending,
+ fJSM_Running = 1 << CNetScheduleAPI::eRunning,
+ fJSM_Canceled = 1 << CNetScheduleAPI::eCanceled,
+ fJSM_Failed = 1 << CNetScheduleAPI::eFailed,
+ fJSM_Done = 1 << CNetScheduleAPI::eDone,
+ fJSM_Reading = 1 << CNetScheduleAPI::eReading,
+ fJSM_Confirmed = 1 << CNetScheduleAPI::eConfirmed,
+ fJSM_ReadFailed = 1 << CNetScheduleAPI::eReadFailed,
+ fJSM_Deleted = 1 << CNetScheduleAPI::eDeleted
+ };
+ typedef int TJobStatusMask;
+
CNetScheduleAPI::EJobStatus WaitForJobEvent(
const string& job_key,
CDeadline& deadline,
CNetScheduleAPI ns_api,
- int status_mask,
- int last_event_index,
- int *new_event_index);
+ TJobStatusMask status_mask,
+ int last_event_index = kMax_Int,
+ int *new_event_index = NULL);
// Worker node methods.
public:
diff --git a/c++/include/connect/services/netservice_api.hpp b/c++/include/connect/services/netservice_api.hpp
index 6c35b09..02fae88 100644
--- a/c++/include/connect/services/netservice_api.hpp
+++ b/c++/include/connect/services/netservice_api.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___NETSERVICE_API__HPP
#define CONNECT_SERVICES___NETSERVICE_API__HPP
-/* $Id: netservice_api.hpp 447471 2014-09-25 20:59:33Z kazimird $
+/* $Id: netservice_api.hpp 456051 2015-01-07 17:38:03Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -106,6 +106,7 @@ class NCBI_XCONNECT_EXPORT CNetService
CNetServiceIterator Iterate(EIterationMode mode = eSortByLoad);
CNetServiceIterator Iterate(CNetServer::TInstance priority_server);
+ CNetServiceIterator IterateByWeight(const string& key);
/// Start iteration excluding 'server' (return the next server
/// after 'server' or NULL).
@@ -144,12 +145,12 @@ class NCBI_XCONNECT_EXPORT CNetService
inline CNetServer CNetService::GetServer(const string& host,
unsigned short port)
{
- return GetServer(g_NetService_gethostbyname(host), port);
+ return GetServer(SServerAddress(host, port));
}
-inline CNetServer CNetService::GetServer(const SServerAddress& server_address)
+inline CNetServer CNetService::GetServer(unsigned host, unsigned short port)
{
- return GetServer(server_address.host, server_address.port);
+ return GetServer(SServerAddress(host, port));
}
/// This class is for use by the grid_cli utility only.
@@ -170,12 +171,20 @@ public:
virtual ~IExecToJson() {}
};
+/// This function is for use by the grid_cli utility only.
+/// @internal
extern NCBI_XCONNECT_EXPORT
CJsonNode g_ExecToJson(IExecToJson& exec_to_json,
CNetService service,
CNetService::EServiceType service_type,
CNetService::EIterationMode iteration_mode = CNetService::eSortByLoad);
+/// This function is for use by the grid_cli utility only.
+/// @internal
+extern NCBI_XCONNECT_EXPORT
+CNetService g_DiscoverService(const string& service_name,
+ const string& client_name);
+
END_NCBI_SCOPE
#endif /* CONNECT_SERVICES___NETSERVICE_API__HPP */
diff --git a/c++/include/connect/services/netstorage.hpp b/c++/include/connect/services/netstorage.hpp
index 9c0492a..1932dda 100644
--- a/c++/include/connect/services/netstorage.hpp
+++ b/c++/include/connect/services/netstorage.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__NETSTORAGE__HPP
#define CONNECT_SERVICES__NETSTORAGE__HPP
-/* $Id: netstorage.hpp 458005 2015-01-29 19:51:18Z kazimird $
+/* $Id: netstorage.hpp 463989 2015-04-02 19:01:11Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -69,7 +69,8 @@ public:
eAuthError, ///< Authentication error (e.g. no FileTrack API key)
eIOError, ///< I/O error encountered while performing an op
eServerError, ///< NetStorage server error
- eTimeout ///< Timeout encountered while performing an op
+ eTimeout, ///< Timeout encountered while performing an op
+ eExpired ///< Object has expired on server
};
virtual const char* GetErrCodeString() const;
NCBI_EXCEPTION_DEFAULT(CNetStorageException, CException);
@@ -77,6 +78,7 @@ public:
/// Enumeration that indicates the current location of the object.
enum ENetStorageObjectLocation {
+ eNFL_Unknown,
eNFL_NotFound,
eNFL_NetCache,
eNFL_FileTrack
@@ -127,18 +129,9 @@ enum ENetStorageFlags {
fNST_NetCache = (1 << 0), ///< Use NetCache as the primary storage
fNST_FileTrack = (1 << 1), ///< Use FileTrack as the primary storage
- ///@{
- /// These are not used runtime (only for compile-time calculations)
- fNST_V1,
- fNST_V2 = (fNST_V1 - 1) << 1,
- ///@}
-
- ///@{
- /// Abstract locations (values and mapping may be changed later)
+ /**@{ @internal */ fNST_V1, fNST_V2 = (fNST_V1 - 1) << 1, /**@}*/
fNST_Fast = fNST_NetCache,
fNST_Persistent = fNST_FileTrack,
- ///@}
-
fNST_AnyLoc = (fNST_V2 - 1), ///< Any location (all location bits are set)
fNST_Movable = (fNST_V2 << 0), ///< Allow the object to move between storages
@@ -146,8 +139,11 @@ enum ENetStorageFlags {
fNST_NoMetaData = (fNST_V2 << 2), ///< Do not use NetStorage relational database
///< to track ownership & changes. Attributes
///< and querying will also be disabled.
+
+ /**@{ @internal */ fNST_V3, fNST_V4 = (fNST_V3 - 1) << 1, /**@}*/
+ fNST_AnyAttr = (fNST_V4 - 1) ^ fNST_AnyLoc
};
-typedef int TNetStorageFlags; ///< Bitwise OR of ENetStorageFlags
+typedef unsigned TNetStorageFlags; ///< Bitwise OR of ENetStorageFlags
@@ -285,13 +281,22 @@ class NCBI_XCONNECT_EXPORT CNetStorageObject
///
Uint8 GetSize(void);
+ /// Get list of names of all attributes set on this object.
+ /// To get value of particular attribute, GetAttribute should be called.
+ ///
+ /// @throw If the underlying storage does not support attributes,
+ /// a CNetStorageException will be thrown.
+ ///
+ typedef list<string> TAttributeList;
+ TAttributeList GetAttributeList() const;
+
/// Get the current value of the specified attribute. Attribute
/// values are not cached by this method.
///
/// @throw If the underlying storage does not support attributes,
/// a CNetStorageException will be thrown.
///
- string GetAttribute(const string& attr_name);
+ string GetAttribute(const string& attr_name) const;
/// Set the new value for the specified attribute.
///
@@ -324,7 +329,7 @@ class NCBI_XCONNECT_EXPORT CNetStorageObject
class NCBI_XCONNECT_EXPORT CNetStorage
{
- NCBI_NET_COMPONENT(NetStorage);
+ NCBI_NET_COMPONENT_IMPL(NetStorage);
/// Construct a CNetStorage object
///
@@ -336,12 +341,22 @@ class NCBI_XCONNECT_EXPORT CNetStorage
/// and the value of the attribute must be separated by the equality
/// sign, and the value must be URL-encoded.
/// The following attributes are recoginzed:
+ /// * namespace - Application domain. This parameter is required.
/// * client - Application name. If omitted, generated from
/// the executable pathname.
/// * nst - NetStorage server address or LBSM service name
/// pointing to a group of NetStorage servers.
+ /// * metadata - Whether to request or disable the metadata DB.
+ /// Valid options:
+ /// - required - Database access must be enabled
+ /// for the specified NetStorage service
+ /// name in the server configuration.
+ /// - disabled - Database access is disabled for
+ /// all operations.
+ /// - monitoring - Read-only access to the metadata
+ /// database.
/// * nc - NetCache service name or server address.
- /// * cache - Application-specific NetCache cache name.
+ /// * cache - Synonym for "namespace".
/// Example: "client=MyApp&nst=NST_Test&nc=NC_MyApp_TEST&cache=myapp"
///
/// @param default_flags
@@ -368,16 +383,10 @@ class NCBI_XCONNECT_EXPORT CNetStorage
///
/// @param object_loc
/// File to open
- /// @param flags
- /// Combination of flags that hints at the current object location
- /// (storage).
- /// and caching. If this combination differs from that embedded in
- /// 'object_loc', a new object ID will be generated for this object.
/// @return
/// New CNetStorageObject
///
- CNetStorageObject Open(const string& object_loc,
- TNetStorageFlags flags = 0);
+ CNetStorageObject Open(const string& object_loc);
/// Relocate a object according to the specified combination of flags
///
@@ -409,6 +418,10 @@ class NCBI_XCONNECT_EXPORT CNetStorage
/// File to remove
///
void Remove(const string& object_loc);
+
+ /// @deprecated To change flags use Relocate(object_loc, flags) instead.
+ NCBI_DEPRECATED
+ CNetStorageObject Open(const string& object_loc, TNetStorageFlags flags);
};
@@ -420,7 +433,7 @@ class NCBI_XCONNECT_EXPORT CNetStorage
class NCBI_XCONNECT_EXPORT CNetStorageByKey
{
- NCBI_NET_COMPONENT(NetStorageByKey);
+ NCBI_NET_COMPONENT_IMPL(NetStorageByKey);
/// Construct a CNetStorageByKey object.
///
@@ -432,14 +445,16 @@ class NCBI_XCONNECT_EXPORT CNetStorageByKey
/// and the value of the attribute must be separated by the equality
/// sign, and the value must be URL-encoded.
/// The following attributes are recoginzed:
- /// * domain - Namespace name, within which the keys passed
+ /// * namespace - Namespace name, within which the keys passed
/// to the methods of this class must be unique.
+ /// This parameter is required.
+ /// * domain - Synonym for "namespace".
/// * client - Application name.
/// * nst - NetStorage server address or LBSM service name
/// pointing to a group of NetStorage servers.
/// * nc - NetCache service name or server address.
- /// * cache - Application-specific NetCache cache name.
- /// Example: "client=MyApp&nst=NST_Test&nc=NC_MyApp_TEST&cache=myapp"
+ /// * cache - Synonym for "namespace".
+ /// Example: "client=MyApp&nst=NST_Test&nc=NC_MyApp_TEST&namespace=myapp"
///
/// @param default_flags
/// Default storage preferences for objects created by this object.
diff --git a/c++/include/connect/services/netstorage_impl.hpp b/c++/include/connect/services/netstorage_impl.hpp
index 0be4d44..032f298 100644
--- a/c++/include/connect/services/netstorage_impl.hpp
+++ b/c++/include/connect/services/netstorage_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___NETSTORAGE_IMPL__HPP
#define CONNECT_SERVICES___NETSTORAGE_IMPL__HPP
-/* $Id: netstorage_impl.hpp 458002 2015-01-29 19:45:57Z kazimird $
+/* $Id: netstorage_impl.hpp 463378 2015-03-26 21:17:57Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,6 +38,7 @@
#include "netcache_api.hpp"
#include <corelib/rwstream.hpp>
+#include <connect/services/neticache_client.hpp>
BEGIN_NCBI_SCOPE
@@ -66,7 +67,8 @@ struct NCBI_XCONNECT_EXPORT SNetStorageObjectImpl :
virtual void Read(string* data);
virtual bool Eof() = 0;
virtual Uint8 GetSize() = 0;
- virtual string GetAttribute(const string& attr_name) = 0;
+ virtual list<string> GetAttributeList() const = 0;
+ virtual string GetAttribute(const string& attr_name) const = 0;
virtual void SetAttribute(const string& attr_name,
const string& attr_value) = 0;
virtual CNetStorageObjectInfo GetInfo() = 0;
@@ -76,7 +78,7 @@ struct NCBI_XCONNECT_EXPORT SNetStorageObjectRWStream : public CRWStream
{
SNetStorageObjectRWStream(SNetStorageObjectImpl* nst_object) :
CRWStream(nst_object, nst_object, /*buf_size*/ 0, /*buf*/ NULL,
- CRWStreambuf::fLeakExceptions),
+ CRWStreambuf::fLeakExceptions),
m_NetStorageObject(nst_object)
{
}
@@ -138,7 +140,12 @@ inline Uint8 CNetStorageObject::GetSize()
return m_Impl->GetSize();
}
-inline string CNetStorageObject::GetAttribute(const string& attr_name)
+inline CNetStorageObject::TAttributeList CNetStorageObject::GetAttributeList() const
+{
+ return m_Impl->GetAttributeList();
+}
+
+inline string CNetStorageObject::GetAttribute(const string& attr_name) const
{
return m_Impl->GetAttribute(attr_name);
}
@@ -163,8 +170,7 @@ inline void CNetStorageObject::Close()
struct NCBI_XCONNECT_EXPORT SNetStorageImpl : public CObject
{
virtual CNetStorageObject Create(TNetStorageFlags flags = 0) = 0;
- virtual CNetStorageObject Open(const string& object_loc,
- TNetStorageFlags flags = 0) = 0;
+ virtual CNetStorageObject Open(const string& object_loc) = 0;
virtual string Relocate(const string& object_loc,
TNetStorageFlags flags) = 0;
virtual bool Exists(const string& object_loc) = 0;
@@ -176,10 +182,15 @@ inline CNetStorageObject CNetStorage::Create(TNetStorageFlags flags)
return m_Impl->Create(flags);
}
+inline CNetStorageObject CNetStorage::Open(const string& object_loc)
+{
+ return m_Impl->Open(object_loc);
+}
+
inline CNetStorageObject CNetStorage::Open(const string& object_loc,
- TNetStorageFlags flags)
+ TNetStorageFlags /*flags*/)
{
- return m_Impl->Open(object_loc, flags);
+ return m_Impl->Open(object_loc);
}
inline string CNetStorage::Relocate(const string& object_loc,
@@ -232,72 +243,50 @@ inline void CNetStorageByKey::Remove(const string& key, TNetStorageFlags flags)
}
/// @internal
-enum ENetStorageObjectCompoundIDCues {
- eNFCIDC_KeyAndNamespace,
- eNFCIDC_NetICache,
- eNFCIDC_AllowXSiteConn,
- eNFCIDC_TTL,
- eNFCIDC_FileTrackDev,
- eNFCIDC_FileTrackQA,
- eNFCIDC_NetStorageService,
-};
+template <TNetStorageFlags MASK>
+class CNetStorageFlagsSubset
+{
+ typedef CNetStorageFlagsSubset TSelf;
+public:
+ CNetStorageFlagsSubset(TNetStorageFlags flags) : m_Flags(flags & MASK) {}
+ TSelf& operator &=(TSelf flag) { m_Flags &= flag; return *this; }
+ TSelf& operator |=(TSelf flag) { m_Flags |= flag; return *this; }
+ TSelf& operator ^=(TSelf flag) { m_Flags ^= flag; return *this; }
+ operator TNetStorageFlags() const { return m_Flags; }
-/// @internal
-enum ENetStorageObjectLocFields {
- fNFID_KeyAndNamespace = (1 << eNFCIDC_KeyAndNamespace),
- fNFID_NetICache = (1 << eNFCIDC_NetICache),
-#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
- fNFID_AllowXSiteConn = (1 << eNFCIDC_AllowXSiteConn),
-#endif
- fNFID_TTL = (1 << eNFCIDC_TTL),
- fNFID_FileTrackDev = (1 << eNFCIDC_FileTrackDev),
- fNFID_FileTrackQA = (1 << eNFCIDC_FileTrackQA),
- fNFID_NetStorageService = (1 << eNFCIDC_NetStorageService),
+private:
+ TNetStorageFlags m_Flags;
};
-///< @internal Bitwise OR of ENetStorageObjectLocFields
-typedef unsigned char TNetStorageObjectLocFields;
-/// @internal
-enum EFileTrackSite {
- eFileTrack_ProdSite,
- eFileTrack_DevSite,
- eFileTrack_QASite,
- eNumberOfFileTrackSites
-};
-
-/// @internal
-NCBI_XCONNECT_EXPORT
-EFileTrackSite g_StringToFileTrackSite(const char* ft_site_name);
+typedef CNetStorageFlagsSubset<fNST_AnyLoc> TNetStorageLocFlags;
+typedef CNetStorageFlagsSubset<fNST_AnyAttr> TNetStorageAttrFlags;
/// @internal
class NCBI_XCONNECT_EXPORT CNetStorageObjectLoc
{
public:
CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
- TNetStorageFlags flags,
+ TNetStorageAttrFlags flags,
+ const string& app_domain,
Uint8 random_number,
const char* ft_site_name);
CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
- TNetStorageFlags flags,
+ TNetStorageAttrFlags flags,
const string& app_domain,
const string& unique_key,
const char* ft_site_name);
CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
const string& object_loc);
-
- void SetStorageFlags(TNetStorageFlags storage_flags)
- {
- m_StorageFlags = storage_flags;
- m_Dirty = true;
- }
-
- TNetStorageFlags GetStorageFlags() const {return m_StorageFlags;}
- TNetStorageObjectLocFields GetFields() const {return m_Fields;}
+ CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
+ const string& object_loc, TNetStorageAttrFlags flags);
void SetObjectID(Uint8 object_id)
{
- m_StorageFlags &= ~(int) fNST_NoMetaData;
+ m_LocatorFlags &= ~(TLocatorFlags) fLF_NoMetaData;
+ m_LocatorFlags |= fLF_HasObjectID;
m_ObjectID = object_id;
+ if ((m_LocatorFlags & fLF_HasUserKey) == 0)
+ x_SetUniqueKeyFromRandom();
m_Dirty = true;
}
@@ -305,45 +294,38 @@ public:
void SetServiceName(const string& service_name)
{
- if (service_name.empty())
- ClearFieldFlags(fNFID_NetStorageService);
+ if (service_name.empty() ||
+ strchr(service_name.c_str(), ':') != NULL)
+ ClearLocatorFlags(fLF_NetStorageService);
else {
m_ServiceName = service_name;
- SetFieldFlags(fNFID_NetStorageService);
+ SetLocatorFlags(fLF_NetStorageService);
}
m_Dirty = true;
}
string GetServiceName() const {return m_ServiceName;}
+ ENetStorageObjectLocation GetLocation() const {return m_Location;}
+
+ bool IsMovable() const {return (m_LocatorFlags & fLF_Movable) != 0;}
+ bool IsCacheable() const {return (m_LocatorFlags & fLF_Cacheable) != 0;}
+ bool IsMetaDataDisabled() const
+ {
+ return (m_LocatorFlags & fLF_NoMetaData) != 0;
+ }
+
Int8 GetTimestamp() const {return m_Timestamp;}
CTime GetCreationTime() const {return CTime(m_Timestamp);}
Uint8 GetRandom() const {return m_Random;}
- bool HasUserKey() const {return (m_Fields & fNFID_KeyAndNamespace) != 0;}
+ bool HasUserKey() const {return (m_LocatorFlags & fLF_HasUserKey) != 0;}
string GetAppDomain() const {return m_AppDomain;}
string GetUserKey() const {return m_UserKey;}
- // A combination of either timestamp+random or app_domain+user_key.
+ string GetICacheKey() const {return m_ICacheKey;}
string GetUniqueKey() const {return m_UniqueKey;}
- void ClearNetICacheParams();
- void SetNetICacheParams(const string& service_name,
- const string& cache_name, Uint4 server_ip, unsigned short server_port
-#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
- , bool allow_xsite_conn
-#endif
- );
-
- string GetNCServiceName() const {return m_NCServiceName;}
- string GetCacheName() const {return m_CacheName;}
- Uint4 GetNetCacheIP() const {return m_NetCacheIP;}
- Uint2 GetNetCachePort() const {return m_NetCachePort;}
-
- void SetFileTrackSite(EFileTrackSite ft_site);
- EFileTrackSite GetFileTrackSite();
- string GetFileTrackURL();
-
void SetCacheChunkSize(size_t cache_chunk_size)
{
m_CacheChunkSize = cache_chunk_size;
@@ -352,76 +334,159 @@ public:
Uint8 GetCacheChunkSize() const {return m_CacheChunkSize;}
- void SetTTL(Uint8 ttl)
+ void SetLocation_NetCache(const string& service_name,
+ Uint4 server_ip, unsigned short server_port,
+ bool allow_xsite_conn);
+
+ string GetNCServiceName() const {return m_NCServiceName;}
+ Uint4 GetNetCacheIP() const {return m_NetCacheIP;}
+ Uint2 GetNetCachePort() const {return m_NetCachePort;}
+
+ bool IsXSiteProxyAllowed() const
{
- if (ttl == 0)
- ClearFieldFlags(fNFID_TTL);
- else {
- m_TTL = ttl;
- SetFieldFlags(fNFID_TTL);
- }
- m_Dirty = true;
+ return (m_NCFlags & fNCF_AllowXSiteConn) != 0;
}
- Uint8 GetTTL() const {return m_TTL;}
+ void SetLocation_FileTrack(const char* ft_site_name);
+
+ string GetFileTrackURL();
- string GetLoc()
+ string GetLocator() const
{
if (m_Dirty)
x_Pack();
return m_Locator;
}
+ TNetStorageAttrFlags GetStorageAttrFlags() const;
+
// Serialize to a JSON object.
void ToJSON(CJsonNode& root) const;
CJsonNode ToJSON() const;
private:
+ enum ELocatorFlags {
+ fLF_NetStorageService = (1 << 0),
+ fLF_NoMetaData = (1 << 1),
+ fLF_HasObjectID = (1 << 2),
+ fLF_HasUserKey = (1 << 3),
+ fLF_Movable = (1 << 4),
+ fLF_Cacheable = (1 << 5),
+ fLF_DevEnv = (1 << 6),
+ fLF_QAEnv = (1 << 7),
+
+ eLF_AttrFlags = (
+ fLF_NoMetaData |
+ fLF_Movable |
+ fLF_Cacheable),
+ eLF_FieldFlags = (
+ fLF_NetStorageService |
+ fLF_HasObjectID |
+ fLF_HasUserKey |
+ fLF_DevEnv |
+ fLF_QAEnv)
+ };
+ typedef unsigned TLocatorFlags;
+
+ enum ENetCacheFlags {
+ fNCF_AllowXSiteConn = (1 << 0),
+ fNCF_ServerSpecified = (1 << 1),
+ };
+ typedef unsigned TNetCacheFlags;
+
+ void Parse(const string& object_loc);
void x_SetFileTrackSite(const char* ft_site_name);
void x_SetUniqueKeyFromRandom();
void x_SetUniqueKeyFromUserDefinedKey();
- void x_Pack();
- void SetFieldFlags(TNetStorageObjectLocFields flags) {m_Fields |= flags;}
- void ClearFieldFlags(TNetStorageObjectLocFields flags) {m_Fields &= ~flags;}
+ void x_Pack() const;
+ void SetLocatorFlags(TLocatorFlags flags) {m_LocatorFlags |= flags;}
+ void ClearLocatorFlags(TLocatorFlags flags) {m_LocatorFlags &= ~flags;}
- CCompoundIDPool m_CompoundIDPool;
+ TLocatorFlags x_StorageFlagsToLocatorFlags(
+ TNetStorageAttrFlags storage_flags);
- TNetStorageFlags m_StorageFlags;
- TNetStorageObjectLocFields m_Fields;
+ mutable CCompoundIDPool m_CompoundIDPool;
+
+ TLocatorFlags m_LocatorFlags;
Uint8 m_ObjectID;
string m_ServiceName;
+ string m_LocationCode;
+ ENetStorageObjectLocation m_Location;
+
+ string m_AppDomain;
Int8 m_Timestamp;
Uint8 m_Random;
- string m_AppDomain;
string m_UserKey;
+ // Either "m_Timestamp-m_Random[-m_ObjectID]" or m_UserKey.
+ string m_ICacheKey;
+ // "m_AppDomain-m_ICacheKey"
string m_UniqueKey;
+ Uint8 m_CacheChunkSize;
+
+ TNetCacheFlags m_NCFlags;
string m_NCServiceName;
- string m_CacheName;
Uint4 m_NetCacheIP;
Uint2 m_NetCachePort;
- Uint8 m_CacheChunkSize;
- Uint8 m_TTL;
- bool m_Dirty;
+ mutable bool m_Dirty;
- string m_Locator;
+ mutable string m_Locator;
};
-NCBI_XCONNECT_EXPORT
-CNetStorageObject g_CreateNetStorage_NetCacheBlob(
- CNetCacheAPI::TInstance nc_api,
+/// @internal
+class NCBI_XCONNECT_EXPORT CDNCNetStorage
+{
+public:
+ static CNetStorageObject Create(CNetCacheAPI::TInstance nc_api);
+ static CNetStorageObject Open(CNetCacheAPI::TInstance nc_api,
const string& blob_key);
-
+};
+
+/// @internal
+class CNetStorageServerError
+{
+public:
+ enum EErrCode {
+ eInvalidArgument = 1001,
+ eMandatoryFieldsMissed = 1002,
+ eHelloRequired = 1003,
+ eInvalidMessageType = 1004,
+ eInvalidIncomingMessage = 1005,
+ ePrivileges = 1006,
+ eInvalidMessageHeader = 1007,
+ eShuttingDown = 1008,
+ eMessageAfterBye = 1009,
+ eStorageError = 1010,
+ eWriteError = 1011,
+ eReadError = 1012,
+ eInternalError = 1013,
+ eNetStorageObjectNotFound = 1014,
+ eNetStorageAttributeNotFound = 1015,
+ eNetStorageAttributeValueNotFound = 1016,
+ eNetStorageClientNotFound = 1017,
+ eNetStorageObjectExpired = 1018,
+ eDatabaseError = 1019,
+ eInvalidConfig = 1020,
+ eRemoteObjectNotFound = 1021,
+
+ // Meta info involving operation requested while the service
+ // is not configured for meta or HELLO metadata option conflict
+ eInvalidMetaInfoRequest = 1022,
+ eUnknownError = 1023
+ };
+};
+
NCBI_XCONNECT_EXPORT
CNetStorageObjectInfo g_CreateNetStorageObjectInfo(const string& object_loc,
- ENetStorageObjectLocation location, const CNetStorageObjectLoc* object_loc_struct,
+ ENetStorageObjectLocation location,
+ const CNetStorageObjectLoc* object_loc_struct,
Uint8 file_size, CJsonNode::TInstance storage_specific_info);
NCBI_XCONNECT_EXPORT
diff --git a/c++/include/connect/services/srv_connections.hpp b/c++/include/connect/services/srv_connections.hpp
index b2ed9ed..0d2abe4 100644
--- a/c++/include/connect/services/srv_connections.hpp
+++ b/c++/include/connect/services/srv_connections.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__SERVER_CONN_HPP_1
#define CONNECT_SERVICES__SERVER_CONN_HPP_1
-/* $Id: srv_connections.hpp 447471 2014-09-25 20:59:33Z kazimird $
+/* $Id: srv_connections.hpp 477824 2015-09-02 12:20:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -49,7 +49,9 @@ struct SNetServerMultilineCmdOutputImpl; ///< @internal
// A host:port pair.
struct SServerAddress {
- SServerAddress(unsigned h, unsigned short p) : host(h), port(p) {}
+ SServerAddress(unsigned h, unsigned short p) : host(h), port(p), name(h) {}
+ SServerAddress(const string &n, unsigned short p)
+ : host(g_NetService_gethostbyname(n)), port(p), name(n, host) {}
bool operator ==(const SServerAddress& h) const
{
@@ -64,7 +66,7 @@ struct SServerAddress {
string AsString() const
{
- string address(g_NetService_gethostnamebyaddr(host));
+ string address(name.get(host));
address += ':';
address += NStr::UIntToString(port);
@@ -73,6 +75,30 @@ struct SServerAddress {
unsigned host;
unsigned short port;
+
+private:
+ struct SName
+ {
+ SName() : host(0) {}
+ SName(unsigned h) : host(h) {}
+ SName(const string &n, unsigned h) : name(n), host(h) {}
+
+ string get(unsigned h)
+ {
+ // Name was not looked up yet or host changed
+ if (name.empty() || host != h) {
+ host = h;
+ name = g_NetService_gethostnamebyaddr(h);
+ }
+
+ return name;
+ }
+
+ string name;
+ unsigned host;
+ };
+
+ mutable SName name;
};
///////////////////////////////////////////////////////////////////////////
@@ -89,15 +115,22 @@ class INetServerConnectionListener : public CObject
public:
virtual CRef<INetServerProperties> AllocServerProperties() = 0;
+ CConfig* PreInit(CObject* api_impl, CConfig* config, string* section);
+
// Event handlers.
public:
- virtual CConfig* LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name) = 0;
+ virtual CConfig* OnPreInit(CObject* api_impl,
+ CConfig* config, string* config_section) { return NULL; }
virtual void OnInit(CObject* api_impl,
CConfig* config, const string& config_section) = 0;
virtual void OnConnected(CNetServerConnection& connection) = 0;
virtual void OnError(const string& err_msg, CNetServer& server) = 0;
virtual void OnWarning(const string& warn_msg, CNetServer& server) = 0;
+
+ string GetClientName() const { return m_ClientName; }
+
+protected:
+ string m_ClientName;
};
///////////////////////////////////////////////////////////////////////////
diff --git a/c++/include/connect/threaded_server.hpp b/c++/include/connect/threaded_server.hpp
index 76ecf71..89bab7b 100644
--- a/c++/include/connect/threaded_server.hpp
+++ b/c++/include/connect/threaded_server.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___THREADED_SERVER__HPP
#define CONNECT___THREADED_SERVER__HPP
-/* $Id: threaded_server.hpp 341365 2011-10-19 14:10:03Z lavr $
+/* $Id: threaded_server.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,6 @@
*
*/
-#include <corelib/ncbistd.hpp>
#include <connect/ncbi_conn_exception.hpp>
#include <connect/ncbi_core_cxx.hpp>
#include <connect/ncbi_socket.hpp>
diff --git a/c++/include/corelib/env_reg.hpp b/c++/include/corelib/env_reg.hpp
index eea709b..5cb1123 100644
--- a/c++/include/corelib/env_reg.hpp
+++ b/c++/include/corelib/env_reg.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___ENV_REG__HPP
#define CORELIB___ENV_REG__HPP
-/* $Id: env_reg.hpp 184972 2010-03-05 17:29:48Z ucko $
+/* $Id: env_reg.hpp 478279 2015-09-08 14:33:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -111,6 +111,8 @@ protected:
void x_SetModifiedFlag(bool modified, TFlags flags);
const string& x_Get(const string& section, const string& name,
TFlags flags) const;
+ const string& x_Get(const string& section, const string& name,
+ TFlags flags, bool& found) const;
bool x_HasEntry(const string& section, const string& name,
TFlags flags) const;
const string& x_GetComment(const string& section, const string& name,
diff --git a/c++/include/corelib/error_codes.hpp b/c++/include/corelib/error_codes.hpp
index e7ab9e6..7a3ac56 100644
--- a/c++/include/corelib/error_codes.hpp
+++ b/c++/include/corelib/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___ERROR_CODES__HPP
#define CORELIB___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 436308 2014-05-27 15:45:33Z grichenk $
+/* $Id: error_codes.hpp 477851 2015-09-02 13:13:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -47,22 +47,23 @@ NCBI_DEFINE_ERRCODE_X(Corelib_Blob, 103, 1);
NCBI_DEFINE_ERRCODE_X(Corelib_Static, 104, 1);
NCBI_DEFINE_ERRCODE_X(Corelib_System, 105, 13);
NCBI_DEFINE_ERRCODE_X(Corelib_App, 106, 21);
-NCBI_DEFINE_ERRCODE_X(Corelib_Diag, 107, 27);
+NCBI_DEFINE_ERRCODE_X(Corelib_Diag, 107, 29);
NCBI_DEFINE_ERRCODE_X(Corelib_File, 108, 4);
NCBI_DEFINE_ERRCODE_X(Corelib_Object, 109, 15);
NCBI_DEFINE_ERRCODE_X(Corelib_Reg, 110, 8);
NCBI_DEFINE_ERRCODE_X(Corelib_Util, 111, 6);
-NCBI_DEFINE_ERRCODE_X(Corelib_StreamBuf, 112, 12);
+NCBI_DEFINE_ERRCODE_X(Corelib_StreamBuf, 112, 14);
NCBI_DEFINE_ERRCODE_X(Corelib_PluginMgr, 113, 4);
NCBI_DEFINE_ERRCODE_X(Corelib_Stack, 114, 12);
NCBI_DEFINE_ERRCODE_X(Corelib_Unix, 115, 2);
NCBI_DEFINE_ERRCODE_X(Corelib_StreamUtil, 116, 1);
NCBI_DEFINE_ERRCODE_X(Corelib_Threads, 117, 4);
-NCBI_DEFINE_ERRCODE_X(Corelib_Dll, 118, 1);
+NCBI_DEFINE_ERRCODE_X(Corelib_Dll, 118, 2);
NCBI_DEFINE_ERRCODE_X(Corelib_TestBoost, 119, 6);
NCBI_DEFINE_ERRCODE_X(Corelib_Process, 120, 2);
NCBI_DEFINE_ERRCODE_X(Corelib_Mutex, 121, 2);
NCBI_DEFINE_ERRCODE_X(Corelib_Cookies, 122, 7);
+NCBI_DEFINE_ERRCODE_X(Corelib_Message, 123, 2);
END_NCBI_SCOPE
diff --git a/c++/include/corelib/expr.hpp b/c++/include/corelib/expr.hpp
index 9b040ef..bd190e4 100644
--- a/c++/include/corelib/expr.hpp
+++ b/c++/include/corelib/expr.hpp
@@ -2,7 +2,7 @@
#define CORELIB___EXPR__HPP
-/* $Id: expr.hpp 395085 2013-04-09 16:23:01Z zakharov $
+/* $Id: expr.hpp 455123 2014-12-23 13:38:22Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -242,7 +242,7 @@ public:
const CException* prev_exception, EErrCode err_code,
const string& message, int pos,
EDiagSev severity = eDiag_Error)
- : CException(info, prev_exception, CException::eInvalid, message)
+ : CException(info, prev_exception, message, severity)
, m_Pos(pos)
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(CExprParserException, CException);
diff --git a/c++/include/corelib/guard.hpp b/c++/include/corelib/guard.hpp
index f5430bb..0b6f35f 100644
--- a/c++/include/corelib/guard.hpp
+++ b/c++/include/corelib/guard.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___GUARD__HPP
#define CORELIB___GUARD__HPP
-/* $Id: guard.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: guard.hpp 451479 2014-11-06 19:47:51Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
*/
#include <corelib/ncbidbg.hpp>
+#include <corelib/ncbimisc.hpp>
BEGIN_NCBI_SCOPE
@@ -94,17 +95,34 @@ enum EEmptyGuard {
eEmptyGuard
};
+
+/// Base class for CGuard<> template.
+class NCBI_XNCBI_EXPORT CGuard_Base
+{
+public:
+ /// Exception reporting options.
+ enum EReportExceptions {
+ eReport, ///< Use ERR_POST to report exceptions.
+ eSilent ///< Silently discard exceptions.
+ };
+
+protected:
+ static void ReportException(std::exception& ex);
+};
+
+
template <class Resource,
class Lock = SSimpleLock<Resource>,
- class Unlock = SSimpleUnlock<Resource> >
-class CGuard
+ class Unlock = SSimpleUnlock<Resource>,
+ CGuard_Base::EReportExceptions ReportExceptions = CGuard_Base::eReport>
+class CGuard : public CGuard_Base
{
public:
typedef Resource resource_type;
typedef resource_type* resource_ptr;
typedef Lock lock_type;
typedef Unlock unlock_type;
- typedef CGuard<Resource, Lock, Unlock> TThisType;
+ typedef CGuard<Resource, Lock, Unlock, ReportExceptions> TThisType;
explicit CGuard(EEmptyGuard /*empty*/)
{
@@ -137,8 +155,11 @@ public:
{
try {
Release();
- } catch(std::exception& ) {
- // catch and ignore std exceptions in destructor
+ } catch(std::exception& ex) {
+ // catch and report or ignore std exceptions in destructor
+ if (ReportExceptions == eReport) {
+ ReportException(ex);
+ }
}
}
diff --git a/c++/include/corelib/hash_impl/stlp_defs.hpp b/c++/include/corelib/hash_impl/stlp_defs.hpp
index 333ee27..a2a878b 100644
--- a/c++/include/corelib/hash_impl/stlp_defs.hpp
+++ b/c++/include/corelib/hash_impl/stlp_defs.hpp
@@ -1,4 +1,4 @@
-/* $Id: stlp_defs.hpp 443320 2014-08-13 02:58:48Z mcelhany $
+/* $Id: stlp_defs.hpp 442546 2014-08-04 22:17:06Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/app/winmasker/win_mask_app.hpp b/c++/include/corelib/impl/listener_stack.hpp
similarity index 56%
copy from c++/src/app/winmasker/win_mask_app.hpp
copy to c++/include/corelib/impl/listener_stack.hpp
index 454f3d8..9f5b288 100644
--- a/c++/src/app/winmasker/win_mask_app.hpp
+++ b/c++/include/corelib/impl/listener_stack.hpp
@@ -1,4 +1,7 @@
-/* $Id: win_mask_app.hpp 139491 2008-09-05 13:20:55Z camacho $
+#ifndef CORELIB___LISTENER_STACK__HPP
+#define CORELIB___LISTENER_STACK__HPP
+
+/* $Id: listener_stack.hpp 477854 2015-09-02 13:14:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -23,57 +26,45 @@
*
* ===========================================================================
*
- * Author: Aleksandr Morgulis
+ * Author: Aleksey Grichenko
*
* File Description:
- * Header file for CWinMaskApplication class.
+ * IMessageListener stack implementation.
*
*/
-#ifndef C_WIN_MASK_APPLICATION_H
-#define C_WIN_MASK_APPLICATION_H
-
-#include <corelib/ncbiapp.hpp>
BEGIN_NCBI_SCOPE
-/**
- **\brief Window based masker main class.
- **
- **/
-class CWinMaskApplication : public CNcbiApplication
+
+class NCBI_XNCBI_EXPORT CMessageListener_Stack
{
public:
+ CMessageListener_Stack(void);
- /// Application constructor
- CWinMaskApplication() {
- CRef<CVersion> version(new CVersion());
- version->SetVersionInfo(1, 0, 0);
- SetFullVersion(version);
- }
+ size_t PushListener(IMessageListener& listener,
+ IMessageListener::EListenFlag flag);
+ void PopListener(size_t depth = 0);
+ bool HaveListeners(void);
+ IMessageListener::EPostResult Post(const IMessage& message);
+ IMessageListener::EPostResult Post(const IProgressMessage& progress);
+private:
+ struct SListenerNode {
+ public:
+ SListenerNode(IMessageListener& listener,
+ IMessageListener::EListenFlag flag)
+ : m_Listener(&listener), m_Flag(flag) {}
- /**
- **\brief Short description of the program.
- **
- **/
- static const char * const USAGE_LINE;
+ CRef<IMessageListener> m_Listener;
+ IMessageListener::EListenFlag m_Flag;
+ };
- /**
- **\brief Initialization.
- **
- ** Setting up descriptions of command line parameters.
- **
- **/
- virtual void Init(void);
+ typedef list<SListenerNode> TListenerStack;
- /**
- **\brief Main routine of the window based masker.
- **
- ** @return the exit status
- **/
- virtual int Run (void);
+ TListenerStack m_Stack;
};
+
END_NCBI_SCOPE
-#endif
+#endif /* CORELIB___LISTENER_STACK__HPP */
diff --git a/c++/include/corelib/impl/ncbi_atomic_defs.h b/c++/include/corelib/impl/ncbi_atomic_defs.h
index 8e5f7c8..f0b6b2b 100644
--- a/c++/include/corelib/impl/ncbi_atomic_defs.h
+++ b/c++/include/corelib/impl/ncbi_atomic_defs.h
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_ATOMIC_DEFS__HPP
#define CORELIB___NCBI_ATOMIC_DEFS__HPP
-/* $Id: ncbi_atomic_defs.h 438620 2014-06-18 13:47:39Z ucko $
+/* $Id: ncbi_atomic_defs.h 471769 2015-07-01 13:53:07Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -106,7 +106,10 @@ extern "C" {
* as function-call overhead can be appreciable, particularly on x86.
*/
#ifdef NCBI_NO_THREADS
- typedef unsigned int TNCBIAtomicValue;
+ typedef size_t TNCBIAtomicValue;
+# if SIZEOF_SIZE_T == 8
+# define NCBI_COUNTER_64_BIT 1
+# endif
# define NCBI_COUNTER_UNSIGNED 1
# define NCBI_COUNTER_ADD(p, d) ((*p) += d)
#elif (defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_ICC)) && \
@@ -114,14 +117,26 @@ extern "C" {
((defined(__i386) || defined(__sparc) || defined(__x86_64)) && \
!defined(__GLIBCPP__) /* < 3.0 or >= 3.4 */) && \
(!defined(__GLIBCXX__) || !defined(NCBI_TCHECK)))
+# if defined(__x86_64)
+# define NCBI_COUNTER_64_BIT
+# endif
+# ifdef NCBI_COUNTER_64_BIT
+ typedef size_t TNCBIAtomicValue;
+# else
typedef unsigned int TNCBIAtomicValue;
+# endif
# define NCBI_COUNTER_UNSIGNED 1
# define NCBI_COUNTER_USE_ASM 1
# if defined(__sparc) && !defined(__sparcv9)
# define NCBI_COUNTER_RESERVED_VALUE 0x3FFFFFFF
# endif
-#elif defined(NCBI_HAVE_CXX11)
- typedef unsigned int TNCBIAtomicValue;
+#elif defined(NCBI_HAVE_CXX11) && !defined(NCBI_OS_MSWIN)
+ /* std::atomic<> in MSVC has non-default constructor so
+ static CAtomicCounter couldn't be initialized in MT-safe manner */
+ typedef size_t TNCBIAtomicValue;
+# if SIZEOF_SIZE_T == 8
+# define NCBI_COUNTER_64_BIT 1
+# endif
# define NCBI_ATOMIC_TYPE(t) std::atomic<t>
# define NCBI_COUNTER_UNSIGNED 1
# define NCBI_COUNTER_ADD(p, d) ((*p) += d)
@@ -245,8 +260,16 @@ extern "C" {
#elif defined(NCBI_OS_MSWIN)
# include <corelib/impl/ncbi_os_mswin.h>
# if !defined(NCBI_COUNTER_ADD) && !defined(NCBI_COUNTER_USE_ASM)
+# if NCBI_PLATFORM_BITS >= 64
+# define NCBI_COUNTER_64_BIT
+# endif
+# ifdef NCBI_COUNTER_64_BIT
+ typedef LONGLONG TNCBIAtomicValue;
+# define NCBI_COUNTER_ADD(p, d) (InterlockedExchangeAdd64(p, d) + d)
+# else
typedef LONG TNCBIAtomicValue;
# define NCBI_COUNTER_ADD(p, d) (InterlockedExchangeAdd(p, d) + d)
+# endif
# endif
# define NCBI_SWAP_POINTERS(loc, nv) (InterlockedExchangePointer(loc, nv))
#elif !defined(NCBI_COUNTER_ADD) && !defined(NCBI_COUNTER_USE_ASM)
diff --git a/c++/include/corelib/impl/ncbi_panfs.h b/c++/include/corelib/impl/ncbi_panfs.h
index b738cc8..e8dd35b 100644
--- a/c++/include/corelib/impl/ncbi_panfs.h
+++ b/c++/include/corelib/impl/ncbi_panfs.h
@@ -1,7 +1,7 @@
#ifndef CORELIB___IMPL___NCBI_PANFS__H
#define CORELIB___IMPL___NCBI_PANFS__H
-/* $Id: ncbi_panfs.h 464911 2015-04-15 14:47:14Z ivanov $
+/* $Id: ncbi_panfs.h 460055 2015-02-24 18:17:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/impl/ncbi_param_impl.hpp b/c++/include/corelib/impl/ncbi_param_impl.hpp
index 1cf04c9..b4be178 100644
--- a/c++/include/corelib/impl/ncbi_param_impl.hpp
+++ b/c++/include/corelib/impl/ncbi_param_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_PARAM_IMPL__HPP
#define CORELIB___NCBI_PARAM_IMPL__HPP
-/* $Id: ncbi_param_impl.hpp 448558 2014-10-07 16:41:06Z ivanov $
+/* $Id: ncbi_param_impl.hpp 450825 2014-10-30 18:31:55Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -430,6 +430,7 @@ CParam<TDescription>::sx_GetDefault(bool force_reset)
def = TParamParser::StringToValue(config_value,
TDescription::sm_ParamDescription);
}
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
sx_GetState() = app && app->FinishedLoadingConfig()
? eState_Config : eState_EnvVar;
diff --git a/c++/include/corelib/impl/rwstreambuf.hpp b/c++/include/corelib/impl/rwstreambuf.hpp
index 60d868f..706cc90 100644
--- a/c++/include/corelib/impl/rwstreambuf.hpp
+++ b/c++/include/corelib/impl/rwstreambuf.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___RWSTREAMBUF__HPP
#define CORELIB___RWSTREAMBUF__HPP
-/* $Id: rwstreambuf.hpp 426324 2014-02-07 17:28:45Z lavr $
+/* $Id: rwstreambuf.hpp 463752 2015-04-01 14:15:52Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -78,8 +78,8 @@ public:
CT_CHAR_TYPE* buf = 0,
TFlags flags = 0);
- /// NOTE: if both reader and writer have actually happened to be
- /// the same object, it will _not_ be deleted twice.
+ /// NOTE: if both reader and writer have actually happened to be the same
+ /// object, then when owned, it will _not_ be deleted twice.
CRWStreambuf(IReader* r,
IWriter* w,
streamsize buf_size = 0,
@@ -113,31 +113,39 @@ protected:
#endif /*NCBI_OS_MSWIN*/
protected:
- CT_POS_TYPE x_GetGPos(void)
+ CT_POS_TYPE x_GetGPos(void)
{ return x_GPos - (CT_OFF_TYPE)(gptr() ? egptr() - gptr() : 0); }
- CT_POS_TYPE x_GetPPos(void)
+
+ CT_POS_TYPE x_GetPPos(void)
{ return x_PPos + (CT_OFF_TYPE)(pbase() ? pbase() - pptr() : 0); }
- int x_sync(void)
- { return pbase() && pptr() > pbase() ? sync() : 0; }
+
+ int x_sync(void)
+ { return pbase() < pptr() ? sync() : 0; }
+
+ ERW_Result x_pushback(void);
protected:
- TFlags m_Flags;
+ TFlags m_Flags;
+
+ AutoPtr<IReader> m_Reader;
+ AutoPtr<IWriter> m_Writer;
- IReader* m_Reader;
- IWriter* m_Writer;
+ size_t m_BufSize;
+ CT_CHAR_TYPE* m_ReadBuf;
+ CT_CHAR_TYPE* m_WriteBuf;
- size_t m_BufSize;
- CT_CHAR_TYPE* m_ReadBuf;
- CT_CHAR_TYPE* m_WriteBuf;
+ CT_CHAR_TYPE* m_pBuf;
+ CT_CHAR_TYPE x_Buf;
- CT_CHAR_TYPE* m_pBuf;
- CT_CHAR_TYPE x_Buf;
+ CT_POS_TYPE x_GPos; ///< get position [for istream.tellg()]
+ CT_POS_TYPE x_PPos; ///< put position [for ostream.tellp()]
- CT_POS_TYPE x_GPos; ///< get position [for istream.tellg()]
- CT_POS_TYPE x_PPos; ///< put position [for ostream.tellp()]
+ bool x_Err; ///< whether there was a _write_ error
+ CT_POS_TYPE x_ErrPos; ///< position of the _write_ error (if x_Err)
- bool x_Err; ///< whether there was a write error
- CT_POS_TYPE x_ErrPos; ///< position of write error (if x_Error)
+private:
+ CRWStreambuf(const CRWStreambuf&);
+ CRWStreambuf operator=(const CRWStreambuf&);
};
diff --git a/c++/include/corelib/impl/stringutf8_deprecated.hpp b/c++/include/corelib/impl/stringutf8_deprecated.hpp
index ae5da3c..0f9b32d 100644
--- a/c++/include/corelib/impl/stringutf8_deprecated.hpp
+++ b/c++/include/corelib/impl/stringutf8_deprecated.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___STRINGUTF8_DEPRECATED__HPP
#define CORELIB___STRINGUTF8_DEPRECATED__HPP
-/* $Id: stringutf8_deprecated.hpp 406607 2013-07-15 13:19:51Z gouriano $
+/* $Id: stringutf8_deprecated.hpp 455122 2014-12-23 13:35:10Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -123,7 +123,9 @@ public:
/// Source string
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED(const TStringUnicode& src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED(const TStringUCS4& src);
+#endif
CStringUTF8_DEPRECATED(const TStringUCS2& src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED(const wstring& src);
@@ -135,7 +137,9 @@ public:
/// Source zero-terminated character buffer
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED(const TUnicodeSymbol* src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED(const TCharUCS4* src);
+#endif
CStringUTF8_DEPRECATED(const TCharUCS2* src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED(const wchar_t* src);
@@ -153,8 +157,10 @@ public:
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED(ECharBufferType type,
const TUnicodeSymbol* src, SIZE_TYPE char_count);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED(ECharBufferType type,
const TCharUCS4* src, SIZE_TYPE char_count);
+#endif
CStringUTF8_DEPRECATED(ECharBufferType type,
const TCharUCS2* src, SIZE_TYPE char_count);
#if defined(HAVE_WSTRING)
@@ -171,7 +177,9 @@ public:
/// Source string
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& operator= (const TStringUnicode& src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& operator= (const TStringUCS4& src);
+#endif
CStringUTF8_DEPRECATED& operator= (const TStringUCS2& src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& operator= (const wstring& src);
@@ -183,7 +191,9 @@ public:
/// Source zero-terminated character buffer
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& operator= (const TUnicodeSymbol* src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& operator= (const TCharUCS4* src);
+#endif
CStringUTF8_DEPRECATED& operator= (const TCharUCS2* src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& operator= (const wchar_t* src);
@@ -198,7 +208,9 @@ public:
/// Source string
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& operator+= (const TStringUnicode& src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& operator+= (const TStringUCS4& src);
+#endif
CStringUTF8_DEPRECATED& operator+= (const TStringUCS2& src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& operator+= (const wstring& src);
@@ -210,7 +222,9 @@ public:
/// Source zero-terminated character buffer
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& operator+= (const TUnicodeSymbol* src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& operator+= (const TCharUCS4* src);
+#endif
CStringUTF8_DEPRECATED& operator+= (const TCharUCS2* src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& operator+= (const wchar_t* src);
@@ -235,7 +249,9 @@ public:
/// Source string
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Assign(const TStringUnicode& src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Assign(const TStringUCS4& src);
+#endif
CStringUTF8_DEPRECATED& Assign(const TStringUCS2& src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& Assign(const wstring& src);
@@ -247,7 +263,9 @@ public:
/// Source zero-terminated character buffer
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Assign(const TUnicodeSymbol* src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Assign(const TCharUCS4* src);
+#endif
CStringUTF8_DEPRECATED& Assign(const TCharUCS2* src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& Assign(const wchar_t* src);
@@ -265,8 +283,10 @@ public:
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Assign(ECharBufferType type,
const TUnicodeSymbol* src, SIZE_TYPE char_count);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Assign(ECharBufferType type,
const TCharUCS4* src, SIZE_TYPE char_count);
+#endif
CStringUTF8_DEPRECATED& Assign(ECharBufferType type,
const TCharUCS2* src, SIZE_TYPE char_count);
#if defined(HAVE_WSTRING)
@@ -302,7 +322,9 @@ public:
/// Source string
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Append(const TStringUnicode& src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Append(const TStringUCS4& src);
+#endif
CStringUTF8_DEPRECATED& Append(const TStringUCS2& src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& Append(const wstring& src);
@@ -314,7 +336,9 @@ public:
/// Source zero-terminated character buffer
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Append(const TUnicodeSymbol* src);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Append(const TCharUCS4* src);
+#endif
CStringUTF8_DEPRECATED& Append(const TCharUCS2* src);
#if defined(HAVE_WSTRING)
CStringUTF8_DEPRECATED& Append(const wchar_t* src);
@@ -332,8 +356,10 @@ public:
/// @deprecated Use utility class CUtf8 instead
CStringUTF8_DEPRECATED& Append(ECharBufferType type,
const TUnicodeSymbol* src, SIZE_TYPE char_count);
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED& Append(ECharBufferType type,
const TCharUCS4* src, SIZE_TYPE char_count);
+#endif
CStringUTF8_DEPRECATED& Append(ECharBufferType type,
const TCharUCS2* src, SIZE_TYPE char_count);
#if defined(HAVE_WSTRING)
diff --git a/c++/include/corelib/impl/stringutf8_deprecated.inl b/c++/include/corelib/impl/stringutf8_deprecated.inl
index b888db0..70d69db 100644
--- a/c++/include/corelib/impl/stringutf8_deprecated.inl
+++ b/c++/include/corelib/impl/stringutf8_deprecated.inl
@@ -1,7 +1,7 @@
#ifndef CORELIB___STRINGUTF8_DEPRECATED__INL
#define CORELIB___STRINGUTF8_DEPRECATED__INL
-/* $Id: stringutf8_deprecated.inl 405847 2013-07-09 13:56:53Z gouriano $
+/* $Id: stringutf8_deprecated.inl 455122 2014-12-23 13:35:10Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -104,9 +104,11 @@ CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUnicode& src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
}
@@ -118,9 +120,11 @@ inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const wstring& src) {
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TUnicodeSymbol* src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
inline CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
}
@@ -135,11 +139,13 @@ CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TUnicodeSymbol* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#endif
inline
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
@@ -180,10 +186,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TStringU
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -198,10 +206,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TUnicode
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator= (const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -216,10 +226,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TString
append( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TStringUCS4& src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TStringUCS2& src) {
append( CUtf8::AsUTF8(src));
return *this;
@@ -234,10 +246,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TUnicod
append( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TCharUCS4* src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::operator+= (const TCharUCS2* src) {
append( CUtf8::AsUTF8(src));
return *this;
@@ -258,10 +272,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TStringUnico
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -276,10 +292,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TUnicodeSymb
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -295,11 +313,13 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Assign(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
@@ -325,10 +345,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TStringUnic
append( CUtf8::AsUTF8( src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TStringUCS4& src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TStringUCS2& src) {
append( CUtf8::AsUTF8( src));
return *this;
@@ -343,10 +365,12 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TUnicodeSymb
append( CUtf8::AsUTF8( src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TCharUCS4* src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(const TCharUCS2* src) {
append( CUtf8::AsUTF8( src));
return *this;
@@ -362,11 +386,13 @@ inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#endif
inline CStringUTF8_DEPRECATED& CStringUTF8_DEPRECATED::Append(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
@@ -562,12 +588,14 @@ basic_string<TUnicodeSymbol> CStringUTF8_DEPRECATED::AsBasicString(
{
return CUtf8::x_AsBasicString(str,substitute_on_error, (CUtf8::EValidate)validate);
}
+#if NCBITOOLKIT_USE_LONG_UCS4
template <> inline
basic_string<TCharUCS4> CStringUTF8_DEPRECATED::AsBasicString(
const CTempString& str, const TCharUCS4* substitute_on_error, EValidate validate)
{
return CUtf8::x_AsBasicString(str,substitute_on_error, (CUtf8::EValidate)validate);
}
+#endif
template <> inline
basic_string<TCharUCS2> CStringUTF8_DEPRECATED::AsBasicString(
const CTempString& str, const TCharUCS2* substitute_on_error, EValidate validate)
diff --git a/c++/include/corelib/metareg.hpp b/c++/include/corelib/metareg.hpp
index 5afa478..98cf380 100644
--- a/c++/include/corelib/metareg.hpp
+++ b/c++/include/corelib/metareg.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___METAREG__HPP
#define CORELIB___METAREG__HPP
-/* $Id: metareg.hpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: metareg.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,9 +35,7 @@
/// files; keeps track of what it loaded from where, for potential
/// reuse.
-#include <corelib/ncbimtx.hpp>
#include <corelib/ncbireg.hpp>
-#include <corelib/ncbitime.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/include/corelib/ncbi_autoinit.hpp b/c++/include/corelib/ncbi_autoinit.hpp
index da5d9a9..b8a5464 100644
--- a/c++/include/corelib/ncbi_autoinit.hpp
+++ b/c++/include/corelib/ncbi_autoinit.hpp
@@ -1,7 +1,7 @@
#ifndef NCBI_AUTOINIT__HPP
#define NCBI_AUTOINIT__HPP
-/* $Id: ncbi_autoinit.hpp 177354 2009-11-30 19:23:37Z grichenk $
+/* $Id: ncbi_autoinit.hpp 478278 2015-09-08 14:32:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -65,6 +65,8 @@ public:
~CAutoInitPtr_Base(void);
+ bool IsInitialized(void) const;
+
protected:
/// Cleanup function type used by derived classes
typedef void (*FSelfCleanup)(void** ptr);
@@ -83,6 +85,9 @@ protected:
m_UserCleanup(user_cleanup)
{}
+ // Make sure the pointer is uninitialized, _ASSERT otherwise.
+ void AssertUninitialized(void) const;
+
/// Pointer to the data
void* m_Ptr;
@@ -244,11 +249,21 @@ private:
//
// Large inline methods
+inline
+bool CAutoInitPtr_Base::IsInitialized(void) const
+{
+ CMutexGuard guard(sm_Mutex);
+ return m_Ptr != NULL;
+}
+
+
template <class T>
inline
void CAutoInitPtr<T>::Set(T* object)
{
CMutexGuard guard(sm_Mutex);
+ AssertUninitialized();
+ if ( m_Ptr ) return;
m_Ptr = object;
}
@@ -258,6 +273,7 @@ inline
void CAutoInitPtr<T>::x_Init(void)
{
CMutexGuard guard(sm_Mutex);
+ if ( m_Ptr ) return;
m_Ptr = new T;
}
@@ -268,6 +284,7 @@ inline
void CAutoInitPtr<T>::x_Init(FUserCreate user_create)
{
CMutexGuard guard(sm_Mutex);
+ if ( m_Ptr ) return;
m_Ptr = user_create();
}
@@ -277,6 +294,8 @@ inline
void CAutoInitRef<T>::Set(T* object)
{
CMutexGuard guard(sm_Mutex);
+ AssertUninitialized();
+ if ( m_Ptr ) return;
if ( object ) {
object->AddReference();
m_Ptr = object;
@@ -289,6 +308,7 @@ inline
void CAutoInitRef<T>::x_Init(void)
{
CMutexGuard guard(sm_Mutex);
+ if ( m_Ptr ) return;
CRef<T> ref(new T);
ref->AddReference();
m_Ptr = ref.Release();
@@ -301,6 +321,7 @@ inline
void CAutoInitRef<T>::x_Init(FUserCreate user_create)
{
CMutexGuard guard(sm_Mutex);
+ if ( m_Ptr ) return;
CRef<T> ref(user_create());
if ( ref ) {
ref->AddReference();
diff --git a/c++/include/corelib/ncbi_config.hpp b/c++/include/corelib/ncbi_config.hpp
index 07e8329..ba9ce06 100644
--- a/c++/include/corelib/ncbi_config.hpp
+++ b/c++/include/corelib/ncbi_config.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_CONFIG__HPP
#define CORELIB___NCBI_CONFIG__HPP
-/* $Id: ncbi_config.hpp 337341 2011-09-11 01:12:03Z lavr $
+/* $Id: ncbi_config.hpp 449355 2014-10-15 20:21:49Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,8 @@ class NCBI_XNCBI_EXPORT CConfigException : public CCoreException
public:
enum EErrCode {
eParameterMissing, ///< Missing mandatory parameter
- eSynonymDuplicate
+ eSynonymDuplicate,
+ eInvalidParameter, ///< Invalid parameter value
};
/// Translate from the error code value to its string representation.
diff --git a/c++/include/corelib/ncbi_cookies.hpp b/c++/include/corelib/ncbi_cookies.hpp
index 41c8bcd..e7b73fc 100644
--- a/c++/include/corelib/ncbi_cookies.hpp
+++ b/c++/include/corelib/ncbi_cookies.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_COOKIES__HPP
#define CORELIB___NCBI_COOKIES__HPP
-/* $Id: ncbi_cookies.hpp 436308 2014-05-27 15:45:33Z grichenk $
+/* $Id: ncbi_cookies.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,8 +33,6 @@
*/
-#include <corelib/ncbistl.hpp>
-#include <corelib/ncbistr.hpp>
#include <corelib/ncbi_url.hpp>
diff --git a/c++/include/corelib/ncbi_limits.hpp b/c++/include/corelib/ncbi_limits.hpp
index 39dc7a2..6999fab 100644
--- a/c++/include/corelib/ncbi_limits.hpp
+++ b/c++/include/corelib/ncbi_limits.hpp
@@ -1,7 +1,7 @@
#ifndef NCBI_LIMITS__HPP
#define NCBI_LIMITS__HPP
-/* $Id: ncbi_limits.hpp 431251 2014-04-02 16:03:33Z kazimird $
+/* $Id: ncbi_limits.hpp 455586 2014-12-31 15:48:34Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -67,6 +67,14 @@
*/
+// Always get rid of the old non-conformant min/max macros
+#ifdef min
+# undef min
+#endif
+#ifdef max
+# undef max
+#endif
+
#if defined(HAVE_LIMITS) && ( !defined(NCBI_COMPILER_WORKSHOP) || NCBI_COMPILER_VERSION >= 550)
// Ideally, we would use std::numeric_limits<> whenever available.
// However, certain compiler versions leave out support for extensions such
diff --git a/c++/include/corelib/ncbi_message.hpp b/c++/include/corelib/ncbi_message.hpp
new file mode 100644
index 0000000..8451e8a
--- /dev/null
+++ b/c++/include/corelib/ncbi_message.hpp
@@ -0,0 +1,309 @@
+#ifndef CORELIB___NCBI_MESSAGE__HPP
+#define CORELIB___NCBI_MESSAGE__HPP
+
+/* $Id: ncbi_message.hpp 477857 2015-09-02 13:15:07Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Authors: Aleksey Grichenko
+ *
+ * File Description: IMessage/IMessageListener interfaces
+ *
+ */
+
+/// @file ncbi_message.hpp
+///
+/// IMessage/IMessageListener interfaces and basic implementations.
+///
+
+#include <corelib/ncbiobj.hpp>
+#include <list>
+#include <corelib/version.hpp>
+
+/** @addtogroup MESSAGE
+ *
+ * @{
+ */
+
+BEGIN_NCBI_SCOPE
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// IMessage_Base::
+///
+/// Common base class for IMessage and IProgressMessage.
+///
+
+class IMessage_Base
+{
+public:
+ virtual ~IMessage_Base(void) {}
+
+ /// Get text message.
+ virtual string GetText(void) const = 0;
+
+ /// Print the message and any additional information to the stream.
+ virtual void Write(CNcbiOstream& out) const = 0;
+
+ /// Get the whole composed message as string.
+ /// The default implementations use Write() to compose the string.
+ virtual string Compose(void) const = 0;
+
+ /// Create a copy of the message. The caller is responsible for
+ /// destroying the copy.
+ virtual IMessage_Base* Clone(void) const = 0;
+};
+
+
+inline
+ostream& operator<<(CNcbiOstream& out, const IMessage_Base& msg)
+{
+ msg.Write(out);
+ return out;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// IMessage::
+///
+/// Generic message interface to be used with IMessageListener to collect and
+/// report error messages.
+///
+
+class IMessage : public IMessage_Base
+{
+public:
+ virtual ~IMessage(void) {}
+
+ /// Get message severity.
+ virtual EDiagSev GetSeverity(void) const = 0;
+
+ /// Get error code. Zero = not set.
+ virtual int GetCode(void) const = 0;
+
+ /// Get error subcode. Zero = not set.
+ virtual int GetSubCode(void) const = 0;
+
+ virtual IMessage* Clone(void) const = 0;
+};
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// IProgressMessage::
+///
+/// Generic progress status interface to be used with IMessageListener.
+/// Unlike IMessage, typical IProgressMessage is intended for immediate
+/// display rather than collecting and reporting later.
+///
+
+class IProgressMessage : public IMessage_Base
+{
+public:
+ virtual ~IProgressMessage(void) {}
+
+ /// Get current progress value (e.g. % or bytes written).
+ virtual Uint8 GetCurrent(void) const = 0;
+
+ /// Get total progress value (e.g. 100% or file size).
+ virtual Uint8 GetTotal(void) const = 0;
+
+ virtual IProgressMessage* Clone(void) const = 0;
+};
+
+
+/// Default IMessage implementation: text and severity only.
+class NCBI_XNCBI_EXPORT CMessage_Basic : public IMessage
+{
+public:
+ CMessage_Basic(const string& txt,
+ EDiagSev sev,
+ int err_code = 0,
+ int sub_code = 0);
+
+ virtual string GetText(void) const;
+ virtual EDiagSev GetSeverity(void) const;
+ virtual int GetCode(void) const;
+ virtual int GetSubCode(void) const;
+ virtual IMessage* Clone(void) const;
+ virtual void Write(CNcbiOstream& out) const;
+ virtual string Compose(void) const;
+
+private:
+ string m_Text;
+ EDiagSev m_Severity;
+ int m_ErrCode;
+ int m_SubCode;
+};
+
+
+/// Default IProgressMessage implementation.
+class NCBI_XNCBI_EXPORT CProgressMessage_Basic : public IProgressMessage
+{
+public:
+ CProgressMessage_Basic(const string& txt,
+ Uint8 current,
+ Uint8 total);
+
+ virtual string GetText(void) const;
+ virtual Uint8 GetCurrent(void) const;
+ virtual Uint8 GetTotal(void) const;
+ virtual CProgressMessage_Basic* Clone(void) const;
+ virtual void Write(CNcbiOstream& out) const;
+ virtual string Compose(void) const;
+
+private:
+ string m_Text;
+ Uint8 m_Current;
+ Uint8 m_Total;
+};
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// IMessageListener::
+///
+/// Interface for IMessage listener/collector.
+///
+
+class NCBI_XNCBI_EXPORT IMessageListener : public CObject
+{
+public:
+ virtual ~IMessageListener(void) {}
+
+ /// Result of PostXXXX() operation.
+ enum EPostResult {
+ eHandled, ///< The message was successfully handled and will not be
+ ///< passed to other listeners installed with
+ ///< eListen_Unhandled flag.
+ eUnhandled ///< The message was not handled and should be passed to
+ ///< other listeners.
+ };
+
+ /// Post new message to the listener.
+ virtual EPostResult PostMessage(const IMessage& message) = 0;
+
+ /// Report progress.
+ /// @param message
+ /// Text message explaining the current state.
+ /// @param current
+ /// Current progress value.
+ /// @param total
+ /// Max progress value.
+ virtual EPostResult PostProgress(const IProgressMessage& progress) = 0;
+
+ /// Get a previously collected message.
+ /// @param index
+ /// Index of the message, must be less than Count().
+ virtual const IMessage& GetMessage(size_t index) const = 0;
+
+ /// Get total number of collected messages.
+ virtual size_t Count(void) const = 0;
+
+ /// Clear all collected messages.
+ virtual void Clear(void) = 0;
+
+ /// Which messages should be passed to the listener
+ enum EListenFlag {
+ eListen_Unhandled, ///< Default flag. The listener only wants messages
+ ///< not handled by previous listeners.
+ eListen_All ///< The listener wants to see all messages, even
+ ///< those already handled.
+ };
+
+ /// Push a new listener to the stack in the current thread.
+ /// @param listener
+ /// The listener to be installed.
+ /// @param flag
+ /// Flag specifying if the new listener should receive all messages
+ /// or only those not handled by other listeners above the current.
+ /// @return
+ /// Total number of listeners in the current thread's stack including
+ /// the new one. This number can be passed to PopListener() for more
+ /// reliable cleanup.
+ /// @sa PopListener()
+ static size_t PushListener(IMessageListener& listener,
+ EListenFlag flag = eListen_Unhandled);
+
+ /// Remove listener(s) from the current thread's stack.
+ /// @param depth
+ /// Index of the listener to be removed, as returned by PushListener().
+ /// If the depth is zero (default), only the topmost listener is removed.
+ /// If there are listeners whose index is larger than (non-zero) depth, then
+ /// all such listeners will be removed too, and a warning will be posted.
+ /// If the current stack size is less than depth, no action is performed,
+ /// and a warning will be posted.
+ /// @sa PushListener()
+ static void PopListener(size_t depth = 0);
+
+ /// Check if there are any listeners installed in the current thread.
+ static bool HaveListeners(void);
+
+ /// Post the message to listener(s), if any. The message is posted
+ /// to each listener starting from the top of the stack. After a
+ /// listener returns eHandled, the message is posted only to the
+ /// listeners which were installed with eListen_All flag.
+ /// @return
+ /// eHandled if at least one listener has handled the message,
+ /// eUnhandled otherwise.
+ /// @sa PostMessage()
+ static EPostResult Post(const IMessage& message);
+
+ /// Post the progress to listener(s), if any. The progress is posted
+ /// to each listener starting from the top of the stack. After a
+ /// listener returns eHandled, the progress is posted only to the
+ /// listeners which were installed with eListen_All flag.
+ /// @return
+ /// eHandled if at least one listener has handled the event,
+ /// eUnhandled otherwise.
+ /// @sa PostProgress()
+ static EPostResult Post(const IProgressMessage& progress);
+};
+
+
+/// Default implementation of IMessageListener: collects all messages
+/// posted.
+class NCBI_XNCBI_EXPORT CMessageListener_Basic : public IMessageListener
+{
+public:
+ virtual EPostResult PostMessage(const IMessage& message);
+ virtual EPostResult PostProgress(const IProgressMessage& progress);
+ virtual const IMessage& GetMessage(size_t index) const;
+ virtual size_t Count(void) const;
+ virtual void Clear(void);
+private:
+ typedef vector< AutoPtr<IMessage> > TMessages;
+
+ TMessages m_Messages;
+};
+
+
+/* @} */
+
+END_NCBI_SCOPE
+
+#include <corelib/impl/listener_stack.hpp>
+
+#endif /* CORELIB___NCBI_MESSAGE__HPP */
diff --git a/c++/include/corelib/ncbi_os_mswin.hpp b/c++/include/corelib/ncbi_os_mswin.hpp
index eed4554..8a9d3a6 100644
--- a/c++/include/corelib/ncbi_os_mswin.hpp
+++ b/c++/include/corelib/ncbi_os_mswin.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_OS_MSWIN__HPP
#define CORELIB___NCBI_OS_MSWIN__HPP
-/* $Id: ncbi_os_mswin.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: ncbi_os_mswin.hpp 477856 2015-09-02 13:14:44Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,6 +63,27 @@ inline int GetObject(HGDIOBJ hGdiObj, int cbBuffer, LPVOID lpvObject)
#endif
+#ifdef GetMessage
+# undef GetMessage
+inline
+WINUSERAPI
+BOOL
+WINAPI
+GetMessage(
+ _Out_ LPMSG lpMsg,
+ _In_opt_ HWND hWnd,
+ _In_ UINT wMsgFilterMin,
+ _In_ UINT wMsgFilterMax)
+{
+# ifdef _UNICODE
+ return GetMessageW(lpMsg, hWnd, wMsgFilterMin, wMsgFilterMax);
+# else
+ return GetMessageA(lpMsg, hWnd, wMsgFilterMin, wMsgFilterMax);
+# endif
+}
+#endif
+
+
// DrawText
#ifdef DrawText
# undef DrawText
diff --git a/c++/include/corelib/ncbi_param.hpp b/c++/include/corelib/ncbi_param.hpp
index 3403edb..9ad97ac 100644
--- a/c++/include/corelib/ncbi_param.hpp
+++ b/c++/include/corelib/ncbi_param.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_PARAM__HPP
#define CORELIB___NCBI_PARAM__HPP
-/* $Id: ncbi_param.hpp 448556 2014-10-07 16:40:16Z ivanov $
+/* $Id: ncbi_param.hpp 445853 2014-09-09 13:27:06Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbi_process.hpp b/c++/include/corelib/ncbi_process.hpp
index 24e7fdc..81c3de8 100644
--- a/c++/include/corelib/ncbi_process.hpp
+++ b/c++/include/corelib/ncbi_process.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_PROCESS__HPP
#define CORELIB___NCBI_PROCESS__HPP
-/* $Id: ncbi_process.hpp 440243 2014-07-10 16:14:32Z kazimird $
+/* $Id: ncbi_process.hpp 465029 2015-04-16 13:28:52Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,6 +42,7 @@
#include <corelib/ncbistr.hpp>
+#include <corelib/interprocess_lock.hpp>
#if defined(NCBI_OS_UNIX)
# include <sys/types.h>
@@ -112,17 +113,41 @@ public:
CProcess(TProcessHandle process, EProcessType type = eHandle);
#endif
+ /// Get type of stored process identifier.
+ /// @note
+ /// On Windows process identifiers and process handles are different.
+ /// On UNIX handle/pid are the same and GetHandle()/GetPid() return
+ /// the same value.
+ EProcessType GetType(void) const { return m_Type; }
+
+ /// Get stored process handle.
+ /// @sa
+ /// GetCurrentHandle
+ TProcessHandle GetHandle(void) const { return (TProcessHandle)m_Process; }
+
+ /// Get stored process identifier (pid).
+ /// @sa
+ /// GetCurrentPid
+ TPid GetPid(void) const { return (TPid)m_Process; }
+
/// Get process handle for the current process (esp. on Windows).
- /// On UNIX returns the same that GetCurrentPid() does.
+ /// @note
+ /// On Windows process identifiers and process handles are different.
+ /// On UNIX handle/pid are the same and GetCurrentHandle()/GetCurrentPid()
+ /// return the same value.
/// @sa
/// GetCurrentPid
static TProcessHandle GetCurrentHandle(void);
/// Get process identifier for the current process.
- static TPid GetCurrentPid(void);
+ /// @sa
+ /// GetCurrentHandle
+ static TPid GetCurrentPid(void);
/// Get process identifier for the parent of the current process.
- static TPid GetParentPid(void);
+ /// @sa
+ /// GetCurrentPid
+ static TPid GetParentPid(void);
/// Check for process existence.
///
@@ -317,6 +342,7 @@ public:
///< but return
fDF_AllowExceptions = 32, ///< Throw an exception in case
///< of an error.
+ fDF_AllowThreads = 64, ///< Do not fail if pre-existing threads are detected
fDontChroot = fDF_KeepCWD, ///< @deprecated Use fDF_KeepCWD instead
fKeepStdin = fDF_KeepStdin, ///< @deprecated Use fDF_KeepStdin instead
@@ -400,8 +426,7 @@ public:
const CException* prev_exception, EErrCode err_code,
const string& message, TPid pid = 0,
EDiagSev severity = eDiag_Error)
- : CException(info, prev_exception, CException::eInvalid,
- message),
+ : CException(info, prev_exception, message, severity),
m_PID(pid)
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(CPIDGuardException, CException);
@@ -427,9 +452,7 @@ private:
/////////////////////////////////////////////////////////////////////////////
///
-/// CPIDGuard --
-///
-/// Define process guard.
+/// CPIDGuard -- Process guard.
///
/// If file already exists, CPIDGuard try to check that the process with PID
/// specified in the file is running or not. If guarded process is still
@@ -438,9 +461,13 @@ private:
/// This means that some CPIDGuard objects can be created for the same PID
/// and file name.
///
-/// NOTE: This method to protect PID file works only within one process.
-/// CPIDGuard know nothing about PID file modification or deletion
-/// by other processes. Be aware.
+/// @note
+/// If you need something just to prevent run some application twice,
+/// please look to CInterProcessLock class.
+/// @note
+/// CPIDGuard know nothing about PID file modification or deletion
+/// by other processes directly, without using this API. Be aware.
+///
class NCBI_XNCBI_EXPORT CPIDGuard
{
@@ -456,9 +483,6 @@ public:
/// Just calls Release();
~CPIDGuard(void);
- /// Returns non-zero if there was a stale file.
- TPid GetOldPID(void) { return m_OldPID; }
-
/// Release PID.
///
/// Decrease reference counter for current PID and remove the file
@@ -478,10 +502,19 @@ public:
/// the parent.
void UpdatePID(TPid pid = 0);
+ /// Returns non-zero if there was a stale file.
+ /// Always return 0, because new implementation don't allow
+ /// any stale file left on the file system.
+ ///
+ /// @deprecated
+ NCBI_DEPRECATED
+ TPid GetOldPID(void) { return 0; }
+
private:
- string m_Path; //< File path to store PID.
- TPid m_OldPID; //< Old PID read from file.
- TPid m_NewPID; //< New PID wroted to file.
+ string m_Path; //< File path to store PID.
+ TPid m_PID; //< Sored PID.
+ auto_ptr<CInterProcessLock> m_MTGuard; //< MT-Safe protection guard.
+ auto_ptr<CInterProcessLock> m_PIDGuard; //< Guard to help with "PID reuse" problem.
};
diff --git a/c++/include/corelib/ncbi_url.hpp b/c++/include/corelib/ncbi_url.hpp
index 315eb37..3eccf73 100644
--- a/c++/include/corelib/ncbi_url.hpp
+++ b/c++/include/corelib/ncbi_url.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_URL__HPP
#define CORELIB___NCBI_URL__HPP
-/* $Id: ncbi_url.hpp 443011 2014-08-08 21:14:52Z mcelhany $
+/* $Id: ncbi_url.hpp 442459 2014-08-04 15:36:07Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbiapp.hpp b/c++/include/corelib/ncbiapp.hpp
index 67742d6..572b482 100644
--- a/c++/include/corelib/ncbiapp.hpp
+++ b/c++/include/corelib/ncbiapp.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIAPP__HPP
#define CORELIB___NCBIAPP__HPP
-/* $Id: ncbiapp.hpp 452158 2014-11-17 15:22:47Z ivanov $
+/* $Id: ncbiapp.hpp 450653 2014-10-29 13:14:43Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbiargs.hpp b/c++/include/corelib/ncbiargs.hpp
index 9007180..1553264 100644
--- a/c++/include/corelib/ncbiargs.hpp
+++ b/c++/include/corelib/ncbiargs.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIARGS__HPP
#define CORELIB___NCBIARGS__HPP
-/* $Id: ncbiargs.hpp 448573 2014-10-07 16:47:45Z ivanov $
+/* $Id: ncbiargs.hpp 466633 2015-05-05 15:36:22Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -282,18 +282,24 @@ public:
return m_Ordinal;
}
+ /// Whether the argument:
+ /// @sa GetDefault()
enum EArgValueFlags {
- fArgValue_HasDefault = (1 << 0), /// argument has default value
- fArgValue_FromDefault = (1 << 1) /// argument was not provided on command line
+ fArgValue_HasDefault = (1 << 0), ///< Has default value
+ fArgValue_FromDefault = (1 << 1) ///< Not provided in command line
};
- typedef unsigned int TArgValueFlags;
+ typedef unsigned int TArgValueFlags; ///< Bitwise OR of "EArgValueFlags"
- /// Get default value if any, as string.
+ /// Get default value of the argument.
///
- /// @param has_default
- /// Flags inidicate whether or not the argument has default value,
- /// and was it set from command line, or from the default.
- const string& GetDefault(TArgValueFlags* has_default = NULL) const;
+ /// @param flags
+ /// Indicate whether the argument has default value, and if the arg's
+ /// value was set from the command line or from the default value.
+ /// @return
+ /// Default value, if specified for this argument.
+ /// If the argument doesn't have a default value: empty string.
+ /// If the argument is a flag: "false" or "true".
+ const string& GetDefault(TArgValueFlags* flags = NULL) const;
protected:
friend class CArgs;
@@ -354,6 +360,17 @@ public:
/// Destructor.
~CArgs(void);
+ /// Creating copy of this object usually makes no sense
+ /// if it is really required, please use Assign method
+ NCBI_DEPRECATED_CTOR(CArgs(const CArgs& other));
+
+ /// Creating copy of this object usually makes no sense
+ /// if it is really required, please use Assign method
+ NCBI_DEPRECATED CArgs& operator=(const CArgs& other);
+
+ /// Copy contents of another object into this one
+ CArgs& Assign(const CArgs& other);
+
/// Check existence of argument description.
///
/// Return TRUE if arg "name" was described in the parent CArgDescriptions.
@@ -602,7 +619,19 @@ public:
fMandatorySeparator = (1 << 7),
/// Hide it in Usage
- fHidden = (1 << 10)
+ fHidden = (1 << 10),
+
+ /// Confidential argument
+ /// Such arguments can be read from command line, from file, or from
+ /// console.
+ /// On command line, they can appear in one of the following forms:
+ /// -key -- read value from console, with automatically
+ /// generated prompt
+ /// -key-file fname -- read value from file 'fname',
+ /// if 'fname' equals '-', read value from
+ /// standard input (stdin) without any prompt
+ /// -key-verbatim value -- read value from the command line, as is
+ fConfidential = (1 << 13)
};
typedef unsigned int TFlags; ///< Bitwise OR of "EFlags"
@@ -668,8 +697,11 @@ public:
EType type, ///< Argument type
const string& default_value, ///< Default value
TFlags flags = 0, ///< Optional flags
- /// Optional name of environment variable that contains default value
- const string& env_var = kEmptyStr
+ /// Optional name of environment variable that
+ /// contains default value
+ const string& env_var = kEmptyStr,
+ /// Default value shown in Usage
+ const char* display_value = nullptr
);
/// Add description for flag argument.
@@ -784,8 +816,11 @@ public:
EType type, ///< Argument type
const string& default_value, ///< Default value
TFlags flags = 0, ///< Optional flags
- /// Optional name of environment variable that contains default value
- const string& env_var = kEmptyStr
+ /// Optional name of environment variable that
+ /// contains default value
+ const string& env_var = kEmptyStr,
+ /// Default value shown in Usage
+ const char* display_value = nullptr
);
/// Add description for the extra, unnamed positional arguments.
diff --git a/c++/include/corelib/ncbicntr.hpp b/c++/include/corelib/ncbicntr.hpp
index b60b584..46fc769 100644
--- a/c++/include/corelib/ncbicntr.hpp
+++ b/c++/include/corelib/ncbicntr.hpp
@@ -1,7 +1,7 @@
#ifndef NCBICNTR__HPP
#define NCBICNTR__HPP
-/* $Id: ncbicntr.hpp 434180 2014-05-05 14:10:19Z ucko $
+/* $Id: ncbicntr.hpp 463582 2015-03-30 18:03:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -232,8 +232,13 @@ THROWS_NONE
*value_p = result;
# elif defined(__i386) || defined(__x86_64)
// Yay CISC. ;-) (WorkShop already handled.)
+# ifdef NCBI_COUNTER_64_BIT
+ asm volatile("lock; xaddq %1, %0" : "=m" (*nv_value_p), "=r" (result)
+ : "1" (Int8(delta)), "m" (*nv_value_p));
+# else
asm volatile("lock; xaddl %1, %0" : "=m" (*nv_value_p), "=r" (result)
: "1" (delta), "m" (*nv_value_p));
+#endif
result += delta;
# else
# error "Unsupported processor type for assembly implementation!"
diff --git a/c++/include/corelib/ncbictype.hpp b/c++/include/corelib/ncbictype.hpp
new file mode 100644
index 0000000..f93c447
--- /dev/null
+++ b/c++/include/corelib/ncbictype.hpp
@@ -0,0 +1,81 @@
+#ifndef CORELIB___NCBICTYPE__HPP
+#define CORELIB___NCBICTYPE__HPP
+
+/* $Id: ncbictype.hpp 453380 2014-12-03 14:39:19Z ucko $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Denis Vakatov, Eugene Vasilchenko
+ *
+ *
+ */
+
+/// @file ncbictype.hpp
+/// Catch attempts to call ctype functions with bad types
+
+
+#include <corelib/ncbistl.hpp>
+#include <corelib/ncbitype.h>
+#include <cctype>
+
+#if !defined(NCBI_NO_STRICT_CTYPE_ARGS)
+# define NCBI_STRICT_CTYPE_ARGS
+#endif
+
+#ifdef NCBI_STRICT_CTYPE_ARGS
+
+# define NCBI_STRICT_CTYPE_ARGS_ACTIVE
+
+BEGIN_STD_NAMESPACE;
+
+#define NCBI_DEFINE_CTYPE_FUNC(name) \
+ inline int name(Uchar c) { return name(int(c)); } \
+ inline int name(char c) { return name(Uchar(c)); } \
+ template<class C> inline int name(C c) \
+ { return See_the_standard_on_proper_argument_type_for_ctype_functions(c); }
+
+NCBI_DEFINE_CTYPE_FUNC(isalpha)
+NCBI_DEFINE_CTYPE_FUNC(isalnum)
+NCBI_DEFINE_CTYPE_FUNC(iscntrl)
+NCBI_DEFINE_CTYPE_FUNC(isdigit)
+NCBI_DEFINE_CTYPE_FUNC(isgraph)
+NCBI_DEFINE_CTYPE_FUNC(islower)
+NCBI_DEFINE_CTYPE_FUNC(isprint)
+NCBI_DEFINE_CTYPE_FUNC(ispunct)
+NCBI_DEFINE_CTYPE_FUNC(isspace)
+NCBI_DEFINE_CTYPE_FUNC(isupper)
+NCBI_DEFINE_CTYPE_FUNC(isxdigit)
+NCBI_DEFINE_CTYPE_FUNC(tolower)
+NCBI_DEFINE_CTYPE_FUNC(toupper)
+//NCBI_DEFINE_CTYPE_FUNC(isblank)
+//NCBI_DEFINE_CTYPE_FUNC(isascii)
+//NCBI_DEFINE_CTYPE_FUNC(toascii)
+
+#undef NCBI_DEFINE_CTYPE_FUNC
+
+END_STD_NAMESPACE;
+
+#endif // NCBI_STRICT_CTYPE_ARGS
+
+#endif /* CORELIB___NCBICTYPE__HPP */
diff --git a/c++/include/corelib/ncbidbg.hpp b/c++/include/corelib/ncbidbg.hpp
index 437e13e..ee7eaff 100644
--- a/c++/include/corelib/ncbidbg.hpp
+++ b/c++/include/corelib/ncbidbg.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIDBG__HPP
#define CORELIB___NCBIDBG__HPP
-/* $Id: ncbidbg.hpp 405291 2013-07-02 14:58:43Z vasilche $
+/* $Id: ncbidbg.hpp 470099 2015-06-11 11:28:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -62,32 +62,30 @@ BEGIN_NCBI_SCOPE
/// Define macros to support debugging.
-#ifdef _DEBUG
-
-# define _TRACE(message) \
+#define _ALWAYS_TRACE(message) \
( NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO, \
NCBI_NS_NCBI::eDiag_Trace).GetRef() \
<< message << NCBI_NS_NCBI::Endm )
-# define _TRACE_EX(err_code, err_subcode, message) \
+#define _ALWAYS_TRACE_EX(err_code, err_subcode, message) \
( NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO \
NCBI_NS_NCBI::eDiag_Trace).GetRef() \
<< NCBI_NS_NCBI::ErrCode( (err_code), (err_subcode) ) \
<< message << NCBI_NS_NCBI::Endm )
-# define _TRACE_X(err_subcode, message) \
- _TRACE_XX(NCBI_USE_ERRCODE_X, err_subcode, message)
+#define _ALWAYS_TRACE_X(err_subcode, message) \
+ _ALWAYS_TRACE_XX(NCBI_USE_ERRCODE_X, err_subcode, message)
-# define _TRACE_XX(error_name, err_subcode, message) \
+#define _ALWAYS_TRACE_XX(error_name, err_subcode, message) \
( (NCBI_CHECK_ERR_SUBCODE_X_NAME(error_name, err_subcode)), \
- _TRACE_EX(NCBI_ERRCODE_X_NAME(error_name), err_subcode, message) )
+ _ALWAYS_TRACE_EX(NCBI_ERRCODE_X_NAME(error_name), err_subcode, message) )
-# define NCBI_TROUBLE(mess) \
+#define NCBI_ALWAYS_TROUBLE(mess) \
NCBI_NS_NCBI::CNcbiDiag::DiagTrouble(DIAG_COMPILE_INFO, mess)
-# ifdef NCBI_COMPILER_MSVC
+#ifdef NCBI_COMPILER_MSVC
// Use standard _ASSERT macro on MSVC in Debug modes
-# define NCBI_ASSERT(expr, mess) \
+# define NCBI_ALWAYS_ASSERT(expr, mess) \
do { \
bool x_expr = ((expr)? true : false); \
const char* x_mess = (mess); \
@@ -103,18 +101,33 @@ BEGIN_NCBI_SCOPE
DIAG_COMPILE_INFO, #expr, mess); \
} \
} while ( 0 )
-# define NCBI_ASSERT_EXPR(expr, mess) \
+# define NCBI_ALWAYS_ASSERT_EXPR(expr, mess) \
((expr)?(void)0:NCBI_NS_NCBI::CNcbiDiag::DiagAssert(DIAG_COMPILE_INFO, #expr, mess))
-# else /* NCBI_COMPILER_MSVC */
-# define NCBI_ASSERT(expr, mess) \
+#else /* NCBI_COMPILER_MSVC */
+# define NCBI_ALWAYS_ASSERT(expr, mess) \
do { if ( !(expr) ) \
NCBI_NS_NCBI::CNcbiDiag::DiagAssert(DIAG_COMPILE_INFO, #expr, mess); \
} while ( 0 )
-# define NCBI_ASSERT_EXPR(expr, mess) \
+# define NCBI_ALWAYS_ASSERT_EXPR(expr, mess) \
((expr)?(void)0:NCBI_NS_NCBI::CNcbiDiag::DiagAssert(DIAG_COMPILE_INFO, #expr, mess))
-# endif
+#endif
-# define NCBI_VERIFY(expr, mess) NCBI_ASSERT(expr, mess)
+#define NCBI_ALWAYS_VERIFY(expr, mess) NCBI_ALWAYS_ASSERT(expr, mess)
+
+
+#ifdef _DEBUG
+
+# define _TRACE(message) _ALWAYS_TRACE(message)
+# define _TRACE_EX(err_code, err_subcode, message) \
+ _ALWAYS_TRACE_EX(err_code, err_subcode, message)
+# define _TRACE_X(err_subcode, message) _ALWAYS_TRACE_X(err_subcode, message)
+# define _TRACE_XX(error_name, err_subcode, message) \
+ _ALWAYS_TRACE_XX(error_name, err_subcode, message)
+
+# define NCBI_TROUBLE(mess) NCBI_ALWAYS_TROUBLE(mess)
+# define NCBI_ASSERT(expr, mess) NCBI_ALWAYS_ASSERT(expr, mess)
+# define NCBI_ASSERT_EXPR(expr, mess) NCBI_ALWAYS_ASSERT_EXPR(expr, mess)
+# define NCBI_VERIFY(expr, mess) NCBI_ALWAYS_VERIFY(expr, mess)
# define _DEBUG_ARG(arg) arg
@@ -142,9 +155,13 @@ BEGIN_NCBI_SCOPE
#ifdef _ASSERT
# undef _ASSERT
#endif
-#define _ASSERT(expr) NCBI_ASSERT(expr, NULL)
-#define _VERIFY(expr) NCBI_VERIFY(expr, NULL)
-#define _TROUBLE NCBI_TROUBLE(NULL)
+#define _ASSERT(expr) NCBI_ASSERT(expr, "")
+#define _VERIFY(expr) NCBI_VERIFY(expr, "")
+#define _TROUBLE NCBI_TROUBLE("")
+
+#define _ALWAYS_ASSERT(expr) NCBI_ALWAYS_ASSERT(expr, "")
+#define _ALWAYS_VERIFY(expr) NCBI_ALWAYS_VERIFY(expr, "")
+#define _ALWAYS_TROUBLE NCBI_ALWAYS_TROUBLE("")
/// Which action to perform.
diff --git a/c++/include/corelib/ncbidiag.hpp b/c++/include/corelib/ncbidiag.hpp
index b699bf6..264bc3a 100644
--- a/c++/include/corelib/ncbidiag.hpp
+++ b/c++/include/corelib/ncbidiag.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIDIAG__HPP
#define CORELIB___NCBIDIAG__HPP
-/* $Id: ncbidiag.hpp 467442 2015-05-13 17:29:03Z ivanov $
+/* $Id: ncbidiag.hpp 483520 2015-11-02 14:44:26Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -187,21 +187,26 @@ NCBI_XNCBI_EXPORT const char* g_DiagUnknownFunction(void);
<< message \
<< NCBI_NS_NCBI::Endm )
-
-/// Log message only without severity, location, prefix information.
-/// This macro is deprecated and it's strongly recomended to move
-/// in all projects (except tests) to macro LOG_POST_X to make possible more
-/// flexible error statistics and logging.
-///
-/// @sa
-/// LOG_POST_EX, LOG_POST_X
+// When printing a message in 'old' (human readable) format LOG_POST skips
+// all fields except the message.
#define LOG_POST(message) \
( NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO, \
NCBI_NS_NCBI::eDiag_Error, \
- NCBI_NS_NCBI::eDPF_Log | NCBI_NS_NCBI::eDPF_IsMessage).GetRef() \
+ NCBI_NS_NCBI::eDPF_Log | NCBI_NS_NCBI::eDPF_IsNote).GetRef() \
<< message \
<< NCBI_NS_NCBI::Endm )
+/// Posting fatal error and abort.
+/// This macro is deprecated and it's strongly recomended to move in all
+/// projects (except tests) to macro ERR_FATAL_X to make possible more
+/// flexible error statistics and logging.
+///
+/// @sa
+/// ERR_FATAL_X, ERR_POST
+#define ERR_FATAL(message) \
+ NCBI_NS_NCBI::EndmFatal(NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO, \
+ NCBI_NS_NCBI::eDiag_Fatal).GetRef() << message )
+
/// Error posting with error codes.
/// This macro should be used only when you need to make non-constant
/// error subcode. In all other cases it's strongly recomended to move
@@ -216,26 +221,23 @@ NCBI_XNCBI_EXPORT const char* g_DiagUnknownFunction(void);
<< message \
<< NCBI_NS_NCBI::Endm )
-/// Log posting with error codes.
-/// This macro should be used only when you need to make non-constant
-/// error subcode. In all other cases it's strongly recomended to move
-/// in all projects (except tests) to macro LOG_POST_X to make possible more
-/// flexible error statistics and logging.
-///
-/// @sa
-/// LOG_POST, LOG_POST_X
-#define LOG_POST_EX(err_code, err_subcode, message) \
+#define LOG_POST_EX(err_code, err_subcode, message) \
( NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO, \
NCBI_NS_NCBI::eDiag_Error, \
- NCBI_NS_NCBI::eDPF_Log | NCBI_NS_NCBI::eDPF_IsMessage).GetRef() \
- << NCBI_NS_NCBI::ErrCode( (err_code), (err_subcode) ) \
- << message << NCBI_NS_NCBI::Endm )
+ NCBI_NS_NCBI::eDPF_Log | NCBI_NS_NCBI::eDPF_IsNote).GetRef() \
+ << NCBI_NS_NCBI::ErrCode( (err_code), (err_subcode) ) \
+ << message \
+ << NCBI_NS_NCBI::Endm )
+#define ERR_FATAL_EX(err_code, err_subcode, message) \
+ NCBI_NS_NCBI::EndmFatal(NCBI_NS_NCBI::CNcbiDiag(DIAG_COMPILE_INFO, \
+ NCBI_NS_NCBI::eDiag_Fatal).GetRef() << \
+ NCBI_NS_NCBI::ErrCode( (err_code), (err_subcode) ) << message )
/// Define global error code name with given value (err_code) and given
/// maximum value of error subcode within this code. To use defined error
/// code you need to define symbol NCBI_USE_ERRCODE_X with name as its value.
-/// This error code is used only in macros LOG_POST_X and ERR_POST_X. Maximum
+/// This error code is used only in ERR_POST_X macro. Maximum
/// value of error subcode is being checked during compilation and
/// exists for developers to know what code they can use in next inserted
/// ERR_POST_X call (i.e. when one want to insert new ERR_POST_X call he has
@@ -256,7 +258,7 @@ NCBI_XNCBI_EXPORT const char* g_DiagUnknownFunction(void);
///
///
/// @sa
-/// NCBI_DEFINE_ERR_SUBCODE_X, LOG_POST_X, ERR_POST_X,
+/// NCBI_DEFINE_ERR_SUBCODE_X, ERR_POST_X,
/// NCBI_ERRCODE_X, NCBI_MAX_ERR_SUBCODE_X
#define NCBI_DEFINE_ERRCODE_X(name, err_code, max_err_subcode) \
namespace err_code_x { \
@@ -362,7 +364,7 @@ NCBI_XNCBI_EXPORT const char* g_DiagUnknownFunction(void);
/// maximum error subcode valid for active error code.
///
/// @sa
-/// NCBI_DEFINE_ERRCODE_X, NCBI_DEFINE_ERR_SUBCODE_X, LOG_POST_X, ERR_POST_X
+/// NCBI_DEFINE_ERRCODE_X, NCBI_DEFINE_ERR_SUBCODE_X, ERR_POST_X
template <int errorCode, int errorSubcode, int maxErrorSubcode, bool isWrong>
struct WRONG_ERROR_SUBCODE_IN_POST_MACRO;
@@ -413,7 +415,7 @@ inline void CheckErrSubcodeX(int)
/// For early versions of gcc used a bit different design to make error
/// message more clear to understand.
///
-/// @sa LOG_POST_X, ERR_POST_X
+/// @sa ERR_POST_X
#define NCBI_CHECK_ERR_SUBCODE_X_NAME(name, subcode) \
NCBI_NS_NCBI::CheckErrSubcodeX( \
NCBI_NS_NCBI::WRONG_ERROR_SUBCODE_IN_POST_MACRO< \
@@ -432,7 +434,7 @@ inline void CheckErrSubcodeX(int)
/// Though for MIPSpro and ICC it's not enough to make error message clear
/// (see addition below).
///
-/// @sa LOG_POST_X, ERR_POST_X
+/// @sa ERR_POST_X
#define NCBI_CHECK_ERR_SUBCODE_X_NAME(name, subcode) \
NCBI_NS_NCBI::CheckErrSubcodeX( \
(int)sizeof(NCBI_NS_NCBI::WRONG_ERROR_SUBCODE_IN_POST_MACRO< \
@@ -450,6 +452,14 @@ inline void CheckErrSubcodeX(int)
#define NCBI_CHECK_ERR_SUBCODE_X(subcode) \
NCBI_CHECK_ERR_SUBCODE_X_NAME(NCBI_USE_ERRCODE_X, subcode)
+/// Pass subcode as argument with check of its validity for given error code.
+#define NCBI_ERR_SUBCODE_X_NAME(name, subcode) \
+ (NCBI_CHECK_ERR_SUBCODE_X_NAME(name, subcode), subcode)
+
+/// Pass subcode as argument with check of its validity for current error code.
+#define NCBI_ERR_SUBCODE_X(subcode) \
+ (NCBI_CHECK_ERR_SUBCODE_X(subcode), subcode)
+
#if defined(NCBI_COMPILER_ICC) || defined(NCBI_COMPILER_MIPSPRO)
/// Additional not implemented template structure for use in
@@ -492,7 +502,7 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
/// Error posting with default error code and given error subcode. Also
/// checks subcode correctness. When error subcode is incorrect (greater than
/// defined in NCBI_DEFINE_ERRCODE_X) compile-time error is issued.
-/// All calls to ERR_POST_X or LOG_POST_X under the same default error code
+/// All calls to ERR_POST_X under the same default error code
/// MUST be with deferent error subcodes to make possible more
/// flexible error statistics and logging.
/// If using of macro leads to compile errors containing in message strings
@@ -528,32 +538,31 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
#define ERR_POST_X(err_subcode, message) \
ERR_POST_XX(NCBI_USE_ERRCODE_X, err_subcode, message)
-/// Log posting with default error code and given error subcode. See comments
-/// to ERR_POST_X for clarifying the way of use and details of behaviour
-/// of this macro.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, NCBI_ERRCODE_X, ERR_POST_X, LOG_POST_EX
#define LOG_POST_X(err_subcode, message) \
LOG_POST_XX(NCBI_USE_ERRCODE_X, err_subcode, message)
+#define ERR_FATAL_X(err_subcode, message) \
+ ERR_FATAL_XX(NCBI_USE_ERRCODE_X, err_subcode, message)
+
/// Error posting with error code having given name and with given error
/// subcode. Macro must be placed in headers instead of ERR_POST_X to not
/// confuse default error codes used in sources where this header is included.
///
/// @sa NCBI_DEFINE_ERRCODE_X, ERR_POST_X
-#define ERR_POST_XX(error_name, err_subcode, message) \
- ( (NCBI_CHECK_ERR_SUBCODE_X_NAME(error_name, err_subcode)), \
- ERR_POST_EX(NCBI_ERRCODE_X_NAME(error_name), err_subcode, message) )
+#define ERR_POST_XX(error_name, err_subcode, message) \
+ ERR_POST_EX(NCBI_ERRCODE_X_NAME(error_name), \
+ NCBI_ERR_SUBCODE_X_NAME(error_name, err_subcode), \
+ message)
-/// Log posting with error code having given name and with given error
-/// subcode. Macro must be placed in headers instead of LOG_POST_X to not
-/// confuse default error codes used in sources where this header is included.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, LOG_POST_X
-#define LOG_POST_XX(error_name, err_subcode, message) \
- ( (NCBI_CHECK_ERR_SUBCODE_X_NAME(error_name, err_subcode)), \
- LOG_POST_EX(NCBI_ERRCODE_X_NAME(error_name), err_subcode, message) )
+#define LOG_POST_XX(error_name, err_subcode, message) \
+ LOG_POST_EX(NCBI_ERRCODE_X_NAME(error_name), \
+ NCBI_ERR_SUBCODE_X_NAME(error_name, err_subcode), \
+ message)
+#define ERR_FATAL_XX(error_name, err_subcode, message) \
+ ERR_FATAL_EX(NCBI_ERRCODE_X_NAME(error_name), \
+ NCBI_ERR_SUBCODE_X_NAME(error_name, err_subcode), \
+ message)
/// Common code for making log or error posting only given number of times
/// during program execution. This macro MUST not be used outside
@@ -569,27 +578,19 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
} while ( false )
-/// Log posting only given number of times during program execution.
-#define LOG_POST_N_TIMES(count, message) \
- NCBI_REPEAT_POST_N_TIMES( LOG_POST, count, (message) )
-
/// Error posting only given number of times during program execution.
#define ERR_POST_N_TIMES(count, message) \
NCBI_REPEAT_POST_N_TIMES( ERR_POST, count, (message) )
-/// Log posting only once during program execution.
-#define LOG_POST_ONCE(message) LOG_POST_N_TIMES(1, message)
+#define LOG_POST_N_TIMES(count, message) \
+ NCBI_REPEAT_POST_N_TIMES( LOG_POST, count, (message) )
+
/// Error posting only once during program execution.
#define ERR_POST_ONCE(message) ERR_POST_N_TIMES(1, message)
+#define LOG_POST_ONCE(message) LOG_POST_N_TIMES(1, message)
-/// Log posting only given number of times during program execution
-/// with default error code and given error subcode.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, NCBI_ERRCODE_X, LOG_POST_X
-#define LOG_POST_X_N_TIMES(count, err_subcode, message) \
- NCBI_REPEAT_POST_N_TIMES( LOG_POST_X, count, (err_subcode, message) )
/// Error posting only given number of times during program execution
/// with default error code and given error subcode.
@@ -598,12 +599,8 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
#define ERR_POST_X_N_TIMES(count, err_subcode, message) \
NCBI_REPEAT_POST_N_TIMES( ERR_POST_X, count, (err_subcode, message) )
-/// Log posting only once during program execution with default
-/// error code and given error subcode.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, NCBI_ERRCODE_X, LOG_POST_X
-#define LOG_POST_X_ONCE(err_subcode, message) \
- LOG_POST_X_N_TIMES(1, err_subcode, message)
+#define LOG_POST_X_N_TIMES(count, err_subcode, message) \
+ NCBI_REPEAT_POST_N_TIMES( LOG_POST_X, count, (err_subcode, message) )
/// Error posting only once during program execution with default
/// error code and given error subcode.
@@ -612,14 +609,8 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
#define ERR_POST_X_ONCE(err_subcode, message) \
ERR_POST_X_N_TIMES(1, err_subcode, message)
-
-/// Log posting only given number of times during program execution
-/// with given error code name and given error subcode.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, LOG_POST_XX
-#define LOG_POST_XX_N_TIMES(count, error_name, err_subcode, message) \
- NCBI_REPEAT_POST_N_TIMES( LOG_POST_XX, count, \
- (error_name, err_subcode, message) )
+#define LOG_POST_X_ONCE(err_subcode, message) \
+ LOG_POST_X_N_TIMES(1, err_subcode, message)
/// Error posting only given number of times during program execution
/// with given error code name and given error subcode.
@@ -629,12 +620,9 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
NCBI_REPEAT_POST_N_TIMES( ERR_POST_XX, count, \
(error_name, err_subcode, message) )
-/// Log posting only once during program execution with given
-/// error code name and given error subcode.
-///
-/// @sa NCBI_DEFINE_ERRCODE_X, LOG_POST_XX
-#define LOG_POST_XX_ONCE(error_name, err_subcode, message) \
- LOG_POST_XX_N_TIMES(1, error_name, err_subcode, message)
+#define LOG_POST_XX_N_TIMES(count, error_name, err_subcode, message) \
+ NCBI_REPEAT_POST_N_TIMES( LOG_POST_XX, count, \
+ (error_name, err_subcode, message) )
/// Error posting only once during program execution with given
/// error code name and given error subcode.
@@ -643,6 +631,8 @@ struct WRONG_USAGE_OF_DEFINE_ERR_SUBCODE_MACRO<errorCode, true> {
#define ERR_POST_XX_ONCE(error_name, err_subcode, message) \
ERR_POST_XX_N_TIMES(1, error_name, err_subcode, message)
+#define LOG_POST_XX_ONCE(error_name, err_subcode, message) \
+ LOG_POST_XX_N_TIMES(1, error_name, err_subcode, message)
/// Severity level for the posted diagnostics.
enum EDiagSev {
@@ -742,13 +732,14 @@ enum EDiagPostFlag {
// "Unusual" flags -- not included in "eDPF_All"
eDPF_ErrCodeMsgInFront = 1 << 19, ///< Put ErrCode text in front of the message
- eDPF_PreMergeLines = 1 << 20, ///< Remove EOLs before calling handler
- eDPF_MergeLines = 1 << 21, ///< Ask diag.handlers to remove EOLs
+ eDPF_MergeLines = 1 << 21, ///< Escape EOLs.
+ eDPF_PreMergeLines = eDPF_MergeLines, ///< Obsolete. Use eDPF_MergeLines.
eDPF_OmitInfoSev = 1 << 22, ///< No sev. indication if eDiag_Info
eDPF_OmitSeparator = 1 << 23, ///< No '---' separator before message
eDPF_AppLog = 1 << 24, ///< Post message to application log
- eDPF_IsMessage = 1 << 25, ///< Print "Message" severity name.
+ eDPF_IsNote = 1 << 25, ///< Print "Note[X]" severity name.
+ eDPF_IsMessage = eDPF_IsNote, // Legacy name
/// This flag is deprecated and ignored - all log writes are atomic.
/// For compatibility IsSetDiagPostFlag always returns true when
@@ -766,8 +757,7 @@ enum EDiagPostFlag {
/// Important bits which should be taken from the globally set flags
/// even if a user attempts to override (or forgets to set) them
/// when calling CNcbiDiag().
- eDPF_ImportantFlagsMask = eDPF_PreMergeLines |
- eDPF_MergeLines |
+ eDPF_ImportantFlagsMask = eDPF_MergeLines |
eDPF_OmitInfoSev |
eDPF_OmitSeparator,
@@ -1054,10 +1044,17 @@ public:
/// Set IsMessage flag to indicate that the current post is a message.
/// Do not flush current post or change the severity. The flag is reset
/// by the next Flush().
+ /// @deprecated Use Note manipulator.
friend const CNcbiDiag& Message (const CNcbiDiag& diag);
+ /// Set IsNote flag to indicate that the current post is a note.
+ /// Do not flush current post or change the severity. The flag is reset
+ /// by the next Flush().
+ friend const CNcbiDiag& Note (const CNcbiDiag& diag);
+
/// Set IsConsole flag to indicate that the current post should
- /// go to console rather that to the default output (file etc.).
+ /// go to console regardless of its severity (in addition to the
+ /// default output -- file etc.).
/// Do not flush current post or change the severity. The flag is reset
/// by the next Flush().
friend const CNcbiDiag& Console (const CNcbiDiag& diag);
@@ -1126,9 +1123,10 @@ public:
/// Get function name of the current message.
const char* GetFunction(void) const;
- /// Check if filters are passed
+ /// Check if filters are passed for the current message.
+ /// In addition check an exception and all its backlog if specified.
NCBI_XNCBI_EXPORT
- bool CheckFilters(void) const;
+ bool CheckFilters(const CException* ex = NULL) const;
/// Get post flags for the current message.
/// If the post flags have "eDPF_Default" set, then in the returned flags
@@ -1145,7 +1143,7 @@ public:
TDiagPostFlags ResetPostFlags(TDiagPostFlags flags) const;
/// Display fatal error message.
- NCBI_XNCBI_EXPORT
+ NCBI_XNCBI_EXPORT NCBI_NORETURN
static void DiagFatal(const CDiagCompileInfo& info,
const char* message);
/// Display trouble error message.
@@ -1172,8 +1170,11 @@ public:
const char* expression,
const char* message);
- /// Reset IsMessage flag.
- void ResetIsMessageFlag(void) const { m_PostFlags &= ~eDPF_IsMessage; }
+ /// @deprecated Use ResetIsNoteFlag()
+ void ResetIsMessageFlag(void) const { ResetIsNoteFlag(); }
+
+ /// Reset IsNote flag.
+ void ResetIsNoteFlag(void) const { m_PostFlags &= ~eDPF_IsNote; }
/// Reset IsConsole flag.
void ResetIsConsoleFlag(void) const { m_PostFlags &= ~eDPF_IsConsole; }
@@ -1433,7 +1434,7 @@ NCBI_XNCBI_EXPORT
extern int CompareDiagPostLevel(EDiagSev sev1, EDiagSev sev2);
/// Check if the specified severity is higher or equal to the currently
-/// selected post level and will be printed by LOG_POST/ERR_POST.
+/// selected post level and will be printed by ERR_POST.
NCBI_XNCBI_EXPORT
extern bool IsVisibleDiagPostLevel(EDiagSev sev);
@@ -1668,13 +1669,13 @@ struct NCBI_XNCBI_EXPORT SDiagMessage {
const string& GetAppName(void) const;
EDiagAppState GetAppState(void) const;
- /// For compatibility x_Write selects old or new message formatting
- /// depending on DIAG_OLD_POST_FORMAT parameter.
- CNcbiOstream& x_Write(CNcbiOstream& os, TDiagWriteFlags fl = fNone) const;
CNcbiOstream& x_OldWrite(CNcbiOstream& os, TDiagWriteFlags fl = fNone) const;
CNcbiOstream& x_NewWrite(CNcbiOstream& os, TDiagWriteFlags fl = fNone) const;
string x_GetModule(void) const;
+ static void s_EscapeNewlines(string& buf);
+ static void s_UnescapeNewlines(string& buf);
+
private:
// Parse extra args formatted as CGI query string. Do not check validity
// of names and values. Split args by '&', split name/value by '=', do
@@ -1906,10 +1907,12 @@ public:
CDiagContext_Extra& SetType(const string& type);
/// Allow bad symbols in argument names. URL-encode names the same way
- /// as values. The method must be called before printing any arguments
- /// or it will have no effect.
+ /// as values.
/// NOTE: Avoid using this method if possible. Argument names with
/// encoded symbols may be incompatible with some logging tools.
+ /// If the flag is not set, any bad symbol is replaced with
+ /// [ILLEGAL_APPLOG_SYMBOL:%##] string, where %## is the URL-encoded
+ /// symbol.
CDiagContext_Extra& AllowBadSymbolsInArgNames(void);
private:
@@ -2160,10 +2163,16 @@ public:
/// Set application name
void SetAppName(const string& app_name);
+ /// Check if exit code has been set.
+ bool IsSetExitCode(void) const { return m_ExitCodeSet; }
/// Get exit code
int GetExitCode(void) const { return m_ExitCode; }
/// Set exit code
- void SetExitCode(int exit_code) { m_ExitCode = exit_code; }
+ void SetExitCode(int exit_code)
+ {
+ m_ExitCode = exit_code;
+ m_ExitCodeSet = true;
+ }
/// Get exit signal
int GetExitSignal(void) const { return m_ExitSig; }
@@ -2197,7 +2206,8 @@ public:
/// or Log.Http_Hit_Id/Log.Hit_Id values in the INI file. The Http-value
/// has higher priority. If none of the values is set, the default hit id
/// is generated automatically.
- string GetDefaultHitID(void) const;
+ string GetDefaultHitID(void) const { return x_GetDefaultHitID(eHitID_Create); }
+
/// Set new global default hit id. This value is used only if the per-request
/// hit id is not set.
void SetDefaultHitID(const string& hit_id);
@@ -2301,8 +2311,21 @@ private:
static void sx_ThreadDataTlsCleanup(CDiagContextThreadData* value,
void* cleanup_data);
friend class CDiagContextThreadData;
-
friend class CDiagBuffer;
+ friend class CRequestContext;
+
+ // Default hit id initialization flags.
+ enum EDefaultHitIDFlags {
+ eHitID_NoCreate, // Do not create new hit id.
+ eHitID_Create // Create new hit id if it's not yet set.
+ };
+
+ // Check if current state is 'PB/P/PE'.
+ bool x_DiagAtApplicationLevel(void) const;
+ bool x_IsSetDefaultHitID(void) const;
+ string x_GetDefaultHitID(EDefaultHitIDFlags flag) const;
+ void x_LogHitID(void) const;
+ void x_LogHitID_WithLock(void) const; // Same as above but with mutex lock.
// Saved messages to be flushed after setting up log files
typedef list<SDiagMessage> TMessages;
@@ -2320,6 +2343,7 @@ private:
mutable auto_ptr<string> m_DefaultHitId;
mutable bool m_LoggedHitId;
int m_ExitCode;
+ bool m_ExitCodeSet;
int m_ExitSig;
EDiagAppState m_AppState;
TProperties m_Properties;
@@ -2701,6 +2725,8 @@ public:
/// initialized, i.e. no earlier than CNcbiApplication::Run() is called.
/// Method can throw CThreadException if dedicated thread failed
/// to start.
+ /// @deprecated Use regular diganostics instead.
+ NCBI_DEPRECATED
void InstallToDiag(void);
/// Remove this DiagHandler from diagnostics.
/// This method must be called if InstallToDiag was called. Object cannot
diff --git a/c++/include/corelib/ncbidiag.inl b/c++/include/corelib/ncbidiag.inl
index 920efef..a8a781d 100644
--- a/c++/include/corelib/ncbidiag.inl
+++ b/c++/include/corelib/ncbidiag.inl
@@ -1,7 +1,7 @@
#if defined(CORELIB___NCBIDIAG__HPP) && !defined(CORELIB___NCBIDIAG__INL)
#define CORELIB___NCBIDIAG__INL
-/* $Id: ncbidiag.inl 448557 2014-10-07 16:40:40Z ivanov $
+/* $Id: ncbidiag.inl 461881 2015-03-13 13:39:13Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -409,6 +409,10 @@ const CNcbiDiag& Endm(const CNcbiDiag& diag) {
return diag;
}
+// No-return version of Endm(), used in ERR_FATAL* set of macros
+NCBI_XNCBI_EXPORT NCBI_NORETURN
+void EndmFatal(const CNcbiDiag& diag);
+
inline
const CNcbiDiag& Info(const CNcbiDiag& diag) {
diag.x_EndMess();
@@ -448,7 +452,13 @@ const CNcbiDiag& Trace(const CNcbiDiag& diag) {
inline
const CNcbiDiag& Message(const CNcbiDiag& diag) {
diag.x_EndMess();
- diag.m_PostFlags |= eDPF_IsMessage;
+ diag.m_PostFlags |= eDPF_IsNote;
+ return diag;
+}
+inline
+const CNcbiDiag& Note(const CNcbiDiag& diag) {
+ diag.x_EndMess();
+ diag.m_PostFlags |= eDPF_IsNote;
return diag;
}
inline
diff --git a/c++/include/corelib/ncbienv.hpp b/c++/include/corelib/ncbienv.hpp
index ca033b1..b5df2de 100644
--- a/c++/include/corelib/ncbienv.hpp
+++ b/c++/include/corelib/ncbienv.hpp
@@ -1,7 +1,7 @@
#ifndef NCBIENV__HPP
#define NCBIENV__HPP
-/* $Id: ncbienv.hpp 360028 2012-04-19 13:20:54Z gouriano $
+/* $Id: ncbienv.hpp 478279 2015-09-08 14:33:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -122,7 +122,7 @@ public:
/// If environmnent value is not cached then call "Load(name)" to load
/// the environmnent value. The loaded name/value pair will then be
/// cached, too, after the call to "Get()".
- const string& Get(const string& name) const;
+ const string& Get(const string& name, bool* found = NULL) const;
/// Find all variable names starting with an optional prefix.
void Enumerate(list<string>& names, const string& prefix = kEmptyStr)
@@ -139,16 +139,19 @@ public:
protected:
/// Load value of specified environment variable.
- virtual string Load(const string& name) const;
+ virtual string Load(const string& name, bool& found) const;
private:
/// Cached environment <name,value> pair.
struct SEnvValue {
SEnvValue(void) : ptr(NULL) {}
- SEnvValue(const string& v, TXChar* p) : value(v), ptr(p) {}
+ SEnvValue(const string& v, const TXChar* p) : value(v), ptr(p) {}
string value; // cached value
- TXChar* ptr; // string created by strdup() or NULL
+ // NULL if the corresponding environment variable is unset.
+ // kEmptyXCStr if the value was loaded from the environment.
+ // A string created by strdup() if the value came from Set().
+ const TXChar* ptr;
};
typedef map<string, SEnvValue> TCache;
mutable TCache m_Cache;
@@ -188,6 +191,8 @@ private:
string m_VariableName;
/// Previous value of the environment variable manipulated
string m_PrevValue;
+ /// Was the variable originally set at all?
+ bool m_WasSet;
};
diff --git a/c++/include/corelib/ncbierror.hpp b/c++/include/corelib/ncbierror.hpp
index 593e200..b780f4b 100644
--- a/c++/include/corelib/ncbierror.hpp
+++ b/c++/include/corelib/ncbierror.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIERROR__HPP
#define CORELIB___NCBIERROR__HPP
-/* $Id: ncbierror.hpp 373165 2012-08-27 14:27:55Z gouriano $
+/* $Id: ncbierror.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,7 +38,6 @@
#include <corelib/ncbistl.hpp>
#include <corelib/ncbimisc.hpp>
#include <errno.h>
-#include <string>
#include <corelib/impl/ncbierror_impl.hpp>
diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp
index a8c0025..ade5dfb 100644
--- a/c++/include/corelib/ncbiexpt.hpp
+++ b/c++/include/corelib/ncbiexpt.hpp
@@ -1,7 +1,7 @@
#ifndef NCBIEXPT__HPP
#define NCBIEXPT__HPP
-/* $Id: ncbiexpt.hpp 467443 2015-05-13 17:30:03Z ivanov $
+/* $Id: ncbiexpt.hpp 459484 2015-02-18 20:00:46Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -889,6 +889,12 @@ public:
CException& UnsetFlag(EFlags flag) { m_Flags &= ~flag; return *this; }
protected:
+ /// Constructor for derived classes
+ CException(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ EDiagSev severity = eDiag_Error,
+ TFlags flags = 0);
/// Constructor with no arguments.
///
/// Required in case of multiple inheritance.
@@ -1110,8 +1116,7 @@ public: \
exception_class(const CDiagCompileInfo& info, \
const CException* prev_exception, EErrCode err_code, \
const string& message, EDiagSev severity = eDiag_Error) \
- : base_class(info, prev_exception, \
- (base_class::EErrCode) CException::eInvalid, (message)) \
+ : base_class(info, prev_exception, (message), severity, 0) \
{ \
x_Init(info, message, prev_exception, severity); \
x_InitErrCode((CException::EErrCode) err_code); \
@@ -1120,13 +1125,22 @@ public: \
const CException* prev_exception, \
const CExceptionArgs<EErrCode>& args, \
const string& message) \
- : base_class(info, prev_exception, \
- (base_class::EErrCode) CException::eInvalid, (message)) \
+ : base_class(info, prev_exception, (message), \
+ args.GetSeverity(), 0) \
{ \
x_Init(info, message, prev_exception, args.GetSeverity()); \
x_InitArgs(args); \
x_InitErrCode((CException::EErrCode) args.GetErrCode()); \
} \
+protected: \
+ exception_class(const CDiagCompileInfo& info, \
+ const CException* prev_exception, \
+ const string& message, \
+ EDiagSev severity, CException::TFlags flags) \
+ : base_class(info, prev_exception, (message), severity, flags) \
+ { \
+ } \
+public: \
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, \
base_class) \
private: \
@@ -1391,34 +1405,7 @@ public:
}
}
- /// Constructor.
- CErrnoTemplExceptionEx(const CDiagCompileInfo& info,
- const CException* prev_exception,
- EErrCode err_code, const string& message,
- EDiagSev severity = eDiag_Error)
- : TBase(info, prev_exception,
- (typename TBase::EErrCode)(CException::eInvalid),
- message)
- {
- m_Errno = PErrCode();
- this->x_Init(info, message, prev_exception, severity);
- this->x_InitErrCode((CException::EErrCode) err_code);
- }
-
- /// Constructor.
- CErrnoTemplExceptionEx(const CDiagCompileInfo& info,
- const CException* prev_exception,
- EErrCode err_code, const string& message,
- int errnum, EDiagSev severity = eDiag_Error)
- : TBase(info, prev_exception,
- (typename TBase::EErrCode)(CException::eInvalid),
- message),
- m_Errno(errnum)
- {
- this->x_Init(info, message, prev_exception, severity);
- this->x_InitErrCode((CException::EErrCode) err_code);
- }
-
+public:
/// Copy constructor.
CErrnoTemplExceptionEx(
const CErrnoTemplExceptionEx<TBase, PErrCode, PErrStr>& other)
@@ -1458,6 +1445,29 @@ public:
protected:
/// Constructor.
+ CErrnoTemplExceptionEx(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ EDiagSev severity = eDiag_Error,
+ CException::TFlags flags = 0)
+ : TBase(info, prev_exception, message, severity, flags)
+ {
+ m_Errno = PErrCode();
+ this->x_Init(info, message, prev_exception, severity);
+ }
+
+ /// Constructor.
+ CErrnoTemplExceptionEx(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ int errnum, EDiagSev severity = eDiag_Error,
+ CException::TFlags flags = 0)
+ : TBase(info, prev_exception, message, severity, flags),
+ m_Errno(errnum)
+ {
+ this->x_Init(info, message, prev_exception, severity);
+ }
+ /// Constructor.
CErrnoTemplExceptionEx(void) { m_Errno = PErrCode(); }
/// Helper clone method.
@@ -1493,9 +1503,17 @@ public:
typename CParent::EErrCode err_code,
const string& message,
EDiagSev severity = eDiag_Error)
- : CParent(info, prev_exception,
- (typename CParent::EErrCode)CException::eInvalid, message)
+ : CParent(info, prev_exception, message, severity, 0)
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException<TBase>, CParent)
+
+protected:
+ CErrnoTemplException<TBase>(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ EDiagSev severity,
+ CException::TFlags flags)
+ : CParent(info, prev_exception, message, severity, flags) {
+ }
};
@@ -1515,9 +1533,17 @@ public:
typename CParent::EErrCode err_code,
const string& message,
EDiagSev severity = eDiag_Error)
- : CParent(info, prev_exception,
- (typename CParent::EErrCode)CException::eInvalid, message)
+ : CParent(info, prev_exception, message, severity, 0)
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException_Win<TBase>, CParent)
+
+protected:
+ CErrnoTemplException_Win<TBase>(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ EDiagSev severity,
+ CException::TFlags flags)
+ : CParent(info, prev_exception, message, severity, flags) {
+ }
};
#endif
@@ -1562,8 +1588,7 @@ public: \
EErrCode err_code,const string& message, \
extra_type extra_param, EDiagSev severity = eDiag_Error) \
: base_class(info, prev_exception, \
- (base_class::EErrCode) CException::eInvalid, \
- (message), extra_param, severity) \
+ (message), extra_param, severity, 0) \
NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class)
END_NCBI_SCOPE
diff --git a/c++/include/corelib/ncbifile.hpp b/c++/include/corelib/ncbifile.hpp
index c0f753d..4496a98 100644
--- a/c++/include/corelib/ncbifile.hpp
+++ b/c++/include/corelib/ncbifile.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIFILE__HPP
#define CORELIB___NCBIFILE__HPP
-/* $Id: ncbifile.hpp 464912 2015-04-15 14:48:07Z ivanov $
+/* $Id: ncbifile.hpp 463266 2015-03-26 12:27:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbifloat.h b/c++/include/corelib/ncbifloat.h
index 09d5cc7..a039e53 100644
--- a/c++/include/corelib/ncbifloat.h
+++ b/c++/include/corelib/ncbifloat.h
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIFLOAT__H
#define CORELIB___NCBIFLOAT__H
-/* $Id: ncbifloat.h 412593 2013-09-09 02:15:57Z ucko $
+/* $Id: ncbifloat.h 453541 2014-12-04 14:58:29Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,7 +68,8 @@ extern "C" {
# ifdef isnan
# undef isnan
# endif
-# if __cplusplus >= 201103L && defined(_GLIBCXX_CONSTEXPR)
+# if __cplusplus >= 201103L && defined(_GLIBCXX_CONSTEXPR) \
+ && !defined(__MIC__)
# define ISNAN_CONSTEXPR _GLIBCXX_CONSTEXPR
# else
# define ISNAN_CONSTEXPR
@@ -85,6 +86,8 @@ namespace boost {
}
}
# define isnan bool_isnan
+#elif defined(NCBI_OS_DARWIN)
+# include <cmath>
#endif
#if defined(NCBI_OS_MSWIN) && !defined(isnan)
@@ -94,15 +97,6 @@ namespace boost {
* Checks double-precision value for not a number (NaN).
*/
# define isnan _isnan
-#elif defined(NCBI_OS_DARWIN) && defined(MATH_ERRNO) && !defined(isnan)
-/**
- * Define value of isnan (Is Not A Number).
- *
- * <math.h> changed a lot between 10.1 and 10.2; the presence of
- * MATH_ERRNO indicates 10.2, which needs this hack, thanks to
- * <cmath>'s obnoxious removal of <math.h>'s isnan macro.
- */
-# define isnan __isnand
#endif
#if defined(NCBI_OS_MSWIN)
@@ -112,6 +106,16 @@ namespace boost {
* Checks whether given double-precision floating point value is finite
*/
# define finite _finite
+#elif defined(NCBI_OS_DARWIN)
+/**
+ * Define value of finite (Is Finite).
+ *
+ * Checks whether given double-precision floating point value is finite
+ */
+# ifdef finite
+# undef finite
+# endif
+# define finite isfinite
#endif
diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp
index 8e000eb..7e40e2f 100644
--- a/c++/include/corelib/ncbimisc.hpp
+++ b/c++/include/corelib/ncbimisc.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIMISC__HPP
#define CORELIB___NCBIMISC__HPP
-/* $Id: ncbimisc.hpp 449468 2014-10-16 19:16:17Z vasilche $
+/* $Id: ncbimisc.hpp 468451 2015-05-22 18:30:31Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,33 +35,16 @@
/// Miscellaneous common-use basic types and functionality
-#include <corelib/ncbistl.hpp>
-
+#include <corelib/ncbidbg.hpp>
#include <stdlib.h>
-
#ifdef HAVE_SYS_TYPES_H
# include <sys/types.h>
#endif
-#ifdef NCBI_COMPILER_ICC
-// Preemptively pull in <cctype>, which breaks if we've already
-// repointed is* at NCBI_is*.
-# include <cctype>
-#else
-# include <ctype.h>
-#endif
-
-#include <corelib/ncbitype.h>
-#include <corelib/ncbistre.hpp>
-#include <corelib/ncbidbg.hpp>
-#if !defined(HAVE_NULLPTR)
+#if !defined(HAVE_NULLPTR) && !defined(nullptr)
# define nullptr NULL
#endif
-#if defined(_DEBUG) && !defined(NCBI_NO_STRICT_CTYPE_ARGS)
-# define NCBI_STRICT_CTYPE_ARGS
-#endif
-
/** @addtogroup AppFramework
*
@@ -444,18 +427,18 @@ struct CDeleter
/// Define an "auto_ptr" like class that can be used inside STL containers.
///
/// The Standard auto_ptr template from STL doesn't allow the auto_ptr to be
-/// put in STL containers (list, vector, map etc.). The reason for this is
+/// put in STL containers (list, vector, map etc.). The reason for this is
/// the absence of copy constructor and assignment operator.
/// We decided that it would be useful to have an analog of STL's auto_ptr
/// without this restriction - AutoPtr.
///
-/// Due to nature of AutoPtr its copy constructor and assignment operator
-/// modify the state of the source AutoPtr object as it transfers ownership
-/// to the target AutoPtr object. Also, we added possibility to redefine the
-/// way pointer will be deleted: the second argument of template allows
+/// Due to the nature of AutoPtr its copy constructor and assignment operator
+/// modify the state of the source AutoPtr object as it transfers the ownership
+/// to the target AutoPtr object. Also, we added possibility to redefine the
+/// way pointer will be deleted: the second argument of the template allows
/// pointers from "malloc" in AutoPtr, or you can use "ArrayDeleter" (see
/// above) to properly delete an array of objects using "delete[]" instead
-/// of "delete". By default, the internal pointer will be deleted by C++
+/// of "delete". By default, the internal pointer is deleted by the C++
/// "delete" operator.
///
/// @sa
@@ -471,26 +454,22 @@ public:
/// Constructor.
AutoPtr(element_type* p = 0)
: m_Ptr(p), m_Data(true)
- {
- }
+ { }
/// Constructor.
AutoPtr(element_type* p, const deleter_type& deleter)
: m_Ptr(p), m_Data(deleter, true)
- {
- }
+ { }
/// Constructor, own the pointed object if ownership == eTakeOwnership
AutoPtr(element_type* p, EOwnership ownership)
: m_Ptr(p), m_Data(ownership != eNoOwnership)
- {
- }
+ { }
/// Constructor, own the pointed object if ownership == eTakeOwnership
AutoPtr(element_type* p, const deleter_type& deleter, EOwnership ownership)
: m_Ptr(p), m_Data(deleter, ownership != eNoOwnership)
- {
- }
+ { }
/// Copy constructor.
AutoPtr(const AutoPtr<X, Del>& p)
@@ -544,8 +523,8 @@ public:
return m_Ptr;
}
- /// Reset will delete old pointer, set content to new value,
- /// and accept ownership upon the new pointer.
+ /// Reset will delete the old pointer (if owned), set content to the new
+ /// value, and assume the ownership upon the new pointer by default.
void reset(element_type* p = 0, EOwnership ownership = eTakeOwnership)
{
if ( m_Ptr != p ) {
@@ -554,15 +533,17 @@ public:
}
m_Ptr = p;
}
- m_Data.second() = p != 0 && ownership == eTakeOwnership;
+ m_Data.second() = ownership != eNoOwnership;
}
void Swap(AutoPtr<X, Del>& a)
{
- swap(m_Ptr, a.m_Ptr);
+ swap(m_Ptr, a.m_Ptr);
swap(m_Data, a.m_Data);
}
+ bool IsOwned(void) const { return m_Ptr && m_Data.second(); }
+
private:
element_type* m_Ptr; ///< Internal pointer representation.
mutable pair_base_member<deleter_type, bool> m_Data; ///< State info.
@@ -582,8 +563,8 @@ private:
/// "AutoPtr" like class for using with arrays
///
/// vector<> template comes with a performance penalty, since it always
-/// initializes its content. This template is not a vector replacement,
-/// it's a version of AutoPtr<> tuned for array pointers. For convenience
+/// initializes its content. This template is not a vector replacement,
+/// it's a version of AutoPtr<> tuned for array pointers. For convenience
/// it defines array style access operator [] and size based contructor.
///
/// @sa AutoPtr
@@ -602,16 +583,15 @@ public:
/// @note In this case you should use ArrayDeleter<> or compatible
explicit AutoArray(size_t size)
: m_Ptr(new element_type[size]), m_Data(true)
- {}
+ { }
explicit AutoArray(element_type* p = 0)
: m_Ptr(p), m_Data(true)
- {}
+ { }
AutoArray(element_type* p, const deleter_type& deleter)
: m_Ptr(p), m_Data(deleter, true)
- {
- }
+ { }
AutoArray(const AutoArray<X, Del>& p)
: m_Ptr(0), m_Data(p.m_Data)
@@ -641,11 +621,12 @@ public:
reset(p);
return *this;
}
+
/// Bool operator for use in if() clause.
DECLARE_OPERATOR_BOOL_PTR(m_Ptr);
/// Get pointer.
- element_type* get (void) const { return m_Ptr; }
+ element_type* get (void) const { return m_Ptr; }
/// Release will release ownership of pointer to caller.
element_type* release(void)
@@ -654,26 +635,28 @@ public:
return m_Ptr;
}
- /// array style dereference (returns value)
+ /// Array style dereference (returns value)
const element_type& operator[](size_t pos) const { return m_Ptr[pos]; }
- /// array style dereference (returns reference)
- element_type& operator[](size_t pos) { return m_Ptr[pos]; }
+ /// Array style dereference (returns reference)
+ element_type& operator[](size_t pos) { return m_Ptr[pos]; }
- /// Reset will delete old pointer, set content to new value,
- /// and accept ownership upon the new pointer.
+ /// Reset will delete the old pointer, set content to the new value,
+ /// and assume the ownership upon the new pointer.
void reset(element_type* p = 0)
{
- if (m_Ptr && m_Data.second()) {
- m_Data.first().Delete(release());
+ if (m_Ptr != p) {
+ if (m_Ptr && m_Data.second()) {
+ m_Data.first().Delete(release());
+ }
+ m_Ptr = p;
}
- m_Ptr = p;
m_Data.second() = true;
}
void Swap(AutoPtr<X, Del>& a)
{
- swap(m_Ptr, a.m_Ptr);
+ swap(m_Ptr, a.m_Ptr);
swap(m_Data, a.m_Data);
}
@@ -685,7 +668,7 @@ private:
}
private:
- element_type* m_Ptr;
+ element_type* m_Ptr;
mutable pair_base_member<deleter_type, bool> m_Data; ///< State info.
};
@@ -811,166 +794,6 @@ extern char* strdup(const char* str);
-// ctype hacks
-//
-
-#ifdef NCBI_STRICT_CTYPE_ARGS
-
-END_NCBI_NAMESPACE;
-
-#define NCBI_CTYPEFAKEBODY \
- { return See_the_standard_on_proper_argument_type_for_ctype_macros(c); }
-
-#ifdef isalpha
-inline int NCBI_isalpha(unsigned char c) { return isalpha(c); }
-inline int NCBI_isalpha(int c) { return isalpha(c); }
-template<class C>
-inline int NCBI_isalpha(C c) NCBI_CTYPEFAKEBODY
-#undef isalpha
-#define isalpha NCBI_isalpha
-#endif
-
-#ifdef isalnum
-inline int NCBI_isalnum(unsigned char c) { return isalnum(c); }
-inline int NCBI_isalnum(int c) { return isalnum(c); }
-template<class C>
-inline int NCBI_isalnum(C c) NCBI_CTYPEFAKEBODY
-#undef isalnum
-#define isalnum NCBI_isalnum
-#endif
-
-#ifdef isascii
-inline int NCBI_isascii(unsigned char c) { return isascii(c); }
-inline int NCBI_isascii(int c) { return isascii(c); }
-template<class C>
-inline int NCBI_isascii(C c) NCBI_CTYPEFAKEBODY
-#undef isascii
-#define isascii NCBI_isascii
-#endif
-
-#ifdef isblank
-inline int NCBI_isblank(unsigned char c) { return isblank(c); }
-inline int NCBI_isblank(int c) { return isblank(c); }
-template<class C>
-inline int NCBI_isblank(C c) NCBI_CTYPEFAKEBODY
-#undef isblank
-#define isblank NCBI_isblank
-#endif
-
-#ifdef iscntrl
-inline int NCBI_iscntrl(unsigned char c) { return iscntrl(c); }
-inline int NCBI_iscntrl(int c) { return iscntrl(c); }
-template<class C>
-inline int NCBI_iscntrl(C c) NCBI_CTYPEFAKEBODY
-#undef iscntrl
-#define iscntrl NCBI_iscntrl
-#endif
-
-#ifdef isdigit
-inline int NCBI_isdigit(unsigned char c) { return isdigit(c); }
-inline int NCBI_isdigit(int c) { return isdigit(c); }
-template<class C>
-inline int NCBI_isdigit(C c) NCBI_CTYPEFAKEBODY
-#undef isdigit
-#define isdigit NCBI_isdigit
-#endif
-
-#ifdef isgraph
-inline int NCBI_isgraph(unsigned char c) { return isgraph(c); }
-inline int NCBI_isgraph(int c) { return isgraph(c); }
-template<class C>
-inline int NCBI_isgraph(C c) NCBI_CTYPEFAKEBODY
-#undef isgraph
-#define isgraph NCBI_isgraph
-#endif
-
-#ifdef islower
-inline int NCBI_islower(unsigned char c) { return islower(c); }
-inline int NCBI_islower(int c) { return islower(c); }
-template<class C>
-inline int NCBI_islower(C c) NCBI_CTYPEFAKEBODY
-#undef islower
-#define islower NCBI_islower
-#endif
-
-#ifdef isprint
-inline int NCBI_isprint(unsigned char c) { return isprint(c); }
-inline int NCBI_isprint(int c) { return isprint(c); }
-template<class C>
-inline int NCBI_isprint(C c) NCBI_CTYPEFAKEBODY
-#undef isprint
-#define isprint NCBI_isprint
-#endif
-
-#ifdef ispunct
-inline int NCBI_ispunct(unsigned char c) { return ispunct(c); }
-inline int NCBI_ispunct(int c) { return ispunct(c); }
-template<class C>
-inline int NCBI_ispunct(C c) NCBI_CTYPEFAKEBODY
-#undef ispunct
-#define ispunct NCBI_ispunct
-#endif
-
-#ifdef isspace
-inline int NCBI_isspace(unsigned char c) { return isspace(c); }
-inline int NCBI_isspace(int c) { return isspace(c); }
-template<class C>
-inline int NCBI_isspace(C c) NCBI_CTYPEFAKEBODY
-#undef isspace
-#define isspace NCBI_isspace
-#endif
-
-#ifdef isupper
-inline int NCBI_isupper(unsigned char c) { return isupper(c); }
-inline int NCBI_isupper(int c) { return isupper(c); }
-template<class C>
-inline int NCBI_isupper(C c) NCBI_CTYPEFAKEBODY
-#undef isupper
-#define isupper NCBI_isupper
-#endif
-
-#ifdef isxdigit
-inline int NCBI_isxdigit(unsigned char c) { return isxdigit(c); }
-inline int NCBI_isxdigit(int c) { return isxdigit(c); }
-template<class C>
-inline int NCBI_isxdigit(C c) NCBI_CTYPEFAKEBODY
-#undef isxdigit
-#define isxdigit NCBI_isxdigit
-#endif
-
-#ifdef toascii
-inline int NCBI_toascii(unsigned char c) { return toascii(c); }
-inline int NCBI_toascii(int c) { return toascii(c); }
-template<class C>
-inline int NCBI_toascii(C c) NCBI_CTYPEFAKEBODY
-#undef toascii
-#define toascii NCBI_toascii
-#endif
-
-#ifdef tolower
-inline int NCBI_tolower(unsigned char c) { return tolower(c); }
-inline int NCBI_tolower(int c) { return tolower(c); }
-template<class C>
-inline int NCBI_tolower(C c) NCBI_CTYPEFAKEBODY
-#undef tolower
-#define tolower NCBI_tolower
-#endif
-
-#ifdef toupper
-inline int NCBI_toupper(unsigned char c) { return toupper(c); }
-inline int NCBI_toupper(int c) { return toupper(c); }
-template<class C>
-inline int NCBI_toupper(C c) NCBI_CTYPEFAKEBODY
-#undef toupper
-#define toupper NCBI_toupper
-#endif
-
-#undef NCBI_CTYPEFAKEBODY
-
-BEGIN_NCBI_NAMESPACE;
-
-#endif // NCBI_STRICT_CTYPE_ARGS
-
// ITERATE
// NON_CONST_ITERATE
// REVERSE_ITERATE
@@ -1094,15 +917,16 @@ typedef int TSignedSeqPos;
//#define NCBI_INT8_GI
#ifdef NCBI_STRICT_GI
-#define NCBI_INT8_GI
+# define NCBI_INT8_GI
#endif
#ifdef NCBI_INT8_GI
-#ifdef NCBI_STRICT_GI
-
+// Generic id type which needs to be the same size as GI.
+typedef Int8 TIntId;
+typedef Uint8 TUintId;
-class CTypeInfo;
+#ifdef NCBI_STRICT_GI
// Strict mode can be enabled only for Int8 GIs.
@@ -1123,82 +947,97 @@ public:
CStrictGi& operator--(void) { m_Gi--; return *this; }
CStrictGi operator--(int) { CStrictGi tmp = *this; m_Gi--; return tmp; }
- CStrictGi operator+(const CStrictGi& gi) const { return CStrictGi(m_Gi + gi.m_Gi); }
- CStrictGi operator-(const CStrictGi& gi) const { return CStrictGi(m_Gi - gi.m_Gi); }
+ CStrictGi operator+(TIntId offset) const { return m_Gi + offset; }
+ CStrictGi operator-(TIntId offset) const { return m_Gi - offset; }
+
+ CStrictGi(TIntId value) : m_Gi(value) {}
+ CStrictGi& operator=(TIntId value) { m_Gi = value; return *this; }
+ operator TIntId(void) const { return m_Gi; }
+ bool operator==(TIntId value) const { return m_Gi == value; }
- CStrictGi(Int8 value) : m_Gi(value) {}
- CStrictGi& operator=(Int8 value) { m_Gi = value; return *this; }
- operator Int8(void) const { return m_Gi; }
+#if defined(NCBI_INT8_GI) && defined(NCBI_TEST_APPLICATION)
+ CStrictGi(Int4 value) : m_Gi(value) {}
+ CStrictGi& operator=(Int4 value) { m_Gi = value; return *this; }
+ bool operator==(Int4 value) const { return m_Gi == value; }
+#endif
- explicit CStrictGi(Int4 value) : m_Gi(value) {}
+ operator bool(void) const { return m_Gi != 0; }
private:
+#if defined(NCBI_INT8_GI) && !defined(NCBI_TEST_APPLICATION)
+ CStrictGi(Int4);
CStrictGi& operator=(Int4);
operator Int4(void) const;
-
+#endif
+ CStrictGi(Int1);
+ CStrictGi(Uint1);
+ CStrictGi(Int2);
+ CStrictGi(Uint2);
CStrictGi(Uint4);
- CStrictGi& operator=(Uint4);
- operator Uint4(void) const;
-
CStrictGi(Uint8);
+ CStrictGi(float);
+ CStrictGi(double);
+ CStrictGi& operator=(Int1);
+ CStrictGi& operator=(Uint1);
+ CStrictGi& operator=(Int2);
+ CStrictGi& operator=(Uint2);
+ CStrictGi& operator=(Uint4);
CStrictGi& operator=(Uint8);
+ CStrictGi& operator=(float);
+ CStrictGi& operator=(double);
+ operator Int1(void) const;
+ operator Uint1(void) const;
+ operator Int2(void) const;
+ operator Uint2(void) const;
+ operator Uint4(void) const;
operator Uint8(void) const;
+ operator float(void) const;
+ operator double(void) const;
private:
- Int8 m_Gi;
+ TIntId m_Gi;
};
inline
CNcbiOstream& operator<<(CNcbiOstream& out, const CStrictGi& gi)
{
- out << Int8(gi);
- return out;
+ return out << TIntId(gi);
}
typedef CStrictGi TGi;
-#define ZERO_GI TGi(0)
-#define INVALID_GI TGi(-1)
-
-
#else // NCBI_STRICT_GI
-
-typedef Int8 TGi;
-#define ZERO_GI 0
-#define INVALID_GI -1
-
+typedef TIntId TGi;
#endif // NCBI_STRICT_GI
-
-// Generic id type which needs to be the same size as GI.
-typedef Int8 TIntId;
-typedef Uint8 TUintId;
-
-
#else // NCBI_INT8_GI
-
typedef int TGi;
typedef Int4 TIntId;
typedef Uint4 TUintId;
-#define ZERO_GI 0
-#define INVALID_GI -1
-
-
#endif
+/// a helper template to enforce constness of argument to GI_CONST macro
+template<TIntId gi>
+class CConstGIChecker {
+public:
+ static const TIntId value = gi;
+};
+#define GI_CONST(gi) (TGi(CConstGIChecker<gi>::value))
+#define ZERO_GI GI_CONST(0)
+#define INVALID_GI GI_CONST(-1)
/// Temporary macros to convert TGi to other types (int, unsigned etc.).
-#define GI_TO(T, gi) (T)(TIntId(gi))
-#define GI_FROM(T, value) TGi(TIntId(value))
+#define GI_TO(T, gi) (static_cast<T>(TIntId(gi)))
+#define GI_FROM(T, value) (TGi(static_cast<TIntId>(value)))
/// Convert gi-compatible int to/from other types.
-#define INT_ID_TO(T, id) (T)(id)
-#define INT_ID_FROM(T, value) TIntId(value)
+#define INT_ID_TO(T, id) (static_cast<T>(id))
+#define INT_ID_FROM(T, value) (static_cast<TIntId>(value))
/// Helper address class
@@ -1333,19 +1172,6 @@ size_t ArraySize(const Element (&)[Size])
END_STD_NAMESPACE;
-/// Definition of packed enum type, to save some memory
-#if defined(NCBI_COMPILER_MSVC)
-# define NCBI_PACKED_ENUM_TYPE(type) : type
-# define NCBI_PACKED_ENUM_END()
-#elif (defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400) || defined(NCBI_COMPILER_ICC)
-# define NCBI_PACKED_ENUM_TYPE(type)
-# define NCBI_PACKED_ENUM_END() __attribute__((packed))
-#else
-# define NCBI_PACKED_ENUM_TYPE(type)
-# define NCBI_PACKED_ENUM_END()
-#endif
-
-
/* @} */
#endif /* CORELIB___NCBIMISC__HPP */
diff --git a/c++/include/corelib/ncbimtx.hpp b/c++/include/corelib/ncbimtx.hpp
index d7e5515..4f8123e 100644
--- a/c++/include/corelib/ncbimtx.hpp
+++ b/c++/include/corelib/ncbimtx.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIMTX__HPP
#define CORELIB___NCBIMTX__HPP
-/* $Id: ncbimtx.hpp 452157 2014-11-17 15:22:17Z ivanov $
+/* $Id: ncbimtx.hpp 450144 2014-10-23 13:52:16Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbimtx.inl b/c++/include/corelib/ncbimtx.inl
index b787612..2cf00d3 100644
--- a/c++/include/corelib/ncbimtx.inl
+++ b/c++/include/corelib/ncbimtx.inl
@@ -1,7 +1,7 @@
#if defined(CORELIB___NCBIMTX__HPP) && !defined(CORELIB___NCBIMTX__INL)
#define CORELIB___NCBIMTX__INL
-/* $Id: ncbimtx.inl 441953 2014-07-29 16:51:39Z ivanov $
+/* $Id: ncbimtx.inl 467328 2015-05-12 18:55:28Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -388,7 +388,17 @@ void CRWLockHolder::RemoveListener(IRWLockHolder_Listener* listener)
_ASSERT(m_Lock);
m_ObjLock.Lock();
- m_Listeners.remove(TRWLockHolder_ListenerWeakRef(listener));
+ // m_Listeners.remove(TRWLockHolder_ListenerWeakRef(listener));
+ // The above gives strange errors about invalid operands to operator==
+ // with the Apple Developer Tools release containing Xcode 6.3.1 and
+ // "Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)".
+ // The below workaround should be equivalent.
+ TRWLockHolder_ListenerWeakRef ref(listener);
+ TListenersList::iterator it;
+ while ((it = find(m_Listeners.begin(), m_Listeners.end(), ref))
+ != m_Listeners.end()) {
+ m_Listeners.erase(it);
+ }
m_ObjLock.Unlock();
}
diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp
index 11b3cc7..d4e6fea 100644
--- a/c++/include/corelib/ncbiobj.hpp
+++ b/c++/include/corelib/ncbiobj.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIOBJ__HPP
#define CORELIB___NCBIOBJ__HPP
-/* $Id: ncbiobj.hpp 440327 2014-07-11 14:23:39Z grichenk $
+/* $Id: ncbiobj.hpp 463582 2015-03-30 18:03:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -138,7 +138,7 @@ public:
void NCBI_OBJECT_LOCKER_EXPORT TransferLock(const CObject* object,
const CObjectCounterLocker& old_locker) const;
- static
+ static NCBI_NORETURN
void NCBI_XNCBI_EXPORT ReportIncompatibleType(const type_info& type);
/// Set monitored object type, e.g. typeid(CScope)
@@ -306,7 +306,7 @@ protected:
NCBI_XNCBI_EXPORT
virtual void DeleteThis(void);
-private:
+public:
typedef CAtomicCounter TCounter; ///< Counter type is CAtomiCounter
typedef TCounter::TValue TCount; ///< Alias for value type of counter
@@ -331,61 +331,32 @@ private:
/// - [0]1c...ccx0 : object not in heap -> cannot be deleted.
/// - [0]1c...cc01 : object in heap pool -> can be deleted via CMemoryPool
/// - [0]1c...cc11 : object in heap -> can be deleted.
- enum EObjectState {
- eStateBitsInHeap = 1 << 0, ///< Detected as in heap
- eStateBitsHeapSignature = 1 << 1, ///< Heap signature was found
-
- /// Mask for 'in heap' state flags
- eStateBitsInHeapMask = eStateBitsInHeap | eStateBitsHeapSignature,
+ /// Detected as in heap
+ static const TCount eCounterBitsCanBeDeleted = 1 << 0;
+ /// Heap signature was found
+ static const TCount eCounterBitsInPlainHeap = 1 << 1;
+ /// Mask for 'in heap' state flags
+ static const TCount eCounterBitsPlaceMask =
+ eCounterBitsCanBeDeleted | eCounterBitsInPlainHeap;
+ /// Skip over the "in heap" bits
+ static const int eCounterStep = 1 << 2;
+
+ /// Minimal value for valid objects (reference counter is zero)
+ /// Must be a single bit value.
+ /// All counter values less than this value are invalid.
#ifdef NCBI_COUNTER_UNSIGNED
- /// 1 in the left most of the valid bits -- unsigned case
- eStateBitsValid = (unsigned int)(1 << (sizeof(TCount) * 8 - 1)),
+ /// 1 in the left most of the valid bits -- unsigned case
+ static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 1);
#else
- /// 1 in the left most of the valid bits -- signed case
- eStateBitsValid = (unsigned int)(1 << (sizeof(TCount) * 8 - 2)),
+ /// 1 in the left most of the valid bits -- signed case
+ static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2);
#endif
- /// Valid object, and object in heap.
- eStateMask = eStateBitsValid | eStateBitsInHeapMask,
-
- /// Skip over the "in heap" bits
- eCounterStep = 1 << 2,
-
- /// Minimal value for valid objects (reference counter is zero)
- eCounterValid = eStateBitsValid,
-
- /// Minimal value for referenced valid objects (reference counter = 1)
- eCounterValidRef1 = eCounterValid + eCounterStep,
-
- /// Minimal value for double referenced objects (reference counter = 2)
- eCounterValidRef2 = eCounterValid + eCounterStep*2,
-
- /// Initial counter value for non-heap objects
- eInitCounterNotInHeap = eStateBitsValid,
-
- /// Initial counter value for in-heap objects
- eInitCounterInHeap = eStateBitsValid | eStateBitsHeapSignature |
- eStateBitsInHeap,
+ /// Valid object, and object in heap.
+ static const TCount eCounterStateMask =
+ eCounterValid | eCounterBitsPlaceMask;
- /// Initial counter value for objects allocated in memory pool
- eInitCounterInPool = eStateBitsValid | eStateBitsInHeap,
-
- /// Initial counter value for probably non-heap objects (w/ signature)
- eInitCounterInStack = eStateBitsValid | eStateBitsHeapSignature,
-
- /// All magic counter values should have all their state bits off.
- /// Magic counter value for deleted objects
- eMagicCounterDeleted = 0x5b4d9f34 & ~eStateMask,
-
- /// Magic counter value for object allocated in heap
- eMagicCounterNew = 0x3423cb13 & ~eStateMask,
-
- /// Magic counter value for deleted object allocated in memory pool
- eMagicCounterPoolDeleted= 0x4229775b & ~eStateMask,
-
- /// Magic counter value for objects allocated in memory pool
- eMagicCounterPoolNew = 0x54917ec2 & ~eStateMask
- };
+private:
friend class CObjectMemoryPool;
friend class CWeakObject;
@@ -439,43 +410,44 @@ private:
inline
bool CObject::ObjectStateCanBeDeleted(TCount count)
{
- return (count & eStateBitsInHeap) != 0;
+ // check only 'CanBeDeleted' bit, include both plain heap and memory pool
+ return (count & eCounterBitsCanBeDeleted) != 0;
}
inline
bool CObject::ObjectStateIsAllocatedInPool(TCount count)
{
- return (count & eStateBitsInHeapMask) ==
- (eInitCounterInPool & eStateBitsInHeapMask);
+ // check if 'CanBeDeleted' is set and InPlainHeap is not set
+ return (count & eCounterBitsPlaceMask) == eCounterBitsCanBeDeleted;
}
inline
bool CObject::ObjectStateValid(TCount count)
{
- return count >= TCount(eCounterValid);
+ return count >= eCounterValid;
}
inline
bool CObject::ObjectStateReferenced(TCount count)
{
- return count >= TCount(eCounterValidRef1);
+ return count >= eCounterValid + eCounterStep;
}
inline
bool CObject::ObjectStateUnreferenced(TCount count)
{
- return (count & ~eStateBitsInHeapMask) == TCount(eCounterValid);
+ return (count & ~eCounterBitsPlaceMask) == eCounterValid;
}
inline
bool CObject::ObjectStateReferencedOnlyOnce(TCount count)
{
- return (count & ~eStateBitsInHeapMask) == TCount(eCounterValidRef1);
+ return (count & ~eCounterBitsPlaceMask) == eCounterValid + eCounterStep;
}
@@ -2067,7 +2039,7 @@ public:
CObject* GetLockedObject(void);
/// Report about trying to convert incompatible interface fo CObject
- NCBI_XNCBI_EXPORT
+ NCBI_XNCBI_EXPORT NCBI_NORETURN
static void ReportIncompatibleType(const type_info& type);
private:
diff --git a/c++/include/corelib/ncbireg.hpp b/c++/include/corelib/ncbireg.hpp
index 395a1f4..1124a66 100644
--- a/c++/include/corelib/ncbireg.hpp
+++ b/c++/include/corelib/ncbireg.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIREG__HPP
#define CORELIB___NCBIREG__HPP
-/* $Id: ncbireg.hpp 463789 2015-04-01 15:38:30Z ivanov $
+/* $Id: ncbireg.hpp 461481 2015-03-10 16:01:30Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp
index 74ef869..c3916ed 100644
--- a/c++/include/corelib/ncbistl.hpp
+++ b/c++/include/corelib/ncbistl.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBISTL__HPP
#define CORELIB___NCBISTL__HPP
-/* $Id: ncbistl.hpp 443319 2014-08-13 02:58:02Z mcelhany $
+/* $Id: ncbistl.hpp 442488 2014-08-04 17:50:17Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp
index dfc089e..a70bb99 100644
--- a/c++/include/corelib/ncbistr.hpp
+++ b/c++/include/corelib/ncbistr.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBISTR__HPP
#define CORELIB___NCBISTR__HPP
-/* $Id: ncbistr.hpp 466626 2015-05-05 14:46:39Z ivanov $
+/* $Id: ncbistr.hpp 479746 2015-09-23 13:17:35Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,8 +35,8 @@
/// The NCBI C++ standard methods for dealing with std::string
-#include <corelib/tempstr.hpp>
#include <corelib/ncbi_limits.hpp>
+#include <corelib/tempstr.hpp>
#include <corelib/ncbierror.hpp>
#ifdef NCBI_OS_OSF1
# include <strings.h>
@@ -68,6 +68,7 @@ class CNcbiEmptyString
{
public:
/// Get string.
+ inline
static const string& Get(void)
{
static string empty_str;
@@ -138,6 +139,11 @@ const SIZE_TYPE NPOS = static_cast<SIZE_TYPE>(-1);
/////////////////////////////////////////////////////////////////////////////
// Unicode-related definitions and conversions
+/// Unicode character
+typedef Uint4 TUnicodeSymbol;
+/// Unicode string
+typedef basic_string<TUnicodeSymbol> TStringUnicode;
+
#if defined(NCBI_OS_MSWIN) && defined(_UNICODE)
typedef wchar_t TXChar;
@@ -444,6 +450,8 @@ public:
/// - If conversion succeeds, set errno to zero and return the
/// converted value.
/// - Otherwise, set errno to non-zero and return zero.
+ /// - Denormal or infinite results are considered successful conversion.
+ /// - To enforce finite and normalized result, use fDecimalPosixFinite flag.
/// - This function is meant to be more "low-level" than other
/// StringToXxx functions - for example, it allows trailing characters
/// (and doesn't include a flags parameter for tweaking such behavior).
@@ -468,6 +476,9 @@ public:
/// converted value.
/// - Otherwise, if fConvErr_NoThrow is not set, throw an exception.
/// - Otherwise, set errno to non-zero and return zero.
+ /// @note
+ /// - Denormal or infinite results are considered successful conversion.
+ /// - To enforce finite and normalized result, use fDecimalPosixFinite flag.
static double StringToDouble(const CTempStringEx& str,
TStringToNumFlags flags = 0);
@@ -670,6 +681,9 @@ public:
static string IntToString(unsigned int value, TNumToStringFlags flags = 0,
int base = 10);
+
+// +++ will be deleted soon
+//private:
/// @deprecated Use NumericToString instead
NCBI_DEPRECATED
static string IntToString(long value, TNumToStringFlags flags = 0,
@@ -688,7 +702,8 @@ public:
static string IntToString(Uint8 value, TNumToStringFlags flags = 0,
int base = 10);
#endif
-
+// --- will be deleted soon
+public:
/// Convert int to string.
///
@@ -713,6 +728,9 @@ public:
static void IntToString(string& out_str, unsigned int value,
TNumToStringFlags flags = 0,
int base = 10);
+
+// +++ will be deleted soon
+//private:
/// @deprecated Use NumericToString instead
NCBI_DEPRECATED
static void IntToString(string& out_str, long value,
@@ -735,6 +753,8 @@ public:
TNumToStringFlags flags = 0,
int base = 10);
#endif
+// --- will be deleted soon
+public:
/// Convert UInt to string.
///
@@ -757,6 +777,9 @@ public:
static string UIntToString(int value,
TNumToStringFlags flags = 0,
int base = 10);
+
+// +++ will be deleted soon
+//private:
/// @deprecated Use NumericToString instead
NCBI_DEPRECATED
static string UIntToString(unsigned long value,
@@ -779,6 +802,8 @@ public:
TNumToStringFlags flags = 0,
int base = 10);
#endif
+// --- will be deleted soon
+public:
/// Convert UInt to string.
///
@@ -803,6 +828,9 @@ public:
static void UIntToString(string& out_str, int value,
TNumToStringFlags flags = 0,
int base = 10);
+
+// +++ will be deleted soon
+//private:
/// @deprecated Use NumericToString instead
NCBI_DEPRECATED
static void UIntToString(string& out_str, unsigned long value,
@@ -825,6 +853,8 @@ public:
TNumToStringFlags flags = 0,
int base = 10);
#endif
+// --- will be deleted soon
+public:
/// Convert Int to string.
///
@@ -1771,6 +1801,37 @@ public:
static bool MatchesMask(CTempString str,
CTempString mask, ECase use_case = eCase);
+ /// Check if a string is blank (has no text).
+ ///
+ /// @param str
+ /// String to check.
+ /// @param pos
+ /// starting position (default 0)
+ static bool IsBlank(const CTempString& str, SIZE_TYPE pos = 0);
+
+ /// Checks if all letters in the given string have a lower case.
+ ///
+ /// @param str
+ /// String to be checked.
+ /// @return
+ /// TRUE if all letter characters in the string are lowercase
+ /// according to the current C locale (std::islower()).
+ /// All non-letter characters will be ignored.
+ /// TRUE if empty or no letters.
+ static bool IsLower(const CTempString& str);
+
+ /// Checks if all letters in the given string have a upper case.
+ ///
+ /// @param str
+ /// String to be checked.
+ /// @return
+ /// TRUE if all letter characters in the string are uppercase
+ /// according to the current C locale (std::isupper()).
+ /// All non-letter characters will be skipped.
+ /// TRUE if empty or no letters.
+ static bool IsUpper(const CTempString& str);
+
+
// The following 4 methods change the passed string, then return it
/// Convert string to lower case -- string& version.
@@ -1815,6 +1876,7 @@ private:
static void/*dummy*/ ToUpper(const char* /*dummy*/);
public:
+
/// Check if a string starts with a specified prefix value.
///
/// @param str
@@ -1894,13 +1956,6 @@ public:
/// and the start of the second string.
static SIZE_TYPE CommonOverlapSize(const CTempString& s1, const CTempString& s2);
- /// Check if a string is blank (has no text).
- ///
- /// @param str
- /// String to check.
- /// @param pos
- /// starting position (default 0)
- static bool IsBlank(const CTempString& str, SIZE_TYPE pos = 0);
/// Whether it is the first or last occurrence.
enum EOccurrence {
@@ -1925,18 +1980,19 @@ public:
/// "pattern" in "str". When set to eLast, this means to find the last
/// occurrence of "pattern" in "str".
/// @param use_case
- /// Whether to do a case sensitive compare(default is eCase), or a
+ /// Whether to do a case sensitive compare (default is eCase), or a
/// case-insensitive compare (eNocase) while searching for the pattern.
/// @return
/// - The start of the first or last (depending on "which" parameter)
/// occurrence of "pattern" in "str", within the string interval
/// ["start", "end"], or
/// - NPOS if there is no occurrence of the pattern.
+ /// @sa FindCase, FindNoCase, FindWord
static SIZE_TYPE Find(const CTempString& str,
const CTempString& pattern,
- SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
+ SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
EOccurrence which = eFirst,
- ECase use_case = eCase);
+ ECase use_case = eCase);
/// Find the pattern in the specified range of a string using a case
/// sensitive search.
@@ -1960,9 +2016,10 @@ public:
/// occurrence of "pattern" in "str", within the string interval
/// ["start", "end"], or
/// - NPOS if there is no occurrence of the pattern.
+ /// @sa Find
static SIZE_TYPE FindCase (const CTempString& str,
const CTempString& pattern,
- SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
+ SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
EOccurrence which = eFirst);
/// Find the pattern in the specified range of a string using a case
@@ -1987,9 +2044,10 @@ public:
/// occurrence of "pattern" in "str", within the string interval
/// ["start", "end"], or
/// - NPOS if there is no occurrence of the pattern.
+ /// @sa Find
static SIZE_TYPE FindNoCase(const CTempString& str,
const CTempString& pattern,
- SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
+ SIZE_TYPE start = 0, SIZE_TYPE end = NPOS,
EOccurrence which = eFirst);
/// Test for presence of a given string in a list or vector of strings
@@ -2015,6 +2073,37 @@ public:
const CTempString& val);
+ /// Find given word in the string.
+ ///
+ /// This function honors word boundaries:
+ /// - starting or ending of the string,
+ /// - any non-word character, all except [a-zA-Z0-9_].
+ ///
+ /// @param str
+ /// String to search.
+ /// @param word
+ /// Pattern to search for in "str". The "word" can have any symbols,
+ /// not letters only. Function treat it as a pattern, even it have
+ /// any non-word characters.
+ /// @param which
+ /// When set to eFirst, this means to find the first occurrence of
+ /// "word" in "str". When set to eLast, this means to find the last
+ /// occurrence of "word" in "str".
+ /// @param use_case
+ /// Whether to do a case sensitive compare (default is eCase), or a
+ /// case-insensitive compare (eNocase) while searching for the word.
+ /// @return
+ /// - The start of the first or last (depending on "which" parameter)
+ /// occurrence of "word" in "str", within the string interval
+ /// ["start", "end"], or
+ /// - NPOS if there is no occurrence of the word.
+ /// @sa Find
+ static SIZE_TYPE FindWord(const CTempString& str,
+ const CTempString& word,
+ EOccurrence which = eFirst,
+ ECase use_case = eCase);
+
+
/// Which end to truncate a string.
enum ETrunc {
eTrunc_Begin, ///< Truncate leading spaces only
@@ -2092,6 +2181,37 @@ public:
static void TruncateSpacesInPlace(string& str, ETrunc where = eTrunc_Both);
static void TruncateSpacesInPlace(CTempString&, ETrunc where = eTrunc_Both);
+
+ /// Trim prefix from a string (in-place)
+ ///
+ /// @param str
+ /// String to trim from.
+ /// @param prefix
+ /// Prefix to remove.
+ /// If string doesn't have specified prefix, it doesn't changes.
+ /// @param use_case
+ /// Whether to do a case sensitive compare (default is eCase), or a
+ /// case-insensitive compare (eNocase) while checking for a prefix.
+ static void TrimPrefixInPlace(string& str, const CTempString& prefix,
+ ECase use_case = eCase);
+ static void TrimPrefixInPlace(CTempString& str, const CTempString& prefix,
+ ECase use_case = eCase);
+
+ /// Trim suffix from a string (in-place)
+ ///
+ /// @param str
+ /// String to trim from.
+ /// @param suffix
+ /// Suffix to remove.
+ /// If string doesn't have specified suffix, it doesn't changes.
+ /// @param use_case
+ /// Whether to do a case sensitive compare (default is eCase), or a
+ /// case-insensitive compare (eNocase) while checking for a prefix.
+ static void TrimSuffixInPlace(string& str, const CTempString& suffix,
+ ECase use_case = eCase);
+ static void TrimSuffixInPlace(CTempString& str, const CTempString& suffix,
+ ECase use_case = eCase);
+
/// Replace occurrences of a substring within a string.
///
/// @param src
@@ -2416,11 +2536,57 @@ public:
/// @return
/// Return a printable version of "str".
/// @sa
- /// ParseEscapes, CEncode, CParse
+ /// ParseEscapes, CEncode, CParse, Sanitize
static string PrintableString(const CTempString& str,
TPrintableMode mode =
fNewLine_Quote | fNonAscii_Passthru);
+ /// Flags for Sanitize().
+ enum ESS_Flags {
+ // Character filters (if no filters are set, then use fSS_print)
+ fSS_alpha = 1 << 1, ///< Check on ::isalpha()
+ fSS_digit = 1 << 2, ///< Check on ::isdigit()
+ fSS_alnum = 1 << 3, ///< Check on ::isalnum()
+ fSS_print = 1 << 4, ///< Check on ::isprint()
+ fSS_cntrl = 1 << 5, ///< Check on ::iscntrl()
+ fSS_punct = 1 << 6, ///< Check on ::ispunct()
+
+ // Filter: in or out?
+ fSS_Reject = 1 << 11, ///< Reject specified characters, allow all other.
+ ///< Revert default behavior, that allow specified
+ ///< characters and reject all other.
+ // Utility flags
+ fSS_Remove = 1 << 12, ///< Remove (rather than replace) rejected chars
+ fSS_NoMerge = 1 << 13, ///< Do not merge adjacent spaces
+ fSS_NoTruncate_Begin = 1 << 14, ///< Do not truncate leading spaces
+ fSS_NoTruncate_End = 1 << 15, ///< Do not truncate trailing spaces
+ fSS_NoTruncate = fSS_NoTruncate_Begin | fSS_NoTruncate_End
+ };
+ typedef int TSS_Flags; ///< Bitwise OR of ESS_Flags
+
+ /// Sanitize a string, allowing only specified classes of characters.
+ ///
+ /// By default:
+ /// - replace all non-printable characters with spaces;
+ /// - merge coalescent spaces;
+ /// - truncate leading and trailing spaces.
+ /// @note
+ /// - All coalescent leading/trailing spaces also will be merged
+ /// by default if fSS_NoMerge has not specified.
+ /// - The truncation of leading/trailing spaces is doing after
+ /// allowing/rejecting characters. Defending on the specified flags,
+ /// all rejected characters adjacent to it can be treat as part
+ /// of leading/trailing spaces.
+ /// @param str
+ /// String to sanitize
+ /// @param flags
+ /// Alternative sanitation options
+ /// @return
+ /// Sanitized string
+ /// @sa
+ /// PrintableString
+ static string Sanitize(CTempString str, TSS_Flags flags = 0);
+
/// C-style escape sequences parsing mode.
/// For escape sequences with a value outside the range of [0-255]
/// the behavior of ParseEscapes() depends from this mode.
@@ -2558,6 +2724,11 @@ public:
EEncoding encoding = eEncoding_Unknown,
THtmlDecode* result_flags = NULL);
+ /// Returns HTML entity name for this symbol if one exists
+ /// (without leading ampersand and trailing semicolon);
+ /// or empty string if suitable HTML entity was not found
+ static string HtmlEntity(TUnicodeSymbol uch);
+
/// Encode a string for JSON.
static string JsonEncode(const CTempString& str);
@@ -2671,7 +2842,42 @@ public:
/// first line.
/// @return
/// Return "arr", the list of wrapped lines.
- static list<string>& Wrap(const string& str, SIZE_TYPE width,
+ template<typename _D>
+ static void WrapIt(const string& str, SIZE_TYPE width,
+ _D& dest, TWrapFlags flags = 0,
+ const string* prefix = 0,
+ const string* prefix1 = 0);
+
+ class IWrapDest
+ {
+ public:
+ virtual void Append(const string& s) = 0;
+ virtual void Append(const CTempString& s) = 0;
+ };
+
+ class CWrapDestStringList : public IWrapDest
+ {
+ protected:
+ list<string>& m_list;
+ public:
+ CWrapDestStringList(list<string>& l) : m_list(l) {};
+ virtual void Append(const string& s)
+ {
+ m_list.push_back(s);
+ }
+ virtual void Append(const CTempString& s)
+ {
+ m_list.push_back(NcbiEmptyString);
+ m_list.back().assign(s.data(), s.length());
+ }
+ };
+
+ static void Wrap(const string& str, SIZE_TYPE width,
+ IWrapDest& dest, TWrapFlags flags,
+ const string* prefix,
+ const string* prefix1);
+
+ static list<string>& Wrap(const string& str, SIZE_TYPE width,
list<string>& arr, TWrapFlags flags = 0,
const string* prefix = 0,
const string* prefix1 = 0);
@@ -2879,15 +3085,16 @@ public:
///
-/// Unicode character
-typedef Uint4 TUnicodeSymbol;
-/// Unicode string
-typedef basic_string<TUnicodeSymbol> TStringUnicode;
-
+#define NCBITOOLKIT_USE_LONG_UCS4 (SIZEOF_LONG == 4)
+#if NCBITOOLKIT_USE_LONG_UCS4
/// UCS-4 character
typedef unsigned long TCharUCS4;
/// UCS-4 string
typedef basic_string<TCharUCS4> TStringUCS4;
+#else
+typedef TUnicodeSymbol TCharUCS4;
+typedef TStringUnicode TStringUCS4;
+#endif
/// Type for character in UCS-2 encoding
typedef Uint2 TCharUCS2;
@@ -2954,8 +3161,10 @@ public:
/// If it equals to NPOS, buffer is assumed to be zero-terminated
static CStringUTF8 AsUTF8(const TUnicodeSymbol* src,
SIZE_TYPE tchar_count = NPOS);
+#if NCBITOOLKIT_USE_LONG_UCS4
static CStringUTF8 AsUTF8(const TCharUCS4* src,
SIZE_TYPE tchar_count = NPOS);
+#endif
static CStringUTF8 AsUTF8(const TCharUCS2* src,
SIZE_TYPE tchar_count = NPOS);
#if defined(HAVE_WSTRING)
@@ -3324,9 +3533,7 @@ public:
const CException* prev_exception,
EErrCode err_code,const string& message,
string::size_type pos, EDiagSev severity = eDiag_Error)
- : TBase(info, prev_exception,
- (typename TBase::EErrCode)(CException::eInvalid),
- message), m_Pos(pos)
+ : TBase(info, prev_exception, message, severity, 0), m_Pos(pos)
{
this->x_Init(info,
string("{") + NStr::SizetToString(m_Pos) +
@@ -3358,20 +3565,31 @@ public:
/// Get exception class type.
virtual const char* GetType(void) const { return "CParseTemplException"; }
+ typedef int TErrCode;
/// Get error code.
- EErrCode GetErrCode(void) const
+ TErrCode GetErrCode(void) const
{
return typeid(*this) == typeid(CParseTemplException<TBase>) ?
- (typename CParseTemplException<TBase>::EErrCode)
- this->x_GetErrCode() :
- (typename CParseTemplException<TBase>::EErrCode)
- CException::eInvalid;
+ (TErrCode) this->x_GetErrCode() :
+ (TErrCode) CException::eInvalid;
}
/// Get error position.
string::size_type GetPos(void) const throw() { return m_Pos; }
protected:
+ CParseTemplException(const CDiagCompileInfo &info,
+ const CException* prev_exception,
+ const string& message,
+ string::size_type pos, EDiagSev severity, CException::TFlags flags)
+ : TBase(info, prev_exception, message, severity, flags), m_Pos(pos)
+ {
+ this->x_Init(info,
+ string("{") + NStr::SizetToString(m_Pos) +
+ "} " + message,
+ prev_exception,
+ severity);
+ }
/// Constructor.
CParseTemplException(void)
{
@@ -4559,21 +4777,21 @@ template<> inline
string NStr::NumericToString(TGi value,
TNumToStringFlags flags, int base)
{
- return NumericToString(GI_TO(TIntId, value), flags, base);
+ return NumericToString<TIntId>(value, flags, base);
}
template<> inline
void NStr::NumericToString(string& out_str, TGi value,
TNumToStringFlags flags, int base)
{
- return NumericToString(out_str, GI_TO(TIntId, value), flags, base);
+ return NumericToString<TIntId>(out_str, value, flags, base);
}
template <> inline
TGi NStr::StringToNumeric(const CTempString& str,
TStringToNumFlags flags, int base)
{
- return GI_FROM(TIntId, StringToNumeric<TIntId>(str, flags, base));
+ return StringToNumeric<TIntId>(str, flags, base);
}
template <> inline
@@ -5143,11 +5361,11 @@ SIZE_TYPE NStr::FindCase(const CTempString& str, const CTempString& pattern,
SIZE_TYPE start, SIZE_TYPE end, EOccurrence where)
{
if (where == eFirst) {
- SIZE_TYPE result = str.find(pattern, start);
- return (result == NPOS || result > end) ? NPOS : result;
+ SIZE_TYPE pos = str.find(pattern, start);
+ return (pos == NPOS || (pos + pattern.length()) > end) ? NPOS : pos;
} else {
- SIZE_TYPE result = str.rfind(pattern, end);
- return (result == NPOS || result < start) ? NPOS : result;
+ SIZE_TYPE pos = str.rfind(pattern, end);
+ return (pos == NPOS || pos < start) ? NPOS : pos;
}
}
@@ -5284,10 +5502,12 @@ template <> inline CStringUTF8 CUtf8::AsUTF8(const basic_string<TUnicodeSymbol>&
CStringUTF8 u8;
return x_Append(u8, src.begin(), src.end());
}
+#if NCBITOOLKIT_USE_LONG_UCS4
template <> inline CStringUTF8 CUtf8::AsUTF8(const basic_string<TCharUCS4>& src) {
CStringUTF8 u8;
return x_Append(u8, src.begin(), src.end());
}
+#endif
template <> inline CStringUTF8 CUtf8::AsUTF8(const basic_string<TCharUCS2>& src) {
CStringUTF8 u8;
return x_Append(u8, src.begin(), src.end());
@@ -5304,11 +5524,13 @@ CUtf8::AsUTF8(const TUnicodeSymbol* src, SIZE_TYPE tchar_count) {
CStringUTF8 u8;
return x_Append(u8, src, tchar_count);
}
+#if NCBITOOLKIT_USE_LONG_UCS4
inline CStringUTF8
CUtf8::AsUTF8(const TCharUCS4* src, SIZE_TYPE tchar_count) {
CStringUTF8 u8;
return x_Append(u8, src, tchar_count);
}
+#endif
inline CStringUTF8
CUtf8::AsUTF8(const TCharUCS2* src, SIZE_TYPE tchar_count) {
CStringUTF8 u8;
@@ -5330,10 +5552,12 @@ template <> inline CStringUTF8&
CUtf8::AppendAsUTF8(CStringUTF8& u8, const TUnicodeSymbol* src, SIZE_TYPE tchar_count) {
return x_Append(u8, src, tchar_count);
}
+#if NCBITOOLKIT_USE_LONG_UCS4
template <> inline CStringUTF8&
CUtf8::AppendAsUTF8(CStringUTF8& u8, const TCharUCS4* src, SIZE_TYPE tchar_count) {
return x_Append(u8, src, tchar_count);
}
+#endif
template <> inline CStringUTF8&
CUtf8::AppendAsUTF8(CStringUTF8& u8, const TCharUCS2* src, SIZE_TYPE tchar_count) {
return x_Append(u8, src, tchar_count);
@@ -5378,11 +5602,13 @@ CUtf8::AsBasicString(const CTempString& str,
const TUnicodeSymbol* on_error, EValidate validate) {
return CUtf8::x_AsBasicString<TUnicodeSymbol>(str,on_error,validate);
}
+#if NCBITOOLKIT_USE_LONG_UCS4
template <> inline basic_string<TCharUCS4>
CUtf8::AsBasicString(const CTempString& str,
const TCharUCS4* on_error, EValidate validate) {
return CUtf8::x_AsBasicString<TCharUCS4>(str,on_error,validate);
}
+#endif
template <> inline basic_string<TCharUCS2>
CUtf8::AsBasicString(const CTempString& str,
const TCharUCS2* on_error, EValidate validate) {
diff --git a/c++/include/corelib/ncbistre.hpp b/c++/include/corelib/ncbistre.hpp
index 7227892..31ac8d9 100644
--- a/c++/include/corelib/ncbistre.hpp
+++ b/c++/include/corelib/ncbistre.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBISTRE__HPP
#define CORELIB___NCBISTRE__HPP
-/* $Id: ncbistre.hpp 438026 2014-06-12 13:06:37Z gouriano $
+/* $Id: ncbistre.hpp 458676 2015-02-09 12:35:49Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,9 +36,7 @@
/// "old" C++ stream libraries.
-#include <corelib/ncbitype.h>
-#include <corelib/ncbistl.hpp>
-
+#include <corelib/ncbictype.hpp>
/// Determine which iostream library to use, include appropriate
/// headers, and #define specific preprocessor variables.
@@ -120,7 +118,6 @@
// Obsolete
#define SEEKOFF PUBSEEKOFF
-#include <string>
#include <stddef.h>
diff --git a/c++/include/corelib/ncbithr.hpp b/c++/include/corelib/ncbithr.hpp
index fcdef2f..7c0b0eb 100644
--- a/c++/include/corelib/ncbithr.hpp
+++ b/c++/include/corelib/ncbithr.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBITHR__HPP
#define CORELIB___NCBITHR__HPP
-/* $Id: ncbithr.hpp 441144 2014-07-21 18:45:59Z vasilche $
+/* $Id: ncbithr.hpp 467434 2015-05-13 16:41:39Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -576,6 +576,10 @@ public:
/// This amount does not contain main thread.
static unsigned int GetThreadsCount();
+ /// Set name for the current thread.
+ /// This works only on Linux, no-op on other platforms
+ static void SetCurrentThreadName(const CTempString&);
+
/// Initialize main thread's TID.
/// The function must be called from the main thread if the application
/// is using non-toolkit threads. Otherwise getting thread id of a
diff --git a/c++/include/corelib/ncbitime.hpp b/c++/include/corelib/ncbitime.hpp
index 0fe52c1..f5d6ea1 100644
--- a/c++/include/corelib/ncbitime.hpp
+++ b/c++/include/corelib/ncbitime.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB__NCBITIME__HPP
#define CORELIB__NCBITIME__HPP
-/* $Id: ncbitime.hpp 467519 2015-05-14 11:30:36Z ivanov $
+/* $Id: ncbitime.hpp 472770 2015-07-14 13:57:15Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,7 @@
///
/// - Do not use Local time and time_t and its dependent functions with
/// dates outside the range January 1, 1970 UTC to January 18, 2038 UTC.
-/// Also avoid to use GMT -> Local time conversion functions.
+/// Also avoid to use universal->local time conversion functions.
///
/// - Do not use DataBase conversion functions for dates
/// prior to January 1, 1900.
@@ -73,6 +73,9 @@ BEGIN_NCBI_SCOPE
class CTimeSpan;
class CFastLocalTime;
+/// Number of seconds.
+typedef Int8 TSeconds;
+
/// Number of nanoseconds in one second.
///
@@ -89,11 +92,14 @@ const long kMicroSecondsPerSecond = 1000000;
/// Interval for it is from 0 to 999.
const long kMilliSecondsPerSecond = 1000;
+/// The average length of the year in the Gregorian (modern) calendar (in days)
+const double kAverageDaysPerYear = 365.2425;
+/// The average length of the year in the Gregorian (modern) calendar (in seconds)
+const TSeconds kAverageSecondsPerYear = 31556952; // 365.2425*24*3600
+const TSeconds kAverageSecondsPerMonth = kAverageSecondsPerYear/12;
-// Time formats in databases (always contain local time only!)
-/// Number of seconds.
-typedef Int8 TSeconds;
+// Time formats in databases (always contain local time only!)
/// Database format for time where day and time is unsigned 16 bit.
typedef struct {
@@ -115,7 +121,7 @@ typedef struct {
///
/// Defines a storage class for time format.
///
-/// See CTime::SetFormat and CTimeSpan::SetFormat for description
+/// See CTime::SetFormat() and CTimeSpan::SetFormat() for description
/// of format symbols for specific class.
class NCBI_XNCBI_EXPORT CTimeFormat
@@ -128,34 +134,50 @@ public:
/// that mean simple format string and strict matching.
/// @sa SetFormat, AsString
enum EFlags {
+ // Format flags
+
/// Use single characters as format symbols.
- fFormat_Simple = (1 << 0),
+ /// (default)
+ fFormat_Simple = (1 << 0),
/// Specify each format symbol with a preceding symbol '$'.
/// This can be useful if your format string includes output characters
/// that otherwise can be treated as format symbols.
/// To include symbol '$' use '$$'.
- fFormat_Ncbi = (1 << 1),
+ fFormat_Ncbi = (1 << 1),
+
+ // Time string parsing flags
/// A time string should strictly match the format string.
- fMatch_Strict = (1 << 5), ///< eg "Y" and "1997"
+ fMatch_Strict = (1 << 5), ///< eg "Y" and "1997"
/// A time/format string can have extra trailing format symbols,
/// that do not have matching symbols in the time string.
- /// Corresponding time components will be initialized by default
+ /// Any missed time components will be initialized by default
/// in the time object.
- fMatch_ShortTime = (1 << 6), ///< eg "Y/M/D h:m:s" and "1997"
- fMatch_ShortFormat = (1 << 7), ///< eg "Y" and "1997/07/16"
+ fMatch_ShortTime = (1 << 6), ///< eg "Y/M/D h:m:s" and "1997"
+ fMatch_ShortFormat = (1 << 7), ///< eg "Y" and "1997/07/16"
/// Combination of both modes above.
/// Note that it matches until time or format string have symbols.
/// It not allow unprocessed symbols left in both time and format
/// strings at the same time.
- fMatch_Weak = fMatch_ShortTime | fMatch_ShortFormat,
+ fMatch_Weak = fMatch_ShortTime | fMatch_ShortFormat,
+ /// Ignore all white spaces in the time and format strings
+ /// on the matching/parsing step (CTime only).
+ /// Use it for backward compatibility with old code only.
+ /// Don't recommended to use, can lead to odd results and incorrect
+ /// time on parsing some time strings.
+ fMatch_IgnoreSpaces = (1 << 8),
+
+ /// Prefer "UTC" over "GMT" abbreviation for universal time.
+ /// Used for output purposes only, parsing accept both.
+ fConf_UTC = (1 << 9),
+
/// Default flags
- fDefault = fFormat_Simple | fMatch_Strict,
+ fDefault = 0, // fFormat_Simple | fMatch_Strict
/// "Enum"s, used for backward compatibility. Please use flags instead.
- eNcbiSimple = fFormat_Simple,
- eNcbi = fFormat_Ncbi,
- eDefault = fDefault
+ eNcbiSimple = fFormat_Simple,
+ eNcbi = fFormat_Ncbi,
+ eDefault = fDefault
};
typedef unsigned int TFlags; ///< Binary OR of "EFlags"
@@ -164,12 +186,12 @@ public:
/// @sa GetPredefined, CTime::SetFormat
enum EPredefined {
// ISO 8601 formats (without time zone)
- eISO8601_Year = 0, ///< Y (eg 1997)
- eISO8601_YearMonth = 1, ///< Y-M (eg 1997-07)
- eISO8601_Date = 2, ///< Y-M-D (eg 1997-07-16)
- eISO8601_DateTimeMin = 3, ///< Y-M-DTh:m (eg 1997-07-16T19:20)
- eISO8601_DateTimeSec = 4, ///< Y-M-DTh:m:s (eg 1997-07-16T19:20:30)
- eISO8601_DateTimeFrac = 5 ///< Y-M-DTh:m:s.l(eg 1997-07-16T19:20:30.123)
+ eISO8601_Year = 0, ///< Y (eg 1997)
+ eISO8601_YearMonth = 1, ///< Y-M (eg 1997-07)
+ eISO8601_Date = 2, ///< Y-M-D (eg 1997-07-16)
+ eISO8601_DateTimeMin = 3, ///< Y-M-DTh:m (eg 1997-07-16T19:20)
+ eISO8601_DateTimeSec = 4, ///< Y-M-DTh:m:s (eg 1997-07-16T19:20:30)
+ eISO8601_DateTimeFrac = 5 ///< Y-M-DTh:m:g (eg 1997-07-16T19:20:30.123)
};
/// Default constructor.
@@ -208,7 +230,7 @@ public:
/// @param flags
/// Flags specifying how to match a time string against format string.
/// @sa
- /// GetFormat, EFormat
+ /// GetFormat, EFormat, CTime::SetFormat, CTimeSpan::SetFormat
void SetFormat(const string& fmt, TFlags flags = fDefault);
/// Get format string.
@@ -257,13 +279,13 @@ private:
/// Defines a standard Date/Time class.
///
/// Can be used to span time (to represent elapsed time). Can operate with
-/// local and GMT (aka UTC) time. The time is kept in class in the format
-/// in which it was originally given.
+/// local and universal (GMT/UTC) time. The time is kept in class in
+/// the format in which it was originally given.
///
/// Throw exception of type CTimeException on errors.
///
/// NOTE: Do not use local time with time span and dates < "1/1/1900"
-/// (use GMT time only!!!).
+/// (use universal time only!!!).
class NCBI_XNCBI_EXPORT CTime
{
@@ -276,8 +298,9 @@ public:
/// Which initial value to use for timezone.
enum ETimeZone {
- eLocal = 1, ///< Use local time
- eGmt ///< Use GMT (Greenwich Mean Time)
+ eLocal = 1, ///< Local time
+ eUTC, ///< UTC (Universal Coordinated Time)
+ eGmt = eUTC, ///< GMT (Greenwich Mean Time)
};
/// Current timezone. Used in AsString() method.
@@ -348,7 +371,7 @@ public:
/// Whether to build time object with current time or empty
/// time (default).
/// @param tz
- /// Whether to use local time (default) or GMT.
+ /// Whether to use local time (default) or UTC.
/// @param tzp
/// What time zone precision to use.
CTime(EInitMode mode = eEmpty,
@@ -357,11 +380,11 @@ public:
/// Conversion constructor for time_t representation of time.
///
- /// Construct time object from GMT time_t value.
- /// The constructed object will be in the eGMT format.
+ /// Construct time object from UTC time_t value.
+ /// The constructed object will be in the eUTC format.
///
/// @param t
- /// Time in the GMT time_t format.
+ /// Time in the UTC time_t format.
/// @param tzp
/// What time zone precision to use.
/// @sa SetTimeT, GetTimeT
@@ -399,7 +422,7 @@ public:
/// @param nanosecond
/// Nanosecond part of time.
/// @param tz
- /// Whether to use local time (default) or GMT.
+ /// Whether to use local time (default) or UTC.
/// @param tzp
/// What time zone precision to use.
CTime(int year, int month, int day,
@@ -416,7 +439,7 @@ public:
/// @param yearDayNumber
/// N-th day of the year.
/// @param tz
- /// Whether to use local time (default) or GMT.
+ /// Whether to use local time (default) or UTC.
/// @param tzp
/// What time zone precision to use.
CTime(int year, int yearDayNumber,
@@ -435,7 +458,8 @@ public:
/// method, or default "M/D/Y h:m:s".
/// @param tz
/// If current format contains 'Z', then objects timezone will be set to:
- /// - eGMT if "str" has word "GMT" in the appropriate position;
+ /// - eUTC if "str" has words "GMT", "UTC" or "Z" (zero UTC offset) in
+ /// the appropriate position;
/// - eLocal otherwise.
/// If current format does not contain 'Z', objects timezone
/// will be set to 'tz' value.
@@ -453,7 +477,8 @@ public:
/// Assignment operator from string.
///
/// If current format contains 'Z', then objects timezone will be set to:
- /// - eGMT if "str" has word "GMT" in the appropriate position;
+ /// - eUTC if "str" has words "GMT", "UTC" or "Z" (zero UTC offset) in
+ /// the appropriate position;
/// - eLocal otherwise.
/// If current format does not contain 'Z', objects timezone
/// will not be changed.
@@ -467,7 +492,7 @@ public:
/// Set time using time_t time value.
///
/// @param t
- /// Time to set in time object. This is always in GMT time format, and
+ /// Time to set in time object. This is always in UTC time format, and
/// nanoseconds will be truncated.
/// @return
/// Time object that is set.
@@ -482,7 +507,7 @@ public:
/// Time in time_t format.
time_t GetTimeT(void) const;
- /// Get current GMT time in time_t format (with nanoseconds).
+ /// Get current UTC time in time_t format (with nanoseconds).
///
/// @param sec
/// The function return the number of seconds elapsed since
@@ -577,11 +602,13 @@ public:
/// - g = same as "G" but w/o leading "0" if number of seconds < 10.
/// - P = am/pm (AM/PM)
/// - p = am/pm (am/pm)
- /// - Z = timezone format (GMT or none)
/// - W = full day of week name (Sunday-Saturday)
/// - w = abbreviated day of week name (Sun-Sat)
- /// following available only on POSIX platforms:
- /// - z = timezone shift ([GMT]+/-HHMM)
+ /// - Z = UTC timezone designator (GMT/UTC/Z or none)
+ ///
+ /// following available on POSIX platforms only:
+ /// - z = timezone shift ([GMT/UTC]+/-HHMM)
+ /// - o = timezone shift (+/-HH:MM)
///
/// Format string can represent date/time partially, in this case
/// current time, or default values, will be used to amplify time
@@ -654,13 +681,14 @@ public:
/// Format specifier used to convert time to string.
/// If "format" is not defined, then GetFormat() will be used.
/// @param out_tz
- /// Output timezone. This is a difference in seconds between GMT time
+ /// Output timezone. This is a difference in seconds between universal
/// and local time for some place (for example, for EST5 timezone
/// its value is 18000). This parameter works only with local time.
- /// If the time object contains GMT time then it is ignored.
- /// Before transformation to string the time will be converted to output
- /// timezone. Timezone can be printed as a string 'GMT[+|-]HHMM' using
- /// the format symbol 'z'. By default the current timezone is used.
+ /// If the time object contains universal (GMT/UTC/Z) time it is ignored.
+ /// Before doing transformation to string, the time will be converted
+ /// to the output timezone. Timezone can be printed as a string
+ /// 'GMT/UTC/Z[+|-]HHMM' using the format symbol 'z'.
+ /// By default the current timezone is used.
/// @sa
/// GetFormat, SetFormat
string AsString(const CTimeFormat& format = kEmptyStr,
@@ -669,6 +697,7 @@ public:
/// Return time as string using the format returned by GetFormat().
operator string(void) const;
+
//
// Get various components of time.
//
@@ -733,6 +762,7 @@ public:
/// MilliSecond, MicroSecond
long NanoSecond(void) const;
+
//
// Set various components of time.
//
@@ -976,6 +1006,7 @@ public:
/// @sa ERoundPrecision, Round
CTime& Truncate(ERoundPrecision precision = eRound_Day);
+
//
// Add/subtract time span
//
@@ -995,6 +1026,7 @@ public:
/// Operator to subtract times.
CTimeSpan operator- (const CTime& t) const;
+
//
// Time comparison ('>' means "later", '<' means "earlier")
//
@@ -1017,6 +1049,7 @@ public:
/// Operator to test if time is earlier or equal.
bool operator<= (const CTime& t) const;
+
//
// Time difference
//
@@ -1042,6 +1075,7 @@ public:
/// Difference in nanoseconds from specified time.
CTimeSpan DiffTimeSpan(const CTime& t) const;
+
//
// Checks
//
@@ -1061,8 +1095,32 @@ public:
/// Is time local time?
bool IsLocalTime (void) const;
- /// Is time GMT time?
- bool IsGmtTime (void) const;
+ /// Is time universal (GMT/UTC/Z)?
+ bool IsUniversalTime(void) const;
+ bool IsGmtTime(void) const { return IsUniversalTime(); };
+
+ /// Is DST (daylight savings time) in effect for this time?
+ /// @note
+ /// This method use current DST rules on current machine, so be aware
+ /// to use it against time in the past or future, because such rules
+ /// can be changed.
+ bool IsDST(void) const;
+
+ /// Validate if string match time format.
+ ///
+ /// @param str
+ /// String representation of time.
+ /// @param fmt
+ /// Format that is used to check time string. Default value of kEmptyStr,
+ /// implies the format, that was previously setup using SetFormat()
+ /// method, or default one.
+ /// @return
+ /// TRUE if CTime can be initialized from "str" using format "fmt",
+ /// FALSE otherwise.
+ /// @sa
+ /// CTimeFormat
+ static bool ValidateString(const string& str, const CTimeFormat& fmt = kEmptyStr);
+
//
// Timezone functions
@@ -1085,8 +1143,9 @@ public:
/// Get the time as local time.
CTime GetLocalTime(void) const;
- /// Get the time as GMT time.
- CTime GetGmtTime(void) const;
+ /// Get the time as universal (GMT/UTC) time.
+ CTime GetUniversalTime(void) const;
+ CTime GetGmtTime(void) const { return GetUniversalTime(); }
/// Convert the time into specified time zone time.
CTime& ToTime(ETimeZone val);
@@ -1094,14 +1153,17 @@ public:
/// Convert the time into local time.
CTime& ToLocalTime(void);
- /// Convert the time into GMT time.
- CTime& ToGmtTime(void);
+ /// Convert the time into universal (GMT/UTC) time.
+ CTime& ToUniversalTime(void);
+ CTime& ToGmtTime(void) { return ToUniversalTime(); };
- /// Get difference between local timezone for current time object and UTC in seconds.
+ /// Get difference between local timezone for current time object
+ /// and UTC in seconds.
/// @deprecated Use CTime::TimeZoneOffset() instead.
NCBI_DEPRECATED TSeconds TimeZoneDiff(void) const;
- /// Get difference between local timezone for current time object and UTC in seconds.
+ /// Get difference between local timezone for current time object
+ /// and UTC in seconds.
TSeconds TimeZoneOffset(void) const;
/// Get time zone offset string in format [+/-]HHMM.
@@ -1119,8 +1181,15 @@ public:
string TimeZoneName(void);
private:
+ /// Defines how to behave on error
+ enum EErrAction {
+ eErr_Throw, ///< Throw an exception on error
+ eErr_NoThrow ///< Return default value on error
+ };
+
/// Helper method to set time value from string "str" using format "fmt".
- void x_Init(const string& str, const CTimeFormat& fmt);
+ bool x_Init(const string& str, const CTimeFormat& fmt,
+ EErrAction err_action = eErr_Throw);
/// Helper method to set time from 'time_t' -- If "t" not specified,
/// then set to current time.
@@ -1137,7 +1206,7 @@ private:
/// barrier of winter & summer times) using "from" as a reference point.
///
/// This does the adjustment only if the time object:
- /// - contains local time (not GMT), and
+ /// - contains local time, and
/// - has TimeZonePrecision != CTime::eNone, and
/// - differs from "from" in the TimeZonePrecision (or larger) part.
CTime& x_AdjustTime(const CTime& from, bool shift_time = true);
@@ -1174,11 +1243,11 @@ private:
unsigned char hour NCBI_TIME_BITFIELD( 5); // 0..23
unsigned char min NCBI_TIME_BITFIELD( 6); // 0..59
unsigned char sec NCBI_TIME_BITFIELD( 6); // 0..61
- // Difference between GMT and local time in seconds,
+ // Difference between universal and local times in seconds,
// as stored during the last call to x_AdjustTime***().
Int4 adjTimeDiff NCBI_TIME_BITFIELD(18);
// Timezone and precision
- ETimeZone tz NCBI_TIME_BITFIELD(3); // local/GMT
+ ETimeZone tz NCBI_TIME_BITFIELD(3); // local/universal
ETimeZonePrecision tzprec NCBI_TIME_BITFIELD(4); // Time zone precision
NCBI_TIME_EMPTY_BITFIELD // Force alignment
Int4 nanosec;
@@ -1196,7 +1265,8 @@ private:
/// CTimeSpan
///
/// Defines a class to represents a relative time span.
-/// Time span can be both positive and negative.
+/// Time span can be both positive and negative and hold value in range
+/// [LONG_MIN - LONG_MAX] seconds (a little more than 68 years in each direction).
///
/// Throw exception of type CTimeException on errors.
@@ -1251,7 +1321,9 @@ public:
/// String representation of time span in format "fmt".
/// @param fmt
/// Format in which "str" is presented. Default value of kEmptyStr,
- /// implies the "-S.n" format.
+ /// implies the format set with SetFormat(), or "-G" if SetFormat()
+ /// has not used before.
+ /// @sa SetFormat
explicit CTimeSpan(const string& str, const CTimeFormat& fmt = kEmptyStr);
/// Copy constructor.
@@ -1287,16 +1359,18 @@ public:
/// - N = total whole number of nanoseconds stored in the time span
/// - n = nanoseconds (-999999999 - 999999999)
/// - G = total whole number of seconds and part of second as double value
- /// ("S.nnn") with floating number (1-9) of digits after dot.
+ /// ("S.n") with floating number (1-9) of digits after dot.
/// - g = seconds, "S" modulo 60 and part of second as double value
- /// ("s.nnn") with floating number (1-9) of digits after dot.
+ /// ("s.n") with floating number (1-9) of digits after dot.
/// @sa
/// CTimeFormat, GetFormat, AsString
static void SetFormat(const CTimeFormat& format);
/// Get the current time span format.
///
- /// The default format is: "-S.n".
+ /// If SetFormat() has not used before, that default formats are:
+ /// "-S.n" - to output with AsString();
+ /// "-G" - to initialize from string.
/// @return
/// An object describing the time format.
/// @sa
@@ -1318,70 +1392,141 @@ public:
operator string(void) const;
+ /// AsSmartString() conversion flags.
+ ///
+ /// @attention
+ /// Use one flag in each group only, or CTimeException exception
+ /// will be thrown. If not specified otherwise default value will be used.
+ /// @sa AsSmartString
+ enum ESmartStringFlags {
+ /// @note precision
+ /// Flags describing how many parts of time span should be
+ /// returned.
+ /// - Values from fSS_Year to fSS_Nanosecond apparently
+ /// describe part of time span which will be last in output string.
+ /// - Floating precision levels fSS_PrecisionN say that only up to 'N'
+ /// of most significant parts of time span will be printed.
+ /// The parts counting begin from first non-zero value.
+ /// - fSS_Smart is default, it tries to represent time span as close
+ /// and short as possible, usually using only one or two most
+ /// significant non-zero parts of the time span.
+ fSS_Year = (1 << 0), ///< Round to years
+ fSS_Month = (1 << 1), ///< Round to months
+ fSS_Day = (1 << 2), ///< Round to days
+ fSS_Hour = (1 << 3), ///< Round to hours
+ fSS_Minute = (1 << 4), ///< Round to minutes
+ fSS_Second = (1 << 5), ///< Round to seconds
+ fSS_Millisecond = (1 << 6), ///< Round to milliseconds
+ fSS_Microsecond = (1 << 7), ///< Round to microseconds
+ fSS_Nanosecond = (1 << 8), ///< Do not round at all (accurate time span)
+ fSS_Precision1 = (1 << 9), ///< Floating precision level 1
+ fSS_Precision2 = (1 << 10), ///< Floating precision level 2
+ fSS_Precision3 = (1 << 11), ///< Floating precision level 3
+ fSS_Precision4 = (1 << 12), ///< Floating precision level 4
+ fSS_Precision5 = (1 << 13), ///< Floating precision level 5
+ fSS_Precision6 = (1 << 14), ///< Floating precision level 6
+ fSS_Precision7 = (1 << 15), ///< Floating precision level 7
+ fSS_Smart = (1 << 16), ///< Be as smart as possible (see above)
+ fSS_PrecisionMask = 0x1FFFF, ///< Mask of precision flags (sum of all above)
+
+ /// @note rounding
+ /// Rounding flags. By default time span will be truncated at last value
+ /// specified by precision. If fSS_Round specified, that time span will be
+ /// arithmetically rounded by precision level.
+ fSS_Round = (1 << 20),
+ fSS_Trunc = (1 << 21),
+
+ /// @note zero parts
+ /// Flags to print or skip zero parts of time span which should be
+ /// printed but have 0 value. Apply to middle and trailing zero parts
+ /// of time span only. Leading zeros will be ignored in common case
+ /// in any mode, they can be printed only if it is impossible
+ /// to represent time span otherwise.
+ /// @attention
+ /// fSS_NoSkipZero is not compatible with fSS_Smart (exception will be thrown).
+ fSS_NoSkipZero = (1 << 22),
+ fSS_SkipZero = (1 << 23),
+
+ /// @note naming
+ /// Specify what kind of names use for output time components,
+ /// short standard abbreviations for time component like "m",
+ /// or full "minutes".
+ fSS_Short = (1 << 24),
+ fSS_Full = (1 << 25),
+
+ /// Default flags
+ fSS_Default = 0 // fSS_Smart | fSS_Trunc | fSS_SkipZero | fSS_Full
+ };
+ typedef unsigned int TSmartStringFlags; ///< Binary OR of "ESmartStringFlags"
+
/// Precision for span "smart" string. Used in AsSmartString() method.
+ /// @deprecated Use ESmartStringFlags instead
enum ESmartStringPrecision {
// Named precision levels
- eSSP_Year, ///< Round to years
- eSSP_Month, ///< Round to months
- eSSP_Day, ///< Round to days
- eSSP_Hour, ///< Round to hours
- eSSP_Minute, ///< Round to minutes
- eSSP_Second, ///< Round to seconds
- eSSP_Millisecond, ///< Round to milliseconds
- eSSP_Microsecond, ///< Round to microseconds
- eSSP_Nanosecond, ///< Do not round at all (accurate time span)
-
- // Floating precision levels (1-7)
- eSSP_Precision1,
- eSSP_Precision2,
- eSSP_Precision3,
- eSSP_Precision4,
- eSSP_Precision5,
- eSSP_Precision6,
- eSSP_Precision7,
-
- /// Be as smart as possible (use most significant levels of time span)
- eSSP_Smart
+ eSSP_Year = fSS_Year,
+ eSSP_Month = fSS_Month,
+ eSSP_Day = fSS_Day,
+ eSSP_Hour = fSS_Hour,
+ eSSP_Minute = fSS_Minute,
+ eSSP_Second = fSS_Second,
+ eSSP_Millisecond = fSS_Millisecond,
+ eSSP_Microsecond = fSS_Microsecond,
+ eSSP_Nanosecond = fSS_Nanosecond,
+ eSSP_Precision1 = fSS_Precision1,
+ eSSP_Precision2 = fSS_Precision2,
+ eSSP_Precision3 = fSS_Precision3,
+ eSSP_Precision4 = fSS_Precision4,
+ eSSP_Precision5 = fSS_Precision5,
+ eSSP_Precision6 = fSS_Precision6,
+ eSSP_Precision7 = fSS_Precision7,
+ eSSP_Smart = fSS_Smart
};
/// Which format use to output zero time span parts.
+ /// @deprecated Use ESmartStringFlags instead
enum ESmartStringZeroMode {
- eSSZ_SkipZero, ///< Skip zero valued parts
- eSSZ_NoSkipZero ///< Print zero valued parts
+ eSSZ_NoSkipZero = fSS_NoSkipZero, ///< Print zero valued parts
+ eSSZ_SkipZero = fSS_SkipZero ///< Skip zero valued parts
};
/// Transform time span to "smart" string.
///
- /// @param precision
- /// Enum value describing how many parts of time span should be
- /// returned. Values from eSSP_Year to eSSP_Nanosecond apparently
- /// describe part of time span which will be last in output string.
- /// Float precision levels eSSP_PrecisionN say that maximum 'N'
- /// parts of time span will be put to output string.
- /// The parts counting begin from first non-zero value.
- /// For special precision value eSSP_Smart it try to represent
- /// time span as close and shorter as possible, usually using only
- /// one or two most significant non-zero parts of the time span.
- /// @param rounding
- /// Rounding mode. By default time span will be truncated at last value
- /// specified by precision. If mode is eRound, that time span will be
- /// arithmetically rounded by precision level.
- /// @param zero_mode
- /// Mode to print or skip zero parts of time span which should be
- /// printed but have 0 value. Apply to middle and trailing zero parts
- /// of time span only. Leading zeros will be ignored in common case
- /// in any mode, they can be printed only if it is impossible
- /// to represent time span otherwise.
- /// This parameters is ignored for eSSP_Smart precision level and
- /// always works as eSSZ_SkipZero.
+ /// @deprecated Use AsSmartString(TSmartStringFlags) instead.
+ NCBI_DEPRECATED
+ string AsSmartString(ESmartStringPrecision precision,
+ ERound rounding,
+ ESmartStringZeroMode zero_mode = eSSZ_SkipZero) const;
+
+ /// Transform time span to "smart" string.
+ ///
+ /// @param flags
+ /// How to convert string to value.
/// @return
/// A string representation of time span.
+ /// It MUST NOT be negative, or an exception will be thrown!
+ /// @sa
+ /// AssignFromSmartString, AsString, ESmartStringFlags
+ /// @note
+ /// For very big time spans it use the average length of the year
+ /// in the Gregorian (modern) calendar (365.2425 days)
+ /// to calculate number of months and years.
+ string AsSmartString(TSmartStringFlags flags = 0) const;
+
+ /// Assign value to time span object from string representation of time
+ /// in formats produced by AsSmartString().
+ ///
+ /// @param str
+ /// String representation of time span in the format produced by AsSmartString().
+ /// All numeric time parts should have letter/word specifiers.
+ /// The string should represent "positive" timespan, the sign (minus)
+ /// is not allowed there.
/// @sa
- /// AsString, ESmartStringPrecision, ERound, ESmartStringZeroMode
- string AsSmartString(ESmartStringPrecision precision = eSSP_Smart,
- ERound rounding = eTrunc,
- ESmartStringZeroMode zero_mode = eSSZ_SkipZero)
- const;
+ /// AsSmartString
+ /// @note
+ /// It use the average length of the year in the Gregorian (modern)
+ /// calendar (365.2425 days) to convert years and months.
+ CTimeSpan& AssignFromSmartString(const string& str);
+
//
// Get various components of time span.
@@ -1487,10 +1632,9 @@ private:
void x_Normalize(void);
/// Helpers for AsSmartString()
- string x_AsSmartString_Smart_Big (ERound rounding);
- string x_AsSmartString_Smart_Small(ERound rounding);
- string x_AsSmartString_Precision (ESmartStringPrecision precision,
- ERound rounding, ESmartStringZeroMode zero_mode);
+ string x_AsSmartString_Smart_Big(TSmartStringFlags flags) const;
+ string x_AsSmartString_Smart_Small(TSmartStringFlags flags) const;
+ string x_AsSmartString_Precision(TSmartStringFlags flags) const;
private:
long m_Sec; ///< Seconds part of the time span
@@ -1528,7 +1672,7 @@ public:
/// Initialize timeout in seconds and microseconds.
/// @note
- /// Use CNanoTimeout ctor to initialize with (seconds and) nanoseconds
+ /// Use CNanoTimeout ctor to initialize with (seconds and) nanoseconds
/// @sa CNanoTimeout
CTimeout(unsigned int sec, unsigned int usec);
@@ -1684,7 +1828,7 @@ private:
};
-/// @deprecated Use CDeadline instead
+/// @deprecated Use CDeadline instead
NCBI_DEPRECATED typedef CDeadline CAbsTimeout;
@@ -1839,12 +1983,25 @@ public:
/// A string representation of elapsed time span.
/// @sa
/// CTimeSpan::AsSmartString, AsString, Elapsed
+ /// @deprecated Use AsSmartString(TSmartStringFlags) instead.
+ NCBI_DEPRECATED
string AsSmartString(
- CTimeSpan::ESmartStringPrecision precision = CTimeSpan::eSSP_Nanosecond,
- ERound rounding = eTrunc,
+ CTimeSpan::ESmartStringPrecision precision,
+ ERound rounding,
CTimeSpan::ESmartStringZeroMode zero_mode = CTimeSpan::eSSZ_SkipZero)
const;
+ /// Transform elapsed time to "smart" string.
+ ///
+ /// For more details see CTimeSpan::AsSmartString().
+ /// @param flags
+ /// How to convert string to value.
+ /// @return
+ /// A string representation of elapsed time span.
+ /// @sa
+ /// CTimeSpan::AsSmartString, AsString, Elapsed
+ string AsSmartString(CTimeSpan::TSmartStringFlags flags = 0) const;
+
protected:
/// Get current time mark.
static double GetTimeMark();
@@ -1974,7 +2131,7 @@ CTime operator+ (const CTimeSpan& ts, const CTime& t)
#ifdef CurrentTime // from <X11/X.h>, perhaps
# undef CurrentTime
#endif
-// Get current time (in local or GMT format)
+// Get current time (in local or universal format)
inline
CTime CurrentTime(
CTime::ETimeZone tz = CTime::eLocal,
@@ -2206,14 +2363,14 @@ inline
double CTime::DiffNanoSecond(const CTime& t) const
{
long dNanoSec = NanoSecond() - t.NanoSecond();
- return (double) DiffSecond(t) * kNanoSecondsPerSecond + dNanoSec;
+ return double(DiffSecond(t)) * double(kNanoSecondsPerSecond) + double(dNanoSec);
}
inline
bool CTime::IsLocalTime(void) const { return m_Data.tz == eLocal; }
inline
-bool CTime::IsGmtTime(void) const { return m_Data.tz == eGmt; }
+bool CTime::IsUniversalTime(void) const { return m_Data.tz == eGmt; }
inline
CTime::ETimeZone CTime::GetTimeZone(void) const
@@ -2263,9 +2420,9 @@ CTime& CTime::ToLocalTime(void)
}
inline
-CTime& CTime::ToGmtTime(void)
+CTime& CTime::ToUniversalTime(void)
{
- ToTime(eGmt);
+ ToTime(eUTC);
return *this;
}
@@ -2359,7 +2516,7 @@ long CTimeSpan::GetNanoSecondsAfterSecond(void) const { return m_NanoSec; }
inline
double CTimeSpan::GetAsDouble(void) const
{
- return m_Sec + double(m_NanoSec) / kNanoSecondsPerSecond;
+ return double(m_Sec) + double(m_NanoSec) / double(kNanoSecondsPerSecond);
}
inline
@@ -2385,13 +2542,6 @@ CTimeSpan& CTimeSpan::operator= (const CTimeSpan& t)
}
inline
-CTimeSpan& CTimeSpan::operator= (const string& str)
-{
- x_Init(str, GetFormat());
- return *this;
-}
-
-inline
CTimeSpan::operator string(void) const { return AsString(); }
inline
@@ -2485,6 +2635,22 @@ bool CTimeSpan::operator<= (const CTimeSpan& t) const
return !(*this > t);
}
+// @deprecated
+inline
+string CTimeSpan::AsSmartString(
+ ESmartStringPrecision precision,
+ ERound rounding,
+ ESmartStringZeroMode zero_mode) const
+{
+ TSmartStringFlags flags = precision;
+ flags |= (rounding == eRound) ?
+ CTimeSpan::fSS_Round : CTimeSpan::fSS_Trunc;
+ flags |= (zero_mode == CTimeSpan::eSSZ_NoSkipZero) ?
+ CTimeSpan::fSS_NoSkipZero : CTimeSpan::fSS_SkipZero;
+ return AsSmartString(flags);
+}
+
+
//
// CTimeout
@@ -2631,6 +2797,7 @@ CStopWatch::operator string(void) const
}
+// @deprecated
inline
string CStopWatch::AsSmartString(
CTimeSpan::ESmartStringPrecision precision,
@@ -2638,7 +2805,19 @@ string CStopWatch::AsSmartString(
CTimeSpan::ESmartStringZeroMode zero_mode)
const
{
- return CTimeSpan(Elapsed()).AsSmartString(precision, rounding, zero_mode);
+ CTimeSpan::TSmartStringFlags flags = precision;
+ flags |= (rounding == eRound) ?
+ CTimeSpan::fSS_Round : CTimeSpan::fSS_Trunc;
+ flags |= (zero_mode == CTimeSpan::eSSZ_NoSkipZero) ?
+ CTimeSpan::fSS_NoSkipZero : CTimeSpan::fSS_SkipZero;
+ return CTimeSpan(Elapsed()).AsSmartString(flags);
+}
+
+
+inline
+string CStopWatch::AsSmartString(CTimeSpan::TSmartStringFlags flags) const
+{
+ return CTimeSpan(Elapsed()).AsSmartString(flags);
}
diff --git a/c++/include/corelib/perf_log.hpp b/c++/include/corelib/perf_log.hpp
index 4302b08..533abe3 100644
--- a/c++/include/corelib/perf_log.hpp
+++ b/c++/include/corelib/perf_log.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___PERF_LOG__HPP
#define CORELIB___PERF_LOG__HPP
-/* $Id: perf_log.hpp 351049 2012-01-25 19:08:52Z grichenk $
+/* $Id: perf_log.hpp 469371 2015-06-03 18:05:11Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -88,6 +88,15 @@ public:
/// Constructor. Starts the timer by default.
CPerfLogger(EStart state = eStart);
+ /// Constructor. Use the provided stopwatch to track time.
+ /// Start or stop the stopwatch according to the 'state'.
+ /// The same stopwatch object can be used multiple times
+ /// to accumulate total time for several operations.
+ /// @note
+ /// The stopwatch is not copied, so the original object must not be
+ /// destroyed while the logger is running.
+ CPerfLogger(CStopWatch& stopwatch, EStart state = eStart);
+
/// Activate and start (or, restart after Suspend()) the timer.
/// @note
/// If the timer is already running, post an error (once).
@@ -108,6 +117,8 @@ public:
/// Verbal description of the status of the timed code.
/// @note
/// If the timer is already inactive, then post an error (once).
+ /// @note
+ /// If an external stopwatch was provided, it is stopped by this method.
/// @sa Discard
CDiagContext_Extra Post(CRequestStatus::ECode status,
CTempString resource,
@@ -132,15 +143,27 @@ public:
/// Turn performance logging on/off globally.
static void SetON(bool enable = true);
+ /// Adjust the printed elapsed time.
+ /// @param timespan
+ /// Adjustment value, can be positive or negative. The value is
+ /// added to the actual elapsed time before logging it in Post(),
+ /// if the resuling adjusted timespan is negative, zero is logged.
+ /// Multiple adjustments are accumulated.
+ /// @note
+ /// The adjustment does not affect the actual elapsed time counted by
+ /// the stopwatch, only the printed value is adjusted.
+ void Adjust(CTimeSpan timespan);
+
private:
bool x_CheckValidity(const CTempString& err_msg) const;
friend class CPerfLogGuard;
private:
- CStopWatch m_StopWatch; ///< Internal timer
- CStopWatch::EStart m_TimerState; ///< Internal timer state to save cycles
- bool m_IsDiscarded; ///< TRUE if Post() or Discard() is already called
-
+ auto_ptr<CStopWatch> m_StopWatchGuard; // Internal timer if auto-created.
+ CStopWatch* m_StopWatch; // Timer (internal or provided by user)
+ CStopWatch::EStart m_TimerState; // Internal timer state to save cycles
+ bool m_IsDiscarded; // TRUE if Post() or Discard() is already called
+ double m_Adjustment; // Accumulated elapsed time adjustment
};
@@ -149,23 +172,46 @@ private:
/// Convenience macro that also saves cycles when the performance logging is
/// globally turned off.
///
+/// @par Usage example:
+/// This example demonstrates logging a variety of performance statistics.
+/// @code
/// CPerfLogger perf_logger;
-/// --- Here, running stored proc "123" on server "MSSQL444" which e.g.
-/// --- has finished successfully (code 200) in 2.345 seconds:
-/// PERF_POST(perf_logger, e200_Ok, "StoredProc123",
-/// .Print("dbserver", "MSSQL444")
-/// .Print("foo", "bar"));
-///
+/// PERF_POST(perf_logger, e200_Ok, "ApacheSlotStats",
+/// .Print("total_slots",
+/// NStr::NumericToString(total))
+/// .Print("free_slots",
+/// NStr::NumericToString(total ? total - used : 0))
+/// .Print("used_slots",
+/// NStr::NumericToString(total ? used : 0))
+/// .Print("used_slots_pct",
+/// NStr::NumericToString(total ? 100 * used / total : 0))
+/// .Print("ratio",
+/// NStr::DoubleToString(ratio, 2))
+/// .Print("penalty", m_Mode == eShmem ? "N/A" :
+/// NStr::DoubleToString(m_Penalty, 0))
+/// .Print("error",
+/// NStr::BoolToString(!okay)));
+/// @endcode
+/// @note The status must come from enum CRequestStatus::ECode (but without
+/// the class scope, which is added by the macro).
#define PERF_POST(perf_logger, status, resource, args) \
do { if ( CPerfLogger::IsON() ) \
perf_logger.Post(CRequestStatus::status, resource) args; \
} while (false)
-/// Adaptation for logging database performance
+/// Adaptation for logging database performance.
+///
+/// @par Usage example:
+/// This example demonstrates logging the results of a stored procedure call.
+/// @code
+/// CPerfLogger perf_logger;
/// PERF_POST_DB(perf_logger, e200_Ok,
/// "StoredProc123", "MSSQL444")
/// .Print("foo", "bar"));
+/// @endcode
+/// @note The status must come from enum CRequestStatus::ECode (but without
+/// the class scope, which is added by the macro).
///
#define PERF_POST_DB(perf_logger, status, resource, server, args) \
do { if ( CPerfLogger::IsON() ) \
@@ -197,6 +243,23 @@ public:
CPerfLogGuard(CTempString resource,
CPerfLogger::EStart state = CPerfLogger::eStart);
+ /// Constructor.
+ /// @param resource
+ /// Name of the resource (must be non-empty, else throws an exception).
+ /// Constructor. Use the provided stopwatch to track time.
+ /// @param stopwatch
+ /// User-provided stopwatch to use for tracking time.
+ /// The same stopwatch object can be used multiple times
+ /// to accumulate total time for several operations.
+ /// @param state
+ /// Whether to start the timer by default.
+ /// @note
+ /// The stopwatch is not copied, so the original object must not be
+ /// destroyed while the logger is running.
+ CPerfLogGuard(CTempString resource,
+ CStopWatch& stopwatch,
+ CPerfLogger::EStart state = CPerfLogger::eStart);
+
/// Activate and start (or, restart after Suspend()) the timer.
/// @note
/// If the timer is already running, post an error (once).
@@ -256,7 +319,23 @@ private:
inline
CPerfLogger::CPerfLogger(EStart state)
{
+ m_StopWatchGuard.reset(new CStopWatch);
+ m_StopWatch = m_StopWatchGuard.get();
+ m_IsDiscarded = false;
+ m_Adjustment = 0.0;
+ m_TimerState = CStopWatch::eStop;
+ if ( state == eStart ) {
+ Start();
+ }
+}
+
+
+inline
+CPerfLogger::CPerfLogger(CStopWatch& stopwatch, EStart state)
+{
+ m_StopWatch = &stopwatch;
m_IsDiscarded = false;
+ m_Adjustment = 0.0;
m_TimerState = CStopWatch::eStop;
if ( state == eStart ) {
Start();
@@ -275,7 +354,7 @@ void CPerfLogger::Start()
return;
}
if ( CPerfLogger::IsON() ) {
- m_StopWatch.Start();
+ m_StopWatch->Start();
}
m_TimerState = CStopWatch::eStart;
}
@@ -288,13 +367,13 @@ void CPerfLogger::Suspend()
return;
}
if ( CPerfLogger::IsON() ) {
- m_StopWatch.Stop();
+ m_StopWatch->Stop();
}
m_TimerState = CStopWatch::eStop;
}
-inline CDiagContext_Extra
+inline CDiagContext_Extra
CPerfLogger::Post(CRequestStatus::ECode status,
CTempString resource,
CTempString status_msg)
@@ -306,16 +385,23 @@ CPerfLogger::Post(CRequestStatus::ECode status,
inline
void CPerfLogger::Discard()
{
- // We don't need to "stop" CStopWatch here, it is nor really running.
+ // We don't need to "stop" CStopWatch here, it is nor actually running.
m_TimerState = CStopWatch::eStop;
m_IsDiscarded = true;
}
inline
+void CPerfLogger::Adjust(CTimeSpan timespan)
+{
+ m_Adjustment += timespan.GetAsDouble();
+}
+
+
+inline
CPerfLogger::~CPerfLogger()
{
- if ( !m_IsDiscarded && m_TimerState != CStopWatch::eStop ) {
+ if (IsON() && !m_IsDiscarded && m_TimerState != CStopWatch::eStop ) {
ERR_POST_ONCE(Error << "CPerfLogger timer is still running");
}
}
@@ -349,6 +435,19 @@ CPerfLogGuard::CPerfLogGuard(CTempString resource, CPerfLogger::EStart state)
inline
+CPerfLogGuard::CPerfLogGuard(CTempString resource,
+ CStopWatch& stopwatch,
+ CPerfLogger::EStart state)
+ : m_Logger(stopwatch, state), m_Resource(resource)
+{
+ if ( resource.empty() ) {
+ NCBI_THROW(CCoreException, eInvalidArg,
+ "CPerfLogGuard:: resource name is not specified");
+ }
+}
+
+
+inline
CPerfLogGuard::~CPerfLogGuard()
{
try {
diff --git a/c++/include/corelib/plugin_manager.hpp b/c++/include/corelib/plugin_manager.hpp
index 2c1e905..1c50271 100644
--- a/c++/include/corelib/plugin_manager.hpp
+++ b/c++/include/corelib/plugin_manager.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___PLUGIN_MANAGER__HPP
#define CORELIB___PLUGIN_MANAGER__HPP
-/* $Id: plugin_manager.hpp 389691 2013-02-20 14:43:09Z ivanov $
+/* $Id: plugin_manager.hpp 460958 2015-03-04 17:53:33Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -761,7 +761,7 @@ TClass* CPluginManager<TClass>::CreateInstanceFromList(
drv = CreateInstance(drv_name, version, driver_params);
}
catch ( exception& e ) {
- LOG_POST_XX(Corelib_PluginMgr, 1,
+ ERR_POST_XX(Corelib_PluginMgr, 1,
drv_name << " is not available ::" << e.what());
}
if ( drv ) {
@@ -1230,8 +1230,10 @@ CPluginManager<TClass>::CPluginManager(void)
// Retrieve a driver name substitution map.
// Get current registry ...
- if (CNcbiApplication::Instance()) {
- registry = &CNcbiApplication::Instance()->GetConfig();
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if (app) {
+ registry = &app->GetConfig();
}
if (registry) {
diff --git a/c++/include/corelib/reader_writer.hpp b/c++/include/corelib/reader_writer.hpp
index d5fdc5d..4e2f8d2 100644
--- a/c++/include/corelib/reader_writer.hpp
+++ b/c++/include/corelib/reader_writer.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___READER_WRITER__HPP
#define CORELIB___READER_WRITER__HPP
-/* $Id: reader_writer.hpp 448174 2014-10-02 18:33:31Z vasilche $
+/* $Id: reader_writer.hpp 463569 2015-03-30 16:23:11Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -101,6 +101,20 @@ public:
/// both eRW_Success and zero "*count", or return eRW_NotImplemented alone.
virtual ERW_Result PendingCount(size_t* count) = 0;
+
+ /// This method gets called by RStream buffer destructor to return buffered
+ /// yet still unread (from the stream) portion of data back to the device.
+ /// It's semantically equivalent to CStreamUtils::Pushback() with the only
+ /// difference that IReader can only assume the ownership of "buf" when
+ /// "del_ptr" is passed non-NULL.
+ /// Return eRW_Success when data have been successfully pushed back and the
+ /// ownership of the pointers has been assumed as described above.
+ /// Any other error code results in pointers remained and handled within
+ /// the stream buffer being deleted, with a error messages suppressed for
+ /// eRW_NotImplemented (default implementation).
+ virtual ERW_Result Pushback(const void* buf, size_t count,
+ void* del_ptr = 0);
+
virtual ~IReader();
};
diff --git a/c++/include/corelib/request_ctx.hpp b/c++/include/corelib/request_ctx.hpp
index d0b04ed..390a9f1 100644
--- a/c++/include/corelib/request_ctx.hpp
+++ b/c++/include/corelib/request_ctx.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___REQUEST_CTX__HPP
#define CORELIB___REQUEST_CTX__HPP
-/* $Id: request_ctx.hpp 448715 2014-10-08 15:41:41Z ivanov $
+/* $Id: request_ctx.hpp 463649 2015-03-31 16:12:18Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -107,15 +107,40 @@ public:
string GetEncodedSessionID(void) const;
/// Hit ID
- /// Get explicit hit id or the default one (from HTTP_NCBI_PHID or
- /// generated automatically at application start).
- string GetHitID(void) const;
- /// Set explicit hit id.
+ /// Allowed source of the current hit id
+ /// @sa IsSetHitID
+ enum EHitIDSource {
+ eHitID_Any = 0, ///< Any hit id - always return true.
+ eHitID_Request = 0x01, ///< Check if per-request hit id is set.
+ eHitID_Default = 0x02, ///< Check if default hit id is set.
+
+ /// Check if any hit is already available (will not be generated
+ /// on request).
+ eHidID_Existing = eHitID_Default | eHitID_Request
+ };
+
+ /// Get explicit hit id or the default one (from HTTP_NCBI_PHID etc).
+ /// If none of the above is available, generate a new id for the current
+ /// request.
+ /// If using the default hit id, it is cached in the request context and
+ /// becomes local one.
+ string GetHitID(void) const
+ { return x_GetHitID(CDiagContext::eHitID_Create); }
+ /// Set explicit hit id. The id is reset on request end.
void SetHitID(const string& hit);
/// Check if there's an explicit hit id or the default one.
- bool IsSetHitID(void) const;
+ /// @param src
+ /// Allowed source(s) of hit id.
+ /// @return
+ /// If 'src' is eHitID_Any, always return 'true' because GetHitID
+ /// always returns a non-empty value. For other options return true
+ /// if the selected hit id source is already not empty.
+ bool IsSetHitID(EHitIDSource src = eHitID_Any) const;
/// Check if there's an explicit hit id.
- bool IsSetExplicitHitID(void) const;
+ /// @deprecated Use IsSetHitID(eHitID_Request) instead.
+ NCBI_DEPRECATED
+ bool IsSetExplicitHitID(void) const
+ { return IsSetHitID(eHitID_Request); }
/// Reset explicit hit id.
void UnsetHitID(void);
/// Generate unique hit id, assign it to this request, return
@@ -125,7 +150,7 @@ public:
/// If hit id is not set, return empty string.
const string& GetNextSubHitID(void);
- /// Request exit startus
+ /// Request exit status
int GetRequestStatus(void) const;
void SetRequestStatus(int status);
void SetRequestStatus(CRequestStatus::ECode code);
@@ -259,7 +284,10 @@ private:
// Log current hit id if not yet logged and if the application state is
// 'in request', otherwise postpone logging until StartRequest is executed.
- void x_LogHitID(void) const;
+ // If 'ignore_app_state' is set, log any available hit id anyway.
+ void x_LogHitID(bool ignore_app_state = false) const;
+
+ string x_GetHitID(CDiagContext::EDefaultHitIDFlags flag) const;
static bool& sx_GetDefaultAutoIncRequestIDOnPost(void);
@@ -280,6 +308,11 @@ private:
bool m_AutoIncOnPost;
TContextFlags m_Flags;
string m_SubHitIDCache;
+
+ // For saving/checking owner TID.
+ friend class CDiagContextThreadData;
+ // TID of the thread currently using this context or -1.
+ Uint8 m_OwnerTID;
};
@@ -395,20 +428,23 @@ void CRequestContext::UnsetSessionID(void)
inline
-bool CRequestContext::IsSetHitID(void) const
+bool CRequestContext::IsSetHitID(EHitIDSource src) const
{
- // Either explicit or default hit id is always available.
- return true;
+ if (src == eHitID_Any) {
+ // Local, default or auto-created hit id is always available.
+ return true;
+ }
+ if ((src & eHitID_Request) && x_IsSetProp(eProp_HitID)) {
+ return true;
+ }
+ if ((src & eHitID_Default) && GetDiagContext().x_IsSetDefaultHitID()) {
+ return true;
+ }
+ return false;
}
inline
-bool CRequestContext::IsSetExplicitHitID(void) const
-{
- return x_IsSetProp(eProp_HitID);
-}
-
-inline
void CRequestContext::UnsetHitID(void)
{
x_UnsetProp(eProp_HitID);
diff --git a/c++/include/corelib/request_status.hpp b/c++/include/corelib/request_status.hpp
index 127ee38..1600b64 100644
--- a/c++/include/corelib/request_status.hpp
+++ b/c++/include/corelib/request_status.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___REQUEST_STATUS__HPP
#define CORELIB___REQUEST_STATUS__HPP
-/* $Id: request_status.hpp 446389 2014-09-15 17:56:35Z ivanov $
+/* $Id: request_status.hpp 441525 2014-07-24 16:55:45Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/resource_info.hpp b/c++/include/corelib/resource_info.hpp
index cd4acc7..1afa75c 100644
--- a/c++/include/corelib/resource_info.hpp
+++ b/c++/include/corelib/resource_info.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___RESOURCE_INFO__HPP
#define CORELIB___RESOURCE_INFO__HPP
-/* $Id: resource_info.hpp 463791 2015-04-01 15:39:43Z ivanov $
+/* $Id: resource_info.hpp 463082 2015-03-24 17:47:35Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/corelib/stream_utils.hpp b/c++/include/corelib/stream_utils.hpp
index 69dbbda..eab590b 100644
--- a/c++/include/corelib/stream_utils.hpp
+++ b/c++/include/corelib/stream_utils.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___STREAM_UTILS__HPP
#define CORELIB___STREAM_UTILS__HPP
-/* $Id: stream_utils.hpp 424653 2014-01-17 20:30:11Z lavr $
+/* $Id: stream_utils.hpp 463569 2015-03-30 16:23:11Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -57,51 +57,54 @@ BEGIN_NCBI_SCOPE
struct NCBI_XNCBI_EXPORT CStreamUtils
{
-// Push the block of data [buf, buf+buf_size) back to the input stream "is".
+// Push a block of data [buf, buf+buf_size) back to the input stream "is".
// If "del_ptr" is not NULL, then `delete[] (CT_CHAR_TYPE*) del_ptr' is called
// some time between the moment you call this function (perhaps, prior to when
// it returns) and when the passed block is no longer needed (i.e. its content
// is stored elsewhere, or its all read out from the stream, or if the stream
-// is destructed). Since this function may, at its own discretion, use the
-// passed "buf" directly in the input stream as long as it needs to, for the
-// sake of data integrity and consistency the block should not be modified
-// from the outside until all of the passed data is read out from the stream.
-// NOTE 1: It's okay to pushback arbitrary data (i.e. not necessarily
-// just what has been last read from the stream).
+// is destructed). Since the first form of this API may, at its own
+// discretion, use the passed "buf" directly in the input stream as long as
+// needed, for the sake of data integrity and consistency the block must not
+// be modified until all of the data is read out from the stream.
+// NOTE 0: The very presence of the "del_ptr" parameter (NULL or non-NULL)
+// denotes that the "buf"'s contents can be directly used as the
+// pushback data (i.e. the stream assumes the ownership of "buf").
+// NOTE 1: It's okay to push back arbitrary data (i.e. not necessarily just
+// what has been last read from the "is" stream).
// NOTE 2: Data does not actually go to the original streambuf of "is".
// NOTE 3: It's okay if "is" is a full-duplex stream (iostream).
// NOTE 4: Data pushed back regardless of the current stream state, so it is
// the caller's responsibility to check and possibly clear stream
// state that can prevent further reading (e.g. an EOF condition
// reached previously).
-// NOTE 5: After a pushback, the stream is allowed to do limited seeks
+// NOTE 5: After the pushback, the stream is allowed to do limited seeks
// relative to current position (ios::cur); only direct-access
// (ios::beg, ios::end) seeks are fully okay (if permitted by "is").
// NOTE 6: Stream re-positioning made after pushback clears all pushback data.
// NOTE 7: The standard specifically says that putbacks must be interleaved
// with reads in order to work properly. That is especially
-// important to keep in mind, when using both the standard
+// important to keep in mind, while using both the standard
// putbacks and the pushbacks offered by this API.
// NOTE 8: Implementation is incomplete (but safe and stable) and may leak
-// memory in Solaris WorkShop MT builds (due to a bug in C++ RTL).
+// memory in Solaris WorkShop MT builds (due to a bug in its C++ RTL).
static void Pushback(CNcbiIstream& is,
CT_CHAR_TYPE* buf,
streamsize buf_size,
void* del_ptr)
{ x_Pushback(is, buf, (size_t) buf_size, del_ptr, ePushback_NoCopy); }
-// Acts just like its counterpart with 4 args (above), but this variant
-// always copies (if necessary) the "pushback data" into an internal buffer,
-// so "buf" is not required to remain read-only in the outer code.
+// Acts just like its counterpart with 4 args (above), but this variant always
+// copies (if necessary) the "pushback data" into an internal buffer, so "buf"
+// is not required to remain read-only in the outer code.
static void Pushback(CNcbiIstream& is,
const CT_CHAR_TYPE* buf,
streamsize buf_size)
{ x_Pushback(is, const_cast<CT_CHAR_TYPE*> (buf), (size_t) buf_size); }
-// Unsafe but fast API that tries to backup "buf_size" bytes in the
-// internal stream buffer, but if that is not possible, will use
-// (perhaps, partially) "buf" and "del_ptr" to pushback as described above.
-// This call relies upon that the data in "buf" is exactly as it has been
+// Unsafe but fast API that tries to backup "buf_size" bytes in the internal
+// stream buffer, but if that is not possible, will use (perhaps, partially)
+// "buf" and "del_ptr" to pushback as described above.
+// This call relies upon that the data in "buf" is exactly same as it has been
// read from the stream previously (otherwise, behavior is undefined).
static void Stepback(CNcbiIstream& is,
CT_CHAR_TYPE* buf,
@@ -139,8 +142,13 @@ private:
/// into a single bi-directional one, e.g.:
/// CRWStream rw(new CStreamReader(cin), new CStreamWriter(cout),
/// 0, 0, CRWStreambuf::fOwnAll);
+///
+/// @note If the stream is not owned by CStreamReader, then any data buffered
+/// yet unread from a CRStream built on top of this reader, will be
+/// pushed back to the original stream when the CRStream gets destroyed.
+///
/// @sa
-/// CStreamWriter
+/// CStreamWriter, CStreamUtils::Pushback
class NCBI_XNCBI_EXPORT CStreamReader : public IReader
{
public:
@@ -150,6 +158,7 @@ public:
virtual ERW_Result Read(void* buf, size_t count, size_t* bytes_read);
virtual ERW_Result PendingCount(size_t* count);
+ virtual ERW_Result Pushback(const void* buf, size_t count, void* del_ptr);
protected:
AutoPtr<CNcbiIstream> m_Stream;
diff --git a/c++/include/corelib/tempstr.hpp b/c++/include/corelib/tempstr.hpp
index 698ecbc..5e70b4e 100644
--- a/c++/include/corelib/tempstr.hpp
+++ b/c++/include/corelib/tempstr.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___TEMPSTR__HPP
#define CORELIB___TEMPSTR__HPP
-/* $Id: tempstr.hpp 423238 2014-01-02 16:06:48Z lavr $
+/* $Id: tempstr.hpp 462543 2015-03-19 13:28:44Z drozdov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,7 +26,7 @@
*
* ===========================================================================
*
- * Authors: Mike DiCuccio, Eugene Vasilchenko, Aaron Ucko
+ * Authors: Mike DiCuccio, Eugene Vasilchenko, Aaron Ucko, Vladimir Ivanov
*
* File Description:
*
@@ -85,9 +85,9 @@ public:
CTempString(const CTempString& str, size_type pos);
CTempString(const CTempString& str, size_type pos, size_type len);
- /// copy a substring into a string
+ /// Copy a substring into a string
/// Somewhat similar to basic_string::assign()
- void Copy(string& dst, size_type pos, size_type length) const;
+ void Copy(string& dst, size_type pos, size_type len) const;
/// @name std::basic_string<> compatibility interface
/// @{
@@ -95,9 +95,7 @@ public:
/// Assign new values to the content of the a string
CTempString& assign(const char* src_str, size_type len);
CTempString& assign(const CTempString& src_str);
- CTempString& assign(const CTempString& src_str,
- size_type off,
- size_type count);
+ CTempString& assign(const CTempString& src_str, size_type pos, size_type len);
CTempString& operator=(const CTempString& str);
@@ -110,18 +108,17 @@ public:
/// Return a pointer to the array represented. As with
/// std::basic_string<>, this is not guaranteed to be NULL terminated.
- const char* data(void) const;
+ const char* data(void) const;
/// Return the length of the represented array.
- size_type length(void) const;
+ size_type length(void) const;
/// Return the length of the represented array.
- size_type size(void) const;
-
+ size_type size(void) const;
/// Return true if the represented string is empty (i.e., the length is
/// zero)
- bool empty(void) const;
+ bool empty(void) const;
/// Clears the string
void clear(void);
@@ -180,43 +177,27 @@ public:
/// a NULL character is returned.
char operator[](size_type pos) const;
- /// operator== for C-style strings
- bool operator==(const char* str) const;
- /// operator== for std::string strings
- bool operator==(const string& str) const;
- /// operator== for CTempString strings
- bool operator==(const CTempString& str) const;
+ /// Compare the current string with a given string.
+ int compare(const CTempString& str) const;
- /// operator!= for C-style strings
- bool operator!=(const char* str) const;
- /// operator!= for std::string strings
- bool operator!=(const string& str) const;
- /// operator!= for CTempString strings
+ // Comparison operators, see compare().
+ bool operator==(const CTempString& str) const;
bool operator!=(const CTempString& str) const;
-
- /// operator< for C-style strings
- bool operator<(const char* str) const;
- /// operator< for std::string strings
- bool operator<(const string& str) const;
- /// operator< for CTempString strings
- bool operator<(const CTempString& str) const;
+ bool operator< (const CTempString& str) const;
+ bool operator> (const CTempString& str) const;
/// @}
operator string(void) const;
private:
-
const char* m_String; ///< Stored pointer to string
size_type m_Length; ///< Length of string
+private:
// Initialize CTempString with bounds checks
- void x_Init(const char* str, size_type str_len,
- size_type pos, size_type len);
- void x_Init(const char* str, size_type str_len,
- size_type pos);
- bool x_Equals(const_iterator it2, size_type len2) const;
- bool x_Less(const_iterator it2, size_type len2) const;
+ void x_Init(const char* str, size_type str_len, size_type pos, size_type len);
+ void x_Init(const char* str, size_type str_len, size_type pos);
#if defined(NCBI_TEMPSTR_USE_A_COPY)
/// @attention This (making copy of the string) is turned off by default!
@@ -231,11 +212,54 @@ NCBI_XNCBI_EXPORT
CNcbiOstream& operator<<(CNcbiOstream& out, const CTempString& str);
-/// Global operator== for string and CTempString
+// Global comparison operators (counterparts for CTempString::operator's).
+
+inline
+bool operator==(const char* str1, const CTempString& str2)
+{
+ return str2.compare(str1) == 0;
+}
+
inline
bool operator==(const string& str1, const CTempString& str2)
{
- return str2 == str1;
+ return str2.compare(str1) == 0;
+}
+
+inline
+bool operator!=(const char* str1, const CTempString& str2)
+{
+ return str2.compare(str1) != 0;
+}
+
+inline
+bool operator!=(const string& str1, const CTempString& str2)
+{
+ return str2.compare(str1) != 0;
+}
+
+inline
+bool operator<(const char* str1, const CTempString& str2)
+{
+ return str2.compare(str1) > 0;
+}
+
+inline
+bool operator<(const string& str1, const CTempString& str2)
+{
+ return str2.compare(str1) > 0;
+}
+
+inline
+bool operator>(const char* str1, const CTempString& str2)
+{
+ return str2.compare(str1) < 0;
+}
+
+inline
+bool operator>(const string& str1, const CTempString& str2)
+{
+ return str2.compare(str1) < 0;
}
/*
@@ -474,8 +498,8 @@ void CTempString::erase(size_type pos)
}
-/// copy a substring into a string
-/// These are analogs of basic_string::assign()
+/// Copy a substring into a string.
+/// These are analogs of basic_string::assign().
inline
void CTempString::Copy(string& dst, size_type pos, size_type len) const
{
@@ -535,7 +559,7 @@ inline
CTempString::size_type CTempString::find_last_of(const CTempString& match,
size_type pos) const
{
- if (match.length() && match.length() <= length() ) {
+ if (match.length()) {
if (pos >= length()) {
pos = length() - 1;
}
@@ -565,7 +589,7 @@ inline
CTempString::size_type CTempString::find_last_not_of(const CTempString& match,
size_type pos) const
{
- if (match.length() && match.length() <= length() ) {
+ if (match.length()) {
if (pos >= length()) {
pos = length() - 1;
}
@@ -710,11 +734,11 @@ CTempString& CTempString::assign(const CTempString& src_str)
inline
CTempString& CTempString::assign(const CTempString& src_str,
- size_type off,
- size_type count)
+ size_type pos,
+ size_type len)
{
NCBI_TEMPSTR_DESTROY_COPY();
- x_Init(src_str.data(), src_str.size(), off, count);
+ x_Init(src_str.data(), src_str.size(), pos, len);
NCBI_TEMPSTR_MAKE_COPY();
return *this;
}
@@ -749,92 +773,60 @@ CTempString::operator string(void) const
inline
-bool CTempString::x_Equals(const_iterator it2, size_type len2) const
+int CTempString::compare(const CTempString& str) const
{
- return len2 == length() && memcmp(data(), it2, len2) == 0;
-}
+ const int kLess = -1;
+ const int kEqual = 0;
+ const int kGreater = 1;
+ size_type n1 = length();
+ size_type n2 = str.length();
-inline
-bool CTempString::operator==(const char* str) const
-{
- if ( !str || !m_String ) {
- return !str && !m_String;
+ if ( !n1 ) {
+ return n2 ? kLess : kEqual;
}
- return x_Equals(str, strlen(str));
-}
-
-
-inline
-bool CTempString::operator==(const string& str) const
-{
- return x_Equals(str.data(), str.size());
+ if ( !n2 ) {
+ return n1 ? kGreater : kEqual;
+ }
+ int res = memcmp(data(), str.data(), min(n1, n2));
+ if ( res ) {
+ return res;
+ }
+ if (n1 < n2) {
+ return kLess;
+ }
+ if (n1 > n2) {
+ return kGreater;
+ }
+ return kEqual;
}
inline
bool CTempString::operator==(const CTempString& str) const
{
- return x_Equals(str.data(), str.size());
-}
-
-
-inline
-bool CTempString::operator!=(const char* str) const
-{
- return !(*this == str);
-}
-
-
-inline
-bool CTempString::operator!=(const string& str) const
-{
- return !(*this == str);
+ return compare(str) == 0;
}
-
inline
bool CTempString::operator!=(const CTempString& str) const
{
- return !(*this == str);
+ return compare(str) != 0;
}
-
inline
-bool CTempString::x_Less(const_iterator it2, size_type other_len) const
+bool CTempString::operator<(const CTempString& str) const
{
- size_type comp_len = min(other_len, length());
- int res = memcmp(begin(), it2, comp_len);
- if ( res != 0 ) {
- return res < 0;
- }
- return length() < other_len;
+ return compare(str) < 0;
}
-
inline
-bool CTempString::operator<(const char* str) const
+bool CTempString::operator>(const CTempString& str) const
{
- if ( !str || !m_String ) {
- return str && !m_String;
- }
- return x_Less(str, strlen(str));
+ return compare(str) > 0;
}
-inline
-bool CTempString::operator<(const string& str) const
-{
- return x_Less(str.data(), str.size());
-}
-
-
-inline
-bool CTempString::operator<(const CTempString& str) const
-{
- return x_Less(str.data(), str.size());
-}
-
class CTempStringEx : public CTempString
{
@@ -913,11 +905,11 @@ public:
return *this = str;
}
CTempStringEx& assign(const CTempString& str,
- size_type off,
+ size_type pos,
size_type count)
{
m_ZeroAtEnd = eNoZeroAtEnd;
- CTempString::assign(str, off, count);
+ CTempString::assign(str, pos, count);
return *this;
}
@@ -969,24 +961,15 @@ private:
/// in the functions which need to modify the strings (e.g. NStr::Splilt).
-class CTempString_Storage
+class NCBI_XNCBI_EXPORT CTempString_Storage
{
public:
typedef CTempString::size_type size_type;
- ~CTempString_Storage(void)
- {
- NON_CONST_ITERATE(TData, it, m_Data) {
- delete[] (*it);
- *it = 0;
- }
- }
+ CTempString_Storage(void);
+ ~CTempString_Storage(void);
- char* Allocate(CTempString::size_type len)
- {
- m_Data.push_back(new char[len]);
- return m_Data.back();
- }
+ char* Allocate(CTempString::size_type len);
private:
typedef char* TBuffer;
diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp
index 1480a71..52f7dfe 100644
--- a/c++/include/corelib/test_boost.hpp
+++ b/c++/include/corelib/test_boost.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___TEST_BOOST__HPP
#define CORELIB___TEST_BOOST__HPP
-/* $Id: test_boost.hpp 467443 2015-05-13 17:30:03Z ivanov $
+/* $Id: test_boost.hpp 462211 2015-03-17 14:17:35Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -244,20 +244,20 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \
// {BOOST,NCBITEST}_REQUIRE* call will bail.
#ifdef __clang_analyzer__
# undef BOOST_REQUIRE
-# define BOOST_REQUIRE(P) _ASSERT(P)
+# define BOOST_REQUIRE(P) _ALWAYS_ASSERT(P)
# undef BOOST_REQUIRE_MESSAGE
-# define BOOST_REQUIRE_MESSAGE(P, M) _ASSERT((FORMAT(M), (P)))
+# define BOOST_REQUIRE_MESSAGE(P, M) _ALWAYS_ASSERT((FORMAT(M), (P)))
# undef BOOST_REQUIRE_EQUAL
-# define BOOST_REQUIRE_EQUAL(L, R) _ASSERT((L) == (R))
+# define BOOST_REQUIRE_EQUAL(L, R) _ALWAYS_ASSERT((L) == (R))
# undef BOOST_REQUIRE_NE
-# define BOOST_REQUIRE_NE(L, R) _ASSERT((L) != (R))
+# define BOOST_REQUIRE_NE(L, R) _ALWAYS_ASSERT((L) != (R))
# undef BOOST_REQUIRE_NO_THROW
-# define BOOST_REQUIRE_NO_THROW(S) try { S; } catch (...) { _TROUBLE; }
+# define BOOST_REQUIRE_NO_THROW(S) try { S; } catch (...) { _ALWAYS_TROUBLE; }
# undef BOOST_REQUIRE_THROW
# define BOOST_REQUIRE_THROW(S, E) \
- do { try { S; } catch (E const&) { break; } _TROUBLE; } while(false)
+ do { try { S; } catch (E const&) { break; } _ALWAYS_TROUBLE; } while(false)
# undef NCBITEST_REQUIRE
-# define NCBITEST_REQUIRE(P) BOOST_REQUIRE_NO_THROW(_ASSERT(P))
+# define NCBITEST_REQUIRE(P) BOOST_REQUIRE_NO_THROW(_ALWAYS_ASSERT(P))
# undef NCBITEST_REQUIRE_MESSAGE
# define NCBITEST_REQUIRE_MESSAGE(P, M) NCBITEST_REQUIRE((FORMAT(M), (P)))
# undef NCBITEST_REQUIRE_EQUAL
diff --git a/c++/include/dbapi/dbapi.hpp b/c++/include/dbapi/dbapi.hpp
index da11b71..3b7677f 100644
--- a/c++/include/dbapi/dbapi.hpp
+++ b/c++/include/dbapi/dbapi.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI___DBAPI__HPP
#define DBAPI___DBAPI__HPP
-/* $Id: dbapi.hpp 447099 2014-09-22 15:55:54Z ucko $
+/* $Id: dbapi.hpp 446742 2014-09-17 19:11:55Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/dbapi/driver/dbapi_conn_factory.hpp b/c++/include/dbapi/driver/dbapi_conn_factory.hpp
index 4de1262..4c2fa14 100644
--- a/c++/include/dbapi/driver/dbapi_conn_factory.hpp
+++ b/c++/include/dbapi/driver/dbapi_conn_factory.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI_CONN_FACTORY_HPP
#define DBAPI_CONN_FACTORY_HPP
-/* $Id: dbapi_conn_factory.hpp 423263 2014-01-02 17:57:22Z ucko $
+/* $Id: dbapi_conn_factory.hpp 471064 2015-06-23 13:56:53Z fukanchi $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -129,14 +129,20 @@ protected:
return *m_Parent;
}
+ void Exclude(const string& service_name, const TSvrRef& server);
+ void CleanExcluded(const string& service_name);
+ const string& GetExcluded(const string& service_name);
+
private:
// Data types
typedef map<string, TSvrRef> TDispatchedSet;
+ typedef map<string, string> TExclusionSummaryMap;
typedef map<string, unsigned int> TServer2NumMap;
const CDBConnectionFactory* m_Parent;
CRef<IDBServiceMapper> m_DBServiceMapper;
TDispatchedSet m_DispatchedSet;
+ TExclusionSummaryMap m_ExclusionSummaryMap;
TServer2NumMap m_DispatchNumMap;
TServer2NumMap m_ValidationFailureMap;
};
@@ -158,7 +164,7 @@ private:
I_DriverContext& driver_ctx;
IConnValidator::EConnStatus conn_status;
impl::CDBHandlerStack handlers;
- unsigned int retries;
+ list<string> tried;
// params deliberately left out (potentially call-specific)
};
diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
index d2344c4..2f7474e 100644
--- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
+++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI_DRIVER_IMPL___DBAPI_DRIVER_UTILS__HPP
#define DBAPI_DRIVER_IMPL___DBAPI_DRIVER_UTILS__HPP
-/* $Id: dbapi_driver_utils.hpp 450675 2014-10-29 17:13:44Z ivanov $
+/* $Id: dbapi_driver_utils.hpp 450609 2014-10-28 18:46:14Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp b/c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp
index 45530ce..b79c38a 100644
--- a/c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp
+++ b/c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp
@@ -2,7 +2,7 @@
#define DBAPI_DRIVER_IMPL___DBAPI_IMPL_CONNECTION__HPP
-/* $Id: dbapi_impl_connection.hpp 459267 2015-02-17 16:40:25Z ivanov $
+/* $Id: dbapi_impl_connection.hpp 482702 2015-10-26 15:43:14Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,6 +36,7 @@
#include <dbapi/driver/impl/dbapi_driver_utils.hpp>
#include <dbapi/driver/impl/handle_stack.hpp>
+#include <corelib/ncbitime.hpp>
BEGIN_NCBI_SCOPE
@@ -225,6 +226,11 @@ public:
//
CDBConnParams::EServerType CalculateServerType(CDBConnParams::EServerType server_type);
+
+ void SetUserData(CObject* data)
+ {
+ m_UserData.Reset(data);
+ }
protected:
/// These methods to allow the children of CConnection to create
@@ -296,6 +302,11 @@ protected:
return m_OpeningMsgHandlers;
}
+ CObject* x_GetUserData(void) const
+ {
+ return const_cast<CObject*>(m_UserData.GetPointerOrNull());
+ }
+
private:
typedef deque<impl::CCommand*> TCommandList;
@@ -314,6 +325,10 @@ private:
const Uint2 m_Port;
const string m_Passwd;
const string m_Pool;
+ unsigned int m_PoolMinSize;
+ CTimeSpan m_PoolIdleTimeParam;
+ CTime m_CleanupTime;
+ CRef<CObject> m_UserData;
unsigned int m_ReuseCount;
const bool m_Reusable;
bool m_OpenFinished;
diff --git a/c++/include/dbapi/driver/impl/dbapi_impl_context.hpp b/c++/include/dbapi/driver/impl/dbapi_impl_context.hpp
index 3676e67..8a46d14 100644
--- a/c++/include/dbapi/driver/impl/dbapi_impl_context.hpp
+++ b/c++/include/dbapi/driver/impl/dbapi_impl_context.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI_DRIVER_IMPL___DBAPI_IMPL_CONTEXT__HPP
#define DBAPI_DRIVER_IMPL___DBAPI_IMPL_CONTEXT__HPP
-/* $Id: dbapi_impl_context.hpp 445018 2014-08-29 15:50:04Z ucko $
+/* $Id: dbapi_impl_context.hpp 480566 2015-10-01 16:55:03Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -73,7 +73,10 @@ struct NCBI_DBAPIDRIVER_EXPORT SDBConfParams
fPoolMaxSizeSet = 0x0800,
fArgsSet = 0x1000,
fPasswordFileSet = 0x2000,
- fPasswordKeySet = 0x4000
+ fPasswordKeySet = 0x4000,
+ fPoolIdleTimeSet = 0x8000,
+ fPoolWaitTimeSet = 0x10000,
+ fPoolAllowTempSet= 0x20000
};
typedef unsigned int TFlags;
@@ -93,6 +96,9 @@ struct NCBI_DBAPIDRIVER_EXPORT SDBConfParams
string pool_name;
string pool_minsize;
string pool_maxsize;
+ string pool_idle_time;
+ string pool_wait_time;
+ string pool_allow_temp_overflow;
string args;
@@ -112,6 +118,10 @@ struct NCBI_DBAPIDRIVER_EXPORT SDBConfParams
bool IsPooledSet(void) { return IsFlagSet(fIsPooledSet); }
bool IsPoolMinSizeSet(void) { return IsFlagSet(fPoolMinSizeSet); }
bool IsPoolMaxSizeSet(void) { return IsFlagSet(fPoolMaxSizeSet); }
+ bool IsPoolIdleTimeSet(void) { return IsFlagSet(fPoolIdleTimeSet); }
+ bool IsPoolWaitTimeSet(void) { return IsFlagSet(fPoolWaitTimeSet); }
+ bool IsPoolAllowTempOverflowSet(void)
+ { return IsFlagSet(fPoolAllowTempSet); }
bool IsArgsSet(void) { return IsFlagSet(fArgsSet); }
void Clear(void);
@@ -214,11 +224,16 @@ public:
void ReadDBConfParams (const string& service_name, SDBConfParams* params);
bool SatisfyPoolMinimum(const CDBConnParams& params);
void CloseConnsForPool (const string& pool_name);
+ void CloseOldIdleConns (unsigned int max_closings,
+ const string& pool_name = kEmptyStr);
protected:
typedef list<CConnection*> TConnPool;
- mutable CMutex m_CtxMtx;
+ virtual SSystemMutex& x_GetCtxMtx(void) const
+ {
+ return m_DefaultCtxMtx;
+ }
// To allow children of CDriverContext to create CDB_Connection
CDB_Connection* MakeCDBConnection(CConnection* connection);
@@ -248,6 +263,13 @@ protected:
private:
+ mutable CMutex m_DefaultCtxMtx;
+#ifdef NCBI_THREADS
+ CSemaphore m_PoolSem;
+ string m_PoolSemSubject;
+ CConnection* m_PoolSemConn;
+#endif
+
unsigned int m_LoginTimeout; //< Login timeout.
unsigned int m_Timeout; //< Connection timeout.
unsigned int m_CancelTimeout;//< Canceling timeout.
diff --git a/c++/include/dbapi/driver/interfaces.hpp b/c++/include/dbapi/driver/interfaces.hpp
index f8c0024..483d23d 100644
--- a/c++/include/dbapi/driver/interfaces.hpp
+++ b/c++/include/dbapi/driver/interfaces.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI_DRIVER___INTERFACES__HPP
#define DBAPI_DRIVER___INTERFACES__HPP
-/* $Id: interfaces.hpp 441150 2014-07-21 19:10:46Z ucko $
+/* $Id: interfaces.hpp 482702 2015-10-26 15:43:14Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1372,6 +1372,8 @@ public:
class NCBI_DBAPIDRIVER_EXPORT I_ConnectionExtra
{
public:
+ virtual ~I_ConnectionExtra(void);
+
#ifdef NCBI_OS_MSWIN
typedef SOCKET TSockHandle;
#else
@@ -1381,7 +1383,14 @@ public:
/// Get OS handle of the socket represented by the connection
virtual TSockHandle GetLowLevelHandle(void) const = 0;
- virtual ~I_ConnectionExtra(void);
+ virtual void SetUserData(CObject* data) = 0;
+ template<typename T> T* GetUserData(void)
+ { return dynamic_cast<T*>(x_GetUserData()); }
+ template<typename T> const T* GetUserData(void) const
+ { return dynamic_cast<T*>(x_GetUserData()); }
+
+protected:
+ virtual CObject* x_GetUserData(void) const = 0;
};
diff --git a/c++/include/dbapi/driver/public.hpp b/c++/include/dbapi/driver/public.hpp
index 0af4b7f..2d3f4ad 100644
--- a/c++/include/dbapi/driver/public.hpp
+++ b/c++/include/dbapi/driver/public.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI_DRIVER___PUBLIC__HPP
#define DBAPI_DRIVER___PUBLIC__HPP
-/* $Id: public.hpp 459267 2015-02-17 16:40:25Z ivanov $
+/* $Id: public.hpp 458199 2015-02-02 19:18:09Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,6 +54,7 @@ namespace impl
}
+class CAutoTrans;
template <class I> class CInterfaceHook;
@@ -304,6 +305,11 @@ public:
virtual string GetDriverName(void) const;
+ bool HasTransaction(void) const
+ {
+ return m_HasTransaction;
+ }
+
public:
// Deprecated legacy methods.
// CXX-601
@@ -348,6 +354,7 @@ public:
private:
impl::CConnection* m_ConnImpl;
+ bool m_HasTransaction;
CDB_Connection(impl::CConnection* c);
@@ -363,6 +370,7 @@ private:
// The constructor should be called by "I_DriverContext" only!
friend class impl::CDriverContext;
+ friend class CAutoTrans;
friend class CInterfaceHook<CDB_Connection>;
};
diff --git a/c++/include/dbapi/error_codes.hpp b/c++/include/dbapi/error_codes.hpp
index cc958cd..c7aca8e 100644
--- a/c++/include/dbapi/error_codes.hpp
+++ b/c++/include/dbapi/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI___ERROR_CODES__HPP
#define DBAPI___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 437697 2014-06-09 18:26:37Z ucko $
+/* $Id: error_codes.hpp 469244 2015-06-02 18:54:37Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,7 +75,7 @@ NCBI_DEFINE_ERRCODE_X(Dbapi_BlobStream, 1134, 3);
NCBI_DEFINE_ERRCODE_X(Dbapi_ObjImpls, 1135, 10);
NCBI_DEFINE_ERRCODE_X(Dbapi_BulkInsert, 1136, 1);
NCBI_DEFINE_ERRCODE_X(Dbapi_DrvrContext, 1137, 1);
-NCBI_DEFINE_ERRCODE_X(Dbapi_Sdbapi, 1138, 17);
+NCBI_DEFINE_ERRCODE_X(Dbapi_Sdbapi, 1138, 18);
END_NCBI_SCOPE
diff --git a/c++/include/dbapi/variant.hpp b/c++/include/dbapi/variant.hpp
index 1560ef5..851873c 100644
--- a/c++/include/dbapi/variant.hpp
+++ b/c++/include/dbapi/variant.hpp
@@ -1,7 +1,7 @@
#ifndef DBAPI___VARIANT__HPP
#define DBAPI___VARIANT__HPP
-/* $Id: variant.hpp 405916 2013-07-09 19:20:40Z ucko $
+/* $Id: variant.hpp 461616 2015-03-11 15:47:00Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -283,8 +283,7 @@ CVariant::ReleaseITDescriptor(void) const
inline
void CVariant::x_Verify_AssignType(EDB_Type db_type, const char* cxx_type) const
{
- if( db_type != GetType() )
- {
+ if (db_type == eDB_UnsupportedType || db_type != GetType()) {
NCBI_THROW(CVariantException, eVariant,
"Cannot assign type '" + string(cxx_type) + "' to type '"
+ string(CDB_Object::GetTypeName(GetType())) + "'");
diff --git a/c++/include/html/htmlhelper.hpp b/c++/include/html/htmlhelper.hpp
index 1b48850..7fdcc3c 100644
--- a/c++/include/html/htmlhelper.hpp
+++ b/c++/include/html/htmlhelper.hpp
@@ -1,7 +1,7 @@
#ifndef HTML___HTMLHELPER__HPP
#define HTML___HTMLHELPER__HPP
-/* $Id: htmlhelper.hpp 367926 2012-06-29 14:04:54Z ivanov $
+/* $Id: htmlhelper.hpp 460167 2015-02-25 15:39:05Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -218,7 +218,7 @@ void CIDs::Decode(const string& str)
cmd = str[end];
pos = end + 1;
}
- id = AddID(cmd, id, GetNumber(str.substr(pos)));
+ AddID(cmd, id, GetNumber(str.substr(pos)));
}
diff --git a/c++/include/ncbi_pch.hpp b/c++/include/ncbi_pch.hpp
index 3a5a266..6c3b09c 100644
--- a/c++/include/ncbi_pch.hpp
+++ b/c++/include/ncbi_pch.hpp
@@ -1,5 +1,5 @@
#if defined(NCBI_USE_PCH) && !defined(NCBI_PCH__HPP)
-/* $Id: ncbi_pch.hpp 469194 2015-06-02 14:03:42Z blastadm $
+/* $Id: ncbi_pch.hpp 485953 2015-11-30 17:53:34Z blastadm $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/ncbi_source_ver.h b/c++/include/ncbi_source_ver.h
index 3c084c1..bdf3e1d 100644
--- a/c++/include/ncbi_source_ver.h
+++ b/c++/include/ncbi_source_ver.h
@@ -1,4 +1,4 @@
-/* $Id: ncbi_source_ver.h 469194 2015-06-02 14:03:42Z blastadm $
+/* $Id: ncbi_source_ver.h 485953 2015-11-30 17:53:34Z blastadm $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/ncbiconf.h b/c++/include/ncbiconf.h
index 2b2bb17..ab8e245 100644
--- a/c++/include/ncbiconf.h
+++ b/c++/include/ncbiconf.h
@@ -1,7 +1,7 @@
#ifndef FORWARDING_NCBICONF_H
#define FORWARDING_NCBICONF_H
-/* $Id: ncbiconf.h 469194 2015-06-02 14:03:42Z blastadm $
+/* $Id: ncbiconf.h 485953 2015-11-30 17:53:34Z blastadm $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/biblio/Auth_list.hpp b/c++/include/objects/biblio/Auth_list.hpp
index 365de55..6d96a38 100644
--- a/c++/include/objects/biblio/Auth_list.hpp
+++ b/c++/include/objects/biblio/Auth_list.hpp
@@ -1,4 +1,4 @@
-/* $Id: Auth_list.hpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Auth_list.hpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/blast/names.hpp b/c++/include/objects/blast/names.hpp
index b404e5b..2fe5991 100644
--- a/c++/include/objects/blast/names.hpp
+++ b/c++/include/objects/blast/names.hpp
@@ -1,4 +1,4 @@
-/* $Id: names.hpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: names.hpp 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/blastdb/defline_extra.hpp b/c++/include/objects/blastdb/defline_extra.hpp
index 95b42c5..590c2cc 100644
--- a/c++/include/objects/blastdb/defline_extra.hpp
+++ b/c++/include/objects/blastdb/defline_extra.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_BLASTDB___DEFLINE_EXTRA__HPP
#define OBJECTS_BLASTDB___DEFLINE_EXTRA__HPP
-/* $Id: defline_extra.hpp 428160 2014-02-27 21:55:46Z camacho $
+/* $Id: defline_extra.hpp 447320 2014-09-24 18:16:04Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,7 +48,8 @@ enum LinkoutTypes {
eStructure = (1<<2), ///< Add Linkout for structure.
eGeo = (1<<3), ///< Add Linkout for Geo
eGene = (1<<4), ///< Add Linkout for Gene
- eHitInMapviewer = (1<<5), ///< NCBI_DEPRECATED, use eMapviewer
+ eFromVerifiedMaterial = (1<<5), ///< Identifies sequences from verified material
+ ///< (Entrez query: 177353[BioProject])
eMapviewer = (1<<6), ///< The main blast link goes to entrez but we put on a linkout icon that goes to mapviewer.
eGenomicSeq = (1<<7), ///< Is a genomic sequence. Used for the genome+transcript database to show the genomic
///< and transcript sequences separately.
diff --git a/c++/include/objects/general/Dbtag.hpp b/c++/include/objects/general/Dbtag.hpp
index 227d5f4..0eb4a40 100644
--- a/c++/include/objects/general/Dbtag.hpp
+++ b/c++/include/objects/general/Dbtag.hpp
@@ -1,4 +1,4 @@
-/* $Id: Dbtag.hpp 462430 2015-03-18 17:23:06Z ivanov $
+/* $Id: Dbtag.hpp 460837 2015-03-03 18:33:15Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/general/Object_id.hpp b/c++/include/objects/general/Object_id.hpp
index 96b86a5..6df3ac2 100644
--- a/c++/include/objects/general/Object_id.hpp
+++ b/c++/include/objects/general/Object_id.hpp
@@ -1,4 +1,4 @@
-/* $Id: Object_id.hpp 416864 2013-10-31 18:48:43Z vasilche $
+/* $Id: Object_id.hpp 455980 2015-01-06 19:59:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,7 +71,18 @@ public:
// e_Str if the Object-id as a string without valid integer
// If the result is e_Id the integer id will be returned by Int8 value,
// otherwise the value will be set to 0.
- E_Choice GetIdType(Int8& value) const;
+ typedef Int8 TId8;
+ E_Choice GetIdType(TId8& value) const;
+
+ bool IsId8(void) const;
+ TId8 GetId8(void) const;
+ NCBI_WARN_UNUSED_RESULT bool GetId8(TId8& value) const;
+ void SetId8(TId8 value);
+
+ bool IsGi(void) const;
+ TIntId GetGi(void) const;
+ NCBI_WARN_UNUSED_RESULT bool GetGi(TIntId& value) const;
+ void SetGi(TIntId value);
// format contents into a stream
ostream& AsString(ostream &s) const;
@@ -100,6 +111,71 @@ bool CObject_id::operator<(const CObject_id& id2) const
}
+inline
+NCBI_WARN_UNUSED_RESULT
+bool CObject_id::GetId8(TId8& value) const
+{
+ return GetIdType(value) == e_Id;
+}
+
+
+inline
+bool CObject_id::IsId8(void) const
+{
+ TId8 value;
+ return GetId8(value);
+}
+
+
+inline
+NCBI_WARN_UNUSED_RESULT
+bool CObject_id::GetGi(TIntId& value) const
+{
+#ifdef NCBI_INT8_GI
+ return GetId8(value);
+#else
+ if ( IsId() ) {
+ value = GetId();
+ return true;
+ }
+ return false;
+#endif
+}
+
+
+inline
+bool CObject_id::IsGi(void) const
+{
+#ifdef NCBI_INT8_GI
+ return IsId8();
+#else
+ return IsId();
+#endif
+}
+
+
+inline
+TIntId CObject_id::GetGi(void) const
+{
+#ifdef NCBI_INT8_GI
+ return GetId8();
+#else
+ return GetId();
+#endif
+}
+
+
+inline
+void CObject_id::SetGi(TIntId value)
+{
+#ifdef NCBI_INT8_GI
+ SetId8(value);
+#else
+ SetId(value);
+#endif
+}
+
+
/////////////////// end of CObject_id inline methods
/////////////////////////////////////////////////////////////////////////////
diff --git a/c++/include/objects/general/User_object.hpp b/c++/include/objects/general/User_object.hpp
index 1ac0ead..d1d158a 100644
--- a/c++/include/objects/general/User_object.hpp
+++ b/c++/include/objects/general/User_object.hpp
@@ -1,4 +1,4 @@
-/* $Id: User_object.hpp 447737 2014-09-30 13:44:49Z ivanov $
+/* $Id: User_object.hpp 478651 2015-09-11 12:01:08Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -155,7 +155,9 @@ public:
eObjectType_StructuredComment,
eObjectType_OriginalId,
eObjectType_Unverified,
- eObjectType_ValidationSuppression
+ eObjectType_ValidationSuppression,
+ eObjectType_Cleanup,
+ eObjectType_AutodefOptions
};
EObjectType GetObjectType() const;
@@ -169,6 +171,8 @@ public:
void AddUnverifiedFeature();
void RemoveUnverifiedFeature();
+ void UpdateNcbiCleanup(int version);
+
private:
/// Prohibit copy constructor and assignment operator
CUser_object(const CUser_object& value);
diff --git a/c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp b/c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp
old mode 100644
new mode 100755
index ff34d8a..4597f9b
--- a/c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp
+++ b/c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp
@@ -1,4 +1,4 @@
-/* $Id: GCClient_GetAssemblyReques.hpp 459043 2015-02-12 17:31:59Z ivanov $
+/* $Id: GCClient_GetAssemblyReques.hpp 479931 2015-09-24 17:18:23Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -64,6 +64,7 @@ public:
eAssemblyMode_eukaryotic_annotation = 2, ///<- use to retrive eukaryotic assemblies for annotation
eAssemblyMode_prokaryotic_annotation = 3, ///<- use to retrive prokaryotic assemblies for annotation
eAssemblyMode_entrez_indexing = 4, ///<- used when building the Entrez index for assembly and gencoll
+ eAssemblyMode_gbench = 4, ///<- used in gbench
eAssemblyMode_assembly_backend = 5, ///<- used in the CGI to provide data to the Entrez Assembly detail page.
eAssemblyMode_sequence_names = 6, ///<- used in retrieving sequences synonyms
eAssemblyMode_ftp_export = 7 ///<- used in export to public FTP site
@@ -78,8 +79,10 @@ public:
int component_flags;
SRequestParam();
+ SRequestParam(int level_, int assembly_flags_, int chromosome_flags_, int scaffold_flags_, int component_flags_);
bool SetMode(EAssemblyMode mode);
+ bool SetMode(const string& mode);
};
private:
diff --git a/c++/include/objects/genomecoll/GC_Assembly.hpp b/c++/include/objects/genomecoll/GC_Assembly.hpp
index 009b13b..00ac70b 100644
--- a/c++/include/objects/genomecoll/GC_Assembly.hpp
+++ b/c++/include/objects/genomecoll/GC_Assembly.hpp
@@ -1,4 +1,4 @@
-/* $Id: GC_Assembly.hpp 468019 2015-05-19 17:49:08Z ivanov $
+/* $Id: GC_Assembly.hpp 467805 2015-05-18 12:53:53Z zherikov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/genomecoll/GC_Sequence.hpp b/c++/include/objects/genomecoll/GC_Sequence.hpp
index e9b31ae..8034cf9 100644
--- a/c++/include/objects/genomecoll/GC_Sequence.hpp
+++ b/c++/include/objects/genomecoll/GC_Sequence.hpp
@@ -1,4 +1,4 @@
-/* $Id: GC_Sequence.hpp 398186 2013-05-03 15:42:06Z kumarv2 $
+/* $Id: GC_Sequence.hpp 479299 2015-09-18 11:47:36Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -95,6 +95,12 @@ public:
bool HasRole(int Role) const;
+ /// Is the length statistic available?
+ bool CanGetLength() const;
+ /// return the length of this sequence.
+ /// if not available throws CUnassignedMember exception.
+ TSeqPos GetLength() const;
+
protected:
CGC_Assembly* m_Assembly;
CGC_AssemblyUnit* m_AssemblyUnit;
@@ -102,6 +108,11 @@ protected:
CGC_Sequence* m_ParentSequence;
CGC_TaggedSequences::TState m_ParentRel;
+ TSeqPos x_GetLength() const;
+ mutable TSeqPos m_SeqLength;
+ mutable bool m_SeqLengthRetrieved;
+
+
private:
// Prohibit copy constructor and assignment operator
CGC_Sequence(const CGC_Sequence& value);
diff --git a/c++/src/util/distribution.cpp b/c++/include/objects/genomecoll/cached_assembly.hpp
similarity index 64%
copy from c++/src/util/distribution.cpp
copy to c++/include/objects/genomecoll/cached_assembly.hpp
index 03832da..dbec443 100644
--- a/c++/src/util/distribution.cpp
+++ b/c++/include/objects/genomecoll/cached_assembly.hpp
@@ -1,4 +1,4 @@
-/* $Id: distribution.cpp 448239 2014-10-03 14:17:45Z kazimird $
+/* $Id
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -23,31 +23,35 @@
*
* ===========================================================================
*
- * Authors:
- * Dmitry Kazimirov
- *
- * File Description:
- * Implementations of the CDiscreteDistribution class.
*/
-#include <ncbi_pch.hpp>
+#ifndef INTERNAL_GPIPE_OBJECTS_GENOMECOLL_CACHED_ASSEMBLY_HPP
+#define INTERNAL_GPIPE_OBJECTS_GENOMECOLL_CACHED_ASSEMBLY_HPP
-#include <util/distribution.hpp>
-#include <util/random_gen.hpp>
+#include <objects/genomecoll/GC_Assembly.hpp>
+#include <util/compress/stream_util.hpp>
BEGIN_NCBI_SCOPE
-unsigned CDiscreteDistribution::GetNextValue() const
+class CCachedAssembly : public CObject
{
- CRandom::TValue random_number = m_RandomGen->GetRand();
+public:
+ CCachedAssembly(CRef<objects::CGC_Assembly> assembly);
+ CCachedAssembly(const string& blob);
+ CCachedAssembly(const vector<char>& blob);
- CRangeList::TRangeVector::const_iterator random_range =
- m_RangeVector.begin() + (random_number % m_RangeVector.size());
+ CRef<objects::CGC_Assembly> Assembly();
+ const string& Blob(CCompressStream::EMethod neededCompression);
- int diff = random_range->second - random_range->first;
+public:
+ static bool ValidBlob(int blobSize);
- return diff <= 0 ? random_range->first :
- random_range->first + (random_number % (diff + 1));
-}
+private:
+ CRef<objects::CGC_Assembly> m_assembly;
+ //TODO: replace with vector<char> after migration to NetCache
+ string m_blob;
+};
END_NCBI_SCOPE
+
+#endif
diff --git a/c++/include/objects/genomecoll/genomic_collections_cli.hpp b/c++/include/objects/genomecoll/genomic_collections_cli.hpp
index 2341a20..5c60dde 100644
--- a/c++/include/objects/genomecoll/genomic_collections_cli.hpp
+++ b/c++/include/objects/genomecoll/genomic_collections_cli.hpp
@@ -1,4 +1,4 @@
-/* $Id: genomic_collections_cli.hpp 457080 2015-01-20 16:54:14Z ivanov $
+/* $Id: genomic_collections_cli.hpp 483522 2015-11-02 14:44:55Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,6 +45,7 @@
#include <objects/genomecoll/GCClient_AttributeFlags.hpp>
#include <objects/genomecoll/GCClient_GetAssemblyReques.hpp>
#include <objects/genomecoll/GCClient_FindBestAssemblyR.hpp>
+#include <objects/genomecoll/cached_assembly.hpp>
// generated classes
BEGIN_NCBI_SCOPE
@@ -60,15 +61,10 @@ class CGenomicCollectionsService : public CGenomicCollectionsService_Base
{
string m_url;
- typedef CGenomicCollectionsService_Base Tparent;
public:
- // constructor
- CGenomicCollectionsService(void);
+ CGenomicCollectionsService();
CGenomicCollectionsService(const string& url);
- // destructor
- ~CGenomicCollectionsService(void);
-
virtual void x_Connect();
// Override this to supply your own URL.
@@ -97,6 +93,21 @@ public:
CRef<CGC_Assembly> GetAssembly(const string& acc, CGCClient_GetAssemblyRequest::EAssemblyMode mode);
CRef<CGC_Assembly> GetAssembly(int releaseId, CGCClient_GetAssemblyRequest::EAssemblyMode mode);
+ CRef<CGC_Assembly> GetAssembly(const string& acc, const string& mode);
+ CRef<CGC_Assembly> GetAssembly(int releaseId, const string& mode);
+
+ //Some general modes
+ //please contact NCBI if you have other needs
+ struct SAssemblyMode
+ {
+ //as defined in GenomeColl_Master.dbo.CodeServiceModeAlias
+ static string kAssemblyOnly() {return "AssemblyOnly";};
+ static string kFTPExport() {return "FTPExport";};
+ };
+
+ CRef<CGC_Assembly> _GetAssemblyNew(const string& acc, const string& mode);
+ CRef<CGC_Assembly> _GetAssemblyNew(int releaseId, const string& mode);
+
string ValidateChrType(const string& chrType, const string& chrLoc);
CRef<CGCClient_AssemblyInfo> FindBestAssembly
@@ -125,17 +136,6 @@ private:
};
-/////////////////// CGenomicCollectionsService inline methods
-
-
-
-/////////////////// end of CGenomicCollectionsService inline methods
-
-
-END_objects_SCOPE // namespace ncbi::objects::
-
+END_objects_SCOPE
END_NCBI_SCOPE
-
-
-#endif // INTERNAL_GPIPE_OBJECTS_GENOMECOLL_GENOMIC_COLLECTIONS_CLI_HPP
-/* Original file checksum: lines: 86, chars: 2754, CRC32: 2b52f173 */
+#endif
diff --git a/c++/include/objects/macro/Search_func.hpp b/c++/include/objects/macro/Search_func.hpp
index acca0ae..de47a7d 100644
--- a/c++/include/objects/macro/Search_func.hpp
+++ b/c++/include/objects/macro/Search_func.hpp
@@ -1,4 +1,4 @@
-/* $Id: Search_func.hpp 436149 2014-05-23 16:11:09Z chenj $
+/* $Id: Search_func.hpp 450811 2014-10-30 17:34:54Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -84,7 +84,7 @@ private:
bool x_ContainsNorMoreSetsOfBracketsOrParentheses(const string& str,
const int& n) const;
char x_GetClose(char bp) const;
- bool x_SkipBracketOrParen(const unsigned& idx, string& start) const;
+ bool x_SkipBracketOrParen(size_t idx, string& start) const;
// e_Three_numbers
bool x_ContainsThreeOrMoreNumbersTogether(const string& str) const;
diff --git a/c++/include/objects/macro/String_constraint.hpp b/c++/include/objects/macro/String_constraint.hpp
index 57024ea..a1ea07c 100644
--- a/c++/include/objects/macro/String_constraint.hpp
+++ b/c++/include/objects/macro/String_constraint.hpp
@@ -1,4 +1,4 @@
-/* $Id: String_constraint.hpp 454550 2014-12-16 16:26:25Z ivanov $
+/* $Id: String_constraint.hpp 454228 2014-12-11 19:24:06Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -97,21 +97,21 @@ private:
bool x_AdvancedStringCompare(const string& str,
const string& str_match,
const char prev_char,
- unsigned int * ini_target_match_len = 0) const;
+ size_t * ini_target_match_len = 0) const;
bool x_AdvancedStringMatch(const string& str,const string& tmp_match) const;
bool x_CaseNCompareEqual(string str1,
string str2,
- unsigned len1, bool case_sensitive) const;
+ size_t len1, bool case_sensitive) const;
string x_StripUnimportantCharacters(const string& str,
bool strip_space, bool strip_punct) const;
bool x_IsWholeWordMatch(const string& start,
- const size_t& found,
- const unsigned& match_len,
+ size_t found,
+ size_t match_len,
bool disallow_slash = false) const;
bool x_DisallowCharacter(const char ch, bool disallow_slash) const;
bool x_GetSpanFromHyphenInString(const string& str,
- const size_t& hyphen,
+ size_t hyphen,
string& first,
string& second) const;
bool x_StringIsPositiveAllDigits(const string& str) const;
diff --git a/c++/include/objects/macro/Suspect_rule_set.hpp b/c++/include/objects/macro/Suspect_rule_set.hpp
index 6e3ef60..9bee407 100644
--- a/c++/include/objects/macro/Suspect_rule_set.hpp
+++ b/c++/include/objects/macro/Suspect_rule_set.hpp
@@ -1,4 +1,4 @@
-/* $Id: Suspect_rule_set.hpp 423489 2014-01-06 13:19:47Z bollin $
+/* $Id: Suspect_rule_set.hpp 467165 2015-05-11 13:55:19Z kachalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,8 +59,8 @@ public:
// destructor
~CSuspect_rule_set(void);
- static CConstRef<CSuspect_rule_set> GetOrganelleProductRules();
- static CConstRef<CSuspect_rule_set> GetProductRules();
+ static CConstRef<CSuspect_rule_set> GetOrganelleProductRules(const string& name = "");
+ static CConstRef<CSuspect_rule_set> GetProductRules(const string& name = "");
private:
// Prohibit copy constructor and assignment operator
diff --git a/c++/include/objects/macro/Word_substitution.hpp b/c++/include/objects/macro/Word_substitution.hpp
index f4c4615..ada7d22 100644
--- a/c++/include/objects/macro/Word_substitution.hpp
+++ b/c++/include/objects/macro/Word_substitution.hpp
@@ -1,4 +1,4 @@
-/* $Id: Word_substitution.hpp 449682 2014-10-20 13:47:49Z ivanov $
+/* $Id: Word_substitution.hpp 449388 2014-10-16 14:55:16Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/misc/error_codes.hpp b/c++/include/objects/misc/error_codes.hpp
index ae184fd..4d8134d 100644
--- a/c++/include/objects/misc/error_codes.hpp
+++ b/c++/include/objects/misc/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS___ERROR_CODES__HPP
#define OBJECTS___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 368051 2012-07-02 14:29:27Z ucko $
+/* $Id: error_codes.hpp 483824 2015-11-04 17:35:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,8 +45,8 @@ NCBI_DEFINE_ERRCODE_X(Objects_UOConv, 1301, 4);
NCBI_DEFINE_ERRCODE_X(Objects_Taxonomy, 1302, 19);
NCBI_DEFINE_ERRCODE_X(Objects_SeqIdMap, 1303, 4);
NCBI_DEFINE_ERRCODE_X(Objects_SeqAlignMap, 1304, 20);
-NCBI_DEFINE_ERRCODE_X(Objects_SeqLocMap, 1305, 30);
-NCBI_DEFINE_ERRCODE_X(Objects_SeqId, 1306, 11);
+NCBI_DEFINE_ERRCODE_X(Objects_SeqLocMap, 1305, 31);
+NCBI_DEFINE_ERRCODE_X(Objects_SeqId, 1306, 12);
NCBI_DEFINE_ERRCODE_X(Objects_SeqLoc, 1307, 3);
NCBI_DEFINE_ERRCODE_X(Objects_SeqAnnot, 1308, 1);
NCBI_DEFINE_ERRCODE_X(Objects_Bioseq, 1309, 1);
diff --git a/c++/include/objects/pub/Pub.hpp b/c++/include/objects/pub/Pub.hpp
index 382a9b8..af2b49e 100644
--- a/c++/include/objects/pub/Pub.hpp
+++ b/c++/include/objects/pub/Pub.hpp
@@ -1,4 +1,4 @@
-/* $Id: Pub.hpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Pub.hpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/pub/Pub_equiv.hpp b/c++/include/objects/pub/Pub_equiv.hpp
index 7a7213c..0d3d189 100644
--- a/c++/include/objects/pub/Pub_equiv.hpp
+++ b/c++/include/objects/pub/Pub_equiv.hpp
@@ -1,4 +1,4 @@
-/* $Id: Pub_equiv.hpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Pub_equiv.hpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seq/Bioseq.hpp b/c++/include/objects/seq/Bioseq.hpp
index ddd1c17..0b8dfda 100644
--- a/c++/include/objects/seq/Bioseq.hpp
+++ b/c++/include/objects/seq/Bioseq.hpp
@@ -1,4 +1,4 @@
-/* $Id: Bioseq.hpp 457722 2015-01-27 17:54:29Z ivanov $
+/* $Id: Bioseq.hpp 455474 2014-12-30 16:36:56Z foleyjp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seq/Seq_descr.hpp b/c++/include/objects/seq/Seq_descr.hpp
index 4731d54..2c87572 100644
--- a/c++/include/objects/seq/Seq_descr.hpp
+++ b/c++/include/objects/seq/Seq_descr.hpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_descr.hpp 450030 2014-10-22 17:53:43Z ivanov $
+/* $Id: Seq_descr.hpp 448516 2014-10-07 14:40:49Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seq/annot_mapper_exception.hpp b/c++/include/objects/seq/annot_mapper_exception.hpp
index 90dafeb..a860bf2 100644
--- a/c++/include/objects/seq/annot_mapper_exception.hpp
+++ b/c++/include/objects/seq/annot_mapper_exception.hpp
@@ -1,7 +1,7 @@
#ifndef ANNOT_MAPPER_EXCEPTION__HPP
#define ANNOT_MAPPER_EXCEPTION__HPP
-/* $Id: annot_mapper_exception.hpp 444821 2014-08-28 12:07:07Z ivanov $
+/* $Id: annot_mapper_exception.hpp 444487 2014-08-25 16:48:54Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seq/seq_align_mapper_base.hpp b/c++/include/objects/seq/seq_align_mapper_base.hpp
index c898c58..4cc414b 100644
--- a/c++/include/objects/seq/seq_align_mapper_base.hpp
+++ b/c++/include/objects/seq/seq_align_mapper_base.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_ALIGN_MAPPER_BASE__HPP
#define SEQ_ALIGN_MAPPER_BASE__HPP
-/* $Id: seq_align_mapper_base.hpp 442903 2014-08-08 01:36:16Z mcelhany $
+/* $Id: seq_align_mapper_base.hpp 454586 2014-12-16 18:43:50Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -275,6 +275,22 @@ private:
int x_GetPartialDenseg(CRef<CSeq_align>& dst,
int start_seg) const;
+ // Collect exons from a single sub-alignment.
+ void x_GetDstSplicedSubAlign(CSpliced_seg& spliced,
+ const CSeq_align_Mapper_Base& sub_align,
+ bool& last_exon_partial,
+ CSeq_id_Handle& gen_id,
+ CSeq_id_Handle& last_gen_id,
+ bool& single_gen_id,
+ ENa_strand& gen_strand,
+ bool& single_gen_str,
+ CSeq_id_Handle& prod_id,
+ CSeq_id_Handle& last_prod_id,
+ bool& single_prod_id,
+ ENa_strand& prod_strand,
+ bool& single_prod_str,
+ bool& partial) const;
+
// Check if both nucs and prots are present in the segments.
bool x_HaveMixedSeqTypes(void) const;
// Check if each row contains only one strand.
diff --git a/c++/include/objects/seq/seq_id_handle.hpp b/c++/include/objects/seq/seq_id_handle.hpp
index b02fb59..a1a8cac 100644
--- a/c++/include/objects/seq/seq_id_handle.hpp
+++ b/c++/include/objects/seq/seq_id_handle.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
#define OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
-/* $Id: seq_id_handle.hpp 420366 2013-12-03 17:35:24Z vasilche $
+/* $Id: seq_id_handle.hpp 463550 2015-03-30 15:20:32Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -91,9 +91,9 @@ public:
x_RemoveLastLock();
}
}
- int GetLockCounter(void) const
+ bool IsLocked(void) const
{
- return m_LockCounter.Get();
+ return m_LockCounter.Get() != 0;
}
CSeq_id::E_Choice GetType(void) const
diff --git a/c++/include/objects/seq/seq_loc_mapper_base.hpp b/c++/include/objects/seq/seq_loc_mapper_base.hpp
index 8573d0b..e3a76df 100644
--- a/c++/include/objects/seq/seq_loc_mapper_base.hpp
+++ b/c++/include/objects/seq/seq_loc_mapper_base.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_LOC_MAPPER_BASE__HPP
#define SEQ_LOC_MAPPER_BASE__HPP
-/* $Id: seq_loc_mapper_base.hpp 460227 2015-02-25 18:24:03Z ivanov $
+/* $Id: seq_loc_mapper_base.hpp 482403 2015-10-22 18:03:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,6 +35,7 @@
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
+#include <corelib/ncbi_message.hpp>
#include <util/range.hpp>
#include <util/rangemap.hpp>
#include <objects/seqloc/Na_strand.hpp>
@@ -358,10 +359,6 @@ public:
/// target row of the alignment. Any other ID is mapped to the
/// target one. Only the first row matching target ID is used,
/// all other rows are considered source.
- /// If the alignment is a spliced-seg, the merging is set to
- /// 'merge by segment' automatically to merge mapped locations
- /// by exon.
- /// @sa SetMergeBySeg
CSeq_loc_Mapper_Base(const CSeq_align& map_align,
const CSeq_id& to_id,
TMapOptions opts = 0,
@@ -369,10 +366,6 @@ public:
/// Sparse alignments require special row indexing since each
/// row contains two seq-ids. Use options to specify mapping
/// direction.
- /// If the alignment is a spliced-seg, the merging is set to
- /// 'merge by segment' automatically to merge mapped locations
- /// by exon.
- /// @sa SetMergeBySeg
CSeq_loc_Mapper_Base(const CSeq_align& map_align,
size_t to_row,
TMapOptions opts = 0,
@@ -399,7 +392,6 @@ public:
CSeq_loc_Mapper_Base& SetMergeAbutting(void);
/// Merge only intervals from the same group. Group is created
/// for each exon, dense-diag, std-seg and disc sub-alignment.
- /// For spliced segs this mode is turned on by default.
CSeq_loc_Mapper_Base& SetMergeBySeg(void);
/// Merge intervals only if one is completely covered by another
CSeq_loc_Mapper_Base& SetMergeContained(void);
@@ -427,6 +419,11 @@ public:
/// correspond to the strand of the mapping source.
CSeq_loc_Mapper_Base& SetCheckStrand(bool value = true);
+ /// When set to 'true' if mapped alignment has exactly one genomic and
+ /// one protein row, convert it to spliced-seg. By default all mixed-type
+ /// alignments are converted to std-seg.
+ CSeq_loc_Mapper_Base& MixedAlignsAsSpliced(bool value = true);
+
/// Include source ranges in the mapped location. If turned
/// on, the resulting seq-loc will be an equiv with the
/// first sub-loc containing the usual mapped seq-loc, and
@@ -436,6 +433,11 @@ public:
/// Merging mode must be set to MergeNone.
CSeq_loc_Mapper_Base& IncludeSourceLocs(bool value = true);
+ /// Report source range trimming as an error. If the flag is set,
+ /// any trimming will result in throwing CAnnotMapperException.
+ /// Intended to be used when mapping GC-Assembly aliases.
+ CSeq_loc_Mapper_Base& SetErrorOnPartial(bool value = true);
+
/// Map seq-loc
CRef<CSeq_loc> Map(const CSeq_loc& src_loc);
/// Map the whole alignment. Searches all rows for ranges
@@ -528,7 +530,8 @@ protected:
// only with cd-region features.
void x_InitializeLocs(const CSeq_loc& source,
const CSeq_loc& target,
- int frame = 0);
+ int src_frame = 0,
+ int dst_frame = 0);
// Initialize the mapper from an alignment. Looks for the first
// row containing the id and sets it as mapping target. All other
// rows become mapping source.
@@ -641,7 +644,7 @@ private:
eMergeNone, // no merging
eMergeAbutting, // merge only abutting intervals, keep overlapping
eMergeContained, // merge if one range is contained in another
- eMergeBySeg, // merge ranges by mapping group (e.g. by exon)
+ eMergeBySeg, // merge abutting and overlapping ranges by mapping group
eMergeAll // merge both abutting and overlapping intervals
};
enum EGapFlags {
@@ -656,7 +659,7 @@ private:
// if the type can not be detected or there are multiple types.
bool x_CheckSeqTypes(const CSeq_loc& loc,
ESeqType& seqtype,
- TSeqPos& len) const;
+ TSeqPos& len);
// If x_CheckSeqTypes returns false, it may indicate that some
// sequence types could not be detected. In this case the mapper
// will attempt to find at least one known type in the location
@@ -809,16 +812,30 @@ private:
EMergeFlags m_MergeFlag;
// How to treat gaps (Null sub-locations) if any.
EGapFlags m_GapFlag;
- // Trim leading/trailing indels (gaps) from mapped spliced-seg alignments.
- bool m_TrimSplicedSegs;
- // Wether to keep or discard ranges which can not be mapped.
- bool m_KeepNonmapping;
- // Wether to check or not if the original location is on the same strand
- // as the mapping source.
- bool m_CheckStrand;
- // Wether to include a source of each mapped range to the mapped seq-loc.
- bool m_IncludeSrcLocs;
+ // Other mapping options.
+ enum EMiscFlags {
+ // Trim leading/trailing indels (gaps) from mapped spliced-seg alignments.
+ fTrimSplicedSegs = 1 << 0,
+ // Wether to keep or discard ranges which can not be mapped.
+ fKeepNonmapping = 1 << 1,
+ // Wether to check or not if the original location is on the same strand
+ // as the mapping source.
+ fCheckStrand = 1 << 2,
+ // Wether to include a source of each mapped range to the mapped seq-loc.
+ fIncludeSrcLocs = 1 << 3,
+ // Prefer spliced-seg for mixed alignments.
+ fMixedAlignsAsSpliced = 1 << 4,
+ // Treat any range truncation as an error (added for mapping to GC-Assembly
+ // aliases).
+ fErrorOnPartial = 1 << 5
+ };
+ typedef int TMiscFlags;
+
+ bool x_IsSetMiscFlag(EMiscFlags flag) const { return m_MiscFlags & flag; }
+ void x_SetMiscFlag(EMiscFlags flag, bool value);
+
+ TMiscFlags m_MiscFlags;
// Mapped ranges collected from the currently parsed sub-location.
mutable TRangesById m_MappedLocs;
@@ -919,6 +936,65 @@ public:
};
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CSeq_loc_Mapper_Message
+///
+/// Class used to report CSeq_loc_Mapper_Base issues through
+/// IMessageListener.
+class NCBI_SEQ_EXPORT CSeq_loc_Mapper_Message : public CMessage_Basic
+{
+public:
+ CSeq_loc_Mapper_Message(const string& msg,
+ EDiagSev sev,
+ int err_code = 0,
+ int sub_code = 0);
+ virtual ~CSeq_loc_Mapper_Message(void);
+
+ virtual CSeq_loc_Mapper_Message* Clone(void) const;
+ virtual void Write(CNcbiOstream& out) const;
+
+ enum EObjectType {
+ eNot_set,
+ eSeq_loc,
+ eSeq_feat,
+ eSeq_align,
+ eSeq_graph
+ };
+
+ /// Check type of the object stored in the message.
+ EObjectType Which(void) const { return m_ObjType; }
+
+ /// Set seq-loc object (copy into the message).
+ void SetLoc(const CSeq_loc& loc);
+ /// Get seq-loc object or null.
+ const CSeq_loc* GetLoc(void) const;
+
+ /// Set seq-feat object (copy into the message).
+ void SetFeat(const CSeq_feat& feat);
+ /// Get seq-feat object or null.
+ const CSeq_feat* GetFeat(void) const;
+
+ /// Set seq-align object (copy into the message).
+ void SetAlign(const CSeq_align& align);
+ /// Get seq-align object or null.
+ const CSeq_align* GetAlign(void) const;
+
+ /// Set seq-graph object (copy into the message).
+ void SetGraph(const CSeq_graph& graph);
+ /// Get seq-graph object or null.
+ const CSeq_graph* GetGraph(void) const;
+
+ /// Set the stored object to null.
+ void ResetObject(void);
+
+private:
+ EObjectType m_ObjType;
+
+ CRef<CObject> m_Obj;
+};
+
+
struct CMappingRangeRef_Less
{
bool operator()(const CRef<CMappingRange>& x,
@@ -1040,7 +1116,7 @@ CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::SetGapRemove(void)
inline
CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::SetTrimSplicedSeg(bool trim)
{
- m_TrimSplicedSegs = trim;
+ x_SetMiscFlag(fTrimSplicedSegs, trim);
return *this;
}
@@ -1048,7 +1124,7 @@ CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::SetTrimSplicedSeg(bool trim)
inline
CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::SetCheckStrand(bool value)
{
- m_CheckStrand = value;
+ x_SetMiscFlag(fCheckStrand, value);
return *this;
}
@@ -1063,7 +1139,7 @@ bool CSeq_loc_Mapper_Base::LastIsPartial(void)
inline
CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::KeepNonmappingRanges(void)
{
- m_KeepNonmapping = true;
+ x_SetMiscFlag(fKeepNonmapping, true);
return *this;
}
@@ -1071,7 +1147,15 @@ CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::KeepNonmappingRanges(void)
inline
CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::TruncateNonmappingRanges(void)
{
- m_KeepNonmapping = false;
+ x_SetMiscFlag(fKeepNonmapping, false);
+ return *this;
+}
+
+
+inline
+CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::MixedAlignsAsSpliced(bool value)
+{
+ x_SetMiscFlag(fMixedAlignsAsSpliced, value);
return *this;
}
@@ -1079,7 +1163,15 @@ CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::TruncateNonmappingRanges(void)
inline
CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::IncludeSourceLocs(bool value)
{
- m_IncludeSrcLocs = value;
+ x_SetMiscFlag(fIncludeSrcLocs, value);
+ return *this;
+}
+
+
+inline
+CSeq_loc_Mapper_Base& CSeq_loc_Mapper_Base::SetErrorOnPartial(bool value)
+{
+ x_SetMiscFlag(fErrorOnPartial, value);
return *this;
}
diff --git a/c++/include/objects/seqalign/Dense_diag.hpp b/c++/include/objects/seqalign/Dense_diag.hpp
index 5f0e092..6d7b24d 100644
--- a/c++/include/objects/seqalign/Dense_diag.hpp
+++ b/c++/include/objects/seqalign/Dense_diag.hpp
@@ -1,4 +1,4 @@
-/* $Id: Dense_diag.hpp 371304 2012-08-07 17:46:06Z vasilche $
+/* $Id: Dense_diag.hpp 482675 2015-10-26 14:12:53Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -110,7 +110,7 @@ TSeqPos CDense_diag::GetSeqStart(TDim row) const
inline
TSeqPos CDense_diag::GetSeqStop(TDim row) const
{
- return GetSeqStart(row) + GetLen();
+ return GetSeqStart(row) + GetLen() - 1;
}
diff --git a/c++/include/objects/seqfeat/BioSource.hpp b/c++/include/objects/seqfeat/BioSource.hpp
index 3d4c788..39f325c 100644
--- a/c++/include/objects/seqfeat/BioSource.hpp
+++ b/c++/include/objects/seqfeat/BioSource.hpp
@@ -1,4 +1,4 @@
-/* $Id: BioSource.hpp 455171 2014-12-23 18:28:37Z ivanov $
+/* $Id: BioSource.hpp 454989 2014-12-22 12:41:16Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seqfeat/Gb_qual.hpp b/c++/include/objects/seqfeat/Gb_qual.hpp
index d85556f..4610800 100644
--- a/c++/include/objects/seqfeat/Gb_qual.hpp
+++ b/c++/include/objects/seqfeat/Gb_qual.hpp
@@ -1,4 +1,4 @@
-/* $Id: Gb_qual.hpp 462219 2015-03-17 15:06:40Z ivanov $
+/* $Id: Gb_qual.hpp 481760 2015-10-15 15:32:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -74,6 +74,11 @@ public:
static bool CleanupRptUnitSeq(string& val);
static bool CleanupReplace(string& val);
static bool CleanupRptUnitRange(string& val);
+
+ static bool IsLegalMobileElementValue(const string& val);
+ static void GetMobileElementValueElements(const string& val, string& element_type, string& element_name);
+
+ static bool IsIllegalQualName(const string& val);
private:
// Prohibit copy constructor and assignment operator
diff --git a/c++/include/objects/seqfeat/Gene_ref.hpp b/c++/include/objects/seqfeat/Gene_ref.hpp
index 9dad1f7..92f35d4 100644
--- a/c++/include/objects/seqfeat/Gene_ref.hpp
+++ b/c++/include/objects/seqfeat/Gene_ref.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_SEQFEAT_GENE_REF_HPP
#define OBJECTS_SEQFEAT_GENE_REF_HPP
-/* $Id: Gene_ref.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: Gene_ref.hpp 465442 2015-04-21 17:46:19Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,6 +63,8 @@ public:
// Checks for an emtpy Gene-ref used for suppressing /gene by overlap
bool IsSuppressed(void) const;
+ bool RefersToSameGene(const CGene_ref& xref) const;
+
private:
// Prohibit copy constructor and assignment operator
CGene_ref(const CGene_ref& value);
diff --git a/c++/include/objects/seqfeat/ISeq_feat.hpp b/c++/include/objects/seqfeat/ISeq_feat.hpp
index 777f915..845e5c1 100644
--- a/c++/include/objects/seqfeat/ISeq_feat.hpp
+++ b/c++/include/objects/seqfeat/ISeq_feat.hpp
@@ -1,4 +1,4 @@
-/* $Id: ISeq_feat.hpp 459295 2015-02-17 18:12:32Z ivanov $
+/* $Id: ISeq_feat.hpp 458821 2015-02-10 17:18:44Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seqfeat/OrgMod.hpp b/c++/include/objects/seqfeat/OrgMod.hpp
index 5f32737..db6460f 100644
--- a/c++/include/objects/seqfeat/OrgMod.hpp
+++ b/c++/include/objects/seqfeat/OrgMod.hpp
@@ -1,4 +1,4 @@
-/* $Id: OrgMod.hpp 463567 2015-03-30 16:19:15Z ivanov $
+/* $Id: OrgMod.hpp 462584 2015-03-19 16:38:52Z kachalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seqfeat/OrgName.hpp b/c++/include/objects/seqfeat/OrgName.hpp
index 62ae7cc..71cd864 100644
--- a/c++/include/objects/seqfeat/OrgName.hpp
+++ b/c++/include/objects/seqfeat/OrgName.hpp
@@ -1,4 +1,4 @@
-/* $Id: OrgName.hpp 453132 2014-12-01 15:30:39Z ivanov $
+/* $Id: OrgName.hpp 452696 2014-11-24 15:23:55Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,13 +58,32 @@ public:
bool GetFlatName(string& name_out, string* lineage = 0) const;
+ // Flag indicating that node's scientific name is "well specified" according to the
+ // respective taxonomic nomenclature (e.g. Genus species subspecies).
+ // Based on "specified" property from Taxonomy database.
+ // Flag is kept along with other flags in orgname.attrib field
+ // (see comments to x_SetAttribFlag() function)
+ bool IsFormalName() const;
+ void SetFormalNameFlag( bool bFormalName );
+
+ // Uncultured flag.
+ // Flag is kept along with other flags in orgname.attrib field
+ // (see comments to x_SetAttribFlag() function)
+ bool IsUncultured() const;
+ void SetUncultured( bool bUncultured );
+
CRef<COrgName> MakeCommon(const COrgName& other) const;
private:
// Prohibit copy constructor and assignment operator
COrgName(const COrgName& value);
COrgName& operator=(const COrgName& value);
-
+ // The proposed format for orgname flags: flagname1;[flagname2;]...
+ // where flagnameX consists of ascii alphanum characters only. Each value of flagnameX is unique.
+ // Presence of flag name in the strings means 'true' value for the flag.
+ void x_SetAttribFlag( const string& name );
+ void x_ResetAttribFlag( const string& name );
+ bool x_GetAttribFlag( const string& name ) const;
};
diff --git a/c++/include/objects/seqfeat/Org_ref.hpp b/c++/include/objects/seqfeat/Org_ref.hpp
index 75ce6d1..54f1120 100644
--- a/c++/include/objects/seqfeat/Org_ref.hpp
+++ b/c++/include/objects/seqfeat/Org_ref.hpp
@@ -1,4 +1,4 @@
-/* $Id: Org_ref.hpp 453132 2014-12-01 15:30:39Z ivanov $
+/* $Id: Org_ref.hpp 452696 2014-11-24 15:23:55Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seqfeat/PCRPrimerSeq.hpp b/c++/include/objects/seqfeat/PCRPrimerSeq.hpp
index c710067..19fcf2d 100644
--- a/c++/include/objects/seqfeat/PCRPrimerSeq.hpp
+++ b/c++/include/objects/seqfeat/PCRPrimerSeq.hpp
@@ -1,4 +1,4 @@
-/* $Id: PCRPrimerSeq.hpp 447117 2014-09-22 18:28:11Z ivanov $
+/* $Id: PCRPrimerSeq.hpp 446399 2014-09-15 18:19:05Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objects/seqfeat/RNA_ref.hpp b/c++/include/objects/seqfeat/RNA_ref.hpp
index d0f601c..c9550ed 100644
--- a/c++/include/objects/seqfeat/RNA_ref.hpp
+++ b/c++/include/objects/seqfeat/RNA_ref.hpp
@@ -1,4 +1,4 @@
-/* $Id: RNA_ref.hpp 170000 2009-09-08 13:00:17Z bollin $
+/* $Id: RNA_ref.hpp 471076 2015-06-23 15:21:05Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,6 +61,9 @@ public:
static string GetRnaTypeName (const CRNA_ref::EType rna_type);
+ const string& GetRnaProductName(void) const;
+ void SetRnaProductName(const string& product, string& remainder);
+
private:
// Prohibit copy constructor and assignment operator
CRNA_ref(const CRNA_ref& value);
diff --git a/c++/include/objects/seqfeat/SeqFeatData.hpp b/c++/include/objects/seqfeat/SeqFeatData.hpp
index f5a54d0..8ada576 100644
--- a/c++/include/objects/seqfeat/SeqFeatData.hpp
+++ b/c++/include/objects/seqfeat/SeqFeatData.hpp
@@ -1,4 +1,4 @@
-/* $Id: SeqFeatData.hpp 458380 2015-02-04 15:35:32Z ivanov $
+/* $Id: SeqFeatData.hpp 478054 2015-09-03 16:30:15Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -105,6 +105,7 @@ BEGIN_objects_SCOPE // namespace ncbi::objects::
class CFeatList;
class CBondList;
class CSiteList;
+class CGb_qual;
class NCBI_SEQFEAT_EXPORT CSeqFeatData : public CSeqFeatData_Base
{
@@ -495,6 +496,12 @@ public:
static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype);
+ static bool AllowStrandBoth(ESubtype subtype);
+ static bool RequireLocationIntervalsInBiologicalOrder(ESubtype subtype);
+ static bool AllowAdjacentIntervals(ESubtype subtype);
+
+ static bool ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, const CGb_qual& qual);
+ static bool ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, CSeqFeatData::EQualifier qual_type);
// Internal structure to hold additional info
struct SFeatDataInfo
diff --git a/c++/include/objects/seqfeat/Seq_feat.hpp b/c++/include/objects/seqfeat/Seq_feat.hpp
index f724c13..6e165fa 100644
--- a/c++/include/objects/seqfeat/Seq_feat.hpp
+++ b/c++/include/objects/seqfeat/Seq_feat.hpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_feat.hpp 459295 2015-02-17 18:12:32Z ivanov $
+/* $Id: Seq_feat.hpp 468197 2015-05-21 12:53:40Z kornbluh $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -171,6 +171,26 @@ public:
/// Non-const version of FindExt().
CRef<CUser_object> FindExt(const string& ext_type);
+ enum EAddExt {
+ fAddExt_ReplaceAll = 1 << 0 ///< Before adding, remove all previous
+ };
+ typedef int TAddExt; ///< binary OR of EAddExt
+
+ /// Add an extension by type in exts container. Note that it's
+ /// always added to the Exts field, never the Ext field.
+ /// Also, it does not check for dups.
+ ///
+ /// @param ext
+ /// The ext to be added. It will NOT be copied.
+ void AddExt(CRef<CUser_object> ext, TAddExt add_flags = 0);
+
+ /// Remove all Exts with the given type. Note: Runs in linear time
+ /// relative to the number of Exts total.
+ ///
+ /// @param ext_type
+ /// String id of the extension to find.
+ void RemoveExt(const string& ext_type);
+
private:
/// Prohibit copy constructor and assignment operator
diff --git a/c++/include/objects/seqfeat/SubSource.hpp b/c++/include/objects/seqfeat/SubSource.hpp
index 12fa7f6..fbaf17c 100644
--- a/c++/include/objects/seqfeat/SubSource.hpp
+++ b/c++/include/objects/seqfeat/SubSource.hpp
@@ -1,4 +1,4 @@
-/* $Id: SubSource.hpp 463565 2015-03-30 16:17:58Z ivanov $
+/* $Id: SubSource.hpp 482191 2015-10-21 15:23:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -108,6 +108,8 @@ public:
static bool IsCollectionDateAfterTime(const CDate& collection_date, time_t t);
static bool IsCollectionDateAfterTime(const CDate& collection_date, CTime& ctime);
+ static bool IsISOFormatTime(const string& orig_time, int& hour, int& min, int& sec);
+ static bool IsISOFormatDateOnly(const string& date);
static bool IsISOFormatDate (const string& orig_date);
static CRef<CDate> GetDateFromISODate(const string& orig_date);
@@ -452,7 +454,7 @@ private:
static bool s_CompareTwoLinesByLatLonThenCountry(const CCountryLine* line1,
const CCountryLine* line2);
- int x_GetLatStartIndex (int y);
+ size_t x_GetLatStartIndex (int y);
const CCountryExtreme * x_FindCountryExtreme (const string& country);
diff --git a/c++/include/objects/seqloc/Seq_id.hpp b/c++/include/objects/seqloc/Seq_id.hpp
index fa2ac4a..3a41bec 100644
--- a/c++/include/objects/seqloc/Seq_id.hpp
+++ b/c++/include/objects/seqloc/Seq_id.hpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_id.hpp 432036 2014-04-09 17:27:03Z grichenk $
+/* $Id: Seq_id.hpp 483962 2015-11-05 15:31:25Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -293,8 +293,8 @@ public:
eAcc_embl_dirsub = e_Embl | eAcc_dirsub | fAcc_nuc, // V
eAcc_embl_patent = e_Embl | eAcc_div_patent | fAcc_nuc, // A
eAcc_embl_tsa_nuc = e_Embl | eAcc_tsa | fAcc_nuc, // IAAA
- eAcc_embl_tsa_prot = e_Embl | eAcc_tsa | fAcc_prot,
- eAcc_embl_genome = e_Embl | eAcc_genome | fAcc_nuc,
+ eAcc_embl_tsa_prot = e_Embl | eAcc_tsa | fAcc_prot, // unused
+ eAcc_embl_genome = e_Embl | eAcc_genome | fAcc_nuc, // unused
eAcc_embl_htgs = e_Embl | eAcc_htgs | fAcc_nuc, // unused
eAcc_embl_con = e_Embl | eAcc_con | fAcc_nuc, // AN
eAcc_embl_wgs_nuc = e_Embl | eAcc_wgs | fAcc_nuc, // CAAA
@@ -341,10 +341,10 @@ public:
eAcc_ddbj_patent = e_Ddbj | eAcc_div_patent | fAcc_nuc, // E
eAcc_ddbj_mrna = e_Ddbj | eAcc_mrna | fAcc_nuc, // AK
eAcc_ddbj_tsa_nuc = e_Ddbj | eAcc_tsa | fAcc_nuc, // FX
- eAcc_ddbj_tsa_prot = e_Ddbj | eAcc_tsa | fAcc_prot,
+ eAcc_ddbj_tsa_prot = e_Ddbj | eAcc_tsa | fAcc_prot, // LAA
eAcc_ddbj_gss = e_Ddbj | eAcc_gss | fAcc_nuc, // DE
eAcc_ddbj_genome = e_Ddbj | eAcc_genome | fAcc_nuc, // AP
- eAcc_ddbj_htgs = e_Ddbj | eAcc_htgs | fAcc_nuc,
+ eAcc_ddbj_htgs = e_Ddbj | eAcc_htgs | fAcc_nuc, // unused
eAcc_ddbj_con = e_Ddbj | eAcc_con | fAcc_nuc, // BA
eAcc_ddbj_wgs_nuc = e_Ddbj | eAcc_wgs | fAcc_nuc, // BAAA
eAcc_ddbj_wgs_prot = e_Ddbj | eAcc_wgs | fAcc_prot, // GAA
@@ -367,7 +367,7 @@ public:
eAcc_embl_tpa_nuc = e_Tpe | eAcc_other | fAcc_nuc, // BN
eAcc_embl_tpa_prot = e_Tpe | eAcc_other | fAcc_prot, // CAD29848
eAcc_embl_tpa_wgs_nuc = e_Tpe | eAcc_wgs | fAcc_nuc, // FAAA
- eAcc_embl_tpa_wgs_prot = e_Tpe | eAcc_wgs | fAcc_prot,
+ eAcc_embl_tpa_wgs_prot = e_Tpe | eAcc_wgs | fAcc_prot, // unused
eAcc_embl_tpa_wgsm_nuc = e_Tpe | eAcc_wgs_master | fAcc_nuc,
eAcc_embl_tpa_wgsm_prot = e_Tpe | eAcc_wgs_master | fAcc_prot,
@@ -691,7 +691,7 @@ struct NCBI_SEQLOC_EXPORT SSeqIdRange
///
/// Define exceptions generated by CSeq_id.
-class CSeqIdException : public CException
+class NCBI_SEQLOC_EXPORT CSeqIdException : public CException
{
public:
/// Error types that CSeq_id can generate.
@@ -701,14 +701,7 @@ public:
};
/// Translate from the error code value to its string representation.
- virtual const char* GetErrCodeString(void) const
- {
- switch (GetErrCode()) {
- case eUnknownType: return "eUnknownType";
- case eFormat: return "eFormat";
- default: return CException::GetErrCodeString();
- }
- }
+ virtual const char* GetErrCodeString(void) const;
// Standard exception boilerplate code.
NCBI_EXCEPTION_DEFAULT(CSeqIdException, CException);
diff --git a/c++/include/objects/seqloc/Seq_loc.hpp b/c++/include/objects/seqloc/Seq_loc.hpp
index 0fff43d..125c779 100644
--- a/c++/include/objects/seqloc/Seq_loc.hpp
+++ b/c++/include/objects/seqloc/Seq_loc.hpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_loc.hpp 410271 2013-08-15 16:52:50Z ucko $
+/* $Id: Seq_loc.hpp 475726 2015-08-11 18:12:56Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -67,6 +67,28 @@ class CSeq_id_Handle;
class ISynonymMapper;
class ILengthGetter;
class CSeq_loc_CI;
+class CSeq_loc_I;
+
+/// Seq-loc exceptions
+class NCBI_SEQ_EXPORT CSeqLocException : public CException
+{
+public:
+ enum EErrCode {
+ eNotSet, ///< Seq-loc is not set
+ eMultipleId, ///< Seq-loc on multiple ids when one id is required
+ eUnsupported, ///< Seq-loc has data that is not supported yet
+ eBadLocation, ///< Seq-loc is incorrectly formed
+ eBadIterator, ///< Seq-loc iterator is in bad state
+ eIncomatible, ///< Seq-loc type is incompatible with operation
+ eOutOfRange, ///< parameter is out of valid range
+
+ eOtherError
+ };
+
+ virtual const char* GetErrCodeString(void) const;
+ NCBI_EXCEPTION_DEFAULT(CSeqLocException, CException);
+};
+
class NCBI_SEQLOC_EXPORT CSeq_loc : public CSeq_loc_Base
{
@@ -350,9 +372,10 @@ private:
kSeveralIds = -3
};
- mutable TRange m_TotalRangeCache;
+ mutable volatile TSeqPos m_TotalRangeCacheFrom;
+ mutable volatile TSeqPos m_TotalRangeCacheToOpen;
// Seq-id for the whole seq-loc or null if multiple IDs were found
- mutable const CSeq_id* m_IdCache;
+ mutable const CSeq_id* volatile m_IdCache;
};
@@ -382,18 +405,19 @@ public:
// Simple location structure: id/from/to
-struct SSeq_loc_CI_RangeInfo {
+struct NCBI_SEQLOC_EXPORT SSeq_loc_CI_RangeInfo {
SSeq_loc_CI_RangeInfo(void);
+ ~SSeq_loc_CI_RangeInfo(void);
+
void SetStrand(ENa_strand strand);
typedef CSeq_loc::TRange TRange;
- typedef vector<SSeq_loc_CI_RangeInfo> TRangeList;
+ CSeq_id_Handle m_IdHandle;
CConstRef<CSeq_id> m_Id;
TRange m_Range;
bool m_IsSetStrand;
ENa_strand m_Strand;
- // The original seq-loc for the interval
CConstRef<CSeq_loc> m_Loc;
pair<CConstRef<CInt_fuzz>, CConstRef<CInt_fuzz> > m_Fuzz;
};
@@ -415,15 +439,18 @@ public:
eOrder_Positional, /// Iterate sub-locations in positional order
eOrder_Biological /// Iterate sub-locations in biological order
};
- typedef SSeq_loc_CI_RangeInfo::TRange TRange;
+ typedef CSeq_loc::TRange TRange;
/// constructors
CSeq_loc_CI(void);
CSeq_loc_CI(const CSeq_loc& loc,
EEmptyFlag empty_flag = eEmpty_Skip,
ESeqLocOrder order = eOrder_Biological);
+ /// construct iterator at a different position in the same location
+ /// @sa GetPos()
+ CSeq_loc_CI(const CSeq_loc_CI& iter, size_t pos);
/// destructor
- ~CSeq_loc_CI(void);
+ virtual ~CSeq_loc_CI(void);
CSeq_loc_CI(const CSeq_loc_CI& iter);
CSeq_loc_CI& operator= (const CSeq_loc_CI& iter);
@@ -434,6 +461,41 @@ public:
bool operator== (const CSeq_loc_CI& iter) const;
bool operator!= (const CSeq_loc_CI& iter) const;
+ /// Location of type equiv define set of equivalent locations.
+ /// Each equiv set consist of several equivalent parts.
+ /// Each equiv part can contain equiv location too,
+ /// so equiv sets are recursive.
+
+ /// Return true if current position is part of a bond
+ bool IsInBond(void) const;
+ /// Return true if current position is A part of a bond
+ bool IsBondA(void) const;
+ /// Return true if current position is B part of a bond
+ bool IsBondB(void) const;
+ /// Return iterators that cover bond of current position
+ /// result.first is the first segment in the equiv set
+ /// result.second is the first segment after the equiv set
+ pair<CSeq_loc_CI, CSeq_loc_CI> GetBondRange(void) const;
+
+ /// Return true if location has equiv parts
+ bool HasEquivSets(void) const;
+ /// Return true if current position is in some equiv part
+ bool IsInEquivSet(void) const;
+ /// Return number of recursuve equiv parts current position in
+ size_t GetEquivSetsCount(void) const;
+ /// Return iterators that cover equiv set of current position
+ /// result.first is the first segment in the equiv set
+ /// result.second is the first segment after the equiv set
+ /// level specify equiv set if there are more than one of them
+ /// level = 0 is the smallest equiv set (innermost)
+ pair<CSeq_loc_CI, CSeq_loc_CI> GetEquivSetRange(size_t level = 0) const;
+ /// Return iterators that cover equiv part of current position
+ /// result.first is the first segment in the equiv part
+ /// result.second is the first segment after the equiv part
+ /// level specify equiv set if there are more than one of them
+ /// level = 0 is the smallest equiv set (innermost)
+ pair<CSeq_loc_CI, CSeq_loc_CI> GetEquivPartRange(size_t level = 0) const;
+
/// Get seq_id of the current location
const CSeq_id& GetSeq_id(void) const;
CSeq_id_Handle GetSeq_id_Handle(void) const;
@@ -475,29 +537,327 @@ public:
/// Reset the iterator to the initial state
void Rewind(void);
-private:
+ /// Get number of ranges.
+ size_t GetSize(void) const;
+
+ /// Get iterator's position.
+ size_t GetPos(void) const;
+
+ /// Set iterator's position.
+ void SetPos(size_t pos);
+
+protected:
const SSeq_loc_CI_RangeInfo& x_GetRangeInfo(void) const;
- typedef SSeq_loc_CI_RangeInfo::TRangeList TRangeList;
CRef<CSeq_loc_CI_Impl> m_Impl;
// Check the iterator position
bool x_IsValid(void) const;
// Check the position, throw exception if not valid
- void x_CheckNotValid(const char* where) const;
+ virtual const char* x_GetIteratorType(void) const;
+ void x_CheckValid(const char* where) const;
void x_ThrowNotValid(const char* where) const;
size_t m_Index;
};
+/// Seq-loc iterator class -- iterates all intervals from a seq-loc
+/// in the correct order.
+class NCBI_SEQLOC_EXPORT CSeq_loc_I : public CSeq_loc_CI
+{
+public:
+ /// Options for creation modified locations
+ /// Bond and equiv types are preserved if possible
+ enum EMakeType {
+ eMake_CompactType, /// use most compact Seq-loc type (default)
+ eMake_PreserveType /// keep original Seq-loc type if possible
+ };
+
+ /// constructors
+ CSeq_loc_I(void);
+ CSeq_loc_I(CSeq_loc& loc);
+ /// construct iterator at a different position in the same location
+ /// @sa GetPos()
+ CSeq_loc_I(const CSeq_loc_I& iter, size_t pos);
+ /// destructor
+ virtual ~CSeq_loc_I(void);
+
+ /// return true of any part was changed since initialization
+ bool HasChanges(void) const;
+
+ /// return constructed CSeq_loc with all changes
+ CRef<CSeq_loc> MakeSeq_loc(EMakeType make_type = eMake_CompactType) const;
+
+ /// Delete current element, and make iterator to point to the next element.
+ /// All other iterators of the same CSeq_loc object will become invalid.
+ /// If the deleted element is contained in any equiv set then the equiv set
+ /// and its corresponding part will be reduced in size appropriately,
+ /// and if the part and/or the set become empty after the deletion
+ /// they will be removed completely.
+ void Delete(void);
+
+ /// Set of Insert*() methods.
+ /// All of them insert new element before the one the iterator points to.
+ /// If the iterator is at the end of CSeq_loc then the new element is
+ /// inserted after the last element of the CSeq_loc.
+ /// After the insertion this iterator will point to the element
+ /// it was pointing before (or end), and the result iterator will point
+ /// to the inserted element.
+ /// All other iterators of the same CSeq_loc object will become invalid.
+ /// If the insertion point is completely within an equiv set (excluding
+ /// the equiv set boundary) the equiv set will be expanded appropriately.
+ /// If the insertion point is completely within an equiv part (excluding
+ /// the equiv part boundary) the new element is added to that equiv part.
+ /// If the insertion point is between two equiv parts of the same set
+ /// then the new element is appended to the part just before
+ /// the insertion point.
+ /// The effect of the insertion on equiv sets can be modified
+ /// by calling SetEquivMode(EEquivMode).
+ /// @sa SetEquivMode()
+ CSeq_loc_I InsertNull(void);
+
+ /// Insert new element before the current one (@sa InsertNull()).
+ CSeq_loc_I InsertEmpty(const CSeq_id_Handle& id);
+ /// Insert new element before the current one (@sa InsertNull()).
+ CSeq_loc_I InsertEmpty(const CSeq_id& id)
+ {
+ return InsertEmpty(CSeq_id_Handle::GetHandle(id));
+ }
+ /// Insert new element before the current one (@sa InsertNull()).
+ CSeq_loc_I InsertWhole(const CSeq_id_Handle& id);
+ /// Insert new element before the current one (@sa InsertNull()).
+ CSeq_loc_I InsertWhole(const CSeq_id& id)
+ {
+ return InsertWhole(CSeq_id_Handle::GetHandle(id));
+ }
+
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertInterval(const CSeq_id_Handle& id,
+ const TRange& range,
+ ENa_strand strand = eNa_strand_unknown);
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertInterval(const CSeq_id& id,
+ const TRange& range,
+ ENa_strand strand = eNa_strand_unknown)
+ {
+ return InsertInterval(CSeq_id_Handle::GetHandle(id), range, strand);
+ }
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertInterval(const CSeq_id& id,
+ TSeqPos from, TSeqPos to,
+ ENa_strand strand = eNa_strand_unknown)
+ {
+ return InsertInterval(id, TRange(from, to), strand);
+ }
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertInterval(const CSeq_id_Handle& id,
+ TSeqPos from, TSeqPos to,
+ ENa_strand strand = eNa_strand_unknown)
+ {
+ return InsertInterval(id, TRange(from, to), strand);
+ }
+
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertPoint(const CSeq_id_Handle& id,
+ TSeqPos pos,
+ ENa_strand strand = eNa_strand_unknown);
+ /// Insert new element before the current one (@sa InsertNull()).
+ /// The strand value eNa_strand_unknown produces strand field not set,
+ /// If eNa_strand_unknown is expicitly required, call SetStrand().
+ CSeq_loc_I InsertPoint(const CSeq_id& id,
+ TSeqPos pos,
+ ENa_strand strand = eNa_strand_unknown)
+ {
+ return InsertPoint(CSeq_id_Handle::GetHandle(id), pos, strand);
+ }
+
+ /// Set seq_id of the current location
+ void SetSeq_id_Handle(const CSeq_id_Handle& id);
+ /// Set seq_id of the current location
+ void SetSeq_id(const CSeq_id& id)
+ {
+ SetSeq_id_Handle(CSeq_id_Handle::GetHandle(id));
+ }
+
+ /// Set the range
+ void SetRange(const TRange& range);
+ /// Set the range from position
+ void SetFrom(TSeqPos from);
+ /// Set the range to position
+ void SetTo(TSeqPos to);
+ /// Set the range from and to positions
+ void SetPoint(TSeqPos pos);
+
+ /// Reset the range strand
+ void ResetStrand(void);
+ /// Set the range strand
+ void SetStrand(ENa_strand strand);
+
+ /// Reset fuzz from
+ void ResetFuzzFrom(void);
+ /// Change fuzz from
+ void SetFuzzFrom(CInt_fuzz& fuzz);
+ /// Reset fuzz to
+ void ResetFuzzTo(void);
+ /// Change fuzz to values
+ void SetFuzzTo(CInt_fuzz& fuzz);
+ /// Reset fuzz of a point
+ void ResetFuzz(void);
+ /// Change fuzz of a point
+ void SetFuzz(CInt_fuzz& fuzz);
+
+ /// Return iterators that cover equiv set of current position
+ /// result.first is the first segment in the equiv set
+ /// result.second is the first segment after the equiv set
+ /// level specify equiv set if there are more than one of them
+ /// level = 0 is the smallest equiv set (innermost)
+ pair<CSeq_loc_I, CSeq_loc_I> GetEquivSetRange(size_t level = 0) const;
+ /// Return iterators that cover equiv part of current position
+ /// result.first is the first segment in the equiv part
+ /// result.second is the first segment after the equiv part
+ /// level specify equiv set if there are more than one of them
+ /// level = 0 is the smallest equiv set (innermost)
+ pair<CSeq_loc_I, CSeq_loc_I> GetEquivPartRange(size_t level = 0) const;
+
+ /// This enum defines a way equiv sets are expanded or created
+ /// when one of Insert*() methods is called.
+ enum EEquivMode {
+ /// By default no equiv sets are created or expanded except
+ /// if insertion point is completely inside of an equiv or its part.
+ eEquiv_none,
+
+ /// A new equiv set will be created, even if the insertion point
+ /// is already inside of an existing equiv, so that new equiv set may
+ /// become a sub-unit of an exisiting equiv set.
+ /// The new equiv set will contain one part with the inserted element
+ /// as its content.
+ /// The mode will switch to eEquiv_append after the insertion.
+ eEquiv_new_equiv,
+
+ /// New equiv part will be started with the inserted element.
+ /// If the insertion point is not in or near any existing equiv part
+ /// then exception is thrown.
+ /// If...
+ /// A. the insertion point is exactly between two equiv sets
+ /// then a new equiv part will be created at the end of the first set
+ /// with the inserted element as its content.
+ /// B. the insertion point is at a boundary of any equiv part
+ /// then a new equiv part will be created at this point
+ /// with the inserted element as its content.
+ /// C. the insertion point is in the middle of existing part
+ /// then the existing part will be split at the insertion point
+ /// and new element will be added to the second part after splitting.
+ ///
+ /// The mode will switch to eEquiv_append after the insertion.
+ eEquiv_new_part,
+
+ /// If the insertion point is just after any equiv part, including
+ /// the last one in an equiv, then the inserted element is appended
+ /// to the part, and the equiv mode will remain eEquiv_append.
+ /// Otherwise the equiv mode will switch to eEquiv_none.
+ /// Change the mode to eEquiv_none explicitly if you want to stop
+ /// expanding existing equiv.
+ eEquiv_append,
+
+ /// If the insertion point is just before any equiv part, including
+ /// the first one in an equiv, then the inserted element is prepended
+ /// to the part, and the equiv mode will remain eEquiv_prepend.
+ /// Otherwise the equiv mode will switch to eEquiv_none.
+ /// Change the mode to eEquiv_none explicitly if you want to stop
+ /// expanding existing equiv.
+ eEquiv_prepend
+ };
+ /// Change equiv modification mode
+ /// @sa InsertNull()
+ void SetEquivMode(EEquivMode mode);
+ /// Change equiv modification mode to add new equiv set for the next
+ /// insert operation.
+ /// @sa SetEquivMode()
+ void StartNewEquiv(void)
+ {
+ SetEquivMode(eEquiv_new_equiv);
+ }
+ /// Change equiv modification mode to add new equiv part for the next
+ /// insert operation.
+ /// @sa SetEquivMode()
+ void StartNewEquivPart(void)
+ {
+ SetEquivMode(eEquiv_new_part);
+ }
+ /// Change equiv modification mode to normal behavior that will only
+ /// update existing equiv sets.
+ /// @sa SetEquivMode()
+ void StopEquiv(void)
+ {
+ SetEquivMode(eEquiv_none);
+ }
+ /// Get equiv modification mode.
+ /// @sa SetEquivMode()
+ EEquivMode GetEquivMode(void) const;
+
+ /// Remove equiv set, all pieces that are part of the set will be
+ /// preserved as independent pieces.
+ void RemoveEquiv(size_t level = 0);
+ /// Create equiv set with one part from current position to
+ /// the position pointed by end_it argument exclusive.
+ /// The end_it position must be after current position.
+ /// If there are any conflicts with existing equiv sets or bond pairs
+ /// no new equiv set will be made and an exception will be thrown.
+ /// New set's level will be assigned depending on its size in relation
+ /// to existing overlapping equiv sets.
+ void MakeEquiv(const CSeq_loc_I& end_it);
+ /// Create equiv set with one part from current position to
+ /// the position pointed by end_it argument exclusive.
+ /// The end_it position must be after current position.
+ /// If there are any conflicts with existing equiv sets or bond pairs
+ /// no new equiv set will be made and an exception will be thrown.
+ void MakeEquivPartBreak(size_t level = 0);
+
+ /// Remove bond at current position - it may be either A or B part
+ void RemoveBond(void);
+ /// Make bond at current position (only A)
+ /// The current part must be a point
+ /// If current posision is already a bond A part, it will be updated
+ void MakeBondA(void);
+ /// Make bond at current position with the next position (A and B)
+ /// The current and next parts must be points
+ /// If current posision is already a bond A part, it will be updated
+ void MakeBondAB(void);
+ /// Make bond at previous position with the current position (A and B)
+ /// The current and previous parts must be points
+ /// If previous posision is already a bond A part, it will be updated
+ void MakeBondB(void);
+
+protected:
+ using CSeq_loc_CI::x_GetRangeInfo;
+ SSeq_loc_CI_RangeInfo& x_GetRangeInfo(void);
+
+ void x_SetSeq_id_Handle(SSeq_loc_CI_RangeInfo& info,
+ const CSeq_id_Handle& id);
+
+ bool x_IsValidForInsert(void) const;
+ void x_CheckValidForInsert(const char* where) const;
+ virtual const char* x_GetIteratorType(void) const;
+};
+
/////////////////// CSeq_loc inline methods
inline
void CSeq_loc::InvalidateTotalRangeCache(void) const
{
- m_TotalRangeCache.SetFrom(TSeqPos(kDirtyCache));
+ m_TotalRangeCacheFrom = TSeqPos(kDirtyCache);
}
@@ -527,11 +887,14 @@ CSeq_loc::CSeq_loc(void)
inline
CSeq_loc::TRange CSeq_loc::GetTotalRange(void) const
{
- TRange range = m_TotalRangeCache;
- if ( range.GetFrom() == TSeqPos(kDirtyCache) ) {
- range = x_UpdateTotalRange();
+ TSeqPos range_from = m_TotalRangeCacheFrom;
+ if ( range_from == TSeqPos(kDirtyCache) ) {
+ return x_UpdateTotalRange();
+ }
+ else {
+ TSeqPos range_to_open = m_TotalRangeCacheToOpen;
+ return COpenRange<TSeqPos>(range_from, range_to_open);
}
- return range;
}
@@ -615,16 +978,6 @@ bool CSeq_loc::IsReverseStrand(void) const
/////////////////// CSeq_loc_CI inline methods
inline
-SSeq_loc_CI_RangeInfo::SSeq_loc_CI_RangeInfo(void)
- : m_Id(0),
- m_IsSetStrand(false),
- m_Strand(eNa_strand_unknown),
- m_Loc(0)
-{
- return;
-}
-
-inline
void SSeq_loc_CI_RangeInfo::SetStrand(ENa_strand strand)
{
m_IsSetStrand = true;
@@ -632,94 +985,111 @@ void SSeq_loc_CI_RangeInfo::SetStrand(ENa_strand strand)
}
inline
-CSeq_loc_CI& CSeq_loc_CI::operator++ (void)
+void CSeq_loc_CI::x_CheckValid(const char* where) const
{
- ++m_Index;
- return *this;
+ if ( !x_IsValid() )
+ x_ThrowNotValid(where);
}
inline
-void CSeq_loc_CI::x_CheckNotValid(const char* where) const
+CSeq_loc_CI& CSeq_loc_CI::operator++ (void)
{
- if ( !x_IsValid() )
- x_ThrowNotValid(where);
+ x_CheckValid("operator++");
+ ++m_Index;
+ return *this;
}
inline
const CSeq_id& CSeq_loc_CI::GetSeq_id(void) const
{
- x_CheckNotValid("GetSeq_id()");
+ x_CheckValid("GetSeq_id()");
return *x_GetRangeInfo().m_Id;
}
inline
CSeq_id_Handle CSeq_loc_CI::GetSeq_id_Handle(void) const
{
- return CSeq_id_Handle::GetHandle(GetSeq_id());
+ x_CheckValid("GetSeq_id_Handle()");
+ return x_GetRangeInfo().m_IdHandle;
}
inline
CSeq_loc_CI::TRange CSeq_loc_CI::GetRange(void) const
{
- x_CheckNotValid("GetRange()");
+ x_CheckValid("GetRange()");
return x_GetRangeInfo().m_Range;
}
inline
bool CSeq_loc_CI::IsSetStrand(void) const
{
- x_CheckNotValid("IsSetStrand()");
+ x_CheckValid("IsSetStrand()");
return x_GetRangeInfo().m_IsSetStrand;
}
inline
ENa_strand CSeq_loc_CI::GetStrand(void) const
{
- x_CheckNotValid("GetStrand()");
+ x_CheckValid("GetStrand()");
return x_GetRangeInfo().m_Strand;
}
inline
const CInt_fuzz* CSeq_loc_CI::GetFuzzFrom(void) const
{
- x_CheckNotValid("GetFuzzFrom()");
+ x_CheckValid("GetFuzzFrom()");
return x_GetRangeInfo().m_Fuzz.first;
}
inline
const CInt_fuzz* CSeq_loc_CI::GetFuzzTo(void) const
{
- x_CheckNotValid("GetFuzzTo()");
+ x_CheckValid("GetFuzzTo()");
return x_GetRangeInfo().m_Fuzz.second;
}
inline
bool CSeq_loc_CI::IsWhole(void) const
{
- x_CheckNotValid("IsWhole()");
+ x_CheckValid("IsWhole()");
return x_GetRangeInfo().m_Range.IsWhole();
}
inline
bool CSeq_loc_CI::IsEmpty(void) const
{
- x_CheckNotValid("IsEmpty()");
+ x_CheckValid("IsEmpty()");
return x_GetRangeInfo().m_Range.Empty();
}
inline
bool CSeq_loc_CI::IsPoint(void) const
{
- x_CheckNotValid("IsPoint()");
+ x_CheckValid("IsPoint()");
return x_GetRangeInfo().m_Range.GetLength() == 1;
}
inline
+size_t CSeq_loc_CI::GetPos(void) const
+{
+ return m_Index;
+}
+
+inline
void CSeq_loc_CI::Rewind(void)
{
m_Index = 0;
}
+/////////////////// CSeq_loc_I inline methods
+
+inline
+void CSeq_loc_I::x_CheckValidForInsert(const char* where) const
+{
+ if ( !x_IsValidForInsert() )
+ x_ThrowNotValid(where);
+}
+
NCBISER_HAVE_POST_READ(CSeq_loc)
/////////////////// end of CSeq_loc_CI inline methods
diff --git a/c++/include/objects/seqtable/Scaled_int_multi_data.hpp b/c++/include/objects/seqtable/Scaled_int_multi_data.hpp
index fb56fac..ae3fa01 100644
--- a/c++/include/objects/seqtable/Scaled_int_multi_data.hpp
+++ b/c++/include/objects/seqtable/Scaled_int_multi_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: Scaled_int_multi_data.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: Scaled_int_multi_data.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,6 +59,13 @@ public:
// destructor
~CScaled_int_multi_data(void);
+ // return size (sizeof) of integer value to store data,
+ // returned value is the size of data in chars.
+ size_t GetIntSize(void) const;
+
+ bool TryGetInt4(size_t row, Int4& v) const;
+ bool TryGetInt8(size_t row, Int8& v) const;
+
private:
// Prohibit copy constructor and assignment operator
CScaled_int_multi_data(const CScaled_int_multi_data& value);
diff --git a/c++/include/objects/seqtable/Scaled_real_multi_data.hpp b/c++/include/objects/seqtable/Scaled_real_multi_data.hpp
index c3c5995..3251547 100644
--- a/c++/include/objects/seqtable/Scaled_real_multi_data.hpp
+++ b/c++/include/objects/seqtable/Scaled_real_multi_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: Scaled_real_multi_data.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: Scaled_real_multi_data.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,6 +59,8 @@ public:
// destructor
~CScaled_real_multi_data(void);
+ bool TryGetReal(size_t row, double& v) const;
+
private:
// Prohibit copy constructor and assignment operator
CScaled_real_multi_data(const CScaled_real_multi_data& value);
diff --git a/c++/include/objects/seqtable/SeqTable_column.hpp b/c++/include/objects/seqtable/SeqTable_column.hpp
index ce30d1e..70809b7 100644
--- a/c++/include/objects/seqtable/SeqTable_column.hpp
+++ b/c++/include/objects/seqtable/SeqTable_column.hpp
@@ -1,4 +1,4 @@
-/* $Id: SeqTable_column.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: SeqTable_column.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -43,6 +43,11 @@
// generated includes
#include <objects/seqtable/SeqTable_column_.hpp>
+// extra includes
+#include <objects/seqtable/SeqTable_sparse_index.hpp>
+#include <objects/seqtable/SeqTable_single_data.hpp>
+#include <objects/seqtable/SeqTable_multi_data.hpp>
+
// generated classes
BEGIN_NCBI_SCOPE
@@ -66,12 +71,42 @@ public:
// return true if there is a value at the row
bool IsSet(size_t row) const;
+ // get value for the row, return false if there is no a value
+ template<class Value>
+ bool TryGetValue(size_t row, Value& v) const {
+ size_t index = row;
+ if ( IsSetSparse() ) {
+ index = GetSparse().GetIndexAt(row);
+ if ( index == CSeqTable_sparse_index::kSkipped ) {
+ if ( !IsSetSparse_other() ) {
+ return false;
+ }
+ GetSparse_other().GetValue(v);
+ return true;
+ }
+ }
+ if ( IsSetData() && GetData().TryGetValue(index, v) ) {
+ return true;
+ }
+ if ( IsSetDefault() ) {
+ GetDefault().GetValue(v);
+ return true;
+ }
+ return false;
+ }
+
// get bool value for the row, return false if there is no a value
- bool TryGetBool(size_t row, bool& v) const;
+ bool TryGetBool(size_t row, bool& v) const {
+ return TryGetValue(row, v);
+ }
// get int value for the row, return false if there is no a value
- bool TryGetInt(size_t row, int& v) const;
+ bool TryGetInt(size_t row, int& v) const {
+ return TryGetValue(row, v);
+ }
// get double value for the row, return false if there is no a value
- bool TryGetReal(size_t row, double& v) const;
+ bool TryGetReal(size_t row, double& v) const {
+ return TryGetValue(row, v);
+ }
// get pointer to a string value for the row, or null if there is none
const string* GetStringPtr(size_t row) const;
diff --git a/c++/include/objects/seqtable/SeqTable_multi_data.hpp b/c++/include/objects/seqtable/SeqTable_multi_data.hpp
index 555f4c7..623e1c2 100644
--- a/c++/include/objects/seqtable/SeqTable_multi_data.hpp
+++ b/c++/include/objects/seqtable/SeqTable_multi_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: SeqTable_multi_data.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: SeqTable_multi_data.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -72,19 +72,103 @@ public:
return row_index < GetSize();
}
+ // return equivalent simpler variant:
+ // e_Bit - bool
+ // e_Int - any integer that fits in Int4
+ // e_Int8 - integer that fits in Int8
+ // e_Real - floating point value
+ // e_String - string
+ // e_Bytes - char/byte vector
+ // e_Loc - CSeq_loc
+ // e_Id - CSeq_id
+ // e_Interval - CSeq_interval
+ // e_notset - no data
+ E_Choice GetValueType(void) const;
+
+ // return true if the value is convertible to integer value (any size).
+ // Bool, Int, Int1, Int2, Int8 are all integer types.
+ // This includes special representations:
+ // bvector for 1-bit values, scaled integers, delta encoding.
+ bool CanGetInt(void) const;
+
+ // return true if the value is convertible to double value.
+ // This includes special representation: scaled values.
+ bool CanGetReal(void) const;
+
+ // return size (sizeof) of integer value to store data from any row,
+ // or zero if the data is not convertible to integer value.
+ // Bool, Int, Int1, Int2, Int8 are all integer types.
+ // This includes special representations:
+ // bvector for 1-bit values, scaled integers, delta encoding.
+ size_t GetIntSize(void) const;
+
// get bool value for the row, return false if there is no a value
bool TryGetBool(size_t row, bool& v) const;
- // get int value for the row, return false if there is no a value
- bool TryGetInt(size_t row, int& v) const;
+
// get double value for the row, return false if there is no a value
bool TryGetReal(size_t row, double& v) const;
+ // get Int1 value for the row, return false if there is no a value
+ bool TryGetInt1(size_t row, Int1& v) const;
+ bool TryGetInt1WithRounding(size_t row, Int1& v) const;
+ // get Int2 value for the row, return false if there is no a value
+ bool TryGetInt2(size_t row, Int2& v) const;
+ bool TryGetInt2WithRounding(size_t row, Int2& v) const;
+ // get Int4 value for the row, return false if there is no a value
+ bool TryGetInt4(size_t row, Int4& v) const;
+ bool TryGetInt4WithRounding(size_t row, Int4& v) const;
+ // get Int8 value for the row, return false if there is no a value
+ bool TryGetInt8(size_t row, Int8& v) const;
+ bool TryGetInt8WithRounding(size_t row, Int8& v) const;
+
+ // for plain int (=Int4)
+ bool TryGetInt(size_t row, int& v) const {
+ return TryGetInt4(row, v);
+ }
+ bool TryGetIntWithRounding(size_t row, int& v) const {
+ return TryGetInt4WithRounding(row, v);
+ }
+
// get pointer to a string value for the row, or null if there is none
const string* GetStringPtr(size_t row) const;
// get pointer to a byte vector value for the row, or null if there is none
typedef vector<char> TBytesValue;
const TBytesValue* GetBytesPtr(size_t row) const;
+ // overloaded methods for use in templates
+ bool TryGetValue(size_t row, Int1& v) const {
+ return TryGetInt1(row, v);
+ }
+ bool TryGetValue(size_t row, Int2& v) const {
+ return TryGetInt2(row, v);
+ }
+ bool TryGetValue(size_t row, Int4& v) const {
+ return TryGetInt4(row, v);
+ }
+ bool TryGetValue(size_t row, Int8& v) const {
+ return TryGetInt8(row, v);
+ }
+ bool TryGetValue(size_t row, bool& v) const {
+ return TryGetBool(row, v);
+ }
+ bool TryGetValue(size_t row, double& v) const {
+ return TryGetReal(row, v);
+ }
+ bool TryGetValue(size_t row, string& v) const {
+ if ( const string* ptr = GetStringPtr(row) ) {
+ v = *ptr;
+ return true;
+ }
+ return false;
+ }
+ bool TryGetValue(size_t row, TBytesValue& v) const {
+ if ( const TBytesValue* ptr = GetBytesPtr(row) ) {
+ v = *ptr;
+ return true;
+ }
+ return false;
+ }
+
// reserve memory for multi-row data vectors
class NCBI_SEQ_EXPORT CReserveHook : public CPreReadChoiceVariantHook
{
@@ -96,7 +180,13 @@ public:
void ChangeTo(E_Choice type);
void ChangeToBit(void); // convert int data with values 0/1 to bits
void ChangeToBit_bvector(void);
- void ChangeToInt(void);
+ void ChangeToInt1(void);
+ void ChangeToInt2(void);
+ void ChangeToInt4(void);
+ void ChangeToInt8(void);
+ void ChangeToInt(void) {
+ ChangeToInt4();
+ }
void ChangeToInt_delta(void);
void ChangeToInt_scaled(int mul, int add);
void ChangeToReal(void);
@@ -118,6 +208,8 @@ public:
protected:
+ bool x_TryGetInt8(size_t row, Int8& v, const char* type_name) const;
+
void x_ResetCache(void);
CIntDeltaSumCache& x_GetIntDeltaCache(void) const;
diff --git a/c++/include/objects/seqtable/SeqTable_single_data.hpp b/c++/include/objects/seqtable/SeqTable_single_data.hpp
new file mode 100644
index 0000000..b54aadd
--- /dev/null
+++ b/c++/include/objects/seqtable/SeqTable_single_data.hpp
@@ -0,0 +1,119 @@
+/* $Id: SeqTable_single_data.hpp 457991 2015-01-29 19:26:03Z vasilche $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ */
+
+/// @file SeqTable_single_data.hpp
+/// User-defined methods of the data storage class.
+///
+/// This file was originally generated by application DATATOOL
+/// using the following specifications:
+/// 'seqtable.asn'.
+///
+/// New methods or data members can be added to it if needed.
+/// See also: SeqTable_single_data_.hpp
+
+
+#ifndef OBJECTS_SEQTABLE_SEQTABLE_SINGLE_DATA_HPP
+#define OBJECTS_SEQTABLE_SEQTABLE_SINGLE_DATA_HPP
+
+
+// generated includes
+#include <objects/seqtable/SeqTable_single_data_.hpp>
+
+// generated classes
+
+BEGIN_NCBI_SCOPE
+
+BEGIN_objects_SCOPE // namespace ncbi::objects::
+
+/////////////////////////////////////////////////////////////////////////////
+class NCBI_SEQ_EXPORT CSeqTable_single_data : public CSeqTable_single_data_Base
+{
+ typedef CSeqTable_single_data_Base Tparent;
+public:
+ // constructor
+ CSeqTable_single_data(void);
+ // destructor
+ ~CSeqTable_single_data(void);
+
+ E_Choice GetValueType(void) const {
+ return Which();
+ }
+
+ // return true if the value is integer of any size.
+ // Bool, Int, Int8 are all integer types.
+ bool CanGetInt(void) const {
+ return IsInt() || IsInt8() || IsBit();
+ }
+ // return size (sizeof) of integer value to store data,
+ // or zero if the data is not convertible to integer value.
+ // Bool, Int, Int8 are all integer types.
+ // returned value is the size of data in chars.
+ size_t GetIntSize(void) const {
+ return IsInt()? sizeof(TInt): IsInt8()? sizeof(TInt8): IsBit()? 1: 0;
+ }
+ // return true if the value is convertible to double value.
+ bool CanGetReal(void) const {
+ return IsReal();
+ }
+
+ void GetValue(bool& v) const;
+ void GetValue(Int1& v) const;
+ void GetValue(Int2& v) const;
+ void GetValue(int& v) const;
+ void GetValue(Int8& v) const;
+ void GetValue(double& v) const;
+ void GetValue(string& v) const;
+ void GetValue(TBytes& v) const;
+
+ void ThrowConversionError(const char* type_name) const;
+ static void ThrowOverflowError(Int8 value, const char* type_name);
+
+private:
+ // Prohibit copy constructor and assignment operator
+ CSeqTable_single_data(const CSeqTable_single_data& value);
+ CSeqTable_single_data& operator=(const CSeqTable_single_data& value);
+
+};
+
+/////////////////// CSeqTable_single_data inline methods
+
+// constructor
+inline
+CSeqTable_single_data::CSeqTable_single_data(void)
+{
+}
+
+
+/////////////////// end of CSeqTable_single_data inline methods
+
+
+END_objects_SCOPE // namespace ncbi::objects::
+
+END_NCBI_SCOPE
+
+
+#endif // OBJECTS_SEQTABLE_SEQTABLE_SINGLE_DATA_HPP
diff --git a/c++/include/objects/seqtable/Seq_table.hpp b/c++/include/objects/seqtable/Seq_table.hpp
index c61597a..17a88c1 100644
--- a/c++/include/objects/seqtable/Seq_table.hpp
+++ b/c++/include/objects/seqtable/Seq_table.hpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_table.hpp 399623 2013-05-15 14:59:37Z vasilche $
+/* $Id: Seq_table.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,6 +68,8 @@ public:
const CSeqTable_column& GetColumn(TColumnId column_id,
CTempString column_name) const;
+ static string GetIdName(TColumnId column_id);
+
private:
// Prohibit copy constructor and assignment operator
CSeq_table(const CSeq_table& value);
@@ -93,4 +95,3 @@ END_NCBI_SCOPE
#endif // OBJECTS_SEQTABLE_SEQ_TABLE_HPP
-/* Original file checksum: lines: 86, chars: 2417, CRC32: e07df33b */
diff --git a/c++/include/objects/seqtable/impl/delta_cache.hpp b/c++/include/objects/seqtable/impl/delta_cache.hpp
index c4ada87..abdf75b 100644
--- a/c++/include/objects/seqtable/impl/delta_cache.hpp
+++ b/c++/include/objects/seqtable/impl/delta_cache.hpp
@@ -1,4 +1,4 @@
-/* $Id: delta_cache.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: delta_cache.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,14 +39,67 @@ BEGIN_objects_SCOPE // namespace ncbi::objects::
class NCBI_SEQ_EXPORT CIntDeltaSumCache : public CObject
{
public:
- CIntDeltaSumCache(size_t size); // size of deltas array
- ~CIntDeltaSumCache(void);
+ virtual ~CIntDeltaSumCache(void);
typedef CSeqTable_multi_data TDeltas;
- typedef int TValue;
- TValue GetDeltaSum(const TDeltas& deltas,
- size_t index);
+ virtual Int4 GetDeltaSum4(const TDeltas& deltas,
+ size_t index);
+ virtual Int8 GetDeltaSum8(const TDeltas& deltas,
+ size_t index);
+};
+
+
+// delta accumulation support
+class NCBI_SEQ_EXPORT CInt4DeltaSumCache : public CIntDeltaSumCache
+{
+public:
+ CInt4DeltaSumCache(size_t size); // size of deltas array
+ ~CInt4DeltaSumCache(void);
+
+ typedef Int4 TValue;
+
+ TValue GetDeltaSum4(const TDeltas& deltas,
+ size_t index);
+
+protected:
+ TValue x_GetDeltaSum2(const TDeltas& deltas,
+ size_t block_index,
+ size_t block_offset);
+
+ // size of blocks of deltas for accumulation
+ static const size_t kBlockSize;
+
+ // accumulated deltas for each block
+ // size = (totaldeltas+kBlockSize-1)/kBlockSize
+ // m_Blocks[0] = sum of deltas in the 1st block (0..kBlockSize-1)
+ // m_Blocks[1] = sum of deltas in first 2 blocks (0..2*kBlockSize-1)
+ AutoArray<TValue> m_Blocks;
+ // number of calculated entries in m_Block
+ size_t m_BlocksFilled;
+
+ // cached accumulated sums per delta within a block
+ // size = kBlockSize
+ // m_CacheBlockInfo[0] = sum of the first delta of cached block
+ // m_CacheBlockInfo[1] = sum of first 2 deltas of cached block
+ // ...
+ AutoArray<TValue> m_CacheBlockInfo;
+ // index of the block with cached sums (or size_t(-1))
+ size_t m_CacheBlockIndex;
+};
+
+
+// delta accumulation support
+class NCBI_SEQ_EXPORT CInt8DeltaSumCache : public CIntDeltaSumCache
+{
+public:
+ CInt8DeltaSumCache(size_t size); // size of deltas array
+ ~CInt8DeltaSumCache(void);
+
+ typedef Int8 TValue;
+
+ TValue GetDeltaSum8(const TDeltas& deltas,
+ size_t index);
protected:
TValue x_GetDeltaSum2(const TDeltas& deltas,
diff --git a/c++/include/objects/seqtable/seq_table_exception.hpp b/c++/include/objects/seqtable/seq_table_exception.hpp
index 233e43f..004aa76 100644
--- a/c++/include/objects/seqtable/seq_table_exception.hpp
+++ b/c++/include/objects/seqtable/seq_table_exception.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_TABLE_EXCEPTION__HPP
#define SEQ_TABLE_EXCEPTION__HPP
-/* $Id: seq_table_exception.hpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: seq_table_exception.hpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -53,7 +53,7 @@ public:
enum EErrCode {
eColumnNotFound, ///< Requested column is missing
eRowNotFound, ///< Requested row is missing
- eIncompatibleRowType, ///< Data cannot be converted to asked type
+ eIncompatibleValueType, ///< Data cannot be converted to asked type
eOtherError
};
virtual const char* GetErrCodeString(void) const;
diff --git a/c++/include/objects/biblio/Auth_list.hpp b/c++/include/objects/taxon1/Taxon2_data.hpp
similarity index 56%
copy from c++/include/objects/biblio/Auth_list.hpp
copy to c++/include/objects/taxon1/Taxon2_data.hpp
index 365de55..465a50d 100644
--- a/c++/include/objects/biblio/Auth_list.hpp
+++ b/c++/include/objects/taxon1/Taxon2_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: Auth_list.hpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Taxon2_data.hpp 454834 2014-12-18 16:56:57Z domrach $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -25,25 +25,23 @@
*
*/
-/// @Auth_list.hpp
+/// @file Taxon2_data.hpp
/// User-defined methods of the data storage class.
///
/// This file was originally generated by application DATATOOL
/// using the following specifications:
-/// 'biblio.asn'.
+/// 'taxon1.asn'.
///
/// New methods or data members can be added to it if needed.
-/// See also: Auth_list_.hpp
+/// See also: Taxon2_data_.hpp
-#ifndef OBJECTS_BIBLIO_AUTH_LIST_HPP
-#define OBJECTS_BIBLIO_AUTH_LIST_HPP
-
+#ifndef OBJECTS_TAXON1_TAXON2_DATA_HPP
+#define OBJECTS_TAXON1_TAXON2_DATA_HPP
+#include <objects/general/general__.hpp>
// generated includes
-#include <objects/biblio/Auth_list_.hpp>
-
-#include <objects/biblio/citation_base.hpp>
+#include <objects/taxon1/Taxon2_data_.hpp>
// generated classes
@@ -52,46 +50,53 @@ BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
/////////////////////////////////////////////////////////////////////////////
-class NCBI_BIBLIO_EXPORT CAuth_list
- : public CAuth_list_Base, public ICitationBase
+class NCBI_TAXON1_EXPORT CTaxon2_data : public CTaxon2_data_Base
{
- typedef CAuth_list_Base Tparent;
+ typedef CTaxon2_data_Base Tparent;
public:
// constructor
- CAuth_list(void);
+ CTaxon2_data(void);
// destructor
- ~CAuth_list(void);
+ ~CTaxon2_data(void);
- size_t GetNameCount(void) const;
+ // Additional properties from lookup
+ void SetProperty( const string& name, const string& value );
+ void SetProperty( const string& name, int value );
+ void SetProperty( const string& name, bool value );
- void ConvertMlToStandard(void);
- bool SameCitation(const CAuth_list& other) const;
-
-protected:
- bool GetLabelV1(string* label, TLabelFlags flags) const;
- bool GetLabelV2(string* label, TLabelFlags flags) const;
+ bool GetProperty( const string& name, string& value ) const;
+ bool GetProperty( const string& name, int& value ) const;
+ bool GetProperty( const string& name, bool& value ) const;
+ void ResetProperty( const string& name );
private:
// Prohibit copy constructor and assignment operator
- CAuth_list(const CAuth_list& value);
- CAuth_list& operator=(const CAuth_list& value);
+ CTaxon2_data(const CTaxon2_data& value);
+ CTaxon2_data& operator=(const CTaxon2_data& value);
+
+protected:
+ typedef list< CRef< CDbtag > > TOrgProperties;
+ TOrgProperties m_props;
+ TOrgProperties::iterator x_FindProperty( const string& name );
+ TOrgProperties::const_iterator x_FindPropertyConst( const string& name ) const;
};
-/////////////////// CAuth_list inline methods
+/////////////////// CTaxon2_data inline methods
// constructor
inline
-CAuth_list::CAuth_list(void)
+CTaxon2_data::CTaxon2_data(void)
{
}
-/////////////////// end of CAuth_list inline methods
+/////////////////// end of CTaxon2_data inline methods
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
-#endif // OBJECTS_BIBLIO_AUTH_LIST_HPP
-/* Original file checksum: lines: 94, chars: 2572, CRC32: 9913f83c */
+
+#endif // OBJECTS_TAXON1_TAXON2_DATA_HPP
+/* Original file checksum: lines: 86, chars: 2448, CRC32: 5537cc62 */
diff --git a/c++/include/objects/taxon3/taxon3.hpp b/c++/include/objects/taxon3/cached_taxon3.hpp
old mode 100644
new mode 100755
similarity index 58%
copy from c++/include/objects/taxon3/taxon3.hpp
copy to c++/include/objects/taxon3/cached_taxon3.hpp
index 0e47197..d2c884f
--- a/c++/include/objects/taxon3/taxon3.hpp
+++ b/c++/include/objects/taxon3/cached_taxon3.hpp
@@ -1,7 +1,7 @@
-#ifndef NCBI_TAXON3_HPP
-#define NCBI_TAXON3_HPP
+#ifndef NCBI_CACHED_TAXON3_HPP
+#define NCBI_CACHED_TAXON3_HPP
-/* $Id: taxon3.hpp 438755 2014-06-19 18:23:50Z gotvyans $
+/* $Id: cached_taxon3.hpp 478049 2015-09-03 16:29:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,19 +26,23 @@
*
* ===========================================================================
*
- * Author: Colleen Bollin, based on work by Vladimir Soussov, Michael Domrachev
+ * Author: Brad Holmes
*
* File Description:
- * NCBI Taxonomy information retreival library
+ * Taxon service that caches a parameterized number of replies
+ * for queries by list of org-ref. It *DOES NOT* cache replies
+ * for request objects.
*
*/
#include <objects/taxon3/taxon3__.hpp>
+#include <objects/taxon3/itaxon3.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <serial/serialdef.hpp>
#include <connect/ncbi_types.h>
#include <corelib/ncbi_limits.hpp>
+#include <util/ncbi_cache.hpp>
#include <list>
#include <vector>
@@ -53,35 +57,53 @@ class CConn_ServiceStream;
BEGIN_objects_SCOPE
-class NCBI_TAXON3_EXPORT CTaxon3 {
+class NCBI_TAXON3_EXPORT CCachedTaxon3 : public ITaxon3,
+ protected CCache<string, CRef<CTaxon3_reply> >
+{
+
+private:
+ CCachedTaxon3(AutoPtr<ITaxon3> taxon, TSizeType capacity);
+
public:
+ virtual ~CCachedTaxon3() {};
- CTaxon3();
- ~CTaxon3();
+ typedef string TCacheKey;
+
+ // The method to create the cache one-off
+ static AutoPtr<CCachedTaxon3> Create(
+ AutoPtr<ITaxon3> taxon, TSizeType capacity = 100000);
+
+ // This should only be used if it will be
+ // immediately wrapped into a safe pointer
+ static CCachedTaxon3* CreateUnSafe(
+ AutoPtr<ITaxon3> taxon, TSizeType capacity = 100000);
//---------------------------------------------
// Taxon1 server init
// Returns: TRUE - OK
// FALSE - Can't open connection to taxonomy service
///
- void Init(void); // default: 120 sec timeout, 5 reconnect attempts,
+ virtual void Init(void); // default: 120 sec timeout, 5 reconnect attempts,
- void Init(const STimeout* timeout, unsigned reconnect_attempts=5);
+ virtual void Init(const STimeout* timeout, unsigned reconnect_attempts=5);
// submit a list of org_refs
- CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list);
- CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request);
+ virtual CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list);
+ virtual CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request);
//--------------------------------------------------
// Get error message after latest erroneous operation
// Returns: error message, or empty string if no error occurred
- ///
- const string& GetLastError() const { return m_sLastError; }
+ // FIXME: Not implemented properly at this time.
+ virtual const string& GetLastError() const { NCBI_USER_THROW("LastError state is not properly implemented"); return m_sLastError; }
+private:
+
+ CRef<CTaxon3_reply> x_AddReplyToCache(const TCacheKey& key, const COrg_ref& org_ref);
+ CRef<CTaxon3_reply> x_GetReplyForOrgRef(const COrg_ref& org_ref);
-private:
ESerialDataFormat m_eDataFormat;
const char* m_pchService;
@@ -92,11 +114,15 @@ private:
string m_sLastError;
+ /// The cached taxon does not own the taxon.
+ AutoPtr<ITaxon3> m_taxon;
+
void SetLastError(const char* err_msg);
+
};
END_objects_SCOPE
END_NCBI_SCOPE
-#endif //NCBI_TAXON1_HPP
+#endif //NCBI_CACHED_TAXON3_HPP
diff --git a/c++/include/objects/taxon3/taxon3.hpp b/c++/include/objects/taxon3/itaxon3.hpp
similarity index 70%
copy from c++/include/objects/taxon3/taxon3.hpp
copy to c++/include/objects/taxon3/itaxon3.hpp
index 0e47197..986b9fa 100644
--- a/c++/include/objects/taxon3/taxon3.hpp
+++ b/c++/include/objects/taxon3/itaxon3.hpp
@@ -1,7 +1,7 @@
-#ifndef NCBI_TAXON3_HPP
-#define NCBI_TAXON3_HPP
+#ifndef NCBI_ITAXON3_HPP
+#define NCBI_ITAXON3_HPP
-/* $Id: taxon3.hpp 438755 2014-06-19 18:23:50Z gotvyans $
+/* $Id: itaxon3.hpp 478049 2015-09-03 16:29:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -27,6 +27,7 @@
* ===========================================================================
*
* Author: Colleen Bollin, based on work by Vladimir Soussov, Michael Domrachev
+ * Brad Holmes : Added ITaxon interface, to support mocking the service.
*
* File Description:
* NCBI Taxonomy information retreival library
@@ -53,50 +54,33 @@ class CConn_ServiceStream;
BEGIN_objects_SCOPE
-class NCBI_TAXON3_EXPORT CTaxon3 {
+class NCBI_TAXON3_EXPORT ITaxon3 {
public:
- CTaxon3();
- ~CTaxon3();
+ virtual ~ITaxon3(){};
//---------------------------------------------
// Taxon1 server init
// Returns: TRUE - OK
// FALSE - Can't open connection to taxonomy service
- ///
- void Init(void); // default: 120 sec timeout, 5 reconnect attempts,
+ virtual void Init(void) = 0;
- void Init(const STimeout* timeout, unsigned reconnect_attempts=5);
+ virtual void Init(const STimeout* timeout, unsigned reconnect_attempts=5) = 0;
// submit a list of org_refs
- CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list);
- CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request);
+ virtual CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list) = 0;
+ virtual CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request) = 0;
//--------------------------------------------------
// Get error message after latest erroneous operation
// Returns: error message, or empty string if no error occurred
///
- const string& GetLastError() const { return m_sLastError; }
-
-
-
-
-private:
-
- ESerialDataFormat m_eDataFormat;
- const char* m_pchService;
- STimeout* m_timeout; // NULL, or points to "m_timeout_value"
- STimeout m_timeout_value;
-
- unsigned m_nReconnectAttempts;
-
- string m_sLastError;
+ virtual const string& GetLastError() const = 0;
- void SetLastError(const char* err_msg);
};
END_objects_SCOPE
END_NCBI_SCOPE
-#endif //NCBI_TAXON1_HPP
+#endif //NCBI_ITAXON1_HPP
diff --git a/c++/include/objects/taxon3/taxon3.hpp b/c++/include/objects/taxon3/taxon3.hpp
index 0e47197..a2c9325 100644
--- a/c++/include/objects/taxon3/taxon3.hpp
+++ b/c++/include/objects/taxon3/taxon3.hpp
@@ -1,7 +1,7 @@
#ifndef NCBI_TAXON3_HPP
#define NCBI_TAXON3_HPP
-/* $Id: taxon3.hpp 438755 2014-06-19 18:23:50Z gotvyans $
+/* $Id: taxon3.hpp 478049 2015-09-03 16:29:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,8 @@
#include <connect/ncbi_types.h>
#include <corelib/ncbi_limits.hpp>
+#include <objects/taxon3/itaxon3.hpp>
+
#include <list>
#include <vector>
#include <map>
@@ -53,30 +55,30 @@ class CConn_ServiceStream;
BEGIN_objects_SCOPE
-class NCBI_TAXON3_EXPORT CTaxon3 {
+class NCBI_TAXON3_EXPORT CTaxon3 : public ITaxon3 {
public:
CTaxon3();
- ~CTaxon3();
+ virtual ~CTaxon3();
//---------------------------------------------
// Taxon1 server init
// Returns: TRUE - OK
// FALSE - Can't open connection to taxonomy service
///
- void Init(void); // default: 120 sec timeout, 5 reconnect attempts,
+ virtual void Init(void); // default: 120 sec timeout, 5 reconnect attempts,
- void Init(const STimeout* timeout, unsigned reconnect_attempts=5);
+ virtual void Init(const STimeout* timeout, unsigned reconnect_attempts=5);
// submit a list of org_refs
- CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list);
- CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request);
+ virtual CRef<CTaxon3_reply> SendOrgRefList(const vector<CRef< COrg_ref> >& list);
+ virtual CRef< CTaxon3_reply > SendRequest(const CTaxon3_request& request);
//--------------------------------------------------
// Get error message after latest erroneous operation
// Returns: error message, or empty string if no error occurred
///
- const string& GetLastError() const { return m_sLastError; }
+ virtual const string& GetLastError() const { return m_sLastError; }
diff --git a/c++/include/objects/trackmgr/gridrpcclient.hpp b/c++/include/objects/trackmgr/gridrpcclient.hpp
index 79d6d28..8d6ba2b 100644
--- a/c++/include/objects/trackmgr/gridrpcclient.hpp
+++ b/c++/include/objects/trackmgr/gridrpcclient.hpp
@@ -1,7 +1,7 @@
#ifndef INTERNAL_MISC_SERIAL___GRID_RPC_CLIENT__HPP
#define INTERNAL_MISC_SERIAL___GRID_RPC_CLIENT__HPP
-/* $Id: gridrpcclient.hpp 439067 2014-06-25 13:02:23Z meric $
+/* $Id: gridrpcclient.hpp 471177 2015-06-24 13:24:03Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
/// Classes pertaining to GRID-based ASN.1 RPC clients
#include <corelib/ncbiobj.hpp>
+#include <corelib/stream_utils.hpp>
#include <serial/serial.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
@@ -41,7 +42,10 @@
#include <connect/services/grid_rw_impl.hpp>
#include <connect/services/grid_client.hpp>
#include <connect/ncbi_conn_stream.hpp>
+#include <corelib/perf_log.hpp>
#include <corelib/rwstream.hpp>
+#include <util/compress/lzo.hpp>
+#include <util/compress/stream_util.hpp>
#include <util/compress/zlib.hpp>
@@ -65,42 +69,24 @@ public:
};
///
-/// Traits class for uncompressed binary ASN.1 streams
+/// Traits class for compressed binary ASN.1 streams
///
-class CAsnBinUncompressed : public CAsnBin
+class CAsnBinCompressed : public CAsnBin
{
public:
- /// Return an object output stream (CObjectOStream)
- ///
- /// @param ostr
- /// underlying output stream
- /// @return
- /// object stream
- static CObjectOStream*
- GetOStream(CNcbiOstream& ostr)
- {
- return CObjectOStream::Open(GetDataFormat(), ostr);
- }
+ typedef int TOwnership;
- /// Return an object input stream (CObjectIStream)
- ///
- /// @param istr
- /// underlying input stream
- /// @return
- /// object stream
- static CObjectIStream*
- GetIStream(CNcbiIstream& istr)
+ struct SStreamProp
{
- return CObjectIStream::Open(GetDataFormat(), istr);
- }
-};
+ SStreamProp(const CCompressStream::EMethod comp_mthd = CCompressStream::eZip)
+ : compress_method(comp_mthd)
+ {
+ }
+
+ CCompressStream::EMethod compress_method;
+ };
+
-///
-/// Traits class for compressed binary ASN.1 streams
-///
-class CAsnBinCompressed : public CAsnBin
-{
-public:
/// Return an object output stream (CObjectOStream)
///
/// @param ostr
@@ -108,17 +94,16 @@ public:
/// @return
/// object stream
static CObjectOStream*
- GetOStream(CNcbiOstream& ostr)
+ GetOStream(CNcbiOstream& ostr, SStreamProp stream_prop = SStreamProp(CCompressStream::eLZO))
{
- static const enum ENcbiOwnership ownership = eTakeOwnership;
auto_ptr<CCompressionOStream> outstr_zip(
new CCompressionOStream(
ostr,
- new CZipStreamCompressor(),
+ CreateStreamCompressor(stream_prop),
CCompressionStream::fOwnProcessor
)
);
- return CObjectOStream::Open(GetDataFormat(), *outstr_zip.release(), ownership);
+ return CObjectOStream::Open(GetDataFormat(), *outstr_zip.release(), eTakeOwnership);
}
/// Return an object input stream (CObjectIStream)
@@ -130,15 +115,122 @@ public:
static CObjectIStream*
GetIStream(CNcbiIstream& istr)
{
- static const enum ENcbiOwnership ownership = eTakeOwnership;
+ return GetIStream(istr, GetIStreamProperties(istr));
+ }
+
+ static CObjectIStream*
+ GetIStream(const string& job_content, CNetCacheAPI& nc_api)
+ {
+ SStreamProp sp;
+ return GetIStream(job_content, nc_api, sp);
+ }
+
+ static CObjectIStream*
+ GetIStream(const string& job_content, CNetCacheAPI& nc_api, SStreamProp& streamprop)
+ {
+ streamprop = GetJobStreamProperties(job_content, nc_api);
+ auto_ptr<CStringOrBlobStorageReader> reader(new CStringOrBlobStorageReader(job_content, nc_api));
+ auto_ptr<CRStream> rstr(new CRStream(reader.release(), CRWStreambuf::fOwnReader));
+ return GetIStream(*rstr.release(), streamprop, CCompressionStream::fOwnAll);
+ }
+
+protected:
+ static CObjectIStream*
+ GetIStream(CNcbiIstream& istr,
+ const SStreamProp& stream_prop,
+ TOwnership ownership = CCompressionStream::fOwnProcessor
+ )
+ {
auto_ptr<CCompressionIStream> instr_zip(
new CCompressionIStream(
istr,
- new CZipStreamDecompressor(CZipCompression::fAllowTransparentRead),
- CCompressionStream::fOwnProcessor
+ CreateStreamDecompressor(stream_prop),
+ ownership
)
);
- return CObjectIStream::Open(GetDataFormat(), *instr_zip.release(), ownership);
+ return CObjectIStream::Open(GetDataFormat(), *instr_zip.release(), eTakeOwnership);
+ }
+
+ static SStreamProp GetJobStreamProperties(const string& job_content, CNetCacheAPI& nc_api)
+ {
+ if (job_content.empty()) {
+ NCBI_THROW(CException, eUnknown, "job content is empty");
+ }
+ CStringOrBlobStorageReader reader(job_content, nc_api);
+ char buf[5];
+ size_t count = ArraySize(buf);
+ size_t bytes_read = 0UL;
+ reader.Read(buf, count, &bytes_read);
+ const bool is_lzo = IsLZOStream(CTempString(buf, bytes_read));
+ return SStreamProp(is_lzo ? CCompressStream::eLZO : CCompressStream::eZip);
+ };
+
+ static SStreamProp
+ GetIStreamProperties(CNcbiIstream& istr)
+ {
+ return SStreamProp(IsLZOStream(istr) ? CCompressStream::eLZO : CCompressStream::eZip);
+ }
+
+ static bool IsLZOStream(CNcbiIstream& istr)
+ {
+ char buf[5];
+ const size_t buflen = ArraySize(buf);
+ const streamsize readlen = CStreamUtils::Readsome(istr, buf, buflen);
+ CStreamUtils::Stepback(istr, buf, readlen);
+ return IsLZOStream(CTempString(buf, readlen));
+ }
+
+ static bool IsLZOStream(const CTempString& str)
+ {
+ /// LZO magic header (see fStreamFormat flag).
+ static const char kMagic[] = { 'L', 'Z', 'O', '\0' };
+ static const size_t kMagicSize = 4UL;
+ return (str.size() < kMagicSize)
+ ? false
+ : NStr::Equal(CTempString(kMagic, kMagicSize), CTempString(str, 0, kMagicSize));
+ }
+
+ static CCompressionStreamProcessor* CreateStreamCompressor(const SStreamProp& stream_prop)
+ {
+ auto_ptr<CCompressionStreamProcessor> sp;
+ if (stream_prop.compress_method == CCompressStream::eLZO) {
+ sp.reset(new CLZOStreamCompressor());
+ }
+ else {
+ sp.reset(new CZipStreamCompressor());
+ }
+ return sp.release();
+ }
+
+ static CCompressionStreamProcessor* CreateStreamDecompressor(const SStreamProp& stream_prop)
+ {
+ auto_ptr<CCompressionStreamProcessor> sp;
+ if (stream_prop.compress_method == CCompressStream::eLZO) {
+ sp.reset(new CLZOStreamDecompressor());
+ }
+ else {
+ sp.reset(new CZipStreamDecompressor());
+ }
+ return sp.release();
+ }
+
+ static string CompMethodToString(const CCompressStream::EMethod method)
+ {
+ switch (method) {
+ case CCompressStream::eNone:
+ return "none";
+ case CCompressStream::eBZip2:
+ return "BZip2";
+ case CCompressStream::eLZO:
+ return "LZO";
+ case CCompressStream::eZip:
+ return "Zip";
+ case CCompressStream::eGZipFile:
+ return "GZipFile";
+ case CCompressStream::eConcatenatedGZipFile:
+ return "GZipFile";
+ };
+ NCBI_THROW(CException, eUnknown, "unexpected compression method");
}
};
@@ -152,6 +244,7 @@ public:
eUnexpectedFailure
};
virtual const char* GetErrCodeString(void) const;
+
NCBI_EXCEPTION_DEFAULT(CGridRPCBaseClientException, CException);
};
@@ -161,9 +254,9 @@ public:
///
/// Base class for GRID-based ASN.1 RPC clients
///
-/// TConnectTraits template classes: CAsnBinCompressed and CAsnBinUncompressed
+/// TConnectTraits template classes: CAsnBinCompressed
///
-template <typename TConnectTraits, int DefaultTimeout = 20>
+template <typename TConnectTraits = CAsnBinCompressed, int DefaultTimeout = 20>
class CGridRPCBaseClient : private TConnectTraits
{
public:
@@ -184,7 +277,7 @@ public:
: m_NS_api(CNetScheduleAPI::eAppRegistry, NS_registry_section),
m_Timeout(DefaultTimeout)
{
- LOG_POST(Trace << "NS: " << NS_registry_section);
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
static const CNcbiRegistry& cfg = CNcbiApplication::Instance()->GetConfig();
const string nc_reg(
NStr::IsBlank(NC_registry_section)
@@ -201,7 +294,6 @@ public:
void x_Init(const string& NC_registry_section)
{
- LOG_POST(Trace << "NS queue NC: " << NC_registry_section);
m_NC_api = CNetCacheAPI(CNetCacheAPI::eAppRegistry, NC_registry_section);
m_Grid_cli.reset(new CGridClient(m_NS_api.GetSubmitter(),
m_NC_api,
@@ -216,7 +308,7 @@ public:
}
template <class TRequest, class TReply>
- void Ask(const TRequest& request, TReply& reply) const
+ pair<CNetScheduleJob, bool> Ask(const TRequest& request, TReply& reply) const
{
CNcbiOstream& job_in = m_Grid_cli->GetOStream(); // job input stream
auto_ptr<CObjectOStream> outstr(TConnectTraits::GetOStream(job_in));
@@ -228,42 +320,100 @@ public:
m_Grid_cli->CloseStream();
CNetScheduleJob& job = m_Grid_cli->GetJob();
+ bool timed_out = false;
+ x_PrepareJob(job);
- CDeadline deadline(m_Timeout, 0);
+ try {
+ const CNetScheduleAPI::EJobStatus evt = m_Grid_cli->SubmitAndWait(m_Timeout);
+ switch (evt) {
+ case CNetScheduleAPI::eDone:
+ {
+ m_NS_api.GetJobDetails(job);
+ auto_ptr<CObjectIStream> instr(TConnectTraits::GetIStream(job.output, m_NC_api));
+ *instr >> reply;
+ break;
+ }
+ case CNetScheduleAPI::eFailed:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job failed");
- CNetScheduleNotificationHandler submit_job_handler;
- submit_job_handler.SubmitJob(m_NS_api.GetSubmitter(),
- job,
- m_Timeout
- );
- LOG_POST(Trace << "job: " << job.job_id);
+ case CNetScheduleAPI::eCanceled:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job canceled");
- CNetScheduleAPI::EJobStatus status(
- submit_job_handler.WaitForJobCompletion(job, deadline, m_NS_api)
- );
+ case CNetScheduleAPI::eRunning:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job running");
+
+ default:
+ NCBI_THROW(CGridRPCBaseClientException,
+ eWaitTimeout,
+ "Unexpected status: " + CNetScheduleAPI::StatusToString(evt)
+ );
+ }
+ }
+ catch (const CGridRPCBaseClientException& e) {
+ switch (e.GetErrCode()) {
+ case CGridRPCBaseClientException::eUnexpectedFailure:
+ timed_out = true;
+ break;
+
+ case CGridRPCBaseClientException::eWaitTimeout:
+ default:
+ break;
+ }
+ throw e;
+ }
+ return make_pair(job, timed_out);
+ }
- // TODO The wait is over; the current job status is in the status
- // variable. CNetScheduleAPI::StatusToString(status) can convert it
- // to a human-readable string.
- if (status == CNetScheduleAPI::eDone) {
- // TODO The job has completed successfully.
- CStringOrBlobStorageReader reader(job.output, m_NC_api);
- CRStream rstr(&reader);
- auto_ptr<CObjectIStream> instr(TConnectTraits::GetIStream(rstr));
+protected:
+ virtual void x_PrepareJob(CNetScheduleJob& job) const
+ {
+ }
+
+ template <class TReply>
+ CNetScheduleJob x_GetJobById(const string job_id, TReply& reply) const
+ {
+ CNetScheduleNotificationHandler job_handler;
+ CNetScheduleJob job;
+ job.job_id = job_id;
+
+ CDeadline deadline(m_Timeout, 0);
+ const int status_mask(
+ CNetScheduleNotificationHandler::fJSM_Done |
+ CNetScheduleNotificationHandler::fJSM_Canceled |
+ CNetScheduleNotificationHandler::fJSM_Failed
+ );
+ const CNetScheduleAPI::EJobStatus evt = job_handler.WaitForJobEvent(job.job_id, deadline, m_NS_api, status_mask);
+ switch (evt) {
+ case CNetScheduleAPI::eDone:
+ {
+ m_NS_api.GetJobDetails(job);
+ auto_ptr<CObjectIStream> instr(TConnectTraits::GetIStream(job.output, m_NC_api));
*instr >> reply;
+ break;
}
- else {
- // TODO Check 'status' to see if the job's still running or
- // it has failed.
- NCBI_THROW(CGridRPCBaseClientException, eWaitTimeout, kEmptyStr);
+ case CNetScheduleAPI::eFailed:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job failed");
+
+ case CNetScheduleAPI::eCanceled:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job canceled");
+
+ case CNetScheduleAPI::eRunning:
+ NCBI_THROW(CGridRPCBaseClientException, eUnexpectedFailure, "Job running");
+
+ default:
+ NCBI_THROW(CGridRPCBaseClientException,
+ eWaitTimeout,
+ "Unexpected status: " + CNetScheduleAPI::StatusToString(evt)
+ );
}
+ return job;
}
private:
mutable CNetScheduleAPI m_NS_api;
mutable CNetCacheAPI m_NC_api;
mutable auto_ptr<CGridClient> m_Grid_cli;
- int m_Timeout;
+ Uint4 m_Timeout;
};
diff --git a/c++/include/objects/valerr/ValidErrItem.hpp b/c++/include/objects/valerr/ValidErrItem.hpp
index 4db6342..5b181c2 100644
--- a/c++/include/objects/valerr/ValidErrItem.hpp
+++ b/c++/include/objects/valerr/ValidErrItem.hpp
@@ -1,4 +1,4 @@
-/* $Id: ValidErrItem.hpp 455335 2014-12-29 13:00:02Z ivanov $
+/* $Id: ValidErrItem.hpp 473633 2015-07-21 17:05:11Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -249,6 +249,8 @@ enum EErrType {
eErr_SEQ_DESCR_OrganismIsUndefinedSpecies,
eErr_SEQ_DESCR_SuspectedContaminatedCellLine,
eErr_SEQ_DESCR_WrongBiomolForTechnique,
+ eErr_SEQ_DESCR_WrongOrganismFor16SrRNA,
+ eErr_SEQ_DESCR_InconsistentWGSFlags,
ERR_CODE_END(SEQ_DESCR),
@@ -518,6 +520,7 @@ enum EErrType {
eErr_SEQ_FEAT_NonsenseIntron,
eErr_SEQ_FEAT_InconsistentPseudogeneValue,
eErr_SEQ_FEAT_MultiIntervalIntron,
+ eErr_SEQ_FEAT_SeqLocTypeProblem,
ERR_CODE_END(SEQ_FEAT),
ERR_CODE_BEGIN(SEQ_ALIGN) = 5000,
diff --git a/c++/include/objects/valerr/ValidError.hpp b/c++/include/objects/valerr/ValidError.hpp
index 14a56d7..e13d4ce 100644
--- a/c++/include/objects/valerr/ValidError.hpp
+++ b/c++/include/objects/valerr/ValidError.hpp
@@ -1,4 +1,4 @@
-/* $Id: ValidError.hpp 447737 2014-09-30 13:44:49Z ivanov $
+/* $Id: ValidError.hpp 447658 2014-09-29 18:29:18Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/bioseq_handle.hpp b/c++/include/objmgr/bioseq_handle.hpp
index faf1615..cbb53d0 100644
--- a/c++/include/objmgr/bioseq_handle.hpp
+++ b/c++/include/objmgr/bioseq_handle.hpp
@@ -1,7 +1,7 @@
#ifndef BIOSEQ_HANDLE__HPP
#define BIOSEQ_HANDLE__HPP
-/* $Id: bioseq_handle.hpp 457723 2015-01-27 17:54:52Z ivanov $
+/* $Id: bioseq_handle.hpp 455474 2014-12-30 16:36:56Z foleyjp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/bioseq_set_handle.hpp b/c++/include/objmgr/bioseq_set_handle.hpp
index 836a884..2f676f3 100644
--- a/c++/include/objmgr/bioseq_set_handle.hpp
+++ b/c++/include/objmgr/bioseq_set_handle.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR__BIOSEQ_SET_HANDLE__HPP
#define OBJMGR__BIOSEQ_SET_HANDLE__HPP
-/* $Id: bioseq_set_handle.hpp 444889 2014-08-28 17:54:38Z ivanov $
+/* $Id: bioseq_set_handle.hpp 444685 2014-08-27 13:07:18Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/data_loader.hpp b/c++/include/objmgr/data_loader.hpp
index 34c74d4..3d893d6 100644
--- a/c++/include/objmgr/data_loader.hpp
+++ b/c++/include/objmgr/data_loader.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR___DATA_LOADER__HPP
#define OBJECTS_OBJMGR___DATA_LOADER__HPP
-/* $Id: data_loader.hpp 428348 2014-03-03 17:39:03Z vasilche $
+/* $Id: data_loader.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -286,6 +286,9 @@ public:
/// Returns fState_not_found|fState_no_data if sequence
/// with requested id is not known.
virtual int GetSequenceState(const CSeq_id_Handle& idh);
+ /// Request for a sequence hash.
+ /// Returns 0 if the sequence or hash is not known.
+ virtual int GetSequenceHash(const CSeq_id_Handle& idh);
/// Bulk loading interface for a small pieces of information per id.
/// The 'loaded' bit set (in/out) marks ids that already processed.
@@ -301,6 +304,7 @@ public:
typedef vector<TSeqPos> TSequenceLengths;
typedef vector<CSeq_inst::TMol> TSequenceTypes;
typedef vector<int> TSequenceStates;
+ typedef vector<int> TSequenceHashes;
/// Bulk request for accession.version Seq-ids of a set of sequences.
virtual void GetAccVers(const TIds& ids, TLoaded& loaded, TIds& ret);
/// Bulk request for gis of a set of sequences.
@@ -318,6 +322,9 @@ public:
/// Bulk request for states of a set of sequences.
virtual void GetSequenceStates(const TIds& ids, TLoaded& loaded,
TSequenceStates& ret);
+ /// Bulk request for hashes of a set of sequences.
+ virtual void GetSequenceHashes(const TIds& ids, TLoaded& loaded,
+ TSequenceHashes& ret);
// Load multiple seq-ids. Same as GetRecords() for multiple ids
// with choise set to eBlob. The map should be initialized with
diff --git a/c++/include/objmgr/gc_assembly_parser.hpp b/c++/include/objmgr/gc_assembly_parser.hpp
index 15ec92b..e06335d 100644
--- a/c++/include/objmgr/gc_assembly_parser.hpp
+++ b/c++/include/objmgr/gc_assembly_parser.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR_GC_ASSEMBLY_PARSER__HPP
#define OBJMGR_GC_ASSEMBLY_PARSER__HPP
-/* $Id: gc_assembly_parser.hpp 427871 2014-02-25 18:00:57Z grichenk $
+/* $Id: gc_assembly_parser.hpp 479618 2015-09-22 15:42:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -104,13 +104,13 @@ private:
const CGC_Sequence* parent_seq,
CRef<CSeq_entry> parent_entry,
CRef<CSeq_id> override_id);
- void x_AddBioseq(CRef<CSeq_entry> parent_entry,
- const TSeqIds& synonyms,
- const CDelta_ext* delta);
+ void x_AddBioseq(CRef<CSeq_entry> parent_entry,
+ const TSeqIds& synonyms,
+ const CGC_Sequence& gc_seq);
void x_InitSeq_entry(CRef<CSeq_entry> entry,
CRef<CSeq_entry> parent);
void x_CopyData(const CGC_AssemblyDesc& assm_desc,
- CSeq_entry& entry);
+ CSeq_entry& entry);
TParserFlags m_Flags;
CRef<CSeq_entry> m_TSE;
diff --git a/c++/include/objmgr/graph_ci.hpp b/c++/include/objmgr/graph_ci.hpp
index 5f3cc00..94b879d 100644
--- a/c++/include/objmgr/graph_ci.hpp
+++ b/c++/include/objmgr/graph_ci.hpp
@@ -1,7 +1,7 @@
#ifndef GRAPH_CI__HPP
#define GRAPH_CI__HPP
-/* $Id: graph_ci.hpp 439367 2014-06-27 17:27:09Z vasilche $
+/* $Id: graph_ci.hpp 464897 2015-04-15 13:12:52Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -158,6 +158,9 @@ public:
if ( m_MappedGraph ) {
return m_MappedGraph->GetNumval();
}
+ if ( !m_GraphRef->GetMappingInfo().IsMapped() ) {
+ return GetOriginalGraph().GetNumval();
+ }
TSeqPos numval = 0;
ITERATE(TGraphRanges, it, GetMappedGraphRanges()) {
numval += it->GetLength();
diff --git a/c++/include/objmgr/impl/annot_collector.hpp b/c++/include/objmgr/impl/annot_collector.hpp
index 70f4123..4b72eb9 100644
--- a/c++/include/objmgr/impl/annot_collector.hpp
+++ b/c++/include/objmgr/impl/annot_collector.hpp
@@ -1,7 +1,7 @@
#ifndef ANNOT_COLLECTOR__HPP
#define ANNOT_COLLECTOR__HPP
-/* $Id: annot_collector.hpp 458847 2015-02-10 19:47:18Z vasilche $
+/* $Id: annot_collector.hpp 458705 2015-02-09 15:12:21Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/impl/annot_type_index.hpp b/c++/include/objmgr/impl/annot_type_index.hpp
index 9f8490b..900f49a 100644
--- a/c++/include/objmgr/impl/annot_type_index.hpp
+++ b/c++/include/objmgr/impl/annot_type_index.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___ANNOT_TYPE_INDEX__HPP
#define OBJECTS_OBJMGR_IMPL___ANNOT_TYPE_INDEX__HPP
-/* $Id: annot_type_index.hpp 151374 2009-02-03 21:03:09Z vasilche $
+/* $Id: annot_type_index.hpp 462572 2015-03-19 15:33:54Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -77,9 +77,18 @@ public:
static SAnnotTypeSelector GetTypeSelector(size_t index);
private:
- typedef vector<TIndexRange> TIndexRangeTable;
- typedef vector<size_t> TIndexTable;
- typedef vector<CSeqFeatData::ESubtype> TSubtypes;
+ enum ETypeSizes {
+ kAnnotType_size = CSeq_annot::C_Data::e_MaxChoice,
+ kFeatType_size = CSeqFeatData::e_MaxChoice,
+ kFeatSubtype_size = CSeqFeatData::eSubtype_max
+ };
+ enum EAnnotIndexValues {
+ kAnnotIndex_Align,
+ kAnnotIndex_Graph,
+ kAnnotIndex_Seq_table,
+ kAnnotIndex_Ftable,
+ kAnnotIndex_size = kAnnotIndex_Ftable + kFeatSubtype_size
+ };
static void x_InitIndexTables(void);
@@ -87,13 +96,13 @@ private:
static bool sm_TablesInitialized;
// Table: annot type -> index
// (for Ftable it's just the first feature type index)
- static TIndexRangeTable sm_AnnotTypeIndexRange;
+ static Uint1 sm_AnnotTypeIndexRange[kAnnotType_size][2];
// Table: feat type -> index range, [)
- static TIndexRangeTable sm_FeatTypeIndexRange;
+ static Uint1 sm_FeatTypeIndexRange[kFeatType_size][2];
// Table feat subtype -> index
- static TIndexTable sm_FeatSubtypeIndex;
+ static Uint1 sm_FeatSubtypeIndex[kFeatSubtype_size];
// Table index -> subtype
- static TSubtypes sm_IndexSubtype;
+ static Uint1 sm_IndexSubtype[kAnnotIndex_size];
};
@@ -111,12 +120,15 @@ CAnnotType_Index::TIndexRange
CAnnotType_Index::GetAnnotTypeRange(CSeq_annot::C_Data::E_Choice type)
{
Initialize();
- if ( size_t(type) < sm_AnnotTypeIndexRange.size() ) {
- return sm_AnnotTypeIndexRange[type];
+ size_t start, end;
+ if ( size_t(type) < kAnnotType_size ) {
+ start = sm_AnnotTypeIndexRange[type][0];
+ end = sm_AnnotTypeIndexRange[type][1];
}
else {
- return TIndexRange(0, 0);
+ start = end = 0;
}
+ return TIndexRange(start, end);
}
@@ -125,12 +137,15 @@ CAnnotType_Index::TIndexRange
CAnnotType_Index::GetFeatTypeRange(CSeqFeatData::E_Choice type)
{
Initialize();
- if ( size_t(type) < sm_FeatTypeIndexRange.size() ) {
- return sm_FeatTypeIndexRange[type];
+ size_t start, end;
+ if ( size_t(type) < kFeatType_size ) {
+ start = sm_FeatTypeIndexRange[type][0];
+ end = sm_FeatTypeIndexRange[type][1];
}
else {
- return TIndexRange(0, 0);
+ start = end = 0;
}
+ return TIndexRange(start, end);
}
@@ -138,7 +153,7 @@ inline
size_t CAnnotType_Index::GetSubtypeIndex(CSeqFeatData::ESubtype subtype)
{
Initialize();
- if ( size_t(subtype) < sm_FeatSubtypeIndex.size() ) {
+ if ( size_t(subtype) < kFeatSubtype_size ) {
return sm_FeatSubtypeIndex[subtype];
}
else {
@@ -151,8 +166,8 @@ inline
CSeqFeatData::ESubtype CAnnotType_Index::GetSubtypeForIndex(size_t index)
{
Initialize();
- if ( index < sm_IndexSubtype.size() ) {
- return sm_IndexSubtype[index];
+ if ( index < kAnnotIndex_size ) {
+ return CSeqFeatData::ESubtype(sm_IndexSubtype[index]);
}
else {
return CSeqFeatData::eSubtype_bad;
diff --git a/c++/include/objmgr/impl/bioseq_base_info.hpp b/c++/include/objmgr/impl/bioseq_base_info.hpp
index c696be1..520ebcb 100644
--- a/c++/include/objmgr/impl/bioseq_base_info.hpp
+++ b/c++/include/objmgr/impl/bioseq_base_info.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___BIOSEQ_BASE_INFO__HPP
#define OBJECTS_OBJMGR_IMPL___BIOSEQ_BASE_INFO__HPP
-/* $Id: bioseq_base_info.hpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: bioseq_base_info.hpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/impl/data_source.hpp b/c++/include/objmgr/impl/data_source.hpp
index 6db245d..2c40b3b 100644
--- a/c++/include/objmgr/impl/data_source.hpp
+++ b/c++/include/objmgr/impl/data_source.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___DATA_SOURCE__HPP
#define OBJECTS_OBJMGR_IMPL___DATA_SOURCE__HPP
-/* $Id: data_source.hpp 436014 2014-05-22 15:54:51Z vasilche $
+/* $Id: data_source.hpp 467006 2015-05-08 11:59:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -182,6 +182,7 @@ public:
const CTSE_LockSet& GetStaticBlobs(void) const;
CDataLoader* GetDataLoader(void) const;
+ void RevokeDataLoader(void);
const CConstRef<CObject>& GetSharedObject(void) const;
TTSE_Lock GetSharedTSE(void) const;
bool CanBeEdited(void) const;
@@ -190,13 +191,25 @@ public:
void UpdateAnnotIndex(const CSeq_entry_Info& entry_info);
void UpdateAnnotIndex(const CSeq_annot_Info& annot_info);
+ // annotations for sequence that is not in this data source
void GetTSESetWithOrphanAnnots(const TSeq_idSet& ids,
TTSE_LockMatchSet& tse_set,
const SAnnotSelector* sel);
+ // annotations for sequence that is provided by this data source
+ // external_only = true means to exclude TSE with the sequence
void GetTSESetWithBioseqAnnots(const CBioseq_Info& bioseq,
const TTSE_Lock& tse,
TTSE_LockMatchSet& tse_set,
- const SAnnotSelector* sel);
+ const SAnnotSelector* sel,
+ bool external_only = false);
+ // external annotations for sequence that is provided by this data source
+ void GetTSESetWithExternalAnnots(const CBioseq_Info& bioseq,
+ const TTSE_Lock& tse,
+ TTSE_LockMatchSet& tse_set,
+ const SAnnotSelector* sel)
+ {
+ GetTSESetWithBioseqAnnots(bioseq, tse, tse_set, sel, true);
+ }
// Fill the set with bioseq handles for all sequences from a given TSE.
// Return empty tse lock if the entry was not found or is not a TSE.
@@ -224,6 +237,7 @@ public:
TSeqPos GetSequenceLength(const CSeq_id_Handle& idh);
CSeq_inst::TMol GetSequenceType(const CSeq_id_Handle& idh);
int GetSequenceState(const CSeq_id_Handle& idh);
+ int GetSequenceHash(const CSeq_id_Handle& idh);
// bulk interface
typedef vector<bool> TLoaded;
@@ -233,6 +247,7 @@ public:
typedef vector<TSeqPos> TSequenceLengths;
typedef vector<CSeq_inst::TMol> TSequenceTypes;
typedef vector<int> TSequenceStates;
+ typedef vector<int> TSequenceHashes;
void GetAccVers(const TIds& ids, TLoaded& loaded, TIds& ret);
void GetGis(const TIds& ids, TLoaded& loaded, TGis& ret);
void GetLabels(const TIds& ids, TLoaded& loaded, TLabels& ret);
@@ -243,6 +258,8 @@ public:
TSequenceTypes& ret);
void GetSequenceStates(const TIds& ids, TLoaded& loaded,
TSequenceStates& ret);
+ void GetSequenceHashes(const TIds& ids, TLoaded& loaded,
+ TSequenceHashes& ret);
typedef map<CSeq_id_Handle, SSeqMatch_DS> TSeqMatchMap;
void GetBlobs(TSeqMatchMap& match_map);
diff --git a/c++/include/objmgr/impl/handle_range_map.hpp b/c++/include/objmgr/impl/handle_range_map.hpp
index e24b117..72c9c56 100644
--- a/c++/include/objmgr/impl/handle_range_map.hpp
+++ b/c++/include/objmgr/impl/handle_range_map.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___HANDLE_RANGE_MAP__HPP
#define OBJECTS_OBJMGR_IMPL___HANDLE_RANGE_MAP__HPP
-/* $Id: handle_range_map.hpp 448087 2014-10-02 14:56:26Z ivanov $
+/* $Id: handle_range_map.hpp 472371 2015-07-09 14:13:53Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -97,16 +97,22 @@ public:
CHandleRangeMap& operator= (const CHandleRangeMap& rmap);
+ enum ETransSplicing {
+ eNoTransSplicing,
+ eTransSplicing
+ };
struct SAddState {
typedef CHandleRange::TRange TRange;
CSeq_id_Handle m_PrevId;
ENa_strand m_PrevStrand;
+ ETransSplicing m_TransSplicing;
TRange m_PrevRange;
};
// Add all ranges for each seq-id from a seq-loc
- void AddLocation(const CSeq_loc& loc);
+ void AddLocation(const CSeq_loc& loc,
+ ETransSplicing trans_splcing = eNoTransSplicing);
void AddLocation(const CSeq_loc& loc, SAddState& state);
// Add range substituting with handle "h"
void AddRange(const CSeq_id_Handle& h,
diff --git a/c++/include/objmgr/impl/scope_impl.hpp b/c++/include/objmgr/impl/scope_impl.hpp
index 8703c10..a077f7e 100644
--- a/c++/include/objmgr/impl/scope_impl.hpp
+++ b/c++/include/objmgr/impl/scope_impl.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR_IMPL_SCOPE_IMPL__HPP
#define OBJMGR_IMPL_SCOPE_IMPL__HPP
-/* $Id: scope_impl.hpp 428346 2014-03-03 17:35:59Z vasilche $
+/* $Id: scope_impl.hpp 474909 2015-08-03 10:48:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -135,7 +135,7 @@ public:
typedef map<CSeq_id_Handle, SSeq_id_ScopeInfo> TSeq_idMap;
typedef TSeq_idMap::value_type TSeq_idMapValue;
typedef set<CSeq_id_Handle> TSeq_idSet;
- typedef vector< pair<CTSE_Handle, CSeq_id_Handle> > TTSE_LockMatchSet;
+ typedef vector< pair<CTSE_Handle, CSeq_id_Handle> > TTSE_LockMatchSet;
typedef int TPriority;
typedef map<CConstRef<CObject>, CRef<CObject> > TEditInfoMap;
typedef map<CRef<CDataSource>, CRef<CDataSource_ScopeInfo> > TDSMap;
@@ -368,6 +368,7 @@ public:
TSeqPos GetSequenceLength(const CSeq_id_Handle& id, bool force_load);
CSeq_inst::TMol GetSequenceType(const CSeq_id_Handle& id, bool force_load);
int GetSequenceState(const CSeq_id_Handle& id, bool force_load);
+ int GetSequenceHash(const CSeq_id_Handle& id);
// Get a set of bioseq lengths
typedef vector<TSeqPos> TSequenceLengths;
@@ -381,6 +382,10 @@ public:
typedef vector<int> TSequenceStates;
void GetSequenceStates(TSequenceStates& ret,
const TIds& idhs, bool force_load);
+ // Get a set of sequence hashes
+ typedef vector<int> TSequenceHashes;
+ void GetSequenceHashes(TSequenceHashes& ret,
+ const TIds& idhs);
private:
@@ -428,6 +433,8 @@ public:
private:
void x_ClearAnnotCache(void);
void x_ClearCacheOnNewAnnot(const CTSE_Info& new_tse);
+ void x_ClearCacheOnRemoveSeqId(const CSeq_id_Handle& id,
+ CBioseq_ScopeInfo& seq);
void x_ClearCacheOnRemoveAnnot(const CTSE_Info& old_tse);
CRef<CDataSource_ScopeInfo>
@@ -551,17 +558,31 @@ private:
typedef CBioseq_ScopeInfo::TTSE_MatchSet TTSE_MatchSet;
typedef CDataSource::TTSE_LockMatchSet TTSE_LockMatchSet_DS;
+
+ void x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ CBioseq_ScopeInfo& binfo);
+ void x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TTSE_MatchSet* save_match,
+ CBioseq_ScopeInfo& binfo,
+ const SAnnotSelector* sel = 0);
+ void x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TSeq_idMapValue& info);
+ void x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TTSE_MatchSet* save_match,
+ TSeq_idMapValue& info,
+ const SAnnotSelector* sel = 0);
+
void x_AddTSESetWithAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
const TTSE_LockMatchSet_DS& add,
CDataSource_ScopeInfo& ds_info);
void x_GetTSESetWithOrphanAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
const TSeq_idSet& ids,
- CDataSource_ScopeInfo* excl_ds,
+ CBioseq_ScopeInfo* binfo,
const SAnnotSelector* sel);
void x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
CBioseq_ScopeInfo& binfo,
const SAnnotSelector* sel);
void x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
diff --git a/c++/include/objmgr/impl/scope_info.hpp b/c++/include/objmgr/impl/scope_info.hpp
index d143424..7cac7f6 100644
--- a/c++/include/objmgr/impl/scope_info.hpp
+++ b/c++/include/objmgr/impl/scope_info.hpp
@@ -1,7 +1,7 @@
#ifndef SCOPE_INFO__HPP
#define SCOPE_INFO__HPP
-/* $Id: scope_info.hpp 425515 2014-01-30 13:12:42Z vasilche $
+/* $Id: scope_info.hpp 467006 2015-05-08 11:59:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -282,8 +282,11 @@ public:
typedef map<CSeq_id_Handle, SSeqMatch_Scope> TSeqMatchMap;
void GetBlobs(TSeqMatchMap& match_map);
+ bool TSEIsReplaced(const TBlobId& blob_id) const;
+
protected:
friend class CScope_Impl;
+ friend class CTSE_ScopeInfo;
SSeqMatch_Scope x_GetSeqMatch(const CSeq_id_Handle& idh);
SSeqMatch_Scope x_FindBestTSE(const CSeq_id_Handle& idh);
@@ -315,6 +318,7 @@ private: // members
TTSE_UnlockQueue m_TSE_UnlockQueue;
mutable TTSE_LockSetMutex m_TSE_UnlockQueueMutex;
CRef<CDataSource_ScopeInfo> m_EditDS;
+ set<TBlobId> m_ReplacedTSEs;
private: // to prevent copying
CDataSource_ScopeInfo(const CDataSource_ScopeInfo&);
@@ -387,8 +391,9 @@ public:
typedef map<CConstRef<CObject>, CRef<CObject> > TEditInfoMap;
void SetEditTSE(const CTSE_Lock& new_tse_lock,
- CDataSource_ScopeInfo& new_ds,
- const TEditInfoMap& edit_map);
+ CDataSource_ScopeInfo& new_ds);
+ void ReplaceTSE(const CTSE_Info& old_tse);
+ void RestoreReplacedTSE(void);
// gets locked CScopeInfo_Base object
typedef CScopeInfo_Ref<CSeq_entry_ScopeInfo> TSeq_entry_Lock;
@@ -467,7 +472,7 @@ private: // members
SUnloadedInfo(const CTSE_Lock& lock);
CTSE_Lock LockTSE(void);
- CRef<CDataLoader> m_Loader;
+ CRef<CDataSource> m_Source;
TBlobId m_BlobId;
TBlobOrder m_BlobOrder;
TSeqIds m_BioseqsIds;
@@ -482,7 +487,7 @@ private: // members
mutable const CTSE_ScopeInfo* m_UsedByTSE;
mutable TUsedTSE_LockSet m_UsedTSE_Set;
- mutable CTSE_ScopeUserLock m_EditLock;
+ TBlobId m_ReplacedTSE;
TScopeInfoMap m_ScopeInfoMap;
@@ -497,7 +502,7 @@ class NCBI_XOBJMGR_EXPORT CBioseq_ScopeInfo : public CScopeInfo_Base
public:
typedef CRef<CTSE_ScopeInfo> TTSE_ScopeInfo;
typedef set<CSeq_id_Handle> TSeq_idSet;
- typedef vector< pair<TTSE_ScopeInfo, CSeq_id_Handle> > TTSE_MatchSet;
+ typedef vector< pair<TTSE_ScopeInfo, CSeq_id_Handle> > TTSE_MatchSet;
typedef CObjectFor<TTSE_MatchSet> TTSE_MatchSetObject;
typedef CInitMutex<TTSE_MatchSetObject> TAnnotRefInfo;
typedef TIndexIds TIds;
diff --git a/c++/include/objmgr/impl/seq_annot_info.hpp b/c++/include/objmgr/impl/seq_annot_info.hpp
index 337f7af..3c6085e 100644
--- a/c++/include/objmgr/impl/seq_annot_info.hpp
+++ b/c++/include/objmgr/impl/seq_annot_info.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_ANNOT_INFO__HPP
#define SEQ_ANNOT_INFO__HPP
-/* $Id: seq_annot_info.hpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: seq_annot_info.hpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/impl/seq_table_info.hpp b/c++/include/objmgr/impl/seq_table_info.hpp
index e9864c7..59df0fa 100644
--- a/c++/include/objmgr/impl/seq_table_info.hpp
+++ b/c++/include/objmgr/impl/seq_table_info.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_TABLE_INFO__HPP
#define SEQ_TABLE_INFO__HPP
-/* $Id: seq_table_info.hpp 386178 2013-01-16 18:34:29Z vasilche $
+/* $Id: seq_table_info.hpp 458003 2015-01-29 19:47:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -90,49 +90,17 @@ public:
bool val = false;
return *this && m_Column->TryGetBool(row, val) && val;
}
- bool GetBool(size_t row, bool& v, bool force = false) const
+ template<class Value>
+ bool GetValue(size_t row, Value& v, bool force = false) const
{
- return m_Column->TryGetBool(row, v) ||
+ return m_Column->TryGetValue(row, v) ||
(force && x_ThrowUnsetValue());
}
- bool GetInt(size_t row, int& v, bool force = false) const
- {
- return m_Column->TryGetInt(row, v) ||
- (force && x_ThrowUnsetValue());
- }
- bool GetReal(size_t row, double& v, bool force = false) const
- {
- return m_Column->TryGetReal(row, v) ||
- (force && x_ThrowUnsetValue());
- }
- bool GetString(size_t row, string& v, bool force = false) const;
- bool GetBytes(size_t row, vector<char>& v, bool force = false) const;
const string* GetStringPtr(size_t row, bool force = false) const;
const vector<char>* GetBytesPtr(size_t row, bool force = false) const;
CConstRef<CSeq_id> GetSeq_id(size_t row, bool force = false) const;
CConstRef<CSeq_loc> GetSeq_loc(size_t row, bool force = false) const;
- bool GetValue(size_t row, bool& value, bool force = false) const
- {
- return GetBool(row, value, force);
- }
- bool GetValue(size_t row, int& value, bool force = false) const
- {
- return GetInt(row, value, force);
- }
- bool GetValue(size_t row, double& value, bool force = false) const
- {
- return GetReal(row, value, force);
- }
- bool GetValue(size_t row, string& value, bool force = false) const
- {
- return GetString(row, value, force);
- }
- bool GetValue(size_t row, vector<char>& value, bool force = false) const
- {
- return GetBytes(row, value, force);
- }
-
void UpdateSeq_loc(CSeq_loc& loc, size_t row,
const CSeqTableSetLocField& setter) const;
void UpdateSeq_loc(CSeq_loc& loc,
diff --git a/c++/include/objmgr/impl/seq_table_setter.hpp b/c++/include/objmgr/impl/seq_table_setter.hpp
index ccd43a9..f2d10d8 100644
--- a/c++/include/objmgr/impl/seq_table_setter.hpp
+++ b/c++/include/objmgr/impl/seq_table_setter.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_TABLE_SETTER__HPP
#define SEQ_TABLE_SETTER__HPP
-/* $Id: seq_table_setter.hpp 116188 2007-12-27 18:22:40Z vasilche $
+/* $Id: seq_table_setter.hpp 458003 2015-01-29 19:47:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,6 +55,7 @@ public:
virtual ~CSeqTableSetLocField();
virtual void SetInt(CSeq_loc& loc, int value) const;
+ virtual void SetInt8(CSeq_loc& loc, Int8 value) const;
virtual void SetReal(CSeq_loc& loc, double value) const;
virtual void SetString(CSeq_loc& loc, const string& value) const;
};
@@ -66,6 +67,7 @@ public:
virtual ~CSeqTableSetFeatField();
virtual void SetInt(CSeq_feat& feat, int value) const;
+ virtual void SetInt8(CSeq_feat& feat, Int8 value) const;
virtual void SetReal(CSeq_feat& feat, double value) const;
virtual void SetString(CSeq_feat& feat, const string& value) const;
virtual void SetBytes(CSeq_feat& feat, const vector<char>& value) const;
diff --git a/c++/include/objmgr/impl/seq_table_setters.hpp b/c++/include/objmgr/impl/seq_table_setters.hpp
index d5e49a2..0c18456 100644
--- a/c++/include/objmgr/impl/seq_table_setters.hpp
+++ b/c++/include/objmgr/impl/seq_table_setters.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_TABLE_SETTERS__HPP
#define SEQ_TABLE_SETTERS__HPP
-/* $Id: seq_table_setters.hpp 197444 2010-07-16 18:05:11Z vasilche $
+/* $Id: seq_table_setters.hpp 458003 2015-01-29 19:47:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -104,6 +104,7 @@ public:
CSeqTableSetExt(const CTempString& name);
virtual void SetInt(CSeq_feat& feat, int value) const;
+ virtual void SetInt8(CSeq_feat& feat, Int8 value) const;
virtual void SetReal(CSeq_feat& feat, double value) const;
virtual void SetString(CSeq_feat& feat, const string& value) const;
virtual void SetBytes(CSeq_feat& feat, const vector<char>& value) const;
@@ -127,6 +128,7 @@ public:
}
virtual void SetInt(CSeq_feat& feat, int value) const;
+ virtual void SetInt8(CSeq_feat& feat, Int8 value) const;
virtual void SetString(CSeq_feat& feat, const string& value) const;
private:
@@ -138,6 +140,7 @@ class CSeqTableSetExtType : public CSeqTableSetFeatField
{
public:
virtual void SetInt(CSeq_feat& feat, int value) const;
+ virtual void SetInt8(CSeq_feat& feat, Int8 value) const;
virtual void SetString(CSeq_feat& feat, const string& value) const;
};
@@ -223,6 +226,7 @@ public:
CObjectInfo GetFinalObject(CObjectInfo obj) const;
void SetObjectField(CObjectInfo obj, int value) const;
+ void SetObjectField(CObjectInfo obj, Int8 value) const;
void SetObjectField(CObjectInfo obj, double value) const;
void SetObjectField(CObjectInfo obj, const string& value) const;
void SetObjectField(CObjectInfo obj, const vector<char>& value) const;
@@ -242,6 +246,7 @@ public:
CSeqTableSetAnyLocField(const CTempString& field);
virtual void SetInt(CSeq_loc& loc, int value) const;
+ virtual void SetInt8(CSeq_loc& loc, Int8 value) const;
virtual void SetReal(CSeq_loc& loc, double value) const;
virtual void SetString(CSeq_loc& loc, const string& value) const;
virtual void SetBytes(CSeq_loc& loc, const vector<char>& value) const;
@@ -255,6 +260,7 @@ public:
CSeqTableSetAnyFeatField(const CTempString& field);
virtual void SetInt(CSeq_feat& feat, int value) const;
+ virtual void SetInt8(CSeq_feat& feat, Int8 value) const;
virtual void SetReal(CSeq_feat& feat, double value) const;
virtual void SetString(CSeq_feat& feat, const string& value) const;
virtual void SetBytes(CSeq_feat& feat, const vector<char>& value) const;
diff --git a/c++/include/objmgr/impl/snp_annot_info.hpp b/c++/include/objmgr/impl/snp_annot_info.hpp
index 1cdbaeb..33dced4 100644
--- a/c++/include/objmgr/impl/snp_annot_info.hpp
+++ b/c++/include/objmgr/impl/snp_annot_info.hpp
@@ -1,7 +1,7 @@
#ifndef SNP_ANNOT_INFO__HPP
#define SNP_ANNOT_INFO__HPP
-/* $Id: snp_annot_info.hpp 406792 2013-07-16 14:30:43Z vasilche $
+/* $Id: snp_annot_info.hpp 468050 2015-05-19 19:16:25Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -191,6 +191,7 @@ public:
TGi GetGi(void) const;
const CSeq_id& GetSeq_id(void) const;
+ void SetGi(TGi gi);
size_t GetSize(void) const;
const SSNP_Info& GetInfo(size_t index) const;
diff --git a/c++/include/objmgr/impl/synonyms.hpp b/c++/include/objmgr/impl/synonyms.hpp
index cbf939a..7956081 100644
--- a/c++/include/objmgr/impl/synonyms.hpp
+++ b/c++/include/objmgr/impl/synonyms.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___SYNONYMS__HPP
#define OBJECTS_OBJMGR_IMPL___SYNONYMS__HPP
-/* $Id: synonyms.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: synonyms.hpp 446824 2014-09-18 14:47:47Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,7 +35,6 @@
#include <corelib/ncbiobj.hpp>
#include <objects/seq/seq_id_handle.hpp>
-#include <objmgr/impl/scope_info.hpp>
#include <vector>
#include <utility>
@@ -55,7 +54,7 @@ class CBioseq_Handle;
class NCBI_XOBJMGR_EXPORT CSynonymsSet : public CObject
{
public:
- typedef pair<const CSeq_id_Handle, SSeq_id_ScopeInfo>* value_type;
+ typedef CSeq_id_Handle value_type;
typedef vector<value_type> TIdSet;
typedef TIdSet::const_iterator const_iterator;
@@ -67,7 +66,6 @@ public:
bool empty(void) const;
static CSeq_id_Handle GetSeq_id_Handle(const const_iterator& iter);
- static CBioseq_Handle GetBioseqHandle(const const_iterator& iter);
void AddSynonym(const value_type& syn);
bool ContainsSynonym(const CSeq_id_Handle& id) const;
diff --git a/c++/include/objmgr/impl/tse_assigner.hpp b/c++/include/objmgr/impl/tse_assigner.hpp
index 04feb55..34765f7 100644
--- a/c++/include/objmgr/impl/tse_assigner.hpp
+++ b/c++/include/objmgr/impl/tse_assigner.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___TSE_ASSIGNER__HPP
#define OBJECTS_OBJMGR_IMPL___TSE_ASSIGNER__HPP
-/* $Id: tse_assigner.hpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: tse_assigner.hpp 472380 2015-07-09 14:16:30Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -72,7 +72,7 @@ public:
const CSeq_descr& descr) = 0;
virtual void LoadAnnot(CTSE_Info&, const TPlace& place,
CRef<CSeq_annot> annot,
- TIntId chunk_id) = 0;
+ int chunk_id) = 0;
virtual void LoadBioseq(CTSE_Info&, const TPlace& place,
CRef<CSeq_entry> entry) = 0;
virtual void LoadSequence(CTSE_Info&, const TPlace& place, TSeqPos pos,
@@ -116,7 +116,7 @@ public:
const CSeq_descr& descr);
virtual void LoadAnnot(CTSE_Info&, const TPlace& place,
CRef<CSeq_annot> annot,
- TIntId chunk_id);
+ int chunk_id);
virtual void LoadBioseq(CTSE_Info&, const TPlace& place,
CRef<CSeq_entry> entry);
virtual void LoadSequence(CTSE_Info&, const TPlace& place, TSeqPos pos,
diff --git a/c++/include/objmgr/impl/tse_info.hpp b/c++/include/objmgr/impl/tse_info.hpp
index e592880..7d7f143 100644
--- a/c++/include/objmgr/impl/tse_info.hpp
+++ b/c++/include/objmgr/impl/tse_info.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___TSE_INFO__HPP
#define OBJECTS_OBJMGR_IMPL___TSE_INFO__HPP
-/* $Id: tse_info.hpp 440696 2014-07-16 15:33:15Z vasilche $
+/* $Id: tse_info.hpp 446824 2014-09-18 14:47:47Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -57,6 +57,7 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
class CScope_Impl;
+class CTSE_ScopeInfo;
class CBioseq_Info;
class CSeq_entry_Info;
class CSeq_annot_Info;
@@ -447,6 +448,7 @@ private:
friend class CTSE_Guard;
friend class CDataSource;
friend class CScope_Impl;
+ friend class CTSE_ScopeInfo;
friend class CDataLoader;
friend class CAnnot_Collector;
friend class CSeq_entry_Info;
diff --git a/c++/include/objmgr/impl/tse_split_info.hpp b/c++/include/objmgr/impl/tse_split_info.hpp
index 1c0b848..1dca9ee 100644
--- a/c++/include/objmgr/impl/tse_split_info.hpp
+++ b/c++/include/objmgr/impl/tse_split_info.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_OBJMGR_IMPL___TSE_SPLIT_INFO__HPP
#define OBJECTS_OBJMGR_IMPL___TSE_SPLIT_INFO__HPP
-/* $Id: tse_split_info.hpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: tse_split_info.hpp 472380 2015-07-09 14:16:30Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,7 +68,7 @@ public:
typedef int TSplitVersion;
typedef CTSE_Chunk_Info::TChunkId TChunkId;
typedef vector<TChunkId> TChunkIds;
- typedef map<CTSE_Info*, CRef<ITSE_Assigner> > TTSE_Set;
+ typedef map<CTSE_Info*, CRef<ITSE_Assigner> > TTSE_Set;
typedef vector<pair<CSeq_id_Handle, TChunkId> > TSeqIdToChunks;
typedef map<TChunkId, CRef<CTSE_Chunk_Info> > TChunks;
typedef CTSE_Chunk_Info::TBioseqId TBioseqId;
@@ -95,6 +95,7 @@ public:
// TSE connection
void x_DSAttach(CDataSource& ds);
+ void x_DSDetach(CDataSource& ds);
void x_TSEAttach(CTSE_Info& tse_info, CRef<ITSE_Assigner>& assigner);
void x_TSEDetach(CTSE_Info& tse_info);
@@ -145,7 +146,7 @@ public:
// loading results
void x_LoadDescr(const TPlace& place, const CSeq_descr& descr);
- void x_LoadAnnot(const TPlace& place, const CSeq_annot& annot, TIntId chunk_id);
+ void x_LoadAnnot(const TPlace& place, const CSeq_annot& annot, int chunk_id);
void x_LoadBioseq(const TPlace& place, const CBioseq& bioseq);
void x_LoadSequence(const TPlace& place, TSeqPos pos,
const TSequence& sequence);
@@ -160,7 +161,7 @@ protected:
private:
// identification of the blob
- CRef<CDataLoader> m_DataLoader;
+ CDataSource* m_DataLoader;
TBlobId m_BlobId;
TBlobVersion m_BlobVersion;
TSplitVersion m_SplitVersion;
diff --git a/c++/include/objmgr/object_manager.hpp b/c++/include/objmgr/object_manager.hpp
index 1b19b8c..a0d7f75 100644
--- a/c++/include/objmgr/object_manager.hpp
+++ b/c++/include/objmgr/object_manager.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECT_MANAGER__HPP
#define OBJECT_MANAGER__HPP
-/* $Id: object_manager.hpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: object_manager.hpp 467023 2015-05-08 14:53:15Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -185,6 +185,25 @@ public:
bool RevokeDataLoader(CDataLoader& loader);
bool RevokeDataLoader(const string& loader_name);
+
+ /// Revoke all registered data loaders, even if they were still used.
+ /// This method should be called at application's end to release
+ /// data loader plugins for unloading of their shared library.
+ void RevokeAllDataLoaders(void);
+
+
+ class NCBI_XOBJMGR_EXPORT IDataLoaderFilter
+ {
+ public:
+ virtual ~IDataLoaderFilter();
+
+ virtual bool IsDataLoaderMatches(CDataLoader& loader) const = 0;
+ };
+
+ /// Revoke data loaders by filter, even if they were still used.
+ /// This method should be called from data loader's plugin unloadin code.
+ void RevokeDataLoaders(IDataLoaderFilter& filter);
+
typedef SRegisterLoaderInfo<CDataLoader> TRegisterLoaderInfo;
void ReleaseDataSource(TDataSourceLock& data_source);
diff --git a/c++/include/objmgr/objmgr_exception.hpp b/c++/include/objmgr/objmgr_exception.hpp
index e1c1050..0f77419 100644
--- a/c++/include/objmgr/objmgr_exception.hpp
+++ b/c++/include/objmgr/objmgr_exception.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR_EXCEPTION__HPP
#define OBJMGR_EXCEPTION__HPP
-/* $Id: objmgr_exception.hpp 435595 2014-05-19 12:06:04Z vasilche $
+/* $Id: objmgr_exception.hpp 457199 2015-01-21 14:46:10Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -157,8 +157,7 @@ public:
TBlobState state,
EDiagSev severity = eDiag_Error)
: CObjMgrException(info, prev_exception,
- (CObjMgrException::EErrCode) CException::eInvalid,
- message, severity),
+ message, severity, 0),
m_BlobState(state)
{
x_Init(info, message, prev_exception, severity);
diff --git a/c++/include/objmgr/scope.hpp b/c++/include/objmgr/scope.hpp
index 7011c39..cc1b5cc 100644
--- a/c++/include/objmgr/scope.hpp
+++ b/c++/include/objmgr/scope.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR_SCOPE__HPP
#define OBJMGR_SCOPE__HPP
-/* $Id: scope.hpp 428346 2014-03-03 17:35:59Z vasilche $
+/* $Id: scope.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -428,6 +428,11 @@ public:
CBioseq_Handle::TBioseqStateFlags GetSequenceState(const CSeq_id_Handle& id,
EForceLoad force_load = eNoForceLoad);
+ // returns 0 if sequence or its hash is not known
+ typedef int TSequenceHash;
+ TSequenceHash GetSequenceHash(const CSeq_id& id);
+ TSequenceHash GetSequenceHash(const CSeq_id_Handle& id);
+
/// Bulk retrieval methods
typedef vector<CSeq_id_Handle> TSeq_id_Handles;
TSeq_id_Handles GetAccVers(const TSeq_id_Handles& idhs,
@@ -472,6 +477,10 @@ public:
void GetSequenceStates(TSequenceStates* results,
const TSeq_id_Handles& idhs,
EForceLoad force_load = eNoForceLoad);
+ typedef vector<TSequenceHash> TSequenceHashes;
+ TSequenceHashes GetSequenceHashes(const TSeq_id_Handles& idhs);
+ void GetSequenceHashes(TSequenceHashes* results,
+ const TSeq_id_Handles& idhs);
/// Get bioseq synonyms, resolving to the bioseq in this scope.
CConstRef<CSynonymsSet> GetSynonyms(const CSeq_id& id);
diff --git a/c++/include/objmgr/seq_entry_ci.hpp b/c++/include/objmgr/seq_entry_ci.hpp
index 9d95c05..fedac06 100644
--- a/c++/include/objmgr/seq_entry_ci.hpp
+++ b/c++/include/objmgr/seq_entry_ci.hpp
@@ -1,7 +1,7 @@
#ifndef OBJMGR__SEQ_ENTRY_CI__HPP
#define OBJMGR__SEQ_ENTRY_CI__HPP
-/* $Id: seq_entry_ci.hpp 414728 2013-09-26 15:15:41Z vasilche $
+/* $Id: seq_entry_ci.hpp 485120 2015-11-18 19:39:01Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -135,9 +135,6 @@ protected:
bool IsValid(void) const;
private:
- typedef vector< CRef<CSeq_entry_Info> > TSeq_set;
- typedef TSeq_set::const_iterator TIterator;
-
void x_Initialize(const CBioseq_set_Handle& set);
void x_SetCurrentEntry(void);
@@ -149,7 +146,7 @@ private:
void x_Next(void);
CBioseq_set_Handle m_Parent;
- TIterator m_Iterator;
+ size_t m_Index;
CSeq_entry_Handle m_Current;
TFlags m_Flags;
CSeq_entry::E_Choice m_Filter;
diff --git a/c++/include/objmgr/seq_feat_handle.hpp b/c++/include/objmgr/seq_feat_handle.hpp
index dce8a35..a626d61 100644
--- a/c++/include/objmgr/seq_feat_handle.hpp
+++ b/c++/include/objmgr/seq_feat_handle.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_FEAT_HANDLE__HPP
#define SEQ_FEAT_HANDLE__HPP
-/* $Id: seq_feat_handle.hpp 459296 2015-02-17 18:12:39Z ivanov $
+/* $Id: seq_feat_handle.hpp 458821 2015-02-10 17:18:44Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objmgr/seq_loc_mapper.hpp b/c++/include/objmgr/seq_loc_mapper.hpp
index 5ab48ca..80d84f1 100644
--- a/c++/include/objmgr/seq_loc_mapper.hpp
+++ b/c++/include/objmgr/seq_loc_mapper.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_LOC_MAPPER__HPP
#define SEQ_LOC_MAPPER__HPP
-/* $Id: seq_loc_mapper.hpp 425911 2014-02-04 17:57:38Z grichenk $
+/* $Id: seq_loc_mapper.hpp 479618 2015-09-22 15:42:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -283,8 +283,8 @@ private:
// Creates and adds to the scope a virtual bioseq. If delta is not null,
// the bioseq uses it for the instance. Otherwise a virtual bioseq without
// length/data is created.
- CBioseq_Handle x_AddVirtualBioseq(const TSynonyms& synonyms,
- const CDelta_ext* delta = 0);
+ CBioseq_Handle x_AddVirtualBioseq(const TSynonyms& synonyms,
+ const CGC_Sequence& gc_seq);
// Helper function to check for UCSC random chromosomes and populate
// the set of synonyms.
diff --git a/c++/include/objmgr/table_field.hpp b/c++/include/objmgr/table_field.hpp
index 0230039..194a828 100644
--- a/c++/include/objmgr/table_field.hpp
+++ b/c++/include/objmgr/table_field.hpp
@@ -1,7 +1,7 @@
#ifndef TABLE_FIELD__HPP
#define TABLE_FIELD__HPP
-/* $Id: table_field.hpp 437701 2014-06-09 18:37:23Z ucko $
+/* $Id: table_field.hpp 458045 2015-01-30 04:26:01Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,6 +38,8 @@
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objects/seqtable/SeqTable_column.hpp>
+#include <objmgr/feat_ci.hpp>
+
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
@@ -47,7 +49,6 @@ class CSeq_annot;
class CSeq_annot_Info;
class CSeq_annot_Handle;
class CTable_annot_Info;
-class CFeat_CI;
class NCBI_XOBJMGR_EXPORT CTableFieldHandle_Base
@@ -66,30 +67,28 @@ public:
return m_FieldName;
}
- bool IsSet(const CFeat_CI& feat_ci) const;
- bool IsSet(const CSeq_annot_Handle& annot, size_t row) const;
-
- void Get(const CFeat_CI& feat_ci, bool& v) const;
- void Get(const CFeat_CI& feat_ci, int& v) const;
- void Get(const CFeat_CI& feat_ci, double& v) const;
- void Get(const CFeat_CI& feat_ci, string& v) const;
- void Get(const CFeat_CI& feat_ci, vector<char>& v) const;
- void Get(const CSeq_annot_Handle& annot, size_t row, bool& v) const;
- void Get(const CSeq_annot_Handle& annot, size_t row, int& v) const;
- void Get(const CSeq_annot_Handle& annot, size_t row, double& v) const;
- void Get(const CSeq_annot_Handle& annot, size_t row, string& v) const;
- void Get(const CSeq_annot_Handle& annot, size_t row, vector<char>& v) const;
-
- bool TryGet(const CFeat_CI& feat_ci, bool& v) const;
- bool TryGet(const CFeat_CI& feat_ci, int& v) const;
- bool TryGet(const CFeat_CI& feat_ci, double& v) const;
- bool TryGet(const CFeat_CI& feat_ci, string& v) const;
- bool TryGet(const CFeat_CI& feat_ci, vector<char>& v) const;
- bool TryGet(const CSeq_annot_Handle& annot, size_t row, bool& v) const;
- bool TryGet(const CSeq_annot_Handle& annot, size_t row, int& v) const;
- bool TryGet(const CSeq_annot_Handle& annot, size_t row, double& v) const;
- bool TryGet(const CSeq_annot_Handle& annot, size_t row, string& v) const;
- bool TryGet(const CSeq_annot_Handle& annot, size_t row, vector<char>& v) const;
+ bool IsSet(const CFeat_CI& feat_ci) const {
+ return x_GetColumn(feat_ci).IsSet(x_GetRow(feat_ci));
+ }
+ bool IsSet(const CSeq_annot_Handle& annot, size_t row) const {
+ return x_GetColumn(annot).IsSet(row);
+ }
+
+ template<class Value>
+ bool TryGet(const CFeat_CI& feat_ci, Value& v) const {
+ if ( const CSeqTable_column* column = x_FindColumn(feat_ci) ) {
+ return column->TryGetValue(x_GetRow(feat_ci), v);
+ }
+ return false;
+ }
+
+ template<class Value>
+ bool TryGet(const CSeq_annot_Handle& annot, size_t row, Value& v) const {
+ if ( const CSeqTable_column* column = x_FindColumn(annot) ) {
+ return column->TryGetValue(row, v);
+ }
+ return false;
+ }
const string* GetPtr(const CFeat_CI& feat_ci,
const string* dummy,
@@ -108,14 +107,27 @@ public:
protected:
bool x_ThrowUnsetValue(void) const;
- const CSeqTable_column* x_FindColumn(const CFeat_CI& feat_ci) const;
+
const CSeqTable_column* x_FindColumn(const CSeq_annot_Info& annot) const;
- const CSeqTable_column* x_FindColumn(const CSeq_annot_Handle& annot) const;
- const CSeqTable_column& x_GetColumn(const CFeat_CI& feat_ci) const;
const CSeqTable_column& x_GetColumn(const CSeq_annot_Info& annot) const;
- const CSeqTable_column& x_GetColumn(const CSeq_annot_Handle& annot) const;
- size_t x_GetRow(const CFeat_CI& feat_ci) const;
+ const CSeqTable_column* x_FindColumn(const CSeq_annot_Handle& annot) const {
+ return x_FindColumn(annot.x_GetInfo());
+ }
+ const CSeqTable_column* x_FindColumn(const CFeat_CI& feat_ci) const {
+ return x_FindColumn(feat_ci.Get().GetSeq_annot_Info());
+ }
+
+ const CSeqTable_column& x_GetColumn(const CSeq_annot_Handle& annot) const {
+ return x_GetColumn(annot.x_GetInfo());
+ }
+ const CSeqTable_column& x_GetColumn(const CFeat_CI& feat_ci) const {
+ return x_GetColumn(feat_ci.Get().GetSeq_annot_Info());
+ }
+
+ size_t x_GetRow(const CFeat_CI& feat_ci) const {
+ return feat_ci.Get().GetAnnotIndex();
+ }
int m_FieldId;
string m_FieldName;
@@ -138,13 +150,34 @@ public:
CTableFieldHandle(const string& field_name)
: CTableFieldHandle_Base(field_name) {
}
+ /*
const TFieldType* GetPtr(const CFeat_CI& feat_ci) const {
const TFieldType* dummy = 0;
return CTableFieldHandle_Base::GetPtr(feat_ci, dummy, false);
}
- const TFieldType& Get(const CFeat_CI& feat_ci) const {
- const TFieldType* dummy = 0;
- return *CTableFieldHandle_Base::GetPtr(feat_ci, dummy, true);
+ */
+ void Get(const CFeat_CI& feat_ci, TFieldType& v) const {
+ if ( !TryGet(feat_ci, v) ) {
+ x_ThrowUnsetValue();
+ }
+ }
+
+ void Get(const CSeq_annot_Handle& annot, size_t row, TFieldType& v) const {
+ if ( !TryGet(annot, row, v) ) {
+ x_ThrowUnsetValue();
+ }
+ }
+
+ TFieldType Get(const CFeat_CI& feat_ci) const {
+ TFieldType value;
+ Get(feat_ci, value);
+ return value;
+ }
+
+ TFieldType Get(const CSeq_annot_Handle& annot, size_t row) const {
+ TFieldType value;
+ Get(annot, row, value);
+ return value;
}
};
diff --git a/c++/include/objmgr/util/create_defline.hpp b/c++/include/objmgr/util/create_defline.hpp
index e11bcca..ec11322 100644
--- a/c++/include/objmgr/util/create_defline.hpp
+++ b/c++/include/objmgr/util/create_defline.hpp
@@ -80,12 +80,13 @@ public:
/// User-settable flags for tuning behavior
enum EUserFlags {
- fIgnoreExisting = 0x1, ///< Generate fresh titles unconditionally.
- fAllProteinNames = 0x2, ///< List all relevant proteins, not just one.
- fLocalAnnotsOnly = 0x4, ///< Never use related sequences' annotations.
+ fIgnoreExisting = 0x1, ///< Generate fresh titles unconditionally.
+ fAllProteinNames = 0x2, ///< List all relevant proteins, not just one.
+ fLocalAnnotsOnly = 0x4, ///< Never use related sequences' annotations.
/// Refrain from anything that could add substantial overhead.
- fNoExpensiveOps = fLocalAnnotsOnly,
- fGpipeMode = 0x8 ///< Use GPipe defaults.
+ fNoExpensiveOps = fLocalAnnotsOnly,
+ fGpipeMode = 0x8, ///< Use GPipe defaults.
+ fOmitTaxonomicName = 0x10 ///< Do not add organism suffix to proteins.
};
typedef int TUserFlags; ///< Binary "OR" of EUserFlags
@@ -179,6 +180,7 @@ private:
bool m_AllProtNames;
bool m_LocalAnnotsOnly;
bool m_GpipeMode;
+ bool m_OmitTaxonomicName;
/// seq-inst fields
bool m_IsNA;
@@ -202,9 +204,9 @@ private:
bool m_TSAMaster;
string m_MainTitle;
- CTempString m_GeneralStr;
- CTempString m_PatentCountry;
- CTempString m_PatentNumber;
+ string m_GeneralStr;
+ string m_PatentCountry;
+ string m_PatentNumber;
int m_PatentSequence;
@@ -230,6 +232,7 @@ private:
bool m_TPAExp;
bool m_TPAInf;
bool m_TPAReasm;
+ bool m_Unordered;
/// pdb block fields
CTempString m_PDBCompound;
@@ -237,6 +240,8 @@ private:
/// biosource fields
CConstRef<CBioSource> m_Source;
CTempString m_Taxname;
+ CTempString m_Genus;
+ CTempString m_Species;
bool m_Multispecies;
CBioSource::TGenome m_Genome;
bool m_IsPlasmid;
diff --git a/c++/include/objmgr/util/feature.hpp b/c++/include/objmgr/util/feature.hpp
index f9d9f6c..a1febb9 100644
--- a/c++/include/objmgr/util/feature.hpp
+++ b/c++/include/objmgr/util/feature.hpp
@@ -1,7 +1,7 @@
#ifndef FEAT__HPP
#define FEAT__HPP
-/* $Id: feature.hpp 467517 2015-05-14 11:25:58Z ivanov $
+/* $Id: feature.hpp 480957 2015-10-06 12:01:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -497,6 +497,67 @@ bool GetFeatureGeneBiotype(feature::CFeatTree ft,
CMappedFeat mf,
string& biotype);
+typedef enum {
+ eLocationInFrame_InFrame = 0,
+ eLocationInFrame_BadStart,
+ eLocationInFrame_BadStop,
+ eLocationInFrame_BadStartAndStop,
+ eLocationInFrame_NotIn
+} ELocationInFrame;
+
+/// Determines whether location loc is in frame with coding region cds
+/// @param cds coding region feature [in]
+/// @param loc location to compare to coding region
+/// @return enumerated return value indicates frame is good or either endpoint is bad
+ELocationInFrame NCBI_XOBJUTIL_EXPORT IsLocationInFrame (const CSeq_feat_Handle& cds, const CSeq_loc& loc);
+
+/// Promotes coding region from Seq-annot on nucleotide sequence to Seq-annot
+/// on nuc-prot-set if necessary and appropriate
+/// @param orig_feat coding region feature [in]
+/// @return enumerated return value indicates whether a change was made
+NCBI_XOBJUTIL_EXPORT bool PromoteCDSToNucProtSet(objects::CSeq_feat_Handle& orig_feat);
+
+/// AdjustFeaturePartialFlagForLocation
+/// A function to ensure that Seq-feat.partial is set if either end of the
+/// feature is partial, and clear if neither end of the feature is partial
+/// @param new_feat The feature to be adjusted (if necessary)
+///
+/// @return Boolean to indicate whether the feature was changed
+bool AdjustFeaturePartialFlagForLocation(CSeq_feat& new_feat);
+
+/// AdjustProteinFeaturePartialsToMatchCDS
+/// A function to change an existing MolInfo to match a coding region
+/// @param new_prot The protein feature to be adjusted (if necessary)
+/// @param cds The CDS to match
+///
+/// @return Boolean to indicate whether the protein feature was changed
+bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat& new_prot, const CSeq_feat& cds);
+
+/// AdjustProteinMolInfoToMatchCDS
+/// A function to change an existing MolInfo to match a coding region
+/// @param molinfo The MolInfo to be adjusted (if necessary)
+/// @param cds The CDS to match
+///
+/// @return Boolean to indicate whether molinfo was changed
+bool AdjustProteinMolInfoToMatchCDS(CMolInfo& molinfo, const CSeq_feat& cds);
+
+/// AdjustForCDSPartials
+/// A function to make all of the necessary related changes to
+/// a Seq-entry after the partialness of a coding region has been
+/// changed.
+/// @param cds The feature for which adjustments are to be made
+/// @param seh The Seq-entry-handle to be adjusted (if necessary)
+///
+/// @return Boolean to indicate whether the Seq-entry-handle was changed
+bool AdjustForCDSPartials(const CSeq_feat& cds, CSeq_entry_Handle seh);
+
+/// RetranslateCDS
+/// A function to replace the protein Bioseq pointed to by cds.product
+/// with the current translation of the coding region cds.
+/// @param cds The feature for which adjustments are to be made
+///
+/// @return Boolean to indicate whether the coding region was retranslated.
+bool RetranslateCDS(const CSeq_feat& cds, CScope& scope);
END_SCOPE(feature)
END_SCOPE(objects)
diff --git a/c++/include/objmgr/util/obj_sniff.hpp b/c++/include/objmgr/util/obj_sniff.hpp
index 91d2c2f..237317e 100644
--- a/c++/include/objmgr/util/obj_sniff.hpp
+++ b/c++/include/objmgr/util/obj_sniff.hpp
@@ -1,7 +1,7 @@
#ifndef OBJ_SNIFF__HPP
#define OBJ_SNIFF__HPP
-/* $Id: obj_sniff.hpp 462547 2015-03-19 14:01:05Z vasilche $
+/* $Id: obj_sniff.hpp 462343 2015-03-18 12:44:25Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/format/utils.hpp b/c++/include/objmgr/util/objutil.hpp
similarity index 92%
rename from c++/src/objtools/format/utils.hpp
rename to c++/include/objmgr/util/objutil.hpp
index 8e5b7a5..d5bf20a 100644
--- a/c++/src/objtools/format/utils.hpp
+++ b/c++/include/objmgr/util/objutil.hpp
@@ -1,7 +1,7 @@
-#ifndef OBJTOOLS_FORMAT___UTILS_HPP
-#define OBJTOOLS_FORMAT___UTILS_HPP
+#ifndef OBJMGR_UTIL___OBJUTILS_HPP
+#define OBJMGR_UTIL___OBJUTILS_HPP
-/* $Id: utils.hpp 434576 2014-05-08 16:38:48Z gotvyans $
+/* $Id: objutil.hpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,7 +70,9 @@ string JoinString(const list<string>& l,
// with one space. Strips all spaces after '(' and before ')'
void StripSpaces(string& str);
bool TrimSpacesAndJunkFromEnds(string& str, bool allow_ellipsis = false);
-void TrimSpaces(string& str, int indent = 0);
+void TrimSpacesAndJunkFromEnds(string& result, const CTempString& str, bool allow_ellipsis = false);
+void TrimSpaces(string& str, size_t indent = 0);
+void CleanAndCompress (string& dest, const CTempString& instr);
string &CompressSpaces( string& str, const bool trim_beginning = true, const bool trim_end = true );
bool RemovePeriodFromEnd(string& str, bool keep_ellipsis = true);
void AddPeriod(string& str);
@@ -124,7 +126,7 @@ struct SModelEvidance
TSpanType span; // start, then end. 0-based
SModelEvidance(void) :
- name(kEmptyStr), method(kEmptyStr), mrnaEv(false), estEv(false), gi(TGi(-1)), span(-1, -1)
+ name(kEmptyStr), method(kEmptyStr), mrnaEv(false), estEv(false), gi(INVALID_GI), span(-1, -1)
{}
};
@@ -192,7 +194,8 @@ bool ConvertQuotesNotInHTMLTags( string &str );
// We use the word "try" in the name because this is NOT airtight security,
// but rather a net that catches the majority of cases.
void TryToSanitizeHtml( std::string &str );
-void TryToSanitizeHtmlList( std::list<std::string> &strs );
+void TryToSanitizeHtml(std::string &result, const CTempString& str);
+void TryToSanitizeHtmlList(std::list<std::string> &strs);
bool CommentHasSuspiciousHtml( const string &str );
diff --git a/c++/include/objmgr/util/seq_loc_util.hpp b/c++/include/objmgr/util/seq_loc_util.hpp
index 84d7d3a..f6912a6 100644
--- a/c++/include/objmgr/util/seq_loc_util.hpp
+++ b/c++/include/objmgr/util/seq_loc_util.hpp
@@ -1,7 +1,7 @@
#ifndef SEQ_LOC_UTIL__HPP
#define SEQ_LOC_UTIL__HPP
-/* $Id: seq_loc_util.hpp 345950 2011-12-01 19:31:27Z kornbluh $
+/* $Id: seq_loc_util.hpp 451986 2014-11-13 20:13:31Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -175,14 +175,27 @@ bool BadSeqLocSortOrder(const CBioseq& seq,
*/
enum ECompare {
- eNoOverlap = 0, ///< CSeq_locs do not overlap
+ eNoOverlap = 0, ///< CSeq_locs do not overlap or abut
eContained, ///< First CSeq_loc contained by second
eContains, ///< First CSeq_loc contains second
eSame, ///< CSeq_locs contain each other
- eOverlap ///< CSeq_locs overlap
+ eOverlap, ///< CSeq_locs overlap
+
+ /// Abutting seq-locs. The flag can be returned only by the 4-argument
+ /// version of Compare() if fCompareAbutting flag is set in the
+ /// TCompareFlags argument.
+ eAbutting,
+ /// Seq-locs do both abut and overlap. The flag can be returned only by
+ /// the 4-argument version of Compare() if fCompareAbutting flag is set
+ /// in the TCompareFlags argument.
+ eAbutAndOverlap
};
-/// Returns the sequence::ECompare containment relationship between CSeq_locs
+/// Returns the sequence::ECompare containment relationship between CSeq_locs.
+/// For backward compatibility the function does not check for abutting
+/// seq-locs and never returns eAbutting or eAbutAndOverlap.
+/// @deprecated Use the new Compare() taking the additional TCompareFlags arg.
+NCBI_DEPRECATED
NCBI_XOBJUTIL_EXPORT
sequence::ECompare Compare(const CSeq_loc& loc1,
const CSeq_loc& loc2,
@@ -191,6 +204,34 @@ sequence::ECompare Compare(const CSeq_loc& loc1,
/* @} */
+/** @name Compare
+ * Check if the two CSeq_locs are abutting
+ * @{
+ */
+
+enum FCompareFlags {
+ /// Check if seq-locs are abutting (loc2 follows loc1)
+ fCompareAbutting = 1 << 0,
+ /// Check if seq-locs are overlapping
+ fCompareOverlapping = 1 << 1,
+ fCompareAll = fCompareAbutting | fCompareOverlapping,
+
+ /// Use positional coordinates (ignore strands) when looking for
+ /// abutting locations.
+ fComparePositional = 1 << 2
+};
+typedef int TCompareFlags;
+
+/// Compare the seq-locs. Depending on the selected flags the function
+/// checks if the seq-locs are abutting (loc2 immediately follows loc1),
+/// overlap (see ECompare) or both.
+NCBI_XOBJUTIL_EXPORT
+sequence::ECompare Compare(const CSeq_loc& loc1,
+ const CSeq_loc& loc2,
+ CScope* scope,
+ TCompareFlags flags);
+
+/* @} */
/** @name Change id
* Replace seq-id with the best or worst rank
* @{
diff --git a/c++/include/objmgr/util/sequence.hpp b/c++/include/objmgr/util/sequence.hpp
index d3d71fb..434fcc0 100644
--- a/c++/include/objmgr/util/sequence.hpp
+++ b/c++/include/objmgr/util/sequence.hpp
@@ -1,7 +1,7 @@
#ifndef SEQUENCE__HPP
#define SEQUENCE__HPP
-/* $Id: sequence.hpp 444616 2014-08-26 15:01:50Z ivanov $
+/* $Id: sequence.hpp 468762 2015-05-27 20:18:13Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -643,11 +643,17 @@ int GetTaxId(const CBioseq_Handle& handle);
/// Retrieve the MolInfo object for a given bioseq handle. If the supplied
/// sequence does not have a MolInfo associated with it, this will return NULL
NCBI_XOBJUTIL_EXPORT
+const CMolInfo* GetMolInfo(const CBioseq& bioseq);
+
+NCBI_XOBJUTIL_EXPORT
const CMolInfo* GetMolInfo(const CBioseq_Handle& handle);
/// Retrieve the BioSource object for a given bioseq handle. If the supplied
/// sequence does not have a MolInfo associated with it, this will return NULL
NCBI_XOBJUTIL_EXPORT
+const CBioSource* GetBioSource(const CBioseq& bioseq);
+
+NCBI_XOBJUTIL_EXPORT
const CBioSource* GetBioSource(const CBioseq_Handle& handle);
diff --git a/c++/include/objtools/align_format/align_format_util.hpp b/c++/include/objtools/align_format/align_format_util.hpp
index 02190d0..754489a 100644
--- a/c++/include/objtools/align_format/align_format_util.hpp
+++ b/c++/include/objtools/align_format/align_format_util.hpp
@@ -1,4 +1,4 @@
-/* $Id: align_format_util.hpp 438223 2014-06-13 14:49:45Z zaretska $
+/* $Id: align_format_util.hpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,7 +71,7 @@ static const char kEntrezUrl[] = "<a title=\"Show report for <@acc@>\" <@cssInf@
static const char kEntrezTMUrl[] = "http://www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>";
//.ncbirc alias: WGS
-static const char kWGSUrl[] = "http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=<@wgsproj@>&page=1&display=contig&search=<@wgsacc@>";
+static const char kWGSUrl[] = "http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=<@wgsproj@>&page=1&display=contigs&search=<@wgsacc@>";
///trace db
@@ -166,8 +166,8 @@ static const char kReprMicrobialGenomesImg[] = "<img border=0 height=16 width=16
//For text link <@lnk@> is substituted by formatted url
static const string kReprMicrobialGenomesDispl = "<div><@lnk@>-<span class=\"rlLink\">Genomic Sequence</span></div>";
-static const char kIdenticalProteinsUrl[] = "<a href=\"http://www.ncbi.nlm.nih.gov/protein?LinkName=protein_protein_identical&from_uid=<@gi@>&RID=<@rid@>&log$=identprot<@log@>&blast_rank=<@blast_rank@>\" title=\"View proteins identical to <@label@>\" <@lnkTarget@>><@lnk_displ@></a>";
-static const string kIdenticalProteinsDispl = "<div><@lnk@>-<span class=\"rlLink\">Proteins identical to the subject</span></div>";
+static const char kIdenticalProteinsUrl[] = "<a href=\"http://www.ncbi.nlm.nih.gov/protein/<@gi@>?report=ipg\" title=\"View proteins identical to <@label@>\" <@lnkTarget@>><@lnk_displ@></a>";
+static const string kIdenticalProteinsDispl = "<div><@lnk@>-<span class=\"rlLink\">Identical proteins to <@label@></span></div>";
///dumpgnl
@@ -482,6 +482,17 @@ public:
static void PrintTildeSepLines(string str, size_t line_len,
CNcbiOstream& out);
+ /// Fills one BLAST dbinfo structure.
+ /// Intended for use in bl2seq mode with multiple subject sequences.
+ /// database title set to "User specified sequence set"
+ /// @param retval return vector [in/out]
+ /// @param is_protein are these databases protein? [in]
+ /// @param numSeqs number of sequecnes in set [in]
+ /// @param numLetters size of the set [in]
+ /// @param tag Hint to user about subject sequences [in]
+ static void FillScanModeBlastDbInfo(vector<SDbInfo>& retval,
+ bool is_protein, int numSeqs, Int8 numLetters, string& tag);
+
/// Retrieve BLAST database information for presentation in BLAST report
/// @param dbname space-separated list of BLAST database names [in]
/// @param is_protein are these databases protein? [in]
@@ -1071,8 +1082,8 @@ public:
///@return:string containing template data replaced by real data
///
///<@tmplParamName@> is replaced by templParamVal
- static string MapTemplate(string inpString,string tmplParamName,int templParamVal);
-
+ static string MapTemplate(string inpString,string tmplParamName,Int8 templParamVal);
+
///Replace template tags by real data
///@param inpString: string containing template data
///@param tmplParamName:string with template tag name
@@ -1189,11 +1200,16 @@ public:
list<TGi>& use_this_gi,
TGi& gi);
- ///Check if accession is WGS
+ ///Check if accession is WGS
///@param accession: string accession [in]
///@param wgsProj: string wgsProj [out]
///@return: bool indicating if accession is WGS
- static bool IsWGSAccession(string &accession, string &wgsProj);
+ static bool IsWGSAccession(string &accession, string &wgsProj);
+
+ ///Check if accession is WGS
+ ///@param accession: string accession [in]
+ ///@return: bool indicating if accession is WGS
+ static bool IsWGSPattern(string &wgsAccession);
///Get Gene symobol for gi
///@param giForGeneLookup: gi
@@ -1203,6 +1219,9 @@ public:
static bool m_geturl_debug_flag;
static auto_ptr<CGeneInfoFileReader> m_GeneInfoReader;
+ /// Calculate the uniq subject query coverage range (blastn only)
+ static int GetUniqSeqCoverage(objects::CSeq_align_set & alnset);
+
protected:
///Wrap a string to specified length. If break happens to be in
diff --git a/c++/include/objtools/align_format/format_flags.hpp b/c++/include/objtools/align_format/format_flags.hpp
index d8bbcbe..cbddb93 100644
--- a/c++/include/objtools/align_format/format_flags.hpp
+++ b/c++/include/objtools/align_format/format_flags.hpp
@@ -1,4 +1,4 @@
-/* $Id: format_flags.hpp 439436 2014-06-30 13:51:29Z fongah2 $
+/* $Id: format_flags.hpp 485058 2015-11-18 16:06:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -124,6 +124,7 @@ enum ETabularField {
eSubjectStrand, ///< Subject Strand
eQueryCovSubject, ///< Query Coverage per Subject
eQueryCovSeqalign, ///< Query Coverage per Seqalign
+ eQueryCovUniqSubject, ///< Query Coverage per Subject
eMaxTabularField ///< Sentinel value
};
@@ -153,6 +154,34 @@ NCBI_ALIGN_FORMAT_EXPORT extern const size_t kNumTabularOutputFormatSpecifiers;
/// Returns a string documenting the available format specifiers
NCBI_ALIGN_FORMAT_EXPORT string DescribeTabularOutputFormatSpecifiers(bool is_igblast=false);
+enum ESAMField {
+ eSAM_SeqData = 0 ///< Include seq data
+};
+
+struct SSAMFormatSpec {
+ /// Format specification name
+ string name;
+ /// A description of what the above name represents
+ string description;
+ /// Enumeration that corresponds to this field
+ ESAMField field;
+
+ /// Constructor
+ /// @param n format specification name [in]
+ /// @param d format specification description [in]
+ /// @param f enumeration value [in]
+ SSAMFormatSpec(string n, string d, ESAMField f)
+ : name(n), description(d), field(f) {}
+};
+
+/// Array containing the supported output formats for SAM output.
+NCBI_ALIGN_FORMAT_EXPORT extern const SSAMFormatSpec sc_SAMFormatSpecifiers[];
+/// Number of elements in the sc_SAMFormatSpecifiers array.
+NCBI_ALIGN_FORMAT_EXPORT extern const size_t kNumSAMOutputFormatSpecifiers;
+
+/// Returns a string documenting the available format specifiers
+NCBI_ALIGN_FORMAT_EXPORT string DescribeSAMOutputFormatSpecifiers();
+
END_SCOPE(align_format)
END_NCBI_SCOPE
diff --git a/c++/include/objtools/align_format/seqalignfilter.hpp b/c++/include/objtools/align_format/seqalignfilter.hpp
index eb38fff..b5c8ea7 100644
--- a/c++/include/objtools/align_format/seqalignfilter.hpp
+++ b/c++/include/objtools/align_format/seqalignfilter.hpp
@@ -1,4 +1,4 @@
-/* $Id: seqalignfilter.hpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: seqalignfilter.hpp 482392 2015-10-22 16:37:19Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -180,7 +180,7 @@ public:
void ReadGiList(const string& fname, list<TGi>& list_gis, bool sorted = false);
/// Read a gi vector from a file and, optionally, sort it.
- void ReadGiVector(const string& fname, vector<int>& vec_gis, bool sorted = false);
+ void ReadGiVector(const string& fname, vector<TGi>& vec_gis, bool sorted = false);
private:
//--- Internal methods ---//
diff --git a/c++/include/objtools/align_format/tabular.hpp b/c++/include/objtools/align_format/tabular.hpp
index 4316744..1e826f6 100644
--- a/c++/include/objtools/align_format/tabular.hpp
+++ b/c++/include/objtools/align_format/tabular.hpp
@@ -1,4 +1,4 @@
-/* $Id: tabular.hpp 446201 2014-09-12 13:53:23Z ivanov $
+/* $Id: tabular.hpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -288,9 +288,11 @@ protected:
void x_PrintSubjectStrand();
void x_PrintSeqalignCoverage();
void x_PrintSubjectCoverage();
+ void x_PrintUniqSubjectCoverage();
void x_SetTaxInfo(const objects::CBioseq_Handle & handle, const CRef<objects::CBlast_def_line_set> & bdlRef);
void x_SetSubjectIds(const objects::CBioseq_Handle& bh, const CRef<objects::CBlast_def_line_set> & bdlRef);
void x_SetQueryCovSubject(const objects::CSeq_align & align);
+ void x_SetQueryCovUniqSubject(const objects::CSeq_align & align);
void x_SetQueryCovSeqalign(const CSeq_align & align, int query_len);
void x_CheckTaxDB();
@@ -341,6 +343,7 @@ private:
string m_SubjectStrand;
pair<string, int> m_QueryCovSubject;
+ pair<string, int> m_QueryCovUniqSubject;
int m_QueryCovSeqalign;
int m_QueryGeneticCode;
@@ -404,7 +407,7 @@ inline void CBlastTabularInfo::x_PrintPercentIdentical(void)
{
double perc_ident =
(m_AlignLength > 0 ? ((double)m_NumIdent)/m_AlignLength * 100 : 0);
- m_Ostream << NStr::DoubleToString(perc_ident, 2);
+ m_Ostream << NStr::DoubleToString(perc_ident, 3);
}
inline void CBlastTabularInfo::x_PrintPercentPositives(void)
diff --git a/c++/include/objtools/alnmgr/aln_converters.hpp b/c++/include/objtools/alnmgr/aln_converters.hpp
index fea15c8..05268e4 100644
--- a/c++/include/objtools/alnmgr/aln_converters.hpp
+++ b/c++/include/objtools/alnmgr/aln_converters.hpp
@@ -1,6 +1,6 @@
#ifndef OBJTOOLS_ALNMGR___ALN_CONVERTERS__HPP
#define OBJTOOLS_ALNMGR___ALN_CONVERTERS__HPP
-/* $Id: aln_converters.hpp 369976 2012-07-25 15:20:22Z grichenk $
+/* $Id: aln_converters.hpp 467310 2015-05-12 17:51:21Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -277,9 +277,17 @@ CRef<CAnchoredAln> CreateAnchoredAlnFromAln(
}
}
+ const CSeq_align& seq_aln = *aln_stats.GetAlnVec()[aln_idx];
// Flags
int anchor_flags = CPairwiseAln::fKeepNormalized;
- int flags = CPairwiseAln::fKeepNormalized | CPairwiseAln::fAllowMixedDir;
+ int flags = CPairwiseAln::fKeepNormalized |
+ CPairwiseAln::fAllowMixedDir;
+ if ( seq_aln.GetSegs().IsStd() ) {
+ // Std-segs may contain overlaps (in this case the alignment will be split
+ // into segments later).
+ anchor_flags |= CPairwiseAln::fAllowOverlap;
+ flags |= CPairwiseAln::fAllowOverlap;
+ }
if ((options.m_MergeFlags & CAlnUserOptions::fIgnoreInsertions) != 0) {
anchor_flags |= CPairwiseAln::fIgnoreInsertions;
@@ -288,7 +296,7 @@ CRef<CAnchoredAln> CreateAnchoredAlnFromAln(
// Create pairwises
typedef typename _TAlnStats::TIdVec TIdVec;
- TIdVec ids = aln_stats.GetSeqIdsForAln(aln_idx);
+ const TIdVec ids = aln_stats.GetSeqIdsForAln(aln_idx);
CAnchoredAln::TPairwiseAlnVector pairwises;
pairwises.resize(dim);
int empty_rows = 0;
@@ -298,12 +306,10 @@ CRef<CAnchoredAln> CreateAnchoredAlnFromAln(
row == anchor_row ? anchor_flags : flags));
ConvertSeqAlignToPairwiseAln(
- *pairwise_aln,
- *aln_stats.GetAlnVec()[aln_idx],
- anchor_row,
- row,
+ *pairwise_aln, seq_aln,
+ anchor_row, row,
row == anchor_row ? CAlnUserOptions::eDirect : options.m_Direction,
- &aln_stats.GetSeqIdsForAln(aln_idx));
+ &ids);
if ( force_widths ) {
// Need to convert coordinates to genomic.
@@ -363,17 +369,63 @@ void CreateAnchoredAlnVec(_TAlnStats& aln_stats,
for (size_t aln_idx = 0; aln_idx < aln_stats.GetAlnCount(); ++aln_idx) {
CRef<CAnchoredAln> anchored_aln =
CreateAnchoredAlnFromAln(aln_stats, aln_idx, options);
-
- if ( anchored_aln ) {
- out_vec.push_back(anchored_aln);
- // Calc scores
- for (typename _TAlnStats::TDim row = 0; row < anchored_aln->GetDim(); ++row) {
- ITERATE(CPairwiseAln, rng_it, *anchored_aln->GetPairwiseAlns()[row]) {
- anchored_aln->SetScore() += rng_it->GetLength();
+ if ( !anchored_aln ) continue;
+
+ const CSeq_align& aln = *aln_stats.GetAlnVec()[aln_idx];
+ if (aln.GetSegs().IsStd()) {
+ bool need_split = false;
+ ITERATE(CAnchoredAln::TPairwiseAlnVector, it, anchored_aln->GetPairwiseAlns()) {
+ const CPairwiseAln& pw = **it;
+ if (pw.IsSet(CPairwiseAln::fMixedDir) ||
+ pw.IsSet(CPairwiseAln::fOverlap)) {
+ need_split = true;
+ break;
+ }
+ }
+ if (need_split) {
+ // The std-seg contains overlaps and needs to be split into
+ // separate rows/segments.
+ CAnchoredAln::TDim anchor_row = anchored_aln->GetAnchorRow();
+ const CPairwiseAln& apw = *anchored_aln->GetPairwiseAlns()[anchor_row];
+ for (CAnchoredAln::TDim row = 0; row < anchored_aln->GetDim(); ++row) {
+ if (row == anchor_row) continue;
+ const CPairwiseAln& rpw = *anchored_aln->GetPairwiseAlns()[row];
+ for (size_t seg = 0; seg < rpw.size(); ++seg) {
+ CRef<CAnchoredAln> sub_anchored_aln(new CAnchoredAln);
+ sub_anchored_aln->SetPairwiseAlns().resize(2);
+ sub_anchored_aln->SetDim(2);
+ CRef<CPairwiseAln> sub_row(new CPairwiseAln(
+ rpw.GetFirstId(), rpw.GetSecondId(), rpw.GetPolicyFlags()));
+ sub_row->insert(sub_row->end(), rpw[seg]);
+ CRef<CPairwiseAln> sub_anchor_row(new CPairwiseAln(
+ apw.GetFirstId(), apw.GetSecondId(), apw.GetPolicyFlags()));
+ sub_anchor_row->insert(sub_anchor_row->end(), apw[seg]);
+ if (anchor_row == 0) {
+ sub_anchored_aln->SetAnchorRow(0);
+ sub_anchored_aln->SetPairwiseAlns()[0] = sub_anchor_row;
+ sub_anchored_aln->SetPairwiseAlns()[1] = sub_row;
+ }
+ else {
+ sub_anchored_aln->SetAnchorRow(1);
+ sub_anchored_aln->SetPairwiseAlns()[0] = sub_row;
+ sub_anchored_aln->SetPairwiseAlns()[1] = sub_anchor_row;
+ }
+ out_vec.push_back(sub_anchored_aln);
+ sub_anchored_aln->SetScore(rpw[seg].GetLength());
+ }
}
+ continue; // Done splitting std-seg
+ }
+ }
+
+ out_vec.push_back(anchored_aln);
+ // Calc scores
+ for (typename _TAlnStats::TDim row = 0; row < anchored_aln->GetDim(); ++row) {
+ ITERATE(CPairwiseAln, rng_it, *anchored_aln->GetPairwiseAlns()[row]) {
+ anchored_aln->SetScore() += rng_it->GetLength();
}
- anchored_aln->SetScore() /= anchored_aln->GetDim();
}
+ anchored_aln->SetScore() /= anchored_aln->GetDim();
}
}
diff --git a/c++/include/objtools/alnmgr/seqids_extractor.hpp b/c++/include/objtools/alnmgr/seqids_extractor.hpp
index 6edf763..43a0128 100644
--- a/c++/include/objtools/alnmgr/seqids_extractor.hpp
+++ b/c++/include/objtools/alnmgr/seqids_extractor.hpp
@@ -1,6 +1,6 @@
#ifndef OBJTOOLS_ALNMGR___SEQIDS_EXTRACTOR__HPP
#define OBJTOOLS_ALNMGR___SEQIDS_EXTRACTOR__HPP
-/* $Id: seqids_extractor.hpp 446395 2014-09-15 17:58:05Z ivanov $
+/* $Id: seqids_extractor.hpp 445727 2014-09-08 13:02:39Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/blast/blastdb_format/blastdb_seqid.hpp b/c++/include/objtools/blast/blastdb_format/blastdb_seqid.hpp
index 0713911..1358a0e 100644
--- a/c++/include/objtools/blast/blastdb_format/blastdb_seqid.hpp
+++ b/c++/include/objtools/blast/blastdb_format/blastdb_seqid.hpp
@@ -1,4 +1,4 @@
-/* $Id: blastdb_seqid.hpp 165919 2009-07-15 16:50:05Z avagyanv $
+/* $Id: blastdb_seqid.hpp 443490 2014-08-14 19:35:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -94,7 +94,7 @@ public:
string retval;
switch (m_EntryChoice) {
case ePig: retval = "PIG " + NStr::IntToString(GetPig()); break;
- case eGi: retval = "GI " + NStr::IntToString(GetGi()); break;
+ case eGi: retval = "GI " + NStr::NumericToString(GetGi()); break;
case eSeqId: retval = "'" + GetStringId() + "'"; break;
case eNone:
if (GetOID() != CBlastDBSeqId::kInvalid) {
@@ -125,7 +125,7 @@ public:
bool IsOID() const { return m_EntryChoice == eNone || m_OID != kInvalid; }
/// Retrieve this object's GI
- int GetGi() const { return m_EntrySpecified.m_GI; }
+ TIntId GetGi() const { return m_EntrySpecified.m_GI; }
/// Retrieve this object's PIG
int GetPig() const { return m_EntrySpecified.m_PIG; }
/// Retrieve this object's string identifier
@@ -154,7 +154,7 @@ private:
/// Union to hold the memory of the data stored
union {
int m_PIG; ///< Store a PIG
- int m_GI; ///< Store a GI
+ TIntId m_GI; ///< Store a GI
string* m_SequenceId; ///< Store a sequence identifier as a string
} m_EntrySpecified;
diff --git a/c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp b/c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
index 9322258..fd41afa 100644
--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS_SEQDB__SEQDBATLAS_HPP
#define OBJTOOLS_READERS_SEQDB__SEQDBATLAS_HPP
-/* $Id: seqdbatlas.hpp 400237 2013-05-20 15:28:07Z maning $
+/* $Id: seqdbatlas.hpp 463291 2015-03-26 14:57:38Z rackerst $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// @file seqdbatlas.hpp
/// The SeqDB memory management layer.
-///
+///
/// Defines classes:
/// CSeqDBFlushCB
/// CSeqDBLockHold
@@ -44,7 +44,7 @@
/// CSeqDB_AtlasRegionHolder
/// CSeqDBAtlas
/// CSeqDBAtlasHolder
-///
+///
/// Implemented for: UNIX, MS-Windows
@@ -158,7 +158,7 @@ string SeqDB_MakeOSPath(const string & dbs);
/// CSeqDBFlushCB
-///
+///
/// This abstract class defines an interface which can be called to
/// free unused regions of Atlas managed memory. If a class derived
/// from this interface is provide to the atlas constructor, it will
@@ -169,7 +169,7 @@ string SeqDB_MakeOSPath(const string & dbs);
class CSeqDBFlushCB {
public:
/// Flush held memory references.
- ///
+ ///
/// This class should be subclassed, and this method overloaded to
/// flush held memory that is not in use. Normally, this amounts
/// to calling the Clear() method on any CSeqDBMemLease objects
@@ -181,9 +181,9 @@ public:
/// the released slices will require searching for the correct
/// memory block. If that block was deleted, it will be remapped,
/// which may trigger another garbage collection.
-
+
virtual void operator()() = 0;
-
+
/// Destructor to avoid warnings.
virtual ~CSeqDBFlushCB() {}
};
@@ -196,7 +196,7 @@ class CSeqDBMemLease;
/// CSeqDBLockHold
-///
+///
/// This class is used to keep track of whether this thread holds the
/// atlas lock. The atlas code will skip subsequent Lock() operations
/// during the same transaction if the lock is already held. This
@@ -208,7 +208,7 @@ class CSeqDBMemLease;
class CSeqDBLockHold {
public:
/// Constructor
- ///
+ ///
/// This object constructs to an unlocked state, which means that
/// the thread owning the stack frame where this object is stored
/// does not hold the atlas lock. This object keeps a reference
@@ -222,47 +222,47 @@ public:
{
INIT_CLASS_MARK();
}
-
+
/// Get a hold a region of memory.
void HoldRegion(CSeqDBMemLease & lease);
-
+
/// Destructor
- ///
+ ///
/// The class will unlock the atlas's lock on destruction (if it
/// is the owner of that lock).
~CSeqDBLockHold();
-
+
private:
CLASS_MARKER_FIELD("LHLD")
-
+
/// Private method to prevent copy construction.
CSeqDBLockHold(CSeqDBLockHold & oth);
CSeqDBLockHold& operator=(CSeqDBLockHold & oth);
-
+
/// Only the atlas code is permitted to modify this object - it
/// does so simply by editing the m_Locked member as needed.
friend class CSeqDBAtlas;
-
+
/// This reference allows unlock on exit.
class CSeqDBAtlas & m_Atlas;
-
+
/// These are memory leases that should not flush during GC.
vector<CRegionMap*> m_Holds;
-
+
/// If this is true, this thread owns the atlas lock.
bool m_Locked;
};
/// CSeqDBMemReg
-///
+///
/// This class is used to keep track of bytes allocated externally to
/// the atlas, but included under its memory bound.
class CSeqDBMemReg {
public:
/// Constructor
- ///
+ ///
/// This object constructs to an empty state, which means that the
/// atlas does not consider this object to "own" any bytes.
///
@@ -273,31 +273,31 @@ public:
m_Bytes(0)
{
}
-
+
/// Destructor
- ///
+ ///
/// The class will unlock the atlas's lock on destruction (if it
/// is the owner of that lock).
inline ~CSeqDBMemReg();
-
+
private:
/// Private method to prevent copy construction.
CSeqDBMemReg(CSeqDBMemReg & oth);
-
+
/// Only the atlas code is permitted to modify this object - it
/// does so simply by editing the m_Locked member as needed.
friend class CSeqDBAtlas;
-
+
/// This reference allows unlock on exit.
class CSeqDBAtlas & m_Atlas;
-
+
/// This object "owns" this many bytes of the atlas memory bound.
size_t m_Bytes;
};
/// CRegionMap
-///
+///
/// This object stores data relevant to a mapped portion of a file.
/// The mapped area may be a memory map or an allocated buffer filled
/// with data read from a file. It also remembers some garbage
@@ -309,9 +309,9 @@ class CRegionMap {
public:
/// The type used for file offsets.
typedef CNcbiStreamoff TIndx;
-
+
/// Constructor
- ///
+ ///
/// Initializes the object, storing the provided filename, file
/// id, and byte range. This object does not own the string
/// containing the filename, and does not map any memory or
@@ -328,14 +328,30 @@ public:
int fid,
TIndx begin,
TIndx end);
-
+
+ /// Set the mmap strategy for index files
+ static void SetMmapStrategy_Index(
+ EMemoryAdvise strategy
+ )
+ {
+ sm_MmapStrategy_Index = strategy;
+ }
+
+ /// Set the mmap strategy for sequence files
+ static void SetMmapStrategy_Sequence(
+ EMemoryAdvise strategy
+ )
+ {
+ sm_MmapStrategy_Sequence = strategy;
+ }
+
/// Destructor
- ///
+ ///
/// Frees or unmaps any memory associated with this region.
~CRegionMap();
-
+
/// Memory map a region of a file
- ///
+ ///
/// This uses CMemoryFile to map the file region associated with
/// this object. The range of memory may be rounded up to the
/// nearest slice boundary, and may trigger (atlas's) garbage
@@ -344,15 +360,15 @@ public:
/// the memory bound requirements are not acheivable, but this
/// will probably result in performance degradation due to
/// thrashing atlas's garbage collector.
- ///
+ ///
/// @param atlas
/// Pointer to the atlas.
/// @return
/// Returns true if the mapping succeeded.
bool MapMmap(CSeqDBAtlas * atlas);
-
+
/// Read a region of a file into memory
- ///
+ ///
/// This uses CNcbiIfstream to read the file region associated
/// with this object into an allocated memory block. The range of
/// memory may be rounded up (but only to the nearest block
@@ -362,15 +378,15 @@ public:
/// requirements are not acheivable, but this will probably result
/// in performance degradation due to thrashing atlas's garbage
/// collector.
- ///
+ ///
/// @param atlas
/// Pointer to the atlas.
/// @return
/// Returns true if the read succeeded.
bool MapFile(CSeqDBAtlas * atlas);
-
+
/// Increment this region's reference count.
- ///
+ ///
/// This increments the count of "users" associated with this
/// region. When too much memory is used, memory regions may be
/// freed. This process (garbage collection) will skip over any
@@ -384,9 +400,9 @@ public:
m_Ref ++;
m_Clock = 0;
}
-
+
/// Decrement this region's reference count.
- ///
+ ///
/// This decrements the count of "users" associated with this
/// region. If the count becomes zero, the region becomes
/// available for the next run of garbage collection. This method
@@ -399,13 +415,13 @@ public:
cout << "refcount non-positive = " << m_Ref << endl;
}
#endif
-
+
_ASSERT(m_Ref > 0);
m_Ref --;
}
-
+
/// Return true if memory region is in use.
- ///
+ ///
/// This returns true if any users (normally, CSeqMemLease
/// objects) are holding a reference on this memory region.
///
@@ -416,14 +432,14 @@ public:
CHECK_MARKER();
return m_Ref != 0;
}
-
+
/// Return true if memory region contains the pointer.
- ///
+ ///
/// This method returns true if the specified pointer points to a
/// character in the memory area managed by this object. It is
/// used to find the region to decrement when a user provides a
/// region to "give back".
- ///
+ ///
/// @return
/// true if this memory region contains the pointer
bool InRange(const char * p) const
@@ -432,9 +448,9 @@ public:
_ASSERT(m_Data);
return ((p >= m_Data) && (p < (m_Data + (m_End - m_Begin))));
}
-
+
/// Return the name of the file.
- ///
+ ///
/// Provides the name of the file from which this data was
/// obtained.
///
@@ -445,12 +461,12 @@ public:
CHECK_MARKER();
return *m_Fname;
}
-
+
/// Return the beginning offset of this region.
- ///
+ ///
/// Provides the file offset corresponding to the beginning of
/// this mapping.
- ///
+ ///
/// @return
/// The index of the beginning of this mapping.
TIndx Begin()
@@ -458,12 +474,12 @@ public:
CHECK_MARKER();
return m_Begin;
}
-
+
/// Return the end offset of this region.
- ///
+ ///
/// Provides the file offset corresponding to the end of this
/// mapping.
- ///
+ ///
/// @return
/// The index of the end of this mapping.
TIndx End()
@@ -471,21 +487,21 @@ public:
CHECK_MARKER();
return m_End;
}
-
+
/// Return the length of this mapping in bytes.
TIndx Length()
{
CHECK_MARKER();
return m_End - m_Begin;
}
-
+
/// Get a pointer to a section of this data.
- ///
+ ///
/// This method takes an offset range (start and end), and returns
/// a pointer to the data at the start offset. The offsets are
/// relative to the file, not the region. The end offset is only
/// used to check that the region contains the entire range.
- ///
+ ///
/// @param begin
/// The offset of the first required byte.
/// @param end
@@ -493,12 +509,12 @@ public:
/// @return
/// A pointer to the beginning of the requested data.
const char * Data(TIndx begin, TIndx end);
-
+
/// Get a pointer to all data in this region.
- ///
+ ///
/// This method returns a pointer to the data at the start offset
/// of this region.
- ///
+ ///
/// @return
/// A pointer to the beginning of the region's data.
const char * Data()
@@ -506,14 +522,14 @@ public:
CHECK_MARKER();
return m_Data;
}
-
+
/// Return the file id associated with this region.
- ///
+ ///
/// This method returns an integer used to identify this file
/// within the atlas code. The integer used here is uniquely
/// associated with the filename (but costs slightly fewer CPU
/// cycles during certain common operations).
- ///
+ ///
/// @return
/// An integer identifying the file this mapping is of.
int Fid()
@@ -521,9 +537,9 @@ public:
CHECK_MARKER();
return m_Fid;
}
-
+
/// Get the garbage collection clock value.
- ///
+ ///
/// This method is used by the atlas code's garbage collection
/// routine. The clock concept is borrowed from certain operating
/// system paging techniques, and is described further in the
@@ -531,7 +547,7 @@ public:
/// plus a penalty, which is used to preferentially page out
/// regions with undesireable "shapes", e.g. that don't have a
/// size of exactly one (large) slice.
- ///
+ ///
/// @return
/// The clock value plus the penalty for this region.
int GetClock()
@@ -539,9 +555,9 @@ public:
CHECK_MARKER();
return m_Clock + m_Penalty;
}
-
+
/// Increase the garbage collection clock count.
- ///
+ ///
/// This method increments the clock value, used by the atlas
/// code's garbage collection routine. This method should never
/// be called on an in-use region. The higher the clock value
@@ -553,9 +569,9 @@ public:
_ASSERT(! m_Ref);
m_Clock++;
}
-
+
/// Test and select this region if the arguments match.
- ///
+ ///
/// This method takes arguments describing a section of a file.
/// If this region has the same fid, and the byte range of this
/// region encompasses the specified range, then the reference
@@ -564,7 +580,7 @@ public:
/// beginning of the requested portion of the region. This method
/// also returns a pointer to the beginning of the input range
/// (before adjusting begin and end).
- ///
+ ///
/// @param fid
/// The number identifying this file to the atlas code.
/// @param begin
@@ -580,16 +596,16 @@ public:
TIndx & begin,
TIndx & end,
const char ** start);
-
+
/// In debugging / verbose code, dump information about this
/// memory region object.
void Show();
-
+
/// Get the data pointer and offset range of this region.
- ///
+ ///
/// This method returns a pointer to this region's data, and the
/// beginning and ending offsets of the region.
- ///
+ ///
/// @param region_start
/// Returns the address of the region data.
/// @param begin_offset
@@ -605,39 +621,39 @@ public:
begin_offset = m_Begin;
end_offset = m_End;
}
-
+
/// Less-than operator.
- ///
+ ///
/// This method defines an partial ordering over CRegionMap
/// objects. The order defined here places the objects in
/// ascending order by fid, then start offset, then region size
/// (equivalently, end offset). The ordering is partial because
/// two region maps could have identical parameters. However,
/// this should never happen for the atlas code as defined.
- ///
+ ///
/// @param other
/// The other region map to compare with.
/// @return
/// True if this object is before "other" in the ordering.
inline bool operator < (const CRegionMap & other) const;
-
+
/// Verify the marker values (only in debug mode).
void Verify()
{
#ifdef _DEBUG
// Cannot do too much, as the client code creates a CRegionMap
// to use as a key, and it will not be completely specified.
-
+
CHECK_MARKER();
_ASSERT(m_Begin < m_End);
#endif
}
-
+
private:
CLASS_MARKER_FIELD("REGM")
-
+
/// Compute the penalty and the expanded offset range.
- ///
+ ///
/// The files are normally divided into "slices". When a mapping
/// request asks for a specific range of offsets, we attempt to
/// expand the offset range to the entire slice that contains the
@@ -647,7 +663,7 @@ private:
/// mapping is thought to be. Mapping one whole slice gets a
/// value of zero. Partial slices, areas overlapping the ends of
/// two slices, and other anomalies get higher penalties.
- ///
+ ///
/// @param begin
/// The starting offset (this method may adjust it).
/// @param end
@@ -666,38 +682,44 @@ private:
TIndx file_size,
bool use_mmap,
CSeqDBAtlas * atlas);
-
+
/// Pointer to allocated or mapped memory area.
const char * m_Data;
-
+
/// The memory mapped file object.
CMemoryFileMap * m_MemFile;
-
+
/// Pointer to the filename (this object does not own it).
const string * m_Fname;
-
+
/// The file offset of the start of the region.
TIndx m_Begin;
-
+
/// The file offset of the end of the region.
TIndx m_End;
-
+
/// An integer identifying this object to the atlas code.
int m_Fid;
-
+
/// Number of current users of this object.
int m_Ref;
-
+
/// GC uses this to rank how recently this range was used.
int m_Clock;
-
+
/// Adjustment to m_Clock to bias region collection.
int m_Penalty;
+
+ /// Index file mmap strategy.
+ static EMemoryAdvise sm_MmapStrategy_Index;
+
+ /// Sequence file mmap strategy.
+ static EMemoryAdvise sm_MmapStrategy_Sequence;
};
/// CSeqDBMemLease
-///
+///
/// This object holds a reference on a region of memory managed by the
/// atlas code, and prevent the region from being unmapped. This
/// allows for rapid access to that memory for the duration of the
@@ -712,11 +734,11 @@ class CSeqDBMemLease {
public:
/// The type used for file offsets.
typedef CRegionMap::TIndx TIndx;
-
+
/// Constructor
- ///
+ ///
/// Initializes a memory lease object.
- ///
+ ///
/// @param atlas
/// The main atlas pointer.
CSeqDBMemLease(CSeqDBAtlas & atlas)
@@ -728,9 +750,9 @@ public:
{
INIT_CLASS_MARK();
}
-
+
/// Destructor
- ///
+ ///
/// Verifies this object is not active at time of destruction.
~CSeqDBMemLease()
{
@@ -738,20 +760,20 @@ public:
_ASSERT(m_Data == 0);
BREAK_MARKER();
}
-
+
/// Clears the lease object.
- ///
+ ///
/// This method releases the reference count on the held region .
/// It assumes the lock is held.
inline void Clear();
-
+
/// Check whether the held area includes an offset range.
- ///
+ ///
/// This checks whether the region associated with this object
/// already encompasses the desired offset range. If so, there is
/// no need to call GetRegion, because you can already access it
/// from this object. It assumes the atlas lock is held.
- ///
+ ///
/// @param begin
/// Start of the offset range.
/// @param end
@@ -759,7 +781,7 @@ public:
/// @return
/// Returns true if the held region includes the offset range.
inline bool Contains(TIndx begin, TIndx end) const;
-
+
/// Get a pointer to the internal region map.
///
/// @return
@@ -768,12 +790,12 @@ public:
{
return m_RMap;
}
-
+
/// Get a pointer to the specified offset.
- ///
+ ///
/// Given an offset (which is assumed to be available here), this
/// method returns a pointer to the data at that offset.
- ///
+ ///
/// @param offset
/// The required offset relative to the start of the file.
/// @return
@@ -783,12 +805,12 @@ public:
CHECK_MARKER();
return (m_Data + (offset - m_Begin));
}
-
+
/// Return true if this object is inactive.
- ///
+ ///
/// An active object holds a reference to a region of a file.
/// This method returns true if this object is not active.
- ///
+ ///
/// @return
/// true, if this object does not hold a reference.
bool Empty() const
@@ -796,13 +818,13 @@ public:
CHECK_MARKER();
return m_Data == 0;
}
-
+
/// Verify the integrity of this object.
void Verify() const
{
CHECK_MARKER();
}
-
+
/// Get another reference to the held CRegionMap object.
///
/// To call this method, this object must be active (already hold
@@ -815,23 +837,23 @@ public:
/// and when the user returns the pointer to the region to CSeqDB,
/// the atlas code will find the region and decrement the count.
inline void IncrementRefCnt();
-
+
private:
CLASS_MARKER_FIELD("LEAS")
-
+
/// This method is declared private to prevent copy construction.
CSeqDBMemLease(const CSeqDBMemLease & ml);
-
+
/// This method is declared private to prevent assignment.
CSeqDBMemLease & operator =(const CSeqDBMemLease & ml);
-
+
/// Active the region, setting its data members.
- ///
+ ///
/// When the GetRegion call returns a region in a MemLease object,
/// it increments the reference count, and calls this method to
/// populate this object with the summary data it needs. This
/// method is private so that only the atlas object can call it.
- ///
+ ///
/// @param begin
/// The starting offset of the area this lease can access.
/// @param end
@@ -847,35 +869,35 @@ private:
{
CHECK_MARKER();
Clear();
-
+
m_Data = data;
m_Begin = begin;
m_End = end;
m_RMap = rmap;
}
-
+
/// Access to the private data is restricted to the atlas code.
friend class CSeqDBAtlas;
-
+
/// The atlas associated with this object.
CSeqDBAtlas & m_Atlas;
-
+
/// Points to the beginning of the data area.
const char * m_Data;
-
+
/// Start offset of the data relative to the start of the file.
TIndx m_Begin;
-
+
/// End offset of the data relative to the start of the file.
TIndx m_End;
-
- /// Points to the object that manages the file region.
+
+ /// Points to the object that manages the file region.
class CRegionMap * m_RMap;
};
/// CSeqDBMovingAverage
-///
+///
/// This implements an exponentially smoothed moving average, which is
/// a technique for smoothing a noisy scalar measurement.
@@ -896,35 +918,35 @@ public:
m_Average(start)
{
}
-
+
/// Add a new measurement.
/// @param value The new measurement.
void AddData(double value)
{
// Each esma is a weighted average of the last esma and the
// new measurement.
-
+
m_Average *= m_Ratio;
m_Average += (value * (1.0 - m_Ratio));
}
-
+
/// Get the current moving average.
double GetAverage() const
{
return m_Average;
}
-
+
private:
/// Ratio of smoothness.
double m_Ratio;
-
+
/// Current value.
double m_Average;
};
/// CSeqDBMapStrategy
-///
+///
/// Some SeqDB clients access OIDs in sequential order; others tend to
/// follow a random access pattern. This class attempts to implement
/// a kind of self-tuning for SeqDB based on client access patterns.
@@ -935,10 +957,10 @@ class CSeqDBMapStrategy {
public:
/// The type used for file offsets.
typedef Int8 TIndx;
-
+
/// Maximum memory: 256 GB for 64 bits.
static const Int8 e_MaxMemory64;
-
+
enum {
// On Linux, malloc() uses mmap() for large requests, which
// means that the heap can shrink when free() is called. In
@@ -946,70 +968,70 @@ public:
// using a large memory bound and handling map failures in
// certain routines. This can cause stack exhaustion on other
// platforms, so it is only currently enabled for Linux.
-
+
#if defined(NCBI_OS_LINUX)
/// Probe address space with special allocations.
e_ProbeMemory = true,
-
+
/// Maximum memory: 2 GB for non-WinOS, 32 bit systems.
e_MaxMemory32 = 768 << 20,
#else
/// Probe address space with special allocations.
e_ProbeMemory = false,
-
+
/// Maximum memory: 1 GB for WinOS, 2 GB for other 32 bit.
e_MaxMemory32 = 768 << 20,
#endif
-
+
// Up to the AppSpace setting, SeqDB will try to consume at
// most half of the available memory. Beyond this point,
// SeqDB will only leave the AppSpace amount for the
// application.
-
+
/// Application space - maximum memory set aside for the app.
e_AppSpace = 256 << 20,
-
+
/// Minimum memory bound.
e_MinMemory = 64 << 20,
-
+
/// Maximum slice to map on a 32 bit system.
e_MaxSlice32 = 128 << 20,
-
+
/// Maximum slice to map on a 64 bit system.
e_MaxSlice64 = 1 << 30,
-
+
/// Minimum slice size to use.
e_MinSlice = 4 << 20,
-
+
/// Maximum overhang.
e_MaxOverhang = 8 << 20,
-
+
/// Minimum overhang.
e_MinOverhang = 256 << 10,
-
+
/// Maximum open (mapped) regions at once.
eMaxOpenRegions = 500,
-
+
/// Maximum new open regions between collections.
eOpenRegionsWindow = 100
};
-
+
/// Constructor
CSeqDBMapStrategy(CSeqDBAtlas & atlas);
-
+
/// Get current overhang amount.
- ///
+ ///
/// This returns the amount of memory to map past the end of the
/// (end-of-map) slice boundary. This should prevent most cases
/// where a memory map 'straddles' the boundary between slices.
- ///
+ ///
/// @return
/// Atlas will map this much data past the slice-end boundary.
TIndx GetOverhang()
{
return m_Overhang;
}
-
+
/// Return the slice size for mmap requests.
TIndx GetSliceSize()
{
@@ -1021,7 +1043,7 @@ public:
{
m_SliceSize = min(m_SliceSize, size);
}
-
+
/// Return the total memory bound.
///
/// This returns the active memory bound. If SeqDB is done
@@ -1040,41 +1062,41 @@ public:
x_CheckAdjusted();
return returning ? m_RetBound : m_MaxBound;
}
-
+
/// An allocation this large will trigger a memory purge.
TIndx GetGCTriggerSize()
{
return m_SliceSize*3;
}
-
+
/// Give this object an OID specified by the user.
/// @param oid The user tried to fetch data via this oid.
/// @param num_oids The total number of OIDs.
void MentionOid(int oid, int num_oids);
-
+
/// Tell SeqDB that a memory mapping failed.
void MentionMapFailure(Uint8 current);
-
+
/// Set the memory bound using a user specified value.
void SetMemoryBound(Uint8 max)
{
x_SetBounds(max);
}
-
+
/// Set global default memory bound.
///
/// This sets the default, global memory bound used for all SeqDB
/// objects. If zero is specified, an appropriate default will be
/// selected based on system information.
static void SetDefaultMemoryBound(Uint8 bytes);
-
+
private:
/// Check if the global bound has been adjusted and use that value.
void x_CheckAdjusted();
-
+
/// Mention an ordered or out-of-order access.
void x_OidOrder(bool in_order);
-
+
/// Restrict a number to a range.
///
/// This method returns a number as close as possible to 'guess',
@@ -1086,43 +1108,43 @@ private:
/// @param high Highest value to return.
/// @param guess The preferred value.
Uint8 x_Pick(Uint8 low, Uint8 high, Uint8 guess);
-
+
/// Set all parameters.
void x_SetBounds(Uint8 bound);
-
+
/// The atlas object.
CSeqDBAtlas & m_Atlas;
-
+
/// Maximum memory bound SeqDB may map.
Int8 m_MaxBound;
-
+
/// Maximum memory bound when returning from Atlas code.
Int8 m_RetBound;
-
+
/// Atlas will try to map files in blocks this size.
Int8 m_SliceSize;
/// Mapped areas of files should overlap this much.
Int8 m_Overhang;
-
+
/// Track sequentiality of OID accesses.
CSeqDBMovingAverage m_Order;
-
+
/// True if SeqDB thinks user is accessing OIDs sequentially.
bool m_InOrder;
-
+
/// True if mmap has failed at least once.
bool m_MapFailed;
-
+
/// Last OID seen.
int m_LastOID;
-
+
/// Block size for mapping.
long m_BlockSize;
-
+
/// Global maximum memory bound.
static Int8 m_GlobalMaxBound;
-
+
/// Has global memory bound been changed?
static bool m_AdjustedBound;
};
@@ -1143,21 +1165,21 @@ class CSeqDB_AtlasRegionHolder : public CObject {
public:
/// Constructor.
CSeqDB_AtlasRegionHolder(CSeqDBAtlas & atlas, const char * ptr);
-
+
/// Destructor.
~CSeqDB_AtlasRegionHolder();
-
+
private:
/// Reference to the memory management layer.
CSeqDBAtlas & m_Atlas;
-
+
/// Pointer to this object.
const char * m_Ptr;
};
/// CSeqDBAtlas class
-///
+///
/// This object manages a collection of (memory) maps. It mmaps or
/// reads data from files on demand, to allow a set of files to be
/// accessed efficiently by SeqDB. The total size of the files used
@@ -1169,26 +1191,26 @@ private:
/// various SeqDB critical regions, some of which are outside of this
/// class. ["Atlas: n. 1. A book or bound collection of maps..."; The
/// American Heritage Dictionary of the English Language, 4th Edition.
-/// Copyright � 2000 by Houghton Mifflin Company.]
+/// Copyright � 2000 by Houghton Mifflin Company.]
class CSeqDBAtlas {
public:
/// The type used for file offsets.
typedef CRegionMap::TIndx TIndx;
-
+
/// Constructor
- ///
+ ///
/// Initializes the atlas object.
- ///
+ ///
/// @param use_mmap
/// If false, use read(); if true, use mmap() or similar.
CSeqDBAtlas(bool use_mmap);
-
+
/// The destructor unmaps and frees all associated memory.
~CSeqDBAtlas();
-
+
/// Check if file exists.
- ///
+ ///
/// If the file exists, this method will return true, otherwise
/// false. Also, if the file exists, the first slice of it will
/// be mapped. This method exists for efficiency reasons; it is
@@ -1198,7 +1220,7 @@ public:
/// already been mapped, this will return true without consulting
/// the file system, so this method will not detect files that
/// have been deleted since the mapping occurred.
- ///
+ ///
/// @param fname
/// The filename of the file to get.
/// @param locked
@@ -1206,11 +1228,11 @@ public:
/// @return
/// True if the file exists.
bool DoesFileExist(const string & fname, CSeqDBLockHold & locked);
-
+
/// Check if file exists.
- ///
+ ///
/// This is like the previous but accepts CSeqDB_Path.
- ///
+ ///
/// @param fname
/// The filename of the file to get.
/// @param locked
@@ -1221,13 +1243,13 @@ public:
{
return DoesFileExist(fname.GetPathS(), locked);
}
-
+
/// Get mapping of an entire file.
- ///
+ ///
/// A file is mapped or read, in its entirety. The region is held
/// in memory until the pointer is returned with RetRegion(). The
/// atlas will be locked if necessary.
- ///
+ ///
/// @param fname
/// The filename of the file to get.
/// @param length
@@ -1239,13 +1261,13 @@ public:
const char * GetFile(const string & fname,
TIndx & length,
CSeqDBLockHold & locked);
-
+
/// Get mapping of an entire file.
- ///
+ ///
/// A file is mapped or read, in its entirety. The region is held
/// in memory until the lease object is cleared. The atlas will
/// be locked if necessary.
- ///
+ ///
/// @param lease
/// The lease which owns the hold on the region.
/// @param fname
@@ -1258,11 +1280,11 @@ public:
const string & fname,
TIndx & length,
CSeqDBLockHold & locked);
-
+
/// Get mapping of an entire file.
- ///
+ ///
/// This version is like the previous but takes CSeqDB_Path.
- ///
+ ///
/// @param lease
/// The lease which owns the hold on the region.
/// @param fname
@@ -1278,11 +1300,11 @@ public:
{
GetFile(lease, fname.GetPathS(), length, locked);
}
-
+
/// Get size of a file.
- ///
+ ///
/// Check whether a file exists and get the file's size.
- ///
+ ///
/// @param fname
/// The filename of the file to get the size of.
/// @param length
@@ -1294,12 +1316,12 @@ public:
bool GetFileSize(const string & fname,
TIndx & length,
CSeqDBLockHold & locked);
-
+
/// Get size of a file.
- ///
+ ///
/// Check whether a file exists and get the file's size. This
/// version assumes the atlas lock is held.
- ///
+ ///
/// @param fname
/// The filename of the file to get the size of.
/// @param length
@@ -1307,16 +1329,16 @@ public:
/// @return
/// true if the file exists.
bool GetFileSizeL(const string & fname, TIndx & length);
-
+
/// Gets a partial mapping of the file.
- ///
+ ///
/// Part of a file is mapped or read. The region is held in
/// memory until the pointer is released with RetRegion(). This
/// method may read or map a larger section of the file than was
/// asked for. It may also return a pointer into an area that was
/// mapped by a previous call. The atlas will be locked if
/// necessary.
- ///
+ ///
/// @param fname
/// The filename of the file to get.
/// @param begin
@@ -1331,15 +1353,15 @@ public:
TIndx begin,
TIndx end,
CSeqDBLockHold & locked);
-
+
/// Gets a partial mapping of the file (assumes lock is held).
- ///
+ ///
/// Part of a file is mapped or read. The region is held in
/// memory until the lease object is cleared. This method may
/// read or map a larger section of the file than was asked for.
/// It may also return a pointer into an area that was mapped by a
/// previous call. The atlas is assumed to be locked.
- ///
+ ///
/// @param lease
/// The memory lease object to store the region hold.
/// @param fname
@@ -1352,82 +1374,82 @@ public:
const string & fname,
TIndx begin,
TIndx end);
-
+
/// Release a hold on a region of memory.
- ///
+ ///
/// This method releases holds kept by CSeqDBMemLease objects. It
/// release the reference count and resets the lease to an
/// inactive state. The atlas lock is assumed to be held. This
/// method assumes the lock is held.
- ///
+ ///
/// @param ml
/// The memory lease object holding the reference.
void RetRegion(CSeqDBMemLease & ml);
-
+
/// Release a mapping of the file, or free allocated memory.
- ///
+ ///
/// This method releases the holds that are gotten by the versions
/// of the GetRegion() and GetFile() methods that return pointers,
/// and by the Alloc() method. Each call to a hold-getting method
/// should be paired with a call to a hold-releasing method. With
/// data known to have originated in Alloc(), it is faster to call
/// the Free() method. This method assumes the lock is held.
- ///
+ ///
/// @param datap
/// Pointer to the data to release or deallocate.
void RetRegion(const char * datap)
{
Verify(true);
-
+
for(int i = 0; i<eNumRecent; i++) {
CRegionMap * rec_map = m_Recent[i];
-
+
if (! rec_map)
break;
-
+
if (rec_map->InRange(datap)) {
rec_map->RetRef();
-
+
if (i) {
x_AddRecent(rec_map);
}
-
+
return;
}
}
-
+
x_RetRegionNonRecent(datap);
-
+
Verify(true);
}
-
+
/// Clean up unreferenced objects
- ///
+ ///
/// This iterates over all file regions managed by the atlas code.
/// If the region has no users, it is a candidate for removal by
/// garbage collection. The lock will be acquired if necessary.
- ///
+ ///
/// @param locked
/// The lock hold object for this thread.
void GarbageCollect(CSeqDBLockHold & locked);
-
+
/// Display memory layout.
- ///
+ ///
/// This method provides a way to examine the set of memory
/// objects in use by the Atlas code, for example when running an
/// application in a debugger. Some or all of the functionality
/// of this code is disabled in a normal compile; it may be
/// necessary to define certain compilation flags to make it
/// available again.
- ///
+ ///
/// @param locked
/// If this is set to false, the atlas lock will be acquired.
/// @param index
/// A value which will be inserted into the output messages.
void ShowLayout(bool locked, TIndx index);
-
+
/// Allocate memory that atlas will keep track of.
- ///
+ ///
/// This method allocates memory for the calling code's use.
/// There are three reasons to do this. First, the allocated
/// memory is guaranteed to be deleted when the atlas destructor
@@ -1443,7 +1465,7 @@ public:
/// thereabouts) does not need to can return allocated memory to
/// the user as "sequence data", and does not have to track
/// whether the data was allocated or mapped.
- ///
+ ///
/// @param length
/// Amount of memory to allocate in bytes.
/// @param locked
@@ -1453,23 +1475,23 @@ public:
/// @return
/// A pointer to the allocation region of memory.
char * Alloc(size_t length, CSeqDBLockHold & locked, bool clear = true);
-
+
/// Return allocated memory.
- ///
+ ///
/// This method returns memory acquired from the Alloc() method.
/// Dynamically allocated memory from other sources should not be
/// freed with this method, and memory allocated via Alloc()
/// should not be freed by any means other than this method or
/// RetRegion().
- ///
+ ///
/// @param freeme
/// A pointer to memory allocated via Alloc().
/// @param locked
/// The lock hold object for this thread.
void Free(const char * freeme, CSeqDBLockHold & locked);
-
+
/// Register externally allocated memory.
- ///
+ ///
/// This method tells the atlas code that memory was allocated
/// external to the atlas code, and should be included under the
/// memory bound enforced by the atlas. These areas of memory
@@ -1478,7 +1500,7 @@ public:
/// unmapped earlier or more often. This method may trigger atlas
/// garbage collection. RegisterFree() should be called when the
/// memory is freed.
- ///
+ ///
/// @param memreg
/// Memory registration tracking object.
/// @param bytes
@@ -1488,24 +1510,24 @@ public:
void RegisterExternal(CSeqDBMemReg & memreg,
size_t bytes,
CSeqDBLockHold & locked);
-
+
/// Unregister externally allocated memory.
- ///
+ ///
/// This method tells the atlas that external memory registered
/// with RegisterExternal() has been freed. The atlas lock is
/// assumed to be held.
- ///
+ ///
/// @param memreg
/// Memory registration tracking object.
void UnregisterExternal(CSeqDBMemReg & memreg);
-
+
/// Lock the atlas.
- ///
+ ///
/// If the lock hold object passed to
/// this method is already in a "locked" state, this call is a
/// noop. Otherwise, the lock hold object is put in a locked
/// state and the lock is acquired.
- ///
+ ///
/// @param locked
/// This object tracks whether this thread owns the mutex.
void Lock(CSeqDBLockHold & locked)
@@ -1515,14 +1537,14 @@ public:
locked.m_Locked = true;
}
}
-
+
/// Unlock the atlas.
- ///
+ ///
/// If the lock hold object passed to
/// this method is already in an "unlocked" state, this call is a
/// noop. Otherwise, the lock hold object is put in an unlocked
/// state and the lock is released.
- ///
+ ///
/// @param locked
/// This object tracks whether this thread owns the mutex.
void Unlock(CSeqDBLockHold & locked)
@@ -1532,9 +1554,9 @@ public:
m_Lock.Unlock();
}
}
-
+
/// Adjust the atlas memory management boundaries.
- ///
+ ///
/// The memory bound determines the total amount of memory the
/// atlas will map before triggering garbage collection. Whenever
/// one of the GetRegion() or GetFile() methods is called, the
@@ -1561,13 +1583,13 @@ public:
/// sequence data for extended periods of time. Also note that if
/// the atlas code thinks these parameters are set to unreasonable
/// values, it will silently adjust them.
- ///
+ ///
/// @param mb
/// Total amount of address space the atlas can use.
void SetMemoryBound(Uint8 mb);
-
+
/// Insure room for a new allocation.
- ///
+ ///
/// This method is used to insure that the atlas code has room for
/// a new address space purchase. When mapping new regions, this
/// method is called. If the memory bound would be exceeded by
@@ -1578,38 +1600,38 @@ public:
/// is possible for the user to exhaust memory simply by calling
/// CSeqDB::GetSequence() once for each slice of a large database
/// without calling CSeqDB::RetSequence().
- ///
+ ///
/// @param space_needed
/// The size in bytes of the new region or allocation.
/// @param returning
/// Specify true if we are about to return to user code.
void PossiblyGarbageCollect(Uint8 space_needed, bool returning);
-
+
/// Return the current overhang amount.
- ///
+ ///
/// This returns the amount of memory to map past the end of the
/// (end-of-map) slice boundary. This should prevent most cases
/// where a memory map 'straddles' the boundary between slices.
- ///
+ ///
/// @return
/// Atlas will map this much data past the slice-end boundary.
Uint8 GetOverhang()
{
return m_Strategy.GetOverhang();
}
-
+
/// Get the current slice size.
- ///
+ ///
/// This returns the current slice size used for mmap() style
/// memory allocations.
- ///
+ ///
/// @return
/// Atlas will try to map this much data at a time.
Uint8 GetSliceSize()
{
return m_Strategy.GetSliceSize();
}
-
+
/// Set the MT slice size.
/// This sets the current slice size used for mmap() allocations.
void SetSliceSize()
@@ -1618,18 +1640,18 @@ public:
}
/// Return the current number of bytes allocated.
- ///
+ ///
/// This returns the number of bytes currently allocated by the
/// atlas code. It does not include overhead or meta-data such as
/// the CRegionMap objects or the atlas object itself.
- ///
+ ///
/// @return
/// The amount of memory allocated in bytes.
TIndx GetCurrentAllocationTotal()
{
return m_CurAlloc;
}
-
+
/// Verify the integrity of this object and subobjects.
/// @param locked
/// The lock hold object for this thread. [in]
@@ -1640,7 +1662,7 @@ public:
Verify(true);
#endif
}
-
+
/// Verify the integrity of this object and subobjects.
/// @param already_locked
/// True if the lock is already held, false if not. [in]
@@ -1648,22 +1670,22 @@ public:
{
#ifdef _DEBUG
CSeqDBLockHold locked(*this);
-
+
if (! already_locked) {
Lock(locked);
}
-
+
ITERATE(TNameOffsetTable, iter, m_NameOffsetLookup) {
CRegionMap & rmp = **iter;
rmp.Verify();
}
-
+
if (! already_locked) {
Unlock(locked);
}
#endif
}
-
+
/// Report a user-specified OID for ordered-access detection.
///
/// This class attempts to reduce thrashing by determining if the
@@ -1684,7 +1706,7 @@ public:
Lock(locked);
m_Strategy.MentionOid(oid, num_oids);
}
-
+
/// Add a garbage collection callback.
///
/// Some classes in the SeqDB library keep holds on regions of
@@ -1706,7 +1728,7 @@ public:
m_Flushers.push_back(flusher);
*flushp = flusher;
}
-
+
/// Remove a garbage collection callback.
///
/// This removes a garbage collection callback from the list
@@ -1718,9 +1740,9 @@ public:
void RemoveRegionFlusher(CSeqDBFlushCB * flusher, CSeqDBLockHold & locked)
{
Lock(locked);
-
+
_ASSERT(m_Flushers.size());
-
+
for(size_t i = 0; i < m_Flushers.size(); i++) {
if (m_Flushers[i] == flusher) {
m_Flushers[i] = m_Flushers.back();
@@ -1730,7 +1752,7 @@ public:
}
_ASSERT(0);
}
-
+
/// Set global default memory bound.
///
/// This sets the default, global memory bound used for all SeqDB
@@ -1741,7 +1763,7 @@ public:
static void SetDefaultMemoryBound(Uint8 bytes);
/// Get BlastDB search path.
- const string GetSearchPath() const
+ const string GetSearchPath() const
{
return m_SearchPath;
}
@@ -1772,16 +1794,16 @@ public:
return path;
}
-
+
private:
/// Private method to prevent copy construction.
CSeqDBAtlas(const CSeqDBAtlas &);
-
+
/// Iterator type for m_Pool member.
typedef map<const char *, size_t>::iterator TPoolIter;
-
+
/// Finds a matching region if any exists.
- ///
+ ///
/// This method searches the list of mapped regions to find one
/// with the same fid, and whose offset range includes the
/// specified range. If found, all of the input fields are
@@ -1791,7 +1813,7 @@ private:
/// the (pre-adjustment) begin offset is returned from the method.
/// If no region was found, NULL is returned and no changes are
/// made to the input parameters.
- ///
+ ///
/// @param fid
/// The number identifying this file to the atlas code.
/// @param begin
@@ -1809,9 +1831,9 @@ private:
TIndx & end,
const char ** startp,
CRegionMap ** rmap);
-
+
/// Gets a partial mapping of the file.
- ///
+ ///
/// This method searches the list of mapped regions to find one
/// with the same fid, and whose offset range includes the
/// specified range. If found, it will be used. If not found, a
@@ -1821,7 +1843,7 @@ private:
/// CRegionMap object is returned in *rmap, and a pointer to the
/// (pre-adjustment) begin offset is returned from the method. If
/// no region could be found or created, an exception is thrown.
- ///
+ ///
/// @param fname
/// The name of the file to get a region of.
/// @param begin
@@ -1839,32 +1861,32 @@ private:
TIndx & end,
const char ** start,
CRegionMap ** rmap);
-
+
/// Try to find the region and free it.
- ///
+ ///
/// This method looks for the region in the memory pool (m_Pool),
/// which means it must have been allocated with Alloc().
- ///
+ ///
/// @param freeme
/// The pointer to free.
/// @return
/// true, if the memory block was found and freed.
bool x_Free(const char * freeme);
-
+
/// Clean up unreferenced objects (non-locking version.)
- ///
+ ///
/// This iterates over all file regions managed by the atlas code.
/// If the region has no users, it is a candidate for removal by
/// garbage collection. The lock is assumed to be already held.
/// If the amount of memory held is reduced to a number below
/// reduce_to, the routine will stop freeing memory and return.
- ///
+ ///
/// @param reduce_to
/// The maximum amount of allocated memory to keep.
void x_GarbageCollect(Uint8 reduce_to);
-
+
/// Find the fid for the filename.
- ///
+ ///
/// Atlas maps filenames to fids. The filename is looked up and
/// the fid is returned. If the filename is not found, it is
/// added to the table and a newly generated fid is returned. The
@@ -1874,7 +1896,7 @@ private:
/// provides a permanent (for the lifetime of CSeqDBAtlas) address
/// for the filename, which can be used by structures like
/// CRegionMap, so that they don't have to copy string data.
- ///
+ ///
/// @param fname
/// The filename to look up.
/// @param map_fname_ptr
@@ -1883,22 +1905,22 @@ private:
/// The fid
int x_LookupFile(const string & fname,
const string ** map_fname_ptr);
-
+
/// Releases or deletes a memory region.
- ///
+ ///
/// The RetRegion method is called many times. The functionality
/// is split into a fast inlined part and a slow non-inlined part.
/// This is the non-inlined part. It searches for the region or
/// allocated block that owns the specified address, and releases
/// it, if found. This method assumes the lock is held.
- ///
+ ///
/// @param datap
/// Pointer to the area to delete or release a hold on.
void x_RetRegionNonRecent(const char * datap);
-
+
/// Clear recent-region lookup table
- ///
+ ///
/// Functions which delete regions call this to flush the fast
/// lookup table for recently used region, on the grounds that it
/// may have been invalidated (it may contain dangling pointers).
@@ -1912,9 +1934,9 @@ private:
m_Recent[i] = 0;
}
}
-
+
/// Add most recently used region to the fast lookup table.
- ///
+ ///
/// Whenever a lookup finds a region, it is added to the beginning
/// of a fast region lookup table (m_Recent). Existing entries in
/// the table will move down one slot. If the new entry already
@@ -1922,33 +1944,33 @@ private:
/// that point (and only entries between that point and the top of
/// the table will need to move. If all slots in the table are
/// used, the last entry will simply be dropped.
- ///
+ ///
/// @param r
/// The most recently used region.
void x_AddRecent(CRegionMap * r)
{
if (m_Recent[0] == r)
return;
-
+
int found_at = eNumRecent-1;
-
+
for(int i = 0; i < eNumRecent-1; i++) {
if (m_Recent[i] == r) {
found_at = i;
break;
}
}
-
+
while(found_at) {
m_Recent[found_at] = m_Recent[found_at-1];
found_at --;
}
-
+
m_Recent[0] = r;
}
-
+
/// Call all callbacks.
- ///
+ ///
/// This method calls all the GC callbacks in preparation for a
/// garbage collection run or similar processing. This method
/// assumes the lock is held.
@@ -1958,45 +1980,45 @@ private:
(*m_Flushers[i])();
}
}
-
+
// Data
-
+
/// Protects most of the critical regions of the SeqDB library.
CMutex m_Lock;
-
+
/// Set to true if memory mapping is enabled.
bool m_UseMmap;
-
+
/// Bytes of "data" currently known to SeqDBAtlas. This does not
/// include metadata, such as the region map class itself..
TIndx m_CurAlloc;
-
+
/// All of the SeqDB region maps.
vector<CRegionMap*> m_Regions;
-
+
/// Maps from pointers to dynamically allocated blocks to the byte
/// size of the allocation.
map<const char *, size_t> m_Pool;
-
+
/// The most recently assigned FID.
int m_LastFID;
-
+
/// Lookup table of fids by filename.
map<string, int> m_FileIDs;
-
+
/// RegionMapLess
- ///
+ ///
/// This functor provides an ordering over CRegionMap objects.
-
+
struct RegionMapLess
: public binary_function<const CRegionMap*, const CRegionMap*, bool>
{
/// Compare regions using less-than.
- ///
+ ///
/// This compares two CRegionMap objects using that class's
/// overloaded less-than operator. It provides a partial
/// ordering for the TNameOffsetTable.
- ///
+ ///
/// @param L
/// The first object.
/// @param R
@@ -2010,40 +2032,40 @@ private:
return *L < *R;
}
};
-
+
/// Defines lookup of regions by fid, offset, and length.
- typedef set<CRegionMap *, RegionMapLess> TNameOffsetTable;
-
+ typedef set<CRegionMap *, RegionMapLess> TNameOffsetTable;
+
/// Defines lookup of regions by starting memory address.
typedef map<const char *, CRegionMap*> TAddressTable;
-
+
/// Map to find regions for Getting (x_FindRegion).
TNameOffsetTable m_NameOffsetLookup;
-
+
/// Map to find regions for Returning (x_RetRegionNonRecent).
TAddressTable m_AddressLookup;
-
+
// Recent region lookup
-
+
/// Number of recently-used-region slots.
enum { eNumRecent = 8 };
-
+
/// Table of recently used regions.
CRegionMap * m_Recent[ eNumRecent ];
-
+
/// Atlas will try to garbage collect if more than this many
/// regions are opened.
int m_OpenRegionsTrigger;
-
+
/// Cache of file existence and length.
map< string, pair<bool, TIndx> > m_FileSize;
/// Maxium file size.
Uint8 m_MaxFileSize;
-
+
/// Callbacks to flush memory leases before a garbage collection.
vector<CSeqDBFlushCB*> m_Flushers;
-
+
/// Flexible memory allocation manager.
CSeqDBMapStrategy m_Strategy;
@@ -2076,20 +2098,20 @@ CRegionMap::MatchAndUse(int fid,
CHECK_MARKER();
_ASSERT(fid);
_ASSERT(m_Fid);
-
+
if ((fid == m_Fid) && (m_Begin <= begin) && (m_End >= end)) {
AddRef();
-
+
const char * location = m_Data + (begin - m_Begin);
-
+
begin = m_Begin;
end = m_End;
*start = m_Data;
_ASSERT(*start);
-
+
return location;
}
-
+
return 0;
}
@@ -2097,21 +2119,21 @@ bool CRegionMap::operator < (const CRegionMap & other) const
{
CHECK_MARKER();
// Sort ascending by fid
-
+
if (m_Fid < other.m_Fid)
return true;
if (other.m_Fid < m_Fid)
return false;
-
+
// Sort ascending by start order
-
+
if (m_Begin < other.m_Begin)
return true;
if (other.m_Begin < m_Begin)
return false;
-
+
// Sort ascending by size of mapping.
-
+
return m_End < other.m_End;
}
@@ -2146,23 +2168,23 @@ public:
CSeqDBAtlasHolder(bool use_mmap,
CSeqDBFlushCB * flusher,
CSeqDBLockHold * lockedp);
-
+
/// Destructor.
~CSeqDBAtlasHolder();
-
+
/// Get the CSeqDBAtlas object.
CSeqDBAtlas & Get();
-
+
private:
/// Garbage collection callback.
CSeqDBFlushCB * m_FlushCB;
-
+
/// Lock protecting this object's fields
DECLARE_CLASS_STATIC_FAST_MUTEX(m_Lock);
-
+
/// Count of users of the CSeqDBAtlas object.
static int m_Count;
-
+
/// The CSeqDBAtlas object itself.
static CSeqDBAtlas * m_Atlas;
};
diff --git a/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp b/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
index c73ff3f..0397d71 100644
--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB__SEQDB__SEQDBGENERAL_HPP
#define CORELIB__SEQDB__SEQDBGENERAL_HPP
-/* $Id: seqdbgeneral.hpp 311249 2011-07-11 14:12:16Z camacho $
+/* $Id: seqdbgeneral.hpp 480560 2015-10-01 16:50:48Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1208,7 +1208,8 @@ void SeqDB_CombineAndQuote(const vector<string> & dbs,
/// @param dbname Combined database name.
/// @param dbs Database names to combine.
void SeqDB_SplitQuoted(const string & dbname,
- vector<CSeqDB_Substring> & dbs);
+ vector<CSeqDB_Substring> & dbs,
+ bool keep_quote = false);
/// Fence Sentry value, which is placed at either end of ranges of
/// data that are included in partially fetched sequences; this only
diff --git a/c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp b/c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
index d5b8455..5c04ceb 100644
--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS_SEQDB__SEQDBISAM_HPP
#define OBJTOOLS_READERS_SEQDB__SEQDBISAM_HPP
-/* $Id: seqdbisam.hpp 311249 2011-07-11 14:12:16Z camacho $
+/* $Id: seqdbisam.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@
/// @file seqdbisam.hpp
/// ISAM index database access object.
-///
+///
/// Defines classes:
/// CSeqDBIsam
-///
+///
/// Implemented for: UNIX, MS-Windows
@@ -55,12 +55,12 @@ s_AdvanceGiList(CSeqDBGiList & gis,
int gis_size,
const T & key)
{
- while( (gi_index < gis_size)
+ while( (gi_index < gis_size)
&& (gis.GetKey<T>(gi_index) < key)) {
++gi_index;
int jump = 2;
-
+
while( (gi_index + jump < gis_size)
&& (gis.GetKey<T>(gi_index + jump) < key)) {
@@ -68,9 +68,9 @@ s_AdvanceGiList(CSeqDBGiList & gis,
jump *= 2;
}
}
-
+
// skipping translated elements
- while( (gi_index < gis_size)
+ while( (gi_index < gis_size)
&& (gis.IsValueSet<T>(gi_index) )) ++gi_index;
}
@@ -82,20 +82,20 @@ s_AdvanceKeyList(const vector<T> & keys,
int num_keys,
const T & target)
{
- while( (index < num_keys)
+ while( (index < num_keys)
&& (keys[index] <= target)) {
-
+
++index;
int jump = 2;
-
- while( (index + jump < num_keys)
+
+ while( (index + jump < num_keys)
&& (keys[index + jump] <= target)) {
index += jump;
jump *= 2;
}
}
- --index;
+ --index;
}
// apply the translation (if we have it) for those GIs.
@@ -106,16 +106,16 @@ s_SetTranslation(CSeqDBGiList & gis,
const T & key,
int value)
{
- while( (gi_index < gis_size)
+ while( (gi_index < gis_size)
&& (gis.GetKey<T>(gi_index) == key)) {
gis.SetValue<T>(gi_index, value);
++gi_index;
}
}
-
+
/// CSeqDBIsam
-///
+///
/// Manages one ISAM file, which will translate either PIGs, GIs, or
/// Accessions to OIDs. Translation in the other direction is done in
/// the CSeqDBVol code. Files managed by this class include those
@@ -128,7 +128,7 @@ class CSeqDBIsam : public CObject {
public:
/// Import the type representing one GI, OID association.
typedef CSeqDBGiList::SGiOid TGiOid;
-
+
/// Types of database this class can access.
enum EIsamDbType {
eNumeric = 0, /// Numeric database with Key/Value pairs in the index file.
@@ -138,31 +138,31 @@ public:
eStringBin = 4, /// This type is not supported.
eNumericLongId = 5 /// Like eNumeric but with 8 bytes of Key data per record.
};
-
+
/// Type which is large enough to span the bytes of an ISAM file.
typedef CSeqDBAtlas::TIndx TIndx;
-
+
/// This class works with OIDs relative to a specific volume.
typedef int TOid;
-
+
/// PIG identifiers for numeric indices over protein volumes.
typedef int TPig;
-
+
/// Genomic IDs, the most common numerical identifier.
- typedef int TGi;
-
+// typedef int TGi;
+
/// Identifier type for trace databases.
typedef Int8 TTi;
-
+
/// Type large enough to hold any numerical ID.
typedef Int8 TId;
-
+
/// Constructor
- ///
+ ///
/// An ISAM file object corresponds to an index file and a data
/// file, and converts identifiers (string, GI, or PIG) into OIDs
/// relative to a particular database volume.
- ///
+ ///
/// @param atlas
/// The memory management object. [in]
/// @param dbname
@@ -178,20 +178,20 @@ public:
char prot_nucl,
char file_ext_char,
ESeqDBIdType ident_type);
-
+
/// Destructor
///
/// Releases all resources associated with this object.
~CSeqDBIsam();
-
+
/// PIG translation
- ///
+ ///
/// A PIG identifier is translated to an OID. PIG identifiers are
/// used exclusively for protein sequences. One PIG corresponds
/// to exactly one sequences of amino acids, and vice versa. They
/// are also stable; the sequence a PIG points to will never be
/// changed.
- ///
+ ///
/// @param pig
/// The PIG to look up. [in]
/// @param oid
@@ -205,15 +205,15 @@ public:
_ASSERT(m_IdentType == ePigId);
return x_IdentToOid(pig, oid, locked);
}
-
+
/// GI or TI translation
- ///
+ ///
/// A GI or TI identifier is translated to an OID. GI identifiers
/// are used for all types of sequences. TI identifiers are used
/// primarily for nucleotide data in the Trace DBs. Multiple GIs
/// may indicate the same sequence of bases and the same OID, but
/// TIs are usually unique.
- ///
+ ///
/// @param id
/// The GI or TI to look up. [in]
/// @param oid
@@ -227,7 +227,7 @@ public:
_ASSERT(m_IdentType == eGiId || m_IdentType == eTiId);
return x_IdentToOid(id, oid, locked);
}
-
+
/// Translate Gis and Tis to Oids for the given ID list.
///
/// This method iterates over a vector of Gi/OID and/or Ti/OID
@@ -248,7 +248,7 @@ public:
int vol_end,
CSeqDBGiList & ids,
CSeqDBLockHold & locked);
-
+
/// Compute list of included OIDs based on a negative ID list.
///
/// This method iterates over a vector of Gis or Tis, along with
@@ -278,9 +278,9 @@ public:
int vol_end,
CSeqDBNegativeList & ids,
CSeqDBLockHold & locked);
-
+
/// String translation
- ///
+ ///
/// A string id is translated to one or more OIDs. String ids are
/// used by some groups which produce sequence data. In some
/// cases, the string may correspond to more than one OID. For
@@ -298,7 +298,7 @@ public:
/// succeeded. CSeqDBVol::x_CheckVersions() can then be called to
/// verify the OIDs; see that method for more information about
/// this scenario.
- ///
+ ///
/// @param acc
/// The string to look up. [in]
/// @param oids
@@ -314,14 +314,14 @@ public:
bool adjusted,
bool & version_check,
CSeqDBLockHold & locked);
-
+
/// Seq-id translation
- ///
+ ///
/// A Seq-id identifier (serialized to a string) is translated
/// into an OID. This routine will attempt to simplify the seqid
/// so as to use the faster numeric lookup techniques whenever
/// possible.
- ///
+ ///
/// @param acc
/// A string containing the Seq-id. [in]
/// @param oid
@@ -329,16 +329,16 @@ public:
/// @param locked
/// The lock hold object for this thread. [in|out]
bool SeqidToOid(const string & acc, TOid & oid, CSeqDBLockHold & locked);
-
+
/// Sequence hash lookup
- ///
+ ///
/// This methods tries to find sequences associated with a given
/// sequence hash value. The provided value is numeric but the
/// ISAM file uses a string format, because string searches can
/// return multiple results per key, and there may be multiple
/// OIDs for a given hash value due to identical sequences and
/// collisions.
- ///
+ ///
/// @param hash
/// The sequence hash value to look up. [in]
/// @param oids
@@ -348,16 +348,16 @@ public:
void HashToOids(unsigned hash,
vector<TOid> & oids,
CSeqDBLockHold & locked);
-
+
/// Return any memory held by this object to the atlas.
void UnLease();
-
+
/// Get Numeric Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of numeric keys in
/// the database index. If the operation fails, zero will be
/// returned for count.
- ///
+ ///
/// @param low_id Lowest numeric id value in database. [out]
/// @param high_id Highest numeric id value in database. [out]
/// @param count Number of numeric id values in database. [out]
@@ -366,13 +366,13 @@ public:
Int8 & high_id,
int & count,
CSeqDBLockHold & locked);
-
+
/// Get String Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of string keys in
/// the database index. If the operation fails, zero will be
/// returned for count.
- ///
+ ///
/// @param low_id Lowest string id value in database. [out]
/// @param high_id Highest string id value in database. [out]
/// @param count Number of string id values in database. [out]
@@ -381,7 +381,7 @@ public:
string & high_id,
int & count,
CSeqDBLockHold & locked);
-
+
/// Check if a given ISAM index exists.
///
/// @param dbname Base name of the database volume.
@@ -390,96 +390,96 @@ public:
static bool IndexExists(const string & dbname,
char prot_nucl,
char file_ext_char);
-
+
private:
/// Stores a key for an ISAM file.
///
/// This class stores a key of either of the types used by ISAM
/// files. It provides functionality for ordering comparisons of
/// keys.
-
+
class SIsamKey {
public:
// If case insensitive string comparisons are desired, the
// keys should be upcased before calling these methods.
-
+
/// Constructor.
SIsamKey()
: m_IsSet(false), m_NKey(-1)
{
}
-
+
/// Returns true if this object has an assigned value.
bool IsSet()
{
return m_IsSet;
}
-
+
/// Assign a numeric value to this object.
void SetNumeric(Int8 ident)
{
m_IsSet = true;
m_NKey = ident;
}
-
+
/// Fetch the numeric value of this object.
Int8 GetNumeric() const
{
return m_NKey;
}
-
+
/// Fetch the string value of this object.
void SetString(const string & ident)
{
m_IsSet = true;
m_SKey = ident;
}
-
+
/// Fetch the numeric value of this object.
string GetString() const
{
return m_SKey;
}
-
+
/// Returns true if the provided integer compares as lower
/// than the assigned lower boundary for this ISAM file.
bool OutsideFirstBound(Int8 ident)
{
return (m_IsSet && (ident < m_NKey));
}
-
+
/// Returns true if the provided string compares as lower than
/// the assigned lower boundary for this ISAM file.
bool OutsideFirstBound(const string & ident)
{
return (m_IsSet && (ident < m_SKey));
}
-
+
/// Returns true if the provided integer compares as higher
/// than the assigned upper boundary for this ISAM file.
bool OutsideLastBound(Int8 ident)
{
return (m_IsSet && (ident > m_NKey));
}
-
+
/// Returns true if the provided string compares as lower than
/// the assigned upper boundary for this ISAM file.
bool OutsideLastBound(const string & ident)
{
return (m_IsSet && (ident > m_SKey));
}
-
+
private:
/// True if this object has an assigned value.
bool m_IsSet;
-
+
/// The key, if it is a number.
Int8 m_NKey;
-
+
/// The key, if it is a string.
string m_SKey;
};
-
+
/// Exit conditions occurring in this code.
enum EErrorCode {
eNotFound = 1, /// The key was not found
@@ -488,7 +488,7 @@ private:
eBadType = -11, /// The requested ISAM type did not match the file.
eWrongFile = -12 /// The file was not found, or was the wrong length.
};
-
+
/// Load and extract all index samples into array at once
template <class T>
void x_LoadIndex(CSeqDBMemLease & lease,
@@ -496,17 +496,17 @@ private:
vector<TIndx> & offs)
{
const char * keydatap = lease.GetPtr(m_KeySampleOffset);
-
+
for (int index=0; index < m_NumSamples; ++index) {
keys.push_back(x_GetNumericKey(keydatap));
// vals.push_back(x_GetNumericData(keydatap));
offs.push_back(index * m_PageSize * m_TermSize);
keydatap += m_TermSize;
- }
+ }
offs.push_back(m_NumTerms * m_TermSize);
}
-
+
/// Load and extract a data page into array at once
template <class T>
void x_LoadData(CSeqDBMemLease & lease,
@@ -521,14 +521,14 @@ private:
keys.push_back(x_GetNumericKey(keydatap));
vals.push_back(x_GetNumericData(keydatap));
keydatap += m_TermSize;
- }
+ }
}
-
+
/// GiList Translation
- ///
+ ///
/// Given a GI list, this routine finds the OID for each ID in the
/// list not already having a translation.
- ///
+ ///
/// @param vol_start
/// The starting OID for this ISAM file's database volume.
/// @param gis
@@ -548,18 +548,18 @@ private:
if(m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
// Most ordinary errors (missing GIs for example) are
// ignored for "multi" mode searches. But if a GI list is
// specified, and cannot be interpreted, it is an error.
-
+
NCBI_THROW(CSeqDBException,
eArgErr,
"Error: Unable to use ISAM index in batch mode.");
}
}
-
+
CSeqDBMemLease lease(m_Atlas);
vector<T> sample_keys;
@@ -571,7 +571,7 @@ private:
page_offs.reserve(m_NumSamples + 1);
keys.reserve(m_PageSize);
vals.reserve(m_PageSize);
-
+
m_Atlas.GetRegion(lease, m_IndexFname, 0, m_IndexFileLength);
x_LoadIndex(lease, sample_keys, page_offs);
m_Atlas.RetRegion(lease);
@@ -580,15 +580,15 @@ private:
int sample_index = 0;
while((gilist_index < gilist_size) && (sample_index < m_NumSamples)) {
-
- s_AdvanceGiList<T>(gis, gilist_index, gilist_size,
- sample_keys[sample_index]);
+
+ s_AdvanceGiList<T>(gis, gilist_index, gilist_size,
+ sample_keys[sample_index]);
if (gilist_index >= gilist_size) break;
- s_AdvanceKeyList<T>(sample_keys, sample_index, m_NumSamples,
+ s_AdvanceKeyList<T>(sample_keys, sample_index, m_NumSamples,
gis.GetKey<T>(gilist_index));
-
+
// Now we should be ready to search a data block.
keys.clear();
vals.clear();
@@ -598,7 +598,7 @@ private:
num_keys = m_NumTerms - sample_index * m_PageSize;
}
- m_Atlas.GetRegion(lease,
+ m_Atlas.GetRegion(lease,
m_DataFname,
page_offs[sample_index],
page_offs[sample_index + 1]);
@@ -618,23 +618,23 @@ private:
++index;
if (index >= num_keys) break;
- s_AdvanceGiList<T>(gis, gilist_index, gilist_size, keys[index]);
+ s_AdvanceGiList<T>(gis, gilist_index, gilist_size, keys[index]);
s_SetTranslation<T>(gis, gilist_index, gilist_size,
keys[index], vals[index] + vol_start);
}
-
+
// We could be finished here because we exhausted the GI list
// We must be done with that one by now..
++sample_index;
}
}
-
+
/// Numeric identifier lookup
- ///
+ ///
/// Given a numeric identifier, this routine finds the OID.
- ///
+ ///
/// @param id
/// The GI or PIG identifier to look up.
/// @param oid
@@ -646,12 +646,12 @@ private:
bool x_IdentToOid(Int8 id,
TOid & oid,
CSeqDBLockHold & locked);
-
+
/// Index file search
- ///
+ ///
/// Given a numeric identifier, this routine finds the OID or the
/// page in the data file where the OID can be found.
- ///
+ ///
/// @param Number
/// The GI or PIG identifier to look up.
/// @param Data
@@ -673,12 +673,12 @@ private:
Int4 & SampleNum,
bool & done,
CSeqDBLockHold & locked);
-
+
/// Negative ID List Translation
- ///
+ ///
/// Given a Negative ID list, this routine turns on the bits for
/// the OIDs found in the volume but not in the negated ID list.
- ///
+ ///
/// @param vol_start
/// The starting OID for this ISAM file's database volume.
/// @param vol_end
@@ -695,12 +695,12 @@ private:
CSeqDBNegativeList & gis,
bool use_tis,
CSeqDBLockHold & locked);
-
+
/// Data file search
- ///
+ ///
/// Given a numeric identifier, this routine finds the OID in the
/// data file.
- ///
+ ///
/// @param Number
/// The GI or PIG identifier to look up.
/// @param Data
@@ -719,11 +719,11 @@ private:
Uint4 * Index,
Int4 SampleNum,
CSeqDBLockHold & locked);
-
+
/// Numeric identifier lookup
- ///
+ ///
/// Given a numeric identifier, this routine finds the OID.
- ///
+ ///
/// @param Number
/// The GI or PIG identifier to look up.
/// @param Data
@@ -739,11 +739,11 @@ private:
int * Data,
Uint4 * Index,
CSeqDBLockHold & locked);
-
+
/// String identifier lookup
- ///
+ ///
/// Given a string identifier, this routine finds the OID(s).
- ///
+ ///
/// @param term_in
/// The string identifier to look up.
/// @param term_out
@@ -762,25 +762,25 @@ private:
vector<string> & value_out,
vector<TIndx> & index_out,
CSeqDBLockHold & locked);
-
+
/// Initialize the search object
- ///
+ ///
/// The first identifier search sets up the object by calling this
/// function, which reads the metadata from the index file and
/// sets all the fields needed for ISAM lookups.
- ///
+ ///
/// @param locked
/// The lock holder object for this thread.
/// @return
/// A non-zero error on failure, or eNoError on success.
EErrorCode
x_InitSearch(CSeqDBLockHold & locked);
-
+
/// Determine the number of elements in the data page.
- ///
+ ///
/// The number of elements is determined based on whether this is
/// the last page and the configured page size.
- ///
+ ///
/// @param SampleNum
/// Which data page will be searched.
/// @param Start
@@ -789,13 +789,13 @@ private:
/// The number of elements in this data page.
int x_GetPageNumElements(Int4 SampleNum,
Int4 * Start);
-
+
/// Lookup a string in a sparse table
- ///
+ ///
/// This does string lookup in a sparse string table. There is no
/// support (code) for this since there are currently no examples
/// of this kind of table to test against.
- ///
+ ///
/// @param acc
/// The string to look up.
/// @param oids
@@ -810,14 +810,14 @@ private:
vector<int> & oids,
bool adjusted,
CSeqDBLockHold & locked);
-
+
/// Find the first character to differ in two strings
- ///
+ ///
/// This finds the index of the first character to differ in
/// meaningful way between two strings. One of the strings is a
/// term that is passed in; the other is assumed to be located in
/// the ISAM table, a lease to which is passed to this function.
- ///
+ ///
/// @param term_in
/// The key string to compare against.
/// @param lease
@@ -845,14 +845,14 @@ private:
TIndx KeyOffset,
bool ignore_case,
CSeqDBLockHold & locked);
-
+
/// Find the first character to differ in two strings
- ///
+ ///
/// This finds the index of the first character to differ in
/// meaningful way between two strings. One of the strings is a
/// term that is passed in; the other is a range of memory
/// represented by two pointers.
- ///
+ ///
/// @param term_in
/// The key string to compare against.
/// @param begin
@@ -868,13 +868,13 @@ private:
const char * begin,
const char * end,
bool ignore_case);
-
+
/// Extract the data from a key-value pair in memory.
- ///
+ ///
/// Given pointers to a location in mapped memory, and the end of
/// the mapped data, this finds the key and data values for the
/// object at that location.
- ///
+ ///
/// @param key_start
/// A pointer to the beginning of the key-value pair in memory.
/// @param entry_end
@@ -887,13 +887,13 @@ private:
const char * entry_end,
vector<string> & key_out,
vector<string> & data_out);
-
+
/// Get the offset of the specified sample.
- ///
+ ///
/// For string ISAM indices, the index file contains a table of
/// offsets of the index file samples. This function gets the
/// offset of the specified sample in the index file's table.
- ///
+ ///
/// @param sample_offset
/// The offset into the file of the set of samples.
/// @param sample_num
@@ -905,12 +905,12 @@ private:
TIndx x_GetIndexKeyOffset(TIndx sample_offset,
Uint4 sample_num,
CSeqDBLockHold & locked);
-
+
/// Read a string from the index file.
- ///
+ ///
/// Given an offset into the index file, and a maximum length,
/// this function returns the bytes in a string object.
- ///
+ ///
/// @param key_offset
/// The offset into the file of the first byte.
/// @param length
@@ -926,14 +926,14 @@ private:
string & prefix,
bool trim_to_null,
CSeqDBLockHold & locked);
-
+
/// Find the first character to differ in two strings
- ///
+ ///
/// This finds the index of the first character to differ between
/// two strings. The first string is provided, the second is one
/// of the sample strings, indicated by the index of that sample
/// value.
- ///
+ ///
/// @param term_in
/// The key string to compare against.
/// @param SampleNum
@@ -946,13 +946,13 @@ private:
Uint4 SampleNum,
TIndx & KeyOffset,
CSeqDBLockHold & locked);
-
+
/// Find matches in the given page of a string ISAM file.
- ///
+ ///
/// This searches the area around a specific page of the data file
/// to find all matches to term_in. The results are returned in
/// vectors. This method may search multiple pages.
- ///
+ ///
/// @param term_in
/// The key string to compare against.
/// @param sample_index
@@ -971,12 +971,12 @@ private:
vector<string> & keys_out,
vector<string> & data_out,
CSeqDBLockHold & locked);
-
+
/// Find matches in the given memory area of a string ISAM file.
- ///
+ ///
/// This searches the specified section of memory to find all
/// matches to term_in. The results are returned in vectors.
- ///
+ ///
/// @param term_in
/// The key string to compare against.
/// @param page_index
@@ -998,14 +998,14 @@ private:
vector<TIndx> & indices_out,
vector<string> & keys_out,
vector<string> & data_out);
-
+
/// Map a page into memory
- ///
+ ///
/// Given two indices, this method maps into memory the area
/// starting at the beginning of the first index and extending to
/// the end of the other. (If the indices are equal, only one
/// page would be mapped.)
- ///
+ ///
/// @param SampleNum1
/// The first page index.
/// @param SampleNum2
@@ -1021,7 +1021,7 @@ private:
const char ** beginp,
const char ** endp,
CSeqDBLockHold & locked);
-
+
/// Test a sample key value from a numeric index.
///
/// This method reads the key value of an index file sample
@@ -1049,7 +1049,7 @@ private:
Int8 key_in,
Int8 & key_out,
int & data_out);
-
+
/// Get a sample key value from a numeric index.
///
/// Given the index of a sample value, this code will get the key.
@@ -1069,7 +1069,7 @@ private:
int index,
Int8 & key_out,
int & data_out);
-
+
/// Find ID in the negative GI list using PBS.
///
/// Use parabolic binary search to find the specified ID in the
@@ -1089,7 +1089,7 @@ private:
int & index,
Int8 key,
bool use_tis);
-
+
/// Map a data page.
///
/// The caller provides an index into the sample file. The page
@@ -1107,7 +1107,7 @@ private:
int & num_elements,
const void ** data_page_begin,
CSeqDBLockHold & locked);
-
+
/// Get a particular data element from a data page.
/// @param dpage A pointer to that page in memory. [in]
/// @param index The index of the element to fetch. [in]
@@ -1117,20 +1117,20 @@ private:
int index,
Int8 & key,
int & data);
-
+
/// Find the least and greatest keys in this ISAM file.
void x_FindIndexBounds(CSeqDBLockHold & locked);
-
+
/// Check whether a numeric key is within this volume's bounds.
/// @param key The key for which to do the check.
/// @param locked The lock holder object for this thread.
bool x_OutOfBounds(Int8 key, CSeqDBLockHold & locked);
-
+
/// Check whether a string key is within this volume's bounds.
/// @param key The key for which to do the check.
/// @param locked The lock holder object for this thread.
bool x_OutOfBounds(string key, CSeqDBLockHold & locked);
-
+
/// Converts a string to lower case.
static void x_Lower(string & s)
{
@@ -1138,15 +1138,15 @@ private:
s[i] = tolower(s[i]);
}
}
-
+
/// Fetch a GI or TI from a GI list.
static Int8 x_GetId(CSeqDBNegativeList & ids, int index, bool use_tis)
{
return (use_tis
? ids.GetTi(index)
- : ids.GetGi(index));
+ : GI_TO(Int8, ids.GetGi(index)));
}
-
+
/// Make filenames for ISAM file.
///
/// @param dbname Base name of the database volume. [in]
@@ -1159,72 +1159,72 @@ private:
char file_ext_char,
string & index_name,
string & data_name);
-
+
// Data
-
+
/// The memory management layer
CSeqDBAtlas & m_Atlas;
-
+
/// The type of identifier this class uses
ESeqDBIdType m_IdentType;
-
+
/// A persistent lease on the ISAM index file.
CSeqDBMemLease m_IndexLease;
-
+
/// A persistent lease on the ISAM data file.
CSeqDBMemLease m_DataLease;
-
+
/// The format type of database files found (eNumeric or eString).
int m_Type;
-
+
/// The filename of the ISAM data file.
string m_DataFname;
-
+
/// The filename of the ISAM index file.
string m_IndexFname;
-
+
/// The length of the ISAM data file.
TIndx m_DataFileLength;
-
+
/// The length of the ISAM index file.
TIndx m_IndexFileLength;
-
+
/// Number of terms in database
Int4 m_NumTerms;
-
+
/// Number of terms in ISAM index
Int4 m_NumSamples;
-
+
/// Page size of ISAM index
Int4 m_PageSize;
-
+
/// Maximum string length in the database
Int4 m_MaxLineSize;
-
+
/// Options set by upper layer
Int4 m_IdxOption;
-
+
/// Flag indicating whether initialization has been done.
bool m_Initialized;
-
+
/// Offset of samples in index file.
TIndx m_KeySampleOffset;
-
+
/// Check if data for String ISAM sorted
bool m_TestNonUnique;
-
+
/// Pointer to index file if no memmap.
char * m_FileStart;
-
+
/// First and last offset's of last page.
Int4 m_FirstOffset;
-
+
/// First and last offset's of last page.
Int4 m_LastOffset;
-
+
/// First volume key
SIsamKey m_FirstKey;
-
+
/// Last volume key
SIsamKey m_LastKey;
@@ -1256,16 +1256,16 @@ CSeqDBIsam::x_TestNumericSample(CSeqDBMemLease & index_lease,
Int8 & key_out,
int & data_out)
{
-
+
const void * keydatap = 0;
TIndx offset_begin = m_KeySampleOffset + (m_TermSize * index);
-
+
keydatap = index_lease.GetPtr(offset_begin);
key_out = x_GetNumericKey(keydatap);
-
+
int rv = 0;
-
+
if (key_in < key_out) {
rv = -1;
} else if (key_in > key_out) {
@@ -1274,7 +1274,7 @@ CSeqDBIsam::x_TestNumericSample(CSeqDBMemLease & index_lease,
rv = 0;
data_out = x_GetNumericData(keydatap);
}
-
+
return rv;
}
@@ -1285,14 +1285,53 @@ CSeqDBIsam::x_GetNumericSample(CSeqDBMemLease & index_lease,
int & data_out)
{
const void * keydatap = 0;
-
+
TIndx offset_begin = m_KeySampleOffset + (m_TermSize * index);
-
+
keydatap = index_lease.GetPtr(offset_begin);
key_out = x_GetNumericKey(keydatap);
data_out = x_GetNumericData(keydatap);
}
+/// Load and extract all index samples into array at once
+template <>
+inline void CSeqDBIsam::x_LoadIndex<TGi>(
+ CSeqDBMemLease & lease,
+ vector<TGi> & keys,
+ vector<TIndx> & offs
+)
+{
+ const char * keydatap = lease.GetPtr(m_KeySampleOffset);
+
+ for (int index=0; index < m_NumSamples; ++index) {
+ keys.push_back(GI_FROM(Uint8, x_GetNumericKey(keydatap)));
+ // vals.push_back(x_GetNumericData(keydatap));
+ offs.push_back(index * m_PageSize * m_TermSize);
+ keydatap += m_TermSize;
+ }
+
+ offs.push_back(m_NumTerms * m_TermSize);
+}
+
+/// Load and extract a data page into array at once
+template <>
+inline void CSeqDBIsam::x_LoadData<TGi>(
+ CSeqDBMemLease & lease,
+ vector<TGi> & keys,
+ vector<int> & vals,
+ int num_keys,
+ TIndx begin
+)
+{
+ const char * keydatap = lease.GetPtr(begin);
+
+ for (int index=0; index < num_keys; ++index) {
+ keys.push_back(GI_FROM(Uint8, x_GetNumericKey(keydatap)));
+ vals.push_back(x_GetNumericData(keydatap));
+ keydatap += m_TermSize;
+ }
+}
+
template <> inline void
CSeqDBIsam::x_LoadIndex<string>(CSeqDBMemLease & lease,
vector<string> & keys,
@@ -1300,7 +1339,7 @@ CSeqDBIsam::x_LoadIndex<string>(CSeqDBMemLease & lease,
{
TIndx offset_begin = m_KeySampleOffset;
TIndx sample_begin = offset_begin + sizeof(Uint4) * (m_NumSamples + 1);
-
+
// load offset array
const Uint4 * offset = (const Uint4 *) lease.GetPtr(offset_begin);
for (int index=0; index <= m_NumSamples; ++index, ++offset) {
@@ -1308,7 +1347,7 @@ CSeqDBIsam::x_LoadIndex<string>(CSeqDBMemLease & lease,
offs.push_back(SeqDB_GetStdOrd((Uint4*) offset));
}
- // load sample array
+ // load sample array
offset = (const Uint4 *) lease.GetPtr(sample_begin);
for (int index=0; index < m_NumSamples; ++index, ++offset) {
// Get the index_offsets
@@ -1324,10 +1363,10 @@ CSeqDBIsam::x_LoadIndex<string>(CSeqDBMemLease & lease,
/* key_begin = ++keydatap;
while (*keydatap != 0x00) ++keydatap;
vals.push_back(NStr::StringToUInt(string(key_begin, keydatap))); */
- }
+ }
}
-
-template <> inline void
+
+template <> inline void
CSeqDBIsam::x_LoadData<string>(CSeqDBMemLease & lease,
vector<string> & keys,
vector<int> & vals,
@@ -1355,29 +1394,29 @@ CSeqDBIsam::x_FindInNegativeList(CSeqDBNegativeList & ids,
bool use_tis)
{
bool found = false;
-
+
// Skip any that are less than key.
-
+
int ids_size = use_tis ? ids.GetNumTis() : ids.GetNumGis();
-
+
while((index < ids_size) && (x_GetId(ids, index, use_tis) < key)) {
index++;
-
+
int jump = 2;
-
+
while((index + jump) < ids_size &&
x_GetId(ids, index + jump, use_tis) < key) {
index += jump;
jump += jump;
}
}
-
+
// Check whether the GI or TI was found.
-
+
if ((index < ids_size) && (x_GetId(ids,index,use_tis) == key)) {
found = true;
}
-
+
return found;
}
@@ -1391,19 +1430,19 @@ CSeqDBIsam::x_MapDataPage(int sample_index,
{
num_elements =
x_GetPageNumElements(sample_index, & start);
-
+
TIndx offset_begin = start * m_TermSize;
TIndx offset_end = offset_begin + m_TermSize * num_elements;
-
+
m_Atlas.Lock(locked);
-
+
if (! m_DataLease.Contains(offset_begin, offset_end)) {
m_Atlas.GetRegion(m_DataLease,
m_DataFname,
offset_begin,
offset_end);
}
-
+
*data_page_begin = m_DataLease.GetPtr(offset_begin);
}
diff --git a/c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp b/c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
index 59a6cd4..2f3d3ed 100644
--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS_SEQDB__SEQDBVOL_HPP
#define OBJTOOLS_READERS_SEQDB__SEQDBVOL_HPP
-/* $Id: seqdbvol.hpp 400237 2013-05-20 15:28:07Z maning $
+/* $Id: seqdbvol.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,13 +50,13 @@ BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
/// CSeqDBGiIndex
-///
-/// This class maintains the OID->GI translation
+///
+/// This class maintains the OID->GI translation
class CSeqDBGiIndex : public CObject {
public:
typedef CSeqDBAtlas::TIndx TIndx;
typedef int TOid;
- typedef int TGi;
+// typedef int TGi;
CSeqDBGiIndex(CSeqDBAtlas & atlas,
const string & dbname,
@@ -77,7 +77,7 @@ public:
string fn(name + '.' + prot_nucl + "og");
return CFile(fn).Exists();
}
-
+
TGi GetSeqGI(TOid oid, CSeqDBLockHold & locked);
private:
@@ -87,7 +87,7 @@ private:
Int4 m_Size;
Int4 m_NumOIDs;
};
-
+
/// CSeqDBRangeList
///
@@ -112,22 +112,22 @@ public:
// performance further, but requires some consideration of the
// design with respect to locking and correctness.
}
-
+
/// Destructor.
~CSeqDBRangeList()
{
FlushSequence();
}
-
+
/// Returns true if the sequence data is cached.
bool IsCached()
{
return false;
}
-
+
/// List of sequence offset ranges.
typedef set< pair<int, int> > TRangeList;
-
+
/// Set ranges of the sequence that will be used.
/// @param ranges Offset ranges of the sequence that are needed. [in]
/// @param append_ranges If true, combine new ranges with old. [in]
@@ -135,46 +135,46 @@ public:
void SetRanges(const TRangeList & ranges,
bool append_ranges,
bool cache_data);
-
+
/// Get ranges of sequence offsets that will be used.
const TRangeList & GetRanges()
{
return m_Ranges;
}
-
+
/// Flush cached sequence data (if any).
void FlushSequence()
{
}
-
+
/// Sequences shorter than this will not use ranges in any case.
static int ImmediateLength()
{
return 10240;
}
-
+
private:
/// Memory management layer.
CSeqDBAtlas & m_Atlas;
-
+
/// Range of offsets needed for this sequence.
TRangeList m_Ranges;
-
+
/// True if caching of sequence data is required for this sequence.
bool m_CacheData;
-
+
/// Pointer to cached sequence data.
const char * m_Sequence;
-
+
/// Length of sequence.
int m_Length;
-
+
/// Number of user-held references to this sequence.
int m_RefCount;
};
/// CSeqDBVol class.
-///
+///
/// This object defines access to one database volume. It aggregates
/// file objects associated with the sequence and header data, and
/// ISAM objects used for translation of GIs and PIGs for data in this
@@ -186,7 +186,7 @@ class CSeqDBVol {
public:
/// Import TIndx definition from the CSeqDBAtlas class.
typedef CSeqDBAtlas::TIndx TIndx;
-
+
/// Constructor.
///
/// All files connected with the database volume will be opened,
@@ -194,7 +194,7 @@ public:
/// and identifier translation indices will be opened. The name
/// of these files is the specified name of the volume plus an
/// extension.
- ///
+ ///
/// @param atlas
/// The memory management layer object. [in]
/// @param name
@@ -218,7 +218,7 @@ public:
CSeqDBLockHold & locked);
/// Open sequence file
- ///
+ ///
/// By default, sequence file is opened on a "lazy" schedule.
/// This method will force the sequence file to be opened.
///
@@ -227,11 +227,11 @@ public:
void OpenSeqFile(CSeqDBLockHold &locked) const;
/// Sequence length for protein databases.
- ///
+ ///
/// This method returns the length of the sequence in bases, and
/// should only be called for protein sequences. It does not
/// require synchronization via the atlas object's lock.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -239,16 +239,16 @@ public:
/// @return
/// The length in bases of the sequence.
int GetSeqLengthProt(int oid, CSeqDBLockHold & locked) const;
-
+
/// Approximate sequence length for nucleotide databases.
- ///
+ ///
/// This method returns the length of the sequence using a fast
/// method that may be off by as much as 4 bases. The method is
/// designed to be unbiased, meaning that the total length of
/// large numbers of sequences will approximate what the exact
/// length would be. The approximate lengths will change if the
/// database is regenerated. It does not require synchronization.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -256,14 +256,14 @@ public:
/// @return
/// The approximate length in bases of the sequence.
int GetSeqLengthApprox(int oid, CSeqDBLockHold & locked) const;
-
+
/// Exact sequence length for nucleotide databases.
- ///
+ ///
/// This method returns the length of the sequence in bases, and
/// should only be called for nucleotide sequences. It requires
/// synchronization via the atlas object's lock, which must be
/// done in the calling code.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -271,9 +271,9 @@ public:
/// @return
/// The length in bases of the sequence.
int GetSeqLengthExact(int oid, CSeqDBLockHold & locked) const;
-
+
/// Get filtered sequence header information.
- ///
+ ///
/// This method returns the set of Blast-def-line objects stored
/// for each sequence. These contain descriptive information
/// related to the sequence. If OID filtering is enabled and a
@@ -282,7 +282,7 @@ public:
/// bit are contained in filt_info. This field may be NULL, in
/// which case OID list bit filtering is not done (in this case
/// the deflines are not cached).
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -292,19 +292,19 @@ public:
CRef<CBlast_def_line_set>
GetFilteredHeader(int oid,
CSeqDBLockHold & locked) const;
-
+
/// Get the sequence type stored in this database.
- ///
+ ///
/// This method returns the type of sequences stored in this
/// database, either kSeqTypeProt for protein, or kSeqTypeNucl for
/// nucleotide.
- ///
+ ///
/// @return
/// Either kSeqTypeProt for protein, or kSeqTypeNucl for nucleotide.
char GetSeqType() const;
-
+
/// Get a CBioseq object for this sequence.
- ///
+ ///
/// This method builds and returns a Bioseq for this sequence.
/// The taxonomy information is cached in this volume, so it
/// should not be modified directly, or other Bioseqs from this
@@ -320,7 +320,7 @@ public:
/// used to allow Bioseq summary data to be provided without the
/// performance penalty of loading (possibly very large) sequence
/// data from disk.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param pref_gi
@@ -337,14 +337,14 @@ public:
/// A CBioseq describing this sequence.
CRef<CBioseq>
GetBioseq(int oid,
- int pref_gi,
+ TGi pref_gi,
const CSeq_id * pref_seq_id,
CRef<CSeqDBTaxInfo> tax_info,
bool seqdata,
CSeqDBLockHold & locked);
-
+
/// Get the sequence data.
- ///
+ ///
/// This method gets the sequence data, returning a pointer and
/// the length of the sequence. The atlas will be locked, but the
/// lock may also be returned during this method. The computation
@@ -356,7 +356,7 @@ public:
/// the reference count we have acquired to return to the user.
/// The returned sequence data is intended for blast searches, and
/// will contain random values in any ambiguous regions.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param buffer
@@ -364,19 +364,19 @@ public:
/// @param locked
/// The lock holder object for this thread. [in]
/// @param in_lease
- /// Only perform sequence retrieval if the requested oid is
+ /// Only perform sequence retrieval if the requested oid is
/// within the previous lease [in]
/// @return
/// The length of this sequence in bases.
- int GetSequence(int oid, const char ** buffer,
+ int GetSequence(int oid, const char ** buffer,
CSeqDBLockHold & locked,
bool in_lease = false) const
{
return x_GetSequence(oid, buffer, true, locked, false, in_lease);
}
-
+
/// Get a sequence with ambiguous regions.
- ///
+ ///
/// This method gets the sequence data, returning a pointer and
/// the length of the sequence. For nucleotide sequences, the
/// data can be returned in one of two encodings. Specify either
@@ -385,7 +385,7 @@ public:
/// ways, enumerated in ESeqDBAllocType. Specify eAtlas to use
/// the Atlas code, eMalloc to use the malloc() function, or eNew
/// to use the new operator.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param buffer
@@ -407,12 +407,12 @@ public:
SSeqDBSlice * region,
CSeqDB::TSequenceRanges * masks,
CSeqDBLockHold & locked) const;
-
+
/// Get the Seq-ids associated with a sequence.
- ///
+ ///
/// This method returns a list containing all the CSeq_id objects
/// associated with a sequence.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -421,7 +421,7 @@ public:
/// The list of Seq-id objects for this sequences.
list< CRef<CSeq_id> > GetSeqIDs(int oid,
CSeqDBLockHold & locked) const;
-
+
/// Get the GI of a sequence
/// This method returns the gi of the sequence
///
@@ -429,24 +429,24 @@ public:
/// The OID of the sequence. [in]
/// @return
/// The oid of the sequence
- int GetSeqGI(int oid, CSeqDBLockHold & locked) const;
+ TGi GetSeqGI(int oid, CSeqDBLockHold & locked) const;
/// Get the volume title.
/// @return The volume's title.
string GetTitle() const;
-
+
/// Get the formatting date of the volume.
/// @return The create-date of the volume.
string GetDate() const;
-
+
/// Get the number of OIDs for this volume.
/// @return The number of OIDs.
int GetNumOIDs() const;
-
+
/// Get the total length of this volume (in bases).
/// @return The total volume length.
Uint8 GetVolumeLength() const;
-
+
/// Get the length of the largest sequence in this volume.
/// @return The largest sequence's length.
int GetMaxLength() const;
@@ -454,21 +454,21 @@ public:
/// Get the length of the smallest sequence in this volume.
/// @return The smallest sequence's length.
int GetMinLength() const;
-
+
/// Get the volume name.
/// @return The volume name.
const string & GetVolName() const
{
return m_VolName;
}
-
+
/// Return expendable resources held by this volume.
- ///
+ ///
/// This volume holds resources acquired via the atlas. This
/// method returns all such resources which can be automatically
/// reacquired (but not, for example, the index file data).
void UnLease();
-
+
/// Find the OID given a PIG.
///
/// A lookup is done for the PIG, and if found, the corresponding
@@ -483,11 +483,11 @@ public:
/// @return
/// True if the PIG was found.
bool PigToOid(int pig, int & oid, CSeqDBLockHold & locked) const;
-
+
/// Find the PIG given an OID.
- ///
+ ///
/// If this OID is associated with a PIG, the PIG is returned.
- ///
+ ///
/// @param oid
/// The oid of the sequence. [in]
/// @param pig
@@ -497,7 +497,7 @@ public:
/// @return
/// True if a PIG was returned.
bool GetPig(int oid, int & pig, CSeqDBLockHold & locked) const;
-
+
/// Find the OID given a TI.
///
/// A lookup is done for the TI, and if found, the corresponding
@@ -514,7 +514,7 @@ public:
bool TiToOid(Int8 ti,
int & oid,
CSeqDBLockHold & locked) const;
-
+
/// Find the OID given a GI.
///
/// A lookup is done for the GI, and if found, the corresponding
@@ -528,8 +528,8 @@ public:
/// The lock holder object for this thread. [in]
/// @return
/// True if an OID was returned.
- bool GiToOid(int gi, int & oid, CSeqDBLockHold & locked) const;
-
+ bool GiToOid(TGi gi, int & oid, CSeqDBLockHold & locked) const;
+
/// Find the GI given an OID.
///
/// If this OID is associated with a GI, the GI is returned.
@@ -543,9 +543,9 @@ public:
/// @return
/// True if a GI was returned.
bool GetGi(int oid,
- int & gi,
+ TGi & gi,
CSeqDBLockHold & locked) const;
-
+
/// Find OIDs for the specified accession or formatted Seq-id.
///
/// An attempt will be made to simplify the string by parsing it
@@ -564,7 +564,7 @@ public:
void AccessionToOids(const string & acc,
vector<int> & oids,
CSeqDBLockHold & locked) const;
-
+
/// Find OIDs for the specified Seq-id.
///
/// The Seq-id will be formatted and the resulting string will be
@@ -581,7 +581,7 @@ public:
void SeqidToOids(CSeq_id & seqid,
vector<int> & oids,
CSeqDBLockHold & locked) const;
-
+
/// Find the OID at a given index into the database.
///
/// This method considers the database as one long array of bases,
@@ -604,7 +604,7 @@ public:
int GetOidAtOffset(int first_seq,
Uint8 residue,
CSeqDBLockHold & locked) const;
-
+
/// Translate Gis to Oids for the given vector of Gi/Oid pairs.
///
/// This method iterates over a vector of Gi/Oid pairs. For each
@@ -619,7 +619,7 @@ public:
/// The lock holder object for this thread. [in]
void IdsToOids(CSeqDBGiList & gis,
CSeqDBLockHold & locked) const;
-
+
/// Add OIDs for this volume, filtered by negative ID lists.
///
/// This method iterates over a vector of Gis or Tis. For each
@@ -634,7 +634,7 @@ public:
/// The lock holder object for this thread. [in]
void IdsToOids(CSeqDBNegativeList & gis,
CSeqDBLockHold & locked) const;
-
+
/// Filter this volume using the specified GI list.
///
/// A volume can be filtered by a GI list. This method attaches a
@@ -647,14 +647,14 @@ public:
{
m_VolumeGiLists.push_back(gilist);
}
-
+
/// Simplify the GI list configuration.
///
/// When all user and volume GI lists have been attached, the user
/// GI list may be removed; this is only possible if neither the
/// user nor volume GI lists contain Seq-id data.
void OptimizeGiLists() const;
-
+
/// Fetch data as a CSeq_data object.
///
/// All or part of the sequence is fetched in a CSeq_data object.
@@ -674,7 +674,7 @@ public:
TSeqPos begin,
TSeqPos end,
CSeqDBLockHold & locked) const;
-
+
/// Get Raw Sequence and Ambiguity Data.
///
/// Get a pointer to the raw sequence and ambiguity data, and the
@@ -697,26 +697,26 @@ public:
int * seq_length,
int * ambig_length,
CSeqDBLockHold & locked) const;
-
+
/// Get GI Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of GIs. If the
/// operation fails, zero will be returned for count.
- ///
+ ///
/// @param low_id Lowest GI value in database. [out]
/// @param high_id Highest GI value in database. [out]
/// @param count Number of GI values in database. [out]
/// @param locked Lock holder object for this thread. [in]
- void GetGiBounds(int & low_id,
- int & high_id,
+ void GetGiBounds(TGi & low_id,
+ TGi & high_id,
int & count,
CSeqDBLockHold & locked) const;
-
+
/// Get PIG Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of PIGs. If the
/// operation fails, zero will be returned for count.
- ///
+ ///
/// @param low_id Lowest PIG value in database. [out]
/// @param high_id Highest PIG value in database. [out]
/// @param count Number of PIG values in database. [out]
@@ -725,13 +725,13 @@ public:
int & high_id,
int & count,
CSeqDBLockHold & locked) const;
-
+
/// Get String Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of string keys in
/// the database index. If the operation fails, zero will be
/// returned for count.
- ///
+ ///
/// @param low_id Lowest string value in database. [out]
/// @param high_id Highest string value in database. [out]
/// @param count Number of string values in database. [out]
@@ -740,10 +740,10 @@ public:
string & high_id,
int & count,
CSeqDBLockHold & locked) const;
-
+
/// List of sequence offset ranges.
typedef set< pair<int, int> > TRangeList;
-
+
/// Apply a range of offsets to a database sequence.
///
/// The GetAmbigSeq() method requires an amount of work (and I/O)
@@ -780,7 +780,7 @@ public:
bool append_ranges,
bool cache_data,
CSeqDBLockHold & locked) const;
-
+
/// Flush all offset ranges cached
/// @param locked Lock holder object for this thread. [in]
void FlushOffsetRangeCache(CSeqDBLockHold& locked);
@@ -793,7 +793,7 @@ public:
/// @param oid The sequence to compute the hash of. [in]
/// @return The sequence hash.
unsigned GetSequenceHash(int oid);
-
+
/// Get the OIDs for a given sequence hash.
///
/// The OIDs corresponding to a hash value (if any) are found and
@@ -808,11 +808,11 @@ public:
void HashToOids(unsigned hash,
vector<int> & oids,
CSeqDBLockHold & locked) const;
-
+
/// List the titles of all columns for this volume.
void ListColumns(set<string> & titles,
CSeqDBLockHold & locked);
-
+
/// Get an ID number for a given column title.
///
/// For a given column title, this returns an ID that can be used
@@ -825,7 +825,7 @@ public:
/// @return Column ID number for this column, or -1. [in]
int GetColumnId(const string & title,
CSeqDBLockHold & locked);
-
+
/// Get all metadata for the specified column.
///
/// Columns may contain user-defined metadata as a list of
@@ -837,14 +837,14 @@ public:
/// If this is unsatisfactory, the two-argument version of this
/// method may be used to get more precise values for specific
/// volumes.
- ///
+ ///
/// @param col_id The column id from GetColumnId. [in]
/// @param locked The lock holder object for this thread. [in]
/// @return The map of metadata for this column. [out]
const map<string,string> &
GetColumnMetaData(int col_id,
CSeqDBLockHold & locked);
-
+
/// Fetch the data blob for the given column and oid.
///
/// This method finds the blob data for this OID and column, and
@@ -873,11 +873,11 @@ public:
CBlastDbBlob & blob,
bool keep,
CSeqDBLockHold & locked);
-
+
/// Set the MEMB_BIT fitlering for this volume.
///
/// This method sets the MEMB_BIT for the volume. If the
- /// MEMB_BIT has already been set, and the new bit is different,
+ /// MEMB_BIT has already been set, and the new bit is different,
/// exception will be thrown. This prevents conflicting MEMB_BIT
/// settings within an alias tree; nevertheless, it also prevents
/// aggregating the same volume with different MEMB_BIT settings,
@@ -905,25 +905,25 @@ private:
/// A set of GI lists.
typedef vector< CRef<CSeqDBGiList> > TGiLists;
-
+
/// Returns true if this volume has a positive ID list.
bool x_HaveGiList() const
{
return ! (m_UserGiList.Empty() && m_VolumeGiLists.empty());
}
-
+
/// Returns true if this volume has a negative ID list.
bool x_HaveNegativeList() const
{
return m_NegativeList.NotEmpty();
}
-
+
/// Returns true if this volume has an ID list.
bool x_HaveIdFilter() const
{
return x_HaveGiList() || x_HaveNegativeList();
}
-
+
/// Determine if a user ID list affects this ID, and how.
///
/// This is used to accumulate information about a Seq-id in two
@@ -956,7 +956,7 @@ private:
have_user = true;
}
}
-
+
if (! have_vol) {
if (m_VolumeGiLists.empty()) {
have_vol = true;
@@ -970,7 +970,7 @@ private:
}
}
}
-
+
/// Returns true if this volume's ID list has this Seq-id.
/// @param L A GI list to test against. [in]
/// @param id A Seq-id to test against L. [in]
@@ -979,7 +979,7 @@ private:
{
return L.FindId(id);
}
-
+
/// Returns true if this ID is not found in the negative ID list.
///
/// This checks whether an ID is found in the negative ID list,
@@ -1001,26 +1001,26 @@ private:
{
// A defline is included IFF either a GI or TI is found, and
// that ID is not on the list.
-
+
// I use the terms 'included' and 'mentioned' to describe the
// negative list processing as follows: "A negative list
// INCLUDES a TI or GI if that ID is not MENTIONED in the
// negative list."
-
+
bool match_type = false;
bool found = L.FindId(id, match_type);
-
+
return (! found) && match_type;
}
-
+
/// Get sequence header object.
- ///
+ ///
/// This method returns the sequence header information as an
/// ASN.1 object. Seq-ids of type "gnl|BL_ORD_ID|#" are stored as
/// values relative to this volume. If they will be returned to
/// the user in any way, specify true for adjust_oids to adjust
/// them to the global OID range.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param adjust_oids
@@ -1036,14 +1036,14 @@ private:
bool adjust_oids,
bool * changed,
CSeqDBLockHold & locked) const;
-
+
/// Get sequence header binary data.
- ///
+ ///
/// This method returns the sequence header information as a
/// reference to raw ASN.1 binary data. This reference can be
/// used until the next access to the Atlas layer or the header
/// data memory lease.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -1051,12 +1051,12 @@ private:
/// @return
/// The Blast-def-line-set describing this sequence.
CTempString x_GetHdrAsn1Binary(int oid, CSeqDBLockHold & locked) const;
-
+
/// Get binary sequence header information.
- ///
+ ///
/// This method reads the sequence header information (as binary
/// encoded ASN.1) into a supplied char vector.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param hdr_data
@@ -1067,15 +1067,15 @@ private:
x_GetFilteredBinaryHeader(int oid,
vector<char> & hdr_data,
CSeqDBLockHold & locked) const;
-
+
/// Get sequence header information.
- ///
+ ///
/// This method returns the set of Blast-def-line objects stored
/// for each sequence. These contain descriptive information
/// related to the sequence. If OID filtering is enabled and a
/// membership bit is used, only deflines with that membership bit
/// set will be returned.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param changed
@@ -1088,14 +1088,14 @@ private:
x_GetFilteredHeader(int oid,
bool * changed,
CSeqDBLockHold & locked) const;
-
+
/// Get sequence header information structures.
- ///
+ ///
/// This method reads the sequence header information and returns
/// a Seqdesc suitable for inclusion in a CBioseq. This object
/// will contain an opaque type, storing the sequence headers as
/// binary ASN.1, wrapped in a C++ ASN.1 structure (CSeqdesc).
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param locked
@@ -1104,12 +1104,12 @@ private:
/// The CSeqdesc to include in the CBioseq.
CRef<CSeqdesc> x_GetAsnDefline(int oid,
CSeqDBLockHold & locked) const;
-
+
/// Returns 'p' for protein databases, or 'n' for nucleotide.
char x_GetSeqType() const;
-
+
/// Get ambiguity information.
- ///
+ ///
/// This method is used to fetch the ambiguity data for sequences
/// in a nucleotide database. The ambiguity data describes
/// sections of the nucleotide sequence for which more than one of
@@ -1118,7 +1118,7 @@ private:
/// the sequence which have such data. This method only returns
/// the array of integers, and does not interpret them, except for
/// byte swapping.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param ambchars
@@ -1128,9 +1128,9 @@ private:
void x_GetAmbChar(int oid,
vector<Int4> & ambchars,
CSeqDBLockHold & locked) const;
-
+
/// Get a sequence with ambiguous regions.
- ///
+ ///
/// This method gets the sequence data, returning a pointer and
/// the length of the sequence. For nucleotide sequences, the
/// data can be returned in one of two encodings. Specify either
@@ -1139,7 +1139,7 @@ private:
/// ways, enumerated in ESeqDBAllocType. Specify eAtlas to use
/// the Atlas code, eMalloc to use the malloc() function, or eNew
/// to use the new operator.
- ///
+ ///
/// @param oid
/// The OID of the sequence. [in]
/// @param buffer
@@ -1161,7 +1161,7 @@ private:
SSeqDBSlice * region,
CSeqDB::TSequenceRanges *masks,
CSeqDBLockHold & locked) const;
-
+
/// Allocate memory in one of several ways.
///
/// This method provides functionality to allocate memory with the
@@ -1180,7 +1180,7 @@ private:
char * x_AllocType(size_t length,
ESeqDBAllocType alloc_type,
CSeqDBLockHold & locked) const;
-
+
/// Get sequence data.
///
/// The sequence data is found and returned for the specified
@@ -1191,7 +1191,7 @@ private:
/// flags are true, this code may return the lock holder object
/// before that point to reduce lock contention in multithreaded
/// code.
- ///
+ ///
/// @param oid
/// The ordinal ID of the sequence to get. [in]
/// @param buffer
@@ -1212,9 +1212,9 @@ private:
CSeqDBLockHold & locked,
bool can_release,
bool in_lease = false) const;
-
+
/// Get partial sequence data.
- ///
+ ///
/// The sequence data is found and returned for the specified oid
/// and offset range. If the region argument is non-null, the
/// region endpoints are verified against the sequence endpoints.
@@ -1222,7 +1222,7 @@ private:
/// that the code returns the length of the region in bases, but
/// buffer is set to a pointer to the beginning of the sequence,
/// not the beginning of the region.
- ///
+ ///
/// @param oid
/// The ordinal ID of the sequence to get. [in]
/// @param buffer
@@ -1243,7 +1243,7 @@ private:
CSeqDBLockHold & locked,
bool can_release,
SSeqDBSlice * region) const;
-
+
/// Get defline filtered by several criteria.
///
/// This method returns the set of deflines for a sequence. If
@@ -1251,20 +1251,23 @@ private:
/// filtered by membership bit. If there is a preferred GI is
/// specified, the defline matching that GI (if found) will be
/// moved to the front of the set.
- ///
+ ///
/// @param oid
/// The ordinal ID of the sequence to get. [in]
/// @param preferred_gi
- /// This GI's defline (if found) will be put at the front of the list. [in]
+ /// This GI's defline (if non-zero and found) will be put at the front of the list. [in]
+ /// @param preferred_seqid
+ /// This SeqID's defline (if non-NULL and found) will be put at the front of the list. [in]
/// @param locked
/// The lock holder object for this thread. [in]
/// @return
/// The defline set for the specified oid.
CRef<CBlast_def_line_set>
x_GetTaxDefline(int oid,
- int preferred_gi,
+ TGi preferred_gi,
+ const CSeq_id * preferred_seq_id,
CSeqDBLockHold & locked);
-
+
/// Get taxonomic descriptions of a sequence.
///
/// This method builds a set of CSeqdesc objects from taxonomic
@@ -1274,11 +1277,13 @@ private:
/// matching that GI (if found) will be moved to the front of the
/// set. This method is called as part of the processing for
/// building a CBioseq object.
- ///
+ ///
/// @param oid
/// The ordinal ID of the sequence to get. [in]
/// @param preferred_gi
- /// This GI's defline (if found) will be put at the front of the list. [in]
+ /// This GI's defline (if non-zero and found) will be put at the front of the list. [in]
+ /// @param preferred_seqid
+ /// This SeqID's defline (if non-NULL and found) will be put at the front of the list. [in]
/// @param tax_info
/// Taxonomic info to encode. [in]
/// @param locked
@@ -1287,10 +1292,11 @@ private:
/// A list of CSeqdesc objects for the specified oid.
list< CRef<CSeqdesc> >
x_GetTaxonomy(int oid,
- int preferred_gi,
+ TGi preferred_gi,
+ const CSeq_id * preferred_seq_id,
CRef<CSeqDBTaxInfo> tax_info,
CSeqDBLockHold & locked);
-
+
/// Returns the base-offset of the specified oid.
///
/// This method finds the starting offset of the OID relative to
@@ -1308,7 +1314,7 @@ private:
/// @return
/// The offset in the volume of that sequence in bytes.
Uint8 x_GetSeqResidueOffset(int oid, CSeqDBLockHold & locked) const;
-
+
/// Find all columns for this volume.
///
/// This method looks for and opens any columns that might be
@@ -1317,7 +1323,7 @@ private:
/// @param locked
/// The lock holder object for this thread. [in]
void x_OpenAllColumns(CSeqDBLockHold & locked);
-
+
/// Check Seq-id versions for special sparse-id support case.
///
/// The BlastDB `sparse indexing' feature omits versions when
@@ -1348,54 +1354,54 @@ private:
void x_OpenTiFile(CSeqDBLockHold &locked) const;
void x_OpenHashFile(CSeqDBLockHold &locked) const;
void x_OpenOidFile(CSeqDBLockHold &locked) const;
-
+
/// The memory management layer.
CSeqDBAtlas & m_Atlas;
-
+
/// True if the volume is protein, false for nucleotide.
bool m_IsAA;
-
+
/// The name of this volume.
string m_VolName;
-
+
/// Metadata plus offsets into the sequence, header, and ambiguity data.
CRef<CSeqDBIdxFile> m_Idx;
-
+
/// Contains sequence data for this volume.
mutable CRef<CSeqDBSeqFile> m_Seq;
-
+
/// Contains header (defline) information for this volume.
mutable CRef<CSeqDBHdrFile> m_Hdr;
-
+
// These are mutable because they defer initialization.
-
+
/// Handles translation of GIs to OIDs.
mutable CRef<CSeqDBIsam> m_IsamPig;
-
+
/// Handles translation of GIs to OIDs.
mutable CRef<CSeqDBIsam> m_IsamGi;
-
+
/// Handles translation of strings (accessions) to OIDs.
mutable CRef<CSeqDBIsam> m_IsamStr;
-
+
/// Handles translation of TI (trace ids) to OIDs.
mutable CRef<CSeqDBIsam> m_IsamTi;
-
+
/// Handles translation of sequence hash value to OIDs.
mutable CRef<CSeqDBIsam> m_IsamHash;
-
+
/// The GI index file (for fast oid->gi conversion)
mutable CRef<CSeqDBGiIndex> m_GiIndex;
/// This cache allows CBioseqs to share taxonomic objects.
mutable CSeqDBIntCache< CRef<CSeqdesc> > m_TaxCache;
-
+
/// The user ID list, if one exists.
mutable CRef<CSeqDBGiList> m_UserGiList;
-
+
/// The negative ID list, if one exists.
mutable CRef<CSeqDBNegativeList> m_NegativeList;
-
+
/// The volume GI lists, if any exist.
mutable TGiLists m_VolumeGiLists;
@@ -1404,22 +1410,22 @@ private:
/// Cached/ranged sequence info type.
typedef map<int, CRef<CSeqDBRangeList> > TRangeCache;
-
+
/// Cached/ranged sequence info.
mutable TRangeCache m_RangeCache;
-
+
/// Starting OID of this volume.
int m_VolStart;
-
+
/// First OID past end of this volume.
int m_VolEnd;
-
+
/// Filtered defline plus whether binary data needed changes.
typedef pair<CRef<CBlast_def_line_set>, bool> TDeflineCacheItem;
-
+
/// Cache of filtered deflines.
mutable CSeqDBIntCache<TDeflineCacheItem> m_DeflineCache;
-
+
/// True if we have opened the columns for this volume.
bool m_HaveColumns;
@@ -1432,7 +1438,7 @@ private:
mutable bool m_TiFileOpened;
mutable bool m_HashFileOpened;
mutable bool m_OidFileOpened;
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Set of columns defined for this volume.
diff --git a/c++/include/objtools/blast/seqdb_reader/seqdb.hpp b/c++/include/objtools/blast/seqdb_reader/seqdb.hpp
index 7bcc466..27c49c6 100644
--- a/c++/include/objtools/blast/seqdb_reader/seqdb.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/seqdb.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_BLAST_SEQDB_READER___SEQDB__HPP
#define OBJTOOLS_BLAST_SEQDB_READER___SEQDB__HPP
-/* $Id: seqdb.hpp 453781 2014-12-08 15:31:31Z ivanov $
+/* $Id: seqdb.hpp 468781 2015-05-28 12:51:59Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -189,6 +189,27 @@ public:
eFilteredRange
};
+ /// File type for which mmap strategy may be set.
+ enum EMmapFileTypes {
+ /// Index files (name ends with ".pin" or ".nin").
+ eMmap_IndexFile,
+
+ /// Sequence files (name ends with ".psq" or ".nsq").
+ eMmap_SequenceFile
+ };
+
+ /// Permitted mmap strategies.
+ enum EMmapStrategies {
+ /// Normal, no special behavior (should undo next two options).
+ eMmap_Normal,
+
+ /// Expect sequential page references.
+ eMmap_Sequential,
+
+ /// Expect access in the near future.
+ eMmap_WillNeed
+ };
+
/// Sequence type accepted and returned for OID indices.
typedef int TOID;
@@ -196,8 +217,8 @@ public:
typedef int TPIG;
/// Sequence type accepted and returned for GI indices.
- typedef int TGI;
-
+ typedef TGi TGI;
+
/// Structure to represent a range
struct TOffsetPair {
TSeqPos first;
@@ -428,6 +449,17 @@ public:
/// been returned by RetSequence().
~CSeqDB();
+ /// Sets mmap strategy to be used when mapping index or sequence files.
+ ///
+ /// This method sets internal flags of type EMemoryAdvise for a call to
+ /// MemoryAdvise in CRegionMap::MapMmap.
+ /// Note that these are only hints, the system may or may not
+ /// actually alter its behavior when mapping these files.
+ static void SetMmapStrategy(
+ EMmapFileTypes filetype,
+ EMmapStrategies strategy
+ );
+
/// Returns the default BLAST database search path
/// configured for this local installation of BLAST
static string GenerateSearchPath();
@@ -440,7 +472,7 @@ public:
/// all filtering is applied (e.g.: GI list restriction or membership bit).
/// If you need those checks, please use GetGis()
/// @sa GetGis
- int GetSeqGI(int oid) const;
+ TGi GetSeqGI(int oid) const;
/// Returns an unbiased, approximate sequence length.
///
@@ -478,7 +510,7 @@ public:
/// If false, the map will be cleared before adding new entries.
void GetLeafTaxIDs(
int oid,
- map<int, set<int> >& gi_to_taxid_set,
+ map<TGi, set<int> >& gi_to_taxid_set,
bool persist = false
) const;
@@ -520,7 +552,7 @@ public:
/// @param persist
/// If false, the map will be cleared before adding new entries.
void GetTaxIDs(int oid,
- map<int, int> & gi_to_taxid,
+ map<TGi, int> & gi_to_taxid,
bool persist = false) const;
/// Get taxids for an OID.
@@ -560,7 +592,7 @@ public:
/// @return
/// A CBioseq object corresponding to the sequence.
CRef<CBioseq> GetBioseq(int oid,
- int target_gi = 0,
+ TGi target_gi = ZERO_GI,
const CSeq_id * target_seq_id = NULL) const;
/// Get a CBioseq for a sequence without sequence data.
@@ -580,7 +612,7 @@ public:
/// A CBioseq object corresponding to the sequence, but without
/// sequence data.
CRef<CBioseq> GetBioseqNoData(int oid,
- int target_gi = 0,
+ TGi target_gi = ZERO_GI,
const CSeq_id * target_seq_id = NULL) const;
/// Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB
@@ -739,7 +771,7 @@ public:
/// The returned list of gis.
/// @param append
/// Specify true to append to gis, keeping existing elements.
- void GetGis(int oid, vector<int> & gis, bool append = false) const;
+ void GetGis(int oid, vector<TGi> & gis, bool append = false) const;
/// Returns the type of database opened - protein or nucleotide.
///
@@ -979,16 +1011,16 @@ public:
bool TiToOid(Int8 ti, int & oid) const;
/// Translate an OID to a GI.
- bool OidToGi(int oid, int & gi) const;
+ bool OidToGi(int oid, TGi & gi) const;
/// Translate a GI to an OID.
- bool GiToOid(int gi, int & oid) const;
+ bool GiToOid(TGi gi, int & oid) const;
/// Translate a GI to a PIG.
- bool GiToPig(int gi, int & pig) const;
+ bool GiToPig(TGi gi, int & pig) const;
/// Translate a PIG to a GI.
- bool PigToGi(int pig, int & gi) const;
+ bool PigToGi(int pig, TGi & gi) const;
/// Translate an Accession to a list of OIDs.
void AccessionToOids(const string & acc, vector<int> & oids) const;
@@ -1025,7 +1057,7 @@ public:
/// The GI of the sequence.
/// @return
/// A CBioseq object corresponding to the sequence.
- CRef<CBioseq> GiToBioseq(int gi) const;
+ CRef<CBioseq> GiToBioseq(TGi gi) const;
/// Get a CBioseq for a given PIG
///
@@ -1433,6 +1465,10 @@ public:
/// Retrieve the disk usage in bytes for this BLAST database
Int8 GetDiskUsage() const;
+
+ /// Set the membership of all volumes
+ void SetVolsMemBit(int mbit);
+
protected:
/// Implementation details are hidden. (See seqdbimpl.hpp).
class CSeqDBImpl * m_Impl;
@@ -1595,7 +1631,7 @@ public:
/// Returns the BLASTDB list originally provided in the constructor
string GetOrigDbList() const { return m_OrigWgsList; }
private:
- typedef map<string, vector<int> > TGiLists;
+ typedef map<string, vector<TGi> > TGiLists;
/// Reads the gi lists for each of the BLAST DBs provided in the
/// constructor, ignoring those that can't be found
TGiLists x_ReadGiListsForDbs();
diff --git a/c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp b/c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp
index 5e6f286..b50cf83 100644
--- a/c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_BLAST_SEQDB_READER___SEQDBCOMMON__HPP
#define OBJTOOLS_BLAST_SEQDB_READER___SEQDBCOMMON__HPP
-/* $Id: seqdbcommon.hpp 448104 2014-10-02 15:01:54Z ivanov $
+/* $Id: seqdbcommon.hpp 484802 2015-11-16 15:18:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@
/// @file seqdbcommon.hpp
/// Defines exception class and several constants for SeqDB.
-///
+///
/// Defines classes:
/// CSeqDBException
-///
+///
/// Implemented for: UNIX, MS-Windows
#include <ncbiconf.h>
@@ -49,7 +49,7 @@ USING_SCOPE(objects);
/// CSeqDBException
-///
+///
/// This exception class is thrown for SeqDB related errors such as
/// corrupted blast database or alias files, incorrect arguments to
/// SeqDB methods, and failures of SeqDB to accomplish tasks for other
@@ -66,14 +66,14 @@ public:
enum EErrCode {
/// Argument validation failed.
eArgErr,
-
+
/// Files were missing or contents were incorrect.
eFileErr,
-
+
/// Memory allocation failed.
eMemErr
};
-
+
/// Get a message describing the situation leading to the throw.
virtual const char* GetErrCodeString() const
{
@@ -83,7 +83,7 @@ public:
default: return CException::GetErrCodeString();
}
}
-
+
/// Include standard NCBI exception behavior.
NCBI_EXCEPTION_DEFAULT(CSeqDBException,CException);
};
@@ -112,8 +112,11 @@ enum ESeqDBAllocType {
};
+typedef Uint8 TTi;
+
+
/// CSeqDBGiList
-///
+///
/// This class defines an interface to a list of GI,OID pairs. It is
/// used by the CSeqDB class for user specified GI lists. This class
/// should not be instantiated directly, instead use a subclass of
@@ -127,18 +130,18 @@ public:
/// Constuct an SGiOid element from the given gi and oid.
/// @param gi_in A GI, or 0 if none is available.
/// @param oid_in An OID, or -1 if none is available.
- SGiOid(int gi_in = 0, int oid_in = -1)
+ SGiOid(TGi gi_in = ZERO_GI, int oid_in = -1)
: gi(gi_in), oid(oid_in)
{
}
-
+
/// The GI or 0 if unknown.
- int gi;
-
+ TGi gi;
+
/// The OID or -1 if unknown.
int oid;
};
-
+
/// Structure that holds TI,OID pairs.
struct STiOid {
/// Constuct an STiOid element from the given TI (trace ID,
@@ -146,18 +149,18 @@ public:
///
/// @param ti_in A TI, or 0 if none is available.
/// @param oid_in An OID, or -1 if none is available.
- STiOid(Int8 ti_in = 0, int oid_in = -1)
+ STiOid(TTi ti_in = 0, int oid_in = -1)
: ti(ti_in), oid(oid_in)
{
}
-
+
/// The TI or 0 if unknown.
- Int8 ti;
-
+ TTi ti;
+
/// The OID or -1 if unknown.
int oid;
};
-
+
/// Structure that holds Seq-id,OID pairs.
struct SSiOid {
/// Constuct a SSiOid element from the given Seq-id and oid.
@@ -169,75 +172,75 @@ public:
// make sure to lower case as this is what's indexed in ISAM
NStr::ToLower(si);
}
-
+
/// The String-id or "" if unknown.
string si;
-
+
/// The OID or -1 if unknown.
int oid;
};
-
+
/// Possible sorting states
enum ESortOrder {
/// The array is unsorted or the sortedness is unknown.
eNone,
-
+
/// The array is sorted by GI.
eGi
/// TODO should we define eTi and eSi?
};
-
+
/// Constructor
CSeqDBGiList();
-
+
/// Destructor
virtual ~CSeqDBGiList()
{
}
-
+
/// Sort if necessary to insure order of elements.
void InsureOrder(ESortOrder order);
-
+
/// Test for existence of a GI.
- bool FindGi(int gi) const;
-
+ bool FindGi(TGi gi) const;
+
/// Try to find a GI and return the associated OID.
/// @param gi The gi for which to search. [in]
/// @param oid The resulting oid if found. [out]
/// @return True if the GI was found.
- bool GiToOid(int gi, int & oid);
-
+ bool GiToOid(TGi gi, int & oid);
+
/// Find a GI, returning the index and the associated OID.
/// @param gi The gi for which to search. [in]
/// @param oid The resulting oid if found. [out]
/// @param index The index of this GI (if found). [out]
/// @return True if the GI was found.
- bool GiToOid(int gi, int & oid, int & index);
-
+ bool GiToOid(TGi gi, int & oid, int & index);
+
/// Test for existence of a TI.
- bool FindTi(Int8 ti) const;
-
+ bool FindTi(TTi ti) const;
+
/// Try to find a TI and return the associated OID.
/// @param ti The ti for which to search. [in]
/// @param oid The resulting oid if found. [out]
/// @return True if the TI was found.
- bool TiToOid(Int8 ti, int & oid);
-
+ bool TiToOid(TTi ti, int & oid);
+
/// Find a TI, returning the index and the associated OID.
/// @param ti The ti for which to search. [in]
/// @param oid The resulting oid if found. [out]
/// @param index The index of this TI (if found). [out]
/// @return True if the TI was found.
- bool TiToOid(Int8 ti, int & oid, int & index);
+ bool TiToOid(TTi ti, int & oid, int & index);
+
-
bool FindSi(const string & si) const;
bool SiToOid(const string &si, int & oid);
bool SiToOid(const string &si, int & oid, int & index);
-
+
/// Test for existence of a Seq-id by type.
- ///
+ ///
/// This method uses FindGi or FindTi if the input ID is a GI or
/// TI. If not, or if not found, it falls back to a Seq-id lookup
/// to find the ID. It returns true iff ID was found, otherwise
@@ -247,7 +250,7 @@ public:
/// @param id The identifier to find.
/// @return true iff the id is found in the list.
bool FindId(const CSeq_id & id);
-
+
/// Access an element of the array.
/// @param index The index of the element to access. [in]
/// @return A reference to the GI/OID pair.
@@ -255,7 +258,7 @@ public:
{
return m_GisOids[index];
}
-
+
/// Access an element of the array.
/// @param index The index of the element to access. [in]
/// @return A reference to the TI/OID pair.
@@ -263,7 +266,7 @@ public:
{
return m_TisOids[index];
}
-
+
/// Access an element of the array.
/// @param index The index of the element to access. [in]
/// @return A reference to the Seq-id/OID pair.
@@ -271,37 +274,37 @@ public:
{
return m_SisOids[index];
}
-
+
/// Get the number of GIs in the array.
int GetNumGis() const
{
return (int) m_GisOids.size();
}
-
+
/// Get the number of TIs in the array.
int GetNumTis() const
{
return (int) m_TisOids.size();
}
-
+
/// Get the number of Seq-ids in the array.
int GetNumSis() const
{
return (int) m_SisOids.size();
}
-
+
/// Return false if there are elements present.
bool Empty() const
{
return ! (GetNumGis() || GetNumSis() || GetNumTis());
}
-
+
/// Return true if there are elements present.
bool NotEmpty() const
{
return ! Empty();
}
-
+
/// Specify the correct OID for a GI.
///
/// When SeqDB translates a GI into an OID, this method is called
@@ -315,7 +318,7 @@ public:
{
m_GisOids[index].oid = oid;
}
-
+
/// Specify the correct OID for a TI.
///
/// When SeqDB translates a TI into an OID, this method is called
@@ -329,7 +332,7 @@ public:
{
m_TisOids[index].oid = oid;
}
-
+
/// Specify the correct OID for a Seq-id.
///
/// When SeqDB translates a Seq-id into an OID, this method is
@@ -343,7 +346,7 @@ public:
{
m_SisOids[index].oid = oid;
}
-
+
int Size() const
{
return (int) m_GisOids.size();
@@ -368,31 +371,31 @@ public:
}
template <class T>
- void SetValue(int index, int oid)
+ void SetValue(int index, int oid)
{
m_GisOids[index].oid = oid;
}
/// Get the gi list
- void GetGiList(vector<int>& gis) const;
-
+ void GetGiList(vector<TGi>& gis) const;
+
/// Get the ti list
- void GetTiList(vector<Int8>& tis) const;
+ void GetTiList(vector<TTi>& tis) const;
/// TODO Get the seqid list?
-
+
/// Add a new GI to the list.
- void AddGi(int gi)
+ void AddGi(TGi gi)
{
m_GisOids.push_back(gi);
}
-
+
/// Add a new TI to the list.
- void AddTi(Int8 ti)
+ void AddTi(TTi ti)
{
m_TisOids.push_back(ti);
}
-
+
/// Add a new SeqId to the list.
void AddSi(const string &si)
{
@@ -404,27 +407,27 @@ public:
{
m_GisOids.reserve(n);
}
-
+
/// Reserve space for TIs.
void ReserveTis(size_t n)
{
m_TisOids.reserve(n);
}
-
+
/// TODO Reserve space for seqids?
protected:
/// Indicates the current sort order, if any, of this container.
ESortOrder m_CurrentOrder;
-
+
/// Pairs of GIs and OIDs.
vector<SGiOid> m_GisOids;
-
+
/// Pairs of GIs and OIDs.
vector<STiOid> m_TisOids;
-
+
/// Pairs of Seq-ids and OIDs.
vector<SSiOid> m_SisOids;
-
+
private:
// The following disabled methods are reasonable things to do in
// some cases. But I suspect they are more likely to happen
@@ -432,34 +435,34 @@ private:
// cost, I have prevented them. If this kind of deep copy is
// desireable, it can easily be enabled for a subclass by
// assigning each of the data fields in the protected section.
-
+
/// Prevent copy constructor.
CSeqDBGiList(const CSeqDBGiList & other);
-
+
/// Prevent assignment.
CSeqDBGiList & operator=(const CSeqDBGiList & other);
};
template < >
-inline int CSeqDBGiList::GetSize<Int8>() const
+inline int CSeqDBGiList::GetSize<TTi>() const
{
return (int) m_TisOids.size();
}
template < >
-inline const Int8 & CSeqDBGiList::GetKey<Int8>(int index) const
+inline const TTi & CSeqDBGiList::GetKey<TTi>(int index) const
{
return m_TisOids[index].ti;
}
template < >
-inline bool CSeqDBGiList::IsValueSet<Int8>(int index) const
+inline bool CSeqDBGiList::IsValueSet<TTi>(int index) const
{
return (m_TisOids[index].oid != -1);
}
template < >
-inline void CSeqDBGiList::SetValue<Int8>(int index, int oid)
+inline void CSeqDBGiList::SetValue<TTi>(int index, int oid)
{
m_TisOids[index].oid = oid;
}
@@ -489,7 +492,7 @@ inline void CSeqDBGiList::SetValue<string>(int index, int oid)
}
/// CSeqDBBitVector
-///
+///
/// This class defines a bit vector that is similar to vector<bool>,
/// but with a differently designed API that performs better on at
/// least some platforms, and slightly altered semantics.
@@ -501,12 +504,12 @@ public:
: m_Size(0)
{
}
-
+
/// Destructor
virtual ~CSeqDBBitVector()
{
}
-
+
/// Set the inclusion of an OID.
///
/// @param oid The OID in question. [in]
@@ -517,7 +520,7 @@ public:
}
x_SetBit(oid);
}
-
+
/// Set the inclusion of an OID.
///
/// @param oid The OID in question. [in]
@@ -528,7 +531,7 @@ public:
}
x_ClearBit(oid);
}
-
+
/// Get the inclusion status of an OID.
///
/// @param oid The OID in question. [in]
@@ -540,76 +543,76 @@ public:
}
return x_GetBit(oid);
}
-
+
/// Get the size of the OID array.
int Size() const
{
return m_Size;
}
-
+
private:
/// Prevent copy constructor.
CSeqDBBitVector(const CSeqDBBitVector & other);
-
+
/// Prevent assignment.
CSeqDBBitVector & operator=(const CSeqDBBitVector & other);
-
+
/// Bit vector element.
typedef int TBits;
-
+
/// Bit vector.
vector<TBits> m_Bitmap;
-
+
/// Maximum enabled OID plus one.
int m_Size;
-
+
/// Resize the OID list.
void x_Resize(int num)
{
int bits = 8*sizeof(TBits);
int need = (num + bits - 1)/bits;
-
+
if ((int)m_Bitmap.size() < need) {
int new_size = 1024;
-
+
while (new_size < need) {
new_size *= 2;
}
-
+
m_Bitmap.resize(new_size);
}
-
+
m_Size = num;
}
-
+
/// Set a specific bit (to 1).
void x_SetBit(int num)
{
int bits = 8*sizeof(TBits);
-
+
m_Bitmap[num/bits] |= (1 << (num % bits));
}
-
+
/// Set a specific bit (to 1).
bool x_GetBit(int num)
{
int bits = 8*sizeof(TBits);
-
+
return !! (m_Bitmap[num/bits] & (1 << (num % bits)));
}
-
+
/// Clear a specific bit (to 0).
void x_ClearBit(int num)
{
int bits = 8*sizeof(TBits);
-
+
m_Bitmap[num/bits] &= ~(1 << (num % bits));
}
};
/// CSeqDBNegativeList
-///
+///
/// This class defines a list of GIs or TIs of sequences that should
/// not be included in a SeqDB instance. It is used by CSeqDB for
/// user specified negative ID lists. This class can be subclassed to
@@ -622,12 +625,12 @@ public:
: m_LastSortSize (0)
{
}
-
+
/// Destructor
virtual ~CSeqDBNegativeList()
{
}
-
+
/// Sort list if not already sorted.
void InsureOrder()
{
@@ -635,23 +638,23 @@ public:
std::sort(m_Gis.begin(), m_Gis.end());
std::sort(m_Tis.begin(), m_Tis.end());
std::sort(m_Sis.begin(), m_Sis.end());
-
+
m_LastSortSize = m_Gis.size() + m_Tis.size() + m_Sis.size();
}
}
-
+
/// Add a new GI to the list.
- void AddGi(int gi)
+ void AddGi(TGi gi)
{
m_Gis.push_back(gi);
}
-
+
/// Add a new TI to the list.
- void AddTi(Int8 ti)
+ void AddTi(TTi ti)
{
m_Tis.push_back(ti);
}
-
+
/// Add a new SeqId to the list.
void AddSi(const string &si)
{
@@ -659,14 +662,14 @@ public:
}
/// Test for existence of a GI.
- bool FindGi(int gi);
-
+ bool FindGi(TGi gi);
+
/// Test for existence of a TI.
- bool FindTi(Int8 ti);
-
+ bool FindTi(TTi ti);
+
/// Test for existence of a TI or GI here and report whether the
/// ID was one of those types.
- ///
+ ///
/// If the input ID is a GI or TI, this method sets match_type to
/// true and returns the output of FindGi or FindTi. If it is
/// neither of those types, it sets match_type to false and
@@ -677,26 +680,26 @@ public:
/// @param match_type The identifier is either a TI or GI.
/// @return true iff the id is found in the list.
bool FindId(const CSeq_id & id, bool & match_type);
-
+
/// Test for existence of a TI or GI included here.
bool FindId(const CSeq_id & id);
-
+
/// Access an element of the GI array.
/// @param index The index of the element to access. [in]
/// @return The GI for that index.
- int GetGi(int index) const
+ TGi GetGi(int index) const
{
return m_Gis[index];
}
-
+
/// Access an element of the TI array.
/// @param index The index of the element to access. [in]
/// @return The TI for that index.
- Int8 GetTi(int index) const
+ TTi GetTi(int index) const
{
return m_Tis[index];
}
-
+
/// Access an element of the SeqId array.
/// @param index The index of the element to access. [in]
/// @return The TI for that index.
@@ -710,31 +713,31 @@ public:
{
return (int) m_Gis.size();
}
-
+
/// Get the number of TIs in the array.
int GetNumTis() const
{
return (int) m_Tis.size();
}
-
+
/// Get the number of SeqIds in the array.
int GetNumSis() const
{
return (int) m_Sis.size();
}
-
+
/// Return false if there are elements present.
bool Empty() const
{
return ! (GetNumGis() || GetNumTis() || GetNumSis());
}
-
+
/// Return true if there are elements present.
bool NotEmpty() const
{
return ! Empty();
}
-
+
/// Include an OID in the iteration.
///
/// The OID will be included by SeqDB in the set returned to users
@@ -745,7 +748,7 @@ public:
{
m_Included.SetBit(oid);
}
-
+
/// Indicate a visible OID.
///
/// The OID will be marked as having been found in a GI or TI
@@ -756,7 +759,7 @@ public:
{
m_Visible.SetBit(oid);
}
-
+
/// Get the inclusion status of an OID.
///
/// This returns true for OIDs that were in the included set and
@@ -768,40 +771,40 @@ public:
{
return m_Included.GetBit(oid) || (! m_Visible.GetBit(oid));
}
-
+
/// Get the size of the OID array.
int GetNumOids()
{
return max(m_Visible.Size(), m_Included.Size());
}
-
+
/// Reserve space for GIs.
void ReserveGis(size_t n)
{
m_Gis.reserve(n);
}
-
+
/// Reserve space for TIs.
void ReserveTis(size_t n)
{
m_Tis.reserve(n);
}
-
+
/// Build ID set for this negative list.
- const vector<int> & GetGiList()
+ const vector<TGi> & GetGiList()
{
return m_Gis;
}
-
+
/// Set ID set for this negative list.
- void SetGiList( const vector<int> & new_list )
+ void SetGiList( const vector<TGi> & new_list )
{
m_Gis.clear();
m_Gis.reserve( new_list.size() );
m_Gis = new_list;
}
/// Build ID set for this negative list.
- const vector<Int8> & GetTiList()
+ const vector<TTi> & GetTiList()
{
return m_Tis;
}
@@ -812,27 +815,27 @@ public:
}
protected:
/// GIs to exclude from the SeqDB instance.
- vector<int> m_Gis;
-
+ vector<TGi> m_Gis;
+
/// TIs to exclude from the SeqDB instance.
- vector<Int8> m_Tis;
-
+ vector<TTi> m_Tis;
+
/// SeqIds to exclude from the SeqDB instance.
vector<string> m_Sis;
-
+
private:
/// Prevent copy constructor.
CSeqDBNegativeList(const CSeqDBNegativeList & other);
-
+
/// Prevent assignment.
CSeqDBNegativeList & operator=(const CSeqDBNegativeList & other);
-
+
/// Included OID bitmap.
CSeqDBBitVector m_Included;
-
+
/// OIDs visible to the ISAM file.
CSeqDBBitVector m_Visible;
-
+
/// Zero if unsorted, or the size it had after the last sort.
size_t m_LastSortSize;
};
@@ -843,7 +846,7 @@ private:
/// @param name The name of the file containing GIs. [in]
/// @param gis The GIs returned by this function. [out]
NCBI_XOBJREAD_EXPORT
-void SeqDB_ReadBinaryGiList(const string & name, vector<int> & gis);
+void SeqDB_ReadBinaryGiList(const string & name, vector<TGi> & gis);
/// Read a text or binary GI list from an area of memory.
///
@@ -965,7 +968,8 @@ void SeqDB_CombineAndQuote(const vector<string> & dbs,
NCBI_XOBJREAD_EXPORT
void SeqDB_SplitQuoted(const string & dbname,
- vector<CTempString> & dbs);
+ vector<CTempString> & dbs,
+ bool keep_quote = false);
/// Read a text or binary GI list from a file.
///
@@ -1052,7 +1056,7 @@ void SeqDB_ReadMixList(const string & fname,
NCBI_XOBJREAD_EXPORT
void SeqDB_ReadGiList(const string & fname,
- vector<int> & gis,
+ vector<TGi> & gis,
bool * in_order = 0);
/// Read a text or binary SeqId list from a file.
@@ -1086,7 +1090,7 @@ NCBI_XOBJREAD_EXPORT
bool SeqDB_IsBinaryTiList(const string & fname);
/// CSeqDBFileGiList
-///
+///
/// This class defines a CSeqDBGiList subclass which reads a GI list
/// file given a filename. It can read text or binary GI list files,
/// and will automatically distinguish between them.
@@ -1121,14 +1125,14 @@ public:
/// The two lists of GIs are sorted and this class is computed as
/// an intersection of them. Note that both arguments to this
/// function are potentially modified (sorted in place).
- CIntersectionGiList(CSeqDBGiList & gilist, vector<int> & gis);
+ CIntersectionGiList(CSeqDBGiList & gilist, vector<TGi> & gis);
/// The two lists of GIs are sorted and this class is computed as
/// an intersection of them. Since gilist is negative this means
/// all gi's in the vector that are NOT in the negative list.
/// Note that both arguments to this
/// function are potentially modified (sorted in place).
- CIntersectionGiList(CSeqDBNegativeList & gilist, vector<int> & gis);
+ CIntersectionGiList(CSeqDBNegativeList & gilist, vector<TGi> & gis);
};
@@ -1142,46 +1146,64 @@ public:
CSeqDBIdSet_Vector()
{
}
-
+
/// Construct from an 'int' set.
- CSeqDBIdSet_Vector(const vector<int> & ids)
+ CSeqDBIdSet_Vector(const vector<Int4> & ids)
{
- ITERATE(vector<int>, iter, ids) {
- m_Ids.push_back(*iter);
+ ITERATE(vector<Int4>, iter, ids) {
+ m_Ids.push_back((Int8) *iter);
}
}
-
+
/// Construct from an 'Int8' set.
CSeqDBIdSet_Vector(const vector<Int8> & ids)
{
m_Ids = ids;
}
-
+
+ /// Construct from an 'Uint8' set.
+ CSeqDBIdSet_Vector(const vector<Uint8> & ids)
+ {
+ ITERATE(vector<Uint8>, iter, ids) {
+ m_Ids.push_back((Int8) *iter);
+ }
+ }
+
+#ifdef NCBI_STRICT_GI
+ /// Construct from a 'TGi' set when NCBI_STRICT_GI is in force.
+ CSeqDBIdSet_Vector(const vector<TGi> & ids)
+ {
+ ITERATE(vector<TGi>, iter, ids) {
+ m_Ids.push_back(GI_TO(Int8, *iter));
+ }
+ }
+#endif
+
/// Access the Int8 set.
vector<Int8> & Set()
{
return m_Ids;
}
-
+
/// Access the Int8 set.
const vector<Int8> & Get() const
{
return m_Ids;
}
-
+
/// Get the number of elements stored here.
size_t Size() const
{
return m_Ids.size();
}
-
+
private:
/// The actual list elements.
vector<Int8> m_Ids;
-
+
/// Prevent copy construction.
CSeqDBIdSet_Vector(CSeqDBIdSet_Vector &);
-
+
/// Prevent copy assignment.
CSeqDBIdSet_Vector & operator=(CSeqDBIdSet_Vector &);
};
@@ -1204,13 +1226,13 @@ public:
eXor, // Found in X or Y, but not both
eOr // Found in either X or Y
};
-
+
/// Type of IDs stored here.
enum EIdType {
eGi, // Found in both X and Y
eTi // Found in X or Y, but not both
};
-
+
/// Construct a 'blank' CSeqDBIdSet object.
///
/// This produces a blank ID set object, which (if applied) would
@@ -1218,7 +1240,7 @@ public:
/// a negative ID list with no elements.
///
CSeqDBIdSet();
-
+
/// Build a computed ID list given an initial set of IDs.
///
/// This initializes a list with an initial set of IDs of the
@@ -1229,8 +1251,8 @@ public:
/// @param ids These IDs will be added to the list.
/// @param t The IDs are assumed to be of this type.
/// @param positive True for a positive ID list, false for negative.
- CSeqDBIdSet(const vector<int> & ids, EIdType t, bool positive = true);
-
+ CSeqDBIdSet(const vector<Int4> & ids, EIdType t, bool positive = true);
+
/// Build a computed ID list given an initial set of IDs.
///
/// This initializes a list with an initial set of IDs of the
@@ -1242,76 +1264,117 @@ public:
/// @param t The IDs are assumed to be of this type.
/// @param positive True for a positive ID list, false for negative.
CSeqDBIdSet(const vector<Int8> & ids, EIdType t, bool positive = true);
-
+
+ /// Build a computed ID list given an initial set of IDs.
+ ///
+ /// This initializes a list with an initial set of IDs of the
+ /// specified type. All further logic operations on the list
+ /// should use vectors of IDs or CSeqDBIdSet objects
+ /// initialized with the same EIdType enumeration.
+ ///
+ /// @param ids These IDs will be added to the list.
+ /// @param t The IDs are assumed to be of this type.
+ /// @param positive True for a positive ID list, false for negative.
+ CSeqDBIdSet(const vector<Uint8> & ids, EIdType t, bool positive = true);
+
+#ifdef NCBI_STRICT_GI
+ /// Build a computed ID list given an initial set of IDs.
+ ///
+ /// This initializes a list with an initial set of IDs of the
+ /// specified type. All further logic operations on the list
+ /// should use vectors of IDs or CSeqDBIdSet objects
+ /// initialized with the same EIdType enumeration.
+ ///
+ /// @param ids These IDs will be added to the list.
+ /// @param t The IDs are assumed to be of this type.
+ /// @param positive True for a positive ID list, false for negative.
+ CSeqDBIdSet(const vector<TGi> & ids, EIdType t, bool positive = true);
+#endif
+
/// Virtual destructor.
virtual ~CSeqDBIdSet()
{
}
-
+
/// Invert the current list.
void Negate();
-
+
/// Perform a logical operation on a list.
- ///
+ ///
/// The logical operation is performed between the current list
/// and the ids parameter, and the 'positive' flag is used to
/// determine if the new input list should be treated as a
/// positive or negative list. For example, using op == eOr and
/// positive == false would perform the operation (X OR NOT Y).
- ///
+ ///
/// @param op Logical operation to perform.
/// @param ids List of ids for the second argument.
/// @param positive True for positive lists, false for negative.
void Compute(EOperation op,
const vector<int> & ids,
bool positive = true);
-
+
/// Perform a logical operation on a list.
- ///
+ ///
/// The logical operation is performed between the current list
/// and the ids parameter, and the 'positive' flag is used to
/// determine if the new input list should be treated as a
/// positive or negative list. For example, using op == eOr and
/// positive == false would perform the operation (X OR NOT Y).
- ///
+ ///
/// @param op Logical operation to perform.
/// @param ids List of ids for the second argument.
/// @param positive If true, ids represent 'negative' ids.
void Compute(EOperation op,
const vector<Int8> & ids,
bool positive = true);
-
+
+ /// Perform a logical operation on a list.
+ ///
+ /// The logical operation is performed between the current list
+ /// and the ids parameter, and the 'positive' flag is used to
+ /// determine if the new input list should be treated as a
+ /// positive or negative list. For example, using op == eOr and
+ /// positive == false would perform the operation (X OR NOT Y).
+ ///
+ /// @param op Logical operation to perform.
+ /// @param ids List of ids for the second argument.
+ /// @param positive If true, ids represent 'negative' ids.
+ void Compute(EOperation op,
+ const vector<Uint8> & ids,
+ bool positive = true);
+
/// Perform a logical operation on a list.
- ///
+ ///
/// The logical operation is performed between the current list
/// and the ids parameter. For example if 'eOr' is specified, the
/// operation performed will be 'X OR Y'. The 'ids' list will not
/// be modified by this operation.
- ///
+ ///
/// @param op Logical operation to perform.
/// @param ids List of ids for the second argument.
void Compute(EOperation op, const CSeqDBIdSet & ids);
-
+
/// Checks whether a positive GI list was produced.
///
/// If this method returns true, a positive list was produced, and
/// can be retrieved with GetPositiveList(). If it returns false,
/// a negative list was produced and can be retrieved with
/// GetNegativeList().
- ///
+ ///
/// @return true If the produced GI list is positive.
bool IsPositive()
{
return m_Positive;
}
-
+
/// Retrieve a positive GI list.
///
/// If IsPositive() returned true, this method should be used to
/// retrieve a positive GI list. If IsPositive() returned false,
/// this method will throw an exception.
CRef<CSeqDBGiList> GetPositiveList();
-
+
/// Retrieve a negative GI list.
///
/// If IsPositive() returned false, this method should be used to
@@ -1320,9 +1383,9 @@ public:
///
/// @return A negative GI list.
CRef<CSeqDBNegativeList> GetNegativeList();
-
+
/// Check if an ID list is blank.
- ///
+ ///
/// An ID list is considered 'blank' iff it is a negative list
/// with no elements. Constructing a database with such a list is
/// equivalent to not specifying a list. Blank lists are produced
@@ -1333,11 +1396,11 @@ public:
///
/// @return True if this list is blank.
bool Blank() const;
-
+
private:
/// Sort and unique the internal set.
static void x_SortAndUnique(vector<Int8> & ids);
-
+
/// Compute inclusion flags for a boolean operation.
///
/// This takes a logical operator (AND, OR, or XOR) and a flag
@@ -1360,7 +1423,7 @@ private:
bool & incl_A,
bool & incl_B,
bool & incl_AB);
-
+
/// Compute boolean operation on two vectors.
///
/// This takes a logical operator (AND, OR, or XOR) and two
@@ -1382,19 +1445,19 @@ private:
bool B_pos,
vector<Int8> & result,
bool & result_pos);
-
+
/// True if the current list is positive.
bool m_Positive;
-
+
/// Id type.
EIdType m_IdType;
-
+
/// Ids stored here.
CRef<CSeqDBIdSet_Vector> m_Ids;
-
+
/// Cached positive list.
CRef<CSeqDBGiList> m_CachedPositive;
-
+
/// Cached negative list.
CRef<CSeqDBNegativeList> m_CachedNegative;
};
@@ -1426,19 +1489,19 @@ struct SSeqDBTaxInfo {
: taxid(t)
{
}
-
+
/// An identifier for this species or taxonomic group.
int taxid;
-
+
/// Scientific name, such as "Aotus vociferans".
string scientific_name;
-
+
/// Common name, such as "noisy night monkey".
string common_name;
-
+
/// A simple category name, such as "birds".
string blast_name;
-
+
/// A string of length 1 indicating the "Super Kingdom".
string s_kingdom;
@@ -1471,23 +1534,23 @@ string SeqDB_ResolveDbPath(const string & filename);
///
/// Identical to SeqDB_ResolveDbPath with the exception that this function does
/// not require the extension to be provided. This is intended to check whether
-/// a BLAST DB exists or not.
+/// a BLAST DB exists or not.
///
/// @param filename Name of file to find.
/// @param dbtype Determines whether the BLAST DB is protein ('p'), nucleotide
/// ('n'), or whether the algorithm should guess it ('-')
/// @return Resolved path or empty string if not found.
NCBI_XOBJREAD_EXPORT
-string SeqDB_ResolveDbPathNoExtension(const string & filename,
+string SeqDB_ResolveDbPathNoExtension(const string & filename,
char dbtype = '-');
/// Resolve a file path using SeqDB's path algorithms.
///
/// Identical to SeqDB_ResolveDbPathNoExtension with the exception that this
-/// function searches for ISAM files, specifically those storing numeric and
+/// function searches for ISAM files, specifically those storing numeric and
/// string data (for LinkoutDB; i.e.: p[ns][id]).
/// This is intended to check whether a pair of ISAM files used in LinkoutDB
-/// exists or not.
+/// exists or not.
///
/// @param filename Name of file to find.
/// @return Resolved path or empty string if not found.
@@ -1496,11 +1559,11 @@ string SeqDB_ResolveDbPathForLinkoutDB(const string & filename);
/// Compares two volume file names and determine the volume order
///
-/// @param volpath1 The 1st volume path
-/// @param volpath2 The 2nd volume path
+/// @param volpath1 The 1st volume path
+/// @param volpath2 The 2nd volume path
/// @return true if vol1 should appear before vol2
NCBI_XOBJREAD_EXPORT
-bool SeqDB_CompareVolume(const string & volpath1,
+bool SeqDB_CompareVolume(const string & volpath1,
const string & volpath2);
/// Returns a path minus filename.
@@ -1540,7 +1603,7 @@ enum ESeqDBIdType {
};
/// Seq-id simplification.
-///
+///
/// Given a Seq-id, this routine devolves it to a GI or PIG if
/// possible. If not, it formats the Seq-id into a canonical form
/// for lookup in the string ISAM files. If the Seq-id was parsed
@@ -1549,12 +1612,12 @@ enum ESeqDBIdType {
/// can recognize. In the case that new Seq-id types are added,
/// support for which has not been added to this code, this
/// mechanism will try to use the original string.
-///
+///
/// @param bestid
/// The Seq-id to look up. [in]
/// @param acc
/// The original string the Seq-id was created from (or NULL). [in]
-/// @param num_id
+/// @param num_id
/// The returned identifier, if numeric. [out]
/// @param str_id
/// The returned identifier, if a string. [out]
@@ -1562,21 +1625,21 @@ enum ESeqDBIdType {
/// Whether an adjustment was done at all. [out]
/// @return
/// The resulting identifier type.
-NCBI_XOBJREAD_EXPORT ESeqDBIdType
+NCBI_XOBJREAD_EXPORT ESeqDBIdType
SeqDB_SimplifySeqid(CSeq_id & bestid,
- const string * acc,
- Int8 & num_id,
- string & str_id,
- bool & simpler);
-
+ const string * acc,
+ Int8 & num_id,
+ string & str_id,
+ bool & simpler);
+
/// String id simplification.
-///
+///
/// This routine tries to produce a numerical type from a string
/// identifier. SeqDB can use faster lookup mechanisms if a PIG,
/// GI, or OID type can be recognized in the string, for example.
/// Even when the output is a string, it may be better formed for
/// the purpose of lookup in the string ISAM file.
-///
+///
/// @param acc
/// The string to look up. [in]
/// @param num_id
@@ -1587,7 +1650,7 @@ SeqDB_SimplifySeqid(CSeq_id & bestid,
/// Whether an adjustment was done at all. [out]
/// @return
/// The resulting identifier type.
-NCBI_XOBJREAD_EXPORT ESeqDBIdType
+NCBI_XOBJREAD_EXPORT ESeqDBIdType
SeqDB_SimplifyAccession(const string & acc,
Int8 & num_id,
string & str_id,
@@ -1608,7 +1671,7 @@ SeqDB_SimplifyAccession(const string &acc);
/// Retrieves a list of all supported file extensions for BLAST databases
/// @param db_is_protein set to true if the database is protein else false [in]
/// @param extensions where the return value will be stored [in|out]
-NCBI_XOBJREAD_EXPORT
+NCBI_XOBJREAD_EXPORT
void SeqDB_GetFileExtensions(bool db_is_protein,
vector<string>& extensions);
diff --git a/c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp b/c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp
index b12a125..26cc440 100644
--- a/c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_BLAST_SEQDB_READER___SEQDBEXPERT__HPP
#define OBJTOOLS_BLAST_SEQDB_READER___SEQDBEXPERT__HPP
-/* $Id: seqdbexpert.hpp 151315 2009-02-03 18:13:26Z camacho $
+/* $Id: seqdbexpert.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,10 +55,10 @@ USING_SCOPE(objects);
class NCBI_XOBJREAD_EXPORT CSeqDBExpert : public CSeqDB {
public:
/// Short Constructor
- ///
+ ///
/// This version of the constructor assumes memory mapping and
/// that the entire possible OID range will be included.
- ///
+ ///
/// @param dbname
/// A list of database or alias names, seperated by spaces
/// @param seqtype
@@ -68,7 +68,7 @@ public:
CSeqDBExpert(const string & dbname,
ESeqType seqtype,
CSeqDBGiList * gilist = 0);
-
+
/// Constructor with MMap Flag and OID Range.
///
/// If the oid_end value is specified as zero, or as a value
@@ -78,7 +78,7 @@ public:
/// version of the constructor is obsolete because the sequence
/// type is specified as a character (eventually only the ESeqType
/// version will exist).
- ///
+ ///
/// @param dbname
/// A list of database or alias names, seperated by spaces.
/// @param seqtype
@@ -101,21 +101,21 @@ public:
int oid_end,
bool use_mmap,
CSeqDBGiList * gi_list = 0);
-
+
/// Null Constructor
- ///
+ ///
/// This version of the constructor does not open a specific blast
/// database. This is provided for cases where the application
/// only needs 'global' resources like the taxonomy database.
CSeqDBExpert();
-
+
/// Destructor.
///
/// This will return resources acquired by this object, including
/// any gotten by the GetSequence() call, whether or not they have
/// been returned by RetSequence().
~CSeqDBExpert();
-
+
/// Raw Sequence and Ambiguity Data
///
/// Get a pointer to the raw sequence and ambiguity data, and the
@@ -136,45 +136,45 @@ public:
const char ** buffer,
int * seq_length,
int * ambig_length) const;
-
+
/// Get GI Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of GIs. A value
/// is returned for each non-null argument. If the operation
/// fails, an exception will be thrown, which probably indicates a
/// missing index file.
- ///
+ ///
/// @param low_id Lowest GI value in database. [out]
/// @param high_id Highest GI value in database. [out]
/// @param count Number of GI values in database. [out]
- void GetGiBounds(int * low_id, int * high_id, int * count);
-
+ void GetGiBounds(TGi * low_id, TGi * high_id, int * count);
+
/// Get PIG Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of PIGs. A value
/// is returned for each non-null argument. If the operation
/// fails, an exception will be thrown, which probably indicates a
/// missing index file.
- ///
+ ///
/// @param low_id Lowest PIG value in database. [out]
/// @param high_id Highest PIG value in database. [out]
/// @param count Number of PIG values in database. [out]
void GetPigBounds(int * low_id, int * high_id, int * count);
-
+
/// Get String Bounds.
- ///
+ ///
/// Fetch the lowest, highest, and total number of string keys in
/// the database index. A value is returned for each non-null
/// argument. If the operation fails, an exception will be
/// thrown, which probably indicates a missing index file. Note
/// that the number of string keys does not directly correspond to
/// the number of deflines, Seq-ids, or accessions.
- ///
+ ///
/// @param low_id Lowest string value in database. [out]
/// @param high_id Highest string value in database. [out]
/// @param count Number of string values in database. [out]
void GetStringBounds(string * low_id, string * high_id, int * count);
-
+
/// Get the sequence hash for a given OID.
///
/// The sequence data is fetched and the sequence hash is
@@ -183,7 +183,7 @@ public:
/// @param oid The sequence to compute the hash of. [in]
/// @return The sequence hash.
unsigned GetSequenceHash(int oid);
-
+
/// Get the OIDs for a given sequence hash.
///
/// The OIDs corresponding to a hash value are found and returned.
@@ -192,7 +192,7 @@ public:
/// @param oids OIDs of sequences with this hash. [out]
/// @return True if the hash value was found, false otherwise.
void HashToOids(unsigned hash, vector<int> & oids);
-
+
/// Verify internal SeqDB data structures for consistency.
void Verify();
};
diff --git a/c++/include/objtools/blast/seqdb_writer/build_db.hpp b/c++/include/objtools/blast/seqdb_writer/build_db.hpp
index 6bf293f..3a99dd2 100644
--- a/c++/include/objtools/blast/seqdb_writer/build_db.hpp
+++ b/c++/include/objtools/blast/seqdb_writer/build_db.hpp
@@ -1,4 +1,4 @@
-/* $Id: build_db.hpp 389699 2013-02-20 15:33:26Z maning $
+/* $Id: build_db.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -85,7 +85,7 @@ public:
/// in the column_blob vector. If this OID does not have a data
/// object for this column, either the column may be missing from
/// the list, or the blob data string should be empty.
- ///
+ ///
/// @param sequence Sequence data packed in BlastDB disk format. [out]
/// @param ambiguities Ambiguities packed in BlastDB disk format. [out]
/// @param deflines This OID's headers as a Blast-def-line-set. [out]
@@ -97,23 +97,23 @@ public:
vector<SBlastDbMaskData> & mask_ranges,
vector<int> & column_ids,
vector<CTempString> & column_blobs) = 0;
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Get the names of all columns defined by this sequence source.
/// @param names A list of column names. [out]
virtual void GetColumnNames(vector<string> & names) = 0;
-
+
/// Get the column ID for a column mentioned by name.
/// @param name The name (column title) of the column. [in]
/// @return The corresponding Column-ID.
virtual int GetColumnId(const string & name) = 0;
-
+
/// Get metadata for the column with the specified Column ID.
/// @param id The column-id for which to get meta-data. [in]
/// @return All meta-data for this column-id.
virtual const map<string,string> & GetColumnMetaData(int id) = 0;
-#endif
+#endif
};
/// An interface providing lookups of mask-data by Seq-id.
@@ -122,12 +122,12 @@ public:
/// Get ranges of masking data for the given Seq-ids.
/// @param id Seq-ids for which to get masking data.
/// @return Masking data for these Seq-ids.
- virtual CMaskedRangesVector &
+ virtual CMaskedRangesVector &
GetRanges(const list< CRef<CSeq_id> > & id) = 0;
};
/// Build BlastDB format databases from various data sources.
-///
+///
/// This class provides an API for building BlastDB format databases.
/// The WriteDB library is used internally to produce the actual
/// database; the functionality provided by this class helps to bridge
@@ -156,11 +156,11 @@ public:
CWriteDB::TIndexType indexing,
bool use_gi_mask,
ostream * logfile);
-
+
// Note -- should deprecate (or just remove) the following one:
// - sparse does nothing
// - parse_seqids is always true
-
+
/// Constructor.
///
/// Create a database with the specified name, type, and other
@@ -185,7 +185,7 @@ public:
ostream * logfile);
~CBuildDatabase();
-
+
/// Specify a mapping of sequence ids to taxonomic ids.
///
/// When adding sequences CBuildDatabase will use the object
@@ -194,7 +194,7 @@ public:
///
/// @param taxids An object providing defline-to-TaxID lookups. [in]
void SetTaxids(CTaxIdSet & taxids);
-
+
/// Specify letters to mask out of protein sequence data.
///
/// Protein sequences sometimes contain rare (or recently defined)
@@ -205,7 +205,7 @@ public:
///
/// @param taxids An object providing defline-to-TaxID lookups. [in]
void SetMaskLetters(const string & mask_letters);
-
+
/// Specify source database(s) via the database name(s).
///
/// The provided name will be used to find a source database (or
@@ -214,7 +214,7 @@ public:
///
/// @param src_db_name Database name of the source database. [in]
void SetSourceDb(const string & src_db_name);
-
+
/// Specify source database.
///
/// The provided source database will be used to look up sequence
@@ -222,7 +222,7 @@ public:
///
/// @param src_db The source database. [in]
void SetSourceDb(CRef<CSeqDBExpert> src_db);
-
+
/// Specify a linkout bit lookup object.
///
/// The provided mapping will be used to look up linkout bits for
@@ -231,7 +231,7 @@ public:
/// @param src_db The source database. [in]
void SetLinkouts(const TLinkoutMap & linkouts,
bool keep_links);
-
+
/// Specify a membership bit lookup object.
///
/// The provided mapping will be used to look up membership bit
@@ -240,7 +240,7 @@ public:
/// @param src_db The source database. [in]
void SetMembBits(const TLinkoutMap & membbits,
bool keep_mbits);
-
+
/// Build the database.
///
/// This method builds a database from the given list of Sequence
@@ -250,17 +250,17 @@ public:
/// additional logging is done with summary information.).
///
/// @param ids List of identifiers to add to the database.
- /// @param fasta_file FASTA format data for
+ /// @param fasta_file FASTA format data for
bool Build(const vector<string> & ids,
CNcbiIstream * fasta_file);
-
+
/// Start building a new database.
///
/// This method sets up a new database to begin receiving
/// sequences. It should be called before AddIds, AddFasta,
/// AddSequences, or AddRawSequences is called.
void StartBuild();
-
+
/// Add the specified sequences from the source database.
///
/// The list of strings are interpreted as GIs if they're composed
@@ -279,7 +279,7 @@ public:
/// @param ids List of sequence IDs as strings.
/// @return true if all sequences were found locally or remotely.
bool AddIds(const vector<string> & ids);
-
+
/// Add sequences from a file containing FASTA data.
///
/// The provided file is expected to contain FASTA data for one or
@@ -289,7 +289,7 @@ public:
/// @param fasta_file A file containing FASTA data.
/// @return True if at least one sequence was added.
bool AddFasta(CNcbiIstream & fasta_file);
-
+
/// Add sequences from an IBioseqSource object.
///
/// The provided `src' object is queried using GetNext() to get a
@@ -302,7 +302,7 @@ public:
/// @param add_pig true if PIG should be added if available
/// @return True if at least one sequence was added.
bool AddSequences(IBioseqSource & src, bool add_pig = false);
-
+
/// Add sequences from an IRawSequenceSource object.
///
/// The provided `src' object is queried using GetNext() to get
@@ -315,7 +315,7 @@ public:
/// @param src An object providing one or more "raw" sequences.
/// @return True if at least one sequence was added.
bool AddSequences(IRawSequenceSource & src);
-
+
/// Finish building a new database.
///
/// This method closes the newly constructed database, flushing
@@ -323,7 +323,7 @@ public:
/// volumes together, and so on.
/// @param erase Will erase all files created if true.
bool EndBuild(bool erase = false);
-
+
/// Specify whether to use remote fetching for locally absent IDs.
///
/// If identifiers in the list provided to Build or to AddIds is
@@ -355,14 +355,14 @@ public:
{
m_UseRemote = use_remote;
}
-
+
/// Specify level of output verbosity.
/// @param v Specify true if output should be more detailed.
void SetVerbosity(bool v)
{
m_Verbose = v;
}
-
+
/// Set the maximum size of database component files.
///
/// This will specify the maximum size of file that will be
@@ -372,7 +372,7 @@ public:
///
/// @param max_file_size Maximum file size in bytes.
void SetMaxFileSize(Uint8 max_file_size);
-
+
/// Define a masking algorithm.
///
/// The returned integer ID will be defined as corresponding to the
@@ -388,10 +388,10 @@ public:
/// The empty string should be used to indicate default parameters. [in]
/// @param name Name of the GI-base mask file [in]
int
- RegisterMaskingAlgorithm(EBlast_filter_program program,
+ RegisterMaskingAlgorithm(EBlast_filter_program program,
const string & options,
const string & name = "");
-
+
/// Define a masking algorithm.
///
/// The returned integer ID will be defined as corresponding to the
@@ -409,7 +409,7 @@ public:
RegisterMaskingAlgorithm(const string & program,
const string & description,
const string & options);
-
+
/// Specify an object mapping Seq-id to subject masking data.
///
/// Masking data is provided to CBuildDatabase by implementing an
@@ -421,17 +421,17 @@ public:
///
/// @param ranges An object mapping Seq-ids to their masking data.
void SetMaskDataSource(IMaskDataSource & ranges);
-
+
private:
/// Get a scope for remote loading of objects.
objects::CScope & x_GetScope();
-
+
/// Duplicate IDs from local databases.
- ///
+ ///
/// This method iterates over the list of IDs, copying sequences
/// found in the source databases to the output database.
void x_DupLocal();
-
+
/// Resolve an ID remotely.
///
/// This method looks up the given ID via remote services in order
@@ -444,8 +444,8 @@ private:
///
/// @param seqid Sequence identifier to look up remotely. [in|out]
/// @param gi Genomic ID if one is found, otherwise 0. [out]
- void x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, int & gi);
-
+ void x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, TGi & gi);
+
/// Resolve various input IDs (as strings) to GIs.
///
/// The input IDs are examined, the type of each is determined as
@@ -456,7 +456,7 @@ private:
/// @param ids List of strings representing IDs to resolve.
/// @return GI list produced from the input ids.
CRef<CInputGiList> x_ResolveGis(const vector<string> & ids);
-
+
/// Modify deflines with linkout and membership bits and taxids.
///
/// The provided deflines are modified: the taxid is set (0 is
@@ -469,7 +469,7 @@ private:
/// Add pig if id can be extracted from the deflines
/// @param headers Headers to extract the id if available.
void x_AddPig(CRef<objects::CBlast_def_line_set> headers);
-
+
/// Modify a Bioseq as needed and add it to the database.
///
/// The provided Bioseq is added to the database. Modifications
@@ -484,14 +484,14 @@ private:
bool x_EditAndAddBioseq(CConstRef<objects::CBioseq> bs,
objects::CSeqVector * sv,
bool add_pig = false);
-
+
/// Add the masks for the Seq-id(s) (usually just one) to the database
/// being created
/// @param ids Seq-id(s) of the sequence to which masks should be added [in]
void x_AddMasksForSeqId(const list< CRef<CSeq_id> >& ids);
/// Duplicate IDs from local databases.
- ///
+ ///
/// This method iterates over the list of IDs; any IDs that were
/// not found in the source database are added by fetching the
/// sequence from remote services. (Whether an ID was found
@@ -501,12 +501,12 @@ private:
/// @param gi_list A list of GIs and Seq-ids.
/// @return True if all IDs could be added.
bool x_AddRemoteSequences(CInputGiList & gi_list);
-
+
/// Write log messages for any unresolved IDs.
/// @param gi_list List of GIs and Seq-ids.
/// @return True if all sequences were resolved.
bool x_ReportUnresolvedIds(const CInputGiList & gi_list) const;
-
+
/// Store linkout and membership bits in provided headers.
///
/// Each Seq-id found in each defline in the provided headers will
@@ -516,11 +516,11 @@ private:
///
/// @param headers These deflines will be modified. [in|out]
void x_SetLinkAndMbit(CRef<objects::CBlast_def_line_set> headers);
-
+
/// Fetch a sequence from the remote service and add it to the db.
///
/// The provided Seq-id will be used to fetch a Bioseq remotely,
- /// and this Bioseq will be added to this database. If
+ /// and this Bioseq will be added to this database. If
///
/// @param seqid Identifies the sequence to fetch. [in]
/// @param found Will be set to true if a sequence was found. [out]
@@ -528,7 +528,7 @@ private:
void x_AddOneRemoteSequence(const objects::CSeq_id & seqid,
bool & found,
bool & error);
-
+
/// Determine if this string ID can be found in the source database.
///
/// The provided string will be looked up as an accession in the
@@ -546,55 +546,55 @@ private:
bool x_ResolveFromSource(const string & acc, CRef<objects::CSeq_id> & id);
bool x_EndBuild(bool erase, const CException * close_exception);
-
+
/// True for a protein database, false for nucleotide.
bool m_IsProtein;
-
+
/// True to keep linkout bits from source dbs, false to discard.
bool m_KeepLinks;
-
+
/// Table of linkout bits to apply to sequences.
TIdToBits m_Id2Links;
-
+
/// True to keep membership bits from source dbs, false to discard.
bool m_KeepMbits;
-
+
/// Table of membership bits to apply to sequences.
TIdToBits m_Id2Mbits;
-
+
/// Object manager, used for remote fetching.
CRef<objects::CObjectManager> m_ObjMgr;
-
+
/// Sequence scope, used for remote fetching.
CRef<objects::CScope> m_Scope;
-
+
/// Set of TaxIDs configured to apply to sequences.
CRef<CTaxIdSet> m_Taxids;
-
+
/// Database being produced here.
CRef<CWriteDB> m_OutputDb;
-
+
/// Database for duplicating sequences locally (-sourcedb option.)
CRef<CSeqDBExpert> m_SourceDb;
-
+
/// Subject masking data.
CRef<IMaskDataSource> m_MaskData;
-
+
/// Logfile.
ostream & m_LogFile;
-
+
/// Whether to use remote resolution and sequence fetching.
bool m_UseRemote;
-
+
/// Define count.
int m_DeflineCount;
-
+
/// Number of OIDs stored in this database.
int m_OIDCount;
-
+
/// If true, more detailed log messages will be produced.
bool m_Verbose;
-
+
/// If true, string IDs found in FASTA input will be parsed as Seq-ids.
bool m_ParseIDs;
diff --git a/c++/include/objtools/blast/seqdb_writer/multisource_util.hpp b/c++/include/objtools/blast/seqdb_writer/multisource_util.hpp
index 7758d32..1aa241e 100644
--- a/c++/include/objtools/blast/seqdb_writer/multisource_util.hpp
+++ b/c++/include/objtools/blast/seqdb_writer/multisource_util.hpp
@@ -1,4 +1,4 @@
-/* $Id: multisource_util.hpp 204413 2010-09-07 20:49:45Z camacho $
+/* $Id: multisource_util.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,7 +48,7 @@ void GetDeflineKeys(const objects::CBlast_def_line & defline,
vector<string> & keys);
/// CMultisourceException
-///
+///
/// This exception class is thrown for errors occurring during
/// traceback.
@@ -59,9 +59,9 @@ public:
/// Argument validation failed.
eArg,
/// Failed to create the output file(s)/directory
- eOutputFileError
+ eOutputFileError
};
-
+
/// Get a message describing the exception.
virtual const char* GetErrCodeString() const
{
@@ -70,7 +70,7 @@ public:
default: return CException::GetErrCodeString();
}
}
-
+
/// Include standard NCBI exception behavior.
NCBI_EXCEPTION_DEFAULT(CMultisourceException, CException);
};
@@ -86,22 +86,22 @@ class NCBI_XOBJWRITE_EXPORT CInputGiList : public CSeqDBGiList {
public:
/// Construct an empty GI list.
CInputGiList(int capacity = 1024)
- : m_Last(0)
+ : m_Last(ZERO_GI)
{
if (capacity > 0) {
m_GisOids.reserve(capacity);
}
-
+
// An empty vector is always sorted, right?
m_CurrentOrder = eGi;
}
-
+
/// Append a GI.
- ///
+ ///
/// This method adds a GI to the list.
- ///
+ ///
/// @param gi A sequence identifier.
- void AppendGi(int gi, int oid = -1)
+ void AppendGi(TGi gi, int oid = -1)
{
if (m_CurrentOrder == eGi) {
if (m_Last > gi) {
@@ -110,15 +110,15 @@ public:
return;
}
}
-
+
m_GisOids.push_back(SGiOid(gi, oid));
m_Last = gi;
}
-
+
/// Append a Seq-id
- ///
+ ///
/// This method adds a Seq-id to the list.
- ///
+ ///
/// @param seqid A sequence identifier.
void AppendSi(const string &si, int oid = -1)
{
@@ -127,14 +127,14 @@ public:
// assume that Seq-ids are out-of order. This also fits the
// basic practice of not making tiny optimizations in code
// paths that are slow.
-
+
m_CurrentOrder = eNone;
string str_id = SeqDB_SimplifyAccession(si);
if (str_id != "") m_SisOids.push_back(SSiOid(str_id, oid));
}
-
+
private:
- int m_Last;
+ TGi m_Last;
};
@@ -148,15 +148,15 @@ public:
: m_SeqDB(seqdb), m_Buffer(buffer)
{
}
-
+
~CSequenceReturn()
{
m_SeqDB.RetSequence(& m_Buffer);
}
-
+
private:
CSequenceReturn & operator=(CSequenceReturn &);
-
+
CSeqDB & m_SeqDB;
const char * m_Buffer;
};
@@ -172,7 +172,7 @@ void MapToLMBits(const TLinkoutMap & gilist, TIdToBits & gi2links);
NCBI_XOBJWRITE_EXPORT
bool CheckAccession(const string & acc,
- int & gi,
+ TGi & gi,
CRef<objects::CSeq_id> & seqid,
bool & specific);
diff --git a/c++/include/objtools/blast/seqdb_writer/writedb.hpp b/c++/include/objtools/blast/seqdb_writer/writedb.hpp
index b9ef65c..bad4d70 100644
--- a/c++/include/objtools/blast/seqdb_writer/writedb.hpp
+++ b/c++/include/objtools/blast/seqdb_writer/writedb.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_BLAST_SEQDB_WRITER___WRITEDB__HPP
#define OBJTOOLS_BLAST_SEQDB_WRITER___WRITEDB__HPP
-/* $Id: writedb.hpp 409815 2013-08-09 22:10:12Z camacho $
+/* $Id: writedb.hpp 480972 2015-10-06 12:06:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -94,46 +94,46 @@ public:
enum ESeqType {
/// Protein database.
eProtein = 0,
-
+
/// Nucleotide database.
eNucleotide = 1
};
-
+
/// Whether and what kind of indices to build.
enum EIndexType {
/// Build a database without any indices.
eNoIndex = 0,
-
+
/// Use only simple accessions in the string index.
eSparseIndex = 0x1,
-
+
/// Use several forms of each Seq-id in the string index.
eFullIndex = 0x2,
-
+
/// OR this in to add an index for trace IDs.
eAddTrace = 0x4,
-
+
/// Like eFullIndex but also build a numeric Trace ID index.
eFullWithTrace = eFullIndex | eAddTrace,
-
+
/// Like eFullIndex but also build a numeric Trace ID index.
eDefault = eFullIndex | eAddTrace,
-
+
// Specialized ISAMs; these can be ORred into the above.
-
+
/// Add an index from sequence hash to OID.
eAddHash = 0x100
};
typedef int TIndexType; ///< Bitwise OR of "EIndexType"
-
+
//
// Setup
//
-
+
/// Constructor
- ///
+ ///
/// Starts construction of a blast database.
- ///
+ ///
/// @param dbname
/// A list of database or alias names, seperated by spaces. [in]
/// @param seqtype
@@ -152,26 +152,26 @@ public:
int itype = eDefault,
bool parse_ids = true,
bool use_gi_mask = false);
-
+
/// Destructor.
///
/// This will return resources acquired by this object, and call Close()
/// if it has not already been called.
~CWriteDB();
-
+
//
// Adding data
//
-
+
// Each new sequence is started when the client calls one of the
// AddSequence() methods. This can optionally be followed by one
// or more calls to Set...() methods or AddDefline(), to add or
// change other data. The accumulated data for the sequence is
// combined and written when the sequence after it is started
// (with another AddSequence() call), or when Close() is called.
-
+
/// Add a sequence as a CBioseq.
- ///
+ ///
/// This adds the sequence data in the specified CBioseq to the
/// database. If the CBioseq contains deflines, they will also be
/// used unless there is a call to SetDeflines() or AddDefline().
@@ -181,12 +181,12 @@ public:
/// GetInst().GetSeq_data(). If this might not be true, it may be
/// better to use the version of this function that also takes a
/// CSeqVector.
- ///
+ ///
/// @param bs The sequence and related data as a CBioseq. [in]
void AddSequence(const CBioseq & bs);
-
+
/// Add a sequence as a CBioseq.
- ///
+ ///
/// This adds the sequence data in the specified CSeqVector, and
/// the meta data in the specified CBioseq, to the database. If
/// the CBioseq contains deflines, they will also be used unless
@@ -194,21 +194,21 @@ public:
/// the CBioseq will be held by CWriteDB at least until the next
/// sequence is provided. This version will use the CSeqVector if
/// the sequence data is not found in the CBioseq.
- ///
+ ///
/// @param bs A CBioseq containing meta data for the sequence. [in]
/// @param sv The sequence data for the sequence. [in]
void AddSequence(const CBioseq & bs, CSeqVector & sv);
-
+
/// Add a sequence as a CBioseq.
- ///
+ ///
/// This adds the sequence found in the given CBioseq_Handle to
/// the database.
- ///
+ ///
/// @param bsh The sequence and related data as a CBioseq_Handle. [in]
void AddSequence(const CBioseq_Handle & bsh);
-
+
/// Add a sequence as raw data.
- ///
+ ///
/// This adds a sequence provided as raw sequence data. The raw
/// data must be (and is assumed to be) encoded correctly for the
/// format of database being produced. For protein databases, the
@@ -216,39 +216,39 @@ public:
/// this version of AddSequence() is used, the user must also
/// provide one or more deflines with SetDeflines() or
/// AddDefline() calls.
- ///
+ ///
/// @param sequence The sequence data as a string of bytes. [in]
/// @param ambiguities The ambiguity data as a string of bytes. [in]
void AddSequence(const CTempString & sequence,
const CTempString & ambiguities = "");
-
+
/// Set the PIG to be used for the sequence.
- ///
+ ///
/// For proteins, this sets the PIG of the protein sequence.
- ///
+ ///
/// @param pig PIG identifier as an integer. [in]
void SetPig(int pig);
/// Set the deflines to be used for the sequence.
- ///
+ ///
/// This method sets all the deflines at once as a complete set,
/// overriding any deflines provided by AddSequence(). If this
/// method is used with the CBioseq version of AddSequence, it
/// replaces the deflines found in the CBioseq.
- ///
+ ///
/// @param deflines Deflines to use for this sequence. [in]
void SetDeflines(const CBlast_def_line_set & deflines);
-
+
/// Register a type of filtering data found in this database.
///
/// @return algorithm ID for the filtering data.
/// @param program Program used to produce this masking data. [in]
/// @param options Algorithm options provided to the program. [in]
/// @param name Name of the GI-based mask. [in]
- int RegisterMaskAlgorithm(EBlast_filter_program program,
+ int RegisterMaskAlgorithm(EBlast_filter_program program,
const string & options = string(),
const string & name = string());
-
+
/// Register a type of filtering data found in this database.
///
/// @return algorithm ID for the filtering data.
@@ -260,23 +260,23 @@ public:
const string & options = string());
/// Set filtering data for a sequence.
- ///
+ ///
/// This method specifies filtered regions for this sequence. A
/// sequence may have filtering data from one or more algorithms.
/// For each algorithm_id value specified in ranges, a description
/// should be added to the database using RegisterMaskAlgorithm().
/// This must be done before the first call to SetMaskData() that
/// uses the algorithm id for a non-empty offset range list.
- ///
+ ///
/// @param ranges Filtered ranges for this sequence and algorithm.
/// @param gis GIs associated with this sequence.
void SetMaskData(const CMaskedRangesVector & ranges,
- const vector<int> & gis);
-
+ const vector<TGi> & gis);
+
//
// Output
//
-
+
/// List Volumes
///
/// Returns the base names of all volumes constructed by this
@@ -285,7 +285,7 @@ public:
///
/// @param vols The set of volumes produced by this class. [out]
void ListVolumes(vector<string> & vols);
-
+
/// List Filenames
///
/// Returns a list of the files constructed by this class; the
@@ -294,23 +294,23 @@ public:
///
/// @param files The set of resolved database path names. [out]
void ListFiles(vector<string> & files);
-
+
/// Close the Database.
///
/// Flush all data to disk and close any open files.
void Close();
-
+
//
// Controls
//
-
+
// The blast volume format has internal limits for these fields;
// these are called 'hard limits' here. If the value specified
// here exceeds that limit, it will be silently reduced. Limits
// are applied simultaneously; creation of a new volume is
// triggered as soon as any of the limits is reached (unless the
// current volume is empty).
-
+
/// Set maximum size for output files.
///
/// The provided size is applied as a limit on the size of output
@@ -323,7 +323,7 @@ public:
///
/// @param sz Maximum size in bytes of any volume component file. [in]
void SetMaxFileSize(Uint8 sz);
-
+
/// Set maximum letters for output volumes.
///
/// The provided size is applied as a limit on the size of output
@@ -336,21 +336,21 @@ public:
///
/// @param letters Maximum letters to pack in one volume. [in]
void SetMaxVolumeLetters(Uint8 letters);
-
+
/// Extract Deflines From Bioseq.
- ///
+ ///
/// Deflines are extracted from the CBioseq and returned to the
/// user. The caller can then modify or inspect the deflines, and
/// apply them to a sequence with SetDeflines().
- ///
+ ///
/// @param bs The bioseq from which to extract a defline set. [in]
/// @param parse_ids If seqid should be parsed [in]
/// @return A set of deflines for this CBioseq.
static CRef<CBlast_def_line_set>
ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids=true);
-
+
/// Set letters that should not be used in sequences.
- ///
+ ///
/// This method specifies letters that should not be used in the
/// resulting database. The masked letters are expected to be
/// specified in an IUPAC (alphabetic) encoding, and will be
@@ -358,10 +358,10 @@ public:
/// This method should be called before any sequences are added.
/// This method only works with protein (the motivating case
/// cannot happen with nucleotide).
- ///
+ ///
/// @param masked Letters to disinclude. [in]
void SetMaskedLetters(const string & masked);
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Find an existing column.
@@ -372,7 +372,7 @@ public:
/// @param title The column title to look for.
/// @return The column ID if this title is defined, otherwise -1.
int FindColumn(const string & title) const;
-
+
/// Set up a user-defined CWriteDB column.
///
/// This method creates a user-defined column associated with this
@@ -390,7 +390,7 @@ public:
/// @param title Name identifying this column.
/// @return Column identifier (a positive integer).
int CreateUserColumn(const string & title);
-
+
/// Add meta data to a user-defined column.
///
/// In addition to normal blob data, database columns can store a
@@ -406,7 +406,7 @@ public:
void AddColumnMetaData(int col_id,
const string & key,
const string & value);
-
+
/// Add blob data to a user-defined column.
///
/// To add data to a user-defined blob column, call this method,
@@ -421,7 +421,7 @@ public:
/// @return Blob data should be written to this object.
CBlastDbBlob & SetBlobData(int column_id);
#endif
-
+
protected:
/// Implementation object.
CWriteDB_Impl * m_Impl;
@@ -445,18 +445,18 @@ public:
enum EIdType {
/// Genomic id.
eGi,
-
+
/// Trace id.
eTi
};
-
+
/// Construct a list of a given type.
CBinaryListBuilder(EIdType id_type);
-
+
/// Write the list to a file.
/// @param fname Filename of the file to write the object to.
void Write(const string & fname);
-
+
/// Write the list to a stream
/// @param stream Stream to write the object to.
void Write(CNcbiOstream& stream);
@@ -466,7 +466,7 @@ public:
{
m_Ids.push_back(id);
}
-
+
/// Add several 4 byte IDs to the list.
///
/// This should take begin and end indicators, such as pointers to
@@ -484,7 +484,7 @@ public:
AppendId(id);
}
}
-
+
/// Returns the number of IDs stored in an instance of this class
size_type Size() const {
return m_Ids.size();
@@ -493,13 +493,13 @@ public:
private:
/// List of identifiers to use.
TContainerType m_Ids;
-
+
/// Whether to use GIs or TIs.
EIdType m_IdType;
-
+
/// Prevent copy construction.
CBinaryListBuilder(CBinaryListBuilder&);
-
+
/// Prevent copy assignment.
CBinaryListBuilder& operator=(CBinaryListBuilder &);
};
@@ -534,7 +534,7 @@ public:
CWriteDB_ColumnBuilder(const string & title,
const string & basename,
char file_id = 'a');
-
+
/// Add meta data to the column.
///
/// In addition to normal blob data, database columns can store a
@@ -547,10 +547,10 @@ public:
/// @param key Key string.
/// @param value Value string.
void AddMetaData(const string & key, const string & value);
-
+
/// Destructor.
~CWriteDB_ColumnBuilder();
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Add a blob to the column.
@@ -561,10 +561,10 @@ public:
/// @param blob The blob to add to the column.
void AddBlob(const CBlastDbBlob & blob);
#endif
-
+
/// Complete and close the column files.
void Close();
-
+
/// List Filenames
///
/// Returns a list of the files constructed by this class; the
@@ -573,14 +573,14 @@ public:
///
/// @param files The list of files created for this column.
void ListFiles(vector<string> & files) const;
-
+
private:
/// Prevent the copy constructor.
CWriteDB_ColumnBuilder(const CWriteDB_ColumnBuilder&);
-
+
/// Prevent copy assignment.
CWriteDB_ColumnBuilder & operator= (CWriteDB_ColumnBuilder&);
-
+
/// Implementation object.
class CWriteDB_Column * m_Impl;
};
@@ -593,9 +593,9 @@ enum EAliasFileFilterType {
eSeqIdList ///< Filter a BLAST database via a Seq-id list
};
-/**
- * @brief Writes an alias file that restricts a database with a gi list.
- *
+/**
+ * @brief Writes an alias file that restricts a database with a gi list.
+ *
* @param file_name alias file name to create, it will overwrite any existing
* files of that name. It can be specified as an absolute path, or a path
* relative to the current working directory [in]
@@ -606,7 +606,7 @@ enum EAliasFileFilterType {
* @param title title to use in this alias file [in]
* @param alias_type Type of alias file to create [in]
*/
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_CreateAliasFile(const string& file_name,
const string& db_name,
CWriteDB::ESeqType seq_type,
@@ -614,10 +614,10 @@ void CWriteDB_CreateAliasFile(const string& file_name,
const string& title = string(),
EAliasFileFilterType alias_type = eGiList);
-/**
+/**
* @brief Writes an alias file that aggregates multiple existing BLAST
* databases.
- *
+ *
* @param file_name alias file name to create, it will overwrite any existing
* files of that name. It can be specified as an absolute path, or a path
* relative to the current working directory [in]
@@ -628,7 +628,7 @@ void CWriteDB_CreateAliasFile(const string& file_name,
* @param title title to use in this alias file [in]
* @param alias_type Type of alias file to create [in]
*/
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_CreateAliasFile(const string& file_name,
const vector <string> & db_names,
CWriteDB::ESeqType seq_type,
@@ -636,12 +636,12 @@ void CWriteDB_CreateAliasFile(const string& file_name,
const string& title = string(),
EAliasFileFilterType alias_type = eGiList);
-/**
+/**
* @brief Writes an alias file that aggregates multiple existing BLAST
* database volumes. For instance, it can be used to request a top level alias
* file for a database called wgs composed of 3 volumes, creating wgs.nal,
* which refers to wgs.00, wgs.01, and wgs.02
- *
+ *
* @param file_name alias file name to create, it will overwrite any existing
* files of that name [in]
* @param num_volumes Number of volumes that will be referred to in the alias
@@ -649,13 +649,13 @@ void CWriteDB_CreateAliasFile(const string& file_name,
* @param seq_type type of sequences stored in the database [in]
* @param title title to use in this alias file [in]
*/
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_CreateAliasFile(const string& file_name,
unsigned int num_volumes,
CWriteDB::ESeqType seq_type,
const string& title = string());
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_CreateAliasFile(const string& file_name,
const vector<string>& db_names,
CWriteDB::ESeqType seq_type,
@@ -671,7 +671,7 @@ void CWriteDB_CreateAliasFile(const string& file_name,
* @throws CWriteDBException if no alias files are provided to write group
* alias file
*/
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
const string& output_directory = kEmptyStr,
bool delete_source_alias_files = false);
@@ -681,7 +681,7 @@ void CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
* deleted [in]
* @throws CWriteDBException if no alias files can be consolidated
*/
-NCBI_XOBJWRITE_EXPORT
+NCBI_XOBJWRITE_EXPORT
void CWriteDB_ConsolidateAliasFiles(bool delete_source_alias_files = false);
END_NCBI_SCOPE
diff --git a/c++/include/objtools/blast/seqdb_writer/writedb_files.hpp b/c++/include/objtools/blast/seqdb_writer/writedb_files.hpp
index 27b423e..a7a0e80 100644
--- a/c++/include/objtools/blast/seqdb_writer/writedb_files.hpp
+++ b/c++/include/objtools/blast/seqdb_writer/writedb_files.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_FILES_HPP
#define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_FILES_HPP
-/* $Id: writedb_files.hpp 200354 2010-08-06 17:58:25Z camacho $
+/* $Id: writedb_files.hpp 446657 2014-09-17 14:26:27Z rackerst $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,13 +50,13 @@ BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
/// CWriteDB_IndexFile class
-///
+///
/// This manufactures blast database index files from input data.
class CWriteDB_File : public CObject {
public:
// Setup and control
-
+
/// Constructor.
///
/// The filename is constructed from basename, extension, and
@@ -76,7 +76,7 @@ public:
int index,
Uint8 max_file_size,
bool always_create);
-
+
/// Create and open the file.
///
/// This method must be called before the first time that data is
@@ -88,12 +88,12 @@ public:
/// be created optionally, such as ISAM files, which should only
/// be created if the corresponding ID types are found.
void Create();
-
+
/// Write contents of a string to the file.
/// @param data Data to write.
/// @return File offset after write.
int Write(const CTempString & data);
-
+
/// Write an Int4 (in bigendian order) to the file.
/// @param data String to write.
/// @return File offset after write.
@@ -103,7 +103,7 @@ public:
m_Offset += 4;
return m_Offset;
}
-
+
/// Write an Int8 (in bigendian order) to the file.
/// @param data String to write.
/// @return File offset after write.
@@ -113,7 +113,7 @@ public:
m_Offset += 8;
return m_Offset;
}
-
+
/// Write contents of a string to the file, appending a NUL.
/// @param data String to write.
/// @return File offset after write.
@@ -122,13 +122,13 @@ public:
Write(data);
return Write(m_Nul);
}
-
+
/// Close the file, flushing any remaining data to disk.
void Close();
-
+
/// Rename this file, disincluding the volume index.
virtual void RenameSingle();
-
+
/// Construct the short name for a volume.
///
/// Volume names consist of the database base name, ".", and the
@@ -140,7 +140,7 @@ public:
/// @param index Volume index.
/// @return A short name.
static string MakeShortName(const string & base, int index);
-
+
/// Get the current filename for this file.
///
/// The filename is returned. The data returned by this method
@@ -153,17 +153,17 @@ public:
{
return m_Fname;
}
-
+
protected:
/// True if the file has already been opened.
bool m_Created;
-
+
/// Underlying 'output file' type used here.
typedef ofstream TFile;
-
+
/// For convenience, a string containing one NUL character.
string m_Nul; // init me
-
+
/// The default value for max_file_size.
/// @return The max file size used if otherwise unspecified.
Uint8 x_DefaultByteLimit()
@@ -171,7 +171,7 @@ protected:
// 1 gb (marketing version) - 1; about a billion
return 1000*1000*1000 - 1;
}
-
+
/// This should flush any unwritten data to disk.
///
/// This method must be implemented by derived classes to flush
@@ -180,20 +180,20 @@ protected:
/// are written as the data is available. For index (pin/nin) and
/// ISAM files, this method does most of the disk I/O.
virtual void x_Flush() = 0;
-
+
/// Build the filename for this file.
void x_MakeFileName();
-
+
// Configuration
-
+
string m_BaseName; ///< Database base name for all files.
string m_Extension; ///< File extension for this file.
int m_Index; ///< Volume index.
int m_Offset; ///< Stream position.
Uint8 m_MaxFileSize; ///< Maximum file size in bytes.
-
+
// The file
-
+
bool m_UseIndex; ///< True if filenames should use volume index.
string m_Fname; ///< Current filename for output file.
TFile m_RealFile; ///< Actual stream implementing the output file.
@@ -217,18 +217,18 @@ public:
const string & date,
int index,
Uint8 max_file_size);
-
+
/// Returns true if another sequence can fit into the file.
bool CanFit()
{
- _ASSERT(m_MaxFileSize > 1024);
-
- if (! m_OIDs)
+ _ASSERT(m_MaxFileSize > 1024UL);
+
+ if (m_OIDs == 0)
return true;
-
- return m_DataSize < (m_MaxFileSize-12);
+
+ return m_DataSize < (m_MaxFileSize - 12UL);
}
-
+
/// Add a sequence to a protein index file (pin).
///
/// The index file does not need sequence data, so this method
@@ -242,15 +242,15 @@ public:
if (length > m_MaxLength) {
m_MaxLength = length;
}
-
- m_OIDs ++;
+
+ m_OIDs++;
m_Letters += length;
m_DataSize += 8;
-
+
m_Hdr.push_back(hdr);
m_Seq.push_back(seq);
}
-
+
/// Add a sequence to a nucleotide index file (nin).
///
/// The index file does not need sequence data, so this method
@@ -259,22 +259,22 @@ public:
/// @param Sequence length in letters.
/// @param hdr Length of binary ASN.1 header data.
/// @param seq Length in bytes of packed sequence data.
- /// @param seq Length in bytes of packed ambiguity data.
+ /// @param amb Length in bytes of packed ambiguity data.
void AddSequence(int length, int hdr, int seq, int amb)
{
if (length > m_MaxLength) {
m_MaxLength = length;
}
-
- m_OIDs ++;
+
+ m_OIDs++;
m_Letters += length;
-
+
m_DataSize += 12;
m_Hdr.push_back(hdr);
m_Seq.push_back(amb); // Not a bug.
m_Amb.push_back(seq); // Also not a bug.
}
-
+
private:
/// Compute index file overhead. This is the overhead used by all
/// fields of the index file, and does account for padding.
@@ -283,10 +283,10 @@ private:
/// @param D Create time string.
/// @return Combined size of all meta-data fields in nin/pin file.
int x_Overhead(const string & T, const string & D);
-
+
/// Flush index data to disk.
virtual void x_Flush();
-
+
bool m_Protein; ///< True if this is a protein database.
string m_Title; ///< Title string for all database volumes.
string m_Date; ///< Database creation time stamp.
@@ -295,24 +295,24 @@ private:
Uint8 m_DataSize; ///< Required space for data once written to disk.
Uint8 m_Letters; ///< Letters of sequence data accumulated so far.
int m_MaxLength; ///< Length of longest sequence.
-
+
// Because the lengths are found via "next offset - this offset",
// each array has an extra element. (This is not necesary in the
// case of m_Amb; the last element is never examined because of
// the alternation of sequences and ambiguities.)
-
+
/// Start offset in header file of each OID's headers.
///
/// The end offset is given by the start offset of the following
/// OID's headers.
vector<int> m_Hdr;
-
+
/// Offset in sequence file of each OID's sequence data.
///
/// The end of the sequence data is given by the start offset of
/// the ambiguity data for the same OID.
vector<int> m_Seq;
-
+
/// Offset in sequence file of each OID's ambiguity data.
///
/// The end of the ambiguity data is given by the start offset of
@@ -332,7 +332,7 @@ public:
bool protein,
int index,
Uint8 max_file_size);
-
+
/// Returns true if the specified amount of data would fit.
///
/// If the specified amount of data (in bytes) would fit in the
@@ -342,13 +342,15 @@ public:
/// @param size Size of new data in bytes.
bool CanFit(int size)
{
- if (! m_DataSize) {
+ _ASSERT(size >= 0);
+
+ if (m_DataSize == 0UL) {
return true;
}
-
- return (m_DataSize + size) < m_MaxFileSize;
+
+ return (m_DataSize + (Uint8) size) < m_MaxFileSize;
}
-
+
/// Add binary header data to this file.
/// @param binhdr Binary ASN.1 version of header data. [in]
/// @param offset Offset of end of header data. [out]
@@ -356,7 +358,7 @@ public:
{
m_DataSize = offset = Write(binhdr);
}
-
+
private:
/// Flush unwritten data to the output file.
virtual void x_Flush()
@@ -364,7 +366,7 @@ private:
// There is nothing to do here - header data is written as
// soon as it is added.
}
-
+
/// Amount of data written so far.
Uint8 m_DataSize;
};
@@ -382,7 +384,7 @@ public:
int index,
Uint8 max_file_size,
Uint8 max_letters);
-
+
/// Returns true if the specified amount of data would fit.
///
/// If the specified amount of data (in bytes) would fit in the
@@ -394,18 +396,21 @@ public:
/// @param letters Number of sequence letters in new data.
bool CanFit(int size, int letters)
{
+ _ASSERT(size >= 0);
+ _ASSERT(letters >= 0);
+
if (m_Offset <= 1) {
return true;
}
-
- if (m_BaseLimit &&
- ((m_Letters + letters) > m_BaseLimit)) {
+
+ if ((m_BaseLimit != 0) &&
+ ((m_Letters + (Uint8) letters) > m_BaseLimit)) {
return false;
}
-
- return ((m_Offset + (unsigned)size) < m_MaxFileSize);
+
+ return ((Uint8)(m_Offset + size) < m_MaxFileSize);
}
-
+
/// Add a protein sequence to this file.
///
/// This method should only be called in the protein case.
@@ -421,7 +426,7 @@ public:
offset = WriteWithNull(sequence);
m_Letters += length;
}
-
+
/// Add a nucleotide sequence to this file.
///
/// This method should only be called in the nucleotide case.
@@ -442,7 +447,7 @@ public:
off_amb = Write(ambig);
m_Letters += length;
}
-
+
private:
/// Flush unwritten data to the output file.
virtual void x_Flush()
@@ -450,7 +455,7 @@ private:
// There is nothing to do here - sequence data is written as
// soon as it is added.
}
-
+
Uint8 m_Letters; ///< Letters of sequence data added so far.
Uint8 m_BaseLimit; ///< Limit on letters of sequence data.
bool m_Protein; ///< True if this is a protein database.
diff --git a/c++/include/objtools/blast/services/blast_services.hpp b/c++/include/objtools/blast/services/blast_services.hpp
index 0c2bc8f..9225870 100644
--- a/c++/include/objtools/blast/services/blast_services.hpp
+++ b/c++/include/objtools/blast/services/blast_services.hpp
@@ -1,7 +1,7 @@
#ifndef ALGO_BLAST_API___REMOTE_SERVICES__HPP
#define ALGO_BLAST_API___REMOTE_SERVICES__HPP
-/* $Id: blast_services.hpp 465078 2015-04-16 17:36:39Z ivanov $
+/* $Id: blast_services.hpp 464987 2015-04-15 19:29:32Z merezhuk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/cleanup/cleanup.hpp b/c++/include/objtools/cleanup/cleanup.hpp
index 47a27b5..3e3a77b 100644
--- a/c++/include/objtools/cleanup/cleanup.hpp
+++ b/c++/include/objtools/cleanup/cleanup.hpp
@@ -1,7 +1,7 @@
#ifndef CLEANUP___CLEANUP__HPP
#define CLEANUP___CLEANUP__HPP
-/* $Id: cleanup.hpp 467195 2015-05-11 16:00:45Z ivanov $
+/* $Id: cleanup.hpp 480959 2015-10-06 12:01:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,7 +63,8 @@ public:
eClean_NoReporting = 0x1,
eClean_GpipeMode = 0x2,
eClean_NoNcbiUserObjects = 0x4,
- eClean_SyncGenCodes = 0x8
+ eClean_SyncGenCodes = 0x8,
+ eClean_NoProteinTitles = 0x10
};
// Construtor / Destructor
@@ -107,6 +108,113 @@ public:
// Handle versions
CConstRef<CCleanupChange> ExtendedCleanup(CSeq_entry_Handle& seh, Uint4 options = 0);
+ // Useful cleanup functions
+
+/// Moves protein-specific features from nucleotide sequences in the Seq-entry to
+/// the appropriate protein sequence.
+/// @param seh Seq-entry Handle to edit [in]
+/// @return Boolean return value indicates whether any changes were made
+ static bool MoveProteinSpecificFeats(CSeq_entry_Handle seh);
+
+/// Calculates whether a Gene-xref is unnecessary (because it refers to the
+/// same gene as would be calculated using overlap)
+/// @param sf Seq-feat with the xref [in]
+/// @param scope Scope in which to search for location [in]
+/// @param gene_xref Gene-ref of gene-xref [in]
+/// @return Boolean return value indicates whether gene-xref is unnecessary
+ static bool IsGeneXrefUnnecessary(const CSeq_feat& sf, CScope& scope, const CGene_ref& gene_xref);
+
+/// Removes unnecessary Gene-xrefs
+/// @param f Seq-feat to edit [in]
+/// @param scope Scope in which to search for locations [in]
+/// @return Boolean return value indicates whether gene-xrefs were removed
+ static bool RemoveUnnecessaryGeneXrefs(CSeq_feat& f, CScope& scope);
+
+/// Removes unnecessary Gene-xrefs on features in Seq-entry
+/// @param seh Seq-entry-Handle to edit [in]
+/// @return Boolean return value indicates whether gene-xrefs were removed
+ static bool RemoveUnnecessaryGeneXrefs(CSeq_entry_Handle seh);
+
+/// Removes non-suppressing Gene-xrefs
+/// @param f Seq-feat to edit [in]
+/// @return Boolean return value indicates whether gene-xrefs were removed
+ static bool RemoveNonsuppressingGeneXrefs(CSeq_feat& f);
+
+/// Detects gene features with matching locus
+/// @param f Seq-feat parent feature of gene_xref [in]
+/// @param gene_xref Gene-ref of gene-xref [in]
+/// @param bsh CBioseq_Handle parent bioseq in which to search for genes [in]
+/// @return Boolean return value indicates whether a gene feature with matching locus has been found
+ static bool FindMatchingLocusGene(CSeq_feat& f, const CGene_ref& gene_xref, CBioseq_Handle bsh);
+
+/// Removes orphaned locus Gene-xrefs
+/// @param f Seq-feat to edit [in]
+/// @param bsh CBioseq_Handle in which to search for gene features [in]
+/// @return Boolean return value indicates whether gene-xrefs were removed
+ static bool RemoveOrphanLocusGeneXrefs(CSeq_feat& f, CBioseq_Handle bsh);
+
+/// Detects gene features with matching locus_tag
+/// @param f Seq-feat parent feature of gene_xref [in]
+/// @param gene_xref Gene-ref of gene-xref [in]
+/// @param bsh CBioseq_Handle parent bioseq in which to search for genes [in]
+/// @return Boolean return value indicates whether a gene feature with matching locus_tag has been found
+ static bool FindMatchingLocus_tagGene(CSeq_feat& f, const CGene_ref& gene_xref, CBioseq_Handle bsh);
+
+/// Removes orphaned locus_tag Gene-xrefs
+/// @param f Seq-feat to edit [in]
+/// @param bsh CBioseq_Handle in which to search for gene features [in]
+/// @return Boolean return value indicates whether gene-xrefs were removed
+ static bool RemoveOrphanLocus_tagGeneXrefs(CSeq_feat& f, CBioseq_Handle bsh);
+
+/// Sets MolInfo::tech for a sequence
+/// @param seq Bioseq to edit
+/// @param tech tech value to set
+/// @return Boolean tech was changed
+ static bool SetMolinfoTech(CBioseq_Handle seq, CMolInfo::ETech tech);
+
+/// Sets MolInfo::biomol for a sequence
+/// @param seq Bioseq to edit
+/// @param biomol biomol value to set
+/// @return Boolean biomol was changed
+ static bool SetMolinfoBiomol(CBioseq_Handle seq, CMolInfo::EBiomol biomol);
+
+
+/// Adds missing MolInfo descriptor to sequence
+/// @param seq Bioseq to edit
+/// @return Boolean return value indicates whether descriptor was added
+ static bool AddMissingMolInfo(CBioseq& seq, bool is_product);
+
+/// Creates missing protein title descriptor
+/// @param seq Bioseq to edit
+/// @return Boolean return value indicates whether title was added
+ static bool AddProteinTitle(CBioseq_Handle bsh);
+
+/// Removes NcbiCleanup User Objects in the Seq-entry
+/// @param seq_entry Seq-entry to edit
+/// @return Boolean return value indicates whether object was removed
+ static bool RemoveNcbiCleanupObject(CSeq_entry &seq_entry);
+
+/// Looks up Org-refs in the Seq-entry
+/// @param seh Seq-entry to edit
+/// @return Boolean return value indicates whether object was updated
+ static bool TaxonomyLookup(CSeq_entry_Handle seh);
+
+/// Performs WGS specific cleanup
+/// @param entry Seq-entry to edit
+/// @return Boolean return value indicates whether object was updated
+ static bool WGSCleanup(CSeq_entry_Handle entry);
+
+/// Normalize Descriptor Order on a specific Seq-entry
+/// @param entry Seq-entry to edit
+/// @return Boolean return value indicates whether object was updated
+ static bool NormalizeDescriptorOrder(CSeq_descr& descr);
+
+/// Normalize Descriptor Order on a specific Seq-entry
+/// @param entry Seq-entry to edit
+/// @return Boolean return value indicates whether object was updated
+ static bool NormalizeDescriptorOrder(CSeq_entry_Handle seh);
+
+
private:
// Prohibit copy constructor & assignment operator
CCleanup(const CCleanup&);
diff --git a/c++/include/objtools/cleanup/cleanup_change.hpp b/c++/include/objtools/cleanup/cleanup_change.hpp
index 51a2c97..411def0 100644
--- a/c++/include/objtools/cleanup/cleanup_change.hpp
+++ b/c++/include/objtools/cleanup/cleanup_change.hpp
@@ -1,7 +1,7 @@
#ifndef CLEANUP___CLEANUP_CHANGE__HPP
#define CLEANUP___CLEANUP_CHANGE__HPP
-/* $Id: cleanup_change.hpp 428916 2014-03-10 13:22:47Z bollin $
+/* $Id: cleanup_change.hpp 468092 2015-05-20 13:08:50Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -158,6 +158,7 @@ public:
eDecodeXML,
eRemoveDupBioSource, // 90
eCleanOrgref,
+ eTrimInternalSemicolons,
// set when any other change is made.
eChangeOther,
diff --git a/c++/include/objtools/cleanup/newcleanup.hpp b/c++/include/objtools/cleanup/newcleanup.hpp
index febf831..b426562 100755
--- a/c++/include/objtools/cleanup/newcleanup.hpp
+++ b/c++/include/objtools/cleanup/newcleanup.hpp
@@ -334,4 +334,4 @@ protected:
END_SCOPE(objects)
END_NCBI_SCOPE
-#endif /* NEWCLEANUP__HPP */
\ No newline at end of file
+#endif /* NEWCLEANUP__HPP */
diff --git a/c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp b/c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp
index 0b8b377..aad87b6 100644
--- a/c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp
+++ b/c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_DATA_LOADERS_BLASTDB___BLASTDB_ADAPTER__HPP
#define OBJTOOLS_DATA_LOADERS_BLASTDB___BLASTDB_ADAPTER__HPP
-/* $Id: blastdb_adapter.hpp 401240 2013-05-29 14:08:40Z madden $
+/* $Id: blastdb_adapter.hpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -102,7 +102,7 @@ public:
/// the header information.
/// @return object corresponding to the sequence, but without
/// sequence data.
- virtual CRef<CBioseq> GetBioseqNoData(int oid, int target_gi = 0, const CSeq_id * target_id = NULL) = 0;
+ virtual CRef<CBioseq> GetBioseqNoData(int oid, TGi target_gi = ZERO_GI, const CSeq_id * target_id = NULL) = 0;
/// Get all or part of the sequence data as a Seq-data object.
/// @param oid Identifies which sequence to get.
diff --git a/c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp b/c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp
index 993bee6..744551a 100644
--- a/c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp
+++ b/c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp
@@ -1,7 +1,7 @@
#ifndef READER_CACHE__HPP_INCLUDED
#define READER_CACHE__HPP_INCLUDED
-/* $Id: reader_cache.hpp 448019 2014-10-01 20:53:51Z vasilche $
+/* $Id: reader_cache.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -77,6 +77,8 @@ struct NCBI_XREADER_CACHE_EXPORT SCacheInfo
static const char* GetLabelSubkey(void);
// Seq-id -> taxid (1 int)
static const char* GetTaxIdSubkey(void);
+ // Seq-id -> hash (1 int)
+ static const char* GetHashSubkey(void);
// Seq-id -> list of Seq-id, binary ASN.1
static const char* GetSeq_idsSubkey(void);
// blob_id -> blob state (1 int)
@@ -163,6 +165,8 @@ public:
const CSeq_id_Handle& seq_id);
bool LoadSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id);
+ bool LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id);
bool LoadSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel);
diff --git a/c++/include/objtools/data_loaders/genbank/cache/writer_cache.hpp b/c++/include/objtools/data_loaders/genbank/cache/writer_cache.hpp
index 483ea2c..121f46d 100644
--- a/c++/include/objtools/data_loaders/genbank/cache/writer_cache.hpp
+++ b/c++/include/objtools/data_loaders/genbank/cache/writer_cache.hpp
@@ -1,7 +1,7 @@
#ifndef WRITER_CACHE__HPP_INCLUDED
#define WRITER_CACHE__HPP_INCLUDED
-/* $Id: writer_cache.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: writer_cache.hpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -63,6 +63,8 @@ public:
const CSeq_id_Handle& seq_id);
virtual void SaveSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id);
+ virtual void SaveSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id);
virtual void SaveSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel);
@@ -118,6 +120,11 @@ protected:
{
StoreUint4(v);
}
+ void StoreInt8(Int8 v)
+ {
+ StoreInt4(v>>32);
+ StoreUint4(Uint4(v));
+ }
void StoreString(const string& s);
static Uint4 ToUint4(size_t size)
diff --git a/c++/include/objtools/data_loaders/genbank/gbloader.hpp b/c++/include/objtools/data_loaders/genbank/gbloader.hpp
index d520bcc..88ade5e 100644
--- a/c++/include/objtools/data_loaders/genbank/gbloader.hpp
+++ b/c++/include/objtools/data_loaders/genbank/gbloader.hpp
@@ -1,7 +1,7 @@
#ifndef GBLOADER__HPP_INCLUDED
#define GBLOADER__HPP_INCLUDED
-/* $Id: gbloader.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: gbloader.hpp 475892 2015-08-12 18:52:12Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -191,6 +191,7 @@ public:
virtual string GetLabel(const CSeq_id_Handle& idh);
virtual int GetTaxId(const CSeq_id_Handle& idh);
virtual int GetSequenceState(const CSeq_id_Handle& idh);
+ virtual int GetSequenceHash(const CSeq_id_Handle& idh);
virtual void GetAccVers(const TIds& ids, TLoaded& loader, TIds& ret);
virtual void GetGis(const TIds& ids, TLoaded& loader, TGis& ret);
@@ -202,6 +203,8 @@ public:
TSequenceTypes& ret);
virtual void GetSequenceStates(const TIds& ids, TLoaded& loader,
TSequenceStates& ret);
+ virtual void GetSequenceHashes(const TIds& ids, TLoaded& loader,
+ TSequenceHashes& ret);
virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh,
EChoice choice);
@@ -352,6 +355,16 @@ public:
m_AlwaysLoadExternal = flag;
}
+ bool GetAlwaysLoadNamedAcc(void) const
+ {
+ return m_AlwaysLoadNamedAcc;
+ }
+
+ void SetAlwaysLoadNamedAcc(bool flag)
+ {
+ m_AlwaysLoadNamedAcc = flag;
+ }
+
bool GetAddWGSMasterDescr(void) const
{
return m_AddWGSMasterDescr;
@@ -395,6 +408,7 @@ private:
TExpirationTimeout m_IdExpirationTimeout;
bool m_AlwaysLoadExternal;
+ bool m_AlwaysLoadNamedAcc;
bool m_AddWGSMasterDescr;
//
diff --git a/c++/include/objtools/data_loaders/genbank/gbloader_params.h b/c++/include/objtools/data_loaders/genbank/gbloader_params.h
index 2d1f729..543711d 100644
--- a/c++/include/objtools/data_loaders/genbank/gbloader_params.h
+++ b/c++/include/objtools/data_loaders/genbank/gbloader_params.h
@@ -1,7 +1,7 @@
#ifndef GBLOADER_PARAMS__HPP_INCLUDED
#define GBLOADER_PARAMS__HPP_INCLUDED
-/* $Id: gbloader_params.h 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: gbloader_params.h 475892 2015-08-12 18:52:12Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,6 +63,8 @@
#define NCBI_GBLOADER_PARAM_ID_EXPIRATION_TIMEOUT "ID_EXPIRATION_TIMEOUT"
/* Load external annotations for other loaders */
#define NCBI_GBLOADER_PARAM_ALWAYS_LOAD_EXTERNAL "ALWAYS_LOAD_EXTERNAL"
+/* Load NANNOT annotations for other loaders */
+#define NCBI_GBLOADER_PARAM_ALWAYS_LOAD_NAMED_ACC "ALWAYS_LOAD_NAMED_ACC"
/* Add WGS master descriptors to all WGS sequences */
#define NCBI_GBLOADER_PARAM_ADD_WGS_MASTER "ADD_WGS_MASTER"
diff --git a/c++/include/objtools/data_loaders/genbank/id1/reader_id1.hpp b/c++/include/objtools/data_loaders/genbank/id1/reader_id1.hpp
index 63fbfe5..db156a9 100644
--- a/c++/include/objtools/data_loaders/genbank/id1/reader_id1.hpp
+++ b/c++/include/objtools/data_loaders/genbank/id1/reader_id1.hpp
@@ -1,7 +1,7 @@
#ifndef READER_ID1__HPP_INCLUDED
#define READER_ID1__HPP_INCLUDED
-/* $Id: reader_id1.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: reader_id1.hpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -92,9 +92,9 @@ protected:
// returns error blob state parsed from ID1server-back.error
TBlobState x_ResolveId(CReaderRequestResult& result,
CID1server_back& id1_reply,
- const CID1server_request& id1_request);
+ CID1server_request& id1_request);
- void x_SendRequest(TConn conn, const CID1server_request& request);
+ void x_SendRequest(TConn conn, CID1server_request& request);
void x_ReceiveReply(TConn conn, CID1server_back& reply);
void x_SendRequest(const CBlob_id& blob_id, TConn conn);
diff --git a/c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp b/c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp
index b0e9358..74118f7 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp
@@ -2,7 +2,7 @@
#define DISPATCHER__HPP_INCLUDED
/* */
-/* $Id: dispatcher.hpp 441625 2014-07-25 16:14:45Z vasilche $
+/* $Id: dispatcher.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -98,12 +98,15 @@ public:
const CSeq_id_Handle& seq_id);
void LoadSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id);
+ void LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id);
// bulk requests
typedef vector<bool> TLoaded;
typedef vector<TGi> TGis;
typedef vector<string> TLabels;
typedef vector<int> TTaxIds;
+ typedef vector<int> THashes;
typedef vector<TBlobState> TStates;
void LoadAccVers(CReaderRequestResult& result,
const TIds ids, TLoaded& loaded, TIds& ret);
@@ -113,6 +116,8 @@ public:
const TIds ids, TLoaded& loaded, TLabels& ret);
void LoadTaxIds(CReaderRequestResult& result,
const TIds ids, TLoaded& loaded, TTaxIds& ret);
+ void LoadHashes(CReaderRequestResult& result,
+ const TIds ids, TLoaded& loaded, THashes& ret);
void LoadStates(CReaderRequestResult& result,
const TIds ids, TLoaded& loaded, TStates& ret);
diff --git a/c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp b/c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp
index 99fd5ad..02b9f18 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp
@@ -1,7 +1,7 @@
#ifndef GENBANK_IMPL_INFO_CACHE
#define GENBANK_IMPL_INFO_CACHE
-/* $Id: info_cache.hpp 448727 2014-10-08 15:47:13Z ivanov $
+/* $Id: info_cache.hpp 448421 2014-10-06 16:04:30Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/data_loaders/genbank/impl/processor.hpp b/c++/include/objtools/data_loaders/genbank/impl/processor.hpp
index 0b66f39..1e3050d 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/processor.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/processor.hpp
@@ -2,7 +2,7 @@
#define PROCESSOR__HPP_INCLUDED
/* */
-/* $Id: processor.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: processor.hpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -40,6 +40,7 @@
BEGIN_NCBI_SCOPE
class CObjectIStream;
+class CBeginInfo;
class CStopWatch;
BEGIN_SCOPE(objects)
@@ -53,6 +54,7 @@ class CID2_Reply_Data;
class CLoadLockBlob;
class CLoadLockSetter;
class CTSE_Chunk_Info;
+class CTSE_SetObjectInfo;
class CDataLoader;
struct STimeSizeStatistics;
@@ -117,6 +119,52 @@ public:
static void LoadWGSMaster(CDataLoader* loader,
CRef<CTSE_Chunk_Info> chunk);
+ static TIntId GetGiOffset(void);
+ static void OffsetGi(TGi& gi, TIntId gi_offset)
+ {
+ if ( gi ) {
+ gi = gi + gi_offset;
+ }
+ }
+#ifdef NCBI_STRICT_GI
+ static void OffsetGi(TIntId& gi, TIntId gi_offset)
+ {
+ if ( gi ) {
+ gi = gi + gi_offset;
+ }
+ }
+#endif
+ static bool OffsetId(CSeq_id& id, TIntId gi_offset);
+ static bool OffsetId(CSeq_id_Handle& id, TIntId gi_offset);
+ static void OffsetAllGis(CBeginInfo obj, TIntId gi_offset);
+ static void OffsetAllGis(CTSE_SetObjectInfo& set_info, TIntId gi_offset);
+
+ static TGi ConvertGiFromOM(TGi gi)
+ {
+ OffsetGi(gi, -GetGiOffset());
+ return gi;
+ }
+ static TGi ConvertGiToOM(TGi gi)
+ {
+ OffsetGi(gi, GetGiOffset());
+ return gi;
+ }
+ static CSeq_id_Handle ConvertIdFromOM(CSeq_id_Handle id)
+ {
+ OffsetId(id, -GetGiOffset());
+ return id;
+ }
+ static void OffsetGiToOM(TGi& gi)
+ {
+ OffsetGi(gi, GetGiOffset());
+ }
+ static void OffsetIdToOM(CSeq_id& id)
+ {
+ OffsetId(id, GetGiOffset());
+ }
+ static void OffsetAllGisFromOM(CBeginInfo obj);
+ static void OffsetAllGisToOM(CBeginInfo obj, CTSE_SetObjectInfo* set_info = 0);
+
protected:
CProcessor(CReadDispatcher& dispatcher);
@@ -181,6 +229,7 @@ NCBI_PARAM_DECL(bool, GENBANK, USE_MEMORY_POOL);
NCBI_PARAM_DECL(int, GENBANK, READER_STATS);
NCBI_PARAM_DECL(bool, GENBANK, CACHE_RECOMPRESS);
NCBI_PARAM_DECL(bool, GENBANK, ADD_WGS_MASTER);
+NCBI_PARAM_DECL(Int8, GENBANK, GI_OFFSET);
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/include/objtools/data_loaders/genbank/impl/processors.hpp b/c++/include/objtools/data_loaders/genbank/impl/processors.hpp
index a6857c5..9d63994 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/processors.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/processors.hpp
@@ -1,6 +1,6 @@
#ifndef PROCESSORS__HPP_INCLUDED
#define PROCESSORS__HPP_INCLUDED
-/* $Id: processors.hpp 442201 2014-07-31 10:36:19Z mcelhany $
+/* $Id: processors.hpp 442103 2014-07-30 16:02:46Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
diff --git a/c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp b/c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
index e977bf3..a01b4ef 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
@@ -1,7 +1,7 @@
#ifndef READER_ID2_BASE__HPP_INCLUDED
#define READER_ID2_BASE__HPP_INCLUDED
-/* $Id: reader_id2_base.hpp 463675 2015-03-31 18:23:39Z vasilche $
+/* $Id: reader_id2_base.hpp 465720 2015-04-23 18:17:30Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -87,6 +87,8 @@ public:
const CSeq_id_Handle& seq_id);
bool LoadSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id);
+ bool LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id);
bool LoadSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel);
@@ -99,6 +101,8 @@ public:
const TIds& ids, TLoaded& loaded, TLabels& ret);
bool LoadTaxIds(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TTaxIds& ret);
+ bool LoadHashes(CReaderRequestResult& result,
+ const TIds& ids, TLoaded& loaded, THashes& ret);
bool LoadStates(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TStates& ret);
@@ -187,10 +191,20 @@ protected:
TErrorFlags x_GetError(CReaderRequestResult& result,
const CID2_Error& error);
TErrorFlags x_GetMessageError(const CID2_Error& error);
+ static void sx_CheckErrorFlag(const CID2_Error& error,
+ TErrorFlags& error_flags,
+ EErrorFlags test_flag,
+ const char* marker1,
+ const char* marker2 = 0);
TErrorFlags x_GetError(CReaderRequestResult& result,
const CID2_Reply& reply);
TErrorFlags x_GetMessageError(const CID2_Reply& reply);
- TBlobState x_GetBlobState(const CID2_Reply& reply,
+ TBlobState x_GetBlobStateFromID2(const CBlob_id& blob_id,
+ SId2LoadedSet& loaded_set,
+ int id2_state);
+ TBlobState x_GetBlobState(const CBlob_id& blob_id,
+ SId2LoadedSet& loaded_set,
+ const CID2_Reply& reply,
TErrorFlags* errors_ptr = 0);
void x_ProcessReply(CReaderRequestResult& result,
@@ -246,7 +260,8 @@ private:
enum {
fAvoidRequest_nested_get_blob_info = 1,
fAvoidRequest_for_Seq_id_label = 2,
- fAvoidRequest_for_Seq_id_taxid = 4
+ fAvoidRequest_for_Seq_id_taxid = 4,
+ fAvoidRequest_for_SequenceHash = 8
};
typedef int TAvoidRequests;
TAvoidRequests m_AvoidRequest;
diff --git a/c++/include/objtools/data_loaders/genbank/impl/request_result.hpp b/c++/include/objtools/data_loaders/genbank/impl/request_result.hpp
index fa7099f..4aea0a2 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/request_result.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/request_result.hpp
@@ -1,7 +1,7 @@
#ifndef GBLOADER_REQUEST_RESULT__HPP_INCLUDED
#define GBLOADER_REQUEST_RESULT__HPP_INCLUDED
-/* $Id: request_result.hpp 448727 2014-10-08 15:47:13Z ivanov $
+/* $Id: request_result.hpp 452490 2014-11-20 15:50:53Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,9 +80,12 @@ public:
typedef TList::const_reference const_reference;
typedef TList::const_iterator const_iterator;
- explicit CFixedSeq_ids(TState state = 0);
- explicit CFixedSeq_ids(const TList& list, TState state = 0);
- CFixedSeq_ids(ENcbiOwnership ownership, TList& list, TState state = 0);
+ enum {
+ kUnknownState = -256
+ };
+ explicit CFixedSeq_ids(TState state = kUnknownState);
+ explicit CFixedSeq_ids(const TList& list, TState state = kUnknownState);
+ CFixedSeq_ids(ENcbiOwnership ownership, TList& list, TState state = kUnknownState);
const TList& Get(void) const
{
@@ -208,9 +211,12 @@ public:
typedef TList::const_reference const_reference;
typedef TList::const_iterator const_iterator;
- explicit CFixedBlob_ids(TState state = 0);
- explicit CFixedBlob_ids(const TList& list, TState state = 0);
- CFixedBlob_ids(ENcbiOwnership ownership, TList& list, TState state = 0);
+ enum {
+ kUnknownState = -256
+ };
+ explicit CFixedBlob_ids(TState state = kUnknownState);
+ explicit CFixedBlob_ids(const TList& list, TState state = kUnknownState);
+ CFixedBlob_ids(ENcbiOwnership ownership, TList& list, TState state = kUnknownState);
TState GetState(void) const
{
@@ -285,6 +291,8 @@ public:
typedef GBL::CInfoCache<TKeyBlobIds, CFixedBlob_ids> TCacheBlobIds;
typedef int TBlobState;
typedef GBL::CInfoCache<CBlob_id, TBlobState> TCacheBlobState;
+ typedef int TSequenceHash;
+ typedef GBL::CInfoCache<CSeq_id_Handle, TSequenceHash> TCacheHash;
typedef int TBlobVersion;
typedef GBL::CInfoCache<CBlob_id, TBlobVersion> TCacheBlobVersion;
typedef GBL::CInfoCache<CBlob_id, CTSE_LoadLock> TCacheBlob;
@@ -297,6 +305,7 @@ public:
TCacheStrGi m_CacheStrGi;
TCacheLabel m_CacheLabel;
TCacheTaxId m_CacheTaxId;
+ TCacheHash m_CacheHash;
TCacheBlobIds m_CacheBlobIds;
TCacheBlobState m_CacheBlobState;
TCacheBlobVersion m_CacheBlobVersion;
@@ -468,6 +477,35 @@ public:
};
+class NCBI_XREADER_EXPORT CLoadLockHash :
+ public CGBInfoManager::TCacheHash::TInfoLock
+{
+ typedef CGBInfoManager::TCacheHash::TInfoLock TParent;
+public:
+ CLoadLockHash(void)
+ {
+ }
+ CLoadLockHash(CReaderRequestResult& result, const CSeq_id_Handle& id);
+
+ bool IsLoadedHash(void) const
+ {
+ return IsLoaded();
+ }
+ TData GetHash(void) const
+ {
+ return GetData();
+ }
+ bool SetLoadedHash(const TData& data)
+ {
+ return SetLoaded(data);
+ }
+ bool SetLoadedHash(const TData& data, TExpirationTime expiration_time)
+ {
+ return SetLoaded(data, expiration_time);
+ }
+};
+
+
class NCBI_XREADER_EXPORT CLoadLockBlobIds :
public CGBInfoManager::TCacheBlobIds::TInfoLock
{
@@ -701,6 +739,8 @@ public:
typedef CGBInfoManager::TCacheLabel::TInfoLock TInfoLockLabel;
typedef CGBInfoManager::TTaxId TTaxId;
typedef CGBInfoManager::TCacheTaxId::TInfoLock TInfoLockTaxId;
+ typedef CGBInfoManager::TSequenceHash TSequenceHash;
+ typedef CGBInfoManager::TCacheHash::TInfoLock TInfoLockHash;
typedef CGBInfoManager::TCacheBlobIds::TInfoLock TInfoLockBlobIds;
typedef CGBInfoManager::TCacheBlobState::TInfoLock TInfoLockBlobState;
typedef CGBInfoManager::TCacheBlobVersion::TInfoLock TInfoLockBlobVersion;
@@ -785,6 +825,13 @@ public:
bool SetLoadedTaxId(const CSeq_id_Handle& id,
const TTaxId& value);
+ bool IsLoadedHash(const CSeq_id_Handle& id);
+ bool MarkLoadingHash(const CSeq_id_Handle& id);
+ TInfoLockHash GetLoadLockHash(const CSeq_id_Handle& id);
+ TInfoLockHash GetLoadedHash(const CSeq_id_Handle& id);
+ bool SetLoadedHash(const CSeq_id_Handle& id,
+ const TSequenceHash& value);
+
bool IsLoadedBlobIds(const CSeq_id_Handle& id,
const SAnnotSelector* sel);
bool MarkLoadingBlobIds(const CSeq_id_Handle& id,
diff --git a/c++/include/objtools/data_loaders/genbank/impl/statistics.hpp b/c++/include/objtools/data_loaders/genbank/impl/statistics.hpp
index 0ad728b..e933fd0 100644
--- a/c++/include/objtools/data_loaders/genbank/impl/statistics.hpp
+++ b/c++/include/objtools/data_loaders/genbank/impl/statistics.hpp
@@ -1,7 +1,7 @@
#ifndef GENBANK__STATISTICS__HPP_INCLUDED
#define GENBANK__STATISTICS__HPP_INCLUDED
-/* $Id: statistics.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: statistics.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -59,6 +59,7 @@ public:
eStat_ParseSNPBlob,
eStat_ParseSplit,
eStat_ParseChunk,
+ eStat_Hash,
eStats_Count,
eStat_Last = eStats_Count-1
diff --git a/c++/include/objtools/data_loaders/genbank/reader.hpp b/c++/include/objtools/data_loaders/genbank/reader.hpp
index 86c5349..5658980 100644
--- a/c++/include/objtools/data_loaders/genbank/reader.hpp
+++ b/c++/include/objtools/data_loaders/genbank/reader.hpp
@@ -1,6 +1,6 @@
#ifndef READER__HPP_INCLUDED
#define READER__HPP_INCLUDED
-/* $Id: reader.hpp 448190 2014-10-02 20:01:18Z vasilche $
+/* $Id: reader.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -88,6 +88,8 @@ public:
const CSeq_id_Handle& seq_id);
virtual bool LoadSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id);
+ virtual bool LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id);
// bulk requests
typedef vector<CSeq_id_Handle> TIds;
@@ -96,6 +98,7 @@ public:
typedef vector<string> TLabels;
typedef vector<int> TTaxIds;
typedef vector<int> TStates;
+ typedef vector<int> THashes;
virtual bool LoadAccVers(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TIds& ret);
virtual bool LoadGis(CReaderRequestResult& result,
@@ -104,6 +107,8 @@ public:
const TIds& ids, TLoaded& loaded, TLabels& ret);
virtual bool LoadTaxIds(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TTaxIds& ret);
+ virtual bool LoadHashes(CReaderRequestResult& result,
+ const TIds& ids, TLoaded& loaded, THashes& ret);
virtual bool LoadStates(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TStates& ret);
@@ -190,6 +195,9 @@ public:
void SetAndSaveSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
int taxid, ESave save = eSave) const;
+ void SetAndSaveSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id,
+ int hash, ESave save = eSave) const;
void SetAndSaveSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel,
diff --git a/c++/include/objtools/data_loaders/genbank/writer.hpp b/c++/include/objtools/data_loaders/genbank/writer.hpp
index c87b74e..1dbc6d2 100644
--- a/c++/include/objtools/data_loaders/genbank/writer.hpp
+++ b/c++/include/objtools/data_loaders/genbank/writer.hpp
@@ -2,7 +2,7 @@
#define WRITER__HPP_INCLUDED
/* */
-/* $Id: writer.hpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: writer.hpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -82,6 +82,8 @@ public:
const CSeq_id_Handle& seq_id) = 0;
virtual void SaveSeq_idTaxId(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id) = 0;
+ virtual void SaveSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id) = 0;
virtual void SaveSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel) = 0;
diff --git a/c++/include/objtools/data_loaders/loaders.hpp b/c++/include/objtools/data_loaders/loaders.hpp
index 49b1fbf..7ab427a 100644
--- a/c++/include/objtools/data_loaders/loaders.hpp
+++ b/c++/include/objtools/data_loaders/loaders.hpp
@@ -1,7 +1,7 @@
#ifndef DATA_LOADERS___LOADERS__HPP
#define DATA_LOADERS___LOADERS__HPP
-/* $Id: loaders.hpp 469194 2015-06-02 14:03:42Z blastadm $
+/* $Id: loaders.hpp 485953 2015-11-30 17:53:34Z blastadm $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/apply_object.hpp b/c++/include/objtools/edit/apply_object.hpp
index 1a7bfe9..737eb5b 100644
--- a/c++/include/objtools/edit/apply_object.hpp
+++ b/c++/include/objtools/edit/apply_object.hpp
@@ -1,4 +1,4 @@
-/* $Id: apply_object.hpp 447186 2014-09-23 14:45:51Z ivanov $
+/* $Id: apply_object.hpp 447037 2014-09-22 11:21:25Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/autodef.hpp b/c++/include/objtools/edit/autodef.hpp
index f2e0fe6..84bd855 100644
--- a/c++/include/objtools/edit/autodef.hpp
+++ b/c++/include/objtools/edit/autodef.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT___AUTODEF__HPP
#define OBJTOOLS_EDIT___AUTODEF__HPP
-/* $Id: autodef.hpp 453920 2014-12-09 15:32:58Z ivanov $
+/* $Id: autodef.hpp 484817 2015-11-16 16:23:10Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,6 +51,7 @@
#include <objtools/edit/autodef_source_group.hpp>
#include <objtools/edit/autodef_mod_combo.hpp>
#include <objtools/edit/autodef_feature_clause.hpp>
+#include <objtools/edit/autodef_options.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
@@ -58,22 +59,7 @@ BEGIN_SCOPE(objects)
class NCBI_XOBJEDIT_EXPORT CAutoDef
{
public:
- enum EFeatureListType {
- eListAllFeatures = 0,
- eCompleteSequence,
- eCompleteGenome,
- ePartialSequence,
- ePartialGenome,
- eSequence
- };
- enum EMiscFeatRule {
- eDelete = 0,
- eNoncodingProductFeat,
- eCommentFeat
- };
-
- typedef set<objects::CFeatListItem> TFeatTypeItemSet;
typedef set<CAutoDefAvailableModifier> TAvailableModifierSet;
CAutoDef();
@@ -88,18 +74,23 @@ public:
string GetOneSourceDescription(CBioseq_Handle bh);
string GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_val);
string GetOneDefLine(CAutoDefModifierCombo* mod_combo, CBioseq_Handle bh);
+ string GetOneDefLine(CBioseq_Handle bh);
static string GetDocsumOrgDescription(CSeq_entry_Handle se);
string GetDocsumDefLine(CSeq_entry_Handle se);
static bool NeedsDocsumDefline(const CBioseq_set& set);
- void DoAutoDef();
+ static bool RegenerateDefLines(CSeq_entry_Handle se);
- void SetFeatureListType(unsigned int feature_list_type);
- void SetMiscFeatRule(unsigned int misc_feat_rule);
- void SetProductFlag (unsigned int product_flag);
+ void SetOptionsObject(const CUser_object& user);
+ CRef<CUser_object> GetOptionsObject() const { return m_Options.MakeUserObject(); }
+
+ void SetFeatureListType(CAutoDefOptions::EFeatureListType feature_list_type);
+ void SetMiscFeatRule(CAutoDefOptions::EMiscFeatRule misc_feat_rule);
+ void SetProductFlag(CBioSource::EGenome product_flag);
void SetSpecifyNuclearProduct (bool specify_nuclear_product);
void SetAltSpliceFlag (bool alt_splice_flag);
void SetSuppressLocusTags(bool suppress_locus_tags);
+ void SetSuppressAllele(bool suppress_allele);
void SetGeneClusterOppStrand(bool gene_opp_strand);
void SetSuppressFeatureAltSplice (bool suppress_alt_splice);
void SuppressMobileElementAndInsertionSequenceSubfeatures(bool suppress);
@@ -109,10 +100,15 @@ public:
void SetKeepLTRs(bool keep);
void SetKeep3UTRs(bool keep);
void SetKeep5UTRs(bool keep);
+ void SetKeepuORFs(bool keep);
+ void SetKeepOptionalMobileElements(bool keep);
+ void SetKeepPrecursorRNA(bool keep);
+ void SetKeepRepeatRegion(bool keep);
void SetUseNcRNAComment (bool use_comment);
void SetUseFakePromoters (bool use_fake);
- void SuppressFeature(objects::CFeatListItem feat);
+ void SuppressFeature(objects::CFeatListItem feat);
+ void SuppressFeature(objects::CSeqFeatData::ESubtype subtype);
typedef vector<CAutoDefModifierCombo *> TModifierComboVector;
@@ -120,6 +116,8 @@ public:
void Cancel() { m_Cancelled = true; }
bool Cancelled() { return m_Cancelled; }
+
+ static string GetKeywordPrefix(CBioseq_Handle bh);
private:
typedef vector<unsigned int> TModifierIndexVector;
@@ -127,26 +125,9 @@ private:
CAutoDefModifierCombo m_OrigModCombo;
- TFeatTypeItemSet m_SuppressedFeatures;
-
+ CAutoDefOptions m_Options;
+
// feature clause specifications
- unsigned int m_FeatureListType;
- unsigned int m_MiscFeatRule;
- bool m_SpecifyNuclearProduct;
- unsigned int m_ProductFlag;
- bool m_AltSpliceFlag;
- bool m_SuppressAltSplicePhrase;
- bool m_SuppressLocusTags;
- bool m_GeneOppStrand;
- bool m_RemoveMobileElementAndInsertionSequenceSubfeatures;
- bool m_KeepExons;
- bool m_KeepIntrons;
- bool m_KeepPromoters;
- bool m_KeepLTRs;
- bool m_Keep3UTRs;
- bool m_Keep5UTRs;
- bool m_UseNcRNAComment;
- bool m_UseFakePromoters;
bool m_Cancelled;
void x_SortModifierListByRank
@@ -160,21 +141,14 @@ private:
string x_GetFeatureClauses(CBioseq_Handle bh);
string x_GetFeatureClauseProductEnding(const string& feature_clauses,
CBioseq_Handle bh);
- bool x_AddIntergenicSpacerFeatures(CBioseq_Handle bh,
- const CSeq_feat& cf,
- const CSeq_loc& mapped_loc,
- CAutoDefFeatureClause_Base& main_clause,
- bool suppress_locus_tags);
bool x_AddMiscRNAFeatures(CBioseq_Handle bh,
const CSeq_feat& cf,
const CSeq_loc& mapped_loc,
- CAutoDefFeatureClause_Base& main_clause,
- bool suppress_locus_tags);
+ CAutoDefFeatureClause_Base& main_clause);
bool x_AddtRNAAndOther(CBioseq_Handle bh,
const CSeq_feat& cf,
const CSeq_loc& mapped_loc,
- CAutoDefFeatureClause_Base& main_clause,
- bool suppress_locus_tags);
+ CAutoDefFeatureClause_Base& main_clause);
void x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause, CBioseq_Handle bh);
@@ -192,124 +166,146 @@ private:
inline
-void CAutoDef::SetFeatureListType(unsigned int feature_list_type)
+void CAutoDef::SetFeatureListType(CAutoDefOptions::EFeatureListType feature_list_type)
{
- m_FeatureListType = feature_list_type;
+ m_Options.SetFeatureListType(feature_list_type);
}
inline
-void CAutoDef::SetMiscFeatRule(unsigned int misc_feat_rule)
+void CAutoDef::SetMiscFeatRule(CAutoDefOptions::EMiscFeatRule misc_feat_rule)
{
- m_MiscFeatRule = misc_feat_rule;
+ m_Options.SetMiscFeatRule(misc_feat_rule);
}
inline
-void CAutoDef::SetProductFlag(unsigned int product_flag)
+void CAutoDef::SetProductFlag(CBioSource::EGenome product_flag)
{
- m_SpecifyNuclearProduct = false;
- m_ProductFlag = product_flag;
+ m_Options.SetProductFlag(product_flag);
}
inline
void CAutoDef::SetSpecifyNuclearProduct (bool specify_nuclear_product)
{
- m_SpecifyNuclearProduct = specify_nuclear_product;
- m_ProductFlag = CBioSource::eGenome_unknown;
+ m_Options.SetSpecifyNuclearProduct(specify_nuclear_product);
}
inline
void CAutoDef::SetAltSpliceFlag (bool alt_splice_flag)
{
- m_AltSpliceFlag = alt_splice_flag;
+ m_Options.SetAltSpliceFlag(alt_splice_flag);
}
inline
void CAutoDef::SetSuppressLocusTags (bool suppress_locus_tags)
{
- m_SuppressLocusTags = suppress_locus_tags;
+ m_Options.SetSuppressLocusTags(suppress_locus_tags);
}
inline
void CAutoDef::SetGeneClusterOppStrand (bool gene_opp_strand)
{
- m_GeneOppStrand = gene_opp_strand;
+ m_Options.SetGeneClusterOppStrand(gene_opp_strand);
}
inline
void CAutoDef::SetSuppressFeatureAltSplice (bool suppress_alt_splice)
{
- m_SuppressAltSplicePhrase = suppress_alt_splice;
+ m_Options.SetSuppressFeatureAltSplice(suppress_alt_splice);
}
inline
void CAutoDef::SuppressMobileElementAndInsertionSequenceSubfeatures(bool suppress)
{
- m_RemoveMobileElementAndInsertionSequenceSubfeatures = suppress;
+ m_Options.SetSuppressMobileElementSubfeatures(suppress);
}
inline
void CAutoDef::SetKeepExons(bool keep)
{
- m_KeepExons = keep;
+ m_Options.SetKeepExons(keep);
}
inline
void CAutoDef::SetKeepIntrons(bool keep)
{
- m_KeepIntrons = keep;
+ m_Options.SetKeepIntrons(keep);
}
inline
void CAutoDef::SetKeepPromoters(bool keep)
{
- m_KeepPromoters = keep;
+ m_Options.SetKeepPromoters(keep);
}
inline
void CAutoDef::SetKeepLTRs(bool keep)
{
- m_KeepLTRs = keep;
+ m_Options.SetKeepLTRs(keep);
}
inline
void CAutoDef::SetKeep3UTRs(bool keep)
{
- m_Keep3UTRs = keep;
+ m_Options.SetKeep3UTRs(keep);
}
inline
void CAutoDef::SetKeep5UTRs(bool keep)
{
- m_Keep5UTRs = keep;
+ m_Options.SetKeep5UTRs(keep);
+}
+
+
+inline
+void CAutoDef::SetKeepuORFs(bool keep)
+{
+ m_Options.SetKeepuORFs(keep);
+}
+
+
+inline
+void CAutoDef::SetKeepOptionalMobileElements(bool keep)
+{
+ m_Options.SetKeepMobileElements(keep);
}
+inline
+void CAutoDef::SetKeepPrecursorRNA(bool keep)
+{
+ m_Options.SetKeepPrecursorRNA(keep);
+}
+
+inline
+void CAutoDef::SetKeepRepeatRegion(bool keep)
+{
+ m_Options.SetKeepRepeatRegion(keep);
+}
inline
void CAutoDef::SetUseNcRNAComment(bool use_comment)
{
- m_UseNcRNAComment = use_comment;
+ m_Options.SetUseNcRNAComment(use_comment);
}
inline
void CAutoDef::SetUseFakePromoters(bool use_fake)
{
- m_UseFakePromoters = use_fake;
- m_KeepPromoters = true;
+ m_Options.SetUseFakePromoters(use_fake);
}
diff --git a/c++/include/objtools/edit/autodef_feature_clause.hpp b/c++/include/objtools/edit/autodef_feature_clause.hpp
index af7de89..c5fbf53 100644
--- a/c++/include/objtools/edit/autodef_feature_clause.hpp
+++ b/c++/include/objtools/edit/autodef_feature_clause.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT___AUTODEF_FEATURE_CLAUSE__HPP
#define OBJTOOLS_EDIT___AUTODEF_FEATURE_CLAUSE__HPP
-/* $Id: autodef_feature_clause.hpp 454552 2014-12-16 16:27:40Z ivanov $
+/* $Id: autodef_feature_clause.hpp 483240 2015-10-29 14:24:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,9 +45,15 @@ class NCBI_XOBJEDIT_EXPORT CAutoDefFeatureClause : public CAutoDefFeatureClause_
public:
CAutoDefFeatureClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefFeatureClause();
+
+ enum EClauseType {
+ eDefault = 0,
+ eEndogenousVirusRepeatRegion
+ };
+ virtual EClauseType GetClauseType();
- virtual void Label();
- virtual CSeqFeatData::ESubtype GetMainFeatureSubtype();
+ virtual void Label(bool suppress_allele);
+ virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const;
virtual bool IsRecognizedFeature();
@@ -57,13 +63,11 @@ public:
virtual bool IsEndogenousVirusSourceFeature();
virtual bool IsGeneCluster();
virtual bool IsNoncodingProductFeat();
- virtual bool IsIntergenicSpacer();
virtual bool IsSatelliteClause();
virtual bool IsPromoter();
static bool IsSatellite(const CSeq_feat& feat);
static bool IsPromoter(const CSeq_feat& feat);
static bool IsGeneCluster (const CSeq_feat& feat);
- static bool IsIntergenicSpacer (const CSeq_feat& feat);
static bool IsControlRegion (const CSeq_feat& feat);
@@ -76,7 +80,7 @@ public:
// functions for grouping
virtual bool AddmRNA (CAutoDefFeatureClause_Base *mRNAClause);
- virtual bool AddGene (CAutoDefFeatureClause_Base *gene_clause);
+ virtual bool AddGene (CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele);
virtual bool OkToGroupUnderByType(CAutoDefFeatureClause_Base *parent_clause);
virtual bool OkToGroupUnderByLocation(CAutoDefFeatureClause_Base *parent_clause, bool gene_cluster_opp_strand);
@@ -90,8 +94,8 @@ public:
protected:
CAutoDefFeatureClause();
- bool x_GetGenericInterval (string &interval);
- bool x_IsPseudo();
+ bool x_GetGenericInterval (string &interval, bool suppress_allele);
+ virtual bool x_IsPseudo();
const CSeq_feat& m_MainFeat;
CRef<CSeq_loc> m_ClauseLocation;
@@ -108,13 +112,25 @@ protected:
bool x_GetNoncodingProductFeatProduct (string &product);
bool x_FindNoncodingFeatureKeywordProduct (string comment, string keyword, string &product_name);
- string x_GetGeneName(const CGene_ref& gref);
- bool x_MatchGene(const CGene_ref& gref);
+ string x_GetGeneName(const CGene_ref& gref, bool suppress_locus_tag) const;
bool x_GetExonDescription(string &description);
};
+class NCBI_XOBJEDIT_EXPORT CAutoDefGeneClause : public CAutoDefFeatureClause
+{
+public:
+ CAutoDefGeneClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, bool suppress_locus_tag);
+ ~CAutoDefGeneClause() {}
+ bool GetSuppressLocusTag() { return m_SuppressLocusTag; }
+
+protected:
+ virtual bool x_IsPseudo();
+ virtual bool x_GetProductName(string &product_name);
+ bool m_SuppressLocusTag;
+};
+
class NCBI_XOBJEDIT_EXPORT CAutoDefNcRNAClause : public CAutoDefFeatureClause
{
public:
@@ -133,8 +149,9 @@ public:
CAutoDefMobileElementClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefMobileElementClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsMobileElement() { return true; }
+ bool IsOptional();
};
@@ -144,7 +161,7 @@ public:
CAutoDefSatelliteClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefSatelliteClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsSatelliteClause() { return true; }
};
@@ -155,7 +172,7 @@ public:
CAutoDefPromoterClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefPromoterClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsPromoter() { return true; }
};
@@ -167,10 +184,9 @@ public:
CAutoDefIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string comment);
~CAutoDefIntergenicSpacerClause();
- virtual void Label();
- virtual bool IsIntergenicSpacer() { return true; }
+ virtual void Label(bool suppress_allele);
protected:
- void InitWithString (string comment);
+ void InitWithString (string comment, bool suppress_allele);
};
class NCBI_XOBJEDIT_EXPORT CAutoDefParsedClause : public CAutoDefFeatureClause
@@ -182,6 +198,7 @@ public:
void SetDescription(string description) { m_Description = description; m_DescriptionChosen = true; }
void SetTypewordFirst(bool typeword_first) { m_ShowTypewordFirst = typeword_first; }
virtual bool IsRecognizedFeature() { return true; }
+ void SetMiscRNAWord(const string& phrase);
protected:
};
@@ -192,16 +209,17 @@ public:
CAutoDefParsedtRNAClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string gene_name, string product_name, bool is_first, bool is_last);
~CAutoDefParsedtRNAClause();
- virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() { return CSeqFeatData::eSubtype_tRNA; }
- virtual bool IsIntergenicSpacer() { return false; }
+ virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const { return CSeqFeatData::eSubtype_tRNA; }
static bool ParseString(string comment, string& gene_name, string& product_name);
};
class NCBI_XOBJEDIT_EXPORT CAutoDefParsedIntergenicSpacerClause : public CAutoDefIntergenicSpacerClause
{
public:
- CAutoDefParsedIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string description, bool is_first, bool is_last);
+ CAutoDefParsedIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const string& description, bool is_first, bool is_last);
~CAutoDefParsedIntergenicSpacerClause();
+
+ void MakeRegion() { if (!NStr::EndsWith(m_Typeword, "region")) m_Typeword += " region"; }
};
@@ -211,7 +229,7 @@ public:
CAutoDefGeneClusterClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefGeneClusterClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsGeneCluster() { return true; }
};
@@ -222,7 +240,7 @@ public:
CAutoDefMiscCommentClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefMiscCommentClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsRecognizedFeature() { return true; }
};
@@ -233,7 +251,7 @@ public:
CAutoDefParsedRegionClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string product);
~CAutoDefParsedRegionClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsRecognizedFeature() { return true; }
};
@@ -244,9 +262,9 @@ public:
CAutoDefFakePromoterClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc);
~CAutoDefFakePromoterClause();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsPromoter() { return true; }
- virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() { return CSeqFeatData::eSubtype_promoter; };
+ virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const { return CSeqFeatData::eSubtype_promoter; };
virtual bool IsRecognizedFeature() { return false; };
@@ -256,7 +274,6 @@ public:
virtual bool IsEndogenousVirusSourceFeature() { return false; };
virtual bool IsGeneCluster() { return false; };
virtual bool IsNoncodingProductFeat() { return false; };
- virtual bool IsIntergenicSpacer() { return false; };
virtual bool IsSatelliteClause() { return false; };
virtual bool OkToGroupUnderByLocation(CAutoDefFeatureClause_Base *parent_clause, bool gene_cluster_opp_strand);
@@ -265,7 +282,6 @@ public:
};
-vector<CAutoDefFeatureClause *> GetIntergenicSpacerClauseList (string comment, CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, bool suppress_locus_tags);
CAutoDefParsedtRNAClause *s_tRNAClauseFromNote(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, string comment, bool is_first, bool is_last);
diff --git a/c++/include/objtools/edit/autodef_feature_clause_base.hpp b/c++/include/objtools/edit/autodef_feature_clause_base.hpp
index 867981d..f5a62d1 100644
--- a/c++/include/objtools/edit/autodef_feature_clause_base.hpp
+++ b/c++/include/objtools/edit/autodef_feature_clause_base.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT___AUTODEF_FEATURE_CLAUSE_BASE__HPP
#define OBJTOOLS_EDIT___AUTODEF_FEATURE_CLAUSE_BASE__HPP
-/* $Id: autodef_feature_clause_base.hpp 446520 2014-09-16 17:13:44Z ivanov $
+/* $Id: autodef_feature_clause_base.hpp 483241 2015-10-29 14:24:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -47,18 +47,18 @@ class NCBI_XOBJEDIT_EXPORT CAutoDefFeatureClause_Base
public:
typedef vector<CAutoDefFeatureClause_Base *> TClauseList;
- CAutoDefFeatureClause_Base(bool suppress_locus_tags);
+ CAutoDefFeatureClause_Base();
virtual ~CAutoDefFeatureClause_Base();
virtual void AddSubclause (CAutoDefFeatureClause_Base *subclause);
- string PrintClause(bool print_typeword, bool typeword_is_plural);
+ string PrintClause(bool print_typeword, bool typeword_is_plural, bool suppress_allele);
- virtual CSeqFeatData::ESubtype GetMainFeatureSubtype();
+ virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const;
size_t GetNumSubclauses() { return m_ClauseList.size(); }
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool AddmRNA (CAutoDefFeatureClause_Base *mRNAClause);
- virtual bool AddGene (CAutoDefFeatureClause_Base *gene_clause);
+ virtual bool AddGene (CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele);
virtual sequence::ECompare CompareLocation(const CSeq_loc& loc);
virtual void AddToOtherLocation(CRef<CSeq_loc> loc);
@@ -71,9 +71,11 @@ public:
virtual bool IsEndogenousVirusSourceFeature() { return false; }
virtual bool IsGeneCluster() { return false; }
virtual bool IsNoncodingProductFeat() { return false; }
- virtual bool IsIntergenicSpacer() { return false; }
virtual bool IsSatelliteClause() { return false; }
virtual bool IsExonList() { return false; }
+
+ static bool IsuORF(const string& product);
+
virtual CAutoDefFeatureClause_Base *FindBestParentClause(CAutoDefFeatureClause_Base * subclause, bool gene_cluster_opp_strand);
void GroupClauses(bool gene_cluster_opp_strand);
@@ -82,9 +84,10 @@ public:
virtual CRef<CSeq_loc> GetLocation();
- string ListClauses(bool allow_semicolons, bool suppress_final_and);
+ string ListClauses(bool allow_semicolons, bool suppress_final_and, bool suppress_allele);
bool IsGeneMentioned(CAutoDefFeatureClause_Base *gene_clause);
+ bool IsUnattachedGene() const;
bool IsTypewordFirst() { return m_ShowTypewordFirst; }
bool DisplayAlleleName ();
@@ -103,7 +106,6 @@ public:
void MarkForDeletion() { m_DeleteMe = true; }
void SetMakePlural() { m_MakePlural = true; }
bool HasmRNA() { return m_HasmRNA; }
- void SetSuppressLocusTag(bool do_suppress) { m_SuppressLocusTag = do_suppress; }
void SetInfoOnly (bool info_only) { m_ClauseInfoOnly = info_only; }
void PluralizeInterval();
void PluralizeDescription();
@@ -113,14 +115,16 @@ public:
// Grouping functions
void RemoveDeletedSubclauses();
- void GroupmRNAs();
- void GroupGenes();
+ void GroupmRNAs(bool suppress_allele);
+ void GroupGenes(bool suppress_allele);
void GroupConsecutiveExons(CBioseq_Handle bh);
- void GroupSegmentedCDSs();
+ void GroupSegmentedCDSs(bool suppress_allele);
void RemoveGenesMentionedElsewhere();
void RemoveTransSplicedLeaders();
- void ConsolidateRepeatedClauses();
- void FindAltSplices();
+ void RemoveuORFs();
+ void RemoveOptionalMobileElements();
+ void ConsolidateRepeatedClauses(bool suppress_allele);
+ void FindAltSplices(bool suppress_allele);
void TransferSubclauses(TClauseList &other_clause_list);
void CountUnknownGenes();
void ExpandExonLists();
@@ -134,7 +138,7 @@ public:
void SuppressSubfeatures() { m_SuppressSubfeatures = true; }
string FindGeneProductName(CAutoDefFeatureClause_Base *gene_clause);
- void AssignGeneProductNames(CAutoDefFeatureClause_Base *main_clause);
+ void AssignGeneProductNames(CAutoDefFeatureClause_Base *main_clause, bool suppress_allele);
void RemoveFeaturesByType(unsigned int feature_type);
bool IsFeatureTypeLonely(unsigned int feature_type);
@@ -146,9 +150,15 @@ public:
virtual bool IsBioseqPrecursorRNA();
void RemoveBioseqPrecursorRNAs();
+
+ void Consolidate(CAutoDefFeatureClause_Base& other, bool suppress_allele);
+ void TakeSubclauses(CAutoDefFeatureClause_Base& other);
+
+ static vector<string> GetMiscRNAElements(const string& product);
+ static vector<string> GetTrnaIntergenicSpacerClausePhrases(const string& comment);
+
protected:
- CAutoDefFeatureClause_Base();
TClauseList m_ClauseList;
string m_GeneName;
@@ -169,7 +179,6 @@ protected:
bool m_DescriptionChosen;
string m_ProductName;
bool m_ProductNameChosen;
- bool m_SuppressLocusTag;
bool m_SuppressSubfeatures;
@@ -179,16 +188,40 @@ protected:
bool x_OkToConsolidate (unsigned int clause1, unsigned int clause2);
bool x_MeetAltSpliceRules (unsigned int clause1, unsigned int clause2, string &splice_name);
+ void x_RemoveNullClauses();
+
+ // for miscRNA elements
+ typedef enum {
+ eMiscRnaWordType_InternalSpacer = 0,
+ eMiscRnaWordType_ExternalSpacer,
+ eMiscRnaWordType_RNAIntergenicSpacer,
+ eMiscRnaWordType_RNA,
+ eMiscRnaWordType_IntergenicSpacer,
+ eMiscRnaWordType_Unrecognized
+ } ERnaMiscWord;
+ static bool x_AddOneMiscWordElement(const string& phrase, vector<string>& elements);
+ static ERnaMiscWord x_GetRnaMiscWordType(const string& phrase);
+ static const string& x_GetRnaMiscWord(ERnaMiscWord word_type);
+
+ // for tRNA/intergenic spacer elements
+ typedef enum {
+ eTRNAIntergenicSpacerType_Gene = 0,
+ eTRNAIntergenicSpacerType_Spacer = 1,
+ eTRNAIntergenicSpacerType_Unrecognized
+ } ETRNAIntergenicSpacerType;
+ static ETRNAIntergenicSpacerType x_GetTRNAIntergenicSpacerType(const string& phrase);
+ static string x_tRNAGeneFromProduct(const string& product);
+ static bool x_AddOnetRNAIntergenicSpacerElement(const string& phrase, vector<string>& elements);
};
class NCBI_XOBJEDIT_EXPORT CAutoDefUnknownGeneList : public CAutoDefFeatureClause_Base
{
public:
- CAutoDefUnknownGeneList(bool suppress_locus_tags);
+ CAutoDefUnknownGeneList();
~CAutoDefUnknownGeneList();
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsRecognizedFeature() { return true; }
};
@@ -196,15 +229,15 @@ public:
class NCBI_XOBJEDIT_EXPORT CAutoDefExonListClause : public CAutoDefFeatureClause_Base
{
public:
- CAutoDefExonListClause(CBioseq_Handle bh, bool suppress_locus_tags);
+ CAutoDefExonListClause(CBioseq_Handle bh);
virtual void AddSubclause (CAutoDefFeatureClause_Base *subclause);
- virtual void Label();
+ virtual void Label(bool suppress_allele);
virtual bool IsRecognizedFeature() { return true; }
virtual bool IsExonList() { return true; }
virtual bool OkToGroupUnderByLocation(CAutoDefFeatureClause_Base *parent_clause, bool gene_cluster_opp_strand);
virtual bool OkToGroupUnderByType(CAutoDefFeatureClause_Base *parent_clause);
- virtual CSeqFeatData::ESubtype GetMainFeatureSubtype();
+ virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const;
void SetSuppressFinalAnd(bool suppress) { m_SuppressFinalAnd = suppress; }
private:
CRef<CSeq_loc> SeqLocIntersect (CRef<CSeq_loc> loc1, CRef<CSeq_loc> loc2);
diff --git a/c++/include/objtools/edit/autodef_mod_combo.hpp b/c++/include/objtools/edit/autodef_mod_combo.hpp
index 50538aa..0d367a8 100644
--- a/c++/include/objtools/edit/autodef_mod_combo.hpp
+++ b/c++/include/objtools/edit/autodef_mod_combo.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT___AUTODEF_MOD_COMBO__HPP
#define OBJTOOLS_EDIT___AUTODEF_MOD_COMBO__HPP
-/* $Id: autodef_mod_combo.hpp 409737 2013-08-09 16:49:23Z bollin $
+/* $Id: autodef_mod_combo.hpp 484815 2015-11-16 16:22:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,6 +48,7 @@
#include <objtools/edit/autodef_available_modifier.hpp>
#include <objtools/edit/autodef_source_desc.hpp>
#include <objtools/edit/autodef_source_group.hpp>
+#include <objtools/edit/autodef_options.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
@@ -57,15 +58,14 @@ class NCBI_XOBJEDIT_EXPORT CAutoDefModifierCombo : public CObject,
public IAutoDefCombo
{
public:
- enum EHIVCloneIsolateRule {
- ePreferClone = 0,
- ePreferIsolate,
- eWantBoth
- };
CAutoDefModifierCombo();
CAutoDefModifierCombo(CAutoDefModifierCombo *orig);
~CAutoDefModifierCombo();
+
+ void InitFromOptions(const CAutoDefOptions& options);
+ void SetOptions(const CAutoDefOptions& options) { InitFromOptions(options); }
+ void InitOptions(CAutoDefOptions& options) const;
unsigned int GetNumGroups();
@@ -87,8 +87,10 @@ public:
void SetUseModifierLabels(bool use);
bool GetUseModifierLabels();
- void SetMaxModifiers(unsigned int max_mods);
- unsigned int GetMaxModifiers();
+ void SetMaxModifiers(int max_mods);
+ int GetMaxModifiers();
+ void SetAllowModAtEndOfTaxname(bool keep);
+ bool GetAllowModAtEndOfTaxname();
void SetKeepCountryText(bool keep);
bool GetKeepCountryText();
void SetExcludeSpOrgs(bool exclude);
@@ -101,10 +103,10 @@ public:
bool GetExcludeAffOrgs ();
void SetKeepParen(bool keep);
bool GetKeepParen();
- void SetKeepAfterSemicolon(bool keep);
- bool GetKeepAfterSemicolon();
- void SetHIVCloneIsolateRule(unsigned int rule_num);
- unsigned int GetHIVCloneIsolateRule();
+ void SetKeepAfterSemicolon(bool keep);
+ bool GetKeepAfterSemicolon();
+ void SetHIVCloneIsolateRule(CAutoDefOptions::EHIVCloneIsolateRule rule_num);
+ CAutoDefOptions::EHIVCloneIsolateRule GetHIVCloneIsolateRule();
string GetSourceDescriptionString(const CBioSource& bsrc);
@@ -135,6 +137,9 @@ public:
vector<CAutoDefModifierCombo *> ExpandByAnyPresent();
bool AreFeatureClausesUnique();
+ static bool IsModifierRequiredByDefault(bool is_orgmod, int subtype);
+ static bool IsModifierInString(const string& find_this, const string& find_in, bool ignore_at_end);
+
private:
TSubSourceTypeVector m_SubSources;
TOrgModTypeVector m_OrgMods;
@@ -142,7 +147,8 @@ private:
CAutoDefSourceDescription::TModifierVector m_Modifiers;
bool m_UseModifierLabels;
- unsigned int m_MaxModifiers;
+ int m_MaxModifiers;
+ bool m_AllowModAtEndOfTaxname;
bool m_KeepCountryText;
bool m_ExcludeSpOrgs;
// NOTE - after the wxWidgets conversion is complete, need to add controls for the following three
@@ -153,16 +159,25 @@ private:
bool m_KeepParen;
bool m_KeepAfterSemicolon;
- unsigned int m_HIVCloneIsolateRule;
+ CAutoDefOptions::EHIVCloneIsolateRule m_HIVCloneIsolateRule;
string x_GetSubSourceLabel (CSubSource::ESubtype st);
string x_GetOrgModLabel(COrgMod::ESubtype st);
void x_CleanUpTaxName (string &tax_name);
bool x_AddSubsourceString (string &source_description, const CBioSource& bsrc, CSubSource::ESubtype st);
bool x_AddOrgModString (string &source_description, const CBioSource& bsrc, COrgMod::ESubtype st);
- unsigned int x_AddHIVModifiers (string &source_description, const CBioSource& bsrc);
- unsigned int x_AddRequiredSubSourceModifiers (string& description, const CBioSource& bsrc);
-
+
+ typedef pair<COrgMod::ESubtype, bool> TExtraOrgMod;
+ typedef map<COrgMod::ESubtype, bool> TExtraOrgMods;
+ typedef pair<CSubSource::ESubtype, bool> TExtraSubSrc;
+ typedef map<CSubSource::ESubtype, bool> TExtraSubSrcs;
+ static bool x_BioSourceHasSubSrc(const CBioSource& src, CSubSource::ESubtype subtype);
+ static bool x_BioSourceHasOrgMod(const CBioSource& src, COrgMod::ESubtype subtype);
+
+ void x_AddHIVModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc);
+ void x_AddRequiredSubSourceModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc);
+ void x_AddTypeStrainModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc);
+ static bool x_HasTypeStrainComment(const CBioSource& bsrc);
};
@@ -181,20 +196,34 @@ bool CAutoDefModifierCombo::GetUseModifierLabels()
inline
-void CAutoDefModifierCombo::SetMaxModifiers(unsigned int max_mods)
+void CAutoDefModifierCombo::SetMaxModifiers(int max_mods)
{
m_MaxModifiers = max_mods;
}
inline
-unsigned int CAutoDefModifierCombo::GetMaxModifiers()
+int CAutoDefModifierCombo::GetMaxModifiers()
{
return m_MaxModifiers;
}
inline
+void CAutoDefModifierCombo::SetAllowModAtEndOfTaxname(bool keep)
+{
+ m_AllowModAtEndOfTaxname = keep;
+}
+
+
+inline
+bool CAutoDefModifierCombo::GetAllowModAtEndOfTaxname()
+{
+ return m_AllowModAtEndOfTaxname;
+}
+
+
+inline
void CAutoDefModifierCombo::SetKeepCountryText(bool keep)
{
m_KeepCountryText = keep;
@@ -293,14 +322,14 @@ bool CAutoDefModifierCombo::GetKeepAfterSemicolon()
inline
-void CAutoDefModifierCombo::SetHIVCloneIsolateRule(unsigned int rule_num)
+void CAutoDefModifierCombo::SetHIVCloneIsolateRule(CAutoDefOptions::EHIVCloneIsolateRule rule_num)
{
m_HIVCloneIsolateRule = rule_num;
}
inline
-unsigned int CAutoDefModifierCombo::GetHIVCloneIsolateRule()
+CAutoDefOptions::EHIVCloneIsolateRule CAutoDefModifierCombo::GetHIVCloneIsolateRule()
{
return m_HIVCloneIsolateRule;
}
diff --git a/c++/include/objtools/edit/autodef_options.hpp b/c++/include/objtools/edit/autodef_options.hpp
new file mode 100644
index 0000000..b9cfe72
--- /dev/null
+++ b/c++/include/objtools/edit/autodef_options.hpp
@@ -0,0 +1,262 @@
+#ifndef OBJTOOLS_EDIT___AUTODEF_OPTIONS__HPP
+#define OBJTOOLS_EDIT___AUTODEF_OPTIONS__HPP
+
+/* $Id: autodef_options.hpp 483235 2015-10-29 14:22:28Z ivanov $
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's official duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author: Colleen Bollin
+*
+* File Description:
+* Creates unique definition lines for sequences in a set using organism
+* descriptions and feature clauses.
+*/
+
+#include <corelib/ncbistd.hpp>
+#include <objects/seqfeat/Seq_feat.hpp>
+#include <objects/general/User_object.hpp>
+#include <objects/general/User_field.hpp>
+#include <objects/general/Object_id.hpp>
+#include <objtools/edit/autodef_available_modifier.hpp>
+#include <objtools/edit/autodef_source_desc.hpp>
+
+BEGIN_NCBI_SCOPE
+BEGIN_SCOPE(objects)
+
+class NCBI_XOBJEDIT_EXPORT CAutoDefOptions
+{
+public:
+ CAutoDefOptions();
+ ~CAutoDefOptions() {}
+
+ CRef<CUser_object> MakeUserObject() const;
+ void InitFromUserObject(const CUser_object& obj);
+
+ enum EOptionFieldType {
+ eOptionFieldType_Unknown = 0,
+ eOptionFieldType_MaxMods,
+ eOptionFieldType_UseLabels,
+ eOptionFieldType_AllowModAtEndOfTaxname,
+ eOptionFieldType_LeaveParenthetical,
+ eOptionFieldType_DoNotApplyToSp,
+ eOptionFieldType_DoNotApplyToNr,
+ eOptionFieldType_DoNotApplyToCf,
+ eOptionFieldType_DoNotApplyToAff,
+ eOptionFieldType_IncludeCountryText,
+ eOptionFieldType_KeepAfterSemicolon,
+ eOptionFieldType_HIVRule,
+ eOptionFieldType_FeatureListType,
+ eOptionFieldType_MiscFeatRule,
+ eOptionFieldType_ProductFlag,
+ eOptionFieldType_SpecifyNuclearProduct,
+ eOptionFieldType_AltSpliceFlag,
+ eOptionFieldType_SuppressLocusTags,
+ eOptionFieldType_SuppressAlleles,
+ eOptionFieldType_GeneClusterOppStrand,
+ eOptionFieldType_SuppressFeatureAltSplice,
+ eOptionFieldType_SuppressMobileElementSubfeatures,
+ eOptionFieldType_KeepExons,
+ eOptionFieldType_KeepIntrons,
+ eOptionFieldType_KeepPromoters,
+ eOptionFieldType_UseFakePromoters,
+ eOptionFieldType_KeepLTRs,
+ eOptionFieldType_Keep3UTRs,
+ eOptionFieldType_Keep5UTRs,
+ eOptionFieldType_KeepuORFs,
+ eOptionFieldType_KeepMobileElements,
+ eOptionFieldType_KeepPrecursorRNA,
+ eOptionFieldType_KeepRepeatRegion,
+ eOptionFieldType_UseNcRNAComment,
+ eOptionFieldType_SuppressedFeatures,
+ eOptionFieldType_ModifierList,
+ eOptionFieldMax
+ };
+
+ enum EFeatureListType {
+ eListAllFeatures = 0,
+ eCompleteSequence,
+ eCompleteGenome,
+ ePartialSequence,
+ ePartialGenome,
+ eSequence
+ };
+
+ typedef unsigned int TFeatureListType;
+ TFeatureListType GetFeatureListType() const { return m_FeatureListType; }
+ void SetFeatureListType(EFeatureListType list_type) { m_FeatureListType = list_type; }
+
+ enum EMiscFeatRule {
+ eDelete = 0,
+ eNoncodingProductFeat,
+ eCommentFeat
+ };
+
+ typedef unsigned int TMiscFeatRule;
+ TMiscFeatRule GetMiscFeatRule() const { return m_MiscFeatRule; }
+ void SetMiscFeatRule(TMiscFeatRule rule) { m_MiscFeatRule = rule; }
+
+ enum EHIVCloneIsolateRule {
+ ePreferClone = 0,
+ ePreferIsolate,
+ eWantBoth
+ };
+ typedef unsigned int THIVRule;
+ THIVRule GetHIVRule() const { return m_HIVRule; }
+ void SetHIVRule(EHIVCloneIsolateRule rule) { m_HIVRule = rule; }
+
+ bool GetUseFakePromoters() const { return m_BooleanFlags[eOptionFieldType_UseFakePromoters]; }
+ void SetUseFakePromoters(bool val = true) {
+ m_BooleanFlags[eOptionFieldType_UseFakePromoters] = val;
+ if (val) {
+ m_BooleanFlags[eOptionFieldType_KeepPromoters] = true;
+ }
+ }
+
+ CBioSource::TGenome GetProductFlag() const { return m_ProductFlag; };
+ void SetProductFlag(CBioSource::EGenome val) {
+ m_ProductFlag = val;
+ m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = false;
+ }
+
+ bool GetSpecifyNuclearProduct() const { return m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct]; }
+ void SetSpecifyNuclearProduct(bool val) {
+ m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = val;
+ if (val) {
+ m_ProductFlag = CBioSource::eGenome_unknown;
+ }
+ }
+
+ int GetMaxMods() const { return m_MaxMods; }
+ void SetMaxMods(int val) { m_MaxMods = val; }
+
+#define AUTODEFBOOLFIELD(Fieldname) \
+ bool Get##Fieldname() const { return m_BooleanFlags[eOptionFieldType_##Fieldname]; }; \
+ void Set##Fieldname(bool val = true) { m_BooleanFlags[eOptionFieldType_##Fieldname] = val; }
+
+ AUTODEFBOOLFIELD(UseLabels)
+ AUTODEFBOOLFIELD(LeaveParenthetical)
+ AUTODEFBOOLFIELD(AllowModAtEndOfTaxname)
+ AUTODEFBOOLFIELD(DoNotApplyToSp)
+ AUTODEFBOOLFIELD(DoNotApplyToNr)
+ AUTODEFBOOLFIELD(DoNotApplyToCf)
+ AUTODEFBOOLFIELD(DoNotApplyToAff)
+ AUTODEFBOOLFIELD(IncludeCountryText)
+ AUTODEFBOOLFIELD(KeepAfterSemicolon)
+ AUTODEFBOOLFIELD(AltSpliceFlag)
+ AUTODEFBOOLFIELD(SuppressLocusTags)
+ AUTODEFBOOLFIELD(SuppressAlleles)
+ AUTODEFBOOLFIELD(GeneClusterOppStrand)
+ AUTODEFBOOLFIELD(SuppressFeatureAltSplice)
+ AUTODEFBOOLFIELD(SuppressMobileElementSubfeatures)
+ AUTODEFBOOLFIELD(KeepExons)
+ AUTODEFBOOLFIELD(KeepIntrons)
+ AUTODEFBOOLFIELD(KeepPromoters)
+ AUTODEFBOOLFIELD(KeepLTRs)
+ AUTODEFBOOLFIELD(Keep3UTRs)
+ AUTODEFBOOLFIELD(Keep5UTRs)
+ AUTODEFBOOLFIELD(KeepuORFs)
+ AUTODEFBOOLFIELD(KeepMobileElements)
+ AUTODEFBOOLFIELD(KeepPrecursorRNA)
+ AUTODEFBOOLFIELD(KeepRepeatRegion)
+ AUTODEFBOOLFIELD(UseNcRNAComment)
+
+ bool IsFeatureSuppressed(CSeqFeatData::ESubtype subtype) const;
+ bool AreAnyFeaturesSuppressed() const { return !m_SuppressedFeatureSubtypes.empty(); }
+ void SuppressFeature(CSeqFeatData::ESubtype subtype);
+ void SuppressAllFeatures();
+ void ClearSuppressedFeatures();
+
+ void AddSubSource(CSubSource::TSubtype subtype);
+ void AddOrgMod(COrgMod::TSubtype subtype);
+ typedef vector<COrgMod::TSubtype> TOrgMods;
+ const TOrgMods& GetOrgMods() const { return m_OrgMods; }
+ typedef vector<CSubSource::TSubtype> TSubSources;
+ const TSubSources& GetSubSources() const { return m_SubSources; }
+ void ClearModifierList();
+
+ string GetFeatureListType(TFeatureListType list_type) const;
+ TFeatureListType GetFeatureListType(const string& list_type) const;
+
+ string GetMiscFeatRule(TMiscFeatRule list_type) const;
+ TMiscFeatRule GetMiscFeatRule(const string& list_type) const;
+
+ string GetHIVRule(TMiscFeatRule list_type) const;
+ TMiscFeatRule GetHIVRule(const string& list_type) const;
+
+ string GetProductFlag(CBioSource::TGenome value) const;
+ CBioSource::TGenome GetProductFlag(const string& value) const;
+
+private:
+
+ bool m_BooleanFlags[eOptionFieldMax];
+ int m_MaxMods;
+ THIVRule m_HIVRule;
+ TFeatureListType m_FeatureListType;
+ TMiscFeatRule m_MiscFeatRule;
+ CBioSource::TGenome m_ProductFlag;
+ typedef vector<CSeqFeatData::ESubtype> TSuppressedFeatureSubtypes;
+ TSuppressedFeatureSubtypes m_SuppressedFeatureSubtypes;
+
+ TOrgMods m_OrgMods;
+ TSubSources m_SubSources;
+
+ typedef unsigned int TFieldType;
+ string GetFieldType(TFieldType field_type) const;
+ TFieldType GetFieldType(const string& field_name) const;
+
+
+
+ bool x_IsBoolean(TFieldType field_type) const;
+ CRef<CUser_field> x_MakeBooleanField(TFieldType field_type) const;
+
+ void x_MakeSuppressedFeatures(CUser_object& user) const;
+ void x_SetSuppressedFeatures(const CUser_field& field);
+
+ void x_MakeModifierList(CUser_object& user) const;
+ void x_SetModifierList(const CUser_field& field);
+
+ CRef<CUser_field> x_MakeMaxMods() const;
+
+#define AUTODEFENUMFIELD(Fieldname) \
+ CRef<CUser_field> x_Make##Fieldname() const { \
+ CRef<CUser_field> field(new CUser_field()); \
+ field->SetLabel().SetStr(GetFieldType(eOptionFieldType_##Fieldname)); \
+ field->SetData().SetStr(Get##Fieldname(m_##Fieldname)); \
+ return field; \
+ }
+
+ AUTODEFENUMFIELD(FeatureListType)
+ AUTODEFENUMFIELD(MiscFeatRule)
+ AUTODEFENUMFIELD(HIVRule)
+ AUTODEFENUMFIELD(ProductFlag)
+
+ void x_Reset();
+};
+
+
+
+END_SCOPE(objects)
+END_NCBI_SCOPE
+
+#endif //OBJTOOLS_EDIT___AUTODEF_OPTIONS__HPP
diff --git a/c++/include/objtools/edit/capitalization_string.hpp b/c++/include/objtools/edit/capitalization_string.hpp
index 63af248..122692c 100644
--- a/c++/include/objtools/edit/capitalization_string.hpp
+++ b/c++/include/objtools/edit/capitalization_string.hpp
@@ -1,6 +1,6 @@
#ifndef _CAPITALIZATION_INSTRINGS_HPP_
#define _CAPITALIZATION_INSTRINGS_HPP_
-/* $Id: capitalization_string.hpp 458727 2015-02-09 16:40:15Z ivanov $
+/* $Id: capitalization_string.hpp 458478 2015-02-05 15:31:46Z filippov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/cds_fix.hpp b/c++/include/objtools/edit/cds_fix.hpp
index 12cf0a1..05b9030 100644
--- a/c++/include/objtools/edit/cds_fix.hpp
+++ b/c++/include/objtools/edit/cds_fix.hpp
@@ -1,4 +1,4 @@
-/* $Id: cds_fix.hpp 459885 2015-02-23 16:49:52Z ivanov $
+/* $Id: cds_fix.hpp 465650 2015-04-23 14:18:20Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -60,7 +60,6 @@ NCBI_XOBJEDIT_EXPORT CRef<CGenetic_code> GetGeneticCodeForBioseq(CBioseq_Handle
NCBI_XOBJEDIT_EXPORT bool TruncateCDSAtStop(CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT bool ExtendCDSToStopCodon (CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT void AdjustCDSFrameForStartChange(CCdregion& cds, int change);
-NCBI_XOBJEDIT_EXPORT bool PromoteCDSToNucProtSet(objects::CSeq_feat_Handle& orig_feat);
NCBI_XOBJEDIT_EXPORT bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat);
class NCBI_XOBJEDIT_EXPORT ApplyCDSFrame
diff --git a/c++/include/objtools/edit/dblink_field.hpp b/c++/include/objtools/edit/dblink_field.hpp
index caedf16..8ecfd63 100644
--- a/c++/include/objtools/edit/dblink_field.hpp
+++ b/c++/include/objtools/edit/dblink_field.hpp
@@ -1,4 +1,4 @@
-/* $Id: dblink_field.hpp 465911 2015-04-27 16:16:16Z ivanov $
+/* $Id: dblink_field.hpp 465633 2015-04-23 12:24:56Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/feattable_edit.hpp b/c++/include/objtools/edit/feattable_edit.hpp
index f5d3342..a84bef0 100644
--- a/c++/include/objtools/edit/feattable_edit.hpp
+++ b/c++/include/objtools/edit/feattable_edit.hpp
@@ -1,4 +1,4 @@
-/* $Id: feattable_edit.hpp 464927 2015-04-15 15:02:18Z ivanov $
+/* $Id: feattable_edit.hpp 478464 2015-09-09 15:29:44Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,6 +37,7 @@
#include <corelib/ncbistd.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objmgr/scope.hpp>
+#include <objmgr/util/feature.hpp>
#include <objtools/readers/message_listener.hpp>
BEGIN_NCBI_SCOPE
@@ -52,7 +53,8 @@ public:
CFeatTableEdit(
CSeq_annot&,
const string& = "",
- IMessageListener* =0);
+ unsigned int = 1,
+ ILineErrorListener* =0);
~CFeatTableEdit();
void GenerateLocusTags();
@@ -61,8 +63,12 @@ public:
void InferPartials();
void EliminateBadQualifiers();
void GenerateProteinAndTranscriptIds();
- void GenerateOrigProteinAndOrigTranscriptIds();
void GenerateLocusIds();
+ void SubmitFixProducts();
+
+ unsigned int PendingLocusTagNumber() const {
+ return mLocusTagNumber;
+ }
protected:
void xGenerateLocusIdsUseExisting();
@@ -71,11 +77,9 @@ protected:
string xNextFeatId();
string xNextLocusTag();
string xNextProteinId(
- const CSeq_feat&);
+ const CMappedFeat&);
string xNextTranscriptId(
- const CSeq_feat&);
- string xCurrentTranscriptId(
- const CSeq_feat&);
+ const CMappedFeat&);
void xPutErrorMissingLocustag(
CMappedFeat);
@@ -84,18 +88,24 @@ protected:
void xPutErrorMissingProteinId(
CMappedFeat);
- CConstRef<CSeq_feat> xGetGeneParent(
- const CSeq_feat&);
- CConstRef<CSeq_feat> xGetMrnaParent(
- const CSeq_feat&);
+ void xFeatureAddQualifier(
+ CMappedFeat,
+ const std::string&, // qual key
+ const std::string&); // qual value
+ void xFeatureAddProteinId(
+ CMappedFeat);
+ void xFeatureAddTranscriptId(
+ CMappedFeat);
+
CRef<CSeq_feat> xMakeGeneForMrna(
- const CSeq_feat&);
+ const CMappedFeat&);
CSeq_annot& mAnnot;
CRef<CScope> mpScope;
CSeq_annot_Handle mHandle;
+ feature::CFeatTree mTree;
CSeq_annot_EditHandle mEditHandle;
- IMessageListener* mpMessageListener;
+ ILineErrorListener* mpMessageListener;
unsigned int mNextFeatId;
unsigned int mLocusTagNumber;
string mLocusTagPrefix;
diff --git a/c++/include/objtools/edit/field_handler.hpp b/c++/include/objtools/edit/field_handler.hpp
index d620ee9..950c138 100644
--- a/c++/include/objtools/edit/field_handler.hpp
+++ b/c++/include/objtools/edit/field_handler.hpp
@@ -1,4 +1,4 @@
-/* $Id: field_handler.hpp 453539 2014-12-04 14:50:14Z ivanov $
+/* $Id: field_handler.hpp 453160 2014-12-01 17:05:32Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/gaps_edit.hpp b/c++/include/objtools/edit/gaps_edit.hpp
index 4473d3b..ddd18c1 100644
--- a/c++/include/objtools/edit/gaps_edit.hpp
+++ b/c++/include/objtools/edit/gaps_edit.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT_GAPS_EDITOR_HPP_INCLUDED
#define OBJTOOLS_EDIT_GAPS_EDITOR_HPP_INCLUDED
-/* $Id: gaps_edit.hpp 458369 2015-02-04 15:31:06Z ivanov $
+/* $Id: gaps_edit.hpp 468747 2015-05-27 18:57:10Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -49,24 +49,27 @@ public:
// sequences may have any packing and will be optimally packed in result
// runs of Ns with exactly length of gap_Unknown_length will be marked appropriate
// optionally specify linkage evidence or leave it default
+ //CLinkage_evidence::EType
+ typedef set<int> TEvidenceSet;
static
- void ConvertNs2Gaps(CSeq_entry& entry,
- TSeqPos gapNmin, TSeqPos gap_Unknown_length,
- CSeq_gap::EType gap_type = (CSeq_gap::EType)-1,
- CLinkage_evidence::EType evidence = (CLinkage_evidence::EType)-1);
+ void ConvertNs2Gaps(CSeq_entry& entry,
+ TSeqPos gapNmin, TSeqPos gap_Unknown_length,
+ CSeq_gap::EType gap_type = (CSeq_gap::EType) - 1,
+ const TEvidenceSet& evidences = TEvidenceSet() );
static
void ConvertNs2Gaps(CBioseq& bioseq,
TSeqPos gapNmin, TSeqPos gap_Unknown_length,
CSeq_gap::EType gap_type,
- CLinkage_evidence::EType evidence);
+ const TEvidenceSet& evidences);
+
static
void ConvertNs2Gaps(CBioseq::TInst& inst, TSeqPos gap_min);
static
void ConvertNs2Gaps(const CSeq_data& data, TSeqPos len, CDelta_ext& ext, TSeqPos gap_min);
static
CRef<CDelta_seq> CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos gap_length,
- CSeq_gap::EType gap_type, CLinkage_evidence::EType evidence);
+ CSeq_gap::EType gap_type, const TEvidenceSet& evidences);
};
END_SCOPE(objects)
diff --git a/c++/include/objtools/edit/loc_edit.hpp b/c++/include/objtools/edit/loc_edit.hpp
index 5499f72..d724d77 100644
--- a/c++/include/objtools/edit/loc_edit.hpp
+++ b/c++/include/objtools/edit/loc_edit.hpp
@@ -1,4 +1,4 @@
-/* $Id: loc_edit.hpp 444273 2014-08-22 15:55:32Z ivanov $
+/* $Id: loc_edit.hpp 443569 2014-08-15 17:02:07Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/edit/parse_text_options.hpp b/c++/include/objtools/edit/parse_text_options.hpp
new file mode 100644
index 0000000..472b70f
--- /dev/null
+++ b/c++/include/objtools/edit/parse_text_options.hpp
@@ -0,0 +1,128 @@
+#ifndef _PARSE_TEXT_OPTIONS_HPP_
+#define _PARSE_TEXT_OPTIONS_HPP_
+/* $Id: parse_text_options.hpp 477905 2015-09-02 15:51:25Z ivanov $
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's official duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Authors: Colleen Bollin, Andrea Asztalos
+*
+* File Description:
+* Classes that implement string parsing.
+*/
+
+#include <corelib/ncbistd.hpp>
+#include <corelib/ncbiobj.hpp>
+
+
+BEGIN_NCBI_SCOPE
+BEGIN_SCOPE(objects)
+BEGIN_SCOPE(edit)
+
+NCBI_XOBJEDIT_EXPORT SIZE_TYPE FindWithOptions(const string& str, const string& pattern,
+ SIZE_TYPE start_search, bool case_insensitive, bool whole_word);
+
+class NCBI_XOBJEDIT_EXPORT CParseTextMarker : public CObject
+{
+public:
+ enum EMarkerType {
+ eMarkerType_None = 0,
+ eMarkerType_Text,
+ eMarkerType_Digits,
+ eMarkerType_Letters
+ };
+
+ CParseTextMarker()
+ : m_MarkerType(eMarkerType_None),
+ m_Text(kEmptyStr) {}
+ ~CParseTextMarker() {}
+
+ void SetText(const string& val);
+ void SetDigits() { m_MarkerType = eMarkerType_Digits; }
+ void SetLetters() { m_MarkerType = eMarkerType_Letters; }
+ bool FindInText(const string& val, size_t& pos, size_t& len, size_t start_search, bool case_insensitive, bool whole_word) const;
+ void Reset();
+
+ static void s_GetDigitsPosition(const string& str, size_t& pos, size_t& len, size_t start_search);
+ static void s_GetLettersPosition(const string& str, size_t& pos, size_t& len, size_t start_search);
+
+private:
+ EMarkerType m_MarkerType;
+ string m_Text;
+};
+
+
+class NCBI_XOBJEDIT_EXPORT CParseTextOptions : public CObject
+{
+public:
+ CParseTextOptions()
+ : m_IncludeStartMarker(false),
+ m_IncludeStopMarker(false),
+ m_RemoveFromParsed(false),
+ m_RemoveBeforePattern(false),
+ m_RemoveAfterPattern(false),
+ m_CaseInsensitive(false),
+ m_WholeWord(false) {}
+ ~CParseTextOptions() {}
+
+ void SetStartText(const string& val) { m_StartMarker.SetText(val); }
+ void SetStopText(const string& val) { m_StopMarker.SetText(val); }
+ void SetStartDigits() { m_StartMarker.SetDigits(); }
+ void SetStopDigits() { m_StopMarker.SetDigits(); }
+ void SetStartLetters() { m_StartMarker.SetLetters(); }
+ void SetStopLetters() { m_StopMarker.SetLetters(); }
+
+ void SetIncludeStart(bool val) { m_IncludeStartMarker = val; }
+ void SetIncludeStop(bool val) { m_IncludeStopMarker = val; }
+ /// if true, removes the parsed text from the parsed text
+ void SetShouldRemove(bool val) { m_RemoveFromParsed = val; }
+ /// if true, removes the lhs delimiter from the parsed text
+ void SetShouldRmvBeforePattern(bool val) { m_RemoveBeforePattern = val; }
+ /// if true, removes the rhs delimiter from the parsed text
+ void SetShouldRmvAfterPattern(bool val) { m_RemoveAfterPattern = val; }
+
+ void SetCaseInsensitive(bool val) { m_CaseInsensitive = val; }
+ void SetWholeWord(bool val) { m_WholeWord = val; }
+ void Reset();
+
+ string GetSelectedText(const string& input) const;
+ void RemoveSelectedText(string& input, bool remove_first_only = true) const;
+ bool ShouldRemoveFromParsed() const { return m_RemoveFromParsed; }
+
+private:
+ CParseTextMarker m_StartMarker;
+ CParseTextMarker m_StopMarker;
+ bool m_IncludeStartMarker;
+ bool m_IncludeStopMarker;
+ bool m_RemoveFromParsed;
+ bool m_RemoveBeforePattern;
+ bool m_RemoveAfterPattern;
+ bool m_CaseInsensitive;
+ bool m_WholeWord;
+};
+
+END_SCOPE(edit)
+END_SCOPE(objects)
+END_NCBI_SCOPE
+
+#endif // _PARSE_TEXT_OPTIONS_HPP_
\ No newline at end of file
diff --git a/c++/include/objtools/edit/remote_updater.hpp b/c++/include/objtools/edit/remote_updater.hpp
index 3de9396..5eb9791 100755
--- a/c++/include/objtools/edit/remote_updater.hpp
+++ b/c++/include/objtools/edit/remote_updater.hpp
@@ -8,7 +8,7 @@ class CSerialObject;
BEGIN_SCOPE(objects)
class CSeq_entry_EditHandle;
-class IMessageListener;
+class ILineErrorListener;
class CSeq_entry;
class CSeqdesc;
class CSeq_descr;
@@ -29,9 +29,9 @@ public:
void UpdatePubReferences(CSerialObject& obj);
void UpdatePubReferences(CSeq_entry_EditHandle& obj);
- void UpdateOrgFromTaxon(IMessageListener* logger, CSeq_entry& entry);
- void UpdateOrgFromTaxon(IMessageListener* logger, CSeq_entry_EditHandle& obj);
- void UpdateOrgFromTaxon(IMessageListener* logger, CSeqdesc& obj);
+ void UpdateOrgFromTaxon(ILineErrorListener* logger, CSeq_entry& entry);
+ void UpdateOrgFromTaxon(ILineErrorListener* logger, CSeq_entry_EditHandle& obj);
+ void UpdateOrgFromTaxon(ILineErrorListener* logger, CSeqdesc& obj);
void ClearCache();
static void ConvertToStandardAuthors(CAuth_list& auth_list);
static void PostProcessPubs(CSeq_entry_EditHandle& obj);
@@ -44,7 +44,7 @@ public:
private:
void xUpdatePubReferences(CSeq_entry& entry);
void xUpdatePubReferences(CSeq_descr& descr);
- void xUpdateOrgTaxname(IMessageListener* logger, COrg_ref& org);
+ void xUpdateOrgTaxname(ILineErrorListener* logger, COrg_ref& org);
CRef<CMLAClient> m_mlaClient;
diff --git a/c++/include/objtools/edit/rna_edit.hpp b/c++/include/objtools/edit/rna_edit.hpp
index d681d10..2bafab0 100644
--- a/c++/include/objtools/edit/rna_edit.hpp
+++ b/c++/include/objtools/edit/rna_edit.hpp
@@ -1,4 +1,4 @@
-/* $Id: rna_edit.hpp 447118 2014-09-22 18:28:38Z ivanov $
+/* $Id: rna_edit.hpp 477902 2015-09-02 15:50:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,9 +26,8 @@
* Authors: Igor Filippov
*/
-
-#ifndef _EDIT_RNA_EDIT_H_
-#define _EDIT_RNA_EDIT__H_
+#ifndef _EDIT_RNA_EDIT__HPP_
+#define _EDIT_RNA_EDIT__HPP_
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
@@ -73,4 +72,4 @@ END_SCOPE(objects)
END_NCBI_SCOPE
#endif
-
+ // _EDIT_RNA_EDIT__HPP_
diff --git a/c++/include/objtools/edit/seq_entry_edit.hpp b/c++/include/objtools/edit/seq_entry_edit.hpp
index 072a395..38f92da 100644
--- a/c++/include/objtools/edit/seq_entry_edit.hpp
+++ b/c++/include/objtools/edit/seq_entry_edit.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_EDIT___SEQ_ENTRY_EDIT__HPP
#define OBJTOOLS_EDIT___SEQ_ENTRY_EDIT__HPP
-/* $Id: seq_entry_edit.hpp 454233 2014-12-11 19:55:51Z ivanov $
+/* $Id: seq_entry_edit.hpp 468566 2015-05-26 16:19:06Z filippov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -154,12 +154,14 @@ bool HasRepairedIDs(const CSeq_entry& entry);
NCBI_XOBJEDIT_EXPORT
void ConvertRawToDeltaByNs(CSeq_inst& inst,
size_t min_unknown, int max_unknown,
- size_t min_known, int max_known);
+ size_t min_known, int max_known,
+ bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkage_evidence = -1 );
NCBI_XOBJEDIT_EXPORT
void ConvertRawToDeltaByNs(CBioseq_Handle bsh,
size_t min_unknown, int max_unknown,
- size_t min_known, int max_known);
+ size_t min_known, int max_known,
+ bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkage_evidence = -1 );
typedef pair<size_t, int> TLocAdjustment;
typedef vector<TLocAdjustment> TLocAdjustmentVector;
diff --git a/c++/include/objtools/edit/source_edit.hpp b/c++/include/objtools/edit/source_edit.hpp
index 651572f..dfa2c4d 100644
--- a/c++/include/objtools/edit/source_edit.hpp
+++ b/c++/include/objtools/edit/source_edit.hpp
@@ -1,4 +1,4 @@
-/* $Id: source_edit.hpp 453265 2014-12-02 15:21:28Z ivanov $
+/* $Id: source_edit.hpp 475824 2015-08-12 11:28:53Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -27,8 +27,8 @@
*/
-#ifndef _EDIT_SOURCE_EDIT_H_
-#define _EDIT_SOURCE_EDIT__H_
+#ifndef _EDIT_SOURCE_EDIT__HPP_
+#define _EDIT_SOURCE_EDIT__HPP_
#include <corelib/ncbistd.hpp>
#include <objmgr/scope.hpp>
@@ -50,5 +50,5 @@ END_SCOPE(edit)
END_SCOPE(objects)
END_NCBI_SCOPE
-#endif
+#endif /* _EDIT_SOURCE_EDIT__HPP_ */
diff --git a/c++/include/objtools/error_codes.hpp b/c++/include/objtools/error_codes.hpp
index 8622074..018abad 100644
--- a/c++/include/objtools/error_codes.hpp
+++ b/c++/include/objtools/error_codes.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS___ERROR_CODES__HPP
#define OBJTOOLS___ERROR_CODES__HPP
-/* $Id: error_codes.hpp 469194 2015-06-02 14:03:42Z blastadm $
+/* $Id: error_codes.hpp 485953 2015-11-30 17:53:34Z blastadm $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/format/cigar_formatter.hpp b/c++/include/objtools/format/cigar_formatter.hpp
index 863b401..4c9d4bb 100644
--- a/c++/include/objtools/format/cigar_formatter.hpp
+++ b/c++/include/objtools/format/cigar_formatter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___CIGAR_FORMATTER__HPP
#define OBJTOOLS_FORMAT___CIGAR_FORMATTER__HPP
-/* $Id: cigar_formatter.hpp 358642 2012-04-04 15:33:22Z grichenk $
+/* $Id: cigar_formatter.hpp 484559 2015-11-12 17:45:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,7 @@ class NCBI_FORMAT_EXPORT CCIGAR_Formatter
{
public:
enum ECIGARFlags {
- fCIGAR_GffForFlybase = 1, ///< Flybase flavour of GFF3.
+ fCIGAR_GffForFlybase = 1 << 0, ///< Flybase flavour of GFF3.
fCIGAR_Default = 0
};
typedef int TCIGARFlags;
@@ -83,11 +83,13 @@ protected:
virtual void StartRows(void) {}
virtual void EndRows(void) {}
virtual void StartRow(void) {}
- virtual void AddRow(const string& cigar) {}
+ virtual void AddRow(const string& /*cigar*/) {}
virtual void EndRow(void) {}
virtual void AddSegment(CNcbiOstream& cigar,
char seg_type,
TSeqPos seg_len);
+ // Force seq-id to the desired type (e.g. gi, acc.ver).
+ virtual void AdjustSeqIdType(CConstRef<CSeq_id>& /*id*/) {};
// Get top level alignment
const CSeq_align& GetSeq_align(void) const { return m_Align; }
diff --git a/c++/include/objtools/format/context.hpp b/c++/include/objtools/format/context.hpp
index c632aa3..4839b6b 100644
--- a/c++/include/objtools/format/context.hpp
+++ b/c++/include/objtools/format/context.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___CONTEXT__HPP
#define OBJTOOLS_FORMAT___CONTEXT__HPP
-/* $Id: context.hpp 462431 2015-03-18 17:23:52Z ivanov $
+/* $Id: context.hpp 478451 2015-09-09 15:24:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -427,6 +427,10 @@ public:
const CSeq_loc* GetLocation(void) const { return m_Loc; }
void SetLocation(const CSeq_loc* loc) { m_Loc.Reset(loc); }
+ const feature::CFeatTree* GetFeatTree(void) const { return m_FeatTree; }
+ feature::CFeatTree* GetFeatTree(void) { return m_FeatTree; }
+ void SetFeatTree(feature::CFeatTree* tree) { m_FeatTree.Reset(tree); }
+
void AddSection(TSection& section) { m_Sections.push_back(section); }
void Reset(void);
@@ -439,6 +443,7 @@ private:
CConstRef<CSubmit_block> m_Submit;
auto_ptr<SAnnotSelector> m_Selector;
CConstRef<CSeq_loc> m_Loc;
+ CRef<feature::CFeatTree> m_FeatTree;
};
/////////////////////////////////////////////////////////////////////////////
diff --git a/c++/include/objtools/format/flat_file_config.hpp b/c++/include/objtools/format/flat_file_config.hpp
index 6d852e4..868aeb7 100644
--- a/c++/include/objtools/format/flat_file_config.hpp
+++ b/c++/include/objtools/format/flat_file_config.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP
#define OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP
-/* $Id: flat_file_config.hpp 439585 2014-07-01 18:08:58Z gotvyans $
+/* $Id: flat_file_config.hpp 481617 2015-10-14 14:42:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -87,7 +87,8 @@ public:
eFormat_GFF, // version 2, w/GTF
eFormat_GFF3,
eFormat_FeaturesOnly,
- eFormat_SAM
+ eFormat_SAM,
+ eFormat_AGP
};
enum EMode {
@@ -142,6 +143,11 @@ public:
fShowSeqSpans = 1 << 30
};
+ enum ECustom {
+ // additional customization flags
+ fHideProteinID = 1
+ };
+
enum EView {
// determines which Bioseqs in an entry to view
fViewNucleotides = 0x1,
@@ -209,10 +215,11 @@ public:
typedef EFormat TFormat;
typedef EMode TMode;
typedef EStyle TStyle;
- typedef unsigned int TFlags; // binary OR of "EFlatFileFlags"
+ typedef unsigned int TFlags; // binary OR of "EFlags"
typedef unsigned int TView;
typedef unsigned int TGffOptions;
typedef unsigned int TGenbankBlocks;
+ typedef unsigned int TCustom; // binary OR of "ECustom"
class NCBI_FORMAT_EXPORT CGenbankBlockCallback : public CObject {
public:
@@ -327,7 +334,7 @@ public:
FGenbankBlocks which_block ) { return eAction_Default; }
};
- // constructors
+ // constructor
CFlatFileConfig(TFormat format = eFormat_GenBank,
TMode mode = eMode_GBench,
TStyle style = eStyle_Normal,
@@ -337,7 +344,8 @@ public:
TGenbankBlocks genbank_blocks = fGenbankBlocks_All,
CGenbankBlockCallback* pGenbankBlockCallback = NULL,
const ICanceled * pCanceledCallback = NULL,
- bool basicCleanup = false );
+ bool basicCleanup = false,
+ TCustom custom = 0 );
// destructor
~CFlatFileConfig(void);
@@ -351,15 +359,17 @@ public:
bool IsFormatFTable (void) const { return m_Format == eFormat_FTable; }
bool IsFormatGFF (void) const { return m_Format == eFormat_GFF; }
bool IsFormatGFF3 (void) const { return m_Format == eFormat_GFF3; }
+ bool IsFormatAGP (void) const { return m_Format == eFormat_AGP; }
// setters
void SetFormat(const TFormat& format) { m_Format = format; }
- void SetFormatGenbank(void) { m_Format = eFormat_GenBank; }
- void SetFormatEMBL (void) { m_Format = eFormat_EMBL; }
- void SetFormatDDBJ (void) { m_Format = eFormat_DDBJ; }
- void SetFormatGBSeq (void) { m_Format = eFormat_GBSeq; }
- void SetFormatFTable (void) { m_Format = eFormat_FTable; }
- void SetFormatGFF (void) { m_Format = eFormat_GFF; }
+ void SetFormatGenbank(void) { m_Format = eFormat_GenBank; }
+ void SetFormatEMBL (void) { m_Format = eFormat_EMBL; }
+ void SetFormatDDBJ (void) { m_Format = eFormat_DDBJ; }
+ void SetFormatGBSeq (void) { m_Format = eFormat_GBSeq; }
+ void SetFormatFTable (void) { m_Format = eFormat_FTable; }
+ void SetFormatGFF (void) { m_Format = eFormat_GFF; }
void SetFormatGFF3 (void) { m_Format = eFormat_GFF3; }
+ void SetFormatAGP (void) { m_Format = eFormat_AGP; }
// -- Mode
// getters
@@ -473,7 +483,7 @@ public:
bool UseEmblMolType (void) const;
bool HideBankItComment (void) const;
bool CheckCDSProductId (void) const;
- bool FrequencyToNote (void) const;
+ bool FrequencyToNote (void) const;
bool SrcQualsToNote (void) const;
bool HideEmptySource (void) const;
bool GoQualsToNote (void) const;
@@ -485,9 +495,6 @@ public:
bool ShowOutOfBoundsFeats(void) const;
bool HideSpecificGeneMaps(void) const;
- // adjust mode dependant flags for RefSeq
- void SetRefSeqConventions(void);
-
// setters (for customization flags)
void SetFlags(const TFlags& flags) { m_Flags = flags; }
CFlatFileConfig& SetDoHTML (bool val = true);
@@ -521,7 +528,19 @@ public:
CFlatFileConfig& SetHideGapFeatures (bool val = true);
CFlatFileConfig& SetNeverTranslateCDS (bool val = true);
CFlatFileConfig& SetShowSeqSpans (bool val = true);
-
+
+ // -- Custom
+ // getters
+ const TCustom& GetCustom(void) const { return m_Custom; }
+ bool HideProteinID (void) const;
+
+ // setters
+ void SetCustom(const TCustom& custom) { m_Custom = custom; }
+ CFlatFileConfig& SetHideProteinID (bool val = true);
+
+ // adjust mode dependant flags for RefSeq
+ void SetRefSeqConventions(void);
+
// -- GffOptions
// getters
bool GffGenerateIdTags (void) const
@@ -616,7 +635,7 @@ public:
// -- BasicCleanup
// getters
- const bool BasicCleanup(void) const { return m_BasicCleanup; }
+ bool BasicCleanup(void) const { return m_BasicCleanup; }
// setters
void BasicCleanup(bool clean) { m_BasicCleanup = clean; }
@@ -654,6 +673,7 @@ private:
CRef<CGenbankBlockCallback> m_GenbankBlockCallback;
const ICanceled * m_pCanceledCallback; // instance does NOT own it
bool m_BasicCleanup;
+ TCustom m_Custom;
};
@@ -661,14 +681,14 @@ private:
// inilne methods
// custom flags
-#define CUSTOM_FLAG_GET(x) \
+#define FLAG_ARG_GET(x) \
inline \
bool CFlatFileConfig::x(void) const \
{ \
return (m_Flags & f##x) != 0; \
}
-#define CUSTOM_FLAG_SET(x) inline \
+#define FLAG_ARG_SET(x) inline \
CFlatFileConfig& CFlatFileConfig::Set##x(bool val) \
{ \
if ( val ) { \
@@ -679,45 +699,74 @@ CFlatFileConfig& CFlatFileConfig::Set##x(bool val) \
return *this; \
}
-#define CUSTOM_FLAG_IMP(x) \
-CUSTOM_FLAG_GET(x) \
-CUSTOM_FLAG_SET(x)
-
-CUSTOM_FLAG_IMP(DoHTML)
-CUSTOM_FLAG_IMP(HideImpFeatures)
-CUSTOM_FLAG_IMP(HideSNPFeatures)
-CUSTOM_FLAG_IMP(HideExonFeatures)
-CUSTOM_FLAG_IMP(HideIntronFeatures)
-CUSTOM_FLAG_IMP(HideMiscFeatures)
-CUSTOM_FLAG_IMP(HideRemoteImpFeatures)
-CUSTOM_FLAG_IMP(HideGeneRIFs)
-CUSTOM_FLAG_IMP(OnlyGeneRIFs)
-CUSTOM_FLAG_IMP(HideCDSProdFeatures)
-CUSTOM_FLAG_IMP(HideCDDFeatures)
-CUSTOM_FLAG_IMP(LatestGeneRIFs)
-CUSTOM_FLAG_IMP(ShowContigFeatures)
-CUSTOM_FLAG_IMP(ShowContigSources)
-CUSTOM_FLAG_IMP(ShowContigAndSeq)
-CUSTOM_FLAG_IMP(CopyGeneToCDNA)
-CUSTOM_FLAG_IMP(ShowContigInMaster)
-CUSTOM_FLAG_IMP(CopyCDSFromCDNA)
-CUSTOM_FLAG_IMP(HideSourceFeatures)
-CUSTOM_FLAG_IMP(AlwaysTranslateCDS)
-CUSTOM_FLAG_IMP(OnlyNearFeatures)
-CUSTOM_FLAG_IMP(FavorFarFeatures)
-CUSTOM_FLAG_IMP(ShowFarTranslations)
-CUSTOM_FLAG_IMP(TranslateIfNoProduct)
-CUSTOM_FLAG_IMP(ShowTranscript)
-CUSTOM_FLAG_IMP(ShowPeptides)
-CUSTOM_FLAG_IMP(ShowFtableRefs)
-CUSTOM_FLAG_IMP(OldFeaturesOrder)
-CUSTOM_FLAG_IMP(HideGapFeatures)
-CUSTOM_FLAG_IMP(NeverTranslateCDS)
-CUSTOM_FLAG_IMP(ShowSeqSpans)
-
-#undef CUSTOM_FLAG_IMP
-#undef CUSTOM_FLAG_GET
-#undef CUSTOM_FLAG_SET
+#define FLAG_ARG_IMP(x) \
+FLAG_ARG_GET(x) \
+FLAG_ARG_SET(x)
+
+FLAG_ARG_IMP(DoHTML)
+FLAG_ARG_IMP(HideImpFeatures)
+FLAG_ARG_IMP(HideSNPFeatures)
+FLAG_ARG_IMP(HideExonFeatures)
+FLAG_ARG_IMP(HideIntronFeatures)
+FLAG_ARG_IMP(HideMiscFeatures)
+FLAG_ARG_IMP(HideRemoteImpFeatures)
+FLAG_ARG_IMP(HideGeneRIFs)
+FLAG_ARG_IMP(OnlyGeneRIFs)
+FLAG_ARG_IMP(HideCDSProdFeatures)
+FLAG_ARG_IMP(HideCDDFeatures)
+FLAG_ARG_IMP(LatestGeneRIFs)
+FLAG_ARG_IMP(ShowContigFeatures)
+FLAG_ARG_IMP(ShowContigSources)
+FLAG_ARG_IMP(ShowContigAndSeq)
+FLAG_ARG_IMP(CopyGeneToCDNA)
+FLAG_ARG_IMP(ShowContigInMaster)
+FLAG_ARG_IMP(CopyCDSFromCDNA)
+FLAG_ARG_IMP(HideSourceFeatures)
+FLAG_ARG_IMP(AlwaysTranslateCDS)
+FLAG_ARG_IMP(OnlyNearFeatures)
+FLAG_ARG_IMP(FavorFarFeatures)
+FLAG_ARG_IMP(ShowFarTranslations)
+FLAG_ARG_IMP(TranslateIfNoProduct)
+FLAG_ARG_IMP(ShowTranscript)
+FLAG_ARG_IMP(ShowPeptides)
+FLAG_ARG_IMP(ShowFtableRefs)
+FLAG_ARG_IMP(OldFeaturesOrder)
+FLAG_ARG_IMP(HideGapFeatures)
+FLAG_ARG_IMP(NeverTranslateCDS)
+FLAG_ARG_IMP(ShowSeqSpans)
+
+// custom flags
+#define CUSTOM_ARG_GET(x) \
+inline \
+bool CFlatFileConfig::x(void) const \
+{ \
+ return (m_Custom & f##x) != 0; \
+}
+
+#define CUSTOM_ARG_SET(x) inline \
+CFlatFileConfig& CFlatFileConfig::Set##x(bool val) \
+{ \
+ if ( val ) { \
+ m_Custom |= f##x; \
+ } else { \
+ m_Custom &= ~f##x; \
+ } \
+ return *this; \
+}
+
+#define CUSTOM_ARG_IMP(x) \
+CUSTOM_ARG_GET(x) \
+CUSTOM_ARG_SET(x)
+
+CUSTOM_ARG_IMP(HideProteinID)
+
+#undef FLAG_ARG_IMP
+#undef FLAG_ARG_GET
+#undef FLAG_ARG_SET
+
+#undef CUSTOM_ARG_IMP
+#undef CUSTOM_ARG_GET
+#undef CUSTOM_ARG_SET
inline
void CFlatFileConfig::SetRefSeqConventions(void)
diff --git a/c++/include/objtools/format/flat_file_generator.hpp b/c++/include/objtools/format/flat_file_generator.hpp
index c37ead5..c1d5edc 100644
--- a/c++/include/objtools/format/flat_file_generator.hpp
+++ b/c++/include/objtools/format/flat_file_generator.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___FLAT_FILE_GENERATOR__HPP
#define OBJTOOLS_FORMAT___FLAT_FILE_GENERATOR__HPP
-/* $Id: flat_file_generator.hpp 429411 2014-03-13 23:10:45Z kans $
+/* $Id: flat_file_generator.hpp 481618 2015-10-14 14:42:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,7 +68,8 @@ public:
CFlatFileConfig::TMode mode = CFlatFileConfig::eMode_GBench,
CFlatFileConfig::TStyle style = CFlatFileConfig::eStyle_Normal,
CFlatFileConfig::TFlags flags = 0,
- CFlatFileConfig::TView view = CFlatFileConfig::fViewNucleotides);
+ CFlatFileConfig::TView view = CFlatFileConfig::fViewNucleotides,
+ CFlatFileConfig::TCustom custom = 0);
// destructor
~CFlatFileGenerator(void);
@@ -76,6 +77,8 @@ public:
// Supply an annotation selector to be used in feature gathering.
SAnnotSelector& SetAnnotSelector(void);
+ void SetFeatTree(feature::CFeatTree* tree);
+
void Generate(CSeq_submit& submit, CScope& scope, CNcbiOstream& os);
void Generate(const CBioseq& bioseq, CScope& scope, CNcbiOstream& os);
void Generate(const CSeq_loc& loc, CScope& scope, CNcbiOstream& os);
diff --git a/c++/include/objtools/format/gather_items.hpp b/c++/include/objtools/format/gather_items.hpp
index 8c850de..b565cc7 100644
--- a/c++/include/objtools/format/gather_items.hpp
+++ b/c++/include/objtools/format/gather_items.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___GATHER_ITEMS__HPP
#define OBJTOOLS_FORMAT___GATHER_ITEMS__HPP
-/* $Id: gather_items.hpp 450148 2014-10-23 14:01:10Z ivanov $
+/* $Id: gather_items.hpp 478451 2015-09-09 15:24:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -79,7 +79,7 @@ protected:
CBioseqContext& Context (void) const { return *m_Current; }
const CFlatFileConfig& Config(void) const { return m_Context->GetConfig(); }
- virtual void x_GatherSeqEntry(const CSeq_entry_Handle& entry,
+ virtual void x_GatherSeqEntry(CFlatFileContext& ctx,
CRef<CTopLevelSeqEntryContext> topLevelSeqEntryContext = CRef<CTopLevelSeqEntryContext>() ) const;
virtual void x_GatherBioseq(
const CBioseq_Handle& prev_seq, const CBioseq_Handle& this_seq, const CBioseq_Handle& next_seq,
@@ -174,6 +174,7 @@ protected:
void x_FeatComments(CBioseqContext& ctx) const;
void x_NameComments(CBioseqContext& ctx) const;
void x_StructuredComments(CBioseqContext& ctx) const;
+ void x_UnorderedComments(CBioseqContext& ctx) const;
// sequence
void x_GatherSequence (void) const;
@@ -187,6 +188,8 @@ protected:
mutable CRef<CBioseqContext> m_Current;
mutable TCommentVec m_Comments;
+ mutable CConstRef<CUser_object> m_FirstGenAnnotSCAD;
+
// Raw pointer because we do NOT own it
const ICanceled * m_pCanceledCallback;
diff --git a/c++/include/objtools/format/genbank_formatter.hpp b/c++/include/objtools/format/genbank_formatter.hpp
index c22f66b..80ed32b 100644
--- a/c++/include/objtools/format/genbank_formatter.hpp
+++ b/c++/include/objtools/format/genbank_formatter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___GENBANK_FORMATTER__HPP
#define OBJTOOLS_FORMAT___GENBANK_FORMATTER__HPP
-/* $Id: genbank_formatter.hpp 360035 2012-04-19 13:43:48Z kornbluh $
+/* $Id: genbank_formatter.hpp 463068 2015-03-24 16:16:20Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -119,10 +119,12 @@ private:
// HTML
void x_LocusHtmlPrefix( std::string &first_line, CBioseqContext& ctx );
- string x_GetFeatureSpanAndScriptStart( const char * strKey,
+ void x_GetFeatureSpanAndScriptStart(IFlatTextOStream& os, const CTempString& strKey,
const CSeq_loc &feat_loc,
CBioseqContext& ctx );
+ void x_SmartWrapQuals(const class CFeatureItemBase& f, const class CFlatFeature& feat, IFlatTextOStream& text_os);
+
// processing data
unsigned int m_uFeatureCount;
diff --git a/c++/include/objtools/format/items/comment_item.hpp b/c++/include/objtools/format/items/comment_item.hpp
index bf090a5..44458fa 100644
--- a/c++/include/objtools/format/items/comment_item.hpp
+++ b/c++/include/objtools/format/items/comment_item.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT_ITEMS___COMMENT_ITEM__HPP
#define OBJTOOLS_FORMAT_ITEMS___COMMENT_ITEM__HPP
-/* $Id: comment_item.hpp 450148 2014-10-23 14:01:10Z ivanov $
+/* $Id: comment_item.hpp 476214 2015-08-17 13:04:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -136,6 +136,7 @@ public:
static string GetStringForTSA(CBioseqContext& ctx);
static string GetStringForMolinfo(const CMolInfo& mi, CBioseqContext& ctx);
static string GetStringForHTGS(CBioseqContext& ctx);
+ static string GetStringForUnordered(CBioseqContext& ctx);
static string GetStringForModelEvidance(const SModelEvidance& me,
ECommentFormat format = eFormat_Text);
static TRefTrackStatus GetRefTrackStatus(const CUser_object& uo,
diff --git a/c++/include/objtools/format/items/feature_item.hpp b/c++/include/objtools/format/items/feature_item.hpp
index 652f34d..89bf531 100644
--- a/c++/include/objtools/format/items/feature_item.hpp
+++ b/c++/include/objtools/format/items/feature_item.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT_ITEMS___FLAT_FEATURE__HPP
#define OBJTOOLS_FORMAT_ITEMS___FLAT_FEATURE__HPP
-/* $Id: feature_item.hpp 454032 2014-12-10 14:51:24Z ivanov $
+/* $Id: feature_item.hpp 463068 2015-03-24 16:16:20Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -91,7 +91,7 @@ public:
const CFlatSeqLoc& GetLoc (void) const { return *m_Loc; }
const TQuals& GetQuals(void) const { return m_Quals; }
//const CSeq_feat& GetFeat (void) const { return m_Feat.GetOriginalFeature(); }
- CMappedFeat GetFeat (void) const { return m_Feat; }
+ const CMappedFeat& GetFeat (void) const { return m_Feat; }
TQuals& SetQuals(void) { return m_Quals; }
@@ -117,8 +117,8 @@ public:
//return m_Feat.Compare(*f2.m_Feat, GetLoc(), f2.GetLoc()) < 0;
return m_Feat < f2.m_Feat;
}
- CMappedFeat GetFeat(void) const { return m_Feat; }
- const CSeq_loc& GetLoc(void) const { return *m_Loc; }
+ const CMappedFeat& GetFeat(void) const { return m_Feat; }
+ const CSeq_loc& GetLoc(void) const { return *m_Loc; }
virtual string GetKey(void) const {
return m_Feat.GetData().GetKey(CSeqFeatData::eVocabulary_genbank);
@@ -296,7 +296,7 @@ protected:
// format
void x_FormatQuals(CFlatFeature& ff) const;
void x_FormatNoteQuals(CFlatFeature& ff) const;
- void x_FormatQual(EFeatureQualifier slot, const CTempString & name,
+ void x_FormatQual(EFeatureQualifier slot, const char* name,
CFlatFeature::TQuals& qvec, TQualFlags flags = 0) const;
void x_FormatNoteQual(EFeatureQualifier slot, const CTempString & name,
CFlatFeature::TQuals& qvec, TQualFlags flags = 0) const;
@@ -419,7 +419,7 @@ private:
void x_FormatQuals(CFlatFeature& ff) const;
void x_FormatGBNoteQuals(CFlatFeature& ff) const;
void x_FormatNoteQuals(CFlatFeature& ff) const;
- void x_FormatQual(ESourceQualifier slot, const string& name,
+ void x_FormatQual(ESourceQualifier slot, const CTempString& name,
CFlatFeature::TQuals& qvec, TQualFlags flags = 0) const;
void x_FormatNoteQual(ESourceQualifier slot, const char* name,
CFlatFeature::TQuals& qvec, TQualFlags flags = 0) const {
diff --git a/c++/include/objtools/format/items/flat_qual_slots.hpp b/c++/include/objtools/format/items/flat_qual_slots.hpp
index c13f2b9..744e284 100644
--- a/c++/include/objtools/format/items/flat_qual_slots.hpp
+++ b/c++/include/objtools/format/items/flat_qual_slots.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FLAT___FLAT_QUAL_SLOTS__HPP
#define OBJTOOLS_FLAT___FLAT_QUAL_SLOTS__HPP
-/* $Id: flat_qual_slots.hpp 450158 2014-10-23 14:04:08Z ivanov $
+/* $Id: flat_qual_slots.hpp 449759 2014-10-20 19:44:53Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/format/items/qualifiers.hpp b/c++/include/objtools/format/items/qualifiers.hpp
index 875050b..2dcff79 100644
--- a/c++/include/objtools/format/items/qualifiers.hpp
+++ b/c++/include/objtools/format/items/qualifiers.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT_ITEMS___QUALIFIERS__HPP
#define OBJTOOLS_FORMAT_ITEMS___QUALIFIERS__HPP
-/* $Id: qualifiers.hpp 377200 2012-10-10 12:16:52Z kornbluh $
+/* $Id: qualifiers.hpp 463068 2015-03-24 16:16:20Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -93,15 +93,15 @@ public:
eTrim_WhitespaceOnly
};
- CFormatQual(const string& name,
- const string& value,
- const string& prefix,
- const string& suffix,
+ CFormatQual(const CTempString& name,
+ const CTempString& value,
+ const CTempString& prefix,
+ const CTempString& suffix,
TStyle style = eQuoted,
TFlags flags = 0,
ETrim trim = eTrim_Normal );
- CFormatQual(const string& name,
- const string& value,
+ CFormatQual(const CTempString& name,
+ const CTempString& value,
TStyle style = eQuoted,
TFlags flags = 0,
ETrim trim = eTrim_Normal );
@@ -149,7 +149,7 @@ public:
static const string kEOL; // "\n" - end of line
static const string kSpace; // " "
- virtual void Format(TFlatQuals& quals, const string& name,
+ virtual void Format(TFlatQuals& quals, const CTempString& name,
CBioseqContext& ctx, TFlags flags = 0) const = 0;
protected:
@@ -159,7 +159,7 @@ protected:
IFlatQVal(const string* pfx = &kSpace, const string* sfx = &kEmptyStr)
: m_Prefix(pfx), m_Suffix(sfx)
{ }
- TFlatQual x_AddFQ(TFlatQuals& q, const string& n, const string& v,
+ TFlatQual x_AddFQ(TFlatQuals& q, const CTempString& n, const CTempString& v,
TStyle st = CFormatQual::eQuoted,
CFormatQual::TFlags flags = 0,
ETrim trim = CFormatQual::eTrim_Normal ) const {
@@ -202,13 +202,13 @@ public:
bool HasQual(const Key& key) const {
return Find(key) != m_Quals.end();
}
+ inline
iterator LowerBound(Key& key) {
- typename TQualMMap::iterator it = m_Quals.lower_bound(key);
- return (it == m_Quals.end() || it->first == key) ? it : m_Quals.end();
+ return m_Quals.find(key);
}
+ inline
const_iterator LowerBound(const Key& key) const {
- typename TQualMMap::const_iterator it = m_Quals.lower_bound(key);
- return (it == m_Quals.end() || it->first == key) ? it : m_Quals.end();
+ return m_Quals.find(key);
}
iterator Erase(iterator it) {
iterator next = it;
@@ -243,7 +243,7 @@ class NCBI_FORMAT_EXPORT CFlatBoolQVal : public IFlatQVal
{
public:
CFlatBoolQVal(bool value) : m_Value(value) { }
- void Format(TFlatQuals& q, const string& n, CBioseqContext&, TFlags) const
+ void Format(TFlatQuals& q, const CTempString& n, CBioseqContext&, TFlags) const
{ if (m_Value) { x_AddFQ(q, n, kEmptyStr, CFormatQual::eEmpty); } }
private:
bool m_Value;
@@ -254,7 +254,7 @@ class NCBI_FORMAT_EXPORT CFlatIntQVal : public IFlatQVal
{
public:
CFlatIntQVal(int value) : m_Value(value) { }
- void Format(TFlatQuals& q, const string& n, CBioseqContext&, TFlags) const;
+ void Format(TFlatQuals& q, const CTempString& n, CBioseqContext&, TFlags) const;
private:
int m_Value;
};
@@ -267,15 +267,15 @@ private:
class NCBI_FORMAT_EXPORT CFlatStringQVal : public IFlatQVal
{
public:
- CFlatStringQVal(const string& value,
+ CFlatStringQVal(const CTempString& value,
TStyle style = CFormatQual::eQuoted,
ETrim trim = CFormatQual::eTrim_Normal );
- CFlatStringQVal(const string& value, const string& pfx, const string& sfx,
+ CFlatStringQVal(const CTempString& value, const string& pfx, const string& sfx,
TStyle style = CFormatQual::eQuoted, ETrim trim = CFormatQual::eTrim_Normal );
- CFlatStringQVal(const string& value,
+ CFlatStringQVal(const CTempString& value,
ETrim trim );
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
const string& GetValue(void) const { return m_Value; }
@@ -296,7 +296,7 @@ public:
CFlatStringQVal(value, CFormatQual::eUnquoted)
{}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
};
@@ -307,7 +307,7 @@ public:
CFlatBondQVal(const string& value) : CFlatStringQVal(value)
{}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
};
@@ -318,7 +318,7 @@ public:
CFlatGeneQVal(const string& value) : CFlatStringQVal(value, CFormatQual::eTrim_WhitespaceOnly)
{}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
};
@@ -329,7 +329,7 @@ public:
CFlatSiteQVal(const string& value) : CFlatStringQVal(value)
{}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
};
@@ -346,7 +346,7 @@ public:
const list<string>::const_iterator& end,
TStyle style = CFormatQual::eQuoted)
: m_Value(begin, end), m_Style(style) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
const TValue& GetValue(void) const { return m_Value; }
@@ -367,7 +367,7 @@ public:
m_Suffix = &kSemicolon;
}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
};
@@ -375,7 +375,7 @@ class NCBI_FORMAT_EXPORT CFlatNomenclatureQVal : public IFlatQVal
{
public:
CFlatNomenclatureQVal( const CGene_ref_Base::TFormal_name& value ) : m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -386,7 +386,7 @@ class NCBI_FORMAT_EXPORT CFlatCodeBreakQVal : public IFlatQVal
{
public:
CFlatCodeBreakQVal(const CCdregion::TCode_break& value) : m_Value(value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -399,7 +399,7 @@ class NCBI_FORMAT_EXPORT CFlatCodonQVal : public IFlatQVal
public:
CFlatCodonQVal(unsigned int codon, unsigned char aa, bool is_ascii = true);
// CFlatCodonQVal(const string& value); // for imports
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -413,7 +413,7 @@ class NCBI_FORMAT_EXPORT CFlatExperimentQVal : public IFlatQVal
public:
CFlatExperimentQVal(
const string& = "" );
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
protected:
string m_str;
@@ -424,7 +424,7 @@ class NCBI_FORMAT_EXPORT CFlatInferenceQVal : public IFlatQVal
{
public:
CFlatInferenceQVal( const string& = "" );
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
protected:
@@ -436,7 +436,7 @@ class NCBI_FORMAT_EXPORT CFlatIllegalQVal : public IFlatQVal
{
public:
CFlatIllegalQVal(const CGb_qual& value) : m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -460,7 +460,7 @@ public:
typedef CSeq_inst::TMol TMol;
CFlatMolTypeQVal(TBiomol biomol, TMol mol) : m_Biomol(biomol), m_Mol(mol) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -475,7 +475,7 @@ public:
CFlatOrgModQVal(const COrgMod& value) :
IFlatQVal(&kSpace, &kSemicolon), m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -487,7 +487,7 @@ class NCBI_FORMAT_EXPORT CFlatOrganelleQVal : public IFlatQVal
{
public:
CFlatOrganelleQVal(CBioSource::TGenome value) : m_Value(value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -499,7 +499,7 @@ class NCBI_FORMAT_EXPORT CFlatPubSetQVal : public IFlatQVal
{
public:
CFlatPubSetQVal(const CPub_set& value) : m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -512,7 +512,7 @@ class NCBI_FORMAT_EXPORT CFlatSeqIdQVal : public IFlatQVal
public:
CFlatSeqIdQVal(const CSeq_id& value, bool add_gi_prefix = false)
: m_Value(&value), m_GiPrefix(add_gi_prefix) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -525,7 +525,7 @@ class NCBI_FORMAT_EXPORT CFlatSeqLocQVal : public IFlatQVal
{
public:
CFlatSeqLocQVal(const CSeq_loc& value) : m_Value(&value) { }
- void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
+ void Format(TFlatQuals& q, const CTempString& n, CBioseqContext& ctx,
TFlags) const
{ x_AddFQ(q, n, CFlatSeqLoc(*m_Value, ctx).GetString()); }
@@ -541,7 +541,7 @@ public:
IFlatQVal(&kSpace, &kSemicolon), m_Value(&value)
{ }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -567,7 +567,7 @@ public:
}
void Format(
- TFlatQuals& quals, const string& name, CBioseqContext& ctx, TFlags flags) const;
+ TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx, TFlags flags) const;
protected:
string m_fwd_name;
@@ -584,7 +584,7 @@ public:
CFlatXrefQVal(const TXref& value, const TQuals* quals = 0)
: m_Value(value), m_Quals(quals) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -599,7 +599,7 @@ class NCBI_FORMAT_EXPORT CFlatModelEvQVal : public IFlatQVal
{
public:
CFlatModelEvQVal(const CUser_object& value) : m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
private:
@@ -611,7 +611,7 @@ class NCBI_FORMAT_EXPORT CFlatGoQVal : public IFlatQVal
{
public:
CFlatGoQVal(const CUser_field& value) : m_Value(&value) { }
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
bool Equals( const CFlatGoQVal &rhs ) const;
@@ -629,7 +629,7 @@ class NCBI_FORMAT_EXPORT CFlatAnticodonQVal : public IFlatQVal
public:
CFlatAnticodonQVal(const CSeq_loc& ac, const string& aa) :
m_Anticodon(&ac), m_Aa(aa){ }
- void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
+ void Format(TFlatQuals& q, const CTempString& n, CBioseqContext& ctx,
TFlags) const;
private:
@@ -644,7 +644,7 @@ public:
CFlatTrnaCodonsQVal(const CTrna_ext& trna, const string& comment) :
IFlatQVal(&kEmptyStr, &kSemicolon), m_Value(&trna), m_Seqfeat_note(comment)
{}
- void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
+ void Format(TFlatQuals& q, const CTempString& n, CBioseqContext& ctx,
TFlags) const;
private:
@@ -660,7 +660,7 @@ public:
IFlatQVal(&kSpace, &kSemicolon), m_Value(value), m_Gene(gene)
{}
- void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
+ void Format(TFlatQuals& quals, const CTempString& name, CBioseqContext& ctx,
TFlags flags) const;
const CProt_ref::TName& GetValue(void) const { return m_Value; }
diff --git a/c++/include/objtools/format/sam_formatter.hpp b/c++/include/objtools/format/sam_formatter.hpp
index d3a07cf..d20e13a 100644
--- a/c++/include/objtools/format/sam_formatter.hpp
+++ b/c++/include/objtools/format/sam_formatter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_FORMAT___SAM_FORMATTER__HPP
#define OBJTOOLS_FORMAT___SAM_FORMATTER__HPP
-/* $Id: sam_formatter.hpp 457255 2015-01-21 18:33:52Z ivanov $
+/* $Id: sam_formatter.hpp 484559 2015-11-12 17:45:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,7 +51,6 @@
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
-
class NCBI_FORMAT_EXPORT CSAM_Formatter
{
public:
@@ -61,6 +60,9 @@ public:
fSAM_NumNucDiff = 1 << 2, ///< Generate NM tags
fSAM_PercentageIdentity = 1 << 3, ///< Generate PI tags
fSAM_BitScore = 1 << 4, ///< Generate BS tags
+ fSAM_PlainSeqIds = 1 << 5, ///< Drop type prefix in seq-ids
+ fSAM_SeqData = 1 << 6, ///< Print sequence data
+ fSAM_ForceGISeqIds = 1 << 7, ///< Force using GI ids
//? Include all tags by default
fSAM_Default = fSAM_AlignmentScore |
@@ -82,6 +84,62 @@ public:
void SetFlag (EFlags flag) { m_Flags |= flag; }
void UnsetFlag(EFlags flag) { m_Flags &= ~flag; }
+ /// @PG tag fields
+ struct SProgramInfo {
+ SProgramInfo(const string& id = kEmptyStr,
+ const string& ver = kEmptyStr,
+ const string& cmd = kEmptyStr)
+ : m_Id(id), m_Version(ver), m_CmdLine(cmd) {}
+
+ string m_Id; ///< ID - program id
+ string m_Version; ///< VN - version
+ string m_CmdLine; ///< CL - command line
+ string m_Desc; ///< DS - description
+ string m_Name; ///< PN - program name
+ };
+
+ void SetProgram(const SProgramInfo& pg) { m_ProgramInfo = pg; }
+ SProgramInfo& SetProgram(void) { return m_ProgramInfo; }
+ const SProgramInfo& GetProgram(void) const { return m_ProgramInfo; }
+
+ enum ESortOrder {
+ eSO_Skip, ///< Do not print SO tag (default)
+ eSO_Unsorted, ///< SO:unsorted
+ eSO_QueryName, ///< SO:queryname
+ eSO_Coordinate, ///< SO:coordinate
+ eSO_User ///< User-provided string
+ };
+
+ /// Set SO tag value.
+ /// @param so
+ /// Predefined SO tag value.
+ /// @param so_value
+ /// User-defined SO tag value. Used only if 'so' is set to eSO_User.
+ void SetSortOrder(ESortOrder so, const string& so_value = kEmptyStr)
+ {
+ m_SO = so;
+ m_SO_Value = so_value;
+ }
+
+ enum EGroupOrder {
+ eGO_Skip, ///< Do not print GO tag
+ eGO_None, ///< GO:none
+ eGO_Query, ///< GO:query (default)
+ eGO_Reference, ///< GO:reference
+ eGO_User ///< User-provided string
+ };
+
+ /// Set GO tag value.
+ /// @param go
+ /// Predefined GO tag value.
+ /// @param go_value
+ /// User-defined GO tag value. Used only if 'go' is set to eGO_User.
+ void SetGroupOrder(EGroupOrder go, const string& go_value = kEmptyStr)
+ {
+ m_GO = go;
+ m_GO_Value = go_value;
+ }
+
CSAM_Formatter& Print(const CSeq_align& aln,
const CSeq_id& query_id);
CSAM_Formatter& Print(const CSeq_align& aln,
@@ -98,10 +156,29 @@ private:
CNcbiOstream* m_Out;
CRef<CScope> m_Scope;
TFlags m_Flags;
+ SProgramInfo m_ProgramInfo;
+ ESortOrder m_SO;
+ string m_SO_Value;
+ EGroupOrder m_GO;
+ string m_GO_Value;
+
+ void x_PrintSOTag(void) const;
+ void x_PrintGOTag(void) const;
+
+ friend class CSAM_CIGAR_Formatter;
typedef list<string> TLines;
- TLines m_Header;
+ class CSAM_Headers
+ {
+ public:
+ CSAM_Headers(void) {}
+ void AddSequence(CSeq_id_Handle id, const string& line);
+ typedef list<pair<CSeq_id_Handle, string> > TData;
+ TData m_Data;
+ };
+
+ CSAM_Headers m_Header;
TLines m_Body;
};
diff --git a/c++/include/objtools/readers/agp_util.hpp b/c++/include/objtools/readers/agp_util.hpp
index 0fc5476..4dc147b 100644
--- a/c++/include/objtools/readers/agp_util.hpp
+++ b/c++/include/objtools/readers/agp_util.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS___AGP_UTIL__HPP
#define OBJTOOLS_READERS___AGP_UTIL__HPP
-/* $Id: agp_util.hpp 429110 2014-03-11 16:48:43Z sapojnik $
+/* $Id: agp_util.hpp 465301 2015-04-20 16:41:10Z sapojnik $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -583,7 +583,9 @@ public:
W_DuplicateEvidence, // CAgpRow (v. >= 2.0 )
W_CompIsNotHtgTypeIs,
W_SingletonsOnly,
+
W_GnlId,
+ W_CompIsLocalTypeNotW,
W_Last, W_First = 31,
// "GenBank" checks that rely on information about the sequence
@@ -645,7 +647,7 @@ public:
};
//static const char* GetMsgEx(int code);
- static string GetPrintableCode(int code); // Returns a string like e01 w12
+ static string GetPrintableCode(int code, bool strict=false); // Returns a string like e01 w12
static void PrintAllMessages(CNcbiOstream& out);
@@ -665,6 +667,29 @@ public:
const string& filename, int linenum, const string& content);
static void PrintLineXml(CNcbiOstream& ostr, const string& filename, int linenum, const string& content, bool two_lines_involved);
+ // Most warnings are treated as errors in the strict mode.
+ bool m_strict;
+ // A bit mask for warnings that are still warnings in the strict mode.
+ // The lowest bit stands for W_First (aka w31, W_GapObjBegin),
+ // the highest, as of 2015/03/25 - W_Last, w66, W_GnlId.
+ static const Uint8 s_StrictModeWarningMask =
+ (Uint8(1) << (W_ExtraTab -W_First)) |
+ (Uint8(1) << (W_GapLineMissingCol9 -W_First)) |
+ (Uint8(1) << (W_NoEolAtEof -W_First)) |
+ (Uint8(1) << (W_GapLineIgnoredCol9 -W_First)) |
+ (Uint8(1) << (W_ObjOrderNotNumerical -W_First)) |
+ (Uint8(1) << (W_GapSizeNot100 -W_First)) |
+ (Uint8(1) << (W_ShortGap -W_First)) |
+ (Uint8(1) << (W_CommentsAfterStart -W_First)) |
+ (Uint8(1) << (W_AssumingVersion -W_First)) |
+ (Uint8(1) << (W_AGPVersionCommentInvalid -W_First)) |
+ (Uint8(1) << (W_AGPVersionCommentUnnecessary-W_First)) ;
+ static inline bool IsStrictModeWarning(int code)
+ {
+ return s_StrictModeWarningMask & (Uint8(1) << (code-W_First));
+ }
+ const char* ErrorWarningOrNoteEx(int code);
+
/// Print the message by code, preceded by "ERROR" or "WARNING".
/// See also: CAgpErr::FormatMessage().
/// Override this you define user errors or warnings -
@@ -751,7 +776,7 @@ public:
protected:
// Count errors of each type, including skipped ones.
int m_MsgCount[CODE_Last];
- bool m_MustSkip[CODE_Last];
+ char m_MustSkip[CODE_Last];
// pp: line before previous (not supported by CAgpReader, but used in agp_validate for W_BreakingGapSameCompId)
diff --git a/c++/include/objtools/readers/agp_validate_reader.hpp b/c++/include/objtools/readers/agp_validate_reader.hpp
index 42f7632..a4cf0d0 100644
--- a/c++/include/objtools/readers/agp_validate_reader.hpp
+++ b/c++/include/objtools/readers/agp_validate_reader.hpp
@@ -1,7 +1,7 @@
#ifndef AGP_VALIDATE_READER
#define AGP_VALIDATE_READER
-/* $Id: agp_validate_reader.hpp 440982 2014-07-18 16:44:52Z sapojnik $
+/* $Id: agp_validate_reader.hpp 465301 2015-04-20 16:41:10Z sapojnik $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -152,6 +152,7 @@ public:
};
class XPrintTotalsItem;
+class CAgpValidateReader;
class NCBI_XOBJREAD_EXPORT CAgpValidateReader : public CAgpReader
{
public:
@@ -180,7 +181,7 @@ public:
typedef map<int,int> TMapIntInt;
protected:
void x_PrintTotals(CNcbiOstream& out=cout, bool use_xml=false); // without comment counts or ids not in AGP
- void x_PrintIdsNotInAgp(CNcbiOstream& out=cout, bool use_xml=false);
+ //void x_PrintIdsNotInAgp(CNcbiOstream& out=cout, bool use_xml=false);
// true: a suspicious mix of ids - some look like GenBank accessions, some do not.
static bool x_PrintPatterns(CAccPatternCounter& namePatterns, const string& strHeader, int fasta_count, const char* count_label=NULL, CNcbiOstream& out=cout, bool use_xml=false);
@@ -277,6 +278,29 @@ protected:
int m_max_comp_beg;
int m_max_obj_beg;
bool m_has_partial_comp, m_has_comp_of_unknown_len;
+
+ // Former CAgpValidateReader::x_PrintIdsNotInAgp(), split into member functions for the purpose of
+ // running CheckIds() earlier, to be able to add this error to the total error/warning counts.
+ class CIdsNotInAgp
+ {
+ CAgpValidateReader& m_reader;
+ CAccPatternCounter m_patterns;
+ set<string> m_ids;
+ int m_cnt;
+ public:
+ CIdsNotInAgp(CAgpValidateReader& reader) : m_reader(reader)
+ {
+ m_cnt=0;
+ }
+
+ // returns: an error/warning message, to be later passed to Print() or PrintXml();
+ // "" if no error.
+ string CheckIds();
+
+ void Print(CNcbiOstream& out, const string& msg);
+ void PrintXml(CNcbiOstream& out, const string& msg);
+ };
+ friend class CIdsNotInAgp;
};
END_NCBI_SCOPE
diff --git a/c++/include/objtools/readers/bed_reader.hpp b/c++/include/objtools/readers/bed_reader.hpp
index 657bf1d..68434f3 100644
--- a/c++/include/objtools/readers/bed_reader.hpp
+++ b/c++/include/objtools/readers/bed_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: bed_reader.hpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: bed_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -180,7 +180,7 @@ public:
virtual CRef< CSerialObject >
ReadObject(
ILineReader& lr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read a single object from given line reader containing BED data. The
/// resulting Seq-annot will contain a feature table.
@@ -192,58 +192,58 @@ public:
virtual CRef< CSeq_annot >
ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
virtual CRef< CSeq_annot >
ReadSeqAnnot(
CNcbiIstream& istr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
virtual bool
ReadTrackData(
ILineReader&,
CRawBedTrack&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
protected:
virtual bool xParseTrackLine(
const string&,
- IMessageListener*);
+ ILineErrorListener*);
bool xParseFeature(
const vector<string>&,
CRef<CSeq_annot>&,
unsigned int,
- IMessageListener*);
+ ILineErrorListener*);
bool xParseFeatureUserFormat(
const vector<string>&,
CRef<CSeq_annot>&,
- IMessageListener*);
+ ILineErrorListener*);
bool xParseFeatureThreeFeatFormat(
const vector<string>&,
CRef<CSeq_annot>&,
unsigned int,
- IMessageListener*);
+ ILineErrorListener*);
bool xAppendFeatureChrom(
const vector<string>&,
CRef<CSeq_annot>&,
unsigned int,
- IMessageListener*);
+ ILineErrorListener*);
bool xAppendFeatureThick(
const vector<string>&,
CRef<CSeq_annot>&,
unsigned int,
- IMessageListener*);
+ ILineErrorListener*);
bool xAppendFeatureBlock(
const vector<string>&,
CRef<CSeq_annot>&,
unsigned int,
- IMessageListener*);
+ ILineErrorListener*);
void x_SetFeatureLocation(
CRef<CSeq_feat>&,
@@ -310,13 +310,13 @@ protected:
xReadBedDataRaw(
ILineReader&,
CRawBedTrack&,
- IMessageListener*);
+ ILineErrorListener*);
bool
xReadBedRecordRaw(
const string&,
CRawBedRecord&,
- IMessageListener*);
+ ILineErrorListener*);
static void xCleanColumnValues(
vector<string>&);
diff --git a/c++/include/objtools/readers/cigar.hpp b/c++/include/objtools/readers/cigar.hpp
index c5fc603..1565bab 100644
--- a/c++/include/objtools/readers/cigar.hpp
+++ b/c++/include/objtools/readers/cigar.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS___CIGAR__HPP
#define OBJTOOLS_READERS___CIGAR__HPP
-/* $Id: cigar.hpp 142435 2008-10-06 20:26:37Z ucko $
+/* $Id: cigar.hpp 466910 2015-05-07 14:26:38Z foleyjp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,8 +33,8 @@
/// @file cigar.hpp
/// Code to handle Concise Idiosyncratic Gapped Alignment Report notation.
///
-/// See http://may2005.archive.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html
-/// for the base format and http://song.sorceforge.net/gff3-jan04.shtml for
+/// See may2005.archive.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html
+/// for the base format and song.sorceforge.net/gff3-jan04.shtml for
/// the frame-shift extensions.
#include <objects/seqalign/Seq_align.hpp>
diff --git a/c++/include/objtools/readers/error_container.hpp b/c++/include/objtools/readers/error_container.hpp
index fcb397c..bbb3c6e 100644
--- a/c++/include/objtools/readers/error_container.hpp
+++ b/c++/include/objtools/readers/error_container.hpp
@@ -1,4 +1,4 @@
-/* $Id: error_container.hpp 407683 2013-07-23 18:14:31Z kornbluh $
+/* $Id: error_container.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -44,7 +44,7 @@ BEGIN_SCOPE(objects) // namespace ncbi::objects::
// be used because old files might have forward declarations
// like "class IErrorContainer;" that would conflict with a typedef.
-class NCBI_DEPRECATED IErrorContainer : public IMessageListener { };
+class NCBI_DEPRECATED IErrorContainer : public ILineErrorListener { };
class NCBI_DEPRECATED CErrorContainerBase : public CMessageListenerBase { };
class NCBI_DEPRECATED CErrorContainerLenient : public CMessageListenerLenient { };
class NCBI_DEPRECATED CErrorContainerStrict : public CMessageListenerStrict { };
diff --git a/c++/include/objtools/readers/fasta.hpp b/c++/include/objtools/readers/fasta.hpp
index 35c476f..c6bdf59 100644
--- a/c++/include/objtools/readers/fasta.hpp
+++ b/c++/include/objtools/readers/fasta.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS___FASTA__HPP
#define OBJTOOLS_READERS___FASTA__HPP
-/* $Id: fasta.hpp 458373 2015-02-04 15:32:20Z ivanov $
+/* $Id: fasta.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -64,7 +64,7 @@ class CSeq_loc;
class CSeqIdGenerator;
-class IMessageListener;
+class ILineErrorListener;
/// Base class for reading FASTA sequences.
///
@@ -117,24 +117,24 @@ public:
virtual ~CFastaReader(void);
/// CReaderBase overrides
- virtual CRef<CSerialObject> ReadObject (ILineReader &lr, IMessageListener *pErrors);
- virtual CRef<CSeq_entry> ReadSeqEntry (ILineReader &lr, IMessageListener *pErrors);
+ virtual CRef<CSerialObject> ReadObject (ILineReader &lr, ILineErrorListener *pErrors);
+ virtual CRef<CSeq_entry> ReadSeqEntry (ILineReader &lr, ILineErrorListener *pErrors);
/// Indicates (negatively) whether there is any more input.
bool AtEOF(void) const { return m_LineReader->AtEOF(); }
/// Read a single effective sequence, which may turn out to be a
/// segmented set.
- virtual CRef<CSeq_entry> ReadOneSeq(IMessageListener * pMessageListener = 0);
+ virtual CRef<CSeq_entry> ReadOneSeq(ILineErrorListener * pMessageListener = 0);
/// Read multiple sequences (by default, as many as are available.)
- CRef<CSeq_entry> ReadSet(int max_seqs = kMax_Int, IMessageListener * pMessageListener = 0);
+ CRef<CSeq_entry> ReadSet(int max_seqs = kMax_Int, ILineErrorListener * pMessageListener = 0);
/// Read as many sequences as are available, and interpret them as
/// an alignment, with hyphens marking relative deletions.
/// @param reference_row
/// 0-based; the special value -1 yields a full (pseudo-?)N-way alignment.
- CRef<CSeq_entry> ReadAlignedSet(int reference_row, IMessageListener * pMessageListener = 0);
+ CRef<CSeq_entry> ReadAlignedSet(int reference_row, ILineErrorListener * pMessageListener = 0);
// also allow changing?
TFlags GetFlags(void) const { return m_Flags.top(); }
@@ -219,7 +219,7 @@ public:
static string CanonicalizeString(const CTempString & sValue);
void SetMinGaps(TSeqPos gapNmin, TSeqPos gap_Unknown_length);
- void SetGapLinkageEvidence(CSeq_gap::EType type, CLinkage_evidence::EType evidence);
+ void SetGapLinkageEvidences(CSeq_gap::EType type, const set<int>& evidences);
void IgnoreProblem(ILineError::EProblem problem);
@@ -241,27 +241,27 @@ protected:
TSeqPos m_iLineNum;
};
- virtual CRef<CSeq_entry> x_ReadSegSet(IMessageListener * pMessageListener);
+ virtual CRef<CSeq_entry> x_ReadSegSet(ILineErrorListener * pMessageListener);
- virtual void ParseDefLine (const TStr& s, IMessageListener * pMessageListener);
- virtual bool ParseIDs (const TStr& s, IMessageListener * pMessageListener);
- virtual size_t ParseRange (const TStr& s, TSeqPos& start, TSeqPos& end, IMessageListener * pMessageListener);
- virtual void ParseTitle (const SLineTextAndLoc & lineInfo, IMessageListener * pMessageListener);
+ virtual void ParseDefLine (const TStr& s, ILineErrorListener * pMessageListener);
+ virtual bool ParseIDs (const TStr& s, ILineErrorListener * pMessageListener);
+ virtual size_t ParseRange (const TStr& s, TSeqPos& start, TSeqPos& end, ILineErrorListener * pMessageListener);
+ virtual void ParseTitle (const SLineTextAndLoc & lineInfo, ILineErrorListener * pMessageListener);
virtual bool IsValidLocalID(const TStr& s);
virtual void GenerateID (void);
- virtual void ParseDataLine (const TStr& s, IMessageListener * pMessageListener);
- virtual void CheckDataLine (const TStr& s, IMessageListener * pMessageListener);
- virtual void x_CloseGap (TSeqPos len, bool atStartOfLine, IMessageListener * pMessageListener);
+ virtual void ParseDataLine (const TStr& s, ILineErrorListener * pMessageListener);
+ virtual void CheckDataLine (const TStr& s, ILineErrorListener * pMessageListener);
+ virtual void x_CloseGap (TSeqPos len, bool atStartOfLine, ILineErrorListener * pMessageListener);
virtual void x_OpenMask (void);
virtual void x_CloseMask (void);
- virtual bool ParseGapLine (const TStr& s, IMessageListener * pMessageListener);
- virtual void AssembleSeq (IMessageListener * pMessageListener);
- virtual void AssignMolType (IMessageListener * pMessageListener);
+ virtual bool ParseGapLine (const TStr& s, ILineErrorListener * pMessageListener);
+ virtual void AssembleSeq (ILineErrorListener * pMessageListener);
+ virtual void AssignMolType (ILineErrorListener * pMessageListener);
virtual bool CreateWarningsForSeqDataInTitle(
const TStr& sLineText,
TSeqPos iLineNum,
- IMessageListener * pMessageListener);
- virtual void PostWarning(IMessageListener * pMessageListener,
+ ILineErrorListener * pMessageListener);
+ virtual void PostWarning(ILineErrorListener * pMessageListener,
EDiagSev _eSeverity, size_t _uLineNum, CTempString _MessageStrmOps,
CObjReaderParseException::EErrCode _eErrCode,
ILineError::EProblem _eProblem,
@@ -273,13 +273,13 @@ protected:
typedef map<TSeqPos, TSubMap> TStartsMap;
typedef vector<CRef<CSeq_id> > TIds;
- CRef<CSeq_entry> x_ReadSeqsToAlign(TIds& ids, IMessageListener * pMessageListener);
+ CRef<CSeq_entry> x_ReadSeqsToAlign(TIds& ids, ILineErrorListener * pMessageListener);
void x_AddPairwiseAlignments(CSeq_annot& annot, const TIds& ids,
TRowNum reference_row);
void x_AddMultiwayAlignment(CSeq_annot& annot, const TIds& ids);
// inline utilities
- void CloseGap(bool atStartOfLine=true, IMessageListener * pMessageListener = 0);
+ void CloseGap(bool atStartOfLine=true, ILineErrorListener * pMessageListener = 0);
void OpenMask(void);
void CloseMask(void)
{ if (m_MaskRangeStart != kInvalidSeqPos) { x_CloseMask(); } }
@@ -306,7 +306,7 @@ protected:
TSeqPos GetCurrentPos(EPosType pos_type);
void x_ApplyAllMods( CBioseq & bioseq, TSeqPos iLineNum,
- IMessageListener * pMessageListener );
+ ILineErrorListener * pMessageListener );
std::string x_NucOrProt(void) const;
@@ -442,7 +442,7 @@ NCBI_XOBJREAD_EXPORT
CRef<CSeq_entry> ReadFasta(CNcbiIstream& in, TReadFastaFlags flags = 0,
int* counter = 0,
vector<CConstRef<CSeq_loc> >* lcv = 0,
- IMessageListener * pMessageListener = 0);
+ ILineErrorListener * pMessageListener = 0);
//////////////////////////////////////////////////////////////////
//
diff --git a/c++/include/objtools/readers/gff2_data.hpp b/c++/include/objtools/readers/gff2_data.hpp
index 30fb1e0..ce6b918 100644
--- a/c++/include/objtools/readers/gff2_data.hpp
+++ b/c++/include/objtools/readers/gff2_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: gff2_data.hpp 455914 2015-01-06 13:06:39Z ivanov $
+/* $Id: gff2_data.hpp 479671 2015-09-22 18:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,7 +50,8 @@ public:
CGff2Record();
virtual ~CGff2Record();
- static string NextId();
+ static unsigned int NextId();
+ static void ResetId();
//
// Input/output:
@@ -61,7 +62,7 @@ public:
//
// Accessors:
//
- string Id() const {
+ const string& Id() const {
return m_strId;
};
size_t SeqStart() const {
@@ -70,10 +71,10 @@ public:
size_t SeqStop() const {
return m_uSeqStop;
};
- string Source() const {
+ const string& Source() const {
return m_strSource;
};
- string Type() const {
+ const string& Type() const {
return m_strType;
};
double Score() const {
@@ -85,7 +86,7 @@ public:
TFrame Phase() const {
return IsSetPhase() ? *m_pePhase : CCdregion::eFrame_not_set;
};
- string AttributesLiteral() const {
+ const string& AttributesLiteral() const {
return m_strAttributes;
};
@@ -129,17 +130,11 @@ public:
int,
CRef<CSeq_feat> ) const;
- static void TokenizeGFF(vector<CTempString>& columns, const CTempString& line);
+ static void TokenizeGFF(vector<CTempStringEx>& columns, const CTempStringEx& line);
protected:
virtual bool x_AssignAttributesFromGff(
const string& );
- static string x_NormalizedAttributeKey(
- const string& );
-
- static string x_NormalizedAttributeValue(
- const string& );
-
bool x_SplitGffAttributes(
const string&,
vector< string >& ) const;
@@ -181,6 +176,28 @@ protected:
CRef<CSeq_feat>,
TAttributes& ) const;
+ //utility helpers:
+ //
+ static string xNormalizedAttributeKey(
+ const string&);
+
+ static string xNormalizedAttributeValue(
+ const string&);
+
+ static bool xMigrateAttributeDefault(
+ TAttributes&,
+ const string&,
+ CRef<CSeq_feat>,
+ const string&,
+ int);
+
+ static bool xMigrateAttributeSingle(
+ TAttributes&,
+ const string&,
+ CRef<CSeq_feat>,
+ const string&,
+ int);
+
//
// Data:
//
@@ -194,6 +211,7 @@ protected:
TFrame* m_pePhase;
string m_strAttributes;
TAttributes m_Attributes;
+ static unsigned int m_nextId;
};
END_objects_SCOPE
diff --git a/c++/include/objtools/readers/gff2_reader.hpp b/c++/include/objtools/readers/gff2_reader.hpp
index d8c64f6..7bca942 100644
--- a/c++/include/objtools/readers/gff2_reader.hpp
+++ b/c++/include/objtools/readers/gff2_reader.hpp
@@ -1,4 +1,4 @@
- /* $Id: gff2_reader.hpp 464926 2015-04-15 15:01:49Z ivanov $
+ /* $Id: gff2_reader.hpp 479677 2015-09-22 18:46:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -64,12 +64,9 @@ public:
fRetainLocusIds = 0x4000,
} TFlags;
- typedef map< string, CRef< CSeq_feat > > IdToFeatureMap;
-
+ typedef map<string, CRef<CSeq_feat> > IdToFeatureMap;
+
public:
- typedef vector< CRef< CSeq_annot > > TAnnots;
- typedef TAnnots::iterator TAnnotIt;
- typedef TAnnots::const_iterator TAnnotCit;
//
// object management:
@@ -92,30 +89,30 @@ public:
CRef< CSeq_entry >
ReadSeqEntry(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual CRef< CSerialObject >
ReadObject(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual void
ReadSeqAnnots(
- TAnnots&,
+ TAnnotList&,
CNcbiIstream&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual void
ReadSeqAnnots(
- TAnnots&,
+ TAnnotList&,
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual void
ReadSeqAnnotsNew(
TAnnots&,
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
//
// class interface:
@@ -142,26 +139,26 @@ public:
virtual bool x_ParseDataGff(
const string&,
TAnnots&,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool x_ParseFeatureGff(
const string&,
TAnnots&,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool x_ParseAlignmentGff(
const string&,
- TAnnots& );
+ TAnnots&);
virtual bool x_InitAnnot(
const CGff2Record&,
CRef< CSeq_annot >,
- IMessageListener* =0);
+ ILineErrorListener* =0);
virtual bool x_UpdateAnnotFeature(
const CGff2Record&,
CRef< CSeq_annot >,
- IMessageListener* =0);
+ ILineErrorListener* =0);
virtual bool x_UpdateAnnotAlignment(
const CGff2Record&,
@@ -249,6 +246,8 @@ public:
virtual bool xAnnotPostProcess(
CRef<CSeq_annot>);
+ virtual bool xGenerateParentChildXrefs(
+ CRef<CSeq_annot>);
bool xAlignmentSetSegment(
const CGff2Record&,
@@ -289,15 +288,22 @@ protected:
CSeq_feat& feat,
const SRecord& );
- static bool s_GetAnnotId(
- const CSeq_annot&,
- string& );
+ static const string* s_GetAnnotId(
+ const CSeq_annot&);
+
+ void xSetAncestryLine(
+ CSeq_feat&,
+ const string&);
+
+ void xSetAncestorXrefs(
+ CSeq_feat&,
+ CSeq_feat&);
// data:
//
protected:
// TFlags m_iFlags;
- IMessageListener* m_pErrors;
+ ILineErrorListener* m_pErrors;
CRef<CAnnotdesc> m_CurrentTrackInfo;
CRef<CAnnotdesc> m_CurrentBrowserInfo;
};
diff --git a/c++/include/objtools/readers/gff3_reader.hpp b/c++/include/objtools/readers/gff3_reader.hpp
index bb5c798..b7f5b8c 100644
--- a/c++/include/objtools/readers/gff3_reader.hpp
+++ b/c++/include/objtools/readers/gff3_reader.hpp
@@ -1,4 +1,4 @@
- /* $Id: gff3_reader.hpp 455916 2015-01-06 13:07:49Z ivanov $
+ /* $Id: gff3_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -93,7 +93,7 @@ protected:
virtual bool x_UpdateAnnotFeature(
const CGff2Record&,
CRef< CSeq_annot >,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool x_UpdateFeatureCds(
const CGff2Record&,
@@ -107,31 +107,31 @@ protected:
const CGff2Record&,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xUpdateAnnotCds(
const CGff2Record&,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xUpdateAnnotGene(
const CGff2Record&,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xUpdateAnnotGeneric(
const CGff2Record&,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xUpdateAnnotMrna(
const CGff2Record&,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xVerifyCdsParents(
const CGff2Record&);
@@ -148,8 +148,14 @@ protected:
string xNextGenericId();
+ void xVerifyExonLocation(
+ const string&,
+ const CGff2Record&,
+ ILineErrorListener*);
+
// Data:
map<string, string> mCdsParentMap;
+ map<string, CRef<CSeq_interval> > mMrnaLocs;
static unsigned int msGenericIdCounter;
};
diff --git a/c++/include/objtools/readers/gff_reader.hpp b/c++/include/objtools/readers/gff_reader.hpp
index 04b8330..1eaf505 100644
--- a/c++/include/objtools/readers/gff_reader.hpp
+++ b/c++/include/objtools/readers/gff_reader.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS___GFF_READER__HPP
#define OBJTOOLS_READERS___GFF_READER__HPP
-/* $Id: gff_reader.hpp 332573 2011-08-29 13:53:51Z ludwigf $
+/* $Id: gff_reader.hpp 466910 2015-05-07 14:26:38Z foleyjp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,9 +37,9 @@
/// heavy use-specific tuning, both via flags and via virtual methods.
///
/// URLs to relevant specifications:
-/// http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml (GFF 2)
-/// http://genes.cs.wustl.edu/GTF2.html
-/// http://song.sourceforge.net/gff3-jan04.shtml (support incomplete)
+/// www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml (GFF 2)
+/// genes.cs.wustl.edu/GTF2.html
+/// song.sourceforge.net/gff3-jan04.shtml (support incomplete)
#include <corelib/ncbiutil.hpp>
diff --git a/c++/include/objtools/readers/gtf_reader.hpp b/c++/include/objtools/readers/gtf_reader.hpp
index d30fe19..7bc9bfe 100644
--- a/c++/include/objtools/readers/gtf_reader.hpp
+++ b/c++/include/objtools/readers/gtf_reader.hpp
@@ -1,4 +1,4 @@
- /* $Id: gtf_reader.hpp 448857 2014-10-09 16:31:19Z ivanov $
+ /* $Id: gtf_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -72,13 +72,13 @@ public:
ReadSeqAnnots(
TAnnots&,
CNcbiIstream&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual void
ReadSeqAnnots(
TAnnots&,
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
protected:
virtual CGff2Record* x_CreateRecord() { return new CGtfReadRecord(); };
@@ -86,7 +86,7 @@ protected:
virtual bool x_UpdateAnnotFeature(
const CGff2Record&,
CRef< CSeq_annot >,
- IMessageListener* =0);
+ ILineErrorListener* =0);
virtual bool x_UpdateAnnotCds(
const CGff2Record&,
diff --git a/c++/include/objtools/readers/gvf_reader.hpp b/c++/include/objtools/readers/gvf_reader.hpp
index dc52040..9af603d 100644
--- a/c++/include/objtools/readers/gvf_reader.hpp
+++ b/c++/include/objtools/readers/gvf_reader.hpp
@@ -1,4 +1,4 @@
- /* $Id: gvf_reader.hpp 411995 2013-09-04 12:36:33Z ludwigf $
+ /* $Id: gvf_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,7 +58,7 @@ class CGvfReadRecord
public:
CGvfReadRecord(
unsigned int lineNumber,
- IMessageListener* pEC = 0):
+ ILineErrorListener* pEC = 0):
mLineNumber(lineNumber),
mpMessageListener(pEC)
{};
@@ -77,7 +77,7 @@ protected:
const string&);
unsigned int mLineNumber;
- IMessageListener* mpMessageListener;
+ ILineErrorListener* mpMessageListener;
};
// ----------------------------------------------------------------------------
@@ -101,7 +101,7 @@ protected:
virtual bool x_ParseFeatureGff(
const string&,
TAnnots&,
- IMessageListener*);
+ ILineErrorListener*);
CRef<CSeq_annot> x_GetAnnotById(
TAnnots& annots,
@@ -110,7 +110,7 @@ protected:
virtual bool x_MergeRecord(
const CGvfReadRecord&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
bool x_FeatureSetLocation(
const CGff2Record&,
@@ -131,7 +131,7 @@ protected:
virtual bool x_FeatureSetExt(
const CGvfReadRecord&,
CRef<CSeq_feat>,
- IMessageListener*);
+ ILineErrorListener*);
bool xVariationMakeSNV(
const CGvfReadRecord&,
diff --git a/c++/include/objtools/readers/idmapper.hpp b/c++/include/objtools/readers/idmapper.hpp
index 9a05b4c..4ee35f5 100644
--- a/c++/include/objtools/readers/idmapper.hpp
+++ b/c++/include/objtools/readers/idmapper.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_IDMAPPER___IDMAPPER_IMPL__HPP
#define OBJTOOLS_IDMAPPER___IDMAPPER_IMPL__HPP
-/* $Id: idmapper.hpp 432036 2014-04-09 17:27:03Z grichenk $
+/* $Id: idmapper.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
*/
#include <corelib/ncbistd.hpp>
+#include <corelib/ncbicntr.hpp>
#include <objtools/readers/iidmapper.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/scope.hpp>
@@ -68,7 +69,7 @@ public:
/// mapping errors result in exceptions that need to be handled.
CIdMapper(const std::string& strContext = "",
bool bInvert = false,
- IMessageListener* pErrors = 0 );
+ ILineErrorListener* pErrors = 0 );
virtual ~CIdMapper() {};
@@ -115,7 +116,7 @@ protected:
typedef std::map<CSeq_id_Handle, SMapper> TMapperCache;
TMapperCache m_Cache;
- IMessageListener* m_pErrors;
+ ILineErrorListener* m_pErrors;
};
@@ -147,7 +148,7 @@ public:
virtual CRef<CSeq_loc> Map(const CSeq_loc& loc);
private:
- typedef int TOrder;
+ typedef CAtomicCounter::TValue TOrder;
struct SNode {
typedef CIdMapperComposite::TPriority TPriority;
typedef CIdMapperComposite::TOrder TOrder;
@@ -155,7 +156,7 @@ private:
AutoPtr<IIdMapper> m_Mapper;
TPriority m_Priority;
TOrder m_Order;
- static CAtomicCounter_WithAutoInit sm_Counter;
+ static CAtomicCounter sm_Counter;
SNode(IIdMapper* mapper, TPriority priority, EOwnership ownership)
: m_Mapper(mapper, ownership),
@@ -241,11 +242,11 @@ public:
CIdMapperConfig(CNcbiIstream& istr,
const std::string& strContext = "",
bool bInvert = false,
- IMessageListener* pErrors = 0);
+ ILineErrorListener* pErrors = 0);
CIdMapperConfig(const std::string& strContext = "",
bool bInvert = false,
- IMessageListener* pErrors = 0);
+ ILineErrorListener* pErrors = 0);
void Initialize(CNcbiIstream& istr);
static void DescribeContexts(CNcbiIstream& istr,
@@ -287,7 +288,7 @@ public:
/// mapping errors result in exceptions that need to be handled.
CIdMapperBuiltin(const std::string& strContext,
bool bInvert = false,
- IMessageListener* pErrors = 0 );
+ ILineErrorListener* pErrors = 0 );
void Initialize();
@@ -325,7 +326,7 @@ public:
const std::string& strDatabase,
const std::string& strContext,
bool bInvert = false,
- IMessageListener* pErrors = 0)
+ ILineErrorListener* pErrors = 0)
: CIdMapper(strContext, bInvert, pErrors),
m_strServer(strServer),
m_strDatabase(strDatabase)
diff --git a/c++/include/objtools/readers/line_error.hpp b/c++/include/objtools/readers/line_error.hpp
index 21f9e8b..732ea89 100644
--- a/c++/include/objtools/readers/line_error.hpp
+++ b/c++/include/objtools/readers/line_error.hpp
@@ -1,4 +1,4 @@
-/* $Id: line_error.hpp 462246 2015-03-17 15:18:38Z ivanov $
+/* $Id: line_error.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,6 +36,7 @@
#include <corelib/ncbistd.hpp>
#include <corelib/ncbimisc.hpp>
#include <corelib/ncbiobj.hpp>
+#include <corelib/ncbi_message.hpp>
#include <objtools/readers/reader_exception.hpp>
@@ -44,7 +45,7 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects) // namespace ncbi::objects::
// ============================================================================
-class NCBI_XOBJUTIL_EXPORT ILineError
+class NCBI_XOBJUTIL_EXPORT ILineError : public IMessage
// ============================================================================
{
public:
@@ -113,9 +114,6 @@ public:
virtual EProblem
Problem(void) const = 0;
- virtual EDiagSev
- Severity(void) const =0;
-
virtual const std::string &
SeqId(void) const = 0;
@@ -163,24 +161,11 @@ public:
std::string
SeverityStr(void) const
{
- switch ( Severity() ) {
- default:
- return "Unknown";
- case eDiag_Info:
- return "Info";
- case eDiag_Warning:
- return "Warning";
- case eDiag_Error:
- return "Error";
- case eDiag_Critical:
- return "Critical";
- case eDiag_Fatal:
- return "Fatal";
- }
+ return CNcbiDiag::SeverityName(Severity());
};
virtual const std::string&
- ErrorMessage(void) const {
+ ErrorMessage(void) const {
static string empty("");
return empty;
}
@@ -342,8 +327,26 @@ public:
out << "</message>" << endl;
};
+
+ // IMessage methods - default implementations or wrappers for ILineError
+ // methods (for backward compatibility).
+ virtual string GetText(void) const { return Message(); }
+ virtual EDiagSev GetSeverity(void) const { return Severity(); }
+ virtual int GetCode(void) const { return 0; }
+ virtual int GetSubCode(void) const { return 0; }
+ virtual void Write(CNcbiOstream& out) const { Dump(out); }
+ virtual std::string Compose(void) const
+ {
+ CNcbiOstrstream out;
+ Write(out);
+ return CNcbiOstrstreamToString(out);
+ }
+
+ // This is required to disambiguate IMessage::GetSeverity() and
+ // CException::GetSeverity() in CObjReaderLineException
+ virtual EDiagSev Severity(void) const { return eDiag_Error; }
};
-
+
// ============================================================================
class NCBI_XOBJUTIL_EXPORT CLineError:
// ============================================================================
@@ -387,7 +390,7 @@ public:
EProblem
Problem(void) const { return m_eProblem; }
- EDiagSev
+ virtual EDiagSev
Severity(void) const { return m_eSeverity; }
const std::string &
@@ -494,7 +497,7 @@ public:
EProblem Problem(void) const { return m_eProblem; }
const std::string &SeqId(void) const { return m_strSeqId; }
- EDiagSev Severity(void) const { return GetSeverity(); }
+ EDiagSev Severity(void) const { return CObjReaderParseException::GetSeverity(); }
unsigned int Line(void) const { return m_uLineNumber; }
const TVecOfLines & OtherLines(void) const { return m_vecOfOtherLines; }
const std::string &FeatureName(void) const { return m_strFeatureName; }
diff --git a/c++/include/objtools/readers/message_listener.hpp b/c++/include/objtools/readers/message_listener.hpp
index 1fa35cb..d3f7b4f 100644
--- a/c++/include/objtools/readers/message_listener.hpp
+++ b/c++/include/objtools/readers/message_listener.hpp
@@ -1,4 +1,4 @@
-/* $Id: message_listener.hpp 446718 2014-09-17 17:39:48Z ivanov $
+/* $Id: message_listener.hpp 477855 2015-09-02 13:14:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -35,6 +35,7 @@
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
+#include <corelib/ncbi_message.hpp>
#include <objtools/readers/line_error.hpp>
BEGIN_NCBI_SCOPE
@@ -42,11 +43,20 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects) // namespace ncbi::objects::
// ============================================================================
-class IMessageListener
+class ILineErrorListener : public ncbi::IMessageListener
// ============================================================================
{
public:
- virtual ~IMessageListener() {}
+ virtual ~ILineErrorListener() {}
+
+ // IListener::Post() implementation
+ virtual void Post(const IMessage& message)
+ {
+ const ILineError* le = dynamic_cast<const ILineError*>(&message);
+ if (!le) return;
+ PutError(*le);
+ }
+
/// Store error in the container, and
/// return true if error was stored fine, and
/// return false if the caller should terminate all further processing.
@@ -55,36 +65,65 @@ public:
PutError(
const ILineError& ) = 0;
+ // IListener::Get() implementation
+ virtual const IMessage& Get(size_t index) const
+ { return const_cast<ILineErrorListener*>(this)->GetError(index); }
+
/// 0-based error retrieval.
virtual const ILineError&
GetError(
size_t ) =0;
-
- /// Return number of errors seen so far.
- virtual size_t
- Count() const =0;
-
+
+ virtual size_t Count(void) const = 0;
+
/// Returns the number of errors seen so far at the given severity.
virtual size_t
LevelCount(
EDiagSev ) =0;
-
+
/// Clear all accumulated messages.
virtual void
ClearAll() =0;
+ // IListener::Progress() implementation
+ virtual void Progress(const string& message,
+ Uint8 current,
+ Uint8 total) { PutProgress(message, current, total); }
+
/// This is used for processing progress messages.
virtual void
PutProgress(
const string & sMessage,
const Uint8 iNumDone = 0,
const Uint8 iNumTotal = 0 ) = 0;
+
+ // IMessageListener proxy methods
+ virtual EPostResult PostMessage(const IMessage& message)
+ { Post(message); return eHandled; }
+
+ virtual EPostResult PostProgress(const IProgressMessage& p)
+ { Progress(p.GetText(), p.GetCurrent(), p.GetTotal()); return eHandled; }
+
+ virtual const IMessage& GetMessage(size_t index) const
+ { return Get(index); }
+
+ virtual void Clear(void)
+ { ClearAll(); }
};
-
+
+
+// Compatibility declaration, avoid using objects::IMessageListener -
+// use ncbi::IMessageListener or objects::ILineErrorListener instead.
+class IMessageListener : public ILineErrorListener
+{
+public:
+ virtual ~IMessageListener(void) {}
+};
+
+
// ============================================================================
-class NCBI_XOBJREAD_EXPORT CMessageListenerBase:
+class NCBI_XOBJREAD_EXPORT CMessageListenerBase : public objects::IMessageListener
// ============================================================================
- public CObject, public IMessageListener
{
public:
CMessageListenerBase() : m_pProgressOstrm(0) {};
diff --git a/c++/include/objtools/readers/microarray_reader.hpp b/c++/include/objtools/readers/microarray_reader.hpp
index c7218f1..49198b3 100644
--- a/c++/include/objtools/readers/microarray_reader.hpp
+++ b/c++/include/objtools/readers/microarray_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: microarray_reader.hpp 448857 2014-10-09 16:31:19Z ivanov $
+/* $Id: microarray_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,12 +68,12 @@ public:
virtual CRef< CSeq_annot >
ReadSeqAnnot(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual CRef< CSerialObject >
ReadObject(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
//
// helpers:
@@ -81,12 +81,12 @@ public:
protected:
virtual bool xParseTrackLine(
const string&,
- IMessageListener*);
+ ILineErrorListener*);
bool xParseFeature(
const vector<string>&,
CRef<CSeq_annot>&,
- IMessageListener*);
+ ILineErrorListener*);
void xSetFeatureLocation(
CRef<CSeq_feat>&,
diff --git a/c++/include/objtools/readers/read_util.hpp b/c++/include/objtools/readers/read_util.hpp
index 4a6acd1..2a3d159 100644
--- a/c++/include/objtools/readers/read_util.hpp
+++ b/c++/include/objtools/readers/read_util.hpp
@@ -1,4 +1,4 @@
-/* $Id: read_util.hpp 443181 2014-08-12 12:25:37Z mcelhany $
+/* $Id: read_util.hpp 441881 2014-07-29 11:14:26Z ludwigf $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/readers/reader_base.hpp b/c++/include/objtools/readers/reader_base.hpp
index b87f838..4946cc1 100644
--- a/c++/include/objtools/readers/reader_base.hpp
+++ b/c++/include/objtools/readers/reader_base.hpp
@@ -1,4 +1,4 @@
-/* $Id: reader_base.hpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: reader_base.hpp 479677 2015-09-22 18:46:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,7 +45,7 @@ BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
class CSeq_entry;
-class IMessageListener;
+class ILineErrorListener;
class CObjReaderLineException;
class CTrackData;
@@ -77,6 +77,10 @@ public:
OT_SEQANNOT,
OT_SEQENTRY
};
+ typedef list< CRef< CSeq_annot > > TAnnotList;
+ typedef TAnnotList TAnnots;
+ typedef TAnnots::iterator TAnnotIt;
+ typedef TAnnots::const_iterator TAnnotCit;
protected:
/// Protected constructor. Use GetReader() to get an actual reader object.
@@ -110,7 +114,7 @@ public:
virtual CRef< CSerialObject >
ReadObject(
CNcbiIstream& istr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read an object from a given line reader, render it as the most
/// appropriate Genbank object.
@@ -125,7 +129,7 @@ public:
virtual CRef< CSerialObject >
ReadObject(
ILineReader& lr,
- IMessageListener* pErrors=0 ) =0;
+ ILineErrorListener* pErrors=0 ) =0;
/// Read an object from a given input stream, render it as a single
/// Seq-annot. Return empty Seq-annot otherwise.
@@ -137,7 +141,7 @@ public:
virtual CRef< CSeq_annot >
ReadSeqAnnot(
CNcbiIstream& istr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read an object from a given line reader, render it as a single
/// Seq-annot, if possible. Return empty Seq-annot otherwise.
@@ -149,7 +153,7 @@ public:
virtual CRef< CSeq_annot >
ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read all objects from given insput stream, returning them as a vector of
/// Seq-annots.
@@ -162,9 +166,9 @@ public:
///
virtual void
ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
CNcbiIstream& istr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read all objects from given insput stream, returning them as a vector of
/// Seq-annots.
@@ -177,9 +181,9 @@ public:
///
virtual void
ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
ILineReader& lr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read an object from a given input stream, render it as a single
/// Seq-entry, if possible. Return empty Seq-entry otherwise.
@@ -191,7 +195,7 @@ public:
virtual CRef< CSeq_entry >
ReadSeqEntry(
CNcbiIstream& istr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
/// Read an object from a given line reader, render it as a single
/// Seq-entry, if possible. Return empty Seq-entry otherwise.
@@ -203,7 +207,7 @@ public:
virtual CRef< CSeq_entry >
ReadSeqEntry(
ILineReader& lr,
- IMessageListener* pErrors=0 );
+ ILineErrorListener* pErrors=0 );
void
SetProgressReportInterval(
@@ -239,20 +243,20 @@ protected:
virtual bool xParseBrowserLine(
const string&,
CRef<CSeq_annot>&,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xParseTrackLine(
const string&,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool xParseBrowserLine(
const string&,
- IMessageListener*);
+ ILineErrorListener*);
virtual void xSetBrowserRegion(
const string&,
CAnnot_descr&,
- IMessageListener*);
+ ILineErrorListener*);
virtual void xSetTrackData(
CRef<CSeq_annot>&,
@@ -262,14 +266,14 @@ protected:
virtual void xAddConversionInfo(
CRef< CSeq_annot >&,
- IMessageListener* );
+ ILineErrorListener* );
virtual void xAddConversionInfo(
CRef< CSeq_entry >&,
- IMessageListener*);
+ ILineErrorListener*);
virtual CRef<CUser_object> xMakeAsnConversionInfo(
- IMessageListener*);
+ ILineErrorListener*);
bool xParseComment(
const CTempString&,
@@ -281,7 +285,7 @@ protected:
ILineReader& istr);
void xReportProgress(
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
bool xIsReportingProgress() const;
@@ -291,22 +295,22 @@ protected:
void
ProcessError(
CObjReaderLineException&,
- IMessageListener* );
+ ILineErrorListener* );
void
ProcessError(
CLineError&,
- IMessageListener* );
+ ILineErrorListener* );
void
ProcessWarning(
CObjReaderLineException&,
- IMessageListener* );
+ ILineErrorListener* );
void
ProcessWarning(
CLineError&,
- IMessageListener* );
+ ILineErrorListener* );
//
// Data:
diff --git a/c++/include/objtools/readers/readfeat.hpp b/c++/include/objtools/readers/readfeat.hpp
index 2915663..cf8ec34 100644
--- a/c++/include/objtools/readers/readfeat.hpp
+++ b/c++/include/objtools/readers/readfeat.hpp
@@ -49,7 +49,7 @@ BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
class CFeature_table_reader_imp;
-class IMessageListener;
+class ILineErrorListener;
class ITableFilter;
class CSeq_entry;
@@ -75,32 +75,32 @@ public:
CFeature_table_reader(TReaderFlags fReaderFlags = 0);
// For CReaderBase
- CRef<CSerialObject> ReadObject (ILineReader &lr, IMessageListener *pErrors);
- CRef<CSeq_annot> ReadSeqAnnot (ILineReader &lr, IMessageListener *pErrors);
+ CRef<CSerialObject> ReadObject (ILineReader &lr, ILineErrorListener *pErrors);
+ CRef<CSeq_annot> ReadSeqAnnot (ILineReader &lr, ILineErrorListener *pErrors);
// read 5-column feature table and return Seq-annot
static CRef<CSeq_annot> ReadSequinFeatureTable(ILineReader& reader,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
static CRef<CSeq_annot> ReadSequinFeatureTable (CNcbiIstream& ifs,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
static CRef<CSeq_annot> ReadSequinFeatureTable (ILineReader& reader,
const string& seqid,
const string& annotname,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
static CRef<CSeq_annot> ReadSequinFeatureTable (CNcbiIstream& ifs,
const string& seqid,
const string& annotname,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
// read all feature tables available from the input, attaching each
@@ -108,20 +108,20 @@ public:
static void ReadSequinFeatureTables(ILineReader& reader,
CSeq_entry& entry,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
static void ReadSequinFeatureTables(CNcbiIstream& ifs,
CSeq_entry& entry,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
ITableFilter *filter = 0);
// create single feature from key
static CRef<CSeq_feat> CreateSeqFeat (const string& feat,
CSeq_loc& location,
const TFlags flags = 0,
- IMessageListener* pMessageListener = 0,
+ ILineErrorListener* pMessageListener = 0,
unsigned int line = 0,
std::string *seq_id = 0,
ITableFilter *filter = 0);
@@ -132,7 +132,7 @@ public:
const string& qual,
const string& val,
const TFlags flags = 0,
- IMessageListener* pMessageListener=0,
+ ILineErrorListener* pMessageListener=0,
int line = 0,
const string &seq_id = std::string() );
diff --git a/c++/include/objtools/readers/rm_reader.hpp b/c++/include/objtools/readers/rm_reader.hpp
index b53e149..3a852a6 100644
--- a/c++/include/objtools/readers/rm_reader.hpp
+++ b/c++/include/objtools/readers/rm_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: rm_reader.hpp 407582 2013-07-23 11:15:22Z kornbluh $
+/* $Id: rm_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -708,13 +708,13 @@ public:
CRef<CSerialObject>
ReadObject(ILineReader& lr,
- IMessageListener* pMessageListener = 0);
+ ILineErrorListener* pMessageListener = 0);
using CReaderBase::ReadSeqAnnot;
CRef<CSeq_annot>
ReadSeqAnnot(ILineReader& lr,
- IMessageListener* pMessageListener = 0);
+ ILineErrorListener* pMessageListener = 0);
/// Use default Seq-id resolution.
///
@@ -821,19 +821,19 @@ END_NCBI_SCOPE
@see https://sp.ncbi.nlm.nih.gov/IEB/mss/Gpipe/RepeatDb/RepeatMasker%20and%20GPipe.docx
for official requirements specifications
- @see http://jira.be-md.ncbi.nlm.nih.gov/browse/GP-1000
+ @see jira.be-md.ncbi.nlm.nih.gov/browse/GP-1000
for developer discussion.
- @see http://www.repeatmasker.org/ for RepeatMasker.
- @see http://www.repeatmasker.org/webrepeatmaskerhelp.html#reading
+ @see www.repeatmasker.org/ for RepeatMasker.
+ @see www.repeatmasker.org/webrepeatmaskerhelp.html#reading
for RepeatMasker file format specifications.
- @see http://www.girinst.org/repbase/update/index.html
+ @see www.girinst.org/repbase/update/index.html
for examples of EMBL format for RepBase repeat libraries.
- @see http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4
+ @see www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4
for EMBL file format specifications, as used by
the RepeatMaskerLib.embl repeat library.
- @see http://www.ebi.ac.uk/ena/WebFeat/repeat_region_s.html
+ @see www.ebi.ac.uk/ena/WebFeat/repeat_region_s.html
for INSDC standards related to annotating repeat features.
- @see http://www.ebi.ac.uk/embl/Standards/web/repetitive.html
+ @see www.ebi.ac.uk/embl/Standards/web/repetitive.html
for examples of EMBL standards for annotating repeat features.
*/
diff --git a/c++/include/objtools/readers/source_mod_parser.hpp b/c++/include/objtools/readers/source_mod_parser.hpp
index cb715f6..f0a82a5 100644
--- a/c++/include/objtools/readers/source_mod_parser.hpp
+++ b/c++/include/objtools/readers/source_mod_parser.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS___SOURCE_MOD_PARSER__HPP
#define OBJTOOLS_READERS___SOURCE_MOD_PARSER__HPP
-/* $Id: source_mod_parser.hpp 467194 2015-05-11 16:00:18Z ivanov $
+/* $Id: source_mod_parser.hpp 466781 2015-05-06 16:05:10Z kornbluh $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/readers/table_filter.hpp b/c++/include/objtools/readers/table_filter.hpp
index 6ad00ee..84ba7a0 100644
--- a/c++/include/objtools/readers/table_filter.hpp
+++ b/c++/include/objtools/readers/table_filter.hpp
@@ -1,4 +1,4 @@
-/* $Id: table_filter.hpp 457081 2015-01-20 16:54:57Z ivanov $
+/* $Id: table_filter.hpp 456525 2015-01-13 16:19:21Z kornbluh $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/objtools/readers/ucscregion_reader.hpp b/c++/include/objtools/readers/ucscregion_reader.hpp
index b6b4a04..83422e9 100644
--- a/c++/include/objtools/readers/ucscregion_reader.hpp
+++ b/c++/include/objtools/readers/ucscregion_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: ucscregion_reader.hpp 433069 2014-04-22 16:34:38Z gotvyans $
+/* $Id: ucscregion_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -53,11 +53,11 @@ public:
CUCSCRegionReader(unsigned int = fNormal);
virtual ~CUCSCRegionReader();
- virtual CRef<CSeq_annot> ReadSeqAnnot(ILineReader& lr, IMessageListener* pEC);
+ virtual CRef<CSeq_annot> ReadSeqAnnot(ILineReader& lr, ILineErrorListener* pEC);
virtual CRef< CSerialObject >
ReadObject(
ILineReader& lr,
- IMessageListener* pErrors=0);
+ ILineErrorListener* pErrors=0);
protected:
@@ -71,7 +71,7 @@ protected:
bool xParseFeature(
const vector<string>&,
CRef<CSeq_annot>&,
- IMessageListener*);
+ ILineErrorListener*);
};
// ----------------------------------------------------------------------------
diff --git a/c++/include/objtools/readers/vcf_reader.hpp b/c++/include/objtools/readers/vcf_reader.hpp
index 45464a4..01c7477 100644
--- a/c++/include/objtools/readers/vcf_reader.hpp
+++ b/c++/include/objtools/readers/vcf_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: vcf_reader.hpp 448858 2014-10-09 16:31:43Z ivanov $
+/* $Id: vcf_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -160,12 +160,12 @@ public:
virtual CRef< CSerialObject >
ReadObject(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual CRef< CSeq_annot >
ReadSeqAnnot(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
//
// helpers:
@@ -179,31 +179,31 @@ protected:
xProcessTrackLine(
const string&,
CRef< CSeq_annot >&,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessMetaLine(
const string&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessMetaLineInfo(
const string&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessMetaLineFilter(
const string&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessMetaLineFormat(
const string&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessHeaderLine(
@@ -214,7 +214,7 @@ protected:
xProcessDataLine(
const string&,
CRef<CSeq_annot>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xAssignVcfMeta(
@@ -269,7 +269,7 @@ protected:
xAssignVariantProps(
CVcfData&,
CRef<CSeq_feat>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessScore(
@@ -285,7 +285,7 @@ protected:
xProcessInfo(
CVcfData&,
CRef<CSeq_feat>,
- IMessageListener*);
+ ILineErrorListener*);
virtual bool
xProcessFormat(
@@ -296,12 +296,12 @@ protected:
xParseData(
const string&,
CVcfData&,
- IMessageListener* =0);
+ ILineErrorListener* =0);
virtual bool
xNormalizeData(
CVcfData&,
- IMessageListener* =0);
+ ILineErrorListener* =0);
//
// data:
diff --git a/c++/include/objtools/readers/wiggle_reader.hpp b/c++/include/objtools/readers/wiggle_reader.hpp
index 7b166af..63498b0 100644
--- a/c++/include/objtools/readers/wiggle_reader.hpp
+++ b/c++/include/objtools/readers/wiggle_reader.hpp
@@ -1,4 +1,4 @@
-/* $Id: wiggle_reader.hpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: wiggle_reader.hpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -269,18 +269,18 @@ public:
virtual CRef< CSeq_annot >
ReadSeqAnnot(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual CRef< CSerialObject >
ReadObject(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
virtual bool
ReadTrackData(
ILineReader&,
CRawWiggleTrack&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
//
// helpers:
@@ -289,60 +289,60 @@ protected:
CRef< CSeq_annot >
xReadSeqAnnotGraph(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
CRef< CSeq_annot >
xReadSeqAnnotTable(
ILineReader&,
- IMessageListener* =0 );
+ ILineErrorListener* =0 );
bool
xProcessBrowserLine(
- IMessageListener*);
+ ILineErrorListener*);
bool
xParseTrackLine(
const string&,
- IMessageListener*);
+ ILineErrorListener*);
void
xGetFixedStepInfo(
SFixedStepInfo&,
- IMessageListener*);
+ ILineErrorListener*);
void
xReadFixedStepData(
const SFixedStepInfo&,
ILineReader&,
- IMessageListener*);
+ ILineErrorListener*);
bool
xReadFixedStepDataRaw(
ILineReader&,
CRawWiggleTrack&,
- IMessageListener*);
+ ILineErrorListener*);
void
xGetVarStepInfo(
SVarStepInfo&,
- IMessageListener*);
+ ILineErrorListener*);
void
xReadVariableStepData(
const SVarStepInfo&,
ILineReader&,
- IMessageListener*);
+ ILineErrorListener*);
bool
xReadVariableStepDataRaw(
ILineReader&,
CRawWiggleTrack&,
- IMessageListener*);
+ ILineErrorListener*);
void
xReadBedLine(
const string& chrom,
- IMessageListener*);
+ ILineErrorListener*);
CRef<CSeq_annot>
xGetAnnot();
@@ -352,23 +352,23 @@ protected:
string
xGetWord(
- IMessageListener*);
+ ILineErrorListener*);
bool
xSkipWS();
string
xGetParamName(
- IMessageListener*);
+ ILineErrorListener*);
string
xGetParamValue(
- IMessageListener*);
+ ILineErrorListener*);
void
xGetPos(
TSeqPos& v,
- IMessageListener*);
+ ILineErrorListener*);
bool
xTryGetDoubleSimple(
@@ -377,17 +377,17 @@ protected:
bool
xTryGetDouble(
double& v,
- IMessageListener*);
+ ILineErrorListener*);
bool
xTryGetPos(
TSeqPos& v,
- IMessageListener*);
+ ILineErrorListener*);
void
xGetDouble(
double& v,
- IMessageListener*);
+ ILineErrorListener*);
CRef<CSeq_id>
xMakeChromId();
diff --git a/c++/include/serial/enumvalues.hpp b/c++/include/serial/enumvalues.hpp
index 9b06b47..8bd41b7 100644
--- a/c++/include/serial/enumvalues.hpp
+++ b/c++/include/serial/enumvalues.hpp
@@ -1,7 +1,7 @@
#ifndef ENUMVALUES__HPP
#define ENUMVALUES__HPP
-/* $Id: enumvalues.hpp 413810 2013-09-18 15:28:07Z gouriano $
+/* $Id: enumvalues.hpp 471532 2015-06-29 11:41:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,6 +55,12 @@ public:
typedef map<CTempString, TEnumValueType, PQuickStringLess> TNameToValue;
typedef map<TEnumValueType, const string*> TValueToName;
+ enum EValueFlags {
+ eNone = 0,
+ eHideName = 1
+ };
+ typedef unsigned int TValueFlags; ///< Binary OR of EValueFlags
+
CEnumeratedTypeValues(const char* name, bool isInteger);
CEnumeratedTypeValues(const string& name, bool isInteger);
~CEnumeratedTypeValues(void);
@@ -95,9 +101,9 @@ public:
}
/// Add name-value pair
- void AddValue(const string& name, TEnumValueType value);
+ void AddValue(const string& name, TEnumValueType value, TValueFlags flags = eNone);
/// Add name-value pair
- void AddValue(const char* name, TEnumValueType value);
+ void AddValue(const char* name, TEnumValueType value, TValueFlags flags = eNone);
/// Find numeric value by the name of the enum
///
@@ -139,6 +145,10 @@ public:
bool IsBitset(void) const {
return m_IsBitset;
}
+
+ TValueFlags GetValueFlags(TEnumValueType) const;
+ const string& FindNameEx(TEnumValueType value, bool allowBadValue) const;
+
private:
string m_Name;
string m_ModuleName;
@@ -147,6 +157,7 @@ private:
bool m_IsBitset;
bool m_IsInternal;
TValues m_Values;
+ map<TEnumValueType, TValueFlags> m_ValueFlags;
mutable auto_ptr<TNameToValue> m_NameToValue;
mutable auto_ptr<TValueToName> m_ValueToName;
};
diff --git a/c++/include/serial/exception.hpp b/c++/include/serial/exception.hpp
index 4a10d58..18cd3d3 100644
--- a/c++/include/serial/exception.hpp
+++ b/c++/include/serial/exception.hpp
@@ -1,6 +1,6 @@
#ifndef EXCEPTION__HPP
#define EXCEPTION__HPP
-/* $Id: exception.hpp 448169 2014-10-02 18:07:36Z vasilche $
+/* $Id: exception.hpp 445781 2014-09-08 17:33:32Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/serial/impl/choice.hpp b/c++/include/serial/impl/choice.hpp
index 4d971c7..f3b848d 100644
--- a/c++/include/serial/impl/choice.hpp
+++ b/c++/include/serial/impl/choice.hpp
@@ -1,7 +1,7 @@
#ifndef CHOICE__HPP
#define CHOICE__HPP
-/* $Id: choice.hpp 380188 2012-11-08 18:49:33Z vasilche $
+/* $Id: choice.hpp 448502 2014-10-07 13:33:03Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -125,6 +125,11 @@ public:
void SetGlobalHook(const CTempString& variant_names,
CReadChoiceVariantHook* hook);
+ void AdjustChoiceTypeInfoFunctions(void);
+ bool MayBeEmpty(void) const {
+ return m_AllowEmpty;
+ }
+
protected:
void SetSelectDelayFunction(TSelectDelayFunction func);
void CallUserOp_Assign(TObjectPtr dst, TConstObjectPtr src) const;
@@ -139,6 +144,7 @@ protected:
TResetFunction m_ResetFunction;
TSelectFunction m_SelectFunction;
TSelectDelayFunction m_SelectDelayFunction;
+ bool m_AllowEmpty;
};
diff --git a/c++/include/serial/impl/classinfohelper.hpp b/c++/include/serial/impl/classinfohelper.hpp
index 611ebbe..9d1eef6 100644
--- a/c++/include/serial/impl/classinfohelper.hpp
+++ b/c++/include/serial/impl/classinfohelper.hpp
@@ -1,7 +1,7 @@
#ifndef CLASSINFOHELPER__HPP
#define CLASSINFOHELPER__HPP
-/* $Id: classinfohelper.hpp 348915 2012-01-05 17:03:37Z vasilche $
+/* $Id: classinfohelper.hpp 448502 2014-10-07 13:33:03Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -199,6 +199,7 @@ public:
const CClassType* object = 0;
NCBISERSetGlobalReadMemberHook(object, info);
NCBISERSetGlobalReadVariantHook(object, info);
+ info->AdjustChoiceTypeInfoFunctions();
}
static CClassTypeInfo* CreateAbstractClassInfo(const char* name)
diff --git a/c++/include/serial/impl/item.hpp b/c++/include/serial/impl/item.hpp
index 516b79b..b8a27df 100644
--- a/c++/include/serial/impl/item.hpp
+++ b/c++/include/serial/impl/item.hpp
@@ -1,7 +1,7 @@
#ifndef ITEM__HPP
#define ITEM__HPP
-/* $Id: item.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: item.hpp 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -83,6 +83,8 @@ public:
bool NonEmpty(void) const;
CItemInfo* SetNonEmpty(void);
+ bool Optional(void) const;
+
private:
friend class CItemsInfo;
@@ -96,6 +98,8 @@ private:
CTypeRef m_Type;
bool m_NonEmpty;
+protected:
+ bool m_Optional;
};
diff --git a/c++/include/serial/impl/item.inl b/c++/include/serial/impl/item.inl
index 9e71e19..7299b4e 100644
--- a/c++/include/serial/impl/item.inl
+++ b/c++/include/serial/impl/item.inl
@@ -1,7 +1,7 @@
#if defined(ITEM__HPP) && !defined(ITEM__INL)
#define ITEM__INL
-/* $Id: item.inl 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: item.inl 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,5 +80,11 @@ bool CItemInfo::NonEmpty(void) const
return m_NonEmpty;
}
+inline
+bool CItemInfo::Optional(void) const
+{
+ return m_Optional;
+}
+
#endif /* def ITEM__HPP && ndef ITEM__INL */
diff --git a/c++/include/serial/impl/member.hpp b/c++/include/serial/impl/member.hpp
index 4a6690b..c78288f 100644
--- a/c++/include/serial/impl/member.hpp
+++ b/c++/include/serial/impl/member.hpp
@@ -1,7 +1,7 @@
#ifndef MEMBER__HPP
#define MEMBER__HPP
-/* $Id: member.hpp 406009 2013-07-10 14:17:14Z gouriano $
+/* $Id: member.hpp 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -198,8 +198,6 @@ private:
// containing class type info
const CClassTypeInfoBase* m_ClassType;
- // is optional
- bool m_Optional;
// default value
TConstObjectPtr m_Default;
// offset of 'SET' flag inside object
diff --git a/c++/include/serial/impl/memberlist.hpp b/c++/include/serial/impl/memberlist.hpp
index 2efd5fe..fa013f1 100644
--- a/c++/include/serial/impl/memberlist.hpp
+++ b/c++/include/serial/impl/memberlist.hpp
@@ -1,7 +1,7 @@
#ifndef MEMBERLIST__HPP
#define MEMBERLIST__HPP
-/* $Id: memberlist.hpp 418737 2013-11-19 18:50:38Z gouriano $
+/* $Id: memberlist.hpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,6 +50,7 @@ BEGIN_NCBI_SCOPE
class CConstObjectInfo;
class CObjectInfo;
+class CClassTypeInfoBase;
// This class supports sets of members with IDs
class NCBI_XSERIAL_EXPORT CItemsInfo
@@ -84,7 +85,8 @@ public:
}
TMemberIndex Find(const CTempString& name) const;
- TMemberIndex FindDeep(const CTempString& name, bool search_attlist = false) const;
+ TMemberIndex FindDeep(const CTempString& name, bool search_attlist = false,
+ const CClassTypeInfoBase** classInfo = nullptr) const;
TMemberIndex FindEmpty(void) const;
TMemberIndex Find(const CTempString& name, TMemberIndex pos) const;
TMemberIndex Find(TTag tag, CAsnBinaryDefs::ETagClass tagclass) const;
diff --git a/c++/include/serial/impl/objstack.hpp b/c++/include/serial/impl/objstack.hpp
index 57aab47..64cc425 100644
--- a/c++/include/serial/impl/objstack.hpp
+++ b/c++/include/serial/impl/objstack.hpp
@@ -1,7 +1,7 @@
#ifndef OBJSTACK__HPP
#define OBJSTACK__HPP
-/* $Id: objstack.hpp 421693 2013-12-13 14:11:00Z gouriano $
+/* $Id: objstack.hpp 461337 2015-03-09 18:00:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -135,6 +135,8 @@ public:
void SetTopMemberId(const CMemberId& memberId);
bool IsNsQualified(void);
+ bool IsCompressed(void) const;
+
#if defined(NCBI_SERIAL_IO_TRACE)
void TracePushFrame(bool push) const;
#endif
diff --git a/c++/include/serial/impl/objstrasnb.hpp b/c++/include/serial/impl/objstrasnb.hpp
index b6d3f37..1ee00a7 100644
--- a/c++/include/serial/impl/objstrasnb.hpp
+++ b/c++/include/serial/impl/objstrasnb.hpp
@@ -1,7 +1,7 @@
#ifndef OBJSTRASNB__HPP
#define OBJSTRASNB__HPP
-/* $Id: objstrasnb.hpp 448579 2014-10-07 16:50:30Z ivanov $
+/* $Id: objstrasnb.hpp 447162 2014-09-23 13:15:30Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp
index 26c30c8..226a8e2 100644
--- a/c++/include/serial/impl/stltypes.hpp
+++ b/c++/include/serial/impl/stltypes.hpp
@@ -1,7 +1,7 @@
#ifndef STLTYPES__HPP
#define STLTYPES__HPP
-/* $Id: stltypes.hpp 354590 2012-02-28 16:30:13Z ucko $
+/* $Id: stltypes.hpp 478074 2015-09-03 17:20:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -118,7 +118,7 @@ protected:
TObjectPtr dataPtr)
{
CTypeConverter<TObjectType>::Get(objectPtr).
- Reset(&CTypeConverter<TDataType>::Get(dataPtr));
+ Reset(CTypeConverter<TDataType>::GetPointer(dataPtr));
}
};
diff --git a/c++/include/serial/impl/variant.hpp b/c++/include/serial/impl/variant.hpp
index fe47cb3..b29b931 100644
--- a/c++/include/serial/impl/variant.hpp
+++ b/c++/include/serial/impl/variant.hpp
@@ -1,7 +1,7 @@
#ifndef VARIANT__HPP
#define VARIANT__HPP
-/* $Id: variant.hpp 358154 2012-03-29 15:05:12Z gouriano $
+/* $Id: variant.hpp 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -95,6 +95,7 @@ public:
EVariantType GetVariantType(void) const;
+ CVariantInfo* SetOptional(void);
CVariantInfo* SetNoPrefix(void);
CVariantInfo* SetNotag(void);
CVariantInfo* SetCompressed(void);
diff --git a/c++/include/serial/impl/variant.inl b/c++/include/serial/impl/variant.inl
index 212aafd..a915dd2 100644
--- a/c++/include/serial/impl/variant.inl
+++ b/c++/include/serial/impl/variant.inl
@@ -1,7 +1,7 @@
#if defined(VARIANT__HPP) && !defined(VARIANT__INL)
#define VARIANT__INL
-/* $Id: variant.inl 282780 2011-05-16 16:02:27Z gouriano $
+/* $Id: variant.inl 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -44,6 +44,14 @@ CVariantInfo::EVariantType CVariantInfo::GetVariantType(void) const
return m_VariantType;
}
+
+inline
+CVariantInfo* CVariantInfo::SetOptional(void)
+{
+ m_Optional = true;
+ return this;
+}
+
inline
CVariantInfo* CVariantInfo::SetNoPrefix(void)
{
diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp
index e0c47bf..da878a1 100644
--- a/c++/include/serial/iterator.hpp
+++ b/c++/include/serial/iterator.hpp
@@ -1,7 +1,7 @@
#ifndef ITERATOR__HPP
#define ITERATOR__HPP
-/* $Id: iterator.hpp 448105 2014-10-02 15:02:16Z ivanov $
+/* $Id: iterator.hpp 444854 2014-08-28 14:30:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/serial/objistrjson.hpp b/c++/include/serial/objistrjson.hpp
index 5bd9ea3..db17b8b 100644
--- a/c++/include/serial/objistrjson.hpp
+++ b/c++/include/serial/objistrjson.hpp
@@ -1,7 +1,7 @@
#ifndef OBJISTRJSON__HPP
#define OBJISTRJSON__HPP
-/* $Id: objistrjson.hpp 427338 2014-02-19 16:14:40Z gouriano $
+/* $Id: objistrjson.hpp 481917 2015-10-19 13:23:10Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,15 @@ public:
CObjectIStreamJson(void);
~CObjectIStreamJson(void);
+ /// Constructor.
+ ///
+ /// @param in
+ /// input stream
+ /// @param deleteIn
+ /// When eTakeOwnership, the input stream will be deleted automatically
+ /// when the reader is deleted
+ CObjectIStreamJson(CNcbiIstream& in, EOwnership deleteIn);
+
/// Get current stream position as string.
/// Useful for diagnostic and information messages.
///
@@ -223,6 +232,7 @@ private:
bool m_FileHeader;
bool m_BlockStart;
bool m_ExpectValue;
+ bool m_GotNameless;
char m_Closing;
EEncoding m_StringEncoding;
string m_LastTag;
diff --git a/c++/include/serial/objistrxml.hpp b/c++/include/serial/objistrxml.hpp
index cec0fb7..542ff10 100644
--- a/c++/include/serial/objistrxml.hpp
+++ b/c++/include/serial/objistrxml.hpp
@@ -1,7 +1,7 @@
#ifndef OBJISTRXML__HPP
#define OBJISTRXML__HPP
-/* $Id: objistrxml.hpp 421693 2013-12-13 14:11:00Z gouriano $
+/* $Id: objistrxml.hpp 459636 2015-02-20 14:45:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,6 +58,15 @@ public:
CObjectIStreamXml(void);
~CObjectIStreamXml(void);
+ /// Constructor.
+ ///
+ /// @param in
+ /// input stream
+ /// @param deleteIn
+ /// When eTakeOwnership, the input stream will be deleted automatically
+ /// when the reader is deleted
+ CObjectIStreamXml(CNcbiIstream& in, EOwnership deleteIn);
+
/// Check if there is still some meaningful data that can be read;
/// this function will skip white spaces and comments
///
diff --git a/c++/include/serial/objostr.hpp b/c++/include/serial/objostr.hpp
index 4a0e7dc..3328092 100644
--- a/c++/include/serial/objostr.hpp
+++ b/c++/include/serial/objostr.hpp
@@ -1,7 +1,7 @@
#ifndef OBJOSTR__HPP
#define OBJOSTR__HPP
-/* $Id: objostr.hpp 406002 2013-07-10 13:16:36Z gouriano $
+/* $Id: objostr.hpp 459636 2015-02-20 14:45:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -750,9 +750,10 @@ public:
MLIOVIR void WriteClassMemberSpecialCase(
const CMemberId& memberId, TTypeInfo memberType,
TConstObjectPtr memberPtr, ESpecialCaseWrite how);
+
protected:
CObjectOStream(ESerialDataFormat format,
- CNcbiOstream& out, bool deleteOut = false);
+ CNcbiOstream& out, EOwnership deleteOut = eNoOwnership);
// low level writers
typedef size_t TObjectIndex;
@@ -789,13 +790,13 @@ protected:
private:
static CObjectOStream* OpenObjectOStreamAsn(CNcbiOstream& out,
- bool deleteOut);
+ EOwnership deleteOut);
static CObjectOStream* OpenObjectOStreamAsnBinary(CNcbiOstream& out,
- bool deleteOut);
+ EOwnership deleteOut);
static CObjectOStream* OpenObjectOStreamXml(CNcbiOstream& out,
- bool deleteOut);
+ EOwnership deleteOut);
static CObjectOStream* OpenObjectOStreamJson(CNcbiOstream& out,
- bool deleteOut);
+ EOwnership deleteOut);
static ESerialVerifyData x_GetVerifyDataDefault(void);
EFixNonPrint m_FixMethod; // method of fixing wrong (eg, non-printable) chars
diff --git a/c++/include/serial/objostrasn.hpp b/c++/include/serial/objostrasn.hpp
index ef10f10..c1433c4 100644
--- a/c++/include/serial/objostrasn.hpp
+++ b/c++/include/serial/objostrasn.hpp
@@ -1,7 +1,7 @@
#ifndef OBJOSTRASN__HPP
#define OBJOSTRASN__HPP
-/* $Id: objostrasn.hpp 448081 2014-10-02 14:54:26Z ivanov $
+/* $Id: objostrasn.hpp 459636 2015-02-20 14:45:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,8 +71,23 @@ public:
/// when the writer is deleted
/// @param how
/// Defines how to fix unprintable characters in ASN VisiableString
+ /// @deprecated
+ /// Use one with EOwnership enum instead
+ NCBI_DEPRECATED_CTOR(CObjectOStreamAsn(CNcbiOstream& out,
+ bool deleteOut,
+ EFixNonPrint how = eFNP_Default));
+
+ /// Constructor.
+ ///
+ /// @param out
+ /// Output stream
+ /// @param deleteOut
+ /// When eTakeOwnership, the output stream will be deleted automatically
+ /// when the writer is deleted
+ /// @param how
+ /// Defines how to fix unprintable characters in ASN VisiableString
CObjectOStreamAsn(CNcbiOstream& out,
- bool deleteOut,
+ EOwnership deleteOut,
EFixNonPrint how = eFNP_Default);
/// Destructor.
diff --git a/c++/include/serial/objostrasnb.hpp b/c++/include/serial/objostrasnb.hpp
index 976817b..f534f70 100644
--- a/c++/include/serial/objostrasnb.hpp
+++ b/c++/include/serial/objostrasnb.hpp
@@ -1,7 +1,7 @@
#ifndef OBJOSTRASNB__HPP
#define OBJOSTRASNB__HPP
-/* $Id: objostrasnb.hpp 448081 2014-10-02 14:54:26Z ivanov $
+/* $Id: objostrasnb.hpp 459636 2015-02-20 14:45:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,9 +76,26 @@ public:
/// when the writer is deleted
/// @param how
/// Defines how to fix unprintable characters in ASN VisiableString
+ /// @deprecated
+ /// Use one with EOwnership enum instead
+ NCBI_DEPRECATED_CTOR(CObjectOStreamAsnBinary(CNcbiOstream& out,
+ bool deleteOut,
+ EFixNonPrint how = eFNP_Default));
+
+ /// Constructor.
+ ///
+ /// @param out
+ /// Output stream
+ /// @param deleteOut
+ /// When eTakeOwnership, the output stream will be deleted automatically
+ /// when the writer is deleted
+ /// @param how
+ /// Defines how to fix unprintable characters in ASN VisiableString
CObjectOStreamAsnBinary(CNcbiOstream& out,
- bool deleteOut,
+ EOwnership deleteOut,
EFixNonPrint how = eFNP_Default);
+
+
/// Destructor.
virtual ~CObjectOStreamAsnBinary(void);
diff --git a/c++/include/serial/objostrjson.hpp b/c++/include/serial/objostrjson.hpp
index f94d4f2..011d22a 100644
--- a/c++/include/serial/objostrjson.hpp
+++ b/c++/include/serial/objostrjson.hpp
@@ -1,7 +1,7 @@
#ifndef OBJOSTRJSON__HPP
#define OBJOSTRJSON__HPP
-/* $Id: objostrjson.hpp 448081 2014-10-02 14:54:26Z ivanov $
+/* $Id: objostrjson.hpp 481916 2015-10-19 13:22:37Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,7 +61,18 @@ public:
/// @param deleteOut
/// when TRUE, the output stream will be deleted automatically
/// when the writer is deleted
- CObjectOStreamJson(CNcbiOstream& out, bool deleteOut);
+ /// @deprecated
+ /// Use one with EOwnership enum instead
+ NCBI_DEPRECATED_CTOR(CObjectOStreamJson(CNcbiOstream& out, bool deleteOut));
+
+ /// Constructor.
+ ///
+ /// @param out
+ /// Output stream
+ /// @param deleteOut
+ /// When eTakeOwnership, the output stream will be deleted automatically
+ /// when the writer is deleted
+ CObjectOStreamJson(CNcbiOstream& out, EOwnership deleteOut);
/// Destructor.
virtual ~CObjectOStreamJson(void);
@@ -212,6 +223,7 @@ private:
void x_WriteString(const string& value,
EStringType type = eStringTypeVisible);
void WriteKey(const string& key);
+ void BeginValue(void);
void WriteValue(const string& value,
EStringType type = eStringTypeVisible);
void WriteKeywordValue(const string& value);
diff --git a/c++/include/serial/objostrxml.hpp b/c++/include/serial/objostrxml.hpp
index 83e18c1..b061ab5 100644
--- a/c++/include/serial/objostrxml.hpp
+++ b/c++/include/serial/objostrxml.hpp
@@ -1,7 +1,7 @@
#ifndef OBJOSTRXML__HPP
#define OBJOSTRXML__HPP
-/* $Id: objostrxml.hpp 448081 2014-10-02 14:54:26Z ivanov $
+/* $Id: objostrxml.hpp 459636 2015-02-20 14:45:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,7 +61,18 @@ public:
/// @param deleteOut
/// when TRUE, the output stream will be deleted automatically
/// when the writer is deleted
- CObjectOStreamXml(CNcbiOstream& out, bool deleteOut);
+ /// @deprecated
+ /// Use one with EOwnership enum instead
+ NCBI_DEPRECATED_CTOR(CObjectOStreamXml(CNcbiOstream& out, bool deleteOut));
+
+ /// Constructor.
+ ///
+ /// @param out
+ /// Output stream
+ /// @param deleteOut
+ /// When eTakeOwnership, the output stream will be deleted automatically
+ /// when the writer is deleted
+ CObjectOStreamXml(CNcbiOstream& out, EOwnership deleteOut);
/// Destructor.
virtual ~CObjectOStreamXml(void);
diff --git a/c++/include/serial/rpcbase.hpp b/c++/include/serial/rpcbase.hpp
index 83e9e93..437a107 100644
--- a/c++/include/serial/rpcbase.hpp
+++ b/c++/include/serial/rpcbase.hpp
@@ -1,7 +1,7 @@
#ifndef SERIAL___RPCBASE__HPP
#define SERIAL___RPCBASE__HPP
-/* $Id: rpcbase.hpp 436798 2014-05-30 18:43:47Z lavr $
+/* $Id: rpcbase.hpp 483519 2015-11-02 14:44:04Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,7 @@
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
+#include <util/retry_ctx.hpp>
/** @addtogroup GenClassSupport
@@ -50,29 +51,19 @@
BEGIN_NCBI_SCOPE
-/// CRPCClient -- prototype client for ASN.1/XML-based RPC.
-/// Normally connects automatically on the first real request and
-/// disconnects automatically in the destructor, but allows both events
-/// to occur explicitly.
-
-template <class TRequest, class TReply>
-class CRPCClient : public CObject,
- protected CConnIniter
+/// Base class for CRPCClient template - defines methods
+/// independent of request and response types.
+class NCBI_XSERIAL_EXPORT CRPCClient_Base
{
public:
- CRPCClient(const string& service = kEmptyStr,
- ESerialDataFormat format = eSerial_AsnBinary,
- unsigned int retry_limit = 3)
- : m_Service(service), m_Format(format), m_Timeout(kDefaultTimeout),
- m_RetryLimit(retry_limit)
- {
- }
- virtual ~CRPCClient(void);
+ CRPCClient_Base(const string& service,
+ ESerialDataFormat format,
+ unsigned int retry_limit);
+ virtual ~CRPCClient_Base(void);
- virtual void Ask(const TRequest& request, TReply& reply);
- void Connect(void);
- void Disconnect(void);
- void Reset(void);
+ void Connect(void);
+ void Disconnect(void);
+ void Reset(void);
const string& GetService(void) const { return m_Service; }
void SetService(const string& service) { m_Service = service; }
@@ -86,130 +77,199 @@ public:
const CTimeSpan GetRetryDelay(void) const { return m_RetryDelay; }
void SetRetryDelay(const CTimeSpan& ts) { m_RetryDelay = ts; }
- EIO_Status SetTimeout(const STimeout* timeout,
- EIO_Event direction = eIO_ReadWrite);
- const STimeout* GetTimeout(EIO_Event direction = eIO_Read) const;
-
protected:
- virtual string GetAffinity(const TRequest& request) const;
- void SetAffinity(const string& affinity);
+ void SetAffinity(const string& affinity);
/// These run with m_Mutex already acquired.
- virtual void x_Connect(void);
+ virtual void x_Connect(void) = 0;
virtual void x_Disconnect(void);
void x_SetStream(CNcbiIostream* stream);
- /// Connect to a URL. (Discouraged; please establish and use a
- /// suitable named service if possible.)
- void x_ConnectURL(const string& url);
- /// Retry policy; by default, just _TRACEs the event and returns
- /// true. May reset the connection (or do anything else, really),
- /// but note that Ask() will always automatically reconnect if the
- /// stream is explicitly bad. (Ask() also takes care of enforcing
- /// m_RetryLimit.)
- virtual bool x_ShouldRetry(unsigned int tries);
+ void x_Ask(const CSerialObject& request, CSerialObject& reply);
+ // Casting stubs.
+ virtual void x_WriteRequest(CObjectOStream& out, const CSerialObject& request) = 0;
+ virtual void x_ReadReply(CObjectIStream& in, CSerialObject& reply) = 0;
+ virtual string x_GetAffinity(const CSerialObject& request) const = 0;
private:
- static bool x_IsSpecial(const STimeout* timeout)
- { return timeout == kDefaultTimeout || timeout == kInfiniteTimeout; }
-
- typedef CRPCClient<TRequest, TReply> TSelf;
/// Prohibit default copy constructor and assignment operator.
- CRPCClient(const TSelf& x);
- bool operator= (const TSelf& x);
+ CRPCClient_Base(const CRPCClient_Base&);
+ bool operator= (const CRPCClient_Base&);
- auto_ptr<CNcbiIostream> m_Stream;
- auto_ptr<CObjectIStream> m_In;
- auto_ptr<CObjectOStream> m_Out;
- string m_Service; ///< Used by default Connect().
- string m_Affinity;
ESerialDataFormat m_Format;
CMutex m_Mutex; ///< To allow sharing across threads.
- const STimeout* m_Timeout; ///< Cloned if not special.
CTimeSpan m_RetryDelay;
+ int m_RetryCount;
+ int m_RecursionCount;
protected:
+ string m_Service; ///< Used by default Connect().
+ auto_ptr<CNcbiIostream> m_Stream; // This must be destroyed after m_In/m_Out.
+ auto_ptr<CObjectIStream> m_In;
+ auto_ptr<CObjectOStream> m_Out;
+ string m_Affinity;
+ const STimeout* m_Timeout; ///< Cloned if not special.
unsigned int m_RetryLimit;
-};
+ CHttpRetryContext m_RetryCtx;
+ // Retry policy; by default, just _TRACEs the event and returns
+ // true. May reset the connection (or do anything else, really),
+ // but note that Ask() will always automatically reconnect if the
+ // stream is explicitly bad. (Ask() also takes care of enforcing
+ // m_RetryLimit.)
+ virtual bool x_ShouldRetry(unsigned int tries);
+
+ // Calculate effective retry delay. Returns value from CRetryContext
+ // if any, or the value set by SetRetryDelay. The returned value never
+ // exceeds max_delay.
+ CTimeSpan x_GetRetryDelay(double max_delay) const;
+
+ // CConn_HttpStream callback for parsing headers.
+ // 'user_data' must point to an instance of CRPCConnStatus.
+ static EHTTP_HeaderParse sx_ParseHeader(const char* http_header,
+ void* user_data,
+ int server_error);
+
+ static bool sx_IsSpecial(const STimeout* timeout);
+};
-///////////////////////////////////////////////////////////////////////////
-// Inline methods
+/// CRPCClient -- prototype client for ASN.1/XML-based RPC.
+/// Normally connects automatically on the first real request and
+/// disconnects automatically in the destructor, but allows both events
+/// to occur explicitly.
template <class TRequest, class TReply>
-inline
-CRPCClient<TRequest, TReply>::~CRPCClient(void)
+class CRPCClient : public CObject,
+ public CRPCClient_Base,
+ protected CConnIniter
{
- Disconnect();
- if ( !x_IsSpecial(m_Timeout) ) {
- delete const_cast<STimeout*>(m_Timeout);
+public:
+ CRPCClient(const string& service = kEmptyStr,
+ ESerialDataFormat format = eSerial_AsnBinary,
+ unsigned int retry_limit = 3)
+ : CRPCClient_Base(service, format, retry_limit) {}
+ virtual ~CRPCClient(void) {}
+
+ virtual void Ask(const TRequest& request, TReply& reply)
+ { x_Ask(request, reply); }
+
+ virtual void WriteRequest(CObjectOStream& out, const TRequest& request)
+ { out << request; }
+
+ virtual void ReadReply(CObjectIStream& in, TReply& reply)
+ { in >> reply; }
+
+ EIO_Status SetTimeout(const STimeout* timeout,
+ EIO_Event direction = eIO_ReadWrite);
+ const STimeout* GetTimeout(EIO_Event direction = eIO_Read) const;
+
+protected:
+ virtual string GetAffinity(const TRequest& request) const
+ {
+ return "";
}
-}
+ virtual void x_WriteRequest(CObjectOStream& out, const CSerialObject& request)
+ {
+ WriteRequest(out, dynamic_cast<const TRequest&>(request));
+ }
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::Connect(void)
-{
- if (m_Stream.get() && m_Stream->good()) {
- return; // already connected
+ virtual void x_ReadReply(CObjectIStream& in, CSerialObject& reply)
+ {
+ ReadReply(in, dynamic_cast<TReply&>(reply));
}
- CMutexGuard LOCK(m_Mutex);
- // repeat test with mutex held to avoid races
- if (m_Stream.get() && m_Stream->good()) {
- return; // already connected
+
+ virtual string x_GetAffinity(const CSerialObject& request) const
+ {
+ return GetAffinity(dynamic_cast<const TRequest&>(request));
}
- x_Connect();
-}
+ virtual void x_Connect(void);
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::Disconnect(void)
+ /// Connect to a URL. (Discouraged; please establish and use a
+ /// suitable named service if possible.)
+ void x_ConnectURL(const string& url);
+};
+
+
+class NCBI_XSERIAL_EXPORT CRPCClientException : public CException
{
- CMutexGuard LOCK(m_Mutex);
- if ( !m_Stream.get() || !m_Stream->good() ) {
- // not connected -- don't call x_Disconnect, which might
- // temporarily reconnect to send a fini!
- return;
- }
- x_Disconnect();
-}
+public:
+ enum EErrCode {
+ eRetry, ///< Request failed, should be retried if possible.
+ eFailed, ///< Request (or retry) failed.
+ eOther
+ };
+ virtual const char* GetErrCodeString(void) const;
-template <class TRequest, class TReply>
+ bool IsSetRetryContext(void) const { return m_RetryCtx; }
+ /// Read retry related data.
+ CRetryContext& GetRetryContext(void) { return *m_RetryCtx; }
+ /// Set new retry context.
+ void SetRetryContext(CRetryContext& ctx) { m_RetryCtx.Reset(&ctx); }
+
+ NCBI_EXCEPTION_DEFAULT(CRPCClientException, CException);
+
+private:
+ CRef<CRetryContext> m_RetryCtx;
+};
+
+
+///////////////////////////////////////////////////////////////////////////
+// Inline methods
+
+template<class TRequest, class TReply>
inline
-void CRPCClient<TRequest, TReply>::Reset(void)
+void CRPCClient<TRequest, TReply>::x_Connect(void)
{
- CMutexGuard LOCK(m_Mutex);
- if (m_Stream.get() && m_Stream->good()) {
- x_Disconnect();
+ if ( m_RetryCtx.IsSetUrl() ) {
+ x_ConnectURL(m_RetryCtx.GetUrl());
+ return;
+ }
+ _ASSERT( !m_Service.empty() );
+ SConnNetInfo* net_info = ConnNetInfo_Create(m_Service.c_str());
+ if ( m_RetryCtx.IsSetArgs() ) {
+ ConnNetInfo_AppendArg(net_info, m_RetryCtx.GetArgs().c_str(), 0);
+ }
+ else if (!m_Affinity.empty()) {
+ ConnNetInfo_PostOverrideArg(net_info, m_Affinity.c_str(), 0);
}
- x_Connect();
-}
+ // Install callback for parsing headers.
+ SSERVICE_Extra x_extra;
+ memset(&x_extra, 0, sizeof(x_extra));
+ x_extra.data = &m_RetryCtx;
+ x_extra.parse_header = sx_ParseHeader;
-template <class TRequest, class TReply>
-inline
-string CRPCClient<TRequest, TReply>::GetAffinity(const TRequest& ) const
-{
- return kEmptyStr;
+ x_SetStream(new CConn_ServiceStream(m_Service, fSERV_Any, net_info,
+ &x_extra, m_Timeout));
+ ConnNetInfo_Destroy(net_info);
}
-template <class TRequest, class TReply>
+template<class TRequest, class TReply>
inline
-void CRPCClient<TRequest, TReply>::SetAffinity(const string& affinity)
+void CRPCClient<TRequest, TReply>::x_ConnectURL(const string& url)
{
- if (m_Affinity != affinity) {
- Disconnect();
- m_Affinity = affinity;
+ SConnNetInfo* net_info = ConnNetInfo_Create(0);
+ ConnNetInfo_ParseURL(net_info, url.c_str());
+ if ( m_RetryCtx.IsSetArgs() ) {
+ ConnNetInfo_PostOverrideArg(net_info, m_RetryCtx.GetArgs().c_str(), 0);
}
+ x_SetStream(new CConn_HttpStream(net_info,
+ kEmptyStr, // user_header
+ sx_ParseHeader, // callback
+ &m_RetryCtx, // user data for the callback
+ 0, // adjust callback
+ 0, // cleanup callback
+ fHTTP_AutoReconnect,
+ m_Timeout));
}
-template <class TRequest, class TReply>
+template<class TRequest, class TReply>
inline
EIO_Status CRPCClient<TRequest, TReply>::SetTimeout(const STimeout* timeout,
EIO_Event direction)
@@ -217,12 +277,12 @@ EIO_Status CRPCClient<TRequest, TReply>::SetTimeout(const STimeout* timeout,
// save for future use, especially if there's no stream at present.
{{
const STimeout* old_timeout = m_Timeout;
- if (x_IsSpecial(timeout)) {
+ if (sx_IsSpecial(timeout)) {
m_Timeout = timeout;
} else { // make a copy
m_Timeout = new STimeout(*timeout);
}
- if ( !x_IsSpecial(old_timeout) ) {
+ if ( !sx_IsSpecial(old_timeout) ) {
delete const_cast<STimeout*>(old_timeout);
}
}}
@@ -239,7 +299,7 @@ EIO_Status CRPCClient<TRequest, TReply>::SetTimeout(const STimeout* timeout,
}
-template <class TRequest, class TReply>
+template<class TRequest, class TReply>
inline
const STimeout* CRPCClient<TRequest, TReply>::GetTimeout(EIO_Event direction)
const
@@ -254,96 +314,6 @@ const STimeout* CRPCClient<TRequest, TReply>::GetTimeout(EIO_Event direction)
}
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::Ask(const TRequest& request, TReply& reply)
-{
- CMutexGuard LOCK(m_Mutex);
-
- unsigned int tries = 0;
- for (;;) {
- try {
- SetAffinity(GetAffinity(request));
- Connect(); // No-op if already connected
- *m_Out << request;
- *m_In >> reply;
- break;
- } catch (CException& e) {
- // Some exceptions tend to correspond to transient glitches;
- // the remainder, however, may as well get propagated immediately.
- if ( !dynamic_cast<CSerialException*>(&e)
- && !dynamic_cast<CIOException*>(&e) ) {
- throw;
- } else if (++tries == m_RetryLimit || !x_ShouldRetry(tries)) {
- throw;
- } else if ( !(tries & 1) ) {
- // reset on every other attempt in case we're out of sync
- try {
- Reset();
- } STD_CATCH_ALL_XX(Serial_RPCClient,1,"CRPCClient<>::Reset()");
- }
- SleepSec(m_RetryDelay.GetCompleteSeconds());
- SleepMicroSec(m_RetryDelay.GetNanoSecondsAfterSecond() / 1000);
- }
- }
-}
-
-
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::x_Connect(void)
-{
- _ASSERT( !m_Service.empty() );
- SConnNetInfo* net_info = ConnNetInfo_Create(m_Service.c_str());
- if (!m_Affinity.empty()) {
- ConnNetInfo_PostOverrideArg(net_info, m_Affinity.c_str(), 0);
- }
- x_SetStream(new CConn_ServiceStream(m_Service, fSERV_Any, net_info, 0,
- m_Timeout));
- ConnNetInfo_Destroy(net_info);
-}
-
-
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::x_Disconnect(void)
-{
- m_In.reset();
- m_Out.reset();
- m_Stream.reset();
-}
-
-
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::x_SetStream(CNcbiIostream* stream)
-{
- m_In .reset();
- m_Out.reset();
- m_Stream.reset(stream);
- m_In .reset(CObjectIStream::Open(m_Format, *stream));
- m_Out.reset(CObjectOStream::Open(m_Format, *stream));
-}
-
-
-template <class TRequest, class TReply>
-inline
-void CRPCClient<TRequest, TReply>::x_ConnectURL(const string& url)
-{
- x_SetStream(new CConn_HttpStream(url, fHTTP_AutoReconnect, m_Timeout));
-}
-
-
-template <class TRequest, class TReply>
-inline
-bool CRPCClient<TRequest, TReply>::x_ShouldRetry(unsigned int tries)
-{
- _TRACE("CRPCClient<>::x_ShouldRetry: retrying after " << tries
- << " failures");
- return true;
-}
-
-
END_NCBI_SCOPE
diff --git a/c++/include/serial/serialimpl.hpp b/c++/include/serial/serialimpl.hpp
index f851972..cc73469 100644
--- a/c++/include/serial/serialimpl.hpp
+++ b/c++/include/serial/serialimpl.hpp
@@ -1,7 +1,7 @@
#ifndef SERIALIMPL__HPP
#define SERIALIMPL__HPP
-/* $Id: serialimpl.hpp 448228 2014-10-03 13:51:14Z vasilche $
+/* $Id: serialimpl.hpp 471531 2015-06-29 11:40:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -549,6 +549,9 @@ const NCBI_NS_NCBI::CEnumeratedTypeValues* MethodName(void) \
#define ADD_ENUM_VALUE(EnumValueName, EnumValueValue) \
enumInfo->AddValue(EnumValueName, enumValue = EnumValueValue)
+#define ADD_ENUM_VALUE_FLAGS(EnumValueName, EnumValueValue, EnumValueFlags) \
+ enumInfo->AddValue(EnumValueName, enumValue = EnumValueValue, EnumValueFlags)
+
#define END_ENUM_IN_INFO END_ENUM_INFO_METHOD
#define END_ENUM_INFO END_ENUM_INFO_METHOD
diff --git a/c++/include/serial/serialutil.hpp b/c++/include/serial/serialutil.hpp
index 18d2f89..e6b4f9b 100644
--- a/c++/include/serial/serialutil.hpp
+++ b/c++/include/serial/serialutil.hpp
@@ -1,7 +1,7 @@
#ifndef SERIALUTIL__HPP
#define SERIALUTIL__HPP
-/* $Id: serialutil.hpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: serialutil.hpp 478074 2015-09-03 17:20:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,6 +61,14 @@ public:
{
return *static_cast<const TObjectType*>(object);
}
+ static TObjectType* GetPointer(TObjectPtr object)
+ {
+ return static_cast<TObjectType*>(object);
+ }
+ static const TObjectType* GetPointer(TConstObjectPtr object)
+ {
+ return static_cast<const TObjectType*>(object);
+ }
// set of SafeCast functions which will check validity of casting by
// dynamic_cast<> in debug mode and will use static_cast<> in release
diff --git a/c++/include/serial/streamiter.hpp b/c++/include/serial/streamiter.hpp
index aebf4e6..515b1b0 100644
--- a/c++/include/serial/streamiter.hpp
+++ b/c++/include/serial/streamiter.hpp
@@ -1,7 +1,7 @@
#ifndef STREAMITER__HPP
#define STREAMITER__HPP
-/* $Id: streamiter.hpp 382850 2012-12-10 15:13:05Z gouriano $
+/* $Id: streamiter.hpp 468542 2015-05-26 14:14:15Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -233,11 +233,14 @@ public:
}
protected:
CIStreamIterator_Base()
+ : m_Reader(nullptr)
{
}
~CIStreamIterator_Base(void)
{
- m_Reader->Stop();
+ if (m_Reader) {
+ m_Reader->Stop();
+ }
}
private:
// prohibit copy
diff --git a/c++/include/util/bitset/bmconst.h b/c++/include/util/bitset/bmconst.h
index aa46c79..e0022ef 100644
--- a/c++/include/util/bitset/bmconst.h
+++ b/c++/include/util/bitset/bmconst.h
@@ -147,11 +147,11 @@ const unsigned DeBruijn_bit_position<T>::_multiply[32] = {
*/
template<bool T> struct first_bit_table
{
- static const char _idx[256];
+ static const signed char _idx[256];
};
template<bool T>
-const char first_bit_table<T>::_idx[256] = {
+const signed char first_bit_table<T>::_idx[256] = {
-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
diff --git a/c++/include/util/checksum.hpp b/c++/include/util/checksum.hpp
index 71f6c65..d41e5c2 100644
--- a/c++/include/util/checksum.hpp
+++ b/c++/include/util/checksum.hpp
@@ -1,7 +1,7 @@
#ifndef CHECKSUM__HPP
#define CHECKSUM__HPP
-/* $Id: checksum.hpp 448175 2014-10-02 18:33:47Z vasilche $
+/* $Id: checksum.hpp 450515 2014-10-27 21:08:39Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,12 +63,23 @@ public:
enum EMethod {
eNone, ///< No checksum in file.
eCRC32, ///< 32-bit Cyclic Redundancy Check.
- eCRC32ZIP, ///< Exact zip CRC32, slightly differs from eCRC32.
+ ///< Most significant bit first, no inversions.
+ eCRC32ZIP, ///< Exact zip CRC32. Same polynomial as eCRC32.
+ ///< Least significant bit are processed first,
+ ///< extra inversions at the beginning and the end.
eCRC32INSD, ///< Inverted CRC32ZIP. Hash function used in
///< the ID system to verify sequence uniqueness.
eMD5, ///< Message Digest version 5.
eAdler32, ///< A bit faster than CRC32ZIP, not recommended
///< for small data sizes.
+ eCRC32CKSUM, ///< CRC32 implemented by cksum utility.
+ ///< Same as eCRC32, but with data length included
+ ///< in CRC, and extra inversion at the end.
+ eCRC32C, ///< CRC32C (Castagnoli). Better polynomial used
+ ///< in some places (iSCSI). This method has
+ ///< hardware support in new Intel processors.
+ ///< Least significant bits are processed first,
+ ///< extra inversions at the beginning and the end.
eDefault = eCRC32
};
enum {
@@ -84,24 +95,22 @@ public:
/// Assignment operator.
CChecksum& operator=(const CChecksum& cks);
- /// Initialize static tables used in checksum calculation.
- /// There is no need to call this method since it's done internally.
- static void InitTables(void);
-
- /// Print C++ code for CRC32 tables for direct inclusion into library.
- /// It also eliminates the need to initialize CRC32 tables.
- static void PrintTables(CNcbiOstream& out);
-
/// Get current method used to compute control sum.
EMethod GetMethod(void) const;
/// Check that method is specified (not equal eNone).
bool Valid(void) const;
+ /// Return size of checksum in bytes.
+ size_t GetChecksumSize(void) const;
+
/// Return calculated checksum.
/// Only valid in CRC32/CRC32ZIP/Adler32 modes!
Uint4 GetChecksum(void) const;
+ /// Return string with checksum in hexadecimal form.
+ string GetHexSum(void) const;
+
/// Return calculated MD5 digest.
/// Only valid in MD5 mode!
void GetMD5Digest(unsigned char digest[16]) const;
@@ -118,6 +127,20 @@ public:
void AddChars(const char* str, size_t length);
void NextLine(void);
+ /// Compute checksum for the file, add it to this checksum.
+ /// On any error an exception will be thrown, and the checksum
+ /// will not change.
+ void AddFile(const string& file_path);
+
+ /// Compute checksum for the stream, add it to this checksum.
+ /// On any error an exception will be thrown, and the checksum
+ /// will not change.
+ /// @is
+ /// Input stream to read data from.
+ /// Please use ios_base::binary flag for the input stream
+ /// if you want to count all symbols there, including end of lines.
+ void AddStream(CNcbiIstream& is);
+
/// Check for checksum line.
bool ValidChecksumLine(const char* line, size_t length) const;
bool ValidChecksumLine(const string& line) const;
@@ -125,6 +148,16 @@ public:
/// Write checksum calculation results into output stream
CNcbiOstream& WriteChecksum(CNcbiOstream& out) const;
CNcbiOstream& WriteChecksumData(CNcbiOstream& out) const;
+ CNcbiOstream& WriteHexSum(CNcbiOstream& out) const;
+
+public:
+ /// Initialize static tables used in checksum calculation.
+ /// There is no need to call this method since it's done internally.
+ static void InitTables(void);
+
+ /// Print C++ code for CRC32 tables for direct inclusion into library.
+ /// It also eliminates the need to initialize CRC32 tables.
+ static void PrintTables(CNcbiOstream& out);
private:
size_t m_LineCount; ///< Number of lines
@@ -150,17 +183,52 @@ private:
CNcbiOstream& operator<<(CNcbiOstream& out, const CChecksum& checksum);
/// Compute checksum for the given file.
-NCBI_XUTIL_EXPORT
+/// @deprecated
+/// Please use CChecksum::AddFile() method instead.
+NCBI_DEPRECATED NCBI_XUTIL_EXPORT
CChecksum ComputeFileChecksum(const string& path, CChecksum::EMethod method);
/// Computes checksum for the given file.
-NCBI_XUTIL_EXPORT
+/// @deprecated
+/// Please use CChecksum::AddFile() method instead.
+NCBI_DEPRECATED NCBI_XUTIL_EXPORT
CChecksum& ComputeFileChecksum(const string& path, CChecksum& checksum);
/// Compute CRC32 checksum for the given file.
+/// @deprecated
+/// Please use CChecksum::AddFile() method instead.
+NCBI_DEPRECATED NCBI_XUTIL_EXPORT
Uint4 ComputeFileCRC32(const string& path);
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CChecksumException --
+///
+/// Define exceptions generated for CChecksum methods.
+///
+/// CChecksumException inherits its basic functionality from CCoreException
+/// and defines additional error codes for CChecksum methods.
+
+class NCBI_XNCBI_EXPORT CChecksumException : public CCoreException
+{
+public:
+ /// Error types that can be generated.
+ enum EErrCode {
+ eStreamIO,
+ eFileIO
+ };
+
+ /// Translate from an error code value to its string representation.
+ virtual const char* GetErrCodeString(void) const;
+
+ // Standard exception boilerplate code.
+ NCBI_EXCEPTION_DEFAULT(CChecksumException, CCoreException);
+};
+
+
+
/////////////////////////////////////////////////////////////////////////////
///
/// CChecksumStreamWriter --
@@ -237,8 +305,8 @@ inline
bool CChecksum::ValidChecksumLine(const char* line, size_t length) const
{
return length > kMinimumChecksumLength &&
- line[0] == '/' && line[1] == '*' && // first four letters of checksum
- line[2] == ' ' && line[3] == 'O' && // see sx_Start in checksum.cpp
+ line[0] == '/' && line[1] == '*' && // first four letters of checksum
+ line[2] == ' ' && line[3] == 'O' && // see sx_Start in checksum.cpp
ValidChecksumLineLong(line, length); // complete check
}
@@ -265,12 +333,6 @@ void CChecksum::GetMD5Digest(string& str) const
}
inline
-Uint4 ComputeFileCRC32(const string& path)
-{
- return ComputeFileChecksum(path, CChecksum::eCRC32).GetChecksum();
-}
-
-inline
const CChecksum& CChecksumStreamWriter::GetChecksum(void) const
{
return m_Checksum;
diff --git a/c++/include/util/compress/archive_.hpp b/c++/include/util/compress/archive_.hpp
index 37bc6cf..306186b 100644
--- a/c++/include/util/compress/archive_.hpp
+++ b/c++/include/util/compress/archive_.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL_COMPRESS__ARCHIVE___HPP
#define UTIL_COMPRESS__ARCHIVE___HPP
-/* $Id: archive_.hpp 394174 2013-04-01 15:49:08Z ivanov $
+/* $Id: archive_.hpp 462539 2015-03-19 12:58:24Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -62,6 +62,7 @@ class NCBI_XUTIL_EXPORT CArchiveException : public CCoreException
public:
/// Error types that file operations can generate.
enum EErrCode {
+ eUnsupported,
eMemory,
eUnsupportedEntryType,
eBadName,
@@ -80,6 +81,7 @@ public:
virtual const char* GetErrCodeString(void) const
{
switch (GetErrCode()) {
+ case eUnsupported: return "eUnsupported";
case eMemory: return "eMemory";
case eUnsupportedEntryType: return "eUnsupportedEntryType";
case eBadName: return "eBadName";
@@ -136,7 +138,7 @@ public:
const string& GetUserName(void) const { return m_UserName; }
const string& GetGroupName(void) const { return m_GroupName; }
const string& GetComment(void) const { return m_Comment; }
- const size_t GetIndex(void) const { return m_Index; }
+ size_t GetIndex(void) const { return m_Index; }
time_t GetModificationTime(void) const { return m_Stat.st_mtime; }
time_t GetLastAccessTime(void) const { return m_Stat.st_atime; }
time_t GetCreationTime(void) const { return m_Stat.st_ctime; }
diff --git a/c++/include/util/compress/zlib/zconf.h b/c++/include/util/compress/zlib/zconf.h
index 53ffaea..52e66d7 100644
--- a/c++/include/util/compress/zlib/zconf.h
+++ b/c++/include/util/compress/zlib/zconf.h
@@ -3,7 +3,7 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
-/* @(#) $Id: zconf.h 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: zconf.h 444593 2014-08-26 12:32:08Z ivanov $ */
#ifndef ZCONF_H
#define ZCONF_H
diff --git a/c++/include/util/compress/zlib/zutil.h b/c++/include/util/compress/zlib/zutil.h
index 23f1256..51be263 100644
--- a/c++/include/util/compress/zlib/zutil.h
+++ b/c++/include/util/compress/zlib/zutil.h
@@ -8,7 +8,7 @@
subject to change. Applications should only use zlib.h.
*/
-/* @(#) $Id: zutil.h 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: zutil.h 444593 2014-08-26 12:32:08Z ivanov $ */
#ifndef ZUTIL_H
#define ZUTIL_H
diff --git a/c++/include/util/distribution.hpp b/c++/include/util/distribution.hpp
index 2471fba..03b2032 100644
--- a/c++/include/util/distribution.hpp
+++ b/c++/include/util/distribution.hpp
@@ -1,4 +1,4 @@
-/* $Id: distribution.hpp 448239 2014-10-03 14:17:45Z kazimird $
+/* $Id: distribution.hpp 448236 2014-10-03 14:05:43Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/util/format_guess.hpp b/c++/include/util/format_guess.hpp
index 5c9a832..44b9187 100644
--- a/c++/include/util/format_guess.hpp
+++ b/c++/include/util/format_guess.hpp
@@ -1,7 +1,7 @@
#ifndef FORMATGUESS__HPP
#define FORMATGUESS__HPP
-/* $Id: format_guess.hpp 432807 2014-04-18 13:52:28Z gotvyans $
+/* $Id: format_guess.hpp 474485 2015-07-29 14:04:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -340,6 +340,7 @@ protected:
unsigned int m_iStatsCountAlNumChars;
unsigned int m_iStatsCountDnaChars;
unsigned int m_iStatsCountAaChars;
+ unsigned int m_iStatsCountBraces;
std::list<std::string> m_TestLines;
CFormatHints m_Hints;
};
diff --git a/c++/include/util/ncbi_cache.hpp b/c++/include/util/ncbi_cache.hpp
index 2217738..84f1a36 100644
--- a/c++/include/util/ncbi_cache.hpp
+++ b/c++/include/util/ncbi_cache.hpp
@@ -1,6 +1,6 @@
#ifndef CORELIB___NCBI_CACHE__HPP
#define CORELIB___NCBI_CACHE__HPP
-/* $Id: ncbi_cache.hpp 448078 2014-10-02 14:52:44Z ivanov $
+/* $Id: ncbi_cache.hpp 444509 2014-08-25 17:24:31Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/util/random_gen.hpp b/c++/include/util/random_gen.hpp
index 8500c6f..221f35e 100644
--- a/c++/include/util/random_gen.hpp
+++ b/c++/include/util/random_gen.hpp
@@ -1,7 +1,7 @@
#ifndef RANDOM_GEN__HPP
#define RANDOM_GEN__HPP
-/* $Id: random_gen.hpp 415936 2013-10-22 18:10:13Z satskyse $
+/* $Id: random_gen.hpp 459009 2015-02-12 15:18:36Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -94,12 +94,42 @@ public:
/// than eGetRand_Sys one
TValue GetRand(TValue min_value, TValue max_value);
+ /// Get random Uint8 number
+ /// @sa EGetRandMethod
+ /// @note eGetRand_LFG generator could be 100 times faster
+ /// than eGetRand_Sys one
+ Uint8 GetRandUint8(void);
+
+ /// Get random number in the interval [min_value..max_value] (inclusive)
+ /// @sa EGetRandMethod
+ /// @note eGetRand_LFG generator could be 100 times faster
+ /// than eGetRand_Sys one
+ Uint8 GetRandUint8(Uint8 min_value, Uint8 max_value);
+
+ /// Get random number in the interval [min_value..max_value] (inclusive)
+ /// @sa EGetRandMethod
+ /// @note eGetRand_LFG generator could be 100 times faster
+ /// than eGetRand_Sys one
+ size_t GetRandSize_t(size_t min_value, size_t max_value);
+
/// Get random number in the interval [0..size-1] (e.g. index in array)
/// @sa EGetRandMethod
/// @note eGetRand_LFG generator could be 100 times faster
/// than eGetRand_Sys one
TValue GetRandIndex(TValue size);
+ /// Get random number in the interval [0..size-1] (e.g. index in array)
+ /// @sa EGetRandMethod
+ /// @note eGetRand_LFG generator could be 100 times faster
+ /// than eGetRand_Sys one
+ Uint8 GetRandIndexUint8(Uint8 size);
+
+ /// Get random number in the interval [0..size-1] (e.g. index in array)
+ /// @sa EGetRandMethod
+ /// @note eGetRand_LFG generator could be 100 times faster
+ /// than eGetRand_Sys one
+ size_t GetRandIndexSize_t(size_t size);
+
/// The max. value GetRand() returns
static TValue GetMax(void);
@@ -136,6 +166,7 @@ private:
TValue m_Seed;
TValue x_GetRand32Bits(void);
+ Uint8 x_GetRand64Bits(void);
TValue x_GetSysRand32Bits(void) const;
// prevent copying
@@ -210,6 +241,13 @@ inline CRandom::TValue CRandom::GetRand(void)
}
+inline Uint8 CRandom::GetRandUint8(void)
+{
+ Uint8 v1 = x_GetRand32Bits();
+ return (v1 << 32)+x_GetRand32Bits();
+}
+
+
inline CRandom::TValue CRandom::GetRandIndex(TValue size)
{
if ( (size & (size-1)) == 0 ) { // only one bit set - power of 2
@@ -226,12 +264,34 @@ inline CRandom::TValue CRandom::GetRandIndex(TValue size)
}
+inline size_t CRandom::GetRandIndexSize_t(size_t size)
+{
+#if SIZEOF_SIZE_T == 4
+ return GetRandIndex(Uint4(size));
+#else
+ return GetRandIndexUint8(size);
+#endif
+}
+
+
inline CRandom::TValue CRandom::GetRand(TValue min_value, TValue max_value)
{
return min_value + GetRandIndex(max_value - min_value + 1);
}
+inline Uint8 CRandom::GetRandUint8(Uint8 min_value, Uint8 max_value)
+{
+ return min_value + GetRandIndexUint8(max_value - min_value + 1);
+}
+
+
+inline size_t CRandom::GetRandSize_t(size_t min_value, size_t max_value)
+{
+ return min_value + GetRandIndexSize_t(max_value - min_value + 1);
+}
+
+
inline CRandom::TValue CRandom::GetMax(void)
{
return 0x7fffffff;
diff --git a/c++/include/util/range_coll.hpp b/c++/include/util/range_coll.hpp
index 5faa657..43c6b49 100644
--- a/c++/include/util/range_coll.hpp
+++ b/c++/include/util/range_coll.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL___RANGE_COLL__HPP
#define UTIL___RANGE_COLL__HPP
-/* $Id: range_coll.hpp 348990 2012-01-06 14:41:19Z grichenk $
+/* $Id: range_coll.hpp 479120 2015-09-16 16:48:06Z mozese2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,7 +51,8 @@ struct PRangeLessPos
///////////////////////////////////////////////////////////////////////////////
// class CRangeCollection<Position> represent a sorted collection of
-// CRange<Position>. It is guaranteed that ranges in collection do not overlap
+// CRange<Position>. It is guaranteed that ranges in collection do not overlap.
+// Unless DivideAt() was explicitly called, it is also guarantees that they
// and aren't adjacent so that there is no gap beween them.
// Adding an interval to the collection leads to possible merging it with
// existing intervals.
@@ -244,6 +245,14 @@ public:
return *this;
}
+ /// If position is in middle of range, divide into two consecutive ranges
+ /// after this position
+ TThisType & DivideAfter(const position_type &p)
+ {
+ x_Divide(p);
+ return *this;
+ }
+
protected:
typedef typename TRangeVector::iterator iterator;
typedef typename TRangeVector::reverse_iterator reverse_iterator;
@@ -385,6 +394,18 @@ protected:
}
m_vRanges = intersection_ranges;
}
+
+ void x_Divide(const position_type& p)
+ {
+ PRangeLessPos<TRange, position_type> P;
+ iterator it = lower_bound(begin_nc(), end_nc(), p, P);
+ if (it != end_nc() && it->GetFrom() <= p && it->GetTo() > p) {
+ position_type end_pos = it->GetTo();
+ it->SetTo(p);
+ m_vRanges.insert(++it, TRange(p+1, end_pos));
+ }
+ }
+
void x_CombineWith(const TThisType &c)
{
ITERATE(typename TThisType, it, c) {
diff --git a/c++/include/util/rangelist.hpp b/c++/include/util/rangelist.hpp
index 69d31e3..4acdcbd 100644
--- a/c++/include/util/rangelist.hpp
+++ b/c++/include/util/rangelist.hpp
@@ -1,4 +1,4 @@
-/* $Id: rangelist.hpp 448239 2014-10-03 14:17:45Z kazimird $
+/* $Id: rangelist.hpp 448236 2014-10-03 14:05:43Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/util/retry_ctx.hpp b/c++/include/util/retry_ctx.hpp
new file mode 100644
index 0000000..a5ce919
--- /dev/null
+++ b/c++/include/util/retry_ctx.hpp
@@ -0,0 +1,499 @@
+#ifndef RETRY_CTX__HPP
+#define RETRY_CTX__HPP
+
+/* $Id: retry_ctx.hpp 483518 2015-11-02 14:43:40Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Aleksey Grichenko
+ *
+ */
+
+/// @file retry_ctx.hpp
+/// Retry context class.
+
+#include <map>
+#include <corelib/ncbistd.hpp>
+#include <corelib/ncbitime.hpp>
+#include <corelib/ncbi_url.hpp>
+
+
+/** @addtogroup Retry Context
+ *
+ * @{
+ */
+
+
+BEGIN_NCBI_SCOPE
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CRetryContext -- Retry context.
+///
+/// The class used to store, send and receive retry related data.
+///
+class NCBI_XUTIL_EXPORT CRetryContext : public CObject
+{
+public:
+ CRetryContext(void);
+ virtual ~CRetryContext(void) {}
+
+ /// Content override flags
+ enum EContentOverride {
+ eNot_set, ///< No content provided, send the original request data
+ eNoContent, ///< Do not send any content on retry
+ eFromResponse, ///< On retry send content from the response body
+ eData ///< On retry send content from the response header
+ };
+
+ /// Check if another retry attempt has been requested (any new headers
+ /// except STOP received in the last reply).
+ bool GetNeedRetry(void) const;
+ void SetNeedRetry(void);
+ void ResetNeedRetry(void);
+
+ /// Clear all options.
+ void Reset(void);
+
+ /// Check if STOP flag is set.
+ bool IsSetStop(void) const;
+ /// Get STOP reason (or empty string).
+ const string& GetStopReason(void) const;
+ /// Set STOP flag, clear all other options.
+ void SetStop(const string& reason);
+ /// Reset STOP flag and reason.
+ void ResetStop(void);
+
+ /// Check if retry delay is set.
+ bool IsSetDelay(void) const;
+ /// Get retry delay.
+ const CTimeSpan& GetDelay(void) const;
+ /// Set retry delay.
+ void SetDelay(CTimeSpan delay);
+ /// Set retry delay in seconds.
+ void SetDelay(double sec);
+ /// Reset delay.
+ void ResetDelay(void);
+
+ /// Check if retry args are set.
+ bool IsSetArgs(void) const;
+ /// Get retry args, URL-decoded.
+ const string& GetArgs(void) const;
+ /// Set retry args. The arguments must be pre-URL-encoded as required.
+ /// The arguments set here will override any values set in the URL.
+ /// @sa SetUrl()
+ void SetArgs(const string& args);
+ /// Set retry args.
+ /// The arguments set here will override any values set in the URL.
+ /// @sa SetUrl()
+ void SetArgs(const CUrlArgs& args);
+ /// Reset args.
+ void ResetArgs(void);
+
+ /// Check if retry URL is set.
+ bool IsSetUrl(void) const;
+ /// Get retry URL.
+ const string& GetUrl(void) const;
+ /// Set retry URL. If the URL contains any arguments, they may be
+ /// overwritten by the values set through SetArgs().
+ void SetUrl(const string& url);
+ /// Set retry URL. If the URL contains any arguments, they may be
+ /// overwritten by the values set through SetArgs().
+ void SetUrl(const CUrl& url);
+ /// Reset URL.
+ void ResetUrl(void);
+
+ /// Check if content source is set.
+ bool IsSetContentOverride(void) const;
+ /// Get content source.
+ EContentOverride GetContentOverride(void) const;
+ /// Set content source.
+ void SetContentOverride(EContentOverride content);
+ /// Reset content source.
+ void ResetContentOverride(void);
+
+ /// Check if retry content is set and content-override flag assumes any
+ /// content (eFromResponse or eData).
+ bool IsSetContent(void) const;
+ /// Get retry content.
+ const string& GetContent(void) const;
+ /// Set retry content. If the content is non-empty and content-override
+ /// is eFromResponse or eData, the value should be sent by the server
+ /// automatically.
+ void SetContent(const string& content);
+ /// Reset content.
+ void ResetContent(void);
+
+ /// Check if the client should reconnect (e.g. if URL or args have changed).
+ bool NeedReconnect(void) const { return m_NeedReconnect; }
+ /// Set need-reconnect flag.
+ void SetNeedReconnect(void) { m_NeedReconnect = true; }
+ /// Reset need-reconnect flag (e.g. after reconnecting to the new
+ /// URL, but before reading new context).
+ void ResetNeedReconnect(void) { m_NeedReconnect = false; }
+
+ /// Map of name-value pairs.
+ typedef map<string, string> TValues;
+ /// Fill name-value pairs (e.g. to be used by a server application
+ /// to serve retry information). The default implementaion does nothing.
+ virtual void GetValues(TValues& /*values*/) const {}
+
+private:
+ enum FFlags {
+ fStop = 1 << 0,
+ fDelay = 1 << 1,
+ fArgs = 1 << 2,
+ fUrl = 1 << 3,
+ fContentOverride = 1 << 4,
+ fContent = 1 << 5
+ };
+ typedef int TFlags;
+
+ bool x_IsSetFlag(FFlags f) const;
+ void x_SetFlag(FFlags f, bool value = true);
+
+ TFlags m_Flags;
+ string m_StopReason;
+ CTimeSpan m_Delay;
+ string m_Args;
+ string m_Url;
+ EContentOverride m_ContentOverride;
+ string m_Content;
+ bool m_NeedRetry;
+ bool m_NeedReconnect;
+};
+
+
+/// HTTP-specific retry context implementation.
+class NCBI_XUTIL_EXPORT CHttpRetryContext : public CRetryContext
+{
+public:
+ CHttpRetryContext(void) {}
+ virtual ~CHttpRetryContext(void) {}
+
+ // Copy functions from CRetryContext - required by CRPCClient_Base
+ CHttpRetryContext(const CRetryContext& ctx);
+ CHttpRetryContext& operator=(const CRetryContext& ctx);
+
+ void ParseHeader(const char* http_header);
+
+ /// Fills HTTP header names and values.
+ virtual void GetValues(TValues& values) const;
+
+ static const char* kHeader_Stop; // X-NCBI-Retry-Stop
+ static const char* kHeader_Delay; // X-NCBI-Retry-Delay
+ static const char* kHeader_Args; // X-NCBI-Retry-Args
+ static const char* kHeader_Url; // X-NCBI-Retry-URL
+ static const char* kHeader_Content; // X-NCBI-Retry-Content
+ static const char* kContent_None; // no_content
+ static const char* kContent_FromResponse; // from_response
+ static const char* kContent_Value; // content:<url-encoded content>
+};
+
+
+/* @} */
+
+
+//////////////////////////////////////////////////////////////////////////////
+//
+// Inline
+//
+
+
+inline
+CRetryContext::CRetryContext(void)
+ : m_Flags(0),
+ m_ContentOverride(eNot_set),
+ m_NeedRetry(false),
+ m_NeedReconnect(false)
+{
+}
+
+
+inline
+bool CRetryContext::GetNeedRetry(void) const
+{
+ return m_NeedRetry;
+}
+
+
+inline
+void CRetryContext::SetNeedRetry(void)
+{
+ m_NeedRetry = true;
+}
+
+
+inline
+void CRetryContext::ResetNeedRetry(void)
+{
+ m_NeedRetry = false;
+}
+
+
+inline
+void CRetryContext::Reset(void)
+{
+ ResetStop();
+ ResetDelay();
+ ResetArgs();
+ ResetUrl();
+ ResetContentOverride();
+ ResetContent();
+ ResetNeedRetry();
+ ResetNeedReconnect();
+}
+
+
+inline
+bool CRetryContext::IsSetStop(void) const
+{
+ return x_IsSetFlag(fStop);
+}
+
+
+inline
+const string& CRetryContext::GetStopReason(void) const
+{
+ return m_StopReason;
+}
+
+
+inline
+void CRetryContext::SetStop(const string& reason)
+{
+ x_SetFlag(fStop);
+ m_StopReason = reason;
+}
+
+
+inline
+void CRetryContext::ResetStop(void)
+{
+ x_SetFlag(fStop, false);
+ m_StopReason.clear();
+}
+
+
+inline
+bool CRetryContext::IsSetDelay(void) const
+{
+ return x_IsSetFlag(fDelay);
+}
+
+
+inline
+const CTimeSpan& CRetryContext::GetDelay(void) const
+{
+ return m_Delay;
+}
+
+
+inline
+void CRetryContext::SetDelay(CTimeSpan delay)
+{
+ x_SetFlag(fDelay);
+ m_Delay = delay;
+}
+
+
+inline
+void CRetryContext::SetDelay(double sec)
+{
+ x_SetFlag(fDelay);
+ m_Delay.Set(sec);
+}
+
+
+inline
+void CRetryContext::ResetDelay(void)
+{
+ x_SetFlag(fDelay, false);
+ m_Delay.Clear();
+}
+
+
+inline
+bool CRetryContext::IsSetArgs(void) const
+{
+ return x_IsSetFlag(fArgs);
+}
+
+
+inline
+const string& CRetryContext::GetArgs(void) const
+{
+ return m_Args;
+}
+
+
+inline
+void CRetryContext::SetArgs(const string& args)
+{
+ x_SetFlag(fArgs);
+ m_Args = args;
+}
+
+
+inline
+void CRetryContext::SetArgs(const CUrlArgs& args)
+{
+ x_SetFlag(fArgs);
+ m_Args = args.GetQueryString(CUrlArgs::eAmp_Char);
+}
+
+
+inline
+void CRetryContext::ResetArgs(void)
+{
+ x_SetFlag(fArgs, false);
+ m_Args.clear();
+}
+
+
+inline
+bool CRetryContext::IsSetUrl(void) const
+{
+ return x_IsSetFlag(fUrl);
+}
+
+
+inline
+const string& CRetryContext::GetUrl(void) const
+{
+ return m_Url;
+}
+
+
+inline
+void CRetryContext::SetUrl(const string& url)
+{
+ x_SetFlag(fUrl);
+ m_Url = url;
+}
+
+
+inline
+void CRetryContext::SetUrl(const CUrl& url)
+{
+ x_SetFlag(fUrl);
+ m_Url = url.ComposeUrl(CUrlArgs::eAmp_Char);
+}
+
+
+inline
+void CRetryContext::ResetUrl(void)
+{
+ x_SetFlag(fUrl, false);
+ m_Url.clear();
+}
+
+
+inline
+bool CRetryContext::IsSetContentOverride(void) const
+{
+ return x_IsSetFlag(fContentOverride) &&
+ m_ContentOverride != eNot_set;
+}
+
+
+inline
+CRetryContext::EContentOverride
+CRetryContext::GetContentOverride(void) const
+{
+ return m_ContentOverride;
+}
+
+
+inline
+void CRetryContext::SetContentOverride(EContentOverride content)
+{
+ x_SetFlag(fContentOverride);
+ m_ContentOverride = content;
+}
+
+
+inline
+void CRetryContext::ResetContentOverride(void)
+{
+ x_SetFlag(fContentOverride, false);
+ m_ContentOverride = eNot_set;
+}
+
+
+inline
+bool CRetryContext::IsSetContent(void) const
+{
+ return x_IsSetFlag(fContent) &&
+ (m_ContentOverride == eData || m_ContentOverride == eFromResponse)
+ && !m_Content.empty();
+}
+
+
+inline
+const string& CRetryContext::GetContent(void) const
+{
+ return m_Content;
+}
+
+
+inline
+void CRetryContext::SetContent(const string& content)
+{
+ x_SetFlag(fContent);
+ m_Content = content;
+}
+
+
+inline
+void CRetryContext::ResetContent(void)
+{
+ x_SetFlag(fContent, false);
+ m_Content.clear();
+}
+
+
+inline
+bool CRetryContext::x_IsSetFlag(FFlags f) const
+{
+ return m_Flags & f;
+}
+
+
+inline
+void CRetryContext::x_SetFlag(FFlags f, bool value)
+{
+ if ( value ) {
+ m_Flags |= f;
+ }
+ else {
+ m_Flags &= ~f;
+ }
+}
+
+
+END_NCBI_SCOPE
+
+#endif /* RETRY_CTX__HPP */
diff --git a/c++/include/util/sequtil/sequtil_convert.hpp b/c++/include/util/sequtil/sequtil_convert.hpp
index fdfa3cc..228b796 100644
--- a/c++/include/util/sequtil/sequtil_convert.hpp
+++ b/c++/include/util/sequtil/sequtil_convert.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL_SEQUTIL___SEQUTIL_CONVERT__HPP
#define UTIL_SEQUTIL___SEQUTIL_CONVERT__HPP
-/* $Id: sequtil_convert.hpp 444998 2014-08-29 14:53:16Z ivanov $
+/* $Id: sequtil_convert.hpp 444660 2014-08-26 20:15:25Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/util/strsearch.hpp b/c++/include/util/strsearch.hpp
index 53a0c1a..d98d8b6 100644
--- a/c++/include/util/strsearch.hpp
+++ b/c++/include/util/strsearch.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL___STRSEARCH__HPP
#define UTIL___STRSEARCH__HPP
-/* $Id: strsearch.hpp 196846 2010-07-09 13:39:06Z gouriano $
+/* $Id: strsearch.hpp 450776 2014-10-30 16:20:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -156,7 +156,8 @@ public:
/// @param pos
/// Position shift in text
/// @return
- /// the position at which the pattern was found, -1 otherwise.
+ /// the position at which the pattern was found,
+ /// size_t(-1) (NPOS) otherwise.
size_t Search(const string& text, size_t pos = 0) const
{
return Search(text.c_str(), pos, text.length());
@@ -172,7 +173,8 @@ public:
/// @param text_len
/// Length of text
/// @return
- /// the position at which the pattern was found, -1 otherwise.
+ /// the position at which the pattern was found,
+ /// SIZE_TYPE(-1) (NPOS) otherwise.
SIZE_TYPE Search(const char* text,
SIZE_TYPE pos,
SIZE_TYPE text_len) const;
diff --git a/c++/include/util/tables/raw_scoremat.h b/c++/include/util/tables/raw_scoremat.h
index aff357d..d0c9ace 100644
--- a/c++/include/util/tables/raw_scoremat.h
+++ b/c++/include/util/tables/raw_scoremat.h
@@ -1,7 +1,7 @@
#ifndef UTIL_TABLES___SCOREMAT__H
#define UTIL_TABLES___SCOREMAT__H
-/* $Id: raw_scoremat.h 459038 2015-02-12 17:28:36Z ivanov $
+/* $Id: raw_scoremat.h 458581 2015-02-06 15:18:12Z boratyng $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/include/util/thread_pool_old.hpp b/c++/include/util/thread_pool_old.hpp
index 249385e..099c6aa 100644
--- a/c++/include/util/thread_pool_old.hpp
+++ b/c++/include/util/thread_pool_old.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL__THREAD_POOL_OLD__HPP
#define UTIL__THREAD_POOL_OLD__HPP
-/* $Id: thread_pool_old.hpp 426855 2014-02-13 18:54:03Z ucko $
+/* $Id: thread_pool_old.hpp 467434 2015-05-13 16:41:39Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -406,7 +406,8 @@ public:
/// The maximum number of urgent threads running simultaneously
CPoolOfThreads(unsigned int max_threads, unsigned int queue_size,
unsigned int spawn_threshold = 1,
- unsigned int max_urgent_threads = kMax_UInt);
+ unsigned int max_urgent_threads = kMax_UInt,
+ const string& thread_name = kEmptyStr);
/// Destructor
virtual ~CPoolOfThreads(void);
@@ -515,6 +516,8 @@ protected:
TQueue m_Queue;
bool m_QueuingForbidden;
+ const string m_ThreadName;
+
private:
friend class CThreadInPool<TRequest>;
TItemHandle x_AcceptRequest(const TRequest& req,
@@ -619,8 +622,10 @@ public:
/// The maximum number of urgent threads running simultaneously
CStdPoolOfThreads(unsigned int max_threads, unsigned int queue_size,
unsigned int spawn_threshold = 1,
- unsigned int max_urgent_threads = kMax_UInt)
- : TParent(max_threads, queue_size, spawn_threshold, max_urgent_threads)
+ unsigned int max_urgent_threads = kMax_UInt,
+ const string& thread_name = kEmptyStr)
+ : TParent(max_threads, queue_size, spawn_threshold, max_urgent_threads,
+ thread_name)
{}
virtual ~CStdPoolOfThreads();
@@ -997,6 +1002,14 @@ void CThreadInPool<TRequest>::x_HandleOneRequest(bool catch_all)
template <typename TRequest>
void* CThreadInPool<TRequest>::Main(void)
{
+ _ASSERT(m_Pool);
+
+ const string& name = m_Pool->m_ThreadName;
+
+ if (!name.empty()) {
+ SetCurrentThreadName(name);
+ }
+
try {
m_Pool->Register(*this);
} catch (CThreadException&) {
@@ -1042,11 +1055,13 @@ template <typename TRequest>
CPoolOfThreads<TRequest>::CPoolOfThreads(unsigned int max_threads,
unsigned int queue_size,
unsigned int spawn_threshold,
- unsigned int max_urgent_threads)
+ unsigned int max_urgent_threads,
+ const string& thread_name)
: m_MaxThreads(max_threads), m_MaxUrgentThreads(max_urgent_threads),
m_Threshold(spawn_threshold), m_Delta(0),
m_Queue(queue_size > 0 ? queue_size : max_threads),
- m_QueuingForbidden(queue_size == 0)
+ m_QueuingForbidden(queue_size == 0),
+ m_ThreadName(thread_name)
{
m_ThreadCount.Set(0);
m_UrgentThreadCount.Set(0);
diff --git a/c++/include/util/xregexp/regexp_template_tester.hpp b/c++/include/util/xregexp/regexp_template_tester.hpp
new file mode 100644
index 0000000..f1cd393
--- /dev/null
+++ b/c++/include/util/xregexp/regexp_template_tester.hpp
@@ -0,0 +1,377 @@
+#ifndef UTIL___REGEXP_TEMPLATE_TESTER__HPP
+#define UTIL___REGEXP_TEMPLATE_TESTER__HPP
+
+/* $Id: regexp_template_tester.hpp 467298 2015-05-12 17:17:00Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Vladimir Ivanov
+ *
+ */
+
+/// @file regexp_template_tester.hpp
+/// Regexp template tester based on the Perl Compatible Regular Expression
+/// (pcre) library. Allow to test delimited text data against template
+/// with regular expression rules.
+
+#include <corelib/ncbistr.hpp>
+
+BEGIN_NCBI_SCOPE
+
+
+/** @addtogroup Regexp
+ *
+ * @{
+ */
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CRegexpTemplateTester --
+///
+/// Match delimited text data against template with regular expression rules.
+///
+/// Template file can have some types of lines:
+/// 1) comment line, started with // symbols (can be changed);
+/// 2) command lines, started with # symbol (can be changed);
+/// 3) regular expressions, that are used to match corresponding line
+/// in the tested file/stream. Usually number of lines in the tested file
+/// should be the same as the number of rule lines in the template,
+/// unless you use 'stop' or 'skip' template commands (see below).
+///
+/// Template commands allow to use variables. Each variable should be surrounded
+/// with figure brackets with preceding $ symbol, like ${var}. Except 'set'
+/// command where we define variable. Note that this can be changed and you can use
+/// any other symbols to separate variables.
+///
+/// Commands:
+///
+/// 1) set var=value
+/// Define variable 'var', set it to 'value'.
+/// 'value' can be string, any other variable or combination of it.
+/// This type of variable works almost as constants in the C++,
+/// they can be useful to predefine some frequently used values
+/// in the regular expression rules. All variable names starts with
+/// a letter and can have numbers, letters, '-' or '_'.
+/// Example:
+/// # set fruit=apple
+/// # set color=red
+/// # set str=${color} ${fruit}
+/// // variable 'str' have value 'red apple' now
+/// This is a rule line with a variable ${str}
+///
+/// 2) echo <string>
+/// Prints string/variables to stdout. Can be useful for debug purposes.
+/// Example:
+/// # set fruit=apple
+/// # echo some string
+/// # echo ${fruit}
+/// # echo We have an ${fruit}
+///
+/// 3) test <expression>
+/// Compare variable with a string value.
+/// 'value' can be string, any other variable or combination of it.
+/// Allowed comparing operators:
+/// == - left value equal to right value
+/// != - left value doesn't equal to right value.
+/// =~ - left value match to regexp on right
+/// !~ - left value doesn't match to regexp on right.
+/// Spaces around the comparison operator counts as part of
+/// the comparing strings on left and right accordingly.
+/// Example:
+/// # set fruit=apple
+/// # set color=red
+/// # test ${fruit}==apple
+/// # test ${fruit}!=orange
+/// # test red ${fruit}==red apple
+/// # test ${color} ${fruit}==red apple
+/// # test ${fruit}=~\w{3,}
+/// # set re=\w{3,}
+/// # test ${fruit}=~${re}
+///
+/// 4) include path
+/// Include sub-template with name 'path' and process it.
+/// This allow to split big templates to parts, or separate common
+/// part of many templates. 'path' defines a relative path to
+/// the sub-template from the directory of the template that includes it.
+/// Sub-templates can include any other templates.
+/// Example:
+/// # include common_header.tpl
+/// # include tests/test1
+/// # include tests/test2
+///
+/// 5) inline variables
+/// One more way to define variables based on the data in the matching
+/// string. For example, comparing file can have such line:
+/// We have 5 apples.
+///
+/// Corresponding template file may have next rules:
+/// We have ${count=[1-9]+} ${fruit=[a-z]+}\.
+/// # test ${count}==5
+/// # test ${fruit}==apples
+///
+/// 6) skip <expression>
+/// Allow to skip lines in the tested file/stream.
+/// It is possible to skip:
+/// - fixed number of lines;
+/// - while lines match specified regular expression (find not);
+/// - until some line will match specified regular expression (find);
+/// Regular expressions can use variables here as well.
+/// Note, that for while/until cases, testing stops on a line that
+/// don't/meet specified criteria. So you can parse it with a different
+/// rule again. If you don't need that line you can use 'skip 1' command
+/// on the next template line or a regular expression that matches any
+/// string, like '.*'.
+/// Example:
+/// // Skip next 5 lines in the tested file/stream
+/// # skip 5
+/// // Skip all next lines started with a capital letter
+/// # skip while ^[A-Z]+
+/// // Skip all next lines until we find a string that have
+/// // some digits followed with 'apple' word.
+/// # set fruit=apple
+/// # skip until \d+ ${fruit}
+/// We have ${count=\d+} ${fruit}
+/// # test ${count}==1
+///
+/// 7) stop
+/// Stops processing the current template. If located in the main template,
+/// it forces Compare() methods to return immediatle. Can be useful for
+/// debug purposes or if you want to check only some part of the file,
+/// ignoring any lines below some point. Note, that if 'stop' command have
+/// used in the sub-template, testing engine will stop processing that
+/// sub-template only and continue processing from the next line in
+/// the parent template.
+/// Example:
+/// # stop
+///
+/// Nested variables.
+///
+/// You can use nested variables in any expression and every command that support it.
+/// They can be useful in some cases, especially if you want to use the same symbols
+/// used to define variables. For example, you can write next template line:
+///
+/// We have ${count=[1-9]+} ${fruit=[a-z]+}\.
+///
+/// It have correct syntax, but what if you want to make it a bit complex or strict?
+/// For example next template line should generate parsing errors:
+///
+/// // Match 2 or more digit numbers and fruits names with 4 letters at least
+/// We have ${count=\d{2,}} ${fruit=\w{4,}}\.
+///
+/// This is because {...} is used inside variable defnition. As solution you can
+/// choice different symbols that will define the start and end sequences for all
+/// variables, or use nested variables as specified below:
+///
+/// # set d2=\d{2,}
+/// # set w4=\w{4,}
+/// We have ${count=${d2}} ${fruit=${w4}}\.
+///
+/// Also, you can construct variable names on the fly:
+///
+/// # set color=red
+/// # echo ${${color}_${apple}}
+///
+///
+/// Note, that all methods throw CRegexpTemplateTesterException on errors,
+/// problems with parsing template commands or data mismatch.
+///
+
+class CRegexpTemplateTester
+{
+public:
+ ///
+ enum EFlags {
+ fSkipEmptySourceLines = (1 << 0), ///< Skip empty lines in the source
+ fSkipEmptyTemplateLines = (1 << 1), ///< Skip empty lines in the template
+ fSkipEmptyLines = fSkipEmptySourceLines | fSkipEmptyTemplateLines
+ };
+ typedef unsigned int TFlags; ///< Binary OR of "EFlags"
+
+ /// Default constructor.
+ CRegexpTemplateTester(TFlags flags = 0);
+
+
+ /// Compare file against template (file version).
+ ///
+ /// @param file_path
+ /// Path to the checking file.
+ /// @param template_path
+ /// Path to the corresponding template.
+ /// @return
+ /// Nothing on success.
+ /// Throw CRegexpTemplateTesterException on error or mismatch.
+ ///
+ void Compare(const string& file_path, const string& template_path);
+
+ /// Compare file against template (stream version).
+ ///
+ /// @param file_stream
+ /// Input stream with checking data.
+ /// @param template_stream
+ /// Input stream with corresponding template data.
+ /// @return
+ /// Nothing on success.
+ /// Throw CRegexpTemplateTesterException on error or mismatch.
+ /// @note
+ /// Due to file-oriented nature of the 'include' command in the
+ /// templates, it works a little different that in the file-based
+ /// version. It is better do not use 'include' with streams at all,
+ /// but if you want it, be aware. We don't have path to the directory
+ /// with the original template, so included sub-template should be
+ /// located in the current directory.
+ ///
+ void Compare(istream& file_stream, istream& template_stream);
+
+
+ // --- Auxiliary methods used to tune up parsing for specific needs.
+
+ /// Change strings defining start/end of variables.
+ /// By default use next syntax: ${var}
+ void SetVarScope(string& start, string& end);
+
+ /// Change string defining start of comments line in templates.
+ /// Default value: "//"
+ void SetCommentStart(string& str);
+
+ /// Change string defining start of template commands and operations.
+ /// Default value: "#"
+ void SetCommandStart(string& str);
+
+ /// Change delimiters string, used for comparing data and templates.
+ /// Default value: "\r\n"
+ void SetDelimiters(string& str);
+
+
+ // --- Debug functions
+
+ void PrintVars(void) const;
+ void PrintVar (const string& name) const;
+ string GetVar (const string& name) const;
+
+ typedef map<string, string> TVarMap;
+ const TVarMap& GetVars(void) const;
+
+private:
+ // Operations
+ void x_Op_Set (CTempString str);
+ void x_Op_Echo (CTempString str);
+ void x_Op_Test (CTempString str);
+ void x_Op_Include (CTempString str, istream& file_stm);
+ void x_Op_Skip (CTempString str, istream& file_stm);
+
+private:
+ // Internal methods
+
+ /// Reset object state
+ void x_Reset(void);
+
+ /// Processing source
+ enum ESource {
+ eFile, ///< source file/stream
+ eTemplate ///< template
+ };
+
+ /// The reason of stopping x_Compare(), if no error.
+ enum EResult {
+ eTemplateEOF,
+ eStop
+ };
+ typedef list<string> TVarList;
+
+ /// Main compare method, compare streams.
+ /// Can be used recursively to process includes.
+ /// Return TRUE if 'stop' command found.
+ EResult x_Compare(istream& file_stream, istream& template_stream);
+
+ /// Process/compare lines.
+ void x_CompareLines(CTempString file_line, CTempString template_line);
+
+ /// Parse variable from string, return its length.
+ /// Can process nested variables.
+ SIZE_TYPE x_ParseVar(CTempString str, SIZE_TYPE pos) const;
+
+ /// Parse/check variable name from string, return its length.
+ SIZE_TYPE x_ParseVarName (CTempString str, SIZE_TYPE pos) const;
+
+ /// Replace all variables in the string with corresponding values.
+ /// Also used for preparing inline variables for consecutive regexp matching.
+ string x_SubstituteVars(CTempString str, TVarList* inline_vars) const;
+
+ /// Get line from the stream 'is'.
+ istream& x_GetLine(istream& is, ESource src);
+
+private:
+ TFlags m_Flags; ///< Processing flags
+ string m_VarStart; ///< Variable definition start
+ string m_VarEnd; ///< Variable definition end
+ string m_OpStart; ///< Start of the template command line
+ string m_CommentStart; ///< Start of the comment line
+ string m_EOLs; ///< Lines delimiters
+ TVarMap m_Vars; ///< Map of variables/values
+
+ // Variables for currently processing file/(sub-)template
+ string m_FileName; ///< Current file name (if any)
+ string m_FileLine; ///< Currently processing file line
+ SIZE_TYPE m_FileLineNum; ///< Current file/stream line number
+ string m_TemplateName; ///< Current template name
+ string m_TemplateLine; ///< Currently processing template line
+ SIZE_TYPE m_TemplateLineNum; ///< Current template line number
+
+ bool m_ReprocessFileLine; ///< TRUE if m_FileLine should be reprocessed
+ ///< with next template data line
+};
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CRegexpTemplateTesterException --
+///
+/// Define exceptions generated by CRegexpTemplateTester.
+
+class CRegexpTemplateTesterException : public CCoreException
+{
+public:
+ /// Error types that tester can generate.
+ enum EErrCode {
+ eOpenFile, ///< file open error
+ eMismatchLength, ///< file/template line number mismatch
+ eMismatchContent, ///< file/template lines do not match
+ eVarNotFound, ///< variable not found
+ eVarErr, ///< variable definition error
+ eOpUnknown, ///< unknown operation
+ eOpErr, ///< operation definition error
+ eOpTest ///< 'test' operation return FALSE
+ } ;
+ virtual const char* GetErrCodeString(void) const;
+ NCBI_EXCEPTION_DEFAULT(CRegexpTemplateTesterException, CCoreException);
+};
+
+
+/* @} */
+
+END_NCBI_SCOPE
+
+
+#endif /* UTIL___REGEXP_TEMPLATE_TESTER__HPP */
diff --git a/c++/scripts/common/add_vdb.sh b/c++/scripts/common/add_vdb.sh
new file mode 100755
index 0000000..7945190
--- /dev/null
+++ b/c++/scripts/common/add_vdb.sh
@@ -0,0 +1,65 @@
+#!/bin/sh
+# $Id: add_vdb.sh 478499 2015-09-09 19:00:24Z ivanov $
+. "`dirname $0`/common.sh"
+
+set -e
+exec 3>&1 >&2
+root=`dirname $0`/../../local
+mkdir -p $root
+cd $root
+root=`pwd`
+ptb_ini=../src/build-system/project_tree_builder.ini
+tag=`sed -ne 's,.*/vdb-versions/,,p' $ptb_ini`
+name=ncbi-vdb${tag+"-$tag"}
+platform=`COMMON_DetectPlatform`
+
+mkdir -p src
+cd src
+if [ -d ncbi-vdb/.git ]; then
+ (cd ncbi-vdb && git fetch)
+else
+ git clone https://github.com/ncbi/ncbi-vdb.git
+fi
+if [ -d ngs/.git ]; then
+ (cd ngs && git fetch)
+else
+ git clone https://github.com/ncbi/ngs.git
+fi
+cd ncbi-vdb
+git checkout "${tag:-master}"
+if [ "$platform" = IntelMAC ]; then
+ archflag=--arch=fat86
+ if [ ! -d $root/tmp/force-clang ]; then
+ mkdir -p $root/tmp/force-clang
+ ln -s /usr/bin/clang $root/tmp/force-clang/gcc
+ fi
+ PATH=$root/tmp/force-clang:$PATH
+else
+ archflag=
+fi
+./configure --prefix=$root/$name --build-prefix=$root/build/$name $archflag \
+ ${LIBXML_LIBPATH:+"LDFLAGS=$LIBXML_LIBPATH"}
+make
+make install
+if [ -f $root/$name/include/klib/rc.h ]; then
+ :
+else
+ (cd interfaces && tar cf - *) | (cd $root/$name/include && tar xf -)
+fi
+if [ -d $root/$name/lib32_64 ]; then
+ for x in lib lib64; do
+ [ -d $root/$name/$x ] || ln -s lib32_64 $root/$name/$x
+ done
+fi
+cat <<EOF
+
+----------------------------------------------------------------------
+NCBI VDB libraries successfully built and installed to
+$root/$name
+
+To take advantage of them, please configure the C++ Toolkit
+--with-vdb=$root/$name
+----------------------------------------------------------------------
+EOF
+
+echo $root/$name >&3
diff --git a/c++/scripts/common/check/check_add.sh b/c++/scripts/common/check/check_add.sh
index 527accd..c7c992a 100755
--- a/c++/scripts/common/check/check_add.sh
+++ b/c++/scripts/common/check/check_add.sh
@@ -1,5 +1,5 @@
#! /bin/sh
-# $Id: check_add.sh 468633 2015-05-27 12:08:08Z ivanov $
+# $Id: check_add.sh 468632 2015-05-27 11:59:00Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
diff --git a/c++/scripts/common/check/check_exec.sh b/c++/scripts/common/check/check_exec.sh
index fce1476..3ba703a 100755
--- a/c++/scripts/common/check/check_exec.sh
+++ b/c++/scripts/common/check/check_exec.sh
@@ -1,6 +1,6 @@
#! /bin/sh
-# $Id: check_exec.sh 453332 2014-12-02 19:11:08Z ivanov $
+# $Id: check_exec.sh 453282 2014-12-02 16:01:34Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
diff --git a/c++/scripts/common/check/check_exec_guard.sh b/c++/scripts/common/check/check_exec_guard.sh
index c9d7894..a434d47 100755
--- a/c++/scripts/common/check/check_exec_guard.sh
+++ b/c++/scripts/common/check/check_exec_guard.sh
@@ -1,6 +1,6 @@
#! /bin/sh
-# $Id: check_exec_guard.sh 457098 2015-01-20 17:30:28Z ivanov $
+# $Id: check_exec_guard.sh 456439 2015-01-12 19:19:30Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
diff --git a/c++/scripts/common/check/check_exec_test.sh b/c++/scripts/common/check/check_exec_test.sh
index faec678..31ae456 100755
--- a/c++/scripts/common/check/check_exec_test.sh
+++ b/c++/scripts/common/check/check_exec_test.sh
@@ -1,6 +1,6 @@
#! /bin/sh
-# $Id: check_exec_test.sh 450806 2014-10-30 17:26:50Z ivanov $
+# $Id: check_exec_test.sh 449804 2014-10-21 14:51:36Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
diff --git a/c++/scripts/common/check/check_make_cfg.sh b/c++/scripts/common/check/check_make_cfg.sh
index 9851fed..d7b7f5e 100755
--- a/c++/scripts/common/check/check_make_cfg.sh
+++ b/c++/scripts/common/check/check_make_cfg.sh
@@ -1,6 +1,6 @@
#! /bin/sh
-# $Id: check_make_cfg.sh 468633 2015-05-27 12:08:08Z ivanov $
+# $Id: check_make_cfg.sh 473888 2015-07-23 12:02:15Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
@@ -269,7 +269,6 @@ case "\$method" in
#----------------------------------------------------------
load_to_db )
is_db_load=true
- rm -f "\$build_dir/test_stat_load.log"
# See RunTest() below
;;
#----------------------------------------------------------
@@ -281,6 +280,8 @@ esac
## Run
+trap "touch \$check_dir/check.failed" 1 2 15
+rm \$check_dir/check.failed \$check_dir/check.success > /dev/null 2>&1
# Set log_site for tests
export NCBI_APPLOG_SITE=testcxx
@@ -693,6 +694,12 @@ if ! \$is_db_load; then
echo
fi
+if test \$count_err -eq 0; then
+ touch \$check_dir/check.success
+else
+ touch \$check_dir/check.failed
+fi
+
exit \$count_err
EOF
diff --git a/c++/scripts/common/check/check_make_unix.sh b/c++/scripts/common/check/check_make_unix.sh
index 9ff9082..844c404 100755
--- a/c++/scripts/common/check/check_make_unix.sh
+++ b/c++/scripts/common/check/check_make_unix.sh
@@ -1,6 +1,6 @@
#! /bin/sh
-# $Id: check_make_unix.sh 468633 2015-05-27 12:08:08Z ivanov $
+# $Id: check_make_unix.sh 471330 2015-06-25 15:56:48Z ivanov $
# Author: Vladimir Ivanov, NCBI
#
###########################################################################
@@ -296,6 +296,9 @@ case "\$method" in
esac
+trap "touch $x_target_dir/check.failed" 1 2 15
+rm $x_target_dir/check.failed $x_target_dir/check.success > /dev/null 2>&1
+
# Set log_site for tests
NCBI_APPLOG_SITE=testcxx
export NCBI_APPLOG_SITE
@@ -881,6 +884,12 @@ if \$no_report_err && \$no_db_load; then
fi
fi
+if test \$count_err -eq 0; then
+ touch $x_target_dir/check.success
+else
+ touch $x_target_dir/check.failed
+fi
+
exit \$count_err
EOF
diff --git a/c++/scripts/common/check/inspxe-suppressions/_vs.sup b/c++/scripts/common/check/inspxe-suppressions/_vs.sup
index 9de1011..4ea2b79 100644
--- a/c++/scripts/common/check/inspxe-suppressions/_vs.sup
+++ b/c++/scripts/common/check/inspxe-suppressions/_vs.sup
@@ -252,4 +252,13 @@ suppression = {
}
}
}
-
+suppression = {
+ name = "GetUserName"
+ type = {invalid_memory_access}
+ stacks = {
+ {
+ ...;
+ mod=ADVAPI32.dll,func=GetUserNameA;
+ }
+ }
+}
diff --git a/c++/scripts/common/check/valgrind.supp b/c++/scripts/common/check/valgrind.supp
index 4be606c..89afb60 100644
--- a/c++/scripts/common/check/valgrind.supp
+++ b/c++/scripts/common/check/valgrind.supp
@@ -1,6 +1,6 @@
-# $Id: valgrind.supp 435732 2014-05-20 15:06:31Z ucko $
+# $Id: valgrind.supp 462287 2015-03-17 18:28:07Z vakatov $
#
-# Valgrind suppression file (version 3.5.0).
+# Valgrind suppression file (version 3.5.0 -> 3.8.1).
#
################################################################################
#
@@ -32,6 +32,256 @@
#
################################################################################
+
+{
+ corelib/CFileUtil::GetTotalDiskSpace, PANFS, CXX-5713 because DLL is not supposed to be closed
+ Memcheck:Leak
+ fun:malloc
+ ...
+ fun:_dl_open
+ ...
+ fun:*s_GetDiskSpace_PANFS*
+ fun:*s_GetFileSystemInfo*
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_fill
+ fun:__log_putr
+ ...
+ fun:__log_put
+ fun:__txn_regop_log
+ fun:__txn_commit
+ fun:__txn_commit_pp
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_ovput() in bt_put.c:886
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_fill
+ fun:__log_putr
+ ...
+ fun:__log_put
+ fun:__db_big_log
+ fun:__db_poff
+ ...
+ fun:__bam_iitem
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 3)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__memp_pgwrite
+ fun:__memp_bhwrite
+ fun:__memp_sync_int
+ ...
+ fun:__db_sync
+ fun:__db_refresh
+ fun:__db_close
+ fun:__db_close_pp
+ fun:_ZN4ncbi12CBDB_RawFile7x_CloseENS0_12EIgnoreErrorE
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 2b)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__memp_pgwrite
+ fun:__memp_bhwrite
+ fun:__memp_sync_int
+ ...
+ fun:__memp_trickle_pp
+ fun:_ZN4ncbi8CBDB_Env11MempTrickleEiPi
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 2a)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_flush_int
+ fun:__log_flush
+ ...
+ fun:__memp_sync_int
+ ...
+ fun:__memp_trickle_pp
+ fun:_ZN4ncbi8CBDB_Env11MempTrickleEiPi
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 1e)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_fill
+ fun:__log_putr
+ ...
+ fun:__log_put
+ fun:__db_addrem_log
+ fun:__db_pitem
+ fun:__bam_iitem
+ fun:__bamc_put
+ fun:__dbc_put
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 1d)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_fill
+ fun:__log_putr
+ ...
+ fun:__log_put
+ fun:__bam_repl_log
+ fun:__bam_ritem
+ fun:__bam_iitem
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__dbc_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile9x_DB_CPutEP5__dbcP8__db_dbtS4_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 1c)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_flush_int
+ ...
+ fun:__log_put
+ ...
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack (Variant 1b5)
+ Memcheck:Param
+ pwrite64(buf)
+ ...
+ fun:__os_io
+ fun:__log_write
+ fun:__log_fill
+ fun:__log_putr
+ ...
+ fun:__log_put
+ ...
+ fun:__bam_split
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack (Variant 1b4)
+ Memcheck:Cond
+ fun:__log_putr
+ ...
+ fun:__log_put
+ fun:__bam_split_log
+ ...
+ fun:__bam_split
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack (Variant 1b3)
+ Memcheck:Cond
+
+ fun:__log_putr
+ fun:__log_put
+ fun:__db_addrem_log
+ ...
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack (Variant 1b2)
+ Memcheck:Cond
+ fun:__log_putr
+ fun:__log_put
+ fun:__db_addrem_log
+ fun:__db_pitem
+ fun:__bam_iitem
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack (Variant 1b1)
+ Memcheck:Cond
+ fun:__log_putr
+ fun:__log_put_next
+ fun:__log_put
+ fun:__db_addrem_log
+ fun:__db_pitem
+ fun:__bam_ovput
+ fun:__bam_iitem
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
+{
+ BerkeleyDB 4.6.21.1 glitch -- uninit value created on stack in __bam_broot() in bt_split.c:519 (Variant 1a)
+ Memcheck:Cond
+ fun:__log_putr
+ fun:__log_put_next
+ fun:__log_put
+ fun:__db_addrem_log
+ fun:__db_pitem
+ fun:__bam_broot
+ fun:__bam_root
+ fun:__bam_split
+ fun:__bamc_put
+ fun:__dbc_put
+ fun:__db_put
+ fun:__db_put_pp
+ fun:_ZN4ncbi12CBDB_RawFile8x_DB_PutEP8__db_dbtS2_j
+}
+
{
Known LIBC bug (https://bugs.kde.org/show_bug.cgi?id=167483)
Memcheck:Free
@@ -99,7 +349,7 @@
fun:__memp_pgwrite
fun:__memp_bhwrite
fun:__memp_sync_int
- fun:__memp_fsync
+ ...
fun:__db_sync
fun:__db_refresh
fun:__db_close
diff --git a/c++/scripts/common/common.sh b/c++/scripts/common/common.sh
index 82bbe61..0c7298a 100755
--- a/c++/scripts/common/common.sh
+++ b/c++/scripts/common/common.sh
@@ -1,5 +1,5 @@
#
-# $Id: common.sh 194912 2010-06-17 19:28:57Z ucko $
+# $Id: common.sh 481670 2015-10-14 18:27:18Z ivanov $
# ATTENTION! This is to be 'included' (using ". common.sh'), not executed!
# Then, you execute the "COMMON_xxx" function(s) you like inside
# your script.
@@ -427,6 +427,7 @@ COMMON_DetectPlatform()
Darwin\ i386 ) echo IntelMAC ;;
Darwin\ x86_64 ) echo IntelMAC ;; # split into IntelMac64?
Darwin\ powerpc ) echo PowerMAC ;;
+ FreeBSD\ amd64 ) echo FreeBSD64 ;;
FreeBSD\ i386 ) echo FreeBSD32 ;;
IRIX64\ * ) echo IRIX64 ;;
Linux\ i?86 ) echo Linux32 ;;
diff --git a/c++/scripts/common/impl/compress_tests.sh b/c++/scripts/common/impl/compress_tests.sh
index 20b20f7..7cc317f 100755
--- a/c++/scripts/common/impl/compress_tests.sh
+++ b/c++/scripts/common/impl/compress_tests.sh
@@ -5,7 +5,7 @@ case "$1" in
* ) def_compress_others= ;;
esac
-compress='gzip -Nf'
+ext='.gz'
ws='[ ]' # Contains a space and a tab.
if [ -f ../../build_info ] \
@@ -13,7 +13,7 @@ if [ -f ../../build_info ] \
&& grep "^$ws*CODEBASE$ws*=$ws*PRODUCTION$ws*\$" ../../build_info \
&& bzip2 --version </dev/null) >/dev/null 2>&1; then
# Some bzip2 releases still try to compress stdin with --version(!)
- compress='bzip2 -f'
+ ext='.bz2'
fi
for dir in "$@"; do
@@ -25,24 +25,29 @@ for dir in "$@"; do
* ) compress_others=no ;;
esac
fi
+ targets=''
for f in $dir/*; do
[ -f "$f" ] || continue
case "`basename $f`" in
plugin_test | speedtest | streamtest | biosample_chk \
| testipub | test_basic_cleanup | test_checksum | test_mghbn \
- | test_ncbi_connutil_hit | test_ncbi_dblb | test_ncbi_http_get \
- | *.*z* )
+ | test_ncbi_connutil_hit | test_ncbi_crypt | test_ncbi_dblb \
+ | test_ncbi_http_get | *.*z* )
;;
*test* | *demo* | *sample* \
| net*che*_c* | ns_*remote_job* | save_to_nc )
- $compress $f
+ targets="$targets `basename $f`$ext"
;;
*blast* | datatool | gbench* | id1_fetch | idwwwget | lbsmc \
| one2all )
;;
*)
- test "$compress_others" = "no" || $compress $f
+ test "$compress_others" = "no" || \
+ targets="$targets `basename $f`$ext"
;;
esac
done
+ ${MAKE-make} -C $dir \
+ -f `dirname $0`/../../../src/build-system/Makefile.compress_tests \
+ $targets
done
diff --git a/c++/scripts/common/impl/if_diff.sh b/c++/scripts/common/impl/if_diff.sh
index a3d299e..d2c3998 100755
--- a/c++/scripts/common/impl/if_diff.sh
+++ b/c++/scripts/common/impl/if_diff.sh
@@ -1,6 +1,6 @@
#! /bin/sh
#################################
-# $Id: if_diff.sh 442382 2014-08-01 18:43:59Z ucko $
+# $Id: if_diff.sh 442076 2014-07-30 14:06:45Z ucko $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
diff --git a/c++/scripts/common/impl/install.sh b/c++/scripts/common/impl/install.sh
index 80505eb..723644a 100755
--- a/c++/scripts/common/impl/install.sh
+++ b/c++/scripts/common/impl/install.sh
@@ -16,7 +16,7 @@
echo "[`date`]"
-svn_location=`echo '$URL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.2.31/c++/scripts/common/impl/install.sh $' | sed "s%\\$[U]RL: *\\([^$][^$]*\\) \\$.*%\\1%"`
+svn_location=`echo '$URL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.3.0/c++/scripts/common/impl/install.sh $' | sed "s%\\$[U]RL: *\\([^$][^$]*\\) \\$.*%\\1%"`
svn_revision=`echo '$Revision: 429376 $' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
script_name=`basename $0`
diff --git a/c++/scripts/common/new_project.sh b/c++/scripts/common/new_project.sh
index bd1fca6..42df854 100755
--- a/c++/scripts/common/new_project.sh
+++ b/c++/scripts/common/new_project.sh
@@ -1,9 +1,9 @@
#! /bin/sh
-# $Id: new_project.sh 443416 2014-08-13 20:54:10Z ucko $
+# $Id: new_project.sh 442644 2014-08-05 20:01:57Z ucko $
# Authors: Denis Vakatov (vakatov at ncbi.nlm.nih.gov),
# Aaron Ucko (ucko at ncbi.nlm.nih.gov)
-svn_revision=`echo '$Revision: 443416 $' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
+svn_revision=`echo '$Revision: 442644 $' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
def_builddir="$NCBI/c++/Debug/build"
repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1'
diff --git a/c++/scripts/projects/blast/Manifest b/c++/scripts/projects/blast/Manifest
index 607afb9..a4500e0 100644
--- a/c++/scripts/projects/blast/Manifest
+++ b/c++/scripts/projects/blast/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 460306 2015-02-26 13:32:41Z camacho $
+# $Id: Manifest 482777 2015-10-26 18:45:55Z camacho $
#
# Author: Christiam Camacho
#
@@ -46,9 +46,9 @@ Linux64-Centos : icc : ICC.sh --with-strip --without-debug --with
DEFAULT_CONFIGURATIONS: Linux64-Centos:icc
-Win32 : plain : static 32 ReleaseMT
-Win64 : plain : static 64 ReleaseMT
+Win32 : plain : static 32 ReleaseMT
+Win64 : plain : static 64 ReleaseMT
-IntelMAC : universal : GCC.sh 4.2 --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public
+IntelMAC : universal : GCC.sh --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public
USE_COMPONENTS
diff --git a/c++/scripts/projects/blast/components.link b/c++/scripts/projects/blast/components.link
index dd77326..0072cc9 100644
--- a/c++/scripts/projects/blast/components.link
+++ b/c++/scripts/projects/blast/components.link
@@ -1,10 +1,10 @@
[components]
-infrastructure 15.0
-core 15.0
-dbase 15.0
-web 15.0
-objects 15.0
-objtools 15.0
-algo 15.0
-blast 15.0
-app 15.0
+infrastructure 16.1
+core 16.1
+dbase 16.1
+web 16.1
+objects 16.1
+objtools 16.1
+algo 16.1
+blast 16.1
+app 16.1
diff --git a/c++/scripts/projects/blast/post_build/rpm/make_rpm.py b/c++/scripts/projects/blast/post_build/rpm/make_rpm.py
index f976f7f..3ea93c4 100755
--- a/c++/scripts/projects/blast/post_build/rpm/make_rpm.py
+++ b/c++/scripts/projects/blast/post_build/rpm/make_rpm.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
"""Script to create a source/binary RPM.
"""
-# $Id: make_rpm.py 460216 2015-02-25 17:58:10Z camacho $
+# $Id: make_rpm.py 478474 2015-09-09 15:57:05Z camacho $
import sys, os, shutil
from optparse import OptionParser
@@ -41,6 +41,7 @@ def setup_rpmbuild():
print >> out, os.path.join(cwd, RPMBUILD_HOME, "tmp"), ")"
print >> out
print >> out, "%packager Christiam E. Camacho (camacho at ncbi.nlm.nih.gov)"
+ print >> out, "%debug_package %{nil}"
finally:
out.close()
if VERBOSE:
diff --git a/c++/scripts/projects/blast/post_build/rpm/ncbi-blast.spec b/c++/scripts/projects/blast/post_build/rpm/ncbi-blast.spec
index c96e5ca..15195b2 100644
--- a/c++/scripts/projects/blast/post_build/rpm/ncbi-blast.spec
+++ b/c++/scripts/projects/blast/post_build/rpm/ncbi-blast.spec
@@ -1,6 +1,6 @@
Name: ncbi-blast
Version: BLAST_VERSION+
-Release: 2
+Release: 1
Source0: %{name}-%{version}.tgz
Summary: NCBI BLAST finds regions of similarity between biological sequences.
Exclusiveos: linux
diff --git a/c++/scripts/projects/blast/project.lst b/c++/scripts/projects/blast/project.lst
index d82320a..f24331e 100644
--- a/c++/scripts/projects/blast/project.lst
+++ b/c++/scripts/projects/blast/project.lst
@@ -22,7 +22,8 @@ cgi$
cgi/impl$
html$
connect$
-connect/services$
+connect/services
+-connect/services/test
connect/ext$
util$
util/creaders$
diff --git a/c++/scripts/projects/cobalt/Manifest b/c++/scripts/projects/cobalt/Manifest
index f698656..fe16c00 100644
--- a/c++/scripts/projects/cobalt/Manifest
+++ b/c++/scripts/projects/cobalt/Manifest
@@ -33,10 +33,8 @@ Linux64-Centos : icc : ICC.sh --with-strip --without-debug --withou
DEFAULT_CONFIGURATIONS: Linux32-Centos:icc Linux64-Centos:icc
-Win32_10 : plain : static 32 ReleaseMT
-Win64_10 : plain : static 64 ReleaseMT
-
-SunOSx86 : plain : WorkShop59.sh 64 --without-debug --without-pcre --with-mt --with-flat-makefile
+Win32_13 : plain : static 32 ReleaseMT
+Win64_13 : plain : static 64 ReleaseMT
IntelMAC : universal : GCC.sh --without-debug --without-pcre --with-mt --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public
diff --git a/c++/scripts/projects/corelib/Manifest b/c++/scripts/projects/corelib/Manifest
index f15656a..72d20a8 100644
--- a/c++/scripts/projects/corelib/Manifest
+++ b/c++/scripts/projects/corelib/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 441031 2014-07-18 20:53:44Z satskyse $
+# $Id: Manifest 474940 2015-08-03 15:56:40Z fukanchi $
#
# Author: Sergey Satskiy
#
@@ -33,7 +33,7 @@ Linux64-Centos : icc : ICC.sh --without-debug --without-mt --with-s
Linux64-Centos : icc_mtdll : ICC.sh --without-debug --with-mt --with-dll --without-runpath --with-flat-makefile
Linux64-Centos : gcc : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
-FreeBSD32 : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
+FreeBSD32 : plain : Clang.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
SunOSx86 : gcc : GCC.sh 4.5.3 --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
SunOSx86 : w55 : WorkShop55.sh 32 --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
diff --git a/c++/scripts/projects/datatool/ChangeLog b/c++/scripts/projects/datatool/ChangeLog
index 6653299..9f7b0e5 100644
--- a/c++/scripts/projects/datatool/ChangeLog
+++ b/c++/scripts/projects/datatool/ChangeLog
@@ -141,3 +141,7 @@ Fixed code generation and serialization of sequences of base64binary elements.
Use HTML entities in Identifier names if needed and possible.
Added possibility to rename enum values from DEF file.
Fixed bugs in schema parsing .
+
+June 29, 2015
+version 2.14.0, CXX-6104
+Added option to selectively write named integers by value only.
diff --git a/c++/scripts/projects/datatool/Manifest b/c++/scripts/projects/datatool/Manifest
index 7fadd34..c19dec7 100644
--- a/c++/scripts/projects/datatool/Manifest
+++ b/c++/scripts/projects/datatool/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 455973 2015-01-06 19:41:00Z gouriano $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Author: Sergey Satskiy
#
@@ -32,15 +32,11 @@ Linux64-Ubuntu : plain : GCC.sh --without-debug --without-mt --with-stati
FreeBSD32 : plain : Clang.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
-#SunOSx86 : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c --without-dll
-#SunOSx86 : plain : WorkShop59.sh 32 --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
-
-#PowerMAC : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
IntelMAC : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
-#Win32_9 : 900 : static 32 ReleaseMT
-Win32_10 : 1000 : static 32 ReleaseMT
+Win32_13 : plain : static 32 ReleaseMT
XCode : plain : Xcode.sh 30 --without-debug --with-universal=i386,x86_64
USE_COMPONENTS
+
diff --git a/c++/scripts/projects/datatool/components.link b/c++/scripts/projects/datatool/components.link
index ea68b5f..373477a 100644
--- a/c++/scripts/projects/datatool/components.link
+++ b/c++/scripts/projects/datatool/components.link
@@ -1,3 +1,3 @@
[components]
-infrastructure 16.0
-core 16.0
+infrastructure 16.1
+core 16.1
diff --git a/c++/scripts/projects/dbapi.lst b/c++/scripts/projects/dbapi.lst
index 607e03d..ffec39e 100644
--- a/c++/scripts/projects/dbapi.lst
+++ b/c++/scripts/projects/dbapi.lst
@@ -3,6 +3,7 @@ util$
util/bitset$
util/compress
util/regexp$
+util/xregexp$
util/cache$
connect$
connect/ext$
diff --git a/c++/scripts/projects/dbsnp-2.0.lst b/c++/scripts/projects/dbsnp-2.0.lst
index d4dd604..64a0707 100644
--- a/c++/scripts/projects/dbsnp-2.0.lst
+++ b/c++/scripts/projects/dbsnp-2.0.lst
@@ -23,12 +23,16 @@ internal/variation/snp/snputils
internal/variation/snp/hgvstest
internal/variation/snp/snphgvs
internal/variation/snp/common
+internal/variation/utils
internal/objects/ads
internal/aligndb
internal/refgene/refseq_aln_source
internal/asn_cache
internal/trackmgr
internal/gpipe/common$
+internal/gpipe/grid_wrapper
+internal/mapview/cgi/cgilib
+internal/mapview/util
sra
-objtools/snputil
-misc/hgvs/test
diff --git a/c++/scripts/projects/dispatcher/Manifest b/c++/scripts/projects/dispatcher/Manifest
index d6810c7..4cda81d 100644
--- a/c++/scripts/projects/dispatcher/Manifest
+++ b/c++/scripts/projects/dispatcher/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 467025 2015-05-08 14:56:11Z satskyse $
+# $Id: Manifest 469726 2015-06-08 16:04:24Z lavr $
#
# Author: Sergey Satskiy
#
@@ -13,7 +13,7 @@ APP: lbsmd lbsmc lbsm_feedback
APP: launcherd fwdaemon dispd.cgi
LIB: libconnect.a libconnext.a libmghbn.a liblbsmdapi.a
-DEFAULT_CONFIGURATIONS: Linux64-Centos:GCC Cygwin32:GCC
+DEFAULT_CONFIGURATIONS: Linux64-Centos:GCC
COPY: $bindir/test_mghbn $installdir/bin/ncbi_mghbn
COPY: $bindir/test_ncbi_dblb $installdir/bin/ncbi_dblb
@@ -37,4 +37,4 @@ Linux64-Centos : ICC : ICC.sh --with-local-lbsm --without-debug --wit
Linux64-Centos : GCC : GCC.sh --with-local-lbsm --without-debug --without-mt --with-static --without-serial --without-runpath --with-flat-makefile
FreeBSD32 : Clang : Clang.sh --with-local-lbsm --without-debug --without-mt --with-static --without-serial --without-runpath --with-flat-makefile
IntelMAC : GCC : GCC.sh --with-local-lbsm --without-debug --without-mt --with-static --without-serial --without-runpath --with-flat-makefile --with-universal=i386,x86_64
-Cygwin64 : GCC : GCC.sh --with-local-lbsm --without-debug --without-mt --with-static --without-serial --without-runpath --without-flat-makefile
+# Cygwin64 : GCC : GCC.sh --with-local-lbsm --without-debug --without-mt --with-static --without-serial --without-runpath --without-flat-makefile
diff --git a/c++/scripts/projects/grid/Manifest b/c++/scripts/projects/grid/Manifest
index 1a2f09e..612061a 100644
--- a/c++/scripts/projects/grid/Manifest
+++ b/c++/scripts/projects/grid/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 468426 2015-05-22 16:15:04Z fukanchi $
+# $Id: Manifest 481183 2015-10-07 16:16:53Z fukanchi $
#
# Author: Dmitry Kazimirov
#
@@ -49,7 +49,7 @@ FreeBSD32 : Release : Clang.sh --without-debug --with-optimization --with-symbol
FreeBSD32 : Debug : Clang.sh --with-debug --with-mt --without-bdb
IntelMAC : Release : GCC.sh --without-debug --with-optimization --with-symbols --with-mt --without-bdb
IntelMAC : Debug : GCC.sh --with-debug --with-mt --without-bdb
-Win32_10 : Release : static 32 ReleaseDLL
-Win32_10 : Debug : static 32 DebugDLL
+Win32_13 : Release : static 32 ReleaseDLL
+Win32_13 : Debug : static 32 DebugDLL
-USE_COMPONENTS
+#USE_COMPONENTS
diff --git a/c++/scripts/projects/grid/components.link b/c++/scripts/projects/grid/components.link
index d39740e..761777f 100644
--- a/c++/scripts/projects/grid/components.link
+++ b/c++/scripts/projects/grid/components.link
@@ -1,5 +1,5 @@
[components]
-infrastructure 16.0
-core 16.0
-misc 16.0
-web 16.0
+infrastructure 16.1
+core 16.1
+misc 16.1
+web 16.1
diff --git a/c++/scripts/projects/grid/project.lst b/c++/scripts/projects/grid/project.lst
index 9e38cc7..50fefd4 100644
--- a/c++/scripts/projects/grid/project.lst
+++ b/c++/scripts/projects/grid/project.lst
@@ -13,6 +13,7 @@ connect$
connect/ext$
connect/impl$
connect/services$
+connect/services/impl$
cgi$
cgi/impl$
html$
diff --git a/c++/scripts/projects/gumbel_params/Manifest b/c++/scripts/projects/gumbel_params/Manifest
index 00f6c73..2428596 100644
--- a/c++/scripts/projects/gumbel_params/Manifest
+++ b/c++/scripts/projects/gumbel_params/Manifest
@@ -34,8 +34,8 @@ Linux64-Centos : icc : ICC.sh --with-strip --without-debug --with
DEFAULT_CONFIGURATIONS: Linux32-Centos:icc Linux64-Centos:icc
-Win32_10 : plain : static 32 ReleaseMT
-Win64_10 : plain : static 64 ReleaseMT
+Win32_13 : plain : static 32 ReleaseMT
+Win64_13 : plain : static 64 ReleaseMT
SunOSx86 : plain : WorkShop59.sh 64 --without-debug --without-pcre --with-mt --with-flat-makefile
diff --git a/c++/scripts/projects/igblast/Manifest b/c++/scripts/projects/igblast/Manifest
index 1d1600d..1fe51ab 100644
--- a/c++/scripts/projects/igblast/Manifest
+++ b/c++/scripts/projects/igblast/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 427344 2014-02-19 16:46:38Z camacho $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Author: Christiam Camacho
#
@@ -37,9 +37,10 @@ Linux64-Centos : icc : ICC.sh --with-strip --without-debug --withou
DEFAULT_CONFIGURATIONS: Linux32-Centos:icc Linux64-Centos:icc
-Win32_10 : plain : static 32 ReleaseMT
-Win64_10 : plain : static 64 ReleaseMT
+Win32_13 : plain : static 32 ReleaseMT
+Win64_13 : plain : static 64 ReleaseMT
IntelMAC : universal : GCC.sh 4.0 --without-debug --without-pcre --with-mt --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public
USE_COMPONENTS
+
diff --git a/c++/scripts/projects/igblast/project.lst b/c++/scripts/projects/igblast/project.lst
index b57e89d..784632e 100644
--- a/c++/scripts/projects/igblast/project.lst
+++ b/c++/scripts/projects/igblast/project.lst
@@ -21,6 +21,7 @@ cgi/impl$
html$
connect$
connect/services$
+connect/services/impl$
connect/ext$
util$
util/creaders$
diff --git a/c++/scripts/projects/ncbi_applog/Manifest b/c++/scripts/projects/ncbi_applog/Manifest
index 4303cdc..0ebfa79 100644
--- a/c++/scripts/projects/ncbi_applog/Manifest
+++ b/c++/scripts/projects/ncbi_applog/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 452489 2014-11-20 15:48:46Z ivanov $
+# $Id: Manifest 481183 2015-10-07 16:16:53Z fukanchi $
#
# Author: Alexey Rafanovich
#
@@ -27,13 +27,13 @@ POSTBUILD: cp $srcdir/src/misc/clog/app/test_ncbi_applog.sh $installdir/bin
# to it. So some standard options may be added by release configurator, such as --build-root-sfx, --with-projects,
# --with-distcc, --with-action etc.
-Linux32-Centos : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
Linux64-Centos : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
Linux64-Ubuntu : plain : GCC.sh --without-debug --with-mt --with-static --without-runpath --with-flat-makefile
FreeBSD32 : plain : Clang.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
IntelMAC : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile
-Win32_10 : 1000 : static 32 ReleaseMT
+Win32_13 : plain : static 32 ReleaseMT
#XCode : plain : Xcode.sh 30 --without-debug --with-universal=i386,x86_64
#USE_COMPONENTS
+#
diff --git a/c++/scripts/projects/ncbi_gui_base.lst b/c++/scripts/projects/ncbi_gui_base.lst
index 194680f..bc59901 100644
--- a/c++/scripts/projects/ncbi_gui_base.lst
+++ b/c++/scripts/projects/ncbi_gui_base.lst
@@ -29,6 +29,8 @@ internal/ID/utils$
internal/mapview/objects
misc/grid_cgi$
misc/xmlwrapp
+misc/eutils_client$
+misc/discrepancy$
misc/discrepancy_report$
objects
objmgr
diff --git a/c++/scripts/projects/netcache/ChangeLog b/c++/scripts/projects/netcache/ChangeLog
index 48c3380..aee0a59 100644
--- a/c++/scripts/projects/netcache/ChangeLog
+++ b/c++/scripts/projects/netcache/ChangeLog
@@ -110,5 +110,32 @@ May 19, 2015
version 6.8.7
Corrected format of alert reports.
-
-
+June 19, 2015
+version 6.8.8
+Bug fix release
+
+June 26, 2015
+version 6.8.9
+Added report of estimated draining end.
+Reviewed and corrected error reporting and command confirmations.
+Added report of synchronization state, corrected synchronization algorithm.
+Modified synchronization in 'drain' state to allow updating of existing blobs.
+
+July 10, 2015
+version 6.8.10
+Corrected synchronization report to hide currently inactive peers.
+Changed way memory and socket statistics is calculated.
+
+July 31, 2015
+version 6.8.11 (CXX-6216)
+Changed way memory and socket statistics is calculated; corrected synchronization reporting to hide currently inactive peers;
+Corrected synchronization of access to database configuration data, blob synchronization finalization, mirror event handling, storage data access.
+Added error checks during synchronization.
+Added database state report.
+Added option of reloading some storage configuration parameters.
+
+September 29, 2015
+version 6.9.0 (CXX-7396)
+Modified periodic sync logic to avoid deadlocks and enhance speed, corrected error handling.
+Added blob enumeration command.
+Reviewed and corrected configuration defaults.
diff --git a/c++/scripts/projects/netcache/project.lst b/c++/scripts/projects/netcache/project.lst
index 479aa23..01a6d4a 100755
--- a/c++/scripts/projects/netcache/project.lst
+++ b/c++/scripts/projects/netcache/project.lst
@@ -4,6 +4,7 @@ util/bitset$ update-only
util/cache$ update-only
connect$
connect/services$
+connect/services/impl$
connect/services/test$
db$
db/sqlite$
diff --git a/c++/scripts/projects/netschedule/ChangeLog b/c++/scripts/projects/netschedule/ChangeLog
index cb9c4c9..dab40ee 100644
--- a/c++/scripts/projects/netschedule/ChangeLog
+++ b/c++/scripts/projects/netschedule/ChangeLog
@@ -1,3 +1,42 @@
+Release 4.23.2 cloned from 4.23.1 (2015-10-19)
+
+Improvements:
+ * NetSchedule: deadlock (JIRA: CXX-7453)
+ * NetSchedule: internal error for the command test (JIRA: CXX-7450)
+ * NetSchedule: DUMP may lead to an internal error report (JIRA: CXX-7448)
+ * Turn DB_LOG_AUTOREMOVE on BDB (JIRA: CXX-7443)
+ * NetSchedule: logging shutdown in case of a signal (JIRA: CXX-7412)
+
+
+Release 4.23.1 based on SC-16.1 (2015-08-28)
+
+Improvements:
+ * NetSchedule: conversion from a list to a bit vector done twice
+ (JIRA: CXX-7254)
+ * NetSchedule: long shutdown (JIRA: CXX-7274)
+
+
+Release 4.23.0 based on SC-16.1 (2015-08-20)
+
+Improvements:
+ * NetSchedule: way too long graceful shutdown (JIRA: CXX-2617)
+ * NetSchedule can't execute SHUTDOWN drain=1 (JIRA: CXX-6186)
+ * NetSchedule: GET2/READ/READ2 to accept a list of groups (JIRA: CXX-6247)
+
+Release 4.22.0 based on SC-16.1 (2015-07-06)
+
+Improvements:
+ * NetSchedule: fresh Berkley DB version (JIRA: CXX-6094)
+ * NetSchedule: RDRB to have blacklist option (JIRA: CXX-6077)
+ * NetSchedule: new GET2/READ2 flag (JIRA: CXX-6054)
+ * NetSchedule -- change default behavior of READ/READ2 with affinity and/or
+ group restriction (JIRA: CXX-5989)
+ * NetSchedule: encrypted admin names support (JIRA: CXX-5809)
+ * NetStorage & NetSchedule: reconfigurable on-the-fly CServer parameters
+ (JIRA: CXX-5580)
+ * NetSchedule -- job lifetime performance metrics (JIRA: CXX-4581)
+
+
Release 4.21.2 cloned from 4.21.1 (2015-04-21)
Improvements:
diff --git a/c++/scripts/projects/netschedule/Manifest b/c++/scripts/projects/netschedule/Manifest
index aa670d7..9afa218 100644
--- a/c++/scripts/projects/netschedule/Manifest
+++ b/c++/scripts/projects/netschedule/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 461767 2015-03-12 15:44:21Z satskyse $
+# $Id: Manifest 472057 2015-07-06 19:39:16Z satskyse $
#
# Author: Sergey Satskiy
#
@@ -21,7 +21,7 @@ APP: $srcdir/src/app/netschedule/test/ns.py+ $srcdir/src/app/netschedule/test/te
APP: $srcdir/src/app/netschedule/utils/ns_health_check.py
ETC: src/app/netschedule/netscheduled.ini
-DEFAULT_CONFIGURATIONS: Linux64-Centos:Bdb4520-O2g
+DEFAULT_CONFIGURATIONS: Linux64-Centos:Bdb6126-O2g
# Each line describes a single configuration
# The format is as follows:
@@ -30,9 +30,9 @@ DEFAULT_CONFIGURATIONS: Linux64-Centos:Bdb4520-O2g
# Release configurator assumes that this script will eventually call standard configure script and pass all options
# to it. So some standard options may be added by release configurator, such as --build-root-sfx, --with-projects,
# --with-distcc, --with-action etc.
-Linux64-Centos : Bdb4520-Release : GCC.sh 4.8.1 --without-debug --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-4.5.20.dio.SuSE-ONLY
-Linux64-Centos : Bdb4520-Debug : GCC.sh 4.8.1 --with-debug --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-4.5.20.dio.SuSE-ONLY
-Linux64-Centos : Bdb4520-O2g : GCC.sh 4.8.1 --without-debug --with-symbols --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-4.5.20.dio.SuSE-ONLY
+Linux64-Centos : Bdb6126-Release : GCC.sh 4.8.1 --without-debug --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-6.1.26
+Linux64-Centos : Bdb6126-Debug : GCC.sh 4.8.1 --with-debug --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-6.1.26
+Linux64-Centos : Bdb6126-O2g : GCC.sh 4.8.1 --without-debug --with-symbols --with-mt --with-flat-makefile --with-bdb=$NCBI/BerkeleyDB-6.1.26
USE_COMPONENTS
diff --git a/c++/scripts/projects/netschedule/components.link b/c++/scripts/projects/netschedule/components.link
index 030537d..b1e583c 100644
--- a/c++/scripts/projects/netschedule/components.link
+++ b/c++/scripts/projects/netschedule/components.link
@@ -1,4 +1,4 @@
[components]
-infrastructure 15.0
-core 15.0
-dbase 15.0
+infrastructure 16.1
+core 16.1
+dbase 16.1
diff --git a/c++/scripts/projects/netschedule/project.lst b/c++/scripts/projects/netschedule/project.lst
index 6d911cc..5d799c2 100644
--- a/c++/scripts/projects/netschedule/project.lst
+++ b/c++/scripts/projects/netschedule/project.lst
@@ -9,6 +9,7 @@ util/cache$ update-only
util/math$ update-only
connect$
connect/services$
+connect/services/impl$
db$
db/bdb$
app$
diff --git a/c++/scripts/projects/netstorage/ChangeLog b/c++/scripts/projects/netstorage/ChangeLog
index a54b41a..3e5ea7e 100644
--- a/c++/scripts/projects/netstorage/ChangeLog
+++ b/c++/scripts/projects/netstorage/ChangeLog
@@ -1,4 +1,37 @@
-Release X.X.X
+Release 2.1.3 based on SC-16.1 (2015-08-25)
+
+ * Bug fix: Implemented a workaround to overcome FileTrack write-once restriction.
+ (JIRA: CXX-6215)
+
+Release 2.1.2 based on SC-16.1 (2015-07-27)
+
+ * Bug fix: client protocol version update at the first HELLO
+ (JIRA: CXX-6162)
+ * Bug fix: Investigate premature closes of connections to FileTrack
+ (JIRA: CXX-5958)
+ * Bug fix: Investigation of suspicious error message in socket API
+ (JRIA: CXX-6179)
+
+Release 2.1.1 based on SC-16.1 (2015-07-14)
+
+Improvements and bug fixes:
+ * NST 2.1.0: can't parse grid_cli HELLO with ProtocolVersion
+ (JIRA: CXX-6157)
+
+
+Release 2.1.0 based on SC-16.1 (2015-07-09)
+
+Improvements and bug fixes:
+ * NetStorage API does not use ICache::fBestReliability for NetCache
+ (JIRA: CXX-6141)
+ * NetStorage: RECONFIGURE when admin names decryptor failed
+ (JIRA: CXX-6123)
+ * NetStorage: new flags for fine grain timing logging control
+ (JIRA: CXX-6041)
+ * NetStorage: protocol version from a client (JIRA: CXX-5992)
+ * NetStorage & NetSchedule: reconfigurable on-the-fly CServer parameters
+ (JIRA: CXX-5580)
+
Improvements and bug fixes:
* Ability to change [server]/max_connections and [server]/network_timeout
diff --git a/c++/scripts/projects/netstorage/components.link b/c++/scripts/projects/netstorage/components.link
index a6a63cd..55e867a 100644
--- a/c++/scripts/projects/netstorage/components.link
+++ b/c++/scripts/projects/netstorage/components.link
@@ -1,6 +1,6 @@
[components]
-infrastructure 16.0
-core 16.0
-dbase 16.0
-misc 16.0
+infrastructure 16.1
+core 16.1
+dbase 16.1
+misc 16.1
diff --git a/c++/scripts/projects/project_tree_builder/Manifest b/c++/scripts/projects/project_tree_builder/Manifest
index 78a86de..219a3cf 100644
--- a/c++/scripts/projects/project_tree_builder/Manifest
+++ b/c++/scripts/projects/project_tree_builder/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 468668 2015-05-27 14:59:17Z gouriano $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Author: Sergey Satskiy
#
@@ -34,17 +34,13 @@ Linux64-Ubuntu : plain : GCC.sh --without-debug --without-mt --with
FreeBSD32 : plain : Clang.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c --without-pcre
-#SunOSx86 : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c --without-dll
-#SunOSx86 : plain : WorkShop59.sh 32 --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
-#SunOSx86 : plain : WorkShop59.sh 64 --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
-
#PowerMAC : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
IntelMAC : plain : GCC.sh --without-debug --without-mt --with-static --without-runpath --with-flat-makefile --without-ncbi-c
#IntelMAC : universal : GCC.sh --without-debug --without-mt --with-static --with-universal=i386,x86_64 --with-flat-makefile --without-ncbi-c
-#Win32_9 : 900 : static 32 ReleaseMT
-Win32_10 : 1000 : static 32 ReleaseMT
+Win32_13 : msvc-13-static-32 : static 32 ReleaseMT
XCode : plain : Xcode.sh 30 --without-debug --with-universal=i386,x86_64 --without-ncbi-c
USE_COMPONENTS
+
diff --git a/c++/scripts/projects/public/Manifest b/c++/scripts/projects/public/Manifest
index aad368f..5a345af 100644
--- a/c++/scripts/projects/public/Manifest
+++ b/c++/scripts/projects/public/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 435790 2014-05-20 18:47:00Z vakatov $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Author:
#
@@ -11,26 +11,38 @@
USE_COMPONENTS
-Win32_10 : MSVC10-32 : dll 32 ReleaseDLL
-Win64_10 : MSVC10-64 : static 64 ReleaseDLL
+# Each line describes a single configuration
+# The format is as follows:
+# <HardwareIdentifier> : <ReleaseSuffix> : <CompilerConfigurationScriptWithKeys>
+# Configuration script is relative to c++/compilers/unix/ .
+# Release configurator assumes that this script will eventually call standard configure script and pass all options
+# to it. So some standard options may be added by release configurator, such as --build-root-sfx, --with-projects,
+# --with-distcc, --with-action etc.
-Linux32-Centos : GCC445 : GCC.sh 4.4.5 --without-debug --with-3psw=system
-Linux32-Centos : GCC460 : GCC.sh 4.6.0 --without-debug --with-mt
-Linux32-Centos : ICC101 : ICC.sh 10.1 --without-debug --with-dll --with-mt
-Linux32-Centos : ICC110 : ICC.sh 11.0 --without-debug --with-dll --with-mt
+Win32_13 : MSVC13-32 : dll 32 ReleaseDLL
+Win64_13 : MSVC13-64 : static 64 ReleaseDLL
-Linux64-Centos : GCC401 : GCC.sh 4.0.1 --without-debug --without-flat-makefile
-Linux64-Centos : GCC442 : GCC.sh 4.4.2 --without-debug --with-mt --with-distcc
-Linux64-Centos : GCC442d : GCC.sh 4.4.2 --with-mt --with-distcc --with-3psw=system
-Linux64-Centos : GCC463 : GCC.sh 4.6.3 --with-distcc
-Linux64-Centos : GCC472 : GCC.sh 4.7.2 --without-debug --with-mt
-Linux64-Centos : ICC101 : ICC.sh 10.1 --with-mt --with-3psw=system
-Linux64-Centos : ICC130 : ICC.sh 13.0 --without-debug --with-mt
+Cygwin64 : GCC : GCC.sh --without-debug --with-mt --with-flat-makefile
-FreeBSD32 : GCC : GCC.sh --without-debug
+Linux64-Centos : GCC442 : GCC.sh 4.4.2 --without-debug --with-mt --with-distcc
+Linux64-Centos : GCC442d : GCC.sh 4.4.2 --with-mt --with-distcc --with-3psw=system
+Linux64-Centos : GCC463 : GCC.sh 4.6.3 --with-distcc
+Linux64-Centos : GCC472 : GCC.sh 4.7.2 --without-debug --with-mt --with-dll
+Linux64-Centos : GCC481 : GCC.sh 4.8.1 --without-debug --without-flat-makefile
+Linux64-Centos : GCC491d : GCC.sh 4.9.1 --with-debug --with-mt --with-flat-makefile
+Linux64-Centos : GCC510 : GCC.sh 5.1.0 --without-debug --with-mt --with-flat-makefile
+Linux64-Centos : ICC130 : ICC.sh 13.0 --without-debug --with-mt --with-dll
+Linux64-Centos : ICC130d : ICC.sh 13.0 --with-debug --with-mt --with-3psw=system
+Linux64-Centos : Clang : Clang.sh --with-debug --with-mt --with-flat-makefile
-SunOSx86 : GCC : GCC.sh 4.5.3 --without-debug --without-mt --with-static
-SunOSx86 : WS64 : WorkShop59.sh 64 --with-debug --with-dll --with-mt
+Linux64-Ubuntu : plain-GCC : GCC.sh --without-debug --with-mt --with-flat-makefile
+Linux32-Ubuntu : plain-GCC : GCC.sh --without-debug --with-mt --with-flat-makefile
+
+FreeBSD32 : plain : Clang.sh --without-debug --with-mt --with-flat-makefile
+#FreeBSD64 : plain : Clang.sh --without-debug --with-mt --with-flat-makefile
+
+IntelMAC : Debug : GCC.sh --with-debug --with-dll --with-mt --with-universal=i386,x86_64 --with-flat-makefile
+IntelMAC : Release : GCC.sh --without-debug --with-dll --with-mt --with-universal=i386,x86_64 --with-flat-makefile
+
+XCode : plain : Xcode.sh 30 --without-debug --with-64
-IntelMAC : GCC401 : GCC.sh 4.0 --with-debug --with-dll --with-mt --with-universal
-IntelMAC : GCC421 : GCC.sh 4.2 --without-debug --with-dll --with-mt --with-universal=i386,x86_64
diff --git a/c++/scripts/projects/public/components.link b/c++/scripts/projects/public/components.link
index 22dd935..daf3cff 100644
--- a/c++/scripts/projects/public/components.link
+++ b/c++/scripts/projects/public/components.link
@@ -1,13 +1,13 @@
[components]
-infrastructure 13.0
-core 13.0
-dbase 13.0
-web 13.0
-objects 13.0
-objtools 13.0
-algo 13.0
-misc 13.0
-blast 13.0
-app 13.0
-sample 13.0
-sra 13.0
+algo 16.1
+app 16.1
+blast 16.1
+core 16.1
+dbase 16.1
+infrastructure 16.1
+misc 16.1
+objects 16.1
+objtools 16.1
+sample 16.1
+sra 16.1
+web 16.1
diff --git a/c++/scripts/projects/python_ncbi_dbapi/ChangeLog b/c++/scripts/projects/python_ncbi_dbapi/ChangeLog
index e98a7c0..56a9257 100644
--- a/c++/scripts/projects/python_ncbi_dbapi/ChangeLog
+++ b/c++/scripts/projects/python_ncbi_dbapi/ChangeLog
@@ -1,3 +1,11 @@
+Version 1.16.0 (2015-09-22):
+* Advance to version 16.1 of the stable C++ Toolkit components, and
+ GCC 4.8.1.
+
+Version 1.15.2 (2015-09-21):
+* Produce wheels for decentralized installation, not tarballs for
+ centralized installation.
+
Version 1.15.1 (2013-02-06):
* Rework exception translation to follow PEP 249 more closely.
diff --git a/c++/scripts/projects/python_ncbi_dbapi/Manifest b/c++/scripts/projects/python_ncbi_dbapi/Manifest
index f06c232..012f10c 100644
--- a/c++/scripts/projects/python_ncbi_dbapi/Manifest
+++ b/c++/scripts/projects/python_ncbi_dbapi/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 416706 2013-10-30 18:50:28Z ucko $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Authors: Pavel Ivanov, Aaron Ucko
#
@@ -17,7 +17,7 @@ COPY: $srcdir/src/dbapi/lang_bind/python/tests/python_dbapi_test.py $installdir/
# Use stable components (per components.link) rather than the trunk.
USE_COMPONENTS
-POSTBUILD: $srcdir/scripts/projects/python_ncbi_dbapi/post_build/post_build.py $bindir $libdir $installdir $version
+POSTBUILD: $srcdir/scripts/projects/python_ncbi_dbapi/post_build/post_build.py $bindir $libdir $installdir $srcdir
# Each line describes a single configuration
@@ -27,7 +27,7 @@ POSTBUILD: $srcdir/scripts/projects/python_ncbi_dbapi/post_build/post_build.py $
# Release configurator assumes that this script will eventually call standard configure script and pass all options
# to it. So some standard options may be added by release configurator, such as --build-root-sfx, --with-projects,
# --with-distcc, --with-action etc.
-Linux32-Centos : 32 : GCC.sh 4.6.0 --without-debug --with-optimization --with-mt --with-dll --with-hard-runpath
-Linux64-Centos : 64 : GCC.sh 4.4.2 --without-debug --with-optimization --with-mt --with-dll --with-hard-runpath
-Win32_10 : 1000 : dll 32 ReleaseDLL
-#Win64_10 : 1000 : dll 64 ReleaseDLL
+#Linux32-Centos : 32 : GCC.sh 4.6.0 --without-debug --with-optimization --with-mt --with-dll --with-hard-runpath
+Linux64-Centos : 64 : GCC.sh 4.8.1 --without-debug --with-optimization --with-mt --with-dll --with-hard-runpath
+#Win32_13 : plain : dll 32 ReleaseDLL
+#Win64_13 : plain : dll 64 ReleaseDLL
diff --git a/c++/scripts/projects/python_ncbi_dbapi/components.link b/c++/scripts/projects/python_ncbi_dbapi/components.link
index 5d85a52..b1e583c 100644
--- a/c++/scripts/projects/python_ncbi_dbapi/components.link
+++ b/c++/scripts/projects/python_ncbi_dbapi/components.link
@@ -1,4 +1,4 @@
[components]
-infrastructure 11.0
-core 11.0
-dbase 11.0
+infrastructure 16.1
+core 16.1
+dbase 16.1
diff --git a/c++/scripts/projects/python_ncbi_dbapi/post_build/build_tarball.sh b/c++/scripts/projects/python_ncbi_dbapi/post_build/build_tarball.sh
deleted file mode 100755
index 45b3a64..0000000
--- a/c++/scripts/projects/python_ncbi_dbapi/post_build/build_tarball.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-
-INSTALL_DIR=$1
-VERSION="${NCBI_PACKAGE_VERSION}"
-
-if [[ -z "$INSTALL_DIR" || -z "$VERSION" ]]; then
- echo "Installation directory or version are empty"
- exit 1
-fi
-
-#PYTHON_DIR="$(which python)"
-#PYTHON_DIR="${PYTHON_DIR%/*}"
-#PYTHON_DIR="${PYTHON_DIR%/*}"
-PYTHON_DIR=/opt/python-2.5.1
-
-if [ -z "$PYTHON_DIR" ]; then
- echo "Cannot find python directory"
- exit 2
-fi
-
-
-PYTHON_SUBDIR="python2.5/site-packages/python_ncbi_dbapi"
-TARBALL_DIR="$INSTALL_DIR/build_tarball"
-
-mkdir -p "$TARBALL_DIR/$PYTHON_SUBDIR/$VERSION" || exit 3
-cp -R "$PYTHON_DIR/lib/$PYTHON_SUBDIR"/* "$TARBALL_DIR/$PYTHON_SUBDIR/" || exit 4
-
-cp "$INSTALL_DIR/lib"/* "$TARBALL_DIR/$PYTHON_SUBDIR/$VERSION" || exit 5
-ln -s "python_ncbi_dbapi/$VERSION/libpython_ncbi_dbapi.so" "$TARBALL_DIR/$PYTHON_SUBDIR/../python_ncbi_dbapi.so" || exit 6
-
-tar -zcf "$INSTALL_DIR/installation.tar.gz" -C "$TARBALL_DIR" python2.5 || exit 7
-
-rm -rf "$TARBALL_DIR"
diff --git a/c++/scripts/projects/python_ncbi_dbapi/post_build/post_build.py b/c++/scripts/projects/python_ncbi_dbapi/post_build/post_build.py
index ef680a5..f742080 100755
--- a/c++/scripts/projects/python_ncbi_dbapi/post_build/post_build.py
+++ b/c++/scripts/projects/python_ncbi_dbapi/post_build/post_build.py
@@ -1,13 +1,14 @@
#!/usr/bin/env python
-# $Id: post_build.py 416703 2013-10-30 18:21:11Z ucko $
+# $Id: post_build.py 479510 2015-09-21 18:29:09Z ucko $
-import glob, os, shutil, sys
+import glob, os, shutil, subprocess, sys
-(bin_dir, lib_dir, install_dir, version) = sys.argv[1:]
-common_stems = ('python_ncbi_dbapi', 'ncbi_xdbapi_?t*')
+(bin_dir, lib_dir, install_dir, src_dir) = sys.argv[1:]
+common_stems = ('python_ncbi_dbapi', 'ncbi_xdbapi_*')
unix_stems = ('dbapi', 'dbapi_driver', 'ct_ftds64', 'tds_ftds64',
'xconne?t', 'xutil', 'xncbi')
windows_stems = ('ncbi_core', 'ncbi_dbapi', 'ncbi_dbapi_driver')
+installations = ('2.7env',)
os.mkdir(install_dir + '/lib')
if os.path.exists(lib_dir + '/python_ncbi_dbapi.so'):
@@ -21,7 +22,36 @@ for s in stems:
for x in glob.glob(template % s):
shutil.copy(x, install_dir + '/lib/' + os.path.basename(x))
-# Build a tarball for system-wide installation only on Linux.
+# Build wheels only on Linux (currently the only supported platform anyway).
if sys.platform == 'linux2':
- build_tarball = os.path.dirname(sys.argv[0]) + '/build_tarball.sh'
- os.execv(build_tarball, [build_tarball, install_dir, version])
+ proj_src_dir = src_dir + '/src/dbapi/lang_bind/python'
+ tmp_dir = install_dir + '/tmp'
+ cpp_build = os.path.dirname(os.path.abspath(lib_dir))
+ #build_tarball = os.path.dirname(sys.argv[0]) + '/build_tarball.sh'
+ #os.execv(build_tarball, [build_tarball, install_dir, version])
+ for x in installations:
+ py_bin_dir = '/opt/python-' + x + '/bin'
+ if os.path.isdir(tmp_dir):
+ shutil.rmtree(tmp_dir)
+ os.mkdir(tmp_dir)
+ if 0 != subprocess.call((py_bin_dir + '/pip', 'install', '-t', tmp_dir,
+ 'packit')):
+ raise RuntimeError('Error installing packit')
+ for x in ('python_ncbi_dbapi.cpp', 'python_ncbi_dbapi.hpp',
+ 'setup.py'):
+ shutil.copy(proj_src_dir + '/' + x, tmp_dir + '/' + x)
+ shutil.copytree(proj_src_dir + '/pythonpp', tmp_dir + '/pythonpp')
+ orig_cwd = os.getcwd()
+ os.chdir(tmp_dir)
+ if 0 != subprocess.call((py_bin_dir + '/python', 'setup.py',
+ '--with-c++-build=' + cpp_build,
+ '--command-packages', 'packit',
+ 'bdist_wheel')):
+ raise RuntimeError('Error running setup.py')
+ os.chdir(orig_cwd)
+ wheels = glob.glob(tmp_dir + '/dist/*.whl')
+ if len(wheels) != 1:
+ raise RuntimeError('Expected to get exactly 1 wheel, but got '
+ + len(wheels))
+ shutil.move(wheels[0], install_dir)
+ shutil.rmtree(tmp_dir)
diff --git a/c++/scripts/projects/python_ncbi_dbapi/project.lst b/c++/scripts/projects/python_ncbi_dbapi/project.lst
index 105aeb6..c8444ba 100644
--- a/c++/scripts/projects/python_ncbi_dbapi/project.lst
+++ b/c++/scripts/projects/python_ncbi_dbapi/project.lst
@@ -1,5 +1,6 @@
corelib$
util$
+util/bitset$
connect$
connect/ext$
dll
diff --git a/c++/scripts/projects/rmblastn/Manifest b/c++/scripts/projects/rmblastn/Manifest
index ee20dc1..f528d2a 100644
--- a/c++/scripts/projects/rmblastn/Manifest
+++ b/c++/scripts/projects/rmblastn/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 427336 2014-02-19 16:05:07Z camacho $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Author: Christiam Camacho
#
@@ -35,8 +35,8 @@ DEFAULT_CONFIGURATIONS: Linux32-Centos:icc Linux64-Centos:icc
DEFAULT_CONFIGURE_FLAGS: --without-debug --with-strip --with-mt --with-build-root=$srcdir/ReleaseMT
-Win32_10 : plain : static 32 ReleaseMT
-Win64_10 : plain : static 64 ReleaseMT
+Win32_13 : plain : static 32 ReleaseMT
+Win64_13 : plain : static 64 ReleaseMT
IntelMAC : universal : GCC.sh 4.0 --without-debug --without-pcre --with-mt --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public
diff --git a/c++/scripts/projects/test_ccpp_read/Manifest b/c++/scripts/projects/test_ccpp_read/Manifest
index 427896a..8f2d515 100644
--- a/c++/scripts/projects/test_ccpp_read/Manifest
+++ b/c++/scripts/projects/test_ccpp_read/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 365317 2012-06-05 14:31:54Z gouriano $
+# $Id: Manifest 483955 2015-11-05 15:16:36Z fukanchi $
#
# Purpose: This file holds all the supported configurations of a package
# It is used by release configurator.
@@ -24,9 +24,9 @@ Linux32-Centos : plain : GCC.sh --without-debug --with-static --without-ru
Linux64-Centos : plain : GCC.sh --without-debug --with-static --without-runpath --with-flat-makefile
IntelMAC : plain : GCC.sh --without-debug --with-static --without-runpath --with-flat-makefile
-Win64_9 : 900 : static 64 ReleaseDLL
-Win32_10 : 1000 : static 32 ReleaseDLL
-Win64_10 : 1000 : static 64 ReleaseDLL
+Win32_13 : plain : static 32 ReleaseDLL
+Win64_13 : plain : static 64 ReleaseDLL
USE_COMPONENTS
+
diff --git a/c++/scripts/projects/testres-kernel/ChangeLog b/c++/scripts/projects/testres-kernel/ChangeLog
index a0e41ec..36905c3 100644
--- a/c++/scripts/projects/testres-kernel/ChangeLog
+++ b/c++/scripts/projects/testres-kernel/ChangeLog
@@ -1,3 +1,4 @@
Oct 21, 2013
First release
-
+Jun 2, 2015
+Version 1.3.0. Multiple bugfixes, improvements
diff --git a/c++/scripts/projects/testres-kernel/Manifest b/c++/scripts/projects/testres-kernel/Manifest
index 501f125..58b2108 100644
--- a/c++/scripts/projects/testres-kernel/Manifest
+++ b/c++/scripts/projects/testres-kernel/Manifest
@@ -1,14 +1,14 @@
#
# Filename: Manifest
#
-# $Id: Manifest 447824 2014-09-30 19:48:47Z zakharov $
+# $Id: Manifest 481816 2015-10-15 22:41:22Z fukanchi $
#
# Author: Mikhail Zakharov (template by Sergey Satskiy)
#
# Purpose: This file holds all the supported configurations of a package
# It is used by release configurator.
#
-#USE_COMPONENTS
+USE_COMPONENTS
APP: testres_kernel
@@ -16,7 +16,7 @@ APP: testres_kernel
COPY: $srcdir/src/internal/cppcore/testres/tool/templates/ $installdir
#copy modules
-POSTBUILD: $srcdir/scripts/projects/testres-kernel/copy_modules.py $srcdir $bindir $installdir
+POSTBUILD: $packagedir/copy_modules.py $srcdir $bindir $installdir
#ini file
COPY: $srcdir/src/internal/cppcore/testres/kernel/testres_kernel.ini $installdir/bin
diff --git a/c++/scripts/projects/testres-kernel/README b/c++/scripts/projects/testres-kernel/README
index 582e105..a5d8452 100644
--- a/c++/scripts/projects/testres-kernel/README
+++ b/c++/scripts/projects/testres-kernel/README
@@ -5,4 +5,5 @@ Started as testipub replacement (CXX-2091)
Package includes:
1. TestRes kernel
2. Test templates specific to the version
+3. TestRes kernel modules for foreign (TCeX and python) test import
diff --git a/c++/scripts/projects/testres-kernel/components.link b/c++/scripts/projects/testres-kernel/components.link
index 727ede5..bbb94f0 100644
--- a/c++/scripts/projects/testres-kernel/components.link
+++ b/c++/scripts/projects/testres-kernel/components.link
@@ -1,6 +1,6 @@
[components]
-infrastructure 13.0
-core 13.0
-web 13.0
-misc 13.0
-app 13.0
+#infrastructure 16.1
+#core 16.1
+web 16.1
+misc 16.1
+app 16.1
diff --git a/c++/scripts/projects/testres-kernel/copy_modules.py b/c++/scripts/projects/testres-kernel/copy_modules.py
index 1cdcb33..056dada 100755
--- a/c++/scripts/projects/testres-kernel/copy_modules.py
+++ b/c++/scripts/projects/testres-kernel/copy_modules.py
@@ -2,6 +2,8 @@
import os
import shutil
import sys
+import re
+import traceback
MODULES_PATH = "src/internal/cppcore/testres/modules"
MODULES_DEST_PATH = "modules"
@@ -37,18 +39,78 @@ try:
gen_conf_path = None
def_run_path = None
+ mod_dir_path = None # TestRes module support directory to be copied into the release
if (os.path.exists(gen_conf_path_bin) and os.path.exists(def_run_path_bin)):
+ # taking modules from binary
gen_conf_path = gen_conf_path_bin
def_run_path = def_run_path_bin
+ mod_dir_path = module_src_dir
else:
+ # modules in src
if os.path.exists(gen_conf_path_src) and os.path.exists(def_run_path_src):
gen_conf_path = gen_conf_path_src
def_run_path = def_run_path_src
+ mod_dir_path = module_src_dir
+
+ #delete Id svn keyword
+ for root, dirs, files in os.walk(mod_dir_path):
+ for fname in files:
+ fpath = os.path.join(root, fname)
+ result = []
+ modified = False
+
+ with open(fpath) as f:
+ for line in f:
+ if "$Id" not in line:
+ result.append(line)
+ else:
+ modified = True
+
+ if modified:
+ with open(fname, "w") as f:
+ f.writelines(result)
if gen_conf_path and def_run_path:
module_dest_dir = os.path.join(modules_dest_dir, dir_entry)
- os.makedirs(module_dest_dir)
+
+ #print "copying module %s from '%s' to '%s'" % (dir_entry, mod_dir_path, module_dest_dir)
+
+ if mod_dir_path:
+ re_fileskip = re.compile(r"(Makefile)|\.((cpp)|(hpp)|(in)|(app)|(lib))$")
+ # filtered shutil.copytree
+ for root, dirs, files in os.walk(mod_dir_path):
+ rel_root_path = root[len(mod_dir_path):].lstrip('/')
+
+ try:
+ os.makedirs(os.path.join(module_dest_dir, rel_root_path))
+ except OSError:
+ pass
+
+
+ for directory in dirs:
+ if directory != "test": # skip module tests
+ new_dir = os.path.join(module_dest_dir, rel_root_path, directory)
+ print "creating " + new_dir
+ try:
+ os.makedirs(new_dir)
+ except OSError:
+ pass
+ print "filtering %s" % str(files)
+ file_names = [x for x in files if not re_fileskip.search(x)]
+ file_names = [x for x in file_names if not x.startswith(".")]
+ print "getting %s" % str(file_names)
+
+ for file_name in file_names:
+ src_path = os.path.join(root, file_name)
+ dst_path = os.path.join(module_dest_dir, rel_root_path, file_name)
+ # generate config and default run are copied
+ # independently
+ if src_path not in [gen_conf_path, def_run_path]:
+ shutil.copy(src_path, dst_path)
+
+ #shutil.copytree(mod_dir_path, module_dest_dir)
+
gen_conf_dest_path = os.path.join(
module_dest_dir,
GENERATE_CONFIG)
@@ -56,7 +118,7 @@ try:
shutil.copy(gen_conf_path, gen_conf_dest_path)
shutil.copy(def_run_path, def_run_dest_path)
except Exception as excpt:
- print excpt
+ traceback.print_exc()
exit(1)
exit(0)
diff --git a/c++/scripts/projects/testres-kernel/project.lst b/c++/scripts/projects/testres-kernel/project.lst
index b104768..fc0375d 100644
--- a/c++/scripts/projects/testres-kernel/project.lst
+++ b/c++/scripts/projects/testres-kernel/project.lst
@@ -5,6 +5,7 @@ util/bitset$ update-only
util/cache$
util/regexp$
util/xregexp$
+util/compress
objects$
objects/misc$
objects/general
@@ -12,6 +13,7 @@ connect$
connect/ext$
connect/impl$
connect/services$
+connect/services/impl$
connect/daemons$
html$
misc$
@@ -19,9 +21,12 @@ misc/xmlwrapp$
misc/xmlwrapp/impl$
serial$
serial/datatool$
+serial/impl$
boost
internal$
internal/cppcore$
internal/cppcore/testres
internal/cppcore/testres/kernel
internal/cppcore/testres/modules
+-internal/cppcore/testres/examples
+
diff --git a/c++/scripts/projects/testres-scheduler/ChangeLog b/c++/scripts/projects/testres-scheduler/ChangeLog
index a0e41ec..5841b7b 100644
--- a/c++/scripts/projects/testres-scheduler/ChangeLog
+++ b/c++/scripts/projects/testres-scheduler/ChangeLog
@@ -1,3 +1,4 @@
Oct 21, 2013
First release
-
+Jun 2, 2015
+Release 1.3.0, Multiple bugfixes, performance improvements
diff --git a/c++/scripts/projects/testres-scheduler/README b/c++/scripts/projects/testres-scheduler/README
index 8f7358b..804e69e 100644
--- a/c++/scripts/projects/testres-scheduler/README
+++ b/c++/scripts/projects/testres-scheduler/README
@@ -10,4 +10,5 @@ TestRes Scheduler Package includes:
2. tr-dev (console test development environment) scripts
3. presenters
4. cgis
+5. TeamCity integration scripts
diff --git a/c++/scripts/projects/testres-scheduler/components.link b/c++/scripts/projects/testres-scheduler/components.link
index 727ede5..bbb94f0 100644
--- a/c++/scripts/projects/testres-scheduler/components.link
+++ b/c++/scripts/projects/testres-scheduler/components.link
@@ -1,6 +1,6 @@
[components]
-infrastructure 13.0
-core 13.0
-web 13.0
-misc 13.0
-app 13.0
+#infrastructure 16.1
+#core 16.1
+web 16.1
+misc 16.1
+app 16.1
diff --git a/c++/scripts/projects/testres-scheduler/project.lst b/c++/scripts/projects/testres-scheduler/project.lst
index 693389d..79517d4 100644
--- a/c++/scripts/projects/testres-scheduler/project.lst
+++ b/c++/scripts/projects/testres-scheduler/project.lst
@@ -5,10 +5,13 @@ util/bitset$ update-only
util/cache$
util/regexp$
util/xregexp$
+util/compress
+common
connect$
connect/ext$
connect/impl$
connect/services$
+connect/services/impl$
connect/daemons$
html$
misc$
@@ -16,8 +19,12 @@ misc/xmlwrapp$
misc/xmlwrapp/impl$
serial$
serial/datatool$
+serial/impl$
boost
internal$
internal/cppcore$
internal/cppcore/testres
-internal/cppcore/testres/kernel
+-internal/cppcore/testres/examples
+-internal/cppcore/testres/modules
+
diff --git a/c++/scripts/projects/xmlwrapp/Manifest b/c++/scripts/projects/xmlwrapp/Manifest
index 5504a67..8feb35b 100644
--- a/c++/scripts/projects/xmlwrapp/Manifest
+++ b/c++/scripts/projects/xmlwrapp/Manifest
@@ -1,7 +1,7 @@
#
# Filename: Manifest
#
-# $Id: Manifest 466970 2015-05-07 19:00:36Z satskyse $
+# $Id: Manifest 482132 2015-10-20 21:07:25Z fukanchi $
#
# Author: Sergey Satskiy
#
@@ -14,6 +14,7 @@ APP: event_parsing test_attributes test_document test_event test_namespace test_
APP: test_xslt tree_parsing xml_generation xslt_transformation
LIB: libxmlwrapp.a
+SRC: src/misc/xmlwrapp/dtd.cpp
DEFAULT_CONFIGURATIONS: Linux64-Centos:plain-GCC
DEFAULT_CONFIGURE_FLAGS: --without-debug --with-mt
@@ -26,7 +27,8 @@ DEFAULT_CONFIGURE_FLAGS: --without-debug --with-mt
# to it. So some standard options may be added by release configurator, such as --build-root-sfx, --with-projects,
# --with-distcc, --with-action etc.
-FreeBSD32 : plain : GCC.sh --without-debug --with-mt --without-runpath --with-flat-makefile
+FreeBSD32 : plain : Clang.sh --without-debug --with-mt --without-runpath --with-flat-makefile
+FreeBSD64 : plain : Clang.sh --without-debug --with-mt --without-runpath --with-flat-makefile
Linux64-Centos : plain-GCC : GCC.sh --without-debug --with-mt --without-runpath --with-flat-makefile
Linux64-Centos : GCC-nomt : GCC.sh --without-debug --without-mt --without-runpath --with-flat-makefile
@@ -40,9 +42,8 @@ Cygwin64 : GCC : GCC.sh --without-debug --with-mt
IntelMAC : GCC-universal : GCC.sh --without-debug --with-mt --without-runpath --with-flat-makefile --with-universal=i386,x86_64 --with-3psw=system:netopt --without-ncbi-public
IntelMAC : GCC : GCC.sh --without-debug --with-mt --without-runpath --with-flat-makefile
-
-Win32_10 : 1000-static-32 : static 32 ReleaseDLL
-Win64_10 : 1000-static-64 : static 64 ReleaseDLL
+Win32_13 : 13-static-32 : static 32 ReleaseDLL
+Win64_13 : 13-static-64 : static 64 ReleaseDLL
XCode : plain : Xcode.sh 30
diff --git a/c++/scripts/projects/xmlwrapp/project.lst b/c++/scripts/projects/xmlwrapp/project.lst
index 658b68e..9f2e0bf 100644
--- a/c++/scripts/projects/xmlwrapp/project.lst
+++ b/c++/scripts/projects/xmlwrapp/project.lst
@@ -22,7 +22,9 @@ internal/demo/misc/xmlwrapp
#define LST_COMMENT5 Make it independent on the pre-installed PTB
util$
util/regexp$
+util/regexp/testdata$
+util/xregexp$
util/bitset$
serial$
serial/datatool$
-
+connect$
diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in
index 675f6ff..091bb09 100644
--- a/c++/src/Makefile.in
+++ b/c++/src/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
# Master (top-level) makefile for all NCBI C++ projects
##################################################################
diff --git a/c++/src/algo/Makefile.in b/c++/src/algo/Makefile.in
index 556c541..66d9094 100644
--- a/c++/src/algo/Makefile.in
+++ b/c++/src/algo/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
# Meta-makefile("ALGO" project)
#################################
diff --git a/c++/src/algo/blast/Makefile.blast_macros.mk b/c++/src/algo/blast/Makefile.blast_macros.mk
index 5106081..d9ca4a3 100644
--- a/c++/src/algo/blast/Makefile.blast_macros.mk
+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
@@ -1,5 +1,5 @@
#################################
-# $Id: Makefile.blast_macros.mk 457396 2015-01-22 18:08:25Z ivanov $
+# $Id: Makefile.blast_macros.mk 457267 2015-01-21 19:46:09Z boratyng $
# This file contains macro definitions for using libraries maintained by the
# BLAST TEAM
# Author: Christiam Camacho (camacho at ncbi.nlm.nih.gov)
diff --git a/c++/src/algo/blast/api/bl2seq.cpp b/c++/src/algo/blast/api/bl2seq.cpp
index 112295e..1c3f261 100644
--- a/c++/src/algo/blast/api/bl2seq.cpp
+++ b/c++/src/algo/blast/api/bl2seq.cpp
@@ -1,4 +1,4 @@
-/* $Id: bl2seq.cpp 303807 2011-06-13 18:22:23Z camacho $
+/* $Id: bl2seq.cpp 478803 2015-09-14 15:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,7 +46,7 @@ USING_SCOPE(objects);
BEGIN_SCOPE(blast)
CBl2Seq::CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject, EProgram p)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ : m_DbScanMode(false), m_InterruptFnx(0), m_InterruptUserData(0)
{
TSeqLocVector queries;
TSeqLocVector subjects;
@@ -64,7 +64,7 @@ void CBl2Seq::x_InitCLocalBlast()
_ASSERT( !m_OptsHandle.Empty() );
CRef<IQueryFactory> query_factory(new CObjMgr_QueryFactory(m_tQueries));
CRef<IQueryFactory> subject_factory(new CObjMgr_QueryFactory(m_tSubjects));
- CRef<CLocalDbAdapter> db(new CLocalDbAdapter(subject_factory, m_OptsHandle));
+ CRef<CLocalDbAdapter> db(new CLocalDbAdapter(subject_factory, m_OptsHandle, m_DbScanMode));
m_Blast.Reset(new CLocalBlast(query_factory, m_OptsHandle, db));
if (m_InterruptFnx != NULL) {
m_Blast->SetInterruptCallback(m_InterruptFnx, m_InterruptUserData);
@@ -76,7 +76,7 @@ void CBl2Seq::x_InitCLocalBlast()
CBl2Seq::CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject,
CBlastOptionsHandle& opts)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ : m_DbScanMode(false), m_InterruptFnx(0), m_InterruptUserData(0)
{
TSeqLocVector queries;
TSeqLocVector subjects;
@@ -88,8 +88,8 @@ CBl2Seq::CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject,
}
CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects,
- EProgram p)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ EProgram p, bool dbscan_mode)
+ : m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)
{
TSeqLocVector queries;
queries.push_back(query);
@@ -99,8 +99,8 @@ CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects,
}
CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects,
- CBlastOptionsHandle& opts)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ CBlastOptionsHandle& opts, bool dbscan_mode)
+ : m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)
{
TSeqLocVector queries;
queries.push_back(query);
@@ -110,16 +110,16 @@ CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects,
}
CBl2Seq::CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects,
- EProgram p)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ EProgram p, bool dbscan_mode)
+ : m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)
{
x_Init(queries, subjects);
m_OptsHandle.Reset(CBlastOptionsFactory::Create(p));
}
CBl2Seq::CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects,
- CBlastOptionsHandle& opts)
- : m_InterruptFnx(0), m_InterruptUserData(0)
+ CBlastOptionsHandle& opts, bool dbscan_mode)
+ : m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)
{
x_Init(queries, subjects);
m_OptsHandle.Reset(&opts);
diff --git a/c++/src/algo/blast/api/blast_aux_priv.cpp b/c++/src/algo/blast/api/blast_aux_priv.cpp
index ab86a24..d2382cb 100644
--- a/c++/src/algo/blast/api/blast_aux_priv.cpp
+++ b/c++/src/algo/blast/api/blast_aux_priv.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_aux_priv.cpp 444370 2014-08-25 11:42:59Z ivanov $";
+ "$Id: blast_aux_priv.cpp 443924 2014-08-20 15:03:37Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
@@ -116,7 +116,7 @@ string
BlastErrorCode2String(Int2 error_code)
{
Blast_Message* blast_msg = NULL;
- Blast_PerrorEx(&blast_msg, error_code, __FILE__, __LINE__, -1);
+ Blast_PerrorWithLocation(&blast_msg, error_code, kBlastMessageNoContext);
string retval(blast_msg != NULL ? blast_msg->message : kEmptyStr);
blast_msg = Blast_MessageFree(blast_msg);
return retval;
diff --git a/c++/src/algo/blast/api/blast_nucl_options.cpp b/c++/src/algo/blast/api/blast_nucl_options.cpp
index 827261d..2d1f83a 100644
--- a/c++/src/algo/blast/api/blast_nucl_options.cpp
+++ b/c++/src/algo/blast/api/blast_nucl_options.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_nucl_options.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_nucl_options.cpp 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_options_builder.cpp b/c++/src/algo/blast/api/blast_options_builder.cpp
index 60794b1..ef8904f 100644
--- a/c++/src/algo/blast/api/blast_options_builder.cpp
+++ b/c++/src/algo/blast/api/blast_options_builder.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_options_builder.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_options_builder.cpp 482876 2015-10-27 11:29:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -98,7 +98,7 @@ CBlastOptionsBuilder::ComputeProgram(const string & program,
p = "vecscreen";
found = true;
}
- if (s == "sra") {
+ if ((s == "sra") || (s == "wgs")) {
found = true;
}
} else if (p == "tblastn") {
@@ -250,7 +250,18 @@ x_ProcessOneOption(CBlastOptionsHandle & opts,
} else if (CBlast4Field::Get(eBlastOpt_GapOpeningCost).Match(p)) {
bo.SetGapOpeningCost(v.GetInteger());
} else if (CBlast4Field::Get(eBlastOpt_GiList).Match(p)) {
+ #ifdef NCBI_STRICT_GI
+ const list<int>& int_list = v.GetInteger_list();
+ list<TGi> gi_list;
+ ITERATE ( list<int>, it, int_list ) {
+ gi_list.push_back(GI_FROM(int, *it));
+ }
+ m_GiList = gi_list;
+ #elif defined(NCBI_INT8_GI)
+ m_GiList = v.GetBig_integer_list();
+ #else
m_GiList = v.GetInteger_list();
+ #endif
} else if (CBlast4Field::Get(eBlastOpt_GapTracebackAlgorithm).Match(p)) {
bo.SetGapTracebackAlgorithm((EBlastTbackExt) v.GetInteger());
} else if (CBlast4Field::Get(eBlastOpt_GapTrigger).Match(p)) {
@@ -345,7 +356,18 @@ x_ProcessOneOption(CBlastOptionsHandle & opts,
case 'N':
if (CBlast4Field::Get(eBlastOpt_NegativeGiList).Match(p)) {
+ #ifdef NCBI_STRICT_GI
+ const list<int>& int_list = v.GetInteger_list();
+ list<TGi> gi_list;
+ ITERATE ( list<int>, it, int_list ) {
+ gi_list.push_back(GI_FROM(int, *it));
+ }
+ m_NegativeGiList = gi_list;
+ #elif defined(NCBI_INT8_GI)
+ m_NegativeGiList = v.GetBig_integer_list();
+ #else
m_NegativeGiList = v.GetInteger_list();
+ #endif
} else {
found = false;
}
@@ -646,7 +668,7 @@ bool CBlastOptionsBuilder::HaveGiList()
return m_GiList.Have();
}
-list<int> CBlastOptionsBuilder::GetGiList()
+list<TGi> CBlastOptionsBuilder::GetGiList()
{
return m_GiList.Get();
}
@@ -687,7 +709,7 @@ bool CBlastOptionsBuilder::HaveNegativeGiList()
return m_NegativeGiList.Have();
}
-list<int> CBlastOptionsBuilder::GetNegativeGiList()
+list<TGi> CBlastOptionsBuilder::GetNegativeGiList()
{
return m_NegativeGiList.Get();
}
diff --git a/c++/src/algo/blast/api/blast_options_cxx.cpp b/c++/src/algo/blast/api/blast_options_cxx.cpp
index 70c7a8a..e6bf3a1 100644
--- a/c++/src/algo/blast/api/blast_options_cxx.cpp
+++ b/c++/src/algo/blast/api/blast_options_cxx.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_options_cxx.cpp 457059 2015-01-20 15:02:34Z ivanov $";
+ "$Id: blast_options_cxx.cpp 456407 2015-01-12 15:47:18Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
diff --git a/c++/src/algo/blast/api/blast_options_handle.cpp b/c++/src/algo/blast/api/blast_options_handle.cpp
index 9643f9d..0a0bd1e 100644
--- a/c++/src/algo/blast/api/blast_options_handle.cpp
+++ b/c++/src/algo/blast/api/blast_options_handle.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_options_handle.cpp 442346 2014-08-01 16:28:16Z mcelhany $
+/* $Id: blast_options_handle.cpp 442215 2014-07-31 14:00:16Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_options_local_priv.cpp b/c++/src/algo/blast/api/blast_options_local_priv.cpp
index 5f90957..4603df7 100644
--- a/c++/src/algo/blast/api/blast_options_local_priv.cpp
+++ b/c++/src/algo/blast/api/blast_options_local_priv.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_options_local_priv.cpp 464888 2015-04-15 11:36:45Z ivanov $";
+ "$Id: blast_options_local_priv.cpp 463310 2015-03-26 17:00:09Z boukn $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
diff --git a/c++/src/algo/blast/api/blast_options_local_priv.hpp b/c++/src/algo/blast/api/blast_options_local_priv.hpp
index 4dbeed3..4c40d0a 100644
--- a/c++/src/algo/blast/api/blast_options_local_priv.hpp
+++ b/c++/src/algo/blast/api/blast_options_local_priv.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_options_local_priv.hpp 463319 2015-03-26 17:26:40Z ivanov $
+/* $Id: blast_options_local_priv.hpp 460349 2015-02-26 16:10:16Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_prot_options.cpp b/c++/src/algo/blast/api/blast_prot_options.cpp
index 7e8055b..e15ff28 100644
--- a/c++/src/algo/blast/api/blast_prot_options.cpp
+++ b/c++/src/algo/blast/api/blast_prot_options.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_prot_options.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_prot_options.cpp 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_results.cpp b/c++/src/algo/blast/api/blast_results.cpp
index 8717f15..23d4b2d 100644
--- a/c++/src/algo/blast/api/blast_results.cpp
+++ b/c++/src/algo/blast/api/blast_results.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_results.cpp 457067 2015-01-20 15:14:35Z ivanov $
+/* $Id: blast_results.cpp 456936 2015-01-16 15:44:23Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_results.cpp 457067 2015-01-20 15:14:35Z ivanov $";
+ "$Id: blast_results.cpp 456936 2015-01-16 15:44:23Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
diff --git a/c++/src/algo/blast/api/blast_rps_options.cpp b/c++/src/algo/blast/api/blast_rps_options.cpp
index e762998..3037194 100644
--- a/c++/src/algo/blast/api/blast_rps_options.cpp
+++ b/c++/src/algo/blast/api/blast_rps_options.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_rps_options.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_rps_options.cpp 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_seqalign.cpp b/c++/src/algo/blast/api/blast_seqalign.cpp
index 90477b4..ef56238 100644
--- a/c++/src/algo/blast/api/blast_seqalign.cpp
+++ b/c++/src/algo/blast/api/blast_seqalign.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_seqalign.cpp 457063 2015-01-20 15:07:32Z ivanov $
+/* $Id: blast_seqalign.cpp 456652 2015-01-14 14:54:51Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/api/blast_setup_cxx.cpp b/c++/src/algo/blast/api/blast_setup_cxx.cpp
index 99d544b..ae3f5ea 100644
--- a/c++/src/algo/blast/api/blast_setup_cxx.cpp
+++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_setup_cxx.cpp 454099 2014-12-10 20:03:21Z ivanov $";
+ "$Id: blast_setup_cxx.cpp 451176 2014-11-04 15:26:36Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
diff --git a/c++/src/algo/blast/api/local_blast.cpp b/c++/src/algo/blast/api/local_blast.cpp
index ffe01ad..b11962e 100644
--- a/c++/src/algo/blast/api/local_blast.cpp
+++ b/c++/src/algo/blast/api/local_blast.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: local_blast.cpp 465306 2015-04-20 16:55:25Z ivanov $";
+ "$Id: local_blast.cpp 478802 2015-09-14 15:44:22Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -62,7 +62,7 @@ SplitQuery_GetChunkSize(EProgram program)
char* chunk_sz_str = getenv("CHUNK_SIZE");
if (chunk_sz_str && !NStr::IsBlank(chunk_sz_str)) {
retval = NStr::StringToInt(chunk_sz_str);
- _TRACE("DEBUG: Using query chunk size " << retval);
+ _TRACE("Using query chunk size from environment " << retval);
} else {
switch (program) {
@@ -184,7 +184,7 @@ CLocalBlast::Run()
size_t index;
EResultType res_type = eDatabaseSearch;
unsigned int num_subjects = 0;
- if (m_LocalDbAdapter.NotEmpty() && !m_LocalDbAdapter->IsBlastDb()) {
+ if (m_LocalDbAdapter.NotEmpty() && !m_LocalDbAdapter->IsBlastDb() && !m_LocalDbAdapter->IsDbScanMode()) {
res_type = eSequenceComparison;
IBlastSeqInfoSrc * subject_infosrc = m_LocalDbAdapter->MakeSeqInfoSrc();
if(subject_infosrc != NULL) {
@@ -262,7 +262,8 @@ CLocalBlast::Run()
m_Opts,
seqinfo_src,
search_msgs));
- if (m_LocalDbAdapter.NotEmpty() && !m_LocalDbAdapter->IsBlastDb()) {
+ if (m_LocalDbAdapter.NotEmpty() && !m_LocalDbAdapter->IsBlastDb()
+ && !m_LocalDbAdapter->IsDbScanMode()) {
m_TbackSearch->SetResultType(eSequenceComparison);
}
m_TbackSearch->SetNumberOfThreads(GetNumberOfThreads());
diff --git a/c++/src/algo/blast/api/local_db_adapter.cpp b/c++/src/algo/blast/api/local_db_adapter.cpp
index 97988e7..fdc0913 100644
--- a/c++/src/algo/blast/api/local_db_adapter.cpp
+++ b/c++/src/algo/blast/api/local_db_adapter.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: local_db_adapter.cpp 403214 2013-06-13 13:25:50Z fongah2 $";
+ "$Id: local_db_adapter.cpp 478802 2015-09-14 15:44:22Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -56,15 +56,16 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
CLocalDbAdapter::CLocalDbAdapter(const CSearchDatabase& dbinfo)
- : m_SeqSrc(0), m_SeqInfoSrc(0), m_DbName(dbinfo.GetDatabaseName())
+ : m_SeqSrc(0), m_SeqInfoSrc(0), m_DbName(dbinfo.GetDatabaseName()), m_DbScanMode(false)
{
m_DbInfo.Reset(new CSearchDatabase(dbinfo));
}
CLocalDbAdapter::CLocalDbAdapter(CRef<IQueryFactory> subject_sequences,
- CConstRef<CBlastOptionsHandle> opts_handle)
+ CConstRef<CBlastOptionsHandle> opts_handle,
+ bool dbscan_mode)
: m_SeqSrc(0), m_SeqInfoSrc(0), m_SubjectFactory(subject_sequences),
- m_OptsHandle(opts_handle), m_DbName(kEmptyStr)
+ m_OptsHandle(opts_handle), m_DbName(kEmptyStr), m_DbScanMode(dbscan_mode)
{
if (subject_sequences.Empty()) {
NCBI_THROW(CBlastException, eInvalidArgument,
@@ -88,7 +89,7 @@ CLocalDbAdapter::CLocalDbAdapter(CRef<IQueryFactory> subject_sequences,
CLocalDbAdapter::CLocalDbAdapter(BlastSeqSrc* seqSrc,
CRef<IBlastSeqInfoSrc> seqInfoSrc)
- : m_SeqSrc(seqSrc), m_SeqInfoSrc(seqInfoSrc), m_DbName(kEmptyStr)
+ : m_SeqSrc(seqSrc), m_SeqInfoSrc(seqInfoSrc), m_DbName(kEmptyStr), m_DbScanMode(false)
{
}
@@ -135,7 +136,7 @@ CLocalDbAdapter::MakeSeqSrc()
m_OptsHandle->GetOptions().GetProgramType();
if ( !m_Subjects.empty() ) {
//m_SeqSrc = QueryFactoryBlastSeqSrcInit(m_Subjects, program);
- m_SeqSrc = MultiSeqBlastSeqSrcInit(m_Subjects, program);
+ m_SeqSrc = MultiSeqBlastSeqSrcInit(m_Subjects, program, m_DbScanMode);
} else {
m_SeqSrc = QueryFactoryBlastSeqSrcInit(m_SubjectFactory,
program);
diff --git a/c++/src/algo/blast/api/msa_pssm_input.cpp b/c++/src/algo/blast/api/msa_pssm_input.cpp
index 9bd38b6..dea2df7 100644
--- a/c++/src/algo/blast/api/msa_pssm_input.cpp
+++ b/c++/src/algo/blast/api/msa_pssm_input.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: msa_pssm_input.cpp 358452 2012-04-02 19:35:30Z camacho $";
+ "$Id: msa_pssm_input.cpp 483267 2015-10-29 16:09:03Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -349,14 +349,55 @@ CPsiBlastInputClustalW::x_ExtractAlignmentData()
_ASSERT(isalpha(kCurrentRes) || kCurrentRes == kGapChar);
m_Msa->data[seq_index][query_idx].letter =
AMINOACID_TO_NCBISTDAA[(int) toupper(kCurrentRes)];
- if (isupper(kCurrentRes) && kCurrentRes != kGapChar) {
- m_Msa->data[seq_index][query_idx].is_aligned = true;
- } else {
- m_Msa->data[seq_index][query_idx].is_aligned = false;
- }
+ m_Msa->data[seq_index][query_idx].is_aligned = true;
query_idx++;
}
}
+
+ // set flanking gaps and long internal gaps as unaligned
+ seq_index = kQueryIndex + 1;
+ const int kGapResidue = 0;
+ const int kLongGapLen = 10;
+ for (; seq_index < m_Msa->dimensions->num_seqs + 1; seq_index++) {
+ size_t i = 0;
+
+ // find left flanking gaps
+ while (i < m_Msa->dimensions->query_length &&
+ m_Msa->data[seq_index][i].letter == kGapResidue) {
+
+ m_Msa->data[seq_index][i].is_aligned = false;
+ i++;
+ }
+
+ // find long internal gaps
+ while (i < m_Msa->dimensions->query_length) {
+ while (i < m_Msa->dimensions->query_length &&
+ m_Msa->data[seq_index][i].letter != kGapResidue) {
+ i++;
+ }
+
+ int k = i + 1;
+ while (k < m_Msa->dimensions->query_length &&
+ m_Msa->data[seq_index][k].letter == kGapResidue) {
+ k++;
+ }
+
+ if (k - i >= kLongGapLen) {
+ for (int j=i;j < k;j++) {
+ m_Msa->data[seq_index][j].is_aligned = false;
+ }
+ }
+
+ i = k;
+ }
+
+ // find right flanking gaps
+ i = m_Msa->dimensions->query_length - 1;
+ while (i >= 0 && m_Msa->data[seq_index][i].letter == kGapResidue) {
+ m_Msa->data[seq_index][i].is_aligned = false;
+ i--;
+ }
+ }
}
END_SCOPE(blast)
diff --git a/c++/src/algo/blast/api/prelim_stage.cpp b/c++/src/algo/blast/api/prelim_stage.cpp
index 1c60600..4a82a09 100644
--- a/c++/src/algo/blast/api/prelim_stage.cpp
+++ b/c++/src/algo/blast/api/prelim_stage.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: prelim_stage.cpp 444369 2014-08-25 11:42:15Z ivanov $";
+ "$Id: prelim_stage.cpp 479619 2015-09-22 15:43:07Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -171,12 +171,14 @@ CBlastPrelimSearch::x_LaunchMultiThreadedSearch(SInternalData& internal_data)
}
// ... and wait for the threads to finish
- long retv(0);
+ Uint8 retv(0);
NON_CONST_ITERATE(TBlastThreads, thread, the_threads) {
- long result(0);
- (*thread)->Join(reinterpret_cast<void**>(&result));
+ void * result(0);
+ (*thread)->Join(&result);
if (result) {
- retv = result;
+ // Thread is not really returning a pointer, it's actually
+ // retruning an int
+ retv = reinterpret_cast<Uint8> (result);
}
}
diff --git a/c++/src/algo/blast/api/remote_blast.cpp b/c++/src/algo/blast/api/remote_blast.cpp
index a998942..0609944 100644
--- a/c++/src/algo/blast/api/remote_blast.cpp
+++ b/c++/src/algo/blast/api/remote_blast.cpp
@@ -1,4 +1,4 @@
-/* $Id: remote_blast.cpp 416408 2013-10-28 15:24:29Z fongah2 $
+/* $Id: remote_blast.cpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -892,6 +892,14 @@ void CRemoteBlast::x_SetAlgoOpts(void)
CBlast4_parameters * algo_opts =
m_CBOH->SetOptions().GetBlast4AlgoOpts();
+ string user_ipv6_address;
+ CNcbiEnvironment env;
+ if( env.Get("HTTP_X_FORWARDED_FOR_IPV6") != kEmptyStr )
+ user_ipv6_address = env.Get("HTTP_X_FORWARDED_FOR_IPV6");
+ if( !user_ipv6_address.empty() ){
+ algo_opts->Add( string("HTTP_X_FORWARDED_FOR_IPV6"), user_ipv6_address );
+ }
+
m_QSR->SetAlgorithm_options().Set() = *algo_opts;
}
@@ -940,6 +948,21 @@ void CRemoteBlast::x_SetOneParam(objects::CBlast4Field & field,
}
void CRemoteBlast::x_SetOneParam(objects::CBlast4Field & field,
+ const list<Int8> * x)
+{
+ CRef<CBlast4_value> v(new CBlast4_value);
+ v->SetBig_integer_list() = *x;
+
+ CRef<CBlast4_parameter> p(new CBlast4_parameter);
+ p->SetName(field.GetName());
+ p->SetValue(*v);
+ _ASSERT(field.Match(*p));
+
+ m_QSR->SetProgram_options().Set().push_back(p);
+}
+
+
+void CRemoteBlast::x_SetOneParam(objects::CBlast4Field & field,
const char ** x)
{
CRef<CBlast4_value> v(new CBlast4_value);
@@ -1384,7 +1407,7 @@ void CRemoteBlast::x_Init(CRef<CBlastOptionsHandle> opts_handle,
{{
const CSearchDatabase::TGiList& tmplist = db.GetGiListLimitation();
if ( !tmplist.empty() ) {
- list<Int4> gilist;
+ list<TGi> gilist;
copy(tmplist.begin(), tmplist.end(), back_inserter(gilist));
SetGIList(gilist);
}
@@ -1395,7 +1418,7 @@ void CRemoteBlast::x_Init(CRef<CBlastOptionsHandle> opts_handle,
const CSearchDatabase::TGiList& tmplist =
db.GetNegativeGiListLimitation();
if ( !tmplist.empty() ) {
- list<Int4> gilist;
+ list<TGi> gilist;
copy(tmplist.begin(), tmplist.end(), back_inserter(gilist));
SetNegativeGIList(gilist);
}
@@ -1427,7 +1450,7 @@ CRemoteBlast::~CRemoteBlast()
{
}
-void CRemoteBlast::SetGIList(const list<Int4> & gi_list)
+void CRemoteBlast::SetGIList(const list<TGi> & gi_list)
{
if (gi_list.empty()) {
return;
@@ -1435,8 +1458,16 @@ void CRemoteBlast::SetGIList(const list<Int4> & gi_list)
NCBI_THROW(CBlastException, eNotSupported,
"Submitting gi lists remotely is currently not supported");
}
- x_SetOneParam(CBlast4Field::Get(eBlastOpt_GiList), & gi_list);
+ #ifdef NCBI_STRICT_GI
+ list<int> int_gi_list;
+ ITERATE ( list<TGi>, it, gi_list ) {
+ int_gi_list.push_back(GI_TO( int, *it));
+ }
+ x_SetOneParam(CBlast4Field::Get(eBlastOpt_GiList), & int_gi_list);
+ #else
+ x_SetOneParam(CBlast4Field::Get(eBlastOpt_GiList), & gi_list);
+ #endif
m_GiList.clear();
copy(gi_list.begin(), gi_list.end(), back_inserter(m_GiList));
}
@@ -1472,7 +1503,7 @@ CRemoteBlast::GetSubjectMaskingType() const
return m_SubjectMaskingType;
}
-void CRemoteBlast::SetNegativeGIList(const list<Int4> & gi_list)
+void CRemoteBlast::SetNegativeGIList(const list<TGi> & gi_list)
{
if (gi_list.empty()) {
return;
@@ -1480,7 +1511,15 @@ void CRemoteBlast::SetNegativeGIList(const list<Int4> & gi_list)
NCBI_THROW(CBlastException, eNotSupported,
"Submitting negative gi lists remotely is currently not supported");
}
- x_SetOneParam(CBlast4Field::Get(eBlastOpt_NegativeGiList), & gi_list);
+ #ifdef NCBI_STRICT_GI
+ list<int> int_gi_list;
+ ITERATE ( list<TGi>, it, gi_list ) {
+ int_gi_list.push_back(GI_TO( int, *it));
+ }
+ x_SetOneParam(CBlast4Field::Get(eBlastOpt_GiList), & int_gi_list);
+ #else
+ x_SetOneParam(CBlast4Field::Get(eBlastOpt_NegativeGiList), & gi_list);
+ #endif
m_NegativeGiList.clear();
copy(gi_list.begin(), gi_list.end(), back_inserter(m_NegativeGiList));
diff --git a/c++/src/algo/blast/api/remote_search.cpp b/c++/src/algo/blast/api/remote_search.cpp
index 67ea75c..44b2668 100644
--- a/c++/src/algo/blast/api/remote_search.cpp
+++ b/c++/src/algo/blast/api/remote_search.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: remote_search.cpp 103491 2007-05-04 17:18:18Z kazimird $";
+ "$Id: remote_search.cpp 482051 2015-10-20 14:16:32Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -112,7 +112,7 @@ CRemoteBlast & CRemoteSeqSearch::x_RemoteBlast()
const CSearchDatabase::TGiList& kGiList =
m_Subject->GetGiListLimitation();
if ( !kGiList.empty() ) {
- list<Int4> temp(kGiList.begin(), kGiList.end());
+ list<TGi> temp(kGiList.begin(), kGiList.end());
m_RemoteBlast->SetGIList(temp);
}
@@ -333,7 +333,7 @@ CRemoteBlast & CRemotePssmSearch::x_RemoteBlast()
const CSearchDatabase::TGiList& kGiList =
m_Subject->GetGiListLimitation();
if ( !kGiList.empty() ) {
- list<Int4> temp(kGiList.begin(), kGiList.end());
+ list<TGi> temp(kGiList.begin(), kGiList.end());
m_RemoteBlast->SetGIList(temp);
}
}
diff --git a/c++/src/algo/blast/api/rpsblast_local.cpp b/c++/src/algo/blast/api/rpsblast_local.cpp
index e46e642..569a8b0 100644
--- a/c++/src/algo/blast/api/rpsblast_local.cpp
+++ b/c++/src/algo/blast/api/rpsblast_local.cpp
@@ -1,4 +1,4 @@
-/* $Id: rpsblast_local.cpp 454092 2014-12-10 20:00:34Z ivanov $
+/* $Id: rpsblast_local.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,7 +46,8 @@
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
-static string delimiter="#rps#";
+static const char delimiter[] = "#rps#";
+static const size_t delimiter_len = sizeof(delimiter) - 1; // exclude \0
static void s_ConvertConcatStringToVectorOfString(const string & s, vector<string> & v)
@@ -59,7 +60,7 @@ static void s_ConvertConcatStringToVectorOfString(const string & s, vector<strin
break;
TSeqPos length = pos_find - pos_start;
v.push_back(s.substr(pos_start, length));
- pos_start = pos_find + delimiter.size();
+ pos_start = pos_find + delimiter_len;
}
v.push_back(s.substr(pos_start, s.size() - pos_start ));
diff --git a/c++/src/algo/blast/api/search_strategy.cpp b/c++/src/algo/blast/api/search_strategy.cpp
index 94babd0..945efee 100644
--- a/c++/src/algo/blast/api/search_strategy.cpp
+++ b/c++/src/algo/blast/api/search_strategy.cpp
@@ -1,4 +1,4 @@
-/* $Id: search_strategy.cpp 421717 2013-12-13 16:07:22Z boratyng $
+/* $Id: search_strategy.cpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -406,14 +406,30 @@ void CExportStrategy::x_Process_SearchDb(CRef<CSearchDatabase> & db)
const CSearchDatabase::TGiList& gi_list_limit = db->GetGiListLimitation();
if (!gi_list_limit.empty())
{
- x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_GiList), gi_list_limit);
+ #ifdef NCBI_STRICT_GI
+ vector<int> int_gi_list;
+ ITERATE ( vector<TGi>, it, gi_list_limit ) {
+ int_gi_list.push_back(GI_TO( int, *it));
+ }
+ x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_GiList), int_gi_list);
+ #else
+ x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_GiList), gi_list_limit);
+ #endif
}
// Set the negative GI list
const CSearchDatabase::TGiList& neg_gi_list = db->GetNegativeGiListLimitation();
if (!neg_gi_list.empty())
{
- x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_NegativeGiList), neg_gi_list);
+ #ifdef NCBI_STRICT_GI
+ vector<int> int_gi_list;
+ ITERATE ( vector<TGi>, it, neg_gi_list) {
+ int_gi_list.push_back(GI_TO( int, *it));
+ }
+ x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_NegativeGiList), int_gi_list);
+ #else
+ x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_NegativeGiList), neg_gi_list);
+ #endif
}
// Set the filtering algorithms
@@ -630,6 +646,24 @@ void CExportStrategy::x_AddParameterToProgramOptions(objects::CBlast4Field & fie
}
void CExportStrategy::x_AddParameterToProgramOptions(objects::CBlast4Field & field,
+ const vector<Int8> & int_list)
+{
+ list<Int8> tmp_list;
+ copy(int_list.begin(), int_list.end(), back_inserter(tmp_list));
+
+ CRef<CBlast4_parameter> p(new CBlast4_parameter);
+ p->SetName(field.GetName());
+
+ CRef<CBlast4_value> v(new CBlast4_value);
+ v->SetBig_integer_list() = tmp_list;
+ p->SetValue(*v);
+ _ASSERT(field.Match(*p));
+
+ m_QueueSearchRequest->SetProgram_options().Set().push_back(p);
+}
+
+
+void CExportStrategy::x_AddParameterToProgramOptions(objects::CBlast4Field & field,
const string & str)
{
CRef<CBlast4_parameter> p(new CBlast4_parameter);
diff --git a/c++/src/algo/blast/api/seedtop.cpp b/c++/src/algo/blast/api/seedtop.cpp
index e84d3ab..3e16f4b 100644
--- a/c++/src/algo/blast/api/seedtop.cpp
+++ b/c++/src/algo/blast/api/seedtop.cpp
@@ -1,4 +1,4 @@
-/* $Id: seedtop.cpp 363725 2012-05-18 14:59:35Z maning $
+/* $Id: seedtop.cpp 442850 2014-08-07 17:34:09Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,7 +70,7 @@ void CSeedTop::x_ParsePattern()
if (ch=='[' || ch=='{' || ch=='X' || (*unit).length()==1 || (*unit)[1]=='(') {
m_Units.push_back(SPatternUnit(*unit));
} else {
- for (int i=0; i<(*unit).length(); ++i) {
+ for (SIZE_TYPE i=0; i<(*unit).length(); ++i) {
m_Units.push_back(SPatternUnit(string(*unit, i, 1)));
}
}
diff --git a/c++/src/algo/blast/api/seqsrc_multiseq.cpp b/c++/src/algo/blast/api/seqsrc_multiseq.cpp
index ee56e1d..890f352 100644
--- a/c++/src/algo/blast/api/seqsrc_multiseq.cpp
+++ b/c++/src/algo/blast/api/seqsrc_multiseq.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqsrc_multiseq.cpp 351200 2012-01-26 19:01:24Z maning $
+/* $Id: seqsrc_multiseq.cpp 481976 2015-10-19 16:59:52Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,13 +54,14 @@ class CMultiSeqInfo : public CObject
public:
/// Constructor from a vector of sequence location/scope pairs and a
/// BLAST program type.
- CMultiSeqInfo(TSeqLocVector& seq_vector, EBlastProgramType program);
+ CMultiSeqInfo(TSeqLocVector& seq_vector, EBlastProgramType program, bool dbscan_mode);
~CMultiSeqInfo();
/// Setter and getter functions for the private fields
Uint4 GetMaxLength();
void SetMaxLength(Uint4 val);
Uint4 GetAvgLength();
void SetAvgLength(Uint4 val);
+ Int8 GetTotLength();
bool GetIsProtein();
Uint4 GetNumSeqs();
BLAST_SequenceBlk* GetSeqBlk(int index);
@@ -70,6 +71,8 @@ private:
vector<BLAST_SequenceBlk*> m_ivSeqBlkVec; ///< Vector of sequence blocks
unsigned int m_iMaxLength; ///< Length of the longest sequence in this set
unsigned int m_iAvgLength; ///< Average length of sequences in this set
+ Int8 m_iTotalLength; ///< Total length of sequences in this set
+ bool m_DbScanMode; ///< Database scanning mode (not pairwise)
};
/// Returns maximal length of a set of sequences
@@ -96,6 +99,12 @@ inline void CMultiSeqInfo::SetAvgLength(Uint4 length)
m_iAvgLength = length;
}
+/// Returns total length
+inline Int8 CMultiSeqInfo::GetTotLength()
+{
+ return m_iTotalLength;
+}
+
/// Answers whether sequences in this object are protein or nucleotide
inline bool CMultiSeqInfo::GetIsProtein()
{
@@ -120,9 +129,12 @@ inline BLAST_SequenceBlk* CMultiSeqInfo::GetSeqBlk(int index)
/// Constructor
CMultiSeqInfo::CMultiSeqInfo(TSeqLocVector& seq_vector,
- EBlastProgramType program)
+ EBlastProgramType program,
+ bool dbscan_mode)
{
m_ibIsProt = Blast_SubjectIsProtein(program) ? true : false;
+ m_DbScanMode = dbscan_mode;
+ m_iTotalLength=0;
// Fix subject location for tblast[nx].
if (Blast_SubjectIsTranslated(program))
@@ -160,6 +172,13 @@ CMultiSeqInfo::CMultiSeqInfo(TSeqLocVector& seq_vector,
else
SetupSubjects(seq_vector, program, &m_ivSeqBlkVec, &m_iMaxLength);
+ if(dbscan_mode)
+ {
+ ITERATE(vector<BLAST_SequenceBlk*>, iter, m_ivSeqBlkVec)
+ {
+ m_iTotalLength += (Int8) (*iter)->length;
+ }
+ }
// Do not set right away
m_iAvgLength = 0;
}
@@ -214,6 +233,9 @@ s_MultiSeqGetMinLength(void* multiseq_handle, void*)
for (index=0; index<(*seq_info)->GetNumSeqs(); ++index)
retval = MIN(retval, (*seq_info)->GetSeqBlk(index)->length);
+ if(retval < BLAST_SEQSRC_MINLENGTH)
+ retval = BLAST_SEQSRC_MINLENGTH;
+
return retval;
}
@@ -265,11 +287,14 @@ s_MultiSeqGetNumSeqsStats(void* /*multiseq_handle*/, void*)
return 0;
}
-/// Returns 0 as total length, indicating that this is NOT a database!
+/// Returns total length in db scan mode.
+/// Returns 0 as total length, indicating that this is not a database search.
static Int8
-s_MultiSeqGetTotLen(void* /*multiseq_handle*/, void*)
+s_MultiSeqGetTotLen(void* multiseq_handle, void*)
{
- return 0;
+ CRef<CMultiSeqInfo>* seq_info =
+ static_cast<CRef<CMultiSeqInfo>*>(multiseq_handle);
+ return (*seq_info)->GetTotLength();
}
/// Returns 0 as this implementation does not use alias files.
@@ -437,9 +462,10 @@ s_MultiSeqIteratorNext(void* multiseq_handle, BlastSeqSrcIterator* itr)
struct SMultiSeqSrcNewArgs {
TSeqLocVector seq_vector; ///< Vector of sequences
EBlastProgramType program; ///< BLAST program
+ bool dbscan_mode; ///< Database mode (not pairwise)
/// Constructor
- SMultiSeqSrcNewArgs(TSeqLocVector sv, EBlastProgramType p)
- : seq_vector(sv), program(p) {}
+ SMultiSeqSrcNewArgs(TSeqLocVector sv, EBlastProgramType p, bool db)
+ : seq_vector(sv), program(p), dbscan_mode(db) {}
};
/// Multi sequence source destructor: frees its internal data structure
@@ -489,7 +515,8 @@ s_MultiSeqSrcNew(BlastSeqSrc* retval, void* args)
CRef<CMultiSeqInfo>* seq_info = new CRef<CMultiSeqInfo>(0);
try {
seq_info->Reset(new CMultiSeqInfo(seqsrc_args->seq_vector,
- seqsrc_args->program));
+ seqsrc_args->program,
+ seqsrc_args->dbscan_mode));
} catch (const ncbi::CException& e) {
_BlastSeqSrcImpl_SetInitErrorStr(retval, strdup(e.ReportAll().c_str()));
} catch (const std::exception& e) {
@@ -526,14 +553,15 @@ s_MultiSeqSrcNew(BlastSeqSrc* retval, void* args)
BlastSeqSrc*
MultiSeqBlastSeqSrcInit(TSeqLocVector& seq_vector,
- EBlastProgramType program)
+ EBlastProgramType program,
+ bool dbscan_mode)
{
BlastSeqSrc* seq_src = NULL;
BlastSeqSrcNewInfo bssn_info;
auto_ptr<SMultiSeqSrcNewArgs> args
(new SMultiSeqSrcNewArgs(const_cast<TSeqLocVector&>(seq_vector),
- program));
+ program, dbscan_mode));
bssn_info.constructor = &s_MultiSeqSrcNew;
bssn_info.ctor_argument = (void*) args.get();
diff --git a/c++/src/algo/blast/api/seqsrc_seqdb.cpp b/c++/src/algo/blast/api/seqsrc_seqdb.cpp
index 46f5971..f94112c 100644
--- a/c++/src/algo/blast/api/seqsrc_seqdb.cpp
+++ b/c++/src/algo/blast/api/seqsrc_seqdb.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqsrc_seqdb.cpp 426803 2014-02-13 14:19:14Z fongah2 $
+/* $Id: seqsrc_seqdb.cpp 482051 2015-10-20 14:16:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -117,7 +117,7 @@ s_SeqDbGetGiList(void* seqdb_handle, void* args)
if (!datap || !oid)
return NULL;
- vector<int> gis;
+ vector<TGi> gis;
datap->GetGis(*oid, gis);
Blast_GiList* retval = Blast_GiListNewEx(gis.size());
@@ -459,7 +459,7 @@ s_SeqDbGetNextChunk(void* seqdb_handle, BlastSeqSrcIterator* itr)
Uint4 index;
if (itr->chunk_sz < new_sz) {
sfree(itr->oid_list);
- itr->oid_list = (int *) malloc (new_sz * sizeof(unsigned int));
+ itr->oid_list = (int *) malloc (new_sz * sizeof(int));
}
itr->chunk_sz = new_sz;
for (index = 0; index < new_sz; ++index)
diff --git a/c++/src/algo/blast/api/setup_factory.cpp b/c++/src/algo/blast/api/setup_factory.cpp
index 4ce0255..46cc54a 100644
--- a/c++/src/algo/blast/api/setup_factory.cpp
+++ b/c++/src/algo/blast/api/setup_factory.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: setup_factory.cpp 459042 2015-02-12 17:31:13Z ivanov $";
+ "$Id: setup_factory.cpp 458896 2015-02-11 15:05:08Z boratyng $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
diff --git a/c++/src/algo/blast/api/split_query_aux_priv.cpp b/c++/src/algo/blast/api/split_query_aux_priv.cpp
index b340ba0..01e1841 100644
--- a/c++/src/algo/blast/api/split_query_aux_priv.cpp
+++ b/c++/src/algo/blast/api/split_query_aux_priv.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: split_query_aux_priv.cpp 458753 2015-02-09 19:43:06Z ivanov $";
+ "$Id: split_query_aux_priv.cpp 458701 2015-02-09 15:05:54Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -59,7 +59,7 @@ SplitQuery_GetOverlapChunkSize(EBlastProgramType program)
char* overlap_sz_str = getenv("OVERLAP_CHUNK_SIZE");
if (overlap_sz_str && !NStr::IsBlank(overlap_sz_str)) {
retval = NStr::StringToInt(overlap_sz_str);
- _TRACE("DEBUG: Using overlap chunk size " << retval);
+ _TRACE("Using overlap chunk size from environment " << retval);
return retval;
}
diff --git a/c++/src/algo/blast/api/split_query_cxx.cpp b/c++/src/algo/blast/api/split_query_cxx.cpp
index 78277a7..55afcb8 100644
--- a/c++/src/algo/blast/api/split_query_cxx.cpp
+++ b/c++/src/algo/blast/api/split_query_cxx.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: split_query_cxx.cpp 388133 2013-02-05 19:47:18Z maning $";
+ "$Id: split_query_cxx.cpp 442852 2014-08-07 17:41:12Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
@@ -85,6 +85,7 @@ ostream& operator<<(ostream& out, const CQuerySplitter& rhs)
_ASSERT(query_id);
for (size_t chunk_index = 0; chunk_index < kNumChunks; chunk_index++) {
+ ASSERT(rhs.m_SplitQueriesInChunk.size());
CRef<CBlastQueryVector> queries_in_chunk =
rhs.m_SplitQueriesInChunk[chunk_index];
diff --git a/c++/src/algo/blast/api/traceback_stage.cpp b/c++/src/algo/blast/api/traceback_stage.cpp
index 68e5155..83f0dc5 100644
--- a/c++/src/algo/blast/api/traceback_stage.cpp
+++ b/c++/src/algo/blast/api/traceback_stage.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: traceback_stage.cpp 419225 2013-11-22 17:08:29Z camacho $";
+ "$Id: traceback_stage.cpp 459518 2015-02-19 13:53:19Z madden $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -296,6 +296,72 @@ CBlastTracebackSearch::Run()
m_ResultType);
}
+BlastHSPResults*
+CBlastTracebackSearch::RunSimple()
+{
+ _ASSERT(m_OptsMemento);
+ SPHIPatternSearchBlk* phi_lookup_table(0);
+
+ // For PHI BLAST we need to pass the pattern search items structure to the
+ // traceback code
+ bool is_phi = !! Blast_ProgramIsPhiBlast(m_OptsMemento->m_ProgramType);
+
+ if (is_phi) {
+ _ASSERT(m_InternalData->m_LookupTable);
+ _ASSERT(m_DBscanInfo && m_DBscanInfo->m_NumPatOccurInDB !=
+ m_DBscanInfo->kNoPhiBlastPattern);
+ phi_lookup_table = (SPHIPatternSearchBlk*)
+ m_InternalData->m_LookupTable->GetPointer()->lut;
+ phi_lookup_table->num_patterns_db = m_DBscanInfo->m_NumPatOccurInDB;
+ }
+ else
+ {
+ m_InternalData->m_LookupTable.Reset(NULL);
+ }
+
+ // When dealing with PSI-BLAST iterations, we need to keep a larger
+ // alignment for the PSSM engine as to replicate blastpgp's behavior
+ if (m_OptsMemento->m_ProgramType == eBlastTypePsiBlast ) {
+ SBlastHitsParameters* bhp = NULL;
+ SBlastHitsParametersNew(m_OptsMemento->m_HitSaveOpts,
+ m_OptsMemento->m_ExtnOpts,
+ m_OptsMemento->m_ScoringOpts,
+ &bhp);
+ m_OptsMemento->m_HitSaveOpts->hitlist_size = bhp->prelim_hitlist_size;
+ SBlastHitsParametersFree(bhp);
+ }
+
+ auto_ptr<CAutoEnvironmentVariable> omp_env;
+ if (m_NumThreads > kMinNumThreads) {
+ omp_env.reset(new CAutoEnvironmentVariable("OMP_WAIT_POLICY", "passive"));
+ }
+
+ BlastHSPResults * hsp_results(0);
+ int status =
+ Blast_RunTracebackSearchWithInterrupt(m_OptsMemento->m_ProgramType,
+ m_InternalData->m_Queries,
+ m_InternalData->m_QueryInfo,
+ m_InternalData->m_SeqSrc->GetPointer(),
+ m_OptsMemento->m_ScoringOpts,
+ m_OptsMemento->m_ExtnOpts,
+ m_OptsMemento->m_HitSaveOpts,
+ m_OptsMemento->m_EffLenOpts,
+ m_OptsMemento->m_DbOpts,
+ m_OptsMemento->m_PSIBlastOpts,
+ m_InternalData->m_ScoreBlk->GetPointer(),
+ m_InternalData->m_HspStream->GetPointer(),
+ m_InternalData->m_RpsData ?
+ (*m_InternalData->m_RpsData)() : 0,
+ phi_lookup_table,
+ & hsp_results,
+ m_InternalData->m_FnInterrupt,
+ m_InternalData->m_ProgressMonitor->Get(), m_NumThreads);
+ if (status) {
+ NCBI_THROW(CBlastException, eCoreBlastError, "Traceback failed");
+ }
+ return hsp_results;
+}
+
END_SCOPE(blast)
END_NCBI_SCOPE
diff --git a/c++/src/algo/blast/api/uniform_search.cpp b/c++/src/algo/blast/api/uniform_search.cpp
index b46dfb2..71e863a 100644
--- a/c++/src/algo/blast/api/uniform_search.cpp
+++ b/c++/src/algo/blast/api/uniform_search.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: uniform_search.cpp 409921 2013-08-12 17:46:49Z maning $";
+ "$Id: uniform_search.cpp 482051 2015-10-20 14:16:32Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -255,7 +255,7 @@ CSearchDatabase::x_InitializeDb() const
m_SeqDb.Reset(new CSeqDB(m_DbName, seq_type, m_GiList));
} else if (! m_NegativeGiList.Empty() && ! m_NegativeGiList->Empty()) {
- vector<int> gis;
+ vector<TGi> gis;
m_NegativeGiList->GetGiList(gis);
CSeqDBIdSet idset(gis, CSeqDBIdSet::eGi, false);
m_SeqDb.Reset(new CSeqDB(m_DbName, seq_type, idset));
diff --git a/c++/src/algo/blast/api/winmask_filter.cpp b/c++/src/algo/blast/api/winmask_filter.cpp
index 6d072bb..d63303e 100644
--- a/c++/src/algo/blast/api/winmask_filter.cpp
+++ b/c++/src/algo/blast/api/winmask_filter.cpp
@@ -1,4 +1,4 @@
-/* $Id: winmask_filter.cpp 394976 2013-04-08 19:18:29Z camacho $
+/* $Id: winmask_filter.cpp 463952 2015-04-02 16:08:53Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,7 +36,7 @@
/// Blast wrappers for WindowMasker filtering.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: winmask_filter.cpp 394976 2013-04-08 19:18:29Z camacho $";
+static char const rcsid[] = "$Id: winmask_filter.cpp 463952 2015-04-02 16:08:53Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -75,6 +75,7 @@ BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(blast)
+static string s_WINDOW_MASKER_STAT_FILE_NAME("wmasker.obinary");
static string s_WINDOW_MASKER_PATH(kEmptyStr);
DEFINE_STATIC_MUTEX(InitMutex);
@@ -407,19 +408,8 @@ string WindowMaskerTaxidToDb(const string& window_masker_path, int taxid)
string path = window_masker_path;
path += CFile::GetPathSeparator() + NStr::IntToString(taxid)
+ CFile::GetPathSeparator();
-
- const string binpath = path + "wmasker.obinary";
- const string ascpath = path + "wmasker.oascii";
-
- string retval;
- // Try the binary file first, as this is faster to process than the ASCII
- // file
- if (CFile(binpath).Exists()) {
- retval = binpath;
- } else if (CFile(ascpath).Exists()) {
- retval = ascpath;
- }
- return retval;
+ const string binpath = path + s_WINDOW_MASKER_STAT_FILE_NAME;
+ return (CFile(binpath).Exists() ? binpath : kEmptyStr);
}
/* Unit test is in bl2seq_unit_test.cpp */
@@ -450,7 +440,7 @@ static void s_OldGetTaxIdWithWindowMaskerSupport(set<int>& supported_taxids)
const string wmpath = s_FindPathToWM();
oss << wmpath << CFile::GetPathSeparator() << "*"
<< CFile::GetPathSeparator() << "*.*"
- << CFile::GetPathSeparator() << "wmasker.o*";
+ << CFile::GetPathSeparator() << s_WINDOW_MASKER_STAT_FILE_NAME;
const string path = CNcbiOstrstreamToString(oss);
list<string> builds;
@@ -472,7 +462,7 @@ void GetTaxIdWithWindowMaskerSupport(set<int>& supported_taxids)
CNcbiOstrstream oss;
const string wmpath = s_FindPathToWM();
oss << wmpath << CFile::GetPathSeparator() << "*"
- << CFile::GetPathSeparator() << "wmasker.o*";
+ << CFile::GetPathSeparator() << s_WINDOW_MASKER_STAT_FILE_NAME;
const string path = CNcbiOstrstreamToString(oss);
list<string> builds;
diff --git a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
index a7f7bef..96ea05b 100644
--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastinput.lib 441754 2014-07-28 17:06:23Z ivanov $
+# $Id: Makefile.blastinput.lib 441606 2014-07-25 14:36:47Z fongah2 $
SRC_CXX = \
blast_input \
diff --git a/c++/src/algo/blast/blastinput/blast_args.cpp b/c++/src/algo/blast/blastinput/blast_args.cpp
index fd40674..2c259dc 100644
--- a/c++/src/algo/blast/blastinput/blast_args.cpp
+++ b/c++/src/algo/blast/blastinput/blast_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_args.cpp 463323 2015-03-26 17:29:40Z ivanov $
+/* $Id: blast_args.cpp 485060 2015-11-18 16:07:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,7 +37,7 @@ Author: Jason Papadopoulos
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blast_args.cpp 463323 2015-03-26 17:29:40Z ivanov $";
+static char const rcsid[] = "$Id: blast_args.cpp 485060 2015-11-18 16:07:34Z ivanov $";
#endif
#include <ncbi_pch.hpp>
@@ -52,6 +52,7 @@ static char const rcsid[] = "$Id: blast_args.cpp 463323 2015-03-26 17:29:40Z iva
#include <util/format_guess.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/blastinput/blast_input.hpp> // for CInputException
+#include <algo/winmask/seq_masker_istat_factory.hpp> // for CSeqMaskerIstatFactory::DiscoverStatType
#include <connect/ncbi_connutil.h>
#include <algo/blast/api/msa_pssm_input.hpp> // for CPsiBlastInputClustalW
@@ -411,10 +412,16 @@ CFilteringArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
if (args.Exist(kArgWindowMaskerDatabase) &&
args[kArgWindowMaskerDatabase]) {
+ const string& stat_file = args[kArgWindowMaskerDatabase].AsString();
+ const CSeqMaskerIstatFactory::EStatType type =
+ CSeqMaskerIstatFactory::DiscoverStatType(stat_file);
+ if (type != CSeqMaskerIstatFactory::eOBinary &&
+ type != CSeqMaskerIstatFactory::eBinary) {
+ string msg("Only optimized binary windowmasker stat files are supported");
+ NCBI_THROW(CInputException, eInvalidInput, msg);
+ }
- opt.SetWindowMaskerDatabase
- (args[kArgWindowMaskerDatabase].AsString().c_str());
-
+ opt.SetWindowMaskerDatabase(stat_file.c_str());
filter_dbs++;
}
@@ -1120,6 +1127,12 @@ CPsiBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
"File name to store ASCII version of PSSM",
CArgDescriptions::eOutputFile);
+ arg_desc.AddFlag(kArgSaveLastPssm, "Save PSSM after the last database "
+ "search");
+ arg_desc.AddFlag(kArgSaveAllPssms, "Save PSSM after each iteration "
+ "(file name is given in -save_pssm or "
+ "-save_ascii_pssm options)");
+
if (!m_IsDeltaBlast) {
vector<string> msa_exclusions;
msa_exclusions.push_back(kArgPSIInputChkPntFile);
@@ -1227,17 +1240,42 @@ CPsiBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
if(m_NumIterations == 1)
m_NumIterations = args[kArgPSINumIterations].AsInteger();
}
+
+ if (args.Exist(kArgSaveLastPssm) && args[kArgSaveLastPssm] &&
+ (!args.Exist(kArgPSIOutputChkPntFile) ||
+ !args[kArgPSIOutputChkPntFile]) &&
+ (!args.Exist(kArgAsciiPssmOutputFile) ||
+ !args[kArgAsciiPssmOutputFile])) {
+
+ NCBI_THROW(CInputException, eInvalidInput, kArgSaveLastPssm +
+ " option requires " + kArgPSIOutputChkPntFile + " or " +
+ kArgAsciiPssmOutputFile);
+ }
+
+ if (args.Exist(kArgSaveAllPssms) && args[kArgSaveAllPssms] &&
+ (!args.Exist(kArgPSIOutputChkPntFile) ||
+ !args[kArgPSIOutputChkPntFile]) &&
+ (!args.Exist(kArgAsciiPssmOutputFile) ||
+ !args[kArgAsciiPssmOutputFile])) {
+
+ NCBI_THROW(CInputException, eInvalidInput, kArgSaveAllPssms +
+ " option requires " + kArgPSIOutputChkPntFile + " or " +
+ kArgAsciiPssmOutputFile);
+ }
+
+ const bool kSaveAllPssms
+ = args.Exist(kArgSaveAllPssms) && args[kArgSaveAllPssms];
if (args.Exist(kArgPSIOutputChkPntFile) &&
args[kArgPSIOutputChkPntFile]) {
m_CheckPointOutput.Reset
(new CAutoOutputFileReset
- (args[kArgPSIOutputChkPntFile].AsString()));
+ (args[kArgPSIOutputChkPntFile].AsString(), kSaveAllPssms));
}
const bool kSaveAsciiPssm = args[kArgAsciiPssmOutputFile];
if (kSaveAsciiPssm) {
m_AsciiMatrixOutput.Reset
(new CAutoOutputFileReset
- (args[kArgAsciiPssmOutputFile].AsString()));
+ (args[kArgAsciiPssmOutputFile].AsString(), kSaveAllPssms));
}
if (args.Exist(kArgMSAInputFile) && args[kArgMSAInputFile]) {
CNcbiIstream& in = args[kArgMSAInputFile].AsInputFile();
@@ -1252,6 +1290,10 @@ CPsiBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
if (!m_IsDeltaBlast) {
opt.SetIgnoreMsaMaster(args[kArgIgnoreMsaMaster]);
}
+
+ if (args.Exist(kArgSaveLastPssm) && args[kArgSaveLastPssm]) {
+ m_SaveLastPssm = true;
+ }
}
if (args.Exist(kArgPSIInputChkPntFile) && args[kArgPSIInputChkPntFile]) {
@@ -1360,7 +1402,7 @@ void
CIgBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
arg_desc.SetCurrentGroup("Ig-BLAST options");
- const static string suffix = "VDJ";
+ const static char suffix[] = "VDJ";
const static int df_num_align[3] = {3,3,3};
int num_genes = (m_IsProtein) ? 1 : 3;
@@ -1548,7 +1590,7 @@ CIgBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
opts_hndl.Reset(CBlastOptionsFactory::Create(eBlastn));
}
- const static string suffix = "VDJ";
+ const static char suffix[] = "VDJ";
int num_genes = (m_IsProtein) ? 1: 3;
for (int gene=0; gene< num_genes; ++gene) {
string arg_sub = kArgGLSubject;
@@ -1896,27 +1938,46 @@ CFormattingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
string kOutputFormatDescription = string(
"alignment view options:\n"
- " 0 = pairwise,\n"
- " 1 = query-anchored showing identities,\n"
- " 2 = query-anchored no identities,\n"
- " 3 = flat query-anchored, show identities,\n"
- " 4 = flat query-anchored, no identities,\n"
- " 5 = XML Blast output,\n"
- " 6 = tabular,\n"
- " 7 = tabular with comment lines,\n"
- " 8 = Text ASN.1,\n"
- " 9 = Binary ASN.1,\n"
+ " 0 = Pairwise,\n"
+ " 1 = Query-anchored showing identities,\n"
+ " 2 = Query-anchored no identities,\n"
+ " 3 = Flat query-anchored showing identities,\n"
+ " 4 = Flat query-anchored no identities,\n"
+ " 5 = BLAST XML,\n"
+ " 6 = Tabular,\n"
+ " 7 = Tabular with comment lines,\n"
+ " 8 = Seqalign (Text ASN.1),\n"
+ " 9 = Seqalign (Binary ASN.1),\n"
" 10 = Comma-separated values,\n"
- " 11 = BLAST archive format (ASN.1),\n"
- " 12 = JSON Seqalign output,\n"
- " 13 = JSON Blast output,\n"
- " 14 = XML2 Blast output\n\n"
- /* " 15 = SAM format \n\n" */
- "Options 6, 7, and 10 can be additionally configured to produce\n"
- "a custom format specified by space delimited format specifiers.\n"
- "The supported format specifiers are:\n") +
- DescribeTabularOutputFormatSpecifiers() +
- string("\n");
+ " 11 = BLAST archive (ASN.1),\n"
+ " 12 = Seqalign (JSON),\n"
+ " 13 = Multiple-file BLAST JSON,\n"
+ " 14 = Multiple-file BLAST XML2,\n"
+ " 15 = Single-file BLAST JSON,\n"
+ " 16 = Single-file BLAST XML2");
+
+ if(m_FormatFlags & eIsSAM) {
+ kOutputFormatDescription +=
+ ",\n 17 = Sequence Alignment/Map (SAM)\n\n"
+ "Options 6, 7, 10 and 17 "
+ "can be additionally configured to produce\n"
+ "a custom format specified by space delimited format specifiers.\n"
+ "The supported format specifiers for options 6, 7 and 10 are:\n";
+ }
+ else {
+ kOutputFormatDescription +=
+ "\n\nOptions 6, 7 and 10 "
+ "can be additionally configured to produce\n"
+ "a custom format specified by space delimited format specifiers.\n"
+ "The supported format specifiers are:\n";
+ }
+ kOutputFormatDescription += DescribeTabularOutputFormatSpecifiers() + string("\n");
+
+ if(m_FormatFlags & eIsSAM) {
+ kOutputFormatDescription +=
+ "The supported format specifier for option 17 is:\n" +
+ DescribeSAMOutputFormatSpecifiers();
+ }
int dft_outfmt = kDfltArgOutputFormat;
@@ -1924,13 +1985,13 @@ CFormattingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
if (m_IsIgBlast) {
kOutputFormatDescription = string(
"alignment view options:\n"
- " 3 = flat query-anchored, show identities,\n"
- " 4 = flat query-anchored, no identities,\n"
- " 7 = tabular with comment lines\n\n"
+ " 3 = Flat query-anchored, show identities,\n"
+ " 4 = Flat query-anchored, no identities,\n"
+ " 7 = Tabular with comment lines\n\n"
"Options 7 can be additionally configured to produce\n"
"a custom format specified by space delimited format specifiers.\n"
"The supported format specifiers are:\n") +
- DescribeTabularOutputFormatSpecifiers(true) +
+ DescribeTabularOutputFormatSpecifiers(true) +
string("\n");
dft_outfmt = 3;
}
@@ -2036,7 +2097,8 @@ CFormattingArgs::ParseFormattingString(const CArgs& args,
fmt_type = static_cast<EOutputFormat>(val);
if ( !(fmt_type == eTabular ||
fmt_type == eTabularWithComments ||
- fmt_type == eCommaSeparatedValues) ) {
+ fmt_type == eCommaSeparatedValues ||
+ fmt_type == eSAM) ) {
custom_fmt_spec.clear();
}
}
@@ -2048,6 +2110,10 @@ CFormattingArgs::ExtractAlgorithmOptions(const CArgs& args,
CBlastOptions& opt)
{
ParseFormattingString(args, m_OutputFormat, m_CustomOutputFormatSpec);
+ if((m_OutputFormat == eSAM) && !(m_FormatFlags & eIsSAM) ){
+ NCBI_THROW(CInputException, eInvalidInput,
+ "SAM format is only applicable to blastn" );
+ }
m_ShowGis = static_cast<bool>(args[kArgShowGIs]);
if(m_IsIgBlast){
m_Html = false;
@@ -2333,7 +2399,7 @@ CMbIndexArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
CArgDescriptions::eBoolean, NStr::BoolToString(kDfltArgUseIndex));
arg_desc.AddOptionalKey(
kArgIndexName, "string",
- "MegaBLAST database index name",
+ "MegaBLAST database index name (deprecated; use only for old style indices)",
CArgDescriptions::eString );
arg_desc.SetCurrentGroup( "" );
}
diff --git a/c++/src/algo/blast/blastinput/blast_fasta_input.cpp b/c++/src/algo/blast/blastinput/blast_fasta_input.cpp
index 342b5c0..e038f30 100644
--- a/c++/src/algo/blast/blastinput/blast_fasta_input.cpp
+++ b/c++/src/algo/blast/blastinput/blast_fasta_input.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_fasta_input.cpp 443518 2014-08-15 01:32:43Z mcelhany $
+/* $Id: blast_fasta_input.cpp 477844 2015-09-02 13:12:06Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_fasta_input.cpp 443518 2014-08-15 01:32:43Z mcelhany $";
+ "$Id: blast_fasta_input.cpp 477844 2015-09-02 13:12:06Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -82,13 +82,13 @@ public:
/// @param len length of the gap? @sa CFastaReader
protected:
virtual void x_CloseGap(TSeqPos /*len*/, bool /*atStartOfLine*/,
- IMessageListener * /*pMessageListener*/)
+ ILineErrorListener * /*pMessageListener*/)
{ }
/// Override logic for assigning the molecule type
/// @note fForceType is ignored if the sequence length is less than the
/// value configured in the constructor
- virtual void AssignMolType(IMessageListener * pMessageListener) {
+ virtual void AssignMolType(ILineErrorListener * pMessageListener) {
if (GetCurrentPos(eRawPos) < m_SeqLenThreshold) {
_ASSERT( (TestFlag(fAssumeNuc) ^ TestFlag(fAssumeProt) ) );
SetCurrentSeq().SetInst().SetMol(TestFlag(fAssumeNuc)
@@ -131,7 +131,7 @@ public:
m_RetrieveSeqData(retrieve_seq_data) {}
/// Overloaded method to attempt to read non-FASTA input types
- virtual CRef<CSeq_entry> ReadOneSeq(IMessageListener * pMessageListener) {
+ virtual CRef<CSeq_entry> ReadOneSeq(ILineErrorListener * pMessageListener) {
const string line = NStr::TruncateSpaces_Unsafe(*++GetLineReader());
if ( !line.empty() && isalnum(line.data()[0]&0xff) ) {
diff --git a/c++/src/algo/blast/blastinput/blast_input.cpp b/c++/src/algo/blast/blastinput/blast_input.cpp
index af1d9fe..2daf968 100644
--- a/c++/src/algo/blast/blastinput/blast_input.cpp
+++ b/c++/src/algo/blast/blastinput/blast_input.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_input.cpp 458748 2015-02-09 19:40:32Z ivanov $
+/* $Id: blast_input.cpp 458462 2015-02-05 14:10:55Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_input.cpp 458748 2015-02-09 19:40:32Z ivanov $";
+ "$Id: blast_input.cpp 458462 2015-02-05 14:10:55Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
diff --git a/c++/src/algo/blast/blastinput/blast_input_aux.cpp b/c++/src/algo/blast/blastinput/blast_input_aux.cpp
index d6f0fdf..93bff85 100644
--- a/c++/src/algo/blast/blastinput/blast_input_aux.cpp
+++ b/c++/src/algo/blast/blastinput/blast_input_aux.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_input_aux.cpp 437339 2014-06-05 13:54:41Z camacho $
+/* $Id: blast_input_aux.cpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_input_aux.cpp 437339 2014-06-05 13:54:41Z camacho $";
+ "$Id: blast_input_aux.cpp 483791 2015-11-04 11:12:47Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -54,12 +54,20 @@ BEGIN_SCOPE(blast)
CNcbiOstream*
CAutoOutputFileReset::GetStream()
{
- CFile file_deleter(m_FileName);
- if (file_deleter.Exists()) {
- _TRACE("Deleting " << m_FileName);
- file_deleter.Remove();
+ string filename = m_FileName;
+ if (!m_Version) {
+ CFile file_deleter(m_FileName);
+ if (file_deleter.Exists()) {
+ _TRACE("Deleting " << m_FileName);
+ file_deleter.Remove();
+ }
+ }
+ else {
+ filename = m_FileName + "." + NStr::IntToString(m_Version);
+ m_Version++;
}
- m_FileStream.reset(new ofstream(m_FileName.c_str()));
+
+ m_FileStream.reset(new ofstream(filename.c_str()));
return m_FileStream.get();
}
diff --git a/c++/src/algo/blast/blastinput/blast_scope_src.cpp b/c++/src/algo/blast/blastinput/blast_scope_src.cpp
index da54034..563e515 100644
--- a/c++/src/algo/blast/blastinput/blast_scope_src.cpp
+++ b/c++/src/algo/blast/blastinput/blast_scope_src.cpp
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_scope_src.cpp 446083 2014-09-11 11:51:47Z ivanov $";
+ "$Id: blast_scope_src.cpp 445894 2014-09-09 15:49:42Z boratyng $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
diff --git a/c++/src/algo/blast/blastinput/blastn_args.cpp b/c++/src/algo/blast/blastinput/blastn_args.cpp
index 2c52eff..ebe050d 100644
--- a/c++/src/algo/blast/blastinput/blastn_args.cpp
+++ b/c++/src/algo/blast/blastinput/blastn_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastn_args.cpp 431056 2014-04-01 15:13:51Z camacho $
+/* $Id: blastn_args.cpp 474652 2015-07-30 16:37:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[]
- = "$Id: blastn_args.cpp 431056 2014-04-01 15:13:51Z camacho $";
+ = "$Id: blastn_args.cpp 474652 2015-07-30 16:37:40Z ivanov $";
#endif
#include <ncbi_pch.hpp>
@@ -50,14 +50,14 @@ USING_SCOPE(objects);
CBlastnAppArgs::CBlastnAppArgs()
{
CRef<IBlastCmdLineArgs> arg;
- static const string kProgram("blastn");
+ static const char kProgram[] = "blastn";
arg.Reset(new CProgramDescriptionArgs(kProgram,
"Nucleotide-Nucleotide BLAST"));
const bool kQueryIsProtein = false;
m_Args.push_back(arg);
- m_ClientId = kProgram + " " + CBlastVersion().Print();
+ m_ClientId = string(kProgram) + " " + CBlastVersion().Print();
- static const string kDefaultTask = "megablast";
+ static const char kDefaultTask[] = "megablast";
SetTask(kDefaultTask);
set<string> tasks
(CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eNuclNucl));
@@ -106,7 +106,7 @@ CBlastnAppArgs::CBlastnAppArgs()
arg.Reset(m_QueryOptsArgs);
m_Args.push_back(arg);
- m_FormattingArgs.Reset(new CFormattingArgs);
+ m_FormattingArgs.Reset(new CFormattingArgs(false, CFormattingArgs::eIsSAM));
arg.Reset(m_FormattingArgs);
m_Args.push_back(arg);
diff --git a/c++/src/algo/blast/blastinput/blastp_args.cpp b/c++/src/algo/blast/blastinput/blastp_args.cpp
index 4e7223d..2d1ee42 100644
--- a/c++/src/algo/blast/blastinput/blastp_args.cpp
+++ b/c++/src/algo/blast/blastinput/blastp_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastp_args.cpp 431056 2014-04-01 15:13:51Z camacho $
+/* $Id: blastp_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blastp_args.cpp 431056 2014-04-01 15:13:51Z camacho $";
+static char const rcsid[] = "$Id: blastp_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -56,7 +56,7 @@ CBlastpAppArgs::CBlastpAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "blastp";
+ static const char kDefaultTask[] = "blastp";
SetTask(kDefaultTask);
set<string> tasks
(CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eProtProt));
diff --git a/c++/src/algo/blast/blastinput/blastx_args.cpp b/c++/src/algo/blast/blastinput/blastx_args.cpp
index bd36a68..fc2e07e 100644
--- a/c++/src/algo/blast/blastinput/blastx_args.cpp
+++ b/c++/src/algo/blast/blastinput/blastx_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastx_args.cpp 431056 2014-04-01 15:13:51Z camacho $
+/* $Id: blastx_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[]
- = "$Id: blastx_args.cpp 431056 2014-04-01 15:13:51Z camacho $";
+ = "$Id: blastx_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -56,7 +56,7 @@ CBlastxAppArgs::CBlastxAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "blastx";
+ static const char kDefaultTask[] = "blastx";
SetTask(kDefaultTask);
set<string> tasks;
tasks.insert(kDefaultTask);
diff --git a/c++/src/algo/blast/blastinput/cmdline_flags.cpp b/c++/src/algo/blast/blastinput/cmdline_flags.cpp
index e7dd526..1774775 100644
--- a/c++/src/algo/blast/blastinput/cmdline_flags.cpp
+++ b/c++/src/algo/blast/blastinput/cmdline_flags.cpp
@@ -1,4 +1,4 @@
-/* $Id: cmdline_flags.cpp 441754 2014-07-28 17:06:23Z ivanov $
+/* $Id: cmdline_flags.cpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: cmdline_flags.cpp 441754 2014-07-28 17:06:23Z ivanov $";
+ "$Id: cmdline_flags.cpp 483791 2015-11-04 11:12:47Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -174,6 +174,8 @@ const string kArgIgnoreMsaMaster("ignore_msa_master");
const string kArgMSAMasterIndex("msa_master_idx");
const string kArgPSIPseudocount("pseudocount");
const string kArgPSIInclusionEThreshold("inclusion_ethresh");
+const string kArgSaveLastPssm("save_pssm_after_last_round");
+const string kArgSaveAllPssms("save_each_pssm");
const string kArgPHIPatternFile("phi_pattern");
const string kArgGLSubject("germline_sequence_");
diff --git a/c++/src/algo/blast/blastinput/deltablast_args.cpp b/c++/src/algo/blast/blastinput/deltablast_args.cpp
index 9ef5ef9..3b955f6 100644
--- a/c++/src/algo/blast/blastinput/deltablast_args.cpp
+++ b/c++/src/algo/blast/blastinput/deltablast_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: deltablast_args.cpp 402743 2013-06-10 17:41:20Z boratyng $
+/* $Id: deltablast_args.cpp 483793 2015-11-04 11:13:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: deltablast_args.cpp 402743 2013-06-10 17:41:20Z boratyng $";
+static char const rcsid[] = "$Id: deltablast_args.cpp 483793 2015-11-04 11:13:41Z ivanov $";
#endif
#include <ncbi_pch.hpp>
@@ -60,7 +60,7 @@ CDeltaBlastAppArgs::CDeltaBlastAppArgs()
bool const kIsCBS2and3Supported = false;
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "deltablast";
+ static const char kDefaultTask[] = "deltablast";
SetTask(kDefaultTask);
m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
@@ -144,6 +144,12 @@ CDeltaBlastAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
return CRef<CBlastOptionsHandle>(new CDeltaBlastOptionsHandle(locality));
}
+bool
+CDeltaBlastAppArgs::GetSaveLastPssm(void) const
+{
+ return m_PsiBlastArgs->GetSaveLastPssm();
+}
+
END_SCOPE(blast)
END_NCBI_SCOPE
diff --git a/c++/src/algo/blast/blastinput/psiblast_args.cpp b/c++/src/algo/blast/blastinput/psiblast_args.cpp
index 2fe9222..9008626 100644
--- a/c++/src/algo/blast/blastinput/psiblast_args.cpp
+++ b/c++/src/algo/blast/blastinput/psiblast_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: psiblast_args.cpp 389688 2013-02-20 14:23:33Z madden $
+/* $Id: psiblast_args.cpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: psiblast_args.cpp 389688 2013-02-20 14:23:33Z madden $";
+static char const rcsid[] = "$Id: psiblast_args.cpp 483791 2015-11-04 11:12:47Z ivanov $";
#endif
#include <ncbi_pch.hpp>
@@ -57,7 +57,7 @@ CPsiBlastAppArgs::CPsiBlastAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "psiblast";
+ static const char kDefaultTask[] = "psiblast";
SetTask(kDefaultTask);
m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
@@ -189,6 +189,12 @@ CPsiBlastAppArgs::GetAsciiPssmStream()
return m_PsiBlastArgs->GetAsciiMatrixOutputStream();
}
+bool
+CPsiBlastAppArgs::GetSaveLastPssm() const
+{
+ return m_PsiBlastArgs->GetSaveLastPssm();
+}
+
END_SCOPE(blast)
END_NCBI_SCOPE
diff --git a/c++/src/algo/blast/blastinput/rpsblast_args.cpp b/c++/src/algo/blast/blastinput/rpsblast_args.cpp
index 14276d2..1a54173 100644
--- a/c++/src/algo/blast/blastinput/rpsblast_args.cpp
+++ b/c++/src/algo/blast/blastinput/rpsblast_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: rpsblast_args.cpp 439077 2014-06-25 14:19:42Z madden $
+/* $Id: rpsblast_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: rpsblast_args.cpp 439077 2014-06-25 14:19:42Z madden $";
+static char const rcsid[] = "$Id: rpsblast_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -59,7 +59,7 @@ CRPSBlastAppArgs::CRPSBlastAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "rpsblast";
+ static const char kDefaultTask[] = "rpsblast";
SetTask(kDefaultTask);
m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, kIsRpsBlast));
diff --git a/c++/src/algo/blast/blastinput/rpstblastn_args.cpp b/c++/src/algo/blast/blastinput/rpstblastn_args.cpp
index 0c2bdf8..624d0fa 100644
--- a/c++/src/algo/blast/blastinput/rpstblastn_args.cpp
+++ b/c++/src/algo/blast/blastinput/rpstblastn_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: rpstblastn_args.cpp 389688 2013-02-20 14:23:33Z madden $
+/* $Id: rpstblastn_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[]
- = "$Id: rpstblastn_args.cpp 389688 2013-02-20 14:23:33Z madden $";
+ = "$Id: rpstblastn_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -57,7 +57,7 @@ CRPSTBlastnAppArgs::CRPSTBlastnAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "rpstblastn";
+ static const char kDefaultTask[] = "rpstblastn";
SetTask(kDefaultTask);
m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, kIsRpsBlast));
diff --git a/c++/src/algo/blast/blastinput/tblastn_args.cpp b/c++/src/algo/blast/blastinput/tblastn_args.cpp
index 0da74e6..a4ec8a0 100644
--- a/c++/src/algo/blast/blastinput/tblastn_args.cpp
+++ b/c++/src/algo/blast/blastinput/tblastn_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: tblastn_args.cpp 442346 2014-08-01 16:28:16Z mcelhany $
+/* $Id: tblastn_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[]
- = "$Id: tblastn_args.cpp 442346 2014-08-01 16:28:16Z mcelhany $";
+ = "$Id: tblastn_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -57,7 +57,7 @@ CTblastnAppArgs::CTblastnAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "tblastn";
+ static const char kDefaultTask[] = "tblastn";
SetTask(kDefaultTask);
set<string> tasks;
tasks.insert(kDefaultTask);
diff --git a/c++/src/algo/blast/blastinput/tblastx_args.cpp b/c++/src/algo/blast/blastinput/tblastx_args.cpp
index 30315e4..a14a977 100644
--- a/c++/src/algo/blast/blastinput/tblastx_args.cpp
+++ b/c++/src/algo/blast/blastinput/tblastx_args.cpp
@@ -1,4 +1,4 @@
-/* $Id: tblastx_args.cpp 389688 2013-02-20 14:23:33Z madden $
+/* $Id: tblastx_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[]
- = "$Id: tblastx_args.cpp 389688 2013-02-20 14:23:33Z madden $";
+ = "$Id: tblastx_args.cpp 448376 2014-10-06 09:52:42Z mcelhany $";
#endif
#include <ncbi_pch.hpp>
@@ -56,7 +56,7 @@ CTblastxAppArgs::CTblastxAppArgs()
m_Args.push_back(arg);
m_ClientId = kProgram + " " + CBlastVersion().Print();
- static const string kDefaultTask = "tblastx";
+ static const char kDefaultTask[] = "tblastx";
SetTask(kDefaultTask);
m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
diff --git a/c++/src/algo/blast/blastinput/unit_test/blastinput_unit_test.cpp b/c++/src/algo/blast/blastinput/unit_test/blastinput_unit_test.cpp
index 53ad945..a874479 100644
--- a/c++/src/algo/blast/blastinput/unit_test/blastinput_unit_test.cpp
+++ b/c++/src/algo/blast/blastinput/unit_test/blastinput_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastinput_unit_test.cpp 458748 2015-02-09 19:40:32Z ivanov $
+/* $Id: blastinput_unit_test.cpp 463574 2015-03-30 16:58:22Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -790,7 +790,7 @@ void s_ReadAndTestQueryFromString(const string& input, TSeqPos expected_length,
BOOST_REQUIRE_EQUAL(expected_length, sv->size());
BOOST_REQUIRE_EQUAL(is_protein, sv->IsProtein());
sv->SetIupacCoding();
- TSeqPos input_pos = input.find_first_of("ACTG");
+ string::size_type input_pos = input.find_first_of("ACTG");
BOOST_REQUIRE(input_pos != string::npos);
for (TSeqPos pos = 0; pos < sv->size(); pos++, input_pos++) {
CNcbiOstrstream oss;
diff --git a/c++/src/algo/blast/composition_adjustment/composition_adjustment.c b/c++/src/algo/blast/composition_adjustment/composition_adjustment.c
index d997b84..7fdae3e 100644
--- a/c++/src/algo/blast/composition_adjustment/composition_adjustment.c
+++ b/c++/src/algo/blast/composition_adjustment/composition_adjustment.c
@@ -30,7 +30,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: composition_adjustment.c 186500 2010-03-22 11:37:29Z madden $";
+ "$Id: composition_adjustment.c 459367 2015-02-18 14:43:02Z madden $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <limits.h>
@@ -1253,7 +1253,7 @@ Blast_CompositionWorkspaceFree(Blast_CompositionWorkspace ** pNRrecord)
free(NRrecord);
}
- pNRrecord = NULL;
+ *pNRrecord = NULL;
}
diff --git a/c++/src/algo/blast/composition_adjustment/redo_alignment.c b/c++/src/algo/blast/composition_adjustment/redo_alignment.c
index 5eb50eb..9a5a008 100644
--- a/c++/src/algo/blast/composition_adjustment/redo_alignment.c
+++ b/c++/src/algo/blast/composition_adjustment/redo_alignment.c
@@ -31,7 +31,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: redo_alignment.c 418086 2013-11-14 16:36:48Z boratyng $";
+ "$Id: redo_alignment.c 474018 2015-07-24 13:27:53Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <stdlib.h>
@@ -688,9 +688,12 @@ s_WindowsFromTranslatedAligns(BlastCompo_Alignment * alignments,
sequence_length, 0, align_copy);
}
if (windows[k] == NULL)
+ {
+ BlastCompo_AlignmentsFree(&align_copy, NULL);
goto error_return;
+ }
}
- qsort(windows, hspcnt, sizeof(BlastCompo_SequenceRange*),
+ qsort(windows, hspcnt, sizeof(s_WindowInfo*),
s_LocationCompareWindows);
/* Join windows that overlap or are too close together. */
@@ -736,7 +739,7 @@ s_WindowsFromTranslatedAligns(BlastCompo_Alignment * alignments,
for (k = 0; k < length_joined; k++) {
s_DistinctAlignmentsSort(&windows[k]->align, windows[k]->hspcnt);
}
- qsort(windows, *nWindows, sizeof(BlastCompo_SequenceRange*),
+ qsort(windows, *nWindows, sizeof(s_WindowInfo*),
s_SubjectCompareWindows);
return 0; /* normal return */
@@ -810,7 +813,7 @@ s_WindowsFromProteinAligns(BlastCompo_Alignment * alignments,
/* shrink to fit */
{
s_WindowInfo ** new_windows =
- realloc(windows, window_index * sizeof(BlastCompo_SequenceRange*));
+ realloc(windows, window_index * sizeof(s_WindowInfo*));
if (new_windows == NULL) {
goto error_return;
} else {
@@ -818,7 +821,7 @@ s_WindowsFromProteinAligns(BlastCompo_Alignment * alignments,
*nWindows = window_index;
}
}
- qsort(windows, *nWindows, sizeof(BlastCompo_SequenceRange*),
+ qsort(windows, *nWindows, sizeof(s_WindowInfo*),
s_SubjectCompareWindows);
*pwindows = windows;
/* Normal return */
diff --git a/c++/src/algo/blast/core/Makefile.blast.lib b/c++/src/algo/blast/core/Makefile.blast.lib
index 4409d2e..e775ed8 100644
--- a/c++/src/algo/blast/core/Makefile.blast.lib
+++ b/c++/src/algo/blast/core/Makefile.blast.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.blast.lib 457061 2015-01-20 15:06:31Z ivanov $
+# $Id: Makefile.blast.lib 456453 2015-01-12 20:01:35Z fongah2 $
SRC_C = aa_ungapped blast_diagnostics blast_engine blast_extend \
blast_filter blast_gapalign blast_hits blast_hspstream blast_itree \
diff --git a/c++/src/algo/blast/core/blast_aalookup.c b/c++/src/algo/blast/core/blast_aalookup.c
index 649b66d..8961a75 100644
--- a/c++/src/algo/blast/core/blast_aalookup.c
+++ b/c++/src/algo/blast/core/blast_aalookup.c
@@ -1,4 +1,4 @@
-/* $Id: blast_aalookup.c 172185 2009-10-01 17:52:28Z camacho $
+/* $Id: blast_aalookup.c 464154 2015-04-06 16:36:18Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_aalookup.c 172185 2009-10-01 17:52:28Z camacho $";
+ "$Id: blast_aalookup.c 464154 2015-04-06 16:36:18Z madden $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/** Structure containing information needed for adding neighboring words.
@@ -1205,13 +1205,16 @@ static Int4 s_CompressedLookupFinalize(BlastCompressedAaLookupTable * lookup)
count++;
}
+/* fprintf(stderr, "SIZE: %ld %ld\n", (long) count, (long) (0.05 * lookup->backbone_size));
+ */
+
/* Compress the PV array if it would be large. Compress it
more if the backbone is sparsely populated. Do not compress
if the PV array is small enough already or the backbone is
mostly full */
pv_array_bts = PV_ARRAY_BTS;
- if (count <= 0.05 * lookup->backbone_size) {
+ if (count <= 0.01 * lookup->backbone_size) {
pv_array_bts += ilog2(lookup->backbone_size / (8 * kTargetPVBytes));
}
diff --git a/c++/src/algo/blast/core/blast_engine.c b/c++/src/algo/blast/core/blast_engine.c
index 3db89aa..8516f2d 100644
--- a/c++/src/algo/blast/core/blast_engine.c
+++ b/c++/src/algo/blast/core/blast_engine.c
@@ -1,4 +1,4 @@
-/* $Id: blast_engine.c 460402 2015-02-26 19:44:33Z ivanov $
+/* $Id: blast_engine.c 484536 2015-11-12 16:04:07Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,7 +55,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_engine.c 460402 2015-02-26 19:44:33Z ivanov $";
+ "$Id: blast_engine.c 484536 2015-11-12 16:04:07Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_engine.h>
@@ -83,9 +83,9 @@ static char const rcsid[] =
#define CONV_NUCL2PROT_COORDINATES(length) (length) / CODON_LENGTH
NCBI_XBLAST_EXPORT const int kBlastMajorVersion = 2;
-NCBI_XBLAST_EXPORT const int kBlastMinorVersion = 2;
-NCBI_XBLAST_EXPORT const int kBlastPatchVersion = 31;
-NCBI_XBLAST_EXPORT const char* kBlastReleaseDate = "March-03-2015";
+NCBI_XBLAST_EXPORT const int kBlastMinorVersion = 3;
+NCBI_XBLAST_EXPORT const int kBlastPatchVersion = 0;
+NCBI_XBLAST_EXPORT const char* kBlastReleaseDate = "12-17-2015";
/** Structure to be passed to s_BlastSearchEngineCore, containing pointers
to various preallocated structures and arrays. */
@@ -679,8 +679,12 @@ s_BlastSearchEngineCore(EBlastProgramType program_number,
const Boolean kNucleotide = (program_number == eBlastTypeBlastn ||
program_number == eBlastTypePhiBlastn);
const int kHspNumMax = BlastHspNumMax(score_options->gapped_calculation, hit_options);
+ Boolean isRPS = FALSE;
+ SubjectSplitStruct backup = {0,};
+
+ if (Blast_ProgramIsRpsBlast(program_number))
+ isRPS = TRUE;
- SubjectSplitStruct backup;
backup.sequence = NULL;
*hsp_list_out_ptr = NULL;
@@ -734,7 +738,7 @@ s_BlastSearchEngineCore(EBlastProgramType program_number,
/* Substitute query info by concatenated database info for RPS BLAST search */
- if (Blast_ProgramIsRpsBlast(program_number)) {
+ if (isRPS) {
BlastRPSLookupTable* lut = (BlastRPSLookupTable*) lookup->lut;
query_info = BlastQueryInfoNew(eBlastTypeRpsBlast, lut->num_profiles);
/* Since this will really be "subject info", not "query info",
@@ -813,14 +817,12 @@ s_BlastSearchEngineCore(EBlastProgramType program_number,
subject->length, gap_align->sbp, hit_params->link_hsp_params,
score_options->gapped_calculation);
} else if (!Blast_ProgramIsPhiBlast(program_number)
- && !(Blast_ProgramIsRpsBlast(program_number) && !sbp->gbp) ){
+ && !(isRPS && !sbp->gbp) ){
/* Calculate e-values for all HSPs. Skip this step
for PHI or RPS with old FSC, since calculating the E values
requires precomputation that has not been done yet */
- Boolean isRPS = FALSE;
double scale_factor = 1.0;
- if (Blast_ProgramIsRpsBlast(program_number)) {
- isRPS = TRUE;
+ if (isRPS) {
scale_factor = score_params->scale_factor;
}
status = Blast_HSPListGetEvalues(program_number, query_info,
diff --git a/c++/src/algo/blast/core/blast_gapalign.c b/c++/src/algo/blast/core/blast_gapalign.c
index 9017b7f..a141735 100644
--- a/c++/src/algo/blast/core/blast_gapalign.c
+++ b/c++/src/algo/blast/core/blast_gapalign.c
@@ -1,4 +1,4 @@
-/* $Id: blast_gapalign.c 457058 2015-01-20 15:00:53Z ivanov $
+/* $Id: blast_gapalign.c 474016 2015-07-24 13:27:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_gapalign.c 457058 2015-01-20 15:00:53Z ivanov $";
+ "$Id: blast_gapalign.c 474016 2015-07-24 13:27:16Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/ncbi_math.h>
@@ -3771,6 +3771,8 @@ Int2 BLAST_GetGappedScore (EBlastProgramType program_number,
if (rpsblast_pssms) {
gap_align->sbp->psi_matrix->pssm->data = rpsblast_pssms;
}
+ sfree(found_high_score);
+ tree = Blast_IntervalTreeFree(tree);
return status;
}
@@ -3795,7 +3797,11 @@ Int2 BLAST_GetGappedScore (EBlastProgramType program_number,
query_frame, subject->frame, gap_align->score,
&(gap_align->edit_script), &new_hsp);
if (status)
+ {
+ sfree(found_high_score);
+ tree = Blast_IntervalTreeFree(tree);
return status;
+ }
status = Blast_HSPListSaveHSP(hsp_list, new_hsp);
if (status)
break;
diff --git a/c++/src/algo/blast/core/blast_hits.c b/c++/src/algo/blast/core/blast_hits.c
index c833db3..79de6ab 100644
--- a/c++/src/algo/blast/core/blast_hits.c
+++ b/c++/src/algo/blast/core/blast_hits.c
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.c 464885 2015-04-15 11:33:59Z ivanov $
+/* $Id: blast_hits.c 461277 2015-03-09 14:02:47Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_hits.c 464885 2015-04-15 11:33:59Z ivanov $";
+ "$Id: blast_hits.c 461277 2015-03-09 14:02:47Z madden $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/ncbi_math.h>
diff --git a/c++/src/algo/blast/core/blast_kappa.c b/c++/src/algo/blast/core/blast_kappa.c
index 7cb0464..710fba2 100644
--- a/c++/src/algo/blast/core/blast_kappa.c
+++ b/c++/src/algo/blast/core/blast_kappa.c
@@ -1,4 +1,4 @@
-/* $Id: blast_kappa.c 450647 2014-10-29 11:47:28Z ivanov $
+/* $Id: blast_kappa.c 484535 2015-11-12 16:03:44Z ivanov $
* ==========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
-"$Id: blast_kappa.c 450647 2014-10-29 11:47:28Z ivanov $";
+"$Id: blast_kappa.c 484535 2015-11-12 16:03:44Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <float.h>
@@ -1168,7 +1168,7 @@ static int s_FindNumIdentical(Uint1* query_seq,
int query_left_len, query_right_len;
int subject_left_len, subject_right_len;
- int align_len_left, align_len_right;
+ int align_len_left=0, align_len_right=0;
match = TRUE;
num_identical += word_size;
@@ -2703,7 +2703,7 @@ Blast_RedoAlignmentCore(EBlastProgramType program_number,
int numAligns[6];
Blast_KarlinBlk * kbp = NULL;
BlastCompo_MatchingSequence matchingSeq = {0,};
- BlastHSPList * hsp_list = Blast_HSPListNew(0);
+ BlastHSPList * hsp_list = NULL;
double best_evalue;
Int4 best_score;
void * discarded_aligns = NULL;
@@ -2757,6 +2757,7 @@ Blast_RedoAlignmentCore(EBlastProgramType program_number,
goto match_loop_cleanup;
}
+ hsp_list = Blast_HSPListNew(0);
for (frame_index=0; frame_index<numFrames; frame_index++, context_index++) {
incoming_aligns = incoming_align_set[frame_index];
if (!incoming_aligns) continue;
@@ -2888,7 +2889,7 @@ function_cleanup:
s_ClearHeap(&redoneMatches[0]);
}
}
- s_FreeBlastCompo_QueryInfoArray(&query_info, numQueries);
+ s_FreeBlastCompo_QueryInfoArray(&query_info, numContexts);
Blast_RedoAlignParamsFree(&redo_align_params);
if (redoneMatches != NULL) {
for (query_index = 0; query_index < numQueries; query_index++) {
diff --git a/c++/src/algo/blast/core/blast_message.c b/c++/src/algo/blast/core/blast_message.c
index d1a0614..e0d4b18 100644
--- a/c++/src/algo/blast/core/blast_message.c
+++ b/c++/src/algo/blast/core/blast_message.c
@@ -1,4 +1,4 @@
-/* $Id: blast_message.c 444369 2014-08-25 11:42:15Z ivanov $
+/* $Id: blast_message.c 442874 2014-08-07 19:26:31Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_message.c 444369 2014-08-25 11:42:15Z ivanov $";
+ "$Id: blast_message.c 442874 2014-08-07 19:26:31Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_def.h>
diff --git a/c++/src/algo/blast/core/blast_options.c b/c++/src/algo/blast/core/blast_options.c
index 5785622..05bdd98 100644
--- a/c++/src/algo/blast/core/blast_options.c
+++ b/c++/src/algo/blast/core/blast_options.c
@@ -1,4 +1,4 @@
-/* $Id: blast_options.c 459037 2015-02-12 17:28:20Z ivanov $
+/* $Id: blast_options.c 458581 2015-02-06 15:18:12Z boratyng $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_options.c 459037 2015-02-12 17:28:20Z ivanov $";
+ "$Id: blast_options.c 458581 2015-02-06 15:18:12Z boratyng $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_options.h>
diff --git a/c++/src/algo/blast/core/blast_psi.c b/c++/src/algo/blast/core/blast_psi.c
index 7ce5873..591f175 100644
--- a/c++/src/algo/blast/core/blast_psi.c
+++ b/c++/src/algo/blast/core/blast_psi.c
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_psi.c 347205 2011-12-14 20:08:44Z boratyng $";
+ "$Id: blast_psi.c 459883 2015-02-23 16:45:34Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
@@ -471,7 +471,7 @@ PSIMsaNew(const PSIMsaDimensions* dimensions)
return NULL;
}
- retval = (PSIMsa*) malloc(sizeof(PSIMsa));
+ retval = (PSIMsa*) calloc(1, sizeof(PSIMsa));
if ( !retval ) {
return PSIMsaFree(retval);
}
diff --git a/c++/src/algo/blast/core/blast_psi_priv.c b/c++/src/algo/blast/core/blast_psi_priv.c
index d7bb7c9..080bd4a 100644
--- a/c++/src/algo/blast/core/blast_psi_priv.c
+++ b/c++/src/algo/blast/core/blast_psi_priv.c
@@ -1,6 +1,6 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_psi_priv.c 464347 2015-04-08 18:17:15Z ivanov $";
+ "$Id: blast_psi_priv.c 464171 2015-04-06 17:39:26Z boratyng $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/* ===========================================================================
*
diff --git a/c++/src/algo/blast/core/blast_seg.c b/c++/src/algo/blast/core/blast_seg.c
index c3837c5..f12ce6f 100644
--- a/c++/src/algo/blast/core/blast_seg.c
+++ b/c++/src/algo/blast/core/blast_seg.c
@@ -1,4 +1,4 @@
-/* $Id: blast_seg.c 170558 2009-09-14 18:45:07Z maning $
+/* $Id: blast_seg.c 474016 2015-07-24 13:27:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,7 +36,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_seg.c 170558 2009-09-14 18:45:07Z maning $";
+ "$Id: blast_seg.c 474016 2015-07-24 13:27:16Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_seg.h>
@@ -1305,6 +1305,16 @@ double lnfact[] =
82108.927837
};
+/* Nat log values for 0.1, 0.2, 0.3, etc. */
+/* Used instead of repeatedly calculating them. */
+double log_win10[] =
+{
+ 0.0, -2.30258509, -1.60943791, -1.203982804, -0.91629073, -0.6931478, -0.510825623, -0.356674944,
+ -0.22314355, -0.105360515, 0.0
+};
+
+
+
const int kProtAlphabet = 2; /**< identifies protein alphabet (FIXME: needed?). */
@@ -1596,11 +1606,21 @@ s_Entropy(Int4* sv)
if (total==0) return(0.);
ent = 0.0;
- for (i=0; sv[i]!=0; i++)
- {
- ent += ((double)sv[i])*log(((double)sv[i])/(double)total)/NCBIMATH_LN2;
- }
-
+ if (total == 10)
+ { /* Use precomputed table. */
+ for (i=0; sv[i]!=0; i++)
+ {
+ ent += ((double)sv[i])*log_win10[sv[i]]/NCBIMATH_LN2;
+ }
+
+ }
+ else
+ {
+ for (i=0; sv[i]!=0; i++)
+ {
+ ent += ((double)sv[i])*log(((double)sv[i])/(double)total)/NCBIMATH_LN2;
+ }
+ }
ent = fabs(ent/(double)total);
return(ent);
@@ -2065,7 +2085,10 @@ s_SegSeq(SSequence* seq, SegParameters* sparamsp, SSeg **segs,
SSeg *leftsegs = (SSeg*) NULL;
status = s_SegSeq(leftseq, sparamsp, &leftsegs, offset+lend);
if (status < 0)
- return status;
+ {
+ sfree(H);
+ return status;
+ }
/* prepend here, order will be restored in s_SegToSeqLoc */
if (leftsegs!=NULL)
@@ -2177,7 +2200,7 @@ s_AA20alphaStd (void)
palpha->lnalphasize = kLn20;
alphaindex = (Int4*) calloc(kCharSet , sizeof(Int4));
- alphaflag = (unsigned char*) calloc(kCharSet , sizeof(char));
+ alphaflag = (unsigned char*) calloc(kCharSet , sizeof(unsigned char));
for (c=0, i=0; c<kCharSet; c++)
{
diff --git a/c++/src/algo/blast/core/blast_seqsrc.c b/c++/src/algo/blast/core/blast_seqsrc.c
index a022f51..0ae743e 100644
--- a/c++/src/algo/blast/core/blast_seqsrc.c
+++ b/c++/src/algo/blast/core/blast_seqsrc.c
@@ -1,4 +1,4 @@
-/* $Id: blast_seqsrc.c 352811 2012-02-09 15:45:51Z maning $
+/* $Id: blast_seqsrc.c 461918 2015-03-13 16:38:36Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,7 +36,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_seqsrc.c 352811 2012-02-09 15:45:51Z maning $";
+ "$Id: blast_seqsrc.c 461918 2015-03-13 16:38:36Z vasilche $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#endif
@@ -404,7 +404,7 @@ BlastSeqSrcIterator* BlastSeqSrcIteratorNewEx(unsigned int chunk_sz)
}
/* Should employ lazy initialization? */
- itr->oid_list = (int*)malloc(chunk_sz * sizeof(unsigned int));
+ itr->oid_list = (int*)malloc(chunk_sz * sizeof(int));
if (!itr->oid_list) {
sfree(itr);
return NULL;
diff --git a/c++/src/algo/blast/core/blast_setup.c b/c++/src/algo/blast/core/blast_setup.c
index e49555c..f7ae99a 100644
--- a/c++/src/algo/blast/core/blast_setup.c
+++ b/c++/src/algo/blast/core/blast_setup.c
@@ -1,4 +1,4 @@
-/* $Id: blast_setup.c 440819 2014-07-17 13:14:07Z madden $
+/* $Id: blast_setup.c 442853 2014-08-07 17:41:32Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_setup.c 440819 2014-07-17 13:14:07Z madden $";
+ "$Id: blast_setup.c 442853 2014-08-07 17:41:32Z camacho $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_setup.h>
@@ -442,7 +442,7 @@ BlastSetup_ScoreBlkInit(BLAST_SequenceBlk* query_blk,
status = Blast_ScoreBlkMatrixInit(program_number, scoring_options, sbp, get_path);
if (status) {
- Blast_Perror(blast_message, status, -1);
+ Blast_PerrorWithLocation(blast_message, status, kBlastMessageNoContext);
return status;
}
@@ -597,7 +597,7 @@ Int2 BLAST_MainSetUp(EBlastProgramType program_number,
if ( (status = BlastSetup_Validate(query_info, *sbpp) != 0)) {
if (*blast_message == NULL) {
- Blast_Perror(blast_message, BLASTERR_INVALIDQUERIES, -1);
+ Blast_PerrorWithLocation(blast_message, status, kBlastMessageNoContext);
}
return 1;
}
diff --git a/c++/src/algo/blast/core/blast_stat.c b/c++/src/algo/blast/core/blast_stat.c
index 467f253..911f978 100644
--- a/c++/src/algo/blast/core/blast_stat.c
+++ b/c++/src/algo/blast/core/blast_stat.c
@@ -1,4 +1,4 @@
-/* $Id: blast_stat.c 459037 2015-02-12 17:28:20Z ivanov $
+/* $Id: blast_stat.c 474016 2015-07-24 13:27:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_stat.c 459037 2015-02-12 17:28:20Z ivanov $";
+ "$Id: blast_stat.c 474016 2015-07-24 13:27:16Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_stat.h>
@@ -4600,6 +4600,7 @@ RPSfindUngappedLambda(const char *matrixName)
sfree(lambda_array);
return retval;
} else {
+ sfree(lambda_array);
return 0.0;
}
}
@@ -5106,6 +5107,7 @@ BLAST_ComputeLengthAdjustment(double K,
return converged ? 0 : 1;
}
+/* UNUSED
static double s_CalculateNormalProbability(double x_, double eps_)
{
double pi = 3.1415926535897932384626433832795;
@@ -5143,6 +5145,8 @@ static double s_CalculateNormalProbability(double x_, double eps_)
res *= h;
return 0.5+const_val*(res);
}
+UNUSED */
+
/*
BlastSpougeStoE() -- given a score, return the associated Expect value
@@ -5212,7 +5216,7 @@ BLAST_SpougeEtoS(double e0,
Blast_GumbelBlk* gbp,
Int4 m, Int4 n)
{
- Int4 a, b, c;
+ Int4 a=0, b, c;
double e;
double db_scale_factor = (gbp->db_length) ?
(double)gbp->db_length : 1.0;
diff --git a/c++/src/algo/blast/core/blast_traceback.c b/c++/src/algo/blast/core/blast_traceback.c
index ef05727..122ad38 100644
--- a/c++/src/algo/blast/core/blast_traceback.c
+++ b/c++/src/algo/blast/core/blast_traceback.c
@@ -1,4 +1,4 @@
-/* $Id: blast_traceback.c 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blast_traceback.c 456407 2015-01-12 15:47:18Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_traceback.c 457059 2015-01-20 15:02:34Z ivanov $";
+ "$Id: blast_traceback.c 456407 2015-01-12 15:47:18Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_traceback.h>
diff --git a/c++/src/algo/blast/core/blast_util.c b/c++/src/algo/blast/core/blast_util.c
index 5c8e46e..f0876ba 100644
--- a/c++/src/algo/blast/core/blast_util.c
+++ b/c++/src/algo/blast/core/blast_util.c
@@ -1,4 +1,4 @@
-/* $Id: blast_util.c 431697 2014-04-07 15:06:02Z madden $
+/* $Id: blast_util.c 474016 2015-07-24 13:27:16Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_util.c 431697 2014-04-07 15:06:02Z madden $";
+ "$Id: blast_util.c 474016 2015-07-24 13:27:16Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_util.h>
@@ -1146,7 +1146,10 @@ int Blast_GetPartialTranslation(const Uint1* nucl_seq,
if (!mixed_seq_ptr) {
if ((translation_buffer =
(Uint1*) malloc(nucl_length/CODON_LENGTH+2)) == NULL)
+ {
+ sfree(nucl_seq_rev);
return -1;
+ }
length =
BLAST_GetTranslation(nucl_seq, nucl_seq_rev,
@@ -1162,7 +1165,10 @@ int Blast_GetPartialTranslation(const Uint1* nucl_seq,
Uint1* seq;
if ((translation_buffer = (Uint1*) malloc(nucl_length+2)) == NULL)
+ {
+ sfree(nucl_seq_rev);
return -1;
+ }
for (index = 1; index <= CODON_LENGTH; ++index) {
length =
diff --git a/c++/src/algo/blast/core/hspfilter_besthit.c b/c++/src/algo/blast/core/hspfilter_besthit.c
index c8058c1..b1d8951 100644
--- a/c++/src/algo/blast/core/hspfilter_besthit.c
+++ b/c++/src/algo/blast/core/hspfilter_besthit.c
@@ -1,4 +1,4 @@
-/* $Id: hspfilter_besthit.c 458750 2015-02-09 19:41:35Z ivanov $
+/* $Id: hspfilter_besthit.c 458578 2015-02-06 15:11:29Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: hspfilter_besthit.c 458750 2015-02-09 19:41:35Z ivanov $";
+ "$Id: hspfilter_besthit.c 458578 2015-02-06 15:11:29Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/algo/blast/core/hspfilter_collector.c b/c++/src/algo/blast/core/hspfilter_collector.c
index 1a4aec8..dc89a52 100644
--- a/c++/src/algo/blast/core/hspfilter_collector.c
+++ b/c++/src/algo/blast/core/hspfilter_collector.c
@@ -1,4 +1,4 @@
-/* $Id: hspfilter_collector.c 454095 2014-12-10 20:01:55Z ivanov $
+/* $Id: hspfilter_collector.c 443210 2014-08-12 13:55:24Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: hspfilter_collector.c 454095 2014-12-10 20:01:55Z ivanov $";
+ "$Id: hspfilter_collector.c 443210 2014-08-12 13:55:24Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/algo/blast/core/na_ungapped.c b/c++/src/algo/blast/core/na_ungapped.c
index ecdf149..ed200a4 100644
--- a/c++/src/algo/blast/core/na_ungapped.c
+++ b/c++/src/algo/blast/core/na_ungapped.c
@@ -1,4 +1,4 @@
-/* $Id: na_ungapped.c 449669 2014-10-20 12:07:51Z ivanov $
+/* $Id: na_ungapped.c 449473 2014-10-16 19:52:47Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: na_ungapped.c 449669 2014-10-20 12:07:51Z ivanov $";
+ "$Id: na_ungapped.c 449473 2014-10-16 19:52:47Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/na_ungapped.h>
diff --git a/c++/src/algo/blast/dbindex/README.usage b/c++/src/algo/blast/dbindex/README.usage
index 705e333..8d9a5f5 100644
--- a/c++/src/algo/blast/dbindex/README.usage
+++ b/c++/src/algo/blast/dbindex/README.usage
@@ -58,7 +58,7 @@ input. 'makembindex' accepts the following command line options:
-old_style_index [true/false]
If set to 'true', the old style index is generated; otherwose the
-new style index is generated. Default value is 'true'.
+new style index is generated. Default value is 'false'.
-input <string>
@@ -130,9 +130,12 @@ This option should be used to specify an index file name prefix
different from the name of the BLAST database. This option can
be useful if the index is in a non-standard location, or if multiple
indices exist for the same database, e.g. for using different
-types of masking.
+types of masking.
This options should not be used with new style indices. New style
-indexing always tries to find index files at location of
+indexing always tries to find index files at the location of
corresponding the BLAST database.
+It is important that the index used matches the blast database.
+Otherwise blastn may crash or produce bogus results.
+
diff --git a/c++/src/algo/blast/dbindex/makeindex/mkindex_app.cpp b/c++/src/algo/blast/dbindex/makeindex/mkindex_app.cpp
index c763dff..02a09a1 100644
--- a/c++/src/algo/blast/dbindex/makeindex/mkindex_app.cpp
+++ b/c++/src/algo/blast/dbindex/makeindex/mkindex_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: mkindex_app.cpp 433127 2014-04-22 22:39:03Z morgulis $
+/* $Id: mkindex_app.cpp 454194 2014-12-11 17:05:52Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,9 +76,11 @@ void CMkIndexApplication::Init()
arg_desc->AddDefaultKey(
"verbosity", "reporting_level", "how much to report",
CArgDescriptions::eString, "normal" );
- arg_desc->AddDefaultKey(
- "iformat", "input_format", "type of input used",
- CArgDescriptions::eString, "fasta" );
+ arg_desc->AddOptionalKey(
+ "iformat", "input_format",
+ "type of input used (default is \"blastdb\" for new style index, "
+ "\"fasta\" for old style index)",
+ CArgDescriptions::eString );
arg_desc->AddDefaultKey(
"legacy", "use_legacy_index_format",
"use legacy (0-terminated offset lists) dbindex format",
@@ -210,7 +212,13 @@ int CMkIndexApplication::Run()
string odir_name( CFile( ofname_base ).GetDir() );
*/
CSequenceIStream * seqstream = 0;
- string iformat = GetArgs()["iformat"].AsString();
+ string iformat( GetArgs()["iformat"] ? GetArgs()["iformat"].AsString()
+ : old_style ? "fasta" : "blastdb" );
+
+ if( !old_style && iformat == "fasta" ) {
+ ERR_POST( Error << "new style index requires input format 'blastdb'" );
+ exit( 1 );
+ }
if( iformat == "fasta" ) {
if( GetArgs()["db_mask"] ) {
@@ -258,11 +266,6 @@ int CMkIndexApplication::Run()
exit( 1 );
}
- if( !old_style && iformat == "fasta" ) {
- ERR_POST( Error << "new style index requires input format 'blastdb'" );
- exit( 1 );
- }
-
if( !old_style && iformat == "blastdb" ) {
if( GetArgs()["output"] ) {
ERR_POST( Warning <<
diff --git a/c++/src/algo/blast/format/Makefile.xblastformat.lib b/c++/src/algo/blast/format/Makefile.xblastformat.lib
index a4b621c..5569e63 100644
--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
@@ -1,13 +1,13 @@
-# $Id: Makefile.xblastformat.lib 438018 2014-06-12 11:52:14Z fongah2 $
+# $Id: Makefile.xblastformat.lib 474226 2015-07-27 17:10:07Z ivanov $
ASN_DEP = blastdb blastxml blastxml2 xnetblast
LIB = xblastformat
-SRC = blastfmtutil blastxml_format blastxml2_format blast_format data4xmlformat data4xml2format build_archive vecscreen_run
+SRC = blastfmtutil blastxml_format blastxml2_format blast_format data4xmlformat data4xml2format build_archive vecscreen_run sam
CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
+DLL_LIB = $(BLAST_LIBS) align_format blastxml blastxml2 xhtml xcgi
WATCHERS = jianye zaretska madden camacho fongah2
diff --git a/c++/src/algo/blast/format/blast_format.cpp b/c++/src/algo/blast/format/blast_format.cpp
index 405b29b..0905951 100644
--- a/c++/src/algo/blast/format/blast_format.cpp
+++ b/c++/src/algo/blast/format/blast_format.cpp
@@ -1,5 +1,5 @@
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blast_format.cpp 469173 2015-06-02 11:39:23Z ivanov $";
+static char const rcsid[] = "$Id: blast_format.cpp 485947 2015-11-30 17:47:26Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
/*
@@ -84,7 +84,9 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& options,
bool is_megablast /* = false */,
bool is_indexed /* = false */,
const blast::CIgBlastOptions *ig_opts /* = NULL */,
- const blast::CLocalDbAdapter* domain_db_adapter /* = NULL*/)
+ const blast::CLocalDbAdapter* domain_db_adapter /* = NULL*/,
+ const string & cmdline /* =kEMptyStr*/,
+ const string& subjectTag /* =kEmptyStr */)
: m_FormatType(format_type), m_IsHTML(is_html),
m_DbIsAA(db_adapter.IsProtein()), m_BelieveQuery(believe_query),
m_Outfile(outfile), m_NumSummary(num_summary),
@@ -97,6 +99,8 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& options,
m_MatrixName(matrix_name),
m_Scope(& scope),
m_IsBl2Seq(false),
+ m_IsDbScan(false),
+ m_SubjectTag(subjectTag),
m_IsRemoteSearch(is_remote_search),
m_QueriesFormatted(0),
m_Megablast(is_megablast),
@@ -109,13 +113,27 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& options,
m_BaseFile(kEmptyStr),
m_XMLFileCount(0),
m_LineLength(align_format::kDfltLineLength),
- m_OrigExceptionMask(outfile.exceptions())
+ m_OrigExceptionMask(outfile.exceptions()),
+ m_Cmdline(cmdline)
{
m_Outfile.exceptions(NcbiBadbit);
m_DbName = db_adapter.GetDatabaseName();
m_IsBl2Seq = (m_DbName == kEmptyStr ? true : false);
+ m_IsDbScan = db_adapter.IsDbScanMode();
if (m_IsBl2Seq) {
m_SeqInfoSrc.Reset(db_adapter.MakeSeqInfoSrc());
+ }
+ if(m_IsDbScan) {
+ int num_seqs=0;
+ int total_length=0;
+ if (!is_remote_search)
+ {
+ BlastSeqSrc* seqsrc = db_adapter.MakeSeqSrc();
+ num_seqs=BlastSeqSrcGetNumSeqs(seqsrc);
+ total_length=BlastSeqSrcGetTotLen(seqsrc);
+ }
+ CBlastFormatUtil::FillScanModeBlastDbInfo(m_DbInfo, m_DbIsAA,
+ num_seqs, total_length, m_SubjectTag);
} else {
CBlastFormatUtil::GetBlastDbInfo(m_DbInfo, m_DbName, m_DbIsAA,
dbfilt_algorithm, is_remote_search);
@@ -125,7 +143,8 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& options,
m_BlastXMLIncremental.Reset(new SBlastXMLIncremental());
}
- if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson)){
+ if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson) ||
+ (m_FormatType == CFormattingArgs::eXml2_S) || (m_FormatType == CFormattingArgs::eJson_S)){
m_AccumulatedQueries.Reset(new CBlastQueryVector());
}
@@ -162,7 +181,7 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& options,
m_IsIterative = options.IsIterativeSearch();
if (m_FormatType == CFormattingArgs::eSAM) {
- m_SamFormatter.reset(new CSAM_Formatter(m_Outfile, *m_Scope));
+ x_InitSAMFormatter();
}
}
@@ -177,7 +196,8 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& opts,
bool is_html,
bool is_remote_search,
const string& custom_output_format,
- bool is_vdb)
+ bool is_vdb,
+ const string & cmdline)
: m_FormatType(format_type),
m_IsHTML(is_html),
m_DbIsAA(!Blast_SubjectIsNucleotide(opts.GetProgramType())),
@@ -196,6 +216,7 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& opts,
m_MatrixName(opts.GetMatrixName()),
m_Scope(&scope),
m_IsBl2Seq(false),
+ m_IsDbScan (false),
m_IsRemoteSearch(is_remote_search),
m_QueriesFormatted(0),
m_Megablast(opts.GetProgram() == eMegablast ||
@@ -208,7 +229,8 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& opts,
m_BaseFile(kEmptyStr),
m_XMLFileCount(0),
m_LineLength(align_format::kDfltLineLength),
- m_OrigExceptionMask(outfile.exceptions())
+ m_OrigExceptionMask(outfile.exceptions()),
+ m_Cmdline(cmdline)
{
m_Outfile.exceptions(NcbiBadbit);
m_DbInfo.assign(dbinfo_list.begin(), dbinfo_list.end());
@@ -228,7 +250,8 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& opts,
m_BlastXMLIncremental.Reset(new SBlastXMLIncremental());
}
- if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson)) {
+ if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson) ||
+ (m_FormatType == CFormattingArgs::eXml2_S) || (m_FormatType == CFormattingArgs::eJson_S)) {
m_AccumulatedQueries.Reset(new CBlastQueryVector());
}
@@ -259,7 +282,7 @@ CBlastFormat::CBlastFormat(const blast::CBlastOptions& opts,
}
m_IsIterative = opts.IsIterativeSearch();
if (m_FormatType == CFormattingArgs::eSAM) {
- m_SamFormatter.reset(new CSAM_Formatter(m_Outfile, *m_Scope));
+ x_InitSAMFormatter();
}
}
@@ -296,8 +319,15 @@ void
CBlastFormat::PrintProlog()
{
// no header for some output types
- if (m_FormatType >= CFormattingArgs::eXml)
+ if (m_FormatType >= CFormattingArgs::eXml) {
+ if(m_FormatType == CFormattingArgs::eXml2_S) {
+ BlastXML2_PrintHeader(&m_Outfile);
+ }
+ else if(m_FormatType == CFormattingArgs::eJson_S){
+ BlastJSON_PrintHeader(&m_Outfile);
+ }
return;
+ }
if (m_IsHTML) {
m_Outfile << kHTML_Prefix << "\n";
@@ -319,7 +349,7 @@ CBlastFormat::PrintProlog()
m_Outfile);
}
- if (m_IsBl2Seq) {
+ if (m_IsBl2Seq && !m_IsDbScan) {
return;
}
@@ -367,7 +397,8 @@ CBlastFormat::PrintProlog()
else {
m_Outfile << "\n\n";
}
- CBlastFormatUtil::PrintDbReport(m_DbInfo, kFormatLineLength,
+ if (!m_IsBl2Seq || m_IsDbScan)
+ CBlastFormatUtil::PrintDbReport(m_DbInfo, kFormatLineLength,
m_Outfile, true);
}
@@ -665,14 +696,14 @@ CBlastFormat::x_PrintStructuredReport(const blast::CSearchResults& results,
m_AccumulatedQueries->clear();
return;
}
- else if(m_FormatType == CFormattingArgs::eXml2 || m_FormatType == CFormattingArgs::eJson) {
+ else if(m_FormatType == CFormattingArgs::eXml2 || m_FormatType == CFormattingArgs::eJson ||
+ m_FormatType == CFormattingArgs::eXml2_S || m_FormatType == CFormattingArgs::eJson_S) {
x_PrintXML2Report(results, queries);
return;
}
else if (m_FormatType == CFormattingArgs::eSAM) {
- ITERATE (CSeq_align_set::Tdata, it, results.GetSeqAlign()->Get()) {
- _ASSERT(m_SamFormatter.get());
- m_SamFormatter->Print(**it, (*it)->GetSeq_id(0));
+ if(results.HasAlignments()) {
+ m_SamFormatter->Print(*(results.GetSeqAlign()));
}
return;
}
@@ -712,8 +743,13 @@ CBlastFormat::x_PrintTabularReport(const blast::CSearchResults& results,
string strProgVersion =
NStr::ToUpper(m_Program) + " " + blast::CBlastVersion().Print();
CConstRef<CBioseq> subject_bioseq = x_CreateSubjectBioseq();
+ string dbname;
+ if (m_IsDbScan)
+ dbname = string("User specified sequence set (Input: ") + m_SubjectTag + string(")");
+ else
+ dbname = m_DbName;
tabinfo.PrintHeader(strProgVersion, *(bhandle.GetBioseqCore()),
- m_DbName, results.GetRID(), itr_num, aln_set,
+ dbname, results.GetRID(), itr_num, aln_set,
subject_bioseq);
}
@@ -721,8 +757,17 @@ CBlastFormat::x_PrintTabularReport(const blast::CSearchResults& results,
CSeq_align_set copy_aln_set;
CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set, m_HitlistSize);
- if(string::npos != m_CustomOutputFormatSpec.find("qcovs"))
- CBlastFormatUtil::InsertSubjectScores (copy_aln_set, bhandle, m_QueryRange);
+ {
+ unsigned int scores = CBlastFormatUtil::eNoQuerySubjCov;
+ if(string::npos != m_CustomOutputFormatSpec.find("qcovs"))
+ scores |= CBlastFormatUtil::eQueryCovPerSubj ;
+ if(string::npos != m_CustomOutputFormatSpec.find("qcovus") &&
+ ncbi::NStr::ToLower(m_Program) == string("blastn"))
+ scores |= CBlastFormatUtil::eQueryCovPerUniqSubj ;
+
+ if(scores != CBlastFormatUtil::eNoQuerySubjCov)
+ CBlastFormatUtil::InsertSubjectScores (copy_aln_set, bhandle, m_QueryRange, (CBlastFormatUtil::ESubjectScores) scores);
+ }
tabinfo.SetQueryGeneticCode(m_QueryGenCode);
tabinfo.SetDbGeneticCode(m_DbGenCode);
ITERATE(CSeq_align_set::Tdata, itr, copy_aln_set.Get()) {
@@ -806,7 +851,7 @@ CBlastFormat::x_PrintIgTabularReport(const blast::CIgBlastResults& results)
CConstRef<objects::CBioseq> CBlastFormat::x_CreateSubjectBioseq()
{
- if ( !m_IsBl2Seq ) {
+ if ( !m_IsBl2Seq && !m_IsDbScan) {
return CConstRef<CBioseq>();
}
@@ -919,6 +964,8 @@ CBlastFormat::PrintOneResultSet(const blast::CSearchResults& results,
|| m_FormatType == CFormattingArgs::eXml
|| m_FormatType == CFormattingArgs::eXml2
|| m_FormatType == CFormattingArgs::eJson
+ || m_FormatType == CFormattingArgs::eXml2_S
+ || m_FormatType == CFormattingArgs::eJson_S
|| m_FormatType == CFormattingArgs::eJsonSeqalign
|| m_FormatType == CFormattingArgs::eSAM)
{
@@ -968,7 +1015,7 @@ CBlastFormat::PrintOneResultSet(const blast::CSearchResults& results,
m_Outfile, m_BelieveQuery,
m_IsHTML, kIsTabularOutput,
results.GetRID());
- if (m_IsBl2Seq) {
+ if (m_IsBl2Seq && !m_IsDbScan) {
m_Outfile << "\n";
// FIXME: this might be configurable in the future
const bool kBelieveSubject = false;
@@ -1001,7 +1048,7 @@ CBlastFormat::PrintOneResultSet(const blast::CSearchResults& results,
// Also disable when program is rmblastn. At this time
// we do not want summary bit scores/evalues for this
// program. -RMH-
- if ( !m_IsBl2Seq && !(m_DisableKAStats || kIsGlobal) ) {
+ if ( (!m_IsBl2Seq || m_IsDbScan) && !(m_DisableKAStats || kIsGlobal) ) {
x_DisplayDeflines(aln_set, itr_num, prev_seqids);
}
@@ -1016,7 +1063,7 @@ CBlastFormat::PrintOneResultSet(const blast::CSearchResults& results,
CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set, m_NumAlignments);
int flags = s_SetFlags(m_Program, m_FormatType, m_IsHTML, m_ShowGi,
- m_IsBl2Seq, (m_DisableKAStats || kIsGlobal));
+ (m_IsBl2Seq && !m_IsDbScan), (m_DisableKAStats || kIsGlobal));
CDisplaySeqalign display(copy_aln_set, *m_Scope, &masklocs, NULL, m_MatrixName);
display.SetDbName(m_DbName);
@@ -1072,7 +1119,9 @@ CBlastFormat::PrintOneResultSet(blast::CIgBlastResults& results,
|| m_FormatType == CFormattingArgs::eXml
|| m_FormatType == CFormattingArgs::eXml2
|| m_FormatType == CFormattingArgs::eJson
- || m_FormatType == CFormattingArgs::eJsonSeqalign)
+ || m_FormatType == CFormattingArgs::eXml2_S
+ || m_FormatType == CFormattingArgs::eJson_S
+ || m_FormatType == CFormattingArgs::eJsonSeqalign)
{
x_PrintStructuredReport(results, queries);
return;
@@ -1369,6 +1418,8 @@ CBlastFormat::PrintPhiResult(const blast::CSearchResultSet& result_set,
|| m_FormatType == CFormattingArgs::eXml
|| m_FormatType == CFormattingArgs::eXml2
|| m_FormatType == CFormattingArgs::eJson
+ || m_FormatType == CFormattingArgs::eXml2_S
+ || m_FormatType == CFormattingArgs::eJson_S
|| m_FormatType == CFormattingArgs::eJsonSeqalign)
{
ITERATE(CSearchResultSet, result, result_set) {
@@ -1452,7 +1503,7 @@ CBlastFormat::PrintPhiResult(const blast::CSearchResultSet& result_set,
int flags = s_SetFlags(m_Program, m_FormatType, m_IsHTML, m_ShowGi,
- m_IsBl2Seq, false);
+ (m_IsBl2Seq && !m_IsDbScan), false);
if (phi_query_info)
{
@@ -1520,7 +1571,8 @@ CBlastFormat::PrintPhiResult(const blast::CSearchResultSet& result_set,
void
CBlastFormat::PrintEpilog(const blast::CBlastOptions& options)
{
- if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson)) {
+ if ((m_FormatType == CFormattingArgs::eXml2) || (m_FormatType == CFormattingArgs::eJson) ||
+ (m_FormatType == CFormattingArgs::eXml2_S) || (m_FormatType == CFormattingArgs::eJson_S)) {
if(!m_AccumulatedResults.empty()) {
CRef <CBlastSearchQuery> q = m_AccumulatedQueries->GetBlastSearchQuery(0);
if(m_IsBl2Seq) {
@@ -1536,20 +1588,18 @@ CBlastFormat::PrintEpilog(const blast::CBlastOptions& options)
m_AccumulatedResults.clear();
m_AccumulatedQueries->clear();
}
- if (m_FormatType == CFormattingArgs::eXml2)
+ if (m_FormatType == CFormattingArgs::eXml2
+ || m_FormatType == CFormattingArgs::eXml2_S) {
x_GenerateXML2MasterFile();
- else
+ }
+ else {
x_GenerateJSONMasterFile();
-
+ }
return;
}
if (m_FormatType == CFormattingArgs::eTabularWithComments) {
CBlastTabularInfo tabinfo(m_Outfile, m_CustomOutputFormatSpec);
- if (m_IsBl2Seq) {
- _ASSERT(m_SeqInfoSrc);
- m_QueriesFormatted /= m_SeqInfoSrc->Size();
- }
tabinfo.PrintNumProcessed(m_QueriesFormatted);
return;
} else if (m_FormatType >= CFormattingArgs::eTabular)
@@ -1571,7 +1621,7 @@ CBlastFormat::PrintEpilog(const blast::CBlastOptions& options)
m_Outfile, false);
}
- if ( !m_IsBl2Seq ) {
+ if ( !m_IsBl2Seq || m_IsDbScan) {
CBlastFormatUtil::PrintDbReport(m_DbInfo, kFormatLineLength,
m_Outfile, false);
}
@@ -1614,8 +1664,11 @@ void CBlastFormat::ResetScopeHistory()
{
// Do not reset the scope for BLAST2Sequences or else we'll loose the
// sequence data! (see x_CreateSubjectBioseq)
- if ((m_IsBl2Seq) || (m_FormatType == CFormattingArgs::eXml2)
- || (m_FormatType == CFormattingArgs::eJson)){
+ if ((m_IsBl2Seq)
+ || (m_FormatType == CFormattingArgs::eXml2)
+ || (m_FormatType == CFormattingArgs::eJson)
+ || (m_FormatType == CFormattingArgs::eXml2_S)
+ || (m_FormatType == CFormattingArgs::eJson_S)){
return;
}
@@ -1632,37 +1685,43 @@ void CBlastFormat::ResetScopeHistory()
}
}
-static string s_GetBaseName(const string & baseFile, bool isXML)
+static string s_GetBaseName(const string & baseFile, bool isXML, bool withPath)
{
- size_t length = baseFile.size();
- size_t ext_length = isXML? 4: 5;
- if(length > ext_length) {
- string last = baseFile.substr(length - ext_length);
- if((isXML && NStr::CompareNocase(last, ".xml") == 0 ) ||
- ( !isXML && NStr::CompareNocase(last, ".json") == 0)){
- return baseFile.substr(0, length - ext_length);
- }
+ string dir = kEmptyStr;
+ string base = kEmptyStr;
+ string ext = kEmptyStr;
+ CDirEntry::SplitPath(baseFile, withPath ? &dir:NULL, &base, &ext );
+ if(!((isXML && NStr::CompareNocase(ext, ".xml") == 0 ) ||
+ (!isXML && NStr::CompareNocase(ext, ".json") == 0))){
+ base += ext;
}
- return baseFile;
+ if(withPath)
+ return dir + base;
+
+ return base;
}
void CBlastFormat::x_WriteXML2(CCmdLineBlastXML2ReportData & report_data)
{
- if(m_BaseFile == kEmptyStr) {
- if(m_FormatType == CFormattingArgs::eXml2)
+ if(m_FormatType == CFormattingArgs::eXml2_S) {
BlastXML2_FormatReport(&report_data, &m_Outfile);
- else
+ }
+ else if (m_FormatType == CFormattingArgs::eJson_S) {
+ m_XMLFileCount++;
+ if(m_XMLFileCount > 1) {
+ m_Outfile << ",\n";
+ }
BlastJSON_FormatReport(&report_data, &m_Outfile);
}
else {
m_XMLFileCount++;
if(m_FormatType == CFormattingArgs::eXml2) {
- string file_name = s_GetBaseName(m_BaseFile, true) + "_" + NStr::IntToString(m_XMLFileCount) + ".xml";
+ string file_name = s_GetBaseName(m_BaseFile, true, true) + "_" + NStr::IntToString(m_XMLFileCount) + ".xml";
BlastXML2_FormatReport(&report_data, file_name);
}
else {
- string file_name = s_GetBaseName(m_BaseFile, false) + "_" + NStr::IntToString(m_XMLFileCount) + ".json";
+ string file_name = s_GetBaseName(m_BaseFile, false, true) + "_" + NStr::IntToString(m_XMLFileCount) + ".json";
BlastJSON_FormatReport(&report_data, file_name);
}
}
@@ -1731,29 +1790,35 @@ void CBlastFormat::x_PrintXML2Report(const blast::CSearchResults& results,
void CBlastFormat::x_GenerateXML2MasterFile(void)
{
- if(m_BaseFile == kEmptyStr)
+ if(m_FormatType == CFormattingArgs::eXml2_S) {
+ m_Outfile << "</BlastXML2>\n";
return;
+ }
- m_Outfile << "<?xml version=\"1.0\"?>\n<BlastXML\n"
+ m_Outfile << "<?xml version=\"1.0\"?>\n<BlastXML2\n"
"xmlns=\"http://www.ncbi.nlm.nih.gov\"\n"
- "xmlns:xi=\"http://www.w3.org/2003/XInclude\">\n";
+ "xmlns:xi=\"http://www.w3.org/2003/XInclude\"\n"
+ "xmlns:xs=\"http://www.w3.org/2001/XMLSchema-instance\"\n"
+ "xs:schemaLocation=\"http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/data_specs/schema_alt/NCBI_BlastOutput2.xsd\">\n";
- string base = s_GetBaseName(m_BaseFile, true);
+ string base = s_GetBaseName(m_BaseFile, true, false);
for(int i = 1; i <= m_XMLFileCount; i ++) {
string file_name = base + "_" + NStr::IntToString(i) + ".xml";
m_Outfile << "\t<xi:include href=\"" + file_name + "\"/>\n";
}
- m_Outfile << "</BlastXML>\n";
+ m_Outfile << "</BlastXML2>\n";
}
void CBlastFormat::x_GenerateJSONMasterFile(void)
{
- if(m_BaseFile == kEmptyStr)
+ if(m_FormatType == CFormattingArgs::eJson_S) {
+ m_Outfile << "]\n}\n";
return;
+ }
m_Outfile << "{\n\t\"BlastJSON\": [\n";
- string base = s_GetBaseName(m_BaseFile, true);
+ string base = s_GetBaseName(m_BaseFile, true, false);
for(int i = 1; i <= m_XMLFileCount; i ++) {
string file_name = base + "_" + NStr::IntToString(i) + ".json";
m_Outfile << "\t\t{\"File\": \"" + file_name + "\" }";
@@ -1764,3 +1829,10 @@ void CBlastFormat::x_GenerateJSONMasterFile(void)
m_Outfile << "\t]\n}";
}
+void CBlastFormat::x_InitSAMFormatter()
+{
+ CSAM_Formatter::SProgramInfo pg("0", blast::CBlastVersion().Print(), m_Cmdline);
+ pg.m_Name = m_Program;
+ m_SamFormatter.reset(new CBlast_SAM_Formatter(m_Outfile, *m_Scope,
+ m_CustomOutputFormatSpec, pg));
+}
diff --git a/c++/src/algo/blast/format/blastfmtutil.cpp b/c++/src/algo/blast/format/blastfmtutil.cpp
index 7cafd73..7cfdf77 100644
--- a/c++/src/algo/blast/format/blastfmtutil.cpp
+++ b/c++/src/algo/blast/format/blastfmtutil.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastfmtutil.cpp 446084 2014-09-11 11:52:44Z ivanov $
+/* $Id: blastfmtutil.cpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blastfmtutil.cpp 446084 2014-09-11 11:52:44Z ivanov $";
+static char const rcsid[] = "$Id: blastfmtutil.cpp 482732 2015-10-26 16:31:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -55,6 +55,8 @@ static char const rcsid[] = "$Id: blastfmtutil.cpp 446084 2014-09-11 11:52:44Z i
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <util/range.hpp>
+
+
BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi);
USING_SCOPE(objects);
@@ -565,18 +567,26 @@ CBlastFormatUtil::GetWholeAlnSeqStrings(string & query,
void CBlastFormatUtil::InsertSubjectScores (CSeq_align_set & org_align_set,
const CBioseq_Handle & query_handle,
- TSeqRange query_range)
+ TSeqRange query_range,
+ ESubjectScores score_type)
{
- if(!org_align_set.IsSet() || org_align_set.Get().empty())
- {
+
+ if(!org_align_set.IsSet() || org_align_set.Get().empty()) {
_TRACE("Empty seq_align_set");
return;
}
-
// Seq align set from
int dont_care = 0;
- if(org_align_set.Get().front()->GetNamedScore("seq_percent_coverage", dont_care))
+ unsigned int check_type = score_type;
+ if(org_align_set.Get().front()->GetNamedScore("seq_percent_coverage", dont_care)) {
+ check_type &= (~eQueryCovPerSubj);
+ }
+ if (org_align_set.Get().front()->GetNamedScore("uniq_seq_percent_coverage", dont_care)) {
+ check_type &= (~eQueryCovPerUniqSubj);
+ }
+ if(check_type == eNoQuerySubjCov){
return;
+ }
CConstRef<CBioseq> query_bioseq = query_handle.GetCompleteBioseq();
int query_len = 0;
@@ -615,16 +625,33 @@ void CBlastFormatUtil::InsertSubjectScores (CSeq_align_set & org_align_set,
}
tmp_align_list.assign(left_it, right_it);
- int master_coverage = align_format::CAlignFormatUtil::GetMasterCoverage(tmp_align_set);
-
- if (master_coverage)
- {
- double subj_coverage = 100.0 * (double) master_coverage/ (double) query_len;
- if(subj_coverage < 99)
- subj_coverage +=0.5;
-
- (*left_it)->SetNamedScore ("seq_percent_coverage", (int) subj_coverage);
- }
+ if((check_type & eQueryCovPerSubj)) {
+ int master_coverage = align_format::CAlignFormatUtil::GetMasterCoverage(tmp_align_set);
+
+ if (master_coverage)
+ {
+ double subj_coverage = 100.0 * (double) master_coverage/ (double) query_len;
+ //cerr << "Query Length: " << query_len << endl;
+ //cerr << "Query coverage Length: " << master_coverage << endl;
+ if(subj_coverage < 99)
+ subj_coverage +=0.5;
+
+ (*left_it)->SetNamedScore ("seq_percent_coverage", (int) subj_coverage);
+ }
+ }
+ if((check_type & eQueryCovPerUniqSubj)) {
+ int uniq_coverage = align_format::CAlignFormatUtil::GetUniqSeqCoverage(tmp_align_set);
+ if (uniq_coverage)
+ {
+ double uniq_subj_coverage = 100.0 * (double) uniq_coverage/ (double) query_len;
+ //cerr << "Query Uniq coverage Length: " << uniq_coverage << endl;
+ //cerr << uniq_coverage << endl;
+ if(uniq_subj_coverage < 99)
+ uniq_subj_coverage +=0.5;
+
+ (*left_it)->SetNamedScore ("uniq_seq_percent_coverage", (int) uniq_subj_coverage);
+ }
+ }
left_it = right_it;
}
}
diff --git a/c++/src/algo/blast/format/blastxml2_format.cpp b/c++/src/algo/blast/format/blastxml2_format.cpp
index ef181aa..cf453d6 100644
--- a/c++/src/algo/blast/format/blastxml2_format.cpp
+++ b/c++/src/algo/blast/format/blastxml2_format.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastxml2_format.cpp 465639 2015-04-23 13:17:46Z ivanov $
+/* $Id: blastxml2_format.cpp 485061 2015-11-18 16:07:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -53,6 +53,7 @@
#include <serial/objostrjson.hpp>
#include <algo/blast/api/version.hpp>
+#include <sstream>
#include <algorithm>
@@ -700,6 +701,29 @@ static void s_FillBlastOutput(blastxml2::CBlastOutput2 & bxmlout, const IBlastXM
}
}
+class CBlastOStreamXml : public CObjectOStreamXml
+{
+public:
+
+ CBlastOStreamXml (CNcbiOstream& stream, EOwnership deleteOut)
+ : CObjectOStreamXml(stream , deleteOut) {}
+ virtual ~CBlastOStreamXml (void) {};
+ // WriteFileHeader() is a dummy to keep xml prolog, doctype
+ // from being printed with each object
+ virtual void WriteFileHeader(TTypeInfo type) {;};
+};
+
+static void
+s_WriteXML2ObjectNoHeader(blastxml2::CBlastOutput2 & bxmlout, CNcbiOstream *out_stream)
+{
+ TTypeInfo typeInfo = bxmlout.GetThisTypeInfo();
+ auto_ptr<CBlastOStreamXml> xml_out(new CBlastOStreamXml (*out_stream, eNoOwnership));
+ xml_out->SetEncoding(eEncoding_Ascii);
+ xml_out->SetVerifyData( eSerialVerifyData_No );
+ xml_out->SetEnforcedStdXml();
+ xml_out->Write(&bxmlout, typeInfo );
+}
+
static void
s_WriteXML2Object(blastxml2::CBlastOutput2 & bxmlout, CNcbiOstream *out_stream)
@@ -723,12 +747,12 @@ s_WriteXML2Object(blastxml2::CBlastOutput2 & bxmlout, CNcbiOstream *out_stream)
/// retrieved [in]
/// @param out_stream Output stream for incremental output, ignore if NULL [out]
void
-BlastXML2_FormatReport(const IBlastXML2ReportData* data, CNcbiOstream *out_stream )
+BlastXML2_FormatReport(const IBlastXML2ReportData* data, CNcbiOstream *out_stream)
{
blastxml2::CBlastOutput2 bxmlout;
try {
s_FillBlastOutput(bxmlout, data);
- s_WriteXML2Object(bxmlout, out_stream);
+ s_WriteXML2ObjectNoHeader(bxmlout, out_stream);
}
catch(CException &e){
ERR_POST(Error << e.GetMsg() << e.what() );
@@ -744,25 +768,38 @@ void
BlastXML2_FormatReport(const IBlastXML2ReportData* data, string file_name)
{
blastxml2::CBlastOutput2 bxmlout;
- try {
CNcbiOfstream out_stream;
out_stream.open(file_name.c_str(), IOS_BASE::out);
if(!out_stream.is_open())
- NCBI_THROW(CException, eInvalid, "Cannot open output file");
+ NCBI_THROW(CArgException, eInvalidArg, "Cannot open output file");
s_FillBlastOutput(bxmlout, data);
s_WriteXML2Object(bxmlout, &out_stream);
- }
- catch(CException &e){
- ERR_POST(Error << e.GetMsg() << e.what() );
- return;
- }
- catch(...){
- ERR_POST(Error << "XML format failed" );
- return;
- }
}
+void
+BlastXML2_PrintHeader(CNcbiOstream *out_stream)
+{
+ CNcbiOstrstream ostr;
+ auto_ptr<CObjectOStreamXml> xml_out(new CObjectOStreamXml (ostr, eNoOwnership));
+ xml_out->SetEncoding(eEncoding_Ascii);
+ xml_out->SetVerifyData( eSerialVerifyData_No );
+ xml_out->SetReferenceSchema();
+ xml_out->SetUseSchemaLocation(true);
+ xml_out->SetEnforcedStdXml();
+ xml_out->SetDTDFilePrefix("http://www.ncbi.nlm.nih.gov/data_specs/schema_alt/");
+ xml_out->SetDefaultSchemaNamespace("http://www.ncbi.nlm.nih.gov");
+
+ blastxml2::CBlastXML2 xml2;
+ TTypeInfo typeInfo = xml2.GetThisTypeInfo();
+ xml_out->Write(&xml2, typeInfo);
+
+ string out_str = string(CNcbiOstrstreamToString(ostr));
+ string::size_type end_pos = out_str.find("</BlastXML2>");
+ out_str.erase(end_pos);
+
+ *out_stream << out_str;
+}
void
BlastXML2_FormatError(int exit_code, string err_msg,
@@ -776,6 +813,41 @@ BlastXML2_FormatError(int exit_code, string err_msg,
s_WriteXML2Object(bxmlout, out_stream);
}
+class CBlastOStreamJson : public CObjectOStreamJson
+{
+public:
+
+ CBlastOStreamJson (CNcbiOstream& stream, EOwnership deleteOut)
+ : CObjectOStreamJson(stream , deleteOut) {}
+ virtual ~CBlastOStreamJson (void) {};
+ // WriteFileHeader() is a dummy to keep xml prolog, doctype
+ // from being printed with each object
+ virtual void WriteFileHeader(TTypeInfo type) {m_Output.IncIndentLevel();};
+ virtual void EndOfWrite(void) {
+ m_Output.DecIndentLevel();
+ m_Output.PutEol();
+ CObjectOStream::EndOfWrite();
+ };
+};
+
+void
+BlastJSON_PrintHeader(CNcbiOstream *out_stream)
+{
+ *out_stream << "{\n\"BlastOutput2\": [\n";
+}
+
+static void
+s_WriteJSONObjectNoHeader(blastxml2::CBlastOutput2 & bxmlout, CNcbiOstream *out_stream)
+{
+ TTypeInfo typeInfo = bxmlout.GetThisTypeInfo();
+ auto_ptr<CObjectOStreamJson> json_out(new CBlastOStreamJson (*out_stream, eNoOwnership));
+ json_out->SetDefaultStringEncoding(eEncoding_Ascii);
+ //json_out.SetUseIndentation(true);
+ //json_out.SetUseEol(true);
+ json_out->Write(&bxmlout, typeInfo );
+}
+
+
static void
s_WriteJSONObject(blastxml2::CBlastOutput2 & bxmlout, CNcbiOstream *out_stream)
{
@@ -792,23 +864,13 @@ void
BlastJSON_FormatReport(const IBlastXML2ReportData* data, string file_name)
{
blastxml2::CBlastOutput2 bxmlout;
- try {
CNcbiOfstream out_stream;
out_stream.open(file_name.c_str(), IOS_BASE::out);
if(!out_stream.is_open())
- NCBI_THROW(CException, eInvalid, "Cannot open output file");
+ NCBI_THROW(CArgException, eInvalidArg, "Cannot open output file");
s_FillBlastOutput(bxmlout, data);
s_WriteJSONObject(bxmlout, &out_stream);
- }
- catch(CException &e){
- ERR_POST(Error << e.GetMsg() << e.what() );
- return;
- }
- catch(...){
- ERR_POST(Error << "JSON format failed" );
- return;
- }
}
void
@@ -817,7 +879,7 @@ BlastJSON_FormatReport(const IBlastXML2ReportData* data, CNcbiOstream *out_strea
blastxml2::CBlastOutput2 bxmlout;
try {
s_FillBlastOutput(bxmlout, data);
- s_WriteJSONObject(bxmlout, out_stream);
+ s_WriteJSONObjectNoHeader(bxmlout, out_stream);
}
catch(CException &e){
ERR_POST(Error << e.GetMsg() << e.what() );
diff --git a/c++/src/algo/blast/format/data4xml2format.cpp b/c++/src/algo/blast/format/data4xml2format.cpp
index 26c60e2..6150e3e 100644
--- a/c++/src/algo/blast/format/data4xml2format.cpp
+++ b/c++/src/algo/blast/format/data4xml2format.cpp
@@ -1,4 +1,4 @@
-/* $Id: data4xml2format.cpp 465307 2015-04-20 16:56:07Z ivanov $
+/* $Id: data4xml2format.cpp 482740 2015-10-26 16:34:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@ CCmdLineBlastXML2ReportData::CCmdLineBlastXML2ReportData (
const vector<align_format::CAlignFormatUtil::SDbInfo> & dbsInfo) :
m_Query(query), m_Options (opts), m_Scope(scope),
m_DbName(kEmptyStr), m_NumSequences(0), m_NumBases(0),
- m_TaxDBFound(false), m_isBl2seq(false), m_isIterative(false)
+ m_TaxDBFound(false), m_isBl2seq(false), m_isIterative(false), m_Matrix(NULL)
{
x_InitCommon(results, opts);
x_InitDB(dbsInfo);
@@ -66,7 +66,7 @@ CCmdLineBlastXML2ReportData::CCmdLineBlastXML2ReportData(
CConstRef<IBlastSeqInfoSrc> subjectsInfo) :
m_Query(query), m_Options (opts), m_Scope(scope),
m_DbName(kEmptyStr), m_NumSequences(0), m_NumBases(0),
- m_TaxDBFound(false), m_isBl2seq(true), m_isIterative(false)
+ m_TaxDBFound(false), m_isBl2seq(true), m_isIterative(false), m_Matrix(NULL)
{
x_InitCommon(results, opts);
x_InitSubjects(subjectsInfo);
@@ -82,7 +82,7 @@ CCmdLineBlastXML2ReportData::CCmdLineBlastXML2ReportData(
const vector<CAlignFormatUtil::SDbInfo> & dbsInfo) :
m_Query(query), m_Options (opts), m_Scope(scope),
m_DbName(kEmptyStr), m_NumSequences(0), m_NumBases(0),
- m_TaxDBFound(false), m_isBl2seq(false), m_isIterative(true)
+ m_TaxDBFound(false), m_isBl2seq(false), m_isIterative(true), m_Matrix(NULL)
{
x_InitCommon(resultSet[0], opts);
x_InitDB(dbsInfo);
@@ -100,7 +100,7 @@ CCmdLineBlastXML2ReportData::CCmdLineBlastXML2ReportData(
CConstRef<IBlastSeqInfoSrc> subjectsInfo) :
m_Query(query), m_Options (opts), m_Scope(scope),
m_DbName(kEmptyStr), m_NumSequences(0), m_NumBases(0),
- m_TaxDBFound(false), m_isBl2seq(true), m_isIterative(true)
+ m_TaxDBFound(false), m_isBl2seq(true), m_isIterative(true), m_Matrix(NULL)
{
x_InitCommon(resultSet[0], opts);
x_InitSubjects(subjectsInfo);
@@ -185,19 +185,19 @@ CCmdLineBlastXML2ReportData::x_InitSubjects(CConstRef<IBlastSeqInfoSrc> subjects
CCmdLineBlastXML2ReportData::~CCmdLineBlastXML2ReportData()
{
- for (unsigned int i = 0; i < kMatrixCols; i++)
- delete [] m_Matrix[i];
+ if(m_Matrix) {
+ delete m_Matrix;
+ }
}
void
CCmdLineBlastXML2ReportData::x_FillScoreMatrix(const char *matrix_name)
{
- for (unsigned int i = 0; i < kMatrixCols; i++)
- m_Matrix[i] = new int[kMatrixCols];
-
if (matrix_name == NULL)
return;
+ int matrix[kMatrixCols][kMatrixCols];
+ int * tmp[kMatrixCols];
const SNCBIPackedScoreMatrix *packed_matrix = 0;
if (strcmp(matrix_name, "BLOSUM45") == 0)
@@ -231,11 +231,14 @@ CCmdLineBlastXML2ReportData::x_FillScoreMatrix(const char *matrix_name)
NCBISM_Unpack(packed_matrix, &m);
for (unsigned int i = 0; i < kMatrixCols; i++) {
+ tmp[i] = matrix[i];
for (unsigned int j = 0; j < kMatrixCols; j++) {
- m_Matrix[i][j] = m.s[i][j];
+ matrix[i][j] = m.s[i][j];
}
}
}
+
+ m_Matrix = (new CBlastFormattingMatrix(tmp, kMatrixCols, kMatrixCols));
}
string
@@ -306,8 +309,7 @@ CCmdLineBlastXML2ReportData::GetEntropy(int num) const
CBlastFormattingMatrix*
CCmdLineBlastXML2ReportData::GetMatrix(void) const
{
- return new CBlastFormattingMatrix((int **)m_Matrix,
- kMatrixCols, kMatrixCols);
+ return m_Matrix;
}
int
diff --git a/c++/src/algo/blast/format/sam.cpp b/c++/src/algo/blast/format/sam.cpp
new file mode 100644
index 0000000..14f03bd
--- /dev/null
+++ b/c++/src/algo/blast/format/sam.cpp
@@ -0,0 +1,104 @@
+/* $Id:
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's offical duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author: Amelia Fong
+*
+* ===========================================================================
+*/
+
+/// @file: tabular.cpp
+/// Formatting of pairwise sequence alignments in tabular form.
+/// One line is printed for each alignment with tab-delimited fielalnVec.
+
+#include <ncbi_pch.hpp>
+
+#include <algo/blast/format/sam.hpp>
+#include <serial/iterator.hpp>
+#include <objtools/align_format/align_format_util.hpp>
+
+BEGIN_NCBI_SCOPE
+USING_SCOPE(objects);
+
+CBlast_SAM_Formatter::CBlast_SAM_Formatter(CNcbiOstream& out, CScope& scope,
+ const string & custom_spec,
+ const CSAM_Formatter::SProgramInfo & info) :
+ CSAM_Formatter(out,scope),
+ m_refRow(1)
+{
+ CSAM_Formatter::SetFlag(CSAM_Formatter::fSAM_PlainSeqIds);
+ x_ProcessCustomSpec(custom_spec, info);
+}
+
+void CBlast_SAM_Formatter::x_Print(const CSeq_align_set & aln)
+{
+ if(m_refRow == 1) {
+ CSeq_align_set sorted;
+ sorted.Set() = aln.Get();
+ sorted.Set().sort(align_format::CAlignFormatUtil::SortHspByMasterStartAscending);
+ CSAM_Formatter::Print(sorted, m_refRow);
+ }
+ else {
+ CSAM_Formatter::Print(aln, m_refRow);
+ }
+}
+
+void CBlast_SAM_Formatter::Print(const CSeq_align_set & aln)
+{
+ if (aln.Get().front()->GetSegs().Which() == CSeq_align::C_Segs::e_Dendiag){
+ CSeq_align_set d_aln;
+ ITERATE(CSeq_align_set::Tdata, itr, aln.Get()){
+ CRef<CSeq_align> dense_seg = align_format::CAlignFormatUtil::CreateDensegFromDendiag(**itr);
+ CDense_seg::TScores & scores = dense_seg->SetSegs().SetDenseg().SetScores();
+ dense_seg->SetScore().swap(scores);
+ d_aln.Set().push_back(dense_seg);
+ }
+ x_Print(d_aln);
+ }
+ else {
+ x_Print(aln);
+ }
+}
+
+void CBlast_SAM_Formatter::x_ProcessCustomSpec(const string & custom_spec,
+ const CSAM_Formatter::SProgramInfo & info)
+{
+ vector<string> format_tokens;
+ NStr::Tokenize(custom_spec, " ", format_tokens);
+ CSAM_Formatter::SetProgram(info);
+ m_refRow = 1;
+ ITERATE (vector<string>, iter, format_tokens) {
+ if ("SQ" == *iter) {
+ CSAM_Formatter::SetFlag(CSAM_Formatter::fSAM_SeqData);
+ }
+ }
+
+ if(m_refRow == 1) {
+ CSAM_Formatter::SetGroupOrder(eGO_Reference);
+ CSAM_Formatter::SetSortOrder(eSO_Coordinate);
+ }
+}
+
+
+END_NCBI_SCOPE
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.aalookup_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.aalookup_unit_test.app
index 56477ec..8f74aee 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.aalookup_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.aalookup_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.aalookup_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.aalookup_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = aalookup_unit_test
SRC = aalookup_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.aascan_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.aascan_unit_test.app
index 9010c7b..6842eae 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.aascan_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.aascan_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.aascan_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.aascan_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = aascan_unit_test
SRC = aascan_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.bl2seq_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.bl2seq_unit_test.app
index e39b230..b754de4 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.bl2seq_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.bl2seq_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.bl2seq_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.bl2seq_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = bl2seq_unit_test
SRC = bl2seq_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test.app
index 7a94a36..da21ad2 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blast_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blast_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blast_unit_test
SRC = blast_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test_util.lib b/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test_util.lib
index 8db01ee..2392dd6 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test_util.lib
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test_util.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.blast_unit_test_util.lib 464344 2015-04-08 18:15:56Z ivanov $
+# $Id: Makefile.blast_unit_test_util.lib 454210 2014-12-11 18:20:43Z camacho $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastdiag_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastdiag_unit_test.app
index fbb219c..dc622a3 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastdiag_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastdiag_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastdiag_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastdiag_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastdiag_unit_test
SRC = blastdiag_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastengine_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastengine_unit_test.app
index e6c84df..2d7280e 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastengine_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastengine_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastengine_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastengine_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastengine_unit_test
SRC = blastengine_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastextend_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastextend_unit_test.app
index 43793ce..9a147be 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastextend_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastextend_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastextend_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastextend_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastextend_unit_test
SRC = blastextend_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastfilter_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastfilter_unit_test.app
index 02fbd37..f175ec0 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastfilter_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastfilter_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastfilter_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastfilter_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastfilter_unit_test
SRC = blastfilter_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blasthits_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blasthits_unit_test.app
index eeab82f..fdfd972 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blasthits_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blasthits_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blasthits_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blasthits_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blasthits_unit_test
SRC = blasthits_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastoptions_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastoptions_unit_test.app
index a353170..7bc6576 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastoptions_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastoptions_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastoptions_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastoptions_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastoptions_unit_test
SRC = blastoptions_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.blastsetup_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.blastsetup_unit_test.app
index f355bc8..242fd23 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.blastsetup_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.blastsetup_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastsetup_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.blastsetup_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = blastsetup_unit_test
SRC = blastsetup_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.delta_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.delta_unit_test.app
index 93e78b0..7d9234c 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.delta_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.delta_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.delta_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.delta_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = delta_unit_test
SRC = delta_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.gapinfo_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.gapinfo_unit_test.app
index 887ed0d..21ee6bf 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.gapinfo_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.gapinfo_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.gapinfo_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.gapinfo_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = gapinfo_unit_test
SRC = gapinfo_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.gencode_singleton_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.gencode_singleton_unit_test.app
index 17cb1b7..83ee07b 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.gencode_singleton_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.gencode_singleton_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.gencode_singleton_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.gencode_singleton_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = gencode_singleton_unit_test
SRC = gencode_singleton_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_besthit_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_besthit_unit_test.app
index 17eb6a9..247b268 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_besthit_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_besthit_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.hspfilter_besthit_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.hspfilter_besthit_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = hspfilter_besthit_unit_test
SRC = hspfilter_besthit_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_culling_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_culling_unit_test.app
index 47d7a5c..817a5ef 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_culling_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_culling_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.hspfilter_culling_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.hspfilter_culling_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = hspfilter_culling_unit_test
SRC = hspfilter_culling_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.hspstream_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.hspstream_unit_test.app
index 3c6e54e..c3e314d 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.hspstream_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.hspstream_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.hspstream_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.hspstream_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = hspstream_unit_test
SRC = hspstream_unit_test hspstream_test_util
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.in b/c++/src/algo/blast/unit_tests/api/Makefile.in
index de6d270..0270bfb 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.in
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.in 454176 2014-12-11 16:00:59Z camacho $
LIB_PROJ = blast_unit_test_util seqalign_util
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.linkhsp_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.linkhsp_unit_test.app
index e62530a..92f3c0e 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.linkhsp_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.linkhsp_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.linkhsp_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.linkhsp_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = linkhsp_unit_test
SRC = linkhsp_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.msa2pssm_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.msa2pssm_unit_test.app
index a8c8889..95d5a5b 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.msa2pssm_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.msa2pssm_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.msa2pssm_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.msa2pssm_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = msa2pssm_unit_test
SRC = msa2pssm_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.ntlookup_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.ntlookup_unit_test.app
index 0218511..f36b5bc 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.ntlookup_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.ntlookup_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.ntlookup_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.ntlookup_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = ntlookup_unit_test
SRC = ntlookup_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.ntscan_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.ntscan_unit_test.app
index bb0b4e8..d7a1ef1 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.ntscan_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.ntscan_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.ntscan_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.ntscan_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = ntscan_unit_test
SRC = ntscan_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.optionshandle_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.optionshandle_unit_test.app
index 9cb8ae1..d7ac7b8 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.optionshandle_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.optionshandle_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.optionshandle_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.optionshandle_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = optionshandle_unit_test
SRC = optionshandle_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.phiblast_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.phiblast_unit_test.app
index d41aee4..3d55f56 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.phiblast_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.phiblast_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.phiblast_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.phiblast_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = phiblast_unit_test
SRC = phiblast_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.prelimsearch_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.prelimsearch_unit_test.app
index 9af7a5e..84bb066 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.prelimsearch_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.prelimsearch_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.prelimsearch_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.prelimsearch_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = prelimsearch_unit_test
SRC = prelimsearch_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.psibl2seq_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.psibl2seq_unit_test.app
index 50fe289..4d20824 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.psibl2seq_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.psibl2seq_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.psibl2seq_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.psibl2seq_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = psibl2seq_unit_test
SRC = psibl2seq_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_iteration_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_iteration_unit_test.app
index a382d72..01106e4 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_iteration_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_iteration_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.psiblast_iteration_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.psiblast_iteration_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = psiblast_iteration_unit_test
SRC = psiblast_iteration_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_unit_test.app
index 10df9ec..d94e8f0 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.psiblast_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.psiblast_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.psiblast_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = psiblast_unit_test
SRC = psiblast_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.pssmcreate_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.pssmcreate_unit_test.app
index 858a77f..b85eb30 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.pssmcreate_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.pssmcreate_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.pssmcreate_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.pssmcreate_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = pssmcreate_unit_test
SRC = pssmcreate_unit_test pssm_test_util pssmcreate_cdd_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.pssmenginefreqratios_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.pssmenginefreqratios_unit_test.app
index 8be62af..6852a51 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.pssmenginefreqratios_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.pssmenginefreqratios_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.pssmenginefreqratios_unit_test.app 464351 2015-04-08 18:18:59Z ivanov $
+# $Id: Makefile.pssmenginefreqratios_unit_test.app 464229 2015-04-07 14:51:55Z fongah2 $
APP = pssmenginefreqratios_unit_test
SRC = pssmenginefreqratios_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.querydata_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.querydata_unit_test.app
index 7c4cf50..e4610be 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.querydata_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.querydata_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.querydata_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.querydata_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = querydata_unit_test
SRC = querydata_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.queryinfo_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.queryinfo_unit_test.app
index f2568d0..a5ff542 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.queryinfo_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.queryinfo_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.queryinfo_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.queryinfo_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = queryinfo_unit_test
SRC = queryinfo_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.redoalignment_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.redoalignment_unit_test.app
index 90281af..75431f4 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.redoalignment_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.redoalignment_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.redoalignment_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.redoalignment_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = redoalignment_unit_test
SRC = redoalignment_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.remote_blast_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.remote_blast_unit_test.app
index 563597c..9aa515c 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.remote_blast_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.remote_blast_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.remote_blast_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.remote_blast_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = remote_blast_unit_test
SRC = remote_blast_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.rps_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.rps_unit_test.app
index cd5633f..3b3193e 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.rps_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.rps_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.rps_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.rps_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = rps_unit_test
SRC = rps_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.scoreblk_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.scoreblk_unit_test.app
index 3f75701..a10ceb4 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.scoreblk_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.scoreblk_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.scoreblk_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.scoreblk_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = scoreblk_unit_test
SRC = scoreblk_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.search_strategy_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.search_strategy_unit_test.app
index e99a4e5..2a68bc7 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.search_strategy_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.search_strategy_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.search_strategy_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.search_strategy_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = search_strategy_unit_test
SRC = search_strategy_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.seqalign_util.lib b/c++/src/algo/blast/unit_tests/api/Makefile.seqalign_util.lib
index e972a54..25b5574 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.seqalign_util.lib
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.seqalign_util.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.seqalign_util.lib 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.seqalign_util.lib 454176 2014-12-11 16:00:59Z camacho $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.seqinfosrc_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.seqinfosrc_unit_test.app
index 96ab8e8..523060c 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.seqinfosrc_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.seqinfosrc_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.seqinfosrc_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.seqinfosrc_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = seqinfosrc_unit_test
SRC = seqinfosrc_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.seqsrc_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.seqsrc_unit_test.app
index 8a79e29..f89fb76 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.seqsrc_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.seqsrc_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.seqsrc_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.seqsrc_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = seqsrc_unit_test
SRC = seqsrc_unit_test seqsrc_mock mockseqsrc1_unit_test mockseqsrc2_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.setupfactory_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.setupfactory_unit_test.app
index 039dc82..dad179e 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.setupfactory_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.setupfactory_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.setupfactory_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.setupfactory_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = setupfactory_unit_test
SRC = setupfactory_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.split_query_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.split_query_unit_test.app
index efba4b3..c6fcc12 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.split_query_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.split_query_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.split_query_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.split_query_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = split_query_unit_test
SRC = split_query_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.subj_ranges_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.subj_ranges_unit_test.app
index 4ac95a3..c98812c 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.subj_ranges_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.subj_ranges_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.subj_ranges_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.subj_ranges_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = subj_ranges_unit_test
SRC = subj_ranges_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.traceback_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.traceback_unit_test.app
index a8859ed..ce666f7 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.traceback_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.traceback_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.traceback_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.traceback_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = traceback_unit_test
SRC = traceback_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.tracebacksearch_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.tracebacksearch_unit_test.app
index 5f09f26..190142f 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.tracebacksearch_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.tracebacksearch_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.tracebacksearch_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.tracebacksearch_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = tracebacksearch_unit_test
SRC = tracebacksearch_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.uniform_search_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.uniform_search_unit_test.app
index 71e6910..f14e404 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.uniform_search_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.uniform_search_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.uniform_search_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.uniform_search_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = uniform_search_unit_test
SRC = uniform_search_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/Makefile.version_reference_unit_test.app b/c++/src/algo/blast/unit_tests/api/Makefile.version_reference_unit_test.app
index 47074ef..c2df777 100644
--- a/c++/src/algo/blast/unit_tests/api/Makefile.version_reference_unit_test.app
+++ b/c++/src/algo/blast/unit_tests/api/Makefile.version_reference_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.version_reference_unit_test.app 464342 2015-04-08 18:14:49Z ivanov $
+# $Id: Makefile.version_reference_unit_test.app 454176 2014-12-11 16:00:59Z camacho $
APP = version_reference_unit_test
SRC = version_reference_unit_test
diff --git a/c++/src/algo/blast/unit_tests/api/aalookup_unit_test.ini b/c++/src/algo/blast/unit_tests/api/aalookup_unit_test.ini
index 7620583..3ef7ff1 100644
--- a/c++/src/algo/blast/unit_tests/api/aalookup_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/aalookup_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: aalookup_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: aalookup_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/aascan_unit_test.ini b/c++/src/algo/blast/unit_tests/api/aascan_unit_test.ini
index d25af7c..c517ebd 100644
--- a/c++/src/algo/blast/unit_tests/api/aascan_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/aascan_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: aascan_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: aascan_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp
index 5d9faf0..b630a48 100644
--- a/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: bl2seq_unit_test.cpp 444370 2014-08-25 11:42:59Z ivanov $
+/* $Id: bl2seq_unit_test.cpp 478802 2015-09-14 15:44:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -872,7 +872,6 @@ BOOST_AUTO_TEST_CASE(FullyMaskedSequence) {
options->SetGapXDropoff(100);
options->SetMaskAtHash(false);
CBl2Seq blaster(*query, *subj, *options);
- bool caught_exception = false;
CRef<CSearchResultSet> results;
BOOST_REQUIRE_NO_THROW(results = blaster.RunEx());
}
@@ -3113,6 +3112,8 @@ BOOST_AUTO_TEST_CASE(BlastpMultipleQueries_MultipleSubjs_CLocalBlast) {
CRef<CLocalDbAdapter> subjects(new CLocalDbAdapter(subj_qf,
opts_handle));
+ BOOST_REQUIRE(subjects->IsDbScanMode() == false);
+
size_t num_queries = query_vec.size();
size_t num_subjects = subj_vec.size();
@@ -3149,6 +3150,83 @@ BOOST_AUTO_TEST_CASE(BlastpMultipleQueries_MultipleSubjs_CLocalBlast) {
testResultAlignments(num_queries, num_subjects, sas_v);
}
+BOOST_AUTO_TEST_CASE(Blastp_MultipleSubjs_SearchAsSet) {
+ vector<TIntId> q_gis, s_gis;
+
+ // Setup the queries
+ q_gis.push_back(816838863);
+
+ // setup the subjects
+ s_gis.push_back(16130156);
+ s_gis.push_back(15644111);
+ s_gis.push_back(126699345);
+ s_gis.push_back(504220075);
+ s_gis.push_back(21222553);
+ s_gis.push_back(24376189);
+ s_gis.push_back(15598078);
+ s_gis.push_back(15599919);
+ s_gis.push_back(15597767);
+ s_gis.push_back(16131833);
+ s_gis.push_back(15599742);
+ s_gis.push_back(15598387);
+ s_gis.push_back(15600358);
+ s_gis.push_back(24375949);
+ s_gis.push_back(126698248);
+ s_gis.push_back(24375956);
+ s_gis.push_back(24375382);
+ s_gis.push_back(126698598);
+
+ TSeqLocVector query_vec;
+ ITERATE(vector<TIntId>, itr, q_gis) {
+ CRef<CSeq_loc> loc(new CSeq_loc());
+ loc->SetWhole().SetGi(GI_FROM(TIntId, *itr));
+
+ CScope* scope = new CScope(CTestObjMgr::Instance().GetObjMgr());
+ scope->AddDefaults();
+ query_vec.push_back(SSeqLoc(loc, scope));
+ }
+ CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(query_vec));
+
+ CRef<CBlastOptionsHandle>
+ opts_handle(CBlastOptionsFactory::Create(eBlastp));
+
+ TSeqLocVector subj_vec;
+ ITERATE(vector<TIntId>, itr, s_gis) {
+ CRef<CSeq_loc> loc(new CSeq_loc());
+ loc->SetWhole().SetGi(GI_FROM(TIntId, *itr));
+
+ CScope* scope = new CScope(CTestObjMgr::Instance().GetObjMgr());
+ scope->AddDefaults();
+ subj_vec.push_back(SSeqLoc(loc, scope));
+ }
+ CRef<IQueryFactory> subj_qf(new CObjMgr_QueryFactory(subj_vec));
+ CRef<CLocalDbAdapter> subjects(new CLocalDbAdapter(subj_qf,
+ opts_handle, true));
+
+ BOOST_REQUIRE(subjects->IsDbScanMode() == true);
+
+ size_t num_queries = query_vec.size();
+ size_t num_subjects = subj_vec.size();
+
+ // BLAST by concatenating all queries
+ CLocalBlast blaster(queries, opts_handle, subjects);
+ CRef<CSearchResultSet> results = blaster.Run();
+ BOOST_REQUIRE(results->GetResultType() == eDatabaseSearch);
+ BOOST_REQUIRE_EQUAL(num_queries,
+ results->GetNumResults());
+ BOOST_REQUIRE_EQUAL(num_queries, results->size());
+ BOOST_REQUIRE_EQUAL(num_queries, results->GetNumQueries());
+
+ // build the seqalign vector from the result set
+ CRef<CSeq_align_set> aln_set;
+ CSearchResults& res = (*results)[0];
+ aln_set.Reset(const_cast<CSeq_align_set*>
+ (res.GetSeqAlign().GetPointer()));
+ // gi|15599742|ref|NP_253236.1| has two alignments, all others have one.
+ BOOST_REQUIRE_EQUAL(num_subjects+1, aln_set->Size());
+
+}
+
BOOST_AUTO_TEST_CASE(BlastOptionsEquality) {
// Create options object through factory
auto_ptr<CBlastOptionsHandle> megablast_options_handle(
diff --git a/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.ini b/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.ini
index 154c26d..12cb45e 100644
--- a/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: bl2seq_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: bl2seq_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
BlastnWithWindowMasker_Db = PLATFORM_BigEndian
diff --git a/c++/src/algo/blast/unit_tests/api/blast_test_util.cpp b/c++/src/algo/blast/unit_tests/api/blast_test_util.cpp
index 6d6a5c1..e175cc9 100644
--- a/c++/src/algo/blast/unit_tests/api/blast_test_util.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blast_test_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_test_util.cpp 464342 2015-04-08 18:14:49Z ivanov $
+/* $Id: blast_test_util.cpp 454176 2014-12-11 16:00:59Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/unit_tests/api/blast_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blast_unit_test.cpp
index 8070a83..e605ce6 100644
--- a/c++/src/algo/blast/unit_tests/api/blast_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blast_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_unit_test.cpp 464342 2015-04-08 18:14:49Z ivanov $
+/* $Id: blast_unit_test.cpp 454176 2014-12-11 16:00:59Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/unit_tests/api/blast_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blast_unit_test.ini
index 21aae0b..d65b6ca 100644
--- a/c++/src/algo/blast/unit_tests/api/blast_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blast_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blast_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blast_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.cpp
index 06250ec..576fdbf 100644
--- a/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdiag_unit_test.cpp 171622 2009-09-25 15:08:10Z avagyanv $
+/* $Id: blastdiag_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,6 +75,7 @@ BOOST_AUTO_TEST_CASE(testDiagClear) {
}
ewp = BlastExtendWordFree(ewp);
+ BOOST_REQUIRE(ewp == NULL);
}
// This test is for a full diag that does get reset.
@@ -111,6 +112,7 @@ BOOST_AUTO_TEST_CASE(testDiagUpdateFull) {
}
ewp = BlastExtendWordFree(ewp);
+ BOOST_REQUIRE(ewp == NULL);
}
// This test is for a not full diag that does not get reset.
@@ -148,6 +150,7 @@ BOOST_AUTO_TEST_CASE(testDiagUpdateNotFull) {
}
ewp = BlastExtendWordFree(ewp);
+ BOOST_REQUIRE(ewp == NULL);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.ini
index b658d26..4c5d0ca 100644
--- a/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blastdiag_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blastdiag_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastengine_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastengine_unit_test.ini
index bdac343..84eb42e 100644
--- a/c++/src/algo/blast/unit_tests/api/blastengine_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastengine_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blastengine_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blastengine_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.cpp
index f628af9..38f4196 100644
--- a/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastextend_unit_test.cpp 415473 2013-10-17 13:43:48Z madden $
+/* $Id: blastextend_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -202,6 +202,7 @@ struct CBlastExtendTestFixture
m_iclsQueryBlk->sequence, m_iclsQueryInfo,
&message);
message = Blast_MessageFree(message);
+ BOOST_REQUIRE(message == NULL);
BOOST_REQUIRE(status == 0);
status = Blast_ScoreBlkKbpGappedCalc(m_ipScoreBlk, m_ScoringOpts,
@@ -391,6 +392,7 @@ BOOST_AUTO_TEST_CASE(testGreedyAlignment) {
// does not influence the BLAST_MbGetGappedScore behavior.
// Free the HSPList
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
// The initial seeds have been modified if they were on reverse strand,
// so setup the initial hit list again.
m_ipInitHitlist = BLAST_InitHitListFree(m_ipInitHitlist);
diff --git a/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.ini
index 1b4c481..09dfec2 100644
--- a/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastextend_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blastextend_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blastextend_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.cpp
index 681de59..c2fcd62 100644
--- a/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastfilter_unit_test.cpp 435845 2014-05-21 14:12:49Z fongah2 $
+/* $Id: blastfilter_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -490,6 +490,7 @@ BOOST_AUTO_TEST_CASE(SegFilter) {
filtering_options,
& filter_slp, NULL);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
BOOST_REQUIRE(status == 0);
Int4 loc_index;
@@ -722,7 +723,8 @@ BOOST_AUTO_TEST_CASE(RepeatsAndDustFilter) {
Blast_FindRepeatFilterLoc(query_v2, &nucl_handle);
Blast_FindDustFilterLoc(query_v2, &nucl_handle);
- BOOST_REQUIRE_EQUAL(sequence::Compare(*(query_v1[0].mask), *(query_v2[0].mask), qsl1->scope), sequence::eSame);
+ BOOST_REQUIRE_EQUAL(sequence::Compare(*(query_v1[0].mask), *(query_v2[0].mask),
+ qsl1->scope, sequence::fCompareOverlapping), sequence::eSame);
}
BOOST_AUTO_TEST_CASE(WindowMaskerAndDustFilter) {
@@ -748,7 +750,8 @@ BOOST_AUTO_TEST_CASE(WindowMaskerAndDustFilter) {
Blast_FindWindowMaskerLoc(query_v2, &nucl_handle);
Blast_FindDustFilterLoc(query_v2, &nucl_handle);
- BOOST_REQUIRE_EQUAL(sequence::Compare(*(query_v1[0].mask), *(query_v2[0].mask), qsl1->scope), sequence::eSame);
+ BOOST_REQUIRE_EQUAL(sequence::Compare(*(query_v1[0].mask), *(query_v2[0].mask),
+ qsl1->scope, sequence::fCompareOverlapping), sequence::eSame);
}
BOOST_AUTO_TEST_CASE(WindowMasker_OnSeqInterval)
@@ -1318,6 +1321,7 @@ BOOST_AUTO_TEST_CASE(FilterLocProtein) {
eBlastTypeBlastp, filter_options,
&filter_out, &blast_message);
filter_options = SBlastFilterOptionsFree(filter_options);
+ BOOST_REQUIRE(filter_options == NULL);
BOOST_REQUIRE(status == 0);
BlastSeqLoc *filter_slp = filter_out->seqloc_array[0];
@@ -1333,6 +1337,7 @@ BOOST_AUTO_TEST_CASE(FilterLocProtein) {
BOOST_REQUIRE_EQUAL(kNumLocs, loc_index);
filter_out = BlastMaskLocFree(filter_out);
+ BOOST_REQUIRE(filter_out == NULL);
}
BOOST_AUTO_TEST_CASE(MaskProteinSequence) {
@@ -1367,6 +1372,7 @@ BOOST_AUTO_TEST_CASE(MaskProteinSequence) {
BlastSetUp_MaskQuery(query_blk, query_info, filter_maskloc,
eBlastTypeBlastp);
filter_maskloc = BlastMaskLocFree(filter_maskloc);
+ BOOST_REQUIRE(filter_maskloc == NULL);
Uint1* buffer = &query_blk->sequence[0];
Int4 query_length = query_info->contexts[0].query_length;
@@ -1418,6 +1424,7 @@ BOOST_AUTO_TEST_CASE(MaskNucleotideBothStrands) {
BlastSetUp_MaskQuery(query_blk, query_info, filter_maskloc,
eBlastTypeBlastn);
filter_maskloc = BlastMaskLocFree(filter_maskloc);
+ BOOST_REQUIRE(filter_maskloc == NULL);
Uint1* buffer = &query_blk->sequence[0];
Int4 query_length = query_info->contexts[0].query_length;
@@ -1700,6 +1707,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromNULLString)
BOOST_REQUIRE(filtering_options->segOptions == NULL);
BOOST_REQUIRE(filtering_options->dustOptions == NULL);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromStringDustMaskAtHash)
@@ -1717,6 +1725,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringDustMaskAtHash)
BOOST_REQUIRE_EQUAL(string("L;m;"), string(retval.get()));
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromStringDust)
@@ -1734,6 +1743,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringDust)
BOOST_REQUIRE(strcmp(retval.get(), "L;") == 0);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromStringSEGWithParams)
@@ -1753,6 +1763,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringSEGWithParams)
BOOST_REQUIRE(strcmp(retval.get(), "S 10 1.0 1.5;") == 0);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromBadStringSEGWithParams)
@@ -1779,6 +1790,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringBlastnL)
BOOST_REQUIRE(strcmp(retval.get(), "L;") == 0);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromStringBlastpL)
{
@@ -1794,6 +1806,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringBlastpL)
BOOST_REQUIRE(strcmp(retval.get(), "L;") == 0);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterOptionsFromStringBlastnW)
{
@@ -1811,6 +1824,7 @@ BOOST_AUTO_TEST_CASE(FilterOptionsFromStringBlastnW)
BOOST_REQUIRE(strcmp(retval.get(), "W -t 9606;") == 0);
filtering_options = SBlastFilterOptionsFree(filtering_options);
+ BOOST_REQUIRE(filtering_options == NULL);
}
BOOST_AUTO_TEST_CASE(FilterMerge)
@@ -1837,6 +1851,7 @@ BOOST_AUTO_TEST_CASE(FilterMerge)
BOOST_REQUIRE_EQUAL(kNewWindow, result->dustOptions->window);
BOOST_REQUIRE(result->repeatFilterOptions);
result = SBlastFilterOptionsFree(result);
+ BOOST_REQUIRE(result == NULL);
status = SBlastFilterOptionsMerge(&result, opt1, NULL);
BOOST_REQUIRE_EQUAL(0, (int) status);
@@ -1844,6 +1859,7 @@ BOOST_AUTO_TEST_CASE(FilterMerge)
BOOST_REQUIRE_EQUAL(kNewLevel, result->dustOptions->level);
BOOST_REQUIRE_EQUAL(kNewWindow, result->dustOptions->window);
result = SBlastFilterOptionsFree(result);
+ BOOST_REQUIRE(result == NULL);
status = SBlastFilterOptionsMerge(&result, NULL, opt2);
BOOST_REQUIRE_EQUAL(0, (int) status);
@@ -1851,6 +1867,7 @@ BOOST_AUTO_TEST_CASE(FilterMerge)
BOOST_REQUIRE_EQUAL(true, !!result->mask_at_hash);
BOOST_REQUIRE(result->repeatFilterOptions);
result = SBlastFilterOptionsFree(result);
+ BOOST_REQUIRE(result == NULL);
SBlastFilterOptionsFree(opt1);
SBlastFilterOptionsFree(opt2);
@@ -1970,6 +1987,7 @@ BOOST_AUTO_TEST_CASE(BlastSeqLocCombineTest) {
}
result = BlastSeqLocFree(result);
+ BOOST_REQUIRE(result == NULL);
}
BOOST_AUTO_TEST_CASE(GetSeqLocInfoVector_AllPrograms) {
@@ -2078,6 +2096,7 @@ BOOST_AUTO_TEST_CASE(TestBlastSeqLocCombine_MergeElems)
BOOST_REQUIRE(mask_itr == NULL);
mask = BlastSeqLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
}
BOOST_AUTO_TEST_CASE(TestBlastSeqLocCombine_MergeIdenticals)
@@ -2108,6 +2127,7 @@ BOOST_AUTO_TEST_CASE(TestBlastSeqLocCombine_MergeIdenticals)
BOOST_REQUIRE(mask_itr == NULL);
mask = BlastSeqLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
}
BOOST_AUTO_TEST_CASE(TestBlastSeqLocCombine_NoMerging)
@@ -2134,6 +2154,7 @@ BOOST_AUTO_TEST_CASE(TestBlastSeqLocCombine_NoMerging)
BOOST_REQUIRE(mask_itr == NULL);
mask = BlastSeqLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
}
extern "C" void BlastSeqLocListReverse(BlastSeqLoc** head);
@@ -2159,6 +2180,7 @@ BOOST_AUTO_TEST_CASE(TestBlastSeqLocListReverse)
BOOST_REQUIRE(mask_itr == NULL);
mask = BlastSeqLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
}
BOOST_AUTO_TEST_CASE(TestGetTaxIdWithWindowMaskerSupport)
diff --git a/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.ini
index f75618a..1f0437c 100644
--- a/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: blastfilter_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blastfilter_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
WindowMasker = PLATFORM_BigEndian
diff --git a/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.cpp
index 5830725..19d0b30 100644
--- a/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blasthits_unit_test.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blasthits_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -210,8 +210,11 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
}
hsp = Blast_HSPFree(hsp);
+ BOOST_REQUIRE(hsp == NULL);
subject_blk = BlastSequenceBlkFree(subject_blk);
+ BOOST_REQUIRE(subject_blk == NULL);
target_t = BlastTargetTranslationFree(target_t);
+ BOOST_REQUIRE(target_t == NULL);
}
@@ -252,6 +255,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
}
combined_hsp_list = Blast_HSPListFree(combined_hsp_list);
+ BOOST_REQUIRE(combined_hsp_list == NULL);
}
/* Test that purge of newly created HSPList works. */
@@ -261,6 +265,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
/* Nothing was put on list, nothing should be purged off. */
BOOST_REQUIRE_EQUAL(0, hsp_list->hspcnt);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Create new HSPList and set the hspcnt to 5, even though all HSP's are NULL.
@@ -273,6 +278,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
/* Nothing was put on list, nothing should be purged off. */
BOOST_REQUIRE_EQUAL(0, hsp_list->hspcnt);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Check that an HSPList with no missing HSP's is not affected. */
@@ -290,6 +296,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
/* Nothing was NULL on list, everything should be there. */
BOOST_REQUIRE_EQUAL(kNumHsps, hsp_list->hspcnt);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Check that a number of HSP's all with same score are saved correctly if there
@@ -318,6 +325,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
BOOST_REQUIRE_EQUAL(30, hsp->subject.offset);
BOOST_REQUIRE_EQUAL(kNumHsps, hsp_list->hspcnt);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Check that an HSPList with some missing HSP's is treated correctly. */
@@ -354,6 +362,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
}
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Check that an HSP is correctly created by Blast_HSPInit. */
@@ -537,13 +546,17 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
LookupTableOptionsNew(program_number, &lookup_options);
LookupTableWrapInit(query_blk, lookup_options, query_options, blast_seq_loc, sbp, &lookup_wrap, NULL, NULL);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BlastInitialWordOptionsNew(program_number, &word_options);
BlastInitialWordParametersNew(program_number, word_options, hit_params,
lookup_wrap, sbp, query_info, kSubjLength, &word_params);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
lookup_wrap = LookupTableWrapFree(lookup_wrap);
+ BOOST_REQUIRE(lookup_wrap == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
word_params->cutoff_score_min = kWordCutoff;
@@ -682,13 +695,17 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
LookupTableOptionsNew(program_number, &lookup_options);
LookupTableWrapInit(query_blk, lookup_options, query_options, blast_seq_loc, sbp, &lookup_wrap, NULL, NULL);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BlastInitialWordOptionsNew(program_number, &word_options);
BlastInitialWordParametersNew(program_number, word_options, hit_params,
lookup_wrap, sbp, query_info, kSubjLength, &word_params);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
lookup_wrap = LookupTableWrapFree(lookup_wrap);
+ BOOST_REQUIRE(lookup_wrap == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
BOOST_REQUIRE_EQUAL(kWordCutoff, word_params->cutoff_score_min);
@@ -956,12 +973,19 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
BOOST_REQUIRE(delete_hsp == TRUE);
hsp = Blast_HSPFree(hsp);
+ BOOST_REQUIRE(hsp == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
score_params = BlastScoringParametersFree(score_params);
+ BOOST_REQUIRE(score_params == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
score_opts = BlastScoringOptionsFree(score_opts);
+ BOOST_REQUIRE(score_opts == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_opts = BlastHitSavingOptionsFree(hit_opts);
+ BOOST_REQUIRE(hit_opts == NULL);
}
BOOST_AUTO_TEST_CASE(testGetOOFNumIdentities)
@@ -1169,6 +1193,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
}
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testSBlastHitsParamsGapped) {
@@ -1191,14 +1216,19 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
&blasthit_params);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
BOOST_REQUIRE_EQUAL(blasthit_params->prelim_hitlist_size,
hit_options->hitlist_size+50);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
blasthit_params = SBlastHitsParametersFree(blasthit_params);
+ BOOST_REQUIRE(blasthit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
BOOST_AUTO_TEST_CASE(testSBlastHitsParamsUngapped) {
@@ -1222,14 +1252,19 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
&blasthit_params);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
BOOST_REQUIRE_EQUAL(blasthit_params->prelim_hitlist_size,
hit_options->hitlist_size);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
blasthit_params = SBlastHitsParametersFree(blasthit_params);
+ BOOST_REQUIRE(blasthit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
BOOST_AUTO_TEST_CASE(testSBlastHitsParamsCompStats) {
@@ -1255,14 +1290,19 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
&blasthit_params);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
BOOST_REQUIRE_EQUAL(blasthit_params->prelim_hitlist_size,
(2*hit_options->hitlist_size)+50);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
blasthit_params = SBlastHitsParametersFree(blasthit_params);
+ BOOST_REQUIRE(blasthit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
BOOST_AUTO_TEST_CASE(testAdjustOddBlastnScores) {
@@ -1315,6 +1355,7 @@ BOOST_AUTO_TEST_CASE(BlastTargetSequence)
BOOST_REQUIRE_EQUAL(60, (int) hit_list->low_score);
BOOST_REQUIRE(hit_list->hsplist_array != NULL);
hit_list = Blast_HitListFree(hit_list);
+ BOOST_REQUIRE(hit_list == NULL);
}
static void
diff --git a/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.ini
index 3c605c6..33b2ef3 100644
--- a/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blasthits_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blasthits_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blasthits_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp
index 8e5c365..d002cb0 100644
--- a/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastoptions_unit_test.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: blastoptions_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -240,6 +240,7 @@ BOOST_AUTO_TEST_CASE( FilterSetUpOptionsDustTest )
BOOST_CHECK(filter_options->dustOptions);
BOOST_CHECK(filter_options->segOptions == NULL);
filter_options = SBlastFilterOptionsFree(filter_options);
+ BOOST_REQUIRE(filter_options == NULL);
}
BOOST_AUTO_TEST_CASE( FilterSetUpOptionsSegTest )
@@ -252,6 +253,7 @@ BOOST_AUTO_TEST_CASE( FilterSetUpOptionsSegTest )
BOOST_CHECK(filter_options->dustOptions == NULL);
BOOST_CHECK(filter_options->segOptions);
filter_options = SBlastFilterOptionsFree(filter_options);
+ BOOST_REQUIRE(filter_options == NULL);
}
BOOST_AUTO_TEST_CASE( FilterSetUpOptionsNULLInput )
@@ -309,9 +311,13 @@ s_GetInitialWordParameters(EBlastProgramType program_number,
lookup_wrap, sbp, query_info, subject_length, &word_params);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
lookup_wrap = LookupTableWrapFree(lookup_wrap);
+ BOOST_REQUIRE(lookup_wrap == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
return word_params;
}
@@ -388,12 +394,19 @@ BOOST_AUTO_TEST_CASE( testCalcLinkHSPCutoffs )
BOOST_CHECK_EQUAL(41, link_hsp_params->cutoff_small_gap);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
word_params = BlastInitialWordParametersFree(word_params);
+ BOOST_REQUIRE(word_params == NULL);
word_options = BlastInitialWordOptionsFree(word_options);
+ BOOST_REQUIRE(word_options == NULL);
return;
}
@@ -468,9 +481,13 @@ BOOST_AUTO_TEST_CASE( testBadKbpForLinkHSPCutoffs )
BOOST_CHECK_EQUAL(0, link_hsp_params->cutoff_small_gap);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
return;
}
@@ -546,12 +563,19 @@ BOOST_AUTO_TEST_CASE( testCalcLinkHSPCutoffsSmallDB )
BOOST_CHECK_EQUAL(0, link_hsp_params->cutoff_small_gap);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
word_params = BlastInitialWordParametersFree(word_params);
+ BOOST_REQUIRE(word_params == NULL);
word_options = BlastInitialWordOptionsFree(word_options);
+ BOOST_REQUIRE(word_options == NULL);
return;
}
@@ -633,13 +657,21 @@ BOOST_AUTO_TEST_CASE( testCalcLinkHSPResetGapProb )
BOOST_CHECK_EQUAL(41, link_hsp_params->cutoff_small_gap);
query_blk = BlastSequenceBlkFree(query_blk);
+ BOOST_REQUIRE(query_blk == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
word_params = BlastInitialWordParametersFree(word_params);
+ BOOST_REQUIRE(word_params == NULL);
word_options = BlastInitialWordOptionsFree(word_options);
+ BOOST_REQUIRE(word_options == NULL);
return;
}
@@ -737,7 +769,9 @@ BOOST_AUTO_TEST_CASE( testExtParamNewSomeInvalidKbp )
sfree(sb.kbp);
sfree(sb.kbp_gap);
ext_params = BlastExtensionParametersFree(ext_params);
+ BOOST_REQUIRE(ext_params == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
}
static void MakeSomeValidKBP(Blast_KarlinBlk** kbp_array, Int4 num,
@@ -787,6 +821,7 @@ BOOST_AUTO_TEST_CASE( testExtensionParamsNew )
BOOST_CHECK_EQUAL(11, ext_params->gap_x_dropoff_final);
ext_params = BlastExtensionParametersFree(ext_params);
+ BOOST_REQUIRE(ext_params == NULL);
// gap_x_dropoff_final less than gap_x_dropoff, gap_x_dropoff_final should be adjusted.
ext_options->gap_x_dropoff = 25;
@@ -806,7 +841,9 @@ BOOST_AUTO_TEST_CASE( testExtensionParamsNew )
sfree(sb.kbp);
sfree(sb.kbp_gap);
ext_params = BlastExtensionParametersFree(ext_params);
+ BOOST_REQUIRE(ext_params == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
}
BOOST_AUTO_TEST_CASE( testHitSavingParamNewSomeInvalidKbp )
@@ -881,10 +918,15 @@ BOOST_AUTO_TEST_CASE( testHitSavingParamNewSomeInvalidKbp )
BOOST_CHECK_EQUAL(10, hit_params->cutoff_score_min);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
// This simulates values calculated by for the human genomic database.
@@ -946,10 +988,15 @@ BOOST_AUTO_TEST_CASE( testHitSavingParamNewGappedTblastnLargeSubjectSequence )
BOOST_CHECK_EQUAL(50, hit_params->prelim_evalue);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
@@ -1011,10 +1058,15 @@ BOOST_AUTO_TEST_CASE( testHitSavingParamNewGappedTblastnMidsizeSubjectSequence )
BOOST_CHECK_EQUAL(50, hit_params->prelim_evalue);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
// This checks that for repeated calls to BlastHitSavingParametersUpdate the
@@ -1093,10 +1145,15 @@ BOOST_AUTO_TEST_CASE( testHitSavingParamUpdateMultipleCalls )
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
// This simulates values calculated by for an EST database.
@@ -1158,10 +1215,15 @@ BOOST_AUTO_TEST_CASE( testHitSavingParamNewGappedTblastnSmallSubjectSequence )
BOOST_CHECK_EQUAL(19, hit_params->cutoffs[0].cutoff_score_max);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
@@ -1242,12 +1304,19 @@ BOOST_AUTO_TEST_CASE( testInitialWordParamNewSomeInvalidKbp )
BOOST_CHECK_EQUAL(11, word_params->x_dropoff_max);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
word_params = BlastInitialWordParametersFree(word_params);
+ BOOST_REQUIRE(word_params == NULL);
word_options = BlastInitialWordOptionsFree(word_options);
+ BOOST_REQUIRE(word_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
BOOST_AUTO_TEST_CASE( testRemoteFilterString)
diff --git a/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.ini
index d049a0d..806e75e 100644
--- a/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blastoptions_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: blastoptions_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.cpp
index ccc41fd..6724191 100644
--- a/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastsetup_unit_test.cpp 401131 2013-05-28 18:34:25Z grichenk $
+/* $Id: blastsetup_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -902,6 +902,7 @@ BOOST_AUTO_TEST_CASE(testCalcEffLengths)
&sbp, 1.0, &blast_message,
&BlastFindMatrixPath);
blast_message = Blast_MessageFree(blast_message);
+ BOOST_REQUIRE(blast_message == NULL);
BOOST_REQUIRE(status == 0);
BlastEffectiveLengthsParameters* eff_len_params = NULL;
@@ -1104,8 +1105,11 @@ BOOST_AUTO_TEST_CASE(testMainSetup)
BOOST_REQUIRE_EQUAL(-2, sbp->matrix->data[0][11]);
lookup_segments = BlastSeqLocFree(lookup_segments);
+ BOOST_REQUIRE(lookup_segments == NULL);
mask = BlastMaskLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
// supported options.
score_opts->reward = 1;
@@ -1121,8 +1125,11 @@ BOOST_AUTO_TEST_CASE(testMainSetup)
BOOST_REQUIRE_EQUAL(0, sbp->matrix->data[0][11]);
lookup_segments = BlastSeqLocFree(lookup_segments);
+ BOOST_REQUIRE(lookup_segments == NULL);
mask = BlastMaskLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
// NOT supported options.
score_opts->reward = 1;
@@ -1136,8 +1143,11 @@ BOOST_AUTO_TEST_CASE(testMainSetup)
BOOST_REQUIRE_EQUAL(1, (int) st);
lookup_segments = BlastSeqLocFree(lookup_segments);
+ BOOST_REQUIRE(lookup_segments == NULL);
mask = BlastMaskLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
// NOT supported options.
score_opts->reward = 3124;
@@ -1149,11 +1159,17 @@ BOOST_AUTO_TEST_CASE(testMainSetup)
BOOST_REQUIRE_EQUAL(-1, (int) st);
lookup_segments = BlastSeqLocFree(lookup_segments);
+ BOOST_REQUIRE(lookup_segments == NULL);
mask = BlastMaskLocFree(mask);
+ BOOST_REQUIRE(mask == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
blast_msg = Blast_MessageFree(blast_msg);
+ BOOST_REQUIRE(blast_msg == NULL);
qsup_opts = BlastQuerySetUpOptionsFree(qsup_opts);
+ BOOST_REQUIRE(qsup_opts == NULL);
score_opts = BlastScoringOptionsFree(score_opts);
+ BOOST_REQUIRE(score_opts == NULL);
}
@@ -1197,10 +1213,12 @@ BOOST_AUTO_TEST_CASE(testDeltaSeqSetup)
&sbp, 1.0, &blast_message,
&BlastFindMatrixPath);
blast_message = Blast_MessageFree(blast_message);
+ BOOST_REQUIRE(blast_message == NULL);
BOOST_REQUIRE(status == 0);
sbp->kbp_std[0] = Blast_KarlinBlkNew();
status = Blast_KarlinBlkUngappedCalc(sbp->kbp_std[0], sbp->sfp[0]);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
BOOST_REQUIRE(status == 0);
diff --git a/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.ini b/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.ini
index 2f1a1bb..760e4d4 100644
--- a/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: blastsetup_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: blastsetup_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/data/freqsprepos.dat b/c++/src/algo/blast/unit_tests/api/data/freqsprepos.dat
index e391879..029a49c 100644
--- a/c++/src/algo/blast/unit_tests/api/data/freqsprepos.dat
+++ b/c++/src/algo/blast/unit_tests/api/data/freqsprepos.dat
@@ -1,2 +1,2 @@
-0.250631 0.262017 0.213684 0.273668 0.0798137 0.0906228 0.167082 0.165455 0.173608 0.0915804 0.231837 0.260851 0.134584 0.108213 0.0653951 0.064799 0.0906228 0.0587905 0.0453511 0.171394 0.140746 0.0653951 0.0915804 0.0716874 0.289045 0.0798137 0.0628968 0.198835 0.134584 0.0466451 0.250119 0.190166 0.0835016 0.171394 0.12359 0.0798137 0.0906228 0.0653951 0.140746 0.127696 0.108213 0.0819539 0.0835016 0.0915804 0.130478 0.256078 0.269003 0.474919 0.664678 0.227109 0.108213 0.304819 0.214 [...]
+0.254313 0.261912 0.213387 0.270388 0.0807692 0.0899649 0.161815 0.162115 0.181873 0.0911783 0.232285 0.255844 0.129312 0.108272 0.0736004 0.0648313 0.0899649 0.0595162 0.0467117 0.171947 0.14044 0.0736004 0.0911783 0.0680861 0.286463 0.0807692 0.0612256 0.198237 0.129312 0.0459333 0.258072 0.188645 0.0817422 0.171947 0.124348 0.0807692 0.0899649 0.0736004 0.14044 0.126057 0.108272 0.0803732 0.0817422 0.0911783 0.127602 0.25208 0.275601 0.472318 0.668845 0.222882 0.108272 0.299592 0.2099 [...]
diff --git a/c++/src/algo/blast/unit_tests/api/delta_unit_test.ini b/c++/src/algo/blast/unit_tests/api/delta_unit_test.ini
index f52bccf..e0efe3c 100644
--- a/c++/src/algo/blast/unit_tests/api/delta_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/delta_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: delta_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: delta_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/gapinfo_unit_test.ini b/c++/src/algo/blast/unit_tests/api/gapinfo_unit_test.ini
index 7909a32..109851a 100644
--- a/c++/src/algo/blast/unit_tests/api/gapinfo_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/gapinfo_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: gapinfo_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: gapinfo_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/gencode_singleton_unit_test.ini b/c++/src/algo/blast/unit_tests/api/gencode_singleton_unit_test.ini
index 808215f..689d691 100644
--- a/c++/src/algo/blast/unit_tests/api/gencode_singleton_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/gencode_singleton_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: gencode_singleton_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: gencode_singleton_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.cpp
index 04d8d9a..921361d 100644
--- a/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: hspfilter_besthit_unit_test.cpp 274418 2011-04-14 13:40:26Z maning $
+/* $Id: hspfilter_besthit_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,9 @@ BlastHSPBestHitParams* s_GetBestHitParams()
BlastHSPBestHitParams* best_hit_params =
BlastHSPBestHitParamsNew(hit_options, best_hit_opts, false, kIsGapped);
best_hit_opts = BlastHSPBestHitOptionsFree(best_hit_opts);
+ BOOST_REQUIRE(best_hit_opts == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
return best_hit_params;
}
diff --git a/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.ini b/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.ini
index cf39746..3510563 100644
--- a/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: hspfilter_besthit_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: hspfilter_besthit_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.cpp
index 80fc20c..36e2903 100644
--- a/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: hspfilter_culling_unit_test.cpp 174149 2009-10-23 19:12:35Z maning $
+/* $Id: hspfilter_culling_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -53,7 +53,9 @@ BlastHSPCullingParams* s_GetCullingParams()
BlastHSPCullingParams* culling_params =
BlastHSPCullingParamsNew(hit_options, culling_opts, false, kIsGapped);
culling_opts = BlastHSPCullingOptionsFree(culling_opts);
+ BOOST_REQUIRE(culling_opts == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
return culling_params;
}
diff --git a/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.ini b/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.ini
index df511b9..313da6e 100644
--- a/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: hspfilter_culling_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: hspfilter_culling_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.cpp
index 46ca49f..a98b852 100644
--- a/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: hspstream_unit_test.cpp 171622 2009-09-25 15:08:10Z avagyanv $
+/* $Id: hspstream_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -93,7 +93,9 @@ void testHSPStream(EHSPStreamType stream_type) {
BlastHSPStreamRegisterMTLock(hsp_stream, lock);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
/* One written HSP list will be split into one per query. */
num_reads = kNumQueries;
num_hsps = 1;
@@ -138,6 +140,7 @@ void testHSPStream(EHSPStreamType stream_type) {
last_oid = hsp_list->oid;
BOOST_REQUIRE_EQUAL(num_hsps, hsp_list->hspcnt);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/* Check whether we can write more results. */
@@ -149,6 +152,7 @@ void testHSPStream(EHSPStreamType stream_type) {
status = BlastHSPStreamRead(hsp_stream, &hsp_list);
}
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
/* Close the stream for writing. Do it here, to imitate the situation
when reading starts before the stream is explicitly closed for
@@ -161,7 +165,9 @@ void testHSPStream(EHSPStreamType stream_type) {
BOOST_REQUIRE_EQUAL(kBlastHSPStream_Eof, status);
BOOST_REQUIRE(hsp_list == NULL);
hsp_stream = BlastHSPStreamFree(hsp_stream);
+ BOOST_REQUIRE(hsp_stream == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
BOOST_AUTO_TEST_CASE(testCollectorHSPStream) {
@@ -198,7 +204,9 @@ BOOST_AUTO_TEST_CASE(testMultiSeqHSPCollector) {
kProgram, ext_options, FALSE, 1, writer);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
BlastHSPList* hsp_list = NULL;
// Create HSPLists for all odd subjects
@@ -223,7 +231,9 @@ BOOST_AUTO_TEST_CASE(testMultiSeqHSPCollector) {
BOOST_REQUIRE_EQUAL(kBlastHSPStream_Eof, status);
BOOST_REQUIRE(hsp_list == NULL);
hsp_stream = BlastHSPStreamFree(hsp_stream);
+ BOOST_REQUIRE(hsp_stream == NULL);
Blast_HSPResultsFree(results);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.ini b/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.ini
index 331cd94..a5ff351 100644
--- a/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/hspstream_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: hspstream_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: hspstream_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.cpp
index 09693e8..b321ea2 100644
--- a/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: linkhsp_unit_test.cpp 415473 2013-10-17 13:43:48Z madden $
+/* $Id: linkhsp_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -166,6 +166,7 @@ struct LinkHspTestFixture {
status = Blast_ScoreBlkKbpUngappedCalc(m_ProgramType, m_ScoreBlk,
seqbuf, m_QueryInfo, &message);
message = Blast_MessageFree(message);
+ BOOST_REQUIRE(message == NULL);
BOOST_REQUIRE(status == 0);
@@ -464,6 +465,7 @@ struct LinkHspTestFixture {
m_QueryInfo, &ext_params);
fillEffectiveLengths(score_options, (Int8)db_length, db_num_seq);
score_options = BlastScoringOptionsFree(score_options);
+ BOOST_REQUIRE(score_options == NULL);
BlastHitSavingParametersNew(m_ProgramType, hit_options,
m_ScoreBlk, m_QueryInfo, subj_length, 0, &m_HitParams);
@@ -477,14 +479,18 @@ struct LinkHspTestFixture {
LookupTableOptionsNew(m_ProgramType, &lookup_options);
LookupTableWrapInit(query_blk, lookup_options, query_options, blast_seq_loc, m_ScoreBlk, &lookup_wrap, NULL, NULL);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
Uint4 avg_subj_length = (Uint4)(db_length/db_num_seq);
BlastInitialWordParametersNew(m_ProgramType, word_options, m_HitParams, lookup_wrap,
m_ScoreBlk, m_QueryInfo, avg_subj_length, &word_params);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
lookup_wrap = LookupTableWrapFree(lookup_wrap);
+ BOOST_REQUIRE(lookup_wrap == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
BlastLinkHSPParametersUpdate(word_params, m_HitParams, (gapped ? TRUE : FALSE));
diff --git a/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.ini b/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.ini
index 6ca6c18..f5443a0 100644
--- a/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/linkhsp_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: linkhsp_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: linkhsp_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/msa2pssm_unit_test.ini b/c++/src/algo/blast/unit_tests/api/msa2pssm_unit_test.ini
index cb70410..8612b38 100644
--- a/c++/src/algo/blast/unit_tests/api/msa2pssm_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/msa2pssm_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: msa2pssm_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: msa2pssm_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp
index 4042f38..f98033d 100644
--- a/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: ntlookup_unit_test.cpp 319713 2011-07-25 13:51:21Z camacho $
+/* $Id: ntlookup_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -189,6 +189,7 @@ BOOST_AUTO_TEST_CASE(testStdLookupTable) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eSmallNaLookupTable,
(ELookupTableType)lookup_wrap_ptr->lut_type);
@@ -202,7 +203,9 @@ BOOST_AUTO_TEST_CASE(testStdLookupTable) {
BOOST_REQUIRE_EQUAL((Int2)(-345), lookup->final_backbone[21076]);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testMegablastLookupTable)
@@ -221,6 +224,7 @@ BOOST_AUTO_TEST_CASE(testMegablastLookupTable)
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL((ELookupTableType)lookup_wrap_ptr->lut_type,
eMBLookupTable);
@@ -242,7 +246,9 @@ BOOST_AUTO_TEST_CASE(testMegablastLookupTable)
BOOST_REQUIRE_EQUAL(-729205454, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize11) {
@@ -262,6 +268,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize11) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -285,7 +292,9 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize11) {
BOOST_REQUIRE_EQUAL(-160576483, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize12) {
@@ -305,6 +314,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize12) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -328,7 +338,9 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize12) {
BOOST_REQUIRE_EQUAL(-630452942, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize11) {
@@ -348,6 +360,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize11) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -371,7 +384,9 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize11) {
BOOST_REQUIRE_EQUAL(932347030, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize12) {
@@ -391,6 +406,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize12) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -414,7 +430,9 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize12) {
BOOST_REQUIRE_EQUAL(558099690, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableTwoTemplatesWordSize11) {
@@ -434,6 +452,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableTwoTemplatesWordSize11) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -461,7 +480,9 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableTwoTemplatesWordSize11) {
BOOST_REQUIRE_EQUAL(-36132604, pv_array_hash);
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
@@ -484,6 +505,7 @@ BOOST_AUTO_TEST_CASE(testStdLookupTableDebruijn) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eNaLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastNaLookupTable* lookup = (BlastNaLookupTable*) lookup_wrap_ptr->lut;
@@ -505,7 +527,9 @@ BOOST_AUTO_TEST_CASE(testStdLookupTableDebruijn) {
}
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
BOOST_AUTO_TEST_CASE(testMegablastLookupTableDebruijn) {
@@ -527,6 +551,7 @@ BOOST_AUTO_TEST_CASE(testMegablastLookupTableDebruijn) {
lookup_options, query_options, lookup_segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eMBLookupTable, (ELookupTableType)lookup_wrap_ptr->lut_type);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -550,7 +575,9 @@ BOOST_AUTO_TEST_CASE(testMegablastLookupTableDebruijn) {
}
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
}
// Test that nothing is put into the lookup table if contiguous unmasked
@@ -574,6 +601,7 @@ BOOST_AUTO_TEST_CASE(testStdTableSmallUnmaskedRegion) {
lookup_options, query_options, segments,
0, &lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL(eSmallNaLookupTable,
(ELookupTableType)lookup_wrap_ptr->lut_type);
@@ -592,8 +620,11 @@ BOOST_AUTO_TEST_CASE(testStdTableSmallUnmaskedRegion) {
}
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
segments = BlastSeqLocFree(segments);
+ BOOST_REQUIRE(segments == NULL);
}
// Test that nothing is put into the lookup table if contiguous unmasked regions are smaller than user specified word size.
@@ -624,6 +655,7 @@ BOOST_AUTO_TEST_CASE(testMegablastTableSmallUnmaskedRegion) {
lookup_options, query_options, segments, 0,
&lookup_wrap_ptr, NULL, NULL), 0);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
BOOST_REQUIRE_EQUAL((ELookupTableType)lookup_wrap_ptr->lut_type, eMBLookupTable);
BlastMBLookupTable* lookup = (BlastMBLookupTable*) lookup_wrap_ptr->lut;
@@ -643,8 +675,11 @@ BOOST_AUTO_TEST_CASE(testMegablastTableSmallUnmaskedRegion) {
}
lookup_wrap_ptr = LookupTableWrapFree(lookup_wrap_ptr);
+ BOOST_REQUIRE(lookup_wrap_ptr == NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
segments = BlastSeqLocFree(segments);
+ BOOST_REQUIRE(segments == NULL);
}
diff --git a/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.ini b/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.ini
index 6c8706a..80f54cf 100644
--- a/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: ntlookup_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: ntlookup_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.cpp
index e7a968c..4c183d4 100644
--- a/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: ntscan_unit_test.cpp 415473 2013-10-17 13:43:48Z madden $
+/* $Id: ntscan_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -271,6 +271,7 @@ struct TestFixture {
&blast_message, NULL);
BOOST_REQUIRE_EQUAL(0, status);
blast_message = Blast_MessageFree(blast_message);
+ BOOST_REQUIRE(blast_message == NULL);
// set discontiguous megablast (if applicable)
@@ -292,6 +293,7 @@ struct TestFixture {
BOOST_REQUIRE_EQUAL(0, status);
BlastChooseNaExtend(lookup_wrap_ptr);
query_options = BlastQuerySetUpOptionsFree(query_options);
+ BOOST_REQUIRE(query_options == NULL);
// create the hit collection arrays
@@ -301,7 +303,9 @@ struct TestFixture {
BOOST_REQUIRE(offset_pairs != NULL);
lookup_options = LookupTableOptionsFree(lookup_options);
+ BOOST_REQUIRE(lookup_options == NULL);
score_options = BlastScoringOptionsFree(score_options);
+ BOOST_REQUIRE(score_options == NULL);
BlastInitialWordOptionsNew(program_number, &word_options);
BlastExtensionOptionsNew(program_number, &ext_options, TRUE);
BlastHitSavingOptionsNew(program_number, &hitsaving_options, TRUE);
@@ -777,9 +781,13 @@ struct TestFixture {
}
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
word_params = BlastInitialWordParametersFree(word_params);
+ BOOST_REQUIRE(word_params == NULL);
ewp = BlastExtendWordFree(ewp);
+ BOOST_REQUIRE(ewp == NULL);
init_hitlist = BLAST_InitHitListFree(init_hitlist);
+ BOOST_REQUIRE(init_hitlist == NULL);
}
};
diff --git a/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.ini b/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.ini
index 260a497..9e8e9c7 100644
--- a/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/ntscan_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: ntscan_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: ntscan_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/optionshandle_unit_test.ini b/c++/src/algo/blast/unit_tests/api/optionshandle_unit_test.ini
index 5db5441..40c4cbf 100644
--- a/c++/src/algo/blast/unit_tests/api/optionshandle_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/optionshandle_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: optionshandle_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: optionshandle_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.cpp
index 6539d31..f9bb4d9 100644
--- a/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: phiblast_unit_test.cpp 415473 2013-10-17 13:43:48Z madden $
+/* $Id: phiblast_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,6 +80,7 @@ public:
Blast_SetPHIPatternInfo(m_Program, pattern_blk, query_blk,
location, m_QueryInfo, &blast_msg);
location = BlastSeqLocFree(location);
+ BOOST_REQUIRE(location == NULL);
}
void x_CheckGappedAlignmentResults(BlastGapAlignStruct* gap_align) {
@@ -304,6 +305,7 @@ BOOST_AUTO_TEST_CASE(testPHICalcEvalues) {
BOOST_REQUIRE_CLOSE(7.568e-59, hsp->evalue, 1);
hsp_list = Blast_HSPListFree(hsp_list);
+ BOOST_REQUIRE(hsp_list == NULL);
}
/// Tests finding of pattern occurrences in subject.
@@ -393,7 +395,9 @@ BOOST_AUTO_TEST_CASE(testPHIBlastHSPResultsSplit) {
x_CheckSplitResults(results_array, pattern_info->num_patterns);
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
pattern_info = SPHIQueryInfoFree(pattern_info);
+ BOOST_REQUIRE(pattern_info == NULL);
}
BOOST_AUTO_TEST_CASE(testPHIBlastHSPResultsSplitNoHits) {
@@ -409,7 +413,9 @@ BOOST_AUTO_TEST_CASE(testPHIBlastHSPResultsSplitNoHits) {
sfree(results_array);
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
pattern_info = SPHIQueryInfoFree(pattern_info);
+ BOOST_REQUIRE(pattern_info == NULL);
}
// mainly tests cutoff score. Would more logically belong in blastoptions-cppunit.cpp,
@@ -435,8 +441,11 @@ BOOST_AUTO_TEST_CASE(testPHIBlastHitSavingParameters) {
BOOST_REQUIRE_EQUAL(28, hit_params->cutoff_score_min);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
}
diff --git a/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.ini b/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.ini
index fffa771..721cbe7 100644
--- a/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/phiblast_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: phiblast_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: phiblast_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/prelimsearch_unit_test.ini b/c++/src/algo/blast/unit_tests/api/prelimsearch_unit_test.ini
index ca0347a..b8159b9 100644
--- a/c++/src/algo/blast/unit_tests/api/prelimsearch_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/prelimsearch_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: prelimsearch_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: prelimsearch_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
; Boost doesn't support MT
diff --git a/c++/src/algo/blast/unit_tests/api/psibl2seq_unit_test.ini b/c++/src/algo/blast/unit_tests/api/psibl2seq_unit_test.ini
index e0bac33..b4e2d4f 100644
--- a/c++/src/algo/blast/unit_tests/api/psibl2seq_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/psibl2seq_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: psibl2seq_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: psibl2seq_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/psiblast_iteration_unit_test.ini b/c++/src/algo/blast/unit_tests/api/psiblast_iteration_unit_test.ini
index d2653d8..f8a245a 100644
--- a/c++/src/algo/blast/unit_tests/api/psiblast_iteration_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/psiblast_iteration_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: psiblast_iteration_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: psiblast_iteration_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/psiblast_unit_test.ini b/c++/src/algo/blast/unit_tests/api/psiblast_unit_test.ini
index a64e9fa..da50bb7 100644
--- a/c++/src/algo/blast/unit_tests/api/psiblast_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/psiblast_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: psiblast_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: psiblast_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp
index 97de1a4..f9b146a 100644
--- a/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: pssmcreate_unit_test.cpp 439568 2014-07-01 16:13:36Z madden $
+/* $Id: pssmcreate_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1241,6 +1241,7 @@ BOOST_AUTO_TEST_CASE(testPsiLowerCaseMatrix) {
SFreqRatios* freq_ratios = _PSIMatrixFrequencyRatiosNew("blosum62");
BOOST_REQUIRE(freq_ratios != NULL);
freq_ratios = _PSIMatrixFrequencyRatiosFree(freq_ratios);
+ BOOST_REQUIRE(freq_ratios == NULL);
}
diff --git a/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.ini b/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.ini
index cff6795..ce8494d 100644
--- a/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/pssmcreate_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: pssmcreate_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: pssmcreate_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
; Disable this based on Vladimir Ivanov's report on msvc8/64 build problems on
diff --git a/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.cpp
index e1d2276..48b9d56 100644
--- a/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: pssmenginefreqratios_unit_test.cpp 464351 2015-04-08 18:18:59Z ivanov $
+/* $Id: pssmenginefreqratios_unit_test.cpp 483267 2015-10-29 16:09:03Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -151,8 +151,8 @@ BOOST_AUTO_TEST_CASE(FreqRatiosFromMsa)
continue;
}
else {
- double ref_value = NStr::StringToDouble(*ref_pt);
BOOST_REQUIRE(ref_pt != ref_data.end());
+ double ref_value = NStr::StringToDouble(*ref_pt);
BOOST_REQUIRE(fabs(ref_value - *pt) < 0.001);
ref_pt ++;
}
@@ -160,6 +160,5 @@ BOOST_AUTO_TEST_CASE(FreqRatiosFromMsa)
}
-
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.ini b/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.ini
index fb307e8..4238a62 100644
--- a/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/pssmenginefreqratios_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: pssmenginefreqratios_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: pssmenginefreqratios_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/querydata_unit_test.ini b/c++/src/algo/blast/unit_tests/api/querydata_unit_test.ini
index 1afd94d..0798254 100644
--- a/c++/src/algo/blast/unit_tests/api/querydata_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/querydata_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: querydata_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: querydata_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/queryinfo_unit_test.ini b/c++/src/algo/blast/unit_tests/api/queryinfo_unit_test.ini
index 98c97be..a0643ad 100644
--- a/c++/src/algo/blast/unit_tests/api/queryinfo_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/queryinfo_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: queryinfo_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: queryinfo_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.cpp
index b8d172a..60c5595 100644
--- a/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: redoalignment_unit_test.cpp 439568 2014-07-01 16:13:36Z madden $
+/* $Id: redoalignment_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -334,7 +334,9 @@ void CRedoAlignmentTestFixture::
BOOST_REQUIRE(query_info->contexts[0].eff_searchsp == effective_searchsp);
eff_len_opts = BlastEffectiveLengthsOptionsFree(eff_len_opts);
+ BOOST_REQUIRE(eff_len_opts == NULL);
eff_len_params = BlastEffectiveLengthsParametersFree(eff_len_params);
+ BOOST_REQUIRE(eff_len_params == NULL);
BlastExtensionParameters* ext_params=NULL;
BlastExtensionParametersNew(program, ext_options, sbp, query_info,
@@ -365,12 +367,19 @@ void CRedoAlignmentTestFixture::
BOOST_REQUIRE_MESSAGE(rv == (Int2)0, "Blast_RedoAlignmentCore failed!");
hsp_stream = BlastHSPStreamFree(hsp_stream);
+ BOOST_REQUIRE(hsp_stream == NULL);
ext_params = BlastExtensionParametersFree(ext_params);
+ BOOST_REQUIRE(ext_params == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
hit_params = BlastHitSavingParametersFree(hit_params);
+ BOOST_REQUIRE(hit_params == NULL);
scoring_params = BlastScoringParametersFree(scoring_params);
+ BOOST_REQUIRE(scoring_params == NULL);
psi_options = PSIBlastOptionsFree(psi_options);
+ BOOST_REQUIRE(psi_options == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
BOOST_REQUIRE(results && results->num_queries == 1);
BOOST_REQUIRE(*results->hitlist_array != NULL);
@@ -429,6 +438,7 @@ void CRedoAlignmentTestFixture::
}
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
}
BOOST_FIXTURE_TEST_SUITE(RedoAlignment, CRedoAlignmentTestFixture)
@@ -491,6 +501,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentWithCompBasedStats) {
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testRedoAlignmentWithConditionalAdjust) {
@@ -550,6 +561,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentWithConditionalAdjust) {
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testPSIRedoAlignmentWithCompBasedStats) {
@@ -612,6 +624,7 @@ BOOST_AUTO_TEST_CASE(testPSIRedoAlignmentWithCompBasedStats) {
kEffSearchSp, eCompositionBasedStats,
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testRedoAlignmentWithCompBasedStatsBadlyBiasedSequence) {
@@ -685,6 +698,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentWithCompBasedStatsBadlyBiasedSequence) {
kEffSearchSp, eCompositionMatrixAdjust,
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testRedoAlignmentWithSW) {
@@ -744,6 +758,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentWithSW) {
kEffSearchSp, eNoCompositionBasedStats,
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testRedoAlignmentWithCompBasedStatsAndSW) {
@@ -799,6 +814,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentWithCompBasedStatsAndSW) {
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
BOOST_AUTO_TEST_CASE(testPSIRedoAlignmentWithCompBasedStatsAndSW) {
@@ -872,6 +888,7 @@ BOOST_AUTO_TEST_CASE(testPSIRedoAlignmentWithCompBasedStatsAndSW) {
kSmithWaterman);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
// Tests following changes from Mike Gertz and Alejandro Schaffer (rev 1.14
@@ -946,6 +963,7 @@ BOOST_AUTO_TEST_CASE(testRedoAlignmentUseXdropEvalue) {
kHitListSize);
ending_hsp_list = Blast_HSPListFree(ending_hsp_list);
+ BOOST_REQUIRE(ending_hsp_list == NULL);
}
// N.B.: the absence of a testPSIRedoAlignmentWithSW is due to the fact
diff --git a/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.ini b/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.ini
index 0f5cc70..930bda9 100644
--- a/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: redoalignment_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: redoalignment_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.cpp
index 90e5fa1..94abdde 100644
--- a/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: remote_blast_unit_test.cpp 431529 2014-04-04 14:15:53Z fongah2 $
+/* $Id: remote_blast_unit_test.cpp 454692 2014-12-17 15:16:27Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,21 @@ using namespace ncbi;
using namespace ncbi::objects;
using namespace ncbi::blast;
+NCBITEST_INIT_TREE()
+{
+ CNcbiEnvironment env;
+ const string& under_valgrind = env.Get("NCBI_RUN_UNDER_VALGRIND");
+ if ( !under_valgrind.empty() ) {
+ try {
+ if (NStr::StringToBool(under_valgrind)) {
+ NCBITEST_DISABLE(CheckPrimerBlastRID);
+ }
+ } catch (const exception&) {
+ ERR_POST(Warning << "Unsupported NCBI_RUN_UNDER_VALGRIND value "
+ << under_valgrind << "; treating as false.");
+ }
+ }
+}
static int
x_CountHits(const string & rid)
diff --git a/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.ini b/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.ini
index 0af0af0..5e1c441 100644
--- a/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: remote_blast_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: remote_blast_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
; Allow additional time for the specified test units (for slow configurations)
diff --git a/c++/src/algo/blast/unit_tests/api/rps_unit_test.ini b/c++/src/algo/blast/unit_tests/api/rps_unit_test.ini
index 59dd5e3..bfb98b2 100644
--- a/c++/src/algo/blast/unit_tests/api/rps_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/rps_unit_test.ini
@@ -1,4 +1,4 @@
-; $Id: rps_unit_test.ini 464344 2015-04-08 18:15:56Z ivanov $
+; $Id: rps_unit_test.ini 454210 2014-12-11 18:20:43Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
WholeSequenceMatch = PLATFORM_BigEndian
diff --git a/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.cpp
index d4c0c28..f6e57ae 100644
--- a/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: scoreblk_unit_test.cpp 171622 2009-09-25 15:08:10Z avagyanv $
+/* $Id: scoreblk_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -102,6 +102,7 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockNucl) {
BOOST_REQUIRE_EQUAL(1, (int) sbp->reward);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
@@ -144,6 +145,7 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockProtein) {
BOOST_REQUIRE_EQUAL(11, (int) sbp->hiscore);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
BOOST_AUTO_TEST_CASE(GetScoreBlockPHI) {
@@ -199,6 +201,7 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockPHI) {
BOOST_REQUIRE_EQUAL(-1, (int)status);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
BOOST_REQUIRE(!strncmp(kErrorMsg.c_str(), blast_message->message,
kErrorMsg.size()));
@@ -225,6 +228,7 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockPHI) {
BOOST_REQUIRE(sbp->kbp[0]->H > 0);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
BOOST_AUTO_TEST_CASE(GetScoreBlockForFullyMaskedProtein) {
@@ -262,6 +266,7 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockForFullyMaskedProtein) {
BlastSetUp_MaskQuery(query_blk, query_info, filter_maskloc, kProgram);
filter_maskloc = BlastMaskLocFree(filter_maskloc);
+ BOOST_REQUIRE(filter_maskloc == NULL);
BlastScoreBlk* sbp;
@@ -283,7 +288,9 @@ BOOST_AUTO_TEST_CASE(GetScoreBlockForFullyMaskedProtein) {
BOOST_REQUIRE_EQUAL(11, (int) sbp->hiscore);
blast_message = Blast_MessageFree(blast_message);
+ BOOST_REQUIRE(blast_message == NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
}
BOOST_AUTO_TEST_CASE(BlastResFreqStdCompProteinTest) {
@@ -309,6 +316,7 @@ BOOST_AUTO_TEST_CASE(BlastResFreqStdCompProteinTest) {
BOOST_REQUIRE_EQUAL(3216, (int)BLAST_Nint(100000*stdrfp->prob[22]));
stdrfp = Blast_ResFreqFree(stdrfp);
+ BOOST_REQUIRE(stdrfp == NULL);
}
BOOST_AUTO_TEST_CASE(BlastResFreqStdCompNucleotideTest) {
@@ -332,6 +340,7 @@ BOOST_AUTO_TEST_CASE(BlastResFreqStdCompNucleotideTest) {
BOOST_REQUIRE_EQUAL(0, (int)(100*stdrfp->prob[index]));
stdrfp = Blast_ResFreqFree(stdrfp);
+ BOOST_REQUIRE(stdrfp == NULL);
}
BOOST_AUTO_TEST_CASE(EqualRewardPenaltyLHtoK)
@@ -526,6 +535,7 @@ BOOST_AUTO_TEST_CASE(NuclGappedCalc)
BOOST_REQUIRE_EQUAL(-2.0, beta);
kbp = Blast_KarlinBlkFree(kbp);
+ BOOST_REQUIRE(kbp == NULL);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.ini b/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.ini
index 56f01c4..c745408 100644
--- a/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/scoreblk_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: scoreblk_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: scoreblk_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/search_strategy_unit_test.ini b/c++/src/algo/blast/unit_tests/api/search_strategy_unit_test.ini
index 376b137..1de8ef1 100644
--- a/c++/src/algo/blast/unit_tests/api/search_strategy_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/search_strategy_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: search_strategy_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: search_strategy_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/seqinfosrc_unit_test.ini b/c++/src/algo/blast/unit_tests/api/seqinfosrc_unit_test.ini
index 7b11bfa..da27c38 100644
--- a/c++/src/algo/blast/unit_tests/api/seqinfosrc_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/seqinfosrc_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: seqinfosrc_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: seqinfosrc_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.cpp
index f711454..59f6158 100644
--- a/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqsrc_unit_test.cpp 199874 2010-08-03 17:21:21Z camacho $
+/* $Id: seqsrc_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -114,6 +114,7 @@ s_TestGetGis(BlastSeqSrc* seqsrc, const pair<string, bool>& dbinfo) {
BOOST_REQUIRE_EQUAL(gilist->data[i], gis[i]);
}
gilist = Blast_GiListFree(gilist);
+ BOOST_REQUIRE(gilist == NULL);
}
BOOST_AUTO_TEST_CASE(testGetGisSeqDb) {
@@ -185,6 +186,7 @@ BOOST_AUTO_TEST_CASE(testMultiSeqSrc) {
max_len = MAX(max_len, length);
}
itr = BlastSeqSrcIteratorFree(itr);
+ BOOST_REQUIRE(itr == NULL);
BOOST_REQUIRE_EQUAL(kNumSeqs, last_index);
avg_len /= kNumSeqs;
@@ -275,6 +277,7 @@ s_checkDbSeqSrcFunctions(BlastSeqSrc* seq_src, const char* dbname)
total_length += (Int8) length;
}
itr = BlastSeqSrcIteratorFree(itr);
+ BOOST_REQUIRE(itr == NULL);
BOOST_REQUIRE_EQUAL(kRealNumSeqs, last_index);
BOOST_REQUIRE_EQUAL(kTotLenRange, (int)total_length);
diff --git a/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.ini b/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.ini
index 8a19354..7421dfa 100644
--- a/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/seqsrc_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: seqsrc_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: seqsrc_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.cpp
index 91d670a..382b761 100644
--- a/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: setupfactory_unit_test.cpp 444369 2014-08-25 11:42:15Z ivanov $
+/* $Id: setupfactory_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -110,7 +110,9 @@ BOOST_AUTO_TEST_CASE(CreateScoreBlockMaskedSequence)
BOOST_REQUIRE(sbp != NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
}
BOOST_AUTO_TEST_CASE(CreateScoreBlockOK)
@@ -142,7 +144,9 @@ BOOST_AUTO_TEST_CASE(CreateScoreBlockOK)
BOOST_REQUIRE(sbp != NULL);
sbp = BlastScoreBlkFree(sbp);
+ BOOST_REQUIRE(sbp == NULL);
blast_seq_loc = BlastSeqLocFree(blast_seq_loc);
+ BOOST_REQUIRE(blast_seq_loc == NULL);
}
diff --git a/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.ini b/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.ini
index 8d16eca..57f1259 100644
--- a/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/setupfactory_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: setupfactory_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: setupfactory_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/split_query_unit_test.ini b/c++/src/algo/blast/unit_tests/api/split_query_unit_test.ini
index fcbb5e4..c227b44 100644
--- a/c++/src/algo/blast/unit_tests/api/split_query_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/split_query_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: split_query_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: split_query_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.ini b/c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.ini
index fba6ac9..3880f9e 100644
--- a/c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: subj_ranges_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: subj_ranges_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/traceback_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/traceback_unit_test.cpp
index fcadc66..8917818 100644
--- a/c++/src/algo/blast/unit_tests/api/traceback_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/traceback_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: traceback_unit_test.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: traceback_unit_test.cpp 462040 2015-03-16 13:14:29Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -196,6 +196,7 @@ BOOST_AUTO_TEST_CASE(testHSPUpdateWithTraceback) {
new_hsp = Blast_HSPFree(new_hsp);
BOOST_REQUIRE(new_hsp == NULL);
gap_align = BLAST_GapAlignStructFree(gap_align);
+ BOOST_REQUIRE(gap_align == NULL);
}
BOOST_AUTO_TEST_CASE(testBLASTNTraceBack) {
@@ -323,7 +324,9 @@ BOOST_AUTO_TEST_CASE(testBLASTNTraceBack) {
}
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
BOOST_AUTO_TEST_CASE(testBLASTNTraceBackLargeXDrop) {
@@ -457,7 +460,9 @@ BOOST_AUTO_TEST_CASE(testBLASTNTraceBackLargeXDrop) {
}
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
BOOST_AUTO_TEST_CASE(testBLASTPTraceBack) {
@@ -579,7 +584,9 @@ BOOST_AUTO_TEST_CASE(testBLASTPTraceBack) {
}
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
BOOST_AUTO_TEST_CASE(testTBLASTNTraceBack) {
@@ -727,7 +734,9 @@ BOOST_AUTO_TEST_CASE(testTBLASTNTraceBack) {
}
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
BOOST_AUTO_TEST_CASE(testNoHSPEvalueCutoffBeforeLink) {
@@ -792,8 +801,11 @@ BOOST_AUTO_TEST_CASE(testNoHSPEvalueCutoffBeforeLink) {
kProgramType, ext_options, FALSE, 1, writer);
hit_options = BlastHitSavingOptionsFree(hit_options);
+ BOOST_REQUIRE(hit_options == NULL);
scoring_options = BlastScoringOptionsFree(scoring_options);
+ BOOST_REQUIRE(scoring_options == NULL);
ext_options = BlastExtensionOptionsFree(ext_options);
+ BOOST_REQUIRE(ext_options == NULL);
// needed after tie-breaking algorithm for scores was changed in
// ScoreCompareHSP (blast_hits.c, revision 1.139)
Blast_HSPListSortByScore(hsp_list);
@@ -922,7 +934,9 @@ BOOST_AUTO_TEST_CASE(testFilterBlastResults_QueryCov) {
BOOST_REQUIRE_EQUAL(k_num_hsps_filtered, hsp_list->hspcnt);
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
@@ -1027,7 +1041,9 @@ BOOST_AUTO_TEST_CASE(testFilterBlastResults_MaxHsps) {
BOOST_REQUIRE_EQUAL(k_num_hsps_filtered, hsp_list->hspcnt);
results = Blast_HSPResultsFree(results);
+ BOOST_REQUIRE(results == NULL);
seq_src = BlastSeqSrcFree(seq_src);
+ BOOST_REQUIRE(seq_src == NULL);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/c++/src/algo/blast/unit_tests/api/traceback_unit_test.ini b/c++/src/algo/blast/unit_tests/api/traceback_unit_test.ini
index 77d983e..9766920 100644
--- a/c++/src/algo/blast/unit_tests/api/traceback_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/traceback_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: traceback_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: traceback_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp
index e6ccf0e..1434f34 100644
--- a/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: tracebacksearch_unit_test.cpp 347872 2011-12-21 17:13:15Z maning $
+/* $Id: tracebacksearch_unit_test.cpp 457458 2015-01-23 12:27:33Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -346,6 +346,57 @@ BOOST_AUTO_TEST_CASE(Traceback) {
BOOST_REQUIRE(use_these.empty());
}
+// Traceback without Seq-align
+BOOST_AUTO_TEST_CASE(SimpleTraceback)
+{
+ // Build uniform search factory, get options
+ CRef<ISearchFactory> sf(new CLocalSearchFactory);
+ CRef<CBlastOptionsHandle> opth(&* sf->GetOptions(eBlastp));
+
+ // Get a SeqDB and a query factory... This uses two SeqDB
+ // objects in the gi_list case, so that it is possible to
+ // fetch the query, which is not in the GI list.
+
+ CRef<CSeqDB> query_seqdb(new CSeqDB("nr", CSeqDB::eProtein));
+ CRef<CSeqDB> subject_seqdb;
+
+ subject_seqdb = query_seqdb;
+
+ CSeq_id query("gi|54607139");
+ auto_ptr<SSeqLoc> sl(CTestObjMgr::Instance().CreateSSeqLoc(query));
+ TSeqLocVector qv;
+ qv.push_back(*sl);
+ CRef<IQueryFactory> qf(new CObjMgr_QueryFactory(qv));
+
+ // Note that the traceback code will (in some cases) modify
+ // the options object.
+
+ CRef<CBlastOptions>
+ opts(& const_cast<CBlastOptions&>(opth->GetOptions()));
+
+ // Construct false HSPs.
+ CRef< CStructWrapper<BlastHSPStream> >
+ hsps(x_GetSampleHspStream(opts, *subject_seqdb));
+
+ // Now to do the traceback..
+
+ // Build the object itself
+ CRef<CBlastTracebackSearch> tbs;
+
+ BOOST_REQUIRE(subject_seqdb.NotEmpty());
+ CBlastSeqSrc seq_src = SeqDbBlastSeqSrcInit(subject_seqdb);
+ CRef<blast::IBlastSeqInfoSrc> seq_info_src(new blast::CSeqDbSeqInfoSrc(subject_seqdb));
+ tbs.Reset(new CBlastTracebackSearch(qf, opts, seq_src.Get(), seq_info_src, hsps));
+
+ BlastHSPResults* hsp = tbs->RunSimple();
+
+ BOOST_REQUIRE_EQUAL(1, (int)hsp->num_queries);
+
+ BlastHitList* hitlist = hsp->hitlist_array[0];
+
+ BOOST_REQUIRE_EQUAL(1, (int)hitlist->hsplist_count);
+}
+
BOOST_AUTO_TEST_CASE(TracebackWithPssm_AndWarning) {
// read the pssm
const string kPssmFile("data/pssm_zero_fratios.asn");
diff --git a/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.ini b/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.ini
index d7480a8..0eb04cf 100644
--- a/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: tracebacksearch_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: tracebacksearch_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/uniform_search_unit_test.ini b/c++/src/algo/blast/unit_tests/api/uniform_search_unit_test.ini
index b1f8ff8..4aff72c 100644
--- a/c++/src/algo/blast/unit_tests/api/uniform_search_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/uniform_search_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: uniform_search_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: uniform_search_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.cpp b/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.cpp
index 35fbfb4..336d11d 100644
--- a/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: version_reference_unit_test.cpp 460402 2015-02-26 19:44:33Z ivanov $
+/* $Id: version_reference_unit_test.cpp 484536 2015-11-12 16:04:07Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -43,8 +43,8 @@ BOOST_AUTO_TEST_SUITE(version_reference)
BOOST_AUTO_TEST_CASE(testVersion) {
const int kMajor = 2;
- const int kMinor = 2;
- const int kPatch = 31;
+ const int kMinor = 3;
+ const int kPatch = 0;
blast::CBlastVersion v;
BOOST_REQUIRE_EQUAL(kMajor, v.GetMajor());
BOOST_REQUIRE_EQUAL(kMinor, v.GetMinor());
diff --git a/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.ini b/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.ini
index 371880a..a2db3e1 100644
--- a/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.ini
+++ b/c++/src/algo/blast/unit_tests/api/version_reference_unit_test.ini
@@ -1,3 +1,3 @@
-; $Id: version_reference_unit_test.ini 464342 2015-04-08 18:14:49Z ivanov $
+; $Id: version_reference_unit_test.ini 454176 2014-12-11 16:00:59Z camacho $
[UNITTESTS_DISABLE]
GLOBAL = OS_Solaris
diff --git a/c++/src/algo/blast/unit_tests/blast_format/blastfmtutil_unit_test.cpp b/c++/src/algo/blast/unit_tests/blast_format/blastfmtutil_unit_test.cpp
index 98e05ec..253e631 100644
--- a/c++/src/algo/blast/unit_tests/blast_format/blastfmtutil_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/blast_format/blastfmtutil_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastfmtutil_unit_test.cpp 457065 2015-01-20 15:11:15Z ivanov $
+/* $Id: blastfmtutil_unit_test.cpp 456661 2015-01-14 15:22:43Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/algo/blast/unit_tests/blast_format/seqalignfilter_unit_test.cpp b/c++/src/algo/blast/unit_tests/blast_format/seqalignfilter_unit_test.cpp
index a63280d..8b68dd4 100644
--- a/c++/src/algo/blast/unit_tests/blast_format/seqalignfilter_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/blast_format/seqalignfilter_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqalignfilter_unit_test.cpp 401131 2013-05-28 18:34:25Z grichenk $
+/* $Id: seqalignfilter_unit_test.cpp 482678 2015-10-26 14:19:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -152,12 +152,12 @@ static bool s_AreListsEqual(list<TGi>& list1, list<TGi>& list2)
/////////////////////////////////////////////////////////////////////////////
// Vector-based static helper functions
-static bool s_IsGiInVector(TGi gi, vector<int>& vec_gis)
+static bool s_IsGiInVector(TGi gi, vector<TGi>& vec_gis)
{
- return binary_search(vec_gis.begin(), vec_gis.end(), GI_TO(int, gi));
+ return binary_search(vec_gis.begin(), vec_gis.end(), gi);
}
-static bool s_GetFilteredGiList(CRef<CSeq_align> sa, vector<int>& vec_all_gis,
+static bool s_GetFilteredGiList(CRef<CSeq_align> sa, vector<TGi>& vec_all_gis,
list<TGi>& list_sa_filtered)
{
list<TGi> list_sa_full;
@@ -195,8 +195,8 @@ s_Check_GiListConsistency(CRef<CSeq_align> /*sa_orig*/,
static void s_Check_GiEquivalenceInDB(TGi gi1, TGi gi2, CRef<CSeqDB> db)
{
int oid1 = -1, oid2 = -1;
- db->GiToOid(GI_TO(int, gi1), oid1);
- db->GiToOid(GI_TO(int, gi2), oid2);
+ db->GiToOid(gi1, oid1);
+ db->GiToOid(gi2, oid2);
BOOST_REQUIRE(oid1 > 0);
BOOST_REQUIRE(oid2 > 0);
@@ -207,7 +207,7 @@ static void s_Check_GiEquivalenceInDB(TGi gi1, TGi gi2, CRef<CSeqDB> db)
// Pre-processing and testing individual seqaligns
static void s_DoConsistencyCheck(CRef<CSeq_align> sa_orig, CRef<CSeq_align> sa_new,
- vector<int>& vec_all_gis)
+ vector<TGi>& vec_all_gis)
{
list<TGi> list_orig_filtered;
list<TGi> list_new, list_new_filtered;
@@ -308,7 +308,7 @@ BOOST_AUTO_TEST_CASE(s_TestDBBasedFiltering)
CSeq_align_set aln_filtered;
s_LoadSeqAlignsFromFile(aln_filtered, fname_out);
- vector<int> vec_gis; // sorted vector of all available gi's
+ vector<TGi> vec_gis; // sorted vector of all available gi's
filter.ReadGiVector(fname_gis, vec_gis, true);
ITERATE(CSeq_align_set::Tdata, iter, aln_all.Get())
diff --git a/c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp b/c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp
index f671b8b..7dc2042 100644
--- a/c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp
+++ b/c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdb_unit_test.cpp 459515 2015-02-19 13:28:03Z ivanov $
+/* $Id: seqdb_unit_test.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
* Unit test.
*
*/
-
+#define NCBI_TEST_APPLICATION
#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/seqdbexpert.hpp>
#include <objtools/blast/seqdb_reader/column_reader.hpp>
@@ -92,7 +92,7 @@ static void s_TestPartialAmbigRange(CSeqDB & db, int oid, int begin, int end)
db.RetAmbigSeq(& slice);
}
-static void s_TestPartialAmbig(CSeqDB & db, int nt_gi)
+static void s_TestPartialAmbig(CSeqDB & db, TGi nt_gi)
{
int oid(-1);
bool success = db.GiToOid(nt_gi, oid);
@@ -839,7 +839,7 @@ BOOST_AUTO_TEST_CASE(TranslateIdents)
CSeqDB nr("nr", CSeqDB::eProtein);
- Uint4 gi_list[] = {
+ TGi gi_list[] = {
329847, 737263, 1708889, 2612955, 2982661, 3115393,
3318935, 3930059, 4868071, 6573653, 7530437, 9657431,
9951219, 12698889
@@ -857,17 +857,18 @@ BOOST_AUTO_TEST_CASE(TranslateIdents)
394, 174
};
- Uint4 L_gi = Uint4(sizeof(gi_list) / sizeof(gi_list[0]));
- Uint4 L_pig = Uint4(sizeof(pig_list) / sizeof(pig_list[0]));
- Uint4 L_len = Uint4(sizeof(len_list) / sizeof(len_list[0]));
+ size_t L_gi = ArraySize(gi_list);
+ size_t L_pig = ArraySize(pig_list);
+ size_t L_len = ArraySize(len_list);
// In case of hand-editing
BOOST_REQUIRE((L_gi == L_len) && (L_len == L_pig));
- for(Uint4 i = 0; i<L_gi; i++) {
- int arr_gi(0), arr_pig(0), arr_len(0),
- gi2pig(0), gi2oid(0), pig2gi(0), pig2oid(0),
- oid2len(0), oid2pig(0), oid2gi(0),
+ for(size_t i = 0; i<L_gi; i++) {
+ TGi arr_gi = ZERO_GI, pig2gi = ZERO_GI, oid2gi = ZERO_GI;
+ int arr_pig(0), arr_len(0),
+ gi2pig(0), gi2oid(0), pig2oid(0),
+ oid2len(0), oid2pig(0),
pig2gi2oid(0);
bool b1,b2,b3,b4,b5,b6,b7;
@@ -947,23 +948,23 @@ BOOST_AUTO_TEST_CASE(StringIdentSearch)
// Each set of strings should produce a set of GIs.
- Uint4 * gi_list[NUM_ITEMS];
+ TGi * gi_list[NUM_ITEMS];
- Uint4 g0[] =
+ TGi g0[] =
{ 32894304, 32894290, 32894276, 32894262, 32894248,
32894234, 32894220, 32894206, 32894192, 32894178,
32894164, 32894150, 32894136, 32894122, 32894108,
32894066, 32894052, 32894038, 32894024, 32894010,
0 };
- Uint4 g1[] =
+ TGi g1[] =
{ 129295, 0 };
- Uint4 g2[] =
+ TGi g2[] =
{ 433552084, 433552085, 0 };
- Uint4 g3[] =
+ TGi g3[] =
{ 433552084, 433552085, 0 };
- Uint4 g4[] =
+ TGi g4[] =
{ 157831779, 0 };
- Uint4 g5[] =
+ TGi g5[] =
{ 157878050, 28948349, 0 };
gi_list[0] = g0;
@@ -989,9 +990,9 @@ BOOST_AUTO_TEST_CASE(StringIdentSearch)
len_list[4] = l4;
len_list[5] = l5;
- Uint4 L_gi = Uint4(sizeof(gi_list) / sizeof(gi_list[0]));
- Uint4 L_str = Uint4(sizeof(gi_list) / sizeof(gi_list[0]));
- Uint4 L_len = Uint4(sizeof(len_list) / sizeof(len_list[0]));
+ size_t L_gi = ArraySize(gi_list);
+ size_t L_str = ArraySize(gi_list);
+ size_t L_len = ArraySize(len_list);
// Verify lengths in case of typo.
@@ -1006,7 +1007,7 @@ BOOST_AUTO_TEST_CASE(StringIdentSearch)
set<int> exp_len;
set<int> oid_len;
- for(Uint4 * gip = gi_list[i]; *gip; gip++) {
+ for(TGi * gip = gi_list[i]; *gip; gip++) {
int oid1(-1);
bool worked = nr.GiToOid(*gip, oid1);
@@ -1084,7 +1085,7 @@ BOOST_AUTO_TEST_CASE(AmbigBioseq)
const char * dbname = "nt";
bool is_prot = false;
- int gi = 12831944;
+ TGi gi = 12831944;
CNcbiOstrstream oss_fn;
oss_fn << "." << dbname << "." << gi;
@@ -1566,8 +1567,8 @@ BOOST_AUTO_TEST_CASE(OidRanges)
BOOST_AUTO_TEST_CASE(GiListOidRange)
{
- int low_gi = 20*1000*1000;
- int high_gi = 30*1000*1000;
+ TGi low_gi = 20*1000*1000;
+ TGi high_gi = 30*1000*1000;
int low_oid = 50;
int high_oid = 150;
@@ -1603,7 +1604,7 @@ BOOST_AUTO_TEST_CASE(GiListOidRange)
ITERATE(list< CRef<CSeq_id> >, seqid, ids) {
if ((**seqid).IsGi()) {
- int gi = GI_TO(int, (**seqid).GetGi());
+ TGi gi = (**seqid).GetGi();
if ((gi > low_gi) && (gi < high_gi)) {
gi_in_range = true;
@@ -1744,7 +1745,7 @@ BOOST_AUTO_TEST_CASE(CSeqDBFileGiList_GetGis)
// Read using CSeqDBFileGiList
CSeqDBFileGiList seqdbgifile(kFileName);
- vector<int> gis;
+ vector<TGi> gis;
seqdbgifile.GetGiList(gis);
BOOST_REQUIRE_EQUAL((size_t) seqdbgifile.GetNumGis(), gis.size());
sort(gis.begin(), gis.end());
@@ -1754,13 +1755,13 @@ BOOST_AUTO_TEST_CASE(CSeqDBFileGiList_GetGis)
ifstream gifile(fn.c_str());
BOOST_REQUIRE(gifile);
- vector<int> reference;
+ vector<TGi> reference;
reference.reserve(gis.size());
while ( !gifile.eof() ) {
- int gi(-1); // gis can't be negative
- gifile >> gi;
- if (gi == -1) break;
- reference.push_back(gi);
+ Int8 tgi = -1; // gis can't be negative
+ gifile >> tgi;
+ if (tgi == -1) break;
+ reference.push_back(GI_FROM(Int8, tgi));
}
sort(reference.begin(), reference.end());
BOOST_REQUIRE_EQUAL(reference.size(), gis.size());
@@ -1780,7 +1781,7 @@ BOOST_AUTO_TEST_CASE(TwoGiListsOneVolume)
dbs.push_back("Test/baylor_wgs_contigs.01");
dbs.push_back(dbs[0] + " " + dbs[1]);
- vector< vector<int> > gis(dbs.size());
+ vector< vector<TGi> > gis(dbs.size());
vector< vector<string> > volumes(dbs.size());
for(int i = 0; i < (int)dbs.size(); i++) {
@@ -1803,7 +1804,7 @@ BOOST_AUTO_TEST_CASE(TwoGiListsOneVolume)
BOOST_REQUIRE(volumes[0] == volumes[2]);
BOOST_REQUIRE_EQUAL(gis[0].size() + gis[1].size(), gis[2].size());
- vector<int> zero_one(gis[0]);
+ vector<TGi> zero_one(gis[0]);
zero_one.insert(zero_one.end(), gis[1].begin(), gis[1].end());
sort(zero_one.begin(), zero_one.end());
@@ -1815,11 +1816,11 @@ BOOST_AUTO_TEST_CASE(TwoGiListsOneVolume)
BOOST_AUTO_TEST_CASE(GetTaxIDs_gi_to_taxid)
{
- int gi1a = 446106212;
+ TGi gi1a = 446106212;
int tax1 = 1386;
- int gi2a = 494110381;
- int gi2b = 30172867;
+ TGi gi2a = 494110381;
+ TGi gi2b = 30172867;
int tax2a = 1678;
int tax2b = 206672;
@@ -1836,7 +1837,7 @@ BOOST_AUTO_TEST_CASE(GetTaxIDs_gi_to_taxid)
BOOST_REQUIRE(oid1 != oid2);
- map<int, int> gi2taxid;
+ map<TGi, int> gi2taxid;
db.GetTaxIDs(oid1, gi2taxid);
BOOST_REQUIRE_EQUAL((int)gi2taxid.size(), 44);
@@ -1860,7 +1861,7 @@ BOOST_AUTO_TEST_CASE(GetTaxIDs_gi_to_taxid)
BOOST_AUTO_TEST_CASE(GetLeafTaxIDs_gi_to_taxid_set)
{
- int gi1a = 446106212;
+ TGi gi1a = 446106212;
int tax1[] = {
1386,
1392,
@@ -1869,7 +1870,7 @@ BOOST_AUTO_TEST_CASE(GetLeafTaxIDs_gi_to_taxid_set)
1234146
};
- int gi2a = 494110381;
+ TGi gi2a = 494110381;
int tax2a[] = {
1678,
216816,
@@ -1890,7 +1891,7 @@ BOOST_AUTO_TEST_CASE(GetLeafTaxIDs_gi_to_taxid_set)
BOOST_REQUIRE(oid1 != oid2);
- map<int, set<int> > gi2taxids;
+ map<TGi, set<int> > gi2taxids;
set<int> expected1;
expected1.insert(BEGIN(tax1), END(tax1));
@@ -1937,7 +1938,7 @@ BOOST_AUTO_TEST_CASE(GetLeafTaxIDs_gi_to_taxid_set)
BOOST_AUTO_TEST_CASE(GetTaxIDs_vector_of_taxids)
{
- int gi1a = 446106212;
+ TGi gi1a = 446106212;
int tax1[] = {
198094,
261594,
@@ -1985,7 +1986,7 @@ BOOST_AUTO_TEST_CASE(GetTaxIDs_vector_of_taxids)
1437442
};
- int gi2a = 494110381;
+ TGi gi2a = 494110381;
int tax2a[] = {
206672,
205913,
@@ -2073,12 +2074,12 @@ BOOST_AUTO_TEST_CASE(GetTaxIDs_vector_of_taxids)
BOOST_AUTO_TEST_CASE(GetLeafTaxIDs_vector_of_taxids)
{
- int gi1a = 446106212;
+ TGi gi1a = 446106212;
int tax1[] = {
1386, 1392, 1396, 1428, 1234146
};
- int gi2a = 494110381;
+ TGi gi2a = 494110381;
int tax2a[] = {
1678, 216816, 469594, 1263059
};
@@ -2361,7 +2362,9 @@ BOOST_AUTO_TEST_CASE(ExpertIdBounds)
// Tests ID bound functions.
{
- int low(0), high(0), count(0);
+ TGi low(ZERO_GI);
+ TGi high(ZERO_GI);
+ int count(0);
nr.GetGiBounds(& low, & high, & count);
@@ -2481,7 +2484,7 @@ BOOST_AUTO_TEST_CASE(GlobalMemoryBound)
class CSimpleGiList : public CSeqDBGiList {
public:
- CSimpleGiList(const vector<int> & gis)
+ CSimpleGiList(const vector<TGi> & gis)
{
for(size_t i = 0; i < gis.size(); i++) {
m_GisOids.push_back(gis[i]);
@@ -2492,23 +2495,23 @@ public:
BOOST_AUTO_TEST_CASE(IntersectionGiList)
{
- vector<int> a3; // multiples of 3 from 0..500
- vector<int> a5; // multiples of 5 from 0..500
+ vector<TGi> a3; // multiples of 3 from 0..500
+ vector<TGi> a5; // multiples of 5 from 0..500
// The number 41 is added to the front of one set and the end of
// the other to verify that the code computing the intersection
// correctly sorts its inputs.
- int special = 41;
+ TGi special = GI_FROM(int, 41);
// Add to start of a3
a3.push_back(special);
for(int i = 0; (i*3) < 500; i++) {
- a3.push_back(i*3);
+ a3.push_back(GI_FROM(int, i*3));
if (i*5 < 500) {
- a5.push_back(i*5);
+ a5.push_back(GI_FROM(int, i*5));
}
}
@@ -2521,10 +2524,11 @@ BOOST_AUTO_TEST_CASE(IntersectionGiList)
CIntersectionGiList both(gi3, a5);
for(int i = 0; i < 500; i++) {
- if (((i % 15) == 0) || (i == special)) {
- BOOST_REQUIRE(true == both.FindGi(i));
+ TGi gi = GI_FROM(int, i);
+ if (((i % 15) == 0) || (gi == special)) {
+ BOOST_REQUIRE(true == both.FindGi(gi));
} else {
- BOOST_REQUIRE(false == both.FindGi(i));
+ BOOST_REQUIRE(false == both.FindGi(gi));
}
}
}
@@ -2532,29 +2536,29 @@ BOOST_AUTO_TEST_CASE(IntersectionGiList)
BOOST_AUTO_TEST_CASE(IntersectionNegGiList)
{
- vector<int> a3; // multiples of 3 from 0..500
- vector<int> a5; // multiples of 5 from 0..500
+ vector<TGi> a3; // multiples of 3 from 0..500
+ vector<TGi> a5; // multiples of 5 from 0..500
// The number 41 is added to the front of one set and the end of
// the other to verify that the code computing the intersection
// correctly sorts its inputs.
- int special = 41;
+ TGi special = GI_FROM(int, 41);
// Add to start of a3
a3.push_back(special);
for(int i = 0; (i*3) < 500; i++) {
- a3.push_back(i*3);
+ a3.push_back(GI_FROM(int, i*3));
if (i*5 < 500) {
- a5.push_back(i*5);
+ a5.push_back(GI_FROM(int, i*5));
}
}
// Add to end of a5
a5.push_back(special);
- a5.push_back(1000);
+ a5.push_back(GI_FROM(int, 1000));
CSeqDBNegativeList gi3;
gi3.SetGiList(a3);
@@ -2574,7 +2578,7 @@ BOOST_AUTO_TEST_CASE(IntersectionNegGiList)
// all elements in the intersect list have to be found in a5
for(int i = 0; i < both.GetNumGis(); i++) {
- const int gi = both.GetKey<int>(i);
+ const TGi gi = both.GetKey<TGi>(i);
BOOST_REQUIRE(std::find(a5.begin(), a5.end(), gi) != a5.end());
}
}
@@ -2866,7 +2870,7 @@ public:
{
for(const char ** p = str; *p; p++) {
if ((*p)[0] == '#') {
- m_GisOids.push_back(atoi((*p) + 1));
+ m_GisOids.push_back(GI_FROM(int, atoi((*p) + 1)));
} else {
string acc(*p);
string str_id = SeqDB_SimplifyAccession(acc);
@@ -2895,7 +2899,7 @@ BOOST_AUTO_TEST_CASE(SeqIdList)
"NP_854766.1",
"NP_688815.1",
"BAB37428.1",
- "YP_651583.1",
+ "WP_002211004.1",
"XP_645408.1",
"AAG07133.1",
NULL };
@@ -2935,7 +2939,7 @@ BOOST_AUTO_TEST_CASE(OidToGiLookup)
{
CSeqDB dbp("data/ranges/twenty", CSeqDB::eProtein);
for(int oid = 0; dbp.CheckOrFindOID(oid); oid++) {
- int gi = dbp.GetSeqGI(oid);
+ TGi gi = dbp.GetSeqGI(oid);
int the_oid;
BOOST_REQUIRE( dbp.GiToOid(gi, the_oid));
BOOST_REQUIRE_EQUAL(oid, the_oid);
@@ -2943,7 +2947,7 @@ BOOST_AUTO_TEST_CASE(OidToGiLookup)
CSeqDB dbn("data/seqn", CSeqDB::eNucleotide);
for(int oid = 0; dbp.CheckOrFindOID(oid); oid++) {
- int gi = dbp.GetSeqGI(oid);
+ TGi gi = dbp.GetSeqGI(oid);
int the_oid;
BOOST_REQUIRE( dbp.GiToOid(gi, the_oid));
BOOST_REQUIRE_EQUAL(oid, the_oid);
@@ -3101,9 +3105,9 @@ BOOST_AUTO_TEST_CASE(EmptyVolume)
BOOST_REQUIRE_THROW(db.GetSeqLengthApprox(0), CSeqDBException);
BOOST_REQUIRE_THROW(db.GetHdr(0), CSeqDBException);
- map<int, int> gi_to_taxid;
+ map<TGi, int> gi_to_taxid;
vector<int> taxids;
- vector<int> gis;
+ vector<TGi> gis;
BOOST_REQUIRE_THROW(db.GetTaxIDs(0, gi_to_taxid), CSeqDBException);
BOOST_REQUIRE_THROW(db.GetTaxIDs(0, taxids), CSeqDBException);
@@ -3172,7 +3176,8 @@ CSeqDBException);
BOOST_REQUIRE_EQUAL(db.GetGiList(), (CSeqDBGiList*)NULL);
BOOST_REQUIRE_NO_THROW(db.SetMemoryBound(1024*1024*512));
- int pig(123), gi(129295);
+ int pig(123);
+ TGi gi = 129295;
string acc("P01013");
CSeq_id seqid("sp|P01013|OVALX_CHICK");
@@ -3294,14 +3299,14 @@ BOOST_AUTO_TEST_CASE(GetSequenceAsString)
string nucl, prot;
- int nucl_gi = 46071107;
+ TGi nucl_gi = 46071107;
string nucl_str = ("AAGCTCTTCATTGATGGTAGAGAGCCTATTAACAGGCAAC"
"AGTCAATGCTCCAAAGTCCAAACAAGATTACCTGTGCAAA"
"GAACTTGCAGTGTAACAAACCCCNTTCACGGCCAGAAGTA"
"TTTGCAACAATGTTGAAAGTCCTTCTGGCAGAGGAGGAGT"
"CTAAT");
- int prot_gi = 43914529;
+ TGi prot_gi = 43914529;
string prot_str = "MINKSGYEAKYKKSIKNNEEFWRKEGKRITWIKPYKKIKNVRYS";
int nucl_oid(-1), prot_oid(-1);
@@ -3369,15 +3374,15 @@ static void s_MapAllGis(CSeqDB & db,
int & total)
{
total = 0;
- vector<int> gis;
+ vector<TGi> gis;
for(int oid = 0; db.CheckOrFindOID(oid); oid++) {
gis.clear();
db.GetGis(oid, gis, false);
- ITERATE(vector<int>, iter, gis) {
- s_ModifyMap(m, *iter, change, total);
+ ITERATE(vector<TGi>, iter, gis) {
+ s_ModifyMap(m, GI_TO(int, *iter), change, total);
}
}
}
@@ -3460,7 +3465,7 @@ BOOST_AUTO_TEST_CASE(NegativeGiList)
// database, I want to check that it affects the header data that
// is reported from SeqDB::GetHdr().
- int gi1 = 27360885;
+ TGi gi1 = 27360885;
int oid1 = -1;
bool ok = have_got.GiToOid(gi1, oid1);
@@ -3501,7 +3506,7 @@ BOOST_AUTO_TEST_CASE(NegativeListNr)
bool found = have_got.GiToOid(gis[0], oid);
BOOST_REQUIRE(found);
- vector<int> gis_w, gis_wo;
+ vector<TGi> gis_w, gis_wo;
have_got.GetGis(oid, gis_w);
have_not.GetGis(oid, gis_wo);
@@ -3535,7 +3540,7 @@ BOOST_AUTO_TEST_CASE(NegativeListSwissprot)
bool found = have_got.GiToOid(gis[0], oid);
BOOST_REQUIRE(found);
- vector<int> gis_w, gis_wo;
+ vector<TGi> gis_w, gis_wo;
have_got.GetGis(oid, gis_w);
have_not.GetGis(oid, gis_wo);
@@ -4197,7 +4202,7 @@ BOOST_AUTO_TEST_CASE(TestOidNotFoundWithUserAliasFileAndGiList)
string blastdb_name = alias_file_tmpfile.GetFileName() + ".pal";
CFileDeleteAtExit::Add(gilist_name);
CFileDeleteAtExit::Add(blastdb_name);
- const int kGiIncluded = 129295;
+ const TGi kGiIncluded = 129295;
{{
ofstream stream(gilist_name.c_str());
@@ -4215,12 +4220,12 @@ BOOST_AUTO_TEST_CASE(TestOidNotFoundWithUserAliasFileAndGiList)
CRef<CSeqDB> db(new CSeqDB(alias_file_tmpfile.GetFileName(),
CSeqDB::eProtein));
vector<int> oids;
- db->AccessionToOids(NStr::IntToString(kGiIncluded), oids);
+ db->AccessionToOids(NStr::NumericToString(kGiIncluded), oids);
BOOST_REQUIRE_EQUAL(1U, oids.size());
- int gi2search = 129; // shouldn't be found
+ TGi gi2search = 129; // shouldn't be found
oids.clear();
- db->AccessionToOids(NStr::IntToString(gi2search), oids);
+ db->AccessionToOids(NStr::NumericToString(gi2search), oids);
BOOST_CHECK_EQUAL(0U, oids.size());
/*
list< CRef< CSeq_id> > filtered_ids = db->GetSeqIDs(oids[0]);
@@ -4259,12 +4264,12 @@ BOOST_AUTO_TEST_CASE(CWgsTrimmerShortExampleNoRemove)
{
const string wgs_dbs = "WGS/AB/D/wgs.ABDC WGS/AA/D/wgs.AADN";
const string gis_in_wgs_results = "data/wb1206.gis.txt";
- vector<int> gis;
+ vector<TGi> gis;
SeqDB_ReadGiList(gis_in_wgs_results, gis);
CAutoEnvironmentVariable env_var("WGS_GILIST_DIR", "data");
CWgsDbTrimmer trimmer(wgs_dbs);
- ITERATE(vector<int>, gi, gis) {
+ ITERATE(vector<TGi>, gi, gis) {
trimmer.AddGi(*gi);
}
const string kExpectedResult = "WGS/AA/D/wgs.AADN WGS/AB/D/wgs.ABDC";
@@ -4277,13 +4282,13 @@ BOOST_AUTO_TEST_CASE(CWgsTrimmerShortExampleRemove)
{
const string wgs_dbs = "WGS/AB/D/wgs.ABDC WGS/AA/D/wgs.AADN";
const string gis_in_wgs_results = "data/wb1206.gis.txt";
- vector<int> gis;
+ vector<TGi> gis;
SeqDB_ReadGiList(gis_in_wgs_results, gis);
gis.erase(gis.begin()+10, gis.end());
CAutoEnvironmentVariable env_var("WGS_GILIST_DIR", "data");
CWgsDbTrimmer trimmer(wgs_dbs);
- ITERATE(vector<int>, gi, gis) {
+ ITERATE(vector<TGi>, gi, gis) {
trimmer.AddGi(*gi);
}
const string kExpectedResult = "WGS/AB/D/wgs.ABDC";
@@ -4298,13 +4303,13 @@ BOOST_AUTO_TEST_CASE(CWgsTrimmerShortExampleWithNtRemove)
{
const string wgs_dbs = "nt WGS/AB/D/wgs.ABDC WGS/AA/D/wgs.AADN";
const string gis_in_wgs_results = "data/wb1206.gis.txt";
- vector<int> gis;
+ vector<TGi> gis;
SeqDB_ReadGiList(gis_in_wgs_results, gis);
gis.erase(gis.begin()+10, gis.end());
CAutoEnvironmentVariable env_var("WGS_GILIST_DIR", "data");
CWgsDbTrimmer trimmer(wgs_dbs);
- ITERATE(vector<int>, gi, gis) {
+ ITERATE(vector<TGi>, gi, gis) {
trimmer.AddGi(*gi);
}
const string kExpectedResult = "WGS/AB/D/wgs.ABDC nt";
@@ -4338,12 +4343,12 @@ BOOST_AUTO_TEST_CASE(CWgsTrimmerLongExample)
const int orig_num_dbs = tokens.size();
tokens.clear();
- vector<int> gis;
+ vector<TGi> gis;
SeqDB_ReadGiList(gis_in_wgs_results, gis);
CAutoEnvironmentVariable env_var("WGS_GILIST_DIR", "data");
CWgsDbTrimmer trimmer(wgs_dbs);
- ITERATE(vector<int>, gi, gis) {
+ ITERATE(vector<TGi>, gi, gis) {
trimmer.AddGi(*gi);
}
diff --git a/c++/src/algo/dustmask/symdust.cpp b/c++/src/algo/dustmask/symdust.cpp
index 3f1e029..8ea454c 100644
--- a/c++/src/algo/dustmask/symdust.cpp
+++ b/c++/src/algo/dustmask/symdust.cpp
@@ -1,4 +1,4 @@
-/* $Id: symdust.cpp 416745 2013-10-30 21:04:30Z morgulis $
+/* $Id: symdust.cpp 464807 2015-04-14 16:29:40Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -295,7 +295,7 @@ void CSymDustMasker::GetMaskedLocs(
const sequence_type & seq,
std::vector< CConstRef< objects::CSeq_loc > > & locs )
{
- typedef std::vector< CConstRef< objects::CSeq_loc > > locs_type;
+ // typedef std::vector< CConstRef< objects::CSeq_loc > > locs_type;
std::auto_ptr< TMaskList > res = (*this)( seq );
locs.clear();
locs.reserve( res->size() );
diff --git a/c++/src/algo/winmask/Makefile.xalgowinmask.lib b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
index c733d20..4929aeb 100644
--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.xalgowinmask.lib 427427 2014-02-20 13:40:13Z gouriano $
+# $Id: Makefile.xalgowinmask.lib 460140 2015-02-25 13:52:50Z morgulis $
WATCHERS = morgulis dicuccio mozese2
@@ -16,7 +16,7 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
seq_masker_ostat_opt_ascii seq_masker_uset_hash seq_masker_istat_oascii \
seq_masker_ostat_opt_bin seq_masker_istat_obinary seq_masker_cache_boost \
win_mask_counts_converter win_mask_dup_table win_mask_gen_counts \
- win_mask_util win_mask_config
+ win_mask_util win_mask_config seq_masker_istat
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
diff --git a/c++/src/algo/winmask/seq_masker.cpp b/c++/src/algo/winmask/seq_masker.cpp
index a91e9af..a65dcdc 100644
--- a/c++/src/algo/winmask/seq_masker.cpp
+++ b/c++/src/algo/winmask/seq_masker.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker.cpp 435370 2014-05-15 15:50:57Z morgulis $
+/* $Id: seq_masker.cpp 464810 2015-04-14 16:29:42Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,9 +31,6 @@
*/
#include <ncbi_pch.hpp>
-#include <algorithm>
-#include <memory>
-#include <sstream>
#include <corelib/ncbi_limits.h>
@@ -49,9 +46,26 @@
#include <algo/winmask/seq_masker_istat_factory.hpp>
#include <algo/winmask/seq_masker_cache_boost.hpp>
+#include <algorithm>
+#include <memory>
+#include <sstream>
+
+
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
+#define WIN_MASK_ALGO_NAME "window-masker-algorithm"
+#define WIN_MASK_ALGO_VER_MAJOR 1
+#define WIN_MASK_ALGO_VER_MINOR 0
+#define WIN_MASK_ALGO_VER_PATCH 0
+
+//-------------------------------------------------------------------------
+CSeqMaskerVersion CSeqMasker::AlgoVersion(
+ WIN_MASK_ALGO_NAME,
+ WIN_MASK_ALGO_VER_MAJOR,
+ WIN_MASK_ALGO_VER_MINOR,
+ WIN_MASK_ALGO_VER_PATCH
+);
//-------------------------------------------------------------------------
CSeqMasker::CSeqMasker( const string & lstat_name,
@@ -150,18 +164,6 @@ CSeqMasker::DoMask(
{
ustat->total_ = 0;
auto_ptr<TMaskList> mask(new TMaskList);
-
- /* This message is confusing. Particularly because DUST later
- can still mask part of the sequence.
- */
- /*
- if( window_size > data.size() )
- {
- ERR_POST( Warning
- << "length of data is shorter than the window size" );
- }
- */
-
Uint4 cutoff_score = ustat->get_threshold();
Uint4 textend = ustat->get_textend();
Uint1 nbits = discontig ? CSeqMaskerUtil::BitCount( pattern ) : 0;
diff --git a/c++/include/common/ncbi_source_ver.h b/c++/src/algo/winmask/seq_masker_istat.cpp
similarity index 85%
copy from c++/include/common/ncbi_source_ver.h
copy to c++/src/algo/winmask/seq_masker_istat.cpp
index 82df691..bcec605 100644
--- a/c++/include/common/ncbi_source_ver.h
+++ b/c++/src/algo/winmask/seq_masker_istat.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_source_ver.h 460595 2015-02-28 05:09:57Z ucko $
+/* $Id: seq_masker_istat.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -22,7 +22,16 @@
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
+ *
+ * Authors: Aleksandr Morgulis
+ *
*/
-#define NCBI_PRODUCTION_VER 20150221
-#define NCBI_DEVELOPMENT_VER 20140721
+#include <ncbi_pch.hpp>
+
+#include <algo/winmask/seq_masker_istat.hpp>
+
+BEGIN_NCBI_SCOPE
+
+END_NCBI_SCOPE
+
diff --git a/c++/src/algo/winmask/seq_masker_istat_ascii.cpp b/c++/src/algo/winmask/seq_masker_istat_ascii.cpp
index 2407102..3bd393f 100644
--- a/c++/src/algo/winmask/seq_masker_istat_ascii.cpp
+++ b/c++/src/algo/winmask/seq_masker_istat_ascii.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_ascii.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_istat_ascii.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,7 +56,8 @@ CSeqMaskerIstatAscii::CSeqMaskerIstatAscii( const string & name,
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count )
+ Uint4 arg_use_min_count,
+ Uint4 start_line )
: CSeqMaskerIstat( arg_threshold, arg_textend,
arg_max_count, arg_use_max_count,
arg_min_count, arg_use_min_count )
@@ -68,9 +69,10 @@ CSeqMaskerIstatAscii::CSeqMaskerIstatAscii( const string & name,
string( "could not open " ) + name );
bool start = true;
- Uint4 linenum = 0UL;
+ Uint4 linenum = start_line;
Uint4 ambig_len = kMax_UI4;
string line;
+ for( Uint4 i( 0 ); i < start_line; ++i ) getline( input_stream, line );
while( input_stream )
{
@@ -78,12 +80,7 @@ CSeqMaskerIstatAscii::CSeqMaskerIstatAscii( const string & name,
getline( input_stream, line );
++linenum;
if( line.length() == 0 ) continue;
-
- if( line[0] == '#' ) {
- if( line.length() < 2 || line[1] != '#' ) continue;
- SetMetaData( line.substr( 2 ) );
- continue;
- }
+ if( line[0] == '#' ) continue;
// Check if we have a precomputed parameter.
if( line[0] == '>' )
diff --git a/c++/src/algo/winmask/seq_masker_istat_bin.cpp b/c++/src/algo/winmask/seq_masker_istat_bin.cpp
index 34e1b9f..94ee788 100644
--- a/c++/src/algo/winmask/seq_masker_istat_bin.cpp
+++ b/c++/src/algo/winmask/seq_masker_istat_bin.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_bin.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_istat_bin.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,7 +59,8 @@ CSeqMaskerIstatBin::CSeqMaskerIstatBin( const string & name,
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count )
+ Uint4 arg_use_min_count,
+ Uint4 skip )
: CSeqMaskerIstat( arg_threshold, arg_textend,
arg_max_count, arg_use_max_count,
arg_min_count, arg_use_min_count )
@@ -79,27 +80,19 @@ CSeqMaskerIstatBin::CSeqMaskerIstatBin( const string & name,
}
CNcbiIfstream in_stream( name.c_str(), IOS_BASE::binary );
+
+ {
+ char * data( new char[skip] );
+ in_stream.read( data, skip );
+ delete[] data;
+ }
+
+ streamsize adj( in_stream.tellg() );
Uint4 data;
in_stream.read( (char *)&data, sizeof( Uint4 ) );
- streamsize adj( 0 );
{
in_stream.read( (char *)&data, sizeof( Uint4 ) );
-
- if( data > 16 ) {
- adj = sizeof( Uint4 ) + data - 16;
- string md( data - 16, 0 );
- char c;
-
- for( Uint4 i( 0 ); i < data - 16; ++i ) {
- in_stream.read( &c, 1 );
- md[i] = c;
- }
-
- SetMetaData( md );
- in_stream.read( (char *)&data, sizeof( Uint4 ) );
- }
-
Uint1 us = (Uint1)data;
if( us == 0 || us > 16 )
diff --git a/c++/src/algo/winmask/seq_masker_istat_factory.cpp b/c++/src/algo/winmask/seq_masker_istat_factory.cpp
index 185f0d7..c4cf875 100644
--- a/c++/src/algo/winmask/seq_masker_istat_factory.cpp
+++ b/c++/src/algo/winmask/seq_masker_istat_factory.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_factory.cpp 359165 2012-04-11 13:45:29Z morgulis $
+/* $Id: seq_masker_istat_factory.cpp 467792 2015-05-18 11:15:48Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,6 +38,10 @@
#include <algo/winmask/seq_masker_istat_bin.hpp>
#include <algo/winmask/seq_masker_istat_obinary.hpp>
+#include <corelib/ncbifile.hpp>
+
+#include <sstream>
+
BEGIN_NCBI_SCOPE
//------------------------------------------------------------------------------
@@ -53,6 +57,152 @@ const char * CSeqMaskerIstatFactory::Exception::GetErrCodeString() const
}
//------------------------------------------------------------------------------
+static bool CheckBin(
+ string const & name, vector< string > & md, size_t & skip ) {
+ skip = 0;
+ CNcbiIfstream input_stream( name.c_str(), IOS_BASE::binary );
+
+ if( input_stream ) {
+ Uint4 word( 0 );
+ input_stream.read( (char *)&word, sizeof( word ) );
+
+ if( word == 3 ) {
+ skip = 8;
+ input_stream.read( (char *)&word, sizeof( word ) );
+ skip += word;
+ char * data( new char[word + 2] );
+ data[word] = data[word + 1] = 0;
+ input_stream.read( data, word );
+
+ for( char * d( data ); *d != 0; d += strlen( d ) + 1 ) {
+ md.push_back( string( d ) );
+ }
+
+ delete[] data;
+ return true;
+ }
+ else if( word < 3 ) return true;
+ else return false;
+ }
+
+ return false;
+}
+
+//------------------------------------------------------------------------------
+static void GetMetaDataLines(
+ string const & name, vector< string > & md, size_t & skip ) {
+ if( !CFile( name ).Exists() ) return;
+ if( CheckBin( name, md, skip ) ) return;
+ CNcbiIfstream check( name.c_str() );
+ string line;
+
+ while( check ) {
+ getline( check, line );
+
+ if( line.size() >= 2 && line[0] == '#' && line[1] == '#' ) {
+ md.push_back( line );
+ }
+ else break;
+ }
+}
+
+//------------------------------------------------------------------------------
+void ExtractStatAlgoVersion(
+ vector< string > const & md, CSeqMaskerVersion & ver ) {
+ static char const * DIGITS = "0123456789";
+ string t;
+
+ for( vector< string >::const_iterator i( md.begin() );
+ i != md.end(); ++i ) {
+ string::size_type p( i->find( ':', 2 ) ), pp;
+
+ if( p != string::npos ) {
+ if( i->substr( 2, p -2 ) ==
+ CSeqMaskerOstat::STAT_ALGO_COMPONENT_NAME ) {
+ int major = 0, minor = 0, patch = 0;
+ pp = p + 1;
+ p = i->find( '.', pp );
+ if( p == string::npos ) continue;
+ t = i->substr( pp, p - pp );
+ if( t.find_first_not_of( DIGITS ) != string::npos ) continue;
+ major = NStr::StringToInt( t );
+ pp = p + 1;
+ p = i->find( '.', pp );
+ if( p == string::npos ) continue;
+ t = i->substr( pp, p - pp );
+ if( t.find_first_not_of( DIGITS ) != string::npos ) continue;
+ minor = NStr::StringToInt( t );
+ t = i->substr( p + 1 );
+ if( t.find_first_not_of( DIGITS ) != string::npos ) continue;
+ patch = NStr::StringToInt( t );
+ ver = CSeqMaskerVersion(
+ CSeqMaskerOstat::STAT_ALGO_COMPONENT_NAME,
+ major, minor, patch );
+ return;
+ }
+ }
+ }
+}
+
+//------------------------------------------------------------------------------
+string ExtractMetaDataStr( vector< string > const & md ) {
+ for( vector< string >::const_iterator i( md.begin() );
+ i != md.end(); ++i ) {
+ string::size_type pos( i->find( ':', 2 ) );
+
+ if( pos != string::npos ) {
+ if( i->substr( 2, pos - 2 ) == "note" ) {
+ return i->substr( pos + 1 );
+ }
+ }
+ }
+
+ return "";
+}
+
+//------------------------------------------------------------------------------
+CSeqMaskerIstatFactory::EStatType CSeqMaskerIstatFactory::DiscoverStatType(
+ string const & name, vector< string > & md, size_t & skip ) {
+ GetMetaDataLines( name, md, skip );
+ CNcbiIfstream check( name.c_str() );
+
+ if( !check ) {
+ NCBI_THROW( Exception, eOpen, string( "could not open " ) + name );
+ }
+
+ if( skip > 0 ) {
+ char * buf( new char[skip] );
+ check.read( buf, skip );
+ delete[] buf;
+ }
+ else if( !md.empty() ) {
+ string line;
+ for( size_t i( 0 ); i < md.size(); ++i ) getline( check, line );
+ }
+
+ if( check ) {
+ Uint4 data = 1;
+
+ if( check.read( (char *)&data, sizeof( Uint4 ) ) ) {
+ if( data == 0 ) return eBinary;
+ if( data == 0x41414141 ) return eOAscii;
+ if( data == 1 || data == 2 ) return eOBinary;
+ return eAscii;
+ }
+ }
+
+ return eUnknown;
+}
+
+//------------------------------------------------------------------------------
+CSeqMaskerIstatFactory::EStatType CSeqMaskerIstatFactory::DiscoverStatType(
+ string const & name ) {
+ size_t skip( 0 );
+ vector< string > md;
+ return DiscoverStatType( name, md, skip );
+}
+
+//------------------------------------------------------------------------------
CSeqMaskerIstat * CSeqMaskerIstatFactory::create( const string & name,
Uint4 threshold,
Uint4 textend,
@@ -64,38 +214,56 @@ CSeqMaskerIstat * CSeqMaskerIstatFactory::create( const string & name,
{
try
{
+ size_t skip( 0 );
+ vector< string > md;
+ EStatType stat_type( DiscoverStatType( name , md, skip ) );
+ CSeqMaskerIstat * res( 0 );
+
+ switch( stat_type ) {
+ case eAscii: res = new CSeqMaskerIstatAscii(
+ name,
+ threshold, textend,
+ max_count, use_max_count,
+ min_count, use_min_count,
+ md.size() );
+ break;
+
+ case eBinary: res = new CSeqMaskerIstatBin(
+ name, threshold, textend,
+ max_count, use_max_count,
+ min_count, use_min_count,
+ skip );
+ break;
+
+ case eOAscii: res = new CSeqMaskerIstatOAscii(
+ name,
+ threshold, textend,
+ max_count, use_max_count,
+ min_count, use_min_count,
+ md.size() );
+ break;
+
+ case eOBinary: res = new CSeqMaskerIstatOBinary(
+ name,
+ threshold, textend,
+ max_count, use_max_count,
+ min_count, use_min_count,
+ use_ba, skip );
+ break;
+
+ default: NCBI_THROW(Exception, eCreateFail, "unrecognized unit counts format");
+ }
+
{
- CNcbiIfstream check( name.c_str() );
-
- if( !check )
- NCBI_THROW( Exception, eOpen,
- string( "could not open " ) + name );
-
- Uint4 data = 1;
- check.read( (char *)&data, sizeof( Uint4 ) );
-
- if( data == 0 )
- return new CSeqMaskerIstatBin( name,
- threshold, textend,
- max_count, use_max_count,
- min_count, use_min_count );
- else if( data == 0x41414141 )
- return new CSeqMaskerIstatOAscii( name,
- threshold, textend,
- max_count, use_max_count,
- min_count, use_min_count );
- else if( data == 1 || data == 2 )
- return new CSeqMaskerIstatOBinary( name,
- threshold, textend,
- max_count, use_max_count,
- min_count, use_min_count,
- use_ba );
+ string md_str( ExtractMetaDataStr( md ) );
+ CSeqMaskerVersion ver(
+ CSeqMaskerOstat::STAT_ALGO_COMPONENT_NAME, 1, 0, 0 );
+ ExtractStatAlgoVersion( md, ver );
+ res->SetStatAlgoVersion( ver );
+ if( !md_str.empty() ) res->SetMetaData( md_str );
}
- return new CSeqMaskerIstatAscii( name,
- threshold, textend,
- max_count, use_max_count,
- min_count, use_min_count );
+ return res;
}
catch( CException & e)
{
diff --git a/c++/src/algo/winmask/seq_masker_istat_oascii.cpp b/c++/src/algo/winmask/seq_masker_istat_oascii.cpp
index d42231e..5ae218e 100644
--- a/c++/src/algo/winmask/seq_masker_istat_oascii.cpp
+++ b/c++/src/algo/winmask/seq_masker_istat_oascii.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_oascii.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_istat_oascii.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,7 +63,8 @@ CSeqMaskerIstatOAscii::CSeqMaskerIstatOAscii( const string & name,
Uint4 arg_max_count,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
- Uint4 arg_use_min_count )
+ Uint4 arg_use_min_count,
+ Uint4 start_line )
: CSeqMaskerIstat( arg_threshold, arg_textend,
arg_max_count, arg_use_max_count,
arg_min_count, arg_use_min_count )
@@ -76,6 +77,7 @@ CSeqMaskerIstatOAscii::CSeqMaskerIstatOAscii( const string & name,
Uint4 linenum = 0;
string line;
+ for( Uint4 i( 0 ); i < start_line; ++i ) getline( input_stream, line );
Uint1 unit_size;
Uint4 k, roff, bc;
Uint4 t_low = 0,
@@ -191,12 +193,6 @@ CSeqMaskerIstatOAscii::CSeqMaskerIstatOAscii( const string & name,
"not enough lines to fill the values table" );
uset.add_vt_info( M, vt );
-
- if( getline( input_stream, line ) ) {
- if( line.size() > 1 && line[0] == '#' && line[1] == '#' ) {
- SetMetaData( line.substr( 2 ) );
- }
- }
}
//------------------------------------------------------------------------------
diff --git a/c++/src/algo/winmask/seq_masker_istat_obinary.cpp b/c++/src/algo/winmask/seq_masker_istat_obinary.cpp
index 9cc8b59..de9dfbe 100644
--- a/c++/src/algo/winmask/seq_masker_istat_obinary.cpp
+++ b/c++/src/algo/winmask/seq_masker_istat_obinary.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_istat_obinary.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_istat_obinary.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -74,7 +74,8 @@ CSeqMaskerIstatOBinary::CSeqMaskerIstatOBinary( const string & name,
Uint4 arg_use_max_count,
Uint4 arg_min_count,
Uint4 arg_use_min_count,
- bool arg_use_ba )
+ bool arg_use_ba,
+ Uint4 skip )
: CSeqMaskerIstat( arg_threshold, arg_textend,
arg_max_count, arg_use_max_count,
arg_min_count, arg_use_min_count )
@@ -86,6 +87,12 @@ CSeqMaskerIstatOBinary::CSeqMaskerIstatOBinary( const string & name,
NCBI_THROW( Exception, eStreamOpenFail,
string( "could not open " ) + name );
+ {
+ char * data( new char[skip] );
+ input_stream.read( data, skip );
+ delete[] data;
+ }
+
Uint4 word;
Uint1 unit_size;
Uint4 k, roff, bc;
@@ -202,19 +209,6 @@ CSeqMaskerIstatOBinary::CSeqMaskerIstatOBinary( const string & name,
"not enough data to fill the values table" );
uset.add_vt_info( M, vt );
- Uint4 mdsz( 0 );
-
- if( input_stream.read( (char *)&mdsz, sizeof( Uint4 ) ) ) {
- string md;
- char c;
-
- for( Uint4 i( 0 ); i < mdsz; ++i ) {
- input_stream.read( &c, 1 );
- md.push_back( c );
- }
-
- SetMetaData( md );
- }
}
//------------------------------------------------------------------------------
diff --git a/c++/src/algo/winmask/seq_masker_ostat.cpp b/c++/src/algo/winmask/seq_masker_ostat.cpp
index 68ab526..3020c39 100644
--- a/c++/src/algo/winmask/seq_masker_ostat.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: seq_masker_ostat.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,8 +34,27 @@
#include <algo/winmask/seq_masker_ostat.hpp>
+#include <sstream>
+
BEGIN_NCBI_SCOPE
+#define STAT_ALGO_VER_MAJOR 1
+#define STAT_ALGO_VER_MINOR 0
+#define STAT_ALGO_VER_PATCH 0
+
+//------------------------------------------------------------------------------
+char const * CSeqMaskerOstat::STAT_ALGO_COMPONENT_NAME =
+ "windowmasker-statistics-algorithm-version";
+
+
+//------------------------------------------------------------------------------
+CSeqMaskerVersion CSeqMaskerOstat::StatAlgoVersion(
+ STAT_ALGO_COMPONENT_NAME,
+ STAT_ALGO_VER_MAJOR,
+ STAT_ALGO_VER_MINOR,
+ STAT_ALGO_VER_PATCH
+);
+
//------------------------------------------------------------------------------
const char * CSeqMaskerOstat::CSeqMaskerOstatException::GetErrCodeString() const
{
@@ -47,6 +66,58 @@ const char * CSeqMaskerOstat::CSeqMaskerOstatException::GetErrCodeString() const
}
//------------------------------------------------------------------------------
+string CSeqMaskerOstat::FormatParameters() const {
+ std::ostringstream os;
+ Uint4 t_low( pvalues[0] == 0 ? 1 : pvalues[0] ), t_high( pvalues[3] );
+ os << "##parameters:unit=" << (Uint4)unit_size << ' '
+ << "t_low=" << t_low << ' ' << "t_high=" << t_high;
+ return os.str();
+}
+
+//------------------------------------------------------------------------------
+void CSeqMaskerOstat::WriteBinMetaData( std::ostream & os ) const {
+ Uint4 sz( 0 );
+ string s1( "##" );
+ s1 += GetStatFmtVersion().Print();
+ sz += s1.size() + 1;
+ string s2( "##" );
+ s2 += fmt_gen_algo_ver.Print();
+ sz += s2.size() + 1;
+ string s3( FormatParameters() ),
+ s4;
+ sz += s3.size() + 1;
+
+ if( !metadata.empty() ) {
+ s4 = string( "##note:" ) + metadata;
+ sz += s4.size() + 1;
+ }
+
+ char zero( 0 );
+ os.write( (char *)&sz, sizeof( sz ) );
+ os.write( s1.c_str(), s1.size() );
+ os.write( &zero, 1 );
+ os.write( s2.c_str(), s2.size() );
+ os.write( &zero, 1 );
+ os.write( s3.c_str(), s3.size() );
+ os.write( &zero, 1 );
+
+ if( !s4.empty() ) {
+ os.write( s4.c_str(), s4.size() );
+ os.write( &zero, 1 );
+ }
+}
+
+//------------------------------------------------------------------------------
+string CSeqMaskerOstat::FormatMetaData() const {
+ std::ostringstream os;
+ os << "##" << GetStatFmtVersion().Print() << endl;
+ os << "##" << fmt_gen_algo_ver.Print() << endl;
+ os << FormatParameters() << endl;
+ if( !metadata.empty() ) os << "##note:" << metadata << endl;
+ return os.str();
+}
+
+//------------------------------------------------------------------------------
void CSeqMaskerOstat::setUnitSize( Uint1 us )
{
if( state != start )
diff --git a/c++/src/algo/winmask/seq_masker_ostat_ascii.cpp b/c++/src/algo/winmask/seq_masker_ostat_ascii.cpp
index f4c17b3..1cbcfe7 100644
--- a/c++/src/algo/winmask/seq_masker_ostat_ascii.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_ascii.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_ascii.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_ascii.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,6 +38,21 @@
BEGIN_NCBI_SCOPE
+#define STAT_FMT_COMPONENT_NAME "windowmasker-statistics-format-version"
+#define STAT_FMT_VER_MAJOR 1
+#define STAT_FMT_VER_MINOR 0
+#define STAT_FMT_VER_PATCH 0
+#define STAT_FMT_VER_PFX "ascii "
+
+//------------------------------------------------------------------------------
+CSeqMaskerVersion CSeqMaskerOstatAscii::FormatVersion(
+ STAT_FMT_COMPONENT_NAME,
+ STAT_FMT_VER_MAJOR,
+ STAT_FMT_VER_MINOR,
+ STAT_FMT_VER_PATCH,
+ STAT_FMT_VER_PFX
+);
+
//------------------------------------------------------------------------------
const char *
CSeqMaskerOstatAscii::CSeqMaskerOstatAsciiException::GetErrCodeString() const
@@ -71,13 +86,6 @@ CSeqMaskerOstatAscii::~CSeqMaskerOstatAscii()
}
//------------------------------------------------------------------------------
-void CSeqMaskerOstatAscii::doSetUnitSize( Uint4 us )
-{
- out_stream << us << endl;
- if( !metadata.empty() ) out_stream << "##" << metadata << endl;
-}
-
-//------------------------------------------------------------------------------
void CSeqMaskerOstatAscii::doSetUnitCount( Uint4 unit, Uint4 count )
{
static Uint4 punit = 0;
@@ -91,19 +99,38 @@ void CSeqMaskerOstatAscii::doSetUnitCount( Uint4 unit, Uint4 count )
NCBI_THROW( CSeqMaskerOstatAsciiException, eBadOrder, s );
}
- out_stream << hex << unit << " " << dec << count << "\n";
+ counts.push_back( std::make_pair( unit, count ) );
punit = unit;
}
//------------------------------------------------------------------------------
void CSeqMaskerOstatAscii::doSetComment( const string & msg )
-{ out_stream << "#" << msg << "\n"; }
+{
+ comments.push_back( msg );
+}
//------------------------------------------------------------------------------
-void CSeqMaskerOstatAscii::doSetParam( const string & name, Uint4 value )
-{ out_stream << ">" << name << " " << value << "\n"; }
+void CSeqMaskerOstatAscii::doFinalize() {
+ out_stream << FormatMetaData();
+ out_stream << (Uint4)unit_size << endl;
-//------------------------------------------------------------------------------
-void CSeqMaskerOstatAscii::doSetBlank() { out_stream << "\n"; }
+ for( size_t i( 0 ); i < counts.size(); ++i ) {
+ out_stream << hex << counts[i].first << ' '
+ << dec << counts[i].second << '\n';
+ }
+
+ out_stream << '\n';
+
+ for( size_t i( 0 ); i < comments.size(); ++i ) {
+ out_stream << '#' << comments[i] << '\n';
+ }
+
+ out_stream << '\n';
+ out_stream << '>' << PARAMS[0] << ' ' << pvalues[0] << '\n';
+ out_stream << '>' << PARAMS[1] << ' ' << pvalues[1] << '\n';
+ out_stream << '>' << PARAMS[2] << ' ' << pvalues[2] << '\n';
+ out_stream << '>' << PARAMS[3] << ' ' << pvalues[3] << '\n';
+ out_stream << endl;
+}
END_NCBI_SCOPE
diff --git a/c++/src/algo/winmask/seq_masker_ostat_bin.cpp b/c++/src/algo/winmask/seq_masker_ostat_bin.cpp
index 8b16b3f..049e88e 100644
--- a/c++/src/algo/winmask/seq_masker_ostat_bin.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_bin.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_bin.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_bin.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,39 +36,38 @@
BEGIN_NCBI_SCOPE
+#define STAT_FMT_COMPONENT_NAME "windowmasker-statistics-format-version"
+#define STAT_FMT_VER_MAJOR 1
+#define STAT_FMT_VER_MINOR 0
+#define STAT_FMT_VER_PATCH 0
+#define STAT_FMT_VER_PFX "binary "
+
//------------------------------------------------------------------------------
-/**\internal
- **\brief Names and order of allowed parameters.
- **/
-static const char * PARAMS[] = { "t_low", "t_extend", "t_threshold", "t_high" };
+CSeqMaskerVersion CSeqMaskerOstatBin::FormatVersion(
+ STAT_FMT_COMPONENT_NAME,
+ STAT_FMT_VER_MAJOR,
+ STAT_FMT_VER_MINOR,
+ STAT_FMT_VER_PATCH,
+ STAT_FMT_VER_PFX
+);
//------------------------------------------------------------------------------
CSeqMaskerOstatBin::CSeqMaskerOstatBin(
const string & name, string const & metadata )
: CSeqMaskerOstat( static_cast< CNcbiOstream& >(
- *new CNcbiOfstream( name.c_str(), IOS_BASE::binary ) ), true, metadata ),
- pvalues( sizeof( PARAMS )/sizeof( const char * ) )
-{ write_word( (Uint4)0 ); } // Format identifier.
+ *new CNcbiOfstream( name.c_str(), IOS_BASE::binary ) ),
+ true, metadata )
+{}
//------------------------------------------------------------------------------
CSeqMaskerOstatBin::CSeqMaskerOstatBin(
CNcbiOstream & os, string const & metadata )
- : CSeqMaskerOstat( os, false, metadata ),
- pvalues( sizeof( PARAMS )/sizeof( const char * ) )
+ : CSeqMaskerOstat( os, false, metadata )
{ write_word( (Uint4)0 ); } // Format identifier.
//------------------------------------------------------------------------------
CSeqMaskerOstatBin::~CSeqMaskerOstatBin()
{
- try{
- for( vector< Uint4 >::const_iterator i = pvalues.begin();
- i != pvalues.end(); ++i )
- write_word( *i );
- }
- catch( std::exception & e )
- { LOG_POST( Error<< "Error writing trailer: " << e.what() ); }
-
- out_stream.flush();
}
//------------------------------------------------------------------------------
@@ -78,38 +77,29 @@ void CSeqMaskerOstatBin::write_word( Uint4 word )
}
//------------------------------------------------------------------------------
-void CSeqMaskerOstatBin::doSetUnitSize( Uint4 us )
-{
- if( !metadata.empty() ) {
- write_word( (Uint4)(metadata.size() + 16) );
- out_stream.write( metadata.c_str(), metadata.size() );
- }
-
- write_word( us );
-}
-
-//------------------------------------------------------------------------------
void CSeqMaskerOstatBin::doSetUnitCount( Uint4 unit, Uint4 count )
{
- write_word( unit );
- write_word( count );
+ counts.push_back( std::make_pair( unit, count ) );
}
//------------------------------------------------------------------------------
-void CSeqMaskerOstatBin::doSetParam( const string & name, Uint4 value )
-{
- string::size_type pos = name.find_first_of( ' ' );
- string real_name = name.substr( 0, pos );
+void CSeqMaskerOstatBin::doFinalize() {
+ write_word( (Uint4)3 ); // new binary id
+ WriteBinMetaData( out_stream );
+ write_word( (Uint4)0 ); // Format identifier.
+ write_word( (Uint4)unit_size );
+
+ for( size_t i( 0 ); i < counts.size(); ++i ) {
+ write_word( counts[i].first );
+ write_word( counts[i].second );
+ }
- for( unsigned ind = 0;
- ind < sizeof( PARAMS )/sizeof( const char * ); ++ind )
- if( real_name == PARAMS[ind] )
- {
- pvalues[ind] = value;
- return;
- }
+ for( vector< Uint4 >::const_iterator i = pvalues.begin();
+ i != pvalues.end(); ++i ) {
+ write_word( *i );
+ }
- LOG_POST( Error << "Unknown parameter name " << real_name );
+ out_stream.flush();
}
END_NCBI_SCOPE
diff --git a/c++/src/algo/winmask/seq_masker_ostat_opt.cpp b/c++/src/algo/winmask/seq_masker_ostat_opt.cpp
index cc8326d..d5f93d8 100644
--- a/c++/src/algo/winmask/seq_masker_ostat_opt.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_opt.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,13 +46,21 @@ BEGIN_NCBI_SCOPE
static const unsigned long MB = 1024L*1024L;
static const unsigned long GROW_CHUNK = MB;
-static const char * PARAMS[] = { "t_low", "t_extend", "t_threshold", "t_high" };
+const char * CSeqMaskerOstat::PARAMS[] = { "t_low", "t_extend", "t_threshold", "t_high" };
+
+//------------------------------------------------------------------------------
+CSeqMaskerOstat::CSeqMaskerOstat(
+ CNcbiOstream & os, bool alloc, string const & metadata )
+ : out_stream( os ), alloc( alloc ), metadata( metadata ),
+ pvalues( sizeof( PARAMS )/sizeof( const char * ) ),
+ fmt_gen_algo_ver( StatAlgoVersion ),
+ state( start )
+{}
//------------------------------------------------------------------------------
CSeqMaskerOstatOpt::CSeqMaskerOstatOpt(
CNcbiOstream & os, Uint2 sz, bool alloc, string const & metadata )
- : CSeqMaskerOstat( os, alloc, metadata ), size_requested( sz ),
- pvalues( sizeof( PARAMS )/sizeof( const char * ) )
+ : CSeqMaskerOstat( os, alloc, metadata ), size_requested( sz )
{}
//------------------------------------------------------------------------------
@@ -65,7 +73,10 @@ const vector< Uint4 > & CSeqMaskerOstatOpt::GetParams() const
//------------------------------------------------------------------------------
void CSeqMaskerOstatOpt::doSetUnitSize( Uint4 us )
-{ unit_bit_size = 2*us; }
+{
+ CSeqMaskerOstat::doSetUnitSize( us );
+ unit_bit_size = 2*us;
+}
//------------------------------------------------------------------------------
void CSeqMaskerOstatOpt::doSetUnitCount( Uint4 unit, Uint4 count )
@@ -88,7 +99,8 @@ void CSeqMaskerOstatOpt::doSetUnitCount( Uint4 unit, Uint4 count )
}
//------------------------------------------------------------------------------
-void CSeqMaskerOstatOpt::doSetParam( const string & name, Uint4 value )
+// void CSeqMaskerOstatOpt::doSetParam( const string & name, Uint4 value )
+void CSeqMaskerOstat::doSetParam( const string & name, Uint4 value )
{
string::size_type pos = name.find_first_of( ' ' );
string real_name = name.substr( 0, pos );
diff --git a/c++/src/algo/winmask/seq_masker_ostat_opt_ascii.cpp b/c++/src/algo/winmask/seq_masker_ostat_opt_ascii.cpp
index 97ed519..230d1a9 100644
--- a/c++/src/algo/winmask/seq_masker_ostat_opt_ascii.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_opt_ascii.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt_ascii.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt_ascii.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,17 +36,27 @@
BEGIN_NCBI_SCOPE
+#define STAT_FMT_COMPONENT_NAME "windowmasker-statistics-format-version"
+#define STAT_FMT_VER_MAJOR 1
+#define STAT_FMT_VER_MINOR 0
+#define STAT_FMT_VER_PATCH 0
+#define STAT_FMT_VER_PFX "oascii "
+
+//------------------------------------------------------------------------------
+CSeqMaskerVersion CSeqMaskerOstatOptAscii::FormatVersion(
+ STAT_FMT_COMPONENT_NAME,
+ STAT_FMT_VER_MAJOR,
+ STAT_FMT_VER_MINOR,
+ STAT_FMT_VER_PATCH,
+ STAT_FMT_VER_PFX
+);
+
//------------------------------------------------------------------------------
CSeqMaskerOstatOptAscii::CSeqMaskerOstatOptAscii(
const string & name, Uint2 sz, string const & metadata )
: CSeqMaskerOstatOpt( static_cast< CNcbiOstream& >(
*new CNcbiOfstream( name.c_str() ) ), sz, true, metadata )
{
- // File format identifier
- out_stream << (char)65;
- out_stream << (char)65;
- out_stream << (char)65;
- out_stream << (char)65 << endl;
}
//------------------------------------------------------------------------------
@@ -54,16 +64,19 @@ CSeqMaskerOstatOptAscii::CSeqMaskerOstatOptAscii(
CNcbiOstream & os, Uint2 sz, string const & metadata )
: CSeqMaskerOstatOpt( os, sz, false, metadata )
{
+}
+
+//------------------------------------------------------------------------------
+void CSeqMaskerOstatOptAscii::write_out( const params & p ) const
+{
+ out_stream << FormatMetaData();
+
// File format identifier
out_stream << (char)65;
out_stream << (char)65;
out_stream << (char)65;
out_stream << (char)65 << endl;
-}
-//------------------------------------------------------------------------------
-void CSeqMaskerOstatOptAscii::write_out( const params & p ) const
-{
out_stream << (Uint4)UnitSize() << "\n";
out_stream << p.M << " "
<< (Uint4)p.k << " " << (Uint4)p.roff << " " << (Uint4)p.bc
@@ -78,7 +91,6 @@ void CSeqMaskerOstatOptAscii::write_out( const params & p ) const
for( Uint4 i = 0; i < p.M; ++i )
out_stream << (Uint4)(p.vt[i]) << "\n";
- if( !metadata.empty() ) out_stream << "##" << metadata << endl;
out_stream << flush;
}
diff --git a/c++/src/algo/winmask/seq_masker_ostat_opt_bin.cpp b/c++/src/algo/winmask/seq_masker_ostat_opt_bin.cpp
index 69d6869..86b2dfe 100644
--- a/c++/src/algo/winmask/seq_masker_ostat_opt_bin.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_opt_bin.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_masker_ostat_opt_bin.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: seq_masker_ostat_opt_bin.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,6 +36,21 @@
BEGIN_NCBI_SCOPE
+#define STAT_FMT_COMPONENT_NAME "windowmasker-statistics-format-version"
+#define STAT_FMT_VER_MAJOR 1
+#define STAT_FMT_VER_MINOR 0
+#define STAT_FMT_VER_PATCH 0
+#define STAT_FMT_VER_PFX "obinary "
+
+//------------------------------------------------------------------------------
+CSeqMaskerVersion CSeqMaskerOstatOptBin::FormatVersion(
+ STAT_FMT_COMPONENT_NAME,
+ STAT_FMT_VER_MAJOR,
+ STAT_FMT_VER_MINOR,
+ STAT_FMT_VER_PATCH,
+ STAT_FMT_VER_PFX
+);
+
//------------------------------------------------------------------------------
CSeqMaskerOstatOptBin::CSeqMaskerOstatOptBin(
const string & name, Uint2 sz, bool arg_use_ba,
@@ -45,9 +60,6 @@ CSeqMaskerOstatOptBin::CSeqMaskerOstatOptBin(
sz, true, metadata ),
use_ba( arg_use_ba )
{
- if( use_ba )
- write_word( (Uint4)2 );
- else write_word( (Uint4)1 );
}
//------------------------------------------------------------------------------
@@ -56,14 +68,18 @@ CSeqMaskerOstatOptBin::CSeqMaskerOstatOptBin(
: CSeqMaskerOstatOpt( os, sz, false, metadata ),
use_ba( arg_use_ba )
{
- if( use_ba )
- write_word( (Uint4)2 );
- else write_word( (Uint4)1 );
}
//------------------------------------------------------------------------------
void CSeqMaskerOstatOptBin::write_out( const params & p ) const
{
+ write_word( (Uint4)3 ); // new binary id
+ WriteBinMetaData( out_stream );
+
+ if( use_ba )
+ write_word( (Uint4)2 );
+ else write_word( (Uint4)1 );
+
write_word( (Uint4)UnitSize() );
write_word( p.M );
write_word( (Uint4)p.k );
@@ -88,13 +104,6 @@ void CSeqMaskerOstatOptBin::write_out( const params & p ) const
Uint4 sz = (1<<p.k);
out_stream.write( (const char *)(p.ht), sz*sizeof( Uint4 ) );
out_stream.write( (const char *)(p.vt), p.M*sizeof( Uint2 ) );
-
- if( !metadata.empty() ) {
- Uint4 sz( metadata.size() );
- out_stream.write( (const char *)&sz, sizeof( Uint4 ) );
- out_stream.write( metadata.c_str(), sz );
- }
-
out_stream << flush;
}
diff --git a/c++/src/algo/winmask/win_mask_config.cpp b/c++/src/algo/winmask/win_mask_config.cpp
index 763726d..394d4e7 100644
--- a/c++/src/algo/winmask/win_mask_config.cpp
+++ b/c++/src/algo/winmask/win_mask_config.cpp
@@ -1,4 +1,4 @@
-/* $Id: win_mask_config.cpp 445928 2014-09-09 18:46:00Z dicuccio $
+/* $Id: win_mask_config.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -156,10 +156,6 @@ void CWinMaskConfig::AddWinMaskArgs(CArgDescriptions &arg_desc,
arg_desc.AddDefaultKey( "text_match", "text_match_ids",
"match ids as strings",
CArgDescriptions::eBoolean, "T" );
- arg_desc.AddDefaultKey( "use_ba", "use_bit_array_optimization",
- "whether to use extra bit array optimization "
- "for optimized binary counts format",
- CArgDescriptions::eBoolean, "T" );
CArgAllow_Strings* strings_allowed = new CArgAllow_Strings();
for (size_t i = 0; i < kNumInputFormats; i++) {
strings_allowed->Allow(kInputFormats[i]);
@@ -235,7 +231,6 @@ void CWinMaskConfig::AddWinMaskArgs(CArgDescriptions &arg_desc,
arg_desc.CArgDescriptions::SetDependency( "convert", CArgDescriptions::eExcludes, "exclude_ids" );
arg_desc.CArgDescriptions::SetDependency( "convert", CArgDescriptions::eExcludes, "ids" );
arg_desc.CArgDescriptions::SetDependency( "convert", CArgDescriptions::eExcludes, "text_match" );
- arg_desc.CArgDescriptions::SetDependency( "convert", CArgDescriptions::eExcludes, "use_ba" );
}
}
@@ -338,7 +333,7 @@ CWinMaskConfig::CWinMaskConfig( const CArgs & args, EAppType type, bool determin
sformat( app_type < eGenerateMasks ? args["sformat"].AsString() : "" ),
smem( app_type < eGenerateMasks ? args["smem"].AsInteger() : 0 ),
ids( 0 ), exclude_ids( 0 ),
- use_ba( app_type != eConvertCounts && args["use_ba"].AsBoolean() ),
+ use_ba( app_type != eConvertCounts ),
text_match( app_type != eConvertCounts && args["text_match"].AsBoolean() )
{
if (args.Exist("meta") && args["meta"]) {
diff --git a/c++/src/algo/winmask/win_mask_counts_converter.cpp b/c++/src/algo/winmask/win_mask_counts_converter.cpp
index 2c2c226..ccd63ac 100644
--- a/c++/src/algo/winmask/win_mask_counts_converter.cpp
+++ b/c++/src/algo/winmask/win_mask_counts_converter.cpp
@@ -1,4 +1,4 @@
-/* $Id: win_mask_counts_converter.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: win_mask_counts_converter.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -113,9 +113,7 @@ int CWinMaskCountsConverter::operator()()
}
LOG_POST( "converting parameters..." );
- ostat->setBlank();
- ostat->setBlank();
Uint4 t_low = istat->get_min_count();
Uint4 t_extend = istat->get_textend();
Uint4 t_threshold = istat->get_threshold();
@@ -124,8 +122,8 @@ int CWinMaskCountsConverter::operator()()
ostat->setParam( "t_extend ", t_extend );
ostat->setParam( "t_threshold", t_threshold );
ostat->setParam( "t_high ", t_high );
- ostat->setBlank();
LOG_POST( "final processing..." );
+ ostat->SetStatAlgoVersion( istat->GetStatAlgoVersion() );
ostat->finalize();
return 0;
}
diff --git a/c++/src/algo/winmask/win_mask_gen_counts.cpp b/c++/src/algo/winmask/win_mask_gen_counts.cpp
index 5b3b698..e99df7d 100644
--- a/c++/src/algo/winmask/win_mask_gen_counts.cpp
+++ b/c++/src/algo/winmask/win_mask_gen_counts.cpp
@@ -1,4 +1,4 @@
-/* $Id: win_mask_gen_counts.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: win_mask_gen_counts.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,7 +58,6 @@
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
-
//------------------------------------------------------------------------------
static Uint4 letter( char c )
{
@@ -307,7 +306,6 @@ void CWinMaskCountsGenerator::operator()()
if( no_extra_pass )
{
- ustat->setBlank();
ostringstream s;
s << " " << total_ecodes << " ecodes";
ustat->setComment( s.str() );
@@ -361,7 +359,6 @@ void CWinMaskCountsGenerator::operator()()
offset = total_ecodes - score_counts[max_count - 1];
{
- ustat->setBlank();
ostringstream s;
s << " " << total_ecodes << " ecodes";
ustat->setComment( s.str() );
@@ -388,12 +385,10 @@ void CWinMaskCountsGenerator::operator()()
ustat->setComment( s.str() );
}
- ustat->setBlank();
ustat->setParam( "t_low ", index[0] );
ustat->setParam( "t_extend ", index[1] );
ustat->setParam( "t_threshold", index[2] );
ustat->setParam( "t_high ", index[3] );
- ustat->setBlank();
ustat->finalize();
}
diff --git a/c++/src/app/Makefile.in b/c++/src/app/Makefile.in
index cb6c55b..6ef8259 100644
--- a/c++/src/app/Makefile.in
+++ b/c++/src/app/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
# Miscellaneous applications
#################################
@@ -7,14 +7,14 @@ SUB_PROJ = asn2asn asn2fasta asn2flat asnval asn_cleanup \
id1_fetch blast convert_seq \
nmer_repeats objmgr gi2taxid netschedule grid netstorage igblast \
winmasker dustmasker segmasker blastdb vecscreen \
- agpconvert id2_fetch agp_validate objextract lds_indexer \
+ agpconvert id2_fetch agp_validate objextract \
bdb_env_keeper nw_aligner speedtest idmapper formatguess \
multireader read_blast_result splign hfilter \
annotwriter compart streamtest lds2_indexer \
- discrep_report discrepancy_report biosample_chk gap_stats \
- table2asn srcchk ncbi_encrypt
+ discrep_report discrepancy_report biosample_chk gap_stats table2asn \
+ srcchk tableval ncbi_encrypt
-EXPENDABLE_SUB_PROJ = split_cache wig2table netcache rmblastn
+EXPENDABLE_SUB_PROJ = split_cache wig2table netcache rmblastn dblb
REQUIRES = app
diff --git a/c++/src/app/blast/Makefile.blastn.app b/c++/src/app/blast/Makefile.blastn.app
index 64c5be6..0692bf2 100644
--- a/c++/src/app/blast/Makefile.blastn.app
+++ b/c++/src/app/blast/Makefile.blastn.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastn.app 457398 2015-01-22 18:08:58Z ivanov $
+# $Id: Makefile.blastn.app 475019 2015-08-04 13:26:53Z ivanov $
WATCHERS = camacho madden fongah2
@@ -13,7 +13,7 @@ CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386)
LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
REQUIRES = objects -Cygwin
diff --git a/c++/src/app/blast/Makefile.blastp.app b/c++/src/app/blast/Makefile.blastp.app
index a09d6fd..1538371 100644
--- a/c++/src/app/blast/Makefile.blastp.app
+++ b/c++/src/app/blast/Makefile.blastp.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastp.app 457398 2015-01-22 18:08:58Z ivanov $
+# $Id: Makefile.blastp.app 457276 2015-01-21 20:17:49Z boratyng $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/app/blast/Makefile.blastx.app b/c++/src/app/blast/Makefile.blastx.app
index b6ccb0b..96402ff 100644
--- a/c++/src/app/blast/Makefile.blastx.app
+++ b/c++/src/app/blast/Makefile.blastx.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.blastx.app 457398 2015-01-22 18:08:58Z ivanov $
+# $Id: Makefile.blastx.app 457276 2015-01-21 20:17:49Z boratyng $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/app/blast/Makefile.tblastn.app b/c++/src/app/blast/Makefile.tblastn.app
index 682611d..51d8c85 100644
--- a/c++/src/app/blast/Makefile.tblastn.app
+++ b/c++/src/app/blast/Makefile.tblastn.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.tblastn.app 457398 2015-01-22 18:08:58Z ivanov $
+# $Id: Makefile.tblastn.app 457276 2015-01-21 20:17:49Z boratyng $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/app/blast/Makefile.tblastx.app b/c++/src/app/blast/Makefile.tblastx.app
index 9f19b47..d8f0dd9 100644
--- a/c++/src/app/blast/Makefile.tblastx.app
+++ b/c++/src/app/blast/Makefile.tblastx.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.tblastx.app 457398 2015-01-22 18:08:58Z ivanov $
+# $Id: Makefile.tblastx.app 457276 2015-01-21 20:17:49Z boratyng $
WATCHERS = camacho madden fongah2
diff --git a/c++/src/app/blast/blast_app_util.cpp b/c++/src/app/blast/blast_app_util.cpp
index 3958d7e..d52bef0 100644
--- a/c++/src/app/blast/blast_app_util.cpp
+++ b/c++/src/app/blast/blast_app_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_app_util.cpp 415477 2013-10-17 14:44:29Z fongah2 $
+/* $Id: blast_app_util.cpp 485060 2015-11-18 16:07:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_app_util.cpp 415477 2013-10-17 14:44:29Z fongah2 $";
+ "$Id: blast_app_util.cpp 485060 2015-11-18 16:07:34Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -216,7 +216,11 @@ InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args,
CRef<IQueryFactory> subjects;
if ( (subjects = db_args->GetSubjects(scope)) ) {
_ASSERT(search_db.Empty());
- db_adapter.Reset(new CLocalDbAdapter(subjects, opts_hndl));
+ char* bl2seq_legacy = getenv("BL2SEQ_LEGACY");
+ if (bl2seq_legacy)
+ db_adapter.Reset(new CLocalDbAdapter(subjects, opts_hndl, false));
+ else
+ db_adapter.Reset(new CLocalDbAdapter(subjects, opts_hndl, true));
} else {
_ASSERT(search_db.NotEmpty());
try {
@@ -477,7 +481,7 @@ s_ImportDatabase(const CBlast4_subject& subj,
if (opts_builder.HaveGiList()) {
CSeqDBGiList *gilist = new CSeqDBGiList();
- ITERATE(list<int>, gi, opts_builder.GetGiList()) {
+ ITERATE(list<TGi>, gi, opts_builder.GetGiList()) {
gilist->AddGi(*gi);
}
search_db->SetGiList(gilist);
@@ -860,4 +864,43 @@ IsIStreamEmpty(CNcbiIstream & in)
return false;
}
+string
+GetCmdlineArgs(const CNcbiArguments & a)
+{
+ string cmd = kEmptyStr;
+ for(unsigned int i=0; i < a.Size(); i++) {
+ cmd += a[i] + " ";
+ }
+ return cmd;
+}
+
+bool
+UseXInclude(const CFormattingArgs & f, const string & s)
+{
+ CFormattingArgs::EOutputFormat fmt = f.GetFormattedOutputChoice();
+ if((fmt == CFormattingArgs::eXml2) || (fmt == CFormattingArgs::eJson)) {
+ if (s == "-"){
+ string f_str = (fmt == CFormattingArgs::eXml2) ? "14.": "13.";
+ NCBI_THROW(CInputException, eEmptyUserInput,
+ "Please provide a file name for outfmt " + f_str);
+ }
+ return true;
+ }
+ return false;
+}
+
+string
+GetSubjectFile(const CArgs& args)
+{
+ string filename="";
+
+ if (args.Exist(kArgSubject) && args[kArgSubject].HasValue())
+ filename = args[kArgSubject].AsString();
+
+ return filename;
+}
+
+
+
+
END_NCBI_SCOPE
diff --git a/c++/src/app/blast/blast_app_util.hpp b/c++/src/app/blast/blast_app_util.hpp
index d8bcfb3..0e3e0e9 100644
--- a/c++/src/app/blast/blast_app_util.hpp
+++ b/c++/src/app/blast/blast_app_util.hpp
@@ -1,4 +1,4 @@
-/* $Id: blast_app_util.hpp 446371 2014-09-15 16:25:19Z ivanov $
+/* $Id: blast_app_util.hpp 482743 2015-10-26 16:39:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -290,6 +290,18 @@ CheckForFreqRatioFile(const string& rps_dbname, CRef<blast::CBlastOptionsHandle>
bool
IsIStreamEmpty(CNcbiIstream & in);
+string
+GetCmdlineArgs(const CNcbiArguments & a);
+
+bool
+UseXInclude(const blast::CFormattingArgs & f, const string & s);
+
+/// Get name of subject file
+/// @parameter args arguments class [in]
+/// @return Name of subject file.
+string
+GetSubjectFile(const CArgs& args);
+
END_NCBI_SCOPE
#endif /* APP__BLAST_APP_UTIL__HPP */
diff --git a/c++/src/app/blast/blast_formatter.cpp b/c++/src/app/blast/blast_formatter.cpp
index 8154eed..4ed21af 100644
--- a/c++/src/app/blast/blast_formatter.cpp
+++ b/c++/src/app/blast/blast_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_formatter.cpp 458745 2015-02-09 19:38:45Z ivanov $
+/* $Id: blast_formatter.cpp 485060 2015-11-18 16:07:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blast_formatter.cpp 458745 2015-02-09 19:38:45Z ivanov $";
+ "$Id: blast_formatter.cpp 485060 2015-11-18 16:07:34Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -116,7 +116,7 @@ void CBlastFormatterApp::Init()
CArgDescriptions::eInputFile);
arg_desc->SetDependency(kArgRid, CArgDescriptions::eExcludes, kArgArchive);
- CFormattingArgs fmt_args;
+ CFormattingArgs fmt_args(false, CFormattingArgs::eIsSAM);
fmt_args.SetArgumentDescriptions(*arg_desc);
arg_desc->SetCurrentGroup("Output configuration options");
@@ -249,7 +249,7 @@ int CBlastFormatterApp::PrintFormattedOutput(void)
const string& kRid = args[kArgRid].HasValue()
? args[kArgRid].AsString() : kEmptyStr;
CNcbiOstream& out = args[kArgOutput].AsOutputFile();
- CFormattingArgs fmt_args;
+ CFormattingArgs fmt_args(false, CFormattingArgs::eIsSAM) ;
CRef<CBlastOptionsHandle> opts_handle = m_RmtBlast->GetSearchOptions();
CBlastOptions& opts = opts_handle->SetOptions();
@@ -264,6 +264,12 @@ int CBlastFormatterApp::PrintFormattedOutput(void)
const EBlastProgramType p = opts.GetProgramType();
+ if((fmt_args.GetFormattedOutputChoice() == CFormattingArgs::eSAM) &&
+ (p != eBlastTypeBlastn )) {
+ NCBI_THROW(CInputException, eInvalidInput,
+ "SAM format is only applicable to blastn results" );
+ }
+
CRef<CBlastQueryVector> queries =
x_ExtractQueries(Blast_QueryIsProtein(p)?true:false);
CRef<CScope> scope = queries->GetScope(0);
@@ -314,12 +320,13 @@ int CBlastFormatterApp::PrintFormattedOutput(void)
filtering_algorithm,
fmt_args.GetCustomOutputFormatSpec(),
kTask == "megablast",
- opts.GetMBIndexLoaded());
+ opts.GetMBIndexLoaded(),
+ NULL, NULL,
+ GetCmdlineArgs(GetArguments()));
formatter.SetLineLength(fmt_args.GetLineLength());
- if((fmt_args.GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args.GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
- formatter.SetBaseFile(args[kArgOutput].AsString());
+ if(UseXInclude(fmt_args, args[kArgOutput].AsString())) {
+ formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
CRef<CSearchResultSet> results = m_RmtBlast->GetResultSet();
formatter.PrintProlog();
bool isPsiBlast = ("psiblast" == kTask);
@@ -362,7 +369,9 @@ int CBlastFormatterApp::PrintFormattedOutput(void)
// That does not work for other formats. Ugly, but that's where it's at now.
if (m_LoadFromArchive == false || (fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eXml
&& fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eXml2
- && fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eJson )
+ && fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eJson
+ && fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eXml2_S
+ && fmt_args.GetFormattedOutputChoice() != CFormattingArgs::eJson_S )
|| !m_RmtBlast->LoadFromArchive()) {
break;
}
@@ -458,6 +467,6 @@ int CBlastFormatterApp::Run(void)
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- return CBlastFormatterApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CBlastFormatterApp().AppMain(argc, argv, 0, eDS_Default, "");
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/blastn_app.cpp b/c++/src/app/blast/blastn_app.cpp
index 032ebc0..e9ce820 100644
--- a/c++/src/app/blast/blastn_app.cpp
+++ b/c++/src/app/blast/blastn_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: blastn_app.cpp 484400 2015-11-10 18:12:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: blastn_app.cpp 484400 2015-11-10 18:12:56Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -135,7 +135,6 @@ int CBlastnApp::Run(void)
CRef<CBlastOptions> my_options(&(opts_hndl->SetOptions()));
CSetupFactory::InitializeMegablastDbIndex(my_options);
}
-
/*** Get the formatting options ***/
CRef<CFormattingArgs> fmt_args(m_CmdLineArgs->GetFormattingArgs());
CBlastFormat formatter(opt, *db_adapter,
@@ -155,14 +154,16 @@ int CBlastnApp::Run(void)
db_adapter->GetFilteringAlgorithm(),
fmt_args->GetCustomOutputFormatSpec(),
m_CmdLineArgs->GetTask() == "megablast",
- opt.GetMBIndexLoaded());
+ opt.GetMBIndexLoaded(),
+ NULL, NULL,
+ GetCmdlineArgs(GetArguments()),
+ GetSubjectFile(args));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -222,8 +223,8 @@ int CBlastnApp::Run(void)
}
#ifndef SKIP_DOXYGEN_PROCESSING
-int main(int argc, const char* argv[] /*, const char* envp[]*/)
+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
- return CBlastnApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CBlastnApp().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/blastp_app.cpp b/c++/src/app/blast/blastp_app.cpp
index 360f013..7abf18b 100644
--- a/c++/src/app/blast/blastp_app.cpp
+++ b/c++/src/app/blast/blastp_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastp_app.cpp 461340 2015-03-09 18:08:15Z ivanov $
+/* $Id: blastp_app.cpp 484400 2015-11-10 18:12:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blastp_app.cpp 461340 2015-03-09 18:08:15Z ivanov $";
+ "$Id: blastp_app.cpp 484400 2015-11-10 18:12:56Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -148,14 +148,16 @@ int CBlastpApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()),
+ GetSubjectFile(args));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -201,8 +203,8 @@ int CBlastpApp::Run(void)
}
#ifndef SKIP_DOXYGEN_PROCESSING
-int main(int argc, const char* argv[] /*, const char* envp[]*/)
+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
- return CBlastpApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CBlastpApp().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/blastx_app.cpp b/c++/src/app/blast/blastx_app.cpp
index c6c25b6..3037eb9 100644
--- a/c++/src/app/blast/blastx_app.cpp
+++ b/c++/src/app/blast/blastx_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastx_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: blastx_app.cpp 484400 2015-11-10 18:12:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blastx_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: blastx_app.cpp 484400 2015-11-10 18:12:56Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -146,13 +146,16 @@ int CBlastxApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()),
+ GetSubjectFile(args));
formatter.SetQueryRange(query_opts->GetRange());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
- formatter.SetBaseFile(args[kArgOutput].AsString());
+ formatter.SetLineLength(fmt_args->GetLineLength());
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
+ formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -198,8 +201,8 @@ int CBlastxApp::Run(void)
}
#ifndef SKIP_DOXYGEN_PROCESSING
-int main(int argc, const char* argv[] /*, const char* envp[]*/)
+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
- return CBlastxApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CBlastxApp().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/deltablast_app.cpp b/c++/src/app/blast/deltablast_app.cpp
index b7eef64..8ca7455 100644
--- a/c++/src/app/blast/deltablast_app.cpp
+++ b/c++/src/app/blast/deltablast_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: deltablast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: deltablast_app.cpp 483793 2015-11-04 11:13:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: deltablast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: deltablast_app.cpp 483793 2015-11-04 11:13:41Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -270,14 +270,14 @@ int CDeltaBlastApp::Run(void)
db_adapter->GetFilteringAlgorithm(),
fmt_args->GetCustomOutputFormatSpec(),
false, false, NULL,
- domain_db_ptr);
+ domain_db_ptr,
+ GetCmdlineArgs(GetArguments()));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -370,12 +370,30 @@ int CDeltaBlastApp::Run(void)
formatter.PrintOneResultSet(**result, query_batch);
}
}
+
+ if (m_CmdLineArgs->GetSaveLastPssm()) {
+ CConstRef<CBioseq> query_bioseq(&pssm->GetQuery().GetSeq());
+ blast::CSearchResults& res = (*results)[0];
+
+ CRef<CPSIBlastOptionsHandle> psi_opts(
+ dynamic_cast<CPSIBlastOptionsHandle*>(&*opts_hndl));
+
+ pssm = ComputePssmForNextPsiBlastIteration(*query_bioseq,
+ res.GetSeqAlign(),
+ psi_opts,
+ scope,
+ res.GetAncillaryData());
+
+ SavePssmToFile(pssm);
+ }
}
else {
// if more than 1 iterations are requested, then
// do PSI-BLAST iterations, this is not allowed for remote blast
+ SavePssmToFile(pssm);
+
// print domain search results if requested
// query_batch_size == 1 if number of iteratins > 1
if (m_CmdLineArgs->GetShowDomainHits()) {
@@ -483,7 +501,7 @@ CDeltaBlastApp::DoPsiBlastIterations(CRef<CBlastOptionsHandle> opts_hndl,
pssm = ComputePssmForNextPsiBlastIteration(*query_bioseq, aln,
psi_opts,
scope,
- results_1st_query.GetAncillaryData());
+ (*results)[0].GetAncillaryData());
if (psiblast.Empty()) {
psiblast.Reset(new CPsiBlast(pssm, db_adapter, psi_opts));
@@ -517,16 +535,26 @@ CDeltaBlastApp::DoPsiBlastIterations(CRef<CBlastOptionsHandle> opts_hndl,
break;
}
- CConstRef<CSeq_align_set> aln(results_1st_query.GetSeqAlign());
- CPsiBlastIterationState::TSeqIds ids;
- CPsiBlastIterationState::GetSeqIds(aln, psi_opts, ids);
+ aln.Reset(results_1st_query.GetSeqAlign());
+ CPsiBlastIterationState::TSeqIds new_ids;
+ CPsiBlastIterationState::GetSeqIds(aln, psi_opts, new_ids);
- itr.Advance(ids);
+ itr.Advance(new_ids);
}
if (itr.HasConverged()) {
converged = true;
}
+ if (m_CmdLineArgs->GetSaveLastPssm()) {
+ CRef<CPssmWithParameters>
+ pssm = ComputePssmForNextPsiBlastIteration(*query_bioseq, aln,
+ psi_opts,
+ scope,
+ results_1st_query.GetAncillaryData());
+
+ SavePssmToFile(pssm);
+ }
+
return converged;
}
@@ -549,7 +577,7 @@ CDeltaBlastApp::ComputePssmForNextPsiBlastIteration(const CBioseq& bioseq,
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- return CDeltaBlastApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CDeltaBlastApp().AppMain(argc, argv, 0, eDS_Default, "");
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/psiblast_app.cpp b/c++/src/app/blast/psiblast_app.cpp
index 1b68821..b3a0eb6 100644
--- a/c++/src/app/blast/psiblast_app.cpp
+++ b/c++/src/app/blast/psiblast_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: psiblast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: psiblast_app.cpp 483791 2015-11-04 11:12:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: psiblast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: psiblast_app.cpp 483791 2015-11-04 11:12:47Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -291,7 +291,7 @@ CPsiBlastApp::x_RunLocalPsiBlastIterations(CRef<CBlastQueryVector> query,
itr.Advance(ids);
- if (itr) {
+ if (itr || m_CmdLineArgs->GetSaveLastPssm()) {
CConstRef<CBioseq> seq =
s_GetQueryBioseq(query, scope, pssm);
pssm =
@@ -305,6 +305,11 @@ CPsiBlastApp::x_RunLocalPsiBlastIterations(CRef<CBlastQueryVector> query,
}
if (itr.HasConverged())
converged = true;
+
+ if (m_CmdLineArgs->GetSaveLastPssm()) {
+ SavePssmToFile(pssm, &itr);
+ }
+
return converged;
}
@@ -469,14 +474,15 @@ int CPsiBlastApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
@@ -545,6 +551,6 @@ int CPsiBlastApp::Run(void)
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- return CPsiBlastApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CPsiBlastApp().AppMain(argc, argv, 0, eDS_Default, "");
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/rpsblast_app.cpp b/c++/src/app/blast/rpsblast_app.cpp
index 092f251..52e30b6 100644
--- a/c++/src/app/blast/rpsblast_app.cpp
+++ b/c++/src/app/blast/rpsblast_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: rpsblast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: rpsblast_app.cpp 482743 2015-10-26 16:39:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: rpsblast_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: rpsblast_app.cpp 482743 2015-10-26 16:39:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -151,14 +151,15 @@ int CRPSBlastApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -208,7 +209,7 @@ int CRPSBlastApp::Run(void)
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- int status = CRPSBlastApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ int status = CRPSBlastApp().AppMain(argc, argv, 0, eDS_Default, "");
return status;
}
diff --git a/c++/src/app/blast/rpstblastn_app.cpp b/c++/src/app/blast/rpstblastn_app.cpp
index 66a5d5c..da3aba5 100644
--- a/c++/src/app/blast/rpstblastn_app.cpp
+++ b/c++/src/app/blast/rpstblastn_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: rpstblastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: rpstblastn_app.cpp 482743 2015-10-26 16:39:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: rpstblastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: rpstblastn_app.cpp 482743 2015-10-26 16:39:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -151,14 +151,15 @@ int CRPSTBlastnApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -205,6 +206,6 @@ int CRPSTBlastnApp::Run(void)
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- return CRPSTBlastnApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CRPSTBlastnApp().AppMain(argc, argv, 0, eDS_Default, "");
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/seedtop_app.cpp b/c++/src/app/blast/seedtop_app.cpp
index 0d2b1ae..79f8a5b 100644
--- a/c++/src/app/blast/seedtop_app.cpp
+++ b/c++/src/app/blast/seedtop_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: seedtop_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: seedtop_app.cpp 482743 2015-10-26 16:39:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: seedtop_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: seedtop_app.cpp 482743 2015-10-26 16:39:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -241,6 +241,6 @@ int CSeedTopApp::Run(void)
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[] /*, const char* envp[]*/)
{
- return CSeedTopApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CSeedTopApp().AppMain(argc, argv, 0, eDS_Default, "");
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/tblastn_app.cpp b/c++/src/app/blast/tblastn_app.cpp
index bfb12fc..b6dfca1 100644
--- a/c++/src/app/blast/tblastn_app.cpp
+++ b/c++/src/app/blast/tblastn_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: tblastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: tblastn_app.cpp 484400 2015-11-10 18:12:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: tblastn_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: tblastn_app.cpp 484400 2015-11-10 18:12:56Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -167,14 +167,16 @@ int CTblastnApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()),
+ GetSubjectFile(args));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -253,8 +255,8 @@ int CTblastnApp::Run(void)
}
#ifndef SKIP_DOXYGEN_PROCESSING
-int main(int argc, const char* argv[] /*, const char* envp[]*/)
+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
- return CTblastnApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CTblastnApp().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/tblastx_app.cpp b/c++/src/app/blast/tblastx_app.cpp
index 6791f64..6a8aa9e 100644
--- a/c++/src/app/blast/tblastx_app.cpp
+++ b/c++/src/app/blast/tblastx_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: tblastx_app.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: tblastx_app.cpp 484400 2015-11-10 18:12:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: tblastx_app.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: tblastx_app.cpp 484400 2015-11-10 18:12:56Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -146,14 +146,16 @@ int CTblastxApp::Run(void)
opt.GetSumStatisticsMode(),
m_CmdLineArgs->ExecuteRemotely(),
db_adapter->GetFilteringAlgorithm(),
- fmt_args->GetCustomOutputFormatSpec());
+ fmt_args->GetCustomOutputFormatSpec(),
+ false, false, NULL, NULL,
+ GetCmdlineArgs(GetArguments()),
+ GetSubjectFile(args));
formatter.SetQueryRange(query_opts->GetRange());
formatter.SetLineLength(fmt_args->GetLineLength());
- if((fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eXml2 ||
- fmt_args->GetFormattedOutputChoice() == CFormattingArgs::eJson)
- && args[kArgOutput].AsString() != "-")
+ if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
formatter.SetBaseFile(args[kArgOutput].AsString());
+ }
formatter.PrintProlog();
/*** Process the input ***/
@@ -199,8 +201,8 @@ int CTblastxApp::Run(void)
}
#ifndef SKIP_DOXYGEN_PROCESSING
-int main(int argc, const char* argv[] /*, const char* envp[]*/)
+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
- return CTblastxApp().AppMain(argc, argv, 0, eDS_Default, 0);
+ return CTblastxApp().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */
diff --git a/c++/src/app/blast/update_blastdb.pl b/c++/src/app/blast/update_blastdb.pl
index 6f59aec..4aba43a 100755
--- a/c++/src/app/blast/update_blastdb.pl
+++ b/c++/src/app/blast/update_blastdb.pl
@@ -1,5 +1,5 @@
#!/usr/bin/perl
-# $Id: update_blastdb.pl 446090 2014-09-11 12:12:27Z ivanov $
+# $Id: update_blastdb.pl 446062 2014-09-10 21:38:05Z camacho $
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
@@ -82,7 +82,7 @@ $|++;
# Connect and download files
my $ftp = &connect_to_ftp() unless ($opt_show_version);
if ($opt_show_version) {
- my $revision = '$Revision: 446090 $';
+ my $revision = '$Revision: 446062 $';
$revision =~ s/\$Revision: | \$//g;
print "$0 version $revision\n";
} elsif ($opt_showall) {
diff --git a/c++/src/app/blastdb/Makefile.blastdbcp.app b/c++/src/app/blastdb/Makefile.blastdbcp.app
index f5e4b8e..e2be992 100644
--- a/c++/src/app/blastdb/Makefile.blastdbcp.app
+++ b/c++/src/app/blastdb/Makefile.blastdbcp.app
@@ -13,3 +13,5 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
REQUIRES = objects -Cygwin
+
+WATCHERS = rackerst camacho madden
diff --git a/c++/src/app/blastdb/blastdb_aliastool.cpp b/c++/src/app/blastdb/blastdb_aliastool.cpp
index 8b66c65..03c641d 100644
--- a/c++/src/app/blastdb/blastdb_aliastool.cpp
+++ b/c++/src/app/blastdb/blastdb_aliastool.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdb_aliastool.cpp 454089 2014-12-10 19:59:22Z ivanov $
+/* $Id: blastdb_aliastool.cpp 442823 2014-08-07 14:40:27Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blastdb_aliastool.cpp 454089 2014-12-10 19:59:22Z ivanov $";
+ "$Id: blastdb_aliastool.cpp 442823 2014-08-07 14:40:27Z fongah2 $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
diff --git a/c++/src/app/blastdb/blastdbcheck.cpp b/c++/src/app/blastdb/blastdbcheck.cpp
index a72a8cd..66076c8 100644
--- a/c++/src/app/blastdb/blastdbcheck.cpp
+++ b/c++/src/app/blastdb/blastdbcheck.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdbcheck.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: blastdbcheck.cpp 461034 2015-03-05 14:22:52Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/app/blastdb/blastdbcmd.cpp b/c++/src/app/blastdb/blastdbcmd.cpp
index cd7bd53..2eecdf6 100644
--- a/c++/src/app/blastdb/blastdbcmd.cpp
+++ b/c++/src/app/blastdb/blastdbcmd.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdbcmd.cpp 461341 2015-03-09 18:08:50Z ivanov $
+/* $Id: blastdbcmd.cpp 479896 2015-09-24 14:50:02Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: blastdbcmd.cpp 461341 2015-03-09 18:08:50Z ivanov $";
+ "$Id: blastdbcmd.cpp 479896 2015-09-24 14:50:02Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -182,7 +182,7 @@ CBlastDBCmdApp::x_AddOid(CBlastDBCmdApp::TQueries& retval,
}
// Not a NR database, add oid instead
- vector<int> gis;
+ vector<TGi> gis;
m_BlastDb->GetGis(oid, gis);
if (gis.empty()) {
list< CRef<CSeq_id> > ids = m_BlastDb->GetSeqIDs(oid);
@@ -194,9 +194,9 @@ CBlastDBCmdApp::x_AddOid(CBlastDBCmdApp::TQueries& retval,
}
// Default: add all possible ids
- ITERATE(vector<int>, gi, gis) {
+ ITERATE(vector<TGi>, gi, gis) {
retval.push_back(CRef<CBlastDBSeqId>
- (new CBlastDBSeqId(NStr::IntToString(*gi))));
+ (new CBlastDBSeqId(NStr::IntToString(GI_TO(TIntId, *gi)))));
}
}
diff --git a/c++/src/app/blastdb/blastdbcp.cpp b/c++/src/app/blastdb/blastdbcp.cpp
index f8cadaf..fbf4fe3 100644
--- a/c++/src/app/blastdb/blastdbcp.cpp
+++ b/c++/src/app/blastdb/blastdbcp.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdbcp.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: blastdbcp.cpp 479896 2015-09-24 14:50:02Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,6 +31,7 @@
#include <corelib/ncbiapp.hpp>
#include <algo/blast/blastinput/cmdline_flags.hpp>
#include <objtools/blast/seqdb_writer/build_db.hpp>
+#include <objtools/blast/seqdb_writer/impl/criteria.hpp>
USING_NCBI_SCOPE;
USING_SCOPE(blast);
@@ -39,7 +40,6 @@ USING_SCOPE(blast);
/////////////////////////////////////////////////////////////////////////////
// BlastdbCopyApplication::
-
class BlastdbCopyApplication : public CNcbiApplication
{
public:
@@ -50,21 +50,32 @@ private: /* Private Methods */
virtual int Run(void);
virtual void Exit(void);
- bool x_ShouldParseSeqIds(const string& dbname,
+ bool x_ShouldParseSeqIds(const string& dbname,
CSeqDB::ESeqType seq_type) const;
bool x_ShouldCopyPIGs(const string& dbname,
CSeqDB::ESeqType seq_type) const;
private: /* Private Data */
- bool m_bCheckOnly;
+ bool m_bCheckOnly;
+
+ typedef map<string, ICriteria::EMembershipBit> TMemBitMap;
+
+ TMemBitMap m_MembershipMap;
+
+ const string kTargetOnly;
+ const string kMembershipBits;
+ const string kCopyOnly;
};
/////////////////////////////////////////////////////////////////////////////
// Constructor
BlastdbCopyApplication::BlastdbCopyApplication()
- : m_bCheckOnly(false)
+ : m_bCheckOnly(false),
+ kTargetOnly("target_only"),
+ kMembershipBits("membership_bits"),
+ kCopyOnly("copy_only")
{
CRef<CVersion> version(new CVersion());
version->SetVersionInfo(1, 0);
@@ -82,50 +93,111 @@ void BlastdbCopyApplication::Init(void)
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
- arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
- "Performs a (deep) copy of a subset of a BLAST database");
+ arg_desc->SetUsageContext(
+ GetArguments().GetProgramBasename(),
+ "Performs a (deep) copy of a subset of a BLAST database"
+ );
arg_desc->SetCurrentGroup("BLAST database options");
- arg_desc->AddDefaultKey(kArgDb, "dbname", "BLAST database name",
- CArgDescriptions::eString, "nr");
- arg_desc->AddDefaultKey(kArgDbType, "molecule_type",
- "Molecule type stored in BLAST database",
- CArgDescriptions::eString, "prot");
- arg_desc->SetConstraint(kArgDbType, &(*new CArgAllow_Strings,
- "nucl", "prot", "guess"));
+ arg_desc->AddDefaultKey(
+ kArgDb,
+ "dbname",
+ "BLAST database name",
+ CArgDescriptions::eString, "nr"
+ );
+
+ arg_desc->AddDefaultKey(
+ kArgDbType,
+ "molecule_type",
+ "Molecule type stored in BLAST database",
+ CArgDescriptions::eString, "prot"
+ );
+ arg_desc->SetConstraint(
+ kArgDbType,
+ &(*new CArgAllow_Strings, "nucl", "prot", "guess")
+ );
arg_desc->SetCurrentGroup("Configuration options");
- arg_desc->AddOptionalKey(kArgDbTitle, "database_title",
- "Title for BLAST database",
- CArgDescriptions::eString);
- arg_desc->AddKey(kArgGiList, "input_file",
- "Text or binary gi file to restrict the BLAST "
- "database provided in -db argument",
- CArgDescriptions::eString);
- arg_desc->AddFlag("membership_bits", "Copy the membershi bits", true);
+
+ arg_desc->AddOptionalKey(
+ kArgDbTitle,
+ "database_title",
+ "Title for BLAST database",
+ CArgDescriptions::eString
+ );
+
+ arg_desc->AddKey(
+ kArgGiList,
+ "input_file",
+ "Text or binary gi file to restrict the BLAST "
+ "database provided in -db argument",
+ CArgDescriptions::eString
+ );
+
+ arg_desc->AddFlag(
+ kMembershipBits,
+ "Copy the membership bits",
+ true
+ );
+
+ arg_desc->AddFlag(
+ kTargetOnly,
+ "Copy only entries specified in gi file",
+ true
+ );
+
+ arg_desc->AddOptionalKey(
+ kCopyOnly,
+ "membership_bit",
+ "Membership bit by which copied entries are filtered",
+ CArgDescriptions::eString
+ );
+
+ const string kSwissprot("swissprot");
+ const string kPdb("pdb");
+ const string kRefseq("refseq");
+
+ m_MembershipMap[kSwissprot] = ICriteria::eSWISSPROT;
+ m_MembershipMap[kPdb] = ICriteria::ePDB;
+ m_MembershipMap[kRefseq] = ICriteria::eREFSEQ;
+
+ arg_desc->SetConstraint(
+ kCopyOnly,
+ &(*new CArgAllow_Strings, kSwissprot, kPdb, kRefseq)
+ );
arg_desc->SetCurrentGroup("Output options");
- arg_desc->AddOptionalKey(kArgOutput, "database_name",
- "Name of BLAST database to be created",
- CArgDescriptions::eString);
- HideStdArgs(fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun);
+
+ arg_desc->AddOptionalKey(
+ kArgOutput,
+ "database_name",
+ "Name of BLAST database to be created",
+ CArgDescriptions::eString
+ );
+
+ HideStdArgs(
+ fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun
+ );
+
SetupArgDescriptions(arg_desc.release());
}
class CBlastDbBioseqSource : public IBioseqSource
{
public:
- CBlastDbBioseqSource(CRef<CSeqDBExpert> blastdb,
- CRef<CSeqDBGiList> gilist,
- bool copy_membership_bits = false)
+ CBlastDbBioseqSource(
+ CRef<CSeqDBExpert> blastdb,
+ CRef<CSeqDBGiList> gilist,
+ bool copy_membership_bits = false
+ )
{
CStopWatch total_timer, bioseq_timer, memb_timer;
total_timer.Start();
for (int i = 0; i < gilist->GetNumGis(); i++) {
const CSeqDBGiList::SGiOid& elem = gilist->GetGiOid(i);
int oid = 0;
- if ( !blastdb->GiToOid(elem.gi, oid)) {
+ if ( !blastdb->GiToOid(GI_FROM(int, elem.gi), oid)) {
// not found on source BLASTDB, skip
continue;
}
@@ -133,20 +205,32 @@ public:
// don't add the same OID twice to avoid duplicates
continue;
}
+
bioseq_timer.Start();
- CConstRef<CBioseq> bs(&*blastdb->GetBioseq(oid));
+ CRef<CBioseq> bs_nc = blastdb->GetBioseq(oid);
+ if (bs_nc.Empty()) {
+ // If we end up here, all sequences were probably filtered
+ // out by the membership bit setting for this gi.
+ bioseq_timer.Stop();
+ continue;
+ }
+
+ CConstRef<CBioseq> bs(&*bs_nc);
m_Bioseqs.push_back(bs);
bioseq_timer.Stop();
- if (copy_membership_bits == false)
+ if (copy_membership_bits == false) {
+ // If we're not copying the membership bits, we're done
+ // with this gi, so loop back for the next one.
continue;
+ }
memb_timer.Start();
CRef<CBlast_def_line_set> hdr = CSeqDB::ExtractBlastDefline(*bs);
ITERATE(CBlast_def_line_set::Tdata, itr, hdr->Get()) {
CRef<CBlast_def_line> bdl = *itr;
- if (bdl->CanGetMemberships() &&
- !bdl->GetMemberships().empty()) {
+ if (bdl->CanGetMemberships() &&
+ !bdl->GetMemberships().empty()) {
int memb_bits = bdl->GetMemberships().front();
if (memb_bits == 0) {
continue;
@@ -158,18 +242,29 @@ public:
memb_timer.Stop();
}
total_timer.Stop();
- ERR_POST(Info << "Will extract " << m_Bioseqs.size()
- << " sequences from the source database");
- ERR_POST(Info << "Processed all input data in " << total_timer.AsSmartString());
- ERR_POST(Info << "Processed bioseqs in " << bioseq_timer.AsSmartString());
- ERR_POST(Info << "Processed membership bits in " << memb_timer.AsSmartString());
+ ERR_POST(
+ Info << "Will extract " << m_Bioseqs.size()
+ << " sequences from the source database"
+ );
+ ERR_POST(
+ Info << "Processed all input data in "
+ << total_timer.AsSmartString()
+ );
+ ERR_POST(
+ Info << "Processed bioseqs in "
+ << bioseq_timer.AsSmartString()
+ );
+ ERR_POST(
+ Info << "Processed membership bits in "
+ << memb_timer.AsSmartString()
+ );
}
const TLinkoutMap GetMembershipBits() const {
return m_MembershipBits;
}
- virtual CConstRef<CBioseq> GetNext()
+ virtual CConstRef<CBioseq> GetNext()
{
if (m_Bioseqs.empty()) {
return CConstRef<CBioseq>(0);
@@ -239,8 +334,8 @@ int BlastdbCopyApplication::Run(void)
// Setup Logging
if (args["logfile"]) {
- SetDiagPostLevel(eDiag_Info);
- SetDiagPostFlag(eDPF_All);
+ SetDiagPostLevel(eDiag_Info);
+ SetDiagPostFlag(eDPF_All);
SetDiagPostPrefix("blastdbcp");
time_t now = time(0);
LOG_POST( Info << string(72,'-') << "\n" << "NEW LOG - " << ctime(&now) );
@@ -250,8 +345,33 @@ int BlastdbCopyApplication::Run(void)
try {{
seq_type = ParseMoleculeTypeString(args[kArgDbType].AsString());
- CRef<CSeqDBGiList> gilist(new CSeqDBFileGiList(args[kArgGiList].AsString()));
- CRef<CSeqDBExpert> sourcedb(new CSeqDBExpert(args[kArgDb].AsString(), seq_type));
+ CRef<CSeqDBGiList> gilist(
+ new CSeqDBFileGiList(args[kArgGiList].AsString())
+ );
+
+ CSeqDBExpert* dbexpert;
+ if (args[kTargetOnly].AsBoolean()) {
+ dbexpert = new CSeqDBExpert(
+ args[kArgDb].AsString(),
+ seq_type,
+ &*gilist
+ );
+ } else {
+ dbexpert = new CSeqDBExpert(
+ args[kArgDb].AsString(),
+ seq_type
+ );
+ }
+ CRef<CSeqDBExpert> sourcedb(dbexpert);
+
+ if (args[kCopyOnly].HasValue()) {
+ string mbitName = args[kCopyOnly].AsString();
+ TMemBitMap::iterator it = m_MembershipMap.find(mbitName);
+ if (it != m_MembershipMap.end()) {
+ sourcedb->SetVolsMemBit(it->second);
+ }
+ }
+
string title;
if (args[kArgDbTitle].HasValue()) {
title = args[kArgDbTitle].AsString();
@@ -263,8 +383,11 @@ int BlastdbCopyApplication::Run(void)
const bool kCopyPIGs = x_ShouldCopyPIGs(args[kArgDb].AsString(),
seq_type);
- CBlastDbBioseqSource bioseq_source(sourcedb, gilist,
- args["membership_bits"]);
+ CBlastDbBioseqSource bioseq_source(
+ sourcedb,
+ gilist,
+ args[kMembershipBits].AsBoolean()
+ );
const bool kIsSparse = false;
const bool kParseSeqids = x_ShouldParseSeqIds(args[kArgDb].AsString(),
seq_type);
@@ -276,7 +399,7 @@ int BlastdbCopyApplication::Run(void)
CBuildDatabase destdb(args[kArgOutput].AsString(), title,
static_cast<bool>(seq_type == CSeqDB::eProtein),
kIsSparse, kParseSeqids, kUseGiMask,
- &(args["logfile"].HasValue()
+ &(args["logfile"].HasValue()
? args["logfile"].AsOutputFile() : cerr));
destdb.SetUseRemote(false);
//destdb.SetVerbosity(true);
@@ -288,7 +411,7 @@ int BlastdbCopyApplication::Run(void)
timer.Stop();
ERR_POST(Info << "Created BLAST database in " << timer.AsSmartString());
}}
- catch (const CException& ex) {
+ catch (CException& ex) {
LOG_POST( Error << ex );
DeleteBlastDb(args[kArgOutput].AsString(), seq_type);
retval = -1;
diff --git a/c++/src/app/blastdb/convert2blastmask.cpp b/c++/src/app/blastdb/convert2blastmask.cpp
index 475038c..7cbfdd7 100644
--- a/c++/src/app/blastdb/convert2blastmask.cpp
+++ b/c++/src/app/blastdb/convert2blastmask.cpp
@@ -1,4 +1,4 @@
-/* # $Id: convert2blastmask.cpp 407582 2013-07-23 11:15:22Z kornbluh $
+/* # $Id: convert2blastmask.cpp 477844 2015-09-02 13:12:06Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,7 +75,7 @@ public:
// hack to deal with interval format
virtual void ParseDataLine(const TStr &s,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
if (s[0] >= '0' && s[0] <= '9' && s.find('-') > 0) {
string s1, s2;
diff --git a/c++/src/app/blastdb/makeblastdb.cpp b/c++/src/app/blastdb/makeblastdb.cpp
index 0b2a522..e3e8bb1 100644
--- a/c++/src/app/blastdb/makeblastdb.cpp
+++ b/c++/src/app/blastdb/makeblastdb.cpp
@@ -1,4 +1,4 @@
-/* $Id: makeblastdb.cpp 461339 2015-03-09 18:07:37Z ivanov $
+/* $Id: makeblastdb.cpp 483792 2015-11-04 11:13:19Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: makeblastdb.cpp 461339 2015-03-09 18:07:37Z ivanov $";
+ "$Id: makeblastdb.cpp 483792 2015-11-04 11:13:19Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -284,7 +284,7 @@ void CMakeBlastDBApp::Init()
arg_desc->AddDefaultKey("max_file_sz", "number_of_bytes",
"Maximum file size for BLAST database files",
CArgDescriptions::eString, "1GB");
- arg_desc->AddOptionalKey("logfile", "File_Name",
+ arg_desc->AddOptionalKey("logfile", "File_Name",
"File to which the program log should be redirected",
CArgDescriptions::eOutputFile,
CArgDescriptions::fAppend);
@@ -446,7 +446,7 @@ public:
// and it's marked "Unverified", skip ALL of the
// Bioseq objects it contains.
if (it_bio_set->GetClass() == CBioseq_set::eClass_nuc_prot) {
- if (IsUnverified(it_bio_set->GetDescr())) {
+ if (it_bio_set->CanGetDescr() && IsUnverified(it_bio_set->GetDescr())) {
for (it_bio = Begin(*it_bio_set); it_bio; ++it_bio) {
m_bio_skipped.insert(&(*it_bio));
}
@@ -457,7 +457,7 @@ public:
// Step through Seq-entry, picking out Bioseq objects.
for (it_bio = Begin(*m_entry); it_bio; ++it_bio) {
// If Bioseq is marked as "Unverified", skip it.
- if (IsUnverified(it_bio->GetDescr())) {
+ if (it_bio->CanGetDescr() && IsUnverified(it_bio->GetDescr())) {
// Because m_bio_skipped is an STL set container,
// inserting an item that's already in the set will leave
// the set unaltered (i.e. no duplicate items).
@@ -1056,14 +1056,14 @@ void CMakeBlastDBApp::x_BuildDatabase()
string title = (args[kArgDbTitle].HasValue()
? args[kArgDbTitle]
: args[kInput]).AsString();
- if (!args[kArgDbTitle].HasValue() && input_fmt == eBlastDb) {
+ if (!args[kArgDbTitle].HasValue() && input_fmt == eBlastDb) {
vector<CTempString> names;
SeqDB_SplitQuoted(args[kInput].AsString(), names);
if (names.size() > 1) {
NCBI_THROW(CInvalidDataException, eInvalidInput,
"Please provide a title using -title");
}
- CRef<CSeqDB> dbhandle(new CSeqDB(names.front(),
+ CRef<CSeqDB> dbhandle(new CSeqDB(names.front(),
(is_protein ? CSeqDB::eProtein : CSeqDB::eNucleotide)));
title = dbhandle->GetTitle();
}
@@ -1120,6 +1120,10 @@ void CMakeBlastDBApp::x_BuildDatabase()
// Max file size
Uint8 bytes = NStr::StringToUInt8_DataSize(args["max_file_sz"].AsString());
+ if (bytes >= (1L << 31)) {
+ NCBI_THROW(CInvalidDataException, eInvalidInput,
+ "max_file_sz must be < 2 GiB");
+ }
*m_LogFile << "Maximum file size: "
<< Uint8ToString_DataSize(bytes) << endl;
diff --git a/c++/src/app/blastdb/makeprofiledb.cpp b/c++/src/app/blastdb/makeprofiledb.cpp
index 882eed3..be7501e 100644
--- a/c++/src/app/blastdb/makeprofiledb.cpp
+++ b/c++/src/app/blastdb/makeprofiledb.cpp
@@ -1,4 +1,4 @@
-/* $Id: makeprofiledb.cpp 454100 2014-12-10 20:03:49Z ivanov $
+/* $Id: makeprofiledb.cpp 452770 2014-11-24 19:17:41Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/app/winmasker/win_mask_app.cpp b/c++/src/app/winmasker/win_mask_app.cpp
index a5aa3e4..fb1f5d6 100644
--- a/c++/src/app/winmasker/win_mask_app.cpp
+++ b/c++/src/app/winmasker/win_mask_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: win_mask_app.cpp 434184 2014-05-05 14:32:02Z morgulis $
+/* $Id: win_mask_app.cpp 462550 2015-03-19 14:07:19Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,10 @@
#include <algo/winmask/win_mask_util.hpp>
#include <algo/winmask/win_mask_counts_converter.hpp>
#include <algo/winmask/win_mask_config.hpp>
+#include <algo/winmask/seq_masker_ostat_ascii.hpp>
+#include <algo/winmask/seq_masker_ostat_bin.hpp>
+#include <algo/winmask/seq_masker_ostat_opt_ascii.hpp>
+#include <algo/winmask/seq_masker_ostat_opt_bin.hpp>
#include "win_mask_app.hpp"
#include "win_mask_sdust_masker.hpp"
@@ -63,11 +67,36 @@
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
+#define WIN_MASK_APP_VER_MAJOR 1
+#define WIN_MASK_APP_VER_MINOR 0
+#define WIN_MASK_APP_VER_PATCH 0
+
//-------------------------------------------------------------------------
const char * const
CWinMaskApplication::USAGE_LINE = "Window based sequence masker";
//-------------------------------------------------------------------------
+CWinMaskApplication::CWinMaskApplication() {
+ CRef<CVersion> version(new CVersion());
+ version->SetVersionInfo( WIN_MASK_APP_VER_MAJOR,
+ WIN_MASK_APP_VER_MINOR,
+ WIN_MASK_APP_VER_PATCH );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMasker::AlgoVersion ) );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMaskerOstat::StatAlgoVersion ) );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMaskerOstatAscii::FormatVersion ) );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMaskerOstatBin::FormatVersion ) );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMaskerOstatOptAscii::FormatVersion ) );
+ version->AddComponentVersion( new CSeqMaskerVersion(
+ CSeqMaskerOstatOptBin::FormatVersion ) );
+ SetFullVersion(version);
+}
+
+//-------------------------------------------------------------------------
void CWinMaskApplication::Init(void)
{
HideStdArgs(fHideLogfile | fHideConffile | fHideVersion | fHideDryRun);
diff --git a/c++/src/app/winmasker/win_mask_app.hpp b/c++/src/app/winmasker/win_mask_app.hpp
index 454f3d8..04724f1 100644
--- a/c++/src/app/winmasker/win_mask_app.hpp
+++ b/c++/src/app/winmasker/win_mask_app.hpp
@@ -1,4 +1,4 @@
-/* $Id: win_mask_app.hpp 139491 2008-09-05 13:20:55Z camacho $
+/* $Id: win_mask_app.hpp 460140 2015-02-25 13:52:50Z morgulis $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,11 +46,7 @@ class CWinMaskApplication : public CNcbiApplication
public:
/// Application constructor
- CWinMaskApplication() {
- CRef<CVersion> version(new CVersion());
- version->SetVersionInfo(1, 0, 0);
- SetFullVersion(version);
- }
+ CWinMaskApplication();
/**
**\brief Short description of the program.
diff --git a/c++/src/app/winmasker/windowmasker_counts_adapter.py b/c++/src/app/winmasker/windowmasker_counts_adapter.py
new file mode 100755
index 0000000..8b223b3
--- /dev/null
+++ b/c++/src/app/winmasker/windowmasker_counts_adapter.py
@@ -0,0 +1,91 @@
+#!/usr/bin/python
+
+#
+# Run this program to convert new style counts files containing version, parameters, and
+# version data inforamtion into the old format.
+#
+
+import sys
+
+HELP_STR = """
+------------------------------------------------------------------------------
+WINDOWMASKER COUNTS FILE CONVERTER
+------------------------------------------------------------------------------
+
+New windowmasker counts files formats were change to incorporate additional
+information, such as version of file formats and algorithms used to compute
+the n-mer counts statistics, windowmasker parameters used for file creation,
+and additional user-defined metadata.
+
+Old versions of windowmasker can not parse new counts files. This program
+converts the new counts files back to the old format.
+
+USAGE: windowmasker_counts_adapter.py <input> <output>
+
+input --- the path to a counts file in new format;
+output --- the path to the result of the conversion to the old format.
+------------------------------------------------------------------------------
+"""
+
+def check_type( fname ):
+ f = open( fname, 'rb' )
+ head = f.read( 4 )
+ if len( head ) < 4:
+ return 'other'
+ if head[0:2] == '##':
+ return 'ascii'
+ v = [ord( a ) for a in head]
+ if v == [0,0,0,3]:
+ return 'binary_be'
+ if v == [3,0,0,0]:
+ return 'binary_le'
+ return 'other'
+
+def convert_ascii( in_fname, out_fname ):
+ outf = open( out_fname, 'w' )
+ for line in file( in_fname ):
+ if len( line ) >= 2 and line[0:2] == '##':
+ continue
+ outf.write( line )
+ outf.flush()
+
+def convert_binary( in_fname, out_fname, t ):
+ outf = open( out_fname, 'wb' )
+ inf = open( in_fname, 'rb' )
+ head = inf.read( 4 )
+ head = inf.read( 4 )
+ if len( head ) < 4:
+ sys.exit( 'metadata length error' )
+ if t == 'binary_le':
+ sz = (ord( head[0] )) + \
+ (ord( head[1] )<<8) + \
+ (ord( head[2] )<<16) + \
+ (ord( head[3] )<<24)
+ else:
+ sz = (ord( head[3] )) + \
+ (ord( head[2] )<<8) + \
+ (ord( head[1] )<<16) + \
+ (ord( head[0] )<<24)
+ head = inf.read( sz )
+ if len( head ) < sz:
+ sys.exit( 'metadata error' )
+ outf.write( inf.read() )
+ outf.flush()
+
+def main():
+ global HELP_STR
+ if len( sys.argv ) < 3:
+ print HELP_STR
+ sys.exit( 1 )
+ (in_fname, out_fname) = (sys.argv[1:3])
+ t = check_type( sys.argv[1] )
+ if t == "ascii":
+ convert_ascii( in_fname, out_fname )
+ elif t[0:6] == "binary":
+ convert_binary( in_fname, out_fname, t )
+ else:
+ sys.exit( "input is already in old format" )
+
+if __name__ == '__main__':
+ main()
+
diff --git a/c++/src/build-system/Makefile.app.in b/c++/src/build-system/Makefile.app.in
index 55a0976..9182d74 100644
--- a/c++/src/build-system/Makefile.app.in
+++ b/c++/src/build-system/Makefile.app.in
@@ -1,6 +1,6 @@
# -*- makefile-gmake -*-
#################################
-# $Id: Makefile.app.in 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.app.in 478076 2015-09-03 17:21:47Z ivanov $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
# This can be used to build/install/clean
@@ -39,16 +39,31 @@ XLIB_FLAGS = $(runpath) @f_libpath@$(libdir)
XLIB = $(XLIB_FLAGS) $(XAPP_LIB:%=@lib_l_pre@%@lib_l_ext@)
XLIBDEP = $(XAPP_LIB:%=$(status_dir)/.%.dep)
+XLIB2 = $(XLIB)
+XAPP_LIBS2 = $(XAPP_LIBS)
+
ifneq "" "$(wildcard Makefile.$(TMPL).app.libdep)"
include Makefile.$(TMPL).app.libdep
ifneq "" "$(GENERATED_LIB_ORDER)"
- XLIB = $(XLIB_FLAGS) $(GENERATED_LIB_ORDER)
+ XLIB2 = $(XLIB_FLAGS) $(GENERATED_LIB_ORDER)
endif
ifneq "" "$(GENERATED_LIB3PARTY_ORDER)"
- XAPP_LIBS = $(GENERATED_LIB3PARTY_ORDER)
+ XAPP_LIBS2 = $(GENERATED_LIB3PARTY_ORDER)
endif
endif
+CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS)
+CMD_TAIL = @f_outexe@$(XAPP) $(LINK_FILTER)
+CMD = $(CMD_BASE) $(XLIB) $(XAPP_LIBS) $(CMD_TAIL)
+CMD2 = $(CMD_BASE) $(XLIB2) $(XAPP_LIBS2) $(CMD_TAIL)
+
+ifeq "$(CMD)" "$(CMD2)"
+ OR_CMD2 =
+else
+ NOTE = "The original settings failed. Trying project_tree_builder's suggestions:"
+ OR_CMD2 = || (echo $(NOTE); echo $(CMD2); $(CMD2))
+endif
+
include $(builddir)/Makefile.$(Rules)
ASK_REBUILD = \
@@ -133,7 +148,8 @@ $(XAPP): $(DLL_DEP) $(XOBJ) $(XLIBDEP)
else
$(XAPP): $(XOBJ) $(XOBJ2) $(XLIBDEP)
@-$(RM) .$(XAPP).stamp
- $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
+ @echo $(CMD)
+ @$(CMD) $(OR_CMD2)
$(STRIP) $(XAPP)
$(POST_LINK) $(XAPP)
ifneq "$(BINCOPY)" "@:"
diff --git a/c++/src/build-system/Makefile.compress_tests b/c++/src/build-system/Makefile.compress_tests
new file mode 100644
index 0000000..370cd1f
--- /dev/null
+++ b/c++/src/build-system/Makefile.compress_tests
@@ -0,0 +1,7 @@
+# $Id: Makefile.compress_tests 453410 2014-12-03 16:25:18Z ucko $
+
+%.gz: %
+ gzip -Nf $<
+
+%.bz2: %
+ bzip2 -f $<
diff --git a/c++/src/build-system/Makefile.configurables.real b/c++/src/build-system/Makefile.configurables.real
index 05f5711..8fc2ddd 100644
--- a/c++/src/build-system/Makefile.configurables.real
+++ b/c++/src/build-system/Makefile.configurables.real
@@ -1,4 +1,4 @@
-# $Id: Makefile.configurables.real 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.configurables.real 442076 2014-07-30 14:06:45Z ucko $
ALL_SUB_PROJ = $(SUB_PROJ) $(POTENTIAL_SUB_PROJ) $(EXPENDABLE_SUB_PROJ)
LOCAL_CONFIGURABLES = Makefile $(ALL_SUB_PROJ:%=%/Makefile) $(EXTRA_CONFIGURABLES)
diff --git a/c++/src/build-system/Makefile.dll.in b/c++/src/build-system/Makefile.dll.in
index 8199100..7a33022 100644
--- a/c++/src/build-system/Makefile.dll.in
+++ b/c++/src/build-system/Makefile.dll.in
@@ -1,6 +1,6 @@
# -*- makefile-gmake -*-
#################################
-# $Id: Makefile.dll.in 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.dll.in 475041 2015-08-04 15:30:53Z ivanov $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
# This can be used to build/install/clean
@@ -68,6 +68,12 @@ ifneq "" "$(wildcard Makefile.$(TMPL).dll.libdep)"
endif
endif
+ifeq "" "$(filter-out 0 N% n% F% f% OFF Off off, $(KEEP_CORELIB))"
+ ifneq "" "$(filter @OSTYPE@, darwin freebsd)"
+ XDLL_LIB := $(filter-out @lib_l_pre at xncbi%@lib_l_ext@, $(XDLL_LIB))
+ endif
+endif
+
include $(builddir)/Makefile.$(Rules)
# This definition loses any trailing #, and is only useful in conditionals.
@@ -134,7 +140,9 @@ else
-$(RM) $(XDLL) .$(XDLL).stamp
@has_dll_loadable at -$(RM) $(XDLL_LOADABLE)
$(LINK_WRAPPER) $(LINK_DLL) $(XDLL) $(LDFLAGS_DLL) $(DLL_LDFLAGS) $(XDLLOBJ) $(XOBJ) $(XDLL_LIB) $(LIBS) $(LINK_FILTER)
+ $(POST_LINK) $(XDLL)
@has_dll_loadable@$(LINK_WRAPPER) $(LINK_LOADABLE) $(XDLL_LOADABLE) $(LDFLAGS_DLL) $(DLL_LDFLAGS) $(XDLLOBJ) $(XOBJ) $(XDLL_LIB) $(LIBS) $(LINK_FILTER)
+ @has_dll_loadable@$(POST_LINK) $(XDLL_LOADABLE)
ifeq "$(wildcard $(XDLLDEP))" ""
@echo $(srcdir) $(CURDIR) $(TMPL) > $(XDLLDEP)
@$(TOUCH) -r $(XDLL) $(XDLLDEP)
diff --git a/c++/src/build-system/Makefile.flat_tuneups b/c++/src/build-system/Makefile.flat_tuneups
index a150ced..a51b2a9 100644
--- a/c++/src/build-system/Makefile.flat_tuneups
+++ b/c++/src/build-system/Makefile.flat_tuneups
@@ -1,5 +1,5 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.flat_tuneups 441975 2014-07-29 17:23:49Z ucko $
+# $Id: Makefile.flat_tuneups 441919 2014-07-29 15:07:28Z ucko $
all: ptb_all
diff --git a/c++/src/build-system/Makefile.in.top b/c++/src/build-system/Makefile.in.top
index 654d7e0..1abe44f 100644
--- a/c++/src/build-system/Makefile.in.top
+++ b/c++/src/build-system/Makefile.in.top
@@ -1,4 +1,4 @@
-# $Id: Makefile.in.top 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.in.top 451817 2014-11-12 16:41:55Z ucko $
# Top-level meta-makefile that simplifies building even further.
# include @builddir@/Makefile.mk
@@ -11,6 +11,7 @@ bindir = @bindir@
libdir = @libdir@
includedir = @includedir@
pincludedir = $(includedir)/$(PACKAGE_NAME)
+BASENAME = @BASENAME@
INSTALL = @INSTALL@
LN_S = @LN_S@
@@ -46,7 +47,7 @@ install-toolkit:
-rm -f $(libdir)/lib*-static.a
cd $(libdir) && \
for x in *.a; do \
- $(LN_S) "$$x" "`/usr/bin/basename \"$$x\" .a`-static.a"; \
+ $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
done
cd $(includedir0) && find * -name CVS -prune -o -print |\
cpio -pd $(pincludedir)
diff --git a/c++/src/build-system/Makefile.lib.tmpl.in b/c++/src/build-system/Makefile.lib.tmpl.in
index b47a31a..b21b792 100644
--- a/c++/src/build-system/Makefile.lib.tmpl.in
+++ b/c++/src/build-system/Makefile.lib.tmpl.in
@@ -1,5 +1,5 @@
#################################
-# $Id: Makefile.lib.tmpl.in 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.lib.tmpl.in 442076 2014-07-30 14:06:45Z ucko $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
diff --git a/c++/src/build-system/Makefile.meta.gmake=no b/c++/src/build-system/Makefile.meta.gmake=no
index 97c114c..17780b8 100644
--- a/c++/src/build-system/Makefile.meta.gmake=no
+++ b/c++/src/build-system/Makefile.meta.gmake=no
@@ -1,4 +1,4 @@
-# $Id: Makefile.meta.gmake=no 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.meta.gmake=no 442076 2014-07-30 14:06:45Z ucko $
ECHO = /bin/echo
GMAKE = gmake
diff --git a/c++/src/build-system/Makefile.meta.gmake=yes b/c++/src/build-system/Makefile.meta.gmake=yes
index 0588acf..e7f069a 100644
--- a/c++/src/build-system/Makefile.meta.gmake=yes
+++ b/c++/src/build-system/Makefile.meta.gmake=yes
@@ -1,5 +1,5 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.meta.gmake=yes 446510 2014-09-16 16:07:55Z ivanov $
+# $Id: Makefile.meta.gmake=yes 470885 2015-06-19 18:58:22Z ivanov $
ifeq "" "$(findstring /,$(MAKE))"
ABSMAKE := $(word 1,$(wildcard $(patsubst %,%/$(MAKE),$(subst :, ,$(PATH)))))
@@ -11,7 +11,11 @@ endif
ifneq "" "$(findstring :,$(LD_LIBRARY_PATH))"
collect_libs = $(top_srcdir)/scripts/common/impl/collect_outside_libs.sh
ifneq "" "$(import_root)"
- outside_lib_root = $(import_root)/../lib/outside
+ ifeq "" "$(filter /%,$(import_root))"
+ outside_lib_root = $(CURDIR)/$(import_root)/../lib/outside
+ else
+ outside_lib_root = $(import_root)/../lib/outside
+ endif
else
ifeq "" "$(build_root)"
build_root = $(CURDIR)/..
diff --git a/c++/src/build-system/Makefile.meta.in b/c++/src/build-system/Makefile.meta.in
index 13a427c..6975797 100644
--- a/c++/src/build-system/Makefile.meta.in
+++ b/c++/src/build-system/Makefile.meta.in
@@ -1,5 +1,5 @@
#################################
-# $Id: Makefile.meta.in 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.meta.in 442076 2014-07-30 14:06:45Z ucko $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
# Meta-makefile(to be configured into "Makefile")
diff --git a/c++/src/build-system/Makefile.meta_l b/c++/src/build-system/Makefile.meta_l
index ba8fbcd..43a47a5 100644
--- a/c++/src/build-system/Makefile.meta_l
+++ b/c++/src/build-system/Makefile.meta_l
@@ -1,10 +1,11 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.meta_l 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.meta_l 485100 2015-11-18 18:35:45Z ivanov $
### Rules for building within a single directory
sources = sources
DATE = /bin/date
+VDB_REQ = VDB
# Interpret command-line specifications of APP_PROJ or LIB_PROJ as a
# cue to clear out all other *_PROJ settings not also provided there.
@@ -25,6 +26,20 @@ endif
RWL = $(abs_top_srcdir)/scripts/common/impl/run_with_lock.sh
+ifeq "$(srcdir)" "."
+ PTB_ROOT = /net/snowman/vol/export2/win-coremake/App/Ncbi/cppcore/ptb
+ BOOTSTRAP_PTB = $(build_root)/bin/project_tree_builder
+ ifeq "$(PREBUILT_PTB_EXE)" "bootstrap"
+ RELEASE_PTB =
+ else
+ COMMON_SH = $(abs_top_srcdir)/scripts/common/common.sh
+ PLATFORM := $(shell . $(COMMON_SH) && COMMON_DetectPlatform)
+ RELEASE_PTB = $(PTB_ROOT)/$(PLATFORM)/project_tree_builder.RELEASE
+ endif
+ PTB_CANDIDATES = $(PREBUILT_PTB_EXE) $(RELEASE_PTB) $(BOOTSTRAP_PTB)
+ PTB := $(word 1, $(wildcard $(PTB_CANDIDATES)))
+endif
+
### Tests config variables
check_run = $(abs_top_srcdir)/scripts/common/check/check_run.sh
@@ -108,7 +123,7 @@ $(ign)+ at i=$(1) ; \
echo "cd $(abs_srcdir) && $(MAKE_$(2)) $(3)" ; \
cd $(abs_srcdir) && \
if MAKE="$(MAKE) $(MFLAGS_NR)" \
- $(RWL) -base make_asn -log "$(CURDIR)/make_$(1).log" $(MAKE_$(2)) $(3) \
+ $(RWL) -base make_asn -log "$(CURDIR)/make_$(1)_src.log" $(MAKE_$(2)) $(3) \
&& $(MAKE_LIB) src-stamp; then \
: ; \
else \
@@ -236,7 +251,7 @@ sources.nonusr:
$(call make_each_lib_proj,export-headers)
$(MAKE_LOCK_MAP)
-all.nonusr: $(sources:%=%.nonusr)
+all.nonusr: $(sources:%=%.nonusr) # $(wildcard Makefile.*.libdep)
@-$(RM) -f .built .built_r
@-echo "`$(DATE)`: starting to build in $(CURDIR)" > .building
$(call make_each_lib_proj,all)
@@ -251,7 +266,7 @@ clean.nonusr purge.nonusr: %.nonusr: # %_sources
clean_sources purge_sources:
$(call make_each_spec,$@)
-libs_l.real: $(sources)
+libs_l.real: $(sources) # $(wildcard Makefile.*.libdep)
$(call make_each_lib_proj,all)
mark-as-disabled%: ign = -
@@ -269,6 +284,26 @@ depend_l.real: $(sources)
$(call make_each_lib_proj,depend)
$(call make_each_app_proj,depend)
+Makefile.%.libdep: $(srcdir)/Makefile.%
+# $(builddir)/Makefile.mk
+ifneq "$(srcdir)" "."
+ cd $(builddir) && $(RWL) -base project_tree_builder \
+ $(abs_top_srcdir)/scripts/common/impl/create_flat_makefile.sh \
+ $(build_root) -s $(abs_top_srcdir) $(PROJECTS_:%=-p %)
+else
+ ifneq "$(PTB)" ""
+ cd $(import_root) && $(RWL) -base project_tree_builder \
+ $(PTB) -ext -extroot $(builddir) -nws \
+ -logfile Flat.full.configuration_log -conffile \
+ $(abs_top_srcdir)/src/build-system/project_tree_builder.ini \
+ -noadddep `cd .. && pwd` src Makefile.flat.full
+ else
+ @echo Not sure how to update $@ from $<.
+ @exit 10
+ endif
+endif
+ @if [ -f "$@" ]; then touch $@; fi
+
base_req_needers = $(filter-out mark-as-disabled_l,$(local_targets))
.PHONY: $(base_targets) $(has_usr_nonusr) $(has_usr_usr)
.PHONY: $(has_usr_locked) $(has_usr_l_real) $(has_usr_real)
diff --git a/c++/src/build-system/Makefile.meta_p b/c++/src/build-system/Makefile.meta_p
index f3077b4..644ca01 100644
--- a/c++/src/build-system/Makefile.meta_p
+++ b/c++/src/build-system/Makefile.meta_p
@@ -1,5 +1,5 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.meta_p 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.meta_p 442076 2014-07-30 14:06:45Z ucko $
### Project-list-based recursive builds
diff --git a/c++/src/build-system/Makefile.meta_r b/c++/src/build-system/Makefile.meta_r
index b8d17ad..7945c09 100644
--- a/c++/src/build-system/Makefile.meta_r
+++ b/c++/src/build-system/Makefile.meta_r
@@ -1,5 +1,5 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.meta_r 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.meta_r 442076 2014-07-30 14:06:45Z ucko $
### Full recursive build -- in the [SUB_PROJ] directories
diff --git a/c++/src/build-system/Makefile.mk.in b/c++/src/build-system/Makefile.mk.in
index 6ac8578..a0b337e 100644
--- a/c++/src/build-system/Makefile.mk.in
+++ b/c++/src/build-system/Makefile.mk.in
@@ -1,5 +1,5 @@
#################################
-# $Id: Makefile.mk.in 450045 2014-10-22 17:57:31Z ivanov $
+# $Id: Makefile.mk.in 478150 2015-09-04 11:53:48Z ivanov $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
#
@@ -343,9 +343,14 @@ PCRE_LIBS = @PCRE_LIBS@
PCREPOSIX_LIBS = @PCREPOSIX_LIBS@
PCRE_LIB = @PCRE_LIB@
-# OpenSSL, GnuTLS: headers and libs; TLS_* points to GNUTLS_* by preference.
+# OpenSSL, GnuTLS, and potential supporting packages: headers and libs.
+# TLS_* points to GNUTLS_* by preference.
+GMP_INCLUDE = @GMP_INCLUDE@
+GMP_LIBS = @GMP_LIBS@
GCRYPT_INCLUDE = @GCRYPT_INCLUDE@
GCRYPT_LIBS = @GCRYPT_LIBS@
+NETTLE_INCLUDE = @NETTLE_INCLUDE@
+NETTLE_LIBS = @NETTLE_LIBS@
GNUTLS_INCLUDE = @GNUTLS_INCLUDE@
GNUTLS_LIBS = @GNUTLS_LIBS@
OPENSSL_INCLUDE = @OPENSSL_INCLUDE@
@@ -395,12 +400,12 @@ ODBC_LIBS = @ODBC_LIBS@
# PYTHON: headers and libs (default + specific versions)
PYTHON_INCLUDE = @PYTHON_INCLUDE@
PYTHON_LIBS = @PYTHON_LIBS@
-PYTHON23_INCLUDE = @PYTHON23_INCLUDE@
-PYTHON23_LIBS = @PYTHON23_LIBS@
-PYTHON24_INCLUDE = @PYTHON24_INCLUDE@
-PYTHON24_LIBS = @PYTHON24_LIBS@
PYTHON25_INCLUDE = @PYTHON25_INCLUDE@
PYTHON25_LIBS = @PYTHON25_LIBS@
+PYTHON26_INCLUDE = @PYTHON26_INCLUDE@
+PYTHON26_LIBS = @PYTHON26_LIBS@
+PYTHON27_INCLUDE = @PYTHON27_INCLUDE@
+PYTHON27_LIBS = @PYTHON27_LIBS@
# Perl: executable, headers and libs
PERL = @PERL@
@@ -483,6 +488,14 @@ sssutils = @sssutils@
NCBILS2_LIB = ncbils2_cli ncbils2_asn ncbils2_cmn
NCBILS_LIB = $(NCBILS2_LIB)
+# NCBI SRA/VDB Toolkit
+VDB_INCLUDE = @VDB_INCLUDE@
+VDB_LIB = @VDB_LIB@
+VDB_LIBS = @VDB_LIBS@
+VDB_STATIC_LIBS = @VDB_STATIC_LIBS@
+VDB_REQ = @VDB_REQ@
+VDB_POST_LINK = @VDB_POST_LINK@
+
# SP: headers, libraries
SP_INCLUDE = @SP_INCLUDE@
SP_LIBS = @SP_LIBS@
@@ -597,11 +610,18 @@ AVRO_LIBS = @AVRO_LIBS@
AVRO_STATIC_LIBS = @AVRO_STATIC_LIBS@
AVROGENCPP = @AVROGENCPP@
+# USC Cereal (header-only)
+CEREAL_INCLUDE = @CEREAL_INCLUDE@
+
# MongoDB
MONGODB_INCLUDE = @MONGODB_INCLUDE@
MONGODB_LIBS = @MONGODB_LIBS@
MONGODB_STATIC_LIBS = @MONGODB_STATIC_LIBS@
+# Google Mock
+GMOCK_INCLUDE = @GMOCK_INCLUDE@
+GMOCK_LIBS = @GMOCK_LIBS@
+
# Compress
COMPRESS_LDEP = $(CMPRS_LIB)
COMPRESS_LIBS = xcompress $(COMPRESS_LDEP)
@@ -658,7 +678,7 @@ EUTILS_LIBS = eutils egquery elink epost esearch espell esummary linkout \
OBJREAD_LIBS = xobjread variation creaders submit
# formatting code
-XFORMAT_LIBS = xformat xcleanup gbseq submit mlacli mla medlars pubmed valid
+XFORMAT_LIBS = xformat xcleanup gbseq submit mlacli mla medlars pubmed valid taxon3
# object editing library
OBJEDIT_LIBS = xobjedit $(OBJREAD_LIBS) taxon3
diff --git a/c++/src/build-system/Makefile.mk.in.msvc b/c++/src/build-system/Makefile.mk.in.msvc
index 7829044..219f2b0 100644
--- a/c++/src/build-system/Makefile.mk.in.msvc
+++ b/c++/src/build-system/Makefile.mk.in.msvc
@@ -26,6 +26,7 @@ RuntimeTypeInfo=true
DisableSpecificWarnings=
UndefinePreprocessorDefinitions=
AdditionalOptions=
+ProgramDataBaseFileName=$(IntDir)$(TargetName).pdb
[Compiler.800]
PreprocessorDefinitions=_CRT_SECURE_NO_DEPRECATE=1;
@@ -58,6 +59,11 @@ BasicRuntimeChecks=3
BrowseInformation=0
EnableFunctionLevelLinking=false
+[Compiler.debug.DebugDLL]
+RuntimeLibrary=3
+
+[Compiler.debug.DebugMT]
+RuntimeLibrary=1
[Compiler.release]
@@ -73,6 +79,12 @@ BasicRuntimeChecks=0
BrowseInformation=0
EnableFunctionLevelLinking=true
+[Compiler.release.ReleaseDLL]
+RuntimeLibrary=2
+
+[Compiler.release.ReleaseMT]
+RuntimeLibrary=0
+
[Compiler.800.release]
PreprocessorDefinitions=_SECURE_SCL=0;_CRT_SECURE_NO_DEPRECATE=1;
@@ -90,7 +102,7 @@ AdditionalLibraryDirectories=
SubSystem=1
AdditionalOptions=
ProgramDatabaseFile=
-ImportLibrary=
+ImportLibrary=$(OutDir)$(TargetName).lib
IgnoreAllDefaultLibraries=false
IgnoreDefaultLibraryNames=
GenerateManifest=true
@@ -172,6 +184,10 @@ Compiler_InlineFunctionExpansion_1 = OnlyExplicitInline
Compiler_InlineFunctionExpansion_2 = AnySuitable
Compiler_Optimization_0 = Disabled
Compiler_Optimization_2 = MaxSpeed
+Compiler_RuntimeLibrary_0 = MultiThreaded
+Compiler_RuntimeLibrary_1 = MultiThreadedDebug
+Compiler_RuntimeLibrary_2 = MultiThreadedDLL
+Compiler_RuntimeLibrary_3 = MultiThreadedDebugDLL
Compiler_UsePrecompiledHeader_0 = NotUsing
Compiler_UsePrecompiledHeader_1 = Create
Compiler_UsePrecompiledHeader_2 = Use
diff --git a/c++/src/build-system/Makefile.mk.in.xcode b/c++/src/build-system/Makefile.mk.in.xcode
index 49f2925..de5cbe1 100644
--- a/c++/src/build-system/Makefile.mk.in.xcode
+++ b/c++/src/build-system/Makefile.mk.in.xcode
@@ -19,6 +19,7 @@ GCC_ENABLE_CPP_EXCEPTIONS = YES
GCC_ENABLE_CPP_RTTI = YES
#SDKROOT = $(DEVELOPER_SDK_DIR)/MacOSX10.8.sdk
SDKROOT =
+OTHER_CPLUSPLUSFLAGS = -std=gnu++11 -stdlib=libc++ -Wno-deprecated-register
FRAMEWORK_SEARCH_PATHS = /System/Library/Frameworks/CoreServices.framework/Frameworks
USE_HEADERMAP = NO
@@ -40,7 +41,7 @@ GCC_PREPROCESSOR_DEFINITIONS = _MT NDEBUG NCBI_XCODE_BUILD
DEAD_CODE_STRIPPING = NO
PREBINDING = NO
#ZERO_LINK = NO
-#OTHER_LDFLAGS =
+OTHER_LDFLAGS = -headerpad_max_install_names
GCC_INLINES_ARE_PRIVATE_EXTERN = NO
GCC_SYMBOLS_PRIVATE_EXTERN = NO
diff --git a/c++/src/build-system/Makefile.requirements b/c++/src/build-system/Makefile.requirements
index c513f90..d3d7eeb 100644
--- a/c++/src/build-system/Makefile.requirements
+++ b/c++/src/build-system/Makefile.requirements
@@ -1,5 +1,5 @@
# -*- makefile-gmake -*-
-# $Id: Makefile.requirements 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.requirements 485094 2015-11-18 18:33:06Z ivanov $
### Requirements handling (at the subtree level)
@@ -24,7 +24,7 @@ ifdef base_req_needers
else
$(req_needers): %.needs-reqs:
@/bin/echo 'NOTE: Skipping project $(notdir $(CURDIR)) due to unmet requirements:'
- @$(foreach r,$(missing_reqs),/bin/echo $(r:$(status_dir)/%.enabled=%))
+ @$(foreach r,$(missing_reqs),/bin/echo $(r:$(status_dir)/%.enabled=%);)
@$(MAKE) $(MFLAGS) $(mark_as_disabled) \
INHERITED_REQUIREMENTS='$(INHERITED_REQUIREMENTS) $(REQUIRES)'
endif
diff --git a/c++/src/build-system/Makefile.rules_with_autodep.in b/c++/src/build-system/Makefile.rules_with_autodep.in
index d596d96..8b0c3ea 100644
--- a/c++/src/build-system/Makefile.rules_with_autodep.in
+++ b/c++/src/build-system/Makefile.rules_with_autodep.in
@@ -1,5 +1,5 @@
#################################
-# $Id: Makefile.rules_with_autodep.in 442382 2014-08-01 18:43:59Z ucko $
+# $Id: Makefile.rules_with_autodep.in 442076 2014-07-30 14:06:45Z ucko $
# Author: Denis Vakatov (vakatov at ncbi.nlm.nih.gov)
#################################
#
diff --git a/c++/src/build-system/Makefile.top_builddir.in b/c++/src/build-system/Makefile.top_builddir.in
index df9b0da..89f6d58 100644
--- a/c++/src/build-system/Makefile.top_builddir.in
+++ b/c++/src/build-system/Makefile.top_builddir.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.top_builddir.in 447105 2014-09-22 17:51:15Z ivanov $
+# $Id: Makefile.top_builddir.in 453410 2014-12-03 16:25:18Z ucko $
# Master (top-level) makefile for all NCBI C++ projects
##################################################################
@@ -32,7 +32,7 @@ include ./Makefile.meta
#
compress_tests:
- $(abs_top_srcdir)/scripts/common/impl/compress_tests.sh \
+ +$(abs_top_srcdir)/scripts/common/impl/compress_tests.sh \
--$(DEBUG_SFX) ../bin
sfi=$(abs_top_srcdir)/scripts/common/impl/strip_for_install.sh
diff --git a/c++/src/build-system/NEWS b/c++/src/build-system/NEWS
index 47942cf..e7727af 100644
--- a/c++/src/build-system/NEWS
+++ b/c++/src/build-system/NEWS
@@ -12,3 +12,8 @@ reconfigure after minor changes.
2012-02-27: new @TOUCH@ variable to avoid hard-coded paths.
2014-07-30: new @SED@ variable to avoid PATH lookup.
+
+2015-03-30: new @VDB_*@ variables to allow use of external SRA/VDB
+installations.
+
+2015-06-01: additional @VDB_*@ variables @VDB_REQ@ and @VDB_POST_LINK at .
diff --git a/c++/src/build-system/aclocal.m4 b/c++/src/build-system/aclocal.m4
index 3ae2a83..5666efc 100644
--- a/c++/src/build-system/aclocal.m4
+++ b/c++/src/build-system/aclocal.m4
@@ -120,6 +120,11 @@ AC_DEFUN(NCBI_RPATHIFY,
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $2; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -128,6 +133,11 @@ AC_DEFUN(NCBI_RPATHIFY,
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $2; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -163,6 +173,10 @@ AC_DEFUN(NCBI_RPATHIFY_OUTPUT,
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$2 | sed -e "$3"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
$1="[$]$1${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -296,7 +310,7 @@ AC_DEFUN(_NCBI_CHECK_PYTHON,
AC_DEFUN(NCBI_LOCAL_FTDS,
[d="dbapi/driver/ftds$1/freetds"
if test $try_local = yes -a -f "${real_srcdir}/src/$d/Makefile.in" ; then
- test "$with_ftds" = $1 && FTDS_PATH="<$d>"
+ test "$ftds_ver" = $1 && FTDS_PATH="<$d>"
FTDS$1[_CTLIB_LIB]="ct_ftds$1${STATIC} tds_ftds$1${STATIC}"
FTDS$1[_CTLIB_LIBS]='$(ICONV_LIBS) $(KRB5_LIBS)'
FTDS$1[_CTLIB_INCLUDE]="-I\$(includedir)/$d -I\$(includedir0)/$d"
diff --git a/c++/src/build-system/config.h.in b/c++/src/build-system/config.h.in
index 487afa0..b640293 100644
--- a/c++/src/build-system/config.h.in
+++ b/c++/src/build-system/config.h.in
@@ -38,16 +38,28 @@
/* Define to 1 if the Berkeley `db_cxx' library is available. */
#undef HAVE_BERKELEY_DB_CXX
+/* Define to 1 if the `Boost.Filesystem' library is available. */
+#undef HAVE_BOOST_FILESYSTEM
+
+/* Define to 1 if the `Boost.Iostreams' library is available. */
+#undef HAVE_BOOST_IOSTREAMS
+
+/* Define to 1 if the `Boost.Program-Options' library is available. */
+#undef HAVE_BOOST_PROGRAM_OPTIONS
+
/* Define to 1 if the `Boost.Regex' library is available. */
#undef HAVE_BOOST_REGEX
/* Define to 1 if the `Boost.Spirit' headers are available. */
#undef HAVE_BOOST_SPIRIT
+/* Define to 1 if the `Boost.System' library is available. */
+#undef HAVE_BOOST_SYSTEM
+
/* Define to 1 if the `Boost.Test' libraries are available. */
#undef HAVE_BOOST_TEST
-/* Define to 1 if the `Boost.Threads' library is available. */
+/* Define to 1 if the `Boost.Thread' library is available. */
#undef HAVE_BOOST_THREAD
/* Define to 1 if the preprocessor supports GNU-style variadic macros. */
@@ -56,6 +68,9 @@
/* Define to 1 if the preprocessor supports C99-style variadic macros. */
#undef HAVE_CPP_STD_VARARGS
+/* Define to 1 if you have the <cpuid.h> header file. */
+#undef HAVE_CPUID_H
+
/* Define to 1 if you have the <dlfcn.h> header file. */
#undef HAVE_DLFCN_H
@@ -234,6 +249,12 @@
/* Define to 1 if you have libglut. */
#undef HAVE_LIBGLUT
+/* Define to 1 if libgmock is available. */
+#undef HAVE_LIBGMOCK
+
+/* Define to 1 if libgmp is available. */
+#undef HAVE_LIBGMP
+
/* Define to 1 if libgnutls is available. */
#undef HAVE_LIBGNUTLS
@@ -272,6 +293,9 @@
/* Define to 1 if libmuparser is available. */
#undef HAVE_LIBMUPARSER
+/* Define to 1 if libhogweed is available. */
+#undef HAVE_LIBNETTLE
+
/* Define to 1 if liboechem is available. */
#undef HAVE_LIBOECHEM
@@ -424,15 +448,15 @@
/* Define to 1 if Python libraries are available. */
#undef HAVE_PYTHON
-/* Define to 1 if Python 2.3 libraries are available. */
-#undef HAVE_PYTHON23
-
-/* Define to 1 if Python 2.4 libraries are available. */
-#undef HAVE_PYTHON24
-
/* Define to 1 if Python 2.5 libraries are available. */
#undef HAVE_PYTHON25
+/* Define to 1 if Python 2.6 libraries are available. */
+#undef HAVE_PYTHON26
+
+/* Define to 1 if Python 2.7 libraries are available. */
+#undef HAVE_PYTHON27
+
/* Define to 1 if you have the `readpassphrase' function. */
#undef HAVE_READPASSPHRASE
@@ -711,6 +735,9 @@
default). */
#undef NCBI_DLL_SUPPORT
+/* Define to the expected Boost version, to help catch skew. */
+#undef NCBI_EXPECTED_BOOST_VERSION
+
/* Define to whatever syntax your compiler supports for marking functions as
to be inlined even if they might not otherwise be. */
#undef NCBI_FORCEINLINE
@@ -769,6 +796,10 @@
/* Define to 1 on Unix. */
#undef NCBI_OS_UNIX
+/* Define to whatever syntax, if any, your compiler supports for marking types
+ as packed to save memory. */
+#undef NCBI_PACKED
+
/* Define to the architecture size. */
#undef NCBI_PLATFORM_BITS
@@ -804,6 +835,10 @@
/* Define to 1 if prototypes can use exception specifications. */
#undef NCBI_USE_THROW_SPEC
+/* Define to whatever syntax, if any, your compiler supports for marking
+ functions whose (status) result is important to check. */
+#undef NCBI_WARN_UNUSED_RESULT
+
/* Define to 1 if the BSD-style netdb interface is reentrant. */
#undef NETDB_REENTRANT
diff --git a/c++/src/build-system/configure b/c++/src/build-system/configure
index 95c4dce..98a50f5 100755
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
@@ -668,6 +668,7 @@ CXX
CXXFLAGS
ac_ct_CXX
MT_SFX
+DPKG_ARCHITECTURE
DLL
DLL_LIB_SETTING
IF_WITH_DLL
@@ -682,6 +683,7 @@ STRIP
DISTCC
CCACHE
TAIL
+BASENAME
SED
TOUCH
GREP
@@ -700,9 +702,13 @@ LZO_INCLUDE
LZO_LIBS
PCRE_INCLUDE
PCRE_LIBS
+GMP_INCLUDE
+GMP_LIBS
LIBGCRYPT_CONFIG
GCRYPT_INCLUDE
GCRYPT_LIBS
+NETTLE_INCLUDE
+NETTLE_LIBS
LIBGNUTLS_CONFIG
GNUTLS_INCLUDE
GNUTLS_LIBS
@@ -728,15 +734,15 @@ mysql_config
PYTHON
PYTHON_INCLUDE
PYTHON_LIBS
-PYTHON23
-PYTHON23_INCLUDE
-PYTHON23_LIBS
-PYTHON24
-PYTHON24_INCLUDE
-PYTHON24_LIBS
PYTHON25
PYTHON25_INCLUDE
PYTHON25_LIBS
+PYTHON26
+PYTHON26_INCLUDE
+PYTHON26_LIBS
+PYTHON27
+PYTHON27_INCLUDE
+PYTHON27_LIBS
PERL
_ACJNI_JAVAC
XMKMF
@@ -794,6 +800,8 @@ AVRO_LIBS
AVROGENCPP
MONGODB_INCLUDE
MONGODB_LIBS
+GMOCK_INCLUDE
+GMOCK_LIBS
signature
build_root
top_srcdir
@@ -964,6 +972,12 @@ NCBI_SSS_LIBPATH
LIBSSSUTILS
LIBSSSDB
sssutils
+VDB_INCLUDE
+VDB_LIB
+VDB_LIBS
+VDB_STATIC_LIBS
+VDB_REQ
+VDB_POST_LINK
SP_INCLUDE
SP_LIBS
ORBACUS_INCLUDE
@@ -993,6 +1007,7 @@ FREETYPE_INCLUDE
FREETYPE_LIBS
GSOAP_PATH
AVRO_STATIC_LIBS
+CEREAL_INCLUDE
MONGODB_STATIC_LIBS
ncbi_xreader_pubseqos
ncbi_xreader_pubseqos2
@@ -1545,13 +1560,14 @@ autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
deactivation makefile-auto-update projects flat-makefile configure-dialog \
check ncbi-public strip pch caution ccache distcc \
ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
-geo included-geo \
-z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
-ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
+geo included-geo vdb downloaded-vdb included-vdb \
+z bz2 lzo pcre gmp gcrypt nettle gnutls openssl krb5 \
+sybase sybase-local sybase-new ftds mysql \
+orbacus freetype ftgl opengl mesa glut glew glew-mx \
bdb python perl jni sqlite3 icu boost boost-tag \
sp expat sablot libxml libxslt libexslt xerces xalan zorba \
oechem sge muparser hdf5 \
-gif jpeg tiff png xpm magic curl mimetic gsoap avro mongodb 3psw \
+gif jpeg tiff png xpm magic curl mimetic gsoap avro cereal mongodb gmock 3psw \
local-lbsm ncbi-crypt connext \
serial objects dbapi app ctools gui algo internal gbench"
@@ -1582,31 +1598,71 @@ for x_arg in "$@" ; do
{ (exit 1); exit 1; }; }
;;
- --with-extra-action=* | --with-build-root=* | --with-build-root-sfx=* \
- | --with-fake-root=* | --with-saved-settings=* \
- | --with-projects=* | --with-check=* | --with-check-tools=* \
- | --with-universal=* | --with-tcheck=* \
- | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
- | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
- | [A-Z]*=* \
- | --with-z=* | --with-bz2=* | --with-lzo=* \
- | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
- | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* | --with-krb5=* \
- | --with-curl=* | --with-gsoap=* | --with-avro=* | --with-mongodb=* \
- | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
- | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
- | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
- | --with-icu=* | --with-xerces=* | --with-xalan=* | --with-zorba=* \
- | --with-libxml=* | --with-libxslt=* | --with-exslt=* \
- | --with-bdb=* | --with-odbc=* | --with-python=* | --with-perl=* \
- | --with-freetype=* | --with-ftgl=* | --with-gif=* | --with-jpeg=* \
- | --with-png=* | --with-tiff=* | --with-xpm=* | --with-opengl=* \
- | --with-mesa=* | --with-glut=* | --with-glew=* | --with-oechem=* \
- | --with-boost=* | --with-boost-tag=* | --with-orbacus=* | --with-sge=* \
- | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
- | --x-includes=* | --x-libraries=* | --with-3psw=* \
- | --target=* | --with-runpath=* | --with-relative-runpath=* \
- | --help | --no-create | --no-recursion)
+ --with-projects=* | --with-saved-settings=* )
+ # Confirm that the specified file exists and is readable.
+ file=`echo $x_arg | sed -e 's/^[^=]*=//'`
+ case "$file" in
+ /* ) ;;
+ * ) file=$srcdir/$file ;;
+ esac
+ if test -f "$file"; then
+ if test -r "$file"; then
+ :
+ else
+ { echo "$as_me: error: $x_arg: requires a readable file; use --help to show usage" >&2
+ { (exit 1); exit 1; }; }
+ fi
+ else
+ { echo "$as_me: error: $x_arg: requires a (readable) file; use --help to show usage" >&2
+ { (exit 1); exit 1; }; }
+ fi
+ ;;
+
+ --srcdir=* | --x-includes=* | --x-libraries=* | --with-tcheck=* \
+ | --with-ncbi-c=* | --with-sss=* | --with-vdb=* | --with-z=* \
+ | --with-bz2=* | --with-lzo=* | --with-pcre=* \
+ | --with-gmp=* | --with-gcrypt=* | --with-nettle=* \
+ | --with-gnutls=* | --with-openssl=* | --with-krb5=* \
+ | --with-sybase-local=* | --with-ftds=*/* | --with-mysql=* \
+ | --with-opengl=* | --with-mesa=* | --with-glut=* | --with-glew=* \
+ | --with-wxwidgets=* | --with-freetype=* | --with-ftgl=* \
+ | --with-fastcgi=*/* | --with-bdb=*/* | --with-orbacus=* \
+ | --with-odbc=* | --with-python=* | --with-perl=* | --with-jni=* \
+ | --with-boost=* | --with-sqlite3=* | --with-icu=* | --with-expat=* \
+ | --with-sablot=* | --with-libxml=* | --with-libxslt=* | --with-exslt=* \
+ | --with-xerces=* | --with-xalan=* | --with-zorba=* | --with-oechem=* \
+ | --with-sge=* | --with-muparser=* | --with-hdf5=* | --with-gif=* \
+ | --with-jpeg=* | --with-png=* | --with-tiff=* | --with-xpm=* \
+ | --with-magic=* | --with-curl=* | --with-mimetic=* | --with-gsoap=* \
+ | --with-avro=* | --with-cereal=* | --with-mongodb=* | --with-gmock=* )
+ # Confirm that the specified directory exists and is readable.
+ dir=`echo $x_arg | sed -e 's/^[^=]*=//'`
+ case "$x_arg" in
+ --srcdir=* | --*=/* ) ;;
+ * ) dir=$srcdir/$dir ;;
+ esac
+ if test -d "$dir"; then
+ if test -r "$dir"; then
+ :
+ else
+ { echo "$as_me: error: $x_arg: requires a readable directory; use --help to show usage" >&2
+ { (exit 1); exit 1; }; }
+ fi
+ else
+ { echo "$as_me: error: $x_arg: requires a (readable) directory; use --help to show usage" >&2
+ { (exit 1); exit 1; }; }
+ fi
+ ;;
+
+ [A-Z]*=* | -h | --help | --help=* | -V | --version | -q | --quiet \
+ | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
+ | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
+ | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+ | --with-universal=* | --with-runpath=* | --with-relative-runpath=* \
+ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+ | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
+ | --with-bdb=[1-9]* | --with-boost-tag=* | --with-3psw=* )
;;
* )
@@ -1731,6 +1787,7 @@ Optional Packages:
--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
--with-lfs enable large file support to the extent possible
--with-limited-linker don't attempt to build especially large projects
+ --with-experimental=... enable named experimental feature(s)
--with-extra-action= script to call after the configuration is complete
--with-autodep automatic generation of dependencies (GNU make)
--with-build-root=DIR specify a non-default build directory name
@@ -1765,6 +1822,10 @@ Optional Packages:
--without-utils do not use NCBI SSS UTIL library
--without-sssdb do not use NCBI SSS DB library
--with-included-sss use the in-tree copy of SSS
+ --with-vdb=DIR use NCBI SRA/VDB Toolkit installation in DIR
+ --without-vdb do not use the NCBI SRA/VDB Toolkit
+ --with-downloaded-vdb download and build SRA/VDB from GitHub
+ --with-included-vdb use the DEPRECATED bundled SRA/VDB Toolkit copy
--with-z=DIR use zlib installation in DIR
--without-z use internal copy of zlib
--with-bz2=DIR use bzlib installation in DIR
@@ -1773,8 +1834,12 @@ Optional Packages:
--without-lzo do not use LZO
--with-pcre=DIR use PCRE installation in DIR
--without-pcre use internal copy of PCRE
+ --with-gmp=DIR use GMP installation in DIR
+ --without-gmp do not use GMP
--with-gcrypt=DIR use gcrypt installation in DIR
--without-gcrypt do not use gcrypt
+ --with-nettle=DIR use Nettle installation in DIR
+ --without-nettle do not use Nettle
--with-gnutls=DIR use GNUTLS installation in DIR
--without-gnutls do not use GNUTLS
--with-openssl=DIR use OpenSSL installation in DIR
@@ -1873,8 +1938,12 @@ Optional Packages:
--without-gsoap do not use gSOAP++
--with-avro=DIR use Apache Avro installation in DIR
--without-avro do not use Apache Avro
+ --with-cereal=DIR use USC Cereal installation in DIR
+ --without-cereal do not use USC Cereal
--with-mongodb=DIR use MongoDB installation in DIR
--without-mongodb do not use MongoDB
+ --with-gmock=DIR use Google Mock installation in DIR
+ --without-gmock do not use Google Mock
--with-3psw=std:netopt favor standard (system) builds of the above pkgs.
--without-3psw do not use any of the above packages
--without-local-lbsm turn off support for IPC with locally running LBSMD
@@ -2061,6 +2130,12 @@ case "$with_3psw" in
else
with_sssdb=no
fi
+ if test "${with_vdb-no}" != "no"; then
+ { echo "$as_me: error: incompatible options: --with-vdb but --without-3psw" >&2
+ { (exit 1); exit 1; }; }
+ else
+ with_vdb=no
+ fi
if test "${with_z-no}" != "no"; then
{ echo "$as_me: error: incompatible options: --with-z but --without-3psw" >&2
{ (exit 1); exit 1; }; }
@@ -2085,12 +2160,24 @@ case "$with_3psw" in
else
with_pcre=no
fi
+ if test "${with_gmp-no}" != "no"; then
+ { echo "$as_me: error: incompatible options: --with-gmp but --without-3psw" >&2
+ { (exit 1); exit 1; }; }
+ else
+ with_gmp=no
+ fi
if test "${with_gcrypt-no}" != "no"; then
{ echo "$as_me: error: incompatible options: --with-gcrypt but --without-3psw" >&2
{ (exit 1); exit 1; }; }
else
with_gcrypt=no
fi
+ if test "${with_nettle-no}" != "no"; then
+ { echo "$as_me: error: incompatible options: --with-nettle but --without-3psw" >&2
+ { (exit 1); exit 1; }; }
+ else
+ with_nettle=no
+ fi
if test "${with_gnutls-no}" != "no"; then
{ echo "$as_me: error: incompatible options: --with-gnutls but --without-3psw" >&2
{ (exit 1); exit 1; }; }
@@ -2367,12 +2454,24 @@ case "$with_3psw" in
else
with_avro=no
fi
+ if test "${with_cereal-no}" != "no"; then
+ { echo "$as_me: error: incompatible options: --with-cereal but --without-3psw" >&2
+ { (exit 1); exit 1; }; }
+ else
+ with_cereal=no
+ fi
if test "${with_mongodb-no}" != "no"; then
{ echo "$as_me: error: incompatible options: --with-mongodb but --without-3psw" >&2
{ (exit 1); exit 1; }; }
else
with_mongodb=no
fi
+ if test "${with_gmock-no}" != "no"; then
+ { echo "$as_me: error: incompatible options: --with-gmock but --without-3psw" >&2
+ { (exit 1); exit 1; }; }
+ else
+ with_gmock=no
+ fi
$as_unset NCBI || test "${NCBI+set}" != set || { NCBI=; export NCBI; }
;;
@@ -2899,6 +2998,12 @@ if test "${with_limited_linker+set}" = set; then
fi
+# Check whether --with-experimental was given.
+if test "${with_experimental+set}" = set; then
+ withval=$with_experimental;
+fi
+
+
## Scripts, make features, and directory naming
# Check whether --with-extra-action was given.
@@ -3106,6 +3211,30 @@ if test "${with_included_sss+set}" = set; then
fi
+# Check whether --with-vdb was given.
+if test "${with_vdb+set}" = set; then
+ withval=$with_vdb;
+fi
+
+
+# Check whether --with-vdb2 was given.
+if test "${with_vdb2+set}" = set; then
+ withval=$with_vdb2;
+fi
+
+
+# Check whether --with-downloaded-vdb was given.
+if test "${with_downloaded_vdb+set}" = set; then
+ withval=$with_downloaded_vdb;
+fi
+
+
+# Check whether --with-included-vdb was given.
+if test "${with_included_vdb+set}" = set; then
+ withval=$with_included_vdb;
+fi
+
+
## Third-party and system packages
# Check whether --with-z was given.
@@ -3156,6 +3285,18 @@ if test "${with_pcre2+set}" = set; then
fi
+# Check whether --with-gmp was given.
+if test "${with_gmp+set}" = set; then
+ withval=$with_gmp;
+fi
+
+
+# Check whether --with-gmp2 was given.
+if test "${with_gmp2+set}" = set; then
+ withval=$with_gmp2;
+fi
+
+
# Check whether --with-gcrypt was given.
if test "${with_gcrypt+set}" = set; then
withval=$with_gcrypt;
@@ -3168,6 +3309,18 @@ if test "${with_gcrypt2+set}" = set; then
fi
+# Check whether --with-nettle was given.
+if test "${with_nettle+set}" = set; then
+ withval=$with_nettle;
+fi
+
+
+# Check whether --with-nettle2 was given.
+if test "${with_nettle2+set}" = set; then
+ withval=$with_nettle2;
+fi
+
+
# Check whether --with-gnutls was given.
if test "${with_gnutls+set}" = set; then
withval=$with_gnutls;
@@ -3756,6 +3909,18 @@ if test "${with_avro2+set}" = set; then
fi
+# Check whether --with-cereal was given.
+if test "${with_cereal+set}" = set; then
+ withval=$with_cereal;
+fi
+
+
+# Check whether --with-cereal2 was given.
+if test "${with_cereal2+set}" = set; then
+ withval=$with_cereal2;
+fi
+
+
# Check whether --with-mongodb was given.
if test "${with_mongodb+set}" = set; then
withval=$with_mongodb;
@@ -3768,6 +3933,18 @@ if test "${with_mongodb2+set}" = set; then
fi
+# Check whether --with-gmock was given.
+if test "${with_gmock+set}" = set; then
+ withval=$with_gmock;
+fi
+
+
+# Check whether --with-gmock2 was given.
+if test "${with_gmock2+set}" = set; then
+ withval=$with_gmock2;
+fi
+
+
# Check whether --with-3psw was given.
if test "${with_3psw+set}" = set; then
withval=$with_3psw;
@@ -3992,6 +4169,33 @@ echo "$as_me: error: incompatible options: --without-mt but --with-openmp" >&2;}
: ${with_mt=yes}
fi
+case "$with_downloaded_vdb:$with_included_vdb:$with_vdb" in
+ yes:yes:* )
+ { { echo "$as_me:$LINENO: error: incompatible options: --with-downloaded-vdb and
+ --with-included-vdb" >&5
+echo "$as_me: error: incompatible options: --with-downloaded-vdb and
+ --with-included-vdb" >&2;}
+ { (exit 1); exit 1; }; }
+ ;;
+ yes:*:no )
+ { { echo "$as_me:$LINENO: error: incompatible options: --without-vdb but
+ --with-downloaded-vdb" >&5
+echo "$as_me: error: incompatible options: --without-vdb but
+ --with-downloaded-vdb" >&2;}
+ { (exit 1); exit 1; }; }
+ ;;
+ *:yes:no )
+ { { echo "$as_me:$LINENO: error: incompatible options: --without-vdb but
+ --with-included-vdb" >&5
+echo "$as_me: error: incompatible options: --without-vdb but
+ --with-included-vdb" >&2;}
+ { (exit 1); exit 1; }; }
+ ;;
+ yes:*: | *:yes: )
+ with_vdb=yes
+ ;;
+esac
+
#### Check for special options
if test "$with_extra_action" = "yes" ; then
{ { echo "$as_me:$LINENO: error: --with-extra-action must have a value after =" >&5
@@ -4056,6 +4260,27 @@ USER_CFLAGS=$CFLAGS
USER_CXXFLAGS=$CXXFLAGS
USER_LDFLAGS=$LDFLAGS
+if test -n "$with_experimental"; then
+ for x in `echo $with_experimental | tr , ' '`; do
+ case "$x" in
+ Int8GI )
+ CPPFLAGS="$CPPFLAGS -DNCBI_INT8_GI"
+ WithFeatures="$WithFeatures${WithFeaturesSep}Int8GI"; WithFeaturesSep=" "
+ ;;
+ StrictGI )
+ CPPFLAGS="$CPPFLAGS -DNCBI_STRICT_GI"
+ WithFeatures="$WithFeatures${WithFeaturesSep}Int8GI"; WithFeaturesSep=" "
+ WithFeatures="$WithFeatures${WithFeaturesSep}StrictGI"; WithFeaturesSep=" "
+ ;;
+ * )
+ { { echo "$as_me:$LINENO: error: unrecognized experimental feature \"$x\"." >&5
+echo "$as_me: error: unrecognized experimental feature \"$x\"." >&2;}
+ { (exit 1); exit 1; }; }
+ ;;
+ esac
+ done
+fi
+
#### Always define this
cat >>confdefs.h <<\_ACEOF
@@ -5819,14 +6044,10 @@ ncbi_compiler_ver="0"
if test "$GCC" = "yes" ; then
compiler_ver="`$real_CXX -dumpversion 2>&1`"
- case "$compiler_ver" in
- 2.95* | 2.96* | 3.* | 4.* )
- compiler="GCC"
- ncbi_compiler="GCC"
- ncbi_compiler_ver="$compiler_ver"
- WithFeatures="$WithFeatures${WithFeaturesSep}GCC"; WithFeaturesSep=" "
- ;;
- esac
+ compiler="GCC"
+ ncbi_compiler="GCC"
+ ncbi_compiler_ver="$compiler_ver"
+ WithFeatures="$WithFeatures${WithFeaturesSep}GCC"; WithFeaturesSep=" "
elif test "$KCC" = "yes" ; then
compiler_ver="$kcc_ver"
compiler="KCC"
@@ -6217,6 +6438,15 @@ case "$host_os:$compiler" in
esac
;;
+ linux*:GCC )
+ if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"
+ then
+ case "$compiler_version" in
+ 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
+ esac
+ fi
+ ;;
+
irix*:GCC )
if test "$with_debug" != "no" ; then
LDFLAGS="-LD_LAYOUT:lgot_buffer=32 $LDFLAGS"
@@ -6349,7 +6579,7 @@ case "$host_os:$compiler" in
fi
# -flat_namespace is necessary for proper handling of shared libraries
# that don't themselves link against all their dependencies.
- LDFLAGS="-flat_namespace $LDFLAGS"
+ LDFLAGS="-flat_namespace -headerpad_max_install_names $LDFLAGS"
if test "$try_old_sdks" = yes; then
sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
@@ -6375,7 +6605,7 @@ case "$host_os:$compiler" in
CXX="$CXX $TARGET"
fi
else
- LDFLAGS="-Wl,-flat_namespace $LDFLAGS"
+ LDFLAGS="-Wl,-flat_namespace -Wl,-headerpad_max_install_names $LDFLAGS"
fi
if test -f /usr/include/dlfcn.h; then
# may be able to do without /sw, so ignore it by default
@@ -7447,6 +7677,53 @@ case "$host_os:$ncbi_cv_prog_cc_wl_rpath" in
;;
esac
+# Extract the first word of "dpkg-architecture", so it can be a program name with args.
+set dummy dpkg-architecture; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_path_DPKG_ARCHITECTURE+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ case $DPKG_ARCHITECTURE in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_DPKG_ARCHITECTURE="$DPKG_ARCHITECTURE" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_DPKG_ARCHITECTURE="$as_dir/$ac_word$ac_exec_ext"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+DPKG_ARCHITECTURE=$ac_cv_path_DPKG_ARCHITECTURE
+if test -n "$DPKG_ARCHITECTURE"; then
+ { echo "$as_me:$LINENO: result: $DPKG_ARCHITECTURE" >&5
+echo "${ECHO_T}$DPKG_ARCHITECTURE" >&6; }
+else
+ { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+if test -x "$DPKG_ARCHITECTURE" \
+ && $DPKG_ARCHITECTURE -qDEB_HOST_MULTIARCH >/dev/null 2>&1; then
+ multiarch=`$DPKG_ARCHITECTURE -qDEB_HOST_MULTIARCH`
+else
+ multiarch=`echo $host | sed -e 's/-unknown-/-/; s/^i[3-9]86-/^i\[3-9\]86/'`
+fi
+
case "$compiler:$compiler_version:$with_bin_release" in
GCC:*:yes )
libstdcxx=`$CXX $LDFLAGS -print-file-name=libstdc++.a`
@@ -7475,7 +7752,8 @@ echo "$as_me: WARNING: Unable to find static libstdc++ requested by --with-bin-r
dir=`dirname "$path"`
abs_dir=`cd "$dir" && pwd`
case "$dir:$abs_dir" in
- *:/lib | *:/usr/lib | *:/usr/lib32 | *:/usr/lib64 )
+ *:/lib | *:/usr/lib | *:/usr/lib32 | *:/usr/lib64 \
+ | *:/usr/lib/$multiarch )
# no rpath needed
break
;;
@@ -8414,6 +8692,46 @@ else
echo "${ECHO_T}no" >&6; }
fi
+# Extract the first word of "basename", so it can be a program name with args.
+set dummy basename; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_path_BASENAME+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ case $BASENAME in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_BASENAME="$BASENAME" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_BASENAME="$as_dir/$ac_word$ac_exec_ext"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+BASENAME=$ac_cv_path_BASENAME
+if test -n "$BASENAME"; then
+ { echo "$as_me:$LINENO: result: $BASENAME" >&5
+echo "${ECHO_T}$BASENAME" >&6; }
+else
+ { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
# Extract the first word of "sed", so it can be a program name with args.
set dummy sed; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
@@ -12399,9 +12717,10 @@ fi
-for ac_header in atomic.h dlfcn.h ieeefp.h poll.h sys/epoll.h sys/mount.h \
- sys/sockio.h sys/statvfs.h sys/sysinfo.h sys/vfs.h \
- x86intrin.h
+
+for ac_header in atomic.h cpuid.h dlfcn.h ieeefp.h poll.h sys/epoll.h \
+ sys/mount.h sys/sockio.h sys/statvfs.h sys/sysinfo.h \
+ sys/vfs.h x86intrin.h
do
as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
@@ -22487,25 +22806,22 @@ cat >>confdefs.h <<_ACEOF
_ACEOF
-{ echo "$as_me:$LINENO: checking syntax for declaring thread-local variables" >&5
-echo $ECHO_N "checking syntax for declaring thread-local variables... $ECHO_C" >&6; }
-if test "${ncbi_cv_c_tls_var+set}" = set; then
+{ echo "$as_me:$LINENO: checking syntax for marking functions whose result should be checked" >&5
+echo $ECHO_N "checking syntax for marking functions whose result should be checked... $ECHO_C" >&6; }
+if test "${ncbi_cv_c_warn_unused_result+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- ncbi_cv_c_tls_var=none
- for tls_var in __thread '__declspec(thread)' _Thread_local; do
- test "$ncbi_cv_c_tls_var" = "none" || break
- cat >conftest.$ac_ext <<_ACEOF
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-$tls_var int i;
+int f(void) __attribute__((warn_unused_result));
int
main ()
{
-static $tls_var int j;
+int status = f();
;
return 0;
}
@@ -22544,46 +22860,45 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_c_tls_var=$tls_var
+ ncbi_cv_c_warn_unused_result='__attribute__((warn_unused_result))'
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-
+ ncbi_cv_c_warn_unused_result=none
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- done
fi
-{ echo "$as_me:$LINENO: result: $ncbi_cv_c_tls_var" >&5
-echo "${ECHO_T}$ncbi_cv_c_tls_var" >&6; }
-tls_var=$ncbi_cv_c_tls_var
-if test "$tls_var" != "none"; then
+{ echo "$as_me:$LINENO: result: $ncbi_cv_c_warn_unused_result" >&5
+echo "${ECHO_T}$ncbi_cv_c_warn_unused_result" >&6; }
+wur=$ncbi_cv_c_warn_unused_result
+test "$wur" = "none" && wur=""
cat >>confdefs.h <<_ACEOF
-#define NCBI_TLS_VAR $tls_var
+#define NCBI_WARN_UNUSED_RESULT $wur
_ACEOF
-fi
-# for FreeTDS
-{ echo "$as_me:$LINENO: checking whether FIONBIO requires BSD_COMP to be defined" >&5
-echo $ECHO_N "checking whether FIONBIO requires BSD_COMP to be defined... $ECHO_C" >&6; }
-if test "${ncbi_cv_decl_fionbio_needs_bsd_comp+set}" = set; then
+{ echo "$as_me:$LINENO: checking syntax for declaring thread-local variables" >&5
+echo $ECHO_N "checking syntax for declaring thread-local variables... $ECHO_C" >&6; }
+if test "${ncbi_cv_c_tls_var+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- cat >conftest.$ac_ext <<_ACEOF
+ ncbi_cv_c_tls_var=none
+ for tls_var in __thread '__declspec(thread)' _Thread_local; do
+ test "$ncbi_cv_c_tls_var" = "none" || break
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #include <sys/types.h>
- #include <sys/ioctl.h>
+$tls_var int i;
int
main ()
{
- int request = FIONBIO;
+static $tls_var int j;
;
return 0;
}
@@ -22622,24 +22937,44 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_decl_fionbio_needs_bsd_comp=no
+ ncbi_cv_c_tls_var=$tls_var
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- cat >conftest.$ac_ext <<_ACEOF
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_c_tls_var" >&5
+echo "${ECHO_T}$ncbi_cv_c_tls_var" >&6; }
+tls_var=$ncbi_cv_c_tls_var
+if test "$tls_var" != "none"; then
+
+cat >>confdefs.h <<_ACEOF
+#define NCBI_TLS_VAR $tls_var
+_ACEOF
+
+fi
+
+{ echo "$as_me:$LINENO: checking syntax for marking types as packed to save memory" >&5
+echo $ECHO_N "checking syntax for marking types as packed to save memory... $ECHO_C" >&6; }
+if test "${ncbi_cv_c_packed+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #define BSD_COMP 1
- #include <sys/types.h>
- #include <sys/ioctl.h>
+
int
main ()
{
- int request = FIONBIO;
+enum E { foo, bar } __attribute__((packed));
;
return 0;
}
@@ -22678,32 +23013,30 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_decl_fionbio_needs_bsd_comp=yes
+ ncbi_cv_c_packed='__attribute__((__packed__))'
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ncbi_cv_decl_fionbio_needs_bsd_comp="never defined at all"
+ ncbi_cv_c_packed=none
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_c_packed" >&5
+echo "${ECHO_T}$ncbi_cv_c_packed" >&6; }
+packed=$ncbi_cv_c_packed
+test "$packed" = "none" && packed=""
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ echo "$as_me:$LINENO: result: $ncbi_cv_decl_fionbio_needs_bsd_comp" >&5
-echo "${ECHO_T}$ncbi_cv_decl_fionbio_needs_bsd_comp" >&6; }
-if test "$ncbi_cv_decl_fionbio_needs_bsd_comp" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define BSD_COMP 1
+cat >>confdefs.h <<_ACEOF
+#define NCBI_PACKED $packed
_ACEOF
-fi
-{ echo "$as_me:$LINENO: checking whether INADDR_NONE is defined" >&5
-echo $ECHO_N "checking whether INADDR_NONE is defined... $ECHO_C" >&6; }
-if test "${ncbi_cv_decl_inaddr_none+set}" = set; then
+# for FreeTDS
+{ echo "$as_me:$LINENO: checking whether FIONBIO requires BSD_COMP to be defined" >&5
+echo $ECHO_N "checking whether FIONBIO requires BSD_COMP to be defined... $ECHO_C" >&6; }
+if test "${ncbi_cv_decl_fionbio_needs_bsd_comp+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -22712,24 +23045,158 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
- #ifdef HAVE_SYS_TYPES_H
- #include <sys/types.h>
- #endif
- #ifdef HAVE_SYS_SOCKET_H
- #include <sys/socket.h>
- #endif
- #ifdef HAVE_NETINET_IN_H
- #include <netinet/in.h>
- #endif
- #ifdef HAVE_ARPA_INET_H
- #include <arpa/inet.h>
- #endif
-
+ #include <sys/types.h>
+ #include <sys/ioctl.h>
int
main ()
{
- unsigned long addr = INADDR_NONE;
+ int request = FIONBIO;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_decl_fionbio_needs_bsd_comp=no
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+ #define BSD_COMP 1
+ #include <sys/types.h>
+ #include <sys/ioctl.h>
+int
+main ()
+{
+ int request = FIONBIO;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_decl_fionbio_needs_bsd_comp=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_decl_fionbio_needs_bsd_comp="never defined at all"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_decl_fionbio_needs_bsd_comp" >&5
+echo "${ECHO_T}$ncbi_cv_decl_fionbio_needs_bsd_comp" >&6; }
+if test "$ncbi_cv_decl_fionbio_needs_bsd_comp" = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define BSD_COMP 1
+_ACEOF
+
+fi
+
+{ echo "$as_me:$LINENO: checking whether INADDR_NONE is defined" >&5
+echo $ECHO_N "checking whether INADDR_NONE is defined... $ECHO_C" >&6; }
+if test "${ncbi_cv_decl_inaddr_none+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+ #ifdef HAVE_SYS_TYPES_H
+ #include <sys/types.h>
+ #endif
+ #ifdef HAVE_SYS_SOCKET_H
+ #include <sys/socket.h>
+ #endif
+ #ifdef HAVE_NETINET_IN_H
+ #include <netinet/in.h>
+ #endif
+ #ifdef HAVE_ARPA_INET_H
+ #include <arpa/inet.h>
+ #endif
+
+int
+main ()
+{
+ unsigned long addr = INADDR_NONE;
;
return 0;
}
@@ -22879,7 +23346,7 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
typedef int TVector __attribute__((vector_size(16)));
- TVector f(TVector v1, TVector v2) { return v1 ^ v2 };
+ TVector f(TVector v1, TVector v2) { return v1 ^ v2; }
int
main ()
{
@@ -25177,7 +25644,7 @@ case "$signature_compiler:$ac_cv_have_decl__LIBCPP_VERSION" in
esac
usr_lib='[/usr]*/lib/*[amdsprcv]*[23469]*'
-no_usr_lib="s,-L$usr_lib ,,g;"
+no_usr_lib="s,-L$usr_lib ,,g; s,-L/usr/lib/$multiarch ,,g"
if test "$with_z" != "no"; then
case "$with_z" in
@@ -25196,6 +25663,11 @@ if test "$with_z" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $Z_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25204,6 +25676,11 @@ if test "$with_z" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $Z_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25217,6 +25694,11 @@ if test "$with_z" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $Z_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25225,6 +25707,11 @@ if test "$with_z" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $Z_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25363,6 +25850,11 @@ if test "$with_bz2" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $BZ2_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25371,6 +25863,11 @@ if test "$with_bz2" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $BZ2_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25384,6 +25881,11 @@ if test "$with_bz2" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $BZ2_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25392,6 +25894,11 @@ if test "$with_bz2" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $BZ2_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25551,6 +26058,11 @@ if test "$with_lzo" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LZO_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25559,6 +26071,11 @@ if test "$with_lzo" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LZO_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25572,6 +26089,11 @@ if test "$with_lzo" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LZO_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25580,6 +26102,11 @@ if test "$with_lzo" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LZO_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25710,6 +26237,11 @@ if test "$with_pcre" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PCRE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25718,6 +26250,11 @@ if test "$with_pcre" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PCRE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25731,6 +26268,11 @@ if test "$with_pcre" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PCRE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25739,6 +26281,11 @@ if test "$with_pcre" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PCRE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -25867,7 +26414,217 @@ else
PCREPOSIX_LIBS=`echo "$PCRE_LIBS" | sed -e 's/-lpcre/-lpcreposix -lpcre/'`
fi
-## SSL/TLS libraries
+## SSL/TLS libraries (and supporting libraries)
+if test "x$with_gmp" != xno; then
+ case "$with_gmp" in
+ yes | '' ) ;;
+ * ) GMP_PATH=$with_gmp ;;
+ esac
+ for pfx in "$compiler_vpfx" "$compiler_pfx" "" ; do
+ vpath=$GMP_PATH/$pfx${DEBUG_SFX}${mt_sfx}${bit64_sfx}
+ if test -d "$vpath" ; then
+ GMP_PATH=$vpath
+ break
+ fi
+ done
+ if test -d "$GMP_PATH"; then
+ ncbi_fix_dir_tmp=`if cd $GMP_PATH; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $GMP_PATH && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ GMP_PATH=$ncbi_fix_dir_tmp2
+ else
+ case "$GMP_PATH" in
+ /*) ;;
+ * ) GMP_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) GMP_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ if test "$with_gmp" != "no"; then
+ case "$with_gmp" in
+ yes | "" ) ;;
+ * ) GMP_PATH=$with_gmp ;;
+ esac
+ if test "$GMP_PATH" != /usr -a -d "$GMP_PATH"; then
+ in_path=" in $GMP_PATH"
+ if test -z "$GMP_INCLUDE" -a -d "$GMP_PATH/include"; then
+ GMP_INCLUDE="-I$GMP_PATH/include"
+ fi
+ if test -n "$GMP_LIBPATH"; then
+ :
+ elif test -d "$GMP_PATH/lib${bit64_sfx}"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $GMP_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ GMP_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $GMP_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ GMP_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ elif test -d "$GMP_PATH/lib"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $GMP_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ GMP_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $GMP_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ GMP_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ fi
+ GMP_LIBS="$GMP_LIBPATH -lgmp "
+ else
+ GMP_INCLUDE=""
+ GMP_LIBS="-lgmp "
+ in_path=
+ fi
+ { echo "$as_me:$LINENO: checking for libgmp$in_path" >&5
+echo $ECHO_N "checking for libgmp$in_path... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_gmp+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ CPPFLAGS=" $GMP_INCLUDE $orig_CPPFLAGS"
+ LIBS="$GMP_LIBS $orig_LIBS"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <gmp.h>
+int
+main ()
+{
+mpz_t x; mpz_init(x);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_lib_gmp=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_lib_gmp=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_gmp" >&5
+echo "${ECHO_T}$ncbi_cv_lib_gmp" >&6; }
+ if test "$ncbi_cv_lib_gmp" = "no"; then
+ if test "${with_gmp:=no}" != no; then
+ { { echo "$as_me:$LINENO: error: --with-gmp explicitly specified, but no usable version found." >&5
+echo "$as_me: error: --with-gmp explicitly specified, but no usable version found." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ fi
+ fi
+ if test "$with_gmp" = "no"; then
+ GMP_PATH="No_GMP"
+ GMP_INCLUDE=
+ GMP_LIBS=
+ else
+ WithPackages="$WithPackages${WithPackagesSep}GMP"; WithPackagesSep=" "
+ GMP_INCLUDE=" $GMP_INCLUDE"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LIBGMP 1
+_ACEOF
+
+ fi
+
+
+
+fi
+if test "$with_gmp" = no; then
+ $as_unset GMP_INCLUDE || test "${GMP_INCLUDE+set}" != set || { GMP_INCLUDE=; export GMP_INCLUDE; }
+ $as_unset GMP_LIBS || test "${GMP_LIBS+set}" != set || { GMP_LIBS=; export GMP_LIBS; }
+else
+ WithPackages="$WithPackages${WithPackagesSep}GMP"; WithPackagesSep=" "
+fi
+
case "$with_gcrypt" in
no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
yes | '' ) ;;
@@ -25946,6 +26703,10 @@ if test "x$with_gcrypt" != xno; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$LIBGCRYPT_CONFIG --exec-prefix | sed -e "s,^,-L,; s,$,/lib,;"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
GCRYPT_LIBPATH="$GCRYPT_LIBPATH${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -25985,6 +26746,11 @@ if test "$with_gcrypt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GCRYPT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -25993,6 +26759,11 @@ if test "$with_gcrypt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GCRYPT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26006,6 +26777,11 @@ if test "$with_gcrypt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GCRYPT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26014,6 +26790,11 @@ if test "$with_gcrypt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GCRYPT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26135,6 +26916,10 @@ if test "x$with_gcrypt" != xno -a -n "$GCRYPT_CONFIG_LIBS"; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `echo $GCRYPT_CONFIG_LIBS | sed -e "$no_usr_lib"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
GCRYPT_LIBS="$GCRYPT_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -26153,6 +26938,268 @@ if test "x$with_gcrypt" != xno -a -n "$GCRYPT_CONFIG_LIBS"; then
fi
fi
+if test "x$with_nettle" != xno; then
+ case "$with_nettle" in
+ yes | '' ) ;;
+ * ) NETTLE_PATH=$with_nettle ;;
+ esac
+ if test -d "$NETTLE_PATH"; then
+ ncbi_fix_dir_tmp=`if cd $NETTLE_PATH; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $NETTLE_PATH && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ NETTLE_PATH=$ncbi_fix_dir_tmp2
+ else
+ case "$NETTLE_PATH" in
+ /*) ;;
+ * ) NETTLE_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) NETTLE_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ if test -d "$NETTLE_PATH/lib$bit64_sfx"; then
+ NETTLE_LIBDIR=$NETTLE_PATH/lib$bit64_sfx
+ else
+ NETTLE_LIBDIR=$NETTLE_PATH/lib
+ fi
+ for pfx in "$compiler_vpfx" "$compiler_pfx" "" ; do
+ vpath=$NETTLE_PATH/$pfx${DEBUG_SFX}${mt_sfx}${bit64_sfx}
+ if test -d "$vpath" ; then
+ NETTLE_LIBDIR=$vpath/lib
+ break
+ fi
+ done
+ if test -d "$NETTLE_LIBDIR"; then
+ ncbi_fix_dir_tmp=`if cd $NETTLE_LIBDIR; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $NETTLE_LIBDIR && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ NETTLE_LIBDIR=$ncbi_fix_dir_tmp2
+ else
+ case "$NETTLE_LIBDIR" in
+ /*) ;;
+ * ) NETTLE_LIBDIR=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) NETTLE_LIBDIR=$ncbi_fix_dir_tmp ;;
+ esac
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $NETTLE_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $NETTLE_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ fi
+ if test "$with_nettle" != "no"; then
+ case "$with_nettle" in
+ yes | "" ) ;;
+ * ) NETTLE_PATH=$with_nettle ;;
+ esac
+ if test "$NETTLE_PATH" != /usr -a -d "$NETTLE_PATH"; then
+ in_path=" in $NETTLE_PATH"
+ if test -z "$NETTLE_INCLUDE" -a -d "$NETTLE_PATH/include"; then
+ NETTLE_INCLUDE="-I$NETTLE_PATH/include"
+ fi
+ if test -n "$NETTLE_LIBPATH"; then
+ :
+ elif test -d "$NETTLE_PATH/lib${bit64_sfx}"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $NETTLE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $NETTLE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ elif test -d "$NETTLE_PATH/lib"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $NETTLE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $NETTLE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ NETTLE_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ fi
+ NETTLE_LIBS="$NETTLE_LIBPATH -lhogweed -lnettle"
+ else
+ NETTLE_INCLUDE=""
+ NETTLE_LIBS="-lhogweed -lnettle"
+ in_path=
+ fi
+ { echo "$as_me:$LINENO: checking for libhogweed$in_path" >&5
+echo $ECHO_N "checking for libhogweed$in_path... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_nettle+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ CPPFLAGS=" $NETTLE_INCLUDE $orig_CPPFLAGS"
+ LIBS="$NETTLE_LIBS $GMP_LIBS $orig_LIBS"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <nettle/sexp.h>
+int
+main ()
+{
+struct sexp_iterator it;
+ sexp_iterator_first(&it, 0, (const uint8_t*) NULL);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_lib_nettle=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_lib_nettle=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_nettle" >&5
+echo "${ECHO_T}$ncbi_cv_lib_nettle" >&6; }
+ if test "$ncbi_cv_lib_nettle" = "no"; then
+ if test "${with_nettle:=no}" != no; then
+ { { echo "$as_me:$LINENO: error: --with-nettle explicitly specified, but no usable version found." >&5
+echo "$as_me: error: --with-nettle explicitly specified, but no usable version found." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ fi
+ fi
+ if test "$with_nettle" = "no"; then
+ NETTLE_PATH="No_NETTLE"
+ NETTLE_INCLUDE=
+ NETTLE_LIBS=
+ else
+ WithPackages="$WithPackages${WithPackagesSep}NETTLE"; WithPackagesSep=" "
+ NETTLE_INCLUDE=" $NETTLE_INCLUDE"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LIBNETTLE 1
+_ACEOF
+
+ fi
+
+
+
+fi
+if test "$with_nettle" = no; then
+ $as_unset NETTLE_INCLUDE || test "${NETTLE_INCLUDE+set}" != set || { NETTLE_INCLUDE=; export NETTLE_INCLUDE; }
+ $as_unset NETTLE_LIBS || test "${NETTLE_LIBS+set}" != set || { NETTLE_LIBS=; export NETTLE_LIBS; }
+else
+ WithPackages="$WithPackages${WithPackagesSep}NETTLE"; WithPackagesSep=" "
+fi
+
case "$with_gnutls" in
no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
yes | '' ) ;;
@@ -26221,11 +27268,11 @@ fi
if test "x$with_gnutls" != xno; then
if test -x "$LIBGNUTLS_CONFIG"; then
if test -z "$GNUTLS_PATH"; then
- p=`libgnutls-config --prefix`
+ p=`$LIBGNUTLS_CONFIG --prefix`
test "x$p" = "x/usr" || GNUTLS_PATH=$p
fi
else
- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib$bit64_sfx/pkgconfig:$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
$LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
fi
case "$LIBGNUTLS_CONFIG" in
@@ -26239,6 +27286,10 @@ if test "x$with_gnutls" != xno; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$LIBGNUTLS_CONFIG --libs-only-L | sed -e ""`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
GNUTLS_LIBPATH="$GNUTLS_LIBPATH${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -26255,6 +27306,8 @@ if test "x$with_gnutls" != xno; then
done
GNUTLS_LIBPATH="$GNUTLS_LIBPATH${ncbi_rp_R_flags}"
fi
+ GNUTLS_CONFIG_LIBS=`$LIBGNUTLS_CONFIG --libs-only-l`
+ GNUTLS_CONFIG_LIBS="$GNUTLS_LIBPATH $GNUTLS_CONFIG_LIBS $Z_LIBS"
;;
no)
;;
@@ -26268,6 +27321,10 @@ if test "x$with_gnutls" != xno; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$LIBGNUTLS_CONFIG --exec-prefix | sed -e "s,^,-L,; s,$,/lib,;"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
GNUTLS_LIBPATH="$GNUTLS_LIBPATH${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -26284,12 +27341,12 @@ if test "x$with_gnutls" != xno; then
done
GNUTLS_LIBPATH="$GNUTLS_LIBPATH${ncbi_rp_R_flags}"
fi
+ GNUTLS_CONFIG_LIBS="`$LIBGNUTLS_CONFIG --libs` $Z_LIBS"
;;
esac
if test "x$LIBGNUTLS_CONFIG" != xno; then
GNUTLS_INCLUDE=`$LIBGNUTLS_CONFIG --cflags`
- GNUTLS_CONFIG_LIBS="`$LIBGNUTLS_CONFIG --libs` $Z_LIBS"
fi
else
$as_unset GNUTLS_CONFIG_LIBS || test "${GNUTLS_CONFIG_LIBS+set}" != set || { GNUTLS_CONFIG_LIBS=; export GNUTLS_CONFIG_LIBS; }
@@ -26311,6 +27368,11 @@ if test "$with_gnutls" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GNUTLS_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26319,6 +27381,11 @@ if test "$with_gnutls" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GNUTLS_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26332,6 +27399,11 @@ if test "$with_gnutls" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GNUTLS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26340,6 +27412,11 @@ if test "$with_gnutls" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GNUTLS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26458,6 +27535,10 @@ if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `echo $GNUTLS_CONFIG_LIBS | sed -e "$no_usr_lib"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
GNUTLS_LIBS="$GNUTLS_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -26505,6 +27586,11 @@ if test "$with_openssl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OPENSSL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26513,6 +27599,11 @@ if test "$with_openssl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OPENSSL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26526,6 +27617,11 @@ if test "$with_openssl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OPENSSL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26534,6 +27630,11 @@ if test "$with_openssl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OPENSSL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26738,6 +27839,11 @@ if test "$with_krb5" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $KRB5_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26746,6 +27852,11 @@ if test "$with_krb5" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $KRB5_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26759,6 +27870,11 @@ if test "$with_krb5" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $KRB5_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26767,6 +27883,11 @@ if test "$with_krb5" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $KRB5_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26893,6 +28014,10 @@ if test "x$with_krb5" != xno; then
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `echo $KRB5_CONFIG_LIBS | sed -e "$no_usr_lib"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
KRB5_LIBS="$KRB5_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -26929,6 +28054,11 @@ if test "$with_curl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $CURL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26937,6 +28067,11 @@ if test "$with_curl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $CURL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -26950,6 +28085,11 @@ if test "$with_curl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $CURL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -26958,6 +28098,11 @@ if test "$with_curl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $CURL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -27074,7 +28219,6 @@ NETWORK_PURE_LIBS="$NETWORK_LIBS"
ncbi_xreader_pubseqos=
UNLESS_PUBSEQOS=
if test "$with_sybase" != "no" ; then
- sybase_lib=lib$bit64_sfx
resolve_sybase=true
default_pointer=default-${NCBI_PLATFORM_BITS}bit
: ${with_sybase_new:="no"}
@@ -27211,15 +28355,30 @@ echo "$as_me: WARNING: ignoring non-standard SYBASE setting: $SYBASE" >&2;} ;;
fi
fi
- SYBASE_LIBPATH="$SYBASE_PATH/${sybase_lib}"
+ if test -f "$SYBASE_PATH/SYBASE.env"; then
+ ocs=`sed -ne 's:^SYBASE_OCS=:/:p' "$SYBASE_PATH/SYBASE.env"`
+ else
+ ocs=
+ fi
+ if test -d "$SYBASE_PATH$ocslib$bit64_sfx"; then
+ SYBASE_LIBPATH="$SYBASE_PATH$ocs/lib$bit64_sfx"
+ else
+ SYBASE_LIBPATH="$SYBASE_PATH$ocs/lib"
+ fi
syb_sfx=$bit64_sfx
+ if test -f "$SYBASE_LIBPATH/libsybct$syb_sfx.a"; then
+ syb_pfx=syb
+ else
+ syb_pfx=
+ fi
+
if test "$with_mt" = "yes" ; then
{ echo "$as_me:$LINENO: checking for reentrant Sybase libraries" >&5
echo $ECHO_N "checking for reentrant Sybase libraries... $ECHO_C" >&6; }
if test "${ncbi_cv_lib_sybase_r+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -f "$SYBASE_LIBPATH/libct_r$bit64_sfx.so"; then
+ if test -f "$SYBASE_LIBPATH/lib${syb_pfx}ct_r$bit64_sfx.so"; then
ncbi_cv_lib_sybase_r=yes
else
ncbi_cv_lib_sybase_r=no
@@ -27233,7 +28392,7 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
fi
case "$host_os" in
linux*) sybtcl=-lsybtcl$syb_sfx; sybtli="" ;;
- *) sybtcl=-ltcl$syb_sfx; sybtli=-ltli$syb_sfx ;;
+ *) sybtcl=-l${syb_pfx}tcl$syb_sfx; sybtli=-ltli$syb_sfx ;;
esac
test -f "$SYBASE_LIBPATH/libtli.so" || sybtli=
@@ -27248,18 +28407,29 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
SYBASE_NETWORK_LIBS="$NETWORK_LIBS"
fi
+ if test -f "$SYBASE_LIBPATH/libsybunic${bit64_sfx}.a"; then
+ sybunic=-lsybunic${bit64_sfx}
+ fi
+
test -n "$bit64_sfx" && SYBASE_INCLUDE="-DSYB_LP64"
- SYBASE_LIBLIST="-lblk$syb_sfx -lct$syb_sfx -lcs$syb_sfx $sybtcl"
- SYBASE_LIBLIST="$SYBASE_LIBLIST -lcomn$syb_sfx -lintl$syb_sfx"
+ SYBASE_LIBLIST="-l${syb_pfx}blk$syb_sfx -l${syb_pfx}ct$syb_sfx"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}cs$syb_sfx $sybtcl"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}comn$syb_sfx"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}intl$syb_sfx $sybunic"
SYBASE_DLLLIST="$sybtli"
# deduce conf.macro: SYBASE_INCLUDE, SYBASE_LIBS, SYBASE_DLLS, SYBASE_DBLIBS
- SYBASE_INCLUDE="-I$SYBASE_PATH/include $SYBASE_INCLUDE"
+ SYBASE_INCLUDE="-I$SYBASE_PATH$ocs/include $SYBASE_INCLUDE"
if test -z "$SYBASE_LCL_PATH" ; then
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SYBASE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -27268,6 +28438,11 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SYBASE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -27277,11 +28452,16 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
SYBASE_LPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
fi
else
- SYBASE_LCL_LIBPATH="$SYBASE_LCL_PATH/${sybase_lib}"
+ SYBASE_LCL_LIBPATH="$SYBASE_LCL_PATH$ocs/${sybase_lib}"
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SYBASE_LCL_LIBPATH $SYBASE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -27290,6 +28470,11 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SYBASE_LCL_LIBPATH $SYBASE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -27298,7 +28483,7 @@ echo "${ECHO_T}$ncbi_cv_lib_sybase_r" >&6; }
done
SYBASE_LPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
fi
- SYBASE_INCLUDE="-I$SYBASE_LCL_PATH/include $SYBASE_INCLUDE"
+ SYBASE_INCLUDE="-I$SYBASE_LCL_PATH$ocs/include $SYBASE_INCLUDE"
fi
SYBASE_LIBS="$SYBASE_LPATH $SYBASE_LIBLIST"
SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
@@ -27415,7 +28600,7 @@ _ACEOF
fi
fi
- SYBASE_DBLIBS="$SYBASE_LPATH -lsybdb${bit64_sfx}"
+ SYBASE_DBLIBS="$SYBASE_LPATH -lsybdb${bit64_sfx} $sybunic"
{ echo "$as_me:$LINENO: checking for Sybase DBLib" >&5
echo $ECHO_N "checking for Sybase DBLib... $ECHO_C" >&6; }
if test "${ncbi_cv_lib_sybdb+set}" = set; then
@@ -27549,6 +28734,11 @@ if test "$with_ftds" != "no" ; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $FTDS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -27557,6 +28747,11 @@ if test "$with_ftds" != "no" ; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $FTDS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -27568,7 +28763,7 @@ if test "$with_ftds" != "no" ; then
FTDS_INCLUDE="-I$FTDS_PATH/include"
d="dbapi/driver/ftds64/freetds"
if test $try_local = yes -a -f "${real_srcdir}/src/$d/Makefile.in" ; then
- test "$with_ftds" = 64 && FTDS_PATH="<$d>"
+ test "$ftds_ver" = 64 && FTDS_PATH="<$d>"
FTDS64_CTLIB_LIB="ct_ftds64${STATIC} tds_ftds64${STATIC}"
FTDS64_CTLIB_LIBS='$(ICONV_LIBS) $(KRB5_LIBS)'
FTDS64_CTLIB_INCLUDE="-I\$(includedir)/$d -I\$(includedir0)/$d"
@@ -27780,6 +28975,10 @@ fi
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$mysql_config --libs${mt_sfx:+_r} | sed -e "s/'//g; $no_usr_lib"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
MYSQL_LIBS="$MYSQL_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -27961,6 +29160,11 @@ if test "$with_bdb" != "no" ; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in ${BERKELEYDB_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -27969,6 +29173,11 @@ if test "$with_bdb" != "no" ; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in ${BERKELEYDB_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -28128,6 +29337,11 @@ _ACEOF
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in ${BERKELEYDB_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -28136,6 +29350,11 @@ _ACEOF
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in ${BERKELEYDB_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -28252,6 +29471,11 @@ case "$ODBC_PATH" in
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in ${ODBC_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -28260,6 +29484,11 @@ case "$ODBC_PATH" in
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in ${ODBC_LIBPATH}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -28775,6 +30004,11 @@ fi
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PYTHON_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -28783,6 +30017,11 @@ fi
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PYTHON_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -28884,27 +30123,27 @@ _ACEOF
- # Extract the first word of "python2.3", so it can be a program name with args.
-set dummy python2.3; ac_word=$2
+ # Extract the first word of "python2.5", so it can be a program name with args.
+set dummy python2.5; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
-if test "${ac_cv_path_PYTHON23+set}" = set; then
+if test "${ac_cv_path_PYTHON25+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- case $PYTHON23 in
+ case $PYTHON25 in
[\\/]* | ?:[\\/]*)
- ac_cv_path_PYTHON23="$PYTHON23" # Let the user override the test with a path.
+ ac_cv_path_PYTHON25="$PYTHON25" # Let the user override the test with a path.
;;
*)
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.3/bin"
+as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.5/bin"
for as_dir in $as_dummy
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_path_PYTHON23="$as_dir/$ac_word$ac_exec_ext"
+ ac_cv_path_PYTHON25="$as_dir/$ac_word$ac_exec_ext"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -28915,51 +30154,61 @@ IFS=$as_save_IFS
;;
esac
fi
-PYTHON23=$ac_cv_path_PYTHON23
-if test -n "$PYTHON23"; then
- { echo "$as_me:$LINENO: result: $PYTHON23" >&5
-echo "${ECHO_T}$PYTHON23" >&6; }
+PYTHON25=$ac_cv_path_PYTHON25
+if test -n "$PYTHON25"; then
+ { echo "$as_me:$LINENO: result: $PYTHON25" >&5
+echo "${ECHO_T}$PYTHON25" >&6; }
else
{ echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi
- if test -x "$PYTHON23"; then
- PYTHON23_VERSION=`$PYTHON23 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
+ if test -x "$PYTHON25"; then
+ PYTHON25_VERSION=`$PYTHON25 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
else
- PYTHON23_VERSION=
- ncbi_cv_lib_python23=no
+ PYTHON25_VERSION=
+ ncbi_cv_lib_python25=no
fi
- if test -n "$PYTHON23_VERSION"; then
- PYTHON23_INCLUDE=`$PYTHON23 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
- PYTHON23_LIBPATH=`$PYTHON23 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
- PYTHON23_DEPS=`$PYTHON23 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
+ if test -n "$PYTHON25_VERSION"; then
+ PYTHON25_INCLUDE=`$PYTHON25 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
+ PYTHON25_LIBPATH=`$PYTHON25 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
+ PYTHON25_DEPS=`$PYTHON25 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
- for x in $PYTHON23_LIBPATH; do
+ for x in $PYTHON25_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
- PYTHON23_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON23_VERSION $PYTHON23_DEPS"
+ PYTHON25_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON25_VERSION $PYTHON25_DEPS"
else
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
- for x in $PYTHON23_LIBPATH; do
+ for x in $PYTHON25_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
ncbi_rp_R_sep=:
done
- PYTHON23_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON23_VERSION $PYTHON23_DEPS"
+ PYTHON25_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON25_VERSION $PYTHON25_DEPS"
fi
- CPPFLAGS="$PYTHON23_INCLUDE $orig_CPPFLAGS"
- LIBS="$PYTHON23_LIBS $orig_LIBS"
- { echo "$as_me:$LINENO: checking for usable Python $PYTHON23_VERSION libraries" >&5
-echo $ECHO_N "checking for usable Python $PYTHON23_VERSION libraries... $ECHO_C" >&6; }
-if test "${ncbi_cv_lib_python23+set}" = set; then
+ CPPFLAGS="$PYTHON25_INCLUDE $orig_CPPFLAGS"
+ LIBS="$PYTHON25_LIBS $orig_LIBS"
+ { echo "$as_me:$LINENO: checking for usable Python $PYTHON25_VERSION libraries" >&5
+echo $ECHO_N "checking for usable Python $PYTHON25_VERSION libraries... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_python25+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -29018,58 +30267,57 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_lib_python23=yes
+ ncbi_cv_lib_python25=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ncbi_cv_lib_python23=no
+ ncbi_cv_lib_python25=no
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
fi
-{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python23" >&5
-echo "${ECHO_T}$ncbi_cv_lib_python23" >&6; }
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python25" >&5
+echo "${ECHO_T}$ncbi_cv_lib_python25" >&6; }
else
- ncbi_cv_lib_python23=no
+ ncbi_cv_lib_python25=no
fi
- if test "$ncbi_cv_lib_python23" = "no"; then
- PYTHON23_INCLUDE=
- PYTHON23_LIBS=
+ if test "$ncbi_cv_lib_python25" = "no"; then
+ PYTHON25_INCLUDE=
+ PYTHON25_LIBS=
else
- WithPackages="$WithPackages${WithPackagesSep}PYTHON23"; WithPackagesSep=" "
+ WithPackages="$WithPackages${WithPackagesSep}PYTHON25"; WithPackagesSep=" "
cat >>confdefs.h <<\_ACEOF
-#define HAVE_PYTHON23 1
+#define HAVE_PYTHON25 1
_ACEOF
fi
- : ${PYTHON_PATH:="/usr/local/python-2.4.4"}
- # Extract the first word of "python2.4", so it can be a program name with args.
-set dummy python2.4; ac_word=$2
+ # Extract the first word of "python2.6", so it can be a program name with args.
+set dummy python2.6; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
-if test "${ac_cv_path_PYTHON24+set}" = set; then
+if test "${ac_cv_path_PYTHON26+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- case $PYTHON24 in
+ case $PYTHON26 in
[\\/]* | ?:[\\/]*)
- ac_cv_path_PYTHON24="$PYTHON24" # Let the user override the test with a path.
+ ac_cv_path_PYTHON26="$PYTHON26" # Let the user override the test with a path.
;;
*)
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.4/bin"
+as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.6/bin"
for as_dir in $as_dummy
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_path_PYTHON24="$as_dir/$ac_word$ac_exec_ext"
+ ac_cv_path_PYTHON26="$as_dir/$ac_word$ac_exec_ext"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -29080,51 +30328,61 @@ IFS=$as_save_IFS
;;
esac
fi
-PYTHON24=$ac_cv_path_PYTHON24
-if test -n "$PYTHON24"; then
- { echo "$as_me:$LINENO: result: $PYTHON24" >&5
-echo "${ECHO_T}$PYTHON24" >&6; }
+PYTHON26=$ac_cv_path_PYTHON26
+if test -n "$PYTHON26"; then
+ { echo "$as_me:$LINENO: result: $PYTHON26" >&5
+echo "${ECHO_T}$PYTHON26" >&6; }
else
{ echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi
- if test -x "$PYTHON24"; then
- PYTHON24_VERSION=`$PYTHON24 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
+ if test -x "$PYTHON26"; then
+ PYTHON26_VERSION=`$PYTHON26 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
else
- PYTHON24_VERSION=
- ncbi_cv_lib_python24=no
+ PYTHON26_VERSION=
+ ncbi_cv_lib_python26=no
fi
- if test -n "$PYTHON24_VERSION"; then
- PYTHON24_INCLUDE=`$PYTHON24 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
- PYTHON24_LIBPATH=`$PYTHON24 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
- PYTHON24_DEPS=`$PYTHON24 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
+ if test -n "$PYTHON26_VERSION"; then
+ PYTHON26_INCLUDE=`$PYTHON26 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
+ PYTHON26_LIBPATH=`$PYTHON26 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
+ PYTHON26_DEPS=`$PYTHON26 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
- for x in $PYTHON24_LIBPATH; do
+ for x in $PYTHON26_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
- PYTHON24_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON24_VERSION $PYTHON24_DEPS"
+ PYTHON26_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON26_VERSION $PYTHON26_DEPS"
else
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
- for x in $PYTHON24_LIBPATH; do
+ for x in $PYTHON26_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
ncbi_rp_R_sep=:
done
- PYTHON24_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON24_VERSION $PYTHON24_DEPS"
+ PYTHON26_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON26_VERSION $PYTHON26_DEPS"
fi
- CPPFLAGS="$PYTHON24_INCLUDE $orig_CPPFLAGS"
- LIBS="$PYTHON24_LIBS $orig_LIBS"
- { echo "$as_me:$LINENO: checking for usable Python $PYTHON24_VERSION libraries" >&5
-echo $ECHO_N "checking for usable Python $PYTHON24_VERSION libraries... $ECHO_C" >&6; }
-if test "${ncbi_cv_lib_python24+set}" = set; then
+ CPPFLAGS="$PYTHON26_INCLUDE $orig_CPPFLAGS"
+ LIBS="$PYTHON26_LIBS $orig_LIBS"
+ { echo "$as_me:$LINENO: checking for usable Python $PYTHON26_VERSION libraries" >&5
+echo $ECHO_N "checking for usable Python $PYTHON26_VERSION libraries... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_python26+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -29183,57 +30441,57 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_lib_python24=yes
+ ncbi_cv_lib_python26=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ncbi_cv_lib_python24=no
+ ncbi_cv_lib_python26=no
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
fi
-{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python24" >&5
-echo "${ECHO_T}$ncbi_cv_lib_python24" >&6; }
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python26" >&5
+echo "${ECHO_T}$ncbi_cv_lib_python26" >&6; }
else
- ncbi_cv_lib_python24=no
+ ncbi_cv_lib_python26=no
fi
- if test "$ncbi_cv_lib_python24" = "no"; then
- PYTHON24_INCLUDE=
- PYTHON24_LIBS=
+ if test "$ncbi_cv_lib_python26" = "no"; then
+ PYTHON26_INCLUDE=
+ PYTHON26_LIBS=
else
- WithPackages="$WithPackages${WithPackagesSep}PYTHON24"; WithPackagesSep=" "
+ WithPackages="$WithPackages${WithPackagesSep}PYTHON26"; WithPackagesSep=" "
cat >>confdefs.h <<\_ACEOF
-#define HAVE_PYTHON24 1
+#define HAVE_PYTHON26 1
_ACEOF
fi
- # Extract the first word of "python2.5", so it can be a program name with args.
-set dummy python2.5; ac_word=$2
+ # Extract the first word of "python2.7", so it can be a program name with args.
+set dummy python2.7; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
-if test "${ac_cv_path_PYTHON25+set}" = set; then
+if test "${ac_cv_path_PYTHON27+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- case $PYTHON25 in
+ case $PYTHON27 in
[\\/]* | ?:[\\/]*)
- ac_cv_path_PYTHON25="$PYTHON25" # Let the user override the test with a path.
+ ac_cv_path_PYTHON27="$PYTHON27" # Let the user override the test with a path.
;;
*)
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.5/bin"
+as_dummy="$PYTHON_PATH/bin:$PATH:/usr/local/python-2.7/bin"
for as_dir in $as_dummy
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_path_PYTHON25="$as_dir/$ac_word$ac_exec_ext"
+ ac_cv_path_PYTHON27="$as_dir/$ac_word$ac_exec_ext"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -29244,51 +30502,61 @@ IFS=$as_save_IFS
;;
esac
fi
-PYTHON25=$ac_cv_path_PYTHON25
-if test -n "$PYTHON25"; then
- { echo "$as_me:$LINENO: result: $PYTHON25" >&5
-echo "${ECHO_T}$PYTHON25" >&6; }
+PYTHON27=$ac_cv_path_PYTHON27
+if test -n "$PYTHON27"; then
+ { echo "$as_me:$LINENO: result: $PYTHON27" >&5
+echo "${ECHO_T}$PYTHON27" >&6; }
else
{ echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi
- if test -x "$PYTHON25"; then
- PYTHON25_VERSION=`$PYTHON25 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
+ if test -x "$PYTHON27"; then
+ PYTHON27_VERSION=`$PYTHON27 -c 'from distutils import sysconfig; print sysconfig.get_config_var("VERSION")' 2>/dev/null`
else
- PYTHON25_VERSION=
- ncbi_cv_lib_python25=no
+ PYTHON27_VERSION=
+ ncbi_cv_lib_python27=no
fi
- if test -n "$PYTHON25_VERSION"; then
- PYTHON25_INCLUDE=`$PYTHON25 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
- PYTHON25_LIBPATH=`$PYTHON25 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
- PYTHON25_DEPS=`$PYTHON25 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
+ if test -n "$PYTHON27_VERSION"; then
+ PYTHON27_INCLUDE=`$PYTHON27 -c 'from distutils import sysconfig; f=sysconfig.get_python_inc; print "-I%s -I%s" % (f(), f(True))'`
+ PYTHON27_LIBPATH=`$PYTHON27 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBDIR", "LIBPL"))'`
+ PYTHON27_DEPS=`$PYTHON27 -c 'from distutils import sysconfig; print " ".join(sysconfig.get_config_vars("LIBS", "SYSLIBS"))'`
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
- for x in $PYTHON25_LIBPATH; do
+ for x in $PYTHON27_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
- PYTHON25_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON25_VERSION $PYTHON25_DEPS"
+ PYTHON27_LIBS="${ncbi_rp_L_flags} -lpython$PYTHON27_VERSION $PYTHON27_DEPS"
else
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
- for x in $PYTHON25_LIBPATH; do
+ for x in $PYTHON27_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
ncbi_rp_R_sep=:
done
- PYTHON25_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON25_VERSION $PYTHON25_DEPS"
+ PYTHON27_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lpython$PYTHON27_VERSION $PYTHON27_DEPS"
fi
- CPPFLAGS="$PYTHON25_INCLUDE $orig_CPPFLAGS"
- LIBS="$PYTHON25_LIBS $orig_LIBS"
- { echo "$as_me:$LINENO: checking for usable Python $PYTHON25_VERSION libraries" >&5
-echo $ECHO_N "checking for usable Python $PYTHON25_VERSION libraries... $ECHO_C" >&6; }
-if test "${ncbi_cv_lib_python25+set}" = set; then
+ CPPFLAGS="$PYTHON27_INCLUDE $orig_CPPFLAGS"
+ LIBS="$PYTHON27_LIBS $orig_LIBS"
+ { echo "$as_me:$LINENO: checking for usable Python $PYTHON27_VERSION libraries" >&5
+echo $ECHO_N "checking for usable Python $PYTHON27_VERSION libraries... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_python27+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -29347,30 +30615,30 @@ eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ncbi_cv_lib_python25=yes
+ ncbi_cv_lib_python27=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ncbi_cv_lib_python25=no
+ ncbi_cv_lib_python27=no
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
fi
-{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python25" >&5
-echo "${ECHO_T}$ncbi_cv_lib_python25" >&6; }
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_python27" >&5
+echo "${ECHO_T}$ncbi_cv_lib_python27" >&6; }
else
- ncbi_cv_lib_python25=no
+ ncbi_cv_lib_python27=no
fi
- if test "$ncbi_cv_lib_python25" = "no"; then
- PYTHON25_INCLUDE=
- PYTHON25_LIBS=
+ if test "$ncbi_cv_lib_python27" = "no"; then
+ PYTHON27_INCLUDE=
+ PYTHON27_LIBS=
else
- WithPackages="$WithPackages${WithPackagesSep}PYTHON25"; WithPackagesSep=" "
+ WithPackages="$WithPackages${WithPackagesSep}PYTHON27"; WithPackagesSep=" "
cat >>confdefs.h <<\_ACEOF
-#define HAVE_PYTHON25 1
+#define HAVE_PYTHON27 1
_ACEOF
fi
@@ -29378,17 +30646,15 @@ _ACEOF
if test "$ncbi_cv_lib_python" = "no"; then
- # Favor python 2.4 as the only version configure historically
- # recognized, but otherwise prefer newer versions.
- if test "$ncbi_cv_lib_python24" = "yes"; then
- PYTHON_INCLUDE=$PYTHON24_INCLUDE
- PYTHON_LIBS=$PYTHON24_LIBS
+ if test "$ncbi_cv_lib_python27" = "yes"; then
+ PYTHON_INCLUDE=$PYTHON27_INCLUDE
+ PYTHON_LIBS=$PYTHON27_LIBS
+ elif test "$ncbi_cv_lib_python26" = "yes"; then
+ PYTHON_INCLUDE=$PYTHON26_INCLUDE
+ PYTHON_LIBS=$PYTHON26_LIBS
elif test "$ncbi_cv_lib_python25" = "yes"; then
PYTHON_INCLUDE=$PYTHON25_INCLUDE
PYTHON_LIBS=$PYTHON25_LIBS
- elif test "$ncbi_cv_lib_python23" = "yes"; then
- PYTHON_INCLUDE=$PYTHON23_INCLUDE
- PYTHON_LIBS=$PYTHON23_LIBS
fi
if test -n "$PYTHON_LIBS"; then
WithPackages="$WithPackages${WithPackagesSep}PYTHON"; WithPackagesSep=" "
@@ -29462,6 +30728,11 @@ fi
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PERL_ARCHLIB/CORE; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -29470,6 +30741,11 @@ fi
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PERL_ARCHLIB/CORE; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -29894,6 +31170,11 @@ if test "$with_boost" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $BOOST_LIBPATH_; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -29902,6 +31183,11 @@ if test "$with_boost" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $BOOST_LIBPATH_; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -29911,19 +31197,29 @@ if test "$with_boost" != "no"; then
BOOST_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
fi
fi
- test -d "$BOOST_PATH" || BOOST_LIBPATH_=/usr/lib
- boost_path_digits=`basename $BOOST_PATH | sed -e 's/-ncbi[0-9]*$//; s/.0$//' | tr -cd 0123456789`
+ if test -d "$BOOST_PATH"; then
+ boost_path_digits=`basename $BOOST_PATH | sed -e 's/-ncbi[0-9]*$//; s/.0$//' | tr -cd 0123456789`
+ else
+ boost_path_digits=
+ BOOST_LIBPATH_=/usr/lib
+ fi
if test -n "$boost_path_digits"; then
boost_version_digits=`echo $ncbi_cv_lib_boost_version | sed -e 's/.0$//' | tr -cd 0123456789`
if test $boost_path_digits != "$boost_version_digits"; then
# presumably stale, particularly if boost_version WASN'T cached;
# uncache all relevant settings
$as_unset ncbi_cv_lib_boost_version || test "${ncbi_cv_lib_boost_version+set}" != set || { ncbi_cv_lib_boost_version=; export ncbi_cv_lib_boost_version; }
+ $as_unset ncbi_cv_lib_boost_version_num || test "${ncbi_cv_lib_boost_version_num+set}" != set || { ncbi_cv_lib_boost_version_num=; export ncbi_cv_lib_boost_version_num; }
$as_unset ncbi_cv_lib_boost_regex || test "${ncbi_cv_lib_boost_regex+set}" != set || { ncbi_cv_lib_boost_regex=; export ncbi_cv_lib_boost_regex; }
$as_unset ncbi_cv_lib_boost_spirit || test "${ncbi_cv_lib_boost_spirit+set}" != set || { ncbi_cv_lib_boost_spirit=; export ncbi_cv_lib_boost_spirit; }
$as_unset ncbi_cv_lib_boost_system || test "${ncbi_cv_lib_boost_system+set}" != set || { ncbi_cv_lib_boost_system=; export ncbi_cv_lib_boost_system; }
+ $as_unset ncbi_cv_lib_boost_filesystem || test "${ncbi_cv_lib_boost_filesystem+set}" != set || { ncbi_cv_lib_boost_filesystem=; export ncbi_cv_lib_boost_filesystem; }
+ $as_unset ncbi_cv_lib_boost_iostreams || test "${ncbi_cv_lib_boost_iostreams+set}" != set || { ncbi_cv_lib_boost_iostreams=; export ncbi_cv_lib_boost_iostreams; }
+ $as_unset ncbi_cv_lib_boost_program_options || test "${ncbi_cv_lib_boost_program_options+set}" != set || { ncbi_cv_lib_boost_program_options=; export ncbi_cv_lib_boost_program_options; }
$as_unset ncbi_cv_lib_boost_test || test "${ncbi_cv_lib_boost_test+set}" != set || { ncbi_cv_lib_boost_test=; export ncbi_cv_lib_boost_test; }
$as_unset ncbi_cv_lib_boost_thread || test "${ncbi_cv_lib_boost_thread+set}" != set || { ncbi_cv_lib_boost_thread=; export ncbi_cv_lib_boost_thread; }
+ elif test -z "$ncbi_cv_lib_boost_version_num"; then
+ $as_unset ncbi_cv_lib_boost_version || test "${ncbi_cv_lib_boost_version+set}" != set || { ncbi_cv_lib_boost_version=; export ncbi_cv_lib_boost_version; }
fi
fi
{ echo "$as_me:$LINENO: checking Boost version" >&5
@@ -29939,6 +31235,7 @@ cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <boost/version.hpp>
+ncbi_cv_lib_boost_version_num=BOOST_VERSION
ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
_ACEOF
@@ -29951,6 +31248,11 @@ _ACEOF
fi
{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_boost_version" >&5
echo "${ECHO_T}$ncbi_cv_lib_boost_version" >&6; }
+
+cat >>confdefs.h <<_ACEOF
+#define NCBI_EXPECTED_BOOST_VERSION $ncbi_cv_lib_boost_version_num
+_ACEOF
+
if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
fi
@@ -29983,7 +31285,7 @@ echo "$as_me: error: --with-boost: Boost library is too old" >&2;}
fi
with_boost=no
;;
- 1_3[5-9] | 1_3[5-9]_* | 1_4* | 1_5[0-3] | 1_5[0-3]_* ) ;;
+ 1_3[5-9] | 1_3[5-9]_* | 1_4* | 1_5[0-7] | 1_5[0-7]_* ) ;;
'' ) with_boost=no ;;
* )
{ echo "$as_me:$LINENO: WARNING: Untested Boost version; may prove incompatible." >&5
@@ -30034,7 +31336,17 @@ echo $ECHO_N "checking for Boost library name tag... $ECHO_C" >&6; }
then
found=yes
break
+ else
+ for ext in .a .so; do
+ name=libboost_system$base$bsfx$ext
+ path=`$CXX -L$BOOST_LIBPATH_ -print-file-name=$name \
+ 2>/dev/null`
+ case "$path" in
+ $BOOST_PATH/*/$name ) found=yes; break ;;
+ esac
+ done
fi
+ test "$found" = yes && break
done
test "$found" = yes && break
done
@@ -30167,10 +31479,24 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <boost/spirit.hpp>
+ using namespace boost::spirit;
+ struct MyGrammar : public grammar<MyGrammar>
+ {
+ template <typename TScanner>
+ struct definition {
+ definition(const MyGrammar&) { }
+ typedef rule<TScanner, parser_context<>,
+ parser_tag<0> >
+ TRule;
+ TRule my_rule;
+ TRule const & start() const
+ { return my_rule; }
+ };
+ };
int
main ()
{
-boost::spirit::parse("123", boost::spirit::int_p);
+MyGrammar g; parse("123", g);
;
return 0;
}
@@ -30655,8 +31981,8 @@ echo "${ECHO_T}$ncbi_cv_lib_boost_test" >&6; }
BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
fi
- { echo "$as_me:$LINENO: checking for Boost.Threads$in_path" >&5
-echo $ECHO_N "checking for Boost.Threads$in_path... $ECHO_C" >&6; }
+ { echo "$as_me:$LINENO: checking for Boost.Thread$in_path" >&5
+echo $ECHO_N "checking for Boost.Thread$in_path... $ECHO_C" >&6; }
if test "${ncbi_cv_lib_boost_thread+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
@@ -30739,7 +32065,12 @@ else
fi
if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
- WithPackages="$WithPackages${WithPackagesSep}Boost.Filesystem"; WithPackagesSep=" "
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BOOST_FILESYSTEM 1
+_ACEOF
+
+ WithPackages="$WithPackages${WithPackagesSep}Boost.Filesystem"; WithPackagesSep=" "
else
boost_fs_lib=
boost_fs_static_lib=
@@ -30748,14 +32079,24 @@ else
fi
if test "$ncbi_cv_lib_boost_iostreams" != "no"; then
- WithPackages="$WithPackages${WithPackagesSep}Boost.Iostreams"; WithPackagesSep=" "
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BOOST_IOSTREAMS 1
+_ACEOF
+
+ WithPackages="$WithPackages${WithPackagesSep}Boost.Iostreams"; WithPackagesSep=" "
else
BOOST_IOSTREAMS_LIBS=
BOOST_IOSTREAMS_STATIC_LIBS=
fi
if test "$ncbi_cv_lib_boost_program_options" != "no"; then
- WithPackages="$WithPackages${WithPackagesSep}Boost.Program-Options"; WithPackagesSep=" "
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BOOST_PROGRAM_OPTIONS 1
+_ACEOF
+
+ WithPackages="$WithPackages${WithPackagesSep}Boost.Program-Options"; WithPackagesSep=" "
else
BOOST_PROGRAM_OPTIONS_LIBS=
BOOST_PROGRAM_OPTIONS_STATIC_LIBS=
@@ -30783,7 +32124,12 @@ _ACEOF
fi
if test "$ncbi_cv_lib_boost_system" != "no"; then
- WithPackages="$WithPackages${WithPackagesSep}Boost.System"; WithPackagesSep=" "
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BOOST_SYSTEM 1
+_ACEOF
+
+ WithPackages="$WithPackages${WithPackagesSep}Boost.System"; WithPackagesSep=" "
# BOOST_SYSTEM(_STATIC)_LIBS already conditionally cleared above
fi
@@ -30814,7 +32160,7 @@ cat >>confdefs.h <<\_ACEOF
#define HAVE_BOOST_THREAD 1
_ACEOF
- WithPackages="$WithPackages${WithPackagesSep}Boost.Threads"; WithPackagesSep=" "
+ WithPackages="$WithPackages${WithPackagesSep}Boost.Thread"; WithPackagesSep=" "
else
BOOST_THREAD_LIBS=
BOOST_THREAD_STATIC_LIBS=
@@ -32845,6 +34191,11 @@ if test "$with_opengl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OPENGL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -32853,6 +34204,11 @@ if test "$with_opengl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OPENGL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -32866,6 +34222,11 @@ if test "$with_opengl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in /usr/lib/mesa; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -32874,6 +34235,11 @@ if test "$with_opengl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in /usr/lib/mesa; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -33010,6 +34376,11 @@ _ACEOF
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OSMESA_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -33018,6 +34389,11 @@ _ACEOF
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OSMESA_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -33140,6 +34516,11 @@ echo "$as_me: error: --with-mesa explicitly specified, but no usable version fou
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GLUT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -33148,6 +34529,11 @@ echo "$as_me: error: --with-mesa explicitly specified, but no usable version fou
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GLUT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -33296,10 +34682,8 @@ echo "$as_me: error: --with-glut explicitly specified, but no usable version fou
GLEW_LIBDIR=$GLEW_LIBDIR$bit64_sfx
fi
fi
- glew_config="eval PKG_CONFIG_PATH=\"$GLEW_LIBDIR/pkgconfig\" pkg-config"
- else
- glew_config=pkg-config
fi
+ glew_config="eval PKG_CONFIG_PATH=\"$GLEW_LIBDIR/pkgconfig\" pkg-config"
if pkg-config --version >/dev/null 2>&1; then
if $glew_config glewmx --exists >/dev/null 2>&1 \
&& test -n "`$glew_config glewmx --libs 2>/dev/null`"; then
@@ -33453,6 +34837,10 @@ echo "$as_me: error: --with-glew-mx explicitly specified, but no usable version
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `echo $GLEW_LDFLAGS $GLEW_LIBS | sed -e ""`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
tmp_LIBS="$tmp_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -33561,8 +34949,7 @@ LDFLAGS=$orig_LDFLAGS
## wxWidgets
-# Insist on single-byte builds by default, per various projects' expectations.
-: ${with_wxwidgets_ucs=no}
+# : ${with_wxwidgets_ucs=no}
if test "$with_wxwidgets" != "no" ; then
case "$with_wxwidgets" in
yes | "" ) ;;
@@ -33663,7 +35050,7 @@ fi
if test -n "$SYSROOT"; then
deps=`"$wxconf" $wxcfflags --libs --static 2>/dev/null \
| sed -e 's/.*\.a//'`
- libsed="$basesed; s/\$/ $deps/"
+ libsed="$basesed; s%\$% $deps%"
else
libsed=$basesed
fi
@@ -33671,9 +35058,14 @@ fi
* )
baseflags=`$gtkconf --cflags 2>/dev/null`
basesed=$no_usr_lib
- libsed=$basesed
+ deps=`$gtkconf --libs 2>/dev/null`
+ libsed="$basesed; s%\$% $deps%"
;;
esac
+ case "`"$wxconf" $wxcfflags --version`" in
+ 1.* | 2.[0-7].* ) wxlibs=std ;;
+ * ) wxlibs=std,richtext,aui,propgrid ;;
+ esac
{ echo "$as_me:$LINENO: checking for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}" >&5
echo $ECHO_N "checking for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}... $ECHO_C" >&6; }
if test "${ncbi_cv_lib_wxwidgets+set}" = set; then
@@ -33682,14 +35074,18 @@ else
if test -x "$wxconf" ; then
WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
- WXWIDGETS_LIBS=`"$wxconf" $wxcfflags --libs | sed -e "$libsed; s/ -lm / /g;"`
+ WXWIDGETS_LIBS=`"$wxconf" $wxcfflags --libs $wxlibs | sed -e "$libsed; s/ -lm / /g;"`
else
WXWIDGETS_LIBS=
ncbi_rp_L_sep=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
- for x in `"$wxconf" $wxcfflags --libs | sed -e "$libsed; s/ -lm / /g;"`; do
+ for x in `"$wxconf" $wxcfflags --libs $wxlibs | sed -e "$libsed; s/ -lm / /g;"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
WXWIDGETS_LIBS="$WXWIDGETS_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -33794,13 +35190,8 @@ if test "$with_wxwidgets" = "no" ; then
else
WithPackages="$WithPackages${WithPackagesSep}wxWidgets"; WithPackagesSep=" "
case "`"$wxconf" $wxcfflags --version`" in
- 1.* | 2.[0-7].*)
- wxlibs=std
- ;;
- * )
- WithPackages="$WithPackages${WithPackagesSep}wx2.8"; WithPackagesSep=" "
- wxlibs=std,richtext,aui,propgrid
- ;;
+ 1.* | 2.[0-7].*) ;;
+ * ) WithPackages="$WithPackages${WithPackagesSep}wx2.8"; WithPackagesSep=" " ;;
esac
# The "yes" may have been cached; get the actual settings again if needed
if test -z "$WXWIDGETS_INCLUDE"; then
@@ -33815,6 +35206,10 @@ else
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$wxconf $wxcfflags --libs $wxlibs | sed -e "$libsed; s/ -lm / /g;"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
WXWIDGETS_LIBS="$WXWIDGETS_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -33886,6 +35281,11 @@ if test "$with_fastcgi" != "no" ; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $FASTCGI_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -33894,6 +35294,11 @@ if test "$with_fastcgi" != "no" ; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $FASTCGI_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -34272,7 +35677,8 @@ cat >>confdefs.h <<\_ACEOF
_ACEOF
WithPackages="$WithPackages${WithPackagesSep}SSSUTILS"; WithPackagesSep=" "
- if test -f "$local_sss/../ncbils2/asn/login.asn"; then
+ if test -f "$local_sss/../ncbils2/asn/login.asn" \
+ -a -n "$GCRYPT_LIBS"; then
if test "$with_included_sss" = yes || \
grep vformat $NCBI_SSS_INCLUDE/String.hpp >/dev/null 2>&1; then
WithPackages="$WithPackages${WithPackagesSep}LocalNCBILS"; WithPackagesSep=" " # temporary compatibility measure
@@ -34548,6 +35954,11 @@ if test "$with_orbacus" != no; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $fullpath/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -34556,6 +35967,11 @@ if test "$with_orbacus" != no; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $fullpath/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -34572,6 +35988,11 @@ if test "$with_orbacus" != no; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $ORBACUS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -34580,6 +36001,11 @@ if test "$with_orbacus" != no; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $ORBACUS_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -34745,6 +36171,10 @@ else
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$ICU_CONFIG --ldflags-searchpath | sed -e ""`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
ICU_LIBS="$ICU_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -34859,6 +36289,10 @@ else
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$ICU_CONFIG --ldflags-searchpath | sed -e ""`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
ICU_LIBS="$ICU_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -34877,8 +36311,9 @@ else
fi
ICU_LIBS="$ICU_LIBS `$ICU_CONFIG --ldflags-libsonly`"
fi
+ ICU_SEARCHPATH=`$ICU_CONFIG --ldflags-searchpath | sed -e "$no_usr_lib"`
ICU_STATIC_LIBS=`$ICU_CONFIG --ldflags-libsonly | sed -e 's/-licu/-lsicu/g'`
- ICU_STATIC_LIBS="`$ICU_CONFIG --ldflags-searchpath` $ICU_STATIC_LIBS"
+ ICU_STATIC_LIBS="$ICU_SEARCHPATH $ICU_STATIC_LIBS"
cat >>confdefs.h <<\_ACEOF
#define HAVE_ICU 1
@@ -34905,6 +36340,11 @@ if test "$with_expat" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $EXPAT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -34913,6 +36353,11 @@ if test "$with_expat" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $EXPAT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -34926,6 +36371,11 @@ if test "$with_expat" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $EXPAT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -34934,6 +36384,11 @@ if test "$with_expat" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $EXPAT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35082,6 +36537,11 @@ if test "$with_sablot" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SABLOT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35090,6 +36550,11 @@ if test "$with_sablot" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SABLOT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35103,6 +36568,11 @@ if test "$with_sablot" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SABLOT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35111,6 +36581,11 @@ if test "$with_sablot" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SABLOT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35278,6 +36753,11 @@ if test "$with_libxml" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LIBXML_LIBPATH_; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35286,6 +36766,11 @@ if test "$with_libxml" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LIBXML_LIBPATH_; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35395,6 +36880,7 @@ cat >>confdefs.h <<\_ACEOF
#define HAVE_LIBXML 1
_ACEOF
+ export LIBXML_LIBPATH
fi
@@ -35423,6 +36909,11 @@ if test "$with_libxslt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LIBXSLT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35431,6 +36922,11 @@ if test "$with_libxslt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LIBXSLT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35444,6 +36940,11 @@ if test "$with_libxslt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LIBXSLT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35452,6 +36953,11 @@ if test "$with_libxslt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LIBXSLT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35635,6 +37141,11 @@ if test "$with_libexslt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LIBEXSLT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35643,6 +37154,11 @@ if test "$with_libexslt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LIBEXSLT_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35656,6 +37172,11 @@ if test "$with_libexslt" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $LIBEXSLT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35664,6 +37185,11 @@ if test "$with_libexslt" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $LIBEXSLT_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -35880,6 +37406,11 @@ if test "$with_xerces" != no; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $XERCES_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -35888,6 +37419,11 @@ if test "$with_xerces" != no; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $XERCES_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36095,6 +37631,11 @@ if test "$with_xalan" != no; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $XALAN_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36103,6 +37644,11 @@ if test "$with_xalan" != no; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $XALAN_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36318,6 +37864,11 @@ if test "$with_zorba" != no; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $ZORBA_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36326,6 +37877,11 @@ if test "$with_zorba" != no; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $ZORBA_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36467,6 +38023,11 @@ ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SQLITE3_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36475,6 +38036,11 @@ ncbi_rp_L_flags=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SQLITE3_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36500,6 +38066,11 @@ if test "$with_sqlite3" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SQLITE3_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36508,6 +38079,11 @@ if test "$with_sqlite3" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SQLITE3_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36521,6 +38097,11 @@ if test "$with_sqlite3" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SQLITE3_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36529,6 +38110,11 @@ if test "$with_sqlite3" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SQLITE3_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36923,6 +38509,272 @@ else
fi
+# NCBI SRA/VDB
+VDB_POST_LINK=:
+VDB_REQ=VDB
+if test "$with_vdb" != "no" ; then
+ # CURL?
+ vdb_deps="$LIBXML_LIBS $NETWORK_LIBS $BZ2_LIBS $Z_LIBS $DL_LIBS"
+ if test "${with_vdb:-yes}" != "yes" -a -d "$with_vdb"; then
+ VDB_PATH=$with_vdb
+ fi
+ if test -d "$VDB_PATH"; then
+ : ${with_downloaded_vdb=no}
+ else
+ : ${with_downloaded_vdb=$with_vdb}
+ fi
+ if test "$with_downloaded_vdb" != "no"; then
+ { echo "$as_me:$LINENO: trying to build the NCBI SRA/VDB Toolkit from GitHub." >&5
+echo "$as_me: trying to build the NCBI SRA/VDB Toolkit from GitHub." >&6;}
+ VDB_PATH=`$real_srcdir/scripts/common/add_vdb.sh 2>&5`
+ status=$?
+ if test $status != 0; then
+ message="SRA/VDB build failed with status $status"
+ elif test ! -d "$VDB_PATH"; then
+ message="SRA/VDB build nominally succeeded, but failed to report where"
+ else
+ message=
+ fi
+ case "$message:$with_downloaded_vdb" in
+ :* ) ;;
+ *:yes ) { { echo "$as_me:$LINENO: error: $message
+See \`config.log' for more details." >&5
+echo "$as_me: error: $message
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; } ;;
+ * ) { echo "$as_me:$LINENO: WARNING: $message" >&5
+echo "$as_me: WARNING: $message" >&2;} ;;
+ esac
+ fi
+ if test "$with_included_vdb" != "yes"; then
+ if test -z "$VDB_PATH"; then
+ in_path=
+ else
+ vdb_parent=`dirname "$VDB_PATH"`
+ ncbi_fix_dir_tmp=`if cd $vdb_parent; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $vdb_parent && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ vdb_parent=$ncbi_fix_dir_tmp2
+ else
+ case "$vdb_parent" in
+ /*) ;;
+ * ) vdb_parent=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) vdb_parent=$ncbi_fix_dir_tmp ;;
+ esac
+ VDB_PATH=$vdb_parent/`basename "$VDB_PATH"`
+ in_path=" in $VDB_PATH"
+ for x in interfaces include; do
+ if test -d "$VDB_PATH/$x"; then
+ : ${VDB_INCLUDE="-I$VDB_PATH/$x"}
+ break
+ fi
+ done
+ case "$DEBUG_SFX" in
+ Debug )
+ VDB_INCLUDE="$VDB_INCLUDE $VDB_INCLUDE/cc/gcc -D_DEBUGGING"
+ vdb_mode=debug
+ ;;
+ Release )
+ vdb_mode=release
+ ;;
+ esac
+ case "$host_os:$host_cpu:$bit64_sfx" in
+ darwin*:*86*:64 ) vdb_libpath=mac/$vdb_mode/x86_64/lib ;;
+ darwin*:*86*:* ) vdb_libpath=mac/$vdb_mode/fat86/lib ;;
+ linux*:*86*:64 ) vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
+ * )
+ if test -n "$with_vdb"; then
+ { { echo "$as_me:$LINENO: error: --with-vdb explicitly specified,
+ but not supported on this platform." >&5
+echo "$as_me: error: --with-vdb explicitly specified,
+ but not supported on this platform." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ ;;
+ esac
+ for x in "$vdb_libpath" "lib${bit64_sfx:-32}" lib; do
+ if test -n "$x" -a -d "$VDB_PATH/$x"; then
+ : ${VDB_LIBDIR=$VDB_PATH/$x}
+ break
+ fi
+ done
+ fi
+ if test -z "${VDB_LIBS+set}"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $VDB_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ VDB_LIBS="${ncbi_rp_L_flags} -lncbi-vdb $vdb_deps"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $VDB_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ VDB_LIBS="${ncbi_rp_L_flags}${ncbi_rp_R_flags} -lncbi-vdb $vdb_deps"
+ fi
+ fi
+ CPPFLAGS="$orig_CPPFLAGS $VDB_INCLUDE"
+ LIBS="$orig_LIBS $VDB_LIBS"
+ { echo "$as_me:$LINENO: checking for ncbi-vdb$in_path" >&5
+echo $ECHO_N "checking for ncbi-vdb$in_path... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_ncbi_vdb+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+
+ /* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <sra/sradb.h>
+int
+main ()
+{
+const SRAMgr* mgr; SRAMgrMakeRead(&mgr);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_lib_ncbi_vdb=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_lib_ncbi_vdb=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_ncbi_vdb" >&5
+echo "${ECHO_T}$ncbi_cv_lib_ncbi_vdb" >&6; }
+ if test "$ncbi_cv_lib_ncbi_vdb" = yes; then
+ WithPackages="$WithPackages${WithPackagesSep}VDB"; WithPackagesSep=" "
+ VDB_LIB=
+ if test -f "$VDB_LIBDIR/libncbi-vdb-static.a"; then
+ VDB_STATIC_LIBS="-L$VDB_LIBDIR -lncbi-vdb-static $vdb_deps"
+ else
+ VDB_STATIC_LIBS=$VDB_LIBS
+ fi
+ case "$host_os" in
+ darwin*)
+ inst_name=`otool -D $VDB_LIBDIR/libncbi-vdb.dylib 2>/dev/null \
+ | grep -v ':$'`
+ case "$inst_name" in
+ @executable_path* )
+ major=`echo $inst_name | sed -ne 's,.*/libncbi-vdb\.\([1-9][0-9]*\).*\.dylib$,\1,p'`
+ test -z "$major" || \
+ VDB_POST_LINK="install_name_tool -change $inst_name @rpath/libncbi-vdb.$major.dylib"
+ ;;
+ esac
+ ;;
+ esac
+ else
+ VDB_INCLUDE=
+ VDB_LIBS=
+ VDB_STATIC_LIBS=
+ fi
+ elif test -d "$real_srcdir/src/sra/sdk/interfaces"; then
+ case "$host_os" in
+ darwin* | linux* | solaris* )
+ { echo "$as_me:$LINENO: Using local NCBI SRA/VDB copy in src/sra/sdk" >&5
+echo "$as_me: Using local NCBI SRA/VDB copy in src/sra/sdk" >&6;}
+ WithPackages="$WithPackages${WithPackagesSep}VDB"; WithPackagesSep=" "
+ WithPackages="$WithPackages${WithPackagesSep}LocalVDB"; WithPackagesSep=" "
+ VDB_INCLUDE='-I$(includedir)/../src/sra/sdk/interfaces'
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(includedir)/../src/sra/sdk/interfaces/C++Toolkit"
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(top_srcdir)/src/sra/sdk/interfaces"
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(top_srcdir)/src/sra/sdk/interfaces/C++Toolkit"
+ if test "$DEBUG_SFX" = Debug; then
+ VDB_INCLUDE="$VDB_INCLUDE -D_DEBUGGING"
+ fi
+ VDB_LIB=ncbi-vdb-read
+ VDB_LIBS=$vdb_deps
+ VDB_STATIC_LIBS=$VDB_LIBS
+ VDB_REQ=LocalVDB
+ ;;
+ * )
+ { { echo "$as_me:$LINENO: error: --with-included-vdb explicitly specified,
+ but not supported on this platform." >&5
+echo "$as_me: error: --with-included-vdb explicitly specified,
+ but not supported on this platform." >&2;}
+ { (exit 1); exit 1; }; }
+ ;;
+ esac
+ else
+ { { echo "$as_me:$LINENO: error: --with-included-vdb explicitly specified,
+ but no local copy exists." >&5
+echo "$as_me: error: --with-included-vdb explicitly specified,
+ but no local copy exists." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ if test -z "$VDB_LIBS"; then
+ if test "${with_vdb:=no}" != no; then
+ { { echo "$as_me:$LINENO: error: --with-vdb explicitly specified, but no usable version found." >&5
+echo "$as_me: error: --with-vdb explicitly specified, but no usable version found." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ fi
+fi
+
+
### OEChem
# somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
# which depend on oechem....
@@ -36943,6 +38795,11 @@ if test "$with_oechem" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OECHEM_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36951,6 +38808,11 @@ if test "$with_oechem" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OECHEM_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -36964,6 +38826,11 @@ if test "$with_oechem" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $OECHEM_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -36972,6 +38839,11 @@ if test "$with_oechem" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $OECHEM_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37108,10 +38980,16 @@ if test -d "$SGE_PATH" -a -z "$SGE_LIBPATH"; then
break
fi
done
+ BASE_SGE_LIBPATH=$SGE_LIBPATH
ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SGE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37120,6 +38998,11 @@ if test -d "$SGE_PATH" -a -z "$SGE_LIBPATH"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SGE_LIBPATH; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37128,6 +39011,12 @@ if test -d "$SGE_PATH" -a -z "$SGE_LIBPATH"; then
done
SGE_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
fi
+ # Try to use a dedicated directory without alternate versions of
+ # system libraries such as OpenSSL.
+ if test -d "$BASE_SGE_LIBPATH" -a -d "$SGE_PATH/lib/drmaa"; then
+ SGE_LIBPATH=`echo $SGE_LIBPATH \
+ | sed -e "s,-L$BASE_SGE_LIBPATH,-L$SGE_PATH/lib/drmaa,g"`
+ fi
fi
if test "$with_sge" != "no"; then
case "$with_sge" in
@@ -37146,6 +39035,11 @@ if test "$with_sge" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SGE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37154,6 +39048,11 @@ if test "$with_sge" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SGE_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37167,6 +39066,11 @@ if test "$with_sge" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $SGE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37175,6 +39079,11 @@ if test "$with_sge" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $SGE_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37331,6 +39240,11 @@ if test "$with_muparser" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MUPARSER_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37339,6 +39253,11 @@ if test "$with_muparser" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MUPARSER_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37352,6 +39271,11 @@ if test "$with_muparser" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MUPARSER_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37360,6 +39284,11 @@ if test "$with_muparser" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MUPARSER_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37515,6 +39444,11 @@ if test "$with_hdf5" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $HDF5_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37523,6 +39457,11 @@ if test "$with_hdf5" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $HDF5_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37536,6 +39475,11 @@ if test "$with_hdf5" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $HDF5_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37544,6 +39488,11 @@ if test "$with_hdf5" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $HDF5_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37674,6 +39623,11 @@ if test "$with_jpeg" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $JPEG_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37682,6 +39636,11 @@ if test "$with_jpeg" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $JPEG_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37695,6 +39654,11 @@ if test "$with_jpeg" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $JPEG_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37703,6 +39667,11 @@ if test "$with_jpeg" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $JPEG_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37837,6 +39806,11 @@ if test "$with_png" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PNG_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37845,6 +39819,11 @@ if test "$with_png" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PNG_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37858,6 +39837,11 @@ if test "$with_png" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $PNG_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -37866,6 +39850,11 @@ if test "$with_png" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $PNG_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -37995,6 +39984,11 @@ if test "$with_tiff" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $TIFF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38003,6 +39997,11 @@ if test "$with_tiff" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $TIFF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38016,6 +40015,11 @@ if test "$with_tiff" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $TIFF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38024,6 +40028,11 @@ if test "$with_tiff" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $TIFF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38153,6 +40162,11 @@ if test "$with_ungif" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $UNGIF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38161,6 +40175,11 @@ if test "$with_ungif" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $UNGIF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38174,6 +40193,11 @@ if test "$with_ungif" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $UNGIF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38182,6 +40206,11 @@ if test "$with_ungif" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $UNGIF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38310,6 +40339,11 @@ if test "$with_ungif" = "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GIF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38318,6 +40352,11 @@ if test "$with_ungif" = "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GIF_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38331,6 +40370,11 @@ if test "$with_ungif" = "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GIF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38339,6 +40383,11 @@ if test "$with_ungif" = "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GIF_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38477,6 +40526,11 @@ if test "$with_xpm" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $XPM_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38485,6 +40539,11 @@ if test "$with_xpm" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $XPM_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38498,6 +40557,11 @@ if test "$with_xpm" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $XPM_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38506,6 +40570,11 @@ if test "$with_xpm" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $XPM_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38674,6 +40743,10 @@ fi
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in `$freetype_config --libs | sed -e "$no_usr_lib"`; do
case "$x" in
+ -L/lib | -L/usr/lib | -L/usr/lib32 | -L/usr/lib64 \
+ | -L/usr/lib/$multiarch )
+ continue
+ ;;
-L*)
FREETYPE_LIBS="$FREETYPE_LIBS${ncbi_rp_L_sep}$x"
x=`echo $x | sed -e "s/^-L//; $ncbi_rpath_sed"`
@@ -38913,6 +40986,11 @@ ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $FTGL_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38921,6 +40999,11 @@ ncbi_rp_L_flags=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $FTGL_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38947,6 +41030,11 @@ if test "$with_ftgl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $FTGL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38955,6 +41043,11 @@ if test "$with_ftgl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $FTGL_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -38968,6 +41061,11 @@ if test "$with_ftgl" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $FTGL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -38976,6 +41074,11 @@ if test "$with_ftgl" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $FTGL_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39103,6 +41206,11 @@ if test "$with_magic" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MAGIC_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39111,6 +41219,11 @@ if test "$with_magic" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MAGIC_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39124,6 +41237,11 @@ if test "$with_magic" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MAGIC_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39132,6 +41250,11 @@ if test "$with_magic" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MAGIC_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39279,6 +41402,11 @@ ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MIMETIC_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39287,6 +41415,11 @@ ncbi_rp_L_flags=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MIMETIC_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39313,6 +41446,11 @@ if test "$with_mimetic" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MIMETIC_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39321,6 +41459,11 @@ if test "$with_mimetic" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MIMETIC_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39334,6 +41477,11 @@ if test "$with_mimetic" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MIMETIC_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39342,6 +41490,11 @@ if test "$with_mimetic" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MIMETIC_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39503,6 +41656,11 @@ ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GSOAP_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39511,6 +41669,11 @@ ncbi_rp_L_flags=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GSOAP_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39621,6 +41784,11 @@ if test "$with_gsoap" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GSOAP_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39629,6 +41797,11 @@ if test "$with_gsoap" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GSOAP_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39642,6 +41815,11 @@ if test "$with_gsoap" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $GSOAP_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39650,6 +41828,11 @@ if test "$with_gsoap" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $GSOAP_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39827,6 +42010,11 @@ if test "$with_avro" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $AVRO_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39835,6 +42023,11 @@ if test "$with_avro" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $AVRO_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -39848,6 +42041,11 @@ if test "$with_avro" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $AVRO_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -39856,6 +42054,11 @@ if test "$with_avro" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $AVRO_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -40013,6 +42216,114 @@ fi
fi
+
+# USC Cereal (header-only)
+case "$with_cereal" in
+ yes | no | '' ) ;;
+ * ) CEREAL_PATH=$with_cereal ;;
+esac
+if test "$with_cereal" != no; then
+ in_cereal=
+ if test -d "$CEREAL_PATH"; then
+ ncbi_fix_dir_tmp=`if cd $CEREAL_PATH; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $CEREAL_PATH && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ CEREAL_PATH=$ncbi_fix_dir_tmp2
+ else
+ case "$CEREAL_PATH" in
+ /*) ;;
+ * ) CEREAL_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) CEREAL_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ in_cereal=" in $CEREAL_PATH"
+ fi
+ CEREAL_INCLUDE=-I$CEREAL_PATH/include
+ { echo "$as_me:$LINENO: checking for USC Cereal$in_cereal" >&5
+echo $ECHO_N "checking for USC Cereal$in_cereal... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_cereal+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ CPPFLAGS="$CEREAL_INCLUDE $orig_CPPFLAGS"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <iostream>
+ #include <cereal/archives/binary.hpp>
+int
+main ()
+{
+cereal::BinaryOutputArchive
+ archive(std::cout);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_lib_cereal=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_lib_cereal=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_cereal" >&5
+echo "${ECHO_T}$ncbi_cv_lib_cereal" >&6; }
+ if test "$ncbi_cv_lib_cereal" = yes; then
+ WithPackages="$WithPackages${WithPackagesSep}Cereal"; WithPackagesSep=" "
+ else
+ if test "${with_cereal:=no}" != no; then
+ { { echo "$as_me:$LINENO: error: --with-cereal explicitly specified, but no usable version found." >&5
+echo "$as_me: error: --with-cereal explicitly specified, but no usable version found." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ CEREAL_INCLUDE=
+ fi
+fi
+
+
# MongoDB
case "$with_mongodb" in
yes | no | '' ) ;;
@@ -40044,6 +42355,11 @@ ncbi_rp_L_flags=
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MONGODB_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -40052,6 +42368,11 @@ ncbi_rp_L_flags=
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MONGODB_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -40077,6 +42398,11 @@ if test "$with_mongodb" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MONGODB_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -40085,6 +42411,11 @@ if test "$with_mongodb" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MONGODB_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -40098,6 +42429,11 @@ if test "$with_mongodb" != "no"; then
ncbi_rp_L_sep=$CONF_f_libpath
if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
for x in $MONGODB_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
done
@@ -40106,6 +42442,11 @@ if test "$with_mongodb" != "no"; then
ncbi_rp_R_flags=
ncbi_rp_R_sep=" $CONF_f_runpath"
for x in $MONGODB_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
ncbi_rp_L_sep=" $CONF_f_libpath"
x=`echo $x | sed -e "$ncbi_rpath_sed"`
@@ -40219,11 +42560,265 @@ _ACEOF
# MongoDB's own library is normally static, but its supporting Boost
# libraries might not be by default.
if test -n "$MONGODB_LIBS"; then
- MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_REGEXP_STATIC_LIBS $BOOST_THREAD_STATIC_LIBS"
+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongoclient $BOOST_LIBPATH $boost_fs_static_lib $BOOST_REGEX_STATIC_LIBS $BOOST_THREAD_STATIC_LIBS"
else
MONGODB_STATIC_LIBS=
fi
+
+# Google Mock
+case "$with_gmock" in
+ yes | no | '' ) ;;
+ * ) GMOCK_PATH=$with_gmock ;;
+esac
+if test -d "$GMOCK_PATH"; then
+ ncbi_fix_dir_tmp=`if cd $GMOCK_PATH; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $GMOCK_PATH && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ GMOCK_PATH=$ncbi_fix_dir_tmp2
+ else
+ case "$GMOCK_PATH" in
+ /*) ;;
+ * ) GMOCK_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) GMOCK_PATH=$ncbi_fix_dir_tmp ;;
+ esac
+ for d in "$GMOCK_PATH/$compiler_vpfx$DEBUG_SFX$mt_sfx$bit64_sfx/lib" \
+ "$GMOCK_PATH/$compiler_pfx$DEBUG_SFX$mt_sfx$bit64_sfx/lib" \
+ "$GMOCK_PATH/$compiler_vpfx$DEBUG_SFX$mt_sfx/lib" \
+ "$GMOCK_PATH/$compiler_pfx$DEBUG_SFX$mt_sfx/lib" \
+ "$GMOCK_PATH/lib$bit64_sfx" "$GMOCK_PATH/lib"; do
+ if test -d "$d"; then
+ GMOCK_LIBDIR=$d
+ ncbi_fix_dir_tmp=`if cd $GMOCK_LIBDIR; then $as_unset PWD || test "${PWD+set}" != set || { PWD=; export PWD; }; /bin/pwd; fi`
+ case "$ncbi_fix_dir_tmp" in
+ /.*) ncbi_fix_dir_tmp2=`cd $GMOCK_LIBDIR && $smart_pwd 2>/dev/null`
+ if test -n "$ncbi_fix_dir_tmp2" -a -d "$ncbi_fix_dir_tmp2"; then
+ GMOCK_LIBDIR=$ncbi_fix_dir_tmp2
+ else
+ case "$GMOCK_LIBDIR" in
+ /*) ;;
+ * ) GMOCK_LIBDIR=$ncbi_fix_dir_tmp ;;
+ esac
+ fi
+ ;;
+ /*) GMOCK_LIBDIR=$ncbi_fix_dir_tmp ;;
+ esac
+ break
+ fi
+ done
+fi
+ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $GMOCK_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $GMOCK_LIBDIR; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+if test "$with_gmock" != "no"; then
+ case "$with_gmock" in
+ yes | "" ) ;;
+ * ) GMOCK_PATH=$with_gmock ;;
+ esac
+ if test "$GMOCK_PATH" != /usr -a -d "$GMOCK_PATH"; then
+ in_path=" in $GMOCK_PATH"
+ if test -z "$GMOCK_INCLUDE" -a -d "$GMOCK_PATH/include"; then
+ GMOCK_INCLUDE="-I$GMOCK_PATH/include"
+ fi
+ if test -n "$GMOCK_LIBPATH"; then
+ :
+ elif test -d "$GMOCK_PATH/lib${bit64_sfx}"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $GMOCK_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $GMOCK_PATH/lib${bit64_sfx}; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ elif test -d "$GMOCK_PATH/lib"; then
+ ncbi_rp_L_flags=
+ ncbi_rp_L_sep=$CONF_f_libpath
+ if test "x${CONF_f_runpath}" = "x${CONF_f_libpath}"; then
+ for x in $GMOCK_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}"
+ else
+ ncbi_rp_R_flags=
+ ncbi_rp_R_sep=" $CONF_f_runpath"
+ for x in $GMOCK_PATH/lib; do
+ case "$x" in
+ /lib | /usr/lib | /usr/lib32 | /usr/lib64 | /usr/lib/$multiarch )
+ continue
+ ;;
+ esac
+ ncbi_rp_L_flags="${ncbi_rp_L_flags}${ncbi_rp_L_sep}$x"
+ ncbi_rp_L_sep=" $CONF_f_libpath"
+ x=`echo $x | sed -e "$ncbi_rpath_sed"`
+ ncbi_rp_R_flags="${ncbi_rp_R_flags}${ncbi_rp_R_sep}$x"
+ ncbi_rp_R_sep=:
+ done
+ GMOCK_LIBPATH="${ncbi_rp_L_flags}${ncbi_rp_R_flags}"
+ fi
+ fi
+ GMOCK_LIBS="$GMOCK_LIBPATH -lgmock -lgtest"
+ else
+ GMOCK_INCLUDE=""
+ GMOCK_LIBS="-lgmock -lgtest"
+ in_path=
+ fi
+ { echo "$as_me:$LINENO: checking for libgmock$in_path" >&5
+echo $ECHO_N "checking for libgmock$in_path... $ECHO_C" >&6; }
+if test "${ncbi_cv_lib_gmock+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ CPPFLAGS=" $GMOCK_INCLUDE $orig_CPPFLAGS"
+ LIBS="$GMOCK_LIBS $orig_LIBS"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <gmock/gmock.h>
+int
+main ()
+{
+int my_argc;
+ char** my_argv;
+ testing::InitGoogleMock(&my_argc, my_argv);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ncbi_cv_lib_gmock=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ncbi_cv_lib_gmock=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ncbi_cv_lib_gmock" >&5
+echo "${ECHO_T}$ncbi_cv_lib_gmock" >&6; }
+ if test "$ncbi_cv_lib_gmock" = "no"; then
+ if test "${with_gmock:=no}" != no; then
+ { { echo "$as_me:$LINENO: error: --with-gmock explicitly specified, but no usable version found." >&5
+echo "$as_me: error: --with-gmock explicitly specified, but no usable version found." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ fi
+ fi
+ if test "$with_gmock" = "no"; then
+ GMOCK_PATH="No_GMOCK"
+ GMOCK_INCLUDE=
+ GMOCK_LIBS=
+ else
+ WithPackages="$WithPackages${WithPackagesSep}GMOCK"; WithPackagesSep=" "
+ GMOCK_INCLUDE=" $GMOCK_INCLUDE"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LIBGMOCK 1
+_ACEOF
+
+ fi
+
+
+
+
+
### Restore original compiler/linker flags
LIBS="$orig_LIBS"
CPPFLAGS="$orig_CPPFLAGS"
@@ -40621,7 +43216,7 @@ FEATURES="$WithFeatures $WithPackages $WithProjects"
### Compute Without{Features,Packages,Projects}. Takes quadratic time,
### but that's life.
-for x in GCC KCC ICC VisualAge CompaqCompiler Cray WorkShop MIPSpro MSVC MT LFS DLL DLL_BUILD MaxDebug MSWin unix WinMain AIX BSD Cygwin CygwinMT Darwin XCODE IRIX Linux OSF Solaris MacOS in-house-resources PubSeqOS JDK Ncbi-JNI check Valgrind LimitedLinker; do
+for x in Int8GI StrictGI GCC KCC ICC VisualAge CompaqCompiler Cray WorkShop MIPSpro MSVC MT LFS DLL DLL_BUILD MaxDebug MSWin unix WinMain AIX BSD Cygwin CygwinMT Darwin XCODE IRIX Linux OSF Solaris MacOS in-house-resources PubSeqOS JDK Ncbi-JNI check Valgrind LimitedLinker; do
case " $WithFeatures " in
*" $x "*) ;;
*) WithoutFeatures="$WithoutFeatures$WithoutFeaturesSep$x"
@@ -40630,7 +43225,7 @@ for x in GCC KCC ICC VisualAge CompaqCompiler Cray WorkShop MIPSpro MSVC MT LFS
;;
esac
done
- for x in UUID FUSE Z LocalZ BZ2 LocalBZ2 LZO PCRE LocalPCRE GCRYPT GNUTLS OPENSSL KRB5 CURL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON23 PYTHON24 PYTHON25 PERL Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.Spirit Boost.System Boost.Test Boost.Test.Included Boost.Threads C-Toolkit OpenGL MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXSLT LIBEXSL [...]
+ for x in UUID FUSE Z LocalZ BZ2 LocalBZ2 LZO PCRE LocalPCRE GMP GCRYPT NETTLE GNUTLS OPENSSL KRB5 CURL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON25 PYTHON26 PYTHON27 PERL Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.Spirit Boost.System Boost.Test Boost.Test.Included Boost.Thread C-Toolkit OpenGL MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXS [...]
case " $WithPackages " in
*" $x "*) ;;
*) WithoutPackages="$WithoutPackages$WithoutPackagesSep$x"
@@ -41000,6 +43595,13 @@ c_ncbi_runpath=`echo "$ncbi_runpath" | sed -e 's:\\$\\$:\\$:g'`
+
+
+
+
+
+
+
#############################################################################
### Create output files and do some post-configuration
@@ -41734,6 +44336,7 @@ CXX!$CXX$ac_delim
CXXFLAGS!$CXXFLAGS$ac_delim
ac_ct_CXX!$ac_ct_CXX$ac_delim
MT_SFX!$MT_SFX$ac_delim
+DPKG_ARCHITECTURE!$DPKG_ARCHITECTURE$ac_delim
DLL!$DLL$ac_delim
DLL_LIB_SETTING!$DLL_LIB_SETTING$ac_delim
IF_WITH_DLL!$IF_WITH_DLL$ac_delim
@@ -41748,6 +44351,7 @@ STRIP!$STRIP$ac_delim
DISTCC!$DISTCC$ac_delim
CCACHE!$CCACHE$ac_delim
TAIL!$TAIL$ac_delim
+BASENAME!$BASENAME$ac_delim
SED!$SED$ac_delim
TOUCH!$TOUCH$ac_delim
GREP!$GREP$ac_delim
@@ -41766,11 +44370,9 @@ LZO_INCLUDE!$LZO_INCLUDE$ac_delim
LZO_LIBS!$LZO_LIBS$ac_delim
PCRE_INCLUDE!$PCRE_INCLUDE$ac_delim
PCRE_LIBS!$PCRE_LIBS$ac_delim
+GMP_INCLUDE!$GMP_INCLUDE$ac_delim
+GMP_LIBS!$GMP_LIBS$ac_delim
LIBGCRYPT_CONFIG!$LIBGCRYPT_CONFIG$ac_delim
-GCRYPT_INCLUDE!$GCRYPT_INCLUDE$ac_delim
-GCRYPT_LIBS!$GCRYPT_LIBS$ac_delim
-LIBGNUTLS_CONFIG!$LIBGNUTLS_CONFIG$ac_delim
-GNUTLS_INCLUDE!$GNUTLS_INCLUDE$ac_delim
_ACEOF
if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
@@ -41812,6 +44414,12 @@ _ACEOF
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
cat >conf$$subs.sed <<_ACEOF
+GCRYPT_INCLUDE!$GCRYPT_INCLUDE$ac_delim
+GCRYPT_LIBS!$GCRYPT_LIBS$ac_delim
+NETTLE_INCLUDE!$NETTLE_INCLUDE$ac_delim
+NETTLE_LIBS!$NETTLE_LIBS$ac_delim
+LIBGNUTLS_CONFIG!$LIBGNUTLS_CONFIG$ac_delim
+GNUTLS_INCLUDE!$GNUTLS_INCLUDE$ac_delim
GNUTLS_LIBS!$GNUTLS_LIBS$ac_delim
OPENSSL_INCLUDE!$OPENSSL_INCLUDE$ac_delim
OPENSSL_LIBS!$OPENSSL_LIBS$ac_delim
@@ -41835,15 +44443,15 @@ mysql_config!$mysql_config$ac_delim
PYTHON!$PYTHON$ac_delim
PYTHON_INCLUDE!$PYTHON_INCLUDE$ac_delim
PYTHON_LIBS!$PYTHON_LIBS$ac_delim
-PYTHON23!$PYTHON23$ac_delim
-PYTHON23_INCLUDE!$PYTHON23_INCLUDE$ac_delim
-PYTHON23_LIBS!$PYTHON23_LIBS$ac_delim
-PYTHON24!$PYTHON24$ac_delim
-PYTHON24_INCLUDE!$PYTHON24_INCLUDE$ac_delim
-PYTHON24_LIBS!$PYTHON24_LIBS$ac_delim
PYTHON25!$PYTHON25$ac_delim
PYTHON25_INCLUDE!$PYTHON25_INCLUDE$ac_delim
PYTHON25_LIBS!$PYTHON25_LIBS$ac_delim
+PYTHON26!$PYTHON26$ac_delim
+PYTHON26_INCLUDE!$PYTHON26_INCLUDE$ac_delim
+PYTHON26_LIBS!$PYTHON26_LIBS$ac_delim
+PYTHON27!$PYTHON27$ac_delim
+PYTHON27_INCLUDE!$PYTHON27_INCLUDE$ac_delim
+PYTHON27_LIBS!$PYTHON27_LIBS$ac_delim
PERL!$PERL$ac_delim
_ACJNI_JAVAC!$_ACJNI_JAVAC$ac_delim
XMKMF!$XMKMF$ac_delim
@@ -41901,14 +44509,8 @@ AVRO_LIBS!$AVRO_LIBS$ac_delim
AVROGENCPP!$AVROGENCPP$ac_delim
MONGODB_INCLUDE!$MONGODB_INCLUDE$ac_delim
MONGODB_LIBS!$MONGODB_LIBS$ac_delim
-signature!$signature$ac_delim
-build_root!$build_root$ac_delim
-top_srcdir!$top_srcdir$ac_delim
-srcdir!$srcdir$ac_delim
-status_dir!$status_dir$ac_delim
-builddir!$builddir$ac_delim
-runpath!$runpath$ac_delim
-ncbi_runpath!$ncbi_runpath$ac_delim
+GMOCK_INCLUDE!$GMOCK_INCLUDE$ac_delim
+GMOCK_LIBS!$GMOCK_LIBS$ac_delim
_ACEOF
if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
@@ -41950,6 +44552,14 @@ _ACEOF
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
cat >conf$$subs.sed <<_ACEOF
+signature!$signature$ac_delim
+build_root!$build_root$ac_delim
+top_srcdir!$top_srcdir$ac_delim
+srcdir!$srcdir$ac_delim
+status_dir!$status_dir$ac_delim
+builddir!$builddir$ac_delim
+runpath!$runpath$ac_delim
+ncbi_runpath!$ncbi_runpath$ac_delim
c_ncbi_runpath!$c_ncbi_runpath$ac_delim
LINK!$LINK$ac_delim
C_LINK!$C_LINK$ac_delim
@@ -42039,14 +44649,6 @@ RPCSVC_LIBS!$RPCSVC_LIBS$ac_delim
CRYPT_LIBS!$CRYPT_LIBS$ac_delim
DL_LIBS!$DL_LIBS$ac_delim
RT_LIBS!$RT_LIBS$ac_delim
-UUID_LIBS!$UUID_LIBS$ac_delim
-DEMANGLE_LIBS!$DEMANGLE_LIBS$ac_delim
-ICONV_LIBS!$ICONV_LIBS$ac_delim
-Z_LIB!$Z_LIB$ac_delim
-BZ2_LIB!$BZ2_LIB$ac_delim
-PCREPOSIX_LIBS!$PCREPOSIX_LIBS$ac_delim
-PCRE_LIB!$PCRE_LIB$ac_delim
-OPENSSL_STATIC_LIBS!$OPENSSL_STATIC_LIBS$ac_delim
_ACEOF
if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
@@ -42088,6 +44690,14 @@ _ACEOF
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
cat >conf$$subs.sed <<_ACEOF
+UUID_LIBS!$UUID_LIBS$ac_delim
+DEMANGLE_LIBS!$DEMANGLE_LIBS$ac_delim
+ICONV_LIBS!$ICONV_LIBS$ac_delim
+Z_LIB!$Z_LIB$ac_delim
+BZ2_LIB!$BZ2_LIB$ac_delim
+PCREPOSIX_LIBS!$PCREPOSIX_LIBS$ac_delim
+PCRE_LIB!$PCRE_LIB$ac_delim
+OPENSSL_STATIC_LIBS!$OPENSSL_STATIC_LIBS$ac_delim
TLS_INCLUDE!$TLS_INCLUDE$ac_delim
TLS_LIBS!$TLS_LIBS$ac_delim
SYBASE_PATH!$SYBASE_PATH$ac_delim
@@ -42153,6 +44763,12 @@ NCBI_SSS_LIBPATH!$NCBI_SSS_LIBPATH$ac_delim
LIBSSSUTILS!$LIBSSSUTILS$ac_delim
LIBSSSDB!$LIBSSSDB$ac_delim
sssutils!$sssutils$ac_delim
+VDB_INCLUDE!$VDB_INCLUDE$ac_delim
+VDB_LIB!$VDB_LIB$ac_delim
+VDB_LIBS!$VDB_LIBS$ac_delim
+VDB_STATIC_LIBS!$VDB_STATIC_LIBS$ac_delim
+VDB_REQ!$VDB_REQ$ac_delim
+VDB_POST_LINK!$VDB_POST_LINK$ac_delim
SP_INCLUDE!$SP_INCLUDE$ac_delim
SP_LIBS!$SP_LIBS$ac_delim
ORBACUS_INCLUDE!$ORBACUS_INCLUDE$ac_delim
@@ -42171,20 +44787,6 @@ LIBEXSLT_STATIC_LIBS!$LIBEXSLT_STATIC_LIBS$ac_delim
XERCES_INCLUDE!$XERCES_INCLUDE$ac_delim
XERCES_LIBS!$XERCES_LIBS$ac_delim
XERCES_STATIC_LIBS!$XERCES_STATIC_LIBS$ac_delim
-XALAN_INCLUDE!$XALAN_INCLUDE$ac_delim
-XALAN_LIBS!$XALAN_LIBS$ac_delim
-XALAN_STATIC_LIBS!$XALAN_STATIC_LIBS$ac_delim
-ZORBA_INCLUDE!$ZORBA_INCLUDE$ac_delim
-ZORBA_LIBS!$ZORBA_LIBS$ac_delim
-ZORBA_STATIC_LIBS!$ZORBA_STATIC_LIBS$ac_delim
-SQLITE3_STATIC_LIBS!$SQLITE3_STATIC_LIBS$ac_delim
-FREETYPE_INCLUDE!$FREETYPE_INCLUDE$ac_delim
-FREETYPE_LIBS!$FREETYPE_LIBS$ac_delim
-GSOAP_PATH!$GSOAP_PATH$ac_delim
-AVRO_STATIC_LIBS!$AVRO_STATIC_LIBS$ac_delim
-MONGODB_STATIC_LIBS!$MONGODB_STATIC_LIBS$ac_delim
-ncbi_xreader_pubseqos!$ncbi_xreader_pubseqos$ac_delim
-ncbi_xreader_pubseqos2!$ncbi_xreader_pubseqos2$ac_delim
_ACEOF
if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
@@ -42226,6 +44828,21 @@ _ACEOF
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
cat >conf$$subs.sed <<_ACEOF
+XALAN_INCLUDE!$XALAN_INCLUDE$ac_delim
+XALAN_LIBS!$XALAN_LIBS$ac_delim
+XALAN_STATIC_LIBS!$XALAN_STATIC_LIBS$ac_delim
+ZORBA_INCLUDE!$ZORBA_INCLUDE$ac_delim
+ZORBA_LIBS!$ZORBA_LIBS$ac_delim
+ZORBA_STATIC_LIBS!$ZORBA_STATIC_LIBS$ac_delim
+SQLITE3_STATIC_LIBS!$SQLITE3_STATIC_LIBS$ac_delim
+FREETYPE_INCLUDE!$FREETYPE_INCLUDE$ac_delim
+FREETYPE_LIBS!$FREETYPE_LIBS$ac_delim
+GSOAP_PATH!$GSOAP_PATH$ac_delim
+AVRO_STATIC_LIBS!$AVRO_STATIC_LIBS$ac_delim
+CEREAL_INCLUDE!$CEREAL_INCLUDE$ac_delim
+MONGODB_STATIC_LIBS!$MONGODB_STATIC_LIBS$ac_delim
+ncbi_xreader_pubseqos!$ncbi_xreader_pubseqos$ac_delim
+ncbi_xreader_pubseqos2!$ncbi_xreader_pubseqos2$ac_delim
UNLESS_PUBSEQOS!$UNLESS_PUBSEQOS$ac_delim
PERL_INCLUDE!$PERL_INCLUDE$ac_delim
PERL_LIBS!$PERL_LIBS$ac_delim
@@ -42264,7 +44881,7 @@ LIBOBJS!$LIBOBJS$ac_delim
LTLIBOBJS!$LTLIBOBJS$ac_delim
_ACEOF
- if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 36; then
+ if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 51; then
break
elif $ac_last_try; then
{ { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
diff --git a/c++/src/build-system/configure.ac b/c++/src/build-system/configure.ac
index 155faec..ef22cf2 100644
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
@@ -1,5 +1,5 @@
#############################################################################
-# $Id: configure.ac 464915 2015-04-15 14:49:12Z ivanov $
+# $Id: configure.ac 485101 2015-11-18 18:36:07Z ivanov $
# Derived from configure.in version 1.173.
# ==========================================================================
#
@@ -64,14 +64,14 @@ case "$with_3psw" in
else
with_ncbi_c=no
fi
- m4_foreach(X, [sss, sssutils, sssdb, z, bz2, lzo, pcre,
- gcrypt, gnutls, openssl, krb5, boost,
+ m4_foreach(X, [sss, sssutils, sssdb, vdb, z, bz2, lzo, pcre,
+ gmp, gcrypt, nettle, gnutls, openssl, krb5, boost,
sybase, ftds, mysql, opengl, mesa, glut, glew,
wxwidgets, freetype, ftgl, fastcgi, bdb, orbacus, odbc,
python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
- magic, curl, gsoap, avro, mongodb],
+ magic, curl, gsoap, avro, cereal, mongodb, gmock],
[if test "${[with_]X-no}" != "no"; then
AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
else
@@ -163,6 +163,8 @@ AC_ARG_WITH(lfs,
[ --with-lfs enable large file support to the extent possible])
AC_ARG_WITH(limited-linker,
[ --with-limited-linker don't attempt to build especially large projects])
+AC_ARG_WITH(experimental,
+ [ --with-experimental=... enable named experimental feature(s)])
## Scripts, make features, and directory naming
AC_ARG_WITH(extra-action,
@@ -235,6 +237,14 @@ AC_ARG_WITH(sssdb,
[ --without-sssdb do not use NCBI SSS DB library])
AC_ARG_WITH(included-sss,
[ --with-included-sss use the in-tree copy of SSS])
+AC_ARG_WITH(vdb,
+ [ --with-vdb=DIR use NCBI SRA/VDB Toolkit installation in DIR])
+AC_ARG_WITH(vdb2,
+ [ --without-vdb do not use the NCBI SRA/VDB Toolkit])
+AC_ARG_WITH(downloaded-vdb,
+ [ --with-downloaded-vdb download and build SRA/VDB from GitHub])
+AC_ARG_WITH(included-vdb,
+ [ --with-included-vdb use the DEPRECATED bundled SRA/VDB Toolkit copy])
## Third-party and system packages
AC_ARG_WITH(z,
@@ -253,10 +263,18 @@ AC_ARG_WITH(pcre,
[ --with-pcre=DIR use PCRE installation in DIR])
AC_ARG_WITH(pcre2,
[ --without-pcre use internal copy of PCRE])
+AC_ARG_WITH(gmp,
+ [ --with-gmp=DIR use GMP installation in DIR])
+AC_ARG_WITH(gmp2,
+ [ --without-gmp do not use GMP])
AC_ARG_WITH(gcrypt,
[ --with-gcrypt=DIR use gcrypt installation in DIR])
AC_ARG_WITH(gcrypt2,
[ --without-gcrypt do not use gcrypt])
+AC_ARG_WITH(nettle,
+ [ --with-nettle=DIR use Nettle installation in DIR])
+AC_ARG_WITH(nettle2,
+ [ --without-nettle do not use Nettle])
AC_ARG_WITH(gnutls,
[ --with-gnutls=DIR use GNUTLS installation in DIR])
AC_ARG_WITH(gnutls2,
@@ -453,10 +471,18 @@ AC_ARG_WITH(avro,
[ --with-avro=DIR use Apache Avro installation in DIR])
AC_ARG_WITH(avro2,
[ --without-avro do not use Apache Avro])
+AC_ARG_WITH(cereal,
+ [ --with-cereal=DIR use USC Cereal installation in DIR])
+AC_ARG_WITH(cereal2,
+ [ --without-cereal do not use USC Cereal])
AC_ARG_WITH(mongodb,
[ --with-mongodb=DIR use MongoDB installation in DIR])
AC_ARG_WITH(mongodb2,
[ --without-mongodb do not use MongoDB])
+AC_ARG_WITH(gmock,
+ [ --with-gmock=DIR use Google Mock installation in DIR])
+AC_ARG_WITH(gmock2,
+ [ --without-gmock do not use Google Mock])
AC_ARG_WITH(3psw,
[ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.])
AC_ARG_WITH(3psw2,
@@ -510,13 +536,14 @@ autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
deactivation makefile-auto-update projects flat-makefile configure-dialog \
check ncbi-public strip pch caution ccache distcc \
ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
-geo included-geo \
-z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
-ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
+geo included-geo vdb downloaded-vdb included-vdb \
+z bz2 lzo pcre gmp gcrypt nettle gnutls openssl krb5 \
+sybase sybase-local sybase-new ftds mysql \
+orbacus freetype ftgl opengl mesa glut glew glew-mx \
bdb python perl jni sqlite3 icu boost boost-tag \
sp expat sablot libxml libxslt libexslt xerces xalan zorba \
oechem sge muparser hdf5 \
-gif jpeg tiff png xpm magic curl mimetic gsoap avro mongodb 3psw \
+gif jpeg tiff png xpm magic curl mimetic gsoap avro cereal mongodb gmock 3psw \
local-lbsm ncbi-crypt connext \
serial objects dbapi app ctools gui algo internal gbench"
@@ -548,31 +575,67 @@ for x_arg in "$@" ; do
AC_MSG_ERROR([$x_arg: requires value; use --help to show usage])
;;
- --with-extra-action=* | --with-build-root=* | --with-build-root-sfx=* \
- | --with-fake-root=* | --with-saved-settings=* \
- | --with-projects=* | --with-check=* | --with-check-tools=* \
- | --with-universal=* | --with-tcheck=* \
- | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
- | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
- | [[A-Z]*=*] \
- | --with-z=* | --with-bz2=* | --with-lzo=* \
- | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
- | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* | --with-krb5=* \
- | --with-curl=* | --with-gsoap=* | --with-avro=* | --with-mongodb=* \
- | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
- | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
- | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
- | --with-icu=* | --with-xerces=* | --with-xalan=* | --with-zorba=* \
- | --with-libxml=* | --with-libxslt=* | --with-exslt=* \
- | --with-bdb=* | --with-odbc=* | --with-python=* | --with-perl=* \
- | --with-freetype=* | --with-ftgl=* | --with-gif=* | --with-jpeg=* \
- | --with-png=* | --with-tiff=* | --with-xpm=* | --with-opengl=* \
- | --with-mesa=* | --with-glut=* | --with-glew=* | --with-oechem=* \
- | --with-boost=* | --with-boost-tag=* | --with-orbacus=* | --with-sge=* \
- | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
- | --x-includes=* | --x-libraries=* | --with-3psw=* \
- | --target=* | --with-runpath=* | --with-relative-runpath=* \
- | --help | --no-create | --no-recursion)
+ --with-projects=* | --with-saved-settings=* )
+ # Confirm that the specified file exists and is readable.
+ file=`echo $x_arg | sed -e 's/^[[^=]]*=//'`
+ case "$file" in
+ /* ) ;;
+ * ) file=$srcdir/$file ;;
+ esac
+ if test -f "$file"; then
+ if test -r "$file"; then
+ :
+ else
+ AC_MSG_ERROR([$x_arg: requires a readable file; use --help to show usage])
+ fi
+ else
+ AC_MSG_ERROR([$x_arg: requires a (readable) file; use --help to show usage])
+ fi
+ ;;
+
+ --srcdir=* | --x-includes=* | --x-libraries=* | --with-tcheck=* \
+ | --with-ncbi-c=* | --with-sss=* | --with-vdb=* | --with-z=* \
+ | --with-bz2=* | --with-lzo=* | --with-pcre=* \
+ | --with-gmp=* | --with-gcrypt=* | --with-nettle=* \
+ | --with-gnutls=* | --with-openssl=* | --with-krb5=* \
+ | --with-sybase-local=* | --with-ftds=*/* | --with-mysql=* \
+ | --with-opengl=* | --with-mesa=* | --with-glut=* | --with-glew=* \
+ | --with-wxwidgets=* | --with-freetype=* | --with-ftgl=* \
+ | --with-fastcgi=*/* | --with-bdb=*/* | --with-orbacus=* \
+ | --with-odbc=* | --with-python=* | --with-perl=* | --with-jni=* \
+ | --with-boost=* | --with-sqlite3=* | --with-icu=* | --with-expat=* \
+ | --with-sablot=* | --with-libxml=* | --with-libxslt=* | --with-exslt=* \
+ | --with-xerces=* | --with-xalan=* | --with-zorba=* | --with-oechem=* \
+ | --with-sge=* | --with-muparser=* | --with-hdf5=* | --with-gif=* \
+ | --with-jpeg=* | --with-png=* | --with-tiff=* | --with-xpm=* \
+ | --with-magic=* | --with-curl=* | --with-mimetic=* | --with-gsoap=* \
+ | --with-avro=* | --with-cereal=* | --with-mongodb=* | --with-gmock=* )
+ # Confirm that the specified directory exists and is readable.
+ dir=`echo $x_arg | sed -e 's/^[[^=]]*=//'`
+ case "$x_arg" in
+ --srcdir=* | --*=/* ) ;;
+ * ) dir=$srcdir/$dir ;;
+ esac
+ if test -d "$dir"; then
+ if test -r "$dir"; then
+ :
+ else
+ AC_MSG_ERROR([$x_arg: requires a readable directory; use --help to show usage])
+ fi
+ else
+ AC_MSG_ERROR([$x_arg: requires a (readable) directory; use --help to show usage])
+ fi
+ ;;
+
+ [[A-Z]*=*] | -h | --help | --help=* | -V | --version | -q | --quiet \
+ | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
+ | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
+ | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+ | --with-universal=* | --with-runpath=* | --with-relative-runpath=* \
+ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+ | --with-check-tools=* | --with-ftds=[[0-9]]* | --with-fastcgi=[[0-9]]* \
+ | --with-bdb=[[1-9]]* | --with-boost-tag=* | --with-3psw=* )
;;
* )
@@ -633,6 +696,24 @@ if test "$with_openmp" = yes; then
: ${with_mt=yes}
fi
+case "$with_downloaded_vdb:$with_included_vdb:$with_vdb" in
+ yes:yes:* )
+ AC_MSG_ERROR([incompatible options: --with-downloaded-vdb and
+ --with-included-vdb])
+ ;;
+ yes:*:no )
+ AC_MSG_ERROR([incompatible options: --without-vdb but
+ --with-downloaded-vdb])
+ ;;
+ *:yes:no )
+ AC_MSG_ERROR([incompatible options: --without-vdb but
+ --with-included-vdb])
+ ;;
+ yes:*: | *:yes: )
+ with_vdb=yes
+ ;;
+esac
+
#### Check for special options
if test "$with_extra_action" = "yes" ; then
AC_MSG_ERROR([--with-extra-action must have a value after =])
@@ -683,6 +764,25 @@ USER_CFLAGS=$CFLAGS
USER_CXXFLAGS=$CXXFLAGS
USER_LDFLAGS=$LDFLAGS
+if test -n "$with_experimental"; then
+ for x in `echo $with_experimental | tr , ' '`; do
+ case "$x" in
+ Int8GI )
+ CPPFLAGS="$CPPFLAGS -DNCBI_INT8_GI"
+ NCBI_FEATURE(Int8GI)
+ ;;
+ StrictGI )
+ CPPFLAGS="$CPPFLAGS -DNCBI_STRICT_GI"
+ NCBI_FEATURE(Int8GI)
+ NCBI_FEATURE(StrictGI)
+ ;;
+ * )
+ AC_MSG_ERROR([unrecognized experimental feature "$x".])
+ ;;
+ esac
+ done
+fi
+
#### Always define this
AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
@@ -800,14 +900,10 @@ ncbi_compiler_ver="0"
if test "$GCC" = "yes" ; then
compiler_ver="`$real_CXX -dumpversion 2>&1`"
- case "$compiler_ver" in
- 2.95* | 2.96* | 3.* | 4.* )
- compiler="GCC"
- ncbi_compiler="GCC"
- ncbi_compiler_ver="$compiler_ver"
- NCBI_FEATURE(GCC)
- ;;
- esac
+ compiler="GCC"
+ ncbi_compiler="GCC"
+ ncbi_compiler_ver="$compiler_ver"
+ NCBI_FEATURE(GCC)
elif test "$KCC" = "yes" ; then
compiler_ver="$kcc_ver"
compiler="KCC"
@@ -1127,6 +1223,15 @@ case "$host_os:$compiler" in
esac
;;
+ linux*:GCC )
+ if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"
+ then
+ case "$compiler_version" in
+ 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
+ esac
+ fi
+ ;;
+
irix*:GCC )
if test "$with_debug" != "no" ; then
LDFLAGS="-LD_LAYOUT:lgot_buffer=32 $LDFLAGS"
@@ -1259,7 +1364,7 @@ case "$host_os:$compiler" in
fi
# -flat_namespace is necessary for proper handling of shared libraries
# that don't themselves link against all their dependencies.
- LDFLAGS="-flat_namespace $LDFLAGS"
+ LDFLAGS="-flat_namespace -headerpad_max_install_names $LDFLAGS"
if test "$try_old_sdks" = yes; then
sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
@@ -1285,7 +1390,7 @@ case "$host_os:$compiler" in
CXX="$CXX $TARGET"
fi
else
- LDFLAGS="-Wl,-flat_namespace $LDFLAGS"
+ LDFLAGS="-Wl,-flat_namespace -Wl,-headerpad_max_install_names $LDFLAGS"
fi
if test -f /usr/include/dlfcn.h; then
# may be able to do without /sw, so ignore it by default
@@ -1805,6 +1910,14 @@ case "$host_os:$ncbi_cv_prog_cc_wl_rpath" in
;;
esac
+AC_PATH_PROG(DPKG_ARCHITECTURE, dpkg-architecture)
+if test -x "$DPKG_ARCHITECTURE" \
+ && $DPKG_ARCHITECTURE -qDEB_HOST_MULTIARCH >/dev/null 2>&1; then
+ multiarch=`$DPKG_ARCHITECTURE -qDEB_HOST_MULTIARCH`
+else
+ multiarch=`echo $host | sed -e 's/-unknown-/-/; [s/^i[3-9]86-/^i\[3-9\]86/]'`
+fi
+
case "$compiler:$compiler_version:$with_bin_release" in
GCC:*:yes )
libstdcxx=`$CXX $LDFLAGS -print-file-name=libstdc++.a`
@@ -1832,7 +1945,8 @@ case "$compiler:$compiler_version:$with_bin_release" in
dir=`dirname "$path"`
abs_dir=`cd "$dir" && pwd`
case "$dir:$abs_dir" in
- *:/lib | *:/usr/lib | *:/usr/lib32 | *:/usr/lib64 )
+ *:/lib | *:/usr/lib | *:/usr/lib32 | *:/usr/lib64 \
+ | *:/usr/lib/$multiarch )
# no rpath needed
break
;;
@@ -2256,6 +2370,7 @@ else
AC_MSG_RESULT(no)
fi
+AC_PATH_PROG(BASENAME, basename)
AC_PATH_PROG(SED, sed)
AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
dnl AC_PATH_PROG(GREP, grep)
@@ -3008,9 +3123,9 @@ fi
AC_CHECK_TYPES(socklen_t,,,[#include <sys/types.h>
#include <sys/socket.h>])
-AC_CHECK_HEADERS(atomic.h dlfcn.h ieeefp.h poll.h sys/epoll.h sys/mount.h \
- sys/sockio.h sys/statvfs.h sys/sysinfo.h sys/vfs.h \
- x86intrin.h)
+AC_CHECK_HEADERS(atomic.h cpuid.h dlfcn.h ieeefp.h poll.h sys/epoll.h \
+ sys/mount.h sys/sockio.h sys/statvfs.h sys/sysinfo.h \
+ sys/vfs.h x86intrin.h)
case "$host_os" in
cygwin*) AC_CHECK_HEADERS(winternl.h) ;;
esac
@@ -3647,6 +3762,19 @@ AC_DEFINE_UNQUOTED(NCBI_NORETURN, $noret,
[Define to whatever syntax, if any, your compiler supports for marking
functions that never return.])
+AC_CACHE_CHECK([syntax for marking functions whose result should be checked],
+ ncbi_cv_c_warn_unused_result,
+ [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+ [[int f(void) __attribute__((warn_unused_result));]],
+ [[int status = f();]])],
+ [ncbi_cv_c_warn_unused_result='__attribute__((warn_unused_result))'],
+ [ncbi_cv_c_warn_unused_result=none])])
+wur=$ncbi_cv_c_warn_unused_result
+test "$wur" = "none" && wur=""
+AC_DEFINE_UNQUOTED(NCBI_WARN_UNUSED_RESULT, $wur,
+ [Define to whatever syntax, if any, your compiler supports for marking
+ functions whose (status) result is important to check.])
+
AC_CACHE_CHECK([syntax for declaring thread-local variables],
ncbi_cv_c_tls_var,
[ncbi_cv_c_tls_var=none
@@ -3663,6 +3791,18 @@ if test "$tls_var" != "none"; then
thread-local variables, or leave undefined if it doesn't.])
fi
+AC_CACHE_CHECK([syntax for marking types as packed to save memory],
+ ncbi_cv_c_packed,
+ [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([],
+ [[enum E { foo, bar } __attribute__((packed));]])],
+ [ncbi_cv_c_packed='__attribute__((__packed__))'],
+ [ncbi_cv_c_packed=none])])
+packed=$ncbi_cv_c_packed
+test "$packed" = "none" && packed=""
+AC_DEFINE_UNQUOTED(NCBI_PACKED, $packed,
+ [Define to whatever syntax, if any, your compiler supports for marking
+ types as packed to save memory.])
+
# for FreeTDS
AC_CACHE_CHECK([whether FIONBIO requires BSD_COMP to be defined],
ncbi_cv_decl_fionbio_needs_bsd_comp,
@@ -3730,7 +3870,7 @@ AC_CACHE_CHECK([whether $CC supports SIMD vector arithmetic],
ncbi_cv_cc_vector_math,
[AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
[typedef int TVector __attribute__((vector_size(16)));
- TVector f(TVector v1, TVector v2) { return v1 ^ v2 };],
+ TVector f(TVector v1, TVector v2) { return v1 ^ v2; }],
[TVector v1, v2, v3; v3 = f(v1, v2);])],
[ncbi_cv_cc_vector_math=yes], [ncbi_cv_cc_vector_math=no])])
if test "$ncbi_cv_cc_vector_math" = yes; then
@@ -3970,7 +4110,7 @@ case "$signature_compiler:$ac_cv_have_decl__LIBCPP_VERSION" in
esac
usr_lib=['[/usr]*/lib/*[amdsprcv]*[23469]*']
-no_usr_lib="s,-L$usr_lib ,,g;"
+no_usr_lib="s,-L$usr_lib ,,g; s,-L/usr/lib/$multiarch ,,g"
NCBI_CHECK_THIRD_PARTY_LIB(z,
[[AC_LANG_PROGRAM([#include <zlib.h>],
@@ -4032,7 +4172,33 @@ else
PCREPOSIX_LIBS=`echo "$PCRE_LIBS" | sed -e 's/-lpcre/-lpcreposix -lpcre/'`
fi
-## SSL/TLS libraries
+## SSL/TLS libraries (and supporting libraries)
+if test "x$with_gmp" != xno; then
+ case "$with_gmp" in
+ yes | '' ) ;;
+ * ) GMP_PATH=$with_gmp ;;
+ esac
+ for pfx in "$compiler_vpfx" "$compiler_pfx" "" ; do
+ vpath=$GMP_PATH/$pfx${DEBUG_SFX}${mt_sfx}${bit64_sfx}
+ if test -d "$vpath" ; then
+ GMP_PATH=$vpath
+ break
+ fi
+ done
+ if test -d "$GMP_PATH"; then
+ NCBI_FIX_DIR(GMP_PATH)
+ fi
+ NCBI_CHECK_THIRD_PARTY_LIB(gmp,
+ [[AC_LANG_PROGRAM([#include <gmp.h>],
+ [[mpz_t x; mpz_init(x);]])]])
+fi
+if test "$with_gmp" = no; then
+ AS_UNSET(GMP_INCLUDE)
+ AS_UNSET(GMP_LIBS)
+else
+ NCBI_PACKAGE(GMP)
+fi
+
case "$with_gcrypt" in
no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
yes | '' ) ;;
@@ -4068,6 +4234,43 @@ if test "x$with_gcrypt" != xno -a -n "$GCRYPT_CONFIG_LIBS"; then
NCBI_RPATHIFY_OUTPUT(GCRYPT_LIBS, [echo $GCRYPT_CONFIG_LIBS], [$no_usr_lib])
fi
+if test "x$with_nettle" != xno; then
+ case "$with_nettle" in
+ yes | '' ) ;;
+ * ) NETTLE_PATH=$with_nettle ;;
+ esac
+ if test -d "$NETTLE_PATH"; then
+ NCBI_FIX_DIR(NETTLE_PATH)
+ fi
+ if test -d "$NETTLE_PATH/lib$bit64_sfx"; then
+ NETTLE_LIBDIR=$NETTLE_PATH/lib$bit64_sfx
+ else
+ NETTLE_LIBDIR=$NETTLE_PATH/lib
+ fi
+ for pfx in "$compiler_vpfx" "$compiler_pfx" "" ; do
+ vpath=$NETTLE_PATH/$pfx${DEBUG_SFX}${mt_sfx}${bit64_sfx}
+ if test -d "$vpath" ; then
+ NETTLE_LIBDIR=$vpath/lib
+ break
+ fi
+ done
+ if test -d "$NETTLE_LIBDIR"; then
+ NCBI_FIX_DIR(NETTLE_LIBDIR)
+ NCBI_RPATHIFY(NETTLE_LIBPATH, $NETTLE_LIBDIR)
+ fi
+ NCBI_CHECK_THIRD_PARTY_LIB_EX(nettle, NETTLE, hogweed,
+ [[AC_LANG_PROGRAM([#include <nettle/sexp.h>],
+ [[struct sexp_iterator it;
+ sexp_iterator_first(&it, 0, (const uint8_t*) NULL);]])]],
+ [-lnettle], [$GMP_LIBS])
+fi
+if test "$with_nettle" = no; then
+ AS_UNSET(NETTLE_INCLUDE)
+ AS_UNSET(NETTLE_LIBS)
+else
+ NCBI_PACKAGE(NETTLE)
+fi
+
case "$with_gnutls" in
no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
yes | '' ) ;;
@@ -4084,29 +4287,31 @@ AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
if test "x$with_gnutls" != xno; then
if test -x "$LIBGNUTLS_CONFIG"; then
if test -z "$GNUTLS_PATH"; then
- p=`libgnutls-config --prefix`
+ p=`$LIBGNUTLS_CONFIG --prefix`
test "x$p" = "x/usr" || GNUTLS_PATH=$p
fi
else
- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib$bit64_sfx/pkgconfig:$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
$LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
fi
case "$LIBGNUTLS_CONFIG" in
eval\ *)
NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBPATH,
[$LIBGNUTLS_CONFIG --libs-only-L])
+ GNUTLS_CONFIG_LIBS=`$LIBGNUTLS_CONFIG --libs-only-l`
+ GNUTLS_CONFIG_LIBS="$GNUTLS_LIBPATH $GNUTLS_CONFIG_LIBS $Z_LIBS"
;;
no)
;;
*)
NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBPATH,
[$LIBGNUTLS_CONFIG --exec-prefix], [s,^,-L,; s,$,/lib,;])
+ GNUTLS_CONFIG_LIBS="`$LIBGNUTLS_CONFIG --libs` $Z_LIBS"
;;
esac
if test "x$LIBGNUTLS_CONFIG" != xno; then
GNUTLS_INCLUDE=`$LIBGNUTLS_CONFIG --cflags`
- GNUTLS_CONFIG_LIBS="`$LIBGNUTLS_CONFIG --libs` $Z_LIBS"
fi
else
AS_UNSET(GNUTLS_CONFIG_LIBS)
@@ -4203,7 +4408,6 @@ NETWORK_PURE_LIBS="$NETWORK_LIBS"
ncbi_xreader_pubseqos=
UNLESS_PUBSEQOS=
if test "$with_sybase" != "no" ; then
- sybase_lib=lib$bit64_sfx
resolve_sybase=true
default_pointer=default-${NCBI_PLATFORM_BITS}bit
: ${with_sybase_new:="no"}
@@ -4338,11 +4542,26 @@ if test "$with_sybase" != "no" ; then
fi
fi
- SYBASE_LIBPATH="$SYBASE_PATH/${sybase_lib}"
+ if test -f "$SYBASE_PATH/SYBASE.env"; then
+ ocs=`sed -ne 's:^SYBASE_OCS=:/:p' "$SYBASE_PATH/SYBASE.env"`
+ else
+ ocs=
+ fi
+ if test -d "$SYBASE_PATH$ocslib$bit64_sfx"; then
+ SYBASE_LIBPATH="$SYBASE_PATH$ocs/lib$bit64_sfx"
+ else
+ SYBASE_LIBPATH="$SYBASE_PATH$ocs/lib"
+ fi
syb_sfx=$bit64_sfx
+ if test -f "$SYBASE_LIBPATH/libsybct$syb_sfx.a"; then
+ syb_pfx=syb
+ else
+ syb_pfx=
+ fi
+
if test "$with_mt" = "yes" ; then
AC_CACHE_CHECK([for reentrant Sybase libraries], ncbi_cv_lib_sybase_r,
- [if test -f "$SYBASE_LIBPATH/libct_r$bit64_sfx.so"; then
+ [if test -f "$SYBASE_LIBPATH/lib${syb_pfx}ct_r$bit64_sfx.so"; then
ncbi_cv_lib_sybase_r=yes
else
ncbi_cv_lib_sybase_r=no
@@ -4353,7 +4572,7 @@ if test "$with_sybase" != "no" ; then
fi
case "$host_os" in
linux*) sybtcl=-lsybtcl$syb_sfx; sybtli="" ;;
- *) sybtcl=-ltcl$syb_sfx; sybtli=-ltli$syb_sfx ;;
+ *) sybtcl=-l${syb_pfx}tcl$syb_sfx; sybtli=-ltli$syb_sfx ;;
esac
test -f "$SYBASE_LIBPATH/libtli.so" || sybtli=
@@ -4368,19 +4587,25 @@ if test "$with_sybase" != "no" ; then
SYBASE_NETWORK_LIBS="$NETWORK_LIBS"
fi
+ if test -f "$SYBASE_LIBPATH/libsybunic${bit64_sfx}.a"; then
+ sybunic=-lsybunic${bit64_sfx}
+ fi
+
test -n "$bit64_sfx" && SYBASE_INCLUDE="-DSYB_LP64"
- SYBASE_LIBLIST="-lblk$syb_sfx -lct$syb_sfx -lcs$syb_sfx $sybtcl"
- SYBASE_LIBLIST="$SYBASE_LIBLIST -lcomn$syb_sfx -lintl$syb_sfx"
+ SYBASE_LIBLIST="-l${syb_pfx}blk$syb_sfx -l${syb_pfx}ct$syb_sfx"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}cs$syb_sfx $sybtcl"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}comn$syb_sfx"
+ SYBASE_LIBLIST="$SYBASE_LIBLIST -l${syb_pfx}intl$syb_sfx $sybunic"
SYBASE_DLLLIST="$sybtli"
# deduce conf.macro: SYBASE_INCLUDE, SYBASE_LIBS, SYBASE_DLLS, SYBASE_DBLIBS
- SYBASE_INCLUDE="-I$SYBASE_PATH/include $SYBASE_INCLUDE"
+ SYBASE_INCLUDE="-I$SYBASE_PATH$ocs/include $SYBASE_INCLUDE"
if test -z "$SYBASE_LCL_PATH" ; then
NCBI_RPATHIFY(SYBASE_LPATH, $SYBASE_LIBPATH)
else
- SYBASE_LCL_LIBPATH="$SYBASE_LCL_PATH/${sybase_lib}"
+ SYBASE_LCL_LIBPATH="$SYBASE_LCL_PATH$ocs/${sybase_lib}"
NCBI_RPATHIFY(SYBASE_LPATH, $SYBASE_LCL_LIBPATH $SYBASE_LIBPATH)
- SYBASE_INCLUDE="-I$SYBASE_LCL_PATH/include $SYBASE_INCLUDE"
+ SYBASE_INCLUDE="-I$SYBASE_LCL_PATH$ocs/include $SYBASE_INCLUDE"
fi
SYBASE_LIBS="$SYBASE_LPATH $SYBASE_LIBLIST"
SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
@@ -4420,7 +4645,7 @@ if test "$with_sybase" != "no" ; then
fi
fi
- SYBASE_DBLIBS="$SYBASE_LPATH -lsybdb${bit64_sfx}"
+ SYBASE_DBLIBS="$SYBASE_LPATH -lsybdb${bit64_sfx} $sybunic"
AC_CACHE_CHECK([for Sybase DBLib], ncbi_cv_lib_sybdb,
[CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
LIBS="$SYBASE_DBLIBS $SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $orig_LIBS"
@@ -4788,22 +5013,19 @@ if test "$with_python" != "no" ; then
*/* ) PYTHON_PATH=$with_python ;;
esac
NCBI_CHECK_PYTHON()
- NCBI_CHECK_PYTHON(2.3)
- : ${PYTHON_PATH:="/usr/local/python-2.4.4"}
- NCBI_CHECK_PYTHON(2.4)
NCBI_CHECK_PYTHON(2.5)
+ NCBI_CHECK_PYTHON(2.6)
+ NCBI_CHECK_PYTHON(2.7)
if test "$ncbi_cv_lib_python" = "no"; then
- # Favor python 2.4 as the only version configure historically
- # recognized, but otherwise prefer newer versions.
- if test "$ncbi_cv_lib_python24" = "yes"; then
- PYTHON_INCLUDE=$PYTHON24_INCLUDE
- PYTHON_LIBS=$PYTHON24_LIBS
+ if test "$ncbi_cv_lib_python27" = "yes"; then
+ PYTHON_INCLUDE=$PYTHON27_INCLUDE
+ PYTHON_LIBS=$PYTHON27_LIBS
+ elif test "$ncbi_cv_lib_python26" = "yes"; then
+ PYTHON_INCLUDE=$PYTHON26_INCLUDE
+ PYTHON_LIBS=$PYTHON26_LIBS
elif test "$ncbi_cv_lib_python25" = "yes"; then
PYTHON_INCLUDE=$PYTHON25_INCLUDE
PYTHON_LIBS=$PYTHON25_LIBS
- elif test "$ncbi_cv_lib_python23" = "yes"; then
- PYTHON_INCLUDE=$PYTHON23_INCLUDE
- PYTHON_LIBS=$PYTHON23_LIBS
fi
if test -n "$PYTHON_LIBS"; then
NCBI_PACKAGE(PYTHON)
@@ -4893,25 +5115,36 @@ if test "$with_boost" != "no"; then
fi
BOOST_LIBPATH_=$BOOST_PATH/lib
NCBI_RPATHIFY_COND(BOOST_LIBPATH, $BOOST_LIBPATH_)
- test -d "$BOOST_PATH" || BOOST_LIBPATH_=/usr/lib
- boost_path_digits=`basename $BOOST_PATH | sed -e 's/-ncbi[[0-9]]*$//; s/.0$//' | tr -cd 0123456789`
+ if test -d "$BOOST_PATH"; then
+ boost_path_digits=`basename $BOOST_PATH | sed -e 's/-ncbi[[0-9]]*$//; s/.0$//' | tr -cd 0123456789`
+ else
+ boost_path_digits=
+ BOOST_LIBPATH_=/usr/lib
+ fi
if test -n "$boost_path_digits"; then
boost_version_digits=`echo $ncbi_cv_lib_boost_version | sed -e 's/.0$//' | tr -cd 0123456789`
if test $boost_path_digits != "$boost_version_digits"; then
# presumably stale, particularly if boost_version WASN'T cached;
# uncache all relevant settings
AS_UNSET(ncbi_cv_lib_boost_version)
+ AS_UNSET(ncbi_cv_lib_boost_version_num)
AS_UNSET(ncbi_cv_lib_boost_regex)
AS_UNSET(ncbi_cv_lib_boost_spirit)
AS_UNSET(ncbi_cv_lib_boost_system)
+ AS_UNSET(ncbi_cv_lib_boost_filesystem)
+ AS_UNSET(ncbi_cv_lib_boost_iostreams)
+ AS_UNSET(ncbi_cv_lib_boost_program_options)
AS_UNSET(ncbi_cv_lib_boost_test)
AS_UNSET(ncbi_cv_lib_boost_thread)
+ elif test -z "$ncbi_cv_lib_boost_version_num"; then
+ AS_UNSET(ncbi_cv_lib_boost_version)
fi
fi
AC_CACHE_CHECK([Boost version],
ncbi_cv_lib_boost_version,
[AC_LANG_CONFTEST([AC_LANG_SOURCE([[
#include <boost/version.hpp>
+ncbi_cv_lib_boost_version_num=BOOST_VERSION
ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
]])])
eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" \
@@ -4920,6 +5153,9 @@ ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
. ./conftest.sh
rm -f contest*
])
+ AC_DEFINE_UNQUOTED(NCBI_EXPECTED_BOOST_VERSION,
+ $ncbi_cv_lib_boost_version_num,
+ [Define to the expected Boost version, to help catch skew.])
if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
fi
@@ -4950,7 +5186,7 @@ ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
fi
with_boost=no
;;
- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
+ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-7]] | 1_5[[0-7]]_* ) ;;
'' ) with_boost=no ;;
* )
AC_MSG_WARN(
@@ -5000,7 +5236,17 @@ ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
then
found=yes
break
+ else
+ for ext in .a .so; do
+ name=libboost_system$base$bsfx$ext
+ path=`$CXX -L$BOOST_LIBPATH_ -print-file-name=$name \
+ 2>/dev/null`
+ case "$path" in
+ $BOOST_PATH/*/$name ) found=yes; break ;;
+ esac
+ done
fi
+ test "$found" = yes && break
done
test "$found" = yes && break
done
@@ -5058,8 +5304,22 @@ ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
LIBS="$RT_LIBS $orig_LIBS"
[AC_LINK_IFELSE(
- [AC_LANG_PROGRAM([[#include <boost/spirit.hpp>]],
- [[boost::spirit::parse("123", boost::spirit::int_p);]])],
+ [AC_LANG_PROGRAM([[#include <boost/spirit.hpp>
+ using namespace boost::spirit;
+ struct MyGrammar : public grammar<MyGrammar>
+ {
+ template <typename TScanner>
+ struct definition {
+ definition(const MyGrammar&) { }
+ typedef rule<TScanner, parser_context<>,
+ parser_tag<0> >
+ TRule;
+ TRule my_rule;
+ TRule const & start() const
+ { return my_rule; }
+ };
+ };]],
+ [[MyGrammar g; parse("123", g);]])],
[ncbi_cv_lib_boost_spirit=yes], [ncbi_cv_lib_boost_spirit=no])])
BOOST_SYSTEM_LIBS=-lboost_system${BOOST_TAG}
@@ -5199,7 +5459,7 @@ ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
fi
- AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
+ AC_CACHE_CHECK([for Boost.Thread$in_path], ncbi_cv_lib_boost_thread,
CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
[AC_LINK_IFELSE(
@@ -5221,8 +5481,8 @@ else
fi
if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
- dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
- dnl [Define to 1 if the `Boost.Filesystem' library is available.])
+ AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
+ [Define to 1 if the `Boost.Filesystem' library is available.])
NCBI_PACKAGE(Boost.Filesystem)
else
boost_fs_lib=
@@ -5232,8 +5492,8 @@ else
fi
if test "$ncbi_cv_lib_boost_iostreams" != "no"; then
- dnl AC_DEFINE(HAVE_BOOST_IOSTREAMS, 1,
- dnl [Define to 1 if the `Boost.Iostreams' library is available.])
+ AC_DEFINE(HAVE_BOOST_IOSTREAMS, 1,
+ [Define to 1 if the `Boost.Iostreams' library is available.])
NCBI_PACKAGE(Boost.Iostreams)
else
BOOST_IOSTREAMS_LIBS=
@@ -5241,8 +5501,8 @@ else
fi
if test "$ncbi_cv_lib_boost_program_options" != "no"; then
- dnl AC_DEFINE(HAVE_BOOST_PROGRAM_OPTIONS, 1,
- dnl [Define to 1 if the `Boost.Program-Options' library is available.])
+ AC_DEFINE(HAVE_BOOST_PROGRAM_OPTIONS, 1,
+ [Define to 1 if the `Boost.Program-Options' library is available.])
NCBI_PACKAGE(Boost.Program-Options)
else
BOOST_PROGRAM_OPTIONS_LIBS=
@@ -5265,8 +5525,8 @@ if test "$ncbi_cv_lib_boost_spirit" != "no"; then
fi
if test "$ncbi_cv_lib_boost_system" != "no"; then
- dnl AC_DEFINE(HAVE_BOOST_SYSTEM, 1,
- dnl [Define to 1 if the `Boost.System' library is available.])
+ AC_DEFINE(HAVE_BOOST_SYSTEM, 1,
+ [Define to 1 if the `Boost.System' library is available.])
NCBI_PACKAGE(Boost.System)
# BOOST_SYSTEM(_STATIC)_LIBS already conditionally cleared above
fi
@@ -5291,8 +5551,8 @@ fi
if test "$ncbi_cv_lib_boost_thread" != "no"; then
AC_DEFINE(HAVE_BOOST_THREAD, 1,
- [Define to 1 if the `Boost.Threads' library is available.])
- NCBI_PACKAGE(Boost.Threads)
+ [Define to 1 if the `Boost.Thread' library is available.])
+ NCBI_PACKAGE(Boost.Thread)
else
BOOST_THREAD_LIBS=
BOOST_THREAD_STATIC_LIBS=
@@ -5527,10 +5787,8 @@ else
GLEW_LIBDIR=$GLEW_LIBDIR$bit64_sfx
fi
fi
- glew_config="eval PKG_CONFIG_PATH=\"$GLEW_LIBDIR/pkgconfig\" pkg-config"
- else
- glew_config=pkg-config
fi
+ glew_config="eval PKG_CONFIG_PATH=\"$GLEW_LIBDIR/pkgconfig\" pkg-config"
if pkg-config --version >/dev/null 2>&1; then
if $glew_config glewmx --exists >/dev/null 2>&1 \
&& test -n "`$glew_config glewmx --libs 2>/dev/null`"; then
@@ -5587,8 +5845,7 @@ LDFLAGS=$orig_LDFLAGS
## wxWidgets
-# Insist on single-byte builds by default, per various projects' expectations.
-: ${with_wxwidgets_ucs=no}
+# : ${with_wxwidgets_ucs=no}
if test "$with_wxwidgets" != "no" ; then
case "$with_wxwidgets" in
yes | "" ) ;;
@@ -5649,7 +5906,7 @@ if test "$with_wxwidgets" != "no" ; then
if test -n "$SYSROOT"; then
deps=`"$wxconf" $wxcfflags --libs --static 2>/dev/null \
| sed -e 's/.*\.a//'`
- libsed="$basesed; s/\$/ $deps/"
+ libsed="$basesed; s%\$% $deps%"
else
libsed=$basesed
fi
@@ -5657,15 +5914,21 @@ if test "$with_wxwidgets" != "no" ; then
* )
baseflags=`$gtkconf --cflags 2>/dev/null`
basesed=$no_usr_lib
- libsed=$basesed
+ deps=`$gtkconf --libs 2>/dev/null`
+ libsed="$basesed; s%\$% $deps%"
;;
esac
+ case "`"$wxconf" $wxcfflags --version`" in
+ 1.* | 2.[[0-7]].* ) wxlibs=std ;;
+ * ) wxlibs=std,richtext,aui,propgrid ;;
+ esac
AC_CACHE_CHECK(
[for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
ncbi_cv_lib_wxwidgets,
[if test -x "$wxconf" ; then
WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
+ NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS,
+ ["$wxconf" $wxcfflags --libs $wxlibs],
[$libsed; s/ -lm / /g;])
CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
@@ -5693,13 +5956,8 @@ if test "$with_wxwidgets" = "no" ; then
else
NCBI_PACKAGE(wxWidgets)
case "`"$wxconf" $wxcfflags --version`" in
- 1.* | 2.[[0-7]].*)
- wxlibs=std
- ;;
- * )
- NCBI_PACKAGE(wx2.8)
- wxlibs=std,richtext,aui,propgrid
- ;;
+ 1.* | 2.[[0-7]].*) ;;
+ * ) NCBI_PACKAGE(wx2.8) ;;
esac
# The "yes" may have been cached; get the actual settings again if needed
if test -z "$WXWIDGETS_INCLUDE"; then
@@ -5851,7 +6109,8 @@ else
AC_DEFINE(HAVE_LIBSSSUTILS, 1,
[Define to 1 if the NCBI SSS UTILS library is available.])
NCBI_PACKAGE(SSSUTILS)
- if test -f "$local_sss/../ncbils2/asn/login.asn"; then
+ if test -f "$local_sss/../ncbils2/asn/login.asn" \
+ -a -n "$GCRYPT_LIBS"; then
if test "$with_included_sss" = yes || \
grep vformat $NCBI_SSS_INCLUDE/String.hpp >/dev/null 2>&1; then
NCBI_PACKAGE(LocalNCBILS) # temporary compatibility measure
@@ -6062,8 +6321,9 @@ else
NCBI_RPATHIFY_OUTPUT(ICU_LIBS, $ICU_CONFIG --ldflags-searchpath)
ICU_LIBS="$ICU_LIBS `$ICU_CONFIG --ldflags-libsonly`"
fi
+ ICU_SEARCHPATH=`$ICU_CONFIG --ldflags-searchpath | sed -e "$no_usr_lib"`
ICU_STATIC_LIBS=`$ICU_CONFIG --ldflags-libsonly | sed -e 's/-licu/-lsicu/g'`
- ICU_STATIC_LIBS="`$ICU_CONFIG --ldflags-searchpath` $ICU_STATIC_LIBS"
+ ICU_STATIC_LIBS="$ICU_SEARCHPATH $ICU_STATIC_LIBS"
AC_DEFINE(HAVE_ICU, 1, [Define to 1 if ICU libraries are available.])
fi
@@ -6159,6 +6419,7 @@ else
NCBI_PACKAGE(LIBXML)
LIBXML_INCLUDE="$LIBXML_INCLUDE"
AC_DEFINE(HAVE_LIBXML, 1, [Define to 1 if libxml2 is available.])
+ export LIBXML_LIBPATH
fi
AC_SUBST(LIBXML_INCLUDE)
AC_SUBST(LIBXML_LIBS)
@@ -6431,6 +6692,146 @@ else
fi
+# NCBI SRA/VDB
+VDB_POST_LINK=:
+VDB_REQ=VDB
+if test "$with_vdb" != "no" ; then
+ # CURL?
+ vdb_deps="$LIBXML_LIBS $NETWORK_LIBS $BZ2_LIBS $Z_LIBS $DL_LIBS"
+ if test "${with_vdb:-yes}" != "yes" -a -d "$with_vdb"; then
+ VDB_PATH=$with_vdb
+ fi
+ if test -d "$VDB_PATH"; then
+ : ${with_downloaded_vdb=no}
+ else
+ : ${with_downloaded_vdb=$with_vdb}
+ fi
+ if test "$with_downloaded_vdb" != "no"; then
+ AC_MSG_NOTICE([trying to build the NCBI SRA/VDB Toolkit from GitHub.])
+ VDB_PATH=`$real_srcdir/scripts/common/add_vdb.sh 2>&AS_MESSAGE_LOG_FD`
+ status=$?
+ if test $status != 0; then
+ message="SRA/VDB build failed with status $status"
+ elif test ! -d "$VDB_PATH"; then
+ message="SRA/VDB build nominally succeeded, but failed to report where"
+ else
+ message=
+ fi
+ case "$message:$with_downloaded_vdb" in
+ :* ) ;;
+ *:yes ) AC_MSG_FAILURE([$message]) ;;
+ * ) AC_MSG_WARN([$message]) ;;
+ esac
+ fi
+ if test "$with_included_vdb" != "yes"; then
+ if test -z "$VDB_PATH"; then
+ in_path=
+ else
+ dnl NCBI_FIX_DIR(VDB_PATH)
+ vdb_parent=`dirname "$VDB_PATH"`
+ NCBI_FIX_DIR(vdb_parent)
+ VDB_PATH=$vdb_parent/`basename "$VDB_PATH"`
+ in_path=" in $VDB_PATH"
+ for x in interfaces include; do
+ if test -d "$VDB_PATH/$x"; then
+ : ${VDB_INCLUDE="-I$VDB_PATH/$x"}
+ break
+ fi
+ done
+ case "$DEBUG_SFX" in
+ Debug )
+ VDB_INCLUDE="$VDB_INCLUDE $VDB_INCLUDE/cc/gcc -D_DEBUGGING"
+ vdb_mode=debug
+ ;;
+ Release )
+ vdb_mode=release
+ ;;
+ esac
+ case "$host_os:$host_cpu:$bit64_sfx" in
+ darwin*:*86*:64 ) vdb_libpath=mac/$vdb_mode/x86_64/lib ;;
+ darwin*:*86*:* ) vdb_libpath=mac/$vdb_mode/fat86/lib ;;
+ linux*:*86*:64 ) vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
+ * )
+ if test -n "$with_vdb"; then
+ AC_MSG_ERROR([--with-vdb explicitly specified,
+ but not supported on this platform.])
+ fi
+ ;;
+ esac
+ for x in "$vdb_libpath" "lib${bit64_sfx:-32}" lib; do
+ if test -n "$x" -a -d "$VDB_PATH/$x"; then
+ : ${VDB_LIBDIR=$VDB_PATH/$x}
+ break
+ fi
+ done
+ fi
+ NCBI_RPATHIFY_COND(VDB_LIBS, $VDB_LIBDIR, [ -lncbi-vdb $vdb_deps])
+ CPPFLAGS="$orig_CPPFLAGS $VDB_INCLUDE"
+ LIBS="$orig_LIBS $VDB_LIBS"
+ AC_CACHE_CHECK([for ncbi-vdb$in_path], ncbi_cv_lib_ncbi_vdb,
+ AC_LINK_IFELSE([
+ AC_LANG_PROGRAM([#include <sra/sradb.h>],
+ [const SRAMgr* mgr; SRAMgrMakeRead(&mgr);])],
+ [ncbi_cv_lib_ncbi_vdb=yes], [ncbi_cv_lib_ncbi_vdb=no]))
+ if test "$ncbi_cv_lib_ncbi_vdb" = yes; then
+ NCBI_PACKAGE(VDB)
+ VDB_LIB=
+ if test -f "$VDB_LIBDIR/libncbi-vdb-static.a"; then
+ VDB_STATIC_LIBS="-L$VDB_LIBDIR -lncbi-vdb-static $vdb_deps"
+ else
+ VDB_STATIC_LIBS=$VDB_LIBS
+ fi
+ case "$host_os" in
+ darwin*)
+ inst_name=`otool -D $VDB_LIBDIR/libncbi-vdb.dylib 2>/dev/null \
+ | grep -v ':$'`
+ case "$inst_name" in
+ @executable_path* )
+ major=`echo $inst_name | sed -ne 's,.*/libncbi-vdb\.\([[1-9]][[0-9]]*\).*\.dylib$,\1,p'`
+ test -z "$major" || \
+ VDB_POST_LINK="install_name_tool -change $inst_name @rpath/libncbi-vdb.$major.dylib"
+ ;;
+ esac
+ ;;
+ esac
+ else
+ VDB_INCLUDE=
+ VDB_LIBS=
+ VDB_STATIC_LIBS=
+ fi
+ elif test -d "$real_srcdir/src/sra/sdk/interfaces"; then
+ case "$host_os" in
+ darwin* | linux* | solaris* )
+ AC_MSG_NOTICE([Using local NCBI SRA/VDB copy in src/sra/sdk])
+ NCBI_PACKAGE(VDB)
+ NCBI_PACKAGE(LocalVDB)
+ VDB_INCLUDE='-I$(includedir)/../src/sra/sdk/interfaces'
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(includedir)/../src/sra/sdk/interfaces/C++Toolkit"
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(top_srcdir)/src/sra/sdk/interfaces"
+ VDB_INCLUDE="$VDB_INCLUDE -I\$(top_srcdir)/src/sra/sdk/interfaces/C++Toolkit"
+ if test "$DEBUG_SFX" = Debug; then
+ VDB_INCLUDE="$VDB_INCLUDE -D_DEBUGGING"
+ fi
+ VDB_LIB=ncbi-vdb-read
+ VDB_LIBS=$vdb_deps
+ VDB_STATIC_LIBS=$VDB_LIBS
+ VDB_REQ=LocalVDB
+ ;;
+ * )
+ AC_MSG_ERROR([--with-included-vdb explicitly specified,
+ but not supported on this platform.])
+ ;;
+ esac
+ else
+ AC_MSG_ERROR([--with-included-vdb explicitly specified,
+ but no local copy exists.])
+ fi
+ if test -z "$VDB_LIBS"; then
+ NCBI_MISSING_PACKAGE(vdb)
+ fi
+fi
+
+
### OEChem
# somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
# which depend on oechem....
@@ -6466,7 +6867,14 @@ if test -d "$SGE_PATH" -a -z "$SGE_LIBPATH"; then
break
fi
done
+ BASE_SGE_LIBPATH=$SGE_LIBPATH
NCBI_RPATHIFY(SGE_LIBPATH, $SGE_LIBPATH)
+ # Try to use a dedicated directory without alternate versions of
+ # system libraries such as OpenSSL.
+ if test -d "$BASE_SGE_LIBPATH" -a -d "$SGE_PATH/lib/drmaa"; then
+ SGE_LIBPATH=`echo $SGE_LIBPATH \
+ | sed -e "s,-L$BASE_SGE_LIBPATH,-L$SGE_PATH/lib/drmaa,g"`
+ fi
fi
NCBI_CHECK_THIRD_PARTY_LIB_EX(sge, SGE, drmaa,
[[AC_LANG_PROGRAM([[#include <sys/types.h>
@@ -6763,6 +7171,36 @@ if test -n "$AVRO_LIBS"; then
AC_PATH_PROG(AVROGENCPP, avrogencpp, [], [$AVRO_PATH/bin:$PATH])
fi
+
+# USC Cereal (header-only)
+case "$with_cereal" in
+ yes | no | '' ) ;;
+ * ) CEREAL_PATH=$with_cereal ;;
+esac
+if test "$with_cereal" != no; then
+ in_cereal=
+ if test -d "$CEREAL_PATH"; then
+ NCBI_FIX_DIR(CEREAL_PATH)
+ in_cereal=" in $CEREAL_PATH"
+ fi
+ CEREAL_INCLUDE=-I$CEREAL_PATH/include
+ AC_CACHE_CHECK([for USC Cereal$in_cereal], ncbi_cv_lib_cereal,
+ [CPPFLAGS="$CEREAL_INCLUDE $orig_CPPFLAGS"
+ AC_COMPILE_IFELSE(
+ [AC_LANG_PROGRAM([[#include <iostream>
+ #include <cereal/archives/binary.hpp>]],
+ [[cereal::BinaryOutputArchive
+ archive(std::cout);]])],
+ [ncbi_cv_lib_cereal=yes], [ncbi_cv_lib_cereal=no])])
+ if test "$ncbi_cv_lib_cereal" = yes; then
+ NCBI_PACKAGE(Cereal)
+ else
+ NCBI_MISSING_PACKAGE(cereal)
+ CEREAL_INCLUDE=
+ fi
+fi
+
+
# MongoDB
case "$with_mongodb" in
yes | no | '' ) ;;
@@ -6788,11 +7226,40 @@ NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
# MongoDB's own library is normally static, but its supporting Boost
# libraries might not be by default.
if test -n "$MONGODB_LIBS"; then
- MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_REGEXP_STATIC_LIBS $BOOST_THREAD_STATIC_LIBS"
+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongoclient $BOOST_LIBPATH $boost_fs_static_lib $BOOST_REGEX_STATIC_LIBS $BOOST_THREAD_STATIC_LIBS"
else
MONGODB_STATIC_LIBS=
fi
+
+# Google Mock
+case "$with_gmock" in
+ yes | no | '' ) ;;
+ * ) GMOCK_PATH=$with_gmock ;;
+esac
+if test -d "$GMOCK_PATH"; then
+ NCBI_FIX_DIR(GMOCK_PATH)
+ for d in "$GMOCK_PATH/$compiler_vpfx$DEBUG_SFX$mt_sfx$bit64_sfx/lib" \
+ "$GMOCK_PATH/$compiler_pfx$DEBUG_SFX$mt_sfx$bit64_sfx/lib" \
+ "$GMOCK_PATH/$compiler_vpfx$DEBUG_SFX$mt_sfx/lib" \
+ "$GMOCK_PATH/$compiler_pfx$DEBUG_SFX$mt_sfx/lib" \
+ "$GMOCK_PATH/lib$bit64_sfx" "$GMOCK_PATH/lib"; do
+ if test -d "$d"; then
+ GMOCK_LIBDIR=$d
+ NCBI_FIX_DIR(GMOCK_LIBDIR)
+ break
+ fi
+ done
+fi
+NCBI_RPATHIFY(GMOCK_LIBPATH, $GMOCK_LIBDIR)
+NCBI_CHECK_THIRD_PARTY_LIB(gmock,
+ [AC_LANG_PROGRAM([#include <gmock/gmock.h>],
+ [int my_argc;
+ char** my_argv;
+ testing::InitGoogleMock(&my_argc, my_argv);])],
+ [-lgtest])
+
+
### Restore original compiler/linker flags
LIBS="$orig_LIBS"
CPPFLAGS="$orig_CPPFLAGS"
@@ -7441,6 +7908,12 @@ AC_SUBST(NCBI_SSS_LIBPATH)
AC_SUBST(LIBSSSUTILS)
AC_SUBST(LIBSSSDB)
AC_SUBST(sssutils)
+AC_SUBST(VDB_INCLUDE)
+AC_SUBST(VDB_LIB)
+AC_SUBST(VDB_LIBS)
+AC_SUBST(VDB_STATIC_LIBS)
+AC_SUBST(VDB_REQ)
+AC_SUBST(VDB_POST_LINK)
AC_SUBST(SP_INCLUDE)
AC_SUBST(SP_LIBS)
AC_SUBST(ORBACUS_INCLUDE)
@@ -7470,6 +7943,7 @@ AC_SUBST(FREETYPE_INCLUDE)
AC_SUBST(FREETYPE_LIBS)
AC_SUBST(GSOAP_PATH)
AC_SUBST(AVRO_STATIC_LIBS)
+AC_SUBST(CEREAL_INCLUDE)
AC_SUBST(MONGODB_STATIC_LIBS)
AC_SUBST(ncbi_xreader_pubseqos)
AC_SUBST(ncbi_xreader_pubseqos2)
diff --git a/c++/src/build-system/datatool_version.txt b/c++/src/build-system/datatool_version.txt
index 46b81d8..edcfe40 100644
--- a/c++/src/build-system/datatool_version.txt
+++ b/c++/src/build-system/datatool_version.txt
@@ -1 +1 @@
-2.11.0
+2.14.0
diff --git a/c++/src/build-system/install.sh.in b/c++/src/build-system/install.sh.in
index 8f9c9b4..9ea7b71 100644
--- a/c++/src/build-system/install.sh.in
+++ b/c++/src/build-system/install.sh.in
@@ -17,7 +17,7 @@
echo "[`date`]"
-svn_location=`echo '$HeadURL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.2.31/c++/src/build-system/install.sh.in $' | sed "s%\\$[H]eadURL: *\\([^$][^$]*\\) \\$.*%\\1%"`
+svn_location=`echo '$HeadURL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.3.0/c++/src/build-system/install.sh.in $' | sed "s%\\$[H]eadURL: *\\([^$][^$]*\\) \\$.*%\\1%"`
svn_revision=`echo '$Revision: 117476 $' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
script_name=`basename $0`
diff --git a/c++/src/build-system/library_relations.txt b/c++/src/build-system/library_relations.txt
index 98fc5cd..bf463ce 100644
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
@@ -1,6 +1,12 @@
-# $Id: library_relations.txt 466266 2015-04-30 12:59:59Z ivanov $
+# $Id: library_relations.txt 477362 2015-08-28 13:25:29Z fukanchi $
# Pregenerated summary of library relations, for use by project_tree_builder.
$(ORIG_LIBS) needs3party
+16S_common needs seqset
+16S_summaries needs 16S_common
+16S_summaries needs gpipe_xmlutil
+16S_summaries needs xregexp
+Assembly2Fscreen needs fscreen
+Assembly2Fscreen needs xid_utils
BlastCgiUtils needs $(CONNEXT)
BlastCgiUtils needs connect
BlastCgiUtils needs xhtml
@@ -28,11 +34,12 @@ GMC needs softparse
GMC needs xgridcgi
GMU needs $(COMPRESS_LIBS)
GMU needs geoauth
-OSMesa includes3party $(OPENGL_LIBS)
+OSMesa needs3party $(OPENGL_LIBS)
OSMesa needs3party $(ORIG_LIBS)
VDBUtils needs bdbasncli
VDBUtils needs ncbi_xloader_csra
VDBUtils needs ncbi_xloader_wgs
+VDBUtils needs vdb2blast
X11 needs3party $(ORIG_LIBS)
Xext needs3party $(ORIG_LIBS)
Xext needs3party X11
@@ -40,11 +47,13 @@ Xpm needs3party $(ORIG_LIBS)
Xpm needs3party X11
access needs xser
accnmap needs dbapi
+ads needs $(SEQ_LIBS)
+ads needs pub
affy needs3party $(CURL_LIBS)
-affy needs3party $(DL_LIBS)
affy needs3party $(ORIG_LIBS)
affy needs3party $(XERCES_LIBS)
-agp_lookup needs gc_utils
+agp_lookup needs $(GPIPE_COMMON_LIBS)
+agp_lookup needs gpipe_objutil
agp_lookup needs xhtml
align_format needs $(OBJMGR_LIBS)
align_format needs $(OBJREAD_LIBS)
@@ -65,18 +74,33 @@ alndb_query needs $(SEQ_LIBS)
alndb_query needs pub
alndbaccess needs alndb_query
alndbaccess needs generic_db_core
-an_core needs bag_access
+an_core needs 16S_common
an_core needs gc_util_sdbapi
+an_core needs gpinit_bag_util
an_core needs gpipe_an_base
-an_core needs gpipe_jira
an_core needs gpipe_kmer
+an_core needs gpipe_val
an_core needs ncbi_xcache_netcache
-an_euk_pipeline needs an_core
+an_core needs pathogen_connection
+an_core needs reftrack_access
+an_euk_pipeline needs $(GPIPE_COMMON_LIBS)
+an_euk_pipeline needs bag_access
+an_euk_pipeline needs gpipe_an_base
an_euk_pipeline needs gpipe_val
-an_prok_pipeline needs an_core
+an_euk_pipeline needs reftrack_admin
+an_euk_pipeline needs3party $(BOOST_FILESYSTEM_LIBS)
+an_euk_pipeline needs3party $(BOOST_SYSTEM_LIBS)
+an_prok_pipeline needs $(GPIPE_COMMON_LIBS)
+an_prok_pipeline needs gpipe_an_base
+an_prok_pipeline needs pathogen_connection
an_prok_pipeline needs xobjwrite
+an_rnaseq needs gpipe_an_base
+an_rnaseq needs matchhits
an_worker_nodes needs gpipe_an_base
asn_cache includes id_dump
+asn_config needs build_config_base
+asn_config needs config_access
+asn_config needs reftrack_access
asn_sample_lib needs xser
asngendefs needs xser
asnmuxdblb needs dbloadb_asn
@@ -95,9 +119,9 @@ bacterial_pipeline_proc needs xalgoalignutil
bag_access needs $(SEQ_LIBS)
bag_access needs gpipe_common
bag_access needs pub
-bamread needs $(SRA_LIBS)
+bamread needs $(VDB_LIB)
bamread needs seqset
-bamread needs3party $(SRA_SDK_SYSLIBS)
+bamread needs3party $(VDB_LIBS)
basic_sample_lib needs xncbi
bdb needs xutil
bdb needs3party $(BERKELEYDB_LIBS)
@@ -109,10 +133,7 @@ biosample needs $(SDBAPI_LIB)
biosample needs xconnect
biosample needs xmlwrapp
biosample needs xregexp
-bioscgi needs biosample
-bioscgi needs xcgi
-biosconvert needs biosample
-biosconvert needs xvalidate
+biosample needs xutil
biotree needs general
biotree_db needs biotree
biotree_db needs gpipe_common
@@ -123,6 +144,9 @@ blast needs tables
blast_app_util needs $(BLAST_INPUT_LIBS)
blast_app_util needs $(BLAST_LIBS)
blast_services needs xnetblastcli
+blast_unit_test_util needs $(BLAST_LIBS)
+blast_unit_test_util needs $(OBJMGR_LIBS)
+blast_unit_test_util needs3party $(BOOST_TEST_LIBS)
blastapi needs3party blast
blastapi needs3party ncbitool
blastdb needs $(SEQ_LIBS)
@@ -144,12 +168,18 @@ blk64 needs3party comn64
blk64 needs3party intl64
bob_g needs splitdbasn_g
bob_g needs3party netblast
+boost_filesystem-gcc44-mt-d-64 needs3party $(BOOST_SYSTEM_LIBS)
+boost_filesystem-gcc44-mt-d-64 needs3party $(ORIG_LIBS)
+boost_system-gcc44-mt-d-64 needs3party $(ORIG_LIBS)
boost_unit_test_framework-gcc44-mt-d-64 needs3party $(ORIG_LIBS)
+build_config needs $(GPIPE_COMMON_LIBS)
build_config needs $(GPIPE_GENCOLL_LIBS)
build_config needs bacterial_pipeline_proc
-build_config needs gpinit
-build_config needs gpinit_access
-build_config needs gpipe_xml
+build_config needs build_config_base
+build_config needs reftrack_access
+build_config_base needs gencoll_client
+build_config_base needs gpinit_bag_util
+build_config_base needs gpinit_register
bz2 needs3party $(ORIG_LIBS)
cache_blob needs $(COMPRESS_LIBS)
cache_blob needs xser
@@ -158,8 +188,8 @@ cdd needs cn3d
cdd needs scoremat
clog needs3party $(ORIG_LIBS)
cluster needs3party $(ORIG_LIBS)
-clustering needs $(SOBJMGR_LIBS)
-clustering needs3party $(DL_LIBS)
+cluster_assignment needs xser
+clustering needs cobalt
cn3d needs mmdb
cobalt needs $(BLAST_LIBS)
cobalt needs xalgoalignnw
@@ -171,6 +201,8 @@ com_err needs3party $(ORIG_LIBS)
comn64 needs3party $(ORIG_LIBS)
comn64 needs3party intl64
composition_adjustment needs3party $(ORIG_LIBS)
+config_access needs gpinit_obj
+config_access needs gpipe_common
configure_ctl needs gpipe_common
connect needs3party $(NETWORK_LIBS)
connect needs3party $(ORIG_LIBS)
@@ -189,26 +221,33 @@ ct64 needs3party $(ORIG_LIBS)
ct64 needs3party comn64
ct64 needs3party intl64
ct_ftds64 needs tds_ftds64
-ctutils needs $(SRA_LIBS)
-ctutils needs3party $(SRA_SDK_SYSLIBS)
+ctransition needs xncbi
+ctutils needs $(VDB_LIB)
+ctutils needs3party $(SYBASE_DLLS)
ctutils needs3party $(SYBASE_LIBS)
+ctutils needs3party $(VDB_LIBS)
ctutils needs3party ncbiobj
-curl needs3party $(DL_LIBS)
curl needs3party $(ORIG_LIBS)
db needs3party $(ORIG_LIBS)
dbapi needs dbapi_driver
dbapi_driver needs xncbi
dbapi_driver_wrap_s needs dbapi_driver
+dbapi_sample_base needs $(DBAPI_CTLIB)
+dbapi_sample_base needs $(DBAPI_ODBC)
dbapi_sample_base needs $(XCONNEXT)
-dbapi_sample_base needs dbapi_driver
+dbapi_sample_base needs ncbi_xdbapi_ftds
dbapi_sample_base needs xconnect
dbapi_sample_base needs xutil
+dbapi_sample_base needs3party $(SYBASE_DLLS)
+dbapi_sample_base needs3party $(SYBASE_LIBS)
dbapi_util_blobstore needs $(COMPRESS_LIBS)
dbapi_util_blobstore needs dbapi_driver
dbapi_util_blobstore needs xutil
dbassist needs dbapi
dbassist needs dbloadb
dbassist needs ncbi_xdbapi_ftds
+dbassist_cgi includes dbassist
+dbgap_data_access needs xid_utils
dbinfoasncpp_g needs xser
dbldasn_g needs splitdbasn_g
dbloadb needs asnmuxdblb
@@ -224,9 +263,9 @@ edirect needs ncqhst
edirect needs txservbase
egenedb needs $(COMPRESS_LIBS)
egenedb needs $(CONNEXT)
-egenedb needs connect
egenedb needs dbapi_driver_wrap_s
egenedb needs entrezgene
+egenedb needs taxon1
egenedomains needs $(OBJMGR_LIBS)
egenedomains needs entrezgene
egquery needs xser
@@ -254,6 +293,8 @@ eutils needs espell
eutils needs esummary
eutils needs uilist
eutils needs xconnect
+eutils_client needs xconnect
+eutils_client needs xmlwrapp
eutilsapp includes eueid
eutilsapp needs ncqhst
eutilsapp needs3party $(FASTCGI_LIBS)
@@ -266,6 +307,7 @@ fastme needs3party $(ORIG_LIBS)
fbsdstd_g needs3party $(ORIG_LIBS)
fcgi needs3party $(ORIG_LIBS)
featdef needs xser
+filter_snps needs xalnmgr
freetype needs3party $(ORIG_LIBS)
fscreen needs agp_lookup
fscreen needs dbapi_util_blobstore
@@ -276,8 +318,10 @@ gbproj needs submit
gbproj needs xconnect
gbseq needs xser
gc_ftp_ctl needs gpipe_objutil
+gc_load_utils needs $(GPIPE_COMMON_LIBS)
gc_load_utils needs gc_utils
gc_load_utils needs xid_utils
+gc_util_sdbapi needs gencoll_client
gc_util_sdbapi needs gpipe_common
gc_utils needs gpipe_objutil
gcaccess_utils needs $(GPIPE_GENCOLL_LIBS)
@@ -285,7 +329,6 @@ gcedit needs agp_lookup
gcedit needs gc_load_utils
gcrypt needs3party $(ORIG_LIBS)
gdsutil needs xncbi
-gencoll needs genome_collection
gencoll_client needs genome_collection
gencoll_client needs xconnect
gencoll_load needs xser
@@ -304,6 +347,7 @@ generic_db_tmpl_utils needs generic_db_utils
generic_db_utils needs $(COMPRESS_LIBS)
generic_db_utils needs xconnect
generic_db_utils needs xser
+generic_db_utils_cgi includes generic_db_utils
genesbyloc needs xser
genome_collection needs $(SEQ_LIBS)
genome_collection needs pub
@@ -329,78 +373,92 @@ geomyncbi needs xmlwrapp
geostat needs xncbi
gif needs3party $(ORIG_LIBS)
gif needs3party X11
+gmap needs xlinear_prog
+gmap needs xmlwrapp
gmp needs3party $(ORIG_LIBS)
gnomon_access needs sqlitewrapp
-gnomon_access needs xobjutil
+gnomon_access needs xalgognomon
gnomon_access needs xqueryparse
gnomon_asn_proc needs xobjutil
gnutls needs $(Z_LIB)
+gnutls needs3party $(GMP_LIBS)
+gnutls needs3party $(NETTLE_LIBS)
gnutls needs3party $(ORIG_LIBS)
gnutls needs3party $(Z_LIBS)
-gnutls needs3party gmp
-gnutls needs3party hogweed
-gnutls needs3party nettle
-gp_python_attr needs $(GPIPE_COMMON_LIBS)
+gp_python_attr needs gpipe_attr
gp_python_attr needs3party $(PYTHON_LIBS)
+gpcgi needs $(SDBAPI_LIB)
+gpcgi needs xcgi
+gpcgi needs xconnect
+gpcgi needs xmlwrapp
+gpcgi needs xregexp
gpexec_query needs gpipe_common
gpexec_query needs monitor_buildrun
gpg-error needs3party $(ORIG_LIBS)
+gpinit includes gpinit_obj
gpinit needs entrez2cli
gpinit needs gc_utils
-gpinit needs gpinit_utils
+gpinit needs gpinit_access
gpinit_access needs gpipe_common
-gpinit_admin needs gc_utils
-gpinit_admin needs gpinit_access
-gpinit_asn_factory needs gpinit
-gpinit_stats_report needs $(GPIPE_COMMON_LIBS)
-gpinit_utils needs $(GPIPE_COMMON_LIBS)
+gpinit_bag_util needs bag_access
+gpinit_bag_util needs gpinit_access
+gpinit_obj needs general
+gpinit_register needs gc_utils
+gpinit_register needs gpinit_access
+gpinit_reports needs xmlwrapp
+gpinit_reports needs xregexp
+gpinit_stats_report needs gpipe_attr
gpipe_align_format needs $(BLAST_FORMATTER_MINIMAL_LIBS)
-gpipe_align_format needs $(XFORMAT_LIBS)
gpipe_align_format needs gpipe_objutil
gpipe_align_format needs prosplign
gpipe_align_format needs xobjwrite
gpipe_alloc needs3party $(ORIG_LIBS)
gpipe_alnutil needs gpipe_objutil
-gpipe_alnutil needs xalgoalignutil
gpipe_an_base needs gencoll_client
gpipe_an_base needs gpinit
+gpipe_an_base needs gpipe_jira
gpipe_an_base needs gpipe_sadb
gpipe_an_base needs gpipe_type_verifier
gpipe_an_base needs gpxlib
gpipe_an_base needs grid_wrapper
gpipe_asn_cleanup needs xvalidate
gpipe_asn_proc needs gpipe_alnutil
+gpipe_asn_proc needs xalgoalignutil
+gpipe_asn_proc needs xalgognomon
gpipe_asn_proc needs xmergetree
gpipe_attr needs gpipe_property
gpipe_best_placement needs gpipe_alnutil
-gpipe_clean_titles needs xdiscrepancy_report
+gpipe_best_placement needs xalgoalignutil
+gpipe_clean_prot_names needs $(SDBAPI_LIB)
+gpipe_clean_prot_names needs xdiscrepancy_report
+gpipe_common includes eutils_client
gpipe_common needs $(SDBAPI_LIB)
gpipe_common needs xcgi
-gpipe_common needs xconnect
-gpipe_common needs xmlwrapp
-gpipe_ftp needs $(XFORMAT_LIBS)
+gpipe_dateutil needs xregexp
gpipe_ftp needs gcaccess_utils
gpipe_ftp needs gpinit
+gpipe_ftp needs gpipe_alnutil
gpipe_ftp needs xalgoalignutil
gpipe_ftp needs xobjwrite
gpipe_ftp needs xrepeatdb
-gpipe_ftp_new needs $(XFORMAT_LIBS)
gpipe_ftp_new needs gcaccess_utils
gpipe_ftp_new needs gpinit
gpipe_ftp_new needs xalgoalignutil
gpipe_ftp_new needs xobjwrite
gpipe_ftp_new needs xrepeatdb
-gpipe_jira needs gpipe_common
+gpipe_jira needs gpinit_access
+gpipe_jira needs gpipe_attr
gpipe_jira needs3party $(GSOAP_LIBS)
-gpipe_kmer needs biotree
-gpipe_kmer needs pathogen_metadata
+gpipe_kmer needs gpipe_objutil
+gpipe_kmer needs sampling
gpipe_kpi needs xmlwrapp
gpipe_kpi needs xncbi
gpipe_meta_access needs gpipe_common
-gpipe_objutil needs $(GPIPE_COMMON_LIBS)
gpipe_objutil needs $(GPIPE_LOADER_LIBS)
+gpipe_objutil needs $(OBJEDIT_LIBS)
gpipe_objutil needs $(OBJMGR_LIBS)
-gpipe_objutil needs pubmed
+gpipe_objutil needs $(XFORMAT_LIBS)
+gpipe_objutil needs gpipe_attr
gpipe_objutil needs taxon1
gpipe_objutil needs writedb
gpipe_objutil needs3party $(GPIPE_LOADER_THIRDPARTY_LIBS)
@@ -413,6 +471,12 @@ gpipe_sadb needs $(COMPRESS_LIBS)
gpipe_sadb needs seqset
gpipe_sadb needs taxon1
gpipe_sadb needs xmlwrapp
+gpipe_sqlite needs $(SDBAPI_LIB)
+gpipe_sqlite needs $(SEQ_LIBS)
+gpipe_sqlite needs pub
+gpipe_sqlite needs sqlitewrapp
+gpipe_sqlite needs xconnect
+gpipe_sqlite needs xregexp
gpipe_standalone needs gpipe_an_base
gpipe_tree needs gpipe_property
gpipe_tree needs xalgophytree
@@ -423,10 +487,13 @@ gpipe_val needs $(SEQ_LIBS)
gpipe_val needs gpipe_common
gpipe_val needs pub
gpipe_val needs valerr
-gpipe_xml needs $(GPIPE_COMMON_LIBS)
gpipe_xml needs connssl
+gpipe_xml needs gpipe_attr
+gpipe_xml needs gpipe_dateutil
gpipe_xml needs taxon1
gpipe_xml needs taxon3
+gpipe_xmlutil needs xmlwrapp
+gpipe_xmlutil needs xutil
gpxapi needs general
gpxapi needs xconnect
gpxlib needs $(COMPRESS_LIBS)
@@ -435,6 +502,7 @@ gpxlib needs gpxapi
gpxlib needs xgp_manifest
grid_wrapper needs gpipe_resource_req
grid_wrapper needs xconnect
+grid_wrapper needs xutil
grid_wrapper needs3party $(SGE_LIBS)
gsoapssl++ needs $(Z_LIB)
gsoapssl++ needs3party $(KRB5_LIBS)
@@ -448,20 +516,19 @@ gssapi_krb5 needs3party com_err
gssapi_krb5 needs3party k5crypto
gui_config needs gui_objutils
gui_core needs $(BLAST_INPUT_LIBS)
+gui_core needs gui_framework
+gui_core needs w_grid_widget
gui_core needs w_loaders
gui_core needs w_object_list
gui_core needs w_seq
-gui_framework needs $(BLAST_INPUT_LIBS)
-gui_framework needs w_loaders
-gui_framework needs w_object_list
-gui_framework needs w_seq
+gui_framework needs w_data
gui_glmesa needs xcgi
gui_glmesa needs xhtml
gui_glmesa needs ximage
gui_glmesa needs3party $(OSMESA_LIBS)
gui_graph needs gui_opengl
-gui_objects needs $(COMPRESS_LIBS)
gui_objects needs gui_objutils
+gui_objutils needs $(COMPRESS_LIBS)
gui_objutils needs $(EUTILS_LIBS)
gui_objutils needs biotree
gui_objutils needs entrez2cli
@@ -469,9 +536,12 @@ gui_objutils needs entrezgene
gui_objutils needs gbproj
gui_objutils needs gencoll_client
gui_objutils needs gui_utils
+gui_objutils needs macro
gui_objutils needs snputil
gui_objutils needs xalgoalignutil
+gui_objutils needs xcgi
gui_objutils needs xmlwrapp
+gui_objutils needs xobjwrite
gui_objutils needs xvalidate
gui_opengl needs gui_utils
gui_opengl needs ximage
@@ -483,8 +553,7 @@ gui_print needs gui_opengl
gui_utils needs tables
gui_utils needs xconnect
gui_utils needs xutil
-guide_tree needs gui_glmesa
-guide_tree needs w_phylo_tree
+guide_tree needs phytree_format
guide_tree needs xconnserv
gumbelparams needs tables
gumbelparams needs xutil
@@ -497,9 +566,10 @@ hgvs needs xregexp
hgvs_name needs $(OBJMGR_LIBS)
hgvs_name needs gui_objutils
hgvs_name needs sv_objects
+hmm_file needs xregexp
+hmm_hit_handle needs xobjutil
+hogweed needs3party $(GMP_LIBS)
hogweed needs3party $(ORIG_LIBS)
-hogweed needs3party gmp
-hogweed needs3party nettle
homologene needs $(SEQ_LIBS)
homologene needs pub
htbbase needs txxmldoc
@@ -528,6 +598,8 @@ ideocoord needs $(SDBAPI_LIB)
ideocoord needs ideocli
idgen needs dbassist
idload needs3party ctutils
+idload_utils needs gpipe_common
+idload_utils needs xobjutil
idx needs $(CONNEXT)
idx needs dbapi_driver
idx needs spellsrvbase
@@ -562,14 +634,15 @@ jiracli needs xconnect
jirasvc needs xser
jpeg needs3party $(ORIG_LIBS)
k5crypto needs3party $(ORIG_LIBS)
+kmer_metadata needs $(GPIPE_COMMON_LIBS)
+kmer_metadata needs biotree
+kmer_metadata needs gpipe_kmer
+kmer_metadata needs pathogen_connection
krb5 needs3party $(NETWORK_LIBS)
krb5 needs3party $(ORIG_LIBS)
krb5 needs3party com_err
krb5 needs3party k5crypto
lbsmdapi needs connect
-lds needs $(OBJREAD_LIBS)
-lds needs bdb
-lds needs xobjutil
lds2 needs $(COMPRESS_LIBS)
lds2 needs $(OBJREAD_LIBS)
lds2 needs sqlitewrapp
@@ -589,6 +662,8 @@ mapview needs mv_entrez
mapview needs mvobjutil
mapview needs seqset
mapviewcli needs mapview
+matchhits needs $(COMPRESS_LIBS)
+matchhits needs seqdb
medlars needs biblio
medline needs biblio
mghbn needs connect
@@ -612,6 +687,8 @@ muscleasn_g needs $(SEQ_LIBS)
muscleasn_g needs pub
mux needs generic_db_utils
mux needs xcgi
+mux_cgi includes mux
+mux_cgi needs generic_db_utils_cgi
muxex-C_g needs dbldasn_g
muxex-C_g needs mux
muxex_g needs alndb_query
@@ -633,28 +710,22 @@ mv_metacli needs mv_meta
mv_types needs $(SEQ_LIBS)
mv_types needs gui_utils
mv_types needs pub
-mv_util needs $(COMPRESS_LIBS)
-mv_util needs mv_webdata
-mv_util needs xconnserv
mv_webdata needs mapview
-mv_xmlcgi needs mv_types
-mv_xmlcgi needs mv_xmlutil
-mv_xmlcgi needs xcgi
-mv_xmlutil needs xncbi
-mv_xmlutil needs3party $(LIBXML_LIBS)
-mv_xmlutil needs3party $(LIBXSLT_LIBS)
mvobjutil needs mv_align
mvobjutil needs mv_metacli
mysqlclient needs $(Z_LIB)
mysqlclient needs3party $(NETWORK_LIBS)
mysqlclient needs3party $(ORIG_LIBS)
mysqlclient needs3party $(Z_LIBS)
-mzXML needs xser
ncbi includes connect
ncbi includes tables
ncbi needs3party $(ORIG_LIBS)
-ncbi-vdb-read needs3party $(ORIG_LIBS)
-ncbi-vdb-read needs3party $(SRA_SDK_SYSLIBS)
+ncbi-vdb includes $(BZ2_LIB)
+ncbi-vdb includes $(Z_LIB)
+ncbi-vdb includes3party $(BZ2_LIBS)
+ncbi-vdb includes3party $(Z_LIBS)
+ncbi-vdb needs3party $(LIBXML_LIBS)
+ncbi-vdb needs3party $(ORIG_LIBS)
ncbiCacc includes3party ncbiacc
ncbiCacc needs3party netentr
ncbiNacc includes3party ncbiacc
@@ -667,10 +738,12 @@ ncbi_xcache_sqlite3 needs xutil
ncbi_xcache_sqlite3 needs3party $(SQLITE3_LIBS)
ncbi_xdbapi_ctlib needs dbapi_driver
ncbi_xdbapi_ctlib needs3party $(NETWORK_LIBS)
+ncbi_xdbapi_ctlib needs3party $(SYBASE_DLLS)
ncbi_xdbapi_ctlib needs3party $(SYBASE_LIBS)
ncbi_xdbapi_dblib needs dbapi_driver
ncbi_xdbapi_dblib needs3party $(NETWORK_LIBS)
ncbi_xdbapi_dblib needs3party $(SYBASE_DBLIBS)
+ncbi_xdbapi_dblib needs3party $(SYBASE_DLLS)
ncbi_xdbapi_ftds needs $(FTDS_LIB)
ncbi_xdbapi_ftds needs dbapi_driver
ncbi_xdbapi_ftds needs3party $(FTDS_LIBS)
@@ -689,25 +762,20 @@ ncbi_xloader_cdd needs $(SOBJMGR_LIBS)
ncbi_xloader_cdd needs xconnect
ncbi_xloader_csra needs $(SOBJMGR_LIBS)
ncbi_xloader_csra needs $(SRAREAD_LIBS)
-ncbi_xloader_csra needs3party $(SRA_SDK_SYSLIBS)
ncbi_xloader_genbank needs ncbi_xreader_cache
ncbi_xloader_genbank needs ncbi_xreader_id1
ncbi_xloader_genbank needs ncbi_xreader_id2
-ncbi_xloader_lds needs lds
ncbi_xloader_lds2 needs $(SOBJMGR_LIBS)
ncbi_xloader_lds2 needs lds2
ncbi_xloader_patcher needs $(SOBJMGR_LIBS)
ncbi_xloader_sra needs $(SOBJMGR_LIBS)
ncbi_xloader_sra needs $(SRAREAD_LIBS)
-ncbi_xloader_sra needs3party $(SRA_SDK_SYSLIBS)
ncbi_xloader_trace needs $(SOBJMGR_LIBS)
ncbi_xloader_trace needs id1cli
ncbi_xloader_vdbgraph needs $(SOBJMGR_LIBS)
ncbi_xloader_vdbgraph needs $(SRAREAD_LIBS)
-ncbi_xloader_vdbgraph needs3party $(SRA_SDK_SYSLIBS)
ncbi_xloader_wgs needs $(SOBJMGR_LIBS)
ncbi_xloader_wgs needs $(SRAREAD_LIBS)
-ncbi_xloader_wgs needs3party $(SRA_SDK_SYSLIBS)
ncbi_xreader needs $(COMPRESS_LIBS)
ncbi_xreader needs $(SOBJMGR_LIBS)
ncbi_xreader needs id1
@@ -746,6 +814,7 @@ ncbils2_authxml needs xser
ncbils2_cli needs ncbils2_asn
ncbils2_cli needs xconnect
ncbils2_cmn needs $(LIBSSSUTILS)
+ncbils2_cmn needs3party $(GCRYPT_LIBS)
ncbils2_dispxml needs xser
ncbimime needs cdd
ncbimla needs3party ncbiobj
@@ -770,6 +839,8 @@ ncbitool needs3party ncbiobj
ncbitxc2 includes3party objtax1
ncbitxc2 needs3party ncbitool
ncbitxc2 needs3party netcli
+ncbitxc2cxx needs taxon1
+ncbitxc2cxx needs3party objtax1
ncbiwww needs3party ncbiacc
ncbiwww needs3party ncbimsc1
ncqhst needs xconnserv
@@ -791,28 +862,36 @@ objtax1 needs3party ncbiobj
odbc_ftds64 needs tds_ftds64
omssa needs $(SEQ_LIBS)
omssa needs pub
+osutils needs3party $(RT_LIBS)
osutils needs3party ctutils
+pathogen_connection needs connssl
+pathogen_connection needs gpipe_common
+pathogen_connection needs gpipe_dateutil
+pathogen_ctl needs $(GPIPE_COMMON_LIBS)
+pathogen_ctl needs $(SRAREAD_LIBS)
pathogen_ctl needs bag_access
-pathogen_ctl needs gc_utils
pathogen_ctl needs gencoll_client
-pathogen_ctl needs pathogen_metadata
+pathogen_ctl needs pathogen_connection
+pathogen_ctl needs taxon1
pathogen_ctl needs xvalidate
-pathogen_ctl needs3party $(SRA_SDK_SYSLIBS)
pathogen_fill_taxa needs gpipe_common
-pathogen_metadata needs gpipe_objutil
-pathogen_metadata needs gpipe_xml
+pathogen_target_loader needs gpinit_register
+pathogen_target_loader needs pathogen_ctl
pcassay needs $(SEQ_LIBS)
pcassay needs pcsubstance
pcre needs3party $(ORIG_LIBS)
pcsubstance needs pub
pepXML needs xser
-peptidome needs general
phytree_format needs taxon1
phytree_format needs xalgophytree
+pn_ctl needs $(GPIPE_GENCOLL_LIBS)
+pn_ctl needs hmm_file
+pn_ctl needs hmm_hit_handle
+pn_ctl needs idload_utils
+pn_ctl needs xid_utils
png needs $(Z_LIB)
png needs3party $(ORIG_LIBS)
png needs3party $(Z_LIBS)
-primer3 needs3party $(ORIG_LIBS)
proj needs pubmed
proj needs seqset
prosplign needs xalgoalignutil
@@ -821,31 +900,33 @@ pstub needs3party $(ORIG_LIBS)
pub needs medline
pubmed needs medline
python2.5 needs3party $(ORIG_LIBS)
-python_ncbi_dbapi includes connect
-python_ncbi_dbapi includes dbapi
+python_ncbi_dbapi needs connect
+python_ncbi_dbapi needs dbapi
python_ncbi_dbapi needs3party $(PYTHON_LIBS)
rcobaltasn_g needs xser
refseq_aln_source needs $(COMPRESS_LIBS)
refseq_aln_source needs dbapi
refseq_aln_source needs ncbi_xdbapi_ftds
refseq_aln_source needs xalgoalignsplign
-refseq_ctl needs $(GPIPE_GENCOLL_LIBS)
refseq_ctl needs bacterial_pipeline_proc
-refseq_ctl needs gpinit_access
+refseq_ctl needs gencoll_client
+refseq_ctl needs xid_utils
+reftrack_access needs gpipe_common
+reftrack_admin needs reftrack_access
remap needs $(SEQ_LIBS)
remap needs pub
remapcli needs remap
remapcli needs xconnect
rt needs3party $(ORIG_LIBS)
-sablot needs3party $(EXPAT_LIBS)
-sablot needs3party $(ORIG_LIBS)
sage_mappings needs xser
sample_asn needs general
+sampling needs3party $(ORIG_LIBS)
scoremat needs seqset
sdbapi needs $(XCONNEXT)
sdbapi needs dbapi
sdbapi needs ncbi_xdbapi_ftds
sdbapi needs xconnect
+sdbapi needs xutil
sdncbiauth needs auxcomm_g
sdncbiauth needs generic_db_core
sdncbiauth needs muxex_g
@@ -853,6 +934,8 @@ sdncbiauth needs xmyncbi
seq needs pub
seq needs seqcode
seq needs sequtil
+seqalign_util needs $(SEQ_LIBS)
+seqalign_util needs pub
seqcode needs xser
seqdb needs $(SOBJMGR_LIBS)
seqdb needs blastdb
@@ -869,6 +952,12 @@ sequtil needs xncbi
smartasn_g needs submit
smartnet needs3party vibrant
smartnetclient needs xconnect
+snphgvs needs $(GPIPE_LOADER_LIBS)
+snphgvs needs $(SDBAPI_LIB)
+snphgvs needs hgvs
+snphgvs needs ncbi_xcache_netcache
+snphgvs needs refseq_aln_source
+snphgvs needs3party $(GPIPE_LOADER_THIRDPARTY_LIBS)
snputil needs $(SOBJMGR_LIBS)
snputil needs variation
soap_dataobj needs xser
@@ -886,9 +975,14 @@ splitdbasncpp_g needs xnetblast
sqlite3 needs3party $(ORIG_LIBS)
sqlitewrapp needs xncbi
sqlitewrapp needs3party $(SQLITE3_LIBS)
-sraread needs $(SRA_LIBS)
+sraread needs $(VDB_LIB)
sraread needs seqset
-sraread needs3party $(SRA_SDK_SYSLIBS)
+sraread needs3party $(VDB_LIBS)
+srprism needs srprism_seq
+srprism_common needs $(COMPRESS_LIBS)
+srprism_common needs xutil
+srprism_seq needs srprism_common
+srprism_setup needs xncbi
ssl needs $(Z_LIB)
ssl needs3party $(KRB5_LIBS)
ssl needs3party $(NETWORK_LIBS)
@@ -902,6 +996,7 @@ ssrvcmn needs xconnect
ssscli needs ssrvcmn
ssscli needs ssssys
sssdb needs ssssys
+sssdb needs3party $(SYBASE_DLLS)
sssdb needs3party $(SYBASE_LIBS)
ssssys needs $(LIBSSSUTILS)
ssssys needs xconnect
@@ -912,6 +1007,7 @@ submit needs seqset
sv_objects needs general
sybase_os needs3party $(NETWORK_LIBS)
sybase_os needs3party $(ORIG_LIBS)
+sybase_os needs3party $(SYBASE_DLLS)
sybase_os needs3party $(SYBASE_LIBS)
sybdb64 includes3party comn64
sybdb64 includes3party intl64
@@ -954,7 +1050,7 @@ tinyseq needs xser
tiol needs $(Z_LIB)
tiol needs3party $(ORIG_LIBS)
tiol needs3party $(Z_LIBS)
-tracking_utils needs $(GPIPE_COMMON_LIBS)
+tracking_utils needs gpipe_attr
trackmgr needs $(SEQ_LIBS)
trackmgr needs pub
trackmgrcli needs trackmgr
@@ -962,6 +1058,12 @@ trackmgrcli needs xconnect
trackmgrgridcli needs $(COMPRESS_LIBS)
trackmgrgridcli needs trackmgr
trackmgrgridcli needs xconnserv
+tv_objects needs biotree
+tvlib needs $(OBJMGR_LIBS)
+tvlib needs gui_glmesa
+tvlib needs tv_objects
+tvlib needs uudutil
+tvlib needs w_phylo_tree
txclient needs xconnect
txserv includes txservbase
txserv needs txxmldoc
@@ -979,10 +1081,11 @@ u2tl needs $(Z_LIB)
u2tl needs3party $(NETWORK_LIBS)
u2tl needs3party $(ORIG_LIBS)
u2tl needs3party $(SYBASE_DBLIBS)
+u2tl needs3party $(SYBASE_DLLS)
u2tl needs3party $(SYBASE_LIBS)
u2tl needs3party $(Z_LIBS)
uilist needs xser
-unimod needs xser
+unicoll_dump_access needs gpipe_sqlite
uudutil needs $(COMPRESS_LIBS)
uudutil needs gbproj
uudutil needs xconnserv
@@ -996,8 +1099,8 @@ variation needs pub
variation_utils needs variation
variation_utils needs xobjutil
vdb2blast needs $(BLAST_LIBS)
-vdb2blast needs $(SRA_LIBS)
-vdb2blast needs3party $(SRA_SDK_SYSLIBS)
+vdb2blast needs $(VDB_LIB)
+vdb2blast needs3party $(VDB_LIBS)
vibgif needs3party $(NCBI_C_ncbi)
vibnet needs3party ncbiacc
vibnet needs3party ncbidesk
@@ -1018,6 +1121,7 @@ w_aln_table needs w_wx
w_data needs w_wx
w_edit needs align_format
w_edit needs ncbi_xloader_blastdb
+w_edit needs prosplign
w_edit needs w_loaders
w_feat_table needs w_wx
w_gl needs w_wx
@@ -1025,22 +1129,24 @@ w_grid_widget needs w_data
w_hapmap needs w_seq_graphic
w_hit_matrix needs gui_graph
w_hit_matrix needs w_gl
+w_loaders needs $(SRAREAD_LIBS)
+w_loaders needs bamread
w_loaders needs gui_objects
w_loaders needs hgvs
w_loaders needs w_wx
+w_loaders needs xalgophytree
w_loaders needs xobjreadex
w_macro_edit needs w_wx
w_object_list needs w_text_widget
w_phylo_tree needs gui_graph
-w_phylo_tree needs gui_print
w_phylo_tree needs w_data
w_phylo_tree needs w_gl
w_phylo_tree needs xalgophytree
w_seq needs w_text_widget
+w_seq_graphic needs genesbyloc
w_seq_graphic needs gui_config
w_seq_graphic needs gui_graph
w_seq_graphic needs gui_objects
-w_seq_graphic needs gui_print
w_seq_graphic needs hgvs
w_seq_graphic needs w_aln_score
w_seq_graphic needs w_gl
@@ -1057,9 +1163,8 @@ w_snp_utils needs xncbi
w_taxtree needs gui_objutils
w_taxtree needs3party $(WXWIDGETS_LIBS)
w_text_widget needs w_data
-w_wx needs $(COMPRESS_LIBS)
w_wx needs gui_objutils
-w_wx needs gui_opengl
+w_wx needs gui_print
w_wx needs3party $(WXWIDGETS_GL_LIBS)
w_wx needs3party $(WXWIDGETS_LIBS)
we_cpp needs xser
@@ -1169,6 +1274,7 @@ xblast needs xalgodustmask
xblast needs xalgowinmask
xblast needs xnetblastcli
xblastformat needs $(BLAST_LIBS)
+xblastformat needs $(XFORMAT_LIBS)
xblastformat needs align_format
xblastformat needs blastxml
xblastformat needs blastxml2
@@ -1205,13 +1311,15 @@ xctools needs xncbi
xctools needs3party $(NCBI_C_ncbi)
xdb needs xncbi
xdiff needs xncbi
+xdiscrepancy needs $(OBJEDIT_LIBS)
+xdiscrepancy needs $(XFORMAT_LIBS)
+xdiscrepancy needs macro
+xdiscrepancy needs xalnmgr
xdiscrepancy_report needs $(OBJMGR_LIBS)
-xdiscrepancy_report needs $(OBJREAD_LIBS)
xdiscrepancy_report needs macro
xdiscrepancy_report needs xmlwrapp
xdiscrepancy_report needs xvalidate
xerces-c needs3party $(CURL_LIBS)
-xerces-c needs3party $(DL_LIBS)
xerces-c needs3party $(ORIG_LIBS)
xfcgi includes xcgi
xfcgi needs3party $(FASTCGI_LIBS)
@@ -1234,8 +1342,8 @@ xgdsdata needs txxmldoc
xgdsdata needs xconnect
xgdsdata_misc needs xncbi
xgencoll needs aligndb_reader
+xgencoll needs gencoll_client
xgencoll needs gpipe_objutil
-xgencoll needs xobjedit
xgencollstats needs $(GPIPE_GENCOLL_LIBS)
xgencollstats needs gencoll_stats
xgp_manifest needs xser
@@ -1246,7 +1354,7 @@ xgpp_console_access needs xgpp_console_commands
xgpp_console_commands needs gpipe_common
xgpp_console_commands needs xgpp_console
xgpsubmit needs gc_load_utils
-xgpsubmit needs gpinit_utils
+xgpsubmit needs gpinit_access
xgpsubmit needs gpipe_asn_cleanup
xgpsubmit needs grid_wrapper
xgpsubmit needs xasmcompare
@@ -1269,11 +1377,13 @@ xid_utils needs dbapi_driver
xid_utils needs pub
xid_utils needs xcgi
xid_utils needs xconnect
-xid_utils needs3party $(LIBXML_LIBS)
+xid_utils needs xmlwrapp
xid_utils_noncorelib needs txclient
xid_utils_noncorelib needs xid_utils
+xid_wgsdb needs xid_utils
ximage needs xncbi
ximage needs3party $(IMAGE_LIBS)
+xlinear_prog needs xncbi
xmergetree needs $(SOBJMGR_LIBS)
xml2 needs3party $(ORIG_LIBS)
xmlreaders needs xmlwrapp
@@ -1295,10 +1405,10 @@ xngalign needs $(BLAST_INPUT_LIBS)
xngalign needs xalgoalignnw
xngalign needs xalgoalignutil
xngalign needs xmergetree
+xobjedit needs $(OBJREAD_LIBS)
+xobjedit needs $(XFORMAT_LIBS)
xobjedit needs taxon3
-xobjedit needs xformat
-xobjedit needs xobjread
-xobjedit needs xobjutil
+xobjedit needs xalnmgr
xobjmanip needs general
xobjmgr needs genome_collection
xobjmgr needs seqedit
@@ -1331,15 +1441,13 @@ xqueryparse needs xncbi
xregexp needs $(PCRE_LIB)
xregexp needs xncbi
xregexp needs3party $(PCRE_LIBS)
+xregexp_template_tester needs xregexp
xrepeatdb needs gpipe_objutil
xsd_sample_lib needs xser
xser needs xutil
xslt needs3party $(LIBXML_LIBS)
xslt needs3party $(ORIG_LIBS)
xslt_libxml needs xid_utils
-xslt_libxml needs3party $(LIBXSLT_LIBS)
-xslt_sablotron needs xid_utils
-xslt_sablotron needs3party $(SABLOT_LIBS)
xslt_xalan needs xid_utils
xslt_xalan needs3party $(CURL_LIBS)
xslt_xalan needs3party $(ICU_LIBS)
@@ -1363,31 +1471,35 @@ xsvcgi needs ncbi_xcache_netcache
xsvcgi needs ncbi_xloader_vdbgraph
xsvcgi needs ncbi_xloader_wgs
xsvcgi needs uudutil
-xsvcgi needs xcgi
+xsvcgi needs3party $(SYBASE_DLLS)
xsvcgi needs3party $(SYBASE_LIBS)
-xsvdata includes gencoll_client
xsvdata needs $(BLAST_INPUT_LIBS)
xsvdata needs $(DBAPI_CTLIB)
xsvdata needs $(ncbi_xreader_pubseqos2)
xsvdata needs gui_objects
xsvdata needs hgvs
+xsvdata needs ncbi_xcache_netcache
xsvdata needs sv_objects
+xsvdata needs trackmgr
xsvdata needs uudutil
+xsvdata needs xalgophytree
xsvdata needs xobjreadex
+xsvdata needs3party $(SYBASE_DLLS)
xsvdata needs3party $(SYBASE_LIBS)
xsvlink needs gui_objutils
xsvlink needs sv_objects
-xsvnaa needs gui_objutils
+xsvnaa needs xutil
+xsvsearchcgi needs hgvs
xsvsearchcgi needs sv_objects
xsvsearchcgi needs xsvcgi
xthrserv needs xconnect
xthrserv needs xutil
xunittestutil needs xobjutil
xutil needs xncbi
+xvalidate needs $(OBJEDIT_LIBS)
xvalidate needs $(XFORMAT_LIBS)
xvalidate needs valerr
xvalidate needs xalnmgr
-xvalidate needs xobjedit
xxconnect needs xncbi
xxconnect needs3party $(NCBI_C_ncbi)
z needs3party $(ORIG_LIBS)
diff --git a/c++/src/build-system/ncbi_package_version b/c++/src/build-system/ncbi_package_version
index c27abc2..cc6612c 100644
--- a/c++/src/build-system/ncbi_package_version
+++ b/c++/src/build-system/ncbi_package_version
@@ -1 +1 @@
-2.2.31
\ No newline at end of file
+2.3.0
\ No newline at end of file
diff --git a/c++/src/build-system/project_tree_builder.ini b/c++/src/build-system/project_tree_builder.ini
index e107b65..2c72592 100644
--- a/c++/src/build-system/project_tree_builder.ini
+++ b/c++/src/build-system/project_tree_builder.ini
@@ -1,4 +1,4 @@
-# $Id: project_tree_builder.ini 459679 2015-02-20 17:09:31Z ivanov $
+# $Id: project_tree_builder.ini 484252 2015-11-09 16:45:11Z ivanov $
###############################################################################
@@ -12,9 +12,11 @@
# Macros used here should be defined either in this section, or in [msvcNNN]
ThirdPartyBasePath = \\\\snowman\\win-coremake\\Lib\\ThirdParty
ThirdPartyAppsBasePath = \\\\snowman\\win-coremake\\App\\ThirdParty
+ThirdPartyVDBBasePath = \\\\snowman\\trace_software
SWIG_PATH = \\\\ncbipc0204\\swig
XCode_ThirdPartyBasePath = /netopt/ncbi_tools
+XCode_ThirdPartyVDBBasePath = /net/snowman/vol/projects/trace_software
#XCode_DefaultLibsInc = /sw/include
XCode_UserInc = /usr/include
@@ -33,6 +35,7 @@ ProvidedRequests = CXX_Toolkit \
LocalBZ2 \
LocalPCRE \
LocalZ \
+ LocalVDB \
MT
# These requiremenst are also met
@@ -102,6 +105,7 @@ Defines = HAVE_BERKELEY_DB \
HAVE_LIBXSLT \
HAVE_LIBEXSLT \
HAVE_LIBMONGODB \
+ HAVE_LOCAL_LBSM \
HAVE_ODBC \
HAVE_ODBCSS_H \
HAVE_OPENGL \
@@ -125,15 +129,15 @@ Defines = HAVE_BERKELEY_DB \
Macros = BDB_LIB BDB_CACHE_LIB NCBI_CRYPT CONNEXT XCONNEXT \
ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS \
FASTCGI_OBJS DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB \
- DBAPI_ODBC LOCAL_LBSM ncbi_java
+ DBAPI_ODBC LOCAL_LBSM ncbi_java VDB_REQ
#----------------------------------------------------------------------------
# Some 3rd party libraries have analog in the toolkit.
# Depending on the availability of 3rd party library,
# the toolkit will use either external or internal one
# See section in this file with the name of the latter entry in each pair
-LibChoices = z/Z bz2/BZ2 regexp/PCRE lzo/LZO
-ComponentChoices = LocalZ/Z LocalBZ2/BZ2 LocalPCRE/PCRE
+LibChoices = z/Z bz2/BZ2 regexp/PCRE lzo/LZO ncbi-vdb-read/VDB
+ComponentChoices = LocalZ/Z LocalBZ2/BZ2 LocalPCRE/PCRE LocalVDB/VDB
#----------------------------------------------------------------------------
# Some toolkit applications require 3rd party DLLs
@@ -163,7 +167,8 @@ ThirdPartyLibsToInstall = BerkeleyDB \
PYTHON \
libxml \
libxslt \
- libexslt
+ libexslt \
+ VDB
#----------------------------------------------------------------------------
@@ -171,8 +176,8 @@ ThirdPartyLibsToInstall = BerkeleyDB \
# Macros used here should be defined either in this section, or in compiler specific section.
ThirdParty_BerkeleyDB = $(ThirdPartyBasePath)\\berkeleydb\\$(msvc_3rd)\\4.6.21.NC
-ThirdParty_Boost_Test = $(ThirdPartyBasePath)\\boost\\$(msvc_3rd)\\1.53.0
-ThirdParty_Boost_Spirit = $(ThirdPartyBasePath)\\boost\\$(msvc_3rd)\\1.53.0
+ThirdParty_Boost_Test = $(ThirdPartyBasePath)\\boost\\$(msvc_3rd)\\1.56.0
+ThirdParty_Boost_Spirit = $(ThirdPartyBasePath)\\boost\\$(msvc_3rd)\\1.56.0
ThirdParty_BZ2 = $(ThirdPartyBasePath)\\bzip2\\$(msvc_3rd)\\1.0.2
ThirdParty_fastcgi = $(ThirdPartyBasePath)\\fastcgi\\$(msvc_3rd)\\2.4.0
ThirdParty_FreeType = $(ThirdPartyBasePath)\\freetype\\$(msvc_3rd)\\2.4.10
@@ -200,6 +205,7 @@ ThirdParty_XML = $(ThirdPartyBasePath)\\xml\\$(msvc_3rd)\\2.7.8
ThirdParty_XSLT = $(ThirdPartyBasePath)\\xslt\\$(msvc_3rd)\\1.1.26
ThirdParty_Z = $(ThirdPartyBasePath)\\z\\$(msvc_3rd)\\1.2.8
ThirdParty_JDK = $(ThirdPartyBasePath)\\jdk\\1.6.0_25
+ThirdParty_VDB = $(ThirdPartyVDBBasePath)\\vdb\\vdb-versions\\2.5.4
PYTHON_PATH = $(ThirdPartyAppsBasePath)\\Python252\\$(msvc_3rd)
@@ -269,6 +275,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = msvc900_prj
# Macro
msvc_3rd = msvc9
+vdb_arch = i386
#----------------------------------------------------------------------------
# Settings for MSVC 2008 (v.9.00, x64)
@@ -283,6 +290,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = msvc900_prj
# Macro
msvc_3rd = msvc9.64
+vdb_arch = x86_64
#----------------------------------------------------------------------------
# Settings for MSVC 2010 (v.10.00, Win32)
@@ -297,6 +305,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = msvc1000_prj
# Macro
msvc_3rd = msvc10
+vdb_arch = i386
#----------------------------------------------------------------------------
# Settings for MSVC 2010 (v.10.00, x64)
@@ -311,6 +320,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = msvc1000_prj
# Macro
msvc_3rd = msvc10.64
+vdb_arch = x86_64
#----------------------------------------------------------------------------
# Settings for MSVC 2012 (v.11, Win32)
@@ -325,6 +335,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = vs2012
# Macro
msvc_3rd = vs2012
+vdb_arch = i386
#----------------------------------------------------------------------------
@@ -340,6 +351,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = vs2012
# Macro
msvc_3rd = vs2012.64
+vdb_arch = x86_64
#----------------------------------------------------------------------------
@@ -355,6 +367,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = vs2013
# Macro
msvc_3rd = vs2013
+vdb_arch = i386
#----------------------------------------------------------------------------
@@ -370,6 +383,7 @@ DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = vs2013
# Macro
msvc_3rd = vs2013.64
+vdb_arch = x86_64
#============================================================================
@@ -403,14 +417,14 @@ Projects = build
# It describes default settings of compiler, linker etc
MetaMakefile = build-system/Makefile.mk.in.xcode
StandardFeatures = unix Darwin XCODE GCC LFS DBLib algo app dbapi gui objects serial gbench FreeTDS
-NotProvidedRequests = MSWin MSVC KCC ICC VisualAge CompaqCompiler WorkShop MIPSpro -LimitedLinker MaxDebug LocalSSS SSSUTILS MESA GEO SSSDB SP ODBC LIBMAGIC GIF GNUTLS
+NotProvidedRequests = MSWin MSVC KCC ICC VisualAge CompaqCompiler WorkShop MIPSpro -LimitedLinker MaxDebug LocalSSS SSSUTILS MESA GEO SSSDB SP ODBC LIBMAGIC GIF
DefinesPath = common/config/ncbiconf_xcode_site.h
ThirdParty_BerkeleyDB = $(XCode_ThirdPartyBasePath)/BerkeleyDB
ThirdParty_Boost_Test = $(XCode_ThirdPartyBasePath)/boost-1.53.0-ncbi1
ThirdParty_JPEG = $(XCode_ThirdPartyBasePath)/safe-sw
-ThirdParty_PNG = /usr/X11
+ThirdParty_PNG = /opt/X11
ThirdParty_TIFF = $(XCode_ThirdPartyBasePath)/safe-sw
ThirdParty_LZO = $(XCode_ThirdPartyBasePath)/lzo-2.05
ThirdParty_SQLITE3 = $(XCode_ThirdPartyBasePath)/sqlite-3.6.14.2-ncbi1
@@ -418,8 +432,12 @@ ThirdParty_XML = $(XCode_ThirdPartyBasePath)/libxml-2.7.8
ThirdParty_XSLT = $(XCode_ThirdPartyBasePath)/libxml-2.7.8
ThirdParty_GLEW = $(XCode_ThirdPartyBasePath)/glew-1.5.8
ThirdParty_wxWidgets = $(XCode_ThirdPartyBasePath)/wxWidgets-3.0.1-ncbi1
-ThirdParty_FreeType = /usr/X11
+ThirdParty_FreeType = /opt/X11
ThirdParty_FTGL = $(XCode_ThirdPartyBasePath)/ftgl-2.1.3-rc5
+ThirdParty_VDB = $(XCode_ThirdPartyVDBBasePath)/vdb/vdb-versions/2.5.4
+ThirdParty_GMP = $(Xcode_ThirdPartyBasePath)/gmp-6.0.0a
+ThirdParty_Nettle = $(Xcode_ThirdPartyBasePath)/nettle-3.1.1
+ThirdParty_GNUTLS = $(Xcode_ThirdPartyBasePath)/gnutls-3.4.0
LIBXML_INCLUDE = $(ThirdParty_XML)/include/libxml2
LIBXSLT_INCLUDE = $(ThirdParty_XSLT)/include
@@ -432,6 +450,8 @@ Configurations = DebugDLL,DebugMT,ReleaseDLL,ReleaseMT
DllConfigurations = DebugDLL ReleaseDLL
DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = xcode30_prj
+# vdb_arch = i386
+vdb_arch = fat86
[xcode30.x86_64]
Version=44
@@ -440,6 +460,7 @@ DllConfigurations = DebugDLL ReleaseDLL
DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = xcode30_prj
sfx64 = 64
+vdb_arch = x86_64
[xcode30.i386_x86_64]
Version=44
@@ -447,6 +468,7 @@ Configurations = DebugDLL,DebugMT,ReleaseDLL,ReleaseMT
DllConfigurations = DebugDLL ReleaseDLL
DllBuildDefine = NCBI_DLL_BUILD
msvc_prj = xcode30_prj
+vdb_arch = fat86
#============================================================================
@@ -460,6 +482,8 @@ Z_INCLUDE = z util/compress/zlib/
BZ2_INCLUDE = bz2 util/compress/bzip2/
LZO_INCLUDE = lzo .
PCRE_INCLUDE = regexp util/regexp/
+VDB_INCLUDE = ncbi-vdb-read ../src/sra/sdk/interfaces \
+ ncbi-vdb-read ../src/sra/sdk/interfaces/C++Toolkit
#============================================================================
@@ -482,6 +506,7 @@ BZ2_LIB = bz2
Z_LIB = z
LZO_LIB = lzo
PCRE_LIB = regexp
+VDB_LIB = ncbi-vdb-read
ftds64 = ftds
FTDS64_INCLUDE = dbapi/driver/ftds64/ dbapi/driver/ftds64/freetds/
@@ -721,6 +746,9 @@ Component = local_lbsm
Value = ncbi_lbsm ncbi_lbsm_ipc ncbi_lbsmd
DefValue = ncbi_lbsmd_stub
+[HAVE_LOCAL_LBSM]
+Component = local_lbsm
+
[HAVE_LIBSYBASE]
Component=Sybase
@@ -818,17 +846,17 @@ LIBPATH = $(ThirdParty_wxWidgets)u\\lib_dll\\releasedll
[wxWidgets.xcode]
LIB = -lwx_osx_cocoa_gl-3.0 -lwx_osx_cocoa_richtext-3.0 -lwx_osx_cocoa_aui-3.0 -lwx_osx_cocoa_propgrid-3.0 -lwx_osx_cocoa_xrc-3.0 -lwx_osx_cocoa_qa-3.0 -lwx_osx_cocoa_html-3.0 -lwx_osx_cocoa_adv-3.0 -lwx_osx_cocoa_core-3.0 -lwx_base_xml-3.0 -lwx_base_net-3.0 -lwx_base-3.0 -framework Cocoa
[wxWidgets.xcode.debug.DebugMT]
-INCLUDE = $(ThirdParty_wxWidgets)/GCC-Debug$(sfx64)MT/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
-LIBPATH = $(ThirdParty_wxWidgets)/GCC-Debug$(sfx64)MT/lib
+INCLUDE = $(ThirdParty_wxWidgets)/Clang-Debug$(sfx64)MT/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
+LIBPATH = $(ThirdParty_wxWidgets)/Clang-Debug$(sfx64)MT/lib
[wxWidgets.xcode.debug.DebugDLL]
-INCLUDE = $(ThirdParty_wxWidgets)/GCC-Debug$(sfx64)/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
-LIBPATH = $(ThirdParty_wxWidgets)/GCC-Debug$(sfx64)/lib
+INCLUDE = $(ThirdParty_wxWidgets)/Clang-Debug$(sfx64)/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
+LIBPATH = $(ThirdParty_wxWidgets)/Clang-Debug$(sfx64)/lib
[wxWidgets.xcode.release.ReleaseMT]
-INCLUDE = $(ThirdParty_wxWidgets)/GCC-Release$(sfx64)MT/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
-LIBPATH = $(ThirdParty_wxWidgets)/GCC-Release$(sfx64)MT/lib
+INCLUDE = $(ThirdParty_wxWidgets)/Clang-Release$(sfx64)MT/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
+LIBPATH = $(ThirdParty_wxWidgets)/Clang-Release$(sfx64)MT/lib
[wxWidgets.xcode.release.ReleaseDLL]
-INCLUDE = $(ThirdParty_wxWidgets)/GCC-Release$(sfx64)/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
-LIBPATH = $(ThirdParty_wxWidgets)/GCC-Release$(sfx64)/lib
+INCLUDE = $(ThirdParty_wxWidgets)/Clang-Release$(sfx64)/lib/wx/include/osx_cocoa-ansi-3.0 $(ThirdParty_wxWidgets)/include/wx-3.0
+LIBPATH = $(ThirdParty_wxWidgets)/Clang-Release$(sfx64)/lib
[wxWidgets.xcode.debug]
DEFINES = __WXDEBUG__,__WXMAC__,__WXOSX__,__WXOSX_COCOA__
@@ -931,6 +959,23 @@ LIBPATH = $(ThirdParty_GNUTLS)\\lib_dll\\debugdll
[GNUTLS.release.ReleaseDLL]
LIBPATH = $(ThirdParty_GNUTLS)\\lib_dll\\releasedll
+[GNUTLS.xcode]
+Component = Nettle
+INCLUDE = $(ThirdParty_GNUTLS)/include
+LIB = -lgnutls
+LIBPATH = $(ThirdParty_GNUTLS)/lib$(sfx64)
+
+[Nettle.xcode]
+Component = GMP
+INCLUDE = $(ThirdParty_Nettle)/include
+LIB = -lnettle -lhogweed
+LIBPATH = $(ThirdParty_Nettle)/lib$(sfx64)
+
+[GMP.xcode]
+INCLUDE = $(ThirdParty_GMP)/Release$(sfx64)/include
+LIB = -lgmp
+LIBPATH = $(ThirdParty_GMP)/lib$(sfx64)
+
[GNUTLS_LIBS]
Component=GNUTLS
@@ -1529,7 +1574,7 @@ LIBPATH = $(ThirdParty_Boost_Test)\\lib_static\\releasedll
[Boost.Test.xcode]
INCLUDE = $(ThirdParty_Boost_Test)/include
-LIB = -lboost_unit_test_framework
+LIB = -lboost_unit_test_framework-clang-darwin
CONFS = Debug DebugMT DebugDLL Release ReleaseMT ReleaseDLL
LIBPATH = $(ThirdParty_Boost_Test)/lib
@@ -1646,8 +1691,7 @@ INCLUDE =
LIBPATH =
LIB = ws2_32.lib dbghelp.lib
[DefaultLibs.xcode]
-INCLUDE = /usr/include/c++/4.2.1 /usr/include/c++/4.2.1/backward
-LIB = -stdlib=libstdc++ -framework CoreServices
+LIB = -stdlib=libc++ -framework CoreServices
[COMCTL32]
INCLUDE =
@@ -1686,6 +1730,42 @@ CONFS = DebugMT DebugDLL ReleaseMT ReleaseDLL
[UUID.xcode]
LIB =
+[VDB]
+#MACRO = VDB_INCLUDE VDB_LIBS VDB_STATIC_LIBS
+INCLUDE = $(ThirdParty_VDB)\\interfaces
+LIB = ncbi-vdb-md.lib
+CONFS = DebugMT DebugDLL ReleaseMT ReleaseDLL
+BINPATH = .
+[VDB.debug]
+# note: use release libraries!
+LIBPATH = $(ThirdParty_VDB)\\win\\release\\$(vdb_arch)\\bin
+[VDB.release]
+LIBPATH = $(ThirdParty_VDB)\\win\\release\\$(vdb_arch)\\bin
+
+[VDB.xcode]
+INCLUDE = $(ThirdParty_VDB)/interfaces
+LIB = -lncbi-vdb
+[VDB.xcode.debug]
+LIBPATH = $(ThirdParty_VDB)/mac/debug/$(vdb_arch)/lib
+[VDB.xcode.release]
+LIBPATH = $(ThirdParty_VDB)/mac/release/$(vdb_arch)/lib
+
+#[VDB_INCLUDE]
+#Component=VDB
+#[VDB_LIB]
+#Component=VDB
+[VDB_LIBS]
+Component=VDB,LIBXML,BZ2,Z
+[VDB_STATIC_LIBS]
+Component=VDB,LIBXML,BZ2,Z
+[LocalVDBReq]
+FILES = src\\sra\\sdk\\Makefile.ncbi-vdb-read.lib
+[VDB_REQ]
+Component=VDB
+Value=VDB
+DefValue=LocalVDBReq
+
+# CURL
# ===========================================================================
# Datatool description
diff --git a/c++/src/build-system/project_tree_builder/mac_prj_generator.cpp b/c++/src/build-system/project_tree_builder/mac_prj_generator.cpp
index 667c3df..6deb63e 100644
--- a/c++/src/build-system/project_tree_builder/mac_prj_generator.cpp
+++ b/c++/src/build-system/project_tree_builder/mac_prj_generator.cpp
@@ -1,4 +1,4 @@
-/* $Id: mac_prj_generator.cpp 439941 2014-07-08 12:50:23Z gouriano $
+/* $Id: mac_prj_generator.cpp 467273 2015-05-12 15:09:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -202,7 +202,8 @@ void CMacProjectGenerator::Generate(const string& solution)
AddString( *dataspec_dependencies, proj_dependency);
}
if (prj.m_ProjType != CProjKey::eLib && prj.m_ProjType != CProjKey::eDll &&
- prj.m_ProjType != CProjKey::eApp && prj.m_ProjType != CProjKey::eDataSpec) {
+ prj.m_ProjType != CProjKey::eApp && prj.m_ProjType != CProjKey::eDataSpec &&
+ prj.m_ProjType != CProjKey::eMsvc) {
continue;
}
if (add_composite) {
@@ -405,8 +406,9 @@ void CMacProjectGenerator::CreateConfigureScript(const string& name, bool with_g
script += "gui_";
}
script += name + ".sh";
+ string candidate = script + ".candidate";
- CNcbiOfstream ofs(script.c_str(), IOS_BASE::out | IOS_BASE::trunc);
+ CNcbiOfstream ofs(candidate.c_str(), IOS_BASE::out | IOS_BASE::trunc);
if ( !ofs )
NCBI_THROW(CProjBulderAppException, eFileCreation, script);
@@ -448,6 +450,7 @@ void CMacProjectGenerator::CreateConfigureScript(const string& name, bool with_g
ofs << "export PTB_PROJECT_REQ=" << GetApp().m_Subtree << "\n";
ofs << "$BUILD_TREE_ROOT/ptb.sh\n";
ofs.close();
+ PromoteIfDifferent(script, candidate);
CDirEntry(script).SetMode(
CDirEntry::fExecute | CDirEntry::fRead | CDirEntry::fWrite,
CDirEntry::fExecute | CDirEntry::fRead | CDirEntry::fWrite,
@@ -815,7 +818,7 @@ string CMacProjectGenerator::CreateProjectBuildPhase(
const CProjItem& prj,
CDict& dict_objects, CRef<CArray>& build_files)
{
- if (prj.m_ProjType == CProjKey::eDataSpec) {
+ if (prj.m_ProjType == CProjKey::eDataSpec || prj.m_ProjType == CProjKey::eMsvc) {
return kEmptyStr;
}
#if USE_VERBOSE_NAMES
@@ -919,14 +922,14 @@ string CMacProjectGenerator::CreateProjectTarget(
}
}
AddArray( *dict_target, "dependencies", dependencies);
- if (prj.m_ProjType == CProjKey::eDataSpec) {
+ if (prj.m_ProjType == CProjKey::eDataSpec || prj.m_ProjType == CProjKey::eMsvc) {
AddString( *dict_target, "isa", "PBXAggregateTarget");
} else {
AddString( *dict_target, "isa", "PBXNativeTarget");
}
AddString( *dict_target, "name", target_name);
AddString( *dict_target, "productName", target_name);
- if (prj.m_ProjType != CProjKey::eDataSpec) {
+ if (prj.m_ProjType != CProjKey::eDataSpec && prj.m_ProjType != CProjKey::eMsvc) {
AddString( *dict_target, "productReference", product_id);
AddString( *dict_target, "productType", product_type);
}
@@ -1085,6 +1088,8 @@ void CMacProjectGenerator::CreateBuildSettings(CDict& dict_cfg, const SConfigInf
AddCompilerSetting( *settings, cfg, "FRAMEWORK_SEARCH_PATHS");
AddCompilerSetting( *settings, cfg, "USE_HEADERMAP");
+ AddCompilerSetting( *settings, cfg, "OTHER_CPLUSPLUSFLAGS");
+
AddLinkerSetting( *settings, cfg, "DEAD_CODE_STRIPPING");
AddLinkerSetting( *settings, cfg, "PREBINDING");
// AddLinkerSetting( *settings, cfg, "ZERO_LINK");
@@ -1172,7 +1177,7 @@ void CMacProjectGenerator::CreateProjectBuildSettings(
AddArray( *settings, "LIBRARY_SEARCH_PATHS", lib_paths);
}
- if (prj.m_ProjType != CProjKey::eDataSpec) {
+ if (prj.m_ProjType != CProjKey::eDataSpec && prj.m_ProjType != CProjKey::eMsvc) {
AddString( *settings, "MACH_O_TYPE", GetMachOType(prj));
}
@@ -1217,7 +1222,7 @@ void CMacProjectGenerator::CreateProjectBuildSettings(
}
AddString( *settings, "PRODUCT_NAME", GetTargetName(prj));
- if (prj.m_ProjType == CProjKey::eDataSpec) {
+ if (prj.m_ProjType == CProjKey::eDataSpec || prj.m_ProjType == CProjKey::eMsvc) {
return;
}
diff --git a/c++/src/build-system/project_tree_builder/msvc_configure.cpp b/c++/src/build-system/project_tree_builder/msvc_configure.cpp
index 132d37a..57d209b 100644
--- a/c++/src/build-system/project_tree_builder/msvc_configure.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_configure.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_configure.cpp 445045 2014-08-29 17:44:10Z ivanov $
+/* $Id: msvc_configure.cpp 455052 2014-12-22 18:23:09Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -100,9 +100,12 @@ static void s_CreateThirdPartyLibsInstallMakefile
site.GetLibInfo(lib, config, &lib_info);
if ( !lib_info.m_LibPath.empty() ) {
string bin_dir = lib_info.m_LibPath;
+ string bin_path = lib_info.m_BinPath;
+ if (bin_path.empty()) {
+ bin_path = site.GetThirdPartyLibsBinSubDir();
+ }
bin_dir =
- CDirEntry::ConcatPath(bin_dir,
- site.GetThirdPartyLibsBinSubDir());
+ CDirEntry::ConcatPath(bin_dir, bin_path);
bin_dir = CDirEntry::NormalizePath(bin_dir);
if ( CDirEntry(bin_dir).Exists() ) {
//
diff --git a/c++/src/build-system/project_tree_builder/msvc_dlls_info.cpp b/c++/src/build-system/project_tree_builder/msvc_dlls_info.cpp
index 5c90e4a..1ad62e9 100644
--- a/c++/src/build-system/project_tree_builder/msvc_dlls_info.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_dlls_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_dlls_info.cpp 445045 2014-08-29 17:44:10Z ivanov $
+/* $Id: msvc_dlls_info.cpp 444883 2014-08-28 17:23:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/build-system/project_tree_builder/msvc_makefile.cpp b/c++/src/build-system/project_tree_builder/msvc_makefile.cpp
index 6fa3a65..db3f031 100644
--- a/c++/src/build-system/project_tree_builder/msvc_makefile.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_makefile.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_makefile.cpp 407351 2013-07-19 17:24:06Z gouriano $
+/* $Id: msvc_makefile.cpp 460951 2015-03-04 17:33:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -259,7 +259,10 @@ string CreateMsvcProjectMakefileName(const string& project_name,
name += "dll.";
break;
case CProjKey::eMsvc:
- name += "msvcproj.";
+ if (CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eMsvcWin32 ||
+ CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eMsvcX64) {
+ name += "msvcproj.";
+ }
break;
case CProjKey::eDataSpec:
name += "dataspec.";
@@ -810,7 +813,7 @@ string GetCompilerOpt(const IMsvcMetaMakefile& meta_file,
const SConfigInfo& config)
{
string val = project_file.GetCompilerOpt(opt, config);
- if ( val.empty() ) {
+ if ( val.empty() && CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
val = meta_file.GetCompilerOpt(opt, config);
}
if (val == "-") {
@@ -826,7 +829,7 @@ string GetLinkerOpt(const IMsvcMetaMakefile& meta_file,
const SConfigInfo& config)
{
string val = project_file.GetLinkerOpt(opt, config);
- if ( val.empty() ) {
+ if ( val.empty() && CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
val = meta_file.GetLinkerOpt(opt, config);
}
if (val == "-") {
@@ -842,7 +845,7 @@ string GetLibrarianOpt(const IMsvcMetaMakefile& meta_file,
const SConfigInfo& config)
{
string val = project_file.GetLibrarianOpt(opt, config);
- if ( val.empty() ) {
+ if ( val.empty() && CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
val = meta_file.GetLibrarianOpt(opt, config);
}
if (val == "-") {
@@ -857,7 +860,7 @@ string GetResourceCompilerOpt(const IMsvcMetaMakefile& meta_file,
const SConfigInfo& config)
{
string val = project_file.GetResourceCompilerOpt(opt, config);
- if ( val.empty() ) {
+ if ( val.empty() && CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
val = meta_file.GetResourceCompilerOpt(opt, config);
}
if (val == "-") {
diff --git a/c++/src/build-system/project_tree_builder/msvc_prj_generator.cpp b/c++/src/build-system/project_tree_builder/msvc_prj_generator.cpp
index 62ba1f1..a42efab 100644
--- a/c++/src/build-system/project_tree_builder/msvc_prj_generator.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_prj_generator.cpp
@@ -823,6 +823,9 @@ void __SET_CLCOMPILE_ELEMENT(
Container& container, const string& name, const string& value,
const string& condition = kEmptyStr)
{
+ if (value.empty() || value == "-") {
+ return;
+ }
CRef<msbuild::CClCompile::C_E> e(new msbuild::CClCompile::C_E);
e->SetAnyContent().SetName(name);
e->SetAnyContent().SetValue(CUtf8::AsUTF8(value,eEncoding_UTF8));
@@ -834,21 +837,33 @@ void __SET_CLCOMPILE_ELEMENT(
#define __SET_CLCOMPILE(container, name) \
__SET_CLCOMPILE_ELEMENT(container, #name, msvc_tool.Compiler()->name())
+#define __SET_CLCOMPILE_BASE(container, name) \
+ __SET_CLCOMPILE_ELEMENT(container, #name, meta_mk.GetCompilerOpt(#name, cfg_info));
+
template<typename Container>
void __SET_LIB_ELEMENT(
Container& container, const string& name, const string& value)
{
+ if (value.empty() || value == "-") {
+ return;
+ }
CRef<msbuild::CLib::C_E> e(new msbuild::CLib::C_E);
e->SetAnyContent().SetName(name);
e->SetAnyContent().SetValue(CUtf8::AsUTF8(value,eEncoding_UTF8));
container->SetLib().Set().push_back(e);
}
+#define __SET_LIB_BASE(container, name) \
+ __SET_LIB_ELEMENT(container, #name, meta_mk.GetLibrarianOpt(#name, cfg_info));
+
template<typename Container>
void __SET_LINK_ELEMENT(
Container& container, const string& name, const string& value)
{
+ if (value.empty() || value == "-") {
+ return;
+ }
CRef<msbuild::CLink::C_E> e(new msbuild::CLink::C_E);
e->SetAnyContent().SetName(name);
e->SetAnyContent().SetValue(CUtf8::AsUTF8(value,eEncoding_UTF8));
@@ -857,11 +872,18 @@ void __SET_LINK_ELEMENT(
#define __SET_LINK(container, name) \
__SET_LINK_ELEMENT(container, #name, msvc_tool.Linker()->name())
+#define __SET_LINK_BASE(container, name) \
+ __SET_LINK_ELEMENT(container, #name, meta_mk.GetLinkerOpt(#name, cfg_info));
+
+
template<typename Container>
void __SET_RC_ELEMENT(
Container& container, const string& name, const string& value,
const string& condition = kEmptyStr)
{
+ if (value.empty() || value == "-") {
+ return;
+ }
CRef<msbuild::CResourceCompile::C_E> e(new msbuild::CResourceCompile::C_E);
e->SetAnyContent().SetName(name);
e->SetAnyContent().SetValue(CUtf8::AsUTF8(value,eEncoding_UTF8));
@@ -871,11 +893,18 @@ void __SET_RC_ELEMENT(
container->SetResourceCompile().SetResourceCompile().push_back(e);
}
+#define __SET_RC_BASE(container, name) \
+ __SET_RC_ELEMENT(container, #name, meta_mk.GetResourceCompilerOpt(#name, cfg_info));
+
+
template<typename Container>
void __SET_NONE_ELEMENT(
Container& container, const string& name, const string& value,
const string& condition = kEmptyStr)
{
+ if (value.empty() || value == "-") {
+ return;
+ }
CRef<msbuild::CNone::C_E> e(new msbuild::CNone::C_E);
e->SetAnyContent().SetName(name);
e->SetAnyContent().SetValue(CUtf8::AsUTF8(value,eEncoding_UTF8));
@@ -900,7 +929,264 @@ void __SET_CUSTOMBUILD_ELEMENT(
}
+#define USE_PERCFG_PROPSHEET 1
+
+void CMsvcProjectGenerator::GeneratePropertySheets()
+{
+ string ps_dir( GetApp().GetBuildDir());
+ string ps_name("ncbi_sln");
+ string ps_base(ps_name + ".base.props");
+ const list<SConfigInfo>& all_cfgs = GetApp().GetRegSettings().m_ConfigInfo;
+ const CMsvcMetaMakefile& meta_mk = GetApp().GetMetaMakefile();
+
+// user props
+#if USE_PERCFG_PROPSHEET
+ ITERATE(list<SConfigInfo>, c , all_cfgs) {
+
+ string ps_user(ps_name + "." + c->GetConfigFullName() + ".user.props");
+ string file_user(CDirEntry::ConcatPath(ps_dir, ps_user));
+ if (!CDirEntry(file_user).Exists())
+ {
+ //default is very simple and empty
+ msbuild::CProject project;
+ project.SetAttlist().SetToolsVersion("4.0");
+
+ // NCBI base prop sheet
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetImportGroup().SetAttlist().SetLabel("PropertySheets");
+ {
+ CRef<msbuild::CImportGroup::C_E> p(new msbuild::CImportGroup::C_E);
+ p->SetImport().SetAttlist().SetProject(ps_base);
+ t->SetImportGroup().SetImportGroup().push_back(p);
+ }
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+ // UserMacros
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup().SetAttlist().SetLabel("UserMacros");
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+
+ // empty PropertyGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup();
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+
+ // ItemDefinitionGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ t->SetItemDefinitionGroup();
+#if 0
+ // compiler
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetClCompile();
+ }
+ // linker
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLink();
+ }
+ // librarian
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLib();
+ }
+#endif
+ }
+ SaveIfNewer(file_user, project);
+ }
+ }
+#else
+ string ps_user(CDirEntry(solution).GetBase() + ".user.props");
+ string file_user(CDirEntry::ConcatPath(ps_dir, ps_user));
+ if (!CDirEntry(file_user).Exists())
+ {
+ //default is very simple and empty
+ msbuild::CProject project;
+ project.SetAttlist().SetToolsVersion("4.0");
+
+ // NCBI base prop sheet
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetImportGroup().SetAttlist().SetLabel("PropertySheets");
+ {
+ CRef<msbuild::CImportGroup::C_E> p(new msbuild::CImportGroup::C_E);
+ p->SetImport().SetAttlist().SetProject(ps_base);
+ t->SetImportGroup().SetImportGroup().push_back(p);
+ }
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+ // UserMacros
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup().SetAttlist().SetLabel("UserMacros");
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+
+ // empty PropertyGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup();
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+
+ ITERATE(list<SConfigInfo>, c , all_cfgs) {
+
+ string cfg_condition("'$(Configuration)|$(Platform)'=='");
+ const SConfigInfo& cfg_info = *c;
+ cfg_condition += c->GetConfigFullName() + "|" + CMsvc7RegSettings::GetMsvcPlatformName() + "'";
+
+ // ItemDefinitionGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ t->SetItemDefinitionGroup().SetAttlist().SetCondition(cfg_condition);
+ // compiler
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetClCompile();
+ }
+ // linker
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLink();
+ }
+ // librarian
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLib();
+ }
+ }
+ }
+ SaveIfNewer(file_user, project);
+ }
+#endif
+
+// base props
+ string file_base(CDirEntry::ConcatPath(ps_dir, ps_base));
+ {
+ msbuild::CProject project;
+ project.SetAttlist().SetToolsVersion("4.0");
+
+ // NCBI base prop sheet
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetImportGroup().SetAttlist().SetLabel("PropertySheets");
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+ // UserMacros
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup().SetAttlist().SetLabel("UserMacros");
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+ // empty PropertyGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetPropertyGroup();
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+ }
+
+ ITERATE(list<SConfigInfo>, c , all_cfgs) {
+
+ string cfg_condition("'$(Configuration)|$(Platform)'=='");
+ const SConfigInfo& cfg_info = *c;
+ cfg_condition += c->GetConfigFullName() + "|" + CMsvc7RegSettings::GetMsvcPlatformName() + "'";
+
+ // ItemDefinitionGroup
+ {
+ CRef<msbuild::CProject::C_ProjectLevelTagType::C_E> t(new msbuild::CProject::C_ProjectLevelTagType::C_E);
+ t->SetItemDefinitionGroup().SetAttlist().SetCondition(cfg_condition);
+ project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
+
+ // compiler
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetClCompile();
+ __SET_CLCOMPILE_BASE(p, AdditionalOptions);
+ __SET_CLCOMPILE_BASE(p, BasicRuntimeChecks);
+ __SET_CLCOMPILE_BASE(p, BrowseInformation);
+ __SET_CLCOMPILE_BASE(p, BufferSecurityCheck);
+ __SET_CLCOMPILE_BASE(p, CallingConvention);
+ __SET_CLCOMPILE_BASE(p, CompileAs);
+ __SET_CLCOMPILE_BASE(p, DebugInformationFormat);
+ __SET_CLCOMPILE_BASE(p, DisableSpecificWarnings);
+ __SET_CLCOMPILE_BASE(p, EnableFunctionLevelLinking);
+ __SET_CLCOMPILE_BASE(p, FavorSizeOrSpeed);
+ __SET_CLCOMPILE_BASE(p, IgnoreStandardIncludePath);
+ __SET_CLCOMPILE_BASE(p, InlineFunctionExpansion);
+ __SET_CLCOMPILE_BASE(p, MinimalRebuild);
+ __SET_CLCOMPILE_BASE(p, OmitFramePointers);
+ __SET_CLCOMPILE_BASE(p, Optimization);
+ __SET_CLCOMPILE_BASE(p, PreprocessorDefinitions);
+ __SET_CLCOMPILE_BASE(p, ProgramDataBaseFileName);
+ __SET_CLCOMPILE_BASE(p, RuntimeLibrary);
+ __SET_CLCOMPILE_BASE(p, RuntimeTypeInfo);
+ __SET_CLCOMPILE_BASE(p, StringPooling);
+ __SET_CLCOMPILE_BASE(p, StructMemberAlignment);
+ __SET_CLCOMPILE_BASE(p, UndefinePreprocessorDefinitions);
+ __SET_CLCOMPILE_BASE(p, WarningLevel);
+ }
+ // linker
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLink();
+ __SET_LINK_BASE(p, AdditionalDependencies);
+ __SET_LINK_BASE(p, AdditionalLibraryDirectories);
+ __SET_LINK_BASE(p, AdditionalOptions);
+ __SET_LINK_BASE(p, EnableCOMDATFolding);
+ __SET_LINK_BASE(p, FixedBaseAddress);
+ __SET_LINK_BASE(p, GenerateDebugInformation);
+ __SET_LINK_BASE(p, ImportLibrary);
+ __SET_LINK_BASE(p, IgnoreAllDefaultLibraries);
+ __SET_LINK_BASE(p, IgnoreDefaultLibraryNames);
+ __SET_LINK_BASE(p, LargeAddressAware);
+ __SET_LINK_BASE(p, OptimizeReferences);
+ __SET_LINK_BASE(p, SubSystem);
+ __SET_LINK_BASE(p, TargetMachine);
+ __SET_LINK_BASE(p, ImageHasSafeExceptionHandlers);
+ }
+ // librarian
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLib();
+ __SET_LIB_BASE(p, AdditionalLibraryDirectories);
+ __SET_LIB_BASE(p, AdditionalOptions);
+ __SET_LIB_BASE(p, IgnoreAllDefaultLibraries);
+ __SET_LIB_BASE(p, IgnoreSpecificDefaultLibraries);
+ __SET_LIB_BASE(p, OutputFile);
+ __SET_LIB_BASE(p, TargetMachine);
+ }
+ // resource compiler
+ {
+ CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
+ t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetResourceCompile();
+ __SET_RC_BASE(p, AdditionalIncludeDirectories);
+ __SET_RC_BASE(p, AdditionalOptions);
+ __SET_RC_BASE(p, PreprocessorDefinitions);
+ }
+ }
+ }
+ SaveIfNewer(file_base, project);
+ }
+}
void CMsvcProjectGenerator::GenerateMsbuild(
CMsvcPrjFilesCollector& collector,
@@ -1001,6 +1287,19 @@ void CMsvcProjectGenerator::GenerateMsbuild(
p->SetImport().SetAttlist().SetLabel("LocalAppDataPlatform");
t->SetImportGroup().SetImportGroup().push_back(p);
}
+ {
+// NCBI user prop sheet
+ CRef<msbuild::CImportGroup::C_E> p(new msbuild::CImportGroup::C_E);
+ string ps_name = "$(ProjectDir)" +
+ CDirEntry::CreateRelativePath(project_context.ProjectDir(), GetApp().GetBuildDir());
+#if USE_PERCFG_PROPSHEET
+ ps_name += "ncbi_sln." + c->GetConfigFullName() + ".user.props";
+#else
+ ps_name += "ncbi_sln.user.props";
+#endif
+ p->SetImport().SetAttlist().SetProject(ps_name);
+ t->SetImportGroup().SetImportGroup().push_back(p);
+ }
project.SetProjectLevelTagType().SetProjectLevelTagType().push_back(t);
}
}
@@ -1025,6 +1324,7 @@ void CMsvcProjectGenerator::GenerateMsbuild(
}
// OutDir/IntDir/TargetName
+ const CMsvcMetaMakefile& meta_mk = GetApp().GetMetaMakefile();
ITERATE(list<SConfigInfo>, c , all_cfgs) {
const SConfigInfo& cfg_info = *c;
@@ -1049,8 +1349,18 @@ void CMsvcProjectGenerator::GenerateMsbuild(
__SET_PROPGROUP_ELEMENT(t, "OutDir", customtargetname ? targetdir : msvc_tool.Configuration()->OutputDirectory(), cfg_condition);
__SET_PROPGROUP_ELEMENT(t, "IntDir", msvc_tool.Configuration()->IntermediateDirectory(), cfg_condition);
__SET_PROPGROUP_ELEMENT(t, "TargetName", customtargetname ? targetname : project_context.ProjectId(), cfg_condition);
- __SET_PROPGROUP_ELEMENT(t, "LinkIncremental", msvc_tool.Linker()->LinkIncremental(), cfg_condition);
- string prop = msvc_tool.Linker()->GenerateManifest();
+
+ string prop;
+ prop = msvc_tool.Linker()->LinkIncremental();
+ if (prop.empty()) {
+ prop = meta_mk.GetLinkerOpt("LinkIncremental", cfg_info);
+ }
+ __SET_PROPGROUP_ELEMENT(t, "LinkIncremental", prop, cfg_condition);
+
+ prop = msvc_tool.Linker()->GenerateManifest();
+ if (prop.empty()) {
+ prop = meta_mk.GetLinkerOpt("GenerateManifest", cfg_info);
+ }
#if __USE_DISABLED_CFGS__
if (all_cfgs.size() != m_project_configs.size() &&
find(m_project_configs.begin(), m_project_configs.end(), *c) == m_project_configs.end()) {
@@ -1058,7 +1368,13 @@ void CMsvcProjectGenerator::GenerateMsbuild(
}
#endif
__SET_PROPGROUP_ELEMENT(t, "GenerateManifest", prop, cfg_condition);
- __SET_PROPGROUP_ELEMENT(t, "EmbedManifest", msvc_tool.Linker()->EmbedManifest(), cfg_condition);
+
+ prop = msvc_tool.Linker()->EmbedManifest();
+ if (prop.empty()) {
+ prop = meta_mk.GetLinkerOpt("EmbedManifest", cfg_info);
+ }
+ __SET_PROPGROUP_ELEMENT(t, "EmbedManifest", prop, cfg_condition);
+
if (customtargetname) {
__SET_PROPGROUP_ELEMENT(t, "TargetExt", targetext, cfg_condition);
}
@@ -1107,6 +1423,7 @@ void CMsvcProjectGenerator::GenerateMsbuild(
{
CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetClCompile();
__SET_CLCOMPILE(p, AdditionalIncludeDirectories);
__SET_CLCOMPILE(p, AdditionalOptions);
@@ -1143,6 +1460,7 @@ void CMsvcProjectGenerator::GenerateMsbuild(
{
CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLink();
__SET_LINK(p, AdditionalDependencies);
__SET_LINK(p, AdditionalLibraryDirectories);
@@ -1167,14 +1485,13 @@ void CMsvcProjectGenerator::GenerateMsbuild(
#endif
__SET_LINK(p, SubSystem);
__SET_LINK(p, TargetMachine);
- if (!msvc_tool.Linker()->ImageHasSafeExceptionHandlers().empty()) {
- __SET_LINK(p, ImageHasSafeExceptionHandlers);
- }
+ __SET_LINK(p, ImageHasSafeExceptionHandlers);
}
// librarian
{
CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetLib();
__SET_LIB_ELEMENT(p, "AdditionalLibraryDirectories", msvc_tool.Librarian()->AdditionalLibraryDirectories());
__SET_LIB_ELEMENT(p, "AdditionalOptions", msvc_tool.Librarian()->AdditionalOptions());
__SET_LIB_ELEMENT(p, "IgnoreAllDefaultLibraries", msvc_tool.Librarian()->IgnoreAllDefaultLibraries());
@@ -1186,6 +1503,7 @@ void CMsvcProjectGenerator::GenerateMsbuild(
{
CRef<msbuild::CItemDefinitionGroup::C_E> p(new msbuild::CItemDefinitionGroup::C_E);
t->SetItemDefinitionGroup().SetItemDefinitionGroup().push_back(p);
+ p->SetResourceCompile();
__SET_RC_ELEMENT(p, "AdditionalIncludeDirectories", msvc_tool.ResourceCompiler()->AdditionalIncludeDirectories());
__SET_RC_ELEMENT(p, "AdditionalOptions", msvc_tool.ResourceCompiler()->AdditionalOptions());
__SET_RC_ELEMENT(p, "PreprocessorDefinitions", msvc_tool.ResourceCompiler()->PreprocessorDefinitions());
diff --git a/c++/src/build-system/project_tree_builder/msvc_prj_generator.hpp b/c++/src/build-system/project_tree_builder/msvc_prj_generator.hpp
index 983d87e..da8db38 100644
--- a/c++/src/build-system/project_tree_builder/msvc_prj_generator.hpp
+++ b/c++/src/build-system/project_tree_builder/msvc_prj_generator.hpp
@@ -1,7 +1,7 @@
#ifndef PROJECT_TREE_BUILDER__MSVC_PRJ_GENERATOR__HPP
#define PROJECT_TREE_BUILDER__MSVC_PRJ_GENERATOR__HPP
-/* $Id: msvc_prj_generator.hpp 408439 2013-07-30 16:41:12Z gouriano $
+/* $Id: msvc_prj_generator.hpp 461137 2015-03-06 15:40:12Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -81,6 +81,7 @@ public:
CMsvcPrjProjectContext& project_context,
CProjItem& prj);
+ static void GeneratePropertySheets(void);
private:
list<SConfigInfo> m_Configs;
list<SConfigInfo> m_project_configs;
diff --git a/c++/src/build-system/project_tree_builder/msvc_prj_utils.cpp b/c++/src/build-system/project_tree_builder/msvc_prj_utils.cpp
index fc0d1c2..ba18f69 100644
--- a/c++/src/build-system/project_tree_builder/msvc_prj_utils.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_prj_utils.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_prj_utils.cpp 454439 2014-12-15 16:05:42Z ivanov $
+/* $Id: msvc_prj_utils.cpp 460951 2015-03-04 17:33:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -77,7 +77,7 @@ void SaveToXmlFile(const string& file_path, const CSerialObject& project)
if ( !ofs )
NCBI_THROW(CProjBulderAppException, eFileCreation, file_path);
- CObjectOStreamXml xs(ofs, false);
+ CObjectOStreamXml xs(ofs, eNoOwnership);
if (CMsvc7RegSettings::GetMsvcVersion() >= CMsvc7RegSettings::eMsvc1000) {
xs.SetReferenceSchema();
xs.SetUseSchemaLocation(false);
@@ -533,6 +533,7 @@ void LoadConfigInfoByNames(const CNcbiRegistry& registry,
"runtimeLibraryOption","0"));
configs->push_back(config);
#if 0
+// per CXX-4211
if (( config.m_Debug && GetApp().m_TweakVTuneD) ||
(!config.m_Debug && GetApp().m_TweakVTuneR))
{
diff --git a/c++/src/build-system/project_tree_builder/msvc_project_context.cpp b/c++/src/build-system/project_tree_builder/msvc_project_context.cpp
index 530e467..2500822 100644
--- a/c++/src/build-system/project_tree_builder/msvc_project_context.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_project_context.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_project_context.cpp 346490 2011-12-07 15:13:54Z gouriano $
+/* $Id: msvc_project_context.cpp 450311 2014-10-24 14:42:48Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -670,6 +670,7 @@ bool CMsvcPrjProjectContext::IsConfigEnabled(const SConfigInfo& config,
continue;
}
+ bool disabled = false;
if ( !site.IsLibEnabledInConfig(requires, config) ) {
if (unmet) {
if (!unmet->empty()) {
@@ -681,19 +682,26 @@ bool CMsvcPrjProjectContext::IsConfigEnabled(const SConfigInfo& config,
!= libs_required.end()) {
result = false;
}
- s_DisabledPackages[config.GetConfigFullName()].insert(requires);
- } else {
- s_EnabledPackages[config.GetConfigFullName()].insert(requires);
+ disabled = true;
}
if ( !site.IsLibOk(lib_info,true) && !site.Is3PartyLibWithChoice(requires) ) {
- if (unmet_req) {
- if (!unmet_req->empty()) {
- *unmet_req += ", ";
+ disabled = true;
+ if (find( libs_required.begin(), libs_required.end(), requires )
+ != libs_required.end()) {
+ if (unmet_req) {
+ if (!unmet_req->empty()) {
+ *unmet_req += ", ";
+ }
+ *unmet_req += requires;
}
- *unmet_req += requires;
}
}
+ if (disabled) {
+ s_DisabledPackages[config.GetConfigFullName()].insert(requires);
+ } else {
+ s_EnabledPackages[config.GetConfigFullName()].insert(requires);
+ }
}
return result;
diff --git a/c++/src/build-system/project_tree_builder/msvc_site.cpp b/c++/src/build-system/project_tree_builder/msvc_site.cpp
index 9d7b7bf..64e8c52 100644
--- a/c++/src/build-system/project_tree_builder/msvc_site.cpp
+++ b/c++/src/build-system/project_tree_builder/msvc_site.cpp
@@ -1,4 +1,4 @@
-/* $Id: msvc_site.cpp 436629 2014-05-29 17:52:19Z gouriano $
+/* $Id: msvc_site.cpp 465021 2015-04-16 13:03:34Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -311,7 +311,7 @@ string CMsvcSite::ProcessMacros(string raw_data, bool preserve_unresolved) const
void CMsvcSite::GetLibInfo(const string& lib,
const SConfigInfo& config, SLibInfo* libinfo) const
{
- string libinfokey(lib + config.GetConfigFullName());
+ string libinfokey(lib + "|" + config.GetConfigFullName());
map<string,SLibInfo>::const_iterator li;
li = m_AllLibInfo.find(libinfokey);
if (li != m_AllLibInfo.end()) {
@@ -341,6 +341,8 @@ void CMsvcSite::GetLibInfo(const string& lib,
libinfo->m_LibPath = ToOSPath(
ProcessMacros(GetOpt(m_Registry, section, "LIBPATH", config),false));
+ libinfo->m_BinPath = ToOSPath(
+ ProcessMacros(GetOpt(m_Registry, section, "BINPATH", config),false));
string libs_str = GetOpt(m_Registry, section, "LIB", config);
NStr::Split(libs_str, LIST_SEPARATOR, libinfo->m_Libs);
@@ -361,9 +363,8 @@ void CMsvcSite::GetLibInfo(const string& lib,
libinfo->m_libinfokey = libinfokey;
libinfo->m_good = IsLibOk(*libinfo);
-// m_AllLibInfo.insert( make_pair<string,SLibInfo>(libinfokey,*libinfo));
+ LOG_POST(Info << "Component " << libinfokey << ": " << (libinfo->m_good ? "good" : "bad"));
m_AllLibInfo.insert( map<string,SLibInfo>::value_type(libinfokey,*libinfo));
-// m_AllLibInfo[ libinfokey ] = *libinfo;
}
@@ -500,7 +501,6 @@ CMsvcSite::SLibChoice::SLibChoice(const CMsvcSite& site,
site.GetLibInfo(m_3PartyLib, config, &lib_info);
if ( !site.IsLibOk(lib_info) ) {
-
m_Choice = eLib;
break;
}
@@ -508,6 +508,7 @@ CMsvcSite::SLibChoice::SLibChoice(const CMsvcSite& site,
} else {
m_Choice = site.IsProvided(lib_3party) ? e3PartyLib : eLib;
}
+ LOG_POST(Info << "LibChoice " << lib << "/" << lib_3party << " = " << (m_Choice == e3PartyLib ? lib_3party : lib));
}
diff --git a/c++/src/build-system/project_tree_builder/msvc_site.hpp b/c++/src/build-system/project_tree_builder/msvc_site.hpp
index 1273002..440a2de 100644
--- a/c++/src/build-system/project_tree_builder/msvc_site.hpp
+++ b/c++/src/build-system/project_tree_builder/msvc_site.hpp
@@ -1,6 +1,6 @@
#ifndef PROJECT_TREE_BUILDER_MSVC_SITE__HPP
#define PROJECT_TREE_BUILDER_MSVC_SITE__HPP
-/* $Id: msvc_site.hpp 408439 2013-07-30 16:41:12Z gouriano $
+/* $Id: msvc_site.hpp 455052 2014-12-22 18:23:09Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,6 +50,7 @@ struct SLibInfo
list<string> m_IncludeDir;
list<string> m_LibDefines;
string m_LibPath;
+ string m_BinPath;
list<string> m_Libs;
list<string> m_StdLibs;
list<string> m_Macro;
@@ -68,6 +69,7 @@ struct SLibInfo
m_IncludeDir = info.m_IncludeDir;
m_LibDefines = info.m_LibDefines;
m_LibPath = info.m_LibPath;
+ m_BinPath = info.m_BinPath;
m_Libs = info.m_Libs;
m_StdLibs = info.m_StdLibs;
m_Macro = info.m_Macro;
@@ -81,6 +83,7 @@ struct SLibInfo
m_IncludeDir = info.m_IncludeDir;
m_LibDefines = info.m_LibDefines;
m_LibPath = info.m_LibPath;
+ m_BinPath = info.m_BinPath;
m_Libs = info.m_Libs;
m_StdLibs = info.m_StdLibs;
m_Macro = info.m_Macro;
@@ -95,6 +98,7 @@ struct SLibInfo
m_IncludeDir.empty() &&
m_LibDefines.empty() &&
m_LibPath.empty() &&
+ m_BinPath.empty() &&
m_Libs.empty() &&
m_StdLibs.empty() &&
m_Macro.empty() &&
@@ -106,6 +110,7 @@ struct SLibInfo
m_IncludeDir.clear();
m_LibDefines.clear();
m_LibPath.erase();
+ m_BinPath.erase();
m_Libs.clear();
m_StdLibs.clear();
m_Macro.clear();
diff --git a/c++/src/build-system/project_tree_builder/msvc_tools_implement.hpp b/c++/src/build-system/project_tree_builder/msvc_tools_implement.hpp
index bb56c74..ecbb158 100644
--- a/c++/src/build-system/project_tree_builder/msvc_tools_implement.hpp
+++ b/c++/src/build-system/project_tree_builder/msvc_tools_implement.hpp
@@ -1,7 +1,7 @@
#ifndef PROJECT_TREE_BUILDER__TOOLS_IMPLEMENT__HPP
#define PROJECT_TREE_BUILDER__TOOLS_IMPLEMENT__HPP
-/* $Id: msvc_tools_implement.hpp 425324 2014-01-28 13:52:04Z gouriano $
+/* $Id: msvc_tools_implement.hpp 460951 2015-03-04 17:33:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -221,12 +221,6 @@ public:
defines += ';';
}
-#if 0
- defines += GetCompilerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "PreprocessorDefinitions",
- m_Config );
-#else
string opt("PreprocessorDefinitions");
string val;
val = m_MsvcProjectMakefile.GetCompilerOpt(opt, m_Config);
@@ -234,32 +228,21 @@ public:
defines += val;
defines += ';';
}
- val = m_MsvcMetaMakefile.GetCompilerOpt(opt, m_Config);
- if (!val.empty()) {
- defines += val;
+
+ if ( CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
+ val = m_MsvcMetaMakefile.GetCompilerOpt(opt, m_Config);
+ if (!val.empty()) {
+ defines += val;
+ }
+ } else {
+ defines += "%(PreprocessorDefinitions)";
}
-#endif
return defines;
}
SUPPORT_COMPILER_OPTION(MinimalRebuild)
- virtual string BasicRuntimeChecks(void) const
- {
-#if 0
- if (m_Config.m_VTuneAddon) {
- return CMsvcMetaMakefile::TranslateOpt("0", "Compiler", "BasicRuntimeChecks");
- }
-#endif
- return GetCompilerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "BasicRuntimeChecks",
- m_Config );
- }
- virtual string RuntimeLibrary(void) const
- {
- return m_RuntimeLibraryOption;
- }
-
+ SUPPORT_COMPILER_OPTION(BasicRuntimeChecks)
+ SUPPORT_COMPILER_OPTION(RuntimeLibrary)
SUPPORT_COMPILER_OPTION(RuntimeTypeInfo)
SUPPORT_COMPILER_OPTION(UsePrecompiledHeader)
SUPPORT_COMPILER_OPTION(WarningLevel)
@@ -280,8 +263,6 @@ public:
SUPPORT_COMPILER_OPTION(StringPooling)
SUPPORT_COMPILER_OPTION(EnableFunctionLevelLinking)
-
- //Latest additions
SUPPORT_COMPILER_OPTION(OptimizeForProcessor)
SUPPORT_COMPILER_OPTION(StructMemberAlignment)
SUPPORT_COMPILER_OPTION(CallingConvention)
@@ -294,20 +275,7 @@ public:
SUPPORT_COMPILER_OPTION(GlobalOptimizations)
SUPPORT_COMPILER_OPTION(FavorSizeOrSpeed)
SUPPORT_COMPILER_OPTION(BrowseInformation)
-
- virtual string ProgramDataBaseFileName(void) const
- {
- string pdb_file =
- GetCompilerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "ProgramDataBaseFileName",
- m_Config );
- if( !pdb_file.empty() )
- return pdb_file;
-
- return string("$(IntDir)") + m_ProjectId + ".pdb";
-// return string("$(OutDir)$(ProjectName).pdb");
- }
+ SUPPORT_COMPILER_OPTION(ProgramDataBaseFileName)
private:
string m_AdditionalIncludeDirectories;
@@ -359,40 +327,19 @@ public:
}
virtual string AdditionalOptions(void) const
{
-#if 0
- return m_AdditionalOptions + " " +
- GetLinkerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "AdditionalOptions",
- m_Config );
-#else
string options(m_AdditionalOptions);
- string add = m_MsvcMetaMakefile.GetLinkerOpt("AdditionalOptions", m_Config);
- if (!add.empty()) {
- options += " " + add;
+ string add;
+ if ( CMsvc7RegSettings::GetMsvcVersion() < CMsvc7RegSettings::eMsvc1000 ) {
+ add = m_MsvcMetaMakefile.GetLinkerOpt("AdditionalOptions", m_Config);
+ if (!add.empty()) {
+ options += " " + add;
+ }
}
add = m_MsvcProjectMakefile.GetLinkerOpt("AdditionalOptions", m_Config);
if (!add.empty()) {
options += " " + add;
}
return options;
-#endif
- }
- virtual string OutputFile(void) const
- {
- string output_file =
- GetLinkerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "OutputFile",
- m_Config );
- if( !output_file.empty() )
- return output_file;
-
-// return string("$(OutDir)") + m_ProjectId + ConfTrait::TargetExtension();
- if (CMsvc7RegSettings::GetMsvcVersion() >= CMsvc7RegSettings::eMsvc1000) {
- return string("$(OutDir)$(TargetName)$(TargetExt)");
- }
- return string("$(OutDir)$(ProjectName)");
}
#define SUPPORT_LINKER_OPTION(opt) \
@@ -404,6 +351,7 @@ public:
m_Config ); \
}
+ SUPPORT_LINKER_OPTION(OutputFile)
SUPPORT_LINKER_OPTION(LinkIncremental)
SUPPORT_LINKER_OPTION(LargeAddressAware)
virtual string GenerateDebugInformation(void) const
@@ -417,28 +365,9 @@ public:
m_Config );
}
- virtual string ProgramDatabaseFile(void) const
- {
- string pdb_file =
- GetLinkerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "ProgramDatabaseFile",
- m_Config );
- if( !pdb_file.empty() )
- return pdb_file;
-
- return string("$(OutDir)") + m_ProjectId + ".pdb";
-// return string("$(OutDir)$(ProjectName).pdb");
- }
-
+ SUPPORT_LINKER_OPTION(ProgramDatabaseFile)
SUPPORT_LINKER_OPTION(SubSystem)
-
- virtual string ImportLibrary(void) const
- {
- return string("$(OutDir)") + m_ProjectId + ".lib";
-// return string("$(OutDir)$(ProjectName).lib");
- }
-
+ SUPPORT_LINKER_OPTION(ImportLibrary)
SUPPORT_LINKER_OPTION(TargetMachine)
SUPPORT_LINKER_OPTION(ImageHasSafeExceptionHandlers)
SUPPORT_LINKER_OPTION(OptimizeReferences)
@@ -460,18 +389,7 @@ public:
return add + m_AdditionalLibraryDirectories;
}
- virtual string FixedBaseAddress(void) const
- {
-#if 0
- if (m_Config.m_VTuneAddon) {
- return CMsvcMetaMakefile::TranslateOpt("1", "Linker", "FixedBaseAddress");
- }
-#endif
- return GetLinkerOpt(m_MsvcMetaMakefile,
- m_MsvcProjectMakefile,
- "FixedBaseAddress",
- m_Config );
- }
+ SUPPORT_LINKER_OPTION(FixedBaseAddress)
SUPPORT_LINKER_OPTION(GenerateManifest)
SUPPORT_LINKER_OPTION(EmbedManifest)
@@ -527,16 +445,8 @@ public:
SUPPORT_DUMMY_OPTION(ImageHasSafeExceptionHandlers)
SUPPORT_DUMMY_OPTION(OptimizeReferences)
SUPPORT_DUMMY_OPTION(EnableCOMDATFolding)
-
- virtual string IgnoreAllDefaultLibraries(void) const
- {
- return "false";
- }
- virtual string IgnoreDefaultLibraryNames(void) const
- {
- return "";
- }
-
+ SUPPORT_DUMMY_OPTION(IgnoreAllDefaultLibraries)
+ SUPPORT_DUMMY_OPTION(IgnoreDefaultLibraryNames)
SUPPORT_DUMMY_OPTION(AdditionalLibraryDirectories)
SUPPORT_DUMMY_OPTION(FixedBaseAddress)
SUPPORT_DUMMY_OPTION(GenerateManifest)
@@ -572,15 +482,6 @@ public:
return "VCLibrarianTool";
}
- virtual string OutputFile(void) const
- {
-// return string("$(OutDir)") + m_ProjectId + ".lib";
- if (CMsvc7RegSettings::GetMsvcVersion() >= CMsvc7RegSettings::eMsvc1000) {
- return string("$(OutDir)$(TargetName)$(TargetExt)");
- }
- return string("$(OutDir)$(ProjectName)");
- }
-
#define SUPPORT_LIBRARIAN_OPTION(opt) \
virtual string opt(void) const \
{ \
@@ -593,6 +494,7 @@ public:
SUPPORT_LIBRARIAN_OPTION(AdditionalLibraryDirectories)
SUPPORT_LIBRARIAN_OPTION(IgnoreAllDefaultLibraries)
SUPPORT_LIBRARIAN_OPTION(IgnoreDefaultLibraryNames)
+ SUPPORT_LIBRARIAN_OPTION(OutputFile)
SUPPORT_LIBRARIAN_OPTION(TargetMachine)
private:
diff --git a/c++/src/build-system/project_tree_builder/proj_builder_app.cpp b/c++/src/build-system/project_tree_builder/proj_builder_app.cpp
index a7498c8..7503d85 100644
--- a/c++/src/build-system/project_tree_builder/proj_builder_app.cpp
+++ b/c++/src/build-system/project_tree_builder/proj_builder_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: proj_builder_app.cpp 440234 2014-07-10 15:45:34Z gouriano $
+/* $Id: proj_builder_app.cpp 469083 2015-06-01 15:28:15Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -405,7 +405,7 @@ struct PIsExcludedByDisuse
//-----------------------------------------------------------------------------
CProjBulderApp::CProjBulderApp(void)
{
- SetVersion( CVersionInfo(3,11,2) );
+ SetVersion( CVersionInfo(4,2,0) );
m_ScanningWholeTree = false;
m_Dll = false;
m_AddMissingLibs = false;
@@ -772,6 +772,7 @@ void CProjBulderApp::GenerateMsvcProjects(CProjectItemsTree& projects_tree)
}
// Projects
CMsvcProjectGenerator prj_gen(*configurations);
+ CMsvcProjectGenerator::GeneratePropertySheets();
NON_CONST_ITERATE(CProjectItemsTree::TProjects, p, projects_tree.m_Projects) {
prj_gen.Generate(p->second);
}
@@ -2640,7 +2641,7 @@ void CProjBulderApp::LoadDepGraph(const string& filename)
}
map<string, set<string> > lib3Precedes;
CSymResolver::StripSuffix(f_name);
- if (third_list.empty()) {
+ if (third_list.empty() && m_GraphDepPrecedes.find(f_name) == m_GraphDepPrecedes.end()) {
m_GraphDepPrecedes[f_name] = set<string>();
}
ITERATE(list<string>, t, third_list) {
@@ -2788,7 +2789,8 @@ void CProjBulderApp::RankDepGraph(void)
vector< set<string> > graph;
for (map<string, set<string> >::const_iterator d= m_GraphDepPrecedes.begin();
d!= m_GraphDepPrecedes.end(); ++d) {
- set<string> done;
+ list<string> done;
+ done.push_back(d->first);
InsertDep(graph, d->first, done);
}
for (size_t s= 0; s<graph.size(); ++s) {
@@ -2798,21 +2800,23 @@ void CProjBulderApp::RankDepGraph(void)
}
}
-void CProjBulderApp::InsertDep(vector< set<string> >& graph, const string& dep, set<string>& done)
+bool CProjBulderApp::InsertDep(vector< set<string> >& graph, const string& dep, list<string>& done)
{
- if (m_GraphDepPrecedes.find(dep) == m_GraphDepPrecedes.end()) {
- return;
- }
- if (done.find(dep) != done.end()) {
- return;
- }
- done.insert(dep);
const set<string>& dependents = m_GraphDepPrecedes[dep];
size_t graphset=0;
for (set<string>::const_iterator d = dependents.begin(); d != dependents.end(); ++d) {
if (m_GraphDepPrecedes.find(*d) == m_GraphDepPrecedes.end()) {
continue;
}
+ if (find(done.begin(), done.end(), *d) != done.end()) {
+ done.push_back(*d);
+ PTB_ERROR_EX(m_Root, ePTB_ConfigurationError,
+ "Library dependency cycle found: " << NStr::Join(done, " - "));
+ done.pop_back();
+ m_GraphDepPrecedes.erase(*d);
+ return false;
+ }
+ done.push_back(*d);
for (bool found=false; !found; ) {
for (size_t s= 0; !found && s<graph.size(); ++s) {
if (graph[s].find(*d) != graph[s].end()) {
@@ -2821,9 +2825,10 @@ void CProjBulderApp::InsertDep(vector< set<string> >& graph, const string& dep,
}
}
if (!found) {
- InsertDep(graph, *d, done);
+ found = !InsertDep(graph, *d, done);
}
}
+ done.pop_back();
}
if (!dependents.empty()) {
++graphset;
@@ -2835,6 +2840,7 @@ void CProjBulderApp::InsertDep(vector< set<string> >& graph, const string& dep,
t.insert(dep);
graph.push_back(t);
}
+ return true;
}
string CProjBulderApp::ProcessLocationMacros(string raw_data)
@@ -2953,6 +2959,14 @@ void CProjBulderApp::SetConfFileData(const string& src, const string& dest)
m_ConfDest= dest;
}
+string CProjBulderApp::GetBuildDir(void)
+{
+ return CDirEntry::AddTrailingPathSeparator(
+ CDirEntry::ConcatPath( CDirEntry::ConcatPath( CDirEntry::ConcatPath(
+ GetProjectTreeInfo().m_Compilers, GetRegSettings().m_CompilersSubdir),
+ GetBuildType().GetTypeStr()), GetRegSettings().m_ProjectsSubdir));
+}
+
CProjBulderApp& GetApp(void)
{
static CProjBulderApp theApp;
@@ -2969,5 +2983,5 @@ int NcbiSys_main(int argc, TXChar* argv[])
// Execute main application function
CDiagContext::SetLogTruncate(true);
GetDiagContext().SetLogRate_Limit(CDiagContext::eLogRate_Err, (unsigned int)-1);
- return GetApp().AppMain(argc, argv, 0, eDS_Default);
+ return GetApp().AppMain(argc, argv);
}
diff --git a/c++/src/build-system/project_tree_builder/proj_builder_app.hpp b/c++/src/build-system/project_tree_builder/proj_builder_app.hpp
index 0d44b24..727d6fe 100644
--- a/c++/src/build-system/project_tree_builder/proj_builder_app.hpp
+++ b/c++/src/build-system/project_tree_builder/proj_builder_app.hpp
@@ -1,7 +1,7 @@
#ifndef PROJECT_TREE_BULDER__PROJ_BUILDER_APP__HPP
#define PROJECT_TREE_BULDER__PROJ_BUILDER_APP__HPP
-/* $Id: proj_builder_app.hpp 435656 2014-05-19 17:14:19Z gouriano $
+/* $Id: proj_builder_app.hpp 469083 2015-06-01 15:28:15Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -217,6 +217,8 @@ public:
string GetUtilityProjectsDir(void) const;
string GetUtilityProjectsSrcDir(void);
void SetConfFileData(const string& src, const string& dest);
+
+ string GetBuildDir(void);
void UpdateDepGraph( CProjectTreeBuilder::TFiles& files);
private:
@@ -225,7 +227,7 @@ private:
void LoadDepGraph(const string& filename);
void CollectDep(const string& libname, const string& depname);
void RankDepGraph(void);
- void InsertDep(vector< set<string> >& graph, const string& dep, set<string>& done);
+ bool InsertDep(vector< set<string> >& graph, const string& dep, list<string>& done);
void GetBuildConfigs (list<SConfigInfo>* configs);
void GenerateMsvcProjects(CProjectItemsTree& projects_tree);
diff --git a/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.cpp b/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.cpp
index 6bde970..a92d4a8 100644
--- a/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.cpp
+++ b/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.cpp
@@ -1,4 +1,4 @@
-/* $Id: proj_datatool_generated_src.cpp 187161 2010-03-29 13:58:42Z gouriano $
+/* $Id: proj_datatool_generated_src.cpp 465020 2015-04-16 13:02:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -108,6 +108,7 @@ void CDataToolGeneratedSrc::LoadFrom(const string& source_file_path,
CDirEntry::SplitPath(source_file_path, &dir, &base, &ext);
src->m_SourceBaseDir = dir;
+ src->m_SourceCPP = base;
src->m_SourceFile = base + ext;
{{
@@ -202,6 +203,7 @@ bool CDataToolGeneratedSrc::IsEmpty(void) const
void CDataToolGeneratedSrc::Clear(void)
{
m_SourceFile.erase();
+ m_SourceCPP.erase();
m_SourceBaseDir.erase();
m_ImportModules.clear();
@@ -219,6 +221,7 @@ void CDataToolGeneratedSrc::Clear(void)
void CDataToolGeneratedSrc::SetFrom(const CDataToolGeneratedSrc& src)
{
m_SourceFile = src.m_SourceFile;
+ m_SourceCPP = src.m_SourceCPP;
m_SourceBaseDir = src.m_SourceBaseDir;
m_ImportModules = src.m_ImportModules;
diff --git a/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.hpp b/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.hpp
index 72ae84e..7c49596 100644
--- a/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.hpp
+++ b/c++/src/build-system/project_tree_builder/proj_datatool_generated_src.hpp
@@ -1,7 +1,7 @@
#ifndef PROJECT_TREE_BUILDER__PROJ_DATATOOL_GENERATED_SRC__HPP
#define PROJECT_TREE_BUILDER__PROJ_DATATOOL_GENERATED_SRC__HPP
-/* $Id: proj_datatool_generated_src.hpp 122761 2008-03-25 16:45:09Z gouriano $
+/* $Id: proj_datatool_generated_src.hpp 465020 2015-04-16 13:02:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,6 +46,7 @@ public:
bool operator< (const CDataToolGeneratedSrc& src) const;
string m_SourceFile;
+ string m_SourceCPP;
string m_SourceBaseDir;
list<string> m_ImportModules;
diff --git a/c++/src/build-system/project_tree_builder/proj_tree_builder.cpp b/c++/src/build-system/project_tree_builder/proj_tree_builder.cpp
index 9d55c1b..691a5ef 100644
--- a/c++/src/build-system/project_tree_builder/proj_tree_builder.cpp
+++ b/c++/src/build-system/project_tree_builder/proj_tree_builder.cpp
@@ -1,4 +1,4 @@
-/* $Id: proj_tree_builder.cpp 439941 2014-07-08 12:50:23Z gouriano $
+/* $Id: proj_tree_builder.cpp 468328 2015-05-21 18:47:59Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -116,7 +116,9 @@ CProjItem::TProjType SMakeProjectT::GetProjType(const string& base_dir,
string fname_dll = CDirEntry::ConcatPath(base_dir, fname + ".dll");
string fname_msvc= CDirEntry::ConcatPath(base_dir, fname);
string fname_msvc2(fname_msvc);
- if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eUnix) {
+
+ if (CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eMsvcWin32 ||
+ CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eMsvcX64) {
fname_msvc += ".msvcproj";
} else {
fname_msvc2 += ".in";
@@ -214,11 +216,13 @@ bool SMakeProjectT::IsMakeAppFile(const string& name)
}
+/*
bool SMakeProjectT::IsUserProjFile(const string& name)
{
return NStr::StartsWith(name, "Makefile") &&
NStr::EndsWith(name, ".msvcproj");
}
+*/
void SMakeProjectT::DoResolveDefs(CSymResolver& resolver,
@@ -277,7 +281,14 @@ void SMakeProjectT::DoResolveDefs(CSymResolver& resolver,
const string& define = *l;
if ( IsConfigurableDefine(define) ) {
string stripped = StripConfigurableDefine(define);
- string resolved_def_str = site.GetDefinesEntry(stripped);
+ string resolved_def_str;
+ list<string> libchoices_includes ;
+ site.GetLibChoiceIncludes(stripped, &libchoices_includes);
+ if (!libchoices_includes.empty()) {
+ resolved_def_str = NStr::Join( libchoices_includes, " ");
+ } else {
+ resolved_def_str = site.GetDefinesEntry(stripped);
+ }
if ( !resolved_def_str.empty() ) {
defs_resolved[define] = resolved_def_str;
list<string> resolved_defs;
@@ -513,14 +524,15 @@ void SMakeProjectT::Create3PartyLibs(
libs_list->push_back(StripConfigurableDefine(flag));
done.insert(flag);
} else if (NStr::StartsWith(flag, "-l")) {
- CSymResolver::StripSuffix(flag);
+ string suffix;
+ CSymResolver::StripSuffix(flag, &suffix);
if (liborder_found && find(
GetApp().m_LibraryOrder[*mkname].begin(),
GetApp().m_LibraryOrder[*mkname].end(), flag.substr(2)) !=
GetApp().m_LibraryOrder[*mkname].end()) {
continue;
}
- libs3.push_back( CProjKey(CProjKey::eLib, flag.substr(2)));
+ libs3.push_back( CProjKey(CProjKey::eLib, flag.substr(2), suffix));
// user cannot be trusted
// GetApp().m_3PartyLibs.insert(flag.substr(2));
done.insert(flag.substr(2));
@@ -674,6 +686,8 @@ void SMakeProjectT::AnalyzeMakeIn
if (CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eUnix) {
p = makein_contents.m_Contents.find("UNIX_PROJ");
+ } else if (CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eXCode) {
+ p = makein_contents.m_Contents.find("XCODE_PROJ");
} else {
p = makein_contents.m_Contents.find("MSVC_PROJ");
}
@@ -712,7 +726,7 @@ string SMakeProjectT::CreateMakeAppLibFileName
if (!CDirEntry( CDirEntry::ConcatPath(base_dir,fname)).Exists()) {
fname += ".in";
}
- } else {
+ } else if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eXCode) {
fname += ".msvcproj";
}
break;
@@ -2124,8 +2138,22 @@ CProjKey SAsnProjectMultipleT::DoCreate(const string& source_base_dir,
else if ( CDirEntry(asn_path_abs + ".xsd").Exists() )
asn_path_abs += ".xsd";
else {
- PTB_ERROR_EX(asn_path_abs, ePTB_FileNotFound,
- "ASN spec file not found");
+ // one level down
+ string asn_dir_abs = CDirEntry::ConcatPath(source_base_dir, asn);
+ asn_dir_abs = CDirEntry::NormalizePath(asn_dir_abs);
+ asn_dir_abs = CDirEntry::AddTrailingPathSeparator(asn_dir_abs);
+
+ asn_path_abs = CDirEntry::ConcatPath(asn_dir_abs, asn);
+ if ( CDirEntry(asn_path_abs + ".asn").Exists() )
+ asn_path_abs += ".asn";
+ else if ( CDirEntry(asn_path_abs + ".dtd").Exists() )
+ asn_path_abs += ".dtd";
+ else if ( CDirEntry(asn_path_abs + ".xsd").Exists() )
+ asn_path_abs += ".xsd";
+ else {
+ PTB_ERROR_EX(asn_path_abs, ePTB_FileNotFound,
+ "ASN spec file not found");
+ }
}
}
@@ -2183,25 +2211,12 @@ CProjKey SAsnProjectMultipleT::DoCreate(const string& source_base_dir,
if ( !CSymResolver::IsDefine(src) )
project.m_Sources.push_front(src);
}
-// project.m_Sources.remove(proj_name);
-// project.m_Sources.push_back(proj_name + "__");
-// project.m_Sources.push_back(proj_name + "___");
- ITERATE(list<string>, p, asn_names) {
- const string& asn = *p;
- string src(1, CDirEntry::GetPathSeparator());
- if (asn == proj_name) {
- src = asn;
- } else {
- src += "..";
- src += CDirEntry::GetPathSeparator();
- src += asn;
- src += CDirEntry::GetPathSeparator();
- src += asn;
- }
-
+ ITERATE( list<CDataToolGeneratedSrc>, dts, datatool_sources) {
+ const string& asn = dts->m_SourceCPP;
project.m_Sources.remove(asn);
project.m_Sources.remove(asn + "__");
project.m_Sources.remove(asn + "___");
+ string src = CDirEntry::ConcatPath(CDirEntry::CreateRelativePath( source_base_dir, dts->m_SourceBaseDir), asn);
project.m_Sources.push_back(src + "__");
project.m_Sources.push_back(src + "___");
}
@@ -2237,7 +2252,8 @@ CProjKey SMsvcProjectT::DoCreate(const string& source_base_dir,
if (CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eUnix) {
proj_id = proj_name;
} else {
- k = m->second.m_Contents.find("MSVC_PROJ");
+ bool is_xcode = CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eXCode;
+ k = m->second.m_Contents.find(is_xcode ? "XCODE_PROJ" : "MSVC_PROJ");
if (k == m->second.m_Contents.end() ||
k->second.empty()) {
@@ -2269,7 +2285,8 @@ CProjKey SMsvcProjectT::DoCreate(const string& source_base_dir,
string vcproj_file;
list<string> sources;
- if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eUnix) {
+ if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eUnix &&
+ CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eXCode) {
// VCPROJ - will map to src
string vcproj_key("VCPROJ");
if (CMsvc7RegSettings::GetMsvcVersion() >= CMsvc7RegSettings::eMsvc1000) {
@@ -2445,7 +2462,7 @@ CProjectTreeBuilder::BuildProjectTree(const IProjectFilter* filter,
if (GetApp().IsScanningWholeTree()) {
*tree = target_tree;
NON_CONST_ITERATE( CProjectItemsTree::TProjects, t, tree->m_Projects) {
- t->second.m_MakeType = eMakeType_Expendable;
+ t->second.m_MakeType = eMakeType_Excluded;
t->second.m_External = true;
}
return;
@@ -2614,7 +2631,8 @@ void CProjectTreeBuilder::ProcessDir(const string& dir_name,
if ( process_projects ) {
string userproj[] = {"UNIX_PROJ","EXPENDABLE_UNIX_PROJ", ""};
if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eUnix) {
- userproj[0] = "MSVC_PROJ";
+ bool is_xcode = CMsvc7RegSettings::GetMsvcPlatform() == CMsvc7RegSettings::eXCode;
+ userproj[0] = is_xcode ? "XCODE_PROJ" : "MSVC_PROJ";
userproj[1] = "";
}
EMakeFileType usertype[] = {eMakeType_Undefined,eMakeType_Expendable};
@@ -2634,7 +2652,10 @@ void CProjectTreeBuilder::ProcessDir(const string& dir_name,
s_WriteBuildOrder(dir_name,"Makefile." + *i + ".in");
}
} else {
- string mkname("Makefile." + *i + ".msvcproj");
+ string mkname("Makefile." + *i);
+ if (CMsvc7RegSettings::GetMsvcPlatform() != CMsvc7RegSettings::eXCode) {
+ mkname += ".msvcproj";
+ }
userprojects[mkname] = max(maketype, usertype[j]);
if (get_order) {
s_WriteBuildOrder(dir_name,mkname);
@@ -2994,6 +3015,11 @@ void CProjectTreeBuilder::ResolveDefs(CSymResolver& resolver,
keys.insert("DLL_DEP");
SMakeProjectT::DoResolveDefs(resolver, makefiles.m_User, keys);
}}
+ {{
+ set<string> keys;
+ SMakeProjectT::DoResolveDefs(resolver, makefiles.m_In, keys);
+ SMakeProjectT::DoResolveDefs(resolver, makefiles.m_Dll, keys);
+ }}
}
diff --git a/c++/src/build-system/project_tree_builder/resolver.cpp b/c++/src/build-system/project_tree_builder/resolver.cpp
index fa3ad97..d006c62 100644
--- a/c++/src/build-system/project_tree_builder/resolver.cpp
+++ b/c++/src/build-system/project_tree_builder/resolver.cpp
@@ -1,4 +1,4 @@
-/* $Id: resolver.cpp 426194 2014-02-06 17:22:06Z gouriano $
+/* $Id: resolver.cpp 455247 2014-12-24 15:36:34Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -188,8 +188,20 @@ void CSymResolver::Resolve(const string& define, list<string>* resolved_def,
}
if ( resolved_def->size() == 1) {
modified = true;
+#if 1
+ if (raw_define == resolved_def->front()) {
+ if (GetApp().GetSite().IsCppflagDescribed(raw_define)) {
+ modified = false;
+ } else {
+ NStr::ReplaceInPlace(data, raw_define, kEmptyStr);
+ }
+ } else {
+ NStr::ReplaceInPlace(data, raw_define, resolved_def->front());
+ }
+#else
NStr::ReplaceInPlace(data, raw_define,
raw_define != resolved_def->front() ? resolved_def->front() : kEmptyStr);
+#endif
resolved_def->clear();
}
}
diff --git a/c++/src/build-system/project_tree_builder_gui/src/ptbgui/ArgsParser.java b/c++/src/build-system/project_tree_builder_gui/src/ptbgui/ArgsParser.java
index 523bb5d..5a44e1b 100644
--- a/c++/src/build-system/project_tree_builder_gui/src/ptbgui/ArgsParser.java
+++ b/c++/src/build-system/project_tree_builder_gui/src/ptbgui/ArgsParser.java
@@ -1,4 +1,4 @@
-/* $Id: ArgsParser.java 446508 2014-09-16 15:29:49Z ivanov $
+/* $Id: ArgsParser.java 446504 2014-09-16 14:46:53Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/build-system/project_tree_builder_gui/src/ptbgui/PtbguiMain.java b/c++/src/build-system/project_tree_builder_gui/src/ptbgui/PtbguiMain.java
index 02f8a6a..de6f569 100644
--- a/c++/src/build-system/project_tree_builder_gui/src/ptbgui/PtbguiMain.java
+++ b/c++/src/build-system/project_tree_builder_gui/src/ptbgui/PtbguiMain.java
@@ -1,4 +1,4 @@
-/* $Id: PtbguiMain.java 446508 2014-09-16 15:29:49Z ivanov $
+/* $Id: PtbguiMain.java 446504 2014-09-16 14:46:53Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/build-system/ptb_version.txt b/c++/src/build-system/ptb_version.txt
index d2c96c0..4d0dcda 100644
--- a/c++/src/build-system/ptb_version.txt
+++ b/c++/src/build-system/ptb_version.txt
@@ -1 +1 @@
-3.11.3
+4.1.2
diff --git a/c++/src/build-system/relocate.sh.in b/c++/src/build-system/relocate.sh.in
index b57417f..77f6724 100644
--- a/c++/src/build-system/relocate.sh.in
+++ b/c++/src/build-system/relocate.sh.in
@@ -1,6 +1,6 @@
@script_shell@
-# $Id: relocate.sh.in 469196 2015-06-02 14:04:23Z blastadm $
+# $Id: relocate.sh.in 485955 2015-11-30 17:54:14Z blastadm $
# Author: Denis Vakatov, NCBI
#
# Adjust paths to this build tree and the relevant source tree
diff --git a/c++/src/cgi/cgi_entry_reader.cpp b/c++/src/cgi/cgi_entry_reader.cpp
index 973f83a..edfdf37 100644
--- a/c++/src/cgi/cgi_entry_reader.cpp
+++ b/c++/src/cgi/cgi_entry_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: cgi_entry_reader.cpp 441971 2014-07-29 17:21:35Z ucko $
+/* $Id: cgi_entry_reader.cpp 441731 2014-07-28 15:30:35Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/cgi/cgi_exception.cpp b/c++/src/cgi/cgi_exception.cpp
index 69fffb8..6169fbf 100644
--- a/c++/src/cgi/cgi_exception.cpp
+++ b/c++/src/cgi/cgi_exception.cpp
@@ -1,4 +1,4 @@
-/* $Id: cgi_exception.cpp 446390 2014-09-15 17:56:49Z ivanov $
+/* $Id: cgi_exception.cpp 441525 2014-07-24 16:55:45Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/cgi/cgiapp.cpp b/c++/src/cgi/cgiapp.cpp
index fe0df8d..e3e034b 100644
--- a/c++/src/cgi/cgiapp.cpp
+++ b/c++/src/cgi/cgiapp.cpp
@@ -1,4 +1,4 @@
-/* $Id: cgiapp.cpp 465281 2015-04-20 14:55:53Z ivanov $
+/* $Id: cgiapp.cpp 483521 2015-11-02 14:44:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -247,7 +247,6 @@ int CCgiApplication::Run(void)
m_Context.reset( CreateContext() );
_ASSERT(m_Context.get());
- m_Context->CheckStatus();
ConfigureDiagnostics(*m_Context);
x_AddLBCookie();
@@ -259,6 +258,8 @@ int CCgiApplication::Run(void)
ProcessHttpReferer();
LogRequest();
+ m_Context->CheckStatus();
+
try {
m_Cache.reset( GetCacheStorage() );
} catch( exception& ex ) {
@@ -504,7 +505,6 @@ void CCgiApplication::Init(void)
{
if ( TMergeLogLines::GetDefault() ) {
// Convert multi-line diagnostic messages into one-line ones by default.
- SetDiagPostFlag(eDPF_PreMergeLines);
SetDiagPostFlag(eDPF_MergeLines);
}
@@ -761,7 +761,7 @@ const CArgs& CCgiApplication::GetArgs(void) const
m_CgiArgs.reset(new CArgs());
// Copy cmd-line arg values to CGI args
- *m_CgiArgs = CParent::GetArgs();
+ m_CgiArgs->Assign(CParent::GetArgs());
// Add CGI parameters to the CGI version of args
GetArgDescriptions()->ConvertKeys(m_CgiArgs.get(),
@@ -1356,6 +1356,7 @@ void CCgiApplication::SetHTTPStatus(unsigned int status, const string& reason)
bool CCgiApplication::x_DoneHeadRequest(void) const
{
+ if (!m_Context.get()) return false; // There was an error initializing context
const CCgiContext& ctx = GetContext();
const CCgiRequest& req = ctx.GetRequest();
const CCgiResponse& res = ctx.GetResponse();
diff --git a/c++/src/cgi/cgictx.cpp b/c++/src/cgi/cgictx.cpp
index adefb64..315b9e4 100644
--- a/c++/src/cgi/cgictx.cpp
+++ b/c++/src/cgi/cgictx.cpp
@@ -1,4 +1,4 @@
-/* $Id: cgictx.cpp 465070 2015-04-16 16:48:33Z ivanov $
+/* $Id: cgictx.cpp 464979 2015-04-15 18:52:49Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -776,6 +776,8 @@ bool CCgiContext::ProcessCORSRequest(const CCgiRequest& request,
if ( !max_age.empty() ) {
response.SetHeaderValue(kAC_MaxAge, max_age);
}
+ response.DisableTrackingCookie();
+ response.RemoveHeaderValue("NCBI-PHID");
response.WriteHeader();
// This was CORS preflight request (valid or not) - skip normap processing.
return true;
diff --git a/c++/src/cgi/ncbicgi.cpp b/c++/src/cgi/ncbicgi.cpp
index 0fb960d..3485a84 100644
--- a/c++/src/cgi/ncbicgi.cpp
+++ b/c++/src/cgi/ncbicgi.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbicgi.cpp 443818 2014-08-19 18:05:44Z ivanov $
+/* $Id: ncbicgi.cpp 464189 2015-04-06 18:54:37Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1230,7 +1230,7 @@ void CCgiRequest::x_SetClientIpProperty(TFlags flags) const
void CCgiRequest::x_SetPageHitId(TFlags flags)
{
CRequestContext& rctx = CDiagContext::GetRequestContext();
- if ( rctx.IsSetExplicitHitID() ) {
+ if ( rctx.IsSetHitID(CRequestContext::eHitID_Request) ) {
return;
}
if ((flags & fIgnorePageHitId) == 0) {
diff --git a/c++/src/cgi/ncbicgir.cpp b/c++/src/cgi/ncbicgir.cpp
index d111cb0..e2b891d 100644
--- a/c++/src/cgi/ncbicgir.cpp
+++ b/c++/src/cgi/ncbicgir.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbicgir.cpp 446388 2014-09-15 17:56:27Z ivanov $
+/* $Id: ncbicgir.cpp 483517 2015-11-02 14:43:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -115,7 +115,7 @@ class CCgiStreamWrapper : public CWStream
{
public:
CCgiStreamWrapper(CNcbiOstream* out)
- : CWStream(new CCgiStreamWrapperWriter, 0, 0, CRWStreambuf::fOwnWriter),
+ : CWStream(new CCgiStreamWrapperWriter, 1, 0, CRWStreambuf::fOwnWriter),
m_Output(out),
m_OldBuf(0),
m_NewBuf(rdbuf())
@@ -162,6 +162,7 @@ CCgiResponse::CCgiResponse(CNcbiOstream* os, int ofd)
m_Output(NULL),
m_OutputFD(0),
m_HeaderWritten(false),
+ m_RequireWriteHeader(true),
m_RequestMethod(CCgiRequest::eMethod_Other),
m_Session(NULL),
m_DisableTrackingCookie(false)
@@ -339,8 +340,10 @@ CNcbiOstream& CCgiResponse::WriteHeader(CNcbiOstream& os) const
if (m_HeaderWritten) {
NCBI_THROW(CCgiResponseException, eDoubleHeader,
"CCgiResponse::WriteHeader() -- called more than once");
- } else
+ }
+ else {
m_HeaderWritten = true;
+ }
}
// HTTP status line (if "raw CGI" response)
@@ -493,6 +496,10 @@ CNcbiOstream& CCgiResponse::WriteHeader(CNcbiOstream& os) const
void CCgiResponse::Finalize(void) const
{
+ if (m_RequireWriteHeader && !m_HeaderWritten) {
+ ERR_POST_X(5, "CCgiResponse::WriteHeader() has not been called - "
+ "HTTP header can be missing.");
+ }
if (!m_JQuery_Callback.empty() && m_Output && m_HeaderWritten) {
*m_Output << ')';
}
@@ -628,4 +635,14 @@ void CCgiResponse::InitCORSHeaders(const string& /*origin*/,
}
+void CCgiResponse::SetRetryContext(const CRetryContext& ctx)
+{
+ CRetryContext::TValues values;
+ ctx.GetValues(values);
+ ITERATE(CRetryContext::TValues, it, values) {
+ SetHeaderValue(it->first, it->second);
+ }
+}
+
+
END_NCBI_SCOPE
diff --git a/c++/src/cgi/user_agent.cpp b/c++/src/cgi/user_agent.cpp
index 282d0be..60b99c6 100644
--- a/c++/src/cgi/user_agent.cpp
+++ b/c++/src/cgi/user_agent.cpp
@@ -1,4 +1,4 @@
-/* $Id: user_agent.cpp 466744 2015-05-06 12:24:35Z ivanov $
+/* $Id: user_agent.cpp 466541 2015-05-04 14:38:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/Makefile.connect.lib b/c++/src/connect/Makefile.connect.lib
index e96762a..0d49408 100644
--- a/c++/src/connect/Makefile.connect.lib
+++ b/c++/src/connect/Makefile.connect.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.connect.lib 427428 2014-02-20 13:41:02Z gouriano $
+# $Id: Makefile.connect.lib 466062 2015-04-28 18:05:57Z lavr $
SRC_C = ncbi_ansi_ext ncbi_buffer ncbi_types ncbi_priv ncbi_core ncbi_util \
ncbi_socket ncbi_connutil ncbi_connection ncbi_connector \
@@ -15,6 +15,6 @@ PROJ_TAG = core mod_loadinfo
LIBS = $(NETWORK_LIBS) $(ORIG_C_LIBS)
+USES_LIBRARIES = $(NETWORK_LIBS) $(ORIG_LIBS)
+
WATCHERS = lavr
-USES_LIBRARIES = \
- $(NETWORK_LIBS) $(ORIG_LIBS)
diff --git a/c++/src/connect/Makefile.connect.lib.unix b/c++/src/connect/Makefile.connect.lib.unix
index 8fa222d..b391268 100644
--- a/c++/src/connect/Makefile.connect.lib.unix
+++ b/c++/src/connect/Makefile.connect.lib.unix
@@ -1,15 +1,27 @@
-# $Id: Makefile.connect.lib.unix 464345 2015-04-08 18:16:26Z ivanov $
+# $Id: Makefile.connect.lib.unix 468572 2015-05-26 16:26:11Z ucko $
# Adjust ICC flags to avoid problematic references to
# __intel_sse2_str* functions (as of ICC [20]13)
ifeq "$(COMPILER)-$(DEBUG_SFX)$(DLL)" "icc-Release"
- strcspn=connutil ftp_connector http_connector lbsmd local server_info version
+ strcspn=ftp_connector http_connector lbsmd local server_info version
$(strcspn:%=ncbi_%.o): %.o: $(srcdir)/%.c
$(CC_WRAPPER) $(CC) $(CFLAGS_ALL) \
-fno-builtin-strcspn -fno-builtin-strspn $< -o $@ $(CC_FILTER)
+ ncbi_ansi_ext.o: $(srcdir)/ncbi_ansi_ext.c
+ $(CC_WRAPPER) $(CC) $(CFLAGS_ALL) -fno-builtin-strncat $< -o $@ \
+ $(CC_FILTER)
+
+ ncbi_connutil.o: $(srcdir)/ncbi_connutil.c
+ $(CC_WRAPPER) $(CC) $(CFLAGS_ALL) -fno-builtin-strcat \
+ -fno-builtin-strcspn -fno-builtin-strspn $< -o $@ $(CC_FILTER)
+
ncbi_service.o: $(srcdir)/ncbi_service.c
- $(CC_WRAPPER) $(CC) $(CFLAGS_ALL) -fno-builtin-strpbrk $< -o $@ \
+ $(CC_WRAPPER) $(CC) $(CFLAGS_ALL) -fno-builtin-strcat \
+ -fno-builtin-strpbrk $< -o $@ $(CC_FILTER)
+
+ ncbi_socket.o: $(srcdir)/ncbi_socket.c
+ $(CC_WRAPPER) $(CC) $(CFLAGS_ALL) -fno-builtin-strcat $< -o $@ \
$(CC_FILTER)
endif
diff --git a/c++/src/connect/Makefile.connssl.lib b/c++/src/connect/Makefile.connssl.lib
index 0d4a55e..54128cd 100644
--- a/c++/src/connect/Makefile.connssl.lib
+++ b/c++/src/connect/Makefile.connssl.lib
@@ -1,14 +1,12 @@
-# $Id: Makefile.connssl.lib 440221 2014-07-10 15:16:25Z gouriano $
+# $Id: Makefile.connssl.lib 466059 2015-04-28 18:03:44Z lavr $
SRC = ncbi_gnutls
-
LIB = connssl
CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS)
-LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS)
-WATCHERS = lavr
+LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS)
+USES_LIBRARIES = $(GCRYPT_LIBS) $(GNUTLS_LIBS) connect
-USES_LIBRARIES = \
- $(GCRYPT_LIBS) $(GNUTLS_LIBS) connect
+WATCHERS = lavr
diff --git a/c++/src/connect/Makefile.xconnect.lib.unix b/c++/src/connect/Makefile.xconnect.lib.unix
index f1983f8..ecf7aab 100644
--- a/c++/src/connect/Makefile.xconnect.lib.unix
+++ b/c++/src/connect/Makefile.xconnect.lib.unix
@@ -1,3 +1,3 @@
-# $Id: Makefile.xconnect.lib.unix 464345 2015-04-08 18:16:26Z ivanov $
+# $Id: Makefile.xconnect.lib.unix 454221 2014-12-11 18:59:10Z ucko $
include $(srcdir)/Makefile.connect.lib.unix
include $(srcdir)/Makefile.xxconnect.lib.unix
diff --git a/c++/src/connect/Makefile.xxconnect.lib.unix b/c++/src/connect/Makefile.xxconnect.lib.unix
index a999165..da44635 100644
--- a/c++/src/connect/Makefile.xxconnect.lib.unix
+++ b/c++/src/connect/Makefile.xxconnect.lib.unix
@@ -1,4 +1,4 @@
-# $Id: Makefile.xxconnect.lib.unix 464345 2015-04-08 18:16:26Z ivanov $
+# $Id: Makefile.xxconnect.lib.unix 454221 2014-12-11 18:59:10Z ucko $
ifeq "$(COMPILER)-$(DEBUG_SFX)$(DLL)" "icc-Release"
ncbi_conn_stream.o: $(srcdir)/ncbi_conn_stream.cpp
$(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL) -fno-builtin-strspn $< -o $@ \
diff --git a/c++/src/connect/_pch.cpp b/c++/src/connect/_pch.cpp
index 8aee821..6efeb38 100644
--- a/c++/src/connect/_pch.cpp
+++ b/c++/src/connect/_pch.cpp
@@ -1,4 +1,4 @@
-/* $Id: _pch.cpp 454526 2014-12-16 13:13:31Z ivanov $
+/* $Id: _pch.cpp 450657 2014-10-29 13:57:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/connection_pool.cpp b/c++/src/connect/connection_pool.cpp
index 1979238..cbec6e1 100644
--- a/c++/src/connect/connection_pool.cpp
+++ b/c++/src/connect/connection_pool.cpp
@@ -1,4 +1,4 @@
-/* $Id: connection_pool.cpp 379961 2012-11-06 19:42:09Z kazimird $
+/* $Id: connection_pool.cpp 462064 2015-03-16 14:27:31Z satskyse $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -41,6 +41,20 @@
BEGIN_NCBI_SCOPE
+std::string g_ServerConnTypeToString(enum EServerConnType conn_type)
+{
+ switch (conn_type) {
+ case eInactiveSocket: return "eInactiveSocket";
+ case eActiveSocket: return "eActiveSocket";
+ case eListener: return "eListener";
+ case ePreDeferredSocket: return "ePreDeferredSocket";
+ case eDeferredSocket: return "eDeferredSocket";
+ case ePreClosedSocket: return "ePreClosedSocket";
+ case eClosedSocket: return "eClosedSocket";
+ }
+ return "UnknownServerConnType";
+}
+
// CServer_ControlConnection
CStdRequest* CServer_ControlConnection::CreateRequest(
@@ -186,7 +200,11 @@ void CServer_ConnectionPool::CloseConnection(TConnBase* conn)
if (conn->type != eActiveSocket && conn->type != ePreDeferredSocket
&& conn->type != ePreClosedSocket)
{
- abort();
+ ERR_POST(Critical << "Unexpected connection type (" <<
+ g_ServerConnTypeToString(conn->type) <<
+ ") when closing the connection. Ignore and continue.");
+ conn->type_lock.Unlock();
+ return;
}
conn->type = ePreClosedSocket;
conn->type_lock.Unlock();
diff --git a/c++/src/connect/ncbi_ansi_ext.c b/c++/src/connect/ncbi_ansi_ext.c
index a7a7fee..0a5af93 100644
--- a/c++/src/connect/ncbi_ansi_ext.c
+++ b/c++/src/connect/ncbi_ansi_ext.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_ansi_ext.c 378137 2012-10-18 13:12:18Z lavr $
+/* $Id: ncbi_ansi_ext.c 451610 2014-11-07 21:00:36Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -178,7 +178,7 @@ char* NCBI_simple_ftoa(char* s, double f, int p)
x = (long)(v + 0.5 / w);
y = (long)(w * (v - x) + 0.5);
assert(p || !y); /* with precision 0, output of "0" is empty */
- return s + sprintf(s, "-%ld%s%.*lu" + !(f < 0.0), x, &"."[!p], p, y);
+ return s + sprintf(s, &"-%ld%s%.*lu"[!(f < 0.0)], x, &"."[!p], p, y);
}
diff --git a/c++/src/connect/ncbi_assert.h b/c++/src/connect/ncbi_assert.h
index 4009a85..e0bacae 100644
--- a/c++/src/connect/ncbi_assert.h
+++ b/c++/src/connect/ncbi_assert.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_ASSERT__H
#define CONNECT___NCBI_ASSERT__H
-/* $Id: ncbi_assert.h 150242 2009-01-22 17:56:37Z gouriano $
+/* $Id: ncbi_assert.h 450208 2014-10-23 15:47:44Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,7 +26,7 @@
*
* ===========================================================================
*
- * Author: Anton Lavrentiev
+ * Author: Denis Vakatov
*
* File Description:
* Run-time debugging
@@ -41,9 +41,11 @@
#if !defined(NDEBUG) && !defined(_DEBUG)
# define NDEBUG
#endif
+
#include <assert.h>
+
#if defined(NDEBUG)
-# define verify(expr) (void)(expr)
+# define verify(expr) while ( expr ) break
#else
# define verify(expr) assert(expr)
#endif
diff --git a/c++/src/connect/ncbi_buffer.c b/c++/src/connect/ncbi_buffer.c
index 28d0460..c2de9c4 100644
--- a/c++/src/connect/ncbi_buffer.c
+++ b/c++/src/connect/ncbi_buffer.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_buffer.c 442195 2014-07-31 02:11:16Z mcelhany $
+/* $Id: ncbi_buffer.c 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -105,6 +105,7 @@ static SBufChunk* s_AllocChunk(size_t data_size, size_t chunk_size)
size_t alloc_size = ((data_size + chunk_size - 1)
/ chunk_size) * chunk_size;
SBufChunk* chunk = (SBufChunk*) malloc(sizeof(*chunk) + alloc_size);
+ assert(!data_size == !alloc_size);
if (!chunk)
return 0;
@@ -235,6 +236,7 @@ extern int/*bool*/ BUF_Write(BUF* buf, const void* src, size_t size)
SBufChunk* next;
if (!(next = s_AllocChunk(size, (*buf)->unit)))
return 0/*false*/;
+ assert(next->data);
memcpy(next->data, (const char*) src + pending, size);
next->size = size;
next->next = 0;
@@ -261,7 +263,7 @@ extern int/*bool*/ BUF_Write(BUF* buf, const void* src, size_t size)
}
-extern int/*bool*/ BUF_PushBack(BUF* buf, const void* src, size_t size)
+extern int/*bool*/ BUF_Pushback(BUF* buf, const void* src, size_t size)
{
SBufChunk* head;
void* dst;
@@ -278,11 +280,14 @@ extern int/*bool*/ BUF_PushBack(BUF* buf, const void* src, size_t size)
head = (*buf)->list;
/* allocate and link a new chunk at the beginning of the chunk list */
- if (!head || !head->extent || head->skip < size) {
+ if (!head || !head->extent || size > head->skip) {
size_t skip = head && head->extent ? head->skip : 0;
SBufChunk* next = head;
- if (!(head = s_AllocChunk(size -= skip, (*buf)->unit)))
+ size -= skip;
+ assert(size);
+ if (!(head = s_AllocChunk(size, (*buf)->unit)))
return 0/*false*/;
+ assert(head->data);
if (skip) {
/* fill up the skip area */
memcpy(next->data, (const char*) src + size, skip);
diff --git a/c++/src/connect/ncbi_conn_reader_writer.cpp b/c++/src/connect/ncbi_conn_reader_writer.cpp
index 521d2b3..f1e1328 100644
--- a/c++/src/connect/ncbi_conn_reader_writer.cpp
+++ b/c++/src/connect/ncbi_conn_reader_writer.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_conn_reader_writer.cpp 180611 2010-01-11 20:53:47Z lavr $
+/* $Id: ncbi_conn_reader_writer.cpp 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,6 +37,20 @@
BEGIN_NCBI_SCOPE
+ERW_Result CSocketReaderWriter::Pushback(const void* buf,
+ size_t count,
+ void* del_ptr)
+{
+ if (!m_Sock.IsOwned()) {
+ ERW_Result result = x_Result(m_Sock->Pushback(buf, count));
+ if (result != eRW_Success)
+ return result;
+ }
+ delete[] (CT_CHAR_TYPE*) del_ptr;
+ return eRW_Success;
+}
+
+
ERW_Result CSocketReaderWriter::PendingCount(size_t* count)
{
static const STimeout kZero = {0, 0};
diff --git a/c++/src/connect/ncbi_conn_stream.cpp b/c++/src/connect/ncbi_conn_stream.cpp
index b3d998e..26b46be 100644
--- a/c++/src/connect/ncbi_conn_stream.cpp
+++ b/c++/src/connect/ncbi_conn_stream.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_conn_stream.cpp 450634 2014-10-28 22:10:36Z vakatov $
+/* $Id: ncbi_conn_stream.cpp 465077 2015-04-16 17:34:16Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,10 +33,12 @@
*/
#include <ncbi_pch.hpp>
-#include <corelib/ncbiapp.hpp>
+#include "ncbi_ansi_ext.h"
#include "ncbi_conn_streambuf.hpp"
+#include "ncbi_socketp.h"
+#include <corelib/ncbiapp.hpp>
#include <connect/ncbi_conn_exception.hpp>
-#define NCBI_CONN_STREAM_EXPERIMENTAL_API 1 // Pick up MS-Win DLL linkage
+#define NCBI_CONN_STREAM_EXPERIMENTAL_API 1 // Pick up MS-Win DLL linkage
#include <connect/ncbi_conn_stream.hpp>
#include <connect/ncbi_file_connector.h>
#include <connect/ncbi_socket.hpp>
@@ -60,7 +62,7 @@ CConn_IOStream::CConn_IOStream(const TConn_Pair& connpair,
CONN conn = csb->GetCONN();
if (conn) {
SOCK s/*dummy*/;
- // CONN_Write(0 bytes) could have caused the same effect as GetSOCK
+ // NB: CONN_Write(0 bytes) could have caused the same effect as GetSOCK
(void) CONN_GetSOCK(conn, &s); // Prompt CONN to actually open
if (CONN_Status(conn, eIO_Open) == eIO_Success) {
init(csb.get());
@@ -83,7 +85,7 @@ CConn_IOStream::CConn_IOStream(CONN conn, bool close,
timeout, buf_size, flags, ptr, size));
if (conn) {
SOCK s/*dummy*/;
- // CONN_Write(0 bytes) could have caused the same effect as GetSOCK
+ // NB: CONN_Write(0 bytes) could have caused the same effect as GetSOCK
(void) CONN_GetSOCK(conn, &s); // Prompt CONN to actually open
if (CONN_Status(conn, eIO_Open) == eIO_Success) {
init(csb.get());
@@ -166,7 +168,7 @@ void CConn_IOStream::x_Destroy(void)
EIO_Status CConn_IOStream::SetCanceledCallback(const ICanceled* canceled)
{
- CONN conn = GetCONN();
+ CONN conn = GET_CONN(m_CSb);
if (!conn)
return eIO_Closed;
@@ -178,13 +180,15 @@ EIO_Status CConn_IOStream::SetCanceledCallback(const ICanceled* canceled)
memset(&cb, 0, sizeof(cb));
cb.func = (FCONN_Callback) x_IsCanceled;
cb.data = this;
- CONN_SetCallback(conn, eCONN_OnRead, &cb, isset ? 0 : &m_CB[0]);
- CONN_SetCallback(conn, eCONN_OnWrite, &cb, isset ? 0 : &m_CB[1]);
- CONN_SetCallback(conn, eCONN_OnFlush, &cb, isset ? 0 : &m_CB[2]);
+ CONN_SetCallback(conn, eCONN_OnOpen, &cb, isset ? 0 : &m_CB[0]);
+ CONN_SetCallback(conn, eCONN_OnRead, &cb, isset ? 0 : &m_CB[1]);
+ CONN_SetCallback(conn, eCONN_OnWrite, &cb, isset ? 0 : &m_CB[2]);
+ CONN_SetCallback(conn, eCONN_OnFlush, &cb, isset ? 0 : &m_CB[3]);
} else if (isset) {
- CONN_SetCallback(conn, eCONN_OnFlush, &m_CB[2], 0);
- CONN_SetCallback(conn, eCONN_OnWrite, &m_CB[1], 0);
- CONN_SetCallback(conn, eCONN_OnRead, &m_CB[0], 0);
+ CONN_SetCallback(conn, eCONN_OnFlush, &m_CB[3], 0);
+ CONN_SetCallback(conn, eCONN_OnWrite, &m_CB[2], 0);
+ CONN_SetCallback(conn, eCONN_OnRead, &m_CB[1], 0);
+ CONN_SetCallback(conn, eCONN_OnOpen, &m_CB[0], 0);
m_Canceled = 0;
}
@@ -200,14 +204,16 @@ EIO_Status CConn_IOStream::x_IsCanceled(CONN conn,
CConn_IOStream* io = reinterpret_cast<CConn_IOStream*>(data);
if (/* io && */ io->m_Canceled.NotNull() && io->m_Canceled->IsCanceled())
return eIO_Interrupt;
- int n = (int) type - (int) eCONN_OnRead;
- _ASSERT(n >= 0 && (size_t) n < sizeof(io->m_CB) / sizeof(io->m_CB[0]));
- _ASSERT((n == 0 && type == eCONN_OnRead) ||
- (n == 1 && type == eCONN_OnWrite) ||
- (n == 2 && type == eCONN_OnFlush));
- if (!io->m_CB[n].func)
- return eIO_Success;
- return io->m_CB[n].func(conn, type, io->m_CB[n].data);
+ int n = (int) type & (int) eIO_ReadWrite;
+ _ASSERT(0 <= n && (size_t) n < sizeof(io->m_CB) / sizeof(io->m_CB[0]));
+ _ASSERT((n == 0 && type == eCONN_OnOpen) ||
+ (n == 1 && type == eCONN_OnRead) ||
+ (n == 2 && type == eCONN_OnWrite) ||
+ (n == 3 && type == eCONN_OnFlush));
+ return io->m_CB[n].func
+ ? io->m_CB[n].func(conn, type, io->m_CB[n].data)
+ : eIO_Success;
+
}
@@ -278,14 +284,18 @@ s_SocketConnectorBuilder(const SConnNetInfo* net_info,
flags &= ~fSOCK_LogDefault;
flags |= fSOCK_LogOn;
}
- if (*net_info->http_proxy_host && net_info->http_proxy_port) {
+ if (net_info->http_proxy_host[0] && net_info->http_proxy_port) {
status = HTTP_CreateTunnel(net_info, fHTTP_NoAutoRetry, &sock);
_ASSERT(!sock ^ !(status != eIO_Success));
if (status == eIO_Success
- && ((flags & ~(fSOCK_LogOn | fSOCK_LogDefault)) || size)) {
+ && (size || (flags & ~(fSOCK_LogOn | fSOCK_LogDefault)))) {
+ SSOCK_Init init;
+ memset(&init, 0, sizeof(init));
+ init.data = data;
+ init.size = size;
+ init.cred = net_info->credentials;
SOCK s;
- status = SOCK_CreateOnTopEx(sock, 0, &s,
- data, size, flags);
+ status = SOCK_CreateOnTopInternal(sock, 0, &s, &init, flags);
_ASSERT(!s ^ !(status != eIO_Success));
SOCK_Destroy(sock);
sock = s;
@@ -293,21 +303,24 @@ s_SocketConnectorBuilder(const SConnNetInfo* net_info,
proxy = true;
}
if (!sock && (!proxy || net_info->http_proxy_leak)) {
- const char* host = (net_info->firewall && *net_info->proxy_host
- ? net_info->proxy_host : net_info->host);
if (timeout == kDefaultTimeout)
timeout = net_info->timeout;
if (!proxy && net_info->debug_printout) {
SConnNetInfo* x_net_info = ConnNetInfo_Clone(net_info);
if (x_net_info) {
+ x_net_info->scheme = eURL_Unspec;
x_net_info->req_method = eReqMethod_Any;
+ x_net_info->firewall = 0;
x_net_info->stateless = 0;
x_net_info->lb_disable = 0;
+ x_net_info->user[0] = '\0';
+ x_net_info->pass[0] = '\0';
+ x_net_info->path[0] = '\0';
+ x_net_info->args[0] = '\0';
x_net_info->http_proxy_host[0] = '\0';
x_net_info->http_proxy_port = 0;
x_net_info->http_proxy_user[0] = '\0';
x_net_info->http_proxy_pass[0] = '\0';
- x_net_info->proxy_host[0] = '\0';
ConnNetInfo_SetUserHeader(x_net_info, 0);
if (x_net_info->http_referer) {
free((void*) x_net_info->http_referer);
@@ -318,8 +331,13 @@ s_SocketConnectorBuilder(const SConnNetInfo* net_info,
ConnNetInfo_Log(x_net_info, eLOG_Note, CORE_GetLOG());
ConnNetInfo_Destroy(x_net_info);
}
- status = SOCK_CreateEx(host, net_info->port, timeout, &sock,
- data, size, flags);
+ SSOCK_Init init;
+ memset(&init, 0, sizeof(init));
+ init.data = data;
+ init.size = size;
+ init.cred = net_info->credentials;
+ status = SOCK_CreateInternal(net_info->host, net_info->port, timeout,
+ &sock, &init, flags);
_ASSERT(!sock ^ !(status != eIO_Success));
}
string hostport(net_info->host);
@@ -383,17 +401,6 @@ CConn_SocketStream::CConn_SocketStream(CSocket& socket,
}
-static void x_SetupUserAgent(SConnNetInfo* net_info)
-{
- CNcbiApplication* theApp = CNcbiApplication::Instance();
- if (theApp) {
- string user_agent("User-Agent: ");
- user_agent += theApp->GetProgramDisplayName();
- ConnNetInfo_ExtendUserHeader(net_info, user_agent.c_str());
- }
-}
-
-
template<>
struct Deleter<SConnNetInfo>
{
@@ -404,16 +411,17 @@ struct Deleter<SConnNetInfo>
static CConn_IOStream::TConn_Pair
s_HttpConnectorBuilder(const SConnNetInfo* net_info,
+ EReqMethod method,
const char* url,
const char* host,
unsigned short port,
const char* path,
const char* args,
const char* user_header,
- FHTTP_ParseHeader parse_header,
void* user_data,
FHTTP_Adjust adjust,
FHTTP_Cleanup cleanup,
+ FHTTP_ParseHeader parse_header,
THTTP_Flags flags,
const STimeout* timeout)
{
@@ -425,6 +433,14 @@ s_HttpConnectorBuilder(const SConnNetInfo* net_info,
NCBI_THROW(CIO_Exception, eUnknown,
"CConn_HttpStream::CConn_HttpStream(): Out of memory");
}
+ if (method/*!= eReqMethod_Any*/) {
+ if (method < eReqMethod_v1)
+ x_net_info->req_method = method;
+ else if (method & ~eReqMethod_v1)
+ x_net_info->req_method = method;
+ else
+ x_net_info->version = 1;
+ }
if (url && !ConnNetInfo_ParseURL(x_net_info.get(), url)) {
NCBI_THROW(CIO_Exception, eInvalidArg,
"CConn_HttpStream::CConn_HttpStream(): Bad URL");
@@ -454,7 +470,6 @@ s_HttpConnectorBuilder(const SConnNetInfo* net_info,
}
if (user_header && *user_header)
ConnNetInfo_OverrideUserHeader(x_net_info.get(), user_header);
- x_SetupUserAgent(x_net_info.get());
if (timeout != kDefaultTimeout)
x_net_info->timeout = timeout;
CONNECTOR c = HTTP_CreateConnectorEx(x_net_info.get(),
@@ -476,21 +491,21 @@ CConn_HttpStream::CConn_HttpStream(const string& host,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_HttpConnectorBuilder(0,
+ eReqMethod_Any,
0,
host.c_str(),
port,
path.c_str(),
args.c_str(),
user_header.c_str(),
- x_ParseHeader,
this,
0,
0,
+ x_ParseHeader,
flags,
timeout),
timeout, buf_size),
- m_UserParseHeader(0), m_UserData(0), m_UserAdjust(0), m_UserCleanup(0),
- m_Code(0)
+ m_UserData(0), m_UserAdjust(0), m_UserCleanup(0), m_UserParseHeader(0)
{
return;
}
@@ -501,21 +516,48 @@ CConn_HttpStream::CConn_HttpStream(const string& url,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_HttpConnectorBuilder(0,
+ eReqMethod_Any,
url.c_str(),
0,
0,
0,
0,
0,
+ this,
+ 0,
+ 0,
x_ParseHeader,
+ flags,
+ timeout),
+ timeout, buf_size),
+ m_UserData(0), m_UserAdjust(0), m_UserCleanup(0), m_UserParseHeader(0)
+{
+ return;
+}
+
+
+CConn_HttpStream::CConn_HttpStream(const string& url,
+ EReqMethod method,
+ const string& user_header,
+ THTTP_Flags flags,
+ const STimeout* timeout,
+ size_t buf_size)
+ : CConn_IOStream(s_HttpConnectorBuilder(0,
+ method,
+ url.c_str(),
+ 0,
+ 0,
+ 0,
+ 0,
+ user_header.c_str(),
this,
0,
0,
+ x_ParseHeader,
flags,
timeout),
timeout, buf_size),
- m_UserParseHeader(0), m_UserData(0), m_UserAdjust(0), m_UserCleanup(0),
- m_Code(0)
+ m_UserData(0), m_UserAdjust(0), m_UserCleanup(0), m_UserParseHeader(0)
{
return;
}
@@ -532,22 +574,22 @@ CConn_HttpStream::CConn_HttpStream(const string& url,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_HttpConnectorBuilder(net_info,
+ eReqMethod_Any,
url.c_str(),
0,
0,
0,
0,
user_header.c_str(),
- x_ParseHeader,
this,
- adjust ? x_Adjust : 0,
+ adjust ? x_Adjust : 0,
cleanup ? x_Cleanup : 0,
+ x_ParseHeader,
flags,
timeout),
timeout, buf_size),
- m_UserParseHeader(parse_header), m_UserData(user_data),
- m_UserAdjust(adjust), m_UserCleanup(cleanup),
- m_Code(0)
+ m_UserData(user_data), m_UserAdjust(adjust),
+ m_UserCleanup(cleanup), m_UserParseHeader(parse_header)
{
return;
}
@@ -563,36 +605,43 @@ CConn_HttpStream::CConn_HttpStream(const SConnNetInfo* net_info,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_HttpConnectorBuilder(net_info,
+ eReqMethod_Any,
0,
0,
0,
0,
0,
user_header.c_str(),
- x_ParseHeader,
this,
- adjust ? x_Adjust : 0,
+ adjust ? x_Adjust : 0,
cleanup ? x_Cleanup : 0,
+ x_ParseHeader,
flags,
timeout),
timeout, buf_size),
- m_UserParseHeader(parse_header), m_UserData(user_data),
- m_UserAdjust(adjust), m_UserCleanup(cleanup),
- m_Code(0)
+ m_UserData(user_data), m_UserAdjust(adjust),
+ m_UserCleanup(cleanup), m_UserParseHeader(parse_header)
{
return;
}
-EHTTP_HeaderParse CConn_HttpStream::x_ParseHeader(const char* header,
- void* data,
- int code)
+// NB: see CConn_ServiceStream::Fetch()
+EIO_Status CConn_HttpStream::Fetch(const STimeout* timeout)
+{
+ CONN conn = GetCONN();
+ return !conn || !flush()
+ ? eIO_Unknown : CONN_Wait(conn, eIO_Read, timeout);
+}
+
+// NB: must never be upcalled (directly or indirectly) from any stream ctor
+// for SHTTP_StatusData may yet be unbuilt (and the text field invalid)!
+static EHTTP_HeaderParse s_ParseHttpHeader(const char* header,
+ SHTTP_StatusData& data)
{
- CConn_HttpStream* http = reinterpret_cast<CConn_HttpStream*>(data);
int c, n;
if (sscanf(header, "%*s %u%n", &c, &n) < 1)
return eHTTP_HeaderError;
- _ASSERT(!code || code == c);
const char* str = header + n;
str += strspn(str, " \t");
const char* eol = strchr(str, '\n');
@@ -603,11 +652,9 @@ EHTTP_HeaderParse CConn_HttpStream::x_ParseHeader(const char* header,
break;
--eol;
}
- http->m_Code = c;
- http->m_Text.assign(str, (size_t)(eol - str));
- return http->m_UserParseHeader
- ? http->m_UserParseHeader(header, http->m_UserData, code)
- : eHTTP_HeaderSuccess;
+ data.code = c;
+ data.text.assign(str, (size_t)(eol - str));
+ return eHTTP_HeaderSuccess;
}
@@ -627,13 +674,34 @@ void CConn_HttpStream::x_Cleanup(void* data)
}
+EHTTP_HeaderParse CConn_HttpStream::x_ParseHeader(const char* header,
+ void* data,
+ int code)
+{
+ CConn_HttpStream* http = reinterpret_cast<CConn_HttpStream*>(data);
+ EHTTP_HeaderParse rv = s_ParseHttpHeader(header, http->m_StatusData);
+ if (rv != eHTTP_HeaderSuccess)
+ return rv;
+ _ASSERT(!code || code == http->m_StatusData.code);
+ return http->m_UserParseHeader
+ ? http->m_UserParseHeader(header, http->m_UserData, code)
+ : eHTTP_HeaderSuccess;
+}
+
+
static CConn_IOStream::TConn_Pair
-s_ServiceConnectorBuilder(const char* service,
- TSERV_Type types,
- const SConnNetInfo* net_info,
- const char* user_header,
- const SSERVICE_Extra* params,
- const STimeout* timeout)
+s_ServiceConnectorBuilder(const char* service,
+ TSERV_Type types,
+ const SConnNetInfo* net_info,
+ const char* user_header,
+ const SSERVICE_Extra* extra,
+ CConn_ServiceStream::SSERVICE_CBData* cbdata,
+ FSERVICE_Reset reset,
+ FHTTP_Adjust adjust,
+ FSERVICE_Cleanup cleanup,
+ FHTTP_ParseHeader parse_header,
+ FSERVICE_GetNextInfo get_next_info,
+ const STimeout* timeout)
{
AutoPtr<SConnNetInfo>
x_net_info(net_info ?
@@ -645,13 +713,29 @@ s_ServiceConnectorBuilder(const char* service,
}
if (user_header && *user_header)
ConnNetInfo_OverrideUserHeader(x_net_info.get(), user_header);
- x_SetupUserAgent(x_net_info.get());
if (timeout != kDefaultTimeout)
x_net_info->timeout = timeout;
+ if (extra)
+ memcpy(&cbdata->extra, extra, sizeof(cbdata->extra));
+ else
+ memset(&cbdata->extra, 0, sizeof(cbdata->extra));
+ _ASSERT(!reset || (extra && extra->reset));
+ _ASSERT(!adjust || (extra && extra->adjust));
+ _ASSERT(!cleanup || (extra && extra->cleanup));
+ _ASSERT(!get_next_info || (extra && extra->get_next_info));
+ SSERVICE_Extra x_extra;
+ memset(&x_extra, 0, sizeof(x_extra));
+ x_extra.data = cbdata;
+ x_extra.reset = reset;
+ x_extra.adjust = adjust;
+ x_extra.cleanup = cleanup;
+ x_extra.parse_header = parse_header;
+ x_extra.get_next_info = get_next_info;
+ x_extra.flags = extra ? extra->flags : 0;
CONNECTOR c = SERVICE_CreateConnectorEx(service,
types,
x_net_info.get(),
- params);
+ &x_extra);
return CConn_IOStream::TConn_Pair(c, eIO_Unknown);
}
@@ -659,14 +743,24 @@ s_ServiceConnectorBuilder(const char* service,
CConn_ServiceStream::CConn_ServiceStream(const string& service,
TSERV_Type types,
const SConnNetInfo* net_info,
- const SSERVICE_Extra* params,
+ const SSERVICE_Extra* extra,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_ServiceConnectorBuilder(service.c_str(),
types,
net_info,
- 0,
- params,
+ 0, // user_header
+ extra,
+ &m_CBData,
+ extra && extra->reset
+ ? x_Reset : 0,
+ extra && extra->adjust
+ ? x_Adjust : 0,
+ extra && extra->cleanup
+ ? x_Cleanup : 0,
+ x_ParseHeader,
+ extra && extra->get_next_info
+ ? x_GetNextInfo : 0,
timeout),
timeout, buf_size)
{
@@ -677,14 +771,24 @@ CConn_ServiceStream::CConn_ServiceStream(const string& service,
CConn_ServiceStream::CConn_ServiceStream(const string& service,
const string& user_header,
TSERV_Type types,
- const SSERVICE_Extra* params,
+ const SSERVICE_Extra* extra,
const STimeout* timeout,
size_t buf_size)
: CConn_IOStream(s_ServiceConnectorBuilder(service.c_str(),
types,
- 0,
+ 0, //net_info
user_header.c_str(),
- params,
+ extra,
+ &m_CBData,
+ extra && extra->reset
+ ? x_Reset : 0,
+ extra && extra->adjust
+ ? x_Adjust : 0,
+ extra && extra->cleanup
+ ? x_Cleanup : 0,
+ x_ParseHeader,
+ extra && extra->get_next_info
+ ? x_GetNextInfo : 0,
timeout),
timeout, buf_size)
{
@@ -692,6 +796,69 @@ CConn_ServiceStream::CConn_ServiceStream(const string& service,
}
+// NB: see CConn_HttpStream::Fetch()
+EIO_Status CConn_ServiceStream::Fetch(const STimeout* timeout)
+{
+ CONN conn = GetCONN();
+ return !conn || !flush()
+ ? eIO_Unknown : CONN_Wait(conn, eIO_Read, timeout);
+}
+
+
+SOCK CConn_ServiceStream::GetSOCK(void)
+{
+ SOCK sock;
+ CONN conn = GetCONN();
+ if (!conn || CONN_GetSOCK(conn, &sock) != eIO_Success)
+ sock = 0;
+ return sock;
+}
+
+
+void CConn_ServiceStream::x_Reset(void* data)
+{
+ SSERVICE_CBData* cbd = static_cast<SSERVICE_CBData*>(data);
+ cbd->extra.reset(cbd->extra.data);
+}
+
+
+int/*bool*/ CConn_ServiceStream::x_Adjust(SConnNetInfo* net_info,
+ void* data,
+ unsigned int count)
+{
+ SSERVICE_CBData* cbd = static_cast<SSERVICE_CBData*>(data);
+ return cbd->extra.adjust(net_info, cbd->extra.data, count);
+}
+
+
+void CConn_ServiceStream::x_Cleanup(void* data)
+{
+ SSERVICE_CBData* cbd = static_cast<SSERVICE_CBData*>(data);
+ cbd->extra.cleanup(cbd->extra.data);
+}
+
+
+EHTTP_HeaderParse CConn_ServiceStream::x_ParseHeader(const char* header,
+ void* data, int code)
+{
+ SSERVICE_CBData* cbd = static_cast<SSERVICE_CBData*>(data);
+ EHTTP_HeaderParse rv = s_ParseHttpHeader(header, cbd->status);
+ if (rv != eHTTP_HeaderSuccess)
+ return rv;
+ _ASSERT(!code || code == cbd->status.code);
+ return cbd->extra.parse_header
+ ? cbd->extra.parse_header(header, cbd->extra.data, code)
+ : eHTTP_HeaderSuccess;
+}
+
+
+const SSERV_Info* CConn_ServiceStream::x_GetNextInfo(void* data,SERV_ITER iter)
+{
+ SSERVICE_CBData* cbd = static_cast<SSERVICE_CBData*>(data);
+ return cbd->extra.get_next_info(cbd->extra.data, iter);
+}
+
+
CConn_MemoryStream::CConn_MemoryStream(size_t buf_size)
: CConn_IOStream(TConn_Pair(MEMORY_CreateConnector(), eIO_Unknown),
kInfiniteTimeout/*0*/, buf_size),
@@ -837,8 +1004,7 @@ CConn_NamedPipeStream::CConn_NamedPipeStream(const string& pipename,
size_t pipesize,
const STimeout* timeout,
size_t buf_size)
- : CConn_IOStream(TConn_Pair(NAMEDPIPE_CreateConnector(pipename,
- pipesize),
+ : CConn_IOStream(TConn_Pair(NAMEDPIPE_CreateConnector(pipename, pipesize),
eIO_Unknown),
timeout, buf_size)
{
@@ -1065,7 +1231,7 @@ public:
};
-static bool x_IsIdentifier(const string& str)
+static bool s_IsIdentifier(const string& str)
{
const char* s = str.c_str();
if (!isalpha((unsigned char)(*s)))
@@ -1087,7 +1253,7 @@ CConn_IOStream* NcbiOpenURL(const string& url, size_t buf_size)
{
} conn_initer; /*NCBI_FAKE_WARNING*/
}
- bool svc = x_IsIdentifier(url);
+ bool svc = s_IsIdentifier(url);
AutoPtr<SConnNetInfo> net_info = ConnNetInfo_Create(svc ? url.c_str() : 0);
@@ -1096,13 +1262,13 @@ CConn_IOStream* NcbiOpenURL(const string& url, size_t buf_size)
unsigned int host;
unsigned short port;
- if (url.size() == CSocketAPI::StringToHostPort(url, &host, &port) && port
- && net_info.get()) {
+ if (url.size() == CSocketAPI::StringToHostPort(url, &host, &port)
+ && port && net_info.get()) {
net_info->req_method = eReqMethod_Connect;
}
if (ConnNetInfo_ParseURL(net_info.get(), url.c_str())) {
- _ASSERT(net_info); // otherwise ConnNetInfo_ParseURL() would fail
+ _ASSERT(net_info); // otherwise ConnNetInfo_ParseURL() would've failed
if (net_info->req_method == eReqMethod_Connect) {
return new CConn_SocketStream(*net_info, 0, 0, fSOCK_LogDefault,
net_info->timeout, buf_size);
@@ -1127,7 +1293,6 @@ CConn_IOStream* NcbiOpenURL(const string& url, size_t buf_size)
net_info->http_proxy_port = 0;
net_info->http_proxy_user[0] = '\0';
net_info->http_proxy_pass[0] = '\0';
- net_info->proxy_host[0] = '\0';
net_info->max_try = 0;
net_info->timeout = kInfiniteTimeout;
ConnNetInfo_SetUserHeader(net_info.get(), 0);
diff --git a/c++/src/connect/ncbi_conn_streambuf.cpp b/c++/src/connect/ncbi_conn_streambuf.cpp
index b9b97b5..4001359 100644
--- a/c++/src/connect/ncbi_conn_streambuf.cpp
+++ b/c++/src/connect/ncbi_conn_streambuf.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_conn_streambuf.cpp 437026 2014-06-02 19:49:11Z lavr $
+/* $Id: ncbi_conn_streambuf.cpp 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -190,7 +190,7 @@ EIO_Status CConn_Streambuf::x_Close(bool close)
EIO_Status status;
// flush only if some data pending
- if (pbase() && pptr() > pbase()) {
+ if (pbase() < pptr()) {
if ((status = CONN_Status(m_Conn, eIO_Write)) != eIO_Success) {
m_Status = status;
if (CONN_Status(m_Conn, eIO_Open) == eIO_Success) {
@@ -248,7 +248,7 @@ CT_INT_TYPE CConn_Streambuf::overflow(CT_INT_TYPE c)
return CT_EOF;
size_t n_written;
- size_t n_towrite = (size_t)(pbase() ? pptr() - pbase() : 0);
+ size_t n_towrite = (size_t)(pptr() - pbase());
if (n_towrite) {
// send buffer
@@ -300,22 +300,18 @@ CT_INT_TYPE CConn_Streambuf::overflow(CT_INT_TYPE c)
streamsize CConn_Streambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
{
- if (!m_Conn)
+ if (!m_Conn || m < 0)
return 0;
- if (m <= 0)
- return 0;
_ASSERT((Uint8) m < numeric_limits<size_t>::max());
- size_t n = (size_t) m;
-
m_Status = eIO_Success;
+ size_t n = (size_t) m;
size_t n_written = 0;
size_t x_written;
do {
- _ASSERT(n);
if (pbase()) {
- if (pbase() + n < epptr()) {
+ if (n && pbase() + n < epptr()) {
// Would entirely fit into the buffer not causing an overflow
x_written = (size_t)(epptr() - pptr());
if (x_written > n)
@@ -349,10 +345,10 @@ streamsize CConn_Streambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
}
}
- _ASSERT(n && m_Status == eIO_Success);
+ _ASSERT(m_Status == eIO_Success);
m_Status = CONN_Write(m_Conn, buf, n, &x_written, eIO_WritePlain);
_ASSERT(x_written <= n);
- if (!x_written) {
+ if (!x_written && n) {
_ASSERT(m_Status != eIO_Success);
ERR_POST_X(7, x_Message("xsputn(): "
" CONN_Write(direct) failed"));
@@ -383,7 +379,7 @@ streamsize CConn_Streambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
CT_INT_TYPE CConn_Streambuf::underflow(void)
{
- _ASSERT(!gptr() || gptr() >= egptr());
+ _ASSERT(gptr() >= egptr());
if (!m_Conn)
return CT_EOF;
@@ -427,32 +423,39 @@ streamsize CConn_Streambuf::xsgetn(CT_CHAR_TYPE* buf, streamsize m)
if (m_Tie && x_sync() != 0)
return 0;
- if (m <= 0)
+ if (m < 0)
return 0;
+
_ASSERT((Uint8) m < numeric_limits<size_t>::max());
size_t n = (size_t) m;
+ size_t n_read;
- // first, read from the memory buffer
- size_t n_read = (size_t)(gptr() ? egptr() - gptr() : 0);
- if (n_read > n)
- n_read = n;
- memcpy(buf, gptr(), n_read);
- gbump(int(n_read));
- buf += n_read;
- n -= n_read;
+ if (n) {
+ // first, read from the memory buffer
+ n_read = (size_t)(egptr() - gptr());
+ if (n_read > n)
+ n_read = n;
+ memcpy(buf, gptr(), n_read);
+ gbump(int(n_read));
+ n -= n_read;
+ if (!n)
+ return (streamsize) n_read;
+ buf += n_read;
+ } else
+ n_read = 0;
- while (n) {
+ do {
// next, read from the connection
- size_t x_toread = n < m_BufSize ? m_BufSize : n;
- CT_CHAR_TYPE* x_buf = n < m_BufSize ? m_ReadBuf : buf;
+ size_t x_toread = n && n < m_BufSize ? m_BufSize : n;
+ CT_CHAR_TYPE* x_buf = n < m_BufSize ? m_ReadBuf : buf;
size_t x_read;
m_Status = CONN_Read(m_Conn, x_buf, x_toread,
&x_read, eIO_ReadPlain);
_ASSERT(x_read <= x_toread);
if (!x_read) {
- _ASSERT(m_Status != eIO_Success);
- if (m_Status != eIO_Closed)
+ _ASSERT(!x_toread || m_Status != eIO_Success);
+ if (m_Status != eIO_Success && m_Status != eIO_Closed)
ERR_POST_X(10, x_Message("xsgetn(): CONN_Read() failed"));
break;
}
@@ -475,7 +478,7 @@ streamsize CConn_Streambuf::xsgetn(CT_CHAR_TYPE* buf, streamsize m)
break;
buf += x_read;
n -= x_read;
- }
+ } while (n);
return (streamsize) n_read;
}
@@ -485,10 +488,10 @@ streamsize CConn_Streambuf::showmanyc(void)
{
static const STimeout kZeroTmo = {0, 0};
- _ASSERT(!gptr() || gptr() >= egptr());
+ _ASSERT(gptr() >= egptr());
if (!m_Conn)
- return -1;
+ return -1L;
// flush output buffer, if tied up to it
if (m_Tie)
@@ -505,7 +508,7 @@ streamsize CConn_Streambuf::showmanyc(void)
size_t x_read;
bool backup = false;
if (m_BufSize > 1) {
- if (eback() && gptr() > eback()) {
+ if (eback() < gptr()) {
x_Buf = gptr()[-1];
backup = true;
}
@@ -525,17 +528,17 @@ streamsize CConn_Streambuf::showmanyc(void)
switch (m_Status) {
case eIO_Success:
_ASSERT(m_BufSize <= 1);
- return 1; // can read at least 1 byte
+ return 1L; // can read at least 1 byte
case eIO_Timeout:
if (!tmo || !(tmo->sec | tmo->usec))
break;
/*FALLTHRU*/
case eIO_Closed:
- return -1; // EOF
+ return -1L; // EOF
default:
break;
}
- return 0; // no data available immediately
+ return 0; // no data available immediately
}
m_ReadBuf[0] = x_Buf;
@@ -550,7 +553,7 @@ int CConn_Streambuf::sync(void)
{
if (CT_EQ_INT_TYPE(overflow(CT_EOF), CT_EOF))
return -1;
- _ASSERT(!pbase() || pbase() == pptr());
+ _ASSERT(pbase() == pptr());
return 0;
}
@@ -572,9 +575,9 @@ CT_POS_TYPE CConn_Streambuf::seekoff(CT_OFF_TYPE off,
// tellp()/tellg() support only
switch (which) {
case IOS_BASE::out:
- return x_PPos + (CT_OFF_TYPE)(pbase() ? pptr() - pbase() : 0);
+ return x_PPos + (CT_OFF_TYPE)(pptr() - pbase());
case IOS_BASE::in:
- return x_GPos - (CT_OFF_TYPE)(gptr() ? egptr() - gptr() : 0);
+ return x_GPos - (CT_OFF_TYPE)(egptr() - gptr());
default:
break;
}
diff --git a/c++/src/connect/ncbi_conn_streambuf.hpp b/c++/src/connect/ncbi_conn_streambuf.hpp
index 5a2ee6f..77df368 100644
--- a/c++/src/connect/ncbi_conn_streambuf.hpp
+++ b/c++/src/connect/ncbi_conn_streambuf.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONN_STREAMBUF__HPP
#define CONNECT___NCBI_CONN_STREAMBUF__HPP
-/* $Id: ncbi_conn_streambuf.hpp 424667 2014-01-17 22:34:51Z lavr $
+/* $Id: ncbi_conn_streambuf.hpp 463569 2015-03-30 16:23:11Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -96,7 +96,7 @@ protected:
protected:
int x_sync(void)
- { return pbase() && pptr() > pbase() ? sync() : 0; }
+ { return pbase() < pptr() ? sync() : 0; }
private:
CONN m_Conn; // underlying connection handle
diff --git a/c++/src/connect/ncbi_conn_test.cpp b/c++/src/connect/ncbi_conn_test.cpp
index 6302764..ed588e6 100644
--- a/c++/src/connect/ncbi_conn_test.cpp
+++ b/c++/src/connect/ncbi_conn_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_conn_test.cpp 434797 2014-05-11 17:54:30Z lavr $
+/* $Id: ncbi_conn_test.cpp 465077 2015-04-16 17:34:16Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -215,6 +215,17 @@ static EHTTP_HeaderParse s_AnyHeader(const char* /*header*/,
}
+static EHTTP_HeaderParse s_GoodHeader(const char* /*header*/,
+ void* data, int server_error)
+{
+ SAuxData* auxdata = reinterpret_cast<SAuxData*>(data);
+ _ASSERT(auxdata);
+ if (server_error)
+ auxdata->m_Failed = true;
+ return eHTTP_HeaderSuccess;
+}
+
+
static EHTTP_HeaderParse s_SvcHeader(const char* header,
void* data, int server_error)
{
@@ -247,7 +258,7 @@ static void s_Cleanup(void* data)
delete auxdata;
}
-}
+} // extern "C"
EIO_Status CConnTest::ExtraCheckOnFailure(void)
@@ -258,12 +269,13 @@ EIO_Status CConnTest::ExtraCheckOnFailure(void)
const char* host;
const char* vhost;
} kTests[] = {
+ // 0. NCBI default
+ { "", 0 }, // NCBI
// 1. External server(s)
{ "www.google.com", 0 },
// NB: Google's public DNS (also @8.8.8.8), responds at :80 as well
{ "8.8.4.4", "www.google.com" },
- // 2. NCBI servers
- { "www.ncbi.nlm.nih.gov", 0 }, // NCBI
+ // 2. NCBI servers, explicitly
{ "www.be-md.ncbi.nlm.nih.gov", "www.ncbi.nlm.nih.gov" }, // NCBI main
{ "www.st-va.ncbi.nlm.nih.gov", "www.ncbi.nlm.nih.gov" }, // NCBI colo
{ "130.14.29.110", "www.ncbi.nlm.nih.gov" }, // NCBI main
@@ -296,7 +308,8 @@ EIO_Status CConnTest::ExtraCheckOnFailure(void)
for (size_t n = 0; n < sizeof(kTests) / sizeof(kTests[0]); ++n) {
char user_header[80];
_ASSERT(::strlen(kTests[n].host) < sizeof(net_info->host) - 1);
- ::strcpy(net_info->host, kTests[n].host);
+ if (kTests[n].host[0])
+ ::strcpy(net_info->host, kTests[n].host);
if (kTests[n].vhost) {
_ASSERT(::strlen(kTests[n].vhost) + 6 < sizeof(user_header) - 1);
::sprintf(user_header, "Host: %s", kTests[n].vhost);
@@ -322,13 +335,17 @@ EIO_Status CConnTest::ExtraCheckOnFailure(void)
}
EIO_Status readst = CONN_Wait(conn, eIO_Read, &kTimeSlice);
if (readst > eIO_Timeout) {
+ if (readst == eIO_Interrupt) {
+ status = eIO_Interrupt;
+ break;
+ }
if (status < readst && (*h)->GetStatusCode() != 404)
status = readst;
VECTOR_ERASE(h, http);
continue;
}
}
- } while (!deadline.IsExpired());
+ } while (status != eIO_Interrupt && !deadline.IsExpired());
if (status == eIO_Success && http.size())
status = eIO_Timeout;
@@ -358,8 +375,8 @@ EIO_Status CConnTest::HttpOkay(string* reason)
? ':' + NStr::UIntToString(net_info->port)
: kEmptyStr);
SAuxData* auxdata = new SAuxData(m_Canceled, 0);
- CConn_HttpStream http("http://" + host + port + "/Service/index.html",
- net_info, kEmptyStr/*user_header*/, s_AnyHeader,
+ CConn_HttpStream http("/Service/index.html",
+ net_info, kEmptyStr/*user_header*/, s_GoodHeader,
auxdata, s_Adjust, s_Cleanup, 0/*flags*/, m_Timeout);
http.SetCanceledCallback(m_Canceled);
string temp;
@@ -402,8 +419,8 @@ EIO_Status CConnTest::HttpOkay(string* reason)
temp += "' specified with [CONN]HTTP_PROXY_{HOST|PORT} is correct";
} else {
if (net_info->http_proxy_host[0] || net_info->http_proxy_port) {
- temp += "Note that your HTTP proxy seems to have been only"
- " partially specified, and thus cannot be used: the ";
+ temp += "Note that your HTTP proxy seems to have been"
+ " specified only partially, and thus cannot be used: the ";
if (net_info->http_proxy_port) {
temp += "host part is missing (for port :"
+ NStr::UIntToString(net_info->http_proxy_port);
@@ -420,7 +437,7 @@ EIO_Status CConnTest::HttpOkay(string* reason)
}
temp += "; and if your proxy server requires authorization, please"
" check that appropriate [CONN]HTTP_PROXY_{USER|PASS} have been"
- " specified\n";
+ " set\n";
if (net_info && (*net_info->user || *net_info->pass)) {
temp += "Make sure there are no stray [CONN]{USER|PASS} that"
" appear in your configuration -- NCBI services neither"
@@ -467,7 +484,7 @@ EIO_Status CConnTest::DispatcherOkay(string* reason)
if (status != eIO_Timeout) {
if (okay) {
temp = "Make sure there are no stray [CONN]{HOST|PORT|PATH}"
- " settings on the way in your configuration\n";
+ " settings in the way in your configuration\n";
}
if (okay == 1) {
temp += "Service response was not recognized; please contact "
@@ -502,8 +519,9 @@ EIO_Status CConnTest::ServiceOkay(string* reason)
"Checking whether NCBI services operational");
CConn_ServiceStream svc(kService, fSERV_Stateless, net_info,
- 0/*params*/, m_Timeout);
+ 0/*extra*/, m_Timeout);
svc.SetCanceledCallback(m_Canceled);
+
svc << kTest << NcbiEndl;
string temp;
svc >> temp;
@@ -577,14 +595,13 @@ EIO_Status CConnTest::ServiceOkay(string* reason)
EIO_Status CConnTest::x_GetFirewallConfiguration(const SConnNetInfo* net_info)
{
- static const char kFWDUrl[] =
- "http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/fwd_check.cgi";
+ static const char kFWDUrl[] = "/IEB/ToolBox/NETWORK/fwd_check.cgi";
char fwdurl[128];
if (!ConnNetInfo_GetValue(0, "FWD_URL", fwdurl, sizeof(fwdurl), kFWDUrl))
return eIO_InvalidArg;
SAuxData* auxdata = new SAuxData(m_Canceled, 0);
- CConn_HttpStream fwdcgi(fwdurl, net_info, kEmptyStr/*usrhdr*/, s_AnyHeader,
+ CConn_HttpStream fwdcgi(fwdurl, net_info, kEmptyStr/*ushdr*/, s_GoodHeader,
auxdata, s_Adjust, s_Cleanup, 0/*flg*/, m_Timeout);
fwdcgi.SetCanceledCallback(m_Canceled);
fwdcgi << "selftest" << NcbiEndl;
@@ -672,21 +689,25 @@ EIO_Status CConnTest::GetFWConnections(string* reason)
_ASSERT(net_info);
switch (net_info->firewall) {
case eFWMode_Adaptive:
- temp += "There are also fallback connection ports such as "
+ temp += "Also, there are usually a few additional ports such as "
STRINGIFY(CONN_PORT_SSH) " and " STRINGIFY(CONN_PORT_HTTPS)
- " at " NCBI_FWD_BEMD ". They will be used if connections to"
- " the ports in the range described above have failed\n";
+ " at " NCBI_FWD_BEMD ", which can be used if connections to"
+ " the ports in the range described above, have failed\n";
break;
case eFWMode_Firewall:
- temp += "Also, your configuration explicitly forbids to use any"
- " fallback firewall ports that may exist to improve network"
- " connectivity\n";
+ temp += "Furthermore, your configuration explicitly forbids to use"
+ " any fallback firewall ports that may exist to improve"
+ " reliability of connection experience\n";
break;
case eFWMode_Fallback:
- temp += "However, your configuration explicitly requests that only"
- " fallback firewall ports (if any exist) are to be used for"
- " connections: this also implies that no conventional ports"
- " from the range above will be used\n";
+ temp += "There are usually a few backup connection ports such as "
+ STRINGIFY(CONN_PORT_SSH) " and " STRINGIFY(CONN_PORT_HTTPS)
+ " at " NCBI_FWD_BEMD ", which can be used as a failover if"
+ " connections to the port range above fail. However, your "
+ " configuration explicitly requests that only those fallback"
+ " firewall ports (if any exist) are to be used for"
+ " connections: this also implies that no conventional ports"
+ " from the default range will be used\n";
break;
default:
temp += "Internal program error, please report!\n";
@@ -694,8 +715,8 @@ EIO_Status CConnTest::GetFWConnections(string* reason)
break;
}
} else {
- temp += "This mode may not be reliable if your site has a restrictive"
- " firewall imposing fine-grained control over which hosts and"
+ temp += "This mode may not be reliable if your site has a restraining"
+ " firewall imposing a fine-grained control over which hosts and"
" ports the outbound connections are allowed to use\n";
}
if (m_HttpProxy) {
@@ -705,22 +726,10 @@ EIO_Status CConnTest::GetFWConnections(string* reason)
temp += ':';
temp += NStr::UIntToString(net_info->http_proxy_port);
temp += "'";
- if (net_info && net_info->http_proxy_leak) {
+ if (net_info->http_proxy_leak) {
temp += ". If that is unsuccessful, a link bypassing the proxy"
" will then be attempted";
}
- if (m_Firewall && *net_info->proxy_host)
- temp += ". In addition, your";
- }
- if (m_Firewall && *net_info->proxy_host) {
- if (!m_HttpProxy)
- temp += "Your";
- temp += " configuration specifies that instead of connecting directly"
- " to NCBI addresses, a forwarding non-transparent proxy host '";
- temp += net_info->proxy_host;
- temp += "' should be used for all links";
- if (m_HttpProxy)
- temp += " (including those originating from the HTTP proxy)";
}
temp += '\n';
@@ -837,7 +846,7 @@ EIO_Status CConnTest::CheckFWConnections(string* reason)
net_info->timeout = m_Timeout;
}
- SERV_InitFirewallMode();
+ SERV_InitFirewallPorts();
PreCheck(eFirewallConnections, 0/*main*/, temp);
@@ -961,8 +970,11 @@ EIO_Status CConnTest::CheckFWConnections(string* reason)
size_t k;
switch (cp->status) {
case eIO_Success:
- if (n && (net_info->firewall & eFWMode_Adaptive))
- SERV_AddFirewallPort(cp->port);
+ if (n && (net_info->firewall & eFWMode_Adaptive)
+ && !SERV_AddFirewallPort(cp->port)) {
+ m_CheckPoint = "Invalid firewall port";
+ cp->status = eIO_Unknown;
+ }
break;
case eIO_Timeout:
m_CheckPoint = "Connection timed out";
@@ -1023,18 +1035,6 @@ EIO_Status CConnTest::CheckFWConnections(string* reason)
}
temp += '\n';
}
- if (m_Firewall && *net_info->proxy_host) {
- temp += "Your non-transparent proxy '";
- temp += net_info->proxy_host;
- temp += "' may not be forwarding connections properly,"
- " please check with your network administrator"
- " that the proxy has been configured correctly";
- if (!url) {
- temp += ": " NCBI_FWDOC_URL;
- url = true;
- }
- temp += '\n';
- }
temp += "The network port required for this connection to"
" succeed may be blocked/diverted at your firewall;";
if (m_Firewall) {
@@ -1098,8 +1098,6 @@ EIO_Status CConnTest::CheckFWConnections(string* reason)
NCBI_FWDOC_URL;
}
} else {
- if (m_Firewall)
- SERV_AddFirewallPort(0);
temp = "All " + string(m_Firewall
? "firewall port(s)"
: "service entry point(s)") + " checked OK";
@@ -1144,12 +1142,12 @@ EIO_Status CConnTest::StatefulOkay(string* reason)
size_t size = rnd(2, (sizeof(buf) - (8 + 1)) >> 3);
size_t i;
- for (i = 1; i < size; i++)
+ for (i = 1; i < size; ++i)
sprintf(buf + (i << 3), "%08X", (unsigned int) rand());
memset(&buf[size <<= 3], 0, 8);
size += 8;
- CConn_ServiceStream echo(kEcho, fSERV_Any, net_info, 0, m_Timeout);
+ CConn_ServiceStream echo(kEcho, fSERV_Any, net_info, 0/*xtra*/, m_Timeout);
echo.SetCanceledCallback(m_Canceled);
streamsize n = 0;
@@ -1221,9 +1219,8 @@ EIO_Status CConnTest::StatefulOkay(string* reason)
} else if (m_Fwd.empty() && net_info
&& net_info->firewall != eFWMode_Fallback) {
temp += "The most likely reason for the failure is that"
- " your ";
- temp += *net_info->proxy_host ? "forwarder" : "firewall";
- temp += " is still blocking ports as reported above\n";
+ " your firewall is still blocking ports as reported"
+ " above\n";
} else if (status != eIO_Timeout || m_Timeout > kTimeout)
temp += "Please contact " + HELP_EMAIL + '\n';
SERV_Close(iter);
@@ -1239,11 +1236,6 @@ EIO_Status CConnTest::StatefulOkay(string* reason)
temp += net_info->http_proxy_host;
temp += ':';
temp += NStr::UIntToString(net_info->http_proxy_port);
- if ((m_Firewall || net_info->firewall)
- && *net_info->proxy_host) {
- temp += "' and/or connection forwarder '";
- temp += net_info->proxy_host;
- }
temp += "' may be buggy."
" Please see your network administrator\n";
} else {
@@ -1378,7 +1370,7 @@ EIO_Status CConnTest::x_CheckTrap(string* reason)
bool CConnTest::IsNcbiInhouseClient(void)
{
static const STimeout kFast = { 2, 0 };
- CConn_HttpStream http("http://www.ncbi.nlm.nih.gov/Service/getenv.cgi",
+ CConn_HttpStream http("/Service/getenv.cgi",
fHTTP_KeepHeader | fHTTP_NoAutoRetry, &kFast);
char line[1024];
if (!http || !http.getline(line, sizeof(line)))
diff --git a/c++/src/connect/ncbi_connection.c b/c++/src/connect/ncbi_connection.c
index 158a015..23f2dc4 100644
--- a/c++/src/connect/ncbi_connection.c
+++ b/c++/src/connect/ncbi_connection.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_connection.c 425989 2014-02-05 03:56:43Z lavr $
+/* $Id: ncbi_connection.c 463881 2015-04-01 21:51:06Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -170,20 +170,51 @@ typedef struct SConnectionTag {
} SConnection;
+static size_t x_CB2IDX(ECONN_Callback type)
+{
+ size_t idx;
+ switch (type) {
+ case eCONN_OnClose:
+ idx = 0;
+ break;
+ case eCONN_OnRead:
+ idx = 1;
+ break;
+ case eCONN_OnWrite:
+ idx = 2;
+ break;
+ case eCONN_OnFlush:
+ idx = 3;
+ break;
+ case eCONN_OnTimeout:
+ idx = 4;
+ break;
+ case eCONN_OnOpen:
+ idx = 5;
+ break;
+ default:
+ idx = CONN_N_CALLBACKS;
+ break;
+ }
+ return idx;
+}
+
+
static EIO_Status x_Callback(CONN conn, ECONN_Callback type, unsigned int flag)
{
- EIO_Status status;
+ size_t idx = x_CB2IDX(type);
FCONN_Callback func;
void* data;
+ EIO_Status status;
assert(!flag || (type == eCONN_OnTimeout
&& (flag | eIO_ReadWrite) == eIO_ReadWrite));
- assert(conn && (int) type >= 0 && (int) type < CONN_N_CALLBACKS);
+ assert(conn && idx < CONN_N_CALLBACKS);
if (conn->state == eCONN_Unusable)
return eIO_Closed;
- if (!(func = conn->cb[type].func))
+ if (!(func = conn->cb[idx].func))
return type == eCONN_OnTimeout ? eIO_Timeout : eIO_Success;
- data = conn->cb[type].data;
+ data = conn->cb[idx].data;
status = (*func)(conn, (TCONN_Callback) type | flag, data);
if (status == eIO_Interrupt)
conn->state = eCONN_Cancel;
@@ -305,7 +336,7 @@ static EIO_Status x_ReInit(CONN conn, CONNECTOR connector, int/*bool*/ close)
static EIO_Status s_Open(CONN conn)
{
- const STimeout* timeout;
+ const STimeout* timeout = 0;
EIO_Status status;
switch (conn->state) {
@@ -319,28 +350,35 @@ static EIO_Status s_Open(CONN conn)
break;
}
assert(conn->state == eCONN_Closed && conn->meta.list);
+ conn->r_pos = 0;
+ conn->w_pos = 0;
- /* call current connector's "OPEN" method */
if (conn->meta.open) {
- timeout = (conn->o_timeout == kDefaultTimeout
- ? conn->meta.default_timeout
- : conn->o_timeout);
- status = conn->meta.open(conn->meta.c_open, timeout);
- } else {
- status = eIO_NotSupported;
- timeout = 0/*dummy*/;
- }
-
+ /* call current connector's "OPEN" method */
+ int/*bool*/ nocb = !conn->cb[x_CB2IDX(eCONN_OnOpen)].func;
+ if ((status = x_Callback(conn, eCONN_OnOpen, 0)) == eIO_Success) {
+ timeout = (conn->o_timeout == kDefaultTimeout
+ ? conn->meta.default_timeout
+ : conn->o_timeout);
+ status = conn->meta.open(conn->meta.c_open, timeout);
+ /* OnTimeout gets called only if OnOpen was there */
+ if (status == eIO_Timeout && !nocb) {
+ status = x_Callback(conn, eCONN_OnTimeout, eIO_Open);
+ if (status == eIO_Success)
+ status = eIO_Timeout;
+ }
+ }
+ } else
+ status = eIO_NotSupported;
if (status == eIO_Success) {
- conn->r_pos = 0;
- conn->w_pos = 0;
conn->flags &= ~fCONN_Flush;
conn->r_status = eIO_Success;
conn->w_status = eIO_Success;
conn->state = eCONN_Open;
} else {
CONN_LOG(5, Open, eLOG_Error, "Failed to open connection");
- conn->state = eCONN_Bad;
+ if (conn->state == eCONN_Closed)
+ conn->state = eCONN_Bad;
}
return status;
}
@@ -730,12 +768,12 @@ extern EIO_Status CONN_Write
}
-extern EIO_Status CONN_PushBack
+extern EIO_Status CONN_Pushback
(CONN conn,
const void* buf,
size_t size)
{
- CONN_NOT_NULL(19, PushBack);
+ CONN_NOT_NULL(19, Pushback);
if (conn->state == eCONN_Unusable)
return eIO_InvalidArg;
@@ -746,7 +784,7 @@ extern EIO_Status CONN_PushBack
if (!conn->meta.read)
return eIO_NotSupported;
- return BUF_PushBack(&conn->buf, buf, size) ? eIO_Success : eIO_Unknown;
+ return BUF_Pushback(&conn->buf, buf, size) ? eIO_Success : eIO_Unknown;
}
@@ -1005,7 +1043,7 @@ extern EIO_Status CONN_ReadLine
}
if (i < x_read) {
assert(done || len >= size);
- if (!BUF_PushBack(&conn->buf, x_buf + i, x_read - i)) {
+ if (!BUF_Pushback(&conn->buf, x_buf + i, x_read - i)) {
static const STimeout* timeout = 0/*dummy*/;
CONN_LOG_EX(35, ReadLine, eLOG_Critical,
"Cannot pushback extra data", 0);
@@ -1082,23 +1120,23 @@ extern EIO_Status CONN_SetCallback
const SCONN_Callback* newcb,
SCONN_Callback* oldcb)
{
- int i;
+ size_t idx;
CONN_NOT_NULL(28, SetCallback);
-
- if ((i = (int) type) >= CONN_N_CALLBACKS) {
+
+ if ((idx = x_CB2IDX(type)) >= CONN_N_CALLBACKS) {
static const STimeout* timeout = 0/*dummy*/;
char errbuf[80];
- sprintf(errbuf, "Unknown callback type #%u", (unsigned int) i);
+ sprintf(errbuf, "Unknown callback type #%u", (unsigned int) type);
CONN_LOG_EX(29, SetCallback, eLOG_Error, errbuf, eIO_InvalidArg);
return eIO_InvalidArg;
}
/* NB: oldcb and newcb may point to the same address */
if (newcb || oldcb) {
- SCONN_Callback cb = conn->cb[i];
+ SCONN_Callback cb = conn->cb[idx];
if (newcb)
- conn->cb[i] = *newcb;
+ conn->cb[idx] = *newcb;
if (oldcb)
*oldcb = cb;
}
@@ -1155,5 +1193,5 @@ extern TCONN_Flags CONN_GetFlags(CONN conn)
{
CONN_CALLTRACE(GetFlags);
- return conn ? 0 : conn->flags & ~fCONN_Flush;
+ return conn ? conn->flags & ~fCONN_Flush : 0;
}
diff --git a/c++/src/connect/ncbi_connssl.h b/c++/src/connect/ncbi_connssl.h
index 2bfd0a9..7ae0ec2 100644
--- a/c++/src/connect/ncbi_connssl.h
+++ b/c++/src/connect/ncbi_connssl.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_CONNSSL__H
#define CONNECT___NCBI_CONNSSL__H
-/* $Id: ncbi_connssl.h 422228 2013-12-18 19:55:01Z lavr $
+/* $Id: ncbi_connssl.h 466061 2015-04-28 18:05:33Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -83,7 +83,7 @@ typedef EIO_Status (*FSSLPush) (SOCK sock, const void* data, size_t size,
typedef EIO_Status (*FSSLInit) (FSSLPull pull, FSSLPush push);
typedef void* (*FSSLCreate)(ESOCK_Side side, SOCK sock,
NCBI_CRED cred, int* error);
-typedef EIO_Status (*FSSLOpen) (void* session, int* error);
+typedef EIO_Status (*FSSLOpen) (void* session, int* error, char** desc);
/* See FSSLPull for behavior. When non-eIO_Success code gets returned,
* the call must set "*error" to indicate specific problem. The "*error" may
diff --git a/c++/src/connect/ncbi_connutil.c b/c++/src/connect/ncbi_connutil.c
index 883729a..49314c5 100644
--- a/c++/src/connect/ncbi_connutil.c
+++ b/c++/src/connect/ncbi_connutil.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_connutil.c 434037 2014-05-01 20:14:52Z lavr $
+/* $Id: ncbi_connutil.c 468423 2015-05-22 16:08:55Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -264,9 +264,9 @@ static EFWMode x_ParseFirewall(const char* str, int/*bool*/ generic)
unsigned short port;
if (sscanf(str, "%hu%n", &port, &n) < 1 || !port)
break;
- str += n;
if (generic)
SERV_AddFirewallPort(port);
+ str += n;
if (!*(str += strspn(str, " \t")))
return eFWMode_Fallback;
}
@@ -289,7 +289,7 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
/* aux. storage */
char str[1024];
size_t len;
- int val;
+ long val;
double dbl;
char* e;
@@ -298,6 +298,7 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
/* NB: *NOT* cleared up with all 0s */
if (!(info = (SConnNetInfo*) malloc(sizeof(*info) + len)))
return 0/*failure*/;
+ info->reserved = 0/*MBZ*/;
/* client host: default */
info->client_host[0] = '\0';
@@ -322,21 +323,21 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
REG_VALUE(REG_CONN_FIREWALL, str, DEF_CONN_FIREWALL);
info->firewall = x_ParseFirewall(str, generic);
- /* stateless client? */
+ /* stateless client */
REG_VALUE(REG_CONN_STATELESS, str, DEF_CONN_STATELESS);
info->stateless = ConnNetInfo_Boolean(str);
- /* prohibit use of the local load balancer? */
+ /* prohibit use of the local load balancer */
REG_VALUE(REG_CONN_LB_DISABLE, str, DEF_CONN_LB_DISABLE);
info->lb_disable = ConnNetInfo_Boolean(str);
- /* turn on debug printout? */
+ /* level of debug printout */
REG_VALUE(REG_CONN_DEBUG_PRINTOUT, str, DEF_CONN_DEBUG_PRINTOUT);
if (ConnNetInfo_Boolean(str)
|| (*str && strcasecmp(str, "some") == 0)) {
info->debug_printout = eDebugPrintout_Some;
- } else if (*str && (strcasecmp(str, "all") == 0 ||
- strcasecmp(str, "data") == 0)) {
+ } else if (*str && (strcasecmp(str, "data") == 0 ||
+ strcasecmp(str, "all") == 0)) {
info->debug_printout = eDebugPrintout_Data;
} else
info->debug_printout = eDebugPrintout_None;
@@ -355,7 +356,7 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
errno = 0;
if (*str && (val = strtoul(str, &e, 10)) > 0 && !errno
&& !*e && val < (1 << 16)) {
- info->port = val;
+ info->port = (unsigned short) val;
} else
info->port = 0/*default*/;
@@ -365,18 +366,17 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
/* args */
REG_VALUE(REG_CONN_ARGS, info->args, DEF_CONN_ARGS);
- /* HTTP proxy server? */
+ /* HTTP proxy server */
REG_VALUE(REG_CONN_HTTP_PROXY_HOST, info->http_proxy_host,
DEF_CONN_HTTP_PROXY_HOST);
- if (*info->http_proxy_host) {
- /* yes, use the specified HTTP proxy server */
+ if (info->http_proxy_host[0]) {
REG_VALUE(REG_CONN_HTTP_PROXY_PORT, str, DEF_CONN_HTTP_PROXY_PORT);
errno = 0;
if (*str && (val = strtoul(str, &e, 10)) > 0
&& !errno && !*e && val < (1 << 16)) {
- info->http_proxy_port = val;
+ info->http_proxy_port = (unsigned short) val;
} else
- info->http_proxy_port = 0/*none*/;
+ info->http_proxy_port = 0/*none*/;
/* HTTP proxy username */
REG_VALUE(REG_CONN_HTTP_PROXY_USER, info->http_proxy_user,
DEF_CONN_HTTP_PROXY_USER);
@@ -393,8 +393,9 @@ extern SConnNetInfo* ConnNetInfo_Create(const char* service)
info->http_proxy_leak = 0;
}
- /* non-transparent CERN-like firewall proxy server? */
- REG_VALUE(REG_CONN_PROXY_HOST, info->proxy_host, DEF_CONN_PROXY_HOST);
+ /* push HTTP auth tags */
+ REG_VALUE(REG_CONN_HTTP_PUSH_AUTH, str, DEF_CONN_HTTP_PUSH_AUTH);
+ info->http_push_auth = ConnNetInfo_Boolean(str);
/* max. # of attempts to establish connection */
REG_VALUE(REG_CONN_MAX_TRY, str, 0);
@@ -475,12 +476,17 @@ extern int/*bool*/ ConnNetInfo_ParseURL(SConnNetInfo* info, const char* url)
}
/* "user:pass at host:port" first [any optional] */
- if ((s = strstr(url, "://")) != 0) {
- len = (size_t)(s - url);
- if ((scheme = x_ParseScheme(url, len)) == eURL_Unspec)
- return 0/*failure*/;
-
- host = s + 3;
+ if ((s = strstr(url, "//")) != 0) {
+ /* scheme is now optional, too */
+ if (s > url) {
+ if (s[-1] != ':')
+ return 0/*failure*/;
+ len = (size_t)(s - url) - 1;
+ if ((scheme = x_ParseScheme(url, len)) == eURL_Unspec)
+ return 0/*failure*/;
+ } else
+ scheme = (EURLScheme) info->scheme;
+ host = s + 2;
hostlen = strcspn(host, "/?#");
path = host + hostlen;
@@ -1170,7 +1176,7 @@ static const char* x_ReqMethod(TReqMethod req_method, char buf[])
default:
break;
}
- return x_Num(req_method, buf);
+ return buf ? x_Num(req_method, buf) : 0;
}
@@ -1334,7 +1340,6 @@ extern void ConnNetInfo_Log(const SConnNetInfo* info, ELOG_Level sev, LOG lg)
} else
s_SaveString(s, "http_proxy_pass", info->http_proxy_pass);
s_SaveBool (s, "http_proxy_leak", info->http_proxy_leak);
- s_SaveString (s, "proxy_host", info->proxy_host);
s_SaveULong (s, "max_try", info->max_try);
if (info->timeout) {
s_SaveULong (s, "timeout(sec)", info->timeout->sec);
@@ -1354,6 +1359,7 @@ extern void ConnNetInfo_Log(const SConnNetInfo* info, ELOG_Level sev, LOG lg)
== eDebugPrintout_Data
? "DATA"
: x_Num(info->debug_printout,buf)));
+ s_SaveBool (s, "http_push_auth", info->http_push_auth);
s_SaveUserHeader(s, "http_user_header",info->http_user_header, uhlen);
s_SaveString (s, "http_referer", info->http_referer);
if (info->credentials)
@@ -1382,9 +1388,10 @@ extern char* ConnNetInfo_URL(const SConnNetInfo* info)
req_method = info->req_method & ~eReqMethod_v1;
scheme = x_Scheme((EURLScheme) info->scheme, buf);
+ assert(!scheme || *scheme);
if ((!scheme && req_method != eReqMethod_Connect) ||
( scheme && !isalpha((unsigned char)(*scheme)))) {
- return 0/*failed*/;
+ return 0/*failure*/;
}
if (req_method == eReqMethod_Connect) {
@@ -1407,7 +1414,7 @@ extern char* ConnNetInfo_URL(const SConnNetInfo* info)
assert(scheme && args);
strlwr((char*) memcpy(url, scheme, schlen + 1));
len = schlen;
- len += sprintf(url + len, "://%s" + (schlen ? 0 : 3), info->host);
+ len += sprintf(url + len, &"://%s"[schlen ? 0 : 3], info->host);
if (info->port || !path/*req_method == eReqMethod_Connect*/)
len += sprintf(url + len, ":%hu", info->port);
sprintf(url + len, "%s%s%s%s",
@@ -1476,21 +1483,19 @@ extern EIO_Status URL_ConnectEx
TSOCK_Flags flags,
SOCK* sock)
{
- static const char* kHttp[] = { " HTTP/1.0\r\n",
- " HTTP/1.1\r\n" };
- static const char kHost[] = "Host: ";
+ static const char kHttp[][12] = { " HTTP/1.0\r\n",
+ " HTTP/1.1\r\n" };
SOCK s;
BUF buf;
char* hdr;
- unsigned ver;
+ const char* str;
SSOCK_Init init;
+ const char* http;
EIO_Status status;
- int add_hdr;
size_t hdr_len;
- char hdr_buf[80];
size_t args_len;
+ char temp[80];
EReqMethod x_req_meth;
- const char* x_req_meth_str;
size_t user_hdr_len = user_hdr && *user_hdr ? strlen(user_hdr) : 0;
/* sanity check first */
@@ -1510,22 +1515,35 @@ extern EIO_Status URL_ConnectEx
/*FIXME: the check to be removed*/
if (cred && cred < (NCBI_CRED) 4096) {
CORE_LOGF(eLOG_Critical,
- ("[URL_ConnectEx; http%s//%s:%hu%s%s] "
+ ("[URL_ConnectEx; http%s://%s:%hu%s%s] "
" Obsolete feature 'encode_args' is no longer supported",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path));
return x_URLConnectErrorReturn(s, eIO_InvalidArg);
}
- ver = req_method >= eReqMethod_v1 ? 1 : 0;
+ /* trim user_hdr */
+ while (user_hdr_len) {
+ if (!isspace((unsigned char) user_hdr[0]))
+ break;
+ ++user_hdr;
+ --user_hdr_len;
+ }
+ while (user_hdr_len) {
+ if (!isspace((unsigned char) user_hdr[user_hdr_len - 1]))
+ break;
+ --user_hdr_len;
+ }
+
+ http = kHttp[req_method < eReqMethod_v1 ? 0 : 1];
x_req_meth = (EReqMethod)(req_method & ~eReqMethod_v1);
/* select request method and its verbal representation */
if (x_req_meth == eReqMethod_Any)
x_req_meth = content_length ? eReqMethod_Post : eReqMethod_Get;
- else if (content_length && (x_req_meth == eReqMethod_Get ||
+ else if (content_length && (x_req_meth == eReqMethod_Get ||
x_req_meth == eReqMethod_Head)) {
CORE_LOGF_X(3, eLOG_Warning,
- ("[URL_Connect; http%s//%s:%hu%s%s] "
+ ("[URL_Connect; http%s://%s:%hu%s%s] "
" Content-Length (%lu) is ignored with request method %s",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path,
@@ -1534,52 +1552,21 @@ extern EIO_Status URL_ConnectEx
content_length = 0;
}
- switch (x_req_meth | (ver ? eReqMethod_v1 : 0)/*FIXME: to remove*/) {
- case eReqMethod_Get:
- x_req_meth_str = "GET ";
- add_hdr = 1;
- break;
- case eReqMethod_Post:
- x_req_meth_str = "POST ";
- add_hdr = 1;
- break;
- case eReqMethod_Head:
- x_req_meth_str = "HEAD ";
- add_hdr = 1;
- break;
- case eReqMethod_Connect:
- x_req_meth_str = "CONNECT ";
- add_hdr = 0;
- break;
- default:
+ if (!(str = x_ReqMethod(x_req_meth, 0))) {
CORE_LOGF_X(4, eLOG_Error,
- ("[URL_Connect; http%s//%s:%hu%s%s] "
+ ("[URL_Connect; http%s://%s:%hu%s%s] "
" Unsupported request method %s",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path,
- x_ReqMethod(req_method, hdr_buf)));
+ x_ReqMethod(req_method, temp)));
assert(0);
return x_URLConnectErrorReturn(s, eIO_NotSupported);
}
- hdr_len = 0;
- if (add_hdr) {
- const char* temp;
- assert(x_req_meth != eReqMethod_Connect);
- /*FIXME: this to be moved to URL_Connect()*/
- for (temp = user_hdr; temp && *temp; temp = strchr(temp, '\n')) {
- if (temp != user_hdr)
- temp++;
- if (strncasecmp(temp, kHost, sizeof(kHost) - 2) == 0) {
- add_hdr = 0;
- break;
- }
- }
- args_len = args ? strcspn(args, "#") : 0;
+ if (x_req_meth != eReqMethod_Connect) {
if (!port)
port = flags & fSOCK_Secure ? CONN_PORT_HTTPS : CONN_PORT_HTTP;
- else if (add_hdr)
- hdr_len = (size_t) sprintf(hdr_buf, ":%hu", port);
+ args_len = args ? strcspn(args, "#") : 0;
} else
args_len = 0;
@@ -1587,40 +1574,33 @@ extern EIO_Status URL_ConnectEx
errno = 0;
/* compose HTTP header */
if (/* METHOD <path>[?<args>] HTTP/1.x\r\n */
- !BUF_Write(&buf, x_req_meth_str, strlen(x_req_meth_str)) ||
- !BUF_Write(&buf, path, strlen(path)) ||
+ !BUF_Write(&buf, str, strlen(str)) ||
+ !BUF_Write(&buf, " ", 1) ||
+ !BUF_Write(&buf, path, strlen(path)) ||
(args_len
- && (!BUF_Write(&buf, "?", 1) ||
- !BUF_Write(&buf, args, args_len))) ||
- !BUF_Write (&buf, kHttp[ver], strlen(kHttp[ver])) ||
-
- (add_hdr
- /* Host: host[:port]\r\n */
- && (!BUF_Write(&buf, kHost, sizeof(kHost) - 1) ||
- !BUF_Write(&buf, host, strlen(host)) ||
- !BUF_Write(&buf, hdr_buf, hdr_len) ||
- !BUF_Write(&buf, "\r\n", 2))) ||
+ && (!BUF_Write(&buf, "?", 1) ||
+ !BUF_Write(&buf, args, args_len))) ||
+ !BUF_Write (&buf, http, sizeof(kHttp[0]) - 1) ||
/* Content-Length: <content_length>\r\n */
- (x_req_meth == eReqMethod_Post/*NB: HTTP/1.0 only*/ && !ver
- && ((add_hdr
- = sprintf(hdr_buf, "Content-Length: %lu\r\n",
- (unsigned long) content_length)) <= 0 ||
- !BUF_Write(&buf, hdr_buf, (size_t) add_hdr))) ||
+ (x_req_meth != eReqMethod_Connect && content_length
+ && !BUF_Write(&buf, temp, (size_t)
+ sprintf(temp, "Content-Length: %lu\r\n",
+ (unsigned long) content_length))) ||
/* <user_header> */
(user_hdr_len
- && !BUF_Write (&buf, user_hdr, user_hdr_len)) ||
+ && !BUF_Write(&buf, user_hdr, user_hdr_len)) ||
/* header separator */
- !BUF_Write(&buf, "\r\n", 2) ||
+ !BUF_Write(&buf, "\r\n\r\n", user_hdr_len ? 4 : 2) ||
/* tunneled data */
(x_req_meth == eReqMethod_Connect && content_length
- && !BUF_Write (&buf, args, content_length))) {
+ && !BUF_Write(&buf, args, content_length))) {
int x_errno = errno;
CORE_LOGF_ERRNO_X(5, eLOG_Error, x_errno,
- ("[URL_Connect; http%s//%s:%hu%s%s%s%.*s] "
+ ("[URL_Connect; http%s://%s:%hu%s%s%s%.*s] "
" Cannot build HTTP header",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path,
@@ -1633,11 +1613,12 @@ extern EIO_Status URL_ConnectEx
|| BUF_Read(buf, hdr, hdr_len) != hdr_len) {
int x_errno = errno;
CORE_LOGF_ERRNO_X(6, eLOG_Error, x_errno,
- ("[URL_Connect; http%s//%s:%hu%s%s%s%.*s] "
- " Cannot maintain HTTP header",
+ ("[URL_Connect; http%s://%s:%hu%s%s%s%.*s] "
+ " Cannot maintain HTTP header (%lu byte%s)",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path,
- &"?"[!args_len], (int) args_len, args));
+ &"?"[!args_len], (int) args_len, args,
+ (unsigned long) hdr_len, &"s"[hdr_len == 1]));
if (hdr)
free(hdr);
BUF_Destroy(buf);
@@ -1665,19 +1646,19 @@ extern EIO_Status URL_ConnectEx
if (status != eIO_Success) {
assert(!*sock);
if (status == eIO_Timeout && o_timeout) {
- sprintf(hdr_buf, "[%u.%06u]",
+ sprintf(temp, "[%u.%06u]",
(unsigned int)(o_timeout->sec + o_timeout->usec/1000000),
(unsigned int) (o_timeout->usec%1000000));
} else
- *hdr_buf = '\0';
+ *temp = '\0';
CORE_LOGF_X(7, eLOG_Error,
- ("[URL_Connect; http%s//%s:%hu%s%s%s%.*s] "
+ ("[URL_Connect; http%s://%s:%hu%s%s%s%.*s] "
" Failed to %s: %s%s",
&"s"[!(flags & fSOCK_Secure)],
host, port, &"/"[*path == '/'], path,
&"?"[!args_len], (int) args_len, args,
s ? "use connection" : "connect",
- IO_StatusStr(status), hdr_buf));
+ IO_StatusStr(status), temp));
} else
verify(SOCK_SetTimeout(*sock, eIO_ReadWrite, rw_timeout)==eIO_Success);
return status;
@@ -1697,40 +1678,78 @@ extern SOCK URL_Connect
int/*bool*/ encode_args,
TSOCK_Flags flags)
{
- SOCK sock;
- char* temp;
- size_t args_len;
-
- if (req_method >= eReqMethod_v1)
- req_method = (EReqMethod)((int) eReqMethod_v1 - 1)/*bad*/;
- if (req_method != eReqMethod_Connect && args && encode_args
- && (args_len = strcspn(args, "#")) > 0) {
- /* URL-encode "args", if any specified */
- size_t rd_len, wr_len;
- size_t size = 3 * args_len;
- if (!(temp = (char*) malloc(size + 1))) {
- CORE_LOGF_ERRNO_X(8, eLOG_Error, errno,
- ("[URL_Connect] Out of memory (%lu)",
- (unsigned long)(size + 1)));
- return 0;
+ static const char kHost[] = "Host: ";
+ const char* x_hdr = user_hdr;
+ char* x_args = 0;
+ SOCK sock;
+
+ if (req_method >= eReqMethod_v1) {
+ CORE_LOG_X(9, eLOG_Error,
+ "[URL_Connect] Unsupported version of HTTP protocol");
+ return 0;
+ }
+
+ if (req_method != eReqMethod_Connect) {
+ size_t x_add = 1/*true*/;
+ while (x_hdr && *x_hdr) {
+ if (x_hdr != user_hdr)
+ x_hdr++;
+ if (strncasecmp(x_hdr, kHost, sizeof(kHost) - 2) == 0) {
+ x_add = 0/*false*/;
+ break;
+ }
+ x_hdr = strchr(x_hdr, '\n');
}
- URL_Encode(args, args_len, &rd_len, temp, size, &wr_len);
- assert(rd_len == args_len);
- assert(wr_len <= size);
- temp[wr_len] = '\0';
- args = temp;
- } else
- temp = 0;
+ if (x_add) {
+ size_t x_len = host && *host ? strlen(host) : 0;
+ char* x_host = x_len ? (char*) malloc(x_len + sizeof(kHost)+6) : 0;
+ if (x_host) {
+ memcpy(x_host, kHost, sizeof(kHost) - 1);
+ memcpy(x_host + sizeof(kHost) - 1, host, x_len);
+ x_len += sizeof(kHost) - 1;
+ if (port)
+ sprintf(x_host + x_len, ":%hu", port);
+ else
+ x_host[x_len] = '\0';
+ if (!(x_hdr = x_StrcatCRLF(x_host, user_hdr))) {
+ x_hdr = user_hdr;
+ free(x_host);
+ }
+ }
+ } else
+ x_hdr = user_hdr;
+
+ if (args && encode_args && (x_add = strcspn(args, "#")) > 0) {
+ /* URL-encode "args", if any specified */
+ size_t size = 3 * x_add;
+ size_t rd_len, wr_len;
+ if (!(x_args = (char*) malloc(size + 1))) {
+ CORE_LOGF_ERRNO_X(8, eLOG_Error, errno,
+ ("[URL_Connect] Out of memory (%lu)",
+ (unsigned long)(size + 1)));
+ if (x_hdr != user_hdr)
+ free((void*) x_hdr);
+ return 0;
+ }
+ URL_Encode(args, x_add, &rd_len, x_args, size, &wr_len);
+ assert(rd_len == x_add);
+ assert(wr_len <= size);
+ x_args[wr_len] = '\0';
+ args = x_args;
+ }
+ }
sock = 0;
verify(URL_ConnectEx(host, port, path, args,
req_method, content_length,
o_timeout, rw_timeout,
- user_hdr, 0/*cred*/, flags, &sock) == eIO_Success
+ x_hdr, 0/*cred*/, flags, &sock) == eIO_Success
|| !sock);
- if (temp)
- free(temp);
+ if (x_args)
+ free(x_args);
+ if (x_hdr != user_hdr)
+ free((void*) x_hdr);
return sock;
}
@@ -1766,30 +1785,54 @@ static EIO_Status s_StripToPattern
/* check args */
if ( n_discarded )
*n_discarded = 0;
- if (!stream || (pattern != 0) != (pattern_size != 0))
+ if ( !stream )
return eIO_InvalidArg;
+ if ( !pattern_size )
+ pattern = 0;
/* allocate a temporary read buffer */
- buf_size = pattern_size << 1;
- if (buf_size <= sizeof(x_buf)) {
+ buf_size = pattern ? pattern_size << 1 : pattern_size;
+ if (buf_size <= sizeof(x_buf) && (pattern || !pattern_size)) {
buf_size = sizeof(x_buf);
buf = x_buf;
} else if ( !(buf = (char*) malloc(buf_size)) )
return eIO_Unknown;
if ( !pattern ) {
- /* read/discard until EOF */
+ /* read/discard the specified # of bytes or until EOF */
+ size_t n_count = 0;
+ char* xx_buf = buf;
do {
- status = io_func(stream, buf, buf_size, &n_read, eIO_Read);
- if ( discard )
- BUF_Write(discard, buf, n_read);
- if ( n_discarded )
- *n_discarded += n_read;
+ status = io_func(stream, xx_buf, buf_size, &n_read, eIO_Read);
+ if (!n_read) {
+ assert(status != eIO_Success);
+ break;
+ }
+ if (discard) {
+ if (!n_count && pattern_size) {
+ assert(buf_size == pattern_size);
+ /* first time enqueue the entire "buf" */
+ if (!BUF_AppendEx(discard, buf, buf_size, buf, n_read))
+ discard = 0;
+ else
+ buf = 0;
+ } else if (!BUF_Write(discard, xx_buf, n_read))
+ discard = 0;
+ }
+ n_count += n_read;
+ if (pattern_size) {
+ if (!(buf_size -= n_read))
+ break;
+ xx_buf += n_read;
+ }
} while (status == eIO_Success);
+ if ( n_discarded )
+ *n_discarded = n_count;
} else {
+ assert(pattern_size);
n_read = 0;
for (;;) {
- /* read; search for the pattern; store the discarded data */
+ /* read; search for the pattern; store/count the discarded data */
size_t x_read, n_stored;
assert(n_read < pattern_size);
@@ -1797,7 +1840,7 @@ static EIO_Status s_StripToPattern
&x_read, eIO_Read);
if ( !x_read ) {
assert(status != eIO_Success);
- break; /*error*/
+ break;
}
n_stored = n_read + x_read;
@@ -1826,8 +1869,8 @@ static EIO_Status s_StripToPattern
}
/* pattern not found yet */
- if ( discard )
- BUF_Write(discard, buf + n_read, x_read);
+ if (discard && !BUF_Write(discard, buf + n_read, x_read))
+ discard = 0;
if ( n_discarded )
*n_discarded += x_read;
@@ -1840,7 +1883,7 @@ static EIO_Status s_StripToPattern
}
/* cleanup & exit */
- if (buf != x_buf)
+ if (buf && buf != x_buf)
free(buf);
return status;
}
@@ -1858,7 +1901,7 @@ static EIO_Status s_CONN_IO
return CONN_Read((CONN) stream, buf, size, n_read, eIO_ReadPlain);
case eIO_Write:
assert(stream);
- return CONN_PushBack((CONN) stream, buf, size);
+ return CONN_Pushback((CONN) stream, buf, size);
default:
break;
}
@@ -1887,7 +1930,7 @@ static EIO_Status s_SOCK_IO
case eIO_Read:
return SOCK_Read((SOCK) stream, buf, size, n_read, eIO_ReadPlain);
case eIO_Write:
- return SOCK_PushBack((SOCK) stream, buf, size);
+ return SOCK_Pushback((SOCK) stream, buf, size);
default:
break;
}
@@ -1921,7 +1964,7 @@ static EIO_Status s_BUF_IO
case eIO_Write:
assert(stream);
b = (BUF) stream;
- return BUF_PushBack(&b, buf, size) ? eIO_Success : eIO_Unknown;
+ return BUF_Pushback(&b, buf, size) ? eIO_Success : eIO_Unknown;
default:
break;
}
@@ -2102,9 +2145,8 @@ extern void URL_EncodeEx
*(++dst) = *(++subst);
*(++dst) = *(++subst);
*dst_written += 2;
- } else {
+ } else
return;
- }
}
assert(src == (unsigned char*) src_buf + *src_read );
assert(dst == (unsigned char*) dst_buf + *dst_written);
@@ -2278,7 +2320,7 @@ extern int/*bool*/ MIME_ParseContentTypeEx
}
-void SERV_InitFirewallMode(void)
+void SERV_InitFirewallPorts(void)
{
memset(s_FWPorts, 0, sizeof(s_FWPorts));
}
@@ -2286,8 +2328,11 @@ void SERV_InitFirewallMode(void)
int/*bool*/ SERV_AddFirewallPort(unsigned short port)
{
- unsigned int n = port / (sizeof(s_FWPorts[0]) << 3);
- unsigned int m = port % (sizeof(s_FWPorts[0]) << 3);
+ unsigned int n, m;
+ if (!port--)
+ return 0/*false*/;
+ n = port / (sizeof(s_FWPorts[0]) << 3);
+ m = port % (sizeof(s_FWPorts[0]) << 3);
if ((size_t) n < SizeOf(s_FWPorts)) {
s_FWPorts[n] |= (TNCBI_BigCount) 1 << m;
return 1/*true*/;
@@ -2298,10 +2343,13 @@ int/*bool*/ SERV_AddFirewallPort(unsigned short port)
int/*bool*/ SERV_IsFirewallPort(unsigned short port)
{
- unsigned int n = port / (sizeof(s_FWPorts[0]) << 3);
- unsigned int m = port % (sizeof(s_FWPorts[0]) << 3);
- if ((size_t) n < SizeOf(s_FWPorts)
- && (s_FWPorts[n] & ((TNCBI_BigCount) 1 << m))) {
+ unsigned int n, m;
+ if (!port--)
+ return 0/*false*/;
+ n = port / (sizeof(s_FWPorts[0]) << 3);
+ m = port % (sizeof(s_FWPorts[0]) << 3);
+ if ((size_t) n < SizeOf(s_FWPorts) &&
+ s_FWPorts[n] & ((TNCBI_BigCount) 1 << m)) {
return 1/*true*/;
}
return 0/*false*/;
@@ -2328,16 +2376,14 @@ void SERV_PrintFirewallPorts(char* buf, size_t bufsize, EFWMode mode)
for (n = m = 0; n < SizeOf(s_FWPorts); ++n, m += sizeof(s_FWPorts[0])<<3) {
unsigned short p;
TNCBI_BigCount mask = s_FWPorts[n];
- for (p = m; mask; p++, mask >>= 1) {
+ for (p = m + 1; mask; ++p, mask >>= 1) {
if (mask & 1) {
char port[10];
- int k = sprintf(port, " %hu" + !len, p);
+ int k = sprintf(port, &" %hu"[!len], p);
if (len + k < bufsize) {
memcpy(buf + len, port, k);
len += k;
}
- if (!p)
- break;
}
}
}
diff --git a/c++/src/connect/ncbi_core_cxx.cpp b/c++/src/connect/ncbi_core_cxx.cpp
index 78b124e..b59835f 100644
--- a/c++/src/connect/ncbi_core_cxx.cpp
+++ b/c++/src/connect/ncbi_core_cxx.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_core_cxx.cpp 449180 2014-10-14 14:01:12Z ivanov $
+/* $Id: ncbi_core_cxx.cpp 451104 2014-11-03 19:33:10Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -257,6 +257,7 @@ static void s_Fini(void) THROWS_NONE
extern "C" {
static const char* s_GetAppName(void)
{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
return app ? app->GetProgramDisplayName().c_str() : 0;
}
@@ -338,6 +339,7 @@ static void s_InitInternal(void)
&& g_CORE_MT_Lock == &g_CORE_MT_Lock_default) {
try {
if (s_ConnectInit == eConnectInit_Intact) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
s_Init(app ? &app->GetConfig() : 0);
}
diff --git a/c++/src/connect/ncbi_dispd.c b/c++/src/connect/ncbi_dispd.c
index 27a1313..d72cac6 100644
--- a/c++/src/connect/ncbi_dispd.c
+++ b/c++/src/connect/ncbi_dispd.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_dispd.c 430184 2014-03-24 17:40:28Z lavr $
+/* $Id: ncbi_dispd.c 451391 2014-11-06 15:31:05Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,7 +45,7 @@
#endif /*fabs*/
#define fabs(v) ((v) < 0.0 ? -(v) : (v))
-#define NCBI_USE_ERRCODE_X Connect_Dispd
+#define NCBI_USE_ERRCODE_X Connect_LBSM
/* Lower bound of up-to-date/out-of-date ratio */
#define DISPD_STALE_RATIO_OK 0.8
@@ -195,7 +195,7 @@ static void s_Resolve(SERV_ITER iter)
/* ...then trigger the header callback */
CONN_Close(conn);
} else {
- CORE_LOGF_X(1, eLOG_Error,
+ CORE_LOGF_X(5, eLOG_Error,
("%s%s%sUnable to create auxiliary HTTP %s: %s",
&"["[!*iter->name], iter->name, *iter->name ? "] " : "",
c ? "connection" : "connector",
@@ -266,7 +266,7 @@ static int/*bool*/ s_Update(SERV_ITER iter, const char* text, int code)
text += sizeof(HTTP_DISP_FAILURES) - 1;
while (*text && isspace((unsigned char)(*text)))
text++;
- CORE_LOGF_X(2, failure ? eLOG_Warning : eLOG_Note,
+ CORE_LOGF_X(6, failure ? eLOG_Warning : eLOG_Note,
("[%s] %s", data->net_info->svc, text));
}
#endif /*_DEBUG && !NDEBUG*/
diff --git a/c++/src/connect/ncbi_file_connector.c b/c++/src/connect/ncbi_file_connector.c
index 9200408..a6610fb 100644
--- a/c++/src/connect/ncbi_file_connector.c
+++ b/c++/src/connect/ncbi_file_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_file_connector.c 419436 2013-11-25 19:58:53Z lavr $
+/* $Id: ncbi_file_connector.c 454485 2014-12-15 20:41:15Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -140,7 +140,7 @@ static EIO_Status s_VT_Open
/* open file for output */
if (xxx->ofname) {
- switch ( xxx->attr.w_mode ) {
+ switch (xxx->attr.w_mode) {
case eFCM_Truncate:
mode = "wb";
break;
diff --git a/c++/src/connect/ncbi_ftp_connector.c b/c++/src/connect/ncbi_ftp_connector.c
index 974422f..a9ff991 100644
--- a/c++/src/connect/ncbi_ftp_connector.c
+++ b/c++/src/connect/ncbi_ftp_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_ftp_connector.c 425008 2014-01-23 20:15:31Z lavr $
+/* $Id: ncbi_ftp_connector.c 451703 2014-11-10 18:32:44Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -877,7 +877,7 @@ static EIO_Status x_FTPPasv(SFTPConnector* xxx,
return eIO_Unknown;
len = 0;
for (i = 0; i < (unsigned int)(sizeof(o) / sizeof(o[0])); i++) {
- if (sscanf(c + len, ",%d%n" + !i, &o[i], &code) < 1)
+ if (sscanf(c + len, &",%d%n"[!i], &o[i], &code) < 1)
break;
len += code;
}
@@ -2181,6 +2181,7 @@ static EIO_Status s_VT_Close
static void s_Setup
(CONNECTOR connector)
{
+ SFTPConnector* xxx = (SFTPConnector*) connector->handle;
SMetaConnector* meta = connector->meta;
/* initialize virtual table */
@@ -2193,7 +2194,7 @@ static void s_Setup
CONN_SET_METHOD(meta, read, s_VT_Read, connector);
CONN_SET_METHOD(meta, status, s_VT_Status, connector);
CONN_SET_METHOD(meta, close, s_VT_Close, connector);
- meta->default_timeout = kInfiniteTimeout;
+ CONN_SET_DEFAULT_TIMEOUT(meta, xxx->info->timeout);
}
@@ -2279,14 +2280,13 @@ extern CONNECTOR s_CreateConnector(const SConnNetInfo* info,
xxx->info->http_proxy_port = 0;
xxx->info->http_proxy_user[0] = '\0';
xxx->info->http_proxy_pass[0] = '\0';
- xxx->info->proxy_host[0] = '\0';
- ConnNetInfo_SetUserHeader(xxx->info, 0);
- if (xxx->info->http_referer) {
- free((void*) xxx->info->http_referer);
- xxx->info->http_referer = 0;
- }
} else
CORE_LOG(eLOG_Critical, "fFTP_UseProxy not yet implemented");
+ ConnNetInfo_SetUserHeader(xxx->info, 0);
+ if (xxx->info->http_referer) {
+ free((void*) xxx->info->http_referer);
+ xxx->info->http_referer = 0;
+ }
/* some uninited fields are taken care of in s_VT_Open */
xxx->cmcb = cmcb ? *cmcb : kNoCmcb;
diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c
index fd922fe..af791ec 100644
--- a/c++/src/connect/ncbi_gnutls.c
+++ b/c++/src/connect/ncbi_gnutls.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_gnutls.c 438654 2014-06-18 17:54:57Z lavr $
+/* $Id: ncbi_gnutls.c 474202 2015-07-27 15:06:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -100,16 +100,6 @@ static struct gcry_thread_cbs gcry_threads_user = {
# endif /*HAVE_LIBGCRYPT*/
-# ifndef LIBGNUTLS_VERSION_NUMBER
-/* backport support for older gnutls */
-# define gnutls_session_t gnutls_session
-# define gnutls_transport_ptr_t gnutls_transport_ptr
-# define gnutls_connection_end_t gnutls_connection_end
-# define gnutls_anon_client_credentials_t gnutls_anon_client_credentials
-# define gnutls_certificate_credentials_t gnutls_certificate_credentials
-# endif /*LIBGNUTLS_VERSION_NUMBER*/
-
-
# ifdef __cplusplus
extern "C" {
# endif /*__cplusplus*/
@@ -117,7 +107,7 @@ extern "C" {
static EIO_Status s_GnuTlsInit (FSSLPull pull, FSSLPush push);
static void* s_GnuTlsCreate(ESOCK_Side side, SOCK sock,
NCBI_CRED cred, int* error);
-static EIO_Status s_GnuTlsOpen (void* session, int* error);
+static EIO_Status s_GnuTlsOpen (void* session, int* error, char** desc);
static EIO_Status s_GnuTlsRead (void* session, void* buf, size_t size,
size_t* done, int* error);
static EIO_Status s_GnuTlsWrite (void* session, const void* data, size_t size,
@@ -136,7 +126,7 @@ static ssize_t x_GnuTlsPush (gnutls_transport_ptr_t, const void*, size_t);
# endif /*__cplusplus*/
-# if defined(LIBGNUTLS_VERSION_NUMBER) || !defined(NCBI_OS_SOLARIS)
+# if LIBGNUTLS_VERSION_NUMBER < 0x030306
static const int kGnuTlsCertPrio[] = {
GNUTLS_CRT_X509,
/*GNUTLS_CRT_OPENPGP,*/
@@ -147,7 +137,7 @@ static const int kGnuTlsCompPrio[] = {
GNUTLS_COMP_NULL,
0
};
-# endif /*LIBGNUTLS_VERSION_NUMBER || !NCBI_OS_SOLARIS*/
+# endif /*LIBGNUTLS_VERSION_NUMBER<3.3.6*/
static int s_GnuTlsLogLevel;
@@ -191,26 +181,45 @@ static EIO_Status x_RetryStatus(gnutls_session_t session, EIO_Event direction)
# ifdef __GNUC__
inline
# endif /*__GNUC__*/
-static EIO_Status x_ErrorToStatus(int error,
+static EIO_Status x_ErrorToStatus(int* error,
gnutls_session_t session,EIO_Event direction)
{
EIO_Status status;
+ SOCK sock = (SOCK) gnutls_transport_get_ptr(session);
- assert(error <= 0);
+ assert(error && *error <= 0);
- if (!error)
+ if (!*error)
return eIO_Success;
- else if (error == GNUTLS_E_AGAIN)
+ else if (*error == GNUTLS_E_AGAIN)
status = x_RetryStatus(session, direction);
- else if (error == GNUTLS_E_INTERRUPTED)
+ else if (*error == GNUTLS_E_INTERRUPTED)
status = eIO_Interrupt;
- else if (gnutls_error_is_fatal(error))
+ else if (*error == GNUTLS_E_WARNING_ALERT_RECEIVED) {
+ status = eIO_Unknown;
+ *error = GNUTLS_E_APPLICATION_ERROR_MAX - gnutls_alert_get(session);
+ }
+ else if (*error == GNUTLS_E_FATAL_ALERT_RECEIVED) {
+ status = eIO_Closed;
+ *error = GNUTLS_E_APPLICATION_ERROR_MAX - gnutls_alert_get(session);
+ }
+ else if (*error == GNUTLS_E_PULL_ERROR
+ && sock->r_status != eIO_Success
+ && sock->r_status != eIO_Unknown) {
+ status = sock->r_status;
+ }
+ else if (*error == GNUTLS_E_PUSH_ERROR
+ && sock->w_status != eIO_Success
+ && sock->w_status != eIO_Unknown) {
+ status = sock->w_status;
+ }
+ else if (gnutls_error_is_fatal(*error))
status = eIO_Closed;
else
status = eIO_Unknown;
#if 0
CORE_TRACEF(("GNUTLS error %d -> CONNECT status %s",
- error, IO_StatusStr(status)));
+ *error, IO_StatusStr(status)));
#endif
return status;
}
@@ -314,18 +323,18 @@ static void* s_GnuTlsCreate(ESOCK_Side side, SOCK sock,
ConnNetInfo_GetValue(0, "GNUTLS_PRIORITY", val, sizeof(val), 0);
if ((err = gnutls_set_default_priority(session)) != 0 ||
-# if defined(LIBGNUTLS_VERSION_NUMBER) || !defined(NCBI_OS_SOLARIS)
-# if LIBGNUTLS_VERSION_NUMBER >= 0x020200
+# if LIBGNUTLS_VERSION_NUMBER >= 0x020200
( *val &&
(err = gnutls_priority_set_direct(session, val, 0)) != 0) ||
-# endif /*LIBGNUTLS_VERSION_NUMBER>=2.2.0*/
+# endif /*LIBGNUTLS_VERSION_NUMBER>=2.2.0*/
+# if LIBGNUTLS_VERSION_NUMBER < 0x030306
(!*val &&
(err = gnutls_compression_set_priority(session,
kGnuTlsCompPrio)) != 0) ||
(!*val &&
(err = gnutls_certificate_type_set_priority(session,
kGnuTlsCertPrio)) != 0) ||
-# endif /*LIBGNUTLS_VERSION_NUMBER || !NCBI_OS_SOLARIS*/
+# endif /*LIBGNUTLS_VERSION_NUMBER<3.3.6*/
(err = gnutls_credentials_set(session, GNUTLS_CRD_CERTIFICATE,
cred ? cred->data : xcred)) != 0 ||
(err = gnutls_credentials_set(session, GNUTLS_CRD_ANON, acred))!= 0) {
@@ -338,11 +347,16 @@ static void* s_GnuTlsCreate(ESOCK_Side side, SOCK sock,
gnutls_transport_set_push_function(session, x_GnuTlsPush);
gnutls_transport_set_ptr(session, ptr);
gnutls_session_set_ptr(session, sock);
+
+# if LIBGNUTLS_VERSION_NUMBER >= 0x030000
+ gnutls_handshake_set_timeout(session, 0);
+# endif /*LIBGNUTLS_VERSION_NUMBER>=3.0.0*/
+
return session;
}
-static EIO_Status s_GnuTlsOpen(void* session, int* error)
+static EIO_Status s_GnuTlsOpen(void* session, int* error, char** desc)
{
EIO_Status status;
int x_error;
@@ -352,12 +366,18 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error)
} while (x_error && x_error == GNUTLS_E_REHANDSHAKE);
if (x_error < 0) {
- status = x_ErrorToStatus(x_error,
+ status = x_ErrorToStatus(&x_error,
(gnutls_session_t) session, eIO_Open);
*error = x_error;
- } else
+ *desc = 0;
+ } else {
+# if LIBGNUTLS_VERSION_NUMBER < 0x030110
+ *desc = 0;
+# else
+ *desc = gnutls_session_get_desc(session);
+# endif /*LIBGNUTLS_VERSION_NUMBER<3.1.10*/
status = eIO_Success;
-
+ }
return status;
}
@@ -374,15 +394,12 @@ static int x_IfToLog(void)
/*ARGSUSED*/
static void x_set_errno(gnutls_session_t session, int error)
{
-# ifdef LIBGNUTLS_VERSION_NUMBER
-# if LIBGNUTLS_VERSION_NUMBER >= 0x010504
+# if LIBGNUTLS_VERSION_NUMBER >= 0x010504
gnutls_transport_set_errno(session, error);
- return;
-# endif /*LIBGNUTLS_VERSION>=1.5.4*/
-# endif /*LIBGNUTLS_VERSION_NUMBER*/
- /*NOTREACHED*/
+# else
if (error)
errno = error;
+# endif /*LIBGNUTLS_VERSION>=1.5.4*/
}
@@ -460,7 +477,7 @@ static EIO_Status s_GnuTlsRead(void* session, void* buf, size_t n_todo,
x_read = gnutls_record_recv((gnutls_session_t) session, buf, n_todo);
if (x_read <= 0) {
- status = x_ErrorToStatus(x_read,
+ status = x_ErrorToStatus(&x_read,
(gnutls_session_t) session, eIO_Read);
*error = x_read;
x_read = 0;
@@ -483,7 +500,7 @@ static EIO_Status s_GnuTlsWrite(void* session, const void* data, size_t n_todo,
x_written = gnutls_record_send((gnutls_session_t) session, data, n_todo);
if (x_written <= 0) {
- status = x_ErrorToStatus(x_written,
+ status = x_ErrorToStatus(&x_written,
(gnutls_session_t) session, eIO_Write);
*error = x_written;
x_written = 0;
@@ -527,19 +544,31 @@ static EIO_Status s_GnuTlsInit(FSSLPull pull, FSSLPush push)
{
gnutls_anon_client_credentials_t acred;
gnutls_certificate_credentials_t xcred;
- char val[32];
+ const char* version;
+ const char* val;
+ char buf[32];
assert(!s_GnuTlsCredAnon);
- ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", val, sizeof(val), 0);
- if (*val) {
- int level = atoi(val);
- s_GnuTlsLogLevel = level < 0 ? 0 : level;
- if (s_GnuTlsLogLevel > 0) {
+ version = gnutls_check_version(0);
+ if (strcasecmp(GNUTLS_VERSION, version) != 0) {
+ CORE_LOGF(eLOG_Critical,
+ ("GNUTLS version mismatch: %s headers vs. %s runtime",
+ GNUTLS_VERSION, version));
+ assert(0);
+ }
+
+ val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0);
+ if (!val || !*val)
+ val = getenv("GNUTLS_DEBUG_LEVEL");
+ if (val && *val) {
+ s_GnuTlsLogLevel = atoi(val);
+ if (s_GnuTlsLogLevel) {
gnutls_global_set_log_function(x_GnuTlsLogger);
- gnutls_global_set_log_level(s_GnuTlsLogLevel);
+ if (val != buf)
+ gnutls_global_set_log_level(s_GnuTlsLogLevel);
CORE_LOGF(eLOG_Note, ("GNUTLS V%s (Loglevel=%d)",
- gnutls_check_version(0), s_GnuTlsLogLevel));
+ version, s_GnuTlsLogLevel));
}
}
@@ -608,7 +637,9 @@ static void s_GnuTlsExit(void)
static const char* s_GnuTlsError(void* session/*unused*/, int error)
{
/* GNUTLS defines only negative error codes */
- return error < 0 ? gnutls_strerror(error) : 0;
+ return error >= 0 ? 0 : error < GNUTLS_E_APPLICATION_ERROR_MAX
+ ? gnutls_alert_get_name(GNUTLS_E_APPLICATION_ERROR_MAX - error)
+ : gnutls_strerror(error);
}
@@ -631,7 +662,7 @@ extern SOCKSSL NcbiSetupGnuTls(void)
};
return &kGnuTlsOps;
#else
- CORE_LOG(eLOG_Critical, "Unavailable GNUTLS feature requested");
+ CORE_LOG(eLOG_Critical, "Unavailable feature GNUTLS");
return 0;
#endif /*HAVE_LIBGNUTLS*/
}
diff --git a/c++/src/connect/ncbi_heapmgr.c b/c++/src/connect/ncbi_heapmgr.c
index a70ea6f..73ac75b 100644
--- a/c++/src/connect/ncbi_heapmgr.c
+++ b/c++/src/connect/ncbi_heapmgr.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_heapmgr.c 437345 2014-06-05 14:01:35Z ucko $
+/* $Id: ncbi_heapmgr.c 456320 2015-01-09 17:51:13Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -357,7 +357,7 @@ static const char* s_HEAP_Id(char* buf, HEAP h)
/* Scan the heap and return a free block, whose size is the minimal to fit the
- * requested one (i.e. previous free block, if any, is smaller). The block
+ * requested one (i.e. its previous free block, if any, is smaller). The block
* returned is still linked into the list of free blocks. Iff no suitable free
* block can be found, *size gets updated with the total free space available.
*/
@@ -626,27 +626,27 @@ SHEAP_Block* HEAP_Alloc(HEAP heap,
TNCBI_Size need;
char _id[32];
- if (!heap) {
+ if (unlikely(!heap)) {
CORE_LOG_X(6, eLOG_Warning, "Heap Alloc: NULL heap");
return 0;
}
assert(!heap->base == !heap->size);
- if (!heap->chunk) {
+ if (unlikely(!heap->chunk)) {
CORE_LOGF_X(7, eLOG_Error,
("Heap Alloc%s: Heap read-only", s_HEAP_Id(_id, heap)));
return 0;
}
- if (size < 1)
+ if (unlikely(size < 1))
return 0;
size += (TNCBI_Size) sizeof(SHEAP_Block);
need = HEAP_ALIGN(size);
- if (heap->free < heap->size) {
+ if (likely(heap->free < heap->size)) {
TNCBI_Size free = need;
- if ((f = s_HEAP_Find(heap, &free, 0)) != 0) {
- /*NB: f is linked, unlink*/
+ if (likely((f = s_HEAP_Find(heap, &free, 0)) != 0)) {
+ /*NB: f is still linked -- unlink*/
n = heap->base + f->nextfree;
if (n == f) {
assert(f == heap->base + heap->free);
@@ -662,31 +662,34 @@ SHEAP_Block* HEAP_Alloc(HEAP heap,
}
}
s_HEAP_Unlink(f);
- } else if (need <= free) {
- /*NB: f is unlinked*/
+ } else if (unlikely(need <= free)) {
+ /*NB: here f returns unlinked*/
f = s_HEAP_Collect(heap, need);
assert(f && HEAP_ISFREE(f) && need <= f->head.size);
+ if (unlikely(f->head.flag & 2/*HEAP_LAST*/))
+ f->head.flag = HEAP_FREE | HEAP_LAST;
n = 0;
} else
f = n = 0;
} else
f = n = 0;
- if (!f) {
+ if (unlikely(!f)) {
TNCBI_Size dsize = HEAP_EXTENT(heap->size);
TNCBI_Size hsize = _HEAP_ALIGN_EX(dsize + need, heap->chunk);
SHEAP_HeapBlock* base = (SHEAP_HeapBlock*)
heap->resize(heap->base, hsize, heap->auxarg);
- if (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base) {
+ if (unlikely
+ (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base)) {
CORE_LOGF_X(9, eLOG_Warning,
("Heap Alloc%s: Unaligned base (0x%08lX)",
s_HEAP_Id(_id, heap), (long) base));
}
- if (!base)
+ if (unlikely(!base))
return 0;
dsize = hsize - dsize;
memset(base + heap->size, 0, dsize); /* security */
f = base + heap->last;
- if (!heap->base) {
+ if (unlikely(!heap->base)) {
assert(!heap->last && !heap->free);
f->head.flag = HEAP_FREE | HEAP_LAST;
f->head.size = hsize;
@@ -695,7 +698,7 @@ SHEAP_Block* HEAP_Alloc(HEAP heap,
} else {
assert(base <= f && f < base + heap->size && HEAP_ISLAST(f));
hsize = HEAP_BLOCKS(hsize);
- if (!HEAP_ISFREE(f)) {
+ if (unlikely(!HEAP_ISFREE(f))) {
f->head.flag &= ~HEAP_LAST;
/* New block is at the very top of the heap */
heap->last = heap->size;
@@ -739,9 +742,14 @@ static void s_HEAP_Free(HEAP heap,
* "flag" must keep its HEAP_LAST bit so that it can be verified. */
unsigned int last = HEAP_ISLAST(b);
+ assert(p < b && b < n);
+ assert((!p || HEAP_NEXT(p) == b) && b && HEAP_NEXT(b) == n);
+ assert((!p || heap->base <= p) && n <= heap->base + heap->size);
+
s_HEAP_Unlink(b);
b->head.flag = HEAP_FREE | last;
if (!last && HEAP_ISFREE(n)) {
+ assert((n->nextfree | n->prevfree) != (TNCBI_Size)(~0));
b->head.size += n->head.size;
if (HEAP_ISLAST(n)) {
last = HEAP_LAST;
@@ -764,6 +772,7 @@ static void s_HEAP_Free(HEAP heap,
s_HEAP_Unlink(n);
}
if (p && HEAP_ISFREE(p)) {
+ assert((p->nextfree | p->prevfree) != (TNCBI_Size)(~0));
p->head.size += b->head.size;
if (last) {
assert(!HEAP_ISLAST(p));
@@ -792,49 +801,44 @@ void HEAP_Free(HEAP heap, SHEAP_Block* ptr)
SHEAP_HeapBlock *b, *p;
char _id[32];
- if (!heap) {
+ if (unlikely(!heap)) {
CORE_LOG_X(10, eLOG_Warning, "Heap Free: NULL heap");
return;
}
assert(!heap->base == !heap->size);
- if (!heap->chunk) {
+ if (unlikely(!heap->chunk)) {
CORE_LOGF_X(11, eLOG_Error,
("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
return;
}
- if (!ptr)
+ if (unlikely(!ptr))
return;
p = 0;
b = heap->base;
e = b + heap->size;
- while (b < e) {
+ while (likely(b < e)) {
SHEAP_HeapBlock* n = HEAP_NEXT(b);
- if (n <= e) {
- if (&b->head == ptr) {
- if (!HEAP_ISFREE(b)) {
- s_HEAP_Free(heap, p, b, n);
- return;
- }
- if (HEAP_ISFREE(b)) {
- CORE_LOGF_X(12, eLOG_Warning,
- ("Heap Free%s: Freeing free block @%u",
- s_HEAP_Id(_id, heap),
- HEAP_INDEX(b, heap->base)));
- return;
- }
- } else {
- p = b;
- b = n;
- continue;
- }
+ if (unlikely(n > e)) {
+ CORE_LOGF_X(13, eLOG_Error,
+ ("Heap Free%s: Heap corrupt @%u/%u (0x%08X, %u)",
+ s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
+ heap->size, b->head.flag, b->head.size));
+ return;
}
- CORE_LOGF_X(13, eLOG_Error,
- ("Heap Free%s: Heap corrupt @%u/%u (0x%08X, %u)",
- s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
- heap->size, b->head.flag, b->head.size));
- return;
+ if (unlikely(&b->head == ptr)) {
+ if (unlikely(HEAP_ISFREE(b))) {
+ CORE_LOGF_X(12, eLOG_Warning,
+ ("Heap Free%s: Freeing free block @%u",
+ s_HEAP_Id(_id, heap),
+ HEAP_INDEX(b, heap->base)));
+ } else
+ s_HEAP_Free(heap, p, b, n);
+ return;
+ }
+ p = b;
+ b = n;
}
CORE_LOGF_X(14, eLOG_Error,
@@ -848,33 +852,33 @@ void HEAP_FreeFast(HEAP heap, SHEAP_Block* ptr, const SHEAP_Block* prev)
SHEAP_HeapBlock *b, *p, *n;
char _id[32];
- if (!heap) {
+ if (unlikely(!heap)) {
CORE_LOG_X(15, eLOG_Warning, "Heap Free: NULL heap");
return;
}
assert(!heap->base == !heap->size);
- if (!heap->chunk) {
+ if (unlikely(!heap->chunk)) {
CORE_LOGF_X(16, eLOG_Error,
("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
return;
}
- if (!ptr)
+ if (unlikely(!ptr))
return;
p = (SHEAP_HeapBlock*) prev;
b = (SHEAP_HeapBlock*) ptr;
n = HEAP_NEXT(b);
- if (!s_HEAP_fast) {
+ if (unlikely(!s_HEAP_fast)) {
const SHEAP_HeapBlock* e = heap->base + heap->size;
- if (b < heap->base || e < n) {
+ if (unlikely(b < heap->base) || unlikely(e < n)) {
CORE_LOGF_X(17, eLOG_Error,
("Heap Free%s: Alien block", s_HEAP_Id(_id, heap)));
return;
}
- if ((!p && b != heap->base) ||
- ( p && (p < heap->base || b != HEAP_NEXT(p)))) {
+ if (unlikely((!p && b != heap->base)) ||
+ unlikely(( p && (p < heap->base || b != HEAP_NEXT(p))))) {
char h[40];
if (!p || p < heap->base || e <= p)
*h = '\0';
@@ -886,7 +890,7 @@ void HEAP_FreeFast(HEAP heap, SHEAP_Block* ptr, const SHEAP_Block* prev)
HEAP_Free(heap, ptr);
return;
}
- if (HEAP_ISFREE(b)) {
+ if (unlikely(HEAP_ISFREE(b))) {
CORE_LOGF_X(19, eLOG_Warning,
("Heap Free%s: Freeing free block @%u",
s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base)));
@@ -1017,7 +1021,7 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
}
if (HEAP_ISLAST(b) &&
- (n < e || (heap->chunk/*RW heap*/ && b < heap->base + heap->last))){
+ (n < e || (heap->chunk/*RW heap*/ && b < heap->base + heap->last))) {
if (heap->chunk/*RW heap*/)
sprintf(msg, " expected @%u", heap->last);
else
@@ -1168,18 +1172,19 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
SHEAP_Block* HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
{
- if (!heap) {
+ if (unlikely(!heap)) {
CORE_LOG_X(29, eLOG_Warning, "Heap Walk: NULL heap");
return 0;
}
assert(!heap->base == !heap->size);
- if (s_HEAP_fast) {
+ if (likely(s_HEAP_fast)) {
SHEAP_HeapBlock* b;
- if (!ptr)
+ if (unlikely(!ptr))
return &heap->base->head;
b = HEAP_NEXT((SHEAP_HeapBlock*) ptr);
- return ptr < &b->head && b < heap->base + heap->size ? &b->head : 0;
+ return likely(ptr < &b->head) && likely(b < heap->base + heap->size)
+ ? &b->head : 0;
}
return s_HEAP_Walk(heap, ptr);
}
@@ -1306,7 +1311,7 @@ int HEAP_Serial(const HEAP heap)
/*ARGSUSED*/
-void HEAP_Options(ESwitch fast, ESwitch ignored)
+void HEAP_Options(ESwitch fast, ESwitch unused)
{
switch (fast) {
case eOff:
diff --git a/c++/src/connect/ncbi_host_info.c b/c++/src/connect/ncbi_host_info.c
index 99718a2..875f660 100644
--- a/c++/src/connect/ncbi_host_info.c
+++ b/c++/src/connect/ncbi_host_info.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_host_info.c 440969 2014-07-18 15:57:23Z lavr $
+/* $Id: ncbi_host_info.c 462396 2015-03-18 16:23:03Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,10 +71,8 @@ HOST_INFO HINFO_Create(unsigned int addr, const void* hinfo, size_t hinfo_size,
host_info->arg = (const char*) memcpy(s, arg, a_s);
s += a_s;
}
- if (v_s) {
+ if (v_s)
host_info->val = (const char*) memcpy(s, val, v_s);
- s += v_s;
- }
host_info->pad = HINFO_MAGIC;
return host_info;
}
diff --git a/c++/src/connect/ncbi_http_connector.c b/c++/src/connect/ncbi_http_connector.c
index a70c02a..b331421 100644
--- a/c++/src/connect/ncbi_http_connector.c
+++ b/c++/src/connect/ncbi_http_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_http_connector.c 457999 2015-01-29 19:41:58Z kazimird $
+/* $Id: ncbi_http_connector.c 468415 2015-05-22 15:38:30Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -114,10 +114,10 @@ typedef struct {
*/
typedef struct {
SConnNetInfo* net_info; /* network configuration parameters */
- FHTTP_ParseHeader parse_header; /* callback to parse HTTP reply header */
void* user_data; /* user data handle for callbacks (CB) */
FHTTP_Adjust adjust; /* on-the-fly net_info adjustment CB */
FHTTP_Cleanup cleanup; /* cleanup callback */
+ FHTTP_ParseHeader parse_header; /* callback to parse HTTP reply header */
TBHTTP_Flags flags; /* as passed to constructor */
unsigned error_header:1; /* only err.HTTP header on SOME debug */
@@ -156,8 +156,9 @@ static int s_MessageIssued = 0;
static FHTTP_NcbiMessageHook s_MessageHook = 0;
-static int/*bool tri-state inverted*/ x_Authorize(SHttpConnector* uuu,
- const SRetry* retry)
+/* -1=nothing to do; 0=failure; 1=success */
+static int/*tri-state*/ x_Authenticate(SHttpConnector* uuu,
+ ERetry auth)
{
static const char kProxyAuthorization[] = "Proxy-Authorization: Basic ";
static const char kAuthorization[] = "Authorization: Basic ";
@@ -165,30 +166,18 @@ static int/*bool tri-state inverted*/ x_Authorize(SHttpConnector* uuu,
size_t taglen, userlen, passlen, len, n;
const char *tag, *user, *pass;
- assert(retry && retry->data);
- assert(strncasecmp(retry->data, "basic", strcspn(retry->data," \t")) == 0);
- switch (retry->mode) {
+ switch (auth) {
case eRetry_Authenticate:
if (uuu->auth_done)
- return 1/*failed*/;
- uuu->auth_done = 1/*true*/;
- if (uuu->net_info->scheme != eURL_Https
- && !(uuu->flags & fHTTP_InsecureRedirect)) {
- return -1/*prohibited*/;
- }
+ return -1/*nothing to do*/;
tag = kAuthorization;
taglen = sizeof(kAuthorization) - 1;
user = uuu->net_info->user;
pass = uuu->net_info->pass;
break;
case eRetry_ProxyAuthenticate:
- if (!uuu->net_info->http_proxy_host[0] ||
- !uuu->net_info->http_proxy_port) {
- return -1/*prohibited*/;
- }
- if (uuu->proxy_auth_done)
- return 1/*failed*/;
- uuu->proxy_auth_done = 1/*true*/;
+ if (uuu->proxy_auth_done)
+ return -1/*nothing to do*/;
tag = kProxyAuthorization;
taglen = sizeof(kProxyAuthorization) - 1;
user = uuu->net_info->http_proxy_user;
@@ -196,11 +185,16 @@ static int/*bool tri-state inverted*/ x_Authorize(SHttpConnector* uuu,
break;
default:
assert(0);
- return 1/*failed*/;
+ return 0/*failure*/;
}
assert(tag && user && pass);
if (!*user)
- return 1/*failed*/;
+ return -1/*nothing to do*/;
+
+ if (auth == eRetry_Authenticate)
+ uuu->auth_done = 1/*true*/;
+ else
+ uuu->proxy_auth_done = 1/*true*/;
userlen = strlen(user);
passlen = strlen(pass);
s = buf + sizeof(buf) - passlen;
@@ -226,9 +220,40 @@ static int/*bool tri-state inverted*/ x_Authorize(SHttpConnector* uuu,
userlen -= taglen + 1;
BASE64_Encode(s, len, &n, buf + taglen, userlen, &passlen, 0);
if (len != n || buf[taglen + passlen])
- return 1/*failed*/;
+ return 0/*failure*/;
memcpy(buf, tag, taglen);
- return !ConnNetInfo_OverrideUserHeader(uuu->net_info, buf);
+ return ConnNetInfo_OverrideUserHeader(uuu->net_info, buf);
+}
+
+
+/* -1=prohibited; 0=okay; 1=failure */
+static int/*bool tri-state inverted*/ x_RetryAuth(SHttpConnector* uuu,
+ const SRetry* retry)
+{
+ int result;
+
+ assert(retry && retry->data);
+ assert(strncasecmp(retry->data, "basic", strcspn(retry->data," \t")) == 0);
+ switch (retry->mode) {
+ case eRetry_Authenticate:
+ if (uuu->net_info->scheme != eURL_Https
+ && !(uuu->flags & fHTTP_InsecureRedirect)) {
+ return -1/*prohibited*/;
+ }
+ break;
+ case eRetry_ProxyAuthenticate:
+ if (!uuu->net_info->http_proxy_host[0] ||
+ !uuu->net_info->http_proxy_port) {
+ return -1/*prohibited*/;
+ }
+ break;
+ default:
+ assert(0);
+ return 1/*failed*/;
+ }
+
+ result = x_Authenticate(uuu, retry->mode);
+ return result < 0 ? 1/*failed*/ : !result/*done*/;
}
@@ -332,7 +357,7 @@ static EIO_Status s_Adjust(SHttpConnector* uuu,
if (!fail) {
fail =
retry->data && strncasecmp(retry->data, "basic ", 6) == 0
- ? x_Authorize(uuu, retry) : -2;
+ ? x_RetryAuth(uuu, retry) : -2;
}
if (fail) {
CORE_LOGF_X(3, eLOG_Error,
@@ -395,20 +420,20 @@ static EIO_Status s_Adjust(SHttpConnector* uuu,
}
-static char* s_HostPort(size_t slack, const char* host, unsigned short aport)
+static char* s_HostPort(size_t reserve, const char* host, unsigned short xport)
{
size_t hostlen = strlen(host), portlen;
char* hostport, port[16];
- if (!aport) {
+ if (!xport) {
portlen = 1;
port[0] = '\0';
} else
- portlen = (size_t) sprintf(port, ":%hu", aport) + 1;
- hostport = (char*) malloc(slack + hostlen + portlen);
+ portlen = (size_t) sprintf(port, ":%hu", xport) + 1;
+ hostport = (char*) malloc(reserve + hostlen + portlen);
if (hostport) {
- memcpy(hostport + slack, host, hostlen);
- hostlen += slack;
+ memcpy(hostport + reserve, host, hostlen);
+ hostlen += reserve;
memcpy(hostport + hostlen, port, portlen);
}
return hostport;
@@ -431,16 +456,6 @@ static int/*bool*/ s_SetHttpHostTag(SConnNetInfo* net_info)
}
-static const char* s_MakePath(const SConnNetInfo* net_info)
-{
- if (net_info->req_method == eReqMethod_Connect
- && net_info->firewall && *net_info->proxy_host) {
- return s_HostPort(0, net_info->proxy_host, net_info->port);
- }
- return ConnNetInfo_URL(net_info);
-}
-
-
static void x_SetRequestIDs(SConnNetInfo* net_info)
{
char* id = CORE_GetNcbiRequestID(eNcbiRequestID_SID);
@@ -527,7 +542,6 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
if (!net_info->port)
net_info->port = CONN_PORT_HTTPS;
net_info->firewall = 0/*false*/;
- net_info->proxy_host[0] = '\0';
ConnNetInfo_DeleteUserHeader(net_info, kHttpHostTag);
status = HTTP_CreateTunnel(net_info, fHTTP_NoUpread, &sock);
assert((status == eIO_Success) ^ !sock);
@@ -539,8 +553,8 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
char* http_user_header;
const char* host;
unsigned short port;
- const char* path;
- const char* args;
+ char* path;
+ char* args;
char* temp;
size_t len;
@@ -549,9 +563,14 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
|| (uuu->net_info->scheme != eURL_Https
&& uuu->net_info->http_proxy_host[0]
&& uuu->net_info->http_proxy_port)) {
+ if (uuu->net_info->http_push_auth
+ && !x_Authenticate(uuu, eRetry_ProxyAuthenticate)) {
+ status = eIO_Unknown;
+ break;
+ }
host = uuu->net_info->http_proxy_host;
port = uuu->net_info->http_proxy_port;
- path = s_MakePath(uuu->net_info);
+ path = ConnNetInfo_URL(uuu->net_info);
if (!path) {
status = eIO_Unknown;
break;
@@ -565,7 +584,7 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
if (temp)
free(temp);
status = eIO_Unknown;
- free((void*) path);
+ free(path);
break;
} else
args = temp;
@@ -574,8 +593,8 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
assert(uuu->net_info->scheme == eURL_Http);
if (!uuu->skip_host && !s_SetHttpHostTag(uuu->net_info)){
status = eIO_Unknown;
- free((void*) path);
assert(!sock);
+ free(path);
break;
}
if (uuu->flags & fHCC_UrlEncodeArgs) {
@@ -588,6 +607,13 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
}
} else {
/* Direct HTTP[S] or tunneled HTTPS */
+ if (uuu->net_info->http_push_auth
+ && (uuu->net_info->scheme == eURL_Https
+ || (uuu->flags & fHTTP_InsecureRedirect))
+ && !x_Authenticate(uuu, eRetry_Authenticate)) {
+ status = eIO_Unknown;
+ break;
+ }
if (!uuu->skip_host && !s_SetHttpHostTag(uuu->net_info)) {
status = eIO_Unknown;
break;
@@ -618,7 +644,7 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
if (temp)
free(temp);
if (path != uuu->net_info->path)
- free((void*) path);
+ free(path);
status = eIO_Unknown;
break;
}
@@ -677,9 +703,9 @@ static EIO_Status s_Connect(SHttpConnector* uuu,
}
if (path != uuu->net_info->path)
- free((void*) path);
+ free(path);
if (args != uuu->net_info->args && args)
- free((void*) args);
+ free(args);
if (sock) {
assert(status == eIO_Success);
@@ -995,7 +1021,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu,
header_header = "HTTP header (redirect)";
else if (retry->mode == eRetry_Redirect303)
header_header = "HTTP header (see other)";
- else if (retry->mode & eRetry_ProxyAuthenticate)
+ else if (retry->mode & eRetry_Authenticate)
header_header = "HTTP header (authentication)";
else if (retry->mode)
header_header = 0, assert(0);
@@ -1402,7 +1428,7 @@ static EIO_Status s_Read(SHttpConnector* uuu, void* buf,
if (uuu->net_info->req_method == eReqMethod_Head) {
status = eIO_Closed;
*n_read = 0;
- } else if (uuu->flags & fHTTP_UrlDecodeInput) {
+ } else if (uuu->flags & fHCC_UrlDecodeInput) {
/* read and URL-decode */
size_t n_peeked, n_decoded;
TNCBI_BigCount remain = uuu->expected - uuu->received;
@@ -1467,7 +1493,7 @@ static EIO_Status s_Read(SHttpConnector* uuu, void* buf,
}
} else {
if (uuu->expected < uuu->received) {
- if (uuu->flags & fHTTP_UrlDecodeInput) {
+ if (uuu->flags & fHCC_UrlDecodeInput) {
assert(*n_read);
--(*n_read);
} else {
@@ -1691,7 +1717,7 @@ static EIO_Status s_VT_Write
uuu->can_connect |= fCC_Once;
/* accumulate all output in the memory buffer */
- if (size && (uuu->flags & fHTTP_UrlEncodeOutput)) {
+ if (size && (uuu->flags & fHCC_UrlEncodeOutput)) {
/* with URL-encoding */
size_t dst_size = 3 * size;
void* dst = malloc(dst_size);
@@ -1843,12 +1869,12 @@ static int/*bool*/ x_FixupUserHeader(SConnNetInfo* net_info,
if ((s = net_info->http_user_header) != 0) {
int/*bool*/ first = 1/*true*/;
while (*s) {
- if (strncasecmp(s, "\nReferer:" + first, 9 - first) == 0) {
+ if (strncasecmp(s, &"\nReferer:"[first], 9 - first) == 0) {
has_referer = 1/*true*/;
- } else if (strncasecmp(s, "\nHost:" + first, 6 - first) == 0) {
+ } else if (strncasecmp(s, &"\nHost:"[first], 6 - first) == 0) {
has_host = 1/*true*/;
#ifdef HAVE_LIBCONNEXT
- } else if (strncasecmp(s, "\nCAF" + first, 4 - first) == 0
+ } else if (strncasecmp(s, &"\nCAF"[first], 4 - first) == 0
&& (s[4 - first] == '-' || s[4 - first] == ':')) {
char* caftag = strndup(s + !first, strcspn(s + !first, " \t"));
if (caftag) {
@@ -1861,7 +1887,7 @@ static int/*bool*/ x_FixupUserHeader(SConnNetInfo* net_info,
}
#endif /*HAVE_LIBCONNEXT*/
} else if (!*has_sid
- && strncasecmp(s, "\n" HTTP_NCBI_SID + first,
+ && strncasecmp(s, &"\n" HTTP_NCBI_SID[first],
sizeof(HTTP_NCBI_SID) - first) == 0) {
*has_sid = 1/*true*/;
}
@@ -1925,6 +1951,10 @@ static EIO_Status s_CreateHttpConnector
ConnNetInfo_OverrideUserHeader(xxx, user_header);
if (tunnel) {
+ if (!xxx->http_proxy_host[0] || !xxx->http_proxy_port) {
+ ConnNetInfo_Destroy(xxx);
+ return eIO_InvalidArg;
+ }
xxx->req_method = eReqMethod_Connect;
xxx->version = 0;
xxx->path[0] = '\0';
@@ -1947,10 +1977,10 @@ static EIO_Status s_CreateHttpConnector
/* initialize internal data structure */
uuu->net_info = xxx;
- uuu->parse_header = 0;
uuu->user_data = 0;
uuu->adjust = 0;
uuu->cleanup = 0;
+ uuu->parse_header = 0;
sid = flags & fHTTP_NoAutomagicSID ? 1 : tunnel;
uuu->skip_host = x_FixupUserHeader(xxx, &sid);
@@ -2006,10 +2036,10 @@ static CONNECTOR s_CreateConnector
}
/* initialize additional internal data structure */
- uuu->parse_header = parse_header;
uuu->user_data = user_data;
uuu->adjust = adjust;
uuu->cleanup = cleanup;
+ uuu->parse_header = parse_header;
ConnNetInfo_GetValue(0, "HTTP_INSECURE_REDIRECT", val, sizeof(val), 0);
if (ConnNetInfo_Boolean(val))
diff --git a/c++/src/connect/ncbi_http_session.cpp b/c++/src/connect/ncbi_http_session.cpp
index d88cd88..c107954 100644
--- a/c++/src/connect/ncbi_http_session.cpp
+++ b/c++/src/connect/ncbi_http_session.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_http_session.cpp 440343 2014-07-11 15:52:35Z grichenk $
+/* $Id: ncbi_http_session.cpp 465171 2015-04-17 15:05:33Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,7 +61,7 @@ static const char* s_HttpHeaderNames[] = {
};
-// Reserved headers can not be set manually.
+// Reserved headers cannot be set manually.
static const char* kReservedHeaders[] = {
"NCBI-SID",
"NCBI-PHID"
@@ -143,10 +143,10 @@ void CHttpHeaders::ClearAll(void)
}
-void CHttpHeaders::ParseHttpHeader(const char* header)
+void CHttpHeaders::ParseHttpHeader(const CTempString& headers)
{
list<string> lines;
- NStr::Split(header, HTTP_EOL, lines);
+ NStr::Split(headers, HTTP_EOL, lines);
string name, value;
ITERATE(list<string>, line, lines) {
@@ -347,10 +347,10 @@ static Int8 s_SimpleRand(Int8 range)
string CHttpFormData::CreateBoundary(void)
{
- static const char* kBoundaryChars =
+ static const char kBoundaryChars[] =
"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_-";
- static const size_t kBoundaryCharsLen = strlen(kBoundaryChars);
- static const int kBoundaryLen = 32;
+ static const size_t kBoundaryCharsLen = sizeof(kBoundaryChars) - 1;
+ static const int kBoundaryLen = 32;
string boundary;
for (int i = 0; i < kBoundaryLen; ++i) {
@@ -398,9 +398,13 @@ void CHttpFormData::WriteFormData(CNcbiOstream& out) const
// Format data as query string.
CUrlArgs args;
ITERATE(TEntries, values, m_Entries) {
- ITERATE(TValues, it, values->second) {
- args.SetValue(values->first, it->m_Value);
+ if (values->second.size() > 1) {
+ NCBI_THROW(CHttpSessionException, eBadFormData,
+ string("No multiple values per entry are allowed "
+ "in URL-encoded form data, entry name '") +
+ values->first + "' ");
}
+ args.SetValue(values->first, values->second.back().m_Value);
}
CFormDataEncoder encoder;
out << args.GetQueryString(CUrlArgs::eAmp_Char, &encoder);
@@ -449,9 +453,9 @@ bool CHttpFormData::IsEmpty(void) const
//
-CHttpResponse::CHttpResponse(CHttpSession& session,
- const CUrl& url,
- CHttpStreamRef& stream)
+CHttpResponse::CHttpResponse(CHttpSession& session,
+ const CUrl& url,
+ CHttpStreamRef& stream)
: m_Session(&session),
m_Url(url),
m_Location(url),
@@ -490,8 +494,7 @@ CNcbiIstream& CHttpResponse::ErrorStream(void) const
bool CHttpResponse::CanGetContentStream(void) const
{
- if (m_StatusCode >= 200 && m_StatusCode < 300) return true;
- return false;
+ return 200 <= m_StatusCode && m_StatusCode < 300;
}
@@ -514,13 +517,6 @@ void CHttpResponse::x_ParseHeader(const char* header)
m_StatusText = status.substr(text_pos);
}
}
-
- // Location must be updated after processing cookies to make sure
- // all current cookies are saved.
- const string& loc = m_Headers->GetValue(CHttpHeaders::eLocation);
- if ( !loc.empty() ) {
- m_Location.SetUrl(loc);
- }
}
@@ -531,19 +527,21 @@ void CHttpResponse::x_ParseHeader(const char* header)
unsigned short SGetHttpDefaultRetries::operator()(void) const
{
- #define STR(s) #s
+#define _STR(s) #s
+#define STR(s) _STR(s)
char buf[16];
ConnNetInfo_GetValue(0, REG_CONN_MAX_TRY, buf, sizeof(buf), STR(DEF_CONN_MAX_TRY));
+#undef STR
+#undef _STR
unsigned short maxtry = atoi(buf);
return maxtry ? maxtry - 1 : 0;
}
inline
-unsigned short RetriesToMaxtry(unsigned short retries)
+unsigned short x_RetriesToMaxtry(unsigned short retries)
{
- retries++;
- return retries ? retries : retries - 1;
+ return ++retries ? retries : retries - 1;
}
@@ -569,7 +567,7 @@ CHttpResponse CHttpRequest::Execute(void)
}
_ASSERT(m_Response);
_ASSERT(m_Stream && m_Stream->IsInitialized());
- CConn_HttpStream& out = m_Stream->GetConnStream();
+ CConn_IOStream& out = m_Stream->GetConnStream();
if ( have_data ) {
m_FormData->WriteFormData(out);
}
@@ -623,6 +621,13 @@ void CHttpRequest::x_InitConnection(bool use_form_data)
SConnNetInfo* connnetinfo = ConnNetInfo_Create(0);
connnetinfo->req_method = m_Method;
+ // Save headers set automatically (e.g. from CONN_HTTP_USER_HEADER).
+ if (connnetinfo->http_user_header) {
+ CHttpHeaders usr_hdr;
+ usr_hdr.ParseHttpHeader(connnetinfo->http_user_header);
+ m_Headers->Merge(usr_hdr);
+ }
+
x_AddCookieHeader(m_Url);
if (use_form_data) {
m_Headers->SetValue(CHttpHeaders::eContentType,
@@ -635,22 +640,40 @@ void CHttpRequest::x_InitConnection(bool use_form_data)
ConnNetInfo_SetTimeout(connnetinfo, g_CTimeoutToSTimeout(m_Timeout, sto));
}
if ( !m_Retries.IsNull() ) {
- connnetinfo->max_try = RetriesToMaxtry(m_Retries);
+ connnetinfo->max_try = x_RetriesToMaxtry(m_Retries);
}
m_Stream.Reset(new TStreamRef);
- m_Stream->SetConnStream(new CConn_HttpStream(
- m_Url.ComposeUrl(CUrlArgs::eAmp_Char),
- connnetinfo,
- headers.c_str(),
- sx_ParseHeader,
- this,
- sx_Adjust,
- 0, // cleanup
- // Always set AdjustOnRedirect flag - we need this to send correct cookies.
- m_Session->GetHttpFlags() | fHTTP_AdjustOnRedirect));
- ConnNetInfo_Destroy(connnetinfo);
m_Response.Reset(new CHttpResponse(*m_Session, m_Url, *m_Stream));
+ if ( m_Url.GetIsGeneric() ) {
+ // Connect using HTTP.
+ m_Stream->SetConnStream(new CConn_HttpStream(
+ m_Url.ComposeUrl(CUrlArgs::eAmp_Char),
+ connnetinfo,
+ headers.c_str(),
+ sx_ParseHeader,
+ this,
+ sx_Adjust,
+ 0, // cleanup
+ // Always set AdjustOnRedirect flag - we need this to send correct cookies.
+ m_Session->GetHttpFlags() | fHTTP_AdjustOnRedirect));
+ }
+ else {
+ // Try to resolve service name.
+ ConnNetInfo_SetUserHeader(connnetinfo, headers.c_str());
+ SSERVICE_Extra x_extra;
+ memset(&x_extra, 0, sizeof(x_extra));
+ x_extra.data = this;
+ x_extra.adjust = sx_Adjust;
+ x_extra.parse_header = sx_ParseHeader;
+ x_extra.flags = m_Session->GetHttpFlags() | fHTTP_AdjustOnRedirect;
+ m_Stream->SetConnStream(new CConn_ServiceStream(
+ m_Url.ComposeUrl(CUrlArgs::eAmp_Char),
+ fSERV_Http,
+ connnetinfo,
+ &x_extra));
+ }
+ ConnNetInfo_Destroy(connnetinfo);
}
@@ -673,8 +696,8 @@ void CHttpRequest::x_AddCookieHeader(const CUrl& url)
// CConn_HttpStream callback for header parsing.
// user_data must contain CHttpRequest*.
EHTTP_HeaderParse CHttpRequest::sx_ParseHeader(const char* http_header,
- void* user_data,
- int server_error)
+ void* user_data,
+ int server_error)
{
if ( !user_data ) return eHTTP_HeaderContinue;
CHttpRequest* req = reinterpret_cast<CHttpRequest*>(user_data);
@@ -694,7 +717,7 @@ EHTTP_HeaderParse CHttpRequest::sx_ParseHeader(const char* http_header,
// user_data must contain CHttpRequest*.
int CHttpRequest::sx_Adjust(SConnNetInfo* net_info,
void* user_data,
- unsigned int failure_count)
+ unsigned int /*failure_count*/)
{
if ( !user_data ) return 1;
// Reset and re-fill headers on redirects (failure_count == 0).
@@ -716,7 +739,13 @@ int CHttpRequest::sx_Adjust(SConnNetInfo* net_info,
break;
}
- // Use new location from the last response rather than the original url.
+ // Update location if it's different from the original url.
+ char* loc = ConnNetInfo_URL(net_info);
+ if (loc) {
+ resp->m_Location.SetUrl(loc);
+ free(loc);
+ }
+ // Discard old cookies, add those for the new location.
req->x_AddCookieHeader(resp->m_Location);
string headers = req->m_Headers->GetHttpHeader();
ConnNetInfo_SetUserHeader(net_info, headers.c_str());
@@ -820,8 +849,22 @@ CHttpResponse g_HttpGet(const CUrl& url,
const CTimeout& timeout,
THttpRetries retries)
{
+ CHttpHeaders hdr;
+ return g_HttpGet(url, hdr, timeout, retries);
+}
+
+
+CHttpResponse g_HttpGet(const CUrl& url,
+ const CHttpHeaders& headers,
+ const CTimeout& timeout,
+ THttpRetries retries)
+{
CRef<CHttpSession> session(new CHttpSession);
- return session->Get(url, timeout, retries);
+ CHttpRequest req = session->NewRequest(url, CHttpSession::eGet);
+ req.SetTimeout(timeout);
+ req.SetRetries(retries);
+ req.Headers().Merge(headers);
+ return req.Execute();
}
@@ -831,8 +874,43 @@ CHttpResponse g_HttpPost(const CUrl& url,
const CTimeout& timeout,
THttpRetries retries)
{
+ CHttpHeaders hdr;
+ return g_HttpPost(url, hdr, data, content_type, timeout, retries);
+}
+
+
+CHttpResponse g_HttpPost(const CUrl& url,
+ const CHttpHeaders& headers,
+ CTempString data,
+ CTempString content_type,
+ const CTimeout& timeout,
+ THttpRetries retries)
+{
CRef<CHttpSession> session(new CHttpSession);
- return session->Post(url, data, content_type, timeout, retries);
+ CHttpRequest req = session->NewRequest(url, CHttpSession::ePost);
+ req.SetTimeout(timeout);
+ req.SetRetries(retries);
+ req.Headers().Merge(headers);
+
+ if ( content_type.empty() ) {
+ if ( headers.HasValue(CHttpHeaders::eContentType) ) {
+ req.Headers().SetValue(CHttpHeaders::eContentType,
+ headers.GetValue(CHttpHeaders::eContentType));
+ }
+ else {
+ req.Headers().SetValue(CHttpHeaders::eContentType,
+ kContentType_FormUrlEnc);
+ }
+ }
+ else {
+ req.Headers().SetValue(CHttpHeaders::eContentType, content_type);
+ }
+
+ if ( !data.empty() ) {
+ req.ContentStream() << data;
+ }
+
+ return req.Execute();
}
diff --git a/c++/src/connect/ncbi_lb.c b/c++/src/connect/ncbi_lb.c
index 7e42657..e0cb031 100644
--- a/c++/src/connect/ncbi_lb.c
+++ b/c++/src/connect/ncbi_lb.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_lb.c 371118 2012-08-05 05:42:45Z lavr $
+/* $Id: ncbi_lb.c 451391 2014-11-06 15:31:05Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -81,8 +81,8 @@ size_t LB_Select(SERV_ITER iter, void* data,
status = cand->status;
latch = iter->host && iter->host == info->host
&& (!iter->port || iter->port == info->port);
- if (latch || (!fixed && !iter->host &&
- info->locl && info->coef < 0.0)) {
+ if (latch || (!fixed && !iter->host && info->coef < 0.0
+ && (info->site & (fSERV_Local | fSERV_Private)))) {
if (fixed < latch) {
fixed = latch;
access = point = 0.0;
diff --git a/c++/src/connect/ncbi_lbsmd.h b/c++/src/connect/ncbi_lbsmd.h
index 7d76c3f..570f365 100644
--- a/c++/src/connect/ncbi_lbsmd.h
+++ b/c++/src/connect/ncbi_lbsmd.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_LBSMD__H
#define CONNECT___NCBI_LBSMD__H
-/* $Id: ncbi_lbsmd.h 371117 2012-08-05 05:03:11Z lavr $
+/* $Id: ncbi_lbsmd.h 458666 2015-02-09 00:47:56Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -91,6 +91,9 @@ NCBI_XCONNECT_EXPORT const char* LBSMD_GetHostParameter(unsigned int addr,
NCBI_XCONNECT_EXPORT ESwitch LBSMD_FastHeapAccess(ESwitch onoff);
+unsigned int LBSMD_GetLocalHostAddress(const void/*SLBSM_Version*/ *v);
+
+
int LBSM_HINFO_CpuCount(const HOST_INFO hinfo);
diff --git a/c++/src/connect/ncbi_lbsmd_stub.c b/c++/src/connect/ncbi_lbsmd_stub.c
index 46fb9a8..ab98eb8 100644
--- a/c++/src/connect/ncbi_lbsmd_stub.c
+++ b/c++/src/connect/ncbi_lbsmd_stub.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_lbsmd_stub.c 338933 2011-09-23 14:08:59Z lavr $
+/* $Id: ncbi_lbsmd_stub.c 458666 2015-02-09 00:47:56Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -73,6 +73,13 @@ extern const char* LBSMD_GetHostParameter(unsigned int host,
/*ARGSUSED*/
+unsigned int LBSMD_GetLocalHostAddress(const void* v)
+{
+ return SOCK_GetLocalHostAddress(eDefault);
+}
+
+
+/*ARGSUSED*/
int LBSM_HINFO_CpuCount(const HOST_INFO hinfo)
{
return -1;
diff --git a/c++/src/connect/ncbi_local.c b/c++/src/connect/ncbi_local.c
index 85643b7..3c719dd 100644
--- a/c++/src/connect/ncbi_local.c
+++ b/c++/src/connect/ncbi_local.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_local.c 440974 2014-07-18 16:13:30Z lavr $
+/* $Id: ncbi_local.c 462401 2015-03-18 16:28:18Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -116,13 +116,13 @@ static int/*bool*/ s_LoadSingleService(const char* name, SERV_ITER iter)
(svc, iter->ismask || iter->reverse_dns ? name : "", 0))) {
continue;
}
- if (iter->external && info->locl)
+ if (iter->external && (info->site & (fSERV_Local | fSERV_Private)))
continue; /* external mapping for local server not allowed */
- if (!info->host || (info->locl & 0x10)) {
+ if (!info->host || (info->site & fSERV_Private)) {
unsigned int localhost = SOCK_GetLocalHostAddress(eDefault);
if (!info->host)
info->host = localhost;
- if ((info->locl & 0x10) && info->host != localhost)
+ if ((info->site & fSERV_Private) && info->host != localhost)
continue; /* private server */
}
if (!iter->reverse_dns && info->type != fSERV_Dns) {
@@ -130,7 +130,7 @@ static int/*bool*/ s_LoadSingleService(const char* name, SERV_ITER iter)
continue; /* type doesn't match */
if (types == fSERV_Any && info->type == fSERV_Dns)
continue; /* DNS entries have to be req'd explicitly */
- if (iter->stateless && info->sful && !(info->type & fSERV_Http))
+ if (iter->stateless && (info->mode & fSERV_Stateful))
continue; /* skip stateful only servers */
}
if (!info->rate)
@@ -299,9 +299,10 @@ static SSERV_Info* s_GetNextInfo(SERV_ITER iter, HOST_INFO* host_info)
}
if (!iter->ismask)
dns_info_seen = 1/*true*/;
- if (iter->external && temp->locl)
+ if (iter->external
+ && (temp->site & (fSERV_Local | fSERV_Private))) {
continue; /* external mapping req'd; local server */
- assert(!(temp->locl & 0x10)); /* no private DNS */
+ }
if (temp->rate > 0.0 || iter->ok_down) {
data->cand[i].status = data->cand[n].status;
info = temp;
@@ -335,7 +336,8 @@ static SSERV_Info* s_GetNextInfo(SERV_ITER iter, HOST_INFO* host_info)
static void s_Reset(SERV_ITER iter)
{
struct SLOCAL_Data* data = (struct SLOCAL_Data*) iter->data;
- if (data && data->cand) {
+ assert(data);
+ if (data->cand) {
size_t i;
assert(data->a_cand);
for (i = 0; i < data->n_cand; i++)
@@ -349,15 +351,16 @@ static void s_Reset(SERV_ITER iter)
static void s_Close(SERV_ITER iter)
{
struct SLOCAL_Data* data = (struct SLOCAL_Data*) iter->data;
- assert(!data->n_cand && data->reset); /* s_Reset() has been called */
+ /* NB: s_Reset() must have been called before */
+ assert(data && !data->n_cand && data->reset);
if (data->cand) {
assert(data->a_cand);
data->a_cand = 0;
free(data->cand);
data->cand = 0;
}
- free(data);
iter->data = 0;
+ free(data);
}
diff --git a/c++/src/connect/ncbi_namedpipe.cpp b/c++/src/connect/ncbi_namedpipe.cpp
index c1fd4e7..f178e33 100644
--- a/c++/src/connect/ncbi_namedpipe.cpp
+++ b/c++/src/connect/ncbi_namedpipe.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_namedpipe.cpp 450563 2014-10-28 15:19:24Z ivanov $
+/* $Id: ncbi_namedpipe.cpp 445730 2014-09-08 13:17:51Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/ncbi_namedpipe_connector.cpp b/c++/src/connect/ncbi_namedpipe_connector.cpp
index e60f94c..a68281e 100644
--- a/c++/src/connect/ncbi_namedpipe_connector.cpp
+++ b/c++/src/connect/ncbi_namedpipe_connector.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_namedpipe_connector.cpp 362029 2012-05-07 15:36:34Z lavr $
+/* $Id: ncbi_namedpipe_connector.cpp 447122 2014-09-22 18:33:27Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,10 +48,9 @@ USING_NCBI_SCOPE;
// All internal data necessary to perform the (re)connect and i/o
typedef struct {
- CNamedPipeClient* pipe; // pipe handle; NULL if not connected yet
+ CNamedPipeClient* pipe; // pipe handle; non-NULL
string pipename; // pipe name
- size_t pipebufsize; // pipe buffer size
- bool is_open; // true if pipe is open
+ size_t pipesize; // pipe size
} SNamedPipeConnector;
@@ -83,21 +82,10 @@ static EIO_Status s_VT_Open
const STimeout* timeout)
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
-
- _ASSERT(!xxx->is_open);
-
if (!xxx->pipe) {
return eIO_Unknown; // blame operator "new" :-/
}
- if (xxx->pipe->SetTimeout(eIO_Open, timeout) != eIO_Success) {
- return eIO_Unknown;
- }
- EIO_Status status = xxx->pipe->Open(xxx->pipename, timeout,
- xxx->pipebufsize);
- if (status == eIO_Success) {
- xxx->is_open = true;
- }
- return status;
+ return xxx->pipe->Open(xxx->pipename, timeout, xxx->pipesize);
}
@@ -108,7 +96,6 @@ static EIO_Status s_VT_Wait
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
_ASSERT(event == eIO_Read || event == eIO_Write);
- _ASSERT(xxx->is_open && xxx->pipe);
return xxx->pipe->Wait(event, timeout);
}
@@ -121,7 +108,6 @@ static EIO_Status s_VT_Write
const STimeout* timeout)
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
if (xxx->pipe->SetTimeout(eIO_Write, timeout) != eIO_Success) {
return eIO_Unknown;
}
@@ -137,7 +123,6 @@ static EIO_Status s_VT_Read
const STimeout* timeout)
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
if (xxx->pipe->SetTimeout(eIO_Read, timeout) != eIO_Success) {
return eIO_Unknown;
}
@@ -150,7 +135,6 @@ static EIO_Status s_VT_Status
EIO_Event dir)
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
return xxx->pipe->Status(dir);
}
@@ -160,8 +144,6 @@ static EIO_Status s_VT_Close
const STimeout* /*timeout*/)
{
SNamedPipeConnector* xxx = (SNamedPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
- xxx->is_open = false;
return xxx->pipe->Close();
}
@@ -210,7 +192,7 @@ BEGIN_NCBI_SCOPE
extern CONNECTOR NAMEDPIPE_CreateConnector
(const string& pipename,
- size_t pipebufsize)
+ size_t pipesize)
{
CONNECTOR ccc;
SNamedPipeConnector* xxx;
@@ -219,11 +201,10 @@ extern CONNECTOR NAMEDPIPE_CreateConnector
return 0;
// Initialize internal data structures
- xxx = new SNamedPipeConnector;
- xxx->pipe = new CNamedPipeClient;
- xxx->pipename = pipename;
- xxx->pipebufsize = pipebufsize;
- xxx->is_open = false;
+ xxx = new SNamedPipeConnector;
+ xxx->pipe = new CNamedPipeClient;
+ xxx->pipename = pipename;
+ xxx->pipesize = pipesize;
// Initialize connector data
ccc->handle = xxx;
diff --git a/c++/src/connect/ncbi_pipe.cpp b/c++/src/connect/ncbi_pipe.cpp
index 5f22b9b..43f4968 100644
--- a/c++/src/connect/ncbi_pipe.cpp
+++ b/c++/src/connect/ncbi_pipe.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_pipe.cpp 450564 2014-10-28 15:19:44Z ivanov $
+/* $Id: ncbi_pipe.cpp 452711 2014-11-24 15:55:22Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -232,6 +232,7 @@ public:
CPipe::TChildPollMask Poll(CPipe::TChildPollMask mask,
const STimeout* timeout) const;
TProcessHandle GetProcessHandle(void) const { return m_ProcHandle; }
+ void Release(void) { x_Clear(); }
private:
// Clear object state.
@@ -903,6 +904,7 @@ public:
CPipe::TChildPollMask Poll(CPipe::TChildPollMask mask,
const STimeout* timeout) const;
TProcessHandle GetProcessHandle(void) const { return m_Pid; }
+ void Release(void) { x_Clear(); }
private:
// Clear object state.
@@ -2047,7 +2049,18 @@ CPipe::EFinish CPipe::ExecWait(const string& cmd,
}
if (!CProcess(pid).IsAlive())
break;
- if (watcher && watcher->Watch(pid) != IProcessWatcher::eContinue) {
+ if (watcher) {
+ switch (watcher->Watch(pid)) {
+ case IProcessWatcher::eContinue:
+ continue;
+ case IProcessWatcher::eStop:
+ break;
+ case IProcessWatcher::eExit:
+ if (pipe.m_PipeHandle) pipe.m_PipeHandle->Release();
+ return eCanceled;
+ }
+
+ // IProcessWatcher::eStop
pipe.SetTimeout(eIO_Close, &ktm);
finish = eCanceled;
break;
diff --git a/c++/src/connect/ncbi_pipe_connector.cpp b/c++/src/connect/ncbi_pipe_connector.cpp
index 58186fa..73e98e7 100644
--- a/c++/src/connect/ncbi_pipe_connector.cpp
+++ b/c++/src/connect/ncbi_pipe_connector.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_pipe_connector.cpp 362029 2012-05-07 15:36:34Z lavr $
+/* $Id: ncbi_pipe_connector.cpp 447122 2014-09-22 18:33:27Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -47,12 +47,12 @@ USING_NCBI_SCOPE;
// All internal data necessary to perform the (re)connect and i/o
typedef struct {
- CPipe* pipe; // pipe handle; NULL if not connected yet
+ CPipe* pipe; // pipe handle; non-NULL
string cmd; // program to execute
vector<string> args; // program arguments
CPipe::TCreateFlags flags; // pipe create flags
- bool is_open; // true if pipe is open
bool own_pipe; // true if pipe is owned
+ size_t pipe_size;
} SPipeConnector;
@@ -97,17 +97,11 @@ static EIO_Status s_VT_Open
const STimeout* /*timeout*/)
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
-
- _ASSERT(!xxx->is_open);
-
if (!xxx->pipe) {
- return eIO_Unknown;
- }
- EIO_Status status = xxx->pipe->Open(xxx->cmd, xxx->args, xxx->flags);
- if (status == eIO_Success) {
- xxx->is_open = true;
+ return eIO_Unknown; // blame operator "new" :-/
}
- return status;
+ return xxx->pipe->Open(xxx->cmd, xxx->args, xxx->flags,
+ kEmptyStr, NULL, xxx->pipe_size);
}
@@ -118,7 +112,6 @@ static EIO_Status s_VT_Wait
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
_ASSERT(event == eIO_Read || event == eIO_Write);
- _ASSERT(xxx->is_open && xxx->pipe);
CPipe::TChildPollMask what = 0;
if (event & eIO_Read)
what |= CPipe::fDefault;
@@ -136,7 +129,6 @@ static EIO_Status s_VT_Write
const STimeout* timeout)
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
if (xxx->pipe->SetTimeout(eIO_Write, timeout) != eIO_Success) {
return eIO_Unknown;
}
@@ -152,7 +144,6 @@ static EIO_Status s_VT_Read
const STimeout* timeout)
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
if (xxx->pipe->SetTimeout(eIO_Read, timeout) != eIO_Success) {
return eIO_Unknown;
}
@@ -165,7 +156,6 @@ static EIO_Status s_VT_Status
EIO_Event dir)
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
return xxx->pipe->Status(dir);
}
@@ -175,8 +165,6 @@ static EIO_Status s_VT_Close
const STimeout* timeout)
{
SPipeConnector* xxx = (SPipeConnector*) connector->handle;
- _ASSERT(xxx->is_open && xxx->pipe);
- xxx->is_open = false;
xxx->pipe->SetTimeout(eIO_Close, timeout);
return xxx->pipe->Close();
}
@@ -229,9 +217,10 @@ BEGIN_NCBI_SCOPE
extern CONNECTOR PIPE_CreateConnector
(const string& cmd,
const vector<string>& args,
- CPipe::TCreateFlags create_flags,
+ CPipe::TCreateFlags flags,
CPipe* pipe,
- EOwnership own_pipe)
+ EOwnership own_pipe,
+ size_t pipe_size)
{
CONNECTOR ccc;
SPipeConnector* xxx;
@@ -240,13 +229,13 @@ extern CONNECTOR PIPE_CreateConnector
return 0;
// Initialize internal data structures
- xxx = new SPipeConnector;
- xxx->pipe = pipe ? pipe : new CPipe;
- xxx->cmd = cmd;
- xxx->args = args;
- xxx->flags = create_flags;
- xxx->is_open = false;
- xxx->own_pipe = pipe ? own_pipe == eTakeOwnership : true;
+ xxx = new SPipeConnector;
+ xxx->pipe = pipe ? pipe : new CPipe;
+ xxx->cmd = cmd;
+ xxx->args = args;
+ xxx->flags = flags;
+ xxx->own_pipe = pipe ? own_pipe == eTakeOwnership : true;
+ xxx->pipe_size = pipe_size;
// Initialize connector data
ccc->handle = xxx;
diff --git a/c++/src/connect/ncbi_priv.h b/c++/src/connect/ncbi_priv.h
index e565b48..9c471d0 100644
--- a/c++/src/connect/ncbi_priv.h
+++ b/c++/src/connect/ncbi_priv.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_PRIV__H
#define CONNECT___NCBI_PRIV__H
-/* $Id: ncbi_priv.h 449177 2014-10-14 13:58:55Z ivanov $
+/* $Id: ncbi_priv.h 456332 2015-01-09 18:46:30Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,26 +76,25 @@ extern "C" {
/* automatic subcode checking is not implemented in C code */ \
}
-/* Here are only error codes used in C sources. For error codes used in
+/* Here are only error codes used in C sources. For error codes used in
* C++ sources (in C++ Toolkit) see include/connect/error_codes.hpp.
*/
NCBI_C_DEFINE_ERRCODE_X(Connect_Conn, 301, 36);
-NCBI_C_DEFINE_ERRCODE_X(Connect_LBSM, 302, 25);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Util, 303, 8);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Dispd, 304, 2);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Socket, 302, 163);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Util, 303, 9);
+NCBI_C_DEFINE_ERRCODE_X(Connect_LBSM, 304, 33);
NCBI_C_DEFINE_ERRCODE_X(Connect_FTP, 305, 13);
-NCBI_C_DEFINE_ERRCODE_X(Connect_HeapMgr, 306, 33);
+NCBI_C_DEFINE_ERRCODE_X(Connect_SMTP, 306, 33);
NCBI_C_DEFINE_ERRCODE_X(Connect_HTTP, 307, 23);
-NCBI_C_DEFINE_ERRCODE_X(Connect_LBSMD, 308, 8);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Sendmail, 309, 33);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Service, 310, 9);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Socket, 311, 163);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Service, 308, 9);
+NCBI_C_DEFINE_ERRCODE_X(Connect_HeapMgr, 309, 33);
+ /* 310 unused */
+NCBI_C_DEFINE_ERRCODE_X(Connect_Mghbn, 311, 16);
NCBI_C_DEFINE_ERRCODE_X(Connect_Crypt, 312, 5);
NCBI_C_DEFINE_ERRCODE_X(Connect_LocalNet, 313, 4);
-NCBI_C_DEFINE_ERRCODE_X(Connect_Mghbn, 314, 16);
/** Make one identifier from 2 parts */
-#define NCBI_C_CONCAT_IDENTIFIER(prefix, postfix) prefix##postfix
+#define NCBI_C_CONCAT_IDENTIFIER(prefix, postfix) prefix##postfix
/** Return value of error code by its name defined by NCBI_DEFINE_ERRCODE_X
*
@@ -109,7 +108,8 @@ NCBI_C_DEFINE_ERRCODE_X(Connect_Mghbn, 314, 16);
*
* @sa NCBI_DEFINE_ERRCODE_X
*/
-#define NCBI_C_ERRCODE_X NCBI_C_ERRCODE_X_NAME(NCBI_USE_ERRCODE_X)
+#define NCBI_C_ERRCODE_X \
+ NCBI_C_ERRCODE_X_NAME(NCBI_USE_ERRCODE_X)
extern NCBI_XCONNECT_EXPORT LOG g_CORE_Log;
@@ -196,15 +196,15 @@ extern NCBI_XCONNECT_EXPORT LOG g_CORE_Log;
#define DO_CORE_LOG_X(_code, _subcode, _level, _message, _dynamic, \
_error, _descr, _raw_data, _raw_size) \
do { \
- ELOG_Level xx_level = (_level); \
- if (g_CORE_Log || xx_level == eLOG_Fatal) { \
+ ELOG_Level _xx_level = (_level); \
+ if (g_CORE_Log || _xx_level == eLOG_Fatal) { \
SLOG_Handler _mess; \
_mess.dynamic = _dynamic; \
_mess.message = NcbiMessagePlusError(&_mess.dynamic, \
- _message, \
- _error, \
- _descr); \
- _mess.level = xx_level; \
+ (_message), \
+ (_error), \
+ (_descr)); \
+ _mess.level = _xx_level; \
_mess.module = THIS_MODULE; \
_mess.func = CORE_CURRENT_FUNCTION; \
_mess.file = __FILE__; \
@@ -308,9 +308,9 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ g_CORE_RegistrySET
* Random generator seeding support
*/
-extern NCBI_XCONNECT_EXPORT int g_NCBI_ConnectRandomSeed;
-extern NCBI_XCONNECT_EXPORT int g_NCBI_ConnectSrandAddend(void);
-#define NCBI_CONNECT_SRAND_ADDEND g_NCBI_ConnectSrandAddend()
+extern NCBI_XCONNECT_EXPORT int g_NCBI_ConnectRandomSeed;
+extern NCBI_XCONNECT_EXPORT int g_NCBI_ConnectSrandAddend(void);
+#define NCBI_CONNECT_SRAND_ADDEND g_NCBI_ConnectSrandAddend()
/******************************************************************************
@@ -331,6 +331,15 @@ typedef char* (*FNcbiGetRequestID)(ENcbiRequestID);
extern NCBI_XCONNECT_EXPORT FNcbiGetRequestID g_CORE_GetRequestID;
+#ifdef __GNUC__
+# define likely(x) __builtin_expect(!!(x),1)
+# define unlikely(x) __builtin_expect(!!(x),0)
+#else
+# define likely(x) (x)
+# define unlikely(x) (x)
+#endif /*__GNUC__*/
+
+
#ifdef __cplusplus
} /* extern "C" */
#endif
diff --git a/c++/src/connect/ncbi_sendmail.c b/c++/src/connect/ncbi_sendmail.c
index 368e9d1..4537088 100644
--- a/c++/src/connect/ncbi_sendmail.c
+++ b/c++/src/connect/ncbi_sendmail.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_sendmail.c 430867 2014-03-29 22:09:21Z lavr $
+/* $Id: ncbi_sendmail.c 453682 2014-12-05 15:49:55Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,7 +39,7 @@
#include <stdlib.h>
#include <time.h>
-#define NCBI_USE_ERRCODE_X Connect_Sendmail
+#define NCBI_USE_ERRCODE_X Connect_SMTP
#define MX_MAGIC_COOKIE 0xBA8ADEDA
#define MX_CRLF "\r\n"
@@ -201,15 +201,12 @@ static void s_MakeFrom(char* buf, size_t size, const char* from,
/* "user@[host]" */
if (buf != from) {
len = (size_t)(at - from);
- if (at[1]) {
- /* "user at host" */
- if (len < size) {
- size_t tmp = len + strlen(at);
- if (tmp < size)
- len = tmp;
- } else
- len = size - 1;
- } /* else "user@" */
+ if (len < size) {
+ size_t tmp = len + strlen(at);
+ if (tmp < size)
+ len = tmp;
+ } else
+ len = size - 1;
strncpy0(buf, from, len);
}
if (*++at)
@@ -236,7 +233,7 @@ static void s_MakeFrom(char* buf, size_t size, const char* from,
strncpy0(buf, "anonymous", size - 1);
len = strlen(buf);
} else
- len = strlen(buf) - 1;
+ len = strlen(buf) - 1/*'@'*/;
size -= len;
buf += len;
if (!at || !*at) {
@@ -365,7 +362,7 @@ static const char* s_SendRcpt(SOCK sock, const char* to,
const char proto_error[])
{
char c;
- while ((c = *to++) != 0) {
+ while ((c = *to++) != '\0') {
char quote = 0;
size_t k = 0;
if (isspace((unsigned char) c))
@@ -412,9 +409,9 @@ static const char* s_SendRcpt(SOCK sock, const char* to,
static size_t s_FromSize(const SSendMailInfo* info)
{
const char* at, *dot;
- size_t len = strlen(info->from);
+ size_t len = *info->from ? strlen(info->from) : 0;
- if (!*info->from || !(info->mx_options & fSendMail_StripNonFQDNHost))
+ if (!len || !(info->mx_options & fSendMail_StripNonFQDNHost))
return len;
if (!(at = (const char*) memchr(info->from, '@', len))
|| at == info->from + len - 1) {
diff --git a/c++/src/connect/ncbi_server_info.c b/c++/src/connect/ncbi_server_info.c
index c816194..28eb087 100644
--- a/c++/src/connect/ncbi_server_info.c
+++ b/c++/src/connect/ncbi_server_info.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_server_info.c 442196 2014-07-31 02:11:31Z mcelhany $
+/* $Id: ncbi_server_info.c 465213 2015-04-17 20:53:10Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -90,19 +90,6 @@ static struct {
};
-/* Any server is not local by default.
- */
-static unsigned char/*bool*/ s_LocalServerDefault = 0/*false*/;
-
-
-int/*bool*/ SERV_SetLocalServerDefault(int/*bool*/ onoff)
-{
- int/*bool*/ retval = s_LocalServerDefault;
- s_LocalServerDefault = onoff ? 0x01/*true*/ : 0x00/*false*/;
- return retval;
-}
-
-
/* Attributes' lookup (by either type or tag)
*/
static const SSERV_Attr* s_GetAttrByType(ESERV_Type type);
@@ -136,6 +123,7 @@ extern const char* SERV_ReadType(const char* str,
extern char* SERV_WriteInfo(const SSERV_Info* info)
{
+ static const char* k_NY[] = { "no", "yes" };
char c_t[MAX_CONTENT_TYPE_LEN];
const SSERV_Attr* attr;
size_t reserve;
@@ -154,10 +142,10 @@ extern char* SERV_WriteInfo(const SSERV_Info* info)
p++;
memmove(c_t, p, strlen(p) + 1);
} else
- *c_t = 0;
+ *c_t = '\0';
reserve = attr->tag_len+1 + MAX_IP_ADDR_LEN + 1+5/*port*/ + 1+12/*flag*/ +
- 1+9/*coef*/ + 3+strlen(c_t)/*cont.type*/ + 1+5/*locl*/ + 1+5/*priv*/ +
- 1+7/*quorum*/ + 1+14/*rate*/ + 1+5/*sful*/ + 1+12/*time*/ + 1/*EOL*/;
+ 1+9/*coef*/ + 3+strlen(c_t)/*cont.type*/ + 3*(1+5)/*site*/ +
+ 1+14/*rate*/ + 2*(1+5)/*mode*/ + 1+12/*time*/ + 1/*EOL*/;
/* write server-specific info */
if ((str = attr->vtable.Write(reserve, &info->u)) != 0) {
char* s = str;
@@ -182,20 +170,16 @@ extern char* SERV_WriteInfo(const SSERV_Info* info)
s = NCBI_simple_ftoa(strcpy(s, " B=") + 3, info->coef, 2);
if (*c_t)
s += sprintf(s, " C=%s", c_t);
- s += sprintf(s, " L=%s", info->locl & 1 ? "yes" : "no");
- if (info->type != fSERV_Dns && (info->locl & 0x10))
+ s += sprintf(s, " L=%s", k_NY[info->site & fSERV_Local]);
+ if (info->type != fSERV_Dns && (info->site & fSERV_Private))
s += sprintf(s, " P=yes");
- if (info->host && info->quorum) {
- if (info->quorum == (unsigned short)(-1))
- s += sprintf(s, " Q=yes");
- else
- s += sprintf(s, " Q=%hu", info->quorum);
- }
s = NCBI_simple_ftoa(strcpy(s," R=") + 3, info->rate,
fabs(info->rate) < 0.01 ? 3 : 2);
if (!(info->type & fSERV_Http) && info->type != fSERV_Dns)
- s += sprintf(s, " S=%s", info->sful ? "yes" : "no");
- s += sprintf(s, " T=%lu", (unsigned long) info->time);
+ s += sprintf(s, " S=%s", k_NY[info->mode & fSERV_Stateful]);
+ if (info->type != fSERV_Dns && (info->mode & fSERV_Secure))
+ s += sprintf(s, " $=yes");
+ sprintf(s, " T=%lu", (unsigned long) info->time);
}
return str;
}
@@ -205,7 +189,7 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
const char* name,
int/*bool*/ lazy)
{
- int/*bool*/ coef, mime, locl, priv, quor, rate, sful, time, flag;
+ int/*bool*/ coef, mime, locl, priv, rate, sful, secu, time, flag;
ESERV_Type type;
unsigned int host; /* network byte order */
unsigned short port; /* host (native) byte order */
@@ -259,8 +243,8 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
info->host = host;
if (port)
info->port = port;
- coef = mime = locl = priv = quor = rate = sful = time = flag = 0;/*false*/
- /* continue reading server info: optional parts: ... */
+ coef = mime = locl = priv = rate = sful = secu = time = flag = 0;/*false*/
+ /* continue reading server info: optional parts... */
while (*str && isspace((unsigned char)(*str)))
++str;
while (*str) {
@@ -268,7 +252,6 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
char* e;
int n;
double d;
- unsigned short h;
unsigned long t;
char s[4];
EMIME_Type mime_t;
@@ -311,10 +294,10 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
locl = 1;
if (sscanf(++str, "%3s%n", s, &n) >= 1) {
if (strcasecmp(s, "YES") == 0) {
- info->locl |= 0x01/*set*/;
+ info->site |= fSERV_Local;
str += n;
} else if (strcasecmp(s, "NO") == 0) {
- info->locl &= ~0x01/*clear*/;
+ info->site &= ~fSERV_Local;
str += n;
}
}
@@ -325,27 +308,14 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
priv = 1;
if (sscanf(++str, "%3s%n", s, &n) >= 1) {
if (strcasecmp(s, "YES") == 0) {
- info->locl |= 0x10;/*set*/
+ info->site |= fSERV_Private;
str += n;
} else if (strcasecmp(s, "NO") == 0) {
- info->locl &= ~0x10;/*clear*/
+ info->site &= ~fSERV_Private;
str += n;
}
}
break;
- case 'Q':
- if (quor || type == fSERV_Firewall || !info->host)
- break;
- quor = 1;
- if (sscanf(++str, "%3s%n", s, &n) >= 1
- && strcasecmp(s, "YES") == 0) {
- info->quorum = (unsigned short)(-1);
- str += n;
- } else if (sscanf(str, "%hu%n", &h, &n) >= 1) {
- info->quorum = h;
- str += n;
- }
- break;
case 'R':
if (rate)
break;
@@ -363,17 +333,29 @@ SSERV_Info* SERV_ReadInfoEx(const char* str,
}
break;
case 'S':
- if (sful || (type & fSERV_Http) != 0)
+ if (sful || type == fSERV_Dns || (type & fSERV_Http))
break;
sful = 1;
if (sscanf(++str, "%3s%n", s, &n) >= 1) {
if (strcasecmp(s, "YES") == 0) {
- if (type == fSERV_Dns)
- break; /*check only here for compatibility*/
- info->sful = 1/*true*/;
+ info->mode |= fSERV_Stateful;
+ str += n;
+ } else if (strcasecmp(s, "NO") == 0) {
+ info->mode &= ~fSERV_Stateful;
+ str += n;
+ }
+ }
+ break;
+ case '$':
+ if (secu || type == fSERV_Dns)
+ break;
+ secu = 1;
+ if (sscanf(++str, "%3s%n", s, &n) >= 1) {
+ if (strcasecmp(s, "YES") == 0) {
+ info->mode |= fSERV_Secure;
str += n;
} else if (strcasecmp(s, "NO") == 0) {
- info->sful = 0/*false*/;
+ info->mode &= ~fSERV_Secure;
str += n;
}
}
@@ -541,22 +523,21 @@ SSERV_Info* SERV_CreateNcbidInfoEx(unsigned int host,
add += args ? strlen(args) : 0;
if ((info = (SSERV_Info*) malloc(sizeof(SSERV_Info) + add + 1)) != 0) {
- info->type = fSERV_Ncbid;
- info->host = host;
- info->port = port;
- info->sful = 0;
- info->locl = s_LocalServerDefault;
- info->time = 0;
- info->coef = 0.0;
- info->rate = 0.0;
- info->mime_t = eMIME_T_Undefined;
- info->mime_s = eMIME_Undefined;
- info->mime_e = eENCOD_None;
- info->flag = SERV_DEFAULT_FLAG;
+ info->type = fSERV_Ncbid;
+ info->host = host;
+ info->port = port;
+ info->mode = 0;
+ info->site = fSERV_Local;
+ info->time = 0;
+ info->coef = 0.0;
+ info->rate = 0.0;
+ info->mime_t = eMIME_T_Undefined;
+ info->mime_s = eMIME_Undefined;
+ info->mime_e = eENCOD_None;
+ info->flag = SERV_DEFAULT_FLAG;
memset(&info->reserved, 0, sizeof(info->reserved));
- info->quorum = 0;
info->u.ncbid.args = (TNCBI_Size) sizeof(info->u.ncbid);
- if (strcmp(args, "''") == 0) /* special case */
+ if (args && strcmp(args, "''"/*special case*/) == 0)
args = 0;
strcpy(SERV_NCBID_ARGS(&info->u.ncbid), args ? args : "");
}
@@ -610,8 +591,8 @@ SSERV_Info* SERV_CreateStandaloneInfoEx(unsigned int host,
info->type = fSERV_Standalone;
info->host = host;
info->port = port;
- info->sful = 0;
- info->locl = s_LocalServerDefault;
+ info->mode = 0;
+ info->site = fSERV_Local;
info->time = 0;
info->coef = 0.0;
info->rate = 0.0;
@@ -620,7 +601,6 @@ SSERV_Info* SERV_CreateStandaloneInfoEx(unsigned int host,
info->mime_e = eENCOD_None;
info->flag = SERV_DEFAULT_FLAG;
memset(&info->reserved, 0, sizeof(info->reserved));
- info->quorum = 0;
memset(&info->u.standalone, 0, sizeof(info->u.standalone));
}
return info;
@@ -678,19 +658,19 @@ static SSERV_Info* s_HttpAny_Read(ESERV_Type type,const char** str, size_t add)
}
-static SSERV_Info *s_HttpGet_Read(const char** str, size_t add)
+static SSERV_Info* s_HttpGet_Read(const char** str, size_t add)
{
return s_HttpAny_Read(fSERV_HttpGet, str, add);
}
-static SSERV_Info *s_HttpPost_Read(const char** str, size_t add)
+static SSERV_Info* s_HttpPost_Read(const char** str, size_t add)
{
return s_HttpAny_Read(fSERV_HttpPost, str, add);
}
-static SSERV_Info *s_Http_Read(const char** str, size_t add)
+static SSERV_Info* s_Http_Read(const char** str, size_t add)
{
return s_HttpAny_Read(fSERV_Http, str, add);
}
@@ -724,20 +704,19 @@ SSERV_Info* SERV_CreateHttpInfoEx(ESERV_Type type,
return 0;
add += (path ? strlen(path) : 0) + 1 + (args ? strlen(args) : 0);
if ((info = (SSERV_Info*) malloc(sizeof(SSERV_Info) + add + 1)) != 0) {
- info->type = type;
- info->host = host;
- info->port = port;
- info->sful = 0;
- info->locl = s_LocalServerDefault;
- info->time = 0;
- info->coef = 0.0;
- info->rate = 0.0;
- info->mime_t = eMIME_T_Undefined;
- info->mime_s = eMIME_Undefined;
- info->mime_e = eENCOD_None;
- info->flag = SERV_DEFAULT_FLAG;
+ info->type = type;
+ info->host = host;
+ info->port = port;
+ info->mode = 0;
+ info->site = fSERV_Local;
+ info->time = 0;
+ info->coef = 0.0;
+ info->rate = 0.0;
+ info->mime_t = eMIME_T_Undefined;
+ info->mime_s = eMIME_Undefined;
+ info->mime_e = eENCOD_None;
+ info->flag = SERV_DEFAULT_FLAG;
memset(&info->reserved, 0, sizeof(info->reserved));
- info->quorum = 0;
info->u.http.path = (TNCBI_Size) sizeof(info->u.http);
info->u.http.args = (TNCBI_Size) (info->u.http.path +
(path ? strlen(path) : 0) + 1);
@@ -809,8 +788,8 @@ SSERV_Info* SERV_CreateFirewallInfoEx(unsigned int host,
info->type = fSERV_Firewall;
info->host = host;
info->port = port;
- info->sful = 0;
- info->locl = s_LocalServerDefault;
+ info->mode = 0;
+ info->site = fSERV_Local;
info->time = 0;
info->coef = 0.0;
info->rate = 0.0;
@@ -819,7 +798,6 @@ SSERV_Info* SERV_CreateFirewallInfoEx(unsigned int host,
info->mime_e = eENCOD_None;
info->flag = SERV_DEFAULT_FLAG;
memset(&info->reserved, 0, sizeof(info->reserved));
- info->quorum = 0;
info->u.firewall.type = type;
}
return info;
@@ -870,8 +848,8 @@ SSERV_Info* SERV_CreateDnsInfoEx(unsigned int host, size_t add)
info->type = fSERV_Dns;
info->host = host;
info->port = 0;
- info->sful = 0;
- info->locl = s_LocalServerDefault;
+ info->mode = 0;
+ info->site = fSERV_Local;
info->time = 0;
info->coef = 0.0;
info->rate = 0.0;
@@ -880,7 +858,6 @@ SSERV_Info* SERV_CreateDnsInfoEx(unsigned int host, size_t add)
info->mime_e = eENCOD_None;
info->flag = SERV_DEFAULT_FLAG;
memset(&info->reserved, 0, sizeof(info->reserved));
- info->quorum = 0;
memset(&info->u.dns, 0, sizeof(info->u.dns));
}
return info;
diff --git a/c++/src/connect/ncbi_server_infop.h b/c++/src/connect/ncbi_server_infop.h
index 14cfe0b..19577da 100644
--- a/c++/src/connect/ncbi_server_infop.h
+++ b/c++/src/connect/ncbi_server_infop.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SERVER_INFOP__H
#define CONNECT___NCBI_SERVER_INFOP__H
-/* $Id: ncbi_server_infop.h 430183 2014-03-24 17:37:03Z lavr $
+/* $Id: ncbi_server_infop.h 451383 2014-11-06 15:18:01Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,9 +42,6 @@ extern "C" {
#endif
-int/*bool*/ SERV_SetLocalServerDefault(int/*bool*/ onoff);
-
-
/* Constructors for the various types of NCBI server meta-addresses
*/
SSERV_Info* SERV_CreateNcbidInfoEx
diff --git a/c++/src/connect/ncbi_service_connector.c b/c++/src/connect/ncbi_service_connector.c
index 0366a18..bef1bb9 100644
--- a/c++/src/connect/ncbi_service_connector.c
+++ b/c++/src/connect/ncbi_service_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_service_connector.c 434796 2014-05-11 17:54:05Z lavr $
+/* $Id: ncbi_service_connector.c 465077 2015-04-16 17:34:16Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,6 +34,7 @@
#include "ncbi_comm.h"
#include "ncbi_priv.h"
#include "ncbi_servicep.h"
+#include "ncbi_socketp.h"
#include <connect/ncbi_service_connector.h>
#include <connect/ncbi_socket_connector.h>
#include <ctype.h>
@@ -54,9 +55,9 @@ typedef struct SServiceConnectorTag {
unsigned short retry; /* Open retry count since last okay */
TSERV_TypeOnly types; /* Server types w/o any specials */
unsigned reset:1; /* Non-zero if iter was just reset */
+ SSERVICE_Extra extra; /* Extra params as passed to ctor */
ticket_t ticket; /* Network byte order (none if zero) */
EIO_Status status; /* Status of last op */
- SSERVICE_Extra params; /* Extra params as passed to ctor */
const char service[1]; /* Untranslated (orig.) service name */
} SServiceConnector;
@@ -131,9 +132,9 @@ static EHTTP_HeaderParse s_ParseHeader(const char* header,
EHTTP_HeaderParse header_parse;
SERV_Update(uuu->iter, header, server_error);
- if (user_callback_enabled && uuu->params.parse_header) {
+ if (user_callback_enabled && uuu->extra.parse_header) {
header_parse
- = uuu->params.parse_header(header, uuu->params.data, server_error);
+ = uuu->extra.parse_header(header, uuu->extra.data, server_error);
if (server_error || !header_parse)
return header_parse;
} else {
@@ -330,11 +331,16 @@ static const char* s_AdjustNetParams(const char* service,
char* temp = (char*) malloc(++len/*w/EOL*/);
if (temp) {
retval = temp;
- memcpy(temp, static_header, sh_len);
- temp += sh_len;
- memcpy(temp, extend_header, eh_len);
- temp += eh_len;
+ if (static_header) {
+ memcpy(temp, static_header, sh_len);
+ temp += sh_len;
+ }
+ if (extend_header) {
+ memcpy(temp, extend_header, eh_len);
+ temp += eh_len;
+ }
strcpy(temp, c_t);
+ assert(*retval);
}
} else
retval = "";
@@ -347,17 +353,18 @@ static const char* s_AdjustNetParams(const char* service,
static SSERV_InfoCPtr s_GetNextInfo(SServiceConnector* uuu, int/*bool*/ http)
{
for (;;) {
- SSERV_InfoCPtr info = uuu->params.get_next_info
- ? (*uuu->params.get_next_info)(uuu->params.data, uuu->iter)
+ SSERV_InfoCPtr info = uuu->extra.get_next_info
+ ? uuu->extra.get_next_info(uuu->extra.data, uuu->iter)
: SERV_GetNextInfo(uuu->iter);
if (info) {
if (http) {
/* Skip any 'stateful_capable' or unconnectable entries here,
- * which might have been left behind by either a failed
- * stateful dispatching with a fallback to stateless HTTP mode
- * or a too relaxed server type selection.
+ * which might have been left behind by either
+ * a/ a failed stateful dispatching that fallen back to
+ * stateless HTTP mode, or
+ * b/ a too relaxed server type selection.
*/
- if (info->sful || info->type == fSERV_Dns)
+ if ((info->mode & fSERV_Stateful) || info->type == fSERV_Dns)
continue;
}
uuu->reset = 0/*false*/;
@@ -372,16 +379,11 @@ static SSERV_InfoCPtr s_GetNextInfo(SServiceConnector* uuu, int/*bool*/ http)
}
-static char* s_HostPort(const char* host, unsigned short nport)
+static char* x_HostPort(const char* host, unsigned short nport)
{
- size_t hostlen = strlen(host), portlen;
char* hostport, port[16];
-
- if (!nport) {
- portlen = 1;
- port[0] = '\0';
- } else
- portlen = (size_t) sprintf(port, ":%hu", nport) + 1;
+ size_t hostlen = strlen(host);
+ size_t portlen = (size_t) sprintf(port, ":%hu", nport) + 1;
hostport = (char*) malloc(hostlen + portlen);
if (hostport) {
memcpy(hostport, host, hostlen);
@@ -392,49 +394,79 @@ static char* s_HostPort(const char* host, unsigned short nport)
/* Until r294766, this code used to send a ticket along with building the
- * tunnel, but for buggy proxies that ignore HTTP body as connection data
- * (and thus violate the standard), this shortcut could not be utilized;
+ * tunnel, but for buggy proxies, which ignore HTTP body as connection data
+ * (and thus violate the standard), that shortcut could not be utilized;
* so the longer multi-step sequence was introduced below, instead.
* Cf. ncbi_conn_stream.cpp: s_SocketConnectorBuilder().
*/
static CONNECTOR s_SocketConnectorBuilder(SConnNetInfo* net_info,
+ const char* hostport,
EIO_Status* status,
const void* data,
- size_t size)
+ size_t size,
+ TSOCK_Flags flags)
{
- CONNECTOR c;
- char* hostport;
- SOCK sock = 0;
int/*bool*/ proxy = 0/*false*/;
- TSOCK_Flags flags = (net_info->debug_printout == eDebugPrintout_Data
- ? fSOCK_LogOn : fSOCK_LogDefault);
- net_info->path[0] = '\0';
- net_info->args[0] = '\0';
- if (*net_info->http_proxy_host && net_info->http_proxy_port) {
+ SOCK sock = 0, s;
+ SSOCK_Init init;
+ CONNECTOR c;
+
+ flags |= (net_info->debug_printout == eDebugPrintout_Data
+ ? fSOCK_LogOn : fSOCK_LogDefault);
+ if (net_info->http_proxy_host[0] && net_info->http_proxy_port) {
+ /* NB: ideally, should have pushed data:size here if proxy not buggy */
*status = HTTP_CreateTunnel(net_info, fHTTP_NoAutoRetry, &sock);
assert(!sock ^ !(*status != eIO_Success));
- if (*status == eIO_Success && size) {
- SOCK s;
- *status = SOCK_CreateOnTopEx(sock, 0, &s,
- data, size, flags);
+ if (*status == eIO_Success
+ && (size || (flags & ~(fSOCK_LogOn | fSOCK_LogDefault)))) {
+ /* push initial data through the proxy, as-is (i.e. clear-text) */
+ TSOCK_Flags tempf = flags;
+ if (size && (flags & fSOCK_Secure)) {
+ tempf &= fSOCK_LogOn | fSOCK_LogDefault;
+ tempf &= ~fSOCK_Secure;
+ }
+ memset(&init, 0, sizeof(init));
+ init.data = data;
+ init.size = size;
+ init.cred = 0;
+ *status = SOCK_CreateOnTopInternal(sock, 0, &s,
+ &init, tempf);
assert(!s ^ !(*status != eIO_Success));
SOCK_Destroy(sock);
sock = s;
+ if (*status == eIO_Success && tempf != flags) {
+ init.data = 0;
+ init.size = 0;
+ init.cred = net_info->credentials;
+ *status = SOCK_CreateOnTopInternal(sock, 0, &s,
+ &init, flags);
+ assert(!s ^ !(*status != eIO_Success));
+ SOCK_Destroy(sock);
+ sock = s;
+ }
}
proxy = 1/*true*/;
}
if (!sock && (!proxy || net_info->http_proxy_leak)) {
- const char* host = (net_info->firewall && *net_info->proxy_host
- ? net_info->proxy_host : net_info->host);
+ TSOCK_Flags tempf = flags;
+ if (size && (flags & fSOCK_Secure)) {
+ tempf &= fSOCK_LogOn | fSOCK_LogDefault;
+ tempf &= ~fSOCK_Secure;
+ }
if (!proxy && net_info->debug_printout) {
+ net_info->scheme = eURL_Unspec;
net_info->req_method = eReqMethod_Any;
+ net_info->firewall = 0;
net_info->stateless = 0;
net_info->lb_disable = 0;
+ net_info->user[0] = '\0';
+ net_info->pass[0] = '\0';
+ net_info->path[0] = '\0';
+ net_info->args[0] = '\0';
net_info->http_proxy_host[0] = '\0';
net_info->http_proxy_port = 0;
net_info->http_proxy_user[0] = '\0';
net_info->http_proxy_pass[0] = '\0';
- net_info->proxy_host[0] = '\0';
ConnNetInfo_SetUserHeader(net_info, 0);
if (net_info->http_referer) {
free((void*) net_info->http_referer);
@@ -442,19 +474,31 @@ static CONNECTOR s_SocketConnectorBuilder(SConnNetInfo* net_info,
}
ConnNetInfo_Log(net_info, eLOG_Note, CORE_GetLOG());
}
- *status = SOCK_CreateEx(host, net_info->port, net_info->timeout, &sock,
- data, size, flags);
+ memset(&init, 0, sizeof(init));
+ init.data = data;
+ init.size = size;
+ init.cred = 0;
+ *status = SOCK_CreateInternal(net_info->host, net_info->port,
+ net_info->timeout, &sock,
+ &init, tempf);
assert(!sock ^ !(*status != eIO_Success));
+ if (*status == eIO_Success && tempf != flags) {
+ init.data = 0;
+ init.size = 0;
+ init.cred = net_info->credentials;
+ *status = SOCK_CreateOnTopInternal(sock, 0, &s,
+ &init, flags);
+ assert(!s ^ !(*status != eIO_Success));
+ SOCK_Destroy(sock);
+ sock = s;
+ }
}
- hostport = s_HostPort(net_info->host, net_info->port);
if (!(c = SOCK_CreateConnectorOnTopEx(sock, 1/*own*/, hostport))) {
if (*status == eIO_Success)
*status = eIO_Unknown;
SOCK_Abort(sock);
SOCK_Close(sock);
}
- if (hostport)
- free(hostport);
return c;
}
@@ -488,11 +532,11 @@ static int/*bool*/ s_Adjust(SConnNetInfo* net_info,
assert(n > 0 && (!net_info->firewall || net_info->stateless));
if (uuu->retry >= uuu->net_info->max_try)
- return 0/*false - too many errors*/;
+ return 0/*failure - too many errors*/;
uuu->retry++;
if (!(info = s_GetNextInfo(uuu, 1/*http*/)))
- return 0/*false - not adjusted*/;
+ return 0/*failure - not adjusted*/;
iter_header = SERV_Print(uuu->iter, 0, 0);
switch (info->type) {
@@ -528,7 +572,7 @@ static int/*bool*/ s_Adjust(SConnNetInfo* net_info,
case fSERV_Standalone:
user_header = "Client-Mode: STATELESS_ONLY\r\n"; /*default*/
user_header = s_AdjustNetParams(uuu->service, net_info,
- eReqMethod_Post,
+ eReqMethod_Any,
uuu->net_info->path, 0,
uuu->net_info->args,
user_header, info->mime_t,
@@ -553,8 +597,8 @@ static int/*bool*/ s_Adjust(SConnNetInfo* net_info,
if (*user_header) {
uuu->user_header = user_header;
if (!ConnNetInfo_OverrideUserHeader(net_info, user_header))
- return 0/*false - not adjusted*/;
- } else
+ return 0/*failure - not adjusted*/;
+ } else /*NB: special case ""*/
uuu->user_header = 0;
if (info->type == fSERV_Ncbid || (info->type & fSERV_Http)) {
@@ -564,7 +608,10 @@ static int/*bool*/ s_Adjust(SConnNetInfo* net_info,
strcpy(net_info->host, uuu->net_info->host);
net_info->port = uuu->net_info->port;
}
- return 1/*true - adjusted*/;
+ return uuu->extra.adjust
+ && !uuu->extra.adjust(net_info, uuu->extra.data, uuu->retry)
+ ? 0/*failure - not adjusted*/
+ : 1/*success - adjusted*/;
}
@@ -631,12 +678,17 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
info->mime_s, info->mime_e, 0);
break;
case fSERV_Standalone:
- if (!net_info->stateless)
- return s_SocketConnectorBuilder(net_info, status, 0, 0);
+ if (!net_info->stateless) {
+ assert(!uuu->descr);
+ uuu->descr = x_HostPort(net_info->host, net_info->port);
+ return s_SocketConnectorBuilder(net_info, uuu->descr, status,
+ 0, 0, info->mode & fSERV_Secure
+ ? fSOCK_Secure : 0);
+ }
/* Otherwise, it will be a pass-thru connection via dispatcher */
user_header = "Client-Mode: STATELESS_ONLY\r\n"; /*default*/
user_header = s_AdjustNetParams(uuu->service, net_info,
- eReqMethod_Post, 0, 0,
+ eReqMethod_Any, 0, 0,
0, user_header, info->mime_t,
info->mime_s, info->mime_e, 0);
but_last = 1/*true*/;
@@ -754,7 +806,7 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
*status = temp;
}
} else {
- /* This should only happen if we're out of memory */
+ /* can only happen if we're out of memory */
const char* error;
if (c) {
error = IO_StatusStr(temp);
@@ -768,12 +820,6 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
error && *error ? ": " : "", error ? error : ""));
assert(!uuu->host);
}
- if (!uuu->host) {
- /* No connection info returned */
- if (*status == eIO_Success)
- *status = eIO_Unknown;
- return 0;
- }
if (uuu->host == (unsigned int)(-1)) {
assert(!info || info->type == fSERV_Firewall);
assert(!net_info->stateless);
@@ -781,26 +827,50 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
/* Fallback to try to use stateless mode instead */
return s_Open(uuu, timeout, info, net_info, status);
}
- SOCK_ntoa(uuu->host, net_info->host, sizeof(net_info->host));
- if ((net_info->firewall & eFWMode_Adaptive)
+ if (!uuu->host || !uuu->port) {
+ /* no connection info found */
+ if (*status == eIO_Success)
+ *status = eIO_Unknown;
+ if (!net_info->scheme)
+ net_info->scheme = eURL_Http;
+ net_info->args[0] = '\0';
+ assert(!uuu->descr);
+ uuu->descr = ConnNetInfo_URL(net_info);
+ return 0;
+ }
+ if (net_info->firewall == eFWMode_Fallback
&& !SERV_IsFirewallPort(uuu->port)) {
- CORE_LOGF_X(9, net_info->firewall == eFWMode_Fallback
- ? eLOG_Warning : eLOG_Trace,
+ CORE_LOGF_X(9, eLOG_Warning,
("[%s] Firewall port :%hu is not in the fallback set",
uuu->service, uuu->port));
}
- net_info->port = uuu->port;
ConnNetInfo_DeleteUserHeader(net_info, uuu->user_header);
- return s_SocketConnectorBuilder(net_info, status, &uuu->ticket,
- uuu->ticket ? sizeof(uuu->ticket) : 0);
+ SOCK_ntoa(uuu->host, net_info->host, sizeof(net_info->host));
+ net_info->port = uuu->port;
+ assert(!uuu->descr);
+ uuu->descr = x_HostPort(net_info->host, net_info->port);
+ return s_SocketConnectorBuilder(net_info, uuu->descr, status,
+ &uuu->ticket,
+ uuu->ticket ? sizeof(uuu->ticket) : 0,
+ info && (info->mode & fSERV_Secure)
+ ? fSOCK_Secure : 0);
}
ConnNetInfo_DeleteUserHeader(net_info, "Host:");
- return HTTP_CreateConnectorEx(net_info,
- (uuu->params.flags
- & (fHTTP_Flushable | fHTTP_NoAutoRetry))
- | fHTTP_AutoReconnect,
- s_ParseHeaderUCB, uuu/*user_data*/,
- s_Adjust, 0/*cleanup*/);
+ if (info && (info->mode & fSERV_Secure))
+ net_info->scheme = eURL_Https;
+ else if (!net_info->scheme)
+ net_info->scheme = eURL_Http;
+ assert(!uuu->descr);
+ uuu->descr = ConnNetInfo_URL(net_info);
+ return !uuu->extra.adjust
+ || uuu->extra.adjust(net_info, uuu->extra.data, 0)
+ ? HTTP_CreateConnectorEx(net_info,
+ (uuu->extra.flags
+ & (fHTTP_Flushable | fHTTP_NoAutoRetry))
+ | fHTTP_AutoReconnect,
+ s_ParseHeaderUCB, uuu/*user_data*/,
+ s_Adjust, 0/*cleanup*/)
+ : 0/*failure*/;
}
@@ -832,8 +902,8 @@ static EIO_Status s_Close(CONNECTOR connector,
status = uuu->meta.close
? uuu->meta.close(uuu->meta.c_close, timeout)
: eIO_Success;
- if (uuu->params.reset)
- uuu->params.reset(uuu->params.data);
+ if (uuu->extra.reset)
+ uuu->extra.reset(uuu->extra.data);
s_CloseDispatcher(uuu);
s_Cleanup(uuu);
} else
@@ -882,7 +952,7 @@ static EIO_Status s_VT_Open(CONNECTOR connector, const STimeout* timeout)
break;
if (uuu->net_info->firewall
- && strcasecmp(uuu->iter->op->mapper, "local") != 0) {
+ && strcasecmp(SERV_MapperName(uuu->iter), "local") != 0) {
info = 0;
} else if (!(info = s_GetNextInfo(uuu, 0/*any*/)))
break;
@@ -900,9 +970,7 @@ static EIO_Status s_VT_Open(CONNECTOR connector, const STimeout* timeout)
break;
}
- net_info->scheme = eURL_Unspec;
c = s_Open(uuu, timeout, info, net_info, &status);
- uuu->descr = ConnNetInfo_URL(net_info);
stateless = net_info->stateless;
ConnNetInfo_Destroy(net_info);
@@ -1011,8 +1079,8 @@ static void s_Destroy(CONNECTOR connector)
SServiceConnector* uuu = (SServiceConnector*) connector->handle;
connector->handle = 0;
- if (uuu->params.cleanup)
- uuu->params.cleanup(uuu->params.data);
+ if (uuu->extra.cleanup)
+ uuu->extra.cleanup(uuu->extra.data);
s_CloseDispatcher(uuu);
s_Cleanup(uuu);
ConnNetInfo_Destroy(uuu->net_info);
@@ -1029,7 +1097,7 @@ extern CONNECTOR SERVICE_CreateConnectorEx
(const char* service,
TSERV_Type types,
const SConnNetInfo* net_info,
- const SSERVICE_Extra* params)
+ const SSERVICE_Extra* extra)
{
char* x_service;
CONNECTOR ccc;
@@ -1084,9 +1152,9 @@ extern CONNECTOR SERVICE_CreateConnectorEx
}
assert(xxx->iter);
- /* finally, store all callback parameters */
- if (params)
- memcpy(&xxx->params, params, sizeof(xxx->params));
+ /* finally, store all callback extras */
+ if (extra)
+ memcpy(&xxx->extra, extra, sizeof(xxx->extra));
/* done */
return ccc;
diff --git a/c++/src/connect/ncbi_servicep.h b/c++/src/connect/ncbi_servicep.h
index 8ff8a48..fc90567 100644
--- a/c++/src/connect/ncbi_servicep.h
+++ b/c++/src/connect/ncbi_servicep.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SERVICEP__H
#define CONNECT___NCBI_SERVICEP__H
-/* $Id: ncbi_servicep.h 430871 2014-03-30 01:39:04Z lavr $
+/* $Id: ncbi_servicep.h 453850 2014-12-08 19:00:36Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,16 +38,29 @@
#include <connect/ncbi_service.h>
-/* CAUTION: There may be other states not classified by the macros below! */
-#define SERV_IsDown(i) ((i)->time && (i)->time != NCBI_TIME_INFINITE \
- && (i)->rate == 0.0)
-#define SERV_IsActive(i) ((i)->time && (i)->time != NCBI_TIME_INFINITE \
- && (i)->rate > 0.0)
-#define SERV_IsStandby(i) ((i)->time && (i)->time != NCBI_TIME_INFINITE \
- && (i)->rate != 0.0 \
- && fabs((i)->rate) < LBSM_STANDBY_THRESHOLD)
-#define SERV_IsSuppressed(i) ((i)->time && (i)->time != NCBI_TIME_INFINITE \
- && (i)->rate < 0.0)
+/* Order:
+ R>0 T>0 Up
+ R<0 T>0 Standby
+ R>0 T=0 Reserved
+ R>0 T=INF Suppressed
+ R<0 T=INF Standby+Suppressed
+ R<0 T=0 Reserved+Suppressed
+ R=0 T>0 Down
+ R=0 T=INF Down+Suppressed
+ R=0 T=0 Off (unseen)
+*/
+
+
+/* SERV_IfSuppressed() can be applied to any of the SERV_Is*() macros below */
+#define SERV_IfSuppressed(i) ( (i)->time == NCBI_TIME_INFINITE || \
+ (!(i)->time && (i)->rate < 0.0))
+#define SERV_IsActive(i) ( (i)->time && (i)->rate > 0.0)
+#define SERV_IsStandby(i) ( (i)->time && (i)->rate < 0.0)
+#define SERV_IsReserved(i) ( !(i)->time && (i)->rate)
+#define SERV_IsDown(i) ( !(i)->rate)
+
+/* Thus, SERV_IsUp() can be defined as follows */
+#define SERV_IsUp(i) (SERV_IsActive(i) && !SERV_IfSuppressed(i))
#ifdef __cplusplus
@@ -89,8 +102,9 @@ struct SSERV_IterTag {
unsigned stateless:1; /* ..SERV_*() calls.. */
unsigned external:1; /* whether this is an external request */
unsigned int localhost; /* local host address if known */
- size_t n_skip; /* actual number of servers in the array */
- size_t a_skip; /* number of allocated slots in the array */
+ size_t o_skip; /* original number of servers passed in "skip" */
+ size_t n_skip; /* actual number of servers in the skip array */
+ size_t a_skip; /* number of allocated slots in the skip array */
SSERV_InfoCPtr* skip; /* servers to skip (always w/names) */
SSERV_InfoCPtr last; /* last server info taken out, points into skip*/
const char* arg; /* argument to match; the original pointer! */
@@ -108,7 +122,7 @@ struct SSERV_IterTag {
extern NCBI_XCONNECT_EXPORT ESwitch SERV_DoFastOpens(ESwitch on);
-/* Modified "fast track" routine for obtaining of a server info in one-shot.
+/* Modified "fast track" routine for obtaining a server info in one-shot.
* Please see <connect/ncbi_service.h> for explanations [SERV_GetInfoEx()].
*
* CAUTION: Unlike the 'service' parameter, for performance reasons 'arg'
@@ -201,30 +215,30 @@ char* SERV_Print
/* Same as SERV_Penalize() but can specify penalty hold time.
*/
extern NCBI_XCONNECT_EXPORT int/*bool*/ SERV_PenalizeEx
-(SERV_ITER iter, /* handle obtained via 'SERV_Open*' call*/
- double fine, /* fine from range [0=min..100=max] (%%)*/
- TNCBI_Time time /* for how long to keep the penalty, sec*/
+(SERV_ITER iter, /* handle obtained via 'SERV_Open*' call*/
+ double fine, /* fine from range [0=min..100=max] (%%)*/
+ TNCBI_Time time /* for how long to keep the penalty, sec*/
);
-/* Get name of underlying service mapper.
+/* Get a name of the underlying service mapper.
*/
extern NCBI_XCONNECT_EXPORT const char* SERV_MapperName(SERV_ITER iter);
-/* Get the final service name, using CONN_SERVICE_NAME_service environment
- * variable, then (if not found) registry section [service] and a key
+/* Get the final service name, using service_CONN_SERVICE_NAME environment
+ * variable(s), then (if not found) registry section [service] and a key
* CONN_SERVICE_NAME. Return the resultant name (perhaps, an exact copy of
- * "service" if no override name has been found in environment/registry), which
- * is to be 'free()'d by the caller when no longer needed.
+ * "service" if no override name has been found in the environment/registry),
+ * which is to be 'free()'d by the caller when no longer needed.
* Return NULL on error.
- * NOTE: This procedure can detect simple cyclical redefinitions, and
- * is limited to a search depth of 8.
+ * NOTE: This procedure can detect simple cyclic redefinitions, and is limited
+ * to a search depth of 8.
*/
char* SERV_ServiceName(const char* service);
-void SERV_InitFirewallMode(void);
+void SERV_InitFirewallPorts(void);
int/*bool*/ SERV_AddFirewallPort
diff --git a/c++/src/connect/ncbi_socket.c b/c++/src/connect/ncbi_socket.c
index 3a2b8cc..0d835fc 100644
--- a/c++/src/connect/ncbi_socket.c
+++ b/c++/src/connect/ncbi_socket.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_socket.c 450562 2014-10-28 15:18:55Z ivanov $
+/* $Id: ncbi_socket.c 466159 2015-04-29 14:48:08Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -144,7 +144,7 @@
*/
#if defined(NCBI_OS_MSWIN)
-# define SOCK_GHB_THREAD_SAFE 1 /* for gethostby...() */
+# define SOCK_GHBX_MT_SAFE 1 /* for gethostby...() */
# define SOCK_SEND_SLICE (1 << 10) /* 1M */
# define SOCK_INVALID INVALID_SOCKET
# define SOCK_ERRNO WSAGetLastError()
@@ -1003,9 +1003,9 @@ static int s_gethostname(char* name, size_t namesize, ESwitch log)
failed = 1/*true*/;
} else if (name[namesize - 1]) {
if (log) {
- CORE_LOG_X(104, eLOG_Error,
- "[SOCK_gethostname] "
- " Buffer too small");
+ CORE_LOGF_X(104, eLOG_Error,
+ ("[SOCK_gethostname] "
+ " Buffer too small (%lu)", (unsigned long) namesize));
}
failed = 1/*true*/;
} else
@@ -1028,7 +1028,7 @@ static unsigned int s_gethostbyname_(const char* hostname, ESwitch log)
if (!hostname || !*hostname) {
if (s_gethostname(buf, sizeof(buf), log) != 0)
return 0;
-#ifdef NCBI_OS_DARWIN
+#if 0/*def NCBI_OS_DARWIN*/
{{
char* p;
if ((p = strchr(buf, '.')) != 0)
@@ -1082,6 +1082,7 @@ static unsigned int s_gethostbyname_(const char* hostname, ESwitch log)
# elif HAVE_GETHOSTBYNAME_R == 6
if (gethostbyname_r(hostname, &x_he, x_buf, sizeof(x_buf),
&he, &error) != 0) {
+ /*NB: retval == errno on error*/
assert(he == 0);
he = 0;
}
@@ -1089,17 +1090,17 @@ static unsigned int s_gethostbyname_(const char* hostname, ESwitch log)
# error "Unknown HAVE_GETHOSTBYNAME_R value"
# endif /*HAVE_GETHOSTNBYNAME_R == N*/
if (!he) {
- if (!error && (error = SOCK_ERRNO) == ERANGE)
- log = eOn;
+ if (!error)
+ error = SOCK_ERRNO;
else
error += DNS_BASE;
}
# else
static const char suffix[] = "";
-# ifndef SOCK_GHB_THREAD_SAFE
+# ifndef SOCK_GHBX_MT_SAFE
CORE_LOCK_WRITE;
-# endif /*!SOCK_GHB_THREAD_SAFE*/
+# endif /*!SOCK_GHBX_MT_SAFE*/
he = gethostbyname(hostname);
error = he ? 0 : h_errno + DNS_BASE;
@@ -1113,26 +1114,28 @@ static unsigned int s_gethostbyname_(const char* hostname, ESwitch log)
memcpy(&host, he->h_addr, sizeof(host));
# ifndef HAVE_GETHOSTBYNAME_R
-# ifndef SOCK_GHB_THREAD_SAFE
+# ifndef SOCK_GHBX_MT_SAFE
CORE_UNLOCK;
-# endif /*!SOCK_GHB_THREAD_SAFE*/
+# endif /*!SOCK_GHBX_MT_SAFE*/
# endif /*HAVE_GETHOSTBYNAME_R*/
- if (!host && log) {
- const char* strerr;
+ if (!host) {
# ifdef NETDB_INTERNAL
if (error == NETDB_INTERNAL + DNS_BASE)
error = SOCK_ERRNO;
# endif /*NETDB_INTERNAL*/
- strerr = SOCK_STRERROR(error);
- CORE_LOGF_ERRNO_EXX(106, eLOG_Warning,
- error, strerr ? strerr : "",
- ("[SOCK_gethostbyname] "
- " Failed gethostbyname%s(\"%.*s\")",
- suffix, MAXHOSTNAMELEN, hostname));
- UTIL_ReleaseBuffer(strerr);
+ if (error == ERANGE)
+ log = eOn;
+ if (log) {
+ const char* strerr = SOCK_STRERROR(error);
+ CORE_LOGF_ERRNO_EXX(106, eLOG_Warning,
+ error, strerr ? strerr : "",
+ ("[SOCK_gethostbyname] "
+ " Failed gethostbyname%s(\"%.*s\")",
+ suffix, MAXHOSTNAMELEN, hostname));
+ UTIL_ReleaseBuffer(strerr);
+ }
}
-
#endif /*HAVE_GETADDRINFO && !__GLIBC__*/
}
@@ -1239,10 +1242,9 @@ static char* s_gethostbyaddr_(unsigned int host, char* name,
name = 0;
}
if (!name && log) {
- const char* strerr;
+ const char* strerr = SOCK_STRERROR(error);
if (SOCK_ntoa(host, addr, sizeof(addr)) != 0)
sprintf(addr, "0x%08X", (unsigned int) ntohl(host));
- strerr = SOCK_STRERROR(error);
CORE_LOGF_ERRNO_EXX(107, eLOG_Warning,
error, strerr ? strerr : "",
("[SOCK_gethostbyaddr] "
@@ -1251,7 +1253,6 @@ static char* s_gethostbyaddr_(unsigned int host, char* name,
UTIL_ReleaseBuffer(strerr);
}
}
-
#else /* use some variant of gethostbyaddr */
struct hostent* he;
# ifdef HAVE_GETHOSTBYADDR_R
@@ -1266,6 +1267,7 @@ static char* s_gethostbyaddr_(unsigned int host, char* name,
# elif HAVE_GETHOSTBYADDR_R == 8
if (gethostbyaddr_r((char*) &host, sizeof(host), AF_INET, &x_he,
x_buf, sizeof(x_buf), &he, &error) != 0) {
+ /*NB: retval == errno on error*/
assert(he == 0);
he = 0;
}
@@ -1273,17 +1275,17 @@ static char* s_gethostbyaddr_(unsigned int host, char* name,
# error "Unknown HAVE_GETHOSTBYADDR_R value"
# endif /*HAVE_GETHOSTBYADDR_R == N*/
if (!he) {
- if (!error && (error = SOCK_ERRNO) == ERANGE)
- log = eOn;
+ if (!error)
+ error = SOCK_ERRNO;
else
error += DNS_BASE;
}
# else /*HAVE_GETHOSTBYADDR_R*/
static const char suffix[] = "";
-# ifndef SOCK_GHB_THREAD_SAFE
+# ifndef SOCK_GHBX_MT_SAFE
CORE_LOCK_WRITE;
-# endif /*!SOCK_GHB_THREAD_SAFE*/
+# endif /*!SOCK_GHBX_MT_SAFE*/
he = gethostbyaddr((char*) &host, sizeof(host), AF_INET);
error = he ? 0 : h_errno + DNS_BASE;
@@ -1304,28 +1306,30 @@ static char* s_gethostbyaddr_(unsigned int host, char* name,
strcpy(name, he->h_name);
# ifndef HAVE_GETHOSTBYADDR_R
-# ifndef SOCK_GHB_THREAD_SAFE
+# ifndef SOCK_GHBX_MT_SAFE
CORE_UNLOCK;
-# endif /*!SOCK_GHB_THREAD_SAFE*/
+# endif /*!SOCK_GHBX_MT_SAFE*/
# endif /*HAVE_GETHOSTBYADDR_R*/
- if (!name && log) {
- const char* strerr;
+ if (!name) {
# ifdef NETDB_INTERNAL
if (error == NETDB_INTERNAL + DNS_BASE)
error = SOCK_ERRNO;
# endif /*NETDB_INTERNAL*/
- if (SOCK_ntoa(host, addr, sizeof(addr)) != 0)
- sprintf(addr, "0x%08X", (unsigned int) ntohl(host));
- strerr = SOCK_STRERROR(error);
- CORE_LOGF_ERRNO_EXX(108, eLOG_Warning,
- error, strerr ? strerr : "",
- ("[SOCK_gethostbyaddr] "
- " Failed gethostbyaddr%s(%s)",
- suffix, addr));
- UTIL_ReleaseBuffer(strerr);
+ if (error == ERANGE)
+ log = eOn;
+ if (log) {
+ const char* strerr = SOCK_STRERROR(error);
+ if (SOCK_ntoa(host, addr, sizeof(addr)) != 0)
+ sprintf(addr, "0x%08X", (unsigned int) ntohl(host));
+ CORE_LOGF_ERRNO_EXX(108, eLOG_Warning,
+ error, strerr ? strerr : "",
+ ("[SOCK_gethostbyaddr] "
+ " Failed gethostbyaddr%s(%s)",
+ suffix, addr));
+ UTIL_ReleaseBuffer(strerr);
+ }
}
-
#endif /*HAVE_GETNAMEINFO && !__GLIBC__*/
} else {
name[0] = 0;
@@ -1346,7 +1350,6 @@ static const char* s_gethostbyaddr(unsigned int host, char* name,
{
static int once = 1/*true*/;
const char* retval = s_gethostbyaddr_(host, name, namesize, log);
-
if (once && retval
&& ((SOCK_IsLoopbackAddress(host)
&& strncasecmp(retval, "localhost", 9) != 0) ||
@@ -2068,7 +2071,7 @@ static EIO_Status s_Poll_(size_t n,
assert(events || ((nfds_t) m < count && count <= j));
}
if ((events & POLLIN)
- && (revents & (POLLIN | POLLHUP | POLLPRI))) {
+ && (revents & (POLLIN | POLLHUP | POLLPRI))) {
polls[i].revent = (EIO_Event)(polls[i].revent | eIO_Read);
}
if ((events & POLLOUT)
@@ -2560,8 +2563,8 @@ static EIO_Status s_IsConnected_(SOCK sock,
}
if (!sock->connected) {
-#if defined(_DEBUG) && !defined(NDEBUG)
if (sock->log == eOn || (sock->log == eDefault && s_Log == eOn)) {
+#if defined(_DEBUG) && !defined(NDEBUG)
char mtu[128];
# if defined(SOL_IP) && defined(IP_MTU)
if (sock->port) {
@@ -2576,9 +2579,12 @@ static EIO_Status s_IsConnected_(SOCK sock,
} else
# endif /*SOL_IP && IP_MTU*/
*mtu = '\0';
- CORE_TRACEF(("%sConnection established%s", s_ID(sock, _id), mtu));
- }
+#else
+ static const char* mtu = "";
#endif /*_DEBUG && !NDEBUG*/
+ CORE_LOGF(eLOG_Trace,
+ ("%sConnection established%s", s_ID(sock, _id), mtu));
+ }
if (s_ReuseAddress == eOn
#ifdef NCBI_OS_UNIX
&& !sock->path[0]
@@ -2605,21 +2611,31 @@ static EIO_Status s_IsConnected_(SOCK sock,
const unsigned int wtv_set = sock->w_tv_set;
struct timeval rtv;
struct timeval wtv;
+ char* desc = 0;
if (rtv_set)
rtv = sock->r_tv;
if (wtv_set)
wtv = sock->w_tv;
SOCK_SET_TIMEOUT(sock, r, tv);
SOCK_SET_TIMEOUT(sock, w, tv);
- status = sslopen(sock->session, error);
+ status = sslopen(sock->session, error, &desc);
if ((sock->w_tv_set = wtv_set) != 0)
x_tvcpy(&sock->w_tv, &wtv);
if ((sock->r_tv_set = rtv_set) != 0)
x_tvcpy(&sock->r_tv, &rtv);
- if (status != eIO_Success)
- *what = "SSL hello";
- else
+ if (status == eIO_Success) {
sock->pending = 0;
+ if (sock->log == eOn
+ || (sock->log == eDefault && s_Log == eOn)) {
+ CORE_LOGF(eLOG_Trace,
+ ("%sSSL session established%s%s",
+ s_ID(sock, _id),
+ &" "[!desc], desc ? desc : ""));
+ if (desc)
+ free(desc);
+ }
+ } else
+ *what = "SSL hello";
} else
status = eIO_NotSupported;
} else
@@ -2798,7 +2814,7 @@ static EIO_Status s_WritePending(SOCK, const struct timeval*, int, int);
* read. Return other (error) code if an error/EOF occurred (zero bytes read).
* (MSG_PEEK is not implemented on Mac, and it is poorly implemented
* on Win32, so we had to implement this feature by ourselves.)
- * NB: peek = {-1=upread, 0=read, 1=peek}
+ * NB: peek = {-1=upread(!buf && !size), 0=read, 1=peek}
*/
static EIO_Status s_Read_(SOCK sock,
void* buf,
@@ -2858,18 +2874,24 @@ static EIO_Status s_Read_(SOCK sock,
size_t n_todo;
char* x_buf;
- if (!buf/*internal upread/skipping*/ ||
- ((n_todo = size - *n_read) < sizeof(xx_buf))) {
- n_todo = sizeof(xx_buf);
- x_buf = xx_buf;
+ if (!buf/*internal upread/skipping*/ && peek) {
+ n_todo = sizeof(xx_buf);
+ x_buf = (char*) malloc(sizeof(xx_buf));
+ if (!x_buf)
+ x_buf = xx_buf;
+ } else if (!buf || (n_todo = size - *n_read) < sizeof(xx_buf)) {
+ n_todo = sizeof(xx_buf);
+ x_buf = xx_buf;
} else
- x_buf = (char*) buf + *n_read;
+ x_buf = (char*) buf + *n_read;
if (sock->session) {
int error;
FSSLRead sslread = s_SSL ? s_SSL->Read : 0;
assert(sock->session != SESSION_INVALID);
if (!sslread) {
+ if (!buf && x_buf != xx_buf)
+ free(x_buf);
status = eIO_NotSupported;
break/*error*/;
}
@@ -2888,6 +2910,8 @@ static EIO_Status s_Read_(SOCK sock,
}
if (status == eIO_Closed && !sock->eof) {
+ if (!buf && x_buf != xx_buf)
+ free(x_buf);
sock->r_status = eIO_Closed;
sock->eof = 1/*true*/;
break/*bad error*/;
@@ -2897,9 +2921,14 @@ static EIO_Status s_Read_(SOCK sock,
status = s_Recv(sock, x_buf, n_todo, &x_read, 0);
assert(status == eIO_Success || !x_read);
}
- if (status != eIO_Success)
+ if (status != eIO_Success) {
+ if (!buf && x_buf != xx_buf)
+ free(x_buf);
break/*error*/;
+ }
if (!x_read) {
+ if (!buf && x_buf != xx_buf)
+ free(x_buf);
status = eIO_Closed;
break/*EOF*/;
}
@@ -2907,6 +2936,7 @@ static EIO_Status s_Read_(SOCK sock,
if (x_read < n_todo)
done = 1/*true*/;
+
if (buf || size) {
n_todo = size - *n_read;
if (n_todo > x_read)
@@ -2914,20 +2944,33 @@ static EIO_Status s_Read_(SOCK sock,
if (buf && x_buf == xx_buf)
memcpy((char*) buf + *n_read, x_buf, n_todo);
} else
- n_todo = x_read;
+ assert(peek < 0);
if (peek || x_read > n_todo) {
/* store the newly read/excess data in the internal input buffer */
- if (!BUF_Write(&sock->r_buf,
- peek ? x_buf : x_buf + n_todo,
- peek ? x_read : x_read - n_todo)) {
+ if (buf || x_buf == xx_buf || x_read < sizeof(xx_buf)/2) {
+ sock->eof = !BUF_Write (&sock->r_buf,
+ peek ? x_buf : x_buf + n_todo,
+ peek ? x_read : x_read - n_todo);
+ if (!buf && x_buf != xx_buf)
+ free(x_buf);
+ } else {
+ assert(peek);
+ sock->eof = !BUF_AppendEx(&sock->r_buf,
+ x_buf, sizeof(xx_buf),
+ x_buf, x_read);
+ if (sock->eof)
+ free(x_buf);
+ }
+ if (sock->eof) {
CORE_LOGF_ERRNO_X(8, eLOG_Error, errno,
("%s[SOCK::Read] "
" Cannot save unread data",
s_ID(sock, xx_buf)));
- sock->eof = 1/*failure*/;
- sock->r_status = eIO_Closed;
+ sock->r_status = eIO_Closed/*failure*/;
status = eIO_Unknown;
+ if (!buf && peek)
+ x_read = 0;
}
if (x_read > n_todo)
x_read = n_todo;
@@ -3347,8 +3390,10 @@ static EIO_Status s_WriteData(SOCK sock,
EIO_Status status;
FSSLWrite sslwrite = s_SSL ? s_SSL->Write : 0;
assert(sock->session != SESSION_INVALID);
- if (!sslwrite || oob)
+ if (!sslwrite || oob) {
+ *n_written = 0;
return eIO_NotSupported;
+ }
status = sslwrite(sock->session, data, size, n_written, &error);
assert((status == eIO_Success) == (*n_written > 0));
assert(status == eIO_Success || error);
@@ -3719,6 +3764,7 @@ static EIO_Status s_Close_(SOCK sock, int abort)
BUF_Erase(sock->r_buf);
if (sock->type == eDatagram) {
sock->r_len = 0;
+ status = eIO_Success;
BUF_Erase(sock->w_buf);
} else if (abort || !sock->keep) {
int/*bool*/ linger = 0/*false*/;
@@ -3785,11 +3831,13 @@ static EIO_Status s_Close_(SOCK sock, int abort)
if (!abort) {
/* orderly shutdown in both directions */
- s_Shutdown(sock, eIO_Close, SOCK_GET_TIMEOUT(sock, c));
+ status = s_Shutdown(sock, eIO_Close, SOCK_GET_TIMEOUT(sock, c));
assert(sock->r_status == eIO_Closed &&
sock->w_status == eIO_Closed);
- } else
+ } else {
sock->r_status = sock->w_status = eIO_Closed;
+ status = eIO_Success;
+ }
#ifdef NCBI_OS_MSWIN
WSAEventSelect(sock->sock, sock->event/*ignored*/, 0/*cancel*/);
@@ -3828,7 +3876,6 @@ static EIO_Status s_Close_(SOCK sock, int abort)
s_DoLog(eLOG_Note, sock, eIO_Close, 0, 0, abort ? "Aborting" : 0);
}
- status = eIO_Success;
if (abort || !sock->keep) {
if (abort < 0)
abort = 1;
@@ -4535,6 +4582,7 @@ static EIO_Status s_CreateOnTop(const void* handle,
}
assert(session != SESSION_INVALID);
x_sock->session = session;
+ x_sock->cred = cred;
}
if (x_sock->port) {
@@ -4739,7 +4787,6 @@ static EIO_Status s_CreateListening(const char* path,
addr.un.sun_len = addrlen;
# endif /*HAVE_SIN_LEN*/
strcpy(addr.un.sun_path, path);
- cp = path;
u = umask(0);
} else
#endif /*NCBI_OS_UNIX*/
@@ -5370,8 +5417,8 @@ static EIO_Status s_RecvMsg(SOCK sock,
/* statistics & logging */
if (sock->log == eOn || (sock->log == eDefault && s_Log == eOn)){
- s_DoLog(eLOG_Note, sock, eIO_Read, x_msg,
- (size_t) x_read, &sin);
+ s_DoLog(eLOG_Note, sock, eIO_Read, x_msg, (size_t) x_read,
+ &sin);
}
sock->n_read += (TNCBI_BigCount) x_read;
@@ -5501,8 +5548,8 @@ static EIO_Status s_SendMsg(SOCK sock,
(struct sockaddr*) &sin, sizeof(sin))) >= 0) {
/* statistics & logging */
if (sock->log == eOn || (sock->log == eDefault && s_Log == eOn)){
- s_DoLog(eLOG_Note, sock, eIO_Write, x_msg,
- (size_t) x_written, &sin);
+ s_DoLog(eLOG_Note, sock, eIO_Write, x_msg, (size_t) x_written,
+ &sin);
}
sock->w_len = (TNCBI_BigCount) x_written;
@@ -6596,7 +6643,7 @@ extern EIO_Status SOCK_Read(SOCK sock,
}
-#define s_PushBack(s, b, l) BUF_PushBack(&(s)->r_buf, b, l)
+#define s_Pushback(s, b, l) BUF_Pushback(&(s)->r_buf, b, l)
extern EIO_Status SOCK_ReadLine(SOCK sock,
@@ -6621,7 +6668,6 @@ extern EIO_Status SOCK_ReadLine(SOCK sock,
}
cr_seen = done = 0/*false*/;
- status = eIO_Success;
len = 0;
do {
size_t i;
@@ -6668,10 +6714,10 @@ extern EIO_Status SOCK_ReadLine(SOCK sock,
done = 1/*true*/;
if (done && cr_seen) {
c = '\r';
- if (!s_PushBack(sock, &c, 1))
+ if (!s_Pushback(sock, &c, 1))
status = eIO_Unknown;
}
- if (i < x_size && !s_PushBack(sock, &x_buf[i], x_size - i))
+ if (i < x_size && !s_Pushback(sock, &x_buf[i], x_size - i))
status = eIO_Unknown;
} while (!done && status == eIO_Success);
@@ -6684,20 +6730,20 @@ extern EIO_Status SOCK_ReadLine(SOCK sock,
}
-extern EIO_Status SOCK_PushBack(SOCK sock,
+extern EIO_Status SOCK_Pushback(SOCK sock,
const void* buf,
size_t size)
{
if (sock->sock == SOCK_INVALID) {
char _id[MAXIDLEN];
CORE_LOGF_X(67, eLOG_Error,
- ("%s[SOCK::PushBack] "
+ ("%s[SOCK::Pushback] "
" Invalid socket",
s_ID(sock, _id)));
return eIO_Closed;
}
- return s_PushBack(sock, buf, size) ? eIO_Success : eIO_Unknown;
+ return s_Pushback(sock, buf, size) ? eIO_Success : eIO_Unknown;
}
@@ -7962,7 +8008,7 @@ extern int SOCK_gethostnameEx(char* buf, size_t bufsize, ESwitch log)
return -1/*failure*/;
}
- return s_gethostname(buf, bufsize, log);
+ return s_gethostname(buf, bufsize, log == eDefault ? s_Log : log);
}
@@ -7978,7 +8024,7 @@ extern unsigned int SOCK_gethostbynameEx(const char* hostname, ESwitch log)
if (s_InitAPI(0) != eIO_Success)
return 0;
- return s_gethostbyname(hostname, log);
+ return s_gethostbyname(hostname, log == eDefault ? s_Log : log);
}
@@ -8001,7 +8047,7 @@ extern const char* SOCK_gethostbyaddrEx(unsigned int host,
return 0;
}
- return s_gethostbyaddr(host, buf, bufsize, log);
+ return s_gethostbyaddr(host, buf, bufsize, log == eDefault ? s_Log : log);
}
diff --git a/c++/src/connect/ncbi_socket_connector.c b/c++/src/connect/ncbi_socket_connector.c
index 2a60701..19f12d5 100644
--- a/c++/src/connect/ncbi_socket_connector.c
+++ b/c++/src/connect/ncbi_socket_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_socket_connector.c 425649 2014-01-31 16:47:23Z lavr $
+/* $Id: ncbi_socket_connector.c 462719 2015-03-20 16:47:04Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -332,8 +332,13 @@ static CONNECTOR s_Init
} else {
char* temp = (char*) xxx + sizeof(*xxx);
xxx->sock = 0;
- xxx->size = data ? size : 0;
- xxx->data = memcpy(temp, data, xxx->size);
+ if (data) {
+ xxx->size = size;
+ xxx->data = size ? memcpy(temp, data, size) : 0;
+ } else {
+ xxx->size = 0;
+ xxx->data = 0;
+ }
xxx->host = strcpy(temp + xxx->size, host);
xxx->port = port;
xxx->try_own = try_own ? try_own : 1;
diff --git a/c++/src/connect/ncbi_socketp.h b/c++/src/connect/ncbi_socketp.h
index 10bb1e4..03b582f 100644
--- a/c++/src/connect/ncbi_socketp.h
+++ b/c++/src/connect/ncbi_socketp.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_SOCKETP__H
#define CONNECT___NCBI_SOCKETP__H
-/* $Id: ncbi_socketp.h 430179 2014-03-24 17:33:39Z lavr $
+/* $Id: ncbi_socketp.h 451558 2014-11-07 15:40:44Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -380,7 +380,7 @@ EIO_Status SOCK_CreateOnTopInternal(const void* handle,
TSOCK_Flags flags);
-/* Addtl socket API for internal use: if flag != 0 and host is nonexitent,
+/* Addtl socket API for internal use: if flag != 0 and host is nonexistent,
* return it as INADDR_NONE (-1) rather than an error.
*/
const char* SOCK_StringToHostPortEx(const char* str,
diff --git a/c++/src/connect/ncbi_util.c b/c++/src/connect/ncbi_util.c
index 61cc4b0..5f796dc 100644
--- a/c++/src/connect/ncbi_util.c
+++ b/c++/src/connect/ncbi_util.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_util.c 449177 2014-10-14 13:58:55Z ivanov $
+/* $Id: ncbi_util.c 456255 2015-01-08 20:52:17Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,7 +48,10 @@
# endif /*!HAVE_GETPWUID*/
# ifndef NCBI_OS_SOLARIS
# include <limits.h>
-# endif
+# endif /*!NCBI_OS_SOLARIS*/
+# ifdef NCBI_OS_LINUX
+# include <sys/user.h>
+# endif /*NCBI_OS_LINUX*/
# include <pwd.h>
# include <unistd.h>
# include <sys/stat.h>
@@ -58,6 +61,11 @@
# include <windows.h>
# include <lmcons.h>
#endif /*NCBI_OS_MSWIN || NCBI_OS_CYGWIN*/
+#if defined(PAGE_SIZE) && !defined(NCBI_OS_CYGWIN)
+# define NCBI_DEFAULT_PAGE_SIZE PAGE_SIZE
+#else
+# define NCBI_DEFAULT_PAGE_SIZE 0/*unknown*/
+#endif /*PAGE_SIZE && !NCBI_OS_CYGWIN*/
#define NCBI_USE_ERRCODE_X Connect_Util
@@ -168,21 +176,21 @@ extern TLOG_FormatFlags CORE_SetLOGFormatFlags(TLOG_FormatFlags flags)
extern size_t UTIL_PrintableStringSize(const char* data, size_t size)
{
const unsigned char* c;
- size_t retval;
+ size_t count;
if (!data)
return 0;
if (!size)
size = strlen(data);
- retval = size;
- for (c = (const unsigned char*) data; size; size--, c++) {
+ count = size;
+ for (c = (const unsigned char*) data; count; --count, ++c) {
if (*c == '\t' || *c == '\v' || *c == '\b' ||
*c == '\r' || *c == '\f' || *c == '\a' ||
*c == '\\' || *c == '\'' || *c == '"') {
- retval++;
+ size++;
} else if (*c == '\n' || !isascii(*c) || !isprint(*c))
- retval += 3;
+ size += 3;
}
- return retval;
+ return size;
}
@@ -327,7 +335,7 @@ extern const char* NcbiMessagePlusError
mlen += 7;
if (error)
- mlen += sprintf(buf + mlen, "%d%s", error, "," + !*descr);
+ mlen += sprintf(buf + mlen, "%d%s", error, &","[!*descr]);
memcpy((char*) memcpy(buf + mlen, descr, dlen) + dlen, "}", 2);
if (release)
@@ -430,10 +438,10 @@ extern char* LOG_ComposeMessage
}
if (call_data->raw_size) {
- data_len = (sizeof(kRawData_Begin) + 20
- + UTIL_PrintableStringSize((const char*)
- call_data->raw_data,
- call_data->raw_size) +
+ data_len = (sizeof(kRawData_Begin)
+ + 20 + UTIL_PrintableStringSize((const char*)
+ call_data->raw_data,
+ call_data->raw_size) +
sizeof(kRawData_End));
}
@@ -809,8 +817,8 @@ extern const char* CORE_GetUsernameEx(char* buf, size_t bufsize,
break;
}
-# if defined(NCBI_OS_SOLARIS) || \
- (defined(HAVE_GETPWUID) && !defined(NCBI_HAVE_GETPWUID_R))
+# if defined(NCBI_OS_SOLARIS) \
+ || (defined(HAVE_GETPWUID) && !defined(NCBI_HAVE_GETPWUID_R))
/* NB: getpwuid() is MT-safe on Solaris, so use it here, if available */
# ifndef NCBI_OS_SOLARIS
CORE_LOCK_WRITE;
@@ -868,14 +876,14 @@ extern const char* CORE_GetUsername(char* buf, size_t bufsize)
extern size_t CORE_GetVMPageSize(void)
{
- static size_t ps = 0;
+ static size_t s_PS = 0;
- if (!ps) {
+ if (!s_PS) {
#if defined(NCBI_OS_MSWIN) || defined(NCBI_OS_CYGWIN)
- /* NB: CYGWIN's PAGESIZE (== PAGE_SIZE) are actually granularity */
+ /* NB: CYGWIN's PAGESIZE (== PAGE_SIZE) is actually the granularity */
SYSTEM_INFO si;
GetSystemInfo(&si);
- ps = (size_t) si.dwPageSize;
+ s_PS = (size_t) si.dwPageSize;
#elif defined(NCBI_OS_UNIX)
# if defined(_SC_PAGESIZE)
# define NCBI_SC_PAGESIZE _SC_PAGESIZE
@@ -893,15 +901,15 @@ extern size_t CORE_GetVMPageSize(void)
if (x <= 0) {
# ifdef HAVE_GETPAGESIZE
if ((x = getpagesize()) <= 0)
- return 0;
+ return NCBI_DEFAULT_PAGE_SIZE;
# else
- return 0;
-# endif
+ return NCBI_DEFAULT_PAGE_SIZE;
+# endif /*HAVE_GETPAGESIZE*/
}
- ps = (size_t) x;
+ s_PS = (size_t) x;
#endif /*OS_TYPE*/
}
- return ps;
+ return s_PS;
}
diff --git a/c++/src/connect/ncbi_version.h b/c++/src/connect/ncbi_version.h
index 07b4a90..ec20c5e 100644
--- a/c++/src/connect/ncbi_version.h
+++ b/c++/src/connect/ncbi_version.h
@@ -1,7 +1,7 @@
#ifndef CONNECT___NCBI_VERSION__H
#define CONNECT___NCBI_VERSION__H
-/* $Id: ncbi_version.h 435097 2014-05-13 19:58:55Z lavr $
+/* $Id: ncbi_version.h 460431 2015-02-26 20:52:10Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,7 +46,6 @@
# define NETDAEMONS_MAJOR NCBI_PACKAGE_VERSION_MAJOR
# define NETDAEMONS_MINOR NCBI_PACKAGE_VERSION_MINOR
# define NETDAEMONS_PATCH NCBI_PACKAGE_VERSION_PATCH
-/*#define NETDAEMONS_FINAL 1 //only when doing final build, not RC!*/
# define NETDAEMONS_VERSION_STR NCBI_PACKAGE_VERSION
@@ -54,7 +53,7 @@
# define NETDAEMONS_MAJOR 2
# define NETDAEMONS_MINOR 2
-# define NETDAEMONS_PATCH 0
+# define NETDAEMONS_PATCH 3
# ifdef NCBI_CXX_TOOLKIT
# define NETDAEMONS_VERSION_STR NCBI_PACKAGE_VERSION_COMPOSE_STR \
diff --git a/c++/src/connect/server.cpp b/c++/src/connect/server.cpp
index fd77164..7fb6ff6 100644
--- a/c++/src/connect/server.cpp
+++ b/c++/src/connect/server.cpp
@@ -1,4 +1,4 @@
-/* $Id: server.cpp 448565 2014-10-07 16:43:56Z ivanov $
+/* $Id: server.cpp 467185 2015-05-11 14:50:34Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,10 +36,6 @@
#include <connect/ncbi_buffer.h>
#include <connect/error_codes.hpp>
-#ifdef NCBI_OS_LINUX
-# include <sys/prctl.h>
-#endif
-
#define NCBI_USE_ERRCODE_X Connect_ThrServer
@@ -219,11 +215,10 @@ void*
CThreadInPool_ForServer::Main(void)
{
if (!m_Pool->m_ThrSuffix.empty()) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
string thr_name = CNcbiApplication::Instance()->GetProgramDisplayName();
thr_name += m_Pool->m_ThrSuffix;
-#if defined(NCBI_OS_LINUX) && defined(PR_SET_NAME)
- prctl(PR_SET_NAME, (unsigned long)thr_name.c_str(), 0, 0, 0);
-#endif
+ SetCurrentThreadName(thr_name.c_str());
}
if ( !m_Pool->Register(*this) ) {
diff --git a/c++/src/connect/services/Makefile.ncbi_xblobstorage_netcache.lib b/c++/src/connect/services/Makefile.ncbi_xblobstorage_netcache.lib
index e4d76fa..e10aceb 100644
--- a/c++/src/connect/services/Makefile.ncbi_xblobstorage_netcache.lib
+++ b/c++/src/connect/services/Makefile.ncbi_xblobstorage_netcache.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.ncbi_xblobstorage_netcache.lib 427428 2014-02-20 13:41:02Z gouriano $
+# $Id: Makefile.ncbi_xblobstorage_netcache.lib 466155 2015-04-29 14:36:10Z sadyrovr $
#
SRC = blob_storage_netcache
@@ -11,7 +11,7 @@ DLL_LIB = xconnserv xconnect xutil xncbi
CPPFLAGS = $(ORIG_CPPFLAGS)
LIBS = $(ORIG_LIBS)
-WATCHERS = kazimird
+WATCHERS = sadyrovr
diff --git a/c++/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/c++/src/connect/services/Makefile.ncbi_xcache_netcache.lib
index 9c19505..e406a91 100644
--- a/c++/src/connect/services/Makefile.ncbi_xcache_netcache.lib
+++ b/c++/src/connect/services/Makefile.ncbi_xcache_netcache.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.ncbi_xcache_netcache.lib 427428 2014-02-20 13:41:02Z gouriano $
+# $Id: Makefile.ncbi_xcache_netcache.lib 466155 2015-04-29 14:36:10Z sadyrovr $
#
SRC = neticache_client
@@ -11,7 +11,7 @@ DLL_LIB = xconnserv xconnect xutil
CPPFLAGS = $(ORIG_CPPFLAGS)
LIBS = $(ORIG_LIBS)
-WATCHERS = kazimird
+WATCHERS = sadyrovr
USES_LIBRARIES = \
diff --git a/c++/src/connect/services/Makefile.xconnserv.lib b/c++/src/connect/services/Makefile.xconnserv.lib
index d8ccad7..17dcad7 100644
--- a/c++/src/connect/services/Makefile.xconnserv.lib
+++ b/c++/src/connect/services/Makefile.xconnserv.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.xconnserv.lib 447459 2014-09-25 20:43:06Z kazimird $
+# $Id: Makefile.xconnserv.lib 466155 2015-04-29 14:36:10Z sadyrovr $
SRC = grid_worker ns_client_factory grid_worker_app \
grid_client grid_client_app \
@@ -24,7 +24,7 @@ LIBS = $(NETWORK_LIBS)
DLL_LIB = xthrserv xconnect xutil xncbi
-WATCHERS = kazimird
+WATCHERS = sadyrovr
USES_LIBRARIES = \
diff --git a/c++/src/connect/services/clparser.cpp b/c++/src/connect/services/clparser.cpp
index b38f36a..2dbd344 100644
--- a/c++/src/connect/services/clparser.cpp
+++ b/c++/src/connect/services/clparser.cpp
@@ -1,4 +1,4 @@
-/* $Id: clparser.cpp 408158 2013-07-26 16:40:11Z kazimird $
+/* $Id: clparser.cpp 475261 2015-08-05 19:52:42Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -408,7 +408,7 @@ void SCommandLineParserImpl::HelpOnCommand(const SCommonParts* common_parts,
void SCommandLineParserImpl::Throw(const string& error, const string& cmd) const
{
- string message(kEmptyStr);
+ string message;
if (error.empty())
message.append(m_Synopsis);
else {
@@ -557,7 +557,7 @@ int SCommandLineParserImpl::ParseAndValidate(int argc, const char* const *argv)
ret_val = 0;
} else {
if (positional_arguments.empty())
- Throw(m_OptionValues.empty() ? kEmptyStr : "a command is required");
+ Throw(m_OptionValues.empty() ? "" : "a command is required");
command_name = positional_arguments.front();
positional_arguments.pop_front();
diff --git a/c++/src/connect/services/compound_id.cpp b/c++/src/connect/services/compound_id.cpp
index 0221483..ad85ce4 100644
--- a/c++/src/connect/services/compound_id.cpp
+++ b/c++/src/connect/services/compound_id.cpp
@@ -1,4 +1,4 @@
-/* $Id: compound_id.cpp 431243 2014-04-02 15:31:07Z kazimird $
+/* $Id: compound_id.cpp 458444 2015-02-04 23:20:49Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,6 +45,7 @@
#define CIC_GENERICID_CLASS_NAME "CompoundID"
#define CIC_NETCACHEBLOBKEY_CLASS_NAME "NetCacheBlobKey"
#define CIC_NETSCHEDULEJOBKEY_CLASS_NAME "NetScheduleJobKey"
+#define CIC_NETSTORAGEOBJECTLOC_CLASS_NAME_V1 "NetStorageObjectLocV1"
#define CIC_NETSTORAGEOBJECTLOC_CLASS_NAME "NetStorageObjectLoc"
#define CIT_ID_TYPE_NAME "id"
@@ -70,10 +71,11 @@
BEGIN_NCBI_SCOPE
static const char* s_ClassNames[eCIC_NumberOfClasses] = {
- /* eCIC_GenericID */ CIC_GENERICID_CLASS_NAME,
- /* eCIC_NetCacheKey */ CIC_NETCACHEBLOBKEY_CLASS_NAME,
- /* eCIC_NetScheduleKey */ CIC_NETSCHEDULEJOBKEY_CLASS_NAME,
- /* eCIC_NetStorageObjectLoc */ CIC_NETSTORAGEOBJECTLOC_CLASS_NAME
+ /* eCIC_GenericID */ CIC_GENERICID_CLASS_NAME,
+ /* eCIC_NetCacheKey */ CIC_NETCACHEBLOBKEY_CLASS_NAME,
+ /* eCIC_NetScheduleKey */ CIC_NETSCHEDULEJOBKEY_CLASS_NAME,
+ /* eCIC_NetStorageObjectLocV1 */ CIC_NETSTORAGEOBJECTLOC_CLASS_NAME_V1,
+ /* eCIC_NetStorageObjectLoc */ CIC_NETSTORAGEOBJECTLOC_CLASS_NAME
};
static const char* s_TypeNames[eCIT_NumberOfTypes] = {
@@ -480,10 +482,12 @@ CCompoundID CCompoundIDDumpParser::ParseID()
new_id_class = eCIC_NetScheduleJobKey;
else if (new_id_class_name == CIC_NETSTORAGEOBJECTLOC_CLASS_NAME)
new_id_class = eCIC_NetStorageObjectLoc;
+ else if (new_id_class_name == CIC_NETSTORAGEOBJECTLOC_CLASS_NAME_V1)
+ new_id_class = eCIC_NetStorageObjectLocV1;
}
if (new_id_class == eCIC_NumberOfClasses) {
- CID_PARSER_EXCEPTION("unknown component ID class '" <<
+ CID_PARSER_EXCEPTION("unknown compound ID class '" <<
new_id_class_name << '\'');
}
diff --git a/c++/src/connect/services/compound_id_v0.cpp b/c++/src/connect/services/compound_id_v0.cpp
index 7637ec2..286992c 100644
--- a/c++/src/connect/services/compound_id_v0.cpp
+++ b/c++/src/connect/services/compound_id_v0.cpp
@@ -1,4 +1,4 @@
-/* $Id: compound_id_v0.cpp 431243 2014-04-02 15:31:07Z kazimird $
+/* $Id: compound_id_v0.cpp 461156 2015-03-06 16:43:46Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -267,7 +267,7 @@ struct SIDUnpacking
Uint8 SIDUnpacking::ExtractNumber()
{
- Uint8 number;
+ Uint8 number = 0;
unsigned number_len = g_UnpackInteger(m_Ptr, m_RemainingBytes, &number);
diff --git a/c++/src/connect/services/grid_client.cpp b/c++/src/connect/services/grid_client.cpp
index a9dba54..c65e067 100644
--- a/c++/src/connect/services/grid_client.cpp
+++ b/c++/src/connect/services/grid_client.cpp
@@ -1,4 +1,4 @@
-/* $Id: grid_client.cpp 420071 2013-12-03 16:36:52Z kazimird $
+/* $Id: grid_client.cpp 475261 2015-08-05 19:52:42Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -139,8 +139,11 @@ string CGridClient::Submit(const string& affinity)
CNetScheduleAPI::EJobStatus CGridClient::SubmitAndWait(unsigned wait_time)
{
CloseStream();
-
- return GetNetScheduleSubmitter().SubmitJobAndWait(m_Job, wait_time);
+ CNetScheduleAPI::EJobStatus status =
+ GetNetScheduleSubmitter().SubmitJobAndWait(m_Job, wait_time);
+ x_CleanUpAllJobBlobs(status);
+ m_JobDetailsRead = true;
+ return status;
}
//////////////////////////////////////////////////////////
@@ -247,13 +250,8 @@ CGridJobBatchSubmitter::CGridJobBatchSubmitter(CGridClient& grid_client)
//////////////////////////////////////////////////////////////////////////////
//
-CNetScheduleAPI::EJobStatus CGridClient::GetStatus()
+bool CGridClient::x_CleanUpAllJobBlobs(CNetScheduleAPI::EJobStatus status)
{
- time_t job_exptime = 0;
-
- CNetScheduleAPI::EJobStatus status =
- GetNetScheduleSubmitter().GetJobDetails(m_Job, &job_exptime);
-
if (m_AutoCleanUp && (
status == CNetScheduleAPI::eDone ||
status == CNetScheduleAPI::eCanceled)) {
@@ -269,9 +267,23 @@ CNetScheduleAPI::EJobStatus CGridClient::GetStatus()
RemoveDataBlob(m_Job.progress_msg.c_str() + 2);
}
}
- } else {
+
+ return true;
+ }
+
+ return false;
+}
+CNetScheduleAPI::EJobStatus CGridClient::GetStatus()
+{
+ time_t job_exptime = 0;
+
+ CNetScheduleAPI::EJobStatus status =
+ GetNetScheduleSubmitter().GetJobDetails(m_Job, &job_exptime);
+
+ if (!x_CleanUpAllJobBlobs(status)) {
x_RenewAllJobBlobs(job_exptime);
}
+ m_JobDetailsRead = true;
return status;
}
@@ -313,7 +325,7 @@ string CGridClient::GetProgressMessage()
return buffer;
}
}
- return kEmptyStr;
+ return string();
}
void CGridClient::SetJobKey(const string& job_key)
diff --git a/c++/src/connect/services/grid_control_thread.cpp b/c++/src/connect/services/grid_control_thread.cpp
index 9e65d27..ac27e6d 100644
--- a/c++/src/connect/services/grid_control_thread.cpp
+++ b/c++/src/connect/services/grid_control_thread.cpp
@@ -1,4 +1,4 @@
-/* $Id: grid_control_thread.cpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: grid_control_thread.cpp 451104 2014-11-03 19:33:10Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -169,10 +169,13 @@ public:
"\nVersion: " << node.GetAppVersion() <<
"\nBuild date: " << node.GetBuildDate() << "\n";
- CNcbiApplication* app = CNcbiApplication::Instance();
- if (app)
- os << "Executable path: " << app->GetProgramExecutablePath()
- << "\nPID: " << CProcess::GetCurrentPid() << "\n";
+ {{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if (app)
+ os << "Executable path: " << app->GetProgramExecutablePath()
+ << "\nPID: " << CProcess::GetCurrentPid() << "\n";
+ }}
CNetScheduleAPI ns_api(node.GetNetScheduleAPI());
diff --git a/c++/src/connect/services/grid_control_thread.hpp b/c++/src/connect/services/grid_control_thread.hpp
index 2ff17a7..ac5b53e 100644
--- a/c++/src/connect/services/grid_control_thread.hpp
+++ b/c++/src/connect/services/grid_control_thread.hpp
@@ -2,7 +2,7 @@
#define _GRID_CONTROL_THREADD_HPP_
-/* $Id: grid_control_thread.hpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: grid_control_thread.hpp 443514 2014-08-14 21:35:38Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/grid_globals.cpp b/c++/src/connect/services/grid_globals.cpp
index b4322db..e3f5023 100644
--- a/c++/src/connect/services/grid_globals.cpp
+++ b/c++/src/connect/services/grid_globals.cpp
@@ -1,4 +1,4 @@
-/* $Id: grid_globals.cpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: grid_globals.cpp 455687 2015-01-02 17:47:12Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -195,7 +195,7 @@ void CWNJobWatcher::x_KillNode(CGridWorkerNode worker)
NON_CONST_ITERATE(TActiveJobs, it, m_ActiveJobs) {
CNetScheduleJob& job = it->first->GetJob();
if (!it->second.flag)
- worker.GetNSExecutor().ReturnJob(job.job_id, job.auth_token);
+ worker.GetNSExecutor().ReturnJob(job);
else {
job.error_msg = "Job execution time exceeded " +
NStr::NumericToString(
diff --git a/c++/src/connect/services/grid_worker.cpp b/c++/src/connect/services/grid_worker.cpp
index 5320014..234a434 100644
--- a/c++/src/connect/services/grid_worker.cpp
+++ b/c++/src/connect/services/grid_worker.cpp
@@ -1,4 +1,4 @@
-/* $Id: grid_worker.cpp 448052 2014-10-02 13:55:39Z kazimird $
+/* $Id: grid_worker.cpp 467434 2015-05-13 16:41:39Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -77,7 +77,8 @@ class CGridControlThread : public CThread
public:
CGridControlThread(SGridWorkerNodeImpl* worker_node,
unsigned int start_port, unsigned int end_port) : m_Control(
- new CWorkerNodeControlServer(worker_node, start_port, end_port))
+ new CWorkerNodeControlServer(worker_node, start_port, end_port)),
+ m_ThreadName(worker_node->GetAppName() + "_ct")
{
}
@@ -94,6 +95,7 @@ public:
protected:
virtual void* Main(void)
{
+ SetCurrentThreadName(m_ThreadName);
m_Control->Run();
return NULL;
}
@@ -107,6 +109,7 @@ protected:
private:
auto_ptr<CWorkerNodeControlServer> m_Control;
+ const string m_ThreadName;
};
/////////////////////////////////////////////////////////////////////////////
@@ -187,6 +190,7 @@ private:
unsigned int m_AutoShutdown;
CStopWatch m_AutoShutdownSW;
mutable CFastMutex m_Mutex;
+ const string m_ThreadName;
CWorkerNodeIdleThread(const CWorkerNodeIdleThread&);
CWorkerNodeIdleThread& operator=(const CWorkerNodeIdleThread&);
@@ -200,11 +204,14 @@ CWorkerNodeIdleThread::CWorkerNodeIdleThread(IWorkerNodeIdleTask* task,
m_Wait1(0,100000), m_Wait2(0,1000000),
m_StopFlag(false), m_ShutdownFlag(false),
m_RunInterval(run_delay),
- m_AutoShutdown(auto_shutdown), m_AutoShutdownSW(CStopWatch::eStart)
+ m_AutoShutdown(auto_shutdown), m_AutoShutdownSW(CStopWatch::eStart),
+ m_ThreadName(worker_node->GetAppName() + "_id")
{
}
void* CWorkerNodeIdleThread::Main()
{
+ SetCurrentThreadName(m_ThreadName);
+
while (!m_ShutdownFlag) {
if ( x_IsAutoShutdownTime() ) {
LOG_POST_X(47, Info <<
@@ -444,7 +451,9 @@ void SGridWorkerNodeImpl::x_StartWorkerThreads()
{
_ASSERT(m_MaxThreads > 0);
- m_ThreadPool = new CStdPoolOfThreads(m_MaxThreads, 0);
+ m_ThreadPool = new CStdPoolOfThreads(m_MaxThreads, 0, 1, kMax_UInt,
+ GetAppName() + "_wr");
+
try {
unsigned init_threads = m_App.GetConfig().GetInt("server",
"init_threads", 1, 0, IRegistry::eReturn);
@@ -543,7 +552,7 @@ int SGridWorkerNodeImpl::Run(
string host, port;
NStr::SplitInTwo(NStr::TruncateSpaces(*it), ":", host, port);
if (!host.empty() && !port.empty())
- m_Masters.insert(SServerAddress(g_NetService_gethostbyname(host),
+ m_Masters.insert(SServerAddress(host,
(unsigned short) NStr::StringToUInt(port)));
}
diff --git a/c++/src/connect/services/grid_worker_app.cpp b/c++/src/connect/services/grid_worker_app.cpp
index e04a1e4..6e660e8 100644
--- a/c++/src/connect/services/grid_worker_app.cpp
+++ b/c++/src/connect/services/grid_worker_app.cpp
@@ -1,4 +1,4 @@
-/* $Id: grid_worker_app.cpp 447462 2014-09-25 20:48:45Z kazimird $
+/* $Id: grid_worker_app.cpp 469237 2015-06-02 18:26:13Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,6 +33,7 @@
#include "grid_worker_impl.hpp"
+#include <corelib/ncbimtx.hpp>
#include <connect/services/grid_worker_app.hpp>
#if defined(NCBI_OS_UNIX)
@@ -43,6 +44,7 @@ extern "C"
void g_GridWorker_TermHandler(int /*sig*/)
{
try {
+ ncbi::CMutexGuard guard(ncbi::CNcbiApplication::GetInstanceMutex());
ncbi::CGridWorkerApp* app = dynamic_cast<ncbi::CGridWorkerApp*>(
ncbi::CNcbiApplication::Instance());
if (app) {
@@ -82,10 +84,6 @@ CNetCacheAPI CDefaultWorkerNodeInitContext::GetNetCacheAPI() const
return grid_app->GetWorkerNode().GetNetCacheAPI();
}
-void IGridWorkerNodeApp_Listener::OnInit(CNcbiApplication* /*app*/)
-{
-}
-
/////////////////////////////////////////////////////////////////////////////
//
diff --git a/c++/src/connect/services/grid_worker_impl.hpp b/c++/src/connect/services/grid_worker_impl.hpp
index e073226..e950dee 100644
--- a/c++/src/connect/services/grid_worker_impl.hpp
+++ b/c++/src/connect/services/grid_worker_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__GRID_WORKER_IMPL__HPP
#define CONNECT_SERVICES__GRID_WORKER_IMPL__HPP
-/* $Id: grid_worker_impl.hpp 452162 2014-11-17 15:23:48Z ivanov $
+/* $Id: grid_worker_impl.hpp 467683 2015-05-15 15:04:08Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,6 +32,8 @@
* Common NetSchedule Worker Node declarations
*/
+#include <corelib/hash_set.hpp>
+
#include "wn_commit_thread.hpp"
#include "wn_cleanup.hpp"
#include "netschedule_api_impl.hpp"
@@ -48,8 +50,11 @@ struct SWorkerNodeJobContextImpl : public CWorkerNodeTimelineEntry
void ResetJobContext();
- void x_SetCanceled() { m_JobCommitted = CWorkerNodeJobContext::eCanceled; }
- void CheckIfCanceled();
+ void MarkJobAsLost()
+ {
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_JobIsLost;
+ }
+ void CheckIfJobIsLost();
void x_PrintRequestStop();
@@ -61,7 +66,7 @@ struct SWorkerNodeJobContextImpl : public CWorkerNodeTimelineEntry
SGridWorkerNodeImpl* m_WorkerNode;
CNetScheduleJob m_Job;
- CWorkerNodeJobContext::ECommitStatus m_JobCommitted;
+ CWorkerNodeJobContext::ECommitStatus m_JobCommitStatus;
bool m_DisableRetries;
size_t m_InputBlobSize;
unsigned int m_JobNumber;
@@ -171,6 +176,8 @@ struct SGridWorkerNodeImpl : public CObject
return m_NetScheduleAPI->m_Service->m_ServiceName;
}
+ string GetAppName() const { return m_App.GetProgramDisplayName(); }
+
bool EnterExclusiveMode();
void LeaveExclusiveMode();
bool IsExclusiveMode() const {return m_IsProcessingExclusiveJob;}
@@ -240,6 +247,30 @@ struct SGridWorkerNodeImpl : public CObject
bool m_ProgressLogRequested;
size_t m_QueueEmbeddedOutputSize;
unsigned m_ThreadPoolTimeout;
+
+ /// Bookkeeping of jobs being executed (to prevent simultaneous runs of the same job)
+ struct SJobsInProgress
+ {
+ bool Add(const string& id)
+ {
+ TFastMutexGuard lock(m_Mutex);
+ return m_Ids.insert(id).second;
+ }
+
+ size_t Remove(const string& id)
+ {
+ TFastMutexGuard lock(m_Mutex);
+ const size_t erased = m_Ids.erase(id);
+ _ASSERT(erased);
+ return erased;
+ }
+
+ private:
+ CFastMutex m_Mutex;
+ hash_set<string> m_Ids;
+ };
+
+ SJobsInProgress m_JobsInProgress;
};
@@ -281,42 +312,24 @@ public:
CMainLoopThread(SGridWorkerNodeImpl* worker_node) :
m_WorkerNode(worker_node),
m_Semaphore(0, 1),
- m_DiscoveryIteration(1),
- m_DiscoveryAction(
- new SNotificationTimelineEntry(SServerAddress(0, 0), 0))
+ m_ThreadName(worker_node->GetAppName() + "_mn")
{
- m_ImmediateActions.Push(m_DiscoveryAction);
}
virtual void* Main();
- virtual ~CMainLoopThread();
-
private:
SGridWorkerNodeImpl* m_WorkerNode;
CSemaphore m_Semaphore;
- unsigned m_DiscoveryIteration;
-
- typedef CWorkerNodeTimeline<SNotificationTimelineEntry,
- SNotificationTimelineEntry::TRef> TNotificationTimeline;
-
- TNotificationTimeline m_ImmediateActions, m_Timeline;
-
- typedef set<SNotificationTimelineEntry*,
- SNotificationTimelineEntry::SLess> TTimelineEntries;
-
- TTimelineEntries m_TimelineEntryByAddress;
-
- SNotificationTimelineEntry::TRef m_DiscoveryAction;
+ const string m_ThreadName;
+ CServerTimeline m_Timeline;
- SNotificationTimelineEntry* x_GetTimelineEntry(SNetServerImpl* server_impl);
- bool x_PerformTimelineAction(TNotificationTimeline& timeline,
+ bool x_PerformTimelineAction(CServerTimeline::TEntryRef timeline_entry,
CNetScheduleJob& job);
bool x_EnterSuspendedState();
void x_ProcessRequestJobNotification();
bool x_WaitForNewJob(CNetScheduleJob& job);
bool x_GetNextJob(CNetScheduleJob& job);
- void x_ReturnJob(const CNetScheduleJob& job);
};
END_NCBI_SCOPE
diff --git a/c++/src/connect/services/json_over_uttp.cpp b/c++/src/connect/services/json_over_uttp.cpp
index a8192b3..8177717 100644
--- a/c++/src/connect/services/json_over_uttp.cpp
+++ b/c++/src/connect/services/json_over_uttp.cpp
@@ -1,4 +1,4 @@
-/* $Id: json_over_uttp.cpp 457749 2015-01-27 19:56:35Z kazimird $
+/* $Id: json_over_uttp.cpp 457651 2015-01-26 20:28:49Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/netcache_api.cpp b/c++/src/connect/services/netcache_api.cpp
index e808dba..5afeffe 100644
--- a/c++/src/connect/services/netcache_api.cpp
+++ b/c++/src/connect/services/netcache_api.cpp
@@ -1,4 +1,4 @@
-/* $Id: netcache_api.cpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netcache_api.cpp 477824 2015-09-02 12:20:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,7 @@
#pragma warning (disable: 4191)
#endif
+#include "netschedule_api_impl.hpp"
#include "netcache_api_impl.hpp"
#include <connect/services/srv_connections_expt.hpp>
@@ -72,8 +73,7 @@ static SServerAddress* s_GetFallbackServer()
string host, port;
if (NStr::SplitInTwo(TCGI_NetCacheFallbackServer::GetDefault(),
":", host, port)) {
- s_FallbackServer->reset(new SServerAddress(
- g_NetService_gethostbyname(host),
+ s_FallbackServer->reset(new SServerAddress(host,
(unsigned short) NStr::StringToInt(port)));
}
} catch (...) {
@@ -87,61 +87,36 @@ CRef<INetServerProperties> CNetCacheServerListener::AllocServerProperties()
return CRef<INetServerProperties>(new SNetCacheServerProperties);
}
-CConfig* CNetCacheServerListener::LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name)
+CConfig* CNetCacheServerListener::OnPreInit(CObject* api_impl,
+ CConfig* config, string* config_section)
{
SNetCacheAPIImpl* nc_impl = static_cast<SNetCacheAPIImpl*>(api_impl);
- auto_ptr<CConfig::TParamTree> result;
+ _ASSERT(nc_impl);
+ _ASSERT(nc_impl->m_Service);
+ _ASSERT(config_section);
- if (nc_impl->m_NetScheduleAPI) {
- CNetScheduleAPI::TQueueParams queue_params;
-
- nc_impl->m_NetScheduleAPI.GetQueueParams(
- nc_impl->m_NetScheduleAPI.GetQueueName(), queue_params);
+ if (CNetScheduleAPI api = nc_impl->m_NetScheduleAPI) {
+ // Use client name from NetSchedule if it's not provided for NetCache
+ if (m_ClientName.empty()) {
+ m_ClientName = api.GetExecutor().GetClientName();
+ }
- ITERATE(CNetScheduleAPI::TQueueParams, param_it, queue_params) {
- if (NStr::StartsWith(param_it->first, "nc.")) {
- string param_name(param_it->first);
- param_name.erase(0, sizeof("nc.") - 1);
- if (result.get() == NULL) {
- result.reset(new CConfig::TParamTree);
- *new_section_name = "netcache_conf_from_netschedule";
- }
- result->AddNode(CConfig::TParamValue(param_name, param_it->second));
- }
+ // If we are not forced to load config from NetSchedule
+ // and have either config or service name, then nothing to do here
+ if (!CNetScheduleConfigLoader::Use(config, *config_section) &&
+ (config || !nc_impl->m_Service->m_ServiceName.empty())) {
+ return NULL;
}
- if (result.get() == NULL)
- try {
- nc_impl->m_NetScheduleAPI.GetQueueParams(queue_params);
-
- ITERATE(CNetScheduleAPI::TQueueParams, param_it, queue_params) {
- if (NStr::StartsWith(param_it->first, "nc::")) {
- string param_name(param_it->first);
- param_name.erase(0, sizeof("nc::") - 1);
- if (result.get() == NULL) {
- result.reset(new CConfig::TParamTree);
- *new_section_name =
- "netcache_conf_from_netschedule_GETP2";
- }
- result->AddNode(CConfig::TParamValue(param_name,
- param_it->second));
- }
- }
- }
- catch (CNetScheduleException&) {
- }
+ const CTempString kLiterals[] = {
+ "nc.", "netcache_conf_from_netschedule",
+ "nc::", "netcache_conf_from_netschedule_GETP2"
+ };
+ return CNetScheduleConfigLoader::Get(kLiterals, api, config_section);
}
- if (result.get() == NULL)
- return NULL;
-
- CConfig* config = new CConfig(result.get());
-
- result.release();
-
- return config;
+ return NULL;
}
void CNetCacheServerListener::OnInit(CObject* api_impl,
@@ -260,8 +235,9 @@ void CNetCacheServerListener::OnWarning(const string& warn_msg,
if (m_EventHandler)
m_EventHandler->OnWarning(warn_msg, server);
else {
- LOG_POST(Warning << server->m_ServerInPool->m_Address.AsString() <<
- ": " << warn_msg);
+ LOG_POST(Warning << "NetCache server at "
+ << server->m_ServerInPool->m_Address.AsString() <<
+ ": WARNING: " << warn_msg);
}
}
@@ -335,7 +311,7 @@ void SNetCacheAPIImpl::AppendClientIPSessionIDPasswordAgeHitID(string* cmd,
}
cmd->append(" ncbi_phid=\"");
- cmd->append(CDiagContext::GetRequestContext().GetHitID());
+ cmd->append(CDiagContext::GetRequestContext().GetNextSubHitID());
cmd->append(1, '\"');
}
@@ -362,50 +338,33 @@ unsigned SNetCacheAPIImpl::x_ExtractBlobAge(
sizeof("AGE=") - 1, NStr::fAllowTrailingSymbols);
}
-class SNetCacheMirrorTraversal : public IServiceTraversal
-{
-public:
- SNetCacheMirrorTraversal(CNetService::TInstance service,
- CNetServer::TInstance primary_server, ESwitch server_check) :
- m_Service(service),
- m_PrimaryServer(primary_server),
- m_PrimaryServerCheck(server_check != eOff)
- {
- }
-
- virtual CNetServer BeginIteration();
- virtual CNetServer NextServer();
-
- CNetService m_Service;
- CNetServiceIterator m_Iterator;
- CNetServer::TInstance m_PrimaryServer;
- bool m_PrimaryServerCheck;
-};
-
CNetServer SNetCacheMirrorTraversal::BeginIteration()
{
if (m_PrimaryServerCheck)
return *(m_Iterator = m_Service.Iterate(m_PrimaryServer));
+ m_Iterator = NULL;
return m_PrimaryServer;
}
CNetServer SNetCacheMirrorTraversal::NextServer()
{
- if (m_PrimaryServerCheck)
- return ++m_Iterator ? *m_Iterator : CNetServer();
-
- m_PrimaryServerCheck = true;
- return *(m_Iterator = m_Service.Iterate(m_PrimaryServer));
+ if (!m_Iterator) {
+ m_Iterator = m_Service.Iterate(m_PrimaryServer);
+ CNetServer first_server = *m_Iterator;
+ if (first_server->m_ServerInPool != m_PrimaryServer->m_ServerInPool)
+ return first_server;
+ }
+ return ++m_Iterator ? *m_Iterator : CNetServer();
}
CNetServer::SExecResult SNetCacheAPIImpl::ExecMirrorAware(
const CNetCacheKey& key, const string& cmd,
bool multiline_output,
const CNetCacheAPIParameters* parameters,
- SNetServiceImpl::EServerErrorHandling error_handling)
+ SNetServiceImpl::EServerErrorHandling error_handling,
+ INetServerConnectionListener* conn_listener)
{
-
const string& service_name(key.GetServiceName());
bool service_name_is_defined = !key.GetServiceName().empty();
@@ -443,7 +402,8 @@ CNetServer::SExecResult SNetCacheAPIImpl::ExecMirrorAware(
// them into host:port immediately.
if (!key_is_mirrored)
- return server.ExecWithRetry(cmd, multiline_output);
+ return server.ExecWithRetry(cmd, multiline_output,
+ conn_listener);
CNetServer::SExecResult exec_result;
@@ -453,7 +413,8 @@ CNetServer::SExecResult SNetCacheAPIImpl::ExecMirrorAware(
through this service */);
service->IterateUntilExecOK(cmd, multiline_output,
- exec_result, &mirror_traversal, error_handling);
+ exec_result, &mirror_traversal, error_handling,
+ conn_listener);
return exec_result;
}
@@ -479,7 +440,7 @@ CNetServer::SExecResult SNetCacheAPIImpl::ExecMirrorAware(
primary_server, server_check);
service->IterateUntilExecOK(cmd, multiline_output, exec_result,
- &mirror_traversal, error_handling);
+ &mirror_traversal, error_handling, conn_listener);
return exec_result;
}
@@ -492,7 +453,7 @@ CNetServer::SExecResult SNetCacheAPIImpl::ExecMirrorAware(
"accessed because it is not registered for the service.");
}
- return primary_server.ExecWithRetry(cmd, multiline_output);
+ return primary_server.ExecWithRetry(cmd, multiline_output, conn_listener);
}
CNetCacheAPI::CNetCacheAPI(CNetCacheAPI::EAppRegistry /* use_app_reg */,
@@ -659,7 +620,8 @@ string CNetCacheAPI::PutData(const string& key,
parameters.LoadNamedParameters(optional);
parameters.SetCachingMode(eCaching_Disable);
- CNetCacheWriter writer(m_Impl, &actual_key, eNetCache_Wait, ¶meters);
+ CNetCacheWriter writer(m_Impl, &actual_key, kEmptyStr,
+ eNetCache_Wait, ¶meters);
writer.WriteBufferAndClose(reinterpret_cast<const char*>(buf), size);
@@ -680,7 +642,8 @@ IEmbeddedStreamWriter* CNetCacheAPI::PutData(string* key,
parameters.LoadNamedParameters(optional);
- return new CNetCacheWriter(m_Impl, key, eNetCache_Wait, ¶meters);
+ return new CNetCacheWriter(m_Impl, key, kEmptyStr,
+ eNetCache_Wait, ¶meters);
}
@@ -753,7 +716,7 @@ CNetServerMultilineCmdOutput CNetCacheAPI::GetBlobInfo(const string& blob_id,
CNetCacheKey key(blob_id, m_Impl->m_CompoundIDPool);
string cmd("GETMETA " + key.StripKeyExtensions());
- cmd.append(m_Impl->m_Service->m_ServerPool->m_EnforcedServerHost == 0 ?
+ cmd.append(m_Impl->m_Service->m_ServerPool->m_EnforcedServer.host == 0 ?
" 0" : " 1");
CNetCacheAPIParameters parameters(&m_Impl->m_DefaultParameters);
diff --git a/c++/src/connect/services/netcache_api_admin.cpp b/c++/src/connect/services/netcache_api_admin.cpp
index ea5e35e..3a58765 100644
--- a/c++/src/connect/services/netcache_api_admin.cpp
+++ b/c++/src/connect/services/netcache_api_admin.cpp
@@ -1,4 +1,4 @@
-/* $Id: netcache_api_admin.cpp 450571 2014-10-28 15:21:52Z ivanov $
+/* $Id: netcache_api_admin.cpp 450470 2014-10-27 18:24:02Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/netcache_api_impl.hpp b/c++/src/connect/services/netcache_api_impl.hpp
index d3eb824..8069b1c 100644
--- a/c++/src/connect/services/netcache_api_impl.hpp
+++ b/c++/src/connect/services/netcache_api_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___NETCACHE_API_IMPL__HPP
#define CONNECT_SERVICES___NETCACHE_API_IMPL__HPP
-/* $Id: netcache_api_impl.hpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netcache_api_impl.hpp 466058 2015-04-28 18:02:57Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,8 +56,8 @@ public:
virtual CRef<INetServerProperties> AllocServerProperties();
public:
- virtual CConfig* LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name);
+ virtual CConfig* OnPreInit(CObject* api_impl,
+ CConfig* config, string* config_section);
virtual void OnInit(CObject* api_impl,
CConfig* config, const string& config_section);
virtual void OnConnected(CNetServerConnection& connection);
@@ -118,7 +118,8 @@ struct NCBI_XCONNECT_EXPORT SNetCacheAPIImpl : public CObject
bool multiline_output,
const CNetCacheAPIParameters* parameters,
SNetServiceImpl::EServerErrorHandling error_handling =
- SNetServiceImpl::eRethrowServerErrors);
+ SNetServiceImpl::eRethrowServerErrors,
+ INetServerConnectionListener* conn_listener = NULL);
CNetCacheServerListener* GetListener()
{
@@ -155,6 +156,26 @@ inline SNetCacheAdminImpl::SNetCacheAdminImpl(SNetCacheAPIImpl* nc_api_impl) :
{
}
+class NCBI_XCONNECT_EXPORT SNetCacheMirrorTraversal : public IServiceTraversal
+{
+public:
+ SNetCacheMirrorTraversal(CNetService::TInstance service,
+ CNetServer::TInstance primary_server, ESwitch server_check) :
+ m_Service(service),
+ m_PrimaryServer(primary_server),
+ m_PrimaryServerCheck(server_check != eOff)
+ {
+ }
+
+ virtual CNetServer BeginIteration();
+ virtual CNetServer NextServer();
+
+ CNetService m_Service;
+ CNetServiceIterator m_Iterator;
+ CNetServer::TInstance m_PrimaryServer;
+ bool m_PrimaryServerCheck;
+};
+
END_NCBI_SCOPE
#endif /* CONNECT_SERVICES___NETCACHE_API_IMPL__HPP */
diff --git a/c++/src/connect/services/netcache_key.cpp b/c++/src/connect/services/netcache_key.cpp
index 6d73fa5..5c75707 100644
--- a/c++/src/connect/services/netcache_key.cpp
+++ b/c++/src/connect/services/netcache_key.cpp
@@ -1,4 +1,4 @@
-/* $Id: netcache_key.cpp 445350 2014-09-03 19:18:38Z kazimird $
+/* $Id: netcache_key.cpp 445349 2014-09-03 19:16:54Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/netcache_params.cpp b/c++/src/connect/services/netcache_params.cpp
index 526ff7d..ff90cbd 100644
--- a/c++/src/connect/services/netcache_params.cpp
+++ b/c++/src/connect/services/netcache_params.cpp
@@ -1,4 +1,4 @@
-/* $Id: netcache_params.cpp 458672 2015-02-09 11:57:13Z kazimird $
+/* $Id: netcache_params.cpp 458433 2015-02-04 21:48:50Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,14 +63,16 @@ void CNetCacheAPIParameters::LoadNamedParameters(
SetServerCheckHint(Get<bool>(optional));
else if (optional->Is(CNetCacheAPI::eNPT_ServerToUse))
SetServerToUse(Get<CNetServer::TInstance>(optional));
+ else if (optional->Is(CNetCacheAPI::eNPT_ServerLastUsedPtr))
+ SetServerLastUsedPtr(Get<CNetServer*>(optional));
else if (optional->Is(CNetCacheAPI::eNPT_MaxBlobAge))
SetMaxBlobAge(Get<unsigned>(optional));
else if (optional->Is(CNetCacheAPI::eNPT_ActualBlobAgePtr))
SetActualBlobAgePtr(Get<unsigned*>(optional));
else if (optional->Is(CNetCacheAPI::eNPT_UseCompoundID))
SetUseCompoundID(Get<bool>(optional));
- else if (optional->Is(CNetCacheAPI::eNPT_TryAllServers))
- SetTryAllServers(Get<bool>(optional));
+ else if (optional->Is(CNetCacheAPI::eNPT_SingleServer))
+ SetSingleServer(Get<bool>(optional));
else if (optional->Is(CNetCacheAPI::eNPT_CacheName))
SetCacheName(Get<string>(optional));
}
@@ -179,6 +181,11 @@ CNetServer CNetCacheAPIParameters::GetServerToUse() const
NETCACHE_API_GET_PARAM_IMPL(ServerToUse);
}
+CNetServer* CNetCacheAPIParameters::GetServerLastUsedPtr() const
+{
+ NETCACHE_API_GET_PARAM_IMPL(ServerLastUsedPtr);
+}
+
unsigned CNetCacheAPIParameters::GetMaxBlobAge() const
{
NETCACHE_API_GET_PARAM_IMPL(MaxBlobAge);
@@ -194,9 +201,9 @@ bool CNetCacheAPIParameters::GetUseCompoundID() const
NETCACHE_API_GET_PARAM_IMPL(UseCompoundID);
}
-bool CNetCacheAPIParameters::GetTryAllServers() const
+bool CNetCacheAPIParameters::GetSingleServer() const
{
- NETCACHE_API_GET_PARAM_IMPL(TryAllServers);
+ NETCACHE_API_GET_PARAM_IMPL(SingleServer);
}
string CNetCacheAPIParameters::GetCacheName() const
diff --git a/c++/src/connect/services/netcache_params.hpp b/c++/src/connect/services/netcache_params.hpp
index 8865e91..90b8381 100644
--- a/c++/src/connect/services/netcache_params.hpp
+++ b/c++/src/connect/services/netcache_params.hpp
@@ -1,7 +1,7 @@
#ifndef CONN___NETCACHE_PARAMS__HPP
#define CONN___NETCACHE_PARAMS__HPP
-/* $Id: netcache_params.hpp 458672 2015-02-09 11:57:13Z kazimird $
+/* $Id: netcache_params.hpp 458433 2015-02-04 21:48:50Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,10 +58,11 @@ public:
eDP_ServerCheckHint = 1 << 4,
eDP_Password = 1 << 5,
eDP_ServerToUse = 1 << 6,
- eDP_MaxBlobAge = 1 << 7,
- eDP_ActualBlobAgePtr = 1 << 8,
- eDP_UseCompoundID = 1 << 9,
- eDP_TryAllServers = 1 << 10,
+ eDP_ServerLastUsedPtr = 1 << 7,
+ eDP_MaxBlobAge = 1 << 8,
+ eDP_ActualBlobAgePtr = 1 << 9,
+ eDP_UseCompoundID = 1 << 10,
+ eDP_SingleServer = 1 << 11,
eDP_CacheName = 1 << 12,
};
typedef unsigned TDefinedParameters;
@@ -80,10 +81,11 @@ public:
m_MirroringMode(CNetCacheAPI::eIfKeyMirrored),
m_ServerCheck(eDefault),
m_ServerCheckHint(true),
+ m_ServerLastUsedPtr(NULL),
m_MaxBlobAge(0),
m_ActualBlobAgePtr(NULL),
m_UseCompoundID(false),
- m_TryAllServers(false)
+ m_SingleServer(false)
{
}
@@ -131,16 +133,22 @@ public:
m_ServerToUse = server_to_use;
}
+ void SetServerLastUsedPtr(CNetServer* server_last_used_ptr)
+ {
+ m_DefinedParameters |= eDP_ServerLastUsedPtr;
+ m_ServerLastUsedPtr = server_last_used_ptr;
+ }
+
void SetMaxBlobAge(unsigned max_age)
{
m_DefinedParameters |= eDP_MaxBlobAge;
m_MaxBlobAge = max_age;
}
- void SetActualBlobAgePtr(unsigned* actual_age)
+ void SetActualBlobAgePtr(unsigned* actual_age_ptr)
{
m_DefinedParameters |= eDP_ActualBlobAgePtr;
- m_ActualBlobAgePtr = actual_age;
+ m_ActualBlobAgePtr = actual_age_ptr;
}
void SetUseCompoundID(bool use_compound_id)
@@ -149,10 +157,10 @@ public:
m_UseCompoundID = use_compound_id;
}
- void SetTryAllServers(bool try_all_servers)
+ void SetSingleServer(bool single_server)
{
- m_DefinedParameters |= eDP_TryAllServers;
- m_TryAllServers = try_all_servers;
+ m_DefinedParameters |= eDP_SingleServer;
+ m_SingleServer = single_server;
}
void SetCacheName(const string& cache_name)
@@ -168,10 +176,11 @@ public:
bool GetServerCheckHint(bool* server_check_hint) const;
std::string GetPassword() const;
CNetServer GetServerToUse() const;
+ CNetServer* GetServerLastUsedPtr() const;
unsigned GetMaxBlobAge() const;
unsigned* GetActualBlobAgePtr() const;
bool GetUseCompoundID() const;
- bool GetTryAllServers() const;
+ bool GetSingleServer() const;
string GetCacheName() const;
static bool StringToBool(const string& bool_str,
@@ -188,10 +197,11 @@ private:
bool m_ServerCheckHint;
std::string m_Password;
CNetServer m_ServerToUse;
+ CNetServer* m_ServerLastUsedPtr;
unsigned m_MaxBlobAge;
unsigned* m_ActualBlobAgePtr;
bool m_UseCompoundID;
- bool m_TryAllServers;
+ bool m_SingleServer;
string m_CacheName;
};
diff --git a/c++/src/connect/services/netcache_rw.cpp b/c++/src/connect/services/netcache_rw.cpp
index ba5a51a..a86c3f6 100644
--- a/c++/src/connect/services/netcache_rw.cpp
+++ b/c++/src/connect/services/netcache_rw.cpp
@@ -1,4 +1,4 @@
-/* $Id: netcache_rw.cpp 447471 2014-09-25 20:59:33Z kazimird $
+/* $Id: netcache_rw.cpp 465280 2015-04-20 14:54:39Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -253,11 +253,13 @@ void CNetCacheReader::SocketRead(void* buf, size_t count, size_t* bytes_read)
/////////////////////////////////////////////////
CNetCacheWriter::CNetCacheWriter(SNetCacheAPIImpl* impl,
string* blob_id,
+ const string& key,
ENetCacheResponseType response_type,
const CNetCacheAPIParameters* parameters) :
m_ResponseType(response_type),
m_NetCacheAPI(impl),
m_BlobID(*blob_id),
+ m_Key(key),
m_Parameters(parameters)
{
switch (parameters->GetCachingMode()) {
@@ -417,11 +419,6 @@ void CNetCacheWriter::Transmit(const void* buf,
ERW_Result res = m_TransmissionWriter->Write(buf, count, bytes_written);
try {
- if (res != eRW_Success /*&& res != eRW_NotImplemented*/) {
- NCBI_THROW(CNetServiceException, eCommunicationError,
- g_RW_ResultToString(res));
- }
-
STimeout to = {0, 0};
switch (m_Connection->m_Socket.Wait(eIO_Read, &to)) {
case eIO_Success:
@@ -435,6 +432,11 @@ void CNetCacheWriter::Transmit(const void* buf,
msg = NStr::ParseEscapes(msg);
}
NCBI_THROW(CNetCacheException, eServerError, msg);
+ }
+
+ if (res != eRW_Success) {
+ NCBI_THROW(CNetServiceException, eCommunicationError,
+ g_RW_ResultToString(res));
} // else FALL THROUGH
}
diff --git a/c++/src/connect/services/netcache_rw.hpp b/c++/src/connect/services/netcache_rw.hpp
index 4b61769..92a836b 100644
--- a/c++/src/connect/services/netcache_rw.hpp
+++ b/c++/src/connect/services/netcache_rw.hpp
@@ -1,7 +1,7 @@
#ifndef CONN___NETCACHE_RW__HPP
#define CONN___NETCACHE_RW__HPP
-/* $Id: netcache_rw.hpp 446411 2014-09-15 18:56:36Z kazimird $
+/* $Id: netcache_rw.hpp 456051 2015-01-07 17:38:03Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -117,6 +117,7 @@ class NCBI_XCONNECT_EXPORT CNetCacheWriter : public IEmbeddedStreamWriter
public:
CNetCacheWriter(SNetCacheAPIImpl* impl,
string* blob_id,
+ const string& key,
ENetCacheResponseType response_type,
const CNetCacheAPIParameters* parameters);
@@ -137,6 +138,7 @@ public:
ENetCacheResponseType GetResponseType() const {return m_ResponseType;}
const string& GetBlobID() const {return m_BlobID;}
+ const string& GetKey() const {return m_Key;}
void SetBlobID(const string& blob_id) {m_BlobID = blob_id;}
@@ -156,6 +158,7 @@ private:
CNetCacheAPI m_NetCacheAPI;
string m_BlobID;
+ string m_Key; // Only for ICache mode.
const CNetCacheAPIParameters* m_Parameters;
CFileIO m_CacheFile;
diff --git a/c++/src/connect/services/neticache_client.cpp b/c++/src/connect/services/neticache_client.cpp
index 74dffa1..9f5d1f8 100644
--- a/c++/src/connect/services/neticache_client.cpp
+++ b/c++/src/connect/services/neticache_client.cpp
@@ -1,4 +1,4 @@
-/* $Id: neticache_client.cpp 458672 2015-02-09 11:57:13Z kazimird $
+/* $Id: neticache_client.cpp 475261 2015-08-05 19:52:42Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -147,7 +147,8 @@ struct SNetICacheClientImpl : public SNetCacheAPIImpl, protected CConnIniter
config, section, s_NetICacheConfigSections);
}
- CNetServer::SExecResult StickToServerAndExec(const string& cmd,
+ CNetServer::SExecResult ChooseServerAndExec(const string& cmd,
+ const string& key,
bool multiline_output,
const CNetCacheAPIParameters* parameters,
INetServerConnectionListener* conn_listener = NULL);
@@ -213,9 +214,9 @@ void CNetICacheServerListener::OnInit(CObject* api_impl,
}
if (config != NULL)
- icache_impl->m_DefaultParameters.SetTryAllServers(
+ icache_impl->m_DefaultParameters.SetSingleServer(
config->GetBool(config_section,
- "try_all_servers", CConfig::eErr_NoThrow, false));
+ "single_server", CConfig::eErr_NoThrow, false));
}
CNetServerConnection SNetICacheClientImpl::InitiateWriteCmd(
@@ -231,7 +232,8 @@ CNetServerConnection SNetICacheClientImpl::InitiateWriteCmd(
cmd.append(" confirm=1");
AppendClientIPSessionIDPasswordAgeHitID(&cmd, parameters);
- return StickToServerAndExec(cmd, false, parameters).conn;
+ return ChooseServerAndExec(cmd, nc_writer->GetKey(),
+ false, parameters).conn;
}
CNetICacheClient::CNetICacheClient(EAppRegistry use_app_reg,
@@ -278,53 +280,85 @@ STimeout CNetICacheClient::GetCommunicationTimeout() const
return m_Impl->m_Service->m_ServerPool.GetCommunicationTimeout();
}
-CNetServer::SExecResult SNetICacheClientImpl::StickToServerAndExec(
+class SWeightedServiceTraversal : public IServiceTraversal
+{
+public:
+ SWeightedServiceTraversal(CNetService::TInstance service,
+ const string& key) :
+ m_Service(service),
+ m_Key(key)
+ {
+ }
+
+ virtual CNetServer BeginIteration();
+ virtual CNetServer NextServer();
+
+private:
+ CNetService m_Service;
+ const string& m_Key;
+ CNetServiceIterator m_Iterator;
+};
+
+CNetServer SWeightedServiceTraversal::BeginIteration()
+{
+ return *(m_Iterator = m_Service.IterateByWeight(m_Key));
+}
+
+CNetServer SWeightedServiceTraversal::NextServer()
+{
+ return ++m_Iterator ? *m_Iterator : CNetServer();
+}
+
+CNetServer::SExecResult SNetICacheClientImpl::ChooseServerAndExec(
const string& cmd,
+ const string& key,
bool multiline_output,
const CNetCacheAPIParameters* parameters,
INetServerConnectionListener* conn_listener)
{
CNetServer selected_server(parameters->GetServerToUse());
+ CNetServer* server_last_used_ptr(parameters->GetServerLastUsedPtr());
- if (selected_server) {
- try {
+ if (parameters->GetSingleServer()) {
+ if (!selected_server)
+ selected_server = m_Service.IterateByWeight(key).GetServer();
+
+ if (server_last_used_ptr == NULL)
return selected_server.ExecWithRetry(cmd,
multiline_output, conn_listener);
- }
- catch (CNetCacheException& ex) {
- if (ex.GetErrCode() != CNetCacheException::eBlobNotFound ||
- !parameters->GetTryAllServers())
- throw;
- }
- catch (CNetSrvConnException& ex) {
- if (ex.GetErrCode() != CNetSrvConnException::eConnectionFailure &&
- ex.GetErrCode() != CNetSrvConnException::eServerThrottle)
- throw;
- ERR_POST(ex.what());
+ else {
+ CNetServer::SExecResult exec_result(
+ selected_server.ExecWithRetry(cmd,
+ multiline_output, conn_listener));
+ *server_last_used_ptr = selected_server;
+ return exec_result;
}
}
- CNetServiceIterator it = m_Service.Iterate();
+ CNetServer::SExecResult exec_result;
- for (;;) {
- try {
- m_DefaultParameters.SetServerToUse(*it);
- return (*it).ExecWithRetry(cmd, multiline_output, conn_listener);
- }
- catch (CNetCacheException& ex) {
- if (ex.GetErrCode() != CNetCacheException::eBlobNotFound ||
- !parameters->GetTryAllServers() ||
- !++it)
- throw;
- }
- catch (CNetSrvConnException& ex) {
- if ((ex.GetErrCode() != CNetSrvConnException::eConnectionFailure &&
- ex.GetErrCode() != CNetSrvConnException::eServerThrottle) ||
- !++it)
- throw;
- ERR_POST(ex.what());
- }
+ if (selected_server) {
+ ESwitch server_check = eDefault;
+ parameters->GetServerCheck(&server_check);
+
+ SNetCacheMirrorTraversal mirror_traversal(m_Service,
+ selected_server, server_check);
+
+ m_Service->IterateUntilExecOK(cmd, multiline_output, exec_result,
+ &mirror_traversal, SNetServiceImpl::eIgnoreServerErrors,
+ conn_listener);
+ } else {
+ SWeightedServiceTraversal service_traversal(m_Service, key);
+
+ m_Service->IterateUntilExecOK(cmd, multiline_output, exec_result,
+ &service_traversal, SNetServiceImpl::eIgnoreServerErrors,
+ conn_listener);
}
+
+ if (server_last_used_ptr != NULL)
+ *server_last_used_ptr = exec_result.conn->m_Server;
+
+ return exec_result;
}
void CNetICacheClient::RegisterSession(unsigned pid)
@@ -404,7 +438,7 @@ void CNetICacheClient::Store(const string& key,
parameters.SetTTL(time_to_live);
parameters.SetCachingMode(CNetCacheAPI::eCaching_Disable);
- CNetCacheWriter writer(m_Impl, &blob_id,
+ CNetCacheWriter writer(m_Impl, &blob_id, key,
m_Impl->m_CacheFlags & ICache::fBestReliability ?
eNetCache_Wait : eICache_NoWait, ¶meters);
@@ -467,7 +501,7 @@ IReader* SNetICacheClientImpl::GetReadStreamPart(
}
CNetServer::SExecResult exec_result(
- StickToServerAndExec(cmd, false, ¶meters));
+ ChooseServerAndExec(cmd, key, false, ¶meters));
unsigned* actual_age_ptr = parameters.GetActualBlobAgePtr();
if (parameters.GetMaxBlobAge() > 0 && actual_age_ptr != NULL)
@@ -585,7 +619,7 @@ IEmbeddedStreamWriter* CNetICacheClient::GetNetCacheWriter(const string& key,
parameters.LoadNamedParameters(optional);
- return new CNetCacheWriter(m_Impl, &blob_id,
+ return new CNetCacheWriter(m_Impl, &blob_id, key,
m_Impl->m_CacheFlags & ICache::fBestReliability ?
eNetCache_Wait : eICache_NoWait, ¶meters);
}
@@ -730,8 +764,8 @@ IReader* SNetICacheClientImpl::ReadCurrentBlobNotOlderThan(const string& key,
cmd = MakeStdCmd("READLAST", blob_id, ¶meters);
}
- CNetServer::SExecResult exec_result(StickToServerAndExec(cmd,
- false, &m_DefaultParameters));
+ CNetServer::SExecResult exec_result(ChooseServerAndExec(cmd,
+ key, false, &m_DefaultParameters));
string::size_type pos = exec_result.response.find("VER=");
@@ -775,6 +809,11 @@ IReader* SNetICacheClientImpl::ReadCurrentBlobNotOlderThan(const string& key,
return NULL;
}
+ catch (CNetCacheException& e) {
+ if (e.GetErrCode() != CNetCacheException::eBlobNotFound)
+ throw;
+ return NULL;
+ }
}
class CSetValidWarningSuppressor : public CNetICacheServerListener
@@ -793,8 +832,8 @@ public:
}
virtual CRef<INetServerProperties> AllocServerProperties();
- virtual CConfig* LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name);
+ virtual CConfig* OnPreInit(CObject* api_impl,
+ CConfig* config, string* config_section);
virtual void OnInit(CObject* api_impl,
CConfig* config, const string& config_section);
virtual void OnConnected(CNetServerConnection& connection);
@@ -812,11 +851,10 @@ CRef<INetServerProperties> CSetValidWarningSuppressor::AllocServerProperties()
return m_DelegateListener->AllocServerProperties();
}
-CConfig* CSetValidWarningSuppressor::LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name)
+CConfig* CSetValidWarningSuppressor::OnPreInit(CObject* api_impl,
+ CConfig* config, string* config_section)
{
- return m_DelegateListener->LoadConfigFromAltSource(api_impl,
- new_section_name);
+ return m_DelegateListener->OnPreInit(api_impl, config, config_section);
}
void CSetValidWarningSuppressor::OnInit(CObject* api_impl,
@@ -863,10 +901,11 @@ void CNetICacheClient::SetBlobVersionAsCurrent(const string& key,
key, subkey, version));
CNetServer::SExecResult exec_result(
- m_Impl->StickToServerAndExec(
+ m_Impl->ChooseServerAndExec(
m_Impl->MakeStdCmd("SETVALID",
s_KeyVersionSubkeyToBlobID(key, version, subkey),
&m_Impl->m_DefaultParameters),
+ key,
false,
&m_Impl->m_DefaultParameters,
warning_suppressor));
@@ -886,10 +925,11 @@ CNetServerMultilineCmdOutput CNetICacheClient::GetBlobInfo(const string& key,
parameters.LoadNamedParameters(optional);
CNetServerMultilineCmdOutput output(
- m_Impl->StickToServerAndExec(
+ m_Impl->ChooseServerAndExec(
m_Impl->MakeStdCmd("GETMETA",
s_KeyVersionSubkeyToBlobID(key, version, subkey),
¶meters),
+ key,
true,
¶meters));
@@ -913,11 +953,6 @@ void CNetICacheClient::PrintBlobInfo(const string& key,
}
}
-CNetServer CNetICacheClient::GetCurrentServer()
-{
- return m_Impl->m_DefaultParameters.GetServerToUse();
-}
-
CNetService CNetICacheClient::GetService()
{
return m_Impl->m_Service;
@@ -948,10 +983,11 @@ string SNetICacheClientImpl::ExecStdCmd(const char* cmd_base,
const string& key, int version, const string& subkey,
const CNetCacheAPIParameters* parameters)
{
- return StickToServerAndExec(
+ return ChooseServerAndExec(
MakeStdCmd(cmd_base,
s_KeyVersionSubkeyToBlobID(key, version, subkey),
parameters),
+ key,
false,
parameters).response;
}
diff --git a/c++/src/connect/services/netschedule_api.cpp b/c++/src/connect/services/netschedule_api.cpp
index 29f13b1..ea430ca 100644
--- a/c++/src/connect/services/netschedule_api.cpp
+++ b/c++/src/connect/services/netschedule_api.cpp
@@ -1,4 +1,4 @@
-/* $Id: netschedule_api.cpp 451468 2014-11-06 19:33:04Z ivanov $
+/* $Id: netschedule_api.cpp 470758 2015-06-18 17:19:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,10 +46,6 @@
#include <memory>
#include <stdio.h>
-#ifdef NCBI_OS_LINUX
-#include <sys/prctl.h>
-#endif
-
#define COMPATIBLE_NETSCHEDULE_VERSION "4.10.0"
@@ -99,8 +95,6 @@ SNetScheduleNotificationThread::SNetScheduleNotificationThread(
m_API(ns_api),
m_StopThread(false)
{
- m_UDPSocket.SetReuseAddress(eOn);
-
STimeout rto;
rto.sec = rto.usec = 0;
m_UDPSocket.SetTimeout(eIO_Read, &rto);
@@ -115,25 +109,21 @@ SNetScheduleNotificationThread::SNetScheduleNotificationThread(
}
void SNetScheduleNotificationThread::CmdAppendPortAndTimeout(
- string* cmd, const CDeadline* deadline)
+ string* cmd, const CDeadline& deadline)
{
- if (deadline != NULL) {
- unsigned remaining_seconds = s_GetRemainingSeconds(*deadline);
+ unsigned remaining_seconds = s_GetRemainingSeconds(deadline);
- if (remaining_seconds > 0) {
- *cmd += " port=";
- *cmd += NStr::UIntToString(GetPort());
+ if (remaining_seconds > 0) {
+ *cmd += " port=";
+ *cmd += NStr::UIntToString(GetPort());
- *cmd += " timeout=";
- *cmd += NStr::UIntToString(remaining_seconds);
- }
+ *cmd += " timeout=";
+ *cmd += NStr::UIntToString(remaining_seconds);
}
}
CNetScheduleNotificationHandler::CNetScheduleNotificationHandler()
{
- m_UDPSocket.SetReuseAddress(eOn);
-
STimeout rto;
rto.sec = rto.usec = 0;
m_UDPSocket.SetTimeout(eIO_Read, &rto);
@@ -255,11 +245,9 @@ bool SServerNotifications::GetNextNotification(string* ns_node)
void* SNetScheduleNotificationThread::Main()
{
-#ifdef NCBI_OS_LINUX
- prctl(PR_SET_NAME, (unsigned long)
+ SetCurrentThreadName(
(CNcbiApplication::Instance()->GetProgramDisplayName() +
- "_nt").c_str(), 0, 0, 0);
-#endif
+ "_nt").c_str());
static const STimeout two_seconds = {2, 0};
@@ -358,7 +346,7 @@ void SNetScheduleAPIImpl::StartNotificationThread()
m_NotificationThread->Run();
}
-void SNetScheduleAPIImpl::StopNotificationThread()
+SNetScheduleAPIImpl::~SNetScheduleAPIImpl()
{
if (m_NotificationThreadStartStopCounter.Add(-1) == 0) {
CFastMutexGuard guard(m_NotificationThreadMutex);
@@ -400,7 +388,59 @@ void SNetScheduleAPIImpl::x_ClearNode()
}
}
-/**********************************************************************/
+CConfig* CNetScheduleConfigLoader::Parse(const TParams& params,
+ const CTempString& prefix, EParseMode mode)
+{
+ auto_ptr<CConfig::TParamTree> result;
+ const string kQueueParameter = "queue_name";
+
+ ITERATE(CNetScheduleAPI::TQueueParams, it, params) {
+ string param;
+ if (mode == eGetQueueName && it->first == kQueueParameter) {
+ param = it->first;
+ } else if (NStr::StartsWith(it->first, prefix)) {
+ param = it->first.substr(prefix.size());
+ } else {
+ continue;
+ }
+
+ if (!result.get()) {
+ result.reset(new CConfig::TParamTree);
+ }
+
+ result->AddNode(CConfig::TParamValue(param, it->second));
+ }
+
+ return result.get() ? new CConfig(result.release()) : NULL;
+}
+
+CConfig* CNetScheduleConfigLoader::Get(const CTempString* literals,
+ SNetScheduleAPIImpl* impl, string* section, EParseMode mode)
+{
+ _ASSERT(literals);
+ _ASSERT(impl);
+
+ TParams queue_params;
+ impl->GetQueueParams(kEmptyStr, queue_params);
+
+ if (CConfig* result = Parse(queue_params, *literals++, mode)) {
+ *section = *literals;
+ return result;
+ }
+
+ try {
+ impl->GetQueueParams(queue_params);
+
+ if (CConfig* result = Parse(queue_params, *++literals, mode)) {
+ *section = *++literals;
+ return result;
+ }
+ }
+ catch (CNetScheduleException&) {
+ }
+
+ return NULL;
+}
void CNetScheduleServerListener::SetAuthString(SNetScheduleAPIImpl* impl)
{
@@ -444,12 +484,15 @@ void CNetScheduleServerListener::SetAuthString(SNetScheduleAPIImpl* impl)
auth += '\"';
}
- CNcbiApplication* app = CNcbiApplication::Instance();
- if (app != NULL) {
- auth += " client_version=\"";
- auth += app->GetFullVersion().GetVersionInfo().Print();
- auth += '\"';
- }
+ {{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if (app != NULL) {
+ auth += " client_version=\"";
+ auth += app->GetFullVersion().GetVersionInfo().Print();
+ auth += '\"';
+ }
+ }}
ITERATE(SNetScheduleAPIImpl::TAuthParams, it, impl->m_AuthParams) {
auth += it->second;
@@ -499,90 +542,109 @@ CRef<INetServerProperties> CNetScheduleServerListener::AllocServerProperties()
return CRef<INetServerProperties>(new SNetScheduleServerProperties);
}
-CConfig* CNetScheduleServerListener::LoadConfigFromAltSource(
- CObject* /*api_impl*/, string* /*new_section_name*/)
-{
- return NULL;
-}
-
void CNetScheduleServerListener::OnInit(
- CObject* api_impl, CConfig* config, const string& config_section)
+ CObject* api_impl, CConfig* config, const string& section)
{
SNetScheduleAPIImpl* ns_impl = static_cast<SNetScheduleAPIImpl*>(api_impl);
+ _ASSERT(ns_impl);
+
+ auto_ptr<CConfig> config_holder;
+
+ // There are two phases of OnInit in case we need to load config from server
+ // 1) Setup as much as possible and try to get config from server
+ // 2) Setup everything using received config from server
+ for (int phase = 0; phase < 2; ++phase) {
+ string config_section = section;
- if (!ns_impl->m_Queue.empty())
- SNetScheduleAPIImpl::VerifyQueueNameAlphabet(ns_impl->m_Queue);
- else if (config != NULL) {
- ns_impl->m_Queue = config->GetString(config_section,
- "queue_name", CConfig::eErr_NoThrow, kEmptyStr);
if (!ns_impl->m_Queue.empty())
SNetScheduleAPIImpl::VerifyQueueNameAlphabet(ns_impl->m_Queue);
- }
-
- if (config == NULL) {
- ns_impl->m_AffinityPreference = CNetScheduleExecutor::eAnyJob;
- ns_impl->m_UseEmbeddedStorage = true;
- } else {
- try {
- ns_impl->m_UseEmbeddedStorage = config->GetBool(config_section,
- "use_embedded_storage", CConfig::eErr_Throw, true);
- }
- catch (CConfigException&) {
- ns_impl->m_UseEmbeddedStorage = config->GetBool(config_section,
- "use_embedded_input", CConfig::eErr_NoThrow, true);
+ else if (config != NULL) {
+ ns_impl->m_Queue = config->GetString(config_section,
+ "queue_name", CConfig::eErr_NoThrow, kEmptyStr);
+ if (!ns_impl->m_Queue.empty())
+ SNetScheduleAPIImpl::VerifyQueueNameAlphabet(ns_impl->m_Queue);
}
- if (!config->GetBool(config_section, "use_affinities",
- CConfig::eErr_NoThrow, false))
+ if (config == NULL) {
ns_impl->m_AffinityPreference = CNetScheduleExecutor::eAnyJob;
- else {
- ns_impl->m_AffinityPreference = config->GetBool(config_section,
- "claim_new_affinities", CConfig::eErr_NoThrow, false) ?
- CNetScheduleExecutor::eClaimNewPreferredAffs :
- config->GetBool(config_section,
- "process_any_job", CConfig::eErr_NoThrow, false) ?
- CNetScheduleExecutor::ePreferredAffsOrAnyJob :
- CNetScheduleExecutor::ePreferredAffinities;
-
- string affinity_list = config->GetString(config_section,
- "affinity_list", CConfig::eErr_NoThrow, kEmptyStr);
-
- if (!affinity_list.empty()) {
- NStr::Split(affinity_list, ", ", ns_impl->m_AffinityList);
- ITERATE(list<string>, it, ns_impl->m_AffinityList) {
- SNetScheduleAPIImpl::VerifyAffinityAlphabet(*it);
- }
+ ns_impl->m_UseEmbeddedStorage = true;
+ } else {
+ try {
+ ns_impl->m_UseEmbeddedStorage = config->GetBool(config_section,
+ "use_embedded_storage", CConfig::eErr_Throw, true);
+ }
+ catch (CConfigException&) {
+ ns_impl->m_UseEmbeddedStorage = config->GetBool(config_section,
+ "use_embedded_input", CConfig::eErr_NoThrow, true);
}
- string affinity_ladder = config->GetString(config_section,
- "affinity_ladder", CConfig::eErr_NoThrow, kEmptyStr);
- list<CTempString> affinities;
- NStr::Split(affinity_ladder, ", ", affinities);
-
- if (!affinities.empty()) {
- list<CTempString>::const_iterator it = affinities.begin();
- affinity_list = *it;
- for (;;) {
- ns_impl->m_AffinityLadder.push_back(affinity_list);
- if (++it == affinities.end())
- break;
- affinity_list += ',';
- affinity_list += *it;
+ if (!config->GetBool(config_section, "use_affinities",
+ CConfig::eErr_NoThrow, false))
+ ns_impl->m_AffinityPreference = CNetScheduleExecutor::eAnyJob;
+ else {
+ ns_impl->m_AffinityPreference = config->GetBool(config_section,
+ "claim_new_affinities", CConfig::eErr_NoThrow, false) ?
+ CNetScheduleExecutor::eClaimNewPreferredAffs :
+ config->GetBool(config_section,
+ "process_any_job", CConfig::eErr_NoThrow, false) ?
+ CNetScheduleExecutor::ePreferredAffsOrAnyJob :
+ CNetScheduleExecutor::ePreferredAffinities;
+
+ string affinity_list = config->GetString(config_section,
+ "affinity_list", CConfig::eErr_NoThrow, kEmptyStr);
+
+ if (!affinity_list.empty()) {
+ NStr::Split(affinity_list, ", ", ns_impl->m_AffinityList);
+ ITERATE(list<string>, it, ns_impl->m_AffinityList) {
+ SNetScheduleAPIImpl::VerifyAffinityAlphabet(*it);
+ }
+ }
+
+ string affinity_ladder = config->GetString(config_section,
+ "affinity_ladder", CConfig::eErr_NoThrow, kEmptyStr);
+ list<CTempString> affinities;
+ NStr::Split(affinity_ladder, ", ", affinities);
+
+ if (!affinities.empty()) {
+ list<CTempString>::const_iterator it = affinities.begin();
+ affinity_list = *it;
+ for (;;) {
+ ns_impl->m_AffinityLadder.push_back(affinity_list);
+ if (++it == affinities.end())
+ break;
+ affinity_list += ',';
+ affinity_list += *it;
+ }
}
}
+
+ ns_impl->m_JobGroup = config->GetString(config_section,
+ "job_group", CConfig::eErr_NoThrow, kEmptyStr);
+
+ ns_impl->m_ClientNode = config->GetString(config_section,
+ "client_node", CConfig::eErr_NoThrow, kEmptyStr);
+
+ if (!ns_impl->m_ClientNode.empty())
+ ns_impl->m_ClientSession = GetDiagContext().GetStringUID();
}
- ns_impl->m_JobGroup = config->GetString(config_section,
- "job_group", CConfig::eErr_NoThrow, kEmptyStr);
+ SetAuthString(ns_impl);
- ns_impl->m_ClientNode = config->GetString(config_section,
- "client_node", CConfig::eErr_NoThrow, kEmptyStr);
+ // If we should not load config from NetSchedule server
+ // or have already done it
+ if (phase || !CNetScheduleConfigLoader::Use(config, config_section)) {
+ break;
+ }
- if (!ns_impl->m_ClientNode.empty())
- ns_impl->m_ClientSession = GetDiagContext().GetStringUID();
+ const CTempString kLiterals[] = {
+ "ns.", "netschedule_conf_from_netschedule",
+ "ns::", "netschedule_conf_from_netschedule_GETP2"
+ };
+ config_holder.reset(
+ CNetScheduleConfigLoader::Get(kLiterals, ns_impl,
+ &config_section, CNetScheduleConfigLoader::eGetQueueName));
+ config = config_holder.get();
}
-
- SetAuthString(ns_impl);
}
void CNetScheduleServerListener::OnConnected(CNetServerConnection& connection)
@@ -852,14 +914,14 @@ CNetScheduleSubmitter CNetScheduleAPI::GetSubmitter()
CNetScheduleExecutor CNetScheduleAPI::GetExecutor()
{
- m_Impl->AllocNotificationThread();
return new SNetScheduleExecutorImpl(m_Impl);
}
-CNetScheduleJobReader CNetScheduleAPI::GetJobReader()
+CNetScheduleJobReader CNetScheduleAPI::GetJobReader(const string& group,
+ const string& affinity)
{
m_Impl->AllocNotificationThread();
- return new SNetScheduleJobReaderImpl(m_Impl);
+ return new SNetScheduleJobReaderImpl(m_Impl, group, affinity);
}
CNetScheduleAdmin CNetScheduleAPI::GetAdmin()
@@ -893,7 +955,7 @@ CNetScheduleAPI::EJobStatus CNetScheduleAPI::GetJobDetails(
time_t* job_exptime,
ENetScheduleQueuePauseMode* pause_mode)
{
- string resp = m_Impl->x_ExecOnce("STATUS2", job.job_id);
+ string resp = m_Impl->x_ExecOnce("STATUS2", job);
static const char* const s_JobStatusAttrNames[] = {
"job_status", // 0
@@ -949,13 +1011,13 @@ CNetScheduleAPI::EJobStatus CNetScheduleAPI::GetJobDetails(
}
CNetScheduleAPI::EJobStatus SNetScheduleAPIImpl::GetJobStatus(const string& cmd,
- const string& job_key, time_t* job_exptime,
+ const CNetScheduleJob& job, time_t* job_exptime,
ENetScheduleQueuePauseMode* pause_mode)
{
string response;
try {
- response = x_ExecOnce(cmd, job_key);
+ response = x_ExecOnce(cmd, job);
}
catch (CNetScheduleException& e) {
if (e.GetErrCode() != CNetScheduleException::eJobNotFound)
@@ -1062,23 +1124,24 @@ const CNetScheduleAPI::SServerParams& CNetScheduleAPI::GetServerParams()
return m_Impl->GetServerParams();
}
-void CNetScheduleAPI::GetQueueParams(
+void SNetScheduleAPIImpl::GetQueueParams(
const string& queue_name, TQueueParams& queue_params)
{
- string cmd;
+ string cmd("QINF2 ");
- if (queue_name.empty())
- cmd = "QINF2 " + m_Impl->m_Queue;
- else {
+ if (!queue_name.empty()) {
SNetScheduleAPIImpl::VerifyQueueNameAlphabet(queue_name);
- cmd = "QINF2 " + queue_name;
+ cmd += queue_name;
+ } else if (!m_Queue.empty()) {
+ cmd += m_Queue;
+ } else {
+ cmd += "service=" + m_Service->m_ServiceName;
}
g_AppendClientIPSessionIDHitID(cmd);
- CUrlArgs url_parser(m_Impl->m_Service.FindServerAndExec(cmd,
- false).response);
+ CUrlArgs url_parser(m_Service.FindServerAndExec(cmd, false).response);
ITERATE(CUrlArgs::TArgs, field, url_parser.GetArgs()) {
queue_params[field->name] = field->value;
@@ -1086,12 +1149,17 @@ void CNetScheduleAPI::GetQueueParams(
}
void CNetScheduleAPI::GetQueueParams(
- CNetScheduleAPI::TQueueParams& queue_params)
+ const string& queue_name, TQueueParams& queue_params)
+{
+ return m_Impl->GetQueueParams(queue_name, queue_params);
+}
+
+void SNetScheduleAPIImpl::GetQueueParams(TQueueParams& queue_params)
{
string cmd("GETP2");
g_AppendClientIPSessionIDHitID(cmd);
- CUrlArgs url_parser(m_Impl->m_Service.FindServerAndExec(cmd,
+ CUrlArgs url_parser(m_Service.FindServerAndExec(cmd,
false).response);
ITERATE(CUrlArgs::TArgs, field, url_parser.GetArgs()) {
@@ -1099,10 +1167,14 @@ void CNetScheduleAPI::GetQueueParams(
}
}
+void CNetScheduleAPI::GetQueueParams(TQueueParams& queue_params)
+{
+ return m_Impl->GetQueueParams(queue_params);
+}
+
void CNetScheduleAPI::GetProgressMsg(CNetScheduleJob& job)
{
- job.progress_msg = NStr::ParseEscapes(
- m_Impl->x_ExecOnce("MGET", job.job_id));
+ job.progress_msg = NStr::ParseEscapes(m_Impl->x_ExecOnce("MGET", job));
}
void SNetScheduleAPIImpl::VerifyQueueNameAlphabet(const string& queue_name)
diff --git a/c++/src/connect/services/netschedule_api_admin.cpp b/c++/src/connect/services/netschedule_api_admin.cpp
index 6e2b04f..d2fa105 100644
--- a/c++/src/connect/services/netschedule_api_admin.cpp
+++ b/c++/src/connect/services/netschedule_api_admin.cpp
@@ -1,4 +1,4 @@
-/* $Id: netschedule_api_admin.cpp 449958 2014-10-22 13:29:15Z ivanov $
+/* $Id: netschedule_api_admin.cpp 449834 2014-10-21 16:34:48Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/netschedule_api_executor.cpp b/c++/src/connect/services/netschedule_api_executor.cpp
index 9814764..1458d0e 100644
--- a/c++/src/connect/services/netschedule_api_executor.cpp
+++ b/c++/src/connect/services/netschedule_api_executor.cpp
@@ -1,4 +1,4 @@
-/* $Id: netschedule_api_executor.cpp 451458 2014-11-06 19:31:25Z ivanov $
+/* $Id: netschedule_api_executor.cpp 466932 2015-05-07 15:31:56Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -208,14 +208,14 @@ bool g_ParseGetJobResponse(CNetScheduleJob& job, const string& response)
}
////////////////////////////////////////////////////////////////////////
-void CNetScheduleExecutor::JobDelayExpiration(const string& job_key,
+void CNetScheduleExecutor::JobDelayExpiration(const CNetScheduleJob& job,
unsigned runtime_inc)
{
- string cmd(g_MakeBaseCmd("JDEX", job_key));
+ string cmd(g_MakeBaseCmd("JDEX", job.job_id));
cmd += ' ';
cmd += NStr::NumericToString(runtime_inc);
g_AppendClientIPSessionIDHitID(cmd);
- m_Impl->m_API->GetServer(job_key).ExecWithRetry(cmd, false);
+ m_Impl->m_API->GetServer(job).ExecWithRetry(cmd, false);
}
class CGetJobCmdExecutor : public INetServerFinder
@@ -342,6 +342,9 @@ bool SNetScheduleExecutorImpl::ExecGET(SNetServerImpl* server,
if (!g_ParseGetJobResponse(job, exec_result.response))
return false;
+ // Remember the server that issued this job.
+ job.server = server;
+
// If a new preferred affinity is given by the server,
// register it with the rest of servers.
ClaimNewPreferredAffinity(server, job.affinity);
@@ -364,10 +367,10 @@ bool SNetScheduleExecutorImpl::x_GetJobWithAffinityList(SNetServerImpl* server,
}
bool SNetScheduleExecutorImpl::x_GetJobWithAffinityLadder(
- SNetServerImpl* server, const CDeadline* timeout, CNetScheduleJob& job)
+ SNetServerImpl* server, const CDeadline& timeout, CNetScheduleJob& job)
{
if (m_API->m_AffinityLadder.empty())
- return x_GetJobWithAffinityList(server, timeout, job,
+ return x_GetJobWithAffinityList(server, &timeout, job,
m_AffinityPreference, kEmptyStr);
list<string>::const_iterator it = m_API->m_AffinityLadder.begin();
@@ -375,7 +378,7 @@ bool SNetScheduleExecutorImpl::x_GetJobWithAffinityLadder(
for (;;) {
string affinity_list = *it;
if (++it == m_API->m_AffinityLadder.end())
- return x_GetJobWithAffinityList(server, timeout, job,
+ return x_GetJobWithAffinityList(server, &timeout, job,
m_AffinityPreference, affinity_list);
else if (x_GetJobWithAffinityList(server, NULL, job,
CNetScheduleExecutor::ePreferredAffinities, affinity_list))
@@ -408,6 +411,9 @@ bool CNetScheduleExecutor::GetJob(CNetScheduleJob& job,
cmd, deadline, m_Impl->m_JobGroup);
if (g_ParseGetJobResponse(job, server.ExecWithRetry(cmd,
false).response)) {
+ // Remember the server that issued this job.
+ job.server = server;
+
// Notify the rest of NetSchedule servers that
// we are no longer listening on the UDP socket.
string cancel_wget_cmd("CWGET");
@@ -558,17 +564,15 @@ void static s_CheckOutputSize(const string& output, size_t max_output_size)
}
}
-void SNetScheduleExecutorImpl::ExecWithOrWithoutRetry(const string& job_key,
- const string& cmd)
+void SNetScheduleExecutorImpl::ExecWithOrWithoutRetry(
+ const CNetScheduleJob& job, const string& cmd)
{
- CNetServer server(m_API->GetServer(job_key));
-
if (!m_WorkerNodeMode)
- server.ExecWithRetry(cmd, false);
+ m_API->GetServer(job).ExecWithRetry(cmd, false);
else {
CNetServer::SExecResult exec_result;
- server->ConnectAndExec(cmd, false, exec_result);
+ m_API->GetServer(job)->ConnectAndExec(cmd, false, exec_result);
}
}
@@ -592,7 +596,7 @@ void CNetScheduleExecutor::PutResult(const CNetScheduleJob& job)
g_AppendClientIPSessionIDHitID(cmd);
- m_Impl->ExecWithOrWithoutRetry(job.job_id, cmd);
+ m_Impl->ExecWithOrWithoutRetry(job, cmd);
}
void CNetScheduleExecutor::PutProgressMsg(const CNetScheduleJob& job)
@@ -607,8 +611,7 @@ void CNetScheduleExecutor::PutProgressMsg(const CNetScheduleJob& job)
cmd += '\"';
g_AppendClientIPSessionIDHitID(cmd);
CNetServer::SExecResult exec_result;
- m_Impl->m_API->GetServer(job.job_id)->ConnectAndExec(cmd,
- false, exec_result);
+ m_Impl->m_API->GetServer(job)->ConnectAndExec(cmd, false, exec_result);
}
void CNetScheduleExecutor::GetProgressMsg(CNetScheduleJob& job)
@@ -647,7 +650,7 @@ void CNetScheduleExecutor::PutFailure(const CNetScheduleJob& job,
if (no_retries)
cmd.append(" no_retries=1");
- m_Impl->ExecWithOrWithoutRetry(job.job_id, cmd);
+ m_Impl->ExecWithOrWithoutRetry(job, cmd);
}
void CNetScheduleExecutor::Reschedule(const CNetScheduleJob& job)
@@ -674,29 +677,27 @@ void CNetScheduleExecutor::Reschedule(const CNetScheduleJob& job)
g_AppendClientIPSessionIDHitID(cmd);
- m_Impl->ExecWithOrWithoutRetry(job.job_id, cmd);
+ m_Impl->ExecWithOrWithoutRetry(job, cmd);
}
CNetScheduleAPI::EJobStatus CNetScheduleExecutor::GetJobStatus(
- const string& job_key, time_t* job_exptime,
+ const CNetScheduleJob& job, time_t* job_exptime,
ENetScheduleQueuePauseMode* pause_mode)
{
- return m_Impl->m_API->GetJobStatus("WST2",
- job_key, job_exptime, pause_mode);
+ return m_Impl->m_API->GetJobStatus("WST2", job, job_exptime, pause_mode);
}
-void CNetScheduleExecutor::ReturnJob(const string& job_key,
- const string& auth_token)
+void CNetScheduleExecutor::ReturnJob(const CNetScheduleJob& job)
{
- string cmd("RETURN2 job_key=" + job_key);
+ string cmd("RETURN2 job_key=" + job.job_id);
- SNetScheduleAPIImpl::VerifyAuthTokenAlphabet(auth_token);
+ SNetScheduleAPIImpl::VerifyAuthTokenAlphabet(job.auth_token);
cmd.append(" auth_token=");
- cmd.append(auth_token);
+ cmd.append(job.auth_token);
g_AppendClientIPSessionIDHitID(cmd);
- m_Impl->ExecWithOrWithoutRetry(job_key, cmd);
+ m_Impl->ExecWithOrWithoutRetry(job, cmd);
}
int SNetScheduleExecutorImpl::AppendAffinityTokens(string& cmd,
diff --git a/c++/src/connect/services/netschedule_api_impl.hpp b/c++/src/connect/services/netschedule_api_impl.hpp
index 016e5f6..49e3197 100644
--- a/c++/src/connect/services/netschedule_api_impl.hpp
+++ b/c++/src/connect/services/netschedule_api_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONN_SERVICES___NETSCHEDULE_API_IMPL__HPP
#define CONN_SERVICES___NETSCHEDULE_API_IMPL__HPP
-/* $Id: netschedule_api_impl.hpp 451458 2014-11-06 19:31:25Z ivanov $
+/* $Id: netschedule_api_impl.hpp 470759 2015-06-18 17:19:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -73,6 +73,31 @@ struct SNetScheduleServerProperties : public INetServerProperties
bool affs_synced;
};
+// A namespace-like helper class to load configuration from NetSchedule server
+class CNetScheduleConfigLoader
+{
+public:
+ enum EParseMode {
+ eDefault,
+ eGetQueueName
+ };
+
+ static bool Use(CConfig* config, const string& section)
+ {
+ return config && config->GetBool(section, "load_config_from_ns",
+ CConfig::eErr_NoThrow, false);
+ }
+
+ static CConfig* Get(const CTempString* literals, SNetScheduleAPIImpl* impl,
+ string* section, EParseMode mode = eDefault);
+
+private:
+ typedef CNetScheduleAPI::TQueueParams TParams;
+
+ static CConfig* Parse(const TParams& params, const CTempString& prefix,
+ EParseMode mode);
+};
+
class CNetScheduleServerListener : public INetServerConnectionListener
{
public:
@@ -92,8 +117,6 @@ public:
virtual CRef<INetServerProperties> AllocServerProperties();
- virtual CConfig* LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name);
virtual void OnInit(CObject* api_impl,
CConfig* config, const string& config_section);
virtual void OnConnected(CNetServerConnection& connection);
@@ -178,7 +201,7 @@ struct SNetScheduleNotificationThread : public CThread
void PrintPortNumber();
- void CmdAppendPortAndTimeout(string* cmd, const CDeadline* deadline);
+ void CmdAppendPortAndTimeout(string* cmd, const CDeadline& deadline);
SNetScheduleAPIImpl* m_API;
@@ -203,35 +226,47 @@ struct SNetScheduleAPIImpl : public CObject
// Special constructor for CNetScheduleAPI::GetServer().
SNetScheduleAPIImpl(SNetServerInPool* server, SNetScheduleAPIImpl* parent);
+ ~SNetScheduleAPIImpl();
+
CNetScheduleServerListener* GetListener()
{
return static_cast<CNetScheduleServerListener*>(
m_Service->m_Listener.GetPointer());
}
- string x_ExecOnce(const string& cmd_name, const string& job_key)
+ string x_ExecOnce(const string& cmd_name, const CNetScheduleJob& job)
{
- string cmd(g_MakeBaseCmd(cmd_name, job_key));
+ string cmd(g_MakeBaseCmd(cmd_name, job.job_id));
g_AppendClientIPSessionIDHitID(cmd);
CNetServer::SExecResult exec_result;
- GetServer(job_key)->ConnectAndExec(cmd, false, exec_result);
+
+ GetServer(job)->ConnectAndExec(cmd, false, exec_result);
return exec_result.response;
}
CNetScheduleAPI::EJobStatus GetJobStatus(const string& cmd,
- const string& job_key, time_t* job_exptime,
+ const CNetScheduleJob& job, time_t* job_exptime,
ENetScheduleQueuePauseMode* pause_mode);
const CNetScheduleAPI::SServerParams& GetServerParams();
+ typedef CNetScheduleAPI::TQueueParams TQueueParams;
+ void GetQueueParams(const string& queue_name, TQueueParams& queue_params);
+ void GetQueueParams(TQueueParams& queue_params);
+
CNetServer GetServer(const string& job_key)
{
CNetScheduleKey nskey(job_key, m_CompoundIDPool);
return m_Service.GetServer(nskey.host, nskey.port);
}
+ CNetServer GetServer(const CNetScheduleJob& job)
+ {
+ return job.server != NULL ? job.server : GetServer(job.job_id);
+ }
+
bool GetServerByNode(const string& ns_node, CNetServer* server);
static void VerifyJobGroupAlphabet(const string& job_group)
@@ -253,7 +288,6 @@ struct SNetScheduleAPIImpl : public CObject
void AllocNotificationThread();
void StartNotificationThread();
- void StopNotificationThread();
// Unregister client-listener. After this call, the
// server will not try to send any notification messages or
@@ -336,10 +370,10 @@ struct SNetScheduleExecutorImpl : public CObject
CNetScheduleExecutor::EJobAffinityPreference affinity_preference,
const string& affinity_list);
bool x_GetJobWithAffinityLadder(SNetServerImpl* server,
- const CDeadline* timeout,
+ const CDeadline& timeout,
CNetScheduleJob& job);
- void ExecWithOrWithoutRetry(const string& job_key, const string& cmd);
+ void ExecWithOrWithoutRetry(const CNetScheduleJob& job, const string& cmd);
enum EChangeAffAction {
eAddAffs,
@@ -359,6 +393,8 @@ struct SNetScheduleExecutorImpl : public CObject
string m_JobGroup;
+ // True when this object is used by a real
+ // worker node application (CGridWorkerNode).
bool m_WorkerNodeMode;
};
@@ -376,86 +412,201 @@ public:
SNetScheduleExecutorImpl* m_Executor;
};
-struct SNotificationTimelineEntry : public CWorkerNodeTimelineEntry
+struct SServerTimelineEntry : public CWorkerNodeTimelineEntry
{
- typedef CRef<SNotificationTimelineEntry> TRef;
+ const SServerAddress server_address;
+ unsigned discovery_iteration;
+ bool more_jobs;
+
+ // If iteration is zero, then it's either discovery action or search pattern
+ SServerTimelineEntry(const SServerAddress& a, unsigned i = 0) :
+ server_address(a),
+ discovery_iteration(i),
+ more_jobs(i) // It's set to false for special entries (see above)
+ {
+ }
+};
- SServerAddress m_ServerAddress;
+class CServerTimelineEntries
+{
+public:
+ ~CServerTimelineEntries();
- unsigned m_DiscoveryIteration;
+ SServerTimelineEntry* GetEntry(SNetServerImpl* server_impl, unsigned iteration);
- SNotificationTimelineEntry(const SServerAddress& server_address,
- unsigned discovery_iteration) :
- m_ServerAddress(server_address),
- m_DiscoveryIteration(discovery_iteration)
- {
- }
+private:
+ typedef SServerTimelineEntry TEntry;
struct SLess
{
- bool operator ()(const SNotificationTimelineEntry* left,
- const SNotificationTimelineEntry* right) const
+ bool operator ()(const TEntry* left, const TEntry* right) const
{
- return left->m_ServerAddress < right->m_ServerAddress;
+ return left->server_address < right->server_address;
}
};
- bool IsDiscoveryAction() const {return m_DiscoveryIteration == 0;}
+ typedef set<TEntry*, SLess> TTimelineEntries;
+ TTimelineEntries m_TimelineEntryByAddress;
};
-struct SNetScheduleJobReaderImpl : public CObject
+class CServerTimeline
{
- SNetScheduleJobReaderImpl(CNetScheduleAPI::TInstance ns_api_impl) :
- m_API(ns_api_impl),
- m_DiscoveryIteration(1),
- m_DiscoveryAction(
- new SNotificationTimelineEntry(SServerAddress(0, 0), 0))
+public:
+ typedef CRef<SServerTimelineEntry> TEntryRef;
+
+ CServerTimeline();
+
+ bool HasImmediateActions() const { return !m_ImmediateActions.IsEmpty(); }
+ bool HasScheduledActions() const { return !m_Timeline.IsEmpty(); }
+
+ void CheckScheduledActions()
{
- m_ImmediateActions.Push(m_DiscoveryAction);
+ while (!m_Timeline.IsEmpty() && m_Timeline.GetHead()->TimeHasCome()) {
+ m_Timeline.MoveHeadTo(&m_ImmediateActions);
+ }
}
- typedef CWorkerNodeTimeline<SNotificationTimelineEntry,
- SNotificationTimelineEntry::TRef> TNotificationTimeline;
+ const CDeadline GetNextTimeout() const
+ {
+ return m_Timeline.GetHead()->GetTimeout();
+ }
- TNotificationTimeline m_ImmediateActions, m_Timeline;
+ TEntryRef PullImmediateAction()
+ {
+ TEntryRef entry;
+ m_ImmediateActions.Shift(entry);
+ return entry;
+ }
- typedef set<SNotificationTimelineEntry*,
- SNotificationTimelineEntry::SLess> TTimelineEntries;
+ TEntryRef PullScheduledAction()
+ {
+ TEntryRef entry;
+ m_Timeline.Shift(entry);
+ return entry;
+ }
- TTimelineEntries m_TimelineEntryByAddress;
+ bool IsDiscoveryAction(TEntryRef entry) const
+ {
+ return !entry->discovery_iteration;
+ }
- CNetScheduleAPI m_API;
+ bool IsOutdatedAction(TEntryRef entry) const
+ {
+ return entry->discovery_iteration != m_DiscoveryIteration;
+ }
+
+ void MoveToImmediateActions(SNetServerImpl* server_impl)
+ {
+ m_ServerTimeline.GetEntry(server_impl, m_DiscoveryIteration)->
+ MoveTo(&m_ImmediateActions);
+ }
+
+ void PushImmediateAction(TEntryRef entry)
+ {
+ m_ImmediateActions.Push(entry);
+ }
+
+ void PushScheduledAction(TEntryRef entry)
+ {
+ m_Timeline.Push(entry);
+ }
+
+ CNetServer GetServer(CNetScheduleAPI api, TEntryRef entry)
+ {
+ return api.GetService().GetServer(entry->server_address);
+ }
+
+ void NextDiscoveryIteration(CNetScheduleAPI api)
+ {
+ ++m_DiscoveryIteration;
+
+ for (CNetServiceIterator it =
+ api.GetService().Iterate(
+ CNetService::eIncludePenalized); it; ++it) {
+ SServerTimelineEntry* srv_entry = m_ServerTimeline.GetEntry(*it,
+ m_DiscoveryIteration);
+ srv_entry->discovery_iteration = m_DiscoveryIteration;
+ if (!srv_entry->IsInTimeline())
+ m_ImmediateActions.Push(srv_entry);
+ }
+ }
+
+ bool MoreJobs() const
+ {
+ for (TEntryRef entry = m_Timeline.GetHead();
+ entry;
+ entry = m_Timeline.GetNext(entry)) {
+ if (entry->more_jobs && !IsOutdatedAction(entry)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ void Suspend(unsigned timeout)
+ {
+ m_ImmediateActions.Clear();
+ m_Timeline.Clear();
+ m_DiscoveryAction->ResetTimeout(timeout);
+ m_Timeline.Push(m_DiscoveryAction);
+ }
+
+ void Resume()
+ {
+ m_DiscoveryAction->MoveTo(&m_ImmediateActions);
+ }
+
+private:
+ CServerTimelineEntries m_ServerTimeline;
+
+ typedef CWorkerNodeTimeline<SServerTimelineEntry, TEntryRef> TTimeline;
+ TTimeline m_ImmediateActions, m_Timeline;
- CAtomicCounter_WithAutoInit m_NotificationThreadIsRunning;
+ unsigned m_DiscoveryIteration;
+ TEntryRef m_DiscoveryAction;
+};
+
+struct SNetScheduleJobReaderImpl : public CObject
+{
+ SNetScheduleJobReaderImpl(CNetScheduleAPI::TInstance ns_api_impl,
+ const string& group, const string& affinity) :
+ m_API(ns_api_impl),
+ m_JobGroup(group),
+ m_Affinity(affinity)
+ {
+ SNetScheduleAPIImpl::VerifyJobGroupAlphabet(group);
+ SNetScheduleAPIImpl::VerifyAffinityAlphabet(affinity);
+ }
+
+ CNetScheduleAPI m_API;
void x_StartNotificationThread()
{
- if (m_NotificationThreadIsRunning.Get() == 0 &&
- m_NotificationThreadIsRunning.Add(1) == 1)
- m_API->StartNotificationThread();
+ m_API->StartNotificationThread();
}
string m_JobGroup;
string m_Affinity;
bool x_ReadJob(SNetServerImpl* server,
- const CDeadline* timeout,
+ const CDeadline& timeout,
CNetScheduleJob& job,
CNetScheduleAPI::EJobStatus* job_status,
bool* no_more_jobs);
- bool x_PerformTimelineAction(TNotificationTimeline& timeline,
+ bool x_PerformTimelineAction(CServerTimeline::TEntryRef timeline_entry,
CNetScheduleJob& job,
CNetScheduleAPI::EJobStatus* job_status,
bool* no_more_jobs);
void x_ProcessReadJobNotifications();
- SNotificationTimelineEntry* x_GetTimelineEntry(SNetServerImpl* server_impl);
-
- virtual ~SNetScheduleJobReaderImpl();
+ CNetScheduleJobReader::EReadNextJobResult ReadNextJob(
+ CNetScheduleJob* job,
+ CNetScheduleAPI::EJobStatus* job_status,
+ const CTimeout* timeout);
- unsigned m_DiscoveryIteration;
-
- SNotificationTimelineEntry::TRef m_DiscoveryAction;
+private:
+ CServerTimeline m_Timeline;
};
struct SNetScheduleAdminImpl : public CObject
diff --git a/c++/src/connect/services/netschedule_api_reader.cpp b/c++/src/connect/services/netschedule_api_reader.cpp
index f5c86cd..c36082d 100644
--- a/c++/src/connect/services/netschedule_api_reader.cpp
+++ b/c++/src/connect/services/netschedule_api_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: netschedule_api_reader.cpp 449958 2014-10-22 13:29:15Z ivanov $
+/* $Id: netschedule_api_reader.cpp 470760 2015-06-18 17:20:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -52,11 +52,11 @@ void CNetScheduleJobReader::SetAffinity(const string& affinity)
m_Impl->m_Affinity = affinity;
}
-SNotificationTimelineEntry*
- SNetScheduleJobReaderImpl::x_GetTimelineEntry(SNetServerImpl* server_impl)
+CServerTimelineEntries::TEntry*
+CServerTimelineEntries::GetEntry(SNetServerImpl* server_impl, unsigned iteration)
{
- SNotificationTimelineEntry search_pattern(
- server_impl->m_ServerInPool->m_Address, 0);
+ const SServerAddress search_address(server_impl->m_ServerInPool->m_Address);
+ TEntry search_pattern(search_address);
TTimelineEntries::iterator it(
m_TimelineEntryByAddress.find(&search_pattern));
@@ -64,8 +64,7 @@ SNotificationTimelineEntry*
if (it != m_TimelineEntryByAddress.end())
return *it;
- SNotificationTimelineEntry* new_entry = new SNotificationTimelineEntry(
- search_pattern.m_ServerAddress, m_DiscoveryIteration);
+ TEntry* new_entry = new TEntry(search_address, iteration);
m_TimelineEntryByAddress.insert(new_entry);
new_entry->AddReference();
@@ -73,14 +72,18 @@ SNotificationTimelineEntry*
return new_entry;
}
-SNetScheduleJobReaderImpl::~SNetScheduleJobReaderImpl()
+CServerTimelineEntries::~CServerTimelineEntries()
{
ITERATE(TTimelineEntries, it, m_TimelineEntryByAddress) {
(*it)->RemoveReference();
}
+}
- if (m_NotificationThreadIsRunning.Get() != 0)
- m_API->StopNotificationThread();
+CServerTimeline::CServerTimeline() :
+ m_DiscoveryIteration(1),
+ m_DiscoveryAction(new SServerTimelineEntry(SServerAddress(0, 0)))
+{
+ m_ImmediateActions.Push(m_DiscoveryAction);
}
// True if a job is returned.
@@ -134,8 +137,10 @@ static bool s_ParseReadJobResponse(const string& response,
case 'n':
if (field->name == "ncbi_phid")
job.page_hit_id = field->value;
- else if (field->name == "no_more_jobs")
+ else if (field->name == "no_more_jobs") {
+ _ASSERT(no_more_jobs);
*no_more_jobs = NStr::StringToBool(field->value.c_str());
+ }
}
}
@@ -143,7 +148,7 @@ static bool s_ParseReadJobResponse(const string& response,
}
bool SNetScheduleJobReaderImpl::x_ReadJob(SNetServerImpl* server,
- const CDeadline* timeout, CNetScheduleJob& job,
+ const CDeadline& timeout, CNetScheduleJob& job,
CNetScheduleAPI::EJobStatus* job_status,
bool* no_more_jobs)
{
@@ -174,53 +179,46 @@ bool SNetScheduleJobReaderImpl::x_ReadJob(SNetServerImpl* server,
}
bool SNetScheduleJobReaderImpl::x_PerformTimelineAction(
- SNetScheduleJobReaderImpl::TNotificationTimeline& timeline,
+ CServerTimeline::TEntryRef timeline_entry,
CNetScheduleJob& job,
CNetScheduleAPI::EJobStatus* job_status,
bool* no_more_jobs)
{
- *no_more_jobs = false;
-
- SNotificationTimelineEntry::TRef timeline_entry;
-
- timeline.Shift(timeline_entry);
+ _ASSERT(no_more_jobs);
+ *no_more_jobs = true;
- if (timeline_entry->IsDiscoveryAction()) {
- ++m_DiscoveryIteration;
- for (CNetServiceIterator it = m_API.GetService().Iterate(
- CNetService::eIncludePenalized); it; ++it) {
- SNotificationTimelineEntry* srv_entry = x_GetTimelineEntry(*it);
- srv_entry->m_DiscoveryIteration = m_DiscoveryIteration;
- if (!srv_entry->IsInTimeline())
- m_ImmediateActions.Push(srv_entry);
- }
+ if (m_Timeline.IsDiscoveryAction(timeline_entry)) {
+ m_Timeline.NextDiscoveryIteration(m_API);
timeline_entry->ResetTimeout(READJOB_TIMEOUT);
- m_Timeline.Push(timeline_entry);
+ m_Timeline.PushScheduledAction(timeline_entry);
return false;
}
// Skip servers that disappeared from LBSM.
- if (timeline_entry->m_DiscoveryIteration != m_DiscoveryIteration)
+ if (m_Timeline.IsOutdatedAction(timeline_entry))
return false;
- CNetServer server(m_API->m_Service.GetServer(
- timeline_entry->m_ServerAddress));
-
+ CNetServer server(m_Timeline.GetServer(m_API, timeline_entry));
timeline_entry->ResetTimeout(READJOB_TIMEOUT);
try {
- if (x_ReadJob(server, &timeline_entry->GetTimeout(),
+ if (x_ReadJob(server, READJOB_TIMEOUT,
job, job_status, no_more_jobs)) {
// A job has been returned; add the server to
- // m_ImmediateActions because there can be more
+ // immediate actions because there can be more
// jobs in the queue.
- m_ImmediateActions.Push(timeline_entry);
+ m_Timeline.PushImmediateAction(timeline_entry);
return true;
} else {
+ // Cache the result for the server,
+ // so we don't need to ask the server again about matching jobs
+ // while waiting for its notifications
+ timeline_entry->more_jobs = !*no_more_jobs;
+
// No job has been returned by this server;
// query the server later.
- m_Timeline.Push(timeline_entry);
+ m_Timeline.PushScheduledAction(timeline_entry);
return false;
}
}
@@ -240,77 +238,73 @@ void SNetScheduleJobReaderImpl::x_ProcessReadJobNotifications()
while (m_API->m_NotificationThread->m_ReadNotifications.GetNextNotification(
&ns_node))
if (m_API->GetServerByNode(ns_node, &server))
- x_GetTimelineEntry(server)->MoveTo(&m_ImmediateActions);
+ m_Timeline.MoveToImmediateActions(server);
}
-CNetScheduleJobReader::EReadNextJobResult CNetScheduleJobReader::ReadNextJob(
+CNetScheduleJobReader::EReadNextJobResult SNetScheduleJobReaderImpl::ReadNextJob(
CNetScheduleJob* job,
CNetScheduleAPI::EJobStatus* job_status,
- CTimeout* timeout)
+ const CTimeout* timeout)
{
- m_Impl->x_StartNotificationThread();
-
- char deadline_object[sizeof(CDeadline)];
-
- CDeadline* deadline = timeout == NULL ? NULL :
- new (deadline_object) CDeadline(*timeout);
+ x_StartNotificationThread();
+ CDeadline deadline(timeout ? *timeout : CTimeout());
bool no_more_jobs;
+ bool matching_job_exists = false;
for (;;) {
- bool matching_job_exists = false;
-
- while (!m_Impl->m_ImmediateActions.IsEmpty()) {
- if (m_Impl->x_PerformTimelineAction(m_Impl->m_ImmediateActions,
+ while (m_Timeline.HasImmediateActions()) {
+ if (x_PerformTimelineAction(m_Timeline.PullImmediateAction(),
*job, job_status, &no_more_jobs))
- return eRNJ_JobReady;
+ return CNetScheduleJobReader::eRNJ_JobReady;
if (!no_more_jobs)
matching_job_exists = true;
- while (!m_Impl->m_Timeline.IsEmpty() &&
- m_Impl->m_Timeline.GetHead()->TimeHasCome())
- m_Impl->m_Timeline.MoveHeadTo(&m_Impl->m_ImmediateActions);
+ m_Timeline.CheckScheduledActions();
// Check if there's a notification in the UDP socket.
- m_Impl->x_ProcessReadJobNotifications();
+ x_ProcessReadJobNotifications();
}
- // All servers from m_ImmediateActions returned 'no_more_jobs'.
- // However, this method can be called again to wait for possible
- // notifications and to query the servers again periodically.
- if (!matching_job_exists)
- return eRNJ_NoMoreJobs;
+ // All servers returned 'no_more_jobs'.
+ if (!matching_job_exists && !m_Timeline.MoreJobs())
+ return CNetScheduleJobReader::eRNJ_NoMoreJobs;
// FIXME Check for interrupt
// if (CGridGlobals::GetInstance().IsShuttingDown())
// return eRNJ_Interrupt;
- if (deadline == NULL || deadline->GetRemainingTime().IsZero())
- return eRNJ_Timeout;
+ if (timeout == NULL || deadline.GetRemainingTime().IsZero())
+ return CNetScheduleJobReader::eRNJ_NotReady;
// There's still time. Wait for notifications and query the servers.
- if (!m_Impl->m_Timeline.IsEmpty()) {
- const CDeadline& next_event_time =
- m_Impl->m_Timeline.GetHead()->GetTimeout();
-
- if (*deadline < next_event_time) {
- if (!m_Impl->m_API->m_NotificationThread->
- m_ReadNotifications.Wait(*deadline))
- return eRNJ_Timeout;
- m_Impl->x_ProcessReadJobNotifications();
- } else if (m_Impl->m_API->m_NotificationThread->
+ if (m_Timeline.HasScheduledActions()) {
+ const CDeadline next_event_time = m_Timeline.GetNextTimeout();
+ if (deadline < next_event_time) {
+ if (!m_API->m_NotificationThread->
+ m_ReadNotifications.Wait(deadline))
+ return CNetScheduleJobReader::eRNJ_NotReady;
+ x_ProcessReadJobNotifications();
+ } else if (m_API->m_NotificationThread->
m_ReadNotifications.Wait(next_event_time))
- m_Impl->x_ProcessReadJobNotifications();
- else if (m_Impl->x_PerformTimelineAction(m_Impl->m_Timeline,
+ x_ProcessReadJobNotifications();
+ else if (x_PerformTimelineAction(m_Timeline.PullScheduledAction(),
*job, job_status, &no_more_jobs))
- return eRNJ_JobReady;
- else if (no_more_jobs)
- return eRNJ_NoMoreJobs;
+ return CNetScheduleJobReader::eRNJ_JobReady;
}
}
}
+CNetScheduleJobReader::EReadNextJobResult CNetScheduleJobReader::ReadNextJob(
+ CNetScheduleJob* job,
+ CNetScheduleAPI::EJobStatus* job_status,
+ const CTimeout* timeout)
+{
+ _ASSERT(m_Impl);
+ return m_Impl->ReadNextJob(job, job_status, timeout);
+}
+
void CNetScheduleJobReader::InterruptReading()
{
m_Impl->x_StartNotificationThread();
diff --git a/c++/src/connect/services/netschedule_api_submitter.cpp b/c++/src/connect/services/netschedule_api_submitter.cpp
index a9590c9..f589be2 100644
--- a/c++/src/connect/services/netschedule_api_submitter.cpp
+++ b/c++/src/connect/services/netschedule_api_submitter.cpp
@@ -1,4 +1,4 @@
-/* $Id: netschedule_api_submitter.cpp 451456 2014-11-06 19:30:58Z ivanov $
+/* $Id: netschedule_api_submitter.cpp 468672 2015-05-27 15:06:02Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -512,11 +512,11 @@ CNetScheduleNotificationHandler::WaitForJobEvent(
const string& job_key,
CDeadline& deadline,
CNetScheduleAPI ns_api,
- int status_mask,
+ TJobStatusMask status_mask,
int last_event_index,
int *new_event_index)
{
- *new_event_index = -1;
+ int index = -1;
CNetScheduleAPI::EJobStatus job_status;
@@ -531,29 +531,33 @@ CNetScheduleNotificationHandler::WaitForJobEvent(
last_wait = true;
}
- if (RequestJobWatching(ns_api, job_key,
- timeout, &job_status, new_event_index) &&
+ if (RequestJobWatching(ns_api, job_key, timeout, &job_status, &index) &&
((status_mask & (1 << job_status)) != 0 ||
- *new_event_index > last_event_index))
+ index > last_event_index))
break;
if (deadline.GetRemainingTime().IsZero())
break;
if (WaitForNotification(timeout) &&
- CheckJobStatusNotification(job_key, &job_status,
- new_event_index) &&
+ CheckJobStatusNotification(job_key, &job_status, &index) &&
((status_mask & (1 << job_status)) != 0 ||
- *new_event_index > last_event_index))
+ index > last_event_index))
break;
} while (!last_wait);
+ if (new_event_index) {
+ *new_event_index = index;
+ }
+
return job_status;
}
void CNetScheduleSubmitter::CancelJob(const string& job_key)
{
- m_Impl->m_API->x_ExecOnce("CANCEL", job_key);
+ CNetScheduleJob job;
+ job.job_id = job_key;
+ m_Impl->m_API->x_ExecOnce("CANCEL", job);
}
void CNetScheduleSubmitter::CancelJobGroup(const string& job_group,
@@ -573,8 +577,9 @@ CNetScheduleAPI::EJobStatus CNetScheduleSubmitter::GetJobStatus(
const string& job_key, time_t* job_exptime,
ENetScheduleQueuePauseMode* pause_mode)
{
- return m_Impl->m_API->GetJobStatus("SST2",
- job_key, job_exptime, pause_mode);
+ CNetScheduleJob job;
+ job.job_id = job_key;
+ return m_Impl->m_API->GetJobStatus("SST2", job, job_exptime, pause_mode);
}
CNetScheduleAPI::EJobStatus CNetScheduleSubmitter::GetJobDetails(
diff --git a/c++/src/connect/services/netservice_api.cpp b/c++/src/connect/services/netservice_api.cpp
index 6220319..67fea06 100644
--- a/c++/src/connect/services/netservice_api.cpp
+++ b/c++/src/connect/services/netservice_api.cpp
@@ -1,4 +1,4 @@
-/* $Id: netservice_api.cpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netservice_api.cpp 477857 2015-09-02 13:15:07Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,8 +45,10 @@
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbi_config.hpp>
+#include <corelib/ncbi_message.hpp>
#include <util/random_gen.hpp>
+#include <util/checksum.hpp>
#define NCBI_USE_ERRCODE_X ConnServ_Connection
@@ -180,6 +182,17 @@ bool SNetServiceIterator_RandomPivot::Next()
return true;
}
+bool SNetServiceIterator_RandomPivot::Prev()
+{
+ if (m_RandomIterators.empty() ||
+ m_RandomIterator == m_RandomIterators.begin())
+ return false;
+
+ m_Position = *--m_RandomIterator;
+
+ return true;
+}
+
bool SNetServiceIterator_Circular::Next()
{
if (++m_Position == m_ServerGroup->m_Servers.end())
@@ -197,14 +210,69 @@ bool SNetServiceIterator_Circular::Prev()
return true;
}
-bool SNetServiceIterator_RandomPivot::Prev()
+SNetServiceIterator_Weighted::SNetServiceIterator_Weighted(
+ SDiscoveredServers* server_group_impl, Uint4 key_crc32) :
+ SNetServiceIteratorImpl(server_group_impl),
+ m_KeyCRC32(key_crc32)
{
- if (m_RandomIterators.empty() ||
- m_RandomIterator == m_RandomIterators.begin())
+ TNetServerList::const_iterator server_list_iter(m_Position);
+
+ if ((m_SingleServer =
+ (++server_list_iter == server_group_impl->m_SuppressedBegin)))
+ // Nothing to do if there's only one server.
+ return;
+
+ // Find the server with the highest rank.
+ SServerRank highest_rank(x_GetServerRank(m_Position));
+
+ do {
+ SServerRank server_rank(x_GetServerRank(server_list_iter));
+ if (highest_rank < server_rank)
+ highest_rank = server_rank;
+ // To avoid unnecessary memory allocations, do not save
+ // the calculated server ranks in hope that Next()
+ // will be called very rarely for this type of iterators.
+ } while (++server_list_iter != server_group_impl->m_SuppressedBegin);
+
+ m_Position = highest_rank.m_ServerListIter;
+}
+
+bool SNetServiceIterator_Weighted::Next()
+{
+ if (m_SingleServer)
return false;
- m_Position = *--m_RandomIterator;
+ if (m_ServerRanks.empty()) {
+ TNetServerList::const_iterator server_list_iter(
+ m_ServerGroup->m_Servers.begin());
+ do
+ m_ServerRanks.push_back(x_GetServerRank(server_list_iter));
+ while (++server_list_iter != m_ServerGroup->m_SuppressedBegin);
+
+ // Sort the ranks in *reverse* order.
+ sort(m_ServerRanks.rbegin(), m_ServerRanks.rend());
+
+ // Skip the server with the highest rank, which was the first
+ // server returned by this iterator object.
+ m_CurrentServerRank = m_ServerRanks.begin() + 1;
+ } else if (++m_CurrentServerRank == m_ServerRanks.end())
+ return false;
+
+ m_Position = m_CurrentServerRank->m_ServerListIter;
+ return true;
+}
+
+bool SNetServiceIterator_Weighted::Prev()
+{
+ if (m_SingleServer)
+ return false;
+ _ASSERT(!m_ServerRanks.empty());
+
+ if (m_CurrentServerRank == m_ServerRanks.begin())
+ return false;
+
+ m_Position = (--m_CurrentServerRank)->m_ServerListIter;
return true;
}
@@ -214,7 +282,7 @@ SNetServerPoolImpl::SNetServerPoolImpl(const string& api_name,
m_APIName(api_name),
m_ClientName(client_name),
m_Listener(listener),
- m_EnforcedServerHost(0),
+ m_EnforcedServer(0, 0),
m_LBSMAffinityName(kEmptyStr),
m_LBSMAffinityValue(NULL),
m_UseOldStyleAuth(false)
@@ -247,9 +315,8 @@ void SNetServiceImpl::Construct()
if (!NStr::SplitInTwo(m_ServiceName, ":", host, port))
m_ServiceType = CNetService::eLoadBalancedService;
else
- Construct(m_ServerPool->FindOrCreateServerImpl(
- g_NetService_gethostbyname(host),
- (unsigned short) NStr::StringToInt(port)));
+ Construct(m_ServerPool->FindOrCreateServerImpl(SServerAddress(host,
+ (unsigned short) NStr::StringToInt(port))));
}
}
@@ -286,10 +353,36 @@ void SNetServiceImpl::AllowXSiteConnections()
}
#endif
+CConfig* FindSection(const char* const* sections, const CConfig::TParamTree* tree,
+ string* section)
+{
+ _ASSERT(section);
+
+ if (section->empty()) {
+ *section = *sections++;
+ }
+
+ for (;;) {
+ if (const CConfig::TParamTree* sub_tree = tree->FindSubNode(*section)) {
+ return new CConfig(sub_tree);
+ }
+
+ if (!*sections) {
+ break;
+ }
+
+ *section = *sections++;
+ }
+
+ return NULL;
+}
+
void SNetServiceImpl::Init(CObject* api_impl, const string& service_name,
CConfig* config, const string& config_section,
const char* const* default_config_sections)
{
+ _ASSERT(m_Listener);
+
// Initialize the connect library and LBSM structures
// used in DiscoverServersIfNeeded().
{
@@ -301,59 +394,38 @@ void SNetServiceImpl::Init(CObject* api_impl, const string& service_name,
conn_initer.NoOp();
}
- const char* const* default_section = default_config_sections;
- string section = !config_section.empty() ?
- config_section : *default_section++;
-
+ string section = config_section;
+
auto_ptr<CConfig> app_reg_config;
auto_ptr<CConfig::TParamTree> param_tree;
if (config == NULL) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
CNcbiRegistry* reg;
if (app != NULL && (reg = &app->GetConfig()) != NULL) {
param_tree.reset(CConfig::ConvertRegToTree(*reg));
- for (;;) {
- const CConfig::TParamTree* section_param_tree =
- param_tree->FindSubNode(section);
-
- if (section_param_tree != NULL)
- app_reg_config.reset(new CConfig(section_param_tree));
- else if (*default_section != NULL) {
- section = *default_section++;
- continue;
- }
- break;
- }
-
+ app_reg_config.reset(FindSection(default_config_sections,
+ param_tree.get(), §ion));
config = app_reg_config.get();
}
} else {
- const CConfig::TParamTree* supplied_param_tree = config->GetTree();
-
- for (;;) {
- const CConfig::TParamTree* section_param_tree =
- supplied_param_tree->FindSubNode(section);
-
- if (section_param_tree != NULL) {
- app_reg_config.reset(new CConfig(section_param_tree));
- config = app_reg_config.get();
- } else if (*default_section != NULL) {
- section = *default_section++;
- continue;
- }
- break;
+ app_reg_config.reset(FindSection(default_config_sections,
+ config->GetTree(), §ion));
+
+ if (app_reg_config.get()) {
+ config = app_reg_config.get();
}
}
m_ServiceName = service_name;
NStr::TruncateSpacesInPlace(m_ServiceName);
- if (m_ServiceName.empty() && config == NULL &&
- (config = m_Listener->LoadConfigFromAltSource(api_impl,
- §ion)) != NULL)
- app_reg_config.reset(config);
+ if (CConfig *alt = m_Listener->PreInit(api_impl, config, §ion)) {
+ app_reg_config.reset(alt);
+ config = alt;
+ }
if (config != NULL) {
if (m_ServiceName.empty()) {
@@ -385,27 +457,37 @@ void SNetServiceImpl::Init(CObject* api_impl, const string& service_name,
m_UseSmartRetries = config->GetBool(section,
"smart_service_retries", CConfig::eErr_NoThrow, true);
+ m_ConnectionMaxRetries = config->GetInt(section,
+ "connection_max_retries", CConfig::eErr_NoThrow, -1);
+ double retry_delay = config->GetDouble(section,
+ "retry_delay", CConfig::eErr_NoThrow, -1);
+ m_ConnectionRetryDelay = retry_delay < 0? -1:
+ (int)SECONDS_DOUBLE_TO_MS_UL(retry_delay);
+ }
+ if ( m_ConnectionMaxRetries < 0 ) {
+ m_ConnectionMaxRetries = (int)TServConn_ConnMaxRetries::GetDefault();
+ }
+ if ( m_ConnectionRetryDelay < 0 ) {
+ m_ConnectionRetryDelay = (int)s_GetRetryDelay();
}
m_ServerPool->Init(config, section, m_Listener.GetPointerOrNull());
- m_Listener->OnInit(api_impl, config, section);
-
Construct();
+
+ m_Listener->OnInit(api_impl, config, section);
}
void SNetServerPoolImpl::Init(CConfig* config, const string& section,
INetServerConnectionListener* listener)
{
- if (config != NULL) {
- if (m_ClientName.empty()) {
- m_ClientName = config->GetString(section, "client_name",
- CConfig::eErr_NoThrow, kEmptyStr);
- if (m_ClientName.empty())
- m_ClientName = config->GetString(section, "client",
- CConfig::eErr_NoThrow, kEmptyStr);
- }
+ _ASSERT(listener);
+
+ if (m_ClientName.empty()) {
+ m_ClientName = listener->GetClientName();
+ }
+ if (config != NULL) {
if (m_LBSMAffinityName.empty())
m_LBSMAffinityName = config->GetString(section,
"use_lbsm_affinity", CConfig::eErr_NoThrow, kEmptyStr);
@@ -518,6 +600,7 @@ void SNetServerPoolImpl::Init(CConfig* config, const string& section,
if (m_ClientName.empty() || m_ClientName == "noname" ||
NStr::FindNoCase(m_ClientName, "unknown") != NPOS) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if (app == NULL) {
NCBI_THROW_FMT(CArgException, eNoValue,
@@ -565,6 +648,7 @@ string SNetServiceImpl::MakeAuthString()
auth += '\"';
}
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if (app != NULL) {
auth += " client_path=\"";
@@ -603,8 +687,7 @@ bool CNetService::IsLoadBalanced() const
void CNetServerPool::StickToServer(const string& host, unsigned short port)
{
- m_Impl->m_EnforcedServerHost = g_NetService_gethostbyname(host);
- m_Impl->m_EnforcedServerPort = port;
+ m_Impl->m_EnforcedServer = SServerAddress(host, port);
}
void CNetService::PrintCmdOutput(const string& cmd,
@@ -655,10 +738,8 @@ void CNetService::PrintCmdOutput(const string& cmd,
}
SNetServerInPool* SNetServerPoolImpl::FindOrCreateServerImpl(
- unsigned host, unsigned short port)
+ const SServerAddress& server_address)
{
- SServerAddress server_address(host, port);
-
pair<TNetServerByAddress::iterator, bool> loc(m_Servers.insert(
TNetServerByAddress::value_type(server_address,
(SNetServerInPool*) NULL)));
@@ -666,7 +747,7 @@ SNetServerInPool* SNetServerPoolImpl::FindOrCreateServerImpl(
if (!loc.second)
return loc.first->second;
- SNetServerInPool* server = new SNetServerInPool(host, port,
+ SNetServerInPool* server = new SNetServerInPool(server_address.host, server_address.port,
m_Listener->AllocServerProperties().GetPointerOrNull());
loc.first->second = server;
@@ -685,17 +766,15 @@ CRef<SNetServerInPool> SNetServerPoolImpl::ReturnServer(
return CRef<SNetServerInPool>(server_impl);
}
-CNetServer CNetService::GetServer(unsigned host, unsigned short port)
+CNetServer CNetService::GetServer(const SServerAddress& server_address)
{
m_Impl->m_ServerPool->m_RebalanceStrategy->OnResourceRequested();
CFastMutexGuard server_mutex_lock(m_Impl->m_ServerPool->m_ServerMutex);
- SNetServerInPool* server = m_Impl->m_ServerPool->m_EnforcedServerHost == 0 ?
- m_Impl->m_ServerPool->FindOrCreateServerImpl(host, port) :
- m_Impl->m_ServerPool->FindOrCreateServerImpl(
- m_Impl->m_ServerPool->m_EnforcedServerHost,
- m_Impl->m_ServerPool->m_EnforcedServerPort);
+ SNetServerInPool* server = m_Impl->m_ServerPool->FindOrCreateServerImpl(
+ m_Impl->m_ServerPool->m_EnforcedServer.host == 0 ?
+ server_address : m_Impl->m_ServerPool->m_EnforcedServer);
server->m_ServerPool = m_Impl->m_ServerPool;
@@ -745,7 +824,8 @@ CNetServer::SExecResult CNetService::FindServerAndExec(const string& cmd,
m_Impl->IterateUntilExecOK(cmd, multiline_output,
exec_result, &random_traversal,
- SNetServiceImpl::eIgnoreServerErrors);
+ SNetServiceImpl::eIgnoreServerErrors,
+ m_Impl->m_Listener);
return exec_result;
}
@@ -793,12 +873,16 @@ void SNetServiceImpl::DiscoverServersIfNeeded()
// FIXME Retry logic can be removed as soon as LBSMD with
// packet compression is installed universally.
int try_count = TServConn_MaxFineLBNameRetries::GetDefault();
+ //LOG_POST("lbname_retries: "<<try_count);
for (;;) {
SConnNetInfo* net_info =
ConnNetInfo_Create(m_ServiceName.c_str());
srv_it = SERV_OpenP(m_ServiceName.c_str(),
- fSERV_Standalone | fSERV_IncludeSuppressed,
+ fSERV_Standalone |
+ fSERV_IncludeStandby |
+ fSERV_IncludeReserved |
+ fSERV_IncludeSuppressed,
SERV_LOCALHOST, 0, 0.0, net_info, NULL, 0, 0 /*false*/,
m_ServerPool->m_LBSMAffinityName.c_str(),
m_ServerPool->m_LBSMAffinityValue);
@@ -839,7 +923,7 @@ void SNetServiceImpl::DiscoverServersIfNeeded()
if (sinfo->time > 0 && sinfo->time != NCBI_TIME_INFINITE &&
sinfo->rate != 0.0) {
SNetServerInPool* server = m_ServerPool->
- FindOrCreateServerImpl(sinfo->host, sinfo->port);
+ FindOrCreateServerImpl(SServerAddress(sinfo->host, sinfo->port));
{{
CFastMutexGuard guard(server->m_ThrottleLock);
server->m_DiscoveredAfterThrottling = true;
@@ -903,46 +987,78 @@ void SNetServiceImpl::IterateUntilExecOK(const string& cmd,
bool multiline_output,
CNetServer::SExecResult& exec_result,
IServiceTraversal* service_traversal,
- SNetServiceImpl::EServerErrorHandling error_handling)
+ SNetServiceImpl::EServerErrorHandling error_handling,
+ INetServerConnectionListener* conn_listener)
{
- int retry_count = (int) TServConn_ConnMaxRetries::GetDefault();
+ if (conn_listener == NULL)
+ conn_listener = m_Listener;
+
+ int retry_count = m_ConnectionMaxRetries;
+ //LOG_POST("retry_count = "<<retry_count);
- const unsigned long retry_delay = s_GetRetryDelay();
+ const unsigned long retry_delay = m_ConnectionRetryDelay;
+ //LOG_POST("retry_delay = "<<retry_delay);
- CDeadline max_connection_time
- (m_ServerPool->m_MaxConnectionTime / 1000,
+ CDeadline max_connection_time(m_ServerPool->m_MaxConnectionTime / 1000,
(m_ServerPool->m_MaxConnectionTime % 1000) * 1000 * 1000);
+ enum EIterationMode {
+ eInitialIteration,
+ eRetry
+ } iteration_mode = eInitialIteration;
CNetServer server = service_traversal->BeginIteration();
+ vector<CNetServer> servers_to_retry;
+ unsigned current_server = 0;
+
+ bool skip_server;
+
unsigned number_of_servers = 0;
unsigned ns_with_submits_disabled = 0;
unsigned servers_throttled = 0;
+ bool blob_not_found = false;
STimeout* timeout = retry_count <= 0 && !m_UseSmartRetries ?
NULL : &m_ServerPool->m_FirstServerTimeout;
+ CMessageListener_Basic err_listener;
+
for (;;) {
+ skip_server = false;
+
try {
- server->ConnectAndExec(cmd, multiline_output, exec_result, timeout);
+ server->ConnectAndExec(cmd, multiline_output, exec_result,
+ timeout, NULL, conn_listener);
return;
}
+ catch (CNetCacheBlobTooOldException& /*ex rethrown*/) {
+ throw;
+ }
catch (CNetCacheException& ex) {
- if (error_handling == eRethrowServerErrors ||
- (retry_count <= 0 && !m_UseSmartRetries))
+ if (retry_count <= 0 && !m_UseSmartRetries)
throw;
- LOG_POST(Warning << server.GetServerAddress() << ": " << ex);
+ if (ex.GetErrCode() == CNetCacheException::eBlobNotFound) {
+ blob_not_found = true;
+ skip_server = true;
+ } else if (error_handling == eRethrowServerErrors)
+ throw;
+ else
+ conn_listener->OnWarning(ex.GetMsg(), server);
+
+ err_listener.PostMessage(CMessage_Basic(ex.GetMsg(), eDiag_Warning));
}
catch (CNetScheduleException& ex) {
if (retry_count <= 0 && !m_UseSmartRetries)
throw;
- if (ex.GetErrCode() == CNetScheduleException::eSubmitsDisabled)
+ if (ex.GetErrCode() == CNetScheduleException::eSubmitsDisabled) {
++ns_with_submits_disabled;
- else if (error_handling == eRethrowServerErrors)
+ skip_server = true;
+ } else if (error_handling == eRethrowServerErrors)
throw;
- else {
- LOG_POST(Warning << server.GetServerAddress() << ": " << ex);
- }
+ else
+ conn_listener->OnWarning(ex.GetMsg(), server);
+
+ err_listener.PostMessage(CMessage_Basic(ex.GetMsg(), eDiag_Warning));
}
catch (CNetSrvConnException& ex) {
if (retry_count <= 0 && !m_UseSmartRetries)
@@ -951,7 +1067,7 @@ void SNetServiceImpl::IterateUntilExecOK(const string& cmd,
case CNetSrvConnException::eReadTimeout:
break;
case CNetSrvConnException::eConnectionFailure:
- LOG_POST(Warning << ex);
+ conn_listener->OnWarning(ex.GetMsg(), server);
break;
case CNetSrvConnException::eServerThrottle:
@@ -961,10 +1077,28 @@ void SNetServiceImpl::IterateUntilExecOK(const string& cmd,
default:
throw;
}
+
+ err_listener.PostMessage(CMessage_Basic(ex.GetMsg(), eDiag_Warning));
}
++number_of_servers;
- server = service_traversal->NextServer();
+
+ if (iteration_mode == eInitialIteration) {
+ if (!skip_server)
+ servers_to_retry.push_back(server);
+ server = service_traversal->NextServer();
+ } else {
+ if (!skip_server)
+ ++current_server;
+ else
+ servers_to_retry.erase(servers_to_retry.begin() +
+ current_server);
+
+ if (current_server < servers_to_retry.size())
+ server = servers_to_retry[current_server];
+ else
+ server = NULL;
+ }
if (m_ServerPool->m_MaxConnectionTime > 0 &&
max_connection_time.GetRemainingTime().GetAsMilliSeconds() <=
@@ -987,22 +1121,32 @@ void SNetServiceImpl::IterateUntilExecOK(const string& cmd,
"Cannot execute [" << cmd <<
"]: all servers are throttled.");
}
- if (retry_count <= 0) {
+ if (retry_count <= 0 || servers_to_retry.empty()) {
+ if (blob_not_found) {
+ NCBI_THROW_FMT(CNetCacheException, eBlobNotFound,
+ "Cannot execute [" << cmd << "]: blob not found.");
+ }
NCBI_THROW_FMT(CNetSrvConnException, eSrvListEmpty,
- "Unable to send [" << cmd <<
- "] to any of the discovered servers.");
+ "Unable to execute [" << cmd <<
+ "] on any of the discovered servers.");
+ }
+
+ for (size_t i = 0; i < err_listener.Count(); ++i) {
+ LOG_POST(Warning << err_listener.GetMessage(i).GetText());
}
+ err_listener.Clear();
LOG_POST(Warning << "Unable to send [" << cmd << "] to any "
"of the discovered servers; will retry after delay.");
SleepMilliSec(retry_delay);
- server = service_traversal->BeginIteration();
-
number_of_servers = 0;
ns_with_submits_disabled = 0;
servers_throttled = 0;
+
+ iteration_mode = eRetry;
+ server = servers_to_retry[current_server = 0];
}
--retry_count;
@@ -1095,6 +1239,24 @@ CNetServiceIterator CNetService::Iterate(CNetServer::TInstance priority_server)
m_Impl->m_ServiceName + " service.");
}
+CNetServiceIterator CNetService::IterateByWeight(const string& key)
+{
+ CRef<SDiscoveredServers> servers;
+ m_Impl->GetDiscoveredServers(servers);
+
+ if (servers->m_Servers.begin() == servers->m_SuppressedBegin) {
+ NCBI_THROW(CNetSrvConnException, eSrvListEmpty,
+ "Couldn't find any available servers for the " +
+ m_Impl->m_ServiceName + " service.");
+ }
+
+ CChecksum key_crc32(CChecksum::eCRC32);
+
+ key_crc32.AddChars(key.data(), key.length());
+
+ return new SNetServiceIterator_Weighted(servers, key_crc32.GetChecksum());
+}
+
CNetServiceIterator CNetService::ExcludeServer(CNetServer::TInstance server)
{
CRef<SDiscoveredServers> servers;
@@ -1105,9 +1267,9 @@ CNetServiceIterator CNetService::ExcludeServer(CNetServer::TInstance server)
if (it->first == server->m_ServerInPool) {
// The server is found. Make an iterator and
// skip to the next server (the iterator may become NULL).
- CNetServiceIterator server_it(
+ CNetServiceIterator circular_iter(
new SNetServiceIterator_Circular(servers, it));
- return ++server_it;
+ return ++circular_iter;
}
}
@@ -1185,4 +1347,42 @@ CJsonNode g_ExecToJson(IExecToJson& exec_to_json, CNetService service,
return result;
}
+namespace {
+ class CDummyServerConnectionListener : public INetServerConnectionListener
+ {
+ public:
+ virtual CRef<INetServerProperties> AllocServerProperties()
+ {
+ return CRef<INetServerProperties>(new INetServerProperties);
+ }
+ virtual void OnInit(CObject* /*api_impl*/,
+ CConfig* /*config*/, const string& /*config_section*/)
+ {
+ }
+ virtual void OnConnected(CNetServerConnection& /*connection*/)
+ {
+ }
+ virtual void OnError(const string& /*err_msg*/, CNetServer& /*server*/)
+ {
+ }
+ virtual void OnWarning(const string& /*warn_msg*/,
+ CNetServer& /*server*/)
+ {
+ }
+ };
+}
+
+CNetService g_DiscoverService(const string& service_name,
+ const string& client_name)
+{
+ CNetService service(new SNetServiceImpl("Discovery", client_name,
+ new CDummyServerConnectionListener));
+
+ static const char* const config_section[] = {"discovery", NULL};
+
+ service->Init(NULL, service_name, NULL, kEmptyStr, config_section);
+
+ return service;
+}
+
END_NCBI_SCOPE
diff --git a/c++/src/connect/services/netservice_api_impl.hpp b/c++/src/connect/services/netservice_api_impl.hpp
index 3b6fe9f..6a28d2b 100644
--- a/c++/src/connect/services/netservice_api_impl.hpp
+++ b/c++/src/connect/services/netservice_api_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___NETSERVICE_API_IMPL__HPP
#define CONNECT_SERVICES___NETSERVICE_API_IMPL__HPP
-/* $Id: netservice_api_impl.hpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netservice_api_impl.hpp 475261 2015-08-05 19:52:42Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -89,8 +89,7 @@ struct NCBI_XCONNECT_EXPORT SNetServerPoolImpl : public CObject
void Init(CConfig* config, const string& section,
INetServerConnectionListener* listener);
- SNetServerInPool* FindOrCreateServerImpl(
- unsigned host, unsigned short port);
+ SNetServerInPool* FindOrCreateServerImpl(const SServerAddress& server_address);
CRef<SNetServerInPool> ReturnServer(SNetServerInPool* server_impl);
void ResetServerConnections();
@@ -101,8 +100,7 @@ struct NCBI_XCONNECT_EXPORT SNetServerPoolImpl : public CObject
string m_ClientName;
CRef<INetServerConnectionListener> m_Listener;
- unsigned m_EnforcedServerHost;
- unsigned short m_EnforcedServerPort;
+ SServerAddress m_EnforcedServer;
CRef<CSimpleRebalanceStrategy> m_RebalanceStrategy;
@@ -194,6 +192,47 @@ struct SNetServiceIterator_Circular : public SNetServiceIteratorImpl
TNetServerList::const_iterator m_Pivot;
};
+struct SNetServiceIterator_Weighted : public SNetServiceIteratorImpl
+{
+ SNetServiceIterator_Weighted(SDiscoveredServers* server_group_impl,
+ Uint4 key_crc32);
+
+ virtual bool Next();
+ virtual bool Prev();
+
+ Uint4 m_KeyCRC32;
+
+ struct SServerRank {
+ TNetServerList::const_iterator m_ServerListIter;
+ Uint4 m_ServerRank;
+ SServerRank(TNetServerList::const_iterator server_list_iter,
+ Uint4 server_rank) :
+ m_ServerListIter(server_list_iter),
+ m_ServerRank(server_rank)
+ {
+ }
+ bool operator <(const SServerRank& that) const
+ {
+ return m_ServerRank < that.m_ServerRank ||
+ (m_ServerRank == that.m_ServerRank &&
+ m_ServerListIter->first->m_Address <
+ that.m_ServerListIter->first->m_Address);
+ }
+ };
+
+ SServerRank x_GetServerRank(TNetServerList::const_iterator server) const
+ {
+ Uint4 rank = (1103515245 *
+ (server->first->m_RankBase ^ m_KeyCRC32) + 12345) & 0x7FFFFFFF;
+ return SServerRank(server, rank);
+ }
+
+ bool m_SingleServer;
+
+ vector<SServerRank> m_ServerRanks;
+ vector<SServerRank>::const_iterator m_CurrentServerRank;
+};
+
class IServiceTraversal
{
public:
@@ -214,7 +253,9 @@ struct NCBI_XCONNECT_EXPORT SNetServiceImpl : public CObject
m_ColoNetwork(0),
m_AllowXSiteConnections(false),
#endif
- m_UseSmartRetries(true)
+ m_UseSmartRetries(true),
+ m_ConnectionMaxRetries(-1),
+ m_ConnectionRetryDelay(-1)
{
ZeroInit();
}
@@ -228,7 +269,9 @@ struct NCBI_XCONNECT_EXPORT SNetServiceImpl : public CObject
m_ColoNetwork(prototype->m_ColoNetwork),
m_AllowXSiteConnections(prototype->m_AllowXSiteConnections),
#endif
- m_UseSmartRetries(prototype->m_UseSmartRetries)
+ m_UseSmartRetries(prototype->m_UseSmartRetries),
+ m_ConnectionMaxRetries(prototype->m_ConnectionMaxRetries),
+ m_ConnectionRetryDelay(prototype->m_ConnectionRetryDelay)
{
ZeroInit();
Construct(server);
@@ -241,7 +284,9 @@ struct NCBI_XCONNECT_EXPORT SNetServiceImpl : public CObject
m_ColoNetwork(prototype->m_ColoNetwork),
m_AllowXSiteConnections(prototype->m_AllowXSiteConnections),
#endif
- m_UseSmartRetries(prototype->m_UseSmartRetries)
+ m_UseSmartRetries(prototype->m_UseSmartRetries),
+ m_ConnectionMaxRetries(prototype->m_ConnectionMaxRetries),
+ m_ConnectionRetryDelay(prototype->m_ConnectionRetryDelay)
{
ZeroInit();
Construct();
@@ -272,7 +317,8 @@ struct NCBI_XCONNECT_EXPORT SNetServiceImpl : public CObject
bool multiline_output,
CNetServer::SExecResult& exec_result,
IServiceTraversal* service_traversal,
- EServerErrorHandling error_handling);
+ EServerErrorHandling error_handling,
+ INetServerConnectionListener* conn_listener);
SDiscoveredServers* AllocServerGroup(unsigned discovery_iteration);
@@ -306,7 +352,10 @@ struct NCBI_XCONNECT_EXPORT SNetServiceImpl : public CObject
bool m_AllowXSiteConnections;
#endif
+ // connection parameters from config
bool m_UseSmartRetries;
+ int m_ConnectionMaxRetries;
+ int m_ConnectionRetryDelay;
};
struct SNetServiceMap {
diff --git a/c++/src/connect/services/netservice_params.cpp b/c++/src/connect/services/netservice_params.cpp
index e460bcb..9b9bd24 100644
--- a/c++/src/connect/services/netservice_params.cpp
+++ b/c++/src/connect/services/netservice_params.cpp
@@ -1,4 +1,4 @@
-/* $Id: netservice_params.cpp 423530 2014-01-06 17:39:49Z kazimird $
+/* $Id: netservice_params.cpp 447439 2014-09-25 17:52:46Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,7 +45,7 @@ NCBI_PARAM_DEF(string, netservice_api, retry_delay,
NCBI_PARAM_DEF(string, netservice_api, communication_timeout,
NCBI_AS_STRING(COMMUNICATION_TIMEOUT_DEFAULT));
NCBI_PARAM_DEF(int, netservice_api, max_find_lbname_retries, 3);
-NCBI_PARAM_DEF(string, netcache_api, fallback_server, kEmptyStr);
+NCBI_PARAM_DEF(string, netcache_api, fallback_server, "");
NCBI_PARAM_DEF(int, netservice_api, max_connection_pool_size, 0); // unlimited
NCBI_PARAM_DEF(unsigned, server, max_wait_for_servers, 24 * 60 * 60);
NCBI_PARAM_DEF(bool, server, stop_on_job_errors, true);
diff --git a/c++/src/connect/services/netstorage_direct_nc.cpp b/c++/src/connect/services/netstorage_direct_nc.cpp
index acdf8ff..4de9d9f 100644
--- a/c++/src/connect/services/netstorage_direct_nc.cpp
+++ b/c++/src/connect/services/netstorage_direct_nc.cpp
@@ -1,4 +1,4 @@
-/* $Id: netstorage_direct_nc.cpp 458002 2015-01-29 19:45:57Z kazimird $
+/* $Id: netstorage_direct_nc.cpp 463064 2015-03-24 15:50:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -137,15 +137,10 @@ ERW_Result SNetStorage_NetCacheBlob::PendingCount(size_t* count)
void SNetStorage_NetCacheBlob::Read(string* data)
{
- m_NetCacheAPI.ReadData(m_BlobKey, *data);
-}
-
-IReader& SNetStorage_NetCacheBlob::GetReader()
-{
- if (m_State != eReading)
- x_InitReader();
-
- return *m_NetCacheReader;
+ try {
+ m_NetCacheAPI.ReadData(m_BlobKey, *data);
+ }
+ CONVERT_NETSERVICEEXCEPTION("reading");
}
bool SNetStorage_NetCacheBlob::Eof()
@@ -193,19 +188,7 @@ ERW_Result SNetStorage_NetCacheBlob::Write(const void* buf_pos, size_t buf_size,
ERW_Result SNetStorage_NetCacheBlob::Flush()
{
- if (m_State != eWriting) {
- NCBI_THROW_FMT(CNetStorageException, eInvalidArg,
- "The blob is not being written; cannot flush.");
- }
- return m_NetCacheWriter->Flush();
-}
-
-IEmbeddedStreamWriter& SNetStorage_NetCacheBlob::GetWriter()
-{
- if (m_State != eWriting)
- x_InitWriter();
-
- return *m_NetCacheWriter;
+ return m_State != eWriting ? eRW_Success : m_NetCacheWriter->Flush();
}
Uint8 SNetStorage_NetCacheBlob::GetSize()
@@ -216,7 +199,13 @@ Uint8 SNetStorage_NetCacheBlob::GetSize()
return m_NetCacheReader->GetBlobSize();
}
-string SNetStorage_NetCacheBlob::GetAttribute(const string& /*attr_name*/)
+list<string> SNetStorage_NetCacheBlob::GetAttributeList() const
+{
+ NCBI_THROW_FMT(CNetStorageException, eInvalidArg, m_BlobKey <<
+ ": attribute retrieval is not implemented for NetCache blobs");
+}
+
+string SNetStorage_NetCacheBlob::GetAttribute(const string& /*attr_name*/) const
{
NCBI_THROW_FMT(CNetStorageException, eInvalidArg, m_BlobKey <<
": attribute retrieval is not implemented for NetCache blobs");
@@ -249,15 +238,18 @@ CNetStorageObjectInfo SNetStorage_NetCacheBlob::GetInfo()
(Uint8) size_node.AsInteger() :
m_NetCacheAPI.GetBlobSize(m_BlobKey);
- return g_CreateNetStorageObjectInfo(m_BlobKey,
- eNFL_NetCache, NULL, blob_size, blob_info);
+ if (m_NetCacheAPI.HasBlob(m_BlobKey)) {
+ return g_CreateNetStorageObjectInfo(m_BlobKey,
+ eNFL_NetCache, NULL, blob_size, blob_info);
+ }
}
catch (CNetCacheException& e) {
if (e.GetErrCode() != CNetCacheException::eBlobNotFound)
throw;
- return g_CreateNetStorageObjectInfo(m_BlobKey,
- eNFL_NotFound, NULL, 0, NULL);
}
+
+ return g_CreateNetStorageObjectInfo(m_BlobKey,
+ eNFL_NotFound, NULL, 0, NULL);
}
void SNetStorage_NetCacheBlob::Close()
@@ -298,8 +290,16 @@ void SNetStorage_NetCacheBlob::Abort()
}
}
-CNetStorageObject g_CreateNetStorage_NetCacheBlob(
- CNetCacheAPI::TInstance nc_api, const string& blob_key)
+CNetStorageObject CDNCNetStorage::Create(CNetCacheAPI::TInstance nc_api)
+{
+ auto_ptr<SNetStorage_NetCacheBlob> result(
+ new SNetStorage_NetCacheBlob(nc_api, kEmptyStr));
+ result->x_InitWriter();
+ return result.release();
+}
+
+CNetStorageObject CDNCNetStorage::Open(CNetCacheAPI::TInstance nc_api,
+ const string& blob_key)
{
return new SNetStorage_NetCacheBlob(nc_api, blob_key);
}
diff --git a/c++/src/connect/services/netstorage_direct_nc.hpp b/c++/src/connect/services/netstorage_direct_nc.hpp
index b344f74..e4c8244 100644
--- a/c++/src/connect/services/netstorage_direct_nc.hpp
+++ b/c++/src/connect/services/netstorage_direct_nc.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__NETSTORAGE_DIRECT_NC__HPP
#define CONNECT_SERVICES__NETSTORAGE_DIRECT_NC__HPP
-/* $Id: netstorage_direct_nc.hpp 451453 2014-11-06 19:30:09Z ivanov $
+/* $Id: netstorage_direct_nc.hpp 463064 2015-03-24 15:50:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,14 +68,12 @@ struct SNetStorage_NetCacheBlob : public SNetStorageObjectImpl
virtual void Close();
virtual void Abort();
- virtual IReader& GetReader();
- virtual IEmbeddedStreamWriter& GetWriter();
-
virtual string GetLoc();
virtual void Read(string* data);
virtual bool Eof();
virtual Uint8 GetSize();
- virtual string GetAttribute(const string& attr_name);
+ virtual list<string> GetAttributeList() const;
+ virtual string GetAttribute(const string& attr_name) const;
virtual void SetAttribute(const string& attr_name,
const string& attr_value);
virtual CNetStorageObjectInfo GetInfo();
diff --git a/c++/src/connect/services/netstorage_rpc.cpp b/c++/src/connect/services/netstorage_rpc.cpp
index 3cdade9..20aa4f0 100644
--- a/c++/src/connect/services/netstorage_rpc.cpp
+++ b/c++/src/connect/services/netstorage_rpc.cpp
@@ -1,4 +1,4 @@
-/* $Id: netstorage_rpc.cpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netstorage_rpc.cpp 468613 2015-05-26 19:15:53Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -44,7 +44,7 @@
#define NCBI_USE_ERRCODE_X NetStorage_RPC
-#define NST_PROTOCOL_VERSION 1
+#define NST_PROTOCOL_VERSION "1.0.0"
#define READ_CHUNK_SIZE (64 * 1024)
@@ -64,6 +64,7 @@ const char* CNetStorageException::GetErrCodeString() const
case eIOError: return "eIOError";
case eServerError: return "eServerError";
case eTimeout: return "eTimeout";
+ case eExpired: return "eExpired";
default: return CException::GetErrCodeString();
}
}
@@ -268,12 +269,11 @@ static void s_TrapErrors(const CJsonNode& request,
}
if (reply.GetString("Status") != "OK") {
+ Int8 code = CNetStorageServerError::eUnknownError;
string errors;
issues = reply.GetByKeyOrNull("Errors");
- bool file_not_found = false;
-
if (!issues)
errors = reply.GetString("Status");
else {
@@ -281,10 +281,8 @@ static void s_TrapErrors(const CJsonNode& request,
for (CJsonIterator it = issues.Iterate(); it; ++it) {
errors += prefix;
- Int8 server_error_code = (*it).GetInteger("Code");
- if (server_error_code == 14)
- file_not_found = true;
- errors += NStr::NumericToString(server_error_code);
+ code = (*it).GetInteger("Code");
+ errors += NStr::NumericToString(code);
errors += ": ";
errors += (*it).GetString("Message");
prefix = ", error ";
@@ -297,10 +295,16 @@ static void s_TrapErrors(const CJsonNode& request,
sock->GetPeerAddress() << ". "
"Server returned " << errors);
- if (file_not_found) {
- NCBI_THROW_FMT(CNetStorageException, eNotExists, err_msg);
- } else {
- NCBI_THROW_FMT(CNetStorageException, eServerError, err_msg);
+ switch (code) {
+ case CNetStorageServerError::eNetStorageObjectNotFound:
+ case CNetStorageServerError::eRemoteObjectNotFound:
+ NCBI_THROW_FMT(CNetStorageException, eNotExists, err_msg);
+ break;
+ case CNetStorageServerError::eNetStorageObjectExpired:
+ NCBI_THROW_FMT(CNetStorageException, eExpired, err_msg);
+ break;
+ default:
+ NCBI_THROW_FMT(CNetStorageException, eServerError, err_msg);
}
}
@@ -337,8 +341,6 @@ public:
virtual CRef<INetServerProperties> AllocServerProperties();
public:
- virtual CConfig* LoadConfigFromAltSource(CObject* api_impl,
- string* new_section_name);
virtual void OnInit(CObject* api_impl,
CConfig* config, const string& config_section);
virtual void OnConnected(CNetServerConnection& connection);
@@ -353,12 +355,6 @@ CRef<INetServerProperties> CNetStorageServerListener::AllocServerProperties()
return CRef<INetServerProperties>(new INetServerProperties);
}
-CConfig* CNetStorageServerListener::LoadConfigFromAltSource(
- CObject* /*api_impl*/, string* /*new_section_name*/)
-{
- return NULL;
-}
-
void CNetStorageServerListener::OnInit(CObject* /*api_impl*/,
CConfig* /*config*/, const string& /*config_section*/)
{
@@ -406,7 +402,7 @@ struct SNetStorageObjectRPC : public SNetStorageObjectImpl
CJsonNode ExchangeUsingOwnService(const CJsonNode& request,
CNetServerConnection* conn = NULL,
- CNetServer::TInstance server_to_use = NULL)
+ CNetServer::TInstance server_to_use = NULL) const
{
return m_NetStorageRPC->Exchange(m_OwnService,
request, conn, server_to_use);
@@ -422,12 +418,13 @@ struct SNetStorageObjectRPC : public SNetStorageObjectImpl
virtual string GetLoc();
virtual bool Eof();
virtual Uint8 GetSize();
- virtual string GetAttribute(const string& attr_name);
+ virtual list<string> GetAttributeList() const;
+ virtual string GetAttribute(const string& attr_name) const;
virtual void SetAttribute(const string& attr_name,
const string& attr_value);
virtual CNetStorageObjectInfo GetInfo();
- CJsonNode x_MkRequest(const string& request_type);
+ CJsonNode x_MkRequest(const string& request_type) const;
CRef<SNetStorageRPC,
CNetComponentCounterLocker<SNetStorageRPC> > m_NetStorageRPC;
@@ -516,18 +513,22 @@ SNetStorageRPC::SNetStorageRPC(const string& init_string,
}
}
break;
+ case 'm':
+ if (field->name == "metadata")
+ m_MetadataOption = field->value;
+ break;
case 'n':
- if (field->name == "nst")
+ if (field->name == "namespace")
+ m_AppDomain = field->value;
+ else if (field->name == "nst")
m_NetStorageServiceName = field->value;
else if (field->name == "nc")
m_NetCacheServiceName = field->value;
break;
case 'c':
- if (field->name == "cache") {
- m_CacheName = field->value;
- if (m_AppDomain.empty())
- m_AppDomain = m_CacheName;
- } else if (field->name == "client")
+ if (field->name == "cache")
+ m_AppDomain = field->value;
+ else if (field->name == "client")
m_ClientName = field->value;
}
}
@@ -588,10 +589,15 @@ SNetStorageRPC::SNetStorageRPC(const string& init_string,
hello.SetString("Client", m_ClientName);
hello.SetString("Service", m_NetStorageServiceName);
- CNcbiApplication* app = CNcbiApplication::Instance();
- if (app != NULL)
- hello.SetString("Application", app->GetProgramExecutablePath());
- hello.SetInteger("ProtocolVersion", NST_PROTOCOL_VERSION);
+ if (!m_MetadataOption.empty())
+ hello.SetString("Metadata", m_MetadataOption);
+ {{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if (app != NULL)
+ hello.SetString("Application", app->GetProgramExecutablePath());
+ }}
+ hello.SetString("ProtocolVersion", NST_PROTOCOL_VERSION);
m_Service = new SNetServiceImpl("NetStorageAPI", m_ClientName,
new CNetStorageServerListener(hello));
@@ -610,7 +616,7 @@ CNetStorageObject SNetStorageRPC::Create(TNetStorageFlags flags)
case eDefaultStorage_NetCache:
x_InitNetCacheAPI();
- return g_CreateNetStorage_NetCacheBlob(m_NetCacheAPI, kEmptyStr);
+ return CDNCNetStorage::Create(m_NetCacheAPI);
default: /* eDefaultStorage_NoCreate */
NCBI_THROW_FMT(CNetStorageException, eAuthError,
@@ -632,20 +638,23 @@ CNetStorageObject SNetStorageRPC::Create(TNetStorageFlags flags)
object_loc, flags, SNetStorageObjectRPC::eWriting);
}
-CNetStorageObject SNetStorageRPC::Open(const string& object_loc,
- TNetStorageFlags flags)
+CNetStorageObject SNetStorageRPC::Open(const string& object_loc)
{
if (x_NetCacheMode(object_loc))
- return g_CreateNetStorage_NetCacheBlob(m_NetCacheAPI, object_loc);
+ return CDNCNetStorage::Open(m_NetCacheAPI, object_loc);
return new SNetStorageObjectRPC(this, NULL, NULL,
SNetStorageObjectRPC::eByGeneratedID,
- object_loc, flags, SNetStorageObjectRPC::eReady);
+ object_loc, 0, SNetStorageObjectRPC::eReady);
}
string SNetStorageRPC::Relocate(const string& object_loc,
TNetStorageFlags flags)
{
+ if (x_NetCacheMode(object_loc))
+ NCBI_THROW_FMT(CNetStorageException, eInvalidArg, object_loc <<
+ ": Relocate for NetCache blobs is not implemented");
+
CJsonNode request(MkObjectRequest("RELOCATE", object_loc));
CJsonNode new_location(CJsonNode::NewObjectNode());
@@ -708,7 +717,7 @@ void CJsonOverUTTPExecHandler::Exec(CNetServerConnection::TInstance conn_impl,
CJsonNode SNetStorageRPC::Exchange(CNetService service,
const CJsonNode& request,
CNetServerConnection* conn,
- CNetServer::TInstance server_to_use)
+ CNetServer::TInstance server_to_use) const
{
CNetServer server(server_to_use != NULL ? server_to_use :
(CNetServer::TInstance)
@@ -740,6 +749,10 @@ void SNetStorageRPC::x_SetStorageFlags(CJsonNode& node, TNetStorageFlags flags)
storage_flags.SetBoolean("Fast", true);
if (flags & fNST_Persistent)
storage_flags.SetBoolean("Persistent", true);
+ if (flags & fNST_NetCache)
+ storage_flags.SetBoolean("NetCache", true);
+ if (flags & fNST_FileTrack)
+ storage_flags.SetBoolean("FileTrack", true);
if (flags & fNST_Movable)
storage_flags.SetBoolean("Movable", true);
if (flags & fNST_Cacheable)
@@ -750,17 +763,17 @@ void SNetStorageRPC::x_SetStorageFlags(CJsonNode& node, TNetStorageFlags flags)
node.SetByKey("StorageFlags", storage_flags);
}
-void SNetStorageRPC::x_SetICacheNames(CJsonNode& node)
+void SNetStorageRPC::x_SetICacheNames(CJsonNode& node) const
{
- if (!m_NetCacheServiceName.empty() && !m_CacheName.empty()) {
+ if (!m_NetCacheServiceName.empty() && !m_AppDomain.empty()) {
CJsonNode icache(CJsonNode::NewObjectNode());
icache.SetString("ServiceName", m_NetCacheServiceName);
- icache.SetString("CacheName", m_CacheName);
+ icache.SetString("CacheName", m_AppDomain);
node.SetByKey("ICache", icache);
}
}
-CJsonNode SNetStorageRPC::MkStdRequest(const string& request_type)
+CJsonNode SNetStorageRPC::MkStdRequest(const string& request_type) const
{
CJsonNode new_request(CJsonNode::NewObjectNode());
@@ -771,16 +784,21 @@ CJsonNode SNetStorageRPC::MkStdRequest(const string& request_type)
if (req.IsSetClientIP()) {
new_request.SetString("ClientIP", req.GetClientIP());
- new_request.SetString("SessionID", req.IsSetSessionID() ?
- req.GetSessionID() : "UNKNOWN");
- new_request.SetString("PageHitID", req.GetHitID());
+ }
+
+ if (req.IsSetSessionID()) {
+ new_request.SetString("SessionID", req.GetSessionID());
+ }
+
+ if (req.IsSetHitID()) {
+ new_request.SetString("ncbi_phid", req.GetHitID());
}
return new_request;
}
CJsonNode SNetStorageRPC::MkObjectRequest(const string& request_type,
- const string& object_loc)
+ const string& object_loc) const
{
CJsonNode new_request(MkStdRequest(request_type));
@@ -790,7 +808,7 @@ CJsonNode SNetStorageRPC::MkObjectRequest(const string& request_type,
}
CJsonNode SNetStorageRPC::MkObjectRequest(const string& request_type,
- const string& unique_key, TNetStorageFlags flags)
+ const string& unique_key, TNetStorageFlags flags) const
{
CJsonNode new_request(MkStdRequest(request_type));
@@ -1070,7 +1088,29 @@ Uint8 SNetStorageObjectRPC::GetSize()
return (Uint8) ExchangeUsingOwnService(request).GetInteger("Size");
}
-string SNetStorageObjectRPC::GetAttribute(const string& attr_name)
+list<string> SNetStorageObjectRPC::GetAttributeList() const
+{
+ if (m_State != eReady) {
+ NCBI_THROW_FMT(CNetStorageException, eInvalidArg,
+ "Cannot get object attribute while reading or writing");
+ }
+
+ CJsonNode request(x_MkRequest("GETATTRLIST"));
+
+ CJsonNode reply(ExchangeUsingOwnService(request));
+ CJsonNode names(reply.GetByKeyOrNull("AttributeNames"));
+ list<string> result;
+
+ if (names) {
+ for (CJsonIterator it = names.Iterate(); it; ++it) {
+ result.push_back((*it).AsString());
+ }
+ }
+
+ return result;
+}
+
+string SNetStorageObjectRPC::GetAttribute(const string& attr_name) const
{
if (m_State != eReady) {
NCBI_THROW_FMT(CNetStorageException, eInvalidArg,
@@ -1142,7 +1182,7 @@ void SNetStorageObjectRPC::Close()
}
}
-CJsonNode SNetStorageObjectRPC::x_MkRequest(const string& request_type)
+CJsonNode SNetStorageObjectRPC::x_MkRequest(const string& request_type) const
{
if (m_ObjectIdentification == eByGeneratedID)
return m_NetStorageRPC->MkObjectRequest(request_type, m_Locator);
@@ -1239,7 +1279,7 @@ string SNetStorageByKeyRPC::Relocate(const string& unique_key,
CJsonNode new_location(CJsonNode::NewObjectNode());
- m_NetStorageRPC->x_SetStorageFlags(new_location, flags);
+ SNetStorageRPC::x_SetStorageFlags(new_location, flags);
request.SetByKey("NewLocation", new_location);
diff --git a/c++/src/connect/services/netstorage_rpc.hpp b/c++/src/connect/services/netstorage_rpc.hpp
index 2f492b1..6524688 100644
--- a/c++/src/connect/services/netstorage_rpc.hpp
+++ b/c++/src/connect/services/netstorage_rpc.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__NETSTORAGE_RPC__HPP
#define CONNECT_SERVICES__NETSTORAGE_RPC__HPP
-/* $Id: netstorage_rpc.hpp 458012 2015-01-29 20:05:22Z kazimird $
+/* $Id: netstorage_rpc.hpp 463064 2015-03-24 15:50:48Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,8 +51,7 @@ struct SNetStorageRPC : public SNetStorageImpl
SNetStorageRPC(const string& init_string, TNetStorageFlags default_flags);
virtual CNetStorageObject Create(TNetStorageFlags flags = 0);
- virtual CNetStorageObject Open(const string& object_loc,
- TNetStorageFlags flags = 0);
+ virtual CNetStorageObject Open(const string& object_loc);
virtual string Relocate(const string& object_loc, TNetStorageFlags flags);
virtual bool Exists(const string& object_loc);
virtual void Remove(const string& object_loc);
@@ -60,15 +59,15 @@ struct SNetStorageRPC : public SNetStorageImpl
CJsonNode Exchange(CNetService service,
const CJsonNode& request,
CNetServerConnection* conn = NULL,
- CNetServer::TInstance server_to_use = NULL);
+ CNetServer::TInstance server_to_use = NULL) const;
- void x_SetStorageFlags(CJsonNode& node, TNetStorageFlags flags);
- void x_SetICacheNames(CJsonNode& node);
- CJsonNode MkStdRequest(const string& request_type);
+ static void x_SetStorageFlags(CJsonNode& node, TNetStorageFlags flags);
+ void x_SetICacheNames(CJsonNode& node) const;
+ CJsonNode MkStdRequest(const string& request_type) const;
CJsonNode MkObjectRequest(const string& request_type,
- const string& object_loc);
+ const string& object_loc) const;
CJsonNode MkObjectRequest(const string& request_type,
- const string& unique_key, TNetStorageFlags flags);
+ const string& unique_key, TNetStorageFlags flags) const;
void x_InitNetCacheAPI();
bool x_NetCacheMode(const string& object_loc);
@@ -90,11 +89,11 @@ struct SNetStorageRPC : public SNetStorageImpl
string m_NetStorageServiceName;
string m_NetCacheServiceName;
- string m_CacheName;
string m_ClientName;
string m_AppDomain;
+ string m_MetadataOption;
- CAtomicCounter m_RequestNumber;
+ mutable CAtomicCounter m_RequestNumber;
CCompoundIDPool m_CompoundIDPool;
diff --git a/c++/src/connect/services/netstorageobjectinfo.cpp b/c++/src/connect/services/netstorageobjectinfo.cpp
index e4ba586..0679b90 100644
--- a/c++/src/connect/services/netstorageobjectinfo.cpp
+++ b/c++/src/connect/services/netstorageobjectinfo.cpp
@@ -1,4 +1,4 @@
-/* $Id: netstorageobjectinfo.cpp 458005 2015-01-29 19:51:18Z kazimird $
+/* $Id: netstorageobjectinfo.cpp 461290 2015-03-09 14:45:57Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -131,7 +131,7 @@ private:
template <>
CTime SLazyInitData::GetTime<eNFL_FileTrack>()
{
- const char* const kISO8601TimeFormat = "Y-M-DTh:m:s.r:z";
+ const char* const kISO8601TimeFormat = "Y-M-DTh:m:s.ro";
if (st_info) {
if (CJsonNode ctime = st_info.GetByKeyOrNull("ctime")) {
@@ -165,7 +165,8 @@ void SLazyInitData::InitData()
loc =
l == "NetCache" ? eNFL_NetCache :
- l == "FileTrack" ? eNFL_FileTrack : eNFL_NotFound;
+ l == "FileTrack" ? eNFL_FileTrack :
+ l == "NotFound" ? eNFL_NotFound : eNFL_Unknown;
loc_info = json.GetByKey("ObjectLocInfo");
file_size = size ? (Uint8) size.AsInteger() : 0;
st_info = json.GetByKeyOrNull("StorageSpecificInfo");
diff --git a/c++/src/connect/services/netstorageobjectloc.cpp b/c++/src/connect/services/netstorageobjectloc.cpp
index 4dc2760..a590d08 100644
--- a/c++/src/connect/services/netstorageobjectloc.cpp
+++ b/c++/src/connect/services/netstorageobjectloc.cpp
@@ -1,4 +1,4 @@
-/* $Id: netstorageobjectloc.cpp 451504 2014-11-06 20:58:45Z kazimird $
+/* $Id: netstorageobjectloc.cpp 460956 2015-03-04 17:37:13Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,9 +48,23 @@
#define DEFAULT_CACHE_CHUNK_SIZE (1024 * 1024)
+#define FILETRACK_STORAGE_CODE "FT"
+#define NETCACHE_STORAGE_CODE "NC"
+
+#define STORAGE_INFO_CUE 0
+
BEGIN_NCBI_SCOPE
-EFileTrackSite g_StringToFileTrackSite(const char* ft_site_name)
+/// @internal
+enum EFileTrackSite {
+ eFileTrack_ProdSite,
+ eFileTrack_DevSite,
+ eFileTrack_QASite,
+ eNumberOfFileTrackSites
+};
+
+/// @internal
+static EFileTrackSite s_StringToFileTrackSite(const char* ft_site_name)
{
if (strcmp(ft_site_name, "submit") == 0 ||
strcmp(ft_site_name, "prod") == 0)
@@ -68,15 +82,21 @@ EFileTrackSite g_StringToFileTrackSite(const char* ft_site_name)
}
CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
- TNetStorageFlags flags, Uint8 random_number,
+ TNetStorageAttrFlags flags,
+ const string& app_domain,
+ Uint8 random_number,
const char* ft_site_name) :
m_CompoundIDPool(cid_pool),
- m_StorageFlags(flags),
- m_Fields(0),
+ m_LocatorFlags(x_StorageFlagsToLocatorFlags(flags)),
m_ObjectID(0),
+ m_Location(eNFL_Unknown),
+ m_AppDomain(app_domain),
m_Timestamp(time(NULL)),
m_Random(random_number),
m_CacheChunkSize(DEFAULT_CACHE_CHUNK_SIZE),
+ m_NCFlags(0),
+ m_NetCacheIP(0),
+ m_NetCachePort(0),
m_Dirty(true)
{
x_SetFileTrackSite(ft_site_name);
@@ -84,71 +104,131 @@ CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
}
CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
- TNetStorageFlags flags,
+ TNetStorageAttrFlags flags,
const string& app_domain,
const string& unique_key,
const char* ft_site_name) :
m_CompoundIDPool(cid_pool),
- m_StorageFlags(flags),
- m_Fields(fNFID_KeyAndNamespace),
+ m_LocatorFlags(x_StorageFlagsToLocatorFlags(flags) | fLF_HasUserKey),
m_ObjectID(0),
+ m_Location(eNFL_Unknown),
m_AppDomain(app_domain),
m_UserKey(unique_key),
m_CacheChunkSize(DEFAULT_CACHE_CHUNK_SIZE),
+ m_NCFlags(0),
+ m_NetCacheIP(0),
+ m_NetCachePort(0),
m_Dirty(true)
{
x_SetFileTrackSite(ft_site_name);
x_SetUniqueKeyFromUserDefinedKey();
}
-#define THROW_INVALID_LOC_ERROR(object_loc) \
+#define INVALID_LOC_ERROR_MSG "Invalid NetStorage object locator"
+
+#define THROW_INVALID_LOC_ERROR(object_loc, msg) \
NCBI_THROW_FMT(CNetStorageException, eInvalidArg, \
- "Invalid NetStorage object locator '" << (object_loc) << '\'')
+ msg " '" << (object_loc) << '\'')
#define VERIFY_FIELD_EXISTS(field) \
if (!(field)) { \
- THROW_INVALID_LOC_ERROR(object_loc); \
+ THROW_INVALID_LOC_ERROR(object_loc, INVALID_LOC_ERROR_MSG); \
}
+ENetStorageObjectLocation s_LocationCodeToLocation(const string& location)
+{
+ if (location.length() == 2) {
+ if (location.data()[0] == FILETRACK_STORAGE_CODE[0] &&
+ location.data()[1] == FILETRACK_STORAGE_CODE[1])
+ return eNFL_FileTrack;
+ if (location.data()[0] == NETCACHE_STORAGE_CODE[0] &&
+ location.data()[1] == NETCACHE_STORAGE_CODE[1])
+ return eNFL_NetCache;
+ }
+ return eNFL_Unknown;
+}
+
CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
const string& object_loc) :
m_CompoundIDPool(cid_pool),
+ m_ObjectID(0),
+ m_Location(eNFL_Unknown),
+ m_CacheChunkSize(DEFAULT_CACHE_CHUNK_SIZE),
+ m_NCFlags(0),
+ m_NetCacheIP(0),
+ m_NetCachePort(0),
+ m_Dirty(false),
+ m_Locator(object_loc)
+{
+ Parse(object_loc);
+}
+
+CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
+ const string& object_loc, TNetStorageAttrFlags flags) :
+ m_CompoundIDPool(cid_pool),
+ m_ObjectID(0),
+ m_Location(eNFL_Unknown),
+ m_CacheChunkSize(DEFAULT_CACHE_CHUNK_SIZE),
+ m_NCFlags(0),
+ m_NetCacheIP(0),
+ m_NetCachePort(0),
m_Dirty(false),
m_Locator(object_loc)
{
+ Parse(object_loc);
+
+ if (flags != GetStorageAttrFlags()) {
+ m_Dirty = true;
+ m_LocatorFlags = (m_LocatorFlags & eLF_FieldFlags) |
+ x_StorageFlagsToLocatorFlags(flags);
+ }
+}
+
+void CNetStorageObjectLoc::Parse(const string& object_loc)
+{
CCompoundID cid = m_CompoundIDPool.FromString(object_loc);
// Check the ID class.
- if (cid.GetClass() != eCIC_NetStorageObjectLoc) {
- THROW_INVALID_LOC_ERROR(object_loc);
+ switch (cid.GetClass()) {
+ case eCIC_NetStorageObjectLocV1:
+ THROW_INVALID_LOC_ERROR(object_loc,
+ "Unsupported NetStorage object locator version");
+ case eCIC_NetStorageObjectLoc:
+ break;
+ default:
+ THROW_INVALID_LOC_ERROR(object_loc, INVALID_LOC_ERROR_MSG);
}
- // Restore the storage flags.
+ // Get locator flags.
CCompoundIDField field = cid.GetFirst(eCIT_Flags);
VERIFY_FIELD_EXISTS(field);
- m_StorageFlags = (TNetStorageFlags) field.GetFlags();
+ m_LocatorFlags = (TLocatorFlags) field.GetFlags();
- // Restore the field flags.
- VERIFY_FIELD_EXISTS(field = field.GetNextHomogeneous());
- m_Fields = (TNetStorageObjectLocFields) field.GetFlags();
+ // Restore NetStorage service name.
+ if (m_LocatorFlags & fLF_NetStorageService) {
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_ServiceName = field.GetServiceName();
+ }
- if ((m_StorageFlags & fNST_NoMetaData) == 0) {
+ // Restore object ID.
+ if (m_LocatorFlags & fLF_HasObjectID) {
VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
m_ObjectID = field.GetID();
}
- // Restore file identification.
- if (m_Fields & fNFID_KeyAndNamespace) {
- // Get the unique file key.
+ // Get the domain name.
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_AppDomain = field.GetString();
+
+ // Restore object identification.
+ if (m_LocatorFlags & fLF_HasUserKey) {
+ // Get the unique object key.
VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
m_UserKey = field.GetString();
- // Get the domain name.
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_AppDomain = field.GetString();
x_SetUniqueKeyFromUserDefinedKey();
} else {
- // Get file creation timestamp.
+ // Get object creation timestamp.
VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
m_Timestamp = field.GetTimestamp();
// Get the random ID.
@@ -160,92 +240,94 @@ CNetStorageObjectLoc::CNetStorageObjectLoc(CCompoundIDPool::TInstance cid_pool,
x_SetUniqueKeyFromRandom();
}
- // Restore NetCache info.
- if (m_Fields & fNFID_NetICache) {
- // Get the service name.
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_NCServiceName = field.GetServiceName();
- // Get the cache name.
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_CacheName = field.GetDatabaseName();
- // Get the primary NetCache server IP and port.
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_NetCacheIP = field.GetIPv4Address();
- m_NetCachePort = field.GetPort();
- }
-
- // If this file is cacheable, load the size of cache chunks.
- if (m_StorageFlags & fNST_Cacheable) {
+ // If this object is cacheable, load the size of cache chunks.
+ if (m_LocatorFlags & fLF_Cacheable) {
VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
m_CacheChunkSize = (Uint8) field.GetInteger();
}
- // Restore the TTL if it's in the key.
- if (m_Fields & fNFID_TTL) {
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_TTL = (Uint8) field.GetInteger();
- }
-
- // Restore NetStorage service name.
- if (m_Fields & fNFID_NetStorageService) {
- VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
- m_ServiceName = field.GetString();
+ // Find storage info (optional).
+ for (field = cid.GetFirst(eCIT_Cue); field; field = field.GetNextHomogeneous()) {
+ if (field.GetCue() == STORAGE_INFO_CUE) {
+ // Restore object location.
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_LocationCode = field.GetDatabaseName();
+ m_Location = s_LocationCodeToLocation(m_LocationCode);
+
+ // Restore storage-specific info.
+ if (m_Location == eNFL_NetCache) {
+ // Get NetCache flags.
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_NCFlags = (TNetCacheFlags) field.GetFlags();
+ // Get the service name.
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_NCServiceName = field.GetServiceName();
+ // Get the primary NetCache server IP and port.
+ if (m_NCFlags & fNCF_ServerSpecified) {
+ VERIFY_FIELD_EXISTS(field = field.GetNextNeighbor());
+ m_NetCacheIP = field.GetIPv4Address();
+ m_NetCachePort = field.GetPort();
+ }
+ }
+
+ break;
+ }
}
}
-void CNetStorageObjectLoc::ClearNetICacheParams()
-{
- m_Dirty = true;
-
- ClearFieldFlags(fNFID_NetICache);
-}
-
-void CNetStorageObjectLoc::SetNetICacheParams(const string& service_name,
- const string& cache_name, Uint4 server_ip, unsigned short server_port
-#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
- , bool allow_xsite_conn
-#endif
- )
+void CNetStorageObjectLoc::SetLocation_NetCache(
+ const string& service_name,
+ Uint4 server_ip, unsigned short server_port,
+ bool allow_xsite_conn)
{
m_Dirty = true;
- SetFieldFlags(fNFID_NetICache);
+ m_LocationCode = NETCACHE_STORAGE_CODE;
+ m_Location = eNFL_NetCache;
m_NCServiceName = service_name;
- m_CacheName = cache_name;
- m_NetCacheIP = server_ip;
- m_NetCachePort = server_port;
-#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
+ if (server_ip != 0 && server_port != 0)
+ m_NCFlags |= fNCF_ServerSpecified;
+ else
+ m_NCFlags &= ~(TNetCacheFlags) fNCF_ServerSpecified;
+
if (allow_xsite_conn)
- SetFieldFlags(fNFID_AllowXSiteConn);
+ m_NCFlags |= fNCF_AllowXSiteConn;
else
- ClearFieldFlags(fNFID_AllowXSiteConn);
-#endif
+ m_NCFlags &= ~(TNetCacheFlags) fNCF_AllowXSiteConn;
+
+ // NB: FileTrack site must not be reset.
}
-void CNetStorageObjectLoc::SetFileTrackSite(EFileTrackSite ft_site)
+void CNetStorageObjectLoc::SetLocation_FileTrack(const char* ft_site_name)
{
+ EFileTrackSite ft_site = s_StringToFileTrackSite(ft_site_name);
+
m_Dirty = true;
- m_Fields &= ~(unsigned char) (fNFID_FileTrackDev | fNFID_FileTrackQA);
+ m_LocationCode = FILETRACK_STORAGE_CODE;
+ m_Location = eNFL_FileTrack;
+
+ m_NCServiceName.clear();
+ m_NCFlags = 0;
+ m_CacheChunkSize = DEFAULT_CACHE_CHUNK_SIZE;
+
+ m_LocatorFlags &= ~(TLocatorFlags) (fLF_DevEnv | fLF_QAEnv);
if (ft_site == eFileTrack_DevSite)
- m_Fields |= fNFID_FileTrackDev;
+ m_LocatorFlags |= fLF_DevEnv;
else if (ft_site == eFileTrack_QASite)
- m_Fields |= fNFID_FileTrackQA;
+ m_LocatorFlags |= fLF_QAEnv;
}
-EFileTrackSite CNetStorageObjectLoc::GetFileTrackSite()
+string CNetStorageObjectLoc::GetFileTrackURL()
{
- return m_Fields & fNFID_FileTrackDev ? eFileTrack_DevSite :
- m_Fields & fNFID_FileTrackQA ? eFileTrack_QASite :
+ EFileTrackSite ft_site = m_LocatorFlags & fLF_DevEnv ? eFileTrack_DevSite :
+ m_LocatorFlags & fLF_QAEnv ? eFileTrack_QASite :
eFileTrack_ProdSite;
-}
-string CNetStorageObjectLoc::GetFileTrackURL()
-{
- switch (GetFileTrackSite()) {
+ switch (ft_site) {
default:
return "https://submit.ncbi.nlm.nih.gov";
break;
@@ -259,12 +341,14 @@ string CNetStorageObjectLoc::GetFileTrackURL()
void CNetStorageObjectLoc::x_SetFileTrackSite(const char* ft_site_name)
{
- switch (g_StringToFileTrackSite(ft_site_name)) {
+ m_LocatorFlags &= ~(TLocatorFlags) (fLF_DevEnv | fLF_QAEnv);
+
+ switch (s_StringToFileTrackSite(ft_site_name)) {
case eFileTrack_DevSite:
- m_Fields |= fNFID_FileTrackDev;
+ m_LocatorFlags |= fLF_DevEnv;
break;
case eFileTrack_QASite:
- m_Fields |= fNFID_FileTrackQA;
+ m_LocatorFlags |= fLF_QAEnv;
default:
break;
}
@@ -272,64 +356,82 @@ void CNetStorageObjectLoc::x_SetFileTrackSite(const char* ft_site_name)
void CNetStorageObjectLoc::x_SetUniqueKeyFromRandom()
{
- m_UniqueKey = NStr::NumericToString(m_Timestamp) + '_';
- m_UniqueKey.append(NStr::NumericToString(m_Random));
+ m_ICacheKey = NStr::NumericToString(m_Timestamp);
+ m_ICacheKey += '-';
+ m_ICacheKey += NStr::NumericToString(m_Random);
+ if (m_LocatorFlags & fLF_HasObjectID) {
+ m_ICacheKey += '-';
+ m_ICacheKey.append(NStr::NumericToString(m_ObjectID));
+ }
+ m_UniqueKey = m_AppDomain + '-';
+ m_UniqueKey += m_ICacheKey;
}
void CNetStorageObjectLoc::x_SetUniqueKeyFromUserDefinedKey()
{
- m_UniqueKey = m_AppDomain + '_';
- m_UniqueKey.append(m_UserKey);
+ m_ICacheKey = m_UserKey;
+ m_UniqueKey = m_AppDomain + '-';
+ m_UniqueKey += m_UserKey;
}
-void CNetStorageObjectLoc::x_Pack()
+void CNetStorageObjectLoc::x_Pack() const
{
// Allocate a new CompoundID object.
CCompoundID cid = m_CompoundIDPool.NewID(eCIC_NetStorageObjectLoc);
- // Save the storage flags.
- cid.AppendFlags(m_StorageFlags);
- // Remember which fields are stored.
- cid.AppendFlags(m_Fields);
+ // Save locator flags.
+ // If its location is not set yet, add "Movable", so the locator can be used
+ cid.AppendFlags(m_Location != eNFL_Unknown ?
+ m_LocatorFlags : (m_LocatorFlags | fLF_Movable));
- // Save file identification.
- if ((m_StorageFlags & fNST_NoMetaData) == 0)
+ // Save NetStorage service name.
+ if (m_LocatorFlags & fLF_NetStorageService)
+ cid.AppendServiceName(m_ServiceName);
+
+ // Save object ID.
+ if (m_LocatorFlags & fLF_HasObjectID)
cid.AppendID(m_ObjectID);
- if (m_Fields & fNFID_KeyAndNamespace) {
- // Save the unique file key.
+ // Save the domain name.
+ cid.AppendString(m_AppDomain);
+
+ // Save object identification
+ if (m_LocatorFlags & fLF_HasUserKey)
+ // Save the unique object key.
cid.AppendString(m_UserKey);
- // Save the domain name.
- cid.AppendString(m_AppDomain);
- } else {
- // Save file creation timestamp.
+ else {
+ // Save object creation timestamp.
cid.AppendTimestamp(m_Timestamp);
// Save the random ID.
cid.AppendRandom(m_Random >> (sizeof(Uint4) * 8));
cid.AppendRandom((Uint4) m_Random);
}
- // (Optional) Save NetCache info.
- if (m_Fields & fNFID_NetICache) {
- // Save the service name.
- cid.AppendServiceName(m_NCServiceName);
- // Save the cache name.
- cid.AppendDatabaseName(m_CacheName);
- // Save the primary NetCache server IP and port.
- cid.AppendIPv4SockAddr(m_NetCacheIP, m_NetCachePort);
- }
-
- // If this file is cacheable, save the size of cache chunks.
- if (m_StorageFlags & fNST_Cacheable)
+ // If this object is cacheable, save the size of cache chunks.
+ if (m_LocatorFlags & fLF_Cacheable)
cid.AppendInteger((Int8) m_CacheChunkSize);
- // Save the TTL if it's defined.
- if (m_Fields & fNFID_TTL)
- cid.AppendInteger((Int8) m_TTL);
-
- // Save NetStorage service name.
- if (m_Fields & fNFID_NetStorageService)
- cid.AppendString(m_ServiceName);
+ // Save storage info (optional).
+ if (m_Location != eNFL_Unknown) {
+ cid.AppendCue(STORAGE_INFO_CUE);
+
+ // Save object location.
+ cid.AppendDatabaseName(m_LocationCode);
+
+ switch (m_Location) {
+ case eNFL_NetCache:
+ // Save NetCache flags.
+ cid.AppendFlags(m_NCFlags);
+ // Save the service name.
+ cid.AppendServiceName(m_NCServiceName);
+ // Save the primary NetCache server IP and port.
+ if (m_NCFlags & fNCF_ServerSpecified)
+ cid.AppendIPv4SockAddr(m_NetCacheIP, m_NetCachePort);
+ break;
+ default:
+ break;
+ }
+ }
// Now pack it all up.
m_Locator = cid.ToString();
@@ -337,6 +439,36 @@ void CNetStorageObjectLoc::x_Pack()
m_Dirty = false;
}
+TNetStorageAttrFlags CNetStorageObjectLoc::GetStorageAttrFlags() const
+{
+ TNetStorageAttrFlags flags = 0;
+
+ if (m_LocatorFlags & fLF_Movable)
+ flags |= fNST_Movable;
+ if (m_LocatorFlags & fLF_Cacheable)
+ flags |= fNST_Cacheable;
+ if (m_LocatorFlags & fLF_NoMetaData)
+ flags |= fNST_NoMetaData;
+
+ return flags;
+}
+
+CNetStorageObjectLoc::TLocatorFlags
+ CNetStorageObjectLoc::x_StorageFlagsToLocatorFlags(
+ TNetStorageAttrFlags storage_flags)
+{
+ TLocatorFlags locator_flags = 0;
+
+ if (storage_flags & fNST_Movable)
+ locator_flags |= fLF_Movable;
+ if (storage_flags & fNST_Cacheable)
+ locator_flags |= fLF_Cacheable;
+ if (storage_flags & fNST_NoMetaData)
+ locator_flags |= fLF_NoMetaData;
+
+ return locator_flags;
+}
+
CJsonNode CNetStorageObjectLoc::ToJSON() const
{
CJsonNode root(CJsonNode::NewObjectNode());
@@ -346,63 +478,62 @@ CJsonNode CNetStorageObjectLoc::ToJSON() const
void CNetStorageObjectLoc::ToJSON(CJsonNode& root) const
{
- root.SetInteger("Version", 1);
+ root.SetInteger("Version", 1 +
+ eCIC_NetStorageObjectLoc - eCIC_NetStorageObjectLocV1);
+
+ root.SetString("Environment",
+ m_LocatorFlags & fLF_DevEnv ? "dev/test" :
+ m_LocatorFlags & fLF_QAEnv ? "QA" : "production");
+
+ if (m_LocatorFlags & fLF_NetStorageService)
+ root.SetString("ServiceName", m_ServiceName);
+
+ if (m_LocatorFlags & fLF_HasObjectID)
+ root.SetInteger("ObjectID", (Int8) m_ObjectID);
CJsonNode storage_flags(CJsonNode::NewObjectNode());
- storage_flags.SetBoolean("Fast",
- (m_StorageFlags & fNST_Fast) != 0);
- storage_flags.SetBoolean("Persistent",
- (m_StorageFlags & fNST_Persistent) != 0);
storage_flags.SetBoolean("Movable",
- (m_StorageFlags & fNST_Movable) != 0);
+ (m_LocatorFlags & fLF_Movable) != 0);
storage_flags.SetBoolean("Cacheable",
- (m_StorageFlags & fNST_Cacheable) != 0);
+ (m_LocatorFlags & fLF_Cacheable) != 0);
storage_flags.SetBoolean("NoMetaData",
- (m_StorageFlags & fNST_NoMetaData) != 0);
+ (m_LocatorFlags & fLF_NoMetaData) != 0);
root.SetByKey("StorageFlags", storage_flags);
- if (m_Fields & fNFID_NetStorageService)
- root.SetString("ServiceName", m_ServiceName);
+ root.SetString("Namespace", m_AppDomain);
- if ((m_StorageFlags & fNST_NoMetaData) == 0)
- root.SetInteger("ObjectID", (Int8) m_ObjectID);
-
- if (m_Fields & fNFID_KeyAndNamespace) {
- root.SetString("AppDomain", m_AppDomain);
+ if (m_LocatorFlags & fLF_HasUserKey)
root.SetString("UserKey", m_UserKey);
- } else {
+ else {
root.SetInteger("Timestamp", (Int8) m_Timestamp);
root.SetInteger("Random", (Int8) m_Random);
}
- if (m_Fields & fNFID_NetICache) {
- CJsonNode icache_params(CJsonNode::NewObjectNode());
-
- icache_params.SetString("ServiceName", m_NCServiceName);
- icache_params.SetString("CacheName", m_CacheName);
- icache_params.SetString("ServerHost",
- g_NetService_gethostnamebyaddr(m_NetCacheIP));
- icache_params.SetInteger("ServerPort", m_NetCachePort);
- icache_params.SetBoolean("AllowXSiteConn",
-#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
- m_Fields & fNFID_AllowXSiteConn ? true :
-#endif
- false);
-
- root.SetByKey("ICache", icache_params);
- }
-
- if (m_StorageFlags & fNST_Cacheable)
+ if (m_LocatorFlags & fLF_Cacheable)
root.SetInteger("CacheChunkSize", (Int8) m_CacheChunkSize);
- if (m_Fields & fNFID_TTL)
- root.SetInteger("TTL", (Int8) m_TTL);
+ if (!m_LocationCode.empty())
+ root.SetString("DefaultLocation", m_LocationCode);
+
+ CJsonNode storage_info(CJsonNode::NewObjectNode());
- if (m_Fields & (fNFID_FileTrackDev | fNFID_FileTrackQA))
- root.SetString("FileTrackSite",
- m_Fields & fNFID_FileTrackDev ? "dev" : "qa");
+ switch (m_Location) {
+ case eNFL_NetCache:
+ storage_info.SetString("ServiceName", m_NCServiceName);
+ if (m_NCFlags & fNCF_ServerSpecified) {
+ storage_info.SetString("ServerHost",
+ g_NetService_gethostnamebyaddr(m_NetCacheIP));
+ storage_info.SetInteger("ServerPort", m_NetCachePort);
+ }
+ storage_info.SetBoolean("AllowXSiteConn", IsXSiteProxyAllowed());
+
+ root.SetByKey("NetCache", storage_info);
+ break;
+ default:
+ break;
+ }
}
END_NCBI_SCOPE
diff --git a/c++/src/connect/services/ns_output_parser.cpp b/c++/src/connect/services/ns_output_parser.cpp
index 2024e64..22dbdb5 100644
--- a/c++/src/connect/services/ns_output_parser.cpp
+++ b/c++/src/connect/services/ns_output_parser.cpp
@@ -1,4 +1,4 @@
-/* $Id: ns_output_parser.cpp 449958 2014-10-22 13:29:15Z ivanov $
+/* $Id: ns_output_parser.cpp 449834 2014-10-21 16:34:48Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/pack_int.cpp b/c++/src/connect/services/pack_int.cpp
index 8bfd907..2e456ec 100644
--- a/c++/src/connect/services/pack_int.cpp
+++ b/c++/src/connect/services/pack_int.cpp
@@ -1,4 +1,4 @@
-/* $Id: pack_int.cpp 398755 2013-05-08 13:40:21Z kazimird $
+/* $Id: pack_int.cpp 461156 2015-03-06 16:43:46Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,6 +37,8 @@
#include <string.h>
+#include <corelib/ncbidbg.hpp>
+
BEGIN_NCBI_SCOPE
unsigned g_PackInteger(void* dst, size_t dst_size, Uint8 number)
@@ -116,6 +118,8 @@ unsigned g_UnpackInteger(const void* src, size_t src_size, Uint8* number)
if (src_size == 0)
return 0;
+ _ASSERT(number);
+
if ((signed char) *ptr >= 0) {
*number = (Uint8) *ptr;
return 1;
diff --git a/c++/src/connect/services/srv_connections.cpp b/c++/src/connect/services/srv_connections.cpp
index e892591..15f4634 100644
--- a/c++/src/connect/services/srv_connections.cpp
+++ b/c++/src/connect/services/srv_connections.cpp
@@ -1,4 +1,4 @@
-/* $Id: srv_connections.cpp 457223 2015-01-21 16:21:32Z kazimird $
+/* $Id: srv_connections.cpp 477824 2015-09-02 12:20:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -119,7 +119,9 @@ void SNetServerConnectionImpl::DeleteThis()
TFastMutexGuard guard(
m_Server->m_ServerInPool->m_FreeConnectionListLock);
+ //int upper_limit = m_Server.m_Impl->m_MaxConnPoolSize;
int upper_limit = TServConn_MaxConnPoolSize::GetDefault();
+ //LOG_POST("pool size: "<<upper_limit);
if (upper_limit == 0 || m_Server->m_ServerInPool->
m_FreeConnectionListSize < upper_limit) {
@@ -240,6 +242,24 @@ void SNetServerConnectionImpl::WriteLine(const string& line)
}
}
+CConfig* INetServerConnectionListener::PreInit(CObject* api_impl,
+ CConfig* config, string* section)
+{
+ _ASSERT(section);
+
+ if (config) {
+ m_ClientName = config->GetString(*section, "client_name",
+ CConfig::eErr_NoThrow);
+
+ if (m_ClientName.empty()) {
+ m_ClientName = config->GetString(*section, "client",
+ CConfig::eErr_NoThrow);
+ }
+ }
+
+ return OnPreInit(api_impl, config, section);
+}
+
namespace {
class CTimeoutKeeper
{
@@ -311,6 +331,13 @@ SNetServerInPool::SNetServerInPool(unsigned host, unsigned short port,
m_FreeConnectionListSize = 0;
ResetThrottlingParameters();
+
+ m_RankBase = 1103515245 *
+ // XOR the network prefix bytes of the IP address with the port
+ // number (in network byte order) and convert the result
+ // to host order so that it can be used in arithmetic operations.
+ CSocketAPI::NetToHostLong(host ^ CSocketAPI::HostToNetShort(port)) +
+ 12345;
}
void SNetServerInPool::DeleteThis()
@@ -479,6 +506,11 @@ inline static bool operator <(const STimeout& t1, const STimeout& t2)
return t1.sec == t2.sec ? t1.usec < t2.usec : t1.sec < t2.sec;
}
+inline ostream& operator<<(ostream& out, const STimeout& tm)
+{
+ return out << (tm.sec+tm.usec*1e-6);
+}
+
CNetServerConnection SNetServerImpl::Connect(STimeout* timeout,
INetServerConnectionListener* conn_listener)
{
@@ -491,6 +523,8 @@ CNetServerConnection SNetServerImpl::Connect(STimeout* timeout,
STimeout internal_timeout = conn_timeout < s_InternalConnectTimeout ?
conn_timeout : s_InternalConnectTimeout;
+ //LOG_POST("internal timeout: "<<internal_timeout);
+
SServerAddress server_address(m_ServerInPool->m_Address);
#ifdef NCBI_GRID_XSITE_CONN_SUPPORT
@@ -604,6 +638,7 @@ CNetServerConnection SNetServerImpl::Connect(STimeout* timeout,
m_ServerInPool->AdjustThrottlingParameters(SNetServerInPool::eCOR_Success);
+ //LOG_POST("comm timeout: "<<*(timeout != NULL ? timeout: &m_ServerInPool->m_ServerPool->m_CommTimeout));
conn->m_Socket.SetDataLogging(eOff);
conn->m_Socket.SetTimeout(eIO_ReadWrite, timeout != NULL ? timeout :
&m_ServerInPool->m_ServerPool->m_CommTimeout);
@@ -702,6 +737,9 @@ void SNetServerImpl::ConnectAndExec(const string& cmd,
INetServerExecListener* exec_listener,
INetServerConnectionListener* conn_listener)
{
+ if (conn_listener == NULL)
+ conn_listener = m_Service->m_Listener;
+
CNetServerExecHandler exec_handler(cmd, multiline_output,
exec_result, exec_listener, conn_listener);
@@ -753,8 +791,7 @@ void SNetServerInPool::CheckIfThrottled()
ResetThrottlingParameters();
return;
}
- NCBI_THROW(CNetSrvConnException, eServerThrottle,
- m_ThrottleMessage);
+ NCBI_THROW(CNetSrvConnException, eServerThrottle, m_ThrottleMessage);
}
if (m_ServerPool->m_MaxConsecutiveIOFailures > 0 &&
@@ -778,8 +815,7 @@ void SNetServerInPool::CheckIfThrottled()
if (m_Throttled) {
m_ThrottledUntil.SetCurrent();
m_ThrottledUntil.AddSecond(m_ServerPool->m_ServerThrottlePeriod);
- NCBI_THROW(CNetSrvConnException, eServerThrottle,
- m_ThrottleMessage);
+ NCBI_THROW(CNetSrvConnException, eServerThrottle, m_ThrottleMessage);
}
}
diff --git a/c++/src/connect/services/srv_connections_impl.hpp b/c++/src/connect/services/srv_connections_impl.hpp
index 7eb4af3..5723f5b 100644
--- a/c++/src/connect/services/srv_connections_impl.hpp
+++ b/c++/src/connect/services/srv_connections_impl.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES___SRV_CONNECTIONS_IMPL__HPP
#define CONNECT_SERVICES___SRV_CONNECTIONS_IMPL__HPP
-/* $Id: srv_connections_impl.hpp 447471 2014-09-25 20:59:33Z kazimird $
+/* $Id: srv_connections_impl.hpp 456051 2015-01-07 17:38:03Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -160,6 +160,7 @@ struct SNetServerInPool : public CObject
string m_ThrottleMessage;
CTime m_ThrottledUntil;
CFastMutex m_ThrottleLock;
+ Uint4 m_RankBase;
};
struct SNetServerInfoImpl : public CObject
diff --git a/c++/src/connect/services/timeline.hpp b/c++/src/connect/services/timeline.hpp
index 8c5420a..5c0eb5b 100644
--- a/c++/src/connect/services/timeline.hpp
+++ b/c++/src/connect/services/timeline.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__TIMELINE_HPP
#define CONNECT_SERVICES__TIMELINE_HPP
-/* $Id: timeline.hpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: timeline.hpp 470756 2015-06-18 17:19:13Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,14 +48,9 @@ public:
bool IsInTimeline() const {return m_Timeline != NULL;}
- bool IsInTimeline(CWorkerNodeTimeline_Base* timeline) const
- {
- return m_Timeline == timeline;
- }
-
void MoveTo(CWorkerNodeTimeline_Base* timeline);
- const CDeadline& GetTimeout() const {return m_Deadline;}
+ const CDeadline GetTimeout() const {return m_Deadline;}
void ResetTimeout(unsigned seconds)
{
@@ -67,6 +62,11 @@ public:
return m_Deadline.GetRemainingTime().IsZero();
}
+ CWorkerNodeTimelineEntry* GetNext() const
+ {
+ return m_Next;
+ }
+
private:
CWorkerNodeTimeline_Base* m_Timeline;
CWorkerNodeTimelineEntry* m_Prev;
@@ -175,6 +175,11 @@ public:
{
return TRefType(static_cast<TTimelineEntry*>(m_Head));
}
+ TRefType GetNext(TRefType ref) const
+ {
+ _ASSERT(ref);
+ return TRefType(static_cast<TTimelineEntry*>(ref->GetNext()));
+ }
void Shift(TRefType& ref)
{
CWorkerNodeTimelineEntry* head = DetachHead();
diff --git a/c++/src/connect/services/wn_cleanup.cpp b/c++/src/connect/services/wn_cleanup.cpp
index 843bcc9..a2f171e 100644
--- a/c++/src/connect/services/wn_cleanup.cpp
+++ b/c++/src/connect/services/wn_cleanup.cpp
@@ -1,4 +1,4 @@
-/* $Id: wn_cleanup.cpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: wn_cleanup.cpp 443514 2014-08-14 21:35:38Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/wn_cleanup.hpp b/c++/src/connect/services/wn_cleanup.hpp
index af9b51a..705d527 100644
--- a/c++/src/connect/services/wn_cleanup.hpp
+++ b/c++/src/connect/services/wn_cleanup.hpp
@@ -1,7 +1,7 @@
#ifndef CONNECT_SERVICES__WN_CLEANUP__HPP
#define CONNECT_SERVICES__WN_CLEANUP__HPP
-/* $Id: wn_cleanup.hpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: wn_cleanup.hpp 443514 2014-08-14 21:35:38Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/connect/services/wn_commit_thread.cpp b/c++/src/connect/services/wn_commit_thread.cpp
index 993ab5b..d470cb8 100644
--- a/c++/src/connect/services/wn_commit_thread.cpp
+++ b/c++/src/connect/services/wn_commit_thread.cpp
@@ -1,4 +1,4 @@
-/* $Id: wn_commit_thread.cpp 448239 2014-10-03 14:17:45Z kazimird $
+/* $Id: wn_commit_thread.cpp 470126 2015-06-11 14:18:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,6 +58,13 @@ static void s_TlsCleanup(IWorkerNodeJob* p_value, void* /* data */ )
/// @internal
static CStaticTls<IWorkerNodeJob> s_tls;
+CJobCommitterThread::CJobCommitterThread(SGridWorkerNodeImpl* worker_node) :
+ m_WorkerNode(worker_node),
+ m_Semaphore(0, 1),
+ m_ThreadName(worker_node->GetAppName() + "_cm")
+{
+}
+
CWorkerNodeJobContext CJobCommitterThread::AllocJobContext()
{
TFastMutexGuard mutex_lock(m_TimelineMutex);
@@ -76,7 +83,8 @@ CWorkerNodeJobContext CJobCommitterThread::AllocJobContext()
}
void CJobCommitterThread::RecycleJobContextAndCommitJob(
- SWorkerNodeJobContextImpl* job_context)
+ SWorkerNodeJobContextImpl* job_context,
+ CRequestContextSwitcher& rctx_switcher)
{
job_context->m_FirstCommitAttempt = true;
@@ -89,6 +97,9 @@ void CJobCommitterThread::RecycleJobContextAndCommitJob(
WakeUp();
m_ImmediateActions.Push(job_context);
+
+ // We must do it here, before m_TimelineMutex is unlocked
+ rctx_switcher.Release();
}
void CJobCommitterThread::Stop()
@@ -100,6 +111,7 @@ void CJobCommitterThread::Stop()
void* CJobCommitterThread::Main()
{
+ SetCurrentThreadName(m_ThreadName);
TFastMutexGuard mutex_lock(m_TimelineMutex);
do {
@@ -149,32 +161,32 @@ bool CJobCommitterThread::x_CommitJob(SWorkerNodeJobContextImpl* job_context)
bool recycle_job_context = false;
try {
- switch (job_context->m_JobCommitted) {
- case CWorkerNodeJobContext::eDone:
+ switch (job_context->m_JobCommitStatus) {
+ case CWorkerNodeJobContext::eCS_Done:
m_WorkerNode->m_NSExecutor.PutResult(job_context->m_Job);
break;
- case CWorkerNodeJobContext::eFailure:
+ case CWorkerNodeJobContext::eCS_Failure:
m_WorkerNode->m_NSExecutor.PutFailure(job_context->m_Job,
job_context->m_DisableRetries);
break;
- default: /* eNotCommitted: job registration error,
- e.g. too many jobs per client IP or
- session ID. Return the job. */
+ default: /* eCS_NotCommitted */
+ // In the unlikely event of eCS_NotCommitted, return the job.
+ /* FALL THROUGH */
- case CWorkerNodeJobContext::eReturn:
- m_WorkerNode->m_NSExecutor.ReturnJob(job_context->m_Job.job_id,
- job_context->m_Job.auth_token);
+ case CWorkerNodeJobContext::eCS_Return:
+ m_WorkerNode->m_NSExecutor.ReturnJob(job_context->m_Job);
break;
- case CWorkerNodeJobContext::eRescheduled:
+ case CWorkerNodeJobContext::eCS_Reschedule:
m_WorkerNode->m_NSExecutor.Reschedule(job_context->m_Job);
break;
- case CWorkerNodeJobContext::eCanceled:
- ERR_POST("Job " << job_context->m_Job.job_id <<
- " has been canceled");
+ case CWorkerNodeJobContext::eCS_JobIsLost:
+ // Job is cancelled or otherwise taken away from the worker
+ // node. Whatever the cause is, it has been reported already.
+ break;
}
recycle_job_context = true;
@@ -204,6 +216,8 @@ bool CJobCommitterThread::x_CommitJob(SWorkerNodeJobContextImpl* job_context)
}
}
+ m_WorkerNode->m_JobsInProgress.Remove(job_context->m_Job.job_id);
+
if (recycle_job_context)
job_context->x_PrintRequestStop();
diff --git a/c++/src/connect/services/wn_commit_thread.hpp b/c++/src/connect/services/wn_commit_thread.hpp
index 13f157f..4f827f3 100644
--- a/c++/src/connect/services/wn_commit_thread.hpp
+++ b/c++/src/connect/services/wn_commit_thread.hpp
@@ -2,7 +2,7 @@
#define WN_COMMIT_THREAD__HPP
-/* $Id: wn_commit_thread.hpp 447459 2014-09-25 20:43:06Z kazimird $
+/* $Id: wn_commit_thread.hpp 470126 2015-06-11 14:18:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,15 +45,25 @@ BEGIN_NCBI_SCOPE
class CRequestContextSwitcher
{
public:
+ CRequestContextSwitcher() {}
+
CRequestContextSwitcher(CRequestContext* new_request_context)
+ : m_SavedRequestContext(&CDiagContext::GetRequestContext())
{
- m_SavedRequestContext = &CDiagContext::GetRequestContext();
CDiagContext::SetRequestContext(new_request_context);
}
+ void Release()
+ {
+ if (m_SavedRequestContext) {
+ CDiagContext::SetRequestContext(m_SavedRequestContext);
+ m_SavedRequestContext.Reset();
+ }
+ }
+
~CRequestContextSwitcher()
{
- CDiagContext::SetRequestContext(m_SavedRequestContext);
+ Release();
}
private:
@@ -66,15 +76,12 @@ private:
class CJobCommitterThread : public CThread
{
public:
- CJobCommitterThread(SGridWorkerNodeImpl* worker_node) :
- m_WorkerNode(worker_node),
- m_Semaphore(0, 1)
- {
- }
+ CJobCommitterThread(SGridWorkerNodeImpl* worker_node);
CWorkerNodeJobContext AllocJobContext();
- void RecycleJobContextAndCommitJob(SWorkerNodeJobContextImpl* job_context);
+ void RecycleJobContextAndCommitJob(SWorkerNodeJobContextImpl* job_context,
+ CRequestContextSwitcher& rctx_switcher);
void Stop();
@@ -96,6 +103,7 @@ private:
CSemaphore m_Semaphore;
TCommitJobTimeline m_ImmediateActions, m_Timeline, m_JobContextPool;
CFastMutex m_TimelineMutex;
+ const string m_ThreadName;
typedef CGuard<CFastMutex, SSimpleUnlock<CFastMutex>,
SSimpleLock<CFastMutex> > TFastMutexUnlockGuard;
diff --git a/c++/src/connect/services/wn_main_loop.cpp b/c++/src/connect/services/wn_main_loop.cpp
index 566d485..74fb811 100644
--- a/c++/src/connect/services/wn_main_loop.cpp
+++ b/c++/src/connect/services/wn_main_loop.cpp
@@ -1,4 +1,4 @@
-/* $Id: wn_main_loop.cpp 452162 2014-11-17 15:23:48Z ivanov $
+/* $Id: wn_main_loop.cpp 470126 2015-06-11 14:18:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -100,18 +100,18 @@ unsigned int CWorkerNodeJobContext::GetJobNumber() const
bool CWorkerNodeJobContext::IsJobCommitted() const
{
- return m_Impl->m_JobCommitted != eNotCommitted;
+ return m_Impl->m_JobCommitStatus != eCS_NotCommitted;
}
CWorkerNodeJobContext::ECommitStatus
CWorkerNodeJobContext::GetCommitStatus() const
{
- return m_Impl->m_JobCommitted;
+ return m_Impl->m_JobCommitStatus;
}
-bool CWorkerNodeJobContext::IsCanceled() const
+bool CWorkerNodeJobContext::IsJobLost() const
{
- return m_Impl->m_JobCommitted == eCanceled;
+ return m_Impl->m_JobCommitStatus == eCS_JobIsLost;
}
IWorkerNodeCleanupEventSource* CWorkerNodeJobContext::GetCleanupEventSource()
@@ -188,30 +188,30 @@ void CWorkerNodeJobContext::CloseStreams()
void CWorkerNodeJobContext::CommitJob()
{
- m_Impl->CheckIfCanceled();
- m_Impl->m_JobCommitted = eDone;
+ m_Impl->CheckIfJobIsLost();
+ m_Impl->m_JobCommitStatus = eCS_Done;
}
void CWorkerNodeJobContext::CommitJobWithFailure(const string& err_msg,
bool no_retries)
{
- m_Impl->CheckIfCanceled();
- m_Impl->m_JobCommitted = eFailure;
+ m_Impl->CheckIfJobIsLost();
+ m_Impl->m_JobCommitStatus = eCS_Failure;
m_Impl->m_DisableRetries = no_retries;
m_Impl->m_Job.error_msg = err_msg;
}
void CWorkerNodeJobContext::ReturnJob()
{
- m_Impl->CheckIfCanceled();
- m_Impl->m_JobCommitted = eReturn;
+ m_Impl->CheckIfJobIsLost();
+ m_Impl->m_JobCommitStatus = eCS_Return;
}
void CWorkerNodeJobContext::RescheduleJob(
const string& affinity, const string& group)
{
- m_Impl->CheckIfCanceled();
- m_Impl->m_JobCommitted = eRescheduled;
+ m_Impl->CheckIfJobIsLost();
+ m_Impl->m_JobCommitStatus = eCS_Reschedule;
m_Impl->m_Job.affinity = affinity;
m_Impl->m_Job.group = group;
}
@@ -225,7 +225,7 @@ void CWorkerNodeJobContext::PutProgressMessage(const string& msg,
void SWorkerNodeJobContextImpl::PutProgressMessage(const string& msg,
bool send_immediately)
{
- CheckIfCanceled();
+ CheckIfJobIsLost();
if (!send_immediately &&
!m_ProgressMsgThrottler.Approve(CRequestRateControl::eErrCode)) {
LOG_POST(Warning << "Progress message \"" <<
@@ -261,13 +261,14 @@ void SWorkerNodeJobContextImpl::PutProgressMessage(const string& msg,
void CWorkerNodeJobContext::JobDelayExpiration(unsigned runtime_inc)
{
+ m_Impl->CheckIfJobIsLost();
m_Impl->JobDelayExpiration(runtime_inc);
}
void SWorkerNodeJobContextImpl::JobDelayExpiration(unsigned runtime_inc)
{
try {
- m_NetScheduleExecutor.JobDelayExpiration(m_Job.job_id, runtime_inc);
+ m_NetScheduleExecutor.JobDelayExpiration(m_Job, runtime_inc);
}
catch (exception& ex) {
ERR_POST_X(8, "CWorkerNodeJobContext::JobDelayExpiration: " <<
@@ -290,8 +291,9 @@ CNetScheduleAdmin::EShutdownLevel SWorkerNodeJobContextImpl::GetShutdownLevel()
if (m_StatusThrottler.Approve(CRequestRateControl::eErrCode))
try {
ENetScheduleQueuePauseMode pause_mode;
- switch (m_NetScheduleExecutor.GetJobStatus(m_Job.job_id,
- NULL, &pause_mode)) {
+ CNetScheduleAPI::EJobStatus job_status =
+ m_NetScheduleExecutor.GetJobStatus(m_Job, NULL, &pause_mode);
+ switch (job_status) {
case CNetScheduleAPI::eRunning:
if (pause_mode == eNSQ_WithPullback) {
m_WorkerNode->SetJobPullbackTimer(
@@ -300,13 +302,18 @@ CNetScheduleAdmin::EShutdownLevel SWorkerNodeJobContextImpl::GetShutdownLevel()
"(default) pullback timeout=" <<
m_WorkerNode->m_DefaultPullbackTimeout);
}
- break;
-
- case CNetScheduleAPI::eCanceled:
- x_SetCanceled();
/* FALL THROUGH */
+ case CNetScheduleAPI::ePending:
+ // NetSchedule will still allow to commit this job.
+ break;
+
default:
+ // The worker node does not "own" the job any longer.
+ ERR_POST("Cannot proceed with job processing: job '" <<
+ m_Job.job_id << "' changed status to '" <<
+ CNetScheduleAPI::StatusToString(job_status) << "'.");
+ MarkJobAsLost();
return CNetScheduleAdmin::eShutdownImmediate;
}
}
@@ -323,10 +330,10 @@ CNetScheduleAdmin::EShutdownLevel SWorkerNodeJobContextImpl::GetShutdownLevel()
return CGridGlobals::GetInstance().GetShutdownLevel();
}
-void SWorkerNodeJobContextImpl::CheckIfCanceled()
+void SWorkerNodeJobContextImpl::CheckIfJobIsLost()
{
- if (m_JobCommitted == CWorkerNodeJobContext::eCanceled) {
- NCBI_THROW_FMT(CGridWorkerNodeException, eJobIsCanceled,
+ if (m_JobCommitStatus == CWorkerNodeJobContext::eCS_JobIsLost) {
+ NCBI_THROW_FMT(CGridWorkerNodeException, eJobIsLost,
"Job " << m_Job.job_id << " has been canceled");
}
}
@@ -335,7 +342,7 @@ void SWorkerNodeJobContextImpl::ResetJobContext()
{
m_JobNumber = CGridGlobals::GetInstance().GetNewJobNumber();
- m_JobCommitted = CWorkerNodeJobContext::eNotCommitted;
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_NotCommitted;
m_DisableRetries = false;
m_InputBlobSize = 0;
m_ExclusiveJob =
@@ -359,16 +366,16 @@ const char* CWorkerNodeJobContext::GetCommitStatusDescription(
CWorkerNodeJobContext::ECommitStatus commit_status)
{
switch (commit_status) {
- case eDone:
+ case eCS_Done:
return "done";
- case eFailure:
+ case eCS_Failure:
return "failed";
- case eReturn:
+ case eCS_Return:
return "returned";
- case eRescheduled:
+ case eCS_Reschedule:
return "rescheduled";
- case eCanceled:
- return "canceled";
+ case eCS_JobIsLost:
+ return "lost";
default:
return "not committed";
}
@@ -380,7 +387,7 @@ void SWorkerNodeJobContextImpl::x_PrintRequestStop()
if (!m_RequestContext->IsSetRequestStatus())
m_RequestContext->SetRequestStatus(
- m_JobCommitted == CWorkerNodeJobContext::eDone &&
+ m_JobCommitStatus == CWorkerNodeJobContext::eCS_Done &&
m_Job.ret_code == 0 ? 200 : 500);
if (m_RequestContext->GetAppState() == eDiagAppState_Request)
@@ -422,14 +429,14 @@ void SWorkerNodeJobContextImpl::x_RunJob()
ERR_POST("Too many jobs with client IP \"" <<
m_Job.client_ip << "\"; job " <<
m_Job.job_id << " will be returned.");
- m_JobCommitted = CWorkerNodeJobContext::eReturn;
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Return;
} else if (!m_Job.session_id.empty() &&
!m_WorkerNode->m_JobsPerSessionID.CountJob(m_Job.session_id,
&session_id_registration)) {
ERR_POST("Too many jobs with session ID \"" <<
m_Job.session_id << "\"; job " <<
m_Job.job_id << " will be returned.");
- m_JobCommitted = CWorkerNodeJobContext::eReturn;
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Return;
} else {
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobStarted);
@@ -440,8 +447,7 @@ void SWorkerNodeJobContextImpl::x_RunJob()
}
catch (CGridWorkerNodeException& ex) {
switch (ex.GetErrCode()) {
- case CGridWorkerNodeException::eJobIsCanceled:
- m_JobCommitted = CWorkerNodeJobContext::eCanceled;
+ case CGridWorkerNodeException::eJobIsLost:
break;
case CGridWorkerNodeException::eExclusiveModeIsAlreadySet:
@@ -451,71 +457,77 @@ void SWorkerNodeJobContextImpl::x_RunJob()
"because it requested exclusive mode while "
"another exclusive job is already running.");
}
- if (m_JobCommitted == CWorkerNodeJobContext::eNotCommitted)
- m_JobCommitted = CWorkerNodeJobContext::eReturn;
+ if (m_JobCommitStatus ==
+ CWorkerNodeJobContext::eCS_NotCommitted)
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Return;
break;
default:
ERR_POST_X(62, ex);
- if (m_JobCommitted == CWorkerNodeJobContext::eNotCommitted)
- m_JobCommitted = CWorkerNodeJobContext::eReturn;
+ if (m_JobCommitStatus ==
+ CWorkerNodeJobContext::eCS_NotCommitted)
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Return;
}
}
catch (CNetScheduleException& e) {
ERR_POST_X(20, "job " << m_Job.job_id << " failed: " << e);
- if (e.GetErrCode() == CNetScheduleException::eJobNotFound)
- m_JobCommitted = CWorkerNodeJobContext::eCanceled;
- else if (m_JobCommitted == CWorkerNodeJobContext::eNotCommitted) {
- m_JobCommitted = CWorkerNodeJobContext::eFailure;
+ if (e.GetErrCode() == CNetScheduleException::eJobNotFound) {
+ ERR_POST("Cannot proceed with job processing: job '" <<
+ m_Job.job_id << "' has expired.");
+ MarkJobAsLost();
+ } else if (m_JobCommitStatus ==
+ CWorkerNodeJobContext::eCS_NotCommitted) {
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Failure;
m_Job.error_msg = e.what();
}
}
catch (exception& e) {
ERR_POST_X(18, "job " << m_Job.job_id << " failed: " << e.what());
- if (m_JobCommitted == CWorkerNodeJobContext::eNotCommitted) {
- m_JobCommitted = CWorkerNodeJobContext::eFailure;
+ if (m_JobCommitStatus == CWorkerNodeJobContext::eCS_NotCommitted) {
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Failure;
m_Job.error_msg = e.what();
}
}
this_job_context.CloseStreams();
- switch (m_JobCommitted) {
- case CWorkerNodeJobContext::eDone:
+ switch (m_JobCommitStatus) {
+ case CWorkerNodeJobContext::eCS_Done:
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobSucceeded);
break;
- case CWorkerNodeJobContext::eNotCommitted:
+ case CWorkerNodeJobContext::eCS_NotCommitted:
if (TWorkerNode_AllowImplicitJobReturn::GetDefault() ||
this_job_context.GetShutdownLevel() !=
CNetScheduleAdmin::eNoShutdown) {
- m_JobCommitted = CWorkerNodeJobContext::eReturn;
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Return;
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobReturned);
break;
}
- m_JobCommitted = CWorkerNodeJobContext::eFailure;
+ m_JobCommitStatus = CWorkerNodeJobContext::eCS_Failure;
m_Job.error_msg = "Job was not explicitly committed";
/* FALL THROUGH */
- case CWorkerNodeJobContext::eFailure:
+ case CWorkerNodeJobContext::eCS_Failure:
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobFailed);
break;
- case CWorkerNodeJobContext::eReturn:
+ case CWorkerNodeJobContext::eCS_Return:
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobReturned);
break;
- case CWorkerNodeJobContext::eRescheduled:
+ case CWorkerNodeJobContext::eCS_Reschedule:
m_WorkerNode->x_NotifyJobWatchers(this_job_context,
IWorkerNodeJobWatcher::eJobRescheduled);
break;
- default: // eCanceled - will be processed in x_SendJobResults().
+ default: // eCanceled - no action needed.
+ // This object will be recycled in x_CommitJob().
break;
}
@@ -529,17 +541,20 @@ void SWorkerNodeJobContextImpl::x_RunJob()
if (!CGridGlobals::GetInstance().IsShuttingDown())
m_CleanupEventSource->CallEventHandlers();
- m_WorkerNode->m_JobCommitterThread->RecycleJobContextAndCommitJob(this);
+ m_WorkerNode->m_JobCommitterThread->RecycleJobContextAndCommitJob(this,
+ request_state_guard);
}
void* CMainLoopThread::Main()
{
+ SetCurrentThreadName(m_ThreadName);
CDeadline max_wait_for_servers(
TWorkerNode_MaxWaitForServers::GetDefault());
CWorkerNodeJobContext job_context(
m_WorkerNode->m_JobCommitterThread->AllocJobContext());
+ CRequestContextSwitcher no_op;
unsigned try_count = 0;
while (!CGridGlobals::GetInstance().IsShuttingDown()) {
try {
@@ -563,10 +578,10 @@ void* CMainLoopThread::Main()
ERR_POST_X(28, ex);
// that must not happen after CBlockingQueue is fixed
_ASSERT(0);
- job_context->m_JobCommitted =
- CWorkerNodeJobContext::eReturn;
+ job_context->m_JobCommitStatus =
+ CWorkerNodeJobContext::eCS_Return;
m_WorkerNode->m_JobCommitterThread->
- RecycleJobContextAndCommitJob(job_context);
+ RecycleJobContextAndCommitJob(job_context, no_op);
}
job_context =
m_WorkerNode->m_JobCommitterThread->AllocJobContext();
@@ -607,81 +622,41 @@ void* CMainLoopThread::Main()
return NULL;
}
-CMainLoopThread::~CMainLoopThread()
-{
- ITERATE(TTimelineEntries, it, m_TimelineEntryByAddress) {
- (*it)->RemoveReference();
- }
-}
-
-SNotificationTimelineEntry*
- CMainLoopThread::x_GetTimelineEntry(SNetServerImpl* server_impl)
-{
- SNotificationTimelineEntry search_pattern(
- server_impl->m_ServerInPool->m_Address, 0);
-
- TTimelineEntries::iterator it(
- m_TimelineEntryByAddress.find(&search_pattern));
-
- if (it != m_TimelineEntryByAddress.end())
- return *it;
-
- SNotificationTimelineEntry* new_entry = new SNotificationTimelineEntry(
- search_pattern.m_ServerAddress, m_DiscoveryIteration);
-
- m_TimelineEntryByAddress.insert(new_entry);
- new_entry->AddReference();
-
- return new_entry;
-}
-
bool CMainLoopThread::x_PerformTimelineAction(
- CMainLoopThread::TNotificationTimeline& timeline, CNetScheduleJob& job)
+ CServerTimeline::TEntryRef timeline_entry, CNetScheduleJob& job)
{
- SNotificationTimelineEntry::TRef timeline_entry;
-
- timeline.Shift(timeline_entry);
-
- if (timeline_entry->IsDiscoveryAction()) {
+ if (m_Timeline.IsDiscoveryAction(timeline_entry)) {
if (!x_EnterSuspendedState()) {
- ++m_DiscoveryIteration;
- for (CNetServiceIterator it =
- m_WorkerNode->m_NetScheduleAPI.GetService().Iterate(
- CNetService::eIncludePenalized); it; ++it) {
- SNotificationTimelineEntry* srv_entry = x_GetTimelineEntry(*it);
- srv_entry->m_DiscoveryIteration = m_DiscoveryIteration;
- if (!srv_entry->IsInTimeline())
- m_ImmediateActions.Push(srv_entry);
- }
+ m_Timeline.NextDiscoveryIteration(m_WorkerNode->m_NetScheduleAPI);
}
timeline_entry->ResetTimeout(m_WorkerNode->m_NSTimeout);
- m_Timeline.Push(timeline_entry);
+ m_Timeline.PushScheduledAction(timeline_entry);
return false;
}
if (x_EnterSuspendedState() ||
// Skip servers that disappeared from LBSM.
- timeline_entry->m_DiscoveryIteration != m_DiscoveryIteration)
+ m_Timeline.IsOutdatedAction(timeline_entry))
return false;
- CNetServer server(m_WorkerNode->m_NetScheduleAPI->m_Service.GetServer(
- timeline_entry->m_ServerAddress));
+ CNetServer server(m_Timeline.GetServer(m_WorkerNode->m_NetScheduleAPI,
+ timeline_entry));
timeline_entry->ResetTimeout(m_WorkerNode->m_NSTimeout);
try {
if (m_WorkerNode->m_NSExecutor->x_GetJobWithAffinityLadder(server,
- &timeline_entry->GetTimeout(), job)) {
+ m_WorkerNode->m_NSTimeout, job)) {
// A job has been returned; add the server to
- // m_ImmediateActions because there can be more
+ // immediate actions because there can be more
// jobs in the queue.
- m_ImmediateActions.Push(timeline_entry);
+ m_Timeline.PushImmediateAction(timeline_entry);
return true;
} else {
// No job has been returned by this server;
// query the server later.
- m_Timeline.Push(timeline_entry);
+ m_Timeline.PushScheduledAction(timeline_entry);
return false;
}
}
@@ -706,16 +681,13 @@ bool CMainLoopThread::x_EnterSuspendedState()
if (!m_WorkerNode->m_TimelineIsSuspended) {
// Stop the timeline.
m_WorkerNode->m_TimelineIsSuspended = true;
- m_ImmediateActions.Clear();
- m_Timeline.Clear();
- m_DiscoveryAction->ResetTimeout(m_WorkerNode->m_NSTimeout);
- m_Timeline.Push(m_DiscoveryAction);
+ m_Timeline.Suspend(m_WorkerNode->m_NSTimeout);
}
} else { /* event == RESUME_EVENT */
if (m_WorkerNode->m_TimelineIsSuspended) {
// Resume the timeline.
m_WorkerNode->m_TimelineIsSuspended = false;
- m_DiscoveryAction->MoveTo(&m_ImmediateActions);
+ m_Timeline.Resume();
}
}
}
@@ -731,19 +703,18 @@ void CMainLoopThread::x_ProcessRequestJobNotification()
if (m_WorkerNode->m_NSExecutor->
m_NotificationHandler.CheckRequestJobNotification(
m_WorkerNode->m_NSExecutor, &server))
- x_GetTimelineEntry(server)->MoveTo(&m_ImmediateActions);
+ m_Timeline.MoveToImmediateActions(server);
}
}
bool CMainLoopThread::x_WaitForNewJob(CNetScheduleJob& job)
{
for (;;) {
- while (!m_ImmediateActions.IsEmpty()) {
- if (x_PerformTimelineAction(m_ImmediateActions, job))
+ while (m_Timeline.HasImmediateActions()) {
+ if (x_PerformTimelineAction(m_Timeline.PullImmediateAction(), job))
return true;
- while (!m_Timeline.IsEmpty() && m_Timeline.GetHead()->TimeHasCome())
- m_Timeline.MoveHeadTo(&m_ImmediateActions);
+ m_Timeline.CheckScheduledActions();
// Check if there's a notification in the UDP socket.
while (m_WorkerNode->m_NSExecutor->
@@ -754,12 +725,13 @@ bool CMainLoopThread::x_WaitForNewJob(CNetScheduleJob& job)
if (CGridGlobals::GetInstance().IsShuttingDown())
return false;
- if (!m_Timeline.IsEmpty()) {
+ if (m_Timeline.HasScheduledActions()) {
if (m_WorkerNode->m_NSExecutor->
m_NotificationHandler.WaitForNotification(
- m_Timeline.GetHead()->GetTimeout()))
+ m_Timeline.GetNextTimeout()))
x_ProcessRequestJobNotification();
- else if (x_PerformTimelineAction(m_Timeline, job))
+ else if (x_PerformTimelineAction(
+ m_Timeline.PullScheduledAction(), job))
return true;
}
}
@@ -775,24 +747,29 @@ bool CMainLoopThread::x_GetNextJob(CNetScheduleJob& job)
if (!m_WorkerNode->WaitForExclusiveJobToFinish())
return false;
- bool job_exists = x_WaitForNewJob(job);
+ if (!x_WaitForNewJob(job)) {
+ return false;
+ }
+
+ // Already executing this job, so do nothing
+ // (and rely on that execution to report its result later)
+ if (!m_WorkerNode->m_JobsInProgress.Add(job.job_id)) {
+ return false;
+ }
- if (job_exists && job.mask & CNetScheduleAPI::eExclusiveJob) {
+ if (job.mask & CNetScheduleAPI::eExclusiveJob) {
if (!m_WorkerNode->EnterExclusiveMode()) {
- x_ReturnJob(job);
- job_exists = false;
+ m_WorkerNode->m_NSExecutor.ReturnJob(job);
+ return false;
}
}
- if (job_exists && x_EnterSuspendedState()) {
- x_ReturnJob(job);
+
+ if (x_EnterSuspendedState()) {
+ m_WorkerNode->m_NSExecutor.ReturnJob(job);
return false;
}
- return job_exists;
-}
-void CMainLoopThread::x_ReturnJob(const CNetScheduleJob& job)
-{
- m_WorkerNode->m_NSExecutor.ReturnJob(job.job_id, job.auth_token);
+ return true;
}
size_t CGridWorkerNode::GetServerOutputSize()
diff --git a/c++/src/connect/services/wn_offline_mode.cpp b/c++/src/connect/services/wn_offline_mode.cpp
index 42fcb24..b77bd29 100644
--- a/c++/src/connect/services/wn_offline_mode.cpp
+++ b/c++/src/connect/services/wn_offline_mode.cpp
@@ -1,4 +1,4 @@
-/* $Id: wn_offline_mode.cpp 452164 2014-11-17 15:24:25Z ivanov $
+/* $Id: wn_offline_mode.cpp 455687 2015-01-02 17:47:12Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -108,8 +108,8 @@ void SOfflineJobContextImpl::x_RunJob()
}
catch (CGridWorkerNodeException& ex) {
switch (ex.GetErrCode()) {
- case CGridWorkerNodeException::eJobIsCanceled:
- x_SetCanceled();
+ case CGridWorkerNodeException::eJobIsLost:
+ ERR_POST(ex);
break;
case CGridWorkerNodeException::eExclusiveModeIsAlreadySet:
@@ -145,22 +145,23 @@ void SOfflineJobContextImpl::x_RunJob()
CNetScheduleJobSerializer job_serializer(m_Job, m_CompoundIDPool);
switch (this_job_context.GetCommitStatus()) {
- case CWorkerNodeJobContext::eDone:
+ case CWorkerNodeJobContext::eCS_Done:
job_serializer.SaveJobOutput(CNetScheduleAPI::eDone,
m_OutputDirName, m_NetCacheAPI);
break;
- case CWorkerNodeJobContext::eNotCommitted:
+ case CWorkerNodeJobContext::eCS_NotCommitted:
this_job_context.CommitJobWithFailure(
"Job was not explicitly committed");
/* FALL THROUGH */
- case CWorkerNodeJobContext::eFailure:
+ case CWorkerNodeJobContext::eCS_Failure:
job_serializer.SaveJobOutput(CNetScheduleAPI::eFailed,
m_OutputDirName, m_NetCacheAPI);
break;
- default: // eReturn, eRescheduled, eCanceled - results won't be saved
+ default: /* eCS_Return, eCS_Rescheduled, etc. */
+ // No job results to save.
break;
}
}
diff --git a/c++/src/corelib/Makefile.corelib.lib b/c++/src/corelib/Makefile.corelib.lib
index 8b0cf31..d3e5317 100644
--- a/c++/src/corelib/Makefile.corelib.lib
+++ b/c++/src/corelib/Makefile.corelib.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.corelib.lib 436308 2014-05-27 15:45:33Z grichenk $
+# $Id: Makefile.corelib.lib 477845 2015-09-02 13:12:10Z ivanov $
SRC = $(ncbicntr) blob_storage ddumpable env_reg metareg ncbi_config \
ncbi_param ncbi_process ncbi_safe_static ncbi_signal ncbi_stack \
@@ -8,7 +8,7 @@ SRC = $(ncbicntr) blob_storage ddumpable env_reg metareg ncbi_config \
plugin_manager plugin_manager_store rwstreambuf stream_utils \
syslog version request_ctx request_control expr ncbi_strings \
resource_info interprocess_lock ncbi_autoinit perf_log ncbi_toolkit \
- ncbierror ncbi_url ncbi_cookies
+ ncbierror ncbi_url ncbi_cookies guard ncbi_message
UNIX_SRC = ncbi_os_unix
diff --git a/c++/src/corelib/blob_storage.cpp b/c++/src/corelib/blob_storage.cpp
index 888d502..2028a30 100644
--- a/c++/src/corelib/blob_storage.cpp
+++ b/c++/src/corelib/blob_storage.cpp
@@ -1,4 +1,4 @@
-/* $Id: blob_storage.cpp 112029 2007-10-10 18:46:30Z ivanovp $
+/* $Id: blob_storage.cpp 460958 2015-03-04 17:53:33Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -107,7 +107,7 @@ IBlobStorage* CBlobStorageFactory::CreateInstance()
);
} catch (CPluginManagerException& ex) {
if (ex.GetErrCode() == CPluginManagerException::eResolveFailure) {
- LOG_POST_X(1, Warning << ex);
+ ERR_POST_X(1, Warning << ex);
} else if (ex.GetErrCode() == CPluginManagerException::eNullInstance) {
} else {
throw;
diff --git a/c++/src/corelib/env_reg.cpp b/c++/src/corelib/env_reg.cpp
index 865d077..0db400b 100644
--- a/c++/src/corelib/env_reg.cpp
+++ b/c++/src/corelib/env_reg.cpp
@@ -1,4 +1,4 @@
-/* $Id: env_reg.cpp 449004 2014-10-10 13:46:25Z ucko $
+/* $Id: env_reg.cpp 478281 2015-09-08 14:34:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -122,17 +122,27 @@ const string& CEnvironmentRegistry::x_Get(const string& section,
const string& name,
TFlags flags) const
{
+ bool found;
+ return x_Get(section, name, flags, found);
+}
+
+
+const string& CEnvironmentRegistry::x_Get(const string& section,
+ const string& name,
+ TFlags flags,
+ bool& found) const
+{
if ((flags & fTPFlags) == fPersistent) {
return kEmptyStr;
}
REVERSE_ITERATE (TPriorityMap, it, m_PriorityMap) {
string var_name = it->second->RegToEnv(section, name);
- const string* resultp = &m_Env->Get(var_name);
- if ((m_Flags & fCaseFlags) == 0 && resultp->empty()) {
+ const string* resultp = &m_Env->Get(var_name, &found);
+ if ((m_Flags & fCaseFlags) == 0 && !found) {
// try capitalizing the name
resultp = &m_Env->Get(NStr::ToUpper(var_name));
}
- if ( !resultp->empty() ) {
+ if (found) {
return *resultp;
}
}
@@ -144,7 +154,9 @@ bool CEnvironmentRegistry::x_HasEntry(const string& section,
const string& name,
TFlags flags) const
{
- return &x_Get(section, name, flags) != &kEmptyStr;
+ bool found = false;
+ x_Get(section, name, flags, found);
+ return found;
}
diff --git a/c++/src/objects/seqtable/Scaled_int_multi_data.cpp b/c++/src/corelib/guard.cpp
similarity index 72%
copy from c++/src/objects/seqtable/Scaled_int_multi_data.cpp
copy to c++/src/corelib/guard.cpp
index 567ae92..761c481 100644
--- a/c++/src/objects/seqtable/Scaled_int_multi_data.cpp
+++ b/c++/src/corelib/guard.cpp
@@ -1,4 +1,4 @@
-/* $Id: Scaled_int_multi_data.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: guard.cpp 451479 2014-11-06 19:47:51Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -23,35 +23,32 @@
*
* ===========================================================================
*
- * Author: .......
+ * Authors: Aleksey Grichenko
*
* File Description:
- * .......
+ * CGuard<> -- implementation of RAII-based locking guard
*
- * Remark:
- * This code was originally generated by application DATATOOL
- * using the following specifications:
- * 'seqtable.asn'.
*/
-// standard includes
-#include <ncbi_pch.hpp>
-// generated includes
-#include <objects/seqtable/Scaled_int_multi_data.hpp>
+#include <ncbi_pch.hpp>
+#include <corelib/guard.hpp>
+#include <corelib/ncbiexpt.hpp>
-// generated classes
BEGIN_NCBI_SCOPE
-BEGIN_objects_SCOPE // namespace ncbi::objects::
-// destructor
-CScaled_int_multi_data::~CScaled_int_multi_data(void)
+void CGuard_Base::ReportException(std::exception& ex)
{
+ CException* ncbi_ex = dynamic_cast<CException*>(&ex);
+ if ( ncbi_ex ) {
+ ERR_POST(Error << "CGuard::~CGuard(): error on release: " << *ncbi_ex);
+ }
+ else {
+ ERR_POST(Error << "CGuard::~CGuard(): error on release: " << ex.what());
+ }
}
-END_objects_SCOPE // namespace ncbi::objects::
-
END_NCBI_SCOPE
diff --git a/c++/src/corelib/metareg.cpp b/c++/src/corelib/metareg.cpp
index eb9bdd8..7130dda 100644
--- a/c++/src/corelib/metareg.cpp
+++ b/c++/src/corelib/metareg.cpp
@@ -1,4 +1,4 @@
-/* $Id: metareg.cpp 414956 2013-09-27 19:50:21Z ucko $
+/* $Id: metareg.cpp 450825 2014-10-30 18:31:55Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -355,6 +355,7 @@ void CMetaRegistry::GetDefaultSearchPath(CMetaRegistry::TSearchPath& path)
#endif
{{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* the_app = CNcbiApplication::Instance();
if ( the_app ) {
const CNcbiArguments& args = the_app->GetArguments();
diff --git a/c++/src/corelib/ncbi_application.xsd b/c++/src/corelib/ncbi_application.xsd
index 35e57ed..baa0f79 100644
--- a/c++/src/corelib/ncbi_application.xsd
+++ b/c++/src/corelib/ncbi_application.xsd
@@ -9,7 +9,7 @@
<xs:annotation>
<xs:documentation>
- $Id: ncbi_application.xsd 427970 2014-02-26 15:21:03Z gouriano $
+ $Id: ncbi_application.xsd 460139 2015-02-25 13:49:33Z gouriano $
===========================================================================
PUBLIC DOMAIN NOTICE
@@ -203,6 +203,7 @@
<xs:element name="createPath" minOccurs="0"/>
<xs:element name="optionalSeparatorAllowConflict" minOccurs="0"/>
<xs:element name="hidden" minOccurs="0"/>
+ <xs:element name="confidential" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:element>
diff --git a/c++/src/corelib/ncbi_autoinit.cpp b/c++/src/corelib/ncbi_autoinit.cpp
index cd6d871..aba6bd9 100644
--- a/c++/src/corelib/ncbi_autoinit.cpp
+++ b/c++/src/corelib/ncbi_autoinit.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_autoinit.cpp 177049 2009-11-24 20:50:12Z grichenk $
+/* $Id: ncbi_autoinit.cpp 478278 2015-09-08 14:32:54Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -64,4 +64,11 @@ CAutoInitPtr_Base::~CAutoInitPtr_Base(void)
}
+void CAutoInitPtr_Base::AssertUninitialized(void) const
+{
+ NCBI_ASSERT(!m_Ptr,
+ "Multiple CAutoInitPtr_Base initializations are not allowed.");
+}
+
+
END_NCBI_SCOPE
diff --git a/c++/src/corelib/ncbi_config.cpp b/c++/src/corelib/ncbi_config.cpp
index e6843e8..0a71853 100644
--- a/c++/src/corelib/ncbi_config.cpp
+++ b/c++/src/corelib/ncbi_config.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_config.cpp 214664 2010-12-07 17:49:09Z gouriano $
+/* $Id: ncbi_config.cpp 449355 2014-10-15 20:21:49Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -471,7 +471,7 @@ const string& CConfig::x_GetString(const string& driver_name,
NCBI_THROW(CConfigException, eParameterMissing, msg);
}
if (tns.size() > 1 ) {
- string msg = "There are more then 1 synonyms paramters (";
+ string msg = "There are more then 1 synonyms parameters (";
ITERATE(list<const TParamTree*>, it, tns) {
if (it != tns.begin()) msg += ", ";
msg += (*it)->GetKey();
@@ -655,6 +655,7 @@ const char* CConfigException::GetErrCodeString(void) const
switch (GetErrCode()) {
case eParameterMissing: return "eParameterMissing";
case eSynonymDuplicate: return "eSynonymDuplicate";
+ case eInvalidParameter: return "eInvalidParameter";
default: return CException::GetErrCodeString();
}
}
diff --git a/c++/src/corelib/ncbi_message.cpp b/c++/src/corelib/ncbi_message.cpp
new file mode 100644
index 0000000..e495dbc
--- /dev/null
+++ b/c++/src/corelib/ncbi_message.cpp
@@ -0,0 +1,311 @@
+/* $Id: ncbi_message.cpp 477857 2015-09-02 13:15:07Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Authors: Aleksey Grichenko
+ *
+ * File Description: IMessage/IMessageListener implementation
+ *
+ */
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbi_message.hpp>
+#include <corelib/ncbithr.hpp>
+#include <corelib/error_codes.hpp>
+#include <stdlib.h>
+#include <list>
+
+#define NCBI_USE_ERRCODE_X Corelib_Message
+
+BEGIN_NCBI_SCOPE
+
+
+CMessageListener_Stack::CMessageListener_Stack(void)
+{
+}
+
+
+size_t CMessageListener_Stack::PushListener(IMessageListener& listener,
+ IMessageListener::EListenFlag flag)
+{
+ m_Stack.push_front(SListenerNode(listener, flag));
+ return m_Stack.size();
+}
+
+
+void CMessageListener_Stack::PopListener(size_t depth)
+{
+ size_t sz = m_Stack.size();
+ if (depth == 0) depth = sz;
+ if (m_Stack.empty() || sz < depth) {
+ // Nothing to pop.
+ ERR_POST_X_ONCE(1, Warning <<
+ "Unbalanced PushListener/PopListener calls: "
+ "listener index " << depth << " has been already removed");
+ return;
+ }
+ if (sz > depth) {
+ // Report lost listeners.
+ ERR_POST_X_ONCE(2, Warning <<
+ "Unbalanced PushListener/PopListener calls: "
+ "removing " << sz - depth << " lost listeners");
+ }
+ while (m_Stack.size() >= depth) {
+ m_Stack.pop_front();
+ }
+}
+
+
+bool CMessageListener_Stack::HaveListeners(void)
+{
+ return !m_Stack.empty();
+}
+
+
+IMessageListener::EPostResult
+CMessageListener_Stack::Post(const IMessage& message)
+{
+ IMessageListener::EPostResult ret = IMessageListener::eUnhandled;
+ NON_CONST_ITERATE(TListenerStack, it, m_Stack) {
+ if (ret == IMessageListener::eHandled &&
+ it->m_Flag == IMessageListener::eListen_Unhandled) continue;
+ if (it->m_Listener->PostMessage(message) == IMessageListener::eHandled) {
+ ret = IMessageListener::eHandled;
+ }
+ }
+ return ret;
+}
+
+
+IMessageListener::EPostResult
+CMessageListener_Stack::Post(const IProgressMessage& progress)
+{
+ IMessageListener::EPostResult ret = IMessageListener::eUnhandled;
+ NON_CONST_ITERATE(TListenerStack, it, m_Stack) {
+ if (ret == IMessageListener::eHandled &&
+ it->m_Flag == IMessageListener::eListen_Unhandled) continue;
+ if (it->m_Listener->PostProgress(progress) == IMessageListener::eHandled) {
+ ret = IMessageListener::eHandled;
+ }
+ }
+ return ret;
+}
+
+
+void s_ListenerStackCleanup(CMessageListener_Stack* value,
+ void* /*cleanup_data*/)
+{
+ if ( !value ) return;
+ delete value;
+}
+
+
+static CStaticTls<CMessageListener_Stack> s_Listeners;
+
+
+CMessageListener_Stack& s_GetListenerStack(void)
+{
+ CMessageListener_Stack* ls = s_Listeners.GetValue();
+ if ( !ls ) {
+ ls = new CMessageListener_Stack;
+ s_Listeners.SetValue(ls, s_ListenerStackCleanup);
+ }
+ _ASSERT(ls);
+ return *ls;
+}
+
+size_t IMessageListener::PushListener(IMessageListener& listener,
+ EListenFlag flag)
+{
+ CMessageListener_Stack& ls = s_GetListenerStack();
+ return ls.PushListener(listener, flag);
+}
+
+
+void IMessageListener::PopListener(size_t depth)
+{
+ CMessageListener_Stack& ls = s_GetListenerStack();
+ return ls.PopListener(depth);
+}
+
+
+bool IMessageListener::HaveListeners(void)
+{
+ return s_GetListenerStack().HaveListeners();
+}
+
+
+IMessageListener::EPostResult
+IMessageListener::Post(const IMessage& message)
+{
+ return s_GetListenerStack().Post(message);
+}
+
+
+IMessageListener::EPostResult
+IMessageListener::Post(const IProgressMessage& progress)
+{
+ return s_GetListenerStack().Post(progress);
+}
+
+
+CMessage_Basic::CMessage_Basic(const string& txt,
+ EDiagSev sev,
+ int err_code,
+ int sub_code)
+ : m_Text(txt),
+ m_Severity(sev),
+ m_ErrCode(err_code),
+ m_SubCode(sub_code)
+{
+}
+
+
+string CMessage_Basic::GetText(void) const
+{
+ return m_Text;
+}
+
+
+EDiagSev CMessage_Basic::GetSeverity(void) const
+{
+ return m_Severity;
+}
+
+
+int CMessage_Basic::GetCode(void) const
+{
+ return m_ErrCode;
+}
+
+
+int CMessage_Basic::GetSubCode(void) const
+{
+ return m_SubCode;
+}
+
+
+IMessage* CMessage_Basic::Clone(void) const
+{
+ return new CMessage_Basic(*this);
+}
+
+
+void CMessage_Basic::Write(CNcbiOstream& out) const
+{
+ out << CNcbiDiag::SeverityName(GetSeverity()) << ": " << GetText() << endl;
+}
+
+
+string CMessage_Basic::Compose(void) const
+{
+ CNcbiOstrstream out;
+ Write(out);
+ return CNcbiOstrstreamToString(out);
+}
+
+
+CProgressMessage_Basic::CProgressMessage_Basic(const string& txt,
+ Uint8 current,
+ Uint8 total)
+ : m_Text(txt),
+ m_Current(current),
+ m_Total(total)
+{
+}
+
+
+string CProgressMessage_Basic::GetText(void) const
+{
+ return m_Text;
+}
+
+
+Uint8 CProgressMessage_Basic::GetCurrent(void) const
+{
+ return m_Current;
+}
+
+
+Uint8 CProgressMessage_Basic::GetTotal(void) const
+{
+ return m_Total;
+}
+
+
+CProgressMessage_Basic* CProgressMessage_Basic::Clone(void) const
+{
+ return new CProgressMessage_Basic(*this);
+}
+
+
+void CProgressMessage_Basic::Write(CNcbiOstream& out) const
+{
+ out << GetText() << " [" << m_Current << "/" << m_Total << "]" << endl;
+}
+
+
+string CProgressMessage_Basic::Compose(void) const
+{
+ CNcbiOstrstream out;
+ Write(out);
+ return CNcbiOstrstreamToString(out);
+}
+
+
+IMessageListener::EPostResult
+CMessageListener_Basic::PostMessage(const IMessage& message)
+{
+ m_Messages.push_back(AutoPtr<IMessage>(message.Clone()));
+ return eHandled;
+}
+
+
+IMessageListener::EPostResult
+CMessageListener_Basic::PostProgress(const IProgressMessage& progress)
+{
+ ERR_POST(Note << progress);
+ return eHandled;
+}
+
+
+const IMessage& CMessageListener_Basic::GetMessage(size_t index) const
+{
+ return *m_Messages[index].get();
+}
+
+
+size_t CMessageListener_Basic::Count(void) const
+{
+ return m_Messages.size();
+}
+
+
+void CMessageListener_Basic::Clear(void)
+{
+ m_Messages.clear();
+}
+
+
+END_NCBI_SCOPE
diff --git a/c++/src/corelib/ncbi_os_unix_p.hpp b/c++/src/corelib/ncbi_os_unix_p.hpp
index a40b7bc..8dada8e 100644
--- a/c++/src/corelib/ncbi_os_unix_p.hpp
+++ b/c++/src/corelib/ncbi_os_unix_p.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBI_OS_UNIX_P__HPP
#define CORELIB___NCBI_OS_UNIX_P__HPP
-/* $Id: ncbi_os_unix_p.hpp 425984 2014-02-05 03:53:01Z lavr $
+/* $Id: ncbi_os_unix_p.hpp 458482 2015-02-05 15:48:25Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,7 +38,7 @@
#include <ncbiconf.h>
#if !defined(NCBI_OS_UNIX)
-# error "ncbi_os_mswin_p.hpp can be used on MS Windows platforms only"
+# error "ncbi_os_unix_p.hpp can be used on UNIX platforms only"
#endif
#include <string>
diff --git a/c++/src/corelib/ncbi_param.cpp b/c++/src/corelib/ncbi_param.cpp
index f3244c8..f585f0b 100644
--- a/c++/src/corelib/ncbi_param.cpp
+++ b/c++/src/corelib/ncbi_param.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_param.cpp 468792 2015-05-28 14:18:49Z grichenk $
+/* $Id: ncbi_param.cpp 468199 2015-05-21 13:10:41Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -112,7 +112,7 @@ namespace {
#define DUMP_CONFIG(code, data) \
if ( !s_InConfigDump ) { \
s_InConfigDump = true; \
- LOG_POST_X(code, data); \
+ ERR_POST_X(code, Note << data); \
s_InConfigDump = false; \
}
@@ -161,6 +161,7 @@ bool NCBI_XNCBI_EXPORT g_GetConfigFlag(const char* section,
}
if ( section && *section ) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if ( app && app->HasLoadedConfig() ) {
const string& str = app->GetConfig().Get(section, variable);
@@ -249,6 +250,7 @@ int NCBI_XNCBI_EXPORT g_GetConfigInt(const char* section,
}
if ( section && *section ) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if ( app && app->HasLoadedConfig() ) {
const string& str = app->GetConfig().Get(section, variable);
@@ -333,6 +335,7 @@ double NCBI_XNCBI_EXPORT g_GetConfigDouble(const char* section,
}
if ( section && *section ) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if ( app && app->HasLoadedConfig() ) {
const string& str = app->GetConfig().Get(section, variable);
diff --git a/c++/src/corelib/ncbi_process.cpp b/c++/src/corelib/ncbi_process.cpp
index 5e1f649..19d6da6 100644
--- a/c++/src/corelib/ncbi_process.cpp
+++ b/c++/src/corelib/ncbi_process.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_process.cpp 440050 2014-07-08 19:48:37Z kazimird $
+/* $Id: ncbi_process.cpp 465029 2015-04-16 13:28:52Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -374,6 +374,13 @@ namespace {
TPid CProcess::x_DaemonizeEx(const char* logfile, CProcess::TDaemonFlags flags)
{
+ if (!(flags & fDF_AllowThreads)) {
+ if (unsigned n = CThread::GetThreadsCount()) {
+ NCBI_THROW_FMT(CCoreException, eCore, "[Daemonize] "
+ "Prohibited, there are already child threads running: " << n);
+ }
+ }
+
bool success_flag = false;
CSafeRedirect stdin_redirector(STDIN_FILENO, &success_flag);
@@ -426,8 +433,10 @@ TPid CProcess::x_DaemonizeEx(const char* logfile, CProcess::TDaemonFlags flags)
// No need to set success_flag to true here, because
// either this process must be terminated or
// the descriptors must be restored.
- if ((flags & fDF_KeepParent) == 0)
+ if ((flags & fDF_KeepParent) == 0) {
+ GetDiagContext().PrintStop();
::_exit(0);
+ }
return (TPid) pid/*success*/;
}
// Child process.
@@ -1057,17 +1066,12 @@ int CProcess::Wait(unsigned long timeout, CExitInfo* info) const
//
// CPIDGuard
//
-
-// Protective mutex
-DEFINE_STATIC_FAST_MUTEX(s_PidGuardMutex);
-
-// NOTE: This method to protect PID file works only within one process.
-// CPIDGuard know nothing about PID file modification or deletion
-// by other processes. Be aware.
+// NOTE: CPIDGuard know nothing about PID file modification or deletion
+// by other processes behind this API. Be aware.
CPIDGuard::CPIDGuard(const string& filename, const string& dir)
- : m_OldPID(0), m_NewPID(0)
+ : m_PID(0)
{
string real_dir;
CDirEntry::SplitPath(filename, &real_dir, 0, 0);
@@ -1081,6 +1085,9 @@ CPIDGuard::CPIDGuard(const string& filename, const string& dir)
} else {
m_Path = filename;
}
+ // Create guard for MT-Safe protect
+ m_MTGuard.reset(new CInterProcessLock(m_Path + ".guard"));
+ // Update PID
UpdatePID();
}
@@ -1088,60 +1095,82 @@ CPIDGuard::CPIDGuard(const string& filename, const string& dir)
CPIDGuard::~CPIDGuard(void)
{
Release();
+ m_MTGuard.reset();
+ m_PIDGuard.reset();
}
void CPIDGuard::Release(void)
{
- if ( !m_Path.empty() ) {
- // MT-Safe protect
- CFastMutexGuard LOCK(s_PidGuardMutex);
+ if ( m_Path.empty() ) {
+ return;
+ }
+ // MT-Safe protect
+ CGuard<CInterProcessLock> LOCK(*m_MTGuard);
- // Read info
- TPid pid = 0;
- unsigned int ref = 0;
- CNcbiIfstream in(m_Path.c_str());
- if ( in.good() ) {
- in >> pid >> ref;
- in.close();
- if ( m_NewPID != pid ) {
- // We do not own this file more
- return;
+ // Read info
+ TPid pid = 0;
+ unsigned int ref = 0;
+ CNcbiIfstream in(m_Path.c_str());
+
+ if ( in.good() ) {
+ in >> pid >> ref;
+ in.close();
+ if ( m_PID != pid ) {
+ // We do not own this file more.
+ return;
+ }
+ if ( ref ) {
+ ref--;
+ }
+ // Check reference counter
+ if ( ref ) {
+ // Write updated reference counter into the file
+ CNcbiOfstream out(m_Path.c_str(),
+ IOS_BASE::out | IOS_BASE::trunc);
+ if ( out.good() ) {
+ out << pid << endl << ref << endl;
}
- if ( ref ) {
- ref--;
+ if ( !out.good() ) {
+ NCBI_THROW(CPIDGuardException, eWrite,
+ "Unable to write into PID file " + m_Path +": "
+ + _T_CSTRING(NcbiSys_strerror(errno)));
}
- // Check reference counter
- if ( ref ) {
- // Write updated reference counter into the file
- CNcbiOfstream out(m_Path.c_str(),
- IOS_BASE::out | IOS_BASE::trunc);
- if ( out.good() ) {
- out << pid << endl << ref << endl;
- }
- if ( !out.good() ) {
- NCBI_THROW(CPIDGuardException, eWrite,
- "Unable to write into PID file " + m_Path +": "
- + _T_CSTRING(NcbiSys_strerror(errno)));
- }
- } else {
- // Remove the file
- CDirEntry(m_Path).Remove();
+ } else {
+ // Remove the file
+ CDirEntry(m_Path).Remove();
+ // Remove modification protect guard
+ LOCK.Release();
+ m_MTGuard->Remove();
+ m_MTGuard.reset();
+ // PID-file can be reused now
+ if ( m_PIDGuard.get() ) {
+ m_PIDGuard->Remove();
+ m_PIDGuard.reset();
}
}
- m_Path.erase();
}
+ m_Path.erase();
}
void CPIDGuard::Remove(void)
{
- if ( !m_Path.empty() ) {
- // MT-Safe protect
- CFastMutexGuard LOCK(s_PidGuardMutex);
- // Remove the file
- CDirEntry(m_Path).Remove();
- m_Path.erase();
+ if ( m_Path.empty() ) {
+ return;
+ }
+ // MT-Safe protect
+ CGuard<CInterProcessLock> LOCK(*m_MTGuard);
+
+ // Remove the PID file
+ CDirEntry(m_Path).Remove();
+ m_Path.erase();
+ // Remove modification protect guard
+ m_MTGuard->Remove();
+ // PID-file can be reused now
+ if ( m_PIDGuard.get() ) {
+ m_PIDGuard->Remove();
+ m_PIDGuard.reset();
}
}
@@ -1151,27 +1180,44 @@ void CPIDGuard::UpdatePID(TPid pid)
if (pid == 0) {
pid = CProcess::GetCurrentPid();
}
-
// MT-Safe protect
- CFastMutexGuard LOCK(s_PidGuardMutex);
-
- // Read old PID
+ CGuard<CInterProcessLock> LOCK(*m_MTGuard);
+
+ // Check PID from valid PID-files only. The file can be left on
+ // the file system from previous session. And stored in the file
+ // PID can be already reused by OS.
+
+ bool valid_file = true;
unsigned int ref = 1;
- CNcbiIfstream in(m_Path.c_str());
- if ( in.good() ) {
- in >> m_OldPID >> ref;
- if ( m_OldPID == pid ) {
- // Guard the same PID. Just increase the reference counter.
- ref++;
- } else {
- if ( CProcess(m_OldPID,CProcess::ePid).IsAlive() ) {
- NCBI_THROW2(CPIDGuardException, eStillRunning,
- "Process is still running", m_OldPID);
+
+ // Create guard for PID file
+ if ( !m_PIDGuard.get() ) {
+ // first call to Update() ?
+ m_PIDGuard.reset(new CInterProcessLock(m_Path + ".start.guard"));
+ // If the guard lock is successfully obtained, the existent PID file
+ // can be a stale lock or a new unused file, so just reuse it.
+ valid_file = !m_PIDGuard->TryLock();
+ }
+
+ if ( valid_file ) {
+ // Read old PID
+ CNcbiIfstream in(m_Path.c_str());
+ if ( in.good() ) {
+ TPid old_pid;
+ in >> old_pid >> ref;
+ if ( old_pid == pid ) {
+ // Guard the same PID. Just increase the reference counter.
+ ref++;
+ } else {
+ if ( CProcess(old_pid,CProcess::ePid).IsAlive() ) {
+ NCBI_THROW2(CPIDGuardException, eStillRunning,
+ "Process is still running", old_pid);
+ }
+ ref = 1;
}
- ref = 1;
}
+ in.close();
}
- in.close();
// Write new PID
CNcbiOfstream out(m_Path.c_str(), IOS_BASE::out | IOS_BASE::trunc);
@@ -1184,9 +1230,10 @@ void CPIDGuard::UpdatePID(TPid pid)
+ _T_CSTRING(NcbiSys_strerror(errno)));
}
// Save updated pid
- m_NewPID = pid;
+ m_PID = pid;
}
+
const char* CPIDGuardException::GetErrCodeString(void) const
{
switch (GetErrCode()) {
diff --git a/c++/src/corelib/ncbi_safe_static.cpp b/c++/src/corelib/ncbi_safe_static.cpp
index 49dac75..a1e72df 100644
--- a/c++/src/corelib/ncbi_safe_static.cpp
+++ b/c++/src/corelib/ncbi_safe_static.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_safe_static.cpp 441144 2014-07-21 18:45:59Z vasilche $
+/* $Id: ncbi_safe_static.cpp 463583 2015-03-30 18:05:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -86,7 +86,7 @@ DEFINE_CLASS_STATIC_MUTEX(CSafeStaticPtr_Base::sm_Mutex);
int CSafeStaticPtr_Base::x_GetCreationOrder(void)
{
static CAtomicCounter s_CreationOrder;
- return s_CreationOrder.Add(1);
+ return int(s_CreationOrder.Add(1));
}
diff --git a/c++/src/corelib/ncbi_stack.cpp b/c++/src/corelib/ncbi_stack.cpp
index 81456d5..a79b67a 100644
--- a/c++/src/corelib/ncbi_stack.cpp
+++ b/c++/src/corelib/ncbi_stack.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_stack.cpp 379373 2012-10-31 15:06:17Z grichenk $
+/* $Id: ncbi_stack.cpp 463583 2015-03-30 18:05:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -135,7 +135,7 @@ unsigned int CStackTrace::s_GetStackTraceMaxDepth(void)
if ( !s_InGetMaxDepth ) {
s_InGetMaxDepth = true;
try {
- val = s_MaxDepth.Get();
+ val = (unsigned int)s_MaxDepth.Get();
if (val > 0) {
return val;
}
diff --git a/c++/src/corelib/ncbi_stack_win64.cpp b/c++/src/corelib/ncbi_stack_win64.cpp
index 46716f4..a14ef55 100644
--- a/c++/src/corelib/ncbi_stack_win64.cpp
+++ b/c++/src/corelib/ncbi_stack_win64.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_stack_win64.cpp 264326 2011-03-24 18:25:12Z grichenk $
+/* $Id: ncbi_stack_win64.cpp 456287 2015-01-09 14:29:15Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -324,6 +324,8 @@ private:
CStackTraceImpl::CStackTraceImpl(void)
{
+ s_SymbolGuard->UpdateSymbols();
+
HANDLE curr_proc = GetCurrentProcess();
HANDLE thread = GetCurrentThread();
diff --git a/c++/src/corelib/ncbi_system.cpp b/c++/src/corelib/ncbi_system.cpp
index dfcfb29..a6037e9 100644
--- a/c++/src/corelib/ncbi_system.cpp
+++ b/c++/src/corelib/ncbi_system.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_system.cpp 430072 2014-03-21 18:25:13Z lavr $
+/* $Id: ncbi_system.cpp 473887 2015-07-23 12:01:53Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -204,13 +204,13 @@ static void s_ExitHandler(void)
#endif
if (tick == (clock_t)(-1))
tick = 0;
- LOG_POST_X(4, "\tuser CPU time : " <<
+ ERR_POST_X(4, Note << "\tuser CPU time : " <<
buffer.tms_utime/(tick ? tick : 1) <<
(tick ? " sec" : " tick"));
- LOG_POST_X(5, "\tsystem CPU time : " <<
+ ERR_POST_X(5, Note << "\tsystem CPU time : " <<
buffer.tms_stime/(tick ? tick : 1) <<
(tick ? " sec" : " tick"));
- LOG_POST_X(6, "\ttotal CPU time : " <<
+ ERR_POST_X(6, Note << "\ttotal CPU time : " <<
(buffer.tms_stime + buffer.tms_utime)/(tick ? tick : 1) <<
(tick ? " sec" : " tick"));
break;
@@ -224,11 +224,11 @@ static void s_ExitHandler(void)
CTime ct(CTime::eCurrent);
CTime et(2000, 1, 1);
et.AddSecond((int) (ct.GetTimeT() - s_TimeSet->GetTimeT()));
- LOG_POST_X(7, "Program's time: " << Endm <<
+ ERR_POST_X(7, Note << "Program's time: " << Endm <<
"\tstart limit - " << s_TimeSet->AsString() << Endm <<
"\ttermination - " << ct.AsString() << Endm);
et.SetFormat("h:m:s");
- LOG_POST_X(8, "\texecution - " << et.AsString());
+ ERR_POST_X(8, Note << "\texecution - " << et.AsString());
}
@@ -1117,6 +1117,24 @@ extern int GetProcessFDCount(int* soft_limit, int* hard_limit)
int fd_count = 0;
struct dirent* dp;
+ rlim_t cur_limit = -1;
+ rlim_t max_limit = -1;
+
+ struct rlimit rlim;
+ if (getrlimit(RLIMIT_NOFILE, &rlim) == 0) {
+ cur_limit = rlim.rlim_cur;
+ max_limit = rlim.rlim_max;
+ } else {
+ // fallback to sysconf
+ ERR_POST_ONCE(Warning << "getrlimit(RLIMIT_NOFILE, ...) call failed. "
+ "Using sysconf(_SC_OPEN_MAX) instead.");
+ long sysconf_limit = sysconf(_SC_OPEN_MAX);
+ if (sysconf_limit > RLIM_INFINITY)
+ cur_limit = RLIM_INFINITY;
+ else
+ cur_limit = static_cast<rlim_t>(sysconf(_SC_OPEN_MAX));
+ }
+
DIR* dir = opendir("/proc/self/fd/");
if (dir) {
while ((dp = readdir(dir)) != NULL)
@@ -1126,51 +1144,42 @@ extern int GetProcessFDCount(int* soft_limit, int* hard_limit)
if (fd_count < 0)
fd_count = -1;
} else {
- // Fallback to rlimit analysis
- struct rlimit rlim;
- if (getrlimit(RLIMIT_NOFILE, &rlim) == 0) {
- // Try till max because the soft limit could be lowered after some
- // FD were opened.
- for (unsigned int fd = 0; fd < rlim.rlim_max; ++fd) {
+ // Fallback to analysis via looping over all fds
+ if (cur_limit > 0) {
+ int max_fd = static_cast<int>(cur_limit);
+ if (cur_limit > INT_MAX)
+ max_fd = INT_MAX;
+ for (int fd = 0; fd < max_fd; ++fd) {
if (fcntl(fd, F_GETFD, 0) == -1) {
if (errno == EBADF)
continue;
}
++fd_count;
}
- if ( soft_limit )
- *soft_limit = rlim.rlim_cur;
- if ( hard_limit )
- *hard_limit = rlim.rlim_max;
} else {
fd_count = -1;
- if ( soft_limit )
- *soft_limit = -1;
- if ( hard_limit )
- *hard_limit = -1;
}
- return fd_count;
}
if (soft_limit || hard_limit) {
- struct rlimit rlim;
- if (getrlimit(RLIMIT_NOFILE, &rlim) == 0) {
- if ( soft_limit )
- *soft_limit = rlim.rlim_cur;
- if ( hard_limit )
- *hard_limit = rlim.rlim_max;
- } else {
- if ( soft_limit )
- *soft_limit = -1;
- if ( hard_limit )
- *hard_limit = -1;
+ if (soft_limit) {
+ if (cur_limit > INT_MAX)
+ *soft_limit = INT_MAX;
+ else
+ *soft_limit = static_cast<int>(cur_limit);
+ }
+ if (hard_limit) {
+ if (max_limit > INT_MAX)
+ *hard_limit = INT_MAX;
+ else
+ *hard_limit = static_cast<int>(max_limit);
}
}
return fd_count;
#else
- if ( soft_limit )
+ if (soft_limit)
*soft_limit = -1;
- if ( hard_limit )
+ if (hard_limit)
*hard_limit = -1;
return -1;
#endif //NCBI_OS_UNIX
diff --git a/c++/src/corelib/ncbi_url.cpp b/c++/src/corelib/ncbi_url.cpp
index 0da4ea5..f5530e8 100644
--- a/c++/src/corelib/ncbi_url.cpp
+++ b/c++/src/corelib/ncbi_url.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbi_url.cpp 443011 2014-08-08 21:14:52Z mcelhany $
+/* $Id: ncbi_url.cpp 442459 2014-08-04 15:36:07Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/corelib/ncbiapp.cpp b/c++/src/corelib/ncbiapp.cpp
index 3e8543e..8f3de04 100644
--- a/c++/src/corelib/ncbiapp.cpp
+++ b/c++/src/corelib/ncbiapp.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbiapp.cpp 452158 2014-11-17 15:22:47Z ivanov $
+/* $Id: ncbiapp.cpp 460403 2015-02-26 19:51:12Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -566,9 +566,11 @@ int CNcbiApplication::AppMain
s_MacArgMunging(*this, &argc, &argv, exepath);
#endif
+ CDiagContext& diag_context = GetDiagContext();
+
// Preparse command line
if (PreparseArgs(argc, argv) == ePreparse_Exit) {
- GetDiagContext().DiscardMessages();
+ diag_context.DiscardMessages();
return 0;
}
@@ -606,7 +608,7 @@ int CNcbiApplication::AppMain
// Print VERSION
cout << GetFullVersion().Print( appname,
CVersion::fVersionInfo | CVersion::fPackageShort );
- GetDiagContext().DiscardMessages();
+ diag_context.DiscardMessages();
return 0;
// Full version
@@ -614,7 +616,7 @@ int CNcbiApplication::AppMain
delete[] v;
// Print full VERSION
cout << GetFullVersion().Print( appname );
- GetDiagContext().DiscardMessages();
+ diag_context.DiscardMessages();
return 0;
// Dry run
@@ -719,10 +721,14 @@ int CNcbiApplication::AppMain
exit_code = 1;
}
+ if (!diag_context.IsSetExitCode()) {
+ diag_context.SetExitCode(got_exception ? 500 : exit_code);
+ }
+
if (m_ExitCodeCond == eAllExits
|| (got_exception && m_ExitCodeCond == eExceptionalExits)) {
_TRACE("Overriding exit code from " << exit_code
- << " to " << m_ExitCodeCond);
+ << " to " << m_ExitCode);
exit_code = m_ExitCode;
}
@@ -1052,6 +1058,7 @@ void CNcbiApplication::SetProgramDisplayName(const string& app_name)
string CNcbiApplication::GetAppName(EAppNameType name_type, int argc,
const char* const* argv)
{
+ CMutexGuard guard(GetInstanceMutex());
CNcbiApplication* instance = Instance();
string app_name;
@@ -1091,10 +1098,12 @@ string CNcbiApplication::FindProgramExecutablePath
const char* const* argv,
string* real_path)
{
+ CMutexGuard guard(GetInstanceMutex());
CNcbiApplication* instance = Instance();
string ret_val;
- if (argc > 0 && argv != NULL && argv[0] != NULL
- && argv[0][0] != '\0') {
+ _ASSERT(argc >= 0); // formally signed for historical reasons
+ _ASSERT(argv != NULL || argc == 0);
+ if (argc > 0 && argv[0] != NULL && argv[0][0] != '\0') {
ret_val = argv[0];
} else if (instance) {
ret_val = instance->GetArguments().GetProgramName();
@@ -1222,7 +1231,9 @@ string CNcbiApplication::FindProgramExecutablePath
}
}
}
- ret_val = CDirEntry::NormalizePath(app_path.empty() ? argv[0] : app_path);
+ ret_val = CDirEntry::NormalizePath
+ ((app_path.empty() && argv != NULL && argv[0] != NULL) ? argv[0]
+ : app_path);
#else // defined (NCBI_OS_MSWIN) || defined(NCBI_OS_UNIX)
@@ -1388,7 +1399,10 @@ void CNcbiApplication::AppStart(void)
void CNcbiApplication::AppStop(int exit_code)
{
- GetDiagContext().SetExitCode(exit_code);
+ CDiagContext& ctx = GetDiagContext();
+ if ( !ctx.IsSetExitCode() ) {
+ ctx.SetExitCode(exit_code);
+ }
}
diff --git a/c++/src/corelib/ncbiargs.cpp b/c++/src/corelib/ncbiargs.cpp
index f1e6849..6067f68 100644
--- a/c++/src/corelib/ncbiargs.cpp
+++ b/c++/src/corelib/ncbiargs.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbiargs.cpp 448573 2014-10-07 16:47:45Z ivanov $
+/* $Id: ncbiargs.cpp 466633 2015-05-05 15:36:22Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,6 +46,11 @@
# include <corelib/ncbi_os_mswin.hpp>
# include <io.h>
# include <fcntl.h>
+# include <conio.h>
+#else
+# include <termios.h>
+# include <unistd.h>
+# include <fcntl.h>
#endif
@@ -885,6 +890,9 @@ const CArgAllow* CArgDesc::GetConstraint(void) const
string CArgDesc::GetUsageConstraint(void) const
{
+ if (GetFlags() & CArgDescriptions::fConfidential) {
+ return kEmptyStr;
+ }
const CArgAllow* constraint = GetConstraint();
if (!constraint)
return kEmptyStr;
@@ -1005,11 +1013,14 @@ string CArgDesc::PrintXml(CNcbiOstream& out) const
if (flags & CArgDescriptions::fHidden) {
out << "<" << "hidden" << "/>";
}
+ if (flags & CArgDescriptions::fConfidential) {
+ out << "<" << "confidential" << "/>";
+ }
out << "</" << "flags" << ">" << endl;
}
const CArgDescDefault* def = dynamic_cast<const CArgDescDefault*>(this);
if (def) {
- s_WriteXmlLine( out, "default", def->GetDefaultValue());
+ s_WriteXmlLine( out, "default", def->GetDisplayValue());
} else if (s_IsFlag(*this)) {
const CArgDesc_Flag* fl = dynamic_cast<const CArgDesc_Flag*>(this);
if (fl && !fl->GetSetValue()) {
@@ -1074,9 +1085,13 @@ CArgDescMandatory::~CArgDescMandatory(void)
string CArgDescMandatory::GetUsageCommentAttr(void) const
{
+ CArgDescriptions::EType type = GetType();
// Print type name
- string str = CArgDescriptions::GetTypeName(GetType());
+ string str = CArgDescriptions::GetTypeName(type);
+ if (type == CArgDescriptions::eDateTime) {
+ str += ", format: \"Y-M-DTh:m:gZ\" or \"Y/M/D h:m:gZ\"";
+ }
// Print constraint info, if any
string constr = GetUsageConstraint();
if ( !constr.empty() ) {
@@ -1153,14 +1168,19 @@ CArgValue* CArgDescMandatory::ProcessArgument(const string& value) const
}
if (err) {
- string err_msg;
- if (m_NegateConstraint == CArgDescriptions::eConstraintInvert) {
- err_msg = "Illegal value, unexpected ";
+ if (GetFlags() & CArgDescriptions::fConfidential) {
+ NCBI_THROW(CArgException, eConstraint, s_ArgExptMsg(GetName(),
+ "Disallowed value",value));
} else {
- err_msg = "Illegal value, expected ";
+ string err_msg;
+ if (m_NegateConstraint == CArgDescriptions::eConstraintInvert) {
+ err_msg = "Illegal value, unexpected ";
+ } else {
+ err_msg = "Illegal value, expected ";
+ }
+ NCBI_THROW(CArgException, eConstraint, s_ArgExptMsg(GetName(),
+ err_msg + m_Constraint->GetUsage(),value));
}
- NCBI_THROW(CArgException, eConstraint, s_ArgExptMsg(GetName(),
- err_msg + m_Constraint->GetUsage(),value));
}
}
@@ -1239,11 +1259,16 @@ CArgDescDefault::CArgDescDefault(const string& name,
CArgDescriptions::EType type,
CArgDescriptions::TFlags flags,
const string& default_value,
- const string& env_var)
+ const string& env_var,
+ const char* display_value)
: CArgDescMandatory(name, comment, type, flags),
CArgDescOptional(name, comment, type, flags),
- m_DefaultValue(default_value), m_EnvVar(env_var)
+ m_DefaultValue(default_value), m_EnvVar(env_var),
+ m_use_display(display_value != nullptr)
{
+ if (m_use_display) {
+ m_DisplayValue = display_value;
+ }
return;
}
@@ -1265,6 +1290,11 @@ const string& CArgDescDefault::GetDefaultValue(void) const
return m_DefaultValue;
}
+const string& CArgDescDefault::GetDisplayValue(void) const
+{
+ return m_use_display ? m_DisplayValue : GetDefaultValue();
+}
+
CArgValue* CArgDescDefault::ProcessDefault(void) const
{
CArgValue* v = ProcessArgument(GetDefaultValue());
@@ -1460,10 +1490,11 @@ CArgDesc_PosDef::CArgDesc_PosDef(const string& name,
CArgDescriptions::EType type,
CArgDescriptions::TFlags flags,
const string& default_value,
- const string& env_var)
+ const string& env_var,
+ const char* display_value)
: CArgDescMandatory (name, comment, type, flags),
CArgDescOptional (name, comment, type, flags),
- CArgDescDefault (name, comment, type, flags, default_value, env_var),
+ CArgDescDefault (name, comment, type, flags, default_value, env_var, display_value),
CArgDesc_PosOpt (name, comment, type, flags)
{
return;
@@ -1562,10 +1593,11 @@ CArgDesc_KeyDef::CArgDesc_KeyDef(const string& name,
CArgDescriptions::TFlags flags,
const string& synopsis,
const string& default_value,
- const string& env_var)
+ const string& env_var,
+ const char* display_value)
: CArgDescMandatory(name, comment, type, flags),
CArgDescOptional (name, comment, type, flags),
- CArgDesc_PosDef (name, comment, type, flags, default_value, env_var),
+ CArgDesc_PosDef (name, comment, type, flags, default_value, env_var, display_value),
CArgDescSynopsis(synopsis)
{
return;
@@ -1648,6 +1680,25 @@ CArgs::~CArgs(void)
return;
}
+CArgs::CArgs(const CArgs& other)
+{
+ Assign(other);
+}
+
+CArgs& CArgs::operator=(const CArgs& other)
+{
+ return Assign(other);
+}
+
+CArgs& CArgs::Assign(const CArgs& other)
+{
+ if (this != &other) {
+ m_Args = other.m_Args;
+ m_nExtra = other.m_nExtra;
+ m_Command = other.m_Command;
+ }
+ return *this;
+}
static string s_ComposeNameExtra(size_t idx)
{
@@ -1829,6 +1880,200 @@ bool CArgs::IsEmpty(void) const
return m_Args.empty();
}
+enum EEchoInput {
+ eNoEcho,
+ eEchoInput
+};
+
+static string s_CArgs_ReadFromFile(const string& name, const string& filename)
+{
+ CArg_InputFile f(name, filename, CArgDescriptions::fBinary);
+ istreambuf_iterator<char> it( f.AsInputFile() );
+ vector<char> value;
+ std::copy( it, istreambuf_iterator<char>(), back_inserter(value));
+ while (value[ value.size()-1] == '\r' || value[ value.size()-1] == '\n') {
+ value.pop_back();
+ }
+ return string( value.data(), value.size());
+}
+
+static string s_CArgs_ReadFromStdin(const string& name, EEchoInput echo_input, const char* cue)
+{
+ string thx("\n");
+ string prompt;
+ if (cue) {
+ prompt = cue;
+ } else {
+ prompt = "Please enter value of parameter '";
+ prompt += name;
+ prompt += "': ";
+ }
+ if (!prompt.empty()) {
+ cout << prompt;
+ cout.flush();
+ }
+
+ string value;
+#if defined(NCBI_OS_MSWIN)
+ DWORD dw = 0;
+ HANDLE hIn = GetStdHandle(STD_INPUT_HANDLE);
+ if (hIn != INVALID_HANDLE_VALUE) {
+
+ DWORD mode = 0, silent_mode = 0;
+ if (echo_input == eNoEcho) {
+ GetConsoleMode(hIn, &mode);
+ silent_mode = mode & ~ENABLE_ECHO_INPUT;
+ SetConsoleMode(hIn, silent_mode);
+ }
+
+ char buffer[256];
+ while( ReadFile(hIn, buffer, 256, &dw, NULL) && dw != 0) {
+ bool eol = false;
+ while ( buffer[dw-1] == '\n' || buffer[dw-1] == '\r') {
+ --dw; eol = true;
+ }
+ value.append(buffer,dw);
+ if (eol) {
+ break;
+ }
+ }
+
+ if (echo_input == eNoEcho) {
+ SetConsoleMode(hIn, mode);
+ }
+ }
+#else
+ size_t i = 0;
+ char ch;
+
+ struct termios mode, silent_mode;
+ if (echo_input == eNoEcho) {
+ tcgetattr( STDIN_FILENO, &mode );
+ silent_mode = mode;
+ silent_mode.c_lflag &= ~ECHO;
+ tcsetattr( STDIN_FILENO, TCSANOW, &silent_mode );
+ }
+
+ for( i = 0; (ch = getchar()) != EOF && (ch != '\n') && (ch != '\r'); i++ ) {
+ if (ch == '\b') {
+ if (value.size() > 0) {
+ value.erase( value.size()-1, 1);
+ }
+ } else {
+ value.append(1, ch);
+ }
+ }
+
+ if (echo_input == eNoEcho) {
+ tcsetattr( STDIN_FILENO, TCSANOW, &mode );
+ }
+#endif
+ if (!prompt.empty()) {
+ cout << thx;
+ }
+ return value;
+}
+
+static string s_CArgs_ReadFromConsole(const string& name, EEchoInput echo_input, const char* cue)
+{
+ string thx("\n");
+ string prompt;
+ if (cue) {
+ prompt = cue;
+ } else {
+ prompt = "Please enter value of parameter '";
+ prompt += name;
+ prompt += "': ";
+ }
+
+ string value;
+#if defined(NCBI_OS_MSWIN)
+ DWORD dw = 0;
+ HANDLE hOut = INVALID_HANDLE_VALUE;
+ if (!prompt.empty()) {
+ hOut = CreateFile(_TX("CONOUT$"),
+ GENERIC_WRITE, FILE_SHARE_WRITE, NULL, OPEN_EXISTING,
+ FILE_ATTRIBUTE_NORMAL, NULL);
+ if (hOut != INVALID_HANDLE_VALUE) {
+ WriteFile(hOut,prompt.data(),prompt.length(), &dw, NULL);
+ }
+ }
+
+ HANDLE hIn = CreateFile(_TX("CONIN$"),
+ GENERIC_READ | GENERIC_WRITE, FILE_SHARE_READ, NULL, OPEN_EXISTING,
+ FILE_ATTRIBUTE_NORMAL, NULL);
+ if (hIn != INVALID_HANDLE_VALUE) {
+ DWORD mode = 0, silent_mode = 0;
+ if (echo_input == eNoEcho) {
+ GetConsoleMode(hIn, &mode);
+ silent_mode = mode & ~ENABLE_ECHO_INPUT;
+ SetConsoleMode(hIn, silent_mode);
+ }
+
+ char buffer[256];
+ while( ReadFile(hIn, buffer, 256, &dw, NULL) && dw != 0) {
+ bool eol = false;
+ while ( buffer[dw-1] == '\n' || buffer[dw-1] == '\r') {
+ --dw;
+ eol = true;
+ }
+ value.append(buffer,dw);
+ if (eol) {
+ break;
+ }
+ }
+
+ if (echo_input == eNoEcho) {
+ SetConsoleMode(hIn, mode);
+ }
+ CloseHandle(hIn);
+ }
+
+ if (hOut != INVALID_HANDLE_VALUE) {
+ WriteFile(hOut,thx.data(),thx.length(), &dw, NULL);
+ CloseHandle(hOut);
+ }
+#else
+ int tty = open("/dev/tty", O_RDWR);
+ if (tty >= 0) {
+ if (!prompt.empty()) {
+ write( tty, prompt.data(), prompt.length());
+ }
+
+ struct termios mode, silent_mode;
+ if (echo_input == eNoEcho) {
+ tcgetattr( tty, &mode );
+ silent_mode = mode;
+ silent_mode.c_lflag &= ~ECHO;
+ tcsetattr( tty, TCSANOW, &silent_mode );
+ }
+
+ char buffer[256];
+ ssize_t i = 0;
+ while ( (i = read(tty, buffer, 256)) > 0) {
+ bool eol = false;
+ while ( i > 0 && (buffer[i-1] == '\n' || buffer[i-1] == '\r')) {
+ --i;
+ eol = true;
+ }
+ value.append(buffer,i);
+ if (eol) {
+ break;
+ }
+ }
+
+ if (echo_input == eNoEcho) {
+ tcsetattr( tty, TCSANOW, &mode );
+ }
+ if (!prompt.empty()) {
+ write( tty, thx.data(), thx.length());
+ }
+ close(tty);
+ }
+#endif
+ return value;
+}
+
///////////////////////////////////////////////////////
// CArgErrorHandler::
@@ -1996,10 +2241,11 @@ void CArgDescriptions::AddDefaultKey
EType type,
const string& default_value,
TFlags flags,
- const string& env_var)
+ const string& env_var,
+ const char* display_value)
{
auto_ptr<CArgDesc_KeyDef> arg(new CArgDesc_KeyDef(name,
- comment, type, flags, synopsis, default_value, env_var));
+ comment, type, flags, synopsis, default_value, env_var, display_value));
x_AddDesc(*arg);
arg.release();
@@ -2064,10 +2310,11 @@ void CArgDescriptions::AddDefaultPositional
EType type,
const string& default_value,
TFlags flags,
- const string& env_var)
+ const string& env_var,
+ const char* display_value)
{
auto_ptr<CArgDesc_PosDef> arg(new CArgDesc_PosDef(name,
- comment, type, flags, default_value, env_var));
+ comment, type, flags, default_value, env_var, display_value));
x_AddDesc(*arg);
arg.release();
@@ -2479,7 +2726,7 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
bool CArgDescriptions::x_CreateArg(const string& arg1,
- const string& name,
+ const string& name_in,
bool have_arg2,
const string& arg2,
unsigned n_plain,
@@ -2490,6 +2737,7 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
if (new_value)
*new_value = 0;
+ string name(name_in);
bool arg2_used = false;
bool no_separator = false;
bool eq_separator = false;
@@ -2508,6 +2756,37 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
throw;
}
}
+
+ // Check for '/' in the arg1
+ bool confidential = it != m_Args.end() &&
+ ((*it)->GetFlags() & CArgDescriptions::fConfidential) != 0;
+ char conf_method = confidential ? 't' : '\0';
+ size_t dash = name.rfind('-');
+ if (it == m_Args.end() && dash != NPOS && dash != 0) {
+ string test(name.substr(0, dash));
+ string suffix(name.substr(dash+1));
+ if (NStr::strcasecmp(suffix.c_str(), "file") == 0 ||
+ NStr::strcasecmp(suffix.c_str(), "verbatim") == 0)
+ {
+ try {
+ it = x_Find(test);
+ } catch (CArgException&) {
+ it = m_Args.end();
+ }
+ if (it != m_Args.end()) {
+// verify that it has Confidential flag
+// and there is something after dash
+ if (((*it)->GetFlags() & CArgDescriptions::fConfidential) &&
+ name.size() > (dash+1)) {
+ confidential = true;
+ conf_method = name[dash+1];
+ name = test;
+ }
+ }
+ }
+ }
+
+
if (it == m_Args.end() && m_NoSeparator.find(name[0]) != NPOS) {
it = x_Find(name.substr(0, 1), &negative);
_ASSERT(it != m_Args.end());
@@ -2533,7 +2812,7 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
// Check value separated by '='
string arg_val;
- if ( s_IsKey(arg) ) {
+ if ( s_IsKey(arg) && !confidential) {
eq_separator = arg1.length() > name.length() &&
(arg1[name.length() + 1] == '=');
if ( !eq_separator ) {
@@ -2547,11 +2826,14 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
}
// Get argument value
- const string* value = 0;
+ string value;
if ( !eq_separator && !no_separator ) {
- if ( s_IsKey(arg) ) {
+ if ( !s_IsKey(arg) || (confidential && conf_method == 't')) {
+ value = arg1;
+ }
+ else {
// <key> <value> arg -- advance from the arg.name to the arg.value
- if ( !have_arg2 && !value ) {
+ if ( !have_arg2 ) {
// if update specified we try to add default value
// (mandatory throws an exception out of the ProcessDefault())
@@ -2565,10 +2847,8 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
NCBI_THROW(CArgException,eNoArg,s_ArgExptMsg(arg1,
"Value is missing", kEmptyStr));
}
- value = &arg2;
+ value = arg2;
arg2_used = true;
- } else {
- value = &arg1;
}
}
else {
@@ -2579,7 +2859,23 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
else {
arg_val = arg1.substr(name.length() + 2);
}
- value = &arg_val;
+ value = arg_val;
+ }
+
+ if (confidential) {
+ switch (conf_method) {
+ default:
+ break;
+ case 'f':
+ case 'F':
+ value = (value != "-") ? s_CArgs_ReadFromFile(name, value)
+ : s_CArgs_ReadFromStdin(name, eNoEcho, "");
+ break;
+ case 't':
+ case 'T':
+ value = s_CArgs_ReadFromConsole(name, eNoEcho, nullptr);
+ break;
+ }
}
CArgValue* av = 0;
@@ -2591,7 +2887,7 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
av = arg.ProcessDefault();
}
else {
- av = arg.ProcessArgument(*value);
+ av = arg.ProcessArgument(value);
}
}
catch (CArgException) {
@@ -2600,7 +2896,7 @@ bool CArgDescriptions::x_CreateArg(const string& arg1,
err_handler = m_ErrorHandler.GetPointerOrNull();
}
_ASSERT(err_handler);
- av = err_handler->HandleError(arg, *value);
+ av = err_handler->HandleError(arg, value);
}
if ( !av ) {
@@ -2910,6 +3206,14 @@ void CArgDescriptions::x_PrintComment(list<string>& arr,
string t;
t += separator;
t += '<' + attr + '>';
+ if (arg.GetFlags() & CArgDescriptions::fConfidential) {
+ arr.push_back( intro + " - read value interactively from console");
+ arr.push_back( intro + "-file <" +
+ CArgDescriptions::GetTypeName(CArgDescriptions::eInputFile) + "> - read value from file");
+ t = "-verbatim";
+ t += separator;
+ t += '<' + attr + '>';
+ }
attr = t;
}
@@ -2953,7 +3257,7 @@ void CArgDescriptions::x_PrintComment(list<string>& arr,
const CArgDescDefault* dflt = dynamic_cast<const CArgDescDefault*> (&arg);
if ( dflt ) {
s_PrintCommentBody
- (arr, "Default = `" + dflt->GetDefaultValue() + '\'', width);
+ (arr, "Default = `" + dflt->GetDisplayValue() + '\'', width);
}
// Print required/excluded args
diff --git a/c++/src/corelib/ncbiargs_p.hpp b/c++/src/corelib/ncbiargs_p.hpp
index cd3ff0f..bb137cb 100644
--- a/c++/src/corelib/ncbiargs_p.hpp
+++ b/c++/src/corelib/ncbiargs_p.hpp
@@ -1,4 +1,4 @@
-/* $Id: ncbiargs_p.hpp 439772 2014-07-03 17:53:32Z gouriano $
+/* $Id: ncbiargs_p.hpp 460139 2015-02-25 13:49:33Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -359,10 +359,12 @@ public:
CArgDescriptions::EType type,
CArgDescriptions::TFlags flags,
const string& default_value,
- const string& env_var);
+ const string& env_var,
+ const char* display_value);
virtual ~CArgDescDefault(void);
const string& GetDefaultValue(void) const;
+ const string& GetDisplayValue(void) const;
virtual CArgValue* ProcessDefault(void) const;
virtual void VerifyDefault (void) const;
@@ -370,6 +372,8 @@ public:
private:
string m_DefaultValue;
string m_EnvVar;
+ string m_DisplayValue;
+ bool m_use_display;
};
@@ -477,7 +481,8 @@ public:
CArgDescriptions::EType type,
CArgDescriptions::TFlags flags,
const string& default_value,
- const string& env_var);
+ const string& env_var,
+ const char* display_value);
virtual ~CArgDesc_PosDef(void);
};
@@ -520,7 +525,8 @@ public:
CArgDescriptions::TFlags flags,
const string& synopsis,
const string& default_value,
- const string& env_var);
+ const string& env_var,
+ const char* display_value);
virtual ~CArgDesc_KeyDef(void);
virtual string GetUsageSynopsis(bool name_only = false) const;
};
diff --git a/c++/src/corelib/ncbidiag.cpp b/c++/src/corelib/ncbidiag.cpp
index 564d98a..aedbf94 100644
--- a/c++/src/corelib/ncbidiag.cpp
+++ b/c++/src/corelib/ncbidiag.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbidiag.cpp 467442 2015-05-13 17:29:03Z ivanov $
+/* $Id: ncbidiag.cpp 483520 2015-11-02 14:44:26Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,10 +55,6 @@
# include <sys/utsname.h>
#endif
-#ifdef NCBI_OS_LINUX
-# include <sys/prctl.h>
-#endif
-
#define NCBI_USE_ERRCODE_X Corelib_Diag
@@ -914,9 +910,37 @@ CRequestContext& CDiagContextThreadData::GetRequestContext(void)
}
+static const Uint8 kOwnerTID_None = Uint8(-1);
+
void CDiagContextThreadData::SetRequestContext(CRequestContext* ctx)
{
- m_RequestCtx->m_Ctx = ctx ? ctx : m_DefaultRequestCtx->m_Ctx;
+ if (m_RequestCtx->m_Ctx) {
+ // If pointers are the same (e.g. consecutive calls with the same ctx)
+ if (ctx == m_RequestCtx->m_Ctx.GetPointer()) {
+ return;
+ }
+
+ // Reset TID in the context.
+ m_RequestCtx->m_Ctx->m_OwnerTID = kOwnerTID_None;
+ }
+
+ if (!ctx) {
+ m_RequestCtx->m_Ctx = m_DefaultRequestCtx->m_Ctx;
+ return;
+ }
+
+ m_RequestCtx->m_Ctx = ctx;
+
+ if (ctx->m_OwnerTID == kOwnerTID_None) {
+ // Save current TID in the context.
+ ctx->m_OwnerTID = m_TID;
+ }
+ else if (ctx->m_OwnerTID != m_TID) {
+ ERR_POST_X_ONCE(29,
+ "Using the same CRequestContext in multiple threads is unsafe!"
+ << CStackTrace());
+ _TROUBLE;
+ }
}
@@ -1141,6 +1165,7 @@ CDiagContext::CDiagContext(void)
m_AppNameSet(false),
m_LoggedHitId(false),
m_ExitCode(0),
+ m_ExitCodeSet(false),
m_ExitSig(0),
m_AppState(eDiagAppState_AppBegin),
m_StopWatch(new CStopWatch(CStopWatch::eStart)),
@@ -1374,6 +1399,7 @@ CDiagContext::TPID CDiagContext::GetPID(void)
bool CDiagContext::UpdatePID(void)
{
+ TPID old_pid = sm_PID;
TPID new_pid = CProcess::GetCurrentPid();
if (sm_PID == new_pid) {
// Parent process does not need to update pid/guid
@@ -1386,9 +1412,8 @@ bool CDiagContext::UpdatePID(void)
ctx.x_CreateUID();
ctx.Extra().
Print("action", "fork").
- Print("parent_guid", ctx.GetStringUID(old_uid));
- //ctx.PrintExtra("New process created by fork(), "
- // "parent GUID=" + );
+ Print("parent_guid", ctx.GetStringUID(old_uid)).
+ Print("parent_pid", NStr::NumericToString(old_pid));
return true;
}
@@ -1874,11 +1899,24 @@ void CDiagContext::PrintProperties(void)
void CDiagContext::PrintStart(const string& message)
{
x_PrintMessage(SDiagMessage::eEvent_Start, message);
+ // Log hit id if already available.
+ x_GetDefaultHitID(eHitID_NoCreate);
}
void CDiagContext::PrintStop(void)
{
+ // If no hit id has been logged until app-stop,
+ // try to force logging now.
+ if (x_IsSetDefaultHitID()) {
+ x_LogHitID_WithLock();
+ }
+ else {
+ CRequestContext& ctx = GetRequestContext();
+ if (ctx.IsSetHitID(CRequestContext::eHitID_Request)) {
+ ctx.x_LogHitID(true);
+ }
+ }
x_PrintMessage(SDiagMessage::eEvent_Stop, kEmptyStr);
}
@@ -1891,16 +1929,7 @@ void CDiagContext::PrintExtra(const string& message)
CDiagContext_Extra CDiagContext::PrintRequestStart(void)
{
- CDiagContext_Extra extra(SDiagMessage::eEvent_RequestStart);
- const string& role = GetHostRole();
- const string& loc = GetHostLocation();
- if ( !role.empty() ) {
- extra.Print("ncbi_role", role);
- }
- if ( !loc.empty() ) {
- extra.Print("ncbi_location", loc);
- }
- return extra;
+ return CDiagContext_Extra(SDiagMessage::eEvent_RequestStart);
}
@@ -1951,9 +1980,7 @@ CDiagContext_Extra::CDiagContext_Extra(const CDiagContext_Extra& args)
CDiagContext_Extra& CDiagContext_Extra::AllowBadSymbolsInArgNames(void)
{
- if (!m_Args || m_Args->empty()) {
- m_AllowBadNames = true;
- }
+ m_AllowBadNames = true;
return *this;
}
@@ -1967,6 +1994,17 @@ void CDiagContext_Extra::Flush(void)
return;
}
+ // Add ncbi-role and ncbi-location just before setting m_Flushed flag.
+ if (m_EventType == SDiagMessage::eEvent_RequestStart) {
+ const string& role = CDiagContext::GetHostRole();
+ const string& loc = CDiagContext::GetHostLocation();
+ if ( !role.empty() ) {
+ Print("ncbi_role", role);
+ }
+ if ( !loc.empty() ) {
+ Print("ncbi_location", loc);
+ }
+ }
// Prevent double-flush
m_Flushed = true;
@@ -2238,6 +2276,9 @@ void CDiagContext::PrintRequestStop(void)
x_PrintMessage(SDiagMessage::eEvent_RequestStop, kEmptyStr);
if ( app_state_updated ) {
SetAppState(eDiagAppState_AppRun);
+ // Now back at application level check if a default hit id
+ // needs to be logged.
+ x_LogHitID_WithLock();
}
}
@@ -2405,10 +2446,48 @@ typedef NCBI_PARAM_TYPE(Log, Hit_Id) TParamHitId;
DEFINE_STATIC_FAST_MUTEX(s_DefaultHidMutex);
-string CDiagContext::GetDefaultHitID(void) const
+bool CDiagContext::x_DiagAtApplicationLevel(void) const
+{
+ EDiagAppState state = GetAppState();
+ return (state == eDiagAppState_AppBegin) ||
+ (state == eDiagAppState_AppRun) ||
+ (state == eDiagAppState_AppEnd);
+}
+
+
+void CDiagContext::x_LogHitID(void) const
+{
+ // NOTE: The method must be always called with s_DefaultHidMutex locked.
+
+ // Log the default hit id only when at application level. Otherwise
+ // pospone it untill request-stop/app-stop.
+ if (m_LoggedHitId || !m_DefaultHitId.get() || m_DefaultHitId->empty() ||
+ !x_DiagAtApplicationLevel()) {
+ return;
+ }
+ Extra().Print(g_GetNcbiString(eNcbiStrings_PHID), *m_DefaultHitId);
+ m_LoggedHitId = true;
+}
+
+
+void CDiagContext::x_LogHitID_WithLock(void) const
+{
+ CFastMutexGuard guard(s_DefaultHidMutex);
+ x_LogHitID();
+}
+
+
+bool CDiagContext::x_IsSetDefaultHitID(void) const
+{
+ CFastMutexGuard guard(s_DefaultHidMutex);
+ return m_DefaultHitId.get() && !m_DefaultHitId->empty();
+}
+
+
+string CDiagContext::x_GetDefaultHitID(EDefaultHitIDFlags flag) const
{
CFastMutexGuard guard(s_DefaultHidMutex);
- if (m_DefaultHitId.get() && !m_DefaultHitId->empty() && m_LoggedHitId) {
+ if (m_DefaultHitId.get() && !m_DefaultHitId->empty()) {
return *m_DefaultHitId;
}
@@ -2422,16 +2501,13 @@ string CDiagContext::GetDefaultHitID(void) const
*m_DefaultHitId = CRequestContext::SelectLastHitID(
TParamHitId::GetDefault());
}
- if ( m_DefaultHitId->empty() ) {
+ if (m_DefaultHitId->empty() && (flag == eHitID_Create)) {
*m_DefaultHitId = GetNextHitID();
}
- m_LoggedHitId = false;
- }
- if ( !m_LoggedHitId ) {
- // Log default hit id automatically.
- m_LoggedHitId = true;
- Extra().Print(g_GetNcbiString(eNcbiStrings_PHID), *m_DefaultHitId);
}
+ _ASSERT(!m_LoggedHitId);
+ // Log hit id if at application level.
+ x_LogHitID();
return *m_DefaultHitId;
}
@@ -2442,8 +2518,10 @@ void CDiagContext::SetDefaultHitID(const string& hit_id)
if ( !m_DefaultHitId.get() ) {
m_DefaultHitId.reset(new string);
}
- m_LoggedHitId = false;
*m_DefaultHitId = hit_id;
+ // Log new hit id when at application level.
+ m_LoggedHitId = false;
+ x_LogHitID();
}
@@ -2583,8 +2661,6 @@ void CDiagContext::x_StartRequest(void)
ctx.StartRequest();
// Print selected environment and registry values.
- CNcbiApplication* app = CNcbiApplication::Instance();
- if ( !app ) return;
static CSafeStatic<TLogEnvironment> s_LogEnvironment;
string log_args = s_LogEnvironment->Get();
if ( !log_args.empty() ) {
@@ -2592,11 +2668,20 @@ void CDiagContext::x_StartRequest(void)
NStr::Split(log_args, " ", log_args_list);
CDiagContext_Extra extra = GetDiagContext().Extra();
extra.Print("LogEnvironment", "true");
- const CNcbiEnvironment& env = app->GetEnvironment();
- ITERATE(list<string>, it, log_args_list) {
- const string& val = env.Get(*it);
- extra.Print(*it, val);
- }
+ {{
+ // The guard must be released before flushing the extra -
+ // otherwise there may be a deadlock when accessing CParam-s
+ // from other threads.
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if ( app ) {
+ const CNcbiEnvironment& env = app->GetEnvironment();
+ ITERATE(list<string>, it, log_args_list) {
+ const string& val = env.Get(*it);
+ extra.Print(*it, val);
+ }
+ }
+ }}
extra.Flush();
}
static CSafeStatic<TLogRegistry> s_LogRegistry;
@@ -2606,17 +2691,23 @@ void CDiagContext::x_StartRequest(void)
NStr::Split(log_args, " ", log_args_list);
CDiagContext_Extra extra = GetDiagContext().Extra();
extra.Print("LogRegistry", "true");
- const CNcbiRegistry& reg = app->GetConfig();
- ITERATE(list<string>, it, log_args_list) {
- string section, name;
- NStr::SplitInTwo(*it, ":", section, name);
- const string& val = reg.Get(section, name);
- extra.Print(*it, val);
- }
+ {{
+ // The guard must be released before flushing the extra -
+ // see above.
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if ( app ) {
+ const CNcbiRegistry& reg = app->GetConfig();
+ ITERATE(list<string>, it, log_args_list) {
+ string section, name;
+ NStr::SplitInTwo(*it, ":", section, name);
+ const string& val = reg.Get(section, name);
+ extra.Print(*it, val);
+ }
+ }
+ }}
extra.Flush();
}
- // Log PHID if not yet logged.
- ctx.GetHitID();
}
@@ -2683,8 +2774,9 @@ void CDiagContext::x_PrintMessage(SDiagMessage::EEventType event,
0, 0, 0); // module/class/function
mess.m_Event = event;
CDiagBuffer::DiagHandler(mess);
- // Now it's safe to reset the request context
+
if (event == SDiagMessage::eEvent_RequestStop) {
+ // Reset request context after stopping the request.
ctx.StopRequest();
}
}
@@ -2742,7 +2834,7 @@ void CDiagContext::FlushMessages(CDiagHandler& handler)
return;
}
auto_ptr<TMessages> tmp(m_Messages.release());
- //ERR_POST_X(1, Message << "***** BEGIN COLLECTED MESSAGES *****");
+ //ERR_POST_X(1, Note << "***** BEGIN COLLECTED MESSAGES *****");
NON_CONST_ITERATE(TMessages, it, *tmp.get()) {
it->m_NoTee = true; // Do not tee duplicate messages to console.
handler.Post(*it);
@@ -2750,7 +2842,7 @@ void CDiagContext::FlushMessages(CDiagHandler& handler)
handler.PostToConsole(*it);
}
}
- //ERR_POST_X(2, Message << "***** END COLLECTED MESSAGES *****");
+ //ERR_POST_X(2, Note << "***** END COLLECTED MESSAGES *****");
m_Messages.reset(tmp.release());
}
@@ -2946,7 +3038,6 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
if ( old_handler ) {
old_log_name = old_handler->GetLogName();
}
- CNcbiApplication* app = CNcbiApplication::Instance();
string config_logfile = s_GetLogConfigString("FILE", kEmptyStr, config);
if ( config_logfile.empty() ) {
@@ -3021,10 +3112,14 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
collect = eDCM_Discard;
break;
case eDS_AppSpecific:
- if ( app ) {
- app->SetupDiag_AppSpecific(); /* NCBI_FAKE_WARNING */
+ {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if ( app ) {
+ app->SetupDiag_AppSpecific(); /* NCBI_FAKE_WARNING */
+ }
+ collect = eDCM_Discard;
}
- collect = eDCM_Discard;
break;
case eDS_ToSyslog:
if (old_log_name != CSysLog::kLogName_Syslog) {
@@ -3042,12 +3137,19 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
case eDS_ToStdlog:
case eDS_Default:
{
- string log_base = app ?
- app->GetProgramExecutablePath() : kEmptyStr;
+ string log_base;
+ string def_log_dir;
+ {{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
+ CNcbiApplication* app = CNcbiApplication::Instance();
+ if ( app ) {
+ log_base = app->GetProgramExecutablePath();
+ def_log_dir = GetDefaultLogLocation(*app);
+ }
+ }}
if ( !log_base.empty() ) {
log_base = CFile(log_base).GetBase() + ".log";
string log_name;
- string def_log_dir = GetDefaultLogLocation(*app);
// Try /log/<port>
if ( !def_log_dir.empty() ) {
log_name = CFile::ConcatPath(def_log_dir, log_base);
@@ -3137,7 +3239,6 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
if ( to_applog ) {
_ASSERT(s_UsingAutoApplog);
ctx.SetOldPostFormat(false);
- SetDiagPostFlag(eDPF_PreMergeLines);
SetDiagPostFlag(eDPF_MergeLines);
s_MergeLinesSetBySetupDiag = true;
TLogSizeLimitParam::SetDefault(0); // No log size limit
@@ -3148,7 +3249,6 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
else {
s_UsingAutoApplog = old_using_applog;
if ( s_MergeLinesSetBySetupDiag ) {
- UnsetDiagPostFlag(eDPF_PreMergeLines);
UnsetDiagPostFlag(eDPF_MergeLines);
}
// Disable throttling
@@ -3158,9 +3258,14 @@ void CDiagContext::SetupDiag(EAppDiagStream ds,
}
CDiagHandler* new_handler = GetDiagHandler();
- if ( new_handler ) {
- log_set = log_set && new_handler->GetLogName() != old_log_name;
+ // Flush collected messages to the log if either its name has changed
+ // or log file truncation is enabled.
+ if (log_set && new_handler && new_handler->GetLogName() == old_log_name) {
+ bool is_file = dynamic_cast<CFileHandleDiagHandler*>(new_handler) ||
+ dynamic_cast<CFileDiagHandler*>(new_handler);
+ log_set = log_set && is_file && GetLogTruncate();
}
+
if (collect == eDCM_Flush) {
// Flush and discard
if ( log_set && new_handler ) {
@@ -3200,8 +3305,10 @@ bool CDiagContext::IsUsingRootLog(void)
CDiagContext& GetDiagContext(void)
{
// Make the context live longer than other diag safe-statics
+ // and +1 longer than TLS safe statics which print app stop
+ // from their cleanup.
static CSafeStatic<CDiagContext> s_DiagContext(
- CSafeStaticLifeSpan::eLifeSpan_Long);
+ CSafeStaticLifeSpan(CSafeStaticLifeSpan::eLifeSpan_Long, 1));
return s_DiagContext.Get();
}
@@ -3219,16 +3326,10 @@ EDiagSev CDiagBuffer::sm_PostSeverity = eDiag_Warning;
EDiagSevChange CDiagBuffer::sm_PostSeverityChange = eDiagSC_Unknown;
// to be set on first request
-static const TDiagPostFlags s_OldDefaultPostFlags =
- eDPF_Prefix | eDPF_Severity | eDPF_ErrorID |
+static const TDiagPostFlags s_DefaultPostFlags =
+ eDPF_Prefix | eDPF_Severity | eDPF_ErrorID |
eDPF_ErrCodeMessage | eDPF_ErrCodeExplanation |
eDPF_ErrCodeUseSeverity;
-static const TDiagPostFlags s_NewDefaultPostFlags =
- s_OldDefaultPostFlags |
-#if defined(NCBI_THREADS)
- eDPF_TID | eDPF_SerialNo_Thread |
-#endif
- eDPF_PID | eDPF_SerialNo;
static TDiagPostFlags s_PostFlags = 0;
static bool s_DiagPostFlagsInitialized = false;
@@ -3236,8 +3337,7 @@ inline
TDiagPostFlags& CDiagBuffer::sx_GetPostFlags(void)
{
if (!s_DiagPostFlagsInitialized) {
- s_PostFlags = TOldPostFormatParam::GetDefault() ?
- s_OldDefaultPostFlags : s_NewDefaultPostFlags;
+ s_PostFlags = s_DefaultPostFlags;
s_DiagPostFlagsInitialized = true;
}
return s_PostFlags;
@@ -3510,8 +3610,9 @@ void CDiagBuffer::Flush(void)
EDiagSev sev = m_Diag->GetSeverity();
bool is_console = (m_Diag->GetPostFlags() & eDPF_IsConsole) != 0;
bool is_disabled = SeverityDisabled(sev);
- // Do nothing if diag severity is lower than allowed
- if ((!is_console && is_disabled) || IsOssEmpty(*m_Stream)) {
+
+ // Do nothing if diag severity is lower than allowed.
+ if (!is_console && is_disabled) {
return;
}
@@ -3526,11 +3627,7 @@ void CDiagBuffer::Flush(void)
flags |= sm_TraceFlags | eDPF_Trace;
}
- if ( m_Diag->CheckFilters() ) {
- if (IsSetDiagPostFlag(eDPF_PreMergeLines, flags)) {
- string src = message;
- NStr::Replace(NStr::Replace(src,"\r",""),"\n",";", message);
- }
+ if ( m_Diag->CheckFilters() ) {
SDiagMessage mess(sev, message.data(), message.size(),
m_Diag->GetFile(),
m_Diag->GetLine(),
@@ -4142,9 +4239,18 @@ bool SDiagMessage::ParseMessage(const string& message)
size_t severity_pos = pos;
tmp = s_ParseStr(message, pos, ':', true);
if ( !tmp.empty() ) {
+ // Support both old (LOG_POST -> message) and new (NOTE_POST -> note) styles.
+ size_t sev_pos = NPOS;
if (tmp.length() == 10 && tmp.find("Message[") == 0) {
+ sev_pos = 8;
+ }
+ else if (tmp.length() == 7 && tmp.find("Note[") == 0) {
+ sev_pos = 5;
+ }
+
+ if (sev_pos != NPOS) {
// Get the real severity
- switch ( tmp[8] ) {
+ switch ( tmp[sev_pos] ) {
case 'T':
m_Severity = eDiag_Trace;
break;
@@ -4166,7 +4272,7 @@ bool SDiagMessage::ParseMessage(const string& message)
default:
return false;
}
- m_Flags |= eDPF_IsMessage;
+ m_Flags |= eDPF_IsNote;
have_severity = true;
}
else {
@@ -4516,30 +4622,6 @@ void SDiagMessage::Write(string& str, TDiagWriteFlags flags) const
CNcbiOstream& SDiagMessage::Write(CNcbiOstream& os,
TDiagWriteFlags flags) const
{
- if (IsSetDiagPostFlag(eDPF_MergeLines, m_Flags)) {
- CNcbiOstrstream ostr;
- string str;
- x_Write(ostr, fNoEndl);
- str = CNcbiOstrstreamToString(ostr);
- if (str.find_first_of("\r\n") != NPOS) {
- list<string> lines;
- NStr::Split(str, "\r\n", lines);
- str = NStr::Join(lines, " ");
- }
- os << str;
- if ((flags & fNoEndl) == 0) {
- os << NcbiEndl;
- }
- return os;
- } else {
- return x_Write(os, flags);
- }
-}
-
-
-CNcbiOstream& SDiagMessage::x_Write(CNcbiOstream& os,
- TDiagWriteFlags flags) const
-{
CNcbiOstream& res =
x_IsSetOldFormat() ? x_OldWrite(os, flags) : x_NewWrite(os, flags);
return res;
@@ -4597,21 +4679,20 @@ private:
string CExtraEncoder::Encode(const CTempString& src, EStringType stype) const
{
- if (stype == eName && !m_AllowBadNames) {
- // Just check the source string, it may contain only valid chars
- ITERATE(CTempString, c, src) {
- const char* enc = s_ExtraEncodeChars[(unsigned char)(*c)];
- if (enc[1] != 0 || enc[0] != *c) {
- NCBI_THROW(CCoreException, eInvalidArg,
- "Invalid char in extra args name: " + string(src));
- }
- }
- return src;
- }
- // Encode value (or name if m_AllowBadNames is set).
string dst;
ITERATE(CTempString, c, src) {
- dst += s_ExtraEncodeChars[(unsigned char)(*c)];
+ const char* enc = s_ExtraEncodeChars[(unsigned char)(*c)];
+ if (stype == eName && !m_AllowBadNames &&
+ (enc[1] != 0 || enc[0] != *c)) {
+ // Replace bad chars in names with [INVALID_APPLOG_SYMBOL:%xx].
+ dst += "[INVALID_APPLOG_SYMBOL:";
+ // Special case - encode 'bad' space as '%20', not '+'
+ dst += (*c == ' ') ? "%20" : enc;
+ dst += "]";
+ }
+ else {
+ dst += s_ExtraEncodeChars[(unsigned char)(*c)];
+ }
}
return dst;
}
@@ -4624,9 +4705,82 @@ string SDiagMessage::FormatExtraMessage(void) const
}
-CNcbiOstream& SDiagMessage::x_OldWrite(CNcbiOstream& os,
+// Merge lines in-place:
+// \n -> \v
+// \v -> 0xFF + \v
+// 0xFF -> 0xFF 0xFF
+void SDiagMessage::s_EscapeNewlines(string& buf)
+{
+ if (buf.find_first_of("\n\v\377") == NPOS) return;
+ for (size_t p = 0; p < buf.size(); p++) {
+ switch (buf[p]) {
+ case '\377':
+ case '\v':
+ buf.insert(p, 1, '\377');
+ p++;
+ break;
+ case '\n':
+ buf[p] = '\v';
+ break;
+ }
+ }
+}
+
+
+void SDiagMessage::s_UnescapeNewlines(string& buf)
+{
+ if (buf.find_first_of("\v\377") == NPOS) return;
+ size_t src = 0, dst = 0;
+ for (; src < buf.size(); src++, dst++) {
+ switch (buf[src]) {
+ case '\377':
+ if (src < buf.size() - 1 &&
+ (buf[src + 1] == '\377' || buf[src + 1] == '\v')) {
+ src++; // skip escape char
+ }
+ break;
+ case '\v':
+ // non-escaped VT
+ buf[dst] = '\n';
+ continue;
+ }
+ if (dst != src) {
+ buf[dst] = buf[src];
+ }
+ }
+ buf.resize(dst);
+}
+
+
+enum EDiagMergeLines {
+ eDiagMergeLines_Default, // Do not force line merging
+ eDiagMergeLines_Off, // Force line breaks
+ eDiagMergeLines_On // Escape line breaks
+};
+
+
+NCBI_PARAM_ENUM_DECL(EDiagMergeLines, Diag, Merge_Lines);
+NCBI_PARAM_ENUM_ARRAY(EDiagMergeLines, Diag, Merge_Lines)
+{
+ {"Default", eDiagMergeLines_Default},
+ {"Off", eDiagMergeLines_Off},
+ {"On", eDiagMergeLines_On}
+};
+
+NCBI_PARAM_ENUM_DEF_EX(EDiagMergeLines, Diag, Merge_Lines,
+ eDiagMergeLines_Default,
+ eParam_NoThread, DIAG_MERGE_LINES);
+typedef NCBI_PARAM_TYPE(Diag, Merge_Lines) TDiagMergeLines;
+
+
+CNcbiOstream& SDiagMessage::x_OldWrite(CNcbiOstream& out_str,
TDiagWriteFlags flags) const
{
+ // Temp stream - the result will be passed to line merging.
+ // Error text, module, prefix etc. can have linebreaks which need to
+ // be escaped.
+ CNcbiOstrstream os;
+
// Date & time
if (IsSetDiagPostFlag(eDPF_DateTime, m_Flags)) {
os << CFastLocalTime().GetLocalTime().AsString("M/D/y h:m:s ");
@@ -4663,7 +4817,7 @@ CNcbiOstream& SDiagMessage::x_OldWrite(CNcbiOstream& os,
bool have_description = false;
SDiagErrCodeDescription description;
if ((m_ErrCode || m_ErrSubCode) &&
- (IsSetDiagPostFlag(eDPF_ErrCodeMessage, m_Flags) ||
+ (IsSetDiagPostFlag(eDPF_ErrCodeMessage, m_Flags) ||
IsSetDiagPostFlag(eDPF_ErrCodeExplanation, m_Flags) ||
IsSetDiagPostFlag(eDPF_ErrCodeUseSeverity, m_Flags)) &&
IsSetDiagErrCodeInfo()) {
@@ -4682,12 +4836,14 @@ CNcbiOstream& SDiagMessage::x_OldWrite(CNcbiOstream& os,
// <severity>:
if (IsSetDiagPostFlag(eDPF_Severity, m_Flags) &&
(m_Severity != eDiag_Info || !IsSetDiagPostFlag(eDPF_OmitInfoSev))) {
- if ( IsSetDiagPostFlag(eDPF_IsMessage, m_Flags) ) {
- os << "Message: ";
+ string sev = CNcbiDiag::SeverityName(m_Severity);
+ if ( IsSetDiagPostFlag(eDPF_IsNote, m_Flags) ) {
+ os << "Note[" << sev[0] << "]";
}
else {
- os << CNcbiDiag::SeverityName(m_Severity) << ": ";
+ os << sev;
}
+ os << ": ";
}
// (<err_code>.<err_subcode>) or (err_text)
@@ -4774,18 +4930,40 @@ CNcbiOstream& SDiagMessage::x_OldWrite(CNcbiOstream& os,
os << NcbiEndl << description.m_Explanation;
}
+ string buf = CNcbiOstrstreamToString(os);
+ bool merge_lines = IsSetDiagPostFlag(eDPF_MergeLines, m_Flags);
+ switch (TDiagMergeLines::GetDefault()) {
+ case eDiagMergeLines_On:
+ merge_lines = true;
+ break;
+ case eDiagMergeLines_Off:
+ merge_lines = false;
+ break;
+ default:
+ break;
+ }
+ if (merge_lines) {
+ NStr::ReplaceInPlace(buf, "\n", ";");
+ }
+ out_str << buf;
+
// Endl
if ((flags & fNoEndl) == 0) {
- os << NcbiEndl;
+ out_str << NcbiEndl;
}
- return os;
+ return out_str;
}
-CNcbiOstream& SDiagMessage::x_NewWrite(CNcbiOstream& os,
+CNcbiOstream& SDiagMessage::x_NewWrite(CNcbiOstream& out_str,
TDiagWriteFlags flags) const
{
+ // Temp stream - the result will be passed to line merging.
+ // Error text, module, prefix etc. can have linebreaks which need to
+ // be escaped.
+ CNcbiOstrstream os;
+
if ((flags & fNoPrefix) == 0) {
GetDiagContext().WriteStdPrefix(os, *this);
}
@@ -4817,8 +4995,8 @@ CNcbiOstream& SDiagMessage::x_NewWrite(CNcbiOstream& os,
string sev = CNcbiDiag::SeverityName(m_Severity);
os << setfill(' ') << setw(13) // add 1 for space
<< setiosflags(IOS_BASE::left) << setw(0);
- if ( IsSetDiagPostFlag(eDPF_IsMessage, m_Flags) ) {
- os << "Message[" << sev[0] << "]:";
+ if ( IsSetDiagPostFlag(eDPF_IsNote, m_Flags) ) {
+ os << "Note[" << sev[0] << "]:";
}
else {
os << sev << ':';
@@ -4907,18 +5085,23 @@ CNcbiOstream& SDiagMessage::x_NewWrite(CNcbiOstream& os,
if (have_description) {
if (IsSetDiagPostFlag(eDPF_ErrCodeMessage, m_Flags) &&
!description.m_Message.empty())
- os << NcbiEndl << description.m_Message << ' ';
+ os << '\n' << description.m_Message << ' ';
if (IsSetDiagPostFlag(eDPF_ErrCodeExplanation, m_Flags) &&
!description.m_Explanation.empty())
- os << NcbiEndl << description.m_Explanation;
+ os << '\n' << description.m_Explanation;
}
+ string buf = CNcbiOstrstreamToString(os);
+ // Line merging in new (applog) format is unconditional.
+ s_EscapeNewlines(buf);
+ out_str << buf;
+
// Endl
if ((flags & fNoEndl) == 0) {
- os << NcbiEndl;
+ // In applog format always use \n only. The stream must be in binary mode.
+ out_str << '\n';
}
-
- return os;
+ return out_str;
}
@@ -5280,20 +5463,6 @@ void CTeeDiagHandler::Post(const SDiagMessage& mess)
CNcbiOstrstream str_os;
mess.x_OldWrite(str_os);
- if (IsSetDiagPostFlag(eDPF_PreMergeLines, mess.m_Flags)) {
- string str = CNcbiOstrstreamToString(str_os);
- if (str.find_first_of("\r\n") != NPOS) {
- list<string> lines;
- NStr::Split(str, "\r\n", lines);
- str = NStr::Join(lines, " ");
- }
- // Re-use the stream for the merged message.
- str_os.seekp(0);
- str_os << str;
- if ((mess.m_Flags & SDiagMessage::fNoEndl) == 0) {
- str_os << endl;
- }
- }
CDiagLock lock(CDiagLock::ePost);
string str = CNcbiOstrstreamToString(str_os);
cerr.write(str.data(), str.size());
@@ -5462,7 +5631,12 @@ CDiagFileHandleHolder::CDiagFileHandleHolder(const string& fname,
CDiagHandler::TReopenFlags flags)
: m_Handle(-1)
{
+#if defined(NCBI_OS_MSWIN)
+ int mode = O_WRONLY | O_APPEND | O_CREAT | O_BINARY;
+#else
int mode = O_WRONLY | O_APPEND | O_CREAT;
+#endif
+
if (flags & CDiagHandler::fTruncate) {
mode |= O_TRUNC;
}
@@ -5845,7 +6019,6 @@ void CFileDiagHandler::SetOwnership(CStreamDiagHandler_Base* handler, bool own)
}
if (m_Perf == handler) {
m_OwnPerf = own;
- own = false;
}
}
@@ -5973,12 +6146,16 @@ CNcbiOstream* CFileDiagHandler::GetLogStream(EDiagFileType file_type)
switch ( file_type ) {
case eDiagFile_Err:
handler = m_Err;
+ break;
case eDiagFile_Log:
handler = m_Log;
+ break;
case eDiagFile_Trace:
handler = m_Trace;
+ break;
case eDiagFile_Perf:
handler = m_Perf;
+ break;
case eDiagFile_All:
return 0;
}
@@ -6370,11 +6547,10 @@ void*
CAsyncDiagThread::Main(void)
{
if (!m_ThreadSuffix.empty()) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
string thr_name = CNcbiApplication::Instance()->GetProgramDisplayName();
thr_name += m_ThreadSuffix;
-#if defined(NCBI_OS_LINUX) && defined(PR_SET_NAME)
- prctl(PR_SET_NAME, (unsigned long)thr_name.c_str(), 0, 0, 0);
-#endif
+ SetCurrentThreadName(thr_name);
}
const int batch_size = TAsyncBatchSizeParam::GetDefault();
@@ -6716,22 +6892,19 @@ const CNcbiDiag& CNcbiDiag::SetFunction(const char* function) const
}
-bool CNcbiDiag::CheckFilters(void) const
+bool CNcbiDiag::CheckFilters(const CException* ex) const
{
EDiagSev current_sev = GetSeverity();
- if (current_sev == eDiag_Fatal)
+ if (current_sev == eDiag_Fatal) {
return true;
-
+ }
CDiagLock lock(CDiagLock::eRead);
if (GetSeverity() == eDiag_Trace) {
// check for trace filter
- return s_TraceFilter->Check(*this, this->GetSeverity())
- != eDiagFilter_Reject;
+ return s_TraceFilter->Check(*this, ex) != eDiagFilter_Reject;
}
-
- // check for post filter and severity
- return s_PostFilter->Check(*this, this->GetSeverity())
- != eDiagFilter_Reject;
+ // check for post filter
+ return s_PostFilter->Check(*this, ex) != eDiagFilter_Reject;
}
@@ -6773,11 +6946,10 @@ s_GetExceptionText(const CException* pex)
const CNcbiDiag& CNcbiDiag::x_Put(const CException& ex) const
{
- if (m_Buffer.SeverityDisabled(GetSeverity()) || !CheckFilters())
+ if (m_Buffer.SeverityDisabled(GetSeverity()) || !CheckFilters(&ex)) {
return *this;
-
- CDiagContextThreadData& thr_data =
- CDiagContextThreadData::GetThreadData();
+ }
+ CDiagContextThreadData& thr_data = CDiagContextThreadData::GetThreadData();
CDiagCollectGuard* guard = thr_data.GetCollectGuard();
EDiagSev print_sev = AdjustApplogPrintableSeverity(CDiagBuffer::sm_PostSeverity);
EDiagSev collect_sev = print_sev;
@@ -6848,7 +7020,6 @@ const CNcbiDiag& CNcbiDiag::x_Put(const CException& ex) const
m_Buffer.PrintMessage(diagmsg, *this);
}
-
return *this;
}
@@ -6883,12 +7054,15 @@ void CNcbiDiag::DiagFatal(const CDiagCompileInfo& info,
const char* message)
{
CNcbiDiag(info, NCBI_NS_NCBI::eDiag_Fatal) << message << Endm;
+ // DiagFatal is non-returnable, so force aborting even if the above
+ // call has returned.
+ Abort();
}
void CNcbiDiag::DiagTrouble(const CDiagCompileInfo& info,
const char* message)
{
- DiagFatal(info, message);
+ CNcbiDiag(info, NCBI_NS_NCBI::eDiag_Fatal) << message << Endm;
}
void CNcbiDiag::DiagAssert(const CDiagCompileInfo& info,
@@ -7108,21 +7282,13 @@ extern void Abort(void)
else if (value && (*value == _TX('N') || *value == _TX('n') || *value == _TX('0'))) {
::abort();
}
- else
-#define NCBI_TOTALVIEW_ABORT_WORKAROUND 1
-#if defined(NCBI_TOTALVIEW_ABORT_WORKAROUND)
- // The condition in the following if statement is always 'true'.
- // It's a workaround for TotalView 6.5 (beta) to properly display
- // stacktrace at this point.
-// if ( !(value && *value == 'Y') )
-#endif
- {
+ else {
#if defined(_DEBUG)
- ::abort();
+ ::abort();
#else
- ::exit(255);
+ ::exit(255);
#endif
- }
+ }
}
@@ -7301,7 +7467,19 @@ CDiagContext_Extra g_PostPerf(int status,
double timespan,
SDiagMessage::TExtraArgs& args)
{
- return CDiagContext_Extra(status, timespan, args);
+ const CRequestContext& rctx = GetDiagContext().GetRequestContext();
+ CDiagContext_Extra perf(status, timespan, args);
+ if (rctx.IsSetHitID(CRequestContext::eHidID_Existing)) {
+ perf.Print("ncbi_phid", rctx.GetHitID());
+ }
+ return perf;
+}
+
+
+void EndmFatal(const CNcbiDiag& diag)
+{
+ Endm(diag);
+ Abort();
}
diff --git a/c++/src/corelib/ncbidiag_p.cpp b/c++/src/corelib/ncbidiag_p.cpp
index 2185acf..8ab11c5 100644
--- a/c++/src/corelib/ncbidiag_p.cpp
+++ b/c++/src/corelib/ncbidiag_p.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbidiag_p.cpp 467521 2015-05-14 11:31:40Z ivanov $
+/* $Id: ncbidiag_p.cpp 456643 2015-01-14 13:08:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -279,7 +279,7 @@ void CDiagMatcher::Print(ostream& out) const
if (m_Action == eDiagFilter_Reject)
out << '!';
- s_PrintMatcher(out, m_ErrCode, "ErrCode" );
+ s_PrintMatcher(out, m_ErrCode, "ErrCode" );
s_PrintMatcher(out, m_File, "File" );
s_PrintMatcher(out, m_Module, "Module" );
s_PrintMatcher(out, m_Class, "Class" );
@@ -325,71 +325,67 @@ void CDiagFilter::Fill(const char* filter_string)
}
}
-
-// Check if the filter accepts the message
-EDiagFilterAction CDiagFilter::Check(const CNcbiDiag& message, EDiagSev sev) const
+EDiagFilterAction CDiagFilter::Check(const CNcbiDiag& msg,
+ const CException* ex) const
{
- // if we do not have any filters accept
- if(m_Matchers.empty())
+ // if we do not have any filters -- accept
+ if (m_Matchers.empty()) {
return eDiagFilter_Accept;
+ }
+ // Check errcode, file and location for the message
EDiagFilterAction action;
- action = CheckErrCode(message.GetErrorCode(),
- message.GetErrorSubCode(),
- sev);
+ EDiagSev sev = msg.GetSeverity();
+ action = x_CheckErrCode(msg.GetErrorCode(), msg.GetErrorSubCode(), sev);
if (action == eDiagFilter_None) {
- action = CheckFile(message.GetFile(), sev);
- if (action == eDiagFilter_None)
- action = x_Check(message.GetModule(),
- message.GetClass(),
- message.GetFunction(),
- sev);
+ action = x_CheckFile(msg.GetFile(), sev);
}
if (action == eDiagFilter_None) {
- action = eDiagFilter_Reject;
+ action = x_CheckLocation(msg.GetModule(), msg.GetClass(), msg.GetFunction(), sev);
}
- return action;
-}
-
+ // If specified, additionally check an exception and its backlog.
+ // Accept if one of the exceptions match.
-// Check if the filter accepts the exception
-EDiagFilterAction CDiagFilter::Check(const CException& ex, EDiagSev sev) const
-{
- // if we do not have any filters accept
- if(m_Matchers.empty())
- return eDiagFilter_Accept;
+ if (action == eDiagFilter_None && ex) {
- bool found = false;
- ITERATE(TMatchers, i, m_Matchers) {
- if (!(*i)->IsErrCodeMatcher()) {
- found = true;
- break;
+ // Fast check on non errcode matchers.
+ // We already did errcode check above, exceptions have file/location only.
+ bool found = false;
+ ITERATE(TMatchers, i, m_Matchers) {
+ if (!(*i)->IsErrCodeMatcher()) {
+ found = true;
+ break;
+ }
+ }
+ // If found at least one, process with check
+ if (found) {
+ const CException* pex;
+ for (pex = ex; pex; pex = pex->GetPredecessor()) {
+ action = x_CheckFile(pex->GetFile().c_str(), sev);
+ if (action == eDiagFilter_None) {
+ action = x_CheckLocation(pex->GetModule().c_str(),
+ pex->GetClass().c_str(),
+ pex->GetFunction().c_str(),
+ sev);
+ }
+ if (action == eDiagFilter_Accept) {
+ return action;
+ }
+ }
}
- }
- if (!found) {
- return eDiagFilter_Accept;
}
- const CException* pex;
- for (pex = &ex; pex; pex = pex->GetPredecessor()) {
- EDiagFilterAction action = CheckFile(pex->GetFile().c_str(), sev);
- if (action == eDiagFilter_None) {
- action = x_Check(pex->GetModule() .c_str(),
- pex->GetClass() .c_str(),
- pex->GetFunction().c_str(),
- sev);
- }
- if (action == eDiagFilter_Accept) {
- return action;
- }
+ // Reject if not accepted
+ if (action == eDiagFilter_None) {
+ action = eDiagFilter_Reject;
}
- return eDiagFilter_Reject;
+ return action;
}
// same logic as in CheckFile()
-EDiagFilterAction CDiagFilter::CheckErrCode(int code, int subcode, EDiagSev sev) const
+EDiagFilterAction CDiagFilter::x_CheckErrCode(int code, int subcode, EDiagSev sev) const
{
size_t not_matchers_processed = 0;
size_t curr_ind = 0;
@@ -440,7 +436,7 @@ EDiagFilterAction CDiagFilter::CheckErrCode(int code, int subcode, EDiagSev sev)
return eDiagFilter_None;
}
-EDiagFilterAction CDiagFilter::CheckFile(const char* file, EDiagSev sev) const
+EDiagFilterAction CDiagFilter::x_CheckFile(const char* file, EDiagSev sev) const
{
size_t not_matchers_processed = 0;
size_t curr_ind = 0;
@@ -499,10 +495,10 @@ EDiagFilterAction CDiagFilter::CheckFile(const char* file, EDiagSev sev) const
}
// Check if the filter accepts module, class and function
-EDiagFilterAction CDiagFilter::x_Check(const char* module,
- const char* nclass,
- const char* function,
- EDiagSev sev) const
+EDiagFilterAction CDiagFilter::x_CheckLocation(const char* module,
+ const char* nclass,
+ const char* function,
+ EDiagSev sev) const
{
size_t not_matchers_processed = 0;
size_t curr_ind = 0;
diff --git a/c++/src/corelib/ncbidiag_p.hpp b/c++/src/corelib/ncbidiag_p.hpp
index 250329b..28de813 100644
--- a/c++/src/corelib/ncbidiag_p.hpp
+++ b/c++/src/corelib/ncbidiag_p.hpp
@@ -1,7 +1,7 @@
#ifndef CORELIB___NCBIDIAG_P__HPP
#define CORELIB___NCBIDIAG_P__HPP
-/* $Id: ncbidiag_p.hpp 467520 2015-05-14 11:31:10Z ivanov $
+/* $Id: ncbidiag_p.hpp 456643 2015-01-14 13:08:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -250,33 +250,28 @@ public:
CDiagFilter(void);
~CDiagFilter(void);
- /// Check if the filter accepts message with the specified severity
- EDiagFilterAction Check(const CNcbiDiag& message, EDiagSev sev) const;
+ /// Check if the filter accepts message.
+ /// In addition check an exception and all its backlog if specified.
+ EDiagFilterAction Check(const CNcbiDiag& msg, const CException* ex = NULL) const;
- // Check if the filter accepts the exception
- // NOTE: iterate through all exceptions and return TRUE
- // if any exception matches
- EDiagFilterAction Check(const CException& ex, EDiagSev sev) const;
-
- // Check if the filter accepts errcode
- EDiagFilterAction CheckErrCode(int code, int subcode, EDiagSev sev) const;
-
- // Check if the filter accepts path
- EDiagFilterAction CheckFile(const char* file, EDiagSev sev) const;
-
-
- // Fill the filter from a string
+ /// Fill the filter from a string
void Fill(const char* filter_string);
- // Print state
+ /// Print state
void Print(ostream& out) const;
private:
+ /// Check if the filter accepts errcode
+ EDiagFilterAction x_CheckErrCode(int code, int subcode, EDiagSev sev) const;
+
+ /// Check if the filter accepts path
+ EDiagFilterAction x_CheckFile(const char* file, EDiagSev sev) const;
+
// Check if the filter accepts the location
- EDiagFilterAction x_Check(const char* module,
- const char* nclass,
- const char* function,
- EDiagSev sev) const;
+ EDiagFilterAction x_CheckLocation(const char* module,
+ const char* nclass,
+ const char* function,
+ EDiagSev sev) const;
// CSyntaxParser can insert CDiagStrMatcher and clean
friend class CDiagSyntaxParser;
@@ -284,7 +279,9 @@ private:
// Insert a new matcher into the end of list
// Take ownership of the matcher
void InsertMatcher(CDiagMatcher *matcher)
- { m_Matchers.push_back(matcher); }
+ {
+ m_Matchers.push_back(matcher);
+ }
// Negative matchers should be processed first
// because they are *AND NOT* matchers, not just *NOT*.
@@ -297,6 +294,7 @@ private:
// Remove and destroy all matchers, if any
void Clean(void);
+private:
typedef deque< AutoPtr<CDiagMatcher> > TMatchers;
TMatchers m_Matchers;
size_t m_NotMatchersNum;
@@ -359,7 +357,6 @@ public:
// Error info type
typedef pair<const char*, int> TErrorInfo;
-
// Constructor
CDiagSyntaxParser();
diff --git a/c++/src/corelib/ncbidll.cpp b/c++/src/corelib/ncbidll.cpp
index 3821d35..3d65abd 100644
--- a/c++/src/corelib/ncbidll.cpp
+++ b/c++/src/corelib/ncbidll.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbidll.cpp 311608 2011-07-12 16:01:42Z gouriano $
+/* $Id: ncbidll.cpp 441333 2014-07-23 12:15:14Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -334,8 +334,10 @@ bool CDllResolver::TryCandidate(const string& file_name,
}
catch (CCoreException& ex)
{
- if (ex.GetErrCode() != CCoreException::eDll)
+ if (ex.GetErrCode() != CCoreException::eDll) {
throw;
+ }
+ NCBI_REPORT_EXCEPTION_X(2, "CDllResolver::TryCandidate() failed", ex);
return false;
}
diff --git a/c++/src/corelib/ncbienv.cpp b/c++/src/corelib/ncbienv.cpp
index 732da80..d2b7a64 100644
--- a/c++/src/corelib/ncbienv.cpp
+++ b/c++/src/corelib/ncbienv.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbienv.cpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: ncbienv.cpp 478280 2015-09-08 14:33:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -100,24 +100,31 @@ void CNcbiEnvironment::Reset(const char* const* envp)
ERR_POST_X(3, "CNcbiEnvironment: bad string '" << s << "'");
continue;
}
- m_Cache[string(s, eq)]
- = SEnvValue(eq + 1, const_cast<TXChar*>(kEmptyXCStr));
+ m_Cache[string(s, eq)] = SEnvValue(eq + 1, kEmptyXCStr);
}
}
-const string& CNcbiEnvironment::Get(const string& name) const
+const string& CNcbiEnvironment::Get(const string& name, bool* found) const
{
CFastMutexGuard LOCK(m_CacheMutex);
TCache::const_iterator i = m_Cache.find(name);
+ bool fake_found;
+ if (found == NULL) {
+ found = &fake_found;
+ }
if ( i != m_Cache.end() ) {
if (i->second.ptr == NULL && i->second.value.empty()) {
+ *found = false;
return kEmptyStr;
} else {
+ *found = true;
return i->second.value;
}
}
- const string& s = (m_Cache[name] = SEnvValue(Load(name), NULL)).value;
+ string loaded_value = Load(name, *found);
+ m_Cache[name] = SEnvValue(loaded_value, *found ? kEmptyXCStr : NULL);
+ const string& s = m_Cache[name].value;
return s.empty() ? kEmptyStr : s;
}
@@ -153,7 +160,7 @@ void CNcbiEnvironment::Set(const string& name, const string& value)
TCache::const_iterator i = m_Cache.find(name);
if ( i != m_Cache.end() ) {
if (i->second.ptr != NULL && i->second.ptr != kEmptyXCStr) {
- free(i->second.ptr);
+ free(const_cast<TXChar*>(i->second.ptr));
}
}
m_Cache[name] = SEnvValue(value, str);
@@ -180,19 +187,22 @@ void CNcbiEnvironment::Unset(const string& name)
TCache::iterator i = m_Cache.find(name);
if ( i != m_Cache.end() ) {
if (i->second.ptr != NULL && i->second.ptr != kEmptyXCStr) {
- free(i->second.ptr);
+ free(const_cast<TXChar*>(i->second.ptr));
}
m_Cache.erase(i);
}
}
-string CNcbiEnvironment::Load(const string& name) const
+string CNcbiEnvironment::Load(const string& name, bool& found) const
{
const TXChar* s = NcbiSys_getenv(_T_XCSTRING(name));
- if ( !s )
+ if (s == NULL) {
+ found = false;
return NcbiEmptyString;
- else
+ } else {
+ found = true;
return _T_STDSTRING(s);
+ }
}
@@ -208,6 +218,7 @@ CAutoEnvironmentVariable::CAutoEnvironmentVariable(const CTempString& var_name,
: m_Env(env, eNoOwnership), m_VariableName(var_name)
{
if ( !env ) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if (app) {
m_Env.reset(&app->SetEnvironment(), eNoOwnership);
@@ -215,7 +226,7 @@ CAutoEnvironmentVariable::CAutoEnvironmentVariable(const CTempString& var_name,
m_Env.reset(new CNcbiEnvironment(NULL), eTakeOwnership);
}
}
- m_PrevValue = m_Env->Get(m_VariableName);
+ m_PrevValue = m_Env->Get(m_VariableName, &m_WasSet);
if ( value.empty() ) {
m_Env->Unset(m_VariableName);
} else {
@@ -225,7 +236,11 @@ CAutoEnvironmentVariable::CAutoEnvironmentVariable(const CTempString& var_name,
CAutoEnvironmentVariable::~CAutoEnvironmentVariable()
{
- m_Env->Set(m_VariableName, m_PrevValue);
+ if (m_WasSet) {
+ m_Env->Set(m_VariableName, m_PrevValue);
+ } else {
+ m_Env->Unset(m_VariableName);
+ }
}
@@ -254,6 +269,7 @@ CEnvironmentCleaner::CEnvironmentCleaner(const char* s, ...)
void CEnvironmentCleaner::Clean(const string& name)
{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if (app) {
app->SetEnvironment().Unset(name);
diff --git a/c++/src/corelib/ncbiexpt.cpp b/c++/src/corelib/ncbiexpt.cpp
index f9a88d6..d0f5b57 100644
--- a/c++/src/corelib/ncbiexpt.cpp
+++ b/c++/src/corelib/ncbiexpt.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbiexpt.cpp 448564 2014-10-07 16:43:31Z ivanov $
+/* $Id: ncbiexpt.cpp 456643 2015-01-14 13:08:34Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -164,7 +164,7 @@ CException::CException(const CDiagCompileInfo& info,
m_Predecessor(0),
m_InReporter(false),
m_MainText(true),
- m_Flags(0)
+ m_Flags(flags)
{
if (CompareDiagPostLevel(severity, eDiag_Critical) >= 0 &&
s_AbortIfCritical->Get()) {
@@ -175,6 +175,26 @@ CException::CException(const CDiagCompileInfo& info,
prev_exception->m_MainText = false;
}
+CException::CException(const CDiagCompileInfo& info,
+ const CException* prev_exception,
+ const string& message,
+ EDiagSev severity,
+ TFlags flags)
+: m_Severity(severity),
+ m_ErrCode(CException::eInvalid),
+ m_Predecessor(0),
+ m_InReporter(false),
+ m_MainText(true),
+ m_Flags(flags)
+{
+ if (CompareDiagPostLevel(severity, eDiag_Critical) >= 0 &&
+ s_AbortIfCritical->Get()) {
+ abort();
+ }
+ x_Init(info, message, prev_exception, severity);
+ if (prev_exception)
+ prev_exception->m_MainText = false;
+}
CException::CException(const CDiagCompileInfo& info,
const CException* prev_exception,
@@ -638,12 +658,7 @@ void CExceptionReporter::ReportDefaultEx(int err_code, int err_subcode,
flags);
} else {
CNcbiDiag d(info, cex->GetSeverity(), flags);
- d << ErrCode(err_code, err_subcode);
- if ((err_code==0 && err_subcode==0) || d.CheckFilters()) {
- d << title << *cex;
- } else {
- Reset(d);
- }
+ d << ErrCode(err_code, err_subcode) << title << " " << *cex;
}
}
diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp
index de02937..4075c3e 100644
--- a/c++/src/corelib/ncbifile.cpp
+++ b/c++/src/corelib/ncbifile.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbifile.cpp 467526 2015-05-14 11:34:11Z ivanov $
+/* $Id: ncbifile.cpp 466209 2015-04-29 18:50:29Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1561,8 +1561,12 @@ bool CDirEntry::StringToMode(const CTempString& mode,
void CDirEntry::GetUmask(TMode* user_mode, TMode* group_mode,
TMode* other_mode, TSpecialModeBits* special)
{
+#ifdef HAVE_GETUMASK
+ mode_t mode = getumask();
+#else
mode_t mode = umask(0);
umask(mode);
+#endif //HAVE_GETUMASK
ModeFromModeT(mode, user_mode, group_mode, other_mode, special);
}
diff --git a/c++/src/corelib/ncbimtx.cpp b/c++/src/corelib/ncbimtx.cpp
index 927d88c..d15ad34 100644
--- a/c++/src/corelib/ncbimtx.cpp
+++ b/c++/src/corelib/ncbimtx.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbimtx.cpp 452157 2014-11-17 15:22:17Z ivanov $
+/* $Id: ncbimtx.cpp 450144 2014-10-23 13:52:16Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/corelib/ncbiobj.cpp b/c++/src/corelib/ncbiobj.cpp
index 498d878..e2059d6 100644
--- a/c++/src/corelib/ncbiobj.cpp
+++ b/c++/src/corelib/ncbiobj.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbiobj.cpp 448564 2014-10-07 16:43:31Z ivanov $
+/* $Id: ncbiobj.cpp 469441 2015-06-04 14:27:27Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,10 @@
//#define USE_SINGLE_ALLOC
//#define USE_DEBUG_NEW
+#ifdef USE_DEBUG_NEW
+# include <cstring>
+#endif
+
// There was a long and bootless discussion:
// is it possible to determine whether the object has been created
// on the stack or on the heap.
@@ -97,6 +101,56 @@
BEGIN_NCBI_SCOPE
+class CObject;
+
+/// Initial counter value for non-heap objects
+static const CObject::TCount eInitCounterNotInHeap =
+ CObject::eCounterValid;
+/// Initial counter value for objects allocated in memory pool
+static const CObject::TCount eInitCounterInPool =
+ CObject::eCounterValid | CObject::eCounterBitsCanBeDeleted;
+/// Initial counter value for in-heap objects
+static const CObject::TCount eInitCounterInHeap =
+ CObject::eCounterValid | CObject::eCounterBitsCanBeDeleted |
+ CObject::eCounterBitsInPlainHeap;
+#if !USE_TLS_PTR
+/// Without unambiguous TLS ptr that tracks allocations
+/// the library has to guess CObject location.
+/// Here's is a value used to mark 'in stack' allocations.
+/// Initial counter value for probably non-heap objects (w/ signature)
+static const CObject::TCount eInitCounterInStack =
+ CObject::eCounterValid | CObject::eCounterBitsInPlainHeap;
+#endif
+
+#ifdef NCBI_COUNTER_64_BIT
+/// All magic counter values should have all their state bits off.
+/// Magic counter value for deleted objects
+static const CObject::TCount eMagicCounterDeleted =
+ NCBI_CONST_UINT8(0x5b0dead10f34) & ~CObject::eCounterStateMask;
+/// Magic counter value for object allocated in heap
+static const CObject::TCount eMagicCounterNew =
+ NCBI_CONST_UINT8(0x3470add10b13) & ~CObject::eCounterStateMask;
+/// Magic counter value for deleted object allocated in memory pool
+static const CObject::TCount eMagicCounterPoolDeleted =
+ NCBI_CONST_UINT8(0x420dead2075b) & ~CObject::eCounterStateMask;
+/// Magic counter value for objects allocated in memory pool
+static const CObject::TCount eMagicCounterPoolNew =
+ NCBI_CONST_UINT8(0x5490add20ec2) & ~CObject::eCounterStateMask;
+#else
+/// All magic counter values should have all their state bits off.
+/// Magic counter value for deleted objects
+static const CObject::TCount eMagicCounterDeleted =
+ 0x5b4d9f34 & ~CObject::eCounterStateMask;
+/// Magic counter value for object allocated in heap
+static const CObject::TCount eMagicCounterNew =
+ 0x3423cb13 & ~CObject::eCounterStateMask;
+/// Magic counter value for deleted object allocated in memory pool
+static const CObject::TCount eMagicCounterPoolDeleted =
+ 0x4229775b & ~CObject::eCounterStateMask;
+/// Magic counter value for objects allocated in memory pool
+static const CObject::TCount eMagicCounterPoolNew =
+ 0x54917ec2 & ~CObject::eCounterStateMask;
+#endif
/////////////////////////////////////////////////////////////////////////////
// CObject::
@@ -723,11 +777,11 @@ void CObject::DeleteThis(void)
TCount count = m_Counter.Get();
// Counter could be changed by some other thread,
// we should take care of that.
- if ( (count & eInitCounterInHeap) == TCount(eInitCounterInHeap) ) {
+ if ( (count & eInitCounterInHeap) == eInitCounterInHeap ) {
delete this;
}
else {
- _ASSERT((count & eInitCounterInPool) == TCount(eInitCounterInPool));
+ _ASSERT((count & eInitCounterInPool) == eInitCounterInPool);
CObjectMemoryPool::Delete(this);
}
}
@@ -855,11 +909,8 @@ void CObject::DoDeleteThisObject(void)
CFastMutexGuard LOCK(sm_ObjectMutex);
count = m_Counter.Get();
// DoDeleteThisObject is not allowed for stack objects
- enum {
- eCheckBits = eStateBitsValid | eStateBitsHeapSignature
- };
-
- if ( (count & eCheckBits) == TCount(eCheckBits) ) {
+ static const TCount eCheckBits = eStateBitsValid | eStateBitsHeapSignature;
+ if ( (count & eCheckBits) == eCheckBits ) {
if ( !(count & eStateBitsInHeap) ) {
// set 'in heap' flag
m_Counter.Add(eStateBitsInHeap);
@@ -967,22 +1018,22 @@ public:
unsigned total_locks = 0;
ITERATE ( TLocks, it, m_Locks ) {
++total_locks;
- LOG_POST("Locked<"<<sx_MonitorType->name()<<">"
+ ERR_POST(Note << "Locked<"<<sx_MonitorType->name()<<">"
"("<<it->first<<","<<m_Object<<")"
" @ " << *it->second);
}
unsigned total_unlocks = 0;
ITERATE ( TUnlocks, it, m_Unlocks ) {
++total_unlocks;
- LOG_POST("Unlocked<"<<sx_MonitorType->name()<<">"
+ ERR_POST(Note << "Unlocked<"<<sx_MonitorType->name()<<">"
"("<<it->first<<","<<m_Object<<")"
" @ " << *it->second);
}
if ( total_locks ) {
- LOG_POST("Total locks for "<<m_Object<<": "<<total_locks);
+ ERR_POST(Note << "Total locks for "<<m_Object<<": "<<total_locks);
}
if ( total_unlocks ) {
- LOG_POST("Total unlocks for "<<m_Object<<": "<<total_unlocks);
+ ERR_POST(Note << "Total unlocks for "<<m_Object<<": "<<total_unlocks);
}
}
int LockCount(void) const
@@ -1082,7 +1133,7 @@ void CObjectCounterLocker::Unlock(const CObject* object) const
void CObjectCounterLocker::UnlockRelease(const CObject* object) const
{
if ( MonitoredType(object) ) {
- LOG_POST("UnlockRelease<"<<typeid(*object).name()<<">"
+ ERR_POST(Note << "UnlockRelease<"<<typeid(*object).name()<<">"
"("<<this<<", "<<object<<")"
" @ " << StackTrace);
sx_LocksMonitor.Get().Unlocked(this, object);
@@ -1141,12 +1192,11 @@ void CObjectCounterLocker::ReportLockedObjects(bool )
void CObjectCounterLocker::ReportIncompatibleType(const type_info& type)
{
#ifdef _DEBUG
- ERR_POST_X(8, Fatal <<
- "Type " << type.name() << " must be derived from CObject" <<
- StackTrace);
+ ERR_FATAL_X(8, "Type "<<type.name()<<" must be derived from CObject"
+ << StackTrace);
#else
- NCBI_THROW(CCoreException, eInvalidArg,
- string("Type ")+type.name()+" must be derived from CObject");
+ NCBI_THROW_FMT(CCoreException, eInvalidArg,
+ "Type "<<type.name()<<" must be derived from CObject");
#endif
}
@@ -1247,12 +1297,11 @@ CObject* CPtrToObjectProxy::GetLockedObject(void)
void CPtrToObjectProxy::ReportIncompatibleType(const type_info& type)
{
#ifdef _DEBUG
- ERR_POST_X(8, Fatal <<
- "Type " << type.name() << " must be derived from CWeakObject"<<
- StackTrace);
+ ERR_FATAL_X(8, "Type "<<type.name()<<" must be derived from CWeakObject"
+ << StackTrace);
#else
- NCBI_THROW(CCoreException, eInvalidArg, string("Type ") +
- type.name() + " must be derived from CWeakObject");
+ NCBI_THROW_FMT(CCoreException, eInvalidArg,
+ "Type "<<type.name()<<" must be derived from CWeakObject");
#endif
}
@@ -1300,8 +1349,6 @@ static const unsigned kAllocMagicFooter = 0x9e8e0e0e;
static const unsigned kFreedMagicHeader = 0x8b0bdead;
static const unsigned kFreedMagicFooter = 0x9e0edead;
-static std::bad_alloc bad_alloc_instance;
-
DEFINE_STATIC_FAST_MUTEX(s_alloc_mutex);
static NCBI_NS_NCBI::CAtomicCounter seq_number;
static const size_t kLogSize = 64 * 1024;
@@ -1496,7 +1543,7 @@ void* operator new(size_t size) throw(std::bad_alloc)
{
void* ret = s_alloc_mem(size, false);
if ( !ret )
- throw bad_alloc_instance;
+ throw std::bad_alloc();
return ret;
}
@@ -1511,7 +1558,7 @@ void* operator new[](size_t size) throw(std::bad_alloc)
{
void* ret = s_alloc_mem(size, true);
if ( !ret )
- throw bad_alloc_instance;
+ throw std::bad_alloc();
return ret;
}
diff --git a/c++/src/corelib/ncbireg.cpp b/c++/src/corelib/ncbireg.cpp
index facb52b..3894f2d 100644
--- a/c++/src/corelib/ncbireg.cpp
+++ b/c++/src/corelib/ncbireg.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbireg.cpp 463789 2015-04-01 15:38:30Z ivanov $
+/* $Id: ncbireg.cpp 461481 2015-03-10 16:01:30Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -659,11 +659,11 @@ IRWRegistry* IRWRegistry::x_Read(CNcbiIstream& is, TFlags flags,
"Invalid registry section name" + in_path
+ ": `" + str + "'", line);
}
- // add section comment
- if ( !comment.empty() ) {
- SetComment(GetComment(section) + comment, section);
- comment.erase();
- }
+ // Unconditional, to ensure the section becomes known
+ // even if it has no comment or contents
+ SetComment(GetComment(section, kEmptyStr, impact) + comment,
+ section, kEmptyStr, flags | fCountCleared);
+ comment.erase();
break;
}
@@ -819,7 +819,7 @@ bool IRWRegistry::SetComment(const string& comment, const string& section,
const string& name, TFlags flags)
{
x_CheckFlags("IRWRegistry::SetComment", flags,
- fTransient | fNoOverride | fInternalSpaces);
+ fTransient | fNoOverride | fInternalSpaces | fCountCleared);
string clean_section = NStr::TruncateSpaces(section);
if ( !clean_section.empty() && !s_IsNameSection(clean_section, flags) ) {
_TRACE("IRWRegistry::SetComment: bad section name \""
@@ -1036,7 +1036,7 @@ bool CMemoryRegistry::x_SetComment(const string& comment,
}
TSections::iterator sit = m_Sections.find(section);
if (sit == m_Sections.end()) {
- if (comment.empty()) {
+ if (comment.empty() && (flags & fCountCleared) == 0) {
return false;
} else {
sit = m_Sections.insert(make_pair(section, SSection(m_Flags)))
@@ -1046,7 +1046,8 @@ bool CMemoryRegistry::x_SetComment(const string& comment,
}
TEntries& entries = sit->second.entries;
if (name.empty()) {
- if (comment.empty() && entries.empty()) {
+ if (comment.empty() && entries.empty()
+ && (flags & fCountCleared) == 0) {
m_Sections.erase(sit);
return true;
} else {
@@ -1672,7 +1673,8 @@ bool CCompoundRWRegistry::LoadBaseRegistries(TFlags flags, int metareg_flags,
}
}
_TRACE("LoadBaseRegistries(" << this << "): using " << s);
- NStr::Split(s, ", ", names, NStr::fSplit_CanSingleQuote);
+ NStr::Split(s, ", ", names,
+ NStr::fSplit_CanSingleQuote | NStr::fSplit_MergeDelims);
}}
typedef pair<string, CRef<IRWRegistry> > TNewBase;
diff --git a/c++/src/corelib/ncbistr.cpp b/c++/src/corelib/ncbistr.cpp
index 347c106..19d1689 100644
--- a/c++/src/corelib/ncbistr.cpp
+++ b/c++/src/corelib/ncbistr.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbistr.cpp 463914 2015-04-02 11:41:05Z ivanov $
+/* $Id: ncbistr.cpp 479746 2015-09-23 13:17:35Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -323,6 +323,30 @@ string& NStr::ToUpper(string& str)
}
+bool NStr::IsLower(const CTempString& str)
+{
+ SIZE_TYPE len = str.length();
+ for (SIZE_TYPE i = 0; i < len; ++i) {
+ if (isalpha((unsigned char)str[i]) && !islower((unsigned char)str[i])) {
+ return false;
+ }
+ }
+ return true;
+}
+
+
+bool NStr::IsUpper(const CTempString& str)
+{
+ SIZE_TYPE len = str.length();
+ for (SIZE_TYPE i = 0; i < len; ++i) {
+ if (isalpha((unsigned char)str[i]) && !isupper((unsigned char)str[i])) {
+ return false;
+ }
+ }
+ return true;
+}
+
+
int NStr::StringToNonNegativeInt(const string& str)
{
int& errno_ref = errno;
@@ -1162,7 +1186,7 @@ static double s_StringToDouble(const char* str, size_t size,
// Because strtod() may just skip such symbols.
if (!(flags & NStr::fAllowLeadingSymbols)) {
char c = str[pos];
- if ( !isdigit((unsigned int)c) && !s_IsDecimalPoint(c,flags) && c != '-' && c != '+') {
+ if ( !isdigit((unsigned char)c) && !s_IsDecimalPoint(c,flags) && c != '-' && c != '+') {
S2N_CONVERT_ERROR_INVAL(double);
}
}
@@ -1191,9 +1215,28 @@ static double s_StringToDouble(const char* str, size_t size,
if ( !endptr || endptr == begptr ) {
S2N_CONVERT_ERROR(double, kEmptyStr, EINVAL, s_DiffPtr(endptr, begptr) + pos);
}
- if ( errno_ref ) {
+ // some libs set ERANGE, others do not
+ // here, we do not consider ERANGE as error
+ if ( errno_ref && errno_ref != ERANGE ) {
S2N_CONVERT_ERROR(double, kEmptyStr, errno_ref, s_DiffPtr(endptr, begptr) + pos);
}
+ // special cases
+ if ((flags & NStr::fDecimalPosixFinite) && n != 0. && !isnan(n))
+ {
+ bool is_negative = n < 0.;
+ if (is_negative) {
+ n = -n;
+ }
+ if ( n < DBL_MIN) {
+ n = DBL_MIN;
+ } else if (!finite(n)) {
+ n = DBL_MAX;
+ }
+ if (is_negative) {
+ n = -n;
+ }
+ }
+
pos += s_DiffPtr(endptr, begptr);
// Skip allowed trailing symbols
@@ -2157,7 +2200,7 @@ void NStr::DoubleToString(string& out_str, double value,
{
char buffer[kMaxDoubleStringSize];
if (precision >= 0 ||
- ((flags & fDoublePosix) && (isnan(value) || !finite(value) || value == 0.))) {
+ ((flags & fDoublePosix) && (!finite(value) || value == 0.))) {
SIZE_TYPE n = DoubleToString(value, precision, buffer,
kMaxDoubleStringSize, flags);
buffer[n] = '\0';
@@ -2198,7 +2241,7 @@ SIZE_TYPE NStr::DoubleToString(double value, unsigned int precision,
{
char buffer[kMaxDoubleStringSize];
int n = 0;
- if ((flags & fDoublePosix) && (isnan(value) || !finite(value) || value == 0.)) {
+ if ((flags & fDoublePosix) && (!finite(value) || value == 0.)) {
if (value == 0.) {
double zero = 0.;
if (memcmp(&value, &zero, sizeof(double)) == 0) {
@@ -2726,13 +2769,15 @@ SIZE_TYPE NStr::FindNoCase(const CTempString& str, const CTempString& pattern,
} else if (islower((unsigned char) pat[0])) {
pat += (char) toupper((unsigned char) pat[0]);
}
+
if (where == eFirst) {
SIZE_TYPE pos = str.find_first_of(pat, start);
- while (pos != NPOS && pos <= end
+ while (pos != NPOS && (pos + l) <= end
&& CompareNocase(str, pos, l, pattern) != 0) {
pos = str.find_first_of(pat, pos + 1);
}
return pos > end ? NPOS : pos;
+
} else { // eLast
SIZE_TYPE pos = str.find_last_of(pat, end);
while (pos != NPOS && pos >= start
@@ -2772,6 +2817,50 @@ const string* NStr::Find(const vector <string>& vec, const CTempString& val,
}
+/// @internal
+// Check that symbol 'ch' is a word boundary character (don't matches [a-zA-Z0-9_]).
+static inline
+bool s_IsWordBoundaryChar(char ch)
+{
+ return !(ch == '_' || isalnum((unsigned char)ch));
+}
+
+
+SIZE_TYPE NStr::FindWord(const CTempString& str, const CTempString& pattern,
+ EOccurrence where, ECase use_case)
+{
+ const SIZE_TYPE slen = str.length();
+ const SIZE_TYPE plen = pattern.length();
+
+ SIZE_TYPE start = 0;
+ SIZE_TYPE end = slen;
+
+ SIZE_TYPE pos = Find(str, pattern, start, end, where, use_case);
+
+ while (pos != NPOS) {
+ // Check word boundaries
+ if ( ((pos == 0) || s_IsWordBoundaryChar(str[pos-1])) &&
+ ((pos + plen == slen) || s_IsWordBoundaryChar(str[pos+plen])) ) {
+ return pos;
+ }
+ // Find next occurrence
+ if (where == eFirst) {
+ if (pos + plen == slen) {
+ return NPOS;
+ }
+ ++start;
+ } else { // eLast
+ if (pos == 0) {
+ return NPOS;
+ }
+ --end;
+ }
+ pos = Find(str, pattern, start, end, where, use_case);
+ }
+ return pos;
+}
+
+
SIZE_TYPE NStr::CommonOverlapSize(const CTempString& s1, const CTempString& s2)
{
const SIZE_TYPE len1 = s1.length();
@@ -2924,6 +3013,54 @@ void NStr::TruncateSpacesInPlace(string& str, ETrunc where)
}
+void NStr::TrimPrefixInPlace(string& str, const CTempString& prefix,
+ ECase use_case)
+{
+ if (!str.length() ||
+ !prefix.length() ||
+ !Equal(str, 0, prefix.length(), prefix, use_case)) {
+ return;
+ }
+ str.erase(0, prefix.length());
+}
+
+
+void NStr::TrimPrefixInPlace(CTempString& str, const CTempString& prefix,
+ ECase use_case)
+{
+ if (!str.length() ||
+ !prefix.length() ||
+ !Equal(str, 0, prefix.length(), prefix, use_case)) {
+ return;
+ }
+ str.assign(str.data() + prefix.length(), str.length() - prefix.length());
+}
+
+
+void NStr::TrimSuffixInPlace(string& str, const CTempString& suffix,
+ ECase use_case)
+{
+ if (!str.length() ||
+ !suffix.length() ||
+ !Equal(str, str.length() - suffix.length(), suffix.length(), suffix, use_case)) {
+ return;
+ }
+ str.erase(str.length() - suffix.length());
+}
+
+
+void NStr::TrimSuffixInPlace(CTempString& str, const CTempString& suffix,
+ ECase use_case)
+{
+ if (!str.length() ||
+ !suffix.length() ||
+ !Equal(str, str.length() - suffix.length(), suffix.length(), suffix, use_case)) {
+ return;
+ }
+ str.erase(str.length() - suffix.length());
+}
+
+
string& NStr::Replace(const string& src,
const string& search, const string& replace,
string& dst, SIZE_TYPE start_pos, SIZE_TYPE max_replace)
@@ -3006,6 +3143,52 @@ string NStr::Replace(const string& src,
return dst;
}
+#if 0
+static
+string& _replace_reduct(string& src,
+ const string& search, const string& replace,
+ SIZE_TYPE start_pos, SIZE_TYPE max_replace)
+{
+ size_t remove_len = 0;
+
+ const char* start_ptr = src.c_str() + start_pos;
+ char* write_pos = (char*) start_ptr;
+
+ for (SIZE_TYPE count = 0; !(max_replace && count >= max_replace); count++) {
+
+ const char* found = strstr(start_ptr, search.c_str());
+
+ SIZE_TYPE len = (found?found:(src.c_str() + src.size())) - start_ptr;
+ if (len && write_pos != start_ptr)
+ {
+ memcpy(write_pos, start_ptr, len);
+ }
+
+ if (found == 0)
+ break;
+
+ write_pos += len;
+ start_ptr = found + search.size();
+
+ if (replace.size() == 1)
+ {
+ *write_pos++ = replace[0];
+ } else
+ if (replace.size() > 0)
+ {
+ memcpy(write_pos, replace.c_str(), replace.size());
+ write_pos += replace.size();
+ }
+
+ remove_len += (search.size() - replace.size());
+ }
+
+ if (remove_len)
+ src.resize(src.size() - remove_len);
+
+ return src;
+}
+#endif
string& NStr::ReplaceInPlace(string& src,
const string& search, const string& replace,
@@ -3015,6 +3198,11 @@ string& NStr::ReplaceInPlace(string& src,
search == replace )
return src;
+#if 0
+ if (search.size() >= replace.size())
+ return _replace_reduct(src, search, replace, start_pos, max_replace);
+#endif
+
bool equal_len = (search.size() == replace.size());
for (SIZE_TYPE count = 0; !(max_replace && count >= max_replace); count++){
start_pos = src.find(search, start_pos);
@@ -3032,6 +3220,28 @@ string& NStr::ReplaceInPlace(string& src,
return src;
}
+#if 0
+struct unit_test
+{
+ string test(const string& str, const string& search, const string& replace)
+ {
+ string s = str;
+ NStr::ReplaceInPlace(s, search, replace);
+ return s;
+ };
+ unit_test()
+ {
+ test("11 222 3333 4444", " ", "");
+ test("11 222 3333 4444", " ", ".");
+ test("11 222 3333 4444", "222", "x");
+ test("11 222 3333 4444", "222", "xxx");
+ test("11 222 3333 4444", "222", "xxxx");
+ }
+};
+
+unit_test t;
+#endif
+
template<typename TString, typename TContainer>
TContainer& s_Split(const TString& str, const TString& delim,
@@ -3273,6 +3483,155 @@ string NStr::Join(const set<CTempString>& arr, const CTempString& delim)
}
+// Auxiliary macros for NStr::Sanitize()
+
+#define SS_WRITE_SUBSTR \
+ if (!out.get()) { \
+ out.reset(new CNcbiOstrstream); \
+ } \
+ out->write(str.data() + pos, n_good); \
+ n_good = 0; \
+ pos = i
+
+#define SS_WRITE_SPACES \
+ if (!out.get()) { \
+ out.reset(new CNcbiOstrstream); \
+ } \
+ SIZE_TYPE n = (flags & fSS_NoMerge) ? n_spaces : 1; \
+ for (SIZE_TYPE i = n; i > 0; i--) { \
+ out->put(' '); \
+ }
+
+string NStr::Sanitize(CTempString str, TSS_Flags flags)
+{
+ auto_ptr<CNcbiOstrstream> out;
+ SIZE_TYPE i;
+ SIZE_TYPE pos = 0; // start position of the substring
+ SIZE_TYPE n_good = 0; // length of substring (good symbols)
+ SIZE_TYPE n_spaces = 0; // number of accumulated spaces
+
+ // Use fSS_print by default if no any other filter
+ if ( !(flags & (fSS_alpha | fSS_digit | fSS_alnum |
+ fSS_print | fSS_cntrl | fSS_punct)) ) {
+ flags |= fSS_print;
+ }
+
+ for (i = 0; i < str.size(); i++)
+ {
+ char c = str[i];
+
+ // Check on bare space.
+ // Do not use ::isspace() here due it interference with ::iscntrl().
+ if ( c == ' ' ) {
+ // Spaces starts and we have good chars before? -- write it immediately
+ if ( n_good ) {
+ SS_WRITE_SUBSTR;
+ }
+ // Count and skip all consecutive spaces
+ ++n_spaces;
+ continue;
+ }
+
+ // Check against filters
+ bool allowed = ((flags & fSS_Reject) != 0);
+ if (((flags & fSS_print) && isprint((unsigned char)c)) ||
+ ((flags & fSS_alnum) && isalnum((unsigned char)c)) ||
+ ((flags & fSS_alpha) && isalpha((unsigned char)c)) ||
+ ((flags & fSS_digit) && isdigit((unsigned char)c)) ||
+ ((flags & fSS_cntrl) && iscntrl((unsigned char)c)) ||
+ ((flags & fSS_punct) && ispunct((unsigned char)c)) ) {
+
+ // If matched and reverse logic -- treat char as rejected
+ allowed = ((flags & fSS_Reject) == 0);
+ }
+
+ // Good character and no spaces before?
+ if ( allowed && !n_spaces ) {
+ // Continue to build substring or start new one
+ if ( n_good ) {
+ ++n_good;
+ } else {
+ n_good = 1;
+ pos = i;
+ }
+ continue;
+ }
+
+ // Rejected character?
+ if ( !allowed ) {
+ // Write previously accumulated substring
+ if ( n_good ) {
+ SS_WRITE_SUBSTR;
+ }
+ // Increase space pool or just ignore
+ if ( !(flags & fSS_Remove) ) {
+ ++n_spaces;
+ }
+ continue;
+ }
+
+ _ASSERT( allowed );
+ _ASSERT( !n_good );
+
+ // Otherwise need to process accumulated spaces first
+ if ( n_spaces ) {
+ // Don't write leading spaces
+ if ( pos || (!pos && (flags & fSS_NoTruncate_Begin))) {
+ SS_WRITE_SPACES;
+ }
+ n_spaces = 0;
+ }
+ // Start new substring
+ n_good = 1;
+ pos = i;
+
+ } /* for */
+
+ // Some good characters?
+ if ( n_good ) {
+ if (i == n_good) {
+ // All are good - return (a copy of) the original string
+ return str;
+ }
+ if ( !out.get() ) {
+ // All leading characters are bad - return a second part of
+ // the original string, to avoid copying (below).
+ return str.substr(pos, n_good);
+ }
+ // Write last accumulated substring
+ SS_WRITE_SUBSTR;
+ }
+
+ // Empty string, or all spaces (or rejected chars replaced with spaces)?
+ if ( (i == n_spaces) || (n_spaces && !out.get()) ) {
+ if (!n_spaces || ((flags & fSS_NoTruncate) != fSS_NoTruncate) ) {
+ return kEmptyStr;
+ }
+ if (flags & fSS_NoMerge) {
+ SS_WRITE_SPACES;
+ return CNcbiOstrstreamToString(*out);
+ } else {
+ return " ";
+ }
+ return kEmptyStr;
+ }
+
+ // Trailing spaces?
+ if ( n_spaces ) {
+ _ASSERT(out.get());
+ if (flags & fSS_NoTruncate_End) {
+ SS_WRITE_SPACES;
+ }
+ }
+ if (out.get()) {
+ // Return sanitized string
+ return CNcbiOstrstreamToString(*out);
+ }
+
+ // All rejected
+ return kEmptyStr;
+}
+
enum ELanguage {
eLanguage_C,
@@ -3629,6 +3988,8 @@ string NStr::HtmlEncode(const CTempString& str, THtmlEncode flags)
// Character entity references
// http://www.w3.org/TR/html4/sgml/entities.html
// http://www.w3.org/TR/1998/REC-html40-19980424/charset.html#h-5.3
+// only some entities from here were added (those shifted to right):
+// http://dev.w3.org/html5/html-author/charref
static struct tag_HtmlEntities
{
@@ -3636,11 +3997,38 @@ static struct tag_HtmlEntities
const char* s;
} const s_HtmlEntities[] = {
+ { 9, "Tab" },
+ { 10, "NewLine" },
+ { 33, "excl" },
{ 34, "quot" },
+ { 35, "num" },
+ { 36, "dollar" },
+ { 37, "percnt" },
{ 38, "amp" },
{ 39, "apos" },
+ { 40, "lpar" },
+ { 41, "rpar" },
+ { 42, "ast" },
+ { 43, "plus" },
+ { 44, "comma" },
+ { 46, "period" },
+ { 47, "sol" },
+ { 58, "colon" },
+ { 59, "semi" },
{ 60, "lt" },
+ { 61, "equals" },
{ 62, "gt" },
+ { 63, "quest" },
+ { 64, "commat" },
+ { 91, "lsqb" },
+ { 92, "bsol" },
+ { 93, "rsqb" },
+ { 94, "Hat" },
+ { 95, "lowbar" },
+ { 96, "grave" },
+ {123, "lcub" },
+ {124, "verbar" },
+ {125, "rcub" },
{ 160, "nbsp" },
{ 161, "iexcl" },
{ 162, "cent" },
@@ -3892,6 +4280,16 @@ static struct tag_HtmlEntities
{ 0, 0 }
};
+string NStr::HtmlEntity(TUnicodeSymbol uch)
+{
+ const struct tag_HtmlEntities* p = s_HtmlEntities;
+ for ( ; p->u != 0; ++p) {
+ if (uch == p->u) {
+ return p->s;
+ }
+ }
+ return kEmptyStr;
+}
string NStr::HtmlDecode(const CTempString& str, EEncoding encoding, THtmlDecode* result_flags)
{
@@ -4042,8 +4440,10 @@ string NStr::ShellEncode(const string& str)
// Aesthetic issue: Most people are not familiar with the BASH-only
// quoting style. Avoid it as much as possible.
- if (find_if(str.begin(),str.end(),not1(ptr_fun(::isprint))) != str.end()) {
- return "$'" + NStr::PrintableString(str) + "'";
+ ITERATE ( string, it, str ) {
+ if ( !isprint(Uchar(*it)) ) {
+ return "$'" + NStr::PrintableString(str) + "'";
+ }
}
/////////////////////////////////////////////////////////////////////////
@@ -4363,250 +4763,284 @@ static SIZE_TYPE s_VisibleHtmlWidth(const string& str)
return width;
}
-list<string>& NStr::Wrap(const string& str, SIZE_TYPE width,
- list<string>& arr, NStr::TWrapFlags flags,
- const string* prefix, const string* prefix1)
-{
- if (prefix == 0) {
- prefix = &kEmptyStr ;
- }
-
- const string* pfx = prefix1 ? prefix1 : prefix;
- SIZE_TYPE pos = 0, len = str.size(), nl_pos = 0;
-
- const bool is_html = flags & fWrap_HTMLPre ? true : false;
- const bool do_flat = (flags & fWrap_FlatFile) != 0;
-
- enum EScore { // worst to best
- eForced,
- ePunct,
- eComma,
- eSpace,
- eNewline
- };
-
- // To avoid copying parts of str when we need to store a
- // substr of str, we store the substr as a pair
- // representing start (inclusive) and end (exclusive).
- typedef pair<SIZE_TYPE, SIZE_TYPE> TWrapSubstr;
-
- // This variable is used for HTML links that cross line boundaries.
- // Since it's aesthetically displeasing for a link to cross a boundary, we
- // close it at the end of each line and re-open it after the next line's
- // prefix
- // (This is needed in, e.g. AE017351)
- TWrapSubstr best_link(0, 0); // last link found before current best_pos
- TWrapSubstr latest_link(0, 0); // last link found at all
-
- while (pos < len) {
- bool hyphen = false; // "-" or empty
- SIZE_TYPE column = is_html? s_VisibleHtmlWidth(*pfx) : pfx->size();
- SIZE_TYPE column0 = column;
- // the next line will start at best_pos
- SIZE_TYPE best_pos = NPOS;
- EScore best_score = eForced;
-
- // certain logic can be skipped if this part has no backspace,
- // which is, by far, the most common case
- bool thisPartHasBackspace = false;
-
- arr.push_back("");
- arr.back().reserve( width );
- arr.back() = *pfx;
-
- // append any still-open links from previous lines
- if( is_html && best_link.second != 0 ) {
- arr.back().append(
- str.begin() + best_link.first,
- str.begin() + best_link.second );
- }
-
- SIZE_TYPE pos0 = pos;
-
- // we can't do this in HTML mode because we might have to deal with
- // link tags that go across lines.
- if( ! is_html ) {
- if (nl_pos <= pos) {
- nl_pos = str.find('\n', pos);
- if (nl_pos == NPOS) {
- nl_pos = len;
- }
- }
- if (column + (nl_pos-pos) <= width ) {
- pos0 = nl_pos;
- }
- }
-
- for (SIZE_TYPE pos2 = pos0; pos2 < len && column <= width;
- ++pos2, ++column) {
- EScore score = eForced;
- SIZE_TYPE score_pos = pos2;
- const char c = str[pos2];
-
- if (c == '\n') {
- best_pos = pos2;
- best_score = eNewline;
- best_link = latest_link;
- break;
- } else if (isspace((unsigned char) c)) {
- if ( !do_flat && pos2 > 0 &&
- isspace((unsigned char) str[pos2 - 1])) {
- if(pos2 < len - 1 && str[pos2 + 1] == '\b') {
- thisPartHasBackspace = true;
- }
- continue; // take the first space of a group
- }
- score = eSpace;
- } else if (is_html && c == '<') {
- // treat tags as zero-width...
- SIZE_TYPE start_of_tag = pos2;
- pos2 = s_EndOfTag(str, pos2);
- --column;
- if (pos2 == NPOS) {
- break;
- }
-
- if( (pos2 - start_of_tag) >= 6 &&
- str[start_of_tag+1] == 'a' &&
- str[start_of_tag+2] == ' ' &&
- str[start_of_tag+3] == 'h' &&
- str[start_of_tag+4] == 'r' &&
- str[start_of_tag+5] == 'e' &&
- str[start_of_tag+6] == 'f' )
- {
- // remember current link in case of line wrap
- latest_link.first = start_of_tag;
- latest_link.second = pos2 + 1;
- }
- if( (pos2 - start_of_tag) >= 3 &&
- str[start_of_tag+1] == '/' &&
- str[start_of_tag+2] == 'a' &&
- str[start_of_tag+3] == '>')
- {
- // link is closed
- latest_link.first = 0;
- latest_link.second = 0;
- }
- } else if (is_html && c == '&') {
- // ...and references as single characters
- pos2 = s_EndOfReference(str, pos2);
- if (pos2 == NPOS) {
- break;
- }
- } else if ( c == ',' && column < width && score_pos < len - 1 ) {
- score = eComma;
- ++score_pos;
- } else if (do_flat ? c == '-' : ispunct((unsigned char) c)) {
- // For flat files, only whitespace, hyphens and commas
- // are special.
- switch(c) {
- case '(': case '[': case '{': case '<': case '`':
- score = ePunct;
- break;
- default:
- if( score_pos < len - 1 && column < width ) {
- score = ePunct;
- ++score_pos;
- }
- break;
- }
- }
-
- if (score >= best_score && score_pos > pos0) {
- best_pos = score_pos;
- best_score = score;
- best_link = latest_link;
- }
-
- while (pos2 < len - 1 && str[pos2 + 1] == '\b') {
- // Account for backspaces
- ++pos2;
- if (column > column0) {
- --column;
- }
- thisPartHasBackspace = true;
- }
- }
-
- if ( best_score != eNewline && column <= width ) {
- if( best_pos != len ) {
- // If the whole remaining text can fit, don't split it...
- best_pos = len;
- best_link = latest_link;
- // Force backspace checking, to play it safe
- thisPartHasBackspace = true;
- }
- } else if ( best_score == eForced && (flags & fWrap_Hyphenate) ) {
- hyphen = true;
- --best_pos;
- }
-
- {{
- string::const_iterator begin = str.begin() + pos;
- string::const_iterator end = str.begin() + best_pos;
- if( thisPartHasBackspace ) {
- // eat backspaces and the characters (if any) that precede them
-
- string::const_iterator bs; // position of next backspace
- while ((bs = find(begin, end, '\b')) != end) {
- if (bs != begin) {
- // add all except the last one
- arr.back().append(begin, bs - 1);
- }
- else {
- // The backspace is at the beginning of next substring,
- // so we should remove previously added symbol if any.
- SIZE_TYPE size = arr.back().size();
- if (size > pfx->size()) { // current size > prefix size
- arr.back().resize(size - 1);
- }
- }
- // skip over backspace
- begin = bs + 1;
- }
- }
- if (begin != end) {
- // add remaining characters
- arr.back().append(begin, end);
- }
- }}
-
- // if we didn't close the link on this line, we
- // close it here
- if( is_html && best_link.second != 0 ) {
- arr.back() += "</a>";
- }
-
- if ( hyphen ) {
- arr.back() += '-';
- }
- pos = best_pos;
- pfx = prefix;
+static
+inline bool _isspace(unsigned char c)
+{
+ return ((c>=0x09 && c<=0x0D) || (c==0x20));
+}
+
+template<typename _D>
+void NStr::WrapIt(const string& str, SIZE_TYPE width,
+ _D& dest, TWrapFlags flags,
+ const string* prefix,
+ const string* prefix1)
+{
+ if (prefix == 0) {
+ prefix = &kEmptyStr;
+ }
+
+ if (prefix1 == 0)
+ prefix1 = prefix;
+
+ SIZE_TYPE pos = 0, len = str.size(), nl_pos = 0;
+
+ const bool is_html = flags & fWrap_HTMLPre ? true : false;
+ const bool do_flat = (flags & fWrap_FlatFile) != 0;
+ string temp_back; temp_back.reserve(width);
+
+ enum EScore { // worst to best
+ eForced,
+ ePunct,
+ eComma,
+ eSpace,
+ eNewline
+ };
+
+ // To avoid copying parts of str when we need to store a
+ // substr of str, we store the substr as a pair
+ // representing start (inclusive) and end (exclusive).
+ typedef pair<SIZE_TYPE, SIZE_TYPE> TWrapSubstr;
+
+ // This variable is used for HTML links that cross line boundaries.
+ // Since it's aesthetically displeasing for a link to cross a boundary, we
+ // close it at the end of each line and re-open it after the next line's
+ // prefix
+ // (This is needed in, e.g. AE017351)
+ TWrapSubstr best_link(0, 0); // last link found before current best_pos
+ TWrapSubstr latest_link(0, 0); // last link found at all
+
+ while (pos < len) {
+ bool hyphen = false; // "-" or empty
+ SIZE_TYPE column = is_html ? s_VisibleHtmlWidth(*prefix1) : prefix1->size();
+ SIZE_TYPE column0 = column;
+ // the next line will start at best_pos
+ SIZE_TYPE best_pos = NPOS;
+ EScore best_score = eForced;
+
+ // certain logic can be skipped if this part has no backspace,
+ // which is, by far, the most common case
+ bool thisPartHasBackspace = false;
+
+ temp_back = *prefix1;
+
+ // append any still-open links from previous lines
+ if (is_html && best_link.second != 0) {
+ temp_back.append(
+ str.begin() + best_link.first,
+ str.begin() + best_link.second);
+ }
+
+ SIZE_TYPE pos0 = pos;
+
+ // we can't do this in HTML mode because we might have to deal with
+ // link tags that go across lines.
+ if (!is_html) {
+ if (nl_pos <= pos) {
+ nl_pos = str.find('\n', pos);
+ if (nl_pos == NPOS) {
+ nl_pos = len;
+ }
+ }
+ if (column + (nl_pos - pos) <= width) {
+ pos0 = nl_pos;
+ }
+ }
+
+ for (SIZE_TYPE pos2 = pos0; pos2 < len && column <= width;
+ ++pos2, ++column) {
+ EScore score = eForced;
+ SIZE_TYPE score_pos = pos2;
+ const char c = str[pos2];
+
+ if (c == '\n') {
+ best_pos = pos2;
+ best_score = eNewline;
+ best_link = latest_link;
+ break;
+ }
+ else if (_isspace((unsigned char)c)) {
+ if (!do_flat && pos2 > 0 &&
+ _isspace((unsigned char)str[pos2 - 1])) {
+ if (pos2 < len - 1 && str[pos2 + 1] == '\b') {
+ thisPartHasBackspace = true;
+ }
+ continue; // take the first space of a group
+ }
+ score = eSpace;
+ }
+ else if (is_html && c == '<') {
+ // treat tags as zero-width...
+ SIZE_TYPE start_of_tag = pos2;
+ pos2 = s_EndOfTag(str, pos2);
+ --column;
+ if (pos2 == NPOS) {
+ break;
+ }
+
+ if ((pos2 - start_of_tag) >= 6 &&
+ str[start_of_tag + 1] == 'a' &&
+ str[start_of_tag + 2] == ' ' &&
+ str[start_of_tag + 3] == 'h' &&
+ str[start_of_tag + 4] == 'r' &&
+ str[start_of_tag + 5] == 'e' &&
+ str[start_of_tag + 6] == 'f')
+ {
+ // remember current link in case of line wrap
+ latest_link.first = start_of_tag;
+ latest_link.second = pos2 + 1;
+ }
+ if ((pos2 - start_of_tag) >= 3 &&
+ str[start_of_tag + 1] == '/' &&
+ str[start_of_tag + 2] == 'a' &&
+ str[start_of_tag + 3] == '>')
+ {
+ // link is closed
+ latest_link.first = 0;
+ latest_link.second = 0;
+ }
+ }
+ else if (is_html && c == '&') {
+ // ...and references as single characters
+ pos2 = s_EndOfReference(str, pos2);
+ if (pos2 == NPOS) {
+ break;
+ }
+ }
+ else if (c == ',' && column < width && score_pos < len - 1) {
+ score = eComma;
+ ++score_pos;
+ }
+ else if (do_flat ? c == '-' : ispunct((unsigned char)c)) {
+ // For flat files, only whitespace, hyphens and commas
+ // are special.
+ switch (c) {
+ case '(': case '[': case '{': case '<': case '`':
+ score = ePunct;
+ break;
+ default:
+ if (score_pos < len - 1 && column < width) {
+ score = ePunct;
+ ++score_pos;
+ }
+ break;
+ }
+ }
+
+ if (score >= best_score && score_pos > pos0) {
+ best_pos = score_pos;
+ best_score = score;
+ best_link = latest_link;
+ }
+
+ while (pos2 < len - 1 && str[pos2 + 1] == '\b') {
+ // Account for backspaces
+ ++pos2;
+ if (column > column0) {
+ --column;
+ }
+ thisPartHasBackspace = true;
+ }
+ }
+
+ if (best_score != eNewline && column <= width) {
+ if (best_pos != len) {
+ // If the whole remaining text can fit, don't split it...
+ best_pos = len;
+ best_link = latest_link;
+ // Force backspace checking, to play it safe
+ thisPartHasBackspace = true;
+ }
+ }
+ else if (best_score == eForced && (flags & fWrap_Hyphenate)) {
+ hyphen = true;
+ --best_pos;
+ }
+
+ {{
+ string::const_iterator begin = str.begin() + pos;
+ string::const_iterator end = str.begin() + best_pos;
+ if (thisPartHasBackspace) {
+ // eat backspaces and the characters (if any) that precede them
+
+ string::const_iterator bs; // position of next backspace
+ while ((bs = find(begin, end, '\b')) != end) {
+ if (bs != begin) {
+ // add all except the last one
+ temp_back.append(begin, bs - 1);
+ }
+ else {
+ // The backspace is at the beginning of next substring,
+ // so we should remove previously added symbol if any.
+ SIZE_TYPE size = temp_back.size();
+ if (size > prefix1->size()) { // current size > prefix size
+ temp_back.resize(size - 1);
+ }
+ }
+ // skip over backspace
+ begin = bs + 1;
+ }
+ }
+ if (begin != end) {
+ // add remaining characters
+ temp_back.append(begin, end);
+ }
+ }}
+
+ // if we didn't close the link on this line, we
+ // close it here
+ if (is_html && best_link.second != 0) {
+ temp_back += "</a>";
+ }
+
+ if (hyphen) {
+ temp_back += '-';
+ }
+ pos = best_pos;
+ prefix1 = prefix;
+
+ if (do_flat) {
+ if (best_score == eSpace) {
+ while (str[pos] == ' ') {
+ ++pos;
+ }
+ if (str[pos] == '\n') {
+ ++pos;
+ }
+ }
+ if (best_score == eNewline) {
+ ++pos;
+ }
+ }
+ else {
+ if (best_score == eSpace || best_score == eNewline) {
+ ++pos;
+ }
+ }
+ while (pos < len && str[pos] == '\b') {
+ ++pos;
+ }
+
+ dest.Append(temp_back);
+ }
+}
+
+
+void NStr::Wrap(const string& str, SIZE_TYPE width,
+ IWrapDest& dest, TWrapFlags flags,
+ const string* prefix,
+ const string* prefix1)
+{
+ WrapIt(str, width, dest, flags, prefix, prefix1);
+}
- if (do_flat) {
- if (best_score == eSpace) {
- while (str[pos] == ' ') {
- ++pos;
- }
- if (str[pos] == '\n') {
- ++pos;
- }
- }
- if (best_score == eNewline) {
- ++pos;
- }
- }
- else {
- if ( best_score == eSpace || best_score == eNewline ) {
- ++pos;
- }
- }
- while (pos < len && str[pos] == '\b') {
- ++pos;
- }
- }
- return arr;
+list<string>& NStr::Wrap(const string& str, SIZE_TYPE width,
+ list<string>& arr2, NStr::TWrapFlags flags,
+ const string* prefix, const string* prefix1)
+{
+ CWrapDestStringList d(arr2);
+ WrapIt(str, width, d, flags, prefix, prefix1);
+ return arr2;
}
@@ -4693,9 +5127,11 @@ list<string>& NStr::Justify(const CTempString& str,
SIZE_TYPE wlen = pos - start;
if (!wlen)
break;
- if (len + wlen + nw > width) {
+ if (width < len + nw + wlen) {
if (nw) {
- pos = start; // Will have to rescan this word again
+ if (width < wlen && len < width - len)
+ big = true; // Big word is coming, no space stretch
+ pos = start; // Will have to rescan this word again
break;
}
big = true; // Long line with a long lonely word :-/
@@ -5681,9 +6117,11 @@ CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUnicode& src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
}
@@ -5695,9 +6133,11 @@ CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const wstring& src) {
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TUnicodeSymbol* src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
}
@@ -5711,10 +6151,12 @@ CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TUnicodeSymbol* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#endif
CStringUTF8_DEPRECATED::CStringUTF8_DEPRECATED(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
@@ -5775,9 +6217,11 @@ CStringUTF8::CStringUTF8(
CStringUTF8::CStringUTF8(const TStringUnicode& src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8::CStringUTF8(const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
CStringUTF8::CStringUTF8(const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
}
@@ -5789,9 +6233,11 @@ CStringUTF8::CStringUTF8(const wstring& src) {
CStringUTF8::CStringUTF8(const TUnicodeSymbol* src) {
assign( CUtf8::AsUTF8(src));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8::CStringUTF8(const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
}
+#endif
CStringUTF8::CStringUTF8(const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
}
@@ -5806,10 +6252,12 @@ CStringUTF8::CStringUTF8(
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8::CStringUTF8(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
}
+#endif
CStringUTF8::CStringUTF8(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
@@ -5824,10 +6272,12 @@ CStringUTF8& CStringUTF8::operator= (const TStringUnicode& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::operator= (const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::operator= (const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -5842,10 +6292,12 @@ CStringUTF8& CStringUTF8::operator= (const TUnicodeSymbol* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::operator= (const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::operator= (const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -5860,10 +6312,12 @@ CStringUTF8& CStringUTF8::operator+= (const TStringUnicode& src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::operator+= (const TStringUCS4& src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::operator+= (const TStringUCS2& src) {
append( CUtf8::AsUTF8(src));
return *this;
@@ -5878,10 +6332,12 @@ CStringUTF8& CStringUTF8::operator+= (const TUnicodeSymbol* src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::operator+= (const TCharUCS4* src) {
append( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::operator+= (const TCharUCS2* src) {
append( CUtf8::AsUTF8(src));
return *this;
@@ -5902,10 +6358,12 @@ CStringUTF8& CStringUTF8::Assign(const TStringUnicode& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Assign(const TStringUCS4& src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Assign(const TStringUCS2& src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -5920,10 +6378,12 @@ CStringUTF8& CStringUTF8::Assign(const TUnicodeSymbol* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Assign(const TCharUCS4* src) {
assign( CUtf8::AsUTF8(src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Assign(const TCharUCS2* src) {
assign( CUtf8::AsUTF8(src));
return *this;
@@ -5939,11 +6399,13 @@ CStringUTF8& CStringUTF8::Assign(
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Assign(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Assign(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
assign( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
@@ -5969,10 +6431,12 @@ CStringUTF8& CStringUTF8::Append(const TStringUnicode& src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Append(const TStringUCS4& src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Append(const TStringUCS2& src) {
append( CUtf8::AsUTF8( src));
return *this;
@@ -5987,10 +6451,12 @@ CStringUTF8& CStringUTF8::Append(const TUnicodeSymbol* src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Append(const TCharUCS4* src) {
append( CUtf8::AsUTF8( src));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Append(const TCharUCS2* src) {
append( CUtf8::AsUTF8( src));
return *this;
@@ -6006,11 +6472,13 @@ CStringUTF8& CStringUTF8::Append(
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#if NCBITOOLKIT_USE_LONG_UCS4
CStringUTF8& CStringUTF8::Append(
ECharBufferType type, const TCharUCS4* src, SIZE_TYPE char_count) {
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
return *this;
}
+#endif
CStringUTF8& CStringUTF8::Append(
ECharBufferType type, const TCharUCS2* src, SIZE_TYPE char_count) {
append( CUtf8::AsUTF8(src, type == eCharBuffer ? char_count : NPOS));
@@ -6770,6 +7238,27 @@ SIZE_TYPE CTempStringList::GetSize(void) const
}
+CTempString_Storage::CTempString_Storage(void)
+{
+}
+
+
+CTempString_Storage::~CTempString_Storage(void)
+{
+ NON_CONST_ITERATE(TData, it, m_Data) {
+ delete[] (*it);
+ *it = 0;
+ }
+}
+
+
+char* CTempString_Storage::Allocate(CTempString::size_type len)
+{
+ m_Data.push_back(new char[len]);
+ return m_Data.back();
+}
+
+
bool CStrTokenizeBase::Advance(CTempStringList* part_collector)
{
SIZE_TYPE pos = m_Pos, part_start = m_Pos, delim_pos = 0, quote_pos = 0;
diff --git a/c++/src/corelib/ncbistre.cpp b/c++/src/corelib/ncbistre.cpp
index 301d11f..d8a0b4b 100644
--- a/c++/src/corelib/ncbistre.cpp
+++ b/c++/src/corelib/ncbistre.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbistre.cpp 450561 2014-10-28 15:18:26Z ivanov $
+/* $Id: ncbistre.cpp 447116 2014-09-22 18:27:54Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -299,7 +299,7 @@ size_t NcbiStreamToString(string* str, CNcbiIstream& is, size_t pos)
str_size += (size_t) count;
if (str) {
if ((size_t) count == buf_size) {
- if (buf_size < (1UL << 16))
+ if (buf_size < (1UL << 20))
buf_size <<= 1;
str->resize(str_size + buf_size);
} else
diff --git a/c++/src/corelib/ncbithr.cpp b/c++/src/corelib/ncbithr.cpp
index 657c0da..62050d1 100644
--- a/c++/src/corelib/ncbithr.cpp
+++ b/c++/src/corelib/ncbithr.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbithr.cpp 445747 2014-09-08 14:38:30Z ivanov $
+/* $Id: ncbithr.cpp 467434 2015-05-13 16:41:39Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,6 +48,9 @@
#ifdef NCBI_POSIX_THREADS
# include <sys/time.h> // for gettimeofday()
#endif
+#ifdef NCBI_OS_LINUX
+# include <sys/prctl.h>
+#endif
#include "ncbidbg_p.hpp"
@@ -136,11 +139,13 @@ static void s_CleanupMainUsedTlsBases(CUsedTlsBases& tls)
}
// Storage for used TLS sets
-CStaticTls<CUsedTlsBases> CUsedTlsBases::sm_UsedTlsBases;
+CStaticTls<CUsedTlsBases>
+ CUsedTlsBases::sm_UsedTlsBases(0, CSafeStaticLifeSpan::eLifeSpan_Long);
// Main thread needs a usual safe-static-ref for proper cleanup --
// there's no thread which can do it on destruction.
static CSafeStatic<CUsedTlsBases>
-s_MainUsedTlsBases(0, s_CleanupMainUsedTlsBases);
+s_MainUsedTlsBases(0, s_CleanupMainUsedTlsBases,
+CSafeStaticLifeSpan::eLifeSpan_Long);
CUsedTlsBases& CUsedTlsBases::GetUsedTlsBases(void)
{
@@ -862,6 +867,18 @@ void CThread::GetSystemID(TThreadSystemID* id)
}
+#if defined(NCBI_OS_LINUX) && defined(PR_SET_NAME)
+void CThread::SetCurrentThreadName(const CTempString& name)
+{
+ prctl(PR_SET_NAME, (unsigned long)name.data(), 0, 0, 0);
+}
+#else
+void CThread::SetCurrentThreadName(const CTempString&)
+{
+}
+#endif
+
+
const char* CThreadException::GetErrCodeString(void) const
{
switch (GetErrCode()) {
diff --git a/c++/src/corelib/ncbitime.cpp b/c++/src/corelib/ncbitime.cpp
index fe0f610..e826d5d 100644
--- a/c++/src/corelib/ncbitime.cpp
+++ b/c++/src/corelib/ncbitime.cpp
@@ -1,4 +1,4 @@
-/* $Id: ncbitime.cpp 457992 2015-01-29 19:30:41Z kazimird $
+/* $Id: ncbitime.cpp 472773 2015-07-14 13:58:13Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -43,6 +43,9 @@
# include <sys/time.h>
#endif
+
+// The current difference in seconds between UTC and local time on this computer.
+// UTC = local time + TimeZone()
#if defined(__CYGWIN__)
# define TimeZone() _timezone
# define Daylight() _daylight
@@ -51,6 +54,14 @@
# define Daylight() daylight
#endif
+// The offset in seconds of daylight saving time.
+// 1 hour for most time zones.
+#if defined(NCBI_COMPILER_MSVC)
+# define DSTBias() _dstbias
+#else
+# define DSTBias() -3600
+#endif
+
#if defined(NCBI_OS_DARWIN) || defined(NCBI_OS_BSD)
# define TIMEZONE_IS_UNDEFINED 1
#endif
@@ -84,7 +95,7 @@ static CSafeStatic<CFastLocalTime> s_FastLocalTime;
//============================================================================
// Number of days per month
- static int s_DaysInMonth[12] = {
+static int s_DaysInMonth[12] = {
31, 0, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31
};
@@ -110,12 +121,13 @@ static const char* kWeekdayFull [7] = {
// Default value for time/timespan format
static const char* kDefaultFormatTime = "M/D/Y h:m:s";
static const char* kDefaultFormatSpan = "-S.n";
+static const char* kDefaultFormatSpanIn = "-G"; // default CTimeSpan init format
static const char* kDefaultFormatStopWatch = "S.n";
// Set of the checked format symbols.
// For CStopWatch class the format symbols are equal
// to kFormatSymbolsSpan also.
-static const char* kFormatSymbolsTime = "yYMbBDdhHmsSlrgGzZwWpP";
+static const char* kFormatSymbolsTime = "yYMbBDdhHmsSlrgGzZwWpPo";
static const char* kFormatSymbolsSpan = "-dhHmMsSnNgG";
// Character used to escape formatted symbols.
@@ -128,21 +140,39 @@ const char kFormatEscapeSymbol = '$';
// CTime::IsValid
// CTime::Set*() methods
-#define CHECK_RANGE(value, what, min, max) \
+#define CHECK_RANGE_EXCEPTION(value, what, min, max) \
if ( value < min || value > max ) { \
NCBI_THROW(CTimeException, eArgument, \
- what " value '" + \
- NStr::Int8ToString((Int8)value) + "' is out of range"); \
+ what " value '" + \
+ NStr::Int8ToString((Int8)value) + "' is out of range"); \
}
-#define CHECK_RANGE_YEAR(value) CHECK_RANGE(value, "Year", 1583, kMax_Int)
-#define CHECK_RANGE_MONTH(value) CHECK_RANGE(value, "Month", 1, 12)
-#define CHECK_RANGE_DAY(value) CHECK_RANGE(value, "Day", 1, 31)
-#define CHECK_RANGE_HOUR(value) CHECK_RANGE(value, "Hour", 0, 23)
-#define CHECK_RANGE_MIN(value) CHECK_RANGE(value, "Minute", 0, 59)
-#define CHECK_RANGE_SEC(value) CHECK_RANGE(value, "Second", 0, 61)
-#define CHECK_RANGE_NSEC(value) CHECK_RANGE(value, "Nanosecond", 0, \
- kNanoSecondsPerSecond - 1)
+#define CHECK_RANGE2(value, what, min, max, err_action) \
+ if ( value < min || value > max ) { \
+ if ( err_action == eErr_Throw ) { \
+ NCBI_THROW(CTimeException, eArgument, \
+ what " value '" + \
+ NStr::Int8ToString((Int8)value) + "' is out of range"); \
+ } else { return false; } \
+ }
+
+#define CHECK_RANGE_YEAR(value) CHECK_RANGE_EXCEPTION(value, "Year", 1583, kMax_Int)
+#define CHECK_RANGE_MONTH(value) CHECK_RANGE_EXCEPTION(value, "Month", 1, 12)
+#define CHECK_RANGE_DAY(value) CHECK_RANGE_EXCEPTION(value, "Day", 1, 31)
+#define CHECK_RANGE_HOUR(value) CHECK_RANGE_EXCEPTION(value, "Hour", 0, 23)
+#define CHECK_RANGE_MIN(value) CHECK_RANGE_EXCEPTION(value, "Minute", 0, 59)
+#define CHECK_RANGE_SEC(value) CHECK_RANGE_EXCEPTION(value, "Second", 0, 61)
+#define CHECK_RANGE_NSEC(value) CHECK_RANGE_EXCEPTION(value, "Nanosecond", 0, \
+ kNanoSecondsPerSecond - 1)
+
+#define CHECK_RANGE2_YEAR(value, err) CHECK_RANGE2(value, "Year", 1583, kMax_Int, err)
+#define CHECK_RANGE2_MONTH(value, err) CHECK_RANGE2(value, "Month", 1, 12, err)
+#define CHECK_RANGE2_DAY(value, err) CHECK_RANGE2(value, "Day", 1, 31, err)
+#define CHECK_RANGE2_HOUR(value, err) CHECK_RANGE2(value, "Hour", 0, 23, err)
+#define CHECK_RANGE2_MIN(value, err) CHECK_RANGE2(value, "Minute", 0, 59, err)
+#define CHECK_RANGE2_SEC(value, err) CHECK_RANGE2(value, "Second", 0, 61, err)
+#define CHECK_RANGE2_NSEC(value, err) CHECK_RANGE2(value, "Nanosecond", 0, \
+ kNanoSecondsPerSecond - 1, err)
//============================================================================
@@ -151,7 +181,7 @@ const char kFormatEscapeSymbol = '$';
static unsigned s_Date2Number(const CTime& date)
{
if ( date.IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eConvert, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
unsigned d = date.Day();
unsigned m = date.Month();
@@ -162,7 +192,7 @@ static unsigned s_Date2Number(const CTime& date)
m -= 3;
} else {
m += 9;
- y--;
+ --y;
}
c = y / 100;
ya = y - 100 * c;
@@ -197,7 +227,7 @@ static CTime s_Number2Date(unsigned num, const CTime& t)
month += 3;
} else {
month -= 9;
- year++;
+ ++year;
}
// Construct new CTime object
return
@@ -260,7 +290,7 @@ void s_AddZeroPadInt(string& str, long value, size_t len, bool ignore_trailing_z
}
char* p = buf + size - len;
if (ignore_trailing_zeros) {
- for (; len > 1 && p[len-1] == '0'; len--) {}
+ for (; len > 1 && p[len-1] == '0'; --len) {}
}
str.append(p, len);
}
@@ -313,21 +343,22 @@ CTimeFormat::CTimeFormat(const string& fmt, TFlags flags)
void CTimeFormat::SetFormat(const string& fmt, TFlags flags)
{
- // Checks flags compatibility
+ // Check flags compatibility
+
TFlags f = fFormat_Simple | fFormat_Ncbi;
- if ( (flags & f) == f ) {
- NCBI_THROW(CTimeException, eFormat,
+ if ((flags & f) == f) {
+ NCBI_THROW(CTimeException, eArgument,
"Incompatible flags specified together: fFormat_Simple | fFormat_Ncbi");
}
- if ( (flags & f) == 0 ) {
+ if ((flags & f) == 0) {
flags |= fFormat_Simple; // default
}
- if ( (flags & fMatch_Strict) && (flags & fMatch_Weak) ) {
- NCBI_THROW(CTimeException, eFormat,
- "Incompatible flags specified together: fMatch_Strict | fMatch_Weak)");
+ if ((flags & fMatch_Strict) && (flags & fMatch_Weak)) {
+ NCBI_THROW(CTimeException, eArgument,
+ "Incompatible flags specified together: fMatch_Strict | fMatch_Weak");
}
- if ( (flags & (fMatch_Strict|fMatch_Weak)) == 0 ) {
+ if ((flags & (fMatch_Strict | fMatch_Weak)) == 0) {
flags |= fMatch_Strict; // default
}
@@ -352,12 +383,12 @@ CTimeFormat CTimeFormat::GetPredefined(EPredefined fmt, TFlags flags)
// Predefined time formats
static const char* s_Predefined[][2] =
{
- {"Y", "$Y"},
- {"Y-M", "$Y-$M"},
- {"Y-M-D", "$Y-$M-$D"},
- {"Y-M-DTh:m", "$Y-$M-$DT$h:$m"},
- {"Y-M-DTh:m:s", "$Y-$M-$DT$h:$m:$s"},
- {"Y-M-DTh:m:s.l", "$Y-$M-$DT$h:$m:$s.$l"},
+ {"Y", "$Y"},
+ {"Y-M", "$Y-$M"},
+ {"Y-M-D", "$Y-$M-$D"},
+ {"Y-M-DTh:m", "$Y-$M-$DT$h:$m"},
+ {"Y-M-DTh:m:s", "$Y-$M-$DT$h:$m:$s"},
+ {"Y-M-DTh:m:G", "$Y-$M-$DT$h:$m:$G"},
};
int fmt_type = (flags & fFormat_Ncbi) ? 1 : 0;
return CTimeFormat(s_Predefined[(int)fmt][(int)fmt_type], flags);
@@ -382,7 +413,7 @@ static string s_TimeDump(const CTime& time)
"min=" + NStr::Int8ToString(time.Minute()) + ", " +
"sec=" + NStr::Int8ToString(time.Second()) + ", " +
"nanosec=" + NStr::Int8ToString(time.NanoSecond()) + ", " +
- "tz=" + (time.IsGmtTime() ? "GMT" : "Local") +
+ "tz=" + (time.IsUniversalTime() ? "UTC" : "Local") +
"]";
return out;
}
@@ -408,46 +439,78 @@ CTime::CTime(int year, int yearDayNumber,
m_Data.day = t.Day();
}
-// This helper takes care of parsing time with ':z' specified
-struct STzFmtParse
+
+// Helper macro for x_Init() errors
+#define X_INIT_ERROR(type, msg) \
+ if (err_action == eErr_Throw) { \
+ NCBI_THROW(CTimeException, type, msg); \
+ } else { \
+ return false; \
+ }
+
+// Skip white spaces
+#define SKIP_SPACES(s) \
+ while (isspace((unsigned char)(*s))) ++s;
+
+
+// The helper to check string with 'o' format symbol specified
+struct STzFormatCheck
{
- STzFmtParse() : m_Active(false) {}
+ STzFormatCheck() : m_Active(false) {}
- void fmt(const char*& f)
- {
+ bool fmt(const char*& f) {
_ASSERT(f);
- if (*f == ':') {
- if (*++f == 'z') {
- m_Active = true;
- } else {
- --f;
- }
- }
+ return m_Active = *f == 'o';
}
-
- bool str(const char*& s)
- {
+ bool str(const char*& s) {
_ASSERT(s);
if (m_Active) {
if (*s != ':') return false;
-
++s;
m_Active = false;
}
-
return true;
}
+private:
+ bool m_Active;
+};
+
+// The helper to compose string with 'o' format symbol specified
+struct STzFormatMake
+{
+ STzFormatMake() : m_Active(false) {}
+
+ void activate() {
+ m_Active = true;
+ }
+ void str(string& s) {
+ if (m_Active) {
+ s += ':';
+ m_Active = false;
+ }
+ }
+ bool active() const { return m_Active; }
private:
bool m_Active;
};
-void CTime::x_Init(const string& str, const CTimeFormat& format)
+
+bool CTime::x_Init(const string& str, const CTimeFormat& format, EErrAction err_action)
{
Clear();
+
+ // Special case, always create empty CTime object if str is empty, ignoring format.
+ // See IsEmpty().
if ( str.empty() ) {
- return;
+ return true;
}
+
+ // Use guard against accidental exceptions from other parts of API or NStr::,
+ // we do best to avoid exceptions if requested, but it is not alway possible
+ // to control all calling code from here, so just to be safe...
+ try {
+
// For partially defined times use default values
bool is_year_present = false;
bool is_month_present = false;
@@ -455,8 +518,8 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
bool is_time_present = false;
const string& fmt = format.GetString();
- bool is_escaped = ((format.GetFlags() & CTimeFormat::fFormat_Simple) == 0);
- bool is_format_symbol = !is_escaped;
+ bool is_escaped_fmt = ((format.GetFlags() & CTimeFormat::fFormat_Simple) == 0);
+ bool is_escaped_symbol = false;
const char* fff;
const char* sss = str.c_str();
@@ -467,41 +530,81 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
e24, eAM, ePM
};
EHourFormat hour_format = e24;
+ int weekday = -1;
bool is_12hour = false;
- int weekday = -1;
- STzFmtParse tz_fmt_parse;
+ // Used to check white spaces for fMatch_IgnoreSpaces
+ bool is_ignore_spaces = ((format.GetFlags() & CTimeFormat::fMatch_IgnoreSpaces) != 0);
+ bool is_format_space = false;
+ STzFormatCheck tz_fmt_check;
- for (fff = fmt.c_str(); *fff != '\0'; fff++) {
- // Skip space symbols in format string
- if ( isspace((unsigned char)(*fff)) ) {
- continue;
+ for (fff = fmt.c_str(); *fff != '\0'; ++fff) {
+
+ // White space processing -- except directly after escape symbols
+
+ if (!is_escaped_symbol) {
+ // Skip space symbols in format string
+ if (isspace((unsigned char)(*fff))) {
+ is_format_space = true;
+ continue;
+ }
+ if (is_ignore_spaces) {
+ // Skip space symbols in time string also
+ SKIP_SPACES(sss);
+ } else {
+ // match spaces
+ if (isspace((unsigned char)(*sss))) {
+ if (is_format_space) {
+ // Skip space symbols in time string
+ SKIP_SPACES(sss);
+ } else {
+ break; // error: non-matching spaces
+ }
+ } else {
+ if (is_format_space) {
+ break; // error: non-matching spaces
+ }
+ }
+ is_format_space = false;
+ }
}
+
// Skip preceding symbols for some formats
- if ( !is_format_symbol ) {
- if ( *fff == kFormatEscapeSymbol ) {
- is_format_symbol = true;
+ if (is_escaped_fmt && !is_escaped_symbol) {
+ if (*fff == kFormatEscapeSymbol) {
+ is_escaped_symbol = true;
continue;
}
}
- if ( is_escaped ) {
- is_format_symbol = false;
- }
- tz_fmt_parse.fmt(fff);
- // Skip space symbols in time string
- while ( isspace((unsigned char)(*sss)) )
- sss++;
+ // Match non-format symbols
- // Non-format symbols
- if (strchr(kFormatSymbolsTime, *fff) == 0) {
- if (*fff == *sss) {
- sss++;
- continue; // skip matching non-format symbols
+ if (is_escaped_fmt) {
+ if (!(is_escaped_symbol && *fff != kFormatEscapeSymbol)) {
+ // Match non-format symbols
+ if (*fff == *sss) {
+ ++sss;
+ continue;
+ }
+ break; // error: non-matching symbols
+ }
+ // format symbol found, process as usual
+ is_escaped_symbol = false;
+ } else {
+ // Regular non-escaped format, each symbol can be a format symbol.
+ // Check allowed format symbols
+ if (strchr(kFormatSymbolsTime, *fff) == 0) {
+ // Match non-format symbols
+ if (*fff == *sss) {
+ ++sss;
+ continue;
+ }
+ break; // error: non-matching symbols
}
- break; // error: non-matching non-format symbols
}
+ // Process format symbols
+
// Month
if (*fff == 'b' || *fff == 'B') {
const char** name;
@@ -510,14 +613,14 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
} else {
name = kMonthFull;
}
- for (unsigned char i = 0; i < 12; i++) {
+ for (unsigned char i = 0; i < 12; ++i) {
size_t namelen = strlen(*name);
if (NStr::strncasecmp(sss, *name, namelen) == 0) {
sss += namelen;
m_Data.month = i + 1;
break;
}
- name++;
+ ++name;
}
is_month_present = true;
continue;
@@ -526,41 +629,42 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
// Day of week
if (*fff == 'w' || *fff == 'W') {
const char** day = (*fff == 'w') ? kWeekdayAbbr : kWeekdayFull;
- for (unsigned char i = 0; i < 7; i++) {
+ for (unsigned char i = 0; i < 7; ++i) {
size_t len = strlen(*day);
if (NStr::strncasecmp(sss, *day, len) == 0) {
sss += len;
weekday = i;
break;
}
- day++;
+ ++day;
}
continue;
}
- // Timezone (GMT time)
+ // Timezone (UTC time)
if (*fff == 'Z') {
- if (NStr::strncasecmp(sss, "GMT", 3) == 0) {
- m_Data.tz = eGmt;
- sss += 3;
+ if ((NStr::strncasecmp(sss, "UTC", 3) == 0) ||
+ (NStr::strncasecmp(sss, "GMT", 3) == 0) ||
+ (*sss == 'Z')) {
+ m_Data.tz = eUTC;
+ sss += ((*sss == 'Z') ? 1 : 3);
} else {
m_Data.tz = eLocal;
}
continue;
}
- // Timezone (local time in format GMT+HHMM)
- if (*fff == 'z') {
- m_Data.tz = eGmt;
- if (NStr::strncasecmp(sss, "GMT", 3) == 0) {
+ // Timezone (local time in format '[GMT/UTC]+/-HHMM')
+ if (*fff == 'z' || tz_fmt_check.fmt(fff)) {
+ m_Data.tz = eUTC;
+ if ((NStr::strncasecmp(sss, "UTC", 3) == 0) ||
+ (NStr::strncasecmp(sss, "GMT", 3) == 0)) {
sss += 3;
}
- while ( isspace((unsigned char)(*sss)) ) {
- sss++;
- }
+ SKIP_SPACES(sss);
int sign = (*sss == '+') ? 1 : ((*sss == '-') ? -1 : 0);
if ( sign ) {
- sss++;
+ ++sss;
} else {
sign = 1;
}
@@ -571,7 +675,7 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
char* s = value_str;
for (size_t len = 2;
len && *sss && isdigit((unsigned char)(*sss));
- len--) {
+ --len) {
*s++ = *sss++;
}
*s = '\0';
@@ -583,14 +687,13 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
}
try {
if ( *sss != '\0' ) {
- if (!tz_fmt_parse.str(sss)) {
+ if (!tz_fmt_check.str(sss)) {
break; // error: not matched format symbol ':'
}
-
s = value_str;
for (size_t len = 2;
len && *sss && isdigit((unsigned char)(*sss));
- len--) {
+ --len) {
*s++ = *sss++;
}
*s = '\0';
@@ -606,7 +709,7 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
continue;
}
- // Timezone (local time in format GMT+HHMM)
+ // AM/PM modifier
if (*fff == 'p' || *fff == 'P') {
if (NStr::strncasecmp(sss, "AM", 2) == 0) {
hour_format = eAM;
@@ -628,7 +731,7 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
case 'l': len = 3; break;
case 'r': len = 6; break;
}
- for ( ; len && *sss && isdigit((unsigned char)(*sss)); len--) {
+ for ( ; len && *sss && isdigit((unsigned char)(*sss)); --len) {
*s++ = *sss++;
}
*s = '\0';
@@ -637,7 +740,7 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
// Set time part
switch ( *fff ) {
case 'Y':
- CHECK_RANGE_YEAR(value);
+ CHECK_RANGE2_YEAR(value, err_action);
m_Data.year = (unsigned int)value;
is_year_present = true;
break;
@@ -647,68 +750,68 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
} else if (value >= 50 && value < 100) {
value += 1900;
}
- CHECK_RANGE_YEAR(value);
+ CHECK_RANGE2_YEAR(value, err_action);
m_Data.year = (unsigned int)value;
is_year_present = true;
break;
case 'M':
- CHECK_RANGE_MONTH(value);
+ CHECK_RANGE2_MONTH(value, err_action);
m_Data.month = (unsigned char)value;
is_month_present = true;
break;
case 'D':
case 'd':
- CHECK_RANGE_DAY(value);
+ CHECK_RANGE2_DAY(value, err_action);
m_Data.day = (unsigned char)value;
is_day_present = true;
break;
case 'h':
- CHECK_RANGE_HOUR(value);
+ CHECK_RANGE2_HOUR(value, err_action);
m_Data.hour = (unsigned char)value;
is_time_present = true;
break;
case 'H':
- CHECK_RANGE_HOUR(value);
+ CHECK_RANGE2_HOUR(value, err_action);
m_Data.hour = (unsigned char)value % 12;
is_12hour = true;
is_time_present = true;
break;
case 'm':
- CHECK_RANGE_MIN(value);
+ CHECK_RANGE2_MIN(value, err_action);
m_Data.min = (unsigned char)value;
is_time_present = true;
break;
case 's':
- CHECK_RANGE_SEC(value);
+ CHECK_RANGE2_SEC(value, err_action);
m_Data.sec = (unsigned char)value;
is_time_present = true;
break;
case 'l':
- CHECK_RANGE_NSEC((Int8)value * 1000000);
+ CHECK_RANGE2_NSEC((Int8)value * 1000000, err_action);
m_Data.nanosec = (Int4)value * 1000000;
is_time_present = true;
break;
case 'r':
- CHECK_RANGE_NSEC((Int8)value * 1000);
+ CHECK_RANGE2_NSEC((Int8)value * 1000, err_action);
m_Data.nanosec = (Int4)value * 1000;
is_time_present = true;
break;
case 'S':
- CHECK_RANGE_NSEC(value);
+ CHECK_RANGE2_NSEC(value, err_action);
m_Data.nanosec = (Int4)value;
is_time_present = true;
break;
case 'g':
case 'G':
- CHECK_RANGE_SEC(value);
+ CHECK_RANGE2_SEC(value, err_action);
m_Data.sec = (unsigned char)value;
if ( *sss == '.' ) {
- sss++;
+ ++sss;
char* s = value_str;
// Limit fraction of second to 9 digits max,
// ignore all other digits in string if any.
for (size_t len = 9;
- len && *sss && isdigit((unsigned char)(*sss)); len--) {
+ len && *sss && isdigit((unsigned char)(*sss)); --len) {
*s++ = *sss++;
}
*s = '\0';
@@ -716,21 +819,21 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
size_t n = strlen(value_str);
// 'n' cannot have more then 9 (max for nanoseconds) - see above.
_ASSERT(n <= 9);
- for (; n < 9; n++) {
+ for (; n < 9; ++n) {
value *= 10;
}
- CHECK_RANGE_NSEC(value);
+ CHECK_RANGE2_NSEC(value, err_action);
m_Data.nanosec = (Int4)value;
// Ignore extra digits
while ( isdigit((unsigned char)(*sss)) ) {
- sss++;
+ ++sss;
}
}
is_time_present = true;
break;
+
default:
- NCBI_THROW(CTimeException, eFormat,
- "Format '" + fmt + "' is incorrect");
+ X_INIT_ERROR(eFormat, "Format '" + fmt + "' has incorrect format symbol '" + *fff + "'");
}
}
@@ -739,26 +842,30 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
m_Data.hour += 12;
}
- while ( isspace((unsigned char)(*sss)) )
- sss++;
+ // Skip all remaining white spaces in the string
+ if (is_ignore_spaces) {
+ SKIP_SPACES(sss);
+ } else {
+ if (isspace((unsigned char)(*sss)) && is_format_space) {
+ SKIP_SPACES(sss);
+ }
+ // else { error: non-matching spaces -- processed below }
+ }
if (*fff != '\0' &&
!(format.GetFlags() & CTimeFormat::fMatch_ShortTime)) {
- NCBI_THROW(CTimeException, eFormat,
- "Time string '" + str +
- "' is too short for time format '" + fmt + "'");
+ X_INIT_ERROR(eFormat, "Time string '" + str +
+ "' is too short for time format '" + fmt + "'");
}
if (*sss != '\0' &&
!(format.GetFlags() & CTimeFormat::fMatch_ShortFormat)) {
- NCBI_THROW(CTimeException, eFormat,
- "Time string '" + str +
- "' is too long for time format '" + fmt + "'");
+ X_INIT_ERROR(eFormat, "Time string '" + str +
+ "' is too long for time format '" + fmt + "'");
}
if (*fff != '\0' && *sss != '\0' &&
((format.GetFlags() & CTimeFormat::fMatch_Weak) == CTimeFormat::fMatch_Weak)) {
- NCBI_THROW(CTimeException, eFormat,
- "Time string '" + str +
- "' do not match time format '" + fmt + "'");
+ X_INIT_ERROR(eFormat, "Time string '" + str +
+ "' does not match time format '" + fmt + "'");
}
// For partially defined times use default values
@@ -811,18 +918,26 @@ void CTime::x_Init(const string& str, const CTimeFormat& format)
// Check on errors for weekday
if (weekday != -1 && weekday != DayOfWeek()) {
- NCBI_THROW(CTimeException, eConvert,
- "Invalid day of week " + NStr::IntToString(weekday));
+ X_INIT_ERROR(eConvert, "Invalid day of week " + NStr::IntToString(weekday));
}
// Validate time value
if ( !IsValid() ) {
- NCBI_THROW(CTimeException, eConvert,
- "Unable to convert string '" + str + "' to CTime");
+ X_INIT_ERROR(eConvert, "Unable to convert string '" + str + "' to CTime");
}
- // Adjust time to GMT time (see 'z' format symbol above)
+ // Adjust time to universal (see 'z' format symbol above)
if ( adjust_needed ) {
AddSecond(-adjust_tz, CTime::eIgnoreDaylight);
}
+
+ // see 'try' at the beginning of the method
+ } catch (CException&) {
+ if (err_action == eErr_Throw) {
+ throw;
+ } else {
+ return false;
+ }
+ }
+ return true;
}
@@ -872,7 +987,7 @@ CTime::CTime(EInitMode mode, ETimeZone tz, ETimeZonePrecision tzp)
CTime::CTime(time_t t, ETimeZonePrecision tzp)
{
memset(&m_Data, 0, sizeof(m_Data));
- m_Data.tz = eGmt;
+ m_Data.tz = eUTC;
m_Data.tzprec = tzp;
SetTimeT(t);
}
@@ -892,6 +1007,7 @@ CTime::CTime(const string& str, const CTimeFormat& fmt,
{
memset(&m_Data, 0, sizeof(m_Data));
_ASSERT(eLocal > 0);
+ _ASSERT(eUTC > 0);
_ASSERT(eGmt > 0);
if ( !m_Data.tz ) {
m_Data.tz = tz;
@@ -905,6 +1021,13 @@ CTime::CTime(const string& str, const CTimeFormat& fmt,
}
+bool CTime::ValidateString(const string& str, const CTimeFormat& fmt)
+{
+ CTime t;
+ return t.x_Init(str, fmt.IsEmpty() ? GetFormat() : fmt, eErr_NoThrow);
+}
+
+
void CTime::SetYear(int year)
{
CHECK_RANGE_YEAR(year);
@@ -1011,7 +1134,7 @@ int CTime::YearDayNumber(void) const
int CTime::YearWeekNumber(EDayOfWeek first_day_of_week) const
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if (first_day_of_week > eSaturday) {
NCBI_THROW(CTimeException, eArgument,
@@ -1034,7 +1157,7 @@ int CTime::YearWeekNumber(EDayOfWeek first_day_of_week) const
if (yday >= wday) {
week_num = yday / 7;
if ( (yday % 7) >= wday ) {
- week_num++;
+ ++week_num;
}
}
// Adjust range from [0..53] to [1..54]
@@ -1054,7 +1177,7 @@ int CTime::MonthWeekNumber(EDayOfWeek first_day_of_week) const
int CTime::DayOfWeek(void) const
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
int y = Year();
int m = Month();
@@ -1067,7 +1190,7 @@ int CTime::DayOfWeek(void) const
int CTime::DaysInMonth(void) const
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
int n_days = s_DaysInMonth[Month()-1];
if (n_days == 0) {
@@ -1080,8 +1203,8 @@ int CTime::DaysInMonth(void) const
int CTime::MonthNameToNum(const string& month)
{
const char** name = month.length() == 3 ? kMonthAbbr : kMonthFull;
- for (int i = 0; i < 12; i++) {
- if (month == name[i]) {
+ for (int i = 0; i < 12; ++i) {
+ if ( NStr::CompareNocase(month, name[i]) == 0 ) {
return i+1;
}
}
@@ -1101,7 +1224,7 @@ string CTime::MonthNumToName(int month, ENameFormat fmt)
NCBI_THROW(CTimeException, eArgument,
"Invalid month number " + NStr::IntToString(month));
}
- month--;
+ --month;
return fmt == eFull ? kMonthFull[month] : kMonthAbbr[month];
}
@@ -1109,8 +1232,8 @@ string CTime::MonthNumToName(int month, ENameFormat fmt)
int CTime::DayOfWeekNameToNum(const string& day)
{
const char** name = day.length() == 3 ? kWeekdayAbbr : kWeekdayFull;
- for (int i = 0; i <= 6; i++) {
- if (day == name[i]) {
+ for (int i = 0; i <= 6; ++i) {
+ if (NStr::CompareNocase(day, name[i]) == 0) {
return i;
}
}
@@ -1154,200 +1277,33 @@ CTimeFormat CTime::GetFormat(void)
return fmt;
}
-// This helper takes care of composing string with ':z' specified
-struct STzFmtMake
-{
- typedef string::const_iterator T_CI;
-
- STzFmtMake() : m_Active(false) {}
-
- void fmt(string& s, T_CI i, T_CI end)
- {
- _ASSERT(i != end);
- T_CI j = i + 1;
-
- if (j != end && *j == 'z') {
- m_Active = true;
- } else {
- s += ':';
- }
- }
-
- bool active() const
- {
- return m_Active;
- }
-
- void str(string& s)
- {
- if (m_Active) {
- s += ':';
- m_Active = false;
- }
- }
-
-private:
- bool m_Active;
-};
-
-string CTime::AsString(const CTimeFormat& format, TSeconds out_tz) const
-{
- if ( !IsValid() ) {
- NCBI_THROW(CTimeException, eInvalid,
- "Invalid time " + s_TimeDump(*this));
- }
- if ( IsEmpty() ) {
- return kEmptyStr;
- }
-#if !defined(TIMEZONE_IS_UNDEFINED)
- // MT-Safe protect
- CFastMutexGuard LOCK(s_TimeMutex);
-#endif
-
- const CTime* t = this;
- CTime* t_out = 0;
- // Adjust time for output timezone
- if (out_tz != eCurrentTimeZone) {
-#if defined(TIMEZONE_IS_UNDEFINED)
- ERR_POST_X(4, "Output timezone is unsupported on this platform");
-#else
- if (out_tz != TimeZone()) {
- t_out = new CTime(*this);
- t_out->AddSecond(TimeZone() - out_tz);
- t = t_out;
- }
-#endif
- }
- string str;
- str.reserve(64); // try to save on memory allocations
- string fmt;
- CTimeFormat::TFlags fmt_flags;
- if ( format.IsEmpty() ) {
- CTimeFormat f = GetFormat();
- fmt = f.GetString();
- fmt_flags = f.GetFlags();
- } else {
- fmt = format.GetString();
- fmt_flags = format.GetFlags();
- }
- bool is_escaped = ((fmt_flags & CTimeFormat::fFormat_Simple) == 0);
- bool is_format_symbol = !is_escaped;
-
- STzFmtMake tz_fmt_make;
-
- ITERATE(string, it, fmt) {
-
- if ( !is_format_symbol ) {
- if ( *it == kFormatEscapeSymbol ) {
- is_format_symbol = true;
- } else {
- str += *it;
- }
- continue;
- }
- if ( is_escaped ) {
- is_format_symbol = false;
- }
- switch ( *it ) {
- case 'y': s_AddZeroPadInt2(str, t->Year() % 100); break;
- case 'Y': s_AddZeroPadInt(str, t->Year(), 4); break;
- case 'M': s_AddZeroPadInt2(str, t->Month()); break;
- case 'b': str += kMonthAbbr[t->Month()-1]; break;
- case 'B': str += kMonthFull[t->Month()-1]; break;
- case 'D': s_AddZeroPadInt2(str, t->Day()); break;
- case 'd': s_AddZeroPadInt(str, t->Day(),1); break;
- case 'h': s_AddZeroPadInt2(str, t->Hour()); break;
- case 'H': s_AddZeroPadInt2(str, (t->Hour()+11) % 12+1);
- break;
- case 'm': s_AddZeroPadInt2(str, t->Minute()); break;
- case 's': s_AddZeroPadInt2(str, t->Second()); break;
- case 'l': s_AddZeroPadInt(str, t->NanoSecond() / 1000000, 3);
- break;
- case 'r': s_AddZeroPadInt(str, t->NanoSecond() / 1000, 6);
- break;
- case 'S': s_AddZeroPadInt(str, t->NanoSecond(), 9); break;
- case 'G': s_AddZeroPadInt2(str, t->Second());
- str += ".";
- s_AddZeroPadInt(str, t->NanoSecond(), 9, true);
- break;
- case 'g': s_AddInt(str, t->Second());
- str += ".";
- s_AddZeroPadInt(str, t->NanoSecond(), 9, true);
- break;
- case 'p': str += ( t->Hour() < 12) ? "am" : "pm" ; break;
- case 'P': str += ( t->Hour() < 12) ? "AM" : "PM" ; break;
- case ':': tz_fmt_make.fmt(str, it, fmt.end()); break;
- case 'z': {
-#if defined(TIMEZONE_IS_UNDEFINED)
- ERR_POST_X(5, "Format symbol 'z' is unsupported "
- "on this platform");
-#else
- if (!tz_fmt_make.active()) {
- str += "GMT";
- if (IsGmtTime()) {
- break;
- }
- }
- TSeconds tz = out_tz;
- if (out_tz == eCurrentTimeZone) {
- tz = TimeZone();
- if ( Daylight() ) {
- tz -= 3600; // DST in effect
- }
- }
- str += (tz > 0) ? '-' : '+';
- if (tz < 0) tz = -tz;
- int tzh = int(tz / 3600);
- s_AddZeroPadInt2(str, tzh);
- tz_fmt_make.str(str);
- s_AddZeroPadInt2(str, (int)(tz - tzh * 3600) / 60);
-#endif
- break;
- }
- case 'Z': if (IsGmtTime()) str += "GMT"; break;
- case 'w': str += kWeekdayAbbr[t->DayOfWeek()]; break;
- case 'W': str += kWeekdayFull[t->DayOfWeek()]; break;
- default : str += *it; break;
- }
- }
- // Free used memory
- if ( t_out ) {
- delete t_out;
- }
- return str;
-}
-
-time_t CTime::GetTimeT(void) const
+// Internal version without checks and locks
+time_t s_GetTimeT(const CTime& ct)
{
- if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
- }
- // MT-Safe protect
- CFastMutexGuard LOCK(s_TimeMutex);
-
struct tm t;
// Convert time to time_t value at base local time
#if defined(HAVE_TIMEGM) || defined(NCBI_OS_DARWIN)
- t.tm_sec = Second();
+ t.tm_sec = ct.Second();
#else
- t.tm_sec = Second() + (int)(IsGmtTime() ? -TimeZone() : 0);
+ // see below
+ t.tm_sec = ct.Second() + (int)(ct.IsUniversalTime() ? -TimeZone() : 0);
#endif
- t.tm_min = Minute();
- t.tm_hour = Hour();
- t.tm_mday = Day();
- t.tm_mon = Month()-1;
- t.tm_year = Year()-1900;
+ t.tm_min = ct.Minute();
+ t.tm_hour = ct.Hour();
+ t.tm_mday = ct.Day();
+ t.tm_mon = ct.Month()-1;
+ t.tm_year = ct.Year()-1900;
t.tm_isdst = -1;
#if defined(NCBI_OS_DARWIN)
time_t tt = mktime(&t);
if ( tt == (time_t)(-1L) ) {
return tt;
}
- return IsGmtTime() ? tt+t.tm_gmtoff : tt;
+ return ct.IsUniversalTime() ? tt+t.tm_gmtoff : tt;
#elif defined(HAVE_TIMEGM)
- return IsGmtTime() ? timegm(&t) : mktime(&t);
+ return ct.IsUniversalTime() ? timegm(&t) : mktime(&t);
#else
struct tm *ttemp;
time_t timer;
@@ -1356,19 +1312,22 @@ time_t CTime::GetTimeT(void) const
return timer;
}
- // Correct timezone for GMT time
- if ( IsGmtTime() ) {
+ // Correct timezone for UTC time
+ if ( ct.IsUniversalTime() ) {
- // Call mktime() second time for GMT time !!!
+ // Somewhat hackish, but seem to work.
+ // Local time is ambiguous and we don't know is DST on
+ // for specified date/time or not, so we call mktime()
+ // second time for GMT/UTC time:
// 1st - to get correct value of TimeZone().
- // 2nd - to get value "timer".
-
- t.tm_sec = Second() - (int)TimeZone();
- t.tm_min = Minute();
- t.tm_hour = Hour();
- t.tm_mday = Day();
- t.tm_mon = Month()-1;
- t.tm_year = Year()-1900;
+ // 2nd - to get value of "timer".
+
+ t.tm_sec = ct.Second() - (int)TimeZone();
+ t.tm_min = ct.Minute();
+ t.tm_hour = ct.Hour();
+ t.tm_mday = ct.Day();
+ t.tm_mon = ct.Month()-1;
+ t.tm_year = ct.Year()-1900;
t.tm_isdst = -1;
timer = mktime(&t);
if ( timer == (time_t)(-1L) ) {
@@ -1385,13 +1344,57 @@ time_t CTime::GetTimeT(void) const
if (ttemp == NULL)
return (time_t)(-1L);
if (ttemp->tm_isdst > 0 && Daylight())
- timer += 3600;
+ timer -= DSTBias(); // +1 hour in common case
}
return timer;
#endif
}
+// Internal version without checks and locks
+bool s_IsDST(const CTime& ct)
+{
+ time_t timer = s_GetTimeT(ct);
+ if (timer == (time_t)(-1L)) {
+ return false;
+ }
+ struct tm *t;
+# if defined(HAVE_LOCALTIME_R)
+ struct tm temp;
+ localtime_r(&timer, &temp);
+ t = &temp;
+# else
+ t = localtime(&timer);
+# endif
+ if (t == NULL) {
+ return false;
+ }
+ return (t->tm_isdst > 0);
+}
+
+
+bool CTime::IsDST(void) const
+{
+ if ( IsEmptyDate() ) {
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
+ }
+ // MT-Safe protect
+ CFastMutexGuard LOCK(s_TimeMutex);
+ return s_IsDST(*this);
+}
+
+
+time_t CTime::GetTimeT(void) const
+{
+ if ( IsEmptyDate() ) {
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
+ }
+ // MT-Safe protect
+ CFastMutexGuard LOCK(s_TimeMutex);
+ return s_GetTimeT(*this);
+}
+
+
struct tm CTime::GetTimeTM(void) const
{
CTime lt = GetLocalTime();
@@ -1430,7 +1433,7 @@ CTime& CTime::SetTimeTM(const struct tm& t)
m_Data.adjTimeDiff = 0;
if ( !IsValid() ) {
- NCBI_THROW(CTimeException, eConvert,
+ NCBI_THROW(CTimeException, eInvalid,
"Invalid time " + s_TimeDump(*this));
}
return *this;
@@ -1485,14 +1488,144 @@ CTime& CTime::SetTimeDBI(const TDBTimeI& t)
// Local time - 1/1/1900 00:00:00.0
CTime time(1900, 1, 1, 0, 0, 0, 0, eLocal);
- time.SetTimeZonePrecision(GetTimeZonePrecision());
- time.AddDay(t.days);
- time.AddSecond(t.time / 300);
- time.AddNanoSecond(long((Int8(t.time % 300) * kNanoSecondsPerSecond)/300));
- time.ToTime(GetTimeZone());
+ time.SetTimeZonePrecision(GetTimeZonePrecision());
+ time.AddDay(t.days);
+ time.AddSecond(t.time / 300);
+ time.AddNanoSecond(long((Int8(t.time % 300) * kNanoSecondsPerSecond)/300));
+ time.ToTime(GetTimeZone());
+
+ *this = time;
+ return *this;
+}
+
+
+string CTime::AsString(const CTimeFormat& format, TSeconds out_tz) const
+{
+ if ( !IsValid() ) {
+ NCBI_THROW(CTimeException, eInvalid,
+ "Invalid time " + s_TimeDump(*this));
+ }
+ if ( IsEmpty() ) {
+ return kEmptyStr;
+ }
+#if !defined(TIMEZONE_IS_UNDEFINED)
+ // MT-Safe protect
+ CFastMutexGuard LOCK(s_TimeMutex);
+#endif
+
+ const CTime* t = this;
+ CTime* t_out = 0;
+ // Adjust time for output timezone
+ if (out_tz != eCurrentTimeZone) {
+#if defined(TIMEZONE_IS_UNDEFINED)
+ ERR_POST_X(4, "Output timezone is unsupported on this platform");
+#else
+ if (out_tz != TimeZone()) {
+ t_out = new CTime(*this);
+ t_out->AddSecond(TimeZone() - out_tz);
+ t = t_out;
+ }
+#endif
+ }
+ string str;
+ str.reserve(64); // try to save on memory allocations
+ string fmt;
+ CTimeFormat::TFlags fmt_flags;
+ if ( format.IsEmpty() ) {
+ CTimeFormat f = GetFormat();
+ fmt = f.GetString();
+ fmt_flags = f.GetFlags();
+ } else {
+ fmt = format.GetString();
+ fmt_flags = format.GetFlags();
+ }
+ bool is_escaped = ((fmt_flags & CTimeFormat::fFormat_Simple) == 0);
+ bool is_format_symbol = !is_escaped;
+ STzFormatMake tz_fmt_make;
+
+ ITERATE(string, it, fmt) {
- *this = time;
- return *this;
+ if ( !is_format_symbol ) {
+ if ( *it == kFormatEscapeSymbol ) {
+ is_format_symbol = true;
+ } else {
+ str += *it;
+ }
+ continue;
+ }
+ if ( is_escaped ) {
+ is_format_symbol = false;
+ }
+ switch ( *it ) {
+ case 'y': s_AddZeroPadInt2(str, t->Year() % 100); break;
+ case 'Y': s_AddZeroPadInt(str, t->Year(), 4); break;
+ case 'M': s_AddZeroPadInt2(str, t->Month()); break;
+ case 'b': str += kMonthAbbr[t->Month()-1]; break;
+ case 'B': str += kMonthFull[t->Month()-1]; break;
+ case 'D': s_AddZeroPadInt2(str, t->Day()); break;
+ case 'd': s_AddZeroPadInt(str, t->Day(),1); break;
+ case 'h': s_AddZeroPadInt2(str, t->Hour()); break;
+ case 'H': s_AddZeroPadInt2(str, (t->Hour()+11) % 12+1);
+ break;
+ case 'm': s_AddZeroPadInt2(str, t->Minute()); break;
+ case 's': s_AddZeroPadInt2(str, t->Second()); break;
+ case 'l': s_AddZeroPadInt(str, t->NanoSecond() / 1000000, 3);
+ break;
+ case 'r': s_AddZeroPadInt(str, t->NanoSecond() / 1000, 6);
+ break;
+ case 'S': s_AddZeroPadInt(str, t->NanoSecond(), 9); break;
+ case 'G': s_AddZeroPadInt2(str, t->Second());
+ str += ".";
+ s_AddZeroPadInt(str, t->NanoSecond(), 9, true);
+ break;
+ case 'g': s_AddInt(str, t->Second());
+ str += ".";
+ s_AddZeroPadInt(str, t->NanoSecond(), 9, true);
+ break;
+ case 'p': str += ( t->Hour() < 12) ? "am" : "pm" ; break;
+ case 'P': str += ( t->Hour() < 12) ? "AM" : "PM" ; break;
+ case 'o': tz_fmt_make.activate(); /* FALL THROUGH */
+ case 'z': {
+#if defined(TIMEZONE_IS_UNDEFINED)
+ ERR_POST_X(5, "Format symbol 'z' is unsupported "
+ "on this platform");
+#else
+ if (!tz_fmt_make.active()) {
+ str += (fmt_flags & CTimeFormat::fConf_UTC) ? "UTC" : "GMT";
+ }
+ if (IsUniversalTime()) {
+ break;
+ }
+ TSeconds tz = out_tz;
+ if (tz == eCurrentTimeZone) {
+ tz = TimeZone();
+ if (s_IsDST(*this)) {
+ tz += DSTBias(); // DST in effect
+ }
+ }
+ str += (tz > 0) ? '-' : '+';
+ if (tz < 0) tz = -tz;
+ tz /= 60;
+ s_AddZeroPadInt2(str, (long)(tz / 60));
+ tz_fmt_make.str(str);
+ s_AddZeroPadInt2(str, (long)(tz % 60));
+#endif
+ break;
+ }
+ case 'Z': if (IsUniversalTime()) {
+ str += (fmt_flags & CTimeFormat::fConf_UTC) ? "UTC" : "GMT";
+ }
+ break;
+ case 'w': str += kWeekdayAbbr[t->DayOfWeek()]; break;
+ case 'W': str += kWeekdayFull[t->DayOfWeek()]; break;
+ default : str += *it; break;
+ }
+ }
+ // Free used memory
+ if ( t_out ) {
+ delete t_out;
+ }
+ return str;
}
@@ -1583,6 +1716,7 @@ CTime& CTime::x_SetTime(const time_t* value)
m_Data.sec = t->tm_sec;
CHECK_RANGE_NSEC(ns);
m_Data.nanosec = (Int4)ns;
+
return *this;
}
@@ -1590,7 +1724,7 @@ CTime& CTime::x_SetTime(const time_t* value)
CTime& CTime::AddMonth(int months, EDaylight adl)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !months ) {
return *this;
@@ -1621,7 +1755,7 @@ CTime& CTime::AddMonth(int months, EDaylight adl)
CTime& CTime::AddDay(int days, EDaylight adl)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !days ) {
return *this;
@@ -1653,7 +1787,7 @@ CTime& CTime::AddDay(int days, EDaylight adl)
CTime& CTime::x_AddHour(int hours, EDaylight adl, bool shift_time)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !hours ) {
return *this;
@@ -1683,7 +1817,7 @@ CTime& CTime::x_AddHour(int hours, EDaylight adl, bool shift_time)
CTime& CTime::AddMinute(int minutes, EDaylight adl)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !minutes ) {
return *this;
@@ -1713,7 +1847,7 @@ CTime& CTime::AddMinute(int minutes, EDaylight adl)
CTime& CTime::AddSecond(TSeconds seconds, EDaylight adl)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !seconds ) {
return *this;
@@ -1729,7 +1863,7 @@ CTime& CTime::AddSecond(TSeconds seconds, EDaylight adl)
CTime& CTime::AddNanoSecond(long ns)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( !ns ) {
return *this;
@@ -1881,7 +2015,7 @@ bool CTime::IsValid(void) const
CTime CTime::GetLocalTime(void) const
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if ( IsLocalTime() ) {
return *this;
@@ -1891,23 +2025,23 @@ CTime CTime::GetLocalTime(void) const
}
-CTime CTime::GetGmtTime(void) const
+CTime CTime::GetUniversalTime(void) const
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
- if ( IsGmtTime() ) {
+ if ( IsUniversalTime() ) {
return *this;
}
CTime t(*this);
- return t.ToGmtTime();
+ return t.ToUniversalTime();
}
CTime& CTime::ToTime(ETimeZone tz)
{
if ( IsEmptyDate() ) {
- NCBI_THROW(CTimeException, eInvalid, "The date is empty");
+ NCBI_THROW(CTimeException, eArgument, "The date is empty");
}
if (GetTimeZone() != tz) {
struct tm* t;
@@ -2048,7 +2182,7 @@ bool CTime::IsLeap(void) const
TSeconds CTime::TimeZoneOffset(void) const
{
const CTime tl(GetLocalTime());
- const CTime tg(GetGmtTime());
+ const CTime tg(GetUniversalTime());
TSeconds dSecs = tl.Second() - tg.Second();
TSeconds dMins = tl.Minute() - tg.Minute();
@@ -2120,8 +2254,8 @@ TSeconds CTime::DiffSecond(const CTime& from) const
if (GetTimeZone() != from.GetTimeZone()) {
t1 = *this;
t2 = from;
- t1.ToGmtTime();
- t2.ToGmtTime();
+ t1.ToUniversalTime();
+ t2.ToUniversalTime();
p1 = &t1;
p2 = &t2;
} else {
@@ -2201,7 +2335,7 @@ CTime& CTime::x_AdjustTimeImmediately(const CTime& from, bool shift_time)
// Time in hours for temporary time shift.
// Shift used for obtainment correct result at changeover daytime saving.
// Must be > 3 (Linux distinction). On other platforms may be == 3.
- const int kShift = 4;
+ const int kShiftHours = 4;
// MT-Safe protect
CFastMutexGuard LOCK(s_TimeAdjustMutex);
@@ -2215,7 +2349,7 @@ CTime& CTime::x_AdjustTimeImmediately(const CTime& from, bool shift_time)
sign = ( *this > from ) ? 1 : -1;
// !!! Run TimeZoneOffset() first for old time value
diff = -tmp.TimeZoneOffset() + TimeZoneOffset();
- // Correction need's if time already in identical timezone
+ // Correction needs if time already in identical timezone
if (!diff || diff == m_Data.adjTimeDiff) {
return *this;
}
@@ -2223,14 +2357,14 @@ CTime& CTime::x_AdjustTimeImmediately(const CTime& from, bool shift_time)
// Recursive procedure call. Inside below
// x_AddHour(*, eAdjustDaylight, false)
else {
- // Correction need't if difference not found
+ // Correction needn't if difference not found
if (diff == m_Data.adjTimeDiff) {
return *this;
}
}
// Make correction with temporary time shift
time_t t = GetTimeT();
- CTime tn(t + (time_t)diff + 3600 * kShift * sign);
+ CTime tn(t + (time_t)diff + 3600 * kShiftHours * sign);
if (from.GetTimeZone() == eLocal) {
tn.ToLocalTime();
}
@@ -2242,7 +2376,7 @@ CTime& CTime::x_AdjustTimeImmediately(const CTime& from, bool shift_time)
// Primary procedure call
if ( shift_time ) {
// Cancel temporary time shift
- tn.x_AddHour(-kShift * sign, eAdjustDaylight, false);
+ tn.x_AddHour(-kShiftHours * sign, eAdjustDaylight, false);
tn.m_Data.adjTimeDiff = (Int4)diff;
}
*this = tn;
@@ -2281,12 +2415,36 @@ CTimeSpan::CTimeSpan(long days, long hours, long minutes, long seconds,
CTimeSpan::CTimeSpan(const string& str, const CTimeFormat& fmt)
{
if (fmt.IsEmpty()) {
- x_Init(str, GetFormat());
+ // Use another format to init from string by default
+ // if global format has not set.
+ CTimeFormat* ptr = s_TlsFormatSpan.GetValue();
+ if (!ptr) {
+ CTimeFormat fmt(kDefaultFormatSpanIn);
+ x_Init(str, fmt);
+ } else {
+ x_Init(str, *ptr);
+ }
} else {
x_Init(str, fmt);
}
}
+
+CTimeSpan& CTimeSpan::operator= (const string& str)
+{
+ // Use another format to init from string by default
+ // if global format has not set.
+ CTimeFormat* ptr = s_TlsFormatSpan.GetValue();
+ if (!ptr) {
+ CTimeFormat fmt(kDefaultFormatSpanIn);
+ x_Init(str, fmt);
+ } else {
+ x_Init(str, *ptr);
+ }
+ return *this;
+}
+
+
void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
{
Clear();
@@ -2294,54 +2452,70 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
return;
}
const string& fmt = format.GetString();
- bool is_escaped = ((format.GetFlags() & CTimeFormat::fFormat_Simple) == 0);
- bool is_format_symbol = !is_escaped;
+ bool is_escaped_fmt = ((format.GetFlags() & CTimeFormat::fFormat_Simple) == 0);
+ bool is_escaped_symbol = false;
const char* fff;
char f;
const char* sss = str.c_str();
int sign = 1;
- for (fff = fmt.c_str(); *fff != '\0'; fff++) {
-
- f = *fff;
+ for (fff = fmt.c_str(); *fff != '\0'; ++fff) {
// Skip preceding symbols for some formats
- if ( !is_format_symbol ) {
- if ( f == kFormatEscapeSymbol ) {
- is_format_symbol = true;
+ if (is_escaped_fmt && !is_escaped_symbol) {
+ if (*fff == kFormatEscapeSymbol) {
+ is_escaped_symbol = true;
continue;
}
}
- if ( is_escaped ) {
- is_format_symbol = false;
- }
- // Non-format symbols
- if (strchr(kFormatSymbolsSpan, f) == 0) {
- if (f == *sss) {
- sss++;
- continue; // skip matching non-format symbols
+
+ // Match non-format symbols
+
+ if (is_escaped_fmt) {
+ if (!(is_escaped_symbol && *fff != kFormatEscapeSymbol)) {
+ // Match non-format symbols
+ if (*fff == *sss) {
+ ++sss;
+ continue;
+ }
+ break; // error: non-matching symbols
+ }
+ // format symbol found, process as usual
+ is_escaped_symbol = false;
+ } else {
+ // Regular non-escaped format, each symbol can be a format symbol.
+ // Check allowed format symbols
+ if (strchr(kFormatSymbolsSpan, *fff) == 0) {
+ // Match non-format symbols
+ if (*fff == *sss) {
+ ++sss;
+ continue;
+ }
+ break; // error: non-matching symbols
}
- break; // error: non-matching non-format symbols
}
+ // Process format symbols
// Sign: if specified that the time span is negative
- if (f == '-') {
+ if (*fff == '-') {
if (*sss == '-') {
sign = -1;
- sss++;
+ ++sss;
}
continue;
}
+ f = *fff;
read_next_value:
// Other format symbols -- read the next data ingredient
- char value_str[10];
+ char value_str[11];
char* s = value_str;
- for (size_t len = 9;
- len && *sss && isdigit((unsigned char)(*sss)); len--) {
+ // Read 9 (special case) or 10 digits only, ignore all other.
+ size_t len = (f == '\1') ? 9 : 10;
+ for (; len && *sss && isdigit((unsigned char)(*sss)); --len) {
*s++ = *sss++;
}
*s = '\0';
@@ -2349,7 +2523,7 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
switch ( f ) {
case 'd':
- m_Sec += value * 86400L;
+ m_Sec += value * 3600L * 24L;
break;
case 'h':
m_Sec += value * 3600L;
@@ -2376,7 +2550,7 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
m_Sec += value;
if ( *sss == '.' ) {
// Read fraction
- sss++;
+ ++sss;
f = '\1';
goto read_next_value;
}
@@ -2385,7 +2559,7 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
m_Sec = value;
if ( *sss == '.' ) {
// Read fraction
- sss++;
+ ++sss;
f = '\1';
goto read_next_value;
}
@@ -2396,28 +2570,23 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
// Process a fraction of a second for format symbols 'g' and 'G'.
// Convert value to nanoseconds.
size_t n = strlen(value_str);
- // 'n' cannot have more then 9 (max for nanoseconds) - see above.
- _ASSERT(n <= 9);
- for (; n < 9; n++) {
+ // 'n' cannot have more then 9 (max for nanoseconds)
+ // ignore all other digits
+ for (; n < 9; ++n) {
value *= 10;
}
m_NanoSec = value;
// Limit fraction of second to 9 digits max,
// ignore all other digits in string if any.
while ( isdigit((unsigned char)(*sss)) ) {
- sss++;
+ ++sss;
}
}
break;
default:
- NCBI_THROW(CTimeException, eFormat, "Format '" + fmt + "' is incorrect");
+ NCBI_THROW(CTimeException, eFormat, "Format '" + fmt + "' has incorrect format symbol '" + f + "'");
}
}
- // Normalize time span
- if (sign < 0) {
- Invert();
- }
- x_Normalize();
// Check on errors
if (*fff != '\0' &&
@@ -2432,6 +2601,11 @@ void CTimeSpan::x_Init(const string& str, const CTimeFormat& format)
"Time string '" + str +
"' is too long for time format '" + fmt + "'");
}
+ // Normalize time span
+ if (sign < 0) {
+ Invert();
+ }
+ x_Normalize();
}
@@ -2441,10 +2615,10 @@ void CTimeSpan::x_Normalize(void)
m_NanoSec %= kNanoSecondsPerSecond;
// If signs are different then make timespan correction
if (m_Sec > 0 && m_NanoSec < 0) {
- m_Sec--;
+ --m_Sec;
m_NanoSec += kNanoSecondsPerSecond;
} else if (m_Sec < 0 && m_NanoSec > 0) {
- m_Sec++;
+ ++m_Sec;
m_NanoSec -= kNanoSecondsPerSecond;
}
}
@@ -2540,127 +2714,174 @@ string CTimeSpan::AsString(const CTimeFormat& format) const
}
-struct SSmartStringItem {
- SSmartStringItem(void) : value(0), str(kEmptyStr) {};
- SSmartStringItem(long v, const string& s) : value(v), str(s) {};
- long value;
- string str;
+// Number of time components
+const unsigned int kUnitCount = 9;
+
+// Time components
+enum EUnit {
+ eYear = 0,
+ eMonth = 1,
+ eDay = 2,
+ eHour = 3,
+ eMinute = 4,
+ eSecond = 5,
+ eMillisecond = 6,
+ eMicrosecond = 7,
+ eNanosecond = 8,
+
+ // Special value, some precision based (see fSS_Precision*).
+ // Must be last and go after eNanosecond.
+ ePrecision = 9
};
+// Structure to store time component names/abbreviations
+struct SUnitName {
+ const char* name_full;
+ const char* name_short;
+};
+static const SUnitName kUnitNames[kUnitCount] = {
+ { "year", "y" },
+ { "month", "mo"},
+ { "day", "d" },
+ { "hour", "h" },
+ { "minute", "m" },
+ { "second", "s" },
+ { "millisecond", "ms" },
+ { "microsecond", "us" },
+ { "nanosecond", "ns" }
+};
+
+// Multipliers for parts of time in seconds/nanoseconds
+static const TSeconds kTimeSpanUnitMultipliers[kUnitCount] = {
+ // second based parts
+ kAverageSecondsPerYear, // year
+ kAverageSecondsPerMonth, // month
+ 3600L * 24L, // day
+ 3600L, // hour
+ 60L, // minute
+ 1, // seconds
+ // nanosecond based parts
+ 1000000L, // milliseconds
+ 1000L, // microseconds
+ 1 // nanoseconds
+};
-// Helper functions for Smart mode and timespans >= 1 min.
-// Do not use with smaller timespans!
-string CTimeSpan::x_AsSmartString_Smart_Big(ERound rounding)
+
+// Helper functions to convert to smart string for "smart" mode
+// and timespans >= 1 min. Do not use with smaller timespans!
+
+string CTimeSpan::x_AsSmartString_Smart_Big(TSmartStringFlags flags) const
{
+ _ASSERT(*this >= CTimeSpan(60,0) );
+ _ASSERT(GetSign() != eNegative);
+ _ASSERT((flags & fSS_Smart) == fSS_Smart);
+
+ // Make a copy (for rounding)
+ CTimeSpan ts(*this);
+
// Round timespan
- if ( rounding == eRound ) {
+ if ( flags & fSS_Round ) {
// Find first non-zero value for proper rounding (2 level max)
- long days = GetCompleteDays();
- int hours = x_Hour();
- int minutes = x_Minute();
- int adjust_level = eSSP_Second;
-
- if ( days >=365 ) {
- adjust_level = eSSP_Year;
- } else if (days >= 30) {
- adjust_level = eSSP_Month;
- } else if (days > 0) {
- adjust_level = eSSP_Day;
- } else if (hours > 0) {
- adjust_level = eSSP_Hour;
- } else if (minutes > 0) {
- adjust_level = eSSP_Minute;
- }
- adjust_level++; // one level down
+ long sec = GetCompleteSeconds();
+ int adjust_level;
+ for (adjust_level = eYear; adjust_level < eSecond; adjust_level++) {
+ if (sec >= kTimeSpanUnitMultipliers[adjust_level]) {
+ break;
+ }
+ }
+ _ASSERT(adjust_level < eMicrosecond);
+ ++adjust_level; // one level down
// Add adjustment time span
- switch (ESmartStringPrecision(adjust_level)) {
- case eSSP_Month:
- *this += CTimeSpan(15, 0, 0, 0);
+ switch ( EUnit(adjust_level) ) {
+ case eMonth:
+ ts += CTimeSpan(15, 0, 0, 0);
break;
- case eSSP_Day:
- *this += CTimeSpan(0, 12, 0, 0);
+ case eDay:
+ ts += CTimeSpan(0, 12, 0, 0);
break;
- case eSSP_Hour:
- *this += CTimeSpan(0, 0, 30, 0);
+ case eHour:
+ ts += CTimeSpan(0, 0, 30, 0);
break;
- case eSSP_Minute:
- *this += CTimeSpan(0, 0, 0, 30);
+ case eMinute:
+ ts += CTimeSpan(0, 0, 0, 30);
break;
- case eSSP_Second:
- *this += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2);
+ case eSecond:
+ ts += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2);
break;
default:
- ; // years, and seconds and below -- nothing to do
+ ; // years, seconds and below -- nothing to do
}
}
// Prepare data
- typedef SSmartStringItem SItem;
const int max_count = 6;
- SItem span[max_count];
+ long span[max_count];
+ long sec = ts.GetCompleteSeconds();
- long days = GetCompleteDays();
- span[0] = SItem(days/365 , "year" ); days %= 365;
- span[1] = SItem(days/30 , "month" ); days %= 30;
- span[2] = SItem(days , "day" );
- span[3] = SItem(x_Hour() , "hour" );
- span[4] = SItem(x_Minute(), "minute");
- span[5] = SItem(x_Second(), "second");
+ span[eYear] = sec/kAverageSecondsPerYear; sec %= kAverageSecondsPerYear;
+ span[eMonth] = sec/kAverageSecondsPerMonth; sec %= kAverageSecondsPerMonth;
+ span[eDay] = sec/(3600L*24); sec %= (3600L*24);
+ span[eHour] = sec/3600L; sec %= 3600L;
+ span[eMinute] = sec/60L; sec %= 60L;
+ span[eSecond] = sec;
string result; // result string
int start = 0; // precision level to start from (first non-zero)
- int precision; // end precision
+ int prec; // end precision
// Get start precision after rounding (it can changes there)
- for (; start < 5; start++) {
- if (span[start].value) {
+ for (; start < 5; ++start) {
+ if ( span[start] ) {
break;
}
}
- // Allow 2 levels max for smart mode
- if (start == eSSP_Second) {
- precision = start;
+ // Allow 2 levels maximum for smart mode
+ if (start == eSecond) {
+ prec = start;
} else {
- precision = start + 1;
+ prec = start + 1;
}
// Compose result string
- while (start <= precision) {
- long val = span[start].value;
+ while (start <= prec) {
+ long val = span[start];
if ( !val ) {
- start++;
+ ++start;
continue;
}
if ( !result.empty() ) {
result += " ";
}
- result += NStr::LongToString(val) + " " + span[start].str;
- if (val != 1) {
- result += "s";
+ result += NStr::LongToString(val);
+ if (flags & fSS_Full) {
+ result += string(" ") + kUnitNames[start].name_full;
+ if (val != 1) {
+ result += "s";
+ }
+ } else {
+ result += kUnitNames[start].name_short;
}
- start++;
+ ++start;
}
return result;
}
-// Helper functions for Smart mode and timespans < 1 min.
-// Do not use with bigger timespans!
-string CTimeSpan::x_AsSmartString_Smart_Small(ERound rounding)
+
+// Helper functions to convert to smart string for "smart" mode
+// and timespans < 1 min. Do not use with sbigger timespans!
+
+string CTimeSpan::x_AsSmartString_Smart_Small(TSmartStringFlags flags) const
{
- enum EUnit {
- eSecond = 0,
- eMillisecond,
- eMicrosecond,
- eNanosecond
- };
- const char* kUnitNames[4] = { "second", "millisecond", "microsecond", "nanosecond" };
+ _ASSERT(*this < CTimeSpan(60, 0));
+ _ASSERT(GetSign() != eNegative);
+ _ASSERT((flags & fSS_Smart) == fSS_Smart);
// Get timespan components
int sec = x_Second();
long nanoseconds = GetNanoSecondsAfterSecond();
- // Split nanoseconds on 3 digit parts AAABBBCCC
+ // Split nanoseconds to 3 digit parts AAABBBCCC
// AAA - milli, BBB - micro, CCC - nano
int milli = nanoseconds / 1000000;
int micro = nanoseconds / 1000 % 1000;
@@ -2689,17 +2910,15 @@ string CTimeSpan::x_AsSmartString_Smart_Small(ERound rounding)
v2 = 0;
} else {
// Empty timespan
- return "0 seconds";
+ return (flags & fSS_Full) ? "0 seconds" : "0s";
}
- string result;
-
- result = NStr::LongToString(v1);
+ string result = NStr::LongToString(v1);
bool plural = (v1 != 1);
size_t len = result.length();
// Rounding
- if (rounding == eRound) {
+ if ( flags & fSS_Round ) {
// Rounding depends on number of digits we already have in v1
if (len == 1) {
v2 += 5;
@@ -2710,12 +2929,12 @@ string CTimeSpan::x_AsSmartString_Smart_Small(ERound rounding)
}
// Check on overflow
if ( v2 > 999 ) {
- v1++;
+ ++v1;
v2 = 0;
if (unit == eSecond) {
if ( v1 > 59 ) {
// Special case, because we work with timespans < 1 min
- return "1 minute";
+ return (flags & fSS_Full) ? "1 minute" : "1m";
}
} else {
if ( v1 > 999 ) {
@@ -2742,78 +2961,93 @@ string CTimeSpan::x_AsSmartString_Smart_Small(ERound rounding)
plural = true;
}
}
- result += string(" ") + kUnitNames[unit];
- if (plural) {
- result += "s";
+ if ( flags & fSS_Full ) {
+ result += string(" ") + kUnitNames[unit].name_full;
+ if (plural) {
+ result += "s";
+ }
+ } else {
+ result += kUnitNames[unit].name_short;
}
return result;
}
-// Helper functions for all modes except Smart.
-string CTimeSpan::x_AsSmartString_Precision(ESmartStringPrecision precision,
- ERound rounding, ESmartStringZeroMode zero_mode)
+// Helper functions for all modes except "smart".
+string CTimeSpan::x_AsSmartString_Precision(TSmartStringFlags flags) const
{
+ _ASSERT(GetSign() != eNegative);
+ _ASSERT((flags & fSS_Smart) != fSS_Smart);
+
+ // Convert precision flags to continuous numeric value (bit position - 1)
+ int precision = -1;
+ TSmartStringFlags pf = flags & fSS_PrecisionMask;
+ while (pf) {
+ pf >>= 1; ++precision;
+ }
+ _ASSERT(precision >= 0);
+
// Named or float precision level
- bool is_named_precision = (precision <= eSSP_Nanosecond);
+ bool is_named_precision = (precision < ePrecision);
+
+ // Make a copy (for rounding)
+ CTimeSpan ts(*this);
- // Round time span
- if (rounding == eRound ) {
+ // Round time span if necessary
+ if ( flags & fSS_Round ) {
int adjust_level = precision;
// Calculate adjustment for floating precision level
if ( !is_named_precision ) {
- adjust_level = eSSP_Nanosecond;
- long days = GetCompleteDays();
- int adjust_shift = precision - eSSP_Nanosecond - 1;
-
- if ( days >=365 ) {
- adjust_level = eSSP_Year + adjust_shift;
- } else if (days >= 30) {
- adjust_level = eSSP_Month + adjust_shift;
- } else if (days > 0) {
- adjust_level = eSSP_Day + adjust_shift;
- } else if (x_Hour() > 0) {
- adjust_level = eSSP_Hour + adjust_shift;
- } else if (x_Minute() > 0) {
- adjust_level = eSSP_Minute + adjust_shift;
- } else if (x_Second() > 0) {
- adjust_level = eSSP_Second + adjust_shift;
+
+ // Find first non-zero value
+ long sec = GetCompleteSeconds();
+ for (adjust_level = eYear; adjust_level <= eSecond; adjust_level++) {
+ if (sec >= kTimeSpanUnitMultipliers[adjust_level]) {
+ break;
+ }
}
- if (adjust_level > eSSP_Second) {
- if ( GetNanoSecondsAfterSecond() % 1000 == 0 ) {
- adjust_level = eSSP_Millisecond;
- } else if ( GetNanoSecondsAfterSecond() % 1000000 == 0 ) {
- adjust_level = eSSP_Microsecond;
+ // Calculate adjustment level
+ if (adjust_level <= eSecond) {
+ adjust_level += (precision - eNanosecond - 1);
+ } else {
+ // ms, us, ns
+ if (GetNanoSecondsAfterSecond() % 1000 == 0) {
+ adjust_level = eMillisecond;
+ }
+ else if (GetNanoSecondsAfterSecond() % 1000000 == 0) {
+ adjust_level = eMicrosecond;
+ } else {
+ // no adjustment otherwise
+ adjust_level = eNanosecond;
}
- // no adjustment otherwise
}
}
// Add adjustment time span
- switch (ESmartStringPrecision(adjust_level)) {
- case eSSP_Year:
- *this += CTimeSpan(365/2, 0, 0, 0);
+ switch ( EUnit(adjust_level) ) {
+ case eYear:
+ ts += CTimeSpan((long)kAverageSecondsPerYear/2);
break;
- case eSSP_Month:
- *this += CTimeSpan(15, 0, 0, 0);
+ case eMonth:
+ ts += CTimeSpan((long)kAverageSecondsPerMonth/2);
break;
- case eSSP_Day:
- *this += CTimeSpan(0, 12, 0, 0);
+ case eDay:
+ ts += CTimeSpan(0, 12, 0, 0);
break;
- case eSSP_Hour:
- *this += CTimeSpan(0, 0, 30, 0);
+ case eHour:
+ ts += CTimeSpan(0, 0, 30, 0);
break;
- case eSSP_Minute:
- *this += CTimeSpan(0, 0, 0, 30);
+ case eMinute:
+ ts += CTimeSpan(0, 0, 0, 30);
break;
- case eSSP_Second:
- *this += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2);
+ case eSecond:
+ ts += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2);
break;
- case eSSP_Millisecond:
- *this += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2000);
+ case eMillisecond:
+ ts += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2000);
break;
- case eSSP_Microsecond:
- *this += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2000000);
+ case eMicrosecond:
+ ts += CTimeSpan(0, 0, 0, 0, kNanoSecondsPerSecond/2000000);
break;
default:
; // nanoseconds -- nothing to do
@@ -2821,27 +3055,35 @@ string CTimeSpan::x_AsSmartString_Precision(ESmartStringPrecision precision,
}
// Prepare data
- typedef SSmartStringItem SItem;
+
+ long sec = ts.GetCompleteSeconds();
+ long nanoseconds = ts.GetNanoSecondsAfterSecond();
+
+ struct SItem {
+ SItem(void) : value(0), unit(eYear) {};
+ SItem(long v, EUnit u) : value(v), unit(u) {};
+ long value;
+ EUnit unit;
+ };
const int max_count = 7;
SItem span[max_count];
- long days = GetCompleteDays();
- long nanoseconds = GetNanoSecondsAfterSecond();
-
- span[0] = SItem(days/365 , "year" ); days %= 365;
- span[1] = SItem(days/30 , "month" ); days %= 30;
- span[2] = SItem(days , "day" );
- span[3] = SItem(x_Hour() , "hour" );
- span[4] = SItem(x_Minute(), "minute");
- span[5] = SItem(x_Second(), "second");
+
+ span[0] = SItem(sec/kAverageSecondsPerYear, eYear ); sec %= kAverageSecondsPerYear;
+ span[1] = SItem(sec/kAverageSecondsPerMonth, eMonth ); sec %= kAverageSecondsPerMonth;
+ span[2] = SItem(sec/(3600L*24), eDay ); sec %= (3600L*24);
+ span[3] = SItem(sec/3600L, eHour ); sec %= 3600L;
+ span[4] = SItem(sec/60L, eMinute); sec %= 60L;
+ span[5] = SItem(sec, eSecond);
+
switch (precision) {
- case eSSP_Millisecond:
- span[6] = SItem(nanoseconds / 1000000, "millisecond");
+ case eMillisecond:
+ span[6] = SItem(nanoseconds / 1000000, eMillisecond);
break;
- case eSSP_Microsecond:
- span[6] = SItem(nanoseconds / 1000, "microsecond");
+ case eMicrosecond:
+ span[6] = SItem(nanoseconds / 1000, eMicrosecond);
break;
- case eSSP_Nanosecond:
- span[6] = SItem(nanoseconds, "nanosecond");
+ case eNanosecond:
+ span[6] = SItem(nanoseconds, eNanosecond);
break;
default:
; // other not-nanoseconds based precisions
@@ -2850,78 +3092,330 @@ string CTimeSpan::x_AsSmartString_Precision(ESmartStringPrecision precision,
// Result string
string result;
// Precision level to start from (first non-zero)
- int start = is_named_precision ? eSSP_Year : eSSP_Precision1;
+ int start = is_named_precision ? eYear : ePrecision;
// Compose resulting string
- for (int i = 0; i < max_count && start <= precision; i++) {
+ for (int i = 0; i < max_count && start <= precision; ++i) {
long val = span[i].value;
// Adjust precision to skip zero values
if ( !val ) {
if ( result.empty() ) {
- if (start == precision && start != eSSP_Precision1) {
+ if (start == precision && start != ePrecision) {
break;
}
if ( is_named_precision ) {
- start++;
+ ++start;
}
continue;
}
- if (zero_mode == eSSZ_SkipZero) {
- start++;
+ if ( flags & fSS_SkipZero ) {
+ ++start;
continue;
} else {
long sum = 0;
int cp = start + 1;
for (int j = i + 1;
- j < max_count && (cp <= precision); j++, cp++) {
+ j < max_count && (cp <= precision); ++j, ++cp) {
sum += span[j].value;
}
if ( !sum ) {
// all trailing parts are zeros -- skip all
- start = precision;
break;
}
}
}
- start++;
+ ++start;
if ( !result.empty() ) {
result += " ";
}
- result += NStr::LongToString(val) + " " + span[i].str;
- if (val != 1) {
- result += "s";
+ result += NStr::LongToString(val);
+ if (flags & fSS_Full) {
+ result += string(" ") + kUnitNames[span[i].unit].name_full;
+ if (val != 1) {
+ result += "s";
+ }
+ } else {
+ result += kUnitNames[span[i].unit].name_short;
}
}
if ( result.empty() ) {
- if ( precision >= eSSP_Second ) {
- return "0 " + span[eSSP_Second].str + "s";
+ if ( precision >= eSecond ) {
+ return (flags & fSS_Full) ? "0 seconds" : "0s";
} else {
- return "0 " + span[precision].str + "s";
+ if (flags & fSS_Full) {
+ return string("0 ") + kUnitNames[span[precision].unit].name_full + "s";
+ }
+ return string("0") + kUnitNames[span[precision].unit].name_short;
}
}
return result;
}
-string CTimeSpan::AsSmartString(ESmartStringPrecision precision,
- ERound rounding,
- ESmartStringZeroMode zero_mode) const
+string CTimeSpan::AsSmartString(TSmartStringFlags flags) const
{
- // Make positive copy
- CTimeSpan diff(*this);
- if ( diff.GetSign() == eNegative ) {
- diff.Invert();
+ // Check on negative value
+ if (GetSign() == eNegative) {
+ NCBI_THROW(CTimeException, eArgument,
+ "Negative CTimeSpan cannot be converted to smart string");
+ }
+
+ // Check flags compatibility
+
+ _ASSERT(fSS_PrecisionMask ==
+ (fSS_Year | fSS_Month | fSS_Day |
+ fSS_Hour | fSS_Minute | fSS_Second |
+ fSS_Millisecond | fSS_Microsecond | fSS_Nanosecond |
+ fSS_Precision1 | fSS_Precision2 | fSS_Precision3 |
+ fSS_Precision4 | fSS_Precision5 | fSS_Precision6 |
+ fSS_Precision7 | fSS_Smart)
+ );
+
+ const string kMsg = "Incompatible flags specified together: ";
+
+ TSmartStringFlags f = flags & fSS_PrecisionMask;
+ if (f == 0) {
+ flags |= fSS_Smart; // default
+ } else {
+ if ( !(f && !(f & (f-1))) ) {
+ NCBI_THROW(CTimeException, eArgument, "Only one precision flag can be specified");
+ }
+ }
+
+ // Default flags
+
+ // Truncation
+ f = fSS_Trunc | fSS_Round;
+ if ((flags & f) == f) {
+ NCBI_THROW(CTimeException, eArgument, kMsg + "fSS_Trunc | fSS_Round");
+ }
+ if ((flags & f) == 0) {
+ flags |= fSS_Trunc;
+ }
+ // SkipZero
+ f = fSS_SkipZero | fSS_NoSkipZero;
+ if ((flags & f) == f) {
+ NCBI_THROW(CTimeException, eArgument, kMsg + "fSS_SkipZero | fSS_NoSkipZero");
+ }
+ f = fSS_Smart | fSS_NoSkipZero;
+ if ((flags & f) == f) {
+ NCBI_THROW(CTimeException, eArgument, kMsg + "fSS_Smart | fSS_NoSkipZero");
}
- if (precision == eSSP_Smart) {
- if ( diff < CTimeSpan(60,0) ) {
- return diff.x_AsSmartString_Smart_Small(rounding);
+ if ((flags & f) == 0) {
+ flags |= fSS_SkipZero;
+ }
+ // Naming
+ f = fSS_Short | fSS_Full;
+ if ((flags & f) == f) {
+ NCBI_THROW(CTimeException, eArgument, kMsg + "fSS_Short | fSS_Full");
+ }
+ if ((flags & f) == 0) {
+ flags |= fSS_Full;
+ }
+
+ // Use specific code depends on precision
+
+ if ((flags & fSS_Smart) == fSS_Smart) {
+ if (*this < CTimeSpan(60, 0)) {
+ return x_AsSmartString_Smart_Small(flags);
}
- return diff.x_AsSmartString_Smart_Big(rounding);
+ return x_AsSmartString_Smart_Big(flags);
} else {
- return diff.x_AsSmartString_Precision(precision, rounding, zero_mode);
+ return x_AsSmartString_Precision(flags);
+ }
+}
+
+
+CTimeSpan& CTimeSpan::AssignFromSmartString(const string& str)
+{
+ Clear();
+ if ( str.empty() ) {
+ return *this;
+ }
+
+ const char* sss = str.c_str();
+ bool numeric_expected = true;
+ long value = 0;
+ long frac = 0;
+ size_t frac_len = 0;
+ bool repetitions[kUnitCount];
+
+ memset(repetitions, 0, kUnitCount * sizeof(repetitions[0]));
+
+ for (; *sss != '\0'; ++sss) {
+
+ // Skip all white spaces
+ if (isspace((unsigned char)(*sss))) {
+ continue;
+ }
+
+ // Numeric data expected
+ if (numeric_expected) {
+
+ value = 0; frac = 0;
+
+ if (isdigit((unsigned char)(*sss))) {
+ // Get numeric value
+ const char* start = sss++;
+ while (*sss && isdigit((unsigned char)(*sss))) ++sss;
+ size_t n = sss - start;
+ if (n > 10) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Too long numeric value '" + (string)CTempString(start, n) +
+ "': string '" + str + "' (pos = " +
+ NStr::NumericToString(start - str.c_str()) + ")" );
+ }
+ value = NStr::StringToULong(CTempString(start, n));
+ } else
+ if (*sss != '.') {
+ // no digits and no fraction part (".n" case)
+ break; // error
+ }
+
+ // Check on fraction
+ if (*sss == '.') {
+ ++sss;
+ if (*sss && isdigit((unsigned char)(*sss))) {
+ const char* start = sss++;
+ while (*sss && isdigit((unsigned char)(*sss))) ++sss;
+ frac_len = sss - start;
+ if (frac_len > 9) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Too long fractional part '" + (string)CTempString(start, frac_len) +
+ "': string '" + str + "' (pos = " +
+ NStr::NumericToString(start - str.c_str()) + ")" );
+ }
+ frac = NStr::StringToULong(CTempString(start, frac_len));
+ }
+ // else { "n." case --= nothing to do }
+ }
+ --sss;
+ numeric_expected = false;
+ continue;
+ }
+
+ // Unit specifier expected after numeric value
+ else {
+ if (!isalpha((unsigned char)(*sss))) {
+ break; // error
+ }
+ const char* start = sss++;
+ while (*sss && isalpha((unsigned char)(*sss))) ++sss;
+ size_t n = sss - start;
+ --sss;
+ string spec(start, n);
+ NStr::ToLower(spec);
+
+ unsigned int i = 0;
+ for (; i < kUnitCount; ++i) {
+ if (spec == kUnitNames[i].name_full ||
+ spec == kUnitNames[i].name_full + string("s") ||
+ spec == kUnitNames[i].name_short) {
+ break;
+ }
+ }
+ if (i >= kUnitCount) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Unknown time specifier '" + spec + "': string '" + str +
+ "' (pos = " + NStr::NumericToString(start - str.c_str()) + ")" );
+ }
+
+ // Use bigger values for calculations to check on possible overflow
+ TSeconds sec = m_Sec;
+ TSeconds ns = m_NanoSec;
+
+ // Add component to timespan
+ switch (EUnit(i)) {
+ case eYear:
+ case eMonth:
+ case eDay:
+ case eHour:
+ case eMinute:
+ case eSecond:
+ sec += value * kTimeSpanUnitMultipliers[i];
+ break;
+ case eMillisecond:
+ case eMicrosecond:
+ ns += value * kTimeSpanUnitMultipliers[i];
+ break;
+ case eNanosecond:
+ ns += value;
+ break;
+ default:
+ _TROUBLE;
+ }
+
+ // Add fractional part
+ if (frac) {
+ // div = 10 ^ frac_len
+ unsigned int div = 10;
+ _ASSERT(frac_len > 0);
+ while (--frac_len) div *= 10;
+
+ if (i < eSecond) {
+ // fraction of year, month, day, hour, minute
+ sec += ((TSeconds)frac * kTimeSpanUnitMultipliers[i] / div);
+ } else
+ if (i == eSecond) {
+ // sec -- increase nanoseconds
+ ns += ((TSeconds)frac * (kNanoSecondsPerSecond / div));
+ } else {
+ if (i == eNanosecond) {
+ // Round fractional nanoseconds to nearest value
+ if (((TSeconds)frac * 10 / div) >=5 ) {
+ ++ns;
+ }
+ } else
+ // us, ms -- increase nanoseconds
+ ns += ((TSeconds)frac * (kTimeSpanUnitMultipliers[i] / div));
+ }
+ }
+
+ // Check repetition of time components -- not allowed
+ if (repetitions[i]) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Time component for '" + string(kUnitNames[i].name_full) +
+ "s' already exists: string '" + str +
+ "' (pos = " + NStr::NumericToString(start - str.c_str()) + ")");
+ }
+ repetitions[i] = true;
+ if (frac && (i >= eSecond)) {
+ // disable all subsequent ms, us, ns and fraction of second
+ repetitions[eMillisecond] = true;
+ repetitions[eMicrosecond] = true;
+ repetitions[eNanosecond] = true;
+ }
+
+ // Check on overflow
+ if ( sec <= kMin_Long || sec >= kMax_Long ||
+ ns <= kMin_Long || ns >= kMax_Long) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Value is too big to convert to CTimeSpan: string '" + str +
+ "' (pos = " + NStr::NumericToString(start - str.c_str()) + ")");
+ }
+ m_Sec = (long)sec;
+ m_NanoSec = (long)ns;
+ numeric_expected = true;
+ }
+ }
+
+ // Check on errors
+ if (!numeric_expected) {
+ NCBI_THROW(CTimeException, eConvert,
+ "Time specifier expected: string '" + str +
+ "' (pos = " + NStr::NumericToString(sss - str.c_str()) + ")");
+ }
+ if (*sss != '\0') {
+ NCBI_THROW(CTimeException, eConvert,
+ "Unexpected symbol: string '" + str +
+ "' (pos = " + NStr::NumericToString(sss - str.c_str()) + ")");
}
+ // Normalize time span
+ x_Normalize();
+
+ return *this;
}
@@ -3040,7 +3534,7 @@ void CTimeout::GetNano(unsigned int *sec, unsigned int *nanosec) const
s_SpecialValueName(m_Type) + " timeout value");
}
if ( sec ) {
- *sec = m_Sec;
+ *sec = m_Sec;
}
if ( nanosec ) {
*nanosec = m_NanoSec;
@@ -3086,12 +3580,12 @@ void CTimeout::SetNano(unsigned int sec, unsigned int nanosec)
void CTimeout::Set(double sec)
{
if (sec < 0) {
- NCBI_THROW(CTimeException, eConvert,
+ NCBI_THROW(CTimeException, eArgument,
"Cannot set negative value " +
NStr::DoubleToString(sec));
}
if (sec > kMax_UInt) {
- NCBI_THROW(CTimeException, eConvert,
+ NCBI_THROW(CTimeException, eArgument,
"Timeout value " +
NStr::DoubleToString(sec) + " too big");
}
@@ -3104,12 +3598,12 @@ void CTimeout::Set(double sec)
void CTimeout::Set(const CTimeSpan& ts)
{
if (ts.GetSign() == eNegative) {
- NCBI_THROW(CTimeException, eConvert,
+ NCBI_THROW(CTimeException, eArgument,
"Cannot convert from negative CTimeSpan(" +
ts.AsString() + ")");
}
if ((Uint8) ts.GetCompleteSeconds() > kMax_UInt) {
- NCBI_THROW(CTimeException, eConvert,
+ NCBI_THROW(CTimeException, eArgument,
"CTimeSpan value (" +
ts.AsString() + ") too big");
// We don't need to check nanoseconds, because CTimeSpan always has it
@@ -3191,7 +3685,7 @@ bool CTimeout::operator>= (const CTimeout& t) const
case COMPARE_TIMEOUT_TYPES(eInfinite, eDefault):
return true; // infinity >= anything
case COMPARE_TIMEOUT_TYPES(eDefault, eFinite):
- if ( t.IsZero() )
+ if ( t.IsZero() )
return true; // default >= zero
// fall through
default:
@@ -3343,7 +3837,7 @@ CNanoTimeout CDeadline::GetRemainingTime(void) const
if (thenNS >= nowNS) {
thenNS -= nowNS;
} else {
- thenS--;
+ --thenS;
thenNS = kNanoSecondsPerSecond - (nowNS - thenNS);
}
_ASSERT(thenS >= nowS);
@@ -3533,7 +4027,7 @@ int CFastLocalTime::GetLocalTimezone(void)
//
//=============================================================================
-// deprecated
+/// @deprecated
CStopWatch::CStopWatch(bool start)
{
m_Total = 0;
diff --git a/c++/src/corelib/perf_log.cpp b/c++/src/corelib/perf_log.cpp
index db93f7e..3f719ba 100644
--- a/c++/src/corelib/perf_log.cpp
+++ b/c++/src/corelib/perf_log.cpp
@@ -1,4 +1,4 @@
-/* $Id: perf_log.cpp 351049 2012-01-25 19:08:52Z grichenk $
+/* $Id: perf_log.cpp 469371 2015-06-03 18:05:11Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -84,7 +84,9 @@ CDiagContext_Extra CPerfLogger::Post(int status,
if ( !status_msg.empty() ) {
args.push_back(SDiagMessage::TExtraArg("status_msg", status_msg));
}
- CDiagContext_Extra extra = g_PostPerf((int)status, m_StopWatch.Elapsed(), args);
+ double elapsed = m_StopWatch->Elapsed() + m_Adjustment;
+ CDiagContext_Extra extra = g_PostPerf((int)status,
+ elapsed < 0.0 ? 0.0 : elapsed, args);
Discard();
return extra;
}
diff --git a/c++/src/corelib/plugin_manager_store.cpp b/c++/src/corelib/plugin_manager_store.cpp
index 6cdef52..4dfed7e 100644
--- a/c++/src/corelib/plugin_manager_store.cpp
+++ b/c++/src/corelib/plugin_manager_store.cpp
@@ -1,4 +1,4 @@
-/* $Id: plugin_manager_store.cpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: plugin_manager_store.cpp 461873 2015-03-13 12:47:31Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,9 +76,9 @@ void CPluginManagerGetterImpl::ReportKeyConflict(const TKey& key,
const TObject* old_pm,
const type_info& new_pm_type)
{
- ERR_POST_X(4, Fatal << "Plugin Manager conflict, key=\"" << key << "\", "
- "old type=" << typeid(*old_pm).name() << ", "
- "new type=" << new_pm_type.name());
+ ERR_FATAL_X(4, "Plugin Manager conflict, key=\"" << key << "\", "
+ "old type=" << typeid(*old_pm).name() << ", "
+ "new type=" << new_pm_type.name());
}
diff --git a/c++/src/corelib/request_ctx.cpp b/c++/src/corelib/request_ctx.cpp
index e92ec52..ffdba9d 100644
--- a/c++/src/corelib/request_ctx.cpp
+++ b/c++/src/corelib/request_ctx.cpp
@@ -1,4 +1,4 @@
-/* $Id: request_ctx.cpp 448715 2014-10-08 15:41:41Z ivanov $
+/* $Id: request_ctx.cpp 472377 2015-07-09 14:15:29Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,7 +56,8 @@ CRequestContext::CRequestContext(TContextFlags flags)
m_PropSet(0),
m_IsRunning(false),
m_AutoIncOnPost(false),
- m_Flags(flags)
+ m_Flags(flags),
+ m_OwnerTID(-1)
{
}
@@ -73,18 +74,21 @@ CRequestContext::TCount CRequestContext::GetNextRequestID(void)
}
-static void s_LogHitID(const string& phid)
+void CRequestContext::x_LogHitID(bool ignore_app_state) const
{
- GetDiagContext().Extra().Print(g_GetNcbiString(eNcbiStrings_PHID), phid);
-}
+ if (m_LoggedHitID || m_HitID.empty()) return;
+ // ignore_app_state can be set by CDiagContext in case if hit-id
+ // was set for request context only (no default one), but request
+ // start/stop never happened and the hit id may be lost. If this
+ // happens, CDiagContext may force logging of the request's hit id
+ // on application stop.
-void CRequestContext::x_LogHitID(void) const
-{
- if (m_LoggedHitID || m_HitID.empty()) return;
- if (m_AppState != eDiagAppState_Request &&
- m_AppState != eDiagAppState_RequestBegin) return;
- s_LogHitID(m_HitID);
+ if (!ignore_app_state &&
+ m_AppState != eDiagAppState_Request &&
+ m_AppState != eDiagAppState_RequestBegin &&
+ m_AppState != eDiagAppState_RequestEnd) return;
+ GetDiagContext().Extra().Print(g_GetNcbiString(eNcbiStrings_PHID), m_HitID);
m_LoggedHitID = true;
}
@@ -92,18 +96,26 @@ void CRequestContext::x_LogHitID(void) const
const string& CRequestContext::SetHitID(void)
{
SetHitID(GetDiagContext().GetNextHitID());
- x_LogHitID();
return m_HitID;
}
-string CRequestContext::GetHitID(void) const
+string CRequestContext::x_GetHitID(CDiagContext::EDefaultHitIDFlags flag) const
{
if ( x_IsSetProp(eProp_HitID) ) {
x_LogHitID();
return m_HitID;
}
- return GetDiagContext().GetDefaultHitID();
+ string phid = GetDiagContext().x_GetDefaultHitID(CDiagContext::eHitID_NoCreate);
+ if (!phid.empty()) {
+ const_cast<CRequestContext*>(this)->SetHitID(phid);
+ return phid;
+ }
+ if (flag != CDiagContext::eHitID_NoCreate) {
+ // If there's no hit id available, create (and log) a new one.
+ return const_cast<CRequestContext*>(this)->SetHitID();
+ }
+ return kEmptyStr;
}
@@ -197,11 +209,16 @@ void CRequestContext::StartRequest(void)
}
GetRequestTimer().Restart();
m_IsRunning = true;
+ x_LogHitID();
}
void CRequestContext::StopRequest(void)
{
+ if (!m_LoggedHitID) {
+ // Hit id has not been set or logged yet. Try to log the default one.
+ x_GetHitID(CDiagContext::eHitID_NoCreate);
+ }
Reset();
m_IsRunning = false;
}
@@ -288,6 +305,11 @@ static bool IsValidHitID(const string& hit) {
void CRequestContext::SetHitID(const string& hit)
{
+ if ( m_LoggedHitID ) {
+ // Show warning when changing hit id after is has been logged.
+ ERR_POST_X(28, Warning << "Changing hit ID after one has been logged. "
+ "New hit id is: " << hit);
+ }
static CSafeStatic<TOnBadHitId> action;
if ( !IsValidHitID(hit) ) {
switch ( action->Get() ) {
@@ -313,22 +335,25 @@ void CRequestContext::SetHitID(const string& hit)
m_SubHitID = 0;
}
m_HitID = hit;
+ m_LoggedHitID = false;
+ x_LogHitID();
}
const string& CRequestContext::GetNextSubHitID(void)
{
- static CSafeStatic<CAtomicCounter_WithAutoInit> s_DefaultSubHitCounter;
+ static CAtomicCounter s_DefaultSubHitCounter;
- if ( !IsSetHitID() ) return kEmptyStr;
+ _ASSERT(IsSetHitID());
// Use global sub-hit counter for default hit id to prevent
// duplicate phids in different threads.
- int sub_hit_id = GetHitID() == GetDiagContext().GetDefaultHitID() ?
- s_DefaultSubHitCounter->Add(1) : ++m_SubHitID;
+ m_SubHitIDCache = GetHitID();
+ int sub_hit_id = m_SubHitIDCache == GetDiagContext().GetDefaultHitID() ?
+ s_DefaultSubHitCounter.Add(1) : ++m_SubHitID;
// Cache the string so that C code can use it.
- m_SubHitIDCache = GetHitID() + "." + NStr::NumericToString(sub_hit_id);
+ m_SubHitIDCache += "." + NStr::NumericToString(sub_hit_id);
return m_SubHitIDCache;
}
diff --git a/c++/src/corelib/resource_info.cpp b/c++/src/corelib/resource_info.cpp
index 57b44d1..38929ab 100644
--- a/c++/src/corelib/resource_info.cpp
+++ b/c++/src/corelib/resource_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: resource_info.cpp 463791 2015-04-01 15:39:43Z ivanov $
+/* $Id: resource_info.cpp 464978 2015-04-15 18:51:39Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -859,7 +859,7 @@ void BlockTEA_Encode_In_Place(Int4* data, Int4 n, const TBlockTEA_Key key)
{
if (n <= 1) return;
Uint4 z = data[n - 1];
- Uint4 y = data[0];
+ Uint4 y;
Uint4 sum = 0;
Uint4 e;
Int4 p;
@@ -881,7 +881,7 @@ void BlockTEA_Encode_In_Place(Int4* data, Int4 n, const TBlockTEA_Key key)
void BlockTEA_Decode_In_Place(Int4* data, Int4 n, const TBlockTEA_Key key)
{
if (n <= 1) return;
- Uint4 z = data[n - 1];
+ Uint4 z;
Uint4 y = data[0];
Uint4 e;
Int4 p;
diff --git a/c++/src/corelib/rwstreambuf.cpp b/c++/src/corelib/rwstreambuf.cpp
index 1db606f..281df59 100644
--- a/c++/src/corelib/rwstreambuf.cpp
+++ b/c++/src/corelib/rwstreambuf.cpp
@@ -1,4 +1,4 @@
-/* $Id: rwstreambuf.cpp 430074 2014-03-21 18:25:58Z lavr $
+/* $Id: rwstreambuf.cpp 463752 2015-04-01 14:15:52Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -112,15 +112,44 @@ const char* g_RW_ResultToString(ERW_Result result)
static const streamsize kDefaultBufSize = 4096;
+static inline EOwnership x_IfToOwnReader(const IReader* r, const IWriter* w,
+ CRWStreambuf::TFlags f)
+{
+ const IReaderWriter* rw = dynamic_cast<const IReaderWriter*> (r);
+ if (!rw || rw != dynamic_cast<const IReaderWriter*> (w)) {
+ if (f & CRWStreambuf::fOwnReader)
+ return eTakeOwnership;
+ } else {
+ if ((f & CRWStreambuf::fOwnAll) == CRWStreambuf::fOwnAll)
+ return eTakeOwnership;
+ }
+ return eNoOwnership;
+}
+
+
+static inline EOwnership x_IfToOwnWriter(const IReader* r, const IWriter* w,
+ CRWStreambuf::TFlags f)
+{
+ const IReaderWriter* rw = dynamic_cast<const IReaderWriter*> (w);
+ if (!rw || rw != dynamic_cast<const IReaderWriter*> (r)) {
+ if (f & CRWStreambuf::fOwnWriter)
+ return eTakeOwnership;
+ } /* else IReader sets the ownership */
+ return eNoOwnership;
+}
+
+
CRWStreambuf::CRWStreambuf(IReaderWriter* rw,
streamsize n,
CT_CHAR_TYPE* s,
CRWStreambuf::TFlags f)
- : m_Flags(f), m_Reader(rw), m_Writer(rw), m_pBuf(0),
+ : m_Flags(f),
+ m_Reader(rw, x_IfToOwnReader(rw, rw, f)),
+ m_Writer(rw, x_IfToOwnWriter(rw, rw, f)), m_pBuf(0),
x_GPos((CT_OFF_TYPE) 0), x_PPos((CT_OFF_TYPE) 0),
x_Err(false), x_ErrPos((CT_OFF_TYPE) 0)
{
- setbuf(s && n ? s : 0, n ? n : kDefaultBufSize << 1);
+ setbuf(n && s ? s : 0, n ? n : kDefaultBufSize << 1);
}
@@ -129,7 +158,9 @@ CRWStreambuf::CRWStreambuf(IReader* r,
streamsize n,
CT_CHAR_TYPE* s,
CRWStreambuf::TFlags f)
- : m_Flags(f), m_Reader(r), m_Writer(w), m_pBuf(0),
+ : m_Flags(f),
+ m_Reader(r, x_IfToOwnReader(r, w, f)),
+ m_Writer(w, x_IfToOwnWriter(r, w, f)), m_pBuf(0),
x_GPos((CT_OFF_TYPE) 0), x_PPos((CT_OFF_TYPE) 0),
x_Err(false), x_ErrPos((CT_OFF_TYPE) 0)
{
@@ -138,28 +169,44 @@ CRWStreambuf::CRWStreambuf(IReader* r,
}
+ERW_Result CRWStreambuf::x_pushback(void)
+{
+ if ( !m_Reader ) {
+ _ASSERT(!gptr() && !egptr());
+ return eRW_Success;
+ }
+
+ ERW_Result result;
+ const CT_CHAR_TYPE* ptr = gptr();
+ size_t count = (size_t)(egptr() - ptr);
+ setg(0, 0, 0);
+ if ( !count )
+ result = eRW_Success;
+ else if ((result = m_Reader->Pushback(ptr, count, m_pBuf)) == eRW_Success)
+ m_pBuf = 0;
+ return result;
+}
+
+
CRWStreambuf::~CRWStreambuf()
{
try {
// Flush only if data pending and no error
if (!x_Err || x_ErrPos != x_GetPPos())
x_sync();
- setg(0, 0, 0);
setp(0, 0);
-
- IReaderWriter* rw = dynamic_cast<IReaderWriter*> (m_Reader);
- if (rw && rw == dynamic_cast<IReaderWriter*> (m_Writer)) {
- if ((m_Flags & fOwnAll) == fOwnAll)
- delete rw;
- } else {
- if (m_Flags & fOwnWriter)
- delete m_Writer;
- if (m_Flags & fOwnReader)
- delete m_Reader;
+ } NCBI_CATCH_ALL_X(2, "Exception in ~CRWStreambuf() [IGNORED]");
+ try {
+ // Push any data still unred in the buffer back to the device
+ ERW_Result result = x_pushback();
+ if (result != eRW_Success && result != eRW_NotImplemented) {
+ ERR_POST_X(13,
+ Critical << "CRWStreambuf::~CRWStreambuf():"
+ " Read data pending");
}
+ } NCBI_CATCH_ALL_X(14, "Exception in ~CRWStreambuf() [IGNORED]");
- delete[] m_pBuf;
- } NCBI_CATCH_ALL_X(2, "Exception in ~CRWStreambuf() [IGNORED]");
+ delete[] m_pBuf;
}
@@ -168,16 +215,18 @@ CNcbiStreambuf* CRWStreambuf::setbuf(CT_CHAR_TYPE* s, streamsize m)
if (!s && !m)
return this;
- if (gptr() && gptr() < egptr())
+ if (x_pushback() != eRW_Success)
ERR_POST_X(3,Critical << "CRWStreambuf::setbuf(): Read data pending");
- if (pbase() && pptr() > pbase())
+ if (x_sync() != 0)
ERR_POST_X(4,Critical << "CRWStreambuf::setbuf(): Write data pending");
+ setp(0, 0);
delete[] m_pBuf;
m_pBuf = 0;
size_t n = (size_t) m;
if ( !n ) {
+ s = 0/*setbuf(s, 0)?!*/;
_ASSERT(kDefaultBufSize > 1);
n = (size_t) kDefaultBufSize << (m_Reader && m_Writer ? 1 : 0);
}
@@ -208,20 +257,21 @@ CT_INT_TYPE CRWStreambuf::overflow(CT_INT_TYPE c)
if ( !m_Writer )
return CT_EOF;
- ERW_Result result;
size_t n_written;
- size_t n_towrite = (size_t)(pbase() ? pptr() - pbase() : 0);
+ size_t n_towrite = (size_t)(pptr() - pbase());
+ ERW_Result result;
if ( n_towrite ) {
// send buffer
do {
+ n_written = 0;
RWSTREAMBUF_HANDLE_EXCEPTIONS(
result = m_Writer->Write(pbase(), n_towrite, &n_written),
5, "CRWStreambuf::overflow(): IWriter::Write()",
(n_written = 0, result = eRW_Error));
_ASSERT(n_written <= n_towrite);
if ( !n_written ) {
- _ASSERT(result == eRW_Error);
+ _ASSERT(result != eRW_Success);
break;
}
// update buffer content (get rid of the data just sent)
@@ -244,6 +294,7 @@ CT_INT_TYPE CRWStreambuf::overflow(CT_INT_TYPE c)
}
} else if ( !CT_EQ_INT_TYPE(c, CT_EOF) ) {
// send char
+ n_written = 0;
CT_CHAR_TYPE b = CT_TO_CHAR_TYPE(c);
RWSTREAMBUF_HANDLE_EXCEPTIONS(
m_Writer->Write(&b, 1, &n_written),
@@ -281,23 +332,19 @@ CT_INT_TYPE CRWStreambuf::overflow(CT_INT_TYPE c)
streamsize CRWStreambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
{
- if ( !m_Writer )
+ if (!m_Writer || m < 0)
return 0;
- if (m <= 0)
- return 0;
_ASSERT((Uint8) m < numeric_limits<size_t>::max());
- size_t n = (size_t) m;
-
ERW_Result result = eRW_Success;
+ size_t n = (size_t) m;
size_t n_written = 0;
size_t x_written;
x_Err = false;
do {
- _ASSERT( n );
if (pbase()) {
- if (pbase() + n < epptr()) {
+ if (n && pbase() + n < epptr()) {
// Would entirely fit into the buffer not causing an overflow
x_written = (size_t)(epptr() - pptr());
if (x_written > n)
@@ -315,6 +362,7 @@ streamsize CRWStreambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
size_t x_towrite = (size_t)(pptr() - pbase());
if ( x_towrite ) {
+ x_written = 0;
RWSTREAMBUF_HANDLE_EXCEPTIONS(
result = m_Writer->Write(pbase(), x_towrite, &x_written),
8, "CRWStreambuf::xsputn(): IWriter::Write()",
@@ -332,13 +380,14 @@ streamsize CRWStreambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
}
}
- _ASSERT(n && result == eRW_Success);
+ x_written = 0;
+ _ASSERT(result == eRW_Success);
RWSTREAMBUF_HANDLE_EXCEPTIONS(
result = m_Writer->Write(buf, n, &x_written),
9, "CRWStreambuf::xsputn(): IWriter::Write()",
x_written = 0);
_ASSERT(x_written <= n);
- if ( !x_written ) {
+ if (!x_written && n) {
x_Err = true;
x_ErrPos = x_GetPPos();
break;
@@ -368,7 +417,7 @@ streamsize CRWStreambuf::xsputn(const CT_CHAR_TYPE* buf, streamsize m)
CT_INT_TYPE CRWStreambuf::underflow(void)
{
- _ASSERT(!gptr() || gptr() >= egptr());
+ _ASSERT(gptr() >= egptr());
if ( !m_Reader )
return CT_EOF;
@@ -384,7 +433,7 @@ CT_INT_TYPE CRWStreambuf::underflow(void)
#endif /*NCBI_COMPILER_MIPSPRO*/
// read from device
- size_t n_read;
+ size_t n_read = 0;
RWSTREAMBUF_HANDLE_EXCEPTIONS(
m_Reader->Read(m_ReadBuf, m_BufSize, &n_read),
10, "CRWStreambuf::underflow(): IReader::Read()",
@@ -410,26 +459,33 @@ streamsize CRWStreambuf::xsgetn(CT_CHAR_TYPE* buf, streamsize m)
if (!(m_Flags & fUntie) && x_sync() != 0)
return 0;
- if (m <= 0)
+ if (m < 0)
return 0;
+
_ASSERT((Uint8) m < numeric_limits<size_t>::max());
size_t n = (size_t) m;
+ size_t n_read;
- // first, read from the memory buffer
- size_t n_read = (size_t)(gptr() ? egptr() - gptr() : 0);
- if (n_read > n)
- n_read = n;
- memcpy(buf, gptr(), n_read);
- gbump((int) n_read);
- buf += n_read;
- n -= n_read;
+ if ( n ) {
+ // first, read from the memory buffer
+ n_read = (size_t)(egptr() - gptr());
+ if (n_read > n)
+ n_read = n;
+ memcpy(buf, gptr(), n_read);
+ gbump(int(n_read));
+ n -= n_read;
+ if ( !n )
+ return (streamsize) n_read;
+ buf += n_read;
+ } else
+ n_read = 0;
- while ( n ) {
+ do {
// next, read directly from the device
- size_t x_toread = n < m_BufSize ? m_BufSize : n;
- CT_CHAR_TYPE* x_buf = n < m_BufSize ? m_ReadBuf : buf;
+ size_t x_toread = n && n < m_BufSize ? m_BufSize : n;
+ CT_CHAR_TYPE* x_buf = n < m_BufSize ? m_ReadBuf : buf;
ERW_Result result = eRW_Success;
- size_t x_read;
+ size_t x_read = 0;
RWSTREAMBUF_HANDLE_EXCEPTIONS(
result = m_Reader->Read(x_buf, x_toread, &x_read),
@@ -457,7 +513,7 @@ streamsize CRWStreambuf::xsgetn(CT_CHAR_TYPE* buf, streamsize m)
break;
buf += x_read;
n -= x_read;
- }
+ } while ( n );
return (streamsize) n_read;
}
@@ -465,7 +521,7 @@ streamsize CRWStreambuf::xsgetn(CT_CHAR_TYPE* buf, streamsize m)
streamsize CRWStreambuf::showmanyc(void)
{
- _ASSERT(!gptr() || gptr() >= egptr());
+ _ASSERT(gptr() >= egptr());
if ( !m_Reader )
return -1L;
@@ -474,7 +530,7 @@ streamsize CRWStreambuf::showmanyc(void)
if (!(m_Flags & fUntie))
x_sync();
- size_t count;
+ size_t count = 0;
ERW_Result result;
RWSTREAMBUF_HANDLE_EXCEPTIONS(
result = m_Reader->PendingCount(&count),
diff --git a/c++/src/corelib/stream_utils.cpp b/c++/src/corelib/stream_utils.cpp
index 3a4ffd4..8489cac 100644
--- a/c++/src/corelib/stream_utils.cpp
+++ b/c++/src/corelib/stream_utils.cpp
@@ -1,4 +1,4 @@
-/* $Id: stream_utils.cpp 448174 2014-10-02 18:33:31Z vasilche $
+/* $Id: stream_utils.cpp 463570 2015-03-30 16:29:21Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -566,6 +566,12 @@ streamsize CStreamUtils::Readsome(CNcbiIstream& is,
}
+ERW_Result IReader::Pushback(const void*, size_t, void*)
+{
+ return eRW_NotImplemented;
+}
+
+
IReader::~IReader()
{
}
@@ -597,9 +603,8 @@ ERW_Result CStreamReader::Read(void* buf,
*bytes_read = (size_t) r;
}
if (!r) {
- m_Stream->setstate(!sb
- ? NcbiBadbit
- : NcbiFailbit | (ok ? NcbiEofbit : NcbiGoodbit));
+ m_Stream->setstate(!sb ? NcbiBadbit
+ : ok ? NcbiEofbit : NcbiFailbit);
return ok ? eRW_Eof : eRW_Error;
}
return eRW_Success;
@@ -620,6 +625,21 @@ ERW_Result CStreamReader::PendingCount(size_t* count)
}
+ERW_Result CStreamReader::Pushback(const void* buf, size_t count,
+ void* del_ptr)
+{
+ if (!m_Stream.IsOwned()) {
+ if (del_ptr) {
+ CStreamUtils::Pushback(*m_Stream,
+ (CT_CHAR_TYPE*) buf, count, del_ptr);
+ } else
+ CStreamUtils::Pushback(*m_Stream, (CT_CHAR_TYPE*) buf, count);
+ } else
+ delete[] (CT_CHAR_TYPE*) del_ptr;
+ return eRW_Success;
+}
+
+
ERW_Result CStreamWriter::Write(const void* buf,
size_t count,
size_t* bytes_written)
@@ -659,7 +679,7 @@ void g_ExtractReaderContents(IReader& reader, string& s)
if (s.size() <= pos + 1024) {
s.resize(s.size() * 2);
}
- size_t n;
+ size_t n = 0;
status = reader.Read(&s[pos], s.size() - pos, &n);
pos += n;
} while (status == eRW_Success);
diff --git a/c++/src/corelib/syslog.cpp b/c++/src/corelib/syslog.cpp
index 8fdcb78..afc07fc 100644
--- a/c++/src/corelib/syslog.cpp
+++ b/c++/src/corelib/syslog.cpp
@@ -1,4 +1,4 @@
-/* $Id: syslog.cpp 112029 2007-10-10 18:46:30Z ivanovp $
+/* $Id: syslog.cpp 460070 2015-02-24 19:18:49Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -103,13 +103,13 @@ void CSysLog::Post(const SDiagMessage& mess)
mess.Write(message_str, SDiagMessage::fNoEndl);
EPriority priority;
switch (mess.m_Severity) {
- case eDiag_Info: priority = eInfo;
- case eDiag_Warning: priority = eWarning;
- case eDiag_Error: priority = eError;
- case eDiag_Critical: priority = eCritical;
- case eDiag_Fatal: priority = eAlert;
- case eDiag_Trace: priority = eDebug;
- default: priority = eNotice;
+ case eDiag_Info: priority = eInfo; break;
+ case eDiag_Warning: priority = eWarning; break;
+ case eDiag_Error: priority = eError; break;
+ case eDiag_Critical: priority = eCritical; break;
+ case eDiag_Fatal: priority = eAlert; break;
+ case eDiag_Trace: priority = eDebug; break;
+ default: priority = eNotice; break;
}
Post(message_str, priority);
}
diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp
index c8c6047..bf6891e 100644
--- a/c++/src/corelib/test_boost.cpp
+++ b/c++/src/corelib/test_boost.cpp
@@ -1,4 +1,4 @@
-/* $Id: test_boost.cpp 422318 2013-12-19 17:48:09Z satskyse $
+/* $Id: test_boost.cpp 467868 2015-05-18 16:00:06Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -842,9 +842,6 @@ CNcbiTestApplication::CNcbiTestApplication(void)
{
m_Reporter = new CNcbiBoostReporter();
m_Logger = new CNcbiBoostLogger();
-
- // Do not show warning about inaccessible configuration file
- SetDiagFilter(eDiagFilter_Post, "!(106.11)");
}
CNcbiTestApplication::~CNcbiTestApplication(void)
@@ -979,7 +976,7 @@ CNcbiTestApplication::CollectTestUnit(but::test_unit* tu)
if (!tu_val) {
tu_val = tu;
if (test_name != unit_name) {
- LOG_POST_X(3, Info << "Duplicate name found: '" << unit_name
+ ERR_POST_X(3, Info << "Duplicate name found: '" << unit_name
<< "' - renamed to '" << test_name << "'");
tu->p_name.set(test_name);
}
@@ -1171,10 +1168,13 @@ static const char* s_NcbiFeatures[] = {
inline void
CNcbiTestApplication::x_InitCommonParserVars(void)
{
+ m_IniParser->AddSymbol("COMPILER_Clang", IS_VAR_DEFINED(__clang__));
m_IniParser->AddSymbol("COMPILER_Compaq", IS_FLAG_DEFINED(COMPILER_COMPAQ));
+ m_IniParser->AddSymbol("COMPILER_Cray", IS_FLAG_DEFINED(COMPILER_CRAY));
m_IniParser->AddSymbol("COMPILER_GCC", IS_FLAG_DEFINED(COMPILER_GCC));
m_IniParser->AddSymbol("COMPILER_ICC", IS_FLAG_DEFINED(COMPILER_ICC));
m_IniParser->AddSymbol("COMPILER_KCC", IS_FLAG_DEFINED(COMPILER_KCC));
+ m_IniParser->AddSymbol("COMPILER_LLVM", IS_VAR_DEFINED(__llvm__));
m_IniParser->AddSymbol("COMPILER_MipsPro", IS_FLAG_DEFINED(COMPILER_MIPSPRO));
m_IniParser->AddSymbol("COMPILER_MSVC", IS_FLAG_DEFINED(COMPILER_MSVC));
m_IniParser->AddSymbol("COMPILER_VisualAge", IS_FLAG_DEFINED(COMPILER_VISUALAGE));
@@ -1240,8 +1240,14 @@ CNcbiTestApplication::x_InitCommonParserVars(void)
bool found = (it != features.end());
m_IniParser->AddSymbol(name.c_str(), found);
}
+
+ // Is it running from TeamCity?
+ m_IniParser->AddSymbol
+ ("TeamCity",
+ !CNcbiEnvironment().Get("TEAMCITY_PROJECT_NAME").empty());
}
+
inline bool
CNcbiTestApplication::x_CalcConfigValue(const string& value)
{
diff --git a/c++/src/corelib/test_mt.cpp b/c++/src/corelib/test_mt.cpp
index d82ff02..8c62d2c 100644
--- a/c++/src/corelib/test_mt.cpp
+++ b/c++/src/corelib/test_mt.cpp
@@ -1,4 +1,4 @@
-/* $Id: test_mt.cpp 355815 2012-03-08 17:05:20Z ivanovp $
+/* $Id: test_mt.cpp 461873 2015-03-13 12:47:31Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,7 +55,7 @@ int s_SpawnBy = 6;
// Next test thread index
static volatile unsigned int s_NextIndex = 0;
-#define TESTAPP_LOG_POST(x) do { ++m_LogMsgCount; LOG_POST(x); } while (0)
+#define TESTAPP_LOG_POST(x) do { ++m_LogMsgCount; ERR_POST(x); } while (0)
/////////////////////////////////////////////////////////////////////////////
// Randomization paramaters
@@ -483,7 +483,7 @@ int CThreadedApp::Run(void)
unsigned int threshold = NCBI_PARAM_TYPE(TEST_MT, Cascading)::GetDefault();
if (threshold > 100) {
- ERR_POST(Fatal << "Cascading threshold must be less than 100");
+ ERR_FATAL("Cascading threshold must be less than 100");
}
bool cascading = ((unsigned int)(rand() % 100)) < threshold;
#if !defined(NCBI_THREADS)
@@ -569,13 +569,13 @@ void CThreadedApp::x_InitializeThreadGroups(void)
}
if(count > s_NumThreads) {
- ERR_POST(Fatal << "Thread groups with no threads are not allowed");
+ ERR_FATAL("Thread groups with no threads are not allowed");
}
unsigned int threshold =
NCBI_PARAM_TYPE(TEST_MT, IntragroupSyncPoint)::GetDefault();
if (threshold > 100) {
- ERR_POST(Fatal << "IntragroupSyncPoint threshold must be less than 100");
+ ERR_FATAL("IntragroupSyncPoint threshold must be less than 100");
}
unsigned int threads_left = s_NumThreads;
diff --git a/c++/src/dbapi/cache/dbapi_blob_cache.cpp b/c++/src/dbapi/cache/dbapi_blob_cache.cpp
index 7968292..02e4b72 100644
--- a/c++/src/dbapi/cache/dbapi_blob_cache.cpp
+++ b/c++/src/dbapi/cache/dbapi_blob_cache.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_blob_cache.cpp 420801 2013-12-05 16:20:55Z ucko $
+/* $Id: dbapi_blob_cache.cpp 478145 2015-09-04 11:52:04Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -266,7 +266,7 @@ public:
*bytes_read = min(count, bytes_left);
::memcpy(buf, m_Buffer + m_ReadPos, *bytes_read);
} else {
- if (&*m_TmpFile) {
+ if (m_TmpFile.get() != NULL) {
m_TmpFile->read((char*)buf, count);
*bytes_read = (size_t)m_TmpFile->gcount();
if (*bytes_read == 0) {
@@ -384,7 +384,7 @@ public:
}
}
- if (&*m_TmpFile) {
+ if (m_TmpFile.get() != NULL) {
m_TmpFile->write((char*)buf, count);
if ( m_TmpFile->good() ) {
*bytes_written = count;
@@ -411,7 +411,7 @@ private:
out.write((char*)m_Buffer, m_BytesInBuffer);
}
- if (&*m_TmpFile) {
+ if (m_TmpFile.get() != NULL) {
_ASSERT(m_Buffer == 0);
m_TmpFile->seekg(0, IOS_BASE::beg);
@@ -439,7 +439,7 @@ private:
ostream& out = cur.GetBlobOStream(1, m_BytesInBuffer);
ret = x_SaveBlob(out);
}
- if (&*m_TmpFile) {
+ if (m_TmpFile.get() != NULL) {
CT_OFF_TYPE total_bytes = m_TmpFile->tellg() - CT_POS_TYPE(0);
ostream& out = cur.GetBlobOStream(1, (size_t)total_bytes);
ret = x_SaveBlob(out);
diff --git a/c++/src/dbapi/conn_impl.cpp b/c++/src/dbapi/conn_impl.cpp
index 8e7d84e..4342dc7 100644
--- a/c++/src/dbapi/conn_impl.cpp
+++ b/c++/src/dbapi/conn_impl.cpp
@@ -1,4 +1,4 @@
-/* $Id: conn_impl.cpp 333164 2011-09-02 16:04:31Z ivanovp $
+/* $Id: conn_impl.cpp 451412 2014-11-06 16:54:28Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -23,7 +23,7 @@
*
* ===========================================================================
*
-* File Name: $Id: conn_impl.cpp 333164 2011-09-02 16:04:31Z ivanovp $
+* File Name: $Id: conn_impl.cpp 451412 2014-11-06 16:54:28Z ucko $
*
* Author: Michael Kholodov
*
@@ -216,9 +216,19 @@ CDB_Connection* CConnection::CloneCDB_Conn()
def_params.SetParam("do_not_dispatch", "true");
def_params.SetParam("do_not_read_conf", "true");
- CDB_Connection* tmp_conn(
- m_ds->GetDriverContext()->MakeConnection(params)
- );
+ I_DriverContext* dctx = m_ds->GetDriverContext();
+ CDB_Connection* tmp_conn = dctx->MakeConnection(params);
+
+ // If the original connection was known to be in a transaction,
+ // operations using the new one could block on its completion,
+ // possibly yielding a deadlock. In such cases, ensure that the
+ // new connection has a reasonable timeout. (MS SQL offers a
+ // finer-grained LOCK_TIMEOUT setting, but that's not portable,
+ // even to Sybase, which is more prone to such deadlocks in the
+ // first place.)
+ if (GetCDB_Connection()->HasTransaction() && dctx->GetTimeout() == 0) {
+ tmp_conn->SetTimeout(5);
+ }
_TRACE("CDB_Connection " << (void*)GetCDB_Connection()
<< " cloned, new CDB_Connection: " << (void*)tmp_conn);
diff --git a/c++/src/dbapi/driver/dbapi_conn_factory.cpp b/c++/src/dbapi/driver/dbapi_conn_factory.cpp
index 17caa43..e47a7b0 100644
--- a/c++/src/dbapi/driver/dbapi_conn_factory.cpp
+++ b/c++/src/dbapi/driver/dbapi_conn_factory.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_conn_factory.cpp 459266 2015-02-17 16:39:29Z ivanov $
+/* $Id: dbapi_conn_factory.cpp 471064 2015-06-23 13:56:53Z fukanchi $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -302,8 +302,7 @@ impl::CDBHandlerStack& CDB_DBLB_Delegate::SetOpeningMsgHandlers(void)
///////////////////////////////////////////////////////////////////////////////
CDBConnectionFactory::SOpeningContext::SOpeningContext
(I_DriverContext& driver_ctx_in)
- : driver_ctx(driver_ctx_in), conn_status(IConnValidator::eInvalidConn),
- retries(0)
+ : driver_ctx(driver_ctx_in), conn_status(IConnValidator::eInvalidConn)
{
}
@@ -384,8 +383,9 @@ CDBConnectionFactory::MakeDBConnection(
// cur_conn_attr,
cur_params);
- } catch(const CDB_Exception& ex) {
- m_Errors.push_back(ex.Clone());
+ } catch (CDB_Exception& ex) {
+ // m_Errors.push_back(ex.Clone());
+ opening_ctx.handlers.PostMsg(&ex);
if (params.GetConnValidator()) {
opening_ctx.conn_status
= params.GetConnValidator()->ValidateException(ex);
@@ -464,7 +464,7 @@ CDBConnectionFactory::DispatchServerName(
if (dsp_srv.Empty() && tried_servers.empty()) {
_TRACE("List of servers for service " << service_name
<< " is exhausted. Giving excluded a try.");
- rt_data.GetDBServiceMapper().CleanExcluded(service_name);
+ rt_data.CleanExcluded(service_name);
dsp_srv = rt_data.GetDBServiceMapper().GetServer(service_name);
}
@@ -488,9 +488,9 @@ CDBConnectionFactory::DispatchServerName(
_TRACE("List of servers for service " << service_name
<< " is exhausted. Giving excluded a try.");
- rt_data.GetDBServiceMapper().CleanExcluded(service_name);
+ rt_data.CleanExcluded(service_name);
ITERATE(list<TSvrRef>, it, tried_servers) {
- rt_data.GetDBServiceMapper().Exclude(service_name, *it);
+ rt_data.Exclude(service_name, *it);
}
full_retry_made = true;
continue;
@@ -503,7 +503,7 @@ CDBConnectionFactory::DispatchServerName(
bool found = false;
ITERATE(list<TSvrRef>, it, tried_servers) {
if (**it == *dsp_srv) {
- rt_data.GetDBServiceMapper().Exclude(service_name, dsp_srv);
+ rt_data.Exclude(service_name, dsp_srv);
found = true;
break;
}
@@ -542,8 +542,9 @@ CDBConnectionFactory::DispatchServerName(
t_con = MakeValidConnection(ctx,
// curr_conn_attr,
cur_params);
- } catch(const CDB_Exception& ex) {
- m_Errors.push_back(ex.Clone());
+ } catch (CDB_Exception& ex) {
+ // m_Errors.push_back(ex.Clone());
+ ctx.handlers.PostMsg(&ex);
if (params.GetConnValidator()) {
ctx.conn_status
= params.GetConnValidator()->ValidateException(ex);
@@ -555,7 +556,6 @@ CDBConnectionFactory::DispatchServerName(
return t_con;
}
else if (!t_con) {
- ++ctx.retries;
bool need_exclude = true;
if (cur_srv_name == service_name && cur_host == 0 && cur_port == 0
&& (ctx.conn_status != IConnValidator::eTempInvalidConn
@@ -575,7 +575,7 @@ CDBConnectionFactory::DispatchServerName(
rt_data.IncNumOfValidationFailures(service_name, dsp_srv);
} else {
// conn_status == IConnValidator::eInvalidConn
- rt_data.GetDBServiceMapper().Exclude(service_name, dsp_srv);
+ rt_data.Exclude(service_name, dsp_srv);
tried_servers.push_back(dsp_srv);
}
}
@@ -598,7 +598,14 @@ CDBConnectionFactory::MakeValidConnection(
const CDBConnParams& params)
{
_TRACE("Trying to connect to server '" << params.GetServerName()
- << "', host " << params.GetHost() << ", port " << params.GetPort());
+ << "', host " << impl::ConvertN2A(params.GetHost())
+ << ", port " << params.GetPort());
+ if (params.GetHost() != 0) {
+ ctx.tried.push_back(impl::ConvertN2A(params.GetHost()) + ':'
+ + NStr::NumericToString(params.GetPort()));
+ } else {
+ ctx.tried.push_back(params.GetServerName());
+ }
auto_ptr<CDB_Connection> conn(CtxMakeConnection(ctx.driver_ctx, params));
@@ -630,13 +637,14 @@ CDBConnectionFactory::MakeValidConnection(
ctx.handlers.PostMsg(&ex);
return NULL;
}
- } catch (const CDB_Exception& ex) {
+ } catch (CDB_Exception& ex) {
if (params.GetConnValidator().NotNull()) {
ctx.conn_status
= params.GetConnValidator()->ValidateException(ex);
}
if (ctx.conn_status != IConnValidator::eValidConn) {
- m_Errors.push_back(ex.Clone());
+ // m_Errors.push_back(ex.Clone());
+ ctx.handlers.PostMsg(&ex);
return NULL;
}
} catch (const CException& ex) {
@@ -650,6 +658,7 @@ CDBConnectionFactory::MakeValidConnection(
<< params.GetUserName() << "'");
throw;
}
+ ctx.tried.pop_back();
conn->FinishOpening();
}
else {
@@ -803,7 +812,18 @@ void CDBConnectionFactory::x_LogConnection(const SOpeningContext& ctx,
extra.Print(prefix + "name_mapper",
rt_data.GetDBServiceMapper().GetName());
- extra.Print(prefix + "retries", ctx.retries);
+ size_t retries = ctx.tried.size();
+ if (ctx.conn_status != IConnValidator::eValidConn) {
+ --retries;
+ }
+ extra.Print(prefix + "retries", retries);
+ if ( !ctx.tried.empty() ) {
+ extra.Print(prefix + "tried", NStr::Join(ctx.tried, " "));
+ }
+ const string& excluded = rt_data.GetExcluded(service);
+ if ( !excluded.empty() ) {
+ extra.Print(prefix + "excluded", excluded);
+ }
if (connection != NULL) {
extra.Print(prefix + "conn_reuse_count", connection->GetReuseCount());
}
@@ -871,10 +891,45 @@ CDBConnectionFactory::CRuntimeData::IncNumOfValidationFailures(
GetNumOfValidationFailures(server_name) >=
GetParent().GetMaxNumOfValidationAttempts()) {
// It is time to finish with this server ...
- GetDBServiceMapper().Exclude(server_name, dsp_srv);
+ Exclude(server_name, dsp_srv);
+ }
+}
+
+void CDBConnectionFactory::CRuntimeData::Exclude(const string& service_name,
+ const TSvrRef& server)
+{
+ GetDBServiceMapper().Exclude(service_name, server);
+ if (server->GetHost() != 0) {
+ string& excluded = m_ExclusionSummaryMap[service_name];
+ if ( !excluded.empty() ) {
+ excluded += ' ';
+ }
+ excluded += (impl::ConvertN2A(server->GetHost()) + ':'
+ + NStr::NumericToString(server->GetPort()));
+ } else if ( !server->GetName().empty() ) {
+ string& excluded = m_ExclusionSummaryMap[service_name];
+ if ( !excluded.empty() ) {
+ excluded += ' ';
+ }
+ excluded += server->GetName();
}
}
+void CDBConnectionFactory::CRuntimeData::CleanExcluded
+(const string& service_name)
+{
+ GetDBServiceMapper().CleanExcluded(service_name);
+ m_ExclusionSummaryMap.erase(service_name);
+}
+
+const string& CDBConnectionFactory::CRuntimeData::GetExcluded
+(const string& service_name)
+{
+ TExclusionSummaryMap::const_iterator it
+ = m_ExclusionSummaryMap.find(service_name);
+ return (it == m_ExclusionSummaryMap.end()) ? kEmptyStr : it->second;
+}
+
///////////////////////////////////////////////////////////////////////////////
CDBConnectionFactory::CMapperFactory::CMapperFactory(
IDBServiceMapper::TFactory svc_mapper_factory,
diff --git a/c++/src/dbapi/driver/dbapi_driver_conn_params.cpp b/c++/src/dbapi/driver/dbapi_driver_conn_params.cpp
index e0c7014..379e495 100644
--- a/c++/src/dbapi/driver/dbapi_driver_conn_params.cpp
+++ b/c++/src/dbapi/driver/dbapi_driver_conn_params.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_driver_conn_params.cpp 441963 2014-07-29 17:18:59Z ucko $
+/* $Id: dbapi_driver_conn_params.cpp 441728 2014-07-28 15:00:40Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/dbapi/driver/dbapi_driver_sample_base.cpp b/c++/src/dbapi/driver/dbapi_driver_sample_base.cpp
index 30b1130..0350d9b 100644
--- a/c++/src/dbapi/driver/dbapi_driver_sample_base.cpp
+++ b/c++/src/dbapi/driver/dbapi_driver_sample_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_driver_sample_base.cpp 441963 2014-07-29 17:18:59Z ucko $
+/* $Id: dbapi_driver_sample_base.cpp 441728 2014-07-28 15:00:40Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/dbapi/driver/dbapi_driver_utils.cpp b/c++/src/dbapi/driver/dbapi_driver_utils.cpp
index 03f6cf5..875acd8 100644
--- a/c++/src/dbapi/driver/dbapi_driver_utils.cpp
+++ b/c++/src/dbapi/driver/dbapi_driver_utils.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_driver_utils.cpp 447262 2014-09-23 21:05:11Z ucko $
+/* $Id: dbapi_driver_utils.cpp 447074 2014-09-22 14:45:33Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/dbapi/driver/dbapi_impl_connection.cpp b/c++/src/dbapi/driver/dbapi_impl_connection.cpp
index bed7996..a290e15 100644
--- a/c++/src/dbapi/driver/dbapi_impl_connection.cpp
+++ b/c++/src/dbapi/driver/dbapi_impl_connection.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_impl_connection.cpp 459266 2015-02-17 16:39:29Z ivanov $
+/* $Id: dbapi_impl_connection.cpp 480564 2015-10-01 16:54:20Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -102,6 +102,9 @@ CConnection::CConnection(CDriverContext& dc,
, m_Port(params.GetPort())
, m_Passwd(params.GetPassword())
, m_Pool(params.GetParam("pool_name"))
+, m_PoolMinSize(0)
+, m_PoolIdleTimeParam(-1, 0)
+, m_CleanupTime(CTime::eEmpty)
, m_ReuseCount(0)
, m_Reusable(params.GetParam("is_pooled") == "true")
, m_OpenFinished(false)
@@ -114,6 +117,16 @@ CConnection::CConnection(CDriverContext& dc,
_ASSERT(m_MsgHandlers.GetSize() > 0);
m_OpeningMsgHandlers = params.GetOpeningMsgHandlers();
+ string pool_min_str = params.GetParam("pool_minsize"),
+ pool_idle_str = params.GetParam("pool_idle_time");
+
+ if ( !pool_min_str.empty() && pool_min_str != "default") {
+ m_PoolMinSize = NStr::StringToUInt(pool_min_str);
+ }
+ if ( !pool_idle_str.empty() && pool_idle_str != "default") {
+ m_PoolIdleTimeParam = CTimeSpan(NStr::StringToDouble(pool_idle_str));
+ }
+
CheckCanOpen();
}
@@ -131,11 +144,9 @@ void CConnection::CheckCanOpen(void)
// Check for maximum number of connections
if (!CDbapiConnMgr::Instance().AddConnect()) {
const string conn_num = NStr::NumericToString(CDbapiConnMgr::Instance().GetMaxConnect());
- const string msg =
- string("Cannot create new connection: maximum connections amount (")
- + conn_num
- + ") is exceeded!!!";
-
+ const string msg =
+ "Cannot create new connection: hit limit of " + conn_num
+ + " simultaneously open connections.";
ERR_POST_X_ONCE(3, msg);
DATABASE_DRIVER_ERROR(msg, 500000);
}
diff --git a/c++/src/dbapi/driver/dbapi_impl_context.cpp b/c++/src/dbapi/driver/dbapi_impl_context.cpp
index 8f7076e..1836101 100644
--- a/c++/src/dbapi/driver/dbapi_impl_context.cpp
+++ b/c++/src/dbapi/driver/dbapi_impl_context.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbapi_impl_context.cpp 445018 2014-08-29 15:50:04Z ucko $
+/* $Id: dbapi_impl_context.cpp 481035 2015-10-06 16:46:46Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,6 +63,9 @@ namespace impl
//
CDriverContext::CDriverContext(void) :
+#ifdef NCBI_THREADS
+ m_PoolSem(0, 1),
+#endif
m_LoginTimeout(0),
m_Timeout(0),
m_CancelTimeout(0),
@@ -81,7 +84,7 @@ CDriverContext::~CDriverContext(void)
void
CDriverContext::SetApplicationName(const string& app_name)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_AppName = app_name;
}
@@ -89,7 +92,7 @@ CDriverContext::SetApplicationName(const string& app_name)
string
CDriverContext::GetApplicationName(void) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
return m_AppName;
}
@@ -97,7 +100,7 @@ CDriverContext::GetApplicationName(void) const
void
CDriverContext::SetHostName(const string& host_name)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_HostName = host_name;
}
@@ -105,21 +108,21 @@ CDriverContext::SetHostName(const string& host_name)
string
CDriverContext::GetHostName(void) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
return m_HostName;
}
unsigned int CDriverContext::GetLoginTimeout(void) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
return m_LoginTimeout;
}
bool CDriverContext::SetLoginTimeout (unsigned int nof_secs)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_LoginTimeout = nof_secs;
@@ -128,7 +131,7 @@ bool CDriverContext::SetLoginTimeout (unsigned int nof_secs)
unsigned int CDriverContext::GetTimeout(void) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
return m_Timeout;
}
@@ -136,7 +139,7 @@ unsigned int CDriverContext::GetTimeout(void) const
bool CDriverContext::SetTimeout(unsigned int nof_secs)
{
bool success = true;
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
try {
m_Timeout = nof_secs;
@@ -153,7 +156,7 @@ bool CDriverContext::SetTimeout(unsigned int nof_secs)
unsigned int CDriverContext::GetCancelTimeout(void) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
return m_CancelTimeout;
}
@@ -161,7 +164,7 @@ unsigned int CDriverContext::GetCancelTimeout(void) const
bool CDriverContext::SetCancelTimeout(unsigned int nof_secs)
{
bool success = true;
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
try {
m_CancelTimeout = nof_secs;
@@ -174,7 +177,7 @@ bool CDriverContext::SetCancelTimeout(unsigned int nof_secs)
bool CDriverContext::SetMaxTextImageSize(size_t nof_bytes)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_MaxTextImageSize = nof_bytes;
@@ -186,26 +189,26 @@ bool CDriverContext::SetMaxTextImageSize(size_t nof_bytes)
void CDriverContext::PushCntxMsgHandler(CDB_UserHandler* h,
EOwnership ownership)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_CntxHandlers.Push(h, ownership);
}
void CDriverContext::PopCntxMsgHandler(CDB_UserHandler* h)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_CntxHandlers.Pop(h);
}
void CDriverContext::PushDefConnMsgHandler(CDB_UserHandler* h,
EOwnership ownership)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_ConnHandlers.Push(h, ownership);
}
void CDriverContext::PopDefConnMsgHandler(CDB_UserHandler* h)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_ConnHandlers.Pop(h);
// Remove this handler from all connections
@@ -263,7 +266,7 @@ void CDriverContext::ResetEnvSybase(void)
void CDriverContext::x_Recycle(CConnection* conn, bool conn_reusable)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
TConnPool::iterator it = find(m_InUse.begin(), m_InUse.end(), conn);
@@ -271,17 +274,39 @@ void CDriverContext::x_Recycle(CConnection* conn, bool conn_reusable)
m_InUse.erase(it);
}
+#ifdef NCBI_THREADS
+ bool for_sem = false;
+ if ( !m_PoolSemSubject.empty() && conn->PoolName() == m_PoolSemSubject) {
+ for_sem = true;
+ m_PoolSemSubject.erase();
+ m_PoolSemConn = NULL;
+ m_PoolSem.TryWait(); // probably redundant, but ensures Post will work
+ m_PoolSem.Post();
+ }
+#endif
+
if (conn_reusable && conn->IsOpeningFinished() && conn->IsValid()) {
+ if (conn->m_PoolIdleTimeParam.GetSign() != eNegative) {
+ CTime now(CTime::eCurrent);
+ conn->m_CleanupTime = now + conn->m_PoolIdleTimeParam;
+ }
m_NotInUse.push_back(conn);
+#ifdef NCBI_THREADS
+ if (for_sem) {
+ m_PoolSemConn = conn;
+ }
+#endif
} else {
delete conn;
}
+
+ CloseOldIdleConns(1);
}
void CDriverContext::CloseUnusedConnections(const string& srv_name,
const string& pool_name)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
TConnPool::value_type con;
@@ -301,7 +326,7 @@ void CDriverContext::CloseUnusedConnections(const string& srv_name,
unsigned int CDriverContext::NofConnections(const TSvrRef& svr_ref,
const string& pool_name) const
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
if ((!svr_ref || !svr_ref->IsValid()) && pool_name.empty()) {
return static_cast<unsigned int>(m_InUse.size() + m_NotInUse.size());
@@ -347,16 +372,34 @@ unsigned int CDriverContext::NofConnections(const string& srv_name,
CDB_Connection* CDriverContext::MakeCDBConnection(CConnection* connection)
{
+ connection->m_CleanupTime.Clear();
m_InUse.push_back(connection);
return new CDB_Connection(connection);
}
+class CDBConnParams_Unpooled : public CDBConnParamsDelegate
+{
+public:
+ CDBConnParams_Unpooled(const CDBConnParams& other)
+ : CDBConnParamsDelegate(other)
+ { }
+
+ string GetParam(const string& key) const
+ {
+ if (key == "is_pooled") {
+ return "false";
+ } else {
+ return CDBConnParamsDelegate::GetParam(key);
+ }
+ }
+};
+
CDB_Connection*
CDriverContext::MakePooledConnection(const CDBConnParams& params)
{
if (params.GetParam("is_pooled") == "true") {
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
string pool_name(params.GetParam("pool_name"));
if (!m_NotInUse.empty()) {
@@ -429,8 +472,39 @@ CDriverContext::MakePooledConnection(const CDBConnParams& params)
if (pool_name == t_con->PoolName())
++total_cnt;
}
- if (total_cnt >= pool_max)
- return NULL;
+ if (total_cnt >= pool_max) {
+#ifdef NCBI_THREADS
+ string timeout_str(params.GetParam("pool_wait_time"));
+ double timeout_val = 0.0;
+ if ( !timeout_str.empty() && timeout_str != "default") {
+ timeout_val = NStr::StringToDouble(timeout_str);
+ }
+ CTimeout timeout(timeout_val);
+ m_PoolSemSubject = pool_name;
+ mg.Release();
+ if (m_PoolSem.TryWait(timeout)) {
+ mg.Guard(x_GetCtxMtx());
+ CConnection* t_con = NULL;
+ NON_CONST_REVERSE_ITERATE(TConnPool, it, m_NotInUse) {
+ if (*it == m_PoolSemConn) {
+ t_con = m_PoolSemConn;
+ m_PoolSemConn = NULL;
+ m_NotInUse.erase((++it).base());
+ }
+ }
+ if (t_con != NULL) {
+ return MakeCDBConnection(t_con);
+ }
+ } else
+#endif
+ if (params.GetParam("pool_allow_temp_overflow")
+ == "true") {
+ return MakePooledConnection
+ (CDBConnParams_Unpooled(params));
+ } else {
+ return NULL;
+ }
+ }
}
}
}
@@ -677,6 +751,9 @@ SDBConfParams::Clear(void)
is_pooled.clear();
pool_name.clear();
pool_maxsize.clear();
+ pool_idle_time.clear();
+ pool_wait_time.clear();
+ pool_allow_temp_overflow.clear();
args.clear();
}
@@ -762,6 +839,22 @@ CDriverContext::ReadDBConfParams(const string& service_name,
params->flags += SDBConfParams::fPoolMaxSizeSet;
params->pool_maxsize = reg.Get(section_name, "conn_pool_maxsize");
}
+ if (reg.HasEntry(section_name, "conn_pool_idle_time",
+ IRegistry::fCountCleared)) {
+ params->flags += SDBConfParams::fPoolIdleTimeSet;
+ params->pool_idle_time = reg.Get(section_name, "conn_pool_idle_time");
+ }
+ if (reg.HasEntry(section_name, "conn_pool_wait_time",
+ IRegistry::fCountCleared)) {
+ params->flags += SDBConfParams::fPoolWaitTimeSet;
+ params->pool_wait_time = reg.Get(section_name, "conn_pool_wait_time");
+ }
+ if (reg.HasEntry(section_name, "conn_pool_allow_temp_overflow",
+ IRegistry::fCountCleared)) {
+ params->flags += SDBConfParams::fPoolAllowTempSet;
+ params->pool_allow_temp_overflow
+ = reg.Get(section_name, "conn_pool_allow_temp_overflow");
+ }
if (reg.HasEntry(section_name, "args", IRegistry::fCountCleared)) {
params->flags += SDBConfParams::fArgsSet;
params->args = reg.Get(section_name, "args");
@@ -771,7 +864,7 @@ CDriverContext::ReadDBConfParams(const string& service_name,
bool
CDriverContext::SatisfyPoolMinimum(const CDBConnParams& params)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
string pool_min_str = params.GetParam("pool_minsize");
if (pool_min_str.empty() || pool_min_str == "default")
@@ -814,7 +907,7 @@ CDriverContext::SatisfyPoolMinimum(const CDBConnParams& params)
CDB_Connection*
CDriverContext::MakeConnection(const CDBConnParams& params)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
CMakeConnActualParams act_params(params);
SDBConfParams conf_params;
@@ -913,11 +1006,41 @@ CDriverContext::MakeConnection(const CDBConnParams& params)
else if (params.GetParam("is_pooled") == "default") {
act_params.SetParam("is_pooled", "false");
}
+ if (conf_params.IsPoolMinSizeSet())
+ act_params.SetParam("pool_minsize", conf_params.pool_minsize);
+ else if (params.GetParam("pool_minsize") == "default") {
+ act_params.SetParam("pool_minsize", "0");
+ }
if (conf_params.IsPoolMaxSizeSet())
act_params.SetParam("pool_maxsize", conf_params.pool_maxsize);
else if (params.GetParam("pool_maxsize") == "default") {
act_params.SetParam("pool_maxsize", "");
}
+ if (conf_params.IsPoolIdleTimeSet())
+ act_params.SetParam("pool_idle_time", conf_params.pool_idle_time);
+ else if (params.GetParam("pool_idle_time") == "default") {
+ act_params.SetParam("pool_idle_time", "");
+ }
+ if (conf_params.IsPoolWaitTimeSet())
+ act_params.SetParam("pool_wait_time", conf_params.pool_wait_time);
+ else if (params.GetParam("pool_wait_time") == "default") {
+ act_params.SetParam("pool_wait_time", "0");
+ }
+ if (conf_params.IsPoolAllowTempOverflowSet()) {
+ if (conf_params.pool_allow_temp_overflow.empty()) {
+ act_params.SetParam("pool_allow_temp_overflow", "false");
+ }
+ else {
+ act_params.SetParam
+ ("pool_allow_temp_overflow",
+ NStr::BoolToString(
+ NStr::StringToBool(
+ conf_params.pool_allow_temp_overflow)));
+ }
+ }
+ else if (params.GetParam("pool_allow_temp_overflow") == "default") {
+ act_params.SetParam("pool_allow_temp_overflow", "false");
+ }
s_TransformLoginData(server_name, user_name, db_name, password);
act_params.SetServerName(server_name);
@@ -964,7 +1087,7 @@ CDriverContext::MakeConnection(const CDBConnParams& params)
void CDriverContext::CloseConnsForPool(const string& pool_name)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
ITERATE(TConnPool, it, m_InUse) {
CConnection* t_con(*it);
@@ -981,6 +1104,39 @@ void CDriverContext::CloseConnsForPool(const string& pool_name)
}
}
+
+void CDriverContext::CloseOldIdleConns(unsigned int max_closings,
+ const string& pool_name)
+{
+ if (max_closings == 0) {
+ return;
+ }
+
+ set<string> at_min;
+ CTime now(CTime::eCurrent);
+ ERASE_ITERATE (TConnPool, it, m_NotInUse) {
+ const string& pool_name_2 = (*it)->PoolName();
+ if (pool_name_2.empty()
+ || ( !pool_name.empty() && pool_name != pool_name_2)
+ || at_min.find(pool_name_2) != at_min.end()
+ || (*it)->m_CleanupTime.IsEmpty()
+ || (*it)->m_CleanupTime > now) {
+ continue;
+ }
+ unsigned int n = NofConnections(TSvrRef(), pool_name_2);
+ if (n > (*it)->m_PoolMinSize) {
+ delete *it;
+ m_NotInUse.erase(it);
+ if (--max_closings == 0) {
+ break;
+ }
+ } else {
+ at_min.insert(pool_name_2);
+ }
+ }
+}
+
+
void CDriverContext::DestroyConnImpl(CConnection* impl)
{
if (impl) {
@@ -991,7 +1147,7 @@ void CDriverContext::DestroyConnImpl(CConnection* impl)
void CDriverContext::SetClientCharset(const string& charset)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_ClientCharset = charset;
m_ClientEncoding = eEncoding_Unknown;
diff --git a/c++/src/dbapi/driver/exception.cpp b/c++/src/dbapi/driver/exception.cpp
index 9565638..659547b 100644
--- a/c++/src/dbapi/driver/exception.cpp
+++ b/c++/src/dbapi/driver/exception.cpp
@@ -1,4 +1,4 @@
-/* $Id: exception.cpp 451248 2014-11-05 12:42:47Z ivanov $
+/* $Id: exception.cpp 451134 2014-11-03 21:52:05Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/dbapi/driver/memory_store.cpp b/c++/src/dbapi/driver/memory_store.cpp
index 1adf0ca..7107ec9 100644
--- a/c++/src/dbapi/driver/memory_store.cpp
+++ b/c++/src/dbapi/driver/memory_store.cpp
@@ -1,4 +1,4 @@
-/* $Id: memory_store.cpp 436010 2014-05-22 15:36:11Z vakatov $
+/* $Id: memory_store.cpp 461604 2015-03-11 15:24:58Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -349,9 +349,8 @@ size_t CMemStore::Truncate(size_t size)
// we have to delete the whole block
delete [] m_Last->body;
SMemBlock* t = m_Last->prev;
- if ( t ) {
- t->next = 0;
- }
+ _ASSERT(t != NULL);
+ t->next = NULL;
delete m_Last;
_ASSERT(m_Last != t);
m_Last = t;
@@ -360,7 +359,7 @@ size_t CMemStore::Truncate(size_t size)
continue;
}
// we have to free some bytes
- m_Last->free_space -= nof_bytes;
+ m_Last->free_space += nof_bytes;
m_Size -= nof_bytes;
break;
}
@@ -438,7 +437,8 @@ size_t CMemStore::Insert(const void* buff, size_t size)
// try to merge the two last blocks
SMemBlock* t_block = m_Current->next;
- if ((m_Current->free_space + t_block->free_space) >= m_BlockSize) {
+ if (t_block != NULL
+ && (m_Current->free_space + t_block->free_space) >= m_BlockSize) {
TSize f_free = m_BlockSize - m_Current->free_space;
TSize k = m_BlockSize - t_block->free_space;
memcpy(&m_Current->body[f_free], t_block->body, k);
diff --git a/c++/src/dbapi/driver/numeric_convert.cpp b/c++/src/dbapi/driver/numeric_convert.cpp
index aaa22a8..4384707 100644
--- a/c++/src/dbapi/driver/numeric_convert.cpp
+++ b/c++/src/dbapi/driver/numeric_convert.cpp
@@ -1,4 +1,4 @@
-/* $Id: numeric_convert.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: numeric_convert.cpp 461606 2015-03-11 15:25:49Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,7 +75,7 @@ unsigned char* longlong_to_numeric (Int8 l_num, unsigned int prec, unsigned cha
l_num = l_num/256;
number--;
if (number <= cs_num) {
- if(needs_del) delete cs_num;
+ if (needs_del) delete[] cs_num;
return 0;
}
}
@@ -95,15 +95,14 @@ Int8 numeric_to_longlong(unsigned int precision, unsigned char* cs_num)
int BYTE_NUM = s_NumericBytesPerPrec[precision - 1];
Int8 my_long = 0;
- if (BYTE_NUM <= 9) {
- for (int i = 1; i < BYTE_NUM; i++) {
- my_long = my_long*256 + cs_num[i];
+ for (int i = 1; i < BYTE_NUM; i++) {
+ if (my_long > kMax_I8 >> 8) {
+ return 0;
}
- if (cs_num[0] != 0) {
- my_long*= -1;
- }
- } else {
- return 0;
+ my_long = my_long*256 + cs_num[i];
+ }
+ if (cs_num[0] != 0) {
+ my_long*= -1;
}
return my_long;
diff --git a/c++/src/dbapi/driver/odbc/context.cpp b/c++/src/dbapi/driver/odbc/context.cpp
index 1f3f2d3..9d41227 100644
--- a/c++/src/dbapi/driver/odbc/context.cpp
+++ b/c++/src/dbapi/driver/odbc/context.cpp
@@ -1,4 +1,4 @@
-/* $Id: context.cpp 441150 2014-07-21 19:10:46Z ucko $
+/* $Id: context.cpp 450236 2014-10-23 18:15:34Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -386,7 +386,7 @@ CODBCContext::~CODBCContext()
void
CODBCContext::x_Close(bool delete_conn)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
if (m_Context) {
// Unregister first for sake of exception safety.
@@ -427,7 +427,7 @@ CODBCContext::x_Close(bool delete_conn)
void
CODBCContext::SetupErrorReporter(const CDBConnParams& params)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_Reporter.SetServerName(params.GetServerName());
m_Reporter.SetUserName(params.GetUserName());
}
@@ -441,7 +441,7 @@ string CODBCContext::GetDriverName(void) const
void CODBCContext::SetPacketSize(SQLUINTEGER packet_size)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
m_PacketSize = packet_size;
}
@@ -450,7 +450,7 @@ void CODBCContext::SetPacketSize(SQLUINTEGER packet_size)
bool CODBCContext::CheckSIE(int rc, SQLHDBC con,
const CODBC_Reporter& opening_reporter)
{
- CMutexGuard mg(m_CtxMtx);
+ CMutexGuard mg(x_GetCtxMtx());
switch(rc) {
case SQL_SUCCESS_WITH_INFO:
diff --git a/c++/src/dbapi/driver/public.cpp b/c++/src/dbapi/driver/public.cpp
index 6dae5ab..6b0bc9c 100644
--- a/c++/src/dbapi/driver/public.cpp
+++ b/c++/src/dbapi/driver/public.cpp
@@ -1,4 +1,4 @@
-/* $Id: public.cpp 459267 2015-02-17 16:40:25Z ivanov $
+/* $Id: public.cpp 458199 2015-02-02 19:18:09Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -280,10 +280,10 @@ string CDBParamVariant::MakePlainName(const CTempString& name)
//
CDB_Connection::CDB_Connection(impl::CConnection* c)
+ : m_ConnImpl(c), m_HasTransaction(false)
{
CHECK_DRIVER_ERROR( !c, "No valid connection provided", 200001 );
- m_ConnImpl = c;
m_ConnImpl->AttachTo(this);
m_ConnImpl->SetResultProcessor(0); // to clean up the result processor if any
}
@@ -1260,6 +1260,7 @@ CAutoTrans::~CAutoTrans(void)
Commit();
}
}
+ m_Conn.m_HasTransaction = (curr_TranCount <= 1);
// Skip commit/rollback if this transaction was previously
// explicitly finished ...
@@ -1270,6 +1271,7 @@ CAutoTrans::~CAutoTrans(void)
void
CAutoTrans::BeginTransaction(void)
{
+ m_Conn.m_HasTransaction = true;
auto_ptr<CDB_LangCmd> auto_stmt(m_Conn.LangCmd("BEGIN TRANSACTION"));
auto_stmt->Send();
auto_stmt->DumpResults();
diff --git a/c++/src/objects/Makefile.in b/c++/src/objects/Makefile.in
index d67dbc2..1db09a8 100644
--- a/c++/src/objects/Makefile.in
+++ b/c++/src/objects/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
# Meta-makefile("objects" project)
#################################
diff --git a/c++/src/objects/Makefile.sources b/c++/src/objects/Makefile.sources
index ec029d1..c03c805 100644
--- a/c++/src/objects/Makefile.sources
+++ b/c++/src/objects/Makefile.sources
@@ -1,4 +1,4 @@
-# $Id: Makefile.sources 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.sources 485953 2015-11-30 17:53:34Z blastadm $
#
# Generate ASN.1 serialization code in the "objects/" projects
diff --git a/c++/src/objects/biblio/Auth_list.cpp b/c++/src/objects/biblio/Auth_list.cpp
index 4b72590..aead49d 100644
--- a/c++/src/objects/biblio/Auth_list.cpp
+++ b/c++/src/objects/biblio/Auth_list.cpp
@@ -1,4 +1,4 @@
-/* $Id: Auth_list.cpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Auth_list.cpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/biblio/Cit_sub.cpp b/c++/src/objects/biblio/Cit_sub.cpp
index c71d374..f0ef6a8 100644
--- a/c++/src/objects/biblio/Cit_sub.cpp
+++ b/c++/src/objects/biblio/Cit_sub.cpp
@@ -1,4 +1,4 @@
-/* $Id: Cit_sub.cpp 442535 2014-08-04 20:57:08Z ucko $
+/* $Id: Cit_sub.cpp 442489 2014-08-04 18:03:35Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/biblio/Makefile.biblio.lib b/c++/src/objects/biblio/Makefile.biblio.lib
index a2e265e..8b5a94e 100644
--- a/c++/src/objects/biblio/Makefile.biblio.lib
+++ b/c++/src/objects/biblio/Makefile.biblio.lib
@@ -1,6 +1,7 @@
LIB = biblio
SRC = biblio__ biblio___ citation_base
+DLL_LIB = general
USES_LIBRARIES = \
general
diff --git a/c++/src/objects/biblio/citation_base.cpp b/c++/src/objects/biblio/citation_base.cpp
index b752f1d..c30b44b 100644
--- a/c++/src/objects/biblio/citation_base.cpp
+++ b/c++/src/objects/biblio/citation_base.cpp
@@ -1,4 +1,4 @@
- /*$Id: citation_base.cpp 408266 2013-07-29 03:59:33Z vakatov $
+ /*$Id: citation_base.cpp 463068 2015-03-24 16:16:20Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -185,7 +185,7 @@ void ICitationBase::NoteSup(string* label, const CImprint& ip)
if (HasText(issue)) {
*label += *issue;
}
- if (HasText(part_sup)) {
+ if (HasText(part_supi)) {
*label += ' ' + *part_supi;
}
*label += ')';
@@ -287,17 +287,33 @@ bool ICitationBase::x_GetLabelV1(string* label,
// constructed from the first character of each whitespace separated
// word in titleunique
if (unique) {
- string tag;
+ //string tag;
+ // NB: add '|' even if tag is empty to maintain backward compatibility.
+ *label += '|';
if (titleunique && !titleunique->empty()) {
+#if 0
CNcbiIstrstream is(titleunique->c_str(), titleunique->size());
string word;
int cnt = 0;
while ( (is >> word) && (cnt++ < 40) ) {
- tag += word[0];
+ *label += word[0];
+ }
+#else
+ size_t pos;
+ CTempString temp = *titleunique;
+ CTempString space(" \t\r\n");
+ while ( (pos = temp.find_first_not_of(space)) != CTempString::npos)
+ {
+ *label += temp[pos];
+ temp.assign(temp, pos, temp.size() - pos);
+ pos = temp.find_first_of(space);
+ if (pos != CTempString::npos)
+ temp.assign(temp, pos, temp.size() - pos);
+ else
+ break;
}
+#endif
}
- // NB: add '|' even if tag is empty to maintain backward compatibility.
- *label += "|" + tag;
}
return true;
diff --git a/c++/src/objects/biotree/biotree.asn b/c++/src/objects/biotree/biotree.asn
index e32af12..c6e7b57 100644
--- a/c++/src/objects/biotree/biotree.asn
+++ b/c++/src/objects/biotree/biotree.asn
@@ -1,4 +1,4 @@
---$Revision: 420728 $
+--$Revision: 480521 $
--*********************************************************************
--
-- biotree.asn
@@ -11,7 +11,7 @@
NCBI-BioTree DEFINITIONS ::=
BEGIN
-EXPORTS BioTreeContainer, DistanceMatrix;
+EXPORTS BioTreeContainer, FeatureDictSet, DistanceMatrix;
IMPORTS User-object, User-field FROM NCBI-General;
@@ -58,4 +58,4 @@ DistanceMatrix ::= SEQUENCE {
}
-END
\ No newline at end of file
+END
diff --git a/c++/src/objects/blast/Makefile.blast.lib b/c++/src/objects/blast/Makefile.blast.lib
index 2d1fa8e..c0d6d59 100644
--- a/c++/src/objects/blast/Makefile.blast.lib
+++ b/c++/src/objects/blast/Makefile.blast.lib
@@ -1,6 +1,8 @@
LIB = xnetblast
SRC = blast__ blast___ names
+DLL_LIB = seqset scoremat
+
WATCHERS = camacho
diff --git a/c++/src/objects/blast/Makefile.xnetblastcli.lib b/c++/src/objects/blast/Makefile.xnetblastcli.lib
index b544c1c..05eb98d 100644
--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
@@ -3,6 +3,7 @@ ASN_DEP = xnetblast
LIB = xnetblastcli
SRC = blastclient blastclient_
+DLL_LIB = xconnect
USES_LIBRARIES = \
xconnect xnetblast
diff --git a/c++/src/objects/blast/names.cpp b/c++/src/objects/blast/names.cpp
index cb5505a..e59149e 100644
--- a/c++/src/objects/blast/names.cpp
+++ b/c++/src/objects/blast/names.cpp
@@ -1,4 +1,4 @@
-/* $Id: names.cpp 457059 2015-01-20 15:02:34Z ivanov $
+/* $Id: names.cpp 468380 2015-05-22 13:46:49Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,15 +34,18 @@
#include <objects/blast/names.hpp>
#include <objects/blast/blast__.hpp>
#include <objects/scoremat/scoremat__.hpp>
+#include <corelib/ncbimtx.hpp>
BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
CBlast4Field::TFieldMap CBlast4Field::m_Fields;
-
CBlast4Field & CBlast4Field::Get(EBlastOptIdx opt)
{
+ {
+ DEFINE_STATIC_MUTEX(mx);
+ CMutexGuard guard(mx);
if (m_Fields.count(opt) == 0) {
switch (opt) {
//case eBlastOpt_Program:
@@ -330,6 +333,7 @@ CBlast4Field & CBlast4Field::Get(EBlastOptIdx opt)
break;
}
}
+ }
_ASSERT(m_Fields.count(opt) != 0);
return m_Fields[opt];
}
diff --git a/c++/src/objects/blastdb/Blast_def_line_set.cpp b/c++/src/objects/blastdb/Blast_def_line_set.cpp
index b1b8f68..b9b8377 100644
--- a/c++/src/objects/blastdb/Blast_def_line_set.cpp
+++ b/c++/src/objects/blastdb/Blast_def_line_set.cpp
@@ -1,4 +1,4 @@
-/* $Id: Blast_def_line_set.cpp 435843 2014-05-21 14:04:06Z madden $
+/* $Id: Blast_def_line_set.cpp 447320 2014-09-24 18:16:04Z camacho $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -221,6 +221,7 @@ void GetLinkoutTypes(vector<TLinkoutTypeString>& rv)
rv.push_back(make_pair(eStructure, string("eStructure")));
rv.push_back(make_pair(eGeo, string("eGeo")));
rv.push_back(make_pair(eGene, string("eGene")));
+ rv.push_back(make_pair(eFromVerifiedMaterial, string("eFromVerifiedMaterial")));
rv.push_back(make_pair(eMapviewer, string("eMapviewer")));
rv.push_back(make_pair(eGenomicSeq, string("eGenomicSeq")));
rv.push_back(make_pair(eBioAssay, string("eBioAssay")));
diff --git a/c++/src/objects/blastdb/Makefile.blastdb.lib b/c++/src/objects/blastdb/Makefile.blastdb.lib
index 8469e4b..0e33ddc 100644
--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
@@ -1,8 +1,10 @@
-# $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
+# $Id: Makefile.blastdb.lib 468761 2015-05-27 20:14:39Z ucko $
LIB = blastdb
SRC = blastdb__ blastdb___
+DLL_LIB = xser
+
WATCHERS = camacho
diff --git a/c++/src/objects/blastdb/blastdb.asn b/c++/src/objects/blastdb/blastdb.asn
index 6f77cc9..166b621 100644
--- a/c++/src/objects/blastdb/blastdb.asn
+++ b/c++/src/objects/blastdb/blastdb.asn
@@ -1,4 +1,4 @@
---$Id: blastdb.asn 419874 2013-12-02 14:45:17Z camacho $
+--$Id: blastdb.asn 451801 2014-11-12 15:05:39Z camacho $
--
-- Notes:
--
diff --git a/c++/src/objects/blastxml2/blastxml2.asn b/c++/src/objects/blastxml2/blastxml2.asn
index f9ecdb5..16ffbe0 100644
--- a/c++/src/objects/blastxml2/blastxml2.asn
+++ b/c++/src/objects/blastxml2/blastxml2.asn
@@ -6,6 +6,8 @@ BlastOutput2 ::= SEQUENCE {
error Err OPTIONAL
}
+BlastXML2 ::= SET OF BlastOutput2
+
Report ::= SEQUENCE {
program VisibleString , -- BLAST program: blastp, tblastx etc.
version VisibleString , -- Program version
diff --git a/c++/src/objects/entrezgene/entrezgene.asn b/c++/src/objects/entrezgene/entrezgene.asn
index 3ace09b..163783d 100644
--- a/c++/src/objects/entrezgene/entrezgene.asn
+++ b/c++/src/objects/entrezgene/entrezgene.asn
@@ -1,4 +1,4 @@
---$Revision: 413470 $
+--$Revision: 463081 $
--**********************************************************************
--
-- NCBI Entrezgene
@@ -43,6 +43,7 @@ Entrezgene ::= SEQUENCE {
transposon (8) ,
miscRNA (9) ,
ncRNA (10) ,
+ biological-region (11),
other (255) } ,
source BioSource ,
gene Gene-ref , -- for locus-tag see note 3
@@ -138,7 +139,8 @@ Gene-commentary ::= SEQUENCE {
properties SEQUENCE OF Gene-commentary OPTIONAL ,
comment SEQUENCE OF Gene-commentary OPTIONAL ,
create-date Date OPTIONAL ,
- update-date Date OPTIONAL }
+ update-date Date OPTIONAL ,
+ rna RNA-ref OPTIONAL }
Other-source ::= SEQUENCE {
src Dbtag OPTIONAL , -- key to non-ncbi source
diff --git a/c++/src/objects/general/Date_std.cpp b/c++/src/objects/general/Date_std.cpp
index 24ccc1e..ffb340b 100644
--- a/c++/src/objects/general/Date_std.cpp
+++ b/c++/src/objects/general/Date_std.cpp
@@ -1,4 +1,4 @@
-/* $Id: Date_std.cpp 187399 2010-03-31 12:59:20Z bollin $
+/* $Id: Date_std.cpp 463068 2015-03-24 16:16:20Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -273,16 +273,14 @@ void CDate_std::GetDate(string* label, const string& format) const
*label += GetSeason();
}
} else { // just a number
- if (length > 0) {
- // We want exactly <length> digits.
- CNcbiOstrstream oss;
- oss << setfill('0') << setw(length) << value;
- string s = CNcbiOstrstreamToString(oss);
- label->append(s, s.size() > length ? s.size() - length : 0,
- length);
- } else {
- *label += NStr::IntToString(value);
- }
+ // We want exactly <length> digits.
+ string s;
+ NStr::IntToString(s, value);
+ size_t zeropad = length < s.length() ? 0 : length-s.length();
+ size_t start = (length > 0 && length < s.length() ) ? s.size() - length : 0;
+ if (zeropad>0)
+ label->append(zeropad, '0');
+ label->append(s, start, s.size() - start);
}
} else {
// missing...roll back label and look for alternatives, or
diff --git a/c++/src/objects/general/Dbtag.cpp b/c++/src/objects/general/Dbtag.cpp
index 68c02a3..af64dee 100644
--- a/c++/src/objects/general/Dbtag.cpp
+++ b/c++/src/objects/general/Dbtag.cpp
@@ -1,4 +1,4 @@
-/* $Id: Dbtag.cpp 462430 2015-03-18 17:23:06Z ivanov $
+/* $Id: Dbtag.cpp 469010 2015-05-29 22:47:32Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -623,7 +623,6 @@ static const TDbtUrl sc_url_prefix[] = {
{ CDbtag::eDbtagType_PDB, "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=" },
{ CDbtag::eDbtagType_PFAM, "http://pfam.sanger.ac.uk/family?acc=" },
{ CDbtag::eDbtagType_PGN, "http://pgn.cornell.edu/cgi-bin/search/seq_search_result.pl?identifier=" },
- { CDbtag::eDbtagType_Pathema, "http://pathema.jcvi.org/cgi-bin/Burkholderia/shared/GenePage.cgi?all=1&locus=" },
{ CDbtag::eDbtagType_Phytozome, "http://www.phytozome.net/genePage.php?db=Phytozome&crown&method=0&search=1&detail=1&searchText=locusname:" },
{ CDbtag::eDbtagType_PomBase, "http://www.pombase.org/spombe/result/" },
{ CDbtag::eDbtagType_PseudoCap, "http://www.pseudomonas.com/getAnnotation.do?locusID=" },
diff --git a/c++/src/objects/general/Makefile.general.lib b/c++/src/objects/general/Makefile.general.lib
index aedd0dd..d3535d4 100644
--- a/c++/src/objects/general/Makefile.general.lib
+++ b/c++/src/objects/general/Makefile.general.lib
@@ -1,6 +1,7 @@
LIB = general
SRC = general__ general___ uoconv
+DLL_LIB = xser
USES_LIBRARIES = \
xser
diff --git a/c++/src/objects/general/Object_id.cpp b/c++/src/objects/general/Object_id.cpp
index 151302c..b1b80a9 100644
--- a/c++/src/objects/general/Object_id.cpp
+++ b/c++/src/objects/general/Object_id.cpp
@@ -1,4 +1,4 @@
-/* $Id: Object_id.cpp 420652 2013-12-04 16:44:17Z vasilche $
+/* $Id: Object_id.cpp 455980 2015-01-06 19:59:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,7 +76,7 @@ bool CObject_id::Match(const CObject_id& oid2) const
}
-CObject_id::E_Choice CObject_id::GetIdType(Int8& value) const
+CObject_id::E_Choice CObject_id::GetIdType(TId8& value) const
{
switch ( Which() ) {
case e_Id:
@@ -125,7 +125,7 @@ CObject_id::E_Choice CObject_id::GetIdType(Int8& value) const
// match for identity
int CObject_id::Compare(const CObject_id& oid2) const
{
- Int8 value, value2;
+ TId8 value, value2;
E_Choice type = GetIdType(value);
E_Choice type2 = oid2.GetIdType(value2);
if ( int diff = type - type2 ) {
@@ -142,6 +142,29 @@ int CObject_id::Compare(const CObject_id& oid2) const
}
+CObject_id::TId8 CObject_id::GetId8(void) const
+{
+ TId8 value;
+ if ( !GetId8(value) ) {
+ NCBI_THROW(CSerialException, eInvalidData,
+ "CObject_id doesn't have Int8 value");
+ }
+ return value;
+}
+
+
+void CObject_id::SetId8(TId8 value)
+{
+ if ( TId(value) == value ) {
+ // fits in id
+ SetId(TId(value));
+ }
+ else {
+ NStr::NumericToString(SetStr(), value);
+ }
+}
+
+
// format contents into a stream
ostream& CObject_id::AsString(ostream &s) const
{
diff --git a/c++/src/objects/general/Person_id.cpp b/c++/src/objects/general/Person_id.cpp
index 566a13b..cda33c1 100644
--- a/c++/src/objects/general/Person_id.cpp
+++ b/c++/src/objects/general/Person_id.cpp
@@ -1,4 +1,4 @@
-/* $Id: Person_id.cpp 448230 2014-10-03 13:53:54Z ivanov $
+/* $Id: Person_id.cpp 448025 2014-10-02 00:45:40Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/general/User_object.cpp b/c++/src/objects/general/User_object.cpp
index ff172d7..fac10ca 100644
--- a/c++/src/objects/general/User_object.cpp
+++ b/c++/src/objects/general/User_object.cpp
@@ -1,4 +1,4 @@
-/* $Id: User_object.cpp 457350 2015-01-22 14:35:39Z ivanov $
+/* $Id: User_object.cpp 482748 2015-10-26 17:00:43Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -582,6 +582,8 @@ const string kOriginalId = "OriginalID";
const string kOrigIdAltSpell = "OrginalID";
const string kUnverified = "Unverified";
const string kValidationSuppression = "ValidationSuppression";
+const string kNcbiCleanup = "NcbiCleanup";
+const string kAutoDefOptions = "AutodefOptions";
CUser_object::EObjectType CUser_object::GetObjectType() const
{
@@ -603,6 +605,10 @@ CUser_object::EObjectType CUser_object::GetObjectType() const
rval = eObjectType_Unverified;
} else if (NStr::Equal(label, kValidationSuppression)) {
rval = eObjectType_ValidationSuppression;
+ } else if (NStr::Equal(label, kNcbiCleanup)) {
+ rval = eObjectType_Cleanup;
+ } else if (NStr::Equal(label, kAutoDefOptions)) {
+ rval = eObjectType_AutodefOptions;
}
return rval;
}
@@ -626,6 +632,12 @@ void CUser_object::SetObjectType(EObjectType obj_type)
case eObjectType_ValidationSuppression:
SetType().SetStr(kValidationSuppression);
break;
+ case eObjectType_Cleanup:
+ SetType().SetStr(kNcbiCleanup);
+ break;
+ case eObjectType_AutodefOptions:
+ SetType().SetStr(kAutoDefOptions);
+ break;
case eObjectType_Unknown:
ResetType();
break;
@@ -722,7 +734,7 @@ void CUser_object::RemoveUnverifiedOrganism()
}
-static const string kUnverifiedFeature = "Feature";
+static const string kUnverifiedFeature = "Features";
bool CUser_object::IsUnverifiedFeature() const
{
@@ -742,7 +754,23 @@ void CUser_object::RemoveUnverifiedFeature()
}
+void CUser_object::UpdateNcbiCleanup(int version)
+{
+ SetObjectType(eObjectType_Cleanup);
+ CRef<CUser_field> method = SetFieldRef("method");
+ method->SetData().SetStr(CUtf8::AsUTF8("ExtendedSeqEntryCleanup", eEncoding_Ascii));
+ CRef<CUser_field> version_field = SetFieldRef("version");
+ version_field->SetData().SetInt(version);
+ // get current time
+ CTime curr_time(CTime::eCurrent);
+ CRef<CUser_field> month = SetFieldRef("month");
+ month->SetData().SetInt(curr_time.Month());
+ CRef<CUser_field> day = SetFieldRef("day");
+ day->SetData().SetInt(curr_time.Day());
+ CRef<CUser_field> year = SetFieldRef("year");
+ year->SetData().SetInt(curr_time.Year());
+}
END_objects_SCOPE // namespace ncbi::objects::
diff --git a/c++/src/objects/genomecoll/GCClient_GetAssemblyReques.cpp b/c++/src/objects/genomecoll/GCClient_GetAssemblyReques.cpp
old mode 100644
new mode 100755
index 9b41e02..464f369
--- a/c++/src/objects/genomecoll/GCClient_GetAssemblyReques.cpp
+++ b/c++/src/objects/genomecoll/GCClient_GetAssemblyReques.cpp
@@ -1,4 +1,4 @@
-/* $Id: GCClient_GetAssemblyReques.cpp 459044 2015-02-12 17:32:29Z ivanov $
+/* $Id: GCClient_GetAssemblyReques.cpp 483944 2015-11-05 13:38:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -60,6 +60,16 @@ CGCClient_GetAssemblyRequest::SRequestParam::SRequestParam()
{
}
+CGCClient_GetAssemblyRequest::SRequestParam::SRequestParam(int level_, int assembly_flags_, int chromosome_flags_,
+ int scaffold_flags_, int component_flags_)
+ : level(level_)
+ , assembly_flags(assembly_flags_)
+ , chromosome_flags(chromosome_flags_)
+ , scaffold_flags(scaffold_flags_)
+ , component_flags(component_flags_)
+{
+}
+
bool CGCClient_GetAssemblyRequest::SRequestParam::SetMode(EAssemblyMode mode)
{
level = CGCClient_GetAssemblyRequest::eLevel_component;
@@ -119,6 +129,33 @@ bool CGCClient_GetAssemblyRequest::SRequestParam::SetMode(EAssemblyMode mode)
return true;
}
+bool CGCClient_GetAssemblyRequest::SRequestParam::SetMode(const string& mode)
+{
+ level = CGCClient_GetAssemblyRequest::eLevel_component;
+ assembly_flags = eGCClient_AttributeFlags_none;
+ chromosome_flags = eGCClient_AttributeFlags_biosource;
+ scaffold_flags = eGCClient_AttributeFlags_none;
+ component_flags = eGCClient_AttributeFlags_none;
+
+ if(mode == "Gbench")
+ {
+ level = CGCClient_GetAssemblyRequest::eLevel_scaffold;
+ assembly_flags = eGCClient_AttributeFlags_none;
+ chromosome_flags = eGCClient_AttributeFlags_biosource |
+ eGCClient_AttributeFlags_exclude_aligndb;
+ }
+ else if(mode == "Gbench_chrs")
+ {
+ level = CGCClient_GetAssemblyRequest::eLevel_replicon;
+ assembly_flags = eGCClient_AttributeFlags_none;
+ chromosome_flags = eGCClient_AttributeFlags_biosource;
+ }
+ else
+ return false;
+
+ return true;
+}
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/genomecoll/GC_Assembly.cpp b/c++/src/objects/genomecoll/GC_Assembly.cpp
index 306cbf9..06afb16 100644
--- a/c++/src/objects/genomecoll/GC_Assembly.cpp
+++ b/c++/src/objects/genomecoll/GC_Assembly.cpp
@@ -1,4 +1,4 @@
-/* $Id: GC_Assembly.cpp 468019 2015-05-19 17:49:08Z ivanov $
+/* $Id: GC_Assembly.cpp 467805 2015-05-18 12:53:53Z zherikov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/genomecoll/GC_Sequence.cpp b/c++/src/objects/genomecoll/GC_Sequence.cpp
index 8d4c7bb..f51b4a1 100644
--- a/c++/src/objects/genomecoll/GC_Sequence.cpp
+++ b/c++/src/objects/genomecoll/GC_Sequence.cpp
@@ -1,4 +1,4 @@
-/* $Id: GC_Sequence.cpp 398188 2013-05-03 15:43:30Z kumarv2 $
+/* $Id: GC_Sequence.cpp 479299 2015-09-18 11:47:36Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,7 @@
// generated includes
#include <objects/genomecoll/GC_Sequence.hpp>
+#include <objects/genomecoll/GC_SequenceStats.hpp>
#include <objects/genomecoll/GC_AssemblyUnit.hpp>
#include <objects/genomecoll/GC_Assembly.hpp>
#include <objects/genomecoll/GC_Replicon.hpp>
@@ -58,6 +59,8 @@ CGC_Sequence::CGC_Sequence(void)
, m_Replicon(NULL)
, m_ParentSequence(NULL)
, m_ParentRel(CGC_TaggedSequences::eState_not_set)
+ , m_SeqLength(0)
+ , m_SeqLengthRetrieved(false)
{
}
@@ -198,6 +201,51 @@ bool CGC_Sequence::HasRole(int Role) const
return false;
}
+
+bool CGC_Sequence::CanGetLength() const
+{
+ return ( x_GetLength() != 0);
+}
+
+TSeqPos CGC_Sequence::GetLength() const
+{
+ TSeqPos result = x_GetLength();
+ if (result == 0) {
+ NCBI_THROW(CUnassignedMember, eGet, "CGC_Sequence::GetLength(): Sequence length not set.");
+ }
+ return result;
+}
+
+TSeqPos CGC_Sequence::x_GetLength() const
+{
+ if ( ! m_SeqLengthRetrieved) {
+ if (HasRole(eGC_SequenceRole_chromosome)) {
+ if (CanGetStats() && GetStats().CanGetOrdered_scaf()) {
+ ITERATE(list< CRef< CGC_Scaf_stats > >, stat_it, GetStats().GetOrdered_scaf()) {
+ if ( (*stat_it)->GetStats_category() == CGC_Scaf_stats::eStats_category_total_length)
+ {
+ m_SeqLength = static_cast<TSeqPos>((*stat_it)->GetValue());
+ break;
+ }
+ }
+ }
+ } else {
+ if (CanGetStats() && GetStats().CanGetAll_scaf()) {
+ ITERATE(list< CRef< CGC_Scaf_stats > >, stat_it, GetStats().GetAll_scaf()) {
+ if ( (*stat_it)->GetStats_category() == CGC_Scaf_stats::eStats_category_total_length)
+ {
+ m_SeqLength = static_cast<TSeqPos>((*stat_it)->GetValue());
+ break;
+ }
+ }
+ }
+ }
+ m_SeqLengthRetrieved = true;
+ }
+ return m_SeqLength;
+}
+
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/genomecoll/Makefile.gencoll_client.lib b/c++/src/objects/genomecoll/Makefile.gencoll_client.lib
index 9f74906..3165234 100644
--- a/c++/src/objects/genomecoll/Makefile.gencoll_client.lib
+++ b/c++/src/objects/genomecoll/Makefile.gencoll_client.lib
@@ -1,10 +1,10 @@
-# $Id: Makefile.gencoll_client.lib 427424 2014-02-20 13:38:50Z gouriano $
+# $Id: Makefile.gencoll_client.lib 481642 2015-10-14 15:58:55Z ivanov $
ASN = gencoll_client
# SRC = $(ASN:%=%__) $(ASN:%=%___)
-SRC = gencoll_client__ gencoll_client___ genomic_collections_cli genomic_collections_cli_
+SRC = gencoll_client__ gencoll_client___ genomic_collections_cli genomic_collections_cli_ cached_assembly
LIB = gencoll_client
@@ -12,8 +12,8 @@ LIB_OR_DLL = lib
#REQUIRES = objects dbapi
-WATCHERS = kumarv2 dicuccio
+WATCHERS = shchekot dicuccio
USES_LIBRARIES = \
- genome_collection xconnect
+ genome_collection xconnect $(COMPRESS_LIBS)
diff --git a/c++/src/objects/genomecoll/Makefile.genome_collection.lib b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
index d7a38ec..5f18821 100644
--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
@@ -1,9 +1,9 @@
-# $Id: Makefile.genome_collection.lib 427424 2014-02-20 13:38:50Z gouriano $
+# $Id: Makefile.genome_collection.lib 481642 2015-10-14 15:58:55Z ivanov $
LIB = genome_collection
SRC = genome_collection__ genome_collection___
-WATCHERS = dicuccio
+WATCHERS = dicuccio shchekot
USES_LIBRARIES = \
diff --git a/c++/src/objects/genomecoll/cached_assembly.cpp b/c++/src/objects/genomecoll/cached_assembly.cpp
new file mode 100644
index 0000000..64bcc31
--- /dev/null
+++ b/c++/src/objects/genomecoll/cached_assembly.cpp
@@ -0,0 +1,182 @@
+/* $Id
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ */
+#include <ncbi_pch.hpp>
+#include <objects/genomecoll/cached_assembly.hpp>
+#include <sstream>
+
+BEGIN_NCBI_SCOPE
+USING_SCOPE(objects);
+
+CCachedAssembly::CCachedAssembly(CRef<CGC_Assembly> assembly)
+ : m_assembly(assembly)
+{}
+
+CCachedAssembly::CCachedAssembly(const string& blob)
+ : m_blob(blob)
+{}
+
+CCachedAssembly::CCachedAssembly(const vector<char>& blob)
+ : m_blob(blob.begin(), blob.end())
+{}
+
+static
+CRef<CGC_Assembly> UncomressAndCreate(const string& blob, CCompressStream::EMethod method) {
+ CStopWatch sw(CStopWatch::eStart);
+
+ CNcbiIstrstream in(blob.data(), blob.size());
+ CDecompressIStream decompress(in, method);
+
+ CRef<CGC_Assembly> m_assembly(new CGC_Assembly);
+ decompress >> MSerial_AsnBinary
+ >> MSerial_SkipUnknownMembers(eSerialSkipUnknown_Yes) // Make reading cache backward compatible
+ >> MSerial_SkipUnknownVariants(eSerialSkipUnknown_Yes)
+ >> (*m_assembly);
+
+ sw.Stop();
+ LOG_POST(Info << "Assebmly uncomressed and created in (sec): " << sw.Elapsed());
+ GetDiagContext().Extra().Print("Create-assembly-from-blob-time", sw.Elapsed() * 1000) // need millisecond
+ .Print("compress-method", method)
+ .Print("blob-size", blob.size());
+ return m_assembly;
+}
+
+//static
+//void Uncomress(const string& blob, CCompressStream::EMethod m) {
+// CStopWatch g(CStopWatch::eStart);
+//
+// CNcbiIstrstream in(blob.data(), blob.size());
+// CDecompressIStream lzip(in, m);
+//
+// size_t n = 1024*1024;
+// char* buf = new char[n];
+// while (!lzip.eof()) lzip.read(buf, n);
+// delete [] buf;
+//
+// LOG_POST(Info << "processed: " << lzip.GetProcessedSize() << ", out: " << lzip.GetOutputSize());
+// LOG_POST(Info << "Assebmly uncomressed in (sec): " << g.Elapsed());
+//}
+
+static
+CCompressStream::EMethod Compression(const string& blob)
+{
+ if (!CCachedAssembly::ValidBlob(blob.size()))
+ NCBI_THROW(CCoreException, eCore, "Invalid blob size detected: " + blob.size());
+ const char bzip2Header[] = {0x42, 0x5a, 0x68};
+ const char zlibHeader[] = {0x78};
+ if (NStr::StartsWith(blob, CTempString(bzip2Header, sizeof(bzip2Header))))
+ return CCompressStream::eBZip2;
+ if (NStr::StartsWith(blob, CTempString(zlibHeader, sizeof(zlibHeader))))
+ return CCompressStream::eZip;
+ NCBI_THROW(CCoreException, eInvalidArg, "Cant determine compression method: " + blob.substr(0, 10));
+}
+
+CRef<CGC_Assembly> CCachedAssembly::Assembly()
+{
+ if (m_assembly.NotNull()) {
+ return m_assembly;
+ }
+
+ if (ValidBlob(m_blob.size())) {
+ m_assembly = UncomressAndCreate(m_blob, Compression(m_blob));
+ }
+ return m_assembly;
+}
+
+static
+void CompressAssembly(string& blob, CRef<CGC_Assembly> assembly, CCompressStream::EMethod method)
+{
+ CStopWatch sw(CStopWatch::eStart);
+
+ LOG_POST(Info << "Creating blob with compression: " << method);
+ _ASSERT(blob.empty());
+
+ CNcbiOstrstream out;
+ CCompressOStream compress(out, method);
+
+ compress << MSerial_AsnBinary << (*assembly);
+ compress.Finalize();
+
+ blob = CNcbiOstrstreamToString(out);
+
+ sw.Stop();
+ GetDiagContext().Extra().Print("Compress-assembly-to-blob-time", sw.Elapsed() * 1000) // need millisecond
+ .Print("compress-method", method)
+ .Print("blob-size", blob.size());
+}
+
+static
+string ChangeCompression(const string& blob,
+ CCompressStream::EMethod from, CCompressStream::EMethod to)
+{
+ CStopWatch sw(CStopWatch::eStart);
+
+ LOG_POST(Info << "Changing compression from " << from << " to " << to);
+ _ASSERT(from != to);
+
+ CNcbiIstrstream in(blob.data(), blob.size());
+ CDecompressIStream from_stream(in, from);
+ CNcbiOstrstream out;
+ CCompressOStream to_stream(out, to);
+
+ to_stream << from_stream.rdbuf();
+ to_stream.Finalize();
+
+ string new_blob = CNcbiOstrstreamToString(out);
+
+ sw.Stop();
+ LOG_POST(Info << "Compression done - processed: " << to_stream.GetProcessedSize() << ", old size:" << blob.size() << ", new size: " << to_stream.GetOutputSize());
+
+ GetDiagContext().Extra().Print("Change-assembly-compression-time", sw.Elapsed() * 1000) // need millisecond
+ .Print("compress-method-old", from)
+ .Print("compress-method-new", to)
+ .Print("blob-size-old", blob.size())
+ .Print("blob-size-new", new_blob.size());
+
+ return new_blob;
+}
+
+const string& CCachedAssembly::Blob(CCompressStream::EMethod neededCompression)
+{
+ _ASSERT(neededCompression == CCompressStream::eBZip2 || neededCompression == CCompressStream::eZip);
+ LOG_POST(Info << "Requested blob with compression: " << neededCompression);
+ if (m_blob.empty()) {
+ CompressAssembly(m_blob, m_assembly, neededCompression);
+ }
+ else if (neededCompression != Compression(m_blob)) {
+ //TODO: remove it once all be switched to new gc_access (conversion will be done inside CGencollCache)
+ m_blob = ChangeCompression(m_blob, Compression(m_blob), neededCompression);
+ }
+ return m_blob;
+}
+
+bool CCachedAssembly::ValidBlob(int blobSize)
+{
+ const int kSmallestZip = 200; // No assembly, let alone a compressed one, will be smaller than this.
+ return blobSize >= kSmallestZip;
+}
+
+END_NCBI_SCOPE
diff --git a/c++/src/objects/genomecoll/gencoll_client.asn b/c++/src/objects/genomecoll/gencoll_client.asn
index 6127b15..bdc5bd5 100755
--- a/c++/src/objects/genomecoll/gencoll_client.asn
+++ b/c++/src/objects/genomecoll/gencoll_client.asn
@@ -1,4 +1,4 @@
--- $Id: gencoll_client.asn 457080 2015-01-20 16:54:14Z ivanov $
+-- $Id: gencoll_client.asn 479931 2015-09-24 17:18:23Z ivanov $
-- **********************************************************************
--
-- NCBI Genome Collections Statistics
@@ -19,7 +19,8 @@ GCClientRequest ::= CHOICE {
get-assembly GCClient-GetAssemblyRequest,
get-chrtype-valid GCClient-ValidateChrTypeLocRequest,
get-best-assembly GCClient-FindBestAssemblyRequest,
- get-equivalent-assemblies GCClient-GetEquivalentAssembliesRequest
+ get-equivalent-assemblies GCClient-GetEquivalentAssembliesRequest,
+ get-assembly-blob GCClient-GetAssemblyBlobRequest
}
@@ -30,7 +31,8 @@ GCClientResponse ::= CHOICE {
get-equivalent-assemblies GCClient-EquivalentAssemblies,
-- errors encountered at the server side.
- srvr-error GCClient-Error
+ srvr-error GCClient-Error,
+ get-assembly-blob OCTET STRING
}
GCClient-Error ::= SEQUENCE {
@@ -112,6 +114,20 @@ GCClient-GetAssemblyRequest ::= SEQUENCE {
component-flags GCClient-AttributeFlags DEFAULT none
}
+GCClient-GetAssemblyBlobRequest ::= SEQUENCE {
+
+ -- One of accession or release id MUST BE SUPPLIED
+
+ -- Assembly accession or accession.version
+ -- (versionless accession is answered with most recent version)
+ accession VisibleString OPTIONAL,
+
+ -- release ID
+ release-id INTEGER OPTIONAL,
+
+ mode VisibleString
+}
+
GCClient-ValidateChrTypeLocRequest ::= SEQUENCE {
-- Validate the Type Location in the request
diff --git a/c++/src/objects/genomecoll/genome_collection.asn b/c++/src/objects/genomecoll/genome_collection.asn
index 0077e5c..6c0040a 100644
--- a/c++/src/objects/genomecoll/genome_collection.asn
+++ b/c++/src/objects/genomecoll/genome_collection.asn
@@ -1,4 +1,4 @@
--- $Id: genome_collection.asn 443902 2014-08-20 12:30:14Z ivanov $
+-- $Id: genome_collection.asn 469353 2015-06-03 16:18:27Z smithrg $
-- **********************************************************************
--
-- NCBI Genome Collections
@@ -522,6 +522,8 @@ GC-Scaf-stats ::= SEQUENCE {
count-alt-scaf-with-alignment (110), -- number of alt scaffolds with alignment to primary assembly
count-alt-loci-scaf (111), -- number of alt-loci scaffolds.
count-real-scaffolds (112), -- number of scaffolds with gb_is_skipped = 0.
+ top-level-count (113), -- Number of chromosomes or plasmids, unplaced/unlocalized scaffolds, alt-loci scaffolds, and patch scaffolds
+ total-gap-length (114), -- Total length of gaps
other (255) -- catch all
},
diff --git a/c++/src/objects/genomecoll/genomic_collections_cli.cpp b/c++/src/objects/genomecoll/genomic_collections_cli.cpp
index ddc3b8e..a3b086b 100644
--- a/c++/src/objects/genomecoll/genomic_collections_cli.cpp
+++ b/c++/src/objects/genomecoll/genomic_collections_cli.cpp
@@ -1,4 +1,4 @@
-/* $Id: genomic_collections_cli.cpp 457080 2015-01-20 16:54:14Z ivanov $
+/* $Id: genomic_collections_cli.cpp 482676 2015-10-26 14:13:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,8 +39,6 @@
// generated includes
#include <objects/genomecoll/genomic_collections_cli.hpp>
-#include <objects/genomecoll/GCClient_AttributeFlags.hpp>
-#include <objects/genomecoll/GCClient_GetAssemblyReques.hpp>
#include <objects/genomecoll/GCClient_AssemblyInfo.hpp>
#include <objects/genomecoll/GCClient_AssemblySequenceI.hpp>
#include <objects/genomecoll/GCClient_AssembliesForSequ.hpp>
@@ -49,30 +47,28 @@
#include <objects/genomecoll/GCClient_ValidateChrTypeLo.hpp>
#include <objects/genomecoll/GCClient_EquivalentAssembl.hpp>
#include <objects/genomecoll/GCClient_GetEquivalentAsse.hpp>
+#include <objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp>
+#include <objects/genomecoll/cached_assembly.hpp>
#include <sstream>
// generated classes
BEGIN_NCBI_SCOPE
+BEGIN_objects_SCOPE
-BEGIN_objects_SCOPE // namespace ncbi::objects::
+static const STimeout kTimeout = {600, 0};
-// constructor
-CGenomicCollectionsService::CGenomicCollectionsService(void)
+CGenomicCollectionsService::CGenomicCollectionsService()
{
+ SetTimeout(&kTimeout);
}
CGenomicCollectionsService::CGenomicCollectionsService(const string& url)
: m_url(url)
{
+ SetTimeout(&kTimeout);
}
-// destructor
-CGenomicCollectionsService::~CGenomicCollectionsService(void)
-{
-}
-
-
string CGenomicCollectionsService::x_GetURL()
{
return m_url;
@@ -83,18 +79,21 @@ void CGenomicCollectionsService::x_Connect()
#ifdef _DEBUG
LOG_POST(Info << "Connecting to url:" << x_GetURL().c_str());
#endif
- STimeout to5Min;
- to5Min.sec=600;
- to5Min.usec=0;
- SetTimeout(&to5Min);
-
- string url = x_GetURL();
- if(url.empty())
+ if(x_GetURL().empty())
CGenomicCollectionsService_Base::x_Connect();
else
- x_ConnectURL(url);
+ x_ConnectURL(x_GetURL());
}
+template<typename TReq>
+void LogRequest(const TReq& req)
+{
+#ifdef _DEBUG
+ ostringstream ostrstrm;
+ ostrstrm << "Making request -" << MSerial_AsnText << req;
+ LOG_POST(Info << ostrstrm.str());
+#endif
+}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc,
int level,
@@ -105,24 +104,20 @@ CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc,
{
CGCClient_GetAssemblyRequest req;
CGCClientResponse reply;
-
+
req.SetAccession(acc);
req.SetLevel(level);
req.SetAssm_flags(asmAttrFlags);
req.SetChrom_flags(chrAttrFlags);
req.SetScaf_flags(scafAttrFlags);
req.SetComponent_flags(compAttrFlags);
-
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request - " << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
-
+
+ LogRequest(req);
+
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
- if(reply.Which() == CGCClientResponse::e_Srvr_error) {
+ if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
@@ -146,17 +141,13 @@ CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(int releaseId,
req.SetChrom_flags(chrAttrFlags);
req.SetScaf_flags(scafAttrFlags);
req.SetComponent_flags(compAttrFlags);
-
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
-
+
+ LogRequest(req);
+
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
- if(reply.Which() == CGCClientResponse::e_Srvr_error) {
+ if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
@@ -191,6 +182,74 @@ CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(int releaseId, CGCCli
params.component_flags);
}
+CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc, const string& mode)
+{
+ CGCClient_GetAssemblyRequest::SRequestParam params;
+ if(!params.SetMode(mode))
+ NCBI_THROW(CException, eUnknown, "GetAssembly: Illegal mode passed.");
+
+ return GetAssembly(acc,
+ params.level,
+ params.assembly_flags,
+ params.chromosome_flags,
+ params.scaffold_flags,
+ params.component_flags);
+}
+
+CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(int releaseId, const string& mode)
+{
+ CGCClient_GetAssemblyRequest::SRequestParam params;
+ if(!params.SetMode(mode))
+ NCBI_THROW(CException, eUnknown, "GetAssembly: Illegal mode passed.");
+
+ return GetAssembly(releaseId,
+ params.level,
+ params.assembly_flags,
+ params.chromosome_flags,
+ params.scaffold_flags,
+ params.component_flags);
+}
+
+CRef<CGC_Assembly> CGenomicCollectionsService::_GetAssemblyNew(const string& acc, const string& mode)
+{
+ CGCClient_GetAssemblyBlobRequest req;
+ CGCClientResponse reply;
+
+ req.SetAccession(acc);
+ req.SetMode(mode);
+
+ LogRequest(req);
+
+ try {
+ return CCachedAssembly(AskGet_assembly_blob(req, &reply)).Assembly();
+ } catch (CException& ex) {
+ if(reply.IsSrvr_error()) {
+ NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
+ }
+ throw;
+ }
+}
+
+CRef<CGC_Assembly> CGenomicCollectionsService::_GetAssemblyNew(int releaseId, const string& mode)
+{
+ CGCClient_GetAssemblyBlobRequest req;
+ CGCClientResponse reply;
+
+ req.SetRelease_id(releaseId);
+ req.SetMode(mode);
+
+ LogRequest(req);
+
+ try {
+ return CCachedAssembly(AskGet_assembly_blob(req, &reply)).Assembly();
+ } catch (CException& ex) {
+ if(reply.IsSrvr_error()) {
+ NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
+ }
+ throw;
+ }
+}
+
string CGenomicCollectionsService::ValidateChrType(const string& chrType, const string& chrLoc)
{
CGCClient_ValidateChrTypeLocRequest req;
@@ -198,17 +257,13 @@ string CGenomicCollectionsService::ValidateChrType(const string& chrType, const
req.SetType(chrType);
req.SetLocation(chrLoc);
-
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
-
+
+ LogRequest(req);
+
try {
return AskGet_chrtype_valid(req, &reply);
} catch (CException& ex) {
- if(reply.Which() == CGCClientResponse::e_Srvr_error) {
+ if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
@@ -226,11 +281,7 @@ CRef<CGCClient_AssemblyInfo> CGenomicCollectionsService::FindBestAssembly(const
req.SetSort(sort_type);
req.SetAssembly_return_limit(1);
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
+ LogRequest(req);
try {
CRef<CGCClient_AssembliesForSequences> assm = AskGet_best_assembly(req, &reply);
@@ -257,11 +308,7 @@ CRef<CGCClient_AssemblySequenceInfo> CGenomicCollectionsService::FindBestAssembl
req.SetSort(sort_type);
req.SetAssembly_return_limit(1);
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
+ LogRequest(req);
try {
CRef<CGCClient_AssembliesForSequences> assm = AskGet_best_assembly(req, &reply);
@@ -271,7 +318,7 @@ CRef<CGCClient_AssemblySequenceInfo> CGenomicCollectionsService::FindBestAssembl
CRef<CGCClient_AssemblySequenceInfo>();
} catch (const CException& ex) {
if(reply.IsSrvr_error()) {
- NCBI_REPORT_EXCEPTION(reply.GetSrvr_error().GetDescription(), ex);
+ NCBI_REPORT_EXCEPTION(reply.GetSrvr_error().GetDescription().c_str(), ex);
}
throw;
}
@@ -287,11 +334,7 @@ CRef<CGCClient_AssembliesForSequences> CGenomicCollectionsService::FindAllAssemb
req.SetFilter(filter_type);
req.SetSort(sort_type);
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
+ LogRequest(req);
try {
CRef<CGCClient_AssembliesForSequences> assm = AskGet_best_assembly(req, &reply);
@@ -314,11 +357,7 @@ CRef<CGCClient_EquivalentAssemblies> CGenomicCollectionsService::GetEquivalentAs
req.SetAccession(acc);
req.SetEquivalency(equivalency);
-#ifdef _DEBUG
- ostringstream ostrstrm;
- ostrstrm << "Making request -" << MSerial_AsnText << req;
- LOG_POST(Info << ostrstrm.str());
-#endif
+ LogRequest(req);
try {
CRef<CGCClient_EquivalentAssemblies> assm = AskGet_equivalent_assemblies(req, &reply);
@@ -332,9 +371,5 @@ CRef<CGCClient_EquivalentAssemblies> CGenomicCollectionsService::GetEquivalentAs
}
}
-
-END_objects_SCOPE // namespace ncbi::objects::
-
+END_objects_SCOPE
END_NCBI_SCOPE
-
-/* Original file checksum: lines: 57, chars: 1793, CRC32: a9ae6ff4 */
diff --git a/c++/src/objects/id1/Makefile.id1.lib b/c++/src/objects/id1/Makefile.id1.lib
index 05543a5..3d978e2 100644
--- a/c++/src/objects/id1/Makefile.id1.lib
+++ b/c++/src/objects/id1/Makefile.id1.lib
@@ -3,6 +3,8 @@ ASN_DEP = seq
LIB = id1
SRC = id1__ id1___
+DLL_LIB = seqset
+
WATCHERS = vasilche
diff --git a/c++/src/objects/id1/Makefile.id1cli.lib b/c++/src/objects/id1/Makefile.id1cli.lib
index b5c302f..3ed07eb 100644
--- a/c++/src/objects/id1/Makefile.id1cli.lib
+++ b/c++/src/objects/id1/Makefile.id1cli.lib
@@ -3,6 +3,8 @@ ASN_DEP = id1
LIB = id1cli
SRC = id1_client id1_client_
+DLL_LIB = id1
+
WATCHERS = vasilche
diff --git a/c++/src/objects/id1/id1.def b/c++/src/objects/id1/id1.def
index ec13766..88d3e0a 100644
--- a/c++/src/objects/id1/id1.def
+++ b/c++/src/objects/id1/id1.def
@@ -33,3 +33,7 @@ getseqidsfromgi._storage_type = ncbi::TIntId
getgihist._storage_type = ncbi::TIntId
getgirev._storage_type = ncbi::TIntId
getgistate._storage_type = ncbi::TIntId
+
+[ID1blob-info]
+gi._type = ncbi::TGi
+gi._storage_type = ncbi::TIntId
diff --git a/c++/src/objects/id2/id2.asn b/c++/src/objects/id2/id2.asn
index b1bdf97..8cc5270 100644
--- a/c++/src/objects/id2/id2.asn
+++ b/c++/src/objects/id2/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 464739 $
+--$Revision: 484991 $
--********************************************************************
--
-- Network Id server network access
@@ -76,8 +76,12 @@ ID2-Request-Get-Seq-id ::= SEQUENCE {
-- in general id with db "LABEL"
taxid (256), -- return a sequence taxonomy ID as integer
-- in general id with db "TAXID"
- hash (512) -- return a sequence hash as integer
+ hash (512), -- return a sequence hash as integer
-- in general id with db "HASH"
+ seq-length (1024), -- return a sequence Seq-inst.length as int
+ -- in general id with db "Seq-inst.length"
+ seq-mol (2048) -- return a sequence Seq-inst.mol as int
+ -- in general id with db "Seq-inst.mol"
} DEFAULT any
}
diff --git a/c++/src/objects/macro/Feature_field.cpp b/c++/src/objects/macro/Feature_field.cpp
index f6903cb..67030ea 100644
--- a/c++/src/objects/macro/Feature_field.cpp
+++ b/c++/src/objects/macro/Feature_field.cpp
@@ -1,4 +1,4 @@
-/* $Id: Feature_field.cpp 443958 2014-08-20 17:34:00Z ivanov $
+/* $Id: Feature_field.cpp 442282 2014-07-31 20:14:08Z chenj $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/macro/Location_constraint.cpp b/c++/src/objects/macro/Location_constraint.cpp
index 4aaeaac..695379c 100644
--- a/c++/src/objects/macro/Location_constraint.cpp
+++ b/c++/src/objects/macro/Location_constraint.cpp
@@ -1,4 +1,4 @@
-/* $Id: Location_constraint.cpp 459332 2015-02-17 21:53:51Z dicuccio $
+/* $Id: Location_constraint.cpp 459331 2015-02-17 21:53:17Z dicuccio $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/macro/Makefile.in b/c++/src/objects/macro/Makefile.in
index 46ecec6..2c9bd16 100644
--- a/c++/src/objects/macro/Makefile.in
+++ b/c++/src/objects/macro/Makefile.in
@@ -1,4 +1,4 @@
-# $Id: Makefile.in 449682 2014-10-20 13:47:49Z ivanov $
+# $Id: Makefile.in 449388 2014-10-16 14:55:16Z bollin $
ASN_PROJ = macro
SUB_PROJ = unit_test
diff --git a/c++/src/objects/macro/Makefile.macro.lib b/c++/src/objects/macro/Makefile.macro.lib
index 52cc121..511467f 100644
--- a/c++/src/objects/macro/Makefile.macro.lib
+++ b/c++/src/objects/macro/Makefile.macro.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.macro.lib 452363 2014-11-19 14:00:39Z ivanov $
+# $Id: Makefile.macro.lib 450410 2014-10-27 12:18:08Z bollin $
LIB = macro
SRC = macro__ macro___
diff --git a/c++/src/objects/macro/Molinfo_field.cpp b/c++/src/objects/macro/Molinfo_field.cpp
index 1432853..487e621 100644
--- a/c++/src/objects/macro/Molinfo_field.cpp
+++ b/c++/src/objects/macro/Molinfo_field.cpp
@@ -1,4 +1,4 @@
-/* $Id: Molinfo_field.cpp 459332 2015-02-17 21:53:51Z dicuccio $
+/* $Id: Molinfo_field.cpp 459331 2015-02-17 21:53:17Z dicuccio $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/macro/Search_func.cpp b/c++/src/objects/macro/Search_func.cpp
index faff844..051a429 100644
--- a/c++/src/objects/macro/Search_func.cpp
+++ b/c++/src/objects/macro/Search_func.cpp
@@ -1,4 +1,4 @@
-/* $Id: Search_func.cpp 443970 2014-08-20 17:37:22Z ivanov $
+/* $Id: Search_func.cpp 450811 2014-10-30 17:34:54Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -65,7 +65,7 @@ bool CSearch_func :: Empty() const
bool CSearch_func :: x_DoesStrContainPlural(const string& word, char last_letter, char second_to_last_letter, char next_letter) const
{
- unsigned len = word.size();
+ size_t len = word.size();
if (last_letter == 's') {
if (len >= 5 && CTempString(word).substr(len-5) == "trans") {
return false; // not plural;
@@ -88,7 +88,7 @@ bool CSearch_func :: x_StringMayContainPlural(const string& str) const
char last_letter, second_to_last_letter, next_letter;
bool may_contain_plural = false;
string word_skip = " ,";
- unsigned len;
+ size_t len;
if (str.empty()) {
return false;
@@ -161,7 +161,7 @@ static const char* skip_bracket_paren[] = {
"[acyl-carrier-protein]",
"(acyl carrier protein)"
};
-bool CSearch_func :: x_SkipBracketOrParen(const unsigned& idx, string& start) const
+bool CSearch_func :: x_SkipBracketOrParen(size_t idx, string& start) const
{
bool rval = false;
size_t ep, ns;
@@ -171,8 +171,8 @@ bool CSearch_func :: x_SkipBracketOrParen(const unsigned& idx, string& start) co
start = CTempString(start).substr(idx + 3);
}
else {
- unsigned len;
- for (unsigned i = 0; i < ArraySize(skip_bracket_paren); i++) {
+ size_t len;
+ for (size_t i = 0; i < ArraySize(skip_bracket_paren); i++) {
len = strlen(skip_bracket_paren[i]);
if (CTempString(start).substr(idx, len) == skip_bracket_paren[i]) {
start = CTempString(start).substr(idx + len);
@@ -243,9 +243,9 @@ static const char* ok_num_prefix[] = {
};
bool CSearch_func :: x_PrecededByOkPrefix (const string& start_str) const
{
- unsigned len_str = start_str.size();
- unsigned len_i;
- for (unsigned i = 0; i < ArraySize(ok_num_prefix); i++) {
+ size_t len_str = start_str.size();
+ size_t len_i;
+ for (size_t i = 0; i < ArraySize(ok_num_prefix); i++) {
len_i = string(ok_num_prefix[i]).size();
if (len_str >= len_i
&& (CTempString(start_str).substr(len_str-len_i) == ok_num_prefix[i])){
@@ -266,7 +266,7 @@ bool CSearch_func :: x_InWordBeforeCytochromeOrCoenzyme(const string& start_str)
strtmp = CTempString(start_str).substr(0, pos);
pos = strtmp.find_last_not_of(' ');
if (pos != string::npos) {
- unsigned len = strtmp.size();
+ size_t len = strtmp.size();
comp_str1 = CTempString(strtmp).substr(len-10);
comp_str2 = CTempString(strtmp).substr(len-8);
if ( (len >= 10 && NStr::EqualNocase(comp_str1, "cytochrome"))
@@ -369,7 +369,7 @@ bool CSearch_func :: x_IsPrefixPlusNumbers(const string& str, const string& pref
{
if (str.empty()) return false;
- unsigned pattern_len = prefix.size();
+ size_t pattern_len = prefix.size();
if (pattern_len > 0 && !NStr::EqualCase(str, 0, pattern_len, prefix)) {
return false;
}
diff --git a/c++/src/objects/macro/String_constraint.cpp b/c++/src/objects/macro/String_constraint.cpp
index 2ea51e9..ebb8391 100644
--- a/c++/src/objects/macro/String_constraint.cpp
+++ b/c++/src/objects/macro/String_constraint.cpp
@@ -1,4 +1,4 @@
-/* $Id: String_constraint.cpp 454553 2014-12-16 16:28:06Z ivanov $
+/* $Id: String_constraint.cpp 454397 2014-12-15 14:13:39Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -85,7 +85,7 @@ bool CString_constraint :: x_IsAllLowerCase(const string& str) const
bool CString_constraint :: x_IsAllPunctuation(const string& str) const
{
for (unsigned i=0; i< str.size(); i++) {
- if (!ispunct(str[i])) return false;
+ if (!ispunct(Uint1(str[i]))) return false;
}
return true;
}
@@ -150,7 +150,7 @@ static const string weasels[] = {
bool CString_constraint :: x_IsWeasel(const string& str) const
{
- unsigned sz = ArraySize(weasels);
+ size_t sz = ArraySize(weasels);
const string *begin = weasels;
const string *end = &(weasels[sz]);
@@ -181,7 +181,7 @@ string CString_constraint :: x_SkipWeasel(const string& str) const
return ret_str;
};
-bool CString_constraint :: x_CaseNCompareEqual(string str1, string str2, unsigned len1, bool case_sensitive) const
+bool CString_constraint :: x_CaseNCompareEqual(string str1, string str2, size_t len1, bool case_sensitive) const
{
if (!len1) return false;
string comp_str1, comp_str2;
@@ -204,7 +204,7 @@ string CString_constraint :: x_StripUnimportantCharacters(const string& str, boo
result.reserve(str.size());
string::const_iterator it = str.begin();
do {
- if ((strip_space && isspace(*it)) || (strip_punct && ispunct(*it)));
+ if ((strip_space && isspace(Uint1(*it))) || (strip_punct && ispunct(Uint1(*it))));
else result += *it;
} while (++it != str.end());
@@ -213,14 +213,14 @@ string CString_constraint :: x_StripUnimportantCharacters(const string& str, boo
bool CString_constraint :: x_DisallowCharacter(const char ch, bool disallow_slash) const
{
- if (isalpha (ch) || isdigit (ch) || ch == '_' || ch == '-') return true;
+ if (isalpha (Uint1(ch)) || isdigit (Uint1(ch)) || ch == '_' || ch == '-') return true;
else if (disallow_slash && ch == '/') return true;
else return false;
};
-bool CString_constraint :: x_IsWholeWordMatch(const string& start, const size_t& found, const unsigned& match_len, bool disallow_slash) const
+bool CString_constraint :: x_IsWholeWordMatch(const string& start, size_t found, size_t match_len, bool disallow_slash) const
{
- unsigned after_idx;
+ size_t after_idx;
if (!match_len) return true;
else if (start.empty() || found == string::npos) return false;
@@ -283,24 +283,24 @@ bool CString_constraint :: x_PartialCompare(const string& str, const string& pat
}
}
if (GetIgnore_space()) {
- if (isspace(str.c_str()[0])) {
+ if (isspace(Uint1(str[0]))) {
match_len++;
- return x_PartialCompare(str.substr(1), pattern, str.c_str()[0], match_len);
- } else if (isspace(pattern.c_str()[0])) {
+ return x_PartialCompare(str.substr(1), pattern, str[0], match_len);
+ } else if (isspace(Uint1(pattern[0]))) {
return x_PartialCompare(str, pattern.substr(1), prev_char, match_len);
}
}
if (GetIgnore_punct()) {
- if (ispunct(str.c_str()[0])) {
+ if (ispunct(Uint1(str[0]))) {
match_len++;
- return x_PartialCompare(str.substr(1), pattern, str.c_str()[0], match_len);
- } else if (ispunct(pattern.c_str()[0])) {
+ return x_PartialCompare(str.substr(1), pattern, str[0], match_len);
+ } else if (ispunct(Uint1(pattern[0]))) {
return x_PartialCompare(str, pattern.substr(1), prev_char, match_len);
}
}
- if (str.c_str()[0] == pattern.c_str()[0]) {
+ if (str[0] == pattern[0]) {
match_len++;
- return x_PartialCompare(str.substr(1), pattern.substr(1), str.c_str()[0], match_len);
+ return x_PartialCompare(str.substr(1), pattern.substr(1), str[0], match_len);
} else if ((!IsSetCase_sensitive() || !GetCase_sensitive()) &&
tolower(Uint1(str[0])) == tolower(Uint1(pattern[0]))) {
match_len++;
@@ -311,7 +311,7 @@ bool CString_constraint :: x_PartialCompare(const string& str, const string& pat
}
-bool CString_constraint :: x_AdvancedStringCompare(const string& str, const string& str_match, const char prev_char, unsigned int * ini_target_match_len) const
+bool CString_constraint :: x_AdvancedStringCompare(const string& str, const string& str_match, const char prev_char, size_t * ini_target_match_len) const
{
bool rval = false;
size_t match_len = 0;
@@ -331,7 +331,7 @@ bool CString_constraint :: x_AdvancedStringMatch(const string& str, const string
string
match_text = CanGetMatch_text() ? tmp_match : kEmptyStr;
- unsigned int match_len = 0;
+ size_t match_len = 0;
if (x_AdvancedStringCompare (str, match_text, 0, &match_len) &&
(GetMatch_location() != eString_location_equals || match_len == str.length())) {
@@ -343,10 +343,10 @@ bool CString_constraint :: x_AdvancedStringMatch(const string& str, const string
}
else {
size_t pos = 1;
- unsigned len = str.size();
+ size_t len = str.size();
while (!rval && pos < len) {
if (GetWhole_word()) {
- while (pos < len && isalpha (str[pos-1])) pos++;
+ while (pos < len && isalpha (Uint1(str[pos-1]))) pos++;
}
if (pos < len) {
if (x_AdvancedStringCompare (CTempString(str).substr(pos),
@@ -363,7 +363,7 @@ bool CString_constraint :: x_AdvancedStringMatch(const string& str, const string
return rval;
};
-bool CString_constraint :: x_GetSpanFromHyphenInString(const string& str, const size_t& hyphen, string& first, string& second) const
+bool CString_constraint :: x_GetSpanFromHyphenInString(const string& str, size_t hyphen, string& first, string& second) const
{
if (!hyphen) return false;
@@ -376,7 +376,7 @@ bool CString_constraint :: x_GetSpanFromHyphenInString(const string& str, const
cp = 0;
}
- unsigned len = hyphen - cp;
+ size_t len = hyphen - cp;
first = CTempString(str).substr(cp, len);
NStr::TruncateSpacesInPlace(first);
@@ -390,7 +390,7 @@ bool CString_constraint :: x_GetSpanFromHyphenInString(const string& str, const
}
len = cp - hyphen;
- if (!isspace (str[cp])) {
+ if (!isspace (Uint1(str[cp]))) {
len--;
}
second = CTempString(str).substr(hyphen+1, len);
@@ -400,8 +400,8 @@ bool CString_constraint :: x_GetSpanFromHyphenInString(const string& str, const
if (first.empty() || second.empty()) {
rval = false;
}
- else if (!isdigit (first[first.size() - 1])
- || !isdigit (second[second.size() - 1])) {
+ else if (!isdigit (Uint1(first[first.size() - 1]))
+ || !isdigit (Uint1(second[second.size() - 1]))) {
/* if this is a span, then neither end point can end with anything other than a number */
rval = false;
}
@@ -477,8 +477,8 @@ bool CString_constraint :: x_IsStringInSpan(const string& str, const string& fir
comp_str2 = CTempString(first).substr(0, prefix_len);
if (prefix_len <= first.size()
&& prefix_len <= second.size()
- && isdigit (first[prefix_len-1])
- && isdigit (second[prefix_len-1])
+ && isdigit (Uint1(first[prefix_len-1]))
+ && isdigit (Uint1(second[prefix_len-1]))
&& comp_str1 == comp_str2) {
new_first = CTempString(first).substr(prefix_len);
new_second = CTempString(second).substr(prefix_len);
@@ -671,7 +671,7 @@ bool CString_constraint::x_ReplaceContains(string& val, const string& replace) c
size_t offset = 0;
while (offset < val.length()) {
- unsigned int match_len = 0;
+ size_t match_len = 0;
if (x_AdvancedStringCompare(val.substr(offset), GetMatch_text(),
offset == 0 ? 0 : val.c_str()[offset - 1],
&match_len)) {
@@ -708,7 +708,7 @@ bool CString_constraint::ReplaceStringConstraintPortionInString(string& val, con
break;
case eString_location_starts:
{{
- unsigned int match_len = 0;
+ size_t match_len = 0;
if (x_AdvancedStringCompare(val, GetMatch_text(), 0, &match_len)) {
val = replace + val.substr(match_len);
rval = true;
@@ -722,7 +722,7 @@ bool CString_constraint::ReplaceStringConstraintPortionInString(string& val, con
{{
size_t offset = 0;
while (!rval && offset < val.length()) {
- unsigned int match_len = 0;
+ size_t match_len = 0;
if (x_AdvancedStringCompare(val.substr(offset),
GetMatch_text(),
(offset == 0 ? 0 : val.c_str()[offset - 1]),
diff --git a/c++/src/objects/macro/Suspect_rule_set.cpp b/c++/src/objects/macro/Suspect_rule_set.cpp
index cd87972..17f433e 100644
--- a/c++/src/objects/macro/Suspect_rule_set.cpp
+++ b/c++/src/objects/macro/Suspect_rule_set.cpp
@@ -1,4 +1,4 @@
-/* $Id: Suspect_rule_set.cpp 423489 2014-01-06 13:19:47Z bollin $
+/* $Id: Suspect_rule_set.cpp 467165 2015-05-11 13:55:19Z kachalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -69,15 +69,15 @@ CSuspect_rule_set::~CSuspect_rule_set(void)
}
-static void s_InitializeOrganelleProductRules(void)
+static void s_InitializeOrganelleProductRules(const string& name)
{
CFastMutexGuard GUARD(s_OrganelleProductRulesMutex);
if (s_OrganelleProductRulesInitialized) {
return;
}
s_OrganelleProductRules.Reset(new CSuspect_rule_set());
- string file = g_FindDataFile("organelle_products.prt");
-
+ string file = name.empty() ? g_FindDataFile("organelle_products.prt") : name;
+
if ( !file.empty() ) {
auto_ptr<CObjectIStream> in;
in.reset(CObjectIStream::Open(file, eSerial_AsnText));
@@ -93,20 +93,20 @@ static void s_InitializeOrganelleProductRules(void)
CNcbiIstrstream istr(all_rules.c_str());
istr >> MSerial_AsnText >> *s_OrganelleProductRules;
}
-
+
s_OrganelleProductRulesInitialized = true;
}
-static void s_InitializeProductRules(void)
+static void s_InitializeProductRules(const string& name)
{
CFastMutexGuard GUARD(s_ProductRulesMutex);
if (s_ProductRulesInitialized) {
return;
}
s_ProductRules.Reset(new CSuspect_rule_set());
- string file = g_FindDataFile("product_rules.prt");
-
+ string file = name.empty() ? g_FindDataFile("product_rules.prt") : name;
+
if ( !file.empty() ) {
auto_ptr<CObjectIStream> in;
in.reset(CObjectIStream::Open(file, eSerial_AsnText));
@@ -122,21 +122,21 @@ static void s_InitializeProductRules(void)
CNcbiIstrstream istr(all_rules.c_str());
istr >> MSerial_AsnText >> *s_ProductRules;
}
-
+
s_ProductRulesInitialized = true;
}
-CConstRef<CSuspect_rule_set> CSuspect_rule_set::GetOrganelleProductRules()
+CConstRef<CSuspect_rule_set> CSuspect_rule_set::GetOrganelleProductRules(const string& name)
{
- s_InitializeOrganelleProductRules();
+ s_InitializeOrganelleProductRules(name);
return CConstRef<CSuspect_rule_set>(s_OrganelleProductRules.GetPointer());
}
-CConstRef<CSuspect_rule_set> CSuspect_rule_set::GetProductRules()
+CConstRef<CSuspect_rule_set> CSuspect_rule_set::GetProductRules(const string& name)
{
- s_InitializeProductRules();
+ s_InitializeProductRules(name);
return CConstRef<CSuspect_rule_set>(s_ProductRules.GetPointer());
}
diff --git a/c++/src/objects/macro/Word_substitution.cpp b/c++/src/objects/macro/Word_substitution.cpp
index deb9dc5..2ac4f08 100644
--- a/c++/src/objects/macro/Word_substitution.cpp
+++ b/c++/src/objects/macro/Word_substitution.cpp
@@ -1,4 +1,4 @@
-/* $Id: Word_substitution.cpp 452500 2014-11-20 16:51:44Z ivanov $
+/* $Id: Word_substitution.cpp 452316 2014-11-18 19:13:59Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/macro/macro.asn b/c++/src/objects/macro/macro.asn
index ce9a95c..3ac1995 100755
--- a/c++/src/objects/macro/macro.asn
+++ b/c++/src/objects/macro/macro.asn
@@ -1,4 +1,4 @@
---$Revision: 455331 $
+--$Revision: 465458 $
--**********************************************************************
--
-- NCBI ASN.1 macro editing language specifications
@@ -87,7 +87,6 @@ Object-type-constraint ::= ENUMERATED {
feature (1) ,
descriptor (2) }
-
-- feature values --
Macro-feature-type ::= ENUMERATED {
@@ -193,8 +192,8 @@ Feat-qual-legal ::= ENUMERATED {
activity (2) ,
anticodon (3) ,
bound-moiety (4) ,
- chromosome (5),
- citation (6),
+ chromosome (5),
+ citation (6),
codon (7) ,
codon-start (8) ,
codons-recognized (9) ,
@@ -249,9 +248,9 @@ Feat-qual-legal ::= ENUMERATED {
translation (58) ,
transl-except (59) ,
transl-table (60) ,
- usedin (61),
- mobile-element-type (62),
- mobile-element-name (63),
+ usedin (61),
+ mobile-element-type (62),
+ mobile-element-name (63),
gene-comment (64) ,
satellite (65) ,
satellite-type (66) ,
@@ -296,7 +295,7 @@ Rna-feat-type ::= CHOICE {
tRNA NULL ,
rRNA NULL ,
ncRNA VisibleString ,
- tmRNA NULL,
+ tmRNA NULL,
miscRNA NULL }
Rna-field ::= ENUMERATED {
@@ -313,11 +312,10 @@ Rna-field ::= ENUMERATED {
gene-synonym (11) ,
gene-comment (12) ,
tag-peptide (13) }
-
Rna-qual ::= SEQUENCE {
type Rna-feat-type ,
- field Rna-field }
+ field Rna-field }
Rna-qual-pair ::= SEQUENCE {
type Rna-feat-type ,
@@ -393,7 +391,7 @@ Source-qual ::= ENUMERATED {
strain (66) ,
subclone (67) ,
subgroup (68) ,
- subsource-note (69),
+ subsource-note (69),
sub-species (70) ,
substrain (71) ,
subtype (72) ,
@@ -414,12 +412,12 @@ Source-qual ::= ENUMERATED {
culture-collection-SpecID (87) ,
bio-material-INST (88) ,
bio-material-COLL (89) ,
- bio-material-SpecID (90),
- all-notes (91),
- mating-type (92),
+ bio-material-SpecID (90),
+ all-notes (91),
+ mating-type (92),
linkage-group (93) ,
- haplogroup (94),
- all-quals (95),
+ haplogroup (94),
+ all-quals (95),
dbxref (96) ,
taxid (97) ,
all-primers (98) ,
@@ -467,18 +465,18 @@ Source-origin ::= ENUMERATED {
Source-qual-choice ::= CHOICE {
textqual Source-qual ,
- location Source-location,
+ location Source-location,
origin Source-origin ,
gcode INTEGER ,
mgcode INTEGER }
Source-qual-text-val ::= SEQUENCE {
srcqual Source-qual ,
- val VisibleString }
-
+ val VisibleString }
+
Source-qual-val-choice ::= CHOICE {
textqual Source-qual-text-val ,
- location Source-location,
+ location Source-location,
origin Source-origin ,
gcode INTEGER ,
mgcode INTEGER }
@@ -530,7 +528,7 @@ Molecule-type ::= ENUMERATED {
macro-other (11) }
Technique-type ::= ENUMERATED {
- unknown (0) ,
+ unknown (0) ,
standard (1) ,
est (2) ,
sts (3) ,
@@ -542,7 +540,7 @@ Technique-type ::= ENUMERATED {
seq-pept (9) ,
both (10) ,
seq-pept-overlap (11) ,
- seq-pept-homol (12) ,
+ seq-pept-homol (12) ,
concept-trans-a (13) ,
htgs-1 (14) ,
htgs-2 (15) ,
@@ -572,7 +570,7 @@ Molecule-class-type ::= ENUMERATED {
dna (1) ,
rna (2) ,
protein (3) ,
- nucleotide (4),
+ nucleotide (4),
other (5) }
Topology-type ::= ENUMERATED {
@@ -657,12 +655,12 @@ Publication-field ::= ENUMERATED {
affil-email (16) ,
affil-fax (17) ,
affil-phone (18) ,
- affil-zipcode (19),
- authors-initials (20),
- pmid (21),
+ affil-zipcode (19),
+ authors-initials (20),
+ pmid (21),
pub-class (22)
}
-
+
-- structured comment fields --
Structured-comment-field ::= CHOICE {
@@ -675,7 +673,7 @@ Structured-comment-field-pair ::= SEQUENCE {
from Structured-comment-field ,
to Structured-comment-field
}
-
+
-- misc fields --
-- these would not appear in pairs --
Misc-field ::= ENUMERATED {
@@ -698,7 +696,7 @@ DBLink-field-pair ::= SEQUENCE {
from DBLink-field-type ,
to DBLink-field-type
}
-
+
-- complex constraints --
Pub-type ::= ENUMERATED {
@@ -722,7 +720,7 @@ Pub-field-special-constraint-type ::= CHOICE {
Pub-field-special-constraint ::= SEQUENCE {
field Publication-field ,
constraint Pub-field-special-constraint-type }
-
+
Publication-constraint ::= SEQUENCE {
type Pub-type ,
field Pub-field-constraint OPTIONAL ,
@@ -870,7 +868,7 @@ Field-pair-type ::= CHOICE {
cds-gene-prot CDSGeneProt-field-pair ,
molinfo-field Molinfo-field-pair ,
struc-comment-field Structured-comment-field-pair ,
- dblink DBLink-field-pair}
+ dblink DBLink-field-pair}
ExistingTextOption ::= ENUMERATED {
replace-old (1) ,
@@ -887,7 +885,6 @@ ExistingTextOption ::= ENUMERATED {
leave-old (12) ,
add-qual (13) }
-
Apply-action ::= SEQUENCE {
field Field-type ,
value VisibleString ,
@@ -1007,7 +1004,6 @@ Parse-action ::= SEQUENCE {
transform Text-transform-set OPTIONAL ,
existing-text ExistingTextOption }
-
Location-interval ::= SEQUENCE {
from INTEGER ,
to INTEGER }
@@ -1021,7 +1017,7 @@ Sequence-list ::= SET OF VisibleString
Sequence-list-choice ::= CHOICE {
list Sequence-list ,
all NULL }
-
+
Apply-feature-action ::= SEQUENCE {
type Macro-feature-type ,
partial5 BOOLEAN DEFAULT FALSE ,
@@ -1033,7 +1029,7 @@ Apply-feature-action ::= SEQUENCE {
add-mrna BOOLEAN DEFAULT FALSE ,
apply-to-parts BOOLEAN DEFAULT FALSE ,
only-seg-num INTEGER DEFAULT -1 ,
- fields Feat-qual-legal-set OPTIONAL,
+ fields Feat-qual-legal-set OPTIONAL,
src-fields Source-qual-val-set OPTIONAL }
Remove-feature-action ::= SEQUENCE {
@@ -1046,7 +1042,7 @@ Convert-from-CDS-options ::= SEQUENCE {
remove-gene BOOLEAN ,
remove-transcript-id BOOLEAN }
-Convert-feature-src-options ::= CHOICE {
+Convert-feature-src-options ::= CHOICE {
cds Convert-from-CDS-options }
Bond-type ::= ENUMERATED {
@@ -1056,7 +1052,6 @@ Bond-type ::= ENUMERATED {
thioether (4) ,
other (5) }
-
Site-type ::= ENUMERATED {
active (1) ,
binding (2) ,
@@ -1088,7 +1083,7 @@ Site-type ::= ENUMERATED {
-- other choice is to create protein sequences, skipping bad --
Region-type ::= SEQUENCE {
- create-nucleotide BOOLEAN }
+ create-nucleotide BOOLEAN }
Convert-feature-dst-options ::= CHOICE {
bond Bond-type ,
@@ -1097,15 +1092,13 @@ Convert-feature-dst-options ::= CHOICE {
ncrna-class VisibleString ,
remove-original BOOLEAN }
-
Convert-feature-action ::= SEQUENCE {
type-from Macro-feature-type ,
type-to Macro-feature-type ,
src-options Convert-feature-src-options OPTIONAL ,
dst-options Convert-feature-dst-options OPTIONAL ,
leave-original BOOLEAN ,
- src-feat-constraint Constraint-choice-set OPTIONAL }
-
+ src-feat-constraint Constraint-choice-set OPTIONAL }
Feature-location-strand-from ::= ENUMERATED {
any (0) ,
@@ -1123,7 +1116,7 @@ Feature-location-strand-to ::= ENUMERATED {
Edit-location-strand ::= SEQUENCE {
strand-from Feature-location-strand-from ,
- strand-to Feature-location-strand-to }
+ strand-to Feature-location-strand-to }
Partial-5-set-constraint ::= ENUMERATED {
all (0) ,
@@ -1165,7 +1158,7 @@ Partial-both-set-action ::= SEQUENCE {
Partial-both-clear-constraint ::= ENUMERATED {
all (0) ,
not-at-end (1) }
-
+
Convert-location-type ::= ENUMERATED {
join (1) ,
order (2) ,
@@ -1175,7 +1168,7 @@ Extend-to-feature ::= SEQUENCE {
type Macro-feature-type ,
include-feat BOOLEAN ,
distance Quantity-constraint OPTIONAL }
-
+
Location-edit-type ::= CHOICE {
strand Edit-location-strand ,
set-5-partial Partial-5-set-action ,
@@ -1218,14 +1211,14 @@ Descriptor-type ::= ENUMERATED {
Remove-descriptor-action ::= SEQUENCE {
type Descriptor-type ,
- constraint Constraint-choice-set OPTIONAL }
+ constraint Constraint-choice-set OPTIONAL }
Autodef-list-type ::= ENUMERATED {
feature-list (1) ,
complete-sequence (2) ,
complete-genome (3) ,
sequence (4) }
-
+
Autodef-misc-feat-parse-rule ::= ENUMERATED {
use-comment-before-first-semicolon (1) ,
look-for-noncoding-products (2) }
@@ -1252,7 +1245,7 @@ Sort-fields-action ::= SEQUENCE {
field Field-type ,
order Sort-order ,
constraint Constraint-choice-set OPTIONAL }
-
+
Fix-author-caps ::= SEQUENCE {
last-name-only BOOLEAN }
@@ -1290,17 +1283,17 @@ Gene-xref-type ::= SEQUENCE {
feature Macro-feature-type ,
suppression Gene-xref-suppression-type ,
necessary Gene-xref-necessary-type }
-
+
Xref-type ::= CHOICE {
gene Gene-xref-type }
Remove-xrefs-action ::= SEQUENCE {
xref-type Xref-type ,
- constraint Constraint-choice-set OPTIONAL }
+ constraint Constraint-choice-set OPTIONAL }
Make-gene-xref-action ::= SEQUENCE {
feature Macro-feature-type ,
- constraint Constraint-choice-set OPTIONAL }
+ constraint Constraint-choice-set OPTIONAL }
Author-fix-type ::= ENUMERATED {
truncate-middle-initials (1) ,
@@ -1309,7 +1302,7 @@ Author-fix-type ::= ENUMERATED {
Author-fix-action ::= SEQUENCE {
fix-type Author-fix-type ,
- constraint Constraint-choice-set OPTIONAL }
+ constraint Constraint-choice-set OPTIONAL }
Update-sequences-action ::= SEQUENCE {
filename VisibleString ,
@@ -1323,7 +1316,7 @@ Create-TSA-ids-src ::= CHOICE {
Create-TSA-ids-action ::= SEQUENCE {
src Create-TSA-ids-src ,
suffix VisibleString OPTIONAL ,
- id-text-portion Text-portion OPTIONAL }
+ id-text-portion Text-portion OPTIONAL }
Autofix-action ::= SEQUENCE {
test-name VisibleString }
@@ -1337,7 +1330,7 @@ Fix-sets-action ::= CHOICE {
Table-match-type ::= CHOICE {
feature-id NULL ,
gene-locus-tag NULL ,
- protein-id NULL,
+ protein-id NULL,
dbxref NULL ,
nuc-id NULL ,
src-qual Source-qual-choice ,
@@ -1351,7 +1344,6 @@ Table-match ::= SEQUENCE {
match-location String-location DEFAULT equals
}
-
Apply-table-extra-data ::= CHOICE {
table NULL }
@@ -1366,7 +1358,7 @@ Apply-table-action ::= SEQUENCE {
Add-file-action ::= SEQUENCE {
filename VisibleString ,
in-memory-table Apply-table-extra-data OPTIONAL
-}
+}
Add-descriptor-list-action ::= SEQUENCE {
descriptor-list Add-file-action ,
@@ -1383,12 +1375,10 @@ Update-replaced-ec-numbers-action ::= SEQUENCE {
delete-multiple-replacement BOOLEAN
}
-
Retranslate-cds-action ::= SEQUENCE {
obey-stop-codon BOOLEAN
}
-
Truncated-ends-partial-type ::= ENUMERATED {
always (1) ,
unless-pseudo (2) ,
@@ -1404,7 +1394,6 @@ Adjust-features-for-gaps-action ::= SEQUENCE {
even-when-gaps-are-in-introns BOOLEAN
}
-
Macro-action-choice ::= CHOICE {
aecr AECR-action ,
parse Parse-action ,
@@ -1457,10 +1446,8 @@ Macro-action-choice ::= CHOICE {
join-short-trnas NULL ,
adjust-features-for-gaps Adjust-features-for-gaps-action }
-
Macro-action-list ::= SET OF Macro-action-choice
-
Search-func ::= CHOICE {
string-constraint String-constraint ,
contains-plural NULL ,
@@ -1474,7 +1461,7 @@ Search-func ::= CHOICE {
has-term VisibleString }
Simple-replace ::= SEQUENCE {
- replace VisibleString OPTIONAL,
+ replace VisibleString OPTIONAL,
whole-string BOOLEAN DEFAULT FALSE ,
weasel-to-putative BOOLEAN DEFAULT FALSE }
@@ -1491,17 +1478,17 @@ Fix-type ::= ENUMERATED {
typo (1) ,
putative-typo (2) ,
quickfix (3) ,
- no-organelle-for-prokaryote (4),
- might-be-nonfunctional (5),
- database (6),
- remove-organism-name (7),
- inappropriate-symbol (8),
- evolutionary-relationship (9),
- use-protein (10),
- hypothetical (11),
- british (12),
- description (13),
- gene (14) }
+ no-organelle-for-prokaryote (4),
+ might-be-nonfunctional (5),
+ database (6),
+ remove-organism-name (7),
+ inappropriate-symbol (8),
+ evolutionary-relationship (9),
+ use-protein (10),
+ hypothetical (11),
+ british (12),
+ description (13),
+ gene (14) }
Suspect-rule ::= SEQUENCE {
find Search-func ,
@@ -1509,10 +1496,10 @@ Suspect-rule ::= SEQUENCE {
feat-constraint Constraint-choice-set OPTIONAL ,
rule-type Fix-type DEFAULT none ,
replace Replace-rule OPTIONAL ,
- description VisibleString OPTIONAL }
+ description VisibleString OPTIONAL ,
+ fatal BOOLEAN DEFAULT FALSE }
Suspect-rule-set ::= SET OF Suspect-rule
-
END
diff --git a/c++/src/objects/macro/product_rules.prt b/c++/src/objects/macro/product_rules.prt
index 5fda90a..277d46f 100644
--- a/c++/src/objects/macro/product_rules.prt
+++ b/c++/src/objects/macro/product_rules.prt
@@ -8154,7 +8154,8 @@ Suspect-rule-set ::= {
is-all-lower FALSE ,
is-all-punct FALSE ,
ignore-weasel TRUE } } ,
- rule-type might-be-nonfunctional } ,
+ rule-type might-be-nonfunctional,
+ fatal TRUE } ,
{
find
string-constraint {
@@ -8197,7 +8198,8 @@ Suspect-rule-set ::= {
is-all-lower FALSE ,
is-all-punct FALSE ,
ignore-weasel FALSE } ,
- rule-type might-be-nonfunctional } ,
+ rule-type might-be-nonfunctional,
+ fatal TRUE } ,
{
find
string-constraint {
@@ -8257,7 +8259,8 @@ Suspect-rule-set ::= {
is-all-lower FALSE ,
is-all-punct FALSE ,
ignore-weasel FALSE } ,
- rule-type might-be-nonfunctional } ,
+ rule-type might-be-nonfunctional,
+ fatal TRUE } ,
{
find
string-constraint {
diff --git a/c++/src/objects/medline/Makefile.medline.lib b/c++/src/objects/medline/Makefile.medline.lib
index 9e0e7f9..cfac0b8 100644
--- a/c++/src/objects/medline/Makefile.medline.lib
+++ b/c++/src/objects/medline/Makefile.medline.lib
@@ -1,6 +1,7 @@
LIB = medline
SRC = medline__ medline___
+DLL_LIB = biblio general
USES_LIBRARIES = \
biblio
diff --git a/c++/src/objects/mla/Makefile.mlacli.lib b/c++/src/objects/mla/Makefile.mlacli.lib
index 0112d71..eefa520 100644
--- a/c++/src/objects/mla/Makefile.mlacli.lib
+++ b/c++/src/objects/mla/Makefile.mlacli.lib
@@ -3,6 +3,7 @@ ASN_DEP = mla
LIB = mlacli
SRC = mla_client mla_client_
+DLL_LIB = xconnect
USES_LIBRARIES = \
mla xconnect
diff --git a/c++/src/objects/nt_sources.sh b/c++/src/objects/nt_sources.sh
index 699d53f..c83cede 100644
--- a/c++/src/objects/nt_sources.sh
+++ b/c++/src/objects/nt_sources.sh
@@ -1,5 +1,5 @@
#! /bin/sh
-# $Id: nt_sources.sh 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: nt_sources.sh 485953 2015-11-30 17:53:34Z blastadm $
#
# Script to update ASN.1 objects' sources on Windows-NT
# (using BASH and DATATOOL)
diff --git a/c++/src/objects/pub/Makefile.pub.lib b/c++/src/objects/pub/Makefile.pub.lib
index a285e41..e1de649 100644
--- a/c++/src/objects/pub/Makefile.pub.lib
+++ b/c++/src/objects/pub/Makefile.pub.lib
@@ -1,6 +1,7 @@
LIB = pub
SRC = pub__ pub___
+DLL_LIB = medline biblio
USES_LIBRARIES = \
medline
diff --git a/c++/src/objects/pub/Pub.cpp b/c++/src/objects/pub/Pub.cpp
index e5cacf0..2ea04f0 100644
--- a/c++/src/objects/pub/Pub.cpp
+++ b/c++/src/objects/pub/Pub.cpp
@@ -1,4 +1,4 @@
-/* $Id: Pub.cpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Pub.cpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/pub/Pub_equiv.cpp b/c++/src/objects/pub/Pub_equiv.cpp
index 66a5248..7547479 100644
--- a/c++/src/objects/pub/Pub_equiv.cpp
+++ b/c++/src/objects/pub/Pub_equiv.cpp
@@ -1,4 +1,4 @@
-/* $Id: Pub_equiv.cpp 452741 2014-11-24 17:50:42Z ivanov $
+/* $Id: Pub_equiv.cpp 452468 2014-11-20 13:44:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/scoremat/Makefile.scoremat.lib b/c++/src/objects/scoremat/Makefile.scoremat.lib
index f965fc1..a83215d 100644
--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
@@ -1,6 +1,7 @@
LIB = scoremat
SRC = scoremat__ scoremat___
+DLL_LIB = seqset
USES_LIBRARIES = \
seqset
diff --git a/c++/src/objects/seq/Bioseq.cpp b/c++/src/objects/seq/Bioseq.cpp
index 7dc32d7..c3eb538 100644
--- a/c++/src/objects/seq/Bioseq.cpp
+++ b/c++/src/objects/seq/Bioseq.cpp
@@ -1,4 +1,4 @@
-/* $Id: Bioseq.cpp 457722 2015-01-27 17:54:29Z ivanov $
+/* $Id: Bioseq.cpp 474382 2015-07-28 16:24:11Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -262,8 +262,10 @@ const CSeq_id* CBioseq::GetFirstId() const
static int s_BestNonLocalRank(const CRef<CSeq_id>& id)
{
- if (id.Empty() || id->IsLocal()) {
+ if (id.Empty()) {
return kMax_Int;
+ } else if (id->IsLocal()) {
+ return kMax_Int - 1;
} else {
return id->BestRankScore();
}
@@ -272,7 +274,9 @@ static int s_BestNonLocalRank(const CRef<CSeq_id>& id)
const CSeq_id* CBioseq::GetNonLocalId() const
{
CRef<CSeq_id> id = FindBestChoice(GetId(), &s_BestNonLocalRank);
- if (id.NotEmpty() && !id->IsLocal()) {
+ if (id.Empty()) {
+ return NULL; // No way to verify potential IDs found elsewhere
+ } else if ( !id->IsLocal() ) {
return &*id;
}
@@ -290,12 +294,11 @@ const CSeq_id* CBioseq::GetNonLocalId() const
continue;
}
- // XXX - check that local ID matches id?
const CSeq_id& id1 = (*it)->GetSeq_id(0);
const CSeq_id& id2 = (*it)->GetSeq_id(1);
- if (id1.IsLocal() && !id2.IsLocal()) {
+ if (id1.IsLocal() && id1.Match(*id) && !id2.IsLocal()) {
return &id2;
- } else if (id2.IsLocal() && !id1.IsLocal()) {
+ } else if (id2.IsLocal() && id2.Match(*id) && !id1.IsLocal()) {
return &id1;
}
}
diff --git a/c++/src/objects/seq/Makefile.seq.lib b/c++/src/objects/seq/Makefile.seq.lib
index 016bb92..444f61d 100644
--- a/c++/src/objects/seq/Makefile.seq.lib
+++ b/c++/src/objects/seq/Makefile.seq.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.seq.lib 427424 2014-02-20 13:38:50Z gouriano $
+# $Id: Makefile.seq.lib 468535 2015-05-26 13:23:32Z ucko $
ASN = seq seqalign seqblock seqfeat seqloc seqres seqtable
@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
seq_loc_from_string seq_loc_reverse_complementer
+DLL_LIB = seqcode pub general xser sequtil
+
WATCHERS = vasilche grichenk
diff --git a/c++/src/objects/seq/Makefile.seq.lib.unix b/c++/src/objects/seq/Makefile.seq.lib.unix
index 2b157c0..6080101 100644
--- a/c++/src/objects/seq/Makefile.seq.lib.unix
+++ b/c++/src/objects/seq/Makefile.seq.lib.unix
@@ -1,4 +1,4 @@
-# $Id: Makefile.seq.lib.unix 464346 2015-04-08 18:17:00Z ivanov $
+# $Id: Makefile.seq.lib.unix 454246 2014-12-11 20:46:10Z ucko $
ifeq "$(COMPILER)-$(DEBUG_SFX)$(DLL)" "icc-Release"
seqfeat__.o: seqfeat__.cpp
$(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL) -fno-builtin-strspn $< -o $@ \
diff --git a/c++/src/objects/seq/MolInfo.cpp b/c++/src/objects/seq/MolInfo.cpp
index 3c9ff0c..5b84b85 100644
--- a/c++/src/objects/seq/MolInfo.cpp
+++ b/c++/src/objects/seq/MolInfo.cpp
@@ -1,4 +1,4 @@
-/* $Id: MolInfo.cpp 447995 2014-10-01 19:21:32Z vasilche $
+/* $Id: MolInfo.cpp 444280 2014-08-22 16:24:25Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seq/Seq_descr.cpp b/c++/src/objects/seq/Seq_descr.cpp
index 75e6998..f56ea8c 100644
--- a/c++/src/objects/seq/Seq_descr.cpp
+++ b/c++/src/objects/seq/Seq_descr.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_descr.cpp 450030 2014-10-22 17:53:43Z ivanov $
+/* $Id: Seq_descr.cpp 448516 2014-10-07 14:40:49Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seq/Seq_gap.cpp b/c++/src/objects/seq/Seq_gap.cpp
index 6d42917..3a71be1 100644
--- a/c++/src/objects/seq/Seq_gap.cpp
+++ b/c++/src/objects/seq/Seq_gap.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_gap.cpp 446221 2014-09-12 15:25:23Z ivanov $
+/* $Id: Seq_gap.cpp 442805 2014-08-07 13:46:05Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seq/seq_align_mapper_base.cpp b/c++/src/objects/seq/seq_align_mapper_base.cpp
index 8e04f93..b5568be 100644
--- a/c++/src/objects/seq/seq_align_mapper_base.cpp
+++ b/c++/src/objects/seq/seq_align_mapper_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_align_mapper_base.cpp 467971 2015-05-19 15:57:45Z ivanov $
+/* $Id: seq_align_mapper_base.cpp 482403 2015-10-22 18:03:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -705,6 +705,7 @@ void CSeq_align_Mapper_Base::InitExon(const CSpliced_seg& spliced,
}
if ( !ex_prod_id ) {
ERR_POST_X(15, Warning << "Missing product id in spliced-seg");
+ return;
}
m_HaveStrands = m_HaveStrands ||
exon.IsSetGenomic_strand() || exon.IsSetProduct_strand();
@@ -1055,7 +1056,8 @@ CSeq_align_Mapper_Base::x_ConvertSegment(TSegments::iterator& seg_it,
for (size_t map_idx = 0; map_idx < mappings.size(); ++map_idx) {
CRef<CMappingRange> mapping(mappings[map_idx]);
if (!mapping->CanMap(start, stop,
- aln_row.m_IsSetStrand && m_LocMapper.m_CheckStrand,
+ aln_row.m_IsSetStrand &&
+ m_LocMapper.x_IsSetMiscFlag(CSeq_loc_Mapper_Base::fCheckStrand),
aln_row.m_Strand)) {
// Mapping does not apply to this segment/row, leave it unchanged.
continue;
@@ -1080,6 +1082,11 @@ CSeq_align_Mapper_Base::x_ConvertSegment(TSegments::iterator& seg_it,
0 : mapping->m_Src_from - start;
TSeqPos dr = mapping->m_Src_to >= stop ?
0 : stop - mapping->m_Src_to;
+ if ((dl || dr) &&
+ m_LocMapper.x_IsSetMiscFlag(CSeq_loc_Mapper_Base::fErrorOnPartial)) {
+ NCBI_THROW(CAnnotMapperException, eCanNotMap,
+ "Alignment segment can not be mapped without trimming.");
+ }
if (dl > 0) {
// Add segment for the skipped range on the left.
// Copy the original segment.
@@ -1386,6 +1393,55 @@ void CSeq_align_Mapper_Base::x_GetDstDenseg(CRef<CSeq_align>& dst) const
void CSeq_align_Mapper_Base::x_GetDstStd(CRef<CSeq_align>& dst) const
{
TStd& std_segs = dst->SetSegs().SetStd();
+ int non_gap_count = 0;
+
+ // Check if there are exactly two rows of different types (nuc-to-prot align).
+ // If true, collect frames from the protein row and use them later to adjust
+ // genomic locations. See CXX-5478
+ bool set_frames = true;
+ int p_row = -1;
+ vector< pair<TSeqPos, TSeqPos> > frames;
+ frames.reserve(m_Segs.size());
+ ITERATE(TSegments, seg_it, m_Segs) {
+ if (seg_it->m_Rows.size() != 2) {
+ set_frames = false;
+ break;
+ }
+ CSeq_loc_Mapper_Base::ESeqType r0_type =
+ m_LocMapper.GetSeqTypeById(seg_it->m_Rows[0].m_Id);
+ CSeq_loc_Mapper_Base::ESeqType r1_type =
+ m_LocMapper.GetSeqTypeById(seg_it->m_Rows[1].m_Id);
+ if (r0_type == r1_type) {
+ set_frames = false;
+ break;
+ }
+ if (p_row == -1) {
+ if (r0_type == CSeq_loc_Mapper_Base::eSeq_prot) {
+ p_row = 0;
+ }
+ else if (r1_type == CSeq_loc_Mapper_Base::eSeq_prot) {
+ p_row = 1;
+ }
+ else {
+ set_frames = false;
+ break;
+ }
+ }
+ _ASSERT(p_row != -1);
+ TSeqPos start = seg_it->m_Rows[p_row].m_Start;
+ TSeqPos start_frame = 0;
+ TSeqPos stop_frame = 0;
+ if (start != kInvalidSeqPos) {
+ start_frame = start % 3; // 1 or 2 bases from codon start.
+ stop_frame = (start + seg_it->m_Len) % 3;
+ if ( stop_frame ) {
+ stop_frame = 3 - stop_frame; // 1 or 2 bases from codon stop.
+ }
+ }
+ frames.push_back(pair<TSeqPos, TSeqPos>(start_frame, stop_frame));
+ }
+
+ size_t seg_n = 0;
ITERATE(TSegments, seg_it, m_Segs) {
// Create new std-seg for each segment.
CRef<CStd_seg> std_seg(new CStd_seg);
@@ -1396,6 +1452,8 @@ void CSeq_align_Mapper_Base::x_GetDstStd(CRef<CSeq_align>& dst) const
seg_it->m_Scores, std_seg->SetScores());
}
// Add rows.
+ non_gap_count = 0;
+ size_t row_n = 0;
ITERATE(SAlignment_Segment::TRows, row, seg_it->m_Rows) {
// Check sequence type, set width to 3 for prots.
int width = (m_LocMapper.GetSeqTypeById(row->m_Id) ==
@@ -1415,18 +1473,93 @@ void CSeq_align_Mapper_Base::x_GetDstStd(CRef<CSeq_align>& dst) const
// Adjust coordinates according to the sequence type.
TSeqPos start = row->m_Start/width;
TSeqPos stop = (row->m_Start + seg_it->m_Len)/width;
+
+ // For pairwise mixed-type alignments indicate frames using 'alt' fuzz.
+ // See CXX-5478
+
+ if ( set_frames ) {
+ const SAlignment_Segment::SAlignment_Row& g_row =
+ seg_it->m_Rows[1 - p_row];
+ TSeqPos start_frame = frames[seg_n].first;
+ TSeqPos stop_frame = frames[seg_n].second;
+ if ( IsReverse(g_row.m_Strand) ) {
+ swap(start_frame, stop_frame);
+ }
+ if ( row_n == p_row ) {
+ // Trim incomplete codon if genomic start can not be
+ // adjusted properly.
+ TSeqPos g_start = g_row.m_Start;
+ if (g_start < start_frame) {
+ if ( IsReverse(g_row.m_Strand) ) {
+ stop--;
+ }
+ else {
+ start++;
+ }
+ // Tricky case: protein row contains just one AA,
+ // which is partial. Start must be adjusted to
+ // remove the incomplete codon, but this makes
+ // the whole segment empty. So, we need to drop
+ // the genomic row too.
+ if (start > stop) {
+ if (p_row == 1) {
+ // Genomic row has been already saved.
+ std_seg->SetLoc().pop_back();
+ }
+ else {
+ // Skip genomic row
+ ++row;
+ }
+ continue;
+ }
+ }
+ }
+ else {
+ // Adjust start and stop to the start/stop of complete
+ // codon, set fuzzes to indicate actual start/stop.
+ if ( start_frame ) {
+ if (start >= start_frame) {
+ // Add 1 or 2 bases to match complete codon.
+ loc->SetInt().SetFuzz_from().SetAlt().push_back(start);
+ start -= start_frame;
+ }
+ else {
+ // Skip the first incomplete codon.
+ start += 3 - start_frame;
+ }
+ }
+ if ( stop_frame ) {
+ loc->SetInt().SetFuzz_to().SetAlt().push_back(stop - 1);
+ stop += stop_frame;
+ }
+ }
+ }
+
loc->SetInt().SetFrom(start);
// len may be 0 after dividing by width, check it before
// decrementing stop.
- loc->SetInt().SetTo(stop ? stop - 1 : 0);
+ loc->SetInt().SetTo(stop > start ? stop - 1 : stop);
if (row->m_IsSetStrand) {
loc->SetInt().SetStrand(row->m_Strand);
}
+ non_gap_count++;
}
std_seg->SetLoc().push_back(loc);
+ row_n++;
+ }
+ seg_n++;
+ // Ignore starting segments with no actually aligned sequences.
+ if (seg_it == m_Segs.begin() && non_gap_count < 2) {
+ continue;
}
+ // Ignore empty segments
+ if ( std_seg->GetLoc().empty() ) continue;
std_segs.push_back(std_seg);
}
+ if (non_gap_count < 2 && !std_segs.empty()) {
+ // Remove the last segment if there are no aligned sequences in it.
+ std_segs.pop_back();
+ }
}
@@ -1596,6 +1729,8 @@ x_GetDstExon(CSpliced_seg& spliced,
bool pstrand_set = false;
bool aln_protein = false;
size_t mapped_gaps = 0;
+ int non_gap_gen_start = 0;
+ int non_gap_prod_start = 0;
int non_gap_gen_end = 0;
int non_gap_prod_end = 0;
@@ -1695,6 +1830,9 @@ x_GetDstExon(CSpliced_seg& spliced,
}
CSpliced_exon_chunk::E_Choice orig_ptype = seg->m_PartType;
+ if (orig_ptype == CSpliced_exon_chunk::e_not_set) {
+ orig_ptype = CSpliced_exon_chunk::e_Match;
+ }
CSpliced_exon_chunk::E_Choice ptype = orig_ptype;
// Check strands consistency
@@ -1869,8 +2007,12 @@ x_GetDstExon(CSpliced_seg& spliced,
}
else {
mapped_gaps = 0;
- non_gap_prod_end = prod_end;
- non_gap_gen_end = gen_end;
+ if (!is_gap) {
+ non_gap_prod_start = prod_start;
+ non_gap_gen_start = gen_start;
+ non_gap_prod_end = prod_end;
+ non_gap_gen_end = gen_end;
+ }
}
}
else {
@@ -1900,6 +2042,8 @@ x_GetDstExon(CSpliced_seg& spliced,
for (; mapped_gaps > 0; mapped_gaps--) {
parts.pop_back();
}
+ gen_start = non_gap_gen_start;
+ prod_start = non_gap_prod_start;
gen_end = non_gap_gen_end;
prod_end = non_gap_prod_end;
}
@@ -1926,21 +2070,25 @@ x_GetDstExon(CSpliced_seg& spliced,
}
if ( IsReverse(gen_strand) ) {
- if ( !partial_right && m_OrigExon->IsSetAcceptor_before_exon() ) {
+ if ( !partial_right && m_OrigExon &&
+ m_OrigExon->IsSetAcceptor_before_exon() ) {
exon->SetAcceptor_before_exon().Assign(
m_OrigExon->GetAcceptor_before_exon());
}
- if ( !partial_left && m_OrigExon->IsSetDonor_after_exon() ) {
+ if ( !partial_left && m_OrigExon &&
+ m_OrigExon->IsSetDonor_after_exon() ) {
exon->SetDonor_after_exon().Assign(
m_OrigExon->GetDonor_after_exon());
}
}
else {
- if ( !partial_left && m_OrigExon->IsSetAcceptor_before_exon() ) {
+ if ( !partial_left && m_OrigExon &&
+ m_OrigExon->IsSetAcceptor_before_exon() ) {
exon->SetAcceptor_before_exon().Assign(
m_OrigExon->GetAcceptor_before_exon());
}
- if ( !partial_right && m_OrigExon->IsSetDonor_after_exon() ) {
+ if ( !partial_right && m_OrigExon &&
+ m_OrigExon->IsSetDonor_after_exon() ) {
exon->SetDonor_after_exon().Assign(
m_OrigExon->GetDonor_after_exon());
}
@@ -1983,7 +2131,7 @@ x_GetDstExon(CSpliced_seg& spliced,
m_SegsScores, exon->SetScores().Set());
}
// Copy ext from the original exon.
- if ( m_OrigExon->IsSetExt() ) {
+ if ( m_OrigExon && m_OrigExon->IsSetExt() ) {
CloneContainer<CUser_object, CSpliced_exon::TExt, CSpliced_exon::TExt>(
m_OrigExon->GetExt(), exon->SetExt());
}
@@ -1993,6 +2141,79 @@ x_GetDstExon(CSpliced_seg& spliced,
}
+void CSeq_align_Mapper_Base::x_GetDstSplicedSubAlign(
+ CSpliced_seg& spliced,
+ const CSeq_align_Mapper_Base& sub_align,
+ bool& last_exon_partial,
+ CSeq_id_Handle& gen_id,
+ CSeq_id_Handle& last_gen_id,
+ bool& single_gen_id,
+ ENa_strand& gen_strand,
+ bool& single_gen_str,
+ CSeq_id_Handle& prod_id,
+ CSeq_id_Handle& last_prod_id,
+ bool& single_prod_id,
+ ENa_strand& prod_strand,
+ bool& single_prod_str,
+ bool& partial) const
+{
+ TSegments::const_iterator seg = sub_align.m_Segs.begin();
+ // Convert the current sub-mapper to an exon.
+ // In some cases the exon can be split (e.g. if a gap is found in
+ // both rows). In this case 'seg' iterator will not be set to
+ // m_Segs.end() by x_GetDstExon and the next iteration will be
+ // performed.
+ while (seg != sub_align.m_Segs.end()) {
+ CSeq_id_Handle ex_gen_id;
+ CSeq_id_Handle ex_prod_id;
+ ENa_strand ex_gen_strand = eNa_strand_unknown;
+ ENa_strand ex_prod_strand = eNa_strand_unknown;
+ bool added_exon = sub_align.x_GetDstExon(spliced, seg, ex_gen_id, ex_prod_id,
+ ex_gen_strand, ex_prod_strand, last_exon_partial,
+ last_gen_id, last_prod_id);
+ partial = partial || last_exon_partial;
+ if (added_exon) {
+ // Check if all exons have the same ids in genomic and product
+ // rows.
+ if (ex_gen_id) {
+ last_gen_id = ex_gen_id;
+ if ( !gen_id ) {
+ gen_id = ex_gen_id;
+ }
+ else {
+ single_gen_id &= gen_id == ex_gen_id;
+ }
+ }
+ if (ex_prod_id) {
+ if ( !prod_id ) {
+ prod_id = ex_prod_id;
+ }
+ else {
+ single_prod_id &= prod_id == ex_prod_id;
+ }
+ }
+ // Check if all exons have the same strands.
+ if (ex_gen_strand != eNa_strand_unknown) {
+ single_gen_str &= (gen_strand == eNa_strand_unknown) ||
+ (gen_strand == ex_gen_strand);
+ gen_strand = ex_gen_strand;
+ }
+ else {
+ single_gen_str &= gen_strand == eNa_strand_unknown;
+ }
+ if (ex_prod_strand != eNa_strand_unknown) {
+ single_prod_str &= (prod_strand == eNa_strand_unknown) ||
+ (prod_strand == ex_prod_strand);
+ prod_strand = ex_prod_strand;
+ }
+ else {
+ single_prod_str &= prod_strand == eNa_strand_unknown;
+ }
+ }
+ }
+}
+
+
// Create spliced-seg.
void CSeq_align_Mapper_Base::x_GetDstSpliced(CRef<CSeq_align>& dst) const
{
@@ -2010,64 +2231,36 @@ void CSeq_align_Mapper_Base::x_GetDstSpliced(CRef<CSeq_align>& dst) const
bool partial = false;
bool last_exon_partial = false;
- ITERATE(TSubAligns, it, m_SubAligns) {
- TSegments::const_iterator seg = (*it)->m_Segs.begin();
- // Convert the current sub-mapper to an exon.
- // In some cases the exon can be split (e.g. if a gap is found in
- // both rows). In this case 'seg' iterator will not be set to
- // m_Segs.end() by x_GetDstExon and the next iteration will be
- // performed.
- while (seg != (*it)->m_Segs.end()) {
- CSeq_id_Handle ex_gen_id;
- CSeq_id_Handle ex_prod_id;
- ENa_strand ex_gen_strand = eNa_strand_unknown;
- ENa_strand ex_prod_strand = eNa_strand_unknown;
- bool added_exon = (*it)->x_GetDstExon(spliced, seg, ex_gen_id, ex_prod_id,
- ex_gen_strand, ex_prod_strand, last_exon_partial,
- last_gen_id, last_prod_id);
- partial = partial || last_exon_partial;
- if (added_exon) {
- // Check if all exons have the same ids in genomic and product
- // rows.
- if (ex_gen_id) {
- last_gen_id = ex_gen_id;
- if ( !gen_id ) {
- gen_id = ex_gen_id;
- }
- else {
- single_gen_id &= gen_id == ex_gen_id;
- }
- }
- if (ex_prod_id) {
- if ( !prod_id ) {
- prod_id = ex_prod_id;
- }
- else {
- single_prod_id &= prod_id == ex_prod_id;
- }
- }
- // Check if all exons have the same strands.
- if (ex_gen_strand != eNa_strand_unknown) {
- single_gen_str &= (gen_strand == eNa_strand_unknown) ||
- (gen_strand == ex_gen_strand);
- gen_strand = ex_gen_strand;
- }
- else {
- single_gen_str &= gen_strand == eNa_strand_unknown;
- }
- if (ex_prod_strand != eNa_strand_unknown) {
- single_prod_str &= (prod_strand == eNa_strand_unknown) ||
- (prod_strand == ex_prod_strand);
- prod_strand = ex_prod_strand;
- }
- else {
- single_prod_str &= prod_strand == eNa_strand_unknown;
- }
+ if ( m_SubAligns.empty() ) {
+ NON_CONST_ITERATE(TSegments, seg, m_Segs) {
+ SAlignment_Segment::SAlignment_Row& gen_row =
+ seg->m_Rows[CSeq_loc_Mapper_Base::eSplicedRow_Gen];
+ SAlignment_Segment::SAlignment_Row& prod_row =
+ seg->m_Rows[CSeq_loc_Mapper_Base::eSplicedRow_Prod];
+ // Check if rows have correct types. If not, try to swap.
+ if (m_LocMapper.GetSeqTypeById(gen_row.m_Id) != CSeq_loc_Mapper_Base::eSeq_nuc) {
+ swap(gen_row, prod_row);
}
}
+ x_GetDstSplicedSubAlign(spliced, *this,
+ last_exon_partial, gen_id, last_gen_id, single_gen_id,
+ gen_strand, single_gen_str,
+ prod_id, last_prod_id, single_prod_id,
+ prod_strand, single_prod_str,
+ partial);
+ }
+ else {
+ ITERATE(TSubAligns, it, m_SubAligns) {
+ x_GetDstSplicedSubAlign(spliced, **it,
+ last_exon_partial, gen_id, last_gen_id, single_gen_id,
+ gen_strand, single_gen_str,
+ prod_id, last_prod_id, single_prod_id,
+ prod_strand, single_prod_str,
+ partial);
+ }
}
- if ( m_LocMapper.m_TrimSplicedSegs ) {
+ if ( m_LocMapper.x_IsSetMiscFlag(CSeq_loc_Mapper_Base::fTrimSplicedSegs) ) {
// Make sure the first and the last parts are not gaps. By now there should
// be no exons with only gaps in them, so no trimming should result in an
// empty exon.
@@ -2263,20 +2456,22 @@ void CSeq_align_Mapper_Base::x_GetDstSpliced(CRef<CSeq_align>& dst) const
}
}
- const CSpliced_seg& orig = m_OrigAlign->GetSegs().GetSpliced();
- // Copy some values from the original alignment.
- if ( orig.IsSetPoly_a() ) {
- spliced.SetPoly_a(orig.GetPoly_a());
- }
- if ( orig.IsSetProduct_length() ) {
- spliced.SetProduct_length(orig.GetProduct_length());
- }
- // Some properties can be copied only if the alignment was not
- // truncated.
- if (!partial && orig.IsSetModifiers()) {
- CloneContainer<CSpliced_seg_modifier,
- CSpliced_seg::TModifiers, CSpliced_seg::TModifiers>(
- orig.GetModifiers(), spliced.SetModifiers());
+ if ( m_OrigAlign->GetSegs().IsSpliced() ) {
+ const CSpliced_seg& orig = m_OrigAlign->GetSegs().GetSpliced();
+ // Copy some values from the original alignment.
+ if ( orig.IsSetPoly_a() ) {
+ spliced.SetPoly_a(orig.GetPoly_a());
+ }
+ if ( orig.IsSetProduct_length() ) {
+ spliced.SetProduct_length(orig.GetProduct_length());
+ }
+ // Some properties can be copied only if the alignment was not
+ // truncated.
+ if (!partial && orig.IsSetModifiers()) {
+ CloneContainer<CSpliced_seg_modifier,
+ CSpliced_seg::TModifiers, CSpliced_seg::TModifiers>(
+ orig.GetModifiers(), spliced.SetModifiers());
+ }
}
}
@@ -2754,7 +2949,15 @@ CRef<CSeq_align> CSeq_align_Mapper_Base::GetDstAlign(void) const
// Since spliced-segs are mapped in a different way (through
// sub-mappers which return mapped exons rather than whole alignments),
// here we should always use std-seg.
- x_GetDstStd(dst);
+ if (m_LocMapper.x_IsSetMiscFlag(CSeq_loc_Mapper_Base::fMixedAlignsAsSpliced) &&
+ row_ids.size() == 2 &&
+ m_LocMapper.GetSeqTypeById(row_ids[0]) != m_LocMapper.GetSeqTypeById(row_ids[1])) {
+ // Try to use spliced-seg for mixed-type pairwise alignments.
+ x_GetDstSpliced(dst);
+ }
+ else {
+ x_GetDstStd(dst);
+ }
}
/*
// Commented out as it looks to be wrong approach - it discards scores and
diff --git a/c++/src/objects/seq/seq_id_tree.cpp b/c++/src/objects/seq/seq_id_tree.cpp
index 4ad3b2e..f6201c0 100644
--- a/c++/src/objects/seq/seq_id_tree.cpp
+++ b/c++/src/objects/seq/seq_id_tree.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_id_tree.cpp 448566 2014-10-07 16:44:32Z ivanov $
+/* $Id: seq_id_tree.cpp 467602 2015-05-14 17:44:35Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -194,16 +194,16 @@ CSeq_id_Info* CSeq_id_Which_Tree::CreateInfo(const CSeq_id& id)
void CSeq_id_Which_Tree::DropInfo(const CSeq_id_Info* info)
{
TWriteLockGuard guard(m_TreeLock);
- if ( info->GetLockCounter() != 0 ) {
+ if ( info->IsLocked() ) {
_ASSERT(info->m_Seq_id_Type != CSeq_id::e_not_set);
return;
}
if ( info->m_Seq_id_Type == CSeq_id::e_not_set ) {
- _ASSERT(info->GetLockCounter() == 0);
+ _ASSERT(!info->IsLocked());
return;
}
x_Unindex(info);
- _ASSERT(info->GetLockCounter()==0);
+ _ASSERT(!info->IsLocked());
_ASSERT(info->m_Seq_id_Type != CSeq_id::e_not_set);
const_cast<CSeq_id_Info*>(info)->m_Seq_id_Type = CSeq_id::e_not_set;
}
@@ -596,7 +596,7 @@ CSeq_id_Handle CSeq_id_Gi_Tree::FindInfo(const CSeq_id& id) const
{
CSeq_id_Handle ret;
_ASSERT(x_Check(id));
- TPacked gi = GI_TO(TPacked, x_Get(id));
+ TPacked gi = x_Get(id);
if (gi) {
ret = CSeq_id_Handle(m_SharedInfo, gi);
}
@@ -1024,13 +1024,6 @@ bool x_IsDefaultSwissprotRelease(const string& release)
}
-static inline
-bool x_IsDefaultSwissprotRelease(const CTextseq_id& tid)
-{
- return tid.IsSetRelease() && x_IsDefaultSwissprotRelease(tid.GetRelease());
-}
-
-
void CSeq_id_Textseq_Tree::x_FindMatchByAcc(TSeq_id_MatchList& id_list,
const string& acc,
const TVersion* ver) const
diff --git a/c++/src/objects/seq/seq_loc_from_string.cpp b/c++/src/objects/seq/seq_loc_from_string.cpp
index 3433a34..f0c4480 100644
--- a/c++/src/objects/seq/seq_loc_from_string.cpp
+++ b/c++/src/objects/seq/seq_loc_from_string.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_loc_from_string.cpp 402244 2013-06-06 12:18:03Z kornbluh $
+/* $Id: seq_loc_from_string.cpp 463555 2015-03-30 15:36:47Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -333,7 +333,7 @@ namespace {
str = copy;
}
- unsigned int s_GetParenLen (string text)
+ size_t s_GetParenLen (string text)
{
string::size_type offset = 0;
unsigned int paren_count;
diff --git a/c++/src/objects/seq/seq_loc_mapper_base.cpp b/c++/src/objects/seq/seq_loc_mapper_base.cpp
index 2c1d4d9..8e6c312 100644
--- a/c++/src/objects/seq/seq_loc_mapper_base.cpp
+++ b/c++/src/objects/seq/seq_loc_mapper_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_loc_mapper_base.cpp 460227 2015-02-25 18:24:03Z ivanov $
+/* $Id: seq_loc_mapper_base.cpp 485927 2015-11-30 16:04:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -221,7 +221,7 @@ bool CMappingRange::CanMap(TSeqPos from,
ENa_strand strand) const
{
// The callers set is_set_strand to true only if the mapper's
- // m_CheckStrand is enabled. Only in this case CanMap() checks
+ // fCheckStrand is enabled. Only in this case CanMap() checks
// if the location's strand is the same as the mapping's one.
if ( is_set_strand && (IsReverse(strand) != IsReverse(m_Src_strand)) ) {
return false;
@@ -282,7 +282,7 @@ CMappingRange::TRange CMappingRange::Map_Range(TSeqPos from,
if( m_Dst_len != kInvalidSeqPos ) {
const TSeqPos src_to_dst_end = m_Dst_from + (m_Src_to - m_Src_from);
const TSeqPos new_dst_end = m_Dst_from + m_Dst_len - 1;
- if ( m_ExtTo && partial_to && to == m_Src_bioseq_len ) {
+ if ( m_ExtTo && partial_to && to+1 == m_Src_bioseq_len ) {
if( ((int)new_dst_end - (int)src_to_dst_end) >= 0 && (new_dst_end - src_to_dst_end) <= 2 ) {
ret.SetTo( new_dst_end );
}
@@ -302,7 +302,7 @@ CMappingRange::TRange CMappingRange::Map_Range(TSeqPos from,
}
// extend to the end, if necessary (Note: reverse strand implies "end" is a lower number )
// ( e.g. NZ_AAOJ01000043 )
- if( m_ExtTo && partial_to && (to == m_Src_bioseq_len) ) {
+ if( m_ExtTo && partial_to && (to+1 == m_Src_bioseq_len) ) {
ret.SetFrom( m_Dst_from );
}
@@ -491,6 +491,128 @@ CMappingRanges::BeginMappingRanges(CSeq_id_Handle id,
/////////////////////////////////////////////////////////////////////
//
+// CSeq_loc_Mapper_Message
+//
+
+
+CSeq_loc_Mapper_Message::CSeq_loc_Mapper_Message(const string& msg,
+ EDiagSev sev,
+ int err_code,
+ int sub_code)
+ : CMessage_Basic(msg, sev, err_code, sub_code),
+ m_ObjType(eNot_set),
+ m_Obj(null)
+{
+}
+
+
+CSeq_loc_Mapper_Message::~CSeq_loc_Mapper_Message(void)
+{
+}
+
+
+CSeq_loc_Mapper_Message* CSeq_loc_Mapper_Message::Clone(void) const
+{
+ return new CSeq_loc_Mapper_Message(*this);
+}
+
+
+void CSeq_loc_Mapper_Message::Write(CNcbiOstream& out) const
+{
+ CMessage_Basic::Write(out);
+ switch ( Which() ) {
+ case CSeq_loc_Mapper_Message::eNot_set:
+ cout << "NULL";
+ break;
+ case CSeq_loc_Mapper_Message::eSeq_loc:
+ cout << MSerial_AsnText << *GetLoc();
+ break;
+ case CSeq_loc_Mapper_Message::eSeq_feat:
+ cout << MSerial_AsnText << *GetFeat();
+ break;
+ case CSeq_loc_Mapper_Message::eSeq_align:
+ cout << MSerial_AsnText << *GetAlign();
+ break;
+ case CSeq_loc_Mapper_Message::eSeq_graph:
+ cout << MSerial_AsnText << *GetGraph();
+ break;
+ }
+}
+
+
+void CSeq_loc_Mapper_Message::SetLoc(const CSeq_loc& loc)
+{
+ m_ObjType = eSeq_loc;
+ CRef<CSeq_loc> ref(new CSeq_loc());
+ ref->Assign(loc);
+ m_Obj = ref;
+}
+
+
+const CSeq_loc* CSeq_loc_Mapper_Message::GetLoc(void) const
+{
+ return m_ObjType == eSeq_loc ?
+ dynamic_cast<const CSeq_loc*>(m_Obj.GetPointerOrNull()) : 0;
+}
+
+
+void CSeq_loc_Mapper_Message::SetFeat(const CSeq_feat& feat)
+{
+ m_ObjType = eSeq_feat;
+ CRef<CSeq_feat> ref(new CSeq_feat());
+ ref->Assign(feat);
+ m_Obj = ref;
+}
+
+
+const CSeq_feat* CSeq_loc_Mapper_Message::GetFeat(void) const
+{
+ return m_ObjType == eSeq_feat ?
+ dynamic_cast<const CSeq_feat*>(m_Obj.GetPointerOrNull()) : 0;
+}
+
+
+void CSeq_loc_Mapper_Message::SetAlign(const CSeq_align& align)
+{
+ m_ObjType = eSeq_align;
+ CRef<CSeq_align> ref(new CSeq_align());
+ ref->Assign(align);
+ m_Obj = ref;
+}
+
+
+const CSeq_align* CSeq_loc_Mapper_Message::GetAlign(void) const
+{
+ return m_ObjType == eSeq_align ?
+ dynamic_cast<const CSeq_align*>(m_Obj.GetPointerOrNull()) : 0;
+}
+
+
+void CSeq_loc_Mapper_Message::SetGraph(const CSeq_graph& graph)
+{
+ m_ObjType = eSeq_graph;
+ CRef<CSeq_graph> ref(new CSeq_graph());
+ ref->Assign(graph);
+ m_Obj = ref;
+}
+
+
+const CSeq_graph* CSeq_loc_Mapper_Message::GetGraph(void) const
+{
+ return m_ObjType == eSeq_graph ?
+ dynamic_cast<const CSeq_graph*>(m_Obj.GetPointerOrNull()) : 0;
+}
+
+
+void CSeq_loc_Mapper_Message::ResetObject(void)
+{
+ m_ObjType = eNot_set;
+ m_Obj.Reset();
+}
+
+
+/////////////////////////////////////////////////////////////////////
+//
// CSeq_loc_Mapper_Base
//
@@ -521,10 +643,7 @@ ENa_strand s_IndexToStrand(size_t idx)
CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(IMapper_Sequence_Info* seqinfo)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(new CMappingRanges),
@@ -540,10 +659,7 @@ CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(CMappingRanges* mapping_ranges,
IMapper_Sequence_Info* seq_info)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(mapping_ranges),
@@ -560,10 +676,7 @@ CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(const CSeq_feat& map_feat,
IMapper_Sequence_Info* seq_info)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(new CMappingRanges),
@@ -581,10 +694,7 @@ CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(const CSeq_loc& source,
IMapper_Sequence_Info* seq_info)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(new CMappingRanges),
@@ -603,10 +713,7 @@ CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(const CSeq_align& map_align,
IMapper_Sequence_Info* seq_info)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(new CMappingRanges),
@@ -625,10 +732,7 @@ CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(const CSeq_align& map_align,
IMapper_Sequence_Info* seq_info)
: m_MergeFlag(eMergeNone),
m_GapFlag(eGapPreserve),
- m_TrimSplicedSegs(true),
- m_KeepNonmapping(false),
- m_CheckStrand(false),
- m_IncludeSrcLocs(false),
+ m_MiscFlags(fTrimSplicedSegs),
m_Partial(false),
m_LastTruncated(false),
m_Mappings(new CMappingRanges),
@@ -721,17 +825,18 @@ void CSeq_loc_Mapper_Base::x_InitializeFeat(const CSeq_feat& map_feat,
frame = map_feat.GetData().GetCdregion().GetFrame();
}
if (dir == eLocationToProduct) {
- x_InitializeLocs(map_feat.GetLocation(), map_feat.GetProduct(), frame);
+ x_InitializeLocs(map_feat.GetLocation(), map_feat.GetProduct(), frame, 0);
}
else {
- x_InitializeLocs(map_feat.GetProduct(), map_feat.GetLocation(), frame);
+ x_InitializeLocs(map_feat.GetProduct(), map_feat.GetLocation(), 0, frame);
}
}
void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
const CSeq_loc& target,
- int frame)
+ int src_frame,
+ int dst_frame)
{
if (source.IsEmpty() || target.IsEmpty()) {
// Ignore mapping from or to an empty location.
@@ -749,6 +854,39 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
ESeqType dst_type = eSeq_unknown; // destination sequence type
bool known_src_types = x_CheckSeqTypes(source, src_type, src_total_len);
bool known_dst_types = x_CheckSeqTypes(target, dst_type, dst_total_len);
+
+ // Non-zero frame indicates genomic sequence in a nuc-to-prot alignment.
+ if (src_frame) {
+ if (src_type == eSeq_unknown) {
+ src_type = eSeq_nuc;
+ }
+ else if (src_type != eSeq_nuc) {
+ NCBI_THROW(CAnnotMapperException, eBadLocation,
+ "Frame can not be specified for a protein source location.");
+ }
+ if (!dst_frame) {
+ if (dst_type == eSeq_unknown) {
+ dst_type = eSeq_prot;
+ }
+ // If frame is not set it's probably a prot, but we are not enforcing this.
+ }
+ }
+ if (dst_frame) {
+ if (dst_type == eSeq_unknown) {
+ dst_type = eSeq_nuc;
+ }
+ else if (dst_type != eSeq_nuc) {
+ NCBI_THROW(CAnnotMapperException, eBadLocation,
+ "Frame can not be specified for a protein target location.");
+ }
+ if (!src_frame) {
+ if (src_type == eSeq_unknown) {
+ src_type = eSeq_prot;
+ }
+ // If frame is not set it's probably a nuc, but we are not enforcing this.
+ }
+ }
+
// Check if all sequence types are known and there are no conflicts.
bool known_types = known_src_types && known_dst_types;
if ( !known_types ) {
@@ -786,12 +924,6 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
else if (dst_type != eSeq_unknown) {
src_type = dst_type;
}
- else if (frame) {
- // Both sequence types are unknown, but frame is set.
- // Assume they are proteins.
- src_type = eSeq_prot;
- dst_type = eSeq_prot;
- }
// By default we assume that both sequences are nucleotides.
// Even if it's a mapping between two proteins, this assumption
// should work fine in most cases.
@@ -802,8 +934,10 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
// ranges according to the new sequence width.
}
// While checking if it's a mapping between nuc and prot,
- // truncate incomplete codons.
- else if (src_total_len/3 == dst_total_len) {
+ // truncate incomplete or stop codons.
+ // NOTE: It's safe to ignore frames here. If frames are set, sequence types
+ // should have been already assigned.
+ else if (src_total_len/3 == dst_total_len || src_total_len == (dst_total_len + 1)*3) {
if (src_type == eSeq_unknown) {
src_type = eSeq_nuc;
}
@@ -817,15 +951,8 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
"Sequence types (nuc to prot) are inconsistent with "
"location lengths");
}
- // Report overhanging bases if any
- if (src_total_len % 3 != 0) {
- ERR_POST_X(28, Warning <<
- "Source and destination lengths do not match, "
- "dropping " << src_total_len % 3 <<
- " overhanging bases on source location");
- }
}
- else if (dst_total_len/3 == src_total_len) {
+ else if (dst_total_len/3 == src_total_len || dst_total_len == (src_total_len + 1)*3) {
if (src_type == eSeq_unknown) {
src_type = eSeq_prot;
}
@@ -839,13 +966,6 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
"Sequence types (prot to nuc) are inconsistent with "
"location lengths");
}
- // Report overhanging bases if any
- if (dst_total_len % 3 != 0) {
- ERR_POST_X(29, Warning <<
- "Source and destination lengths do not match, "
- "dropping " << dst_total_len % 3 <<
- " overhanging bases on destination location");
- }
}
else {
// If location lengths are not 1:1 or 1:3, there's no way
@@ -856,6 +976,59 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
}
}
}
+ // If both source and destination total length are known, check if
+ // they match each other.
+ if (src_total_len != kInvalidSeqPos && dst_total_len != kInvalidSeqPos) {
+ if ( src_frame ) src_total_len -= src_frame - 1;
+ if ( dst_frame ) dst_total_len -= dst_frame - 1;
+ // Check for incomplete and stop codons.
+ if (src_type == eSeq_nuc && dst_type == eSeq_prot) {
+ // Report overhanging bases if any
+ if (src_total_len == (dst_total_len + 1)*3) {
+ // Skip stop codon
+ dst_total_len++;
+ }
+ else if (src_total_len/3 == dst_total_len && src_total_len % 3 != 0) {
+ ERR_POST_X(28, Info <<
+ "Source and destination lengths do not match, "
+ "dropping " << src_total_len % 3 <<
+ " overhanging bases on source location");
+ src_total_len -= src_total_len % 3;
+ }
+ // Allow partial codon mismatch
+ if (dst_total_len*3 >= src_total_len + 3 ||
+ dst_total_len*3 + 3 <= src_total_len) {
+ ERR_POST_X(31, Warning <<
+ "Source and destination lengths do not match.");
+ }
+ }
+ else if (dst_type == eSeq_nuc && src_type == eSeq_prot) {
+ // Report overhanging bases if any
+ if (dst_total_len == (src_total_len + 1)*3) {
+ // Skip stop codon
+ src_total_len++;
+ }
+ else if (dst_total_len/3 == src_total_len && dst_total_len % 3 != 0) {
+ ERR_POST_X(28, Info <<
+ "Source and destination lengths do not match, "
+ "dropping " << dst_total_len % 3 <<
+ " overhanging bases on destination location");
+ dst_total_len -= dst_total_len % 3;
+ }
+ // Allow partial codon mismatch
+ if (src_total_len*3 >= dst_total_len + 3 ||
+ src_total_len*3 + 3 <= dst_total_len) {
+ ERR_POST_X(31, Warning <<
+ "Source and destination lengths do not match.");
+ }
+ }
+ // Same sequence types
+ else if (src_total_len != dst_total_len) {
+ ERR_POST_X(31, Warning <<
+ "Source and destination lengths do not match.");
+ }
+ }
+
// At this point all sequence types should be known or forced.
// Set the widths.
int src_width = (src_type == eSeq_prot) ? 3 : 1;
@@ -871,6 +1044,8 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
// Start with an empty range
TSeqPos src_start = kInvalidSeqPos;
TSeqPos src_len = 0;
+ // For whole ranges don't fetch their actual length since it is allowed
+ // to be different from its genomic couterpart.
if ( rg.IsWhole() ) {
src_start = 0;
src_len = kInvalidSeqPos;
@@ -879,7 +1054,6 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
src_start = src_it.GetRange().GetFrom()*src_width;
src_len = x_GetRangeLength(src_it)*src_width;
}
-
rg = dst_it.GetRange();
TSeqPos dst_start = kInvalidSeqPos;
TSeqPos dst_len = 0;
@@ -892,27 +1066,26 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
dst_len = x_GetRangeLength(dst_it)*dst_width;
}
- if ( frame ) {
- const int shift = frame - 1;
- if (dst_type == eSeq_prot && src_start != kInvalidSeqPos &&
- static_cast<TSeqPos>(shift) < src_len ) {
- if( ! source.IsReverseStrand() ) {
- src_start += shift;
- }
- src_len -= shift;
+ if (src_frame && dst_type == eSeq_prot && src_start != kInvalidSeqPos &&
+ static_cast<TSeqPos>(src_frame) <= src_len ) {
+ if( !source.IsReverseStrand() ) {
+ src_start += src_frame - 1;
}
- if (src_type == eSeq_prot && dst_start != kInvalidSeqPos &&
- static_cast<TSeqPos>(shift) < dst_len ) {
- if( ! target.IsReverseStrand() ) {
- dst_start += shift;
- }
- dst_len -= shift;
+ src_len -= src_frame - 1;
+ }
+ if (dst_frame && src_type == eSeq_prot && dst_start != kInvalidSeqPos &&
+ static_cast<TSeqPos>(dst_frame) <= dst_len ) {
+ if( !target.IsReverseStrand() ) {
+ dst_start += dst_frame - 1;
}
+ dst_len -= dst_frame - 1;
}
// Iterate source and destination ranges.
- const TSeqPos src_bioseq_len =
- (source.GetId() ? src_width*(GetSequenceLength( *source.GetId()) - 1)
- + (src_width - 1) : src_total_len);
+ TSeqPos src_bioseq_len = (source.GetId() ? GetSequenceLength( *source.GetId())
+ : src_total_len);
+ if (src_bioseq_len != kInvalidSeqPos) {
+ src_bioseq_len = src_width*src_bioseq_len;
+ }
TSeqPos last_src_start = 0, last_src_len = 0;
TSeqPos last_dst_start = 0, last_dst_len = 0;
bool last_src_reverse = false, last_dst_reverse = false;
@@ -964,7 +1137,9 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
x_NextMappingRange(
src_it.GetSeq_id(), src_start, src_len, src_it.GetStrand(),
dst_it.GetSeq_id(), dst_start, dst_len, dst_it.GetStrand(),
- dst_it.GetFuzzFrom(), dst_it.GetFuzzTo(), frame, dst_total_len, src_bioseq_len );
+ dst_it.GetFuzzFrom(), dst_it.GetFuzzTo(),
+ src_frame ? src_frame : dst_frame,
+ dst_total_len, src_bioseq_len);
// Start new group on a gap in src or dst.
// If the whole source or destination range was used, increment the
// iterator.
@@ -974,6 +1149,8 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
// two whole locations (one per source range), dst_it will never be
// incremented and both source ranges will be mapped to the same
// sequence.
+ last_src_id = src_it.GetSeq_id_Handle();
+ last_src_reverse = IsReverse(src_it.GetStrand());
if (src_len == 0 && ++src_it) {
TRange rg = src_it.GetRange();
if ( rg.Empty() ) {
@@ -992,9 +1169,9 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
last_src_reverse != IsReverse(src_it.GetStrand())) {
m_CurrentGroup++;
}
- last_src_id = src_it.GetSeq_id_Handle();
- last_src_reverse = IsReverse(src_it.GetStrand());
}
+ last_dst_id = dst_it.GetSeq_id_Handle();
+ last_dst_reverse = IsReverse(dst_it.GetStrand());
if (dst_len == 0 && ++dst_it) {
TRange rg = dst_it.GetRange();
if ( rg.Empty() ) {
@@ -1013,8 +1190,6 @@ void CSeq_loc_Mapper_Base::x_InitializeLocs(const CSeq_loc& source,
last_dst_reverse != IsReverse(dst_it.GetStrand())) {
m_CurrentGroup++;
}
- last_dst_id = dst_it.GetSeq_id_Handle();
- last_dst_reverse = IsReverse(dst_it.GetStrand());
}
}
// Remember the direction of source and destination. This information
@@ -1906,6 +2081,13 @@ CSeq_loc_Mapper_Base::CollectSynonyms(const CSeq_id_Handle& id) const
m_SeqInfo->CollectSynonyms(id, synonyms);
ITERATE(TSynonyms, syn, synonyms) {
m_SynonymMap[*syn] = id;
+ // Add matching (e.g. versionless) synonyms.
+ CConstRef<CSeq_id> syn_id = syn->GetSeqId();
+ CSeq_id::TSeqIdHandles matches;
+ syn_id->GetMatchingIds(matches);
+ ITERATE(CSeq_id::TSeqIdHandles, mit, matches) {
+ m_SynonymMap[*mit] = id;
+ }
}
return id;
}
@@ -1947,7 +2129,7 @@ void CSeq_loc_Mapper_Base::SetSeqTypeById(const CSeq_id_Handle& idh,
bool CSeq_loc_Mapper_Base::x_CheckSeqTypes(const CSeq_loc& loc,
ESeqType& seqtype,
- TSeqPos& len) const
+ TSeqPos& len)
{
// Iterate the seq-loc, try to get sequence types used in it.
len = 0;
@@ -1970,7 +2152,7 @@ bool CSeq_loc_Mapper_Base::x_CheckSeqTypes(const CSeq_loc& loc,
// Adjust total length or reset it.
if (len != kInvalidSeqPos) {
if ( it.GetRange().IsWhole() ) {
- len = kInvalidSeqPos;
+ len = GetSequenceLength(it.GetSeq_id());
}
else {
len += it.GetRange().GetLength();
@@ -2515,7 +2697,7 @@ bool CSeq_loc_Mapper_Base::x_MapNextRange(const TRange& src_rg,
{
const CMappingRange& cvt = *mappings[cvt_idx];
if ( !cvt.CanMap(src_rg.GetFrom(), src_rg.GetTo(),
- is_set_strand && m_CheckStrand, src_strand) ) {
+ is_set_strand && x_IsSetMiscFlag(fCheckStrand), src_strand) ) {
// Can not map the range through this mapping.
return false;
}
@@ -2531,8 +2713,11 @@ bool CSeq_loc_Mapper_Base::x_MapNextRange(const TRange& src_rg,
bool reverse = IsReverse(src_strand);
+ // Have to save trimmed parts for error reporting (see below).
+ TRange trimmed_left, trimmed_right;
// Check if the source range is truncated by the mapping.
if (left < cvt.m_Src_from) {
+ trimmed_left.SetOpen(left, cvt.m_Src_from);
used_rg.SetFrom(cvt.m_Src_from - left);
left = cvt.m_Src_from;
if ( !reverse ) {
@@ -2547,6 +2732,7 @@ bool CSeq_loc_Mapper_Base::x_MapNextRange(const TRange& src_rg,
}
}
if (right > cvt.m_Src_to) {
+ trimmed_right.Set(cvt.m_Src_to + 1, right);
used_rg.SetLength(cvt.m_Src_to - left + 1);
right = cvt.m_Src_to;
if ( !reverse ) {
@@ -2560,6 +2746,20 @@ bool CSeq_loc_Mapper_Base::x_MapNextRange(const TRange& src_rg,
(right + 1 != *last_src_to);
}
}
+ if ((partial_left || partial_right) && x_IsSetMiscFlag(fErrorOnPartial)) {
+ string err_msg = "Unmapped sequence: " + cvt.m_Src_id_Handle.AsString();
+ if ( partial_left ) {
+ err_msg += " " + NStr::NumericToString(trimmed_left.GetFrom()) + ".." +
+ NStr::NumericToString(trimmed_left.GetTo());
+ }
+ if ( partial_right ) {
+ if ( partial_left ) err_msg += ",";
+ err_msg += " " + NStr::NumericToString(trimmed_right.GetFrom()) + ".." +
+ NStr::NumericToString(trimmed_right.GetTo());
+ }
+ err_msg += " not mapped to " + cvt.m_Dst_id_Handle.AsString();
+ NCBI_THROW(CAnnotMapperException, eCanNotMap, err_msg);
+ }
if (right < left) {
// Empty range - ignore it.
return false;
@@ -2663,7 +2863,7 @@ void CSeq_loc_Mapper_Base::x_SetLastTruncated(void)
{
// The flag indicates if the last range could not be mapped
// or preserved and was dropped.
- if ( m_LastTruncated || m_KeepNonmapping ) {
+ if ( m_LastTruncated || x_IsSetMiscFlag(fKeepNonmapping) ) {
return;
}
m_LastTruncated = true;
@@ -2798,7 +2998,7 @@ void CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(const CSeq_interval& si)
if ( !res ) {
// If the interval could not be mapped, we may need to keep
// the original one.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
// Propagate collected mapped ranges to the destination seq-loc.
x_PushRangesToDstMix();
// Add a copy of the original interval.
@@ -2835,7 +3035,7 @@ void CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(const CPacked_seqpnt& pp,
if ( !res ) {
// If the point could not be mapped, we may need to keep
// the original one.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
// Propagate collected mapped ranges to the destination seq-loc.
x_PushRangesToDstMix();
// Add a copy of the original point.
@@ -2903,7 +3103,7 @@ void CSeq_loc_Mapper_Base::x_MapSeq_loc(const CSeq_loc& src_loc)
if ( !res ) {
// If we don't have any mappings for this seq-id we may
// still need to keep the original.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
x_PushRangesToDstMix();
CRef<CSeq_loc> loc(new CSeq_loc);
loc->Assign(src_loc);
@@ -2934,7 +3134,7 @@ void CSeq_loc_Mapper_Base::x_MapSeq_loc(const CSeq_loc& src_loc)
if ( !res ) {
// If nothing could be mapped, we may still need to keep
// the original.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
x_PushRangesToDstMix();
CRef<CSeq_loc> loc(new CSeq_loc);
loc->Assign(src_loc);
@@ -2969,7 +3169,7 @@ void CSeq_loc_Mapper_Base::x_MapSeq_loc(const CSeq_loc& src_loc)
if ( !res ) {
// If nothing could be mapped, we may still need to keep
// the original.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
x_PushRangesToDstMix();
CRef<CSeq_loc> loc(new CSeq_loc);
loc->Assign(src_loc);
@@ -3011,7 +3211,7 @@ void CSeq_loc_Mapper_Base::x_MapSeq_loc(const CSeq_loc& src_loc)
if ( !res ) {
// If nothing could be mapped, we may still need to keep
// the original.
- if ( m_KeepNonmapping ) {
+ if ( x_IsSetMiscFlag(fKeepNonmapping) ) {
x_PushRangesToDstMix();
CRef<CSeq_loc> loc(new CSeq_loc);
loc->Assign(src_loc);
@@ -3146,7 +3346,7 @@ void CSeq_loc_Mapper_Base::x_MapSeq_loc(const CSeq_loc& src_loc)
m_Dst_loc = prev;
// Now we check the non-mapping flag. Only if both A and B
// failed to map and the flag is not set, we can discard the bond.
- if ( resA || resB || m_KeepNonmapping ) {
+ if ( resA || resB || x_IsSetMiscFlag(fKeepNonmapping) ) {
if (pntA->IsPnt() && pntB->IsPnt()) {
// Mapped locations are points - pack into bond
CSeq_bond& dst_bond = dst_loc->SetBond();
@@ -3330,7 +3530,7 @@ void CSeq_loc_Mapper_Base::x_PushMappedRange(const CSeq_id_Handle& id,
{
// It is impossible to collect source locations and do merging
// at the same time.
- if (m_IncludeSrcLocs && m_MergeFlag != eMergeNone) {
+ if (x_IsSetMiscFlag(fIncludeSrcLocs) && m_MergeFlag != eMergeNone) {
NCBI_THROW(CAnnotMapperException, eOtherError,
"Merging ranges is incompatible with "
"including source locations.");
@@ -3340,6 +3540,7 @@ void CSeq_loc_Mapper_Base::x_PushMappedRange(const CSeq_id_Handle& id,
switch ( m_MergeFlag ) {
case eMergeContained:
case eMergeAll:
+ case eMergeBySeg:
{
// Merging will be done later, while constructing the mapped
// seq-loc. Now just add new range in the right order.
@@ -3369,7 +3570,6 @@ void CSeq_loc_Mapper_Base::x_PushMappedRange(const CSeq_id_Handle& id,
break;
}
case eMergeAbutting:
- case eMergeBySeg:
default:
{
// Some special processing is required.
@@ -3441,7 +3641,7 @@ void CSeq_loc_Mapper_Base::x_PushSourceRange(const CSeq_id_Handle& idh,
const TRange& range,
bool push_reverse)
{
- if ( !m_IncludeSrcLocs ) return; // No need to store source ranges.
+ if ( !x_IsSetMiscFlag(fIncludeSrcLocs) ) return; // No need to store source ranges.
if ( !m_SrcLocs ) {
m_SrcLocs.Reset(new CSeq_loc);
}
@@ -3566,8 +3766,11 @@ CRef<CSeq_loc> CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(void)
TSeqPos from = kInvalidSeqPos;
TSeqPos to = kInvalidSeqPos;
TRangeFuzz fuzz(kEmptyFuzz, kEmptyFuzz);
+ int group = -1;
// Some merge flags require the ranges to be sorted.
- if (m_MergeFlag == eMergeContained || m_MergeFlag == eMergeAll) {
+ if (m_MergeFlag == eMergeContained ||
+ m_MergeFlag == eMergeAll ||
+ m_MergeFlag == eMergeBySeg) {
id_it->second[str].sort();
}
// Iterate mapped ranges.
@@ -3590,42 +3793,46 @@ CRef<CSeq_loc> CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(void)
from = rg_it->range.GetFrom();
to = rg_it->range.GetTo();
fuzz = rg_it->fuzz;
+ group = rg_it->group;
continue;
}
- // Merge abutting ranges. The ranges are sorted by 'from',
- // so we need to check only one end.
- if (m_MergeFlag == eMergeAbutting) {
- if (rg_it->range.GetFrom() == to + 1) {
- to = rg_it->range.GetTo();
- fuzz.second = rg_it->fuzz.second;
- continue;
- }
- }
- // Merge contained ranges
- if (m_MergeFlag == eMergeContained) {
- // Ignore interval completely covered by another one.
- // Check only 'to', since the ranges are sorted by 'from'.
- if (rg_it->range.GetTo() <= to) {
- continue;
- }
- // If the old range is contaied in the new one, adjust
- // its 'to'.
- if (rg_it->range.GetFrom() == from) {
- to = rg_it->range.GetTo();
- fuzz.second = rg_it->fuzz.second;
- continue;
+ if (m_MergeFlag != eMergeBySeg || rg_it->group == group) {
+ // Merge abutting ranges. The ranges are sorted by 'from',
+ // so we need to check only one end.
+ if (m_MergeFlag == eMergeAbutting) {
+ if (rg_it->range.GetFrom() == to + 1) {
+ to = rg_it->range.GetTo();
+ fuzz.second = rg_it->fuzz.second;
+ continue;
+ }
}
- }
- // Merge all overlapping ranges.
- if (m_MergeFlag == eMergeAll) {
- if (rg_it->range.GetFrom() <= to + 1) {
- if (rg_it->range.GetTo() > to) {
+ // Merge contained ranges
+ if (m_MergeFlag == eMergeContained) {
+ // Ignore interval completely covered by another one.
+ // Check only 'to', since the ranges are sorted by 'from'.
+ if (rg_it->range.GetTo() <= to) {
+ continue;
+ }
+ // If the old range is contaied in the new one, adjust
+ // its 'to'.
+ if (rg_it->range.GetFrom() == from) {
to = rg_it->range.GetTo();
fuzz.second = rg_it->fuzz.second;
+ continue;
+ }
+ }
+ // Merge all overlapping ranges.
+ if (m_MergeFlag == eMergeAll || m_MergeFlag == eMergeBySeg) {
+ if (rg_it->range.GetFrom() <= to + 1) {
+ if (rg_it->range.GetTo() > to) {
+ to = rg_it->range.GetTo();
+ fuzz.second = rg_it->fuzz.second;
+ }
+ continue;
}
- continue;
}
}
+
// No merging happened - store the previous interval
// or point.
if ( x_ReverseRangeOrder(str) ) {
@@ -3641,6 +3848,7 @@ CRef<CSeq_loc> CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(void)
from = rg_it->range.GetFrom();
to = rg_it->range.GetTo();
fuzz = rg_it->fuzz;
+ group = rg_it->group;
}
// If there were only empty ranges, do not try to add them as points.
if (from == kInvalidSeqPos && to == kInvalidSeqPos) {
@@ -3827,35 +4035,52 @@ CSeq_loc_Mapper_Base::Map(CSeq_annot& annot, TAnnotMapFlags flags)
case CSeq_annot::C_Data::e_Ftable:
{
CSeq_annot::C_Data::TFtable& ftable = annot.SetData().SetFtable();
+ string error;
+ bool mapped = false;
ERASE_ITERATE(CSeq_annot::C_Data::TFtable, it, ftable) {
- bool mapped = false;
- CSeq_feat& feat = **it;
- CRef<CSeq_loc> loc;
- if (flags & fAnnotMap_Location) {
- loc = Map(feat.GetLocation());
- if ( loc ) {
- feat.SetLocation(*loc);
- mapped = mapped || !loc->IsNull();
+ error.clear();
+ mapped = false;
+ try {
+ // For error reporting we may need the original feature.
+ CSeq_feat& feat = **it;
+ CRef<CSeq_loc> loc;
+ if (flags & fAnnotMap_Location) {
+ loc = Map(feat.GetLocation());
+ if ( loc && !loc->IsNull() ) {
+ feat.SetLocation(*loc);
+ mapped = true;
+ }
}
- }
- if ((flags & fAnnotMap_Product) && feat.IsSetProduct() ) {
- loc = Map(feat.GetProduct());
- if ( loc ) {
- feat.SetProduct(*loc);
- mapped = mapped || !loc->IsNull();
+ if ((flags & fAnnotMap_Product) && feat.IsSetProduct() ) {
+ loc = Map(feat.GetProduct());
+ if ( loc && !loc->IsNull() ) {
+ feat.SetProduct(*loc);
+ mapped = true;
+ }
}
}
+ catch (CAnnotMapperException& e) {
+ error = e.GetMsg();
+ mapped = false;
+ }
if ( mapped ) {
mapped_count++;
}
else {
+ if ( IMessageListener::HaveListeners() ) {
+ CSeq_loc_Mapper_Message msg(
+ error.empty() ? "Failed to map seq-feat" : error,
+ eDiag_Error);
+ msg.SetFeat(**it);
+ IMessageListener::Post(msg);
+ }
non_mapped_count++;
if (flags & fAnnotMap_RemoveNonMapping) {
ftable.erase(it);
}
if (flags & fAnnotMap_ThrowOnFailure) {
NCBI_THROW(CAnnotMapperException, eCanNotMap,
- "Can not map seq-feat.");
+ error.empty() ? string("Failed to map seq-feat.") : error);
}
}
}
@@ -3864,20 +4089,38 @@ CSeq_loc_Mapper_Base::Map(CSeq_annot& annot, TAnnotMapFlags flags)
case CSeq_annot::C_Data::e_Align:
{
CSeq_annot::C_Data::TAlign& aligns = annot.SetData().SetAlign();
+ string error;
+ bool mapped = false;
ERASE_ITERATE(CSeq_annot::C_Data::TAlign, it, aligns) {
- CRef<CSeq_align> align = Map(**it);
+ error.clear();
+ mapped = false;
+ CRef<CSeq_align> align;
+ try {
+ align = Map(**it);
+ }
+ catch (CAnnotMapperException& e) {
+ error = e.GetMsg();
+ mapped = false;
+ }
if ( align ) {
*it = align;
mapped_count++;
}
else {
+ if ( IMessageListener::HaveListeners() ) {
+ CSeq_loc_Mapper_Message msg(
+ error.empty() ? "Failed to map seq-align" : error,
+ eDiag_Error);
+ msg.SetAlign(**it);
+ IMessageListener::Post(msg);
+ }
non_mapped_count++;
if (flags & fAnnotMap_RemoveNonMapping) {
aligns.erase(it);
}
if (flags & fAnnotMap_ThrowOnFailure) {
NCBI_THROW(CAnnotMapperException, eCanNotMap,
- "Can not map seq-align.");
+ error.empty() ? string("Failed to map seq-align") : error);
}
}
}
@@ -3886,20 +4129,38 @@ CSeq_loc_Mapper_Base::Map(CSeq_annot& annot, TAnnotMapFlags flags)
case CSeq_annot::C_Data::e_Graph:
{
CSeq_annot::C_Data::TGraph& graphs = annot.SetData().SetGraph();
+ string error;
+ bool mapped = false;
ERASE_ITERATE(CSeq_annot::C_Data::TGraph, it, graphs) {
- CRef<CSeq_graph> graph = Map(**it);
+ error.clear();
+ mapped = false;
+ CRef<CSeq_graph> graph;
+ try {
+ graph = Map(**it);
+ }
+ catch (CAnnotMapperException& e) {
+ error = e.GetMsg();
+ mapped = false;
+ }
if ( graph ) {
*it = graph;
mapped_count++;
}
else {
+ if ( IMessageListener::HaveListeners() ) {
+ CSeq_loc_Mapper_Message msg(
+ error.empty() ? "Failed to map seq-graph" : error,
+ eDiag_Error);
+ msg.SetGraph(**it);
+ IMessageListener::Post(msg);
+ }
non_mapped_count++;
if (flags & fAnnotMap_RemoveNonMapping) {
graphs.erase(it);
}
if (flags & fAnnotMap_ThrowOnFailure) {
NCBI_THROW(CAnnotMapperException, eCanNotMap,
- "Can not map seq-graph.");
+ error.empty() ? string("Failed to map seq-graph") : error);
}
}
}
@@ -3922,5 +4183,16 @@ CSeq_loc_Mapper_Base::Map(CSeq_annot& annot, TAnnotMapFlags flags)
}
+void CSeq_loc_Mapper_Base::x_SetMiscFlag(EMiscFlags flag, bool value)
+{
+ if ( value ) {
+ m_MiscFlags |= flag;
+ }
+ else {
+ m_MiscFlags &= ~flag;
+ }
+}
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objects/seq/seqport_util.cpp b/c++/src/objects/seq/seqport_util.cpp
index 04cf4e9..75f19ca 100644
--- a/c++/src/objects/seq/seqport_util.cpp
+++ b/c++/src/objects/seq/seqport_util.cpp
@@ -1,4 +1,4 @@
- /*$Id: seqport_util.cpp 448002 2014-10-01 19:34:01Z vasilche $
+ /*$Id: seqport_util.cpp 462182 2015-03-16 22:40:36Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -2391,7 +2391,7 @@ TSeqPos CSeqportUtil_implementation::Complement
retval = CSeqManip::Complement(*in_str, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_str);
CSeq_data temp(out_str, in_code);
out_seq->Assign(temp);
- } else {
+ } else if (in_vec != 0) {
vector<char> out_vec;
retval = CSeqManip::Complement(*in_vec, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_vec);
CSeq_data temp(out_vec, in_code);
@@ -2446,7 +2446,7 @@ TSeqPos CSeqportUtil_implementation::Reverse
retval = CSeqManip::Reverse(*in_str, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_str);
CSeq_data temp(out_str, in_code);
out_seq->Assign(temp);
- } else {
+ } else if (in_vec != NULL) {
vector<char> out_vec;
retval = CSeqManip::Reverse(*in_vec, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_vec);
CSeq_data temp(out_vec, in_code);
@@ -2478,8 +2478,10 @@ TSeqPos CSeqportUtil_implementation::ReverseComplement
if ( in_str ) {
return CSeqManip::ReverseComplement(*in_str, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength);
- } else {
+ } else if (in_vec != NULL) {
return CSeqManip::ReverseComplement(*in_vec, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength);
+ } else {
+ return 0;
}
}
@@ -2511,7 +2513,7 @@ TSeqPos CSeqportUtil_implementation::ReverseComplement
retval = CSeqManip::ReverseComplement(*in_str, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_str);
CSeq_data temp(out_str, in_code);
out_seq->Assign(temp);
- } else {
+ } else if (in_vec != NULL) {
vector<char> out_vec;
retval = CSeqManip::ReverseComplement(*in_vec, s_SeqDataToSeqUtil[in_code], uBeginIdx, uLength, out_vec);
CSeq_data temp(out_vec, in_code);
diff --git a/c++/src/objects/seqalign/Dense_seg.cpp b/c++/src/objects/seqalign/Dense_seg.cpp
index 24c1c58..eff7518 100644
--- a/c++/src/objects/seqalign/Dense_seg.cpp
+++ b/c++/src/objects/seqalign/Dense_seg.cpp
@@ -1,4 +1,4 @@
-/* $Id: Dense_seg.cpp 448566 2014-10-07 16:44:32Z ivanov $
+/* $Id: Dense_seg.cpp 464942 2015-04-15 15:46:17Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1490,18 +1490,23 @@ void CDense_seg::CReserveHook::PreReadClassMember(CObjectIStream& in,
}
CDense_seg& ds = *CType<CDense_seg>::Get(member.GetClassObject());
size_t numseg = ds.GetNumseg();
- switch ( member.GetMemberIndex() ) {
- case 4: // "starts"
- ds.SetStarts().reserve(ds.GetDim()*numseg);
- break;
- case 5: // "lens"
- ds.SetLens().reserve(numseg);
- break;
- case 6: // "strands"
- ds.SetStrands().reserve(ds.GetDim()*numseg);
- break;
- default:
- break;
+ try {
+ switch ( member.GetMemberIndex() ) {
+ case 4: // "starts"
+ ds.SetStarts().reserve(ds.GetDim()*numseg);
+ break;
+ case 5: // "lens"
+ ds.SetLens().reserve(numseg);
+ break;
+ case 6: // "strands"
+ ds.SetStrands().reserve(ds.GetDim()*numseg);
+ break;
+ default:
+ break;
+ }
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
}
}
@@ -1531,7 +1536,14 @@ void CDenseSegReserveStartsHook::ReadClassMember(CObjectIStream& in,
const CObjectInfoMI& member)
{
CDense_seg& ds = *CType<CDense_seg>::Get(member.GetClassObject());
- ds.SetStarts().reserve(ds.GetDim()*ds.GetNumseg());
+ size_t size = ds.GetDim()*ds.GetNumseg();
+ CDense_seg::TStarts& array = ds.SetStarts();
+ try {
+ array.reserve(size);
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
+ }
DefaultRead(in, member);
}
@@ -1561,7 +1573,14 @@ void CDenseSegReserveLensHook::ReadClassMember(CObjectIStream& in,
const CObjectInfoMI& member)
{
CDense_seg& ds = *CType<CDense_seg>::Get(member.GetClassObject());
- ds.SetLens().reserve(ds.GetNumseg());
+ size_t size = ds.GetNumseg();
+ CDense_seg::TLens& array = ds.SetLens();
+ try {
+ array.reserve(size);
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
+ }
DefaultRead(in, member);
}
@@ -1591,7 +1610,14 @@ void CDenseSegReserveStrandsHook::ReadClassMember(CObjectIStream& in,
const CObjectInfoMI& member)
{
CDense_seg& ds = *CType<CDense_seg>::Get(member.GetClassObject());
- ds.SetStrands().reserve(ds.GetDim()*ds.GetNumseg());
+ size_t size = ds.GetDim()*ds.GetNumseg();
+ CDense_seg::TStrands& array = ds.SetStrands();
+ try {
+ array.reserve(size);
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
+ }
DefaultRead(in, member);
}
diff --git a/c++/src/objects/seqalign/Seq_align.cpp b/c++/src/objects/seqalign/Seq_align.cpp
index 2c187af..f5f2af5 100644
--- a/c++/src/objects/seqalign/Seq_align.cpp
+++ b/c++/src/objects/seqalign/Seq_align.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_align.cpp 459114 2015-02-13 15:21:48Z mozese2 $
+/* $Id: Seq_align.cpp 461118 2015-03-06 13:29:39Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -763,7 +763,6 @@ CSeq_align::CreateDensegFromStdseg(SSeqIdChooser* SeqIdChooser) const
seg_lens.push_back(0);
TSeqPos& seg_len = seg_lens.back();
- row_len = 0;
row_lens.clear();
widths_determined.push_back(false);
@@ -831,11 +830,7 @@ CSeq_align::CreateDensegFromStdseg(SSeqIdChooser* SeqIdChooser) const
"Inconsistent strands!");
}
}
- } else {
- strand = eNa_strand_unknown;
}
-
-
} else if ((*i)->IsEmpty()) {
starts.push_back(-1);
if (seg == 0) {
@@ -843,7 +838,6 @@ CSeq_align::CreateDensegFromStdseg(SSeqIdChooser* SeqIdChooser) const
}
seq_id = &(*i)->GetEmpty();
row_lens.push_back(0);
-
}
// determine/check the id
diff --git a/c++/src/objects/seqfeat/BioSource.cpp b/c++/src/objects/seqfeat/BioSource.cpp
index 237d7c7..fe98624 100644
--- a/c++/src/objects/seqfeat/BioSource.cpp
+++ b/c++/src/objects/seqfeat/BioSource.cpp
@@ -1,4 +1,4 @@
-/* $Id: BioSource.cpp 460793 2015-03-03 14:52:45Z ivanov $
+/* $Id: BioSource.cpp 483244 2015-10-29 14:26:03Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -161,31 +161,43 @@ CBioSource::EGenome CBioSource::GetGenomeByOrganelle (const string& organelle, N
{
CBioSource::EGenome gtype = CBioSource::eGenome_unknown;
- if (use_case == NStr::eCase && !starts_with) {
+ if (use_case == NStr::eCase && !starts_with) {
TGenomeMap::const_iterator g_iter = sm_GenomeKeys.find (organelle.c_str ());
- if (g_iter != sm_GenomeKeys.end ()) {
+ if (g_iter == sm_GenomeKeys.end()) {
+ if (NStr::Equal(organelle, "mitochondrial")) {
+ gtype = CBioSource::eGenome_mitochondrion;
+ }
+ } else {
gtype = g_iter->second;
}
} else {
TGenomeMap::const_iterator g_iter = sm_GenomeKeys.begin();
if (starts_with) {
- string match;
- while (g_iter != sm_GenomeKeys.end() && gtype == CBioSource::eGenome_unknown) {
- match = g_iter->first;
- if (NStr::StartsWith(organelle, match.c_str(), use_case)) {
- if (organelle.length() == match.length()
- || (match.length() < organelle.length() && isspace (organelle[match.length()]))) {
- gtype = g_iter->second;
+ if (NStr::StartsWith(organelle, "mitochondrial", use_case)){
+ gtype = CBioSource::eGenome_mitochondrion;
+ } else {
+ string match;
+ while (g_iter != sm_GenomeKeys.end() && gtype == CBioSource::eGenome_unknown) {
+ match = g_iter->first;
+ if (NStr::StartsWith(organelle, match.c_str(), use_case)) {
+ if (organelle.length() == match.length()
+ || (match.length() < organelle.length() && isspace(organelle[match.length()]))) {
+ gtype = g_iter->second;
+ }
}
+ ++g_iter;
}
- ++g_iter;
}
} else {
- while (g_iter != sm_GenomeKeys.end() && gtype == CBioSource::eGenome_unknown) {
- if (NStr::Equal(organelle, g_iter->first, use_case)) {
- gtype = g_iter->second;
+ if (NStr::Equal(organelle, "mitochondrial", use_case)) {
+ gtype = CBioSource::eGenome_mitochondrion;
+ } else {
+ while (g_iter != sm_GenomeKeys.end() && gtype == CBioSource::eGenome_unknown) {
+ if (NStr::Equal(organelle, g_iter->first, use_case)) {
+ gtype = g_iter->second;
+ }
+ ++g_iter;
}
- ++g_iter;
}
}
}
@@ -650,6 +662,9 @@ void CBioSource::UpdateWithBioSample(const CBioSource& biosample, bool force, bo
ITERATE(TFieldDiffList, it, diffs) {
if (NStr::EqualNocase((*it)->GetFieldName(), "Organism Name")) {
SetOrg().SetTaxname((*it)->GetSampleVal());
+ if (GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetName()) {
+ SetOrg().SetOrgname().ResetName();
+ }
} else if (NStr::EqualNocase((*it)->GetFieldName(), "Tax ID")) {
try {
SetOrg().SetTaxId(atoi((*it)->GetSampleVal().c_str()));
@@ -864,7 +879,7 @@ static const char* const s_TaxNameElementQuals[] = {
"forma",
"forma-specialis",
"genotype",
- "pathova",
+ "pathovar",
"serotype",
"serovar",
"subspecies",
diff --git a/c++/src/objects/seqfeat/Gb_qual.cpp b/c++/src/objects/seqfeat/Gb_qual.cpp
index 39d67e7..bf0db9c 100644
--- a/c++/src/objects/seqfeat/Gb_qual.cpp
+++ b/c++/src/objects/seqfeat/Gb_qual.cpp
@@ -1,4 +1,4 @@
-/* $Id: Gb_qual.cpp 462231 2015-03-17 15:12:15Z ivanov $
+/* $Id: Gb_qual.cpp 481760 2015-10-15 15:32:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -216,6 +216,87 @@ void CInferencePrefixList::GetPrefixAndRemainder (const string& inference, strin
}
+static string s_LegalMobileElementStrings[] = {
+ "transposon",
+ "retrotransposon",
+ "integron",
+ "superintegron",
+ "insertion sequence",
+ "non-LTR retrotransposon",
+ "P-element",
+ "transposable element",
+ "SINE",
+ "MITE",
+ "LINE",
+ "other"
+};
+
+
+void CGb_qual::GetMobileElementValueElements(const string& val, string& element_type, string& element_name)
+{
+ element_type = "";
+ element_name = "";
+ for (size_t i = 0;
+ i < sizeof(s_LegalMobileElementStrings) / sizeof(string);
+ ++i) {
+ if (NStr::StartsWith(val, s_LegalMobileElementStrings[i], NStr::eNocase)) {
+ element_name = val.substr(s_LegalMobileElementStrings[i].length());
+ if (!NStr::IsBlank(element_name) &&
+ (!NStr::StartsWith(element_name, ":") || NStr::Equal(element_name, ":"))) {
+ element_name = "";
+ } else {
+ element_type = s_LegalMobileElementStrings[i];
+ }
+ break;
+ }
+ }
+}
+
+
+bool CGb_qual::IsLegalMobileElementValue(const string& val)
+{
+ string element_type;
+ string element_name;
+ GetMobileElementValueElements(val, element_type, element_name);
+ if (NStr::IsBlank(element_type)) {
+ return false;
+ } else if (NStr::Equal(element_type, "other") && NStr::IsBlank(element_name)) {
+ return false;
+ } else {
+ return true;
+ }
+}
+
+
+static string s_IllegalQualNameStrings[] = {
+ "anticodon",
+ "citation",
+ "codon_start",
+ "db_xref",
+ "evidence",
+ "exception",
+ "gene",
+ "note",
+ "protein_id",
+ "pseudo",
+ "transcript_id",
+ "translation",
+ "transl_except",
+ "transl_table"
+};
+
+bool CGb_qual::IsIllegalQualName(const string& val)
+{
+ for (size_t i = 0;
+ i < sizeof(s_IllegalQualNameStrings) / sizeof(string);
+ ++i) {
+ if (NStr::EqualNocase(val, s_IllegalQualNameStrings[i])) {
+ return true;
+ }
+ }
+ return false;
+}
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/seqfeat/Gene_ref.cpp b/c++/src/objects/seqfeat/Gene_ref.cpp
index e9595cd..9efee0e 100644
--- a/c++/src/objects/seqfeat/Gene_ref.cpp
+++ b/c++/src/objects/seqfeat/Gene_ref.cpp
@@ -1,4 +1,4 @@
-/* $Id: Gene_ref.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: Gene_ref.cpp 465396 2015-04-21 14:47:55Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -87,6 +87,26 @@ bool CGene_ref::IsSuppressed(void) const
}
+// Examines criteria to determine if this gene is referred to by another gene xref
+bool CGene_ref::RefersToSameGene(const CGene_ref& xref) const
+{
+ if (IsSetLocus_tag() && !NStr::IsBlank(GetLocus_tag())
+ && xref.IsSetLocus_tag() && !NStr::IsBlank(xref.GetLocus_tag())) {
+ return NStr::Equal(GetLocus_tag(), xref.GetLocus_tag());
+ }
+ if (IsSetLocus() && !NStr::IsBlank(GetLocus())
+ && xref.IsSetLocus() && !NStr::IsBlank(xref.GetLocus())) {
+ return NStr::Equal(GetLocus(), xref.GetLocus());
+ }
+ if (IsSetSyn() && GetSyn().size() > 0 && !NStr::IsBlank(GetSyn().front())
+ && xref.IsSetSyn() && xref.GetSyn().size() > 0 && !NStr::IsBlank(xref.GetSyn().front())) {
+ return NStr::Equal(GetSyn().front(), xref.GetSyn().front());
+ }
+
+ return false;
+}
+
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/seqfeat/OrgMod.cpp b/c++/src/objects/seqfeat/OrgMod.cpp
index 54eb094..b6e8fe3 100644
--- a/c++/src/objects/seqfeat/OrgMod.cpp
+++ b/c++/src/objects/seqfeat/OrgMod.cpp
@@ -1,4 +1,4 @@
-/* $Id: OrgMod.cpp 463567 2015-03-30 16:19:15Z ivanov $
+/* $Id: OrgMod.cpp 485528 2015-11-23 16:15:43Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -519,8 +519,7 @@ COrgMod::FixStructuredVoucher(string& val, const string& v_type)
string id = "";
if (!ParseStructuredVoucher(val, inst_code, coll_code, id)
|| NStr::IsBlank(inst_code)) {
- //return AddStructureToVoucher(val, v_type);
- return false;
+ return AddStructureToVoucher(val, v_type);
}
bool rval = false;
bool found = false;
@@ -821,24 +820,6 @@ string COrgMod::AutoFix(TSubtype subtype, const string& value)
{
string new_val = "";
switch (subtype) {
- case COrgMod::eSubtype_bio_material:
- new_val = value;
- if (!FixStructuredVoucher(new_val, "b")) {
- new_val = "";
- }
- break;
- case COrgMod::eSubtype_culture_collection:
- new_val = value;
- if (!FixStructuredVoucher(new_val, "c")) {
- new_val = "";
- }
- break;
- case COrgMod::eSubtype_specimen_voucher:
- new_val = value;
- if (!FixStructuredVoucher(new_val, "s")) {
- new_val = "";
- }
- break;
case COrgMod::eSubtype_strain:
new_val = FixStrain(value);
break;
diff --git a/c++/src/objects/seqfeat/OrgName.cpp b/c++/src/objects/seqfeat/OrgName.cpp
index fbe38b0..948f556 100644
--- a/c++/src/objects/seqfeat/OrgName.cpp
+++ b/c++/src/objects/seqfeat/OrgName.cpp
@@ -1,4 +1,4 @@
-/* $Id: OrgName.cpp 453132 2014-12-01 15:30:39Z ivanov $
+/* $Id: OrgName.cpp 452696 2014-11-24 15:23:55Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -109,6 +109,89 @@ bool COrgName::GetFlatName(string& name_out, string* lineage) const
}
}
+// The proposed format for orgname flags: flagname1[;flagname2]...[;flagnameN]
+// where flagnameX consists of ascii alphanum characters only. Each value of flagnameX is unique.
+// Presence of flag name in the strings means 'true' value for the flag.
+const CTempString s_flagDelim = ";";
+
+void COrgName::x_SetAttribFlag( const string& name )
+{
+ if( !x_GetAttribFlag( name ) ) {
+ if( IsSetAttrib() && !GetAttrib().empty() ) {
+ SetAttrib().append(s_flagDelim).append(name);
+ } else {
+ SetAttrib( name );
+ }
+ }
+}
+
+void COrgName::x_ResetAttribFlag( const string& name )
+{
+ if( !name.empty() && IsSetAttrib() ) {
+ const string& attr = GetAttrib();
+ list< CTempString > lVals;
+ NStr::Split( attr, s_flagDelim, lVals );
+ for( list< CTempString >::iterator i = lVals.begin(), li = lVals.end(); i != li; ) {
+ NStr::TruncateSpacesInPlace( *i );
+ if( NStr::EqualNocase( *i, name ) ) {
+ i = lVals.erase( i );
+ } else {
+ ++i;
+ }
+ }
+ SetAttrib( NStr::Join( lVals, s_flagDelim ) );
+ if( SetAttrib().empty() ) {
+ ResetAttrib();
+ }
+ }
+}
+
+bool COrgName::x_GetAttribFlag( const string& name ) const
+{
+ if( !name.empty() && IsSetAttrib() ) {
+ const string& attr = GetAttrib();
+ list< CTempString > lVals;
+ NStr::Split( attr, s_flagDelim, lVals );
+ NON_CONST_ITERATE( list< CTempString >, i, lVals ) {
+ NStr::TruncateSpacesInPlace( *i );
+ if( NStr::EqualNocase( *i, name ) ) {
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
+// Flag indicating that node's scientific name is "well specified" according to the
+// respective taxonomic nomenclature (e.g. Genus species subspecies).
+// Based on "specified" property from Taxonomy database
+bool COrgName::IsFormalName() const
+{
+ return x_GetAttribFlag( "specified" );
+}
+
+void COrgName::SetFormalNameFlag( bool bFormalName )
+{
+ if( bFormalName ) {
+ x_SetAttribFlag( "specified" );
+ } else {
+ x_ResetAttribFlag( "specified" );
+ }
+}
+
+bool COrgName::IsUncultured() const
+{
+ return x_GetAttribFlag( "uncultured" );
+}
+
+void COrgName::SetUncultured( bool bUncultured )
+{
+ if( bUncultured ) {
+ x_SetAttribFlag( "uncultured" );
+ } else {
+ x_ResetAttribFlag( "uncultured" );
+ }
+}
#define MAKE_COMMON(o1,o2,o3,Field) if (o1.IsSet##Field() && o2.IsSet##Field() && NStr::Equal(o1.Get##Field(), o2.Get##Field())) o3.Set##Field(o1.Get##Field());
diff --git a/c++/src/objects/seqfeat/Org_ref.cpp b/c++/src/objects/seqfeat/Org_ref.cpp
index ad4476f..a2e5562 100644
--- a/c++/src/objects/seqfeat/Org_ref.cpp
+++ b/c++/src/objects/seqfeat/Org_ref.cpp
@@ -1,4 +1,4 @@
-/* $Id: Org_ref.cpp 453132 2014-12-01 15:30:39Z ivanov $
+/* $Id: Org_ref.cpp 472019 2015-07-06 16:40:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,6 +70,9 @@ static const char* const s_taxonName = "taxon" ;
int
COrg_ref::GetTaxId() const
{
+ if( ! IsSetDb() ) {
+ return 0;
+ }
const TDb& lDbTags = GetDb();
for(TDb::const_iterator i = lDbTags.begin();
diff --git a/c++/src/objects/seqfeat/PCRPrimerSeq.cpp b/c++/src/objects/seqfeat/PCRPrimerSeq.cpp
index b34342c..d2753a2 100644
--- a/c++/src/objects/seqfeat/PCRPrimerSeq.cpp
+++ b/c++/src/objects/seqfeat/PCRPrimerSeq.cpp
@@ -1,4 +1,4 @@
-/* $Id: PCRPrimerSeq.cpp 450152 2014-10-23 14:02:34Z ivanov $
+/* $Id: PCRPrimerSeq.cpp 450796 2014-10-30 16:55:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -220,15 +220,15 @@ bool CPCRPrimerSeq::TrimJunk(string& seq)
string orig(seq);
for(int i=0; starts[i] != NULL; i++) {
- unsigned int len = strlen(starts[i]);
- unsigned int pos = seq.find(starts[i]);
+ size_t len = strlen(starts[i]);
+ size_t pos = seq.find(starts[i]);
if (pos == 0 && len < seq.length())
seq = seq.substr(len);
}
for(int i=0; ends[i] != NULL; i++) {
- unsigned int len = strlen(ends[i]);
- unsigned int pos = seq.rfind(ends[i]);
+ size_t len = strlen(ends[i]);
+ size_t pos = seq.rfind(ends[i]);
if (len < seq.length() && pos == seq.length()-len)
seq = seq.substr(0,seq.length()-len);
}
diff --git a/c++/src/objects/seqfeat/Prot_ref.cpp b/c++/src/objects/seqfeat/Prot_ref.cpp
index ba3ac6f..1abc79a 100644
--- a/c++/src/objects/seqfeat/Prot_ref.cpp
+++ b/c++/src/objects/seqfeat/Prot_ref.cpp
@@ -1,4 +1,4 @@
-/* $Id: Prot_ref.cpp 448001 2014-10-01 19:31:37Z vasilche $
+/* $Id: Prot_ref.cpp 444281 2014-08-22 16:25:37Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/RNA_gen.cpp b/c++/src/objects/seqfeat/RNA_gen.cpp
index 1ec519c..1317ea6 100644
--- a/c++/src/objects/seqfeat/RNA_gen.cpp
+++ b/c++/src/objects/seqfeat/RNA_gen.cpp
@@ -1,4 +1,4 @@
-/* $Id: RNA_gen.cpp 452179 2014-11-17 15:52:15Z ivanov $
+/* $Id: RNA_gen.cpp 451322 2014-11-05 19:23:13Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/RNA_ref.cpp b/c++/src/objects/seqfeat/RNA_ref.cpp
index bd31234..4aabf07 100644
--- a/c++/src/objects/seqfeat/RNA_ref.cpp
+++ b/c++/src/objects/seqfeat/RNA_ref.cpp
@@ -1,4 +1,4 @@
-/* $Id: RNA_ref.cpp 359375 2012-04-12 17:22:36Z vasilche $
+/* $Id: RNA_ref.cpp 473602 2015-07-21 16:58:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,6 +39,8 @@
// generated includes
#include <objects/seqfeat/RNA_ref.hpp>
+#include <objects/seqfeat/Trna_ext.hpp>
+#include <util/sequtil/sequtil_convert.hpp>
// generated classes
@@ -79,7 +81,149 @@ string CRNA_ref::GetRnaTypeName (const CRNA_ref::EType rna_type)
return rna_type_name;
}
+static const string s_TrnaList[] = {
+ "tRNA-Gap",
+ "tRNA-Ala",
+ "tRNA-Asx",
+ "tRNA-Cys",
+ "tRNA-Asp",
+ "tRNA-Glu",
+ "tRNA-Phe",
+ "tRNA-Gly",
+ "tRNA-His",
+ "tRNA-Ile",
+ "tRNA-Xle",
+ "tRNA-Lys",
+ "tRNA-Leu",
+ "tRNA-Met",
+ "tRNA-Asn",
+ "tRNA-Pyl",
+ "tRNA-Pro",
+ "tRNA-Gln",
+ "tRNA-Arg",
+ "tRNA-Ser",
+ "tRNA-Thr",
+ "tRNA-Sec",
+ "tRNA-Val",
+ "tRNA-Trp",
+ "tRNA-OTHER",
+ "tRNA-Tyr",
+ "tRNA-Glx",
+ "tRNA-TERM"
+};
+
+static const string& s_AaName(int aa)
+{
+ int idx = 255;
+
+ if (aa != '*') {
+ idx = aa - 64;
+ } else {
+ idx = 28;
+ }
+ if ( idx > 0 && idx < 28 ) {
+ return s_TrnaList [idx];
+ }
+ return kEmptyStr;
+}
+
+static int s_ToIupacaa(int aa)
+{
+ vector<char> n(1, static_cast<char>(aa));
+ vector<char> i;
+ CSeqConvert::Convert(n, CSeqUtil::e_Ncbieaa, 0, 1, i, CSeqUtil::e_Iupacaa);
+ return i.front();
+}
+
+static const string& s_GetTrnaProduct(const CTrna_ext& trna)
+{
+ int aa = 0;
+ if ( trna.IsSetAa() && trna.GetAa().IsNcbieaa() ) {
+ aa = trna.GetAa().GetNcbieaa();
+ }
+ aa = s_ToIupacaa(aa);
+
+ return s_AaName(aa);
+}
+const string& CRNA_ref::GetRnaProductName(void) const
+{
+ if (!IsSetExt()) {
+ return kEmptyStr;
+ }
+
+ if (GetExt().IsName()) {
+ return GetExt().GetName();
+ } else if (GetExt().IsGen() && GetExt().GetGen().IsSetProduct()) {
+ return GetExt().GetGen().GetProduct();
+ } else if (GetExt().IsTRNA()) {
+ return s_GetTrnaProduct(GetExt().GetTRNA());
+ }
+
+ return kEmptyStr;
+}
+
+static void s_SetTrnaProduct(CTrna_ext& trna, const string& product, string& remainder)
+{
+ remainder = kEmptyStr;
+ if (NStr::IsBlank(product)) {
+ trna.ResetAa();
+ return;
+ }
+
+ int num_names = sizeof(s_TrnaList) / sizeof (string);
+ string test = product;
+ if (!NStr::StartsWith(product, "tRNA-")) {
+ test = "tRNA-" + test;
+ }
+
+ if (NStr::StartsWith(test, "tRNA-TERM", NStr::eNocase)
+ || NStr::StartsWith(test, "tRNA-STOP", NStr::eNocase)) {
+ trna.SetAa().SetNcbieaa(42);
+ if (test.length() > 9) {
+ remainder = test.substr(9);
+ NStr::TruncateSpacesInPlace(remainder);
+ }
+ } else {
+ remainder = product;
+ for (int i = 0; i < num_names - 1; i++) {
+ if (NStr::StartsWith(test, s_TrnaList[i], NStr::eNocase)) {
+ trna.SetAa().SetNcbieaa(i + 64);
+ remainder = test.substr(s_TrnaList[i].length());
+ break;
+ }
+ }
+ }
+}
+
+void CRNA_ref::SetRnaProductName(const string& product, string& remainder)
+{
+ remainder = kEmptyStr;
+ switch (GetType()) {
+ case CRNA_ref::eType_rRNA:
+ case CRNA_ref::eType_mRNA:
+ case CRNA_ref::eType_premsg:
+ if (NStr::IsBlank(product)) {
+ ResetExt();
+ } else {
+ SetExt().SetName(product);
+ }
+ break;
+ case CRNA_ref::eType_tRNA:
+ s_SetTrnaProduct(SetExt().SetTRNA(), product, remainder);
+ break;
+ default:
+ if (NStr::IsBlank(product)) {
+ SetExt().SetGen().ResetProduct();
+ if (!GetExt().GetGen().IsSetClass() && !GetExt().GetGen().IsSetQuals()) {
+ ResetExt();
+ }
+ } else {
+ SetExt().SetGen().SetProduct(product);
+ }
+ break;
+ }
+}
END_objects_SCOPE // namespace ncbi::objects::
diff --git a/c++/src/objects/seqfeat/SeqFeatData.cpp b/c++/src/objects/seqfeat/SeqFeatData.cpp
index 4ff89b0..872fd7d 100644
--- a/c++/src/objects/seqfeat/SeqFeatData.cpp
+++ b/c++/src/objects/seqfeat/SeqFeatData.cpp
@@ -1,4 +1,4 @@
-/* $Id: SeqFeatData.cpp 458380 2015-02-04 15:35:32Z ivanov $
+/* $Id: SeqFeatData.cpp 481786 2015-10-15 18:26:27Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1305,6 +1305,8 @@ START_SUBTYPE(attenuator)
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
ADD_QUAL(phenotype);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -1346,6 +1348,8 @@ START_SUBTYPE(CAAT_signal)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -1459,6 +1463,8 @@ START_SUBTYPE(enhancer)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
@@ -1505,6 +1511,8 @@ START_SUBTYPE(GC_signal)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -1526,6 +1534,8 @@ START_SUBTYPE(iDNA)
ADD_QUAL(note);
ADD_QUAL(number);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -1748,6 +1758,9 @@ START_SUBTYPE(misc_signal)
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
ADD_QUAL(phenotype);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
+ ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -1851,6 +1864,8 @@ START_SUBTYPE(polyA_signal)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -2001,6 +2016,8 @@ START_SUBTYPE(RBS)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
@@ -2271,6 +2288,8 @@ START_SUBTYPE(TATA_signal)
ADD_QUAL(map);
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(usedin);
END_SUBTYPE
@@ -2290,6 +2309,8 @@ START_SUBTYPE(terminator)
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
@@ -2498,6 +2519,8 @@ START_SUBTYPE(10_signal)
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
@@ -2518,6 +2541,8 @@ START_SUBTYPE(35_signal)
ADD_QUAL(note);
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
ADD_QUAL(usedin);
@@ -2848,6 +2873,8 @@ START_SUBTYPE(regulatory)
ADD_QUAL(old_locus_tag);
ADD_QUAL(operon);
ADD_QUAL(phenotype);
+ ADD_QUAL(pseudo);
+ ADD_QUAL(pseudogene);
ADD_QUAL(regulatory_class);
ADD_QUAL(standard_name);
END_SUBTYPE
@@ -3745,6 +3772,181 @@ CSeqFeatData::EFeatureLocationAllowed CSeqFeatData::AllowedFeatureLocation(ESubt
}
+bool CSeqFeatData::AllowStrandBoth(ESubtype subtype)
+{
+ bool rval = false;
+
+ switch (subtype) {
+ case eSubtype_regulatory:
+ case eSubtype_protein_bind:
+ case eSubtype_misc_feature:
+ case eSubtype_repeat_region:
+ case eSubtype_rep_origin:
+ case eSubtype_misc_recomb:
+ case eSubtype_S_region:
+ case eSubtype_centromere:
+ case eSubtype_telomere:
+ case eSubtype_variation:
+ case eSubtype_misc_binding:
+ case eSubtype_misc_difference:
+ case eSubtype_misc_structure:
+ case eSubtype_mobile_element:
+ case eSubtype_assembly_gap:
+ case eSubtype_LTR:
+ rval = true;
+ break;
+ default:
+ rval = false;
+ break;
+ }
+
+ return rval;
+}
+
+
+bool CSeqFeatData::RequireLocationIntervalsInBiologicalOrder(CSeqFeatData::ESubtype feat_subtype)
+{
+ bool required = true;
+ switch (feat_subtype)
+ {
+ case CSeqFeatData::eSubtype_pub:
+ case CSeqFeatData::eSubtype_het:
+ case CSeqFeatData::eSubtype_primer_bind:
+ case CSeqFeatData::eSubtype_misc_recomb:
+ required = false;
+ break;
+ default:
+ break;
+ }
+ return required;
+}
+
+
+bool CSeqFeatData::AllowAdjacentIntervals(CSeqFeatData::ESubtype feat_subtype)
+{
+ bool allowed = false;
+ switch (feat_subtype)
+ {
+ case CSeqFeatData::eSubtype_pub:
+ case CSeqFeatData::eSubtype_het:
+ case CSeqFeatData::eSubtype_primer_bind:
+ case CSeqFeatData::eSubtype_misc_recomb:
+ allowed = true;
+ break;
+ default:
+ break;
+ }
+ return allowed;
+}
+
+
+bool CSeqFeatData::ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, CSeqFeatData::EQualifier qual_type)
+{
+ // experiment and inference get their own panels
+ if (qual_type == CSeqFeatData::eQual_experiment || qual_type == CSeqFeatData::eQual_inference) {
+ return false;
+ }
+ // pseudo and pseudogene are handled separately
+ if (qual_type == CSeqFeatData::eQual_pseudogene || qual_type == CSeqFeatData::eQual_pseudo) {
+ return false;
+ }
+
+ if (qual_type == CSeqFeatData::eQual_product) {
+ if (feat_subtype == CSeqFeatData::eSubtype_mat_peptide
+ || feat_subtype == CSeqFeatData::eSubtype_sig_peptide
+ || feat_subtype == CSeqFeatData::eSubtype_transit_peptide
+ || feat_subtype == CSeqFeatData::eSubtype_C_region
+ || feat_subtype == CSeqFeatData::eSubtype_D_segment
+ || feat_subtype == CSeqFeatData::eSubtype_exon
+ || feat_subtype == CSeqFeatData::eSubtype_J_segment
+ || feat_subtype == CSeqFeatData::eSubtype_misc_feature
+ || feat_subtype == CSeqFeatData::eSubtype_N_region
+ || feat_subtype == CSeqFeatData::eSubtype_S_region
+ || feat_subtype == CSeqFeatData::eSubtype_V_region
+ || feat_subtype == CSeqFeatData::eSubtype_V_segment
+ || feat_subtype == CSeqFeatData::eSubtype_variation) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ if (feat_subtype == CSeqFeatData::eSubtype_gene)
+ {
+ if ( qual_type == CSeqFeatData::eQual_allele ||
+ qual_type == CSeqFeatData::eQual_gene_synonym ||
+ qual_type == CSeqFeatData::eQual_locus_tag ||
+ qual_type == CSeqFeatData::eQual_map
+ )
+ return true;
+ else
+ return false;
+ }
+
+
+ if (qual_type == CSeqFeatData::eQual_citation
+ || qual_type == CSeqFeatData::eQual_db_xref
+ || qual_type == CSeqFeatData::eQual_evidence
+ || qual_type == CSeqFeatData::eQual_exception
+ || qual_type == CSeqFeatData::eQual_gene
+ || qual_type == CSeqFeatData::eQual_gene_synonym
+ || qual_type == CSeqFeatData::eQual_insertion_seq
+ || qual_type == CSeqFeatData::eQual_label
+ || qual_type == CSeqFeatData::eQual_locus_tag
+ || qual_type == CSeqFeatData::eQual_note
+ || qual_type == CSeqFeatData::eQual_partial
+ || qual_type == CSeqFeatData::eQual_product
+ || qual_type == CSeqFeatData::eQual_pseudo
+ || qual_type == CSeqFeatData::eQual_rpt_unit
+ || qual_type == CSeqFeatData::eQual_transposon
+ || qual_type == CSeqFeatData::eQual_experiment
+ || qual_type == CSeqFeatData::eQual_trans_splicing
+ || qual_type == CSeqFeatData::eQual_ribosomal_slippage
+ || qual_type == CSeqFeatData::eQual_standard_name
+ || qual_type == CSeqFeatData::eQual_usedin) {
+ return false;
+ }
+ if (feat_subtype == CSeqFeatData::eSubtype_cdregion) {
+ if (qual_type == CSeqFeatData::eQual_codon_start
+ || qual_type == CSeqFeatData::eQual_codon
+ || qual_type == CSeqFeatData::eQual_EC_number
+ || qual_type == CSeqFeatData::eQual_gdb_xref
+ || qual_type == CSeqFeatData::eQual_number
+ || qual_type == CSeqFeatData::eQual_protein_id
+ //|| qual_type == CSeqFeatData::eQual_transl_except
+ || qual_type == CSeqFeatData::eQual_transl_table
+ || qual_type == CSeqFeatData::eQual_translation
+ || qual_type == CSeqFeatData::eQual_allele
+ || qual_type == CSeqFeatData::eQual_translation
+ || qual_type == CSeqFeatData::eQual_function
+ || qual_type == CSeqFeatData::eQual_old_locus_tag) {
+ return false;
+ }
+ }
+
+
+
+ if (qual_type == CSeqFeatData::eQual_map
+ && feat_subtype != CSeqFeatData::eSubtype_repeat_region
+ && feat_subtype != CSeqFeatData::eSubtype_gap) {
+ return false;
+ }
+ if (qual_type == CSeqFeatData::eQual_operon
+ && feat_subtype != CSeqFeatData::eSubtype_operon) {
+ return false;
+ }
+ return true;
+}
+
+
+bool CSeqFeatData::ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, const CGb_qual& qual)
+{
+ if (!qual.IsSetQual()) {
+ return false;
+ }
+ return ShouldRepresentAsGbqual(feat_subtype, CSeqFeatData::GetQualifierType(qual.GetQual()));
+}
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/seqfeat/Seq_feat.cpp b/c++/src/objects/seqfeat/Seq_feat.cpp
index ec18ae3..3a7d8aa 100644
--- a/c++/src/objects/seqfeat/Seq_feat.cpp
+++ b/c++/src/objects/seqfeat/Seq_feat.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_feat.cpp 459295 2015-02-17 18:12:32Z ivanov $
+/* $Id: Seq_feat.cpp 468197 2015-05-21 12:53:40Z kornbluh $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -508,6 +508,71 @@ CRef<CUser_object> CSeq_feat::FindExt(const string& ext_type)
return ret;
}
+void
+CSeq_feat::AddExt(CRef<CUser_object> ext, TAddExt add_flags)
+{
+ // ext must have type set
+ if( ! ext->IsSetType() || ! ext->GetType().IsStr()) {
+ NCBI_USER_THROW("Seq-feat Ext must have a type");
+ }
+
+ // if requested, remove all previous ones, effectively simulating
+ // a replace function.
+ if( add_flags & fAddExt_ReplaceAll ) {
+ const string & ext_type = ext->GetType().GetStr();
+ RemoveExt(ext_type);
+ }
+
+ SetExts().push_back(ext);
+}
+
+void
+CSeq_feat::RemoveExt(const string& ext_type)
+{
+ if ( IsSetExts() ) {
+ TExts & exts = SetExts();
+ // Exts are list, so constant time removal per element
+ ERASE_ITERATE(TExts, it, exts) {
+ const CObject_id& obj_type = (*it)->GetType();
+ if ( obj_type.IsStr() && obj_type.GetStr() == ext_type ) {
+ exts.erase(it);
+ }
+ }
+ if( exts.empty() ) {
+ ResetExts();
+ }
+ }
+ if ( IsSetExt()) {
+ if (GetExt().GetType().IsStr()) {
+ if (GetExt().GetType().GetStr() == ext_type) {
+ ResetExt();
+ }
+ else if (GetExt().GetType().GetStr() == "CombinedFeatureUserObjects") {
+ // build new ext vector since cannot remove easily as
+ // we go along.
+ TExt::TData new_ext_data;
+ TExt::TData & curr_ext_data = SetExt().SetData();
+ NON_CONST_ITERATE (TExt::TData, it, curr_ext_data) {
+ CUser_field& f = **it;
+ if (f.GetData().IsObject() &&
+ f.GetData().GetObject().GetType().IsStr() &&
+ f.GetData().GetObject().GetType().GetStr() == ext_type) {
+ continue;
+ }
+ new_ext_data.push_back(*it);
+ }
+
+ if( new_ext_data.empty() ) {
+ ResetExt();
+ } else if( new_ext_data.size() != curr_ext_data.size() ) {
+ // swap is constant time
+ new_ext_data.swap(curr_ext_data);
+ }
+ }
+ }
+ }
+}
+
ISeq_feat::~ISeq_feat(void)
{
diff --git a/c++/src/objects/seqfeat/SubSource.cpp b/c++/src/objects/seqfeat/SubSource.cpp
index 52c7d66..2984518 100644
--- a/c++/src/objects/seqfeat/SubSource.cpp
+++ b/c++/src/objects/seqfeat/SubSource.cpp
@@ -1,4 +1,4 @@
-/* $Id: SubSource.cpp 463567 2015-03-30 16:19:15Z ivanov $
+/* $Id: SubSource.cpp 484821 2015-11-16 16:24:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -170,9 +170,10 @@ string CSubSource::GetSubtypeName(CSubSource::TSubtype stype,
bool CSubSource::IsMultipleValuesAllowed(TSubtype subtype)
{
return subtype != eSubtype_chromosome
+ && subtype != eSubtype_sex
&& subtype != eSubtype_germline
&& subtype != eSubtype_rearranged
- && subtype != eSubtype_plastid_name
+ && subtype != eSubtype_plasmid_name
&& subtype != eSubtype_segment
&& subtype != eSubtype_country
&& subtype != eSubtype_transgenic
@@ -328,7 +329,7 @@ CRef<CDate> CSubSource::DateFromCollectionDate (const string& test) THROWS((CExc
if (!NStr::IsBlank(month)) {
for (size_t i = 0; i < ArraySize(sm_LegalMonths); i++) {
if (NStr::Equal(month, sm_LegalMonths[i])) {
- month_val = i + 1;
+ month_val = int(i + 1);
break;
}
}
@@ -517,6 +518,10 @@ string CSubSource::x_ParseDateRangeWithDelimiter(const string& orig_date, const
if (pos == string::npos) {
return "";
}
+ size_t second_pos = NStr::Find(orig_date.substr(pos + 1), delim, NStr::eNocase);
+ if (second_pos != string::npos) {
+ return "";
+ }
bool month_ambig = false;
string first_date = FixDateFormat(orig_date.substr(0, pos), true, month_ambig);
if (month_ambig || NStr::IsBlank(first_date)) {
@@ -550,8 +555,89 @@ string CSubSource::FixDateFormat (const string& orig_date)
return fix;
}
+// ISO Format for time is one of these:
+// HH:MM:SS
+// HH:MM
+// HH
+// Followed by either Z or +hh:mm to indicate an offset from Zulu
+bool CSubSource::IsISOFormatTime(const string& orig_time, int& hour, int& min, int& sec)
+{
+ int offset_hour = 0;
+ int offset_min = 0;
+ size_t suffix = NStr::Find(orig_time, "Z");
+ if (suffix == string::npos) {
+ suffix = NStr::Find(orig_time, "+");
+ if (suffix == string::npos ||
+ orig_time.substr(suffix).length() != 6 ||
+ !isdigit(orig_time.c_str()[suffix + 1]) ||
+ !isdigit(orig_time.c_str()[suffix + 2]) ||
+ orig_time.c_str()[suffix + 3] != ':' ||
+ !isdigit(orig_time.c_str()[suffix + 4]) ||
+ !isdigit(orig_time.c_str()[suffix + 5])) {
+ return false;
+ }
+ try {
+ offset_hour = NStr::StringToInt(orig_time.substr(suffix + 1, 2));
+ offset_min = NStr::StringToInt(orig_time.substr(suffix + 4, 2));
+ } catch (...) {
+ return false;
+ }
+ }
+ if (suffix != 2 && suffix != 5 && suffix != 8) {
+ return false;
+ }
+
+ if (!isdigit(orig_time.c_str()[0]) || !isdigit(orig_time.c_str()[1])) {
+ return false;
+ }
+ hour = 0;
+ min = 0;
+ sec = 0;
+ try {
+ hour = NStr::StringToInt(orig_time.substr(0, 2));
+ if (hour < 0 || hour > 23) {
+ return false;
+ }
+ hour -= offset_hour;
+ } catch (...) {
+ return false;
+ }
+ if (suffix > 2) {
+ if (!isdigit(orig_time.c_str()[3]) || !isdigit(orig_time.c_str()[4])) {
+ return false;
+ }
+ try {
+ min = NStr::StringToInt(orig_time.substr(3, 2));
+ if (min < 0 || min > 59) {
+ return false;
+ }
+ } catch (...) {
+ return false;
+ }
+ min -= offset_min;
+ }
+ if (suffix == 8) {
+ if (!isdigit(orig_time.c_str()[6]) || !isdigit(orig_time.c_str()[7])) {
+ return false;
+ }
+ try {
+ sec = NStr::StringToInt(orig_time.substr(6, 2));
+ if (sec < 0) {
+ // negative number bad
+ return false;
+ } else if (sec > 59) {
+ // too big
+ return false;
+ }
+ } catch (...) {
+ return false;
+ }
+ }
+
+ return true;
+}
-// ISO Formate for date is exactly 10 characters long OR exactly 7 characters long.
+// ISO Format for date is exactly 10 characters long OR exactly 7 characters long.
// For ten characters:
// First four characters must be digits, represent year.
// Fifth character must be dash.
@@ -562,16 +648,14 @@ string CSubSource::FixDateFormat (const string& orig_date)
// First four characters must be digits, represent year.
// Fifth character must be dash.
// Sixth and seventh characters must be digits, represent month, use zero padding.
-bool CSubSource::IsISOFormatDate (const string& orig_date)
+bool CSubSource::IsISOFormatDateOnly (const string& cpy)
{
- string cpy = orig_date;
- NStr::TruncateSpacesInPlace(cpy);
if (cpy.length() != 10 && cpy.length() != 7) {
return false;
}
bool rval = true;
size_t pos = 0;
- string::iterator it = cpy.begin();
+ string::const_iterator it = cpy.begin();
while (it != cpy.end() && rval) {
if (pos == 4 || pos == 7) {
if (*it != '-') {
@@ -603,6 +687,20 @@ bool CSubSource::IsISOFormatDate (const string& orig_date)
return rval;
}
+bool CSubSource::IsISOFormatDate(const string& orig_date)
+{
+ string cpy = orig_date;
+ NStr::TruncateSpacesInPlace(cpy);
+ size_t time_pos = NStr::Find(cpy, "T");
+ if (time_pos == string::npos) {
+ return IsISOFormatDateOnly(cpy);
+ } else {
+ int h, m, s;
+ return (IsISOFormatDateOnly(cpy.substr(0, time_pos)) &&
+ IsISOFormatTime(cpy.substr(time_pos + 1), h, m, s));
+ }
+
+}
CRef<CDate> CSubSource::GetDateFromISODate(const string& orig_date)
{
@@ -626,11 +724,12 @@ CRef<CDate> CSubSource::GetDateFromISODate(const string& orig_date)
// return 1-based month number if found, 0 for error
-size_t GetMonthNumberFromString(const string& month)
+static
+int GetMonthNumberFromString(const string& month)
{
for (size_t i = 0; i < ArraySize(sm_LegalMonths); i++) {
if (NStr::StartsWith(month, sm_LegalMonths[i], NStr::eNocase)) {
- return i + 1;
+ return int(i + 1);
}
}
return 0;
@@ -829,7 +928,7 @@ string CSubSource::FixDateFormat (const string& test, bool month_first, bool& mo
try {
val1 = NStr::StringToInt (tokens[0]);
val2 = NStr::StringToInt (tokens[1]);
- } catch (CException& e) {
+ } catch (CException& /*e*/) {
// not actually numbers
return "";
}
@@ -861,7 +960,7 @@ string CSubSource::FixDateFormat (const string& test, bool month_first, bool& mo
// make sure day is valid
if (day > 0 && !NStr::IsBlank(month) && year > -1) {
- size_t month_num = GetMonthNumberFromString(month);
+ int month_num = GetMonthNumberFromString(month);
if (month_num == 0) {
return "";
} else if (!IsDayValueOkForMonth(day, month_num, year)) {
@@ -1004,12 +1103,12 @@ void CSubSource::IsCorrectLatLonFormat (string lat_lon, bool& format_correct, bo
int precision_lat = 0;
size_t pos = NStr::Find(pieces[0], ".");
if (pos != string::npos) {
- precision_lat = pieces[0].length() - pos - 1;
+ precision_lat = int(pieces[0].length() - pos - 1);
}
int precision_lon = 0;
pos = NStr::Find(pieces[2], ".");
if (pos != string::npos) {
- precision_lon = pieces[2].length() - pos - 1;
+ precision_lon = int(pieces[2].length() - pos - 1);
}
char reformatted[1000];
@@ -1069,6 +1168,20 @@ string s_GetDefaultDir(bool is_negative, string default_dir)
return dir;
}
+static void s_RemoveLeadingZeros(string& token)
+{
+
+ size_t index = 0;
+ while (index < token.size() &&
+ token[index] == '0' &&
+ (index + 1 < token.size() && isdigit(token[index + 1]))) {
+ ++index;
+ }
+ if (index != 0) {
+ token = token.substr(index);
+ }
+}
+
static string s_GetNumFromLatLonToken (string token, string default_dir)
{
@@ -1095,6 +1208,7 @@ static string s_GetNumFromLatLonToken (string token, string default_dir)
is_negative = true;
token = token.substr(1);
}
+
if (NStr::IsBlank(dir)) {
dir = s_GetDefaultDir(is_negative, default_dir);
} else if (is_negative) {
@@ -1196,6 +1310,8 @@ static string s_GetNumFromLatLonToken (string token, string default_dir)
}
}
+ s_RemoveLeadingZeros(token);
+
if (prev_start == 0) {
if (!NStr::IsBlank(dir)) {
token = token + " " + dir;
@@ -1411,6 +1527,7 @@ string CSubSource::FixLatLonFormat (string orig_lat_lon, bool guess)
NStr::ReplaceInPlace (cpy, "EAST", "E");
NStr::ReplaceInPlace (cpy, "WEST", "W");
NStr::ReplaceInPlace (cpy, " AND ", " "); // treat AND like a space delimiter
+ NStr::ReplaceInPlace (cpy, "_", " ");
NStr::ReplaceInPlace (cpy, " ", " "); // double-spaces become single spaces
size_t lat_pos = NStr::Find (cpy, "LAT");
@@ -1883,6 +2000,7 @@ string CSubSource::ValidateLatLonCountry (const string& input_countryname, strin
if (m_LatLonWaterMap->IsCountryInLatLon(country, lat_value, lon_value)) {
return "";
}
+ } else if (NStr::EqualNocase (country, "Palestine") || NStr::EqualNocase (country, "State of Palestine")) {
} else {
// report unrecognized country
return "";
@@ -1898,6 +2016,15 @@ string CSubSource::ValidateLatLonCountry (const string& input_countryname, strin
if (NStr::EqualNocase (country, "China") && NStr::EqualNocase (cguess, "Hong Kong")) {
return "";
}
+ if (NStr::EqualNocase (country, "USA") && NStr::EqualNocase (cguess, "Puerto Rico")) {
+ return "";
+ }
+ if ((NStr::EqualNocase (country, "Palestine") ||
+ NStr::EqualNocase (country, "State of Palestine")) &&
+ (NStr::EqualNocase (cguess, "Gaza Strip") ||
+ NStr::EqualNocase (cguess, "West Bank"))) {
+ return "";
+ }
if (NStr::IsBlank (cguess) && (! NStr::IsBlank (wguess))) {
string parent = x_FindSurroundingOcean (wguess);
@@ -2309,7 +2436,7 @@ bool CSubSource::IsAltitudeValid (const string& value)
string number = "";
string units = "";
s_CollectNumberAndUnits(value, number, units);
- if (NStr::IsBlank(number) || !NStr::EqualCase(units, "m.")) {
+ if (NStr::IsBlank(number) || !NStr::EqualCase(units, "m")) {
return false;
} else {
return true;
@@ -2333,14 +2460,14 @@ string CSubSource::FixAltitude (const string& value)
double val = NStr::StringToDouble(number);
val *= 0.3048;
NStr::NumericToString(number, val);
- units = "m.";
+ units = "m";
}
if (NStr::Equal(units, "m.")
|| NStr::Equal(units, "meters")
|| NStr::Equal(units, "meter")
|| NStr::Equal(units, "m")) {
- return number + " " + "m.";
+ return number + " " + "m";
} else {
return "";
}
@@ -2609,6 +2736,7 @@ static const char* const s_Countries[] = {
"Pacific Ocean",
"Pakistan",
"Palau",
+ "Palestine",
"Palmyra Atoll",
"Panama",
"Papua New Guinea",
@@ -2654,6 +2782,7 @@ static const char* const s_Countries[] = {
"Spain",
"Spratly Islands",
"Sri Lanka",
+ "State of Palestine",
"Sudan",
"Suriname",
"Svalbard",
@@ -3372,11 +3501,8 @@ string CCountries::NewFixCountry (const string& test)
string input = test;
- if (NStr::StartsWith(input, "\"")) {
- input = input.substr(1);
- }
- if (NStr::EndsWith(input, "\"")) {
- input = input.substr(0, input.length() - 1);
+ if (NStr::StartsWith(input, "\"") && NStr::EndsWith(input, "\"")) {
+ input = input.substr(1, input.length() - 2);
}
NStr::TruncateSpacesInPlace(input);
@@ -3479,16 +3605,25 @@ string CCountries::CountryFixupItem(const string &input, bool capitalize_after_c
{
string country = NewFixCountry (input);
string new_country = country;
- SIZE_TYPE pos = NStr::Find(country,":");
- if (pos != NPOS)
+ SIZE_TYPE country_end_pos = NStr::Find(country,":");
+ if (country_end_pos != NPOS)
{
- string after = country.substr(pos+1);
- if (!after.empty())
+ SIZE_TYPE pos = country_end_pos;
+ while (country.c_str()[pos] == ',' || country.c_str()[pos] == ':'
+ || isspace(country.c_str()[pos]))
{
+ pos++;
+ }
+ string after = country.substr(pos);
+ if (after.empty()) {
+ if (pos > country_end_pos) {
+ new_country = country.substr(0, country_end_pos);
+ }
+ } else {
NStr::TruncateSpacesInPlace(after,NStr::eTrunc_Begin);
if (capitalize_after_colon)
after = CapitalizeFirstLetterOfEveryWord (after);
- new_country = country.substr(0,pos);
+ new_country = country.substr(0,country_end_pos);
new_country += ": " + after;
}
}
@@ -4695,13 +4830,12 @@ bool CLatLonCountryMap::IsCountryInLatLon(const string& country, double lat,
const CCountryExtreme *
CLatLonCountryMap::x_FindCountryExtreme(const string& country)
{
- int L, R, mid;
+ size_t L, R, mid;
if (NStr::IsBlank (country)) return NULL;
L = 0;
R = m_CountryExtremes.size() - 1;
- mid = 0;
while (L < R) {
mid = (L + R) / 2;
@@ -4729,9 +4863,9 @@ bool CLatLonCountryMap::HaveLatLonForRegion(const string& region)
}
-int CLatLonCountryMap::x_GetLatStartIndex (int y)
+size_t CLatLonCountryMap::x_GetLatStartIndex (int y)
{
- int L, R, mid;
+ size_t L, R, mid;
L = 0;
R = m_LatLonSortedList.size() - 1;
diff --git a/c++/src/objects/seqfeat/Variation_ref.cpp b/c++/src/objects/seqfeat/Variation_ref.cpp
index cfefa5f..289d090 100644
--- a/c++/src/objects/seqfeat/Variation_ref.cpp
+++ b/c++/src/objects/seqfeat/Variation_ref.cpp
@@ -1,4 +1,4 @@
-/* $Id: Variation_ref.cpp 341192 2011-10-17 23:59:36Z dicuccio $
+/* $Id: Variation_ref.cpp 450796 2014-10-30 16:55:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -771,7 +771,7 @@ static void s_SetReplaces(CVariation_ref& ref,
has_del = true;
} else {
CRef<CDelta_item> item(new CDelta_item);
- item->SetSeq().SetLiteral().SetLength(rep.size());
+ item->SetSeq().SetLiteral().SetLength(TSeqPos(rep.size()));
if (seq_type == CVariation_ref::eSeqType_na) {
item->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(rep);
} else {
diff --git a/c++/src/objects/seqfeat/cell_line.inc b/c++/src/objects/seqfeat/cell_line.inc
index 674d703..d25336d 100644
--- a/c++/src/objects/seqfeat/cell_line.inc
+++ b/c++/src/objects/seqfeat/cell_line.inc
@@ -1,4 +1,4 @@
-/* $Id: cell_line.inc 458907 2015-02-11 15:50:55Z ivanov $
+/* $Id: cell_line.inc 458797 2015-02-10 15:36:36Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/ecnum_ambiguous.inc b/c++/src/objects/seqfeat/ecnum_ambiguous.inc
index 4a97049..9c68845 100644
--- a/c++/src/objects/seqfeat/ecnum_ambiguous.inc
+++ b/c++/src/objects/seqfeat/ecnum_ambiguous.inc
@@ -1,4 +1,4 @@
-/* $Id: ecnum_ambiguous.inc 454031 2014-12-10 14:50:55Z ivanov $
+/* $Id: ecnum_ambiguous.inc 453849 2014-12-08 18:54:49Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/ecnum_deleted.inc b/c++/src/objects/seqfeat/ecnum_deleted.inc
index 41d574a..9298deb 100644
--- a/c++/src/objects/seqfeat/ecnum_deleted.inc
+++ b/c++/src/objects/seqfeat/ecnum_deleted.inc
@@ -1,4 +1,4 @@
-/* $Id: ecnum_deleted.inc 454031 2014-12-10 14:50:55Z ivanov $
+/* $Id: ecnum_deleted.inc 453849 2014-12-08 18:54:49Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/ecnum_replaced.inc b/c++/src/objects/seqfeat/ecnum_replaced.inc
index 72f9bd4..b95e017 100644
--- a/c++/src/objects/seqfeat/ecnum_replaced.inc
+++ b/c++/src/objects/seqfeat/ecnum_replaced.inc
@@ -1,4 +1,4 @@
-/* $Id: ecnum_replaced.inc 454031 2014-12-10 14:50:55Z ivanov $
+/* $Id: ecnum_replaced.inc 453849 2014-12-08 18:54:49Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/ecnum_specific.inc b/c++/src/objects/seqfeat/ecnum_specific.inc
index 80e22a4..021e2d5 100644
--- a/c++/src/objects/seqfeat/ecnum_specific.inc
+++ b/c++/src/objects/seqfeat/ecnum_specific.inc
@@ -1,4 +1,4 @@
-/* $Id: ecnum_specific.inc 457367 2015-01-22 14:42:41Z ivanov $
+/* $Id: ecnum_specific.inc 457265 2015-01-21 19:09:40Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqfeat/institution_codes.inc b/c++/src/objects/seqfeat/institution_codes.inc
index de39bb9..16f96ba 100644
--- a/c++/src/objects/seqfeat/institution_codes.inc
+++ b/c++/src/objects/seqfeat/institution_codes.inc
@@ -1,4 +1,4 @@
-/* $Id: institution_codes.inc 467816 2015-05-18 13:40:32Z ivanov $
+/* $Id: institution_codes.inc 484377 2015-11-10 16:38:18Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -182,7 +182,8 @@ static const char* const kInstitutionCollectionCodeList[] = {
"AM:Mineralogy s Australian Museum, Earth Sciences: Mineralogy and Petrology Collection",
"AM:Ornithology s Australian Museum, Vertebrate Collections: Ornithology",
"AM:Palaeontology s Australian Museum, Palaeontology Collection",
-"AM<BLG> s Asenovgrad Museum",
+"AM<ARG> s Acatushun Museum at the Estancia Haberton",
+"AM<BLG> s Asenovgrad Paleontology Museum",
"AMAZ s Universidad Nacional de la Amazonia Peruana",
"AMC c Department of Biologics Research",
"AMCC s Ambrose Monell Cryo Collection, American Museum of Natural History",
@@ -216,6 +217,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"ANDES:A s La Universidad de Los Andes, Amphibian Collection",
"ANDES:O s La Universidad de Los Andes, Ornithology Collection",
"ANES s Anadolu University, Biology Department",
+"ANFC s Australian National Fish Collection",
"ANFM s Associazione Naturalisti Forlivesi Pro Museo",
"ANG s Arboretum de la Maulevrie",
"ANGU s Instituto Nacional de Tecnologia Agropecuaria",
@@ -1160,7 +1162,8 @@ static const char* const kInstitutionCollectionCodeList[] = {
"CO s Museum National d'Histoire Naturelle, Department of Marine Biology",
"COA s Herbario, Universidad de Cordoba - Jardin Botanico de Cordoba",
"COA<USA-ME> s College of the Atlantic, Museum",
-"COAH s Instituto Amazonico de Investigaciones Cientificas SINCHI",
+"COAD c Colecao Octavio de Almeida Drumond",
+"COAH s Herbario Amazonico Colombiano (Instituto Amazonico de Investigaciones Cientificas SINCHI)",
"COCA s Comision Tecnico Consultiva de Coeficientes de Agostadero (COTECOCA)",
"COCH s Universidad Mayor de San Simon, Departamento de Botanica",
"COCO s Colorado College, Biology Department",
@@ -1618,6 +1621,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"EDNC s Raleigh, North Carolina Department of Agriculture",
"EEBP s Estacao Experimental de Biologia e Piscicultura de Pirassununga",
"EELM s Estacion Experimental Agricola de la Molina",
+"EERU s Economic Entomology Research Unit",
"EFC s Escola de Florestas",
"EFCC s Epping Forest Conservation Centre",
"EFH s Forestry Commission",
@@ -2045,7 +2049,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"GOD s Charterhouse School Museum",
"GOE<DEU> s Institut und Museum fuer Geologie und Palaeontologie",
"GOE<GBR> s Goole Scientific Society",
-"GOET s Universitaet Goettingen, Abteilung Systematische Botanik",
+"GOET s Herbarium Universitat Gottingen",
"GOFS s Free State National Botanical Garden",
"GOW s Clydebank High School",
"GP s Instituto de Geociencias, Universidade de Sao Paulo",
@@ -2103,6 +2107,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"GUBIOTJT c Freshwater microalgae collection and culture laboratory",
"GUH s HNB Garhwal University, Botany Department",
"GUM s Glasgow University Museum (Hunter Museum)",
+"GUM<IRN> s Mycological herbarium of University of Guilan",
"GUMACC c Gotheburg University Marine Algal Culture Collection",
"GUYN s Fundacion Jardin Botanico del Orinoco",
"GVF s George Vanderbilt Foundation",
@@ -2528,6 +2533,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"IEAU s Istituto di Entomologia Agraria dell'Universita",
"IEB s Instituto de Ecologia, A.C.",
"IEBC c International Entomopathogenic Bacillus Centre (WHO)",
+"IEBR s Institute of Ecology and Biological Resources",
"IEC s Centre D'Etude sur les Ressources Vegetales",
"IECA s Czech Academy of Science, Institute of Entomology",
"IEEUACH s Universidad Austral de Chile, Instituto de Ecologia y Evolucion",
@@ -2864,7 +2870,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"JCM c Japan Collection of Microorganisms",
"JCRB c Japanese Collection of Research Bioresources Cell Bank",
"JCT c James Cook Townsville",
-"JE s Friedrich-Schiller-Universitaet Jena",
+"JE s Herbarium Haussknecht, Jena",
"JEF s Indiana University Southeast, Biology Department",
"JEL c Joyce E. Longcore Chytrid Collection at the University of Maine",
"JEL<LVA> s Latvian Agricultural Academy, Plant Protection Department",
@@ -2954,6 +2960,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"KCFS s King's College",
"KCK s Dick Institute",
"KCLB c Korean Cell Line Bank",
+"KCOM c Korean Collection for Oral Microbiology",
"KCS s University of London, King's College, Botany Department",
"KCTC c Korean Collection for Type Cultures",
"KDL s Kendal Museum",
@@ -3775,6 +3782,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"MMB s Moravske Muzeum",
"MMBC s Moravske Muzeum [Moravian Museum]",
"MMBS s Mukaishima Marine Biological Station",
+"MMCC c MARDI Microbial Culture Collection",
"MMChPV s Museo Municipal El Chocon",
"MMCM s Museum of Malawi",
"MMF s Museu Municipal do Funchal",
@@ -4032,7 +4040,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"MUDH s The Hague, Museon",
"MUFE s University of Marmara, Department of Botany",
"MUFM s Manipur University Fish Museum",
-"MUFS s Department of Animal Science",
+"MUFS s Department of Animal Science, Miyazaki University",
"MUGM s Museo de Ciencias Naturales, Coleccion \"Gustavo Orces\" (Ecuador)",
"MUHW s Marshall University, Biological Sciences Department",
"MUJ s Museo Javeriano de Historia Natural, Laboratoriao de Entomologia",
@@ -4554,6 +4562,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"NTM<FRA> s Museum d'Histoire Naturelle de Nantes",
"NTN s Central Museum and Art Gallery",
"NTNU s National Taiwan Normal University",
+"NTNU-VM s Norwegian University of Science and Technology, Museum of Natural History and Archaeology",
"NTOU sc Institute of Marine Biology, National Taiwan Ocean University",
"NTS s Nevada Operations Office, U.S. Department of Energy",
"NTSC s University of North Texas, Biological Sciences Department",
@@ -4785,7 +4794,8 @@ static const char* const kInstitutionCollectionCodeList[] = {
"PECA s Pratt Education Center and Aquarium",
"PECS s Janus Pannonius Museum, Natural History Department",
"PEFO s Petrified Forest",
-"PEI s Agriculture and Agri-Food Canada",
+"PEI cb Paul-Ehrlich-Institut",
+"PEI<CAN> s Agriculture and Agri-Food Canada",
"PEL s Universidade Federal de Pelotas, Departamento de Botanica",
"PEM<CHN> s Beijing Medical University, Botany Department",
"PEM<ZAF> s Port Elizabeth Museum",
@@ -4819,6 +4829,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"PH s Academy of Natural Sciences, Botany Department",
"PHA s Pharmaceutical Society of Great Britain",
"PHBL c Philip Harris Biological Ltd.",
+"PHEL s Plant Health and Environment Laboratory",
"PHG s Peper Harow",
"PHIL s University of the Sciences in Philadelphia, Biological Sciences Department",
"PI<DEU> s Institut und Museum fuer Geologie und Palaeontologie",
@@ -4833,6 +4844,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"PIN<RUS> s Paleontological Institute, Russian Academy of Sciences",
"PINN s Pinnacles National Monument",
"PIR c Bulgarian Research Culture Collection",
+"PISR s Pechora-Ilych State Reserve, Russia",
"PIUU s Paleontological Institut, University of Uppsala",
"PKDC s Divisao de Museu de Historia Natural",
"PKM s V. G. Belinsk Pedagogical Institute of Penza",
@@ -5557,6 +5569,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"SMN s Simao District National Medical and Pharmaceutical Institute",
"SMNG s Senckenberg Museum fuer Naturkunde Goerlitz",
"SMNH<CAN> s Saskatchewan Museum of Natural History",
+"SMNH<ISR> s Steinhardt Museum of Natural History",
"SMNH<SWE> s Swedish Museum of Natural History",
"SMNH<UKR> s State Museum of Natural History",
"SMNH<USA-KS> s Schmidt Museum of Natural History, Emporia State University",
@@ -5596,6 +5609,8 @@ static const char* const kInstitutionCollectionCodeList[] = {
"SNOMNH s Sam Nobel Oklahoma Museum of Natural History",
"SNP<MYS> s Sabah Parks, Botany Section",
"SNPH s Sehlabathebe National Park",
+"SNSD s Senckenberg Natural History Collections Dresden, Museum of Zoology",
+"SNSD:Moll s Senckenberg Natural History Collections Dresden, Museum of Zoology, ",
"SNU s Seoul National University, School of Biological Sciences",
"SNUA s Seoul National University, The Arboretum",
"SNW s Shropshire and North Wales Natural History and Antiquarian Society",
@@ -5904,6 +5919,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"TJDC s Tianjin Municipal Institute for Drug Control, Department of Traditional Chinese Medicine",
"TJMP s Tianjin Institute of Medical and Pharmaceutical Sciences",
"TK s Tomsk State University",
+"TK<MEX> s Coleccion de mamiferos del Centro Interdisciplinario de Investigacion para el Desarrollo Integral Regional Unidad Durango",
"TKB s University of Tsukuba",
"TKNM s Twickenham Girls' School",
"TKPM s Tokushima Prefectural Museum",
@@ -6302,7 +6318,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"UMNH:Mamm s Utah Museum of Natural History, Mammal collection",
"UMO<GBR> s University Museum of Natural History",
"UMO<USA-ME> s University of Maine",
-"UMO<USA-MO> s University of Missouri, Museum Support Center",
+"UMO<USA-MO> s Dunn-Palmer Herbarium, University of Missouri, Museum Support Center",
"UMOC s University of Missouri, Museum of Zoology",
"UMRC c University of Minnesota Rhizobium Collection",
"UMRM s W.R. Enns Entomology Museum",
@@ -6364,6 +6380,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"UNLV s University of Nevada, Las Vegas, Department of Biological Sciences",
"UNM s University of New Mexico, Department of Biology",
"UNMC s University of New Mexico",
+"UNMDP s Universidad Nacional de Mar del Plata, Mar del Plata, Argentina",
"UNN s University of Nigeria, Botany Department",
"UNNF s Universite de Nancy",
"UNO s University of Nebraska at Omaha",
@@ -6508,6 +6525,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"UT<USA-UT> s University of Utah Herbarium",
"UTA s University of Texas at Arlington",
"UTA:A s University of Texas at Arlington, Amphibian Collection",
+"UTA:R s University of Texas at Arlington, Reptile collection",
"UTAI s Tel Aviv University",
"UTC s Utah State University, Biology Department",
"UTCI s University of Tennessee at Chattanooga Insect Collection",
@@ -6972,7 +6990,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
"ZIA s National Academy of Sciences of Armenia",
"ZIAN s Zoological Institute, Academy of Sciences",
"ZICUP s Zoological Institute Charles University",
-"ZIHU s Zoological Institute, Hokkaido University",
+"ZIHU s Hiroshima University, Zoological Institute",
"ZIK s Ukrainian Academy of Sciences, Zoological Institute",
"ZIKU s Zoological Institute, Kochi University",
"ZIL s Academy of Sciences, Zoological Institute",
diff --git a/c++/src/objects/seqfeat/institution_codes.txt b/c++/src/objects/seqfeat/institution_codes.txt
index 91af3d2..15578fa 100644
--- a/c++/src/objects/seqfeat/institution_codes.txt
+++ b/c++/src/objects/seqfeat/institution_codes.txt
@@ -149,7 +149,8 @@ AM:Marine_Invertebrates s Australian Museum, Invertebrate Collections: Marine an
AM:Mineralogy s Australian Museum, Earth Sciences: Mineralogy and Petrology Collection
AM:Ornithology s Australian Museum, Vertebrate Collections: Ornithology
AM:Palaeontology s Australian Museum, Palaeontology Collection
-AM<BLG> s Asenovgrad Museum
+AM<ARG> s Acatushun Museum at the Estancia Haberton
+AM<BLG> s Asenovgrad Paleontology Museum
AMAZ s Universidad Nacional de la Amazonia Peruana
AMC c Department of Biologics Research
AMCC s Ambrose Monell Cryo Collection, American Museum of Natural History
@@ -183,6 +184,7 @@ ANDES s La Universidad de Los Andes
ANDES:A s La Universidad de Los Andes, Amphibian Collection
ANDES:O s La Universidad de Los Andes, Ornithology Collection
ANES s Anadolu University, Biology Department
+ANFC s Australian National Fish Collection
ANFM s Associazione Naturalisti Forlivesi Pro Museo
ANG s Arboretum de la Maulevrie
ANGU s Instituto Nacional de Tecnologia Agropecuaria
@@ -1127,7 +1129,8 @@ CNWGRGL b Chinese National Waterfowl Germplasm Resources Gene Library
CO s Museum National d'Histoire Naturelle, Department of Marine Biology
COA s Herbario, Universidad de Cordoba - Jardin Botanico de Cordoba
COA<USA-ME> s College of the Atlantic, Museum
-COAH s Instituto Amazonico de Investigaciones Cientificas SINCHI
+COAD c Colecao Octavio de Almeida Drumond
+COAH s Herbario Amazonico Colombiano (Instituto Amazonico de Investigaciones Cientificas SINCHI)
COCA s Comision Tecnico Consultiva de Coeficientes de Agostadero (COTECOCA)
COCH s Universidad Mayor de San Simon, Departamento de Botanica
COCO s Colorado College, Biology Department
@@ -1585,6 +1588,7 @@ EDH s Plinian Society
EDNC s Raleigh, North Carolina Department of Agriculture
EEBP s Estacao Experimental de Biologia e Piscicultura de Pirassununga
EELM s Estacion Experimental Agricola de la Molina
+EERU s Economic Entomology Research Unit
EFC s Escola de Florestas
EFCC s Epping Forest Conservation Centre
EFH s Forestry Commission
@@ -2012,7 +2016,7 @@ GO s Philosophical Society
GOD s Charterhouse School Museum
GOE<DEU> s Institut und Museum fuer Geologie und Palaeontologie
GOE<GBR> s Goole Scientific Society
-GOET s Universitaet Goettingen, Abteilung Systematische Botanik
+GOET s Herbarium Universitat Gottingen
GOFS s Free State National Botanical Garden
GOW s Clydebank High School
GP s Instituto de Geociencias, Universidade de Sao Paulo
@@ -2070,6 +2074,7 @@ GUAY s Universidad de Guayaquil
GUBIOTJT c Freshwater microalgae collection and culture laboratory
GUH s HNB Garhwal University, Botany Department
GUM s Glasgow University Museum (Hunter Museum)
+GUM<IRN> s Mycological herbarium of University of Guilan
GUMACC c Gotheburg University Marine Algal Culture Collection
GUYN s Fundacion Jardin Botanico del Orinoco
GVF s George Vanderbilt Foundation
@@ -2495,6 +2500,7 @@ IEAS s Institute of Entomology
IEAU s Istituto di Entomologia Agraria dell'Universita
IEB s Instituto de Ecologia, A.C.
IEBC c International Entomopathogenic Bacillus Centre (WHO)
+IEBR s Institute of Ecology and Biological Resources
IEC s Centre D'Etude sur les Ressources Vegetales
IECA s Czech Academy of Science, Institute of Entomology
IEEUACH s Universidad Austral de Chile, Instituto de Ecologia y Evolucion
@@ -2831,7 +2837,7 @@ JCE s Jiangxi College of Education, Biology Department
JCM c Japan Collection of Microorganisms
JCRB c Japanese Collection of Research Bioresources Cell Bank
JCT c James Cook Townsville
-JE s Friedrich-Schiller-Universitaet Jena
+JE s Herbarium Haussknecht, Jena
JEF s Indiana University Southeast, Biology Department
JEL c Joyce E. Longcore Chytrid Collection at the University of Maine
JEL<LVA> s Latvian Agricultural Academy, Plant Protection Department
@@ -2921,6 +2927,7 @@ KCCM c Korean Culture Center of Microorganisms, Department of Food Engineering
KCFS s King's College
KCK s Dick Institute
KCLB c Korean Cell Line Bank
+KCOM c Korean Collection for Oral Microbiology
KCS s University of London, King's College, Botany Department
KCTC c Korean Collection for Type Cultures
KDL s Kendal Museum
@@ -3742,6 +3749,7 @@ MM<FRA> s University of Montpellier
MMB s Moravske Muzeum
MMBC s Moravske Muzeum [Moravian Museum]
MMBS s Mukaishima Marine Biological Station
+MMCC c MARDI Microbial Culture Collection
MMChPV s Museo Municipal El Chocon
MMCM s Museum of Malawi
MMF s Museu Municipal do Funchal
@@ -3999,7 +4007,7 @@ MUCV s Monash University, Biological Sciences Department
MUDH s The Hague, Museon
MUFE s University of Marmara, Department of Botany
MUFM s Manipur University Fish Museum
-MUFS s Department of Animal Science
+MUFS s Department of Animal Science, Miyazaki University
MUGM s Museo de Ciencias Naturales, Coleccion "Gustavo Orces" (Ecuador)
MUHW s Marshall University, Biological Sciences Department
MUJ s Museo Javeriano de Historia Natural, Laboratoriao de Entomologia
@@ -4521,6 +4529,7 @@ NTM s Museum and Art Gallery of the Northern Territory
NTM<FRA> s Museum d'Histoire Naturelle de Nantes
NTN s Central Museum and Art Gallery
NTNU s National Taiwan Normal University
+NTNU-VM s Norwegian University of Science and Technology, Museum of Natural History and Archaeology
NTOU sc Institute of Marine Biology, National Taiwan Ocean University
NTS s Nevada Operations Office, U.S. Department of Energy
NTSC s University of North Texas, Biological Sciences Department
@@ -4752,7 +4761,8 @@ PE s Institute of Botany, Chinese Academy of Sciences
PECA s Pratt Education Center and Aquarium
PECS s Janus Pannonius Museum, Natural History Department
PEFO s Petrified Forest
-PEI s Agriculture and Agri-Food Canada
+PEI cb Paul-Ehrlich-Institut
+PEI<CAN> s Agriculture and Agri-Food Canada
PEL s Universidade Federal de Pelotas, Departamento de Botanica
PEM<CHN> s Beijing Medical University, Botany Department
PEM<ZAF> s Port Elizabeth Museum
@@ -4786,6 +4796,7 @@ PGSC<USA-NC> c Pseudomonas Genetic Stock Center
PH s Academy of Natural Sciences, Botany Department
PHA s Pharmaceutical Society of Great Britain
PHBL c Philip Harris Biological Ltd.
+PHEL s Plant Health and Environment Laboratory
PHG s Peper Harow
PHIL s University of the Sciences in Philadelphia, Biological Sciences Department
PI<DEU> s Institut und Museum fuer Geologie und Palaeontologie
@@ -4800,6 +4811,7 @@ PIN<GBR> s Philosophical Institution of Newport
PIN<RUS> s Paleontological Institute, Russian Academy of Sciences
PINN s Pinnacles National Monument
PIR c Bulgarian Research Culture Collection
+PISR s Pechora-Ilych State Reserve, Russia
PIUU s Paleontological Institut, University of Uppsala
PKDC s Divisao de Museu de Historia Natural
PKM s V. G. Belinsk Pedagogical Institute of Penza
@@ -5524,6 +5536,7 @@ SMMC s Second Military Medical College
SMN s Simao District National Medical and Pharmaceutical Institute
SMNG s Senckenberg Museum fuer Naturkunde Goerlitz
SMNH<CAN> s Saskatchewan Museum of Natural History
+SMNH<ISR> s Steinhardt Museum of Natural History
SMNH<SWE> s Swedish Museum of Natural History
SMNH<UKR> s State Museum of Natural History
SMNH<USA-KS> s Schmidt Museum of Natural History, Emporia State University
@@ -5563,6 +5576,8 @@ SNMNH s Saudi Arabian National Museum of Natural History
SNOMNH s Sam Nobel Oklahoma Museum of Natural History
SNP<MYS> s Sabah Parks, Botany Section
SNPH s Sehlabathebe National Park
+SNSD s Senckenberg Natural History Collections Dresden, Museum of Zoology
+SNSD:Moll s Senckenberg Natural History Collections Dresden, Museum of Zoology,
SNU s Seoul National University, School of Biological Sciences
SNUA s Seoul National University, The Arboretum
SNW s Shropshire and North Wales Natural History and Antiquarian Society
@@ -5871,6 +5886,7 @@ TIU s Tokyo Imperial University, Science College Museum
TJDC s Tianjin Municipal Institute for Drug Control, Department of Traditional Chinese Medicine
TJMP s Tianjin Institute of Medical and Pharmaceutical Sciences
TK s Tomsk State University
+TK<MEX> s Coleccion de mamiferos del Centro Interdisciplinario de Investigacion para el Desarrollo Integral Regional Unidad Durango
TKB s University of Tsukuba
TKNM s Twickenham Girls' School
TKPM s Tokushima Prefectural Museum
@@ -6269,7 +6285,7 @@ UMNH s Utah Museum of Natural History
UMNH:Mamm s Utah Museum of Natural History, Mammal collection
UMO<GBR> s University Museum of Natural History
UMO<USA-ME> s University of Maine
-UMO<USA-MO> s University of Missouri, Museum Support Center
+UMO<USA-MO> s Dunn-Palmer Herbarium, University of Missouri, Museum Support Center
UMOC s University of Missouri, Museum of Zoology
UMRC c University of Minnesota Rhizobium Collection
UMRM s W.R. Enns Entomology Museum
@@ -6331,6 +6347,7 @@ UNLP s Universidad Nacional de La Plata
UNLV s University of Nevada, Las Vegas, Department of Biological Sciences
UNM s University of New Mexico, Department of Biology
UNMC s University of New Mexico
+UNMDP s Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
UNN s University of Nigeria, Botany Department
UNNF s Universite de Nancy
UNO s University of Nebraska at Omaha
@@ -6475,6 +6492,7 @@ UT<USA-TN> s University of Tennessee
UT<USA-UT> s University of Utah Herbarium
UTA s University of Texas at Arlington
UTA:A s University of Texas at Arlington, Amphibian Collection
+UTA:R s University of Texas at Arlington, Reptile collection
UTAI s Tel Aviv University
UTC s Utah State University, Biology Department
UTCI s University of Tennessee at Chattanooga Insect Collection
@@ -6939,7 +6957,7 @@ ZhM s Zhejinag Museum
ZIA s National Academy of Sciences of Armenia
ZIAN s Zoological Institute, Academy of Sciences
ZICUP s Zoological Institute Charles University
-ZIHU s Zoological Institute, Hokkaido University
+ZIHU s Hiroshima University, Zoological Institute
ZIK s Ukrainian Academy of Sciences, Zoological Institute
ZIKU s Zoological Institute, Kochi University
ZIL s Academy of Sciences, Zoological Institute
diff --git a/c++/src/objects/seqfeat/lat_lon_country.txt b/c++/src/objects/seqfeat/lat_lon_country.txt
index c58e357..1f952ef 100644
--- a/c++/src/objects/seqfeat/lat_lon_country.txt
+++ b/c++/src/objects/seqfeat/lat_lon_country.txt
@@ -93,7 +93,7 @@ Afghanistan
37.59 69.51 69.60 69.69 69.95 70.19 71.51
37.58 65.75 65.79 69.49 69.97 70.18 71.51
37.57 65.74 65.81 69.49 70.00 70.17 71.50
- 37.56 65.74 65.82 69.49 70.00 70.15 71.50
+ 37.56 65.74 65.82 69.49 70.01 70.15 71.50
37.55 65.74 65.82 69.48 70.08 70.13 71.50
37.54 65.74 65.83 69.47 71.51
37.53 65.65 65.83 69.45 71.51
@@ -124,7 +124,7 @@ Afghanistan
37.28 65.54 67.16 67.47 67.53 68.65 68.78 68.81 69.03 69.39 71.49 72.91 73.65 73.90 74.84
37.27 65.53 67.18 67.45 67.53 68.64 69.04 69.39 71.49 72.90 73.62 73.84 74.70 74.73 74.85
37.26 65.51 67.20 67.44 67.54 67.61 67.65 68.64 69.04 69.39 71.49 72.88 73.61 73.82 74.69 74.74 74.86
- 37.25 65.28 67.21 67.43 67.54 67.57 67.66 68.63 69.05 69.39 71.49 72.85 73.61 73.63 73.69 73.81 74.68 74.74 74.88
+ 37.25 65.27 67.21 67.43 67.54 67.57 67.66 68.63 69.05 69.39 71.49 72.85 73.61 73.63 73.69 73.81 74.68 74.74 74.88
37.24 65.04 67.21 67.42 67.74 68.63 69.07 69.39 71.48 72.81 73.70 73.73 73.76 73.79 74.67 74.75 74.90
37.23 65.00 67.22 67.40 67.77 68.62 69.09 69.39 71.48 72.78 74.65 74.75 74.90
37.22 64.96 67.22 67.32 67.77 68.62 69.10 69.41 71.47 72.77 74.56 74.59 74.64 74.76 74.90
@@ -160,19 +160,19 @@ Afghanistan
36.92 64.75 71.49 72.17 74.30
36.91 64.75 71.50 72.15 74.28
36.90 64.74 71.50 72.14 74.26
- 36.89 64.74 71.51 72.12 74.24
+ 36.89 64.73 71.51 72.12 74.24
36.88 64.73 71.52 72.11 74.14 74.17 74.23
36.87 64.72 71.52 72.09 73.61 73.80 74.12
- 36.86 64.72 71.53 72.07 73.32 73.35 73.41 73.48 73.54 73.84 74.11
- 36.85 64.71 71.53 72.06 73.12 73.23 73.30 73.87 74.11
+ 36.86 64.71 71.53 72.07 73.32 73.35 73.41 73.48 73.54 73.84 74.11
+ 36.85 64.70 71.53 72.06 73.12 73.23 73.30 73.87 74.11
36.84 64.70 71.54 72.04 73.04 73.89 74.11
- 36.83 64.70 71.54 72.03 73.02 73.91 74.11
+ 36.83 64.69 71.54 72.03 73.02 73.91 74.11
36.82 64.69 71.54 72.01 72.91 73.93 74.10
36.81 64.68 71.55 71.99 72.60 72.73 72.82 73.95 74.08
- 36.80 64.68 71.55 71.98 72.55 73.98 74.05
+ 36.80 64.67 71.55 71.98 72.55 73.98 74.05
36.79 64.67 71.55 71.96 72.53
36.78 64.66 71.56 71.95 72.51
- 36.77 64.66 71.56 71.93 72.50
+ 36.77 64.65 71.56 71.93 72.50
36.76 64.65 71.57 71.91 72.49
36.75 64.64 71.57 71.90 72.47
36.74 64.64 71.58 71.88 72.46
@@ -245,7 +245,7 @@ Afghanistan
36.07 64.02 71.21
36.06 64.02 71.20
36.05 64.02 71.18
- 36.04 63.90 63.94 64.02 71.18
+ 36.04 63.89 63.94 64.02 71.18
36.03 63.84 63.96 64.02 71.18
36.02 63.82 64.00 64.02 71.20
36.01 63.80 71.23
@@ -357,10 +357,10 @@ Afghanistan
34.95 61.07 71.48
34.94 61.06 71.48
34.93 61.06 71.47
- 34.92 61.06 71.44
- 34.91 61.06 71.42
- 34.90 61.06 71.39
- 34.89 61.06 71.36
+ 34.92 61.06 71.45
+ 34.91 61.06 71.43
+ 34.90 61.06 71.40
+ 34.89 61.06 71.37
34.88 61.06 71.34
34.87 61.06 71.32
34.86 61.06 71.30
@@ -711,8 +711,8 @@ Afghanistan
31.41 61.24 67.65 67.69 67.76
31.40 61.34 67.78
31.39 61.44 67.78
- 31.38 61.53 67.78
- 31.37 61.61 67.78
+ 31.38 61.51 67.78
+ 31.37 61.57 67.78
31.36 61.67 67.78
31.35 61.68 67.78
31.34 61.69 67.78
@@ -894,7 +894,7 @@ Afghanistan
29.58 61.75 65.27
29.57 61.78 65.22
29.56 61.81 65.20
- 29.55 61.84 64.46 64.57 65.16
+ 29.55 61.84 64.46 64.58 65.16
29.54 61.88 64.42 64.86 65.11
29.53 61.92 64.39 64.94 65.06
29.52 61.96 64.36
@@ -909,8 +909,8 @@ Afghanistan
29.43 62.28 63.00 63.85 64.15
29.42 62.32 62.85 63.89 64.14
29.41 62.35 62.75 63.94 64.14
- 29.40 62.39 62.60 63.98 64.13
- 29.39 62.44 62.52 64.01 64.13
+ 29.40 62.39 62.62 63.98 64.13
+ 29.39 62.44 62.54 64.01 64.13
29.38 64.03 64.12
29.37 64.06 64.10
Albania
@@ -955,7 +955,7 @@ Albania
42.28 19.34 20.43
42.27 19.34 20.45
42.26 19.33 20.46
- 42.25 19.32 20.48
+ 42.25 19.32 20.47
42.24 19.31 20.49
42.23 19.30 20.50
42.22 19.29 20.51
@@ -999,7 +999,7 @@ Albania
41.84 19.35 19.40 19.45 20.55
41.83 19.47 20.55
41.82 19.50 20.55
- 41.81 19.53 20.55
+ 41.81 19.53 20.56
41.80 19.56 20.56
41.79 19.58 20.56
41.78 19.56 20.56
@@ -1021,7 +1021,7 @@ Albania
41.62 19.57 20.53
41.61 19.56 20.54
41.60 19.56 20.54
- 41.59 19.43 19.49 19.54 20.54
+ 41.59 19.43 19.49 19.53 20.54
41.58 19.43 20.54
41.57 19.43 20.54
41.56 19.44 20.53
@@ -1056,9 +1056,9 @@ Albania
41.27 19.49 20.50
41.26 19.50 20.50
41.25 19.50 20.51
- 41.24 19.50 20.51
- 41.23 19.49 20.51
- 41.22 19.48 20.52
+ 41.24 19.49 20.51
+ 41.23 19.48 20.51
+ 41.22 19.47 20.52
41.21 19.47 20.53
41.20 19.46 20.53
41.19 19.45 20.54
@@ -1084,11 +1084,11 @@ Albania
40.99 19.43 20.69
40.98 19.46 20.70
40.97 19.46 20.70
- 40.96 19.46 20.70
+ 40.96 19.45 20.70
40.95 19.43 20.71
40.94 19.41 20.71
40.93 19.40 20.71 20.80 20.87
- 40.92 19.38 20.72 20.79 20.92
+ 40.92 19.37 20.73 20.79 20.92
40.91 19.37 20.74 20.78 20.95
40.90 19.37 20.96
40.89 19.37 20.96
@@ -1117,12 +1117,12 @@ Albania
40.66 19.29 21.04
40.65 19.29 21.04
40.64 19.29 21.04
- 40.63 19.30 21.04
- 40.62 19.31 21.04
+ 40.63 19.29 21.04
+ 40.62 19.30 21.04
40.61 19.31 21.04
40.60 19.32 21.04
- 40.59 19.33 21.04
- 40.58 19.34 21.03
+ 40.59 19.32 21.04
+ 40.58 19.33 21.03
40.57 19.34 21.03
40.56 19.35 21.03
40.55 19.36 21.03
@@ -1136,10 +1136,10 @@ Albania
40.47 19.41 20.95
40.46 19.43 20.94
40.45 19.44 20.84 20.87 20.93
- 40.44 19.30 19.35 19.46 20.83 20.89 20.92
- 40.43 19.28 19.36 19.46 20.82
- 40.42 19.28 19.37 19.47 20.81
- 40.41 19.28 19.38 19.47 20.79
+ 40.44 19.29 19.35 19.46 20.83 20.89 20.92
+ 40.43 19.27 19.36 19.46 20.82
+ 40.42 19.27 19.37 19.47 20.81
+ 40.41 19.27 19.38 19.47 20.79
40.40 19.28 19.39 19.47 20.78
40.39 19.29 19.40 19.46 20.78
40.38 19.30 19.40 19.46 20.78
@@ -1151,7 +1151,7 @@ Albania
40.32 19.35 20.76
40.31 19.35 20.75
40.30 19.35 20.75
- 40.29 19.36 20.74
+ 40.29 19.35 20.74
40.28 19.37 20.73
40.27 19.38 20.71
40.26 19.39 20.70
@@ -1195,8 +1195,8 @@ Albania
39.88 19.93 20.37
39.87 19.94 20.37
39.86 19.95 20.38
- 39.85 20.00 20.39
- 39.84 20.00 20.40
+ 39.85 19.99 20.39
+ 39.84 19.99 20.40
39.83 20.00 20.40
39.82 19.99 20.40
39.81 19.99 20.40
@@ -1221,40 +1221,40 @@ Albania
39.62 20.17 20.19
Algeria
37.10 6.39 6.49
- 37.09 6.36 6.51 7.17 7.25 7.27 7.30 7.35 7.39
+ 37.09 6.36 6.51 7.17 7.25 7.27 7.32 7.35 7.39
37.08 6.34 6.53 7.17 7.39
37.07 6.31 6.54 7.17 7.40
- 37.06 6.31 6.55 7.17 7.41 7.48 7.50
+ 37.06 6.31 6.55 7.17 7.41 7.46 7.50
37.05 6.30 6.55 7.18 7.52
37.04 6.28 6.57 7.20 7.53
37.03 6.26 6.58 7.21 7.54
37.02 6.25 6.58 7.23 7.55
37.01 6.25 6.58 7.24 7.56
37.00 6.24 6.59 7.24 7.58 7.78 7.80
- 36.99 6.24 6.60 7.23 7.69 7.77 7.80
- 36.98 6.24 6.65 7.22 7.71 7.77 7.80
+ 36.99 6.24 6.59 7.23 7.69 7.77 7.80
+ 36.98 6.24 6.65 7.22 7.71 7.76 7.80
36.97 6.24 6.67 7.20 7.80
36.96 6.24 6.83 7.19 7.80 8.21 8.25
36.95 6.24 6.86 7.17 7.79 8.18 8.26
- 36.94 6.23 6.87 7.16 7.78 8.16 8.28 8.58 8.61
+ 36.94 6.23 6.86 7.16 7.78 8.16 8.28 8.58 8.61
36.93 6.22 6.88 7.07 7.12 7.15 7.79 8.13 8.40 8.54 8.61
- 36.92 3.80 3.92 4.25 4.29 4.41 4.45 6.20 6.89 7.03 7.80 8.10 8.42 8.50 8.61
- 36.91 3.76 3.94 4.13 4.19 4.23 4.32 4.35 4.49 6.17 6.90 6.99 7.80 8.08 8.61
- 36.90 3.73 4.50 4.56 4.80 6.14 6.93 6.95 7.80 8.07 8.61
- 36.89 3.71 4.83 6.11 7.79 8.06 8.62
- 36.88 3.69 4.86 6.07 7.81 8.02 8.63
+ 36.92 3.80 3.92 4.25 4.29 4.41 4.46 6.20 6.89 7.03 7.80 8.10 8.42 8.50 8.61
+ 36.91 3.76 3.94 4.13 4.19 4.23 4.32 4.35 4.49 6.17 6.89 6.99 7.80 8.08 8.61
+ 36.90 3.73 4.50 4.56 4.80 6.14 7.80 8.07 8.61
+ 36.89 3.71 4.83 6.11 7.79 8.05 8.62
+ 36.88 3.69 4.85 6.07 7.80 8.01 8.63
36.87 3.68 4.88 6.04 7.84 7.97 8.63
36.86 3.67 4.91 6.00 7.89 7.92 8.64
- 36.85 3.66 4.94 5.94 8.65
- 36.84 3.65 4.96 5.72 5.79 5.88 8.65
- 36.83 3.64 4.97 5.70 8.65
- 36.82 2.95 3.02 3.21 3.25 3.62 5.02 5.69 8.65
+ 36.85 3.65 4.93 5.94 8.65
+ 36.84 3.64 4.96 5.72 5.79 5.88 8.65
+ 36.83 3.63 4.97 5.70 8.65
+ 36.82 2.95 3.02 3.21 3.25 3.61 5.02 5.69 8.65
36.81 2.92 3.04 3.21 3.27 3.55 5.02 5.67 8.64
36.80 2.90 3.05 3.21 3.29 3.54 5.04 5.63 8.61
36.79 2.88 3.07 3.21 3.41 3.49 5.11 5.60 8.57
36.78 2.86 3.08 3.21 5.11 5.58 8.54
- 36.77 2.85 3.10 3.21 5.11 5.56 8.43
- 36.76 2.84 3.13 3.19 5.11 5.56 8.45
+ 36.77 2.84 3.10 3.21 5.11 5.56 8.43
+ 36.76 2.83 3.13 3.19 5.11 5.56 8.45
36.75 2.83 5.10 5.55 8.46
36.74 2.82 5.10 5.55 8.47
36.73 2.81 5.09 5.54 8.47
@@ -1262,21 +1262,21 @@ Algeria
36.71 2.79 5.11 5.53 8.47
36.70 2.77 5.13 5.50 8.47
36.69 2.75 5.16 5.47 8.46
- 36.68 2.73 5.19 5.47 8.46
- 36.67 2.71 5.22 5.40 8.45
+ 36.68 2.73 5.19 5.46 8.46
+ 36.67 2.71 5.22 5.39 8.45
36.66 2.69 5.25 5.33 8.45
36.65 2.68 8.44
- 36.64 2.29 2.39 2.66 8.43
- 36.63 2.25 2.40 2.65 8.41
- 36.62 2.22 2.40 2.63 8.40
- 36.61 2.18 2.41 2.61 8.38
- 36.60 2.14 2.45 2.52 8.36
- 36.59 2.11 8.34
- 36.58 2.07 8.32
+ 36.64 2.27 2.39 2.66 8.43
+ 36.63 2.23 2.40 2.65 8.41
+ 36.62 2.19 2.40 2.63 8.40
+ 36.61 2.15 2.41 2.61 8.38
+ 36.60 2.11 2.45 2.52 8.36
+ 36.59 2.07 8.34
+ 36.58 1.88 1.94 2.01 8.32
36.57 1.75 1.79 1.82 8.30
- 36.56 1.73 8.27
- 36.55 1.32 1.41 1.61 8.24
- 36.54 1.29 1.45 1.49 8.22
+ 36.56 1.71 8.27
+ 36.55 1.32 1.41 1.60 8.24
+ 36.54 1.29 1.44 1.49 8.22
36.53 1.27 8.20
36.52 1.16 8.19
36.51 1.14 8.17
@@ -1287,7 +1287,7 @@ Algeria
36.46 0.93 8.34
36.45 0.92 8.35
36.44 0.92 8.36
- 36.43 0.92 8.36
+ 36.43 0.91 8.36
36.42 0.91 8.36
36.41 0.90 8.36
36.40 0.88 8.36
@@ -1317,8 +1317,8 @@ Algeria
36.16 0.30 8.32
36.15 0.28 8.32
36.14 0.26 8.32
- 36.13 0.23 8.32
- 36.12 0.21 8.32
+ 36.13 0.22 8.32
+ 36.12 0.20 8.32
36.11 0.19 8.31
36.10 0.18 8.30
36.09 0.16 8.30
@@ -1330,21 +1330,21 @@ Algeria
36.03 0.11 8.28
36.02 0.10 8.28
36.01 0.10 8.28
- 36.00 0.10 8.28
+ 36.00 0.09 8.28
35.99 0.09 8.28
- 35.98 0.09 8.28
+ 35.98 0.08 8.28
35.97 0.08 8.28
- 35.96 0.08 8.28
+ 35.96 0.07 8.28
35.95 0.07 8.27
- 35.94 0.07 8.27
- 35.93 0.06 8.27
+ 35.94 0.06 8.27
+ 35.93 0.05 8.26
35.92 0.05 8.26
- 35.91 -0.38 -0.32 0.05 8.26
+ 35.91 -0.38 -0.32 0.04 8.26
35.90 -0.48 -0.46 -0.40 -0.32 0.04 8.25
35.89 -0.49 -0.29 0.03 8.25
35.88 -0.49 -0.29 0.03 8.25
35.87 -0.49 -0.28 0.02 8.25
- 35.86 -0.48 -0.28 0.01 8.25
+ 35.86 -0.49 -0.28 0.01 8.25
35.85 -0.49 -0.28 0.00 8.25
35.84 -0.49 -0.28 -0.01 8.25
35.83 -0.50 -0.26 -0.03 8.25
@@ -1352,17 +1352,17 @@ Algeria
35.81 -0.51 -0.15 -0.07 8.25
35.80 -0.52 -0.12 -0.10 8.25
35.79 -0.52 8.25
- 35.78 -0.81 -0.79 -0.58 -0.55 -0.53 8.25
+ 35.78 -0.81 -0.78 -0.58 8.25
35.77 -0.83 -0.77 -0.58 8.26
35.76 -0.84 -0.73 -0.59 8.26
35.75 -0.84 -0.70 -0.59 8.27
35.74 -0.85 -0.69 -0.61 8.27
- 35.73 -0.93 -0.89 -0.87 -0.69 -0.63 8.28
+ 35.73 -0.93 -0.90 -0.87 -0.69 -0.63 8.28
35.72 -0.97 8.29
35.71 -0.97 8.30
35.70 -0.98 8.30
35.69 -1.04 8.31
- 35.68 -1.04 8.32
+ 35.68 -1.05 8.32
35.67 -1.06 8.32
35.66 -1.07 8.33
35.65 -1.08 8.33
@@ -1371,15 +1371,15 @@ Algeria
35.62 -1.12 8.33
35.61 -1.13 8.33
35.60 -1.14 8.33
- 35.59 -1.18 8.34
+ 35.59 -1.18 8.33
35.58 -1.19 8.34
- 35.57 -1.19 8.34
+ 35.57 -1.20 8.34
35.56 -1.20 8.34
- 35.55 -1.20 8.34
+ 35.55 -1.21 8.34
35.54 -1.21 8.34
- 35.53 -1.21 8.34
+ 35.53 -1.22 8.34
35.52 -1.22 8.34
- 35.51 -1.22 8.34
+ 35.51 -1.23 8.34
35.50 -1.23 8.34
35.49 -1.23 8.34
35.48 -1.24 8.34
@@ -1400,11 +1400,11 @@ Algeria
35.33 -1.36 8.30
35.32 -1.38 8.30
35.31 -1.50 8.31
- 35.30 -1.51 8.31
- 35.29 -1.53 8.34
- 35.28 -1.54 8.38
+ 35.30 -1.52 8.31
+ 35.29 -1.54 8.34
+ 35.28 -1.55 8.38
35.27 -1.56 8.41
- 35.26 -1.57 8.43
+ 35.26 -1.58 8.43
35.25 -1.59 8.44
35.24 -1.60 8.44
35.23 -1.62 8.44
@@ -1457,7 +1457,7 @@ Algeria
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25.47 -5.63 9.91
25.46 -5.61 9.92
25.45 -5.59 9.93
@@ -2490,13 +2490,13 @@ Algeria
24.43 -3.97 11.17
24.42 -3.96 11.20
24.41 -3.94 11.23
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24.33 -3.82 11.49
24.32 -3.80 11.52
24.31 -3.79 11.54
@@ -2529,20 +2529,20 @@ Algeria
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@@ -2748,8 +2748,8 @@ Algeria
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@@ -3025,8 +3025,8 @@ Algeria
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@@ -3044,12 +3044,12 @@ American Samoa
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Andorra
42.65 1.45 1.56
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@@ -3496,7 +3496,7 @@ Angola
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@@ -3526,7 +3526,7 @@ Angola
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- -79.25 -164.29 -160.25 -152.42 -81.23 -80.47 -79.44 -71.69 -69.31 -68.16 -67.03 -50.70 -43.28 -36.86 -34.00 -32.88 -32.74 -30.56 160.53
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- -79.38 -164.06 -159.66 -151.81 -81.21 -80.55 -76.18 -71.78 -69.58 -68.44 -67.44 -50.35 -43.04 -30.00 160.66
- -79.39 -164.03 -159.63 -151.73 -81.20 -80.55 -76.15 -71.79 -69.59 -68.52 -67.44 -50.35 -43.02 -30.04 160.69
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- -79.41 -163.98 -159.57 -151.58 -81.17 -80.55 -76.08 -71.81 -69.49 -68.57 -67.29 -50.34 -42.97 -30.12 160.98
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- -79.45 -163.70 -159.51 -151.27 -81.08 -80.52 -76.02 -71.82 -69.72 -68.56 -67.23 -50.26 -42.93 -30.28 161.04
- -79.46 -163.61 -159.50 -151.19 -81.02 -80.49 -76.01 -71.82 -69.69 -68.44 -67.23 -50.26 -42.93 -30.32 160.60 160.65 161.04
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- -79.48 -163.52 -159.43 -151.04 -80.91 -80.44 -75.99 -71.82 -69.62 -68.40 -67.28 -50.24 -42.92 -30.40 160.50 160.81 161.04
- -79.49 -163.50 -159.39 -150.96 -80.85 -80.42 -75.97 -71.82 -69.60 -68.24 -67.33 -50.25 -42.92 -30.44 160.48 160.94 161.03
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- -79.52 -163.30 -159.31 -150.73 -80.68 -80.40 -75.91 -71.80 -69.48 -67.81 -67.64 -50.27 -42.92 -30.56 160.45
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- -79.54 -163.15 -159.31 -150.57 -80.57 -80.42 -75.91 -71.77 -69.48 -67.84 -67.45 -50.37 -42.92 -30.64 160.33
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- -79.56 -163.00 -159.26 -150.47 -75.91 -71.73 -69.69 -67.84 -66.90 -50.42 -42.92 -30.67 159.73 159.85 160.21
- -79.57 -162.92 -159.22 -150.36 -75.92 -71.71 -69.67 -67.84 -66.85 -50.44 -42.93 -30.68 159.73 159.93 160.19
- -79.58 -162.85 -159.21 -150.19 -75.93 -71.69 -69.65 -67.84 -66.83 -50.46 -42.93 -30.68 159.73 160.02 160.17
- -79.59 -162.77 -159.20 -150.02 -75.95 -71.67 -69.63 -67.82 -66.78 -65.93 -65.80 -50.49 -42.93 -30.68 159.73
- -79.60 -162.70 -159.19 -149.85 -75.96 -71.65 -69.63 -67.76 -66.44 -66.07 -65.78 -50.51 -42.93 -30.53 159.75 160.74 160.85
- -79.61 -162.62 -159.19 -149.69 -75.97 -71.62 -69.63 -67.75 -65.77 -50.53 -42.93 -30.23 159.78 160.54 160.85
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- -79.63 -162.47 -159.18 -149.35 -76.00 -71.57 -69.75 -67.71 -65.77 -50.60 -42.94 -32.03 -31.57 -29.63 159.85 160.16 160.84
- -79.64 -162.40 -159.16 -149.18 -76.01 -71.54 -69.83 -67.69 -65.82 -60.11 -60.05 -50.64 -42.94 -32.05 -31.55 -30.86 -30.76 -29.34 159.87 159.96 160.82
- -79.65 -162.32 -159.13 -149.08 -76.02 -71.50 -69.91 -67.66 -65.86 -60.17 -60.03 -50.67 -42.94 -32.08 -31.52 -30.89 -30.73 -29.04 160.80
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- -79.69 -162.03 -159.01 -149.02 -76.05 -70.76 -70.22 -67.47 -66.50 -60.42 -60.05 -50.82 -42.95 -32.17 -31.41 -30.93 -30.70 -27.85 160.62
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- -79.72 -161.80 -158.94 -148.66 -76.07 -67.33 -66.20 -60.61 -60.26 -50.93 -42.95 -32.08 -31.28 -30.88 -30.59 -26.96 160.45
- -79.73 -161.73 -158.94 -148.53 -76.07 -67.29 -66.16 -60.68 -60.34 -50.95 -42.95 -31.98 -31.24 -30.88 -30.50 -26.66 160.40
- -79.74 -161.65 -158.94 -148.39 -76.08 -67.24 -66.12 -65.77 -65.63 -60.74 -60.10 -50.98 -42.96 -31.96 -31.20 -30.87 -30.40 -26.36 -24.35 -24.28 160.34
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- -79.78 -161.35 -158.95 -147.95 -76.15 -67.05 -65.54 -60.99 -59.78 -51.08 -42.97 -32.06 -31.11 -30.65 -30.03 -25.17 -24.61 -24.29 160.11
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- -79.89 -148.85 -148.03 -147.90 -76.42 -67.03 -65.48 -61.53 -59.61 -51.45 -43.04 -31.62 -30.19 -29.90 -29.62 -23.00 159.71 160.05 160.58 161.11 161.48
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- -79.93 -148.61 -76.57 -66.99 -66.86 -66.75 -65.45 -61.44 -59.68 -51.57 -43.08 -30.99 -30.62 -30.51 -30.00 -29.82 -29.63 -22.85 160.77 160.87 161.44
- -79.94 -148.65 -76.61 -66.73 -65.43 -61.38 -59.66 -51.61 -43.09 -30.85 -30.62 -30.50 -29.99 -29.74 -29.68 -22.85 161.42
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- -79.97 -148.95 -76.87 -66.47 -65.48 -61.27 -59.82 -59.71 -59.68 -51.71 -43.14 -30.48 -29.97 -23.10 161.26
- -79.98 -148.95 -76.97 -66.38 -65.54 -61.25 -59.81 -51.75 -43.63 -43.52 -43.18 -30.48 -30.00 -23.48 161.18
- -79.99 -148.52 -77.06 -66.36 -65.61 -61.27 -59.81 -51.78 -43.71 -43.36 -43.23 -30.48 -30.05 -23.87 161.09
- -80.00 -148.52 -79.64 -79.31 -77.16 -66.38 -65.68 -61.71 -59.79 -51.82 -43.75 -30.47 -30.10 -24.11 161.01
- -80.01 -148.52 -79.59 -78.55 -77.26 -66.42 -65.74 -61.71 -59.77 -51.85 -43.71 -30.45 -30.15 -24.13 160.92
- -80.02 -148.50 -79.49 -77.79 -77.36 -66.42 -65.75 -61.76 -59.76 -51.89 -43.67 -30.43 -30.26 -24.15 160.84
- -80.03 -148.47 -79.39 -66.42 -65.77 -61.80 -59.76 -51.92 -43.64 -24.17 160.76
- -80.04 -148.24 -79.29 -66.41 -65.82 -61.81 -59.76 -52.42 -52.32 -51.96 -43.60 -24.19 160.67
- -80.05 -148.30 -79.20 -66.40 -65.89 -61.81 -59.76 -52.46 -52.28 -51.99 -43.56 -24.23 160.59
- -80.06 -150.37 -150.23 -148.57 -79.10 -66.40 -65.96 -61.81 -59.77 -52.50 -52.26 -52.03 -43.52 -24.74 160.50
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- -80.15 -150.19 -78.30 -78.21 -77.73 -77.46 -76.25 -61.66 -59.32 -53.46 -53.17 -52.85 -43.42 -29.42 159.75
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- -80.17 -150.18 -76.24 -61.67 -59.27 -53.46 -43.44 -29.82 159.58
- -80.18 -150.26 -76.23 -66.27 -66.19 -61.67 -59.27 -53.44 -43.46 -29.84 159.50
- -80.19 -150.35 -76.21 -66.27 -66.16 -61.64 -59.27 -53.48 -43.48 -29.86 159.41
- -80.20 -150.74 -150.55 -150.43 -76.19 -66.45 -66.15 -61.61 -59.26 -53.52 -43.51 -29.87 159.33
- -80.21 -150.76 -76.17 -66.59 -66.15 -61.59 -59.26 -53.56 -43.59 -29.87 159.25
- -80.22 -150.79 -76.15 -66.62 -66.15 -61.56 -59.46 -59.33 -59.26 -53.59 -43.71 -29.87 159.16
- -80.23 -150.81 -76.14 -66.65 -66.15 -61.56 -59.59 -53.61 -43.84 -29.84 159.08
- -80.24 -150.81 -76.13 -66.69 -66.16 -61.55 -59.59 -53.62 -43.97 -29.80 158.99
- -80.25 -150.81 -76.12 -66.72 -66.18 -61.52 -59.58 -53.64 -44.09 -29.90 158.91
- -80.26 -150.74 -76.11 -76.05 -75.94 -66.75 -66.17 -61.48 -59.57 -53.65 -44.22 -29.91 158.83
- -80.27 -150.64 -76.09 -76.07 -75.93 -66.77 -66.17 -61.31 -59.56 -53.67 -44.34 -30.60 158.79
- -80.28 -150.60 -75.93 -66.79 -66.17 -61.37 -59.56 -53.68 -44.47 -31.29 158.79
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- -80.33 -150.73 -150.55 -150.37 -75.73 -66.81 -66.17 -61.66 -59.67 -53.76 -45.10 -31.24 158.74
- -80.34 -150.33 -75.70 -66.81 -66.12 -61.72 -59.68 -53.78 -45.23 -31.19 158.70
- -80.35 -150.28 -75.67 -66.79 -66.06 -62.44 -59.75 -53.80 -45.35 -31.14 158.64
- -80.36 -150.24 -75.64 -66.78 -66.00 -63.83 -59.76 -53.82 -45.48 -31.10 158.57
- -80.37 -150.16 -75.61 -66.78 -65.94 -65.22 -59.76 -53.84 -45.61 -31.05 158.50 160.62 160.80
- -80.38 -150.89 -75.58 -66.77 -59.76 -53.86 -45.73 -31.00 158.44 160.38 160.83
- -80.39 -150.89 -75.56 -66.76 -59.74 -53.88 -45.86 -30.95 158.37 160.14 160.85
- -80.40 -150.98 -75.55 -66.76 -59.72 -53.90 -45.98 -30.90 158.30 159.90 160.86
- -80.41 -151.02 -75.54 -66.74 -59.72 -53.92 -46.11 -30.85 158.24 159.66 160.86
- -80.42 -151.02 -75.52 -66.72 -59.72 -53.94 -46.24 -32.07 -31.82 -30.80 158.19 159.42 160.87
- -80.43 -151.02 -75.49 -66.67 -59.77 -53.96 -46.36 -32.15 -31.44 -30.76 158.23 159.18 160.97
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Armenia
41.30 44.99 45.01
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- 12.56 -70.06 -69.95
+ 12.56 -70.07 -69.95
12.55 -70.07 -69.93
12.54 -70.07 -69.92
12.53 -70.07 -69.92
@@ -10902,24 +10961,24 @@ Aruba
12.51 -70.03 -69.91
12.50 -70.02 -69.90
12.49 -70.01 -69.89
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12.44 -69.95 -69.86
12.43 -69.95 -69.86
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Ashmore and Cartier Islands
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Australia
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@@ -10945,7 +11004,7 @@ Australia
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-10.16 142.11 142.34
-10.17 142.11 142.35
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@@ -10953,17 +11012,17 @@ Australia
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@@ -11002,60 +11061,60 @@ Australia
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@@ -11065,73 +11124,73 @@ Australia
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@@ -15821,8 +15880,8 @@ Australia: Northern Territory
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@@ -19530,41 +19644,41 @@ Australia: South Australia
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@@ -19581,7 +19695,7 @@ Australia: South Australia
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@@ -19594,28 +19708,28 @@ Australia: South Australia
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@@ -19630,9 +19744,9 @@ Australia: South Australia
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@@ -19662,8 +19776,8 @@ Australia: South Australia
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@@ -19682,9 +19796,9 @@ Australia: South Australia
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@@ -19693,10 +19807,10 @@ Australia: South Australia
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@@ -19881,7 +19995,7 @@ Australia: South Australia
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@@ -19902,6 +20016,14 @@ Australia: South Australia
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Australia: Tasmania
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@@ -19947,50 +20069,50 @@ Australia: Tasmania
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@@ -20016,16 +20138,16 @@ Australia: Tasmania
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@@ -20033,7 +20155,7 @@ Australia: Tasmania
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@@ -20046,8 +20168,8 @@ Australia: Tasmania
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@@ -20057,7 +20179,7 @@ Australia: Tasmania
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@@ -20086,9 +20208,9 @@ Australia: Tasmania
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@@ -20161,16 +20283,16 @@ Australia: Tasmania
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@@ -22850,15 +22972,15 @@ Australia: Western Australia
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@@ -22872,14 +22994,14 @@ Australia: Western Australia
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@@ -22894,7 +23016,7 @@ Australia: Western Australia
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@@ -22915,8 +23037,8 @@ Australia: Western Australia
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@@ -22934,19 +23056,19 @@ Australia: Western Australia
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@@ -22963,14 +23085,14 @@ Australia: Western Australia
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@@ -22988,7 +23110,7 @@ Austria
48.94 14.95 15.48
48.93 14.95 15.50
48.92 14.95 15.52
- 48.91 14.95 15.55
+ 48.91 14.95 15.56
48.90 14.95 15.59
48.89 14.95 15.62
48.88 14.95 15.65 15.76 15.82
@@ -23026,7 +23148,7 @@ Austria
48.56 13.43 13.66 13.72 16.96
48.55 13.43 13.67 13.71 16.96
48.54 13.43 16.96
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48.52 13.43 16.95
48.51 13.44 16.94
48.50 13.44 16.93
@@ -23067,7 +23189,7 @@ Austria
48.15 12.77 17.02
48.14 12.76 17.05
48.13 12.73 17.06
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48.11 12.72 17.08
48.10 12.72 17.09
48.09 12.72 17.09
@@ -23113,7 +23235,7 @@ Austria
47.69 12.16 12.43 12.93 12.99 13.02 16.52 16.70 17.08
47.68 12.16 12.43 12.63 12.72 13.03 16.50 16.70 16.83 16.85 17.02
47.67 12.17 12.44 12.58 12.77 13.04 16.47 16.72 16.82 16.85 16.95
- 47.66 12.19 12.45 12.57 12.77 13.05 16.44 16.76 16.81
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47.65 12.19 12.47 12.55 12.77 13.05 16.47 16.49 16.52
47.64 12.19 12.49 12.52 12.78 13.06 16.56
47.63 12.19 12.81 13.05 16.64
@@ -23125,7 +23247,7 @@ Austria
47.57 9.72 9.82 10.40 10.47 10.57 10.62 11.57 12.78 13.02 16.68
47.56 9.71 9.82 10.40 10.47 10.55 10.65 11.57 12.79 13.02 16.69
47.55 9.70 9.87 9.93 9.95 10.40 10.47 10.54 10.69 11.57 12.81 13.01 16.69
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47.53 9.53 9.95 10.41 10.75 10.81 10.88 11.55 12.85 13.01 16.69
47.52 9.53 9.97 10.41 10.90 11.53 12.87 13.01 16.69
47.51 9.53 9.98 10.40 10.90 11.40 12.88 13.01 16.69
@@ -23173,7 +23295,7 @@ Austria
47.09 9.59 16.49
47.08 9.58 16.48
47.07 9.58 16.49
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47.05 9.57 12.10 12.18 16.50
47.04 9.57 12.07 12.16 16.50
47.03 9.68 12.03 12.13 16.50
@@ -23213,11 +23335,11 @@ Austria
46.69 12.37 15.64 15.68 15.77 15.90 16.02
46.68 12.39 15.64 15.92 16.02
46.67 12.41 15.64 15.98 16.02
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46.65 12.50 15.54
46.64 12.52 15.54
46.63 12.68 15.53
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46.61 12.78 15.00 15.42 15.52
46.60 12.80 14.99 15.45 15.51
46.59 12.82 14.91 14.95 14.97
@@ -23228,7 +23350,7 @@ Austria
46.54 13.19 13.33 13.48 14.82
46.53 13.49 14.82
46.52 13.56 14.81
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46.50 13.64 14.80
46.49 13.74 13.83 13.90 14.79
46.48 13.93 14.78
@@ -23237,9 +23359,9 @@ Austria
46.45 14.08 14.69
46.44 14.10 14.68
46.43 14.12 14.66
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46.41 14.40 14.59
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46.39 14.50 14.57
46.38 14.50 14.57
46.37 14.51 14.56
@@ -23251,7 +23373,7 @@ Azerbaijan
41.87 46.40 46.55
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21.35 -73.04 -73.01
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21.33 -73.06 -73.00
@@ -24084,67 +24207,67 @@ Bahamas
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Bahrain
26.25 50.47 50.51 50.57 50.59
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@@ -24300,12 +24423,12 @@ Bangladesh
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25.36 88.80 89.80
25.35 88.80 89.80
@@ -24327,7 +24450,7 @@ Bangladesh
25.19 88.43 88.52 88.57 88.68 88.79 88.87 88.89 90.30 91.05 91.28 91.98 92.05
25.18 88.42 88.71 88.79 90.33 90.60 90.64 90.99 91.30 91.84 91.93 91.96 92.08
25.17 88.42 90.35 90.47 90.66 90.72 90.77 90.95 91.34 91.53 91.56 91.71 92.10
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25.15 88.42 91.42 91.49 91.59 91.66 92.12
25.14 88.42 91.59 91.66 92.18
25.13 88.42 92.18
@@ -24391,7 +24514,7 @@ Bangladesh
24.55 88.07 92.17
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@@ -24537,7 +24660,7 @@ Bangladesh
23.09 88.84 90.59 90.61 91.33 91.36 91.49 91.78 92.35
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23.05 88.83 90.52 90.61 91.51 91.74 92.36
23.04 88.83 90.52 90.55 90.59 90.62 91.52 91.73 92.36
23.03 88.83 90.52 90.54 90.60 90.62 91.52 91.72 92.36
@@ -24550,104 +24673,104 @@ Bangladesh
22.96 88.82 92.36
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22.06 89.04 89.87 89.90 90.36 90.41 90.45 90.47 90.78 91.85 92.56
22.05 89.04 89.84 89.90 90.39 90.41 90.44 90.47 90.57 90.59 90.77 91.85 92.57
22.04 89.04 89.85 89.90 90.45 90.47 90.57 90.59 90.73 91.85 92.57
22.03 89.05 89.85 89.90 90.57 90.59 90.72 91.86 92.57
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21.99 89.08 89.86 89.91 90.54 90.58 90.60 90.62 90.70 91.87 92.58
21.98 89.08 89.86 89.92 90.53 90.56 90.60 90.63 90.68 91.87 92.58
- 21.97 89.08 89.86 89.94 89.99 90.01 90.31 90.33 90.49 90.54 90.60 91.87 92.58
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21.95 89.07 89.53 89.55 89.87 90.02 90.31 90.33 90.49 90.51 90.61 91.87 92.59
21.94 89.07 89.53 89.55 89.87 90.02 90.48 90.50 90.61 91.85 92.59
21.93 89.07 89.53 89.55 89.88 90.02 90.48 90.50 90.61 91.84 92.60
@@ -24660,17 +24783,17 @@ Bangladesh
21.86 89.04 89.34 89.36 89.48 89.53 89.87 90.01 90.35 90.49 90.55 91.82 92.60
21.85 89.04 89.33 89.36 89.48 89.52 89.85 90.01 90.35 90.49 90.54 91.82 92.60
21.84 89.05 89.33 89.36 89.47 89.52 89.83 90.03 90.28 90.30 90.35 91.82 92.60
- 21.83 89.05 89.33 89.35 89.47 89.52 89.82 90.04 90.27 90.30 90.34 91.83 92.59
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21.80 89.04 89.31 89.35 89.47 89.51 89.70 90.11 90.22 91.82 92.59
21.79 89.04 89.31 89.35 89.47 89.51 89.71 90.14 90.21 91.82 92.59
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21.74 89.07 89.15 89.19 89.30 89.35 89.46 89.52 89.61 89.63 89.68 91.81 92.58
- 21.73 89.08 89.15 89.20 89.30 89.35 89.45 89.53 89.61 91.81 92.58
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21.72 89.09 89.15 89.20 89.30 89.36 89.44 89.53 89.61 91.81 92.58
21.71 89.11 89.14 89.20 89.30 89.37 89.43 89.54 89.61 91.82 92.58
21.70 89.19 89.29 89.38 89.41 89.55 89.61 91.83 92.58
@@ -24695,24 +24818,24 @@ Bangladesh
21.51 91.84 92.60
21.50 91.84 92.60
21.49 91.84 92.60
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21.47 91.85 91.90 91.96 92.60
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21.43 91.94 92.31 92.34 92.61
21.42 91.94 92.31 92.35 92.61
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21.39 91.95 92.24 92.36 92.62
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21.37 91.98 92.23 92.37 92.63
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21.35 91.99 92.22 92.41 92.63
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21.33 92.00 92.21 92.52 92.64
21.32 92.01 92.21 92.52 92.64
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21.30 92.02 92.19 92.53 92.65
21.29 92.02 92.19 92.53 92.65
21.28 92.03 92.18 92.54 92.65
@@ -24747,17 +24870,17 @@ Bangladesh
20.99 92.17 92.26
20.98 92.18 92.26
20.97 92.18 92.26
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20.94 92.19 92.27
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20.91 92.20 92.28
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20.89 92.21 92.29
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20.87 92.22 92.31
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20.85 92.23 92.31
20.84 92.24 92.31
20.83 92.24 92.31
@@ -24775,14 +24898,14 @@ Bangladesh
Barbados
13.35 -59.62 -59.59
13.34 -59.64 -59.58
- 13.33 -59.65 -59.57
- 13.32 -59.66 -59.56
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13.31 -59.66 -59.56
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13.29 -59.66 -59.55
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13.27 -59.66 -59.54
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13.25 -59.66 -59.53
13.24 -59.66 -59.52
13.23 -59.66 -59.51
@@ -24796,12 +24919,12 @@ Barbados
13.15 -59.65 -59.41
13.14 -59.65 -59.41
13.13 -59.65 -59.41
- 13.12 -59.64 -59.41
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13.06 -59.57 -59.47
13.05 -59.55 -59.48
13.04 -59.54 -59.49
@@ -24809,13 +24932,10 @@ Bassas da India
-21.43 39.71 39.74
-21.44 39.71 39.74
-21.45 39.71 39.74
- -21.48 39.68 39.70
- -21.49 39.68 39.70
- -21.50 39.68 39.70
Belarus
56.16 28.08 28.13
- 56.15 28.05 28.15
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+ 56.14 28.02 28.16
56.13 28.00 28.17
56.12 27.92 28.19
56.11 27.90 28.21
@@ -24870,7 +24990,7 @@ Belarus
55.62 26.59 30.73 30.82 30.87
55.61 26.59 30.74 30.78 30.89
55.60 26.59 30.90
- 55.59 26.59 30.91
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55.58 26.58 30.92
55.57 26.58 30.92
55.56 26.56 30.92
@@ -24904,7 +25024,7 @@ Belarus
55.28 26.77 30.82
55.27 26.78 30.84
55.26 26.77 30.86
- 55.25 26.73 30.87
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55.24 26.67 30.87
55.23 26.65 30.88
55.22 26.64 30.88
@@ -25148,7 +25268,7 @@ Belarus
52.84 23.90 31.52
52.83 23.90 31.52
52.82 23.90 31.53
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52.80 23.91 31.56
52.79 23.91 31.57
52.78 23.91 31.57
@@ -25239,7 +25359,7 @@ Belarus
51.93 23.61 30.84
51.92 23.61 25.12 25.22 30.82
51.91 23.61 25.07 25.30 30.82
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51.89 23.60 24.96 25.92 30.81
51.88 23.59 24.87 26.08 30.78
51.87 23.59 24.52 24.66 24.77 26.10 30.74
@@ -25293,7 +25413,7 @@ Belarus
51.39 28.71 28.74 29.26 29.49 30.28 30.64
51.38 29.27 29.48 30.31 30.65
51.37 29.27 29.37 29.42 29.47 30.31 30.65
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51.35 29.30 29.33 30.30 30.65
51.34 30.30 30.64
51.33 30.30 30.64
@@ -25309,46 +25429,46 @@ Belarus
51.23 30.52 30.56
51.22 30.52 30.56
Belgium
- 51.50 4.74 4.80
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51.49 4.72 4.82
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51.47 4.40 4.54 4.69 4.83 4.99 5.07
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51.45 4.36 4.54 4.67 4.83 4.98 5.08
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51.38 3.31 3.35 4.38 5.08
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51.35 3.18 3.36 4.20 5.11
51.34 3.14 3.36 4.19 5.11
51.33 3.10 3.36 4.18 5.12
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51.31 3.05 3.36 4.16 5.21
51.30 3.03 3.36 3.59 3.62 4.14 5.22
51.29 3.00 3.36 3.50 3.67 4.12 5.22 5.43 5.51
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51.27 2.95 3.37 3.49 3.77 4.06 5.22 5.25 5.33 5.39 5.54
51.26 2.93 3.39 3.49 3.78 4.03 5.54
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51.22 2.82 3.79 3.93 5.56
51.21 2.80 5.60
51.20 2.77 5.64
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51.18 2.72 5.75
51.17 2.69 5.76
51.16 2.67 5.83
51.15 2.65 5.84
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51.10 2.53 5.85
51.09 2.51 5.85
51.08 2.51 5.84
@@ -25374,24 +25494,24 @@ Belgium
50.88 2.57 5.69
50.87 2.57 5.67
50.86 2.57 5.66
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50.84 2.57 5.63
50.83 2.57 5.64
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50.81 2.60 5.68
50.80 2.61 5.71
50.79 2.68 5.71
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50.77 2.69 5.70 5.73 5.78
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50.72 2.75 2.94 3.16 6.02 6.04 6.10
50.71 2.77 2.93 3.16 6.11
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50.67 3.22 6.15
50.66 3.21 6.16
50.65 3.21 6.17
@@ -25404,15 +25524,15 @@ Belgium
50.58 3.24 6.25
50.57 3.24 6.24
50.56 3.25 6.23
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50.54 3.25 6.18
50.53 3.25 6.18
50.52 3.25 6.20
50.51 3.26 6.20
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50.46 3.59 6.33
50.45 3.61 6.34
50.44 3.62 6.36
@@ -25433,11 +25553,11 @@ Belgium
50.29 3.66 3.72 4.06 6.37
50.28 3.68 3.70 4.08 6.28
50.27 4.09 6.28
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50.25 4.10 6.28
50.24 4.11 6.27
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50.21 4.14 6.17
50.20 4.14 6.17
50.19 4.13 6.17
@@ -25446,31 +25566,31 @@ Belgium
50.16 4.12 6.16
50.15 4.11 6.16
50.14 4.11 5.96 6.00 6.13
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50.12 4.11 4.76 4.86 5.95 6.09 6.13
50.11 4.11 4.75 4.85 5.95 6.09 6.13
50.10 4.17 4.74 4.83 5.94
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50.08 4.18 4.71 4.82 5.88
50.07 4.18 4.69 4.81 5.87
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50.05 4.15 4.69 4.81 5.87
50.04 4.13 4.69 4.81 5.85
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50.01 4.11 4.68 4.79 5.84
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49.99 4.11 4.67 4.78 5.82
49.98 4.12 4.67 4.77 5.82
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49.91 4.84 5.75
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49.88 4.83 5.74
49.87 4.83 5.75
49.86 4.82 5.76
@@ -25482,7 +25602,7 @@ Belgium
49.80 4.83 5.73
49.79 4.83 5.77
49.78 4.83 5.78
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49.76 5.00 5.80
49.75 5.01 5.81
49.74 5.03 5.81
@@ -25491,27 +25611,27 @@ Belgium
49.71 5.10 5.86
49.70 5.11 5.86
49.69 5.12 5.86
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49.66 5.27 5.88
49.65 5.28 5.89
49.64 5.28 5.89
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49.62 5.28 5.88
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49.56 5.41 5.85
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49.52 5.44 5.63 5.67 5.73 5.76 5.81
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Belize
18.50 -88.42 -88.40
18.49 -88.49 -88.46 -88.44 -88.29
@@ -25536,7 +25656,7 @@ Belize
18.30 -88.60 -88.08
18.29 -88.61 -88.08
18.28 -88.61 -88.08
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18.26 -88.62 -88.07
18.25 -88.62 -88.07
18.24 -88.62 -88.07
@@ -25557,10 +25677,10 @@ Belize
18.09 -88.73 -88.08 -87.98 -87.85
18.08 -88.73 -88.08 -87.99 -87.86
18.07 -88.73 -88.09 -87.99 -87.86
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18.05 -88.75 -88.10 -87.95 -87.87
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18.02 -88.79 -88.11 -87.96 -87.88
18.01 -88.79 -88.11 -87.96 -87.89
18.00 -89.07 -89.01 -88.79 -88.12 -87.96 -87.89
@@ -25593,188 +25713,188 @@ Belize
17.73 -89.17 -88.21 -88.09 -88.06
17.72 -89.17 -88.21 -88.11 -88.06
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15.87 -89.23 -89.20 -89.00 -88.91
15.86 -88.97 -88.93
@@ -25831,11 +25951,11 @@ Benin
11.91 2.36 3.31
11.90 2.36 3.32 3.35 3.39
11.89 2.37 3.41
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11.86 2.36 3.47
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11.82 2.35 3.52
11.81 2.34 3.52
@@ -25869,13 +25989,13 @@ Benin
11.53 2.09 3.51
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11.43 1.37 1.59 1.69 1.94 1.99 3.47
11.42 1.37 1.59 1.65 3.47
11.41 1.37 1.60 1.62 3.48
@@ -25998,10 +26118,10 @@ Benin
10.24 0.92 3.60
10.23 0.93 3.61
10.22 0.95 3.62
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10.20 0.98 3.64
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10.17 1.03 3.67
10.16 1.05 3.67
10.15 1.07 3.67
@@ -26089,9 +26209,9 @@ Benin
9.33 1.38 3.16
9.32 1.38 3.16
9.31 1.39 3.16
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9.27 1.41 3.16
9.26 1.42 3.16
9.25 1.43 3.15
@@ -26148,7 +26268,7 @@ Benin
8.74 1.59 2.73
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8.70 1.59 2.74
8.69 1.59 2.74
8.68 1.59 2.74
@@ -26160,9 +26280,9 @@ Benin
8.62 1.59 2.74
8.61 1.59 2.74
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@@ -26249,7 +26369,7 @@ Benin
7.73 1.61 2.73
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7.71 1.61 2.73
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7.69 1.61 2.72
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@@ -26369,13 +26489,13 @@ Benin
6.53 1.65 2.74
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6.42 1.72 2.71
6.41 1.73 2.71
@@ -26402,47 +26522,52 @@ Benin
6.20 1.60 1.64
Bermuda
32.39 -64.68 -64.66
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Bhutan
- 28.33 89.98 90.02
- 28.32 89.96 90.08
- 28.31 89.86 89.88 89.94 90.14
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28.07 89.46 90.74 91.17 91.31
28.06 89.45 90.77 91.16 91.32
28.05 89.44 90.88 91.15 91.34
@@ -26470,58 +26595,58 @@ Bhutan
27.83 89.24 91.63
27.82 89.22 91.63
27.81 89.21 91.63
- 27.80 89.19 91.63
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27.50 88.96 91.65
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27.32 88.88 92.08
27.31 88.88 92.09
27.30 88.87 92.09
- 27.29 88.87 92.09
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27.28 88.84 92.09
27.27 88.81 92.09
27.26 88.78 92.09
@@ -26537,7 +26662,7 @@ Bhutan
27.16 88.72 92.01
27.15 88.72 92.01
27.14 88.72 92.00
- 27.13 88.73 92.00
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27.12 88.75 92.00
27.11 88.77 91.99
27.10 88.79 91.99
@@ -26561,21 +26686,21 @@ Bhutan
26.92 88.91 92.09
26.91 88.91 92.09
26.90 88.92 88.97 89.00 92.09
- 26.89 89.02 92.08
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26.88 89.03 92.08
26.87 89.05 90.32 90.38 92.08
26.86 89.05 90.32 90.40 92.07
26.85 89.06 90.31 90.41 91.42 91.44 91.90 91.92 92.06
26.84 89.06 90.30 90.43 91.40 91.47 91.90 91.94 92.04
26.83 89.06 90.21 90.44 91.38 91.47 91.79 91.83 91.89 91.96 92.01
- 26.82 89.07 89.27 89.36 90.19 90.46 91.38 91.48 91.77 91.83 91.89
+ 26.82 89.07 89.27 89.35 90.19 90.46 91.38 91.48 91.77 91.83 91.89
26.81 89.08 89.26 89.37 90.18 90.48 91.38 91.48 91.76 91.83 91.89
26.80 89.10 89.25 89.39 90.17 90.50 91.37 91.49 91.74 91.84 91.89
26.79 89.41 90.17 90.52 91.36 91.49 91.57 91.60 91.72 91.85 91.88
26.78 89.43 89.48 89.52 90.17 90.54 91.05 91.21 91.35 91.51 91.55 91.62 91.68
- 26.77 89.56 90.16 90.56 91.02 91.23 91.34
- 26.76 89.58 90.16 90.61 90.93 91.25 91.33
- 26.75 89.60 90.15 90.67 90.79
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+ 26.75 89.60 90.15 90.67 90.83
26.74 89.59 90.13
26.73 89.58 90.11
26.72 89.58 90.03
@@ -26715,7 +26840,7 @@ Bolivia
-10.94 -69.58 -69.18 -68.27 -65.30
-10.95 -69.58 -69.13 -69.10 -69.05 -68.28 -65.28
-10.96 -69.58 -69.03 -68.30 -65.28
- -10.97 -69.57 -69.01 -68.31 -65.28
+ -10.97 -69.58 -69.01 -68.31 -65.28
-10.98 -69.57 -68.99 -68.82 -68.78 -68.32 -65.28
-10.99 -69.56 -68.92 -68.84 -68.75 -68.38 -65.28
-11.00 -69.56 -68.74 -68.40 -65.29
@@ -27572,14 +27697,14 @@ Bolivia
-19.51 -68.55 -60.99 -58.73 -58.00
-19.52 -68.56 -61.04 -58.71 -58.00
-19.53 -68.57 -61.09 -58.69 -58.01
- -19.54 -68.58 -61.14 -58.67 -58.01
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-19.55 -68.58 -61.19 -58.65 -58.02
-19.56 -68.59 -61.24 -58.63 -58.02
- -19.57 -68.60 -61.29 -58.61 -58.03
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-19.58 -68.60 -61.33 -58.59 -58.03
-19.59 -68.61 -61.38 -58.58 -58.04
-19.60 -68.62 -61.43 -58.56 -58.04
- -19.61 -68.63 -61.48 -58.55 -58.05
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-19.62 -68.63 -61.51 -58.53 -58.05
-19.63 -68.64 -61.59 -58.52 -58.06
-19.64 -68.64 -61.68 -58.50 -58.06
@@ -27666,8 +27791,8 @@ Bolivia
-20.45 -68.76 -62.17
-20.46 -68.76 -62.18
-20.47 -68.75 -62.19
- -20.48 -68.73 -62.19
- -20.49 -68.72 -62.20
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+ -20.49 -68.72 -62.21
-20.50 -68.72 -62.21
-20.51 -68.71 -62.22
-20.52 -68.69 -62.23
@@ -27711,7 +27836,7 @@ Bolivia
-20.90 -68.57 -62.26
-20.91 -68.57 -62.26
-20.92 -68.56 -62.26
- -20.93 -68.55 -62.26
+ -20.93 -68.54 -62.26
-20.94 -68.53 -62.26
-20.95 -68.52 -68.46 -68.44 -62.26
-20.96 -68.42 -62.26
@@ -27819,7 +27944,7 @@ Bolivia
-21.98 -68.10 -66.27 -65.91 -62.55
-21.99 -68.09 -66.27 -65.90 -62.55
-22.00 -68.08 -66.27 -65.89 -62.56
- -22.01 -68.06 -66.27 -65.88 -63.91 -63.86 -63.64 -63.32 -62.92 -62.84 -62.56
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-22.02 -68.05 -66.28 -65.88 -63.94 -63.80 -63.67 -62.81 -62.56
-22.03 -68.04 -66.28 -65.87 -63.94 -63.79 -63.69 -62.81 -62.56
-22.04 -68.03 -66.28 -65.86 -63.95 -63.77 -63.70 -62.81 -62.57
@@ -27829,7 +27954,7 @@ Bolivia
-22.08 -67.98 -66.29 -65.82 -63.96 -62.80 -62.58
-22.09 -67.98 -66.32 -65.81 -63.98 -62.80 -62.58
-22.10 -67.97 -66.33 -65.80 -65.58 -65.54 -63.99 -62.80 -62.58
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-22.12 -67.97 -66.35 -65.76 -65.70 -64.95 -63.99 -62.80 -62.59
-22.13 -67.97 -66.36 -64.91 -63.99 -62.80 -62.59
-22.14 -67.98 -66.38 -64.86 -64.00 -62.79 -62.59
@@ -27920,14 +28045,14 @@ Borneo
4.99 114.88 115.06
4.98 114.86 115.05
4.97 114.85 115.05
- 4.96 114.83 115.05
+ 4.96 114.84 115.05
4.95 114.82 115.04
- 4.94 114.80 115.04
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- 4.90 114.74 115.01 115.10 115.15
- 4.89 114.72 115.00 115.10 115.15
+ 4.94 114.81 115.04
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+ 4.89 114.73 115.00 115.10 115.15
4.88 114.71 115.00 115.10 115.16
4.87 114.70 114.99 115.10 115.19
4.86 114.69 114.98 115.11 115.19
@@ -27947,7 +28072,7 @@ Borneo
4.72 114.54 114.76 115.01 115.25
4.71 114.52 114.75 115.01 115.25
4.70 114.50 114.75 115.01 115.26
- 4.69 114.48 114.75 115.01 115.26
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4.68 114.45 114.76 115.01 115.27
4.67 114.42 114.76 115.01 115.27
4.66 114.40 114.77 115.01 115.27
@@ -28040,18 +28165,18 @@ Borneo
4.21 115.68 117.42
4.20 115.67 117.43
4.19 115.66 117.45
- 4.18 115.64 117.55 117.79 117.91
- 4.17 115.63 117.56 117.68 117.91
- 4.16 115.63 117.57 117.68 117.92
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4.14 115.62 117.57 117.62 117.92
4.13 115.62 117.55 117.62 117.69 117.71 117.92
4.12 115.62 117.41 117.45 117.54 117.61 117.70 117.72 117.92
4.11 115.62 117.41 117.48 117.53 117.60 117.92
4.10 115.62 117.45 117.60 117.92
- 4.09 115.62 117.46 117.59 117.92
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4.08 115.61 117.47 117.59 117.93
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4.06 115.61 117.48 117.50 117.52 117.58 117.76 117.79 117.94
4.05 115.61 117.53 117.58 117.76 117.80 117.94
4.04 115.61 117.54 117.59 117.76 117.81 117.94
@@ -28070,7 +28195,7 @@ Borneo
3.91 115.52 117.69
3.90 115.52 117.69
3.89 115.52 117.69
- 3.88 115.52 117.71 117.74 117.78
+ 3.88 115.52 117.70 117.74 117.78
3.87 115.54 117.80
3.86 115.56 117.82
3.85 115.56 117.83
@@ -28084,7 +28209,7 @@ Borneo
3.77 115.56 117.79
3.76 115.55 117.79
3.75 115.55 117.77
- 3.74 115.55 117.80
+ 3.74 115.55 117.82
3.73 115.55 117.83
3.72 115.54 117.83
3.71 115.54 117.83
@@ -28098,8 +28223,8 @@ Borneo
3.63 115.53 117.53 117.59 117.77
3.62 115.53 117.21 117.25 117.53 117.61 117.76
3.61 115.53 117.22 117.44 117.53 117.63 117.70
- 3.60 115.53 117.22 117.24 117.27 117.46 117.53 117.79 117.82
- 3.59 115.53 117.29 117.48 117.52 117.77 117.84
+ 3.60 115.53 117.22 117.24 117.27 117.46 117.52 117.79 117.82
+ 3.59 115.53 117.29 117.48 117.51 117.77 117.84
3.58 115.53 117.35 117.77 117.85
3.57 115.54 117.40 117.76 117.86
3.56 115.54 117.41 117.76 117.87
@@ -28129,13 +28254,13 @@ Borneo
3.32 115.49 117.67
3.31 115.49 117.67
3.30 115.49 117.54 117.56 117.67
- 3.29 115.49 117.38 117.40 117.54 117.57 117.67
+ 3.29 115.49 117.37 117.40 117.54 117.57 117.67
3.28 115.48 117.37 117.40 117.53 117.59 117.67
3.27 115.48 117.37 117.40 117.46 117.51 117.53 117.61 117.67
- 3.26 115.48 117.37 117.42 117.45 117.61 117.67
+ 3.26 115.48 117.37 117.42 117.44 117.61 117.67
3.25 115.48 117.37 117.62 117.67
- 3.24 115.48 117.37 117.62 117.67
- 3.23 115.47 117.36 117.62 117.66
+ 3.24 115.48 117.37 117.62 117.66
+ 3.23 115.47 117.36 117.62 117.65
3.22 115.47 117.35
3.21 115.47 117.33
3.20 115.47 117.35
@@ -28201,13 +28326,13 @@ Borneo
2.60 115.04 117.85
2.59 115.04 117.86
2.58 115.06 115.10 115.14 117.87
- 2.57 108.97 109.00 115.15 117.88
- 2.56 108.96 109.04 115.16 117.89
+ 2.57 108.97 109.01 115.15 117.88
+ 2.56 108.96 109.03 115.16 117.89
2.55 108.95 109.05 115.17 117.90
2.54 108.95 109.11 115.18 117.91
2.53 108.95 109.12 115.18 117.92
2.52 108.96 109.12 115.19 117.93
- 2.51 108.97 109.12 115.19 117.94
+ 2.51 108.96 109.12 115.19 117.94
2.50 109.00 109.12 115.18 117.95
2.49 109.00 109.11 115.14 117.96
2.48 109.00 109.09 115.11 117.97
@@ -28226,7 +28351,7 @@ Borneo
2.35 114.91 118.08
2.34 114.90 118.09
2.33 114.90 118.09
- 2.32 114.90 118.10 118.54 118.59
+ 2.32 114.90 118.10 118.54 118.58
2.31 114.90 118.10 118.54 118.60
2.30 114.90 118.10 118.54 118.62
2.29 114.89 118.10 118.54 118.63
@@ -28251,12 +28376,12 @@ Borneo
2.10 114.75 117.93
2.09 109.63 109.65 114.76 117.92
2.08 109.62 109.65 114.75 117.92
- 2.07 109.61 109.65 114.75 117.89
- 2.06 109.61 109.65 114.75 117.90
+ 2.07 109.61 109.65 114.75 117.90
+ 2.06 109.61 109.65 114.75 117.91
2.05 109.60 109.64 114.75 117.91
2.04 109.60 109.64 114.76 117.91
- 2.03 109.59 109.64 114.76 117.91
- 2.02 109.59 109.63 114.77 114.80 114.83 117.89
+ 2.03 109.59 109.64 114.76 117.89
+ 2.02 109.59 109.63 114.77 114.80 114.83 117.87
2.01 109.58 109.63 114.83 117.84
2.00 109.54 109.63 114.83 117.88
1.99 109.50 109.62 114.83 117.88
@@ -28277,7 +28402,7 @@ Borneo
1.84 109.31 109.54 114.66 117.92
1.83 109.31 109.54 114.66 117.92
1.82 109.30 109.55 114.66 117.96
- 1.81 109.29 109.56 114.66 117.99
+ 1.81 109.28 109.56 114.66 117.99
1.80 109.27 109.58 114.66 118.01
1.79 109.27 109.65 114.66 118.05
1.78 109.27 109.65 114.66 118.06
@@ -28304,9 +28429,9 @@ Borneo
1.57 109.08 109.69 112.43 112.62 112.81 113.01 114.57 118.29
1.56 109.07 109.70 112.41 112.78 112.81 113.02 114.56 118.31
1.55 109.07 109.71 112.41 113.02 114.56 118.34
- 1.54 109.06 109.73 112.40 113.03 114.55 118.37
- 1.53 109.06 109.74 112.38 113.03 114.55 118.38
- 1.52 109.06 109.75 112.30 113.03 114.55 118.39
+ 1.54 109.06 109.73 112.40 113.03 114.55 118.36
+ 1.53 109.06 109.74 112.38 113.03 114.55 118.37
+ 1.52 109.06 109.75 112.30 113.03 114.55 118.38
1.51 109.05 109.76 112.28 113.03 114.33 114.41 114.55 118.39
1.50 109.05 109.77 112.26 113.03 114.31 114.43 114.55 118.42
1.49 109.05 109.78 112.24 113.03 114.29 114.45 114.55 118.43
@@ -28361,22 +28486,22 @@ Borneo
1.00 108.96 110.33 110.84 111.49 111.52 117.97 118.00 119.01
0.99 108.97 110.37 110.83 117.98 118.00 119.02
0.98 108.97 110.38 110.82 117.98 118.01 119.02
- 0.97 108.97 110.39 110.80 117.99 118.01 119.02
- 0.96 108.97 110.40 110.79 117.99 118.02 119.02
- 0.95 108.97 110.40 110.78 117.99 118.02 119.01
+ 0.97 108.97 110.39 110.80 117.98 118.01 119.02
+ 0.96 108.97 110.40 110.79 117.98 118.02 119.02
+ 0.95 108.97 110.40 110.78 117.98 118.02 119.01
0.94 108.96 110.41 110.77 117.99 118.03 119.00
0.93 108.96 110.42 110.77 117.99 118.04 118.99
0.92 108.95 110.42 110.74 118.00 118.04 118.98
0.91 108.95 110.43 110.69 118.00 118.05 118.97
0.90 108.94 110.45 110.59 110.63 110.68 118.01 118.06 118.96
0.89 108.93 110.46 110.59 110.64 110.67 118.02 118.08 118.95
- 0.88 108.89 110.48 110.58 118.03 118.10 118.94
- 0.87 108.88 110.50 110.56 118.03 118.13 118.92
- 0.86 108.86 118.04 118.16 118.90
- 0.85 108.85 118.04 118.21 118.88
+ 0.88 108.89 110.48 110.58 118.03 118.10 118.93
+ 0.87 108.88 110.50 110.56 118.03 118.13 118.91
+ 0.86 108.86 118.04 118.16 118.89
+ 0.85 108.85 118.04 118.21 118.87
0.84 108.84 118.04 118.27 118.86
0.83 108.84 118.04 118.32 118.86
- 0.82 108.84 118.04 118.33 118.63 118.69 118.85
+ 0.82 108.84 118.04 118.33 118.42 118.44 118.63 118.69 118.85
0.81 108.84 117.89 117.94 118.04 118.34 118.42 118.49 118.61 118.70 118.85
0.80 108.84 117.82 117.95 118.04 118.35 118.41 118.52 118.59 118.74 118.84
0.79 108.85 117.81 117.95 118.04 118.37 118.40 118.54 118.58 118.75 118.82
@@ -28455,17 +28580,17 @@ Borneo
0.06 109.20 117.50
0.05 109.21 117.50
0.04 109.15 109.19 109.22 117.51
- 0.03 109.15 117.51
+ 0.03 109.14 117.51
0.02 109.14 117.52
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@@ -28563,12 +28688,12 @@ Borneo
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6.58 116.52 117.42 117.48 117.55
6.57 116.51 117.44 117.47 117.56
6.56 116.50 117.57
6.55 116.50 117.57
- 6.54 116.50 117.58
- 6.53 116.50 117.59 117.63 117.65
+ 6.54 116.49 117.58
+ 6.53 116.49 117.59 117.63 117.65
6.52 116.49 117.66
6.51 116.49 117.67
6.50 116.49 117.67
@@ -28986,7 +29111,7 @@ Borneo
5.99 116.08 117.68 117.90 118.08
5.98 116.08 117.68 117.89 118.08
5.97 116.07 117.68 117.88 118.08
- 5.96 116.06 117.67 117.77 117.79 117.85 118.08
+ 5.96 116.06 117.67 117.77 117.80 117.85 118.08
5.95 116.06 117.67 117.76 118.08
5.94 116.05 117.66 117.76 118.08
5.93 116.05 117.65 117.76 118.09
@@ -28997,7 +29122,7 @@ Borneo
5.88 116.04 118.13
5.87 116.04 118.13
5.86 116.04 118.13 118.17 118.24
- 5.85 116.04 118.13 118.16 118.24
+ 5.85 116.04 118.13 118.15 118.24
5.84 116.03 118.12 118.15 118.24
5.83 116.02 118.12 118.15 118.29
5.82 116.00 118.11 118.15 118.31 118.34 118.37
@@ -29006,9 +29131,9 @@ Borneo
5.79 115.94 117.93 117.96 118.07 118.14 118.44
5.78 115.93 117.93 118.14 118.46
5.77 115.92 117.93 118.14 118.47
- 5.76 115.92 117.94 118.14 118.49
- 5.75 115.91 117.94 118.14 118.51
- 5.74 115.91 117.94 118.14 118.52
+ 5.76 115.91 117.94 118.14 118.49
+ 5.75 115.90 117.94 118.14 118.51
+ 5.74 115.90 117.94 118.14 118.52
5.73 115.90 117.95 118.13 118.53
5.72 115.90 117.95 118.02 118.11 118.13 118.54
5.71 115.90 117.96 118.00 118.56
@@ -29024,9 +29149,9 @@ Borneo
5.61 115.57 115.62 115.86 118.69
5.60 115.56 115.62 115.86 118.70
5.59 115.56 115.62 115.85 118.71
- 5.58 115.55 115.61 115.85 118.71
- 5.57 115.55 115.62 115.84 118.72
- 5.56 115.54 115.64 115.83 118.73
+ 5.58 115.55 115.61 115.84 118.71
+ 5.57 115.55 115.62 115.83 118.72
+ 5.56 115.54 115.64 115.82 118.73
5.55 115.54 115.65 115.81 118.77
5.54 115.53 115.67 115.80 118.80
5.53 115.51 118.81
@@ -29047,31 +29172,31 @@ Borneo
5.38 115.20 115.25 115.36 119.27
5.37 115.19 115.25 115.36 119.28
5.36 115.18 115.25 115.35 119.28
- 5.35 115.17 115.26 115.35 119.28
+ 5.35 115.17 115.25 115.35 119.28
5.34 115.17 115.26 115.35 119.28
- 5.33 115.17 115.27 115.35 119.28
- 5.32 115.16 115.27 115.34 119.28
- 5.31 115.16 115.27 115.34 119.28
- 5.30 115.16 115.27 115.34 119.28
- 5.29 115.16 115.27 115.35 119.28
- 5.28 115.15 115.26 115.39 119.27
- 5.27 115.15 115.26 115.40 119.27
- 5.26 115.14 115.20 115.22 115.25 115.41 119.27
+ 5.33 115.17 115.26 115.35 119.28
+ 5.32 115.16 115.26 115.34 119.28
+ 5.31 115.16 115.26 115.34 119.28
+ 5.30 115.16 115.26 115.34 119.28
+ 5.29 115.16 115.26 115.35 119.28
+ 5.28 115.15 115.26 115.40 119.27
+ 5.27 115.15 115.26 115.41 119.27
+ 5.26 115.14 115.20 115.22 115.25 115.42 119.27
5.25 115.14 115.19 115.43 119.27
5.24 115.14 115.17 115.44 119.27
5.23 115.45 119.27
- 5.22 115.47 119.27
- 5.21 115.48 119.27
+ 5.22 115.46 119.27
+ 5.21 115.47 119.27
5.20 115.49 119.27
5.19 115.51 119.27
- 5.18 115.57 119.26
+ 5.18 115.56 119.26
5.17 115.56 119.25
5.16 115.56 119.24
5.15 115.56 119.23
- 5.14 115.56 119.23
- 5.13 115.56 119.22
- 5.12 115.56 119.21
- 5.11 115.56 119.20
+ 5.14 115.55 119.23
+ 5.13 115.55 119.22
+ 5.12 115.55 119.21
+ 5.11 115.55 119.20
5.10 115.55 119.19
5.09 115.55 119.17
5.08 115.55 119.14
@@ -29079,8 +29204,8 @@ Borneo
5.06 115.53 119.09
5.05 115.52 119.07
5.04 115.48 119.04
- 5.03 115.47 119.01
- 5.02 115.46 118.99
+ 5.03 115.46 119.01
+ 5.02 115.45 118.99
5.01 115.45 118.35 118.39 118.96
5.00 115.44 118.33 118.41 118.92
4.99 115.43 118.32 118.42 118.88
@@ -29090,8 +29215,8 @@ Borneo
4.95 115.18 115.24 115.39 118.23 118.46 118.57 118.59 118.76
4.94 115.18 115.29 115.38 118.21 118.46 118.56 118.63 118.74
4.93 115.17 115.30 115.37 118.20 118.47 118.54 118.65 118.72
- 4.92 115.00 115.02 115.17 115.30 115.36 118.20 118.48 118.52
- 4.91 115.00 115.02 115.13 115.32 115.34 118.19
+ 4.92 115.00 115.02 115.16 115.30 115.36 118.20 118.48 118.52
+ 4.91 114.99 115.02 115.13 118.19
4.90 114.98 115.03 115.13 118.18
4.89 114.97 115.03 115.13 118.17
4.88 114.95 115.03 115.13 118.16
@@ -29108,7 +29233,7 @@ Borneo
4.77 114.79 115.03 115.20 118.21
4.76 114.77 115.03 115.21 118.22
4.75 114.75 115.03 115.21 118.23
- 4.74 114.74 115.03 115.22 118.24
+ 4.74 114.73 115.03 115.22 118.24
4.73 114.73 115.03 115.22 118.25
4.72 114.73 115.03 115.22 118.26
4.71 114.73 115.03 115.23 118.27
@@ -29148,7 +29273,7 @@ Borneo
4.37 113.95 114.29 114.82 115.18 115.32 117.63 117.68 118.59
4.36 113.95 114.29 114.82 115.24 115.33 116.51 116.53 117.64 117.68 118.58
4.35 113.95 114.29 114.81 115.28 115.33 116.13 116.15 116.27 116.31 116.50 116.54 117.64 117.69 118.57
- 4.34 113.95 114.30 114.81 115.30 115.34 115.83 115.86 116.12 116.19 116.24 116.32 116.50 116.55 117.64 117.71 118.50 118.52 118.55
+ 4.34 113.95 114.30 114.81 115.30 115.34 115.83 115.86 116.12 116.19 116.24 116.32 116.50 116.55 117.64 117.71 118.50
4.33 113.95 114.30 114.80 115.32 115.34 115.83 115.88 116.11 116.35 116.50 116.55 116.70 116.74 117.19 117.21 117.64 117.74 118.35 118.37 118.45
4.32 113.95 114.30 114.79 115.83 115.95 116.10 116.35 116.50 116.56 116.69 116.75 116.85 116.93 117.18 117.22 117.64 117.77 118.34
4.31 113.94 114.30 114.78 115.83 115.96 116.09 116.36 116.50 116.96 117.08 117.22 117.64 117.80 118.31
@@ -29162,14 +29287,14 @@ Borneo
4.23 113.89 114.45 114.78 115.78 117.35 117.80 117.91 118.04
4.22 113.88 114.45 114.78 115.78 117.36 117.81 117.95 118.02
4.21 113.88 114.45 114.77 115.78 117.38 117.61 117.63 117.82
- 4.20 113.87 114.46 114.77 115.72 117.39 117.88
+ 4.20 113.87 114.46 114.77 115.72 117.39 117.87
4.19 113.86 114.46 114.77 115.70 117.40 117.90
4.18 113.85 114.46 114.77 115.69 117.41 117.63 117.65 117.91
4.17 113.84 114.47 114.77 115.68 117.42 117.63 117.66 117.91
4.16 113.84 114.47 114.76 115.67 117.44 117.63 117.67 117.91
- 4.15 113.83 114.48 114.76 115.65 117.54 117.60 117.68 117.80
- 4.14 113.82 114.49 114.75 115.65 117.55 117.58
- 4.13 113.81 114.50 114.74 115.65
+ 4.15 113.83 114.48 114.76 115.65 117.54 117.60 117.68 117.91
+ 4.14 113.82 114.49 114.75 115.65 117.55 117.58 117.71 117.91
+ 4.13 113.81 114.50 114.74 115.64
4.12 113.81 114.52 114.73 115.64
4.11 113.80 114.53 114.72 115.64
4.10 113.79 114.54 114.71 115.64
@@ -29268,10 +29393,10 @@ Borneo
3.17 112.99 115.52
3.16 112.97 115.52
3.15 112.95 115.52
- 3.14 112.92 115.52
- 3.13 112.89 115.51
- 3.12 112.87 115.51
- 3.11 112.84 115.50
+ 3.14 112.91 115.52
+ 3.13 112.88 115.51
+ 3.12 112.85 115.51
+ 3.11 112.81 115.50
3.10 112.77 115.49
3.09 112.75 115.49
3.08 112.73 115.48
@@ -29302,14 +29427,14 @@ Borneo
2.83 111.62 115.10
2.82 111.60 115.09
2.81 111.58 115.09
- 2.80 111.57 115.09
- 2.79 111.30 111.34 111.55 115.10
- 2.78 111.30 111.36 111.53 115.10
- 2.77 111.29 111.36 111.52 115.11
- 2.76 111.29 111.37 111.51 115.11
+ 2.80 111.56 115.09
+ 2.79 111.30 111.33 111.54 115.10
+ 2.78 111.30 111.35 111.52 115.10
+ 2.77 111.29 111.36 111.51 115.11
+ 2.76 111.29 111.36 111.50 115.11
2.75 111.29 111.37 111.49 115.11
- 2.74 111.29 111.38 111.48 115.11
- 2.73 111.28 111.38 111.47 115.10
+ 2.74 111.29 111.38 111.47 115.11
+ 2.73 111.28 111.38 111.46 115.10
2.72 111.28 111.38 111.45 115.10
2.71 111.28 111.39 111.44 115.09
2.70 111.28 111.39 111.43 115.06
@@ -29375,8 +29500,8 @@ Borneo
2.10 111.23 114.78
2.09 109.63 109.65 111.23 114.78
2.08 109.63 109.65 111.20 114.78
- 2.07 109.62 109.66 111.19 114.78
- 2.06 109.62 109.66 111.19 114.78
+ 2.07 109.62 109.65 111.19 114.78
+ 2.06 109.62 109.65 111.19 114.78
2.05 109.62 109.66 111.19 114.84
2.04 109.61 109.66 111.19 114.85
2.03 109.61 109.66 111.18 114.85
@@ -29400,9 +29525,9 @@ Borneo
1.85 109.52 109.73 111.11 114.77
1.84 109.52 109.75 111.10 114.70
1.83 109.52 109.78 111.10 114.68
- 1.82 109.52 109.80 111.10 114.68
- 1.81 109.52 109.82 110.31 110.34 111.10 114.68
- 1.80 109.53 109.84 110.30 110.35 111.10 114.68
+ 1.82 109.52 109.80 111.09 114.68
+ 1.81 109.52 109.82 110.31 110.34 111.09 114.68
+ 1.80 109.53 109.84 110.30 110.35 111.09 114.68
1.79 109.54 109.86 110.30 110.35 111.09 114.68
1.78 109.55 109.88 110.29 110.36 111.08 114.69
1.77 109.57 109.89 110.28 110.36 111.08 114.69
@@ -29414,8 +29539,8 @@ Borneo
1.71 109.63 109.92 110.00 110.18 110.22 110.27 110.29 110.39 110.43 110.53 111.10 114.68
1.70 109.63 109.94 109.96 110.20 110.22 110.52 111.10 114.68
1.69 109.63 110.51 111.06 114.67
- 1.68 109.63 110.51 111.02 114.67
- 1.67 109.63 110.51 111.01 114.67
+ 1.68 109.63 110.50 111.02 114.67
+ 1.67 109.63 110.50 111.01 114.67
1.66 109.63 110.50 111.01 114.67
1.65 109.63 110.50 111.01 114.66
1.64 109.63 110.52 111.01 114.66
@@ -29505,42 +29630,42 @@ Bosnia and Herzegovina
45.27 16.88 16.94
45.26 16.87 16.97
45.25 16.85 17.01
- 45.24 16.84 17.04
- 45.23 16.51 16.60 16.82 17.05
- 45.22 15.81 16.03 16.50 16.64 16.82 17.05
- 45.21 15.80 16.03 16.48 16.67 16.81 17.06
- 45.20 15.79 16.03 16.47 16.71 16.81 17.07
- 45.19 15.78 16.04 16.46 16.76 16.79 17.09 17.25 17.29
- 45.18 15.78 16.06 16.45 17.12 17.24 17.31
- 45.17 15.76 16.07 16.45 17.15 17.24 17.34 17.43 17.45 17.63 17.70
- 45.16 15.76 16.09 16.44 17.36 17.42 17.46 17.61 17.72 18.20 18.27
- 45.15 15.76 16.09 16.43 17.46 17.48 17.50 17.60 17.74 17.97 18.04 18.19 18.28
- 45.14 15.76 16.10 16.42 17.50 17.59 17.75 17.96 18.05 18.19 18.30
- 45.13 15.76 16.10 16.38 17.76 17.95 18.07 18.18 18.36
- 45.12 15.76 16.11 16.37 17.77 17.93 18.09 18.18 18.42
- 45.11 15.77 16.12 16.37 17.78 17.92 18.13 18.16 18.43
+ 45.24 16.85 17.04
+ 45.23 16.51 16.61 16.83 17.05
+ 45.22 15.81 16.03 16.50 16.65 16.82 17.05
+ 45.21 15.80 16.03 16.48 16.69 16.81 17.06
+ 45.20 15.79 16.03 16.47 16.73 16.81 17.08
+ 45.19 15.78 16.03 16.46 16.77 16.79 17.09 17.25 17.29
+ 45.18 15.78 16.06 16.45 17.11 17.24 17.32
+ 45.17 15.77 16.08 16.45 17.14 17.24 17.34 17.43 17.45 17.63 17.70
+ 45.16 15.77 16.09 16.44 17.36 17.42 17.46 17.61 17.72 18.20 18.27
+ 45.15 15.77 16.09 16.43 17.46 17.48 17.50 17.60 17.74 17.97 18.04 18.19 18.29
+ 45.14 15.77 16.10 16.42 17.50 17.59 17.75 17.96 18.06 18.19 18.30
+ 45.13 15.77 16.10 16.38 17.76 17.95 18.07 18.19 18.36
+ 45.12 15.77 16.11 16.37 17.77 17.93 18.09 18.18 18.42
+ 45.11 15.77 16.12 16.37 17.78 17.92 18.13 18.16 18.43 18.59 18.61
45.10 15.77 16.13 16.37 17.79 17.91 18.45 18.52 18.63
- 45.09 15.76 16.15 16.37 17.80 17.90 18.46 18.52 18.63 18.65 18.69
- 45.08 15.76 16.16 16.36 17.82 17.85 18.48 18.52 18.70
- 45.07 15.75 16.17 16.36 18.70
+ 45.09 15.76 16.15 16.37 17.81 17.90 18.46 18.52 18.63 18.65 18.69
+ 45.08 15.76 16.16 16.36 17.83 17.85 18.48 18.52 18.70
+ 45.07 15.75 16.18 16.35 18.70
45.06 15.75 16.19 16.35 18.71
45.05 15.74 16.21 16.34 18.72
- 45.04 15.74 16.23 16.34 18.72
+ 45.04 15.74 16.22 16.34 18.72
45.03 15.74 16.24 16.33 18.73
- 45.02 15.74 16.27 16.33 18.78
+ 45.02 15.74 16.26 16.33 18.78
45.01 15.74 18.80
45.00 15.74 18.80
- 44.99 15.74 18.80
+ 44.99 15.75 18.80
44.98 15.75 18.81
44.97 15.74 18.81
44.96 15.73 18.81
44.95 15.72 18.81
- 44.94 15.72 18.80
+ 44.94 15.72 18.79
44.93 15.72 18.79 19.16 19.20
- 44.92 15.72 18.79 19.14 19.26 19.29 19.31
+ 44.92 15.72 18.79 19.14 19.26 19.29 19.32
44.91 15.72 18.80 19.12 19.33
44.90 15.72 18.81 19.10 19.37
- 44.89 15.72 18.84 19.08 19.38
+ 44.89 15.72 18.83 19.08 19.38
44.88 15.72 18.85 19.02 19.38
44.87 15.73 19.38
44.86 15.74 19.38
@@ -29558,17 +29683,17 @@ Bosnia and Herzegovina
44.74 15.72 19.34
44.73 15.73 19.33
44.72 15.74 19.33
- 44.71 15.77 19.33
- 44.70 15.77 19.32
+ 44.71 15.76 19.33
+ 44.70 15.78 19.32
44.69 15.78 19.31
44.68 15.79 15.83 15.89 19.30
44.67 15.90 19.28
44.66 15.93 19.28
- 44.65 15.94 19.27
+ 44.65 15.93 19.27
44.64 15.94 19.27
44.63 15.94 19.26
44.62 15.95 19.25
- 44.61 15.99 19.24
+ 44.61 16.00 19.24
44.60 16.02 19.24
44.59 16.02 19.23
44.58 16.02 19.22
@@ -29578,7 +29703,7 @@ Bosnia and Herzegovina
44.54 15.99 19.19
44.53 15.99 19.19
44.52 16.00 19.18
- 44.51 16.01 16.06 16.10 19.17
+ 44.51 16.01 16.07 16.10 19.17
44.50 16.10 19.15
44.49 16.11 19.14
44.48 16.11 19.14
@@ -29589,7 +29714,7 @@ Bosnia and Herzegovina
44.43 16.13 19.15
44.42 16.14 19.15
44.41 16.14 19.14
- 44.40 16.13 19.13
+ 44.40 16.14 19.13
44.39 16.12 19.12
44.38 16.12 19.12
44.37 16.12 19.11
@@ -29609,7 +29734,7 @@ Bosnia and Herzegovina
44.23 16.18 19.36
44.22 16.19 19.36
44.21 16.19 19.36
- 44.20 16.19 19.37
+ 44.20 16.20 19.37
44.19 16.20 19.38
44.18 16.22 19.40
44.17 16.23 19.42
@@ -29618,9 +29743,9 @@ Bosnia and Herzegovina
44.14 16.26 19.48
44.13 16.27 19.49
44.12 16.28 19.50
- 44.11 16.28 19.51
+ 44.11 16.29 19.51
44.10 16.29 19.52
- 44.09 16.29 19.54
+ 44.09 16.30 19.54
44.08 16.30 19.56
44.07 16.31 19.61
44.06 16.32 19.62
@@ -29630,7 +29755,7 @@ Bosnia and Herzegovina
44.02 16.41 19.62
44.01 16.42 19.62
44.00 16.42 19.62
- 43.99 16.46 19.27 19.29 19.61
+ 43.99 16.45 19.27 19.29 19.61
43.98 16.49 19.25 19.31 19.59
43.97 16.49 19.25 19.32 19.57
43.96 16.50 19.25 19.34 19.54
@@ -29647,31 +29772,31 @@ Bosnia and Herzegovina
43.85 16.62 19.36
43.84 16.64 19.38
43.83 16.66 19.39
- 43.82 16.67 19.40
+ 43.82 16.66 19.40
43.81 16.67 19.42
43.80 16.67 19.43
43.79 16.67 19.44
- 43.78 16.68 19.46
+ 43.78 16.67 19.46
43.77 16.68 19.47
43.76 16.70 19.47
43.75 16.71 19.48
43.74 16.73 19.48
- 43.73 16.75 19.49
- 43.72 16.77 19.49
+ 43.73 16.74 19.49
+ 43.72 16.76 19.49
43.71 16.78 19.50
- 43.70 16.80 19.50
+ 43.70 16.79 19.50
43.69 16.81 19.51
43.68 16.82 19.51
- 43.67 16.83 19.51
+ 43.67 16.84 19.51
43.66 16.85 19.51
43.65 16.86 19.51
- 43.64 16.87 19.51
+ 43.64 16.88 19.51
43.63 16.89 19.51
43.62 16.90 19.50
- 43.61 16.91 19.49
+ 43.61 16.92 19.49
43.60 16.93 19.48
43.59 16.94 19.48
- 43.58 16.95 19.33 19.36 19.49
+ 43.58 16.96 19.33 19.36 19.49
43.57 16.97 19.31 19.37 19.50
43.56 16.98 19.25 19.37 19.50
43.55 16.99 19.24 19.38 19.43 19.46 19.50
@@ -29679,16 +29804,16 @@ Bosnia and Herzegovina
43.53 17.02 19.23 19.39 19.42
43.52 17.03 18.97 19.00 19.22
43.51 17.05 18.96 19.01 19.12
- 43.50 17.07 18.94 19.01 19.10
+ 43.50 17.07 18.94 19.02 19.10
43.49 17.09 18.94 19.04 19.09
43.48 17.11 18.95
43.47 17.13 18.96
43.46 17.18 18.96
43.45 17.25 18.98
43.44 17.26 18.99
- 43.43 17.26 19.00
+ 43.43 17.27 19.00
43.42 17.27 19.01
- 43.41 17.27 19.01
+ 43.41 17.26 19.01
43.40 17.26 19.02
43.39 17.26 19.02
43.38 17.26 19.03
@@ -29696,12 +29821,12 @@ Bosnia and Herzegovina
43.36 17.25 19.04
43.35 17.25 19.05
43.34 17.25 19.05
- 43.33 17.26 18.88 18.90 19.06
+ 43.33 17.25 18.87 18.90 19.06
43.32 17.26 18.84 18.93 19.06
- 43.31 17.27 18.84 18.94 19.07
- 43.30 17.27 18.83 18.94 19.07
- 43.29 17.28 18.80 18.94 19.07
- 43.28 17.29 18.78 18.95 19.03
+ 43.31 17.26 18.84 18.94 19.07
+ 43.30 17.27 18.82 18.94 19.07
+ 43.29 17.27 18.80 18.94 19.07
+ 43.28 17.28 18.78 18.95 19.03
43.27 17.29 18.76 18.96 19.02
43.26 17.30 18.74 18.97 19.01
43.25 17.31 18.72 18.98 19.00
@@ -29710,19 +29835,19 @@ Bosnia and Herzegovina
43.22 17.35 18.69
43.21 17.37 18.69
43.20 17.39 18.68
- 43.19 17.39 18.68
- 43.18 17.40 18.67
- 43.17 17.40 18.66
+ 43.19 17.39 18.67
+ 43.18 17.39 18.66
+ 43.17 17.40 18.65
43.16 17.40 18.64
43.15 17.41 18.64
- 43.14 17.42 18.63
- 43.13 17.45 18.63
- 43.12 17.47 18.63
- 43.11 17.49 18.63
- 43.10 17.51 18.63
- 43.09 17.53 18.63
- 43.08 17.55 18.63
- 43.07 17.57 18.63
+ 43.14 17.43 18.63
+ 43.13 17.44 18.63
+ 43.12 17.46 18.63
+ 43.11 17.48 18.63
+ 43.10 17.50 18.63
+ 43.09 17.52 18.63
+ 43.08 17.54 18.63
+ 43.07 17.56 18.63
43.06 17.58 18.64
43.05 17.59 18.64
43.04 17.60 18.64
@@ -29730,7 +29855,7 @@ Bosnia and Herzegovina
43.02 17.62 18.64
43.01 17.62 18.64
43.00 17.63 18.51
- 42.99 17.64 18.48
+ 42.99 17.63 18.48
42.98 17.64 18.46
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@@ -29746,14 +29871,14 @@ Bosnia and Herzegovina
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@@ -29772,7 +29897,7 @@ Bosnia and Herzegovina
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42.59 18.28 18.53
42.58 18.33 18.51
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@@ -29893,11 +30018,11 @@ Botswana
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- -7.23 72.43 72.47
+ -7.21 72.42 72.45
+ -7.22 72.42 72.46
+ -7.23 72.42 72.47
-7.24 72.43 72.47
- -7.25 72.34 72.37 72.44 72.48
+ -7.25 72.34 72.37 72.43 72.48
-7.26 72.34 72.38 72.44 72.49
-7.27 72.34 72.40 72.45 72.49
-7.28 72.35 72.42 72.46 72.50
@@ -34666,7 +34792,7 @@ British Virgin Islands
18.74 -64.41 -64.27
18.73 -64.41 -64.27
18.72 -64.40 -64.26
- 18.71 -64.38 -64.26
+ 18.71 -64.39 -64.26
18.70 -64.32 -64.26
18.69 -64.29 -64.26
18.52 -64.42 -64.39 -64.33 -64.31
@@ -34676,15 +34802,15 @@ British Virgin Islands
18.48 -64.54 -64.51 -64.42 -64.32
18.47 -64.54 -64.51 -64.43 -64.33
18.46 -64.75 -64.71 -64.65 -64.51 -64.44 -64.37
- 18.45 -64.78 -64.71 -64.66 -64.52 -64.45 -64.38
- 18.44 -64.78 -64.71 -64.67 -64.54 -64.45 -64.39
- 18.43 -64.78 -64.71 -64.68 -64.54 -64.45 -64.40
- 18.42 -64.74 -64.72 -64.69 -64.54
- 18.41 -64.70 -64.55
+ 18.45 -64.78 -64.71 -64.67 -64.51 -64.45 -64.38
+ 18.44 -64.78 -64.71 -64.67 -64.50 -64.45 -64.39
+ 18.43 -64.78 -64.71 -64.67 -64.50 -64.45 -64.40
+ 18.42 -64.74 -64.72 -64.68 -64.50
+ 18.41 -64.68 -64.55
18.40 -64.71 -64.56
- 18.39 -64.71 -64.61
- 18.38 -64.71 -64.63
- 18.37 -64.67 -64.64 -64.58 -64.56
+ 18.39 -64.72 -64.62
+ 18.38 -64.72 -64.63
+ 18.37 -64.72 -64.64 -64.58 -64.56
18.36 -64.61 -64.55
18.35 -64.61 -64.55
18.34 -64.61 -64.55
@@ -34701,14 +34827,14 @@ Brunei
4.99 114.88 115.06
4.98 114.86 115.05
4.97 114.85 115.05
- 4.96 114.83 115.05
+ 4.96 114.84 115.05
4.95 114.82 115.04
- 4.94 114.80 115.04
- 4.93 114.78 115.03
- 4.92 114.77 115.03
- 4.91 114.75 115.02 115.10 115.15
- 4.90 114.74 115.01 115.10 115.15
- 4.89 114.72 115.00 115.10 115.15
+ 4.94 114.81 115.04
+ 4.93 114.79 115.03
+ 4.92 114.78 115.03
+ 4.91 114.76 115.02 115.10 115.15
+ 4.90 114.75 115.01 115.10 115.15
+ 4.89 114.73 115.00 115.10 115.15
4.88 114.71 115.00 115.10 115.16
4.87 114.70 114.99 115.10 115.19
4.86 114.69 114.98 115.11 115.19
@@ -34728,7 +34854,7 @@ Brunei
4.72 114.54 114.76 115.01 115.25
4.71 114.52 114.75 115.01 115.25
4.70 114.50 114.75 115.01 115.26
- 4.69 114.48 114.75 115.01 115.26
+ 4.69 114.47 114.75 115.01 115.26
4.68 114.45 114.76 115.01 115.27
4.67 114.42 114.76 115.01 115.27
4.66 114.40 114.77 115.01 115.27
@@ -34799,9 +34925,9 @@ Brunei
4.01 114.57 114.65
4.00 114.60 114.63
Bulgaria
- 44.23 22.65 22.71
+ 44.23 22.66 22.71
44.22 22.63 22.73
- 44.21 22.62 22.75
+ 44.21 22.63 22.75
44.20 22.62 22.77
44.19 22.61 22.79
44.18 22.59 22.81 27.01 27.04
@@ -34811,11 +34937,11 @@ Bulgaria
44.14 22.58 22.89 26.81 27.18
44.13 22.58 22.93 26.79 27.26
44.12 22.58 22.97 26.76 27.27
- 44.11 22.58 23.01 26.68 27.27
+ 44.11 22.58 23.02 26.68 27.27
44.10 22.58 23.04 26.62 27.27
44.09 22.58 23.04 26.56 27.28
- 44.08 22.59 23.05 26.46 27.30
- 44.07 22.54 23.05 26.36 27.33
+ 44.08 22.58 23.05 26.46 27.30
+ 44.07 22.54 23.05 26.37 27.33
44.06 22.52 23.05 26.29 27.35
44.05 22.51 23.05 26.27 27.36
44.04 22.50 23.04 26.24 27.37
@@ -34837,28 +34963,28 @@ Bulgaria
43.88 22.36 22.86 23.21 23.52 25.92 27.98
43.87 22.35 22.86 23.17 23.54 25.92 27.98
43.86 22.35 22.87 23.14 23.56 25.91 27.99
- 43.85 22.35 22.88 23.02 23.58 23.67 23.75 25.90 28.00
+ 43.85 22.35 22.88 22.98 23.58 23.67 23.75 25.90 28.00
43.84 22.34 23.77 25.89 28.03
43.83 22.34 23.79 25.87 28.06
- 43.82 22.34 23.83 25.86 28.09
- 43.81 22.33 23.89 24.44 24.49 25.85 28.12
- 43.80 22.33 23.95 24.42 24.53 25.83 28.15
- 43.79 22.33 24.01 24.40 24.57 25.82 28.18
- 43.78 22.34 24.07 24.38 24.61 25.80 28.21
- 43.77 22.35 24.13 24.25 24.65 25.79 28.26
+ 43.82 22.34 23.82 25.86 28.09
+ 43.81 22.33 23.88 24.44 24.49 25.85 28.12
+ 43.80 22.33 23.94 24.42 24.53 25.83 28.15
+ 43.79 22.33 24.00 24.40 24.57 25.82 28.18
+ 43.78 22.34 24.06 24.38 24.61 25.80 28.21
+ 43.77 22.35 24.12 24.34 24.65 25.79 28.26
43.76 22.36 24.69 25.79 28.33
43.75 22.36 24.73 24.85 24.99 25.78 28.40 28.50 28.58
43.74 22.37 25.03 25.76 28.58
43.73 22.37 25.07 25.74 28.58
43.72 22.37 25.24 25.66 28.58
- 43.71 22.37 25.26 25.64 28.58
- 43.70 22.38 25.28 25.62 28.58
+ 43.71 22.37 25.27 25.64 28.58
+ 43.70 22.38 25.29 25.62 28.58
43.69 22.38 25.30 25.58 28.58
43.68 22.38 25.32 25.47 25.51 25.54 28.58
43.67 22.39 25.34 25.44 28.58
43.66 22.40 28.58
43.65 22.41 28.58
- 43.64 22.44 28.58
+ 43.64 22.43 28.58
43.63 22.45 28.58
43.62 22.46 28.58
43.61 22.46 28.58
@@ -34878,7 +35004,7 @@ Bulgaria
43.47 22.49 28.58
43.46 22.50 28.58
43.45 22.52 28.57
- 43.44 22.55 28.57
+ 43.44 22.54 28.57
43.43 22.56 28.56
43.42 22.57 28.54
43.41 22.58 28.53
@@ -34888,18 +35014,18 @@ Bulgaria
43.37 22.70 28.11 28.43 28.48
43.36 22.73 28.11 28.45 28.48
43.35 22.74 28.10 28.46 28.48
- 43.34 22.75 28.10
+ 43.34 22.75 28.09
43.33 22.77 28.09
- 43.32 22.78 28.09
+ 43.32 22.78 28.08
43.31 22.79 28.08
- 43.30 22.80 28.08
+ 43.30 22.80 28.07
43.29 22.81 28.07
- 43.28 22.81 28.07
+ 43.28 22.81 28.06
43.27 22.81 28.06
- 43.26 22.82 28.06
+ 43.26 22.82 28.05
43.25 22.83 28.05
- 43.24 22.84 28.05
- 43.23 22.86 28.04
+ 43.24 22.84 28.04
+ 43.23 22.85 28.04
43.22 22.87 28.03
43.21 22.88 28.01
43.20 22.90 27.99
@@ -34933,7 +35059,7 @@ Bulgaria
42.92 22.73 27.91
42.91 22.73 27.91
42.90 22.72 27.91
- 42.89 22.55 22.64 22.70 27.90
+ 42.89 22.55 22.63 22.70 27.90
42.88 22.49 27.90
42.87 22.48 27.90
42.86 22.48 27.91
@@ -34952,12 +35078,12 @@ Bulgaria
42.73 22.45 27.90
42.72 22.45 27.90
42.71 22.44 27.90
- 42.70 22.43 27.90
+ 42.70 22.44 27.90
42.69 22.43 27.73 27.81 27.87
42.68 22.43 27.72
- 42.67 22.43 27.75
- 42.66 22.43 27.75
- 42.65 22.43 27.75
+ 42.67 22.43 27.74
+ 42.66 22.43 27.74
+ 42.65 22.43 27.74
42.64 22.43 27.73
42.63 22.43 27.69
42.62 22.42 27.64
@@ -34974,8 +35100,8 @@ Bulgaria
42.51 22.48 27.50
42.50 22.50 27.50
42.49 22.51 27.50
- 42.48 22.51 27.50
- 42.47 22.52 27.49
+ 42.48 22.52 27.50
+ 42.47 22.52 27.49 27.53 27.55
42.46 22.52 27.49 27.52 27.65
42.45 22.51 27.65
42.44 22.51 27.65
@@ -34986,7 +35112,7 @@ Bulgaria
42.39 22.45 27.72
42.38 22.44 27.72
42.37 22.43 27.72
- 42.36 22.43 27.72
+ 42.36 22.43 27.71
42.35 22.42 27.72
42.34 22.42 27.79
42.33 22.35 27.79
@@ -34999,7 +35125,7 @@ Bulgaria
42.26 22.37 27.77
42.25 22.38 27.79
42.24 22.39 27.79
- 42.23 22.40 27.81
+ 42.23 22.40 27.80
42.22 22.41 27.82
42.21 22.42 27.83
42.20 22.43 27.84
@@ -35008,16 +35134,16 @@ Bulgaria
42.17 22.47 27.86
42.16 22.48 27.88
42.15 22.48 27.89
- 42.14 22.49 27.90
- 42.13 22.50 27.90
+ 42.14 22.48 27.90
+ 42.13 22.49 27.90
42.12 22.51 27.92
42.11 22.52 27.94
42.10 22.54 27.96
42.09 22.56 27.97
42.08 22.58 27.99
42.07 22.60 27.21 27.27 27.99
- 42.06 22.62 27.04 27.07 27.20 27.29 27.99
- 42.05 22.65 27.02 27.10 27.19 27.30 28.00
+ 42.06 22.61 27.04 27.07 27.20 27.29 27.99
+ 42.05 22.64 27.02 27.10 27.19 27.30 28.00
42.04 22.68 27.02 27.15 27.18 27.32 28.01
42.03 22.70 27.01 27.33 28.02
42.02 22.77 27.00 27.34 28.02
@@ -35053,7 +35179,7 @@ Bulgaria
41.72 22.99 26.19 26.23 26.34
41.71 22.99 26.12 26.25 26.34
41.70 22.98 26.10 26.26 26.34
- 41.69 22.97 26.08
+ 41.69 22.98 26.08
41.68 22.97 26.06
41.67 22.96 26.06
41.66 22.96 26.06
@@ -35165,16 +35291,16 @@ Burkina Faso
14.48 -2.00 0.17
14.47 -2.00 0.18
14.46 -2.01 0.18
- 14.45 -2.01 0.19
- 14.44 -2.01 0.20
- 14.43 -2.01 0.21
+ 14.45 -2.01 0.20
+ 14.44 -2.01 0.21
+ 14.43 -2.01 0.22
14.42 -2.01 0.23
14.41 -2.01 0.24
14.40 -2.01 0.25
14.39 -2.01 0.26
- 14.38 -2.02 0.27
- 14.37 -2.02 0.28
- 14.36 -2.02 0.29
+ 14.38 -2.02 0.28
+ 14.37 -2.02 0.29
+ 14.36 -2.02 0.30
14.35 -2.02 0.31
14.34 -2.02 0.32
14.33 -2.02 0.33
@@ -35191,9 +35317,9 @@ Burkina Faso
14.22 -2.61 -2.26 -2.03 0.40
14.21 -2.62 -2.24 -2.03 0.39
14.20 -2.63 -2.22 -2.03 0.38
- 14.19 -2.64 -2.20 -2.05 0.38
- 14.18 -2.65 -2.18 -2.07 0.38
- 14.17 -2.66 -2.16 -2.09 0.38
+ 14.19 -2.64 -2.20 -2.04 0.38
+ 14.18 -2.65 -2.18 -2.06 0.38
+ 14.17 -2.66 -2.16 -2.08 0.38
14.16 -2.67 0.37
14.15 -2.68 0.37
14.14 -2.69 0.36
@@ -35245,7 +35371,7 @@ Burkina Faso
13.68 -3.29 -3.10 -2.91 0.77
13.67 -3.27 -3.09 -2.91 0.77
13.66 -3.27 -3.08 -2.91 0.77
- 13.65 -3.26 -3.07 -2.93 0.77
+ 13.65 -3.26 -3.07 -2.92 0.77
13.64 -3.26 -3.06 -3.03 -2.97 -2.95 0.79
13.63 -3.27 -3.06 -3.04 0.88
13.62 -3.27 0.91
@@ -35322,11 +35448,11 @@ Burkina Faso
12.91 -4.23 1.23
12.90 -4.23 1.24
12.89 -4.23 1.25
- 12.88 -4.23 1.27
+ 12.88 -4.23 1.26
12.87 -4.23 1.28
12.86 -4.23 1.29
12.85 -4.23 1.30
- 12.84 -4.23 1.32
+ 12.84 -4.23 1.31
12.83 -4.23 1.33
12.82 -4.22 1.34
12.81 -4.22 1.35
@@ -35402,7 +35528,7 @@ Burkina Faso
12.11 -4.64 2.22
12.10 -4.65 2.22
12.09 -4.65 2.23
- 12.08 -4.65 2.24
+ 12.08 -4.66 2.24
12.07 -4.71 -4.68 -4.66 2.25
12.06 -4.73 2.25
12.05 -4.73 2.26
@@ -35423,12 +35549,12 @@ Burkina Faso
11.90 -5.22 2.40
11.89 -5.24 2.40
11.88 -5.25 2.40
- 11.87 -5.26 2.39
- 11.86 -5.26 2.38
- 11.85 -5.32 2.38
+ 11.87 -5.26 2.40
+ 11.86 -5.26 2.39
+ 11.85 -5.32 2.39
11.84 -5.41 2.38
11.83 -5.42 2.38
- 11.82 -5.42 2.37
+ 11.82 -5.42 2.38
11.81 -5.42 2.37
11.80 -5.41 2.37
11.79 -5.40 2.36
@@ -35462,13 +35588,13 @@ Burkina Faso
11.51 -5.23 2.11
11.50 -5.23 2.10
11.49 -5.23 2.09
- 11.48 -5.23 2.09
- 11.47 -5.23 2.08
- 11.46 -5.23 2.07
- 11.45 -5.23 2.06
- 11.44 -5.23 1.44 1.51 2.05
- 11.43 -5.23 1.42 1.55 2.04
- 11.42 -5.23 1.40 1.55 1.82 1.88 2.03
+ 11.48 -5.23 2.08
+ 11.47 -5.23 2.07
+ 11.46 -5.23 2.06
+ 11.45 -5.23 2.05
+ 11.44 -5.23 1.44 1.51 2.04
+ 11.43 -5.23 1.42 1.55 2.03
+ 11.42 -5.23 1.40 1.55 1.82 1.88 2.02
11.41 -5.25 1.40 1.55 1.80 1.91 2.02
11.40 -5.27 1.40 1.57 1.70 1.93 2.00
11.39 -5.27 1.40 1.58 1.66
@@ -35509,8 +35635,8 @@ Burkina Faso
11.04 -5.51 -0.43 0.19 0.97 1.02 1.12
11.03 -5.51 -0.44 0.25 0.96 1.02 1.05 1.08 1.12
11.02 -5.51 -0.44 0.30 0.96 1.09 1.12
- 11.01 -5.51 -0.44 0.35 0.97 1.10 1.12
- 11.00 -5.50 -1.56 -1.42 -0.46 0.40 0.98
+ 11.01 -5.51 -0.44 0.34 0.97 1.10 1.12
+ 11.00 -5.50 -1.56 -1.43 -0.46 0.39 0.98
10.99 -5.50 -1.57 -1.40 -1.07 -1.00 -0.48 0.45 0.98
10.98 -5.51 -1.58 -1.37 -1.09 -0.92 -0.49 0.47 0.98
10.97 -5.51 -2.82 -2.76 -2.30 -0.91 -0.86 -0.70 -0.50 0.47 0.73 0.90 0.98
@@ -35676,7 +35802,7 @@ Burkina Faso
Burundi
-2.29 30.35 30.40
-2.30 29.92 29.95 30.34 30.43
- -2.31 29.91 29.95 30.33 30.43
+ -2.31 29.91 29.96 30.33 30.43
-2.32 29.91 29.97 30.19 30.21 30.33 30.44
-2.33 29.91 30.02 30.19 30.24 30.30 30.45
-2.34 29.91 30.03 30.19 30.46
@@ -35722,9 +35848,9 @@ Burundi
-2.74 28.98 29.34 29.73 29.77 29.83 30.46
-2.75 28.98 29.34 29.72 30.46
-2.76 28.97 29.33 29.72 30.45
- -2.77 28.97 29.33 29.59 29.64 29.72 30.45
+ -2.77 28.97 29.33 29.59 29.63 29.72 30.45
-2.78 28.97 29.33 29.57 29.66 29.71 30.45
- -2.79 28.97 29.34 29.39 29.46 29.53 30.45
+ -2.79 28.97 29.34 29.39 29.47 29.53 30.45
-2.80 28.97 29.34 29.37 29.50 29.52 30.44
-2.81 28.97 30.44
-2.82 28.98 30.43
@@ -35813,13 +35939,13 @@ Burundi
-3.65 29.21 30.42
-3.66 29.21 30.41
-3.67 29.21 30.40
- -3.68 29.21 30.40
+ -3.68 29.20 30.40
-3.69 29.20 30.39
-3.70 29.20 30.39
-3.71 29.20 30.38
-3.72 29.20 30.38
-3.73 29.20 30.38
- -3.74 29.20 30.39
+ -3.74 29.19 30.39
-3.75 29.19 30.39
-3.76 29.19 30.39
-3.77 29.19 30.39
@@ -35862,10 +35988,10 @@ Burundi
-4.14 29.33 30.11
-4.15 29.34 30.10
-4.16 29.34 30.09
- -4.17 29.35 30.08
+ -4.17 29.34 30.08
-4.18 29.35 30.07
-4.19 29.35 30.06
- -4.20 29.36 30.05
+ -4.20 29.35 30.05
-4.21 29.36 30.05
-4.22 29.36 30.04
-4.23 29.36 30.04
@@ -35925,12 +36051,12 @@ Cambodia
14.43 103.54 103.56 103.61 103.68 104.67 104.71 104.73 104.81 106.20 106.72 107.00 107.05 107.12 107.47
14.42 103.52 103.58 103.60 103.68 104.58 104.64 104.66 104.89 106.20 106.73 107.00 107.06 107.10 107.46
14.41 103.50 103.68 104.16 104.19 104.23 104.26 104.58 104.90 106.19 106.73 106.99 107.45
- 14.40 103.48 103.68 104.16 104.19 104.22 104.29 104.57 104.93 106.19 106.74 106.98 107.39 107.41 107.44
+ 14.40 103.48 103.68 104.16 104.19 104.22 104.29 104.57 104.94 106.19 106.74 106.98 107.39 107.41 107.44
14.39 103.39 103.43 103.46 103.73 104.09 104.12 104.15 104.31 104.56 104.98 106.18 106.75 106.97 107.39
14.38 103.38 103.76 104.06 104.38 104.47 104.52 104.56 104.98 106.05 106.11 106.17 106.75 106.97 107.38
14.37 103.37 103.84 103.90 103.98 104.04 104.98 105.96 106.01 106.05 106.76 106.95 107.37
14.36 103.25 103.85 103.90 104.98 105.95 106.76 106.95 107.37
- 14.35 103.23 104.98 105.16 105.19 105.95 106.77 106.94 107.36
+ 14.35 103.22 104.98 105.16 105.19 105.95 106.77 106.94 107.36
14.34 103.20 104.98 105.14 105.19 105.95 106.79 106.86 106.92 106.94 107.36
14.33 103.16 104.98 105.14 105.19 105.95 106.80 106.86 107.36
14.32 103.10 104.98 105.13 105.19 105.95 106.82 106.84 107.36
@@ -35938,7 +36064,7 @@ Cambodia
14.30 103.07 104.98 105.12 105.19 105.97 107.37
14.29 103.06 104.99 105.12 105.19 105.98 107.37
14.28 103.05 104.99 105.11 105.20 105.98 107.37
- 14.27 103.04 105.00 105.11 105.21 105.99 107.37
+ 14.27 103.03 105.00 105.11 105.21 105.99 107.37
14.26 103.02 105.00 105.10 105.21 105.99 107.37
14.25 103.01 105.01 105.10 105.22 105.99 107.37
14.24 103.00 105.02 105.08 105.23 105.99 107.37
@@ -36036,17 +36162,17 @@ Cambodia
13.32 102.31 107.60
13.31 102.31 107.59
13.30 102.31 107.59
- 13.29 102.31 107.59
+ 13.29 102.31 107.58
13.28 102.31 107.58
13.27 102.31 107.58
13.26 102.31 107.57
13.25 102.31 107.57
- 13.24 102.32 107.56
+ 13.24 102.32 107.57
13.23 102.32 107.56
13.22 102.33 107.56
13.21 102.33 107.55
13.20 102.34 107.55
- 13.19 102.34 107.54
+ 13.19 102.34 107.55
13.18 102.34 107.54
13.17 102.35 107.54
13.16 102.35 107.53
@@ -36058,7 +36184,7 @@ Cambodia
13.10 102.38 107.51
13.09 102.39 107.50
13.08 102.40 107.50
- 13.07 102.41 107.49
+ 13.07 102.41 107.50
13.06 102.41 107.49
13.05 102.42 107.49
13.04 102.43 107.48
@@ -36135,8 +36261,8 @@ Cambodia
12.33 102.70 107.52
12.32 102.70 107.51
12.31 102.70 107.50
- 12.30 102.69 107.26 107.33 107.49
- 12.29 102.69 107.23 107.34 107.47
+ 12.30 102.69 107.25 107.33 107.49
+ 12.29 102.69 107.22 107.34 107.47
12.28 102.69 107.21 107.34 107.45
12.27 102.69 107.19 107.35 107.44
12.26 102.69 107.17 107.35 107.44
@@ -36161,7 +36287,7 @@ Cambodia
12.07 102.72 106.97
12.06 102.73 106.95
12.05 102.74 106.93
- 12.04 102.75 106.76
+ 12.04 102.74 106.76
12.03 102.75 106.75
12.02 102.76 106.74
12.01 102.76 106.74
@@ -36203,7 +36329,7 @@ Cambodia
11.65 102.90 105.96 106.39 106.43
11.64 102.90 105.95
11.63 102.90 105.84 105.88 105.94
- 11.62 102.91 105.82
+ 11.62 102.90 105.82
11.61 102.92 105.81
11.60 102.93 105.81
11.59 102.93 105.80
@@ -36220,8 +36346,8 @@ Cambodia
11.48 102.99 103.05 103.07 105.87
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@@ -36269,16 +36395,16 @@ Cambodia
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@@ -36311,13 +36437,13 @@ Cambodia
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@@ -36332,50 +36458,50 @@ Cameroon
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@@ -36392,7 +36518,7 @@ Cameroon
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@@ -36541,7 +36667,7 @@ Cameroon
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@@ -36624,7 +36750,7 @@ Cameroon
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@@ -36640,7 +36766,7 @@ Cameroon
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9.93 13.21 14.17 14.62 14.85 14.97 15.07 15.32 15.50
@@ -36720,35 +36846,35 @@ Cameroon
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@@ -36912,7 +37038,7 @@ Cameroon
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@@ -36970,11 +37096,11 @@ Cameroon
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@@ -36983,9 +37109,9 @@ Cameroon
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Canada
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@@ -38697,421 +38823,421 @@ Canada
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- 70.17 -130.56 -130.45 -130.41 -130.37 -129.83 -129.50 -128.21 -127.02 -125.09 -124.94 -124.56 -124.53 -116.57 -101.61 -101.39 -101.29 -101.15 -100.96 -96.55 -92.26 -92.23 -91.50 -87.12 -87.08 -86.43 -78.74 -77.70 -69.70 -69.48 -68.64 -68.35 -67.59
- 70.16 -130.56 -130.45 -130.41 -130.36 -129.85 -129.50 -129.48 -129.45 -128.25 -127.01 -125.11 -124.94 -124.71 -124.62 -124.57 -124.52 -124.47 -124.39 -116.69 -101.59 -101.40 -101.27 -101.18 -100.96 -96.54 -92.38 -92.16 -91.50 -87.13 -87.05 -86.41 -78.74 -77.70 -69.73 -69.56 -68.64 -68.35 -67.55
- 70.15 -130.65 -130.62 -130.59 -130.46 -130.41 -130.35 -129.86 -129.44 -128.28 -127.01 -125.12 -124.94 -124.72 -124.38 -116.80 -101.58 -101.40 -101.25 -101.21 -100.96 -96.54 -92.37 -92.11 -91.50 -87.14 -87.03 -86.38 -78.74 -77.70 -69.77 -69.64 -68.63 -68.34 -67.52
- 70.14 -130.74 -130.70 -130.66 -130.31 -129.87 -129.44 -129.42 -129.40 -128.32 -127.00 -125.12 -124.97 -124.75 -124.37 -116.91 -101.57 -101.40 -100.96 -96.54 -92.37 -92.08 -91.50 -87.15 -87.01 -86.36 -78.74 -77.70 -69.82 -69.70 -68.63 -68.34 -67.50
- 70.13 -130.77 -130.69 -130.67 -130.31 -129.87 -129.39 -128.35 -126.99 -125.13 -124.97 -124.76 -124.37 -117.00 -101.55 -101.51 -100.96 -96.54 -92.37 -92.07 -91.51 -87.15 -86.96 -86.67 -86.61 -86.34 -78.73 -77.70 -69.82 -69.73 -68.63 -68.34 -67.48
- 70.12 -130.77 -130.69 -130.67 -130.31 -130.10 -130.08 -129.87 -129.39 -128.37 -126.98 -125.13 -124.98 -124.76 -124.37 -117.08 -100.96 -96.54 -92.41 -92.05 -91.61 -87.36 -86.89 -86.72 -86.58 -86.32 -78.72 -77.69 -69.82 -69.75 -68.65 -68.27 -67.47
- 70.11 -130.90 -130.88 -130.82 -130.69 -130.67 -130.28 -130.19 -130.14 -130.11 -130.06 -129.99 -129.93 -129.88 -129.39 -128.37 -126.97 -125.13 -125.03 -124.76 -124.39 -117.16 -100.96 -96.53 -92.43 -92.03 -91.85 -87.38 -86.83 -86.78 -86.57 -86.30 -81.73 -81.65 -78.72 -77.69 -69.83 -69.77 -68.68 -68.25 -67.46
- 70.10 -130.91 -130.88 -130.86 -130.28 -130.21 -130.14 -130.12 -130.06 -130.03 -129.92 -129.90 -129.39 -128.37 -126.95 -125.09 -125.06 -124.76 -124.37 -117.21 -100.97 -96.51 -92.44 -92.34 -92.20 -87.38 -86.55 -86.28 -81.71 -81.59 -78.72 -77.68 -69.84 -69.79 -68.70 -68.27 -67.44
- 70.09 -130.93 -129.40 -128.37 -126.94 -125.02 -124.98 -124.74 -124.36 -117.23 -100.97 -96.50 -92.45 -92.38 -92.07 -87.38 -86.54 -86.24 -81.69 -81.57 -78.72 -77.68 -69.85 -69.80 -68.73 -68.30 -67.43
- 70.08 -130.95 -129.40 -128.37 -126.92 -125.02 -124.97 -124.83 -124.81 -124.74 -124.35 -117.26 -100.97 -96.49 -92.46 -92.43 -92.02 -87.37 -86.52 -86.20 -85.56 -85.48 -85.39 -85.31 -81.62 -81.38 -78.71 -77.67 -69.87 -69.80 -68.72 -68.45 -68.39 -68.32 -67.40
- 70.07 -130.97 -129.41 -128.37 -126.91 -125.04 -124.96 -124.86 -124.35 -117.28 -100.95 -96.48 -92.00 -87.33 -86.51 -86.16 -85.50 -85.16 -81.54 -81.18 -81.09 -81.06 -78.69 -77.67 -69.91 -69.81 -68.72 -68.46 -67.39
- 70.06 -130.98 -129.41 -128.37 -126.91 -125.07 -124.96 -124.92 -124.35 -117.32 -100.94 -96.46 -91.98 -87.30 -86.50 -86.12 -85.45 -85.10 -84.90 -84.88 -81.51 -81.06 -78.67 -77.67 -69.90 -69.81 -68.72 -68.57 -68.48 -68.46 -67.37
- 70.05 -131.00 -129.42 -128.36 -126.90 -125.11 -124.96 -124.93 -124.35 -117.37 -100.93 -96.44 -91.96 -87.28 -86.50 -86.08 -85.41 -85.00 -84.93 -84.87 -81.48 -81.05 -80.94 -80.88 -78.67 -77.68 -69.85 -69.81 -68.73 -68.57 -67.36
- 70.04 -131.03 -129.44 -128.36 -126.89 -125.13 -124.35 -117.39 -100.92 -96.42 -91.94 -87.28 -86.49 -86.04 -85.32 -84.86 -81.46 -81.35 -81.28 -80.84 -78.66 -77.68 -69.84 -69.81 -68.75 -68.57 -67.35
- 70.03 -131.03 -129.48 -128.36 -126.88 -125.15 -124.35 -117.41 -100.92 -96.40 -91.93 -87.28 -86.46 -86.00 -85.29 -84.85 -81.44 -81.38 -81.24 -80.68 -78.65 -77.68 -68.77 -68.57 -67.35
- 70.02 -131.03 -129.48 -128.35 -126.86 -125.18 -124.35 -117.42 -100.91 -96.38 -91.93 -87.28 -86.44 -85.96 -85.27 -84.84 -81.44 -81.41 -81.20 -80.53 -78.65 -77.69 -68.79 -68.58 -67.34
- 70.01 -131.01 -129.49 -128.33 -126.83 -125.21 -124.36 -117.43 -100.91 -96.36 -91.93 -87.25 -86.44 -85.92 -85.24 -84.80 -81.18 -80.49 -78.65 -77.69 -68.81 -68.60 -67.33
- 70.00 -131.01 -129.52 -128.32 -126.80 -125.21 -124.39 -117.44 -100.91 -96.34 -91.94 -87.21 -86.44 -85.88 -85.22 -84.76 -81.16 -80.45 -78.65 -77.70 -68.84 -68.66 -67.32
- 69.99 -131.02 -129.54 -128.32 -126.78 -125.21 -124.90 -124.86 -124.40 -117.45 -100.91 -96.32 -91.96 -87.17 -87.01 -86.97 -86.45 -85.84 -85.62 -85.54 -85.22 -84.72 -84.60 -84.51 -83.27 -83.25 -83.19 -83.15 -83.08 -83.05 -81.15 -80.42 -80.21 -80.13 -78.65 -77.70 -68.89 -68.68 -67.28
- 69.98 -131.02 -129.57 -128.94 -128.87 -128.33 -126.76 -125.20 -125.02 -124.96 -124.91 -124.86 -124.40 -117.45 -100.91 -96.30 -92.00 -87.13 -87.03 -86.93 -86.46 -85.80 -85.69 -85.42 -85.22 -84.45 -83.29 -83.04 -81.14 -80.38 -80.26 -80.05 -78.65 -77.70 -68.96 -68.68 -67.25
- 69.97 -131.41 -131.38 -131.03 -129.61 -128.97 -128.85 -128.33 -126.76 -125.20 -125.03 -124.86 -124.46 -117.45 -100.91 -97.47 -97.35 -96.28 -92.07 -87.10 -87.06 -86.88 -86.48 -85.31 -85.23 -84.39 -83.32 -83.03 -81.14 -80.33 -80.28 -80.06 -78.65 -77.70 -69.04 -68.68 -67.23
- 69.96 -131.43 -131.31 -131.04 -129.67 -128.99 -128.84 -128.36 -126.76 -125.21 -125.03 -124.86 -124.41 -117.43 -100.91 -97.48 -97.33 -96.26 -92.07 -86.81 -86.63 -84.04 -83.40 -82.98 -81.13 -80.06 -78.65 -77.69 -69.09 -68.96 -68.75 -68.67 -67.22
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- 69.91 -131.45 -131.19 -131.08 -129.84 -129.03 -128.89 -128.51 -126.77 -124.96 -124.42 -117.38 -100.89 -97.50 -97.32 -96.13 -92.18 -82.81 -81.71 -81.56 -81.03 -79.80 -78.69 -77.69 -69.21 -69.15 -67.20
- 69.90 -131.49 -131.19 -131.15 -131.11 -131.09 -129.88 -129.04 -128.90 -128.53 -126.79 -124.97 -124.43 -117.37 -102.23 -102.21 -100.88 -98.00 -97.89 -97.49 -97.24 -96.13 -92.20 -82.79 -82.72 -82.69 -81.73 -81.46 -80.99 -79.80 -78.71 -77.68 -69.23 -69.19 -67.20
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- 69.88 -131.63 -129.96 -129.07 -128.94 -128.58 -126.77 -125.01 -124.43 -117.35 -102.23 -102.18 -100.87 -98.04 -97.83 -97.44 -97.21 -96.18 -92.23 -91.82 -91.67 -91.49 -91.39 -82.65 -81.72 -81.41 -80.94 -79.79 -78.77 -77.68 -67.20
- 69.87 -131.66 -130.00 -129.10 -128.93 -128.60 -126.76 -125.03 -124.40 -117.35 -102.23 -102.18 -100.87 -98.06 -97.76 -97.35 -97.21 -96.21 -92.24 -91.84 -91.65 -91.50 -91.39 -84.88 -84.84 -82.62 -81.72 -81.39 -80.92 -79.78 -79.15 -78.86 -78.78 -77.68 -67.19
- 69.86 -131.69 -130.04 -129.21 -128.92 -128.62 -126.75 -125.21 -125.15 -125.03 -124.39 -117.34 -102.22 -102.18 -100.87 -98.07 -97.69 -97.33 -97.21 -96.21 -92.25 -91.87 -91.63 -91.50 -91.39 -85.57 -85.32 -84.90 -84.81 -84.71 -84.31 -82.58 -81.84 -81.77 -81.72 -81.35 -80.90 -79.74 -79.45 -78.83 -78.78 -77.68 -67.18
- 69.85 -131.72 -130.08 -129.37 -128.92 -128.64 -126.74 -125.23 -125.15 -125.03 -124.39 -117.33 -102.22 -102.18 -100.87 -98.08 -97.68 -97.31 -97.22 -96.21 -92.29 -91.87 -91.63 -91.50 -91.41 -85.58 -85.29 -84.90 -84.78 -84.75 -84.29 -82.54 -82.02 -81.98 -81.84 -81.33 -80.88 -79.72 -79.51 -77.68 -77.41 -77.32 -67.17
- 69.84 -131.75 -130.14 -129.48 -128.92 -128.66 -126.74 -125.25 -125.15 -125.03 -124.39 -122.99 -122.92 -122.75 -122.72 -117.32 -102.22 -102.18 -100.86 -98.08 -97.68 -97.29 -97.23 -96.17 -92.34 -91.87 -91.63 -91.59 -91.43 -85.59 -85.26 -84.90 -84.19 -83.86 -83.80 -82.50 -82.39 -82.36 -82.04 -81.98 -81.87 -81.31 -80.86 -79.70 -79.57 -77.68 -77.48 -77.32 -67.16
- 69.83 -131.77 -130.22 -129.62 -128.92 -128.67 -126.73 -125.27 -125.15 -125.04 -124.42 -123.01 -122.88 -122.75 -122.68 -122.66 -122.60 -117.31 -102.30 -102.18 -102.06 -102.03 -101.50 -101.48 -100.86 -98.09 -97.68 -96.11 -92.36 -91.87 -91.43 -85.59 -85.23 -84.89 -84.14 -83.88 -83.70 -82.46 -82.41 -82.33 -82.06 -81.97 -81.93 -81.28 -80.84 -79.68 -79.63 -77.69 -77.49 -77.32 -67.15
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- 69.81 -131.77 -130.35 -129.67 -129.14 -128.71 -126.71 -125.29 -125.15 -125.07 -124.45 -123.05 -122.79 -122.77 -121.83 -117.29 -102.29 -102.03 -101.52 -101.47 -100.86 -98.20 -97.61 -96.05 -92.46 -91.85 -91.79 -91.71 -91.45 -85.47 -85.18 -85.04 -84.10 -83.91 -83.53 -82.33 -82.11 -81.20 -80.79 -80.46 -80.36 -80.25 -80.17 -79.70 -79.55 -79.52 -79.44 -77.69 -77.44 -77.18 -77.11 -77.08 -67.14
- 69.80 -131.78 -130.36 -129.69 -129.13 -128.74 -126.71 -125.29 -124.46 -123.06 -121.70 -117.28 -102.28 -102.03 -101.52 -101.46 -100.86 -98.22 -97.57 -96.04 -92.49 -91.74 -91.46 -85.36 -85.14 -85.06 -84.08 -83.92 -83.51 -82.31 -82.11 -81.16 -80.76 -80.48 -80.33 -80.29 -80.15 -79.75 -79.42 -77.68 -77.43 -77.16 -77.13 -77.08 -67.14
- 69.79 -131.80 -130.38 -129.74 -129.13 -128.75 -126.70 -125.27 -124.46 -123.09 -121.61 -117.28 -102.28 -102.03 -101.53 -101.46 -100.86 -98.24 -97.50 -96.02 -92.53 -91.74 -91.45 -85.45 -85.38 -85.35 -85.10 -85.06 -84.06 -83.92 -83.51 -82.31 -82.11 -81.15 -80.75 -80.50 -80.13 -79.76 -79.40 -77.67 -77.43 -76.90 -67.14
- 69.78 -132.32 -132.25 -131.93 -131.87 -131.82 -130.42 -129.80 -129.12 -128.77 -126.70 -125.27 -124.46 -123.13 -121.57 -117.28 -102.28 -102.02 -101.54 -101.45 -100.86 -98.26 -97.45 -96.01 -92.53 -91.74 -91.45 -85.49 -85.38 -85.34 -84.04 -83.92 -83.51 -82.22 -82.12 -81.13 -80.75 -80.51 -80.12 -79.76 -79.39 -77.67 -77.43 -76.91 -67.13
- 69.77 -132.37 -132.24 -131.95 -130.45 -129.86 -129.12 -128.79 -126.68 -125.26 -124.47 -123.16 -121.39 -117.27 -102.29 -102.01 -101.54 -101.44 -100.86 -98.28 -97.44 -95.99 -95.73 -95.70 -92.53 -91.72 -91.45 -85.52 -83.99 -83.92 -83.52 -82.16 -82.12 -81.12 -80.75 -80.51 -80.12 -79.82 -79.79 -79.76 -79.39 -77.66 -77.50 -76.91 -67.12
- 69.76 -132.47 -132.24 -131.97 -130.53 -129.98 -129.12 -128.87 -126.66 -125.24 -124.47 -123.16 -121.35 -117.27 -102.48 -102.44 -102.40 -102.38 -102.30 -101.99 -101.55 -101.44 -100.87 -98.29 -97.43 -95.88 -95.85 -95.83 -95.75 -95.64 -92.64 -92.62 -92.54 -91.70 -91.45 -85.52 -83.59 -81.10 -80.75 -80.73 -80.67 -80.51 -80.11 -80.09 -80.03 -79.85 -79.39 -78.20 -78.14 -77.66 -77.50 -76.91 -67.87 -67.72 -67.12
- 69.75 -132.55 -132.24 -132.02 -130.54 -130.03 -129.12 -128.95 -126.65 -125.23 -125.19 -125.12 -124.47 -123.16 -121.30 -117.26 -102.50 -102.38 -102.32 -101.98 -101.55 -101.43 -100.88 -98.31 -97.42 -95.83 -95.75 -95.62 -92.64 -92.60 -92.55 -91.67 -91.46 -85.52 -83.61 -81.09 -80.76 -80.73 -80.62 -80.50 -79.99 -79.92 -79.36 -78.21 -78.12 -77.65 -77.51 -76.90 -68.02 -67.68 -67.11
- 69.74 -132.56 -132.28 -132.07 -130.55 -130.09 -129.12 -128.97 -126.64 -125.09 -124.47 -124.21 -124.13 -123.14 -121.26 -117.24 -102.52 -102.19 -102.12 -101.97 -101.55 -101.42 -100.89 -98.32 -97.40 -95.81 -95.76 -95.61 -92.66 -91.65 -91.47 -85.50 -83.65 -81.06 -80.76 -80.74 -80.59 -80.50 -79.34 -78.28 -78.05 -77.64 -77.53 -76.89 -68.07 -67.64 -67.11
- 69.73 -134.50 -134.44 -134.39 -134.30 -132.56 -132.28 -132.11 -130.55 -130.14 -129.12 -128.97 -126.62 -125.16 -124.39 -124.24 -124.05 -123.12 -121.22 -117.20 -102.55 -102.23 -102.12 -101.95 -101.55 -101.40 -100.90 -98.32 -97.38 -95.79 -95.77 -95.59 -92.69 -91.64 -91.48 -85.48 -83.64 -81.02 -79.33 -78.28 -78.03 -77.62 -77.55 -76.80 -68.08 -67.60 -67.10
- 69.72 -134.50 -134.30 -132.57 -132.28 -132.25 -132.22 -132.13 -130.55 -130.25 -129.13 -128.98 -126.60 -125.19 -124.37 -124.27 -124.03 -123.12 -121.17 -117.16 -102.59 -102.24 -102.11 -101.94 -101.88 -101.83 -101.56 -101.38 -100.90 -98.33 -97.35 -95.57 -92.52 -91.59 -91.50 -85.45 -83.64 -80.98 -79.32 -78.28 -78.00 -76.93 -76.89 -76.81 -68.10 -67.96 -67.92 -67.90 -67.86 -67.57 -67.10
- 69.71 -134.50 -134.30 -132.58 -132.20 -132.13 -130.56 -130.35 -129.13 -128.98 -126.58 -125.35 -125.29 -125.22 -124.33 -124.30 -124.02 -123.11 -121.13 -117.14 -102.57 -102.24 -102.11 -101.80 -101.58 -101.38 -100.90 -98.33 -97.33 -95.52 -92.52 -92.39 -92.32 -91.57 -91.53 -85.44 -83.63 -83.29 -83.18 -82.70 -82.60 -80.98 -80.85 -80.81 -79.31 -78.38 -78.33 -78.28 -77.98 -77.02 -76.98 -76.95 -76.89 -76.83 -68.15 -67.98 -67.85 -67.50 -67.10
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- 69.69 -134.47 -134.21 -132.62 -130.57 -130.38 -129.00 -128.96 -126.54 -125.39 -124.02 -123.11 -121.04 -117.10 -102.47 -102.24 -102.10 -101.75 -101.61 -101.37 -100.90 -98.33 -97.21 -95.48 -92.32 -85.52 -82.55 -80.82 -79.31 -78.40 -78.29 -78.26 -77.95 -77.15 -68.21 -67.98 -67.79
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@@ -40756,238 +40882,238 @@ Canada
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@@ -43439,49 +43565,49 @@ Canada: British Columbia
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@@ -43489,7 +43615,7 @@ Canada: British Columbia
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@@ -43499,49 +43625,49 @@ Canada: British Columbia
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51.85 -128.25 -128.01 -127.89 -116.99
@@ -43584,8 +43710,8 @@ Canada: British Columbia
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51.41 -127.95 -127.88 -127.66 -116.28
@@ -43620,13 +43746,13 @@ Canada: British Columbia
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51.00 -127.54 -115.65
@@ -43637,27 +43763,27 @@ Canada: British Columbia
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@@ -43670,12 +43796,12 @@ Canada: British Columbia
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@@ -43683,7 +43809,7 @@ Canada: British Columbia
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@@ -43701,7 +43827,7 @@ Canada: British Columbia
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@@ -43728,30 +43854,30 @@ Canada: British Columbia
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@@ -43761,14 +43887,14 @@ Canada: British Columbia
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@@ -43777,27 +43903,27 @@ Canada: British Columbia
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49.29 -126.25 -126.06 -126.02 -124.09 -123.17 -114.42
@@ -43805,21 +43931,21 @@ Canada: British Columbia
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49.07 -125.87 -123.77 -123.70 -123.63 -123.15 -114.08
@@ -43827,52 +43953,52 @@ Canada: British Columbia
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@@ -43885,11 +44011,11 @@ Canada: British Columbia
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@@ -44014,7 +44140,7 @@ Canada: Manitoba
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@@ -44024,10 +44150,10 @@ Canada: Manitoba
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@@ -44076,8 +44202,8 @@ Canada: Manitoba
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@@ -44177,10 +44303,10 @@ Canada: Manitoba
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@@ -44215,7 +44341,7 @@ Canada: Manitoba
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@@ -44987,23 +45113,23 @@ Canada: Manitoba
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Canada: New Brunswick
@@ -45014,8 +45140,8 @@ Canada: New Brunswick
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@@ -45032,9 +45158,9 @@ Canada: New Brunswick
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@@ -45087,19 +45213,19 @@ Canada: New Brunswick
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@@ -45188,19 +45314,19 @@ Canada: New Brunswick
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@@ -45211,7 +45337,7 @@ Canada: New Brunswick
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46.02 -67.79 -64.05
46.01 -67.79 -64.04
@@ -45224,7 +45350,7 @@ Canada: New Brunswick
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@@ -45233,7 +45359,7 @@ Canada: New Brunswick
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45.79 -67.81 -64.60 -64.50 -64.39
@@ -45247,7 +45373,7 @@ Canada: New Brunswick
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@@ -45256,7 +45382,7 @@ Canada: New Brunswick
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@@ -45297,44 +45423,43 @@ Canada: New Brunswick
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Canada: Newfoundland and Labrador
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@@ -45374,7 +45499,7 @@ Canada: Newfoundland and Labrador
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@@ -45404,25 +45529,25 @@ Canada: Newfoundland and Labrador
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@@ -45466,7 +45591,7 @@ Canada: Newfoundland and Labrador
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59.05 -64.82 -64.66 -64.35 -63.11
@@ -45494,15 +45619,15 @@ Canada: Newfoundland and Labrador
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@@ -45526,14 +45651,14 @@ Canada: Newfoundland and Labrador
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@@ -45594,17 +45719,17 @@ Canada: Newfoundland and Labrador
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@@ -45621,7 +45746,7 @@ Canada: Newfoundland and Labrador
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@@ -45650,10 +45775,10 @@ Canada: Newfoundland and Labrador
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57.18 -63.86 -63.84 -63.79 -61.65
@@ -45687,11 +45812,11 @@ Canada: Newfoundland and Labrador
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@@ -45708,9 +45833,9 @@ Canada: Newfoundland and Labrador
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56.61 -64.04 -61.90 -61.72 -61.65 -61.46 -61.37 -61.24 -61.04
@@ -45722,7 +45847,7 @@ Canada: Newfoundland and Labrador
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@@ -45734,8 +45859,8 @@ Canada: Newfoundland and Labrador
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@@ -45773,462 +45898,462 @@ Canada: Newfoundland and Labrador
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@@ -46289,14 +46414,14 @@ Canada: Newfoundland and Labrador
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@@ -46305,12 +46430,12 @@ Canada: Newfoundland and Labrador
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@@ -46350,22 +46475,22 @@ Canada: Newfoundland and Labrador
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@@ -46379,7 +46504,7 @@ Canada: Newfoundland and Labrador
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@@ -46393,7 +46518,7 @@ Canada: Newfoundland and Labrador
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@@ -46413,7 +46538,7 @@ Canada: Newfoundland and Labrador
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@@ -46422,11 +46547,11 @@ Canada: Newfoundland and Labrador
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49.47 -58.17 -55.66 -55.60 -55.34 -55.28 -55.11 -54.86 -54.79 -54.73 -54.42 -54.11 -53.98
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49.45 -58.19 -55.66 -55.61 -55.30 -55.28 -55.11 -54.76 -54.43 -54.14 -53.89
@@ -46438,8 +46563,8 @@ Canada: Newfoundland and Labrador
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49.33 -58.24 -55.20 -55.09 -54.99 -54.89 -54.82 -54.79 -53.58
49.32 -58.24 -55.20 -55.08 -54.99 -54.87 -54.82 -54.79 -53.57
@@ -46512,7 +46637,7 @@ Canada: Newfoundland and Labrador
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48.61 -59.12 -58.93 -58.86 -58.83 -58.69 -53.76 -53.45 -53.31 -53.18 -52.97
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48.59 -59.16 -58.88 -58.86 -58.82 -58.70 -53.79 -53.47 -53.29 -53.18 -52.97
@@ -46530,9 +46655,9 @@ Canada: Newfoundland and Labrador
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48.46 -59.27 -59.20 -58.55 -58.48 -58.45 -53.03
48.45 -58.58 -58.48 -58.46 -53.03
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48.41 -58.62 -53.05
48.40 -58.63 -53.07
48.39 -58.67 -53.09
@@ -46558,11 +46683,11 @@ Canada: Newfoundland and Labrador
48.19 -58.93 -53.50
48.18 -58.94 -53.50 -52.93 -52.90
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48.13 -59.02 -53.51 -52.98 -52.84
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48.11 -59.06 -53.52 -53.00 -52.82
48.10 -59.08 -53.52 -53.01 -52.82
48.09 -59.11 -53.52 -53.02 -52.82
@@ -46587,7 +46712,7 @@ Canada: Newfoundland and Labrador
47.90 -59.41 -53.67 -53.37 -53.05
47.89 -59.41 -53.67 -53.37 -53.05
47.88 -59.41 -53.68 -53.40 -53.05
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47.86 -59.39 -53.71 -53.43 -53.05
47.85 -59.39 -53.71 -53.44 -53.05
47.84 -59.38 -53.72 -53.44 -53.06
@@ -46607,16 +46732,16 @@ Canada: Newfoundland and Labrador
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47.55 -59.18 -59.06 -57.14 -57.08 -56.93 -56.69 -56.03 -55.38 -54.89 -54.37 -54.25 -54.15 -54.11 -54.05 -53.91 -53.17 -52.94 -52.65
@@ -46625,53 +46750,53 @@ Canada: Newfoundland and Labrador
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47.00 -55.96 -55.14 -54.16 -53.77 -53.64 -52.85
@@ -46712,8 +46837,8 @@ Canada: Newfoundland and Labrador
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46.64 -53.63 -53.44 -53.24 -53.06
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+ 46.61 -53.60 -53.50 -53.20 -53.12
46.60 -53.57 -53.52
Canada: Northwest Territories
78.77 -110.57 -110.40
@@ -46751,34 +46876,34 @@ Canada: Northwest Territories
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78.44 -113.07 -109.99
78.43 -113.12 -109.99
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@@ -47278,7 +47403,7 @@ Canada: Northwest Territories
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@@ -47562,8 +47687,8 @@ Canada: Northwest Territories
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@@ -47589,9 +47714,9 @@ Canada: Northwest Territories
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@@ -47600,20 +47725,20 @@ Canada: Northwest Territories
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@@ -47624,19 +47749,19 @@ Canada: Northwest Territories
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@@ -47661,19 +47786,19 @@ Canada: Northwest Territories
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69.03 -136.00 -135.87 -135.73 -120.67
@@ -47687,7 +47812,7 @@ Canada: Northwest Territories
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@@ -48675,9 +48800,9 @@ Canada: Nova Scotia
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46.06 -61.53 -59.85
@@ -48701,15 +48826,15 @@ Canada: Nova Scotia
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@@ -48738,7 +48863,7 @@ Canada: Nova Scotia
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@@ -48747,8 +48872,8 @@ Canada: Nova Scotia
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@@ -48797,7 +48922,7 @@ Canada: Nova Scotia
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44.86 -65.47 -62.40
@@ -48837,7 +48962,7 @@ Canada: Nova Scotia
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@@ -49346,45 +49471,45 @@ Canada: Nunavut
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@@ -49403,103 +49528,103 @@ Canada: Nunavut
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@@ -49612,104 +49737,104 @@ Canada: Nunavut
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@@ -49721,28 +49846,28 @@ Canada: Nunavut
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@@ -49756,12 +49881,12 @@ Canada: Nunavut
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@@ -49770,7 +49895,7 @@ Canada: Nunavut
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@@ -49785,37 +49910,37 @@ Canada: Nunavut
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@@ -49831,9 +49956,9 @@ Canada: Nunavut
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@@ -49850,24 +49975,24 @@ Canada: Nunavut
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@@ -49879,11 +50004,11 @@ Canada: Nunavut
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@@ -49893,24 +50018,24 @@ Canada: Nunavut
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@@ -49919,7 +50044,7 @@ Canada: Nunavut
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@@ -49927,11 +50052,11 @@ Canada: Nunavut
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@@ -49947,7 +50072,7 @@ Canada: Nunavut
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@@ -49956,17 +50081,17 @@ Canada: Nunavut
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@@ -49982,56 +50107,56 @@ Canada: Nunavut
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@@ -50050,39 +50175,39 @@ Canada: Nunavut
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@@ -50090,8 +50215,8 @@ Canada: Nunavut
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@@ -50111,24 +50236,24 @@ Canada: Nunavut
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@@ -50139,21 +50264,21 @@ Canada: Nunavut
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@@ -50163,20 +50288,20 @@ Canada: Nunavut
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@@ -50195,30 +50320,30 @@ Canada: Nunavut
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@@ -50228,133 +50353,133 @@ Canada: Nunavut
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@@ -50363,8 +50488,8 @@ Canada: Nunavut
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@@ -50479,37 +50604,37 @@ Canada: Nunavut
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@@ -50521,13 +50646,13 @@ Canada: Nunavut
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@@ -50538,11 +50663,11 @@ Canada: Nunavut
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@@ -50554,8 +50679,8 @@ Canada: Nunavut
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@@ -50572,109 +50697,109 @@ Canada: Nunavut
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@@ -50683,35 +50808,35 @@ Canada: Nunavut
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@@ -50739,9 +50864,9 @@ Canada: Nunavut
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@@ -50749,31 +50874,31 @@ Canada: Nunavut
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@@ -50784,40 +50909,40 @@ Canada: Nunavut
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@@ -50833,13 +50958,13 @@ Canada: Nunavut
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@@ -50849,141 +50974,141 @@ Canada: Nunavut
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@@ -50992,84 +51117,84 @@ Canada: Nunavut
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@@ -51548,6 +51744,10 @@ Canada: Nunavut
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@@ -51555,6 +51755,17 @@ Canada: Nunavut
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@@ -51562,35 +51773,47 @@ Canada: Nunavut
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@@ -51601,17 +51824,17 @@ Canada: Nunavut
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@@ -51641,11 +51864,12 @@ Canada: Nunavut
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@@ -51660,30 +51884,40 @@ Canada: Nunavut
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Canada: Ontario
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@@ -51776,7 +52010,7 @@ Canada: Ontario
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@@ -51784,52 +52018,52 @@ Canada: Ontario
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@@ -51853,8 +52087,8 @@ Canada: Ontario
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@@ -52046,7 +52280,7 @@ Canada: Ontario
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@@ -52235,7 +52469,7 @@ Canada: Ontario
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@@ -52445,9 +52679,9 @@ Canada: Ontario
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@@ -52501,7 +52735,7 @@ Canada: Ontario
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@@ -52510,17 +52744,17 @@ Canada: Ontario
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@@ -52537,38 +52771,38 @@ Canada: Ontario
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@@ -52663,24 +52897,24 @@ Canada: Ontario
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@@ -52718,21 +52952,21 @@ Canada: Ontario
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@@ -52780,13 +53014,13 @@ Canada: Ontario
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@@ -52802,17 +53036,17 @@ Canada: Ontario
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@@ -52822,15 +53056,15 @@ Canada: Ontario
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@@ -52852,8 +53086,8 @@ Canada: Ontario
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@@ -52880,10 +53114,10 @@ Canada: Ontario
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@@ -52908,46 +53142,46 @@ Canada: Ontario
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@@ -52987,12 +53221,12 @@ Canada: Ontario
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@@ -53055,8 +53289,8 @@ Canada: Ontario
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@@ -53089,14 +53323,14 @@ Canada: Ontario
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@@ -53106,12 +53340,12 @@ Canada: Ontario
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@@ -53123,11 +53357,11 @@ Canada: Ontario
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@@ -53138,14 +53372,14 @@ Canada: Ontario
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@@ -53154,22 +53388,22 @@ Canada: Ontario
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@@ -53178,24 +53412,24 @@ Canada: Ontario
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@@ -53219,10 +53453,10 @@ Canada: Prince Edward Island
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@@ -53282,7 +53516,7 @@ Canada: Prince Edward Island
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@@ -53294,7 +53528,7 @@ Canada: Prince Edward Island
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@@ -53335,9 +53569,9 @@ Canada: Quebec
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@@ -53354,7 +53588,7 @@ Canada: Quebec
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@@ -53363,10 +53597,10 @@ Canada: Quebec
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@@ -53391,14 +53625,14 @@ Canada: Quebec
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@@ -53503,12 +53737,12 @@ Canada: Quebec
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@@ -53598,8 +53832,8 @@ Canada: Quebec
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@@ -53727,7 +53961,7 @@ Canada: Quebec
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@@ -53739,24 +53973,24 @@ Canada: Quebec
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@@ -53773,7 +54007,7 @@ Canada: Quebec
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@@ -53804,18 +54038,18 @@ Canada: Quebec
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@@ -54791,7 +55025,7 @@ Canada: Quebec
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47.88 -79.53 -69.84 -69.56 -68.36 -67.47 -67.13 -66.97 -66.94
@@ -54823,7 +55057,7 @@ Canada: Quebec
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47.56 -79.53 -70.19 -69.90 -68.36 -61.67 -61.58 -61.56 -61.44
@@ -54838,15 +55072,15 @@ Canada: Quebec
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47.33 -79.51 -70.52 -70.18 -69.35 -69.07 -68.81 -61.95 -61.90
@@ -54856,7 +55090,7 @@ Canada: Quebec
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@@ -54890,28 +55124,28 @@ Canada: Quebec
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@@ -54920,17 +55154,17 @@ Canada: Quebec
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@@ -54952,7 +55186,7 @@ Canada: Quebec
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@@ -54971,7 +55205,7 @@ Canada: Quebec
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@@ -55002,7 +55236,7 @@ Canada: Quebec
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@@ -55014,17 +55248,17 @@ Canada: Quebec
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@@ -55053,13 +55287,13 @@ Canada: Quebec
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@@ -55083,7 +55317,7 @@ Canada: Quebec
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Canada: Saskatchewan
60.01 -110.00 -101.99
@@ -56265,8 +56499,8 @@ Canada: Yukon
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@@ -57123,49 +57357,49 @@ Canada: Yukon
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Cape Verde
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@@ -57174,29 +57408,29 @@ Cape Verde
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@@ -57206,28 +57440,28 @@ Cape Verde
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16.50 -24.35 -24.30
@@ -57268,47 +57502,47 @@ Cape Verde
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14.88 -24.75 -24.67 -24.52 -24.28
14.87 -24.76 -24.67 -24.51 -24.28
14.86 -24.76 -24.67 -24.50 -24.28
@@ -57318,38 +57552,37 @@ Cape Verde
14.82 -24.76 -24.67 -24.45 -24.32
14.81 -24.75 -24.67 -24.43 -24.33
14.80 -24.73 -24.68 -24.39 -24.35
- 14.79 -24.72 -24.69
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Cayman Islands
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Central African Republic
11.01 22.45 22.47 22.50 22.52
11.00 22.42 22.53
@@ -57425,7 +57658,7 @@ Central African Republic
10.30 21.68 23.39
10.29 21.67 23.39
10.28 21.67 23.40
- 10.27 21.66 23.41
+ 10.27 21.66 23.40
10.26 21.66 23.41
10.25 21.65 23.42
10.24 21.64 23.42
@@ -57433,7 +57666,7 @@ Central African Republic
10.22 21.51 23.44
10.21 21.50 23.44
10.20 21.49 23.45
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10.18 21.48 23.46
10.17 21.47 23.47
10.16 21.47 23.47
@@ -57441,7 +57674,7 @@ Central African Republic
10.14 21.46 23.49
10.13 21.45 23.49
10.12 21.45 23.50
- 10.11 21.45 23.51
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10.10 21.44 23.51
10.09 21.44 23.52
10.08 21.43 23.52
@@ -57449,7 +57682,7 @@ Central African Republic
10.06 21.42 23.54
10.05 21.42 23.54
10.04 21.41 23.55
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10.02 21.40 23.56
10.01 21.39 23.57
10.00 21.38 23.57
@@ -57457,7 +57690,7 @@ Central African Republic
9.98 21.24 21.31 21.36 23.59
9.97 21.23 23.59
9.96 21.22 23.60
- 9.95 21.22 23.61
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9.94 21.21 23.61
9.93 21.20 23.62
9.92 21.19 23.62
@@ -57537,7 +57770,7 @@ Central African Republic
9.18 20.45 23.57
9.17 20.44 23.55
9.16 20.09 20.11 20.44 23.54
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9.14 20.05 20.13 20.16 20.24 20.39 23.47
9.13 20.03 20.32 20.36 23.46
9.12 19.99 23.46
@@ -57582,13 +57815,13 @@ Central African Republic
8.73 19.02 23.50 23.55 23.64 23.75 23.82
8.72 19.03 23.52 23.54 23.71 23.73 23.85 23.89 23.94
8.71 19.04 23.96
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8.69 19.08 24.24
8.68 19.09 24.24
8.67 19.09 24.24
8.66 19.08 24.24
8.65 19.08 24.24
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8.63 19.05 24.22
8.62 19.05 24.22
8.61 19.04 24.24
@@ -57725,7 +57958,7 @@ Central African Republic
7.30 15.28 25.44
7.29 15.26 25.45
7.28 15.25 25.47 25.49 25.51
- 7.27 15.24 25.54
+ 7.27 15.23 25.54
7.26 15.22 25.55
7.25 15.21 25.56
7.24 15.21 25.56
@@ -57784,11 +58017,11 @@ Central African Republic
6.71 14.92 26.29
6.70 14.91 26.31
6.69 14.91 26.33
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6.67 14.90 26.37
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6.65 14.89 26.38
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6.63 14.88 26.38
6.62 14.88 26.38
6.61 14.87 26.38
@@ -57797,9 +58030,9 @@ Central African Republic
6.58 14.86 26.37
6.57 14.85 26.37
6.56 14.85 26.36
- 6.55 14.84 26.36
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6.54 14.84 26.35
- 6.53 14.83 26.34
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6.52 14.83 26.33
6.51 14.83 26.33
6.50 14.82 26.32
@@ -57820,7 +58053,7 @@ Central African Republic
6.35 14.77 26.36
6.34 14.77 26.37
6.33 14.77 26.37
- 6.32 14.76 26.38
+ 6.32 14.76 26.39
6.31 14.75 26.42
6.30 14.74 26.45
6.29 14.73 26.46
@@ -57961,7 +58194,7 @@ Central African Republic
4.94 14.66 19.20 20.02 24.27 24.64 24.90 25.05 25.09
4.93 14.66 19.19 20.03 24.20 24.23 24.27 24.64 24.88
4.92 14.66 19.11 20.04 24.19 24.24 24.27 24.64 24.86
- 4.91 14.67 19.11 20.05 24.19 24.24 24.26 24.64 24.81
+ 4.91 14.67 19.10 20.05 24.19 24.24 24.26 24.64 24.81
4.90 14.67 19.10 20.07 24.08 24.10 24.18 24.69 24.80
4.89 14.67 19.09 20.09 24.07 24.12 24.17
4.88 14.67 19.08 20.13 24.06
@@ -58086,11 +58319,11 @@ Central African Republic
3.69 15.21 18.60
3.68 15.22 17.44 17.47 18.60
3.67 15.23 17.42 17.48 18.61
- 3.66 15.24 17.40 17.50 18.61
- 3.65 15.25 17.38 17.51 18.61
+ 3.66 15.24 17.41 17.50 18.61
+ 3.65 15.25 17.39 17.51 18.61
3.64 15.26 17.37 17.53 18.61
3.63 15.27 17.37 17.54 18.61
- 3.62 15.27 17.36 17.56 18.61
+ 3.62 15.28 17.36 17.56 18.61
3.61 15.28 17.35 17.60 18.61
3.60 15.29 17.25 17.28 17.34 17.73 18.45 18.48 18.61
3.59 15.30 17.24 17.79 18.44 18.49 18.62
@@ -58177,13 +58410,13 @@ Central African Republic
2.78 16.04 16.47
2.77 16.04 16.46
2.76 16.04 16.46
- 2.75 16.04 16.46
+ 2.75 16.04 16.45
2.74 16.04 16.45
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2.72 16.04 16.44
- 2.71 16.04 16.44
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2.70 16.04 16.43
- 2.69 16.05 16.43
+ 2.69 16.05 16.42
2.68 16.08 16.42
2.67 16.08 16.42
2.66 16.08 16.41
@@ -58277,13 +58510,13 @@ Chad
23.03 15.03 16.85
23.02 15.00 16.87
23.01 14.98 16.89
- 23.00 14.97 16.91
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- 22.98 14.97 16.96
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22.96 14.97 17.00
22.95 14.97 17.02
- 22.94 14.98 17.04
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22.93 14.98 17.06
22.92 14.98 17.08
22.91 14.98 17.10
@@ -58775,7 +59008,7 @@ Chad
18.05 15.56 23.99
18.04 15.56 23.99
18.03 15.56 23.99
- 18.02 15.56 23.99
+ 18.02 15.55 23.99
18.01 15.55 23.99
18.00 15.55 23.99
17.99 15.55 23.99
@@ -58886,7 +59119,7 @@ Chad
16.94 15.46 23.99
16.93 15.46 23.99
16.92 15.46 23.99
- 16.91 15.46 23.99
+ 16.91 15.45 23.99
16.90 15.45 23.99
16.89 15.45 23.99
16.88 15.44 23.99
@@ -59008,7 +59241,7 @@ Chad
15.72 14.33 23.56 23.76 23.99
15.71 14.32 23.51 23.83 23.99
15.70 14.32 23.49 23.86 23.99
- 15.69 14.31 23.13 23.18 23.46 23.89 23.98
+ 15.69 14.31 23.14 23.18 23.46 23.89 23.98
15.68 14.31 23.09 23.24 23.43 23.92 23.98
15.67 14.30 23.07 23.29 23.41
15.66 14.29 23.06
@@ -59124,7 +59357,7 @@ Chad
14.56 13.65 22.39
14.55 13.64 22.38
14.54 13.62 22.38
- 14.53 13.60 22.38
+ 14.53 13.61 22.38
14.52 13.53 22.38
14.51 13.51 22.39
14.50 13.49 22.41
@@ -59188,13 +59421,13 @@ Chad
13.92 13.54 22.20
13.91 13.54 22.19
13.90 13.54 22.18
- 13.89 13.55 22.18
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13.88 13.55 22.17
13.87 13.55 22.16
13.86 13.56 22.15
13.85 13.56 22.14
13.84 13.56 22.13
- 13.83 13.56 22.13
+ 13.83 13.56 22.12
13.82 13.56 22.12
13.81 13.56 22.11
13.80 13.56 22.10
@@ -59221,37 +59454,37 @@ Chad
13.59 13.66 22.20
13.58 13.67 22.20
13.57 13.68 22.21
- 13.56 13.68 22.21
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13.55 13.69 22.22
13.54 13.70 22.22
13.53 13.71 22.22
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13.51 13.72 22.22
13.50 13.73 22.22
13.49 13.74 22.22
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13.47 13.75 22.22
13.46 13.76 22.22
13.45 13.77 22.23
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13.43 13.78 22.25
13.42 13.79 22.25
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13.39 13.81 22.27
13.38 13.82 22.28
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13.36 13.83 22.28
13.35 13.84 22.28
13.34 13.85 22.28
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13.32 13.86 22.27
13.31 13.87 22.26
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13.29 13.88 22.25
13.28 13.89 22.25
13.27 13.90 22.24
- 13.26 13.90 22.23
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13.25 13.91 22.22
13.24 13.92 22.21
13.23 13.93 22.20
@@ -59262,7 +59495,7 @@ Chad
13.18 13.96 22.14
13.17 13.97 22.13
13.16 13.98 22.11
- 13.15 13.98 22.08
+ 13.15 13.99 22.08
13.14 13.99 22.06
13.13 14.00 22.03
13.12 14.01 22.01
@@ -59275,10 +59508,10 @@ Chad
13.05 14.43 21.95
13.04 14.43 21.94
13.03 14.44 21.93
- 13.02 14.44 21.93
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13.00 14.46 21.92
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12.98 14.47 21.91
12.97 14.48 21.90
12.96 14.48 21.90
@@ -59470,11 +59703,11 @@ Chad
11.10 15.01 22.93
11.09 15.01 22.93
11.08 15.01 22.93
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11.02 15.02 22.90
11.01 15.02 22.90
11.00 15.02 22.90
@@ -59578,7 +59811,7 @@ Chad
10.02 15.60 21.43
10.01 15.62 21.43
10.00 14.37 14.47 15.63 21.42
- 9.99 14.24 14.51 15.09 15.23 15.63 21.41
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9.98 14.16 14.55 15.07 15.27 15.59 21.40
9.97 14.16 14.59 14.87 14.92 15.07 15.30 15.54 21.39
9.96 14.16 14.63 14.84 14.98 15.06 15.33 15.49 21.38
@@ -59664,35 +59897,35 @@ Chad
9.16 14.33 20.47
9.15 14.33 20.46
9.14 14.34 20.46
- 9.13 14.35 20.45
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9.12 14.37 20.19 20.22 20.44
9.11 14.38 20.06 20.12 20.17 20.23 20.40
- 9.10 14.39 20.04 20.14 20.16 20.24 20.27 20.31 20.37
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9.09 14.41 20.04
9.08 14.42 20.04
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9.02 14.50 19.74
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8.91 14.64 18.95
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8.88 14.68 18.92
8.87 14.69 18.89
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8.84 14.73 18.91
8.83 14.74 18.91
8.82 14.75 18.92
@@ -59716,7 +59949,7 @@ Chad
8.64 15.01 19.10
8.63 15.04 19.10
8.62 15.04 19.09
- 8.61 15.05 19.08
+ 8.61 15.05 19.07
8.60 15.06 19.07
8.59 15.06 19.06
8.58 15.07 19.06
@@ -59732,30 +59965,30 @@ Chad
8.48 15.15 18.98
8.47 15.16 18.98
8.46 15.17 18.97
- 8.45 15.17 18.96
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8.44 15.18 18.95
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8.42 15.19 18.93
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8.40 15.20 18.92
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8.38 15.21 18.91
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8.34 15.23 18.88
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8.32 15.24 18.86
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8.30 15.25 18.85
8.29 15.25 18.84
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8.27 15.26 18.83
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8.25 15.27 18.81
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8.23 15.28 18.79
- 8.22 15.28 18.76
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8.21 15.29 18.73
8.20 15.29 18.71
8.19 15.30 18.69
@@ -59917,21 +60150,21 @@ Chile
-18.28 -70.10 -69.08
-18.29 -70.12 -69.07
-18.30 -70.14 -69.07
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China
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@@ -64921,7 +65154,7 @@ China
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37.42 75.10 118.95 119.97 122.53 122.59 122.69
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36.00 75.93 120.18 120.21 120.24 120.26 120.31
@@ -65449,23 +65682,23 @@ China
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@@ -66814,93 +67047,93 @@ China
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@@ -67219,6 +67452,33 @@ China
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18.16 109.55 109.58 109.60 109.62
18.15 109.55 109.57
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China: Hainan
20.17 110.66 110.68
20.16 110.66 110.69
@@ -67231,11 +67491,11 @@ China: Hainan
20.09 110.37 110.39 110.56 110.72
20.08 110.36 110.40 110.55 110.72
20.07 110.14 110.18 110.31 110.34 110.36 110.41 110.55 110.73
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20.05 110.13 110.24 110.29 110.47 110.55 110.76
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20.03 110.12 110.53 110.56 110.78
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20.01 109.64 109.73 110.09 110.53 110.56 110.85 110.88 110.93
20.00 109.58 109.73 109.80 109.82 109.90 109.95 110.07 110.94
19.99 109.57 109.73 109.80 109.83 109.87 109.95 110.05 110.94
@@ -67251,10 +67511,10 @@ China: Hainan
19.89 109.24 109.37 109.50 110.97
19.88 109.24 109.39 109.43 109.45 109.50 110.98
19.87 109.23 109.46 109.51 110.98
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19.82 109.16 110.99
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19.80 109.15 110.99
@@ -67289,8 +67549,8 @@ China: Hainan
19.51 108.91 110.81
19.50 108.89 110.81
19.49 108.88 110.81
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19.46 108.84 110.79
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@@ -67319,14 +67579,14 @@ China: Hainan
19.21 108.61 110.63
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19.19 108.65 110.62
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19.13 108.63 110.59
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19.10 108.60 110.58
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@@ -67336,14 +67596,14 @@ China: Hainan
19.04 108.62 110.57
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19.02 108.62 110.55
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18.93 108.64 110.51
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@@ -67394,13 +67654,13 @@ China: Hainan
18.46 108.80 110.09
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18.36 108.96 109.76
18.35 108.98 109.76
18.34 109.11 109.75
@@ -67409,9 +67669,9 @@ China: Hainan
18.31 109.13 109.74
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@@ -67431,27 +67691,27 @@ Christmas Island
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Clipperton Island
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Cocos Islands
-12.11 96.81 96.83
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-12.17 96.81 96.87
@@ -67459,6 +67719,9 @@ Cocos Islands
-12.19 96.82 96.87
-12.20 96.83 96.86
Colombia
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13.37 -81.38 -81.34
13.36 -81.38 -81.34
@@ -67469,7 +67732,7 @@ Colombia
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@@ -67482,12 +67745,12 @@ Colombia
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@@ -67496,18 +67759,18 @@ Colombia
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@@ -67536,7 +67799,7 @@ Colombia
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@@ -67544,7 +67807,7 @@ Colombia
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@@ -67586,8 +67849,8 @@ Colombia
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@@ -67596,8 +67859,8 @@ Colombia
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@@ -67658,16 +67921,16 @@ Colombia
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@@ -67676,12 +67939,12 @@ Colombia
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@@ -67690,14 +67953,14 @@ Colombia
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@@ -67705,22 +67968,22 @@ Colombia
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@@ -67729,68 +67992,68 @@ Colombia
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Costa Rica
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+ 19.87 -77.74 -77.30 -77.13 -77.01 -75.56 -75.44 -75.41 -75.26
19.86 -77.74 -77.30 -75.54 -75.46
19.85 -77.74 -77.33
19.84 -77.74 -77.41
- 19.83 -77.73 -77.49
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19.82 -77.72 -77.62
- 19.81 -77.71 -77.65
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Curacao
12.40 -69.17 -69.14
- 12.39 -69.17 -69.12
- 12.38 -69.18 -69.10
+ 12.39 -69.17 -69.13
+ 12.38 -69.18 -69.11
12.37 -69.18 -69.08
12.36 -69.18 -69.07
12.35 -69.17 -69.06
- 12.34 -69.17 -69.05
- 12.33 -69.17 -69.04
- 12.32 -69.17 -69.04
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12.31 -69.17 -69.04
- 12.30 -69.17 -69.03
+ 12.30 -69.17 -69.04
12.29 -69.17 -69.03
12.28 -69.16 -69.03
12.27 -69.15 -69.03
@@ -71144,15 +71419,15 @@ Curacao
12.21 -69.11 -68.93
12.20 -69.10 -68.89
12.19 -69.08 -68.85
- 12.18 -69.07 -68.81
- 12.17 -69.03 -68.80
- 12.16 -69.03 -68.80
- 12.15 -69.02 -68.80
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+ 12.15 -69.03 -68.80
12.14 -69.02 -68.80
12.13 -69.01 -68.80
12.12 -69.00 -68.79
- 12.11 -68.98 -68.77
- 12.10 -68.97 -68.76
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+ 12.10 -68.97 -68.77
12.09 -68.95 -68.75
12.08 -68.92 -68.74
12.07 -68.89 -68.73
@@ -71170,30 +71445,30 @@ Cyprus
35.13 32.50 32.74 33.01 33.27 33.30 33.44
35.12 32.49 32.79 32.99 33.45
35.11 32.49 32.80 32.97 33.46
- 35.10 32.26 32.30 32.48 32.81 32.88 32.90 32.95 33.46
- 35.09 32.26 32.31 32.47 32.81 32.87 32.92 32.94 33.46
- 35.08 32.26 32.32 32.46 32.82 32.86 33.47 33.87 33.89
- 35.07 32.26 32.33 32.45 32.82 32.84 33.47 33.81 33.83 33.85 33.91
- 35.06 32.26 32.35 32.43 33.47 33.80 34.03
+ 35.10 32.26 32.30 32.47 32.81 32.88 32.90 32.95 33.46
+ 35.09 32.26 32.31 32.46 32.81 32.87 32.92 32.94 33.46
+ 35.08 32.26 32.32 32.45 32.82 32.86 33.47 33.87 33.89
+ 35.07 32.26 32.33 32.44 32.82 32.84 33.47 33.81 33.83 33.85 33.91
+ 35.06 32.26 32.35 32.42 33.47 33.80 34.03
35.05 32.26 33.46 33.50 33.52 33.79 34.05
- 35.04 32.26 33.46 33.50 33.53 33.78 34.06
+ 35.04 32.26 33.46 33.49 33.53 33.78 34.06
35.03 32.26 33.46 33.48 33.53 33.78 34.06
- 35.02 32.27 33.46 33.48 33.53 33.56 33.64 33.78 34.07
- 35.01 32.28 33.46 33.48 33.53 33.55 33.67 33.81 34.07
- 35.00 32.28 33.46 33.48 33.70 33.81 34.07
- 34.99 32.29 33.71 33.81 34.08
- 34.98 32.29 33.71 33.83 34.09
- 34.97 32.30 33.71 33.82 34.10
- 34.96 32.30 33.71 33.82 33.95 34.02 34.10
- 34.95 32.30 33.70 33.82 33.93 34.04 34.10
+ 35.02 32.27 33.46 33.48 33.53 33.56 33.64 33.73 33.76 33.78 34.07
+ 35.01 32.28 33.46 33.48 33.53 33.55 33.67 33.72 33.76 33.81 34.07
+ 35.00 32.28 33.46 33.48 33.70 33.72 33.77 33.81 34.07
+ 34.99 32.29 34.08
+ 34.98 32.29 33.71 33.74 33.80 33.83 34.09
+ 34.97 32.30 33.71 33.74 33.80 33.82 34.10
+ 34.96 32.30 33.71 33.77 33.80 33.82 33.94 34.02 34.10
+ 34.95 32.30 33.70 33.82 33.91 34.04 34.10
34.94 32.30 33.68 33.83 33.90
34.93 32.31 33.66
34.92 32.31 33.65
34.91 32.31 33.65
- 34.90 32.31 33.65
- 34.89 32.31 33.65
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+ 34.89 32.31 33.64
34.88 32.31 33.64
- 34.87 32.32 33.64
+ 34.87 32.31 33.64
34.86 32.32 33.64
34.85 32.33 33.64
34.84 32.35 33.64
@@ -71204,7 +71479,7 @@ Cyprus
34.79 32.38 33.54
34.78 32.39 33.53
34.77 32.39 33.52
- 34.76 32.39 33.49
+ 34.76 32.39 33.48
34.75 32.40 33.45
34.74 32.40 33.43
34.73 32.40 33.40
@@ -71216,7 +71491,7 @@ Cyprus
34.67 32.57 32.82 32.85 33.08
34.66 32.59 32.80 32.85 33.07
34.65 32.61 32.77 32.87 33.05
- 34.64 32.64 32.77 32.90 33.03
+ 34.64 32.64 32.77 32.92 33.03
34.63 32.68 32.76 32.94 33.03
34.62 32.94 33.02
34.61 32.94 32.97
@@ -71224,38 +71499,38 @@ Cyprus
35.70 34.58 34.60
35.69 34.55 34.60
35.68 34.52 34.60
- 35.67 34.49 34.59
- 35.66 34.46 34.58
- 35.65 34.43 34.58
- 35.64 34.40 34.58
- 35.63 34.37 34.58
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35.61 34.34 34.53
35.60 34.32 34.51
- 35.59 34.30 34.49
- 35.58 34.28 34.47
- 35.57 34.25 34.45
- 35.56 34.17 34.20 34.22 34.44
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35.55 34.16 34.42
- 35.54 34.15 34.41
- 35.53 34.14 34.39
- 35.52 34.13 34.38
- 35.51 34.11 34.36
- 35.50 34.09 34.35
- 35.49 34.07 34.33
- 35.48 34.04 34.31
- 35.47 34.01 34.29
- 35.46 33.98 34.27
- 35.45 33.94 34.25
- 35.44 33.91 34.23
- 35.43 33.88 34.21
- 35.42 33.85 34.19
- 35.41 33.77 34.17
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+ 35.47 33.98 34.29
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+ 35.45 33.92 34.25
+ 35.44 33.89 34.23
+ 35.43 33.86 34.21
+ 35.42 33.77 33.81 33.84 34.19
+ 35.41 33.75 34.17
35.40 32.91 32.96 33.73 34.15
35.39 32.91 32.98 33.71 34.13
35.38 32.91 33.00 33.69 34.11
- 35.37 32.91 33.05 33.67 34.10
- 35.36 32.92 33.17 33.62 34.10
+ 35.37 32.91 33.04 33.10 33.18 33.67 34.10
+ 35.36 32.92 33.24 33.62 34.10
35.35 32.92 33.32 33.54 34.09
35.34 32.92 33.39 33.46 34.08
35.33 32.92 34.08
@@ -71266,14 +71541,14 @@ Cyprus
35.28 32.92 33.95
35.27 32.92 33.94
35.26 32.92 33.93
- 35.25 32.91 33.93
+ 35.25 32.91 33.92
35.24 32.91 33.92
35.23 32.91 33.91
35.22 32.90 33.91
35.21 32.90 33.91
35.20 32.89 33.91
35.19 32.60 32.65 32.70 32.73 32.89 33.91
- 35.18 32.59 32.65 32.70 32.78 32.88 33.91
+ 35.18 32.59 32.65 32.70 32.78 32.88 33.90
35.17 32.59 32.65 32.70 32.80 32.86 33.91
35.16 32.59 32.64 32.70 32.82 32.84 33.14 33.20 33.39 33.41 33.92
35.15 32.60 32.63 32.70 33.13 33.25 33.36 33.41 33.94
@@ -71294,8 +71569,8 @@ Cyprus
35.00 33.45 33.48
34.99 33.45 33.48
Cyprus
- 34.71 32.82 32.84
- 34.70 32.81 32.87
+ 34.71 32.82 32.86
+ 34.70 32.81 32.86
34.69 32.79 32.87
34.68 32.75 32.88 32.94 32.99
34.67 32.75 32.99
@@ -71304,8 +71579,8 @@ Cyprus
34.64 32.75 32.79 32.88 33.02
34.63 32.90 33.02
34.62 32.90 33.02
- 34.61 32.91 33.02
- 34.60 32.91 33.02
+ 34.61 32.91 33.01
+ 34.60 32.91 33.01
34.59 32.92 33.03
34.58 32.93 33.04
34.57 32.93 33.04
@@ -71319,7 +71594,7 @@ Cyprus
35.08 33.86 33.93
35.07 33.69 33.72 33.80 33.93
35.06 33.66 33.72 33.78 33.92
- 35.05 33.66 33.90
+ 35.05 33.66 33.91
35.04 33.66 33.86
35.03 33.66 33.84
35.02 33.66 33.84
@@ -71328,9 +71603,9 @@ Cyprus
34.99 33.68 33.86
34.98 33.69 33.86
34.97 33.69 33.88
- 34.96 33.69 33.89
- 34.95 33.81 33.89
- 34.94 33.82 33.89
+ 34.96 33.69 33.90
+ 34.95 33.80 33.90
+ 34.94 33.81 33.90
34.93 33.83 33.89
34.92 33.85 33.87
Czech Republic
@@ -71397,7 +71672,7 @@ Czech Republic
50.45 12.79 12.84 12.99 16.26
50.44 12.72 12.86 12.98 16.24 16.87 16.93
50.43 12.71 12.88 12.97 16.22 16.85 16.95
- 50.42 12.70 12.90 12.95 16.22 16.85 17.01
+ 50.42 12.70 12.90 12.96 16.22 16.85 17.01
50.41 12.69 16.24 16.85 17.06
50.40 12.53 16.24 16.85 17.11
50.39 12.49 16.25 16.85 17.13 17.15 17.18
@@ -71419,7 +71694,7 @@ Czech Republic
50.23 12.06 12.25 12.30 16.51 16.94 17.74
50.22 12.07 12.26 12.29 16.53 16.89 17.75
50.21 12.09 12.27 12.29 16.54 16.89 17.75
- 50.20 12.11 12.27 12.29 16.54 16.86 17.75
+ 50.20 12.11 12.27 12.29 16.54 16.87 17.75
50.19 12.13 12.27 12.29 16.55 16.80 17.74
50.18 12.15 16.55 16.78 17.73
50.17 12.16 16.56 16.77 17.71
@@ -71551,7 +71826,7 @@ Czech Republic
48.91 13.60 14.97 15.47 17.87
48.90 13.60 14.97 15.49 17.79
48.89 13.61 14.97 15.51 17.77
- 48.88 13.62 14.97 15.54 17.77
+ 48.88 13.62 14.97 15.55 17.77
48.87 13.64 14.97 15.58 17.76
48.86 13.66 14.97 15.61 17.75
48.85 13.71 14.96 15.64 15.77 15.81 17.74
@@ -71632,7 +71907,7 @@ Democratic Republic of the Congo
4.96 19.18 20.04 24.19 24.68 24.87 27.51
4.95 19.10 20.05 24.18 24.68 24.80 24.83 24.85 27.51
4.94 19.09 20.06 24.17 24.68 24.80 27.51
- 4.93 19.09 20.08 24.07 24.11 24.17 24.70 24.75 24.77 24.79 27.52
+ 4.93 19.08 20.08 24.07 24.11 24.17 24.70 24.75 24.77 24.79 27.52
4.92 19.08 20.10 24.06 24.13 24.16 27.53
4.91 19.07 20.14 24.05 27.60
4.90 19.05 20.16 24.04 27.65
@@ -71669,13 +71944,13 @@ Democratic Republic of the Congo
4.59 18.83 20.47 22.71 27.81 29.43 29.71 29.73 29.76
4.58 18.83 20.47 22.71 27.82 29.42 29.77
4.57 18.82 20.46 22.70 27.83 27.90 27.94 29.41 29.79
- 4.56 18.81 20.46 22.70 28.02 28.74 28.77 29.40 29.80
+ 4.56 18.81 20.46 22.70 28.02 28.74 28.76 29.40 29.80
4.55 18.81 20.45 22.69 28.02 28.72 28.78 29.40 29.80
4.54 18.80 20.46 22.68 28.02 28.68 28.79 29.40 29.80
4.53 18.80 20.46 22.68 28.02 28.68 28.79 29.40 29.80
4.52 18.79 20.47 22.68 28.02 28.67 28.79 29.39 29.79
4.51 18.79 20.48 22.68 28.02 28.67 28.79 29.39 29.78
- 4.50 18.79 20.49 22.67 28.02 28.66 28.79 28.95 29.00 29.38 29.79
+ 4.50 18.79 20.49 22.67 28.02 28.66 28.79 28.95 28.99 29.38 29.79
4.49 18.78 20.50 22.60 28.02 28.66 28.80 28.83 28.88 28.91 29.00 29.37 29.79
4.48 18.78 20.51 22.58 28.02 28.65 29.02 29.36 29.79
4.47 18.77 20.52 22.58 28.02 28.65 29.04 29.34 29.79
@@ -71732,14 +72007,14 @@ Democratic Republic of the Congo
3.96 18.63 30.24
3.95 18.63 30.29
3.94 18.62 30.32
- 3.93 18.61 30.35
- 3.92 18.61 30.37
+ 3.93 18.61 30.34
+ 3.92 18.61 30.36
3.91 18.60 30.38
- 3.90 18.60 30.40
+ 3.90 18.60 30.39
3.89 18.60 30.41
3.88 18.60 30.44 30.50 30.52
3.87 18.60 30.53
- 3.86 18.60 30.54
+ 3.86 18.60 30.53
3.85 18.60 30.54
3.84 18.60 30.54
3.83 18.60 30.54
@@ -71812,10 +72087,10 @@ Democratic Republic of the Congo
3.16 18.61 30.79
3.15 18.60 30.78
3.14 18.60 30.78
- 3.13 18.60 30.77
+ 3.13 18.60 30.78
3.12 18.58 30.77
3.11 18.56 30.77
- 3.10 18.55 30.76
+ 3.10 18.55 30.77
3.09 18.53 30.76
3.08 18.52 30.76
3.07 18.51 30.75
@@ -71908,7 +72183,7 @@ Democratic Republic of the Congo
2.20 18.07 31.24
2.19 18.07 31.26
2.18 18.06 31.27
- 2.17 18.06 31.28
+ 2.17 18.06 31.27
2.16 18.06 31.29
2.15 18.06 31.29
2.14 18.06 31.29
@@ -71992,11 +72267,11 @@ Democratic Republic of the Congo
1.36 17.99 30.59
1.35 17.98 30.58
1.34 17.98 30.57
- 1.33 17.98 30.56
+ 1.33 17.98 30.57
1.32 17.97 30.56
1.31 17.97 30.55
1.30 17.96 30.54
- 1.29 17.96 30.53
+ 1.29 17.96 30.54
1.28 17.96 30.53
1.27 17.95 30.52
1.26 17.95 30.51
@@ -72043,7 +72318,7 @@ Democratic Republic of the Congo
0.85 17.86 30.03
0.84 17.86 30.01
0.83 17.86 29.99
- 0.82 17.87 29.97
+ 0.82 17.87 29.98
0.81 17.87 29.96
0.80 17.87 29.95
0.79 17.87 29.94
@@ -72082,11 +72357,11 @@ Democratic Republic of the Congo
0.46 17.94 29.94
0.45 17.94 29.93
0.44 17.94 29.92
- 0.43 17.94 29.91
+ 0.43 17.94 29.92
0.42 17.93 29.91
0.41 17.93 29.90
0.40 17.93 29.89
- 0.39 17.93 29.88
+ 0.39 17.93 29.89
0.38 17.93 29.88
0.37 17.92 29.87
0.36 17.91 29.86
@@ -72146,24 +72421,24 @@ Democratic Republic of the Congo
-0.18 17.70 29.68
-0.19 17.70 29.68
-0.20 17.70 29.68
- -0.21 17.70 29.67
- -0.22 17.70 29.67
- -0.23 17.70 29.67
+ -0.21 17.70 29.68
+ -0.22 17.70 29.68
+ -0.23 17.70 29.68
-0.24 17.70 29.67
-0.25 17.70 29.67
-0.26 17.70 29.67
- -0.27 17.71 29.66
+ -0.27 17.71 29.67
-0.28 17.71 29.66
-0.29 17.71 29.66
-0.30 17.71 29.66
-0.31 17.72 29.66
-0.32 17.72 29.66
- -0.33 17.72 29.65
- -0.34 17.73 29.65
+ -0.33 17.72 29.66
+ -0.34 17.73 29.66
-0.35 17.73 29.65
-0.36 17.73 29.65
-0.37 17.73 29.65
- -0.38 17.73 29.64
+ -0.38 17.73 29.65
-0.39 17.73 29.64
-0.40 17.73 29.64
-0.41 17.73 29.64
@@ -72195,13 +72470,13 @@ Democratic Republic of the Congo
-0.67 17.59 29.62
-0.68 17.58 29.62
-0.69 17.57 29.62
- -0.70 17.57 29.61
+ -0.70 17.56 29.61
-0.71 17.56 29.61
-0.72 17.55 29.61
-0.73 17.54 29.61
-0.74 17.53 29.61
-0.75 17.52 29.61
- -0.76 17.52 29.62
+ -0.76 17.51 29.62
-0.77 17.51 29.62
-0.78 17.50 29.62
-0.79 17.49 29.62
@@ -72273,9 +72548,9 @@ Democratic Republic of the Congo
-1.45 16.72 29.49
-1.46 16.71 29.48
-1.47 16.70 29.47
- -1.48 16.70 29.47
+ -1.48 16.70 29.46
-1.49 16.69 29.46
- -1.50 16.69 29.46
+ -1.50 16.69 29.45
-1.51 16.68 29.45
-1.52 16.67 29.35
-1.53 16.67 29.35
@@ -72300,16 +72575,16 @@ Democratic Republic of the Congo
-1.72 16.60 29.21
-1.73 16.59 29.20
-1.74 16.59 29.19
- -1.75 16.58 29.19
- -1.76 16.58 29.18
+ -1.75 16.58 29.18
+ -1.76 16.57 29.18
-1.77 16.57 29.17
-1.78 16.56 29.16
-1.79 16.55 29.16
- -1.80 16.55 29.15
- -1.81 16.54 29.15
+ -1.80 16.54 29.15
+ -1.81 16.53 29.15
-1.82 16.53 29.15
-1.83 16.52 29.14
- -1.84 16.52 29.14
+ -1.84 16.51 29.14
-1.85 16.51 29.14
-1.86 16.50 29.14
-1.87 16.50 29.13
@@ -72418,7 +72693,7 @@ Democratic Republic of the Congo
-2.90 16.16 29.09
-2.91 16.16 29.10
-2.92 16.16 29.12
- -2.93 16.16 29.13
+ -2.93 16.17 29.13
-2.94 16.17 29.14
-2.95 16.17 29.15
-2.96 16.17 29.15
@@ -72495,13 +72770,13 @@ Democratic Republic of the Congo
-3.67 16.01 29.23
-3.68 16.00 29.23
-3.69 16.00 29.23
- -3.70 16.00 29.23
+ -3.70 16.00 29.22
-3.71 15.99 29.22
-3.72 15.98 29.22
-3.73 15.98 29.22
-3.74 15.97 29.22
-3.75 15.97 29.22
- -3.76 15.96 29.22
+ -3.76 15.96 29.21
-3.77 15.96 29.21
-3.78 15.96 29.21
-3.79 15.95 29.21
@@ -72540,10 +72815,10 @@ Democratic Republic of the Congo
-4.12 15.49 29.35
-4.13 15.49 29.36
-4.14 15.49 29.36
- -4.15 15.48 29.37
+ -4.15 15.48 29.36
-4.16 15.48 29.37
-4.17 15.47 29.37
- -4.18 15.46 29.38
+ -4.18 15.46 29.37
-4.19 15.45 29.38
-4.20 15.44 29.38
-4.21 15.42 29.38
@@ -72565,14 +72840,14 @@ Democratic Republic of the Congo
-4.37 14.11 14.42 15.16 29.40
-4.38 14.07 14.42 15.16 29.40
-4.39 14.03 14.44 15.15 29.40
- -4.40 14.01 14.46 15.14 29.41
- -4.41 13.76 13.82 14.00 14.47 15.13 29.41
+ -4.40 14.01 14.46 15.15 29.41
+ -4.41 13.76 13.82 14.00 14.47 15.14 29.41
-4.42 13.73 13.83 14.00 14.47 15.13 29.41
-4.43 13.71 13.84 13.99 14.47 15.12 29.41
-4.44 13.70 13.85 13.97 14.47 15.11 29.41
- -4.45 13.70 13.85 13.97 14.47 15.10 29.41
+ -4.45 13.70 13.85 13.97 14.47 15.11 29.41
-4.46 13.70 13.86 13.96 14.47 15.10 29.41
- -4.47 13.70 13.92 13.95 14.46 15.09 29.41
+ -4.47 13.70 13.91 13.95 14.46 15.09 29.41
-4.48 13.70 14.45 15.08 29.42
-4.49 13.70 14.44 15.07 29.42
-4.50 13.70 14.44 15.07 29.42
@@ -72618,11 +72893,11 @@ Democratic Republic of the Congo
-4.90 12.67 29.33
-4.91 12.66 29.33
-4.92 12.60 29.33
- -4.93 12.59 29.33
+ -4.93 12.59 29.34
-4.94 12.59 29.34
-4.95 12.59 29.34
-4.96 12.59 29.34
- -4.97 12.58 29.34
+ -4.97 12.58 29.35
-4.98 12.58 29.35
-4.99 12.57 29.35
-5.00 12.55 29.35
@@ -72708,30 +72983,30 @@ Democratic Republic of the Congo
-5.80 12.21 29.60
-5.81 12.22 29.60
-5.82 12.22 29.59
- -5.83 12.23 12.89 12.94 29.59
- -5.84 12.24 29.58
- -5.85 12.24 12.98 13.01 29.57
- -5.86 12.25 12.98 13.06 13.88 13.96 29.56
- -5.87 12.26 12.98 13.08 13.14 13.22 13.38 13.50 13.55 13.60 13.73 13.99 16.03 16.33 29.56
- -5.88 12.27 12.95 13.28 13.37 14.01 14.09 14.17 15.39 16.34 29.55
- -5.89 12.28 12.91 13.31 13.36 14.20 14.75 16.36 29.54
- -5.90 12.30 12.86 13.33 13.35 14.29 14.46 14.49 14.67 16.38 16.44 16.52 29.53
- -5.91 12.31 12.84 14.52 14.61 16.54 29.52
- -5.92 12.32 12.82 16.56 29.52
- -5.93 12.33 12.82 16.57 29.51
- -5.94 12.33 12.81 16.57 29.50
- -5.95 12.34 12.71 12.73 12.80 16.57 29.50
- -5.96 12.36 12.71 16.57 29.49
- -5.97 12.37 12.70 16.58 29.49
- -5.98 12.37 12.69 16.58 29.49
- -5.99 12.37 12.56 16.58 29.49
- -6.00 12.38 12.54 16.58 29.48
- -6.01 12.41 12.52 16.58 29.48
- -6.02 12.41 12.51 16.58 29.48
- -6.03 12.41 12.49 16.59 29.48
- -6.04 12.42 12.47 16.59 29.48
- -6.05 16.59 29.49
- -6.06 16.59 29.49
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+ -5.85 12.24 12.80 12.83 12.92 12.96 29.57
+ -5.86 12.25 12.78 12.81 13.88 13.96 29.56
+ -5.87 12.26 12.77 12.79 13.00 13.04 13.14 13.22 13.38 13.50 13.55 13.60 13.73 13.99 16.03 16.33 29.56
+ -5.88 12.27 12.99 13.28 13.37 14.01 14.09 14.17 15.39 16.34 29.55
+ -5.89 12.28 12.97 13.31 13.36 14.20 14.78 16.36 29.54
+ -5.90 12.30 12.96 13.33 13.35 14.29 14.46 14.49 14.67 16.38 16.44 16.52 29.53
+ -5.91 12.31 12.92 14.52 14.61 16.54 29.52
+ -5.92 12.32 12.88 16.56 29.52
+ -5.93 12.33 12.86 16.57 29.51
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+ -5.96 12.36 12.73 12.75 12.81 16.57 29.49
+ -5.97 12.36 12.73 12.77 12.80 16.58 29.49
+ -5.98 12.36 12.73 16.58 29.49
+ -5.99 12.37 12.72 16.58 29.49
+ -6.00 12.37 12.70 16.58 29.48
+ -6.01 12.38 12.40 12.42 12.60 12.63 12.68 16.58 29.48
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+ -6.05 12.42 12.50 16.59 29.49
+ -6.06 12.42 12.46 16.59 29.49
-6.07 16.59 29.49
-6.08 16.60 29.49
-6.09 16.60 29.50
@@ -72799,13 +73074,13 @@ Democratic Republic of the Congo
-6.71 16.75 29.84
-6.72 16.76 29.85
-6.73 16.76 29.87
- -6.74 16.77 29.89
- -6.75 16.78 29.91
- -6.76 16.79 29.93
- -6.77 16.79 29.95
- -6.78 16.80 29.97
- -6.79 16.81 29.99
- -6.80 16.81 30.01
+ -6.74 16.77 29.88
+ -6.75 16.78 29.90
+ -6.76 16.79 29.92
+ -6.77 16.79 29.94
+ -6.78 16.80 29.96
+ -6.79 16.81 29.98
+ -6.80 16.81 30.00
-6.81 16.81 30.02
-6.82 16.81 30.03
-6.83 16.82 30.04
@@ -72964,8 +73239,8 @@ Democratic Republic of the Congo
-8.36 21.89 29.73
-8.37 21.89 29.67
-8.38 21.90 29.62
- -8.39 21.90 29.56
- -8.40 21.91 29.48
+ -8.39 21.90 29.54
+ -8.40 21.91 29.47
-8.41 21.91 29.40
-8.42 21.92 29.33
-8.43 21.92 29.25
@@ -73348,9 +73623,9 @@ Democratic Republic of the Congo
-12.20 27.52 28.96 29.51 29.80
-12.21 27.52 28.96 29.49 29.80
-12.22 27.53 28.97 29.47 29.80
- -12.23 27.55 28.97 29.46 29.80
+ -12.23 27.54 28.97 29.46 29.80
-12.24 27.56 28.98 29.45 29.80
- -12.25 27.58 28.98 29.45 29.80
+ -12.25 27.57 28.98 29.45 29.80
-12.26 27.59 28.99 29.45 29.80
-12.27 27.60 28.99 29.44 29.80
-12.28 27.60 27.82 27.87 29.00 29.44 29.80
@@ -73492,8 +73767,8 @@ Denmark
57.60 9.95 10.46
57.59 9.94 10.46
57.58 9.93 10.45
- 57.57 9.92 10.45
- 57.56 9.91 10.45
+ 57.57 9.91 10.45
+ 57.56 9.90 10.45
57.55 9.89 10.45
57.54 9.88 10.46
57.53 9.86 10.46
@@ -73515,23 +73790,23 @@ Denmark
57.37 9.68 10.52
57.36 9.67 10.52
57.35 9.66 10.52
- 57.34 9.65 10.52 11.08 11.19
- 57.33 9.64 10.52 11.00 11.20
- 57.32 9.63 10.52 10.93 11.20
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- 57.29 9.60 10.53 10.88 11.13 11.15 11.17
- 57.28 9.59 10.53 10.84 11.09
- 57.27 9.58 10.53 10.84 11.09
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- 57.24 9.54 10.54 10.86 11.08
- 57.23 9.53 10.54 10.94 11.07
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- 57.21 9.49 10.53 10.95 11.04
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+ 57.18 9.42 10.47 10.98 11.01
57.17 8.97 9.05 9.38 10.45
57.16 8.95 9.17 9.34 10.44
57.15 8.93 10.44
@@ -73548,18 +73823,18 @@ Denmark
57.04 8.49 10.38
57.03 8.47 10.37
57.02 8.45 10.37
- 57.01 8.44 10.36
- 57.00 8.43 10.36
- 56.99 8.42 10.35
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56.97 8.39 10.32
56.96 8.38 10.31
56.95 8.37 10.29
- 56.94 8.36 10.29
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- 56.91 8.33 10.27
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56.89 8.30 10.28
56.88 8.29 10.28
56.87 8.28 10.29
@@ -73570,17 +73845,17 @@ Denmark
56.82 8.23 10.29
56.81 8.23 10.29
56.80 8.23 10.29
- 56.79 8.22 10.29
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56.78 8.22 10.30
56.77 8.22 10.31
56.76 8.22 10.31
56.75 8.22 10.32
56.74 8.22 10.33
- 56.73 8.22 10.34 11.56 11.66
- 56.72 8.20 10.35 11.51 11.66
- 56.71 8.19 10.35 11.50 11.66
- 56.70 8.18 10.35 11.50 11.64
- 56.69 8.17 10.36 11.50 11.61
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56.68 8.16 10.36 11.50 11.61
56.67 8.16 10.36 11.51 11.60
56.66 8.15 10.36 11.53 11.58
@@ -73594,10 +73869,10 @@ Denmark
56.58 8.12 10.36
56.57 8.11 10.37
56.56 8.11 10.38
- 56.55 8.11 10.42
- 56.54 8.11 10.46 10.72 10.84
- 56.53 8.11 10.52 10.60 10.87
- 56.52 8.11 10.88
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+ 56.53 8.11 10.51 10.60 10.86
+ 56.52 8.11 10.87
56.51 8.11 10.89
56.50 8.11 10.90
56.49 8.11 10.91
@@ -73619,21 +73894,21 @@ Denmark
56.33 8.12 10.93
56.32 8.12 10.92
56.31 8.12 10.91
- 56.30 8.12 10.90
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56.29 8.12 10.88
56.28 8.12 10.87
- 56.27 8.12 10.86
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56.26 8.12 10.84
- 56.25 8.12 10.83
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56.24 8.12 10.81
56.23 8.12 10.79
56.22 8.12 10.77
56.21 8.12 10.62 10.65 10.76
56.20 8.12 10.32 10.34 10.60 10.65 10.76
- 56.19 8.12 10.31 10.34 10.60 10.63 10.76
- 56.18 8.12 10.29 10.35 10.59 10.63 10.76
- 56.17 8.11 10.27 10.36 10.58 10.63 10.76
- 56.16 8.11 10.25 10.38 10.56 10.64 10.75
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+ 56.17 8.11 10.25 10.36 10.58 10.63 10.76
+ 56.16 8.11 10.24 10.38 10.56 10.64 10.75
56.15 8.10 10.24 10.39 10.45 10.48 10.56 10.66 10.75
56.14 8.10 10.23 10.48 10.57 10.68 10.74
56.13 8.09 10.24 10.48 10.57 12.22 12.34
@@ -73641,7 +73916,7 @@ Denmark
56.11 8.09 10.25 10.48 10.58 12.14 12.40
56.10 8.09 10.26 10.49 10.58 12.12 12.52
56.09 8.09 10.26 10.50 10.57 12.10 12.54
- 56.08 8.09 10.27 10.52 10.54 12.08 12.56
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56.07 8.09 10.27 12.06 12.59
56.06 8.09 10.27 12.04 12.61
56.05 8.09 10.27 12.02 12.63
@@ -73651,123 +73926,123 @@ Denmark
56.01 8.09 10.28 11.92 12.61
56.00 8.10 10.28 10.53 10.56 11.26 11.30 11.89 12.60
55.99 8.10 10.27 10.51 10.56 11.26 11.34 11.87 12.59
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55.94 8.12 10.26 10.50 10.60 11.34 11.78 11.83 12.55
55.93 8.12 10.26 10.51 10.63 11.41 11.77 11.83 12.54
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55.88 8.14 10.23 10.56 10.67 11.49 11.70 11.91 12.56
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55.86 8.14 10.06 10.10 10.20 10.51 10.67 11.47 11.72 11.93 12.57
55.85 8.14 9.98 10.11 10.20 10.50 10.66 11.43 11.73 11.93 12.57
55.84 8.15 9.98 10.12 10.20 10.50 10.65 11.33 11.36 11.40 11.74 11.93 12.58
55.83 8.15 10.00 10.13 10.20 10.50 10.63 11.33 11.74 11.92 12.58
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55.80 8.16 10.05 10.50 10.63 11.36 11.74 11.85 12.61
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55.78 8.16 10.04 10.51 10.63 11.35 11.76 11.84 12.61
55.77 8.16 10.03 10.51 10.63 11.35 11.76 11.83 12.60
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55.72 8.17 10.04 10.86 11.78 11.83 12.60
55.71 8.16 10.02 10.91 11.79 11.82 12.61
55.70 8.16 10.02 10.95 11.79 11.81 12.62
55.69 8.15 10.02 10.97 12.62
55.68 8.15 9.93 10.99 12.63
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55.60 8.10 9.85 10.17 10.39 10.59 10.66 11.08 12.68
55.59 8.10 9.82 10.13 10.42 10.59 10.67 11.10 12.39 12.43 12.49 12.51 12.68
55.58 8.09 9.80 10.09 10.43 10.58 10.69 11.12 12.35 12.51 12.67
55.57 8.08 9.78 10.05 10.43 10.58 10.70 11.12 12.33 12.51 12.66
55.56 8.08 8.26 8.30 9.82 10.01 10.47 10.58 10.71 11.13 12.31 12.52 12.64
55.55 8.08 8.26 8.30 9.84 9.99 10.50 10.59 10.71 11.12 12.29 12.52 12.62
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55.53 8.08 8.28 8.32 9.86 9.95 10.52 10.55 10.72 11.07 12.25
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55.51 8.17 8.30 8.34 10.50 10.55 10.74 11.07 12.23
55.50 8.20 8.31 8.36 9.64 9.66 10.50 10.56 10.75 11.07 12.23
55.49 8.22 8.32 8.37 10.50 10.54 10.75 11.07 11.11 11.15 12.22
55.48 8.24 8.33 8.38 10.75 11.15 12.21
55.47 8.26 8.33 8.36 9.67 9.69 10.75 11.16 12.21
55.46 8.28 8.33 8.36 9.67 9.69 10.72 11.17 12.22
- 55.45 8.30 8.32 8.35 9.67 9.69 10.69 11.17 12.22
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- 55.41 8.36 8.47 8.61 9.61 9.77 10.74 11.19 12.36
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55.38 8.38 8.47 8.62 9.61 9.76 10.78 11.13 12.43
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55.34 8.41 8.48 8.63 9.65 9.80 10.81 11.07 12.45
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55.32 8.44 8.47 8.64 9.65 9.87 10.82 11.09 12.46
55.31 8.64 9.66 9.87 10.83 11.14 12.46 14.75 14.78
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- 55.27 8.63 9.71 9.87 10.84 11.20 12.47 14.72 14.84
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- 55.25 8.63 9.72 9.87 10.81 11.22 12.43 14.70 14.88
- 55.24 8.64 9.72 9.87 10.82 11.22 12.41 14.69 14.92
- 55.23 8.64 9.72 9.88 10.82 11.22 12.36 14.69 14.97
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54.90 8.65 9.58 9.60 10.07 10.23 10.41 10.44 10.48 10.67 10.83 11.00 11.36 11.63 11.70 11.73 12.26
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54.87 8.67 8.75 8.92 9.56 9.61 9.75 9.86 10.07 10.28 10.50 10.65 10.82 11.00 11.43 11.63 12.22
54.86 8.96 9.55 9.61 9.75 9.88 10.06 10.30 10.52 10.64 10.81 11.01 11.47 11.58 12.17
54.85 9.03 9.51 9.61 9.76 9.94 10.00 10.32 10.52 10.63 10.81 11.02 11.51 11.56 12.18
54.84 9.13 9.49 9.63 9.76 9.95 9.98 10.33 10.52 10.59 10.80 11.04 11.54 11.56 12.18
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54.81 9.20 9.45 10.39 10.42 10.61 10.79 10.99 12.16
54.80 9.20 9.44 10.63 10.78 10.99 12.14
54.79 9.21 9.35 9.39 9.43 10.64 10.78 10.98 12.12
@@ -73776,8 +74051,8 @@ Denmark
54.76 10.65 10.76 10.99 12.06
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54.71 11.19 11.84 11.86 12.01
54.70 11.22 11.85 11.87 11.99
54.69 11.24 11.98
@@ -73805,17 +74080,17 @@ Djibouti
12.65 42.95 43.17
12.64 42.93 43.18
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12.51 42.40 42.51 42.77 43.28
12.50 42.39 42.53 42.77 43.29
12.49 42.38 42.54 42.77 43.33
@@ -73828,7 +74103,7 @@ Djibouti
12.42 42.32 42.62 42.73 43.34
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12.38 42.30 43.37
12.37 42.29 43.37
12.36 42.29 43.37
@@ -73876,10 +74151,10 @@ Djibouti
11.94 42.00 43.22
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11.87 41.95 43.14
11.86 41.94 43.13
11.85 41.93 43.12
@@ -73908,8 +74183,8 @@ Djibouti
11.62 41.76 42.72 43.14 43.16
11.61 41.75 42.71 43.13 43.16
11.60 41.75 42.71 42.83 42.86 43.05 43.08 43.12 43.16
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11.57 41.74 42.69 42.72 43.17
11.56 41.74 43.18
11.55 41.73 43.18
@@ -73925,33 +74200,33 @@ Djibouti
11.45 41.73 43.24
11.44 41.74 43.23
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11.29 41.77 43.13
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11.26 41.77 43.11
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11.15 41.77 43.04
11.14 41.77 43.03
11.13 41.77 43.03
@@ -73959,10 +74234,10 @@ Djibouti
11.11 41.77 43.01
11.10 41.77 43.01
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11.06 41.77 42.55 42.64 42.98
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11.04 41.76 42.49 42.72 42.97
11.03 41.76 42.47 42.72 42.96
11.02 41.76 42.45 42.73 42.96
@@ -73970,7 +74245,7 @@ Djibouti
11.00 41.75 42.42 42.74 42.94
10.99 41.75 42.32 42.36 42.41 42.75 42.94
10.98 41.75 42.27 42.76 42.93
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10.96 41.78 42.06 42.86 42.88
10.95 41.81 42.05
10.94 41.85 42.04
@@ -73980,10 +74255,10 @@ Djibouti
Dominica
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15.57 -61.49 -61.29
15.56 -61.49 -61.28
@@ -74033,26 +74308,26 @@ Dominican Republic
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@@ -74082,7 +74357,7 @@ Dominican Republic
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19.34 -71.77 -69.79 -69.55 -69.49 -69.47 -69.42 -69.31 -69.21
@@ -74098,8 +74373,8 @@ Dominican Republic
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19.18 -71.65 -69.61 -69.44 -69.21
19.17 -71.65 -69.61 -69.29 -69.22
@@ -74107,7 +74382,7 @@ Dominican Republic
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@@ -74116,9 +74391,9 @@ Dominican Republic
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@@ -74138,19 +74413,19 @@ Dominican Republic
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@@ -74178,58 +74453,58 @@ Dominican Republic
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-0.97 -91.45 -90.90
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+ -0.99 -91.45 -91.02
-1.00 -91.44 -91.03
-1.01 -91.44 -91.05
-1.02 -91.43 -91.08
@@ -75218,7 +75493,7 @@ Ecuador: Galapagos
-1.20 -90.48 -90.46
-1.21 -90.49 -90.42
-1.22 -90.50 -90.39
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+ -1.23 -90.50 -90.38
-1.24 -90.50 -90.36
-1.25 -90.50 -90.35
-1.26 -90.50 -90.35
@@ -75250,60 +75525,60 @@ Egypt
31.57 25.05 25.18 25.61 26.21 30.88 31.26
31.56 25.04 25.18 25.57 26.25 30.85 31.29
31.55 25.04 25.19 25.53 26.30 30.82 31.31
- 31.54 25.03 25.21 25.49 26.34 30.78 31.34 31.85 31.93
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31.53 25.03 25.28 25.45 26.40 30.75 31.36 31.81 31.95
31.52 25.02 25.30 25.34 25.37 25.41 26.47 30.72 31.39 31.79 31.95
31.51 25.02 26.55 30.35 30.38 30.68 31.41 31.77 31.96
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31.45 24.94 26.85 26.92 26.98 30.34 32.00
31.44 24.92 26.99 30.33 32.00
31.43 24.91 27.03 30.33 32.01
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31.38 24.85 27.34 30.31 32.08
31.37 24.84 27.35 30.31 32.11
31.36 24.84 27.35 30.30 32.12
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31.29 24.83 27.38 29.99 30.12 30.19 32.31 34.13 34.22
31.28 24.83 27.39 29.98 32.34 34.11 34.23
31.27 24.83 27.39 29.97 32.34 34.09 34.23
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31.10 24.85 28.17 29.70 32.53 32.77 33.16 33.22 34.29
31.09 24.85 28.18 28.36 28.44 29.69 32.55 32.74 33.15 33.20 34.30
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31.05 24.86 28.55 29.63 34.31
31.04 24.86 28.57 29.61 34.31
31.03 24.87 28.61 29.60 34.32
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31.00 24.87 28.72 29.54 34.33
30.99 24.88 28.74 29.53 34.33
30.98 24.88 28.76 29.51 34.34
@@ -75417,10 +75692,10 @@ Egypt
29.90 24.79 32.47 32.57 34.77
29.89 24.79 32.48 32.59 34.77
29.88 24.80 32.50 32.60 34.78
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29.83 24.79 32.49 32.59 34.79
29.82 24.79 32.48 32.59 34.80
29.81 24.78 32.47 32.59 34.80
@@ -75445,22 +75720,22 @@ Egypt
29.62 24.86 32.36 32.67 34.86
29.61 24.86 32.36 32.67 34.86
29.60 24.86 32.36 32.67 34.86
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29.56 24.85 32.37 32.70 34.85
29.55 24.85 32.37 32.70 34.86
29.54 24.85 32.38 32.71 34.86
29.53 24.85 32.39 32.71 34.87
29.52 24.85 32.41 32.71 34.87
29.51 24.85 32.43 32.71 34.88
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29.49 24.85 32.46 32.71 34.89
29.48 24.85 32.47 32.71 34.89
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29.43 24.87 32.53 32.74 34.85
29.42 24.87 32.54 32.76 34.84
29.41 24.88 32.55 32.78 34.84
@@ -75484,21 +75759,21 @@ Egypt
29.23 24.96 32.64 32.87 34.73
29.22 24.96 32.64 32.88 34.73
29.21 24.96 32.64 32.89 34.73
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29.18 24.97 32.64 32.95 34.73
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29.16 24.97 32.65 32.98 34.72
29.15 24.97 32.65 32.99 34.70
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29.13 24.97 32.66 32.99 34.70
29.12 24.97 32.66 33.02 34.70
29.11 24.97 32.66 33.02 34.70
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29.05 24.97 32.64 33.06 34.68
29.04 24.97 32.64 33.07 34.68
29.03 24.97 32.64 33.09 34.68
@@ -75508,8 +75783,8 @@ Egypt
28.99 24.97 32.63 33.16 34.69
28.98 24.97 32.63 33.15 34.69
28.97 24.97 32.64 33.15 34.69
- 28.96 24.97 32.65 33.15 34.67
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28.94 24.97 32.67 33.15 34.65
28.93 24.97 32.68 33.16 34.65
28.92 24.97 32.68 33.16 34.65
@@ -75525,7 +75800,7 @@ Egypt
28.82 24.97 32.74 33.16 34.63
28.81 24.97 32.77 33.16 34.63
28.80 24.97 32.79 33.17 34.63
- 28.79 24.97 32.80 33.18 34.63
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28.78 24.97 32.81 33.19 34.64
28.77 24.97 32.82 33.20 34.64
28.76 24.97 32.82 33.20 34.64
@@ -75533,7 +75808,7 @@ Egypt
28.74 24.97 32.83 33.20 34.63
28.73 24.97 32.84 33.20 34.63
28.72 24.97 32.84 33.19 34.63
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28.70 24.97 32.84 33.19 34.62
28.69 24.97 32.85 33.19 34.61
28.68 24.97 32.85 33.18 34.60
@@ -75546,8 +75821,8 @@ Egypt
28.61 24.97 32.87 33.20 34.58
28.60 24.97 32.87 33.20 34.57
28.59 24.97 32.87 33.20 34.56
- 28.58 24.97 32.90 33.21 34.56
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+ 28.57 24.97 32.91 33.21 34.55
28.56 24.97 32.93 33.21 34.54
28.55 24.97 32.95 33.21 34.53
28.54 24.97 32.96 33.22 34.53
@@ -75571,9 +75846,9 @@ Egypt
28.36 24.97 33.10 33.41 34.45
28.35 24.97 33.11 33.42 34.44
28.34 24.97 33.11 33.43 34.43
- 28.33 24.97 33.11 33.45 34.43
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28.32 24.97 33.12 33.47 34.43
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28.30 24.97 33.13 33.51 34.42
28.29 24.97 33.14 33.53 34.41
28.28 24.97 33.15 33.55 34.42
@@ -75589,33 +75864,33 @@ Egypt
28.18 24.97 33.25 33.62 34.46
28.17 24.97 33.25 33.62 34.46
28.16 24.97 33.25 33.63 34.46
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28.14 24.97 33.29 33.66 34.45
28.13 24.97 33.30 33.66 34.45
28.12 24.97 33.30 33.66 34.45
28.11 24.97 33.31 33.67 34.45
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28.06 24.97 33.37 33.70 34.45
28.05 24.97 33.37 33.71 34.45
28.04 24.97 33.39 33.73 34.45
28.03 24.97 33.42 33.75 34.45
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+ 27.93 24.97 33.53 33.86 34.39 34.49 34.63 34.65 34.74
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+ 27.89 24.97 33.56 33.94 34.34 34.69 34.72
27.88 24.97 33.57 33.95 34.34
27.87 24.97 33.57 33.96 34.34
27.86 24.97 33.58 33.98 34.33
@@ -75627,13 +75902,13 @@ Egypt
27.80 24.97 33.60 34.04 34.28
27.79 24.97 33.60 34.06 34.27
27.78 24.97 33.60 34.12 34.25
- 27.77 24.97 33.56 34.18 34.26
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27.76 24.97 33.56 34.19 34.26
27.75 24.97 33.56 34.20 34.26
27.74 24.97 33.56 34.21 34.27
27.73 24.97 33.56 34.22 34.27
27.72 24.97 33.56 34.23 34.27
- 27.71 24.97 33.56 34.24 34.26
+ 27.71 24.97 33.56 34.23 34.26
27.70 24.97 33.56
27.69 24.97 33.58
27.68 24.97 33.58
@@ -75650,7 +75925,7 @@ Egypt
27.57 24.97 33.57
27.56 24.97 33.57
27.55 24.97 33.57
- 27.54 24.97 33.57 33.91 33.98
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27.53 24.97 33.59 33.90 33.99
27.52 24.97 33.61 33.90 34.00
27.51 24.97 33.63 33.90 34.03
@@ -75661,12 +75936,12 @@ Egypt
27.46 24.97 33.65 33.99 34.06
27.45 24.97 33.66 34.00 34.06
27.44 24.97 33.67 34.02 34.06
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27.42 24.97 33.68
27.41 24.97 33.68
27.40 24.97 33.68
27.39 24.97 33.68
- 27.38 24.97 33.68
+ 27.38 24.97 33.69
27.37 24.97 33.69
27.36 24.97 33.69
27.35 24.97 33.70
@@ -75724,18 +75999,18 @@ Egypt
26.83 24.97 34.01
26.82 24.97 34.00
26.81 24.97 33.95
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26.68 24.97 33.94
26.67 24.97 33.95
26.66 24.97 33.95
@@ -75762,13 +76037,13 @@ Egypt
26.45 24.97 34.10
26.44 24.97 34.11
26.43 24.97 34.11
- 26.42 24.97 34.12
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@@ -75862,10 +76137,10 @@ Egypt
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@@ -75909,12 +76184,12 @@ Egypt
24.98 24.97 34.95
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24.89 24.97 35.00
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24.87 24.97 35.00
@@ -75943,103 +76218,103 @@ Egypt
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23.64 24.97 35.51
23.63 24.97 35.51
23.62 24.97 35.51
@@ -76073,29 +76348,29 @@ Egypt
23.34 24.97 35.56
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23.06 24.97 35.66
@@ -76107,9 +76382,9 @@ Egypt
23.00 24.97 35.67
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22.94 24.97 35.75
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22.92 24.97 35.76
@@ -76122,20 +76397,20 @@ Egypt
22.85 24.97 35.79
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22.68 24.97 36.14
22.67 24.97 36.18
22.66 24.97 36.20
@@ -76149,42 +76424,42 @@ Egypt
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22.19 24.97 31.38 31.46 36.70
22.18 24.97 31.37 31.47 36.71 36.74 36.78
22.17 24.97 31.36 31.47 36.79
@@ -76194,11 +76469,11 @@ Egypt
22.13 24.97 31.34 31.47 36.81
22.12 24.97 31.34 31.47 36.81
22.11 24.97 31.33 31.46 36.83
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22.05 24.97 31.30 31.44 36.90
22.04 24.97 31.30 31.43 36.90
22.03 24.97 31.29 31.43 36.90
@@ -76211,7 +76486,7 @@ El Salvador
14.45 -89.41 -89.38
14.44 -89.42 -89.38
14.43 -89.51 -89.45 -89.43 -89.36
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14.41 -89.59 -89.28
14.40 -89.59 -89.24 -89.13 -89.09
14.39 -89.60 -89.21 -89.14 -89.08
@@ -76253,7 +76528,7 @@ El Salvador
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13.99 -89.96 -88.49 -88.25 -88.07
13.98 -89.97 -88.48 -88.25 -88.07
13.97 -89.99 -88.48 -88.25 -88.07
@@ -76267,7 +76542,7 @@ El Salvador
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13.85 -90.11 -87.73
13.84 -90.11 -87.72
13.83 -90.12 -87.70
@@ -76279,33 +76554,33 @@ El Salvador
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13.47 -89.37 -87.70
13.46 -89.29 -87.70
13.45 -89.24 -87.71
@@ -76319,8 +76594,8 @@ El Salvador
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13.32 -88.99 -87.79
13.31 -88.97 -87.78
13.30 -88.95 -87.77
@@ -76328,17 +76603,17 @@ El Salvador
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13.14 -87.99 -87.90
Equatorial Guinea
3.78 8.72 8.75
@@ -76372,7 +76647,7 @@ Equatorial Guinea
3.50 8.56 8.87
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3.48 8.57 8.86
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3.46 8.45 8.86
3.45 8.44 8.85
3.44 8.44 8.85
@@ -76392,19 +76667,19 @@ Equatorial Guinea
3.30 8.42 8.78
3.29 8.43 8.77
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3.24 8.45 8.73
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3.22 8.53 8.72
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3.20 8.63 8.71
3.19 8.66 8.70
3.18 8.67 8.69
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2.32 9.75 9.82
2.31 9.75 9.82
2.30 9.75 9.82
@@ -76445,7 +76720,7 @@ Equatorial Guinea
1.95 9.79 11.34
1.94 9.79 11.34
1.93 9.79 11.34
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1.91 9.78 11.34
1.90 9.77 11.34
1.89 9.77 11.34
@@ -76460,8 +76735,8 @@ Equatorial Guinea
1.80 9.72 11.34
1.79 9.72 11.34
1.78 9.70 11.34
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1.75 9.67 11.34
1.74 9.66 11.34
1.73 9.66 11.34
@@ -76488,7 +76763,7 @@ Equatorial Guinea
1.52 9.55 11.34
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1.50 9.54 11.34
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1.48 9.53 11.34
1.47 9.52 11.34
1.46 9.51 11.34
@@ -76521,17 +76796,17 @@ Equatorial Guinea
1.19 9.33 11.34
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1.17 9.33 11.34
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1.13 9.35 11.34
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1.07 9.55 9.66 9.78 11.34
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1.05 9.56 9.65 9.78 11.34
1.04 9.56 9.63 9.78 11.34
1.03 9.57 9.60 9.78 11.34
@@ -76539,7 +76814,7 @@ Equatorial Guinea
1.01 9.79 11.34
1.00 9.79 11.34
0.99 9.79 11.34
- 0.98 9.79 10.01 11.18 11.34
+ 0.98 9.79 10.02 11.18 11.34
0.97 9.83 9.98
0.96 9.85 9.98
0.95 9.86 9.98
@@ -76572,9 +76847,9 @@ Eritrea
17.89 38.44 38.67
17.88 38.43 38.67
17.87 38.43 38.67
- 17.86 38.42 38.68
+ 17.86 38.42 38.67
17.85 38.42 38.68
- 17.84 38.41 38.69
+ 17.84 38.41 38.68
17.83 38.41 38.70
17.82 38.41 38.70
17.81 38.40 38.70
@@ -76582,37 +76857,37 @@ Eritrea
17.79 38.39 38.71
17.78 38.39 38.72
17.77 38.39 38.73
- 17.76 38.38 38.74
+ 17.76 38.38 38.73
17.75 38.38 38.74
- 17.74 38.38 38.75
- 17.73 38.37 38.76
+ 17.74 38.38 38.74
+ 17.73 38.37 38.75
17.72 38.37 38.76
- 17.71 38.36 38.77
- 17.70 38.36 38.78
- 17.69 38.35 38.79
- 17.68 38.35 38.79
- 17.67 38.34 38.80
- 17.66 38.33 38.80
- 17.65 38.31 38.81
- 17.64 38.29 38.81
- 17.63 38.27 38.82
- 17.62 38.26 38.82
- 17.61 38.24 38.83
- 17.60 38.24 38.83
- 17.59 38.24 38.84
- 17.58 38.24 38.84
- 17.57 38.24 38.85
- 17.56 38.14 38.17 38.24 38.85
- 17.55 38.02 38.07 38.10 38.19 38.24 38.86
- 17.54 38.00 38.08 38.10 38.20 38.23 38.86
- 17.53 37.98 38.08 38.10 38.87
- 17.52 37.96 38.08 38.10 38.87
+ 17.71 38.36 38.76
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+ 17.56 38.14 38.17 38.24 38.84
+ 17.55 38.02 38.07 38.10 38.19 38.24 38.85
+ 17.54 38.00 38.08 38.10 38.20 38.23 38.85
+ 17.53 37.98 38.08 38.10 38.86
+ 17.52 37.96 38.08 38.10 38.86
17.51 37.94 38.08 38.10 38.87
- 17.50 37.93 38.88
+ 17.50 37.93 38.87
17.49 37.92 38.88
- 17.48 37.78 37.82 37.92 38.89
+ 17.48 37.78 37.82 37.92 38.88
17.47 37.76 37.83 37.91 38.89
- 17.46 37.75 37.84 37.90 38.90
+ 17.46 37.75 37.84 37.90 38.89
17.45 37.74 37.86 37.88 38.90
17.44 37.74 38.91
17.43 37.73 38.91
@@ -76680,15 +76955,15 @@ Eritrea
16.81 36.97 39.13
16.80 36.97 39.13
16.79 36.97 39.13
- 16.78 36.97 39.14
+ 16.78 36.97 39.13
16.77 36.97 39.14
16.76 36.97 39.14
- 16.75 36.96 39.15
- 16.74 36.96 39.15
- 16.73 36.96 39.16
- 16.72 36.95 39.16
- 16.71 36.95 39.16
- 16.70 36.93 39.16
+ 16.75 36.96 39.14
+ 16.74 36.96 39.14
+ 16.73 36.96 39.15
+ 16.72 36.95 39.15
+ 16.71 36.95 39.15
+ 16.70 36.93 39.15
16.69 36.92 39.16
16.68 36.91 39.16
16.67 36.90 39.16
@@ -76771,10 +77046,10 @@ Eritrea
15.90 36.76 39.32 39.94 40.01
15.89 36.76 39.34 39.94 40.04
15.88 36.76 39.35 39.94 40.06
- 15.87 36.75 39.37 39.94 40.07
+ 15.87 36.75 39.37 39.94 40.08
15.86 36.75 39.38 39.95 40.09
15.85 36.74 39.39 40.00 40.10
- 15.84 36.74 39.41 40.02 40.10
+ 15.84 36.74 39.41 40.02 40.11
15.83 36.74 39.43 39.98 40.11
15.82 36.73 39.44 39.96 40.13
15.81 36.73 39.44 39.96 40.14
@@ -76787,7 +77062,7 @@ Eritrea
15.74 36.67 39.45 39.91 40.14
15.73 36.66 39.45 39.91 40.14
15.72 36.66 39.45 39.92 40.14
- 15.71 36.65 39.45 39.92 40.14 40.23 40.29
+ 15.71 36.65 39.45 39.92 40.14 40.23 40.30
15.70 36.65 39.46 39.92 40.14 40.21 40.32
15.69 36.65 39.47 39.92 40.15 40.20 40.33
15.68 36.64 39.47 39.92 40.16 40.20 40.33
@@ -76798,19 +77073,19 @@ Eritrea
15.63 36.63 39.49 39.94 40.41
15.62 36.63 39.49 39.95 40.41
15.61 36.62 39.49 39.95 40.42
- 15.60 36.62 39.49 39.95 40.42
- 15.59 36.62 39.48 39.96 39.99 40.01 40.42
+ 15.60 36.62 39.49 39.96 40.42
+ 15.59 36.62 39.48 39.96 40.42
15.58 36.61 39.45 40.04 40.42
- 15.57 36.61 39.46 40.07 40.11 40.14 40.18 40.23 40.42
- 15.56 36.61 39.46 40.25 40.33 40.38 40.41
+ 15.57 36.61 39.46 40.07 40.11 40.14 40.18 40.23 40.41
+ 15.56 36.61 39.46 40.25 40.33 40.38 40.40
15.55 36.60 39.46 39.54 39.57
15.54 36.60 39.46 39.52 39.59
- 15.53 36.60 39.47 39.51 39.60
+ 15.53 36.60 39.47 39.50 39.60
15.52 36.60 39.60
15.51 36.60 39.61 39.86 39.88
- 15.50 36.60 39.62 39.85 39.89
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15.49 36.60 39.62 39.85 39.89
- 15.48 36.60 39.63 39.82 39.90
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15.47 36.60 39.63 39.82 39.91
15.46 36.60 39.63 39.79 39.92
15.45 36.60 39.64 39.79 39.93
@@ -76819,12 +77094,12 @@ Eritrea
15.42 36.57 39.64 39.78 39.97
15.41 36.57 39.65 39.76 39.99
15.40 36.56 39.65 39.76 40.00
- 15.39 36.56 39.65 39.76 40.02
- 15.38 36.55 39.66 39.76 40.04
- 15.37 36.55 39.66 39.76 40.06
+ 15.39 36.56 39.65 39.76 40.01
+ 15.38 36.55 39.66 39.76 40.03
+ 15.37 36.55 39.66 39.76 40.07
15.36 36.55 39.66 39.76 40.08
- 15.35 36.54 39.67 39.77 40.09
- 15.34 36.54 39.68 39.77 40.09
+ 15.35 36.54 39.67 39.76 40.08
+ 15.34 36.54 39.68 39.76 40.09
15.33 36.54 39.70 39.77 40.09
15.32 36.53 39.70 39.76 40.09
15.31 36.53 39.70 39.76 40.09
@@ -76834,7 +77109,7 @@ Eritrea
15.27 36.52 39.72 39.76 40.05
15.26 36.51 39.72 39.77 40.05
15.25 36.51 39.72 39.77 40.05
- 15.24 36.50 39.72 39.78 40.05
+ 15.24 36.50 39.72 39.77 39.79 39.81 40.05
15.23 36.49 39.72 39.81 40.06
15.22 36.48 39.72 39.82 40.06
15.21 36.47 39.71 39.82 40.06
@@ -76845,9 +77120,9 @@ Eritrea
15.16 36.42 39.71 39.83 40.09
15.15 36.42 39.71 39.82 40.09
15.14 36.41 39.70 39.81 40.10
- 15.13 36.41 39.70 39.81 40.10
- 15.12 36.41 39.72 39.81 40.11
- 15.11 36.41 39.72 39.81 40.11
+ 15.13 36.41 39.70 39.80 40.10
+ 15.12 36.41 39.71 39.80 40.11
+ 15.11 36.41 39.72 39.80 40.11
15.10 36.41 39.72 39.74 39.76 39.81 40.11
15.09 36.41 39.76 39.80 40.11
15.08 36.41 40.11
@@ -76857,15 +77132,15 @@ Eritrea
15.04 36.42 40.16
15.03 36.42 40.16
15.02 36.42 40.16 40.50 40.52
- 15.01 36.42 40.16 40.38 40.40 40.43 40.46 40.50 40.53
- 15.00 36.42 40.16 40.37 40.47 40.50 40.56
- 14.99 36.42 40.17 40.36 40.47 40.50 40.56
+ 15.01 36.42 40.16 40.37 40.39 40.43 40.46 40.50 40.53
+ 15.00 36.42 40.16 40.37 40.39 40.41 40.47 40.50 40.56
+ 14.99 36.42 40.17 40.36 40.39 40.41 40.47 40.50 40.56
14.98 36.42 40.20 40.36 40.56
14.97 36.42 40.22 40.35 40.56
14.96 36.42 40.24 40.34 40.61
14.95 36.43 40.27 40.33 40.62
- 14.94 36.43 40.29 40.31 40.63
- 14.93 36.43 40.63
+ 14.94 36.43 40.28 40.31 40.63
+ 14.93 36.43 40.28 40.30 40.63
14.92 36.43 40.63
14.91 36.43 40.63 40.65 40.69
14.90 36.43 40.70
@@ -76878,7 +77153,7 @@ Eritrea
14.83 36.44 37.89 37.91 40.74
14.82 36.44 37.88 37.92 40.74
14.81 36.44 37.88 37.92 40.74
- 14.80 36.44 37.87 37.93 40.74
+ 14.80 36.45 37.87 37.93 40.74
14.79 36.45 37.87 37.93 40.74
14.78 36.45 37.86 37.94 40.74
14.77 36.45 37.86 37.94 40.74
@@ -76886,7 +77161,7 @@ Eritrea
14.75 36.45 37.85 37.95 40.74
14.74 36.45 37.85 37.97 40.75
14.73 36.45 37.84 37.98 40.76 40.79 40.82
- 14.72 36.45 37.84 37.98 40.77 40.79 40.89
+ 14.72 36.46 37.84 37.98 40.77 40.79 40.89
14.71 36.46 37.83 37.99 40.91
14.70 36.46 37.83 38.01 40.92
14.69 36.46 37.82 38.04 40.94
@@ -76894,7 +77169,7 @@ Eritrea
14.67 36.46 37.81 38.09 41.07
14.66 36.46 37.81 38.12 38.17 38.21 41.13
14.65 36.46 37.80 38.22 41.16
- 14.64 36.46 37.80 38.22 41.17
+ 14.64 36.46 37.80 38.23 41.17
14.63 36.46 37.79 38.23 41.18
14.62 36.46 37.79 38.23 39.00 39.05 41.18
14.61 36.47 37.79 38.24 39.00 39.09 41.19
@@ -76910,7 +77185,7 @@ Eritrea
14.51 36.48 37.75 38.29 38.91 39.15 39.49 39.57 41.30
14.50 36.48 37.74 38.30 38.90 39.16 39.48 39.58 41.30
14.49 36.48 37.74 38.31 38.89 39.16 39.46 39.60 41.31
- 14.48 36.48 37.73 38.33 38.88 39.16 39.43 39.63 39.71 39.77 41.32
+ 14.48 36.48 37.73 38.33 38.88 39.16 39.43 39.63 39.70 39.77 41.32
14.47 36.48 37.73 38.34 38.85 39.17 39.28 39.31 39.39 39.79 41.32
14.46 36.49 37.73 38.36 38.81 39.17 39.26 39.81 41.33
14.45 36.49 37.72 38.38 38.78 39.18 39.25 39.82 41.33
@@ -76922,19 +77197,19 @@ Eritrea
14.39 36.49 37.12 37.34 37.69 40.26 41.37
14.38 36.50 37.11 37.34 37.69 40.27 41.38
14.37 36.50 37.11 37.35 37.68 40.28 41.39
- 14.36 36.50 37.10 37.36 37.68 40.29 41.40
- 14.35 36.50 37.10 37.37 37.67 40.31 41.41
- 14.34 36.50 37.10 37.38 37.67 40.32 41.41
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+ 14.35 36.50 37.10 37.37 37.67 40.31 41.40
+ 14.34 36.50 37.10 37.38 37.67 40.32 41.40
14.33 36.50 37.10 37.38 37.66 40.33 41.41
- 14.32 36.50 37.10 37.38 37.66 40.34 41.42
+ 14.32 36.50 37.10 37.38 37.66 40.34 41.41
14.31 36.50 36.74 36.82 37.10 37.38 37.66 40.35 41.42
14.30 36.50 36.72 36.85 37.10 37.38 37.65 40.36 41.43
14.29 36.51 36.63 36.89 37.10 37.38 37.65 40.37 41.44
14.28 36.51 36.61 36.95 37.09 37.40 37.64 40.39 41.45
- 14.27 36.51 36.56 36.95 37.08 37.41 37.64 40.40 41.47
- 14.26 36.51 36.56 36.96 37.07 37.43 37.64 40.41 41.48
- 14.25 36.51 36.55 36.97 37.02 37.44 37.63 40.42 41.49
- 14.24 37.44 37.63 40.44 41.50
+ 14.27 36.51 36.56 36.95 37.08 37.41 37.64 40.40 41.46
+ 14.26 36.51 36.56 36.96 37.07 37.43 37.64 40.41 41.47
+ 14.25 36.51 36.55 36.97 37.02 37.44 37.63 40.42 41.48
+ 14.24 37.44 37.63 40.44 41.49
14.23 37.44 37.63 40.46 41.50
14.22 37.45 37.62 40.48 41.51
14.21 37.45 37.62 40.50 41.51
@@ -76972,7 +77247,7 @@ Eritrea
13.89 41.00 41.85
13.88 41.01 41.93
13.87 41.02 41.95
- 13.86 41.03 41.97
+ 13.86 41.03 41.96
13.85 41.04 41.98
13.84 41.04 41.99
13.83 41.05 41.99
@@ -76992,7 +77267,7 @@ Eritrea
13.69 41.13 42.09
13.68 41.13 42.10
13.67 41.14 42.10 42.15 42.19
- 13.66 41.14 42.11 42.13 42.21
+ 13.66 41.14 42.10 42.12 42.21
13.65 41.15 42.22
13.64 41.16 42.23
13.63 41.16 42.24
@@ -77035,10 +77310,10 @@ Eritrea
13.26 41.66 42.38
13.25 41.67 42.38
13.24 41.69 42.38 42.51 42.54
- 13.23 41.70 42.39 42.51 42.54
+ 13.23 41.70 42.39 42.50 42.54
13.22 41.71 42.41 42.50 42.54
13.21 41.72 42.43 42.49 42.55
- 13.20 41.73 42.57
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13.19 41.74 42.57
13.18 41.75 42.58
13.17 41.75 42.59
@@ -77053,9 +77328,9 @@ Eritrea
13.08 41.81 42.66
13.07 41.81 42.70
13.06 41.82 42.71
- 13.05 41.82 42.73
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+ 13.03 41.83 42.73
13.02 41.84 42.74
13.01 41.84 42.74
13.00 41.85 42.74
@@ -77122,7 +77397,7 @@ Eritrea
12.39 42.61 42.75
12.38 42.62 42.74
12.37 42.64 42.73
- 12.36 42.65 42.71
+ 12.36 42.65 42.70
12.35 42.66 42.69
Estonia
59.68 25.68 25.71
@@ -77140,15 +77415,15 @@ Estonia
59.56 24.47 24.56 24.76 24.85 25.48 26.44 26.55 26.69
59.55 24.47 24.56 24.76 24.87 25.49 26.48 26.52 26.71
59.54 24.47 24.56 24.76 24.88 25.11 25.17 25.42 26.73
- 59.53 24.49 24.55 24.76 24.90 25.09 25.23 25.40 26.74
- 59.52 24.77 24.92 24.97 25.06 25.09 25.30 25.39 26.76
- 59.51 24.77 25.37 25.39 26.78
- 59.50 24.65 24.70 24.77 26.80
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+ 59.51 24.77 25.37 25.39 26.79
+ 59.50 24.65 24.70 24.77 26.81
59.49 24.65 24.71 24.79 26.82 28.00 28.02
59.48 24.32 24.44 24.61 24.72 24.79 26.85 27.99 28.03
- 59.47 24.32 24.45 24.53 24.56 24.61 24.72 24.79 26.90 27.99 28.06
- 59.46 24.31 24.47 24.52 24.58 24.61 24.74 24.77 26.93 27.33 27.45 27.98 28.09
- 59.45 24.31 27.53 27.97 28.10
+ 59.47 24.31 24.45 24.53 24.58 24.61 24.72 24.79 26.90 27.99 28.06
+ 59.46 24.31 24.47 24.52 27.03 27.33 27.45 27.98 28.09
+ 59.45 24.30 27.53 27.97 28.10
59.44 24.30 27.64 27.95 28.11
59.43 24.30 27.76 27.93 28.12
59.42 24.22 27.84 27.89 28.12
@@ -77167,7 +77442,7 @@ Estonia
59.29 23.74 23.87 23.90 28.09
59.28 23.72 27.93
59.27 23.71 27.90
- 59.26 23.63 23.68 23.71 27.90
+ 59.26 23.61 23.68 23.71 27.90
59.25 23.60 27.90
59.24 23.50 23.53 23.58 27.90
59.23 23.48 27.89
@@ -77189,15 +77464,15 @@ Estonia
59.07 22.56 22.72 23.43 27.80
59.06 22.56 22.72 23.42 27.79
59.05 22.55 22.72 23.12 23.24 23.41 27.78
- 59.04 22.54 22.71 23.10 23.36 23.41 27.77
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59.03 22.49 22.72 23.10 23.37 23.39 27.76
59.02 22.47 22.73 23.10 27.75
59.01 22.47 22.86 23.10 27.74
59.00 22.47 22.91 23.10 27.73
- 58.99 22.43 22.95 23.11 23.40 23.42 27.73
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+ 58.98 22.38 22.95 23.11 23.40 23.44 27.72
58.97 22.23 22.96 23.12 23.39 23.49 27.71
- 58.96 22.04 22.96 23.13 23.22 23.25 23.32 23.35 23.38 23.52 27.70
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58.95 22.04 22.96 23.15 23.20 23.43 27.68
58.94 22.03 22.96 23.42 27.66
58.93 22.03 22.97 23.41 27.64
@@ -77209,45 +77484,45 @@ Estonia
58.87 22.17 22.26 22.36 23.04 23.44 27.51
58.86 22.38 23.04 23.44 27.49
58.85 22.40 23.05 23.45 27.48
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58.81 22.43 22.89 23.00 23.03 23.45 27.46
58.80 22.43 22.89 23.44 27.45
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58.73 22.47 22.70 23.51 27.43
58.72 22.45 22.70 23.51 27.43
58.71 22.45 22.69 23.49 27.43
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58.69 22.47 22.66 23.16 23.22 23.48 27.44
58.68 22.49 22.64 23.14 23.26 23.48 27.44
58.67 22.52 22.59 23.12 23.31 23.48 27.45
58.66 23.12 23.34 23.48 27.45
58.65 23.12 23.35 23.48 27.45
58.64 22.56 22.59 23.11 23.35 23.49 27.46
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58.59 22.31 23.38 23.49 27.48
58.58 22.29 23.39 23.48 27.48
58.57 22.27 23.40 23.48 27.49
58.56 22.27 23.41 23.48 27.49
58.55 22.17 22.22 22.27 23.12 23.14 23.41 23.49 27.50
58.54 22.17 22.23 22.27 23.13 23.16 23.41 23.50 23.53 23.56 27.50
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58.52 21.82 21.85 21.91 22.00 22.13 22.24 22.27 23.25 23.33 23.38 23.59 27.51
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58.49 21.83 22.04 22.09 23.30 23.67 27.52
58.48 21.84 22.05 22.08 23.32 23.67 27.53
58.47 21.85 22.06 22.08 23.33 23.67 27.53
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58.44 21.90 23.15 23.18 23.34 23.66 27.54
58.43 21.91 23.14 23.20 23.28 23.30 23.33 23.66 27.55
@@ -77258,31 +77533,31 @@ Estonia
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58.09 22.07 22.12 22.14 22.27 23.94 24.01 24.45 27.64
58.08 22.06 22.26 23.96 23.99 24.45 27.64
@@ -77291,9 +77566,9 @@ Estonia
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@@ -77303,7 +77578,7 @@ Estonia
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@@ -77313,7 +77588,7 @@ Estonia
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@@ -77337,8 +77612,8 @@ Estonia
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@@ -77367,7 +77642,7 @@ Ethiopia
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@@ -77644,10 +77919,10 @@ Ethiopia
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@@ -78276,11 +78551,11 @@ Ethiopia
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Faroe Islands
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@@ -78710,11 +78991,11 @@ Faroe Islands
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@@ -78768,14 +79049,14 @@ Fiji
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@@ -79054,15 +79350,15 @@ Finland
69.80 26.30 28.47
69.79 26.29 28.51
69.78 26.27 28.57
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69.68 25.97 29.14
69.67 25.95 29.15
69.66 25.95 29.16
@@ -79107,24 +79403,24 @@ Finland
69.27 21.18 21.67 25.75 29.03
69.26 21.14 21.69 25.74 29.01
69.25 21.10 21.70 25.74 28.99
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69.06 20.64 21.01 21.09 21.97 25.73 28.91
69.05 20.62 21.06 21.08 21.99 25.73 28.93
69.04 20.61 22.00 25.74 28.95
@@ -79213,14 +79509,14 @@ Finland
68.21 23.13 28.67
68.20 23.13 28.69
68.19 23.13 28.71
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68.10 23.33 29.26
68.09 23.33 29.32
68.08 23.34 29.34
@@ -79385,10 +79681,10 @@ Finland
66.49 23.68 29.53
66.48 23.66 29.54
66.47 23.65 29.54
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66.45 23.64 29.55
66.44 23.63 29.55
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66.42 23.63 29.56
66.41 23.63 29.56
66.40 23.64 29.56
@@ -79453,8 +79749,8 @@ Finland
65.81 24.15 30.09
65.80 24.15 30.09
65.79 24.16 30.10
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65.76 24.19 24.24 24.34 24.43 24.54 30.11
65.75 24.37 24.41 24.54 30.11
65.74 24.54 30.11
@@ -79467,7 +79763,7 @@ Finland
65.67 24.66 30.12
65.66 24.66 30.12
65.65 24.66 29.97 30.03 30.12
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65.63 24.66 24.74 24.89 29.81
65.62 24.66 24.72 24.91 29.75
65.61 24.92 29.75
@@ -79482,8 +79778,8 @@ Finland
65.52 25.25 29.80
65.51 25.27 29.78
65.50 25.29 29.76
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65.47 25.34 29.73
65.46 25.34 29.73
65.45 25.34 29.72
@@ -79504,14 +79800,14 @@ Finland
65.30 25.29 29.72
65.29 25.28 29.70
65.28 25.28 29.68
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65.19 25.26 29.84
65.18 25.24 29.84
65.17 25.22 29.84
@@ -79521,33 +79817,33 @@ Finland
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64.94 24.69 24.77 25.19 29.62
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64.91 25.00 25.13 25.23 29.64
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64.89 24.91 25.18 25.29 29.66
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64.87 24.75 25.19 25.34 29.67
64.86 24.72 25.20 25.34 29.68
64.85 24.72 25.23 25.34 29.69
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64.83 24.66 25.26 25.30 29.73
64.82 24.65 29.75
64.81 24.52 24.60 24.65 29.77
@@ -79559,8 +79855,8 @@ Finland
64.75 24.52 30.13
64.74 24.52 30.12
64.73 24.52 30.12
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64.70 24.45 30.17
64.69 24.43 30.18
64.68 24.41 30.18
@@ -79581,7 +79877,7 @@ Finland
64.53 24.29 29.99
64.52 24.27 30.00
64.51 24.27 30.02
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64.49 24.20 30.07
64.48 24.20 30.08
64.47 24.20 30.08
@@ -79614,10 +79910,10 @@ Finland
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64.18 23.70 30.56
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64.13 23.63 30.57
64.12 23.62 30.57
64.11 23.56 30.58
@@ -79625,12 +79921,12 @@ Finland
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64.07 23.57 30.59
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64.05 23.37 23.46 23.49 23.52 23.59 30.59
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64.00 23.35 30.55
63.99 23.35 30.53
63.98 23.35 30.51
@@ -79658,7 +79954,7 @@ Finland
63.76 22.67 22.83 22.89 30.13
63.75 22.67 22.83 22.86 30.08
63.74 22.67 22.82 22.86 30.04
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63.72 22.69 30.01
63.71 22.57 22.61 22.64 22.78 22.82 30.03
63.70 22.57 22.70 22.85 30.05
@@ -79683,7 +79979,7 @@ Finland
63.51 22.26 22.34 22.42 30.44
63.50 22.26 22.35 22.42 30.45
63.49 22.26 22.39 22.41 30.46
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63.47 22.19 30.50
63.46 22.18 30.54
63.45 22.18 30.58
@@ -79698,23 +79994,23 @@ Finland
63.36 21.29 21.37 21.95 22.09 22.29 30.87
63.35 21.26 21.38 21.93 22.09 22.21 22.23 22.30 30.88
63.34 21.22 21.38 21.93 22.01 22.03 22.07 22.20 22.24 22.32 30.90
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63.32 21.21 21.38 21.93 22.24 22.34 30.93
63.31 21.21 21.37 21.97 22.29 22.34 30.95
63.30 21.23 21.36 21.96 22.30 22.33 30.97
63.29 21.06 21.10 21.17 21.35 21.96 30.99
63.28 21.06 21.25 21.30 21.34 21.96 31.03
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63.26 21.07 21.25 21.30 21.42 21.84 21.90 21.97 31.09
63.25 21.07 21.22 21.29 21.43 21.74 21.78 21.80 21.90 22.03 31.13
63.24 21.08 21.21 21.28 21.43 21.53 21.57 21.72 21.90 22.00 22.07 22.09 31.16
63.23 21.08 21.24 21.28 21.43 21.51 21.59 21.69 21.89 22.00 31.19
63.22 21.09 21.42 21.49 21.61 21.65 21.89 22.00 31.21
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63.20 21.12 21.43 21.48 21.90 21.96 31.23
63.19 21.12 21.43 21.48 21.90 21.94 31.23
63.18 21.12 21.43 21.49 21.92 21.94 31.24
- 63.17 21.13 21.33 21.36 21.39 21.50 31.24
+ 63.17 21.13 21.33 21.50 31.24
63.16 21.19 21.32 21.49 31.24
63.15 21.20 21.32 21.49 31.24
63.14 21.22 21.31 21.49 31.25
@@ -79723,7 +80019,7 @@ Finland
63.11 21.51 31.27
63.10 21.52 31.28
63.09 21.54 31.30
- 63.08 21.48 21.51 21.55 31.34
+ 63.08 21.48 21.51 21.54 31.34
63.07 21.48 31.36
63.06 21.47 31.38
63.05 21.43 31.39
@@ -79740,8 +80036,8 @@ Finland
62.94 21.13 21.23 21.41 31.53
62.93 21.15 21.22 21.40 31.53
62.92 21.39 31.55
- 62.91 21.39 31.57
- 62.90 21.39 31.57
+ 62.91 21.38 31.57
+ 62.90 21.38 31.57
62.89 21.38 31.57
62.88 21.37 31.56
62.87 21.23 21.30 21.35 31.55
@@ -79750,7 +80046,7 @@ Finland
62.84 21.21 31.52
62.83 21.21 31.51
62.82 21.20 31.50
- 62.81 21.20 31.49
+ 62.81 21.19 31.49
62.80 21.11 31.48
62.79 21.10 31.47
62.78 21.10 31.46
@@ -79760,15 +80056,15 @@ Finland
62.74 21.09 31.43
62.73 21.10 31.42
62.72 21.13 31.41
- 62.71 21.14 31.41
- 62.70 21.12 31.40
+ 62.71 21.13 31.41
+ 62.70 21.10 31.40
62.69 21.08 31.40
62.68 21.06 31.39
62.67 21.06 31.39
62.66 21.06 31.38
62.65 21.06 31.38
62.64 21.06 31.37
- 62.63 21.06 31.36
+ 62.63 21.05 31.36
62.62 21.05 31.36
62.61 21.05 31.35
62.60 21.05 31.34
@@ -79779,7 +80075,7 @@ Finland
62.55 21.11 31.29
62.54 21.11 31.28
62.53 21.12 31.28
- 62.52 21.12 31.27
+ 62.52 21.11 31.27
62.51 21.11 31.27
62.50 21.10 31.26
62.49 21.10 31.25
@@ -79787,7 +80083,7 @@ Finland
62.47 21.10 31.21
62.46 21.10 31.18
62.45 21.10 31.16
- 62.44 21.10 31.15
+ 62.44 21.11 31.15
62.43 21.12 31.14
62.42 21.12 31.13
62.41 21.12 31.12
@@ -79795,10 +80091,10 @@ Finland
62.39 21.12 21.14 21.17 31.08
62.38 21.17 31.06
62.37 21.18 31.05
- 62.36 21.18 21.23 21.25 31.03
- 62.35 21.18 21.22 21.25 31.01
- 62.34 21.18 21.22 21.25 30.99
- 62.33 21.18 21.22 21.26 30.98
+ 62.36 21.17 21.23 21.25 31.03
+ 62.35 21.17 21.22 21.25 31.01
+ 62.34 21.17 21.22 21.25 30.99
+ 62.33 21.17 21.22 21.26 30.98
62.32 21.18 21.22 21.32 30.96
62.31 21.32 30.96
62.30 21.32 30.95
@@ -79826,61 +80122,61 @@ Finland
62.08 21.27 30.53
62.07 21.27 30.52
62.06 21.26 30.51
- 62.05 21.26 30.49
+ 62.05 21.25 30.49
62.04 21.25 30.47
- 62.03 21.25 30.45
+ 62.03 21.24 30.45
62.02 21.24 30.43
62.01 21.23 30.41
62.00 21.23 30.39
61.99 21.22 30.37
61.98 21.22 30.35
61.97 21.22 30.33
- 61.96 21.25 30.32
+ 61.96 21.25 30.31
61.95 21.26 30.30
61.94 21.26 30.29
- 61.93 21.28 30.28
+ 61.93 21.28 30.27
61.92 21.30 30.26
- 61.91 21.38 30.25
- 61.90 21.38 30.24
+ 61.91 21.37 30.25
+ 61.90 21.38 30.23
61.89 21.38 30.22
61.88 21.38 30.21
- 61.87 21.38 30.20
+ 61.87 21.38 30.19
61.86 21.39 30.18
61.85 21.40 30.17
- 61.84 21.41 30.16
+ 61.84 21.41 30.15
61.83 21.43 30.14
61.82 21.43 30.13
- 61.81 21.43 30.12
+ 61.81 21.43 30.11
61.80 21.44 30.10
61.79 21.47 30.09
- 61.78 21.46 30.08
+ 61.78 21.46 30.07
61.77 21.46 30.06
- 61.76 21.46 30.05
- 61.75 21.46 30.04
- 61.74 21.46 30.02
+ 61.76 21.45 30.05
+ 61.75 21.45 30.03
+ 61.74 21.45 30.02
61.73 21.46 30.01
- 61.72 21.47 30.00
+ 61.72 21.47 29.99
61.71 21.49 29.98
61.70 21.50 29.96
61.69 21.50 29.94
61.68 21.51 29.92
- 61.67 21.52 29.90
+ 61.67 21.53 29.90
61.66 21.52 29.88
61.65 21.47 29.86
61.64 21.46 29.84
- 61.63 21.45 29.83
- 61.62 21.45 21.53 21.56 29.82
- 61.61 21.45 21.53 21.58 29.82
+ 61.63 21.44 29.83
+ 61.62 21.44 21.53 21.56 29.82
+ 61.61 21.44 21.53 21.58 29.82
61.60 21.48 21.51 21.58 29.81
61.59 21.59 29.80
- 61.58 21.59 29.79
- 61.57 21.45 21.54 21.60 29.77
+ 61.58 21.49 21.53 21.59 29.79
+ 61.57 21.45 21.57 21.60 29.77
61.56 21.45 29.75
61.55 21.45 29.73
61.54 21.45 29.71
- 61.53 21.46 29.70
- 61.52 21.47 29.68
- 61.51 21.49 29.66
+ 61.53 21.45 29.70
+ 61.52 21.46 29.68
+ 61.51 21.48 29.66
61.50 21.50 29.64
61.49 21.41 29.63
61.48 21.41 29.61
@@ -79897,14 +80193,14 @@ Finland
61.37 21.49 29.42
61.36 21.51 29.40
61.35 21.51 29.38
- 61.34 21.52 29.36
- 61.33 21.52 29.34
+ 61.34 21.51 29.36
+ 61.33 21.51 29.34
61.32 21.52 29.32
61.31 21.52 29.31
61.30 21.53 29.29
61.29 21.53 29.28
61.28 21.49 29.27
- 61.27 21.49 29.26
+ 61.27 21.48 29.26
61.26 21.47 29.25
61.25 21.46 29.24
61.24 21.46 29.22
@@ -79924,7 +80220,7 @@ Finland
61.10 21.44 28.87
61.09 21.44 28.84
61.08 21.44 28.81
- 61.07 21.37 28.79
+ 61.07 21.28 28.79
61.06 21.28 28.78
61.05 21.28 28.76
61.04 21.28 28.75
@@ -79961,15 +80257,15 @@ Finland
60.73 21.39 28.14
60.72 21.41 28.12
60.71 21.41 28.11
- 60.70 21.42 28.09
- 60.69 21.34 21.39 21.42 28.08
- 60.68 21.34 28.07
- 60.67 21.34 28.05
- 60.66 21.34 28.04
- 60.65 21.24 21.28 21.35 28.02
- 60.64 21.23 21.28 21.36 28.01
- 60.63 21.20 21.28 21.37 27.99
- 60.62 21.20 21.30 21.39 27.97
+ 60.70 21.34 21.37 21.42 28.09
+ 60.69 21.34 28.08
+ 60.68 21.34 28.06
+ 60.67 21.34 28.04
+ 60.66 21.34 28.03
+ 60.65 21.24 21.28 21.35 28.01
+ 60.64 21.23 21.28 21.35 28.00
+ 60.63 21.20 21.29 21.36 27.99
+ 60.62 21.20 21.30 21.38 27.97
60.61 21.20 21.30 21.40 27.95
60.60 21.20 21.30 21.40 27.93
60.59 21.21 21.29 21.39 27.91
@@ -79978,15 +80274,15 @@ Finland
60.56 21.21 21.30 21.32 21.71 21.79 27.85
60.55 21.21 21.47 21.50 21.67 21.79 27.76 27.78 27.83
60.54 21.21 21.29 21.31 21.48 21.51 21.67 21.79 27.76 27.79 27.81
- 60.53 21.22 21.49 21.53 21.67 21.73 21.77 21.79 27.75
- 60.52 21.24 21.49 21.54 21.67 21.71 21.77 21.79 27.03 27.05 27.76
- 60.51 21.24 21.49 21.56 21.66 21.70 27.03 27.06 27.10 27.12 27.76
+ 60.53 21.22 21.49 21.52 21.67 21.73 21.77 21.79 27.75
+ 60.52 21.24 21.49 21.54 21.67 21.71 27.03 27.05 27.76
+ 60.51 21.24 21.49 21.55 21.66 21.70 27.03 27.06 27.10 27.12 27.76
60.50 21.24 21.34 21.36 21.47 21.54 21.66 21.69 21.86 21.92 27.03 27.16 27.19 27.22 27.76
- 60.49 21.24 21.33 21.36 21.47 21.54 21.66 21.68 21.76 21.78 21.87 21.92 27.02 27.23 27.76
+ 60.49 21.24 21.33 21.36 21.47 21.54 21.66 21.68 21.87 21.92 27.02 27.23 27.76
60.48 21.24 21.33 21.37 21.47 21.54 21.65 21.68 21.75 21.77 21.88 21.92 27.01 27.34 27.50 27.53 27.75
- 60.47 21.25 21.33 21.38 21.45 21.56 21.63 21.67 21.73 21.77 21.88 21.96 27.00 27.37 27.51 27.55 27.64 27.66 27.73
- 60.46 21.40 21.45 21.67 21.72 21.77 21.88 21.97 26.97 27.40 27.51 27.57 27.64
- 60.45 21.67 21.72 21.78 21.91 21.99 26.75 26.78 26.89 26.91 26.97 27.43 27.51
+ 60.47 21.28 21.33 21.38 21.45 21.56 21.63 21.67 21.73 21.77 21.88 21.96 27.00 27.37 27.51 27.55 27.63 27.66 27.73
+ 60.46 21.40 21.45 21.67 21.72 21.77 21.88 21.97 26.97 27.40 27.51 27.57 27.63
+ 60.45 21.67 21.72 21.78 21.91 22.00 26.75 26.78 26.89 26.91 26.97 27.43 27.51
60.44 21.67 21.71 21.78 21.91 22.00 26.75 26.78 26.85 26.92 26.97 27.47 27.51
60.43 21.78 21.94 22.01 26.75 26.94 26.97
60.42 21.79 21.95 22.03 22.08 22.10 26.48 26.50 26.74
@@ -79994,50 +80290,50 @@ Finland
60.40 21.30 21.33 21.78 21.96 22.21 26.05 26.10 26.46 26.49 26.64 26.67 26.71
60.39 21.29 21.35 21.77 21.96 22.13 22.21 22.23 26.05 26.12 26.18 26.22 26.43 26.49 26.61
60.38 21.28 21.36 21.77 21.96 22.11 26.06 26.13 26.17 26.30 26.43 26.50 26.57
- 60.37 21.28 21.36 21.77 21.99 22.10 22.37 22.45 26.08 26.31 26.35 26.51 26.56
- 60.36 21.28 21.36 21.78 22.00 22.09 22.30 22.36 22.41 22.45 26.09 26.33 26.35 26.52 26.55
+ 60.37 21.28 21.36 21.77 21.99 22.10 22.37 22.45 26.07 26.31 26.35 26.51 26.56
+ 60.36 21.28 21.36 21.78 22.00 22.09 22.30 22.36 22.41 22.45 26.08 26.33 26.35 26.52 26.55
60.35 21.29 21.36 21.80 22.00 22.09 22.30 22.33 22.42 22.54 26.11
60.34 21.32 21.36 21.82 22.00 22.09 22.29 22.31 22.47 22.53 26.11
60.33 21.88 22.00 22.16 22.25 22.30 22.48 22.53 25.91 25.99 26.11
- 60.32 21.86 22.00 22.09 22.27 22.30 22.48 22.52 25.62 25.64 25.90 26.01 26.11
- 60.31 21.86 21.99 22.07 25.57 25.64 25.90 26.02 26.11
- 60.30 21.86 22.01 22.07 25.55 25.57 25.60 25.64 25.90 26.02 26.11
- 60.29 21.86 22.01 22.06 25.62 25.64 25.91 26.03 26.10
+ 60.32 21.86 22.00 22.09 22.27 22.30 22.48 22.52 25.90 26.01 26.11
+ 60.31 21.86 21.99 22.07 25.57 25.64 25.89 26.02 26.11
+ 60.30 21.86 22.01 22.07 25.55 25.57 25.60 25.63 25.90 26.02 26.10
+ 60.29 21.86 22.01 22.06 25.91 26.03 26.10
60.28 21.86 22.01 22.06 22.96 22.99 25.92 26.03 26.07
- 60.27 21.57 21.61 21.87 22.00 22.06 22.35 22.44 25.93
+ 60.27 21.57 21.61 21.87 22.00 22.06 22.34 22.44 25.93
60.26 21.56 21.63 21.91 21.95 22.06 22.34 22.44 25.93
- 60.25 21.56 21.63 22.07 22.10 22.12 22.34 22.43 22.81 22.83 25.53 25.55 25.94
+ 60.25 21.56 21.63 22.07 22.34 22.43 22.81 22.83 25.53 25.55 25.94
60.24 21.55 21.63 22.14 22.17 22.19 22.30 22.43 22.79 22.81 25.33 25.35 25.52 25.56 25.82 25.87 25.94
60.23 21.55 21.63 22.21 22.30 22.43 25.31 25.35 25.52 25.58 25.69 25.72 25.79 25.88 25.94
- 60.22 21.32 21.36 21.55 21.62 22.03 22.06 22.20 22.30 22.43 22.48 22.53 25.20 25.59 25.68 25.81 25.88
- 60.21 21.27 21.36 21.55 21.61 22.00 22.07 22.19 22.30 22.34 22.38 22.42 22.48 22.51 25.21 25.59 25.66 25.80 25.88
+ 60.22 21.32 21.36 21.55 21.62 22.03 22.06 22.20 22.30 22.43 22.48 22.52 25.20 25.59 25.68 25.81 25.88
+ 60.21 21.27 21.36 21.55 21.61 22.00 22.07 22.19 22.30 22.34 22.38 22.42 22.48 22.51 25.21 25.59 25.65 25.80 25.88
60.20 21.26 21.45 21.73 21.87 21.97 22.08 22.19 22.39 22.42 22.47 22.51 25.21 25.59 25.64 25.80 25.88
60.19 21.26 21.45 21.71 21.89 21.94 22.08 22.19 22.39 22.42 25.21 25.62 25.64 25.80 25.87
- 60.18 21.26 21.45 21.56 21.60 21.69 21.89 21.92 22.08 22.20 22.39 22.41 25.20 25.81 25.86
- 60.17 21.29 21.45 21.54 21.64 21.69 21.89 21.92 22.07 22.22 22.25 22.28 22.38 22.41 25.19
- 60.16 21.30 21.40 21.52 21.66 21.69 21.89 21.92 22.05 22.28 22.37 22.40 25.15
- 60.15 21.37 21.39 21.50 21.66 21.69 21.87 21.93 22.04 22.27 22.36 22.40 25.07
- 60.14 21.48 21.66 21.69 21.87 21.92 22.04 22.27 22.34 22.40 24.97 25.00 25.06
- 60.13 21.48 21.65 21.68 21.83 21.91 22.03 22.27 22.34 22.40 24.80 24.83 24.96 25.02 25.05
- 60.12 21.47 21.64 21.68 21.81 21.91 22.02 22.41 24.75 24.85 24.91
- 60.11 21.47 21.64 21.68 21.80 21.91 22.02 22.41 24.61 24.63 24.69
+ 60.18 21.26 21.45 21.55 21.60 21.69 21.89 21.92 22.08 22.20 22.39 22.41 25.20 25.81 25.86
+ 60.17 21.29 21.45 21.53 21.64 21.69 21.89 21.92 22.06 22.22 22.25 22.28 22.38 22.41 25.19
+ 60.16 21.30 21.40 21.51 21.66 21.69 21.89 21.92 22.04 22.28 22.37 22.40 25.15
+ 60.15 21.37 21.39 21.49 21.66 21.69 21.87 21.93 22.04 22.27 22.36 22.40 25.07
+ 60.14 21.48 21.66 21.69 21.87 21.92 22.04 22.27 22.34 22.40 24.97 25.00 25.07
+ 60.13 21.48 21.65 21.68 21.83 21.91 22.03 22.27 22.34 22.40 24.80 24.83 24.96 25.01 25.04
+ 60.12 21.47 21.64 21.68 21.81 21.91 22.02 22.41 24.75
+ 60.11 21.47 21.64 21.68 21.80 21.91 22.02 22.41 24.61 24.63 24.68
60.10 21.47 21.64 21.70 21.77 21.92 22.01 22.41 24.61 24.63 24.68
- 60.09 21.48 21.63 22.36 22.38 22.40 24.61 24.64 24.68
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60.08 21.50 21.53 22.34 24.61
60.07 22.33 22.96 22.98 24.60
60.06 22.33 22.81 22.84 22.93 22.98 24.60
- 60.05 22.33 22.79 22.84 22.93 22.98 24.30 24.35 24.60
- 60.04 22.33 22.77 22.84 22.92 23.00 24.30 24.34 24.60
- 60.03 22.33 22.76 22.84 22.92 23.02 24.28 24.32 24.58
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+ 60.03 22.33 22.76 22.84 22.92 23.02 24.28 24.32 24.56
60.02 22.34 22.76 22.84 22.91 23.04 23.16 23.21 24.19 24.21 24.26 24.30 24.54
- 60.01 22.35 22.75 22.84 22.90 23.20 24.09 24.12 24.19 24.30 24.52
- 60.00 22.35 22.75 22.84 22.89 23.16 23.98 24.00 24.04 24.15 24.18 24.30 24.51
- 59.99 22.36 22.54 22.56 22.62 22.66 22.74 22.86 22.88 23.11 23.97 24.01 24.03 24.30 24.38 24.40 24.49
- 59.98 22.37 22.39 22.42 22.48 22.59 22.61 22.67 22.69 23.10 23.95 24.30 24.33 24.40 24.48
+ 60.01 22.34 22.75 22.84 22.90 23.20 24.09 24.12 24.19 24.30 24.52
+ 60.00 22.35 22.54 22.56 22.75 22.84 22.89 23.16 24.04 24.15 24.18 24.30 24.51
+ 59.99 22.36 22.53 22.56 22.62 22.66 22.74 22.86 22.88 23.11 23.97 24.01 24.03 24.30 24.34 24.36 24.38 24.40 24.49
+ 59.98 22.37 22.39 22.42 22.48 22.59 22.61 22.67 22.69 23.10 23.95 24.30 24.32 24.40 24.48
59.97 22.59 22.61 23.10 23.93
- 59.96 23.09 23.40 23.42 23.93
- 59.95 23.09 23.39 23.42 23.53 23.58 23.93
- 59.94 23.09 23.38 23.42 23.48 23.59 23.69 23.78 23.81 23.83 23.93
+ 59.96 23.09 23.93
+ 59.95 23.09 23.39 23.41 23.53 23.58 23.93
+ 59.94 23.09 23.38 23.41 23.48 23.59 23.69 23.78 23.81 23.83 23.93
59.93 23.09 23.37 23.86 23.90
59.92 23.09 23.13 23.15 23.36
59.91 23.09 23.12 23.15 23.34
@@ -80064,7 +80360,7 @@ Finland
60.40 19.81 19.91
60.39 19.80 19.92
60.38 19.79 19.92
- 60.37 19.78 19.92 19.94 19.99 20.01 20.03 20.74 20.79
+ 60.37 19.78 19.92 19.94 19.98 20.01 20.03 20.74 20.79
60.36 19.76 20.10 20.73 20.80
60.35 19.76 20.12 20.73 20.80
60.34 19.76 20.15 20.72 20.80
@@ -80080,32 +80376,34 @@ Finland
60.24 19.52 19.78 19.80 20.26 20.33 20.45 20.77 20.86
60.23 19.52 20.25 20.33 20.45 20.65 20.70 20.78 20.85
60.22 19.52 20.24 20.33 20.44 20.65 20.71 20.78 20.82
- 60.21 19.52 20.24 20.34 20.43 20.65 20.72
- 60.20 19.52 20.24 20.37 20.42 20.65 20.72
- 60.19 19.50 20.24 20.37 20.41 20.65 20.72
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60.18 19.50 20.21 20.37 20.40 20.66 20.71
60.17 19.50 20.05 20.07 20.19
60.16 19.50 20.05 20.08 20.18 20.64 20.66
- 60.15 19.50 20.05 20.14 20.18 20.21 20.28 20.62 20.67
- 60.14 19.50 19.61 19.63 20.04 20.20 20.29 20.62 20.69
- 60.13 19.51 19.61 19.70 20.04 20.19 20.30 20.62 20.69
- 60.12 19.53 19.60 19.71 20.04 20.19 20.30 20.62 20.69
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+ 60.13 19.51 19.60 19.70 20.04 20.19 20.30 20.62 20.69
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60.11 19.55 19.58 19.71 20.05 20.18 20.30 20.63 20.69
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- 60.08 19.74 19.88 19.91 20.06 20.18 20.28 20.50 20.55
- 60.07 19.74 19.78 19.81 19.87 19.91 19.96 20.01 20.05 20.19 20.28 20.43 20.55
- 60.06 19.75 19.77 19.82 19.85 19.92 19.96 20.22 20.28 20.41 20.61
- 60.05 19.92 19.96 20.24 20.28 20.39 20.62
- 60.04 19.92 19.96 20.39 20.62
- 60.03 19.93 19.95 20.38 20.62
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+ 59.98 20.09 20.22 20.27 20.45
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@@ -80126,14 +80424,14 @@ France
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@@ -80994,13 +81292,13 @@ France
France: Corsica
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@@ -81021,19 +81319,19 @@ France: Corsica
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42.36 8.53 9.54
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42.34 8.54 9.55
42.33 8.54 9.55
- 42.32 8.54 8.57 8.59 9.56
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- 42.28 8.65 9.57
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42.21 8.54 9.56
42.20 8.55 9.56
42.19 8.55 9.56
42.18 8.55 9.56
42.17 8.55 9.56
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42.12 8.57 9.56
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42.10 8.63 9.56
42.09 8.64 9.55
42.08 8.70 9.54
@@ -81132,7 +81430,7 @@ France: Corsica
41.65 8.82 9.39
41.64 8.79 9.38
41.63 8.78 9.38
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41.61 8.77 9.35
41.60 8.76 9.36
41.59 8.76 9.36
@@ -81142,15 +81440,15 @@ France: Corsica
41.55 8.78 9.35
41.54 8.78 9.32
41.53 8.81 9.30
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41.50 8.86 9.28
41.49 8.89 9.28
41.48 8.91 9.28
41.47 8.92 9.28
41.46 9.00 9.28
41.45 9.00 9.28
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41.43 9.09 9.26
41.42 9.09 9.26
41.41 9.08 9.26
@@ -81167,72 +81465,68 @@ France: Saint Barthelemy
17.90 -62.87 -62.78
17.89 -62.87 -62.78
17.88 -62.86 -62.79
- 17.87 -62.84 -62.80
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France: Saint Martin
18.13 -63.04 -63.00
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18.11 -63.08 -63.00
18.10 -63.08 -63.00
18.09 -63.09 -63.00
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18.07 -63.15 -63.00
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French Guiana
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5.35 -54.18 -52.81
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5.28 -54.26 -52.75
5.27 -54.27 -52.74
5.26 -54.28 -52.72
@@ -81264,9 +81558,9 @@ French Guiana
5.00 -54.46 -52.41
4.99 -54.46 -52.40
4.98 -54.46 -52.39
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4.94 -54.46 -52.26
4.93 -54.48 -52.26
4.92 -54.49 -52.25
@@ -81285,10 +81579,10 @@ French Guiana
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4.72 -54.47 -52.03
4.71 -54.45 -52.02
4.70 -54.45 -52.01
@@ -81322,9 +81616,9 @@ French Guiana
4.42 -54.45 -51.72
4.41 -54.45 -51.72
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4.36 -54.44 -51.68
4.35 -54.44 -51.69
4.34 -54.43 -51.70
@@ -81341,9 +81635,9 @@ French Guiana
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4.22 -54.41 -51.64
4.21 -54.42 -51.64
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4.17 -54.41 -51.63
4.16 -54.40 -51.63
4.15 -54.39 -51.63
@@ -81574,14 +81868,14 @@ French Polynesia
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-8.95 -140.21 -140.16 -139.62 -139.59
-8.96 -140.20 -140.17 -139.62 -139.60
@@ -81590,10 +81884,10 @@ French Polynesia
-9.33 -140.13 -140.01
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-9.35 -140.15 -140.01
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-9.40 -140.15 -140.03
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@@ -81605,14 +81899,14 @@ French Polynesia
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-9.83 -139.15 -139.04
@@ -81620,8 +81914,8 @@ French Polynesia
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@@ -81633,22 +81927,22 @@ French Polynesia
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@@ -81667,10 +81961,10 @@ French Polynesia
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@@ -81687,46 +81981,46 @@ French Polynesia
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@@ -81741,20 +82035,20 @@ French Polynesia
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@@ -81766,7 +82060,7 @@ French Polynesia
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@@ -81778,15 +82072,15 @@ French Polynesia
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-49.39 68.86 69.93 70.24 70.41
-49.40 68.86 69.93 70.25 70.43
@@ -82245,7 +82556,7 @@ French Southern and Antarctic Lands
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-49.48 68.81 69.81 69.85 69.93
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-49.52 68.81 69.71 69.75 69.98 70.03 70.30
-49.53 68.80 69.71 69.76 69.86 69.88 70.00 70.03 70.31
@@ -82257,10 +82568,10 @@ French Southern and Antarctic Lands
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@@ -82402,7 +82713,7 @@ Gabon
1.04 9.64 9.78 11.32 14.38
1.03 9.63 9.78 11.32 14.38
1.02 9.58 9.78 11.32 14.38
- 1.01 9.56 9.79 10.00 11.19 11.32 14.38
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1.00 9.56 9.84 9.97 14.39
0.99 9.55 9.86 9.96 14.40
0.98 9.55 9.87 9.96 14.41
@@ -82412,8 +82723,8 @@ Gabon
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0.89 9.57 14.47
0.88 9.57 14.47
0.87 9.58 14.45
@@ -82422,9 +82733,9 @@ Gabon
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@@ -82478,12 +82789,12 @@ Gabon
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0.27 9.28 9.38 9.57 13.92
0.26 9.29 9.38 9.59 13.91
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0.24 9.30 9.37 9.62 13.90
0.23 9.30 9.38 9.63 13.89
0.22 9.30 9.38 9.64 13.89
0.21 9.30 9.43 9.65 13.88
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0.19 9.31 9.45 9.49 9.53 9.72 13.88
0.18 9.31 9.46 9.49 9.56 9.73 13.88
0.17 9.31 9.57 9.76 13.88
@@ -82513,11 +82824,11 @@ Gabon
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@@ -82567,17 +82878,17 @@ Gabon
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@@ -82595,8 +82906,8 @@ Gabon
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@@ -82671,14 +82982,14 @@ Gabon
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@@ -82697,8 +83008,8 @@ Gabon
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@@ -82708,11 +83019,11 @@ Gabon
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@@ -82741,9 +83052,9 @@ Gabon
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@@ -82752,88 +83063,88 @@ Gabon
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Gambia
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13.81 -15.15 -15.02
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13.79 -15.37 -15.29 -15.20 -14.86
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13.77 -15.41 -15.27 -15.22 -14.84
13.76 -15.43 -15.27 -15.24 -14.83
13.75 -15.44 -14.83
@@ -82924,10 +83237,10 @@ Gambia
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13.51 -16.56 -15.19 -15.06 -14.43 -14.24 -13.87
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13.49 -16.70 -16.66 -16.56 -15.20 -15.03 -14.40 -14.27 -13.84
@@ -82949,10 +83262,10 @@ Gambia
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13.29 -16.83 -16.46 -16.39 -16.37 -16.35 -15.81 -14.53 -13.93
13.28 -16.83 -15.81 -14.48 -13.98
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13.26 -16.82 -15.81 -14.46 -14.11
13.25 -16.81 -15.81 -14.45 -14.13
13.24 -16.81 -15.81 -14.42 -14.14
@@ -83051,7 +83364,7 @@ Georgia
43.27 40.23 41.50
43.26 40.24 41.51
43.25 40.25 41.53
- 43.24 40.25 41.55 42.26 42.39
+ 43.24 40.25 41.55 42.26 42.40
43.23 40.25 41.57 41.64 41.71 42.16 42.44
43.22 40.25 41.76 42.13 42.46
43.21 40.25 41.95 42.11 42.48
@@ -83067,8 +83380,8 @@ Georgia
43.11 40.49 42.99
43.10 40.52 43.01
43.09 40.53 43.01
- 43.08 40.56 43.01
- 43.07 40.57 40.62 40.73 43.01
+ 43.08 40.55 43.01
+ 43.07 40.56 40.62 40.73 43.01
43.06 40.79 43.01
43.05 40.83 43.00
43.04 40.85 43.02
@@ -83099,43 +83412,43 @@ Georgia
42.79 41.13 43.66
42.78 41.14 41.19 41.23 43.71
42.77 41.26 43.77
- 42.76 41.28 43.79 44.48 44.58 44.84 44.91
- 42.75 41.29 43.81 44.45 44.63 44.83 44.93
+ 42.76 41.28 43.80 44.48 44.58 44.84 44.91
+ 42.75 41.29 43.81 44.45 44.64 44.83 44.93
42.74 41.34 43.81 44.43 44.66 44.82 44.95
42.73 41.39 43.82 44.41 44.69 44.82 44.97
42.72 41.41 43.82 44.38 44.70 44.81 44.99
- 42.71 41.42 43.82 44.26 44.72 44.80 45.01 45.09 45.14
- 42.70 41.44 43.82 44.24 44.73 44.80 45.02 45.07 45.16
+ 42.71 41.42 43.82 44.26 44.72 44.80 45.01 45.08 45.14
+ 42.70 41.44 43.82 44.24 44.73 44.80 45.02 45.06 45.16
42.69 41.45 43.81 44.23 44.73 44.79 45.18
- 42.68 41.45 43.79 44.23 44.74 44.78 45.19
- 42.67 41.46 43.78 44.22 44.74 44.78 45.20
+ 42.68 41.46 43.79 44.23 44.74 44.78 45.19
+ 42.67 41.47 43.78 44.22 44.74 44.78 45.20
42.66 41.47 43.76 44.22 44.75 44.78 45.21
42.65 41.48 43.75 44.21 44.75 44.78 45.22
- 42.64 41.48 43.73 44.19 45.24
- 42.63 41.49 43.73 44.17 45.25
+ 42.64 41.48 43.73 44.20 45.24
+ 42.63 41.49 43.73 44.16 45.25
42.62 41.49 43.74 44.03 45.26
42.61 41.49 43.75 44.00 45.27
42.60 41.50 43.78 43.99 45.28
42.59 41.50 43.87 43.98 45.29
42.58 41.50 43.90 43.97 45.30
- 42.57 41.50 43.92 43.96 45.31
+ 42.57 41.50 43.92 43.96 45.30
42.56 41.50 45.31
42.55 41.51 45.32 45.45 45.58
42.54 41.51 45.33 45.41 45.64
42.53 41.51 45.35 45.37 45.66
42.52 41.51 45.68
42.51 41.51 45.70
- 42.50 41.51 45.72
+ 42.50 41.52 45.72
42.49 41.52 45.73
42.48 41.52 45.74
42.47 41.52 45.74
- 42.46 41.52 45.74
- 42.45 41.52 45.74
+ 42.46 41.53 45.74
+ 42.45 41.53 45.74
42.44 41.53 45.74
42.43 41.53 45.74
42.42 41.53 45.74
- 42.41 41.53 45.73
- 42.40 41.53 45.73
+ 42.41 41.54 45.73
+ 42.40 41.54 45.73
42.39 41.54 45.72
42.38 41.54 45.72
42.37 41.54 45.71
@@ -83169,7 +83482,7 @@ Georgia
42.09 41.66 45.90
42.08 41.67 45.91
42.07 41.68 45.91
- 42.06 41.69 45.92
+ 42.06 41.68 45.92
42.05 41.69 45.92
42.04 41.70 45.93 45.97 46.01
42.03 41.71 46.02 46.04 46.06
@@ -83200,9 +83513,9 @@ Georgia
41.78 41.73 46.37
41.77 41.73 46.36
41.76 41.73 46.34
- 41.75 41.73 46.33
- 41.74 41.72 46.32
- 41.73 41.71 46.20 46.25 46.29
+ 41.75 41.72 46.33
+ 41.74 41.71 46.32
+ 41.73 41.70 46.20 46.25 46.29
41.72 41.70 46.19
41.71 41.69 46.19
41.70 41.68 46.18
@@ -83219,7 +83532,7 @@ Georgia
41.59 41.56 46.27
41.58 41.55 46.28
41.57 41.54 46.28
- 41.56 41.54 42.60 42.73 46.28
+ 41.56 41.54 42.59 42.73 46.28
41.55 41.53 42.58 42.79 46.29
41.54 41.52 42.56 42.79 46.29
41.53 41.52 42.56 42.78 46.29
@@ -83237,14 +83550,14 @@ Georgia
41.41 41.79 41.83 42.95 45.22 45.36 46.53
41.40 42.95 45.21 45.46 46.56
41.39 42.96 45.19 45.48 46.58
- 41.38 42.97 45.17 45.50 46.60
+ 41.38 42.97 45.18 45.50 46.60
41.37 42.99 45.16 45.52 46.60
- 41.36 43.00 45.14 45.56 46.61
+ 41.36 43.00 45.15 45.56 46.61
41.35 43.02 45.13 45.59 46.64
- 41.34 43.04 45.11 45.63 46.65
- 41.33 43.06 45.09 45.68 46.66
- 41.32 43.07 45.08 45.69 46.67
- 41.31 43.09 45.06 45.68 46.67
+ 41.34 43.04 45.12 45.63 46.65
+ 41.33 43.06 45.10 45.68 46.66
+ 41.32 43.07 45.09 45.69 46.67
+ 41.31 43.09 45.07 45.68 46.67
41.30 43.11 45.05 45.67 46.68
41.29 43.13 45.03 45.67 46.69
41.28 43.16 45.01 45.67 46.69
@@ -83252,8 +83565,8 @@ Georgia
41.26 43.11 44.99 45.68 46.70
41.25 43.09 44.97 45.69 46.70
41.24 43.09 44.85 45.71 46.68
- 41.23 43.09 44.85 45.73 46.68
- 41.22 43.17 44.86 45.75 46.68
+ 41.23 43.09 44.86 45.73 46.68
+ 41.22 43.17 44.86 45.76 46.68
41.21 43.18 44.86 45.77 46.67
41.20 43.18 44.17 44.21 44.61 44.64 44.86 45.79 46.66
41.19 43.19 44.17 44.23 44.33 44.36 44.59 44.66 44.85 45.81 46.65
@@ -83294,25 +83607,25 @@ Germany
54.90 8.27 8.41 8.54 8.68 8.74 8.93
54.89 8.27 8.97
54.88 8.27 9.04
- 54.87 8.27 9.14 9.57 9.59
- 54.86 8.27 8.48 8.63 9.21 9.55 9.59
- 54.85 8.27 8.32 8.36 8.47 8.63 9.22 9.52 9.59
- 54.84 8.26 8.30 8.63 9.22 9.51 9.59
- 54.83 8.26 8.30 8.63 9.22 9.48 9.61
+ 54.87 8.27 9.14 9.55 9.58
+ 54.86 8.27 8.48 8.63 9.21 9.55 9.58
+ 54.85 8.27 8.32 8.36 8.47 8.63 9.22 9.51 9.59
+ 54.84 8.26 8.30 8.63 9.22 9.51 9.60
+ 54.83 8.26 8.30 8.63 9.22 9.48 9.62
54.82 8.26 8.30 8.63 9.22 9.34 9.40 9.42 9.72
54.81 8.26 8.30 8.63 9.75
54.80 8.26 8.30 8.63 9.79 9.88 9.92
54.79 8.26 8.30 8.65 9.81 9.88 9.94
54.78 8.26 8.30 8.66 9.81 9.88 9.96
- 54.77 8.26 8.30 8.67 9.82 9.87 9.98
+ 54.77 8.26 8.30 8.67 9.82 9.86 9.98
54.76 8.26 8.30 8.44 8.57 8.67 9.98
54.75 8.26 8.30 8.42 8.58 8.67 9.98
54.74 8.26 8.30 8.40 8.59 8.67 9.99
54.73 8.27 8.30 8.39 8.60 8.67 10.00
- 54.72 8.34 8.60 8.67 10.01
+ 54.72 8.32 8.60 8.67 10.01
54.71 8.32 8.60 8.70 10.02
54.70 8.31 8.59 8.72 10.02
- 54.69 8.30 8.37 8.40 8.59 8.74 10.02 13.35 13.43
+ 54.69 8.30 8.36 8.40 8.59 8.74 10.02 13.35 13.45
54.68 8.29 8.36 8.43 8.58 8.76 10.04 13.28 13.45
54.67 8.28 8.36 8.46 8.57 8.78 10.04 13.24 13.45
54.66 8.28 8.37 8.80 10.04 13.22 13.45
@@ -83320,26 +83633,26 @@ Germany
54.64 8.30 8.41 8.81 10.04 13.21 13.42
54.63 8.31 8.41 8.82 10.04 13.21 13.40
54.62 8.32 8.41 8.83 10.04 13.21 13.39
- 54.61 8.33 8.40 8.80 10.04 13.10 13.16 13.25 13.40
+ 54.61 8.33 8.40 8.80 10.04 13.09 13.16 13.25 13.40
54.60 8.34 8.37 8.80 10.04 13.09 13.16 13.24 13.42 13.55 13.62
54.59 8.80 10.04 13.09 13.16 13.24 13.45 13.49 13.65
- 54.58 8.81 8.83 8.88 10.04 13.08 13.16 13.24 13.67
- 54.57 8.89 10.04 13.08 13.16 13.24 13.68
- 54.56 8.66 8.70 8.90 10.04 13.07 13.16 13.20 13.68
+ 54.58 8.81 8.83 8.88 10.04 13.08 13.16 13.23 13.67
+ 54.57 8.89 10.04 13.08 13.16 13.23 13.68
+ 54.56 8.66 8.70 8.90 10.04 13.07 13.15 13.20 13.68
54.55 8.62 8.71 8.92 10.04 13.07 13.68
54.54 8.61 8.71 8.89 10.03 11.06 11.15 13.06 13.68
- 54.53 8.59 8.71 8.86 10.03 11.05 11.19 13.06 13.68
+ 54.53 8.59 8.71 8.85 10.03 11.05 11.19 13.06 13.68
54.52 8.58 8.71 8.82 10.02 11.03 11.22 13.05 13.11 13.15 13.67
54.51 8.58 8.70 8.80 10.01 11.02 11.24 13.05 13.11 13.15 13.67
54.50 8.58 8.69 8.80 8.96 8.98 9.99 10.08 10.16 11.01 11.25 13.05 13.09 13.15 13.66
54.49 8.58 8.67 8.80 8.96 9.00 10.18 11.01 11.25 12.50 12.54 13.05 13.08 13.17 13.64
54.48 8.59 8.66 8.80 8.95 9.00 10.20 11.00 11.26 12.49 12.54 13.05 13.08 13.22 13.62
- 54.47 8.80 8.93 8.99 10.21 10.99 11.27 12.48 12.57 13.05 13.08 13.21 13.60
- 54.46 8.81 8.92 8.96 10.21 10.99 11.28 12.48 12.84 13.05 13.08 13.17 13.58
+ 54.47 8.80 8.93 8.99 10.21 10.99 11.27 12.48 12.57 13.05 13.07 13.21 13.60
+ 54.46 8.81 8.92 8.96 10.21 10.99 11.28 12.48 12.84 13.05 13.07 13.17 13.58
54.45 8.83 8.90 8.93 10.21 10.29 10.38 10.99 11.29 12.47 12.92 13.05 13.07 13.16 13.58
54.44 8.91 10.20 10.28 10.40 10.99 11.30 12.46 12.93 12.98 13.04 13.15 13.59
- 54.43 8.89 10.20 10.27 10.42 11.02 11.05 11.09 11.31 12.45 13.04 13.14 13.61
- 54.42 8.71 10.44 11.09 11.32 12.44 13.04 13.14 13.63
+ 54.43 8.89 10.20 10.25 10.42 11.02 11.04 11.09 11.31 12.45 13.04 13.14 13.60
+ 54.42 8.70 10.44 11.09 11.32 12.44 13.04 13.14 13.62
54.41 8.63 10.47 11.09 11.32 12.43 13.04 13.14 13.18 13.20 13.69
54.40 8.62 10.51 11.08 11.18 11.24 11.32 12.42 13.06 13.22 13.70
54.39 8.61 10.55 10.97 11.02 11.06 11.14 12.41 13.08 13.15 13.19 13.22 13.71
@@ -83347,46 +83660,46 @@ Germany
54.37 8.61 10.61 10.87 11.14 12.38 13.10 13.12 13.74
54.36 8.61 10.63 10.85 11.13 12.37 13.76
54.35 8.60 10.65 10.83 11.11 12.36 13.09 13.11 13.77
- 54.34 8.59 10.67 10.81 11.09 12.35 13.77
- 54.33 8.59 10.69 10.79 11.08 12.35 13.55 13.60 13.77
- 54.32 8.59 10.72 10.75 11.09 12.34 13.50 13.60 13.76
- 54.31 8.59 11.09 12.33 13.47 13.60 13.75
+ 54.34 8.58 10.67 10.81 11.09 12.35 13.77
+ 54.33 8.58 10.69 10.79 11.08 12.35 13.55 13.60 13.77
+ 54.32 8.58 11.09 12.34 13.49 13.60 13.76
+ 54.31 8.58 11.09 12.33 13.47 13.60 13.75
54.30 8.59 11.09 12.31 13.44 13.60 13.74
54.29 8.60 11.10 12.29 13.42 13.64 13.73
- 54.28 8.60 11.10 12.26 13.42 13.64 13.73
- 54.27 8.61 8.72 8.84 11.10 12.22 13.42 13.68 13.73
- 54.26 8.63 8.70 8.83 11.09 12.20 13.42 13.70 13.73
- 54.25 8.66 8.69 8.83 11.09 12.17 13.43
- 54.24 8.83 11.10 12.16 13.43
- 54.23 8.83 11.10 12.16 13.43
+ 54.28 8.61 11.10 12.26 13.42 13.64 13.73
+ 54.27 8.62 8.72 8.84 11.10 12.22 13.42 13.68 13.73
+ 54.26 8.64 8.70 8.82 11.09 12.20 13.42 13.70 13.73
+ 54.25 8.66 8.69 8.82 11.09 12.17 13.43
+ 54.24 8.82 11.10 12.16 13.43
+ 54.23 8.82 11.10 12.16 13.43
54.22 8.82 11.10 12.15 13.31 13.33 13.43
54.21 8.81 11.10 12.13 13.32 13.38 13.42
- 54.20 8.81 11.10 12.07 12.09 12.11 13.34
- 54.19 8.80 11.10 12.05 13.35
- 54.18 8.80 11.09 12.01 13.41 13.69 13.72 13.76 13.82
- 54.17 8.80 11.07 11.93 13.41 13.66 13.72 13.75 13.83
- 54.16 8.80 11.05 11.67 11.77 11.85 13.42 13.64 13.72 13.74 13.84
+ 54.20 7.86 7.93 8.81 11.10 12.07 12.09 12.11 13.34
+ 54.19 7.86 7.94 8.80 11.10 12.05 13.35
+ 54.18 7.86 7.94 8.80 11.09 12.01 13.41 13.69 13.72 13.76 13.82
+ 54.17 7.88 7.94 8.80 11.07 11.93 13.41 13.66 13.72 13.75 13.83
+ 54.16 7.88 7.90 8.80 11.05 11.66 11.77 11.85 13.42 13.64 13.72 13.74 13.84
54.15 8.81 11.03 11.64 13.43 13.61 13.84
54.14 8.82 11.01 11.63 13.43 13.53 13.85
- 54.13 8.83 10.99 11.63 13.85
+ 54.13 8.83 8.94 8.96 10.99 11.63 13.85
54.12 8.84 8.90 8.96 10.97 11.60 13.87
54.11 8.85 8.88 8.96 10.95 11.58 13.90
54.10 8.97 10.94 11.54 13.92
54.09 8.99 10.92 11.52 13.94
- 54.08 9.00 10.88 11.51 13.99
- 54.07 9.00 10.80 10.82 10.84 11.51 14.01
- 54.06 9.00 10.79 11.51 14.02
- 54.05 8.85 8.93 8.99 10.78 11.51 14.04
- 54.04 8.82 8.95 8.99 10.77 11.44 11.48 11.50 14.06
- 54.03 8.82 10.77 11.41 14.07
- 54.02 8.82 10.78 11.11 11.20 11.39 14.09
- 54.01 8.83 10.82 11.02 11.20 11.38 13.82 13.84 14.11
- 54.00 8.84 10.88 10.99 11.20 11.37 13.82 13.84 14.12
- 53.99 8.84 10.89 10.95 11.25 11.36 14.14
- 53.98 8.85 10.89 10.93 11.25 11.36 13.85 13.89 14.15
+ 54.08 9.00 10.88 11.51 14.00
+ 54.07 9.00 10.80 11.51 14.02
+ 54.06 9.00 10.79 11.51 14.04
+ 54.05 8.85 8.93 8.99 10.78 11.51 11.55 11.57 14.05
+ 54.04 8.82 8.95 8.98 10.77 11.44 11.48 11.50 14.07
+ 54.03 8.82 10.77 11.41 14.08
+ 54.02 8.82 10.78 11.11 11.20 11.39 14.10
+ 54.01 8.83 10.81 11.02 11.20 11.38 13.82 13.84 14.11
+ 54.00 8.84 10.88 10.99 11.20 11.37 13.82 13.84 14.13
+ 53.99 8.84 10.89 10.95 11.24 11.36 14.14
+ 53.98 8.85 10.89 10.93 11.25 11.36 13.85 13.89 14.16
53.97 8.86 11.25 11.32 11.34 11.36 13.86 13.89 14.17
53.96 8.87 11.25 11.30 11.35 11.38 14.19
- 53.95 8.88 14.21
+ 53.95 8.88 14.20
53.94 8.88 11.41 11.45 14.22
53.93 8.89 11.42 11.45 14.22
53.92 8.90 14.22
@@ -83401,16 +83714,16 @@ Germany
53.83 8.54 13.97
53.82 8.53 13.92
53.81 8.53 13.94
- 53.80 7.84 7.94 8.53 13.96
+ 53.80 7.84 7.94 8.52 13.96
53.79 7.67 7.82 7.84 7.96 8.52 13.98
- 53.78 7.66 7.82 7.84 7.96 8.52 14.00
+ 53.78 7.66 7.82 7.84 7.96 8.51 14.00
53.77 7.47 7.62 7.65 7.82 7.84 7.96 8.51 14.03 14.22 14.25
- 53.76 7.46 7.63 7.65 7.82 7.86 7.88 8.51 14.08 14.21 14.27
- 53.75 7.46 7.63 7.65 7.79 8.50 14.15 14.19 14.27
- 53.74 7.37 7.43 7.46 7.63 7.65 7.68 7.70 7.74 8.12 8.19 8.49 14.27
- 53.73 7.16 7.44 7.46 7.53 7.58 7.63 7.90 7.98 8.11 8.20 8.49 14.27
+ 53.76 7.46 7.63 7.65 7.82 7.86 7.88 8.50 14.08 14.21 14.27
+ 53.75 7.45 7.63 7.65 7.79 8.50 14.15 14.19 14.27
+ 53.74 7.37 7.43 7.45 7.63 7.65 7.68 7.70 7.73 8.12 8.19 8.49 14.27
+ 53.73 7.16 7.53 7.58 7.63 7.90 7.98 8.11 8.20 8.49 14.27
53.72 7.14 7.44 7.46 7.52 7.80 8.02 8.11 8.20 8.48 14.27
- 53.71 7.12 7.44 7.47 7.52 7.70 8.04 8.11 8.20 8.47 14.27
+ 53.71 7.12 7.44 7.47 7.52 7.70 8.04 8.11 8.20 8.47 14.26
53.70 6.97 7.07 7.12 7.32 7.37 7.48 7.61 8.04 8.11 8.17 8.47 14.27
53.69 6.89 7.09 7.12 7.24 7.28 7.50 7.53 8.04 8.47 14.27
53.68 6.86 7.09 7.24 8.04 8.47 14.27
@@ -83418,17 +83731,17 @@ Germany
53.66 6.86 6.98 7.19 8.04 8.47 14.27
53.65 7.17 8.05 8.47 14.27
53.64 7.15 8.06 8.48 14.28
- 53.63 7.13 8.08 8.49 14.28
+ 53.63 6.76 6.79 7.13 8.08 8.49 14.28
53.62 6.70 6.79 7.12 8.09 8.26 8.36 8.49 14.29
53.61 6.66 6.80 7.10 8.11 8.24 8.37 8.49 14.29
- 53.60 6.65 6.80 7.09 8.13 8.24 8.37 8.49 14.30
- 53.59 6.65 6.80 7.07 8.13 8.23 8.38 8.50 14.30
- 53.58 6.65 6.76 7.07 8.13 8.23 8.41 8.51 14.30
+ 53.60 6.64 6.80 7.09 8.13 8.23 8.37 8.50 14.30
+ 53.59 6.64 6.80 7.07 8.13 8.23 8.38 8.50 14.30
+ 53.58 6.64 6.76 7.07 8.13 8.23 8.41 8.51 14.30
53.57 6.65 6.76 7.07 8.16 8.23 8.47 8.53 14.30
53.56 6.66 6.76 7.07 8.17 8.23 14.30
53.55 6.73 6.76 7.09 8.17 8.23 14.30
53.54 7.11 8.17 8.22 14.30
- 53.53 7.05 8.17 8.22 14.30
+ 53.53 7.04 8.17 8.22 14.30
53.52 7.04 8.17 8.22 14.30
53.51 7.04 8.16 8.22 14.31
53.50 7.03 8.15 8.29 14.32
@@ -83438,22 +83751,22 @@ Germany
53.46 7.01 8.15 8.29 14.35
53.45 7.01 8.17 8.28 14.36
53.44 7.01 8.18 8.27 14.36
- 53.43 7.01 8.19 8.27 14.37
- 53.42 7.01 8.22 8.24 14.37
+ 53.43 7.01 8.20 8.27 14.37
+ 53.42 7.01 8.21 8.24 14.37
53.41 7.01 14.38
53.40 7.01 14.38
53.39 7.01 14.38
- 53.38 7.01 14.38
+ 53.38 7.01 14.39
53.37 7.01 14.39
53.36 7.01 14.39
- 53.35 7.01 14.39
- 53.34 7.02 14.39
+ 53.35 7.01 14.40
+ 53.34 7.02 14.40
53.33 7.02 14.40
53.32 7.05 14.40
- 53.31 7.23 14.40
- 53.30 7.22 14.40
- 53.29 7.22 14.41
- 53.28 7.22 14.42
+ 53.31 7.22 14.40
+ 53.30 7.21 14.40
+ 53.29 7.21 14.41
+ 53.28 7.21 14.42
53.27 7.21 14.43
53.26 7.20 14.45
53.25 7.18 14.45
@@ -83497,7 +83810,7 @@ Germany
52.87 7.07 14.17
52.86 7.06 14.17
52.85 7.06 14.16
- 52.84 7.05 14.15
+ 52.84 7.06 14.15
52.83 7.05 14.21
52.82 7.05 14.22
52.81 7.04 14.24
@@ -83519,8 +83832,8 @@ Germany
52.65 6.75 6.89 7.02 14.53
52.64 6.72 14.55
52.63 6.70 14.57
- 52.62 6.69 14.59
- 52.61 6.69 14.61
+ 52.62 6.69 14.58
+ 52.61 6.69 14.60
52.60 6.69 14.62
52.59 6.69 14.64
52.58 6.69 14.65
@@ -83569,7 +83882,7 @@ Germany
52.15 6.85 14.71
52.14 6.84 14.71
52.13 6.83 14.70
- 52.12 6.79 14.70
+ 52.12 6.80 14.70
52.11 6.73 14.71
52.10 6.72 14.73
52.09 6.71 14.75
@@ -83640,8 +83953,8 @@ Germany
51.44 6.19 14.96
51.43 6.19 14.96
51.42 6.18 14.96
- 51.41 6.18 14.95
- 51.40 6.18 14.95
+ 51.41 6.18 14.96
+ 51.40 6.18 14.96
51.39 6.18 14.96
51.38 6.18 14.96
51.37 6.19 14.96
@@ -83723,7 +84036,7 @@ Germany
50.61 6.14 13.50
50.60 6.16 13.36 13.38 13.48
50.59 6.22 13.34 13.39 13.47
- 50.58 6.20 13.32 13.41 13.46
+ 50.58 6.19 13.32 13.41 13.46
50.57 6.16 13.32
50.56 6.16 13.23 13.25 13.31
50.55 6.15 13.23 13.27 13.30
@@ -83734,7 +84047,7 @@ Germany
50.50 6.16 13.20
50.49 6.17 13.19
50.48 6.18 13.18
- 50.47 6.19 6.23 6.26 13.01
+ 50.47 6.19 6.24 6.26 13.01
50.46 6.31 13.01
50.45 6.31 13.01
50.44 6.31 13.01
@@ -83742,7 +84055,7 @@ Germany
50.42 6.33 12.80 12.83 13.00
50.41 6.34 12.73 12.85 12.99
50.40 6.33 12.72 12.87 12.98
- 50.39 6.33 12.71 12.89 12.96
+ 50.39 6.33 12.71 12.89 12.97
50.38 6.32 12.70
50.37 6.32 12.54
50.36 6.32 12.50
@@ -83755,7 +84068,7 @@ Germany
50.29 6.25 12.11 12.15 12.39
50.28 6.25 12.12 12.16 12.39
50.27 6.25 12.12 12.16 12.38
- 50.26 6.21 12.12 12.16 12.37
+ 50.26 6.23 12.12 12.16 12.37
50.25 6.17 12.11 12.16 12.35
50.24 6.16 12.11 12.19 12.34
50.23 6.14 12.12 12.21 12.34
@@ -83828,8 +84141,8 @@ Germany
49.56 6.34 12.57
49.55 6.34 12.57
49.54 6.34 12.57
- 49.53 6.34 12.59
- 49.52 6.34 12.62
+ 49.53 6.33 12.59
+ 49.52 6.33 12.62
49.51 6.33 12.63
49.50 6.33 12.63
49.49 6.33 12.63
@@ -83866,7 +84179,7 @@ Germany
49.18 6.69 6.84 6.93 13.13
49.17 6.69 6.84 6.96 13.14
49.16 6.69 6.84 6.99 13.15
- 49.15 6.69 6.84 6.99 7.38 7.40 13.16
+ 49.15 6.69 6.84 6.99 13.16
49.14 6.70 6.84 6.99 7.36 7.40 13.17
49.13 6.78 6.83 6.99 7.35 7.46 13.17
49.12 7.00 7.34 7.46 13.19
@@ -83883,7 +84196,7 @@ Germany
49.01 7.94 13.39
49.00 7.97 13.39
48.99 7.99 13.39
- 48.98 8.02 13.40 13.50 13.53
+ 48.98 8.02 13.40 13.50 13.52
48.97 8.05 13.42 13.49 13.55
48.96 8.07 13.44 13.48 13.59
48.95 8.13 13.61
@@ -84018,7 +84331,7 @@ Germany
47.66 7.50 8.43 8.49 8.61 8.84 12.24 12.41 13.08
47.65 7.52 8.61 8.85 8.99 9.17 12.21 12.42 12.64 12.71 13.08
47.64 7.54 8.61 8.87 8.97 9.18 12.21 12.43 12.59 12.74 13.08
- 47.63 7.55 8.61 9.28 12.21 12.44 12.58 12.74 13.08
+ 47.63 7.55 8.61 9.28 12.21 12.44 12.57 12.74 13.08
47.62 7.55 8.61 9.30 12.21 12.46 12.56 12.75 13.08
47.61 7.56 8.59 9.32 12.21 12.48 12.53 12.77 13.08
47.60 7.56 8.21 8.26 8.59 9.34 12.20 12.77 13.07
@@ -84027,10 +84340,10 @@ Germany
47.57 7.57 7.82 7.86 8.12 8.30 8.46 8.55 8.57 9.41 11.85 12.76 13.05
47.56 7.59 7.81 7.89 8.11 9.43 9.75 9.79 11.60 11.79 11.84 12.76 13.05
47.55 7.59 7.80 7.89 8.09 9.46 9.74 9.79 11.59 12.76 13.05
- 47.54 7.61 7.78 9.48 9.73 9.79 10.58 10.61 11.59 12.76 13.05
- 47.53 7.64 7.73 9.50 9.72 9.80 10.56 10.64 11.59 12.78 13.04
+ 47.54 7.62 7.78 9.48 9.73 9.79 10.58 10.61 11.59 12.76 13.05
+ 47.53 7.65 7.71 9.50 9.72 9.80 10.56 10.64 11.59 12.78 13.04
47.52 9.52 9.71 9.82 10.43 10.45 10.55 10.68 11.58 12.80 13.04
- 47.51 9.57 9.69 9.93 10.43 10.50 10.54 10.71 11.57 12.83 13.04
+ 47.51 9.58 9.69 9.93 10.43 10.50 10.54 10.71 11.57 12.83 13.04
47.50 9.94 10.43 10.74 10.82 10.84 11.56 12.84 13.04
47.49 9.96 10.45 10.84 11.54 12.86 13.04
47.48 9.97 10.45 10.84 11.41 12.87 13.04
@@ -84071,7 +84384,7 @@ Ghana
11.06 -0.45 0.02
11.05 -0.46 0.02
11.04 -0.46 0.02
- 11.03 -1.58 -1.41 -0.47 0.02
+ 11.03 -1.58 -1.42 -0.47 0.02
11.02 -1.58 -1.39 -1.08 -0.99 -0.49 0.02
11.01 -1.59 -1.36 -1.10 -0.91 -0.84 -0.81 -0.50 0.02
11.00 -2.84 -2.74 -2.31 -0.90 -0.87 -0.68 -0.51 0.02
@@ -84104,9 +84417,9 @@ Ghana
10.73 -2.93 -0.07
10.72 -2.93 -0.07
10.71 -2.93 -0.07
- 10.70 -2.93 -0.07
- 10.69 -2.92 -0.07
- 10.68 -2.92 -0.07
+ 10.70 -2.92 -0.07
+ 10.69 -2.92 -0.08
+ 10.68 -2.92 -0.08
10.67 -2.92 -0.08
10.66 -2.92 -0.08
10.65 -2.93 -0.08
@@ -84309,50 +84622,50 @@ Ghana
8.68 -2.59 0.40
8.67 -2.59 0.41
8.66 -2.59 0.42
- 8.65 -2.58 0.42
+ 8.65 -2.59 0.42
8.64 -2.58 0.43
8.63 -2.58 0.44
8.62 -2.58 0.44
8.61 -2.58 0.45
8.60 -2.58 0.47
- 8.59 -2.57 0.48
- 8.58 -2.57 0.50
+ 8.59 -2.58 0.48
+ 8.58 -2.58 0.50
8.57 -2.57 0.51
8.56 -2.57 0.52
8.55 -2.57 0.52
8.54 -2.57 0.53
- 8.53 -2.56 0.55
- 8.52 -2.56 0.57
- 8.51 -2.56 0.59
+ 8.53 -2.57 0.55
+ 8.52 -2.57 0.57
+ 8.51 -2.57 0.59
8.50 -2.56 0.61
8.49 -2.56 0.62
8.48 -2.56 0.63
8.47 -2.56 0.63
- 8.46 -2.55 0.64
- 8.45 -2.55 0.64
+ 8.46 -2.56 0.64
+ 8.45 -2.56 0.64
8.44 -2.55 0.64
8.43 -2.55 0.65
8.42 -2.55 0.65
8.41 -2.55 0.67
- 8.40 -2.54 0.68
- 8.39 -2.54 0.69
+ 8.40 -2.55 0.68
+ 8.39 -2.55 0.69
8.38 -2.54 0.69
8.37 -2.54 0.69
8.36 -2.54 0.69
8.35 -2.54 0.69
- 8.34 -2.53 0.69
- 8.33 -2.53 0.71
+ 8.34 -2.54 0.69
+ 8.33 -2.54 0.71
8.32 -2.53 0.71
8.31 -2.53 0.72
8.30 -2.53 0.72
8.29 -2.53 0.72
- 8.28 -2.52 0.72
+ 8.28 -2.53 0.72
8.27 -2.52 0.71
8.26 -2.52 0.70
8.25 -2.52 0.68
8.24 -2.52 0.66
8.23 -2.52 0.64
- 8.22 -2.51 0.62
+ 8.22 -2.52 0.62
8.21 -2.51 0.61
8.20 -2.52 0.60
8.19 -2.53 0.59
@@ -84550,8 +84863,8 @@ Ghana
6.27 -3.19 1.00
6.26 -3.19 1.01
6.25 -3.19 1.01
- 6.24 -3.18 1.02
- 6.23 -3.17 1.03
+ 6.24 -3.19 1.02
+ 6.23 -3.18 1.03
6.22 -3.16 1.05
6.21 -3.15 1.06
6.20 -3.14 1.06
@@ -84600,7 +84913,7 @@ Ghana
5.77 -3.02 0.95
5.76 -3.03 0.35 0.42 0.93
5.75 -3.03 0.29 0.54 0.87
- 5.74 -3.03 0.28 0.66 0.77
+ 5.74 -3.03 0.27 0.66 0.77
5.73 -3.03 0.24
5.72 -3.03 0.21
5.71 -3.03 0.17
@@ -84626,14 +84939,14 @@ Ghana
5.51 -2.78 -0.22
5.50 -2.78 -0.25
5.49 -2.78 -0.28
- 5.48 -2.78 -0.35
+ 5.48 -2.78 -0.34
5.47 -2.77 -0.37
5.46 -2.77 -0.38
5.45 -2.77 -0.39
5.44 -2.77 -0.41
5.43 -2.77 -0.42
5.42 -2.76 -0.43
- 5.41 -2.76 -0.43
+ 5.41 -2.76 -0.44
5.40 -2.75 -0.44
5.39 -2.75 -0.44
5.38 -2.74 -0.45
@@ -84646,10 +84959,10 @@ Ghana
5.31 -2.80 -0.61
5.30 -2.80 -0.66
5.29 -2.80 -0.67
- 5.28 -2.80 -0.68
- 5.27 -2.80 -0.70
+ 5.28 -2.80 -0.70
+ 5.27 -2.80 -0.71
5.26 -2.80 -0.72
- 5.25 -2.79 -0.73
+ 5.25 -2.79 -0.74
5.24 -2.78 -0.75
5.23 -2.78 -0.76
5.22 -2.78 -0.76
@@ -84672,14 +84985,14 @@ Ghana
5.05 -3.05 -1.40
5.04 -3.02 -1.42
5.03 -2.98 -1.44
- 5.02 -2.94 -1.48
- 5.01 -2.89 -1.54
- 5.00 -2.85 -1.61 -1.57 -1.55
- 4.99 -2.67 -1.61
- 4.98 -2.64 -1.61
+ 5.02 -2.93 -1.48
+ 5.01 -2.86 -1.54
+ 5.00 -2.76 -1.61 -1.57 -1.55
+ 4.99 -2.68 -1.61
+ 4.98 -2.65 -1.61
4.97 -2.62 -1.61
- 4.96 -2.59 -1.62
- 4.95 -2.56 -1.63
+ 4.96 -2.60 -1.62
+ 4.95 -2.57 -1.63
4.94 -2.54 -1.65
4.93 -2.50 -1.67
4.92 -2.46 -1.69
@@ -84701,15 +85014,15 @@ Ghana
4.76 -2.13 -1.94
4.75 -2.11 -1.94
4.74 -2.11 -1.95
- 4.73 -2.11 -2.00
- 4.72 -2.10 -2.04
+ 4.73 -2.11 -2.01
+ 4.72 -2.10 -2.05
Gibraltar
- 36.15 -5.39 -5.35
- 36.14 -5.39 -5.34
- 36.13 -5.39 -5.34
- 36.12 -5.39 -5.34
- 36.11 -5.38 -5.34
- 36.10 -5.37 -5.35
+ 36.15 -5.36 -5.32
+ 36.14 -5.36 -5.32
+ 36.13 -5.36 -5.32
+ 36.12 -5.36 -5.32
+ 36.11 -5.36 -5.32
+ 36.10 -5.36 -5.33
Glorioso Islands
-11.54 47.28 47.30
-11.55 47.27 47.31
@@ -84779,9 +85092,9 @@ Greece
41.16 22.03 22.05 22.15 22.28 22.61 22.69 22.71 26.34
41.15 22.02 22.07 22.14 22.31 22.60 26.34
41.14 21.99 22.08 22.12 22.31 22.35 22.39 22.59 26.34
- 41.13 21.94 22.40 22.49 22.53 22.58 26.33
+ 41.13 21.94 22.40 22.49 22.53 22.57 26.33
41.12 21.92 26.34
- 41.11 21.90 26.34
+ 41.11 21.91 26.34
41.10 21.89 26.34
41.09 21.88 26.34
41.08 21.88 26.33
@@ -84793,22 +85106,22 @@ Greece
41.02 21.83 26.38
41.01 21.83 26.38
41.00 21.82 26.38
- 40.99 21.80 26.37
- 40.98 21.78 25.05 25.12 26.35
- 40.97 21.77 25.05 25.12 26.36
+ 40.99 21.80 25.10 25.13 26.37
+ 40.98 21.78 25.04 25.12 26.35
+ 40.97 21.77 25.04 25.12 26.36
40.96 21.77 25.03 25.12 26.36
40.95 21.77 25.01 25.12 26.36
- 40.94 21.76 25.00 25.12 26.35
- 40.93 21.66 21.71 21.74 24.47 24.55 25.00 25.17 25.30 25.32 26.34
- 40.92 21.64 24.41 24.55 24.95 25.21 25.29 25.34 26.32
+ 40.94 21.76 25.00 25.13 26.35
+ 40.93 21.66 21.71 21.74 24.47 24.55 25.00 25.16 25.29 25.31 26.34
+ 40.92 21.64 24.41 24.55 24.95 25.21 25.28 25.34 26.32
40.91 21.37 21.51 21.64 24.39 24.56 24.93 25.24 25.27 25.36 26.31
40.90 21.36 21.53 21.61 24.38 24.57 24.89 25.37 26.31
- 40.89 21.34 21.55 21.60 24.37 24.58 24.87 25.40 26.31
+ 40.89 21.34 21.55 21.60 24.37 24.58 24.87 25.39 26.31
40.88 21.16 21.20 21.33 24.35 24.58 24.86 25.45 26.25
40.87 21.12 24.34 24.59 24.85 25.49 26.24
- 40.86 21.03 24.34 24.61 24.84 25.50 26.22
- 40.85 20.95 24.34 24.61 24.83 25.54 25.59 25.62 26.22
- 40.84 20.95 24.35 24.61 24.64 24.68 24.75 24.78 24.81 25.66 26.22
+ 40.86 21.03 24.34 24.60 24.84 25.50 26.22
+ 40.85 20.95 24.34 24.60 24.83 25.54 25.59 25.65 26.22
+ 40.84 20.95 24.35 24.61 24.64 24.68 24.75 24.78 24.81 25.67 26.22
40.83 20.95 24.35 25.81 25.91 25.93 26.22
40.82 20.95 24.35 25.96 26.21
40.81 20.95 24.33 24.63 24.66 25.97 26.19
@@ -84816,7 +85129,7 @@ Greece
40.79 20.95 24.29 24.60 24.74 25.99 26.16
40.78 20.94 24.27 24.58 24.74 26.01 26.15
40.77 20.93 24.25 24.56 24.74 26.01 26.15
- 40.76 20.93 23.79 23.85 24.23 24.55 24.77 26.02 26.14
+ 40.76 20.93 23.79 23.86 24.23 24.55 24.77 26.02 26.14
40.75 20.93 23.77 23.88 24.21 24.54 24.79 26.02 26.14
40.74 20.94 23.75 23.91 24.19 24.54 24.79 26.02 26.13
40.73 20.94 23.73 23.93 24.17 24.53 24.79 26.03 26.12
@@ -84831,7 +85144,7 @@ Greece
40.64 21.02 23.77 24.50 24.78
40.63 21.02 23.78 24.50 24.79
40.62 21.02 22.87 22.92 23.78 24.50 24.79
- 40.61 21.02 22.87 22.93 23.79 24.56 24.79
+ 40.61 21.02 22.87 22.92 23.79 24.56 24.79
40.60 21.01 22.87 22.93 23.79 24.59 24.79
40.59 21.01 22.86 22.93 23.81 24.59 24.75
40.58 21.01 22.86 22.93 23.83 24.59 24.71
@@ -84851,57 +85164,57 @@ Greece
40.44 20.78 22.61 22.85 23.85 23.98 24.03 25.45 25.70
40.43 20.76 22.61 22.85 23.86 23.98 24.04 25.46 25.70
40.42 20.75 22.61 22.86 23.87 23.98 24.04 25.48 25.70
- 40.41 20.75 22.62 22.87 23.90 23.98 24.05 25.50 25.69
- 40.40 20.75 22.64 22.88 23.92 23.99 24.06 25.52 25.67
+ 40.41 20.75 22.62 22.86 23.89 23.98 24.05 25.50 25.69
+ 40.40 20.75 22.63 22.87 23.91 23.99 24.06 25.52 25.67
40.39 20.75 22.65 22.87 24.07 25.53 25.64
40.38 20.76 22.66 22.87 24.08 25.55 25.60
40.37 20.76 22.67 22.87 24.15
- 40.36 20.75 22.67 22.95 24.19
+ 40.36 20.75 22.67 22.95 24.18
40.35 20.75 22.67 22.97 23.82 23.86 24.19
40.34 20.74 22.66 22.99 23.80 23.94 24.19
- 40.33 20.73 22.65 23.00 23.78 23.95 24.20
- 40.32 20.73 22.64 23.01 23.72 23.97 24.24
- 40.31 20.72 22.64 23.01 23.71 23.98 24.25
- 40.30 20.70 22.63 23.03 23.71 24.00 24.26
+ 40.33 20.73 22.65 23.00 23.77 23.95 24.20
+ 40.32 20.73 22.64 23.01 23.71 23.97 24.24
+ 40.31 20.72 22.64 23.01 23.70 23.98 24.25
+ 40.30 20.70 22.63 23.03 23.70 24.00 24.26
40.29 20.69 22.63 23.07 23.71 24.02 24.27
- 40.28 20.68 22.62 23.09 23.71 24.06 24.28
- 40.27 20.68 22.62 23.11 23.72 24.10 24.29
- 40.26 20.68 22.61 23.13 23.72 24.14 24.30
- 40.25 20.68 22.61 23.19 23.38 23.45 23.74 24.16 24.31
+ 40.28 20.68 22.62 23.09 23.71 24.08 24.28
+ 40.27 20.68 22.62 23.11 23.72 24.13 24.29
+ 40.26 20.68 22.61 23.13 23.72 24.15 24.30
+ 40.25 20.68 22.61 23.18 23.38 23.45 23.74 24.16 24.31
40.24 20.68 22.60 23.21 23.37 23.49 23.76 24.17 24.32
40.23 20.68 22.60 23.26 23.36 23.52 23.76 24.18 24.33
40.22 20.68 22.60 23.28 23.36 23.58 23.77 24.19 24.34
- 40.21 20.68 22.60 23.29 23.35 23.64 23.79 24.19 24.36
+ 40.21 20.68 22.59 23.29 23.35 23.64 23.79 24.19 24.36
40.20 20.67 22.59 23.30 23.35 23.66 23.81 24.20 24.37
- 40.19 20.65 22.59 23.30 23.35 23.67 23.85 24.21 24.38
+ 40.19 20.65 22.58 23.30 23.35 23.67 23.85 24.21 24.38
40.18 20.64 22.58 23.30 23.36 23.68 23.91 24.21 24.39
40.17 20.64 22.57 23.31 23.36 23.69 23.92 24.22 24.39
40.16 20.64 22.57 23.31 23.37 23.70 23.92 24.24 24.40
- 40.15 20.65 22.56 23.31 23.41 23.71 23.97 24.27 24.40
- 40.14 20.65 22.56 23.31 23.41 23.72 23.99 24.27 24.40
+ 40.15 20.65 22.56 23.30 23.41 23.71 23.97 24.27 24.40
+ 40.14 20.65 22.56 23.30 23.41 23.72 23.99 24.27 24.40
40.13 20.65 22.56 23.30 23.42 23.73 23.99 24.28 24.39
- 40.12 20.64 22.57 23.30 23.43 23.74 24.00 24.28 24.37
- 40.11 20.64 22.57 23.29 23.44 23.75 24.00 24.29 24.34
+ 40.12 20.64 22.57 23.29 23.43 23.74 24.00 24.28 24.37
+ 40.11 20.64 22.57 23.29 23.44 23.75 24.00 24.28 24.34
40.10 20.62 22.58 23.29 23.44 23.75 24.00
40.09 20.60 22.58 23.29 23.45 23.76 24.00
40.08 20.48 20.53 20.58 22.58 23.29 23.46 23.77 24.01
40.07 20.42 22.58 23.30 23.47 23.77 24.01
40.06 20.40 22.58 23.32 23.49 23.77 24.01
40.05 20.39 22.59 23.33 23.51 23.77 24.02
- 40.04 20.38 22.60 23.34 23.53 23.78 24.02 25.43 25.46
- 40.03 20.37 22.60 23.34 23.55 23.79 24.02 25.37 25.46
- 40.02 20.37 22.61 23.35 23.57 23.79 24.02 25.35 25.46
- 40.01 20.37 22.63 23.35 23.59 23.80 24.02 25.09 25.15 25.19 25.26 25.34 25.45
+ 40.04 20.38 22.60 23.34 23.53 23.77 24.02 25.43 25.45
+ 40.03 20.37 22.60 23.34 23.55 23.78 24.02 25.37 25.45
+ 40.02 20.37 22.61 23.35 23.57 23.79 24.02 25.35 25.45
+ 40.01 20.37 22.63 23.35 23.59 23.79 24.02 25.09 25.15 25.19 25.26 25.34 25.45
40.00 20.33 22.65 23.36 23.64 23.80 24.02 25.02 25.27 25.33 25.45
- 39.99 20.28 22.66 23.36 23.68 23.81 23.83 23.85 24.01 25.02 25.27 25.33 25.46
- 39.98 20.28 22.68 23.35 23.68 23.87 24.00 25.02 25.28 25.32 25.46
- 39.97 20.28 22.71 23.35 23.68 23.88 24.00 25.02 25.46
+ 39.99 20.28 22.66 23.36 23.68 23.81 23.83 23.85 24.01 25.02 25.27 25.33 25.45
+ 39.98 20.28 22.68 23.35 23.68 23.87 24.00 25.02 25.28 25.31 25.45
+ 39.97 20.28 22.71 23.35 23.68 23.88 24.00 25.02 25.45
39.96 20.29 22.72 23.35 23.68 23.88 24.00 25.03 25.44
39.95 20.29 22.72 23.35 23.41 23.48 23.71 23.89 24.00 25.03 25.42
- 39.94 20.29 22.72 23.51 23.75 23.91 24.00 25.03 25.40
+ 39.94 20.29 22.72 23.51 23.75 23.90 24.00 25.03 25.40
39.93 20.29 22.72 23.54 23.75 25.03 25.39
39.92 20.30 22.72 23.56 23.75 25.04 25.39
- 39.91 20.30 22.73 23.59 23.75 25.05 25.39
+ 39.91 20.30 22.73 23.59 23.75 25.04 25.39
39.90 20.30 22.73 23.65 23.74 25.04 25.39
39.89 20.32 22.74 25.04 25.37
39.88 20.33 22.75 25.03 25.37
@@ -84910,9 +85223,9 @@ Greece
39.85 20.35 22.81 25.03 25.36
39.84 20.36 22.81 25.03 25.37
39.83 19.83 19.87 20.37 22.82 25.03 25.22 25.25 25.37
- 39.82 19.80 19.88 20.38 22.84 25.03 25.06 25.11 25.22 25.26 25.38
- 39.81 19.78 19.91 20.27 20.32 20.38 22.85 25.13 25.23 25.28 25.38
- 39.80 19.65 19.95 20.26 20.35 20.37 22.86 25.13 25.23 25.28 25.38
+ 39.82 19.80 19.88 20.38 22.84 25.03 25.06 25.11 25.22 25.26 25.37
+ 39.81 19.77 19.91 20.27 20.32 20.38 22.85 25.13 25.23 25.28 25.37
+ 39.80 19.65 19.95 20.26 20.35 20.37 22.86 25.13 25.23 25.28 25.37
39.79 19.65 19.95 20.26 22.86 25.15 25.23 25.28 25.36
39.78 19.64 19.95 20.26 22.86 25.31 25.36
39.77 19.63 19.95 20.26 22.86 25.33 25.35
@@ -84922,26 +85235,26 @@ Greece
39.73 19.61 19.94 20.27 22.87
39.72 19.64 19.93 20.28 22.88
39.71 19.64 19.90 20.00 20.03 20.27 22.88
- 39.70 19.64 19.87 19.99 20.07 20.25 22.89
- 39.69 19.66 19.85 19.99 20.10 20.23 22.89
- 39.68 19.66 19.84 19.99 20.12 20.23 22.90
- 39.67 19.66 19.86 20.01 20.14 20.19 22.90
+ 39.70 19.64 19.87 19.98 20.07 20.25 22.89
+ 39.69 19.66 19.85 19.98 20.10 20.23 22.89
+ 39.68 19.66 19.84 19.98 20.12 20.23 22.90
+ 39.67 19.67 19.86 20.01 20.14 20.19 22.90
39.66 19.67 19.86 20.06 20.16 20.19 22.91
39.65 19.71 19.88 20.08 22.91
39.64 19.71 19.90 20.10 22.92
39.63 19.72 19.93 20.12 22.92
39.62 19.72 19.93 20.13 22.92
39.61 19.73 19.93 20.17 22.93
- 39.60 19.73 19.93 20.16 22.93
- 39.59 19.77 19.93 20.16 22.94
- 39.58 19.78 19.92 20.13 22.95
- 39.57 19.80 19.92 20.13 22.97 24.98 25.02
- 39.56 19.81 19.93 20.13 22.99 24.98 25.04
- 39.55 19.82 19.93 20.13 23.02 24.98 25.05
+ 39.60 19.75 19.93 20.16 22.93
+ 39.59 19.77 19.93 20.16 22.95
+ 39.58 19.78 19.92 20.13 22.96
+ 39.57 19.79 19.92 20.13 22.98 24.98 25.02
+ 39.56 19.81 19.93 20.13 23.00 24.98 25.04
+ 39.55 19.82 19.93 20.13 23.02 24.97 25.05
39.54 19.83 19.93 20.13 23.04 24.96 25.05
39.53 19.83 19.93 20.12 23.07 24.96 25.05
39.52 19.83 19.93 20.12 23.09 24.96 25.05
- 39.51 19.83 19.93 20.12 20.15 20.18 23.10 24.96 25.05
+ 39.51 19.83 19.93 20.12 20.14 20.18 23.10 24.96 25.05
39.50 19.83 19.94 20.20 23.11 24.96 25.04
39.49 19.83 19.94 20.20 23.11 24.96 25.03
39.48 19.83 19.94 20.20 23.12 24.96 25.03
@@ -84955,42 +85268,42 @@ Greece
39.40 19.96 20.11 20.22 23.20
39.39 19.98 20.11 20.22 23.21 26.25 26.36
39.38 19.98 20.12 20.22 23.22 26.15 26.37
- 39.37 20.03 20.12 20.26 23.22 24.04 24.07 26.15 26.37
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39.36 20.05 20.12 20.26 23.23 24.04 24.09 26.15 26.37
39.35 20.09 20.11 20.28 23.25 24.03 24.10 26.15 26.41
39.34 20.28 23.27 24.03 24.10 26.16 26.42
39.33 20.28 22.95 22.99 23.28 24.03 24.10 26.14 26.42
39.32 20.28 22.94 23.00 23.28 24.03 24.10 26.08 26.42
- 39.31 20.29 22.95 23.01 23.29 24.03 24.10 26.03 26.42
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39.30 20.30 22.95 23.01 23.29 24.04 24.09 25.90 25.93 26.03 26.41
- 39.29 20.31 22.95 23.10 23.29 23.94 23.96 24.04 24.09 25.90 25.93 25.98 26.41
- 39.28 20.33 22.93 23.12 23.30 23.93 23.98 24.05 24.08 25.88 26.40
- 39.27 20.35 22.87 23.14 23.30 23.92 23.98 25.85 26.41
- 39.26 20.45 22.84 23.14 23.31 23.91 23.98 25.84 26.42
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39.25 20.13 20.15 20.46 22.83 23.15 23.31 23.90 23.98 25.84 26.44
- 39.24 20.11 20.15 20.46 22.83 23.16 23.32 23.89 23.97 25.84 26.46
- 39.23 20.11 20.17 20.46 22.83 23.16 23.33 23.88 23.97 25.83 26.48
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39.22 20.11 20.19 20.46 22.83 23.16 23.34 23.46 23.48 23.59 23.61 23.87 23.96 25.83 26.49
- 39.21 20.11 20.20 20.46 22.84 23.17 23.34 23.44 23.50 23.57 23.62 23.87 23.96 25.83 26.49
- 39.20 20.11 20.20 20.47 22.84 22.86 22.89 23.18 23.35 23.43 23.51 23.57 23.63 23.87 23.94 25.83 26.50
+ 39.21 20.11 20.20 20.46 22.84 23.17 23.34 23.44 23.50 23.57 23.62 23.87 23.95 25.83 26.49
+ 39.20 20.11 20.20 20.47 22.84 22.86 22.89 23.18 23.35 23.43 23.51 23.57 23.63 23.86 23.94 25.83 26.50
39.19 20.12 20.21 20.49 22.90 23.19 23.35 23.42 23.51 23.57 23.64 23.86 23.93 25.82 26.51
39.18 20.13 20.21 20.51 22.91 23.20 23.35 23.40 23.52 23.58 23.66 23.86 23.93 25.82 26.53
- 39.17 20.14 20.21 20.52 22.92 23.20 23.35 23.38 23.52 23.58 23.68 23.83 23.92 25.82 26.55
- 39.16 20.17 20.21 20.53 22.92 23.09 23.12 23.16 23.35 23.38 23.52 23.59 23.72 23.83 23.91 25.82 26.55
- 39.15 20.54 22.92 23.07 23.12 23.16 23.33 23.38 23.52 23.60 23.74 23.82 23.90 25.85 26.55
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+ 39.16 20.19 20.21 20.53 22.92 23.09 23.12 23.16 23.35 23.38 23.52 23.59 23.72 23.83 23.91 25.82 26.54
+ 39.15 20.54 22.92 23.07 23.12 23.16 23.33 23.38 23.52 23.60 23.74 23.82 23.90 25.85 26.54
39.14 20.55 22.94 23.05 23.12 23.15 23.31 23.38 23.51 23.61 23.74 23.82 23.89 25.86 26.55
39.13 20.56 22.96 23.05 23.30 23.38 23.48 23.61 23.80 23.82 23.87 25.87 26.55
39.12 20.57 22.97 23.05 23.24 23.44 23.47 23.62 23.80 25.89 26.57
39.11 20.58 22.98 23.05 23.24 23.64 23.80 25.93 26.57
39.10 20.59 22.98 23.04 23.24 23.64 23.80 25.94 26.57
39.09 20.61 22.99 23.04 23.21 23.64 23.79 25.97 26.57
- 39.08 20.63 22.99 23.04 23.14 23.64 23.77 26.01 26.58
- 39.07 20.65 23.00 23.07 23.13 23.67 23.76 26.07 26.59
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+ 39.07 20.66 23.00 23.07 23.13 23.67 23.76 26.07 26.59
39.06 20.67 23.00 23.69 23.73 26.07 26.61
- 39.05 20.68 23.00 23.05 23.08 23.28 23.30 26.10 26.62
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39.04 20.68 23.08 23.25 23.32 26.11 26.62
39.03 20.69 23.08 23.23 23.35 26.12 26.62
- 39.02 20.69 23.08 23.21 23.38 26.13 26.62
+ 39.02 20.69 23.08 23.20 23.38 26.13 26.62
39.01 20.69 23.07 23.11 23.39 26.14 26.62
39.00 20.69 23.05 23.09 23.39 26.24 26.61
38.99 20.69 23.03 23.08 23.39 24.48 24.50 26.28 26.55
@@ -84999,43 +85312,43 @@ Greece
38.96 20.70 23.01 23.06 23.43 24.44 24.56 26.35 26.54
38.95 20.71 23.01 23.03 23.43 24.44 24.57 26.38 26.46
38.94 20.71 23.00 23.03 23.43 24.44 24.58
- 38.93 20.72 22.96 23.02 23.44 24.44 24.58
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38.92 20.74 22.95 22.99 23.44 24.44 24.58
38.91 20.74 23.45 24.43 24.58
38.90 20.74 22.85 22.88 23.45 24.42 24.58
- 38.89 20.74 22.85 22.89 23.46 24.42 24.58
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38.88 20.75 22.84 22.86 23.46 24.42 24.60
38.87 20.75 22.80 22.84 23.46 24.42 24.62
- 38.86 20.73 22.80 22.82 23.47 24.42 24.44 24.46 24.64
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38.85 20.65 20.70 20.73 22.71 22.82 23.00 23.03 23.48 24.47 24.65
38.84 20.64 20.71 20.73 22.72 22.82 23.00 23.04 23.51 24.49 24.66
38.83 20.63 22.72 22.82 22.99 23.05 23.10 23.15 23.53 24.49 24.67
38.82 20.62 22.73 22.82 22.91 23.17 23.55 24.53 24.67
38.81 20.62 22.74 22.82 22.85 23.19 23.56 24.55 24.69
- 38.80 20.61 22.77 23.21 23.58 24.52 24.69
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38.79 20.59 22.84 23.23 23.60 24.52 24.69
- 38.78 20.59 22.93 23.25 23.62 24.52 24.69
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38.77 20.58 20.73 20.75 20.84 20.86 22.94 23.27 23.73 24.53 24.69
38.76 20.58 20.73 20.75 20.83 20.87 23.03 23.29 23.73 24.54 24.58 24.60 24.67
38.75 20.57 20.73 20.75 20.82 20.87 23.05 23.31 23.74 24.55 24.57 24.61 24.66
- 38.74 20.57 20.74 20.87 23.06 23.31 23.75
- 38.73 20.57 20.74 20.88 23.07 23.31 23.75
- 38.72 20.56 20.74 20.88 23.07 23.32 23.77
- 38.71 20.56 20.73 20.88 23.08 23.35 23.80
- 38.70 20.55 20.73 20.88 23.08 23.36 23.84
- 38.69 20.55 20.73 20.89 23.08 23.17 23.21 23.37 23.88 23.97 24.00
- 38.68 20.55 20.73 20.77 20.80 20.89 23.09 23.15 23.23 23.39 23.94 23.96 24.11
+ 38.74 20.57 20.73 20.87 23.05 23.31 23.75
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+ 38.72 20.56 20.73 20.88 23.06 23.32 23.77
+ 38.71 20.56 20.73 20.88 23.07 23.35 23.80
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+ 38.68 20.55 20.73 20.77 20.79 20.89 23.08 23.15 23.23 23.39 24.11
38.67 20.54 20.81 20.90 23.09 23.15 23.27 23.41 24.15
- 38.66 20.54 20.81 20.91 23.10 23.14 23.32 23.43 24.16
- 38.65 20.54 20.81 20.89 23.10 23.13 23.33 23.44 24.16
+ 38.66 20.54 20.81 20.91 23.09 23.14 23.32 23.43 24.16
+ 38.65 20.54 20.81 20.89 23.10 23.13 23.33 23.43 24.16
38.64 20.54 20.81 20.88 23.34 23.44 24.16
38.63 20.54 20.79 20.87 20.96 20.98 23.34 23.46 24.15
- 38.62 20.53 20.79 20.87 20.96 20.98 23.34 23.48 24.13 25.57 25.59
- 38.61 20.53 20.72 20.74 20.80 20.86 20.95 20.99 23.34 23.49 24.13 25.51 25.60 25.95 26.03
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+ 38.60 20.53 20.71 20.75 20.81 20.85 20.95 21.00 23.34 23.49 24.13 25.51 25.62 25.87 26.07
38.59 20.53 20.58 20.60 20.69 20.76 20.81 20.85 20.95 21.01 23.34 23.49 24.15 25.51 25.63 25.83 26.07
38.58 20.53 20.57 20.61 20.65 20.77 20.81 20.85 20.94 21.01 23.33 23.49 24.16 25.51 25.63 25.83 26.08
- 38.57 20.53 20.57 20.62 20.65 20.86 20.93 21.01 23.33 23.50 24.18 25.53 25.63 25.83 26.15
+ 38.57 20.53 20.57 20.62 20.65 20.86 20.93 21.01 23.32 23.50 24.18 25.53 25.63 25.83 26.15
38.56 20.53 20.56 20.88 20.92 21.00 23.34 23.56 24.19 25.53 25.63 25.82 26.16
38.55 20.53 20.56 20.88 20.91 21.00 23.38 23.59 24.21 25.54 25.62 25.82 26.17
38.54 20.88 20.91 21.00 23.39 23.60 24.23 25.54 25.61 25.82 26.17
@@ -85043,47 +85356,47 @@ Greece
38.52 21.00 23.39 23.53 23.56 23.61 24.24 25.55 25.61 25.82 26.16
38.51 20.64 20.67 21.01 23.47 23.53 23.57 23.61 24.24 25.82 26.16
38.50 20.64 20.68 21.02 23.59 23.61 24.23 25.83 26.15
- 38.49 20.61 20.68 21.02 21.04 21.06 24.21 25.84 26.15
- 38.48 20.52 20.58 20.61 20.68 21.06 24.20 25.85 26.15
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+ 38.48 20.52 20.58 20.60 20.68 21.06 24.20 25.85 26.15
38.47 20.52 20.58 20.60 20.68 21.06 24.20 25.86 26.16
- 38.46 20.52 20.70 21.09 24.19 25.88 26.16
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38.45 20.52 20.71 21.07 24.19 25.89 26.16
- 38.44 20.53 20.71 21.06 24.19 25.93 26.16
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38.43 20.52 20.60 20.63 20.71 21.06 24.20 25.94 26.15
38.42 20.52 20.60 20.63 20.71 21.06 24.21 25.94 26.14
38.41 20.52 20.61 20.63 20.71 21.07 24.21 25.94 26.14
- 38.40 20.52 20.61 20.63 20.72 21.07 24.21 25.94 26.15
- 38.39 20.52 20.75 21.08 23.68 23.72 24.21 25.94 26.15
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+ 38.39 20.52 20.75 21.08 23.68 23.71 24.21 25.94 26.14
38.38 20.52 20.62 20.64 20.76 21.09 21.34 21.36 23.66 23.75 23.81 23.87 24.22 25.95 26.15
- 38.37 20.39 20.43 20.52 20.76 21.08 21.32 21.41 23.67 24.04 24.22 25.96 26.15
- 38.36 20.39 20.44 20.52 20.63 20.65 20.76 21.08 21.30 21.41 23.69 24.04 24.22 25.97 26.16
- 38.35 20.38 20.44 20.52 20.63 20.66 20.75 21.07 21.30 21.41 23.71 23.75 23.80 24.04 24.22 25.97 26.16
- 38.34 20.38 20.47 20.51 20.63 20.67 20.77 21.07 21.28 21.41 23.83 24.01 24.22 25.96 26.16
+ 38.37 20.38 20.43 20.52 20.76 21.08 21.31 21.41 23.67 24.03 24.22 25.96 26.15
+ 38.36 20.38 20.44 20.52 20.63 20.65 20.76 21.08 21.30 21.41 23.68 24.04 24.22 25.97 26.15
+ 38.35 20.38 20.44 20.52 20.63 20.66 20.75 21.07 21.30 21.41 23.70 23.75 23.80 24.04 24.22 25.97 26.15
+ 38.34 20.38 20.47 20.51 20.63 20.67 20.77 21.07 21.28 21.41 23.83 24.01 24.22 25.96 26.15
38.33 20.38 20.47 20.49 20.63 20.67 20.77 21.07 21.27 21.41 21.64 21.71 23.85 24.01 24.23 25.96 26.16
- 38.32 20.38 20.63 20.67 20.77 21.10 21.26 21.41 21.58 21.73 23.88 24.01 24.24 25.96 26.17
- 38.31 20.38 20.63 20.68 20.77 21.13 21.24 21.43 21.56 21.75 23.90 24.03 24.25 25.92 26.17
- 38.30 20.38 20.62 20.69 20.75 21.13 21.19 21.45 21.54 21.75 23.96 24.09 24.26 25.91 26.17
- 38.29 20.38 20.62 20.67 20.69 21.14 21.18 21.46 21.54 21.74 23.96 24.10 24.26 25.87 26.17
- 38.28 20.37 20.62 20.66 20.69 21.50 21.53 21.74 23.97 24.09 24.26 25.86 26.15
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+ 38.31 20.38 20.63 20.68 20.77 21.13 21.20 21.22 21.24 21.43 21.56 21.75 23.90 24.03 24.25 25.92 26.17
+ 38.30 20.37 20.62 20.69 20.73 21.13 21.19 21.45 21.54 21.75 23.96 24.08 24.26 25.91 26.17
+ 38.29 20.37 20.62 20.67 20.69 21.14 21.18 21.46 21.54 21.74 23.96 24.10 24.26 25.87 26.17
+ 38.28 20.36 20.62 20.66 20.69 21.50 21.53 21.74 23.97 24.09 24.26 25.86 26.15
38.27 20.35 20.70 21.73 23.99 24.09 24.26 25.86 26.13
- 38.26 20.34 20.71 21.72 24.00 24.09 24.26 25.85 26.12
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38.25 20.34 20.71 21.72 24.02 24.09 24.26 25.85 26.12
38.24 20.34 20.71 21.71 24.03 24.09 24.26 25.85 26.12
38.23 20.34 20.71 21.36 21.38 21.70 24.04 24.12 24.26 25.85 26.12
38.22 20.34 20.73 21.36 21.41 21.70 24.06 24.11 24.28 25.86 26.12
- 38.21 20.32 20.75 21.36 21.47 21.69 24.07 24.11 24.30 25.88 26.12
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38.20 20.32 20.76 21.36 21.48 21.68 24.08 24.11 24.15 24.17 24.32 25.90 26.10
- 38.19 20.32 20.76 21.36 21.50 21.67 24.08 24.17 24.33 25.91 26.07
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38.18 20.32 20.77 21.36 21.52 21.65 24.08 24.18 24.34 25.92 26.05
38.17 20.33 20.44 20.46 20.78 21.36 21.57 21.63 24.09 24.18 24.40 25.94 26.04
38.16 20.34 20.43 20.46 20.78 21.36 24.09 24.19 24.42 24.53 24.59 25.95 26.04
38.15 20.36 20.42 20.47 20.79 21.36 24.09 24.17 24.59 25.96 26.03
- 38.14 20.37 20.39 20.47 20.80 21.36 24.07 24.17 24.59 25.99 26.03
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38.13 20.48 20.80 21.35 24.07 24.17 24.59
- 38.12 20.48 20.81 21.34 24.02 24.05 24.07 24.17 24.59
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38.11 20.48 20.81 21.34 24.00 24.17 24.58
- 38.10 20.50 20.81 21.33 24.00 24.19 24.58
- 38.09 20.52 20.58 20.65 20.81 21.33 24.00 24.19 24.59
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+ 38.09 20.52 20.58 20.65 20.81 21.33 24.00 24.19 24.58
38.08 20.55 20.57 20.67 20.81 21.32 24.01 24.19 24.59
38.07 20.68 20.81 21.31 24.01 24.27 24.60
38.06 20.69 20.81 21.30 24.01 24.27 24.60
@@ -85092,28 +85405,28 @@ Greece
38.03 21.28 24.02 24.30 24.59
38.02 21.27 23.51 23.58 24.03 24.30 24.59
38.01 21.26 23.51 23.57 24.04 24.30 24.59 24.76 24.79
- 38.00 21.25 24.04 24.31 24.58 24.73 24.80
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37.99 21.25 24.04 24.32 24.41 24.44 24.58 24.71 24.80
37.98 21.24 24.04 24.32 24.41 24.45 24.58 24.69 24.83
37.97 21.22 24.03 24.34 24.41 24.46 24.57 24.68 24.84
37.96 21.20 23.28 23.36 24.02 24.36 24.40 24.46 24.56 24.68 24.84
37.95 21.12 21.15 21.19 23.22 23.41 24.02 24.46 24.55 24.68 24.84
- 37.94 21.12 23.20 23.41 23.58 23.60 24.02 24.47 24.50 24.67 24.84
- 37.93 20.67 20.72 21.11 23.18 23.39 23.57 23.61 24.04 24.67 24.84
- 37.92 20.65 20.72 21.11 23.17 23.39 23.55 23.61 23.66 23.68 24.05 24.67 24.86
- 37.91 20.64 20.73 21.10 23.15 23.39 23.55 23.69 24.05 24.68 24.96
- 37.90 20.63 20.73 21.10 23.02 23.07 23.12 23.39 23.54 23.70 24.05 24.68 24.97
- 37.89 20.63 20.74 21.09 23.02 23.39 23.53 23.71 24.05 24.69 24.97
- 37.88 20.62 20.74 21.09 23.02 23.39 23.52 23.71 24.06 24.70 24.97
- 37.87 20.61 20.75 21.09 23.01 23.43 23.49 23.72 24.07 24.70 24.97
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- 37.85 20.61 20.83 21.09 23.13 23.73 24.07 24.76 24.96
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37.84 20.61 20.86 21.09 23.14 23.73 24.07 24.77 24.97
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37.78 20.65 20.92 21.25 23.19 23.48 23.56 23.87 24.09 24.83 24.99 26.63 27.07
37.77 20.65 20.92 21.27 23.19 23.41 23.57 23.87 24.09 24.84 25.00 26.58 27.07
37.76 20.66 20.94 21.28 23.19 23.41 23.57 23.87 24.09 24.85 25.00 26.57 27.07
@@ -85122,29 +85435,29 @@ Greece
37.73 20.69 20.99 21.29 23.17 23.41 23.55 23.90 24.08 24.89 25.00 26.57 27.07
37.72 20.69 20.99 21.30 23.18 23.42 23.55 23.90 24.08 24.89 24.99 26.57 27.07
37.71 20.70 20.89 20.93 21.00 21.30 23.18 23.43 23.54 23.91 24.08 24.90 24.99 26.57 27.07
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37.68 20.74 20.86 20.98 21.00 21.28 23.17 23.44 23.53 23.93 24.08 24.31 24.39 24.93 25.07 26.27 26.37 26.57 26.65 26.73 26.99
37.67 20.76 20.86 21.28 23.17 23.46 23.52 23.93 24.08 24.29 24.40 24.94 25.07 26.25 26.37 26.57 26.63 26.75 26.96
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37.65 20.78 20.86 21.29 23.18 23.99 24.06 24.27 24.41 24.97 25.20 26.22 26.36 26.76 26.90
37.64 20.79 20.86 21.30 21.33 21.37 23.18 23.33 23.40 24.01 24.04 24.27 24.41 24.70 24.74 24.97 25.22 26.05 26.35 26.77 26.89
37.63 21.30 21.32 21.40 23.18 23.31 23.41 24.26 24.41 24.69 24.75 24.98 25.25 26.04 26.34 26.77 26.88
37.62 21.30 21.32 21.41 23.18 23.30 23.41 24.26 24.40 24.68 24.75 24.98 25.25 26.03 26.32
37.61 21.42 23.21 23.30 23.41 24.26 24.40 24.64 24.75 25.01 25.26 26.01 26.31
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37.53 21.55 22.74 22.80 23.53 24.26 24.33 25.14 25.23 25.96 26.12
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37.49 21.58 22.74 22.97 23.50 24.42 24.45 24.88 24.95 25.30 25.44
- 37.48 21.59 22.75 22.98 23.51 24.41 24.45 24.88 24.96 25.29 25.46
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37.47 21.60 22.76 22.98 23.52 24.39 24.45 24.89 24.96 25.29 25.47
37.46 21.60 22.76 22.98 23.53 24.38 24.45 24.89 24.96 25.29 25.47
37.45 21.61 22.76 22.99 23.53 24.37 24.45 24.88 24.96 25.31 25.47
@@ -85161,108 +85474,108 @@ Greece
37.34 21.68 22.82 23.06 23.28 23.41 23.58 24.36 24.45 26.52 26.61
37.33 21.68 22.83 23.10 23.28 23.39 23.56 24.36 24.45 26.52 26.61
37.32 21.68 22.83 23.10 23.20 23.37 23.51 24.35 24.44 26.52 26.56 26.59 26.61
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37.29 21.67 22.85 23.09 23.21 23.36 23.43 24.35 24.38 26.51 26.57
37.28 21.65 22.86 23.08 23.20 26.52 26.57
37.27 21.64 22.86 23.08 23.17 26.53 26.57
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37.21 21.57 22.90 24.45 24.53 25.52 25.55 26.79 26.81
37.20 21.56 22.91 24.43 24.53 25.49 25.56 26.77 26.84
37.19 21.56 22.92 24.42 24.54 25.48 25.57 26.76 26.86
37.18 21.56 22.92 24.42 24.54 25.48 25.58 26.76 26.86
37.17 21.55 22.92 24.42 24.54 25.46 25.59 26.76 26.86
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36.99 21.63 21.98 22.14 23.02 24.65 24.76 25.01 25.08 25.10 25.24 25.37 25.58 26.91 27.05
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36.96 21.64 21.94 22.13 23.02 24.65 24.77 25.02 25.09 25.39 25.57 26.91 27.05
36.95 21.65 21.94 22.13 23.02 24.65 24.77 25.03 25.09 25.41 25.56 26.90 27.05
36.94 21.65 21.94 22.12 23.02 24.66 24.77 25.05 25.09 25.41 25.54 25.98 26.01 26.90 27.05
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36.91 21.68 21.93 22.12 23.04 23.43 23.47 24.68 24.74 25.43 25.49 25.62 25.67 25.94 26.07 26.93 26.99 27.21 27.29
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36.89 21.67 21.93 22.13 23.05 23.44 23.47 24.70 24.72 25.59 25.69 25.92 26.08 27.13 27.35
36.88 21.67 21.93 22.15 22.19 22.21 23.05 25.46 25.48 25.59 25.69 25.89 26.08 27.11 27.35
36.87 21.67 21.93 22.22 23.05 25.44 25.48 25.59 25.69 25.86 26.03 27.10 27.36
36.86 21.67 21.93 22.23 23.06 25.43 25.48 25.64 25.68 25.84 26.00 27.08 27.36
36.85 21.67 21.94 22.24 23.07 23.86 23.89 24.53 24.61 25.42 25.48 25.83 25.98 27.06 27.36
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36.80 21.69 21.98 22.28 23.10 24.51 24.65 25.29 25.31 25.72 25.91 27.00 27.21
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36.66 22.35 22.56 22.80 23.04 24.31 24.53 24.83 24.90 25.06 25.15 25.31 25.40 26.96 26.98
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36.58 22.36 22.49 22.91 23.10 24.92 24.97 26.25 26.47 27.11 27.21 27.75 27.88
36.57 22.36 22.49 22.92 23.13 26.25 26.47 27.11 27.21 27.75 27.88
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36.55 22.35 22.49 22.93 23.16 26.25 26.37 27.11 27.20 27.78 27.88
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36.53 22.34 22.49 22.94 23.16 26.25 26.35 27.81 27.88
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36.49 22.34 22.51 23.05 23.17 26.30 26.35
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36.47 22.36 22.52 23.05 23.20 25.35 25.45 27.28 27.38
36.46 22.38 22.52 23.05 23.21 25.35 25.46 27.28 27.38 28.20 28.23
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36.41 22.46 22.51 25.41 25.49 25.75 25.78 27.28 27.45 28.05 28.24
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36.37 22.91 22.97 25.36 25.50 25.72 25.86 27.36 27.43 27.96 28.24
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36.34 22.89 22.99 25.35 25.49 25.73 25.85 27.88 28.22
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36.29 22.89 23.07 27.81 28.19
36.28 22.89 23.08 27.79 28.18
36.27 22.90 23.09 27.79 28.18
@@ -85272,23 +85585,23 @@ Greece
36.23 22.89 23.11 27.50 27.62 27.76 28.17
36.22 22.89 23.11 27.50 27.62 27.76 28.17
36.21 22.89 23.08 27.50 27.62 27.75 28.15
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36.17 22.91 23.06 27.69 28.14
36.16 22.91 23.06 27.67 28.10
36.15 22.93 23.06 27.67 28.10
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36.13 22.97 23.06 27.68 28.08
36.12 22.98 23.00 27.69 28.08
36.11 27.69 28.10
36.10 27.70 28.10
36.09 27.72 28.10
36.08 27.73 28.10
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36.03 27.74 27.97
36.02 27.73 27.95
36.01 27.73 27.94
@@ -85303,9 +85616,9 @@ Greece
35.92 27.71 27.86
35.91 23.26 23.28 27.72 27.85
35.90 23.26 23.29 27.72 27.83
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35.86 23.27 23.34
35.85 23.27 23.34
35.84 23.28 23.34
@@ -85314,7 +85627,7 @@ Greece
35.81 23.31 23.34 27.14 27.24
35.80 27.14 27.24
35.79 27.14 27.23
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35.77 27.14 27.22
35.76 27.15 27.22
35.75 27.15 27.22
@@ -85333,30 +85646,30 @@ Greece
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35.61 23.59 23.61 23.70 23.78 24.10 24.14 27.05 27.18
35.60 23.58 23.61 23.70 23.78 24.08 24.18 27.05 27.19
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35.58 23.57 23.61 23.70 23.78 24.07 24.19 27.05 27.20
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35.52 23.55 23.65 23.70 24.21 27.09 27.23
35.51 23.55 23.67 23.69 24.20 27.09 27.24
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35.41 23.54 24.27 24.60 25.06 26.87 27.01 27.11 27.17
35.40 23.53 24.27 24.57 25.06 26.86 27.01 27.12 27.16
35.39 23.53 24.27 24.52 25.06 26.85 27.01 27.12 27.15
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35.37 23.52 24.30 24.40 25.06 26.83 26.95
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35.35 23.52 25.21 25.27 25.32 25.35 25.38 25.61 25.69 26.84 26.92
35.34 23.53 25.39 25.58 25.77 26.85 26.90
35.33 23.53 25.40 25.55 25.77 26.86 26.88
@@ -85369,21 +85682,21 @@ Greece
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35.06 24.73 26.26
@@ -85397,10 +85710,10 @@ Greece
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34.87 24.06 24.13
34.86 24.03 24.13
34.85 24.03 24.13
@@ -85410,94 +85723,94 @@ Greece
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Greenland
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Grenada
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Guadeloupe
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@@ -87964,187 +88277,187 @@ Guatemala
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@@ -88154,10 +88467,10 @@ Guatemala
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@@ -88310,58 +88623,60 @@ Guatemala
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Guernsey
49.74 -2.18 -2.16
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@@ -88986,12 +89301,12 @@ Guinea-Bissau
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Haiti
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@@ -90094,101 +90409,103 @@ Honduras
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15.43 -88.60 -83.75
@@ -90196,19 +90513,19 @@ Honduras
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@@ -90232,18 +90549,18 @@ Honduras
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14.96 -89.17 -83.50
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14.92 -89.19 -83.54
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14.90 -89.20 -83.56
14.89 -89.22 -83.58
14.88 -89.23 -83.59
@@ -90295,7 +90612,7 @@ Honduras
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14.36 -89.22 -89.12 -89.10 -85.14
@@ -90337,7 +90654,7 @@ Honduras
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@@ -90351,7 +90668,7 @@ Honduras
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13.82 -87.74 -86.27 -85.76 -85.72
13.81 -87.73 -86.28 -85.75 -85.73
13.80 -87.72 -86.28
@@ -90404,13 +90721,13 @@ Honduras
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13.28 -87.68 -87.60 -87.52 -86.69
13.27 -87.68 -87.60 -87.52 -86.83 -86.80 -86.70
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13.25 -87.67 -87.60 -87.51 -86.86 -86.76 -86.72
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13.23 -87.65 -87.62 -87.48 -86.89
13.22 -87.47 -86.90
13.21 -87.46 -86.90
@@ -90433,8 +90750,8 @@ Honduras
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13.02 -87.32 -86.96
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12.99 -87.32 -86.99
12.98 -87.32 -87.00
12.97 -87.32 -87.19 -87.05 -87.01
@@ -90449,16 +90766,16 @@ Hong Kong
22.51 114.03 114.34
22.50 114.02 114.34
22.49 113.98 114.34
- 22.48 113.97 114.35
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22.47 113.97 114.36
22.46 113.96 114.37
22.45 113.94 114.38
22.44 113.94 114.40
22.43 113.93 114.40
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22.38 113.90 114.39
22.37 113.90 114.39
22.36 113.90 114.28 114.32 114.39
@@ -90471,7 +90788,7 @@ Hong Kong
22.29 113.88 114.03 114.11 114.32
22.28 113.85 114.03 114.10 114.32
22.27 113.84 114.02 114.10 114.31
- 22.26 113.83 114.02 114.10 114.31
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22.25 113.83 114.02 114.10 114.31
22.24 113.82 114.01 114.09 114.26 114.28 114.30
22.23 113.82 114.02 114.09 114.26
@@ -90483,9 +90800,9 @@ Hong Kong
22.17 114.10 114.15 114.19 114.21
22.16 114.10 114.15
Howland Island
- 0.81 -176.64 -176.62
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+ 0.79 -176.65 -176.62
0.78 -176.64 -176.62
Hungary
48.57 20.74 20.82 21.39 21.43
@@ -90538,8 +90855,8 @@ Hungary
48.10 19.43 22.81
48.09 19.27 22.83
48.08 19.06 19.16 19.24 22.84
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48.05 18.82 22.86
48.04 18.81 22.86
48.03 17.17 17.21 18.80 22.87
@@ -90566,9 +90883,9 @@ Hungary
47.82 17.02 17.65 18.74 22.77
47.81 17.02 17.66 18.73 22.76
47.80 17.03 17.67 18.49 18.61 18.71 22.72
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47.78 17.03 17.73 18.32 22.68
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47.76 16.54 16.62 17.03 22.43 22.46 22.65
47.75 16.52 16.65 17.03 22.42 22.50 22.62
47.74 16.51 16.67 17.03 22.42 22.54 22.59
@@ -90589,7 +90906,7 @@ Hungary
47.59 16.63 22.17
47.58 16.63 22.17
47.57 16.64 22.17
- 47.56 16.64 22.16
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47.55 16.64 22.09
47.54 16.67 22.07
47.53 16.67 22.06
@@ -90661,8 +90978,8 @@ Hungary
46.87 16.08 21.60
46.86 16.08 21.60
46.85 16.08 21.60
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46.82 16.31 21.56
46.81 16.30 21.53
46.80 16.30 21.52
@@ -90683,7 +91000,7 @@ Hungary
46.65 16.35 21.43
46.64 16.35 21.43
46.63 16.35 21.42
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46.61 16.36 21.40
46.60 16.38 21.33 21.35 21.39
46.59 16.41 21.31
@@ -90716,7 +91033,7 @@ Hungary
46.32 16.86 21.17
46.31 16.86 21.17
46.30 16.86 21.17
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46.28 16.87 21.16
46.27 16.88 21.15
46.26 16.90 21.14
@@ -90732,24 +91049,24 @@ Hungary
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46.12 17.07 19.50 19.75 19.84 20.12 20.16 20.18 20.28 20.56 20.68
46.11 17.09 19.50 19.78 19.81 20.20 20.27 20.59 20.64
46.10 17.19 19.50 20.21 20.26
46.09 17.20 19.50 20.23 20.25
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46.07 17.23 19.47
46.06 17.24 19.46
46.05 17.24 19.45
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46.02 17.25 19.38
46.01 17.25 19.37
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45.98 17.28 19.05 19.11 19.28
45.97 17.28 19.05 19.13 19.27
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45.95 17.33 19.05
45.94 17.33 19.00
45.93 17.39 17.42 17.53 18.99
@@ -90778,23 +91095,23 @@ Iceland
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66.34 -23.19 -22.19 -16.51 -15.66 -15.02 -14.63
@@ -90802,96 +91119,96 @@ Iceland
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@@ -91180,7 +91497,7 @@ India
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34.62 73.90 75.26 75.92 78.32
@@ -91414,7 +91731,7 @@ India
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@@ -91627,7 +91944,7 @@ India
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@@ -91698,71 +92015,71 @@ India
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28.80 72.39 80.13 93.86 96.58
@@ -91772,43 +92089,43 @@ India
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28.36 72.13 81.18 93.06 96.91 97.02 97.14
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28.34 72.12 81.20 93.03 97.16
@@ -91873,7 +92190,7 @@ India
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27.73 70.05 70.75 70.92 82.35 88.12 88.83 91.61 97.06
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27.70 70.04 82.39 82.58 82.68 88.11 88.83 91.59 96.99
27.69 70.03 82.40 82.54 82.69 88.11 88.82 91.59 96.98
@@ -91901,7 +92218,7 @@ India
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27.43 69.84 83.18 83.34 83.70 83.82 84.24 88.02 88.77 91.72 91.94 91.98 96.90
27.42 69.83 83.20 83.34 83.72 83.82 84.25 88.01 88.77 91.73 91.84 91.99 96.90
27.41 69.82 83.21 83.34 83.74 83.82 84.26 88.01 88.78 91.73 91.82 91.99 96.91
@@ -91919,7 +92236,7 @@ India
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27.24 69.61 84.65 87.98 88.82 92.02 96.18 96.83 97.05
27.23 69.60 84.65 87.98 88.79 92.02 96.13 96.84 97.06
@@ -91938,7 +92255,7 @@ India
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27.06 69.49 84.64 87.98 88.85 91.98 95.94
27.05 69.49 84.63 87.98 88.85 91.99 95.93
27.04 69.49 84.64 87.99 88.85 92.00 95.92
@@ -91954,20 +92271,20 @@ India
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26.90 69.47 84.97 88.10 89.06 90.31 90.39 92.06 95.72
26.89 69.46 85.01 88.11 89.07 90.30 90.41 91.88 91.92 92.06 95.71
26.88 69.46 85.02 88.12 89.07 90.30 90.42 91.41 91.45 91.88 91.93 92.05 95.70
26.87 69.46 85.02 85.08 85.15 88.12 89.08 90.29 90.44 91.39 91.48 91.88 91.95 92.03 95.66
26.86 69.46 85.02 85.05 85.17 85.57 85.62 88.13 89.08 89.32 89.35 90.20 90.45 91.37 91.49 91.78 91.84 91.88 91.97 92.00 95.63
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26.84 69.46 85.17 85.52 85.66 88.14 89.09 89.25 89.38 90.16 90.49 91.36 91.50 91.75 95.62
26.83 69.45 85.17 85.50 85.68 88.14 89.11 89.24 89.40 90.16 90.51 91.36 91.50 91.73 95.61
26.82 69.45 85.17 85.48 85.69 88.14 89.42 90.15 90.53 91.35 91.51 91.56 91.61 91.71 95.61
26.81 69.45 85.17 85.46 85.70 88.14 89.44 89.47 89.53 90.15 90.55 91.04 91.22 91.34 91.52 91.54 91.63 91.67 95.60
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26.77 69.45 85.19 85.35 85.71 88.14 89.62 90.12 95.48
26.76 69.46 85.22 85.34 85.71 88.15 89.62 90.10 95.47
26.75 69.46 85.26 85.31 85.71 88.15 89.62 90.02 95.47
@@ -91992,7 +92309,7 @@ India
26.56 70.09 86.44 86.98 87.05 88.08 88.36 88.38 95.12
26.55 70.11 86.46 86.97 87.05 88.07 88.36 88.38 95.12
26.54 70.12 86.49 86.95 87.05 88.07 88.35 88.38 95.11
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26.52 70.14 86.52 86.89 87.06 88.06 88.35 88.42 95.10
26.51 70.14 86.53 86.87 87.06 88.06 88.34 88.45 95.09
26.50 70.14 86.55 86.86 87.06 88.06 88.34 88.46 95.08
@@ -92003,7 +92320,7 @@ India
26.45 70.14 86.65 86.72 86.77 86.82 87.08 87.74 87.80 87.82 87.90 88.05 88.47 88.53 95.06
26.44 70.14 86.67 86.72 87.09 87.74 87.91 88.05 88.48 88.58 95.06
26.43 70.14 86.69 86.71 87.10 87.39 87.49 87.66 87.69 87.73 87.91 88.04 88.48 88.59 95.07
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26.41 70.14 87.12 87.19 87.22 87.34 87.53 87.62 87.92 88.03 88.49 88.61 95.07
26.40 70.14 87.23 87.34 87.55 87.61 87.94 88.02 88.49 88.63 95.07
26.39 70.14 87.24 87.33 87.57 87.59 87.96 88.01 88.50 88.63 95.07
@@ -92100,12 +92417,12 @@ India
25.48 70.63 88.64 88.67 88.81 89.81 94.78
25.47 70.63 88.81 89.80 94.76
25.46 70.63 88.82 89.80 94.71
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25.42 70.63 88.82 89.79 94.65
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25.39 70.64 88.82 89.78 94.62
25.38 70.64 88.82 89.78 94.61
25.37 70.65 88.82 89.78 94.61
@@ -92132,7 +92449,7 @@ India
25.16 70.82 88.44 88.51 88.58 88.67 88.81 88.86 88.93 90.29 91.06 91.27 91.99 92.04 94.66
25.15 70.83 88.44 88.70 88.80 88.88 88.93 90.32 90.61 90.63 91.00 91.29 91.85 91.92 91.97 92.07 94.68
25.14 70.83 88.44 90.34 90.48 90.65 90.73 90.76 90.96 91.33 91.73 92.09 94.69
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25.12 70.84 88.44 91.41 91.50 91.57 91.68 92.10 94.70
25.11 70.84 88.44 91.58 91.67 92.14 94.71
25.10 70.85 88.44 92.17 94.71
@@ -92190,7 +92507,7 @@ India
24.58 70.94 88.09 92.15 94.48
24.57 70.94 88.09 92.15 94.47
24.56 70.94 88.09 92.15 94.45
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24.54 70.94 88.10 92.12 94.42
24.53 70.96 88.10 92.11 94.42
24.52 70.96 88.10 92.10 94.42
@@ -92262,8 +92579,8 @@ India
23.86 68.18 88.67 91.20 93.36 94.06 94.14
23.85 68.17 88.66 91.21 93.36 94.06 94.14
23.84 68.17 88.59 91.21 93.36 94.07 94.14
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23.81 68.16 88.58 91.20 93.37
23.80 68.16 88.58 91.20 93.37
23.79 68.16 88.58 91.19 93.37
@@ -92324,8 +92641,8 @@ India
23.24 68.54 88.76 88.79 88.85 91.27 91.75 92.33 93.39
23.23 68.58 88.89 91.27 91.37 91.40 91.76 92.32 93.39
23.22 68.58 88.91 91.27 91.37 91.40 91.76 92.31 93.39
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23.19 68.59 88.96 91.28 91.36 91.43 91.77 92.31 93.39
23.18 68.61 88.96 91.28 91.36 91.43 91.77 92.31 93.38
23.17 68.63 88.96 91.28 91.36 91.45 91.78 92.31 93.38
@@ -92349,15 +92666,15 @@ India
22.99 68.87 88.84 91.50 91.73 92.34 93.15 93.23 93.29
22.98 68.90 88.84 91.51 91.71 92.34 93.15
22.97 68.93 88.85 91.52 91.70 92.34 93.15
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22.92 69.05 70.14 70.29 88.88 92.34 93.18
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22.90 69.08 70.10 70.36 88.89 92.35 93.18
22.89 69.09 70.05 70.35 88.90 92.36 93.18
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22.87 69.12 69.97 70.34 88.92 92.40 93.18
22.86 69.14 69.93 70.34 88.94 92.41 93.18
22.85 69.16 69.90 70.33 88.95 92.41 93.17
@@ -92385,9 +92702,9 @@ India
22.63 70.20 88.95 92.49 93.10
22.62 70.19 88.96 92.49 93.11
22.61 70.19 88.96 92.49 93.11
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22.59 70.18 88.96 92.49 93.12
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22.57 70.16 88.96 92.49 93.12
22.56 70.01 70.10 70.14 88.96 92.49 93.11
22.55 69.96 88.96 92.49 93.11
@@ -92396,24 +92713,24 @@ India
22.52 69.93 88.98 92.49 93.10
22.51 69.91 88.98 92.50 93.10
22.50 69.90 88.98 92.50 93.10
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22.48 69.04 69.09 69.72 69.75 69.87 88.99 92.50 93.11
22.47 69.03 69.09 69.71 69.76 69.82 88.99 92.50 93.12
22.46 69.01 69.09 69.53 69.55 69.71 69.77 69.81 89.00 92.50 93.13
22.45 68.99 69.09 69.50 69.55 69.70 69.77 69.80 89.00 92.51 93.14
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22.43 68.98 69.08 69.15 69.20 69.50 69.56 69.69 89.01 92.51 93.16
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22.40 68.96 69.21 69.50 69.57 69.64 89.01 92.51 93.17
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22.37 68.95 69.20 69.49 89.00 92.52 93.17
22.36 68.95 69.20 69.48 89.00 92.52 93.17
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22.34 68.94 69.19 69.39 89.01 92.53 93.17
22.33 68.94 69.19 69.33 89.01 92.53 93.17
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22.31 68.93 69.19 69.31 72.35 72.37 89.02 92.53 93.18
22.30 68.93 69.21 69.29 72.35 72.37 89.03 92.53 93.18
22.29 68.93 69.22 69.24 72.35 72.37 89.03 92.53 93.18
@@ -92425,7 +92742,7 @@ India
22.23 68.96 72.31 72.40 72.52 72.70 89.06 92.55 93.17
22.22 68.97 72.31 72.44 72.49 72.60 72.65 72.78 89.07 92.55 93.14
22.21 68.97 72.31 72.58 72.66 72.77 89.07 92.55 93.14
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22.19 68.98 72.32 72.55 72.72 72.75 89.08 92.55 93.15
22.18 68.99 72.32 72.54 89.08 92.55 93.03 93.08 93.15
22.17 69.00 72.32 72.54 89.08 92.56 93.03 93.09 93.15
@@ -92434,31 +92751,31 @@ India
22.14 69.03 72.32 72.52 89.08 92.53 93.03
22.13 69.04 72.32 72.52 89.08 92.52 93.03
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22.02 69.15 72.28 72.50 88.12 88.16 89.06 92.55 92.66 92.83 92.98
22.01 69.15 72.28 72.49 88.10 88.15 89.06 92.55 92.66 92.84 92.98
22.00 69.16 72.27 72.49 88.05 88.14 89.07 92.55 92.66 92.84 92.98
21.99 69.16 72.25 72.49 88.06 88.14 89.07 92.56 92.62 92.85 92.91 92.93 92.98
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21.96 69.18 72.13 72.15 72.18 72.49 88.05 88.13 89.07 92.56 92.58 92.85 92.89
21.95 69.20 72.12 72.49 88.05 88.09 89.07 92.85 92.89
21.94 69.21 72.11 72.50 88.04 88.08 89.07 92.86 92.88
21.93 69.23 72.16 72.50 88.04 88.07 89.07
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21.91 69.25 72.16 72.52 88.03 88.06 88.68 88.70 89.05
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21.86 69.31 72.17 72.57 88.00 88.06 88.66 88.69 89.02
21.85 69.32 72.17 72.55 88.00 88.06 88.66 88.68 89.02
21.84 69.34 72.17 72.55 87.99 88.06 88.66 88.68 89.02
@@ -92469,51 +92786,51 @@ India
21.79 69.39 72.10 72.12 72.18 72.54 87.93 88.07 88.17 88.19 88.65 88.69 89.04
21.78 69.40 72.18 72.54 87.91 88.07 88.17 88.19 88.48 88.51 88.57 88.59 88.65 88.68 89.04
21.77 69.41 72.19 72.54 87.90 88.06 88.17 88.19 88.47 88.50 88.65 88.68 89.04
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21.75 69.43 72.21 72.54 87.89 88.06 88.17 88.19 88.47 88.49 88.64 88.68 89.05
21.74 69.45 72.21 72.53 87.87 88.05 88.17 88.20 88.46 88.49 88.64 88.68 89.05
21.73 69.47 72.22 72.53 87.86 88.05 88.17 88.19 88.46 88.49 88.64 88.68 89.05
21.72 69.47 72.22 72.52 87.85 88.04 88.17 88.19 88.46 88.49 88.64 88.67 89.06
21.71 69.48 72.23 72.52 87.84 88.04 88.46 88.49 88.64 88.67 89.07
21.70 69.49 72.28 72.51 87.82 88.04 88.46 88.49 88.63 88.67 89.08
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21.67 69.52 72.29 72.51 87.75 88.03 88.15 88.17 88.48 88.50 88.60 88.67 89.09
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21.65 69.54 72.30 72.54 72.57 72.81 87.72 88.03 88.15 88.17 88.35 88.37 88.48 88.51 88.60 88.68 89.09
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21.61 69.59 72.30 72.78 87.53 88.10 88.14 88.18 88.35 88.37 88.46 88.50 88.60 88.70 88.87 88.95 89.09
21.60 69.61 72.30 72.77 87.49 88.18 88.34 88.38 88.45 88.49 88.60 88.70 88.88 88.96 89.09
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21.53 69.69 72.27 72.66 87.20 88.47 88.55 88.82 88.92
21.52 69.70 72.26 72.65 87.18 88.48 88.55 88.82 88.91
21.51 69.71 72.26 72.64 87.16 88.50 88.53 88.84 88.90
21.50 69.72 72.26 72.62 87.14
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21.39 69.82 72.18 72.55 87.00
21.38 69.82 72.17 72.55 86.99
21.37 69.83 72.17 72.55 86.98
21.36 69.84 72.16 72.55 86.97
21.35 69.85 72.16 72.56 86.96
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21.31 69.89 72.12 72.57 86.92
21.30 69.90 72.12 72.58 86.91
21.29 69.91 72.12 72.58 86.91
@@ -92524,7 +92841,7 @@ India
21.24 69.96 72.10 72.60 86.87
21.23 69.97 72.11 72.64 86.87
21.22 69.97 72.11 72.66 86.86
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21.20 69.99 72.11 72.69 86.86
21.19 70.00 72.11 72.69 86.85
21.18 70.00 72.10 72.68 86.85
@@ -92534,25 +92851,25 @@ India
21.14 70.03 72.05 72.62 86.84
21.13 70.04 72.03 72.61 86.85
21.12 70.05 72.01 72.60 86.85
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@@ -92576,7 +92893,7 @@ India
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Indonesia
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5.91 95.20 95.25
5.90 95.20 95.26 95.31 95.35
5.89 95.20 95.27 95.30 95.36
@@ -93944,7 +94262,7 @@ Indonesia
5.85 95.22 95.39
5.84 95.24 95.39
5.83 95.24 95.39
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5.81 95.25 95.39
5.80 95.25 95.39
5.79 95.26 95.39
@@ -93960,8 +94278,8 @@ Indonesia
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5.64 95.05 95.07 95.10 95.17 95.37 95.47 95.55 95.60
5.63 95.09 95.18 95.35 95.49 95.52 95.63
5.62 95.09 95.19 95.32 95.50 95.52 95.66
@@ -93983,9 +94301,9 @@ Indonesia
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5.40 95.24 95.97
5.39 95.24 95.98
5.38 95.23 95.99
@@ -93997,25 +94315,25 @@ Indonesia
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5.08 95.29 97.67
@@ -94025,14 +94343,14 @@ Indonesia
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4.92 95.37 97.89
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@@ -94047,8 +94365,8 @@ Indonesia
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4.76 95.46 97.97 107.97 108.02 127.11 127.15
4.75 95.47 97.97 107.97 108.02 127.11 127.15
@@ -94071,116 +94389,116 @@ Indonesia
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3.50 97.01 99.27 115.56 117.52 117.80 117.90 125.49 125.65
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3.45 97.03 99.33 115.58 117.51 117.85 117.90 125.49 125.67
3.44 97.04 99.34 115.58 117.45 117.47 117.50 117.55 117.67 117.86 117.90 125.51 125.67
3.43 97.05 99.35 115.54 117.45 117.53 117.68 125.53 125.67
@@ -94191,19 +94509,19 @@ Indonesia
3.38 97.07 99.45 115.51 117.45 117.52 117.69 125.59 125.63
3.37 97.08 99.46 106.26 106.30 115.50 117.45 117.52 117.69
3.36 97.09 99.47 106.25 106.30 115.50 117.45 117.52 117.69
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3.31 97.12 99.50 106.23 106.30 115.49 117.67
3.30 97.12 99.51 106.23 106.30 115.49 117.54 117.56 117.67
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3.28 97.13 99.53 106.22 106.30 115.48 117.37 117.40 117.53 117.59 117.67
3.27 97.14 99.54 106.22 106.30 115.48 117.37 117.40 117.46 117.51 117.53 117.61 117.67
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3.25 97.15 99.56 106.22 106.29 115.48 117.37 117.62 117.67
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3.22 97.22 99.66 106.19 106.28 115.47 117.35
3.21 97.24 99.70 106.19 106.27 115.47 117.33
3.20 97.26 99.73 106.19 106.28 115.47 117.35
@@ -94225,8 +94543,8 @@ Indonesia
3.04 97.31 99.86 105.67 105.74 115.22 115.26 115.45 117.64
3.03 97.31 99.86 105.68 105.74 107.76 107.80 115.22 115.27 115.42 117.63
3.02 97.32 99.90 105.67 105.74 107.74 107.81 115.21 115.27 115.38 117.62
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+ 3.00 97.34 99.93 105.67 105.74 105.78 105.83 107.73 107.82 108.84 108.89 115.20 115.30 115.32 117.67
2.99 97.34 99.93 105.68 105.86 107.73 107.82 108.83 108.90 115.19 117.68
2.98 97.35 99.95 105.69 105.86 107.73 107.82 108.83 108.90 115.19 117.69
2.97 97.36 99.96 105.70 105.86 107.73 107.82 108.83 108.90 115.18 117.69
@@ -94243,7 +94561,7 @@ Indonesia
2.86 95.75 95.92 97.55 100.00 105.68 105.77 108.79 108.88 115.08 117.72
2.85 95.70 95.94 97.59 100.00 105.68 105.77 108.79 108.86 115.08 117.68
2.84 95.68 95.96 97.59 100.00 105.69 105.77 108.80 108.85 115.05 117.66
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2.82 95.68 95.98 97.59 100.00 105.71 105.73 106.19 106.23 115.05 117.65 125.39 125.43
2.81 95.68 95.98 97.59 100.00 106.18 106.24 115.05 117.67 125.37 125.44
2.80 95.68 95.99 97.60 100.00 106.18 106.24 115.06 117.74 125.36 125.45
@@ -94255,127 +94573,127 @@ Indonesia
2.74 95.72 96.13 97.61 100.04 106.20 106.25 115.08 117.80 125.34 125.45
2.73 95.73 96.13 97.61 100.06 106.22 106.25 115.05 117.80 125.34 125.44
2.72 95.74 96.14 97.61 100.06 106.22 106.25 115.04 117.80 125.34 125.42
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2.70 95.75 96.14 97.62 100.07 100.13 100.22 115.04 117.80 125.35 125.41
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2.68 95.77 96.17 97.62 100.08 100.12 100.24 115.04 117.81 125.36 125.41
2.67 95.77 96.18 97.63 100.08 100.11 100.25 115.05 117.81 125.36 125.42
2.66 95.77 96.19 97.63 100.08 100.11 100.26 115.05 117.81 125.36 125.43
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2.55 96.06 96.35 97.64 100.32 108.95 109.05 115.17 117.90 128.41 128.64
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2.53 96.09 96.36 96.38 96.40 97.65 100.33 108.95 109.12 115.18 117.92 128.40 128.66
2.52 96.10 96.36 96.38 96.43 97.65 100.33 108.96 109.12 115.19 117.93 128.38 128.67
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2.50 96.13 96.45 97.65 100.34 109.00 109.12 115.18 117.95 128.34 128.68
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2.47 96.17 96.46 97.64 100.35 109.01 109.07 115.09 117.98 128.32 128.69
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2.44 96.21 96.47 97.64 100.36 115.06 118.00 128.30 128.70
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2.41 96.28 96.48 97.64 100.37 115.02 118.02 128.14 128.18 128.28 128.70
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2.38 96.29 96.49 97.65 100.38 114.99 118.06 125.35 125.46 128.13 128.19 128.27 128.69
2.37 96.29 96.49 97.65 100.39 114.92 114.96 114.98 118.07 125.35 125.46 128.12 128.20 128.26 128.68
2.36 96.29 96.49 97.66 100.39 114.91 118.08 125.35 125.46 128.11 128.20 128.25 128.68
2.35 96.31 96.49 97.67 100.39 114.91 118.08 125.35 125.46 128.11 128.20 128.25 128.67
2.34 96.32 96.47 97.68 100.40 114.90 118.09 125.36 125.46 128.11 128.20 128.24 128.67
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2.31 97.70 100.42 114.90 118.10 118.54 118.60 125.38 125.45 128.11 128.19 128.21 128.65
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2.29 97.72 100.43 100.83 101.06 114.89 118.10 118.54 118.63 128.12 128.65
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2.24 97.14 97.18 97.23 97.28 97.80 97.91 97.96 100.47 100.80 101.06 114.76 118.09 118.55 118.61 127.73 127.82 128.20 128.64
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2.22 97.09 97.19 97.21 97.29 97.99 100.49 100.79 101.07 114.75 118.08 118.56 118.63 127.73 127.82 128.22 128.63
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2.15 97.20 97.33 98.12 100.59 100.79 101.19 114.74 117.95 127.89 128.06 128.23 128.60
2.14 97.21 97.33 98.14 100.61 100.63 100.67 100.79 101.20 114.74 117.95 125.39 125.41 127.88 128.06 128.23 128.59
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1.98 98.41 101.33 101.39 101.78 109.47 109.62 114.82 117.88 127.73 127.95 128.25 128.28
1.97 98.44 101.33 101.38 101.78 109.43 109.61 114.82 117.88 127.72 127.95
1.96 98.46 101.33 101.38 101.78 109.38 109.60 114.81 117.88 127.71 127.95
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1.60 98.78 101.84 101.99 102.13 109.13 109.66 114.61 118.24 124.83 125.17 127.53 128.03
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@@ -94384,26 +94702,26 @@ Indonesia
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@@ -94412,68 +94730,68 @@ Indonesia
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1.06 97.35 97.90 98.91 102.20 102.23 103.03 103.30 103.42 103.89 104.15 104.22 104.67 108.94 110.25 111.09 111.27 111.85 117.92 117.97 119.00 120.36 120.41 120.59 120.68 120.79 121.96 122.03 122.12 124.31 124.98 127.38 127.76 127.96 128.71 131.24 131.28
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1.04 97.36 97.91 98.92 102.21 102.24 103.05 103.31 103.44 103.87 104.14 104.23 104.67 104.78 104.81 107.52 107.58 108.95 110.26 111.02 111.32 111.60 111.67 111.83 117.94 117.99 119.01 120.35 120.41 120.63 120.69 120.77 121.97 122.01 122.20 124.30 124.96 127.38 127.73 127.94 128.65 131.23 131.27
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0.50 99.08 103.09 103.16 103.19 103.25 103.48 108.90 117.64 119.93 120.48 120.69 121.52 121.62 121.66 121.70 124.52 127.54 128.69
@@ -94482,11 +94800,11 @@ Indonesia
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@@ -94495,261 +94813,261 @@ Indonesia
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@@ -95461,7 +95779,7 @@ Indonesia
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@@ -95481,29 +95799,29 @@ Indonesia
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@@ -95512,8 +95830,8 @@ Indonesia
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@@ -95529,24 +95847,24 @@ Indonesia
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@@ -95558,7 +95876,7 @@ Indonesia
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@@ -95585,7 +95903,7 @@ Indonesia
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-10.62 121.51 121.64 123.14 123.43
-10.63 121.51 121.63 123.12 123.43
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@@ -95608,10 +95926,10 @@ Indonesia
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@@ -95632,8 +95950,8 @@ Iran
39.68 44.44 44.75 47.80 48.03
39.67 44.44 44.77 47.79 48.05
39.66 44.44 44.78 47.77 48.06
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39.63 44.44 44.88 47.72 48.09
39.62 44.43 44.88 47.70 48.10
39.61 44.42 44.89 47.68 48.11
@@ -95659,13 +95977,13 @@ Iran
39.41 44.05 44.22 44.34 45.03 47.31 48.32
39.40 44.03 44.25 44.32 45.05 47.30 48.33
39.39 44.01 45.06 47.29 48.33
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39.37 44.00 45.07 47.22 48.34
39.36 44.00 45.09 47.19 48.34
39.35 44.01 45.10 47.16 48.32
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39.33 44.02 45.11 47.12 48.26
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39.31 44.04 45.12 47.09 48.18
39.30 44.04 45.13 47.08 48.16
39.29 44.04 45.13 47.07 48.15
@@ -95678,7 +95996,7 @@ Iran
39.22 44.07 45.20 47.03 48.12
39.21 44.06 45.26 45.29 45.32 47.02 48.12
39.20 44.06 45.32 47.02 48.14
- 39.19 44.06 45.32 47.00 48.15
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39.18 44.07 45.34 46.87 46.91 46.96 48.16
39.17 44.09 45.35 46.85 48.17
39.16 44.11 45.36 46.84 48.18
@@ -95698,11 +96016,11 @@ Iran
39.02 44.14 45.43 46.68 48.31
39.01 44.13 45.45 46.66 48.31
39.00 44.12 45.47 46.64 48.31
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38.98 44.12 45.53 46.62 48.29
38.97 44.13 45.60 46.62 48.28
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38.94 44.14 45.82 46.60 48.15
38.93 44.16 45.87 46.35 46.41 46.59 48.09
38.92 44.16 45.93 46.28 46.43 46.58 48.06
@@ -95726,7 +96044,7 @@ Iran
38.74 44.24 48.20
38.73 44.23 48.23
38.72 44.23 48.23
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38.70 44.23 48.24
38.69 44.24 48.24
38.68 44.24 48.24
@@ -95770,7 +96088,7 @@ Iran
38.30 44.42 48.88
38.29 44.40 48.88
38.28 44.39 48.88 56.70 56.73 57.15 57.21
- 38.27 44.38 48.88 56.66 56.75 57.13 57.22
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38.26 44.37 48.88 56.41 56.55 56.64 56.77 57.12 57.23
38.25 44.36 48.88 56.39 56.57 56.61 56.79 57.11 57.23
38.24 44.36 48.88 56.37 56.81 57.10 57.24
@@ -96105,7 +96423,7 @@ Iran
34.95 45.85 61.10
34.94 45.84 61.09
34.93 45.84 61.09
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34.91 45.74 45.80 45.84 61.08
34.90 45.73 61.08
34.89 45.73 61.08
@@ -96456,8 +96774,8 @@ Iran
31.44 47.67 61.25
31.43 47.67 61.35
31.42 47.66 61.45
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31.39 47.66 61.68
31.38 47.66 61.69
31.37 47.66 61.70
@@ -96566,43 +96884,43 @@ Iran
30.34 48.17 48.88 48.97 61.34
30.33 48.17 48.88 48.98 61.33
30.32 48.18 48.88 48.98 61.32
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30.30 48.20 48.26 48.28 48.87 48.99 61.30
30.29 48.30 48.88 48.99 61.29
30.28 48.30 48.90 49.00 61.28
30.27 48.31 48.92 49.02 61.27
30.26 48.32 48.93 49.04 61.26
30.25 48.33 48.93 49.06 61.25
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30.22 48.37 48.94 49.13 61.22
30.21 48.38 48.94 49.15 61.21
30.20 48.39 48.94 49.21 61.20
- 30.19 48.39 48.94 49.22 49.94 50.03 61.19
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30.18 48.39 48.95 49.22 49.91 50.06 61.18
30.17 48.38 48.95 49.22 49.89 50.06 61.17
30.16 48.37 48.95 49.22 49.87 50.06 61.16
30.15 48.37 48.95 49.22 49.32 49.36 49.85 50.07 61.15
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30.12 48.37 48.94 49.48 49.80 50.10 61.12
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29.99 48.44 48.67 50.12 60.99
29.98 48.44 48.67 50.12 60.98
29.97 48.45 48.66 50.12 60.97
29.96 48.46 48.66 50.12 60.96
- 29.95 48.51 48.65 50.12 60.95
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29.94 48.57 48.63 50.12 60.95
29.93 50.13 60.94
29.92 50.13 60.93
@@ -96668,24 +96986,24 @@ Iran
29.32 50.65 61.35
29.31 50.65 61.35
29.30 50.65 61.35
- 29.29 50.28 50.31 50.65 61.34
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29.24 50.28 50.34 50.64 61.37
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29.18 50.62 61.40
29.17 50.62 61.40
29.16 50.62 61.40
29.15 50.62 61.43
29.14 50.63 61.44
29.13 50.63 61.45
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29.11 50.65 50.71 50.83 61.46
29.10 50.83 61.47
29.09 50.83 61.49
@@ -96693,8 +97011,8 @@ Iran
29.07 50.88 61.50
29.06 50.89 61.50
29.05 50.89 61.49
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29.02 50.91 61.51
29.01 50.91 61.52
29.00 50.81 50.85 50.91 61.52
@@ -96785,38 +97103,38 @@ Iran
28.15 51.25 62.77
28.14 51.25 62.76
28.13 51.25 62.76
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28.03 51.33 62.75
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27.86 51.55 62.78
27.85 51.56 62.78
27.84 51.57 62.79
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27.80 52.04 62.79
27.79 52.05 62.79
27.78 52.07 62.79
@@ -96835,8 +97153,8 @@ Iran
27.65 52.30 62.80
27.64 52.35 62.80
27.63 52.39 62.80
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27.60 52.47 62.80
27.59 52.48 62.81
27.58 52.49 62.81
@@ -96866,8 +97184,8 @@ Iran
27.34 52.59 62.77
27.33 52.61 62.78
27.32 52.63 62.79
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27.29 52.71 62.79
27.28 52.73 62.78
27.27 52.74 62.78
@@ -96880,7 +97198,7 @@ Iran
27.20 52.83 63.28
27.19 52.86 63.29
27.18 52.90 56.33 56.36 63.29
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27.16 52.91 56.24 56.41 63.30
27.15 52.92 56.23 56.53 63.31
27.14 52.94 56.12 56.56 63.31
@@ -96888,7 +97206,7 @@ Iran
27.12 52.99 56.10 56.72 63.32
27.11 52.99 56.10 56.44 56.48 56.73 63.32
27.10 53.00 56.08 56.43 56.50 56.80 63.28 63.30 63.32
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27.08 53.03 56.05 56.42 56.51 56.82 63.25
27.07 53.08 56.03 56.42 56.51 56.84 63.25
27.06 53.12 56.01 56.42 56.51 56.85 63.24
@@ -96903,35 +97221,35 @@ Iran
26.97 53.41 55.66 56.01 56.28 56.92 63.24
26.96 53.43 55.65 55.74 55.77 55.99 56.29 56.91 63.24
26.95 53.44 55.64 55.72 55.80 55.97 56.29 56.91 63.24
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26.93 53.45 55.60 55.72 55.85 55.93 56.28 56.92 63.25
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26.91 53.45 55.59 55.74 56.23 56.95 63.26
26.90 53.45 55.59 55.75 56.19 56.38 56.41 56.95 63.27
26.89 53.46 55.59 55.76 56.18 56.35 56.41 56.95 63.27
26.88 53.46 55.59 55.76 56.17 56.33 56.41 56.96 63.27
26.87 53.46 55.59 55.77 56.17 56.31 56.41 56.97 63.27
26.86 53.14 53.20 53.46 55.59 55.77 56.16 56.31 56.41 56.99 63.27
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26.84 53.13 53.30 53.48 55.59 55.77 56.15 56.31 56.40 57.01 63.25
26.83 53.13 53.37 53.49 55.58 55.77 56.14 56.31 56.39 57.01 63.20
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26.79 53.19 53.39 53.54 55.55 55.68 56.10 57.02 63.19
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26.77 53.57 55.27 55.29 55.53 55.63 56.09 57.03 63.19
26.76 53.59 55.25 55.33 55.52 55.62 56.08 57.03 63.19
26.75 53.61 55.24 55.37 55.50 55.60 56.06 57.04 63.19
26.74 53.63 55.23 55.41 55.47 55.58 56.04 57.04 63.18
26.73 53.65 55.23 55.56 56.02 57.04 63.18
26.72 53.66 53.98 54.04 55.22 55.51 56.01 57.04 63.18
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26.69 53.59 53.66 53.70 53.74 53.79 53.87 54.13 54.21 54.30 55.14 55.41 55.81 55.91 55.97 57.05 63.18
26.68 53.59 53.66 54.32 55.10 55.39 55.80 55.87 55.90 55.93 55.95 57.06 63.18
- 26.67 53.59 53.66 54.33 55.09 55.37 55.68 55.72 55.79 55.85 55.91 57.06 63.18
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26.65 53.60 53.66 54.34 55.06 55.26 55.65 55.84 55.91 57.07 63.18
26.64 53.61 53.65 54.35 55.05 55.26 55.63 55.84 55.91 57.07 63.17
26.63 54.35 55.04 55.26 55.62 55.84 55.91 57.07 63.17
@@ -96940,16 +97258,16 @@ Iran
26.60 54.37 54.99 55.27 55.55 55.85 55.88 57.08 62.73
26.59 54.37 54.98 55.27 55.53 57.08 62.72
26.58 54.39 54.97 55.27 55.52 57.08 62.63 62.65 62.69
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26.55 53.90 54.04 54.57 54.93 55.27 55.39 57.08 62.47
26.54 53.89 54.04 54.58 54.91 55.27 55.34 57.07 62.42
26.53 53.89 54.05 54.58 54.89 55.28 55.33 57.07 62.41
26.52 53.89 54.06 54.59 54.87 57.07 62.40
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26.50 53.90 54.06 54.60 54.83 57.07 62.32
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26.47 53.99 54.04 57.06 62.30
26.46 57.06 62.30
26.45 57.06 62.30
@@ -97000,20 +97318,20 @@ Iran
26.00 57.18 61.79
25.99 57.18 61.79
25.98 57.18 61.79
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25.96 57.23 61.79
25.95 57.23 61.79
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25.93 54.51 54.55 57.24 61.78
25.92 54.49 54.56 57.25 61.78
25.91 54.49 54.56 57.25 61.78
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25.83 57.28 61.77
25.82 57.28 61.77
25.81 57.28 61.77
@@ -97022,13 +97340,13 @@ Iran
25.78 57.29 61.73
25.77 57.30 61.68
25.76 57.31 61.68
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25.74 57.46 61.67
25.73 57.50 61.67
25.72 57.60 57.66 57.76 61.67
25.71 57.76 61.68
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25.68 57.76 57.91 57.94 61.68
25.67 57.76 57.88 57.96 61.68
25.66 57.76 57.86 57.96 61.68
@@ -97038,7 +97356,7 @@ Iran
25.62 57.76 57.80 57.99 61.66
25.61 58.00 61.65
25.60 58.00 61.65
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25.58 58.02 58.35 58.40 61.65
25.57 58.02 58.34 58.42 58.52 58.57 61.65
25.56 58.03 58.32 58.63 61.64
@@ -97046,52 +97364,54 @@ Iran
25.54 58.08 58.23 58.82 61.64
25.53 58.11 58.21 58.82 61.64
25.52 58.83 61.64
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25.50 58.90 61.64
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25.24 60.74 61.62
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25.19 61.00 61.59
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+ 25.04 61.39 61.42
Iraq
37.38 42.75 42.80 43.09 43.13
37.37 42.73 42.81 43.03 43.15
@@ -97274,12 +97594,12 @@ Iraq
35.60 41.33 46.01
35.59 41.32 46.01
35.58 41.31 46.01
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35.54 41.28 45.99
35.53 41.27 45.99
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35.51 41.26 45.99
35.50 41.25 45.98
35.49 41.25 45.97
@@ -97524,7 +97844,7 @@ Iraq
33.10 38.85 46.11
33.09 38.85 46.07
33.08 38.85 46.12
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33.06 38.86 46.13
33.05 38.86 46.13
33.04 38.86 46.13
@@ -97543,42 +97863,42 @@ Iraq
32.91 38.90 46.46
32.90 38.91 46.48
32.89 38.91 46.49
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32.87 38.92 46.52
32.86 38.92 46.54
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32.83 38.93 46.61
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32.80 38.94 46.65
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32.77 38.95 46.71
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32.74 38.96 46.74
- 32.73 38.96 46.75
- 32.72 38.96 46.76
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32.71 38.97 46.78
- 32.70 38.97 46.79
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32.68 38.98 46.82
- 32.67 38.98 46.83
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32.65 38.99 46.86
32.64 38.99 46.87
- 32.63 38.99 46.88
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32.62 39.00 46.90
32.61 39.00 46.91
- 32.60 39.00 46.93
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32.58 39.01 46.95
32.57 39.01 46.97
- 32.56 39.01 46.98
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32.55 39.02 46.99
32.54 39.02 47.01
- 32.53 39.02 47.02
+ 32.53 39.03 47.02
32.52 39.03 47.03
32.51 39.03 47.05
32.50 39.03 47.07
@@ -97620,8 +97940,8 @@ Iraq
32.14 39.14 47.53
32.13 39.13 47.54
32.12 39.13 47.57
- 32.11 39.13 47.58
- 32.10 39.13 39.15 39.18 47.59
+ 32.11 39.13 47.59
+ 32.10 39.13 39.16 39.18 47.59
32.09 39.25 47.60
32.08 39.31 47.60
32.07 39.38 47.61
@@ -97777,11 +98097,11 @@ Iraq
30.57 42.72 48.02
30.56 42.73 48.02
30.55 42.75 48.02
- 30.54 42.76 48.02
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30.52 42.79 48.02
30.51 42.80 48.02
- 30.50 42.81 48.02
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30.49 42.83 48.02
30.48 42.84 48.02
30.47 42.85 48.07
@@ -97833,7 +98153,7 @@ Iraq
30.01 43.50 47.19 47.85 48.02 48.18 48.46
30.00 43.52 47.17 47.88 48.00 48.21 48.46
29.99 43.53 47.15 47.90 47.98 48.23 48.47
- 29.98 43.54 47.14 47.92 47.95 48.25 48.52
+ 29.98 43.54 47.14 47.92 47.95 48.25 48.51
29.97 43.56 47.14 48.27 48.54
29.96 43.57 47.13 48.30 48.56
29.95 43.59 47.12 48.32 48.56
@@ -97851,9 +98171,9 @@ Iraq
29.83 43.76 47.06
29.82 43.77 47.06
29.81 43.79 47.05
- 29.80 43.80 47.05
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29.79 43.82 47.04
- 29.78 43.83 47.04
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29.77 43.85 47.03
29.76 43.86 47.03
29.75 43.88 47.02
@@ -97928,44 +98248,44 @@ Iraq
29.06 46.13 46.47
29.05 46.30 46.38
Ireland
- 55.39 -7.39 -7.34
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55.36 -7.40 -7.21
55.35 -7.38 -7.19
55.34 -7.36 -7.18
55.33 -7.36 -7.17
55.32 -7.37 -7.15
55.31 -7.47 -7.44 -7.38 -7.14
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55.29 -7.53 -7.09
55.28 -7.68 -7.63 -7.53 -7.05
55.27 -7.70 -7.62 -7.53 -7.01
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55.15 -8.29 -7.08
55.14 -8.30 -7.10
55.13 -8.30 -7.15
55.12 -8.32 -7.17
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55.07 -8.36 -7.22
55.06 -8.37 -7.23
55.05 -8.37 -7.23
55.04 -8.41 -7.26
55.03 -8.41 -7.28
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55.01 -8.56 -8.48 -8.46 -7.36
55.00 -8.57 -7.37
54.99 -8.57 -7.39
@@ -98005,8 +98325,8 @@ Ireland
54.65 -8.80 -7.85
54.64 -8.80 -7.78
54.63 -8.73 -7.76 -7.73 -7.70
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54.60 -8.68 -8.54 -8.49 -8.33 -8.30 -8.24 -8.18 -7.69
54.59 -8.57 -8.55 -8.48 -8.34 -8.30 -8.27 -8.19 -7.69
54.58 -8.46 -8.36 -8.21 -7.71
@@ -98019,10 +98339,10 @@ Ireland
54.51 -8.28 -8.01
54.50 -8.26 -8.02
54.49 -8.27 -8.03
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54.47 -8.47 -8.44 -8.40 -8.06
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54.44 -8.48 -8.13
54.43 -8.51 -8.12
54.42 -8.53 -8.11 -7.05 -6.99
@@ -98034,22 +98354,22 @@ Ireland
54.36 -8.67 -7.99 -7.12 -6.90
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54.28 -10.07 -9.91 -9.86 -9.20 -9.07 -8.87 -8.77 -8.74 -8.70 -8.65 -8.61 -7.86 -7.21 -6.84
54.27 -10.08 -9.19 -9.07 -7.86 -7.19 -6.82
54.26 -10.09 -9.19 -9.08 -7.86 -7.19 -6.82
54.25 -10.09 -9.18 -9.08 -7.85 -7.19 -6.81
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54.23 -10.12 -9.18 -9.10 -7.85 -7.16 -6.80
54.22 -10.12 -9.18 -9.12 -7.83 -7.20 -6.78
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54.20 -10.10 -7.67 -7.26 -6.74 -6.72 -6.66
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54.17 -10.10 -10.00 -9.98 -7.61 -7.31 -6.63
54.16 -10.11 -10.02 -9.97 -7.61 -7.33 -6.62
54.15 -10.12 -10.02 -9.96 -7.60 -7.45 -7.40 -7.34 -6.62
@@ -98063,13 +98383,13 @@ Ireland
54.07 -9.99 -6.64 -6.50 -6.43 -6.41 -6.19
54.06 -9.98 -6.63 -6.60 -6.57 -6.54 -6.17
54.05 -9.96 -6.16
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54.03 -10.07 -9.95 -9.91 -6.10
54.02 -10.19 -10.13 -10.09 -9.94 -9.91 -6.09
54.01 -10.20 -9.93 -9.90 -6.09
54.00 -10.21 -9.93 -9.90 -6.09
53.99 -10.27 -9.92 -9.89 -6.33 -6.29 -6.10
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53.97 -10.27 -9.92 -9.89 -6.35 -6.21 -6.12
53.96 -10.27 -6.35 -6.19 -6.13
53.95 -10.21 -10.11 -10.07 -6.36
@@ -98089,7 +98409,7 @@ Ireland
53.81 -9.63 -6.22
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53.79 -9.80 -9.76 -9.71 -6.21
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53.77 -9.91 -6.22
53.76 -9.91 -6.23
53.75 -9.91 -6.23
@@ -98102,14 +98422,14 @@ Ireland
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53.55 -10.21 -6.06
@@ -98135,29 +98455,29 @@ Ireland
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53.33 -9.91 -9.70 -9.66 -6.17
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53.30 -9.89 -9.85 -9.83 -9.72 -9.62 -6.10
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53.09 -9.72 -9.63 -9.34 -6.02
53.08 -9.68 -9.63 -9.35 -6.02
53.07 -9.36 -6.02
@@ -98183,20 +98503,20 @@ Ireland
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52.83 -9.46 -6.07
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52.70 -9.67 -6.15
52.69 -9.68 -6.16
52.68 -9.70 -6.17
@@ -98211,7 +98531,7 @@ Ireland
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52.55 -9.94 -9.79 -9.68 -6.19
52.54 -9.94 -9.88 -9.68 -6.19
52.53 -9.69 -6.19
@@ -98235,7 +98555,7 @@ Ireland
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52.30 -10.06 -10.00 -9.89 -6.36
52.29 -10.20 -10.15 -10.06 -10.00 -9.89 -6.36
@@ -98248,10 +98568,10 @@ Ireland
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52.21 -10.38 -6.31
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52.18 -10.47 -6.80 -6.63 -6.33
52.17 -10.47 -6.80 -6.62 -6.53 -6.40 -6.34
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52.14 -10.48 -6.97 -6.95 -6.87
52.13 -10.48 -7.15 -7.11 -6.98 -6.95 -6.89
@@ -98278,17 +98598,17 @@ Ireland
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51.77 -10.35 -10.32 -10.23 -9.97 -9.90 -8.28
51.76 -10.21 -9.99 -9.93 -8.28
@@ -98307,11 +98627,11 @@ Ireland
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@@ -98322,9 +98642,9 @@ Ireland
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Isle of Man
54.42 -4.39 -4.34
54.41 -4.46 -4.34
@@ -98333,10 +98653,10 @@ Isle of Man
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@@ -98345,27 +98665,26 @@ Isle of Man
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+ 54.06 -4.80 -4.59
+ 54.05 -4.80 -4.72 -4.68 -4.59
+ 54.04 -4.78 -4.74 -4.62 -4.60
Israel
33.41 35.81 35.83
33.40 35.79 35.83
@@ -98399,7 +98718,7 @@ Israel
33.12 35.48 35.83
33.11 35.25 35.29 35.47 35.84
33.10 35.19 35.30 35.47 35.85
- 33.09 35.09 35.31 35.43 35.85
+ 33.09 35.08 35.31 35.43 35.85
33.08 35.08 35.32 35.41 35.85
33.07 35.08 35.33 35.37 35.85
33.06 35.08 35.85
@@ -98420,7 +98739,7 @@ Israel
32.91 35.05 35.88
32.90 35.06 35.86
32.89 35.06 35.86
- 32.88 35.06 35.85
+ 32.88 35.05 35.85
32.87 35.05 35.85
32.86 35.05 35.85
32.85 34.96 34.98 35.04 35.85
@@ -98449,8 +98768,8 @@ Israel
32.62 34.90 35.58
32.61 34.90 35.58
32.60 34.90 35.58
- 32.59 34.90 35.58
- 32.58 34.90 35.58
+ 32.59 34.89 35.58
+ 32.58 34.89 35.58
32.57 34.89 35.58
32.56 34.89 35.58
32.55 34.89 35.58
@@ -98468,11 +98787,11 @@ Israel
32.43 34.86 35.06 35.39 35.57
32.42 34.85 35.05 35.39 35.56
32.41 34.85 35.05 35.39 35.56
- 32.40 34.85 35.04 35.39 35.56
+ 32.40 34.85 35.05 35.39 35.56
32.39 34.85 35.04 35.41 35.57
32.38 34.84 35.04 35.50 35.57
32.37 34.84 35.04 35.54 35.57
- 32.36 34.84 35.03
+ 32.36 34.84 35.04
32.35 34.84 35.03
32.34 34.83 35.03
32.33 34.83 35.03
@@ -98516,22 +98835,22 @@ Israel
31.95 34.69 34.99
31.94 34.69 34.98
31.93 34.68 34.99
- 31.92 34.68 34.99
+ 31.92 34.67 34.99
31.91 34.67 35.00
- 31.90 34.67 35.00
+ 31.90 34.66 35.00
31.89 34.66 35.01
- 31.88 34.66 35.01
- 31.87 34.65 35.01
- 31.86 34.65 35.01
- 31.85 34.64 35.00 35.03 35.05
- 31.84 34.64 34.97 35.02 35.07
- 31.83 34.63 34.96 35.01 35.10
- 31.82 34.63 35.15
- 31.81 34.62 35.19
- 31.80 34.62 35.20
- 31.79 34.61 35.21
- 31.78 34.61 35.21
- 31.77 34.60 35.21
+ 31.88 34.65 35.01
+ 31.87 34.64 35.01
+ 31.86 34.64 35.01
+ 31.85 34.63 35.00 35.03 35.05
+ 31.84 34.63 34.97 35.02 35.07
+ 31.83 34.62 34.95 35.01 35.10
+ 31.82 34.62 35.15
+ 31.81 34.61 35.19
+ 31.80 34.61 35.20
+ 31.79 34.60 35.21
+ 31.78 34.60 35.21
+ 31.77 34.59 35.21
31.76 34.59 35.21
31.75 34.58 35.21
31.74 34.58 35.21
@@ -98549,7 +98868,7 @@ Israel
31.62 34.48 34.98
31.61 34.47 34.97
31.60 34.47 34.96
- 31.59 34.47 34.95
+ 31.59 34.47 34.96
31.58 34.47 34.95
31.57 34.47 34.94
31.56 34.48 34.94
@@ -98617,7 +98936,7 @@ Israel
30.94 34.33 35.39
30.93 34.33 35.38
30.92 34.34 35.37
- 30.91 34.34 35.36
+ 30.91 34.34 35.35
30.90 34.35 35.34
30.89 34.35 35.34
30.88 34.35 35.33
@@ -98759,11 +99078,11 @@ Israel
29.52 34.84 34.95
29.51 34.85 34.94
29.50 34.85 34.93
- 29.49 34.86 34.93
- 29.48 34.86 34.92
- 29.47 34.87 34.92
+ 29.49 34.86 34.92
+ 29.48 34.87 34.92
+ 29.47 34.89 34.92
Italy
- 47.09 12.14 12.20
+ 47.09 12.15 12.20
47.08 12.09 12.21
47.07 12.06 12.21
47.06 12.02 12.21
@@ -98854,7 +99173,7 @@ Italy
46.21 8.09 8.52 9.17 13.53
46.20 8.09 8.53 9.16 13.55
46.19 8.10 8.54 9.16 13.64
- 46.18 8.11 8.55 9.15 13.64
+ 46.18 8.11 8.55 9.15 13.65
46.17 8.11 8.56 9.13 13.65
46.16 8.11 8.58 9.11 13.65
46.15 8.11 8.59 9.09 13.65
@@ -98867,7 +99186,7 @@ Italy
46.08 8.00 8.83 9.05 13.57
46.07 8.00 8.84 9.04 13.55
46.06 8.00 8.84 9.01 13.53
- 46.05 8.00 8.84 9.00 13.51
+ 46.05 8.00 8.84 9.00 13.52
46.04 8.00 8.83 8.99 13.50
46.03 7.99 8.82 8.98 13.50
46.02 7.98 8.81 8.98 13.50
@@ -98875,21 +99194,21 @@ Italy
46.00 7.92 8.80 8.99 13.49
45.99 7.53 7.57 7.88 8.80 8.98 13.49 13.58 13.61
45.98 7.51 7.62 7.87 8.82 8.97 13.50 13.55 13.62
- 45.97 7.50 7.67 7.86 8.84 8.96 13.63
- 45.96 7.46 7.68 7.85 8.87 8.96 13.63
- 45.95 7.44 7.69 7.84 8.88 8.96 13.63
+ 45.97 7.50 7.67 7.87 8.84 8.96 13.63
+ 45.96 7.46 7.68 7.86 8.87 8.96 13.63
+ 45.95 7.44 7.69 7.85 8.88 8.96 13.63
45.94 7.42 7.70 7.72 7.75 7.83 8.89 8.98 13.63
45.93 6.99 7.03 7.40 7.77 7.83 8.89 8.98 13.62
45.92 6.98 7.05 7.26 7.33 7.37 8.90 8.99 13.62
45.91 6.98 7.06 7.24 8.90 9.00 13.61
45.90 6.97 7.08 7.21 8.91 9.03 13.60
- 45.89 6.97 7.11 7.16 8.92 9.04 13.60
+ 45.89 6.97 7.11 7.16 8.92 9.04 13.59
45.88 6.96 8.92 9.04 13.59
45.87 6.95 8.92 9.03 13.58
45.86 6.93 8.92 9.03 13.58
- 45.85 6.83 8.92 9.02 13.57
+ 45.85 6.86 8.92 9.02 13.57
45.84 6.80 8.96 9.00 13.57
- 45.83 6.79 13.58
+ 45.83 6.79 13.57
45.82 6.77 13.58
45.81 6.77 13.60
45.80 6.77 13.67
@@ -98898,12 +99217,12 @@ Italy
45.77 6.77 13.72
45.76 6.77 13.54 13.59 13.76
45.75 6.77 13.19 13.22 13.54 13.63 13.78
- 45.74 6.77 13.17 13.23 13.56 13.64 13.79
+ 45.74 6.77 13.16 13.23 13.56 13.64 13.79
45.73 6.77 13.13 13.30 13.56 13.66 13.80
- 45.72 6.77 13.13 13.36 13.56 13.67 13.80
- 45.71 6.78 13.16 13.37 13.54 13.68 13.81
- 45.70 6.78 13.16 13.39 13.51 13.70 13.82
- 45.69 6.79 13.16 13.36 13.48 13.71 13.83
+ 45.72 6.77 13.13 13.37 13.56 13.67 13.80
+ 45.71 6.78 13.15 13.40 13.54 13.68 13.81
+ 45.70 6.78 13.15 13.39 13.51 13.70 13.82
+ 45.69 6.79 13.15 13.36 13.48 13.71 13.83
45.68 6.80 13.15 13.36 13.46 13.72 13.84
45.67 6.82 13.14 13.36 13.44 13.73 13.84
45.66 6.85 13.13 13.38 13.42 13.74 13.85
@@ -98914,7 +99233,7 @@ Italy
45.61 6.94 12.97 13.70 13.90
45.60 6.94 12.93 13.70 13.89
45.59 6.94 12.91 13.70 13.88
- 45.58 6.94 12.89 13.70 13.87
+ 45.58 6.94 12.89 13.70 13.86
45.57 6.94 12.87 13.78 13.85
45.56 6.95 12.84
45.55 6.95 12.82
@@ -98924,22 +99243,22 @@ Italy
45.51 6.96 12.71
45.50 6.97 12.69
45.49 6.99 12.66
- 45.48 7.01 12.35 12.37 12.63
- 45.47 7.03 12.33 12.41 12.59
- 45.46 7.05 12.31 12.40 12.54
- 45.45 7.06 12.29 12.40 12.51
- 45.44 7.07 12.27 12.40 12.49
- 45.43 7.07 12.27 12.40 12.45
- 45.42 7.08 12.26 12.40 12.43
- 45.41 7.10 12.26
- 45.40 7.13 12.26
- 45.39 7.14 12.26
- 45.38 7.13 12.26
- 45.37 7.13 12.25
- 45.36 7.12 12.25
- 45.35 7.11 12.25
- 45.34 7.09 12.24
- 45.33 7.08 12.24
+ 45.48 7.01 12.34 12.37 12.63
+ 45.47 7.03 12.32 12.41 12.59
+ 45.46 7.05 12.36 12.40 12.54
+ 45.45 7.06 12.28 12.30 12.37 12.40 12.51
+ 45.44 7.07 12.27 12.30 12.49
+ 45.43 7.07 12.27 12.30 12.45
+ 45.42 7.08 12.26 12.30 12.44
+ 45.41 7.10 12.26 12.31 12.44
+ 45.40 7.13 12.26 12.33 12.37 12.42 12.44
+ 45.39 7.14 12.26 12.32 12.37
+ 45.38 7.13 12.26 12.31 12.36
+ 45.37 7.13 12.25 12.31 12.36
+ 45.36 7.12 12.25 12.31 12.35
+ 45.35 7.11 12.25 12.31 12.34
+ 45.34 7.09 12.24 12.31 12.34
+ 45.33 7.08 12.24 12.31 12.33
45.32 7.08 12.24
45.31 7.08 12.23
45.30 7.08 12.22
@@ -98959,7 +99278,7 @@ Italy
45.16 6.71 6.78 6.85 12.33
45.15 6.66 6.80 6.85 12.33
45.14 6.64 12.33
- 45.13 6.62 12.33
+ 45.13 6.61 12.33
45.12 6.60 12.33
45.11 6.59 12.33
45.10 6.59 12.34
@@ -98969,16 +99288,16 @@ Italy
45.06 6.62 12.40
45.05 6.62 12.42
45.04 6.62 12.42
- 45.03 6.63 12.42
+ 45.03 6.63 12.43
45.02 6.64 12.45
45.01 6.65 12.46
45.00 6.70 12.51
- 44.99 6.71 12.52
- 44.98 6.71 12.53
+ 44.99 6.71 12.53
+ 44.98 6.71 12.54
44.97 6.71 12.54
44.96 6.71 12.54
44.95 6.71 12.54
- 44.94 6.71 12.54
+ 44.94 6.71 12.53
44.93 6.71 12.53
44.92 6.71 12.52
44.91 6.71 12.52
@@ -99040,36 +99359,36 @@ Italy
44.35 6.85 8.61 9.11 12.33
44.34 6.86 8.57 9.12 12.34
44.33 6.87 8.56 9.13 12.35
- 44.32 6.88 8.55 9.13 9.22 9.25 12.35
- 44.31 6.89 8.53 9.13 9.22 9.27 12.35
- 44.30 6.90 8.51 9.15 9.22 9.29 12.35
+ 44.32 6.88 8.54 9.13 9.22 9.25 12.35
+ 44.31 6.89 8.52 9.13 9.22 9.27 12.35
+ 44.30 6.90 8.50 9.15 9.22 9.29 12.35
44.29 6.90 8.48 9.18 9.22 9.32 12.36
44.28 6.92 8.46 9.34 12.36
- 44.27 6.94 8.46 9.35 12.37
- 44.26 6.94 8.46 9.36 12.37
- 44.25 6.95 8.46 9.38 12.38
- 44.24 6.95 8.45 9.40 12.39
- 44.23 6.96 8.44 9.41 12.40
- 44.22 6.98 7.02 7.05 8.44 9.42 12.41
+ 44.27 6.94 8.45 9.35 12.37
+ 44.26 6.94 8.45 9.36 12.37
+ 44.25 6.95 8.45 9.38 12.38
+ 44.24 6.95 8.44 9.40 12.38
+ 44.23 6.96 8.44 9.41 12.39
+ 44.22 6.98 7.02 7.05 8.44 9.42 12.40
44.21 7.07 8.42 9.48 12.41
44.20 7.09 8.41 9.50 12.42
- 44.19 7.12 8.41 9.52 12.44
- 44.18 7.15 8.41 9.54 12.45
+ 44.19 7.12 8.41 9.53 12.44
+ 44.18 7.15 8.41 9.56 12.45
44.17 7.18 8.40 9.56 12.46
- 44.16 7.20 8.38 9.57 12.47
+ 44.16 7.20 8.38 9.56 12.47
44.15 7.23 7.60 7.63 8.34 9.58 12.47
44.14 7.26 7.57 7.63 8.31 9.60 12.49
44.13 7.29 7.53 7.63 8.29 9.61 12.51
44.12 7.31 7.47 7.63 8.28 9.67 12.52
- 44.11 7.32 7.41 7.64 8.27 9.68 12.54
- 44.10 7.65 8.25 9.70 12.56
+ 44.11 7.32 7.41 7.64 8.26 9.68 12.54
+ 44.10 7.65 8.25 9.69 12.56
44.09 7.66 8.24 9.72 12.58
44.08 7.67 8.24 9.73 12.59
- 44.07 7.67 8.24 9.75 12.60
- 44.06 7.66 8.24 9.76 9.85 9.89 12.61
- 44.05 7.65 8.24 9.79 9.85 9.91 12.62
- 44.04 7.64 8.23 9.81 9.85 9.93 12.63
- 44.03 7.63 8.22 9.82 9.85 9.94 9.99 10.02 12.64
+ 44.07 7.67 8.24 9.75 12.61
+ 44.06 7.66 8.24 9.76 9.85 9.89 12.62
+ 44.05 7.65 8.24 9.79 9.85 9.91 12.63
+ 44.04 7.64 8.23 9.81 9.85 9.93 12.64
+ 44.03 7.63 8.22 9.82 9.85 9.94 9.99 10.02 12.65
44.02 7.63 8.21 10.04 12.66
44.01 7.62 8.20 10.06 12.68
44.00 7.62 8.18 10.09 12.71
@@ -99088,10 +99407,10 @@ Italy
43.87 7.46 8.05 10.22 13.00
43.86 7.46 8.02 10.22 13.02
43.85 7.46 8.00 10.23 13.03
- 43.84 7.46 7.98 10.23 13.05
- 43.83 7.47 7.94 10.24 13.07
- 43.82 7.47 7.88 10.24 13.08
- 43.81 7.48 7.82 10.24 13.10
+ 43.84 7.46 7.97 10.23 13.05
+ 43.83 7.47 7.93 10.24 13.07
+ 43.82 7.47 7.87 10.24 13.08
+ 43.81 7.48 7.81 10.24 13.10
43.80 7.48 7.78 10.25 13.12
43.79 7.49 7.76 10.25 13.13
43.78 7.49 7.74 10.25 13.15
@@ -99106,9 +99425,9 @@ Italy
43.69 10.26 13.32
43.68 10.26 13.34
43.67 10.26 13.36
- 43.66 10.27 13.39
- 43.65 10.27 13.40
- 43.64 10.27 13.43 13.49 13.52
+ 43.66 10.27 13.38
+ 43.65 10.27 13.39
+ 43.64 10.27 13.42 13.49 13.52
43.63 10.27 13.46 13.48 13.54
43.62 10.27 13.55
43.61 10.27 13.55
@@ -99163,34 +99482,34 @@ Italy
43.12 10.52 13.84
43.11 10.52 13.85
43.10 10.52 13.85
- 43.09 9.81 9.83 10.52 13.85
- 43.08 9.80 9.84 10.52 13.85
- 43.07 9.80 9.85 10.52 13.86
- 43.06 9.79 9.86 10.51 13.86
- 43.05 9.79 9.86 10.51 13.86
+ 43.09 10.52 13.85
+ 43.08 9.81 9.84 10.52 13.85
+ 43.07 9.79 9.85 10.52 13.86
+ 43.06 9.79 9.85 10.51 13.86
+ 43.05 9.78 9.86 10.51 13.86
43.04 9.78 9.86 10.50 13.86
- 43.03 9.78 9.86 10.50 13.87
- 43.02 9.78 9.85 10.50 13.87
- 43.01 9.79 9.84 10.49 13.87
- 43.00 9.80 9.83 10.47 13.87
- 42.99 10.46 13.88
+ 43.03 9.77 9.86 10.50 13.87
+ 43.02 9.77 9.86 10.50 13.87
+ 43.01 9.77 9.85 10.48 13.87
+ 43.00 9.78 9.84 10.46 13.87
+ 42.99 9.79 9.83 10.46 13.88
42.98 10.46 13.88
42.97 10.46 13.89
42.96 10.47 13.89
42.95 10.47 13.89
42.94 10.48 13.90
- 42.93 10.49 10.56 10.65 13.90
- 42.92 10.49 10.55 10.69 13.90
+ 42.93 10.48 10.56 10.65 13.90
+ 42.92 10.49 10.55 10.69 13.91
42.91 10.50 10.53 10.73 13.91
42.90 10.75 13.91
42.89 10.75 13.92
42.88 10.40 10.43 10.75 13.92
- 42.87 10.39 10.44 10.75 13.92
+ 42.87 10.38 10.44 10.75 13.92
42.86 10.38 10.44 10.75 13.93
42.85 10.38 10.45 10.75 13.93
- 42.84 10.37 10.45 10.75 13.93
+ 42.84 10.37 10.45 10.75 13.94
42.83 10.26 10.33 10.35 10.45 10.75 13.94
- 42.82 10.12 10.21 10.24 10.44 10.74 13.94
+ 42.82 10.12 10.20 10.24 10.44 10.74 13.94
42.81 10.10 10.44 10.72 13.95
42.80 10.10 10.44 10.72 13.95
42.79 10.09 10.44 10.72 13.96
@@ -99201,8 +99520,8 @@ Italy
42.74 10.09 10.43 10.90 13.99
42.73 10.11 10.32 10.35 10.44 10.92 13.99
42.72 10.13 10.24 10.35 10.44 10.94 14.00
- 42.71 10.36 10.44 10.95 14.00
- 42.70 10.38 10.43 10.96 14.01
+ 42.71 10.36 10.44 10.96 14.00
+ 42.70 10.38 10.43 10.97 14.01
42.69 10.40 10.42 10.98 14.02
42.68 10.98 14.03
42.67 10.98 14.04
@@ -99214,35 +99533,35 @@ Italy
42.61 10.06 10.09 11.06 14.07
42.60 10.05 10.10 11.07 14.08
42.59 10.04 10.10 11.08 14.09
- 42.58 10.04 10.10 11.09 14.10
+ 42.58 10.04 10.10 11.09 14.11
42.57 10.04 10.10 11.09 14.12
42.56 10.04 10.10 11.10 14.13
42.55 11.10 14.14
- 42.54 11.11 14.15
- 42.53 11.15 14.16
- 42.52 11.16 14.17
- 42.51 11.17 14.18
- 42.50 11.17 14.20
- 42.49 11.17 14.21
- 42.48 11.17 14.22
- 42.47 11.16 14.23
- 42.46 11.16 14.25
- 42.45 11.08 14.26
- 42.44 11.07 14.28
+ 42.54 11.11 14.16
+ 42.53 11.15 14.17
+ 42.52 11.16 14.18
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+ 42.50 11.17 14.21
+ 42.49 11.17 14.22
+ 42.48 11.17 14.23
+ 42.47 11.16 14.24
+ 42.46 11.16 14.26
+ 42.45 11.08 11.13 11.16 14.27
+ 42.44 11.08 14.28
42.43 11.07 14.30
42.42 11.07 14.32
42.41 11.07 14.34
42.40 10.87 10.89 11.07 11.22 11.27 14.36
- 42.39 10.86 10.90 11.08 11.21 11.31 14.38
- 42.38 10.86 10.91 11.09 11.21 11.38 14.39
- 42.37 10.85 10.91 11.11 11.20 11.40 14.40
+ 42.39 10.86 10.91 11.08 11.21 11.31 14.38
+ 42.38 10.86 10.92 11.09 11.21 11.38 14.39
+ 42.37 10.85 10.92 11.11 11.20 11.40 14.40
42.36 10.29 10.31 10.85 10.93 11.13 11.19 11.43 14.41
- 42.35 10.28 10.32 10.85 10.94 11.14 11.19 11.45 14.41
+ 42.35 10.28 10.32 10.85 10.93 11.14 11.19 11.45 14.41
42.34 10.28 10.32 10.86 10.94 11.47 14.42
42.33 10.28 10.32 10.87 10.94 11.50 14.43
- 42.32 10.28 10.32 10.88 10.93 11.53 14.45
- 42.31 10.28 10.32 10.89 10.92 11.55 14.46
- 42.30 11.57 14.47
+ 42.32 10.28 10.32 10.88 10.94 11.53 14.45
+ 42.31 10.28 10.32 10.89 10.94 11.55 14.46
+ 42.30 10.91 10.93 11.57 14.47
42.29 11.59 14.49
42.28 11.60 14.50
42.27 11.62 14.52
@@ -99255,19 +99574,19 @@ Italy
42.20 11.69 14.68
42.19 11.70 14.70
42.18 11.70 14.71
- 42.17 11.71 14.71
+ 42.17 11.71 14.72
42.16 11.71 14.72
42.15 11.72 14.72
- 42.14 11.73 14.72
+ 42.14 11.73 14.73
42.13 11.73 14.73
42.12 11.73 14.73
42.11 11.74 14.73
42.10 11.75 14.74
42.09 11.76 14.75
- 42.08 11.77 14.80
+ 42.08 11.76 14.79
42.07 11.78 14.81
- 42.06 11.79 14.83
- 42.05 11.80 14.86
+ 42.06 11.78 14.83
+ 42.05 11.79 14.86
42.04 11.80 14.92
42.03 11.81 14.98
42.02 11.81 15.00
@@ -99276,11 +99595,11 @@ Italy
41.99 11.96 15.03
41.98 11.97 15.04
41.97 12.01 15.08
- 41.96 12.02 15.10
+ 41.96 12.01 15.10
41.95 12.02 15.12 15.95 16.05
- 41.94 12.04 15.15 15.83 16.09
- 41.93 12.05 15.32 15.56 16.13
- 41.92 12.07 15.38 15.48 16.15
+ 41.94 12.04 15.16 15.83 16.09
+ 41.93 12.06 15.32 15.56 16.13
+ 41.92 12.08 15.38 15.48 16.15
41.91 12.09 16.16
41.90 12.11 16.18
41.89 12.13 16.18
@@ -99302,15 +99621,15 @@ Italy
41.73 12.21 16.15
41.72 12.22 16.12
41.71 12.25 16.10
- 41.70 12.29 16.09
+ 41.70 12.29 16.08
41.69 12.33 16.07
41.68 12.34 16.06
41.67 12.36 16.05
41.66 12.37 16.03
41.65 12.39 16.01
- 41.64 12.40 15.99
- 41.63 12.41 15.96
- 41.62 12.43 15.94
+ 41.64 12.40 15.98
+ 41.63 12.41 15.94
+ 41.62 12.43 15.92
41.61 12.44 15.92
41.60 12.45 15.91
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39.07 8.33 9.04 16.07 17.14
39.06 8.33 9.05 16.07 17.15
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39.04 8.33 8.48 8.53 9.05 16.08 17.20
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39.02 8.34 8.47 8.55 9.03 16.09 17.21
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38.95 8.39 8.44 8.57 8.98 16.13 17.18
38.94 8.59 8.96 16.14 17.17
38.93 8.60 8.95 16.15 17.16
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38.87 8.62 8.66 8.79 8.87 16.21 16.77
38.86 8.62 8.66 8.84 8.86 16.21 16.74
38.85 8.63 8.65 16.21 16.72
38.84 16.21 16.70
- 38.83 16.20 16.69
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38.82 15.20 15.23 16.20 16.67
38.81 15.19 15.24 16.20 16.65
38.80 15.17 15.24 16.20 16.63
@@ -99620,44 +99939,44 @@ Italy
38.55 14.33 14.36 14.54 14.59 14.79 14.88 15.89 16.57
38.54 14.33 14.37 14.56 14.59 14.81 14.87 15.90 16.58
38.53 14.33 14.37 14.83 14.87 14.91 14.96 15.90 16.58
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38.46 14.89 14.97 15.88 16.58
38.45 14.91 14.97 15.87 16.58
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38.40 14.93 15.01 15.84 16.57
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38.34 15.81 16.49
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38.26 15.22 15.25 15.42 16.31
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38.21 13.22 13.33 15.20 15.58 15.62 16.26
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- 38.18 12.71 12.77 13.07 13.38 14.83 14.96 15.18 15.57 15.62 16.22
- 38.17 12.71 12.77 13.07 13.38 14.73 14.76 14.78 14.97 15.17 15.57 15.62 16.21
- 38.16 12.71 12.78 13.05 13.38 14.72 15.05 15.14 15.56 15.62 16.20
- 38.15 12.71 12.78 13.04 13.38 14.71 15.06 15.11 15.55 15.63 16.19
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+ 38.18 12.70 12.77 13.07 13.38 14.83 14.96 15.18 15.57 15.62 16.22
+ 38.17 12.70 12.77 13.07 13.38 14.73 14.76 14.78 14.97 15.17 15.57 15.62 16.21
+ 38.16 12.70 12.78 13.05 13.38 14.72 15.05 15.14 15.56 15.62 16.20
+ 38.15 12.70 12.78 13.04 13.38 14.71 15.06 15.11 15.55 15.63 16.19
38.14 12.71 12.79 13.04 13.38 14.69 15.54 15.63 16.18
38.13 12.71 12.79 13.04 13.39 14.68 15.54 15.63 16.17
38.12 12.65 12.80 13.04 13.39 13.45 13.52 14.67 15.53 15.62 16.17
@@ -99665,10 +99984,10 @@ Italy
38.10 12.64 12.81 13.05 13.55 14.64 15.52 15.61 16.16
38.09 12.63 12.81 13.05 13.55 14.61 15.52 15.61 16.16
38.08 12.56 12.59 12.61 12.82 13.03 13.55 14.58 15.51 15.61 16.15
- 38.07 12.55 12.84 13.00 13.55 14.55 15.51 15.61 16.15
- 38.06 12.54 12.87 12.98 13.55 14.52 15.50 15.62 16.15
- 38.05 12.52 12.88 12.95 13.57 14.01 14.04 14.41 14.45 14.48 15.49 15.63 16.15
- 38.04 12.50 12.90 12.92 13.60 13.96 14.06 14.39 15.48 15.63 16.14
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+ 38.05 12.52 12.88 12.95 13.57 14.01 14.05 14.41 14.45 14.48 15.49 15.63 16.15
+ 38.04 12.50 12.90 12.92 13.60 13.96 14.08 14.39 15.48 15.63 16.14
38.03 12.48 13.62 13.91 14.22 14.35 15.47 15.62 16.14
38.02 12.48 13.64 13.90 15.46 15.62 16.14
38.01 12.48 13.68 13.87 15.45 15.62 16.14
@@ -99682,7 +100001,7 @@ Italy
37.93 12.26 12.37 12.46 15.38 15.69 16.10
37.92 12.26 12.37 12.45 15.37 15.71 16.09
37.91 12.26 12.37 12.45 15.36 15.74 15.86 15.95 16.04
- 37.90 12.29 12.36 12.45 15.35 15.98 16.01
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37.89 12.45 15.34
37.88 12.45 15.33
37.87 12.46 15.33
@@ -99736,10 +100055,10 @@ Italy
37.39 13.25 15.10
37.38 13.26 15.10
37.37 13.27 15.10
- 37.36 13.31 15.10
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- 37.33 13.36 15.13
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37.32 13.37 15.15
37.31 13.39 15.17
37.30 13.41 15.20
@@ -99752,7 +100071,7 @@ Italy
37.23 13.59 15.27
37.22 13.60 15.23 15.25 15.27
37.21 13.62 15.23
- 37.20 13.63 15.23
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37.19 13.64 15.20
37.18 13.66 15.20
37.17 13.67 15.24
@@ -99760,10 +100079,10 @@ Italy
37.15 13.72 15.25
37.14 13.74 15.25
37.13 13.80 15.24
- 37.12 13.82 15.26
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37.11 13.84 15.31
37.10 13.86 15.31
- 37.09 13.88 14.03 14.13 15.31
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37.08 13.91 13.96 14.16 15.31
37.07 14.18 15.31
37.06 14.20 15.31
@@ -99771,13 +100090,13 @@ Italy
37.04 14.24 15.33
37.03 14.26 15.33
37.02 14.27 15.34
- 37.01 14.29 15.34
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37.00 14.30 15.34
- 36.99 14.32 15.29 15.31 15.33
- 36.98 14.33 15.28
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36.97 14.34 15.27
- 36.96 14.36 15.27
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36.94 14.37 15.22
36.93 14.38 15.19
36.92 14.39 15.17
@@ -99788,7 +100107,7 @@ Italy
36.87 14.41 15.14
36.86 14.42 15.14
36.85 11.93 11.96 14.43 15.13
- 36.84 11.92 11.97 11.99 12.01 14.43 15.13
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36.83 11.91 12.02 14.44 15.12
36.82 11.91 12.03 14.44 15.12
36.81 11.91 12.05 14.45 15.11
@@ -99823,27 +100142,27 @@ Italy
35.47 12.60 12.62
Jamaica
18.53 -77.88 -77.78
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18.49 -77.95 -77.48
18.48 -77.96 -77.43
18.47 -77.96 -77.29
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18.43 -78.26 -77.14
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18.38 -78.31 -76.87
18.37 -78.34 -76.86
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18.33 -78.35 -76.80
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18.31 -78.35 -76.79
18.30 -78.35 -76.78
18.29 -78.36 -76.78
@@ -99851,21 +100170,21 @@ Jamaica
18.27 -78.38 -76.68
18.26 -78.38 -76.67
18.25 -78.38 -76.66
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18.20 -78.33 -76.46
18.19 -78.29 -76.43
18.18 -78.24 -78.20 -78.17 -76.39
18.17 -78.06 -76.36
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18.15 -78.05 -76.34
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18.13 -78.04 -76.32
18.12 -78.04 -76.31
18.11 -78.03 -76.30
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18.09 -78.02 -76.29
18.08 -77.99 -76.28
18.07 -77.98 -76.28
@@ -99874,41 +100193,41 @@ Jamaica
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17.84 -77.74 -77.64 -77.56 -77.44 -77.40 -77.14 -77.04 -76.90
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17.82 -77.37 -77.14 -76.97 -76.92
17.81 -77.35 -77.14
17.80 -77.33 -77.14
17.79 -77.32 -77.16
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17.70 -77.22 -77.12
17.69 -77.20 -77.13
Jan Mayen
- 71.19 -8.02 -7.98
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71.18 -8.16 -7.95
71.17 -8.17 -7.93
71.16 -8.25 -7.92
@@ -99917,7 +100236,7 @@ Jan Mayen
71.13 -8.38 -7.92
71.12 -8.40 -7.92
71.11 -8.41 -7.93
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71.09 -8.44 -7.98
71.08 -8.45 -7.98
71.07 -8.46 -7.97
@@ -99930,38 +100249,38 @@ Jan Mayen
71.00 -8.63 -8.08
70.99 -8.71 -8.14
70.98 -8.74 -8.19
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70.95 -8.81 -8.51 -8.45 -8.37
70.94 -8.92 -8.57
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70.92 -8.98 -8.66
70.91 -9.00 -8.70
70.90 -9.02 -8.72
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70.87 -9.12 -8.79
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70.83 -9.08 -8.91
70.82 -9.08 -8.92
70.81 -9.08 -8.93
70.80 -9.08 -8.95
70.79 -9.06 -8.99
Japan
- 45.53 141.92 141.95
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45.51 141.88 141.97
- 45.50 141.87 141.97
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45.49 141.86 141.98
45.48 141.86 141.98
45.47 140.95 141.00 141.86 142.01
45.46 140.95 141.00 141.04 141.06 141.65 141.67 141.86 142.02
45.45 140.95 141.07 141.64 141.68 141.84 142.03
45.44 140.96 141.07 141.63 141.69 141.82 142.04
- 45.43 140.96 141.08 141.62 141.69 141.79 142.04
- 45.42 140.97 141.08 141.62 141.69 141.74 142.05
+ 45.43 140.97 141.08 141.62 141.69 141.79 142.04
+ 45.42 140.98 141.08 141.62 141.69 141.74 142.05
45.41 140.98 141.08 141.62 142.06
45.40 140.99 141.08 141.62 142.08
45.39 140.98 141.08 141.62 142.09
@@ -99970,13 +100289,13 @@ Japan
45.36 140.98 141.07 141.63 142.14
45.35 140.98 141.07 141.63 142.16
45.34 140.98 141.07 141.62 142.18
- 45.33 140.98 141.06 141.62 142.19
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45.32 140.99 141.06 141.61 142.21
45.31 141.00 141.06 141.61 142.22
45.30 141.01 141.06 141.61 142.23
45.29 141.01 141.05 141.60 142.24
- 45.28 141.01 141.05 141.60 142.25
- 45.27 141.01 141.05 141.59 142.26
+ 45.28 141.01 141.05 141.59 142.25
+ 45.27 141.01 141.05 141.58 142.26
45.26 141.01 141.04 141.57 142.27
45.25 141.02 141.04 141.16 141.24 141.57 142.29
45.24 141.15 141.26 141.57 142.30
@@ -99985,16 +100304,16 @@ Japan
45.21 141.12 141.30 141.56 142.33
45.20 141.12 141.31 141.56 142.34
45.19 141.12 141.32 141.56 142.35
- 45.18 141.13 141.33 141.56 142.36
+ 45.18 141.12 141.33 141.56 142.36
45.17 141.12 141.33 141.56 142.37
45.16 141.12 141.34 141.57 142.39
- 45.15 141.12 141.34 141.57 142.40
+ 45.15 141.13 141.34 141.57 142.40
45.14 141.13 141.34 141.58 142.41
45.13 141.14 141.33 141.58 142.42
45.12 141.15 141.32 141.59 142.43
45.11 141.17 141.32 141.60 142.44
- 45.10 141.19 141.31 141.60 142.45
- 45.09 141.21 141.29 141.61 142.46
+ 45.10 141.19 141.30 141.60 142.45
+ 45.09 141.21 141.28 141.61 142.46
45.08 141.24 141.26 141.62 142.47
45.07 141.62 142.49
45.06 141.63 142.50
@@ -100038,10 +100357,10 @@ Japan
44.68 141.78 142.88
44.67 141.78 142.89
44.66 141.78 142.90
- 44.65 141.78 142.93
- 44.64 141.78 142.95
- 44.63 141.78 142.96
- 44.62 141.78 142.97
+ 44.65 141.78 142.92
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+ 44.62 141.78 142.96
44.61 141.78 142.97
44.60 141.78 142.98
44.59 141.78 143.00
@@ -100071,7 +100390,7 @@ Japan
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30.50 130.87 130.99 140.29 140.32
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+ 29.99 129.89 129.94
29.98 129.88 129.94
29.97 129.88 129.95
29.96 129.88 129.95
- 29.95 129.89 129.95
- 29.94 129.90 129.95
- 29.93 129.91 129.94
+ 29.95 129.90 129.95
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29.91 129.51 129.56
29.90 129.51 129.56
- 29.89 129.51 129.56
- 29.88 129.52 129.56 129.85 129.90
- 29.87 129.52 129.55 129.84 129.91
- 29.86 129.84 129.91
- 29.85 129.84 129.92
- 29.84 129.84 129.93
- 29.83 129.85 129.93
- 29.82 129.87 129.93
- 29.81 129.89 129.93
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+ 29.89 129.51 129.56 129.84 129.87
+ 29.88 129.52 129.56 129.82 129.90
+ 29.87 129.52 129.55 129.82 129.90
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+ 29.81 129.85 129.93
+ 29.80 129.89 129.93
29.67 129.72 129.75
29.66 129.70 129.75
29.65 129.70 129.76
@@ -101522,8 +101840,8 @@ Japan
28.39 129.39 129.65
28.38 129.38 129.62 130.02 130.04
28.37 129.32 129.62 130.00 130.04
- 28.36 129.31 129.60 129.98 130.04
- 28.35 129.30 129.58 129.96 130.04
+ 28.36 129.30 129.60 129.98 130.04
+ 28.35 129.29 129.58 129.96 130.04
28.34 129.27 129.58 129.95 130.04
28.33 129.24 129.57 129.94 130.04
28.32 129.23 129.57 129.92 130.03
@@ -101544,8 +101862,8 @@ Japan
28.17 129.17 129.42
28.16 129.17 129.41
28.15 129.18 129.41
- 28.14 129.18 129.28 129.30 129.38
- 28.13 129.19 129.38
+ 28.14 129.19 129.28 129.30 129.38
+ 28.13 129.20 129.38
28.12 129.20 129.38
28.11 129.20 129.38
28.10 129.20 129.38
@@ -101572,10 +101890,10 @@ Japan
27.76 128.88 129.03
27.75 128.88 129.03
27.74 128.88 129.03
- 27.73 128.88 129.02 142.09 142.12
- 27.72 128.88 129.02 142.09 142.12
- 27.71 128.88 129.01 142.09 142.12
- 27.70 128.90 129.00 142.09 142.11
+ 27.73 128.88 129.02 142.06 142.12
+ 27.72 128.88 129.02 142.06 142.12
+ 27.71 128.88 129.01 142.06 142.12
+ 27.70 128.90 129.00 142.07 142.11
27.69 128.91 128.99
27.68 128.91 128.98
27.67 128.91 128.97
@@ -101589,10 +101907,10 @@ Japan
27.44 128.64 128.71
27.43 128.55 128.59 128.62 128.71
27.42 128.52 128.70
- 27.41 128.51 128.69
- 27.40 128.51 128.67
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+ 27.40 128.51 128.66
27.39 128.51 128.66
- 27.38 128.51 128.66
+ 27.38 128.51 128.65
27.37 128.51 128.65
27.36 128.51 128.64
27.35 128.52 128.62
@@ -101601,7 +101919,7 @@ Japan
27.23 140.85 140.88
27.22 140.85 140.88
27.21 140.85 140.88
- 27.20 140.86 140.88
+ 27.20 140.85 140.87
27.19 142.18 142.21
27.18 142.17 142.21
27.17 142.17 142.21
@@ -101614,9 +101932,9 @@ Japan
27.08 127.97 128.01 142.17 142.25
27.07 127.96 128.01 128.41 128.45 142.17 142.25
27.06 127.95 128.00 128.39 128.46 142.17 142.25
- 27.05 127.94 128.00 128.38 128.46 142.17 142.25
+ 27.05 127.94 128.00 128.38 128.46 142.17 142.24
27.04 127.93 127.99 128.38 128.46 142.18 142.24
- 27.03 127.92 127.99 128.38 128.46 142.20 142.24
+ 27.03 127.92 127.99 128.38 128.46 142.20 142.23
27.02 127.92 127.98 128.39 128.46
27.01 127.91 127.97 128.42 128.46
27.00 127.91 127.96
@@ -101636,20 +101954,20 @@ Japan
26.77 128.15 128.34
26.76 128.15 128.34
26.75 128.15 128.34
- 26.74 127.75 127.82 128.14 128.34
- 26.73 127.74 127.82 128.13 128.33 142.10 142.13
- 26.72 127.74 127.82 128.11 128.33 142.10 142.14
- 26.71 127.74 127.82 128.10 128.32 142.10 142.17
- 26.70 127.74 127.82 127.86 127.99 128.09 128.32 142.10 142.17
- 26.69 127.76 127.82 127.86 128.00 128.09 128.32 142.11 142.17
+ 26.74 127.75 127.81 128.14 128.34
+ 26.73 127.74 127.81 128.13 128.33 142.10 142.13
+ 26.72 127.74 127.82 128.11 128.32 142.10 142.14
+ 26.71 127.74 127.82 128.10 128.31 142.10 142.17
+ 26.70 127.74 127.82 127.86 128.00 128.09 128.31 142.10 142.17
+ 26.69 127.76 127.82 127.86 128.01 128.09 128.31 142.11 142.17
26.68 127.86 128.01 128.09 128.29 142.11 142.19
26.67 127.86 128.01 128.08 128.29 142.11 142.19
- 26.66 127.86 128.01 128.06 128.28 142.12 142.19
+ 26.66 127.86 128.00 128.06 128.28 142.12 142.19
26.65 127.87 128.00 128.03 128.28 142.12 142.20
26.64 127.87 128.27 142.13 142.20
- 26.63 127.87 128.26 142.14 142.20
- 26.62 127.87 128.25 142.15 142.19
- 26.61 127.22 127.24 127.87 128.23 142.16 142.19
+ 26.63 127.87 128.26 142.13 142.20
+ 26.62 127.87 128.25 142.14 142.19
+ 26.61 127.22 127.24 127.87 128.23 142.15 142.19
26.60 127.20 127.25 127.87 128.17 142.17 142.19
26.59 127.19 127.25 127.88 128.15
26.58 127.19 127.25 127.94 128.15
@@ -101670,18 +101988,18 @@ Japan
26.43 127.71 127.95
26.42 127.71 127.86
26.41 127.71 127.87
- 26.40 126.74 126.77 127.71 127.88
- 26.39 126.71 126.78 127.71 127.88
+ 26.40 126.74 126.76 127.71 127.87
+ 26.39 126.71 126.79 127.71 127.87
26.38 126.69 126.80 127.71 127.88
26.37 126.68 126.81 127.71 127.88
26.36 126.68 126.82 127.71 127.88
26.35 126.68 126.82 127.71 127.88
26.34 126.69 126.82 127.72 127.90
- 26.33 126.71 126.82 127.72 127.92
- 26.32 126.75 126.81 127.72 127.92
- 26.31 126.75 126.81 127.72 127.93
- 26.30 126.76 126.80 127.72 127.93
- 26.29 126.76 126.80 127.72 127.82 127.89 127.93
+ 26.33 126.70 126.82 127.72 127.92
+ 26.32 126.74 126.81 127.72 127.92
+ 26.31 126.75 126.81 127.72 127.92
+ 26.30 126.76 126.80 127.72 127.92
+ 26.29 126.76 126.80 127.72 127.82 127.89 127.92
26.28 127.69 127.82
26.27 127.69 127.81
26.26 127.68 127.81
@@ -101706,29 +102024,26 @@ Japan
26.07 127.64 127.73
25.96 131.27 131.32
25.95 131.27 131.33
- 25.94 123.66 123.68 131.27 131.33
- 25.93 123.66 123.69 131.27 131.33
- 25.92 123.66 123.69 131.28 131.33
- 25.91 123.66 123.69 131.29 131.33
- 25.90 123.66 123.69 124.55 124.57
- 25.89 124.55 124.57
- 25.88 124.55 124.57 131.22 131.26
+ 25.94 131.27 131.33
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+ 25.91 123.66 123.68 131.29 131.33
+ 25.88 131.22 131.26
25.87 131.22 131.27
25.86 131.21 131.28
25.85 131.20 131.28
25.84 131.20 131.28
25.83 131.20 131.27
25.82 131.20 131.26
- 25.81 123.58 123.60 131.20 131.26
- 25.80 123.58 123.60 131.23 131.26
- 25.79 123.58 123.60
- 25.78 123.52 123.54 123.58 123.62
- 25.77 123.50 123.55 123.60 123.62
- 25.76 123.50 123.62
- 25.75 123.50 123.61
- 25.74 123.50 123.52 123.54 123.61
- 25.73 123.58 123.61
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+ 25.81 131.20 131.26
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+ 25.74 123.50 123.52 123.59 123.61
+ 25.73 123.59 123.61
+ 25.72 123.59 123.61
25.46 141.26 141.29
25.45 141.26 141.30
25.44 141.26 141.30
@@ -101748,9 +102063,9 @@ Japan
24.80 125.13 125.22 125.26 125.35 141.30 141.35
24.79 125.14 125.21 125.25 125.40 141.28 141.36
24.78 125.25 125.42 141.28 141.37
- 24.77 125.25 125.44 141.28 141.37
- 24.76 125.24 125.45 141.28 141.37
- 24.75 125.24 125.46 141.28 141.34
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+ 24.75 125.24 125.46 141.27 141.34
24.74 125.24 125.46 141.27 141.33
24.73 125.24 125.46 141.27 141.32
24.72 125.24 125.45 141.27 141.31
@@ -101769,14 +102084,14 @@ Japan
24.49 124.23 124.29
24.48 122.94 123.01 124.22 124.29
24.47 122.93 123.02 124.10 124.14 124.21 124.28
- 24.46 122.92 123.02 124.10 124.15 124.21 124.28
- 24.45 122.92 123.02 124.09 124.16 124.19 124.28
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+ 24.45 122.92 123.02 124.09 124.28
24.44 122.92 123.02 124.06 124.27
24.43 122.92 123.02 124.06 124.27
- 24.42 122.93 123.01 123.76 123.79 124.06 124.27
+ 24.42 122.93 123.01 123.75 123.79 124.06 124.27
24.41 123.75 123.81 124.06 124.27
- 24.40 123.75 123.86 124.09 124.26
- 24.39 123.75 123.90 124.11 124.26
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+ 24.39 123.75 123.91 124.11 124.26
24.38 123.74 123.93 124.12 124.26
24.37 123.74 123.94 124.11 124.26
24.36 123.74 123.94 124.11 124.25
@@ -101792,7 +102107,7 @@ Japan
24.26 123.75 123.90
24.25 123.79 123.89
24.24 123.83 123.88
- 24.23 141.44 141.48
+ 24.23 141.44 141.47
24.22 141.44 141.48
24.21 141.44 141.48
24.20 141.44 141.48
@@ -101811,11 +102126,11 @@ Jersey
49.21 -2.24 -1.99
49.20 -2.24 -1.99
49.19 -2.24 -2.00
- 49.18 -2.24 -2.14 -2.12 -2.01
- 49.17 -2.24 -2.15 -2.10 -2.01
- 49.16 -2.18 -2.15 -2.08 -2.01
+ 49.18 -2.24 -2.01
+ 49.17 -2.24 -2.15 -2.11 -2.01
+ 49.16 -2.17 -2.15 -2.08 -2.01
Johnston Atoll
- 16.77 -169.53 -169.50
+ 16.77 -169.54 -169.50
16.76 -169.54 -169.50
16.75 -169.54 -169.50
16.74 -169.54 -169.50
@@ -101841,14 +102156,14 @@ Jordan
33.23 38.47 38.83
33.22 38.45 38.83
33.21 38.43 38.84
- 33.20 38.42 38.84
- 33.19 38.40 38.84
- 33.18 38.38 38.85
- 33.17 38.36 38.85
- 33.16 38.34 38.85
- 33.15 38.32 38.86
- 33.14 38.31 38.86
- 33.13 38.29 38.86
+ 33.20 38.41 38.84
+ 33.19 38.39 38.84
+ 33.18 38.37 38.85
+ 33.17 38.35 38.85
+ 33.16 38.33 38.85
+ 33.15 38.31 38.86
+ 33.14 38.30 38.86
+ 33.13 38.28 38.86
33.12 38.27 38.87
33.11 38.25 38.87
33.10 38.23 38.87
@@ -101887,12 +102202,12 @@ Jordan
32.77 37.62 38.98
32.76 37.60 38.98
32.75 35.73 35.78 37.58 38.99
- 32.74 35.71 35.81 37.57 38.99
- 32.73 35.69 35.87 37.55 38.99
- 32.72 35.67 35.90 37.53 39.00
- 32.71 35.66 35.92 37.51 39.00
- 32.70 35.65 35.95 37.49 39.00
- 32.69 35.60 35.95 37.47 39.01
+ 32.74 35.71 35.81 37.56 38.99
+ 32.73 35.69 35.87 37.54 38.99
+ 32.72 35.67 35.90 37.52 39.00
+ 32.71 35.66 35.92 37.50 39.00
+ 32.70 35.65 35.95 37.48 39.00
+ 32.69 35.60 35.95 37.46 39.01
32.68 35.58 35.95 37.45 39.01
32.67 35.57 35.95 37.43 39.01
32.66 35.56 36.01 37.41 39.01
@@ -101924,8 +102239,8 @@ Jordan
32.40 35.53 36.37 36.93 39.01
32.39 35.53 36.38 36.92 39.01
32.38 35.53 36.44 36.90 39.01
- 32.37 35.54 36.53 36.88 39.02
- 32.36 35.54 36.61 36.86 39.02 39.21 39.25
+ 32.37 35.54 36.50 36.88 39.02
+ 32.36 35.54 36.59 36.86 39.02 39.21 39.25
32.35 35.54 36.66 36.85 39.02 39.17 39.26
32.34 35.54 36.67 36.83 39.03 39.13 39.27
32.33 35.54 36.76 36.81 39.03 39.09 39.27
@@ -101941,7 +102256,7 @@ Jordan
32.23 35.54 39.30
32.22 35.54 39.29
32.21 35.55 39.28
- 32.20 35.55 39.27
+ 32.20 35.54 39.27
32.19 35.54 39.26
32.18 35.54 39.25
32.17 35.54 39.23
@@ -101985,17 +102300,17 @@ Jordan
31.79 35.52 38.23
31.78 35.53 38.19
31.77 35.53 38.15
- 31.76 35.53 38.11
- 31.75 35.52 38.07
- 31.74 35.51 38.02
- 31.73 35.51 37.98
- 31.72 35.50 37.93
- 31.71 35.50 37.89
- 31.70 35.49 37.85
- 31.69 35.49 37.81
- 31.68 35.48 37.77
- 31.67 35.48 37.73
- 31.66 35.47 37.69
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+ 31.69 35.49 37.82
+ 31.68 35.49 37.78
+ 31.67 35.48 37.74
+ 31.66 35.48 37.69
31.65 35.47 37.65
31.64 35.47 37.62
31.63 35.47 37.58
@@ -102036,12 +102351,12 @@ Jordan
31.28 35.39 37.19
31.27 35.38 37.20
31.26 35.38 37.21
- 31.25 35.38 37.22
- 31.24 35.38 37.23
- 31.23 35.38 37.24
- 31.22 35.39 37.25
- 31.21 35.39 37.26
- 31.20 35.40 37.27
+ 31.25 35.38 37.23
+ 31.24 35.38 37.24
+ 31.23 35.38 37.25
+ 31.22 35.39 37.26
+ 31.21 35.39 37.27
+ 31.20 35.40 37.28
31.19 35.40 37.29
31.18 35.40 37.30
31.17 35.41 37.31
@@ -102067,7 +102382,7 @@ Jordan
30.97 35.37 37.53
30.96 35.37 37.54
30.95 35.36 37.55
- 30.94 35.35 37.56
+ 30.94 35.34 37.56
30.93 35.33 37.57
30.92 35.32 37.58
30.91 35.32 37.59
@@ -102239,8 +102554,8 @@ Jordan
29.25 35.49 36.17
29.24 35.54 36.15
29.23 35.59 36.14
- 29.22 35.66 36.12
- 29.21 35.74 36.10
+ 29.22 35.68 36.12
+ 29.21 35.76 36.10
29.20 35.82 36.09
29.19 35.88 36.07
29.18 35.93 36.06
@@ -102325,15 +102640,15 @@ Kazakhstan
54.74 66.72 71.12
54.73 66.71 71.21
54.72 66.41 71.22
- 54.71 65.91 65.95 66.36 71.24
- 54.70 65.87 65.96 66.32 71.25
- 54.69 65.83 65.96 66.27 71.26
- 54.68 65.81 65.96 66.22 71.26
- 54.67 65.80 65.96 66.18 71.27
- 54.66 65.79 65.97 66.13 71.27
- 54.65 65.78 65.97 66.08 71.27
- 54.64 65.45 65.53 65.77 65.97 66.04 71.27
- 54.63 65.43 65.60 65.77 65.97 65.99 71.27
+ 54.71 65.91 65.95 66.37 71.24
+ 54.70 65.87 65.96 66.33 71.25
+ 54.69 65.83 65.96 66.28 71.26
+ 54.68 65.81 65.96 66.24 71.26
+ 54.67 65.80 65.96 66.19 71.27
+ 54.66 65.79 65.97 66.15 71.27
+ 54.65 65.78 65.97 66.11 71.27
+ 54.64 65.45 65.53 65.77 65.97 66.06 71.27
+ 54.63 65.43 65.60 65.77 65.97 66.00 71.27
54.62 65.43 65.65 65.75 71.27
54.61 65.43 65.69 65.72 71.26
54.60 65.43 71.25
@@ -102378,13 +102693,13 @@ Kazakhstan
54.21 63.45 63.87 63.89 71.06 71.31 71.34 71.70 72.03 72.05 72.34 75.98 76.78
54.20 63.42 71.06 71.29 71.37 71.70 72.33 75.95 76.78
54.19 63.13 63.19 63.40 71.07 71.28 71.46 71.70 72.32 75.91 76.77
- 54.18 63.11 63.28 63.37 71.09 71.27 71.47 71.70 72.32 75.87 76.76
+ 54.18 63.11 63.27 63.37 71.09 71.27 71.47 71.70 72.32 75.87 76.76
54.17 63.11 71.11 71.26 71.47 71.70 72.36 75.84 76.74
54.16 63.10 71.12 71.25 71.47 71.70 72.41 75.80 76.72
54.15 63.10 71.13 71.24 71.47 71.70 72.46 75.76 76.71
54.14 63.10 71.13 71.23 71.47 71.69 72.49 72.59 72.69 75.73 76.39 76.49 76.70
54.13 63.10 71.14 71.21 71.48 71.51 71.60 71.68 72.49 72.55 72.82 72.91 72.95 75.70 76.40 76.53 76.68
- 54.12 63.10 71.16 71.19 71.61 71.66 72.49 72.53 72.96 75.68 76.41 76.57 76.67
+ 54.12 63.10 71.16 71.19 71.61 71.66 72.49 72.53 72.96 75.67 76.41 76.57 76.67
54.11 63.11 72.49 72.51 72.97 75.44 75.55 75.65 76.42
54.10 62.78 62.85 62.96 63.04 63.09 72.48 72.51 72.97 75.41 76.43
54.09 62.71 62.87 62.92 72.47 72.50 72.98 75.39 76.44
@@ -102448,10 +102763,10 @@ Kazakhstan
53.51 61.22 61.30 61.53 73.40 73.53 74.30 74.41 77.49
53.50 61.20 61.31 61.50 73.39 73.51 74.31 74.40 77.51
53.49 61.20 61.32 61.48 73.39 73.49 74.33 74.40 77.53
- 53.48 61.20 61.33 61.47 73.38 73.47 74.35 74.39 77.56
- 53.47 61.20 61.34 61.45 73.37 73.46 77.58
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+ 53.45 61.19 61.37 61.42 73.40 73.43 77.62
53.44 61.19 77.64
53.43 61.18 77.65
53.42 61.16 77.67
@@ -102460,10 +102775,10 @@ Kazakhstan
53.39 61.13 77.71
53.38 61.12 77.73
53.37 61.12 77.74
- 53.36 61.12 77.76
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53.35 61.12 77.77
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53.32 61.12 77.81
53.31 61.13 77.83
53.30 61.14 77.84
@@ -102624,7 +102939,7 @@ Kazakhstan
51.75 50.73 50.85 52.27 52.35 60.43 79.26
51.74 50.73 50.87 52.26 52.36 60.43 79.27
51.73 50.73 50.88 52.15 52.36 60.42 79.28
- 51.72 50.73 50.88 52.13 52.36 60.39 79.29
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51.71 50.73 50.89 52.12 52.37 60.36 79.29
51.70 50.73 50.90 52.11 52.37 60.34 79.30
51.69 50.73 50.92 51.20 51.25 52.11 52.37 60.34 79.31
@@ -102732,7 +103047,7 @@ Kazakhstan
50.67 48.96 54.41 54.63 55.32 55.38 55.46 55.95 59.21 59.89 60.65 60.76 84.03
50.66 48.94 54.41 54.64 55.48 55.93 59.23 59.88 84.05
50.65 48.57 48.62 48.92 54.40 54.64 55.50 55.91 59.24 59.87 84.07
- 50.64 48.55 48.64 48.90 54.40 54.65 55.51 55.88 59.24 59.35 59.45 59.86 84.09
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50.63 48.55 48.67 48.88 54.39 54.65 55.51 55.85 59.27 59.31 59.47 59.84 84.11
50.62 48.55 48.70 48.86 54.39 54.66 55.52 55.83 59.48 59.83 84.13
50.61 48.55 48.72 48.84 54.39 54.66 55.54 55.80 59.49 59.83 84.14
@@ -102742,7 +103057,7 @@ Kazakhstan
50.57 48.65 54.42 54.61 55.60 55.72 59.57 59.80 84.15
50.56 48.66 54.43 54.59 55.61 55.71 59.57 59.79 84.16
50.55 48.66 54.45 54.57 55.64 55.69 59.57 59.77 84.17
- 50.54 48.66 54.47 54.52 59.57 59.74 84.18
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50.53 48.66 59.47 59.50 59.55 59.61 84.19
50.52 48.66 59.46 59.59 84.20
50.51 48.66 59.48 59.57 84.20
@@ -102758,9 +103073,9 @@ Kazakhstan
50.41 47.44 47.67 48.67 84.20
50.40 47.43 47.68 48.67 84.21
50.39 47.42 47.71 48.67 84.21
- 50.38 47.41 47.74 48.68 84.22
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50.37 47.41 47.75 48.68 84.23
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50.35 47.40 47.77 48.68 84.24
50.34 47.39 47.77 48.69 84.24
50.33 47.37 47.80 48.69 84.25
@@ -102840,27 +103155,27 @@ Kazakhstan
49.59 46.82 85.64 86.26 86.60
49.58 46.82 85.65 85.70 85.76 86.25 86.60
49.57 46.82 85.77 85.87 85.92 86.24 86.61
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49.55 46.81 85.95 86.23 86.77
49.54 46.81 85.95 86.22 86.79
49.53 46.81 85.95 86.04 86.12 86.22 86.81
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49.51 46.80 85.94 85.99 86.13 86.21 86.83
49.50 46.80 85.94 85.98 86.14 86.20 86.83
49.49 46.80 86.16 86.19 86.83
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49.47 46.79 86.83
49.46 46.79 86.82
49.45 46.79 86.82
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49.43 46.78 86.87
49.42 46.78 86.89
49.41 46.78 86.92
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49.39 46.77 86.94
49.38 46.77 86.94
49.37 46.77 86.94
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49.35 46.76 86.92
49.34 46.76 86.93
49.33 46.76 86.94
@@ -102914,41 +103229,41 @@ Kazakhstan
48.85 46.70 86.78
48.84 46.70 86.79
48.83 46.69 86.79
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48.81 46.68 86.78
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48.79 46.67 86.77
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48.77 46.66 86.75
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48.61 46.57 86.66
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48.59 46.56 86.63
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48.56 46.54 86.60
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48.54 46.53 86.59
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48.52 46.52 86.58
48.51 46.51 86.57
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48.49 46.50 86.53
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48.47 46.49 86.32 86.38 86.45
48.46 46.48 86.30
48.45 46.48 86.29
@@ -103093,8 +103408,8 @@ Kazakhstan
47.06 48.71 51.08 51.39 83.01 83.48 85.51
47.05 48.72 51.04 51.41 83.01 83.50 85.51
47.04 48.73 51.00 51.51 83.01 83.54 85.50
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47.01 48.75 50.85 50.87 50.93 51.54 51.63 51.67 83.00 83.66 85.20
47.00 48.76 50.85 50.89 50.92 51.55 51.63 51.67 82.99 83.71 85.19
46.99 48.77 50.84 51.56 51.63 51.66 82.99 83.75 85.18
@@ -103103,27 +103418,27 @@ Kazakhstan
46.96 48.80 50.81 51.66 52.43 52.54 83.00 83.87 84.13 84.45 84.59 84.67 85.15
46.95 48.81 50.80 51.67 52.43 52.56 83.00 84.02 84.11 84.49 84.55 84.69 85.13
46.94 48.82 50.80 51.69 52.43 52.58 83.00 84.71 85.11
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46.92 48.83 50.69 50.72 50.78 51.72 52.41 52.93 82.98 84.73 85.07
46.91 48.84 50.62 50.64 50.67 50.72 50.77 51.73 52.40 52.94 82.98 84.73 85.05
46.90 48.85 50.62 50.72 50.76 51.75 52.39 52.95 82.97 84.73 85.04
46.89 48.86 50.62 50.73 50.75 51.77 51.82 51.84 52.38 52.96 82.96 84.73 85.02
46.88 48.87 50.62 51.84 52.37 52.98 82.95 84.73 84.97
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- 46.86 48.89 50.42 50.47 50.61 51.92 51.96 52.01 52.31 53.05 82.94 84.71 84.95
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46.83 48.92 50.40 50.54 50.60 52.05 52.25 53.07 82.92 84.70 84.90
46.82 48.93 50.40 50.54 50.59 52.05 52.25 53.08 82.91 84.70 84.86
46.81 48.94 50.39 50.55 50.58 52.06 52.25 53.08 82.90 84.70 84.83
46.80 48.94 50.39 52.09 52.25 53.08 82.90 84.72 84.79
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46.78 48.58 48.63 48.96 50.30 53.09 82.88
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46.72 48.48 48.73 48.92 50.16 50.20 50.25 53.09 82.84
46.71 48.47 48.73 48.87 50.14 50.20 50.24 53.13 82.84
46.70 48.47 48.75 48.79 50.13 53.16 82.83
@@ -103140,17 +103455,17 @@ Kazakhstan
46.59 48.53 49.94 53.09 82.79
46.58 48.53 49.91 53.03 53.05 53.08 82.79
46.57 48.52 49.90 53.02 53.05 53.08 82.78
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46.53 48.70 49.63 49.65 49.82 52.99 82.77
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46.51 48.73 49.38 49.44 49.50 49.56 49.63 49.68 49.71 52.98 82.76
46.50 48.74 49.39 49.44 49.51 49.56 49.63 49.69 49.71 52.98 82.76
46.49 48.75 49.39 49.44 49.51 49.56 49.60 52.98 82.75
46.48 48.77 49.40 49.48 49.51 49.56 49.59 52.98 82.75
46.47 48.78 49.40 52.98 82.74
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46.45 48.91 49.35 53.03 82.73
46.44 48.93 49.36 53.04 82.72
46.43 48.94 49.38 53.06 82.72
@@ -103160,10 +103475,10 @@ Kazakhstan
46.39 49.02 49.30 49.32 49.38 53.10 82.71
46.38 49.04 49.30 49.34 49.38 53.11 82.70
46.37 49.06 49.23 49.26 49.28 49.35 49.37 53.12 82.70
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46.32 49.18 49.23 49.71 49.83 53.14 82.68
46.31 49.20 49.23 49.71 49.83 53.14 82.67
46.30 49.72 49.84 53.14 82.66
@@ -103214,8 +103529,8 @@ Kazakhstan
45.85 52.95 82.47
45.84 52.94 82.47
45.83 52.93 82.46
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45.80 52.89 82.44
45.79 52.87 82.43
45.78 52.86 82.43
@@ -103241,7 +103556,7 @@ Kazakhstan
45.58 52.72 82.32
45.57 52.72 82.31
45.56 52.72 82.31
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45.54 52.72 82.30
45.53 52.58 52.66 52.72 58.50 58.56 82.31
45.52 52.58 52.67 52.72 58.43 58.59 82.31
@@ -103251,28 +103566,28 @@ Kazakhstan
45.48 52.54 52.69 52.82 58.24 58.69 82.48
45.47 52.54 52.69 52.84 58.18 58.71 82.53
45.46 51.74 51.77 52.54 52.70 52.86 58.14 58.73 82.57
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45.41 51.70 51.84 52.32 52.71 52.99 57.92 58.83 82.64
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45.38 51.39 51.44 51.62 52.69 53.11 57.76 58.89 82.64
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45.36 51.39 51.45 51.59 52.72 53.16 57.67 58.93 82.64
45.35 51.39 51.48 51.56 52.79 53.20 57.63 58.95 82.64
45.34 51.38 52.85 53.20 57.58 58.97 82.64
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45.32 51.36 53.06 53.13 57.50 59.01 81.65 81.68 82.64
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45.30 51.33 57.41 59.06 81.60 81.74 82.64
45.29 51.32 57.36 59.08 81.58 81.75 82.63
45.28 51.31 57.32 59.10 81.56 81.75 82.63
45.27 51.30 57.27 59.13 81.52 81.76 82.63
45.26 51.29 57.22 59.15 81.48 81.76 82.63
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45.23 51.28 57.08 59.21 81.35 81.77 82.62
45.22 51.27 57.03 59.23 81.30 81.77 82.62
45.21 51.26 56.99 59.25 81.26 81.77 82.22 82.26 82.61
@@ -103282,43 +103597,43 @@ Kazakhstan
45.17 51.23 56.85 59.34 81.11 81.79 82.10 82.35 82.59
45.16 51.23 56.80 59.36 81.08 81.88 82.07 82.36 82.59
45.15 51.23 56.75 59.38 81.05 81.89 82.05 82.38 82.58
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45.12 51.23 56.61 59.44 80.68 80.76 80.90 82.41 82.55
45.11 51.23 56.57 59.46 80.64 80.80 80.87 82.43 82.54
45.10 51.23 56.52 59.48 80.60 82.45 82.51
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45.08 50.05 50.12 50.26 50.36 51.23 56.42 59.52 80.44
45.07 50.04 50.12 50.26 50.36 51.16 51.21 51.24 56.38 59.54 80.43
45.06 50.03 50.12 50.26 50.36 51.13 56.33 59.56 80.42
45.05 50.02 50.12 50.26 50.36 51.11 56.28 59.58 80.42
45.04 50.02 50.11 50.25 50.35 51.09 56.24 59.60 80.41
45.03 50.01 50.09 50.25 50.34 51.08 56.21 59.62 80.40
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45.01 50.00 50.05 50.25 50.34 51.06 56.14 59.66 80.10 80.17 80.24
45.00 49.99 50.04 50.25 50.34 50.99 56.10 59.68 80.08
44.99 49.98 50.04 50.24 50.34 50.96 56.05 59.70 80.06
44.98 49.98 50.04 50.24 50.34 50.94 56.00 59.72 80.04
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44.94 49.97 50.04 50.27 50.31 50.61 50.73 50.94 55.98 59.81 79.97
44.93 49.97 50.06 50.62 50.74 50.95 55.98 59.83 79.95
44.92 49.98 50.06 50.63 50.74 50.97 55.98 59.85 79.93
44.91 49.99 50.06 50.65 50.74 50.95 55.98 59.88 79.91
44.90 50.00 50.06 50.67 50.74 50.95 55.98 59.90 79.89
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- 44.87 50.04 50.09 50.17 50.19 50.67 50.77 50.95 55.98 59.96 79.86
- 44.86 50.04 50.11 50.15 50.19 50.68 50.77 50.95 55.98 59.98 79.86
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44.85 50.04 50.19 50.68 50.77 50.95 55.98 60.00 79.88
44.84 50.04 50.19 50.68 50.72 50.95 55.98 60.02 79.90
- 44.83 50.05 50.19 50.96 55.98 60.04 79.93
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44.82 50.06 50.18 50.98 55.98 60.06 79.96 80.16 80.26
- 44.81 50.09 50.18 51.00 55.98 60.08 79.98 80.07 80.28
- 44.80 50.12 50.16 51.02 55.98 60.10 80.30
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44.79 51.03 55.98 60.12 80.33
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44.77 51.10 55.98 60.17 80.40
44.76 51.11 55.98 60.19 80.43
44.75 51.13 55.98 60.21 80.46
@@ -103337,12 +103652,12 @@ Kazakhstan
44.62 50.27 50.92 51.27 55.98 60.48 80.38
44.61 50.27 50.93 51.27 55.98 60.51 80.39
44.60 50.26 50.94 51.28 55.98 60.53 80.39
- 44.59 50.22 50.24 50.26 50.95 51.29 51.39 51.42 55.98 60.55 80.39
- 44.58 50.22 50.96 51.30 51.34 51.44 55.98 60.58 80.38
- 44.57 50.21 51.01 51.46 55.98 60.60 80.38
- 44.56 50.21 51.02 51.28 51.39 51.48 55.98 60.63 80.37
- 44.55 50.21 51.02 51.27 51.39 51.50 55.98 60.65 80.37
- 44.54 50.21 51.02 51.26 51.39 51.43 55.98 60.67 80.37
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44.53 50.21 51.02 51.25 55.98 60.69 80.36
44.52 50.21 51.05 51.23 55.98 60.71 80.36
44.51 50.21 51.08 51.22 55.98 60.73 80.35
@@ -103436,7 +103751,7 @@ Kazakhstan
43.63 51.12 55.98 61.78 64.69 64.99 80.63
43.62 51.13 55.98 61.79 64.67 65.01 80.64
43.61 51.14 55.98 61.81 64.64 65.02 80.64
- 43.60 51.19 55.98 61.82 63.16 63.28 64.62 65.03 80.65
+ 43.60 51.20 55.98 61.82 63.16 63.28 64.62 65.03 80.65
43.59 51.20 55.98 61.84 63.07 63.43 64.60 65.04 80.65
43.58 51.20 55.98 61.85 62.98 63.58 64.58 65.05 80.66
43.57 51.22 55.98 61.86 62.89 63.73 64.55 65.06 80.66
@@ -103453,11 +103768,11 @@ Kazakhstan
43.46 51.29 55.98 65.18 80.72
43.45 51.30 55.98 65.20 80.72
43.44 51.30 55.98 65.21 80.72
- 43.43 51.31 55.98 65.22 80.72
- 43.42 51.31 55.98 65.23 80.72
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- 43.39 51.31 55.98 65.28 80.71
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43.38 51.30 55.98 65.30 80.70
43.37 51.30 55.98 65.32 80.69
43.36 51.30 55.98 65.34 80.69
@@ -103504,10 +103819,10 @@ Kazakhstan
42.95 51.78 55.98 65.73 66.04 66.08 73.54 74.87 76.83 77.05 80.46
42.94 51.79 55.98 65.73 66.02 66.08 73.54 74.90 76.81 77.10 80.50
42.93 51.80 55.98 65.74 65.99 66.08 73.53 74.92 76.80 77.13 80.54
- 42.92 51.81 55.98 65.74 65.97 66.08 73.53 74.94 76.79 77.14 80.55
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42.91 51.81 55.98 65.75 65.94 66.08 73.52 74.96 75.78 75.91 76.05 76.12 76.75 77.15 80.55
- 42.90 51.82 55.98 65.76 65.92 66.08 73.52 74.98 75.77 75.95 76.01 76.27 76.73 77.16 77.41 77.44 80.56
- 42.89 51.83 55.98 65.76 65.90 66.08 73.51 75.03 75.77 76.31 76.46 76.51 76.64 77.20 77.39 77.51 80.56
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+ 42.89 51.82 55.98 65.76 65.90 66.08 73.51 75.03 75.77 76.31 76.46 76.51 76.64 77.20 77.39 77.51 80.56
42.88 51.84 55.98 65.77 65.87 66.08 73.50 75.07 75.76 76.38 76.45 76.53 76.62 77.27 77.35 77.52 77.61 77.74 80.56
42.87 51.85 55.98 65.77 65.85 66.07 73.50 75.09 75.75 76.39 76.44 77.54 77.59 77.77 77.86 77.91 80.56
42.86 51.86 52.10 52.17 55.98 65.78 65.83 66.07 73.50 75.10 75.75 77.78 77.85 77.93 78.41 78.45 80.55
@@ -103530,7 +103845,7 @@ Kazakhstan
42.69 52.56 52.64 52.72 55.98 66.06 71.22 72.42 73.45 79.16 80.19
42.68 52.56 52.66 52.72 55.98 66.05 71.21 72.44 73.45 79.17 80.18
42.67 52.58 52.67 52.72 55.98 66.05 71.18 72.46 73.44 79.17 80.18
- 42.66 52.60 52.68 52.73 55.98 66.05 71.15 72.49 73.44 79.18 80.17
+ 42.66 52.60 52.67 52.73 55.98 66.05 71.15 72.49 73.44 79.18 80.17
42.65 52.61 52.68 52.73 55.98 66.05 71.15 72.61 73.43 79.18 80.16
42.64 52.62 52.69 52.73 55.98 66.05 71.15 72.68 73.43 79.19 80.16
42.63 52.63 52.69 52.73 55.98 66.05 71.15 72.73 73.43 79.20 80.15
@@ -103547,9 +103862,9 @@ Kazakhstan
42.52 52.65 55.98 66.04 71.03 72.88 72.98 73.14 73.45 79.36 80.20
42.51 52.65 55.98 66.04 71.05 73.16 73.45 79.36 80.21
42.50 52.65 55.98 66.04 71.06 73.19 73.46 79.37 80.22
- 42.49 52.65 55.98 66.04 71.07 73.28 73.47 79.37 80.22
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42.48 52.64 55.98 66.04 71.07 73.30 73.47 79.38 80.22
- 42.47 52.64 55.98 66.04 71.07 73.30 73.48 79.39 80.22
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42.46 52.63 55.98 66.04 71.07 73.30 73.49 79.40 80.22
42.45 52.63 55.98 66.04 71.06 73.30 73.50 79.41 80.21
42.44 52.63 55.98 66.03 70.96 71.00 71.05 73.30 73.50 79.44 79.64 79.67 80.21
@@ -103683,7 +103998,7 @@ Kazakhstan
41.16 66.70 67.69 67.76 67.90 67.93 68.99
41.15 66.71 67.45 67.80 67.88 67.94 68.96
41.14 66.72 67.23 67.81 67.86 67.94 68.90
- 41.13 66.75 66.98 67.95 68.88
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41.12 67.97 68.87
41.11 67.98 68.86
41.10 67.99 68.85
@@ -103731,9 +104046,9 @@ Kazakhstan
40.68 68.18 68.63
40.67 68.19 68.63
40.66 68.21 68.63
- 40.65 68.23 68.63
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40.62 68.32 68.63
40.61 68.35 68.63
40.60 68.37 68.62
@@ -103741,96 +104056,50 @@ Kazakhstan
40.58 68.42 68.50 68.58 68.60
40.57 68.44 68.47
Kenya
- 5.50 35.25 35.27
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4.60 34.34 35.93
4.59 34.33 35.94
4.58 34.32 35.94
@@ -103941,7 +104210,7 @@ Kenya
3.53 34.42 38.88 38.94 38.97 39.03 39.09 39.59 41.59
3.52 34.41 39.11 39.58 41.58
3.51 34.41 39.13 39.57 41.57
- 3.50 34.39 39.15 39.29 39.32 39.56 41.57
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3.49 34.37 39.17 39.27 39.33 39.56 41.56
3.48 34.37 39.20 39.25 39.33 39.55 41.55
3.47 34.37 39.45 39.55 41.54
@@ -104068,9 +104337,9 @@ Kenya
2.26 34.88 40.97
2.25 34.89 40.97
2.24 34.89 40.97
- 2.23 34.90 40.97
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2.22 34.90 40.97
- 2.21 34.91 40.97
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2.20 34.91 40.97
2.19 34.91 40.97
2.18 34.92 40.97
@@ -104155,7 +104424,7 @@ Kenya
1.39 34.76 40.97
1.38 34.76 40.97
1.37 34.76 40.97
- 1.36 34.76 40.97
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1.35 34.77 40.97
1.34 34.77 40.97
1.33 34.77 40.97
@@ -104180,7 +104449,7 @@ Kenya
1.14 34.56 40.97
1.13 34.56 40.97
1.12 34.56 40.97
- 1.11 34.49 34.52 34.56 40.97
+ 1.11 34.49 34.52 34.55 40.97
1.10 34.48 40.97
1.09 34.47 40.97
1.08 34.47 40.97
@@ -104235,7 +104504,7 @@ Kenya
0.59 34.12 40.97
0.58 34.12 40.97
0.57 34.12 40.97
- 0.56 34.11 40.97
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0.55 34.11 40.97
0.54 34.11 40.97
0.53 34.11 40.97
@@ -104430,7 +104699,7 @@ Kenya
-1.36 34.59 41.38
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- -1.39 34.65 41.40
+ -1.39 34.64 41.40
-1.40 34.66 41.41
-1.41 34.68 41.41
-1.42 34.70 41.42
@@ -104461,15 +104730,15 @@ Kenya
-1.67 35.15 41.54
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- -1.78 35.34 41.46
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-1.79 35.36 41.45
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-1.81 35.40 41.44
@@ -104495,34 +104764,34 @@ Kenya
-2.01 35.76 41.08
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+ -2.31 36.29 40.80 40.90 40.95
-2.32 36.31 40.80 40.91 40.94
-2.33 36.33 40.80
-2.34 36.34 40.82
@@ -104546,10 +104815,10 @@ Kenya
-2.52 36.67 40.68
-2.53 36.69 40.67
-2.54 36.70 40.48 40.53 40.66
- -2.55 36.72 40.46 40.56 40.65
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+ -2.58 36.77 40.38
-2.59 36.79 40.37
-2.60 36.81 40.35
-2.61 36.83 40.32
@@ -104583,9 +104852,9 @@ Kenya
-2.89 37.34 40.18
-2.90 37.36 40.17
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+ -2.94 37.43 40.19
-2.95 37.45 40.19
-2.96 37.47 40.19 40.22 40.24
-2.97 37.49 40.24
@@ -104601,31 +104870,31 @@ Kenya
-3.07 37.64 40.17
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-3.35 37.62 40.02
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-3.37 37.59 40.01
@@ -104696,14 +104965,14 @@ Kenya
-4.02 38.25 39.72
-4.03 38.27 39.72
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-4.15 38.44 39.65
@@ -104749,7 +105018,7 @@ Kenya
-4.55 38.99 39.47
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+ -4.58 39.04 39.41 39.43 39.46
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-4.60 39.06 39.41
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@@ -104790,18 +105059,18 @@ Kerguelen Archipelago
-48.81 68.83 69.17 69.39 69.44
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@@ -104826,24 +105095,24 @@ Kerguelen Archipelago
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@@ -104856,7 +105125,7 @@ Kerguelen Archipelago
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@@ -104868,10 +105137,10 @@ Kerguelen Archipelago
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-49.68 68.75 69.09 69.84 70.26
@@ -104900,32 +105169,32 @@ Kiribati
4.72 -160.42 -160.36
4.71 -160.42 -160.36
4.70 -160.42 -160.36
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3.82 -159.37 -159.23
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3.15 172.95 172.97
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3.08 172.87 172.89
3.07 172.81 172.89
3.06 172.80 172.89
@@ -104935,20 +105204,22 @@ Kiribati
3.02 172.74 172.81
3.01 172.74 172.80
3.00 172.74 172.79
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1.90 -157.58 -157.51 -157.45 -157.33 172.93 172.98
1.89 -157.59 -157.53 -157.48 -157.33 172.94 172.99
1.88 -157.59 -157.53 -157.48 -157.33 172.95 173.00
@@ -104961,14 +105232,14 @@ Kiribati
1.81 -157.49 -157.25 173.01 173.03
1.80 -157.47 -157.23 173.01 173.03
1.79 -157.45 -157.22 173.01 173.04
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1.74 -157.32 -157.16 173.02 173.04
1.73 -157.29 -157.16 173.00 173.04
1.72 -157.28 -157.16 172.98 173.04
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1.70 -157.25 -157.16 172.98 173.03
1.69 -157.24 -157.21 172.99 173.02
1.63 172.93 172.97
@@ -104988,7 +105259,7 @@ Kiribati
1.37 173.06 173.18
1.36 173.04 173.18
1.35 173.02 173.18
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1.33 173.00 173.05
1.32 173.00 173.03
1.03 172.98 173.01
@@ -104997,18 +105268,18 @@ Kiribati
1.00 172.98 173.04
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0.83 172.95 173.01
@@ -105032,13 +105303,13 @@ Kiribati
0.18 173.62 173.65
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@@ -105057,10 +105328,16 @@ Kiribati
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@@ -105086,19 +105363,19 @@ Kiribati
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@@ -105114,11 +105391,11 @@ Kiribati
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@@ -105135,49 +105412,73 @@ Kiribati
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Kosovo
- 43.27 20.75 20.81
+ 43.27 20.75 20.80
43.26 20.73 20.83
43.25 20.71 20.84
43.24 20.70 20.86
@@ -105189,8 +105490,8 @@ Kosovo
43.18 20.58 20.85
43.17 20.58 20.87
43.16 20.59 20.89
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43.13 20.60 20.96
43.12 20.61 20.98
43.11 20.61 21.00
@@ -105201,8 +105502,8 @@ Kosovo
43.06 20.63 21.13
43.05 20.62 21.13
43.04 20.61 21.13
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43.01 20.54 21.14
43.00 20.54 21.21
42.99 20.52 21.22
@@ -105214,10 +105515,10 @@ Kosovo
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42.92 20.44 21.24
42.91 20.44 21.25
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42.89 20.45 21.31
42.88 20.47 21.33
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42.86 20.44 21.40
42.85 20.40 21.41
42.84 20.36 21.41
@@ -105229,16 +105530,16 @@ Kosovo
42.78 20.06 20.10 20.19 21.41
42.77 20.04 20.12 20.19 21.40
42.76 20.02 20.14 20.18 21.40
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42.73 20.01 21.58
42.72 20.01 21.59
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42.70 20.01 21.61
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42.68 20.03 21.76
42.67 20.05 21.77
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42.65 20.08 21.78
42.64 20.08 21.78
42.63 20.08 21.78
@@ -105252,14 +105553,14 @@ Kosovo
42.55 20.05 21.73
42.54 20.05 21.72
42.53 20.05 21.71
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42.51 20.08 21.70
42.50 20.10 21.69
42.49 20.12 21.68
42.48 20.14 21.67
42.47 20.15 21.66
42.46 20.15 21.65
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42.44 20.16 21.63
42.43 20.17 21.62
42.42 20.17 21.63
@@ -105269,8 +105570,8 @@ Kosovo
42.38 20.18 21.63
42.37 20.18 21.62
42.36 20.20 21.61
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42.33 20.21 21.53
42.32 20.21 21.52
42.31 20.21 21.53
@@ -105282,22 +105583,22 @@ Kosovo
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42.24 20.44 21.57
42.23 20.45 21.57
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42.21 20.48 21.43
42.20 20.49 21.36 21.39 21.43
42.19 20.49 21.35
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42.17 20.50 21.09 21.11 21.33
42.16 20.51 21.07 21.13 21.33
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42.13 20.52 21.02 21.18 21.31
42.12 20.53 20.99 21.19 21.31
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42.06 20.54 20.78
42.05 20.54 20.77
42.04 20.54 20.77
@@ -105308,7 +105609,7 @@ Kosovo
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41.98 20.57 20.75
41.97 20.57 20.75
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41.95 20.58 20.76
41.94 20.58 20.76
41.93 20.57 20.76
@@ -105340,12 +105641,12 @@ Kuwait
29.96 47.10 47.97 48.00 48.05 48.10 48.22
29.95 47.09 47.98 48.01 48.03 48.11 48.22
29.94 47.09 47.98 48.13 48.23
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29.87 47.05 47.99 48.07 48.29
29.86 47.05 47.99 48.07 48.30
29.85 47.04 47.99 48.10 48.31
@@ -105372,79 +105673,79 @@ Kuwait
29.64 46.95 48.32
29.63 46.94 48.31
29.62 46.93 48.30
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29.06 46.69 48.15
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29.03 46.91 48.16
29.02 47.02 48.16
29.01 47.12 48.17
29.00 47.22 48.17
28.99 47.32 48.18
28.98 47.40 48.19
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28.96 47.43 48.20
28.95 47.44 48.21
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28.93 47.45 48.22
28.92 47.46 48.24
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28.88 47.48 48.29
28.87 47.49 48.29
28.86 47.49 48.29
@@ -105468,9 +105769,9 @@ Kuwait
28.68 47.54 48.39
28.67 47.54 48.39
28.66 47.55 48.39
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28.62 47.57 48.40
28.61 47.57 48.40
28.60 47.58 48.40
@@ -105592,7 +105893,7 @@ Kyrgyzstan
42.21 71.16 80.18
42.20 71.18 80.20
42.19 71.20 80.22
- 42.18 71.23 80.22
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42.17 71.22 80.22
42.16 71.20 80.22
42.15 71.17 80.22
@@ -105696,7 +105997,7 @@ Kyrgyzstan
41.17 70.99 71.43 71.88 71.94 71.98 72.10 72.14 78.25
41.16 71.04 71.19 71.23 71.43 71.99 72.08 72.14 78.24
41.15 71.05 71.19 71.23 71.43 72.00 72.06 72.15 78.23
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41.13 71.12 71.19 71.24 71.43 72.16 78.22
41.12 71.13 71.19 71.24 71.31 71.34 71.42 72.16 78.21
41.11 71.14 71.19 71.25 71.30 71.36 71.42 72.16 78.21
@@ -105712,7 +106013,7 @@ Kyrgyzstan
41.01 72.15 72.30 72.38 76.93 77.05 77.73
41.00 72.15 72.27 72.40 76.89 77.07 77.32 77.35 77.70
40.99 72.15 72.23 72.47 76.86 77.17 77.28 77.39 77.68
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40.97 72.47 76.84 77.45 77.55
40.96 72.47 76.83
40.95 72.49 76.82
@@ -105755,7 +106056,7 @@ Kyrgyzstan
40.58 72.33 72.44 72.65 72.70 72.72 75.46 75.58 76.61
40.57 72.33 72.45 72.64 75.44 75.58 76.60
40.56 72.34 72.47 72.64 75.43 75.59 76.58
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40.54 72.35 72.54 72.64 75.39 75.59 76.55
40.53 72.35 72.56 72.64 75.38 75.59 76.55
40.52 72.35 72.58 72.60 75.36 75.60 76.54
@@ -105765,7 +106066,7 @@ Kyrgyzstan
40.48 72.37 74.83 74.87 75.29 75.60 76.52
40.47 72.39 74.82 74.89 75.27 75.61 76.51
40.46 72.14 72.27 72.40 74.82 74.91 75.26 75.62 76.51
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40.44 72.10 72.27 72.41 74.81 74.95 75.10 75.14 75.23 75.65 76.49
40.43 72.08 72.28 72.41 74.80 74.98 75.08 75.16 75.22 75.65 76.49
40.42 72.08 72.30 72.40 74.80 75.64 76.48
@@ -105853,7 +106154,7 @@ Kyrgyzstan
39.60 69.28 73.93
39.59 69.27 70.18 70.20 71.44 71.46 73.93
39.58 69.27 70.18 70.20 71.42 71.48 73.93
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39.56 69.27 70.17 70.20 70.40 70.51 71.36 71.50 73.91
39.55 69.27 69.58 69.72 70.03 70.07 70.16 70.19 70.33 70.60 71.34 71.51 73.89
39.54 69.27 69.56 69.75 70.01 70.09 70.15 70.19 70.31 70.61 71.32 71.51 73.89
@@ -106059,8 +106360,8 @@ Laos
20.89 100.50 103.10 103.89 104.29
20.88 100.50 103.11 103.86 104.30
20.87 100.50 103.13 103.84 104.31
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20.84 100.37 100.41 100.58 103.19 103.23 103.26 103.76 104.33
20.83 100.35 100.45 100.56 103.27 103.41 103.44 103.76 104.33
20.82 100.34 100.50 100.54 103.29 103.40 103.45 103.75 104.36
@@ -106166,7 +106467,7 @@ Laos
19.82 100.41 104.82
19.81 100.40 104.82
19.80 100.39 104.82
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19.78 100.38 104.81
19.77 100.37 104.80
19.76 100.37 104.79
@@ -106177,8 +106478,8 @@ Laos
19.71 100.38 104.69
19.70 100.39 104.67
19.69 100.39 104.67
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19.66 100.40 104.13 104.27 104.34 104.38 104.65
19.65 100.40 104.00 104.04 104.12 104.27 104.32 104.39 104.65
19.64 100.40 104.01 104.05 104.11 104.28 104.30 104.40 104.65
@@ -106195,7 +106496,7 @@ Laos
19.53 100.44 100.82 101.24 104.08
19.52 100.45 100.60 100.64 100.81 101.24 104.08
19.51 100.46 100.59 100.67 100.80 101.24 104.09
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19.49 100.50 100.58 100.71 100.78 101.23 104.10
19.48 100.53 100.57 100.72 100.77 101.22 104.10
19.47 100.73 100.76 101.20 104.09
@@ -106328,13 +106629,13 @@ Laos
18.20 101.12 103.16 104.05 105.30 105.38 105.46
18.19 101.14 102.08 102.16 103.16 104.05 105.32 105.37 105.47
18.18 101.15 102.07 102.16 103.15 104.06 105.34 105.37 105.48
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18.10 101.13 101.99 102.23 103.07 104.10 105.51
18.09 101.13 101.98 102.23 103.07 104.10 105.52
18.08 101.13 101.97 102.24 103.07 104.11 105.53
@@ -106391,8 +106692,8 @@ Laos
17.57 100.87 101.24 104.58 105.88
17.56 100.87 101.24 104.60 105.88
17.55 100.89 101.23 104.62 105.89
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17.52 100.99 101.21 104.67 105.92
17.51 101.00 101.21 104.69 105.93
17.50 101.02 101.20 104.70 105.94
@@ -106441,9 +106742,9 @@ Laos
17.07 104.75 106.40
17.06 104.74 106.40
17.05 104.74 106.40
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17.03 104.73 106.40
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17.01 104.73 106.41
17.00 104.73 106.42
16.99 104.73 106.45 106.51 106.53
@@ -106518,7 +106819,7 @@ Laos
16.30 104.95 107.08
16.29 104.96 107.09
16.28 104.96 107.10
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16.26 105.00 107.12
16.25 105.00 107.12
16.24 105.01 107.12
@@ -106539,7 +106840,7 @@ Laos
16.09 105.06 107.28
16.08 105.08 107.29 107.39 107.44
16.07 105.11 107.31 107.36 107.44
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16.05 105.18 107.44
16.04 105.21 107.44
16.03 105.23 107.44
@@ -106643,7 +106944,7 @@ Laos
15.05 105.48 107.60
15.04 105.51 107.59
15.03 105.51 107.58
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15.01 105.52 107.45
15.00 105.53 107.46
14.99 105.54 107.46
@@ -106760,9 +107061,9 @@ Latvia
58.08 25.25 25.29
58.07 25.05 25.16 25.24 25.30
58.06 25.03 25.17 25.23 25.31
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58.02 24.95 25.19 25.25 25.42
58.01 24.85 25.20 25.26 25.43
58.00 24.72 24.75 24.83 25.21 25.24 25.45
@@ -106772,7 +107073,7 @@ Latvia
57.96 24.69 25.56
57.95 24.52 25.56
57.94 24.50 25.56
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57.92 24.46 25.74
57.91 24.41 25.75
57.90 24.41 25.75
@@ -106788,27 +107089,27 @@ Latvia
57.80 24.27 26.02
57.79 24.27 26.02
57.78 24.27 26.04
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57.76 22.53 22.62 24.28 26.08
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57.61 21.97 22.64 24.36 26.29 26.82 27.00
57.60 21.86 22.65 24.36 26.32 26.81 27.01
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57.56 21.68 22.73 24.34 26.45 26.61 27.08
57.55 21.67 22.75 24.34 26.47 26.59 27.19
57.54 21.66 22.78 24.34 26.48 26.58 27.24
@@ -106816,9 +107117,9 @@ Latvia
57.52 21.64 22.82 24.35 27.53
57.51 21.63 22.84 24.36 27.53
57.50 21.63 22.86 24.36 27.53
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57.46 21.59 22.93 24.37 27.53
57.45 21.58 22.95 24.37 27.53
57.44 21.57 22.97 24.37 27.53
@@ -106828,23 +107129,23 @@ Latvia
57.40 21.51 23.05 24.38 27.63
57.39 21.50 23.07 24.38 27.65
57.38 21.49 23.14 24.38 27.67
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57.36 21.48 23.14 24.38 27.70
57.35 21.48 23.14 24.39 27.72
57.34 21.47 23.15 24.39 27.76
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57.31 21.42 23.17 24.39 27.84
57.30 21.42 23.18 24.39 27.85
57.29 21.41 23.18 24.39 27.85
57.28 21.40 23.19 24.39 27.85
57.27 21.40 23.19 24.39 27.85
57.26 21.40 23.20 24.39 27.85
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57.22 21.40 23.22 24.34 27.85
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57.20 21.40 23.23 24.31 27.85
57.19 21.40 23.24 24.29 27.85
57.18 21.40 23.24 24.26 27.84
@@ -106853,22 +107154,22 @@ Latvia
57.15 21.39 23.25 24.22 27.83
57.14 21.39 23.25 24.20 27.83
57.13 21.39 23.26 24.19 27.81
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57.11 21.40 23.26 24.14 27.75
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57.08 21.40 23.32 24.05 27.74
57.07 21.40 23.34 24.02 27.75
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57.04 21.39 23.52 23.98 27.76
57.03 21.38 23.53 23.96 27.76
57.02 21.38 23.54 23.93 27.75
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56.96 21.27 27.73
56.95 21.26 27.72
56.94 21.25 27.72
@@ -106880,7 +107181,7 @@ Latvia
56.88 21.12 27.67 27.76 27.81
56.87 21.10 27.66 27.72 27.85
56.86 21.07 27.65 27.70 27.86
- 56.85 21.05 27.65 27.67 27.88
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56.84 21.05 27.89
56.83 21.04 27.92
56.82 21.04 27.92
@@ -106926,22 +107227,22 @@ Latvia
56.42 20.98 28.17
56.41 20.96 24.86 24.90 28.17
56.40 20.96 24.86 24.90 28.17
- 56.39 20.96 22.07 22.16 22.91 22.93 24.85 24.91 28.17
- 56.38 20.96 22.03 22.18 22.87 22.95 24.78 24.91 28.17
- 56.37 20.95 21.99 22.54 22.84 22.96 24.74 24.92 28.17
+ 56.39 20.96 22.08 22.16 22.91 22.93 24.85 24.91 28.17
+ 56.38 20.96 22.04 22.18 22.87 22.95 24.78 24.91 28.17
+ 56.37 20.95 22.00 22.54 22.84 22.96 24.74 24.92 28.17
56.36 20.95 21.95 22.58 22.80 22.97 24.70 24.92 28.17
- 56.35 20.95 21.91 22.61 22.76 22.98 23.26 23.33 24.67 24.92 28.18
- 56.34 20.95 21.87 22.63 22.71 22.98 23.20 23.37 24.65 24.93 28.19
- 56.33 20.96 21.83 22.65 22.68 22.99 23.17 23.41 23.59 23.71 24.63 24.93 28.19
+ 56.35 20.95 21.91 22.61 22.76 22.98 23.26 23.32 24.67 24.92 28.18
+ 56.34 20.95 21.87 22.63 22.71 22.98 23.20 23.35 24.65 24.93 28.19
+ 56.33 20.96 21.83 22.65 22.68 22.99 23.17 23.39 23.59 23.71 24.63 24.93 28.19
56.32 20.96 21.79 22.99 23.16 23.45 23.56 23.71 24.62 24.94 28.20
- 56.31 20.97 21.75 23.00 23.14 23.49 23.53 23.71 23.79 23.88 24.60 24.94 28.21
- 56.30 20.97 21.71 23.02 23.12 23.94 24.59 24.95 28.21
+ 56.31 20.97 21.75 23.00 23.14 23.49 23.53 23.71 23.79 23.89 24.60 24.94 28.21
+ 56.30 20.97 21.71 23.02 23.12 23.95 24.59 24.95 28.21
56.29 20.97 21.64 23.04 23.09 23.99 24.58 24.96 28.22
56.28 20.97 21.58 24.01 24.56 24.97 28.22
56.27 20.97 21.54 24.03 24.27 24.36 24.55 24.98 28.22
56.26 20.95 21.52 24.05 24.23 24.38 24.52 24.99 28.22
56.25 20.95 21.50 24.08 24.19 24.40 24.50 25.00 28.22
- 56.24 20.95 21.47 24.11 24.15 25.01 28.22
+ 56.24 20.95 21.47 24.11 24.16 25.01 28.22
56.23 20.95 21.45 25.02 28.21
56.22 20.96 21.43 25.02 28.20
56.21 20.96 21.34 25.03 28.20
@@ -106950,11 +107251,11 @@ Latvia
56.18 20.98 21.29 25.06 28.19
56.17 20.99 21.27 25.08 28.18
56.16 20.99 21.25 25.14 28.18
- 56.15 21.00 21.23 25.23 28.17
- 56.14 21.00 21.23 25.31 28.16
- 56.13 21.01 21.22 25.40 25.49 25.54 28.09 28.12 28.15
- 56.12 21.02 21.22 25.65 28.06
- 56.11 21.02 21.22 25.65 28.04
+ 56.15 21.00 21.23 25.22 28.17
+ 56.14 21.00 21.23 25.30 28.16
+ 56.13 21.01 21.22 25.39 25.49 25.54 28.09 28.12 28.15
+ 56.12 21.02 21.22 25.65 28.05
+ 56.11 21.02 21.22 25.65 28.03
56.10 21.03 21.21 25.66 28.01
56.09 21.03 21.21 25.66 27.93
56.08 21.03 21.21 25.67 27.92
@@ -106962,16 +107263,16 @@ Latvia
56.06 21.04 21.18 25.71 27.90
56.05 25.73 27.89
56.04 25.75 27.87
- 56.03 25.76 27.85
- 56.02 25.78 27.83
- 56.01 25.80 27.81
- 56.00 25.82 27.79
+ 56.03 25.77 27.85
+ 56.02 25.79 27.83
+ 56.01 25.81 27.81
+ 56.00 25.83 27.79
55.99 25.84 27.79
55.98 25.86 27.78
55.97 25.88 27.77
55.96 25.90 27.77
55.95 25.92 27.76
- 55.94 25.95 27.75
+ 55.94 25.94 27.75
55.93 25.97 27.73
55.92 25.99 27.70
55.91 26.01 27.66
@@ -107006,21 +107307,21 @@ Lebanon
34.68 36.27 36.33
34.67 36.27 36.34
34.66 35.97 35.99 36.27 36.34
- 34.65 35.96 36.01 36.27 36.35
- 34.64 35.96 36.03 36.07 36.12 36.16 36.19 36.26 36.36
- 34.63 35.96 36.45
+ 34.65 35.95 36.01 36.27 36.35
+ 34.64 35.95 36.03 36.07 36.10 36.16 36.19 36.26 36.36
+ 34.63 35.95 36.45
34.62 35.97 36.45
34.61 35.97 36.45
34.60 35.97 36.45
- 34.59 35.98 36.44
- 34.58 35.98 36.44
+ 34.59 35.97 36.44
+ 34.58 35.97 36.44
34.57 35.97 36.39
34.56 35.97 36.39
34.55 35.97 36.39
34.54 35.97 36.39
- 34.53 35.96 36.38
- 34.52 35.94 36.36
- 34.51 35.93 36.41
+ 34.53 35.94 36.38
+ 34.52 35.93 36.36
+ 34.51 35.92 36.41
34.50 35.91 36.44
34.49 35.90 36.44
34.48 35.86 36.44
@@ -107050,7 +107351,7 @@ Lebanon
34.24 35.63 36.57
34.23 35.63 36.58
34.22 35.63 36.59
- 34.21 35.61 36.60
+ 34.21 35.61 36.61
34.20 35.61 36.61
34.19 35.61 36.61
34.18 35.61 36.61
@@ -107102,9 +107403,9 @@ Lebanon
33.72 35.42 35.98
33.71 35.41 35.97
33.70 35.41 35.96
- 33.69 35.41 35.95
+ 33.69 35.40 35.95
33.68 35.40 35.95
- 33.67 35.40 35.95
+ 33.67 35.39 35.95
33.66 35.39 35.95
33.65 35.38 35.95
33.64 35.38 35.95
@@ -107130,9 +107431,9 @@ Lebanon
33.44 35.25 35.91
33.43 35.25 35.89
33.42 35.24 35.88
- 33.41 35.24 35.86
+ 33.41 35.24 35.87
33.40 35.23 35.85
- 33.39 35.23 35.83
+ 33.39 35.23 35.84
33.38 35.23 35.82
33.37 35.23 35.81
33.36 35.23 35.80
@@ -107140,18 +107441,18 @@ Lebanon
33.34 35.22 35.79
33.33 35.22 35.78
33.32 35.21 35.76
- 33.31 35.21 35.74
- 33.30 35.20 35.69
- 33.29 35.18 35.69
+ 33.31 35.20 35.74
+ 33.30 35.19 35.69
+ 33.29 35.17 35.69
33.28 35.17 35.68
33.27 35.17 35.67
- 33.26 35.17 35.66
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33.25 35.18 35.61
33.24 35.19 35.54 35.57 35.61
33.23 35.19 35.53 35.58 35.61
- 33.22 35.19 35.53
+ 33.22 35.18 35.53
33.21 35.18 35.53
- 33.20 35.18 35.53
+ 33.20 35.17 35.53
33.19 35.17 35.53
33.18 35.15 35.52
33.17 35.15 35.52
@@ -107160,10 +107461,10 @@ Lebanon
33.14 35.11 35.52
33.13 35.10 35.52
33.12 35.09 35.51
- 33.11 35.09 35.50
- 33.10 35.09 35.50
- 33.09 35.09 35.49
- 33.08 35.09 35.26 35.28 35.49
+ 33.11 35.08 35.50
+ 33.10 35.08 35.50
+ 33.09 35.08 35.49
+ 33.08 35.09 35.49
33.07 35.09 35.20 35.29 35.49
33.06 35.30 35.44
33.05 35.31 35.42
@@ -107181,7 +107482,7 @@ Lesotho
-28.65 28.34 28.69
-28.66 28.33 28.69
-28.67 28.32 28.75
- -28.68 28.19 28.25 28.31 28.75
+ -28.68 28.22 28.25 28.31 28.75
-28.69 28.14 28.76
-28.70 28.13 28.77
-28.71 28.12 28.77
@@ -107238,8 +107539,8 @@ Lesotho
-29.22 27.51 29.38
-29.23 27.51 29.39
-29.24 27.51 29.40
- -29.25 27.49 29.41
- -29.26 27.47 29.41
+ -29.25 27.50 29.41
+ -29.26 27.48 29.41
-29.27 27.45 29.42
-29.28 27.44 29.42
-29.29 27.44 29.42
@@ -107290,27 +107591,27 @@ Lesotho
-29.74 27.07 29.13
-29.75 27.07 29.13
-29.76 27.07 29.12
- -29.77 27.07 29.12
+ -29.77 27.08 29.12
-29.78 27.08 29.12
- -29.79 27.08 29.12
+ -29.79 27.09 29.12
-29.80 27.09 29.11
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-29.82 27.10 29.12
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-29.84 27.11 29.14
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-29.86 27.12 29.14
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-29.88 27.13 29.14
- -29.89 27.13 29.15
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-29.90 27.14 29.16
- -29.91 27.14 29.16
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-29.92 27.15 29.16
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-29.94 27.16 29.12
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+ -29.95 27.17 29.09
-29.96 27.17 29.07
- -29.97 27.17 29.05
+ -29.97 27.18 29.05
-29.98 27.18 29.03
-29.99 27.19 29.01
-30.00 27.20 28.99
@@ -107330,7 +107631,7 @@ Lesotho
-30.14 27.30 28.50 28.58 28.65
-30.15 27.35 28.47
-30.16 27.35 28.38
- -30.17 27.34 28.36
+ -30.17 27.34 28.37
-30.18 27.34 28.36
-30.19 27.33 28.35
-30.20 27.33 28.35
@@ -107353,7 +107654,7 @@ Lesotho
-30.37 27.48 28.24
-30.38 27.49 28.24
-30.39 27.51 28.23
- -30.40 27.51 28.21
+ -30.40 27.52 28.21
-30.41 27.52 28.20
-30.42 27.53 28.18
-30.43 27.55 28.17
@@ -107475,13 +107776,13 @@ Liberia
7.66 -10.78 -9.36 -8.72 -8.55
7.65 -10.79 -9.36 -8.73 -8.56
7.64 -10.80 -9.35 -8.73 -8.55
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7.62 -10.81 -9.34 -8.73 -8.54
7.61 -10.82 -9.34 -8.73 -8.53
7.60 -10.83 -9.35 -8.74 -8.52
7.59 -10.84 -9.36 -8.74 -8.51
7.58 -10.85 -9.36 -8.74 -8.50
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7.56 -10.86 -9.36 -8.74 -8.46
7.55 -10.87 -9.37 -8.74 -8.44
7.54 -10.88 -9.37 -8.74 -8.43
@@ -107504,7 +107805,7 @@ Liberia
7.37 -11.13 -9.20 -8.86 -8.38
7.36 -11.14 -9.20 -8.87 -8.38
7.35 -11.15 -9.20 -8.87 -8.38
- 7.34 -11.15 -9.20 -8.87 -8.38
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7.33 -11.16 -9.19 -8.87 -8.38
7.32 -11.17 -9.19 -8.87 -8.37
7.31 -11.18 -9.19 -8.87 -8.37
@@ -107569,7 +107870,7 @@ Liberia
6.72 -11.38 -8.36
6.71 -11.38 -8.37
6.70 -11.37 -8.38
- 6.69 -11.36 -8.39
+ 6.69 -11.36 -8.38
6.68 -11.34 -8.39
6.67 -11.32 -8.40
6.66 -11.30 -8.41
@@ -107597,15 +107898,15 @@ Liberia
6.44 -10.85 -8.39
6.43 -10.84 -8.39
6.42 -10.83 -8.39
- 6.41 -10.82 -8.40
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6.40 -10.82 -8.40
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6.38 -10.81 -8.39
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6.36 -10.80 -8.33
6.35 -10.80 -8.29
6.34 -10.80 -8.28
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6.32 -10.81 -8.25
6.31 -10.81 -8.21 -8.08 -8.01
6.30 -10.81 -8.19 -8.11 -7.99
@@ -107693,7 +107994,7 @@ Liberia
5.48 -9.62 -7.41
5.47 -9.60 -7.41
5.46 -9.60 -7.42
- 5.45 -9.59 -7.42
+ 5.45 -9.60 -7.42
5.44 -9.60 -7.42
5.43 -9.60 -7.42
5.42 -9.60 -7.42
@@ -107744,11 +108045,11 @@ Liberia
4.97 -9.03 -7.55
4.96 -9.02 -7.55
4.95 -9.00 -7.54
- 4.94 -8.98 -7.54
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4.93 -8.92 -7.53
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+ 4.90 -8.85 -7.53
4.89 -8.84 -7.58
4.88 -8.83 -7.59
4.87 -8.82 -7.58
@@ -107777,22 +108078,22 @@ Liberia
4.64 -8.40 -7.56
4.63 -8.37 -7.56
4.62 -8.35 -7.56
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4.58 -8.28 -7.56
4.57 -8.27 -7.56
4.56 -8.26 -7.56
4.55 -8.24 -7.56
4.54 -8.16 -7.56
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4.50 -7.98 -7.56
4.49 -7.95 -7.56
4.48 -7.94 -7.56
4.47 -7.92 -7.56
- 4.46 -7.89 -7.56
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4.45 -7.87 -7.56
4.44 -7.85 -7.55
4.43 -7.83 -7.55
@@ -107844,8 +108145,8 @@ Libya
32.85 11.44 12.33 12.96 13.50 21.48 22.43
32.84 11.44 12.39 12.92 13.52 21.46 22.44
32.83 11.45 12.49 12.88 13.54 21.45 22.45
- 32.82 11.45 12.59 12.84 13.56 21.44 22.47
- 32.81 11.45 12.69 12.77 13.60 21.42 22.49
+ 32.82 11.45 12.58 12.84 13.56 21.44 22.47
+ 32.81 11.45 12.68 12.77 13.60 21.42 22.49
32.80 11.45 13.86 21.39 22.53
32.79 11.45 13.90 21.07 21.19 21.35 22.60
32.78 11.45 13.93 21.03 22.64
@@ -107858,8 +108159,8 @@ Libya
32.71 11.43 14.21 20.88 22.86
32.70 11.43 14.23 20.86 22.88
32.69 11.43 14.25 20.85 22.91
- 32.68 11.43 14.26 20.83 23.02
- 32.67 11.43 14.27 20.81 23.04
+ 32.68 11.43 14.26 20.83 23.01
+ 32.67 11.43 14.27 20.81 23.03
32.66 11.43 14.29 20.79 23.07
32.65 11.43 14.31 20.77 23.10
32.64 11.43 14.32 20.75 23.11
@@ -107874,8 +108175,8 @@ Libya
32.55 11.50 14.43 20.53 23.10
32.54 11.51 14.44 20.52 23.11
32.53 11.52 14.46 20.50 23.11
- 32.52 11.53 14.52 20.49 23.11
- 32.51 11.53 14.60 20.47 23.12
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32.50 11.54 14.64 20.46 23.12
32.49 11.55 14.66 20.44 23.14
32.48 11.55 14.68 20.43 23.15
@@ -107891,36 +108192,36 @@ Libya
32.38 11.44 15.21 20.27 23.09 23.11 23.13
32.37 11.42 15.22 20.26 23.09
32.36 11.40 15.23 20.26 23.09
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32.33 11.32 15.28 20.24 23.11
- 32.32 11.30 15.29 20.23 23.14
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32.31 11.27 15.29 20.21 23.17
- 32.30 11.25 15.30 20.20 23.20
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- 32.27 11.17 15.31 20.17 23.23
- 32.26 11.15 15.31 20.15 23.24
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- 32.22 11.05 15.34 20.11 23.38
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32.20 11.00 15.35 20.08 23.47
- 32.19 10.98 15.36 20.07 23.70
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- 32.17 10.93 15.37 20.05 23.78
+ 32.19 10.97 15.36 20.07 23.69
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+ 32.17 10.92 15.37 20.05 23.78
32.16 10.90 15.38 20.04 23.82
32.15 10.88 15.38 20.03 23.86
32.14 10.86 15.38 20.02 23.89
32.13 10.84 15.38 20.02 23.92
32.12 10.83 15.37 20.01 23.95
32.11 10.83 15.37 20.01 23.98
- 32.10 10.82 15.37 20.00 24.00
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- 32.08 10.81 15.37 19.99 24.00
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- 32.06 10.80 15.37 19.98 24.01
+ 32.10 10.82 15.36 20.00 24.00
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+ 32.06 10.80 15.36 19.98 24.01
32.05 10.80 15.36 19.97 24.03
32.04 10.79 15.36 19.97 24.04 24.66 24.74
32.03 10.78 15.36 19.96 24.06 24.64 24.75
@@ -107940,14 +108241,14 @@ Libya
31.89 10.58 15.40 19.92 25.04
31.88 10.58 15.40 19.92 25.04
31.87 10.58 15.41 19.92 25.03
- 31.86 10.57 15.41 19.92 25.03
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- 31.84 10.56 15.42 19.91 25.04
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31.83 10.55 15.43 19.91 25.05
- 31.82 10.54 15.43 19.91 25.06
- 31.81 10.53 15.44 19.91 25.07
- 31.80 10.52 15.44 19.91 25.08
- 31.79 10.52 15.44 19.91 25.08
+ 31.82 10.54 15.43 19.90 25.06
+ 31.81 10.53 15.44 19.90 25.07
+ 31.80 10.52 15.44 19.90 25.08
+ 31.79 10.52 15.44 19.90 25.08
31.78 10.51 15.45 19.90 25.09
31.77 10.51 15.45 19.90 25.10
31.76 10.50 15.46 19.90 25.11
@@ -108025,20 +108326,20 @@ Libya
31.04 10.23 17.46 20.13 24.89
31.03 10.23 17.49 20.12 24.89
31.02 10.23 17.54 20.12 24.89
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31.00 10.23 17.63 20.11 24.90
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30.98 10.23 17.67 20.10 24.92
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+ 30.95 10.24 17.76 20.08 24.93
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30.93 10.25 17.86 20.08 24.94
- 30.92 10.25 17.87 20.08 24.94
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30.91 10.26 17.87 20.07 24.94
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30.89 10.25 17.88 20.06 24.95
- 30.88 10.25 17.90 20.06 24.96
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30.87 10.25 17.92 20.05 24.96
30.86 10.24 17.95 20.04 24.97
30.85 10.24 17.99 20.04 24.98
@@ -108062,22 +108363,22 @@ Libya
30.67 10.11 18.32 19.88 24.97
30.66 10.10 18.33 19.87 24.97
30.65 10.09 18.35 19.86 24.97
- 30.64 10.08 18.36 19.85 24.97
+ 30.64 10.08 18.37 19.85 24.97
30.63 10.08 18.38 19.84 24.96
- 30.62 10.07 18.39 19.83 24.96
+ 30.62 10.07 18.40 19.83 24.96
30.61 10.06 18.41 19.82 24.96
- 30.60 10.05 18.42 19.81 24.96
- 30.59 10.05 18.44 19.80 24.95
- 30.58 10.04 18.45 19.79 24.95
- 30.57 10.03 18.47 19.78 24.94
- 30.56 10.02 18.48 19.77 24.94
- 30.55 10.02 18.50 19.76 24.93
- 30.54 10.01 18.51 19.75 24.93
- 30.53 10.00 18.53 19.74 24.93
- 30.52 9.99 18.54 19.73 24.92
- 30.51 9.99 18.56 19.71 24.92
- 30.50 9.98 18.57 19.70 24.92
- 30.49 9.97 18.58 19.68 24.91
+ 30.60 10.05 18.43 19.81 24.96
+ 30.59 10.05 18.45 19.80 24.95
+ 30.58 10.04 18.46 19.79 24.95
+ 30.57 10.03 18.48 19.78 24.94
+ 30.56 10.02 18.49 19.77 24.94
+ 30.55 10.02 18.51 19.76 24.93
+ 30.54 10.01 18.53 19.75 24.93
+ 30.53 10.00 18.54 19.74 24.93
+ 30.52 9.99 18.56 19.73 24.92
+ 30.51 9.99 18.57 19.71 24.92
+ 30.50 9.98 18.58 19.70 24.92
+ 30.49 9.97 18.59 19.68 24.91
30.48 9.96 18.60 19.67 24.91
30.47 9.95 18.61 19.66 24.90
30.46 9.95 18.62 19.64 24.90
@@ -108098,7 +108399,7 @@ Libya
30.31 9.66 18.92 19.34 24.78
30.30 9.64 18.94 19.31 24.77
30.29 9.62 18.96 19.26 24.76
- 30.28 9.60 19.01 19.19 24.76
+ 30.28 9.60 19.01 19.18 24.76
30.27 9.58 24.75
30.26 9.56 24.74
30.25 9.54 24.74
@@ -108122,9 +108423,9 @@ Libya
30.07 9.30 24.73
30.06 9.31 24.74
30.05 9.32 24.74
- 30.04 9.33 24.75
- 30.03 9.34 24.75
- 30.02 9.35 24.76
+ 30.04 9.32 24.75
+ 30.03 9.33 24.75
+ 30.02 9.34 24.76
30.01 9.35 24.76
30.00 9.36 24.77
29.99 9.37 24.77
@@ -108250,46 +108551,46 @@ Libya
28.79 9.84 24.99
28.78 9.84 24.99
28.77 9.84 24.99
- 28.76 9.84 24.99
+ 28.76 9.83 24.99
28.75 9.83 24.99
28.74 9.83 24.99
28.73 9.83 24.99
28.72 9.83 24.99
28.71 9.83 24.99
- 28.70 9.83 24.99
+ 28.70 9.82 24.99
28.69 9.82 24.99
28.68 9.82 24.99
28.67 9.82 24.99
28.66 9.82 24.99
28.65 9.82 24.99
- 28.64 9.82 24.99
- 28.63 9.82 24.99
+ 28.64 9.81 24.99
+ 28.63 9.81 24.99
28.62 9.81 24.99
28.61 9.81 24.99
28.60 9.81 24.99
28.59 9.81 24.99
- 28.58 9.81 24.99
- 28.57 9.81 24.99
+ 28.58 9.80 24.99
+ 28.57 9.80 24.99
28.56 9.80 24.99
28.55 9.80 24.99
28.54 9.80 24.99
28.53 9.80 24.99
28.52 9.80 24.99
- 28.51 9.80 24.99
- 28.50 9.80 24.99
+ 28.51 9.79 24.99
+ 28.50 9.79 24.99
28.49 9.79 24.99
28.48 9.79 24.99
28.47 9.79 24.99
28.46 9.79 24.99
28.45 9.79 24.99
- 28.44 9.79 24.99
+ 28.44 9.78 24.99
28.43 9.78 24.99
28.42 9.78 24.99
28.41 9.78 24.99
28.40 9.78 24.99
28.39 9.78 24.99
28.38 9.78 24.99
- 28.37 9.78 24.99
+ 28.37 9.77 24.99
28.36 9.77 24.99
28.35 9.77 24.99
28.34 9.77 24.99
@@ -108345,16 +108646,16 @@ Libya
27.84 9.92 24.99
27.83 9.92 24.99
27.82 9.92 24.99
- 27.81 9.91 24.99
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27.80 9.91 24.99
27.79 9.91 24.99
- 27.78 9.90 24.99
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27.77 9.90 24.99
27.76 9.90 24.99
- 27.75 9.89 24.99
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27.74 9.89 24.99
27.73 9.89 24.99
- 27.72 9.88 24.99
+ 27.72 9.89 24.99
27.71 9.88 24.99
27.70 9.88 24.99
27.69 9.87 24.99
@@ -108689,13 +108990,13 @@ Libya
24.40 11.16 24.99
24.39 11.19 24.99
24.38 11.22 24.99
- 24.37 11.26 24.99
- 24.36 11.29 24.99
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+ 24.36 11.28 24.99
24.35 11.32 24.99
24.34 11.35 24.99
24.33 11.38 24.99
- 24.32 11.42 24.99
- 24.31 11.45 24.99
+ 24.32 11.41 24.99
+ 24.31 11.44 24.99
24.30 11.48 24.99
24.29 11.51 24.99
24.28 11.53 24.99
@@ -108728,19 +109029,19 @@ Libya
24.01 11.68 24.99
24.00 11.68 24.99
23.99 11.69 24.99
- 23.98 11.70 24.99
- 23.97 11.70 24.99
- 23.96 11.71 24.99
- 23.95 11.71 24.99
- 23.94 11.72 24.99
- 23.93 11.72 24.99
- 23.92 11.73 24.99
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+ 23.92 11.74 24.99
23.91 11.74 24.99
- 23.90 11.74 24.99
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23.89 11.75 24.99
- 23.88 11.75 24.99
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23.87 11.76 24.99
- 23.86 11.76 24.99
+ 23.86 11.77 24.99
23.85 11.77 24.99
23.84 11.78 24.99
23.83 11.78 24.99
@@ -109208,22 +109509,22 @@ Lithuania
56.45 24.86 24.89
56.44 24.84 24.91
56.43 24.84 24.92
- 56.42 22.06 22.17 22.90 22.94 24.84 24.92
- 56.41 22.02 22.19 22.86 22.96 24.77 24.93
- 56.40 21.98 22.55 22.83 22.97 24.73 24.93
+ 56.42 22.07 22.17 22.90 22.94 24.84 24.92
+ 56.41 22.03 22.19 22.86 22.96 24.77 24.93
+ 56.40 21.99 22.55 22.83 22.97 24.73 24.93
56.39 21.94 22.59 22.79 22.98 24.69 24.94
- 56.38 21.90 22.62 22.75 22.99 23.25 23.34 24.66 24.94
- 56.37 21.86 22.64 22.70 23.00 23.19 23.38 24.64 24.94
- 56.36 21.82 23.00 23.14 23.42 23.58 23.72 24.62 24.95
+ 56.38 21.90 22.62 22.75 22.99 23.25 23.33 24.66 24.94
+ 56.37 21.86 22.64 22.70 23.00 23.19 23.36 24.64 24.94
+ 56.36 21.82 23.00 23.14 23.40 23.58 23.72 24.62 24.95
56.35 21.78 23.01 23.14 23.46 23.55 23.73 24.61 24.95
- 56.34 21.74 23.01 23.13 23.50 23.52 23.73 23.78 23.89 24.59 24.96
- 56.33 21.70 23.03 23.11 23.95 24.58 24.96
+ 56.34 21.74 23.01 23.13 23.50 23.52 23.73 23.78 23.90 24.59 24.96
+ 56.33 21.70 23.03 23.11 23.96 24.58 24.96
56.32 21.63 23.05 23.08 24.00 24.57 24.97
56.31 21.57 24.02 24.55 24.98
56.30 21.53 24.04 24.26 24.37 24.54 24.99
56.29 21.51 24.06 24.22 24.39 24.51 25.00
56.28 21.49 24.09 24.18 24.41 24.49 25.01
- 56.27 21.46 24.12 24.14 25.03
+ 56.27 21.46 24.12 24.15 25.03
56.26 21.44 25.03
56.25 21.42 25.04
56.24 21.33 25.04
@@ -109232,9 +109533,9 @@ Lithuania
56.21 21.28 25.07
56.20 21.26 25.09
56.19 21.24 25.15
- 56.18 21.22 25.24
- 56.17 21.21 25.32
- 56.16 21.21 25.41 25.48 25.55
+ 56.18 21.22 25.23
+ 56.17 21.21 25.31
+ 56.16 21.21 25.40 25.48 25.55
56.15 21.20 25.67
56.14 21.20 25.67
56.13 21.20 25.67
@@ -109244,16 +109545,16 @@ Lithuania
56.09 21.17 25.72
56.08 21.04 25.74
56.07 21.04 25.76
- 56.06 21.04 25.77
- 56.05 21.04 25.79
- 56.04 21.04 25.81
- 56.03 21.04 25.83
+ 56.06 21.04 25.78
+ 56.05 21.04 25.80
+ 56.04 21.04 25.82
+ 56.03 21.04 25.84
56.02 21.04 25.85
56.01 21.04 25.87
56.00 21.04 25.89
55.99 21.04 25.91
55.98 21.04 25.93
- 55.97 21.04 25.96
+ 55.97 21.04 25.95
55.96 21.04 25.98
55.95 21.04 26.00
55.94 21.04 26.02
@@ -109275,8 +109576,8 @@ Lithuania
55.78 21.05 26.25
55.77 21.05 26.26
55.76 21.05 26.27
- 55.75 21.06 26.29
- 55.74 21.06 26.31
+ 55.75 21.05 26.29
+ 55.74 21.05 26.31
55.73 21.06 26.33
55.72 21.07 26.36
55.71 21.07 26.40
@@ -109299,26 +109600,26 @@ Lithuania
55.54 21.07 21.14 21.18 26.59
55.53 21.07 21.14 21.18 26.57
55.52 21.07 21.13 21.18 26.56
- 55.51 21.07 21.13 21.19 26.55
- 55.50 21.07 21.13 21.21 26.54
- 55.49 21.07 21.13 21.21 26.54
- 55.48 21.06 21.13 21.22 26.55
- 55.47 21.06 21.13 21.22 26.55
- 55.46 21.05 21.12 21.22 26.55
+ 55.51 21.07 21.12 21.19 26.55
+ 55.50 21.07 21.12 21.21 26.54
+ 55.49 21.07 21.12 21.21 26.54
+ 55.48 21.06 21.12 21.22 26.55
+ 55.47 21.06 21.12 21.22 26.55
+ 55.46 21.05 21.11 21.22 26.55
55.45 21.05 21.11 21.22 26.55
55.44 21.04 21.10 21.23 26.55
55.43 21.04 21.11 21.23 26.54
55.42 21.03 21.11 21.23 26.52
55.41 21.02 21.11 21.22 26.50
- 55.40 21.02 21.10 21.21 26.50
+ 55.40 21.01 21.10 21.21 26.50
55.39 21.01 21.09 21.20 26.49
55.38 21.00 21.08 21.19 26.49
- 55.37 21.00 21.07 21.19 26.48
- 55.36 20.99 21.07 21.18 26.47
- 55.35 20.98 21.06 21.17 26.47
- 55.34 20.97 21.06 21.17 26.46
- 55.33 20.96 21.06 21.17 21.22 21.24 26.48
- 55.32 20.94 21.05 21.17 21.20 21.24 26.51 26.57 26.69
+ 55.37 20.99 21.07 21.19 26.48
+ 55.36 20.98 21.07 21.18 26.47
+ 55.35 20.97 21.06 21.17 26.47
+ 55.34 20.96 21.06 21.17 21.22 21.24 26.46
+ 55.33 20.95 21.06 21.17 21.21 21.24 26.48
+ 55.32 20.94 21.05 21.17 21.19 21.24 26.51 26.57 26.69
55.31 20.93 21.04 21.26 26.78
55.30 20.92 21.03 21.27 26.80
55.29 20.91 21.01 21.25 26.80
@@ -109328,7 +109629,7 @@ Lithuania
55.25 21.25 21.32 21.40 26.80
55.24 21.25 21.30 21.41 26.79
55.23 21.25 21.28 21.42 26.78
- 55.22 21.43 26.74
+ 55.22 21.43 26.72
55.21 21.44 26.68
55.20 21.45 26.66
55.19 21.47 26.65
@@ -109345,8 +109646,8 @@ Lithuania
55.08 21.86 26.24
55.07 21.88 21.97 22.00 26.24
55.06 21.93 21.95 22.00 26.24
- 55.05 22.00 22.23 22.29 22.52 22.55 26.23
- 55.04 22.00 22.17 22.38 22.46 22.57 26.23
+ 55.05 22.00 22.23 22.25 22.52 22.55 26.23
+ 55.04 22.00 22.17 22.34 22.46 22.57 26.23
55.03 22.01 22.14 22.57 26.22
55.02 22.03 22.12 22.58 26.21
55.01 22.05 22.11 22.58 26.21
@@ -109472,7 +109773,7 @@ Luxembourg
50.14 5.93 6.11
50.13 5.93 6.12
50.12 5.90 6.12
- 50.11 5.86 6.12
+ 50.11 5.87 6.12
50.10 5.85 6.12
50.09 5.85 6.12
50.08 5.85 6.11
@@ -109486,13 +109787,13 @@ Luxembourg
50.00 5.79 6.13
49.99 5.79 6.13
49.98 5.79 6.14
- 49.97 5.78 6.15
+ 49.97 5.79 6.15
49.96 5.76 6.18
49.95 5.74 6.18
49.94 5.74 6.19
49.93 5.73 6.20
- 49.92 5.73 6.21
- 49.91 5.72 6.21
+ 49.92 5.72 6.21
+ 49.91 5.71 6.21
49.90 5.70 6.22
49.89 5.70 6.23
49.88 5.70 6.26
@@ -109521,7 +109822,7 @@ Luxembourg
49.65 5.83 6.43
49.64 5.86 6.42
49.63 5.85 6.42
- 49.62 5.85 6.42
+ 49.62 5.84 6.42
49.61 5.84 6.41
49.60 5.83 6.40
49.59 5.81 6.39
@@ -109532,8 +109833,8 @@ Luxembourg
49.54 5.78 6.36
49.53 5.78 6.36
49.52 5.78 6.36
- 49.51 5.79 6.36
- 49.50 5.81 6.36
+ 49.51 5.79 6.35
+ 49.50 5.81 6.35
49.49 5.81 6.35
49.48 5.82 6.35
49.47 5.89 6.15 6.24 6.35
@@ -109542,12 +109843,13 @@ Luxembourg
49.44 5.94 6.08 6.30 6.35
49.43 5.95 6.07
Macau
+ 22.23 113.52 113.54
22.22 113.51 113.56
22.21 113.51 113.56
22.20 113.51 113.56
- 22.19 113.51 113.56
- 22.18 113.51 113.56
- 22.17 113.51 113.58
+ 22.19 113.50 113.56
+ 22.18 113.50 113.56
+ 22.17 113.50 113.58
22.16 113.51 113.58
22.15 113.52 113.58
22.14 113.52 113.59
@@ -109560,34 +109862,34 @@ Macedonia
42.38 22.25 22.27
42.37 22.24 22.28
42.36 22.23 22.28
- 42.35 22.20 22.28
- 42.34 21.90 21.96 22.16 22.29
- 42.33 21.89 21.98 22.12 22.31
- 42.32 21.88 22.00 22.10 22.35
+ 42.35 22.21 22.28
+ 42.34 21.90 21.96 22.17 22.29
+ 42.33 21.89 21.98 22.14 22.30
+ 42.32 21.88 22.01 22.10 22.35
42.31 21.79 22.36
42.30 21.77 22.37
- 42.29 21.75 22.38
- 42.28 21.73 22.39
- 42.27 21.71 22.40
+ 42.29 21.74 22.38
+ 42.28 21.72 22.39
+ 42.27 21.70 22.40
42.26 21.69 22.41
- 42.25 21.40 21.45 21.47 21.49 21.53 21.63 21.68 22.42
+ 42.25 21.40 21.45 21.47 21.49 21.53 21.64 21.68 22.42
42.24 21.40 22.43
42.23 21.35 22.44
42.22 21.34 22.46
42.21 21.33 22.48
42.20 21.08 21.12 21.32 22.49
42.19 21.06 21.14 21.31 22.49
- 42.18 21.04 21.16 21.31 22.50
- 42.17 21.02 21.17 21.30 22.50
- 42.16 21.01 21.19 21.29 22.51
+ 42.18 21.05 21.16 21.31 22.50
+ 42.17 21.04 21.17 21.30 22.50
+ 42.16 21.01 21.19 21.29 22.50
42.15 20.98 21.20 21.28 22.52
- 42.14 20.94 21.21 21.28 22.53
- 42.13 20.90 21.22 21.28 22.55
- 42.12 20.86 21.22 21.28 22.57
- 42.11 20.82 21.23 21.28 22.59
- 42.10 20.79 21.26 21.28 22.61
- 42.09 20.77 22.63
- 42.08 20.76 22.66
+ 42.14 20.95 21.21 21.28 22.53
+ 42.13 20.91 21.22 21.28 22.55
+ 42.12 20.87 21.22 21.28 22.57
+ 42.11 20.83 21.23 21.28 22.59
+ 42.10 20.79 22.61
+ 42.09 20.77 22.62
+ 42.08 20.76 22.65
42.07 20.75 22.69
42.06 20.75 22.72
42.05 20.74 22.79
@@ -109601,7 +109903,7 @@ Macedonia
41.97 20.73 22.86
41.96 20.73 22.86
41.95 20.73 22.86
- 41.94 20.73 22.86
+ 41.94 20.74 22.86
41.93 20.74 22.87
41.92 20.74 22.87
41.91 20.74 22.88
@@ -109628,7 +109930,7 @@ Macedonia
41.70 20.49 23.01
41.69 20.49 23.01
41.68 20.49 23.00
- 41.67 20.49 22.99
+ 41.67 20.49 23.00
41.66 20.49 22.99
41.65 20.49 22.98
41.64 20.49 22.98
@@ -109685,9 +109987,9 @@ Macedonia
41.13 20.55 22.16 22.27 22.62 22.68 22.72
41.12 20.55 22.03 22.05 22.15 22.29 22.61 22.69 22.71
41.11 20.55 22.00 22.07 22.13 22.29 22.60
- 41.10 20.55 21.95 22.39 22.50 22.52 22.59
+ 41.10 20.55 21.95 22.39 22.50 22.52 22.58
41.09 20.55 21.93
- 41.08 20.56 21.91
+ 41.08 20.56 21.92
41.07 20.58 21.90
41.06 20.64 21.90
41.05 20.64 21.90
@@ -109706,7 +110008,7 @@ Macedonia
40.92 20.69 21.78
40.91 20.69 21.77
40.90 20.70 20.81 20.86 21.67 21.70 21.75
- 40.89 20.71 20.80 20.91 21.66
+ 40.89 20.72 20.80 20.91 21.66
40.88 20.73 20.79 20.94 21.38 21.50 21.65
40.87 20.94 21.37 21.52 21.62
40.86 20.95 21.35 21.54 21.61
@@ -109724,7 +110026,7 @@ Madagascar
-12.00 49.19 49.33
-12.01 49.18 49.33
-12.02 49.17 49.33
- -12.03 49.17 49.34
+ -12.03 49.17 49.33
-12.04 49.15 49.34
-12.05 49.13 49.35
-12.06 49.11 49.35
@@ -109744,7 +110046,7 @@ Madagascar
-12.20 49.15 49.38
-12.21 49.15 49.40
-12.22 49.15 49.41
- -12.23 49.11 49.13 49.15 49.41
+ -12.23 49.10 49.13 49.15 49.41
-12.24 49.09 49.42
-12.25 49.09 49.42
-12.26 49.05 49.43
@@ -109759,22 +110061,22 @@ Madagascar
-12.35 48.96 49.53
-12.36 48.96 49.54
-12.37 48.96 49.54
- -12.38 48.75 48.78 48.95 49.55
+ -12.38 48.74 48.78 48.95 49.55
-12.39 48.74 48.84 48.95 49.55
- -12.40 48.74 48.86 48.95 49.55
+ -12.40 48.73 48.86 48.95 49.55
-12.41 48.73 48.87 48.95 49.56
-12.42 48.72 48.88 48.94 49.56
-12.43 48.72 48.89 48.94 49.57
-12.44 48.72 48.89 48.94 49.57
-12.45 48.74 48.90 48.94 49.58
- -12.46 48.76 48.90 48.94 49.58
+ -12.46 48.76 48.90 48.93 49.58
-12.47 48.77 48.91 48.93 49.59
-12.48 48.78 49.59
-12.49 48.78 49.60
-12.50 48.79 49.60
- -12.51 48.81 49.60
- -12.52 48.82 49.60
- -12.53 48.82 49.60
+ -12.51 48.80 49.60
+ -12.52 48.81 49.60
+ -12.53 48.81 49.60
-12.54 48.82 49.60
-12.55 48.82 49.60
-12.56 48.82 49.59
@@ -109793,7 +110095,7 @@ Madagascar
-12.69 48.89 49.66
-12.70 48.89 49.67
-12.71 48.89 49.67
- -12.72 48.89 49.67 49.72 49.74
+ -12.72 48.89 49.67 49.70 49.74
-12.73 48.90 49.68 49.70 49.75
-12.74 48.90 49.68 49.70 49.75
-12.75 48.90 49.77
@@ -109801,8 +110103,8 @@ Madagascar
-12.77 48.91 49.80
-12.78 48.91 49.81
-12.79 48.92 49.81
- -12.80 48.94 49.81
- -12.81 48.94 49.81
+ -12.80 48.93 49.81
+ -12.81 48.93 49.81
-12.82 48.94 49.81
-12.83 48.94 49.81
-12.84 48.93 49.82
@@ -109856,21 +110158,21 @@ Madagascar
-13.32 48.18 48.36 48.77 49.98
-13.33 48.18 48.35 48.77 50.03
-13.34 48.18 48.35 48.77 50.03
- -13.35 48.19 48.35 48.47 48.50 48.78 50.04
- -13.36 48.19 48.36 48.47 48.51 48.78 50.04
- -13.37 48.19 48.37 48.46 48.52 48.77 50.04
- -13.38 48.19 48.37 48.46 48.53 48.76 50.04
+ -13.35 48.18 48.35 48.47 48.50 48.78 50.04
+ -13.36 48.18 48.36 48.47 48.51 48.78 50.04
+ -13.37 48.18 48.37 48.46 48.52 48.77 50.04
+ -13.38 48.18 48.37 48.46 48.53 48.76 50.04
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+ -23.60 43.65 47.62
-23.61 43.64 47.62
-23.62 43.63 47.63
-23.63 43.63 47.63
@@ -110916,36 +111218,36 @@ Madagascar
-23.92 43.64 47.55
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+ -24.24 43.65 47.39
-24.25 43.65 47.39
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-24.27 43.65 47.38
@@ -110971,8 +111273,8 @@ Madagascar
-24.47 43.77 47.32
-24.48 43.79 47.32
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+ -24.51 43.82 47.31
-24.52 43.83 47.31
-24.53 43.83 47.30
-24.54 43.83 47.30
@@ -111027,7 +111329,7 @@ Madagascar
-25.03 44.06 47.01
-25.04 44.07 47.00
-25.05 44.09 46.99
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+ -25.06 44.10 46.98
-25.07 44.16 46.90 46.94 46.97
-25.08 44.18 46.89 46.94 46.96
-25.09 44.19 46.87
@@ -111044,12 +111346,12 @@ Madagascar
-25.20 44.31 46.26
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-25.22 44.32 46.20
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-25.29 44.48 46.03
-25.30 44.64 46.01
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@@ -111076,10 +111378,10 @@ Madagascar
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+ -25.58 45.12 45.53
-25.59 45.12 45.35
-25.60 45.13 45.19
Malawi
@@ -111243,8 +111545,8 @@ Malawi
-10.94 33.27 34.64
-10.95 33.27 34.64
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@@ -111366,7 +111668,7 @@ Malawi
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+ -12.20 33.28 34.36
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@@ -111477,7 +111779,7 @@ Malawi
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+ -13.31 32.90 34.55
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@@ -111485,7 +111787,7 @@ Malawi
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@@ -111570,7 +111872,7 @@ Malawi
-14.21 33.31 35.51
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+ -14.24 33.34 35.52
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@@ -111601,9 +111903,9 @@ Malawi
-14.52 33.58 33.69 33.74 33.85 34.42 35.75
-14.53 33.59 33.69 33.75 33.84 34.43 35.76
-14.54 33.59 33.68 33.76 33.82 34.44 35.77
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-14.56 33.60 33.68 34.47 35.78
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-14.58 33.61 33.68 34.49 35.80
-14.59 33.61 33.68 34.49 35.81
-14.60 33.62 33.68 34.50 35.82
@@ -111663,14 +111965,14 @@ Malawi
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-15.25 34.55 35.81
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-15.27 34.55 35.81
@@ -111691,10 +111993,10 @@ Malawi
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+ -15.48 34.40 35.84
-15.49 34.40 35.84
-15.50 34.40 35.84
-15.51 34.40 35.84
@@ -111738,10 +112040,10 @@ Malawi
-15.89 34.22 35.81
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-15.96 34.29 35.80
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-15.98 34.31 35.80
@@ -111768,7 +112070,7 @@ Malawi
-16.19 34.37 35.33
-16.20 34.37 35.32
-16.21 34.38 35.31
- -16.22 34.38 35.30
+ -16.22 34.38 35.29
-16.23 34.39 35.29
-16.24 34.39 35.28
-16.25 34.40 35.28
@@ -111817,7 +112119,7 @@ Malawi
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-16.74 34.89 35.29
@@ -111865,11 +112167,11 @@ Malaysia
7.36 116.99 117.01 117.20 117.26
7.35 116.98 117.02 117.14 117.28
7.34 116.97 117.02 117.13 117.29
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7.31 116.92 117.03 117.09 117.29
7.30 116.90 117.03 117.07 117.29
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7.28 116.88 117.03 117.05 117.29
7.27 116.88 117.03 117.05 117.29
7.26 116.87 117.02 117.05 117.29
@@ -111893,7 +112195,7 @@ Malaysia
7.03 116.75 116.79
7.02 116.73 116.79
7.01 116.73 116.80 117.13 117.16
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6.99 116.72 116.83 117.06 117.20
6.98 116.70 116.84 117.06 117.22
6.97 116.70 116.84 117.06 117.24
@@ -111918,10 +112220,10 @@ Malaysia
6.78 116.63 116.86 116.99 117.26
6.77 116.63 116.86 116.98 117.27 117.45 117.47
6.76 116.63 116.86 116.97 117.28 117.40 117.48
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6.71 100.16 100.20 100.23 100.27 116.63 116.83 116.96 117.28 117.39 117.52
6.70 100.15 100.28 116.62 116.83 116.94 117.29 117.43 117.52
6.69 100.15 100.29 116.61 116.82 116.93 117.29 117.35 117.52
@@ -111929,86 +112231,86 @@ Malaysia
6.67 100.15 100.30 116.59 116.81 116.90 117.29 117.33 117.51
6.66 100.15 100.30 116.59 116.81 116.89 117.29 117.33 117.51
6.65 100.15 100.30 116.58 116.80 116.88 117.29 117.33 117.50
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6.63 100.14 100.31 116.57 116.79 116.86 117.47 117.51 117.54
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6.58 100.14 100.32 116.52 117.42 117.48 117.55
6.57 100.15 100.32 116.51 117.44 117.47 117.56
6.56 100.15 100.34 116.50 117.57
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6.52 100.13 100.47 116.49 117.66
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6.50 100.13 100.51 100.70 100.73 116.49 117.67
6.49 100.13 100.53 100.68 100.74 116.47 117.68
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6.47 99.82 99.86 100.13 100.59 100.66 100.74 116.44 117.72
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6.41 99.63 99.90 100.12 100.81 116.37 117.74
6.40 99.63 99.92 100.12 100.81 116.35 117.75
6.39 99.63 99.92 100.12 100.81 116.34 117.75
6.38 99.63 99.92 100.12 100.81 116.33 117.75
6.37 99.63 99.92 100.12 100.81 116.32 117.75
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6.19 99.76 99.84 100.24 101.10 102.05 102.33 116.17 117.61
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5.88 100.35 101.03 101.43 101.60 101.90 102.53 116.04 118.13
5.87 100.35 101.02 101.40 101.62 101.90 102.54 116.04 118.13
5.86 100.35 101.01 101.38 101.64 101.90 102.55 116.04 118.13 118.17 118.24
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5.84 100.35 101.00 101.35 101.64 101.87 102.58 116.03 118.12 118.15 118.24
5.83 100.36 101.00 101.33 101.64 101.85 102.60 116.02 118.12 118.15 118.29
5.82 100.36 100.99 101.29 101.64 101.85 102.61 116.00 118.11 118.15 118.31 118.34 118.37
@@ -112017,9 +112319,9 @@ Malaysia
5.79 100.36 100.97 101.23 101.66 101.70 101.75 101.82 102.64 115.94 117.93 117.96 118.07 118.14 118.44
5.78 100.36 100.98 101.23 101.66 101.69 101.75 101.81 102.65 115.93 117.93 118.14 118.46
5.77 100.36 100.99 101.23 101.76 101.81 102.65 115.92 117.93 118.14 118.47
- 5.76 100.36 100.99 101.22 101.76 101.80 102.66 115.92 117.94 118.14 118.49
- 5.75 100.35 101.00 101.22 101.78 101.80 102.66 115.91 117.94 118.14 118.51
- 5.74 100.35 101.00 101.22 102.66 115.91 117.94 118.14 118.52
+ 5.76 100.36 100.99 101.22 101.76 101.80 102.66 115.91 117.94 118.14 118.49
+ 5.75 100.35 101.00 101.22 101.78 101.80 102.66 115.90 117.94 118.14 118.51
+ 5.74 100.35 101.00 101.22 102.66 115.90 117.94 118.14 118.52
5.73 100.35 101.04 101.22 102.68 115.90 117.95 118.13 118.53
5.72 100.35 101.05 101.22 102.70 115.90 117.95 118.02 118.11 118.13 118.54
5.71 100.35 101.06 101.22 102.71 115.90 117.96 118.00 118.56
@@ -112035,9 +112337,9 @@ Malaysia
5.61 100.33 102.84 115.57 115.62 115.86 118.69
5.60 100.34 102.86 115.56 115.62 115.86 118.70
5.59 100.34 102.87 115.56 115.62 115.85 118.71
- 5.58 100.34 102.89 115.55 115.61 115.85 118.71
- 5.57 100.34 102.91 115.55 115.62 115.84 118.72
- 5.56 100.34 102.94 115.54 115.64 115.83 118.73
+ 5.58 100.34 102.89 115.55 115.61 115.84 118.71
+ 5.57 100.34 102.91 115.55 115.62 115.83 118.72
+ 5.56 100.34 102.94 115.54 115.64 115.82 118.73
5.55 100.34 102.97 115.54 115.65 115.81 118.77
5.54 100.34 102.98 115.53 115.67 115.80 118.80
5.53 100.35 102.99 115.51 118.81
@@ -112046,9 +112348,9 @@ Malaysia
5.50 100.36 103.02 115.47 118.85
5.49 100.37 103.03 115.46 118.86
5.48 100.37 103.04 115.45 118.87
- 5.47 100.18 100.20 100.22 100.31 100.37 103.05 115.45 118.91
- 5.46 100.16 100.32 100.37 103.06 115.44 118.92 119.17 119.20
- 5.45 100.16 100.32 100.36 103.07 115.42 118.93 119.15 119.21
+ 5.47 100.18 100.20 100.22 100.30 100.37 103.05 115.45 118.91
+ 5.46 100.16 100.31 100.37 103.06 115.44 118.92 119.17 119.20
+ 5.45 100.16 100.31 100.36 103.07 115.42 118.93 119.15 119.21
5.44 100.16 100.33 100.36 103.08 115.40 118.94 118.97 119.02 119.13 119.21
5.43 100.16 100.34 100.36 103.09 115.39 118.94 118.96 119.04 119.11 119.22
5.42 100.16 103.10 115.38 118.94 118.96 119.07 119.09 119.23
@@ -112058,31 +112360,31 @@ Malaysia
5.38 100.18 100.34 100.37 103.14 115.20 115.25 115.36 119.27
5.37 100.18 100.33 100.37 103.14 115.19 115.25 115.36 119.28
5.36 100.18 100.33 100.37 103.15 115.18 115.25 115.35 119.28
- 5.35 100.18 100.33 100.38 103.15 115.17 115.26 115.35 119.28
+ 5.35 100.18 100.33 100.38 103.15 115.17 115.25 115.35 119.28
5.34 100.18 100.33 100.38 103.16 115.17 115.26 115.35 119.28
- 5.33 100.18 100.33 100.39 103.17 115.17 115.27 115.35 119.28
- 5.32 100.18 100.33 100.40 103.17 115.16 115.27 115.34 119.28
- 5.31 100.18 100.32 100.40 103.18 115.16 115.27 115.34 119.28
- 5.30 100.18 100.32 100.41 103.19 115.16 115.27 115.34 119.28
- 5.29 100.18 100.31 100.42 103.19 115.16 115.27 115.35 119.28
- 5.28 100.16 100.31 100.42 103.20 115.15 115.26 115.39 119.27
- 5.27 100.16 100.30 100.41 103.20 115.15 115.26 115.40 119.27
- 5.26 100.16 100.30 100.41 103.21 115.14 115.20 115.22 115.25 115.41 119.27
+ 5.33 100.18 100.33 100.39 103.17 115.17 115.26 115.35 119.28
+ 5.32 100.18 100.33 100.40 103.17 115.16 115.26 115.34 119.28
+ 5.31 100.18 100.32 100.40 103.18 115.16 115.26 115.34 119.28
+ 5.30 100.18 100.32 100.41 103.19 115.16 115.26 115.34 119.28
+ 5.29 100.18 100.31 100.42 103.19 115.16 115.26 115.35 119.28
+ 5.28 100.16 100.31 100.42 103.20 115.15 115.26 115.40 119.27
+ 5.27 100.16 100.30 100.41 103.20 115.15 115.26 115.41 119.27
+ 5.26 100.16 100.30 100.41 103.21 115.14 115.20 115.22 115.25 115.42 119.27
5.25 100.17 100.20 100.25 100.29 100.40 103.22 115.14 115.19 115.43 119.27
5.24 100.40 103.22 115.14 115.17 115.44 119.27
5.23 100.40 103.23 115.45 119.27
- 5.22 100.41 103.23 115.47 119.27
- 5.21 100.42 103.24 115.48 119.27
+ 5.22 100.41 103.23 115.46 119.27
+ 5.21 100.42 103.24 115.47 119.27
5.20 100.42 103.24 115.49 119.27
5.19 100.42 103.24 115.51 119.27
- 5.18 100.41 103.25 115.57 119.26
+ 5.18 100.41 103.25 115.56 119.26
5.17 100.41 103.25 115.56 119.25
5.16 100.40 103.25 115.56 119.24
5.15 100.40 103.26 115.56 119.23
- 5.14 100.39 103.26 115.56 119.23
- 5.13 100.39 103.27 115.56 119.22
- 5.12 100.39 103.27 115.56 119.21
- 5.11 100.37 103.28 115.56 119.20
+ 5.14 100.39 103.26 115.55 119.23
+ 5.13 100.39 103.27 115.55 119.22
+ 5.12 100.39 103.27 115.55 119.21
+ 5.11 100.37 103.28 115.55 119.20
5.10 100.35 103.28 115.55 119.19
5.09 100.35 103.29 115.55 119.17
5.08 100.35 103.30 115.55 119.14
@@ -112090,8 +112392,8 @@ Malaysia
5.06 100.35 103.31 115.53 119.09
5.05 100.36 103.32 115.52 119.07
5.04 100.36 103.32 115.48 119.04
- 5.03 100.37 103.33 115.47 119.01
- 5.02 100.37 103.33 115.46 118.99
+ 5.03 100.37 103.33 115.46 119.01
+ 5.02 100.37 103.33 115.45 118.99
5.01 100.38 103.34 115.45 118.35 118.39 118.96
5.00 100.38 103.35 115.44 118.33 118.41 118.92
4.99 100.38 103.35 115.43 118.32 118.42 118.88
@@ -112101,8 +112403,8 @@ Malaysia
4.95 100.41 103.38 115.18 115.24 115.39 118.23 118.46 118.57 118.59 118.76
4.94 100.41 103.38 115.18 115.29 115.38 118.21 118.46 118.56 118.63 118.74
4.93 100.42 103.39 115.17 115.30 115.37 118.20 118.47 118.54 118.65 118.72
- 4.92 100.42 103.39 115.00 115.02 115.17 115.30 115.36 118.20 118.48 118.52
- 4.91 100.43 103.40 115.00 115.02 115.13 115.32 115.34 118.19
+ 4.92 100.42 103.39 115.00 115.02 115.16 115.30 115.36 118.20 118.48 118.52
+ 4.91 100.43 103.40 114.99 115.02 115.13 118.19
4.90 100.43 103.40 114.98 115.03 115.13 118.18
4.89 100.44 100.46 100.48 103.41 114.97 115.03 115.13 118.17
4.88 100.48 103.41 114.95 115.03 115.13 118.16
@@ -112119,7 +112421,7 @@ Malaysia
4.77 100.60 103.45 114.79 115.03 115.20 118.21
4.76 100.59 103.45 114.77 115.03 115.21 118.22
4.75 100.58 103.45 114.75 115.03 115.21 118.23
- 4.74 100.58 103.45 114.74 115.03 115.22 118.24
+ 4.74 100.58 103.45 114.73 115.03 115.22 118.24
4.73 100.58 103.45 114.73 115.03 115.22 118.25
4.72 100.58 103.46 114.73 115.03 115.22 118.26
4.71 100.58 103.46 114.73 115.03 115.23 118.27
@@ -112130,7 +112432,7 @@ Malaysia
4.66 100.59 103.46 114.74 115.03 115.25 118.59
4.65 100.59 103.46 114.74 115.03 115.25 118.60
4.64 100.60 103.46 114.75 115.04 115.25 118.60
- 4.63 100.59 103.46 114.75 115.04 115.26 118.60
+ 4.63 100.59 103.47 114.75 115.04 115.26 118.60
4.62 100.58 103.47 114.76 115.04 115.26 118.40 118.42 118.60
4.61 100.58 103.47 113.98 114.01 114.76 115.05 115.26 118.58
4.60 100.58 103.47 113.96 114.03 114.76 115.05 115.26 118.48 118.50 118.58
@@ -112156,15 +112458,15 @@ Malaysia
4.40 100.57 103.48 113.97 114.28 114.83 115.11 115.28 118.63
4.39 100.57 103.48 113.96 114.28 114.83 115.13 115.29 117.63 117.67 118.60
4.38 100.57 103.49 113.96 114.28 114.83 115.15 115.30 117.62 117.67 118.60
- 4.37 100.57 103.49 113.95 114.29 114.82 115.18 115.32 117.63 117.68 118.59
- 4.36 100.57 103.49 113.95 114.29 114.82 115.24 115.33 116.51 116.53 117.64 117.68 118.58
+ 4.37 100.56 103.49 113.95 114.29 114.82 115.18 115.32 117.63 117.68 118.59
+ 4.36 100.56 103.49 113.95 114.29 114.82 115.24 115.33 116.51 116.53 117.64 117.68 118.58
4.35 100.56 103.50 113.95 114.29 114.81 115.28 115.33 116.13 116.15 116.27 116.31 116.50 116.54 117.64 117.69 118.57
- 4.34 100.56 103.50 113.95 114.30 114.81 115.30 115.34 115.83 115.86 116.12 116.19 116.24 116.32 116.50 116.55 117.64 117.71 118.50 118.52 118.55
+ 4.34 100.56 103.50 113.95 114.30 114.81 115.30 115.34 115.83 115.86 116.12 116.19 116.24 116.32 116.50 116.55 117.64 117.71 118.50
4.33 100.55 103.50 113.95 114.30 114.80 115.32 115.34 115.83 115.88 116.11 116.35 116.50 116.55 116.70 116.74 117.19 117.21 117.64 117.74 118.35 118.37 118.45
4.32 100.55 103.50 113.95 114.30 114.79 115.83 115.95 116.10 116.35 116.50 116.56 116.69 116.75 116.85 116.93 117.18 117.22 117.64 117.77 118.34
4.31 100.55 103.50 113.94 114.30 114.78 115.83 115.96 116.09 116.36 116.50 116.96 117.08 117.22 117.64 117.80 118.31
4.30 100.55 103.50 113.94 114.30 114.77 115.83 115.97 116.08 116.36 116.49 117.24 117.65 117.80 118.27
- 4.29 100.57 103.50 113.93 114.30 114.77 115.83 115.97 116.07 116.37 116.44 117.26 117.66 117.81 118.21
+ 4.29 100.58 103.50 113.93 114.30 114.77 115.83 115.97 116.07 116.37 116.44 117.26 117.66 117.81 118.21
4.28 100.58 103.50 113.93 114.29 114.77 115.82 115.97 116.06 116.38 116.43 117.27 117.66 117.84 118.15
4.27 100.58 103.50 113.92 114.34 114.38 114.42 114.77 115.82 115.98 116.05 116.40 116.42 117.29 117.74 117.85 118.12
4.26 100.58 103.49 113.91 114.43 114.77 115.81 115.99 116.04 117.31 117.78 117.86 118.10
@@ -112173,14 +112475,14 @@ Malaysia
4.23 100.59 103.48 113.89 114.45 114.78 115.78 117.35 117.80 117.91 118.04
4.22 100.59 103.47 113.88 114.45 114.78 115.78 117.36 117.81 117.95 118.02
4.21 100.59 103.46 113.88 114.45 114.77 115.78 117.38 117.61 117.63 117.82
- 4.20 100.60 103.45 113.87 114.46 114.77 115.72 117.39 117.88
+ 4.20 100.60 103.45 113.87 114.46 114.77 115.72 117.39 117.87
4.19 100.60 103.46 113.86 114.46 114.77 115.70 117.40 117.90
4.18 100.60 103.46 113.85 114.46 114.77 115.69 117.41 117.63 117.65 117.91
4.17 100.61 103.46 113.84 114.47 114.77 115.68 117.42 117.63 117.66 117.91
4.16 100.61 103.45 113.84 114.47 114.76 115.67 117.44 117.63 117.67 117.91
- 4.15 100.61 103.45 113.83 114.48 114.76 115.65 117.54 117.60 117.68 117.80
- 4.14 100.62 100.65 100.68 103.43 113.82 114.49 114.75 115.65 117.55 117.58
- 4.13 100.69 103.42 113.81 114.50 114.74 115.65
+ 4.15 100.61 103.45 113.83 114.48 114.76 115.65 117.54 117.60 117.68 117.91
+ 4.14 100.62 100.65 100.68 103.43 113.82 114.49 114.75 115.65 117.55 117.58 117.71 117.91
+ 4.13 100.69 103.42 113.81 114.50 114.74 115.64
4.12 100.70 103.41 113.81 114.52 114.73 115.64
4.11 100.71 103.41 113.80 114.53 114.72 115.64
4.10 100.72 103.40 113.79 114.54 114.71 115.64
@@ -112200,7 +112502,7 @@ Malaysia
3.96 100.69 103.44 113.66 115.61
3.95 100.69 103.44 113.65 115.60
3.94 100.69 103.44 113.64 115.60
- 3.93 100.69 103.44 113.63 115.59
+ 3.93 100.69 103.41 113.63 115.59
3.92 100.69 103.40 113.62 115.58
3.91 100.69 103.40 113.61 115.56
3.90 100.69 103.40 113.59 115.55
@@ -112232,8 +112534,8 @@ Malaysia
3.64 100.98 103.39 113.37 115.55
3.63 101.00 103.39 113.36 115.55
3.62 101.01 103.40 113.35 115.55
- 3.61 101.03 103.40 113.34 115.55
- 3.60 101.03 103.41 113.33 115.55
+ 3.61 101.03 103.41 113.34 115.55
+ 3.60 101.03 103.42 113.33 115.55
3.59 101.04 103.42 113.32 115.56
3.58 101.04 103.43 113.32 115.56
3.57 101.05 103.44 113.30 115.57
@@ -112249,12 +112551,12 @@ Malaysia
3.47 101.09 103.48 113.24 115.60
3.46 101.09 103.47 113.23 115.60
3.45 101.10 103.47 113.21 115.61
- 3.44 101.12 103.46 113.20 115.61
- 3.43 101.13 103.46 113.19 115.61
- 3.42 101.14 103.45 113.18 115.61
+ 3.44 101.11 103.46 113.20 115.61
+ 3.43 101.12 103.46 113.19 115.61
+ 3.42 101.13 103.45 113.18 115.61
3.41 101.14 103.45 113.17 115.60
- 3.40 101.15 103.44 113.17 115.59
- 3.39 101.16 103.44 113.16 115.54
+ 3.40 101.14 103.44 113.17 115.59
+ 3.39 101.15 103.44 113.16 115.54
3.38 101.16 103.44 113.16 115.54
3.37 101.17 103.44 113.15 115.53
3.36 101.17 103.43 113.15 115.53
@@ -112279,12 +112581,12 @@ Malaysia
3.17 101.30 103.46 112.99 115.52
3.16 101.30 103.46 112.97 115.52
3.15 101.30 103.46 112.95 115.52
- 3.14 101.31 103.46 112.92 115.52
- 3.13 101.31 103.46 112.89 115.51
- 3.12 101.31 103.45 112.87 115.51
- 3.11 101.31 103.45 112.84 115.50
- 3.10 101.32 103.45 112.77 115.49
- 3.09 101.33 103.45 112.75 115.49
+ 3.14 101.31 103.46 112.91 115.52
+ 3.13 101.31 103.46 112.88 115.51
+ 3.12 101.31 103.45 112.85 115.51
+ 3.11 101.31 103.45 112.81 115.50
+ 3.10 101.31 103.45 112.77 115.49
+ 3.09 101.32 103.45 112.75 115.49
3.08 101.31 103.45 112.73 115.48
3.07 101.29 103.45 112.69 115.48
3.06 101.25 101.27 101.29 103.45 112.64 115.48
@@ -112313,14 +112615,14 @@ Malaysia
2.83 101.27 103.50 104.14 104.22 111.62 115.10
2.82 101.29 103.51 104.15 104.22 111.60 115.09
2.81 101.33 103.52 104.14 104.22 111.58 115.09
- 2.80 101.37 103.52 104.12 104.23 111.57 115.09
- 2.79 101.40 103.53 104.11 104.23 111.30 111.34 111.55 115.10
- 2.78 101.42 103.54 104.11 104.23 111.30 111.36 111.53 115.10
- 2.77 101.42 103.55 104.11 104.23 111.29 111.36 111.52 115.11
- 2.76 101.43 103.56 104.11 104.23 111.29 111.37 111.51 115.11
- 2.75 101.43 103.57 104.11 104.23 111.29 111.37 111.49 115.11
- 2.74 101.44 103.58 104.12 104.23 111.29 111.38 111.48 115.11
- 2.73 101.44 103.59 104.12 104.23 111.28 111.38 111.47 115.10
+ 2.80 101.37 103.52 104.12 104.23 111.56 115.09
+ 2.79 101.40 103.53 104.11 104.23 111.30 111.33 111.54 115.10
+ 2.78 101.42 103.54 104.11 104.23 111.30 111.35 111.52 115.10
+ 2.77 101.42 103.55 104.11 104.23 111.29 111.36 111.51 115.11
+ 2.76 101.43 103.56 104.11 104.23 111.29 111.36 111.50 115.11
+ 2.75 101.43 103.57 104.12 104.23 111.29 111.37 111.49 115.11
+ 2.74 101.44 103.58 104.12 104.23 111.29 111.38 111.47 115.11
+ 2.73 101.44 103.59 104.12 104.23 111.28 111.38 111.46 115.10
2.72 101.45 103.60 104.12 104.23 111.28 111.38 111.45 115.10
2.71 101.45 103.61 104.13 104.23 111.28 111.39 111.44 115.09
2.70 101.46 103.62 104.14 104.22 111.28 111.39 111.43 115.06
@@ -112338,12 +112640,12 @@ Malaysia
2.58 101.70 103.82 111.29 115.18
2.57 101.76 103.83 111.29 115.19
2.56 101.77 103.83 111.30 115.20
- 2.55 101.77 103.84 111.30 115.20
+ 2.55 101.77 103.83 111.30 115.20
2.54 101.78 103.84 111.30 115.21
- 2.53 101.78 103.85 111.30 115.21
- 2.52 101.78 103.85 111.30 111.39 111.41 115.21
- 2.51 101.79 103.85 111.30 111.39 111.42 115.21
- 2.50 101.79 103.85 111.30 111.39 111.43 115.21
+ 2.53 101.78 103.84 111.30 115.21
+ 2.52 101.78 103.84 111.30 111.39 111.41 115.21
+ 2.51 101.79 103.84 111.30 111.39 111.42 115.21
+ 2.50 101.79 103.84 111.30 111.39 111.43 115.21
2.49 101.80 103.84 111.30 115.21
2.48 101.81 103.84 111.30 115.20
2.47 101.83 103.84 111.29 115.19
@@ -112386,8 +112688,8 @@ Malaysia
2.10 102.41 104.04 111.23 114.78
2.09 102.43 104.05 109.63 109.65 111.23 114.78
2.08 102.46 104.05 109.63 109.65 111.20 114.78
- 2.07 102.49 104.06 109.62 109.66 111.19 114.78
- 2.06 102.51 104.06 109.62 109.66 111.19 114.78
+ 2.07 102.49 104.06 109.62 109.65 111.19 114.78
+ 2.06 102.51 104.06 109.62 109.65 111.19 114.78
2.05 102.52 104.07 109.62 109.66 111.19 114.84
2.04 102.53 104.07 109.61 109.66 111.19 114.85
2.03 102.54 104.08 109.61 109.66 111.18 114.85
@@ -112404,16 +112706,16 @@ Malaysia
1.92 102.64 104.13 109.52 109.67 111.14 114.84
1.91 102.65 104.13 109.51 109.68 111.14 114.84
1.90 102.65 104.13 109.51 109.68 111.13 114.84
- 1.89 102.66 104.13 109.51 109.69 111.13 114.84
+ 1.89 102.66 104.12 109.51 109.69 111.13 114.84
1.88 102.66 104.13 109.51 109.70 111.12 114.83
1.87 102.67 104.13 109.51 109.71 111.12 114.81
1.86 102.67 104.14 109.51 109.72 111.11 114.79
1.85 102.67 104.17 109.52 109.73 111.11 114.77
1.84 102.68 104.18 109.52 109.75 111.10 114.70
- 1.83 102.70 102.76 102.81 104.18 109.52 109.78 111.10 114.68
- 1.82 102.83 104.19 109.52 109.80 111.10 114.68
- 1.81 102.85 104.19 109.52 109.82 110.31 110.34 111.10 114.68
- 1.80 102.86 104.20 109.53 109.84 110.30 110.35 111.10 114.68
+ 1.83 102.70 102.76 102.82 104.18 109.52 109.78 111.10 114.68
+ 1.82 102.83 104.19 109.52 109.80 111.09 114.68
+ 1.81 102.85 104.19 109.52 109.82 110.31 110.34 111.09 114.68
+ 1.80 102.86 104.20 109.53 109.84 110.30 110.35 111.09 114.68
1.79 102.87 104.20 109.54 109.86 110.30 110.35 111.09 114.68
1.78 102.88 104.20 109.55 109.88 110.29 110.36 111.08 114.69
1.77 102.89 104.21 109.57 109.89 110.28 110.36 111.08 114.69
@@ -112425,8 +112727,8 @@ Malaysia
1.71 103.00 104.23 109.63 109.92 110.00 110.18 110.22 110.27 110.29 110.39 110.43 110.53 111.10 114.68
1.70 103.02 104.23 109.63 109.94 109.96 110.20 110.22 110.52 111.10 114.68
1.69 103.03 104.23 109.63 110.51 111.06 114.67
- 1.68 103.05 104.23 109.63 110.51 111.02 114.67
- 1.67 103.07 104.24 109.63 110.51 111.01 114.67
+ 1.68 103.05 104.23 109.63 110.50 111.02 114.67
+ 1.67 103.07 104.24 109.63 110.50 111.01 114.67
1.66 103.08 104.25 109.63 110.50 111.01 114.67
1.65 103.10 104.25 109.63 110.50 111.01 114.66
1.64 103.12 104.26 109.63 110.52 111.01 114.66
@@ -112443,16 +112745,16 @@ Malaysia
1.53 103.34 104.29 109.69 110.95 111.00 112.43 112.77 112.82 113.00 114.58
1.52 103.35 104.01 104.03 104.29 109.70 110.96 111.01 112.42 113.01 114.57
1.51 103.36 104.01 104.03 104.29 109.72 110.97 111.02 112.41 113.01 114.57
- 1.50 103.37 104.01 104.04 104.29 109.73 110.98 111.02 112.39 113.00 114.57
+ 1.50 103.37 104.01 104.03 104.29 109.73 110.98 111.02 112.39 113.00 114.57
1.49 103.38 104.01 104.04 104.30 109.74 110.99 111.02 112.31 113.00 114.57
1.48 103.38 104.02 104.04 104.30 109.75 111.00 111.03 112.29 112.99 114.34 114.40 114.57
1.47 103.39 104.02 104.04 104.30 109.76 111.01 111.03 112.27 112.99 114.32 114.42 114.57
1.46 103.39 104.02 104.04 104.30 109.76 112.25 112.98 114.30 114.44 114.57
- 1.45 103.40 103.81 103.85 104.02 104.04 104.30 109.76 112.23 112.96 114.28 114.45 114.57
- 1.44 103.40 103.79 103.87 104.02 104.05 104.30 109.76 112.21 112.95 114.02 114.11 114.26 114.46 114.57
- 1.43 103.41 103.69 103.73 103.77 103.89 104.02 104.05 104.30 109.79 112.19 112.94 113.94 114.13 114.24 114.48 114.56
- 1.42 103.41 103.68 103.91 104.01 104.06 104.29 109.80 112.18 112.94 113.90 114.14 114.22 114.49 114.55
- 1.41 103.41 103.68 103.93 104.00 104.07 104.28 109.80 112.19 112.94 113.04 113.09 113.89 114.15 114.20 114.51 114.54
+ 1.45 103.40 103.81 103.84 104.02 104.04 104.30 109.76 112.23 112.96 114.28 114.45 114.57
+ 1.44 103.40 103.79 103.86 104.02 104.05 104.30 109.76 112.21 112.95 114.02 114.11 114.26 114.46 114.57
+ 1.43 103.41 103.69 103.73 103.77 103.88 104.01 104.05 104.30 109.79 112.19 112.94 113.94 114.13 114.24 114.48 114.56
+ 1.42 103.41 103.68 103.90 104.00 104.06 104.29 109.80 112.18 112.94 113.90 114.14 114.22 114.49 114.55
+ 1.41 103.41 103.68 103.93 103.99 104.07 104.28 109.80 112.19 112.94 113.04 113.09 113.89 114.15 114.20 114.51 114.54
1.40 103.41 103.67 103.95 103.98 104.09 104.29 109.81 112.19 112.94 113.00 113.11 113.87
1.39 103.42 103.66 104.09 104.29 109.83 112.19 113.12 113.86
1.38 103.42 103.65 104.09 104.29 109.91 112.19 113.13 113.86
@@ -112516,10 +112818,10 @@ Maldives
7.09 72.87 72.92
7.08 72.89 72.92
7.07 72.89 72.92
- 7.06 72.93 72.96
- 7.05 72.93 72.96
- 7.04 72.93 72.96
- 7.03 72.96 72.99
+ 7.06 72.93 72.95
+ 7.05 72.93 72.95
+ 7.04 72.93 72.95
+ 7.03 72.96 72.98
7.02 72.96 72.99
7.01 72.96 72.99
7.00 72.88 72.90 72.96 72.99
@@ -112541,8 +112843,8 @@ Maldives
6.83 72.96 73.00 73.08 73.10 73.12 73.15 73.17 73.20
6.82 72.97 73.00 73.12 73.15 73.17 73.20
6.81 73.17 73.20
- 6.79 73.15 73.17
- 6.78 73.15 73.17
+ 6.79 73.14 73.17
+ 6.78 73.14 73.17
6.77 72.90 72.92 73.14 73.17
6.76 72.90 72.92 73.02 73.04 73.13 73.17
6.75 72.90 72.92 73.02 73.04 73.12 73.17
@@ -112560,7 +112862,7 @@ Maldives
6.62 73.02 73.05
6.61 73.02 73.05
6.60 73.02 73.05
- 6.59 73.01 73.04
+ 6.59 73.01 73.03
6.58 73.01 73.04
6.57 72.91 72.96 73.01 73.04
6.56 72.91 72.97 73.01 73.04
@@ -112604,10 +112906,10 @@ Maldives
6.08 73.23 73.26
6.07 73.23 73.26
6.06 73.23 73.25
- 5.99 72.90 72.92
- 5.98 72.90 72.92 73.38 73.40
- 5.97 72.90 72.94 73.37 73.40
- 5.96 72.90 72.94 73.37 73.40
+ 5.99 72.89 72.92
+ 5.98 72.89 72.92 73.37 73.39
+ 5.97 72.89 72.94 73.37 73.39
+ 5.96 72.89 72.94 73.37 73.40
5.95 72.91 72.94 73.37 73.40
5.94 72.92 72.94 73.38 73.40
5.92 73.41 73.43
@@ -112616,10 +112918,10 @@ Maldives
5.89 73.41 73.43
5.87 72.95 72.97
5.86 72.95 72.97
- 5.85 72.95 72.97 73.43 73.46
- 5.84 72.95 72.97 73.42 73.46
- 5.83 73.42 73.46
- 5.82 72.96 72.98 73.42 73.45
+ 5.85 72.95 72.97 73.43 73.45
+ 5.84 72.95 72.97 73.42 73.45
+ 5.83 73.42 73.45
+ 5.82 72.96 72.98 73.42 73.44
5.81 72.96 72.98
5.80 72.96 72.98 73.37 73.39
5.79 72.96 72.98 73.36 73.39
@@ -112632,7 +112934,7 @@ Maldives
5.72 72.98 73.01 73.36 73.40
5.71 72.98 73.01 73.36 73.40
5.70 72.98 73.01 73.36 73.39
- 5.69 72.99 73.01
+ 5.69 72.98 73.01
5.68 72.99 73.02
5.67 72.99 73.02
5.66 72.99 73.02
@@ -112642,9 +112944,9 @@ Maldives
5.55 73.44 73.47
5.54 73.44 73.47
5.53 73.44 73.47
- 5.50 72.86 72.89 73.00 73.02
- 5.49 72.86 72.89 73.00 73.02
- 5.48 72.86 72.89 73.00 73.02
+ 5.50 72.86 72.89 72.99 73.02
+ 5.49 72.86 72.89 72.99 73.02
+ 5.48 72.86 72.89 72.99 73.02
5.47 72.86 72.89 72.92 72.95 72.98 73.02 73.35 73.37
5.46 72.92 72.95 72.98 73.01 73.35 73.37 73.52 73.54
5.45 72.92 72.95 72.98 73.01 73.35 73.37 73.52 73.54
@@ -112657,9 +112959,9 @@ Maldives
5.38 73.62 73.64
5.37 73.30 73.34 73.38 73.40 73.62 73.64
5.36 72.94 72.96 73.30 73.34 73.38 73.41
- 5.35 72.93 72.96 73.30 73.34 73.38 73.41 73.63 73.65
+ 5.35 72.93 72.96 73.30 73.34 73.38 73.41 73.62 73.65
5.34 72.93 72.96 73.38 73.41 73.61 73.65
- 5.33 72.93 72.96 73.61 73.65
+ 5.33 72.93 72.95 73.61 73.65
5.32 73.61 73.63
5.31 73.45 73.48
5.30 73.09 73.12 73.45 73.48
@@ -112667,15 +112969,15 @@ Maldives
5.28 73.09 73.12 73.56 73.60
5.27 73.56 73.60
5.26 73.56 73.59
- 5.25 73.11 73.14 73.48 73.51
- 5.24 72.84 72.87 73.11 73.14 73.48 73.51
- 5.23 72.84 72.87 73.11 73.14 73.48 73.51
+ 5.25 73.11 73.14 73.48 73.50
+ 5.24 72.84 72.87 73.11 73.14 73.48 73.50
+ 5.23 72.84 72.87 73.11 73.14 73.48 73.50
5.22 72.84 72.87
5.18 73.09 73.12
5.17 73.08 73.12
5.16 73.07 73.12
5.15 73.07 73.10
- 5.14 73.03 73.10
+ 5.14 73.03 73.05 73.07 73.10
5.13 73.03 73.06
5.12 73.03 73.06
5.11 73.03 73.06
@@ -112697,13 +112999,13 @@ Maldives
4.70 73.47 73.50
4.64 73.39 73.41
4.63 73.39 73.41 73.54 73.56
- 4.62 73.39 73.41 73.54 73.56
- 4.61 73.39 73.41 73.54 73.56
- 4.60 73.54 73.56
+ 4.62 73.39 73.41 73.53 73.56
+ 4.61 73.39 73.41 73.53 73.56
+ 4.60 73.53 73.56
4.48 73.36 73.38
4.47 73.36 73.38
- 4.46 73.36 73.38 73.69 73.71
- 4.45 73.36 73.38 73.69 73.71
+ 4.46 73.36 73.38 73.68 73.71
+ 4.45 73.36 73.38 73.68 73.71
4.44 72.93 72.96 73.68 73.71
4.43 72.93 72.96 73.68 73.71
4.42 72.93 72.96 73.68 73.71
@@ -112711,25 +113013,24 @@ Maldives
4.40 73.65 73.67
4.39 73.65 73.67
4.38 73.62 73.67
- 4.37 73.60 73.67
+ 4.37 73.59 73.67
4.36 73.59 73.64
4.35 73.57 73.64
4.34 73.57 73.62
4.33 73.57 73.60
4.27 72.93 72.98
4.26 72.93 72.98
- 4.25 72.93 72.98 73.49 73.53
- 4.24 73.49 73.53
- 4.23 73.49 73.53
- 4.22 73.48 73.53
- 4.21 73.48 73.53
- 4.20 73.47 73.53
- 4.19 73.47 73.52
- 4.18 73.46 73.52
- 4.17 73.46 73.52
- 4.16 73.46 73.52
+ 4.25 72.93 72.98 73.53 73.55
+ 4.24 73.52 73.56
+ 4.23 73.52 73.56
+ 4.22 73.51 73.56
+ 4.21 73.51 73.56
+ 4.20 73.42 73.48 73.51 73.55
+ 4.19 73.42 73.55
+ 4.18 73.42 73.54
+ 4.17 73.42 73.54
+ 4.16 73.44 73.53
4.15 73.46 73.52
- 4.14 73.47 73.51
4.12 73.40 73.43
4.11 73.40 73.43 73.49 73.51
4.10 73.40 73.43 73.49 73.51
@@ -112754,15 +113055,15 @@ Maldives
3.77 72.93 72.95
3.76 72.93 72.95
3.75 72.93 72.95
- 3.74 72.94 72.96
- 3.73 72.68 72.70 72.93 72.96
- 3.72 72.68 72.70 72.93 72.96
- 3.71 72.68 72.70 72.93 72.96
- 3.70 72.68 72.70
+ 3.74 72.93 72.96
+ 3.73 72.67 72.70 72.93 72.96
+ 3.72 72.67 72.70 72.93 72.96
+ 3.71 72.67 72.70 72.93 72.96
+ 3.70 72.67 72.70
3.62 72.92 72.95
3.61 72.92 72.95
3.60 72.92 72.95
- 3.56 72.91 72.93
+ 3.56 72.90 72.93
3.55 72.90 72.93
3.54 72.90 72.93
3.53 72.90 72.92
@@ -112781,16 +113082,13 @@ Maldives
3.34 73.50 73.52
3.32 72.82 72.84
3.31 72.82 72.84
- 3.30 72.82 72.84 73.40 73.43
- 3.29 72.82 72.84 73.38 73.45
- 3.28 73.37 73.45
- 3.27 73.37 73.45
- 3.26 73.02 73.04 73.36 73.45
- 3.25 73.01 73.04 73.36 73.45
- 3.24 73.01 73.04 73.36 73.44
- 3.23 73.01 73.04 73.36 73.44
- 3.22 73.37 73.43
- 3.21 73.03 73.05 73.39 73.42
+ 3.30 72.82 72.84
+ 3.29 72.82 72.84
+ 3.26 73.02 73.04
+ 3.25 73.01 73.04
+ 3.24 73.01 73.04
+ 3.23 73.01 73.04
+ 3.21 73.03 73.05
3.20 73.03 73.05
3.19 73.03 73.05
3.18 73.03 73.05
@@ -112804,7 +113102,7 @@ Maldives
2.97 72.85 72.88 73.57 73.59
2.96 72.85 72.88 72.99 73.01 73.55 73.59
2.95 72.85 72.88 72.99 73.02 73.55 73.59
- 2.94 72.85 72.87 72.99 73.02 73.55 73.59
+ 2.94 72.85 72.87 72.99 73.02 73.55 73.58
2.93 72.99 73.02 73.55 73.57
2.91 73.34 73.37
2.90 73.34 73.37 73.53 73.56
@@ -112819,7 +113117,7 @@ Maldives
2.74 73.01 73.04
2.73 73.01 73.04
2.72 73.01 73.03
- 2.70 72.86 72.88
+ 2.70 72.85 72.88
2.69 72.85 72.91
2.68 72.85 72.91
2.67 72.85 72.91
@@ -112869,44 +113167,39 @@ Maldives
1.98 73.30 73.33 73.53 73.56
1.97 73.30 73.33 73.53 73.56
1.96 73.53 73.56
- 1.95 73.53 73.56
+ 1.95 73.53 73.55
1.94 73.54 73.56
- 1.93 73.54 73.56
+ 1.93 73.53 73.56
1.92 73.53 73.56
1.91 73.53 73.56
- 1.90 73.23 73.26 73.53 73.56
+ 1.90 73.23 73.26 73.53 73.55
1.89 73.23 73.26 73.53 73.55
1.88 73.23 73.26 73.52 73.55
1.87 73.23 73.25 73.52 73.54
1.86 73.52 73.54
1.85 73.50 73.54
- 1.84 73.49 73.54
+ 1.84 73.49 73.52
1.83 73.44 73.52
- 1.82 73.44 73.51
- 1.81 73.38 73.41 73.44 73.50
+ 1.82 73.44 73.52
+ 1.81 73.38 73.41 73.44 73.51
1.80 73.35 73.41
1.79 73.35 73.41
1.78 73.35 73.41
1.77 73.35 73.38
- 0.85 73.12 73.14 73.34 73.36
- 0.84 73.12 73.14 73.34 73.36
- 0.83 73.12 73.14 73.34 73.36
- 0.82 73.12 73.14
- 0.81 73.16 73.18
- 0.80 73.15 73.18
- 0.79 73.15 73.18
- 0.78 73.15 73.18
+ 0.85 73.33 73.36
+ 0.84 73.33 73.36
+ 0.83 73.33 73.36
0.77 73.35 73.38
0.76 73.35 73.38
0.75 73.35 73.38
- 0.74 73.36 73.38
+ 0.74 73.35 73.38
0.65 73.37 73.39
0.64 73.37 73.39
0.63 73.37 73.39
0.62 73.37 73.39
- 0.51 73.48 73.50
- 0.50 72.92 72.95 73.48 73.50
- 0.49 72.92 72.95 73.48 73.50
+ 0.51 73.47 73.50
+ 0.50 72.92 72.95 73.47 73.50
+ 0.49 72.92 72.95 73.47 73.50
0.48 72.92 72.95 73.48 73.50
0.47 72.93 72.95
0.41 72.94 72.96
@@ -112916,10 +113209,10 @@ Maldives
0.37 73.49 73.52
0.31 72.97 72.99
0.30 72.97 72.99
- 0.29 72.97 72.99 73.36 73.38
+ 0.29 72.97 72.99 73.35 73.38
0.28 72.97 72.99 73.35 73.38
0.27 73.02 73.04 73.35 73.38
- 0.26 73.02 73.05 73.35 73.37
+ 0.26 73.02 73.05
0.25 73.02 73.05
0.24 73.03 73.05 73.19 73.22
0.23 73.08 73.11 73.19 73.22
@@ -113139,8 +113432,8 @@ Mali
23.10 -6.38 -1.88
23.09 -6.38 -1.87
23.08 -6.38 -1.86
- 23.07 -6.37 -1.84
- 23.06 -6.37 -1.83
+ 23.07 -6.38 -1.84
+ 23.06 -6.38 -1.83
23.05 -6.37 -1.82
23.04 -6.37 -1.80
23.03 -6.37 -1.78
@@ -113261,8 +113554,8 @@ Mali
21.88 -6.23 -0.02
21.87 -6.23 -0.01
21.86 -6.23 0.00
- 21.85 -6.23 0.02
- 21.84 -6.23 0.04
+ 21.85 -6.23 0.01
+ 21.84 -6.23 0.03
21.83 -6.22 0.05
21.82 -6.22 0.07
21.81 -6.22 0.08
@@ -113538,8 +113831,8 @@ Mali
19.11 -5.91 3.13 3.98 4.23
19.10 -5.91 3.15 3.94 4.23
19.09 -5.91 3.17 3.90 4.23
- 19.08 -5.91 3.19 3.85 4.23
- 19.07 -5.91 3.21 3.79 4.23
+ 19.08 -5.91 3.19 3.83 4.23
+ 19.07 -5.91 3.21 3.77 4.23
19.06 -5.90 3.23 3.73 4.23
19.05 -5.90 3.24 3.68 4.23
19.04 -5.90 3.25 3.62 4.23
@@ -113874,7 +114167,7 @@ Mali
15.75 -5.47 3.89
15.74 -5.47 3.89
15.73 -5.47 3.89
- 15.72 -5.47 3.89
+ 15.72 -5.47 3.88
15.71 -5.47 3.88
15.70 -9.36 -9.33 -5.47 3.88
15.69 -9.38 -9.32 -5.47 3.87
@@ -114030,9 +114323,9 @@ Mali
14.19 -12.02 -2.60 -2.27 -2.01
14.18 -12.01 -2.61 -2.25 -2.01
14.17 -12.01 -2.62 -2.23 -2.01
- 14.16 -12.00 -2.63 -2.21 -2.04
- 14.15 -12.00 -2.64 -2.19 -2.06
- 14.14 -12.00 -2.65 -2.17 -2.08
+ 14.16 -12.00 -2.63 -2.21 -2.03
+ 14.15 -12.00 -2.64 -2.19 -2.05
+ 14.14 -12.00 -2.65 -2.17 -2.07
14.13 -12.00 -2.66 -2.13 -2.10
14.12 -12.01 -2.67
14.11 -12.01 -2.68
@@ -114083,8 +114376,8 @@ Mali
13.66 -12.08 -3.24 -3.20 -2.88
13.65 -12.07 -3.24 -3.11 -2.88
13.64 -12.07 -3.24 -3.10 -2.88
- 13.63 -12.06 -3.24 -3.09 -2.90
- 13.62 -12.05 -3.24 -3.08 -2.92
+ 13.63 -12.06 -3.24 -3.09 -2.89
+ 13.62 -12.05 -3.24 -3.08 -2.91
13.61 -12.05 -3.25 -3.08 -3.02 -2.98 -2.94
13.60 -12.05 -3.25 -3.08 -3.03
13.59 -12.04 -3.25 -3.07 -3.05
@@ -114202,12 +114495,12 @@ Mali
12.47 -11.41 -9.33 -9.31 -9.27 -9.24 -4.40
12.46 -11.41 -9.36 -9.20 -4.41
12.45 -11.38 -9.39 -9.16 -4.42
- 12.44 -11.39 -9.39 -9.14 -4.43
- 12.43 -11.39 -9.37 -9.12 -4.43
- 12.42 -11.39 -9.36 -9.10 -4.43
- 12.41 -11.39 -9.34 -9.08 -4.43
- 12.40 -11.39 -9.33 -9.06 -4.42
- 12.39 -11.44 -9.33 -9.04 -4.42
+ 12.44 -11.39 -9.39 -9.13 -4.43
+ 12.43 -11.39 -9.37 -9.11 -4.43
+ 12.42 -11.39 -9.36 -9.09 -4.43
+ 12.41 -11.39 -9.34 -9.07 -4.43
+ 12.40 -11.39 -9.33 -9.05 -4.42
+ 12.39 -11.44 -9.33 -9.03 -4.42
12.38 -11.45 -9.32 -9.02 -4.41
12.37 -11.45 -9.30 -9.00 -4.41
12.36 -11.46 -9.29 -8.99 -4.40
@@ -114240,7 +114533,7 @@ Mali
12.09 -11.42 -11.11 -10.82 -10.49 -9.99 -9.67 -8.93 -4.62
12.08 -11.40 -11.11 -10.81 -10.49 -9.97 -9.67 -8.93 -4.63
12.07 -11.39 -11.12 -10.81 -10.49 -9.93 -9.67 -8.93 -4.63
- 12.06 -11.38 -11.14 -10.81 -10.50 -9.91 -9.67 -8.93 -4.63
+ 12.06 -11.38 -11.14 -10.81 -10.50 -9.91 -9.67 -8.93 -4.64
12.05 -11.38 -11.14 -10.82 -10.50 -9.89 -9.67 -8.93 -4.64
12.04 -11.37 -11.15 -10.82 -10.50 -9.88 -9.68 -8.93 -4.65
12.03 -11.36 -11.15 -10.82 -10.51 -9.82 -9.69 -8.93 -4.71
@@ -114302,7 +114595,7 @@ Mali
11.47 -8.64 -5.21
11.46 -8.62 -5.21
11.45 -8.55 -5.21
- 11.44 -8.55 -5.20
+ 11.44 -8.54 -5.20
11.43 -8.54 -5.20
11.42 -8.54 -5.20
11.41 -8.53 -5.20
@@ -114453,12 +114746,12 @@ Malta
35.93 14.32 14.52
35.92 14.32 14.52
35.91 14.33 14.52
- 35.90 14.33 14.53
- 35.89 14.33 14.55
- 35.88 14.33 14.56
+ 35.90 14.33 14.55
+ 35.89 14.33 14.56
+ 35.88 14.33 14.57
35.87 14.33 14.57
35.86 14.33 14.57
- 35.85 14.35 14.57
+ 35.85 14.34 14.57
35.84 14.36 14.57
35.83 14.37 14.57
35.82 14.39 14.57
@@ -114469,8 +114762,8 @@ Marshall Islands
14.62 169.00 169.02
14.61 168.99 169.02
14.60 168.98 169.02
- 14.59 168.97 169.02
- 14.58 168.97 169.01
+ 14.59 168.97 169.01
+ 14.58 168.97 169.00
14.57 168.97 168.99
11.72 165.27 165.29
11.71 165.27 165.29
@@ -114497,11 +114790,11 @@ Marshall Islands
9.45 170.22 170.25
9.44 170.22 170.25
9.43 170.23 170.25
- 8.91 170.83 170.85
+ 8.91 170.83 170.86
8.90 170.83 170.86
8.89 170.82 170.86
8.88 170.82 170.86
- 8.87 170.82 170.84
+ 8.87 170.82 170.85
8.75 167.73 167.75
8.74 167.72 167.75
8.73 167.72 167.75
@@ -114557,10 +114850,10 @@ Marshall Islands
6.96 171.72 171.76
6.11 171.71 171.73
6.10 171.71 171.74
- 6.09 171.71 171.74
- 6.08 171.71 171.74
- 6.07 171.71 171.74 171.93 172.01
- 6.06 171.71 171.74 171.93 172.03
+ 6.09 171.71 171.75
+ 6.08 171.71 171.75
+ 6.07 171.71 171.75 171.93 172.01
+ 6.06 171.71 171.75 171.93 172.03
6.05 171.93 172.03
6.04 171.95 172.03
6.02 169.72 169.74
@@ -114579,10 +114872,10 @@ Marshall Islands
5.89 169.62 169.66
5.88 169.62 169.66
5.87 169.62 169.66
- 5.86 169.62 169.65
+ 5.86 169.61 169.65
5.85 169.61 169.65
5.84 169.61 169.65
- 5.83 169.61 169.65
+ 5.83 169.61 169.64
5.82 169.60 169.64
5.81 169.58 169.64
5.80 169.58 169.63
@@ -114607,7 +114900,7 @@ Marshall Islands
Martinique
14.88 -61.18 -61.11
14.87 -61.20 -61.09
- 14.86 -61.21 -61.07
+ 14.86 -61.22 -61.07
14.85 -61.22 -61.05
14.84 -61.23 -61.02
14.83 -61.23 -61.00
@@ -114617,21 +114910,21 @@ Martinique
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@@ -114646,15 +114939,15 @@ Martinique
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Mauritania
27.29 -8.69 -8.67
27.28 -8.69 -8.65
@@ -114827,14 +115120,14 @@ Mauritania
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25.49 -12.02 -5.60
25.48 -12.02 -5.58
@@ -115076,8 +115369,8 @@ Mauritania
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23.07 -12.95 -6.35
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23.05 -12.98 -6.35
@@ -115144,8 +115437,8 @@ Mauritania
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22.39 -13.09 -6.27
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22.37 -13.09 -6.27
@@ -115156,13 +115449,13 @@ Mauritania
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@@ -115175,10 +115468,10 @@ Mauritania
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@@ -115206,8 +115499,8 @@ Mauritania
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@@ -115219,9 +115512,9 @@ Mauritania
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@@ -115231,8 +115524,8 @@ Mauritania
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@@ -115279,15 +115572,15 @@ Mauritania
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20.95 -17.07 -16.99 -16.82 -6.11
@@ -115323,13 +115616,13 @@ Mauritania
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20.54 -16.40 -6.05
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@@ -115342,9 +115635,9 @@ Mauritania
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@@ -115411,23 +115704,23 @@ Mauritania
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@@ -115451,7 +115744,7 @@ Mauritania
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@@ -115462,8 +115755,8 @@ Mauritania
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19.19 -16.36 -5.90
@@ -115485,9 +115778,9 @@ Mauritania
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@@ -115525,19 +115818,19 @@ Mauritania
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@@ -115874,7 +116167,7 @@ Mauritania
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15.08 -12.70 -12.65 -12.62 -11.84
@@ -115915,23 +116208,25 @@ Mauritania
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Mauritius
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@@ -115939,17 +116234,17 @@ Mauritius
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@@ -115980,7 +116275,7 @@ Mauritius
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@@ -116051,7 +116346,7 @@ Mexico
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@@ -116062,13 +116357,13 @@ Mexico
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@@ -116115,916 +116410,916 @@ Mexico
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@@ -117789,10 +118084,10 @@ Mexico
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@@ -117848,12 +118143,16 @@ Mexico
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Micronesia
+ 9.78 140.51 140.54
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9.59 138.16 138.20
9.58 138.13 138.20
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@@ -117885,17 +118184,6 @@ Micronesia
8.58 149.65 149.69 150.39 150.41
8.57 149.65 149.68 150.39 150.41
8.56 149.65 149.67 150.39 150.41
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7.47 151.85 151.90
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@@ -117905,7 +118193,7 @@ Micronesia
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7.37 149.17 149.19 151.57 151.66 151.84 151.87
7.36 149.17 149.19 151.58 151.66 151.84 151.87
7.35 151.55 151.66 151.84 151.87
@@ -117955,17 +118243,32 @@ Micronesia
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Midway Islands
28.22 -177.38 -177.31
28.21 -177.39 -177.31
28.20 -177.39 -177.31
28.19 -177.39 -177.31
- 28.18 -177.39 -177.36
+ 28.18 -177.39 -177.37
Moldova
48.49 27.56 27.61
48.48 27.49 27.61
@@ -117976,8 +118279,8 @@ Moldova
48.43 27.29 27.38 27.42 27.82
48.42 27.28 27.84
48.41 27.27 27.86
- 48.40 26.82 26.86 27.01 27.06 27.25 27.87
- 48.39 26.81 26.88 27.01 27.09 27.24 27.88
+ 48.40 26.82 26.86 27.01 27.06 27.26 27.87
+ 48.39 26.81 26.88 27.01 27.09 27.25 27.88
48.38 26.77 26.90 27.01 27.15 27.22 27.89
48.37 26.76 26.93 26.98 27.91
48.36 26.76 27.92
@@ -118005,7 +118308,7 @@ Moldova
48.14 26.95 28.44 28.50 28.65
48.13 26.95 28.44 28.49 28.79
48.12 26.97 28.44 28.49 28.80
- 48.11 27.00 28.43 28.49 28.81
+ 48.11 27.00 28.43 28.48 28.81
48.10 27.02 28.44 28.48 28.81
48.09 27.02 28.45 28.48 28.82
48.08 27.02 28.82
@@ -118015,8 +118318,8 @@ Moldova
48.04 27.04 28.84
48.03 27.06 28.84
48.02 27.07 28.85
- 48.01 27.07 28.86
- 48.00 27.07 28.87
+ 48.01 27.07 28.87
+ 48.00 27.07 28.88
47.99 27.08 28.88 29.08 29.11
47.98 27.12 28.89 29.06 29.13
47.97 27.13 28.91 29.05 29.14
@@ -118168,7 +118471,7 @@ Moldova
46.51 28.20 29.15 29.19 29.97
46.50 28.20 29.12 29.19 30.01
46.49 28.20 29.09 29.19 30.02
- 46.48 28.21 29.06 29.19 30.03
+ 46.48 28.21 29.07 29.19 30.03
46.47 28.21 29.04 29.19 30.03
46.46 28.22 29.01 29.19 30.04
46.45 28.23 28.99 29.19 29.43 29.46 30.06
@@ -118192,7 +118495,7 @@ Moldova
46.27 28.12 28.94
46.26 28.12 28.95
46.25 28.12 28.96
- 46.24 28.09 28.97
+ 46.24 28.09 28.98
46.23 28.09 28.99
46.22 28.09 29.00
46.21 28.10 29.01
@@ -118275,10 +118578,12 @@ Moldova
Monaco
43.77 7.39 7.42
43.76 7.37 7.43
- 43.75 7.36 7.43
- 43.74 7.36 7.43
- 43.73 7.36 7.43
- 43.72 7.36 7.42
+ 43.75 7.36 7.44
+ 43.74 7.35 7.44
+ 43.73 7.35 7.44
+ 43.72 7.35 7.44
+ 43.71 7.35 7.42
+ 43.70 7.37 7.41
Mongolia
52.13 98.87 98.95
52.12 98.85 98.97
@@ -118464,8 +118769,8 @@ Mongolia
50.32 90.77 94.34 98.26 102.91 104.43 104.53 104.59 106.18 106.33 106.72
50.31 90.74 94.34 98.26 102.95 103.05 103.17 104.39 106.20 106.27 106.77
50.30 90.71 94.34 98.25 103.21 104.37 106.79
- 50.29 90.70 94.34 98.25 103.22 104.36 106.81
- 50.28 90.70 94.34 98.24 103.23 104.34 106.83 114.26 114.35
+ 50.29 90.70 94.34 98.25 103.22 104.35 106.81
+ 50.28 90.70 94.34 98.24 103.23 104.33 106.83 114.26 114.35
50.27 90.70 94.35 98.24 103.23 104.32 106.84 114.22 114.38
50.26 90.70 94.35 98.23 103.24 104.31 106.86 114.18 114.41 114.60 114.68
50.25 90.70 94.35 98.22 103.25 104.29 106.88 114.15 114.45 114.51 114.73
@@ -118502,7 +118807,7 @@ Mongolia
49.94 89.69 95.41 95.57 96.27 97.62 107.95 113.41 115.30 115.87 116.56
49.93 89.65 95.43 95.55 96.29 96.45 96.52 97.58 107.96 113.40 115.32 115.84 116.58
49.92 89.63 95.46 95.53 96.31 96.42 96.53 96.69 96.75 97.55 107.96 113.38 115.34 115.81 116.60
- 49.91 89.61 95.48 95.52 96.32 96.40 96.54 96.67 96.84 97.55 107.96 113.36 115.36 115.79 116.61
+ 49.91 89.61 95.47 95.52 96.32 96.40 96.54 96.67 96.84 97.55 107.96 113.36 115.36 115.79 116.61
49.90 89.61 95.50 95.52 96.34 96.38 96.55 96.65 96.92 97.55 107.96 113.34 115.47 115.53 115.60 115.76 116.62
49.89 89.61 96.55 96.63 96.98 97.55 107.96 113.32 115.66 115.73 116.64
49.88 89.61 96.56 96.61 97.00 97.56 107.96 113.30 116.65
@@ -118511,7 +118816,7 @@ Mongolia
49.85 89.60 97.03 97.56 107.94 113.24 116.67
49.84 89.60 97.04 97.54 107.94 113.22 116.68
49.83 89.60 97.05 97.53 107.94 113.20 116.69
- 49.82 89.61 97.08 97.51 107.95 113.18 116.69
+ 49.82 89.61 97.07 97.51 107.95 113.18 116.69
49.81 89.62 97.11 97.49 107.95 113.17 116.69
49.80 89.61 97.12 97.47 107.96 113.16 116.68
49.79 89.61 97.12 97.46 107.96 113.15 116.68
@@ -118542,15 +118847,15 @@ Mongolia
49.54 88.85 88.91 89.19 108.25 112.45 112.53 112.84 116.51
49.53 88.84 88.92 89.18 108.26 112.41 112.60 112.81 116.50
49.52 88.84 88.92 89.16 108.26 112.37 112.63 112.78 116.49
- 49.51 88.84 88.93 89.14 108.26 112.33 112.66 112.75 116.49
+ 49.51 88.84 88.93 89.14 108.26 112.34 112.66 112.75 116.49
49.50 88.60 88.64 88.84 88.94 89.10 108.27 112.30 116.48
- 49.49 88.57 88.65 88.84 88.95 89.06 108.28 112.26 116.47
- 49.48 88.32 88.43 88.54 88.66 88.84 88.96 89.02 108.29 112.23 116.46
- 49.47 88.23 88.67 88.84 88.97 88.99 108.31 112.19 116.45
- 49.46 88.18 88.69 88.84 108.32 112.15 116.45
- 49.45 88.16 88.80 88.85 108.33 112.12 116.44
- 49.44 88.15 108.34 112.08 116.43
- 49.43 88.15 108.36 112.04 116.43
+ 49.49 88.57 88.65 88.84 88.95 89.06 108.28 112.27 116.47
+ 49.48 88.32 88.43 88.54 88.66 88.84 88.96 89.02 108.29 112.24 116.46
+ 49.47 88.23 88.67 88.84 88.97 88.99 108.31 112.20 116.45
+ 49.46 88.18 88.69 88.84 108.32 112.17 116.45
+ 49.45 88.16 88.80 88.85 108.33 112.13 116.44
+ 49.44 88.15 108.34 112.09 116.43
+ 49.43 88.15 108.36 112.05 116.43
49.42 88.14 108.38 111.93 116.42
49.41 88.14 108.40 111.75 116.41
49.40 88.13 108.41 111.63 116.41
@@ -118865,7 +119170,7 @@ Mongolia
46.31 90.88 116.73
46.30 90.88 116.68
46.29 90.88 116.63
- 46.28 90.88 116.59
+ 46.28 90.88 116.60
46.27 90.88 116.57
46.26 90.88 116.56
46.25 90.89 116.56
@@ -119217,27 +119522,27 @@ Mongolia
42.79 96.33 110.44
42.78 96.33 110.43
42.77 96.33 110.43
- 42.76 96.33 97.12 97.24 110.42
- 42.75 96.34 96.98 97.34 110.41
- 42.74 96.34 96.84 97.44 110.39
- 42.73 96.34 96.69 97.55 110.35
- 42.72 96.34 96.55 97.65 110.32
- 42.71 96.34 96.43 97.76 110.29
- 42.70 97.86 110.25
- 42.69 97.96 110.22
- 42.68 98.07 110.19
- 42.67 98.17 110.15
- 42.66 98.27 110.13
- 42.65 98.38 99.95 100.05 110.11
- 42.64 98.48 99.91 100.13 110.10
- 42.63 98.58 99.86 100.21 110.08
- 42.62 98.69 99.82 100.29 110.07
- 42.61 98.79 99.77 100.37 109.95
- 42.60 98.90 99.73 100.45 109.90
- 42.59 99.00 99.68 100.53 109.87
- 42.58 99.10 99.63 100.61 109.84
- 42.57 99.21 99.59 100.69 109.81
- 42.56 99.31 99.54 100.77 109.77
+ 42.76 96.33 97.14 97.24 110.42
+ 42.75 96.34 97.02 97.35 110.41
+ 42.74 96.34 96.90 97.46 110.39
+ 42.73 96.34 96.75 97.57 110.35
+ 42.72 96.34 96.57 97.68 110.32
+ 42.71 96.34 96.43 97.79 110.29
+ 42.70 97.90 110.25
+ 42.69 98.00 110.22
+ 42.68 98.10 110.19
+ 42.67 98.20 110.15
+ 42.66 98.30 110.13
+ 42.65 98.40 99.95 100.05 110.11
+ 42.64 98.50 99.91 100.13 110.10
+ 42.63 98.60 99.87 100.21 110.08
+ 42.62 98.71 99.82 100.29 110.07
+ 42.61 98.81 99.78 100.37 109.95
+ 42.60 98.91 99.73 100.45 109.90
+ 42.59 99.01 99.69 100.53 109.87
+ 42.58 99.11 99.65 100.61 109.84
+ 42.57 99.21 99.60 100.69 109.81
+ 42.56 99.31 99.55 100.77 109.77
42.55 99.41 99.50 100.85 109.74
42.54 100.93 109.71
42.53 101.01 109.68
@@ -119250,47 +119555,47 @@ Mongolia
42.46 101.70 109.54
42.45 101.72 109.52
42.44 101.73 109.50
- 42.43 101.74 108.13 108.25 109.49
- 42.42 101.74 108.05 108.29 108.95 109.05 109.32
- 42.41 101.75 107.97 108.56 108.93 109.18 109.30
- 42.40 101.76 107.88 108.62 108.90
- 42.39 101.77 107.80 108.69 108.88
- 42.38 101.78 107.72 108.75 108.81
- 42.37 101.78 107.64
- 42.36 101.79 107.55
- 42.35 101.80 107.47
- 42.34 101.81 107.39
- 42.33 101.81 107.30
- 42.32 101.82 107.22
- 42.31 101.83 107.14
- 42.30 101.84 107.06
- 42.29 101.85 106.97
+ 42.43 101.74 108.14 108.25 109.49
+ 42.42 101.74 108.08 108.29 108.95 109.05 109.32
+ 42.41 101.75 108.00 108.56 108.93 109.18 109.30
+ 42.40 101.76 107.92 108.62 108.90
+ 42.39 101.77 107.84 108.69 108.88
+ 42.38 101.78 107.75 108.75 108.81
+ 42.37 101.78 107.67
+ 42.36 101.79 107.58
+ 42.35 101.80 107.50
+ 42.34 101.81 107.41
+ 42.33 101.81 107.32
+ 42.32 101.82 107.24
+ 42.31 101.83 107.15
+ 42.30 101.84 107.07
+ 42.29 101.85 106.98
42.28 101.85 106.89
42.27 101.86 106.81
42.26 101.87 106.75
42.25 101.88 106.72
- 42.24 101.89 106.69
- 42.23 101.91 106.66
- 42.22 101.92 106.63
+ 42.24 101.89 106.68
+ 42.23 101.91 106.65
+ 42.22 101.92 106.62
42.21 101.93 106.59
42.20 101.95 106.56
- 42.19 101.96 106.53
- 42.18 101.98 106.50
- 42.17 102.01 106.47
- 42.16 102.05 106.44
- 42.15 102.11 106.41
- 42.14 102.17 106.38
- 42.13 102.23 106.35
- 42.12 102.29 106.32
- 42.11 102.34 106.28
- 42.10 102.40 106.25
- 42.09 102.46 106.22
- 42.08 102.52 106.19
- 42.07 102.57 106.16
- 42.06 102.63 106.13
- 42.05 102.69 106.10
- 42.04 102.75 106.07
- 42.03 102.81 106.04
+ 42.19 101.96 106.52
+ 42.18 101.98 106.49
+ 42.17 102.01 106.46
+ 42.16 102.05 106.43
+ 42.15 102.11 106.40
+ 42.14 102.17 106.36
+ 42.13 102.23 106.33
+ 42.12 102.29 106.30
+ 42.11 102.35 106.27
+ 42.10 102.40 106.24
+ 42.09 102.46 106.21
+ 42.08 102.52 106.18
+ 42.07 102.57 106.15
+ 42.06 102.63 106.12
+ 42.05 102.69 106.09
+ 42.04 102.74 106.06
+ 42.03 102.80 106.03
42.02 102.86 106.00
42.01 102.92 105.97
42.00 102.98 105.94
@@ -119300,20 +119605,20 @@ Mongolia
41.96 103.13 105.83
41.95 103.16 105.80
41.94 103.18 105.77
- 41.93 103.21 105.75
+ 41.93 103.20 105.75
41.92 103.23 105.72
41.91 103.25 105.70
41.90 103.28 105.67
41.89 103.30 105.64
- 41.88 103.33 105.62
+ 41.88 103.32 105.62
41.87 103.35 105.59
- 41.86 103.38 105.57
+ 41.86 103.37 105.57
41.85 103.40 104.47 104.49 105.54
- 41.84 103.43 104.41 104.49 105.51
+ 41.84 103.42 104.41 104.49 105.51
41.83 103.45 104.34 104.49 105.49
- 41.82 103.48 104.28 104.49 105.46
+ 41.82 103.47 104.28 104.49 105.46
41.81 103.50 104.21 104.49 105.44
- 41.80 103.53 104.15 104.49 105.42
+ 41.80 103.52 104.15 104.49 105.42
41.79 103.55 104.08 104.49 105.40
41.78 103.57 104.02 104.49 105.38
41.77 103.60 103.95 104.48 105.36
@@ -119342,10 +119647,10 @@ Montenegro
43.54 18.95 19.02 19.11 19.20
43.53 18.93 19.03 19.09 19.20
43.52 18.91 19.05 19.08 19.20
- 43.51 18.89 19.19
+ 43.51 18.90 19.19
43.50 18.89 19.19
43.49 18.89 19.18
- 43.48 18.89 19.18
+ 43.48 18.89 19.19
43.47 18.90 19.19
43.46 18.92 19.20
43.45 18.93 19.21
@@ -119357,11 +119662,11 @@ Montenegro
43.39 18.99 19.38
43.38 19.00 19.39
43.37 19.00 19.40
- 43.36 18.87 18.91 19.01 19.40
+ 43.36 18.86 18.91 19.01 19.40
43.35 18.81 18.94 19.01 19.41
- 43.34 18.81 18.96 19.02 19.43
+ 43.34 18.81 18.96 19.02 19.42
43.33 18.81 18.96 19.03 19.44
- 43.32 18.79 18.96 19.03 19.46
+ 43.32 18.79 18.96 19.03 19.45
43.31 18.77 18.96 19.02 19.47
43.30 18.75 18.97 19.00 19.48
43.29 18.73 18.98 19.00 19.49
@@ -119369,14 +119674,14 @@ Montenegro
43.27 18.69 19.50
43.26 18.67 19.51
43.25 18.66 19.52
- 43.24 18.65 19.52
+ 43.24 18.65 19.53
43.23 18.65 19.54
- 43.22 18.65 19.56
- 43.21 18.66 19.57
- 43.20 18.65 19.58
+ 43.22 18.65 19.55
+ 43.21 18.65 19.57
+ 43.20 18.64 19.58
43.19 18.63 19.59
43.18 18.62 19.61
- 43.17 18.62 19.65 19.68 19.72
+ 43.17 18.62 19.64 19.68 19.72
43.16 18.61 19.73
43.15 18.61 19.73
43.14 18.61 19.74
@@ -119388,12 +119693,12 @@ Montenegro
43.08 18.61 19.97
43.07 18.61 19.99
43.06 18.61 20.01
- 43.05 18.61 20.02
- 43.04 18.62 20.04
- 43.03 18.50 20.05
+ 43.05 18.61 20.03
+ 43.04 18.62 20.05
+ 43.03 18.50 20.06
43.02 18.47 20.07
- 43.01 18.45 20.08
- 43.00 18.44 20.09
+ 43.01 18.45 20.09
+ 43.00 18.44 20.10
42.99 18.44 20.11
42.98 18.43 20.17
42.97 18.43 20.21
@@ -119401,7 +119706,7 @@ Montenegro
42.95 18.42 20.25
42.94 18.42 20.27
42.93 18.42 20.29
- 42.92 18.42 20.31
+ 42.92 18.42 20.32
42.91 18.42 20.35
42.90 18.43 20.36
42.89 18.44 20.36
@@ -119417,7 +119722,7 @@ Montenegro
42.79 18.43 20.25
42.78 18.44 20.21
42.77 18.44 20.21
- 42.76 18.44 20.21
+ 42.76 18.45 20.21
42.75 18.45 20.07 20.09 20.21
42.74 18.46 20.05 20.11 20.20
42.73 18.47 20.03 20.13 20.19
@@ -119454,16 +119759,16 @@ Montenegro
42.42 18.48 19.50
42.41 18.48 19.48
42.40 18.48 19.47
- 42.39 18.50 18.54 18.56 19.46
+ 42.39 18.50 18.53 18.56 19.46
42.38 18.56 19.45
42.37 18.57 19.43
42.36 18.59 18.66 18.68 19.42
42.35 18.60 18.66 18.68 19.42
42.34 18.68 19.41
- 42.33 18.69 19.41
+ 42.33 18.68 19.41
42.32 18.70 19.41
42.31 18.70 19.41
- 42.30 18.72 19.40
+ 42.30 18.71 19.40
42.29 18.73 19.39
42.28 18.75 19.38
42.27 18.75 18.85 18.87 19.37
@@ -119482,8 +119787,8 @@ Montenegro
42.14 18.99 19.35
42.13 18.99 19.36
42.12 19.00 19.37
- 42.11 19.04 19.38
- 42.10 19.05 19.38
+ 42.11 19.05 19.38
+ 42.10 19.06 19.38
42.09 19.06 19.38
42.08 19.06 19.38
42.07 19.07 19.37
@@ -119517,27 +119822,27 @@ Montserrat
16.79 -62.22 -62.16
16.78 -62.22 -62.15
16.77 -62.22 -62.14
- 16.76 -62.22 -62.14
+ 16.76 -62.23 -62.14
16.75 -62.23 -62.13
- 16.74 -62.23 -62.13
- 16.73 -62.23 -62.13
- 16.72 -62.23 -62.13
- 16.71 -62.23 -62.13
- 16.70 -62.23 -62.12
- 16.69 -62.23 -62.12
- 16.68 -62.22 -62.12
+ 16.74 -62.24 -62.13
+ 16.73 -62.24 -62.13
+ 16.72 -62.24 -62.13
+ 16.71 -62.24 -62.13
+ 16.70 -62.24 -62.13
+ 16.69 -62.23 -62.13
+ 16.68 -62.23 -62.13
16.67 -62.22 -62.13
16.66 -62.19 -62.14
Morocco
- 35.93 -5.42 -5.38
+ 35.93 -5.41 -5.38
35.92 -5.47 -5.38
35.91 -5.48 -5.37
35.90 -5.49 -5.37
35.89 -5.50 -5.36
35.88 -5.52 -5.36
35.87 -5.53 -5.35
- 35.86 -5.54 -5.34
- 35.85 -5.56 -5.33
+ 35.86 -5.55 -5.34
+ 35.85 -5.57 -5.33
35.84 -5.72 -5.33
35.83 -5.73 -5.33
35.82 -5.75 -5.33
@@ -119554,14 +119859,14 @@ Morocco
35.71 -5.95 -5.30
35.70 -5.95 -5.30
35.69 -5.96 -5.26
- 35.68 -5.96 -5.26
+ 35.68 -5.97 -5.26
35.67 -5.97 -5.26
- 35.66 -5.97 -5.26
- 35.65 -5.97 -5.26
- 35.64 -5.98 -5.25
- 35.63 -5.98 -5.25
- 35.62 -5.99 -5.24
- 35.61 -5.99 -5.24
+ 35.66 -5.98 -5.26
+ 35.65 -5.98 -5.26
+ 35.64 -5.99 -5.26
+ 35.63 -5.99 -5.25
+ 35.62 -5.99 -5.25
+ 35.61 -6.00 -5.25
35.60 -6.00 -5.24
35.59 -6.00 -5.23
35.58 -6.01 -5.22
@@ -119591,22 +119896,22 @@ Morocco
35.34 -6.11 -4.91 -3.04 -2.93
35.33 -6.12 -4.90 -3.04 -2.93
35.32 -6.12 -4.87 -3.05 -2.93
- 35.31 -6.12 -4.85 -3.06 -2.94
- 35.30 -6.13 -4.84 -3.71 -3.67 -3.12 -3.09 -3.07 -2.95
- 35.29 -6.13 -4.83 -3.73 -3.65 -3.13 -2.95
- 35.28 -6.14 -4.82 -3.74 -3.64 -3.14 -2.90
- 35.27 -6.14 -4.81 -3.94 -3.90 -3.75 -3.62 -3.16 -2.89
- 35.26 -6.15 -4.78 -3.98 -3.89 -3.75 -3.61 -3.17 -2.88
- 35.25 -6.15 -4.74 -4.02 -3.89 -3.76 -3.59 -3.18 -2.86
- 35.24 -6.16 -4.70 -4.06 -3.88 -3.76 -3.54 -3.21 -2.85
- 35.23 -6.16 -4.67 -4.08 -3.88 -3.76 -3.49 -3.25 -2.84
- 35.22 -6.17 -4.63 -4.11 -3.86 -3.77 -3.44 -3.29 -2.82
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+ 35.31 -6.12 -4.85 -3.06 -2.93
+ 35.30 -6.13 -4.84 -3.71 -3.67 -3.12 -3.09 -3.07 -2.94
+ 35.29 -6.13 -4.82 -3.73 -3.65 -3.13 -2.95
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+ 35.27 -6.14 -4.79 -3.94 -3.90 -3.75 -3.62 -3.16 -2.88
+ 35.26 -6.15 -4.77 -3.98 -3.89 -3.75 -3.61 -3.17 -2.88
+ 35.25 -6.15 -4.75 -4.02 -3.89 -3.76 -3.59 -3.18 -2.86
+ 35.24 -6.16 -4.71 -4.06 -3.89 -3.76 -3.54 -3.21 -2.85
+ 35.23 -6.16 -4.67 -4.09 -3.90 -3.76 -3.49 -3.25 -2.84
+ 35.22 -6.17 -4.63 -4.12 -3.88 -3.77 -3.44 -3.29 -2.82
+ 35.21 -6.17 -4.58 -4.17 -3.41 -3.34 -2.81
35.20 -6.18 -4.52 -4.23 -2.80
35.19 -6.18 -4.46 -4.27 -2.79
35.18 -6.19 -4.42 -4.29 -2.78
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@@ -120290,29 +120595,29 @@ Morocco
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28.08 -12.17 -8.67
28.07 -12.23 -8.67
@@ -120350,9 +120655,9 @@ Morocco
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@@ -120425,17 +120730,17 @@ Morocco
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@@ -120478,8 +120783,8 @@ Morocco
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26.42 -14.19 -11.52
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26.40 -14.21 -11.53
@@ -120495,19 +120800,19 @@ Morocco
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26.12 -14.50 -11.69
@@ -120515,12 +120820,12 @@ Morocco
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@@ -120640,7 +120945,7 @@ Morocco
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@@ -120662,7 +120967,7 @@ Morocco
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@@ -120718,7 +121023,7 @@ Morocco
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@@ -120740,20 +121045,20 @@ Morocco
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23.67 -16.01 -15.93 -15.86 -13.89
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@@ -120787,22 +121092,22 @@ Morocco
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23.17 -16.15 -14.07
@@ -120814,9 +121119,9 @@ Morocco
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23.03 -16.16 -14.10
@@ -120834,7 +121139,7 @@ Morocco
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22.85 -16.31 -14.13
@@ -120892,7 +121197,7 @@ Morocco
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22.28 -16.71 -14.22
22.27 -16.72 -14.23
@@ -120947,18 +121252,18 @@ Morocco
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21.61 -16.98 -14.64
@@ -120982,6 +121287,7 @@ Morocco
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Mozambique
-10.45 40.44 40.46
-10.46 40.42 40.47 40.50 40.52
@@ -121001,7 +121307,7 @@ Mozambique
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@@ -121009,8 +121315,8 @@ Mozambique
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@@ -121160,7 +121466,7 @@ Mozambique
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@@ -121201,9 +121507,9 @@ Mozambique
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@@ -121238,13 +121544,13 @@ Mozambique
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@@ -121301,7 +121607,7 @@ Mozambique
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@@ -121352,15 +121658,15 @@ Mozambique
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@@ -121391,9 +121697,9 @@ Mozambique
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@@ -121453,18 +121759,18 @@ Mozambique
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@@ -121481,10 +121787,10 @@ Mozambique
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@@ -121557,30 +121863,30 @@ Mozambique
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@@ -121589,7 +121895,7 @@ Mozambique
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@@ -121988,9 +122294,9 @@ Mozambique
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@@ -122090,19 +122396,19 @@ Mozambique
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@@ -122152,8 +122458,8 @@ Mozambique
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@@ -122181,10 +122487,10 @@ Mozambique
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@@ -122321,8 +122627,8 @@ Mozambique
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@@ -122343,7 +122649,7 @@ Mozambique
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@@ -122365,7 +122671,7 @@ Mozambique
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@@ -122478,18 +122784,18 @@ Mozambique
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@@ -122504,14 +122810,14 @@ Mozambique
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@@ -122521,17 +122827,17 @@ Mozambique
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@@ -122620,7 +122926,7 @@ Mozambique
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@@ -122706,7 +123012,7 @@ Myanmar
27.78 97.05 98.21
27.77 97.05 98.22
27.76 97.05 98.22
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27.74 96.99 98.22
27.73 96.98 98.21
27.72 96.97 98.22
@@ -122771,7 +123077,7 @@ Myanmar
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27.11 95.94 97.02 97.12 98.69
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27.09 95.93 98.72
27.08 95.92 98.73
27.07 95.91 98.74
@@ -122936,7 +123242,7 @@ Myanmar
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25.47 94.66 98.11
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25.44 94.63 98.12
25.43 94.62 98.12
25.42 94.61 98.12
@@ -123095,7 +123401,7 @@ Myanmar
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23.88 93.34 94.08 94.12 97.62 97.64 98.67
23.87 93.34 94.08 94.12 98.67
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23.85 93.34 98.68
23.84 93.34 98.68
23.83 93.34 98.68
@@ -123399,7 +123705,7 @@ Myanmar
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20.84 92.31 100.63
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20.81 92.33 100.38 100.40 100.59
20.80 92.33 100.36 100.44 100.57
20.79 92.33 100.36 100.49 100.55
@@ -123413,7 +123719,7 @@ Myanmar
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20.70 92.36 100.24
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20.67 92.39 100.21
20.66 92.41 100.21
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20.44 92.61 92.78 92.82 100.14
20.43 92.62 92.74 92.82 100.14
20.42 92.63 92.74 92.82 99.91 99.94 100.13
@@ -123468,7 +123774,7 @@ Myanmar
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20.12 92.84 92.90 92.96 99.49
20.11 92.85 92.89 92.96 99.48
20.10 92.96 99.14 99.19 99.47
@@ -123478,8 +123784,8 @@ Myanmar
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20.05 92.89 93.32 93.34 99.03 99.28 99.34
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20.00 92.92 92.98 93.02 93.17 93.39 99.02
19.99 92.93 92.99 93.02 93.17 93.39 99.01
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19.90 92.98 93.02 93.07 93.13 93.16 93.21 93.39 93.49 93.53 99.01
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19.85 92.99 93.03 93.10 93.14 93.19 93.24 93.41 93.51 93.63 99.01
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19.83 93.00 93.03 93.11 93.16 93.20 93.24 93.42 93.51 93.61 99.01
19.82 93.00 93.03 93.12 93.16 93.20 93.24 93.42 93.51 93.61 99.01
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19.80 93.14 93.17 93.43 93.51 93.59 99.00
19.79 93.15 93.17 93.43 93.52 93.59 99.00
19.78 93.44 93.52 93.59 98.03 98.05 98.99
@@ -123521,12 +123827,12 @@ Myanmar
19.63 93.72 98.02
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19.54 93.65 93.75 93.80 97.84
19.53 93.64 93.76 93.81 97.84
19.52 93.63 93.77 93.83 97.85
@@ -123549,9 +123855,9 @@ Myanmar
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19.29 93.49 93.72 93.75 97.81
19.28 93.49 93.73 93.76 97.81
19.27 93.50 93.73 93.77 97.80
@@ -123579,10 +123885,10 @@ Myanmar
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18.98 93.71 93.99 94.02 97.72
18.97 93.72 93.99 94.02 97.72
18.96 93.74 93.99 94.03 97.72
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18.44 94.29 97.43
18.43 94.30 97.43
18.42 94.31 97.44
@@ -123647,7 +123953,7 @@ Myanmar
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18.35 94.35 97.45
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18.33 94.38 97.46 97.55 97.61
18.32 94.39 97.47 97.55 97.63
18.31 94.32 94.35 94.39 97.48 97.54 97.64
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17.57 94.54 97.90
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17.55 94.54 97.93
17.54 94.54 97.94
17.53 94.54 97.96
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17.22 94.49 96.86 97.06 98.22
17.21 94.49 96.86 97.06 98.23
17.20 94.50 96.85 97.07 98.24
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17.18 94.44 96.86 97.07 98.25
17.17 94.44 96.86 97.08 98.25
17.16 94.44 96.87 97.08 98.26
@@ -123801,41 +124107,41 @@ Myanmar
16.83 94.38 96.85 97.19 98.52
16.82 94.39 96.85 97.19 98.53
16.81 94.39 96.84 97.20 98.53
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11.72 98.01 98.09 98.24 98.33 98.36 98.56 98.60 98.72 98.79 99.62
@@ -124326,7 +124632,7 @@ Myanmar
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11.52 98.17 98.29 98.51 98.54 98.70 99.45
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10.93 97.90 97.95 98.10 98.23 98.49 98.51 98.70 99.00 99.03 99.06
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Namibia
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@@ -125144,7 +125450,7 @@ Namibia
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@@ -125168,7 +125474,7 @@ Namibia
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@@ -125189,10 +125495,10 @@ Namibia
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@@ -125212,9 +125518,9 @@ Namibia
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@@ -125262,7 +125568,7 @@ Namibia
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@@ -125309,21 +125615,21 @@ Namibia
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@@ -125365,8 +125671,8 @@ Namibia
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@@ -125389,11 +125695,11 @@ Namibia
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@@ -125420,9 +125726,9 @@ Namibia
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@@ -125502,7 +125808,7 @@ Namibia
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@@ -125534,7 +125840,7 @@ Namibia
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@@ -125597,8 +125903,8 @@ Namibia
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@@ -125607,7 +125913,7 @@ Namibia
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@@ -125673,7 +125979,7 @@ Namibia
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@@ -125747,7 +126053,7 @@ Nepal
30.23 81.36 82.09
30.22 80.87 80.89 81.36 82.11
30.21 80.85 80.89 81.35 82.13
- 30.20 80.85 80.90 80.96 81.01 81.35 82.15
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30.19 80.84 81.01 81.34 82.16
30.18 80.82 81.02 81.34 82.16
30.17 80.82 81.03 81.34 82.16
@@ -125759,7 +126065,7 @@ Nepal
30.11 80.79 81.06 81.25 82.13
30.10 80.78 81.06 81.25 82.14
30.09 80.76 81.07 81.26 82.14
- 30.08 80.75 81.08 81.26 82.14
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30.07 80.74 81.08 81.24 82.15 82.18 82.22
30.06 80.73 81.08 81.21 82.24
30.05 80.73 81.09 81.21 82.25
@@ -125887,7 +126193,7 @@ Nepal
28.83 80.02 84.40
28.82 80.02 84.41
28.81 80.04 84.42
- 28.80 80.06 84.43
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28.79 80.09 84.43
28.78 80.11 84.43
28.77 80.11 84.44
@@ -125901,7 +126207,7 @@ Nepal
28.69 80.24 84.62
28.68 80.25 84.63
28.67 80.28 84.67
- 28.66 80.28 80.51 80.53 84.69
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28.65 80.29 80.50 80.54 84.69
28.64 80.29 80.49 80.54 84.69 85.02 85.08
28.63 80.30 80.49 80.55 84.69 85.01 85.10
@@ -125930,8 +126236,8 @@ Nepal
28.40 80.98 85.09
28.39 80.98 85.09
28.38 80.99 85.09
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28.35 81.15 85.09
28.34 81.16 85.09 85.66 85.70
28.33 81.17 85.09 85.66 85.70
@@ -125985,7 +126291,7 @@ Nepal
27.85 81.81 81.91 82.09 87.13 87.32 87.39 87.77 88.17
27.84 81.83 81.90 82.11 87.15 87.31 87.39 87.49 87.56 87.76 88.17
27.83 81.86 81.89 82.13 87.27 87.30 87.39 87.44 87.56 87.62 87.65 87.74 88.17
- 27.82 82.15 87.57 87.60 87.68 87.72 88.17
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27.81 82.17 88.17
27.80 82.18 88.16
27.79 82.20 88.16
@@ -126116,7 +126422,7 @@ Nepal
26.54 86.41 87.01 87.03 88.10
26.53 86.43 86.99 87.03 88.09
26.52 86.45 86.98 87.03 88.09
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26.50 86.50 86.92 87.04 88.09
26.49 86.51 86.90 87.04 88.09
26.48 86.52 86.88 87.04 88.09
@@ -126128,7 +126434,7 @@ Nepal
26.42 86.64 86.74 86.76 86.83 87.07 87.76 87.79 87.83 87.89 88.07
26.41 86.66 86.73 87.08 87.75 87.89 88.06
26.40 86.68 86.72 87.08 87.40 87.48 87.75 87.89 88.06
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26.38 87.11 87.36 87.52 87.63 87.91 88.04
26.37 87.22 87.35 87.54 87.62 87.93 88.03
26.36 87.23 87.34 87.56 87.60 87.95 88.02
@@ -126139,7 +126445,7 @@ Netherlands
53.56 6.43 6.49
53.55 6.43 6.52
53.54 6.43 6.52
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53.52 6.26 6.33 6.47 6.50
53.51 6.16 6.34
53.50 6.13 6.34
@@ -126150,16 +126456,16 @@ Netherlands
53.45 5.46 5.59 5.62 5.96 6.11 6.18 6.53 6.86
53.44 5.41 5.59 5.62 5.93 6.11 6.15 6.45 6.87
53.43 5.36 5.58 5.62 5.88 6.37 6.87
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53.40 5.20 5.49 5.92 6.89
53.39 5.16 5.48 5.88 6.89
53.38 5.16 5.41 5.86 6.90
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53.32 5.03 5.08 5.63 7.01
53.31 5.01 5.11 5.58 7.09
53.30 4.99 5.11 5.56 7.09
@@ -126173,14 +126479,14 @@ Netherlands
53.22 4.86 4.95 5.42 7.20
53.21 4.86 4.94 5.42 7.20
53.20 4.89 4.93 5.41 7.20
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53.18 4.82 4.90 5.40 7.20
53.17 4.81 4.90 5.40 7.20
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53.11 4.74 4.92 5.37 7.19
53.10 4.73 4.92 5.36 7.19
53.09 4.72 4.92 5.30 7.19
@@ -126188,18 +126494,18 @@ Netherlands
53.07 4.71 4.91 5.26 7.20
53.06 4.70 4.90 5.24 7.20
53.05 4.70 4.89 5.22 7.20
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53.00 4.70 4.81 5.13 7.20
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52.96 4.72 4.83 5.05 7.19
52.95 4.72 4.83 4.98 7.19
52.94 4.71 4.83 4.96 7.18
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52.92 4.71 4.86 4.92 7.17
52.91 4.71 7.16
52.90 4.71 7.15
@@ -126209,18 +126515,18 @@ Netherlands
52.86 4.69 7.10
52.85 4.69 7.09
52.84 4.68 7.08
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52.75 4.64 7.06
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52.71 4.62 7.05
52.70 4.62 7.05
52.69 4.62 7.05
@@ -126283,7 +126589,7 @@ Netherlands
52.12 4.27 6.86
52.11 4.26 6.85
52.10 4.24 6.84
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52.08 4.22 6.74
52.07 4.21 6.73
52.06 4.19 6.72
@@ -126303,30 +126609,30 @@ Netherlands
51.92 4.02 6.78
51.91 4.02 6.77
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51.86 4.02 6.55
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51.83 3.87 6.07 6.09 6.16 6.27 6.39 6.42 6.47
51.82 3.85 6.02 6.33 6.39
51.81 3.85 6.00 6.33 6.39
51.80 3.85 5.96
51.79 3.85 5.96
51.78 3.86 3.95 3.99 5.97
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51.76 4.03 5.97
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51.74 3.70 3.98 4.04 5.97
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51.71 3.67 4.02 4.05 6.03
51.70 3.67 4.03 4.06 6.03
51.69 3.67 4.06 4.10 6.03
51.68 3.67 6.03
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51.65 3.87 6.10
51.64 3.88 6.10
51.63 3.89 6.10
@@ -126345,38 +126651,38 @@ Netherlands
51.50 3.45 6.20
51.49 3.47 6.21
51.48 3.48 6.21
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51.46 3.51 4.73 4.81 6.21
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51.44 3.52 4.41 4.51 4.70 4.80 5.01 5.05 6.21
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51.42 3.51 3.56 3.71 3.94 3.97 4.00 4.02 4.39 4.51 4.68 4.75 4.99 5.06 6.21
51.41 3.48 3.59 3.73 3.93 3.96 4.39 4.51 4.66 4.75 4.98 5.05 6.21
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51.39 3.36 3.68 3.78 3.91 3.95 4.06 4.10 4.42 4.77 4.95 5.05 6.21
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51.37 3.33 3.73 3.90 4.12 4.15 4.42 5.05 6.21
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51.35 3.33 4.23 4.25 4.42 5.07 6.21
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51.33 3.34 4.22 5.09 6.20
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51.31 3.34 4.20 5.10 6.17
51.30 3.34 4.19 5.10 6.15
51.29 3.34 4.18 5.13 6.14
51.28 3.34 4.17 5.20 6.13
51.27 3.34 4.15 5.20 6.13
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51.25 3.35 3.51 3.72 4.10 5.20 5.42 5.52 6.11
51.24 3.36 3.51 3.76 4.07 5.20 5.26 5.32 5.40 5.52 6.10
51.23 3.38 3.51 3.76 4.04 5.53 6.09
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51.18 5.59 6.16
51.17 5.63 6.16
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51.15 5.74 6.15
51.14 5.75 6.15
51.13 5.81 6.15
@@ -126386,7 +126692,7 @@ Netherlands
51.09 5.79 6.05
51.08 5.79 6.03
51.07 5.76 6.01
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51.05 5.75 5.98
51.04 5.75 5.97
51.03 5.75 5.96
@@ -126404,22 +126710,22 @@ Netherlands
50.91 5.68 6.07
50.90 5.66 6.07
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50.82 5.61 6.01
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50.77 5.67 6.00
50.76 5.67 6.00
50.75 5.67 6.00
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Netherlands Antilles
17.65 -63.25 -63.22
17.64 -63.25 -63.22
@@ -126427,29 +126733,30 @@ Netherlands Antilles
17.62 -63.26 -63.21
17.61 -63.26 -63.21
17.60 -63.24 -63.21
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12.30 -68.41 -68.34
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12.25 -68.42 -68.25
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12.22 -68.41 -68.18
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12.17 -68.29 -68.20
12.16 -68.29 -68.19
12.15 -68.29 -68.19
@@ -126461,39 +126768,13 @@ Netherlands Antilles
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12.08 -68.29 -68.21
12.07 -68.29 -68.21
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12.05 -68.28 -68.21
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12.03 -68.27 -68.21
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12.01 -68.26 -68.22
New Caledonia
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@@ -126506,12 +126787,12 @@ New Caledonia
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@@ -126561,10 +126842,10 @@ New Caledonia
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-20.51 164.16 164.79 166.56 166.61
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@@ -126573,7 +126854,7 @@ New Caledonia
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@@ -126596,10 +126877,10 @@ New Caledonia
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@@ -126614,7 +126895,7 @@ New Caledonia
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@@ -126626,7 +126907,7 @@ New Caledonia
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-21.13 164.81 165.56 167.27 167.43
-21.14 164.81 165.58 167.31 167.43
@@ -126651,7 +126932,7 @@ New Caledonia
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-21.39 165.01 165.93 167.79 167.98
@@ -126671,14 +126952,14 @@ New Caledonia
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-21.54 165.24 166.18 167.87 168.14
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-21.65 165.46 166.38 167.96 168.09
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@@ -126732,7 +127013,7 @@ New Caledonia
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@@ -126747,10 +127028,10 @@ New Caledonia
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@@ -126812,12 +127093,12 @@ New Zealand
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@@ -126871,9 +127152,9 @@ New Zealand
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@@ -126888,12 +127169,12 @@ New Zealand
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@@ -126911,14 +127192,14 @@ New Zealand
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@@ -126931,11 +127212,11 @@ New Zealand
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@@ -126943,32 +127224,32 @@ New Zealand
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@@ -127005,10 +127286,10 @@ New Zealand
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@@ -127016,9 +127297,9 @@ New Zealand
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@@ -127026,8 +127307,8 @@ New Zealand
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@@ -127042,18 +127323,18 @@ New Zealand
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@@ -127082,7 +127363,7 @@ New Zealand
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@@ -127127,8 +127408,8 @@ New Zealand
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@@ -127164,7 +127445,7 @@ New Zealand
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@@ -127175,7 +127456,7 @@ New Zealand
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@@ -127196,11 +127477,11 @@ New Zealand
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@@ -127234,11 +127515,11 @@ New Zealand
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@@ -127331,12 +127612,12 @@ New Zealand
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@@ -127440,23 +127721,23 @@ New Zealand
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@@ -127464,21 +127745,21 @@ New Zealand
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@@ -127487,14 +127768,14 @@ New Zealand
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@@ -127524,16 +127805,16 @@ New Zealand
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@@ -127557,12 +127838,12 @@ New Zealand
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@@ -127607,10 +127888,10 @@ New Zealand
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@@ -127627,8 +127908,8 @@ New Zealand
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@@ -127636,7 +127917,7 @@ New Zealand
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@@ -127677,8 +127958,8 @@ New Zealand
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@@ -127693,8 +127974,8 @@ New Zealand
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@@ -127740,24 +128021,24 @@ New Zealand
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@@ -127767,27 +128048,27 @@ New Zealand
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@@ -127859,12 +128140,12 @@ New Zealand
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@@ -127945,7 +128226,7 @@ New Zealand
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@@ -127968,7 +128249,7 @@ New Zealand
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@@ -127988,13 +128269,13 @@ New Zealand
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@@ -128024,16 +128305,16 @@ New Zealand
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@@ -128069,14 +128350,14 @@ New Zealand
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@@ -128105,7 +128386,7 @@ New Zealand
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@@ -128118,7 +128399,7 @@ New Zealand
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@@ -128161,31 +128442,31 @@ New Zealand
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Nicaragua
15.04 -83.40 -83.37
15.03 -83.40 -83.36
15.02 -83.51 -83.47 -83.40 -83.34
15.01 -83.52 -83.47 -83.41 -83.26
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14.97 -83.53 -83.12
14.96 -83.55 -83.13
14.95 -83.55 -83.15
@@ -128208,38 +128489,38 @@ Nicaragua
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14.74 -85.01 -84.72 -84.27 -84.19 -84.14 -83.27
14.73 -85.02 -84.71 -84.27 -84.19 -84.15 -83.27
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@@ -128321,7 +128602,7 @@ Nicaragua
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13.45 -86.74 -83.53
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13.26 -86.90 -83.55
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11.29 -85.92 -83.85
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11.11 -85.80 -85.65 -85.44 -83.80
11.10 -85.79 -85.66 -85.42 -83.80
@@ -128579,10 +128860,10 @@ Nicaragua
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10.98 -85.08 -84.80 -84.50 -83.72
@@ -128668,10 +128949,10 @@ Niger
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23.01 11.08 13.74
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22.95 10.98 13.82 14.86 15.00
22.94 10.96 13.83 14.84 15.00
22.93 10.94 13.84 14.82 15.00
@@ -129167,7 +129448,7 @@ Niger
18.03 4.22 15.58
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17.99 4.22 15.57
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@@ -129278,7 +129559,7 @@ Niger
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16.88 4.18 15.47
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@@ -129393,7 +129674,7 @@ Niger
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15.73 3.86 14.37
15.72 3.86 14.36
15.71 3.85 14.36
@@ -129517,7 +129798,7 @@ Niger
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@@ -129525,16 +129806,16 @@ Niger
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@@ -129585,24 +129866,24 @@ Niger
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13.68 0.58 4.53 6.00 13.33
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13.64 0.75 4.43 6.10 6.19 6.30 13.29
13.63 0.75 4.41 6.11 6.17 6.32 13.28
13.62 0.76 4.40 6.33 13.27
@@ -129632,16 +129913,16 @@ Niger
13.38 1.13 4.13 6.59 12.81
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13.28 0.96 4.13 6.68 7.71 8.09 10.33 11.68 12.69
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13.25 0.96 4.13 6.69 7.66 8.13 10.19 11.78 12.59
13.24 0.96 4.13 6.70 7.64 8.15 10.14 11.80 12.58
13.23 0.96 4.13 6.70 7.63 8.16 10.11 11.83 12.57
@@ -129649,13 +129930,13 @@ Niger
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13.17 0.96 4.12 6.73 7.52 8.27 10.01 11.94 12.56
13.16 0.96 4.12 6.74 7.51 8.27 9.99 11.96 12.56
13.15 0.96 4.12 6.74 7.49 8.28 9.98 11.98 12.55
13.14 0.96 4.12 6.75 7.47 8.29 9.96 11.99 12.55
13.13 0.96 4.12 6.75 7.46 8.30 9.94 12.00 12.54
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13.11 0.96 4.11 6.77 7.42 8.32 9.92 12.02 12.50
13.10 0.96 4.11 6.78 7.21 7.24 7.40 8.34 9.91 12.04 12.18 12.21 12.50
13.09 0.96 4.11 6.79 7.19 7.29 7.38 8.35 9.91 12.08 12.17 12.23 12.50
@@ -129670,24 +129951,24 @@ Niger
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12.86 1.24 4.01 8.82 9.69
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12.79 1.33 3.96 9.22 9.32 9.53 9.62
12.78 1.34 3.96
12.77 1.35 3.95
@@ -129805,24 +130086,24 @@ Nigeria
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13.77 4.76 4.88 5.27 5.85
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13.74 4.64 4.96 5.00 5.93
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13.67 4.42 6.11 6.18 6.31 13.28 13.64
13.66 4.40 6.13 6.16 6.33 13.27 13.65
13.65 4.39 6.34 13.26 13.65
@@ -129832,37 +130113,37 @@ Nigeria
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13.53 4.26 6.48 12.98 13.74
13.52 4.25 6.49 12.96 13.75
13.51 4.24 6.50 12.94 13.76
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13.49 4.20 6.52 12.83 13.77
13.48 4.11 6.53 12.83 13.78
13.47 4.11 6.54 12.83 13.79
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13.41 4.11 6.60 12.80 13.83
13.40 4.11 6.61 12.78 13.84
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13.31 4.11 6.69 7.70 8.10 10.32 11.69 12.62 12.65 12.68 13.90
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13.27 4.11 6.71 7.63 8.16 10.13 11.81 12.57 13.93
13.26 4.11 6.72 7.62 8.17 10.10 11.84 12.56 13.94
13.25 4.11 6.72 7.60 8.19 10.08 11.86 12.55 13.95
@@ -129870,13 +130151,13 @@ Nigeria
13.23 4.11 6.73 7.57 8.21 10.05 11.90 12.54 13.96
13.22 4.11 6.74 7.55 8.25 10.03 11.92 12.54 13.97
13.21 4.11 6.74 7.53 8.27 10.02 11.93 12.53 13.98
- 13.20 4.10 6.75 7.51 8.28 10.00 11.95 12.52 13.98
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13.19 4.10 6.75 7.50 8.29 9.98 11.97 12.52 13.99
13.18 4.10 6.76 7.48 8.29 9.97 11.99 12.52 14.00
- 13.17 4.10 6.76 7.46 8.30 9.95 12.00 12.53 14.00
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13.16 4.10 6.77 7.45 8.31 9.93 12.01 12.53 14.01
13.15 4.10 6.77 7.43 8.32 9.92 12.02 12.51 14.02
- 13.14 4.09 6.78 7.41 8.33 9.91 12.03 12.48 14.03
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13.13 4.09 6.79 7.20 7.25 7.39 8.35 9.90 12.05 12.17 12.22 12.48 14.03
13.12 4.09 6.80 7.18 7.30 7.37 8.36 9.89 12.09 12.16 12.24 12.48 14.04
13.11 4.09 6.81 7.17 8.37 9.89 12.27 12.48 14.05
@@ -129889,45 +130170,45 @@ Nigeria
13.04 4.08 6.88 7.11 8.58 9.81 14.08
13.03 4.08 6.89 7.10 8.59 9.80 14.08
13.02 4.07 6.90 7.09 8.60 9.79 14.08
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13.00 4.07 8.61 9.77 14.09
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12.95 4.04 8.65 9.73 14.10
12.94 4.03 8.67 9.72 14.10
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12.81 3.94 14.13
12.80 3.94 14.13
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12.76 3.91 14.14
12.75 3.90 14.14
12.74 3.89 14.14
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12.71 3.87 14.15
12.70 3.86 14.15
12.69 3.85 14.15
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12.67 3.82 14.16
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12.65 3.79 14.16
12.64 3.78 14.16
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12.62 3.75 14.17
12.61 3.74 14.17
12.60 3.72 14.17
@@ -129943,8 +130224,8 @@ Nigeria
12.50 3.63 14.18
12.49 3.63 14.18
12.48 3.63 14.18
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12.45 3.63 14.19
12.44 3.63 14.19
12.43 3.63 14.19
@@ -130097,7 +130378,7 @@ Nigeria
10.96 3.72 13.76
10.95 3.73 13.76
10.94 3.73 13.76
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10.92 3.73 13.75
10.91 3.74 13.74
10.90 3.74 13.74
@@ -130181,7 +130462,7 @@ Nigeria
10.12 3.65 13.43
10.11 3.64 13.42
10.10 3.63 13.40
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10.08 3.60 13.32
10.07 3.60 13.28
10.06 3.59 13.26
@@ -130321,7 +130602,7 @@ Nigeria
8.72 2.71 12.71
8.71 2.71 12.71
8.70 2.71 12.70
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8.68 2.72 12.69
8.67 2.72 12.69
8.66 2.72 12.68
@@ -130333,9 +130614,9 @@ Nigeria
8.60 2.72 12.46 12.48 12.59
8.59 2.72 12.45 12.50 12.57
8.58 2.72 12.44
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8.54 2.73 12.41
8.53 2.73 12.41
8.52 2.73 12.41
@@ -130418,7 +130699,7 @@ Nigeria
7.75 2.71 12.05
7.74 2.71 12.04
7.73 2.71 12.04
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7.71 2.70 12.03
7.70 2.70 12.02
7.69 2.70 12.02
@@ -130538,29 +130819,29 @@ Nigeria
6.55 2.72 9.71 11.05 11.42
6.54 2.71 9.71 11.05 11.42
6.53 2.71 9.70 11.05 11.41
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6.51 2.70 9.69 11.06 11.41
6.50 2.70 9.62 11.06 11.41
6.49 2.70 9.60 11.06 11.40
6.48 2.70 9.59 11.06 11.40
6.47 2.70 9.58 11.06 11.40
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6.45 2.69 9.57 11.07 11.38
6.44 2.69 9.57 11.08 11.37
6.43 2.69 9.56 11.08 11.36
6.42 2.69 9.54 11.10 11.27 11.29 11.33
6.41 2.69 3.77 3.93 9.52 11.24 11.26
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6.33 4.41 9.44
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6.29 4.50 9.34
6.28 4.52 9.33
6.27 4.53 9.33
@@ -130721,7 +131002,7 @@ Nigeria
4.72 5.54 8.34 8.41 8.54
4.71 5.54 8.34 8.45 8.54
4.70 5.54 8.34 8.45 8.54
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4.68 5.54 8.33
4.67 5.55 8.33
4.66 5.55 8.35
@@ -130736,33 +131017,33 @@ Nigeria
4.57 5.63 7.18 7.21 7.28 7.33 8.32
4.56 5.64 7.18 7.21 7.30 7.35 8.31
4.55 5.65 7.17 7.22 7.32 7.40 7.50 7.52 8.31
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4.36 5.86 6.88 6.95 7.02
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4.30 5.98 6.41
4.29 6.03 6.23 6.25 6.37
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4.27 6.07 6.20
4.26 6.08 6.17
Niue
@@ -130770,7 +131051,7 @@ Niue
-18.96 -169.90 -169.81
-18.97 -169.91 -169.81
-18.98 -169.91 -169.80
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@@ -130778,10 +131059,10 @@ Niue
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-19.13 -169.94 -169.84
@@ -130799,6 +131080,7 @@ Norfolk Island
-29.06 167.91 167.99
-29.07 167.91 167.98
-29.08 167.95 167.97
+ -29.09 167.95 167.97
North Korea
43.02 129.91 129.93
43.01 129.89 129.95
@@ -130871,23 +131153,23 @@ North Korea
42.34 129.21 130.67
42.33 129.22 130.67
42.32 129.18 130.68
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42.24 129.17 130.41
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42.22 129.17 130.37
42.21 129.18 130.36
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42.14 129.05 130.21
42.13 129.04 130.21
42.12 129.02 130.21
@@ -130896,14 +131178,14 @@ North Korea
42.09 128.95 130.20
42.08 128.94 130.18
42.07 128.94 130.17
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42.01 128.12 128.48 128.52 130.05
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41.98 128.01 130.04
41.97 128.01 130.01
41.96 128.01 130.01
@@ -130914,60 +131196,60 @@ North Korea
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41.75 126.68 126.72 126.84 127.03 128.12 129.86
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41.73 126.66 126.75 126.79 127.05 128.13 129.78
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41.46 126.50 127.61 127.86 128.02 128.21 129.68
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41.36 126.44 129.81
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41.34 126.42 129.80
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@@ -130976,20 +131258,20 @@ North Korea
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41.10 126.13 129.73
@@ -131007,108 +131289,108 @@ North Korea
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@@ -131118,51 +131400,51 @@ North Korea
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@@ -131170,7 +131452,7 @@ North Korea
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@@ -131190,29 +131472,29 @@ North Korea
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37.76 125.27 125.63 126.08 126.17 126.56 126.61
37.75 125.26 125.51 125.57 125.63 126.09 126.17
- 37.74 125.23 125.50 126.09 126.17
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- 37.69 125.20 125.27 125.32 125.38
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37.68 125.21 125.26 125.32 125.38
- 37.67 125.32 125.38
- 37.66 125.33 125.37
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Northern Mariana Islands
20.56 144.89 144.93
20.55 144.89 144.94
@@ -131353,35 +131635,35 @@ Northern Mariana Islands
20.01 145.21 145.28
20.00 145.23 145.27
19.99 145.24 145.26
- 19.69 145.37 145.42
+ 19.69 145.37 145.41
19.68 145.37 145.42
19.67 145.37 145.42
19.66 145.37 145.42
19.65 145.38 145.42
19.64 145.39 145.41
- 18.81 145.65 145.70
- 18.80 145.64 145.71
- 18.79 145.63 145.71
- 18.78 145.63 145.71
- 18.77 145.63 145.71
- 18.76 145.63 145.71
- 18.75 145.63 145.71
- 18.74 145.63 145.71
- 18.73 145.63 145.71
- 18.72 145.64 145.71
+ 18.81 145.64 145.70
+ 18.80 145.63 145.71
+ 18.79 145.62 145.71
+ 18.78 145.62 145.71
+ 18.77 145.62 145.71
+ 18.76 145.62 145.71
+ 18.75 145.62 145.71
+ 18.74 145.62 145.71
+ 18.73 145.62 145.71
+ 18.72 145.63 145.71
18.71 145.65 145.70
- 18.18 145.78 145.82
- 18.17 145.76 145.83
- 18.16 145.76 145.84
- 18.15 145.76 145.84
- 18.14 145.76 145.84
- 18.13 145.76 145.84
- 18.12 145.76 145.84
- 18.11 145.74 145.84
+ 18.18 145.76 145.82
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+ 18.16 145.74 145.84
+ 18.15 145.74 145.84
+ 18.14 145.74 145.84
+ 18.13 145.74 145.84
+ 18.12 145.74 145.84
+ 18.11 145.73 145.84
18.10 145.72 145.83
- 18.09 145.72 145.81
- 18.08 145.71 145.80
- 18.07 145.71 145.79
+ 18.09 145.71 145.81
+ 18.08 145.70 145.80
+ 18.07 145.70 145.79
18.06 145.70 145.77
18.05 145.70 145.76
18.04 145.70 145.75
@@ -131397,6 +131679,7 @@ Northern Mariana Islands
17.29 145.82 145.87
17.28 145.83 145.87
17.27 145.84 145.86
+ 16.71 145.77 145.80
16.70 145.75 145.81
16.69 145.75 145.81
16.68 145.75 145.81
@@ -131410,7 +131693,7 @@ Northern Mariana Islands
16.34 145.62 145.72
16.33 145.63 145.72
16.32 145.65 145.68
- 15.28 145.79 145.81
+ 15.28 145.79 145.82
15.27 145.77 145.83
15.26 145.75 145.83
15.25 145.72 145.83
@@ -131424,7 +131707,7 @@ Northern Mariana Islands
15.17 145.68 145.79
15.16 145.68 145.79
15.15 145.67 145.79
- 15.14 145.67 145.79
+ 15.14 145.67 145.78
15.13 145.67 145.75
15.12 145.67 145.74
15.11 145.67 145.75
@@ -131449,7 +131732,7 @@ Northern Mariana Islands
14.92 145.59 145.66
14.91 145.59 145.65
14.90 145.61 145.64
- 14.21 145.23 145.29
+ 14.21 145.23 145.28
14.20 145.21 145.29
14.19 145.19 145.30
14.18 145.16 145.30
@@ -131457,7 +131740,7 @@ Northern Mariana Islands
14.16 145.13 145.30
14.15 145.12 145.29
14.14 145.11 145.28
- 14.13 145.10 145.26
+ 14.13 145.10 145.25
14.12 145.10 145.25
14.11 145.10 145.24
14.10 145.18 145.23
@@ -131467,10 +131750,10 @@ Norway
71.15 25.54 25.81
71.14 25.54 25.81
71.13 25.54 25.81 25.99 26.02 27.64 27.67
- 71.12 25.56 25.80 25.83 25.89 25.97 26.04 27.64 27.70
- 71.11 24.70 24.77 25.46 25.51 25.58 26.04 27.63 27.72
- 71.10 24.69 24.84 25.44 25.56 25.61 26.04 27.54 27.73
- 71.09 24.63 24.84 25.34 25.59 25.61 26.04 27.52 27.73 28.15 28.23
+ 71.12 25.56 25.80 25.83 25.89 25.97 26.03 27.64 27.70
+ 71.11 24.70 24.77 25.46 25.51 25.58 26.03 27.63 27.72
+ 71.10 24.69 24.84 25.44 26.04 27.54 27.73
+ 71.09 24.63 24.84 25.34 26.04 27.52 27.73 28.15 28.22
71.08 24.61 24.84 25.30 26.04 27.51 27.73 28.00 28.06 28.13 28.25
71.07 24.60 24.83 25.30 26.04 27.51 27.72 27.98 28.07 28.11 28.26
71.06 24.60 24.83 25.30 26.03 27.51 27.84 27.97 28.07 28.09 28.27
@@ -131478,241 +131761,241 @@ Norway
71.04 24.60 24.79 25.28 25.97 26.10 26.22 27.51 28.27
71.03 23.94 24.09 24.62 24.79 25.28 25.97 26.08 26.22 27.23 27.31 27.51 28.27
71.02 23.91 24.09 24.67 24.79 25.28 25.97 26.06 26.22 27.21 27.42 27.51 28.26
- 71.01 23.88 24.21 24.71 24.78 25.28 25.98 26.03 26.22 27.21 27.49 27.52 28.25 28.32 28.42
- 71.00 23.87 24.23 25.29 26.21 27.21 28.25 28.28 28.52
- 70.99 23.87 24.23 25.31 25.36 25.40 26.20 27.21 28.54
+ 71.01 23.88 24.21 24.71 24.78 25.28 25.98 26.00 26.22 27.21 27.49 27.52 28.24 28.32 28.42
+ 71.00 23.87 24.23 25.29 26.21 27.21 28.24 28.28 28.52
+ 70.99 23.87 24.23 25.31 25.36 25.40 26.19 27.21 28.54
70.98 23.87 24.23 24.59 24.72 24.98 25.04 25.35 26.15 27.22 28.55
70.97 23.89 24.23 24.57 24.79 24.96 25.06 25.34 26.10 27.13 28.55
- 70.96 23.89 24.25 24.57 24.80 24.96 25.07 25.33 26.09 26.65 26.70 27.13 28.55
+ 70.96 23.89 24.25 24.57 24.80 24.96 25.07 25.33 26.09 26.65 26.70 27.12 28.55
70.95 23.89 24.25 24.57 24.84 24.96 25.07 25.33 25.94 26.59 26.70 27.12 28.55
- 70.94 23.89 24.25 24.56 24.86 24.96 25.07 25.33 25.76 26.56 26.71 27.12 28.54
+ 70.94 23.89 24.25 24.56 24.86 24.96 25.07 25.33 25.76 26.56 26.71 27.11 28.54
70.93 23.94 24.22 24.56 24.87 24.95 25.07 25.13 25.15 25.33 25.76 26.53 26.73 27.11 28.54
70.92 23.98 24.18 24.56 24.87 24.90 25.06 25.12 25.17 25.34 25.64 26.50 26.73 27.11 28.53
- 70.91 23.99 24.10 24.13 24.17 24.57 25.06 25.10 25.19 25.35 25.58 26.47 26.73 27.11 28.52
+ 70.91 23.99 24.10 24.14 24.17 24.57 25.06 25.10 25.19 25.35 25.58 26.47 26.73 27.11 28.52
70.90 24.01 24.09 24.58 25.05 25.08 25.21 25.36 25.54 25.63 25.72 25.83 25.90 26.44 26.74 27.12 28.51
70.89 24.59 25.23 25.37 25.54 25.57 25.73 25.78 25.92 26.41 26.74 27.14 28.50 28.92 29.10
- 70.88 24.59 25.24 25.37 25.53 25.56 25.73 25.77 25.92 26.38 26.74 27.17 28.50 28.77 29.11
+ 70.88 24.59 25.24 25.37 25.53 25.56 25.73 25.76 25.92 26.38 26.74 27.17 28.50 28.77 29.11
70.87 23.30 23.37 24.34 24.41 24.61 25.25 25.37 25.53 25.56 25.93 26.35 26.74 27.26 28.49 28.75 29.11
70.86 23.30 23.38 24.31 24.42 24.60 25.25 25.36 25.93 26.33 26.72 27.38 28.45 28.73 29.24
- 70.85 23.30 23.41 24.28 24.46 24.60 25.26 25.36 25.93 26.31 26.71 27.45 28.45 28.71 29.26
- 70.84 23.30 23.43 24.26 24.47 24.60 25.26 25.35 25.93 26.29 26.75 27.47 28.44 28.69 29.27
- 70.83 23.15 23.18 23.30 23.45 24.25 24.47 24.59 25.27 25.35 25.91 26.28 26.75 27.31 27.42 27.47 28.41 28.68 29.27
+ 70.85 23.30 23.41 24.27 24.46 24.60 25.26 25.35 25.93 26.31 26.71 27.45 28.45 28.71 29.26
+ 70.84 23.30 23.43 24.25 24.47 24.60 25.26 25.34 25.93 26.29 26.75 27.47 28.44 28.69 29.27
+ 70.83 23.15 23.18 23.30 23.45 24.25 24.47 24.59 25.27 25.34 25.91 26.28 26.75 27.31 27.42 27.47 28.41 28.68 29.27
70.82 23.05 23.11 23.15 23.20 23.31 23.45 24.25 24.54 24.59 25.88 26.26 26.75 27.30 28.37 28.67 29.27
70.81 23.05 23.13 23.15 23.22 23.31 23.48 24.25 24.56 24.59 25.85 26.25 26.75 27.29 28.37 28.65 29.30
- 70.80 23.02 23.24 23.31 23.49 24.25 25.82 26.23 26.74 27.28 28.31 28.64 29.40
- 70.79 23.02 23.26 23.32 23.49 24.23 25.80 26.20 26.73 27.28 27.98 28.00 28.30 28.62 29.41
- 70.78 23.02 23.49 24.23 25.78 26.18 26.72 27.27 27.96 28.00 28.28 28.59 29.41
- 70.77 22.77 22.81 23.03 23.46 24.23 25.76 26.16 26.71 27.27 27.95 28.10 28.25 28.56 29.41
- 70.76 22.73 22.81 23.04 23.46 23.75 23.83 24.24 25.74 26.15 26.70 27.27 28.00 28.54 29.40
- 70.75 22.71 22.86 23.06 23.45 23.68 23.85 24.25 25.68 26.14 26.70 27.13 28.12 28.53 29.39 29.67 29.75
+ 70.80 23.01 23.24 23.31 23.49 24.24 25.82 26.23 26.74 27.28 28.31 28.64 29.40
+ 70.79 23.01 23.26 23.32 23.49 24.23 25.80 26.20 26.73 27.28 28.30 28.62 29.41
+ 70.78 23.01 23.49 24.23 25.78 26.18 26.71 27.27 27.96 27.99 28.28 28.59 29.41
+ 70.77 22.77 22.81 23.02 23.46 24.23 25.76 26.16 26.71 27.27 27.94 28.10 28.25 28.56 29.41
+ 70.76 22.73 22.81 23.04 23.46 23.75 23.83 24.24 25.74 26.14 26.70 27.27 28.00 28.54 29.40
+ 70.75 22.71 22.86 23.06 23.45 23.68 23.85 24.25 25.68 26.14 26.70 27.12 28.12 28.53 29.39 29.66 29.75
70.74 22.71 22.86 23.08 23.42 23.67 23.85 24.40 25.66 26.13 26.70 27.11 28.14 28.52 29.42 29.62 29.77
- 70.73 22.71 22.93 23.01 23.33 23.36 23.41 23.66 23.85 24.53 25.66 26.12 26.70 27.10 28.14 28.51 29.42 29.58 29.78
+ 70.73 22.71 22.93 23.01 23.33 23.36 23.41 23.66 23.85 24.53 25.66 26.12 26.70 27.10 28.14 28.51 29.42 29.57 29.78
70.72 22.50 22.58 22.71 22.94 23.01 23.33 23.65 23.85 24.54 25.66 26.06 26.70 27.08 28.14 28.23 28.30 28.51 29.42 29.53 29.78 29.97 30.12
70.71 22.37 22.43 22.49 22.61 22.72 22.94 23.01 23.33 23.63 23.99 24.55 25.65 26.05 26.69 27.07 28.13 28.21 28.31 28.51 29.41 29.45 29.78 29.94 30.16
70.70 22.36 22.44 22.48 22.64 22.74 22.94 23.00 23.33 23.62 24.02 24.34 24.37 24.59 25.64 26.04 26.67 27.07 28.11 28.18 28.31 28.52 29.79 29.92 30.19
- 70.69 22.36 22.46 22.48 22.66 22.76 22.93 22.96 23.33 23.62 24.05 24.32 24.49 24.63 25.61 26.03 26.65 27.07 28.09 28.16 28.31 28.53 29.79 29.90 30.21
- 70.68 22.22 22.30 22.36 22.66 22.77 23.28 23.62 24.06 24.30 24.51 24.64 25.58 26.03 26.62 27.08 28.04 28.12 28.31 28.50 29.79 29.88 30.21
- 70.67 21.97 22.02 22.22 22.34 22.36 22.70 22.77 23.28 23.63 24.07 24.28 24.53 24.65 25.55 26.02 26.58 27.10 27.97 28.06 28.30 28.49 29.79 29.86 30.21
- 70.66 21.95 22.08 22.22 22.71 22.77 23.19 23.65 24.07 24.27 24.56 24.67 25.53 26.02 26.64 27.09 27.92 28.00 28.30 28.48 29.78 29.84 30.20
- 70.65 21.94 22.16 22.23 22.71 22.73 23.19 23.64 24.08 24.26 24.58 24.70 25.48 26.01 26.66 27.09 27.89 27.94 28.29 28.48 29.77 29.83 30.19
- 70.64 21.94 23.19 23.64 24.10 24.26 24.60 24.71 25.44 26.01 26.66 27.09 28.29 28.47 30.26
- 70.63 21.94 23.18 23.42 23.50 23.64 24.12 24.26 24.63 24.70 25.43 26.00 26.66 27.09 28.28 28.46 30.29
- 70.62 21.96 23.17 23.38 23.58 23.65 24.13 24.26 25.42 25.99 26.65 27.06 28.27 28.45 30.32
- 70.61 22.01 23.15 23.38 23.58 23.64 24.13 24.23 25.40 25.98 26.65 27.03 28.25 28.44 30.34
+ 70.69 22.36 22.46 22.48 22.66 22.76 22.93 22.96 23.32 23.62 24.05 24.32 24.49 24.63 25.61 26.03 26.65 27.07 28.09 28.16 28.31 28.52 29.79 29.90 30.21
+ 70.68 22.21 22.30 22.36 22.66 22.77 23.28 23.62 24.06 24.30 24.51 24.64 25.58 26.03 26.62 27.08 28.04 28.12 28.31 28.50 29.79 29.88 30.21
+ 70.67 21.97 22.02 22.21 22.34 22.36 22.70 22.77 23.28 23.63 24.07 24.28 24.53 24.65 25.55 26.02 26.58 27.10 27.97 28.06 28.30 28.49 29.79 29.86 30.21
+ 70.66 21.95 22.08 22.21 22.71 22.75 23.19 23.65 24.07 24.27 24.56 24.67 25.53 26.02 26.64 27.09 27.92 28.00 28.30 28.48 29.78 29.84 30.20
+ 70.65 21.94 22.16 22.23 22.71 22.73 23.19 23.64 24.08 24.26 24.58 24.70 25.48 26.01 26.66 27.08 27.88 27.94 28.29 28.48 29.77 29.83 30.19
+ 70.64 21.94 23.19 23.64 24.11 24.26 24.60 24.71 25.44 26.01 26.66 27.08 28.29 28.47 30.26
+ 70.63 21.94 23.18 23.42 23.50 23.64 24.13 24.26 24.63 24.70 25.43 26.00 26.66 27.08 28.28 28.46 30.29
+ 70.62 21.96 23.16 23.38 23.58 23.65 24.13 24.26 25.42 25.99 26.65 27.04 28.27 28.45 30.32
+ 70.61 22.01 23.15 23.38 23.58 23.64 24.13 24.23 25.40 25.98 26.65 27.02 28.25 28.44 30.34
70.60 22.00 23.12 23.38 23.58 23.63 24.13 24.22 25.38 25.96 26.64 27.00 28.24 28.43 30.35
70.59 22.00 23.11 23.42 23.60 23.63 24.12 24.19 25.36 25.94 26.64 26.98 28.22 28.42 30.35
70.58 22.00 22.09 22.22 23.01 23.03 23.10 23.42 23.61 23.63 24.12 24.17 25.33 25.87 26.63 26.97 28.20 28.41 30.35
70.57 22.22 23.01 23.06 23.09 23.40 23.61 23.68 24.11 24.14 25.28 25.85 26.63 26.96 28.18 28.40 30.34 30.41 30.48
70.56 22.22 23.00 23.18 23.23 23.29 23.35 23.38 23.61 23.68 24.08 24.12 25.26 25.83 26.62 26.96 28.15 28.39 30.55
- 70.55 22.19 22.99 23.16 23.26 23.28 23.60 23.69 24.04 24.09 25.25 25.81 26.62 26.96 28.11 28.38 30.59
- 70.54 22.17 22.64 22.72 22.94 23.16 23.59 23.70 24.00 24.09 25.22 25.79 26.61 26.95 28.07 28.38 30.59
- 70.53 22.16 22.64 22.75 22.93 23.10 23.14 23.16 23.59 23.71 23.98 24.09 25.27 25.78 26.61 26.95 28.05 28.38 30.60
- 70.52 22.15 22.64 22.75 22.82 22.85 22.91 23.06 23.65 23.72 23.96 24.10 25.29 25.76 26.60 26.95 28.03 28.27 28.34 28.40 30.60
- 70.51 22.15 22.64 22.76 22.81 23.02 23.66 23.74 24.05 24.17 25.29 25.74 26.59 26.96 28.01 28.11 28.19 28.23 28.34 28.42 30.62
- 70.50 22.14 22.48 22.52 22.59 23.00 23.66 23.77 25.29 25.72 26.57 26.98 27.99 28.03 28.34 28.37 30.65
+ 70.55 22.19 22.99 23.16 23.25 23.28 23.60 23.68 24.04 24.09 25.25 25.81 26.62 26.96 28.11 28.38 30.59
+ 70.54 22.17 22.64 22.72 22.94 23.16 23.59 23.69 24.00 24.09 25.22 25.79 26.61 26.95 28.07 28.38 30.59
+ 70.53 22.16 22.64 22.75 22.93 23.10 23.14 23.16 23.59 23.70 23.98 24.09 25.27 25.78 26.61 26.95 28.05 28.38 30.60
+ 70.52 22.15 22.64 22.75 22.82 22.85 22.91 23.06 23.65 23.72 23.96 24.10 25.29 25.76 26.60 26.95 28.03 28.24 28.34 28.40 30.60
+ 70.51 22.15 22.64 22.76 22.80 23.02 23.66 23.74 24.05 24.17 25.29 25.74 26.59 26.96 28.01 28.11 28.19 28.22 28.34 28.42 30.62
+ 70.50 22.14 22.48 22.52 22.59 23.00 23.66 23.77 25.29 25.72 26.57 26.98 27.98 28.03 28.34 28.37 30.65
70.49 22.13 22.26 22.29 22.39 22.42 22.48 22.54 22.58 22.99 23.66 23.80 25.28 25.71 26.58 26.87 26.95 27.00 30.68
70.48 22.13 22.26 22.32 22.36 22.43 22.47 22.95 23.66 23.78 25.27 25.69 26.59 26.80 26.95 26.99 30.72
70.47 22.13 22.25 22.92 23.67 23.77 25.28 25.67 26.59 26.79 30.74
- 70.46 22.14 22.21 22.88 23.67 23.75 25.29 25.65 26.59 26.78 30.74 30.89 30.94
- 70.45 22.88 23.67 23.73 25.29 25.63 26.57 26.78 30.76 30.85 30.95
+ 70.46 22.14 22.21 22.88 23.67 23.75 25.29 25.65 26.59 26.78 30.74 30.89 30.95
+ 70.45 22.88 23.67 23.73 25.29 25.63 26.57 26.78 30.76 30.85 30.96
70.44 22.88 23.66 23.69 25.29 25.61 26.54 26.76 30.78 30.82 30.97
- 70.43 22.88 25.26 25.59 26.53 26.64 26.68 26.70 30.98
+ 70.43 22.88 25.26 25.59 26.53 26.64 30.98
70.42 22.86 25.26 25.57 26.53 26.62 31.00
70.41 22.84 25.27 25.55 26.53 26.61 31.01
70.40 22.65 22.69 22.74 22.77 22.84 25.27 25.53 26.53 26.61 31.03
- 70.39 21.69 21.73 22.47 22.50 22.56 22.58 22.60 22.70 22.72 22.79 22.84 25.27 25.51 26.53 26.59 31.04
- 70.38 21.68 21.75 22.46 22.52 22.54 22.70 22.72 22.79 22.87 25.18 25.20 25.27 25.49 26.53 26.57 31.06
+ 70.39 21.69 21.73 22.46 22.50 22.55 22.70 22.72 22.79 22.84 25.27 25.51 26.53 26.59 31.04
+ 70.38 21.68 21.75 22.46 22.70 22.72 22.79 22.87 25.18 25.20 25.27 25.49 26.53 26.57 31.06
70.37 21.67 21.78 22.40 22.43 22.45 22.70 22.72 22.80 22.89 25.15 25.23 25.26 25.47 26.52 26.56 31.07
70.36 21.67 21.80 22.38 22.70 22.72 22.80 22.90 25.14 25.45 31.07
70.35 21.67 21.80 22.36 22.82 22.92 23.45 23.48 25.14 25.43 31.07
- 70.34 21.67 21.80 22.36 22.89 22.94 23.42 23.47 25.21 25.42 31.06
- 70.33 21.54 21.57 21.67 21.80 21.96 22.03 22.36 22.96 22.99 23.38 23.46 25.21 25.41 31.04
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70.32 21.52 21.59 21.66 21.80 21.94 22.04 22.36 22.96 23.07 23.39 23.45 25.21 25.41 31.05
70.31 21.50 21.59 21.66 21.80 21.91 22.11 22.37 22.96 23.07 23.39 23.45 25.21 25.41 31.07
- 70.30 19.65 19.69 21.50 21.59 21.66 21.79 21.88 22.11 22.20 22.29 22.39 23.00 23.07 23.39 23.45 25.21 25.46 31.07
- 70.29 19.62 19.70 21.50 21.59 21.66 21.79 21.86 22.11 22.13 22.31 22.41 23.01 23.07 23.36 23.43 25.21 25.51 31.08
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70.28 19.59 19.70 21.50 21.61 21.66 21.78 21.83 22.11 22.13 22.32 22.43 23.01 23.08 23.30 23.37 25.19 25.50 31.08
- 70.27 19.57 19.70 21.38 21.44 21.50 21.77 21.81 22.11 22.13 22.32 22.41 22.45 22.47 23.02 23.09 23.24 23.33 25.16 25.48 31.08
- 70.26 19.15 19.22 19.53 19.70 21.35 21.44 21.49 21.76 21.79 22.11 22.13 22.32 22.38 23.02 23.12 23.19 23.30 25.13 25.46 31.02
- 70.25 19.09 19.23 19.52 19.71 21.28 21.44 21.49 21.74 21.79 22.11 22.14 22.32 22.36 22.60 22.62 23.02 23.28 25.10 25.44 30.96
- 70.24 19.07 19.24 19.52 19.73 20.55 20.76 21.25 21.45 21.48 21.75 21.79 22.31 22.36 22.61 22.69 23.02 23.28 25.07 25.42 30.84
- 70.23 19.07 19.24 19.52 19.79 20.53 20.81 21.22 21.77 21.79 22.30 22.35 22.61 22.63 22.75 22.86 23.01 23.25 25.04 25.42 30.64
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70.22 19.07 19.24 19.54 19.80 19.85 19.91 20.53 20.82 21.20 22.28 22.35 22.89 23.23 25.01 25.41 30.53
- 70.21 19.08 19.25 19.57 19.80 19.85 19.93 20.49 20.83 21.19 22.28 22.34 22.97 23.23 24.99 25.40 30.52
- 70.20 19.10 19.25 19.61 19.81 19.84 19.95 20.44 20.83 21.19 22.28 22.34 22.98 23.23 24.98 25.35 30.52
- 70.19 19.08 19.26 19.64 19.81 19.84 19.95 20.42 20.83 21.19 22.29 22.33 22.98 23.25 24.98 25.31 30.50
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70.18 19.05 19.26 19.66 19.95 20.40 20.83 21.22 22.29 22.32 22.98 23.27 24.98 25.30 30.44
- 70.17 19.02 19.26 19.38 19.43 19.68 19.95 20.40 20.82 21.26 22.98 23.28 24.98 25.29 30.39
- 70.16 18.98 19.26 19.35 19.46 19.70 19.97 20.39 20.85 21.27 22.97 23.28 24.98 25.05 25.10 25.28 30.39
- 70.15 18.98 19.25 19.33 19.50 19.70 20.01 20.39 20.86 21.30 23.02 23.28 24.97 25.01 25.10 25.28 28.76 28.79 30.39
- 70.14 18.98 19.23 19.33 19.54 19.71 20.05 20.38 20.88 21.42 23.02 23.30 24.96 25.00 25.13 25.27 28.75 28.88 30.39
- 70.13 18.99 19.23 19.32 19.57 19.72 20.09 20.13 20.16 20.38 20.89 21.42 23.02 23.34 24.95 25.00 25.14 25.26 28.74 28.98 30.38
- 70.12 18.69 18.77 19.04 19.23 19.32 19.58 19.73 20.16 20.38 20.91 21.42 23.02 23.26 24.95 24.99 25.14 25.25 28.72 28.76 28.80 29.07 30.37
- 70.11 18.69 18.79 18.87 18.92 19.06 19.21 19.32 19.58 19.73 20.16 20.38 20.92 21.43 23.01 23.23 24.95 24.99 25.14 25.23 28.67 28.74 28.82 29.17 30.36
- 70.10 18.69 18.79 18.85 18.95 19.08 19.23 19.33 19.58 19.73 20.16 20.38 20.92 21.44 23.01 23.16 24.96 24.99 25.11 25.21 28.86 29.31 30.34
- 70.09 18.69 18.80 18.83 18.97 19.13 19.23 19.28 19.31 19.38 19.57 19.73 20.11 20.38 20.92 21.45 23.00 23.16 28.86 29.49 30.27
- 70.08 18.68 18.98 19.05 19.23 19.26 19.33 19.45 19.56 19.73 20.04 20.38 20.92 21.47 23.00 23.16 28.94 29.68 30.19
- 70.07 18.66 18.98 19.05 19.33 19.73 20.04 20.39 20.91 21.00 21.05 21.63 23.01 23.18 28.98 29.87 30.16
- 70.06 18.65 18.98 19.05 19.33 19.49 19.57 19.74 20.04 20.40 20.90 20.98 21.05 21.65 23.01 23.20 29.14 30.05 30.16
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- 70.04 18.64 18.96 19.00 19.31 19.42 19.59 19.79 20.00 20.48 20.52 20.57 20.67 20.73 20.89 20.95 21.05 21.31 21.37 21.78 23.13 23.24 27.61 27.72 27.81 27.91 29.20
- 70.03 18.64 19.33 19.41 19.59 19.62 19.66 19.91 19.99 20.57 20.64 20.77 20.91 20.94 21.05 21.28 21.42 21.78 23.13 23.26 27.59 27.92 29.20
- 70.02 18.65 19.36 19.40 19.68 19.89 20.00 20.76 21.10 21.26 21.46 21.78 23.13 23.28 27.58 27.93 29.20 29.24 29.37
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70.01 18.65 19.38 19.40 19.69 19.75 19.83 19.89 20.00 20.76 21.10 21.24 21.50 21.80 23.13 23.47 27.57 27.95 29.42
70.00 18.66 18.78 18.82 19.69 19.73 19.84 19.89 20.00 20.75 21.10 21.23 21.54 21.84 23.13 23.26 23.32 23.46 27.54 27.96 29.50
- 69.99 18.66 18.76 18.82 19.69 19.72 19.85 19.93 19.98 20.75 21.08 21.22 21.56 21.91 23.14 23.23 23.34 23.44 27.48 27.97 29.57
- 69.98 18.66 18.74 18.82 19.86 20.28 20.31 20.75 21.04 21.21 21.57 21.91 23.15 23.19 23.34 23.40 27.44 27.98 29.65
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69.97 18.67 18.72 18.83 19.86 20.26 20.32 20.75 21.00 21.21 21.59 21.91 23.34 23.37 27.42 28.00 29.69
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69.95 18.71 19.85 20.15 20.17 20.21 20.35 20.77 20.98 21.03 21.10 21.20 21.61 21.65 21.74 21.90 27.36 28.03 29.69
69.94 18.71 19.85 20.14 20.37 20.78 20.97 20.99 21.10 21.19 21.61 21.65 21.74 21.90 27.36 28.05 29.65
69.93 18.71 19.84 20.13 20.38 20.79 21.10 21.19 21.60 21.65 21.74 21.90 27.36 28.07 29.62
- 69.92 18.72 19.83 20.12 20.39 20.82 21.08 21.19 21.62 21.66 21.74 21.90 27.35 28.08 29.59 29.68 29.73 29.85 29.93
- 69.91 18.73 19.81 20.12 20.41 20.56 20.73 20.87 21.05 21.19 21.64 21.67 21.70 21.91 26.62 26.73 26.82 26.92 27.33 28.10 29.75 29.82 29.99
- 69.90 18.75 19.79 20.11 20.42 20.54 20.73 20.83 21.03 21.19 21.67 21.91 26.52 27.02 27.26 28.11 29.75 29.80 30.00
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69.89 18.66 18.73 18.79 19.78 20.11 20.42 20.54 20.73 20.80 21.00 21.19 21.77 21.91 26.50 27.06 27.16 28.13 29.75 29.80 30.00 30.26 30.31
69.88 18.66 18.75 18.77 19.76 20.10 20.43 20.53 20.73 20.78 20.98 21.12 21.79 21.91 26.49 28.15 29.75 29.79 30.00 30.15 30.32
69.87 18.65 18.86 18.88 19.75 20.09 20.43 20.52 20.71 20.78 20.96 21.06 21.82 21.91 26.47 28.17 29.75 29.79 30.02 30.15 30.33
69.86 18.65 18.86 18.91 19.74 20.07 20.43 20.51 20.72 20.78 20.94 21.04 21.84 21.92 26.45 28.21 29.76 29.79 30.03 30.15 30.33
- 69.85 18.65 19.73 19.99 20.01 20.06 20.43 20.51 20.72 20.79 20.96 21.04 21.87 21.92 26.45 28.28 29.77 29.79 30.03 30.15 30.39
- 69.84 18.65 19.70 19.96 20.01 20.05 20.42 20.51 20.73 20.80 20.97 21.02 26.45 28.34 29.78 29.80 30.11 30.15 30.41
- 69.83 18.66 19.63 19.95 20.01 20.04 20.41 20.51 20.73 20.81 26.44 28.36 30.11 30.15 30.41
- 69.82 18.67 19.41 19.45 19.53 19.68 19.76 19.95 20.01 20.04 20.40 20.51 20.73 20.79 26.42 28.36 30.11 30.14 30.41 30.44 30.59
- 69.81 18.56 19.39 19.59 19.79 19.94 20.01 20.03 20.40 20.51 20.72 20.75 26.40 28.36 30.11 30.14 30.41 30.44 30.71 30.81 30.85
- 69.80 18.34 18.42 18.54 19.36 19.51 19.79 19.93 20.40 20.52 26.38 28.37 30.10 30.14 30.41 30.44 30.73 30.77 30.85
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69.59 17.45 17.55 17.64 17.71 17.80 17.87 17.98 18.84 18.93 20.39 20.56 26.01 29.17 30.23 30.32 30.94
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69.54 17.30 17.39 17.45 17.60 17.65 17.90 18.13 18.87 18.96 20.31 20.43 20.63 20.66 25.98 29.22 30.24 30.44 30.91
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68.16 13.28 13.37 13.46 13.99 14.18 14.33 15.62 15.67 15.86 16.11 16.38 18.18
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68.02 12.94 13.13 13.15 13.39 15.16 15.25 15.27 15.44 15.51 16.10 16.35 17.21 17.58 18.02
68.01 12.94 13.12 13.15 13.38 15.09 15.12 15.15 15.44 15.47 16.14 16.19 16.29 16.32 17.18 17.62 18.00
68.00 12.93 13.12 13.15 13.32 13.34 13.37 15.07 15.12 15.14 15.28 15.30 15.44 15.47 17.14 17.66 17.99
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67.96 12.89 13.14 14.95 15.29 15.71 15.80 15.91 17.02 17.82 17.93
67.95 12.88 13.14 14.95 15.31 15.63 15.82 15.89 16.98 17.86 17.91
67.94 12.88 13.14 14.95 15.31 15.59 15.83 15.87 16.95
67.93 12.87 13.13 14.95 15.31 15.59 15.84 15.86 16.92
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67.90 12.84 13.05 14.96 15.27 15.29 16.82
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67.83 12.78 12.89 14.77 16.75
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67.81 12.77 12.88 14.74 16.74
67.80 12.77 12.86 14.74 16.73
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67.71 14.77 15.21 15.27 16.67
67.70 14.77 15.20 15.26 16.66
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67.67 14.73 15.09 15.24 16.64
67.66 14.71 15.06 15.20 16.63
67.65 14.71 15.00 15.18 16.62
@@ -131836,9 +132119,9 @@ Norway
67.46 14.75 16.17
67.45 14.35 14.40 14.75 16.16
67.44 14.31 14.41 14.81 16.16
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67.42 14.27 14.42 14.61 16.15
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67.40 14.23 14.42 14.56 16.17
67.39 14.21 14.41 14.56 16.19
67.38 14.21 14.40 14.56 16.20
@@ -131858,27 +132141,27 @@ Norway
67.24 14.31 14.60 14.65 16.40
67.23 14.31 14.50 14.62 16.41
67.22 14.33 14.39 14.60 16.43
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67.18 14.23 14.26 14.50 16.45
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67.14 14.04 14.08 14.19 14.27 14.31 16.44
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67.08 13.98 14.22 14.25 16.43
67.07 13.98 14.21 14.25 16.43
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67.05 14.02 16.42
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67.03 14.00 14.09 14.12 16.41
67.02 14.00 14.10 14.13 14.22 14.25 16.40
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67.00 13.89 13.98 14.01 14.12 14.14 16.35
66.99 13.87 13.98 14.02 16.33
66.98 13.85 13.98 14.02 16.30
@@ -131921,8 +132204,8 @@ Norway
66.61 13.22 15.71
66.60 13.22 15.70
66.59 13.20 15.68
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66.56 13.19 15.63
66.55 13.06 13.13 13.19 15.61
66.54 13.00 13.16 13.19 15.58
@@ -131966,23 +132249,23 @@ Norway
66.16 12.42 12.62 12.99 15.14
66.15 12.42 12.45 12.50 12.62 12.90 15.11
66.14 12.47 12.63 12.84 15.07
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66.10 12.35 12.66 12.71 14.56
66.09 12.33 12.66 12.69 14.56
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66.07 12.33 12.63 12.66 14.57
66.06 12.33 12.59 12.66 14.57
66.05 12.32 12.56 12.66 14.58
66.04 12.31 12.51 12.70 12.87 12.94 14.58
66.03 12.29 12.46 12.58 12.64 12.70 12.89 12.94 14.59
66.02 12.28 12.42 12.54 12.66 12.72 12.91 12.94 14.59
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66.00 12.28 12.32 12.48 12.66 12.68 14.60
65.99 12.46 14.60
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65.96 12.44 14.61
65.95 12.43 14.61
65.94 12.42 14.62
@@ -132008,21 +132291,21 @@ Norway
65.74 12.48 14.61
65.73 12.46 14.61
65.72 12.43 14.60
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65.70 11.81 12.00 12.41 14.58
65.69 11.79 12.01 12.40 14.57
65.68 11.78 12.01 12.38 14.57
65.67 11.77 12.01 12.36 14.57
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65.65 11.76 11.98 12.34 14.56
65.64 11.75 11.98 12.33 14.56
65.63 11.75 11.98 12.33 14.56
65.62 11.74 11.98 12.33 14.56
65.61 11.74 11.97 12.34 14.55
65.60 11.74 11.95 12.34 14.55
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65.58 11.84 11.87 11.89 11.93 12.24 12.29 12.35 14.55
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65.56 12.23 12.31 12.38 14.54
65.55 12.21 12.32 12.38 14.54
65.54 12.21 12.33 12.38 14.54
@@ -132046,7 +132329,7 @@ Norway
65.36 12.11 14.52
65.35 12.09 14.52
65.34 12.09 14.52
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65.32 12.08 12.36 12.40 14.52
65.31 12.07 12.29 12.33 14.52
65.30 12.07 12.24 12.32 14.52
@@ -132055,10 +132338,10 @@ Norway
65.27 12.09 12.25 12.28 14.49
65.26 12.08 12.24 12.26 14.47
65.25 12.07 12.22 12.24 14.45
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65.22 12.04 12.20 12.23 12.29 12.34 14.38
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65.20 12.04 12.23 12.34 12.37 12.42 14.37
65.19 12.09 12.24 12.42 14.37
65.18 12.08 12.26 12.37 14.36
@@ -132069,7 +132352,7 @@ Norway
65.13 12.07 12.26 12.37 14.35
65.12 11.62 11.78 12.05 12.31 12.40 14.34
65.11 11.55 11.78 12.03 12.31 12.47 14.34
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65.09 11.52 11.77 11.96 14.33
65.08 11.51 11.76 11.96 14.33
65.07 11.51 11.73 11.93 14.32
@@ -132095,26 +132378,26 @@ Norway
64.87 10.70 10.99 11.05 14.04
64.86 10.70 10.96 11.03 14.03
64.85 10.70 10.94 11.03 14.01
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64.81 11.22 11.59 11.63 13.96
64.80 11.24 11.28 11.31 11.56 11.69 13.95
64.79 11.33 11.47 11.72 13.94
64.78 11.35 11.46 11.61 13.92
64.77 11.32 11.45 11.54 13.91
64.76 11.28 11.44 11.54 13.90
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64.73 11.22 11.35 11.48 13.86
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64.71 11.38 13.83
64.70 11.27 11.31 11.38 13.82
64.69 11.21 11.33 11.38 13.81
64.68 11.17 11.35 11.38 13.79
64.67 11.16 11.36 11.38 13.78
64.66 11.05 11.10 11.15 11.36 11.38 13.77
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64.64 11.03 11.37 11.40 13.74
64.63 11.03 13.73
64.62 11.02 13.72
@@ -132123,20 +132406,20 @@ Norway
64.59 10.90 13.68
64.58 10.90 11.28 11.30 13.70
64.57 10.90 11.28 11.33 13.73
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64.54 10.94 11.07 11.11 13.83
64.53 10.93 11.45 11.49 13.86
64.52 10.81 10.84 10.91 13.90
64.51 10.79 10.86 10.91 13.93
64.50 10.79 10.87 10.90 13.97
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64.47 10.68 11.18 11.30 14.10
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64.45 10.58 11.33 11.38 14.12
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64.42 10.46 14.13
64.41 10.45 14.13
64.40 10.45 14.13
@@ -132147,8 +132430,8 @@ Norway
64.35 10.44 14.14
64.34 10.44 14.14
64.33 10.44 14.14
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64.30 10.43 14.15
64.29 10.38 14.15
64.28 10.31 14.16
@@ -132159,9 +132442,9 @@ Norway
64.23 10.23 14.17
64.22 10.23 14.17
64.21 10.22 14.17
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64.17 10.16 14.17
64.16 10.14 14.16
64.15 10.14 14.15
@@ -132172,14 +132455,14 @@ Norway
64.10 9.98 14.10
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64.08 9.98 14.08
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+ 64.00 9.84 9.95 9.97 12.85 13.82 13.99
63.99 9.84 12.81 13.89 13.98
63.98 9.88 12.77
63.97 9.93 12.75
@@ -132196,33 +132479,33 @@ Norway
63.86 9.77 12.59
63.85 9.74 12.57
63.84 9.71 11.22 11.31 12.56
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63.82 8.77 8.81 9.64 11.08 11.41 12.53
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63.78 8.67 8.82 9.53 10.99 11.25 12.48
63.77 8.66 8.82 9.53 10.99 11.23 12.47
63.76 8.64 8.82 9.53 10.99 11.22 12.45
63.75 8.60 8.83 9.55 10.98 11.20 12.44
63.74 8.56 8.83 9.57 10.97 11.19 12.43
- 63.73 8.52 8.83 9.54 10.95 11.18 12.42
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63.68 8.26 8.80 9.54 9.69 9.78 10.76 10.88 12.35
63.67 8.26 8.77 9.04 9.10 9.53 9.65 9.78 10.71 10.86 12.34
63.66 8.28 8.39 8.44 8.65 8.89 8.97 9.03 9.16 9.53 9.61 9.78 10.66 10.85 12.33
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63.56 8.39 9.18 9.32 9.39 9.44 9.81 9.87 10.43 10.64 12.20
63.55 8.37 9.18 9.30 9.39 9.42 9.82 9.88 10.35 10.64 10.73 10.79 12.20
63.54 8.34 9.16 9.22 9.27 9.29 9.38 9.41 9.82 9.89 10.24 10.64 10.71 10.77 12.20
@@ -132231,18 +132514,18 @@ Norway
63.51 8.29 9.08 9.15 9.84 9.89 10.15 10.74 12.22
63.50 8.28 9.03 9.14 9.86 9.90 10.13 10.74 12.22
63.49 8.27 8.98 9.13 9.88 9.93 10.10 10.75 12.22
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63.47 7.96 8.11 8.26 8.88 8.99 9.04 9.13 9.92 10.22 10.33 10.76 12.22
63.46 7.94 8.11 8.26 8.70 8.97 9.06 9.14 9.94 10.13 10.35 10.39 10.50 10.66 10.70 10.79 12.22
- 63.45 7.92 8.12 8.26 8.68 8.96 9.08 9.15 9.95 10.10 10.53 10.60 10.73 10.82 12.22
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63.41 7.76 8.18 8.63 9.13 9.15 9.97 10.03 12.17
- 63.40 7.76 8.18 8.62 9.13 9.15 9.96 10.03 12.16
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63.39 7.77 8.19 8.62 9.96 10.03 12.15
63.38 7.77 8.19 8.62 9.95 10.03 12.14
- 63.37 7.77 8.19 8.64 12.12
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63.36 7.79 8.18 8.66 12.11
63.35 7.84 8.17 8.67 12.10
63.34 7.90 8.16 8.68 12.09
@@ -132251,36 +132534,36 @@ Norway
63.31 7.95 8.09 8.49 12.05
63.30 7.96 8.01 8.46 12.04
63.29 8.40 12.03
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63.26 8.26 8.37 8.39 8.48 8.51 12.02
63.25 8.05 8.10 8.26 8.50 8.53 12.03
63.24 8.03 8.13 8.25 8.52 8.55 12.04
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63.20 7.96 12.07
63.19 7.92 12.08
63.18 7.91 12.09
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63.15 7.92 8.50 8.55 12.11
63.14 7.94 12.12
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63.12 7.57 7.64 7.99 8.08 8.15 12.14
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63.02 7.21 7.29 7.38 7.69 7.71 12.22
63.01 7.18 7.30 7.36 7.71 7.76 7.83 7.86 12.23
63.00 7.08 7.32 7.35 7.71 7.86 12.23
- 62.99 7.05 7.74 7.87 12.23
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62.98 7.03 7.79 7.92 12.22
62.97 7.01 7.79 7.90 12.20
62.96 6.98 7.79 7.83 12.19
@@ -132297,55 +132580,55 @@ Norway
62.85 6.76 12.12
62.84 6.76 6.95 6.98 12.12
62.83 6.76 6.95 6.99 12.12
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62.80 6.76 6.92 6.96 12.14
62.79 6.77 6.91 6.95 12.14
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62.73 6.67 6.91 6.93 12.16
62.72 6.66 7.23 7.35 12.16
62.71 6.66 6.92 6.95 7.06 7.37 12.16
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62.66 6.63 6.79 6.90 7.10 7.50 12.13
62.65 6.65 6.81 6.87 7.10 7.42 7.46 7.50 12.13
62.64 6.66 6.83 6.87 7.10 7.40 7.48 7.50 12.12
62.63 6.62 6.64 6.66 6.85 6.87 7.10 7.14 7.19 7.40 12.12
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62.61 6.27 6.58 6.60 7.10 7.13 7.34 7.40 12.11
62.60 6.25 7.37 7.40 12.10
62.59 6.24 12.10
62.58 6.23 12.11
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62.56 6.23 12.12
62.55 6.24 12.13
62.54 6.25 12.14
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62.52 6.25 12.15
62.51 6.25 6.40 6.44 12.16
62.50 6.42 12.17
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62.47 6.23 12.19
62.46 6.21 12.20
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62.44 6.01 12.21
62.43 5.87 5.96 6.01 12.22
62.42 5.84 5.97 6.01 12.23
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62.40 5.81 5.99 6.05 6.34 6.41 12.24
62.39 5.80 6.00 6.07 6.33 6.39 12.25
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62.33 5.50 5.75 5.80 12.30
62.32 5.51 5.74 5.80 12.30
62.31 5.59 5.73 5.81 12.31
@@ -132358,11 +132641,11 @@ Norway
62.24 5.50 5.89 5.93 12.32
62.23 5.49 5.85 5.91 12.32
62.22 5.15 5.19 5.49 5.80 5.91 12.32
- 62.21 5.13 5.21 5.49 5.87 5.91 12.32
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62.20 5.07 5.23 5.44 5.47 5.50 12.31
62.19 5.06 5.25 5.42 12.31
62.18 5.06 5.27 5.41 12.31
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62.16 5.06 5.28 5.39 12.30
62.15 5.06 5.28 5.39 12.30
62.14 5.07 5.28 5.38 12.30
@@ -132372,37 +132655,37 @@ Norway
62.10 5.08 12.28
62.09 5.09 12.28
62.08 5.21 12.28
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62.06 5.25 12.27
62.05 5.27 12.27
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62.03 4.97 5.04 5.09 5.13 5.30 12.26
62.02 4.97 5.14 5.30 12.26
62.01 4.97 5.15 5.29 12.26
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61.99 4.97 5.16 5.25 12.25
61.98 4.98 5.17 5.19 5.21 5.23 12.25
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61.96 5.00 12.24
61.95 5.00 12.24
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61.93 5.00 12.23
61.92 5.01 12.23
61.91 5.05 12.23
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61.89 4.85 5.04 5.11 5.19 5.24 12.22
61.88 4.85 5.09 5.14 5.18 5.29 12.22
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61.86 4.81 5.20 5.28 12.21
61.85 4.79 5.23 5.27 12.21
61.84 4.79 12.21
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61.82 4.81 12.20
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61.80 4.86 5.09 5.11 12.20
61.79 4.86 12.19
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61.76 4.99 12.18
61.75 4.97 12.18
61.74 4.96 12.18
@@ -132411,9 +132694,9 @@ Norway
61.71 4.83 4.88 4.95 12.21
61.70 4.82 4.89 4.94 12.23
61.69 4.82 4.90 4.93 12.25
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61.65 4.83 4.91 4.93 12.33
61.64 4.85 4.91 4.94 12.34
61.63 4.95 12.36
@@ -132440,7 +132723,7 @@ Norway
61.42 4.93 12.82
61.41 4.93 12.84
61.40 4.93 12.85
- 61.39 4.93 12.87
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61.38 4.98 12.88
61.37 4.98 12.89
61.36 4.98 12.89
@@ -132459,8 +132742,8 @@ Norway
61.23 4.97 12.85
61.22 4.97 12.85
61.21 4.85 4.87 4.97 12.84
- 61.20 4.83 4.88 4.91 4.94 5.00 12.83
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61.18 4.83 4.97 5.04 12.81
61.17 4.82 4.97 5.03 12.79
61.16 4.78 4.98 5.03 12.78
@@ -132475,7 +132758,7 @@ Norway
61.07 4.63 4.72 4.78 4.96 5.03 12.73
61.06 4.63 4.72 4.78 4.83 4.86 4.94 5.01 12.72
61.05 4.63 4.73 4.78 4.82 4.87 4.92 5.00 12.72
- 61.04 4.63 4.74 4.78 4.82 4.88 4.91 4.99 12.72
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61.03 4.63 4.74 4.79 4.81 4.99 12.54 12.62 12.71
61.02 4.63 4.74 4.99 12.48
61.01 4.63 4.74 4.99 12.40
@@ -132485,23 +132768,23 @@ Norway
60.97 4.69 4.71 4.98 12.28
60.96 4.97 12.28
60.95 4.81 4.84 4.97 12.29
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60.93 4.76 4.89 4.97 12.31
60.92 4.76 4.89 4.99 12.31
60.91 4.77 4.90 4.99 12.32
- 60.90 4.77 4.91 5.00 12.32
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60.89 4.82 4.92 5.00 12.32
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60.87 4.85 4.93 5.01 12.33
60.86 4.86 4.93 5.02 12.33
60.85 4.86 4.93 5.02 12.33
60.84 4.88 4.93 5.03 12.34
60.83 5.03 12.34
60.82 5.05 12.35
- 60.81 4.93 5.02 5.10 12.35
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+ 60.81 4.91 5.02 5.10 12.35
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60.79 4.91 5.05 5.23 12.36
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60.77 4.95 5.14 5.22 12.37
60.76 4.97 5.16 5.22 12.38
60.75 4.98 5.20 5.22 12.39
@@ -132539,14 +132822,14 @@ Norway
60.43 4.93 4.99 5.10 5.21 5.24 12.62
60.42 4.93 5.00 5.10 5.21 5.24 12.62
60.41 4.93 5.00 5.10 5.21 5.25 12.61
- 60.40 4.93 5.01 5.10 5.20 5.26 12.61
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60.39 4.94 5.03 5.11 12.61
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60.37 4.95 5.05 5.13 12.59
60.36 4.95 5.07 5.13 12.58
60.35 4.95 5.08 5.13 12.57
60.34 4.95 5.09 5.13 12.56
- 60.33 4.95 5.09 5.13 12.55
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60.32 4.96 5.10 5.16 12.53
60.31 4.96 5.10 5.15 12.51
60.30 4.93 5.10 5.15 12.50
@@ -132563,22 +132846,22 @@ Norway
60.19 5.04 5.12 5.23 5.27 5.29 5.51 5.55 5.96 6.06 12.53
60.18 5.04 5.11 5.29 5.50 5.55 5.94 6.06 12.53
60.17 5.07 5.10 5.31 5.48 5.53 5.93 6.06 12.53
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60.15 5.34 5.43 5.53 5.66 5.69 5.92 6.07 12.53
60.14 5.34 5.43 5.54 5.66 5.70 5.90 6.08 12.53
60.13 5.36 5.43 5.56 5.65 5.70 5.86 6.08 12.53
60.12 5.19 5.23 5.39 5.42 5.58 5.61 5.71 5.87 6.09 12.52
60.11 5.19 5.24 5.69 5.87 6.09 12.52
60.10 5.19 5.25 5.69 5.88 6.08 12.52
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60.06 5.16 5.31 5.45 5.88 6.00 12.48
60.05 5.16 5.31 5.43 5.88 5.99 12.47
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60.00 5.19 5.29 5.35 5.67 5.69 5.85 5.93 12.39
59.99 5.20 5.28 5.35 5.66 5.69 5.83 5.93 12.38
59.98 5.23 5.65 5.71 5.76 5.93 12.36
@@ -132586,33 +132869,33 @@ Norway
59.96 5.26 5.62 5.83 12.33
59.95 5.26 5.62 5.79 12.32
59.94 5.26 5.63 5.76 12.30
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59.89 5.24 5.54 5.72 12.18
59.88 5.10 5.16 5.24 5.52 5.70 11.92 12.02 12.16
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59.86 5.09 5.17 5.24 5.50 5.63 11.86
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59.84 5.10 5.21 5.26 5.50 5.63 11.85
59.83 5.08 5.23 5.27 5.50 5.64 11.86
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59.78 5.06 5.50 5.77 11.91
59.77 5.06 5.49 5.78 11.91
59.76 5.06 5.48 5.79 11.91
59.75 5.06 5.33 5.35 5.46 5.88 11.91
59.74 5.13 5.33 5.37 5.44 5.47 5.49 5.84 11.91
59.73 5.13 5.21 5.23 5.34 5.45 5.49 5.79 11.90
- 59.72 5.12 5.20 5.25 5.34 5.43 5.50 5.79 11.90
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59.66 5.10 5.21 5.35 5.51 5.53 11.86
59.65 5.10 5.20 5.33 11.85
59.64 5.10 5.21 5.31 11.83
@@ -132626,14 +132909,14 @@ Norway
59.56 5.21 10.60 10.63 11.68
59.55 5.19 10.59 10.63 11.69
59.54 5.19 10.58 10.63 11.69
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59.52 5.17 10.39 10.41 10.55 10.63 11.70
59.51 5.17 10.38 10.41 10.53 10.64 11.71
59.50 5.17 10.34 10.42 10.50 10.63 11.71
59.49 5.17 10.35 10.62 11.72
59.48 5.17 10.35 10.61 11.73
59.47 5.17 10.36 10.60 11.73
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59.45 5.18 10.46 10.59 11.74
59.44 5.18 10.47 10.58 11.75
59.43 5.18 10.48 10.58 11.76
@@ -132643,118 +132926,118 @@ Norway
59.39 5.17 10.49 10.64 11.78
59.38 5.17 5.86 5.88 10.48 10.63 11.78
59.37 5.17 5.86 5.89 10.47 10.63 11.79
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58.31 6.20 8.56
58.30 6.23 8.55
58.29 6.28 8.54
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58.24 6.50 8.51
58.23 6.54 8.41
58.22 6.65 8.34
@@ -132767,39 +133050,39 @@ Norway
58.15 6.57 8.24
58.14 6.55 8.23
58.13 6.52 8.23
- 58.12 6.52 7.99 8.01 8.15 8.17 8.23
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58.11 6.52 7.97 8.02 8.15 8.19 8.22
58.10 6.52 7.96 8.03 8.14
58.09 6.53 7.96 8.07 8.13
58.08 6.54 7.96
58.07 6.56 6.79 6.82 7.94
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58.04 6.74 6.78 6.89 7.71
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58.00 6.98 7.08 7.35 7.58
57.99 6.98 7.08
57.98 6.98 7.05
Oman
- 26.39 56.35 56.38
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26.38 56.35 56.41
26.37 56.35 56.42
- 26.36 56.35 56.43 56.47 56.51
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26.34 56.34 56.52
26.33 56.32 56.52
26.32 56.31 56.52
26.31 56.31 56.51
- 26.30 56.30 56.47
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26.29 56.30 56.45
26.28 56.30 56.43
26.27 56.19 56.21 56.30 56.42
26.26 56.18 56.21 56.30 56.42
26.25 56.17 56.21 56.29 56.43 56.45 56.48
- 26.24 56.16 56.22 56.29 56.49
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+ 26.23 56.16 56.22 56.25 56.49
26.22 56.15 56.49
26.21 56.14 56.48
26.20 56.13 56.48
@@ -132807,9 +133090,9 @@ Oman
26.18 56.12 56.47
26.17 56.12 56.48
26.16 56.11 56.48
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26.12 56.09 56.38
26.11 56.08 56.38
26.10 56.08 56.48
@@ -132831,10 +133114,10 @@ Oman
25.94 56.16 56.46
25.93 56.16 56.46
25.92 56.16 56.45
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25.87 56.15 56.40
25.86 56.14 56.39
25.85 56.14 56.39
@@ -132863,38 +133146,41 @@ Oman
25.62 56.17 56.28
25.61 56.18 56.28
25.60 56.19 56.26
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25.20 56.20 56.26
24.98 55.91 55.98 56.31 56.39
24.97 55.88 56.00 56.30 56.39
24.96 55.86 56.01 56.30 56.39
- 24.95 55.85 56.01 56.30 56.40
- 24.94 55.83 56.02 56.30 56.40
+ 24.95 55.84 56.01 56.30 56.40
+ 24.94 55.82 56.02 56.30 56.40
24.93 55.81 56.02 56.30 56.40
24.92 55.80 56.02 56.30 56.40
24.91 55.80 56.02 56.30 56.41
- 24.90 55.79 56.02 56.29 56.41
- 24.89 55.78 56.03 56.28 56.42
- 24.88 55.78 56.03 56.27 56.42
- 24.87 55.77 56.03 56.26 56.43
+ 24.90 55.79 56.03 56.29 56.41
+ 24.89 55.78 56.03 56.28 56.41
+ 24.88 55.78 56.03 56.26 56.42
+ 24.87 55.77 56.03 56.25 56.42
24.86 55.77 56.03 56.24 56.43
- 24.85 55.77 56.03 56.23 56.44
+ 24.85 55.77 56.03 56.23 56.43
24.84 55.77 56.00 56.17 56.44
- 24.83 55.77 56.01 56.16 56.45
- 24.82 55.77 56.01 56.16 56.46
- 24.81 55.77 56.02 56.15 56.46
- 24.80 55.77 56.02 56.15 56.47
- 24.79 55.78 56.03 56.14 56.47
+ 24.83 55.77 56.01 56.16 56.44
+ 24.82 55.77 56.01 56.16 56.45
+ 24.81 55.77 56.02 56.15 56.45
+ 24.80 55.77 56.02 56.15 56.46
+ 24.79 55.78 56.03 56.14 56.46
24.78 55.78 56.03 56.13 56.48
24.77 55.78 56.04 56.12 56.49
24.76 55.78 56.04 56.12 56.49
@@ -132987,9 +133273,9 @@ Oman
23.89 55.48 57.34
23.88 55.50 57.38
23.87 55.51 57.42
- 23.86 55.52 57.46
- 23.85 55.52 57.50
- 23.84 55.52 57.53
+ 23.86 55.52 57.45
+ 23.85 55.52 57.49
+ 23.84 55.52 57.52
23.83 55.52 57.55
23.82 55.52 57.57
23.81 55.52 57.62
@@ -132998,7 +133284,7 @@ Oman
23.78 55.52 57.81
23.77 55.52 57.81
23.76 55.52 57.82
- 23.75 55.51 57.83
+ 23.75 55.51 57.85
23.74 55.50 57.87
23.73 55.50 57.90 57.97 58.11
23.72 55.49 58.15
@@ -133091,8 +133377,8 @@ Oman
22.85 55.18 59.28
22.84 55.18 59.29
22.83 55.18 59.29
- 22.82 55.18 59.30
- 22.81 55.18 59.30
+ 22.82 55.18 59.29
+ 22.81 55.18 59.29
22.80 55.18 59.30
22.79 55.18 59.31
22.78 55.18 59.34
@@ -133111,8 +133397,8 @@ Oman
22.65 55.20 59.45
22.64 55.20 59.46
22.63 55.21 59.48
- 22.62 55.22 59.49
- 22.61 55.23 59.50
+ 22.62 55.22 59.50
+ 22.61 55.23 59.51
22.60 55.23 59.52
22.59 55.24 59.54
22.58 55.25 59.54 59.60 59.64
@@ -133172,21 +133458,21 @@ Oman
22.04 55.59 59.69
22.03 55.60 59.68
22.02 55.60 59.68
- 22.01 55.61 59.68
+ 22.01 55.61 59.67
22.00 55.61 59.67
- 21.99 55.62 59.67
- 21.98 55.62 59.67
- 21.97 55.62 59.67
- 21.96 55.61 59.67
+ 21.99 55.62 59.66
+ 21.98 55.62 59.66
+ 21.97 55.62 59.66
+ 21.96 55.61 59.66
21.95 55.61 59.66
21.94 55.61 59.66
- 21.93 55.60 59.66
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21.92 55.60 59.66
21.91 55.60 59.65
- 21.90 55.59 59.63
- 21.89 55.59 59.61
+ 21.90 55.60 59.63
+ 21.89 55.60 59.61
21.88 55.59 59.60
- 21.87 55.58 59.60
+ 21.87 55.59 59.60
21.86 55.58 59.59
21.85 55.58 59.59
21.84 55.57 59.58
@@ -133261,10 +133547,10 @@ Oman
21.15 55.34 58.94
21.14 55.34 58.93
21.13 55.34 58.92
- 21.12 55.33 58.91
+ 21.12 55.34 58.91
21.11 55.33 58.91
21.10 55.33 58.90
- 21.09 55.32 58.89
+ 21.09 55.33 58.89
21.08 55.32 58.89
21.07 55.32 58.88
21.06 55.32 58.87
@@ -133301,7 +133587,7 @@ Oman
20.75 55.21 58.73
20.74 55.21 58.72
20.73 55.21 58.71
- 20.72 55.20 58.70
+ 20.72 55.20 58.69
20.71 55.20 58.67
20.70 55.20 58.66 58.88 58.91
20.69 55.19 58.66 58.87 58.92
@@ -133326,9 +133612,9 @@ Oman
20.50 55.13 58.07 58.22 58.55 58.77 58.96
20.49 55.12 58.08 58.21 58.55 58.77 58.96
20.48 55.12 58.08 58.21 58.54 58.77 58.94
- 20.47 55.12 58.08 58.20 58.54 58.77 58.93
- 20.46 55.12 58.08 58.20 58.54 58.75 58.91
- 20.45 55.11 58.06 58.20 58.54 58.75 58.90
+ 20.47 55.12 58.08 58.20 58.54 58.76 58.93
+ 20.46 55.12 58.07 58.20 58.54 58.75 58.91
+ 20.45 55.11 58.06 58.20 58.54 58.74 58.90
20.44 55.11 58.03 58.19 58.53 58.69 58.88
20.43 55.11 58.01 58.19 58.53 58.68 58.86
20.42 55.10 57.99 58.19 58.53 58.68 58.85
@@ -133336,7 +133622,7 @@ Oman
20.40 55.10 57.97 58.19 58.52 58.66 58.84
20.39 55.10 57.97 58.19 58.49 58.64 58.83
20.38 55.09 57.97 58.21 58.48 58.64 58.82
- 20.37 55.09 57.98 58.26 58.48 58.63 58.82
+ 20.37 55.09 57.98 58.25 58.48 58.63 58.82
20.36 55.09 57.98 58.26 58.31 58.36 58.47 58.63 58.81
20.35 55.08 57.98 58.26 58.29 58.38 58.47 58.63 58.81
20.34 55.08 57.98 58.40 58.46 58.63 58.81
@@ -133357,7 +133643,7 @@ Oman
20.19 55.03 57.83 58.62 58.70
20.18 55.02 57.83 58.63 58.69
20.17 55.02 57.83 58.63 58.69
- 20.16 55.02 57.84 58.64 58.68
+ 20.16 55.02 57.84 58.63 58.68
20.15 55.01 57.84
20.14 55.01 57.85
20.13 55.00 57.85
@@ -133407,8 +133693,8 @@ Oman
19.69 54.02 57.71
19.68 53.98 57.71
19.67 53.95 57.72
- 19.66 53.92 57.73
- 19.65 53.89 57.73
+ 19.66 53.92 57.72
+ 19.65 53.89 57.72
19.64 53.87 57.73
19.63 53.84 57.73
19.62 53.81 57.73
@@ -133464,13 +133750,13 @@ Oman
19.12 52.33 57.82
19.11 52.30 57.81
19.10 52.27 57.81
- 19.09 52.24 57.82
- 19.08 52.21 57.82
- 19.07 52.17 57.83
- 19.06 52.14 57.83
- 19.05 52.11 57.84
- 19.04 52.08 57.84
- 19.03 52.05 57.85
+ 19.09 52.24 57.81
+ 19.08 52.20 57.82
+ 19.07 52.17 57.82
+ 19.06 52.13 57.83
+ 19.05 52.09 57.83
+ 19.04 52.06 57.84
+ 19.03 52.03 57.84
19.02 52.01 57.85
19.01 51.98 57.85
19.00 51.96 57.85
@@ -133511,14 +133797,14 @@ Oman
18.65 52.11 56.74
18.64 52.11 56.73
18.63 52.12 56.72
- 18.62 52.12 56.71
- 18.61 52.13 56.70
- 18.60 52.13 56.69
- 18.59 52.14 56.68
- 18.58 52.14 56.67
- 18.57 52.15 56.67
+ 18.62 52.12 56.70
+ 18.61 52.13 56.69
+ 18.60 52.13 56.68
+ 18.59 52.14 56.67
+ 18.58 52.14 56.66
+ 18.57 52.15 56.66
18.56 52.15 56.66
- 18.55 52.15 56.66
+ 18.55 52.15 56.65
18.54 52.16 56.65
18.53 52.16 56.65
18.52 52.17 56.65
@@ -133536,13 +133822,13 @@ Oman
18.40 52.22 56.63
18.39 52.22 56.63
18.38 52.23 56.62
- 18.37 52.23 56.62
- 18.36 52.24 56.62
- 18.35 52.24 56.62
- 18.34 52.25 56.62
- 18.33 52.25 56.62
- 18.32 52.26 56.62
- 18.31 52.26 56.62
+ 18.37 52.23 56.61
+ 18.36 52.24 56.61
+ 18.35 52.24 56.61
+ 18.34 52.25 56.61
+ 18.33 52.25 56.61
+ 18.32 52.26 56.61
+ 18.31 52.26 56.61
18.30 52.27 56.61
18.29 52.27 56.61
18.28 52.28 56.61
@@ -133581,7 +133867,7 @@ Oman
17.95 52.42 56.36
17.94 52.43 56.36
17.93 52.43 56.15 56.22 56.36
- 17.92 52.44 56.00 56.07 56.13 56.30 56.36
+ 17.92 52.44 56.00 56.07 56.13 56.30 56.35
17.91 52.44 55.98
17.90 52.45 55.96
17.89 52.45 55.93
@@ -133621,7 +133907,7 @@ Oman
17.55 52.60 55.25 56.00 56.06
17.54 52.60 55.24 55.98 56.08
17.53 52.61 55.24 55.96 56.09
- 17.52 52.61 55.23 55.83 55.88 55.95 56.10
+ 17.52 52.61 55.23 55.82 55.88 55.95 56.10
17.51 52.62 55.23 55.82 55.90 55.95 56.10
17.50 52.62 55.23 55.82 55.90 55.95 56.10
17.49 52.62 55.24 55.82 55.90 55.95 56.09
@@ -133676,9 +133962,9 @@ Oman
17.00 52.90 54.21 54.65 55.03
16.99 52.91 54.08 54.67 54.99
16.98 52.91 54.06 54.67 54.98
- 16.97 52.92 54.04 54.68 54.95
+ 16.97 52.92 54.04 54.67 54.95
16.96 52.92 54.02 54.68 54.91
- 16.95 52.93 54.02 54.68 54.90
+ 16.95 52.93 54.02 54.70 54.90
16.94 52.93 54.02 54.72 54.83
16.93 52.94 54.02
16.92 52.94 54.01
@@ -133773,7 +134059,7 @@ Pakistan
36.48 71.76 75.97
36.47 71.76 75.98
36.46 71.60 71.66 71.76 75.98
- 36.45 71.59 71.68 71.76 75.98
+ 36.45 71.59 71.68 71.76 75.99
36.44 71.58 71.70 71.76 75.99
36.43 71.58 71.71 71.76 75.99
36.42 71.57 71.72 71.77 75.99
@@ -133923,10 +134209,10 @@ Pakistan
34.98 71.47 77.03
34.97 71.46 77.02
34.96 71.46 77.01
- 34.95 71.43 76.99
- 34.94 71.41 76.98
- 34.93 71.38 76.96
- 34.92 71.35 76.80 76.86 76.95
+ 34.95 71.44 76.99
+ 34.94 71.42 76.98
+ 34.93 71.39 76.96
+ 34.92 71.36 76.80 76.86 76.95
34.91 71.33 76.78 76.88 76.94
34.90 71.31 76.76
34.89 71.29 76.76
@@ -133956,7 +134242,7 @@ Pakistan
34.65 71.05 73.99 74.74 76.02 76.10 76.18
34.64 71.05 73.94 74.80 76.00
34.63 71.05 73.92 74.86 76.00
- 34.62 71.05 73.92 74.92 75.15 75.22 75.99
+ 34.62 71.05 73.92 74.92 75.15 75.21 75.99
34.61 71.06 73.92 74.98 75.07 75.23 75.98
34.60 71.06 73.93 75.24 75.97
34.59 71.06 73.93 75.24 75.93
@@ -134184,7 +134470,7 @@ Pakistan
32.37 69.22 75.27
32.36 69.22 75.28
32.35 69.23 75.29
- 32.34 69.23 75.31
+ 32.34 69.23 75.30
32.33 69.24 75.32
32.32 69.24 75.33
32.31 69.25 75.34
@@ -134460,7 +134746,7 @@ Pakistan
29.61 61.06 61.76 65.26 73.27
29.60 61.06 61.79 65.21 73.27
29.59 61.07 61.82 65.19 73.26
- 29.58 61.08 61.85 64.45 64.58 65.15 73.26
+ 29.58 61.08 61.85 64.45 64.59 65.15 73.26
29.57 61.09 61.89 64.41 64.87 65.10 73.26
29.56 61.10 61.93 64.38 64.95 65.05 73.25
29.55 61.11 61.97 64.35 73.25
@@ -134475,8 +134761,8 @@ Pakistan
29.46 61.20 62.29 62.99 63.86 64.13 73.20
29.45 61.21 62.33 62.84 63.90 64.13 73.19
29.44 61.22 62.36 62.74 63.95 64.12 73.19
- 29.43 61.22 62.40 62.59 63.99 64.12 73.18
- 29.42 61.23 62.45 62.51 64.02 64.11 73.17
+ 29.43 61.22 62.40 62.61 63.99 64.12 73.18
+ 29.42 61.23 62.45 62.53 64.02 64.11 73.17
29.41 61.24 64.04 64.11 73.17
29.40 61.25 64.07 64.09 73.16
29.39 61.26 73.16
@@ -134884,41 +135170,41 @@ Pakistan
25.37 61.61 65.35 65.37 65.80 66.53 70.69
25.36 61.61 63.64 63.76 65.33 65.37 65.44 65.49 65.78 66.53 70.70
25.35 61.61 63.59 63.81 65.23 65.28 65.31 65.39 65.42 65.53 65.72 66.53 70.71
- 25.34 61.61 63.57 63.85 65.23 65.57 65.70 66.54 70.72
- 25.33 61.61 63.55 63.88 65.22 65.61 65.68 66.55 70.72
+ 25.34 61.61 63.57 63.85 65.23 65.56 65.70 66.54 70.72
+ 25.33 61.61 63.55 63.88 65.22 65.60 65.68 66.55 70.72
25.32 61.61 63.53 63.92 64.03 64.08 65.21 66.57 70.72
25.31 61.61 63.53 64.11 65.20 66.59 70.72
25.30 61.61 63.52 64.15 64.73 64.84 64.88 64.95 65.19 66.60 70.73
- 25.29 61.61 63.51 64.24 64.71 65.07 65.19 66.61 70.73
+ 25.29 61.61 63.51 64.24 64.71 65.06 65.19 66.61 70.73
25.28 61.61 63.50 64.25 64.70 65.12 65.18 66.62 70.73
25.27 61.60 63.49 64.33 64.69 66.63 70.74
- 25.26 61.60 63.49 64.37 64.68 66.65 70.75
+ 25.26 61.60 63.50 64.37 64.68 66.64 70.75
25.25 61.59 63.50 64.38 64.51 64.57 64.68 66.66 70.76
- 25.24 61.59 62.57 62.79 63.13 63.15 63.51 64.39 64.51 64.60 64.67 66.67 70.77
- 25.23 61.58 62.49 62.83 63.11 63.20 63.52 64.40 64.50 64.60 64.67 66.69 70.79
+ 25.24 61.59 62.50 62.79 63.13 63.15 63.51 64.39 64.51 64.60 64.67 66.67 70.77
+ 25.23 61.58 62.48 62.83 63.11 63.20 63.52 64.40 64.50 64.60 64.67 66.69 70.79
25.22 61.58 62.49 62.87 63.09 63.25 63.52 64.42 64.46 64.61 64.67 66.70 70.80
25.21 61.57 62.49 62.91 63.07 63.27 63.52 64.61 64.69 66.70 70.81
- 25.20 61.57 62.17 62.26 62.49 63.41 63.52 64.60 64.71 66.71 70.83
- 25.19 61.57 62.13 62.27 62.43 62.45 62.48 63.43 63.52 64.60 64.71 66.71 70.84
- 25.18 61.69 62.10 62.28 62.40 63.45 63.51 64.59 64.72 66.72 70.84
- 25.17 61.70 62.08 62.30 62.38 64.59 64.72 66.72 70.85
- 25.16 61.73 62.08 62.30 62.37 64.59 64.72 66.72 70.85
- 25.15 61.75 62.09 62.30 62.36 64.62 64.68 66.72 70.86
- 25.14 61.75 62.10 62.30 62.35 66.71 70.86
- 25.13 61.75 62.10 62.27 62.35 66.70 70.86
- 25.12 61.75 62.11 62.26 62.40 66.70 70.87
- 25.11 61.73 62.11 62.26 62.40 66.69 70.87
- 25.10 61.72 61.92 61.98 62.11 62.26 62.40 66.69 70.87
- 25.09 61.71 61.90 62.05 62.10 62.28 62.39 66.69 70.88
- 25.08 61.71 61.88 62.31 62.38 66.69 70.88
- 25.07 61.71 61.88 66.69 70.88
- 25.06 61.71 61.87 66.69 70.88
+ 25.20 61.57 62.17 62.20 62.49 63.41 63.52 64.60 64.71 66.71 70.83
+ 25.19 61.57 62.13 62.25 62.43 62.45 62.48 63.43 63.52 64.60 64.71 66.71 70.84
+ 25.18 61.69 62.10 62.26 62.40 63.45 63.51 64.59 64.72 66.72 70.84
+ 25.17 61.70 62.08 62.28 62.38 64.59 64.72 66.72 70.85
+ 25.16 61.73 62.08 62.28 62.37 64.59 64.72 66.72 70.85
+ 25.15 61.75 62.08 62.29 62.36 64.62 64.68 66.72 70.86
+ 25.14 61.75 62.08 62.29 62.35 66.71 70.86
+ 25.13 61.75 62.08 62.27 62.35 66.70 70.86
+ 25.12 61.75 62.09 62.27 62.37 66.70 70.87
+ 25.11 61.73 62.10 62.25 62.39 66.69 70.87
+ 25.10 61.72 62.10 62.24 62.39 66.69 70.87
+ 25.09 61.71 62.10 62.24 62.39 66.68 70.88
+ 25.08 61.71 61.88 62.24 62.39 66.68 70.88
+ 25.07 61.71 61.87 62.30 62.39 66.68 70.88
+ 25.06 61.71 61.87 66.68 70.88
25.05 61.71 61.86 66.68 70.89
25.04 61.71 61.86 66.68 70.89
- 25.03 61.72 61.85 66.68 70.89
- 25.02 61.73 61.78 61.82 61.85 66.68 70.90
- 25.01 66.68 70.90
- 25.00 66.68 70.90
+ 25.03 61.71 61.85 66.68 70.89
+ 25.02 61.71 61.85 66.68 70.90
+ 25.01 61.71 61.83 66.68 70.90
+ 25.00 61.73 61.81 66.68 70.90
24.99 66.68 70.91
24.98 66.67 70.91
24.97 66.67 70.91
@@ -134939,15 +135225,15 @@ Pakistan
24.82 66.64 66.71 66.79 66.82 66.89 71.00
24.81 66.91 71.01
24.80 66.93 66.97 66.99 71.01
- 24.79 66.95 66.97 67.01 71.02
- 24.78 67.03 71.02
+ 24.79 67.02 71.02
+ 24.78 67.04 71.02
24.77 67.05 67.09 67.15 71.02
24.76 67.07 67.09 67.15 71.03
24.75 67.15 71.03
- 24.74 67.15 71.04
- 24.73 67.21 71.04
- 24.72 67.19 71.05
- 24.71 67.18 71.05
+ 24.74 67.16 71.04
+ 24.73 67.20 71.04
+ 24.72 67.18 71.05
+ 24.71 67.17 71.05
24.70 67.17 71.06
24.69 67.16 71.07
24.68 67.15 71.07
@@ -135023,7 +135309,7 @@ Pakistan
23.98 67.44 68.73
23.97 67.44 68.73
23.96 67.48 68.73
- 23.95 67.49 68.73
+ 23.95 67.48 68.73
23.94 67.48 68.38
23.93 67.48 68.37
23.92 67.48 68.36
@@ -135034,10 +135320,10 @@ Pakistan
23.87 67.48 68.24
23.86 67.51 68.21
23.85 67.57 68.20
- 23.84 67.59 68.20
- 23.83 67.60 67.84 67.89 68.19
- 23.82 67.61 67.84 67.90 68.18
- 23.81 67.61 67.84 67.92 68.18
+ 23.84 67.58 68.20
+ 23.83 67.62 67.84 67.89 68.19
+ 23.82 67.61 67.84 67.89 68.18
+ 23.81 67.61 67.84 67.92 68.17
23.80 67.61 67.75 67.78 67.84 67.93 68.17
23.79 67.62 67.75 67.81 67.84 67.94 68.16
23.78 67.67 67.74 67.99 68.16
@@ -135052,6 +135338,13 @@ Pakistan
23.69 68.07 68.10 68.12 68.16
23.68 68.13 68.16
Palau
+ 8.10 134.69 134.73
+ 8.09 134.69 134.73
+ 8.08 134.68 134.73
+ 8.07 134.68 134.73
+ 8.06 134.68 134.73
+ 8.05 134.68 134.72
+ 8.04 134.69 134.72
7.74 134.61 134.64
7.73 134.61 134.65
7.72 134.61 134.65
@@ -135077,7 +135370,7 @@ Palau
7.52 134.50 134.63
7.51 134.50 134.64
7.50 134.50 134.64
- 7.49 134.49 134.64
+ 7.49 134.48 134.64
7.48 134.48 134.64
7.47 134.47 134.64
7.46 134.47 134.63
@@ -135113,8 +135406,8 @@ Palau
7.05 134.24 134.29
7.04 134.24 134.29
7.03 134.23 134.29
- 7.02 134.23 134.29
- 7.01 134.22 134.29
+ 7.02 134.23 134.28
+ 7.01 134.22 134.28
7.00 134.22 134.28
6.99 134.22 134.26
6.98 134.22 134.25
@@ -135126,7 +135419,7 @@ Palau
6.90 134.12 134.18
6.89 134.12 134.18
6.88 134.13 134.18
- 6.87 134.15 134.17
+ 6.87 134.14 134.17
5.32 132.21 132.23
5.31 132.20 132.23
5.30 132.20 132.23
@@ -135154,198 +135447,198 @@ Palmyra Atoll
5.86 -162.10 -162.05
5.85 -162.08 -162.06
Panama
- 9.63 -79.54 -79.52
- 9.62 -79.56 -79.51
- 9.61 -82.85 -82.81 -79.58 -79.51
- 9.60 -82.86 -82.79 -79.63 -79.51 -79.46 -79.44
- 9.59 -82.87 -82.77 -79.64 -79.48 -79.46 -79.40
- 9.58 -82.87 -82.76 -82.58 -82.56 -79.66 -79.34
- 9.57 -82.88 -82.74 -82.58 -82.55 -79.68 -79.28
- 9.56 -82.88 -82.72 -82.58 -82.53 -79.68 -79.26 -79.03 -78.98
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Papua New Guinea
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Philippines
21.13 121.94 121.96
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@@ -139107,16 +139399,16 @@ Philippines
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@@ -139204,7 +139496,7 @@ Philippines
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@@ -139214,8 +139506,8 @@ Philippines
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@@ -139378,11 +139670,11 @@ Philippines
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@@ -139424,7 +139716,7 @@ Philippines
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@@ -139456,7 +139748,7 @@ Philippines
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@@ -139464,10 +139756,10 @@ Philippines
16.12 119.76 120.11 120.36 121.97 122.02 122.09
16.11 119.76 120.11 120.35 121.93 122.01 122.08
16.10 119.76 120.11 120.34 121.86 122.01 122.08
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- 16.06 119.74 120.13 120.24 121.80 121.99 122.06
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16.05 119.74 120.16 120.23 121.75 121.99 122.05
16.04 119.74 121.73 121.98 122.03
16.03 119.74 121.72 121.98 122.01
@@ -139505,8 +139797,8 @@ Philippines
15.71 119.86 121.64
15.70 119.87 121.63
15.69 119.89 121.62
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15.66 119.91 121.63
15.65 119.90 121.63
15.64 119.90 121.62
@@ -139538,7 +139830,7 @@ Philippines
15.38 119.90 121.45
15.37 119.91 121.44
15.36 119.92 121.43
- 15.35 119.93 121.40
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15.34 119.94 121.39
15.33 119.95 121.39
15.32 119.95 121.39
@@ -139567,7 +139859,7 @@ Philippines
15.09 120.03 121.51
15.08 120.03 121.51
15.07 120.03 121.51
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15.05 120.04 121.53 121.83 121.85 121.89 122.00
15.04 120.04 121.54 121.82 121.87 121.89 122.01
15.03 120.04 121.54 121.82 122.02
@@ -139575,35 +139867,35 @@ Philippines
15.01 120.04 121.56 121.81 122.04
15.00 120.04 121.56 121.81 122.05
14.99 120.04 121.57 121.81 122.06
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14.89 120.04 121.61 121.85 121.98
14.88 120.04 121.62 121.86 121.98
14.87 120.04 121.62 121.87 121.98
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14.85 120.05 121.61 121.86 122.00 122.09 122.14
14.84 120.05 121.62 121.86 122.00 122.09 122.21
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14.74 120.15 120.18 120.24 120.55 120.83 121.73 121.92 122.03 122.21 122.26 122.38 122.41
14.73 120.23 120.54 120.83 121.73 121.90 122.03 122.23 122.26 122.35 122.42
14.72 120.23 120.54 120.85 121.73 121.90 122.03 122.23 122.25 122.33 122.42
14.71 120.23 120.54 120.87 121.73 121.90 122.03 122.31 122.42
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14.69 120.24 120.56 120.89 121.64 121.90 122.02 122.30 122.42
14.68 120.24 120.56 120.90 121.63 121.89 122.02 122.30 122.41
14.67 120.25 120.57 120.90 121.62 121.89 122.01 122.30 122.40
@@ -139611,7 +139903,7 @@ Philippines
14.65 120.26 120.59 120.92 121.61 121.89 122.00
14.64 120.27 120.59 120.93 121.61 121.90 121.99
14.63 120.28 120.59 120.93 121.61 121.90 121.98
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14.61 120.35 120.59 120.94 121.62
14.60 120.35 120.59 120.94 121.62
14.59 120.36 120.59 120.94 121.63
@@ -139637,8 +139929,8 @@ Philippines
14.39 120.78 121.69
14.38 120.77 121.70
14.37 120.76 121.71
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14.34 120.74 121.73 122.44 122.56 122.66 122.71 122.74 122.76
14.33 120.72 121.74 122.40 122.61 122.66 122.77
14.32 120.72 121.74 122.40 122.63 122.66 122.79
@@ -139655,17 +139947,17 @@ Philippines
14.21 120.57 121.76 121.91 121.99 122.22 122.27 122.32 122.94
14.20 120.57 121.76 121.91 122.00 122.20 122.27 122.32 122.94
14.19 120.57 121.75 121.91 122.02 122.18 122.27 122.31 122.95
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14.17 120.56 121.76 121.92 122.04 122.15 122.27 122.31 122.96
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14.15 120.57 121.77 121.93 122.06 122.15 122.30 122.33 122.98
14.14 120.57 121.78 121.94 122.08 122.15 122.30 122.33 122.99
14.13 120.57 121.79 121.95 122.09 122.16 122.30 122.33 123.00
14.12 120.57 121.80 121.97 122.10 122.16 123.03
14.11 120.59 121.82 121.98 122.11 122.16 123.04
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14.09 120.60 121.84 122.01 122.14 122.18 123.05 123.31 123.35 124.17 124.22
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14.07 120.61 121.86 122.03 122.17 122.19 123.05 123.24 123.36 124.11 124.24
14.06 120.61 121.87 122.05 122.18 122.21 123.05 123.24 123.37 124.11 124.25
14.05 120.61 121.88 122.06 122.18 122.24 123.05 123.24 123.37 124.11 124.26
@@ -139673,55 +139965,55 @@ Philippines
14.03 120.60 121.90 122.09 122.19 122.26 123.04 123.22 123.40 124.11 124.27
14.02 120.60 121.91 122.10 122.19 122.27 123.05 123.22 123.40 124.11 124.27
14.01 120.60 121.93 122.11 122.19 122.28 123.06 123.21 123.40 124.11 124.28
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13.90 120.60 120.71 120.82 121.67 121.80 122.47 122.57 123.09 123.27 123.65 123.68 123.74 124.11 124.40
13.89 120.60 120.71 120.88 121.64 121.80 122.47 122.57 123.09 123.27 123.75 124.11 124.41
13.88 120.60 120.72 120.89 121.63 121.81 122.48 122.60 123.09 123.27 123.76 124.11 124.42
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13.81 120.07 120.24 120.61 120.67 120.89 121.47 121.96 122.51 122.64 123.05 123.29 123.89 124.11 124.42
13.80 120.07 120.25 120.61 120.67 120.89 121.46 121.97 122.51 122.65 122.67 122.71 123.05 123.29 123.94 124.11 124.42
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13.76 120.09 120.28 120.65 120.67 120.89 120.98 121.00 121.45 122.09 122.51 122.74 123.08 123.26 123.96 124.10 124.40
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13.73 120.14 120.27 120.87 120.95 121.03 121.45 122.11 122.52 122.80 123.98 124.08 124.40
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13.71 120.20 120.29 120.87 120.94 121.04 121.45 122.12 122.49 122.82 123.85 123.91 123.98 124.06 124.40
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13.60 121.07 121.09 121.22 121.30 122.19 122.56 122.83 123.54 124.03 124.35
13.59 121.23 121.29 122.24 122.58 122.84 123.54 124.03 124.35
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13.51 120.32 120.59 120.85 120.99 121.83 122.05 122.38 122.64 122.96 123.64 124.16 124.19
13.50 120.32 120.71 120.81 120.98 121.82 122.05 122.38 122.61 123.00 123.66
13.49 120.31 120.72 120.78 120.98 121.82 122.09 122.39 122.62 123.02 123.67
@@ -139744,28 +140036,28 @@ Philippines
13.32 120.45 121.34 121.81 122.11 122.50 122.68 123.20 123.79 123.83 123.93
13.31 120.46 121.35 121.82 122.10 122.50 122.68 123.21 123.80 123.83 123.93
13.30 120.46 121.35 121.83 122.09 122.50 122.68 123.21 123.80 123.83 123.92
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13.19 120.57 121.45 121.98 122.01 122.53 122.66 123.29 123.76 124.05 124.21
13.18 120.58 121.45 122.54 122.65 123.28 123.76 124.07 124.21
13.17 120.61 121.45 122.56 122.64 123.28 123.76 124.10 124.21
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13.15 120.64 121.54 122.98 123.02 123.27 123.76 123.86 123.90
- 13.14 120.65 121.55 122.97 123.04 123.27 123.76 123.85 123.90
- 13.13 120.65 121.55 122.96 123.05 123.26 123.77 123.85 123.94
- 13.12 120.66 121.56 122.93 123.06 123.26 123.78 123.84 123.94
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13.11 120.66 121.56 122.93 123.06 123.26 123.78 123.83 123.96
13.10 120.67 121.56 122.93 123.07 123.26 123.78 123.82 124.00
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13.07 120.69 121.55 122.93 123.09 123.27 123.76 123.80 124.03 124.10 124.18
13.06 120.70 121.54 122.93 123.09 123.27 124.03 124.10 124.19
13.05 120.70 121.53 122.94 123.10 123.27 124.04 124.09 124.19
@@ -139773,24 +140065,24 @@ Philippines
13.03 120.72 121.50 122.94 123.12 123.27 124.19
13.02 120.73 121.49 122.95 123.13 123.28 123.38 123.40 124.19
13.01 120.73 121.49 122.95 123.13 123.28 123.36 123.44 124.19
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12.98 120.74 121.49 123.03 123.15 123.45 124.16
12.97 120.74 121.49 123.05 123.15 123.47 124.15
12.96 120.74 121.50 121.69 121.71 123.05 123.16 123.48 124.15
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12.94 120.75 121.50 121.67 121.73 123.07 123.17 123.50 124.14
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12.92 120.75 121.50 121.67 121.74 123.08 123.20 123.54 124.13
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12.87 120.76 121.49 123.14 123.29 123.60 124.14
12.86 120.76 121.49 123.15 123.29 123.67 124.14
12.85 120.75 121.49 123.16 123.29 123.68 124.14
12.84 120.75 121.49 123.17 123.29 123.71 123.75 123.78 124.15
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12.82 120.75 121.49 123.24 123.29 123.78 124.15
12.81 120.76 121.49 123.25 123.30 123.79 124.15
12.80 120.76 121.49 123.26 123.31 123.80 124.15
@@ -139811,33 +140103,33 @@ Philippines
12.65 120.87 121.55 122.09 122.16 123.57 123.67 123.86 124.13
12.64 120.88 121.55 122.07 122.16 123.57 123.69 123.86 124.12
12.63 120.89 121.55 122.04 122.16 123.57 123.71 123.86 124.10
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12.60 120.91 121.55 121.98 122.13 122.25 122.29 123.22 123.26 123.58 123.74 123.90 124.10 124.86 124.89
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12.56 120.91 121.52 121.98 122.14 122.23 122.31 123.22 123.35 123.60 123.74 123.94 124.10 124.26 124.35 124.38 124.43 124.87 125.02 125.08 125.20
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12.53 120.90 121.50 121.98 122.14 122.24 122.32 123.22 123.36 123.40 123.43 123.62 123.75 123.97 124.08 124.26 124.64 124.71 125.24
12.52 120.90 121.49 121.98 122.14 122.24 122.32 123.22 123.45 123.63 123.76 123.99 124.06 124.26 125.25
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12.45 120.94 121.44 121.98 122.11 122.41 122.66 123.23 123.57 123.68 123.78 124.12 124.17 124.29 125.32
12.44 120.95 121.44 121.97 122.11 122.41 122.67 123.24 123.58 123.69 123.79 124.12 124.18 124.30 125.32
12.43 120.96 121.43 121.97 122.11 122.41 122.67 123.25 123.58 123.69 123.79 124.12 124.18 124.30 125.33
12.42 120.96 121.42 121.96 122.11 122.41 122.68 123.26 123.59 123.70 123.79 124.12 124.19 124.31 125.34
12.41 120.97 121.42 121.94 122.11 122.41 122.69 123.26 123.59 123.71 123.79 124.12 124.19 124.31 125.34
12.40 120.97 121.43 121.93 122.10 122.41 122.69 123.26 123.60 123.71 123.80 124.13 124.19 124.32 125.35
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12.38 121.00 121.44 121.92 122.10 122.43 122.69 123.25 123.64 123.73 123.80 124.15 124.18 124.33 125.35
12.37 121.01 121.45 121.92 122.10 122.45 122.69 123.24 123.64 123.74 123.80 124.33 125.34
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12.35 121.02 121.45 121.91 122.10 122.50 122.69 123.24 123.68 123.75 123.80 124.34 125.32
12.34 121.03 121.39 121.42 121.45 121.91 122.10 122.51 122.69 123.24 123.69 123.75 123.80 124.34 125.32
12.33 119.87 119.92 121.04 121.39 121.91 122.09 122.52 122.68 123.24 123.71 123.76 123.80 124.34 125.33
@@ -139846,22 +140138,22 @@ Philippines
12.30 119.86 119.94 121.08 121.40 121.91 122.09 122.54 122.68 123.23 123.73 124.35 125.40
12.29 119.86 119.94 121.08 121.40 121.91 122.09 122.57 122.67 123.22 123.73 124.35 125.45
12.28 119.86 119.97 121.04 121.32 121.36 121.40 121.91 122.08 122.58 122.65 123.22 123.74 124.36 125.46
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12.26 119.86 120.03 121.02 121.29 121.93 122.07 122.59 122.62 123.20 123.75 124.36 125.48
12.25 119.86 120.04 121.02 121.28 121.95 122.07 123.20 123.75 123.78 123.81 124.37 125.51
12.24 119.85 120.05 121.02 121.27 121.96 122.06 123.20 123.82 124.37 125.51
12.23 119.85 120.06 121.03 121.27 121.95 122.06 123.20 123.83 124.37 125.52
12.22 119.85 120.07 120.21 120.24 121.03 121.11 121.19 121.26 121.95 122.05 123.20 123.84 123.86 123.89 124.38 125.53
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12.17 119.83 119.88 119.90 120.12 120.21 120.26 121.07 121.14 121.94 122.07 123.25 123.42 123.53 123.91 124.41 125.54
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12.15 119.83 119.87 119.90 120.15 120.21 120.26 121.08 121.14 121.95 122.04 123.23 123.41 123.55 123.93 124.42 125.51
12.14 119.85 119.87 119.90 120.17 120.21 120.29 121.10 121.13 121.97 122.02 123.20 123.40 123.56 123.94 124.43 125.51
12.13 119.91 120.30 121.97 122.02 123.20 123.39 123.57 123.94 124.44 125.51
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12.11 119.92 120.32 121.34 121.38 121.98 122.02 123.20 123.38 123.58 123.97 124.45 125.51
12.10 119.92 120.34 121.34 121.39 121.99 122.02 123.20 123.38 123.59 123.98 124.46 125.51
12.09 119.92 120.35 121.34 121.39 122.00 122.02 123.20 123.37 123.59 123.99 124.17 124.22 124.47 125.51
@@ -139871,20 +140163,20 @@ Philippines
12.05 119.95 120.35 121.35 121.42 123.18 123.32 123.64 124.00 124.13 124.23 124.53 125.53
12.04 119.96 120.35 121.35 121.42 123.18 123.31 123.64 124.00 124.13 124.20 124.55 125.53
12.03 119.96 120.35 121.35 121.42 123.18 123.30 123.64 124.01 124.14 124.19 124.62 125.53
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11.88 119.86 120.07 120.21 120.28 121.87 122.05 123.85 124.06 124.76 125.46
11.87 119.86 120.09 120.22 120.28 121.41 121.50 121.87 122.06 123.86 124.07 124.78 125.46
11.86 119.87 120.09 120.22 120.27 121.41 121.52 121.87 122.07 123.88 124.07 124.78 125.46
@@ -139894,46 +140186,46 @@ Philippines
11.82 119.89 120.06 120.24 120.28 121.40 121.52 121.87 122.17 123.93 124.07 124.83 125.48
11.81 119.89 120.08 120.24 120.28 121.46 121.51 121.86 122.21 123.95 124.07 124.83 125.49
11.80 119.90 120.08 120.25 120.27 121.85 122.25 123.97 124.06 124.84 125.50
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11.76 119.91 120.08 121.84 122.32 124.01 124.07 124.87 125.49
11.75 119.93 120.07 121.84 122.33 124.02 124.08 124.88 124.98 125.02 125.49
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11.73 119.94 120.07 121.97 122.39 124.03 124.08 124.72 124.74 124.91 124.95 125.02 125.50
11.72 119.94 120.07 122.00 122.40 124.03 124.08 124.72 124.75 125.01 125.51
11.71 119.94 120.06 122.07 122.40 124.04 124.07 124.71 124.76 125.00 125.51
11.70 119.94 120.06 122.08 122.41 124.39 124.52 124.71 124.78 124.99 125.51
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11.68 119.94 120.04 122.09 122.42 124.33 124.55 124.71 124.80 124.98 125.51
11.67 119.94 120.02 122.09 122.44 124.33 124.56 124.71 124.81 124.98 125.50
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11.64 122.09 122.48 124.35 124.57 124.73 124.82 124.98 125.48
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11.62 122.09 122.50 122.71 122.82 124.37 124.58 124.75 124.83 124.98 125.48
11.61 122.08 122.51 122.71 122.85 124.37 124.58 124.76 124.86 124.97 125.48
11.60 122.08 122.53 122.71 122.86 123.14 123.17 124.37 124.59 124.76 124.86 124.96 125.50
11.59 122.08 122.56 122.71 122.86 123.14 123.17 124.37 124.59 124.76 124.86 124.96 125.50
11.58 122.08 122.58 122.70 122.87 123.13 123.17 124.38 124.60 124.76 124.86 124.88 125.50
11.57 122.08 122.59 122.64 122.87 123.12 123.17 124.38 124.61 124.77 124.86 124.88 125.50
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11.55 122.08 122.60 122.63 122.92 123.10 123.17 124.29 124.35 124.39 124.63 124.79 125.50
11.54 122.08 122.60 122.63 122.94 123.08 123.17 124.29 124.36 124.40 124.63 124.80 125.51
11.53 119.83 119.86 122.07 122.60 122.63 122.95 123.06 123.17 124.28 124.36 124.40 124.63 124.81 125.52
11.52 119.82 119.87 122.07 122.95 123.03 123.17 124.28 124.37 124.40 124.63 124.82 125.52
11.51 119.81 119.87 122.07 122.95 123.02 123.16 124.28 124.38 124.41 124.63 124.81 125.53
- 11.50 119.77 119.79 119.81 119.87 122.07 122.94 123.00 123.16 124.28 124.40 124.42 124.63 124.81 125.54
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11.49 119.77 119.88 122.06 122.93 122.96 123.18 124.29 124.41 124.43 124.62 124.81 125.54
11.48 119.71 119.74 119.77 119.88 122.06 123.18 124.29 124.42 124.44 124.62 124.82 125.54
11.47 119.70 119.75 119.77 119.88 122.06 123.18 124.29 124.43 124.45 124.61 124.83 125.55
11.46 119.70 119.88 122.06 123.18 124.30 124.49 124.84 125.55
- 11.45 119.70 119.88 122.06 123.18 124.30 124.45 124.47 124.51 124.86 124.90 124.92 125.56
- 11.44 119.72 119.88 122.06 123.17 124.30 124.53 124.83 124.91 124.94 125.56
- 11.43 119.48 119.51 119.72 119.88 122.06 123.17 124.31 124.54 124.82 124.93 124.97 125.56
- 11.42 119.47 119.51 119.72 119.88 122.05 123.17 124.31 124.54 124.81 124.95 124.98 125.59
- 11.41 119.47 119.51 119.74 119.79 119.81 119.87 122.05 123.17 124.31 124.55 124.80 124.96 124.99 125.60
- 11.40 119.47 119.52 119.75 119.79 119.81 119.87 122.05 123.17 124.32 124.55 124.80 125.62
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11.39 119.47 119.52 119.76 119.78 119.81 119.86 122.05 123.17 124.32 124.56 124.79 125.63
11.38 119.46 119.52 119.81 119.85 122.05 123.17 124.32 124.56 124.78 125.64
11.37 119.46 119.52 119.81 119.85 122.05 123.17 124.33 124.56 124.77 125.64
@@ -139941,7 +140233,7 @@ Philippines
11.35 119.45 119.52 122.05 123.15 124.33 124.57 124.75 125.64
11.34 119.42 119.56 122.05 123.15 124.33 124.58 124.74 125.64
11.33 119.42 119.56 122.04 123.14 124.33 124.59 124.72 125.64
- 11.32 119.41 119.57 122.04 123.13 124.33 124.62 124.69 125.64
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11.31 119.41 119.57 122.03 123.13 124.34 125.64
11.30 119.41 119.57 122.03 123.13 123.73 123.75 124.35 125.63
11.29 119.41 119.57 122.03 123.13 123.72 123.76 124.37 125.62
@@ -139949,74 +140241,74 @@ Philippines
11.27 119.41 119.57 122.03 123.12 123.70 123.77 124.01 124.08 124.39 125.60
11.26 119.41 119.57 122.03 123.12 123.69 123.77 124.00 124.08 124.39 125.02 125.14 125.58
11.25 119.41 119.57 122.03 123.12 123.69 123.78 123.99 124.08 124.39 125.05 125.16 125.57
- 11.24 119.41 119.57 122.04 123.12 123.69 123.78 123.99 124.08 124.39 125.05 125.16 125.57 125.60 125.63
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11.23 119.41 119.57 122.04 123.12 123.69 123.78 123.98 124.07 124.39 125.05 125.17 125.56 125.60 125.65
11.22 119.41 119.57 122.04 123.14 123.69 123.78 123.97 124.07 124.39 125.05 125.17 125.56 125.60 125.67
- 11.21 119.41 119.57 119.60 119.62 122.04 123.14 123.69 123.79 123.97 124.07 124.39 125.05 125.18 125.57 125.60 125.69
- 11.20 119.40 119.63 122.04 123.14 123.69 123.79 123.96 124.06 124.39 125.05 125.18 125.70
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11.19 119.37 119.56 119.58 119.64 122.04 123.14 123.69 123.80 123.95 124.06 124.39 125.05 125.18 125.70
11.18 119.37 119.64 122.04 123.14 123.70 123.81 123.94 124.06 124.39 125.04 125.19 125.71
11.17 119.37 119.64 122.04 123.14 123.70 123.82 123.94 124.06 124.39 125.03 125.19 125.71
11.16 119.38 119.63 122.04 123.13 123.71 123.82 123.94 124.06 124.40 125.03 125.19 125.72
- 11.15 119.38 119.63 122.04 123.12 123.71 123.82 123.94 124.06 124.40 125.04 125.19 125.72
- 11.14 119.38 119.62 122.04 123.05 123.09 123.11 123.72 123.82 123.94 124.05 124.40 125.05 125.20 125.72
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+ 11.14 119.38 119.61 122.04 123.05 123.09 123.11 123.72 123.82 123.94 124.05 124.40 125.05 125.20 125.72
11.13 119.39 119.54 119.56 119.60 122.04 123.04 123.72 123.82 123.94 124.05 124.40 125.05 125.20 125.73
11.12 119.40 119.53 119.57 119.59 122.04 123.04 123.73 123.75 123.95 124.05 124.40 125.05 125.20 125.29 125.31 125.54 125.57 125.64 125.66 125.73
11.11 119.32 119.34 119.41 119.53 122.04 123.04 123.95 124.04 124.39 125.05 125.20 125.28 125.36 125.54 125.57 125.62 125.67 125.75
- 11.10 119.31 119.34 119.40 119.53 119.56 119.60 122.04 123.03 123.93 124.04 124.39 125.05 125.20 125.27 125.37 125.47 125.49 125.54 125.59 125.61 125.69 125.76
- 11.09 119.31 119.35 119.40 119.63 122.04 123.03 123.93 124.03 124.38 125.05 125.21 125.26 125.38 125.46 125.50 125.54 125.69 125.77
- 11.08 119.31 119.36 119.40 119.63 122.04 123.02 123.93 124.02 124.38 125.05 125.22 125.26 125.41 125.45 125.51 125.53 125.69 125.78
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+ 11.09 119.31 119.35 119.40 119.63 122.04 123.03 123.93 124.03 124.38 125.04 125.21 125.26 125.38 125.46 125.50 125.54 125.69 125.77
+ 11.08 119.31 119.36 119.40 119.63 122.04 123.02 123.93 124.02 124.38 125.05 125.22 125.26 125.41 125.45 125.51 125.53 125.69 125.77
11.07 119.31 119.37 119.40 119.64 122.04 123.01 123.93 124.02 124.04 124.06 124.37 125.05 125.69 125.78
- 11.06 119.31 119.65 122.04 123.00 123.92 124.06 124.37 125.06 125.70 125.79
- 11.05 119.31 119.65 122.04 122.99 123.91 124.06 124.37 125.06 125.70 125.79
- 11.04 119.32 119.65 122.03 122.98 123.91 124.06 124.37 125.06 125.70 125.79
- 11.03 119.31 119.65 122.03 122.98 123.90 124.06 124.38 125.06 125.70 125.78
- 11.02 119.31 119.65 122.03 122.97 123.90 124.06 124.38 125.06 125.73 125.78
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11.01 119.31 119.65 122.02 122.93 123.90 124.07 124.39 125.06 125.75 125.77
11.00 119.31 119.65 122.02 122.87 123.20 123.27 123.91 124.07 124.40 125.06
10.99 119.31 119.52 119.54 119.58 119.60 119.62 122.01 122.83 123.18 123.27 123.91 124.07 124.40 125.06
10.98 119.31 119.51 122.00 122.82 123.16 123.31 123.92 124.07 124.40 124.58 124.62 125.06
- 10.97 119.30 119.51 122.00 122.81 123.14 123.32 123.92 124.07 124.39 124.56 124.62 125.06
- 10.96 119.22 119.24 119.30 119.51 121.99 122.79 123.12 123.34 123.36 123.41 123.91 124.07 124.38 124.55 124.63 125.06
- 10.95 119.21 119.25 119.30 119.51 121.99 122.79 123.10 123.41 123.43 123.46 123.91 124.07 124.38 124.56 124.65 125.06
- 10.94 119.21 119.52 121.98 122.79 123.08 123.49 123.90 124.07 124.38 124.57 124.66 125.06
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10.93 119.21 119.52 121.97 122.79 123.07 123.52 123.90 124.06 124.38 124.57 124.67 125.05
10.92 119.21 119.52 121.08 121.10 121.97 122.79 122.99 123.53 123.89 124.06 124.38 124.57 124.68 125.05
10.91 119.21 119.52 121.07 121.10 121.96 122.80 122.98 123.54 123.89 124.06 124.39 124.41 124.43 124.57 124.69 125.05
10.90 119.21 119.52 121.05 121.10 121.96 122.80 122.97 123.54 123.88 124.07 124.43 124.56 124.69 125.04
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10.88 119.23 119.51 121.02 121.10 121.95 122.80 122.95 123.55 123.88 124.07 124.47 124.55 124.70 125.04
- 10.87 119.22 119.51 121.01 121.10 121.95 122.80 122.94 123.55 123.87 124.07 124.48 124.54 124.71 125.03
- 10.86 119.21 119.52 121.01 121.10 121.95 122.80 122.94 123.55 123.87 124.07 124.49 124.53 124.71 125.03
- 10.85 119.21 119.52 121.00 121.10 121.95 122.80 122.94 123.56 123.87 124.07 124.72 125.03
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10.84 119.21 119.52 119.56 119.60 121.00 121.09 121.94 122.79 122.94 123.58 123.86 124.07 124.73 125.02
10.83 119.22 119.53 119.55 119.61 121.00 121.09 121.94 122.79 122.94 123.58 123.86 124.06 124.75 125.02
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10.81 119.25 119.61 121.01 121.09 121.93 122.78 122.94 123.58 123.85 124.05 124.76 125.02 125.67 125.74
- 10.80 119.26 119.61 121.02 121.08 121.93 122.77 122.95 123.58 123.85 124.05 124.76 125.01 125.67 125.74
- 10.79 119.26 119.61 121.93 122.76 122.96 123.58 123.84 124.05 124.77 125.01 125.66 125.74
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10.78 119.26 119.60 121.92 122.68 122.70 122.75 122.96 123.58 123.84 124.05 124.77 125.01 125.66 125.75
10.77 119.26 119.61 121.92 122.68 122.71 122.74 122.96 123.58 123.83 124.04 124.77 125.02 125.66 125.75
- 10.76 119.26 119.61 121.92 122.70 122.96 123.58 123.83 124.04 124.77 125.02 125.66 125.76
- 10.75 119.27 119.61 121.92 122.71 122.96 123.58 123.83 124.03 124.78 125.04 125.66 125.82
- 10.74 119.31 119.61 121.93 122.72 122.96 123.57 123.82 124.03 124.78 125.06 125.67 125.83
- 10.73 119.32 119.61 121.94 122.72 122.96 123.56 123.82 124.03 124.78 125.08 125.69 125.83
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10.72 119.33 119.61 121.95 122.73 122.95 123.55 123.81 124.03 124.33 124.36 124.42 124.48 124.79 125.10 125.71 125.84
10.71 119.33 119.61 121.96 122.73 122.95 123.54 123.80 124.03 124.31 124.37 124.41 124.50 124.79 125.13 125.73 125.84
- 10.70 119.32 119.61 121.96 122.74 122.94 123.54 123.79 124.03 124.31 124.38 124.40 124.51 124.79 125.13 125.74 125.84
- 10.69 119.32 119.61 121.96 122.74 122.94 123.53 123.78 124.04 124.31 124.52 124.79 125.13 125.75 125.83
- 10.68 119.32 119.60 119.63 119.66 121.96 122.74 122.93 123.53 123.77 124.04 124.30 124.52 124.79 125.14 125.77 125.81
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10.67 119.32 119.66 121.96 122.74 122.93 123.52 123.76 124.04 124.29 124.53 124.79 125.14
- 10.66 119.32 119.67 121.97 122.41 122.55 122.74 122.92 123.52 123.76 124.05 124.29 124.53 124.78 125.15
- 10.65 119.31 119.67 119.83 119.87 121.97 122.35 122.54 122.74 122.92 123.52 123.75 124.05 124.29 124.53 124.78 125.16
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10.64 119.31 119.67 119.82 119.89 121.97 122.34 122.54 122.74 122.92 123.51 123.75 124.06 124.29 124.52 124.77 125.16
- 10.63 119.31 119.65 119.81 119.91 121.97 122.28 122.53 122.74 122.91 123.51 123.75 124.06 124.28 124.51 124.77 125.17
- 10.62 119.31 119.66 119.81 119.94 121.97 122.26 122.53 122.74 122.91 123.51 123.75 124.06 124.27 124.39 124.43 124.49 124.77 125.19
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10.61 119.30 119.66 119.80 119.97 121.97 122.21 122.52 122.74 122.90 123.51 123.74 124.06 124.27 124.38 124.76 125.20
- 10.60 119.30 119.66 119.80 119.99 121.96 122.20 122.51 122.74 122.90 123.51 123.74 124.06 124.27 124.37 124.76 125.20
- 10.59 119.30 119.67 119.79 120.01 121.96 122.18 122.51 122.73 122.89 123.50 123.73 124.06 124.27 124.35 124.76 125.20
- 10.58 119.29 119.67 119.78 120.01 121.96 122.17 122.51 122.73 122.87 123.50 123.72 124.06 124.28 124.33 124.75 125.20
- 10.57 119.29 119.67 119.77 120.02 121.95 122.14 122.51 122.73 122.86 123.50 123.71 124.06 124.29 124.31 124.75 125.20
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10.56 119.24 119.69 119.75 120.02 121.95 122.12 122.51 122.73 122.85 123.50 123.71 124.05 124.75 125.20
10.55 119.23 119.71 119.74 120.02 121.94 122.11 122.51 122.72 122.83 123.49 123.70 124.05 124.75 125.20
10.54 119.23 119.72 119.74 120.01 121.94 122.10 122.51 122.72 122.81 123.49 123.70 124.05 124.75 125.19
@@ -140024,33 +140316,33 @@ Philippines
10.52 119.24 120.00 121.93 122.09 122.51 122.71 122.80 123.49 123.70 124.05 124.75 125.19
10.51 119.24 119.73 119.76 119.98 121.92 122.08 122.47 122.70 122.80 123.48 123.70 124.05 124.73 125.19
10.50 119.24 119.73 119.76 119.95 121.92 122.08 122.47 122.70 122.80 123.47 123.71 124.05 124.73 125.20
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- 10.48 119.08 119.13 119.22 119.72 119.76 119.93 121.91 122.06 122.47 122.68 122.80 123.45 123.70 124.05 124.73 125.20
- 10.47 119.07 119.13 119.21 119.69 119.76 119.92 121.91 122.05 122.48 122.68 122.81 123.44 123.69 124.05 124.72 125.20 125.62 125.65
- 10.46 119.07 119.12 119.18 119.67 119.77 119.91 121.91 122.05 122.49 122.67 122.81 123.44 123.68 124.05 124.72 125.20 125.61 125.66
- 10.45 119.07 119.12 119.18 119.66 119.77 119.88 121.91 122.04 122.50 122.66 122.81 123.43 123.68 124.04 124.72 125.20 125.61 125.67
- 10.44 119.07 119.12 119.18 119.66 119.77 119.85 121.92 122.03 122.50 122.65 122.82 123.42 123.67 124.04 124.72 125.20 125.61 125.68
- 10.43 119.07 119.12 119.17 119.65 119.79 119.83 121.92 122.02 122.50 122.64 122.82 123.41 123.66 124.03 124.72 125.20 125.60 125.68
- 10.42 119.06 119.13 119.16 119.63 121.93 122.00 122.51 122.62 122.82 123.40 123.65 124.03 124.72 125.21 125.60 125.68
- 10.41 119.00 119.13 119.15 119.62 122.52 122.56 122.83 123.39 123.65 124.03 124.72 125.21 125.60 125.69
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10.40 118.99 119.61 122.52 122.54 122.83 123.38 123.64 124.02 124.72 125.25 125.60 125.69
- 10.39 118.98 119.60 122.84 123.37 123.63 124.02 124.72 125.26 125.55 125.58 125.60 125.69
- 10.38 118.98 119.59 122.84 123.37 123.62 124.02 124.72 125.26 125.54 125.69
- 10.37 118.97 119.58 122.84 123.37 123.62 124.02 124.74 125.27 125.54 125.69
- 10.36 118.96 119.57 122.84 123.36 123.61 124.02 124.76 125.00 125.02 125.27 125.54 125.69
- 10.35 118.96 119.44 122.85 123.36 123.60 124.01 124.76 125.00 125.03 125.28 125.54 125.69
+ 10.39 118.97 119.60 122.84 123.37 123.63 124.02 124.72 125.26 125.55 125.58 125.60 125.69
+ 10.38 118.97 119.59 122.84 123.37 123.62 124.02 124.72 125.26 125.54 125.69
+ 10.37 118.96 119.58 122.84 123.37 123.62 124.02 124.73 125.27 125.54 125.69
+ 10.36 118.96 119.57 122.84 123.36 123.61 124.02 124.75 124.99 125.02 125.27 125.54 125.69
+ 10.35 118.96 119.44 122.85 123.36 123.60 124.01 124.76 124.99 125.03 125.28 125.54 125.69
10.34 118.96 119.42 122.85 123.35 123.59 124.00 124.77 125.00 125.03 125.28 125.55 125.69
10.33 118.97 119.39 122.85 123.35 123.59 123.98 124.77 125.00 125.03 125.28 125.53 125.68
10.32 119.01 119.37 122.85 123.35 123.58 123.98 124.78 125.00 125.03 125.28 125.51 125.68
10.31 118.98 119.36 122.85 123.35 123.58 123.98 124.78 125.00 125.03 125.28 125.51 125.68
10.30 118.96 119.35 122.85 123.35 123.58 123.96 124.78 125.00 125.03 125.28 125.51 125.68
- 10.29 118.94 119.34 122.84 123.35 123.58 123.94 124.78 125.00 125.04 125.28 125.51 125.67
- 10.28 118.94 119.33 122.84 123.35 123.57 123.92 124.77 125.00 125.05 125.28 125.51 125.67
- 10.27 118.94 119.31 122.84 123.35 123.57 123.90 124.77 125.00 125.05 125.28 125.51 125.67
- 10.26 118.94 119.30 122.84 123.35 123.57 123.89 124.77 125.01 125.05 125.28 125.51 125.67
- 10.25 118.94 119.29 122.84 123.35 123.56 123.89 124.77 125.01 125.05 125.15 125.18 125.27 125.51 125.66
+ 10.29 118.93 119.34 122.84 123.35 123.58 123.94 124.78 125.00 125.04 125.28 125.51 125.67
+ 10.28 118.93 119.33 122.84 123.35 123.57 123.92 124.77 125.00 125.05 125.28 125.51 125.67
+ 10.27 118.93 119.31 122.84 123.35 123.57 123.90 124.77 125.00 125.05 125.28 125.51 125.67
+ 10.26 118.93 119.30 122.84 123.35 123.57 123.89 124.77 125.01 125.05 125.28 125.51 125.67
+ 10.25 118.94 119.29 122.84 123.35 123.56 123.88 124.77 125.01 125.05 125.15 125.18 125.27 125.51 125.66
10.24 118.94 119.28 122.84 123.35 123.55 123.88 124.76 125.01 125.05 125.14 125.20 125.25 125.52 125.66
- 10.23 118.94 119.28 122.84 123.34 123.55 123.87 124.76 125.01 125.06 125.14 125.52 125.67
+ 10.23 118.93 119.28 122.84 123.34 123.55 123.87 124.76 125.01 125.06 125.14 125.52 125.67
10.22 118.86 118.91 118.93 119.27 122.84 123.34 123.54 123.82 124.76 125.01 125.06 125.14 125.51 125.67
10.21 118.85 119.26 122.84 123.33 123.53 123.80 124.76 125.01 125.07 125.15 125.50 125.67
10.20 118.81 119.26 122.84 123.33 123.52 123.79 124.75 125.01 125.08 125.15 125.50 125.67
@@ -140061,11 +140353,11 @@ Philippines
10.15 118.80 119.24 122.85 123.31 123.51 123.74 124.17 124.35 124.37 124.40 124.57 124.61 124.76 125.03 125.11 125.19 125.48 125.69
10.14 118.76 118.78 118.80 119.24 122.86 123.31 123.50 123.72 124.14 124.41 124.57 124.61 124.77 125.03 125.11 125.21 125.48 125.68
10.13 118.75 118.78 118.80 119.24 122.86 123.31 123.49 123.72 124.14 124.41 124.53 124.61 124.78 125.03 125.11 125.23 125.48 125.68
- 10.12 118.75 118.78 118.80 119.24 122.86 123.31 123.48 123.72 124.13 124.44 124.51 124.61 124.80 125.03 125.11 125.23 125.48 125.69
- 10.11 118.74 118.78 118.81 119.23 122.86 123.31 123.48 123.72 124.12 124.45 124.51 124.60 124.88 125.04 125.11 125.24 125.48 125.69
- 10.10 118.74 118.78 118.81 119.23 122.85 123.30 123.47 123.72 124.11 124.46 124.51 124.60 124.89 125.04 125.11 125.24 125.48 125.70
- 10.09 118.73 118.78 118.82 119.23 122.85 123.30 123.46 123.71 124.10 124.46 124.51 124.60 124.89 125.04 125.11 125.25 125.48 125.71
- 10.08 118.73 118.78 118.81 119.23 122.84 123.30 123.45 123.70 124.10 124.47 124.51 124.60 124.90 125.04 125.12 125.25 125.50 125.71
+ 10.12 118.75 118.78 118.80 119.24 122.86 123.30 123.48 123.72 124.13 124.44 124.51 124.61 124.80 125.03 125.11 125.23 125.48 125.69
+ 10.11 118.74 118.78 118.81 119.23 122.86 123.30 123.48 123.71 124.12 124.45 124.51 124.60 124.88 125.04 125.11 125.24 125.48 125.69
+ 10.10 118.74 118.78 118.81 119.23 122.85 123.30 123.47 123.71 124.11 124.46 124.51 124.60 124.89 125.04 125.11 125.24 125.48 125.70
+ 10.09 118.73 118.78 118.82 119.23 122.85 123.30 123.46 123.71 124.10 124.47 124.51 124.60 124.89 125.04 125.11 125.25 125.48 125.71
+ 10.08 118.73 118.78 118.81 119.23 122.84 123.30 123.45 123.70 124.10 124.48 124.51 124.60 124.90 125.04 125.12 125.25 125.50 125.71
10.07 118.72 118.78 118.80 119.23 122.79 123.29 123.43 123.69 124.09 124.59 124.94 125.05 125.12 125.25 125.50 125.71
10.06 118.72 119.22 122.77 123.29 123.42 123.68 124.07 124.57 124.94 125.05 125.13 125.25 125.50 125.71 126.06 126.09
10.05 118.71 119.21 122.76 123.28 123.42 123.66 124.06 124.56 124.95 125.05 125.14 125.26 125.51 125.55 125.58 125.71 126.04 126.09
@@ -140075,7 +140367,7 @@ Philippines
10.01 118.65 119.13 122.72 123.25 123.40 123.65 124.05 124.59 125.00 125.05 125.19 125.28 125.57 125.69 126.03 126.11
10.00 118.64 119.10 122.71 123.25 123.40 123.65 124.05 124.59 125.19 125.29 125.57 125.69 126.03 126.11
9.99 118.64 119.08 122.51 122.60 122.67 123.24 123.38 123.65 124.04 124.59 125.20 125.29 125.57 125.70 126.02 126.12
- 9.98 118.64 119.01 122.46 123.23 123.37 123.65 124.03 124.59 125.21 125.30 125.58 125.70 126.02 126.12
+ 9.98 118.64 119.01 122.46 123.23 123.37 123.65 124.02 124.59 125.21 125.30 125.58 125.70 126.02 126.12
9.97 118.64 118.99 122.45 123.23 123.37 123.65 123.98 124.59 125.21 125.30 125.60 125.70 126.01 126.13
9.96 118.63 118.93 122.45 123.22 123.37 123.65 123.95 124.59 125.22 125.30 125.60 125.70 126.00 126.13
9.95 118.63 118.87 122.44 123.22 123.37 123.65 123.93 124.57 125.23 125.31 125.60 125.70 126.00 126.13
@@ -140084,15 +140376,15 @@ Philippines
9.92 118.61 118.82 122.42 123.21 123.37 123.65 123.87 124.58 125.25 125.31 125.64 125.72 125.98 126.14
9.91 118.60 118.77 122.42 123.20 123.39 123.64 123.87 124.58 125.25 125.30 125.65 125.72 125.97 126.14
9.90 118.60 118.76 122.41 123.19 123.39 123.64 123.87 124.59 125.26 125.29 125.65 125.73 125.97 126.14
- 9.89 118.59 118.76 122.41 123.18 123.39 123.64 123.86 124.59 125.65 125.73 125.97 126.14
- 9.88 118.59 118.76 122.40 123.17 123.39 123.64 123.85 124.59 125.65 125.73 125.97 126.14
- 9.87 118.59 118.76 122.40 123.17 123.39 123.63 123.84 124.59 125.65 125.72 125.97 126.14
- 9.86 118.58 118.76 122.39 123.16 123.38 123.63 123.83 124.59 125.66 125.71 125.95 126.14
+ 9.89 118.59 118.76 122.41 123.18 123.39 123.64 123.86 124.59 125.65 125.73 125.96 126.14
+ 9.88 118.59 118.76 122.40 123.17 123.39 123.64 123.85 124.59 125.65 125.73 125.96 126.14
+ 9.87 118.59 118.76 122.40 123.17 123.39 123.63 123.84 124.59 125.65 125.72 125.96 126.14
+ 9.86 118.58 118.76 122.39 123.16 123.38 123.63 123.83 124.59 125.66 125.71 125.95 126.15
9.85 118.57 118.76 122.38 123.16 123.38 123.61 123.81 124.58 125.95 126.16
9.84 118.55 118.77 122.38 123.16 123.37 123.61 123.81 124.59 125.95 126.16
9.83 118.54 118.77 122.38 123.16 123.37 123.60 123.80 124.61 125.44 125.46 125.96 126.17
9.82 118.53 118.78 122.38 123.17 123.36 123.60 123.80 124.62 125.44 125.47 125.97 126.18
- 9.81 118.53 118.78 122.39 123.17 123.36 123.59 123.79 124.63 125.43 125.48 125.98 126.19
+ 9.81 118.53 118.78 122.38 123.17 123.36 123.59 123.79 124.63 125.43 125.48 125.98 126.19
9.80 118.52 118.79 122.39 123.17 123.35 123.59 123.79 124.63 125.43 125.49 125.98 126.19
9.79 118.52 118.79 122.39 123.17 123.35 123.58 123.79 124.63 125.42 125.50 125.99 126.19
9.78 118.52 118.79 122.39 123.17 123.35 123.58 123.79 124.63 125.42 125.55 125.99 126.19
@@ -140111,19 +140403,19 @@ Philippines
9.65 118.33 118.76 121.24 121.26 122.41 123.17 123.33 123.51 123.83 124.42 125.39 125.62 125.91 126.01
9.64 118.33 118.74 121.24 121.26 122.41 123.17 123.32 123.51 123.80 124.42 125.39 125.62 125.90 126.00
9.63 118.33 118.74 121.23 121.26 122.44 123.17 123.32 123.51 123.77 124.41 125.39 125.64 125.90 126.00
- 9.62 118.33 118.73 121.22 121.26 122.44 123.14 123.32 123.51 123.75 124.39 125.39 125.65 125.90 126.00
+ 9.62 118.33 118.73 121.21 121.26 122.44 123.14 123.32 123.51 123.75 124.39 125.39 125.66 125.90 126.00
9.61 118.33 118.73 121.21 121.26 122.45 123.16 123.32 123.51 123.74 123.87 123.90 124.37 125.40 125.70 125.90 125.99
9.60 118.32 118.72 121.21 121.25 122.45 123.17 123.32 123.51 123.71 123.87 123.92 124.35 125.40 125.70 125.90 125.99
- 9.59 118.32 118.72 121.20 121.25 122.46 123.18 123.31 123.51 123.71 123.87 123.96 124.32 125.40 125.71 125.90 125.99
+ 9.59 118.32 118.71 121.20 121.25 122.46 123.18 123.31 123.51 123.71 123.87 123.96 124.32 125.40 125.71 125.91 125.99
9.58 118.31 118.71 121.20 121.24 122.46 123.18 123.31 123.50 123.71 123.86 124.02 124.15 125.41 125.76 125.91 125.99
9.57 118.29 118.70 121.20 121.23 122.47 123.18 123.31 123.50 123.71 123.85 125.41 125.77 125.91 125.99
9.56 118.28 118.70 121.20 121.22 122.47 123.18 123.31 123.49 123.72 123.84 125.41 125.78 125.93 125.98
9.55 118.28 118.67 122.48 123.18 123.31 123.49 123.72 123.82 125.41 125.82 125.93 125.97
9.54 118.27 118.66 122.49 123.19 123.31 123.49 123.73 123.80 125.42 125.86
- 9.53 118.27 118.66 122.50 123.20 123.30 123.48 123.75 123.78 125.42 125.87
- 9.52 118.26 118.65 122.52 123.20 123.30 123.48 125.42 125.89
+ 9.53 118.27 118.66 122.50 123.19 123.30 123.48 123.75 123.78 125.42 125.87
+ 9.52 118.26 118.65 122.51 123.19 123.30 123.48 125.42 125.89
9.51 118.24 118.65 122.52 123.20 123.30 123.47 125.42 125.90
- 9.50 118.23 118.64 122.53 123.20 123.30 123.45 125.43 125.94
+ 9.50 118.23 118.64 122.52 123.20 123.30 123.45 125.43 125.94
9.49 118.21 118.64 122.53 123.21 123.30 123.44 125.43 125.98
9.48 118.20 118.63 122.54 123.22 123.30 123.44 125.44 125.98
9.47 118.20 118.62 122.55 123.23 123.30 123.43 125.44 125.98
@@ -140131,7 +140423,7 @@ Philippines
9.45 118.19 118.61 122.57 123.26 123.30 123.41 125.45 125.98
9.44 118.18 118.61 122.58 123.26 123.30 123.40 125.45 125.98
9.43 118.18 118.60 122.58 123.26 123.31 123.39 125.45 125.97
- 9.42 118.17 118.59 122.58 123.27 123.31 123.38 125.45 125.97
+ 9.42 118.17 118.59 122.58 123.27 123.31 123.38 125.45 125.96
9.41 118.15 118.58 122.60 123.27 123.31 123.37 125.45 125.94
9.40 118.13 118.56 122.63 123.27 123.31 123.36 125.45 125.92 125.97 126.00
9.39 118.12 118.56 122.63 123.28 123.31 123.35 125.45 126.00
@@ -140142,18 +140434,18 @@ Philippines
9.34 118.11 118.53 122.81 123.33 125.47 126.00
9.33 118.09 118.52 122.83 123.33 125.48 126.00
9.32 118.07 118.52 122.84 123.33 125.48 126.01
- 9.31 118.05 118.51 122.85 123.33 125.49 126.01 126.18 126.23
+ 9.31 118.05 118.51 122.85 123.33 125.49 126.01 126.18 126.22
9.30 118.04 118.50 122.86 123.33 123.61 123.65 125.49 126.02 126.16 126.23
9.29 118.03 118.50 122.87 123.33 123.60 123.66 125.49 126.03 126.15 126.23
9.28 118.02 118.49 122.87 123.33 123.59 123.67 125.49 126.04 126.14 126.23
9.27 117.89 117.93 117.97 117.99 118.02 118.47 122.87 123.33 123.59 123.67 125.50 126.04 126.12 126.23
- 9.26 117.88 117.99 118.01 118.44 122.87 123.32 123.58 123.68 125.51 126.05 126.09 126.22
- 9.25 117.87 118.43 122.87 123.32 123.57 123.68 124.66 124.73 125.51 126.22
- 9.24 117.87 118.42 122.87 123.32 123.56 123.71 124.65 124.75 125.51 126.21
+ 9.26 117.87 117.99 118.01 118.44 122.87 123.32 123.58 123.68 124.68 124.72 125.51 126.05 126.09 126.22
+ 9.25 117.87 118.43 122.87 123.32 123.57 123.68 124.66 124.74 125.51 126.22
+ 9.24 117.86 118.42 122.87 123.32 123.56 123.71 124.65 124.75 125.51 126.21
9.23 117.86 118.41 122.88 123.32 123.49 123.51 123.55 123.71 124.64 124.76 125.51 126.21
- 9.22 117.86 118.40 122.88 123.31 123.48 123.71 124.63 124.77 125.51 126.21
+ 9.22 117.85 118.40 122.88 123.31 123.48 123.71 124.63 124.77 125.51 126.21
9.21 117.85 118.39 122.88 123.31 123.47 123.71 124.63 124.78 125.51 126.20
- 9.20 117.84 118.38 122.88 123.30 123.46 123.71 124.62 124.80 125.52 126.20
+ 9.20 117.83 118.38 122.88 123.30 123.46 123.71 124.62 124.80 125.52 126.20
9.19 117.82 118.38 122.89 123.29 123.46 123.70 124.62 124.80 125.52 126.20
9.18 117.80 118.37 122.89 123.29 123.46 123.69 124.62 124.81 125.52 126.20
9.17 117.78 118.36 122.90 123.28 123.46 123.71 124.62 124.81 125.53 126.19
@@ -140165,13 +140457,13 @@ Philippines
9.11 117.76 118.14 122.92 123.24 123.53 123.71 124.66 124.81 125.53 126.19
9.10 117.76 118.14 122.92 123.24 123.55 123.65 124.68 124.81 125.53 126.19
9.09 117.70 117.72 117.75 118.13 122.93 123.24 123.56 123.65 124.70 124.81 125.19 125.22 125.53 126.19
- 9.08 117.69 117.72 117.75 118.13 122.93 123.23 123.62 123.65 124.72 124.81 125.18 125.23 125.53 126.22
- 9.07 117.65 118.13 122.94 123.21 124.74 124.80 125.18 125.24 125.53 126.23
- 9.06 117.64 118.12 122.95 123.19 124.75 124.78 125.18 125.25 125.52 126.23
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+ 9.07 117.65 118.13 122.94 123.21 124.74 124.80 125.18 125.23 125.53 126.23
+ 9.06 117.64 118.12 122.95 123.19 124.75 124.78 125.18 125.24 125.52 126.23
9.05 117.63 118.12 122.96 123.17 125.18 125.25 125.52 126.24
- 9.04 117.63 118.12 122.97 123.11 125.17 125.26 125.52 126.24
+ 9.04 117.63 118.12 122.97 123.11 125.17 125.25 125.52 126.24
9.03 117.63 118.12 122.98 123.07 125.17 125.26 125.51 126.25
- 9.02 117.62 118.10 123.01 123.05 124.81 124.84 125.17 125.28 125.50 126.26
+ 9.02 117.62 118.10 123.01 123.05 124.81 124.84 125.16 125.28 125.50 126.26
9.01 117.62 118.10 124.79 124.91 125.16 125.30 125.48 126.27
9.00 117.61 118.09 124.78 124.93 125.16 125.40 125.46 126.28
8.99 117.60 118.09 124.78 124.94 125.16 126.29
@@ -140182,14 +140474,14 @@ Philippines
8.94 117.54 118.06 124.77 125.00 125.18 126.33
8.93 117.53 118.05 124.77 125.02 125.18 126.33
8.92 117.52 118.05 124.77 125.04 125.17 126.33
- 8.91 117.52 118.04 124.77 125.05 125.17 126.33
- 8.90 117.51 118.04 119.95 119.97 124.77 125.05 125.17 126.34
- 8.89 117.50 118.03 119.94 119.98 124.77 125.07 125.17 126.34
- 8.88 117.50 118.03 119.94 119.98 124.77 125.08 125.17 126.34
- 8.87 117.49 118.02 119.94 119.98 124.77 125.08 125.16 126.34
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+ 8.90 117.50 118.04 119.95 119.97 124.77 125.05 125.17 126.34
+ 8.89 117.49 118.03 119.94 119.98 124.77 125.07 125.17 126.34
+ 8.88 117.49 118.03 119.94 119.98 124.77 125.08 125.17 126.34
+ 8.87 117.48 118.02 119.94 119.98 124.77 125.08 125.16 126.34
8.86 117.48 118.01 119.94 119.97 124.77 125.09 125.14 126.35
- 8.85 117.48 118.00 124.77 125.09 125.12 126.35
- 8.84 117.47 117.98 124.77 126.35
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+ 8.84 117.46 117.98 124.77 126.35
8.83 117.46 117.96 124.77 126.35
8.82 117.45 117.94 124.77 126.34
8.81 117.45 117.92 124.77 126.34
@@ -140199,31 +140491,31 @@ Philippines
8.77 117.41 117.87 124.77 126.32
8.76 117.39 117.85 124.77 126.32
8.75 117.36 117.84 124.77 126.31
- 8.74 117.35 117.83 124.77 126.27
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8.73 117.34 117.82 123.38 123.44 124.77 126.26
- 8.72 117.34 117.81 123.38 123.46 124.76 126.25
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8.71 117.33 117.80 123.38 123.47 124.75 126.26
8.70 117.32 117.79 123.38 123.52 124.74 126.27
8.69 117.32 117.78 123.38 123.52 124.74 126.27
8.68 117.32 117.77 123.39 123.52 123.60 123.63 124.73 126.27
- 8.67 117.31 117.76 123.40 123.52 123.59 123.64 124.73 126.21 126.23 126.26
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8.66 117.29 117.71 123.41 123.52 123.59 123.65 124.73 126.19
8.65 117.28 117.58 117.61 117.68 123.41 123.52 123.59 123.69 124.73 126.18
8.64 117.28 117.57 123.36 123.52 123.59 123.72 124.74 126.16
- 8.63 117.27 117.56 123.35 123.55 123.58 123.73 124.43 124.48 124.74 126.13
- 8.62 117.27 117.56 123.35 123.76 124.41 124.48 124.75 126.12
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+ 8.62 117.25 117.56 123.35 123.76 124.41 124.48 124.75 126.12
8.61 117.25 117.56 123.34 123.76 124.39 124.48 124.75 126.12
8.60 117.25 117.56 123.34 123.76 124.37 124.48 124.76 126.13
- 8.59 117.25 117.56 123.33 123.77 124.36 124.50 124.76 126.14
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8.58 117.25 117.56 123.33 123.77 124.35 124.54 124.75 126.14
8.57 117.24 117.56 123.33 123.78 124.35 124.55 124.74 126.14
8.56 117.23 117.56 123.33 123.79 124.34 124.56 124.74 126.15 126.21 126.28
8.55 117.23 117.55 123.17 123.22 123.32 123.79 124.33 124.56 124.74 126.15 126.20 126.33 126.35 126.38
8.54 117.22 117.55 123.14 123.22 123.30 123.79 124.32 124.57 124.73 126.15 126.20 126.38
- 8.53 117.22 117.54 123.10 123.24 123.27 123.80 124.32 124.60 124.73 126.38
+ 8.53 117.22 117.54 123.10 123.24 123.27 123.80 124.32 124.59 124.73 126.38
8.52 117.22 117.53 123.05 123.81 124.31 124.66 124.73 126.40
8.51 117.21 117.53 123.04 123.81 124.31 124.66 124.73 126.41
- 8.50 117.21 117.52 123.04 123.82 124.30 124.66 124.72 126.41
+ 8.50 117.21 117.52 123.03 123.82 124.30 124.66 124.72 126.41
8.49 117.21 117.52 123.03 123.83 124.30 126.41
8.48 117.21 117.43 117.48 117.50 123.02 123.84 124.29 126.41
8.47 117.21 117.39 123.01 123.84 124.29 126.42
@@ -140233,8 +140525,8 @@ Philippines
8.43 117.20 117.32 122.99 123.86 124.28 126.39
8.42 117.19 117.32 122.98 123.86 124.28 126.39
8.41 117.19 117.31 122.98 123.86 124.28 126.39
- 8.40 117.19 117.29 122.98 123.86 124.28 126.39
- 8.39 117.19 117.28 122.98 123.86 124.27 126.39
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+ 8.39 117.18 117.28 122.98 123.86 124.27 126.39
8.38 117.18 117.27 122.98 123.87 124.26 126.39
8.37 117.17 117.26 122.98 123.87 124.26 126.38
8.36 117.17 117.24 122.98 123.87 124.26 126.37
@@ -140242,7 +140534,7 @@ Philippines
8.34 117.17 117.25 122.97 123.87 124.25 126.35
8.33 117.18 117.33 122.97 123.87 124.25 126.35
8.32 117.18 117.35 122.95 123.87 124.25 126.36
- 8.31 117.18 117.36 122.94 123.87 124.25 126.39
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8.30 117.17 117.36 122.94 123.87 124.25 126.39
8.29 117.17 117.36 122.94 123.87 124.25 126.39
8.28 117.17 117.36 122.94 123.87 124.26 126.39
@@ -140255,16 +140547,16 @@ Philippines
8.21 117.26 117.36 122.99 123.88 124.20 126.35 126.38 126.47
8.20 117.26 117.36 122.97 123.89 124.09 126.47
8.19 117.14 117.16 117.26 117.36 122.96 123.89 123.99 126.47
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8.16 117.14 117.21 122.66 122.69 122.91 123.89 123.93 126.46
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8.14 117.03 117.05 117.15 117.21 122.64 122.70 122.82 123.88 123.92 126.46
8.13 117.01 117.06 122.64 122.71 122.77 123.87 123.91 126.46
8.12 116.99 117.06 122.63 123.86 123.89 126.46
8.11 116.98 117.07 122.61 126.46
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8.08 116.99 117.07 122.44 126.47
8.07 116.95 116.97 117.00 117.08 122.41 126.46
8.06 116.95 117.09 122.37 126.45
@@ -140274,11 +140566,11 @@ Philippines
8.02 116.95 117.10 122.30 126.44
8.01 116.95 117.10 122.28 126.44
8.00 116.95 117.10 122.26 126.45
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7.97 116.94 117.08 122.22 126.46
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7.94 116.94 117.09 122.21 126.43
7.93 116.94 117.09 122.20 126.42
7.92 116.94 117.09 122.19 126.40
@@ -140292,8 +140584,8 @@ Philippines
7.84 116.97 117.08 122.13 126.41
7.83 116.97 117.07 122.12 126.42
7.82 116.98 117.06 122.11 126.43
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7.79 116.98 117.04 122.10 123.45 123.69 126.47
7.78 117.01 117.03 122.09 123.45 123.71 126.47
7.77 122.09 123.45 123.72 126.48
@@ -140309,15 +140601,15 @@ Philippines
7.67 122.11 122.51 122.78 123.08 123.12 123.50 123.92 126.58
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7.60 122.10 122.46 122.79 123.05 123.17 123.41 124.04 126.58
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7.58 122.11 122.49 122.79 123.05 123.11 123.40 124.06 126.59
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7.55 122.09 122.49 122.81 123.04 123.11 123.38 124.08 126.60
7.54 122.08 122.49 122.78 123.03 123.11 123.39 124.08 126.60
7.53 122.06 122.49 122.78 123.02 123.11 123.39 124.09 126.61
@@ -140326,28 +140618,28 @@ Philippines
7.50 122.05 122.47 122.77 122.89 122.92 123.02 123.13 123.24 123.27 123.41 124.10 126.61
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7.48 122.05 122.41 122.43 122.45 122.77 122.88 122.93 123.02 123.15 123.22 123.27 123.43 124.11 126.61
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7.45 122.03 122.36 122.79 122.87 122.98 123.00 123.29 123.46 124.13 126.61
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7.43 122.03 122.36 122.80 122.85 122.88 122.94 123.31 123.46 124.14 126.60
7.42 122.03 122.37 122.79 122.85 122.88 122.95 123.32 123.46 124.15 126.59
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7.35 122.02 122.37 122.78 122.96 123.42 123.44 124.21 126.59
7.34 122.02 122.36 122.78 122.96 124.21 126.59
7.33 122.02 122.36 122.78 122.95 124.20 125.80 125.83 126.59
7.32 122.02 122.35 122.78 122.92 124.20 125.79 125.84 126.59
7.31 122.03 122.34 122.79 122.90 124.20 125.78 125.84 126.59
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7.25 121.95 122.28 124.18 125.68 125.84 126.62
7.24 121.94 122.27 124.17 125.67 125.84 126.62
7.23 121.93 122.27 124.17 125.67 125.84 126.61
@@ -140360,9 +140652,9 @@ Philippines
7.16 121.89 122.26 124.07 125.66 125.69 125.76 125.87 126.56
7.15 121.88 122.26 124.05 125.66 125.68 125.78 125.88 126.55
7.14 121.88 122.26 124.04 125.66 125.68 125.79 125.88 126.55
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7.12 121.88 122.25 124.01 125.79 125.88 126.54
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7.10 121.88 122.25 124.00 125.79 125.88 126.53
7.09 121.88 122.25 124.00 125.79 125.89 126.52
7.08 121.88 122.25 123.99 125.79 125.89 126.51
@@ -140375,9 +140667,9 @@ Philippines
7.01 118.41 118.55 121.89 122.20 123.97 125.54 125.71 125.79 125.96 126.47
7.00 118.41 118.55 121.90 122.20 123.97 125.52 125.71 125.79 125.96 126.47
6.99 118.41 118.54 121.90 122.19 123.96 125.51 125.71 125.79 125.97 126.47
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6.95 121.93 122.17 123.96 125.49 125.72 125.80 125.96 126.32
6.94 121.95 122.17 123.96 125.49 125.72 125.80 125.96 126.32
6.93 121.96 122.17 123.96 125.49 125.73 125.80 125.96 126.31
@@ -140385,10 +140677,10 @@ Philippines
6.91 122.00 122.16 123.96 125.49 125.73 125.79 125.97 126.31
6.90 122.02 122.15 123.96 125.49 125.74 125.79 125.98 126.20 126.23 126.31
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6.87 123.96 125.46 126.00 126.20 126.25 126.33
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6.83 123.95 125.43 126.05 126.20 126.27 126.35
6.82 123.95 125.42 126.07 126.21 126.28 126.35
@@ -140413,7 +140705,7 @@ Philippines
6.63 121.57 121.63 121.79 122.32 124.04 125.40 126.07 126.24
6.62 121.57 121.63 121.79 122.33 124.04 125.40 125.42 125.44 126.07 126.23
6.61 121.57 121.63 121.79 122.34 124.04 125.40 125.42 125.46 126.07 126.23
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6.59 121.59 121.63 121.79 122.34 124.04 125.48 126.07 126.23
6.58 121.59 121.63 121.80 122.34 124.04 125.48 126.07 126.23
6.57 121.59 121.63 121.82 122.33 124.04 125.49 126.07 126.23
@@ -140422,8 +140714,8 @@ Philippines
6.54 121.86 122.23 124.02 125.51 126.08 126.23
6.53 121.86 122.22 124.02 125.57 126.08 126.23
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6.48 121.88 122.21 124.03 125.60 126.09 126.23
6.47 121.89 122.20 124.03 125.60 126.09 126.23
@@ -140444,17 +140736,17 @@ Philippines
6.32 120.52 120.61 124.11 125.65 126.16 126.21
6.31 120.52 120.61 124.12 125.65 126.17 126.21
6.30 120.52 120.61 124.13 125.65 126.17 126.21
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6.26 120.47 120.59 124.16 125.67
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@@ -140466,31 +140758,31 @@ Philippines
6.10 121.02 121.13 124.40 125.72
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6.08 121.00 121.17 121.76 121.80 124.44 125.16 125.18 125.71
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5.99 120.87 121.43 121.84 121.90 124.58 125.14 125.26 125.69
5.98 120.86 121.43 121.85 121.88 124.58 125.13 125.26 125.69
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5.87 120.91 120.96 121.06 121.09 121.24 121.33 124.88 125.09 125.19 125.62
5.86 121.25 121.32 124.90 125.08 125.19 125.61
5.85 121.14 121.20 121.26 121.31 124.92 125.00 125.02 125.07 125.18 125.60
5.84 121.13 121.21 121.27 121.30 124.94 124.98 125.18 125.59
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5.82 121.12 121.24 125.17 125.58
5.81 121.12 121.24 125.17 125.57
5.80 121.12 121.24 125.17 125.56
@@ -140516,15 +140808,15 @@ Philippines
5.60 125.29 125.44
5.59 125.29 125.44
5.58 120.83 120.88 125.29 125.43
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5.48 120.86 120.90
5.44 125.36 125.41
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@@ -140539,8 +140831,8 @@ Philippines
5.34 120.15 120.22
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5.27 120.07 120.26
@@ -140551,8 +140843,8 @@ Philippines
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@@ -140567,7 +140859,7 @@ Philippines
5.06 119.73 119.97
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4.93 119.78 119.82
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@@ -140604,25 +140896,25 @@ Pitcairn Islands
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-25.08 -130.12 -130.07
Poland
54.84 18.01 18.35
@@ -140631,49 +140923,49 @@ Poland
54.81 17.73 18.43
54.80 17.67 18.46
54.79 17.59 18.49
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54.35 16.24 23.05
54.34 16.23 23.05
54.33 16.21 23.05
@@ -140682,13 +140974,13 @@ Poland
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54.29 16.10 23.17
54.28 16.04 23.19
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54.20 15.62 23.38
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54.18 15.49 23.43
@@ -140773,11 +141065,11 @@ Poland
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53.31 14.38 23.78
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@@ -140826,7 +141118,7 @@ Poland
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52.80 14.20 23.93
@@ -140850,8 +141142,8 @@ Poland
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52.55 14.60 23.53
@@ -140970,8 +141262,8 @@ Poland
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@@ -141043,9 +141335,9 @@ Poland
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50.63 15.98 16.22 16.31 24.11
50.62 15.97 16.08 16.13 16.21 16.33 24.11
50.61 15.96 16.06 16.15 16.20 16.35 24.11
@@ -141092,7 +141384,7 @@ Poland
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50.19 16.52 16.91 16.99 17.01 17.68 23.47
50.18 16.52 16.90 17.65 23.45
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50.15 16.54 16.79 17.57 23.40
50.14 16.54 16.78 17.57 23.38
@@ -141169,7 +141461,7 @@ Poland
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49.42 18.94 19.19 19.61 21.24 21.28 22.69
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49.39 18.94 19.18 19.61 21.07 21.14 21.21 21.39 21.47 21.63 22.72
49.38 18.94 19.04 19.08 19.16 19.63 20.60 20.62 20.66 20.68 21.08 21.16 21.19 21.69 22.72
49.37 18.95 19.02 19.66 20.31 20.34 20.43 20.47 20.59 20.69 21.09 21.70 22.73
@@ -141232,14 +141524,14 @@ Portugal
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41.87 -8.86 -8.19 -8.00 -7.88 -7.86 -7.59 -7.53 -7.49 -7.27 -6.51
@@ -141247,43 +141539,43 @@ Portugal
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@@ -141296,13 +141588,13 @@ Portugal
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@@ -141504,47 +141796,47 @@ Portugal
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@@ -141673,15 +141965,15 @@ Portugal
37.59 -8.83 -7.49
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37.46 -8.81 -7.45
37.45 -8.81 -7.45
@@ -141691,48 +141983,50 @@ Portugal
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Portugal: Azores
39.73 -31.15 -31.07
39.72 -31.15 -31.07
@@ -141880,7 +142174,7 @@ Portugal: Madeira
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32.75 -17.24 -16.66
@@ -141920,71 +142214,72 @@ Portugal: Madeira
Puerto Rico
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Qatar
- 26.16 51.24 51.27
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26.13 51.16 51.34
26.12 51.14 51.34
26.11 51.13 51.35
@@ -142035,7 +142330,7 @@ Qatar
25.66 50.84 51.56
25.65 50.83 51.56
25.64 50.83 51.56
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25.62 50.78 51.55
25.61 50.77 51.54
25.60 50.77 51.53
@@ -142045,8 +142340,8 @@ Qatar
25.56 50.81 51.50
25.55 50.81 51.50
25.54 50.81 51.50
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25.51 50.75 51.49
25.50 50.74 51.49
25.49 50.74 51.50
@@ -142074,7 +142369,7 @@ Qatar
25.27 50.74 51.60
25.26 50.74 51.61
25.25 50.74 51.61
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25.23 50.74 51.62
25.22 50.74 51.62
25.21 50.75 51.62
@@ -142101,10 +142396,10 @@ Qatar
25.00 50.78 51.61
24.99 50.78 51.61
24.98 50.78 51.60
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24.93 50.81 51.59
24.92 50.82 51.58
24.91 50.82 51.57
@@ -142116,13 +142411,13 @@ Qatar
24.85 50.84 51.52
24.84 50.84 51.51
24.83 50.84 51.51
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24.75 50.79 51.48
24.74 50.79 51.48
24.73 50.79 51.47
@@ -142134,22 +142429,22 @@ Qatar
24.67 50.83 51.45
24.66 50.84 51.45
24.65 50.85 51.44
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24.62 50.87 51.22 51.33 51.39
24.61 50.88 51.22 51.33 51.39
24.60 50.89 51.21 51.32 51.38
24.59 50.89 51.19 51.31 51.38
24.58 50.90 51.18 51.31 51.37
24.57 50.91 51.17 51.31 51.36
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24.55 50.95 51.12 51.33 51.35
24.54 51.00 51.07
Republic of the Congo
3.71 17.43 17.49
3.70 17.41 17.49
- 3.69 17.39 17.51
- 3.68 17.37 17.52
+ 3.69 17.40 17.51
+ 3.68 17.38 17.52
3.67 17.36 17.54
3.66 17.35 17.55
3.65 17.35 17.57
@@ -142240,13 +142535,13 @@ Republic of the Congo
2.80 16.45 18.43
2.79 16.44 18.43
2.78 16.44 18.43
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2.76 16.43 18.42
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2.74 16.42 18.41
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2.72 16.41 18.41
- 2.71 16.41 18.40
+ 2.71 16.40 18.40
2.70 16.40 18.40
2.69 16.40 18.39
2.68 16.39 18.39
@@ -142525,11 +142820,11 @@ Republic of the Congo
-0.05 13.90 17.75
-0.06 13.89 17.75
-0.07 13.88 17.75
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+ -0.12 13.84 17.74
-0.13 13.84 17.73
-0.14 13.83 17.73
-0.15 13.83 17.73
@@ -142589,13 +142884,13 @@ Republic of the Congo
-0.69 14.46 17.62
-0.70 14.46 17.60
-0.71 14.45 17.59
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+ -0.78 14.43 17.53
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-0.80 14.43 17.52
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@@ -142695,21 +142990,21 @@ Republic of the Congo
-1.75 14.39 16.61
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-1.84 12.52 12.70 14.38 16.55
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+ -1.86 12.50 12.72 14.38 16.53
+ -1.87 12.41 12.45 12.49 12.74 14.38 16.53
+ -1.88 12.41 12.46 12.49 12.77 14.39 16.52
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-1.94 12.41 12.82 14.26 16.46
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@@ -142764,7 +143059,7 @@ Republic of the Congo
-2.44 11.57 13.85 14.10 16.21
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-2.48 11.56 13.98 14.00 16.21
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@@ -142798,7 +143093,7 @@ Republic of the Congo
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-2.79 11.52 16.21
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@@ -142808,7 +143103,7 @@ Republic of the Congo
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@@ -142886,13 +143181,13 @@ Republic of the Congo
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-3.67 11.21 11.66 11.86 16.04
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@@ -142900,32 +143195,32 @@ Republic of the Congo
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@@ -142939,13 +143234,13 @@ Republic of the Congo
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@@ -142957,69 +143252,69 @@ Republic of the Congo
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+ -5.02 11.99 12.01
Reunion
-20.85 55.39 55.49
-20.86 55.37 55.59
@@ -143047,9 +143342,9 @@ Reunion
-21.08 55.22 55.78
-21.09 55.23 55.80
-21.10 55.23 55.82
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-21.14 55.26 55.86
-21.15 55.27 55.86
-21.16 55.28 55.86
@@ -143064,17 +143359,17 @@ Reunion
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-21.37 55.54 55.72
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+ -21.38 55.58 55.62 55.66 55.70
Romania
48.28 26.64 26.70 26.72 26.74
48.27 26.62 26.74
@@ -143109,8 +143404,8 @@ Romania
47.98 22.90 23.81 25.99 27.17
47.97 22.90 23.83 23.95 24.02 25.88 27.17
47.96 22.88 23.84 23.92 24.05 24.39 24.46 25.79 27.17
- 47.95 22.86 23.85 23.88 24.09 24.37 24.58 25.76 27.18
- 47.94 22.85 24.11 24.35 24.60 25.68 27.18
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+ 47.94 22.85 24.11 24.35 24.59 25.68 27.18
47.93 22.84 24.13 24.31 24.61 25.56 27.18
47.92 22.83 24.17 24.27 24.63 25.44 27.19
47.91 22.82 24.19 24.24 24.64 25.32 27.20
@@ -143131,7 +143426,7 @@ Romania
47.76 22.40 24.85 25.08 27.29
47.75 22.39 24.86 25.05 27.30
47.74 22.28 24.87 25.02 27.30
- 47.73 22.26 24.87 24.95 27.30
+ 47.73 22.26 24.87 24.97 27.30
47.72 22.25 27.30
47.71 22.23 27.30
47.70 22.22 27.30
@@ -143145,8 +143440,8 @@ Romania
47.62 22.16 27.36
47.61 22.15 27.37
47.60 22.15 27.39
- 47.59 22.15 27.43
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47.57 22.06 27.44
47.56 22.05 27.45
47.55 22.03 27.45
@@ -143301,13 +143596,13 @@ Romania
46.06 20.27 28.10
46.05 20.28 28.10
46.04 20.29 28.10
- 46.03 20.30 28.10
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46.02 20.30 28.09
46.01 20.30 28.09
46.00 20.31 28.10
45.99 20.31 28.10
45.98 20.32 28.11
- 45.97 20.34 28.11
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45.96 20.34 28.12
45.95 20.36 28.12
45.94 20.39 28.12
@@ -143317,7 +143612,7 @@ Romania
45.90 20.47 28.13
45.89 20.48 28.13
45.88 20.54 28.14
- 45.87 20.55 28.14
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45.86 20.57 28.14
45.85 20.57 28.13
45.84 20.58 28.12
@@ -143332,7 +143627,7 @@ Romania
45.75 20.65 28.16
45.74 20.66 28.16
45.73 20.67 20.74 20.76 28.16
- 45.72 20.68 20.73 20.76 28.16
+ 45.72 20.69 20.73 20.76 28.16
45.71 20.76 28.17
45.70 20.76 28.17
45.69 20.76 28.17
@@ -143348,10 +143643,10 @@ Romania
45.59 20.74 28.10
45.58 20.74 28.13
45.57 20.74 28.15
- 45.56 20.76 28.15
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45.55 20.76 28.16
45.54 20.77 28.17
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45.52 20.78 28.17
45.51 20.77 28.17
45.50 20.75 28.17
@@ -143362,7 +143657,7 @@ Romania
45.45 20.78 28.27 29.31 29.34
45.44 20.82 28.28 29.29 29.45
45.43 20.83 28.29 29.21 29.48
- 45.42 20.84 28.29 29.19 29.52
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45.41 20.84 28.29 29.18 29.55
45.40 20.85 28.29 29.16 29.57
45.39 20.86 28.30 29.13 29.59
@@ -143372,25 +143667,25 @@ Romania
45.35 20.92 28.32 29.01 29.66
45.34 20.94 28.33 29.00 29.66
45.33 20.95 28.35 28.77 28.84 28.96 29.67
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45.31 20.99 28.39 28.77 28.89 28.95 29.67
45.30 21.02 28.43 28.77 28.91 28.94 29.67
45.29 21.04 28.47 28.75 29.68
45.28 21.07 28.51 28.74 29.68
45.27 21.08 21.12 21.15 28.54 28.74 29.68
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45.25 21.16 28.61 28.75 29.67
45.24 21.17 28.68 28.72 29.67
45.23 21.19 29.67
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45.21 21.22 29.67
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45.18 21.38 29.66
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45.13 21.48 29.68
45.12 21.45 29.68
45.11 21.43 29.67
@@ -143402,7 +143697,7 @@ Romania
45.05 21.41 29.66
45.04 21.41 29.66
45.03 21.36 29.66
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45.01 21.34 29.66
45.00 21.34 29.66
44.99 21.34 29.65
@@ -143411,9 +143706,9 @@ Romania
44.96 21.37 29.64
44.95 21.37 29.64
44.94 21.39 29.64
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44.92 21.49 29.64
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44.90 21.52 29.64
44.89 21.50 29.64
44.88 21.37 21.43 21.46 29.63
@@ -143423,7 +143718,7 @@ Romania
44.84 21.33 29.62
44.83 21.33 29.62
44.82 21.33 29.58
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+ 44.81 21.34 29.57
44.80 21.36 29.48
44.79 21.37 29.42
44.78 21.38 29.35
@@ -143437,24 +143732,24 @@ Romania
44.70 21.60 22.41 22.48 29.03
44.69 21.61 22.39 22.49 29.02
44.68 21.63 22.38 22.50 29.02
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44.65 21.94 22.30 22.54 28.99
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44.60 22.01 22.26 22.71 28.93
44.59 22.02 22.26 22.72 28.92
44.58 22.02 22.25 22.74 28.92
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44.55 22.03 22.23 22.55 28.90
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44.49 22.09 22.18 22.46 28.86
44.48 22.46 28.85
44.47 22.46 28.84
@@ -143475,7 +143770,7 @@ Romania
44.32 22.55 28.66
44.31 22.57 28.65
44.30 22.60 28.64
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44.28 22.67 28.64
44.27 22.67 28.64
44.26 22.67 28.64
@@ -143496,11 +143791,11 @@ Romania
44.11 22.88 26.82 27.17 28.65
44.10 22.92 26.80 27.25 28.65
44.09 22.96 26.77 27.25 28.65
- 44.08 23.00 26.69 27.25 28.65
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44.07 23.02 26.63 27.25 28.66
44.06 23.02 26.57 27.27 28.66
44.05 23.02 26.47 27.29 28.66
- 44.04 23.01 26.37 27.32 28.67
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44.03 22.99 26.30 27.34 28.67
44.02 22.94 26.28 27.35 28.68
44.01 22.89 26.25 27.36 28.68
@@ -143522,258 +143817,258 @@ Romania
43.85 22.84 23.22 23.51 25.94 27.96 28.61
43.84 22.85 23.18 23.53 25.93 27.97 28.61
43.83 22.86 23.15 23.55 25.92 27.97 28.61
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43.81 23.76 25.90 28.02 28.60
43.80 23.78 25.88 28.05 28.60
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43.73 24.68 25.80 28.32 28.58
43.72 24.72 24.86 24.98 25.79 28.39 28.51
43.71 25.02 25.77
43.70 25.06 25.75
43.69 25.23 25.67
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43.67 25.27 25.63
43.66 25.29 25.59
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43.64 25.33 25.45
Russia
81.86 59.03 59.26
81.85 58.68 59.36
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81.34 55.67 55.72 56.36 57.44 57.58 57.71 58.45 59.39
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80.04 49.94 50.07 50.62 51.27 58.76 59.85 90.87 92.45 93.22 94.31 94.78 95.22 95.33 98.09 98.46 99.25
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76.38 64.44 68.44 99.01 112.65 113.10 113.44
@@ -144077,252 +144372,252 @@ Russia
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74.33 55.48 58.66 85.89 109.97 111.44 113.36 115.87 116.13
74.32 55.53 58.67 85.90 109.96 111.44 113.35 115.87 116.13
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74.30 55.16 55.27 55.57 58.73 85.93 109.98 111.44 113.31 115.87 116.13
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73.87 54.06 57.91 85.99 87.10 87.17 108.67 109.73 111.31 112.92 113.15 124.27 124.66 136.09 136.17 141.05 142.33
73.86 54.06 57.91 85.95 87.10 87.19 108.64 109.67 111.34 112.92 113.16 124.28 124.64 136.11 136.16 141.02 142.43
73.85 54.05 57.94 85.91 87.11 87.22 108.62 109.59 111.37 112.92 113.17 124.30 124.61 140.99 142.51
@@ -144331,130 +144626,130 @@ Russia
73.82 53.64 53.67 53.98 57.38 57.41 57.94 85.56 87.10 87.30 108.58 109.52 111.46 112.93 113.21 140.91 142.63
73.81 53.64 53.69 53.95 57.38 57.45 57.95 85.54 87.08 87.34 108.57 109.51 111.51 112.94 113.22 124.32 124.40 140.88 142.65
73.80 53.63 53.71 53.91 57.40 57.48 57.95 85.52 87.07 87.48 108.56 109.51 111.57 112.93 113.23 124.31 124.41 140.87 142.68
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73.78 53.62 57.45 57.52 57.93 85.49 87.05 87.38 108.50 109.51 111.67 112.90 113.26 123.86 123.95 124.28 124.51 140.85 142.74
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- 73.75 53.62 57.50 57.59 57.86 84.50 84.90 85.46 86.94 87.30 108.48 109.53 110.59 110.81 111.85 112.76 113.32 123.87 124.01 124.22 124.60 124.64 124.70 140.82 142.82
- 73.74 53.62 57.51 57.60 57.83 84.46 84.95 85.46 86.85 87.28 108.43 109.54 110.55 110.86 111.93 112.68 113.34 123.89 124.03 124.22 124.71 140.81 142.84
- 73.73 53.63 57.53 57.61 57.81 84.42 84.99 85.47 86.82 87.27 108.38 109.55 110.50 110.86 112.02 112.45 112.55 112.62 113.35 123.89 124.06 124.16 124.71 124.81 124.86 140.80 142.87
- 73.72 53.65 57.57 57.63 57.78 84.38 85.02 85.05 86.80 87.26 108.35 109.56 110.45 110.86 112.10 112.39 113.36 115.37 115.49 123.53 123.62 123.89 124.06 124.11 124.71 124.75 124.86 140.79 142.91
- 73.71 53.69 57.60 57.66 57.76 84.04 86.78 86.87 86.91 87.24 108.33 109.58 110.40 110.87 113.38 115.29 115.65 123.52 123.62 123.89 124.06 124.09 124.86 125.12 125.14 140.79 142.94
- 73.70 53.77 57.60 83.69 86.76 86.82 86.91 87.23 108.30 109.59 110.36 110.89 113.39 115.22 115.80 123.51 123.63 123.89 124.06 124.09 124.91 125.12 125.14 140.78 142.96
+ 73.77 53.62 57.47 57.54 57.91 84.68 84.82 85.47 87.03 87.34 108.50 109.51 111.73 112.87 113.27 123.86 123.97 124.24 124.52 140.84 142.76
+ 73.76 53.62 57.49 57.57 57.88 84.54 84.86 85.46 87.02 87.31 108.50 109.52 110.64 110.70 111.78 112.83 113.30 123.86 123.99 124.22 124.58 140.83 142.79
+ 73.75 53.62 57.50 57.59 57.86 84.49 84.90 85.46 86.94 87.30 108.48 109.53 110.59 110.79 111.85 112.76 113.32 123.87 124.01 124.22 124.60 124.64 124.70 140.82 142.82
+ 73.74 53.62 57.51 57.61 57.83 84.43 84.95 85.46 86.85 87.28 108.43 109.54 110.55 110.86 111.93 112.68 113.34 123.89 124.03 124.22 124.71 140.81 142.84
+ 73.73 53.63 57.53 57.61 57.81 84.38 84.99 85.47 86.82 87.27 108.38 109.55 110.50 110.86 112.02 112.45 112.55 112.62 113.35 123.89 124.06 124.16 124.71 124.81 124.86 140.80 142.87
+ 73.72 53.65 57.57 57.63 57.78 84.20 85.02 85.05 86.80 87.26 108.35 109.56 110.45 110.86 112.10 112.39 113.36 115.37 115.49 123.53 123.62 123.89 124.06 124.11 124.71 124.75 124.86 140.79 142.91
+ 73.71 53.69 57.60 57.66 57.76 83.88 86.78 86.87 86.91 87.24 108.33 109.58 110.40 110.87 113.38 115.29 115.65 123.52 123.62 123.89 124.06 124.09 124.86 125.12 125.14 140.78 142.94
+ 73.70 53.77 57.60 83.69 86.76 86.82 86.91 87.23 108.30 109.59 110.36 110.89 113.39 115.22 115.80 123.51 123.63 123.89 124.06 124.09 124.91 125.12 125.14 140.77 142.96
73.69 53.79 54.70 54.81 57.60 83.63 86.74 86.77 86.91 87.23 108.27 109.60 110.31 110.84 113.40 115.14 116.03 123.47 123.63 123.89 124.92 125.03 125.15 140.76 142.98
- 73.68 53.81 54.52 54.81 57.61 83.57 86.90 87.23 108.24 109.62 109.79 110.76 113.41 115.09 116.64 123.39 123.63 123.89 124.93 124.95 124.99 125.03 125.16 140.75 143.00
- 73.67 53.83 54.48 54.83 57.62 81.84 82.82 83.51 86.89 87.24 108.22 109.64 109.79 110.68 113.41 115.05 116.72 123.35 123.61 123.90 124.99 125.03 125.17 140.73 143.02
- 73.66 53.85 54.46 54.74 57.62 81.63 86.87 87.22 108.19 109.66 109.79 110.60 113.42 115.01 116.80 123.35 123.60 123.90 124.99 125.03 125.18 140.72 143.10
- 73.65 53.86 54.45 54.70 57.62 81.47 86.85 87.20 107.95 108.06 108.16 109.70 109.79 110.44 113.42 114.98 116.87 123.35 123.65 123.91 124.99 125.03 125.22 140.71 143.17
- 73.64 53.89 54.44 54.68 57.61 81.36 86.83 87.19 107.92 108.05 108.13 110.41 113.43 114.94 116.95 123.37 123.66 123.88 124.99 125.01 125.22 140.70 143.19
- 73.63 53.92 54.42 54.64 57.61 81.29 86.81 87.17 107.89 108.05 108.11 110.39 113.43 114.90 117.03 123.36 123.66 123.75 125.22 140.69 143.22
- 73.62 53.93 54.39 54.52 57.61 81.26 86.80 87.13 107.85 108.05 108.08 110.38 113.44 114.86 117.13 123.36 123.66 123.71 125.22 140.68 143.24
- 73.61 53.95 54.33 54.49 57.61 81.16 86.80 86.82 107.35 107.51 107.82 110.37 113.44 114.70 117.26 123.36 125.22 140.67 143.27
- 73.60 54.02 54.29 54.46 57.60 80.99 107.16 107.70 107.79 110.29 113.44 114.08 117.38 117.82 118.19 123.30 125.22 140.66 143.29
- 73.59 54.06 54.10 54.20 54.29 54.43 57.58 80.52 80.71 80.87 86.31 86.38 107.14 110.11 113.44 114.05 118.51 123.30 125.21 125.35 125.37 140.66 143.32
- 73.58 54.40 57.54 75.92 76.05 80.51 86.24 86.38 107.13 110.10 113.43 114.02 118.63 123.30 125.19 125.34 125.37 125.42 125.47 140.64 143.34
- 73.57 54.37 57.46 75.71 76.07 76.14 76.21 80.50 86.16 86.29 107.17 110.08 113.42 113.98 118.74 123.25 125.18 125.22 125.24 125.33 125.38 125.42 125.47 140.60 143.37
- 73.56 54.33 57.38 75.59 76.08 76.12 76.28 80.50 107.18 109.18 109.21 110.07 113.39 113.95 118.82 123.24 125.24 125.31 125.48 126.20 126.31 140.57 143.39
- 73.55 54.30 57.07 57.18 57.36 75.56 76.08 76.10 76.32 80.50 107.18 109.17 109.24 110.07 113.31 113.92 118.87 123.23 125.27 125.29 125.60 125.92 125.96 126.17 126.33 126.97 127.12 127.47 127.72 140.54 143.41
- 73.54 54.27 57.12 57.29 57.36 75.53 76.36 80.50 107.18 109.16 109.27 110.07 113.29 113.79 118.91 123.23 125.65 125.89 125.98 126.14 126.35 126.84 127.22 127.40 127.78 140.51 143.43
- 73.53 54.24 57.18 75.49 76.40 80.50 107.17 109.16 109.32 110.11 113.27 113.58 118.93 123.23 125.66 125.89 125.98 126.11 126.38 126.83 127.29 127.38 127.84 140.48 143.44
- 73.52 54.21 57.23 70.86 70.97 75.46 76.02 76.06 76.54 80.50 107.16 109.16 109.35 110.05 113.25 113.47 118.96 123.25 125.66 125.86 125.98 126.02 126.41 126.82 127.35 127.38 127.90 140.45 143.45
- 73.51 54.19 57.25 70.72 71.03 75.43 75.96 76.06 76.58 80.50 107.14 109.17 109.38 109.98 113.23 113.45 118.98 123.27 125.66 125.82 125.98 126.00 126.41 126.82 127.96 140.41 143.46
- 73.50 54.17 57.26 70.44 70.49 70.60 71.09 75.41 75.91 76.09 76.63 80.49 107.12 109.17 109.41 109.93 113.22 113.45 119.00 123.27 125.65 125.80 126.41 126.82 128.07 140.38 143.47
- 73.49 54.17 57.26 70.38 70.52 70.54 71.14 75.39 75.89 76.31 76.67 80.49 107.08 109.17 109.44 109.87 113.22 113.45 119.00 123.27 125.65 125.80 126.40 126.90 128.07 140.35 143.48
- 73.48 54.17 57.26 70.33 71.20 75.37 75.91 76.41 76.71 80.49 107.04 109.25 109.47 109.81 113.21 113.47 119.00 123.30 125.65 125.72 125.78 125.80 126.40 126.90 128.07 140.32 143.49
- 73.47 54.20 57.26 70.27 71.24 75.34 75.91 76.51 76.74 80.52 80.56 80.60 107.00 109.18 109.50 109.74 113.20 113.48 118.99 123.27 126.40 126.89 128.05 140.07 140.20 140.29 143.51
- 73.46 54.25 57.26 70.22 71.26 75.32 75.91 76.58 76.75 80.60 106.96 109.18 113.19 113.48 118.48 118.59 118.97 123.25 126.40 126.89 127.99 139.91 143.53
- 73.45 54.29 57.26 70.17 71.27 75.31 75.46 75.48 75.88 76.62 76.76 80.59 106.93 109.18 113.17 113.49 118.46 118.60 118.95 123.25 126.40 126.71 126.75 126.84 127.99 139.75 143.54
- 73.44 54.29 57.26 70.11 71.27 75.31 75.42 75.48 75.83 76.66 76.76 80.57 106.92 109.18 113.20 113.50 118.45 118.61 118.92 123.25 126.39 126.67 126.77 126.82 127.98 139.66 143.54
- 73.43 54.29 57.19 70.06 71.27 75.29 75.40 75.48 75.65 76.68 76.76 80.48 106.91 109.19 113.21 113.51 118.44 118.65 118.72 118.78 118.85 123.26 126.37 126.65 126.77 126.82 128.02 139.64 140.60 140.78 143.54
- 73.42 54.20 57.18 70.00 71.13 71.18 71.32 75.29 75.38 76.70 76.76 80.47 106.88 109.21 113.23 113.52 118.39 123.22 126.41 126.64 126.78 126.82 128.07 139.64 140.42 140.85 143.52
- 73.41 54.09 57.18 69.96 71.14 71.22 71.35 75.29 75.38 76.73 76.76 80.45 106.88 109.23 113.24 113.54 118.37 123.20 126.44 126.64 126.78 126.83 128.08 139.64 140.37 140.91 143.50
- 73.40 54.05 57.16 69.94 71.14 71.21 71.35 75.29 75.38 80.44 106.87 109.22 113.25 113.56 118.36 123.20 126.46 126.64 126.80 126.82 128.08 139.64 140.31 140.98 143.48
- 73.39 54.03 57.14 69.94 71.14 71.19 71.36 75.29 75.38 80.34 80.40 80.42 106.86 109.14 113.27 113.58 118.37 123.20 126.46 126.55 126.59 126.62 128.08 139.65 140.26 141.05 143.46
- 73.38 54.02 55.99 56.01 57.11 69.94 71.14 71.17 71.36 75.31 75.37 80.33 106.86 109.02 113.30 113.62 118.43 123.23 126.51 126.55 128.07 139.65 140.22 141.11 143.46
- 73.37 54.02 54.46 54.48 55.99 56.01 57.08 69.94 71.13 71.15 71.36 80.32 106.85 108.95 113.37 113.66 118.43 123.27 126.53 126.55 128.05 128.12 128.20 128.29 128.36 139.66 140.18 141.18 143.46
- 73.36 54.02 54.43 54.45 55.99 56.02 57.06 69.95 71.12 71.14 71.35 71.42 71.45 80.30 106.84 108.86 113.47 113.70 118.43 123.32 128.23 128.27 128.37 139.67 140.14 141.25 143.48
- 73.35 54.05 54.40 54.43 55.99 56.02 57.03 69.96 71.11 71.13 71.36 71.41 71.47 80.27 106.83 108.74 113.49 113.73 118.42 123.32 128.37 139.68 140.10 141.31 143.48
- 73.34 54.09 54.37 54.41 55.99 56.02 57.00 69.98 71.10 71.13 71.36 71.41 71.49 80.25 106.82 108.64 113.50 113.75 118.41 123.32 128.37 139.69 140.04 141.38 143.48
- 73.33 54.14 54.34 54.40 55.99 56.03 56.80 56.83 56.98 69.99 71.09 71.13 71.36 71.40 71.51 80.24 106.80 108.56 113.50 113.71 118.40 123.32 128.36 141.44 143.48
- 73.32 54.18 54.31 54.35 55.81 55.83 55.99 56.03 56.80 56.85 56.96 69.99 71.10 71.13 71.53 80.24 106.77 108.31 113.50 113.69 118.38 123.33 128.34 141.48 143.49
- 73.31 53.80 53.90 54.22 55.81 55.85 55.99 56.04 56.80 56.86 56.94 70.00 71.10 71.13 71.55 80.24 106.73 108.23 113.50 113.68 118.38 123.34 128.32 141.52 143.50
- 73.30 53.72 53.98 54.25 55.95 56.05 56.79 56.87 56.92 70.01 71.10 71.12 71.57 80.25 106.22 106.31 106.45 106.54 106.70 108.21 113.50 113.65 118.38 123.35 128.32 141.56 143.50
- 73.29 53.67 54.05 54.21 55.95 56.06 56.77 70.02 71.09 71.12 71.59 80.26 106.18 106.58 106.66 108.19 113.50 113.62 118.38 123.36 128.32 141.61 141.68 141.73 143.51
- 73.28 53.63 56.04 56.08 56.75 70.02 71.62 80.30 106.15 108.18 113.50 113.60 118.37 123.38 128.32 141.77 143.52
- 73.27 53.61 56.74 70.03 71.63 80.48 106.12 108.18 113.50 113.57 118.37 123.40 128.38 128.54 128.67 141.90 143.53
- 73.26 53.59 56.21 56.23 56.77 70.04 71.64 80.52 106.08 108.18 113.51 113.55 118.38 123.45 128.40 128.50 128.70 142.12 143.54
- 73.25 53.39 53.46 53.57 56.30 56.45 56.77 70.04 71.65 80.53 106.06 108.02 108.16 108.36 113.51 113.53 118.39 123.46 128.42 128.45 128.73 142.25 143.54
- 73.24 53.37 53.51 53.54 56.39 56.58 56.77 70.05 71.66 80.53 106.05 107.94 108.22 108.34 113.51 113.53 118.42 123.46 128.76 142.29 142.59 142.69 143.54
- 73.23 53.30 56.46 56.62 56.75 70.05 71.67 80.54 106.06 107.92 118.45 123.47 128.86 142.33 142.45 142.78 143.54
- 73.22 53.28 56.47 70.04 71.68 76.13 76.24 80.51 106.06 107.89 118.46 123.49 128.90 142.87 143.54
- 73.21 53.25 56.48 70.03 71.68 76.12 76.36 80.29 106.06 107.86 118.49 123.51 128.90 142.96 143.40 143.46 143.53
- 73.20 53.22 56.50 70.02 71.68 76.12 76.47 76.58 76.68 80.26 106.06 106.34 106.41 107.84 118.54 123.49 128.95 143.05 143.36
- 73.19 53.20 56.53 70.01 71.68 76.12 76.71 80.24 106.05 106.32 106.49 107.01 107.08 107.80 118.59 123.42 128.97
- 73.18 53.18 56.55 69.99 71.68 76.13 76.73 80.22 106.04 106.30 106.57 106.98 107.18 107.44 107.61 107.74 118.64 123.39 128.97
- 73.17 53.16 56.57 69.97 71.68 76.15 76.74 80.22 106.03 106.28 106.65 106.94 107.28 107.36 118.69 119.77 120.05 123.37 128.97
- 73.16 53.14 56.58 69.95 71.66 76.18 76.74 80.22 80.28 80.34 106.02 106.27 106.73 106.91 118.74 119.73 120.09 123.36 128.97
- 73.15 53.14 56.58 69.93 71.33 71.49 71.64 76.22 76.74 80.38 106.02 106.20 118.79 119.69 120.14 123.36 128.97
- 73.14 53.14 56.59 69.92 71.31 74.40 74.52 76.25 76.74 80.46 106.01 106.19 118.84 119.65 120.18 123.36 128.96
- 73.13 53.14 56.59 69.91 71.29 74.27 74.60 76.29 76.73 80.54 105.99 106.17 118.89 119.62 120.22 123.37 129.12
- 73.12 53.15 56.59 69.90 71.20 74.19 74.68 76.47 76.67 80.48 105.96 106.17 119.00 119.62 120.26 123.37 129.12
- 73.11 53.11 56.59 69.89 71.05 74.17 74.79 79.15 79.19 80.42 105.92 106.17 119.11 119.62 120.28 123.38 129.12
- 73.10 53.11 56.48 69.89 70.89 74.15 74.87 79.12 79.22 80.42 105.89 106.16 119.17 119.63 120.28 123.39 129.12
- 73.09 53.11 56.36 69.88 70.74 74.14 74.91 79.10 79.25 80.42 105.87 106.16 119.23 119.64 120.28 123.38 129.12
- 73.08 53.12 56.24 69.87 70.65 74.13 74.95 79.08 79.27 80.43 105.86 106.16 119.42 119.69 120.28 123.37 129.12
- 73.07 53.13 56.43 69.87 70.07 70.14 70.61 74.12 74.73 74.77 74.97 79.05 79.29 80.45 105.86 106.16 119.52 119.73 120.27 123.35 129.11
- 73.06 53.14 56.47 69.86 70.04 70.14 70.57 74.11 74.71 74.83 74.97 79.03 79.31 80.48 105.86 106.17 119.54 119.71 120.26 123.34 129.10
- 73.05 53.16 56.47 69.86 70.08 70.15 70.53 74.10 74.70 74.89 74.97 79.00 79.35 80.57 105.86 106.17 119.56 119.69 120.24 123.32 129.09
- 73.04 53.26 56.47 69.86 70.10 70.17 70.49 74.09 74.70 74.93 74.97 78.98 79.38 80.66 105.86 106.17 119.57 119.69 120.24 122.57 122.64 123.31 129.08
- 73.03 53.27 56.46 69.86 70.11 70.19 70.41 74.08 74.70 78.96 79.39 80.69 105.85 106.17 119.58 119.69 120.24 122.49 122.69 123.30 129.07
- 73.02 53.13 56.45 69.86 70.11 70.22 70.31 74.08 74.70 78.93 79.40 80.73 105.85 106.17 119.58 119.71 120.24 122.45 122.73 123.30 129.06
- 73.01 53.12 56.44 69.87 69.96 70.03 70.11 74.08 74.70 78.91 79.40 80.74 105.85 106.18 119.61 119.75 120.01 122.45 122.81 123.30 129.05
- 73.00 53.12 56.42 70.07 70.11 74.08 74.69 78.88 79.40 80.74 105.85 106.19 119.69 119.75 120.16 122.45 122.87 123.30 129.03
- 72.99 53.12 56.39 74.09 74.68 78.86 79.42 80.75 105.84 106.20 119.70 119.75 120.54 122.42 122.88 123.31 129.02
- 72.98 53.12 56.35 69.43 69.79 74.11 74.67 78.84 79.44 80.78 105.82 106.20 119.71 119.75 120.68 121.34 121.68 121.76 121.88 122.42 122.88 123.29 129.00
- 72.97 53.12 56.26 69.37 69.80 74.13 74.66 78.81 79.46 80.79 105.80 106.14 119.72 119.76 120.74 121.28 121.97 122.42 122.89 123.26 128.96
- 72.96 53.12 56.26 69.34 69.80 74.16 74.65 78.79 79.48 80.80 105.77 106.01 120.80 121.19 121.97 122.42 122.93 123.25 128.85
- 72.95 53.13 56.26 69.32 69.80 74.18 74.65 78.76 79.51 80.80 105.75 105.99 120.94 121.09 121.97 122.29 122.40 122.46 122.99 123.24 128.76
- 72.94 53.14 56.26 69.30 69.80 74.21 74.66 78.74 79.53 80.80 105.73 105.97 121.96 122.29 123.05 123.22 128.73
- 72.93 52.98 53.05 53.16 56.25 69.29 69.80 74.27 74.68 78.72 79.55 80.81 105.71 105.96 121.95 122.29 123.11 123.16 128.69
- 72.92 52.91 53.11 53.20 56.25 69.29 69.79 71.49 71.58 74.32 74.70 78.69 79.55 80.81 105.69 105.95 121.99 122.30 128.63
- 72.91 52.84 53.17 53.28 56.24 69.29 69.73 70.93 71.15 71.30 71.62 74.33 74.71 78.67 79.56 80.82 105.67 105.94 122.03 122.32 128.53
- 72.90 52.78 53.22 53.28 56.24 69.29 69.63 70.02 70.42 70.74 71.66 74.36 74.71 78.63 79.56 80.82 105.66 105.93 122.14 122.36 128.66 140.58 140.76 140.80 140.87
- 72.89 52.71 56.24 69.29 69.58 69.73 71.71 74.40 74.71 75.00 75.07 78.61 79.56 80.81 105.64 105.87 122.33 122.40 128.82 140.57 140.95
- 72.88 52.64 56.24 69.28 71.79 74.44 74.70 74.95 75.11 78.60 79.53 80.81 105.61 105.80 128.98 140.57 141.04
- 72.87 52.60 56.24 69.28 71.87 74.57 74.70 74.91 75.12 78.58 79.53 80.80 105.57 105.76 129.08 140.57 141.31
- 72.86 52.58 56.24 69.27 71.95 74.57 74.69 74.87 75.14 78.58 79.53 80.80 105.54 105.74 128.24 128.27 129.12 140.57 141.37
- 72.85 52.57 56.23 69.26 72.00 74.59 74.69 74.83 75.16 78.57 79.53 80.79 105.50 105.72 128.24 128.27 129.16 140.57 141.41
- 72.84 52.55 56.23 69.25 72.01 72.09 72.16 74.63 74.67 74.79 75.23 78.57 79.54 80.78 105.46 105.70 128.25 128.28 129.20 140.58 141.42
- 72.83 52.53 56.23 69.24 72.01 72.03 72.20 74.76 75.29 78.57 79.55 80.76 105.42 105.68 128.25 128.30 129.24 140.61 141.44
- 72.82 52.51 56.23 69.23 72.24 74.73 75.33 78.57 78.62 78.64 79.55 80.76 105.38 105.64 128.25 128.30 129.28 140.64 141.46
- 72.81 52.49 56.23 69.22 72.28 74.73 75.37 78.58 78.62 78.64 79.55 80.76 105.35 105.56 128.24 128.30 129.30 140.64 141.48
- 72.80 52.47 56.19 69.20 72.40 74.73 75.40 78.58 78.62 78.65 79.55 80.74 105.33 105.54 129.30 140.64 141.51
- 72.79 52.46 56.18 69.18 72.51 74.73 75.44 78.59 78.61 78.66 79.55 80.72 105.31 105.52 129.30 140.65 141.54
- 72.78 52.46 55.83 55.89 56.17 69.16 72.55 74.74 75.48 78.68 79.56 80.70 105.30 105.49 128.65 128.82 129.28 140.68 141.61
- 72.77 52.45 55.77 55.96 56.15 69.13 72.58 74.76 75.52 78.70 79.57 80.67 128.77 129.01 129.26 140.72 141.68
- 72.76 52.38 55.83 56.02 56.10 69.10 72.61 74.78 75.53 78.75 79.57 80.65 128.89 129.07 129.21 140.77 141.72
- 72.75 52.37 55.85 69.08 72.65 74.80 75.54 78.80 79.58 80.63 129.01 140.81 141.80
- 72.74 52.36 55.86 69.05 72.69 74.82 75.54 78.83 79.58 80.62 129.13 140.84 141.92
- 72.73 52.36 55.87 69.02 72.75 74.84 75.54 78.86 79.58 80.62 129.25 140.86 142.05
+ 73.68 53.81 54.52 54.81 57.61 83.57 86.90 87.23 108.24 109.62 109.79 110.76 113.41 115.09 116.64 123.39 123.63 123.89 124.93 124.95 124.98 125.03 125.16 140.74 143.00
+ 73.67 53.83 54.48 54.83 57.62 81.84 82.82 83.51 86.88 87.24 108.22 109.64 109.79 110.68 113.41 115.05 116.72 123.35 123.61 123.90 124.98 125.03 125.17 140.73 143.02
+ 73.66 53.85 54.46 54.74 57.62 81.62 86.86 87.22 108.19 109.66 109.79 110.60 113.42 115.01 116.79 123.35 123.60 123.90 124.98 125.03 125.18 140.72 143.10
+ 73.65 53.86 54.44 54.70 57.62 81.46 86.84 87.20 107.95 108.06 108.16 109.70 109.79 110.44 113.42 114.98 116.87 123.35 123.65 123.91 124.99 125.03 125.22 140.71 143.17
+ 73.64 53.89 54.43 54.68 57.61 81.36 86.82 87.19 107.92 108.05 108.13 110.41 113.43 114.94 116.94 123.37 123.66 123.87 124.99 125.01 125.22 140.70 143.19
+ 73.63 53.92 54.41 54.64 57.61 81.29 86.80 87.17 107.89 108.05 108.11 110.39 113.43 114.90 117.02 123.36 123.66 123.75 125.22 140.69 143.22
+ 73.62 53.93 54.39 54.52 57.61 81.26 86.80 87.13 107.85 108.05 108.08 110.38 113.44 114.86 117.12 123.36 123.66 123.71 125.22 140.68 143.24
+ 73.61 53.95 54.33 54.49 57.61 81.16 86.80 86.82 107.35 107.51 107.82 110.37 113.44 114.70 117.25 123.36 125.22 140.67 143.27
+ 73.60 54.02 54.29 54.46 57.60 80.99 107.16 107.69 107.79 110.29 113.44 114.08 117.38 117.82 118.32 123.30 125.22 140.66 143.29
+ 73.59 54.06 54.10 54.19 54.29 54.43 57.58 80.52 80.71 80.87 86.31 86.38 107.14 110.11 113.44 114.05 118.51 123.30 125.21 125.35 125.37 140.65 143.32
+ 73.58 54.40 57.53 75.92 76.05 80.51 86.24 86.38 107.13 110.10 113.43 114.02 118.63 123.30 125.19 125.34 125.37 125.42 125.47 140.63 143.34
+ 73.57 54.37 57.45 75.71 76.07 76.14 76.21 80.50 86.16 86.27 107.16 110.08 113.42 113.98 118.74 123.25 125.18 125.22 125.24 125.33 125.38 125.40 125.47 140.61 143.37
+ 73.56 54.33 57.37 75.59 76.08 76.12 76.28 80.50 107.17 109.18 109.21 110.07 113.39 113.95 118.82 123.24 125.24 125.31 125.48 126.20 126.31 140.59 143.39
+ 73.55 54.30 57.07 57.18 57.36 75.56 76.08 76.10 76.32 80.50 107.17 109.17 109.24 110.07 113.31 113.92 118.87 123.23 125.27 125.29 125.60 125.92 125.96 126.17 126.33 126.97 127.12 127.47 127.72 140.57 143.41
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72.59 52.73 55.68 68.91 72.75 75.03 75.69 77.45 78.16 80.76 128.16 128.18 128.98 140.92 145.06
72.58 52.72 55.69 68.91 72.75 75.04 75.70 77.41 78.21 80.75 128.18 128.22 128.98 140.94 145.20
72.57 52.72 55.69 68.90 72.76 75.04 75.71 77.37 78.26 80.72 128.86 140.91 145.34
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72.55 52.71 52.79 52.87 55.68 68.87 72.80 75.04 75.71 77.30 78.31 80.69 128.83 140.87 145.48
72.54 52.71 52.75 52.85 55.65 68.85 72.83 75.04 75.71 77.29 78.33 80.69 128.82 140.76 145.53
72.53 52.85 55.63 68.85 72.85 75.04 75.71 77.27 78.35 80.69 128.44 128.51 128.79 140.70 145.59
@@ -144463,246 +144758,246 @@ Russia
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@@ -144711,59 +145006,59 @@ Russia
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- 69.68 30.88 32.12 32.15 33.12 59.71 59.95 60.14 60.31 60.44 63.44 66.78 67.01 67.05 72.58 73.54 160.33 160.36 160.67 162.31 162.68 162.89 164.30 167.42 168.07 168.16 169.31 170.17 176.78
- 69.67 30.89 32.11 32.14 33.12 59.88 59.94 60.18 63.48 66.78 67.01 67.11 72.57 73.55 160.74 162.30 162.72 162.80 164.33 167.39 168.03 168.19 169.32 170.15 176.85
- 69.66 30.91 32.11 32.14 33.12 59.89 59.94 60.17 63.52 66.77 67.01 67.15 72.57 73.56 160.78 162.17 162.25 162.28 164.36 167.36 167.97 168.25 169.32 170.14 176.90
- 69.65 30.16 30.21 30.91 32.10 32.14 33.12 59.90 59.94 60.16 63.56 66.77 67.01 67.18 72.56 73.58 160.82 160.87 160.93 161.47 161.51 162.16 164.39 167.33 167.96 168.30 169.32 170.13 176.95
- 69.64 30.10 30.27 30.91 32.08 32.16 33.12 60.15 63.61 66.77 67.01 67.22 72.54 73.59 160.94 161.45 161.57 162.16 164.42 167.30 167.99 168.35 169.32 170.12 177.02
- 69.63 30.10 30.31 30.91 32.06 32.25 33.11 60.14 63.67 66.77 67.00 67.25 72.54 73.60 160.95 161.45 161.59 162.16 164.46 167.27 168.04 168.41 169.31 170.12 177.12
- 69.62 30.10 30.33 30.91 32.07 32.33 32.40 32.46 33.09 60.14 63.73 66.77 66.96 67.29 72.56 73.62 160.96 161.45 161.60 162.12 164.51 167.24 168.08 168.46 169.30 170.11 177.38
- 69.61 30.11 30.35 30.92 32.07 32.53 33.07 60.14 63.79 66.77 66.88 67.38 72.57 73.63 160.98 161.42 161.61 162.10 165.10 167.21 168.12 168.52 169.28 170.11 177.44
- 69.60 30.13 30.38 30.92 32.21 32.61 33.05 60.13 63.86 66.77 66.89 67.46 72.58 73.65 161.00 161.38 161.62 162.05 165.70 167.18 168.15 168.57 169.27 170.11 177.50
- 69.59 30.17 30.40 30.92 32.24 32.33 32.42 32.68 33.01 60.13 63.92 66.77 66.90 67.23 67.32 67.50 72.58 73.67 161.00 161.38 161.63 162.02 165.81 167.15 168.17 168.62 169.26 170.12 170.42 170.51 177.56
- 69.58 30.21 30.43 30.91 32.43 32.75 32.96 60.12 63.98 66.77 66.92 67.16 67.33 67.54 72.59 73.69 161.01 161.38 161.64 162.00 165.87 167.12 168.20 168.68 169.24 170.14 170.34 170.55 177.62
- 69.57 30.21 30.45 30.90 32.44 32.83 32.90 60.12 64.04 66.78 66.93 67.14 67.33 67.63 72.60 73.70 161.01 161.39 161.64 162.00 165.92 167.09 168.23 168.73 169.22 170.17 170.25 170.59 177.67
- 69.56 30.21 30.47 30.89 32.44 60.12 64.10 66.80 66.94 67.12 67.34 67.65 72.60 73.72 161.01 161.39 161.64 162.00 165.96 167.06 168.25 168.78 169.20 170.60 177.69
- 69.55 30.21 30.50 30.88 32.44 60.14 64.15 66.81 66.95 67.10 67.35 67.67 72.61 73.74 161.00 161.32 161.64 161.98 165.99 167.03 168.26 168.84 168.96 170.62 177.69
- 69.54 30.21 30.64 30.86 32.45 60.20 64.19 66.83 66.96 67.09 67.35 67.69 72.62 73.75 160.99 161.25 161.38 161.40 161.63 161.81 161.88 161.95 166.02 166.34 166.64 167.00 168.26 170.63 177.79
- 69.53 30.20 32.49 60.20 64.23 66.85 66.96 67.07 67.35 67.72 68.04 68.08 72.62 73.76 160.98 161.23 161.38 161.40 161.63 161.79 166.68 166.97 168.26 170.65 177.82
- 69.52 30.15 32.51 48.99 49.18 60.20 64.27 66.87 66.96 67.05 67.35 67.75 68.03 68.08 72.63 73.78 160.96 161.20 161.62 161.77 166.70 166.94 168.26 170.66 177.85
- 69.51 30.14 32.56 32.65 32.71 48.85 49.29 60.21 64.31 66.90 66.94 67.03 67.35 67.77 68.03 68.08 72.63 73.79 160.96 161.18 161.39 161.41 161.62 161.73 166.70 166.91 168.26 170.66 177.88
- 69.50 30.13 32.58 32.62 32.77 32.81 32.89 48.78 49.33 60.22 64.35 67.02 67.34 67.80 68.04 68.08 72.64 73.80 160.95 161.15 161.63 161.68 168.25 170.66 177.94
- 69.49 30.13 32.90 48.75 49.37 60.24 64.40 67.02 67.34 67.85 68.05 68.08 72.64 73.81 160.95 161.12 161.63 161.66 168.25 170.66 178.03 178.28 178.39
- 69.48 30.13 32.90 32.93 33.09 48.72 49.41 60.25 64.46 67.01 67.33 67.92 68.05 68.09 72.64 73.83 160.94 161.10 161.63 161.65 168.25 170.66 178.11 178.26 178.45
- 69.47 30.13 33.09 48.69 49.45 60.26 64.52 67.01 67.32 68.00 68.05 68.08 72.64 73.84 160.94 161.08 168.25 170.66 178.17 178.26 178.51
+ 69.92 31.90 32.19 58.85 60.48 66.82 72.64 73.65 159.73 167.88 169.16 170.51 172.85 173.16 173.61
+ 69.91 31.90 32.21 58.87 60.48 66.82 72.65 73.65 159.72 167.85 169.25 170.51 172.89 173.15 173.65
+ 69.90 31.92 32.23 58.90 60.47 66.82 72.66 73.64 159.70 167.83 169.33 170.52 172.94 173.15 173.69 176.05 176.14
+ 69.89 31.95 32.26 58.92 59.12 59.20 60.47 66.81 72.67 73.64 159.70 167.81 169.40 170.53 172.99 173.15 173.71 173.76 173.81 174.01 174.17 174.28 174.35 175.60 175.72 175.77 176.16
+ 69.88 31.97 32.42 58.94 59.14 59.22 60.46 66.81 72.68 73.64 159.71 167.80 169.43 170.54 173.05 173.15 173.71 173.73 173.85 173.97 174.48 175.45 175.73 175.77 176.17
+ 69.87 31.97 32.46 58.94 59.14 59.25 59.34 59.41 60.47 60.88 60.99 61.08 61.12 66.80 72.68 73.64 159.73 167.78 169.44 170.54 173.10 173.15 173.71 173.73 173.87 173.95 174.68 175.35 175.73 175.77 176.19
+ 69.86 31.73 31.86 31.97 32.50 58.96 59.14 59.44 60.51 60.80 61.01 61.06 61.13 66.80 72.69 73.64 159.74 167.77 169.44 170.54 173.91 173.93 174.94 175.23 175.73 175.78 176.22
+ 69.85 31.71 31.88 31.98 32.52 59.00 59.13 59.46 60.52 60.75 61.14 66.79 72.69 73.62 159.76 167.75 169.45 170.54 175.68 175.81 176.24
+ 69.84 31.71 31.90 32.00 32.53 59.00 59.11 59.48 60.53 60.71 61.23 66.79 72.70 73.61 159.77 167.74 169.45 170.54 175.74 175.88 176.26
+ 69.83 31.70 31.94 32.03 32.53 59.50 60.54 60.69 61.32 66.78 72.70 73.59 159.79 167.74 169.46 170.53 175.78 176.10 176.27
+ 69.82 31.70 31.98 32.05 32.53 59.53 60.55 60.68 61.36 66.78 72.70 73.58 159.80 167.74 169.46 170.53 175.80 176.12 176.28
+ 69.81 30.83 30.88 31.69 32.00 32.07 32.55 59.56 60.55 60.67 61.39 66.77 72.69 73.56 159.81 167.75 169.46 170.53 175.82 176.14 176.29
+ 69.80 30.83 30.94 31.69 32.02 32.08 32.60 32.67 32.82 59.58 60.55 60.67 61.47 66.77 72.69 73.55 159.81 167.77 169.46 170.53 175.85 176.14 176.29
+ 69.79 30.83 31.00 31.69 32.93 59.55 60.55 60.67 61.59 66.76 72.68 73.53 159.90 167.78 169.45 170.54 175.90 176.12 176.29
+ 69.78 30.83 31.17 31.69 32.96 59.53 60.53 60.67 61.71 66.76 72.68 73.52 159.94 164.00 164.05 167.65 169.43 170.08 170.28 170.54 175.96 176.08 176.36
+ 69.77 30.83 31.19 31.23 31.30 31.70 32.99 59.53 60.48 60.67 61.87 66.75 72.67 73.51 159.97 163.96 164.09 167.62 167.85 167.90 169.42 170.03 170.28 170.56 176.46
+ 69.76 30.83 31.32 31.69 33.03 59.52 60.46 60.67 62.07 66.75 72.67 73.51 160.01 163.93 164.12 167.59 167.87 167.94 169.42 169.99 170.28 170.52 176.52
+ 69.75 30.83 31.34 31.68 33.13 59.52 60.45 60.67 62.68 66.75 72.66 73.50 160.05 163.90 164.13 167.57 167.89 168.00 169.31 169.35 169.42 169.96 170.28 170.46 176.54
+ 69.74 30.84 31.37 31.68 33.13 59.52 60.47 60.63 62.78 66.75 72.66 73.50 160.08 163.87 164.14 167.55 167.92 168.05 169.31 169.95 170.24 170.39 176.59
+ 69.73 30.85 31.40 31.68 32.12 32.15 33.14 59.55 60.48 60.62 62.88 66.76 72.65 73.50 160.20 163.14 163.32 163.84 164.15 167.53 167.95 168.00 168.05 168.07 169.31 169.94 170.24 170.32 176.63
+ 69.72 30.86 31.41 31.69 32.12 32.15 33.14 59.55 60.48 60.62 62.97 66.76 72.64 73.51 160.28 163.10 163.34 163.37 163.41 163.81 164.17 167.52 169.30 169.94 170.23 170.28 176.64
+ 69.71 30.87 31.41 31.54 31.62 31.71 32.12 32.16 33.14 59.55 60.37 60.42 60.48 60.62 63.07 66.77 72.63 73.51 160.32 162.31 162.36 163.06 163.44 163.78 164.20 167.50 169.29 169.94 170.22 170.26 176.66
+ 69.70 30.87 31.41 31.46 31.50 31.52 32.12 32.16 33.13 59.55 60.02 60.06 60.36 60.62 63.17 66.78 72.61 73.52 160.33 162.31 162.38 163.03 163.47 163.67 164.22 167.48 168.09 168.12 169.30 169.96 170.20 170.24 176.68
+ 69.69 30.87 31.41 31.44 32.12 32.16 33.12 59.61 59.97 60.10 60.34 60.64 63.32 66.78 72.59 73.53 160.33 160.41 160.57 162.31 162.40 162.51 162.64 162.97 164.26 167.45 168.09 168.14 169.31 170.04 170.18 170.22 176.71
+ 69.68 30.88 32.12 32.15 33.12 59.71 59.95 60.14 60.31 60.44 63.44 66.78 67.01 67.05 72.58 73.54 160.33 160.36 160.67 162.31 162.68 162.89 164.30 167.43 168.07 168.16 169.31 170.05 170.15 170.21 176.78
+ 69.67 30.89 32.11 32.14 33.12 59.88 59.94 60.18 63.48 66.78 67.01 67.11 72.57 73.55 160.74 162.30 162.72 162.80 164.33 167.40 168.03 168.19 169.31 170.08 170.12 170.19 176.85
+ 69.66 30.91 32.11 32.14 33.12 59.89 59.94 60.17 63.52 66.77 67.01 67.15 72.57 73.56 160.78 161.78 161.90 162.17 162.25 162.28 164.36 167.37 167.97 168.25 169.31 170.18 176.90
+ 69.65 30.16 30.21 30.91 32.09 32.14 33.12 59.90 59.94 60.16 63.56 66.77 67.01 67.18 72.56 73.58 160.82 160.87 160.93 161.47 161.51 161.72 161.91 162.16 164.39 167.34 167.96 168.31 169.31 170.17 176.95
+ 69.64 30.10 30.27 30.91 32.07 32.15 33.12 60.15 63.61 66.77 67.00 67.22 72.54 73.59 160.94 161.45 161.57 161.65 161.91 162.16 164.42 167.31 167.99 168.37 169.31 170.16 177.02
+ 69.63 30.10 30.31 30.91 32.06 32.29 33.11 60.14 63.67 66.77 66.99 67.25 72.54 73.60 160.95 161.45 161.59 161.65 161.91 162.16 164.46 167.29 168.04 168.43 169.31 170.16 177.12
+ 69.62 30.10 30.33 30.91 32.07 32.48 33.09 60.14 63.73 66.77 66.90 67.29 72.56 73.62 160.96 161.45 161.60 161.65 161.91 162.11 164.51 167.26 168.08 168.49 169.30 170.15 177.39
+ 69.61 30.11 30.35 30.92 32.07 32.53 33.07 60.14 63.79 66.77 66.88 67.38 72.57 73.63 160.98 161.42 161.61 161.65 161.90 162.09 164.57 167.23 168.12 168.54 169.28 170.15 177.46
+ 69.60 30.13 30.38 30.92 32.21 32.61 33.05 60.13 63.86 66.77 66.89 67.46 72.58 73.65 161.00 161.38 161.62 161.65 161.90 162.05 164.65 165.18 165.71 167.20 168.15 168.59 169.27 170.15 177.54
+ 69.59 30.17 30.40 30.92 32.24 32.33 32.42 32.68 33.01 60.13 63.94 66.77 66.90 67.23 67.32 67.50 72.58 73.67 161.00 161.38 161.63 161.66 161.90 162.02 164.72 165.04 165.81 167.17 168.17 168.64 169.26 170.16 177.61
+ 69.58 30.21 30.43 30.91 32.43 32.75 32.96 60.12 64.01 66.77 66.92 67.16 67.33 67.54 72.59 73.69 161.01 161.38 161.64 161.68 161.90 162.00 164.80 164.90 165.87 167.13 168.20 168.69 169.24 170.16 170.49 170.54 177.66
+ 69.57 30.21 30.45 30.90 32.44 32.83 32.90 60.12 64.09 66.78 66.93 67.14 67.33 67.63 72.60 73.70 161.01 161.39 161.64 161.70 161.90 162.00 165.92 167.10 168.23 168.74 169.22 170.17 170.42 170.59 177.68
+ 69.56 30.21 30.47 30.89 32.44 60.12 64.14 66.80 66.94 67.12 67.34 67.65 72.60 73.72 161.01 161.34 161.37 161.39 161.64 161.71 161.90 162.00 165.96 167.07 168.25 168.79 169.20 170.23 170.33 170.60 177.69
+ 69.55 30.21 30.50 30.88 32.44 60.14 64.18 66.81 66.95 67.10 67.35 67.67 72.61 73.74 161.00 161.32 161.64 161.72 161.89 161.98 165.99 167.04 168.26 168.84 168.96 170.62 177.69
+ 69.54 30.21 30.64 30.86 32.45 60.20 64.21 66.83 66.96 67.09 67.35 67.69 72.62 73.75 160.99 161.25 161.38 161.40 161.63 161.74 161.88 161.95 166.02 166.48 166.64 167.01 168.26 170.63 177.79
+ 69.53 30.20 32.49 60.20 64.25 66.85 66.96 67.07 67.35 67.72 68.04 68.08 72.62 73.76 160.97 161.23 161.38 161.40 161.63 161.76 166.68 166.97 168.26 170.65 177.82
+ 69.52 30.15 32.51 48.99 49.18 60.20 64.29 66.87 66.96 67.05 67.35 67.75 68.03 68.08 72.63 73.78 160.96 161.20 161.62 161.77 166.70 166.94 168.26 170.66 177.85
+ 69.51 30.14 32.56 32.65 32.71 48.85 49.29 60.21 64.32 66.90 66.94 67.03 67.35 67.77 68.03 68.08 72.63 73.79 160.95 161.18 161.39 161.41 161.62 161.71 166.70 166.91 168.26 170.66 177.88
+ 69.50 30.13 32.58 32.62 32.77 32.81 32.89 48.78 49.33 60.22 64.36 67.02 67.34 67.80 68.04 68.08 72.64 73.80 160.95 161.15 161.39 161.41 161.62 161.68 168.25 170.66 177.94
+ 69.49 30.13 32.90 48.75 49.37 60.24 64.40 67.02 67.34 67.85 68.05 68.08 72.64 73.81 160.95 161.12 161.39 161.41 161.63 161.66 168.25 170.66 178.03 178.28 178.39
+ 69.48 30.13 32.90 32.93 33.09 48.72 49.41 60.25 64.46 67.01 67.33 67.92 68.05 68.09 72.64 73.83 160.94 161.10 161.39 161.41 161.63 161.65 168.25 170.66 178.11 178.26 178.45
+ 69.47 30.13 33.09 48.69 49.45 60.26 64.52 67.01 67.32 68.00 68.05 68.08 72.64 73.84 160.94 161.08 161.39 161.41 168.25 170.66 178.17 178.26 178.51
69.46 30.12 33.09 33.30 33.33 48.66 49.49 60.27 64.56 66.94 66.98 67.01 67.31 68.08 72.64 73.85 160.93 161.07 161.39 161.41 168.25 170.67 178.20 178.25 178.57
69.45 30.10 33.08 33.25 33.34 33.39 33.47 48.63 49.52 60.29 64.58 66.93 67.29 68.07 72.64 73.85 160.94 161.06 168.25 170.69 178.63
69.44 30.08 33.06 33.19 33.51 48.60 49.56 60.30 64.61 66.92 67.31 68.07 72.64 73.86 160.95 161.06 168.25 170.72 178.69
@@ -144774,567 +145069,567 @@ Russia
69.39 29.97 33.51 33.97 34.31 48.47 49.74 60.39 64.74 66.95 67.26 68.07 72.58 73.87 160.98 161.06 161.40 161.44 168.22 170.73 178.91
69.38 29.95 33.50 33.97 34.35 48.43 49.78 60.42 64.78 66.97 67.23 68.06 72.60 73.86 160.99 161.07 161.36 161.42 168.21 170.73 178.94
69.37 29.92 33.50 33.96 34.39 48.42 49.81 60.42 64.82 66.98 67.20 68.04 72.61 73.86 160.99 161.08 161.37 161.42 168.22 170.75 178.98
- 69.36 29.71 33.50 33.96 34.41 48.41 49.84 60.42 64.86 67.03 67.17 68.03 72.62 73.85 160.99 161.10 161.37 161.42 168.23 170.77 179.01
- 69.35 29.69 33.49 33.96 34.41 48.40 49.88 58.77 58.83 60.42 64.90 67.08 67.15 68.02 72.63 73.85 161.00 161.12 161.37 161.44 168.23 170.80 179.03
- 69.34 29.67 33.47 33.67 33.74 33.84 34.41 48.39 49.91 58.75 58.87 60.43 64.93 68.01 72.63 73.84 161.00 161.14 161.37 161.40 168.24 170.82 179.07
- 69.33 29.63 33.46 33.60 33.75 33.84 34.40 48.37 49.94 58.75 58.91 60.46 64.96 68.01 72.64 73.84 161.01 161.14 161.36 161.40 168.24 170.84 179.07
- 69.32 29.40 33.44 33.58 34.43 48.35 49.98 58.75 58.95 60.49 64.99 68.01 72.64 73.83 161.01 161.15 161.37 161.40 168.25 170.85 179.07
- 69.31 29.36 33.42 33.56 34.43 48.33 50.01 58.77 58.99 60.51 65.01 68.01 72.65 73.82 161.02 161.15 161.37 161.40 168.25 170.87 179.07
+ 69.36 29.71 33.50 33.96 34.41 48.41 49.84 60.42 64.86 67.03 67.17 68.02 72.62 73.85 160.99 161.10 161.37 161.42 168.23 170.77 179.01
+ 69.35 29.69 33.49 33.96 34.41 48.40 49.88 58.77 58.83 60.42 64.90 67.08 67.15 68.01 72.63 73.85 161.00 161.12 161.37 161.44 168.23 170.80 179.03
+ 69.34 29.67 33.47 33.67 33.74 33.84 34.41 48.39 49.91 58.75 58.87 60.43 64.93 68.00 72.63 73.84 161.00 161.14 161.36 161.40 168.24 170.82 179.07
+ 69.33 29.63 33.46 33.60 33.75 33.84 34.40 48.37 49.94 58.75 58.91 60.46 64.96 68.00 72.64 73.84 161.01 161.14 161.36 161.40 168.24 170.84 179.07
+ 69.32 29.40 33.44 33.58 34.43 48.35 49.98 58.75 58.95 60.49 64.99 68.00 72.64 73.83 161.01 161.15 161.37 161.40 168.25 170.85 179.07
+ 69.31 29.36 33.42 33.56 34.43 48.33 50.01 58.77 58.99 60.51 65.01 68.00 72.65 73.82 161.02 161.15 161.37 161.40 168.25 170.87 179.07
69.30 29.35 33.42 33.55 34.43 48.32 50.05 58.79 59.02 60.53 65.01 68.01 72.65 73.82 161.03 161.15 161.38 161.41 168.25 170.88 179.12
- 69.29 29.33 33.45 33.55 34.47 48.30 50.10 58.83 59.06 60.54 65.01 68.02 72.65 73.81 161.03 161.14 161.38 161.43 168.25 170.90 179.22
- 69.28 29.32 33.47 33.55 34.52 34.56 34.60 35.16 35.36 48.29 50.14 58.86 59.10 60.55 65.05 68.03 72.65 73.80 161.03 161.14 161.38 161.44 168.25 170.90 179.28
- 69.27 29.31 33.48 33.55 34.63 35.13 35.42 48.28 50.17 58.90 59.14 60.55 65.08 68.04 72.65 73.79 161.03 161.13 161.38 161.43 168.26 170.90 179.30
- 69.26 29.31 33.48 33.55 34.66 35.13 35.48 48.27 50.19 58.93 59.16 60.56 65.12 68.05 72.64 73.78 161.03 161.13 161.37 161.41 168.28 170.91 179.32
- 69.25 29.30 33.48 33.55 34.75 35.13 35.54 48.27 50.20 58.97 59.18 60.57 65.16 68.06 72.62 73.77 161.03 161.12 161.36 161.40 168.30 170.91 179.34
- 69.24 29.30 33.45 33.55 34.91 35.15 35.60 48.26 50.22 59.00 59.20 60.58 65.20 68.07 72.59 73.77 75.48 75.55 161.02 161.11 161.34 161.39 168.32 170.91 179.36
- 69.23 29.29 33.52 33.55 34.99 35.02 35.13 35.18 35.66 48.26 50.23 59.04 59.21 60.58 65.24 68.09 72.57 73.76 75.44 75.65 161.02 161.11 161.35 161.38 168.52 170.91 179.38
- 69.22 29.29 35.15 35.22 35.72 48.26 50.25 59.06 59.21 60.58 65.28 68.10 72.54 73.75 75.42 75.75 161.03 161.11 168.69 170.90 179.40
- 69.21 29.29 35.15 35.21 35.78 48.25 50.27 59.07 59.21 60.57 65.32 68.11 72.52 73.75 75.40 76.06 161.04 161.12 168.76 170.89 179.43
- 69.20 29.28 35.15 35.20 35.90 48.25 50.28 59.08 59.23 60.57 65.36 68.12 72.51 73.74 75.37 76.10 161.04 161.12 161.38 161.40 168.82 170.88 179.45
- 69.19 29.27 35.95 48.25 50.29 59.10 59.24 60.57 65.40 68.14 72.50 73.74 75.35 76.12 161.04 161.11 161.39 161.42 168.87 170.88 179.48
- 69.18 29.26 35.98 48.25 50.31 59.11 59.25 60.57 65.48 68.15 72.49 73.74 75.33 76.14 161.04 161.11 161.39 161.44 168.91 170.88 179.51
- 69.17 29.25 36.01 48.25 50.32 59.13 59.25 60.57 65.62 68.17 72.49 73.74 75.28 76.19 161.04 161.11 161.39 161.45 168.95 170.88 179.53
- 69.16 29.25 36.03 48.25 50.33 59.15 59.25 60.57 65.75 68.19 72.48 73.74 75.21 76.25 161.04 161.11 161.39 161.43 169.00 170.89 179.56
- 69.15 29.24 36.04 48.25 50.33 59.16 59.25 60.57 60.73 60.78 65.84 68.20 72.48 73.74 75.16 76.30 161.04 161.11 161.39 161.43 169.05 170.90 179.58
- 69.14 29.24 36.05 36.07 36.14 48.25 50.33 59.22 59.25 60.57 60.73 60.82 65.88 68.22 72.49 73.76 75.14 76.34 161.03 161.11 161.39 161.43 169.08 170.93 179.61
- 69.13 29.24 36.22 48.25 50.16 50.19 50.33 59.23 59.25 60.57 60.74 60.85 65.90 68.23 72.49 73.77 75.15 76.39 76.60 76.62 161.02 161.11 161.39 161.44 169.10 170.97 179.63
- 69.12 29.23 36.26 48.25 50.12 50.18 50.33 60.58 60.75 60.87 65.91 68.25 72.50 73.79 74.22 74.40 75.16 76.45 76.59 76.65 161.00 161.12 161.39 161.46 169.14 170.97 179.66
- 69.11 29.22 36.27 48.23 50.10 50.17 50.32 60.59 60.75 60.89 65.91 68.26 72.51 73.80 74.18 74.52 75.16 76.51 76.56 76.74 160.98 161.12 161.40 161.47 169.23 170.98 179.69
- 69.10 29.21 36.28 48.22 50.08 50.16 50.32 60.61 60.75 60.90 65.91 68.28 72.51 73.82 74.14 74.56 75.16 76.76 161.00 161.12 161.41 161.47 169.32 170.98 179.71
- 69.09 29.19 36.28 48.22 50.06 50.14 50.32 60.64 60.73 60.90 65.90 68.29 72.52 73.84 74.10 74.60 75.13 76.78 161.02 161.12 161.42 161.47 169.36 170.99 179.74
- 69.08 29.17 36.28 48.21 50.04 50.13 50.31 60.91 65.82 68.31 72.53 73.87 74.06 74.64 74.90 76.80 161.04 161.12 161.43 161.47 169.38 170.99 179.76
- 69.07 29.15 36.30 48.20 50.01 50.12 50.29 60.91 65.91 68.33 72.53 73.92 74.00 74.68 74.82 76.81 161.11 161.13 161.44 161.47 169.39 170.99 179.79
+ 69.29 29.33 33.46 33.55 34.47 48.30 50.10 58.83 59.06 60.54 65.01 68.02 72.65 73.81 161.03 161.14 161.38 161.43 168.25 170.90 179.22
+ 69.28 29.32 33.48 33.55 34.52 34.56 34.62 35.13 35.36 48.29 50.14 58.86 59.10 60.55 65.05 68.02 72.65 73.80 161.03 161.14 161.38 161.44 168.25 170.90 179.28
+ 69.27 29.31 33.48 33.55 34.64 35.13 35.42 48.28 50.17 58.90 59.14 60.55 65.08 68.03 72.65 73.79 161.03 161.13 161.38 161.43 168.26 170.90 179.30
+ 69.26 29.31 33.48 33.55 34.66 35.13 35.48 48.27 50.19 58.93 59.16 60.56 65.12 68.04 72.64 73.78 161.03 161.13 161.37 161.41 168.28 170.91 179.32
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+ 69.24 29.30 33.43 33.55 34.91 35.16 35.60 48.26 50.22 59.00 59.20 60.57 65.20 68.07 72.59 73.77 75.48 75.55 161.01 161.11 161.34 161.39 168.32 170.91 179.36
+ 69.23 29.29 33.41 33.45 33.52 33.55 34.99 35.02 35.13 35.18 35.66 48.26 50.23 59.04 59.21 60.58 65.24 68.08 72.57 73.76 75.44 75.65 161.02 161.11 161.35 161.38 168.52 170.91 179.38
+ 69.22 29.29 35.15 35.22 35.72 48.26 50.25 59.06 59.21 60.58 65.28 68.09 72.54 73.75 75.42 75.75 161.03 161.11 168.69 170.90 179.40
+ 69.21 29.29 35.15 35.21 35.78 48.25 50.27 59.07 59.22 60.57 65.32 68.11 72.52 73.75 75.40 76.06 161.04 161.12 168.76 170.89 179.43
+ 69.20 29.28 35.15 35.20 35.90 48.25 50.28 59.08 59.24 60.57 65.36 68.12 72.51 73.74 75.37 76.10 161.04 161.12 161.38 161.40 168.82 170.88 179.45
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+ 69.18 29.26 35.98 48.25 50.31 59.11 59.25 60.57 65.48 68.15 72.49 73.74 75.33 76.14 161.04 161.11 161.39 161.44 168.91 170.88 179.50
+ 69.17 29.25 36.01 48.25 50.32 59.13 59.25 60.57 65.62 68.17 72.49 73.74 75.28 76.19 161.04 161.11 161.39 161.45 168.95 170.88 179.52
+ 69.16 29.25 36.03 48.25 50.33 59.15 59.25 60.57 65.75 68.19 72.48 73.74 75.21 76.25 161.04 161.11 161.39 161.43 169.00 170.89 179.55
+ 69.15 29.24 36.04 48.25 50.33 59.16 59.25 60.57 60.73 60.78 65.84 68.20 72.48 73.74 75.16 76.30 161.04 161.11 161.39 161.43 169.05 170.90 179.57
+ 69.14 29.24 36.05 36.07 36.13 48.25 50.33 59.22 59.25 60.57 60.73 60.82 65.88 68.22 72.49 73.76 75.14 76.34 161.03 161.11 161.39 161.43 169.08 170.93 179.59
+ 69.13 29.24 36.21 48.25 50.16 50.19 50.33 59.23 59.25 60.57 60.74 60.85 65.90 68.23 72.49 73.77 75.15 76.39 76.60 76.62 161.02 161.11 161.39 161.44 169.10 170.97 179.62
+ 69.12 29.23 36.25 48.25 50.12 50.18 50.33 60.58 60.75 60.87 65.91 68.25 72.50 73.79 74.22 74.40 75.16 76.48 76.59 76.65 161.00 161.12 161.39 161.46 169.14 170.97 179.64
+ 69.11 29.22 36.27 48.23 50.10 50.17 50.32 60.59 60.75 60.89 65.91 68.26 72.51 73.80 74.18 74.52 75.16 76.74 160.98 161.12 161.40 161.47 169.23 170.98 179.67
+ 69.10 29.21 36.28 48.22 50.08 50.16 50.32 60.61 60.75 60.90 65.91 68.28 72.51 73.82 74.14 74.56 75.16 76.76 161.00 161.12 161.41 161.47 169.32 170.98 179.70
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+ 69.07 29.15 36.30 48.20 50.01 50.12 50.29 60.91 65.91 68.33 72.53 73.92 74.00 74.68 74.82 76.81 161.11 161.13 161.44 161.47 169.39 170.99 179.78
69.06 29.13 36.35 48.20 49.97 50.12 50.28 60.92 66.00 68.34 72.54 76.82 161.46 161.48 169.40 170.95 179.81
- 69.05 29.09 36.42 48.20 49.95 50.11 50.27 60.92 66.10 68.36 72.54 76.83 161.47 161.49 169.40 170.94 179.84
- 69.04 28.96 36.48 48.20 49.93 50.11 50.25 60.92 66.13 68.37 72.54 76.84 161.48 161.51 169.41 170.94 179.87
- 69.03 28.93 36.54 48.21 49.92 50.11 50.24 60.92 66.16 68.39 72.55 76.85 161.49 161.53 169.42 170.93 179.89
- 69.02 28.90 36.58 48.20 49.91 50.11 50.22 54.31 54.44 60.92 66.21 68.40 72.55 76.86 161.50 161.53 169.42 170.91 179.92
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69.01 28.87 36.62 48.20 49.92 50.11 50.20 54.06 54.56 54.61 54.69 58.84 59.22 60.92 66.25 68.40 72.55 76.88 161.50 161.54 169.43 170.90 179.94
69.00 28.84 36.66 48.20 49.92 50.10 50.18 53.98 54.57 54.60 54.70 58.78 59.24 60.93 66.27 68.41 72.55 76.26 76.43 76.90 161.51 161.55 169.43 170.87 179.96
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- 68.98 -180.00 -179.92 28.74 36.75 48.20 49.91 50.10 50.13 53.83 54.70 58.67 59.25 60.93 66.31 68.43 72.57 76.08 76.60 76.99 161.42 161.45 161.52 161.55 169.44 170.80 180.00
- 68.97 -180.00 -179.88 -179.55 -179.50 28.68 36.75 48.22 49.90 50.07 50.11 53.76 54.70 58.61 59.25 60.92 66.35 68.44 72.57 76.04 76.61 77.15 161.42 161.45 161.52 161.55 169.44 170.76 180.00
- 68.96 -180.00 -179.84 -179.55 -179.47 28.64 36.78 48.22 49.88 50.06 50.11 53.68 54.46 54.51 54.54 54.56 54.70 58.55 59.14 60.92 66.40 68.45 72.58 75.92 76.62 77.25 161.42 161.45 161.52 161.55 169.44 170.71 180.00
- 68.95 -180.00 -179.80 -179.55 -179.47 28.60 36.86 48.21 49.84 50.02 50.11 53.61 54.41 54.56 54.69 54.91 54.95 55.30 55.47 58.49 59.05 60.91 66.45 68.47 72.58 75.80 76.63 77.28 161.42 161.44 161.52 161.55 169.44 170.67 180.00
- 68.94 -180.00 -179.76 -179.55 -179.46 28.55 36.90 48.21 49.82 49.99 50.10 53.54 54.37 54.57 54.66 54.90 55.02 55.26 55.49 58.44 58.99 60.90 66.50 68.50 68.96 69.00 72.59 75.76 76.64 77.30 161.41 161.43 161.52 161.55 169.44 170.67 180.00
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- 68.90 -180.00 -179.38 28.40 37.02 48.20 49.77 49.79 49.85 53.31 53.78 54.93 55.02 55.21 55.31 55.43 55.51 58.19 58.24 58.26 59.14 60.80 66.76 68.66 68.80 68.93 72.66 75.34 76.67 77.62 161.37 161.39 169.44 170.53 180.00
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- 68.85 -180.00 -179.33 28.43 28.55 28.68 37.22 48.28 49.63 53.11 54.03 57.94 59.25 60.72 67.12 69.08 72.75 75.03 76.70 77.68 161.30 161.41 169.46 170.43 180.00
- 68.84 -180.00 -179.34 28.73 37.23 48.29 49.59 53.05 54.03 57.93 59.27 60.71 67.13 69.07 72.78 74.98 76.70 77.68 161.30 161.39 169.48 170.43 180.00
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- 68.82 -180.00 -179.17 28.77 37.24 48.35 49.60 53.00 54.01 54.18 54.29 57.93 59.32 60.68 67.13 69.01 72.82 74.88 76.67 77.68 161.28 161.35 169.52 170.13 170.41 170.44 180.00
- 68.81 -180.00 -179.15 28.76 37.29 48.36 49.60 52.97 53.99 54.18 54.35 57.93 59.34 60.66 67.10 69.00 72.84 74.80 76.65 77.68 161.27 161.33 169.54 169.98 180.00
- 68.80 -180.00 -179.05 28.76 37.33 48.37 49.45 49.48 49.60 52.95 53.97 54.18 54.39 57.94 59.36 60.64 67.06 69.00 72.88 74.73 76.64 77.68 161.26 161.31 169.58 169.83 180.00
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- 68.77 -180.00 -178.88 28.73 37.43 48.47 49.28 49.48 49.53 52.78 53.86 54.26 54.40 57.92 59.42 60.58 67.13 68.99 73.01 74.57 76.68 77.70 161.22 161.29 180.00
- 68.76 -180.00 -178.86 28.72 37.45 48.49 49.26 52.75 53.85 54.34 54.39 57.76 59.43 60.56 67.15 68.99 73.05 74.55 76.72 77.70 161.22 161.28 180.00
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- 68.68 -180.00 -178.69 28.63 37.80 43.26 43.52 48.75 49.10 52.49 53.83 57.48 59.19 59.78 67.40 68.93 73.29 74.43 76.95 77.73 161.21 161.26 180.00
- 68.67 -180.00 -178.67 28.61 37.83 43.25 43.56 48.82 49.13 52.46 53.82 55.97 56.02 57.46 59.17 59.76 67.43 68.93 73.32 74.43 76.99 77.72 161.20 161.24 180.00
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- 67.74 -180.00 -175.54 29.80 40.80 40.88 40.95 44.08 45.51 48.76 73.16 74.75 77.25 77.48 77.75 77.80 180.00
- 67.73 -180.00 -175.51 29.82 40.97 44.07 45.44 48.76 73.16 74.74 77.28 77.52 77.75 77.80 180.00
- 67.72 -180.00 -175.42 29.85 40.99 44.05 45.38 48.63 48.72 48.76 73.16 74.74 77.31 77.58 77.74 77.81 180.00
- 67.71 -180.00 -175.40 29.88 41.01 44.05 45.35 48.61 48.74 48.76 73.15 74.73 77.35 77.86 180.00
- 67.70 -180.00 -175.38 29.90 41.02 44.05 45.33 48.58 73.01 73.08 73.15 74.73 77.38 77.85 180.00
- 67.69 -180.00 -175.29 29.93 41.04 44.03 45.35 48.24 48.39 48.55 72.99 73.08 73.14 74.71 77.42 77.85 180.00
- 67.68 -180.00 -175.28 29.96 41.05 44.02 45.35 48.22 48.43 48.53 72.94 73.09 73.13 74.69 77.48 77.85 180.00
- 67.67 -180.00 -175.28 29.96 41.05 44.02 45.36 48.20 72.90 74.66 77.53 77.86 77.91 78.02 180.00
- 67.66 -180.00 -175.28 29.96 41.06 44.01 45.36 47.98 48.07 48.19 72.90 74.64 77.56 78.04 78.43 78.45 180.00
- 67.65 -180.00 -175.29 29.96 41.06 44.00 45.36 47.95 48.09 48.17 72.90 74.61 77.60 78.07 78.29 78.33 78.42 78.47 180.00
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- 67.63 -180.00 -175.32 29.96 41.06 44.00 45.35 47.88 48.10 48.13 72.89 74.56 77.66 78.37 78.41 78.45 180.00
- 67.62 -180.00 -175.31 29.96 41.06 43.99 45.35 47.85 72.87 74.53 77.68 78.39 78.41 78.45 180.00
- 67.61 -180.00 -175.29 29.95 41.06 43.98 45.35 47.83 72.83 74.51 77.70 78.47 180.00
- 67.60 -180.00 -175.28 29.95 41.06 43.96 45.34 47.81 72.60 74.48 77.71 78.49 180.00
- 67.59 -180.00 -175.28 29.95 41.05 43.95 45.33 47.80 72.57 74.46 77.71 78.18 78.27 78.53 180.00
- 67.58 -180.00 -175.27 29.94 41.04 43.94 45.32 47.80 72.55 74.43 77.71 77.81 77.89 78.16 78.30 78.54 180.00
- 67.57 -180.00 -175.27 29.94 41.02 43.93 45.29 47.80 72.55 74.41 77.70 77.74 77.90 77.92 77.98 78.14 78.34 78.52 180.00
- 67.56 -180.00 -175.26 29.93 41.00 43.92 45.15 47.80 72.55 74.38 77.70 77.72 77.99 78.08 180.00
- 67.55 -180.00 -175.23 29.93 41.01 43.91 45.11 47.81 72.55 74.35 180.00
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- 67.13 -180.00 -174.91 -173.74 -173.59 29.26 32.28 32.32 41.40 44.17 45.63 47.72 72.08 73.89 180.00
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- 66.91 -180.00 -174.76 -174.09 -171.68 29.04 32.49 32.93 41.30 44.48 45.82 47.27 71.56 71.66 71.77 73.58 180.00
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- 66.89 -180.00 -174.76 -174.09 -171.69 29.04 32.55 32.98 41.28 44.47 45.88 47.15 71.49 73.55 180.00
- 66.88 -180.00 -174.75 -174.09 -171.69 29.04 32.57 33.00 41.27 44.47 45.94 46.45 46.58 47.10 71.52 73.54 180.00
- 66.87 -180.00 -174.75 -174.07 -171.69 29.05 32.59 33.02 41.26 44.47 45.98 46.41 46.59 46.96 47.01 47.04 71.52 73.54 180.00
- 66.86 -180.00 -174.75 -174.05 -171.69 29.05 32.63 33.04 41.25 44.47 45.99 46.36 46.60 46.93 71.52 73.53 180.00
- 66.85 -180.00 -174.75 -174.05 -171.67 29.06 32.66 33.06 41.24 44.47 46.01 46.32 46.60 46.78 69.89 69.91 71.51 73.53 180.00
- 66.84 -180.00 -174.75 -174.04 -171.65 29.06 32.67 33.08 41.23 44.46 46.60 46.70 69.89 69.93 71.49 73.50 180.00
- 66.83 -180.00 -174.75 -174.04 -171.63 29.07 32.68 33.11 41.22 44.46 46.60 46.62 69.89 69.94 71.49 73.45 180.00
- 66.82 -180.00 -174.75 -174.04 -171.60 29.07 32.68 33.14 41.21 44.41 69.89 69.94 71.51 73.39 180.00
- 66.81 -180.00 -174.74 -174.04 -171.55 29.08 32.69 33.17 41.20 44.36 69.11 69.13 69.88 69.95 71.53 73.33 180.00
- 66.80 -180.00 -174.74 -174.04 -171.49 29.10 32.80 33.21 41.19 42.52 42.60 44.36 69.05 69.12 69.64 69.68 69.85 69.95 71.54 73.26 180.00
- 66.79 -180.00 -174.73 -174.03 -171.43 29.12 32.90 33.24 41.18 42.45 42.64 44.35 69.05 69.12 69.64 69.72 69.79 69.96 71.55 73.20 180.00
- 66.78 -180.00 -174.73 -174.02 -171.41 29.13 32.91 33.27 33.61 33.67 41.17 42.43 42.66 44.35 69.49 69.51 69.64 69.98 71.55 73.15 180.00
- 66.77 -180.00 -174.73 -174.01 -171.39 29.15 32.92 33.30 33.61 33.69 41.15 42.43 42.68 44.35 69.11 69.13 69.50 69.53 69.76 69.99 71.55 73.13 180.00
- 66.76 -180.00 -174.73 -174.01 -171.38 29.16 32.93 33.33 33.62 33.71 41.13 42.43 42.69 44.36 69.12 69.14 69.51 69.53 69.78 70.01 71.54 73.09 180.00
- 66.75 -180.00 -174.73 -174.00 -171.38 29.18 32.94 33.36 33.63 33.74 41.11 42.43 42.71 44.37 69.12 69.16 69.33 69.41 69.51 69.53 69.79 70.03 71.57 73.03 180.00
- 66.74 -180.00 -174.73 -174.00 -171.38 29.20 32.94 33.40 33.63 33.77 41.08 42.44 42.72 44.38 69.12 69.18 69.30 69.42 69.82 70.05 71.59 72.98 180.00
- 66.73 -180.00 -174.81 -174.78 -174.74 -174.00 -171.39 29.21 32.94 33.43 33.58 33.60 33.63 33.78 41.06 42.44 42.72 44.40 69.12 69.22 69.30 69.44 69.91 70.13 71.59 72.97 180.00
- 66.72 -180.00 -174.86 -174.77 -174.74 -174.01 -171.40 29.23 32.93 33.46 33.56 33.78 41.04 42.45 42.72 44.42 69.12 69.45 69.92 69.98 70.03 70.14 71.60 72.97 180.00
- 66.71 -180.00 -174.86 -174.77 -174.75 -174.01 -171.41 29.24 32.96 33.49 33.56 33.79 41.02 42.47 42.72 44.43 69.12 69.46 70.06 70.14 71.60 72.97 180.00
- 66.70 -180.00 -174.87 -174.01 -171.39 29.26 33.20 33.80 41.00 42.49 42.72 44.43 69.12 69.48 70.08 70.14 71.60 72.96 180.00
- 66.69 -180.00 -174.91 -174.01 -171.37 29.28 33.23 33.81 40.98 42.53 42.72 44.44 69.11 69.49 70.09 70.16 71.60 72.94 180.00
- 66.68 -180.00 -174.93 -174.03 -171.35 29.29 33.26 33.82 33.86 33.90 34.06 34.08 40.96 42.57 42.72 44.45 69.11 69.50 70.09 70.19 71.60 72.94 180.00
- 66.67 -180.00 -174.93 -174.05 -171.34 29.31 33.29 33.91 34.02 34.08 40.94 42.61 42.71 44.46 69.11 69.51 70.09 70.25 71.59 72.94 180.00
- 66.66 -180.00 -174.94 -174.11 -171.32 29.32 33.32 34.08 34.16 34.19 40.92 44.45 69.11 69.51 70.09 70.29 71.58 72.86 180.00
- 66.65 -180.00 -174.93 -174.15 -171.30 29.32 33.33 34.10 34.14 34.31 40.90 44.42 69.11 69.52 70.08 70.29 71.58 72.82 180.00
- 66.64 -180.00 -174.92 -174.19 -171.28 29.33 33.33 34.36 40.88 44.40 69.11 69.53 70.09 70.28 71.58 72.72 180.00
- 66.63 -180.00 -174.89 -174.22 -171.25 29.34 33.33 34.34 40.86 44.38 69.11 69.54 70.09 70.28 71.32 71.37 71.56 72.56 180.00
- 66.62 -180.00 -174.82 -174.25 -171.21 29.34 33.33 34.34 40.84 44.38 69.13 69.56 70.09 70.28 71.31 71.42 71.50 72.46 180.00
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- 66.59 -180.00 -174.60 -174.31 -171.11 29.38 33.45 34.36 34.79 34.82 40.78 44.37 69.18 69.52 70.09 70.29 71.13 72.44 180.00
- 66.58 -180.00 -174.54 -174.31 -171.08 29.38 33.46 34.38 34.75 34.86 40.76 44.37 69.20 69.53 70.11 70.30 71.13 72.44 180.00
- 66.57 -180.00 -174.50 -174.30 -171.02 29.38 33.46 34.39 34.71 34.89 40.74 44.36 69.22 69.55 70.13 70.32 71.13 72.44 180.00
- 66.56 -180.00 -174.48 -174.28 -170.97 29.39 33.48 34.40 34.69 34.92 40.73 44.36 69.26 69.58 70.14 70.36 71.12 72.42 180.00
- 66.55 -180.00 -174.47 -174.26 -170.95 29.39 33.53 34.40 34.66 34.94 40.73 44.36 69.30 69.61 70.14 70.39 71.00 71.05 71.10 72.38 180.00
- 66.54 -180.00 -174.46 -174.24 -170.92 29.40 33.54 34.41 34.63 34.97 40.73 42.17 42.25 44.36 69.33 69.64 70.14 70.43 71.00 72.33 180.00
- 66.53 -180.00 -174.46 -174.12 -170.90 29.42 33.29 33.34 33.54 34.42 34.59 35.00 40.73 42.14 42.33 44.36 69.37 69.66 70.10 70.49 70.99 72.30 180.00
- 66.52 -180.00 -174.45 -174.08 -170.84 29.44 33.31 33.40 33.54 34.45 34.55 35.03 40.72 42.12 42.39 44.36 69.41 69.69 70.10 70.54 70.99 72.28 180.00
- 66.51 -180.00 -174.44 -174.00 -170.82 29.46 33.31 33.46 33.52 33.58 33.62 35.05 40.71 42.11 42.44 44.35 69.46 69.72 70.09 70.59 70.91 72.27 180.00
- 66.50 -180.00 -174.43 -174.12 -174.06 -173.92 -170.80 29.47 33.32 33.56 33.63 35.08 40.69 42.10 42.48 44.32 69.65 69.75 70.08 70.65 70.76 72.27 180.00
- 66.49 -180.00 -174.43 -174.27 -174.24 -174.15 -174.01 -173.91 -170.77 29.49 33.34 33.54 33.63 35.11 40.66 42.09 42.53 44.30 69.74 69.78 70.06 72.27 72.32 72.36 180.00
- 66.48 -180.00 -174.42 -174.27 -174.21 -174.17 -173.98 -173.90 -170.75 29.51 33.43 33.51 33.64 35.13 40.62 42.08 42.58 44.27 69.78 69.80 69.93 72.35 180.00
- 66.47 -180.00 -174.42 -174.27 -173.98 -173.89 -170.74 29.51 33.64 35.16 40.60 42.07 42.62 44.25 69.90 72.35 180.00
- 66.46 -180.00 -174.41 -174.27 -173.98 -173.83 -170.71 29.52 33.67 35.19 40.59 42.05 42.66 44.23 69.83 69.86 69.88 72.35 180.00
- 66.45 -180.00 -174.49 -174.45 -174.41 -174.26 -173.98 -173.80 -170.70 29.52 33.71 35.21 40.58 42.04 42.67 44.22 69.85 72.35 180.00
- 66.44 -180.00 -174.49 -174.43 -174.41 -174.23 -173.98 -173.78 -170.68 29.53 33.73 35.26 40.57 42.03 42.67 43.18 43.28 44.21 69.87 72.36 180.00
- 66.43 -180.00 -174.48 -174.22 -173.99 -173.78 -170.66 29.53 33.74 35.31 40.55 42.02 42.67 43.03 43.31 44.21 69.89 72.36 180.00
- 66.42 -180.00 -174.47 -174.26 -174.00 -173.79 -170.65 29.53 33.74 35.33 40.52 42.01 42.67 42.89 43.32 44.20 69.94 72.37 180.00
- 66.41 -180.00 -174.47 -174.31 -174.01 -173.79 -170.63 29.54 33.74 35.35 40.50 41.99 42.67 42.79 43.33 44.20 70.02 72.38 180.00
- 66.40 -180.00 -174.47 -174.33 -174.01 -173.79 -170.61 29.54 33.71 35.37 40.48 41.98 43.34 44.18 70.09 72.38 180.00
- 66.39 -180.00 -174.46 -174.35 -173.98 -173.79 -170.59 29.54 33.62 35.40 40.46 41.97 43.34 44.16 70.16 72.38 180.00
- 66.38 -180.00 -179.16 -179.14 -178.54 -178.52 -174.44 -174.37 -173.97 -173.79 -170.57 29.54 33.65 35.46 40.43 41.95 43.35 44.15 70.24 72.38 180.00
- 66.37 -180.00 -179.16 -179.13 -178.55 -178.52 -174.43 -174.39 -173.97 -173.80 -170.56 29.55 33.67 35.52 40.36 41.94 43.36 44.15 70.29 70.99 71.24 72.37 180.00
- 66.36 -180.00 -179.16 -179.12 -178.56 -178.52 -173.97 -173.94 -170.52 29.55 33.68 35.69 40.29 41.92 43.36 44.14 70.32 70.78 71.45 72.37 180.00
- 66.35 -180.00 -179.16 -179.12 -178.63 -178.52 -173.97 -173.94 -170.47 29.56 33.68 35.74 40.27 41.91 43.39 44.13 70.35 70.66 71.50 72.36 180.00
- 66.34 -180.00 -179.16 -179.11 -178.63 -178.52 -173.97 -173.94 -170.44 29.57 33.68 35.83 40.24 41.89 43.46 44.13 71.60 72.35 180.00
- 66.33 -180.00 -179.16 -179.10 -178.63 -178.52 -173.97 -173.94 -170.40 29.58 33.65 35.95 40.22 41.88 43.57 44.12 71.70 72.35 180.00
- 66.32 -180.00 -179.16 -179.10 -178.63 -178.52 -174.03 -173.94 -170.40 29.59 33.64 36.08 40.19 41.87 43.59 44.11 71.72 72.34 180.00
- 66.31 -180.00 -179.16 -179.10 -178.64 -178.51 -174.05 -173.90 -170.29 29.60 33.66 36.20 40.17 41.85 43.62 44.10 71.74 72.33 180.00
- 66.30 -180.00 -179.16 -179.09 -178.65 -178.51 -174.06 -173.91 -170.27 29.61 33.72 36.29 40.15 41.84 43.64 44.10 71.75 72.24 72.29 72.31 180.00
- 66.29 -180.00 -179.16 -179.11 -178.66 -178.52 -174.06 -173.95 -170.25 29.62 33.78 36.33 40.13 41.82 43.66 44.09 71.76 72.20 180.00
- 66.28 -180.00 -179.16 -179.13 -178.67 -178.53 -174.07 -173.98 -170.23 29.63 33.84 36.37 40.11 41.80 43.68 44.09 71.78 72.17 180.00
- 66.27 -180.00 -179.30 -179.21 -179.16 -179.13 -178.69 -178.54 -174.07 -174.00 -170.21 29.64 33.88 36.57 36.69 36.78 40.09 41.78 43.69 44.08 71.79 72.14 180.00
- 66.26 -180.00 -179.29 -179.13 -178.70 -178.54 -174.07 -174.00 -170.19 29.65 33.89 33.95 34.03 36.91 40.06 41.76 43.69 44.08 71.81 71.89 71.94 72.10 180.00
- 66.25 -180.00 -179.28 -179.13 -178.72 -178.54 -174.07 -174.01 -170.18 29.67 33.89 33.92 34.13 36.99 40.00 41.74 43.70 44.07 71.83 71.85 71.97 72.02 180.00
- 66.24 -180.00 -179.28 -179.13 -178.73 -178.54 -174.05 -174.02 -170.17 29.68 34.15 37.07 39.94 41.72 43.70 44.07 180.00
- 66.23 -180.00 -179.27 -179.12 -178.74 -178.53 -170.16 29.69 34.17 37.15 39.88 41.70 43.70 44.07 180.00
- 66.22 -180.00 -179.25 -179.11 -178.74 -178.54 -170.14 29.71 34.17 37.23 39.83 41.68 43.70 44.06 180.00
- 66.21 -180.00 -179.24 -179.09 -178.75 -178.56 -170.12 29.72 34.17 37.28 39.80 41.66 43.69 44.06 180.00
- 66.20 -180.00 -179.23 -179.07 -178.76 -178.58 -170.12 -170.05 -170.00 29.74 34.17 37.31 39.76 41.64 43.67 44.06 180.00
- 66.19 -180.00 -179.23 -179.06 -178.77 -178.58 -170.12 -170.05 -169.93 29.75 34.20 37.34 39.72 41.62 43.74 43.79 43.86 44.06 180.00
- 66.18 -180.00 -179.23 -179.05 -178.80 -178.58 -170.12 -170.05 -169.91 29.76 34.25 37.39 39.67 41.62 43.88 44.06 180.00
- 66.17 -180.00 -179.25 -179.02 -178.84 -178.57 -169.85 29.78 34.35 37.44 39.59 41.58 43.89 44.06 180.00
- 66.16 -180.00 -179.27 -178.96 -178.88 -178.56 -169.78 29.79 34.38 37.46 39.51 41.54 43.91 44.07 180.00
- 66.15 -180.00 -179.29 -178.57 -169.73 29.81 34.42 37.48 39.45 41.52 43.93 44.07 180.00
- 66.14 -180.00 -179.31 -178.64 -178.61 -178.58 -169.69 29.83 34.45 37.50 39.43 41.50 43.95 44.07 180.00
- 66.13 -180.00 -179.34 -178.66 -169.68 29.84 34.48 37.52 39.40 41.46 43.97 44.08 180.00
- 66.12 -180.00 -179.72 -179.68 -179.38 -178.68 -169.68 29.86 34.50 37.56 39.37 41.45 43.98 44.09 180.00
- 66.11 -180.00 -179.73 -179.67 -179.52 -178.69 -169.68 29.87 34.55 37.62 39.30 41.43 44.00 44.10 180.00
- 66.10 -180.00 -179.74 -178.69 -169.68 29.88 34.56 37.73 39.21 41.42 44.03 44.12 180.00
- 66.09 -180.00 -179.75 -178.70 -169.68 29.89 34.57 37.83 38.97 39.01 39.11 41.38 44.05 44.13 180.00
- 66.08 -180.00 -179.75 -178.70 -169.68 29.89 34.57 37.87 38.90 41.35 44.06 44.13 180.00
- 66.07 -180.00 -179.76 -178.70 -169.68 29.90 34.60 37.90 38.82 41.30 44.06 44.14 180.00
- 66.06 -180.00 -179.76 -178.71 -169.68 29.90 34.62 38.02 38.75 41.22 44.06 44.14 180.00
- 66.05 -180.00 -179.76 -178.98 -178.91 -178.71 -169.68 29.91 34.63 38.23 38.67 41.14 44.06 44.13 180.00
- 66.04 -180.00 -179.76 -178.98 -178.89 -178.72 -169.69 29.91 34.65 38.44 38.59 41.08 44.05 44.13 180.00
- 66.03 -180.00 -179.77 -178.98 -178.87 -178.73 -169.70 29.92 34.67 41.05 44.05 44.12 180.00
- 66.02 -180.00 -179.77 -178.97 -178.84 -178.76 -170.09 -170.00 -169.72 29.92 34.69 41.02 44.04 44.11 180.00
- 66.01 -180.00 -179.78 -178.96 -178.81 -178.78 -170.11 -169.94 -169.73 29.92 34.71 40.90 44.04 44.11 180.00
- 66.00 -180.00 -179.79 -178.95 -170.14 -169.90 -169.74 29.92 34.72 40.77 44.05 44.11 180.00
- 65.99 -180.00 -179.80 -178.93 -170.17 -169.87 -169.75 29.93 34.73 40.73 44.06 44.11 180.00
- 65.98 -180.00 -179.80 -178.92 -170.19 -169.85 -169.77 29.93 34.73 40.70 44.07 44.11 180.00
- 65.97 -180.00 -179.80 -178.91 -170.22 29.93 34.73 40.68 44.08 44.11 180.00
- 65.96 -180.00 -179.80 -178.90 -170.25 29.94 34.72 40.66 44.09 44.12 180.00
- 65.95 -180.00 -179.80 -178.89 -170.28 29.95 34.71 40.64 44.10 44.13 180.00
- 65.94 -180.00 -179.81 -178.89 -170.31 29.96 34.72 40.62 44.11 44.14 180.00
- 65.93 -180.00 -179.81 -178.89 -170.33 29.97 34.72 40.61 180.00
- 65.92 -180.00 -179.80 -178.91 -170.36 29.98 34.80 40.59 180.00
- 65.91 -180.00 -179.80 -178.91 -170.42 29.98 34.86 40.58 180.00
- 65.90 -180.00 -179.79 -178.91 -170.44 29.99 34.86 40.57 180.00
- 65.89 -180.00 -179.79 -178.90 -170.46 30.00 34.86 40.55 180.00
- 65.88 -180.00 -179.78 -178.88 -170.48 30.00 34.87 40.54 180.00
- 65.87 -180.00 -179.78 -178.86 -170.50 30.01 34.87 40.53 180.00
- 65.86 -180.00 -179.77 -178.84 -170.52 30.01 34.87 40.51 180.00
- 65.85 -180.00 -179.77 -178.82 -170.51 30.02 34.85 40.50 180.00
- 65.84 -180.00 -179.76 -178.80 -170.51 30.03 34.84 40.49 180.00
- 65.83 -180.00 -179.76 -178.78 -170.50 -169.07 -169.01 30.04 34.91 40.47 180.00
- 65.82 -180.00 -179.75 -178.76 -170.50 -169.09 -168.98 30.05 34.91 40.45 180.00
- 65.81 -180.00 -179.74 -178.75 -170.50 -169.09 -168.98 30.06 34.91 40.43 180.00
- 65.80 -180.00 -179.72 -178.74 -171.46 -171.41 -170.51 -169.10 -168.98 30.06 34.91 40.41 180.00
- 65.79 -180.00 -179.70 -178.72 -171.45 -171.38 -170.52 -169.10 -168.98 30.07 34.90 40.39 180.00
- 65.78 -180.00 -179.68 -178.71 -171.44 -171.35 -170.53 -169.10 -168.99 30.07 34.90 40.37 180.00
- 65.77 -180.00 -179.65 -178.70 -171.42 -171.33 -170.54 -169.10 -169.00 30.08 34.69 34.71 34.89 40.35 180.00
- 65.76 -180.00 -179.63 -178.66 -171.39 -171.30 -170.54 -169.10 -169.01 30.08 34.69 34.75 34.91 40.33 180.00
- 65.75 -180.00 -179.60 -178.66 -171.34 -171.28 -170.53 -169.10 -169.02 30.08 34.70 34.77 34.93 40.31 180.00
- 65.74 -180.00 -179.58 -178.50 -171.30 -171.26 -170.52 -169.08 -169.04 30.09 34.70 34.79 34.95 40.29 180.00
- 65.73 -180.00 -179.56 -178.48 -171.30 -171.25 -170.52 30.09 34.75 34.81 34.97 40.26 180.00
- 65.72 -180.00 -179.53 -178.47 -171.30 -171.24 -170.51 30.09 34.76 34.83 34.97 40.22 180.00
- 65.71 -180.00 -179.51 -178.47 -171.31 -171.22 -170.51 30.10 34.76 34.85 34.97 40.18 180.00
- 65.70 -180.00 -179.48 -178.47 -171.31 -171.21 -170.51 30.10 34.76 34.87 34.96 40.15 180.00
- 65.69 -180.00 -179.46 -178.48 -171.29 -171.20 -170.51 30.10 34.76 34.89 34.95 40.11 180.00
- 65.68 -180.00 -179.43 -178.48 -172.65 -172.63 -171.27 -171.18 -170.51 29.96 30.04 30.10 34.75 40.07 180.00
- 65.67 -180.00 -179.39 -178.48 -172.65 -172.52 -171.26 -171.11 -170.51 29.88 30.08 30.10 34.75 40.02 180.00
- 65.66 -180.00 -179.36 -178.49 -172.65 -172.45 -171.19 -171.03 -170.51 29.80 34.75 39.96 180.00
- 65.65 -180.00 -179.33 -178.49 -172.65 -172.37 -171.12 -170.99 -170.52 29.74 34.75 39.93 180.00
- 65.64 -180.00 -179.31 -178.50 -172.66 -172.38 -171.10 -170.95 -170.53 29.71 34.76 39.90 180.00
- 65.63 -180.00 -179.31 -178.52 -172.59 -172.38 -171.08 -170.91 -170.54 29.69 34.77 39.86 180.00
- 65.62 -180.00 -179.31 -178.54 -172.51 -172.38 -171.05 -170.90 -170.56 29.69 34.77 39.83 180.00
- 65.61 -180.00 -179.31 -178.54 -172.43 -172.34 -171.03 -170.90 -170.58 29.69 34.78 39.81 180.00
- 65.60 -180.00 -179.32 -178.54 -172.38 -172.32 -171.02 -170.78 -170.61 29.70 34.78 39.79 180.00
- 65.59 -180.00 -179.34 -178.54 -177.12 -177.03 -172.38 -172.31 -171.01 29.72 34.78 39.78 180.00
- 65.58 -180.00 -179.33 -178.53 -177.18 -176.93 -172.38 -172.31 -171.01 29.74 34.78 39.76 180.00
- 65.57 -180.00 -179.32 -178.55 -177.22 -176.85 -172.39 -172.32 -171.01 29.78 34.77 39.74 180.00
- 65.56 -180.00 -179.31 -178.56 -177.25 -176.77 -172.40 -172.34 -171.01 29.80 34.75 39.73 180.00
- 65.55 -180.00 -179.30 -178.57 -177.27 -176.69 -172.42 -172.34 -171.01 29.79 34.75 39.73 180.00
- 65.54 -180.00 -179.30 -178.57 -177.29 -176.61 -172.40 -172.34 -172.31 -172.28 -172.14 -172.07 -171.01 29.77 34.75 39.72 180.00
- 65.53 -180.00 -179.30 -178.58 -177.30 -176.55 -172.37 -172.26 -172.16 -172.06 -171.02 29.75 34.75 39.72 180.00
- 65.52 -180.00 -179.31 -178.58 -177.32 -176.51 -172.35 -172.24 -172.21 -172.05 -171.44 -171.39 -171.02 29.73 34.74 39.71 180.00
- 65.51 -180.00 -179.32 -178.58 -177.34 -176.46 -172.33 -171.96 -171.52 -171.35 -171.03 29.72 34.72 39.71 180.00
- 65.50 -180.00 -179.34 -178.57 -177.36 -176.42 -172.32 -172.19 -172.13 -172.04 -171.60 -171.31 -171.03 29.71 34.70 39.70 180.00
- 65.49 -180.00 -179.36 -178.52 -177.40 -176.39 -172.31 -172.21 -172.13 -172.09 -171.70 -171.27 -171.04 29.71 34.68 39.70 180.00
- 65.48 -180.00 -179.38 -178.50 -177.44 -176.36 -172.31 -172.23 -172.13 -172.09 -171.83 -171.24 -171.05 29.71 34.68 39.70 180.00
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- 65.46 -180.00 -179.42 -176.08 -172.42 -172.39 -172.33 -172.27 -172.15 -171.17 -171.08 29.70 34.69 39.70 180.00
- 65.45 -180.00 -179.44 -176.07 -172.41 -172.29 -172.16 29.70 34.69 39.70 180.00
- 65.44 -180.00 -179.47 -176.05 -172.41 -172.35 -172.17 29.70 34.69 39.70 180.00
- 65.43 -180.00 -179.51 -176.03 -172.18 29.70 34.51 34.58 34.68 39.70 180.00
- 65.42 -180.00 -179.52 -175.99 -172.18 29.70 34.52 39.70 180.00
- 65.41 -180.00 -179.53 -175.96 -172.19 29.71 34.52 39.70 180.00
- 65.40 -180.00 -179.53 -175.95 -172.19 29.71 34.52 39.70 180.00
- 65.39 -180.00 -179.52 -175.94 -172.20 29.71 34.51 39.70 180.00
- 65.38 -180.00 -179.52 -175.94 -172.21 29.71 34.46 39.70 180.00
- 65.37 -180.00 -179.52 -175.94 -172.22 29.72 34.47 39.71 180.00
- 65.36 -180.00 -179.53 -175.94 -172.22 29.72 34.47 39.71 180.00
- 65.35 -180.00 -179.54 -175.94 -172.23 29.72 34.48 39.72 180.00
- 65.34 -180.00 -179.55 -175.94 -172.24 29.71 34.49 39.73 180.00
- 65.33 -180.00 -179.55 -175.93 -172.24 29.71 34.49 39.74 180.00
- 65.32 -180.00 -179.55 -175.92 -172.24 29.69 34.49 39.76 180.00
- 65.31 -180.00 -179.55 -175.91 -172.23 29.67 34.48 39.77 180.00
- 65.30 -180.00 -179.55 -175.92 -172.23 29.65 34.48 39.78 180.00
- 65.29 -180.00 -179.55 -175.92 -172.23 29.63 34.49 39.80 180.00
- 65.28 -180.00 -179.55 -175.92 -172.23 29.61 34.54 39.82 180.00
- 65.27 -180.00 -179.55 -175.92 -172.23 29.60 34.54 39.84 180.00
- 65.26 -180.00 -179.55 -175.91 -172.23 29.59 34.63 39.86 180.00
- 65.25 -180.00 -179.55 -175.90 -172.23 29.58 34.65 39.87 180.00
- 65.24 -180.00 -179.56 -175.88 -172.23 29.57 34.65 39.88 180.00
- 65.23 -180.00 -179.57 -175.87 -172.23 29.57 34.65 39.90 180.00
- 65.22 -180.00 -179.59 -175.86 -172.23 29.57 34.66 39.91 180.00
- 65.21 -180.00 -179.61 -175.85 -172.25 29.59 34.67 36.96 37.12 39.92 180.00
- 65.20 -180.00 -179.63 -175.84 -172.24 29.61 34.69 35.68 35.80 35.97 36.00 36.94 37.15 39.93 180.00
- 65.19 -180.00 -179.65 -175.82 -172.22 29.79 34.69 35.56 35.59 35.66 35.82 35.93 36.02 36.83 37.18 39.94 180.00
- 65.18 -180.00 -179.66 -175.81 -172.21 29.82 34.69 35.55 35.60 35.64 35.84 35.93 36.03 36.83 37.21 39.96 180.00
- 65.17 -180.00 -179.67 -175.80 -172.20 29.82 34.69 35.51 35.85 35.93 36.06 36.82 37.28 39.97 180.00
- 65.16 -180.00 -179.68 -175.80 -172.19 29.80 34.68 35.51 35.85 35.93 36.27 36.82 37.39 39.98 180.00
- 65.15 -180.00 -179.70 -175.80 -172.18 29.79 34.68 35.51 35.85 35.93 36.27 36.82 37.46 39.99 180.00
- 65.14 -180.00 -179.71 -175.80 -172.18 29.79 34.68 35.51 35.85 35.93 36.27 36.82 37.48 40.00 180.00
- 65.13 -180.00 -179.81 -175.81 -172.18 29.79 34.68 35.51 35.86 35.94 36.25 36.83 37.50 40.02 180.00
- 65.12 -180.00 -179.82 -175.81 -172.19 29.79 34.73 35.51 35.86 35.98 36.22 36.84 37.52 40.03 180.00
- 65.11 -180.00 -179.84 -175.81 -172.22 -172.16 -172.13 29.81 34.77 35.52 35.86 36.03 36.08 36.85 37.53 40.04 180.00
- 65.10 -180.00 -179.87 -175.81 -172.21 -172.17 -172.11 29.78 34.78 35.52 35.86 36.85 37.55 40.05 180.00
- 65.09 -180.00 -179.91 -175.81 -172.11 29.70 34.78 35.53 35.87 36.85 37.59 40.06 180.00
- 65.08 -180.00 -179.94 -175.82 -172.11 29.64 34.78 35.54 35.87 36.85 37.66 40.08 180.00
- 65.07 -180.00 -179.96 -175.82 -172.12 29.61 34.77 35.56 35.87 36.85 37.70 40.09 180.00
- 65.06 -180.00 -179.97 -175.83 -172.13 29.60 34.80 35.57 35.87 35.90 36.02 36.84 37.72 40.10 180.00
- 65.05 -180.00 -179.98 -175.85 -172.14 29.59 34.82 35.59 35.86 35.88 36.03 36.83 37.73 40.12 180.00
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63.75 29.97 178.74
63.74 29.97 178.75
63.73 29.97 178.75
@@ -145357,8 +145652,8 @@ Russia
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63.49 30.41 178.83
@@ -145441,820 +145736,820 @@ Russia
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54.82 19.93 22.85 30.75 67.27 70.98 135.19 137.24 137.37 137.50 138.01 155.63 162.13 166.34 166.65 167.43 167.57
54.81 19.93 22.85 30.75 67.26 70.98 135.20 137.23 137.35 137.51 138.01 155.63 162.12 166.47 166.65 167.43 167.57
54.80 19.94 22.85 30.75 67.24 70.98 135.21 137.23 137.34 137.52 138.01 155.63 162.13 166.47 166.65 167.44 167.62
54.79 19.94 22.85 30.75 67.23 70.98 135.22 137.22 137.32 137.52 138.00 155.63 162.13 166.47 166.65 167.46 167.67
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54.54 19.73 22.69 31.07 65.33 65.39 65.45 71.13 136.85 137.56 137.63 155.68 160.84 161.20 161.79 167.97 168.09
54.53 19.72 22.69 31.07 65.30 71.13 136.84 137.54 137.64 155.68 160.80 161.20 161.79 167.99 168.11
@@ -146263,126 +146558,126 @@ Russia
54.50 19.66 22.68 31.05 65.21 71.13 136.84 137.53 137.66 137.82 137.92 155.69 160.71 161.22 161.61 161.64 161.76 168.05 168.12
54.49 19.64 22.68 31.05 65.20 71.13 136.85 137.53 137.66 137.82 137.93 155.69 160.69 161.24 161.45 161.67 161.74 168.07 168.12
54.48 19.62 22.68 31.05 65.21 71.13 136.85 137.55 137.66 137.82 137.93 155.69 160.67 161.27 161.39
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54.42 19.65 22.71 31.20 65.20 71.15 76.69 76.72 136.85 137.53 137.64 137.76 137.86 142.67 142.75 155.71 160.54
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54.40 20.15 22.73 31.21 65.20 71.15 76.66 76.75 136.76 137.53 137.65 137.70 137.85 142.66 142.76 155.71 160.51
54.39 20.49 22.74 31.22 65.21 71.16 76.65 76.75 136.77 137.54 137.65 137.70 137.84 142.66 142.76 155.72 160.49
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54.35 21.85 22.77 31.25 64.55 64.60 64.82 64.99 65.22 71.18 76.65 76.75 136.79 137.70 137.77 142.65 142.80 155.73 160.42
54.34 22.13 22.77 31.26 64.45 64.62 64.80 65.00 65.22 70.99 71.05 71.18 72.09 72.16 76.64 76.78 136.81 137.69 137.73 142.62 142.81 155.74 160.40
- 54.33 22.39 22.73 31.27 64.29 64.31 64.39 64.64 64.77 65.01 65.22 70.97 71.08 71.18 72.10 72.19 76.53 76.82 136.82 137.67 137.74 142.61 142.82 155.74 160.39
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54.32 31.28 64.27 64.66 64.74 65.03 65.21 70.97 72.11 72.21 76.21 76.26 76.51 76.82 136.83 137.40 137.49 137.66 137.74 138.68 138.75 142.57 142.82 155.74 160.37
- 54.31 31.28 64.20 65.04 65.20 70.96 72.11 72.22 76.20 76.33 76.49 76.82 136.83 137.38 137.53 137.65 137.75 138.65 138.79 139.71 139.78 142.27 142.32 142.53 142.83 155.75 160.36
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54.30 31.28 64.08 64.12 64.17 65.06 65.19 70.96 72.11 72.23 76.19 76.39 76.46 76.82 136.83 137.36 137.75 138.63 138.82 139.69 139.80 142.27 142.34 142.50 142.84 155.75 160.34
54.29 31.28 64.07 65.07 65.13 70.96 72.10 72.24 76.18 76.82 136.82 137.33 137.75 138.63 138.85 139.67 139.81 142.27 142.36 142.47 142.85 155.75 160.33
54.28 31.28 64.01 70.96 72.09 72.24 76.18 76.81 136.81 137.29 137.74 138.63 138.89 139.65 139.81 142.27 142.41 142.45 142.86 155.76 160.31
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- 54.26 31.28 64.03 70.96 72.08 72.25 76.19 76.78 136.81 137.27 137.70 138.70 138.96 139.58 139.81 142.32 142.53 142.56 142.89 155.76 160.28
- 54.25 31.28 64.03 71.00 72.08 72.26 76.19 76.77 136.82 137.27 137.68 138.72 139.02 139.54 139.80 142.35 142.54 142.56 142.90 155.77 160.27
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54.24 31.29 64.03 71.04 72.07 72.29 76.19 76.77 136.82 137.26 137.66 138.72 139.07 139.50 139.80 142.37 142.91 155.77 160.26
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54.21 31.31 63.63 63.78 64.01 71.04 71.73 71.99 72.16 72.30 76.10 76.75 136.79 137.16 137.62 138.71 139.24 139.38 139.85 139.90 139.92 142.40 142.93 155.78 160.15
54.20 31.33 63.59 63.81 63.99 71.04 71.72 72.00 72.18 72.30 76.06 76.73 136.79 137.14 137.61 138.71 139.87 139.89 139.92 142.41 142.94 155.79 160.13
- 54.19 31.35 63.56 63.83 63.93 71.03 71.72 72.01 72.18 72.29 76.03 76.71 136.80 137.13 137.59 138.71 139.92 142.42 142.94 155.79 160.11
- 54.18 31.37 63.46 63.86 63.90 71.03 71.72 72.02 72.19 72.28 75.99 76.70 136.81 137.11 137.59 138.71 139.93 142.42 142.95 155.80 160.09
- 54.17 31.40 63.43 71.03 71.30 71.36 71.72 72.03 72.19 72.28 75.96 76.38 76.50 76.69 136.81 137.09 137.59 138.71 139.95 142.43 142.96 155.80 160.08
- 54.16 31.42 63.14 63.18 63.41 71.06 71.29 71.45 71.72 72.03 72.20 72.28 75.92 76.36 76.54 76.67 136.82 137.07 137.57 138.71 139.97 142.43 142.98 155.81 160.06
- 54.15 31.44 63.13 63.27 63.38 71.08 71.28 71.45 71.72 72.04 72.20 72.31 75.88 76.36 76.58 76.66 136.82 137.05 137.55 138.71 139.98 142.44 143.00 155.81 160.05
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+ 54.16 31.42 63.14 63.18 63.41 71.06 71.29 71.45 71.72 72.03 72.20 72.28 75.92 76.36 76.54 76.67 136.82 137.07 137.57 138.71 139.97 142.43 142.99 155.81 160.06
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54.14 31.46 63.12 71.10 71.27 71.45 71.72 72.05 72.20 72.35 75.85 76.36 136.82 137.05 137.53 138.70 140.00 142.44 143.01 155.82 160.04
54.13 31.49 63.13 71.11 71.26 71.45 71.72 72.06 72.19 72.40 75.81 76.36 136.82 137.05 137.52 138.69 140.01 142.45 143.01 155.82 160.02
54.12 31.51 63.13 71.11 71.25 71.45 71.71 72.08 72.18 72.45 75.77 76.37 136.81 137.06 137.37 137.44 137.51 138.68 140.07 142.46 143.02 155.83 160.01
54.11 31.55 63.13 71.12 71.24 71.46 71.70 72.10 72.17 72.40 72.60 72.68 75.74 76.38 136.80 137.07 137.33 137.43 137.50 138.67 140.10 142.48 143.02 155.83 160.01
54.10 31.60 63.13 71.13 71.22 71.46 71.52 71.59 71.69 72.34 72.38 72.40 72.56 72.81 72.92 72.94 75.71 76.39 136.80 137.08 137.32 137.43 137.49 138.66 140.13 142.49 143.02 155.84 160.01
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53.27 32.43 61.39 77.83 120.97 121.07 121.27 124.32 141.42 141.79 143.25 156.04 159.93 159.97 160.02
53.26 32.44 61.41 77.85 120.86 121.12 121.23 124.33 141.41 141.79 143.25 156.04 159.93 159.96 160.02
53.25 32.45 61.43 61.62 61.66 77.86 120.84 124.33 141.41 141.79 143.25 156.04 160.02
@@ -146405,57 +146700,57 @@ Russia
53.08 31.30 62.11 78.03 120.62 125.40 141.37 141.87 143.30 156.07 159.07 160.04 160.06
53.07 31.29 62.12 78.04 120.60 125.46 141.37 141.88 143.31 156.07 159.05
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53.02 31.23 62.12 78.09 120.50 125.63 140.95 141.00 141.27 141.91 143.32 156.08 158.48 158.61 158.95
53.01 31.23 62.11 78.10 120.49 125.64 140.95 141.02 141.26 141.91 143.32 156.08 158.45 158.62 158.93
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52.53 31.54 60.83 78.54 120.73 126.16 141.26 141.80 143.32 156.27 158.53
52.52 31.54 60.86 78.55 120.72 126.19 141.25 141.79 143.32 156.27 158.52
@@ -146468,79 +146763,79 @@ Russia
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52.44 31.57 60.96 78.62 120.70 126.27 141.13 141.72 143.30 156.31 158.54
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52.08 31.83 32.27 34.04 60.38 78.94 98.85 98.96 120.77 126.51 141.37 141.63 143.14 156.44 158.34
52.07 31.86 32.25 34.05 60.36 78.95 98.85 98.96 120.76 126.50 141.37 141.63 143.14 156.44 158.34
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52.03 31.87 32.11 34.05 60.29 78.99 98.85 99.00 120.71 126.44 141.32 141.63 143.14 156.45 158.30
52.02 31.88 31.96 32.04 32.09 34.05 60.28 78.99 98.85 99.04 120.71 126.43 141.31 141.64 143.15 156.45 158.29
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52.00 34.07 60.24 79.01 98.83 99.12 120.72 126.42 141.35 141.64 143.16 156.46 158.29
51.99 34.08 60.23 79.02 98.82 99.16 120.72 126.42 141.38 141.65 143.16 156.46 158.29
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51.88 34.21 60.05 60.11 60.21 79.11 98.75 99.52 120.56 126.50 141.34 141.62 143.17 143.21 143.25 156.48 158.20
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51.86 34.22 34.26 34.28 60.25 79.12 98.74 99.70 120.54 126.52 141.28 141.64 143.25 156.48 158.17
51.85 34.29 60.27 79.13 98.73 99.72 120.49 126.53 141.27 141.66 143.26 156.48 158.16
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51.83 34.33 60.37 79.15 98.72 99.75 120.48 126.55 141.25 141.70 143.27 156.48 158.14
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51.81 34.36 60.46 79.17 98.70 99.78 120.42 126.56 141.21 141.76 143.28 156.48 158.13
51.80 34.37 60.47 79.18 98.69 99.79 120.40 126.57 141.21 141.78 143.29 156.49 158.12
51.79 34.38 60.48 79.18 98.68 99.81 120.38 126.58 141.20 141.79 143.30 156.49 158.11
51.78 34.38 60.48 79.19 98.66 99.82 120.37 126.59 141.20 141.79 143.30 156.49 158.09
51.77 34.39 60.48 79.20 98.64 99.83 120.35 126.60 141.19 141.79 143.31 156.49 158.07
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51.73 34.39 50.76 50.82 52.29 52.33 60.45 79.24 98.45 99.90 120.28 126.63 141.16 141.67 143.32 156.48 158.01
51.72 34.37 50.75 50.84 52.28 52.34 60.45 79.25 98.41 99.95 120.26 126.65 141.15 141.68 143.32 156.48 158.01
51.71 34.24 50.75 50.86 52.27 52.34 60.44 79.26 98.38 100.15 120.25 126.68 141.14 141.69 143.32 156.48 158.00
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51.69 34.11 50.76 50.87 52.14 52.35 60.40 79.27 98.33 100.55 120.22 126.69 141.14 141.73 143.32 156.48 157.98
51.68 34.09 50.77 50.88 52.13 52.35 60.37 79.28 98.32 100.60 120.21 126.69 141.14 141.75 143.28 156.47 157.96
51.67 34.07 50.77 50.89 52.13 52.35 60.43 79.29 98.31 100.64 120.19 126.69 141.13 141.77 143.27 156.47 157.96
@@ -146548,42 +146843,42 @@ Russia
51.65 34.06 50.79 51.04 51.18 51.25 51.86 51.96 52.11 52.36 60.50 79.31 98.29 100.70 120.17 126.70 141.08 141.81 143.27 143.35 143.37 156.47 157.93
51.64 34.06 50.79 51.26 51.85 51.98 52.10 52.37 60.50 79.32 98.28 100.73 120.11 126.70 141.02 141.82 143.26 143.33 143.38 156.47 157.93
51.63 34.06 50.80 51.27 51.84 52.38 60.50 79.32 98.28 100.76 120.10 126.70 140.98 141.83 143.26 143.33 143.38 156.47 157.93
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51.50 34.21 50.54 51.24 51.55 51.61 51.79 52.46 61.02 79.43 98.24 101.22 120.02 126.81 140.91 141.99 143.45 156.47 157.60
51.49 34.21 50.54 51.25 51.54 51.61 51.79 52.46 53.16 53.18 61.04 61.06 61.10 79.44 98.24 101.24 120.00 126.80 140.91 142.01 143.46 156.47 157.58
51.48 34.21 50.54 51.26 51.53 51.61 51.79 52.48 52.76 52.79 53.16 53.19 53.23 53.26 61.13 61.19 61.25 79.45 98.23 101.26 119.99 126.79 140.91 142.02 143.46 156.47 157.56
51.47 34.20 50.54 51.27 51.50 51.61 51.78 52.48 52.75 52.81 52.85 52.87 53.16 53.38 61.28 79.46 98.23 101.27 119.98 126.79 140.90 142.04 143.47 156.47 157.54
51.46 34.20 50.53 51.29 51.48 51.62 51.76 52.49 52.71 52.87 52.99 53.40 61.38 79.46 98.10 98.17 98.23 101.29 119.99 126.78 140.82 142.06 143.47 156.47 157.53
51.45 34.20 50.53 51.33 51.42 51.62 51.73 52.51 52.70 52.87 52.98 53.41 61.42 79.47 98.08 101.30 101.46 101.58 119.99 126.78 140.81 142.07 143.47 156.47 157.52
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51.30 34.26 50.35 53.57 61.57 79.58 97.93 102.17 119.89 126.79 140.70 142.16 143.52 156.51 157.35
51.29 34.24 50.34 53.57 61.59 79.59 97.92 102.16 119.88 126.79 140.70 142.15 143.53 156.51 157.33
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51.26 34.19 50.25 53.59 61.67 79.61 80.64 80.76 80.88 80.90 97.93 102.13 119.84 126.80 140.72 142.15 143.54 156.53 157.29
51.25 34.17 50.22 53.61 61.67 79.62 80.63 80.79 80.86 80.90 97.93 102.12 119.82 126.81 140.72 142.15 143.54 156.56 157.29
51.24 34.17 50.16 53.63 61.67 79.63 80.63 80.82 80.85 80.90 97.94 102.12 119.82 126.83 126.87 126.90 140.72 142.16 143.54 156.61 157.28
@@ -146592,66 +146887,66 @@ Russia
51.21 34.23 34.29 34.49 34.55 34.61 50.00 53.64 61.56 79.65 80.61 80.90 97.94 102.12 119.82 126.89 140.68 142.18 143.55 156.66 157.26
51.20 34.61 49.98 53.66 61.55 79.66 80.61 80.91 97.93 102.12 119.82 126.89 140.68 142.19 143.55 156.67 157.24
51.19 34.61 34.93 34.97 35.03 35.06 49.96 53.70 61.54 79.67 80.60 80.92 97.93 102.13 119.78 126.89 140.69 142.20 143.55 156.68 157.22
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+ 50.66 35.40 49.01 54.38 54.67 55.27 56.00 58.90 59.92 60.36 60.89 83.98 91.73 92.62 92.69 92.97 98.02 102.26 119.43 127.27 140.50 142.05 143.70 155.86 156.13 156.19 156.44
+ 50.65 35.38 48.99 54.37 54.67 55.29 55.98 59.05 59.91 60.50 60.84 84.00 91.71 92.97 98.03 102.26 119.39 127.28 140.50 142.05 143.70 155.86 156.13 156.21 156.43
50.64 35.36 48.97 54.37 54.68 55.31 55.39 55.45 55.96 59.20 59.90 60.64 60.77 84.02 91.69 92.98 98.03 102.26 119.39 127.29 140.51 142.05 143.70 155.86 156.13 156.24 156.41
- 50.63 35.36 48.95 54.37 54.68 55.47 55.94 59.22 59.89 84.04 91.67 92.98 98.04 102.26 119.38 127.30 140.51 142.04 143.71 155.85 156.14 156.29 156.41
- 50.62 35.36 48.93 54.36 54.68 55.49 55.92 59.22 59.88 84.06 91.65 92.99 98.06 102.26 119.37 127.31 140.52 142.04 143.71 155.85 156.15 156.31 156.41
- 50.61 35.36 48.91 54.36 54.68 55.49 55.89 59.23 59.36 59.44 59.87 84.08 91.65 93.00 98.08 102.26 119.35 127.33 140.52 142.04 143.71 155.85 156.16 156.36 156.41
- 50.60 35.36 48.89 54.36 54.68 55.50 55.86 59.26 59.32 59.46 59.85 84.10 91.64 93.01 98.10 102.26 119.34 127.33 140.52 142.04 143.71 155.84 156.16
- 50.59 35.37 48.87 54.36 54.68 55.51 55.84 59.47 59.85 84.12 91.63 93.03 98.12 102.27 119.33 127.34 140.49 142.04 143.72 155.83 156.16
+ 50.63 35.36 48.95 54.37 54.68 55.47 55.94 59.22 59.89 84.04 91.67 92.98 98.04 102.26 119.38 127.30 140.51 142.04 143.71 155.85 156.14 156.25 156.41
+ 50.62 35.36 48.93 54.36 54.68 55.49 55.92 59.22 59.88 84.06 91.65 92.99 98.06 102.26 119.37 127.31 140.52 142.04 143.71 155.85 156.15 156.26 156.41
+ 50.61 35.36 48.91 54.36 54.68 55.49 55.89 59.23 59.36 59.44 59.87 84.09 91.65 93.00 98.08 102.26 119.35 127.33 140.52 142.04 143.71 155.84 156.16
+ 50.60 35.36 48.89 54.36 54.68 55.50 55.86 59.26 59.32 59.46 59.85 84.10 91.64 93.01 98.10 102.26 119.34 127.33 140.52 142.04 143.71 155.83 156.16
+ 50.59 35.37 48.87 54.36 54.68 55.51 55.84 59.47 59.85 84.12 91.63 93.03 98.12 102.27 119.33 127.34 140.49 142.04 143.72 155.82 156.16
50.58 35.37 48.68 48.71 48.85 54.37 54.67 55.53 55.81 59.48 59.84 84.12 91.62 93.07 93.31 93.44 98.15 102.27 119.30 127.34 140.48 142.04 143.72 155.81 156.16
50.57 35.38 48.68 54.37 54.66 55.55 55.78 59.52 59.83 84.13 91.62 93.50 98.20 102.28 119.29 127.35 140.48 142.04 143.72 155.80 156.16
50.56 35.38 48.68 54.38 54.65 55.57 55.76 59.46 59.83 84.13 91.61 93.70 98.26 102.28 119.29 127.35 140.47 142.03 143.72 155.79 156.16
@@ -146659,11 +146954,11 @@ Russia
50.54 35.39 48.68 54.41 54.62 55.59 55.73 59.44 59.81 84.14 91.56 94.24 98.28 102.30 119.28 127.33 140.46 142.03 143.73 155.78 156.16
50.53 35.39 48.68 54.42 54.60 55.60 55.72 59.44 59.80 84.15 91.53 94.26 98.29 102.31 119.28 127.32 140.45 142.03 143.73 155.77 156.16
50.52 35.40 48.68 54.44 54.58 55.63 55.70 59.44 59.78 84.16 91.49 94.26 98.30 102.34 119.27 127.31 140.46 142.03 143.74 155.77 156.16
- 50.51 35.40 48.68 54.46 54.53 59.44 59.75 84.17 91.47 94.26 98.30 102.42 119.27 127.31 140.47 142.03 143.74 155.77 156.16
+ 50.51 35.40 48.68 54.46 54.52 59.44 59.75 84.17 91.47 94.26 98.30 102.42 119.27 127.31 140.47 142.03 143.74 155.77 156.16
50.50 35.41 48.68 59.44 59.62 84.18 91.46 94.26 98.31 102.48 119.27 127.30 140.48 142.04 143.74 155.77 156.16
50.49 35.41 48.68 59.45 59.60 84.18 91.46 94.26 98.31 102.50 119.27 127.30 140.49 142.04 143.75 155.77 156.13
50.48 35.42 48.68 59.47 59.58 84.17 91.45 94.26 98.31 102.51 119.27 127.29 140.50 142.05 143.75 155.76 156.12
- 50.47 35.42 48.68 59.49 59.56 84.17 91.45 94.27 98.31 102.52 119.27 127.27 140.51 142.05 143.75 155.75 156.08
+ 50.47 35.42 48.68 59.49 59.56 84.17 91.45 94.27 98.31 102.52 119.27 127.27 140.51 142.05 143.75 155.75 156.06
50.46 35.43 48.68 59.51 59.54 84.17 91.44 94.27 98.30 102.52 119.27 127.27 140.51 142.06 143.75 155.74 156.05
50.45 35.46 48.69 84.16 91.43 94.28 98.30 102.53 105.27 105.35 119.26 127.27 140.52 142.06 143.76 155.72 156.05
50.44 35.51 48.69 84.16 91.25 91.33 91.40 94.28 98.30 102.54 105.25 105.41 119.26 127.29 140.52 142.07 143.76 155.71 156.05
@@ -146672,20 +146967,20 @@ Russia
50.41 35.54 35.89 36.01 37.37 37.42 47.50 47.63 48.69 84.17 91.15 94.30 98.28 102.56 105.20 105.59 119.22 127.33 140.52 142.09 143.77 155.67 156.05
50.40 35.55 35.83 36.11 37.30 37.43 47.48 47.64 48.70 84.17 91.00 94.30 98.28 102.57 105.18 105.82 119.21 127.34 140.53 142.10 143.77 155.55 155.60 155.65 156.05
50.39 35.55 35.80 36.12 37.28 37.43 47.46 47.65 48.70 84.18 90.97 94.31 98.27 102.58 105.16 105.87 119.15 127.34 140.53 142.10 143.78 155.54 156.04
- 50.38 35.55 35.79 36.13 37.26 37.44 47.45 47.66 48.70 84.19 90.95 94.31 98.27 102.60 105.14 105.96 119.18 127.34 140.53 142.11 143.78 155.43 156.02
- 50.37 35.55 35.78 36.15 37.25 37.44 47.44 47.67 48.70 84.19 90.94 94.31 98.27 102.64 104.92 104.99 105.09 105.99 119.19 127.33 140.54 142.11 143.78 155.41 156.01
- 50.36 35.56 35.74 36.16 37.23 37.45 47.43 47.70 48.71 84.20 90.93 94.31 98.27 102.72 104.87 106.01 119.24 119.28 119.33 127.32 140.54 142.12 143.78 155.39 155.99
+ 50.38 35.55 35.79 36.13 37.26 37.44 47.45 47.66 48.70 84.19 90.95 94.31 98.27 102.60 105.14 105.96 119.18 127.34 140.53 142.11 143.78 155.42 156.02
+ 50.37 35.55 35.78 36.15 37.25 37.44 47.44 47.67 48.70 84.19 90.94 94.31 98.27 102.64 104.92 104.99 105.09 105.99 119.19 127.33 140.54 142.11 143.78 155.40 156.01
+ 50.36 35.56 35.74 36.16 37.23 37.45 47.44 47.70 48.71 84.20 90.93 94.31 98.27 102.72 104.87 106.01 119.24 119.28 119.33 127.32 140.54 142.12 143.78 155.38 155.99
50.35 35.58 35.73 36.17 37.21 37.45 47.43 47.73 48.71 84.21 90.92 94.31 98.28 102.77 104.85 106.03 119.36 127.32 140.55 142.13 143.79 155.37 155.98
- 50.34 35.60 35.72 36.18 37.17 37.46 47.42 47.74 48.71 84.21 90.90 94.31 98.28 102.79 104.83 106.03 119.36 127.32 140.55 142.13 143.79 155.36 155.98
+ 50.34 35.60 35.72 36.18 37.17 37.46 47.43 47.74 48.71 84.21 90.90 94.31 98.28 102.79 104.83 106.03 119.36 127.32 140.55 142.13 143.79 155.36 155.98
50.33 35.62 35.71 36.19 37.13 37.47 47.42 47.75 48.71 84.22 90.89 94.32 98.28 102.81 104.69 106.03 119.37 127.32 140.55 142.14 143.79 155.35 155.97
- 50.32 36.20 36.95 37.01 37.08 37.49 47.41 47.75 48.72 84.22 90.88 94.32 98.28 102.83 104.67 106.03 119.37 127.32 140.55 142.14 143.80 155.34 155.96
+ 50.32 36.20 36.95 37.01 37.08 37.49 47.41 47.75 48.72 84.22 90.88 94.32 98.28 102.83 104.67 106.03 119.37 127.32 140.54 142.14 143.80 155.34 155.96
50.31 36.21 36.88 37.52 47.40 47.76 48.72 84.22 90.86 94.32 98.28 102.85 104.65 106.09 106.49 106.59 119.37 127.32 140.54 142.13 143.80 155.21 155.28 155.33 155.96
50.30 36.22 36.83 37.54 47.38 47.79 48.72 84.22 90.82 94.32 98.28 102.87 104.63 106.14 106.40 106.67 119.37 127.33 140.53 142.12 143.81 155.19 155.95
50.29 36.23 36.81 37.56 47.34 47.80 48.72 84.22 90.78 94.32 98.28 102.90 104.44 104.52 104.60 106.17 106.34 106.71 119.37 127.33 140.53 142.12 143.81 155.18 155.94
50.28 36.24 36.38 36.42 36.78 37.58 47.32 47.82 48.73 84.22 90.75 94.32 98.27 102.94 103.06 103.16 104.40 106.19 106.28 106.76 119.35 127.34 140.52 142.12 143.82 155.17 155.93
- 50.27 36.25 36.35 36.46 36.75 37.58 47.31 47.84 48.73 84.22 90.72 94.32 98.27 103.20 104.38 106.78 119.34 127.36 140.53 142.12 143.83 155.17 155.91
- 50.26 36.27 36.33 36.49 36.73 37.58 47.32 47.85 48.74 84.22 90.72 94.32 98.26 103.21 104.37 106.80 119.34 127.38 140.54 142.13 143.84 155.17 155.90
- 50.25 36.52 36.70 37.59 47.32 47.86 48.75 84.22 90.72 94.33 98.26 103.21 104.35 106.82 114.27 114.34 119.34 127.41 140.54 142.13 143.84 155.17 155.90
+ 50.27 36.25 36.35 36.46 36.75 37.58 47.31 47.84 48.73 84.22 90.72 94.32 98.27 103.20 104.38 106.78 119.34 127.36 140.52 142.12 143.83 155.17 155.91
+ 50.26 36.27 36.33 36.49 36.73 37.58 47.32 47.85 48.74 84.22 90.72 94.32 98.26 103.21 104.36 106.80 119.34 127.38 140.53 142.13 143.84 155.17 155.90
+ 50.25 36.52 36.70 37.59 47.32 47.86 48.75 84.22 90.72 94.33 98.26 103.21 104.34 106.82 114.27 114.34 119.34 127.41 140.53 142.13 143.84 155.17 155.90
50.24 36.52 36.68 37.59 47.33 47.88 48.76 84.23 90.72 94.33 98.25 103.22 104.33 106.83 114.23 114.37 119.34 127.45 140.54 142.13 143.85 155.18 155.89
50.23 36.52 36.67 37.58 47.33 47.90 48.77 84.27 90.72 94.33 98.24 103.23 104.32 106.85 114.19 114.40 114.61 114.67 119.34 127.48 140.54 142.14 143.86 155.19 155.88
50.22 36.52 36.66 37.57 47.33 47.91 48.78 84.30 90.72 94.33 98.23 103.23 104.30 106.87 114.16 114.44 114.52 114.72 119.34 127.51 140.54 142.14 143.87 155.21 155.83
@@ -146712,7 +147007,7 @@ Russia
50.01 37.86 38.18 38.31 47.29 48.10 48.89 85.01 90.00 94.58 94.70 94.97 98.05 107.14 113.62 115.12 119.23 127.47 140.61 142.14 144.01 155.35 155.43
50.00 37.88 38.18 38.32 47.28 48.10 48.89 84.94 90.00 94.59 94.67 94.98 95.81 95.84 98.03 107.15 113.59 115.14 119.22 127.47 140.58 142.14 144.02 155.35 155.42
49.99 37.90 38.18 38.32 47.26 48.11 48.88 84.94 90.00 94.98 95.78 95.86 98.00 107.17 113.56 115.15 116.12 116.23 119.20 127.47 140.56 142.14 144.02 155.35 155.41
- 49.98 37.91 38.18 38.33 47.25 48.11 48.87 84.94 90.00 94.99 95.76 95.88 97.98 107.20 107.27 107.32 113.54 115.17 116.08 116.27 119.16 127.48 140.54 142.14 144.02 155.35 155.40
+ 49.98 37.91 38.18 38.33 47.25 48.11 48.87 84.94 90.00 94.99 95.76 95.88 97.98 107.20 107.27 107.32 113.54 115.17 116.08 116.27 119.16 127.48 140.54 142.14 144.02 155.37 155.40
49.97 37.92 38.18 38.34 47.24 48.12 48.86 84.94 89.99 95.00 95.75 95.88 96.02 96.09 97.95 107.33 113.52 115.18 116.04 116.31 119.12 127.48 140.51 142.14 144.03
49.96 37.93 38.18 38.36 47.22 48.12 48.85 84.94 89.98 95.00 95.75 95.89 96.01 96.12 97.92 107.35 113.51 115.20 116.01 116.35 118.90 118.97 119.05 127.48 140.49 142.13 144.03
49.95 37.94 38.18 38.42 47.21 48.13 48.83 84.94 89.97 95.01 95.74 95.89 95.99 96.15 97.90 107.73 113.49 115.21 115.99 116.39 118.85 127.49 140.49 142.12 144.03
@@ -146721,30 +147016,30 @@ Russia
49.92 37.97 38.16 38.66 47.16 48.17 48.79 84.94 89.80 95.37 95.64 95.93 95.95 96.24 97.67 97.80 97.85 107.87 113.44 115.27 115.91 116.51 118.61 127.51 140.47 142.12 144.04
49.91 37.98 38.14 38.66 47.12 48.19 48.77 84.94 89.70 95.40 95.58 96.26 97.63 97.81 97.84 107.94 113.42 115.29 115.88 116.55 118.59 127.52 140.46 142.12 144.05
49.90 37.98 38.06 38.10 38.12 38.67 47.08 48.19 48.75 84.94 89.66 95.42 95.56 96.28 96.46 96.51 97.59 107.94 113.41 115.31 115.85 116.57 118.57 127.51 140.46 142.11 144.05
- 49.89 37.98 38.04 38.69 47.05 48.20 48.72 84.94 89.64 95.45 95.54 96.30 96.43 96.52 96.70 96.74 97.58 107.93 113.39 115.33 115.82 116.59 118.56 127.51 140.45 142.11 144.06
- 49.88 37.99 38.02 38.71 47.01 48.20 48.70 84.96 89.63 95.47 95.54 96.31 96.41 96.53 96.68 96.83 97.59 107.93 113.37 115.35 115.80 116.60 118.54 127.50 140.45 142.11 144.06
- 49.87 38.73 46.97 48.21 48.66 85.00 89.63 95.49 95.53 96.33 96.39 96.53 96.66 96.91 97.59 107.92 113.35 115.46 115.54 115.59 115.77 116.61 118.52 127.50 140.44 142.12 144.07
- 49.86 38.76 46.95 48.21 48.62 85.04 89.63 96.54 96.64 96.97 97.59 107.92 113.33 115.65 115.74 116.63 118.50 127.50 140.43 142.12 144.08
- 49.85 38.82 46.93 48.22 48.58 85.05 89.62 96.55 96.62 96.99 97.59 107.92 113.31 116.64 118.50 127.49 140.43 142.13 144.08
- 49.84 38.85 39.11 39.17 46.92 48.31 48.54 85.06 89.63 96.57 96.60 97.00 97.58 107.92 113.29 116.65 118.49 127.49 140.44 142.13 144.09 154.37 154.45
- 49.83 38.87 39.09 39.18 46.92 48.33 48.50 85.06 89.64 97.01 97.58 107.92 113.27 116.65 118.49 127.49 140.45 142.13 144.09 154.36 154.45
- 49.82 38.88 39.08 39.18 46.91 48.34 48.47 85.06 89.65 97.02 97.57 107.92 113.25 116.66 118.48 127.49 140.45 142.14 144.10 154.35 154.46
- 49.81 38.90 39.07 39.19 46.90 48.36 48.46 85.06 89.65 97.03 97.55 107.92 113.23 116.67 118.47 127.49 140.47 142.14 144.10 154.35 154.46
- 49.80 38.91 39.06 39.19 46.90 48.39 48.45 85.06 89.65 97.04 97.54 107.93 113.21 116.69 118.39 127.50 140.49 142.14 144.10 154.35 154.46
- 49.79 38.92 39.04 39.20 46.90 48.41 48.44 85.07 89.65 97.07 97.52 107.93 113.19 116.71 118.39 127.50 140.53 142.14 144.11 154.35 154.46
- 49.78 39.20 46.89 85.07 89.66 97.10 97.50 107.94 113.18 116.73 118.38 127.51 140.54 142.14 144.11 154.34 154.46
- 49.77 39.21 46.89 85.08 86.61 86.65 89.70 97.10 97.48 107.94 113.17 116.75 118.38 127.52 140.54 142.14 144.12 154.34 154.46
- 49.76 39.21 46.89 85.09 86.60 86.67 89.71 97.11 97.47 107.94 113.16 116.78 118.37 127.55 140.55 142.14 144.12 154.34 154.45
- 49.75 39.22 46.89 85.11 86.59 86.73 89.71 97.12 97.45 107.94 113.15 116.80 118.32 127.61 140.55 142.14 144.13 154.34 154.44
- 49.74 39.23 46.88 85.12 86.58 86.72 89.72 97.14 97.43 107.94 113.14 116.83 118.30 127.64 140.55 142.14 144.13 154.36 154.43
- 49.73 39.25 46.88 85.13 86.57 86.72 89.72 97.16 97.41 107.93 113.14 116.85 118.28 127.65 140.54 142.14 144.13 154.38 154.43
- 49.72 39.27 39.39 39.45 46.88 85.15 86.54 86.72 89.72 97.18 97.37 107.93 113.13 116.88 118.27 127.66 140.53 142.14 144.13 154.41 154.43
- 49.71 39.30 39.35 39.48 46.88 85.16 86.53 86.73 89.72 97.23 97.33 107.92 113.12 116.91 118.25 127.66 140.53 142.14 144.13
+ 49.89 37.98 38.04 38.69 47.05 48.20 48.72 84.94 89.64 95.45 95.54 96.30 96.43 96.52 96.70 96.74 97.58 107.93 113.39 115.33 115.82 116.59 118.56 127.51 140.45 142.11 144.05
+ 49.88 37.99 38.02 38.71 47.01 48.20 48.70 84.96 89.63 95.46 95.54 96.31 96.41 96.53 96.68 96.83 97.59 107.93 113.37 115.35 115.80 116.60 118.54 127.50 140.45 142.11 144.06
+ 49.87 38.73 46.97 48.21 48.66 85.00 89.63 95.49 95.53 96.33 96.39 96.53 96.66 96.91 97.59 107.92 113.35 115.46 115.54 115.59 115.77 116.61 118.52 127.50 140.44 142.12 144.06
+ 49.86 38.76 46.95 48.21 48.62 85.04 89.63 96.54 96.64 96.97 97.59 107.92 113.33 115.65 115.74 116.63 118.50 127.50 140.43 142.12 144.07
+ 49.85 38.82 46.93 48.22 48.58 85.05 89.62 96.55 96.62 96.99 97.59 107.92 113.31 116.64 118.50 127.49 140.43 142.13 144.07
+ 49.84 38.85 39.11 39.17 46.92 48.31 48.54 85.06 89.63 96.57 96.60 97.00 97.58 107.92 113.29 116.65 118.49 127.49 140.44 142.13 144.08
+ 49.83 38.87 39.09 39.18 46.92 48.33 48.50 85.06 89.64 97.01 97.58 107.92 113.27 116.65 118.49 127.49 140.45 142.13 144.09
+ 49.82 38.88 39.08 39.18 46.91 48.34 48.47 85.06 89.65 97.02 97.57 107.92 113.25 116.66 118.48 127.49 140.45 142.14 144.09 154.40 154.49
+ 49.81 38.90 39.07 39.19 46.90 48.36 48.46 85.06 89.65 97.03 97.55 107.92 113.23 116.67 118.47 127.49 140.47 142.14 144.10 154.38 154.49
+ 49.80 38.91 39.06 39.19 46.90 48.39 48.45 85.06 89.65 97.04 97.54 107.93 113.21 116.69 118.39 127.50 140.49 142.14 144.10 154.38 154.50
+ 49.79 38.92 39.04 39.20 46.90 48.41 48.44 85.07 89.65 97.06 97.52 107.93 113.19 116.71 118.39 127.50 140.53 142.14 144.11 154.37 154.50
+ 49.78 39.20 46.89 85.07 89.66 97.10 97.50 107.94 113.18 116.73 118.38 127.51 140.54 142.14 144.11 154.36 154.50
+ 49.77 39.21 46.89 85.08 86.61 86.65 89.70 97.10 97.48 107.94 113.17 116.75 118.38 127.52 140.54 142.14 144.12 154.36 154.50
+ 49.76 39.21 46.89 85.09 86.60 86.67 89.71 97.11 97.47 107.94 113.16 116.78 118.37 127.55 140.55 142.14 144.12 154.36 154.49
+ 49.75 39.22 46.89 85.11 86.59 86.73 89.71 97.12 97.45 107.94 113.15 116.80 118.32 127.61 140.55 142.14 144.13 154.36 154.48
+ 49.74 39.23 46.88 85.12 86.58 86.72 89.72 97.14 97.43 107.94 113.14 116.83 118.30 127.64 140.55 142.14 144.13 154.37 154.48
+ 49.73 39.25 46.88 85.13 86.57 86.72 89.72 97.16 97.41 107.93 113.14 116.85 118.28 127.65 140.54 142.14 144.13 154.38 154.47
+ 49.72 39.27 39.39 39.45 46.88 85.15 86.54 86.72 89.72 97.18 97.37 107.93 113.13 116.88 118.27 127.66 140.53 142.14 144.13 154.40 154.46
+ 49.71 39.30 39.35 39.48 46.88 85.16 86.53 86.73 89.72 97.23 97.33 107.92 113.12 116.91 118.25 127.66 140.53 142.14 144.13 154.42 154.45
49.70 39.56 46.87 85.16 86.51 86.74 89.71 107.92 113.11 116.93 118.23 127.67 140.52 142.14 144.14
49.69 39.56 46.87 85.17 86.49 86.74 89.70 107.91 113.11 116.96 118.22 127.67 140.52 142.14 144.14
- 49.68 39.57 46.87 85.17 86.49 86.72 89.67 107.91 113.10 116.98 118.21 127.67 140.53 142.15 144.14
- 49.67 39.57 46.87 85.17 86.49 86.65 89.63 107.91 113.09 117.01 118.20 127.67 140.53 142.15 144.14
- 49.66 39.57 46.86 85.17 86.49 86.63 89.59 107.91 113.09 117.03 118.18 127.68 140.53 142.14 144.14
+ 49.68 39.57 46.87 85.17 86.49 86.72 89.67 107.91 113.10 116.98 118.21 127.67 140.53 142.14 144.14
+ 49.67 39.57 46.87 85.17 86.49 86.65 89.63 107.91 113.09 117.01 118.20 127.67 140.53 142.14 144.14
+ 49.66 39.57 46.86 85.17 86.49 86.63 89.59 107.91 113.09 117.03 118.18 127.68 140.53 142.14 144.14 154.82 154.85
49.65 39.58 46.86 85.17 86.47 86.62 89.55 107.92 113.08 117.07 118.15 127.69 140.54 142.14 144.14 154.81 154.86
49.64 39.58 46.86 85.18 86.45 86.61 89.51 107.99 113.08 117.11 118.12 127.70 140.54 142.13 144.14 154.80 154.91
49.63 39.58 46.86 85.18 86.43 86.60 89.49 107.99 113.08 117.15 118.10 127.71 140.54 142.13 144.15 154.78 154.91
@@ -146753,58 +147048,58 @@ Russia
49.60 39.61 46.85 85.19 86.36 86.58 89.19 89.26 89.41 107.99 113.08 117.36 118.07 127.78 140.56 142.13 144.18 154.74 154.91
49.59 39.62 46.85 85.20 85.36 85.39 85.58 85.61 86.32 86.58 89.20 89.28 89.41 108.00 113.08 117.48 118.05 127.79 140.56 142.13 144.19 154.73 154.91
49.58 39.64 39.97 40.06 46.84 85.21 85.34 85.41 85.56 85.62 86.30 86.58 89.21 89.30 89.40 108.01 113.07 117.51 118.03 127.81 127.95 127.97 128.66 128.69 140.57 142.13 144.20 154.73 154.90
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49.56 39.72 39.94 40.11 46.84 85.63 86.27 86.58 89.22 108.04 112.96 117.56 117.98 128.01 128.47 128.58 128.64 128.74 140.57 142.13 144.21 154.73 154.89
49.55 39.74 39.92 40.09 46.84 85.64 85.71 85.75 86.26 86.59 89.22 108.06 112.94 117.59 117.95 128.02 128.37 128.79 140.57 142.12 144.22 154.74 154.89
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49.53 39.77 39.87 40.05 46.83 85.78 85.85 85.92 86.25 86.62 86.69 86.74 89.22 108.11 112.90 117.65 117.90 128.05 128.24 128.29 128.35 128.75 140.55 142.12 144.23 154.72 154.88
49.52 40.04 46.83 85.79 85.82 85.92 86.24 86.76 89.21 108.21 112.88 117.68 117.89 128.14 128.21 128.75 140.54 142.11 144.23 154.71 154.87
49.51 40.03 46.83 85.92 86.24 86.78 88.86 88.90 89.20 108.24 112.46 112.52 112.85 117.70 117.89 128.74 140.53 142.11 144.23 154.70 154.86
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- 49.48 40.02 46.82 85.92 86.00 86.12 86.22 86.80 88.86 88.92 89.15 108.25 112.34 112.65 112.76 128.74 140.52 142.11 144.23 154.68 154.83
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- 49.43 40.04 46.81 86.80 88.19 88.68 88.88 108.31 112.16 128.93 140.48 142.09 144.23 154.62 154.81
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49.36 40.10 46.79 86.89 88.13 108.42 111.60 129.04 129.17 129.25 129.38 129.51 140.45 142.06 144.26 154.59 154.84
49.35 40.11 46.79 86.89 88.13 108.44 111.57 129.05 129.16 129.27 129.38 129.52 140.45 142.06 144.26 154.59 154.84
49.34 40.12 46.79 86.89 88.13 108.46 111.33 111.39 111.55 129.07 129.14 129.29 129.38 129.52 140.45 142.06 144.26 154.59 154.84
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49.32 40.14 46.85 86.90 88.14 108.50 108.72 108.95 109.14 109.22 111.30 129.52 140.45 142.05 144.27 154.59 154.83
49.31 40.14 46.87 86.92 88.14 108.52 108.64 109.00 109.08 109.32 111.29 129.52 140.44 142.05 144.27 154.59 154.82
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49.28 40.13 46.93 86.97 88.15 109.45 111.16 129.54 140.44 142.05 143.51 143.73 144.28 154.59 154.80
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49.26 40.13 46.97 87.00 88.15 109.45 111.11 129.56 140.40 142.05 143.32 143.88 144.29 154.62 154.74
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49.24 40.12 46.99 87.00 88.13 109.50 109.62 109.75 111.07 129.71 140.38 142.06 143.24 144.02 144.30
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49.22 40.08 47.02 87.04 87.12 87.17 88.09 109.79 111.03 129.72 140.38 142.06 143.16 144.08 144.31
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49.20 40.05 47.03 87.22 88.04 109.87 110.34 110.41 110.99 129.72 140.38 142.06 143.12 144.12 144.32
49.19 40.04 47.04 87.25 88.02 109.93 110.33 110.42 110.97 129.72 140.38 142.06 143.11 144.13 144.33
49.18 40.03 47.04 87.26 88.00 109.99 110.31 110.44 110.95 129.73 140.38 142.05 143.10 144.14 144.33 154.44 154.51
49.17 40.01 47.05 87.27 87.99 110.04 110.30 110.47 110.92 129.74 140.37 142.05 143.08 144.16 144.34 154.43 154.53
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49.15 39.96 47.05 87.28 87.97 110.15 110.25 110.53 110.86 129.83 140.38 142.03 143.06 144.19 144.35 154.42 154.59
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49.13 39.94 47.05 87.28 87.69 110.58 110.79 129.83 140.38 142.02 143.03 144.21 144.36 154.44 154.60
49.12 39.93 47.04 87.28 87.64 110.62 110.75 129.83 140.37 142.02 143.02 144.23 144.37 154.44 154.61
49.11 39.92 47.04 87.29 87.60 129.83 140.37 142.01 143.01 144.24 144.37 154.45 154.61
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49.08 39.91 47.03 87.30 87.49 129.87 140.36 142.01 143.00 144.26 144.39 154.46 154.57
49.07 39.91 47.02 87.31 87.48 129.90 140.35 142.01 142.99 144.26 144.40 154.47 154.55
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49.05 39.80 47.00 129.90 140.35 142.01 142.99 144.28 144.41
49.04 39.76 46.99 129.90 140.35 142.01 142.98 144.30 144.42
49.03 39.67 46.98 129.90 140.36 142.00 142.98 144.32 144.44
@@ -146812,7 +147107,7 @@ Russia
49.01 39.67 46.96 129.91 140.38 142.00 142.98 144.35 144.47
49.00 39.66 46.95 129.94 140.40 141.99 142.98 144.37 144.49
48.99 39.66 46.94 129.98 140.40 141.99 142.98 144.39 144.50 153.90 153.94
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48.97 39.66 46.90 130.01 140.40 141.99 142.99 144.44 144.54 153.89 154.00
48.96 39.66 46.87 130.02 140.39 141.99 142.99 144.45 144.56 153.89 154.02
48.95 39.66 46.85 130.03 140.39 141.98 142.99 144.46 144.57 153.89 154.02
@@ -146821,50 +147116,50 @@ Russia
48.92 39.71 46.79 130.09 140.36 141.95 142.99 144.50 144.62 153.90 154.01 154.13 154.22
48.91 39.71 46.77 130.11 140.36 141.95 142.99 144.51 144.64 153.92 154.00 154.11 154.23
48.90 39.72 46.76 130.13 140.36 141.95 142.99 144.52 144.66 154.10 154.24
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48.87 39.76 46.74 130.19 130.36 130.45 140.32 141.95 142.98 144.55 144.70 154.09 154.24
48.86 39.82 40.00 40.03 46.74 130.21 130.32 130.46 140.30 141.95 142.97 144.55 144.70 154.09 154.23
48.85 39.91 39.98 40.04 46.73 130.23 130.27 130.47 130.61 130.65 140.28 141.93 142.96 144.56 144.70 154.09 154.22
48.84 39.92 39.97 40.02 46.73 130.49 130.58 130.64 140.27 141.91 142.96 144.57 144.70 154.09 154.20
48.83 40.01 46.72 130.63 140.26 141.90 142.95 144.58 144.70 154.07 154.19
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48.81 39.76 39.88 39.99 46.71 130.62 140.25 141.87 142.94 144.60 144.71 154.04 154.16
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48.44 39.86 46.50 130.73 140.18 142.03 142.75
48.43 39.86 46.50 130.72 140.17 142.04 142.75
@@ -146886,29 +147181,29 @@ Russia
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48.26 39.86 39.90 39.98 47.12 130.77 133.98 134.62 139.91 142.13 142.67
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48.06 39.81 47.20 130.66 133.06 134.56 139.67 142.16 142.57 153.16 153.30
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48.01 39.74 47.14 130.71 132.96 134.54 139.60 142.17 142.55
48.00 39.74 47.12 130.72 132.94 134.54 139.59 142.17 142.55
47.99 39.75 47.10 130.73 132.92 134.54 139.57 142.17 142.55
@@ -146928,22 +147223,22 @@ Russia
47.85 38.82 39.08 39.24 39.35 39.75 47.16 130.90 132.66 134.65 139.36 142.08 142.54
47.84 38.81 39.11 39.15 39.37 39.43 39.47 39.53 39.59 39.74 47.16 47.40 47.45 130.91 132.65 134.65 139.35 142.07 142.54
47.83 38.79 39.66 39.73 47.14 47.38 47.48 130.92 132.64 134.66 139.34 142.07 142.54
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47.66 38.60 48.23 131.03 131.12 131.55 131.66 131.76 131.82 131.87 131.95 134.70 139.21 141.98 142.60
47.65 38.59 48.24 131.56 131.64 131.89 131.93 134.68 139.21 141.97 142.60
47.64 38.57 48.25 134.67 139.20 141.97 142.61
@@ -146953,7 +147248,7 @@ Russia
47.60 38.30 48.28 134.67 139.16 141.95 142.63
47.59 38.29 48.29 134.67 139.15 141.95 142.64
47.58 38.29 48.30 134.65 139.15 141.95 142.65
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47.56 38.28 48.32 134.62 139.13 141.95 142.66
47.55 38.27 48.33 134.61 139.12 141.95 142.67
47.54 38.27 48.34 134.60 139.11 141.94 142.68
@@ -146972,19 +147267,19 @@ Russia
47.41 38.24 48.53 134.28 139.05 141.95 142.85
47.40 38.24 48.54 134.26 139.05 141.95 142.87
47.39 38.23 48.54 134.25 139.04 141.95 142.89 152.41 152.52
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47.27 38.21 38.24 38.28 48.61 134.15 138.88 141.97 143.01
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47.25 38.27 39.05 39.16 48.62 134.14 138.85 141.99 143.02
47.24 38.25 39.03 39.26 48.62 134.14 138.84 141.99 143.03
47.23 38.23 38.95 39.26 48.63 134.14 138.83 142.00 143.03
@@ -146998,7 +147293,7 @@ Russia
47.15 38.18 38.87 39.23 48.68 134.17 138.74 142.04 143.05 152.15 152.30
47.14 38.18 38.75 39.23 48.68 134.18 138.73 142.04 143.05 152.14 152.30
47.13 38.19 38.70 39.23 48.69 134.19 138.72 142.05 143.05 152.13 152.30
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47.11 38.19 38.39 38.48 38.57 39.25 48.70 134.20 138.69 142.05 143.05 152.11 152.27
47.10 38.20 38.31 38.50 38.57 39.25 48.71 134.20 138.68 142.05 143.05 152.10 152.26
47.09 38.20 38.25 39.25 48.72 134.13 138.67 142.04 143.05 152.09 152.24
@@ -147021,31 +147316,31 @@ Russia
46.92 38.82 48.87 134.05 138.52 141.97 143.11 151.90 152.05
46.91 38.81 48.88 134.05 138.52 141.96 143.12 151.89 152.04
46.90 38.78 48.89 134.04 138.51 141.96 143.12 151.88 152.04
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46.87 38.46 38.50 38.64 48.92 134.03 138.51 141.94 143.18 151.73 151.79 151.84 152.00
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46.83 38.39 48.96 134.01 138.48 141.92 143.26 143.42 143.48 151.69 151.92
46.82 38.39 48.96 134.00 138.47 141.91 143.28 143.41 143.49 151.70 151.91
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46.74 38.26 38.28 38.35 48.55 48.65 49.00 134.02 138.40 141.87 143.52
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46.72 38.23 38.29 38.35 38.41 38.49 48.51 48.69 48.98 134.01 138.39 141.86 143.52
46.71 38.22 38.30 38.36 38.39 38.52 48.50 48.70 48.96 134.01 138.39 141.86 142.70 142.72 143.52
46.70 38.13 38.30 38.36 38.39 38.54 48.50 48.71 48.95 134.01 138.38 141.86 142.64 142.72 143.52
46.69 38.11 38.31 38.36 38.38 38.55 48.49 48.71 48.93 134.00 138.38 141.85 142.60 142.72 143.52
46.68 37.72 37.75 38.09 38.34 38.57 48.49 48.72 48.88 134.00 138.37 141.85 142.57 142.72 143.52
46.67 37.72 37.77 38.08 38.39 38.57 48.48 48.74 48.80 134.00 138.37 141.84 142.54 142.72 143.52
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46.64 37.73 37.84 38.04 48.54 133.98 138.35 141.83 142.49 142.73 143.53
46.63 37.74 37.91 38.00 48.54 133.97 138.35 141.83 142.48 142.74 143.54
46.62 37.74 48.55 133.95 138.35 141.82 142.46 142.74 143.54
@@ -147061,16 +147356,16 @@ Russia
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46.51 37.79 48.78 133.85 138.32 141.80 142.40 143.27 143.56
46.50 37.80 48.79 133.84 138.31 141.80 142.39 143.28 143.56
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46.39 37.90 49.09 133.91 138.18 141.82 142.34 143.32 143.62
46.38 37.92 38.02 38.07 49.12 133.91 138.18 141.83 142.33 143.33 143.63
46.37 37.93 38.02 38.09 49.14 133.89 138.17 141.83 142.33 143.33 143.63
@@ -147082,79 +147377,79 @@ Russia
46.31 38.17 49.26 133.85 138.14 141.86 142.29 143.36 143.58
46.30 38.19 49.27 133.86 138.14 141.87 142.29 143.37 143.58
46.29 38.20 49.29 133.88 138.13 141.87 142.28 143.37 143.58
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46.26 38.26 49.10 49.18 49.31 133.87 138.12 141.88 142.27 143.39 143.54
46.25 38.26 49.11 49.23 49.31 133.85 138.12 141.88 142.27 143.39 143.54
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- 46.10 38.15 38.34 38.53 48.89 48.91 48.96 133.68 137.96 141.92 142.23 143.40 143.48 150.08 150.41
- 46.09 38.15 38.36 38.56 48.67 48.75 48.89 48.91 48.96 133.68 137.95 141.92 142.23 143.40 143.48 150.06 150.40
- 46.08 38.15 38.37 38.56 48.68 48.77 48.88 48.91 48.96 133.69 137.95 141.92 142.22 143.40 143.48 150.04 150.39
- 46.07 38.15 38.39 38.56 48.69 48.77 48.88 48.92 48.95 133.69 137.95 141.92 142.22 143.40 143.48 150.02 150.37
- 46.06 38.01 38.10 38.15 38.40 38.56 48.71 48.78 48.83 48.85 48.88 133.70 137.94 141.92 142.21 143.40 143.46 150.01 150.36
- 46.05 37.98 38.10 38.13 38.42 38.55 48.72 48.79 48.83 133.70 137.93 141.92 142.21 143.40 143.46 149.99 150.34
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- 42.74 43.76 47.73 130.39 131.28 132.80 132.88 133.01 133.28
- 42.73 43.78 44.49 44.57 44.85 44.90 47.72 130.38 131.28 132.82 132.87 132.98 133.25
- 42.72 43.79 44.46 44.62 44.84 44.92 47.72 130.38 131.27 132.98 133.23
- 42.71 43.78 44.44 44.65 44.84 44.94 47.72 130.37 131.27 132.98 133.22
+ 42.78 43.62 47.72 130.46 131.37 132.44 132.47 132.78 132.91 132.99 133.49
+ 42.77 43.63 47.72 130.44 131.37 132.78 132.90 133.01 133.46
+ 42.76 43.65 47.73 130.42 131.28 131.33 131.36 132.79 132.90 133.03 133.45
+ 42.75 43.70 47.73 130.40 131.27 132.79 132.89 133.02 133.40
+ 42.74 43.76 47.73 130.39 131.26 132.80 132.88 133.01 133.28
+ 42.73 43.79 44.49 44.57 44.85 44.90 47.72 130.38 131.26 132.82 132.87 132.98 133.25
+ 42.72 43.79 44.46 44.63 44.84 44.92 47.72 130.38 131.25 132.98 133.23
+ 42.71 43.78 44.44 44.65 44.84 44.94 47.72 130.37 131.25 132.98 133.22
42.70 43.77 44.42 44.68 44.83 44.96 47.72 130.36 131.26 133.00 133.21
42.69 43.75 44.39 44.69 44.82 44.98 47.72 130.36 131.27 133.00 133.20
- 42.68 43.74 44.27 44.71 44.82 45.00 45.10 45.13 47.73 130.36 131.27 133.01 133.19
- 42.67 43.72 44.25 44.71 44.81 45.01 45.08 45.15 47.73 130.37 131.27 133.04 133.17
- 42.66 43.71 44.25 44.72 44.80 45.17 47.74 130.39 130.70 130.78 131.26
+ 42.68 43.74 44.27 44.71 44.82 45.00 45.09 45.13 47.73 130.36 131.27 133.01 133.19
+ 42.67 43.72 44.25 44.71 44.81 45.01 45.07 45.15 47.73 130.37 130.70 130.73 131.27 133.04 133.17
+ 42.66 43.71 44.25 44.72 44.80 45.17 47.74 130.39 130.69 130.77 131.26
42.65 43.71 44.24 44.72 44.80 45.18 47.75 130.51 130.69 130.77 131.26
42.64 43.71 44.24 44.73 44.80 45.19 47.77 130.52 130.71 130.77 131.23
- 42.63 43.71 44.23 44.73 44.80 45.20 47.80 130.54 130.73 130.77 131.22
- 42.62 43.71 44.22 44.74 44.79 45.21 47.82 130.55 130.74 130.80 130.99 131.05 131.22
- 42.61 43.71 44.20 44.74 44.79 45.23 47.84 130.56 130.74 130.82 130.97 131.07 131.11 131.13 131.23
- 42.60 43.72 44.18 44.75 44.79 45.24 47.86 130.56 130.78 130.84 130.96 131.09 131.11 131.13 131.24
- 42.59 43.73 44.04 44.76 44.78 45.25 47.87 130.57 130.78 130.86 130.94 131.15 131.24
- 42.58 43.74 44.01 45.26 47.88 130.57 130.80 130.88 130.91 131.15 131.24
+ 42.63 43.71 44.23 44.73 44.80 45.20 47.80 130.54 130.73 130.80 131.09 131.11 131.22
+ 42.62 43.71 44.22 44.74 44.79 45.21 47.82 130.55 130.74 130.80 130.99 131.05 131.08 131.11 131.21
+ 42.61 43.71 44.21 44.74 44.79 45.23 47.84 130.56 130.74 130.82 130.97 131.11 131.23
+ 42.60 43.72 44.17 44.75 44.79 45.24 47.86 130.56 130.78 130.84 130.95 131.11 131.23
+ 42.59 43.73 44.04 44.76 44.78 45.25 47.87 130.57 130.78 130.86 130.94 131.14 131.24
+ 42.58 43.74 44.01 45.26 47.88 130.57 130.80 130.87 130.90 131.15 131.24
42.57 43.77 44.00 45.27 47.88 130.57 130.83 131.15 131.24
42.56 43.86 43.99 45.28 47.89 130.55 130.85 131.15 131.23
- 42.55 43.89 43.98 45.29 47.90 130.53 130.86 131.17 131.23
- 42.54 43.91 43.97 45.29 47.90 130.52 130.88 131.19 131.22
+ 42.55 43.89 43.98 45.28 47.90 130.53 130.86 131.16 131.23
+ 42.54 43.91 43.97 45.29 47.90 130.52 130.87 131.17 131.22
42.53 45.30 47.91 130.52 130.88
42.52 45.31 45.46 45.57 47.92 130.52 130.88
42.51 45.32 45.42 45.63 47.93 130.52 130.88
@@ -147473,16 +147768,16 @@ Russia
42.40 45.70 48.03 130.61 130.77
42.39 45.69 48.05 130.63 130.77
42.38 45.69 48.07 130.63 130.77
- 42.37 45.68 48.08 130.64 130.77
+ 42.37 45.68 48.08 130.64 130.76
42.36 45.68 48.09 130.64 130.76
- 42.35 45.67 48.10 130.65 130.76
- 42.34 45.67 48.11 130.65 130.76
- 42.33 45.66 48.12 130.65 130.76
- 42.32 45.66 48.12 130.65 130.75
- 42.31 45.65 48.13 130.65 130.74
+ 42.35 45.67 48.10 130.65 130.75
+ 42.34 45.67 48.11 130.65 130.75
+ 42.33 45.66 48.12 130.65 130.75
+ 42.32 45.66 48.12 130.65 130.74
+ 42.31 45.65 48.13 130.65 130.73
42.30 45.65 48.14 130.66 130.73
42.29 45.64 48.15 130.67 130.72
- 42.28 45.64 48.15 130.69 130.71
+ 42.28 45.64 48.15 130.68 130.71
42.27 45.63 48.16
42.26 45.63 48.17
42.25 45.62 48.18
@@ -147529,7 +147824,7 @@ Russia
41.84 46.53 48.58
41.83 46.53 48.58
41.82 46.53 48.57
- 41.81 46.53 46.71 46.73 48.57
+ 41.81 46.53 46.70 46.73 48.57
41.80 46.53 46.65 46.74 48.56
41.79 46.53 46.63 46.74 48.55
41.78 46.53 46.61 46.74 48.55
@@ -147537,7 +147832,7 @@ Russia
41.76 46.75 48.53
41.75 46.76 48.52
41.74 46.78 48.51
- 41.73 46.80 48.50
+ 41.73 46.80 48.49
41.72 46.82 48.48
41.71 46.84 48.47
41.70 46.85 48.46
@@ -147586,12 +147881,12 @@ Russia
41.27 47.29 47.90
41.26 47.31 47.90
41.25 47.33 47.90
- 41.24 47.35 47.90
+ 41.24 47.36 47.90
41.23 47.48 47.90
41.22 47.50 47.90
41.21 47.50 47.90
41.20 47.51 47.60 47.65 47.90
- 41.19 47.53 47.58 47.68 47.89
+ 41.19 47.53 47.58 47.67 47.89
41.18 47.70 47.85
Rwanda
-1.04 30.43 30.46
@@ -147636,9 +147931,9 @@ Rwanda
-1.43 29.47 29.88 29.98 30.75
-1.44 29.46 29.89 29.96 30.75
-1.45 29.45 29.91 29.94 30.75
- -1.46 29.45 30.75
+ -1.46 29.44 30.75
-1.47 29.44 30.75
- -1.48 29.44 30.75
+ -1.48 29.43 30.75
-1.49 29.34 30.75
-1.50 29.33 30.76
-1.51 29.33 30.77
@@ -147663,7 +147958,7 @@ Rwanda
-1.70 29.19 30.83
-1.71 29.18 30.83
-1.72 29.17 30.83
- -1.73 29.17 30.84
+ -1.73 29.16 30.84
-1.74 29.16 30.84
-1.75 29.15 30.84
-1.76 29.14 30.84
@@ -147724,7 +148019,7 @@ Rwanda
-2.31 28.96 30.85
-2.32 28.94 30.36 30.39 30.85
-2.33 28.94 30.35 30.41 30.85
- -2.34 28.93 30.35 30.41 30.85
+ -2.34 28.93 29.93 29.95 30.35 30.41 30.85
-2.35 28.91 29.93 29.96 30.34 30.43 30.84
-2.36 28.87 29.93 30.01 30.21 30.23 30.31 30.44 30.83
-2.37 28.86 29.93 30.02 30.21 30.45 30.67 30.70 30.82
@@ -147770,37 +148065,37 @@ Rwanda
-2.77 29.30 29.74 29.76 29.84
-2.78 29.31 29.74
-2.79 29.31 29.74
- -2.80 29.31 29.60 29.63 29.74
+ -2.80 29.31 29.60 29.62 29.74
-2.81 29.32 29.59 29.65 29.72
- -2.82 29.32 29.40 29.45 29.54
+ -2.82 29.32 29.40 29.46 29.54
-2.83 29.32 29.38 29.49 29.53
Saint Helena
-7.86 -14.38 -14.36
-7.87 -14.40 -14.34
-7.88 -14.40 -14.33
- -7.89 -14.40 -14.31
- -7.90 -14.41 -14.30
- -7.91 -14.41 -14.29
+ -7.89 -14.40 -14.32
+ -7.90 -14.41 -14.31
+ -7.91 -14.41 -14.30
-7.92 -14.42 -14.29
-7.93 -14.42 -14.28
-7.94 -14.42 -14.28
-7.95 -14.42 -14.28
-7.96 -14.42 -14.29
-7.97 -14.42 -14.30
- -7.98 -14.41 -14.32
+ -7.98 -14.41 -14.33
-15.89 -5.73 -5.65
-15.90 -5.74 -5.64
- -15.91 -5.75 -5.64
- -15.92 -5.76 -5.64
- -15.93 -5.77 -5.63
- -15.94 -5.77 -5.63
- -15.95 -5.78 -5.63
- -15.96 -5.78 -5.63
+ -15.91 -5.76 -5.64
+ -15.92 -5.77 -5.64
+ -15.93 -5.78 -5.64
+ -15.94 -5.78 -5.64
+ -15.95 -5.78 -5.64
+ -15.96 -5.79 -5.64
-15.97 -5.79 -5.64
-15.98 -5.79 -5.65
-15.99 -5.79 -5.66
-16.00 -5.79 -5.67
- -16.01 -5.78 -5.68
+ -16.01 -5.79 -5.68
-16.02 -5.77 -5.72
-37.04 -12.30 -12.22
-37.05 -12.30 -12.21
@@ -147809,25 +148104,25 @@ Saint Helena
-37.08 -12.33 -12.18
-37.09 -12.34 -12.18
-37.10 -12.34 -12.18
- -37.11 -12.34 -12.18
+ -37.11 -12.34 -12.19
-37.12 -12.33 -12.20
-37.13 -12.31 -12.21
-37.14 -12.30 -12.23
-37.15 -12.28 -12.24
-40.29 -10.03 -9.93
- -40.30 -10.03 -9.93
- -40.31 -10.03 -9.93
+ -40.30 -10.04 -9.93
+ -40.31 -10.04 -9.93
-40.32 -10.04 -9.92
-40.33 -10.04 -9.91
-40.34 -10.04 -9.90
-40.35 -10.03 -9.89
- -40.36 -10.01 -9.88
+ -40.36 -10.01 -9.89
-40.37 -10.00 -9.88
-40.38 -9.99 -9.88
-40.39 -9.97 -9.88
-40.40 -9.94 -9.90
Saint Kitts and Nevis
- 17.42 -62.82 -62.80
+ 17.42 -62.83 -62.80
17.41 -62.85 -62.78
17.40 -62.86 -62.76
17.39 -62.86 -62.75
@@ -147836,19 +148131,19 @@ Saint Kitts and Nevis
17.36 -62.87 -62.70
17.35 -62.87 -62.69
17.34 -62.86 -62.68
- 17.33 -62.86 -62.68
- 17.32 -62.85 -62.67
- 17.31 -62.84 -62.67
- 17.30 -62.82 -62.66
- 17.29 -62.80 -62.66
- 17.28 -62.77 -62.64
+ 17.33 -62.85 -62.68
+ 17.32 -62.84 -62.67
+ 17.31 -62.83 -62.67
+ 17.30 -62.81 -62.66
+ 17.29 -62.79 -62.66
+ 17.28 -62.77 -62.65
17.27 -62.71 -62.63
- 17.26 -62.69 -62.62
- 17.25 -62.67 -62.61
- 17.24 -62.67 -62.61
+ 17.26 -62.70 -62.62
+ 17.25 -62.68 -62.61
+ 17.24 -62.68 -62.61
17.23 -62.67 -62.61
- 17.22 -62.66 -62.61
- 17.21 -62.66 -62.55
+ 17.22 -62.67 -62.61
+ 17.21 -62.66 -62.56
17.20 -62.65 -62.54
17.19 -62.62 -62.53
17.18 -62.62 -62.53
@@ -147868,9 +148163,9 @@ Saint Lucia
14.09 -60.96 -60.90
14.08 -60.97 -60.89
14.07 -60.98 -60.88
- 14.06 -60.98 -60.87
- 14.05 -60.98 -60.87
- 14.04 -60.99 -60.87
+ 14.06 -60.98 -60.88
+ 14.05 -60.98 -60.88
+ 14.04 -60.99 -60.88
14.03 -61.01 -60.87
14.02 -61.01 -60.87
14.01 -61.02 -60.87
@@ -147906,12 +148201,12 @@ Saint Lucia
13.71 -60.97 -60.93
13.70 -60.96 -60.93
Saint Pierre and Miquelon
- 47.15 -56.36 -56.34
+ 47.15 -56.37 -56.34
47.14 -56.38 -56.33
47.13 -56.39 -56.33
47.12 -56.40 -56.33
47.11 -56.40 -56.34
- 47.10 -56.40 -56.33
+ 47.10 -56.40 -56.34
47.09 -56.40 -56.29
47.08 -56.40 -56.27
47.07 -56.40 -56.25
@@ -147924,10 +148219,10 @@ Saint Pierre and Miquelon
47.00 -56.38 -56.24
46.99 -56.37 -56.25
46.98 -56.37 -56.26
- 46.97 -56.36 -56.26
+ 46.97 -56.36 -56.27
46.96 -56.35 -56.29
46.95 -56.35 -56.29
- 46.94 -56.34 -56.29
+ 46.94 -56.34 -56.30
46.93 -56.34 -56.30
46.92 -56.34 -56.30
46.91 -56.33 -56.30
@@ -147943,24 +148238,24 @@ Saint Pierre and Miquelon
46.81 -56.40 -56.25 -56.20 -56.13
46.80 -56.38 -56.27 -56.21 -56.13
46.79 -56.38 -56.28 -56.22 -56.13
- 46.78 -56.38 -56.30 -56.23 -56.14
- 46.77 -56.37 -56.32 -56.24 -56.13
- 46.76 -56.24 -56.13
- 46.75 -56.24 -56.13
+ 46.78 -56.38 -56.30 -56.24 -56.14
+ 46.77 -56.38 -56.32 -56.25 -56.13
+ 46.76 -56.25 -56.13
+ 46.75 -56.25 -56.13
46.74 -56.23 -56.14
Saint Vincent and the Grenadines
13.39 -61.19 -61.15
13.38 -61.20 -61.13
- 13.37 -61.22 -61.12
+ 13.37 -61.22 -61.13
13.36 -61.22 -61.12
13.35 -61.23 -61.12
13.34 -61.23 -61.12
13.33 -61.24 -61.11
13.32 -61.24 -61.11
13.31 -61.24 -61.11
- 13.30 -61.25 -61.11
- 13.29 -61.27 -61.11
- 13.28 -61.27 -61.11
+ 13.30 -61.28 -61.11
+ 13.29 -61.28 -61.11
+ 13.28 -61.28 -61.11
13.27 -61.27 -61.11
13.26 -61.28 -61.11
13.25 -61.28 -61.11
@@ -147974,9 +148269,9 @@ Saint Vincent and the Grenadines
13.17 -61.28 -61.12
13.16 -61.27 -61.13
13.15 -61.25 -61.13
- 13.14 -61.23 -61.14
- 13.13 -61.21 -61.15
- 13.12 -61.19 -61.16
+ 13.14 -61.24 -61.14
+ 13.13 -61.22 -61.15
+ 13.12 -61.20 -61.16
13.06 -61.21 -61.19
13.05 -61.22 -61.18
13.04 -61.24 -61.18
@@ -148008,11 +148303,11 @@ Saint Vincent and the Grenadines
12.57 -61.46 -61.42
Samoa
-13.45 -172.40 -172.30
- -13.46 -172.42 -172.28
- -13.47 -172.55 -172.27
- -13.48 -172.56 -172.26
- -13.49 -172.62 -172.25
- -13.50 -172.77 -172.70 -172.63 -172.24
+ -13.46 -172.42 -172.29
+ -13.47 -172.55 -172.28
+ -13.48 -172.56 -172.27
+ -13.49 -172.62 -172.26
+ -13.50 -172.77 -172.70 -172.63 -172.25
-13.51 -172.79 -172.24
-13.52 -172.79 -172.23
-13.53 -172.79 -172.22
@@ -148026,28 +148321,28 @@ Samoa
-13.61 -172.72 -172.18
-13.62 -172.71 -172.18
-13.63 -172.70 -172.18
- -13.64 -172.68 -172.17
+ -13.64 -172.68 -172.18
-13.65 -172.66 -172.17
-13.66 -172.66 -172.17
-13.67 -172.65 -172.16
-13.68 -172.65 -172.16
-13.69 -172.64 -172.16
-13.70 -172.61 -172.16
- -13.71 -172.60 -172.16
- -13.72 -172.60 -172.17
+ -13.71 -172.60 -172.17
+ -13.72 -172.60 -172.18
-13.73 -172.59 -172.18
-13.74 -172.59 -172.19
- -13.75 -172.58 -172.20
+ -13.75 -172.59 -172.20
-13.76 -172.58 -172.20
-13.77 -172.58 -172.20
-13.78 -172.56 -172.20
-13.79 -172.55 -172.33 -172.28 -172.20 -171.92 -171.80
-13.80 -172.54 -172.39 -172.27 -172.20 -171.98 -171.77
-13.81 -172.53 -172.47 -172.26 -172.20 -172.00 -171.75
- -13.82 -172.03 -171.72
+ -13.82 -172.03 -171.73
-13.83 -172.05 -171.70
- -13.84 -172.05 -171.67
- -13.85 -172.06 -171.65
+ -13.84 -172.05 -171.68
+ -13.85 -172.06 -171.66
-13.86 -172.06 -171.58
-13.87 -172.07 -171.56
-13.88 -172.07 -171.55
@@ -148066,14 +148361,14 @@ Samoa
-14.01 -171.93 -171.42
-14.02 -171.81 -171.42
-14.03 -171.79 -171.43
- -14.04 -171.77 -171.42
- -14.05 -171.77 -171.70 -171.67 -171.42
- -14.06 -171.76 -171.72 -171.50 -171.42
+ -14.04 -171.78 -171.43
+ -14.05 -171.77 -171.70 -171.67 -171.43
+ -14.06 -171.76 -171.72 -171.50 -171.43
San Marino
43.99 12.46 12.49
43.98 12.43 12.49
43.97 12.41 12.49
- 43.96 12.39 12.50
+ 43.96 12.40 12.50
43.95 12.38 12.50
43.94 12.38 12.50
43.93 12.37 12.50
@@ -148083,14 +148378,14 @@ San Marino
43.89 12.38 12.48
43.88 12.40 12.47
Sao Tome and Principe
- 1.70 7.37 7.46
- 1.69 7.37 7.47
+ 1.70 7.37 7.45
+ 1.69 7.37 7.46
1.68 7.36 7.47
1.67 7.36 7.47
1.66 7.35 7.47
1.65 7.35 7.46
1.64 7.35 7.47
- 1.63 7.35 7.47
+ 1.63 7.34 7.47
1.62 7.32 7.47
1.61 7.32 7.46
1.60 7.31 7.44
@@ -148104,8 +148399,8 @@ Sao Tome and Principe
1.52 7.37 7.41
0.42 6.63 6.67
0.41 6.61 6.70
- 0.40 6.60 6.71
- 0.39 6.59 6.72
+ 0.40 6.59 6.71
+ 0.39 6.58 6.72
0.38 6.57 6.72
0.37 6.55 6.73
0.36 6.53 6.74
@@ -148120,7 +148415,7 @@ Sao Tome and Principe
0.27 6.46 6.77
0.26 6.45 6.77
0.25 6.45 6.77
- 0.24 6.45 6.77
+ 0.24 6.45 6.76
0.23 6.45 6.76
0.22 6.45 6.75
0.21 6.45 6.75
@@ -148179,16 +148474,16 @@ Saudi Arabia
31.82 38.22 40.65
31.81 38.18 40.67
31.80 38.14 40.69
- 31.79 38.10 40.71
- 31.78 38.06 40.73
- 31.77 38.01 40.75
- 31.76 37.97 40.76
- 31.75 37.92 40.78
- 31.74 37.88 40.80
- 31.73 37.84 40.82
- 31.72 37.80 40.84
- 31.71 37.76 40.86
- 31.70 37.72 40.88
+ 31.79 38.09 40.71
+ 31.78 38.05 40.73
+ 31.77 38.00 40.75
+ 31.76 37.96 40.76
+ 31.75 37.93 40.78
+ 31.74 37.89 40.80
+ 31.73 37.85 40.82
+ 31.72 37.81 40.84
+ 31.71 37.77 40.86
+ 31.70 37.73 40.88
31.69 37.68 40.90
31.68 37.64 40.92
31.67 37.61 40.94
@@ -148236,12 +148531,12 @@ Saudi Arabia
31.25 37.18 41.76
31.24 37.19 41.78
31.23 37.20 41.80
- 31.22 37.21 41.82
- 31.21 37.22 41.84
- 31.20 37.23 41.86
- 31.19 37.24 41.87
- 31.18 37.25 41.89
- 31.17 37.26 41.91
+ 31.22 37.22 41.82
+ 31.21 37.23 41.84
+ 31.20 37.24 41.86
+ 31.19 37.25 41.87
+ 31.18 37.26 41.89
+ 31.17 37.27 41.91
31.16 37.28 41.93
31.15 37.29 41.95
31.14 37.30 41.97
@@ -148301,11 +148596,11 @@ Saudi Arabia
30.60 37.86 42.73
30.59 37.86 42.74
30.58 37.87 42.76
- 30.57 37.88 42.77
- 30.56 37.89 42.78
+ 30.57 37.88 42.78
+ 30.56 37.89 42.79
30.55 37.90 42.80
30.54 37.91 42.81
- 30.53 37.92 42.82
+ 30.53 37.92 42.83
30.52 37.93 42.84
30.51 37.94 42.85
30.50 37.95 42.86
@@ -148375,9 +148670,9 @@ Saudi Arabia
29.86 36.71 43.77
29.85 36.70 43.78
29.84 36.69 43.80
- 29.83 36.68 43.81
+ 29.83 36.68 43.82
29.82 36.68 43.83
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@@ -148433,12 +148728,12 @@ Saudi Arabia
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29.19 34.88 44.85
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@@ -148459,10 +148754,10 @@ Saudi Arabia
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@@ -148537,7 +148832,7 @@ Saudi Arabia
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@@ -148556,19 +148851,19 @@ Saudi Arabia
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23.01 38.77 52.50
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22.99 38.78 52.51
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22.97 38.80 52.53
22.96 38.84 52.54
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22.89 38.85 52.99
22.88 38.86 53.10
22.87 38.86 53.20
@@ -149080,7 +149375,7 @@ Saudi Arabia
22.81 38.90 53.65
22.80 38.91 53.75
22.79 38.92 53.82
- 22.78 38.93 53.89
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22.77 38.93 53.96
22.76 38.94 54.07
22.75 38.95 54.17
@@ -149104,8 +149399,8 @@ Saudi Arabia
22.57 39.05 55.29
22.56 39.06 55.29
22.55 39.06 55.30
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22.52 39.06 55.32
22.51 39.06 55.33
22.50 39.06 55.33
@@ -149114,17 +149409,17 @@ Saudi Arabia
22.47 39.06 55.35
22.46 39.06 55.36
22.45 39.06 55.36
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22.42 39.06 55.38
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22.33 39.08 55.44
22.32 39.07 55.45
22.31 39.07 55.45
@@ -149154,29 +149449,29 @@ Saudi Arabia
22.07 39.02 55.60
22.06 39.00 55.61
22.05 39.00 55.62
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21.90 38.93 55.62
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21.86 38.95 55.61
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21.81 39.00 55.59
21.80 39.00 55.59
21.79 39.00 55.59
@@ -149208,23 +149503,23 @@ Saudi Arabia
21.53 39.09 55.50
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21.51 39.10 55.49
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21.46 39.14 55.47
21.45 39.15 55.47
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21.41 39.16 55.45
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21.36 39.12 55.44
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21.33 39.08 55.43
21.32 39.07 55.43
21.31 39.07 55.43
@@ -149248,10 +149543,10 @@ Saudi Arabia
21.13 39.14 55.36
21.12 39.15 55.36
21.11 39.15 55.36
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21.09 39.16 55.35
21.08 39.17 55.35
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21.06 39.20 55.34
21.05 39.21 55.34
21.04 39.22 55.34
@@ -149273,11 +149568,11 @@ Saudi Arabia
20.88 39.32 55.28
20.87 39.32 55.28
20.86 39.33 55.27
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20.83 39.37 55.26
20.82 39.38 55.26
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20.80 39.40 55.25
20.79 39.40 55.25
20.78 39.40 55.25
@@ -149287,8 +149582,8 @@ Saudi Arabia
20.74 39.42 55.23
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20.69 39.48 55.22
20.68 39.49 55.22
20.67 39.50 55.21
@@ -149327,18 +149622,18 @@ Saudi Arabia
20.34 39.75 55.11
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20.27 39.87 55.08
20.26 39.89 40.02 40.07 55.08
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20.24 39.93 39.95 40.10 55.07
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20.22 40.12 55.06
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20.19 40.14 55.05
20.18 40.17 55.05
20.17 40.20 55.05
@@ -149453,12 +149748,12 @@ Saudi Arabia
19.08 41.13 52.31
19.07 41.15 52.28
19.06 41.15 52.25
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19.04 41.15 52.18
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18.99 41.13 52.02
18.98 41.13 51.99
18.97 41.13 51.94
@@ -149476,8 +149771,8 @@ Saudi Arabia
18.85 41.19 51.06
18.84 41.21 50.98
18.83 41.22 50.90
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18.80 41.22 50.66
18.79 41.22 50.58
18.78 41.21 50.50
@@ -149506,7 +149801,7 @@ Saudi Arabia
18.55 41.34 49.03
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18.53 41.35 48.98
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18.51 41.36 48.94
18.50 41.38 48.92
18.49 41.40 48.90
@@ -149516,9 +149811,9 @@ Saudi Arabia
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18.44 41.42 48.79
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18.39 41.43 48.69
18.38 41.43 48.66
18.37 41.43 48.64
@@ -149534,7 +149829,7 @@ Saudi Arabia
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18.26 41.46 48.42
18.25 41.49 48.40
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18.23 41.48 48.36
18.22 41.48 48.34
18.21 41.48 48.32
@@ -149585,10 +149880,10 @@ Saudi Arabia
17.76 41.90 47.86
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17.69 42.00 47.80
17.68 42.01 47.79
17.67 42.02 47.78
@@ -149617,7 +149912,7 @@ Saudi Arabia
17.44 42.26 43.31 43.60 47.59
17.43 42.29 43.30 43.61 47.58
17.42 42.29 43.29 43.62 47.58
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17.40 42.30 43.26 43.64 44.61 45.19 47.57
17.39 42.30 43.25 43.65 44.36 44.49 44.58 45.22 47.57
17.38 42.30 43.23 43.66 44.14 44.18 44.27 45.24 47.56
@@ -149656,60 +149951,60 @@ Saudi Arabia
17.05 42.34 42.38 42.42 43.14 46.87 47.39
17.04 42.34 42.38 42.42 43.14 46.88 47.37
17.03 42.34 42.38 42.43 43.14 46.89 47.35
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17.01 41.83 41.91 42.35 42.37 42.51 43.14 46.90 47.32
17.00 41.83 41.93 42.51 43.14 46.91 47.31
16.99 41.83 41.93 42.53 43.14 46.92 47.29
16.98 41.83 41.94 42.53 43.14 46.93 47.27
16.97 41.89 41.94 42.53 43.14 46.94 47.26
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16.95 41.91 41.95 42.53 43.13 46.95 47.22
16.94 41.90 41.95 42.53 43.12 46.96 47.20
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16.48 42.75 42.98
16.47 42.76 42.94
16.46 42.77 42.91
@@ -149880,7 +150175,7 @@ Senegal
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15.13 -16.97 -12.72
15.12 -16.98 -12.71
15.11 -16.99 -12.69 -12.66 -12.61
@@ -149921,12 +150216,12 @@ Senegal
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14.67 -17.48 -17.41 -17.22 -12.17
14.66 -17.47 -17.41 -17.21 -12.17
14.65 -17.46 -17.42 -17.20 -12.15
@@ -149949,14 +150244,14 @@ Senegal
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14.37 -16.96 -12.12
14.36 -16.95 -12.10
14.35 -16.95 -12.09
@@ -149980,7 +150275,7 @@ Senegal
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14.12 -16.83 -11.98
14.11 -16.82 -11.98
@@ -150018,26 +150313,26 @@ Senegal
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13.55 -15.20 -15.06 -14.50 -14.00 -13.95 -11.98
13.54 -15.21 -15.05 -14.50 -14.03 -13.93 -11.96
@@ -150045,7 +150340,7 @@ Senegal
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13.47 -15.23 -14.92 -14.42 -14.24 -13.86 -11.88
13.46 -15.23 -14.86 -14.41 -14.26 -13.85 -11.87
@@ -150111,12 +150406,12 @@ Senegal
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12.76 -16.79 -11.39
12.75 -16.80 -11.39
@@ -150157,7 +150452,7 @@ Senegal
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12.39 -16.78 -16.30 -12.63 -11.93 -11.91 -11.65 -11.43 -11.37
12.38 -16.77 -16.32 -12.62 -12.10 -12.06 -11.94 -11.88 -11.67
- 12.37 -16.75 -16.34 -12.61 -12.12 -12.03 -11.96 -11.85 -11.70
+ 12.37 -16.76 -16.34 -12.61 -12.12 -12.03 -11.96 -11.85 -11.70
12.36 -16.75 -16.36 -12.60 -12.52 -12.45 -12.13
12.35 -16.75 -16.39 -12.60 -12.55 -12.43 -12.14
12.34 -16.74 -16.47 -12.41 -12.15
@@ -150168,9 +150463,9 @@ Senegal
12.29 -12.37 -12.33
Serbia
46.18 19.61 19.68
- 46.17 19.53 19.70 19.90 19.96
- 46.16 19.50 19.72 19.86 20.02 20.06 20.12
- 46.15 19.48 19.76 19.83 20.13 20.15 20.19
+ 46.17 19.53 19.71 19.90 19.96
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+ 46.15 19.49 19.76 19.83 20.13 20.15 20.19
46.14 19.47 20.21
46.13 19.47 20.22
46.12 19.47 20.24
@@ -150180,102 +150475,102 @@ Serbia
46.08 19.44 20.29
46.07 19.39 20.30
46.06 19.38 20.31
- 46.05 19.37 20.32
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46.04 19.36 20.32
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46.02 19.05 19.12 19.27 20.33
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45.98 19.03 20.37
45.97 18.99 20.40
45.96 18.97 20.42
45.95 18.96 20.44
45.94 18.89 18.94 18.96 20.46
45.93 18.89 20.48
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45.91 18.87 20.55
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45.89 18.86 20.58
45.88 18.86 20.59
45.87 18.88 20.59
45.86 18.84 20.60
45.85 18.84 20.62
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45.83 18.83 20.64
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45.81 18.83 20.65
45.80 18.83 20.65
45.79 18.83 20.65
45.78 18.85 20.66
45.77 18.86 20.67 20.74 20.78
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45.50 18.99 20.80
45.49 18.99 20.79
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45.47 18.98 20.83
45.46 18.98 20.84
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45.43 19.00 20.86
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45.40 18.96 20.90
45.39 18.96 20.92
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45.37 18.96 20.95
45.36 18.97 20.96
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45.34 19.01 21.00
45.33 19.08 21.03
45.32 19.08 21.05
45.31 19.08 21.08 21.11 21.15
45.30 19.08 21.09 21.11 21.16
45.29 19.09 21.17
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45.27 19.14 21.18
45.26 19.18 21.20
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45.24 19.28 21.23
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45.21 19.36 21.39
- 45.20 19.11 19.16 19.38 21.43
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45.19 19.11 19.17 19.39 21.45
- 45.18 19.11 19.18 19.26 19.30 19.39 21.46
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45.17 19.11 21.48
45.16 19.12 21.49
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45.14 19.03 21.50
45.13 19.03 21.50
45.12 19.03 21.50
45.11 19.03 21.50
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45.09 19.06 21.46
45.08 19.06 21.45
45.07 19.07 21.45
@@ -150285,20 +150580,20 @@ Serbia
45.03 19.08 21.43
45.02 19.08 21.43
45.01 19.08 21.42
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44.99 19.07 21.39
44.98 19.07 21.39
44.97 19.07 21.40
- 44.96 19.07 21.46
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44.95 19.10 21.50
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44.93 19.00 19.04 19.08 21.54
44.92 18.98 21.54
44.91 18.98 21.54
44.90 18.98 21.54
44.89 18.98 19.15 19.19 19.22 19.25 21.54
44.88 18.98 19.13 19.32 21.54
- 44.87 18.98 19.11 19.35 21.54
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44.86 18.99 19.09 19.35 21.51
44.85 19.00 19.03 19.35 21.38 21.42 21.47
44.84 19.34 21.36
@@ -150309,33 +150604,33 @@ Serbia
44.79 19.33 21.46 21.52 21.57
44.78 19.32 21.59
44.77 19.32 21.60
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44.75 19.31 21.61
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44.73 19.31 21.62 22.40 22.49
44.72 19.30 21.62 22.38 22.50
44.71 19.29 21.64 22.37 22.51
- 44.70 19.27 21.65 21.81 21.89 22.34 22.53
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44.64 19.23 22.02 22.26 22.71
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44.62 19.22 22.03 22.24 22.73
44.61 19.21 22.04 22.24 22.75
44.60 19.20 22.04 22.23 22.76
44.59 19.18 22.04 22.22 22.77
- 44.58 19.17 22.05 22.22 22.77
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44.57 19.17 22.06 22.21 22.77
44.56 19.17 22.08 22.20 22.77
44.55 19.17 22.08 22.19 22.76
- 44.54 19.16 22.09 22.19 22.58 22.64 22.75
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44.53 19.14 22.09 22.18 22.57 22.66 22.73
- 44.52 19.12 22.10 22.17 22.56
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44.51 19.11 22.56
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44.49 19.11 22.54
44.48 19.11 22.49
44.47 19.12 22.48
@@ -150353,7 +150648,7 @@ Serbia
44.35 19.09 22.56
44.34 19.09 22.58
44.33 19.10 22.61
- 44.32 19.10 22.67
+ 44.32 19.10 22.68
44.31 19.11 22.69
44.30 19.11 22.69
44.29 19.12 22.69
@@ -150365,7 +150660,7 @@ Serbia
44.23 19.33 22.70
44.22 19.33 22.70
44.21 19.34 22.70
- 44.20 19.34 22.66
+ 44.20 19.34 22.67
44.19 19.34 22.65
44.18 19.35 22.64
44.17 19.36 22.63
@@ -150374,8 +150669,8 @@ Serbia
44.14 19.41 22.61
44.13 19.42 22.61
44.12 19.46 22.60
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44.09 19.49 22.61
44.08 19.50 22.61
44.07 19.51 22.61
@@ -150417,9 +150712,9 @@ Serbia
43.71 19.47 22.40
43.70 19.47 22.40
43.69 19.48 22.41
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43.65 19.49 22.47
43.64 19.48 22.48
43.63 19.47 22.48
@@ -150438,8 +150733,8 @@ Serbia
43.50 19.16 22.51
43.49 19.16 22.51
43.48 19.16 22.53
- 43.47 19.16 22.56
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43.45 19.17 22.58
43.44 19.18 22.59
43.43 19.19 22.65
@@ -150452,92 +150747,92 @@ Serbia
43.36 19.37 22.78
43.35 19.38 22.79
43.34 19.38 22.80
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43.32 19.40 22.82
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43.30 19.43 22.83
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43.28 19.46 22.84
43.27 19.47 22.85
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43.25 19.48 22.88
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43.23 19.50 20.74 20.82 22.91
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43.20 19.53 20.69 20.82 22.99
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43.18 19.56 20.61 20.82 22.99
43.17 19.57 20.61 20.82 22.99
43.16 19.58 20.62 20.82 22.99
43.15 19.60 20.62 20.84 22.99
- 43.14 19.64 20.63 20.86 22.98
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43.13 19.71 20.63 20.88 22.98
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43.10 19.74 20.67 20.95 22.97
43.09 19.75 19.90 19.92 20.67 20.97 22.96
43.08 19.77 19.89 19.93 20.67 20.99 22.95
- 43.07 19.81 19.86 19.93 20.67 21.09 22.94
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43.06 19.94 20.66 21.10 22.92
43.05 19.96 20.66 21.10 22.91
43.04 19.98 20.65 21.11 22.90
43.03 20.00 20.64 21.11 22.89
43.02 20.02 20.63 21.11 22.89
- 43.01 20.03 20.62 21.11 22.88
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42.96 20.10 20.54 21.21 22.78
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42.94 20.20 20.47 21.21 22.77
42.93 20.22 20.46 21.21 22.77
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42.91 20.26 20.48 21.22 22.76
42.90 20.28 20.49 21.22 22.75
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42.88 20.34 20.50 21.24 22.74
42.87 20.34 20.50 21.25 22.73
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42.83 20.33 20.45 21.39 22.49
42.82 20.33 20.41 21.39 22.46
42.81 20.33 20.37 21.39 22.44
42.80 21.39 22.44
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42.78 21.38 22.45
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42.76 21.37 22.46
42.75 21.36 22.48
42.74 21.36 22.49
42.73 21.36 22.49
42.72 21.37 22.49
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42.70 21.57 22.48
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42.67 21.60 22.45
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42.65 21.75 22.45
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42.60 21.70 22.44
42.59 21.70 22.44
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42.57 21.70 22.45
42.56 21.70 22.46
42.55 21.69 22.48
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42.53 21.68 22.51
42.52 21.67 22.52
42.51 21.66 22.53
42.50 21.65 22.54
42.49 21.64 22.54
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42.47 21.61 22.54
42.46 21.61 22.54
42.45 21.60 22.54
@@ -150547,83 +150842,92 @@ Serbia
42.41 21.60 22.52
42.40 21.61 22.52
42.39 21.60 22.51
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42.36 21.52 22.46
42.35 21.50 22.45
42.34 21.50 22.45
42.33 21.50 22.24 22.26 22.44
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42.28 21.52 21.80
42.27 21.53 21.78
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42.23 21.55 21.70
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Seychelles
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-6.98 52.73 52.75
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@@ -150652,18 +150956,18 @@ Seychelles
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+ -9.73 46.46 46.51
-9.74 46.46 46.51
-9.75 46.46 46.51
- -9.76 46.47 46.50
+ -9.76 46.46 46.50
Sierra Leone
10.00 -11.92 -11.22
9.99 -11.92 -11.18
@@ -150674,7 +150978,7 @@ Sierra Leone
9.94 -11.92 -11.16
9.93 -12.30 -12.23 -11.95 -11.16
9.92 -12.35 -12.21 -11.99 -11.16
- 9.91 -12.40 -12.20 -12.03 -11.16
+ 9.91 -12.40 -12.20 -12.04 -11.16
9.90 -12.45 -12.19 -12.08 -11.15
9.89 -12.48 -12.17 -12.12 -11.15
9.88 -12.50 -11.15
@@ -150781,20 +151085,20 @@ Sierra Leone
8.87 -13.16 -10.59
8.86 -13.22 -13.18 -13.14 -10.59
8.85 -13.23 -10.58
- 8.84 -13.23 -10.58
- 8.83 -13.24 -10.58
- 8.82 -13.24 -10.58
- 8.81 -13.24 -10.57
- 8.80 -13.24 -10.56
- 8.79 -13.24 -10.55
- 8.78 -13.24 -10.55
- 8.77 -13.24 -10.54
- 8.76 -13.24 -10.53
+ 8.84 -13.24 -10.58
+ 8.83 -13.25 -10.58
+ 8.82 -13.25 -10.58
+ 8.81 -13.25 -10.57
+ 8.80 -13.25 -10.56
+ 8.79 -13.25 -10.55
+ 8.78 -13.25 -10.55
+ 8.77 -13.25 -10.54
+ 8.76 -13.25 -10.53
8.75 -13.24 -10.53
8.74 -13.24 -10.52
8.73 -13.24 -10.51
- 8.72 -13.24 -10.50
- 8.71 -13.24 -10.49
+ 8.72 -13.25 -10.50
+ 8.71 -13.25 -10.49
8.70 -13.25 -10.49
8.69 -13.25 -10.48
8.68 -13.25 -10.47
@@ -150834,9 +151138,9 @@ Sierra Leone
8.34 -13.23 -10.61 -10.52 -10.29
8.33 -13.23 -10.60 -10.54 -10.29
8.32 -13.22 -10.58 -10.56 -10.29
- 8.31 -13.20 -10.30
+ 8.31 -13.21 -10.30
8.30 -13.20 -10.30
- 8.29 -13.19 -10.30
+ 8.29 -13.20 -10.30
8.28 -13.19 -10.31
8.27 -13.18 -10.31
8.26 -13.17 -10.32
@@ -150844,8 +151148,8 @@ Sierra Leone
8.24 -13.17 -10.32
8.23 -13.17 -10.31
8.22 -13.17 -10.31
- 8.21 -13.17 -13.06 -12.99 -10.30
- 8.20 -13.17 -13.08 -12.99 -10.30
+ 8.21 -13.17 -13.07 -12.99 -10.30
+ 8.20 -13.17 -13.09 -12.99 -10.30
8.19 -13.17 -13.10 -12.99 -10.30
8.18 -13.17 -13.11 -12.99 -10.30
8.17 -13.17 -13.13 -12.99 -10.31
@@ -150888,7 +151192,7 @@ Sierra Leone
7.80 -12.87 -10.60
7.79 -12.85 -10.60
7.78 -12.83 -10.60
- 7.77 -12.79 -10.60
+ 7.77 -12.80 -10.60
7.76 -12.79 -10.60
7.75 -12.79 -10.60
7.74 -12.78 -10.64
@@ -150901,16 +151205,16 @@ Sierra Leone
7.67 -12.61 -12.57 -12.55 -10.74
7.66 -12.55 -10.74
7.65 -12.55 -10.75
- 7.64 -12.70 -12.58 -12.55 -10.76
+ 7.64 -12.70 -12.57 -12.55 -10.76
7.63 -12.86 -12.57 -12.54 -10.77
- 7.62 -12.90 -12.57 -12.53 -10.78
- 7.61 -12.90 -10.79
- 7.60 -12.91 -10.79
+ 7.62 -12.90 -12.57 -12.52 -10.78
+ 7.61 -12.91 -10.78
+ 7.60 -12.92 -10.79
7.59 -12.93 -10.80
7.58 -12.96 -10.81
7.57 -12.96 -10.82
7.56 -12.96 -10.83
- 7.55 -12.96 -10.84
+ 7.55 -12.96 -10.83
7.54 -12.93 -12.49 -12.45 -10.84
7.53 -12.87 -12.48 -12.45 -10.85
7.52 -12.82 -12.48 -12.45 -10.86
@@ -150933,7 +151237,7 @@ Sierra Leone
7.35 -12.46 -11.11
7.34 -12.43 -11.12
7.33 -12.39 -11.13
- 7.32 -12.36 -11.13
+ 7.32 -12.36 -11.14
7.31 -12.33 -11.14
7.30 -12.30 -11.15
7.29 -12.27 -11.16
@@ -150978,7 +151282,7 @@ Sierra Leone
6.90 -11.48 -11.46
Singapore
1.45 103.77 103.85
- 1.44 103.70 103.73 103.75 103.87
+ 1.44 103.70 103.87
1.43 103.68 103.90
1.42 103.68 103.92
1.41 103.67 103.95
@@ -151001,12 +151305,12 @@ Singapore
Sint Maarten
18.07 -63.11 -63.08
18.06 -63.12 -63.06
- 18.05 -63.12 -63.03
+ 18.05 -63.12 -63.02
18.04 -63.12 -63.00
18.03 -63.12 -63.00
18.02 -63.10 -63.00
- 18.01 -63.08 -63.00
- 18.00 -63.04 -63.01
+ 18.01 -63.08 -63.01
+ 18.00 -63.05 -63.02
Slovakia
49.61 19.42 19.45
49.60 19.42 19.46
@@ -151026,7 +151330,7 @@ Slovakia
49.46 18.51 18.96 19.19 19.57
49.45 18.50 18.96 19.17 19.64 21.23 21.29
49.44 18.48 18.97 19.17 19.64 21.22 21.32
- 49.43 18.47 18.97 19.17 19.64 21.08 21.14 21.21 21.36 21.50 21.63
+ 49.43 18.47 18.97 19.17 19.64 21.08 21.14 21.21 21.36 21.51 21.63
49.42 18.45 18.97 19.16 19.64 21.04 21.15 21.20 21.40 21.46 21.64
49.41 18.43 18.97 19.03 19.09 19.15 19.64 20.41 20.45 20.59 20.63 20.65 20.69 21.03 21.70
49.40 18.42 18.96 19.01 19.67 19.74 19.77 20.30 20.35 20.41 20.48 20.58 20.70 21.02 21.71
@@ -151085,7 +151389,7 @@ Slovakia
48.87 17.18 17.24 17.70 22.42
48.86 17.14 17.28 17.66 22.41
48.85 17.12 17.31 17.43 17.46 17.62 22.39
- 48.84 17.10 17.33 17.40 17.47 17.58 22.37
+ 48.84 17.10 17.33 17.40 17.47 17.58 22.38
48.83 17.09 17.36 17.38 17.49 17.54 22.37
48.82 17.09 22.37
48.81 17.08 22.37
@@ -151114,7 +151418,7 @@ Slovakia
48.58 16.93 22.18
48.57 16.93 22.16
48.56 16.94 22.15
- 48.55 16.94 22.14
+ 48.55 16.93 22.14
48.54 16.93 20.75 20.81 21.40 21.42 22.14
48.53 16.92 20.68 20.83 21.36 21.45 22.14
48.52 16.90 20.61 20.89 21.32 21.48 22.15
@@ -151159,14 +151463,14 @@ Slovakia
48.13 16.99 19.50 19.76 19.81 19.84 19.96
48.12 17.01 19.49 19.86 19.94
48.11 17.04 19.49 19.87 19.92
- 48.10 17.04 19.49
+ 48.10 17.05 19.49
48.09 17.05 19.48
48.08 17.05 19.46
48.07 17.04 19.44
48.06 17.04 19.28
48.05 17.04 19.07 19.15 19.25
- 48.04 17.05 18.95
- 48.03 17.05 18.87
+ 48.04 17.05 18.96
+ 48.03 17.05 18.89
48.02 17.05 18.83
48.01 17.07 18.82
48.00 17.10 17.18 17.20 18.82
@@ -151193,12 +151497,12 @@ Slovakia
47.79 17.64 18.75
47.78 17.65 18.74
47.77 17.66 18.50 18.60 18.72
- 47.76 17.68 18.40 18.62 18.71
+ 47.76 17.69 18.40 18.62 18.71
47.75 17.72 18.33
- 47.74 17.78 17.97 18.17 18.29
+ 47.74 17.78 18.00 18.17 18.29
Slovenia
- 46.87 16.08 16.12 16.20 16.28
- 46.86 16.06 16.30
+ 46.87 16.08 16.12 16.22 16.28
+ 46.86 16.06 16.29
46.85 16.04 16.32
46.84 15.97 16.33
46.83 15.96 16.33
@@ -151219,8 +151523,8 @@ Slovenia
46.68 15.53 16.41
46.67 15.52 16.42
46.66 15.52 16.42
- 46.65 15.03 15.14 15.29 15.40 15.51 16.42
- 46.64 14.99 15.43 15.50 16.41
+ 46.65 15.03 15.19 15.26 15.40 15.51 16.42
+ 46.64 14.99 15.43 15.50 16.40
46.63 14.92 14.94 14.98 15.46 15.50 16.39
46.62 14.90 16.42
46.61 14.84 16.44
@@ -151231,7 +151535,7 @@ Slovenia
46.56 14.80 16.50
46.55 14.80 16.51
46.54 14.79 16.51
- 46.53 14.78 16.51
+ 46.53 14.79 16.51
46.52 13.69 13.75 13.82 13.91 14.78 16.52
46.51 13.68 13.94 14.77 16.31 16.42 16.52
46.50 13.67 13.97 14.69 16.28 16.43 16.52
@@ -151239,9 +151543,9 @@ Slovenia
46.48 13.67 14.09 14.67 16.24
46.47 13.67 14.11 14.65 16.24
46.46 13.66 14.13 14.65 16.24
- 46.45 13.59 14.26 14.37 14.40 14.62 16.25
+ 46.45 13.59 14.20 14.37 14.40 14.62 16.25
46.44 13.57 14.42 14.58 16.25
- 46.43 13.56 14.44 14.57 16.26
+ 46.43 13.56 14.43 14.57 16.26
46.42 13.55 14.51 14.56 16.26
46.41 13.54 14.52 14.55 16.26
46.40 13.53 14.52 14.55 16.28
@@ -151255,12 +151559,12 @@ Slovenia
46.32 13.39 16.06
46.31 13.37 16.06
46.30 13.35 16.06
- 46.29 13.35 16.05
+ 46.29 13.35 16.04
46.28 13.35 16.03
46.27 13.36 15.99
- 46.26 13.36 15.94
- 46.25 13.36 15.92
- 46.24 13.36 15.90
+ 46.26 13.36 15.93
+ 46.25 13.36 15.91
+ 46.24 13.36 15.89
46.23 13.37 15.80
46.22 13.38 15.78
46.21 13.38 15.78
@@ -151275,11 +151579,11 @@ Slovenia
46.12 13.58 15.59
46.11 13.56 15.60
46.10 13.54 15.61
- 46.09 13.52 15.63
- 46.08 13.50 15.64
+ 46.09 13.52 15.62
+ 46.08 13.51 15.64
46.07 13.49 15.66
46.06 13.48 15.69
- 46.05 13.47 15.69
+ 46.05 13.47 15.70
46.04 13.47 15.70
46.03 13.47 15.70
46.02 13.46 15.70
@@ -151293,7 +151597,7 @@ Slovenia
45.94 13.60 15.68
45.93 13.59 15.68
45.92 13.58 15.68
- 45.91 13.58 15.68
+ 45.91 13.57 15.68
45.90 13.57 15.68
45.89 13.56 15.67
45.88 13.56 15.67
@@ -151303,15 +151607,15 @@ Slovenia
45.84 13.55 15.68
45.83 13.55 15.68
45.82 13.55 15.67
- 45.81 13.56 15.66
- 45.80 13.56 15.51 15.55 15.61
+ 45.81 13.55 15.66
+ 45.80 13.56 15.51 15.56 15.61
45.79 13.57 15.45
45.78 13.59 15.45
45.77 13.66 15.45
45.76 13.68 15.44
- 45.75 13.69 15.41
- 45.74 13.71 15.37
- 45.73 13.75 15.33
+ 45.75 13.69 15.40
+ 45.74 13.71 15.36
+ 45.73 13.75 15.32
45.72 13.77 15.29
45.71 13.78 15.26
45.70 13.78 15.27
@@ -151323,28 +151627,29 @@ Slovenia
45.64 13.83 14.56 14.58 15.38
45.63 13.84 14.56 14.58 15.38
45.62 13.87 14.55 14.58 15.35
- 45.61 13.86 14.54 14.58 15.31
+ 45.61 13.85 14.54 14.58 15.31
45.60 13.70 13.79 13.84 14.53 14.58 15.30
45.59 13.70 14.51 14.59 15.29
45.58 13.70 14.50 14.60 15.29
45.57 13.71 14.50 14.62 15.29
45.56 13.71 14.50 14.64 15.29
- 45.55 13.63 14.49 14.65 15.29
+ 45.55 13.62 14.50 14.65 15.29
45.54 13.55 14.49 14.65 15.29
45.53 13.55 14.49 14.65 15.30
45.52 13.55 14.48 14.65 15.31
45.51 13.56 14.47 14.67 15.33
45.50 13.57 14.46 14.69 15.35
45.49 13.57 14.44 14.73 14.91 14.93 15.37
- 45.48 13.58 13.99 14.03 14.42 14.76 14.91 14.95 15.37
- 45.47 13.58 13.99 14.05 14.18 14.26 14.41 14.77 14.90 14.98 15.37
- 45.46 13.59 13.99 14.07 14.16 14.30 14.39 14.78 14.90 15.02 15.36
+ 45.48 13.57 13.99 14.03 14.42 14.76 14.91 14.95 15.37
+ 45.47 13.57 13.99 14.05 14.18 14.26 14.41 14.77 14.90 14.98 15.37
+ 45.46 13.58 13.99 14.07 14.16 14.30 14.39 14.78 14.90 15.02 15.36
45.45 13.60 13.98 14.78 14.89 15.06 15.35
- 45.44 13.61 13.69 13.76 13.96 14.81 14.86 15.08 15.34
+ 45.44 13.61 13.71 13.76 13.96 14.81 14.86 15.08 15.34
45.43 13.78 13.94 15.10 15.27
45.42 13.80 13.92 15.12 15.24
- 45.41 13.82 13.90 15.15 15.20
+ 45.41 13.82 13.90 15.15 15.21
Solomon Islands
+ -6.58 156.49 156.52
-6.59 156.47 156.54
-6.60 156.46 156.55
-6.61 156.45 156.57
@@ -151367,11 +151672,11 @@ Solomon Islands
-6.78 156.49 156.85
-6.79 156.50 156.86
-6.80 156.06 156.10 156.51 156.88
- -6.81 156.05 156.10 156.52 156.90
- -6.82 156.04 156.10 156.54 156.92
- -6.83 156.04 156.10 156.55 156.95
+ -6.81 156.04 156.10 156.52 156.90
+ -6.82 156.03 156.10 156.54 156.92
+ -6.83 156.03 156.10 156.55 156.95
-6.84 156.03 156.08 156.56 156.98
- -6.85 156.03 156.09 156.57 157.00
+ -6.85 156.03 156.08 156.57 157.00
-6.86 156.03 156.11 156.58 157.01
-6.87 156.03 156.11 156.61 157.01
-6.88 156.04 156.11 156.63 157.05
@@ -151410,7 +151715,7 @@ Solomon Islands
-7.21 156.91 157.29
-7.22 156.92 157.29
-7.23 156.93 157.30
- -7.24 156.96 157.30
+ -7.24 156.98 157.30
-7.25 156.99 157.31
-7.26 157.00 157.33
-7.27 157.00 157.36
@@ -151418,20 +151723,20 @@ Solomon Islands
-7.29 157.00 157.04 157.07 157.41 157.47 157.52
-7.30 157.07 157.53
-7.31 155.53 155.58 157.08 157.53
- -7.32 155.52 155.59 157.08 157.54
- -7.33 155.51 155.60 157.09 157.54
- -7.34 155.50 155.61 157.09 157.54
- -7.35 155.50 155.62 157.10 157.14 157.21 157.54
- -7.36 155.49 155.62 157.23 157.54
- -7.37 155.49 155.62 157.25 157.54 157.71 157.74
+ -7.32 155.52 155.59 157.08 157.53
+ -7.33 155.51 155.60 157.09 157.53
+ -7.34 155.50 155.61 157.09 157.53
+ -7.35 155.50 155.62 157.10 157.14 157.21 157.53
+ -7.36 155.49 155.62 157.23 157.53
+ -7.37 155.49 155.62 157.25 157.53 157.71 157.74
-7.38 155.49 155.61 157.26 157.28 157.30 157.59 157.70 157.76 158.24 158.27
-7.39 155.51 155.60 157.30 157.62 157.69 157.78 158.22 158.27
-7.40 157.31 157.62 157.68 157.78 158.19 158.29
-7.41 157.36 157.62 157.67 157.78 158.19 158.29
- -7.42 157.41 157.62 157.67 157.79 158.18 158.29
+ -7.42 157.41 157.62 157.67 157.78 158.18 158.29
-7.43 157.43 157.46 157.52 157.62 157.66 157.79 158.18 158.28
- -7.44 157.43 157.45 157.53 157.62 157.66 157.80 158.18 158.28
- -7.45 157.53 157.62 157.66 157.80 158.21 158.28
+ -7.44 157.43 157.45 157.53 157.62 157.66 157.79 158.18 158.28
+ -7.45 157.53 157.62 157.66 157.79 158.21 158.28
-7.46 157.53 157.62 157.68 157.80 158.21 158.30
-7.47 157.69 157.80 158.22 158.33
-7.48 157.70 157.80 158.23 158.34
@@ -151453,8 +151758,8 @@ Solomon Islands
-7.64 156.49 156.68 158.35 158.81
-7.65 156.48 156.69 158.39 158.43 158.47 158.82
-7.66 156.48 156.72 158.48 158.53 158.56 158.83
- -7.67 156.48 156.72 158.49 158.52 158.57 158.83
- -7.68 156.48 156.76 158.57 158.84
+ -7.67 156.48 156.72 158.57 158.83
+ -7.68 156.48 156.77 158.57 158.84
-7.69 156.48 156.78 158.57 158.85
-7.70 156.49 156.80 158.57 158.86
-7.71 156.49 156.81 158.57 158.87
@@ -151469,17 +151774,17 @@ Solomon Islands
-7.80 156.50 156.56 156.58 156.78 158.63 158.99
-7.81 156.50 156.56 156.60 156.78 158.64 158.99
-7.82 156.50 156.56 156.60 156.77 158.67 159.00
- -7.83 156.52 156.55 156.59 156.76 158.69 159.03
- -7.84 156.59 156.75 157.04 157.11 158.70 159.05
+ -7.83 156.52 156.55 156.59 156.76 158.69 159.04
+ -7.84 156.59 156.75 157.04 157.11 158.70 159.06
-7.85 156.59 156.74 157.01 157.13 158.70 159.07
-7.86 156.59 156.72 156.99 157.14 158.70 159.07 160.60 160.63
- -7.87 156.59 156.72 156.97 157.15 158.71 159.08 160.59 160.63
- -7.88 156.60 156.71 156.97 157.16 158.71 159.10 160.59 160.64
- -7.89 156.63 156.72 156.97 157.17 158.72 159.20 160.59 160.64
- -7.90 156.64 156.72 156.96 157.18 158.76 159.21 160.59 160.65
- -7.91 156.64 156.73 156.96 157.18 158.76 159.21 160.60 160.65
- -7.92 156.54 156.56 156.64 156.73 156.95 157.19 158.77 159.23 160.61 160.65
- -7.93 156.52 156.56 156.64 156.73 156.95 157.19 158.79 159.25 160.62 160.65
+ -7.87 156.59 156.72 156.97 157.16 158.71 159.08 160.59 160.63
+ -7.88 156.60 156.71 156.97 157.17 158.71 159.10 160.59 160.64
+ -7.89 156.63 156.72 156.97 157.18 158.72 159.20 160.59 160.64
+ -7.90 156.64 156.72 156.96 157.18 158.75 159.21 160.59 160.65
+ -7.91 156.64 156.73 156.96 157.19 158.75 159.21 160.60 160.65
+ -7.92 156.53 156.55 156.64 156.73 156.95 157.19 158.77 159.23 160.61 160.65
+ -7.93 156.52 156.56 156.64 156.73 156.95 157.20 158.79 159.25 160.62 160.65
-7.94 156.52 156.57 156.64 156.73 156.94 157.20 157.49 157.51 158.83 159.28
-7.95 156.52 156.58 156.68 156.72 156.93 157.20 157.46 157.51 158.83 159.29
-7.96 156.52 156.59 156.93 157.20 157.43 157.53 158.83 159.30 159.34 159.37
@@ -151490,30 +151795,30 @@ Solomon Islands
-8.01 156.53 156.61 156.94 157.21 157.38 157.61 158.89 159.43
-8.02 156.53 156.61 156.95 157.21 157.37 157.61 158.92 159.44
-8.03 156.53 156.61 156.95 157.21 157.36 157.61 158.93 159.46
- -8.04 156.52 156.62 156.78 156.82 156.96 157.21 157.35 157.61 158.93 159.48
- -8.05 156.52 156.62 156.78 156.83 156.96 157.21 157.35 157.62 158.93 159.49
+ -8.04 156.52 156.62 156.77 156.82 156.96 157.21 157.35 157.61 158.93 159.48
+ -8.05 156.52 156.62 156.77 156.83 156.96 157.21 157.35 157.62 158.93 159.49
-8.06 156.52 156.62 156.77 156.83 156.97 157.21 157.34 157.62 158.97 159.51
- -8.07 156.52 156.62 156.77 156.84 156.98 157.20 157.34 157.62 158.99 159.52
- -8.08 156.52 156.62 156.77 156.84 156.98 157.20 157.33 157.62 158.99 159.53
- -8.09 156.52 156.62 156.77 156.85 156.99 157.20 157.32 157.62 159.00 159.54
+ -8.07 156.52 156.62 156.77 156.84 156.98 157.20 157.34 157.62 158.99 159.51
+ -8.08 156.52 156.62 156.77 156.84 156.98 157.20 157.33 157.62 158.99 159.52
+ -8.09 156.52 156.62 156.77 156.85 156.99 157.20 157.32 157.62 158.99 159.54
-8.10 156.52 156.62 156.78 156.85 157.00 157.19 157.31 157.62 159.04 159.55
-8.11 156.53 156.62 156.79 156.85 157.01 157.19 157.31 157.62 159.07 159.56
-8.12 156.54 156.62 156.80 156.85 157.03 157.18 157.31 157.62 159.07 159.58
- -8.13 156.54 156.62 157.04 157.18 157.31 157.62 159.12 159.59
+ -8.13 156.54 156.62 157.04 157.18 157.31 157.62 159.11 159.59
-8.14 156.55 156.62 157.08 157.17 157.31 157.62 159.13 159.61
- -8.15 156.55 156.62 157.08 157.17 157.31 157.62 159.15 159.62
+ -8.15 156.55 156.62 157.08 157.17 157.31 157.62 159.14 159.62
-8.16 156.55 156.62 157.08 157.18 157.28 157.63 159.16 159.64
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@@ -151878,8 +152186,8 @@ Somalia
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@@ -151954,34 +152262,34 @@ Somalia
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@@ -152010,8 +152318,8 @@ Somalia
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@@ -152119,12 +152427,12 @@ Somalia
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@@ -152132,15 +152440,15 @@ Somalia
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@@ -152148,18 +152456,18 @@ Somalia
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@@ -152258,24 +152566,24 @@ Somalia
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@@ -152406,23 +152714,23 @@ Somalia
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@@ -152450,11 +152758,11 @@ Somalia
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@@ -152584,7 +152892,7 @@ Somalia
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@@ -152598,7 +152906,7 @@ Somalia
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@@ -152655,7 +152963,7 @@ Somalia
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@@ -152733,13 +153041,13 @@ Somalia
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@@ -152790,37 +153098,37 @@ Somalia
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@@ -152889,8 +153197,8 @@ Somalia
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@@ -153047,17 +153355,17 @@ Somalia
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@@ -153066,16 +153374,16 @@ Somalia
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@@ -153118,8 +153426,8 @@ Somalia
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@@ -153187,33 +153495,33 @@ Somalia
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11.15 43.01 43.58 47.29 47.61 48.14 48.94
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10.71 42.70 43.96 45.50 46.36 46.46 48.94
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South Georgia and the South Sandwich Islands
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@@ -155166,32 +155453,32 @@ South Korea
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@@ -155261,196 +155548,196 @@ South Korea
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34.28 126.01 126.09 126.51 126.56 126.69 126.78
34.27 126.01 126.09 126.72 126.77
34.26 126.05 126.07
@@ -155480,44 +155767,45 @@ South Korea
34.01 127.27 127.33
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South Sudan
12.22 32.71 33.21
@@ -155541,7 +155829,7 @@ South Sudan
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@@ -155644,29 +155932,29 @@ South Sudan
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@@ -155693,54 +155981,54 @@ South Sudan
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@@ -155784,7 +156072,7 @@ South Sudan
9.61 24.78 26.49 27.06 27.57 27.62 27.68 28.99 33.89
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@@ -155807,8 +156095,8 @@ South Sudan
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4.54 27.82 29.42 29.77 34.32
@@ -156352,13 +156640,13 @@ South Sudan
3.93 30.23 33.71
3.92 30.28 33.70
3.91 30.31 33.69
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3.83 30.52 32.94 33.04 33.61
3.82 30.52 32.92 33.05 33.60
3.81 30.52 32.91 33.06 33.59
@@ -156367,8 +156655,8 @@ South Sudan
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3.77 30.53 31.16 31.23 31.75 31.82 32.83 33.12 33.55
3.76 30.53 31.14 31.27 31.74 31.83 32.80 33.13 33.54
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3.73 30.54 31.10 31.33 31.72 31.85 32.51 33.36 33.50
3.72 30.54 31.08 31.34 31.71 31.86 32.40
3.71 30.54 31.06 31.36 31.70 31.87 32.37
@@ -156387,7 +156675,7 @@ South Sudan
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3.54 30.81 30.88 32.04 32.18
3.53 30.81 30.87 32.05 32.18
3.52 30.81 30.87 32.06 32.18
@@ -156396,117 +156684,116 @@ South Sudan
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42.69 -9.04 0.26 0.29 1.37
42.68 -9.04 1.37
@@ -156533,100 +156820,100 @@ Spain
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@@ -157189,16 +157477,22 @@ Spain
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Spain: Canary Islands
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@@ -157219,8 +157513,8 @@ Spain: Canary Islands
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@@ -157357,11 +157651,11 @@ Spain: Canary Islands
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27.65 -18.04 -17.95
@@ -157483,24 +157777,24 @@ Sri Lanka
9.83 79.97 80.03 80.08 80.12 80.14 80.26
9.82 79.96 80.27
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9.69 79.83 79.90 79.93 80.35
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9.62 79.86 79.98 80.03 80.42
9.61 79.87 79.98 80.05 80.44
9.60 79.88 79.92 79.94 79.98 80.04 80.46
@@ -157541,7 +157835,7 @@ Sri Lanka
9.25 80.10 80.84
9.24 80.10 80.84
9.23 80.10 80.85
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Sudan
22.23 31.39 31.46
22.22 31.37 31.47
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15.71 23.08 23.25 23.42 23.93 23.96 36.68
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10.41 23.29 31.84 33.60 34.30
10.40 23.29 31.83 33.61 34.30
10.39 23.30 25.81 25.84 31.83 33.62 34.30
- 10.38 23.30 25.78 25.85 31.82 33.64 34.30
- 10.37 23.31 25.68 25.85 31.82 33.65 34.31
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10.36 23.32 25.61 25.86 31.81 33.66 34.31
- 10.35 23.32 25.57 25.87 31.80 33.68 34.31
- 10.34 23.33 25.55 25.88 31.79 33.69 34.31
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10.32 23.34 25.41 25.88 31.77 33.71 34.32
- 10.31 23.35 25.39 25.88 31.76 33.73 34.32
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10.29 23.36 25.18 25.88 31.75 33.75 34.33
10.28 23.37 25.10 25.88 31.74 33.76 34.33
- 10.27 23.37 25.08 25.88 31.73 33.78 34.33
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10.26 23.38 25.07 25.88 31.72 33.79 34.33
- 10.25 23.39 25.07 25.89 31.71 33.80 34.33
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10.24 23.39 25.06 25.89 29.99 30.03 31.70 33.81 34.33
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10.22 23.40 25.05 25.89 29.96 30.06 31.69 33.84 34.33
- 10.21 23.41 25.05 25.89 29.94 30.08 31.68 33.85 34.33
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10.20 23.42 25.04 25.89 29.92 30.09 31.67 33.86 34.33
- 10.19 23.42 25.04 25.89 29.90 30.11 31.66 33.88 34.33
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10.18 23.43 25.03 25.89 29.88 30.12 31.65 33.89 34.32
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10.16 23.44 25.02 25.90 29.84 30.15 31.63 33.90 34.32
10.15 23.45 25.02 25.90 29.82 30.17 31.62 33.90 34.31
- 10.14 23.45 25.02 25.92 29.80 30.19 31.61 33.91 34.31
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10.13 23.46 25.02 25.94 29.78 30.20 31.60 33.91 34.31
- 10.12 23.47 25.03 25.98 29.76 30.22 31.59 33.92 34.31
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10.11 23.47 25.03 25.99 29.74 30.23 31.58 33.92 34.31
- 10.10 23.48 25.03 26.00 29.72 30.25 31.57 33.93 34.31
- 10.09 23.49 25.03 26.01 29.70 30.26 31.56 33.93 34.30
- 10.08 23.49 25.03 26.01 29.68 30.28 31.55 33.94 34.30
- 10.07 23.50 25.03 26.02 29.66 30.29 31.54 33.94 34.29
- 10.06 23.50 25.03 26.02 29.64 30.31 31.53 33.95 34.28
- 10.05 23.51 25.02 26.03 29.63 30.33 31.52 33.95 34.27
- 10.04 23.52 25.02 26.04 29.62 30.34 31.51 33.95 34.26
- 10.03 23.52 25.02 26.04 29.62 30.36 31.50 33.95 34.25
- 10.02 23.53 25.01 26.05 29.62 30.37 31.49 33.95 34.24
- 10.01 23.54 25.01 26.05 29.62 30.39 31.48 33.95 34.23
- 10.00 23.54 25.00 26.06 29.62 30.40 31.47 33.95 34.23
- 9.99 23.55 25.00 26.07 29.62 30.42 31.46 33.95 34.22
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9.98 23.55 25.00 26.08 29.62 30.44 31.44 33.95 34.22
9.97 23.56 24.99 26.09 29.62 30.45 31.43 33.94 34.22
9.96 23.57 24.99 26.11 29.62 30.47 31.42 33.94 34.21
9.95 23.57 24.98 26.13 29.62 30.48 31.41 33.94 34.21
9.94 23.58 24.97 26.15 29.62 30.49 31.40 33.94 34.20
- 9.93 23.59 24.96 26.17 29.62 30.50 31.39 33.94 34.20
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9.92 23.59 24.95 26.18 29.62 30.51 31.38 33.94 34.20
9.91 23.60 24.95 26.19 29.62 30.52 31.37 33.94 34.19
- 9.90 23.60 24.94 26.20 29.62 30.53 31.36 33.94 34.19
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9.89 23.61 24.93 26.20 29.61 30.55 31.35 33.94 34.19
9.88 23.61 24.92 26.21 29.61 30.56 31.34 33.94 34.18
9.87 23.62 24.91 26.22 29.60 30.57 31.33 33.95 34.18
9.86 23.62 24.90 26.23 29.59 30.58 31.32 33.95 34.17
9.85 23.63 24.88 26.24 29.58 30.59 31.31 33.96 34.17
9.84 23.63 24.87 26.25 29.58 30.60 31.30 33.95 34.17
- 9.83 23.63 24.85 26.26 29.57 30.61 31.29 33.95 34.16
- 9.82 23.64 24.84 26.27 29.56 30.62 31.28 33.94 34.16
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9.81 23.64 24.81 26.27 29.55 30.63 31.27 33.94 34.16
9.80 23.64 24.80 26.28 29.54 30.64 31.26 33.93 34.15
9.79 23.64 24.80 26.29 29.53 30.65 31.25 33.93 34.15
9.78 23.64 24.80 26.30 29.52 30.66 31.24 33.92 34.14
9.77 23.64 24.80 26.31 29.51 30.68 31.22 33.92 34.14
9.76 23.65 24.80 26.32 29.50 30.69 31.20 33.91 34.14
- 9.75 23.65 24.80 26.33 29.49 30.70 31.18 33.91 34.13
- 9.74 23.65 24.80 26.34 29.46 30.71 31.06 33.90 34.13
- 9.73 23.65 24.80 26.35 29.42 30.72 30.90 33.90 34.13
+ 9.75 23.65 24.80 26.32 29.49 30.70 31.18 33.91 34.13
+ 9.74 23.65 24.80 26.33 29.46 30.71 31.06 33.90 34.13
+ 9.73 23.65 24.80 26.34 29.42 30.72 30.89 33.90 34.13
9.72 23.65 24.80 26.35 29.37 30.73 30.82 33.89 34.12
9.71 23.65 24.80 26.36 29.32 30.75 30.80 33.89 34.12
9.70 23.66 24.80 26.37 29.28 30.76 30.79 33.89 34.11
9.69 23.66 24.80 26.38 29.24 33.88 34.11
9.68 23.66 24.80 26.39 29.22 33.88 34.11
9.67 23.65 24.80 26.40 29.20 33.88 34.10
- 9.66 23.65 24.80 26.41 29.17 33.88 34.10
- 9.65 23.65 24.80 26.42 29.15 33.88 34.10
- 9.64 23.64 24.80 26.43 29.12 33.87 34.10
+ 9.66 23.65 24.80 26.40 29.17 33.88 34.10
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+ 9.64 23.64 24.80 26.42 29.12 33.87 34.10
9.63 23.64 24.80 26.43 29.10 33.87 34.09
9.62 23.63 24.80 26.44 29.08 33.87 34.09
9.61 23.63 24.80 26.45 29.06 33.87 34.09
@@ -159141,7 +159435,7 @@ Sudan
9.59 23.61 24.80 26.47 27.21 27.35 29.02 33.87 34.09
9.58 23.61 24.80 26.48 27.07 27.56 27.63 27.67 29.00 33.86 34.08
9.57 23.60 24.80 26.49 27.04 27.73 28.99 33.86 34.08
- 9.56 23.60 24.80 26.50 27.01 27.89 28.98 33.86 34.08
+ 9.56 23.60 24.80 26.49 27.01 27.89 28.98 33.86 34.08
9.55 23.59 24.80 26.50 26.98 27.89 28.97 33.86 34.08
9.54 23.59 24.80 26.51 26.95 27.90 28.96 33.86 34.07
9.53 23.59 24.80 26.52 26.92 27.90 28.94 33.86 34.07
@@ -159166,7 +159460,7 @@ Sudan
9.34 23.61 24.69 28.01 28.84
9.33 23.61 24.69 28.02 28.85
9.32 23.61 24.69 28.03 28.85
- 9.31 23.61 24.68 28.44 28.85
+ 9.31 23.61 24.68 28.24 28.85
9.30 23.61 24.68
9.29 23.62 24.68
9.28 23.62 24.68
@@ -159180,7 +159474,7 @@ Sudan
9.20 23.54 24.67
9.19 23.53 24.67
9.18 23.46 24.67
- 9.17 23.45 24.67
+ 9.17 23.46 24.67
9.16 23.45 24.66
9.15 23.44 24.66
9.14 23.44 24.65
@@ -159232,57 +159526,58 @@ Sudan
8.68 23.95 24.18
8.67 24.05 24.18
Suriname
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5.76 -57.14 -53.98
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5.72 -57.14 -53.98
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5.70 -57.14 -53.99
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5.65 -57.15 -54.02
5.64 -57.15 -54.02
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5.59 -57.16 -54.03
5.58 -57.16 -54.03
5.57 -57.17 -54.03
5.56 -57.17 -54.03
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5.52 -57.21 -54.04
- 5.51 -57.23 -54.04
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5.50 -57.24 -54.05
5.49 -57.25 -54.05
5.48 -57.25 -54.06
@@ -159300,7 +159595,7 @@ Suriname
5.36 -57.31 -54.14
5.35 -57.32 -54.15
5.34 -57.33 -54.15
- 5.33 -57.34 -54.15
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5.32 -57.34 -54.17
5.31 -57.34 -54.18
5.30 -57.34 -54.19
@@ -159498,7 +159793,7 @@ Suriname
3.38 -57.66 -54.02
3.37 -57.65 -54.03
3.36 -57.63 -57.32 -57.30 -54.04
- 3.35 -57.61 -57.41 -57.38 -57.34 -57.30 -54.05
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3.34 -57.59 -57.43 -57.29 -54.05
3.33 -57.57 -57.53 -57.49 -57.45 -57.29 -54.05
3.32 -57.48 -57.46 -57.29 -54.05
@@ -159659,7 +159954,7 @@ Svalbard
80.75 20.50 20.71
80.74 20.50 20.78
80.73 20.51 20.99
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80.71 20.63 21.01 21.09 21.34
80.70 20.65 21.35
80.69 20.66 20.72 20.76 21.37
@@ -159683,21 +159978,21 @@ Svalbard
80.46 19.45 20.04 22.78 23.29 24.06 24.28
80.45 19.45 20.04 22.43 22.51 22.78 23.34 24.15 24.28
80.44 19.45 20.08 22.39 22.63 22.78 23.37 24.15 24.31
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80.42 19.45 20.10 20.16 20.43 22.36 22.69 22.80 23.37 24.14 24.35
80.41 19.45 20.10 20.15 20.43 22.34 22.69 22.80 23.36 24.11 24.38
80.40 19.45 20.10 20.14 20.44 22.33 22.69 22.79 23.32 24.11 24.39
80.39 19.45 20.47 22.32 22.68 22.79 23.31 24.11 24.39
80.38 19.47 20.50 22.32 22.66 22.75 23.22 24.13 24.39
80.37 18.28 18.38 19.50 20.53 22.32 22.65 22.72 23.22 24.15 24.43
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80.32 18.14 18.75 18.98 19.38 19.76 20.58 20.74 20.82 22.37 23.36 24.19 24.61 24.74 24.89
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- 80.30 18.11 18.76 19.04 19.43 19.79 20.84 22.51 23.31 23.72 23.85 23.88 24.14 24.19 24.27 24.29 24.61 24.69 24.88
- 80.29 18.10 18.76 19.07 19.46 19.79 20.84 21.69 21.79 22.51 23.31 23.72 24.52 24.63 24.87 25.29 25.36
+ 80.31 18.12 18.76 19.00 19.41 19.76 20.61 20.66 20.84 22.42 23.33 23.74 23.81 23.88 24.09 24.29 24.61 24.73 24.89
+ 80.30 18.11 18.76 19.04 19.43 19.79 20.84 22.51 23.31 23.72 23.85 23.88 24.13 24.19 24.27 24.29 24.61 24.69 24.88
+ 80.29 18.10 18.76 19.07 19.46 19.79 20.84 21.69 21.79 22.50 23.31 23.72 24.17 24.19 24.52 24.63 24.87 25.29 25.36
80.28 18.10 18.73 19.08 19.49 19.78 20.80 21.50 21.55 21.66 21.86 22.45 23.31 23.72 24.50 24.58 24.85 25.17 25.36
80.27 18.10 18.69 19.08 19.52 19.74 20.77 21.30 21.33 21.45 21.58 21.65 21.87 22.43 23.31 23.70 24.51 24.56 24.97 25.07 25.36
80.26 18.13 18.66 19.08 19.55 19.72 20.78 21.25 21.33 21.41 21.60 21.64 21.88 22.43 23.29 23.70 25.35
@@ -159707,7 +160002,7 @@ Svalbard
80.22 18.46 18.52 19.14 21.90 22.45 23.05 23.40 23.48 23.72 25.61 25.63 25.79 32.96 33.65
80.21 18.69 18.78 19.17 21.90 22.44 23.05 23.38 23.50 23.73 25.79 32.85 33.65
80.20 17.98 18.05 18.69 18.88 19.19 21.90 22.43 23.04 23.21 23.31 23.38 23.50 23.74 25.79 32.69 33.63
- 80.19 17.96 18.08 18.10 18.37 18.42 18.59 18.69 18.92 19.20 21.89 22.41 23.04 23.20 23.32 23.37 23.50 23.73 25.78 25.88 26.37 32.53 33.61
+ 80.19 17.96 18.07 18.10 18.24 18.42 18.59 18.69 18.92 19.20 21.89 22.41 23.04 23.21 23.32 23.37 23.50 23.73 25.78 25.88 26.16 32.53 33.61
80.18 17.91 18.63 18.71 18.94 19.21 21.83 22.39 23.03 23.07 23.17 23.20 23.32 23.37 23.50 23.65 26.83 32.37 33.57
80.17 17.86 18.98 19.24 21.79 22.39 23.02 23.07 23.34 23.37 23.50 23.63 26.88 32.21 33.42
80.16 17.82 19.02 19.32 21.84 22.39 23.03 23.07 23.54 23.61 26.92 32.05 33.16
@@ -159716,8 +160011,8 @@ Svalbard
80.13 17.77 19.16 19.38 21.99 22.38 26.99 31.57 32.91
80.12 17.77 19.20 19.37 22.07 22.36 27.12 31.47 32.86
80.11 17.79 17.87 17.94 18.02 18.04 19.23 19.34 22.07 22.36 27.22 31.46 32.73
- 80.10 17.98 18.00 18.07 19.26 19.31 22.11 22.36 27.24 31.46 32.53
- 80.09 18.09 22.13 22.38 27.24 31.46 32.33
+ 80.10 17.98 18.00 18.07 19.26 19.31 22.10 22.36 27.24 31.46 32.53
+ 80.09 18.09 22.13 22.38 27.24 31.46 32.32
80.08 18.12 22.15 22.33 27.24 31.48 32.12
80.07 16.23 16.35 18.14 22.18 22.33 27.22 31.52 31.92
80.06 16.19 16.46 18.14 22.21 22.33 27.19 31.58 31.72
@@ -159735,70 +160030,70 @@ Svalbard
79.94 15.94 16.73 16.86 17.34 18.21 27.21
79.93 15.94 16.73 16.86 17.38 18.16 27.23
79.92 15.94 16.72 16.85 17.45 18.12 27.23
- 79.91 15.96 16.75 16.85 17.53 18.10 27.24
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79.90 15.97 16.78 16.85 17.58 18.10 27.24
79.89 13.75 13.82 15.99 16.81 16.87 17.61 18.10 27.24
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- 79.86 13.32 13.92 15.64 17.74 18.25 27.21
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79.82 11.53 11.58 11.61 11.90 12.16 12.48 12.94 13.96 14.53 14.58 15.63 17.85 18.35 26.89
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- 79.80 11.51 11.95 12.15 12.53 12.87 13.97 14.49 14.74 15.63 17.91 18.42 21.67 21.73 26.83
- 79.79 10.69 10.79 11.20 11.33 11.51 11.95 12.15 12.54 12.79 13.97 14.48 14.82 15.64 17.93 18.43 21.24 21.72 26.82
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79.76 10.63 10.99 11.18 12.00 12.17 13.98 14.42 14.93 15.63 18.05 18.69 20.15 21.78 26.64
79.75 10.63 11.02 11.20 12.02 12.18 13.97 14.40 14.95 15.63 18.07 18.69 20.11 21.78 26.64
79.74 10.64 11.02 11.20 12.03 12.19 13.95 14.38 14.97 15.66 18.09 18.69 20.06 21.83 26.63
79.73 10.66 11.02 11.18 12.04 12.22 13.93 14.35 14.99 15.67 18.10 18.70 20.02 21.83 26.54
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79.69 10.72 11.07 11.20 12.09 12.13 12.25 12.33 13.76 14.24 15.07 15.67 18.08 20.46 26.40
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79.67 10.72 11.08 11.25 13.03 14.21 15.11 15.71 18.05 20.46 26.28
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79.62 10.87 12.85 14.13 15.29 15.76 17.85 18.15 18.42 19.62 20.31 20.59 25.98
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79.59 10.84 12.71 12.93 13.48 13.97 15.30 15.81 17.77 18.09 18.58 19.62 25.90
79.58 10.84 12.67 12.80 13.49 13.94 15.29 15.81 17.77 18.07 18.62 19.63 25.91
79.57 10.69 13.50 13.92 15.29 15.81 17.76 18.06 18.66 19.63 25.92
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79.55 10.66 13.50 13.87 15.31 15.84 17.76 18.05 18.73 19.65 25.95
79.54 10.66 13.49 13.87 15.31 15.84 17.77 18.04 18.75 19.67 25.96
79.53 10.66 13.47 13.87 15.33 15.84 17.77 18.03 18.76 19.72 25.97
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79.49 10.72 13.29 13.42 13.62 13.92 15.38 15.87 17.79 18.00 18.78 20.02 25.96
79.48 10.81 13.32 13.42 13.63 13.92 15.38 15.88 17.79 18.00 18.79 20.05 25.94
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79.41 10.84 13.86 14.00 15.45 15.91 17.78 17.86 18.91 19.64 19.84 20.77 25.77
79.40 10.84 13.88 14.00 15.45 15.91 18.92 19.61 19.91 20.78 25.73
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79.32 10.88 13.92 14.12 15.62 15.94 18.88 19.68 19.79 20.09 20.16 22.63 24.63 24.95 25.22
79.31 10.90 13.92 14.11 15.63 15.94 18.88 22.63 24.59
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79.27 11.01 11.62 11.70 12.01 12.08 15.72 16.01 18.82 22.67 24.28
79.26 11.02 11.64 11.71 11.91 12.08 15.76 16.03 18.86 22.69 24.28
79.25 11.04 11.65 11.73 11.92 12.05 15.78 16.06 18.89 22.71 24.28
@@ -159806,17 +160101,17 @@ Svalbard
79.23 11.08 11.69 11.76 11.92 12.05 15.79 16.10 18.95 22.80 24.27
79.22 11.12 11.70 11.78 11.91 12.05 15.79 16.14 18.95 22.84 24.25
79.21 11.14 11.71 11.82 11.90 11.97 15.79 16.14 18.95 22.89 24.22
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79.16 11.16 11.72 11.85 15.69 15.77 15.92 16.15 19.84
79.15 11.16 11.71 11.83 15.67 15.75 15.94 16.16 19.84
79.14 11.16 11.67 11.83 15.67 15.73 15.97 16.17 19.84 20.13 20.20
79.13 11.17 11.61 11.82 15.68 15.71 15.99 16.17 19.83 20.08 20.22 20.32 20.48
79.12 11.17 11.55 11.79 16.01 16.18 19.82 20.08 20.55
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79.09 11.21 11.37 11.74 16.09 16.24 19.87 20.10 20.79
79.08 11.24 11.31 11.70 16.11 16.27 19.91 20.10 20.81
79.07 11.67 16.12 16.28 19.93 20.10 20.83
@@ -159838,11 +160133,11 @@ Svalbard
78.91 10.49 10.61 11.40 20.98 28.10 29.70
78.90 10.47 10.71 11.42 21.10 28.08 29.71
78.89 10.47 10.80 11.47 21.22 28.04 28.80 28.87 29.71
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78.83 10.55 11.01 11.75 15.37 15.39 21.55 27.83 28.24
78.82 10.55 11.01 11.72 15.34 15.41 21.55 26.46 26.56 27.90 28.18
78.81 10.53 11.01 11.70 15.32 15.44 21.54 26.43 26.63 28.02 28.13
@@ -159852,7 +160147,7 @@ Svalbard
78.77 10.51 11.14 11.65 15.24 15.41 21.56 26.38 26.71
78.76 10.53 11.16 11.64 15.23 15.42 21.56 26.38 26.73
78.75 10.54 11.18 11.63 15.23 15.45 21.55 26.39 26.75
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78.73 10.60 11.19 11.63 15.23 15.46 21.51 26.43 26.81
78.72 10.63 11.19 11.64 15.23 15.46 21.50 26.44 26.88
78.71 10.64 11.17 11.66 14.66 14.80 15.23 15.48 21.42 26.44 26.98
@@ -159863,26 +160158,26 @@ Svalbard
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78.65 10.77 11.16 11.84 14.55 14.79 15.27 15.44 16.44 16.81 20.64 20.89 21.20 21.27 21.40 26.65 26.96
78.64 10.79 11.21 11.84 14.55 14.79 15.24 15.43 16.40 16.70 20.63 20.92 21.13 21.31 21.39 26.68 26.96
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78.62 10.85 11.28 11.89 14.55 14.81 15.05 15.22 16.38 16.67 20.21 20.47 20.61 21.06 21.11 21.13 21.43 26.70 26.76
78.61 10.87 11.28 11.96 14.55 14.84 15.05 15.20 16.38 16.65 20.08 21.11 21.45 21.65 21.74 26.72 26.74
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78.56 10.94 11.30 12.35 14.59 15.23 16.34 16.50 19.60 20.81 20.92 21.05 22.11
78.55 10.94 11.30 11.32 11.47 12.36 14.59 15.24 16.32 16.48 19.62 20.69 22.12
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78.53 10.97 11.48 12.40 14.58 15.25 16.21 16.44 19.67 20.46 22.15
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78.51 10.99 11.53 12.48 14.44 15.28 16.08 16.43 19.69 20.23 22.22
78.50 10.99 11.56 12.40 14.42 15.29 16.05 16.42 19.69 20.16 22.23
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78.43 11.09 11.27 11.32 11.91 12.46 14.70 16.36 19.02 20.40 22.22
78.42 11.11 11.20 11.37 11.91 12.48 14.71 16.38 16.47 16.56 19.04 20.46 22.23
78.41 11.42 11.91 12.51 14.73 16.57 19.05 20.49 22.23
@@ -159890,25 +160185,25 @@ Svalbard
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78.38 11.54 11.94 12.57 14.74 16.67 19.07 20.60 22.24
78.37 11.57 11.96 12.60 14.30 14.35 14.70 16.07 16.18 16.79 19.07 20.66 22.25
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78.35 11.61 12.00 12.70 14.30 14.41 14.45 15.76 15.85 15.94 19.07 20.51 22.25
78.34 11.63 12.02 12.80 14.31 15.71 19.07 20.49 22.25
78.33 11.67 12.04 12.84 14.32 15.66 19.06 20.47 22.25
78.32 11.71 12.07 12.84 14.32 15.62 19.05 20.45 22.24
78.31 11.74 12.09 12.84 14.33 15.60 19.02 20.45 22.24
78.30 11.78 12.11 12.86 14.33 15.59 19.00 20.45 22.24
- 78.29 11.82 12.11 12.90 14.33 15.58 18.99 20.59 22.25
+ 78.29 11.81 12.11 12.90 14.33 15.58 18.99 20.59 22.25
78.28 11.80 12.11 12.92 14.27 15.58 18.98 20.73 22.27
78.27 11.80 12.13 12.92 14.23 15.58 19.02 20.72 22.28
78.26 11.80 12.14 12.91 13.96 14.03 14.19 15.59 19.05 20.70 22.28 22.85 22.99
78.25 11.81 12.14 12.90 13.95 14.03 14.15 15.60 19.08 20.70 22.28 22.63 23.04
- 78.24 11.83 12.15 12.90 13.95 14.03 14.12 15.35 19.09 20.68 22.17 22.52 23.17
+ 78.24 11.83 12.15 12.90 13.95 14.03 14.12 15.35 19.08 20.68 22.17 22.52 23.17
78.23 11.85 12.15 12.90 13.95 14.03 14.09 15.27 19.09 20.65 21.97 22.50 23.23
- 78.22 11.87 12.17 12.91 13.86 13.90 13.95 15.24 19.09 20.64 22.05 22.44 23.29
- 78.21 11.90 12.17 12.94 13.86 13.93 13.95 15.21 19.08 20.61 23.34
- 78.20 12.06 12.17 12.97 13.12 13.49 13.86 15.17 19.07 20.61 20.75 20.90 21.37 21.47 23.36
- 78.19 12.08 12.16 12.99 13.06 15.14 19.06 20.61 20.74 21.00 21.17 21.38 23.39
- 78.18 12.10 12.15 15.12 19.04 20.63 20.73 21.29 23.41
+ 78.22 11.87 12.17 12.91 13.86 13.90 13.95 15.24 19.09 20.64 21.87 22.46 23.29
+ 78.21 11.90 12.17 12.94 13.86 13.93 13.95 15.21 19.09 20.61 22.22 22.41 23.34
+ 78.20 12.06 12.17 12.97 13.12 13.67 13.86 15.18 19.07 20.61 20.75 20.90 21.37 21.47 23.36
+ 78.19 12.08 12.16 12.99 13.06 15.16 19.06 20.61 20.74 21.00 21.17 21.38 23.39
+ 78.18 12.10 12.15 15.14 19.04 20.63 20.73 21.29 23.41
78.17 15.06 18.95 21.20 23.45
78.16 15.03 18.97 21.12 23.48
78.15 15.00 18.99 21.03 23.48
@@ -159925,7 +160220,7 @@ Svalbard
78.04 13.57 14.18 14.26 18.96 20.98 23.07
78.03 13.59 14.21 14.28 18.54 18.61 18.92 21.02 23.07
78.02 13.61 14.23 14.30 18.47 18.69 18.88 21.06 23.07
- 78.01 13.63 14.26 14.33 18.45 18.77 18.84 21.10 23.09
+ 78.01 13.63 14.26 14.32 18.45 18.77 18.84 21.10 23.09
78.00 13.64 14.27 14.33 18.49 21.14 23.11
77.99 13.63 14.27 14.33 18.51 21.18 23.17
77.98 13.63 14.28 14.33 18.51 21.22 23.25
@@ -159939,72 +160234,72 @@ Svalbard
77.90 13.64 18.37 21.52 23.58 24.05 24.34
77.89 13.65 16.75 16.79 18.36 21.52 23.60 24.02 24.37
77.88 13.66 16.73 16.77 18.39 21.52 23.71 24.01 24.40
- 77.87 13.65 16.72 16.77 18.43 21.53 23.87 23.99 24.47
- 77.86 13.65 15.51 15.57 16.72 16.77 18.44 21.53 24.55
- 77.85 13.64 15.43 15.61 16.70 16.78 18.45 21.49 24.56
- 77.84 13.64 15.35 15.66 16.54 16.80 18.45 21.45 24.58
- 77.83 13.64 15.29 15.70 16.24 16.81 18.45 21.42 24.62
- 77.82 13.71 15.25 15.75 15.94 16.73 18.45 21.42 24.67
- 77.81 13.76 15.22 16.46 18.45 21.42 24.72
- 77.80 13.79 15.18 16.30 18.46 21.42 24.78
- 77.79 13.78 15.15 16.26 18.46 21.38 24.83
- 77.78 13.74 15.11 16.15 18.46 21.35 24.88
- 77.77 13.70 14.93 15.99 18.46 21.33 24.91
- 77.76 13.70 14.15 14.22 14.75 15.83 18.46 21.30 24.91
- 77.75 13.70 14.10 14.24 14.73 15.67 18.46 21.27 24.91
- 77.74 13.72 14.08 14.40 14.62 15.51 18.45 21.25 24.90
- 77.73 13.73 14.05 15.35 18.44 21.24 24.89
- 77.72 13.74 13.83 13.89 14.03 15.19 18.43 21.23 24.83
- 77.71 13.93 13.99 15.09 18.41 21.23 24.72
- 77.70 15.05 18.40 21.23 24.61
- 77.69 14.82 18.39 21.23 24.51
- 77.68 14.76 18.37 21.23 24.40
- 77.67 14.73 18.36 21.22 24.29
- 77.66 14.73 18.36 21.21 24.21
- 77.65 14.73 18.37 21.21 24.17
- 77.64 14.74 18.37 21.21 24.12
+ 77.87 13.65 16.72 16.77 18.43 21.53 23.87 23.99 24.41
+ 77.86 13.65 15.51 15.57 16.72 16.77 18.44 21.53 24.41
+ 77.85 13.64 15.43 15.61 16.70 16.78 18.45 21.49 24.42
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+ 77.83 13.64 15.29 15.70 16.12 16.81 18.45 21.42 24.43
+ 77.82 13.71 15.25 15.75 15.90 16.73 18.45 21.42 24.43
+ 77.81 13.76 15.22 16.46 18.45 21.42 24.43
+ 77.80 13.79 15.18 16.30 18.46 21.42 24.41
+ 77.79 13.78 15.15 16.26 18.46 21.38 24.38
+ 77.78 13.74 15.11 16.17 18.46 21.35 24.35
+ 77.77 13.70 14.93 16.05 18.46 21.33 24.32
+ 77.76 13.70 14.14 14.21 14.75 15.92 18.46 21.30 24.30
+ 77.75 13.70 14.09 14.23 14.73 15.76 18.46 21.27 24.28
+ 77.74 13.71 14.07 14.25 14.28 14.40 14.62 15.58 18.45 21.25 24.26
+ 77.73 13.72 14.05 15.39 18.44 21.24 24.25
+ 77.72 13.74 13.83 13.88 14.03 15.20 18.43 21.23 24.24
+ 77.71 13.90 14.00 15.09 18.41 21.23 24.24
+ 77.70 13.93 13.97 15.05 18.40 21.23 24.23
+ 77.69 14.82 18.39 21.23 24.21
+ 77.68 14.76 18.37 21.23 24.19
+ 77.67 14.73 18.36 21.22 24.17
+ 77.66 14.73 18.36 21.21 24.15
+ 77.65 14.73 18.37 21.21 24.13
+ 77.64 14.74 18.37 21.21 24.11
77.63 14.76 18.37 21.22 24.09
77.62 14.82 18.36 21.21 24.07
77.61 14.84 18.35 21.14 24.06
- 77.60 14.87 14.94 15.04 18.33 21.06 24.04
- 77.59 14.34 14.49 15.22 18.32 20.98 24.01
- 77.58 14.16 14.53 15.40 18.31 20.90 23.99
- 77.57 14.05 14.55 14.96 15.07 15.57 18.31 20.86 23.98
- 77.56 14.01 14.57 14.92 15.12 15.75 18.32 20.86 23.98
- 77.55 13.97 14.59 14.75 15.50 15.86 18.32 20.82 22.41 22.53 23.97
+ 77.60 14.87 14.94 15.07 18.33 21.06 24.04
+ 77.59 14.34 14.48 15.29 18.32 20.98 24.01
+ 77.58 14.16 14.53 15.47 18.31 20.90 23.99
+ 77.57 14.05 14.55 14.96 15.07 15.62 18.31 20.86 23.98
+ 77.56 14.01 14.57 14.92 15.12 15.76 18.32 20.86 23.98
+ 77.55 13.97 14.59 14.75 15.32 15.86 18.32 20.82 22.41 22.53 23.97
77.54 13.90 14.60 14.75 18.32 20.82 22.33 22.54 23.96
77.53 13.90 14.60 14.75 18.31 20.82 22.28 22.54 23.95
- 77.52 13.90 14.60 14.75 18.31 20.85 22.27 22.54 23.93
- 77.51 13.90 14.59 14.73 18.30 20.85 22.25 22.54 23.92
- 77.50 13.90 18.29 20.87 22.23 22.54 23.91
- 77.49 13.90 17.91 17.96 18.27 20.88 22.21 22.59 23.90
- 77.48 13.90 17.85 17.98 18.07 18.14 18.25 20.86 22.06 22.57 23.88
- 77.47 13.93 17.74 20.85 21.78 22.53 23.85
- 77.46 13.94 17.74 20.85 21.50 22.49 23.82
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+ 77.51 13.90 14.59 14.73 18.30 20.84 22.25 22.54 23.92
+ 77.50 13.90 18.29 20.86 22.23 22.54 23.91
+ 77.49 13.90 17.91 17.96 18.27 20.87 22.21 22.59 23.90
+ 77.48 13.90 17.85 17.98 18.07 18.14 18.25 20.86 22.09 22.57 23.88
+ 77.47 13.93 17.74 20.85 21.88 22.53 23.85
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77.45 13.94 17.74 20.85 21.35 22.45 23.78
77.44 13.94 17.72 20.85 21.33 22.41 23.75
77.43 13.94 17.67 20.87 21.26 22.40 23.70
77.42 13.94 17.66 21.06 21.15 22.40 23.64
77.41 13.94 17.66 22.40 23.58
- 77.40 13.96 17.66 22.40 23.53
- 77.39 13.97 17.65 22.41 23.49
+ 77.40 13.95 17.66 22.40 23.53
+ 77.39 13.96 17.65 22.41 23.49
77.38 13.98 17.63 22.43 23.45
- 77.37 14.00 17.61 22.46 23.12 23.25 23.41
- 77.36 14.04 17.61 22.48 23.04 23.31 23.38
- 77.35 14.07 17.60 22.48 23.02
- 77.34 14.10 17.59 22.48 23.00
- 77.33 14.13 17.56 22.44 22.94
- 77.32 14.12 17.53 22.40 22.91
- 77.31 14.12 17.50 22.38 22.91
- 77.30 14.12 17.50 22.38 22.91
- 77.29 14.12 17.50 22.38 22.91
- 77.28 14.14 17.51 22.38 22.90
- 77.27 14.23 17.51 22.39 22.87
- 77.26 14.29 17.51 22.40 22.83
- 77.25 14.29 17.51 22.41 22.50 22.60 22.79
- 77.24 14.29 17.51
- 77.23 14.29 17.50
- 77.22 14.31 17.48
+ 77.37 14.00 17.61 22.46 23.41
+ 77.36 14.04 17.61 22.48 23.38
+ 77.35 14.07 17.60 22.48 23.35
+ 77.34 14.10 17.59 22.48 23.33
+ 77.33 14.13 17.56 22.44 23.31
+ 77.32 14.12 17.53 22.40 23.29
+ 77.31 14.12 17.50 22.38 23.28
+ 77.30 14.12 17.50 22.38 23.29
+ 77.29 14.12 17.50 22.38 23.29
+ 77.28 14.14 17.51 22.38 23.29
+ 77.27 14.23 17.51 22.39 23.28
+ 77.26 14.29 17.51 22.40 23.26
+ 77.25 14.29 17.51 22.41 23.24
+ 77.24 14.29 17.51 22.50 23.08
+ 77.23 14.29 17.50 22.57 22.87
+ 77.22 14.31 17.48 22.65 22.76
77.21 14.32 17.46
77.20 14.33 17.44
77.19 14.35 17.44
@@ -160045,7 +160340,7 @@ Svalbard
76.84 15.63 17.07
76.83 15.69 17.07
76.82 15.73 17.07
- 76.81 15.76 17.03
+ 76.81 15.76 17.02
76.80 15.79 16.96
76.79 15.83 16.98
76.78 15.86 17.05
@@ -160089,11 +160384,11 @@ Svalbard
74.52 18.84 19.20
74.51 18.81 19.22
74.50 18.80 19.24
- 74.49 18.79 19.30
- 74.48 18.78 19.30
- 74.47 18.78 19.30
- 74.46 18.78 19.30
- 74.45 18.80 19.29
+ 74.49 18.78 19.30
+ 74.48 18.77 19.30
+ 74.47 18.77 19.30
+ 74.46 18.77 19.30
+ 74.45 18.79 19.29
74.44 18.81 19.29
74.43 18.83 19.29
74.42 18.85 19.28
@@ -160127,8 +160422,8 @@ Swaziland
-25.89 31.11 31.71
-25.90 31.10 31.73
-25.91 31.10 31.74
- -25.92 31.09 31.76
- -25.93 31.09 31.78
+ -25.92 31.09 31.75
+ -25.93 31.09 31.77
-25.94 31.09 31.79 31.93 31.95
-25.95 31.08 31.81 31.91 31.96
-25.96 31.08 31.83 31.89 31.97
@@ -160215,7 +160510,7 @@ Swaziland
-26.77 30.78 32.12
-26.78 30.78 32.12
-26.79 30.78 32.12
- -26.80 30.78 30.86 30.88 32.12
+ -26.80 30.78 32.12
-26.81 30.79 30.85 30.88 32.12
-26.82 30.88 32.00 32.06 32.12
-26.83 30.89 32.00 32.07 32.12
@@ -160259,7 +160554,7 @@ Swaziland
-27.21 31.14 31.95
-27.22 31.16 31.95
-27.23 31.19 31.95
- -27.24 31.23 31.95
+ -27.24 31.22 31.95
-27.25 31.26 31.95
-27.26 31.29 31.96
-27.27 31.33 31.96
@@ -160269,7 +160564,7 @@ Swaziland
-27.31 31.46 31.97
-27.32 31.50 31.97
Sweden
- 69.04 20.36 20.64
+ 69.04 20.49 20.64
69.03 20.09 20.66
69.02 20.09 20.81
69.01 20.09 20.83
@@ -160317,8 +160612,8 @@ Sweden
68.59 20.07 21.78
68.58 18.39 18.46 20.03 21.87
68.57 18.33 18.50 20.00 21.93
- 68.56 18.26 18.53 19.97 21.95
- 68.55 18.20 18.55 19.95 21.97
+ 68.56 18.27 18.53 19.97 21.95
+ 68.55 18.21 18.55 19.95 21.97
68.54 18.15 18.58 19.95 21.99
68.53 18.15 18.61 19.95 22.01
68.52 18.14 18.63 19.98 22.03
@@ -160557,9 +160852,9 @@ Sweden
66.19 15.13 23.77
66.18 15.10 23.84
66.17 15.06 23.89
- 66.16 14.96 23.91
- 66.15 14.79 23.92
- 66.14 14.62 23.93
+ 66.16 14.98 23.91
+ 66.15 14.85 23.92
+ 66.14 14.66 23.93
66.13 14.53 23.94
66.12 14.53 23.94
66.11 14.53 23.95
@@ -160590,21 +160885,21 @@ Sweden
65.86 14.62 22.69 22.73 24.16
65.85 14.62 22.69 22.76 24.17
65.84 14.63 22.38 22.43 22.69 22.78 24.17
- 65.83 14.63 22.37 22.46 22.70 22.79 24.17
+ 65.83 14.63 22.37 22.45 22.70 22.79 24.17
65.82 14.63 22.36 22.48 22.70 22.80 24.17
- 65.81 14.63 22.37 22.50 22.71 22.80 24.17
- 65.80 14.63 22.37 22.50 22.71 22.81 23.19 23.23 23.67 23.75 24.16
- 65.79 14.62 22.37 22.49 22.71 22.82 23.21 23.25 23.33 23.36 23.44 23.50 23.65 23.76 24.15
- 65.78 14.61 22.37 22.49 22.71 22.73 22.76 22.84 23.23 23.27 23.32 23.36 23.44 23.61 23.64 23.77 24.06
- 65.77 14.60 22.37 22.49 22.55 22.62 22.70 22.72 22.78 22.91 23.24 23.36 23.44 23.79 23.97 24.00 24.04
+ 65.81 14.63 22.37 22.50 22.70 22.80 23.69 23.71 24.17
+ 65.80 14.63 22.37 22.50 22.70 22.81 23.19 23.23 23.45 23.47 23.67 23.75 24.16
+ 65.79 14.62 22.37 22.49 22.70 22.82 23.21 23.25 23.33 23.36 23.44 23.56 23.65 23.76 24.15
+ 65.78 14.61 22.37 22.49 22.70 22.73 22.76 22.84 23.23 23.27 23.32 23.36 23.44 23.61 23.64 23.77 24.06
+ 65.77 14.60 22.37 22.49 22.55 22.62 22.70 22.72 22.78 22.91 23.24 23.36 23.44 23.79 23.97
65.76 14.59 22.37 22.50 22.53 22.63 22.69 22.72 22.80 22.92 23.24 23.37 23.44 23.70 23.72 23.78 23.80 23.86 23.96
- 65.75 14.59 22.37 22.63 22.68 22.72 22.80 22.89 23.24 23.39 23.44 23.67 23.81 23.88 23.95
- 65.74 14.58 22.36 22.63 22.67 22.71 22.81 22.87 22.96 23.04 23.21 23.67 23.81
- 65.73 14.57 22.36 22.71 22.81 22.87 22.96 23.05 23.17 23.67 23.81
+ 65.75 14.59 22.37 22.63 22.68 22.72 22.80 22.89 23.24 23.39 23.44 23.67 23.81 23.90 23.95
+ 65.74 14.58 22.36 22.63 22.67 22.72 22.81 22.87 22.96 23.04 23.19 23.67 23.81
+ 65.73 14.57 22.35 22.71 22.81 22.87 22.96 23.05 23.15 23.67 23.81
65.72 14.56 22.37 22.71 22.82 22.87 22.97 23.06 23.14 23.67 23.80
- 65.71 14.55 22.37 22.71 22.82 22.87 22.99 23.06 23.14 23.67 23.80
- 65.70 14.55 22.38 22.72 22.82 22.87 22.99 23.06 23.14 23.67 23.79
- 65.69 14.55 22.38 22.75 22.81 22.88 22.99 23.06 23.12 23.68 23.77
+ 65.71 14.55 22.38 22.71 22.82 22.87 22.99 23.06 23.13 23.67 23.80
+ 65.70 14.55 22.38 22.72 22.82 22.87 22.99 23.06 23.13 23.67 23.79
+ 65.69 14.55 22.39 22.75 22.81 22.88 22.99 23.06 23.12 23.68 23.77
65.68 14.54 22.39 22.89 22.99 23.71 23.75
65.67 14.54 22.39 22.91 22.98
65.66 14.54 22.39 22.93 22.98
@@ -160619,8 +160914,8 @@ Sweden
65.57 14.52 22.42 22.51 22.65
65.56 14.52 22.26 22.28 22.42 22.51 22.64
65.55 14.52 22.26 22.33 22.43 22.52 22.62
- 65.54 14.51 22.29 22.36 22.43 22.54 22.61
- 65.53 14.51 22.33 22.37 22.43 22.54 22.62
+ 65.54 14.51 22.29 22.37 22.43 22.54 22.61
+ 65.53 14.51 22.33 22.39 22.43 22.54 22.62
65.52 14.51 22.35 22.54 22.62
65.51 14.51 22.09 22.18 22.36 22.54 22.62
65.50 14.51 22.08 22.19 22.36 22.55 22.62
@@ -160634,10 +160929,10 @@ Sweden
65.42 14.50 22.02 22.13 22.24 22.27 22.40
65.41 14.50 21.95 21.97 22.01 22.17 22.24 22.28 22.34
65.40 14.50 21.95 22.20 22.24
- 65.39 14.50 21.94
- 65.38 14.50 21.71 21.76 21.81
- 65.37 14.50 21.50
- 65.36 14.50 21.50
+ 65.39 14.50 21.60 21.62 21.71 21.74 21.94
+ 65.38 14.50 21.60 21.64 21.71
+ 65.37 14.50 21.49
+ 65.36 14.50 21.49
65.35 14.50 21.51
65.34 14.50 21.52 21.57 21.62
65.33 14.50 21.54 21.57 21.63
@@ -160652,12 +160947,12 @@ Sweden
65.24 14.36 21.67
65.23 14.36 21.65
65.22 14.35 21.60
- 65.21 14.35 21.58
- 65.20 14.34 21.59
- 65.19 14.34 21.60
- 65.18 14.34 21.61
- 65.17 14.33 21.62
- 65.16 14.33 21.62
+ 65.21 14.35 21.57
+ 65.20 14.34 21.58
+ 65.19 14.34 21.59
+ 65.18 14.34 21.60
+ 65.17 14.33 21.61
+ 65.16 14.33 21.61
65.15 14.33 21.62
65.14 14.32 21.62
65.13 14.32 21.62
@@ -160679,7 +160974,7 @@ Sweden
64.97 14.12 21.40
64.96 14.11 21.40
64.95 14.09 21.40
- 64.94 14.08 21.39
+ 64.94 14.08 21.32
64.93 14.07 21.26
64.92 14.06 21.26
64.91 14.04 21.25
@@ -160688,14 +160983,14 @@ Sweden
64.88 14.00 21.22
64.87 13.99 21.22
64.86 13.98 21.22
- 64.85 13.96 21.21
+ 64.85 13.97 21.21
64.84 13.95 21.19
64.83 13.94 21.19
64.82 13.93 21.19
64.81 13.91 21.18
64.80 13.90 21.09
64.79 13.89 21.25
- 64.78 13.87 21.30
+ 64.78 13.88 21.30
64.77 13.86 21.31
64.76 13.85 21.32
64.75 13.84 21.32
@@ -160705,7 +161000,7 @@ Sweden
64.71 13.78 21.30
64.70 13.77 21.32
64.69 13.76 21.32
- 64.68 13.74 21.32
+ 64.68 13.75 21.32
64.67 13.73 21.31
64.66 13.72 21.31
64.65 13.71 21.26 21.28 21.31
@@ -160713,10 +161008,10 @@ Sweden
64.63 13.68 21.26
64.62 13.67 21.31
64.61 13.65 21.32 21.35 21.40
- 64.60 13.64 21.32 21.35 21.41
+ 64.60 13.64 21.33 21.35 21.41
64.59 13.63 21.43 21.45 21.49
- 64.58 13.63 21.50
- 64.57 13.63 21.50
+ 64.58 13.63 21.49
+ 64.57 13.63 21.49
64.56 13.65 21.50
64.55 13.69 21.51
64.54 13.72 21.56
@@ -160724,9 +161019,9 @@ Sweden
64.52 13.79 21.56
64.51 13.82 21.55
64.50 13.85 21.49
- 64.49 13.89 21.50
- 64.48 13.92 21.50 21.52 21.60
- 64.47 13.96 21.50 21.52 21.61
+ 64.49 13.89 21.49 21.56 21.59
+ 64.48 13.92 21.49 21.52 21.60
+ 64.47 13.96 21.49 21.52 21.61
64.46 14.02 21.61
64.45 14.07 21.61
64.44 14.09 21.61
@@ -160741,7 +161036,7 @@ Sweden
64.35 14.12 21.45
64.34 14.12 21.43
64.33 14.12 21.41
- 64.32 14.12 21.40
+ 64.32 14.12 21.34 21.36 21.40
64.31 14.12 21.34
64.30 14.13 21.34
64.29 14.13 21.30
@@ -160763,19 +161058,19 @@ Sweden
64.13 14.09 20.97
64.12 14.08 20.97
64.11 14.07 20.97
- 64.10 13.19 13.27 14.06 20.97
- 64.09 13.13 13.35 14.04 20.97
- 64.08 13.07 13.43 14.03 20.96
- 64.07 13.01 13.51 14.02 20.95
- 64.06 12.96 13.59 14.01 20.94
- 64.05 12.92 13.66 14.00 20.93
- 64.04 12.88 13.74 13.99 20.92
- 64.03 12.84 13.82 13.98 20.92
+ 64.10 13.19 13.28 14.06 20.97
+ 64.09 13.13 13.37 14.04 20.97
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64.02 12.80 13.90 13.97 20.92
64.01 12.76 20.92
64.00 12.74 20.91
63.99 12.72 20.91
- 63.98 12.70 20.91
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63.97 12.68 20.90
63.96 12.67 20.90
63.95 12.66 20.87
@@ -160800,7 +161095,7 @@ Sweden
63.76 12.41 20.46 20.53 20.56 20.82 20.95
63.75 12.39 20.45 20.82 20.95
63.74 12.38 20.42 20.86 20.95
- 63.73 12.37 20.42 20.86 20.94
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63.72 12.35 20.32 20.34 20.43 20.86 20.94
63.71 12.34 20.32 20.34 20.43 20.85 20.94
63.70 12.33 20.32 20.34 20.43 20.85 20.94
@@ -160815,7 +161110,7 @@ Sweden
63.61 12.18 20.04
63.60 12.16 20.04
63.59 12.16 19.91 19.99 20.04
- 63.58 12.16 19.89
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63.57 12.16 19.88
63.56 12.17 19.87
63.55 12.17 19.86
@@ -160830,17 +161125,17 @@ Sweden
63.46 12.19 19.51 19.62 19.78
63.45 12.18 19.51 19.62 19.78
63.44 12.16 19.29 19.31 19.38 19.40 19.52 19.62 19.76
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63.41 12.13 19.28 19.45 19.52
63.40 12.11 19.28 19.47 19.52
63.39 12.10 19.28
63.38 12.09 19.28
63.37 12.08 19.28
- 63.36 12.07 19.28
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63.32 12.02 19.27
63.31 12.00 19.26
63.30 11.99 19.18
@@ -160848,30 +161143,30 @@ Sweden
63.28 11.98 19.16
63.27 11.98 19.15
63.26 11.99 19.14
- 63.25 12.00 19.14
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63.24 12.00 18.88 18.91 19.14
63.23 12.01 18.89 18.94 19.13
63.22 12.02 18.92 18.95 19.12
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63.18 12.05 18.90 18.99 19.07
63.17 12.06 18.81 19.01 19.06
63.16 12.07 18.81 19.02 19.06
- 63.15 12.08 18.80
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63.13 12.09 18.66
63.12 12.10 18.66
63.11 12.11 18.66
63.10 12.12 18.57 18.60 18.66
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63.07 12.14 18.56
63.06 12.15 18.56
63.05 12.16 18.55
63.04 12.17 18.53
63.03 12.18 18.50
- 63.02 12.19 18.50
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63.01 12.19 18.49
63.00 12.19 18.54
62.99 12.18 18.57
@@ -160891,13 +161186,13 @@ Sweden
62.85 12.09 18.48
62.84 12.09 18.46
62.83 12.10 18.42
- 62.82 12.10 18.28 18.32 18.39
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62.81 12.10 18.27
62.80 12.11 18.26
62.79 12.11 17.97 17.99 18.26
62.78 12.12 17.96 17.99 18.25
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62.75 12.13 17.98 18.01 18.16
62.74 12.13 17.99 18.01 18.17
62.73 12.14 18.17
@@ -160905,41 +161200,41 @@ Sweden
62.71 12.13 18.16
62.70 12.13 18.15
62.69 12.12 18.15
- 62.68 12.11 18.13
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62.67 12.11 18.13
62.66 12.10 18.00 18.04 18.10
62.65 12.10 18.00
62.64 12.09 18.02
62.63 12.09 18.05
62.62 12.08 18.05
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62.60 12.08 18.07
62.59 12.08 18.07
62.58 12.08 18.07
62.57 12.08 17.92 17.95 18.03
62.56 12.09 17.92 17.95 18.01
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62.54 12.10 17.92
62.53 12.11 17.91
62.52 12.12 17.90
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62.50 12.13 17.40 17.45 17.89
62.49 12.14 17.39 17.47 17.87
62.48 12.15 17.35 17.48 17.72 17.79 17.86
- 62.47 12.16 17.35 17.49 17.69 17.80 17.85
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62.46 12.16 17.36 17.50 17.70
62.45 12.17 17.37 17.51 17.70
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- 62.41 12.20 17.39
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62.38 12.22 17.37
62.37 12.23 17.37
62.36 12.24 17.37
- 62.35 12.25 17.38
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62.33 12.26 17.46
62.32 12.27 17.47
62.31 12.28 17.47
@@ -160953,8 +161248,8 @@ Sweden
62.23 12.30 17.66
62.22 12.29 17.66
62.21 12.29 17.64
- 62.20 12.29 17.51 17.53 17.62
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62.18 12.28 17.51
62.17 12.28 17.51
62.16 12.28 17.51
@@ -160964,31 +161259,31 @@ Sweden
62.12 12.26 17.49
62.11 12.26 17.49
62.10 12.26 17.48
- 62.09 12.26 17.48
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62.08 12.25 17.48
62.07 12.25 17.48
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62.05 12.24 17.47
62.04 12.24 17.47
62.03 12.24 17.46
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62.01 12.23 17.47
62.00 12.23 17.47
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61.98 12.22 17.46
61.97 12.22 17.39
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61.95 12.21 17.39
61.94 12.21 17.38
61.93 12.21 17.35
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61.91 12.20 17.36
61.90 12.20 17.37
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61.88 12.19 17.37
61.87 12.19 17.37
61.86 12.19 17.37
- 61.85 12.19 17.36
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61.84 12.18 17.36
61.83 12.18 17.41
61.82 12.18 17.41
@@ -161004,13 +161299,13 @@ Sweden
61.72 12.15 17.52
61.71 12.15 17.53
61.70 12.16 17.53
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61.62 12.32 17.24 17.42 17.50
61.61 12.33 17.25 17.45 17.49
61.60 12.35 17.25
@@ -161063,10 +161358,10 @@ Sweden
61.13 12.72 17.19
61.12 12.72 17.19
61.11 12.71 17.20
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61.06 12.53 12.63 12.70 17.18
61.05 12.47 17.18
61.04 12.39 17.19
@@ -161112,8 +161407,8 @@ Sweden
60.64 12.47 17.62
60.63 12.48 17.64
60.62 12.49 17.65
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60.59 12.51 17.66 17.79 17.98
60.58 12.52 17.65 17.77 17.99
60.57 12.52 17.63 17.75 17.99
@@ -161121,7 +161416,7 @@ Sweden
60.55 12.54 17.63 17.72 18.00
60.54 12.55 17.63 17.71 18.00
60.53 12.56 17.63 17.71 18.00
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60.51 12.57 18.02 18.36 18.42
60.50 12.58 18.04 18.36 18.43
60.49 12.58 18.06 18.36 18.43
@@ -161136,7 +161431,7 @@ Sweden
60.40 12.58 18.22 18.37 18.47
60.39 12.57 18.27 18.37 18.48
60.38 12.56 18.27 18.37 18.48
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60.36 12.54 18.34 18.38 18.54
60.35 12.52 18.54
60.34 12.50 18.55
@@ -161154,7 +161449,7 @@ Sweden
60.22 12.49 18.45 18.48 18.61 18.70 18.75
60.21 12.50 18.45 18.53 18.59 18.70 18.77
60.20 12.50 18.45 18.70 18.78
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60.18 12.51 18.48 18.53 18.55 18.70 18.81
60.17 12.51 18.50 18.53 18.55 18.70 18.81
60.16 12.51 18.55 18.60 18.64 18.70 18.81
@@ -161165,7 +161460,7 @@ Sweden
60.11 12.49 18.83
60.10 12.48 18.83
60.09 12.47 18.83
- 60.08 12.46 18.83
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60.07 12.44 18.83
60.06 12.43 18.84
60.05 12.41 18.84
@@ -161183,7 +161478,7 @@ Sweden
59.93 12.20 18.98
59.92 12.17 19.01
59.91 11.91 12.03 12.15 19.07
- 59.90 11.87 19.08
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59.89 11.85 19.08
59.88 11.83 19.08
59.87 11.83 19.07
@@ -161191,7 +161486,7 @@ Sweden
59.85 11.83 19.07
59.84 11.83 19.07
59.83 11.83 19.07
- 59.82 11.83 19.07
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59.81 11.84 19.01
59.80 11.85 19.01
59.79 11.87 19.07
@@ -161202,7 +161497,7 @@ Sweden
59.74 11.88 19.08
59.73 11.88 19.08
59.72 11.88 19.07
- 59.71 11.88 18.90 18.93 19.05
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59.70 11.87 18.87 18.94 19.01
59.69 11.85 18.82
59.68 11.84 18.77
@@ -161216,7 +161511,7 @@ Sweden
59.60 11.66 18.69 18.79 18.97
59.59 11.66 18.69 18.76 18.92
59.58 11.66 18.67 18.74 18.92
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59.56 11.66 18.62 18.64 18.67 18.74 18.80 18.87 18.89
59.55 11.66 18.68 18.71 18.74
59.54 11.66 18.74
@@ -161235,7 +161530,7 @@ Sweden
59.41 11.74 18.34 18.41 18.57 18.84 18.93
59.40 11.74 18.34 18.42 18.56 18.83 18.95
59.39 11.75 18.34 18.43 18.60 18.83 18.95
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59.37 11.76 18.73 18.83 18.87 18.89 18.95
59.36 11.76 18.75 18.91 18.95
59.35 11.77 18.75
@@ -161255,40 +161550,40 @@ Sweden
59.21 11.76 18.42 18.51 18.56 18.68 18.76
59.20 11.76 18.43 18.66 18.76
59.19 11.75 18.43 18.65 18.76
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59.17 11.74 18.44 18.64 18.72
59.16 11.74 18.44 18.64 18.68
59.15 11.73 18.44
59.14 11.73 18.44
59.13 11.73 18.43
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59.11 11.73 18.33 18.42 18.49
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59.03 11.10 11.39 11.69 17.71 17.75 18.06 18.09 18.22 18.33 18.45
59.02 11.10 11.41 11.69 17.71 17.74 18.06 18.08 18.22 18.33 18.43
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58.99 11.10 11.45 11.69 17.71 17.73 18.01 18.04 18.20 18.35 18.41
58.98 11.11 11.45 11.68 17.71 17.73 18.00 18.04 18.20 18.33 18.36
58.97 11.10 11.46 11.67 17.71 17.73 17.98 18.04 18.16 18.26 18.36
58.96 11.09 11.46 11.67 17.71 17.73 17.98 18.04 18.16 18.24 18.36
58.95 11.09 11.46 11.66 17.71 17.73 17.97 18.04 18.08 18.10 18.15 18.21 18.36
58.94 11.09 11.46 11.66 17.71 17.73 17.98 18.04 18.07 18.20 18.35
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58.91 11.16 11.46 11.61 17.70 17.73 17.97 18.18 18.32
58.90 11.18 11.47 11.57 17.70 17.76 17.81 17.85 17.96 18.18 18.28
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58.88 11.18 17.61 17.76 17.80 17.85 17.90
58.87 11.18 17.60 17.76 17.79 17.85 17.90
58.86 11.18 17.47 17.49 17.60 17.85 17.90
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58.84 11.19 17.47 17.53 17.59
58.83 11.21 17.47
58.82 11.22 17.47
@@ -161297,20 +161592,20 @@ Sweden
58.79 11.21 17.49
58.78 11.19 17.49
58.77 11.19 17.38
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58.75 11.17 17.38
58.74 11.16 17.37
58.73 11.16 17.29
58.72 11.16 17.28
58.71 11.16 17.15
58.70 11.16 17.15
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58.68 11.20 17.15
58.67 11.20 17.14
58.66 11.20 17.12
58.65 11.21 17.11
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58.62 11.24 16.99
58.61 11.24 16.79 16.83 16.95
58.60 11.24 16.79
@@ -161337,16 +161632,16 @@ Sweden
58.39 11.19 16.72 16.77 16.87 19.17 19.28
58.38 11.20 16.72 16.74 16.87 19.17 19.32
58.37 11.20 16.86 19.18 19.34
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58.32 11.22 11.24 11.37 16.92
58.31 11.37 16.91
58.30 11.37 11.73 11.79 16.80 16.82 16.89
58.29 11.37 11.74 11.79 16.79 16.82 16.89
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58.26 11.38 11.43 11.48 11.62 11.65 11.78 11.80 16.79 16.83 16.87
58.25 11.38 11.41 11.48 11.61 11.64 16.81
58.24 11.48 11.81 11.83 16.81
@@ -161358,39 +161653,39 @@ Sweden
58.18 11.43 16.83
58.17 11.41 16.83
58.16 11.40 16.83
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58.05 11.49 11.74 11.77 16.74
58.04 11.49 11.75 11.77 16.75
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58.02 11.48 11.75 11.78 16.76
58.01 11.48 11.75 11.78 16.76
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57.98 11.50 11.67 11.69 16.74 19.08 19.33
57.97 11.50 11.67 11.74 16.75 19.07 19.34
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+ 57.95 11.51 11.66 11.73 16.75 19.06 19.34
57.94 11.51 11.66 11.72 16.77 19.05 19.34
57.93 11.54 11.62 11.72 16.78 18.68 18.74 18.88 18.92 19.03 19.24 19.26 19.31
- 57.92 11.56 11.60 11.72 16.79 18.66 18.75 18.82 18.92 18.96 19.01 19.03 19.22
+ 57.92 11.57 11.60 11.72 16.79 18.66 18.75 18.82 18.92 18.96 19.00 19.02 19.22
57.91 11.72 16.79 18.64 18.76 18.82 19.19
57.90 11.69 16.58 16.60 16.79 18.64 18.76 18.82 19.17
- 57.89 11.68 16.58 16.60 16.77 18.63 18.78 18.82 19.17
- 57.88 11.68 16.58 16.60 16.77 18.62 18.78 18.83 19.17
+ 57.89 11.68 16.58 16.60 16.77 18.63 18.77 18.82 19.17
+ 57.88 11.68 16.58 16.60 16.68 16.70 16.77 18.62 18.77 18.83 19.17
57.87 11.68 16.57 16.71 16.77 18.61 18.78 18.81 19.17
57.86 11.66 16.54 16.73 16.76 18.61 18.78 18.80 19.16
57.85 11.65 16.55 18.60 18.78 18.80 19.15
57.84 11.64 16.57 18.52 19.14
- 57.83 11.64 16.59 18.48 19.14
+ 57.83 11.64 16.59 18.48 19.13
57.82 11.64 16.60 18.46 19.09
57.81 11.69 16.62 18.45 19.09
57.80 11.70 16.63 18.44 19.01
@@ -161400,17 +161695,17 @@ Sweden
57.76 11.75 16.71 18.40 18.99
57.75 11.73 16.71 18.39 18.94
57.74 11.71 16.71 18.37 18.94
- 57.73 11.69 16.71 18.36 18.95
+ 57.73 11.69 16.70 18.36 18.95
57.72 11.69 16.71 18.35 18.95
57.71 11.69 16.72 18.34 18.82 18.84 18.95
57.70 11.69 16.72 18.33 18.82
57.69 11.69 11.76 11.78 16.72 18.32 18.82
57.68 11.69 11.76 11.80 16.71 18.31 18.81
- 57.67 11.82 16.63 16.66 16.71 18.29 18.81
- 57.66 11.82 16.63 18.28 18.80
+ 57.67 11.82 16.62 16.66 16.71 18.29 18.81
+ 57.66 11.82 16.62 18.28 18.80
57.65 11.82 16.63 18.26 18.79
57.64 11.83 16.63 18.24 18.78
- 57.63 11.84 16.64 18.23 18.78
+ 57.63 11.83 16.64 18.23 18.78
57.62 11.84 16.64 18.21 18.79
57.61 11.84 16.64 18.20 18.82
57.60 11.85 16.61 18.18 18.82
@@ -161420,7 +161715,7 @@ Sweden
57.56 11.90 16.63 18.12 18.80
57.55 11.90 16.64 18.11 18.80
57.54 11.90 16.64 18.11 18.80
- 57.53 11.89 16.65 18.10 18.80
+ 57.53 11.89 16.65 18.10 18.79
57.52 11.89 16.66 18.10 18.79
57.51 11.89 16.67 18.10 18.78
57.50 11.90 16.68 18.10 18.78
@@ -161428,45 +161723,45 @@ Sweden
57.48 11.90 16.69 18.10 18.78
57.47 11.89 16.69 18.10 18.81
57.46 11.89 16.69 18.10 18.81
- 57.45 11.89 16.68 18.11 18.81 18.86 18.90
+ 57.45 11.89 16.68 18.11 18.90
57.44 11.89 16.68 18.11 18.92
57.43 11.89 12.03 12.05 16.65 18.12 18.93
- 57.42 11.89 12.02 12.07 16.68 18.13 18.93
+ 57.42 11.89 12.02 12.06 16.68 18.13 18.93
57.41 11.89 12.01 12.07 16.68 18.13 18.94
57.40 11.89 12.01 12.05 16.68 18.13 18.94
57.39 11.89 12.01 12.05 16.67 18.13 18.94
57.38 11.89 12.00 12.05 16.64 18.14 18.93
57.37 11.90 12.00 12.05 16.64 18.15 18.92
- 57.36 11.92 12.00 12.04 16.56 17.02 17.11 18.15 18.82
- 57.35 11.92 12.00 12.04 16.58 17.00 17.11 18.15 18.79
- 57.34 11.96 11.99 12.04 16.58 16.99 17.13 18.15 18.77
- 57.33 11.96 11.98 12.04 16.58 16.98 17.13 18.15 18.75
- 57.32 12.05 16.57 16.97 17.13 18.14 18.74
+ 57.36 11.92 12.00 12.03 16.56 17.02 17.11 18.15 18.82
+ 57.35 11.92 12.00 12.03 16.57 17.00 17.11 18.15 18.79
+ 57.34 11.96 11.99 12.03 16.57 16.99 17.12 18.15 18.77
+ 57.33 11.96 11.98 12.04 16.57 16.98 17.13 18.15 18.75
+ 57.32 12.05 12.08 12.10 16.57 16.97 17.13 18.14 18.74
57.31 12.11 16.57 16.95 17.13 18.12 18.72
57.30 12.12 16.57 16.95 17.13 18.10 18.70
57.29 12.13 16.55 16.95 17.09 18.10 18.68
- 57.28 12.11 16.51 16.95 17.07 18.09 18.72
+ 57.28 12.10 16.51 16.95 17.07 18.09 18.72
57.27 12.09 16.48 16.95 17.06 18.09 18.72
57.26 12.08 16.49 16.94 17.06 18.08 18.72
57.25 12.08 16.50 16.94 17.07 18.08 18.72
57.24 12.08 16.50 16.94 17.07 18.08 18.72
57.23 12.09 16.50 16.94 17.07 18.10 18.72
57.22 12.09 16.49 16.92 17.07 18.12 18.70
- 57.21 12.11 16.47 16.90 17.07 18.14 18.69
- 57.20 12.12 16.47 16.89 17.07 18.15 18.64
+ 57.21 12.11 16.47 16.89 17.07 18.14 18.69
+ 57.20 12.12 16.47 16.89 17.07 18.14 18.64
57.19 12.13 16.47 16.89 17.06 18.15 18.58
- 57.18 12.13 16.47 16.89 17.06 18.16 18.58
- 57.17 12.13 16.48 16.88 17.05 18.16 18.54
+ 57.18 12.13 16.47 16.89 17.06 18.15 18.58
+ 57.17 12.13 16.48 16.88 17.05 18.15 18.54
57.16 12.18 16.49 16.88 17.03 18.16 18.51
57.15 12.18 16.50 16.88 17.03 18.16 18.48
57.14 12.19 16.50 16.88 17.02 18.17 18.45
- 57.13 12.19 16.52 16.87 17.02 18.17 18.46
- 57.12 12.20 16.55 16.87 17.01 18.20 18.46
+ 57.13 12.19 16.53 16.87 17.02 18.17 18.46
+ 57.12 12.20 16.56 16.87 17.01 18.20 18.46
57.11 12.22 16.56 16.86 17.00 18.20 18.46
57.10 12.20 16.57 16.86 16.99 18.20 18.45
- 57.09 12.20 16.58 16.85 16.98 18.20 18.42
- 57.08 12.20 16.58 16.84 16.98 18.19 18.38
- 57.07 12.22 16.58 16.84 16.97 18.19 18.36
+ 57.09 12.20 16.57 16.85 16.98 18.20 18.42
+ 57.08 12.20 16.57 16.84 16.98 18.19 18.38
+ 57.07 12.22 16.57 16.84 16.97 18.19 18.35
57.06 12.23 16.58 16.83 16.97 18.19 18.35
57.05 12.23 16.59 16.82 16.97 18.19 18.35
57.04 12.24 16.59 16.81 16.96 18.23 18.34
@@ -161474,8 +161769,8 @@ Sweden
57.02 12.27 16.51 16.79 16.94 18.19 18.39
57.01 12.29 16.48 16.78 16.94 18.19 18.41
57.00 12.33 16.45 16.77 16.94 18.19 18.41
- 56.99 12.33 16.45 16.76 16.93 18.19 18.41
- 56.98 12.34 16.45 16.76 16.91 18.18 18.36
+ 56.99 12.33 16.44 16.76 16.93 18.19 18.41
+ 56.98 12.33 16.44 16.76 16.91 18.18 18.36
56.97 12.33 16.46 16.75 16.89 18.17 18.36
56.96 12.33 16.47 16.74 16.89 18.15 18.35
56.95 12.33 16.47 16.73 16.88 18.14 18.33
@@ -161483,40 +161778,40 @@ Sweden
56.93 12.33 16.47 16.73 16.89 18.12 18.32
56.92 12.33 16.47 16.72 16.89 18.12 18.28
56.91 12.34 16.46 16.72 16.89 18.12 18.25
- 56.90 12.36 16.44 16.70 16.89 18.15 18.22
- 56.89 12.39 16.45 16.62 16.88
- 56.88 12.42 16.45 16.61 16.86
- 56.87 12.47 16.45 16.60 16.86
- 56.86 12.47 16.45 16.60 16.86
- 56.85 12.48 16.45 16.59 16.85
+ 56.90 12.36 16.44 16.69 16.89 18.14 18.22
+ 56.89 12.39 16.44 16.62 16.88
+ 56.88 12.42 16.44 16.61 16.86
+ 56.87 12.47 16.44 16.60 16.86
+ 56.86 12.47 16.44 16.60 16.86
+ 56.85 12.48 16.44 16.59 16.85
56.84 12.51 16.44 16.58 16.85
- 56.83 12.52 16.43 16.57 16.85
+ 56.83 12.51 16.43 16.57 16.85
56.82 12.54 16.43 16.57 16.85
56.81 12.57 16.42 16.56 16.84
56.80 12.58 16.42 16.44 16.48 16.55 16.81
56.79 12.58 16.48 16.55 16.78
56.78 12.58 16.48 16.54 16.77
56.77 12.58 16.48 16.53 16.77
- 56.76 12.58 16.48 16.53 16.77
+ 56.76 12.59 16.48 16.53 16.77
56.75 12.59 16.39 16.43 16.46 16.52 16.77
- 56.74 12.59 16.37 16.51 16.77
- 56.73 12.60 16.38 16.50 16.76
+ 56.74 12.60 16.37 16.51 16.77
+ 56.73 12.61 16.38 16.50 16.76
56.72 12.62 16.38 16.50 16.75
56.71 12.63 16.39 16.49 16.75
56.70 12.65 16.39 16.48 16.74
56.69 12.65 16.39 16.48 16.74
56.68 12.66 16.39 16.47 16.73
56.67 12.66 16.39 16.46 16.72
- 56.66 12.67 16.38 16.45 16.72
+ 56.66 12.66 16.38 16.45 16.72
56.65 12.68 16.38 16.45 16.71
56.64 12.70 16.28 16.31 16.37 16.44 16.71
56.63 12.72 12.80 12.85 16.25 16.44 16.70
56.62 12.87 16.24 16.43 16.70
- 56.61 12.87 16.24 16.43 16.70
- 56.60 12.88 16.23 16.42 16.70
- 56.59 12.88 16.23 16.41 16.69
+ 56.61 12.87 16.24 16.43 16.69
+ 56.60 12.88 16.23 16.41 16.69
+ 56.59 12.88 16.23 16.40 16.69
56.58 12.89 16.23 16.40 16.69
- 56.57 12.90 16.23 16.40 16.68
+ 56.57 12.90 16.23 16.39 16.68
56.56 12.90 16.22 16.39 16.67
56.55 12.91 16.22 16.38 16.65
56.54 12.91 16.22 16.38 16.64
@@ -161527,7 +161822,7 @@ Sweden
56.49 12.91 16.17 16.38 16.63
56.48 12.90 16.16 16.38 16.63
56.47 12.68 12.75 12.89 16.15 16.38 16.63
- 56.46 12.64 12.81 12.86 16.14 16.38 16.63
+ 56.46 12.64 12.81 12.86 16.14 16.38 16.62
56.45 12.63 16.13 16.38 16.62
56.44 12.63 16.12 16.38 16.61
56.43 12.62 16.12 16.38 16.60
@@ -161536,10 +161831,10 @@ Sweden
56.40 12.61 16.10 16.39 16.59
56.39 12.62 16.10 16.39 16.58
56.38 12.63 16.09 16.39 16.58
- 56.37 12.65 16.09 16.39 16.58
- 56.36 12.67 16.09 16.39 16.58
- 56.35 12.69 16.08 16.39 16.58
- 56.34 12.71 16.08 16.39 16.58
+ 56.37 12.65 16.09 16.39 16.57
+ 56.36 12.67 16.09 16.39 16.57
+ 56.35 12.69 16.08 16.39 16.57
+ 56.34 12.71 16.08 16.39 16.57
56.33 12.73 16.07 16.39 16.57
56.32 12.73 16.07 16.39 16.56
56.31 12.44 12.47 12.74 16.07 16.39 16.55
@@ -161558,23 +161853,23 @@ Sweden
56.18 12.54 15.98
56.17 12.54 15.64 15.66 15.96
56.16 12.55 15.05 15.07 15.52 15.56 15.63 15.68 15.94
- 56.15 12.56 14.94 14.96 15.05 15.07 15.39 15.44 15.49 15.58 15.62 15.69 15.93
- 56.14 12.57 14.70 14.79 14.86 15.01 15.05 15.17 15.25 15.28 15.38 15.47 15.49 15.72 15.92
- 56.13 12.57 14.69 14.80 14.86 15.28 15.38 15.65 15.68 15.79 15.91
+ 56.15 12.56 14.94 14.96 15.05 15.07 15.39 15.44 15.49 15.58 15.62 15.71 15.93
+ 56.14 12.57 14.70 14.80 14.85 15.01 15.05 15.17 15.25 15.28 15.38 15.46 15.49 15.72 15.92
+ 56.13 12.57 14.69 14.82 14.85 15.28 15.38 15.65 15.68 15.79 15.91
56.12 12.58 14.70 15.31 15.35 15.64 15.73 15.78 15.91
56.11 12.59 14.72 15.63 15.73 15.77 15.90
56.10 12.59 14.72 15.63 15.73 15.77 15.89
- 56.09 12.60 14.73 15.63 15.72 15.77 15.88
- 56.08 12.62 14.74 15.63 15.71 15.79 15.87
- 56.07 12.63 14.75 15.64 15.71 15.82 15.86
- 56.06 12.65 14.75 15.66 15.71
+ 56.09 12.60 14.72 15.63 15.72 15.77 15.88
+ 56.08 12.62 14.74 15.64 15.71 15.79 15.87
+ 56.07 12.63 14.75 15.65 15.71 15.82 15.86
+ 56.06 12.65 14.75 15.67 15.71
56.05 12.66 14.76
56.04 12.68 14.77
56.03 12.69 14.55 14.57 14.77
56.02 12.69 14.49 14.59 14.77
- 56.01 12.69 14.47 14.60 14.76
- 56.00 12.71 14.46 14.60 14.74
- 55.99 12.72 14.45 14.61 14.68 14.70 14.73
+ 56.01 12.69 14.47 14.59 14.76
+ 56.00 12.70 14.46 14.59 14.74
+ 55.99 12.72 14.45 14.64 14.68 14.70 14.73
55.98 12.74 14.44
55.97 12.75 14.43
55.96 12.75 14.41
@@ -161584,7 +161879,7 @@ Sweden
55.92 12.78 14.34
55.91 12.79 14.34
55.90 12.79 14.33
- 55.89 12.79 14.32
+ 55.89 12.80 14.32
55.88 12.80 14.30
55.87 12.81 14.27
55.86 12.82 14.26
@@ -161603,12 +161898,12 @@ Sweden
55.73 12.91 14.20
55.72 12.95 14.20
55.71 12.96 14.22
- 55.70 13.01 14.24
- 55.69 13.03 14.26
+ 55.70 13.01 14.25
+ 55.69 13.03 14.27
55.68 13.04 14.27
55.67 13.04 14.28
55.66 13.04 14.28
- 55.65 13.04 14.28
+ 55.65 13.03 14.28
55.64 13.02 14.28
55.63 13.00 14.29
55.62 12.98 14.31
@@ -161623,23 +161918,23 @@ Sweden
55.53 12.90 14.37
55.52 12.90 14.37
55.51 12.91 14.37
- 55.50 12.91 14.36
- 55.49 12.92 14.34
- 55.48 12.93 14.33
+ 55.50 12.92 14.36
+ 55.49 12.93 14.34
+ 55.48 12.94 14.33
55.47 12.95 14.31
55.46 12.95 14.30
- 55.45 12.95 14.29
- 55.44 12.85 12.88 12.95 14.26
- 55.43 12.84 12.90 12.94 14.25
- 55.42 12.83 14.24
- 55.41 12.82 13.87 13.94 14.23
+ 55.45 12.94 14.29
+ 55.44 12.84 12.88 12.94 14.26
+ 55.43 12.83 12.90 12.93 14.25
+ 55.42 12.82 14.24
+ 55.41 12.81 13.87 13.94 14.23
55.40 12.81 13.64 13.96 14.22
- 55.39 12.81 13.61 13.99 14.22
- 55.38 12.81 13.60 14.01 14.21
+ 55.39 12.81 13.61 13.99 14.21
+ 55.38 12.81 12.95 12.99 13.60 14.01 14.20
55.37 12.82 12.88 12.90 12.94 13.01 13.52 13.55 13.59 14.07 14.17
- 55.36 13.08 13.49
- 55.35 13.13 13.46
- 55.34 13.19 13.43
+ 55.36 13.13 13.49
+ 55.35 13.17 13.46
+ 55.34 13.21 13.43
55.33 13.25 13.40
Switzerland
47.81 8.54 8.60
@@ -161667,7 +161962,7 @@ Switzerland
47.59 7.56 7.66 7.80 7.91 8.09 9.44
47.58 7.53 7.66 7.79 7.91 8.08 9.47
47.57 7.51 7.66 7.77 9.49
- 47.56 7.49 7.65 7.72 9.51
+ 47.56 7.49 7.66 7.70 9.51
47.55 7.47 9.53
47.54 7.47 9.55
47.53 7.47 9.55
@@ -161706,8 +162001,8 @@ Switzerland
47.20 6.84 9.49
47.19 6.84 9.49
47.18 6.83 9.49
- 47.17 6.83 9.49
- 47.16 6.81 9.50
+ 47.17 6.82 9.49
+ 47.16 6.80 9.50
47.15 6.79 9.51
47.14 6.77 9.51
47.13 6.73 9.52
@@ -161789,9 +162084,9 @@ Switzerland
46.37 6.11 6.30 6.75 8.30 8.43 9.27 9.43 10.14
46.36 6.12 6.28 6.74 8.30 8.43 9.28 9.43 10.13
46.35 6.11 6.26 6.74 8.28 8.43 9.28 9.46 9.88 9.92 10.12
- 46.34 6.11 6.26 6.74 8.26 8.42 9.28 9.47 9.84 9.94 10.10
+ 46.34 6.10 6.26 6.74 8.26 8.42 9.28 9.47 9.84 9.94 10.10
46.33 6.10 6.25 6.74 8.24 8.42 9.28 9.48 9.72 9.74 9.80 9.95 10.10
- 46.32 6.10 6.24 6.74 8.23 8.41 9.28 9.48 9.71 9.75 9.78 9.96 10.10
+ 46.32 6.09 6.24 6.74 8.23 8.41 9.28 9.48 9.71 9.75 9.78 9.96 10.10
46.31 6.09 6.22 6.75 8.22 8.41 9.28 9.49 9.71 9.96 10.12
46.30 6.09 6.22 6.76 8.21 8.41 9.27 9.49 9.71 9.96 10.14
46.29 6.08 6.23 6.78 8.20 8.41 9.27 9.50 9.71 9.96 10.15
@@ -161828,10 +162123,10 @@ Switzerland
45.98 6.97 7.99 8.75 9.02
45.97 6.98 7.93 8.75 9.01
45.96 6.98 7.54 7.56 7.89 8.79 9.00
- 45.95 6.99 7.52 7.61 7.88 8.81 9.00
- 45.94 6.99 7.51 7.66 7.87 8.83 9.01
- 45.93 6.99 7.47 7.67 7.86 8.86 9.04
- 45.92 7.00 7.45 7.68 7.85 8.87 9.06
+ 45.95 6.99 7.52 7.61 7.89 8.81 9.00
+ 45.94 6.99 7.51 7.66 7.88 8.83 9.01
+ 45.93 6.99 7.47 7.67 7.88 8.86 9.04
+ 45.92 7.00 7.45 7.68 7.86 8.87 9.06
45.91 7.01 7.43 7.68 7.85 8.87 9.06
45.90 7.02 7.41 7.76 7.85 8.88 9.07
45.89 7.04 7.27 7.32 7.38 8.88 9.07
@@ -161860,10 +162155,10 @@ Syria
37.20 42.03 42.36
37.19 42.01 42.35
37.18 41.97 42.35
- 37.17 41.92 42.34
+ 37.17 41.91 42.34
37.16 41.86 42.36
37.15 41.81 42.36
- 37.14 41.76 42.36
+ 37.14 41.75 42.36
37.13 40.84 40.93 41.70 42.36
37.12 40.74 40.99 41.65 42.36
37.11 40.68 41.05 41.60 42.36
@@ -161882,8 +162177,8 @@ Syria
36.98 40.34 42.29
36.97 40.32 42.28
36.96 40.30 42.27
- 36.95 40.29 42.25
- 36.94 40.27 42.24
+ 36.95 40.28 42.25
+ 36.94 40.26 42.24
36.93 40.25 42.23
36.92 40.23 42.22
36.91 38.17 38.30 40.21 42.21
@@ -161895,20 +162190,20 @@ Syria
36.85 38.03 38.51 40.04 42.13
36.84 38.01 38.53 40.02 42.12
36.83 36.62 36.67 37.99 38.54 40.00 42.11
- 36.82 36.62 36.71 37.96 38.55 39.98 42.10
+ 36.82 36.62 36.71 37.96 38.56 39.98 42.10
36.81 36.62 36.75 37.92 38.57 39.95 42.09
36.80 36.62 36.79 37.89 38.58 39.91 42.08
36.79 36.62 36.83 37.86 38.59 39.88 42.06
36.78 36.61 36.92 37.82 38.60 39.84 42.05
- 36.77 36.60 36.96 37.78 38.61 39.81 42.04
- 36.76 36.60 36.98 37.73 38.62 39.77 42.03
+ 36.77 36.60 36.96 37.78 38.62 39.81 42.04
+ 36.76 36.60 36.98 37.73 38.63 39.77 42.03
36.75 36.59 36.99 37.67 38.64 39.72 42.02
36.74 36.59 37.00 37.63 38.65 39.66 42.00
- 36.73 36.58 37.01 37.60 38.66 39.59 41.99
- 36.72 36.58 37.02 37.58 38.68 39.52 41.98
- 36.71 36.58 37.02 37.56 38.71 39.00 39.05 39.46 41.97
- 36.70 36.58 37.02 37.54 38.76 38.87 39.08 39.39 41.96
- 36.69 36.58 37.02 37.52 39.11 39.32 41.95
+ 36.73 36.58 37.01 37.60 38.66 39.60 41.99
+ 36.72 36.58 37.02 37.58 38.68 39.53 41.98
+ 36.71 36.58 37.02 37.56 38.71 39.00 39.05 39.47 41.97
+ 36.70 36.58 37.02 37.54 38.76 38.87 39.08 39.40 41.96
+ 36.69 36.58 37.02 37.52 39.11 39.33 41.95
36.68 36.58 37.02 37.50 39.14 39.26 41.94
36.67 36.57 37.02 37.48 39.17 39.20 41.93
36.66 36.57 37.02 37.09 37.12 37.18 37.29 37.46 41.92
@@ -162022,12 +162317,12 @@ Syria
35.58 35.71 41.35
35.57 35.71 41.34
35.56 35.71 41.33
- 35.55 35.72 41.33
- 35.54 35.74 41.32
- 35.53 35.76 41.31
+ 35.55 35.72 41.32
+ 35.54 35.74 41.31
+ 35.53 35.76 41.30
35.52 35.76 41.30
35.51 35.76 41.29
- 35.50 35.76 41.29
+ 35.50 35.76 41.28
35.49 35.76 41.28
35.48 35.77 35.79 35.82 41.27
35.47 35.83 41.27
@@ -162076,7 +162371,7 @@ Syria
35.04 35.87 41.20
35.03 35.88 41.20
35.02 35.88 41.20
- 35.01 35.88 41.20
+ 35.01 35.87 41.20
35.00 35.87 41.20
34.99 35.87 41.20
34.98 35.86 41.20
@@ -162114,9 +162409,9 @@ Syria
34.66 35.94 41.14
34.65 35.95 36.29 36.32 41.14
34.64 35.95 36.29 36.32 41.13
- 34.63 35.96 36.29 36.33 41.12
+ 34.63 35.95 36.29 36.33 41.12
34.62 36.00 36.29 36.34 41.12
- 34.61 36.02 36.08 36.11 36.27 36.35 41.11
+ 34.61 36.02 36.27 36.35 41.11
34.60 36.37 41.11
34.59 36.37 41.10
34.58 36.37 41.09
@@ -162128,8 +162423,8 @@ Syria
34.52 36.30 41.06
34.51 36.30 41.05
34.50 36.30 41.04
- 34.49 36.31 41.04
- 34.48 36.32 36.38 36.40 41.03
+ 34.49 36.30 41.04
+ 34.48 36.31 36.38 36.40 41.03
34.47 36.42 41.02
34.46 36.42 41.02
34.45 36.43 41.01
@@ -162233,9 +162528,9 @@ Syria
33.47 35.90 39.01
33.46 35.88 38.99
33.45 35.87 38.97
- 33.44 35.85 38.95
+ 33.44 35.86 38.95
33.43 35.84 38.93
- 33.42 35.82 38.91
+ 33.42 35.83 38.91
33.41 35.81 38.89
33.40 35.80 38.87
33.39 35.80 38.85
@@ -162260,14 +162555,14 @@ Syria
33.20 35.79 38.48
33.19 35.79 38.46
33.18 35.81 38.44
- 33.17 35.82 38.43
- 33.16 35.82 38.41
- 33.15 35.81 38.39
- 33.14 35.81 38.37
- 33.13 35.80 38.35
- 33.12 35.80 38.33
- 33.11 35.80 38.32
- 33.10 35.80 38.30
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+ 33.14 35.81 38.36
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+ 33.12 35.80 38.32
+ 33.11 35.80 38.31
+ 33.10 35.80 38.29
33.09 35.81 38.28
33.08 35.83 38.26
33.07 35.83 38.24
@@ -162306,12 +162601,12 @@ Syria
32.74 35.74 37.63
32.73 35.74 37.61
32.72 35.77 37.59
- 32.71 35.80 37.58
- 32.70 35.86 37.56
- 32.69 35.89 37.54
- 32.68 35.91 37.52
- 32.67 35.92 37.50
- 32.66 35.92 37.48
+ 32.71 35.80 37.57
+ 32.70 35.86 37.55
+ 32.69 35.89 37.53
+ 32.68 35.91 37.51
+ 32.67 35.92 37.49
+ 32.66 35.92 37.47
32.65 35.93 37.46
32.64 35.94 37.44
32.63 35.99 37.42
@@ -162343,8 +162638,8 @@ Syria
32.37 36.36 36.94
32.36 36.37 36.93
32.35 36.43 36.91
- 32.34 36.52 36.89
- 32.33 36.60 36.87
+ 32.34 36.49 36.89
+ 32.33 36.58 36.87
32.32 36.65 36.86
32.31 36.66 36.84
32.30 36.67 36.70 36.75 36.82
@@ -162356,7 +162651,7 @@ Taiwan
25.25 121.42 121.62
25.24 121.42 121.63
25.23 121.41 121.64
- 25.22 121.41 121.65
+ 25.22 121.41 121.64
25.21 121.40 121.69
25.20 121.38 121.69
25.19 121.38 121.69
@@ -162366,13 +162661,13 @@ Taiwan
25.15 121.34 121.78
25.14 121.30 121.83
25.13 121.24 121.87
- 25.12 121.20 121.90
- 25.11 121.18 121.91
- 25.10 121.15 121.91
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25.09 121.13 121.91
25.08 121.10 121.90
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+ 25.06 121.04 121.90
25.05 121.03 121.91
25.04 121.03 121.91
25.03 121.02 121.98
@@ -162381,13 +162676,13 @@ Taiwan
25.00 120.98 122.01
24.99 120.98 122.01
24.98 120.97 122.00
- 24.97 120.96 121.98
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24.96 120.96 121.96
24.95 120.95 121.94
24.94 120.95 121.92
- 24.93 120.94 121.91
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+ 24.91 120.93 121.88
24.90 120.92 121.88
24.89 120.91 121.87
24.88 120.91 121.86
@@ -162411,7 +162706,7 @@ Taiwan
24.70 120.82 121.83
24.69 120.81 121.83
24.68 120.78 121.83
- 24.67 120.76 121.83
+ 24.67 120.76 121.82
24.66 120.75 121.82
24.65 120.74 121.82
24.64 120.72 121.82
@@ -162422,25 +162717,25 @@ Taiwan
24.59 120.68 121.89
24.58 120.68 121.89
24.57 120.67 121.86
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24.54 120.65 121.86
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24.37 120.53 121.78
24.36 120.53 121.78
24.35 120.53 121.77
@@ -162498,56 +162793,56 @@ Taiwan
23.83 120.21 121.58
23.82 120.20 121.58
23.81 120.20 121.58
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23.79 120.18 121.57
23.78 120.17 121.57
23.77 120.17 121.57
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23.74 120.16 121.56
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23.55 119.43 119.49 119.52 119.68 120.10 121.51
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23.40 120.13 121.48
23.39 120.13 121.48
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23.35 120.11 121.47
23.34 120.11 121.47
23.33 120.11 121.47
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23.30 120.10 121.45
23.29 120.09 121.44
23.28 120.09 121.43
@@ -162556,7 +162851,7 @@ Taiwan
23.25 120.08 121.42
23.24 120.07 121.41
23.23 120.07 121.41
- 23.22 120.06 121.41
+ 23.22 120.07 121.41
23.21 120.06 121.41
23.20 120.06 121.41
23.19 120.06 121.41
@@ -162588,22 +162883,22 @@ Taiwan
22.93 120.15 121.29
22.92 120.15 121.29
22.91 120.15 121.28
- 22.90 120.16 121.28
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22.89 120.16 121.27
22.88 120.16 121.26
22.87 120.16 121.25
22.86 120.16 121.24
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22.83 120.18 121.20
22.82 120.18 121.20
22.81 120.18 121.20
22.80 120.18 121.20
22.79 120.18 121.20
- 22.78 120.19 121.19
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22.76 120.19 121.18
- 22.75 120.20 121.17
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22.74 120.20 121.16
22.73 120.21 121.15
22.72 120.21 121.14
@@ -162622,18 +162917,18 @@ Taiwan
22.59 120.27 121.01
22.58 120.27 121.01
22.57 120.27 121.00
- 22.56 120.27 120.99
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22.55 120.28 120.99
22.54 120.29 120.98
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22.51 120.31 120.95
22.50 120.32 120.95
22.49 120.33 120.95
22.48 120.35 120.95
22.47 120.37 120.95
22.46 120.41 120.95
- 22.45 120.43 120.94
+ 22.45 120.42 120.94
22.44 120.44 120.94
22.43 120.46 120.94
22.42 120.48 120.93
@@ -162668,7 +162963,7 @@ Taiwan
22.13 120.67 120.88
22.12 120.67 120.88
22.11 120.68 120.88
- 22.10 120.68 120.88
+ 22.10 120.67 120.88
22.09 120.67 120.88 121.48 121.57
22.08 120.67 120.88 121.48 121.57
22.07 120.67 120.88 121.48 121.57
@@ -162783,9 +163078,9 @@ Tajikistan
40.15 68.57 69.81 70.07 70.84 70.86 70.91
40.14 68.58 69.77 70.09 70.82
40.13 68.59 69.73 70.11 70.78
- 40.12 68.61 68.89 68.94 69.70 70.13 70.77
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- 40.10 68.66 68.73 68.96 69.63 70.26 70.71
+ 40.12 68.61 68.90 68.94 69.70 70.13 70.77
+ 40.11 68.63 68.82 68.96 69.66 70.25 70.75
+ 40.10 68.66 68.74 68.96 69.63 70.26 70.71
40.09 68.97 69.59 70.27 70.68
40.08 68.76 68.80 68.87 68.92 68.97 69.51 70.28 70.66
40.07 68.75 68.80 68.85 69.50 70.29 70.64
@@ -162835,7 +163130,7 @@ Tajikistan
39.63 67.69 67.79 68.57 69.30
39.62 67.67 67.84 68.56 69.30 70.17 70.21 71.43 71.47
39.61 67.65 67.89 68.55 69.30 70.16 70.22 70.46 70.49 71.41 71.49
- 39.60 67.63 67.94 68.53 69.30 70.16 70.22 70.41 70.51 71.35 71.51
+ 39.60 67.63 67.94 68.53 69.30 70.16 70.22 70.41 70.51 71.35 71.50
39.59 67.61 67.98 68.51 69.30 70.15 70.22 70.39 70.52 71.35 71.52
39.58 67.59 68.03 68.50 69.30 69.57 69.73 70.02 70.08 70.15 70.22 70.32 70.61 71.33 71.52
39.57 67.54 68.08 68.49 69.29 69.55 69.76 70.00 70.10 70.14 70.22 70.30 70.63 71.31 71.53
@@ -162873,7 +163168,7 @@ Tajikistan
39.25 67.33 72.21 72.26 73.62
39.24 67.33 72.21 72.26 73.62
39.23 67.33 72.21 72.25 73.61
- 39.22 67.33 72.21 72.25 73.61
+ 39.22 67.34 72.21 72.25 73.61
39.21 67.34 72.22 72.24 73.61
39.20 67.34 72.22 72.24 73.62
39.19 67.35 73.63
@@ -163000,7 +163295,7 @@ Tajikistan
37.98 68.25 70.31 71.25 74.90
37.97 68.24 70.29 71.25 74.90
37.96 68.24 70.28 71.24 74.90
- 37.95 68.23 70.26 71.24 74.90
+ 37.95 68.22 70.26 71.24 74.90
37.94 68.15 70.27 71.24 74.89
37.93 68.12 70.27 71.24 74.89
37.92 68.12 70.27 71.24 71.48 71.53 74.90
@@ -163170,7 +163465,7 @@ Tanzania
-1.33 30.55 34.60
-1.34 30.56 34.62
-1.35 30.58 34.64
- -1.36 30.60 34.66
+ -1.36 30.60 34.65
-1.37 30.61 34.67
-1.38 30.64 34.69
-1.39 30.66 34.71
@@ -163201,15 +163496,15 @@ Tanzania
-1.64 30.82 35.16
-1.65 30.82 35.18
-1.66 30.82 35.20
- -1.67 30.81 35.21
- -1.68 30.81 35.23
+ -1.67 30.81 35.22
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-1.69 30.81 35.25
-1.70 30.81 35.27
- -1.71 30.81 35.28
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-1.72 30.81 35.30
-1.73 30.81 35.32
-1.74 30.81 35.34
- -1.75 30.82 35.35
+ -1.75 30.82 35.36
-1.76 30.81 35.37
-1.77 30.81 35.39
-1.78 30.81 35.41
@@ -163323,9 +163618,9 @@ Tanzania
-2.86 30.40 37.35
-2.87 30.41 37.37
-2.88 30.42 37.39
- -2.89 30.43 37.41
- -2.90 30.44 37.43
- -2.91 30.45 37.45
+ -2.89 30.43 37.40
+ -2.90 30.44 37.42
+ -2.91 30.45 37.44
-2.92 30.45 30.52 30.55 37.46
-2.93 30.46 30.51 30.57 37.48
-2.94 30.47 30.51 30.59 37.50
@@ -163352,12 +163647,12 @@ Tanzania
-3.15 30.81 37.68
-3.16 30.82 37.68
-3.17 30.82 37.68
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+ -3.18 30.81 37.69
-3.19 30.80 37.69
-3.20 30.79 37.69
-3.21 30.79 37.69
- -3.22 30.79 37.69
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+ -3.22 30.79 37.70
+ -3.23 30.79 37.70
-3.24 30.79 37.70
-3.25 30.79 37.70
-3.26 30.78 37.70
@@ -163441,9 +163736,9 @@ Tanzania
-4.04 30.15 38.33
-4.05 30.15 38.34
-4.06 30.14 38.36
- -4.07 30.13 38.37
+ -4.07 30.13 38.38
-4.08 30.12 38.39
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+ -4.09 30.12 38.41
-4.10 30.11 38.42
-4.11 30.10 38.43
-4.12 30.09 38.45
@@ -163522,25 +163817,25 @@ Tanzania
-4.85 29.31 39.22
-4.86 29.31 39.22
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- -4.88 29.31 39.21 39.67 39.69 39.84 39.87
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-5.00 29.33 39.14 39.66 39.88
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-5.07 29.35 39.15 39.68 39.84
-5.08 29.36 39.15 39.68 39.84
-5.09 29.36 39.15 39.68 39.86
@@ -163552,9 +163847,9 @@ Tanzania
-5.15 29.39 39.10 39.71 39.87
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-5.21 29.43 39.08 39.64 39.86
-5.22 29.43 39.09 39.65 39.86
-5.23 29.44 39.09 39.69 39.86
@@ -163572,17 +163867,17 @@ Tanzania
-5.35 29.47 39.04 39.63 39.82
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@@ -163641,13 +163936,13 @@ Tanzania
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@@ -163675,10 +163970,10 @@ Tanzania
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@@ -163711,13 +164006,13 @@ Tanzania
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@@ -163765,7 +164060,7 @@ Tanzania
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@@ -163773,8 +164068,8 @@ Tanzania
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@@ -163801,9 +164096,9 @@ Tanzania
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@@ -163819,12 +164114,12 @@ Tanzania
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@@ -163832,23 +164127,23 @@ Tanzania
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@@ -163880,8 +164175,8 @@ Tanzania
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@@ -163909,8 +164204,8 @@ Tanzania
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@@ -163921,8 +164216,8 @@ Tanzania
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@@ -163942,7 +164237,7 @@ Tanzania
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@@ -163961,11 +164256,11 @@ Tanzania
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@@ -163975,7 +164270,7 @@ Tanzania
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@@ -164034,7 +164329,7 @@ Tanzania
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@@ -164057,8 +164352,8 @@ Tanzania
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@@ -164130,7 +164425,7 @@ Tanzania
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@@ -164239,7 +164534,7 @@ Thailand
20.19 99.50 100.48
20.18 99.51 100.49
20.17 99.51 100.51 100.53 100.55
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20.15 99.47 100.55
20.14 99.47 100.55
20.13 99.13 99.20 99.46 100.56
@@ -164278,7 +164573,7 @@ Thailand
19.80 98.01 98.07 98.77 98.85 98.97 100.43
19.79 98.00 98.07 98.76 98.86 98.95 100.42
19.78 98.00 98.13 98.74 98.87 98.92 100.41
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19.76 98.00 98.16 98.68 100.40
19.75 97.99 98.17 98.63 100.39
19.74 97.99 98.19 98.61 100.39
@@ -164297,13 +164592,13 @@ Thailand
19.61 97.93 100.44 100.85 101.03
19.60 97.91 100.45 100.84 101.05
19.59 97.89 100.46 100.83 101.06 101.17 101.23
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19.57 97.83 100.46 100.81 101.26
19.56 97.82 100.46 100.81 101.26
19.55 97.82 100.46 100.59 100.65 100.80 101.26
19.54 97.82 100.47 100.58 100.68 100.79 101.26
19.53 97.82 100.49 100.57 100.70 100.78 101.26
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19.51 97.82 100.54 100.56 100.73 100.76 101.26
19.50 97.83 101.26
19.49 97.83 101.26
@@ -164435,14 +164730,14 @@ Thailand
18.23 97.60 101.14 103.14 104.06
18.22 97.60 101.15 102.06 102.17 103.14 104.07
18.21 97.61 101.16 102.06 102.18 103.14 104.07
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18.12 97.67 101.15 101.97 102.25 103.05 104.12
18.11 97.67 101.15 101.96 102.25 103.05 104.12
18.10 97.67 101.15 101.95 102.26 103.05 104.13
@@ -164468,7 +164763,7 @@ Thailand
17.90 97.68 101.04 101.62 102.62 102.72 104.27
17.89 97.67 101.03 101.60 102.62 102.70 104.27
17.88 97.67 101.01 101.60 102.61 102.67 104.28
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17.86 97.67 101.01 101.56 102.61 102.65 104.29
17.85 97.67 101.01 101.56 102.60 102.65 104.31
17.84 97.66 101.01 101.56 102.62 102.65 104.33
@@ -164492,17 +164787,17 @@ Thailand
17.66 97.75 100.95 101.31 104.48
17.65 97.76 100.95 101.30 104.49
17.64 97.77 100.94 101.28 104.51
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17.62 97.80 100.92 101.26 104.55
17.61 97.81 100.91 101.24 104.57
17.60 97.82 100.90 101.23 104.59
17.59 97.83 100.90 101.22 104.61
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17.55 97.88 101.00 101.20 104.68
17.54 97.89 101.01 101.19 104.70
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17.52 97.92 101.04 101.15 104.72
17.51 97.93 101.04 101.15 104.73
17.50 97.95 101.07 101.15 104.73
@@ -164625,7 +164920,7 @@ Thailand
16.33 98.63 98.76 98.88 104.96
16.32 98.64 98.74 98.88 104.97
16.31 98.64 98.73 98.88 104.98
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16.29 98.64 98.72 98.87 105.01
16.28 98.64 98.71 98.87 105.02
16.27 98.65 98.70 98.87 105.02
@@ -164646,7 +164941,7 @@ Thailand
16.12 98.64 105.07
16.11 98.64 105.09
16.10 98.64 105.12
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16.08 98.63 105.19
16.07 98.62 105.22
16.06 98.54 98.57 98.60 105.24
@@ -164732,7 +165027,7 @@ Thailand
15.26 98.24 105.57
15.25 98.23 105.56
15.24 98.23 105.54
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15.22 98.16 105.51
15.21 98.16 105.50
15.20 98.16 105.49
@@ -164818,12 +165113,12 @@ Thailand
14.40 98.51 103.62 103.66 104.74 104.80 105.39
14.39 98.51 103.53 103.57 103.61 103.66 104.60 104.63 104.67 104.70 104.73 104.88 105.36
14.38 98.52 103.51 103.66 104.59 104.88 105.35
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14.36 98.53 103.40 103.42 103.47 103.72 104.16 104.19 104.21 104.30 104.58 104.96 105.28
14.35 98.54 103.39 103.75 104.07 104.11 104.15 104.37 104.48 104.51 104.57 104.96 105.27
14.34 98.55 103.38 103.83 103.92 103.97 104.05 104.43 104.47 104.96 105.26
14.33 98.56 103.26 103.84 103.91 103.99 104.02 104.96 105.23
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14.31 98.58 103.21 104.96 105.16
14.30 98.59 103.17 104.96 105.15
14.29 98.60 103.11 104.96 105.15
@@ -164831,7 +165126,7 @@ Thailand
14.27 98.64 103.08 104.97 105.14
14.26 98.65 103.07 104.97 105.13
14.25 98.66 103.06 104.98 105.13
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14.23 98.70 103.03 104.99 105.12
14.22 98.71 103.02 105.00 105.11
14.21 98.72 103.01 105.01 105.09
@@ -164905,10 +165200,10 @@ Thailand
13.53 99.15 102.32
13.52 99.15 100.59 100.61 102.33
13.51 99.15 100.59 100.63 102.33
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13.46 99.16 100.25 100.83 102.33
13.45 99.16 100.22 100.87 102.33
13.44 99.16 100.20 100.96 102.34
@@ -164933,7 +165228,7 @@ Thailand
13.25 99.17 99.98 100.91 102.34
13.24 99.17 99.98 100.92 102.35
13.23 99.17 99.99 100.92 102.35
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13.21 99.17 100.02 100.93 102.36
13.20 99.12 100.03 100.93 102.36
13.19 99.10 100.05 100.92 102.37
@@ -164960,7 +165255,7 @@ Thailand
12.98 99.14 100.08 100.88 102.50
12.97 99.14 100.07 100.88 102.49
12.96 99.15 100.07 100.88 102.48
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5.83 100.97 101.39 101.62 101.91
@@ -165706,8 +166001,8 @@ Togo
11.07 -0.11 -0.06 -0.02 0.20
11.06 -0.01 0.26
11.05 0.00 0.31
- 11.04 0.00 0.36
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11.02 0.00 0.46
11.01 0.00 0.49
11.00 0.00 0.50 0.72 0.91
@@ -165739,8 +166034,8 @@ Togo
10.74 -0.09 0.84
10.73 -0.09 0.83
10.72 -0.09 0.81
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10.69 -0.10 0.79
10.68 -0.10 0.79
10.67 -0.10 0.79
@@ -165786,10 +166081,10 @@ Togo
10.27 0.36 0.93
10.26 0.36 0.94
10.25 0.35 0.96
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10.23 0.34 0.99
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10.20 0.34 1.04
10.19 0.34 1.06
10.18 0.34 1.08
@@ -165878,9 +166173,9 @@ Togo
9.35 0.51 1.40
9.34 0.51 1.40
9.33 0.51 1.41
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9.31 0.51 1.42
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9.29 0.51 1.43
9.28 0.50 1.44
9.27 0.49 1.45
@@ -165937,7 +166232,7 @@ Togo
8.76 0.35 1.61
8.75 0.35 1.61
8.74 0.35 1.61
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8.72 0.36 1.61
8.71 0.36 1.61
8.70 0.36 1.61
@@ -166191,17 +166486,17 @@ Togo
6.22 1.00 1.63
6.21 1.01 1.62
6.20 1.02 1.62
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6.13 1.16 1.32
6.12 1.17 1.29
6.11 1.17 1.26
6.10 1.17 1.24
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Tokelau
-9.08 -171.87 -171.83
-9.09 -171.88 -171.83
@@ -166233,13 +166528,6 @@ Tonga
-15.61 -175.69 -175.60
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@@ -166254,16 +166542,16 @@ Tonga
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@@ -166276,11 +166564,11 @@ Tonga
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-19.77 -175.10 -175.03 -174.34 -174.29
@@ -166288,8 +166576,8 @@ Tonga
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@@ -166297,22 +166585,22 @@ Tonga
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@@ -166331,15 +166619,15 @@ Tonga
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Trinidad and Tobago
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11.33 -60.62 -60.51
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11.31 -60.67 -60.51
@@ -166365,7 +166653,7 @@ Trinidad and Tobago
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10.78 -61.47 -61.43 -61.40 -60.91
@@ -166382,7 +166670,7 @@ Trinidad and Tobago
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10.61 -61.50 -61.01
@@ -166399,11 +166687,11 @@ Trinidad and Tobago
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10.40 -61.49 -61.01
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Tromelin Island
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Tunisia
37.35 9.72 9.75
37.34 9.63 9.82
@@ -166458,15 +166746,15 @@ Tunisia
37.30 9.52 9.87
37.29 9.50 9.87
37.28 9.40 9.87
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37.25 9.36 10.11
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37.23 9.18 10.17
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37.18 9.08 10.28
37.17 9.05 10.28
37.16 9.02 10.28
@@ -166478,7 +166766,7 @@ Tunisia
37.10 8.96 10.24
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37.06 8.93 10.18 10.91 11.07
37.05 8.92 10.19 10.89 11.07
37.04 8.91 10.19 10.88 11.06
@@ -166486,101 +166774,101 @@ Tunisia
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@@ -166606,146 +166894,146 @@ Tunisia
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34.37 7.80 10.27
@@ -166756,23 +167044,23 @@ Tunisia
34.32 7.78 10.17
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34.12 7.52 10.02
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34.10 7.50 10.02
@@ -166795,58 +167083,58 @@ Tunisia
33.93 7.47 10.10
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33.54 7.61 10.68 10.87 11.12
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33.51 7.63 10.70 10.80 11.12
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33.38 7.69 11.14
33.37 7.69 11.15
33.36 7.69 11.16
@@ -166857,15 +167145,15 @@ Tunisia
33.31 7.69 11.25
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33.25 7.69 11.17 11.34 11.38
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33.19 7.74 11.51
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@@ -166954,24 +167242,24 @@ Tunisia
32.34 8.60 11.43
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32.13 8.93 10.91
32.12 8.95 10.89
32.11 8.97 10.87
@@ -166981,11 +167269,11 @@ Tunisia
32.07 9.02 10.84
32.06 9.03 10.83
32.05 9.03 10.83
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31.99 9.05 10.78
31.98 9.05 10.77
31.97 9.05 10.75
@@ -167189,37 +167477,37 @@ Turkey
41.90 26.53 28.05 32.94 35.11
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41.86 26.53 27.97 32.72 35.15
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41.78 26.32 28.03 32.44 35.22
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41.75 26.30 28.04 32.36 35.27
41.74 26.30 28.05 32.34 35.28 35.92 35.96
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41.71 26.31 28.07 32.24 35.34 35.85 36.05
41.70 26.32 28.08 32.23 35.41 35.82 36.06
41.69 26.37 28.09 32.22 35.42 35.79 36.07
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41.65 26.45 28.09 32.17 35.51 35.64 36.11
41.64 26.45 28.09 32.16 35.56 35.59 36.12
41.63 26.45 28.11 32.16 36.13
41.62 26.47 28.12 32.15 36.13
41.61 26.49 28.14 32.13 36.14
41.60 26.51 28.15 32.10 36.14
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41.56 26.58 28.18 31.99 36.14 42.54 42.82
41.55 26.58 28.20 31.97 36.14 42.54 42.82
41.54 26.58 28.21 31.94 36.14 42.54 42.81
@@ -167227,7 +167515,7 @@ Turkey
41.52 26.58 28.25 31.88 36.13 41.51 41.54 42.53 42.81
41.51 26.59 28.27 31.86 36.13 41.50 41.58 41.92 41.96 42.07 42.09 42.12 42.15 42.53 42.80 42.85 42.87
41.50 26.59 28.29 31.84 36.13 41.49 41.61 41.89 42.00 42.03 42.18 42.52 42.80 42.84 42.88
- 41.49 26.60 28.31 31.82 36.13 41.47 41.71 41.88 42.28 42.51 42.89
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41.48 26.60 28.33 31.80 36.13 41.46 41.71 41.87 42.32 42.50 42.89
41.47 26.60 28.35 31.78 36.14 41.44 41.71 41.86 42.35 42.49 42.91
41.46 26.60 28.37 31.76 36.15 41.42 41.77 41.85 42.38 42.48 42.94
@@ -167238,13 +167526,13 @@ Turkey
41.41 26.62 28.53 31.66 36.21 41.41 42.98
41.40 26.62 28.56 31.63 36.22 41.39 43.00
41.39 26.62 28.59 31.59 36.22 41.39 43.01
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41.37 26.62 28.65 31.51 36.23 36.59 36.80 41.29 43.05
41.36 26.53 26.55 26.62 28.67 31.48 36.25 36.59 36.85 41.27 43.07
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41.34 26.50 28.73 31.47 36.29 36.58 36.90 41.24 43.10
41.33 26.48 28.76 31.41 36.34 36.58 36.92 41.22 43.12
- 41.32 26.47 28.78 31.39 36.35 36.57 36.95 41.21 43.14
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41.31 26.46 28.81 31.38 36.35 36.56 36.97 41.19 43.17
41.30 26.44 28.84 31.38 36.35 36.56 36.99 41.15 43.19
41.29 26.42 28.86 31.38 36.37 36.54 37.01 41.11 43.19
@@ -167252,36 +167540,36 @@ Turkey
41.27 26.40 28.93 31.40 36.40 36.50 37.03 41.08 43.19
41.26 26.32 28.98 29.02 29.08 31.40 36.43 36.48 37.03 41.06 43.18
41.25 26.31 29.10 29.22 29.27 31.39 37.04 41.05 43.18
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- 41.23 26.31 29.11 29.14 29.39 31.39 37.04 41.00 43.20
- 41.22 26.31 29.45 30.26 30.29 31.39 37.04 40.95 43.20
- 41.21 26.31 29.50 30.25 30.35 31.39 37.04 40.82 40.85 40.93 43.21
- 41.20 26.31 29.54 30.23 30.37 31.39 37.04 40.81 40.88 40.90 43.21 43.29 43.37
- 41.19 26.31 29.59 30.22 30.40 31.38 37.05 40.79 43.23 43.25 43.40
- 41.18 26.31 29.66 30.21 30.46 31.36 37.09 40.77 43.42
- 41.17 26.31 29.75 30.19 30.51 31.35 37.11 40.75 43.43
+ 41.24 26.31 29.11 29.15 29.18 29.20 29.33 31.39 37.04 41.03 43.19
+ 41.23 26.31 29.11 29.13 29.39 31.39 37.04 41.00 43.20
+ 41.22 26.31 29.44 30.26 30.29 31.39 37.04 40.94 43.20
+ 41.21 26.31 29.49 30.25 30.34 31.39 37.04 40.82 40.85 40.92 43.21
+ 41.20 26.31 29.54 30.23 30.36 31.39 37.04 40.81 40.88 40.90 43.21 43.29 43.37
+ 41.19 26.31 29.59 30.22 30.39 31.38 37.05 40.79 43.23 43.25 43.40
+ 41.18 26.31 29.66 30.21 30.45 31.36 37.09 40.77 43.42
+ 41.17 26.31 29.75 30.19 30.50 31.35 37.11 40.75 43.43
41.16 26.31 29.84 30.17 30.56 31.33 37.13 40.74 43.44
- 41.15 26.31 30.62 31.32 37.30 37.68 37.70 40.73 43.45
- 41.14 26.30 30.67 31.31 37.32 37.66 37.70 40.72 43.46
+ 41.15 26.31 30.61 31.32 37.30 37.67 37.69 40.73 43.45
+ 41.14 26.30 30.67 31.31 37.32 37.66 37.69 40.72 43.46
41.13 26.30 30.70 31.29 37.33 37.65 37.71 37.74 37.79 40.71 43.46
- 41.12 26.30 30.72 31.26 37.39 37.64 37.79 39.42 39.47 40.70 43.46
+ 41.12 26.30 30.72 31.26 37.39 37.64 37.79 39.40 39.47 40.70 43.46
41.11 26.30 30.73 31.23 37.40 37.63 37.79 39.39 39.50 40.69 43.46
- 41.10 26.31 30.77 31.10 37.41 37.62 37.79 39.38 39.50 40.67 43.45
- 41.09 26.31 30.81 30.96 37.43 37.61 37.79 39.35 39.51 40.61 43.45
+ 41.10 26.31 30.77 31.10 37.41 37.62 37.79 39.38 39.51 40.67 43.45
+ 41.09 26.31 30.81 30.96 37.43 37.61 37.79 39.35 39.52 40.61 43.45
41.08 26.31 37.46 37.61 37.79 39.14 39.23 39.32 39.53 40.60 43.45
41.07 26.31 37.49 37.60 37.79 39.12 39.25 39.30 39.54 40.58 43.45
- 41.06 26.31 28.14 28.17 28.22 28.24 37.50 37.59 37.80 39.08 39.56 40.45 40.48 40.56 43.45
- 41.05 26.31 28.12 28.31 37.52 37.54 37.82 38.91 39.57 40.43 40.50 40.53 43.46
+ 41.06 26.31 28.14 28.17 28.22 28.24 37.50 37.59 37.80 39.08 39.56 40.45 40.47 40.56 43.45
+ 41.05 26.31 28.12 28.31 37.52 37.54 37.82 38.91 39.57 40.43 40.49 40.53 43.46
41.04 26.32 28.08 28.34 37.84 38.89 39.59 40.41 43.46
41.03 26.33 28.04 28.38 37.86 38.88 39.61 40.39 43.47
- 41.02 26.35 28.01 28.44 37.87 38.83 39.63 39.70 39.75 40.38 43.47
+ 41.02 26.35 28.01 28.44 37.87 38.83 39.63 39.69 39.75 40.38 43.47
41.01 26.33 27.99 28.46 37.88 38.77 39.80 40.36 43.54
41.00 26.32 27.98 28.47 37.89 37.91 38.00 38.76 39.82 40.34 43.56
40.99 26.32 27.70 27.79 27.98 28.49 38.03 38.75 39.83 39.95 40.00 40.32 43.58
40.98 26.32 27.63 27.82 27.97 28.50 28.56 28.58 28.94 29.01 38.06 38.61 38.66 38.73 39.85 39.92 40.02 40.30 43.60
40.97 26.32 27.56 27.83 27.96 28.52 28.55 28.58 28.91 29.01 38.09 38.58 38.67 38.72 39.87 39.90 40.03 40.27 43.61
- 40.96 26.33 27.51 27.85 27.96 28.58 28.88 29.03 38.19 38.24 38.28 38.57 40.05 40.24 43.62
- 40.95 26.31 27.49 28.60 28.69 28.77 28.85 29.05 38.29 38.55 40.06 40.21 43.63
+ 40.96 26.33 27.51 27.85 27.96 28.58 28.72 28.75 28.88 29.03 38.19 38.24 38.28 38.57 40.05 40.24 43.62
+ 40.95 26.31 27.49 28.60 28.66 28.77 28.85 29.05 38.29 38.55 40.06 40.21 43.63
40.94 26.29 27.49 29.07 38.31 38.54 40.08 40.15 43.64
40.93 26.25 27.48 29.09 38.33 38.36 38.41 38.45 43.64
40.92 26.25 27.48 29.10 43.65
@@ -167299,92 +167587,92 @@ Turkey
40.80 26.13 27.41 29.24 43.71
40.79 26.13 27.39 29.31 43.72
40.78 26.12 27.38 29.31 43.72
- 40.77 26.12 27.37 29.33 43.73
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40.76 26.11 27.35 29.33 29.55 29.70 43.73
40.75 26.09 27.34 29.34 29.41 29.72 43.73
40.74 26.02 27.33 29.36 29.39 29.75 43.73
40.73 26.02 27.32 29.46 29.53 29.71 43.73
40.72 26.02 27.32 29.45 29.54 29.65 43.73
- 40.71 26.02 27.31 29.37 29.40 29.45 29.55 29.59 43.73
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40.70 26.03 27.30 29.35 43.73
40.69 26.03 27.29 29.33 43.73
40.68 26.04 27.28 29.30 43.73
40.67 26.04 27.26 27.53 27.55 27.58 27.65 29.20 43.73
40.66 26.04 27.24 27.52 27.72 29.05 43.73
40.65 26.04 27.22 27.52 27.73 28.97 43.73
- 40.64 26.04 26.76 26.78 27.20 27.51 27.73 28.96 43.72
+ 40.64 26.04 27.20 27.51 27.73 28.96 43.72
40.63 26.05 26.71 26.79 27.20 27.51 27.74 28.94 43.71
40.62 26.05 26.69 26.79 27.19 27.51 27.74 28.92 43.71
40.61 26.05 26.58 26.80 27.17 27.52 27.74 28.90 43.71
40.60 26.06 26.56 26.80 27.13 27.52 27.73 28.87 43.71
- 40.59 26.08 26.33 26.38 26.43 26.47 26.54 26.80 27.04 27.52 27.70 28.83 43.70
+ 40.59 26.08 26.33 26.38 26.43 26.47 26.54 26.80 27.04 27.52 27.67 28.83 43.70
40.58 26.49 26.52 26.78 27.03 27.54 27.65 28.81 43.69
40.57 26.72 27.02 27.56 27.63 28.79 43.68
40.56 26.70 27.01 27.59 27.62 28.78 43.67
40.55 26.69 27.00 28.77 43.67
- 40.54 26.69 26.98 27.72 27.77 28.77 43.66
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40.53 26.68 26.91 27.71 27.85 28.76 43.66
40.52 26.58 26.89 27.69 27.93 28.76 43.66
- 40.51 26.56 26.87 27.59 27.63 27.67 28.00 28.76 43.66
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40.50 26.54 26.85 27.58 27.65 27.67 28.02 28.79 43.61
40.49 26.52 26.83 27.58 27.65 27.67 28.03 28.83 43.60
40.48 26.51 26.79 27.56 27.65 27.67 28.04 28.85 43.59
40.47 26.49 26.75 27.25 27.30 27.56 27.66 27.68 28.04 28.87 43.58
40.46 26.47 26.74 27.08 27.16 27.22 27.31 27.56 27.66 27.69 28.04 28.89 29.01 29.07 43.58
- 40.45 26.44 26.72 27.06 27.32 27.57 27.66 27.71 28.03 28.94 29.00 29.09 43.60
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40.44 26.42 26.69 27.05 27.32 27.58 27.66 27.72 28.02 29.12 43.62
- 40.43 26.40 26.69 27.04 27.33 27.63 27.66 27.74 28.01 29.08 43.63
- 40.42 26.38 26.68 27.04 27.33 27.74 27.99 29.07 43.63
- 40.41 26.36 26.68 26.72 26.82 26.87 26.92 27.02 27.33 27.75 27.97 28.22 28.38 28.76 28.81 29.07 43.63
- 40.40 26.34 26.67 26.70 26.97 27.00 27.33 27.76 27.95 28.08 28.57 28.74 28.87 29.06 43.63
- 40.39 26.32 26.66 26.69 27.33 27.77 27.93 28.04 28.61 28.71 28.90 29.06 43.63
- 40.38 26.32 26.64 26.68 27.35 27.78 27.93 27.98 28.92 29.05 43.62
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40.37 26.28 26.63 26.67 27.37 27.83 43.62
40.36 26.26 26.63 26.66 27.39 27.82 43.61
40.35 26.22 27.41 27.80 43.61
- 40.34 26.20 27.44 27.60 27.63 27.79 43.61
- 40.33 26.20 27.47 27.57 27.66 27.69 27.73 27.77 43.62
- 40.32 26.20 27.51 27.55 43.64
- 40.31 26.20 26.58 26.60 43.65
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40.30 26.20 26.57 26.59 43.66
40.29 26.20 26.55 26.58 43.66
- 40.28 26.20 26.53 26.56 43.67
- 40.27 26.21 26.51 26.55 43.68
- 40.26 26.23 26.49 26.54 43.69
- 40.25 25.89 25.94 26.24 26.48 26.52 43.69
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40.24 25.86 25.95 26.25 26.47 26.51 43.70
40.23 25.83 25.98 26.25 26.45 26.50 43.70
- 40.22 25.78 25.98 26.26 26.44 26.48 43.70
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40.21 25.74 25.98 26.25 26.42 26.45 43.70
- 40.20 25.72 25.98 26.25 43.71
- 40.19 25.70 25.97 26.24 26.37 26.39 43.72
- 40.18 25.68 25.98 26.23 26.36 26.38 43.72
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40.17 25.67 26.02 26.22 43.73
40.16 25.66 26.02 26.21 43.73
40.15 25.66 26.02 26.20 43.73
40.14 25.65 26.02 26.19 43.72
- 40.13 25.65 26.02 26.19 26.37 26.39 43.69
- 40.12 25.65 26.01 26.19 26.36 26.39 43.68
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40.11 25.65 25.94 26.19 43.70
40.10 25.68 25.89 26.18 26.33 26.35 43.74
- 40.09 25.69 25.87 26.16 26.32 26.35 43.78
- 40.08 25.73 25.81 26.15 26.30 26.35 43.82
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40.07 26.15 26.27 26.35 43.84
40.06 26.14 26.25 26.34 43.86
40.05 26.14 26.24 26.33 43.88 44.22 44.31
40.04 26.14 26.21 26.32 43.90 44.07 44.12 44.17 44.34
40.03 26.15 26.17 26.31 43.95 44.05 44.36
40.02 26.28 44.01 44.03 44.38
- 40.01 26.17 26.23 26.25 44.41
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40.00 26.16 44.43
39.99 26.16 44.45
39.98 26.15 44.47
39.97 26.15 44.49
39.96 26.15 44.50
39.95 26.14 44.52
- 39.94 26.14 44.53
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39.91 26.14 44.55
39.90 26.14 44.56
39.89 26.14 44.57
@@ -167395,10 +167683,10 @@ Turkey
39.84 25.96 26.09 26.12 44.62
39.83 25.96 26.09 26.12 44.63
39.82 25.96 26.09 26.12 44.64
- 39.81 25.97 26.09 26.14 44.66
- 39.80 25.98 26.09 26.14 44.70
- 39.79 26.00 26.09 26.14 44.70
- 39.78 26.02 26.09 26.14 44.71
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+ 39.78 26.02 26.09 26.13 44.71
39.77 26.04 26.08 26.12 44.72
39.76 26.12 44.73
39.75 26.12 44.74
@@ -167413,7 +167701,7 @@ Turkey
39.66 26.14 44.47 44.72 44.80
39.65 26.14 44.47 44.74 44.80
39.64 26.14 44.47 44.76 44.81
- 39.63 26.13 44.47 44.77 44.81
+ 39.63 26.13 44.46 44.77 44.81
39.62 26.12 44.46 44.79 44.81
39.61 26.11 44.46
39.60 26.10 44.45
@@ -167426,10 +167714,10 @@ Turkey
39.53 26.07 26.63 26.93 44.42
39.52 26.07 26.56 26.92 44.42
39.51 26.06 26.49 26.92 44.42
- 39.50 26.06 26.45 26.92 44.42
+ 39.50 26.06 26.45 26.91 44.42
39.49 26.06 26.43 26.89 44.42
- 39.48 26.06 26.41 26.85 44.41
- 39.47 26.06 26.39 26.84 44.41
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+ 39.47 26.06 26.38 26.84 44.41
39.46 26.06 26.26 26.84 44.41
39.45 26.08 26.25 26.84 44.41
39.44 26.10 26.18 26.79 44.41
@@ -167461,8 +167749,8 @@ Turkey
39.18 26.72 44.14
39.17 26.74 44.16
39.16 26.76 44.18
- 39.15 26.78 44.19
- 39.14 26.80 44.19
+ 39.15 26.77 44.19
+ 39.14 26.79 44.19
39.13 26.81 44.20
39.12 26.82 44.20
39.11 26.84 44.20
@@ -167483,8 +167771,8 @@ Turkey
38.96 26.78 44.17
38.95 26.78 44.18
38.94 26.79 44.18
- 38.93 26.79 44.18
- 38.92 26.81 44.19
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+ 38.92 26.83 44.19
38.91 26.83 26.91 26.96 44.19
38.90 26.84 26.89 26.97 27.01 27.03 44.20
38.89 27.03 44.20
@@ -167492,8 +167780,8 @@ Turkey
38.87 26.99 44.24
38.86 26.98 44.26
38.85 26.94 44.28
- 38.84 26.94 44.28
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+ 38.83 26.90 44.28
38.82 26.88 44.28
38.81 26.88 44.28
38.80 26.88 44.28
@@ -167511,35 +167799,35 @@ Turkey
38.68 26.39 26.48 26.71 44.27
38.67 26.34 26.50 26.72 44.27
38.66 26.34 26.51 26.70 44.27
- 38.65 26.34 26.53 26.70 44.29
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38.62 26.33 26.55 26.73 44.30
38.61 26.33 26.56 26.74 44.30
- 38.60 26.33 26.56 26.74 44.30
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38.58 26.34 26.58 26.78 44.30
38.57 26.34 26.59 26.82 44.30
38.56 26.34 26.60 26.82 44.30
38.55 26.35 26.60 26.80 44.30
- 38.54 26.36 26.61 26.80 44.31
- 38.53 26.36 26.63 26.80 44.31
- 38.52 26.36 26.64 26.80 44.31
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+ 38.52 26.35 26.64 26.80 44.31
38.51 26.36 26.64 26.81 44.31
- 38.50 26.37 26.64 26.83 44.31
- 38.49 26.38 26.64 26.84 44.31
- 38.48 26.39 26.64 26.88 44.31
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38.47 26.38 26.65 26.89 44.31
38.46 26.37 26.65 26.89 44.30
38.45 26.37 26.65 26.90 44.30
- 38.44 26.37 26.42 26.46 26.61 26.70 26.73 26.91 27.01 27.05 44.29
- 38.43 26.44 26.61 26.69 26.74 26.92 26.98 27.11 44.30
+ 38.44 26.37 26.42 26.46 26.61 26.69 26.73 26.91 27.01 27.05 44.29
+ 38.43 26.44 26.61 26.68 26.74 26.92 26.97 27.11 44.30
38.42 26.44 26.62 26.67 26.74 26.92 26.95 27.00 44.30
38.41 26.44 26.63 26.66 26.75 26.98 44.30
38.40 26.44 26.63 26.66 26.75 26.95 44.30
- 38.39 26.45 26.64 26.66 26.76 26.93 44.29 44.39 44.42
- 38.38 26.30 26.33 26.45 26.79 26.83 44.34 44.37 44.43
- 38.37 26.28 26.33 26.46 26.79 26.81 44.45
+ 38.39 26.45 26.63 26.66 26.76 26.93 44.29 44.39 44.42
+ 38.38 26.30 26.33 26.45 26.64 26.66 26.79 26.83 44.34 44.37 44.43
+ 38.37 26.28 26.33 26.46 26.64 26.66 44.45
38.36 26.27 26.33 26.43 44.46
38.35 26.27 26.33 26.37 26.39 26.41 44.46
38.34 26.27 26.34 26.37 44.46
@@ -167601,20 +167889,20 @@ Turkey
37.78 27.25 44.52
37.77 27.24 44.55
37.76 27.24 44.56
- 37.75 27.24 44.57
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37.74 27.22 44.58
37.73 27.21 44.59
37.72 27.19 44.60
37.71 27.16 44.60
- 37.70 27.13 44.60
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37.69 27.01 44.60
37.68 27.01 44.59
37.67 27.00 44.58
37.66 27.00 44.56
37.65 27.00 44.55
- 37.64 27.01 44.55
- 37.63 27.03 44.56
- 37.62 27.08 44.58
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+ 37.63 27.06 44.56
+ 37.62 27.10 44.58
37.61 27.14 44.59
37.60 27.16 44.59
37.59 27.18 44.59
@@ -167660,12 +167948,12 @@ Turkey
37.19 27.51 42.07 42.32 42.61 43.79 43.84 44.23 44.76
37.18 27.51 42.06 42.32 42.60 43.79 43.82 44.23 44.77
37.17 27.51 42.04 42.32 42.59 44.23 44.78
- 37.16 27.31 27.39 27.53 42.02 42.32 42.58 44.20 44.78
+ 37.16 27.31 27.39 27.52 42.02 42.32 42.58 44.20 44.78
37.15 27.31 27.39 27.53 41.98 42.32 42.58 44.19 44.60 44.67 44.78
- 37.14 27.31 27.40 27.53 41.93 42.33 42.57 44.18 44.57 44.74 44.78
+ 37.14 27.31 27.41 27.53 41.92 42.33 42.57 44.18 44.57 44.74 44.78
37.13 27.24 27.29 27.31 27.44 27.52 41.87 42.34 42.57 44.17 44.55 44.75 44.77
37.12 27.24 27.44 27.51 41.82 42.34 42.52 44.17 44.53
- 37.11 27.24 27.44 27.48 41.77 42.34 42.48 44.17 44.52
+ 37.11 27.24 27.44 27.48 41.76 42.34 42.48 44.17 44.52
37.10 27.24 40.85 40.92 41.71 42.34 42.43 44.17 44.51
37.09 27.22 40.75 40.98 41.66 42.34 42.38 44.17 44.50
37.08 27.22 40.69 41.04 41.61 44.17 44.48
@@ -167676,102 +167964,102 @@ Turkey
37.03 27.22 40.58 44.18 44.37
37.02 27.23 40.56 44.19 44.34
37.01 27.23 27.97 28.03 28.12 28.20 40.54 44.19 44.34
- 37.00 27.23 27.42 27.44 27.87 28.10 28.12 28.20 40.50 44.20 44.34
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36.99 27.23 27.34 27.36 27.40 27.45 27.83 28.18 40.43 44.20 44.33
- 36.98 27.23 27.34 27.36 27.39 27.46 27.67 27.73 27.79 28.18 40.41 44.21 44.32
+ 36.98 27.23 27.34 27.36 27.39 27.46 27.67 27.72 27.79 28.18 40.41 44.21 44.32
36.97 27.24 27.33 27.52 27.57 27.60 27.65 28.18 40.39 44.22 44.32
36.96 27.24 27.32 27.54 27.57 28.18 40.37 44.23 44.31
36.95 27.25 27.31 28.14 40.35 44.26 44.30
36.94 27.27 27.31 28.03 40.33
36.93 28.01 40.31
- 36.92 28.01 40.30
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36.90 28.01 36.01 36.03 40.26
36.89 28.01 35.98 36.06 40.24
36.88 28.02 35.96 36.08 38.18 38.29 40.22
36.87 28.00 35.95 36.09 38.14 38.33 40.20
- 36.86 27.99 30.66 30.70 35.94 36.11 38.12 38.37 40.18
- 36.85 27.99 30.65 30.71 35.93 36.12 38.10 38.41 40.14
- 36.84 27.99 30.63 30.73 35.92 36.13 38.08 38.45 40.10
- 36.83 27.99 30.62 30.75 30.86 30.98 35.91 36.14 38.06 38.48 40.07
- 36.82 27.88 27.90 27.99 30.61 31.06 35.90 36.14 38.04 38.50 40.05
- 36.81 27.61 27.66 27.77 27.92 27.99 30.60 31.14 35.89 36.15 38.02 38.52 40.03
- 36.80 27.61 27.68 27.76 28.42 28.45 30.60 31.22 35.86 36.16 38.00 38.53 40.01
- 36.79 27.60 28.42 28.47 28.53 28.57 30.59 31.30 34.68 34.75 35.85 36.17 36.65 36.70 37.97 38.54 39.99
- 36.78 27.60 28.41 28.48 28.53 28.58 30.59 31.35 34.66 34.81 35.84 36.17 36.65 36.74 37.93 38.56 39.96
- 36.77 27.51 28.26 28.35 28.40 28.51 28.53 28.60 30.58 31.36 34.64 34.83 35.83 36.18 36.64 36.78 37.90 38.57 39.92
- 36.76 27.44 28.28 28.60 30.58 31.36 34.58 34.85 35.82 36.18 36.63 36.82 37.87 38.58 39.89
- 36.75 27.42 28.29 28.60 30.58 31.36 34.56 34.86 35.79 36.19 36.62 36.91 37.83 38.59 39.85
- 36.74 27.41 28.01 28.07 28.29 28.59 30.58 31.41 34.55 34.87 35.67 36.19 36.62 36.95 37.79 38.60 39.82
- 36.73 27.41 27.71 27.83 27.98 28.06 28.30 28.59 30.58 31.44 34.54 34.88 35.70 36.19 36.61 36.97 37.74 38.61 39.78
- 36.72 27.34 27.36 27.41 27.70 28.02 28.30 28.59 30.58 31.46 34.53 34.89 35.71 36.19 36.61 36.98 37.68 38.63 39.73
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36.71 27.34 27.69 27.99 28.30 28.59 28.91 28.94 30.57 31.49 34.51 34.89 35.71 36.19 36.60 36.99 37.64 38.64 39.67
- 36.70 27.34 27.69 27.96 28.25 28.28 28.30 28.60 28.90 28.97 30.57 31.52 34.50 34.89 34.91 34.98 35.71 36.19 36.60 37.00 37.61 38.65 39.60
- 36.69 27.34 27.69 27.95 28.24 28.60 28.90 29.01 30.58 31.54 34.48 35.00 35.70 36.19 36.60 37.00 37.59 38.67 39.53
- 36.68 27.35 27.69 27.95 28.24 28.61 28.63 28.65 28.69 28.72 28.90 29.03 30.58 31.57 34.47 35.02 35.69 36.19 36.60 37.00 37.57 38.70 39.01 39.04 39.47
- 36.67 27.35 27.68 27.95 28.21 28.75 28.90 29.05 30.58 31.60 34.45 35.05 35.68 36.19 36.60 37.00 37.55 38.75 38.88 39.07 39.40
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36.65 27.39 27.50 27.64 27.68 28.03 28.16 28.77 28.91 29.08 30.57 31.63 34.42 35.09 35.66 36.20 36.59 37.00 37.51 39.13 39.27
36.64 27.45 27.49 27.66 27.68 28.03 28.15 28.77 28.91 29.07 30.56 31.66 34.41 35.11 35.66 36.20 36.59 37.00 37.49 39.16 39.21
36.63 28.03 28.15 28.80 28.90 29.03 30.56 31.68 34.39 35.13 35.65 36.19 36.58 37.00 37.19 37.28 37.47
36.62 28.03 28.14 28.80 28.89 29.02 30.56 31.73 34.37 35.15 35.64 36.18 36.58 37.01 37.08 37.36 37.45
36.61 27.94 28.14 28.80 28.88 29.02 30.58 31.74 34.35 35.17 35.64 36.17 36.57 37.02 37.07
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36.57 27.95 28.09 29.01 30.59 31.80 34.28 35.25 35.43 35.50 35.59 36.09 36.58
36.56 27.95 28.05 29.02 30.59 31.88 34.27 35.27 35.41 36.07 36.58
36.55 27.96 28.05 29.00 30.59 31.89 34.26 35.29 35.40 36.05 36.58
36.54 27.98 28.00 29.00 30.58 31.96 34.25 35.31 35.37 36.03 36.58
36.53 29.00 29.05 29.08 30.58 31.97 34.24 35.32 35.35 36.02 36.57
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36.48 29.08 30.54 32.07 34.20 35.96 36.54
36.47 29.08 30.53 32.09 34.19 35.93 36.54
36.46 29.08 30.52 32.09 34.18 35.92 36.54
36.45 29.10 30.52 32.10 34.17 35.90 36.55
36.44 29.11 30.51 32.11 34.16 35.90 36.55
36.43 29.11 30.50 32.11 34.14 35.90 36.55
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36.41 29.09 30.49 32.14 34.12 35.87 36.56
36.40 29.08 30.49 32.15 34.10 35.86 36.58
36.39 29.08 30.48 32.16 34.08 35.86 36.60
36.38 29.08 30.50 32.16 34.08 35.85 36.60
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36.32 29.16 30.52 32.21 34.08 35.77 36.64
36.31 29.20 30.51 32.22 34.08 35.77 36.65
36.30 29.23 30.50 32.24 34.07 35.77 36.66
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36.28 29.24 30.20 30.26 30.49 32.25 33.85 33.92 34.00 35.77 36.67
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36.26 29.27 30.15 30.31 30.48 32.26 33.83 33.93 34.00 35.79 36.67
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36.23 29.31 29.37 29.40 30.13 30.39 30.45 32.27 33.81 33.94 33.97 35.83 36.68
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36.19 29.50 29.91 30.38 30.40 32.32 33.74 35.84 36.47
36.18 29.57 29.89 32.33 33.73 35.85 36.38 36.43 36.46
36.17 29.57 29.84 32.34 33.71 35.86 36.37
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36.11 29.66 29.68 32.44 33.14 33.17 33.23 33.26 33.30 33.54 33.56 35.90 36.36
36.10 32.47 33.13 35.91 36.36
36.09 32.49 33.12 35.92 36.36
36.08 32.52 32.93 32.97 33.11 35.92 36.36
- 36.07 32.57 32.91 33.00 33.04 33.06 33.10 35.93 36.36
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36.04 32.64 32.85 35.94 36.36
36.03 32.66 32.84 35.95 36.36
36.02 32.69 32.82 35.95 36.36
@@ -167910,7 +168198,7 @@ Turkmenistan
41.71 52.46 55.05 56.95 60.07
41.70 52.48 55.06 56.95 60.07
41.69 52.50 55.07 56.95 60.08
- 41.68 52.52 55.08 56.95 60.09
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41.67 52.52 55.09 56.95 60.10
41.66 52.56 55.10 56.95 60.11
41.65 52.56 55.11 56.95 60.12
@@ -167947,7 +168235,7 @@ Turkmenistan
41.34 52.75 55.40 57.10 60.24
41.33 52.76 55.41 55.85 56.06 57.07 60.26
41.32 52.76 55.41 55.82 56.24 57.06 60.28
- 41.31 52.78 55.42 55.79 56.45 57.05 60.31 61.42 61.46
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41.30 52.78 55.43 55.73 56.69 57.04 60.33 61.40 61.50
41.29 52.79 55.45 55.67 56.84 57.03 60.35 61.39 61.54
41.28 52.79 55.47 55.64 56.92 57.02 60.37 61.38 61.58
@@ -168005,12 +168293,12 @@ Turkmenistan
40.76 52.83 62.04
40.75 52.82 62.04
40.74 52.82 62.04
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40.72 52.81 62.05
40.71 52.81 62.06
40.70 52.81 62.07
40.69 52.82 62.08
- 40.68 52.84 62.10
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40.67 52.85 62.11
40.66 52.85 62.11
40.65 52.84 62.12
@@ -168086,7 +168374,7 @@ Turkmenistan
39.95 52.83 52.93 53.04 53.09 53.20 53.34 53.55 62.52
39.94 52.85 52.93 53.22 53.33 53.54 62.54
39.93 52.87 52.93 53.26 53.30 53.52 62.56
- 39.92 52.88 52.94 53.27 53.29 53.51 62.57
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39.91 52.88 52.94 53.51 62.59
39.90 52.88 52.94 53.49 62.60
39.89 52.88 52.94 53.47 62.62
@@ -168097,17 +168385,17 @@ Turkmenistan
39.84 52.90 52.99 53.45 62.71
39.83 52.93 53.00 53.44 62.72
39.82 52.95 53.01 53.43 62.74
- 39.81 52.95 53.01 53.42 62.76
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39.80 52.96 53.02 53.41 62.78
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39.78 52.97 53.05 53.38 62.82
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39.76 52.98 53.06 53.37 62.85
39.75 52.99 53.06 53.37 62.87
39.74 53.01 53.05 53.38 62.89
39.73 53.03 53.05 53.41 62.91
- 39.72 53.41 62.93
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39.70 53.40 62.96
39.69 53.40 62.98
39.68 53.40 63.00
@@ -168123,10 +168411,10 @@ Turkmenistan
39.58 53.19 53.25 53.45 53.52 53.61 63.17
39.57 53.19 53.25 53.45 53.52 53.61 63.19
39.56 53.18 53.24 53.45 53.53 53.61 63.20
- 39.55 53.18 53.24 53.45 53.54 53.62 63.22
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39.51 53.16 53.61 53.63 63.29
39.50 53.15 53.53 53.55 63.31
39.49 53.13 53.52 53.55 63.33
@@ -168170,9 +168458,9 @@ Turkmenistan
39.11 53.63 63.87
39.10 53.04 53.09 53.64 63.89
39.09 53.03 53.09 53.65 63.91
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39.05 53.01 53.06 53.70 63.98
39.04 53.01 53.06 53.72 64.00
39.03 53.01 53.06 53.73 64.02
@@ -168184,7 +168472,7 @@ Turkmenistan
38.97 53.02 53.07 53.87 64.13 64.24 64.35
38.96 53.02 53.07 53.88 64.15 64.21 64.36
38.95 53.02 53.07 53.90 64.37
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38.93 53.02 53.07 53.93 64.39
38.92 53.02 53.07 53.96 64.40
38.91 53.02 53.07 53.96 64.41
@@ -168194,21 +168482,21 @@ Turkmenistan
38.87 53.04 53.08 53.94 64.46
38.86 53.04 53.08 53.93 64.48
38.85 53.05 53.09 53.93 64.49
- 38.84 53.05 53.09 53.93 64.51
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38.82 53.06 53.10 53.92 64.54
38.81 53.06 53.10 53.90 64.55
38.80 53.07 53.11 53.90 64.57
38.79 53.07 53.11 53.90 64.58
38.78 53.07 53.11 53.90 64.60
38.77 53.08 53.11 53.91 64.61
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38.75 53.08 53.11 53.90 64.65
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38.72 53.88 64.71
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38.69 53.86 64.78
38.68 53.85 64.82
38.67 53.84 64.86
@@ -168282,7 +168570,7 @@ Turkmenistan
37.99 53.79 55.31 57.31 66.63
37.98 53.79 55.28 57.31 66.64
37.97 53.79 55.24 57.32 66.64
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37.95 53.79 55.22 57.34 66.65
37.94 53.80 55.18 57.36 66.65
37.93 53.80 55.13 57.40 66.65
@@ -168327,22 +168615,22 @@ Turkmenistan
37.54 53.85 54.81 59.13 65.76 65.80 66.50
37.53 53.86 54.80 59.14 65.76 65.80 66.50
37.52 53.86 54.80 59.16 65.76 65.81 66.50
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37.50 53.87 54.79 59.20 59.25 59.32 65.66 65.82 66.52
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37.41 53.89 54.50 59.33 65.63 66.08 66.53
37.40 53.89 54.48 59.33 65.63 66.09 66.52
37.39 53.89 54.46 59.33 65.63 66.10 66.51
- 37.38 53.90 54.44 59.33 65.63 66.11 66.51
- 37.37 53.90 54.42 59.34 65.63 66.13 66.52
- 37.36 53.90 54.40 59.34 65.63 66.15 66.52
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37.35 53.90 54.38 59.35 65.63 66.22 66.52
37.34 53.90 54.35 59.35 65.63 66.24 66.51
37.33 53.90 54.26 59.35 65.63 66.26 66.50
@@ -168356,7 +168644,7 @@ Turkmenistan
37.25 59.43 65.55
37.24 59.44 65.54
37.23 59.45 65.52
- 37.22 59.44 65.29
+ 37.22 59.44 65.28
37.21 59.44 65.05
37.20 59.44 65.01
37.19 59.45 64.97
@@ -168391,19 +168679,19 @@ Turkmenistan
36.90 60.09 64.77
36.89 60.09 64.77
36.88 60.10 64.76
- 36.87 60.11 64.76
+ 36.87 60.11 64.75
36.86 60.12 64.75
36.85 60.13 64.74
- 36.84 60.14 64.74
- 36.83 60.15 64.73
+ 36.84 60.14 64.73
+ 36.83 60.15 64.72
36.82 60.16 64.72
- 36.81 60.17 64.72
+ 36.81 60.17 64.71
36.80 60.17 64.71
36.79 60.18 64.70
- 36.78 60.19 64.70
+ 36.78 60.19 64.69
36.77 60.20 64.69
36.76 60.21 64.68
- 36.75 60.22 64.68
+ 36.75 60.22 64.67
36.74 60.23 64.67
36.73 60.24 64.66
36.72 60.24 64.66
@@ -168477,7 +168765,7 @@ Turkmenistan
36.04 61.16 64.04
36.03 61.16 64.05
36.02 61.16 64.05
- 36.01 61.16 63.91 63.93 64.05
+ 36.01 61.16 63.90 63.93 64.05
36.00 61.15 63.85 63.95 64.05
35.99 61.13 63.83 63.99 64.05
35.98 61.11 63.81 64.02 64.05
@@ -168575,21 +168863,21 @@ Turks and Caicos Islands
21.91 -72.03 -71.90
21.90 -72.03 -71.90
21.89 -72.10 -72.07 -72.03 -71.89
- 21.88 -72.11 -72.07 -72.02 -71.98 -71.96 -71.89
- 21.87 -72.33 -72.30 -72.11 -72.07 -71.96 -71.89
- 21.86 -72.33 -72.29 -72.13 -72.07 -71.96 -71.88 -71.85 -71.81
- 21.85 -72.33 -72.28 -72.14 -72.08 -71.96 -71.74 -71.70 -71.66
- 21.84 -72.33 -72.27 -72.14 -72.10 -71.95 -71.65
+ 21.88 -72.11 -72.07 -72.02 -71.89
+ 21.87 -72.34 -72.31 -72.11 -72.07 -71.97 -71.89
+ 21.86 -72.34 -72.29 -72.13 -72.07 -71.97 -71.88 -71.86 -71.80
+ 21.85 -72.34 -72.28 -72.14 -72.08 -71.96 -71.74 -71.71 -71.66
+ 21.84 -72.34 -72.27 -72.14 -72.10 -71.95 -71.65
21.83 -72.34 -72.26 -72.16 -72.11 -71.93 -71.64
- 21.82 -72.34 -72.25 -72.17 -72.11 -71.90 -71.64
- 21.81 -72.34 -72.24 -72.18 -72.11 -71.88 -71.63
- 21.80 -72.34 -72.11 -71.85 -71.63
+ 21.82 -72.35 -72.25 -72.17 -72.11 -71.90 -71.64
+ 21.81 -72.35 -72.24 -72.18 -72.11 -71.88 -71.63
+ 21.80 -72.35 -72.11 -71.85 -71.63
21.79 -72.34 -72.11 -71.85 -71.62
- 21.78 -72.34 -72.12 -71.84 -71.62
- 21.77 -72.34 -72.14 -71.83 -71.76 -71.73 -71.62 -71.58 -71.56
- 21.76 -72.34 -72.14 -71.71 -71.62 -71.59 -71.54
- 21.75 -72.34 -72.17 -71.71 -71.63 -71.59 -71.52
- 21.74 -72.34 -72.32 -72.30 -72.26 -71.70 -71.63 -71.59 -71.48
+ 21.78 -72.35 -72.12 -71.84 -71.62
+ 21.77 -72.35 -72.14 -71.83 -71.76 -71.73 -71.62 -71.58 -71.56
+ 21.76 -72.35 -72.14 -71.71 -71.62 -71.60 -71.54
+ 21.75 -72.34 -72.17 -71.70 -71.63 -71.60 -71.52
+ 21.74 -72.30 -72.26 -71.67 -71.63 -71.60 -71.48
21.73 -72.30 -72.27 -71.66 -71.63 -71.59 -71.46
21.72 -71.58 -71.45
21.71 -72.47 -72.42 -71.56 -71.45
@@ -168598,7 +168886,7 @@ Turks and Caicos Islands
21.68 -72.47 -72.42 -71.50 -71.44
21.67 -72.47 -72.42 -71.50 -71.44
21.66 -72.47 -72.42 -71.49 -71.44
- 21.65 -72.47 -72.43 -71.48 -71.44
+ 21.65 -72.48 -72.43 -71.48 -71.44
21.64 -72.49 -72.43
21.63 -72.49 -72.44
21.62 -72.49 -72.46
@@ -168609,8 +168897,8 @@ Turks and Caicos Islands
21.53 -71.53 -71.48
21.52 -71.54 -71.48 -71.14 -71.12
21.51 -71.54 -71.48 -71.14 -71.12
- 21.50 -71.54 -71.48 -71.15 -71.11
- 21.49 -71.54 -71.48 -71.15 -71.11
+ 21.50 -71.54 -71.48 -71.15 -71.12
+ 21.49 -71.54 -71.48 -71.15 -71.12
21.48 -71.54 -71.49 -71.16 -71.11
21.47 -71.53 -71.50 -71.16 -71.11
21.46 -71.16 -71.11
@@ -168670,7 +168958,7 @@ Tuvalu
-8.49 179.18 179.21
-8.50 179.18 179.22
-8.51 179.19 179.22
- -8.52 179.18 179.22
+ -8.52 179.19 179.22
-8.53 179.18 179.22
-8.54 179.18 179.21
-8.55 179.18 179.20
@@ -168730,8 +169018,8 @@ Uganda
3.81 31.75 31.81 32.84 33.11 33.55 34.17
3.80 31.15 31.24 31.74 31.83 32.82 33.13 33.54 34.18
3.79 31.13 31.28 31.73 31.84 32.79 33.14 33.53 34.18 34.22 34.25
- 3.78 31.11 31.30 31.72 31.85 32.76 33.16 33.52 34.25
- 3.77 31.10 31.32 31.72 31.86 32.67 33.18 33.51 34.26
+ 3.78 31.12 31.30 31.72 31.85 32.76 33.16 33.51 34.25
+ 3.77 31.10 31.32 31.72 31.86 32.67 33.18 33.50 34.26
3.76 31.09 31.34 31.71 31.87 32.50 33.37 33.49 34.27
3.75 31.07 31.35 31.70 31.87 32.39 34.27
3.74 31.05 31.37 31.69 31.88 32.36 34.27 34.31 34.35
@@ -168751,7 +169039,7 @@ Uganda
3.60 30.89 31.99 32.16 34.45
3.59 30.88 32.04 32.16 34.45
3.58 30.87 32.05 32.16 34.45
- 3.57 30.86 32.06 32.16 34.45
+ 3.57 30.86 32.05 32.16 34.45
3.56 30.86 32.06 32.16 34.45
3.55 30.85 32.07 32.16 34.45
3.54 30.85 32.09 32.16 34.45
@@ -168793,10 +169081,10 @@ Uganda
3.18 30.77 34.44
3.17 30.76 34.45
3.16 30.76 34.46
- 3.15 30.75 34.49
+ 3.15 30.76 34.49
3.14 30.75 34.52
3.13 30.75 34.53
- 3.12 30.74 34.54
+ 3.12 30.75 34.54
3.11 30.74 34.54
3.10 30.74 34.55
3.09 30.73 34.55
@@ -168883,9 +169171,9 @@ Uganda
2.28 31.03 34.90
2.27 31.07 31.14 31.16 34.91
2.26 31.16 34.91
- 2.25 31.16 34.92
+ 2.25 31.16 34.91
2.24 31.16 34.92
- 2.23 31.16 34.93
+ 2.23 31.16 34.92
2.22 31.17 34.93
2.21 31.18 34.93
2.20 31.19 34.94
@@ -168893,8 +169181,8 @@ Uganda
2.18 31.21 34.94
2.17 31.23 34.95
2.16 31.25 34.95
- 2.15 31.26 34.96
- 2.14 31.27 34.96
+ 2.15 31.25 34.96
+ 2.14 31.26 34.96
2.13 31.26 34.96
2.12 31.26 34.97
2.11 31.26 34.97
@@ -168973,11 +169261,11 @@ Uganda
1.38 30.57 34.79
1.37 30.56 34.79
1.36 30.55 34.79
- 1.35 30.54 34.79
+ 1.35 30.55 34.79
1.34 30.54 34.80
1.33 30.53 34.80
1.32 30.52 34.81
- 1.31 30.51 34.81
+ 1.31 30.52 34.81
1.30 30.51 34.81
1.29 30.50 34.82
1.28 30.49 34.82
@@ -168999,7 +169287,7 @@ Uganda
1.12 30.22 34.58
1.11 30.22 34.58
1.10 30.22 34.58
- 1.09 30.21 34.58
+ 1.09 30.21 34.57
1.08 30.20 34.57
1.07 30.20 34.49 34.53 34.56
1.06 30.20 34.49
@@ -169023,7 +169311,7 @@ Uganda
0.88 30.02 34.44
0.87 30.00 34.43
0.86 29.98 34.43
- 0.85 29.96 34.42
+ 0.85 29.97 34.42
0.84 29.95 34.41
0.83 29.93 34.41
0.82 29.93 34.40
@@ -169054,7 +169342,7 @@ Uganda
0.57 29.91 34.14
0.56 29.91 34.14
0.55 29.91 34.14
- 0.54 29.91 34.13
+ 0.54 29.91 34.14
0.53 29.92 34.13
0.52 29.92 34.13
0.51 29.92 34.13
@@ -169063,11 +169351,11 @@ Uganda
0.48 29.92 34.12
0.47 29.91 34.11
0.46 29.90 34.11
- 0.45 29.89 34.11
+ 0.45 29.90 34.11
0.44 29.89 34.10
0.43 29.88 34.10
0.42 29.87 34.09
- 0.41 29.86 34.08
+ 0.41 29.87 34.08
0.40 29.86 34.08
0.39 29.85 34.08
0.38 29.84 34.09
@@ -169127,24 +169415,24 @@ Uganda
-0.16 29.66 33.96
-0.17 29.66 33.96
-0.18 29.66 33.96
- -0.19 29.65 33.96
- -0.20 29.65 33.96
- -0.21 29.65 33.95
+ -0.19 29.66 33.96
+ -0.20 29.66 33.96
+ -0.21 29.66 33.95
-0.22 29.65 33.95
-0.23 29.65 33.95
-0.24 29.65 33.95
- -0.25 29.64 33.95
+ -0.25 29.65 33.95
-0.26 29.64 33.95
-0.27 29.64 33.95
-0.28 29.64 33.95
-0.29 29.64 33.94
-0.30 29.64 33.94
- -0.31 29.63 33.94
- -0.32 29.63 33.94
+ -0.31 29.64 33.94
+ -0.32 29.64 33.94
-0.33 29.63 33.94
-0.34 29.63 33.94
-0.35 29.63 33.94
- -0.36 29.62 33.94
+ -0.36 29.63 33.94
-0.37 29.62 33.94
-0.38 29.62 33.93
-0.39 29.62 33.93
@@ -169224,7 +169512,7 @@ Uganda
-1.13 29.54 30.33
-1.14 29.54 30.32
-1.15 29.54 30.32
- -1.16 29.54 30.29
+ -1.16 29.54 30.30
-1.17 29.54 30.29
-1.18 29.54 30.29
-1.19 29.54 30.29
@@ -169302,7 +169590,7 @@ Ukraine
51.96 30.83 34.16
51.95 25.11 25.23 30.81 34.17
51.94 25.06 25.31 30.79 34.19
- 51.93 25.02 25.52 25.72 25.82 30.79 34.20
+ 51.93 25.02 25.45 25.72 25.82 30.79 34.20
51.92 24.95 25.93 30.79 34.21
51.91 24.86 26.09 30.77 34.23
51.90 24.51 24.67 24.76 26.11 30.72 34.24
@@ -169356,7 +169644,7 @@ Ukraine
51.42 23.65 29.28 29.48 30.29 30.57 34.22
51.41 23.66 29.28 29.47 30.33 30.57 34.22
51.40 23.66 29.29 29.36 29.43 29.46 30.33 30.60 34.22
- 51.39 23.66 29.29 29.34 30.34 30.61 34.21
+ 51.39 23.66 29.29 29.35 30.34 30.61 34.21
51.38 23.66 30.34 30.62 34.23
51.37 23.65 30.34 30.62 34.31
51.36 23.63 30.34 30.62 34.31
@@ -169431,7 +169719,7 @@ Ukraine
50.67 24.06 35.47
50.66 24.07 35.47
50.65 24.07 35.47
- 50.64 24.07 35.45
+ 50.64 24.08 35.45
50.63 24.08 35.41
50.62 24.08 35.39
50.61 24.07 35.39
@@ -169658,8 +169946,8 @@ Ukraine
48.40 22.12 27.30 27.37 27.43 27.81 39.91
48.39 22.12 22.19 22.25 27.29 27.83 39.92
48.38 22.24 27.28 27.85 39.93
- 48.37 22.24 26.83 26.85 27.26 27.86 39.93
- 48.36 22.24 26.83 26.87 27.04 27.08 27.25 27.87 39.93
+ 48.37 22.24 26.83 26.85 27.27 27.86 39.93
+ 48.36 22.24 26.83 26.87 27.04 27.08 27.26 27.87 39.93
48.35 22.24 26.79 26.89 27.04 27.14 27.23 27.88 39.92
48.34 22.24 26.79 26.92 27.03 27.90 39.90
48.33 22.28 26.79 27.90 39.89
@@ -169686,7 +169974,7 @@ Ukraine
48.12 22.56 26.29 28.30 28.36 28.40 28.52 28.61 39.86
48.11 22.57 26.29 28.31 28.35 28.40 28.51 28.64 39.86
48.10 22.58 26.29 28.41 28.51 28.78 39.85
- 48.09 22.59 22.72 22.75 26.28 28.41 28.51 28.79 39.85
+ 48.09 22.59 22.72 22.75 26.28 28.41 28.50 28.79 39.85
48.08 22.59 22.62 22.78 26.28 28.42 28.50 28.79 39.84
48.07 22.80 23.11 23.17 26.27 28.43 28.50 28.79 39.84
48.06 22.82 23.10 23.21 26.26 28.44 28.50 28.80 39.84
@@ -169697,14 +169985,14 @@ Ukraine
48.01 22.84 23.08 23.29 26.20 28.82 39.81
48.00 22.83 23.08 23.31 26.20 28.82 39.79
47.99 22.83 23.07 23.33 26.19 28.84 39.79
- 47.98 22.82 22.93 22.96 23.06 23.35 23.52 23.61 26.18 28.85 39.80
+ 47.98 22.82 22.93 22.96 23.06 23.35 23.52 23.61 26.18 28.86 39.80
47.97 22.82 22.93 22.97 23.04 23.40 23.50 23.66 26.16 28.86 39.80
47.96 22.82 22.93 23.44 23.49 23.79 26.14 28.87 39.80
47.95 22.83 22.93 23.80 26.00 28.88 29.07 29.12 39.80
47.94 22.84 22.92 23.82 23.96 24.01 25.89 28.90 29.06 29.13 39.80
47.93 22.86 22.89 23.83 23.93 24.04 24.40 24.45 25.80 28.92 29.04 29.13 39.80
- 47.92 23.84 23.89 24.08 24.38 24.57 25.77 28.94 29.02 29.14 39.80
- 47.91 24.10 24.36 24.59 25.69 28.96 29.00 29.14 39.79
+ 47.92 23.84 23.89 24.08 24.38 24.55 25.77 28.94 29.02 29.14 39.80
+ 47.91 24.10 24.36 24.58 25.69 28.96 29.00 29.14 39.79
47.90 24.12 24.32 24.60 25.57 29.15 39.79
47.89 24.16 24.28 24.62 25.45 29.15 39.79
47.88 24.18 24.25 24.63 25.33 29.16 39.79
@@ -169725,7 +170013,7 @@ Ukraine
47.73 24.84 25.09 29.19 38.76
47.72 24.85 25.06 29.18 38.76
47.71 24.85 25.03 29.18 38.76
- 47.70 24.86 24.96 29.18 38.76
+ 47.70 24.86 24.98 29.18 38.76
47.69 29.18 38.75
47.68 29.18 38.75
47.67 29.18 38.75
@@ -169748,7 +170036,7 @@ Ukraine
47.50 29.11 38.28
47.49 29.11 38.27
47.48 29.12 38.27
- 47.47 29.13 38.27
+ 47.47 29.12 38.27
47.46 29.13 38.27
47.45 29.14 38.27
47.44 29.14 38.27
@@ -169822,29 +170110,29 @@ Ukraine
46.76 29.92 36.87
46.75 29.92 36.61 36.72 36.86
46.74 29.93 36.60 36.74 36.85
- 46.73 29.94 36.51 36.75 36.85
- 46.72 29.94 36.46 36.77 36.84
- 46.71 29.94 36.42 36.78 36.84
- 46.70 29.94 36.40 36.79 36.83
- 46.69 29.93 36.38 36.78 36.83
- 46.68 29.93 36.37 36.78 36.83
+ 46.73 29.94 36.51 36.75 36.84
+ 46.72 29.94 36.46 36.77 36.83
+ 46.71 29.94 36.42 36.78 36.83
+ 46.70 29.94 36.40 36.79 36.82
+ 46.69 29.93 36.38 36.78 36.82
+ 46.68 29.93 36.37 36.78 36.82
46.67 29.93 36.35 36.77 36.82
46.66 29.93 36.34 36.77 36.81
- 46.65 29.92 36.33 36.73 36.81
- 46.64 29.92 31.45 31.47 36.00 36.20 36.31 36.73 36.80
+ 46.65 29.92 36.03 36.09 36.33 36.73 36.81
+ 46.64 29.92 31.45 31.47 35.96 36.20 36.31 36.73 36.80
46.63 29.92 31.44 31.47 35.89 36.22 36.30 36.73 36.79
46.62 29.92 31.43 31.47 35.87 36.23 36.29 36.75 36.77
46.61 29.92 31.42 31.48 35.84 36.23 36.29
- 46.60 29.92 31.14 31.21 31.39 31.53 35.81 36.23 36.28
+ 46.60 29.92 31.13 31.21 31.39 31.53 35.81 36.23 36.28
46.59 29.92 31.04 31.26 31.37 31.49 35.79 36.26 36.28
46.58 29.92 30.99 31.49 35.77
46.57 29.93 30.97 31.49 35.75
46.56 29.88 30.92 31.50 35.74
46.55 29.88 30.90 31.51 35.73
- 46.54 29.14 29.20 29.88 30.88 31.52 35.72
+ 46.54 29.14 29.20 29.88 30.80 30.83 30.88 31.52 35.72
46.53 29.11 29.21 29.88 30.79 31.54 35.71
46.52 29.08 29.21 29.89 30.78 31.55 35.69
- 46.51 29.05 29.21 29.89 30.77 31.57 35.68
+ 46.51 29.06 29.21 29.89 30.77 31.57 35.68
46.50 29.03 29.21 29.90 30.77 31.58 35.67
46.49 29.00 29.21 29.44 29.49 29.93 30.77 31.60 35.66
46.48 28.98 29.21 29.29 29.32 29.42 29.49 29.70 29.72 29.95 30.78 31.61 35.64
@@ -169856,102 +170144,102 @@ Ukraine
46.42 28.90 29.21 29.27 29.55 29.63 29.79 30.05 30.79 31.67 31.69 32.00 35.22 35.26 35.49
46.41 28.90 29.21 29.27 29.56 29.63 29.80 30.06 30.79 31.67 31.69 32.01 35.22 35.26 35.47
46.40 28.90 29.21 29.24 29.56 29.63 29.81 30.09 30.78 32.03 35.22 35.25 35.46
- 46.39 28.90 29.21 29.23 29.57 29.63 29.81 30.08 30.78 32.02 35.22 35.25 35.45
- 46.38 28.90 29.58 29.63 29.81 29.89 29.98 30.05 30.78 31.49 31.52 32.00 35.22 35.24 35.44
- 46.37 28.90 29.81 29.87 30.77 31.49 31.53 31.98 35.21 35.24 35.43
+ 46.39 28.90 29.21 29.23 29.57 29.63 29.81 30.08 30.78 32.01 35.22 35.25 35.45
+ 46.38 28.90 29.58 29.63 29.81 29.89 29.98 30.05 30.78 31.49 31.52 31.99 35.21 35.24 35.44
+ 46.37 28.90 29.81 29.87 30.77 31.49 31.53 31.97 35.21 35.24 35.43
46.36 28.91 29.81 29.85 30.76 31.49 31.53 31.92 35.20 35.24 35.41
- 46.35 28.91 30.75 31.49 31.53 31.79 35.18 35.24 35.39
- 46.34 28.91 30.74 31.49 31.54 31.77 35.16 35.25 35.38
+ 46.35 28.91 30.75 31.49 31.53 31.78 35.18 35.24 35.39
+ 46.34 28.91 30.74 31.49 31.54 31.76 35.16 35.25 35.38
46.33 28.92 30.73 31.49 31.54 31.76 35.15 35.26 35.37
46.32 28.92 30.69 31.50 31.55 31.75 35.14 35.28 35.36
46.31 28.93 30.69 31.50 31.55 31.75 35.14 35.29 35.35
46.30 28.93 30.69 31.51 31.56 31.75 35.13 35.28 35.34
46.29 28.92 30.69 31.52 31.57 31.76 35.12 35.27 35.34
- 46.28 28.92 30.69 31.52 31.59 31.77 35.11 35.27 35.33
- 46.27 28.92 30.68 31.53 31.61 31.79 31.90 31.93 35.10 35.26 35.32
+ 46.28 28.92 30.69 31.52 31.59 31.77 31.89 31.92 35.11 35.27 35.33
+ 46.27 28.92 30.68 31.53 31.61 31.79 31.89 31.93 35.10 35.26 35.32
46.26 28.92 30.68 31.55 31.65 31.84 31.89 31.95 35.08 35.25 35.31
46.25 28.92 30.67 31.57 31.71 31.97 35.07 35.24 35.30
46.24 28.92 30.66 31.59 31.78 31.99 35.05 35.22 35.29
- 46.23 28.94 30.65 31.63 31.85 32.06 35.01 35.21 35.28
+ 46.23 28.94 30.65 31.63 31.85 32.06 35.01 35.21 35.27
46.22 28.95 30.64 31.67 31.91 32.07 34.96 35.21 35.26
- 46.21 28.96 30.63 31.71 31.98 32.09 34.89 35.20 35.26
+ 46.21 28.97 30.63 31.71 31.98 32.09 34.89 35.20 35.26
46.20 28.98 30.61 31.76 32.04 32.10 34.87 35.20 35.25
- 46.19 28.99 30.60 31.82 32.09 32.11 34.85 35.18 35.25
- 46.18 28.99 30.59 31.88 32.12 32.16 34.83 35.15 35.24
+ 46.19 28.99 30.60 31.82 32.09 32.11 34.85 35.18 35.24
+ 46.18 28.99 30.59 31.88 32.12 32.16 34.83 35.15 35.23
46.17 28.99 30.58 31.94 32.14 32.23 34.82 35.11 35.23
- 46.16 28.99 30.58 32.00 32.16 32.23 34.82 35.06 35.23
- 46.15 28.98 30.57 32.06 32.17 32.23 33.19 33.21 34.82 35.03 35.22
- 46.14 28.97 30.56 32.12 32.17 32.24 33.18 33.21 34.82 35.03 35.21
+ 46.16 28.99 30.58 32.00 32.16 32.23 34.82 35.06 35.22
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USA
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@@ -173478,164 +173767,164 @@ USA
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@@ -178351,335 +178642,335 @@ USA: Alaska
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- 58.88 -161.80 -160.75 -160.17 -159.75 -159.63 -158.66 -158.51 -157.05 -157.02 -153.25 -137.96 -135.31 -135.14 -134.27
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- 58.53 -159.18 -158.75 -157.44 -153.91 -152.67 -152.36 -137.46 -136.13 -135.85 -135.14 -134.87 -133.54
- 58.52 -159.17 -158.75 -157.45 -153.91 -152.65 -152.38 -137.44 -136.07 -135.85 -135.13 -134.85 -133.53
- 58.51 -159.17 -158.70 -157.46 -153.91 -152.65 -152.40 -137.42 -136.07 -135.85 -135.13 -134.83 -133.51
- 58.50 -159.16 -158.69 -157.47 -153.91 -152.65 -152.42 -137.40 -136.07 -135.87 -135.13 -134.83 -133.49
- 58.49 -159.14 -158.69 -157.49 -153.93 -152.66 -152.44 -137.38 -136.07 -135.87 -135.12 -134.81 -133.47
- 58.48 -159.12 -158.69 -157.50 -153.94 -152.67 -152.45 -137.35 -136.05 -135.92 -135.11 -134.79 -133.45
- 58.47 -159.09 -158.70 -157.51 -154.08 -152.68 -152.47 -137.33 -136.05 -135.96 -135.11 -134.79 -133.44
- 58.46 -159.09 -158.72 -157.52 -154.08 -152.75 -152.71 -152.68 -152.48 -137.31 -136.05 -135.96 -135.09 -134.78 -133.42
- 58.45 -159.09 -158.73 -157.52 -154.07 -152.75 -152.48 -137.29 -136.05 -135.96 -135.08 -134.78 -133.40
- 58.44 -159.08 -158.73 -157.53 -154.06 -152.76 -152.48 -137.27 -136.04 -135.96 -135.08 -134.78 -133.38
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- 58.42 -159.07 -158.76 -157.54 -154.05 -152.87 -152.46 -152.37 -152.25 -137.19 -136.03 -135.91 -135.07 -134.78 -133.37
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@@ -178687,18 +178978,18 @@ USA: Alaska
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@@ -178706,48 +178997,48 @@ USA: Alaska
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56.96 -158.70 -156.77 -154.46 -154.14 -154.11 -154.06 -153.98 -153.55 -135.36 -134.71 -133.94 -133.01 -132.92 -132.04
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@@ -178755,7 +179046,7 @@ USA: Alaska
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@@ -178780,103 +179071,103 @@ USA: Alaska
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@@ -178888,58 +179179,58 @@ USA: Alaska
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@@ -178955,29 +179246,30 @@ USA: Alaska
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@@ -178988,23 +179280,23 @@ USA: Alaska
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USA: Missouri
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@@ -191919,8 +192282,8 @@ USA: New Jersey
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@@ -192507,10 +192870,10 @@ USA: New York
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USA: South Carolina
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USA: Wyoming
45.01 -111.06 -104.04
45.00 -111.06 -104.04
@@ -199627,7 +199995,7 @@ Uzbekistan
45.37 57.57 58.98
45.36 57.53 59.00
45.35 57.49 59.02
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45.33 57.40 59.07
45.32 57.35 59.09
45.31 57.31 59.11
@@ -199644,8 +200012,8 @@ Uzbekistan
45.20 56.84 59.35
45.19 56.79 59.37
45.18 56.74 59.39
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45.15 56.60 59.45
45.14 56.56 59.47
45.13 56.51 59.49
@@ -199940,7 +200308,7 @@ Uzbekistan
42.24 55.96 57.89 59.90 66.02 70.91 71.17
42.23 55.96 57.88 59.91 66.02 70.90 71.19
42.22 55.96 57.84 59.93 66.02 70.88 71.21
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42.20 55.96 57.86 59.97 66.02 70.71 71.26
42.19 55.96 57.86 59.99 66.02 70.70 71.26
42.18 55.96 57.86 60.01 66.02 70.70 71.26
@@ -200033,7 +200401,7 @@ Uzbekistan
41.31 55.96 57.11 60.23 66.66 69.04 70.78 71.40 71.87
41.30 56.05 57.08 60.25 66.66 69.04 70.77 71.40 71.87
41.29 56.23 57.07 60.27 66.67 69.03 70.77 71.40 71.87
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41.27 56.68 57.05 60.32 61.41 61.49 66.67 69.03 70.77 71.40 71.87
41.26 56.83 57.04 60.34 61.40 61.53 66.67 69.03 70.76 71.40 71.87
41.25 56.91 57.03 60.36 61.40 61.57 66.68 69.03 70.86 71.40 71.87
@@ -200045,7 +200413,7 @@ Uzbekistan
41.19 60.96 60.99 61.11 61.36 61.71 66.71 67.68 67.77 67.89 67.95 68.98 71.05 71.17 71.24 71.41 72.01 72.07 72.16
41.18 61.13 61.35 61.73 66.72 67.44 67.81 67.87 67.96 68.95 71.06 71.17 71.25 71.41 72.01 72.05 72.16
41.17 61.15 61.34 61.75 66.73 67.22 67.82 67.85 67.96 68.89 71.11 71.17 71.25 71.41 72.17
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41.15 61.19 61.31 61.78 67.98 68.85 71.14 71.17 71.26 71.30 71.35 71.41 72.18
41.14 61.22 61.29 61.80 67.99 68.85 71.15 71.17 71.26 71.29 71.37 71.40 72.18
41.13 61.82 68.00 68.84 72.18
@@ -200093,9 +200461,9 @@ Uzbekistan
40.71 62.02 68.19 68.56 69.32 69.55 69.89 70.74 72.97
40.70 62.03 68.20 68.58 69.32 69.56 69.85 70.74 72.95
40.69 62.04 68.22 68.59 69.31 69.57 69.82 70.72 72.93
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40.65 62.09 68.33 68.60 69.31 69.61 69.76 70.66 72.79
40.64 62.09 68.36 68.59 69.31 69.62 69.75 70.64 72.78
40.63 62.10 68.38 68.59 69.32 69.63 69.74 70.62 72.77
@@ -200104,7 +200472,7 @@ Uzbekistan
40.60 62.10 69.32 70.59 72.76
40.59 62.11 69.32 70.58 72.76
40.58 62.11 69.31 70.55 72.36 72.39 72.76
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40.56 62.12 69.23 70.51 72.38 72.41 72.75
40.55 62.13 69.21 70.50 72.38 72.43 72.66 72.69 72.73
40.54 62.14 69.21 70.49 72.38 72.44 72.66
@@ -200113,8 +200481,8 @@ Uzbekistan
40.51 62.16 69.23 70.42 72.38 72.53 72.66
40.50 62.17 69.24 70.38 72.40 72.55 72.65
40.49 62.17 69.24 70.36 72.41 72.57 72.61
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40.46 62.23 69.25 70.34 72.43
40.45 62.27 69.26 70.34 72.43
40.44 62.29 69.26 70.34 72.43
@@ -200134,7 +200502,7 @@ Uzbekistan
40.30 62.38 69.31 70.54 71.97
40.29 62.38 69.31 70.54 71.23 71.26 71.97
40.28 62.39 69.22 69.24 69.31 70.54 71.23 71.27 71.99
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40.26 62.39 69.24 70.55 71.22 71.38 72.03
40.25 62.39 69.25 70.55 71.03 71.10 71.21 71.41 72.03
40.24 62.39 69.26 70.55 70.99 71.43 72.03
@@ -200146,9 +200514,9 @@ Uzbekistan
40.18 62.42 68.82 69.12 69.29 70.61 70.69 71.54 71.60 71.65 71.79
40.17 62.42 68.67 68.74 68.79 69.16 69.27 71.65 71.79
40.16 62.42 68.63 70.98 71.02 71.65 71.78
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40.12 62.41 68.98 70.94 71.06
40.11 62.41 68.99 70.94 71.06
40.10 62.41 68.99 70.94 71.07
@@ -200237,7 +200605,7 @@ Uzbekistan
39.27 63.59 67.36
39.26 63.60 67.35
39.25 63.60 67.35
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39.23 63.62 67.36
39.22 63.63 67.36
39.21 63.64 67.37
@@ -200459,8 +200827,8 @@ Vanuatu
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-13.20 166.60 166.64
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@@ -200489,10 +200857,10 @@ Vanuatu
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@@ -200543,8 +200911,8 @@ Vanuatu
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@@ -200558,7 +200926,7 @@ Vanuatu
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@@ -200574,12 +200942,12 @@ Vanuatu
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@@ -200610,7 +200978,7 @@ Vanuatu
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@@ -200643,8 +201011,8 @@ Vanuatu
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@@ -200711,15 +201079,15 @@ Vanuatu
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@@ -200733,7 +201101,7 @@ Vanuatu
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@@ -200750,9 +201118,9 @@ Vanuatu
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@@ -200760,8 +201128,8 @@ Vanuatu
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@@ -200794,7 +201162,7 @@ Vanuatu
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@@ -200832,8 +201200,8 @@ Vanuatu
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@@ -200848,7 +201216,7 @@ Vanuatu
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@@ -200856,8 +201224,8 @@ Vanuatu
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@@ -200881,8 +201249,8 @@ Vanuatu
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@@ -200895,10 +201263,10 @@ Vanuatu
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@@ -200924,8 +201292,12 @@ Vanuatu
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Venezuela
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12.18 -70.08 -69.93
12.17 -70.09 -69.92
12.16 -70.10 -69.91
@@ -200937,7 +201309,7 @@ Venezuela
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12.09 -70.22 -69.87
12.08 -70.22 -69.86
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12.06 -70.22 -69.85 -67.69 -67.66
12.05 -70.23 -69.84 -67.69 -67.66
12.04 -70.24 -69.83 -67.68 -67.66
@@ -200958,243 +201330,243 @@ Venezuela
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0.82 -66.44 -65.93 -65.54 -65.37
0.81 -66.43 -65.94 -65.55 -65.38
0.80 -66.42 -65.95 -65.55 -65.39
@@ -202103,7 +202475,7 @@ Viet Nam
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@@ -202149,13 +202521,13 @@ Viet Nam
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22.63 102.36 102.77 103.15 103.44 103.52 103.82 103.99 106.71
22.62 102.36 102.80 103.14 103.45 103.52 103.82 103.99 106.70
@@ -202258,7 +202630,7 @@ Viet Nam
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21.61 102.95 107.47 107.51 107.86
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21.30 102.84 107.61 107.70 107.75
21.29 102.81 107.61 107.70 107.73
@@ -202307,27 +202679,27 @@ Viet Nam
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20.91 103.06 104.04 104.17 106.95 107.38 107.56
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@@ -202335,7 +202707,7 @@ Viet Nam
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20.84 103.12 103.85 104.30 106.88 106.90 107.05 107.33 107.38 107.46 107.50
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20.82 103.17 103.78 104.31 106.76 106.82 107.10 107.33 107.39 107.45 107.50
@@ -202343,7 +202715,7 @@ Viet Nam
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+ 10.91 105.01 105.16 105.34 105.83 106.11 108.16 108.28 108.31
+ 10.90 105.00 105.23 105.34 105.83 105.92 105.94 106.11 108.12 108.28 108.31
10.89 105.00 105.26 105.33 105.84 105.91 105.95 106.11 108.10
10.88 105.00 105.27 105.33 105.84 105.91 105.96 106.12 108.09
10.87 105.00 105.29 105.32 105.85 105.91 105.97 106.12 108.08
@@ -203366,19 +203738,19 @@ Viet Nam
10.57 104.87 107.62
10.56 104.86 107.60 108.93 108.95
10.55 104.85 107.58 108.91 108.95
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10.52 104.54 107.55 108.91 108.97
10.51 104.53 107.54 108.91 108.97
10.50 104.53 107.54 108.92 108.97
10.49 104.52 106.71 106.74 107.53 108.93 108.97
10.48 104.51 107.50
10.47 104.51 107.48
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10.41 103.95 104.06 104.44 106.98 107.09 107.31
10.40 103.94 104.07 104.44 106.98 107.06 107.30
10.39 103.94 104.08 104.44 106.79 106.82 106.85 106.87 106.98 107.06 107.30
@@ -203396,7 +203768,7 @@ Viet Nam
10.27 103.89 104.09 104.52 106.80
10.26 103.90 104.09 104.56 106.79
10.25 103.92 104.09 104.57 106.76
- 10.24 103.93 104.09 104.57 106.63 106.65 106.76
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10.23 103.93 104.09 104.58 106.66 106.69 106.76
10.22 103.94 104.09 104.58 106.76
10.21 103.94 104.08 104.58 104.72 104.75 106.75
@@ -203421,7 +203793,7 @@ Viet Nam
10.02 104.00 104.05 105.04 106.69
10.01 104.02 104.06 105.05 106.69
10.00 104.02 104.06 105.06 106.69
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9.98 105.07 106.67
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9.96 105.09 106.66
@@ -203434,57 +203806,57 @@ Viet Nam
9.89 104.98 106.70
9.88 104.96 106.70
9.87 104.96 106.70
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9.55 104.82 106.30 106.34 106.52
9.54 104.82 106.20 106.23 106.30 106.36 106.51
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9.52 104.82 106.21 106.23 106.28
9.51 104.82 106.21
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9.33 104.81 106.14
@@ -203493,102 +203865,103 @@ Viet Nam
9.30 104.81 106.03
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9.26 104.80 105.93
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Virgin Islands
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17.76 -64.89 -64.54
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17.71 -64.89 -64.62
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17.68 -64.90 -64.76
17.67 -64.90 -64.83
Wake Island
@@ -203600,14 +203973,14 @@ Wake Island
19.26 166.62 166.65
Wallis and Futuna
-13.19 -176.16 -176.14
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- -13.21 -176.17 -176.13
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@@ -203627,13 +204000,7 @@ Wallis and Futuna
-14.29 -178.17 -178.04
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-14.31 -178.16 -178.03
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+ -14.32 -178.15 -178.03
West Bank
32.55 35.18 35.22
32.54 35.16 35.23
@@ -203648,11 +204015,11 @@ West Bank
32.45 35.04 35.41
32.44 35.03 35.41
32.43 35.03 35.41
- 32.42 35.02 35.42
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32.41 35.02 35.51
32.40 35.02 35.55
32.39 35.02 35.57
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32.37 35.01 35.57
32.36 35.01 35.57
32.35 35.00 35.57
@@ -203672,7 +204039,7 @@ West Bank
32.21 34.95 35.58
32.20 34.94 35.57
32.19 34.93 35.57
- 32.18 34.93 35.57
+ 32.18 34.93 35.56
32.17 34.93 35.56
32.16 34.93 35.56
32.15 34.94 35.56
@@ -203705,7 +204072,7 @@ West Bank
31.88 34.98 35.54
31.87 34.96 35.54
31.86 34.94 35.54
- 31.85 34.94 35.55
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31.84 34.93 35.55
31.83 34.93 35.55
31.82 34.93 35.55
@@ -203724,12 +204091,12 @@ West Bank
31.69 35.04 35.52
31.68 35.02 35.51
31.67 35.01 35.51
- 31.66 34.99 35.50
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31.65 34.97 35.50
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31.63 34.95 35.49
31.62 34.94 35.49
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31.60 34.93 35.48
31.59 34.92 35.48
31.58 34.92 35.48
@@ -203759,631 +204126,631 @@ West Bank
31.34 34.87 35.02
31.33 34.89 34.97
Western Sahara
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20.80 -17.09 -17.05
20.79 -17.08 -17.05
20.78 -17.07 -17.04
@@ -204609,7 +204976,7 @@ Yemen
17.47 43.30 43.61 47.57 52.66
17.46 43.29 43.62 47.57 52.66
17.45 43.28 43.63 47.56 52.67
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17.43 43.25 43.65 44.60 45.20 47.56 52.68
17.42 43.24 43.66 44.35 44.50 44.57 45.23 47.55 52.68
17.41 43.22 43.67 44.13 44.19 44.26 45.25 47.55 52.69
@@ -204740,7 +205107,7 @@ Yemen
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16.12 42.82 52.23
16.11 42.82 52.23
16.10 42.83 52.23
@@ -204795,27 +205162,27 @@ Yemen
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15.60 42.70 52.23
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15.52 42.73 51.98
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15.44 42.58 42.64 42.76 51.87
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15.42 42.56 42.63 42.76 51.75
15.41 42.55 42.62 42.76 51.73
15.40 42.54 42.63 42.76 51.71
15.39 42.54 42.63 42.77 51.69
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15.37 42.54 42.63 42.70 42.72 42.78 51.67
15.36 42.54 42.63 42.69 42.72 42.78 51.67
15.35 42.54 42.63 42.68 42.72 42.78 51.68
@@ -204837,13 +205204,13 @@ Yemen
15.19 42.60 42.69 42.72 51.28
15.18 42.62 42.68 42.76 51.25
15.17 42.64 42.68 42.77 51.22
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15.11 42.85 50.99
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15.09 42.87 50.88
15.08 42.87 50.84
15.07 42.86 50.80
@@ -204869,8 +205236,8 @@ Yemen
14.87 42.87 42.90 42.94 50.26
14.86 42.87 42.91 42.94 50.24
14.85 42.87 42.92 42.94 50.22
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14.82 42.89 49.98 50.02 50.11
14.81 42.90 49.93 50.02 50.09
14.80 42.90 49.89 50.03 50.06
@@ -204907,62 +205274,62 @@ Yemen
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14.10 43.08 48.78
14.09 43.08 48.77
14.08 42.75 42.77 43.08 48.76
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13.90 42.76 42.79 43.18 47.78
13.89 43.19 47.75
13.88 43.20 47.71
@@ -205011,19 +205378,19 @@ Yemen
13.45 43.24 46.81
13.44 43.24 46.78
13.43 43.23 46.75
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13.39 43.23 46.14
13.38 43.23 46.03
13.37 43.23 45.91
13.36 43.23 45.83 45.85 45.89
13.35 43.23 45.78
13.34 43.23 45.74
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13.31 43.22 45.64
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13.29 43.21 45.62
13.28 43.21 45.61
13.27 43.21 45.60
@@ -205047,9 +205414,9 @@ Yemen
13.09 43.31 45.45
13.08 43.31 45.44
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13.03 43.34 45.34
13.02 43.35 45.30
13.01 43.36 45.26
@@ -205061,7 +205428,7 @@ Yemen
12.95 43.38 45.12
12.94 43.38 45.12
12.93 43.39 45.11
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12.91 43.40 45.10
12.90 43.40 45.10
12.89 43.41 45.09
@@ -205076,70 +205443,71 @@ Yemen
12.80 43.47 44.94 44.97 45.06
12.79 43.47 44.57 44.67 44.93 44.96 45.07
12.78 43.47 44.55 44.69 44.93 44.96 45.07
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12.75 43.46 44.51 44.71 44.93 44.98 45.06
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Zambia
-8.18 30.70 30.76
-8.19 30.62 30.76
@@ -205159,8 +205527,8 @@ Zambia
-8.33 29.72 30.81
-8.34 29.66 30.81
-8.35 29.61 30.82
- -8.36 29.55 30.82
- -8.37 29.47 30.83
+ -8.36 29.53 30.82
+ -8.37 29.46 30.83
-8.38 29.39 30.84
-8.39 29.32 30.85
-8.40 29.24 30.85
@@ -205228,7 +205596,7 @@ Zambia
-9.02 28.64 31.92
-9.03 28.63 31.93 32.02 32.06
-9.04 28.62 31.93 32.00 32.08
- -9.05 28.61 31.96 31.99 32.15
+ -9.05 28.61 31.96 31.99 32.14
-9.06 28.60 32.16
-9.07 28.59 32.17
-9.08 28.58 32.18
@@ -205418,8 +205786,8 @@ Zambia
-10.92 23.96 24.12 28.52 33.29
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-10.94 23.97 24.12 28.52 33.29
- -10.95 23.98 24.12 28.51 33.29
- -10.96 23.98 24.12 28.50 33.29
+ -10.95 23.98 24.12 28.51 33.30
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-10.97 23.99 24.12 28.49 33.30
-10.98 23.99 24.12 28.49 33.30
-10.99 23.98 24.12 28.49 33.30
@@ -205543,9 +205911,9 @@ Zambia
-12.17 23.94 27.53 28.88 29.75 29.78 33.29
-12.18 23.94 27.54 28.90 29.73 29.78 33.30
-12.19 23.94 27.54 28.91 29.71 29.78 33.31
- -12.20 23.94 27.56 28.92 29.57 29.59 29.70 29.78 33.31
+ -12.20 23.94 27.55 28.92 29.57 29.59 29.70 29.78 33.31
-12.21 23.95 27.57 28.93 29.56 29.60 29.68 29.78 33.32
- -12.22 23.96 27.59 28.94 29.55 29.61 29.66 29.78 33.32
+ -12.22 23.96 27.58 28.94 29.55 29.61 29.66 29.78 33.32
-12.23 23.97 27.60 28.94 29.52 29.78 33.33
-12.24 23.98 27.61 27.82 27.85 28.95 29.50 29.78 33.33
-12.25 23.98 27.62 27.80 27.88 28.95 29.48 29.78 33.33
@@ -205656,7 +206024,7 @@ Zambia
-13.30 21.97 28.94 29.39 29.67 29.78 32.92
-13.31 21.97 28.95 29.37 29.67 29.78 32.92
-13.32 21.97 28.95 29.34 29.66 29.78 32.92
- -13.33 21.97 28.96 29.31 29.63 29.78 32.91
+ -13.33 21.97 28.96 29.31 29.63 29.78 32.92
-13.34 21.97 28.96 29.29 29.63 29.78 32.91
-13.35 21.97 28.97 29.28 29.63 29.78 32.91
-13.36 21.97 28.98 29.26 29.63 29.78 32.91
@@ -205920,7 +206288,7 @@ Zambia
-15.94 21.97 29.06
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+ -15.97 21.97 28.94
-15.98 21.97 28.93
-15.99 21.97 28.92
-16.00 21.97 28.90
@@ -206009,13 +206377,13 @@ Zambia
-16.83 22.44 28.12
-16.84 22.45 28.10
-16.85 22.46 28.08
- -16.86 22.46 28.05
- -16.87 22.47 28.03
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- -16.89 22.48 27.98
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-16.91 22.49 27.93
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+ -16.92 22.51 27.91
-16.93 22.53 27.88
-16.94 22.55 27.86
-16.95 22.55 27.84
@@ -206166,7 +206534,7 @@ Zimbabwe
-15.91 29.05 30.41
-15.92 29.04 30.41
-15.93 29.02 30.41
- -15.94 28.94 30.41
+ -15.94 28.93 30.41
-15.95 28.92 30.41
-15.96 28.91 30.41
-15.97 28.89 30.41
@@ -206255,13 +206623,13 @@ Zimbabwe
-16.80 28.11 32.95
-16.81 28.09 32.94
-16.82 28.07 32.94
- -16.83 28.04 32.93
- -16.84 28.02 32.93
- -16.85 27.99 32.92
- -16.86 27.97 32.92
- -16.87 27.94 32.91
+ -16.83 28.05 32.93
+ -16.84 28.03 32.93
+ -16.85 28.00 32.92
+ -16.86 27.98 32.92
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-16.88 27.92 32.90
- -16.89 27.89 32.89
+ -16.89 27.90 32.89
-16.90 27.87 32.88
-16.91 27.85 32.87
-16.92 27.83 32.85
@@ -206311,7 +206679,7 @@ Zimbabwe
-17.36 27.55 33.03
-17.37 27.54 33.03
-17.38 27.53 33.02
- -17.39 27.52 33.01
+ -17.39 27.52 33.02
-17.40 27.51 33.01
-17.41 27.50 33.00
-17.42 27.49 32.99
@@ -206467,11 +206835,11 @@ Zimbabwe
-18.92 25.92 32.72
-18.93 25.93 32.71
-18.94 25.93 32.70
- -18.95 25.93 32.69
+ -18.95 25.94 32.69
-18.96 25.94 32.69
-18.97 25.94 32.70
-18.98 25.94 32.70
- -18.99 25.94 32.70
+ -18.99 25.95 32.70
-19.00 25.95 32.70 32.75 32.81
-19.01 25.95 32.83
-19.02 25.94 32.83
diff --git a/c++/src/objects/seqfeat/lat_lon_island.txt b/c++/src/objects/seqfeat/lat_lon_island.txt
index ea24b86..99caa86 100644
--- a/c++/src/objects/seqfeat/lat_lon_island.txt
+++ b/c++/src/objects/seqfeat/lat_lon_island.txt
@@ -4,7 +4,7 @@ Unnamed Islands
81.35 54.17 54.23
81.34 54.17 54.28
81.33 54.17 54.34
- 81.32 54.21 54.40
+ 81.32 54.19 54.40
81.31 54.24 54.44
81.30 54.25 54.44
81.29 54.28 54.44
@@ -16,17 +16,6 @@ Unnamed Islands
80.83 -66.38 -66.28
80.82 -66.38 -66.28
80.81 -66.38 -66.28
- 80.68 -66.99 -66.83
- 80.67 -66.99 -66.77
- 80.66 -66.99 -66.71
- 80.65 -66.99 -66.67
- 80.64 -66.98 -66.63
- 80.63 -66.96 -66.58
- 80.62 -66.96 -66.57
- 80.61 -66.94 -66.57
- 80.60 -66.92 -66.57
- 80.59 -66.85 -66.58
- 80.58 -66.81 -66.75
80.51 -67.30 -67.17
80.50 -67.30 -67.14
80.49 -67.30 -67.14
@@ -42,15 +31,6 @@ Unnamed Islands
77.13 90.11 90.26
77.12 90.11 90.26
77.11 90.11 90.25
- 76.78 97.50 97.64
- 76.77 97.33 97.65
- 76.76 97.15 97.65
- 76.75 97.15 97.65
- 76.74 97.15 97.65
- 76.73 97.15 97.55 97.59 97.65
- 76.72 97.43 97.51 97.61 97.63
- 76.71 97.43 97.49
- 76.70 97.44 97.47
75.99 92.53 92.68
75.98 92.53 92.68
75.97 92.53 92.68
@@ -59,10 +39,10 @@ Unnamed Islands
75.94 92.54 92.66
71.05 24.93 24.98
71.04 24.92 25.05
- 71.03 24.91 25.05
- 71.02 24.91 25.05
- 71.01 24.91 25.05
- 71.00 24.92 25.04
+ 71.03 24.92 25.05
+ 71.02 24.92 25.05
+ 71.01 24.92 25.05
+ 71.00 24.93 25.04
70.99 24.94 25.03
70.98 24.95 25.01
70.71 25.81 25.88
@@ -101,8 +81,8 @@ Unnamed Islands
70.15 18.77 18.90 19.93 20.07
70.14 18.77 18.90 19.96 20.07
70.13 18.78 18.90 20.00 20.06 21.29 21.34
- 70.12 18.79 18.85 21.28 21.36
- 70.11 18.79 18.86 21.27 21.37
+ 70.12 18.78 18.85 21.28 21.36
+ 70.11 18.78 18.86 21.27 21.37
70.10 18.79 18.86 21.27 21.37
70.09 18.79 18.86 21.27 21.37
70.08 18.80 18.85 21.32 21.35
@@ -148,16 +128,11 @@ Unnamed Islands
68.94 16.64 16.77
68.93 16.65 16.74
68.92 16.66 16.70
- 68.83 37.29 37.33 67.20 67.26
- 68.82 37.29 37.36 67.14 67.31
- 68.81 37.29 37.37 67.11 67.36
- 68.80 37.29 37.37 67.10 67.39
- 68.79 37.30 37.37 67.10 67.40
- 68.78 67.10 67.19 67.21 67.41
- 68.77 67.12 67.17 67.23 67.41
- 68.76 67.26 67.41
- 68.75 67.29 67.41
- 68.74 67.31 67.34 67.37 67.40
+ 68.83 37.29 37.33
+ 68.82 37.29 37.36
+ 68.81 37.29 37.37
+ 68.80 37.29 37.37
+ 68.79 37.30 37.37
68.40 38.44 38.46
68.39 38.42 38.47
68.38 38.41 38.48
@@ -213,7 +188,7 @@ Unnamed Islands
67.53 12.07 12.17
67.52 12.06 12.17
67.51 12.06 12.17
- 67.50 12.06 12.15
+ 67.50 12.06 12.16
67.49 12.06 12.11
67.48 -174.65 -174.59 11.93 11.95 12.06 12.09
67.47 -174.65 -174.58 11.92 11.96
@@ -331,12 +306,12 @@ Unnamed Islands
65.85 12.22 12.28
65.84 12.22 12.27
65.83 12.22 12.25
- 65.82 12.22 12.25 22.45 22.48 22.74 22.77
- 65.81 12.46 12.50 22.38 22.40 22.45 22.49 22.71 22.78 24.11 24.14
- 65.80 12.44 12.50 22.37 22.42 22.45 22.49 22.71 22.78 23.20 23.24 23.45 23.49 24.09 24.17
- 65.79 12.40 12.50 22.37 22.43 22.45 22.49 22.59 22.64 22.71 22.78 23.20 23.25 23.45 23.49 23.94 23.98 24.09 24.17 24.50 24.53 34.93 34.99
- 65.78 12.39 12.50 22.37 22.43 22.45 22.49 22.59 22.64 22.73 22.78 23.20 23.25 23.45 23.49 23.94 23.98 24.09 24.22 24.49 24.54 34.90 34.99
- 65.77 12.38 12.49 22.37 22.43 22.46 22.49 22.59 22.64 23.21 23.28 23.36 23.38 23.41 23.43 23.46 23.49 23.87 23.89 23.94 23.98 24.09 24.12 24.14 24.24 24.47 24.54 34.90 35.00
+ 65.82 -67.38 -67.30 -67.24 -67.21 12.22 12.25 22.45 22.48 22.74 22.77
+ 65.81 -67.40 -67.21 12.46 12.50 22.38 22.40 22.45 22.49 22.71 22.78 24.11 24.14
+ 65.80 -67.42 -67.21 12.44 12.50 22.37 22.42 22.45 22.49 22.71 22.78 23.20 23.24 23.45 23.49 24.09 24.17
+ 65.79 -67.42 -67.21 12.40 12.50 22.37 22.43 22.45 22.49 22.59 22.64 22.71 22.78 23.20 23.25 23.45 23.49 23.94 23.98 24.09 24.17 24.50 24.53 34.93 34.99
+ 65.78 -67.42 -67.22 12.39 12.50 22.37 22.43 22.45 22.49 22.59 22.64 22.73 22.78 23.20 23.25 23.45 23.49 23.94 23.98 24.09 24.22 24.49 24.54 34.90 34.99
+ 65.77 -67.34 -67.26 12.38 12.49 22.37 22.43 22.46 22.49 22.59 22.64 23.21 23.28 23.36 23.38 23.41 23.43 23.46 23.49 23.87 23.89 23.94 23.98 24.09 24.12 24.14 24.24 24.47 24.54 34.90 35.00
65.76 12.38 12.49 22.46 22.49 22.59 22.64 23.17 23.28 23.36 23.38 23.40 23.43 23.87 23.90 23.95 23.97 24.05 24.07 24.18 24.24 24.46 24.54 34.90 35.02
65.75 12.36 12.48 22.47 22.49 23.17 23.28 23.36 23.43 23.47 23.50 23.52 23.55 23.87 23.90 24.04 24.07 24.18 24.24 24.46 24.52 34.90 35.02
65.74 12.36 12.43 22.55 22.57 23.15 23.28 23.36 23.43 23.47 23.56 23.87 23.90 24.04 24.07 24.20 24.23 24.46 24.52 34.91 35.02
@@ -362,7 +337,7 @@ Unnamed Islands
65.54 22.31 22.36 22.40 22.43 22.63 22.82 23.54 23.56 23.74 23.77 24.80 24.83
65.53 22.31 22.38 22.40 22.43 22.63 22.82 23.52 23.56
65.52 22.06 22.11 22.31 22.43 22.63 22.73 22.77 22.82 23.52 23.56
- 65.51 21.97 22.04 22.06 22.12 22.34 22.39 22.49 22.56 22.65 22.73 22.77 22.81 23.52 23.56
+ 65.51 21.97 22.03 22.06 22.12 22.34 22.39 22.49 22.56 22.65 22.73 22.77 22.81 23.52 23.56
65.50 21.97 22.12 22.35 22.39 22.49 22.57 22.65 22.74 22.79 22.81
65.49 21.97 22.12 22.36 22.38 22.49 22.58 22.65 22.75
65.48 12.13 12.18 21.98 22.11 22.49 22.58 22.62 22.75
@@ -459,7 +434,7 @@ Unnamed Islands
64.51 -22.38 -22.32 10.76 10.85 24.24 24.27
64.50 -166.24 -166.18 -22.37 -22.35 10.77 10.85 24.24 24.27
64.49 -166.24 -166.18 24.24 24.27
- 64.48 -166.24 -166.18
+ 64.48 -166.24 -166.18 24.25 24.27
64.47 -166.23 -166.18
64.46 -166.22 -166.19
64.32 23.50 23.52
@@ -481,11 +456,11 @@ Unnamed Islands
64.13 23.62 23.66
64.10 23.39 23.41
64.09 23.39 23.42 23.50 23.55
- 64.08 9.93 10.00 23.39 23.42 23.50 23.55
+ 64.08 9.92 10.00 23.39 23.42 23.50 23.55
64.07 9.92 10.02 23.39 23.42 23.50 23.55
64.06 9.92 10.02 23.51 23.55 36.74 36.78
64.05 9.92 10.02 23.53 23.55 36.74 36.79
- 64.04 9.93 10.02 36.74 36.79
+ 64.04 9.92 10.02 36.74 36.79
64.03 9.93 10.02 36.74 36.79
64.02 9.98 10.01 36.74 36.79
64.01 36.74 36.78
@@ -494,7 +469,7 @@ Unnamed Islands
63.98 9.09 9.15
63.97 9.09 9.15
63.96 9.10 9.13 23.17 23.21
- 63.95 23.17 23.23 23.28 23.32
+ 63.95 23.17 23.22 23.28 23.32
63.94 23.17 23.23 23.27 23.32
63.93 22.73 22.82 23.18 23.23 23.27 23.32
63.92 22.73 22.83 23.18 23.23 23.27 23.31
@@ -576,12 +551,12 @@ Unnamed Islands
63.10 -164.64 -164.57 18.75 18.77 20.78 20.82
63.09 -164.64 -164.57 18.71 18.74 20.78 20.82
63.08 -164.65 -164.57 18.59 18.63 18.71 18.74
- 63.07 -164.65 -164.58 18.52 18.55 18.59 18.63 18.71 18.74
- 63.06 -164.65 -164.60 18.49 18.57 18.59 18.63 18.71 18.74
- 63.05 18.49 18.57 18.60 18.63 18.72 18.74
- 63.04 18.48 18.57 18.60 18.63
- 63.03 18.48 18.56 21.18 21.21
- 63.02 18.48 18.55 18.63 18.66 21.18 21.23
+ 63.07 -164.65 -164.58 -164.51 -164.39 18.52 18.55 18.59 18.63 18.71 18.74
+ 63.06 -164.65 -164.60 -164.53 -164.38 18.49 18.57 18.59 18.63 18.71 18.74
+ 63.05 -164.53 -164.37 18.49 18.57 18.60 18.63 18.72 18.74
+ 63.04 -164.53 -164.37 18.48 18.57 18.60 18.63
+ 63.03 -164.52 -164.37 18.48 18.56 21.18 21.21
+ 63.02 -164.43 -164.37 18.48 18.55 18.63 18.66 21.18 21.23
63.01 18.48 18.54 18.61 18.67 21.18 21.24
63.00 18.48 18.52 18.61 18.67 21.18 21.26
62.99 18.60 18.67 20.82 20.84 21.18 21.26
@@ -703,9 +678,9 @@ Unnamed Islands
61.32 4.68 4.74 4.82 4.84
61.31 4.67 4.75
61.30 4.67 4.78
- 61.29 4.67 4.79
- 61.28 4.67 4.79
- 61.27 4.68 4.79
+ 61.29 4.67 4.78
+ 61.28 4.67 4.78
+ 61.27 4.68 4.78
61.22 21.41 21.44
61.21 21.40 21.46
61.20 21.40 21.47
@@ -825,16 +800,16 @@ Unnamed Islands
60.01 -144.40 -144.35 5.11 5.21 19.95 20.02 20.83 20.87 21.44 21.48 22.89 22.97 28.34 28.40
60.00 -144.40 -144.35 5.08 5.22 19.97 20.02 20.83 20.87 22.35 22.38 22.61 22.63 22.89 22.96 28.35 28.40
59.99 -144.40 -144.35 5.08 5.22 19.97 20.01 22.33 22.38 22.42 22.46 22.50 22.56 22.60 22.63 22.89 22.93 28.36 28.39
- 59.98 -144.40 -144.35 5.08 5.22 20.28 20.30 21.27 21.31 22.32 22.38 22.40 22.47 22.49 22.56 22.59 22.64
- 59.97 -79.85 -79.83 5.08 5.22 20.27 20.30 21.27 21.31 21.74 21.79 22.32 22.37 22.40 22.47 22.49 22.56 22.58 22.65
- 59.96 -79.87 -79.82 5.09 5.21 20.27 20.30 21.27 21.31 21.58 21.63 21.74 21.79 22.32 22.47 22.49 22.66
- 59.95 -79.89 -79.82 5.11 5.18 20.27 20.29 21.58 21.63 21.73 21.79 22.32 22.47 22.49 22.66
+ 59.98 -144.40 -144.35 5.08 5.22 21.27 21.31 22.32 22.38 22.40 22.47 22.49 22.56 22.59 22.64
+ 59.97 -79.85 -79.83 5.08 5.22 21.27 21.31 21.74 21.79 22.32 22.37 22.40 22.47 22.49 22.56 22.58 22.65
+ 59.96 -79.87 -79.82 5.09 5.21 21.27 21.31 21.58 21.63 21.74 21.79 22.32 22.47 22.49 22.66
+ 59.95 -79.89 -79.82 5.11 5.18 21.58 21.63 21.73 21.79 22.32 22.47 22.49 22.66
59.94 -79.90 -79.82 21.58 21.63 21.73 21.79 22.32 22.66
59.93 -79.95 -79.84 21.59 21.63 21.73 21.81 22.32 22.48 22.54 22.66 23.09 23.11
59.92 -79.96 -79.85 21.44 21.47 21.76 21.81 22.32 22.48 22.61 22.65 23.08 23.13
59.91 -79.96 -79.86 21.44 21.47 21.76 21.81 22.34 22.48 22.53 22.56 23.08 23.13
59.90 -79.96 -79.85 21.44 21.47 21.76 21.80 22.34 22.39 22.46 22.56 23.08 23.13 23.28 23.33
- 59.89 -79.95 -79.85 21.45 21.47 22.34 22.37 22.46 22.56 23.09 23.13 23.27 23.44
+ 59.89 -79.95 -79.85 21.44 21.47 22.34 22.37 22.46 22.56 23.09 23.13 23.27 23.44
59.88 -79.89 -79.85 -77.43 -77.40 5.56 5.60 22.17 22.21 22.46 22.55 23.10 23.13 23.27 23.44
59.87 -79.89 -79.86 -77.43 -77.39 5.54 5.61 19.10 19.15 21.93 21.97 22.06 22.10 22.16 22.21 22.46 22.53 23.27 23.44 27.17 27.21
59.86 -79.89 -79.87 -77.43 -77.37 5.54 5.62 19.10 19.15 21.93 21.97 22.05 22.10 22.16 22.21 22.36 22.41 22.46 22.49 23.35 23.44 27.16 27.22
@@ -924,13 +899,13 @@ Unnamed Islands
59.01 18.51 18.53
58.98 18.02 18.04
58.97 18.00 18.04
- 58.96 -152.05 -152.01 -78.60 -78.56 17.99 18.04
- 58.95 -152.07 -152.00 -78.61 -78.55 17.99 18.04 18.19 18.22
- 58.94 -152.07 -152.00 -78.61 -78.55 17.98 18.04 18.15 18.22
- 58.93 -152.08 -152.00 -78.61 -78.55 17.98 18.03 18.15 18.22
- 58.92 -152.08 -152.00 -78.60 -78.57 10.97 11.03 17.98 18.03 18.13 18.22
- 58.91 -152.08 -152.02 10.97 11.05 18.00 18.02 18.13 18.21
- 58.90 -152.08 -152.04 10.97 11.06 17.83 17.87 18.12 18.19
+ 58.96 -78.60 -78.56 17.99 18.04
+ 58.95 -78.61 -78.55 17.99 18.04 18.19 18.22
+ 58.94 -78.61 -78.55 17.98 18.04 18.15 18.22
+ 58.93 -78.61 -78.55 17.98 18.03 18.15 18.22
+ 58.92 -78.60 -78.57 10.97 11.03 17.98 18.03 18.13 18.22
+ 58.91 10.97 11.05 18.00 18.02 18.13 18.21
+ 58.90 10.97 11.06 17.83 17.87 18.12 18.19
58.89 10.97 11.07 17.81 17.87 18.10 18.17
58.88 10.97 11.07 17.80 17.87 18.09 18.15
58.87 10.97 11.07 17.68 17.70 17.80 17.86 18.08 18.15
@@ -1075,9 +1050,9 @@ Unnamed Islands
56.97 -76.70 -76.64
56.96 -76.70 -76.65
56.95 -76.70 -76.65
- 56.94 -158.72 -158.67 -76.70 -76.66
- 56.93 -158.73 -158.67
- 56.92 -158.73 -158.67
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+ 56.92 -158.73 -158.68
56.91 -158.73 -158.70
56.89 -76.67 -76.65
56.88 -76.67 -76.63
@@ -1219,21 +1194,15 @@ Unnamed Islands
54.90 -162.90 -162.86
54.89 -162.90 -162.86
54.88 -162.89 -162.86
- 54.84 -133.55 -133.51
- 54.83 -133.55 -133.51
- 54.82 -133.55 -133.51
- 54.81 -133.55 -133.51
- 54.80 -133.55 -133.50
- 54.79 -133.55 -133.50
- 54.78 -133.55 -133.50
- 54.77 -133.55 -133.50
- 54.76 -133.55 -133.50
- 54.75 -133.53 -133.51
54.65 -162.38 -162.34
54.64 -162.39 -162.34
54.63 -162.39 -162.34
54.62 -162.39 -162.34
54.61 -162.39 -162.35
+ 54.50 -57.17 -57.10
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+ 54.47 -57.19 -57.11
54.44 -162.85 -162.82
54.43 -162.86 -162.81
54.42 -162.86 -162.79 -79.56 -79.51
@@ -1323,9 +1292,9 @@ Unnamed Islands
53.23 -132.07 -132.03 -9.77 -9.71
53.22 -132.11 -132.02 -9.77 -9.71
53.21 -132.13 -132.02 -9.77 -9.71
- 53.20 -132.14 -132.02
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- 53.18 -132.14 -132.04
+ 53.20 -132.13 -132.02
+ 53.19 -132.13 -132.02
+ 53.18 -132.13 -132.04
53.17 -132.13 -132.09
53.05 -79.02 -78.99
53.04 -79.03 -78.99
@@ -1351,11 +1320,11 @@ Unnamed Islands
52.73 -131.67 -131.60 -4.81 -4.79
52.59 -171.16 -171.12 -131.38 -131.35
52.58 -171.17 -171.10 -131.41 -131.35
- 52.57 -171.18 -171.10 -131.44 -131.34
- 52.56 -171.18 -171.10 -131.45 -131.33 -79.18 -79.14
- 52.55 -171.18 -171.10 -131.45 -131.33 -79.18 -79.14
- 52.54 -171.16 -171.12 -131.45 -131.33 -79.18 -79.14
- 52.53 -131.43 -131.34 -79.18 -79.14
+ 52.57 -171.18 -171.10 -131.44 -131.34 -129.41 -129.39
+ 52.56 -171.18 -171.10 -131.45 -131.33 -129.42 -129.38 -79.18 -79.14
+ 52.55 -171.18 -171.10 -131.45 -131.33 -129.42 -129.38 -79.18 -79.14
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52.52 -131.40 -131.36 -79.18 -79.14
52.51 -79.18 -79.15
52.19 -175.53 -175.49
@@ -1428,7 +1397,7 @@ Unnamed Islands
50.85 -127.65 -127.60 -126.93 -126.73
50.84 -127.65 -127.60 -126.93 -126.73
50.83 -127.64 -127.60 -126.93 -126.76
- 50.82 -127.64 -127.60 -126.91 -126.85
+ 50.82 -127.64 -127.60
50.81 -127.62 -127.60
50.77 -126.70 -126.64
50.76 -126.72 -126.62
@@ -1546,7 +1515,7 @@ Unnamed Islands
48.42 -123.26 -123.21
48.41 -123.26 -123.21
48.40 -123.25 -123.22
- 47.81 -61.47 -61.43
+ 47.81 -61.47 -61.41
47.80 -61.49 -61.41
47.79 -61.51 -61.41
47.78 -61.51 -61.41
@@ -1617,7 +1586,7 @@ Unnamed Islands
44.93 13.72 13.77 14.75 14.81
44.92 13.72 13.78 14.75 14.82
44.91 13.72 13.78 14.75 14.83
- 44.90 13.73 13.78 14.75 14.84
+ 44.90 13.72 13.78 14.75 14.84
44.89 13.73 13.78 14.76 14.84
44.88 13.73 13.76 14.78 14.84
44.87 13.73 13.76 14.81 14.84
@@ -1647,40 +1616,63 @@ Unnamed Islands
44.41 14.65 14.71 14.91 14.97 47.50 47.54 141.28 141.34 141.38 141.42
44.40 14.65 14.71 14.92 14.97 141.28 141.33
44.39 14.65 14.71 14.93 14.97
- 44.38 14.65 14.71
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- 44.33 15.02 15.07
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+ 44.38 -68.43 -68.41 14.65 14.71
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44.07 15.06 15.11
44.06 15.06 15.11
44.05 15.06 15.13
44.04 15.06 15.14
44.03 15.07 15.15
44.02 15.09 15.15
- 44.01 15.10 15.16
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+ 44.01 -69.39 -69.36 15.10 15.16
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43.72 15.66 15.70
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43.70 15.66 15.73 15.81 15.86
@@ -1694,6 +1686,10 @@ Unnamed Islands
43.62 146.25 146.36
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43.47 145.86 145.88
43.46 16.11 16.16 145.85 145.95
43.45 9.88 9.92 16.11 16.17 145.85 145.95 146.07 146.10
@@ -1713,11 +1709,11 @@ Unnamed Islands
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42.95 15.98 16.03 131.70 131.76
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42.93 131.70 131.75
@@ -1747,7 +1743,7 @@ Unnamed Islands
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42.63 131.41 131.47
42.62 131.42 131.47
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42.47 130.89 130.94
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42.45 130.89 130.94
@@ -1897,12 +1893,12 @@ Unnamed Islands
39.49 124.60 124.64 125.09 125.12
39.48 124.60 124.64
39.47 124.61 124.64 124.75 124.79
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39.40 -9.52 -9.50 24.14 24.19 124.70 124.74
39.39 24.14 24.19 124.70 124.72
39.38 24.13 24.19
@@ -1912,9 +1908,11 @@ Unnamed Islands
39.34 24.30 24.34
39.33 24.30 24.34
39.32 24.30 24.33
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39.21 122.48 122.55 127.50 127.54 127.60 127.65 139.53 139.56
39.20 122.48 122.50 127.51 127.54 139.52 139.57
39.19 139.52 139.57
@@ -1931,17 +1929,23 @@ Unnamed Islands
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38.88 -9.03 -8.99 121.80 121.84 141.59 141.64
38.87 -9.03 -8.99 121.80 121.84 141.59 141.64
38.86 -9.03 -8.99 24.34 24.36 121.80 121.84 141.59 141.64
@@ -1961,8 +1965,8 @@ Unnamed Islands
38.56 25.49 25.52
38.55 25.49 25.53 26.17 26.21 26.69 26.72
38.54 25.48 25.53 26.17 26.24 26.69 26.73
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38.51 25.49 25.52 26.18 26.29 26.68 26.74
38.50 26.19 26.30 26.68 26.74 139.24 139.26
38.49 -8.85 -8.82 26.22 26.30 26.68 26.75 139.23 139.26
@@ -1979,16 +1983,23 @@ Unnamed Islands
38.33 141.10 141.14
38.32 141.10 141.14 141.40 141.42 141.55 141.57
38.31 141.11 141.13 141.39 141.43 141.54 141.59
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38.02 24.23 24.27
@@ -1997,21 +2008,24 @@ Unnamed Islands
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37.76 23.74 23.77 24.12 24.15 124.71 124.78 125.20 125.24 125.87 125.93
@@ -2041,11 +2055,11 @@ Unnamed Islands
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37.51 8.89 8.96 26.49 26.51 122.15 122.20 126.31 126.38 126.42 126.48
37.50 8.89 8.96 23.88 23.91 122.15 122.21 126.42 126.48
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37.44 26.93 27.01
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37.42 26.70 26.72
@@ -2054,19 +2068,20 @@ Unnamed Islands
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37.22 126.61 126.65
37.21 126.61 126.65
37.20 126.62 126.65
@@ -2078,11 +2093,11 @@ Unnamed Islands
37.14 10.78 10.82 126.27 126.29
37.13 10.78 10.82
37.12 10.78 10.83 126.37 126.39
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37.06 21.52 21.56 27.06 27.11 125.93 125.96 126.40 126.45
37.05 21.52 21.56 27.06 27.11 125.93 125.99 126.40 126.45
37.04 21.52 21.56 27.06 27.11 125.96 126.00 126.40 126.45
@@ -2153,6 +2168,12 @@ Unnamed Islands
36.01 14.31 14.36
36.00 14.31 14.36
35.99 14.31 14.36
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35.86 126.35 126.38
35.85 126.35 126.39
35.84 126.35 126.39 126.43 126.45
@@ -2186,14 +2207,21 @@ Unnamed Islands
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35.26 126.12 126.16
35.25 126.13 126.15
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35.03 126.11 126.16 139.15 139.18
35.02 126.10 126.17 128.62 128.66 139.15 139.18
35.01 126.08 126.17 126.23 126.26 128.62 128.66
@@ -2224,36 +2252,36 @@ Unnamed Islands
34.76 119.43 119.50 126.29 126.33 127.43 127.46 128.27 128.31 128.45 128.56 131.11 131.17
34.75 119.43 119.50 126.30 126.32 128.27 128.31 128.45 128.56 131.12 131.17
34.74 119.45 119.50 128.27 128.31 128.45 128.56 131.13 131.15
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34.72 125.19 125.22 126.09 126.11 127.70 127.74 128.16 128.18 128.47 128.52
34.71 125.19 125.22 126.08 126.11 127.70 127.75 128.15 128.20
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34.59 125.80 125.86 127.08 127.11 127.39 127.41 127.51 127.57 127.63 127.67
34.58 125.80 125.85 127.08 127.11 127.39 127.41 127.53 127.56 127.63 127.70
34.57 127.38 127.41 127.62 127.70
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@@ -2291,14 +2319,14 @@ Unnamed Islands
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33.98 126.90 126.94 130.70 130.72 130.85 130.87 131.69 131.74 131.83 131.88 132.25 132.28 132.48 132.57 132.65 132.67 133.34 133.38
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33.96 126.29 126.35 126.90 126.94 130.85 130.87 131.71 131.73 131.80 131.88 132.32 132.36 132.48 132.56 132.64 132.68
@@ -2342,11 +2370,11 @@ Unnamed Islands
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@@ -2552,17 +2580,17 @@ Unnamed Islands
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@@ -2599,12 +2627,21 @@ Unnamed Islands
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@@ -2613,36 +2650,45 @@ Unnamed Islands
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@@ -2657,6 +2703,11 @@ Unnamed Islands
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@@ -2669,7 +2720,13 @@ Unnamed Islands
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@@ -2697,14 +2754,12 @@ Unnamed Islands
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@@ -2716,11 +2771,11 @@ Unnamed Islands
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@@ -2843,13 +2898,13 @@ Unnamed Islands
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25.13 -80.72 -80.67 -80.65 -80.62 -80.49 -80.47 52.86 52.89 55.10 55.17
@@ -2904,12 +2959,6 @@ Unnamed Islands
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@@ -2959,7 +3008,7 @@ Unnamed Islands
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@@ -2977,23 +3026,21 @@ Unnamed Islands
23.61 36.17 36.21 116.95 116.97
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@@ -3069,52 +3116,53 @@ Unnamed Islands
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8.24 93.21 93.26 117.06 117.12
8.23 93.21 93.26 117.06 117.13
8.22 93.21 93.26 117.06 117.13
@@ -4085,11 +4136,11 @@ Unnamed Islands
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@@ -4110,22 +4161,40 @@ Unnamed Islands
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6.69 99.84 99.86
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6.57 99.26 99.32
@@ -4137,10 +4206,10 @@ Unnamed Islands
6.51 99.27 99.33
6.50 99.27 99.32
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@@ -4160,8 +4229,8 @@ Unnamed Islands
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6.17 118.04 118.06 118.09 118.11 120.41 120.47 120.89 121.00 121.78 121.83
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6.15 118.03 118.06 118.09 118.11 120.40 120.47 120.52 120.56 120.87 120.93 121.78 121.86
@@ -4169,11 +4238,9 @@ Unnamed Islands
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6.12 117.99 118.03 120.43 120.45 120.52 120.57 120.87 120.92 121.79 121.86
6.11 117.99 118.03 120.52 120.56 120.88 120.92 121.80 121.86
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@@ -4186,28 +4253,30 @@ Unnamed Islands
5.96 117.65 117.71 120.07 120.11 121.54 121.60 169.42 169.44
5.95 117.65 117.71 119.97 120.00 120.08 120.12 121.54 121.60 169.42 169.45
5.94 117.65 117.70 119.96 120.00 120.08 120.12 121.54 121.60 169.42 169.45
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@@ -4315,10 +4384,6 @@ Unnamed Islands
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3.92 107.88 107.93
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@@ -4478,32 +4543,32 @@ Unnamed Islands
1.00 103.74 103.81 104.14 104.19 104.24 104.27
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0.96 103.77 103.81 104.04 104.08 104.13 104.19 104.22 104.27 107.41 107.48
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0.78 103.52 103.56 104.67 104.76 108.68 108.72
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0.75 103.52 103.55 103.64 103.68 104.29 104.36 104.61 104.66 104.68 104.76 108.69 108.74
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0.71 103.65 103.75 104.58 104.65
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0.69 103.68 103.75 104.26 104.33 104.58 104.63
@@ -4576,15 +4641,15 @@ Unnamed Islands
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0.00 129.58 129.60
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@@ -4656,26 +4721,33 @@ Unnamed Islands
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@@ -4898,7 +4970,7 @@ Unnamed Islands
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@@ -5035,12 +5107,12 @@ Unnamed Islands
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@@ -5049,12 +5121,12 @@ Unnamed Islands
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@@ -5071,18 +5143,10 @@ Unnamed Islands
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@@ -5100,14 +5164,13 @@ Unnamed Islands
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+ -51.51 -74.99 -74.88
+ -51.52 -74.99 -74.87
+ -51.53 -74.99 -74.87 -74.77 -74.71 -74.38 -74.34
+ -51.54 -74.99 -74.87 -74.77 -74.68 -74.39 -74.34
+ -51.55 -74.98 -74.88 -74.77 -74.67 -74.41 -74.33 -60.81 -60.77
+ -51.56 -74.93 -74.89 -74.77 -74.67 -74.42 -74.33 -60.82 -60.73
+ -51.57 -74.76 -74.67 -74.59 -74.57 -74.42 -74.33 -60.82 -60.72
+ -51.58 -74.70 -74.67 -74.61 -74.55 -74.42 -74.33 -60.82 -60.72
+ -51.59 -74.61 -74.54 -74.42 -74.34 -60.81 -60.72 -60.70 -60.67
+ -51.60 -74.61 -74.54 -74.40 -74.36 -60.70 -60.66
+ -51.61 -74.60 -74.50 -60.70 -60.66
+ -51.62 -74.59 -74.50 -60.70 -60.66
+ -51.63 -74.58 -74.50 -60.69 -60.66
+ -51.64 -74.56 -74.50 -60.69 -60.64
-51.65 -60.70 -60.64
-51.66 -60.70 -60.64
-51.67 -60.70 -60.64
@@ -5960,9 +6148,15 @@ Unnamed Islands
-51.82 -59.62 -59.59
-52.41 -59.14 -59.03
-52.42 -59.15 -59.03
- -52.43 -59.15 -59.03
- -52.44 -59.15 -59.03
- -52.45 -59.15 -59.08
+ -52.43 -74.57 -74.53 -59.15 -59.03
+ -52.44 -74.59 -74.51 -59.15 -59.03
+ -52.45 -74.59 -74.49 -59.15 -59.08
+ -52.46 -74.59 -74.47
+ -52.47 -74.59 -74.46
+ -52.48 -74.58 -74.46
+ -52.49 -74.55 -74.46
+ -52.50 -74.53 -74.47
+ -52.51 -74.51 -74.49
-52.89 -59.21 -59.18
-52.90 -59.21 -59.18
-52.91 -59.22 -59.18
diff --git a/c++/src/objects/seqfeat/lat_lon_water.txt b/c++/src/objects/seqfeat/lat_lon_water.txt
index 3bab10e..a191d26 100644
--- a/c++/src/objects/seqfeat/lat_lon_water.txt
+++ b/c++/src/objects/seqfeat/lat_lon_water.txt
@@ -6744,9 +6744,9 @@ Aral Sea
46.53 59.98 60.85
46.52 59.98 60.86
46.51 59.97 60.88
- 46.50 59.97 60.91
+ 46.50 59.97 60.92
46.49 59.97 61.03
- 46.48 59.97 61.10 61.20 61.24
+ 46.48 59.97 61.10
46.47 59.97 61.12 61.17 61.27
46.46 59.98 61.28
46.45 59.98 61.28
@@ -6807,10 +6807,10 @@ Aral Sea
45.90 58.78 59.29 59.63 59.91 59.94 60.49
45.89 58.73 59.28 59.63 59.89 59.99 60.49
45.88 58.72 59.28 59.63 59.86 60.01 60.48
- 45.87 58.71 59.27 59.62 59.87 60.05 60.09 60.18 60.48
- 45.86 58.71 59.26 59.62 59.88 60.25 60.47
- 45.85 58.70 59.26 59.61 59.88 60.26 60.47
- 45.84 58.69 59.25 59.61 59.88 60.27 60.32 60.35 60.46
+ 45.87 58.71 59.27 59.62 59.87 60.18 60.48
+ 45.86 58.71 59.26 59.62 59.87 60.25 60.47
+ 45.85 58.70 59.26 59.61 59.87 60.26 60.47
+ 45.84 58.69 59.25 59.61 59.87 60.27 60.32 60.35 60.46
45.83 58.68 59.25 59.61 59.84 60.37 60.45
45.82 58.68 59.24 59.61 59.83 60.40 60.42
45.81 58.68 59.24 59.61 59.83
@@ -6935,7 +6935,7 @@ Aral Sea
44.62 58.28 58.67 59.23 59.99
44.61 58.26 58.66 59.24 59.99
44.60 58.25 58.65 59.25 59.99
- 44.59 58.25 58.64 59.26 59.99
+ 44.59 58.24 58.64 59.26 59.99
44.58 58.24 58.63 59.28 60.00
44.57 58.23 58.62 59.29 60.01
44.56 58.23 58.61 59.30 60.02
@@ -6984,7 +6984,6 @@ Aral Sea
44.13 59.53 59.66
Arctic Ocean
90.00 -180.00 180.00
- 90.00 -180.00 180.00
89.99 -180.00 180.00
89.98 -180.00 180.00
89.97 -180.00 180.00
@@ -58327,7 +58326,7 @@ Great Bear Lake
66.61 -122.52 -122.48 -122.42 -122.32 -122.21 -120.05 -118.04 -117.58
66.60 -122.54 -122.48 -122.45 -122.31 -122.26 -120.07 -118.06 -117.60
66.59 -122.55 -122.48 -122.46 -122.31 -122.28 -120.12 -118.08 -117.64
- 66.58 -122.57 -120.13 -118.09 -117.67
+ 66.58 -122.56 -120.13 -118.09 -117.67
66.57 -122.57 -120.14 -118.11 -117.69
66.56 -122.91 -122.85 -122.81 -122.67 -122.57 -120.15 -118.12 -117.70
66.55 -122.93 -120.16 -118.15 -117.70
@@ -58340,9 +58339,9 @@ Great Bear Lake
66.48 -123.26 -123.12 -123.07 -120.23 -118.24 -117.83 -117.60 -117.51
66.47 -123.34 -120.23 -118.25 -117.85 -117.66 -117.51 -117.49 -117.45
66.46 -123.37 -120.24 -118.26 -117.84 -117.68 -117.45
- 66.45 -123.51 -120.25 -118.27 -117.82 -117.70 -117.45
- 66.44 -123.52 -120.45 -120.38 -120.31 -118.28 -117.82 -117.72 -117.45
- 66.43 -123.54 -120.46 -118.28 -117.82 -117.80 -117.45
+ 66.45 -123.44 -120.25 -118.27 -117.82 -117.70 -117.45
+ 66.44 -123.51 -120.45 -120.38 -120.31 -118.28 -117.82 -117.72 -117.45
+ 66.43 -123.53 -120.46 -118.28 -117.82 -117.80 -117.45
66.42 -123.66 -120.46 -118.29 -117.46
66.41 -123.70 -120.46 -120.18 -120.11 -118.31 -117.57 -117.54 -117.47
66.40 -123.76 -120.46 -120.40 -120.33 -120.20 -120.06 -118.34 -117.58
@@ -58362,7 +58361,7 @@ Great Bear Lake
66.26 -125.09 -117.60
66.25 -125.09 -117.63
66.24 -125.09 -117.63
- 66.23 -125.09 -123.01 -122.47 -117.64
+ 66.23 -125.09 -123.01 -122.09 -117.64
66.22 -125.10 -122.97 -121.88 -117.65
66.21 -125.11 -122.95 -121.84 -117.66
66.20 -125.12 -122.94 -121.80 -117.68
@@ -58370,11 +58369,11 @@ Great Bear Lake
66.18 -125.13 -122.92 -121.72 -117.67
66.17 -125.13 -122.92 -121.68 -117.67
66.16 -125.13 -122.92 -121.65 -117.69
- 66.15 -125.13 -124.28 -124.16 -123.31 -123.26 -122.93 -121.63 -117.80 -117.78 -117.71
- 66.14 -125.13 -124.48 -124.14 -123.41 -123.25 -122.95 -121.62 -117.80 -117.77 -117.73
- 66.13 -125.13 -124.59 -124.13 -123.51 -123.24 -122.97 -121.61 -117.93 -117.84 -117.80
- 66.12 -125.12 -124.57 -124.11 -123.61 -123.23 -122.99 -121.60 -117.96
- 66.11 -125.11 -124.55 -124.10 -123.71 -123.22 -123.01 -121.60 -117.97
+ 66.15 -125.13 -124.28 -124.16 -123.31 -123.26 -122.93 -121.63 -117.71
+ 66.14 -125.13 -124.48 -124.14 -123.39 -123.25 -122.95 -121.62 -117.80 -117.77 -117.73
+ 66.13 -125.13 -124.59 -124.13 -123.47 -123.24 -122.97 -121.61 -117.93 -117.84 -117.80
+ 66.12 -125.12 -124.57 -124.11 -123.58 -123.23 -122.99 -121.60 -117.96
+ 66.11 -125.11 -124.55 -124.10 -123.70 -123.22 -123.01 -121.60 -117.97
66.10 -125.10 -124.54 -124.08 -123.79 -123.21 -123.03 -121.59 -117.97
66.09 -125.09 -124.54 -123.95 -123.83 -123.20 -123.04 -121.59 -121.46 -121.44 -121.39 -121.31 -117.97
66.08 -125.08 -124.54 -123.19 -123.08 -121.57 -121.52 -121.27 -117.97 -117.93 -117.88
@@ -58462,8 +58461,8 @@ Great Bear Lake
65.26 -122.92 -121.58 -120.61 -119.98
65.25 -122.94 -121.60 -120.63 -119.99
65.24 -123.07 -123.00 -122.96 -121.57 -120.65 -120.00
- 65.23 -123.09 -121.57 -120.66 -120.00
- 65.22 -123.26 -121.57 -120.70 -120.01
+ 65.23 -123.18 -121.57 -120.66 -120.00
+ 65.22 -123.35 -121.57 -120.70 -120.01
65.21 -123.45 -121.57 -120.70 -120.01
65.20 -123.47 -121.58 -120.71 -120.02
65.19 -123.49 -121.58 -120.78 -120.02
@@ -58533,7 +58532,7 @@ Great Salt Lake
41.47 -113.02 -112.67 -112.38 -112.34
41.46 -113.01 -112.66 -112.40 -112.28
41.45 -113.01 -112.64 -112.41 -112.26
- 41.44 -113.00 -112.61 -112.59 -112.53 -112.41 -112.26
+ 41.44 -113.00 -112.61 -112.59 -112.52 -112.41 -112.26
41.43 -112.99 -112.51 -112.41 -112.25
41.42 -112.99 -112.50 -112.41 -112.25 -112.15 -112.09
41.41 -112.98 -112.50 -112.41 -112.25 -112.16 -112.05
@@ -58547,10 +58546,10 @@ Great Salt Lake
41.33 -113.00 -112.46 -112.40 -112.07
41.32 -113.01 -112.46 -112.39 -112.25 -112.19 -112.14 -112.11 -112.08
41.31 -113.01 -112.46 -112.39 -112.26 -112.17 -112.14
- 41.30 -113.02 -112.93 -112.91 -112.46 -112.38 -112.28
+ 41.30 -113.02 -112.93 -112.91 -112.46 -112.39 -112.28
41.29 -113.02 -112.95 -112.90 -112.46 -112.38 -112.29
41.28 -113.02 -112.95 -112.89 -112.47 -112.38 -112.29
- 41.27 -113.02 -112.95 -112.87 -112.47 -112.37 -112.24
+ 41.27 -113.02 -112.95 -112.87 -112.47 -112.38 -112.24
41.26 -113.02 -112.95 -112.85 -112.46 -112.37 -112.24
41.25 -112.99 -112.96 -112.84 -112.46 -112.35 -112.24
41.24 -112.84 -112.45 -112.36 -112.23
@@ -58644,8 +58643,8 @@ Great Slave Lake
62.52 -115.78 -115.12 -111.46 -109.88
62.51 -115.77 -115.10 -111.48 -109.91
62.50 -115.75 -115.08 -111.50 -109.95
- 62.49 -115.73 -115.03 -111.52 -109.98
- 62.48 -115.72 -114.97 -111.54 -110.01
+ 62.49 -115.73 -114.98 -111.52 -109.98
+ 62.48 -115.72 -114.96 -111.54 -110.01
62.47 -115.72 -115.37 -115.31 -114.85 -111.56 -110.05
62.46 -115.71 -115.63 -115.54 -115.45 -115.28 -114.85 -111.58 -110.08
62.45 -115.30 -114.85 -111.59 -110.11
@@ -58723,7 +58722,7 @@ Great Slave Lake
61.73 -115.58 -112.05
61.72 -115.58 -112.06
61.71 -115.58 -112.07
- 61.70 -115.57 -112.10
+ 61.70 -115.58 -112.10
61.69 -115.59 -112.13
61.68 -115.62 -112.14
61.67 -115.64 -112.14
@@ -58755,26 +58754,26 @@ Great Slave Lake
61.41 -115.96 -113.37 -113.01 -112.85
61.40 -116.04 -113.38 -113.02 -112.86
61.39 -116.06 -113.39 -113.02 -112.87
- 61.38 -116.07 -113.40 -113.02 -112.90
- 61.37 -116.07 -113.48 -112.99 -112.93
+ 61.38 -116.07 -113.40 -113.02 -112.92
+ 61.37 -116.07 -113.48 -112.99 -112.94
61.36 -116.07 -113.50
61.35 -116.02 -113.51
61.34 -116.76 -116.63 -116.01 -113.51
61.33 -116.78 -116.52 -115.96 -113.51
- 61.32 -116.80 -116.50 -115.92 -113.59
- 61.31 -117.69 -117.58 -116.80 -116.46 -115.91 -113.62
+ 61.32 -116.80 -116.50 -115.92 -113.58
+ 61.31 -117.69 -117.58 -116.80 -116.46 -115.91 -113.61
61.30 -117.69 -117.54 -116.80 -116.45 -115.87 -113.64
61.29 -117.69 -117.51 -116.80 -116.44 -116.37 -116.25 -115.86 -113.66
- 61.28 -117.67 -117.47 -116.80 -116.18 -115.88 -113.67
+ 61.28 -117.67 -117.48 -116.80 -116.18 -115.88 -113.67
61.27 -117.64 -117.44 -116.79 -116.17 -115.96 -113.68
- 61.26 -117.61 -117.40 -116.78 -116.17 -115.98 -113.69
- 61.25 -117.58 -117.37 -116.77 -116.14 -116.01 -113.69
- 61.24 -117.50 -117.33 -116.76 -116.10 -116.03 -113.69
- 61.23 -117.49 -117.29 -116.78 -116.07 -116.03 -113.68
- 61.22 -117.49 -117.26 -116.80 -116.05 -116.03 -113.67
- 61.21 -117.48 -117.22 -116.85 -113.66
+ 61.26 -117.61 -117.41 -116.78 -116.17 -115.98 -113.69
+ 61.25 -117.58 -117.38 -116.77 -116.14 -116.01 -113.69
+ 61.24 -117.50 -117.34 -116.76 -116.10 -116.03 -113.69
+ 61.23 -117.49 -117.31 -116.78 -116.07 -116.03 -113.68
+ 61.22 -117.49 -117.27 -116.80 -116.05 -116.03 -113.67
+ 61.21 -117.48 -117.23 -116.85 -113.66
61.20 -117.47 -117.19 -116.91 -113.66
- 61.19 -117.47 -117.15 -116.96 -113.66
+ 61.19 -117.47 -117.16 -116.96 -113.66
61.18 -117.46 -117.12 -116.98 -113.66
61.17 -117.41 -117.08 -117.00 -113.64
61.16 -117.37 -117.05 -117.03 -113.63
@@ -58795,10 +58794,10 @@ Great Slave Lake
61.01 -116.72 -116.57 -116.52 -113.68
61.00 -116.70 -116.68 -116.65 -116.59 -116.50 -113.70
60.99 -116.51 -114.23 -114.20 -113.73
- 60.98 -116.51 -114.25 -114.19 -113.80
- 60.97 -116.51 -114.28 -114.07 -113.89
- 60.96 -116.46 -114.32 -114.06 -113.99
- 60.95 -116.45 -114.36
+ 60.98 -116.51 -114.25 -114.19 -113.79
+ 60.97 -116.51 -114.28 -114.07 -113.86
+ 60.96 -116.46 -114.32 -114.06 -113.93
+ 60.95 -116.45 -114.36 -114.05 -114.00
60.94 -116.43 -114.40
60.93 -116.42 -114.48
60.92 -116.39 -114.54
@@ -75614,16 +75613,16 @@ IJsselmeer
52.60 5.02 5.86
52.59 5.02 5.86
52.58 5.02 5.86
- 52.57 5.03 5.87
+ 52.57 5.03 5.86
52.56 5.04 5.87
- 52.55 5.05 5.88
+ 52.55 5.05 5.87
52.54 5.05 5.88
52.53 5.06 5.88
52.52 5.06 5.88
52.51 5.07 5.88
52.50 5.07 5.88
52.49 5.06 5.88
- 52.48 5.06 5.88
+ 52.48 5.05 5.88
52.47 5.04 5.87
52.46 5.04 5.87
52.45 5.04 5.86
@@ -83847,474 +83846,289 @@ Internal Canada Arctic Waters
69.73 -80.74 -80.68 -80.61 -80.44 -80.14 -79.88
69.72 -80.51 -80.45 -80.13 -80.08 -80.02 -79.94
Internal Denmark Waters
- 56.38 10.88 10.90
- 56.37 10.88 10.91
- 56.36 10.88 10.93
- 56.35 10.87 10.94
- 56.34 10.87 10.95
- 56.33 10.86 10.96
- 56.32 10.85 10.98
- 56.31 10.85 10.99
- 56.30 10.84 11.00
- 56.29 10.82 11.01
- 56.28 10.40 10.43 10.80 11.03
- 56.27 10.38 10.45 10.78 11.04
- 56.26 10.36 10.46 10.76 11.05
- 56.25 10.34 10.48 10.73 11.06
- 56.24 10.33 10.50 10.70 11.07
- 56.23 10.31 10.51 10.66 11.09
- 56.22 10.30 10.53 10.63 11.10
- 56.21 10.30 11.11
- 56.20 10.29 11.12
- 56.19 10.29 11.14
- 56.18 10.28 11.15
- 56.17 10.28 11.16
- 56.16 10.27 11.17
- 56.15 10.27 11.19
- 56.14 10.27 11.20
- 56.13 10.26 11.21
- 56.12 10.26 11.22
- 56.11 10.25 11.24
- 56.10 10.25 11.25
- 56.09 10.24 11.26
- 56.08 10.24 11.27
- 56.07 10.24 11.29
- 56.06 10.23 11.30
- 56.05 10.23 11.31
- 56.04 10.22 11.32
- 56.03 10.22 11.33
- 56.02 10.21 11.35
- 56.01 10.21 11.36
- 56.00 10.21 11.37
- 55.99 10.20 11.38
- 55.98 10.20 11.40
- 55.97 10.20 11.41
- 55.96 10.20 11.42
- 55.95 10.19 11.43
- 55.94 10.19 11.45
- 55.93 10.19 11.46
- 55.92 10.18 11.47
- 55.91 10.18 11.47
- 55.90 10.18 11.47
- 55.89 10.18 11.47
- 55.88 9.99 10.12 10.17 11.47
- 55.87 9.95 10.14 10.16 11.47
- 55.86 9.91 11.47
- 55.85 9.89 11.46
- 55.84 9.89 11.45
- 55.83 9.89 11.44
- 55.82 9.91 11.42
- 55.81 9.93 11.41
- 55.80 9.95 11.40
- 55.79 9.96 11.39
- 55.78 9.97 11.38
- 55.77 9.99 11.37
- 55.76 10.00 11.35
- 55.75 9.99 11.34
- 55.74 9.97 11.33
- 55.73 9.94 11.31
- 55.72 9.90 11.03 11.13 11.29
- 55.71 9.88 10.99
- 55.70 9.86 10.99
- 55.69 9.85 10.99
- 55.68 9.83 11.00
- 55.67 9.81 11.00
- 55.66 9.80 11.01
- 55.65 9.79 11.02
- 55.64 9.78 11.06
- 55.63 9.78 11.09
- 55.62 9.77 11.11
- 55.61 9.75 11.13
- 55.60 9.73 11.13
- 55.59 9.71 11.13
- 55.58 9.69 11.13
- 55.57 9.67 11.13
- 55.56 9.65 11.12
- 55.55 9.64 11.13
- 55.54 9.63 11.13
- 55.53 9.61 11.14
- 55.52 9.60 11.15
- 55.51 9.59 11.16
- 55.50 9.58 11.16
- 55.49 9.58 11.17
- 55.48 9.58 11.18
- 55.47 9.58 11.19
- 55.46 9.59 11.19
- 55.45 9.59 11.19
- 55.44 9.59 11.19
- 55.43 9.60 11.19
- 55.42 9.60 11.19
- 55.41 9.61 11.19
- 55.40 9.61 11.19
- 55.39 9.61 11.19
- 55.38 9.62 11.19
- 55.37 9.62 11.18
- 55.36 9.62 11.18
- 55.35 9.62 11.18
- 55.34 9.63 11.18
- 55.33 9.63 11.18
- 55.32 9.63 11.19
- 55.31 9.64 11.20
- 55.30 9.64 11.21
- 55.29 9.64 11.22
- 55.28 9.65 11.23
- 55.27 9.65 11.23
- 55.26 9.66 11.24
- 55.25 9.65 11.25
- 55.24 9.65 11.26
- 55.23 9.64 11.27
- 55.22 9.64 11.28 11.37 11.51
- 55.21 9.63 11.30 11.33 11.57
- 55.20 9.61 11.63
- 55.19 9.60 11.66
- 55.18 9.58 11.66
- 55.17 9.57 11.67
- 55.16 9.55 11.67
- 55.15 9.53 11.68
- 55.14 9.52 11.68
- 55.13 9.50 11.69
- 55.12 9.49 11.69
- 55.11 9.48 11.70
- 55.10 9.48 11.70
- 55.09 9.47 11.70
- 55.08 9.47 11.70
- 55.07 9.46 11.70
- 55.06 9.45 11.71
- 55.05 9.45 11.71
- 55.04 9.44 11.71
- 55.03 9.44 11.71
- 55.02 9.44 9.52 9.58 11.72
- 55.01 9.62 11.72
- 55.00 9.65 11.73
- 54.99 9.67 11.73
- 54.98 9.68 11.74
- 54.97 9.69 11.74
- 54.96 9.71 11.74
- 54.95 9.71 11.74
- 54.94 9.70 11.75
- 54.93 9.69 11.16 11.25 11.75
- 54.92 9.69 11.06 11.27 11.75
- 54.91 9.69 11.06 11.29 11.76
- 54.90 9.69 11.05 11.31 11.77
- 54.89 9.70 11.05 11.33 11.77
- 54.88 9.70 11.05 11.35 11.78
- 54.87 9.70 11.05 11.37 11.79
- 54.86 9.71 11.05 11.39 11.80
- 54.85 9.71 11.05 11.42 11.80
- 54.84 9.71 11.05 11.44 11.81
- 54.83 9.72 11.05 11.46 11.82
- 54.82 9.72 11.05 11.49 11.83
- 54.81 9.72 11.04 11.51 11.60 11.66 11.84
- 54.80 9.73 11.04 11.69 11.84
- 54.79 9.73 11.04 11.71 11.85
- 54.78 9.77 11.05 11.72 11.86
- 54.77 9.85 11.08 11.73 11.86
- 54.76 9.89 11.11 11.73 11.86
- 54.75 9.90 11.14 11.74 11.84
- 54.74 9.92 11.17 11.74 11.81
- 54.73 9.93 11.19 11.75 11.78
- 54.72 9.94 11.22
- 54.71 9.95 11.25
- 54.70 9.96 11.28
- 54.69 9.97 11.31
- 54.68 9.99 11.34
- 54.67 10.00 11.36
- 54.66 10.01 11.36
- 54.65 10.01 11.36
- 54.64 10.01 11.35
- 54.63 10.01 11.34
- 54.62 10.01 11.33
- 54.61 10.01 11.32
- 54.60 10.01 11.31
- 54.59 10.01 11.30
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- 54.51 9.91 11.22
- 54.50 9.89 11.06 11.13 11.21
- 54.49 9.87 11.04 11.17 11.20
- 54.48 9.85 11.04
- 54.47 9.85 11.05
- 54.46 9.85 10.01 10.14 11.08
- 54.45 10.15 11.10
- 54.44 10.16 11.11
- 54.43 10.17 11.12
- 54.42 10.18 11.12
- 54.41 10.18 10.34 10.37 11.12
- 54.40 10.19 10.29 10.40 11.11
- 54.39 10.20 10.24 10.43 11.10
- 54.38 10.46 11.09
- 54.37 10.49 11.08
- 54.36 10.52 11.06
- 54.35 10.56 10.94 11.00 11.05
- 54.34 10.59 10.90 11.01 11.04
- 54.33 10.62 10.86 11.01 11.03
- 54.32 10.65 10.83
- 54.31 10.68 10.79
- 54.30 10.71 10.75
+ 54.85 12.04 12.06
+ 54.84 12.04 12.07
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+ 54.82 12.02 12.09
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+ 54.66 11.33 11.39 11.53 12.23
+ 54.65 11.32 11.42 11.49 12.24
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+ 54.43 11.10 11.12 11.26 12.44
+ 54.42 11.09 12.45
+ 54.41 11.08 12.46
+ 54.40 11.07 12.47
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+ 54.38 11.04 12.47
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+ 54.35 11.01 12.42
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+ 53.97 11.17 11.51
+ 53.96 11.22 11.49
+ 53.95 11.26 11.47
+ 53.94 11.31 11.45
+ 53.93 11.36 11.41
Internal Philippines Waters
- 10.37 125.66 125.68
- 10.36 125.66 125.69
- 10.35 125.66 125.70
- 10.34 125.65 125.72
- 10.33 125.65 125.73
- 10.32 125.65 125.74
- 10.31 125.65 125.75
- 10.30 125.64 125.76
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- 10.21 125.64 125.87
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- 9.62 125.66 126.13
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- 9.59 125.71 126.13
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- 9.57 125.74 126.13
- 9.56 125.76 126.13
- 9.55 125.77 126.14
- 9.54 125.79 126.14
- 9.53 125.81 126.14
- 9.52 125.82 126.14
- 9.51 125.84 126.14
- 9.50 125.86 126.14
- 9.49 125.87 126.14
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- 9.47 125.89 126.15
- 9.46 125.90 126.15
- 9.45 125.90 126.15
- 9.44 125.91 126.15
- 9.43 125.92 126.15
- 9.42 125.93 126.15
- 9.41 125.94 126.15
- 9.40 125.94 126.15
- 9.39 125.95 126.16
- 9.38 125.95 126.16
- 9.37 125.96 126.16
- 9.36 125.96 126.16
- 9.35 125.97 126.16
- 9.34 125.97 126.16
- 9.33 125.98 126.16
- 9.32 125.98 126.16
- 9.31 125.99 126.17
- 9.30 126.00 126.17
- 9.29 126.02 126.17
- 9.28 126.03 126.17
- 9.27 126.04 126.17
- 9.26 126.06 126.17
- 9.25 126.07 126.13
+ 10.61 125.49 125.67
+ 10.60 125.47 125.67
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+ 10.28 125.13 125.20 125.24 125.53
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+ 9.75 125.45 125.58
+ 9.74 125.46 125.57
+ 9.73 125.52 125.57
+ 9.72 125.53 125.56
+ 9.71 125.54 125.56
Internal Philippines Waters
- 10.79 123.55 123.58
- 10.78 123.55 123.62
- 10.77 123.54 123.65
- 10.76 123.54 123.69
- 10.75 123.54 123.73
- 10.74 123.53 123.76
- 10.73 123.53 123.80
- 10.72 123.53 123.82
- 10.71 123.52 123.82
- 10.70 123.52 123.82
- 10.69 123.52 123.81
- 10.68 123.51 123.81
- 10.67 123.51 123.80
- 10.66 123.51 123.80
- 10.65 123.50 123.79
- 10.64 123.50 123.78
- 10.63 123.50 123.78
- 10.62 123.49 123.77
- 10.61 123.49 123.77
- 10.60 123.48 123.76
- 10.59 123.48 123.75
- 10.58 123.47 123.75
- 10.57 123.47 123.74
- 10.56 123.46 123.74
- 10.55 123.45 123.73
- 10.54 123.45 123.73
- 10.53 123.44 123.73
- 10.52 123.43 123.73
- 10.51 123.42 123.73
- 10.50 123.42 123.72
- 10.49 123.41 123.72
- 10.48 123.40 123.72
- 10.47 123.40 123.72
- 10.46 123.39 123.72
- 10.45 123.39 123.71
- 10.44 123.38 123.71
- 10.43 123.38 123.70
- 10.42 123.37 123.69
- 10.41 123.37 123.68
- 10.40 123.36 123.68
- 10.39 123.36 123.67
- 10.38 123.35 123.66
- 10.37 123.35 123.66
- 10.36 123.34 123.65
- 10.35 123.34 123.64
- 10.34 123.33 123.64
- 10.33 123.33 123.63
- 10.32 123.33 123.62
- 10.31 123.33 123.61
- 10.30 123.32 123.61
- 10.29 123.32 123.60
- 10.28 123.32 123.60
- 10.27 123.32 123.59
- 10.26 123.31 123.59
- 10.25 123.31 123.58
- 10.24 123.31 123.58
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- 10.21 123.30 123.56
- 10.20 123.30 123.56
- 10.19 123.30 123.55
- 10.18 123.29 123.55
- 10.17 123.29 123.54
- 10.16 123.29 123.54
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- 10.14 123.28 123.53
- 10.13 123.28 123.52
- 10.12 123.28 123.51
- 10.11 123.27 123.51
- 10.10 123.27 123.50
- 10.09 123.26 123.49
- 10.08 123.26 123.48
- 10.07 123.25 123.48
- 10.06 123.25 123.47
- 10.05 123.24 123.46
- 10.04 123.24 123.46
- 10.03 123.23 123.45
- 10.02 123.22 123.44
- 10.01 123.22 123.43
- 10.00 123.21 123.43
- 9.99 123.20 123.42
- 9.98 123.20 123.41
- 9.97 123.19 123.40
- 9.96 123.18 123.40
- 9.95 123.18 123.39
- 9.94 123.17 123.40
- 9.93 123.17 123.40
- 9.92 123.16 123.40
- 9.91 123.16 123.40
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- 9.88 123.15 123.41
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- 9.81 123.15 123.39
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- 9.60 123.13 123.34
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- 9.55 123.16 123.33
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- 9.53 123.17 123.33
- 9.52 123.18 123.33
- 9.51 123.18 123.32
- 9.50 123.19 123.32
- 9.49 123.20 123.32
- 9.48 123.20 123.32
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- 9.46 123.21 123.33
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- 9.42 123.24 123.33
- 9.41 123.25 123.33
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- 9.39 123.26 123.32
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+ 13.93 122.47 122.56
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+ 13.57 122.56 122.96
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+ 13.21 122.68 123.30
+ 13.20 122.70 123.30
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+ 13.11 122.88 123.30
+ 13.10 122.90 123.30
+ 13.09 122.92 122.99 123.04 123.30
+ 13.08 122.94 122.96 123.05 123.31
+ 13.07 123.05 123.31
+ 13.06 123.06 123.32
+ 13.05 123.07 123.32
+ 13.04 123.08 123.32
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+ 13.02 123.09 123.30
+ 13.01 123.10 123.27
+ 13.00 123.11 123.24
+ 12.99 123.11 123.22
+ 12.98 123.12 123.19
+ 12.97 123.13 123.16
Internal U.S. (Alaska) Waters
59.42 -135.37 -135.33
59.41 -135.38 -135.33
@@ -93355,10 +93169,10 @@ Lake Baikal
54.59 108.70 109.53
54.58 108.69 109.53
54.57 108.68 109.53
- 54.56 108.66 109.53
- 54.55 108.64 109.53
- 54.54 108.62 109.53
- 54.53 108.61 109.53
+ 54.56 108.67 109.53
+ 54.55 108.65 109.53
+ 54.54 108.64 109.53
+ 54.53 108.62 109.53
54.52 108.60 109.53
54.51 108.58 109.52
54.50 108.57 109.52
@@ -93397,11 +93211,11 @@ Lake Baikal
54.17 108.31 109.57
54.16 108.30 109.57
54.15 108.29 109.57
- 54.14 108.29 109.57
- 54.13 108.29 109.56
- 54.12 108.29 109.56
- 54.11 108.29 109.55
- 54.10 108.29 109.53
+ 54.14 108.28 109.57
+ 54.13 108.28 109.56
+ 54.12 108.28 109.56
+ 54.11 108.28 109.55
+ 54.10 108.28 109.53
54.09 108.29 109.52
54.08 108.29 109.52
54.07 108.28 109.51
@@ -93444,9 +93258,9 @@ Lake Baikal
53.70 107.74 108.74 109.04 109.20
53.69 107.72 108.73 109.04 109.21
53.68 107.70 108.72 109.02 109.22
- 53.67 107.68 108.72 109.00 109.22
+ 53.67 107.68 108.71 109.00 109.22
53.66 107.66 108.71 108.98 109.22
- 53.65 107.64 108.71 108.97 109.21
+ 53.65 107.64 108.70 108.97 109.21
53.64 107.63 108.70 108.97 109.19
53.63 107.62 108.69 108.97 109.19
53.62 107.62 108.68 108.97 109.18
@@ -93492,9 +93306,9 @@ Lake Baikal
53.22 107.00 108.53
53.21 106.99 108.52
53.20 106.98 108.50
- 53.19 106.97 108.48
- 53.18 106.96 108.47
- 53.17 106.95 108.45
+ 53.19 106.98 108.48
+ 53.18 106.97 108.47
+ 53.17 106.96 108.45
53.16 106.92 108.44
53.15 106.89 108.42
53.14 106.87 108.40
@@ -93514,9 +93328,9 @@ Lake Baikal
53.00 106.73 106.79 106.89 108.32
52.99 106.88 108.31
52.98 106.86 108.30
- 52.97 106.84 108.29
- 52.96 106.82 108.28
- 52.95 106.80 108.26
+ 52.97 106.84 108.28
+ 52.96 106.82 108.27
+ 52.95 106.80 108.25
52.94 106.79 108.24
52.93 106.78 108.23
52.92 106.77 108.22
@@ -93681,9 +93495,9 @@ Lake Chad
13.15 14.29 14.70
13.14 14.26 14.71
13.13 14.26 14.72
- 13.12 14.26 14.73
- 13.11 14.27 14.73
- 13.10 14.28 14.73
+ 13.12 14.26 14.72
+ 13.11 14.27 14.72
+ 13.10 14.28 14.72
13.09 14.29 14.74
13.08 14.29 14.76
13.07 14.27 14.77
@@ -93922,8 +93736,8 @@ Lake Erie
42.38 -81.82 -79.48
42.37 -81.82 -79.50
42.36 -81.82 -79.52
- 42.35 -81.83 -79.53
- 42.34 -81.83 -79.54
+ 42.35 -81.83 -79.54
+ 42.34 -81.83 -79.55
42.33 -81.86 -79.57
42.32 -81.88 -79.60
42.31 -83.09 -83.06 -81.90 -79.62
@@ -94054,12 +93868,12 @@ Lake Huron
45.72 -81.66 -80.60
45.71 -81.67 -80.58
45.70 -81.67 -80.57
- 45.69 -81.68 -80.57
+ 45.69 -81.67 -80.57
45.68 -81.69 -80.56
45.67 -81.70 -80.56
45.66 -81.71 -80.55
45.65 -81.72 -80.53
- 45.64 -81.72 -80.51
+ 45.64 -81.72 -80.50
45.63 -81.73 -80.50 -80.44 -80.40
45.62 -81.73 -80.50 -80.44 -80.39
45.61 -81.73 -80.50 -80.44 -80.39
@@ -94101,8 +93915,8 @@ Lake Huron
45.25 -81.61 -80.08
45.24 -81.61 -80.10
45.23 -81.30 -80.09
- 45.22 -81.29 -80.04
- 45.21 -81.31 -80.04
+ 45.22 -81.30 -80.04
+ 45.21 -81.32 -80.04
45.20 -81.33 -80.01
45.19 -81.33 -80.00
45.18 -81.33 -80.00
@@ -94199,7 +94013,7 @@ Lake Huron
46.19 -84.25 -83.00 -82.96 -82.63 -82.57 -82.30
46.18 -84.24 -82.30
46.17 -84.23 -84.17 -84.15 -82.23
- 46.16 -84.22 -84.20 -84.12 -82.21
+ 46.16 -84.22 -84.19 -84.12 -82.21
46.15 -84.11 -82.18
46.14 -84.06 -82.17 -82.12 -82.06
46.13 -84.05 -82.02 -81.64 -81.61
@@ -94209,9 +94023,9 @@ Lake Huron
46.09 -84.06 -81.70 -81.67 -81.53
46.08 -84.05 -81.53
46.07 -84.04 -81.53
- 46.06 -84.66 -84.61 -84.03 -81.53
- 46.05 -84.68 -84.54 -84.02 -81.49
- 46.04 -84.68 -84.54 -84.01 -81.49
+ 46.06 -84.66 -84.61 -84.04 -81.53
+ 46.05 -84.68 -84.54 -84.03 -81.49
+ 46.04 -84.68 -84.54 -84.02 -81.49
46.03 -84.68 -84.53 -84.00 -81.49
46.02 -84.69 -84.53 -84.46 -84.41 -83.95 -81.47 -81.19 -81.14
46.01 -84.69 -84.48 -84.46 -84.37 -84.35 -84.29 -83.93 -81.47 -81.23 -81.14
@@ -94251,7 +94065,7 @@ Lake Huron
45.67 -84.50 -80.56
45.66 -84.47 -80.55
45.65 -84.29 -80.53
- 45.64 -84.25 -80.51
+ 45.64 -84.25 -80.50
45.63 -84.23 -80.50 -80.44 -80.40
45.62 -84.22 -80.50 -80.44 -80.39
45.61 -84.20 -80.50 -80.44 -80.39
@@ -94293,8 +94107,8 @@ Lake Huron
45.25 -83.42 -81.65 -81.63 -80.08
45.24 -83.42 -81.68 -81.63 -80.10
45.23 -83.42 -81.68 -81.30 -80.09
- 45.22 -83.41 -81.64 -81.29 -80.04
- 45.21 -83.41 -81.64 -81.31 -80.04
+ 45.22 -83.41 -81.64 -81.30 -80.04
+ 45.21 -83.41 -81.64 -81.32 -80.04
45.20 -83.40 -81.62 -81.58 -81.56 -81.33 -80.01
45.19 -83.39 -81.56 -81.33 -80.00
45.18 -83.39 -81.56 -81.33 -80.00
@@ -94306,7 +94120,7 @@ Lake Huron
45.12 -83.31 -81.51 -81.31 -79.99
45.11 -83.31 -81.50 -81.29 -80.01
45.10 -83.33 -81.50 -81.28 -80.05
- 45.09 -83.33 -81.48 -81.27 -80.05
+ 45.09 -83.33 -81.49 -81.27 -80.05
45.08 -83.42 -83.36 -83.33 -81.47 -81.27 -80.00
45.07 -83.44 -81.47 -81.27 -79.99
45.06 -83.44 -81.45 -81.27 -79.98
@@ -94327,7 +94141,7 @@ Lake Huron
44.91 -83.41 -81.35 -81.15 -79.80
44.90 -83.39 -81.35 -81.15 -81.11 -81.09 -81.05 -81.01 -79.78
44.89 -83.37 -81.34 -81.09 -81.07 -81.01 -79.78 -79.70 -79.68
- 44.88 -83.36 -81.31 -81.01 -79.78 -79.72 -79.67
+ 44.88 -83.36 -81.32 -81.01 -79.78 -79.72 -79.67
44.87 -83.34 -81.31 -81.01 -79.76 -79.74 -79.66
44.86 -83.34 -81.31 -81.02 -79.76 -79.74 -79.66
44.85 -83.33 -81.31 -81.03 -79.76 -79.74 -79.66
@@ -94384,7 +94198,7 @@ Lake Huron
44.34 -83.35 -81.53
44.33 -83.40 -81.55
44.32 -83.41 -81.57
- 44.31 -83.42 -81.58
+ 44.31 -83.42 -81.57
44.30 -83.43 -81.57
44.29 -83.50 -81.57
44.28 -83.52 -81.57
@@ -94658,13 +94472,13 @@ Lake Malawi
-9.50 33.96 34.08
-9.51 33.95 34.11
-9.52 33.94 34.12
- -9.53 33.93 34.12
+ -9.53 33.94 34.12
-9.54 33.93 34.13
-9.55 33.93 34.13
-9.56 33.93 34.15
- -9.57 33.94 34.16
+ -9.57 33.93 34.16
-9.58 33.94 34.18
- -9.59 33.95 34.20
+ -9.59 33.94 34.20
-9.60 33.95 34.21
-9.61 33.95 34.22
-9.62 33.94 34.23
@@ -94761,7 +94575,7 @@ Lake Malawi
-10.53 34.19 34.59
-10.54 34.18 34.59
-10.55 34.18 34.60
- -10.56 34.17 34.60
+ -10.56 34.17 34.61
-10.57 34.17 34.63
-10.58 34.17 34.63
-10.59 34.17 34.63
@@ -94770,8 +94584,8 @@ Lake Malawi
-10.62 34.19 34.65
-10.63 34.19 34.66
-10.64 34.19 34.66
- -10.65 34.19 34.66
- -10.66 34.19 34.66
+ -10.65 34.19 34.67
+ -10.66 34.19 34.67
-10.67 34.19 34.67
-10.68 34.19 34.67
-10.69 34.19 34.67
@@ -94837,7 +94651,7 @@ Lake Malawi
-11.29 34.22 34.76
-11.30 34.24 34.75
-11.31 34.24 34.75
- -11.32 34.25 34.82
+ -11.32 34.25 34.83
-11.33 34.25 34.86
-11.34 34.25 34.87
-11.35 34.26 34.88
@@ -95072,9 +94886,9 @@ Lake Malawi
-13.64 34.56 34.86
-13.65 34.57 34.86
-13.66 34.58 34.86
- -13.67 34.58 34.86
+ -13.67 34.59 34.86
-13.68 34.59 34.86
- -13.69 34.61 34.88
+ -13.69 34.61 34.87
-13.70 34.61 34.89
-13.71 34.61 35.04
-13.72 34.60 35.06
@@ -95091,13 +94905,13 @@ Lake Malawi
-13.83 34.58 35.12
-13.84 34.58 35.12
-13.85 34.58 35.12
- -13.86 34.57 35.12
+ -13.86 34.58 35.12
-13.87 34.57 35.13
-13.88 34.57 35.13
-13.89 34.56 35.13
-13.90 34.55 35.13
- -13.91 34.55 35.13
- -13.92 34.54 35.13
+ -13.91 34.54 35.13
+ -13.92 34.53 35.13
-13.93 34.53 35.13
-13.94 34.52 35.13
-13.95 34.52 35.14
@@ -95145,8 +94959,8 @@ Lake Malawi
-14.37 35.19 35.29
-14.38 35.20 35.29
-14.39 35.21 35.28
- -14.40 35.21 35.27
- -14.41 35.22 35.26
+ -14.40 35.21 35.26
+ -14.41 35.22 35.25
Lake Michigan
46.12 -85.43 -85.38
46.11 -85.53 -85.37 -85.35 -85.30
@@ -95183,12 +94997,12 @@ Lake Michigan
45.80 -87.07 -86.97 -86.82 -86.54 -86.44 -84.76
45.79 -87.07 -86.97 -86.82 -86.55 -86.45 -84.76
45.78 -87.08 -86.97 -86.83 -86.55 -86.46 -84.76
- 45.77 -87.08 -86.96 -86.84 -86.55 -86.53 -84.78
- 45.76 -87.08 -86.96 -86.85 -86.61 -86.58 -86.55 -86.53 -84.79
+ 45.77 -87.08 -86.96 -86.84 -86.55 -86.53 -84.77
+ 45.76 -87.08 -86.96 -86.85 -86.61 -86.58 -86.55 -86.53 -84.78
45.75 -87.08 -86.96 -86.86 -86.62 -86.53 -84.80
- 45.74 -87.09 -86.96 -86.86 -86.62 -86.54 -84.93
+ 45.74 -87.08 -86.96 -86.86 -86.62 -86.54 -84.93
45.73 -87.09 -86.96 -86.88 -86.63 -86.55 -84.93
- 45.72 -87.10 -86.97 -86.93 -86.64 -86.57 -84.93
+ 45.72 -87.09 -86.97 -86.93 -86.64 -86.57 -84.93
45.71 -87.10 -86.65 -86.59 -84.94
45.70 -87.12 -86.65 -86.59 -84.95
45.69 -87.14 -86.66 -86.60 -84.96
@@ -95243,7 +95057,7 @@ Lake Michigan
45.20 -87.57 -85.38
45.19 -87.59 -85.37
45.18 -87.61 -85.37
- 45.17 -87.61 -85.63 -85.57 -85.37
+ 45.17 -87.61 -85.62 -85.57 -85.37
45.16 -87.61 -85.64 -85.59 -85.37
45.15 -87.61 -85.64 -85.61 -85.37
45.14 -87.61 -85.65 -85.61 -85.37
@@ -95258,11 +95072,11 @@ Lake Michigan
45.05 -87.64 -85.75 -85.61 -85.37
45.04 -87.64 -85.75 -85.62 -85.37
45.03 -87.64 -85.75 -85.63 -85.37
- 45.02 -87.64 -85.76 -85.63 -85.38
+ 45.02 -87.64 -85.76 -85.63 -85.37
45.01 -87.64 -85.76 -85.64 -85.38
45.00 -87.65 -85.77 -85.64 -85.38
44.99 -87.67 -85.77 -85.65 -85.38
- 44.98 -87.73 -85.78 -85.65 -85.39
+ 44.98 -87.73 -85.78 -85.65 -85.38
44.97 -87.79 -85.79 -85.65 -85.39
44.96 -87.81 -85.94 -85.92 -85.79 -85.61 -85.39
44.95 -87.83 -85.94 -85.89 -85.80 -85.61 -85.40
@@ -95598,8 +95412,8 @@ Lake Michigan
41.65 -87.44 -87.07
41.64 -87.43 -87.10
41.63 -87.41 -87.14
- 41.62 -87.36 -87.18
- 41.61 -87.32 -87.24
+ 41.62 -87.39 -87.18
+ 41.61 -87.34 -87.24
Lake Okeechobee
27.20 -80.82 -80.76
27.19 -80.84 -80.74
@@ -95638,9 +95452,9 @@ Lake Okeechobee
26.86 -81.04 -80.62
26.85 -80.99 -80.62
26.84 -80.99 -80.63
- 26.83 -80.97 -80.64
- 26.82 -80.97 -80.65
- 26.81 -80.96 -80.66
+ 26.83 -80.97 -80.63
+ 26.82 -80.97 -80.64
+ 26.81 -80.96 -80.65
26.80 -80.96 -80.67
26.79 -80.95 -80.68
26.78 -80.95 -80.68
@@ -95713,7 +95527,7 @@ Lake Ontario
43.97 -78.21 -76.05
43.96 -78.30 -76.06
43.95 -78.35 -76.09
- 43.94 -78.40 -76.11
+ 43.94 -78.40 -76.12
43.93 -78.44 -76.13
43.92 -78.62 -78.53 -78.47 -76.13
43.91 -78.66 -76.13
@@ -95726,7 +95540,7 @@ Lake Ontario
43.84 -79.04 -76.24
43.83 -79.10 -76.23
43.82 -79.12 -76.23
- 43.81 -79.12 -76.22
+ 43.81 -79.12 -76.23
43.80 -79.13 -76.22
43.79 -79.14 -76.22
43.78 -79.17 -76.21
@@ -95746,7 +95560,7 @@ Lake Ontario
43.64 -79.49 -76.16
43.63 -79.49 -76.17
43.62 -79.50 -76.19
- 43.61 -79.50 -76.20
+ 43.61 -79.51 -76.20
43.60 -79.56 -76.18
43.59 -79.58 -76.17
43.58 -79.59 -76.17
@@ -95889,7 +95703,7 @@ Lake Shasta
40.80 -122.40 -122.33 -122.30 -122.26 -122.20 -122.15
40.79 -122.42 -122.33 -122.31 -122.26 -122.22 -122.15 -122.11 -122.08
40.78 -122.42 -122.15 -122.13 -122.08
- 40.77 -122.42 -122.08
+ 40.77 -122.43 -122.08
40.76 -122.43 -122.08
40.75 -122.44 -122.09
40.74 -122.45 -122.10
@@ -95922,8 +95736,8 @@ Lake Superior
48.81 -88.53 -88.32 -88.18 -87.30 -87.01 -86.95 -86.74 -86.65
48.80 -88.54 -88.32 -88.15 -87.29 -87.06 -87.03 -87.01 -86.93 -86.75 -86.61
48.79 -88.55 -88.31 -88.13 -87.29 -87.19 -86.91 -86.78 -86.60
- 48.78 -88.55 -88.31 -88.11 -87.26 -87.21 -86.89 -86.83 -86.60 -86.47 -86.41
- 48.77 -88.55 -88.30 -88.12 -86.87 -86.85 -86.60 -86.54 -86.41
+ 48.78 -88.55 -88.31 -88.11 -87.26 -87.21 -86.88 -86.83 -86.60 -86.47 -86.41
+ 48.77 -88.55 -88.30 -88.12 -86.60 -86.54 -86.41
48.76 -88.55 -88.30 -88.12 -86.60 -86.54 -86.38
48.75 -88.55 -88.30 -88.12 -86.58 -86.56 -86.37
48.74 -88.55 -88.30 -88.12 -86.37
@@ -95934,7 +95748,7 @@ Lake Superior
48.69 -88.56 -88.32 -88.14 -86.35
48.68 -88.56 -88.32 -88.15 -86.35
48.67 -88.55 -88.33 -88.16 -86.34
- 48.66 -88.55 -88.30 -88.17 -86.29
+ 48.66 -88.55 -88.31 -88.17 -86.29
48.65 -88.55 -88.30 -88.23 -88.21 -88.18 -86.29
48.64 -88.61 -88.29 -88.24 -88.21 -88.19 -86.29
48.63 -88.63 -88.28 -88.26 -86.30
@@ -96051,36 +95865,36 @@ Lake Superior
47.52 -90.96 -84.88
47.51 -91.00 -84.85
47.50 -91.02 -84.83
- 47.49 -91.04 -84.78
+ 47.49 -91.03 -84.78
47.48 -91.05 -84.77
47.47 -91.06 -84.75
- 47.46 -91.08 -84.73
+ 47.46 -91.07 -84.73
47.45 -91.09 -84.71
47.44 -91.10 -84.71
- 47.43 -91.12 -84.70
+ 47.43 -91.11 -84.70
47.42 -91.13 -84.69
47.41 -91.14 -84.69
- 47.40 -91.16 -84.68
+ 47.40 -91.15 -84.68
47.39 -91.17 -84.68
47.38 -91.18 -84.62
- 47.37 -91.20 -84.61
+ 47.37 -91.19 -84.61
47.36 -91.21 -84.60
47.35 -91.22 -84.60
- 47.34 -91.24 -84.59
+ 47.34 -91.23 -84.59
47.33 -91.25 -84.59
47.32 -91.26 -84.57
- 47.31 -91.28 -84.57
+ 47.31 -91.27 -84.57
47.30 -91.29 -84.57
- 47.29 -91.31 -84.57
- 47.28 -91.32 -84.57
+ 47.29 -91.30 -84.57
+ 47.28 -91.31 -84.57
47.27 -91.33 -84.57
- 47.26 -91.35 -84.58
+ 47.26 -91.34 -84.58
47.25 -91.36 -84.61
47.24 -91.37 -84.62
- 47.23 -91.39 -84.63
+ 47.23 -91.38 -84.63
47.22 -91.40 -84.63
47.21 -91.41 -88.66 -88.64 -84.64
- 47.20 -91.43 -88.68 -88.64 -84.65
+ 47.20 -91.42 -88.68 -88.64 -84.65
47.19 -91.44 -88.70 -88.64 -84.66
47.18 -91.45 -88.72 -88.64 -84.67
47.17 -91.47 -88.73 -88.64 -84.68
@@ -96112,15 +95926,15 @@ Lake Superior
46.91 -91.92 -91.00 -90.79 -89.22 -88.47 -88.08 -87.98 -84.36
46.90 -91.93 -91.03 -90.79 -89.24 -88.48 -88.14 -87.88 -84.35
46.89 -91.95 -91.04 -90.79 -89.26 -88.48 -88.19 -87.82 -84.35
- 46.88 -91.97 -91.04 -90.79 -89.28 -88.48 -88.31 -88.27 -88.20 -87.79 -84.34
+ 46.88 -91.97 -91.04 -90.79 -89.28 -88.48 -88.30 -88.27 -88.20 -87.79 -84.34
46.87 -91.99 -91.08 -90.80 -89.31 -88.48 -88.32 -88.28 -88.20 -87.78 -84.34
46.86 -92.01 -91.09 -90.80 -89.34 -88.48 -88.33 -88.29 -88.21 -87.75 -84.34
46.85 -92.03 -91.24 -91.21 -91.10 -90.81 -89.37 -88.49 -88.37 -88.30 -88.22 -87.75 -84.35
46.84 -92.05 -91.26 -91.13 -91.11 -90.81 -89.45 -88.49 -88.37 -88.30 -88.23 -87.74 -84.35
- 46.83 -92.07 -91.27 -90.82 -89.58 -88.49 -88.38 -88.30 -88.25 -87.73 -84.47 -84.44 -84.36
- 46.82 -92.09 -91.29 -90.82 -89.72 -88.48 -88.39 -88.30 -88.27 -87.67 -84.50 -84.41 -84.38
+ 46.83 -92.07 -91.27 -90.82 -89.58 -88.49 -88.38 -88.30 -88.24 -87.73 -84.47 -84.44 -84.36
+ 46.82 -92.09 -91.29 -90.82 -89.72 -88.48 -88.39 -88.30 -88.26 -87.67 -84.50 -84.41 -84.37
46.81 -92.10 -91.31 -90.84 -89.79 -88.47 -88.40 -87.67 -84.53
- 46.80 -92.11 -91.33 -90.86 -89.81 -88.48 -88.42 -87.63 -84.53
+ 46.80 -92.11 -91.33 -90.86 -89.81 -88.48 -88.42 -87.67 -84.53
46.79 -92.11 -91.35 -90.87 -89.83 -88.49 -88.43 -87.62 -84.53
46.78 -92.12 -91.37 -90.87 -89.85 -88.49 -88.44 -87.62 -84.53
46.77 -92.12 -91.39 -90.88 -89.86 -88.49 -88.45 -87.61 -84.53
@@ -96154,8 +95968,8 @@ Lake Superior
46.49 -87.28 -87.19 -86.96 -86.54 -85.04 -84.48
46.48 -86.95 -86.55 -85.03 -84.96 -84.94 -84.66 -84.64 -84.48
46.47 -86.94 -86.78 -86.74 -86.56 -84.93 -84.68 -84.62 -84.48
- 46.46 -86.90 -86.80 -86.74 -86.57 -84.89 -84.70 -84.61 -84.47
- 46.45 -86.90 -86.81 -86.73 -86.58 -84.86 -84.72 -84.61 -84.47
+ 46.46 -86.90 -86.80 -86.73 -86.57 -84.89 -84.70 -84.61 -84.47
+ 46.45 -86.90 -86.81 -86.72 -86.58 -84.86 -84.72 -84.61 -84.47
46.44 -86.89 -86.83 -86.69 -86.59 -84.84 -84.75 -84.61 -84.47
46.43 -86.66 -86.61 -84.61 -84.47
46.42 -86.66 -86.63 -84.61 -84.48
@@ -96181,7 +95995,7 @@ Lake Superior
46.85 -84.93 -84.35
46.84 -84.94 -84.35
46.83 -84.95 -84.47 -84.44 -84.36
- 46.82 -84.95 -84.50 -84.41 -84.38
+ 46.82 -84.95 -84.50 -84.41 -84.37
46.81 -84.96 -84.53
46.80 -84.97 -84.53
46.79 -84.98 -84.53
@@ -96351,8 +96165,8 @@ Lake Tanganyika
-4.19 29.09 29.20 29.23 29.54
-4.20 29.09 29.20 29.22 29.54
-4.21 29.09 29.19 29.22 29.55
- -4.22 29.09 29.19 29.22 29.55
- -4.23 29.07 29.19 29.22 29.55
+ -4.22 29.07 29.19 29.22 29.55
+ -4.23 29.06 29.19 29.22 29.55
-4.24 29.05 29.18 29.22 29.55
-4.25 29.05 29.17 29.22 29.56
-4.26 29.04 29.17 29.22 29.57
@@ -96473,9 +96287,9 @@ Lake Tanganyika
-5.41 29.23 29.75
-5.42 29.24 29.75
-5.43 29.25 29.75
- -5.44 29.25 29.75
- -5.45 29.26 29.75
- -5.46 29.27 29.76
+ -5.44 29.25 29.76
+ -5.45 29.26 29.76
+ -5.46 29.27 29.77
-5.47 29.27 29.77
-5.48 29.28 29.78
-5.49 29.28 29.79
@@ -96564,14 +96378,14 @@ Lake Tanganyika
-6.32 29.34 29.79
-6.33 29.35 29.80
-6.34 29.35 29.81
- -6.35 29.35 29.82
+ -6.35 29.36 29.82
-6.36 29.36 29.83
- -6.37 29.36 29.84
+ -6.37 29.37 29.84
-6.38 29.37 29.84
- -6.39 29.37 29.85
+ -6.39 29.38 29.85
-6.40 29.38 29.86
-6.41 29.38 29.87
- -6.42 29.38 29.89
+ -6.42 29.39 29.89
-6.43 29.39 29.90
-6.44 29.39 29.92 30.04 30.15
-6.45 29.39 29.94 30.01 30.16
@@ -96641,7 +96455,7 @@ Lake Tanganyika
-7.09 29.86 30.57
-7.10 29.91 30.57
-7.11 29.93 30.56
- -7.12 29.96 30.55
+ -7.12 29.96 30.53
-7.13 29.97 30.53
-7.14 29.98 30.54
-7.15 29.99 30.54
@@ -96728,8 +96542,8 @@ Lake Tanganyika
-7.96 30.40 30.88
-7.97 30.41 30.89
-7.98 30.42 30.90
- -7.99 30.42 30.90
- -8.00 30.43 30.91
+ -7.99 30.43 30.90
+ -8.00 30.44 30.91
-8.01 30.44 30.91
-8.02 30.44 30.91
-8.03 30.48 30.91
@@ -96824,11 +96638,11 @@ Lake Victoria
0.41 33.17 33.37
0.40 33.17 33.37
0.39 33.18 33.37
- 0.38 33.19 33.37
+ 0.38 33.20 33.37
0.37 33.25 33.37
0.36 33.22 33.37 33.42 33.47
- 0.35 33.20 33.47
- 0.34 33.18 33.48 33.69 33.73
+ 0.35 33.21 33.47
+ 0.34 33.19 33.48 33.68 33.73
0.33 33.16 33.49 33.61 33.65 33.67 33.74
0.32 33.14 33.50 33.60 33.76
0.31 33.14 33.51 33.60 33.76
@@ -96838,10 +96652,10 @@ Lake Victoria
0.27 32.62 32.67 33.06 33.09 33.14 33.51 33.60 33.75 33.96 33.99
0.26 32.61 32.67 33.06 33.11 33.13 33.50 33.60 33.75 33.95 34.00
0.25 32.61 32.67 33.06 33.45 33.61 33.75 33.94 34.00
- 0.24 32.61 32.68 33.04 33.45 33.47 33.51 33.61 33.75 33.78 33.80 33.93 34.01
+ 0.24 32.61 32.68 33.04 33.45 33.47 33.51 33.61 33.75 33.77 33.80 33.93 34.01
0.23 32.60 32.69 33.03 33.44 33.47 33.54 33.60 33.74 33.77 33.81 33.92 34.01
0.22 32.60 32.69 33.03 33.54 33.58 33.73 33.77 33.81 33.91 34.01
- 0.21 32.56 32.73 33.03 33.72 33.77 33.84 33.90 34.01
+ 0.21 32.56 32.73 33.03 33.55 33.57 33.72 33.77 33.84 33.90 34.01
0.20 32.55 32.74 32.86 32.90 33.08 33.86 33.88 34.01
0.19 32.55 32.74 32.84 32.90 33.08 34.01
0.18 32.55 32.75 32.84 32.90 33.07 34.00
@@ -96867,7 +96681,7 @@ Lake Victoria
-0.02 32.06 32.09 32.19 34.00
-0.03 32.00 32.11 32.19 34.03
-0.04 32.00 32.13 32.19 34.04 34.08 34.13
- -0.05 32.00 32.15 32.17 34.04 34.06 34.14
+ -0.05 32.00 34.04 34.06 34.14
-0.06 32.00 34.14
-0.07 31.98 34.14 34.66 34.70 34.72 34.74
-0.08 31.96 34.14 34.65 34.74
@@ -96953,13 +96767,13 @@ Lake Victoria
-0.88 31.75 34.19
-0.89 31.75 34.18
-0.90 31.75 34.16
- -0.91 31.75 34.16
- -0.92 31.75 34.15
- -0.93 31.75 34.15
+ -0.91 31.75 34.15
+ -0.92 31.75 34.14
+ -0.93 31.75 34.14
-0.94 31.75 34.14
- -0.95 31.75 34.14
- -0.96 31.76 34.13
- -0.97 31.76 34.13
+ -0.95 31.75 34.13
+ -0.96 31.75 34.13
+ -0.97 31.75 34.13
-0.98 31.76 34.14
-0.99 31.76 34.14
-1.00 31.76 34.14
@@ -97107,15 +96921,15 @@ Lake Victoria
-2.42 31.76 32.10 32.34 32.92 33.10 33.53
-2.43 31.77 32.11 32.35 32.92 33.11 33.54
-2.44 31.77 32.11 32.36 32.91 33.11 33.54
- -2.45 31.77 32.12 32.42 32.64 32.66 32.91 33.12 33.54
+ -2.45 31.77 32.14 32.42 32.64 32.66 32.91 33.12 33.54
-2.46 31.78 32.14 32.42 32.64 32.67 32.91 33.12 33.46
-2.47 31.77 32.16 32.46 32.63 32.67 32.91 33.13 33.45
-2.48 31.76 32.17 32.49 32.62 32.67 32.91 33.16 33.46
-2.49 31.70 32.17 32.51 32.61 32.66 32.88 33.16 33.47
-2.50 31.70 32.18 32.50 32.60 32.66 32.89 33.16 33.47
-2.51 31.70 32.18 32.50 32.59 32.66 32.76 32.81 32.90 33.18 33.47
- -2.52 31.70 32.00 32.05 32.18 32.49 32.57 32.66 32.69 32.72 32.76 32.81 32.91 33.19 33.46
- -2.53 31.70 32.00 32.06 32.17 32.49 32.56 32.72 32.75 32.81 32.91 33.33 33.46
+ -2.52 31.70 32.00 32.04 32.18 32.49 32.57 32.66 32.69 32.72 32.76 32.81 32.91 33.19 33.46
+ -2.53 31.70 32.00 32.05 32.07 32.09 32.17 32.49 32.56 32.72 32.75 32.80 32.91 33.33 33.46
-2.54 31.70 32.00 32.09 32.17 32.49 32.55 32.72 32.74 32.80 32.91 33.34 33.45
-2.55 31.72 32.00 32.12 32.17 32.49 32.54 32.80 32.91 33.38 33.43
-2.56 31.73 32.00 32.12 32.16 32.51 32.53 32.80 32.91 33.38 33.43
@@ -97146,7 +96960,7 @@ Lake Victoria
-2.81 31.77 31.84 32.82 32.97
-2.82 31.77 31.83 32.77 32.97
-2.83 31.77 31.82 32.75 33.02
- -2.84 31.78 31.80 32.73 33.03
+ -2.84 31.78 31.81 32.73 33.03
-2.85 32.71 32.86 32.90 33.03
-2.86 32.71 32.85 32.92 33.03
-2.87 32.71 32.84 32.94 33.03
@@ -97293,7 +97107,7 @@ Lake Winnipeg
53.18 -99.26 -97.40
53.17 -99.24 -97.40
53.16 -99.20 -97.40
- 53.15 -99.16 -97.41
+ 53.15 -99.18 -97.41
53.14 -99.16 -97.42
53.13 -99.15 -97.41
53.12 -99.14 -97.40
@@ -97474,8 +97288,8 @@ Lake Winnipeg
51.37 -96.92 -96.44
51.36 -96.93 -96.42
51.35 -96.94 -96.37
- 51.34 -96.94 -96.74 -96.71 -96.35
- 51.33 -96.94 -96.76 -96.71 -96.34
+ 51.34 -96.94 -96.73 -96.71 -96.35
+ 51.33 -96.94 -96.75 -96.71 -96.34
51.32 -96.93 -96.76 -96.70 -96.33
51.31 -96.93 -96.76 -96.65 -96.33
51.30 -96.95 -96.77 -96.66 -96.32
@@ -97491,7 +97305,7 @@ Lake Winnipeg
51.20 -96.99 -96.88 -96.81 -96.25
51.19 -96.99 -96.89 -96.82 -96.25
51.18 -96.99 -96.91 -96.83 -96.31
- 51.17 -96.99 -96.93 -96.83 -96.33
+ 51.17 -96.99 -96.93 -96.84 -96.33
51.16 -96.84 -96.32
51.15 -96.84 -96.31
51.14 -96.84 -96.30
@@ -97568,10 +97382,10 @@ Lake Winnipeg
50.43 -96.93 -96.57
50.42 -96.93 -96.58
50.41 -96.92 -96.59
- 50.40 -96.91 -96.61
- 50.39 -96.88 -96.63
- 50.38 -96.84 -96.66
- 50.37 -96.80 -96.68
+ 50.40 -96.91 -96.60
+ 50.39 -96.88 -96.62
+ 50.38 -96.84 -96.64
+ 50.37 -96.80 -96.67
Laptev Sea
81.27 96.18 96.24
81.26 96.18 96.32
@@ -159638,7 +159452,7 @@ Yellowstone Lake
44.43 -110.57 -110.46 -110.42 -110.24
44.42 -110.57 -110.47 -110.40 -110.22
44.41 -110.56 -110.48 -110.40 -110.20
- 44.40 -110.55 -110.48 -110.41 -110.19
+ 44.40 -110.55 -110.48 -110.40 -110.19
44.39 -110.43 -110.19
44.38 -110.43 -110.18
44.37 -110.43 -110.18
diff --git a/c++/src/objects/seqloc/Seq_id.cpp b/c++/src/objects/seqloc/Seq_id.cpp
index 34bccf6..3086a9e 100644
--- a/c++/src/objects/seqloc/Seq_id.cpp
+++ b/c++/src/objects/seqloc/Seq_id.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_id.cpp 467227 2015-05-11 19:16:04Z vasilche $
+/* $Id: Seq_id.cpp 483824 2015-11-04 17:35:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -89,6 +89,17 @@ BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
+// CSeqIdException
+const char* CSeqIdException::GetErrCodeString(void) const
+{
+ switch (GetErrCode()) {
+ case eUnknownType: return "eUnknownType";
+ case eFormat: return "eFormat";
+ default: return CException::GetErrCodeString();
+ }
+}
+
+
// constructor
CSeq_id::CSeq_id(void)
{
@@ -762,11 +773,14 @@ private:
void SAccGuide::AddRule(const CTempString& rule)
{
CTempString tmp1, tmp2;
- vector<CTempString> tokens;
+ vector<CTempStringEx> tokens;
SIZE_TYPE pos, pos2;
++count;
- tmp1.assign(rule, 0, rule.find("#")); // strip comment
+ tmp1.assign(rule, 0, rule.find('#')); // strip comment
+ if (tmp1.empty())
+ return;
+ tokens.reserve(3);
NStr::Tokenize(tmp1, " \t", tokens, NStr::eMergeDelims);
if (tokens.empty()) {
return;
@@ -928,20 +942,57 @@ SAccGuide::TAccInfo SAccGuide::Find(TFormatCode fmt,
}
+static bool s_IsFileOld(const string& file)
+{
+ static const char vcs_id_start[] = "# $Id: accguide.inc ";
+ if ( !NStr::StartsWith(kBuiltInGuide[0], vcs_id_start) ) {
+ return false;
+ }
+ const char* rev_start = kBuiltInGuide[0] + sizeof(vcs_id_start);
+ const char* date_start = strchr(rev_start, ' ');
+ if (date_start != NULL) {
+ ++date_start;
+ } else {
+ return false;
+ }
+ const char* time_start = strchr(date_start + 1, ' ');
+ if (time_start != NULL) {
+ ++time_start;
+ } else {
+ return false;
+ }
+ const char* time_end = strchr(time_start + 1, ' ');
+ if (time_end == NULL) {
+ return false;
+ }
+ string builtin_timestamp_str(date_start, time_end - date_start);
+ CTime builtin_timestamp(builtin_timestamp_str, "Y-M-D h:m:sZ");
+ CTime file_timestamp;
+ CFile(file).GetTime(&file_timestamp);
+ return file_timestamp < builtin_timestamp;
+}
+
+
SAccGuide::SAccGuide(void)
: count(0)
{
+ bool file_is_old = false;
{{
string file = g_FindDataFile("accguide.txt");
- if ( !file.empty() ) {
+ if ( !file.empty() && !(file_is_old = s_IsFileOld(file))) {
try {
x_Load(file);
} STD_CATCH_ALL_X(1, "SAccGuide::SAccGuide")
}
}}
if (count == 0) {
- ERR_POST_X(6, Info << "CSeq_id::IdentifyAccession: " // minor lie
- "falling back on built-in rules.");
+ if (file_is_old) {
+ ERR_POST_X(12, Info << "CSeq_id::IdentifyAccession: " // minor lie
+ "using built-in rules because accguide.txt is older.");
+ } else {
+ ERR_POST_X(6, Info << "CSeq_id::IdentifyAccession: "
+ "falling back on built-in rules.");
+ }
static const unsigned int kNumBuiltInRules
= sizeof(kBuiltInGuide) / sizeof(*kBuiltInGuide);
for (unsigned int i = 0; i < kNumBuiltInRules; ++i) {
@@ -1015,7 +1066,8 @@ CSeq_id::EAccessionInfo
CSeq_id::x_IdentifyAccession(const CTempString& main_acc, bool has_version)
{
SIZE_TYPE digit_pos = main_acc.find_first_of(kDigits),
- main_size = main_acc.size(), scaffold_flag_len = 0;
+ main_size = main_acc.size();
+ char flag_char = '\0';
if (digit_pos == NPOS) {
return eAcc_unknown;
} else {
@@ -1074,11 +1126,12 @@ CSeq_id::x_IdentifyAccession(const CTempString& main_acc, bool has_version)
// followed in some rare cases by a tag such as :PDB=...
return eAcc_prf;
} else if (digit_pos >= 4 && non_dig_pos == digit_pos + 2
- && main_acc[non_dig_pos] == 'S'
- && main_size - non_dig_pos >= 6
+ && main_size - non_dig_pos >= 6 && main_acc[3] != '_'
+ && (main_acc[non_dig_pos] == 'S'
+ || main_acc[non_dig_pos] == 'P')
&& (main_acc.find_first_not_of
(kDigits, non_dig_pos + 1) == NPOS)) {
- scaffold_flag_len = 1;
+ flag_char = main_acc[non_dig_pos];
} else {
return eAcc_unknown;
}
@@ -1098,9 +1151,30 @@ CSeq_id::x_IdentifyAccession(const CTempString& main_acc, bool has_version)
s_Guide->Reset(new SAccGuide);
}
- SIZE_TYPE digit_count = main_size - digit_pos - scaffold_flag_len;
+ SIZE_TYPE flag_len = (flag_char == '\0') ? 0 : 1;
+ SIZE_TYPE digit_count = main_size - digit_pos - flag_len;
EAccessionInfo ai
= (*s_Guide)->Find(SAccGuide::s_Key(digit_pos, digit_count), main_acc);
+ if (flag_char == 'P') {
+ switch (ai & eAcc_division_mask) {
+ case eAcc_targeted:
+ case eAcc_wgs:
+ // case eAcc_wgs_intermed:
+ ai = EAccessionInfo((ai & eAcc_type_mask) | eAcc_wgs | fAcc_prot);
+ break;
+ case eAcc_tsa:
+ ai = EAccessionInfo((ai & eAcc_type_mask) | eAcc_tsa | fAcc_prot);
+ break;
+ default:
+ ERR_POST_X(11,
+ Warning << main_acc
+ << ": Protein flag found with unexpected division "
+ << ((ai & eAcc_division_mask) >> 8));
+ ai = EAccessionInfo((ai & (eAcc_type_mask | eAcc_division_mask))
+ | fAcc_prot);
+ break;
+ }
+ }
switch (ai & eAcc_division_mask) {
case eAcc_targeted:
case eAcc_tsa:
@@ -1108,7 +1182,7 @@ CSeq_id::x_IdentifyAccession(const CTempString& main_acc, bool has_version)
case eAcc_wgs_intermed:
if (digit_pos >= 4
&& (main_acc.find_first_not_of
- ("0", digit_pos /* + scaffold_flag_len */ + 2) == NPOS)) {
+ ("0", digit_pos /* + flag_len */ + 2) == NPOS)) {
return EAccessionInfo(ai | fAcc_master);
}
default:
diff --git a/c++/src/objects/seqloc/Seq_loc.cpp b/c++/src/objects/seqloc/Seq_loc.cpp
index c681c39..203b27c 100644
--- a/c++/src/objects/seqloc/Seq_loc.cpp
+++ b/c++/src/objects/seqloc/Seq_loc.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_loc.cpp 449954 2014-10-22 13:28:16Z ivanov $
+/* $Id: Seq_loc.cpp 475726 2015-08-11 18:12:56Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,6 +59,24 @@
BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
+
+// CSeqLocException
+const char* CSeqLocException::GetErrCodeString(void) const
+{
+ switch (GetErrCode()) {
+ case eNotSet: return "eNotSet";
+ case eMultipleId: return "eMultipleId";
+ case eUnsupported: return "eUnsupported";
+ case eBadLocation: return "eBadLocation";
+ case eBadIterator: return "eBadIterator";
+ case eIncomatible: return "eIncomatible";
+ case eOutOfRange: return "eOutOfRange";
+ case eOtherError: return "eOtherError";
+ default: return CException::GetErrCodeString();
+ }
+}
+
+
// constructors
CSeq_loc::CSeq_loc(E_Choice index)
{
@@ -193,8 +211,8 @@ void x_Assign(CInt_fuzz& dst, const CInt_fuzz& src)
dst.SetAlt() = src.GetAlt();
break;
default:
- NCBI_THROW(CException, eUnknown,
- "Invalid Int-fuzz variant");
+ NCBI_THROW(CSeqLocException, eNotSet,
+ "Int-fuzz is not set");
}
}
@@ -365,15 +383,19 @@ void CSeq_loc::Assign(const CSerialObject& obj, ESerialRecursionMode how)
CSeq_loc::TRange CSeq_loc::x_UpdateTotalRange(void) const
{
- TRange range = m_TotalRangeCache;
- if ( range.GetFrom() == TSeqPos(kDirtyCache) ) {
+ TSeqPos range_from = m_TotalRangeCacheFrom;
+ if ( range_from == TSeqPos(kDirtyCache) ) {
const CSeq_id* id = 0;
- range = x_CalculateTotalRangeCheckId(id);
+ TRange range = x_CalculateTotalRangeCheckId(id);
m_IdCache = id;
- m_TotalRangeCache.SetToOpen(range.GetToOpen());
- m_TotalRangeCache.SetFrom(range.GetFrom());
+ m_TotalRangeCacheToOpen = range.GetToOpen();
+ m_TotalRangeCacheFrom = range.GetFrom();
+ return range;
+ }
+ else {
+ TSeqPos range_to_open = m_TotalRangeCacheToOpen;
+ return COpenRange<TSeqPos>(range_from, range_to_open);
}
- return range;
}
@@ -388,7 +410,7 @@ bool CSeq_loc::x_UpdateId(const CSeq_id*& total_id, const CSeq_id* id,
total_id = id;
} else if ( (id && !total_id->Equals(*id)) ) {
if (may_throw) {
- NCBI_THROW(CException, eUnknown,
+ NCBI_THROW(CSeqLocException, eMultipleId,
"CSeq_loc::GetTotalRange() is not defined "
"for seq-loc with several different seq-ids");
} else {
@@ -501,13 +523,13 @@ CSeq_loc::TRange CSeq_loc::x_CalculateTotalRangeCheckId(const CSeq_id*& id) cons
}
break;
}
+
case e_Feat:
default:
- {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::CalculateTotalRange -- "
- "unsupported location type");
- }
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc::CalculateTotalRange(): "
+ "unsupported location type: "<<
+ SelectionName(Which()));
}
return total_range;
@@ -518,7 +540,7 @@ int CSeq_loc::x_CompareSingleId(const CSeq_loc& loc, const CSeq_id* id1,
const CSeq_id* id2) const
{
if ( !id1 || !id2 ) {
- NCBI_THROW(CException, eUnknown,
+ NCBI_THROW(CSeqLocException, eMultipleId,
"CSeq_loc::Compare(): "
"cannot compare locations with several different seq-ids");
}
@@ -669,17 +691,14 @@ static inline
bool s_CheckIfMatchesBioseq( const CSeq_loc &loc,
const CSeq_loc::ISubLocFilter *filter )
{
- if( NULL == filter ) {
- return true;
- }
- return (*filter)( loc.GetId() );
+ return !filter || (*filter)( loc.GetId() );
}
static inline
bool s_CheckIfMatchesBioseq( const CSeq_interval &loc,
const CSeq_loc::ISubLocFilter *filter )
{
- return true;
+ return !filter || (*filter)( &loc.GetId() );
}
// Compare two ranges (reversed on minus strand)
@@ -868,9 +887,9 @@ ENa_strand CSeq_loc::GetStrand(void) const
case e_Equiv:
case e_Feat:
default:
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::GetStrand -- unsupported location type" +
- CSeq_loc::SelectionName(Which()));
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc::GetStrand(): unsupported location type"<<
+ SelectionName(Which()));
}
}
@@ -916,11 +935,9 @@ TSeqPos CSeq_loc::GetStart(ESeqLocExtremes ext) const
case e_Equiv:
case e_Feat:
default:
- {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::GetStart -- "
- "unsupported location type");
- }
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc::GetStart(): "
+ "unsupported location type: "<<SelectionName(Which()));
}
}
@@ -963,408 +980,2009 @@ TSeqPos CSeq_loc::GetStop(ESeqLocExtremes ext) const
return GetBond().GetStop(ext);
}
- case e_Equiv:
- case e_Feat:
- default:
- {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::GetStart -- "
- "unsupported location type");
- }
- }
+ case e_Equiv:
+ case e_Feat:
+ default:
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc::GetStop(): "
+ "unsupported location type: "<<SelectionName(Which()));
+ }
+}
+
+
+TSeqPos CSeq_loc::GetCircularLength(TSeqPos seq_len) const
+{
+ if (seq_len == kInvalidSeqPos) {
+ return GetTotalRange().GetLength();
+ }
+ TSeqPos start = GetStart(eExtreme_Biological);
+ TSeqPos stop = GetStop (eExtreme_Biological);
+ bool minus = IsReverseStrand();
+
+ if (start < stop) {
+ return minus ? (seq_len - stop + start + 1) : (stop - start + 1);
+ } else {
+ return minus ? (start - stop + 1) : (seq_len - start + stop + 1);
+ }
+}
+
+
+CSeq_loc::const_iterator CSeq_loc::begin(void) const
+{
+ return CSeq_loc_CI(*this);
+}
+
+
+CSeq_loc::const_iterator CSeq_loc::end(void) const
+{
+ return CSeq_loc_CI();
+}
+
+
+// CSeq_loc_CI implementation
+
+SSeq_loc_CI_RangeInfo::SSeq_loc_CI_RangeInfo(void)
+ : m_IsSetStrand(false),
+ m_Strand(eNa_strand_unknown)
+{
+}
+
+
+SSeq_loc_CI_RangeInfo::~SSeq_loc_CI_RangeInfo(void)
+{
+}
+
+
+class CSeq_loc_CI_Impl : public CObject
+{
+public:
+ CSeq_loc_CI_Impl(void);
+ CSeq_loc_CI_Impl(const CSeq_loc& loc,
+ CSeq_loc_CI::EEmptyFlag empty_flag,
+ CSeq_loc_CI::ESeqLocOrder order);
+ virtual ~CSeq_loc_CI_Impl(void) {}
+
+ typedef SSeq_loc_CI_RangeInfo::TRange TRange;
+ typedef vector<SSeq_loc_CI_RangeInfo> TRanges;
+
+ struct SEquivSet {
+ size_t m_StartIndex;
+
+ // parts' end offsets within the equiv set, ordered by position
+ // must contain at least one element - the only part
+ // all parts must be not empty - contain at least one element
+ typedef vector<size_t> TParts;
+ typedef TParts::const_iterator TPart_CI;
+ typedef TParts::iterator TPart_I;
+
+ TParts m_Parts;
+
+ // return number of Seq-loc element in all equiv parts (always > 0)
+ size_t GetElementsCount(void) const
+ {
+ _ASSERT(!m_Parts.empty());
+ _ASSERT(m_Parts.back() > 0);
+ return m_Parts.back();
+ }
+ // return index of the first element in the equiv set
+ size_t GetStartIndex(void) const
+ {
+ return m_StartIndex;
+ }
+ // return index of element after the equiv set
+ size_t GetEndIndex(void) const // exclusive
+ {
+ return GetStartIndex()+GetElementsCount();
+ }
+
+ // return true if the equiv set contains element with specified index
+ bool Contains(size_t idx) const
+ {
+ return idx >= GetStartIndex() && idx < GetEndIndex();
+ }
+
+ // return number of equiv parts (always > 0)
+ size_t GetPartsCount(void) const
+ {
+ _ASSERT(!m_Parts.empty());
+ return m_Parts.size();
+ }
+
+ // return offset of the first element in equiv part within equiv set
+ size_t GetPartStartOffset(TPart_CI part) const
+ {
+ _ASSERT(part < m_Parts.end());
+ return part == m_Parts.begin()? 0: *--part;
+ }
+ // return offset of the end element in equiv part within equiv set
+ size_t GetPartEndOffset(TPart_CI part) const
+ {
+ _ASSERT(part < m_Parts.end());
+ return *part;
+ }
+
+ // return index of the first element in equiv part within equiv set
+ size_t GetPartStartIndex(TPart_CI part) const
+ {
+ return GetStartIndex()+GetPartStartOffset(part);
+ }
+ // return index of the end element in equiv part within equiv set
+ size_t GetPartEndIndex(TPart_CI part) const
+ {
+ return GetStartIndex()+GetPartEndOffset(part);
+ }
+
+ // return part containing element with specified index
+ TPart_I FindPartByElementIndex(size_t idx)
+ {
+ _ASSERT(Contains(idx));
+ return upper_bound(m_Parts.begin(), m_Parts.end(),
+ idx - GetStartIndex());
+ }
+ // return part containing element with specified index
+ TPart_CI FindPartByElementIndex(size_t idx) const
+ {
+ _ASSERT(Contains(idx));
+ return upper_bound(m_Parts.begin(), m_Parts.end(),
+ idx - GetStartIndex());
+ }
+ };
+ struct PByLevel {
+ bool operator()(const SEquivSet* e1, const SEquivSet* e2) const
+ {
+ size_t s1 = e1->GetElementsCount();
+ size_t s2 = e2->GetElementsCount();
+ if ( s1 != s2 ) {
+ // smallest first
+ return s1 < s2;
+ }
+ s1 = e1->GetPartsCount();
+ s2 = e2->GetPartsCount();
+ if ( s1 != s2 ) {
+ // enclosing set must have single part with the inner set
+ _ASSERT(s1 == 1 || s2 == 1);
+ // more parts (inner) first
+ return s1 > s2;
+ }
+ // it's still possible that both equiv sets contain
+ // one part with the same set of elements
+ // in this case the sets are equivalent and one set contains
+ // another, no matter which one, but we still order the sets
+ // by their creation order
+ return e1 < e2;
+ }
+ };
+ typedef vector<SEquivSet> TEquivSets;
+
+ TRanges& GetRanges(void) { return m_Ranges; }
+ const TRanges& GetRanges(void) const { return m_Ranges; }
+
+ bool IsEnd(size_t idx) const { return idx >= m_Ranges.size(); }
+
+ void DeleteRange(size_t idx);
+ SSeq_loc_CI_RangeInfo& InsertRange(size_t idx, CSeq_loc::E_Choice type);
+
+ // Point/Interval support
+
+ // If any part of the location part is changed the embedding location
+ // becomes invalid.
+ // This method resets embedding location if it's related to the part only.
+ bool WasPoint(const SSeq_loc_CI_RangeInfo& info) const
+ {
+ return info.m_Loc && info.m_Loc->IsPnt();
+ }
+ bool ShouldBePoint(const SSeq_loc_CI_RangeInfo& info) const
+ {
+ if ( !info.m_Loc ) {
+ return false;
+ }
+ switch ( info.m_Loc->Which() ) {
+ case CSeq_loc::e_Pnt:
+ case CSeq_loc::e_Packed_pnt:
+ case CSeq_loc::e_Bond:
+ return true;
+ default:
+ return false;
+ }
+ }
+ // Update CSeq_point object if any
+ void UpdatePoint(CSeq_point& pnt,
+ const SSeq_loc_CI_RangeInfo& info) const;
+ // Update CSeq_point object if any
+ void UpdatePoint(SSeq_loc_CI_RangeInfo& info);
+ // Create CSeq_point object
+ void SetPoint(SSeq_loc_CI_RangeInfo& info);
+ // Update embedded personal Seq-loc object, making sure it's not a point
+ void UpdateLoc(SSeq_loc_CI_RangeInfo& info);
+
+ bool CanBePoint(const SSeq_loc_CI_RangeInfo& info) const;
+
+ bool CanBeInterval(const SSeq_loc_CI_RangeInfo& info) const;
+ bool CanBePoint(size_t idx) const
+ {
+ return CanBePoint(m_Ranges[idx]);
+ }
+ bool CanBeInterval(size_t idx) const
+ {
+ return CanBeInterval(m_Ranges[idx]);
+ }
+ bool CanBePacked_pnt(size_t idx_begin, size_t idx_end) const;
+ bool CanBePacked_int(size_t idx_begin, size_t idx_end) const;
+
+ CRef<CInt_fuzz> MakeFuzz(const CInt_fuzz& fuzz) const;
+ CRef<CSeq_point> MakePoint(const SSeq_loc_CI_RangeInfo& info) const;
+ CRef<CSeq_loc> MakeLocPoint(const SSeq_loc_CI_RangeInfo& info) const;
+
+ CRef<CSeq_interval> MakeInterval(const SSeq_loc_CI_RangeInfo& info) const;
+ CRef<CSeq_loc> MakeLocInterval(const SSeq_loc_CI_RangeInfo& info) const;
+
+ CRef<CSeq_loc> MakeLocPacked_pnt(size_t idx_begin, size_t idx_end) const;
+ CRef<CSeq_loc> MakeLocPacked_int(size_t idx_begin, size_t idx_end) const;
+
+ // Bond support
+ bool CanBeBond(size_t idx_begin, size_t idx_end) const;
+ size_t GetBondBegin(size_t idx) const;
+ size_t GetBondEnd(size_t idx) const;
+ pair<size_t, size_t> GetBondRange(size_t idx) const
+ {
+ return make_pair(GetBondBegin(idx), GetBondEnd(idx));
+ }
+ bool IsInBond(const SSeq_loc_CI_RangeInfo& info) const
+ {
+ return info.m_Loc && info.m_Loc->IsBond();
+ }
+ bool IsInBond(size_t idx) const
+ {
+ return IsInBond(m_Ranges[idx]);
+ }
+ bool IsBondPartA(size_t idx) const
+ {
+ return IsInBond(idx) && idx == GetBondBegin(idx);
+ }
+ bool IsBondPartB(size_t idx) const
+ {
+ return IsInBond(idx) && idx == GetBondBegin(idx)+1;
+ }
+ void x_BreakBond(size_t idx)
+ {
+ SetPoint(m_Ranges[idx]);
+ }
+ void x_CreateBond(size_t idx)
+ {
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ loc->SetBond();
+ m_Ranges[idx].m_Loc = loc;
+ }
+ void x_AddBondPartB(size_t idx)
+ {
+ // add part B be to the bond
+ m_Ranges[idx+1].m_Loc = m_Ranges[idx].m_Loc;
+ }
+ void RemoveBond(size_t idx);
+ void MakeBondA(size_t idx);
+ void MakeBondAB(size_t idx);
+ void MakeBondB(size_t idx);
+ CRef<CSeq_loc> MakeLocBond(size_t idx_begin, size_t idx_end) const;
+
+ // Equiv support
+ bool HasEquivSets(void) const
+ {
+ return !m_EquivSets.empty();
+ }
+ bool IsInEquivSet(size_t idx) const
+ {
+ ITERATE ( TEquivSets, it, m_EquivSets ) {
+ if ( it->Contains(idx) ) {
+ return true;
+ }
+ }
+ return false;
+ }
+ size_t GetEquivSetsCount(size_t idx) const
+ {
+ size_t count = 0;
+ ITERATE ( TEquivSets, it, m_EquivSets ) {
+ if ( it->Contains(idx) ) {
+ ++count;
+ }
+ }
+ return count;
+ }
+ const SEquivSet& GetEquivSet(size_t idx, size_t level) const
+ {
+ vector<const SEquivSet*> sets;
+ ITERATE ( TEquivSets, it, m_EquivSets ) {
+ if ( it->Contains(idx) ) {
+ sets.push_back(&*it);
+ }
+ }
+ if ( level >= sets.size() ) {
+ NCBI_THROW_FMT(CSeqLocException, eOutOfRange,
+ "CSeq_loc_CI: bad equiv set level: "<<level);
+ }
+ sort(sets.begin(), sets.end(), PByLevel());
+ return *sets[level];
+ }
+ pair<size_t, size_t> GetEquivSetRange(size_t idx, size_t level) const
+ {
+ const SEquivSet& s = GetEquivSet(idx, level);
+ return make_pair(s.GetStartIndex(), s.GetEndIndex());
+ }
+ pair<size_t, size_t> GetEquivPartRange(size_t idx, size_t level) const
+ {
+ const SEquivSet& s = GetEquivSet(idx, level);
+ SEquivSet::TPart_CI p = s.FindPartByElementIndex(idx);
+ return make_pair(s.GetPartStartIndex(p), s.GetPartEndIndex(p));
+ }
+ // Return first equiv part bound point that fall into the range.
+ // Beginning and ending points are not counted, so 0 is not possible.
+ // Return 0 if there are no such breaks.
+ size_t HasEquivBreak(size_t begin, size_t end) const;
+
+ typedef set<const SEquivSet*> TUsedEquivs;
+ const SEquivSet* FindInnerEquivSet(size_t begin, size_t end,
+ const TUsedEquivs& used_equivs) const;
+
+ CRef<CSeq_loc> MakeLocOther(const SSeq_loc_CI_RangeInfo& info) const;
+ CRef<CSeq_loc> MakeRangeLoc(const SSeq_loc_CI_RangeInfo& info) const;
+ CRef<CSeq_loc> MakeLoc(CSeq_loc_I::EMakeType make_type) const;
+ CRef<CSeq_loc> MakeLoc(size_t idx_begin,
+ size_t idx_end,
+ CSeq_loc_I::EMakeType make_type,
+ TUsedEquivs& used_equivs) const;
+
+ bool HasChanges(void) const
+ {
+ return m_HasChanges;
+ }
+
+ void SetHasChanges(void)
+ {
+ m_HasChanges = true;
+ }
+
+ CSeq_loc_I::EEquivMode GetEquivMode(void) const
+ {
+ return m_EquivMode;
+ }
+ void SetEquivMode(CSeq_loc_I::EEquivMode mode)
+ {
+ m_EquivMode = mode;
+ }
+
+private:
+ // Never copy this object
+ CSeq_loc_CI_Impl(const CSeq_loc_CI_Impl&);
+ CSeq_loc_CI_Impl& operator=(const CSeq_loc_CI_Impl&);
+
+ // Process the location, fill the list
+ void x_ProcessLocation(const CSeq_loc& loc);
+ void x_ProcessInterval(const CSeq_interval& seq_int,
+ const CSeq_loc& loc);
+ void x_ProcessPoint(const CSeq_point& seq_pnt,
+ const CSeq_loc& loc);
+
+ static void x_SetId(SSeq_loc_CI_RangeInfo& info, const CSeq_id& id);
+
+ // Prevent seq-loc destruction
+ CConstRef<CSeq_loc> m_Location;
+ // List of intervals
+ TRanges m_Ranges;
+ // List of equiv parts
+ TEquivSets m_EquivSets;
+ // Empty locations processing option
+ CSeq_loc_CI::EEmptyFlag m_EmptyFlag;
+ // true if anything was changed in the Seq-loc
+ bool m_HasChanges;
+ // equiv editing mode
+ CSeq_loc_I::EEquivMode m_EquivMode;
+};
+
+
+CSeq_loc_CI_Impl::CSeq_loc_CI_Impl(void)
+ : m_HasChanges(false),
+ m_EquivMode(CSeq_loc_I::eEquiv_none)
+{
+}
+
+
+CSeq_loc_CI_Impl::CSeq_loc_CI_Impl(const CSeq_loc& loc,
+ CSeq_loc_CI::EEmptyFlag empty_flag,
+ CSeq_loc_CI::ESeqLocOrder order)
+ : m_Location(&loc),
+ m_EmptyFlag(empty_flag),
+ m_HasChanges(false),
+ m_EquivMode(CSeq_loc_I::eEquiv_none)
+{
+ x_ProcessLocation(loc);
+ if ( order == CSeq_loc_CI::eOrder_Positional && loc.IsReverseStrand() ) {
+ reverse(m_Ranges.begin(), m_Ranges.end());
+ }
+}
+
+
+void CSeq_loc_CI_Impl::x_SetId(SSeq_loc_CI_RangeInfo& info,
+ const CSeq_id& id)
+{
+ info.m_Id = &id;
+ info.m_IdHandle = CSeq_id_Handle::GetHandle(id);
+}
+
+
+template<class Container>
+static void s_ReserveMore(Container& cont, size_t add_size)
+{
+ if ( cont.size()+add_size > cont.capacity() ) {
+ cont.reserve(max(cont.size()+add_size, cont.capacity()*2));
+ }
+}
+
+
+void CSeq_loc_CI_Impl::x_ProcessLocation(const CSeq_loc& loc)
+{
+ switch ( loc.Which() ) {
+ case CSeq_loc::e_not_set:
+ /*
+ NCBI_THROW(CSeqLocException, eNotSet,
+ "CSeq_loc_CI: location is not set");
+ */
+ case CSeq_loc::e_Null:
+ case CSeq_loc::e_Empty:
+ {
+ if (m_EmptyFlag == CSeq_loc_CI::eEmpty_Allow) {
+ SSeq_loc_CI_RangeInfo info;
+ if (loc.Which() == CSeq_loc::e_Empty) {
+ x_SetId(info, loc.GetEmpty());
+ }
+ else {
+ info.m_Id.Reset(new CSeq_id);
+ }
+ info.m_Range = TRange::GetEmpty();
+ info.m_Loc = &loc;
+ m_Ranges.push_back(info);
+ }
+ return;
+ }
+ case CSeq_loc::e_Whole:
+ {
+ SSeq_loc_CI_RangeInfo info;
+ x_SetId(info, loc.GetWhole());
+ info.m_Range = TRange::GetWhole();
+ info.m_Loc = &loc;
+ m_Ranges.push_back(info);
+ return;
+ }
+ case CSeq_loc::e_Int:
+ {
+ x_ProcessInterval(loc.GetInt(), loc);
+ return;
+ }
+ case CSeq_loc::e_Pnt:
+ {
+ x_ProcessPoint(loc.GetPnt(), loc);
+ return;
+ }
+ case CSeq_loc::e_Packed_int:
+ {
+ const CPacked_seqint::Tdata& data = loc.GetPacked_int().Get();
+ s_ReserveMore(m_Ranges, data.size());
+ ITERATE ( CPacked_seqint::Tdata, ii, data ) {
+ x_ProcessInterval(**ii, loc);
+ }
+ return;
+ }
+ case CSeq_loc::e_Packed_pnt:
+ {
+ const CPacked_seqpnt& pack_pnt = loc.GetPacked_pnt();
+ s_ReserveMore(m_Ranges, pack_pnt.GetPoints().size());
+ SSeq_loc_CI_RangeInfo info;
+ x_SetId(info, pack_pnt.GetId());
+ if ( pack_pnt.IsSetStrand() ) {
+ info.SetStrand(pack_pnt.GetStrand());
+ }
+ if (pack_pnt.IsSetFuzz()) {
+ info.m_Fuzz.first = info.m_Fuzz.second = &pack_pnt.GetFuzz();
+ }
+ info.m_Loc = &loc;
+ ITERATE ( CPacked_seqpnt::TPoints, pi, pack_pnt.GetPoints() ) {
+ info.m_Range.Set(*pi, *pi);
+ m_Ranges.push_back(info);
+ }
+ return;
+ }
+ case CSeq_loc::e_Mix:
+ {
+ const CSeq_loc_mix::Tdata& data = loc.GetMix().Get();
+ s_ReserveMore(m_Ranges, data.size());
+ ITERATE(CSeq_loc_mix::Tdata, li, data) {
+ x_ProcessLocation(**li);
+ }
+ return;
+ }
+ case CSeq_loc::e_Equiv:
+ {
+ const CSeq_loc_equiv::Tdata& data = loc.GetEquiv().Get();
+ s_ReserveMore(m_Ranges, data.size());
+ SEquivSet eq_set;
+ size_t start = m_Ranges.size();
+ eq_set.m_StartIndex = start;
+ ITERATE(CSeq_loc_equiv::Tdata, li, data) {
+ size_t part_start = m_Ranges.size();
+ x_ProcessLocation(**li);
+ size_t part_end = m_Ranges.size();
+ if ( part_start != part_end ) {
+ // add only non-empty parts
+ eq_set.m_Parts.push_back(part_end-start);
+ }
+ }
+ if ( !eq_set.m_Parts.empty() ) {
+ // add only non-empty equiv sets
+ m_EquivSets.push_back(eq_set);
+ }
+ return;
+ }
+ case CSeq_loc::e_Bond:
+ {
+ const CSeq_bond& bond = loc.GetBond();
+ x_ProcessPoint(bond.GetA(), loc);
+ if ( bond.IsSetB() ) {
+ x_ProcessPoint(bond.GetB(), loc);
+ }
+ return;
+ }
+ default:
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc_CI: unsupported location type: "<<
+ loc.SelectionName(loc.Which()));
+ }
+}
+
+
+void CSeq_loc_CI_Impl::x_ProcessInterval(const CSeq_interval& seq_int,
+ const CSeq_loc& loc)
+{
+ _ASSERT(loc.Which() == CSeq_loc::e_Int ||
+ loc.Which() == CSeq_loc::e_Packed_int);
+ SSeq_loc_CI_RangeInfo info;
+ x_SetId(info, seq_int.GetId());
+ info.m_Range.Set(seq_int.GetFrom(), seq_int.GetTo());
+ if ( seq_int.IsSetStrand() ) {
+ info.SetStrand(seq_int.GetStrand());
+ }
+ info.m_Loc = &loc;
+ if (seq_int.IsSetFuzz_from()) {
+ info.m_Fuzz.first = &seq_int.GetFuzz_from();
+ }
+ if (seq_int.IsSetFuzz_to()) {
+ info.m_Fuzz.second = &seq_int.GetFuzz_to();
+ }
+ m_Ranges.push_back(info);
+}
+
+
+void CSeq_loc_CI_Impl::x_ProcessPoint(const CSeq_point& seq_pnt,
+ const CSeq_loc& loc)
+{
+ _ASSERT(loc.Which() == CSeq_loc::e_Pnt ||
+ loc.Which() == CSeq_loc::e_Bond);
+ SSeq_loc_CI_RangeInfo info;
+ x_SetId(info, seq_pnt.GetId());
+ info.m_Range.Set(seq_pnt.GetPoint(), seq_pnt.GetPoint());
+ if ( seq_pnt.IsSetStrand() ) {
+ info.SetStrand(seq_pnt.GetStrand());
+ }
+ info.m_Loc = &loc;
+ if (seq_pnt.IsSetFuzz()) {
+ info.m_Fuzz.first = info.m_Fuzz.second = &seq_pnt.GetFuzz();
+ }
+ m_Ranges.push_back(info);
+}
+
+
+size_t CSeq_loc_CI_Impl::HasEquivBreak(size_t begin,
+ size_t end) const
+{
+ size_t ret = end;
+ ITERATE ( TEquivSets, it, m_EquivSets ) {
+ const SEquivSet& eq_set = *it;
+ size_t eq_begin = eq_set.GetStartIndex();
+ size_t eq_end = eq_set.GetEndIndex();
+ if ( eq_end <= begin || eq_begin >= end ) {
+ // no overlaps
+ continue;
+ }
+ if ( eq_begin > begin && eq_begin < end ) {
+ // range overlaps with the beginning of the equiv set
+ ret = min(ret, eq_begin);
+ continue;
+ }
+ // otherwise the equiv starts before the range and ends somewhere
+ // after beginning of the range.
+ // so the first part that contains range's begin point is the one,
+ // end its end point is one of the breaking points we are looking for.
+ SEquivSet::TPart_CI part = eq_set.FindPartByElementIndex(begin);
+ ret = min(ret, eq_set.GetPartEndIndex(part));
+ }
+ // the first break point may be after the requested range
+ return ret == end? 0: ret;
+}
+
+
+const CSeq_loc_CI_Impl::SEquivSet*
+CSeq_loc_CI_Impl::FindInnerEquivSet(size_t begin,
+ size_t end,
+ const TUsedEquivs& used_equivs) const
+{
+ const SEquivSet* ret = 0;
+ ITERATE ( TEquivSets, it, m_EquivSets ) {
+ const SEquivSet& eq_set = *it;
+ size_t eq_begin = eq_set.GetStartIndex();
+ size_t eq_end = eq_set.GetEndIndex();
+ if ( eq_begin < begin || eq_end > end ) {
+ continue;
+ }
+ if ( used_equivs.find(&eq_set) != used_equivs.end() ) {
+ // already processed
+ continue;
+ }
+ if ( !ret || PByLevel()(ret, &eq_set) ) {
+ ret = &eq_set;
+ }
+ }
+ return ret;
+}
+
+
+void CSeq_loc_CI_Impl::DeleteRange(size_t idx)
+{
+ SetHasChanges();
+ m_Ranges.erase(m_Ranges.begin()+idx);
+ // update equiv sets
+ ERASE_ITERATE ( TEquivSets, it, m_EquivSets ) {
+ SEquivSet& eq_set = *it;
+ size_t start_index = eq_set.GetStartIndex();
+ if ( idx < start_index ) {
+ // shift whole equiv set because an element before is deleted
+ --eq_set.m_StartIndex;
+ continue;
+ }
+ size_t offset = idx - start_index;
+ size_t prev_offset = 0;
+ ERASE_ITERATE ( SEquivSet::TParts, it2, eq_set.m_Parts ) {
+ if ( offset < *it2 ) {
+ --*it2;
+ if ( *it2 == prev_offset ) {
+ VECTOR_ERASE(it2, eq_set.m_Parts);
+ }
+ else {
+ prev_offset = *it2;
+ }
+ }
+ }
+ if ( eq_set.GetElementsCount() == 0 ) {
+ VECTOR_ERASE(it, m_EquivSets);
+ }
+ }
+}
+
+
+static inline bool s_InsertExpands(size_t idx, size_t start, size_t end)
+{
+ return (idx > start && idx <= end) || (idx == start && idx == 0);
+}
+
+
+SSeq_loc_CI_RangeInfo& CSeq_loc_CI_Impl::InsertRange(size_t idx,
+ CSeq_loc::E_Choice type)
+{
+ SetHasChanges();
+ SSeq_loc_CI_RangeInfo& info =
+ *m_Ranges.insert(m_Ranges.begin()+idx, SSeq_loc_CI_RangeInfo());
+ CConstRef<CSeq_loc> loc;
+ // connect with previous or next part (if any)
+ if ( idx > 0 ) {
+ loc = m_Ranges[idx-1].m_Loc;
+ }
+ else if ( idx < m_Ranges.size() ) {
+ loc = m_Ranges[idx].m_Loc;
+ }
+ if ( loc ) {
+ // if type is incompatible with part it's connected to, do not connect
+ switch ( loc->Which() ) {
+ case CSeq_loc::e_Null:
+ case CSeq_loc::e_Empty:
+ case CSeq_loc::e_Whole:
+ case CSeq_loc::e_Pnt:
+ case CSeq_loc::e_Int:
+ loc = null;
+ break;
+ case CSeq_loc::e_Bond:
+ if ( type != CSeq_loc::e_Pnt ) {
+ loc = null;
+ }
+ break;
+ case CSeq_loc::e_Packed_pnt:
+ if ( type != CSeq_loc::e_Pnt ) {
+ loc = null;
+ }
+ break;
+ case CSeq_loc::e_Packed_int:
+ if ( type != CSeq_loc::e_Pnt || type != CSeq_loc::e_Int ) {
+ loc = null;
+ }
+ break;
+ default:
+ break;
+ }
+ }
+ info.m_Loc = loc;
+
+ SEquivSet* add_to_set_beg = 0;
+ vector<SEquivSet*> add_to_set_mid;
+ SEquivSet* add_to_set_end = 0;
+ // update existing equiv sets
+ NON_CONST_ITERATE ( TEquivSets, it, m_EquivSets ) {
+ SEquivSet& eq_set = *it;
+ size_t eq_start = eq_set.GetStartIndex();
+ size_t eq_end = eq_set.GetEndIndex();
+ if ( idx == eq_start &&
+ (GetEquivMode() == CSeq_loc_I::eEquiv_prepend ||
+ GetEquivMode() == CSeq_loc_I::eEquiv_new_part) ) {
+ // new element is inserted just before the equiv and will be added
+ // shift it for now
+ ++eq_set.m_StartIndex;
+ if ( !add_to_set_beg || PByLevel()(&eq_set, add_to_set_beg) ) {
+ add_to_set_beg = &eq_set;
+ }
+ }
+ else if ( idx == eq_end &&
+ (GetEquivMode() == CSeq_loc_I::eEquiv_append ||
+ GetEquivMode() == CSeq_loc_I::eEquiv_new_part) ) {
+ // new element is inserted just after the equiv and will be added
+ if ( !add_to_set_end || PByLevel()(&eq_set, add_to_set_end) ) {
+ add_to_set_end = &eq_set;
+ }
+ }
+ else if ( idx > eq_start && idx < eq_end ) {
+ // new element is completely within eq_set, so it will be added
+ add_to_set_mid.push_back(&eq_set);
+ }
+ else if ( idx <= eq_start ) {
+ // new element is completely before the equiv - shift right
+ ++eq_set.m_StartIndex;
+ }
+ }
+ sort(add_to_set_mid.begin(), add_to_set_mid.end(), PByLevel());
+ if ( add_to_set_beg ) {
+ // add at the beginning of the set
+ NON_CONST_ITERATE ( SEquivSet::TParts, it, add_to_set_beg->m_Parts ) {
+ ++*it;
+ }
+ if ( GetEquivMode() == CSeq_loc_I::eEquiv_new_part ) {
+ // add as a new part
+ add_to_set_beg->m_Parts.insert(add_to_set_beg->m_Parts.begin(), 1);
+ SetEquivMode(CSeq_loc_I::eEquiv_append);
+ }
+ }
+ else if ( add_to_set_end ) {
+ // add at the end of the set
+ if ( GetEquivMode() == CSeq_loc_I::eEquiv_new_part ) {
+ // add as a new part
+ add_to_set_end->m_Parts.push_back(add_to_set_end->m_Parts.back()+1);
+ SetEquivMode(CSeq_loc_I::eEquiv_append);
+ }
+ else {
+ ++add_to_set_end->m_Parts.back();
+ }
+ }
+ if ( GetEquivMode() == CSeq_loc_I::eEquiv_new_part &&
+ !add_to_set_mid.empty() ) {
+ SEquivSet& eq_set = **add_to_set_mid.begin();
+ add_to_set_mid.erase(add_to_set_mid.begin());
+ SEquivSet::TPart_I it = eq_set.FindPartByElementIndex(idx);
+ it = eq_set.m_Parts.insert(it, idx-eq_set.GetStartIndex()+1)+1;
+ for ( ; it != eq_set.m_Parts.end(); ++it ) {
+ ++*it;
+ }
+ SetEquivMode(CSeq_loc_I::eEquiv_append);
+ }
+ ITERATE ( vector<SEquivSet*>, set_it, add_to_set_mid ) {
+ SEquivSet& eq_set = **set_it;
+ SEquivSet::TPart_I it = eq_set.FindPartByElementIndex(idx);
+ for ( ; it != eq_set.m_Parts.end(); ++it ) {
+ ++*it;
+ }
+ }
+ // now all existing equivs were updated
+
+ if ( GetEquivMode() == CSeq_loc_I::eEquiv_new_equiv ) {
+ // create new equiv
+ SEquivSet eq_set;
+ eq_set.m_StartIndex = idx;
+ eq_set.m_Parts.push_back(1);
+ m_EquivSets.push_back(eq_set);
+ SetEquivMode(CSeq_loc_I::eEquiv_append);
+ }
+ return info;
+}
+
+
+bool CSeq_loc_CI_Impl::CanBePoint(const SSeq_loc_CI_RangeInfo& info) const
+{
+ if ( info.m_Range.GetLength() != 1 ) {
+ return false;
+ }
+ if ( info.m_Fuzz.first != info.m_Fuzz.second ) {
+ return false;
+ }
+ if ( !info.m_IdHandle ) {
+ return false;
+ }
+ return true;
+}
+
+
+bool CSeq_loc_CI_Impl::CanBeInterval(const SSeq_loc_CI_RangeInfo& info) const
+{
+ if ( info.m_Range.Empty() || info.m_Range.IsWhole() ) {
+ return false;
+ }
+ if ( !info.m_IdHandle ) {
+ return false;
+ }
+ return true;
+}
+
+
+bool CSeq_loc_CI_Impl::CanBeBond(size_t idx_begin, size_t idx_end) const
+{
+ size_t count = idx_end - idx_begin;
+ if ( count != 1 && count != 2 ) {
+ return false;
+ }
+ if ( !IsInBond(idx_begin) ) {
+ return false;
+ }
+ if ( GetBondRange(idx_begin) != make_pair(idx_begin, idx_end) ) {
+ return false;
+ }
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ _ASSERT(IsInBond(idx));
+ const SSeq_loc_CI_RangeInfo& info = m_Ranges[idx];
+ if ( !CanBePoint(info) ) {
+ return false;
+ }
+ }
+ if ( HasEquivBreak(idx_begin, idx_end) ) {
+ return false;
+ }
+ return true;
+}
+
+
+size_t CSeq_loc_CI_Impl::GetBondBegin(size_t idx) const
+{
+ const CSeq_loc* loc = m_Ranges[idx].m_Loc.GetPointerOrNull();
+ _ASSERT(loc && loc->IsBond());
+ while ( idx > 0 && m_Ranges[idx-1].m_Loc == loc ) {
+ --idx;
+ }
+ return idx;
+}
+
+
+size_t CSeq_loc_CI_Impl::GetBondEnd(size_t idx) const
+{
+ const CSeq_loc* loc = m_Ranges[idx].m_Loc.GetPointerOrNull();
+ _ASSERT(loc && loc->IsBond());
+ while ( idx < m_Ranges.size() && m_Ranges[idx].m_Loc == loc ) {
+ ++idx;
+ }
+ return idx;
+}
+
+
+void CSeq_loc_CI_Impl::RemoveBond(size_t idx)
+{
+ if ( !IsInBond(idx) ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::RemoveBond(): "
+ "there is no bond at current position");
+ }
+ pair<size_t, size_t> range = GetBondRange(idx);
+ SetHasChanges();
+ // unbond all parts
+ for ( idx = range.first; idx < range.second; ++idx ) {
+ x_BreakBond(idx);
+ }
+}
+
+
+void CSeq_loc_CI_Impl::MakeBondA(size_t idx)
+{
+ pair<size_t, size_t> range;
+ if ( IsInBond(idx) ) {
+ range = GetBondRange(idx);
+ }
+ size_t bond_len = range.second-range.first;
+ if ( bond_len > 0 ) {
+ // update existing bond
+ if ( idx != range.first ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::MakeBondA(): "
+ "current position is B part of other bond");
+ }
+ if ( bond_len == 1 ) {
+ // already bond with only part A
+ return;
+ }
+ SetHasChanges();
+ // unbond other parts
+ for ( idx = range.first+1; idx < range.second; ++idx ) {
+ x_BreakBond(idx);
+ }
+ }
+ else {
+ SetHasChanges();
+ x_CreateBond(idx);
+ }
+}
+
+
+void CSeq_loc_CI_Impl::MakeBondAB(size_t idx)
+{
+ if ( idx+1 >= m_Ranges.size() ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::MakeBondAB(): "
+ "no more parts in the location");
+ }
+ pair<size_t, size_t> range;
+ if ( IsInBond(idx) ) {
+ range = GetBondRange(idx);
+ }
+ size_t bond_len = range.second-range.first;
+ if ( bond_len > 0 ) {
+ // update existing bond
+ if ( idx != range.first ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::MakeBondAB(): "
+ "current position is B part of other bond");
+ }
+ if ( bond_len == 2 ) {
+ // already a bond with both parts A and B
+ return;
+ }
+ SetHasChanges();
+ if ( bond_len > 2 ) {
+ // unbond extra parts after B
+ for ( idx = range.first+2; idx < range.second; ++idx ) {
+ x_BreakBond(idx);
+ }
+ return;
+ }
+ x_AddBondPartB(idx);
+ }
+ else {
+ SetHasChanges();
+ x_CreateBond(idx);
+ x_AddBondPartB(idx);
+ }
+}
+
+
+void CSeq_loc_CI_Impl::MakeBondB(size_t idx)
+{
+ if ( idx == 0 ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::MakeBondB(): "
+ "no parts before current");
+ }
+ pair<size_t, size_t> range;
+ if ( IsInBond(idx) ) {
+ range = GetBondRange(idx);
+ }
+ else if ( IsInBond(idx-1) ) {
+ range = GetBondRange(idx-1);
+ }
+ size_t bond_len = range.second-range.first;
+ if ( bond_len > 0 ) {
+ // update existing bond
+ if ( range.first != idx + 1 ) {
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ "CSeq_loc_I::MakeBondB(): "
+ "current position is not a B part of other bond");
+ }
+ if ( bond_len == 2 ) {
+ // already a bond with both parts A and B
+ return;
+ }
+ SetHasChanges();
+ if ( bond_len > 2 ) {
+ // unbond extra parts after B
+ for ( idx = range.first+2; idx < range.second; ++idx ) {
+ x_BreakBond(idx);
+ }
+ return;
+ }
+ _ASSERT(bond_len == 1);
+ x_AddBondPartB(idx);
+ }
+ else {
+ SetHasChanges();
+ x_CreateBond(idx);
+ x_AddBondPartB(idx);
+ }
+}
+
+
+CRef<CSeq_loc> CSeq_loc_CI_Impl::MakeLocBond(size_t idx_begin,
+ size_t idx_end) const
+{
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ loc->SetBond().SetA(*MakePoint(m_Ranges[idx_begin]));
+ if ( idx_begin+1 < idx_end ) {
+ loc->SetBond().SetB(*MakePoint(m_Ranges[idx_begin+1]));
+ }
+ return loc;
+}
+
+
+static
+CRef<CSeq_id> MakeId(const SSeq_loc_CI_RangeInfo& info)
+{
+ if ( !info.m_IdHandle ) {
+ NCBI_THROW(CSeqLocException, eNotSet,
+ "CSeq_loc_I: part id is null");
+ }
+ return Ref(&const_cast<CSeq_id&>(*info.m_Id));
+}
+
+
+CRef<CInt_fuzz> CSeq_loc_CI_Impl::MakeFuzz(const CInt_fuzz& fuzz) const
+{
+ return Ref(&const_cast<CInt_fuzz&>(fuzz));
+}
+
+
+void CSeq_loc_CI_Impl::UpdatePoint(CSeq_point& pnt,
+ const SSeq_loc_CI_RangeInfo& info) const
+{
+ pnt.SetId(*MakeId(info));
+ pnt.SetPoint(info.m_Range.GetFrom());
+ if ( info.m_IsSetStrand ) {
+ pnt.SetStrand(info.m_Strand);
+ }
+ else {
+ pnt.ResetStrand();
+ }
+ if ( info.m_Fuzz.first ) {
+ pnt.SetFuzz(*MakeFuzz(*info.m_Fuzz.first));
+ }
+ else {
+ pnt.ResetFuzz();
+ }
+}
+
+
+void CSeq_loc_CI_Impl::SetPoint(SSeq_loc_CI_RangeInfo& info)
+{
+ info.m_Loc = MakeLocPoint(info);
+}
+
+
+CRef<CSeq_point>
+CSeq_loc_CI_Impl::MakePoint(const SSeq_loc_CI_RangeInfo& info) const
+{
+ CRef<CSeq_point> seq_pnt(new CSeq_point);
+ UpdatePoint(*seq_pnt, info);
+ return seq_pnt;
+}
+
+
+CRef<CSeq_loc>
+CSeq_loc_CI_Impl::MakeLocPoint(const SSeq_loc_CI_RangeInfo& info) const
+{
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ loc->SetPnt(*MakePoint(info));
+ return loc;
+}
+
+
+void CSeq_loc_CI_Impl::UpdatePoint(SSeq_loc_CI_RangeInfo& info)
+{
+ SetHasChanges();
+ if ( WasPoint(info) ) {
+ UpdatePoint(const_cast<CSeq_point&>(info.m_Loc->GetPnt()), info);
+ }
+}
+
+
+void CSeq_loc_CI_Impl::UpdateLoc(SSeq_loc_CI_RangeInfo& info)
+{
+ SetHasChanges();
+ if ( info.m_Loc ) {
+ switch ( info.m_Loc->Which() ) {
+ case CSeq_loc::e_Whole:
+ case CSeq_loc::e_Empty:
+ case CSeq_loc::e_Null:
+ case CSeq_loc::e_Int:
+ case CSeq_loc::e_Pnt:
+ info.m_Loc = null;
+ break;
+ default:
+ break;
+ }
+ }
+}
+
+
+CRef<CSeq_interval>
+CSeq_loc_CI_Impl::MakeInterval(const SSeq_loc_CI_RangeInfo& info) const
+{
+ CRef<CSeq_interval> seq_int(new CSeq_interval);
+ seq_int->SetId(*MakeId(info));
+ seq_int->SetFrom(info.m_Range.GetFrom());
+ seq_int->SetTo(info.m_Range.GetTo());
+ if ( info.m_IsSetStrand ) {
+ seq_int->SetStrand(info.m_Strand);
+ }
+ if ( info.m_Fuzz.first ) {
+ seq_int->SetFuzz_from(*MakeFuzz(*info.m_Fuzz.first));
+ }
+ if ( info.m_Fuzz.second ) {
+ seq_int->SetFuzz_to(*MakeFuzz(*info.m_Fuzz.second));
+ }
+ return seq_int;
+}
+
+
+CRef<CSeq_loc>
+CSeq_loc_CI_Impl::MakeLocInterval(const SSeq_loc_CI_RangeInfo& info) const
+{
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ loc->SetInt(*MakeInterval(info));
+ return loc;
+}
+
+
+CRef<CSeq_loc>
+CSeq_loc_CI_Impl::MakeLocOther(const SSeq_loc_CI_RangeInfo& info) const
+{
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ if ( info.m_Range.IsWhole() ) {
+ loc->SetWhole(*MakeId(info));
+ }
+ else {
+ if ( !info.m_Range.Empty() ) {
+ NCBI_THROW(CSeqLocException, eOtherError,
+ "CSeq_loc_I::MakeSeq_loc(): "
+ "cannot determine type of loc part");
+ }
+ if ( info.m_IdHandle ) {
+ loc->SetEmpty(*MakeId(info));
+ }
+ else {
+ loc->SetNull();
+ }
+ }
+ return loc;
+}
+
+
+CRef<CSeq_loc>
+CSeq_loc_CI_Impl::MakeRangeLoc(const SSeq_loc_CI_RangeInfo& info) const
+{
+ if ( ShouldBePoint(info) && CanBePoint(info) ) {
+ return MakeLocPoint(info);
+ }
+ else if ( info.m_Range.IsWhole() || info.m_Range.Empty() ) {
+ return MakeLocOther(info);
+ }
+ else {
+ return MakeLocInterval(info);
+ }
+}
+
+
+bool CSeq_loc_CI_Impl::CanBePacked_pnt(size_t idx_begin,
+ size_t idx_end) const
+{
+ _ASSERT(idx_end >= idx_begin);
+ if ( idx_end == idx_begin ) {
+ return false;
+ }
+ const SSeq_loc_CI_RangeInfo& info0 = m_Ranges[idx_begin];
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ if ( IsInBond(idx) ) {
+ return false;
+ }
+ const SSeq_loc_CI_RangeInfo& info = m_Ranges[idx];
+ if ( !CanBePoint(m_Ranges[idx]) ) {
+ return false;
+ }
+ if ( idx != idx_begin ) {
+ if ( info.m_IdHandle != info0.m_IdHandle ) {
+ return false;
+ }
+ if ( info.m_IsSetStrand != info0.m_IsSetStrand ) {
+ return false;
+ }
+ if ( info0.m_IsSetStrand && info.m_Strand != info0.m_Strand ) {
+ return false;
+ }
+ if ( info.m_Fuzz.first != info0.m_Fuzz.first ) {
+ return false;
+ }
+ }
+ }
+ if ( HasEquivBreak(idx_begin, idx_end) ) {
+ return false;
+ }
+ return true;
+}
+
+
+bool CSeq_loc_CI_Impl::CanBePacked_int(size_t idx_begin,
+ size_t idx_end) const
+{
+ _ASSERT(idx_end >= idx_begin);
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ if ( IsInBond(idx) ) {
+ return false;
+ }
+ if ( !CanBeInterval(idx) ) {
+ return false;
+ }
+ }
+ if ( HasEquivBreak(idx_begin, idx_end) ) {
+ return false;
+ }
+ return true;
+}
+
+
+CRef<CSeq_loc> CSeq_loc_CI_Impl::MakeLocPacked_pnt(size_t idx_begin,
+ size_t idx_end) const
+{
+ const SSeq_loc_CI_RangeInfo& info0 = m_Ranges[idx_begin];
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ CPacked_seqpnt& pnts = loc->SetPacked_pnt();
+ pnts.SetId(*MakeId(info0));
+ if ( info0.m_IsSetStrand ) {
+ pnts.SetStrand(info0.m_Strand);
+ }
+ if ( info0.m_Fuzz.first ) {
+ pnts.SetFuzz(*MakeFuzz(*info0.m_Fuzz.first));
+ }
+ pnts.SetPoints().reserve(idx_end-idx_begin);
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ const SSeq_loc_CI_RangeInfo& info = m_Ranges[idx];
+ pnts.SetPoints().push_back(info.m_Range.GetFrom());
+ }
+ return loc;
+}
+
+
+CRef<CSeq_loc> CSeq_loc_CI_Impl::MakeLocPacked_int(size_t idx_begin,
+ size_t idx_end) const
+{
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ CPacked_seqint::Tdata& ints = loc->SetPacked_int().Set();
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ ints.push_back(MakeInterval(m_Ranges[idx]));
+ }
+ return loc;
+}
+
+
+static
+void AddLoc(CRef<CSeq_loc>& loc, CRef<CSeq_loc> loc2)
+{
+ if ( !loc ) {
+ loc = loc2;
+ return;
+ }
+ if ( !loc->IsMix() ) {
+ CRef<CSeq_loc> loc1 = loc;
+ loc = new CSeq_loc;
+ loc->SetMix().Set().push_back(loc1);
+ }
+ loc->SetMix().Set().push_back(loc2);
+}
+
+
+CRef<CSeq_loc> CSeq_loc_CI_Impl::MakeLoc(size_t idx_begin,
+ size_t idx_end,
+ CSeq_loc_I::EMakeType make_type,
+ TUsedEquivs& used_equivs) const
+{
+ if ( const SEquivSet* eq_set = FindInnerEquivSet(idx_begin, idx_end, used_equivs) ) {
+ used_equivs.insert(eq_set);
+ size_t idx = eq_set->GetStartIndex();
+ CRef<CSeq_loc> loc;
+ if ( idx > idx_begin ) {
+ loc = MakeLoc(idx_begin, idx, make_type, used_equivs);
+ }
+ CRef<CSeq_loc> loc2(new CSeq_loc);
+ CSeq_loc_equiv& equiv = loc2->SetEquiv();
+ ITERATE ( SEquivSet::TParts, it, eq_set->m_Parts ) {
+ size_t part_end = eq_set->GetPartEndIndex(it);
+ CRef<CSeq_loc> part_loc =
+ MakeLoc(idx, part_end, make_type, used_equivs);
+ equiv.Set().push_back(part_loc);
+ idx = part_end;
+ }
+ AddLoc(loc, loc2);
+ if ( idx < idx_end ) {
+ loc2 = MakeLoc(idx, idx_end, make_type, used_equivs);
+ if ( loc2->IsMix() ) {
+ ITERATE ( CSeq_loc_mix::Tdata, it, loc2->GetMix().Get() ) {
+ AddLoc(loc, *it);
+ }
+ }
+ else {
+ AddLoc(loc, loc2);
+ }
+ }
+ return loc;
+ }
+
+ if ( HasEquivBreak(idx_begin, idx_end) ) {
+ NCBI_THROW(CSeqLocException, eBadLocation,
+ "CSeq_loc_I::MakeSeq_loc: equiv set overlaps with range");
+ }
+
+ if ( idx_begin == idx_end ) {
+ CRef<CSeq_loc> loc(new CSeq_loc);
+ loc->SetMix();
+ return loc;
+ }
+
+ // check bonds
+ const SSeq_loc_CI_RangeInfo& info0 = m_Ranges[idx_begin];
+ if ( make_type == CSeq_loc_I::eMake_PreserveType && info0.m_Loc ) {
+ // try to restore original CSeq_loc type
+ if ( info0.m_Loc->IsPacked_pnt() &&
+ CanBePacked_pnt(idx_begin, idx_end) ) {
+ return MakeLocPacked_pnt(idx_begin, idx_end);
+ }
+ if ( info0.m_Loc->IsPacked_int() &&
+ CanBePacked_int(idx_begin, idx_end) ) {
+ return MakeLocPacked_int(idx_begin, idx_end);
+ }
+ }
+ if ( make_type == CSeq_loc_I::eMake_CompactType &&
+ idx_end - idx_begin > 1 ) {
+ // try to make compact variants
+ if ( CanBePacked_pnt(idx_begin, idx_end) ) {
+ return MakeLocPacked_pnt(idx_begin, idx_end);
+ }
+ if ( CanBePacked_int(idx_begin, idx_end) ) {
+ return MakeLocPacked_int(idx_begin, idx_end);
+ }
+ }
+
+ CRef<CSeq_loc> loc;
+ for ( size_t idx = idx_begin; idx < idx_end; ++idx ) {
+ if ( IsInBond(idx) ) {
+ pair<size_t, size_t> range = GetBondRange(idx);
+ if ( range.first < idx || range.second > idx_end ||
+ !CanBeBond(range.first, range.second) ) {
+ NCBI_THROW(CSeqLocException, eIncomatible,
+ "CSeq_loc_I::MakeSeq_loc: "
+ "invalid bond");
+ }
+ AddLoc(loc, MakeLocBond(range.first, range.second));
+ idx = range.second-1;
+ continue;
+ }
+ const SSeq_loc_CI_RangeInfo& info = m_Ranges[idx];
+ if ( make_type == CSeq_loc_I::eMake_PreserveType ) {
+ if ( WasPoint(info) && CanBePoint(info) ) {
+ AddLoc(loc, MakeLocPoint(info));
+ continue;
+ }
+ if ( (!info.m_Loc || info.m_Loc->IsInt()) &&
+ CanBeInterval(info) ) {
+ AddLoc(loc, MakeLocInterval(info));
+ continue;
+ }
+ }
+ if ( CanBePoint(info) ) {
+ AddLoc(loc, MakeLocPoint(info));
+ continue;
+ }
+ if ( CanBeInterval(info) ) {
+ AddLoc(loc, MakeLocInterval(info));
+ continue;
+ }
+ AddLoc(loc, MakeLocOther(info));
+ }
+ if ( !loc ) {
+ loc = new CSeq_loc;
+ }
+ return loc;
+}
+
+
+CRef<CSeq_loc> CSeq_loc_CI_Impl::MakeLoc(CSeq_loc_I::EMakeType make_type) const
+{
+ TUsedEquivs used_equivs;
+ return MakeLoc(0, m_Ranges.size(), make_type, used_equivs);
+}
+
+
+CSeq_loc_CI::CSeq_loc_CI(void)
+ : m_Impl(new CSeq_loc_CI_Impl),
+ m_Index(0)
+{
+}
+
+
+CSeq_loc_CI::CSeq_loc_CI(const CSeq_loc& loc,
+ EEmptyFlag empty_flag,
+ ESeqLocOrder order)
+ : m_Impl(new CSeq_loc_CI_Impl(loc, empty_flag, order)),
+ m_Index(0)
+{
+}
+
+
+CSeq_loc_CI::CSeq_loc_CI(const CSeq_loc_CI& iter, size_t pos)
+ : m_Impl(iter.m_Impl),
+ m_Index(0)
+{
+ SetPos(pos);
+}
+
+
+CSeq_loc_CI::~CSeq_loc_CI()
+{
+}
+
+
+CSeq_loc_CI::CSeq_loc_CI(const CSeq_loc_CI& iter)
+ : m_Impl(iter.m_Impl),
+ m_Index(iter.m_Index)
+{
+}
+
+
+CSeq_loc_CI& CSeq_loc_CI::operator= (const CSeq_loc_CI& iter)
+{
+ m_Impl = iter.m_Impl;
+ m_Index = iter.m_Index;
+ return *this;
+}
+
+
+bool CSeq_loc_CI::operator== (const CSeq_loc_CI& iter) const
+{
+ // Check if both are at end.
+ bool is_end = m_Impl->IsEnd(m_Index);
+ if ( iter.m_Impl->IsEnd(iter.m_Index) ) {
+ return is_end;
+ }
+ else {
+ return !is_end && m_Impl == iter.m_Impl && m_Index == iter.m_Index;
+ }
+}
+
+
+bool CSeq_loc_CI::operator!= (const CSeq_loc_CI& iter) const
+{
+ return !(*this == iter);
+}
+
+
+bool CSeq_loc_CI::IsInBond(void) const
+{
+ x_CheckValid("IsInBond()");
+ return m_Impl->IsInBond(m_Index);
+}
+
+
+bool CSeq_loc_CI::IsBondA(void) const
+{
+ x_CheckValid("IsBondA()");
+ return m_Impl->IsBondPartA(m_Index);
+}
+
+
+bool CSeq_loc_CI::IsBondB(void) const
+{
+ x_CheckValid("IsBondB()");
+ return m_Impl->IsBondPartB(m_Index);
+}
+
+
+pair<CSeq_loc_CI, CSeq_loc_CI>
+CSeq_loc_CI::GetBondRange(void) const
+{
+ x_CheckValid("GetBondRange()");
+ pair<size_t, size_t> indexes = m_Impl->GetBondRange(m_Index);
+ return make_pair(CSeq_loc_CI(*this, indexes.first),
+ CSeq_loc_CI(*this, indexes.second));
+}
+
+
+bool CSeq_loc_CI::HasEquivSets(void) const
+{
+ return m_Impl->HasEquivSets();
+}
+
+
+bool CSeq_loc_CI::IsInEquivSet(void) const
+{
+ x_CheckValid("IsInEquivSet()");
+ return m_Impl->IsInEquivSet(m_Index);
+}
+
+
+size_t CSeq_loc_CI::GetEquivSetsCount(void) const
+{
+ x_CheckValid("GetEquivSetsCount()");
+ return m_Impl->GetEquivSetsCount(m_Index);
+}
+
+
+pair<CSeq_loc_CI, CSeq_loc_CI>
+CSeq_loc_CI::GetEquivSetRange(size_t level) const
+{
+ x_CheckValid("GetEquivSetRange()");
+ pair<size_t, size_t> indexes = m_Impl->GetEquivSetRange(m_Index, level);
+ return make_pair(CSeq_loc_CI(*this, indexes.first),
+ CSeq_loc_CI(*this, indexes.second));
+}
+
+
+pair<CSeq_loc_CI, CSeq_loc_CI>
+CSeq_loc_CI::GetEquivPartRange(size_t level) const
+{
+ x_CheckValid("GetEquivPartRange()");
+ pair<size_t, size_t> indexes = m_Impl->GetEquivPartRange(m_Index, level);
+ return make_pair(CSeq_loc_CI(*this, indexes.first),
+ CSeq_loc_CI(*this, indexes.second));
+}
+
+
+const CSeq_loc& CSeq_loc_CI::GetSeq_loc(void) const
+{
+ return GetEmbeddingSeq_loc();
+}
+
+
+const CSeq_loc& CSeq_loc_CI::GetEmbeddingSeq_loc(void) const
+{
+ x_CheckValid("GetEmbeddingSeq_loc()");
+ CConstRef<CSeq_loc> loc = x_GetRangeInfo().m_Loc;
+ if ( !loc ) {
+ NCBI_THROW(CSeqLocException, eNotSet,
+ "CSeq_loc_CI::GetSeq_loc(): NULL seq-loc");
+ }
+ return *loc;
+}
+
+
+CConstRef<CSeq_loc> CSeq_loc_CI::GetRangeAsSeq_loc(void) const
+{
+ x_CheckValid("GetRangeAsSeq_loc()");
+ const SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Loc ) {
+ switch ( info.m_Loc->Which() ) {
+ // Single-range, empty or whole seq-loc can be used as-is.
+ case CSeq_loc::e_not_set:
+ case CSeq_loc::e_Null:
+ case CSeq_loc::e_Empty:
+ case CSeq_loc::e_Whole:
+ case CSeq_loc::e_Int:
+ case CSeq_loc::e_Pnt:
+ return info.m_Loc;
+ default:
+ break;
+ }
+ }
+ // Create a new seq-loc for the current range.
+ CRef<CSeq_loc> loc = m_Impl->MakeRangeLoc(info);
+ return ConstRef(loc.Release());
+}
+
+
+bool CSeq_loc_CI::x_IsValid(void) const
+{
+ return m_Impl && m_Index < m_Impl->GetRanges().size();
+}
+
+
+void CSeq_loc_CI::x_ThrowNotValid(const char* where) const
+{
+ NCBI_THROW_FMT(CSeqLocException, eBadIterator,
+ x_GetIteratorType() << "::" << where << ": "
+ "iterator is not valid");
+}
+
+
+const char* CSeq_loc_CI::x_GetIteratorType(void) const
+{
+ return "CSeq_loc_CI";
+}
+
+
+const SSeq_loc_CI_RangeInfo& CSeq_loc_CI::x_GetRangeInfo(void) const
+{
+ // The index validity must be checked by the caller.
+ return m_Impl->GetRanges()[m_Index];
+}
+
+
+size_t CSeq_loc_CI::GetSize(void) const
+{
+ return m_Impl->GetRanges().size();
+}
+
+
+void CSeq_loc_CI::SetPos(size_t pos)
+{
+ if ( pos > GetSize() ) {
+ NCBI_THROW_FMT(CSeqLocException, eOtherError,
+ x_GetIteratorType() << "::SetPos(): "
+ "position is too big: "<<pos<<" > "<<GetSize());
+ }
+ m_Index = pos;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////
+// CSeq_loc_I
+
+CSeq_loc_I::CSeq_loc_I(void)
+{
+}
+
+
+CSeq_loc_I::CSeq_loc_I(CSeq_loc& loc)
+ : CSeq_loc_CI(loc, eEmpty_Allow, eOrder_Biological)
+{
+}
+
+
+CSeq_loc_I::CSeq_loc_I(const CSeq_loc_I& iter, size_t pos)
+ : CSeq_loc_CI(iter)
+{
+ SetPos(pos);
+}
+
+
+CSeq_loc_I::~CSeq_loc_I()
+{
+}
+
+
+bool CSeq_loc_I::x_IsValidForInsert(void) const
+{
+ return m_Impl && m_Index <= m_Impl->GetRanges().size();
+}
+
+
+const char* CSeq_loc_I::x_GetIteratorType(void) const
+{
+ return "CSeq_loc_I";
+}
+
+
+SSeq_loc_CI_RangeInfo& CSeq_loc_I::x_GetRangeInfo(void)
+{
+ // The index validity must be checked by the caller.
+ return m_Impl->GetRanges()[m_Index];
+}
+
+
+void CSeq_loc_I::x_SetSeq_id_Handle(SSeq_loc_CI_RangeInfo& info,
+ const CSeq_id_Handle& id)
+{
+ info.m_Id = id.GetSeqId();
+ info.m_IdHandle = id;
+}
+
+
+bool CSeq_loc_I::HasChanges(void) const
+{
+ return m_Impl->HasChanges();
+}
+
+
+CSeq_loc_I::EEquivMode CSeq_loc_I::GetEquivMode(void) const
+{
+ return m_Impl->GetEquivMode();
}
-TSeqPos CSeq_loc::GetCircularLength(TSeqPos seq_len) const
+void CSeq_loc_I::SetEquivMode(EEquivMode mode)
{
- if (seq_len == kInvalidSeqPos) {
- return GetTotalRange().GetLength();
- }
- TSeqPos start = GetStart(eExtreme_Biological);
- TSeqPos stop = GetStop (eExtreme_Biological);
- bool minus = IsReverseStrand();
+ m_Impl->SetEquivMode(mode);
+}
- if (start < stop) {
- return minus ? (seq_len - stop + start + 1) : (stop - start + 1);
- } else {
- return minus ? (start - stop + 1) : (seq_len - start + stop + 1);
- }
+
+void CSeq_loc_I::Delete(void)
+{
+ x_CheckValid("Delete()");
+ m_Impl->DeleteRange(m_Index);
}
-CSeq_loc::const_iterator CSeq_loc::begin(void) const
+CSeq_loc_I CSeq_loc_I::InsertNull(void)
{
- return CSeq_loc_CI(*this);
+ x_CheckValidForInsert("InsertNull()");
+ m_Impl->InsertRange(m_Index, CSeq_loc::e_Null);
+ return CSeq_loc_I(*this, m_Index++);
}
-CSeq_loc::const_iterator CSeq_loc::end(void) const
+CSeq_loc_I CSeq_loc_I::InsertEmpty(const CSeq_id_Handle& id)
{
- static CSeq_loc_CI s_Seq_loc_CI_end;
- return s_Seq_loc_CI_end;
+ x_CheckValidForInsert("InsertEmpty()");
+ SSeq_loc_CI_RangeInfo& info =
+ m_Impl->InsertRange(m_Index, CSeq_loc::e_Empty);
+ x_SetSeq_id_Handle(info, id);
+ return CSeq_loc_I(*this, m_Index++);
}
-// CSeq_loc_CI implementation
+CSeq_loc_I CSeq_loc_I::InsertWhole(const CSeq_id_Handle& id)
+{
+ x_CheckValidForInsert("InsertWhole()");
+ SSeq_loc_CI_RangeInfo& info =
+ m_Impl->InsertRange(m_Index, CSeq_loc::e_Whole);
+ x_SetSeq_id_Handle(info, id);
+ info.m_Range = TRange::GetWhole();
+ return CSeq_loc_I(*this, m_Index++);
+}
-class CSeq_loc_CI_Impl : public CObject
+
+CSeq_loc_I CSeq_loc_I::InsertPoint(const CSeq_id_Handle& id,
+ TSeqPos pos,
+ ENa_strand strand)
{
-public:
- CSeq_loc_CI_Impl(void);
- CSeq_loc_CI_Impl(const CSeq_loc& loc,
- CSeq_loc_CI::EEmptyFlag empty_flag,
- CSeq_loc_CI::ESeqLocOrder order);
- virtual ~CSeq_loc_CI_Impl(void) {}
+ x_CheckValidForInsert("InsertPoint()");
+ SSeq_loc_CI_RangeInfo& info =
+ m_Impl->InsertRange(m_Index, CSeq_loc::e_Pnt);
+ x_SetSeq_id_Handle(info, id);
+ info.m_Range.SetFrom(pos).SetLength(1);
+ if ( strand != eNa_strand_unknown ) {
+ info.SetStrand(strand);
+ }
+ m_Impl->SetPoint(info);
+ return CSeq_loc_I(*this, m_Index++);
+}
- typedef SSeq_loc_CI_RangeInfo::TRange TRange;
- typedef SSeq_loc_CI_RangeInfo::TRangeList TRanges;
- const TRanges& GetRanges(void) const { return m_Ranges; }
+CSeq_loc_I CSeq_loc_I::InsertInterval(const CSeq_id_Handle& id,
+ const TRange& range,
+ ENa_strand strand)
+{
+ x_CheckValidForInsert("InsertInterval()");
+ SSeq_loc_CI_RangeInfo& info =
+ m_Impl->InsertRange(m_Index, CSeq_loc::e_Int);
+ x_SetSeq_id_Handle(info, id);
+ info.m_Range = range;
+ if ( strand != eNa_strand_unknown ) {
+ info.SetStrand(strand);
+ }
+ if ( !range.IsWhole() && !range.Empty() ) {
+ info.m_Loc = m_Impl->MakeLocInterval(info);
+ }
+ return CSeq_loc_I(*this, m_Index++);
+}
- bool IsEnd(size_t idx) const { return idx >= m_Ranges.size(); }
-private:
- // Never copy this object
- CSeq_loc_CI_Impl(const CSeq_loc_CI_Impl&);
- CSeq_loc_CI_Impl& operator=(const CSeq_loc_CI_Impl&);
+void CSeq_loc_I::SetSeq_id_Handle(const CSeq_id_Handle& id)
+{
+ x_CheckValid("SetSeq_id_Handle()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_IdHandle != id ) {
+ x_SetSeq_id_Handle(info, id);
+ m_Impl->UpdatePoint(info);
+ }
+}
- // Process the location, fill the list
- void x_ProcessLocation(const CSeq_loc& loc);
- // Prevent seq-loc destruction
- CConstRef<CSeq_loc> m_Location;
- // List of intervals
- TRanges m_Ranges;
- // Empty locations processing option
- CSeq_loc_CI::EEmptyFlag m_EmptyFlag;
-};
+void CSeq_loc_I::SetRange(const TRange& range)
+{
+ x_CheckValid("SetRange()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Range != range ) {
+ info.m_Range = range;
+ m_Impl->UpdateLoc(info);
+ }
+}
-CSeq_loc_CI_Impl::CSeq_loc_CI_Impl(void)
+void CSeq_loc_I::SetFrom(TSeqPos from)
{
+ x_CheckValid("SetFrom()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Range.GetFrom() != from ) {
+ info.m_Range.SetFrom(from);
+ m_Impl->UpdateLoc(info);
+ }
}
-CSeq_loc_CI_Impl::CSeq_loc_CI_Impl(const CSeq_loc& loc,
- CSeq_loc_CI::EEmptyFlag empty_flag,
- CSeq_loc_CI::ESeqLocOrder order)
- : m_Location(&loc),
- m_EmptyFlag(empty_flag)
+void CSeq_loc_I::SetTo(TSeqPos to)
{
- x_ProcessLocation(loc);
- if ( order == CSeq_loc_CI::eOrder_Positional && loc.IsReverseStrand() ) {
- reverse(m_Ranges.begin(), m_Ranges.end());
+ x_CheckValid("SetTo()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Range.GetTo() != to ) {
+ info.m_Range.SetTo(to);
+ m_Impl->UpdateLoc(info);
}
}
-void CSeq_loc_CI_Impl::x_ProcessLocation(const CSeq_loc& loc)
+void CSeq_loc_I::SetPoint(TSeqPos pos)
{
- switch ( loc.Which() ) {
- case CSeq_loc::e_not_set:
- case CSeq_loc::e_Null:
- case CSeq_loc::e_Empty:
- {
- if (m_EmptyFlag == CSeq_loc_CI::eEmpty_Allow) {
- SSeq_loc_CI_RangeInfo info;
- if (loc.Which() == CSeq_loc::e_Empty) {
- info.m_Id = &loc.GetEmpty();
- }
- else {
- info.m_Id.Reset(new CSeq_id);
- }
- info.m_Range = TRange::GetEmpty();
- info.m_Loc = &loc;
- m_Ranges.push_back(info);
- }
- return;
- }
- case CSeq_loc::e_Whole:
- {
- SSeq_loc_CI_RangeInfo info;
- info.m_Id = &loc.GetWhole();
- info.m_Range = TRange::GetWhole();
- info.m_Loc = &loc;
- m_Ranges.push_back(info);
- return;
- }
- case CSeq_loc::e_Int:
- {
- const CSeq_interval& seq_int = loc.GetInt();
- SSeq_loc_CI_RangeInfo info;
- info.m_Id = &seq_int.GetId();
- info.m_Range.Set(seq_int.GetFrom(), seq_int.GetTo());
- if ( seq_int.IsSetStrand() ) {
- info.SetStrand(seq_int.GetStrand());
- }
- info.m_Loc = &loc;
- if (seq_int.IsSetFuzz_from()) {
- info.m_Fuzz.first = &seq_int.GetFuzz_from();
- }
- if (seq_int.IsSetFuzz_to()) {
- info.m_Fuzz.second = &seq_int.GetFuzz_to();
- }
- m_Ranges.push_back(info);
- return;
- }
- case CSeq_loc::e_Pnt:
- {
- const CSeq_point& pnt = loc.GetPnt();
- SSeq_loc_CI_RangeInfo info;
- info.m_Id = &pnt.GetId();
- info.m_Range.Set(pnt.GetPoint(), pnt.GetPoint());
- if ( pnt.IsSetStrand() ) {
- info.SetStrand(pnt.GetStrand());
- }
- info.m_Loc = &loc;
- if (pnt.IsSetFuzz()) {
- info.m_Fuzz.first = info.m_Fuzz.second = &pnt.GetFuzz();
- }
- m_Ranges.push_back(info);
- return;
- }
- case CSeq_loc::e_Packed_int:
- {
- const CPacked_seqint::Tdata& data = loc.GetPacked_int().Get();
- m_Ranges.reserve(m_Ranges.size() + data.size());
- ITERATE ( CPacked_seqint::Tdata, ii, data ) {
- const CSeq_interval& seq_int = **ii;
- SSeq_loc_CI_RangeInfo info;
- info.m_Id = &seq_int.GetId();
- info.m_Range.Set(seq_int.GetFrom(), seq_int.GetTo());
- if ( seq_int.IsSetStrand() ) {
- info.SetStrand(seq_int.GetStrand());
- }
- info.m_Loc = &loc;
- if (seq_int.IsSetFuzz_from()) {
- info.m_Fuzz.first = &seq_int.GetFuzz_from();
- }
- if (seq_int.IsSetFuzz_to()) {
- info.m_Fuzz.second = &seq_int.GetFuzz_to();
- }
- m_Ranges.push_back(info);
- }
- return;
+ x_CheckValid("SetPoint()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( !m_Impl->WasPoint(info) || info.m_Range != TRange(pos, pos) ) {
+ info.m_Range = TRange(pos, pos);
+ if ( m_Impl->WasPoint(info) ) {
+ m_Impl->UpdatePoint(info);
}
- case CSeq_loc::e_Packed_pnt:
- {
- const CPacked_seqpnt& pack_pnt = loc.GetPacked_pnt();
- m_Ranges.reserve(m_Ranges.size() + pack_pnt.GetPoints().size());
- SSeq_loc_CI_RangeInfo info;
- info.m_Id = &pack_pnt.GetId();
- if ( pack_pnt.IsSetStrand() ) {
- info.SetStrand(pack_pnt.GetStrand());
- }
- if (pack_pnt.IsSetFuzz()) {
- info.m_Fuzz.first = info.m_Fuzz.second = &pack_pnt.GetFuzz();
- }
- info.m_Loc = &loc;
- ITERATE ( CPacked_seqpnt::TPoints, pi, pack_pnt.GetPoints() ) {
- info.m_Range.Set(*pi, *pi);
- m_Ranges.push_back(info);
- }
- return;
- }
- case CSeq_loc::e_Mix:
- {
- const CSeq_loc_mix::Tdata& data = loc.GetMix().Get();
- m_Ranges.reserve(m_Ranges.size() + data.size());
- ITERATE(CSeq_loc_mix::Tdata, li, data) {
- x_ProcessLocation(**li);
- }
- return;
- }
- case CSeq_loc::e_Equiv:
- {
- const CSeq_loc_equiv::Tdata& data = loc.GetEquiv().Get();
- m_Ranges.reserve(m_Ranges.size() + data.size());
- ITERATE(CSeq_loc_equiv::Tdata, li, data) {
- x_ProcessLocation(**li);
- }
- return;
- }
- case CSeq_loc::e_Bond:
- {
- const CSeq_bond& bond = loc.GetBond();
- const CSeq_point& a = bond.GetA();
- SSeq_loc_CI_RangeInfo infoA;
- infoA.m_Id = &a.GetId();
- infoA.m_Range.Set(a.GetPoint(), a.GetPoint());
- if ( a.IsSetStrand() ) {
- infoA.SetStrand(a.GetStrand());
- }
- infoA.m_Loc = &loc;
- if (a.IsSetFuzz()) {
- infoA.m_Fuzz.first = infoA.m_Fuzz.second = &a.GetFuzz();
- }
- m_Ranges.push_back(infoA);
- if ( bond.IsSetB() ) {
- const CSeq_point& b = bond.GetB();
- SSeq_loc_CI_RangeInfo infoB;
- infoB.m_Id = &b.GetId();
- infoB.m_Range.Set(b.GetPoint(), b.GetPoint());
- if ( b.IsSetStrand() ) {
- infoB.SetStrand(b.GetStrand());
- }
- infoB.m_Loc = &loc;
- if (b.IsSetFuzz()) {
- infoB.m_Fuzz.first = infoB.m_Fuzz.second = &b.GetFuzz();
- }
- m_Ranges.push_back(infoB);
- }
- return;
- }
- case CSeq_loc::e_Feat:
- default:
- {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc_CI -- unsupported location type");
+ else {
+ m_Impl->SetPoint(info);
}
}
}
-CSeq_loc_CI::CSeq_loc_CI(void)
- : m_Impl(new CSeq_loc_CI_Impl),
- m_Index(0)
+void CSeq_loc_I::ResetStrand(void)
{
+ x_CheckValid("ResetStrand()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_IsSetStrand ) {
+ info.m_IsSetStrand = false;
+ info.m_Strand = eNa_strand_unknown;
+ m_Impl->UpdatePoint(info);
+ }
}
-CSeq_loc_CI::CSeq_loc_CI(const CSeq_loc& loc,
- EEmptyFlag empty_flag,
- ESeqLocOrder order)
- : m_Impl(new CSeq_loc_CI_Impl(loc, empty_flag, order)),
- m_Index(0)
+void CSeq_loc_I::SetStrand(ENa_strand strand)
{
+ x_CheckValid("SetStrand()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( !info.m_IsSetStrand || info.m_Strand != strand ) {
+ info.SetStrand(strand);
+ m_Impl->UpdatePoint(info);
+ }
}
-CSeq_loc_CI::~CSeq_loc_CI()
+void CSeq_loc_I::ResetFuzzFrom(void)
{
+ x_CheckValid("ResetFuzzFrom()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Fuzz.first ) {
+ info.m_Fuzz.first = null;
+ m_Impl->UpdateLoc(info);
+ }
}
-CSeq_loc_CI::CSeq_loc_CI(const CSeq_loc_CI& iter)
- : m_Impl(iter.m_Impl),
- m_Index(iter.m_Index)
+void CSeq_loc_I::SetFuzzFrom(CInt_fuzz& fuzz)
{
+ x_CheckValid("SetFuzzFrom()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( !info.m_Fuzz.first || !info.m_Fuzz.first->Equals(fuzz) ) {
+ info.m_Fuzz.first = SerialClone(fuzz);
+ m_Impl->UpdateLoc(info);
+ }
}
-CSeq_loc_CI& CSeq_loc_CI::operator= (const CSeq_loc_CI& iter)
+void CSeq_loc_I::ResetFuzzTo(void)
{
- m_Impl = iter.m_Impl;
- m_Index = iter.m_Index;
- return *this;
+ x_CheckValid("ResetFuzzTo()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Fuzz.second ) {
+ info.m_Fuzz.second = null;
+ m_Impl->UpdateLoc(info);
+ }
}
-bool CSeq_loc_CI::operator== (const CSeq_loc_CI& iter) const
+void CSeq_loc_I::SetFuzzTo(CInt_fuzz& fuzz)
{
- // Check if both are at end.
- if (m_Impl->IsEnd(m_Index) && iter.m_Impl->IsEnd(iter.m_Index)) {
- return true;
+ x_CheckValid("SetFuzzTo()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( !info.m_Fuzz.second || !info.m_Fuzz.second->Equals(fuzz) ) {
+ info.m_Fuzz.second = SerialClone(fuzz);
+ m_Impl->UpdateLoc(info);
}
- return m_Impl == iter.m_Impl && m_Index == iter.m_Index;
}
-bool CSeq_loc_CI::operator!= (const CSeq_loc_CI& iter) const
+void CSeq_loc_I::ResetFuzz(void)
{
- return !(*this == iter);
+ x_CheckValid("ResetFuzz()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( info.m_Fuzz.first || info.m_Fuzz.second ) {
+ info.m_Fuzz.first = info.m_Fuzz.second = null;
+ m_Impl->UpdatePoint(info);
+ }
}
-const CSeq_loc& CSeq_loc_CI::GetSeq_loc(void) const
+void CSeq_loc_I::SetFuzz(CInt_fuzz& fuzz)
{
- return GetEmbeddingSeq_loc();
+ x_CheckValid("SetFuzz()");
+ SSeq_loc_CI_RangeInfo& info = x_GetRangeInfo();
+ if ( !info.m_Fuzz.first || !info.m_Fuzz.first->Equals(fuzz) ||
+ info.m_Fuzz.first != info.m_Fuzz.second ) {
+ info.m_Fuzz.first = info.m_Fuzz.second = SerialClone(fuzz);
+ m_Impl->UpdatePoint(info);
+ }
}
-const CSeq_loc& CSeq_loc_CI::GetEmbeddingSeq_loc(void) const
+CRef<CSeq_loc> CSeq_loc_I::MakeSeq_loc(EMakeType make_type) const
{
- x_CheckNotValid("GetEmbeddingSeq_loc()");
- CConstRef<CSeq_loc> loc = x_GetRangeInfo().m_Loc;
- if ( !loc ) {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc_CI::GetSeq_loc() -- NULL seq-loc");
- }
- return *loc;
+ return m_Impl->MakeLoc(make_type);
}
-CConstRef<CSeq_loc> CSeq_loc_CI::GetRangeAsSeq_loc(void) const
+pair<CSeq_loc_I, CSeq_loc_I>
+CSeq_loc_I::GetEquivSetRange(size_t level) const
{
- x_CheckNotValid("GetRangeAsSeq_loc()");
- const CSeq_loc& parent = GetEmbeddingSeq_loc();
- switch ( parent.Which() ) {
- // Single-range, empty or whole seq-loc can be used as-is.
- case CSeq_loc::e_not_set:
- case CSeq_loc::e_Null:
- case CSeq_loc::e_Empty:
- case CSeq_loc::e_Whole:
- case CSeq_loc::e_Int:
- case CSeq_loc::e_Pnt:
- return ConstRef(&parent);
- default:
- break;
- }
- // Create a new seq-loc for the current range.
- CRef<CSeq_loc> loc(new CSeq_loc);
- const SSeq_loc_CI_RangeInfo& rg_info = x_GetRangeInfo();
- if ( rg_info.m_Range.IsWhole() ) {
- // Whole location
- loc->SetWhole(const_cast<CSeq_id&>(*rg_info.m_Id));
- }
- else if ( rg_info.m_Range.Empty() ) {
- // Empty location
- loc->SetEmpty(const_cast<CSeq_id&>(*rg_info.m_Id));
- }
- else {
- loc->SetInt().SetFrom(rg_info.m_Range.GetFrom());
- loc->SetInt().SetTo(rg_info.m_Range.GetTo());
- loc->SetInt().SetId(const_cast<CSeq_id&>(*rg_info.m_Id));
- if ( rg_info.m_IsSetStrand ) {
- loc->SetInt().SetStrand(rg_info.m_Strand);
- }
- if ( rg_info.m_Fuzz.first ) {
- loc->SetInt().SetFuzz_from(
- const_cast<CInt_fuzz&>(*rg_info.m_Fuzz.first));
- }
- if ( rg_info.m_Fuzz.second ) {
- loc->SetInt().SetFuzz_to(
- const_cast<CInt_fuzz&>(*rg_info.m_Fuzz.second));
- }
- }
- return ConstRef(loc.Release());
+ x_CheckValid("GetEquivSetRange()");
+ pair<size_t, size_t> indexes = m_Impl->GetEquivSetRange(m_Index, level);
+ return make_pair(CSeq_loc_I(*this, indexes.first),
+ CSeq_loc_I(*this, indexes.second));
}
-bool CSeq_loc_CI::x_IsValid(void) const
+pair<CSeq_loc_I, CSeq_loc_I>
+CSeq_loc_I::GetEquivPartRange(size_t level) const
{
- return m_Index < m_Impl->GetRanges().size();
+ x_CheckValid("GetEquivPartRange()");
+ pair<size_t, size_t> indexes = m_Impl->GetEquivPartRange(m_Index, level);
+ return make_pair(CSeq_loc_I(*this, indexes.first),
+ CSeq_loc_I(*this, indexes.second));
}
-void CSeq_loc_CI::x_ThrowNotValid(const char* where) const
+void CSeq_loc_I::RemoveBond(void)
{
- string msg;
- msg += "CSeq_loc_CI::";
- msg += where;
- msg += " -- iterator is not valid";
- NCBI_THROW(CException, eUnknown,
- msg);
+ x_CheckValid("RemoveBond()");
+ m_Impl->RemoveBond(m_Index);
}
-const SSeq_loc_CI_RangeInfo& CSeq_loc_CI::x_GetRangeInfo(void) const
+void CSeq_loc_I::MakeBondA(void)
{
- // The index validity must be checked by the caller.
- return m_Impl->GetRanges()[m_Index];
+ x_CheckValid("MakeBondA()");
+ m_Impl->MakeBondA(m_Index);
+}
+
+
+void CSeq_loc_I::MakeBondAB(void)
+{
+ x_CheckValid("MakeBondAB()");
+ m_Impl->MakeBondAB(m_Index);
+}
+
+
+void CSeq_loc_I::MakeBondB(void)
+{
+ x_CheckValid("MakeBondB()");
+ m_Impl->MakeBondB(m_Index);
}
+// CSeq_loc_I
+/////////////////////////////////////////////////////////////////////////////
+
+
// Append a string representation of a CSeq_id to label
inline
void s_GetLabel(const CSeq_id& id, string* label)
@@ -1982,15 +3600,13 @@ bool CSeq_loc::x_CheckId(const CSeq_id*& id, bool may_throw) const
}
case e_Feat:
default:
- {
- if (may_throw) {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::CheckId -- "
- "unsupported location type");
- } else {
- return false;
- }
+ if (may_throw) {
+ NCBI_THROW_FMT(CSeqLocException, eUnsupported,
+ "CSeq_loc::CheckId(): "
+ "unsupported location type: "<<
+ SelectionName(Which()));
}
+ return false;
}
}
@@ -2095,10 +3711,10 @@ void CSeq_loc::ChangeToPackedInt(void)
return;
}
default:
- {
- NCBI_THROW(CException, eUnknown,
- "Can not convert location to packed-int");
- }
+ NCBI_THROW_FMT(CSeqLocException, eIncomatible,
+ "CSeq_loc::ChangeToPackedInt(): "
+ "Can not convert location to packed-int: "<<
+ SelectionName(Which()));
}
}
@@ -2323,11 +3939,10 @@ void CSeq_loc::Add(const CSeq_loc& other)
}
case e_Feat:
default:
- {
- NCBI_THROW(CException, eUnknown,
- "CSeq_loc::Add -- "
- "unsupported location type");
- }
+ NCBI_THROW_FMT(CSeqLocException, eIncomatible,
+ "CSeq_loc::Add(): "
+ "cannot add sub-location to location of type: "<<
+ SelectionName(Which()));
}
}
@@ -2829,8 +4444,8 @@ void x_SingleRange(CSeq_loc& dst,
if ( first_id ) {
// Seq-id may be missing for NULL seq-loc
if (next_id && first_id != next_id) {
- NCBI_THROW(CException, eUnknown,
- "Can not merge multi-id seq-loc");
+ NCBI_THROW(CSeqLocException, eMultipleId,
+ "Can not merge multi-id seq-loc");
}
}
else {
@@ -2955,6 +4570,10 @@ void x_MergeNoSort(CSeq_loc& dst,
}
+static const bool force_strand_merge = true;
+static const bool force_strand_subtract = true;
+
+
static
void x_MergeAndSort(CSeq_loc& dst,
const CSeq_loc& src,
@@ -2970,7 +4589,7 @@ void x_MergeAndSort(CSeq_loc& dst,
*pid_map_minus.get() : id_map_plus;
// Prepare default strands
- ENa_strand default_plus = use_strand ?
+ ENa_strand default_plus = force_strand_merge && use_strand ?
eNa_strand_plus : eNa_strand_unknown;
ENa_strand default_minus = use_strand ?
eNa_strand_minus : eNa_strand_unknown;
@@ -3016,8 +4635,8 @@ void x_SingleRange(CSeq_loc& dst,
if ( first_id ) {
// Seq-id may be missing for NULL seq-loc
if (next_id && first_id != next_id) {
- NCBI_THROW(CException, eUnknown,
- "Can not merge multi-id seq-loc");
+ NCBI_THROW(CSeqLocException, eMultipleId,
+ "Can not merge multi-id seq-loc");
}
}
else {
@@ -3190,7 +4809,7 @@ void x_SubAndSort(CSeq_loc& dst,
*p_id_map_minus.get() : id_map_plus;
// Prepare default strands
- ENa_strand default_plus = use_strand ?
+ ENa_strand default_plus = force_strand_subtract && use_strand ?
eNa_strand_plus : eNa_strand_unknown;
ENa_strand default_minus = use_strand ?
eNa_strand_minus : eNa_strand_unknown;
diff --git a/c++/src/objects/seqloc/accguide.inc b/c++/src/objects/seqloc/accguide.inc
index 9207cb9..5f27b80 100644
--- a/c++/src/objects/seqloc/accguide.inc
+++ b/c++/src/objects/seqloc/accguide.inc
@@ -1,4 +1,4 @@
-/* $Id: accguide.inc 468963 2015-05-29 16:42:36Z ucko $
+/* $Id: accguide.inc 485916 2015-11-30 15:11:54Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
*/
static const char* const kBuiltInGuide[] = {
- "# $Id: accguide.inc 468963 2015-05-29 16:42:36Z ucko $",
+ "# $Id: accguide.inc 485916 2015-11-30 15:11:54Z ucko $",
"version 1 # of file format",
"",
"# 8-character protein accessions",
@@ -50,6 +50,8 @@ static const char* const kBuiltInGuide[] = {
"3+5 J?? gb_tsa_prot",
"3+5 K?? gb_wgs_prot",
"3+5 L?? ddbj_tsa_prot",
+ "3+5 M?? gb_wgs_prot",
+ "3+5 N?? gb_wgs_prot",
"3+5 ??? unreserved_prot",
"",
"# Genome pipeline accessions",
@@ -131,9 +133,9 @@ static const char* const kBuiltInGuide[] = {
"4+8 O??? embl_tpa_wgs_nuc",
"4+9 O??? embl_tpa_wgs_nuc",
"4+10 O??? embl_tpa_wgs_nuc",
- "4+8 P??? ddbj_tsa_nuc",
- "4+9 P??? ddbj_tsa_nuc",
- "4+10 P??? ddbj_tsa_nuc",
+ "4+8 P??? ddbj_wgs_nuc",
+ "4+9 P??? ddbj_wgs_nuc",
+ "4+10 P??? ddbj_wgs_nuc",
"",
"# Mass sequence Genome for Annotation",
"5+7 A???? ddbj_other_nuc",
@@ -471,17 +473,19 @@ static const char* const kBuiltInGuide[] = {
"2+6 KR gb_dirsub",
"2+6 KS gb_gss",
"2+6 KT gb_dirsub",
+ "2+6 KU gb_dirsub",
+ "2+6 KV gb_con",
"2+6 K? gb_other_nuc",
"2+6 LA ddbj_tsa_nuc",
"2+6 LB ddbj_gss",
"2+6 LC ddbj_dirsub",
"2+6 LD ddbj_con",
"2+6 LE ddbj_tsa_nuc",
- "2+6 LF ddbj_other_nuc",
- "2+6 LG ddbj_other_nuc",
- "2+6 LH ddbj_other_nuc",
- "2+6 LI ddbj_other_nuc",
- "2+6 LJ ddbj_other_nuc",
+ "2+6 LF ddbj_patent",
+ "2+6 LG ddbj_patent",
+ "2+6 LH ddbj_tsa_nuc",
+ "2+6 LI ddbj_tsa_nuc",
+ "2+6 LJ ddbj_tsa_nuc",
"2+6 LK embl_other_nuc",
"2+6 LL embl_other_nuc",
"2+6 LM embl_other_nuc",
@@ -492,6 +496,16 @@ static const char* const kBuiltInGuide[] = {
"2+6 LR embl_other_nuc",
"2+6 LS embl_other_nuc",
"2+6 LT embl_other_nuc",
+ "2+6 LU ddbj_other_nuc",
+ "2+6 LV ddbj_other_nuc",
+ "2+6 LX ddbj_other_nuc",
+ "2+6 LY ddbj_other_nuc",
+ "2+6 LZ ddbj_other_nuc",
+ "2+6 MA ddbj_other_nuc",
+ "2+6 MB ddbj_other_nuc",
+ "2+6 MC ddbj_other_nuc",
+ "2+6 MD ddbj_other_nuc",
+ "2+6 ME ddbj_other_nuc",
"2+6 ?? unreserved_nuc",
"",
"# Specially handled type-general Dbtag names; commented out for now in",
@@ -9659,6 +9673,7 @@ static const char* const kBuiltInGuide[] = {
"special CCD22089-CCD22162 embl_tpa_prot",
"special CCE69367-CCE71257 embl_tpa_prot",
"special CCH35981-CCH35984 embl_tpa_prot",
+ "special CCP37863-CCP38020 embl_tpa_prot",
"special CCQ18550 embl_tpa_prot",
"special CDG31911-CDG32165 embl_tpa_prot",
"special CDG58552 embl_tpa_prot",
@@ -9670,6 +9685,7 @@ static const char* const kBuiltInGuide[] = {
"special CDK02602-CDK08087 embl_tpa_prot",
"special CDK08089-CDK12444 embl_tpa_prot",
"special CDM98735-CDM98850 embl_tpa_prot",
+ "special CDW51382-CDW51481 embl_tpa_prot",
"special CEL64082-CEL71605 embl_tpa_prot",
"special CEL71607-CEL73228 embl_tpa_prot",
"special CEL73230-CEL73266 embl_tpa_prot",
@@ -9682,7 +9698,8 @@ static const char* const kBuiltInGuide[] = {
"special CEL77190-CEL78176 embl_tpa_prot",
"special CEL78178-CEL78353 embl_tpa_prot",
"special CEL78355-CEL78878 embl_tpa_prot",
+ "special CRK77046 embl_tpa_prot",
"## Err on the side of caution on as yet unassigned IDs, and hope that",
"## there's not *too* much more backfilling.",
- "#special CRI73780-CZZ99999 unreserved_prot"
+ "#special CUL03805-CZZ99999 unreserved_prot"
};
diff --git a/c++/src/objects/seqloc/accguide.txt b/c++/src/objects/seqloc/accguide.txt
index 4ad68a9..ef2153c 100644
--- a/c++/src/objects/seqloc/accguide.txt
+++ b/c++/src/objects/seqloc/accguide.txt
@@ -1,4 +1,4 @@
-# $Id: accguide.txt 468963 2015-05-29 16:42:36Z ucko $
+# $Id: accguide.txt 485916 2015-11-30 15:11:54Z ucko $
version 1 # of file format
# 8-character protein accessions
@@ -17,6 +17,8 @@ version 1 # of file format
3+5 J?? gb_tsa_prot
3+5 K?? gb_wgs_prot
3+5 L?? ddbj_tsa_prot
+3+5 M?? gb_wgs_prot
+3+5 N?? gb_wgs_prot
3+5 ??? unreserved_prot
# Genome pipeline accessions
@@ -98,9 +100,9 @@ version 1 # of file format
4+8 O??? embl_tpa_wgs_nuc
4+9 O??? embl_tpa_wgs_nuc
4+10 O??? embl_tpa_wgs_nuc
-4+8 P??? ddbj_tsa_nuc
-4+9 P??? ddbj_tsa_nuc
-4+10 P??? ddbj_tsa_nuc
+4+8 P??? ddbj_wgs_nuc
+4+9 P??? ddbj_wgs_nuc
+4+10 P??? ddbj_wgs_nuc
# Mass sequence Genome for Annotation
5+7 A???? ddbj_other_nuc
@@ -438,17 +440,19 @@ version 1 # of file format
2+6 KR gb_dirsub
2+6 KS gb_gss
2+6 KT gb_dirsub
+2+6 KU gb_dirsub
+2+6 KV gb_con
2+6 K? gb_other_nuc
2+6 LA ddbj_tsa_nuc
2+6 LB ddbj_gss
2+6 LC ddbj_dirsub
2+6 LD ddbj_con
2+6 LE ddbj_tsa_nuc
-2+6 LF ddbj_other_nuc
-2+6 LG ddbj_other_nuc
-2+6 LH ddbj_other_nuc
-2+6 LI ddbj_other_nuc
-2+6 LJ ddbj_other_nuc
+2+6 LF ddbj_patent
+2+6 LG ddbj_patent
+2+6 LH ddbj_tsa_nuc
+2+6 LI ddbj_tsa_nuc
+2+6 LJ ddbj_tsa_nuc
2+6 LK embl_other_nuc
2+6 LL embl_other_nuc
2+6 LM embl_other_nuc
@@ -459,6 +463,16 @@ version 1 # of file format
2+6 LR embl_other_nuc
2+6 LS embl_other_nuc
2+6 LT embl_other_nuc
+2+6 LU ddbj_other_nuc
+2+6 LV ddbj_other_nuc
+2+6 LX ddbj_other_nuc
+2+6 LY ddbj_other_nuc
+2+6 LZ ddbj_other_nuc
+2+6 MA ddbj_other_nuc
+2+6 MB ddbj_other_nuc
+2+6 MC ddbj_other_nuc
+2+6 MD ddbj_other_nuc
+2+6 ME ddbj_other_nuc
2+6 ?? unreserved_nuc
# Specially handled type-general Dbtag names; commented out for now in
@@ -9626,6 +9640,7 @@ special CCC21095-CCC21104 embl_tpa_prot
special CCD22089-CCD22162 embl_tpa_prot
special CCE69367-CCE71257 embl_tpa_prot
special CCH35981-CCH35984 embl_tpa_prot
+special CCP37863-CCP38020 embl_tpa_prot
special CCQ18550 embl_tpa_prot
special CDG31911-CDG32165 embl_tpa_prot
special CDG58552 embl_tpa_prot
@@ -9637,6 +9652,7 @@ special CDI70965-CDI70967 embl_tpa_prot
special CDK02602-CDK08087 embl_tpa_prot
special CDK08089-CDK12444 embl_tpa_prot
special CDM98735-CDM98850 embl_tpa_prot
+special CDW51382-CDW51481 embl_tpa_prot
special CEL64082-CEL71605 embl_tpa_prot
special CEL71607-CEL73228 embl_tpa_prot
special CEL73230-CEL73266 embl_tpa_prot
@@ -9649,6 +9665,7 @@ special CEL76768-CEL77188 embl_tpa_prot
special CEL77190-CEL78176 embl_tpa_prot
special CEL78178-CEL78353 embl_tpa_prot
special CEL78355-CEL78878 embl_tpa_prot
+special CRK77046 embl_tpa_prot
## Err on the side of caution on as yet unassigned IDs, and hope that
## there's not *too* much more backfilling.
-#special CRI73780-CZZ99999 unreserved_prot
+#special CUL03805-CZZ99999 unreserved_prot
diff --git a/c++/src/objects/seqloc/seqloc.asn b/c++/src/objects/seqloc/seqloc.asn
index 8735a39..3cb05a5 100644
--- a/c++/src/objects/seqloc/seqloc.asn
+++ b/c++/src/objects/seqloc/seqloc.asn
@@ -1,4 +1,4 @@
---$Revision: 182744 $
+--$Revision: 454827 $
--**********************************************************************
--
-- NCBI Sequence location and identifier elements
@@ -62,10 +62,12 @@ Giimport-id ::= SEQUENCE {
db VisibleString OPTIONAL , -- dbase used in
release VisibleString OPTIONAL } -- the release
-PDB-seq-id ::= SEQUENCE {
- mol PDB-mol-id , -- the molecule name
- chain INTEGER DEFAULT 32 , -- a single ASCII character, chain id
- rel Date OPTIONAL } -- release date, month and year
+PDB-seq-id ::= SEQUENCE { -- must set either chain or chain_id, but not both
+ mol PDB-mol-id , -- the molecule name
+ chain INTEGER DEFAULT 32 , -- Deprecated : For single ASCII character
+ -- chain identifiers of pre-2015 PDB structures
+ rel Date OPTIONAL , -- release date, month and year
+ chain-id VisibleString OPTIONAL } -- chain identifier
PDB-mol-id ::= VisibleString -- name of mol, 4 chars
diff --git a/c++/src/objects/seqres/Seq_graph.cpp b/c++/src/objects/seqres/Seq_graph.cpp
index f606bf7..797aff2 100644
--- a/c++/src/objects/seqres/Seq_graph.cpp
+++ b/c++/src/objects/seqres/Seq_graph.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_graph.cpp 448566 2014-10-07 16:44:32Z ivanov $
+/* $Id: Seq_graph.cpp 464942 2015-04-15 15:46:17Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,18 +70,23 @@ void CSeq_graph::CReserveHook::PreReadChoiceVariant(
}
if ( CSeq_graph* graph = CType<CSeq_graph>::GetParent(in) ) {
size_t size = graph->GetNumval();
- switch ( variant.GetVariantIndex() ) {
- case C_Graph::e_Real:
- graph->SetGraph().SetReal().SetValues().reserve(size);
- break;
- case C_Graph::e_Int:
- graph->SetGraph().SetInt().SetValues().reserve(size);
- break;
- case C_Graph::e_Byte:
- graph->SetGraph().SetByte().SetValues().reserve(size);
- break;
- default:
- break;
+ try {
+ switch ( variant.GetVariantIndex() ) {
+ case C_Graph::e_Real:
+ graph->SetGraph().SetReal().SetValues().reserve(size);
+ break;
+ case C_Graph::e_Int:
+ graph->SetGraph().SetInt().SetValues().reserve(size);
+ break;
+ case C_Graph::e_Byte:
+ graph->SetGraph().SetByte().SetValues().reserve(size);
+ break;
+ default:
+ break;
+ }
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
}
}
}
diff --git a/c++/src/objects/seqset/Bioseq_set.cpp b/c++/src/objects/seqset/Bioseq_set.cpp
index 9dcb333..6f9f8a6 100644
--- a/c++/src/objects/seqset/Bioseq_set.cpp
+++ b/c++/src/objects/seqset/Bioseq_set.cpp
@@ -1,4 +1,4 @@
-/* $Id: Bioseq_set.cpp 448086 2014-10-02 14:55:59Z ivanov $
+/* $Id: Bioseq_set.cpp 444516 2014-08-25 17:31:21Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/seqsplit/seqsplit.asn b/c++/src/objects/seqsplit/seqsplit.asn
index 11bcb40..71dfc8e 100644
--- a/c++/src/objects/seqsplit/seqsplit.asn
+++ b/c++/src/objects/seqsplit/seqsplit.asn
@@ -1,4 +1,4 @@
---$Revision: 181915 $
+--$Revision: 464673 $
--********************************************************************
--
-- Network Id server network access
@@ -21,8 +21,7 @@ EXPORTS ID2S-Chunk-Id, ID2S-Seq-annot-Info;
IMPORTS Seq-id FROM NCBI-Seqloc
Seq-entry FROM NCBI-Seqset
Bioseq, Seq-annot, Seq-descr, Seq-literal FROM NCBI-Sequence
- Seq-align FROM NCBI-Seqalign
- Feat-id FROM NCBI-Seqfeat;
+ Seq-align FROM NCBI-Seqalign;
----------------------------------------------------------------------------
-- Blob split info types
diff --git a/c++/src/objects/seqtable/Scaled_int_multi_data.cpp b/c++/src/objects/seqtable/Scaled_int_multi_data.cpp
index 567ae92..47c4e4a 100644
--- a/c++/src/objects/seqtable/Scaled_int_multi_data.cpp
+++ b/c++/src/objects/seqtable/Scaled_int_multi_data.cpp
@@ -1,4 +1,4 @@
-/* $Id: Scaled_int_multi_data.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: Scaled_int_multi_data.cpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,8 @@
// generated includes
#include <objects/seqtable/Scaled_int_multi_data.hpp>
+#include <objects/seqtable/SeqTable_multi_data.hpp>
+
// generated classes
BEGIN_NCBI_SCOPE
@@ -52,6 +54,36 @@ CScaled_int_multi_data::~CScaled_int_multi_data(void)
}
+size_t CScaled_int_multi_data::GetIntSize(void) const
+{
+ if ( (IsSetMax() && GetMax() > kMax_Int) ||
+ (IsSetMin() && GetMin() < kMin_Int) ) {
+ return sizeof(Int8);
+ }
+ return sizeof(int);
+}
+
+
+bool CScaled_int_multi_data::TryGetInt4(size_t row, Int4& v) const
+{
+ if ( !GetData().TryGetInt4(row, v) ) {
+ return false;
+ }
+ v = v*GetMul()+GetAdd();
+ return true;
+}
+
+
+bool CScaled_int_multi_data::TryGetInt8(size_t row, Int8& v) const
+{
+ if ( !GetData().TryGetInt8(row, v) ) {
+ return false;
+ }
+ v = v*GetMul()+GetAdd();
+ return true;
+}
+
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/seqtable/Scaled_real_multi_data.cpp b/c++/src/objects/seqtable/Scaled_real_multi_data.cpp
index 98a62c1..83cd300 100644
--- a/c++/src/objects/seqtable/Scaled_real_multi_data.cpp
+++ b/c++/src/objects/seqtable/Scaled_real_multi_data.cpp
@@ -1,4 +1,4 @@
-/* $Id: Scaled_real_multi_data.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: Scaled_real_multi_data.cpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -52,6 +52,16 @@ CScaled_real_multi_data::~CScaled_real_multi_data(void)
}
+bool CScaled_real_multi_data::TryGetReal(size_t row, double& v) const
+{
+ if ( !GetData().TryGetReal(row, v) ) {
+ return false;
+ }
+ v = v*GetMul()+GetAdd();
+ return true;
+}
+
+
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
diff --git a/c++/src/objects/seqtable/SeqTable_column.cpp b/c++/src/objects/seqtable/SeqTable_column.cpp
index e723d94..1b2c35d 100644
--- a/c++/src/objects/seqtable/SeqTable_column.cpp
+++ b/c++/src/objects/seqtable/SeqTable_column.cpp
@@ -1,4 +1,4 @@
-/* $Id: SeqTable_column.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: SeqTable_column.cpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,82 +75,6 @@ bool CSeqTable_column::IsSet(size_t row) const
}
-bool CSeqTable_column::TryGetBool(size_t row, bool& v) const
-{
- size_t index = row;
- if ( IsSetSparse() ) {
- index = GetSparse().GetIndexAt(row);
- if ( index == CSeqTable_sparse_index::kSkipped ) {
- if ( IsSetSparse_other() ) {
- v = GetSparse_other().GetBit();
- return true;
- }
- return false;
- }
- }
- if ( IsSetData() && GetData().TryGetBool(index, v) ) {
- return true;
- }
- if ( IsSetDefault() ) {
- v = GetDefault().GetBit();
- return true;
- }
- return false;
-}
-
-
-bool CSeqTable_column::TryGetInt(size_t row, int& v) const
-{
- size_t index = row;
- if ( IsSetSparse() ) {
- index = GetSparse().GetIndexAt(row);
- if ( index == CSeqTable_sparse_index::kSkipped ) {
- if ( IsSetSparse_other() ) {
- v = GetSparse_other().GetInt();
- return true;
- }
- return false;
- }
- }
- if ( IsSetData() && GetData().TryGetInt(index, v) ) {
- return true;
- }
- if ( IsSetDefault() ) {
- v = GetDefault().GetInt();
- return true;
- }
- return false;
-}
-
-
-bool CSeqTable_column::TryGetReal(size_t row, double& v) const
-{
- size_t index = row;
- if ( IsSetSparse() ) {
- index = GetSparse().GetIndexAt(row);
- if ( index == CSeqTable_sparse_index::kSkipped ) {
- if ( IsSetSparse_other() ) {
- v = GetSparse_other().GetReal();
- return true;
- }
- return false;
- }
- }
- if ( IsSetData() ) {
- const CSeqTable_multi_data::TReal& arr = GetData().GetReal();
- if ( index < arr.size() ) {
- v = arr[index];
- return true;
- }
- }
- if ( IsSetDefault() ) {
- v = GetDefault().GetReal();
- return true;
- }
- return false;
-}
-
-
const string* CSeqTable_column::GetStringPtr(size_t row) const
{
size_t index = row;
diff --git a/c++/src/objects/seqtable/SeqTable_multi_data.cpp b/c++/src/objects/seqtable/SeqTable_multi_data.cpp
index 3587d6a..f244a03 100644
--- a/c++/src/objects/seqtable/SeqTable_multi_data.cpp
+++ b/c++/src/objects/seqtable/SeqTable_multi_data.cpp
@@ -1,4 +1,4 @@
-/* $Id: SeqTable_multi_data.cpp 448566 2014-10-07 16:44:32Z ivanov $
+/* $Id: SeqTable_multi_data.cpp 464942 2015-04-15 15:46:17Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -82,7 +82,13 @@ CIntDeltaSumCache& CSeqTable_multi_data::x_GetIntDeltaCache(void) const
{
CIntDeltaSumCache* info = m_Cache.GetNCPointerOrNull();
if ( !info ) {
- m_Cache = info = new CIntDeltaSumCache(GetInt_delta().GetSize());
+ if ( GetInt_delta().GetIntSize() <= sizeof(Int4) ) {
+ info = new CInt4DeltaSumCache(GetInt_delta().GetSize());
+ }
+ else {
+ info = new CInt8DeltaSumCache(GetInt_delta().GetSize());
+ }
+ m_Cache = info;
}
return *info;
}
@@ -92,11 +98,42 @@ CIntDeltaSumCache& CSeqTable_multi_data::x_GetIntDeltaCache(void) const
// CIntDeltaSumCache
/////////////////////////////////////////////////////////////////////////////
+CIntDeltaSumCache::~CIntDeltaSumCache(void)
+{
+}
+
+
+Int4 CIntDeltaSumCache::GetDeltaSum4(const TDeltas& deltas,
+ size_t index)
+{
+ Int8 v8 = GetDeltaSum8(deltas, index);
+ Int4 v = Int4(v8);
+ if ( v != v8 ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CIntDeltaSumCache::GetDeltaSum4(): "
+ "Int8 value doesn't fit in Int4");
+ }
+ return v;
+}
+
+
+Int8 CIntDeltaSumCache::GetDeltaSum8(const TDeltas& deltas,
+ size_t index)
+{
+ return GetDeltaSum4(deltas, index);
+}
+
+
#define USE_DELTA_CACHE
-const size_t CIntDeltaSumCache::kBlockSize = 128;
+/////////////////////////////////////////////////////////////////////////////
+// CInt4DeltaSumCache
+/////////////////////////////////////////////////////////////////////////////
-CIntDeltaSumCache::CIntDeltaSumCache(size_t size)
+const size_t CInt4DeltaSumCache::kBlockSize = 128;
+
+
+CInt4DeltaSumCache::CInt4DeltaSumCache(size_t size)
: m_Blocks(new TValue[(size+kBlockSize-1)/kBlockSize]),
m_BlocksFilled(0),
#ifdef USE_DELTA_CACHE
@@ -107,16 +144,15 @@ CIntDeltaSumCache::CIntDeltaSumCache(size_t size)
}
-CIntDeltaSumCache::~CIntDeltaSumCache(void)
+CInt4DeltaSumCache::~CInt4DeltaSumCache(void)
{
}
inline
-CIntDeltaSumCache::TValue
-CIntDeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
- size_t block_index,
- size_t block_offset)
+Int4 CInt4DeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
+ size_t block_index,
+ size_t block_offset)
{
#ifdef USE_DELTA_CACHE
_ASSERT(block_index <= m_BlocksFilled);
@@ -128,8 +164,8 @@ CIntDeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
_ASSERT(block_offset < block_size);
TValue sum = block_index == 0? 0: m_Blocks[block_index-1];
for ( size_t i = 0; i < block_size; ++i ) {
- int v;
- if ( deltas.TryGetInt(block_pos+i, v) ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
sum += v;
}
m_CacheBlockInfo[i] = sum;
@@ -149,16 +185,16 @@ CIntDeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
_ASSERT(block_offset < block_size);
TValue sum = block_index == 0? 0: m_Blocks[block_index-1];
for ( size_t i = 0; i <= block_offset; ++i ) {
- int v;
- if ( deltas.TryGetInt(block_pos+i, v) ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
sum += v;
}
}
if ( block_index == m_BlocksFilled ) {
TValue sum2 = sum;
for ( size_t i = block_offset+1; i < block_size; ++i ) {
- int v;
- if ( deltas.TryGetInt(block_pos+i, v) ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
sum2 += v;
}
}
@@ -170,9 +206,8 @@ CIntDeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
}
-CIntDeltaSumCache::TValue
-CIntDeltaSumCache::GetDeltaSum(const TDeltas& deltas,
- size_t index)
+Int4 CInt4DeltaSumCache::GetDeltaSum4(const TDeltas& deltas,
+ size_t index)
{
_ASSERT(index < deltas.GetSize());
size_t block_index = index / kBlockSize;
@@ -185,125 +220,364 @@ CIntDeltaSumCache::GetDeltaSum(const TDeltas& deltas,
/////////////////////////////////////////////////////////////////////////////
+// CInt8DeltaSumCache
+/////////////////////////////////////////////////////////////////////////////
+const size_t CInt8DeltaSumCache::kBlockSize = 128;
-bool CSeqTable_multi_data::TryGetBool(size_t row, bool& v) const
+
+CInt8DeltaSumCache::CInt8DeltaSumCache(size_t size)
+ : m_Blocks(new TValue[(size+kBlockSize-1)/kBlockSize]),
+ m_BlocksFilled(0),
+#ifdef USE_DELTA_CACHE
+ m_CacheBlockInfo(new TValue[kBlockSize]),
+#endif
+ m_CacheBlockIndex(size_t(0)-1)
{
- if ( IsBit() ) {
- const TBit& bits = GetBit();
- size_t i = row/8;
- if ( i >= bits.size() ) {
- return false;
+}
+
+
+CInt8DeltaSumCache::~CInt8DeltaSumCache(void)
+{
+}
+
+
+inline
+Int8 CInt8DeltaSumCache::x_GetDeltaSum2(const TDeltas& deltas,
+ size_t block_index,
+ size_t block_offset)
+{
+#ifdef USE_DELTA_CACHE
+ _ASSERT(block_index <= m_BlocksFilled);
+ if ( block_index != m_CacheBlockIndex ) {
+ size_t size = deltas.GetSize();
+ size_t block_pos = block_index*kBlockSize;
+ _ASSERT(block_pos < size);
+ size_t block_size = min(kBlockSize, size-block_pos);
+ _ASSERT(block_offset < block_size);
+ TValue sum = block_index == 0? 0: m_Blocks[block_index-1];
+ for ( size_t i = 0; i < block_size; ++i ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
+ sum += v;
+ }
+ m_CacheBlockInfo[i] = sum;
+ }
+ m_CacheBlockIndex = block_index;
+ if ( block_index == m_BlocksFilled ) {
+ m_Blocks[block_index] = sum;
+ m_BlocksFilled = block_index+1;
}
- size_t j = row%8;
- Uint1 bb = bits[i];
- v = ((bb<<j)&0x80) != 0;
- return true;
}
- else if ( IsBit_bvector() ) {
- const bm::bvector<>& bv = GetBit_bvector().GetBitVector();
- if ( row >= bv.size() ) {
- return false;
+ return m_CacheBlockInfo[block_offset];
+#else
+ size_t size = deltas.GetSize();
+ size_t block_pos = block_index*kBlockSize;
+ _ASSERT(block_pos < size);
+ size_t block_size = min(kBlockSize, size-block_pos);
+ _ASSERT(block_offset < block_size);
+ TValue sum = block_index == 0? 0: m_Blocks[block_index-1];
+ for ( size_t i = 0; i <= block_offset; ++i ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
+ sum += v;
}
- v = bv.get_bit(row);
- return true;
}
- else if ( IsInt() ) {
- const TInt& arr = GetInt();
- if ( row >= arr.size() ) {
- return false;
+ if ( block_index == m_BlocksFilled ) {
+ TValue sum2 = sum;
+ for ( size_t i = block_offset+1; i < block_size; ++i ) {
+ TValue v;
+ if ( deltas.TryGetValue(block_pos+i, v) ) {
+ sum2 += v;
+ }
}
- v = arr[row] != 0;
- return true;
+ m_Blocks[block_index] = sum2;
+ m_BlocksFilled = block_index+1;
}
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
- "CSeqTable_multi_data::TryGetBool(): "
- "data cannot be converted to bool");
+ return sum;
+#endif
}
-bool CSeqTable_multi_data::TryGetInt(size_t row, int& v) const
+Int8 CInt8DeltaSumCache::GetDeltaSum8(const TDeltas& deltas,
+ size_t index)
{
- if ( IsInt() ) {
- const TInt& arr = GetInt();
- if ( row >= arr.size() ) {
- return false;
- }
- v = arr[row];
- return true;
+ _ASSERT(index < deltas.GetSize());
+ size_t block_index = index / kBlockSize;
+ size_t block_offset = index % kBlockSize;
+ while ( block_index >= m_BlocksFilled ) {
+ x_GetDeltaSum2(deltas, m_BlocksFilled, 0);
}
- else if ( IsInt_delta() ) {
- const CSeqTable_multi_data& deltas = GetInt_delta();
- if ( row >= deltas.GetSize() ) {
- return false;
- }
- CMutexGuard guard(sx_PrepareMutex_multi_data);
- v = x_GetIntDeltaCache().GetDeltaSum(deltas, row);
- return true;
+ return x_GetDeltaSum2(deltas, block_index, block_offset);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////
+
+
+CSeqTable_multi_data::E_Choice CSeqTable_multi_data::GetValueType(void) const
+{
+ switch ( Which() ) {
+ case e_Bit_bvector:
+ return e_Bit;
+ case e_Int1:
+ case e_Int2:
+ return e_Int;
+ case e_Int_delta:
+ return GetInt_delta().GetValueType();
+ case e_Int_scaled:
+ return GetInt_scaled().GetIntSize() <= sizeof(Int4)? e_Int: e_Int8;
+ default:
+ return Which();
}
- else if ( IsInt_scaled() ) {
- const TInt_scaled& scaled = GetInt_scaled();
- if ( !scaled.GetData().TryGetInt(row, v) ) {
- return false;
- }
- v = v*scaled.GetMul()+scaled.GetAdd();
+}
+
+
+bool CSeqTable_multi_data::CanGetInt(void) const
+{
+ switch ( GetValueType() ) {
+ case e_Bit:
+ case e_Int:
+ case e_Int8:
return true;
+ default:
+ return false;
}
- // up cast from bool
- bool v1;
- try {
- if ( !TryGetBool(row, v1) ) {
- return false;
- }
- v = v1;
+}
+
+
+bool CSeqTable_multi_data::CanGetReal(void) const
+{
+ switch ( GetValueType() ) {
+ case e_Bit:
+ case e_Int:
+ case e_Int8:
+ case e_Real:
return true;
+ default:
+ return false;
}
- catch ( CSeqTableException& exc ) {
- if ( exc.GetErrCode() == exc.eIncompatibleRowType ) {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
- "CSeqTable_multi_data::TryGetInt(): "
- "data cannot be converted to int");
- }
- throw;
+}
+
+
+size_t CSeqTable_multi_data::GetIntSize(void) const
+{
+ switch ( Which() ) {
+ case e_Int:
+ return sizeof(TInt::value_type);
+ case e_Int1:
+ return sizeof(TInt1::value_type);
+ case e_Int2:
+ return sizeof(TInt2::value_type);
+ case e_Int8:
+ return sizeof(TInt8::value_type);
+ case e_Bit:
+ case e_Bit_bvector:
+ return 1; // one char is enough to store bit value
+ case e_Int_delta:
+ return GetInt_delta().GetIntSize();
+ case e_Int_scaled:
+ return GetInt_scaled().GetIntSize();
+ default:
+ return 0;
}
}
-bool CSeqTable_multi_data::TryGetReal(size_t row, double& v) const
+size_t CSeqTable_multi_data::GetSize(void) const
{
- if ( IsReal() ) {
- const TReal& arr = GetReal();
- if ( row >= arr.size() ) {
+ switch ( Which() ) {
+ case e_Int:
+ return GetInt().size();
+ case e_Int1:
+ return GetInt1().size();
+ case e_Int2:
+ return GetInt2().size();
+ case e_Int8:
+ return GetInt8().size();
+ case e_Real:
+ return GetReal().size();
+ case e_String:
+ return GetString().size();
+ case e_Bytes:
+ return GetBytes().size();
+ case e_Common_string:
+ return GetCommon_string().GetIndexes().size();
+ case e_Common_bytes:
+ return GetCommon_bytes().GetIndexes().size();
+ case e_Bit:
+ return GetBit().size()*8;
+ case e_Loc:
+ return GetLoc().size();
+ case e_Id:
+ return GetId().size();
+ case e_Interval:
+ return GetInterval().size();
+ case e_Bit_bvector:
+ return GetBit_bvector().GetSize();
+ case e_Int_delta:
+ return GetInt_delta().GetSize();
+ case e_Int_scaled:
+ return GetInt_scaled().GetData().GetSize();
+ case e_Real_scaled:
+ return GetReal_scaled().GetData().GetSize();
+ default:
+ break;
+ }
+ return 0;
+}
+
+
+template<class DstInt>
+static inline
+bool sx_DownCastInt8(DstInt& v, const Int8& value, const char* type_name)
+{
+ v = DstInt(value);
+ if ( Int8(v) != value ) {
+ NCBI_THROW_FMT(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::TryGet"<<type_name<<"(): "
+ "value is too big for requested type: "<<value);
+ }
+ return true;
+}
+
+
+template<class DstInt>
+static inline
+bool sx_Round(DstInt& v, double value, const char* cast_error)
+{
+ // Round and check range.
+ // Function round() is not everywhere available,
+ // so we are using either floor() or ceil() depending on value sign.
+ bool range_error;
+ if ( value > 0 ) {
+ value = floor(value + .5);
+ range_error = value > numeric_limits<DstInt>::max();
+ }
+ else {
+ value = ceil(value-.5);
+ range_error = value < numeric_limits<DstInt>::min();
+ }
+ if ( range_error ) {
+ // range check failed
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType, cast_error);
+ }
+ v = DstInt(value);
+ return true;
+}
+
+
+template<class Arr, class Int>
+static inline
+bool sx_TryGet(const Arr& arr, size_t row, Int& v)
+{
+ if ( row >= arr.size() ) {
+ return false;
+ }
+ v = arr[row];
+ return true;
+}
+
+
+bool CSeqTable_multi_data::TryGetBool(size_t row, bool& v) const
+{
+ Int8 value;
+ return x_TryGetInt8(row, value, "Bool") &&
+ sx_DownCastInt8(v, value, "Bool");
+}
+
+
+bool CSeqTable_multi_data::TryGetInt1(size_t row, Int1& v) const
+{
+ Int8 value;
+ return x_TryGetInt8(row, value, "Int1") &&
+ sx_DownCastInt8(v, value, "Int1");
+}
+
+
+bool CSeqTable_multi_data::TryGetInt2(size_t row, Int2& v) const
+{
+ Int8 value;
+ return x_TryGetInt8(row, value, "Int2") &&
+ sx_DownCastInt8(v, value, "Int2");
+}
+
+
+bool CSeqTable_multi_data::TryGetInt4(size_t row, Int4& v) const
+{
+ Int8 value;
+ return x_TryGetInt8(row, value, "Int4") &&
+ sx_DownCastInt8(v, value, "Int4");
+}
+
+
+bool CSeqTable_multi_data::x_TryGetInt8(size_t row, Int8& v,
+ const char* type_name) const
+{
+ switch ( Which() ) {
+ case e_Bit:
+ {
+ const TBit& bits = GetBit();
+ size_t i = row/8;
+ if ( i >= bits.size() ) {
return false;
}
- v = arr[row];
+ size_t j = row%8;
+ Uint1 bb = bits[i];
+ v = ((bb<<j)&0x80) != 0;
return true;
}
- else if ( IsReal_scaled() ) {
- const TReal_scaled& scaled = GetReal_scaled();
- if ( !scaled.GetData().TryGetReal(row, v) ) {
+ case e_Bit_bvector:
+ return sx_TryGet(GetBit_bvector().GetBitVector(), row, v);
+ case e_Int1:
+ return sx_TryGet(GetInt1(), row, v);
+ case e_Int2:
+ return sx_TryGet(GetInt2(), row, v);
+ case e_Int:
+ return sx_TryGet(GetInt(), row, v);
+ case e_Int8:
+ return sx_TryGet(GetInt8(), row, v);
+ case e_Int_delta:
+ {
+ const CSeqTable_multi_data& deltas = GetInt_delta();
+ if ( row >= deltas.GetSize() ) {
return false;
}
- v = v*scaled.GetMul()+scaled.GetAdd();
+ CMutexGuard guard(sx_PrepareMutex_multi_data);
+ v = x_GetIntDeltaCache().GetDeltaSum8(deltas, row);
return true;
}
- // up cast from int
- int v1;
- try {
- if ( !TryGetInt(row, v1) ) {
+ case e_Int_scaled:
+ return GetInt_scaled().TryGetInt8(row, v);
+ default:
+ NCBI_THROW_FMT(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::TryGet"<<type_name<<"(): "
+ "value cannot be converted to requested type");
+ }
+}
+
+
+bool CSeqTable_multi_data::TryGetInt8(size_t row, Int8& v) const
+{
+ return x_TryGetInt8(row, v, "Int8");
+}
+
+
+bool CSeqTable_multi_data::TryGetReal(size_t row, double& v) const
+{
+ switch ( Which() ) {
+ case e_Real:
+ return sx_TryGet(GetReal(), row, v);
+ case e_Real_scaled:
+ return GetReal_scaled().TryGetReal(row, v);
+ default:
+ Int8 value_int8;
+ if ( !x_TryGetInt8(row, value_int8, "Real") ) {
return false;
}
- v = v1;
+ v = double(value_int8);
return true;
}
- catch ( CSeqTableException& exc ) {
- if ( exc.GetErrCode() == exc.eIncompatibleRowType ) {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
- "CSeqTable_multi_data::TryGetReal() "
- "data cannot be converted to real");
- }
- throw;
- }
}
@@ -327,7 +601,7 @@ const string* CSeqTable_multi_data::GetStringPtr(size_t row) const
}
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::GetStringPtr() "
"data cannot be converted to string");
}
@@ -335,6 +609,58 @@ const string* CSeqTable_multi_data::GetStringPtr(size_t row) const
}
+bool CSeqTable_multi_data::TryGetInt1WithRounding(size_t row, Int1& v) const
+{
+ if ( GetValueType() == e_Real ) {
+ double value;
+ return TryGetReal(row, value) &&
+ sx_Round(v, value,
+ "CSeqTable_multi_data::TryGetInt1WithRounding(): "
+ "real value doesn't fit in Int1");
+ }
+ return TryGetInt1(row, v);
+}
+
+
+bool CSeqTable_multi_data::TryGetInt2WithRounding(size_t row, Int2& v) const
+{
+ if ( GetValueType() == e_Real ) {
+ double value;
+ return TryGetReal(row, value) &&
+ sx_Round(v, value,
+ "CSeqTable_multi_data::TryGetInt2WithRounding(): "
+ "real value doesn't fit in Int2");
+ }
+ return TryGetInt2(row, v);
+}
+
+
+bool CSeqTable_multi_data::TryGetInt4WithRounding(size_t row, int& v) const
+{
+ if ( GetValueType() == e_Real ) {
+ double value;
+ return TryGetReal(row, value) &&
+ sx_Round(v, value,
+ "CSeqTable_multi_data::TryGetInt4WithRounding(): "
+ "real value doesn't fit in Int4");
+ }
+ return TryGetInt4(row, v);
+}
+
+
+bool CSeqTable_multi_data::TryGetInt8WithRounding(size_t row, Int8& v) const
+{
+ if ( GetValueType() == e_Real ) {
+ double value;
+ return TryGetReal(row, value) &&
+ sx_Round(v, value,
+ "CSeqTable_multi_data::TryGetInt8WithRounding(): "
+ "real value doesn't fit in Int8");
+ }
+ return TryGetInt8(row, v);
+}
+
+
const vector<char>* CSeqTable_multi_data::GetBytesPtr(size_t row) const
{
if ( IsBytes() ) {
@@ -355,7 +681,7 @@ const vector<char>* CSeqTable_multi_data::GetBytesPtr(size_t row) const
}
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::GetBytesPtr() "
"data cannot be converted to OCTET STRING");
}
@@ -363,44 +689,6 @@ const vector<char>* CSeqTable_multi_data::GetBytesPtr(size_t row) const
}
-size_t CSeqTable_multi_data::GetSize(void) const
-{
- switch ( Which() ) {
- case e_Int:
- return GetInt().size();
- case e_Real:
- return GetReal().size();
- case e_String:
- return GetString().size();
- case e_Bytes:
- return GetBytes().size();
- case e_Common_string:
- return GetCommon_string().GetIndexes().size();
- case e_Common_bytes:
- return GetCommon_bytes().GetIndexes().size();
- case e_Bit:
- return GetBit().size()*8;
- case e_Loc:
- return GetLoc().size();
- case e_Id:
- return GetId().size();
- case e_Interval:
- return GetInterval().size();
- case e_Bit_bvector:
- return GetBit_bvector().GetSize();
- case e_Int_delta:
- return GetInt_delta().GetSize();
- case e_Int_scaled:
- return GetInt_scaled().GetData().GetSize();
- case e_Real_scaled:
- return GetReal_scaled().GetData().GetSize();
- default:
- break;
- }
- return 0;
-}
-
-
NCBI_PARAM_DECL(bool, OBJECTS, SEQ_TABLE_RESERVE);
NCBI_PARAM_DEF_EX(bool, OBJECTS, SEQ_TABLE_RESERVE, true,
eParam_NoThread, OBJECTS_SEQ_TABLE_RESERVE);
@@ -418,39 +706,53 @@ void CSeqTable_multi_data::CReserveHook::PreReadChoiceVariant(
size_t size = table->GetNum_rows();
CSeqTable_multi_data* data =
CType<CSeqTable_multi_data>::Get(variant.GetChoiceObject());
- switch ( variant.GetVariantIndex() ) {
- case e_Int:
- data->SetInt().reserve(size);
- break;
- case e_Real:
- data->SetReal().reserve(size);
- break;
- case e_String:
- data->SetString().reserve(size);
- break;
- case e_Bytes:
- data->SetBytes().reserve(size);
- break;
- case e_Common_string:
- data->SetCommon_string().SetIndexes().reserve(size);
- break;
- case e_Common_bytes:
- data->SetCommon_bytes().SetIndexes().reserve(size);
- break;
- case e_Bit:
- data->SetBit().reserve((size+7)/8);
- break;
- case e_Loc:
- data->SetLoc().reserve(size);
- break;
- case e_Id:
- data->SetId().reserve(size);
- break;
- case e_Interval:
- data->SetInterval().reserve(size);
- break;
- default:
- break;
+ try {
+ switch ( variant.GetVariantIndex() ) {
+ case e_Int:
+ data->SetInt().reserve(size);
+ break;
+ case e_Int1:
+ data->SetInt1().reserve(size);
+ break;
+ case e_Int2:
+ data->SetInt2().reserve(size);
+ break;
+ case e_Int8:
+ data->SetInt8().reserve(size);
+ break;
+ case e_Real:
+ data->SetReal().reserve(size);
+ break;
+ case e_String:
+ data->SetString().reserve(size);
+ break;
+ case e_Bytes:
+ data->SetBytes().reserve(size);
+ break;
+ case e_Common_string:
+ data->SetCommon_string().SetIndexes().reserve(size);
+ break;
+ case e_Common_bytes:
+ data->SetCommon_bytes().SetIndexes().reserve(size);
+ break;
+ case e_Bit:
+ data->SetBit().reserve((size+7)/8);
+ break;
+ case e_Loc:
+ data->SetLoc().reserve(size);
+ break;
+ case e_Id:
+ data->SetId().reserve(size);
+ break;
+ case e_Interval:
+ data->SetInterval().reserve(size);
+ break;
+ default:
+ break;
+ }
+ }
+ catch ( bad_alloc& /*ignored*/ ) {
+ // ignore insufficient memory exception from advisory reserve()
}
}
}
@@ -465,6 +767,15 @@ void CSeqTable_multi_data::ChangeTo(E_Choice type)
case e_Int:
ChangeToInt();
break;
+ case e_Int1:
+ ChangeToInt1();
+ break;
+ case e_Int2:
+ ChangeToInt2();
+ break;
+ case e_Int8:
+ ChangeToInt8();
+ break;
case e_Real:
ChangeToReal();
break;
@@ -490,15 +801,15 @@ void CSeqTable_multi_data::ChangeTo(E_Choice type)
ChangeToBit_bvector();
break;
case e_Int_scaled: // scaling requires extra parameters
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeTo(e_Int_scaled): "
"scaling parameters are unknown");
case e_Real_scaled: // scaling requires extra parameters
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeTo(e_Real_scaled): "
"scaling parameters are unknown");
default:
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeTo(): "
"requested multi-data type is invalid");
}
@@ -526,7 +837,7 @@ void CSeqTable_multi_data::ChangeToString(const string* omitted_value)
arr.push_back(*omitted_value);
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToString(): "
"common string table is sparse");
}
@@ -534,7 +845,7 @@ void CSeqTable_multi_data::ChangeToString(const string* omitted_value)
swap(SetString(), arr);
return;
}
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToString(): "
"requested mult-data type is invalid");
}
@@ -568,7 +879,7 @@ void CSeqTable_multi_data::ChangeToCommon_string(const string* omit_value)
SetCommon_string(*common);
return;
}
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToCommon_string(): "
"requested mult-data type is invalid");
}
@@ -596,7 +907,7 @@ void CSeqTable_multi_data::ChangeToBytes(const TBytesValue* omitted_value)
value = omitted_value;
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToBytes(): "
"common bytes table is sparse");
}
@@ -605,7 +916,7 @@ void CSeqTable_multi_data::ChangeToBytes(const TBytesValue* omitted_value)
swap(SetBytes(), arr);
return;
}
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToBytes(): "
"requested mult-data type is invalid");
}
@@ -639,7 +950,7 @@ void CSeqTable_multi_data::ChangeToCommon_bytes(const TBytesValue* omit_value)
SetCommon_bytes(*common);
return;
}
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToBytes(): "
"requested mult-data type is invalid");
}
@@ -679,9 +990,10 @@ void CSeqTable_multi_data::ChangeToInt_scaled(int mul, int add)
if ( IsInt_scaled() ) {
return;
}
- TInt arr;
+ int min_v = 0, max_v = 0;
if ( IsInt() ) {
// in-place
+ TInt arr;
swap(arr, SetInt());
NON_CONST_ITERATE ( TInt, it, arr ) {
TInt::value_type value = *it;
@@ -693,14 +1005,23 @@ void CSeqTable_multi_data::ChangeToInt_scaled(int mul, int add)
*it = value*mul+add;
}
swap(arr, SetInt());
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToInt_scaled(): "
"value is not round for scaling");
}
- *it = value/mul;
+ value /= mul;
+ if ( value < min_v ) {
+ min_v = value;
+ }
+ else if ( value > max_v ) {
+ max_v = value;
+ }
+ *it = value;
}
+ swap(SetInt_scaled().SetData().SetInt(), arr);
}
- else {
+ else if ( GetIntSize() <= sizeof(Int4) ) {
+ TInt arr;
for ( size_t row = 0; ; ++row ) {
TInt::value_type value;
if ( !TryGetInt(row, value) ) {
@@ -708,14 +1029,74 @@ void CSeqTable_multi_data::ChangeToInt_scaled(int mul, int add)
}
value -= add;
if ( value % mul != 0 ) {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToInt_scaled(): "
"value is not round for scaling");
}
- arr.push_back(value/mul);
+ value /= mul;
+ if ( value > max_v ) {
+ max_v = value;
+ }
+ else if ( value < min_v ) {
+ min_v = value;
+ }
+ arr.push_back(value);
}
+ swap(SetInt_scaled().SetData().SetInt(), arr);
+ }
+ else { // Int8 -> scaled
+ TInt8 arr;
+ Int8 min_v8 = 0, max_v8 = 0;
+ for ( size_t row = 0; ; ++row ) {
+ Int8 value;
+ if ( !TryGetInt8(row, value) ) {
+ break;
+ }
+ value -= add;
+ if ( value % mul != 0 ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::ChangeToInt_scaled(): "
+ "value is not round for scaling");
+ }
+ value /= mul;
+ if ( value > max_v8 ) {
+ max_v8 = value;
+ }
+ else if ( value < min_v8 ) {
+ min_v8 = value;
+ }
+ arr.push_back(value);
+ }
+ CScaled_int_multi_data& scaled = SetInt_scaled();
+ swap(scaled.SetData().SetInt8(), arr);
+ bool is_int8 = false;
+ if ( min_v < kMin_Int ) {
+ scaled.SetMin(min_v);
+ is_int8 = true;
+ }
+ if ( max_v > kMax_Int ) {
+ scaled.SetMax(max_v);
+ is_int8 = true;
+ }
+ if ( is_int8 ) {
+ return;
+ }
+ min_v = int(min_v8);
+ max_v = int(max_v8);
+ }
+ // compact scaled data
+ if ( min_v == 0 && max_v <= 1 ) {
+ SetInt_scaled().SetData().ChangeToBit();
+ }
+ else if ( min_v >= kMin_I1 && max_v <= kMax_I1 ) {
+ SetInt_scaled().SetData().ChangeToInt1();
+ }
+ else if ( min_v >= kMin_I2 && max_v <= kMax_I2 ) {
+ SetInt_scaled().SetData().ChangeToInt2();
+ }
+ else {
+ SetInt_scaled().SetData().ChangeToInt4();
}
- swap(SetInt_scaled().SetData().SetInt(), arr);
}
@@ -751,7 +1132,7 @@ void CSeqTable_multi_data::ChangeToInt_delta(void)
}
-void CSeqTable_multi_data::ChangeToInt(void)
+void CSeqTable_multi_data::ChangeToInt4(void)
{
if ( IsInt() ) {
return;
@@ -771,28 +1152,69 @@ void CSeqTable_multi_data::ChangeToInt(void)
return;
}
TInt arr;
- if ( IsReal() || IsReal_scaled() ) {
- for ( size_t row = 0; ; ++row ) {
- double value;
- if ( !TryGetReal(row, value) ) {
- break;
- }
- TInt::value_type int_value =
- TInt::value_type(value > 0? floor(value+.5): ceil(value-.5));
- arr.push_back(int_value);
+ for ( size_t row = 0; ; ++row ) {
+ TInt::value_type value;
+ if ( !TryGetIntWithRounding(row, value) ) {
+ break;
}
+ arr.push_back(value);
}
- else {
- for ( size_t row = 0; ; ++row ) {
- TInt::value_type value;
- if ( !TryGetInt(row, value) ) {
- break;
- }
- arr.push_back(value);
+ Reset();
+ swap(SetInt(), arr);
+}
+
+
+void CSeqTable_multi_data::ChangeToInt1(void)
+{
+ if ( IsInt1() ) {
+ return;
+ }
+ TInt1 arr;
+ for ( size_t row = 0; ; ++row ) {
+ Int1 value;
+ if ( !TryGetInt1WithRounding(row, value) ) {
+ break;
}
+ arr.push_back(value);
}
Reset();
- swap(SetInt(), arr);
+ swap(SetInt1(), arr);
+}
+
+
+void CSeqTable_multi_data::ChangeToInt2(void)
+{
+ if ( IsInt2() ) {
+ return;
+ }
+ TInt2 arr;
+ for ( size_t row = 0; ; ++row ) {
+ Int2 value;
+ if ( !TryGetInt2WithRounding(row, value) ) {
+ break;
+ }
+ arr.push_back(value);
+ }
+ Reset();
+ swap(SetInt2(), arr);
+}
+
+
+void CSeqTable_multi_data::ChangeToInt8(void)
+{
+ if ( IsInt8() ) {
+ return;
+ }
+ TInt8 arr;
+ for ( size_t row = 0; ; ++row ) {
+ Int8 value;
+ if ( !TryGetInt8WithRounding(row, value) ) {
+ break;
+ }
+ arr.push_back(value);
+ }
+ Reset();
+ swap(SetInt8(), arr);
}
@@ -845,18 +1267,28 @@ void CSeqTable_multi_data::ChangeToBit(void)
}
arr.resize((bv.size()+7)/8);
}
- else if ( IsInt() ) {
- const TInt& src = GetInt();
- size_t size = src.size();
+ else if ( CanGetInt() ) {
+ size_t size = GetSize();
arr.resize((size+7)/8);
for ( size_t i = 0; i < size; ++i ) {
- if ( src[i] ) {
+ int v;
+ if ( !TryGetInt(i, v) ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::ChangeToBit(): "
+ "multi-data value cannot be converted to int");
+ }
+ if ( v < 0 || v > 1 ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::ChangeToBit(): "
+ "multi-data value is not 0 or 1");
+ }
+ if ( v ) {
arr[i/8] |= 0x80 >> i%8;
}
}
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToBit(): "
"requested mult-data type is invalid");
}
@@ -870,34 +1302,40 @@ void CSeqTable_multi_data::ChangeToBit_bvector(void)
if ( IsBit_bvector() ) {
return;
}
- AutoPtr<bm::bvector<> > bv(new bm::bvector<>(GetSize()));
+ size_t size = GetSize();
+ AutoPtr<bm::bvector<> > bv(new bm::bvector<>(size));
if ( IsBit() ) {
const TBit& src = GetBit();
- size_t size = src.size();
- for ( size_t i = 0; i < size; ++i ) {
- if ( Uint1 b = src[i] ) {
- // the following cycle assumes that Uint1 is exactly 8-bit
- for ( size_t j = 0; b; ++j, b <<= 1 ) {
- if ( b&0x80 ) {
- bv->set_bit(i*8+j);
- }
+ for ( size_t i = 0; i < size; i += 8 ) {
+ for ( Uint1 b = src[i/8], j = 0; b & 0xff; ++j, b <<= 1 ) {
+ if ( b&0x80 ) {
+ bv->set_bit(i+j);
}
}
}
}
- else if ( IsInt() ) {
- const TInt& src = GetInt();
- size_t size = src.size();
+ else if ( CanGetInt() ) {
for ( size_t i = 0; i < size; ++i ) {
- if ( src[i] ) {
+ int v;
+ if ( !TryGetInt(i, v) ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::ChangeToBit_bvector(): "
+ "multi-data value cannot be converted to int");
+ }
+ if ( v < 0 || v > 1 ) {
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_multi_data::ChangeToBit_bvector(): "
+ "multi-data value is not 0 or 1");
+ }
+ if ( v ) {
bv->set_bit(i);
}
}
}
else {
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_multi_data::ChangeToBit_bvector(): "
- "requested mult-data type is invalid");
+ "requested multi-data type is invalid");
}
bv->optimize();
SetBit_bvector().SetBitVector(bv.release());
diff --git a/c++/src/objects/seqtable/SeqTable_single_data.cpp b/c++/src/objects/seqtable/SeqTable_single_data.cpp
new file mode 100644
index 0000000..88a70f5
--- /dev/null
+++ b/c++/src/objects/seqtable/SeqTable_single_data.cpp
@@ -0,0 +1,224 @@
+/* $Id: SeqTable_single_data.cpp 461050 2015-03-05 16:08:06Z vasilche $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: .......
+ *
+ * File Description:
+ * .......
+ *
+ * Remark:
+ * This code was originally generated by application DATATOOL
+ * using the following specifications:
+ * 'seqtable.asn'.
+ */
+
+// standard includes
+#include <ncbi_pch.hpp>
+
+// generated includes
+#include <objects/seqtable/SeqTable_single_data.hpp>
+
+// generated classes
+
+BEGIN_NCBI_SCOPE
+
+BEGIN_objects_SCOPE // namespace ncbi::objects::
+
+// destructor
+CSeqTable_single_data::~CSeqTable_single_data(void)
+{
+}
+
+
+void CSeqTable_single_data::ThrowOverflowError(Int8 value,
+ const char* type_name)
+{
+ NCBI_THROW_FMT(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_single_data::GetValue("<<type_name<<"&): "
+ "value is too big for requested type: "<<value);
+}
+
+
+void CSeqTable_single_data::ThrowConversionError(const char* type_name) const
+{
+ NCBI_THROW_FMT(CSeqTableException, eIncompatibleValueType,
+ "CSeqTable_single_data::GetValue("<<type_name<<"&): "
+ <<SelectionName(Which())<<
+ " value cannot be converted to requested type");
+}
+
+
+template<class DstInt, class SrcInt>
+static inline
+bool sx_DownCast(DstInt& v, const SrcInt& value, const char* type_name)
+{
+ v = DstInt(value);
+ if ( SrcInt(v) != value ) {
+ CSeqTable_single_data::ThrowOverflowError(value, type_name);
+ }
+ return true;
+}
+
+
+void CSeqTable_single_data::GetValue(bool& v) const
+{
+ static const char* const type_name = "bool";
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ sx_DownCast(v, GetInt(), type_name);
+ break;
+ case e_Int8:
+ sx_DownCast(v, GetInt8(), type_name);
+ break;
+ default:
+ ThrowConversionError(type_name);
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(Int1& v) const
+{
+ static const char* const type_name = "Int1";
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ sx_DownCast(v, GetInt(), type_name);
+ break;
+ case e_Int8:
+ sx_DownCast(v, GetInt8(), type_name);
+ break;
+ default:
+ ThrowConversionError(type_name);
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(Int2& v) const
+{
+ static const char* const type_name = "Int2";
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ sx_DownCast(v, GetInt(), type_name);
+ break;
+ case e_Int8:
+ sx_DownCast(v, GetInt8(), type_name);
+ break;
+ default:
+ ThrowConversionError(type_name);
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(int& v) const
+{
+ static const char* const type_name = "int";
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ v = GetInt();
+ break;
+ case e_Int8:
+ sx_DownCast(v, GetInt8(), type_name);
+ break;
+ default:
+ ThrowConversionError(type_name);
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(Int8& v) const
+{
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ v = GetInt();
+ break;
+ case e_Int8:
+ v = GetInt8();
+ break;
+ default:
+ ThrowConversionError("Int8");
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(double& v) const
+{
+ switch ( Which() ) {
+ case e_Bit:
+ v = GetBit();
+ break;
+ case e_Int:
+ v = GetInt();
+ break;
+ case e_Int8:
+ v = GetInt8();
+ break;
+ case e_Real:
+ v = GetReal();
+ break;
+ default:
+ ThrowConversionError("double");
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(string& v) const
+{
+ if ( IsString() ) {
+ v = GetString();
+ }
+ else {
+ ThrowConversionError("string");
+ }
+}
+
+
+void CSeqTable_single_data::GetValue(TBytes& v) const
+{
+ if ( IsBytes() ) {
+ v = GetBytes();
+ }
+ else {
+ ThrowConversionError("vector<char>");
+ }
+}
+
+
+END_objects_SCOPE // namespace ncbi::objects::
+
+END_NCBI_SCOPE
diff --git a/c++/src/objects/seqtable/SeqTable_sparse_index.cpp b/c++/src/objects/seqtable/SeqTable_sparse_index.cpp
index b70617e..53f14b0 100644
--- a/c++/src/objects/seqtable/SeqTable_sparse_index.cpp
+++ b/c++/src/objects/seqtable/SeqTable_sparse_index.cpp
@@ -1,4 +1,4 @@
-/* $Id: SeqTable_sparse_index.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: SeqTable_sparse_index.cpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -626,7 +626,7 @@ void CSeqTable_sparse_index::ChangeTo(E_Choice type)
ChangeToBit_set_bvector();
break;
default:
- NCBI_THROW(CSeqTableException, eIncompatibleRowType,
+ NCBI_THROW(CSeqTableException, eIncompatibleValueType,
"CSeqTable_sparse_index::ChangeTo(): "
"requested sparse index type is invalid");
}
diff --git a/c++/src/objects/seqtable/Seq_table.cpp b/c++/src/objects/seqtable/Seq_table.cpp
index 004b582..5ee0d42 100644
--- a/c++/src/objects/seqtable/Seq_table.cpp
+++ b/c++/src/objects/seqtable/Seq_table.cpp
@@ -1,4 +1,4 @@
-/* $Id: Seq_table.cpp 428967 2014-03-10 16:26:03Z vasilche $
+/* $Id: Seq_table.cpp 457991 2015-01-29 19:26:03Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,12 @@ CSeq_table::~CSeq_table(void)
}
+string CSeq_table::GetIdName(TColumnId column_id)
+{
+ return CSeqTable_column_info::ENUM_METHOD_NAME(EField_id)()->FindName(column_id, true);
+}
+
+
const CSeqTable_column& CSeq_table::GetColumn(CTempString column_name) const
{
ITERATE ( TColumns, it, GetColumns() ) {
@@ -80,7 +86,7 @@ const CSeqTable_column& CSeq_table::GetColumn(TColumnId column_id) const
}
}
NCBI_THROW(CSeqTableException, eColumnNotFound,
- "Column not found: "+CSeqTable_column_info::ENUM_METHOD_NAME(EField_id)()->FindName(column_id, true));
+ "Column not found: "+GetIdName(column_id));
}
@@ -98,7 +104,7 @@ const CSeqTable_column& CSeq_table::GetColumn(TColumnId column_id,
}
}
NCBI_THROW(CSeqTableException, eColumnNotFound,
- "Column not found: "+string(column_name)+"/"+CSeqTable_column_info::ENUM_METHOD_NAME(EField_id)()->FindName(column_id, true));
+ "Column not found: "+string(column_name)+"/"+GetIdName(column_id));
}
@@ -107,8 +113,8 @@ const char* CSeqTableException::GetErrCodeString(void) const
switch ( GetErrCode() ) {
case eColumnNotFound: return "eColumnNotFound";
case eRowNotFound: return "eRowNotFound";
+ case eIncompatibleValueType:return "eIncompatibleValueType";
case eOtherError: return "eOtherError";
- case eIncompatibleRowType: return "eIncompatibleRowType";
default: return CException::GetErrCodeString();
}
}
@@ -116,5 +122,3 @@ const char* CSeqTableException::GetErrCodeString(void) const
END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
-
-/* Original file checksum: lines: 57, chars: 1726, CRC32: d9ae38b2 */
diff --git a/c++/src/objects/seqtable/seqtable.asn b/c++/src/objects/seqtable/seqtable.asn
index 4d143a1..c9ceb94 100644
--- a/c++/src/objects/seqtable/seqtable.asn
+++ b/c++/src/objects/seqtable/seqtable.asn
@@ -1,4 +1,4 @@
---$Revision: 428967 $
+--$Revision: 457991 $
-- ----------------------------------------------------------------------------
--
-- PUBLIC DOMAIN NOTICE
@@ -132,7 +132,12 @@ Scaled-int-multi-data ::= SEQUENCE {
-- output data[i] = data[i]*mul+add
mul INTEGER,
add INTEGER,
- data SeqTable-multi-data
+ data SeqTable-multi-data,
+
+ -- min/max scaled value
+ -- should be set if scaled values may not fit in 32-bit signed integer
+ min INTEGER OPTIONAL,
+ max INTEGER OPTIONAL
}
@@ -154,7 +159,7 @@ BVector-data ::= SEQUENCE {
SeqTable-multi-data ::= CHOICE {
- -- a set of integers, one per row
+ -- a set of 4-byte integers, one per row
int SEQUENCE OF INTEGER,
-- a set of reals, one per row
@@ -192,7 +197,16 @@ SeqTable-multi-data ::= CHOICE {
-- a set of bit, represented as serialized bvector,
-- see include/util/bitset/bm.h
- bit-bvector BVector-data
+ bit-bvector BVector-data,
+
+ -- a set of signed 1-byte integers encoded as sequential octets
+ int1 OCTET STRING,
+
+ -- a set of signed 2-byte integers
+ int2 SEQUENCE OF INTEGER,
+
+ -- a set of signed 8-byte integers
+ int8 SEQUENCE OF INTEGER
}
@@ -215,7 +229,9 @@ SeqTable-single-data ::= CHOICE {
-- location
loc Seq-loc,
id Seq-id,
- interval Seq-interval
+ interval Seq-interval,
+
+ int8 INTEGER
}
diff --git a/c++/src/objects/seqtable/seqtable.def b/c++/src/objects/seqtable/seqtable.def
index 2d24f26..1b6f845 100644
--- a/c++/src/objects/seqtable/seqtable.def
+++ b/c++/src/objects/seqtable/seqtable.def
@@ -6,6 +6,10 @@ columns._type = vector
[SeqTable-multi-data]
int._type = vector
+int2._type = vector
+int8._type = vector
+int2.E._type = Int2
+int8.E._type = Int8
real._type = vector
string._type = vector
bytes._type = vector
@@ -30,3 +34,7 @@ indexes-delta.E._type = unsigned
[BVector-data]
size._type = unsigned
+
+[Scaled-int-multi-data]
+min._type = Int8
+max._type = Int8
diff --git a/c++/src/objects/taxon1/Makefile.taxon1.lib b/c++/src/objects/taxon1/Makefile.taxon1.lib
index 7058116..4d8c561 100644
--- a/c++/src/objects/taxon1/Makefile.taxon1.lib
+++ b/c++/src/objects/taxon1/Makefile.taxon1.lib
@@ -3,6 +3,8 @@ ASN_PROJ = taxon1
LIB = taxon1
SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont
+DLL_LIB = xconnect
+
WATCHERS = domrach
diff --git a/c++/src/objects/taxon1/Taxon2_data.cpp b/c++/src/objects/taxon1/Taxon2_data.cpp
new file mode 100644
index 0000000..63a3640
--- /dev/null
+++ b/c++/src/objects/taxon1/Taxon2_data.cpp
@@ -0,0 +1,186 @@
+/* $Id: Taxon2_data.cpp 454841 2014-12-18 17:45:33Z domrach $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Michael Domrachev
+ *
+ * File Description:
+ * Taxon2_data is returned to caller in various taxonomy-related lookups
+ *
+ * Remark:
+ * This code was originally generated by application DATATOOL
+ * using the following specifications:
+ * 'taxon1.asn'.
+ */
+
+// standard includes
+#include <ncbi_pch.hpp>
+
+// generated includes
+#include <objects/taxon1/Taxon2_data.hpp>
+
+// generated classes
+
+BEGIN_NCBI_SCOPE
+
+BEGIN_objects_SCOPE // namespace ncbi::objects::
+
+// destructor
+CTaxon2_data::~CTaxon2_data(void)
+{
+}
+
+CTaxon2_data::TOrgProperties::iterator
+CTaxon2_data::x_FindProperty( const string& name )
+{
+ NON_CONST_ITERATE( TOrgProperties, i, m_props ) {
+ if( NStr::Equal( (*i)->GetDb(), name ) ) {
+ return i;
+ }
+ }
+ return m_props.end();
+}
+
+CTaxon2_data::TOrgProperties::const_iterator
+CTaxon2_data::x_FindPropertyConst( const string& name ) const
+{
+ ITERATE( TOrgProperties, i, m_props ) {
+ if( NStr::Equal( (*i)->GetDb(), name ) ) {
+ return i;
+ }
+ }
+ return m_props.end();
+}
+
+void
+CTaxon2_data::SetProperty( const string& name, const string& value )
+{
+ if( !name.empty() ) {
+ TOrgProperties::iterator i = x_FindProperty( name );
+ if( i != m_props.end() ) {
+ (*i)->SetTag().SetStr( value );
+ } else {
+ CRef< CDbtag > pProp( new CDbtag );
+ pProp->SetDb( name );
+ pProp->SetTag().SetStr( value );
+ m_props.push_back( pProp );
+ }
+ }
+}
+
+void
+CTaxon2_data::SetProperty( const string& name, int value )
+{
+ if( !name.empty() ) {
+ TOrgProperties::iterator i = x_FindProperty( name );
+ if( i != m_props.end() ) {
+ (*i)->SetTag().SetId( value );
+ } else {
+ CRef< CDbtag > pProp( new CDbtag );
+ pProp->SetDb( name );
+ pProp->SetTag().SetId( value );
+ m_props.push_back( pProp );
+ }
+ }
+}
+
+void
+CTaxon2_data::SetProperty( const string& name, bool value )
+{
+ if( !name.empty() ) {
+ TOrgProperties::iterator i = x_FindProperty( name );
+ if( i != m_props.end() ) {
+ (*i)->SetTag().SetId( value ? 1 : 0 );
+ } else {
+ CRef< CDbtag > pProp( new CDbtag );
+ pProp->SetDb( name );
+ pProp->SetTag().SetId( value ? 1 : 0 );
+ m_props.push_back( pProp );
+ }
+ }
+}
+
+bool
+CTaxon2_data::GetProperty( const string& name, string& value ) const
+{
+ if( !name.empty() ) {
+ TOrgProperties::const_iterator i = x_FindPropertyConst( name );
+ if( i != m_props.end() && (*i)->IsSetTag() ) {
+ switch( (*i)->GetTag().Which() ) {
+ case CObject_id::e_Str: value = (*i)->GetTag().GetStr(); return true;
+ case CObject_id::e_Id: value = NStr::IntToString( (*i)->GetTag().GetId() ); return true;
+ default: break; // unknown type
+ }
+ }
+ }
+ return false;
+}
+
+bool
+CTaxon2_data::GetProperty( const string& name, int& value ) const
+{
+ if( !name.empty() ) {
+ TOrgProperties::const_iterator i = x_FindPropertyConst( name );
+ if( i != m_props.end() && (*i)->IsSetTag() ) {
+ switch( (*i)->GetTag().Which() ) {
+ case CObject_id::e_Str: value = NStr::StringToInt( (*i)->GetTag().GetStr(), NStr::fConvErr_NoThrow ); return true;
+ case CObject_id::e_Id: value = (*i)->GetTag().GetId(); return true;
+ default: break; // unknown type
+ }
+ }
+ }
+ return false;
+}
+
+bool
+CTaxon2_data::GetProperty( const string& name, bool& value ) const
+{
+ if( !name.empty() ) {
+ TOrgProperties::const_iterator i = x_FindPropertyConst( name );
+ if( i != m_props.end() && (*i)->IsSetTag() ) {
+ switch( (*i)->GetTag().Which() ) {
+ case CObject_id::e_Str: value = NStr::StringToBool( (*i)->GetTag().GetStr() ); return true;
+ case CObject_id::e_Id: value = (*i)->GetTag().GetId() != 0; return true;
+ default: break; // unknown type
+ }
+ }
+ }
+ return false;
+}
+
+void
+CTaxon2_data::ResetProperty( const string& name )
+{
+ TOrgProperties::iterator i = x_FindProperty( name );
+ while( i != m_props.end() ) {
+ m_props.erase(i);
+ i = x_FindProperty( name );
+ }
+}
+
+END_objects_SCOPE // namespace ncbi::objects::
+
+END_NCBI_SCOPE
+
+/* Original file checksum: lines: 57, chars: 1728, CRC32: 2b99c14d */
diff --git a/c++/src/objects/taxon1/cache.cpp b/c++/src/objects/taxon1/cache.cpp
index f9c9b04..08c5d13 100644
--- a/c++/src/objects/taxon1/cache.cpp
+++ b/c++/src/objects/taxon1/cache.cpp
@@ -1,4 +1,4 @@
-/* $Id: cache.cpp 428223 2014-02-28 16:54:26Z domrach $
+/* $Id: cache.cpp 454784 2014-12-17 22:26:37Z domrach $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -257,7 +257,7 @@ COrgRefCache::Lookup( int tax_id, CTaxon2_data** ppData )
}
bool
-s_BuildLineage( string& str, CTaxon1Node* pNode, unsigned sz, int sp_rank )
+s_BuildLineage( string& str, CTaxon1Node* pNode, size_t sz, int sp_rank )
{
if( !pNode->IsRoot() ) {
// if( pNode->GetRank() > sp_rank-1 ) {
@@ -663,14 +663,16 @@ COrgRefCache::BuildOrgRef( CTaxon1Node& node, COrg_ref& org, bool& is_species )
pProp->SetIval1( node.GetTaxId() );
pProp->SetIval2( -1 ); // Get string property by name
pProp->SetSval( "orgname" );
+ CTaxon1_req req1;
+ CTaxon1_resp resp1;
- req.SetGetorgprop( *pProp );
+ req1.SetGetorgprop( *pProp );
try {
- if( m_host.SendRequest( req, resp ) ) {
- if( resp.IsGetorgprop() ) {
- if( resp.GetGetorgprop().size() > 0 ) {
+ if( m_host.SendRequest( req1, resp1 ) ) {
+ if( resp1.IsGetorgprop() ) {
+ if( resp1.GetGetorgprop().size() > 0 ) {
CRef<CTaxon1_info> pInfo
- = resp.GetGetorgprop().front();
+ = resp1.GetGetorgprop().front();
if( pInfo->IsSetSval() && !pInfo->GetSval().empty() ) {
try {
CObjectIStreamAsn is( pInfo->GetSval().c_str(),
@@ -686,7 +688,7 @@ COrgRefCache::BuildOrgRef( CTaxon1Node& node, COrg_ref& org, bool& is_species )
}
}
}
- } catch( exception& e ) {
+ } catch( exception& /*e*/ ) {
}
// Fill some other orgname fields
short div_id( node.GetDivision() );
@@ -816,7 +818,7 @@ COrgRefCache::BuildOrgRef( CTaxon1Node& node, COrg_ref& org, bool& is_species )
}
}
}
- } catch( exception& e ) {
+ } catch( exception& /*e*/ ) {
}
return true;
}
diff --git a/c++/src/objects/taxon1/ctreecont.cpp b/c++/src/objects/taxon1/ctreecont.cpp
index 89f5882..cc58f91 100644
--- a/c++/src/objects/taxon1/ctreecont.cpp
+++ b/c++/src/objects/taxon1/ctreecont.cpp
@@ -1,4 +1,4 @@
-/* $Id: ctreecont.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: ctreecont.cpp 460171 2015-02-25 15:50:50Z domrach $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -695,7 +695,7 @@ bool CTreeIterator::AddChild(CTreeContNodeBase* new_node,
if( prev ) { // insert after prevtmp
prev->m_sibling = new_node;
} else { // insert as first child
- prev->Parent()->m_child = next;
+ new_node->Parent()->m_child = new_node;
}
// Restore state
GoParent();
diff --git a/c++/src/objects/taxon1/taxon1.cpp b/c++/src/objects/taxon1/taxon1.cpp
index d5532a9..d5bf59e 100644
--- a/c++/src/objects/taxon1/taxon1.cpp
+++ b/c++/src/objects/taxon1/taxon1.cpp
@@ -1,4 +1,4 @@
-/* $Id: taxon1.cpp 428223 2014-02-28 16:54:26Z domrach $
+/* $Id: taxon1.cpp 455142 2014-12-23 15:34:46Z domrach $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -113,6 +113,8 @@ CTaxon1::Init(const STimeout* timeout, unsigned reconnect_attempts,
SetLastError( "ERROR: Init(): Already initialized" );
return false;
}
+ SConnNetInfo* pNi = NULL;
+
try {
// Open connection to Taxonomy service
CTaxon1_req req;
@@ -134,9 +136,19 @@ CTaxon1::Init(const STimeout* timeout, unsigned reconnect_attempts,
}
auto_ptr<CObjectOStream> pOut;
auto_ptr<CObjectIStream> pIn;
+ pNi = ConnNetInfo_Create( m_pchService );
+ if( pNi == NULL ) {
+ SetLastError( "ERROR: Init(): Unable to create net info" );
+ return false;
+ }
+ pNi->max_try = reconnect_attempts + 1;
+ ConnNetInfo_SetTimeout( pNi, timeout );
+
auto_ptr<CConn_ServiceStream>
pServer( new CConn_ServiceStream(m_pchService, fSERV_Any,
- 0, 0, m_timeout) );
+ pNi, 0, m_timeout) );
+ ConnNetInfo_Destroy( pNi );
+ pNi = NULL;
#ifdef USE_TEXT_ASN
m_eDataFormat = eSerial_AsnText;
@@ -168,13 +180,16 @@ CTaxon1::Init(const STimeout* timeout, unsigned reconnect_attempts,
} catch( exception& e ) {
SetLastError( e.what() );
}
- // Clean streams
+ // Clean up streams
delete m_pIn;
delete m_pOut;
delete m_pServer;
m_pIn = NULL;
m_pOut = NULL;
m_pServer = NULL;
+ if( pNi ) {
+ ConnNetInfo_Destroy( pNi );
+ }
return false;
}
@@ -484,19 +499,20 @@ CTaxon1::OrgRefAdjust( COrg_ref& inp_orgRef, const COrg_ref& db_orgRef,
i != lSrcMod.end();
++i ) {
switch( (*i)->GetSubtype() ) {
- case COrgMod::eSubtype_gb_acronym:
- case COrgMod::eSubtype_gb_anamorph:
- case COrgMod::eSubtype_gb_synonym:
+ //case COrgMod::eSubtype_gb_acronym:
+ //case COrgMod::eSubtype_gb_anamorph:
+ //case COrgMod::eSubtype_gb_synonym:
+ default:
pMod.Reset( new COrgMod() );
pMod->Assign( *(*i) );
lDstMod.push_back( pMod );
- default:
+ case COrgMod::eSubtype_other:
break;
}
}
// Remove 'other' modifiers
- PFindModByType fmbt( COrgMod::eSubtype_other );
- remove_if( lDstMod.begin(), lDstMod.end(), fmbt );
+ //PFindModByType fmbt( COrgMod::eSubtype_other );
+ //remove_if( lDstMod.begin(), lDstMod.end(), fmbt );
}
// Remove 'synonym' or 'anamorph' it if coincides with taxname
PRemoveSynAnamorph rsa( inp_orgRef.GetTaxname() );
diff --git a/c++/src/objects/taxon3/Makefile.taxon3.lib b/c++/src/objects/taxon3/Makefile.taxon3.lib
index 66a7390..4f7c359 100644
--- a/c++/src/objects/taxon3/Makefile.taxon3.lib
+++ b/c++/src/objects/taxon3/Makefile.taxon3.lib
@@ -1,9 +1,11 @@
-# $Id: Makefile.taxon3.lib 427424 2014-02-20 13:38:50Z gouriano $
+# $Id: Makefile.taxon3.lib 478176 2015-09-04 15:51:52Z ivanov $
LIB = taxon3
-SRC = taxon3__ taxon3___ taxon3
+SRC = taxon3__ taxon3___ taxon3 cached_taxon3
-WATCHERS = bollin
+DLL_LIB = xconnect
+
+WATCHERS = bollin holmesbr
USES_LIBRARIES = \
diff --git a/c++/src/objects/taxon3/cached_taxon3.cpp b/c++/src/objects/taxon3/cached_taxon3.cpp
new file mode 100755
index 0000000..96e004a
--- /dev/null
+++ b/c++/src/objects/taxon3/cached_taxon3.cpp
@@ -0,0 +1,207 @@
+/* $Id: cached_taxon3.cpp 478176 2015-09-04 15:51:52Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Brad Holmes
+ *
+ * File Description:
+ * NCBI Taxonomy 3 service that caches a parameterized number of replies
+ *
+ */
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbistr.hpp>
+#include <objects/taxon3/cached_taxon3.hpp>
+#include <objects/seqfeat/seqfeat__.hpp>
+#include <objects/misc/error_codes.hpp>
+#include <connect/ncbi_conn_stream.hpp>
+#include <serial/serial.hpp>
+#include <serial/enumvalues.hpp>
+#include <serial/objistr.hpp>
+#include <serial/objostr.hpp>
+
+#include <algorithm>
+
+
+#define NCBI_USE_ERRCODE_X Objects_Taxonomy
+
+
+
+BEGIN_NCBI_SCOPE
+BEGIN_objects_SCOPE // namespace ncbi::objects::
+
+const string kInvalidReplyMsg = "Taxonomy service returned invalid reply";
+
+
+CCachedTaxon3::CCachedTaxon3(AutoPtr<ITaxon3> taxon, TSizeType capacity)
+ : CCache<string, CRef<CTaxon3_reply> >(capacity),
+ m_taxon(taxon)
+{
+}
+
+
+// The method to create the cache one-off
+AutoPtr<CCachedTaxon3> CCachedTaxon3::Create(
+ AutoPtr<ITaxon3> taxon, TSizeType capacity)
+{
+ return AutoPtr<CCachedTaxon3>(CreateUnSafe(taxon, capacity));
+}
+
+// This should only be used if it will be
+// immediately wrapped into a safe pointer
+CCachedTaxon3* CCachedTaxon3::CreateUnSafe(
+ AutoPtr<ITaxon3> taxon, TSizeType capacity)
+{
+ CCachedTaxon3* c = new CCachedTaxon3(taxon, capacity);
+ return c;
+}
+
+void
+CCachedTaxon3::Init(void)
+{
+ static const STimeout def_timeout = { 120, 0 };
+ CCachedTaxon3::Init(&def_timeout);
+}
+
+
+void
+CCachedTaxon3::Init(const STimeout* timeout, unsigned reconnect_attempts)
+{
+ if ( timeout ) {
+ m_timeout_value = *timeout;
+ m_timeout = &m_timeout_value;
+ } else {
+ m_timeout = 0;
+ }
+
+ m_nReconnectAttempts = reconnect_attempts;
+ m_pchService = "TaxService3";
+ const char* tmp;
+ if( ( (tmp=getenv("NI_TAXON3_SERVICE_NAME")) != NULL ) ||
+ ( (tmp=getenv("NI_SERVICE_NAME_TAXON3")) != NULL ) ) {
+ m_pchService = tmp;
+ }
+
+
+#ifdef USE_TEXT_ASN
+ m_eDataFormat = eSerial_AsnText;
+#else
+ m_eDataFormat = eSerial_AsnBinary;
+#endif
+
+}
+
+
+CRef< CTaxon3_reply >
+CCachedTaxon3::SendRequest(const CTaxon3_request& request)
+{
+ return m_taxon->SendRequest(request);
+}
+
+
+CRef<CTaxon3_reply> CCachedTaxon3::x_AddReplyToCache(
+ const TCacheKey& key,
+ const COrg_ref& org_ref)
+{
+ //Build a request for the Org-ref
+ CRef<CTaxon3_request> request(new CTaxon3_request);
+ CRef<CT3Request> rq(new CT3Request);
+ rq->SetOrg(*SerialClone(org_ref));
+ request->SetRequest().push_back(rq);
+
+ //Send the request
+ CRef<CTaxon3_reply> reply = m_taxon->SendRequest(*request);
+
+ //Check for valid reply
+ if (!reply->IsSetReply()) {
+
+ //Do not cache, and return error.
+ reply = Ref(new CTaxon3_reply);
+ CRef<CT3Reply> t3reply = Ref(new CT3Reply);
+ t3reply->SetError().SetLevel(CT3Reply::TError::eLevel_error);
+ t3reply->SetError().SetMessage(kInvalidReplyMsg);
+ reply->SetReply().push_back(t3reply);
+
+ return reply;
+ }
+
+ // Cache the reply we do have, and return it.
+ try {
+ static const TAddFlags addflags = fAdd_NoReplace;
+ const TOrder ord = Add(key, reply, 1, addflags);
+ if (ord < 0) {
+ LOG_POST(Warning << "Unable to add data for key: " << key);
+ }
+ static const int cache_getflags = fGet_NoTouch | fGet_NoCreate | fGet_NoInsert;
+ return Get(key, cache_getflags);
+ }
+ catch (const CException& e) {
+ LOG_POST(Error << "Unable to add reply to taxon cache: " << e.GetMsg());
+ }
+ return CRef<CTaxon3_reply>();
+}
+
+CRef<CTaxon3_reply> CCachedTaxon3::x_GetReplyForOrgRef(
+ const COrg_ref& org_ref)
+{
+
+ string key = NStr::IntToString(org_ref.GetTaxId());
+ if (org_ref.IsSetTaxname()) {
+ key += org_ref.GetTaxname();
+ }
+ //First, try to get the item from the cache
+ static const int cache_getflags = fGet_NoTouch | fGet_NoCreate | fGet_NoInsert;
+ try {
+ EGetResult retcode;
+ CRef<CTaxon3_reply> reply = Get(key, cache_getflags, &retcode);
+ if (retcode == eGet_Found) {
+ return reply;
+ }
+ }
+ catch (const CException& e) {
+ LOG_POST(Trace << "Taxon cache miss for key " << key);
+ }
+
+ //Couldn't find it, so create a new one
+ return x_AddReplyToCache(key, org_ref);
+}
+
+CRef<CTaxon3_reply> CCachedTaxon3::SendOrgRefList(const vector<CRef< COrg_ref> >& org_list)
+{
+
+ CRef<CTaxon3_reply> result(new CTaxon3_reply);
+
+ ITERATE(vector<CRef< COrg_ref> >, it, org_list)
+ {
+ const COrg_ref& org_ref = **it;
+ result->SetReply().push_back(x_GetReplyForOrgRef(org_ref)->SetReply().front());
+ }
+
+ return result;
+}
+
+
+
+END_objects_SCOPE
+END_NCBI_SCOPE
diff --git a/c++/src/objects/taxon3/taxon3.cpp b/c++/src/objects/taxon3/taxon3.cpp
index 2d1d8b5..38d415d 100644
--- a/c++/src/objects/taxon3/taxon3.cpp
+++ b/c++/src/objects/taxon3/taxon3.cpp
@@ -1,4 +1,4 @@
-/* $Id: taxon3.cpp 438755 2014-06-19 18:23:50Z gotvyans $
+/* $Id: taxon3.cpp 483221 2015-10-29 14:17:48Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/trackmgr/Makefile.trackmgrgridcli.lib b/c++/src/objects/trackmgr/Makefile.trackmgrgridcli.lib
index 81f7852..0d301d0 100644
--- a/c++/src/objects/trackmgr/Makefile.trackmgrgridcli.lib
+++ b/c++/src/objects/trackmgr/Makefile.trackmgrgridcli.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.trackmgrgridcli.lib 439067 2014-06-25 13:02:23Z meric $
+# $Id: Makefile.trackmgrgridcli.lib 471666 2015-06-30 14:25:22Z ivanov $
LIB = trackmgrgridcli
@@ -12,6 +12,8 @@ ASN_DEP = trackmgr
WATCHERS = meric clausen
-
USES_LIBRARIES = \
$(COMPRESS_LIBS) trackmgr xconnserv
+
+REQUIRES = LZO
+
diff --git a/c++/src/objects/trackmgr/trackmgr.asn b/c++/src/objects/trackmgr/trackmgr.asn
index 5a8c9d5..d6f6e97 100644
--- a/c++/src/objects/trackmgr/trackmgr.asn
+++ b/c++/src/objects/trackmgr/trackmgr.asn
@@ -1,4 +1,4 @@
---- $Id: trackmgr.asn 441086 2014-07-21 10:47:30Z clausen $
+--- $Id: trackmgr.asn 469220 2015-06-02 17:28:19Z meric $
---
--- Definitions for the TrackManager service
---
@@ -11,7 +11,7 @@ EXPORTS TMgr-Request, TMgr-Reply, TMgr-GenomeContext,
TMgr-DisplayTrackReply, TMgr-AssemblySpec,TMgr-AttrSpec,
TMgr-BlastRIDDetail, TMgr-Assembly, TMgr-Attribute, TMgr-DisplayTrack,
TMgr-DTrackId, TMgr-DatasetItem, TMgr-DisplayTrackChoice,
- TMgr-CreateUserTrackRequest, TMgr-CreateUserTrackReply,
+ TMgr-CreateUserTrackRequest, TMgr-CreateUserTrackReply, TMgr-Identity,
TMgr-TrackAttrValueRequest, TMgr-TrackAttrValueReply,
TMgr-AttrRequest, TMgr-AttrReply, TMgr-ValueRequest, TMgr-AttrValueReply,
TMgr-TrackAttributes, TMgr-MessageLevel, TMgr-Message, TMgr-DatasetItemSeq;
@@ -85,7 +85,8 @@ TMgr-DTrackId ::= Dbtag
TMgr-SwitchTrackContextRequest ::= SEQUENCE {
client TMgr-ClientInfo,
new-genome-context TMgr-GenomeContext,
- current-dtrack-ids SET OF TMgr-DTrackId
+ current-dtrack-ids SET OF TMgr-DTrackId,
+ annotation-release-number INTEGER OPTIONAL
}
TMgr-SwitchTrackContextReply ::= SEQUENCE {
diff --git a/c++/src/objects/trackmgr/trackmgr_client.cpp b/c++/src/objects/trackmgr/trackmgr_client.cpp
index 1439c59..e7dc238 100644
--- a/c++/src/objects/trackmgr/trackmgr_client.cpp
+++ b/c++/src/objects/trackmgr/trackmgr_client.cpp
@@ -1,4 +1,4 @@
-/* $Id: trackmgr_client.cpp 371920 2012-08-13 20:14:57Z meric $
+/* $Id: trackmgr_client.cpp 450827 2014-10-30 18:38:02Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -101,6 +101,7 @@ CTrackMgrClient::AskDefault_display_tracks(
CRef<CTMgr_DisplayTrackReply>
CTrackMgrClient::s_Ask(const CTMgr_DisplayTrackRequest& request)
{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
static const CNcbiApplication* app = CNcbiApplication::Instance();
const CNcbiRegistry& cfg = app->GetConfig();
const string type = cfg.GetString("TrackMgr", "type", "service");
diff --git a/c++/src/objects/valerr/ValidErrItem.cpp b/c++/src/objects/valerr/ValidErrItem.cpp
index 2cf880b..3518c30 100644
--- a/c++/src/objects/valerr/ValidErrItem.cpp
+++ b/c++/src/objects/valerr/ValidErrItem.cpp
@@ -1,4 +1,4 @@
-/* $Id: ValidErrItem.cpp 455335 2014-12-29 13:00:02Z ivanov $
+/* $Id: ValidErrItem.cpp 473633 2015-07-21 17:05:11Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -422,8 +422,9 @@ BioSource feature." } },
"The RefGeneTracking user object does not have the required Status field set." } },
{ eErr_SEQ_DESCR_UnwantedCompleteFlag,
{ "UnwantedCompleteFlag",
-"The Mol-info.completeness flag should not be set on a genomic sequence unless \
-the title also says it is a complete sequence or complete genome." } },
+"The Mol-info.completeness flag should not be set on a genomic sequence, unless \
+the title also says it is a complete sequence or complete genome, nor should it \
+be set on a plasmid, chromosome, or organelle." } },
{ eErr_SEQ_DESCR_CollidingPublications,
{ "CollidingPublications",
"Multiple publication descriptors with the same PMID or MUID apply to a Bioseq. \
@@ -665,6 +666,12 @@ other. Please make them consistent." } },
{ eErr_SEQ_DESCR_WrongBiomolForTechnique,
{ "WrongBiomolForTechnique",
"TSA records are expected to make use of a very limited set of MolInfo.biomol values: transcribed-RNA, mRNA, rRNA, ncRNA." } },
+ { eErr_SEQ_DESCR_WrongOrganismFor16SrRNA,
+ { "WrongOrganismFor16SrRNA",
+"16S ribosomal RNA is not present in eukaryotic ribosomes." } },
+ { eErr_SEQ_DESCR_InconsistentWGSFlags,
+ { "InconsistentWGSFlags",
+"WGS indicators are used inconsistently in this record." } },
/* SEQ_GENERIC */
@@ -1609,6 +1616,9 @@ same id type" } },
{ eErr_SEQ_FEAT_MultiIntervalIntron,
{ "MultiIntervalIntron",
"Introns should only have a single interval." } },
+ { eErr_SEQ_FEAT_SeqLocTypeProblem,
+ { "SeqLocTypeProblem",
+"A sequence location component is not the expected type." } },
/* SEQ_ALIGN */
diff --git a/c++/src/objects/valerr/ValidError.cpp b/c++/src/objects/valerr/ValidError.cpp
index 61a493b..99b5fd5 100644
--- a/c++/src/objects/valerr/ValidError.cpp
+++ b/c++/src/objects/valerr/ValidError.cpp
@@ -1,4 +1,4 @@
-/* $Id: ValidError.cpp 447737 2014-09-30 13:44:49Z ivanov $
+/* $Id: ValidError.cpp 447658 2014-09-29 18:29:18Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objects/valid/validrules.inc b/c++/src/objects/valid/validrules.inc
index 1a79065..eef21bb 100644
--- a/c++/src/objects/valid/validrules.inc
+++ b/c++/src/objects/valid/validrules.inc
@@ -1,4 +1,4 @@
-/* $Id: validrules.inc 432553 2014-04-15 15:26:42Z bollin $
+/* $Id: validrules.inc 462948 2015-03-23 17:57:46Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -26,7 +26,7 @@
* Author: Jonathan Kans et al.
*
* File Description:
- * Built-in copy of validrules.txt.
+ * Built-in copy of validrules.prt.
*
*/
@@ -997,7 +997,35 @@ static const char* const s_Defaultvalidrules[] = {
" {",
" field-name \"Transcript_exon_combination_evidence\" ,",
" required FALSE } } ,",
- " allow-unlisted TRUE } ",
+ " allow-unlisted TRUE } ,",
+ " {",
+ " prefix \"##BWP:1.0-START##\" ,",
+ " fields {",
+ " {",
+ " field-name \"chainOfCustody\" ,",
+ " required FALSE } , ",
+ " {",
+ " field-name \"typeStatus\" ,",
+ " required TRUE ,",
+ " severity info } ,",
+ " {",
+ " field-name \"basisOfIdentification\" ,",
+ " required TRUE ,",
+ " severity info } ,",
+ " {",
+ " field-name \"identificationConfidence\" ,",
+ " match-expression \"^\\([Hh]igh\\|[Mm]edium\\|[Pp]reliminary\\)$\" ,",
+ " required TRUE ,",
+ " severity info } ,",
+ " {",
+ " field-name \"identificationDate\" ,",
+ " required TRUE ,",
+ " severity info } ,",
+ " {",
+ " field-name \"coordinatePrecision\" ,",
+ " required FALSE } } ,",
+ " require-order FALSE ,",
+ " allow-unlisted TRUE }",
"}",
""
};
diff --git a/c++/src/objects/valid/validrules.prt b/c++/src/objects/valid/validrules.prt
index 58cd601..301b274 100644
--- a/c++/src/objects/valid/validrules.prt
+++ b/c++/src/objects/valid/validrules.prt
@@ -964,6 +964,34 @@ AR\|APR\|MAY\|JUN\|JUL\|AUG\|SEP\|OCT\|NOV\|DEC\)-\(19\|20\)\(0\|1\|2\|3\|4\|5
{
field-name "Transcript_exon_combination_evidence" ,
required FALSE } } ,
- allow-unlisted TRUE }
+ allow-unlisted TRUE } ,
+ {
+ prefix "##BWP:1.0-START##" ,
+ fields {
+ {
+ field-name "chainOfCustody" ,
+ required FALSE } ,
+ {
+ field-name "typeStatus" ,
+ required TRUE ,
+ severity info } ,
+ {
+ field-name "basisOfIdentification" ,
+ required TRUE ,
+ severity info } ,
+ {
+ field-name "identificationConfidence" ,
+ match-expression "^\([Hh]igh\|[Mm]edium\|[Pp]reliminary\)$" ,
+ required TRUE ,
+ severity info } ,
+ {
+ field-name "identificationDate" ,
+ required TRUE ,
+ severity info } ,
+ {
+ field-name "coordinatePrecision" ,
+ required FALSE } } ,
+ require-order FALSE ,
+ allow-unlisted TRUE }
}
diff --git a/c++/src/objects/variation/variation.asn b/c++/src/objects/variation/variation.asn
index 7d49e97..88cc8f1 100644
--- a/c++/src/objects/variation/variation.asn
+++ b/c++/src/objects/variation/variation.asn
@@ -1,4 +1,4 @@
---$Revision: 438976 $
+--$Revision: 460847 $
--**********************************************************************
--
-- NCBI Variation container
@@ -47,7 +47,9 @@ VariationException ::= SEQUENCE
seqfetch-too-long (13), --can't fetch sequence because location is longer than specified threshold
seqfetch-intronic (14), --can't fetch sequence for an intronic (anchor+offset)-based location
seqfetch-invalid (15), --can't fetch sequence because location is invalid (e.g. extends past the end)
- no-mapping-from-newer-version (16) --have mapping from older version of a sequence, but not from newer
+ no-mapping-from-newer-version (16), --have mapping from older version of a sequence, but not from newer
+ source-location-overhang (17), --The source location overhangs the alignment by at least 5kb (VAR-1307)
+ hgvs-exon-boundary-induced (18) --Similar to (2), except induced by 5'/3'-terminal or an exon extension (VAR-1309)
} OPTIONAL,
message VisibleString
@@ -234,6 +236,7 @@ Variation ::= SEQUENCE
package (9), -- set represents a package of observations at
-- a given location, generally containing
-- asserted + reference
+ chimeric (10), -- e.g. c.[1C>T//2G>T]
other (255)
},
variations SET OF Variation,
diff --git a/c++/src/objmgr/annot_collector.cpp b/c++/src/objmgr/annot_collector.cpp
index 62ab383..26e6ebc 100644
--- a/c++/src/objmgr/annot_collector.cpp
+++ b/c++/src/objmgr/annot_collector.cpp
@@ -1,4 +1,4 @@
-/* $Id: annot_collector.cpp 458847 2015-02-10 19:47:18Z vasilche $
+/* $Id: annot_collector.cpp 478075 2015-09-03 17:21:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -574,25 +574,23 @@ struct CAnnotObjectType_Less
}
+ DECLARE_OPERATOR_BOOL(m_BioseqHandle);
+
bool operator()( const CSeq_id *id ) const {
- if( NULL == id ) {
- return false;
- }
- return m_BioseqHandle.IsSynonym(*id);
+ return id && m_BioseqHandle.IsSynonym(*id);
}
private:
- const CBioseq_Handle &m_BioseqHandle;
+ CBioseq_Handle m_BioseqHandle;
};
CNearnessTester m_TesterForIgnoreFarLocationsForSorting;
- explicit CAnnotObjectType_Less(const SAnnotSelector* sel = 0,
+ explicit CAnnotObjectType_Less(const SAnnotSelector* sel,
CScope* scope = 0)
- : m_ByProduct(sel && sel->GetFeatProduct()),
- m_FeatComparator(sel? sel->GetFeatComparator(): 0),
+ : m_ByProduct(sel->GetFeatProduct()),
+ m_FeatComparator(sel->GetFeatComparator()),
m_Scope(scope),
- m_TesterForIgnoreFarLocationsForSorting( sel->GetIgnoreFarLocationsForSorting() )
+ m_TesterForIgnoreFarLocationsForSorting(sel->GetIgnoreFarLocationsForSorting())
{
- m_DoWeIgnoreFarLocationsForSorting = (!! sel->GetIgnoreFarLocationsForSorting() );
}
bool operator()(const CAnnotObject_Ref& x,
@@ -915,7 +913,7 @@ bool CAnnotObjectType_Less::operator()(const CAnnotObject_Ref& x,
if ( x_complex ) {
int diff = 0;
- if( m_DoWeIgnoreFarLocationsForSorting ) {
+ if( m_TesterForIgnoreFarLocationsForSorting ) {
diff = x_loc->CompareSubLoc(*y_loc, x_strand, &m_TesterForIgnoreFarLocationsForSorting);
} else {
diff = x_loc->CompareSubLoc(*y_loc, x_strand);
@@ -1014,13 +1012,11 @@ bool CAnnotObjectType_Less::operator()(const CAnnotObject_Ref& x,
struct CAnnotObject_Less
{
- explicit CAnnotObject_Less(const SAnnotSelector* sel = 0,
+ explicit CAnnotObject_Less(const SAnnotSelector* sel,
CScope* scope = 0)
- : type_less(sel, scope)
+ : type_less(sel, scope),
+ ignore_far_handle(sel->GetIgnoreFarLocationsForSorting())
{
- if( sel ) {
- ignore_far_handle = sel->GetIgnoreFarLocationsForSorting();
- }
}
void x_GetExtremes( TSeqPos &out_from, TSeqPos &out_to,
@@ -1181,7 +1177,7 @@ struct CAnnotObject_Less
struct CAnnotObject_LessReverse
{
- explicit CAnnotObject_LessReverse(const SAnnotSelector* sel = 0,
+ explicit CAnnotObject_LessReverse(const SAnnotSelector* sel,
CScope* scope = 0)
: type_less(sel, scope)
{
@@ -1351,9 +1347,11 @@ CCreatedFeat_Ref::GetMappedLocation(const CAnnotMapping_Info& map,
mapped_feat.Reset();
}
else {
- // hack with null ptr as ResetLocation doesn't reset CRef<>
- CSeq_loc* loc = 0;
- mapped_feat->SetLocation(*loc);
+ CRef<CSeq_loc> null_loc(new CSeq_loc);
+ null_loc->SetNull();
+ // ResetLocation doesn't do what we'd like because
+ // Seq-feat.location isn't optional.
+ mapped_feat->SetLocation(*null_loc);
mapped_feat->ResetProduct();
}
}
diff --git a/c++/src/objmgr/annot_object.cpp b/c++/src/objmgr/annot_object.cpp
index 7810074..f649b98 100644
--- a/c++/src/objmgr/annot_object.cpp
+++ b/c++/src/objmgr/annot_object.cpp
@@ -1,4 +1,4 @@
-/* $Id: annot_object.cpp 448090 2014-10-02 14:57:32Z ivanov $
+/* $Id: annot_object.cpp 472371 2015-07-09 14:13:53Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -430,11 +430,16 @@ void CAnnotObject_Info::x_ProcessFeat(vector<CHandleRangeMap>& hrmaps,
hrmaps.resize(feat.IsSetProduct()? 2: 1);
hrmaps[0].clear();
hrmaps[0].SetMasterSeq(master);
- hrmaps[0].AddLocation(feat.GetLocation());
+ CHandleRangeMap::ETransSplicing mode = CHandleRangeMap::eNoTransSplicing;
+ if ( feat.IsSetExcept_text() &&
+ feat.GetExcept_text().find("trans-splicing") != NPOS ) {
+ mode = CHandleRangeMap::eTransSplicing;
+ }
+ hrmaps[0].AddLocation(feat.GetLocation(), mode);
if ( feat.IsSetProduct() ) {
hrmaps[1].clear();
hrmaps[1].SetMasterSeq(master);
- hrmaps[1].AddLocation(feat.GetProduct());
+ hrmaps[1].AddLocation(feat.GetProduct(), mode);
}
}
/* static */
diff --git a/c++/src/objmgr/annot_type_index.cpp b/c++/src/objmgr/annot_type_index.cpp
index 25869bf..24d1a53 100644
--- a/c++/src/objmgr/annot_type_index.cpp
+++ b/c++/src/objmgr/annot_type_index.cpp
@@ -1,4 +1,4 @@
-/* $Id: annot_type_index.cpp 151374 2009-02-03 21:03:09Z vasilche $
+/* $Id: annot_type_index.cpp 463178 2015-03-25 15:31:16Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,24 +46,13 @@ BEGIN_SCOPE(objects)
// All ranges are in format [x, y)
-const size_t kAnnotTypeMax = CSeq_annot::C_Data::e_MaxChoice - 1;
-const size_t kFeatTypeMax = CSeqFeatData::e_MaxChoice - 1;
-const size_t kFeatSubtypeMax = CSeqFeatData::eSubtype_max;
-const size_t kAlignIndex = 0;
-const size_t kGraphIndex = 1;
-const size_t kTableIndex = 2;
-const size_t kFtableIndex = 3;
-
-CAnnotType_Index::TIndexRangeTable CAnnotType_Index::sm_AnnotTypeIndexRange;
-
-CAnnotType_Index::TIndexRangeTable CAnnotType_Index::sm_FeatTypeIndexRange;
-
-CAnnotType_Index::TIndexTable CAnnotType_Index::sm_FeatSubtypeIndex;
-CAnnotType_Index::TSubtypes CAnnotType_Index::sm_IndexSubtype;
-
DEFINE_STATIC_FAST_MUTEX(sm_TablesInitializeMutex);
bool CAnnotType_Index::sm_TablesInitialized = false;
+Uint1 CAnnotType_Index::sm_AnnotTypeIndexRange[CAnnotType_Index::kAnnotType_size][2];
+Uint1 CAnnotType_Index::sm_FeatTypeIndexRange[CAnnotType_Index::kFeatType_size][2];
+Uint1 CAnnotType_Index::sm_FeatSubtypeIndex[CAnnotType_Index::kFeatSubtype_size];
+Uint1 CAnnotType_Index::sm_IndexSubtype[CAnnotType_Index::kAnnotIndex_size];
void CAnnotType_Index::x_InitIndexTables(void)
{
@@ -73,56 +62,70 @@ void CAnnotType_Index::x_InitIndexTables(void)
}
// Check flag, lock tables
_ASSERT(!sm_TablesInitialized);
- sm_AnnotTypeIndexRange.resize(kAnnotTypeMax + 1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set].first = 0;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align] =
- TIndexRange(kAlignIndex, kAlignIndex+1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph] =
- TIndexRange(kGraphIndex, kGraphIndex+1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Seq_table] =
- TIndexRange(kTableIndex, kTableIndex+1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable].first =
- kFtableIndex;
-
- vector< vector<size_t> > type_subtypes(kFeatTypeMax+1);
- for ( size_t subtype = 0; subtype <= kFeatSubtypeMax; ++subtype ) {
- size_t type = CSeqFeatData::
- GetTypeFromSubtype(CSeqFeatData::ESubtype(subtype));
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set][0] = 0;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align][0] = kAnnotIndex_Align;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align][1] = kAnnotIndex_Align+1;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph][0] = kAnnotIndex_Graph;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph][1] = kAnnotIndex_Graph+1;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Seq_table][0] = kAnnotIndex_Seq_table;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Seq_table][1] = kAnnotIndex_Seq_table+1;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable][0] = kAnnotIndex_Ftable;
+
+ _ASSERT(kFeatType_size < kMax_UI1);
+ _ASSERT(kFeatSubtype_size < kMax_UI1);
+ _ASSERT(kAnnotIndex_size < kMax_UI1);
+ vector< vector<Uint1> > type_subtypes(kFeatType_size);
+ for ( Uint1 subtype = 0; subtype < kFeatSubtype_size; ++subtype ) {
+ Uint1 type =
+ CSeqFeatData::GetTypeFromSubtype(CSeqFeatData::ESubtype(subtype));
if ( type != CSeqFeatData::e_not_set ||
subtype == CSeqFeatData::eSubtype_bad ) {
type_subtypes[type].push_back(subtype);
}
}
-
- sm_FeatTypeIndexRange.resize(kFeatTypeMax + 1);
- sm_FeatSubtypeIndex.resize(kFeatSubtypeMax + 1);
-
- size_t cur_idx = kFtableIndex;
- sm_IndexSubtype.assign(cur_idx, CSeqFeatData::eSubtype_bad);
- for ( size_t type = 0; type <= kFeatTypeMax; ++type ) {
- sm_FeatTypeIndexRange[type].first = cur_idx;
- if ( type != CSeqFeatData::e_not_set ) {
- sm_FeatTypeIndexRange[type].second =
- cur_idx + type_subtypes[type].size();
- }
- ITERATE ( vector<size_t>, it, type_subtypes[type] ) {
- sm_FeatSubtypeIndex[*it] = cur_idx++;
- sm_IndexSubtype.push_back(CSeqFeatData::ESubtype(*it));
+
+ Uint1 cur_idx = kAnnotIndex_Ftable;
+ fill_n(sm_IndexSubtype, cur_idx,
+ CSeqFeatData::eSubtype_bad);
+ for ( Uint1 type = 0; type < kFeatType_size; ++type ) {
+ sm_FeatTypeIndexRange[type][0] = cur_idx;
+ ITERATE ( vector<Uint1>, it, type_subtypes[type] ) {
+ _ASSERT(cur_idx < kAnnotIndex_size);
+ sm_FeatSubtypeIndex[*it] = cur_idx;
+ sm_IndexSubtype[cur_idx] = *it;
+ ++cur_idx;
}
+ sm_FeatTypeIndexRange[type][1] = cur_idx;
}
- sm_FeatTypeIndexRange[CSeqFeatData::e_not_set].second = cur_idx;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable].second = cur_idx;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set].second = cur_idx;
+ sm_FeatTypeIndexRange[CSeqFeatData::e_not_set][1] = cur_idx;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable][1] = cur_idx;
+ sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set][1] = cur_idx;
+ _ASSERT(cur_idx <= kAnnotIndex_size);
+ fill(sm_IndexSubtype+cur_idx, sm_IndexSubtype+kAnnotIndex_size,
+ CSeqFeatData::eSubtype_bad);
sm_TablesInitialized = true;
#if defined(_DEBUG)
- for ( size_t type = 1; type <= kFeatTypeMax; ++type ) {
+ _TRACE("Index size: "<<cur_idx<<" of "<<kAnnotIndex_size);
+ _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_not_set) == TIndexRange(0, cur_idx));
+ _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_Locs) == TIndexRange(0, 0));
+ _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_Ids) == TIndexRange(0, 0));
+ //_ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_MaxChoice) == TIndexRange(0, 0));
+ _ASSERT(GetFeatTypeRange(CSeqFeatData::e_not_set) == TIndexRange(kAnnotIndex_Ftable, cur_idx));
+ //_ASSERT(GetFeatTypeRange(CSeqFeatData::e_MaxChoice) == TIndexRange(0, 0));
+ _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_bad) == kAnnotIndex_Ftable);
+ _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_max) == 0);
+ _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_any) == 0);
+ for ( size_t type = 0; type < kFeatType_size; ++type ) {
CSeqFeatData::E_Choice feat_type = CSeqFeatData::E_Choice(type);
TIndexRange range = GetFeatTypeRange(feat_type);
_TRACE("type: "<<feat_type
<< " range: "<<range.first<<"-"<<range.second);
+ if ( type == 0 ) {
+ continue;
+ }
for ( size_t ind = range.first; ind < range.second; ++ind ) {
SAnnotTypeSelector sel = GetTypeSelector(ind);
_TRACE("index: "<<ind
@@ -198,12 +201,15 @@ SAnnotTypeSelector CAnnotType_Index::GetTypeSelector(size_t index)
{
SAnnotTypeSelector sel;
switch (index) {
- case 0:
+ case kAnnotIndex_Align:
sel.SetAnnotType(CSeq_annot::C_Data::e_Align);
break;
- case 1:
+ case kAnnotIndex_Graph:
sel.SetAnnotType(CSeq_annot::C_Data::e_Graph);
break;
+ case kAnnotIndex_Seq_table:
+ sel.SetAnnotType(CSeq_annot::C_Data::e_Seq_table);
+ break;
default:
sel.SetFeatSubtype(GetSubtypeForIndex(index));
break;
diff --git a/c++/src/objmgr/bioseq_base_info.cpp b/c++/src/objmgr/bioseq_base_info.cpp
index a1b4966..4f6f544 100644
--- a/c++/src/objmgr/bioseq_base_info.cpp
+++ b/c++/src/objmgr/bioseq_base_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: bioseq_base_info.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: bioseq_base_info.cpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/bioseq_ci.cpp b/c++/src/objmgr/bioseq_ci.cpp
index 3734190..b0e0f2a 100644
--- a/c++/src/objmgr/bioseq_ci.cpp
+++ b/c++/src/objmgr/bioseq_ci.cpp
@@ -1,4 +1,4 @@
-/* $Id: bioseq_ci.cpp 448103 2014-10-02 15:01:44Z ivanov $
+/* $Id: bioseq_ci.cpp 444539 2014-08-25 18:43:02Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/bioseq_handle.cpp b/c++/src/objmgr/bioseq_handle.cpp
index 58648c7..89525a8 100644
--- a/c++/src/objmgr/bioseq_handle.cpp
+++ b/c++/src/objmgr/bioseq_handle.cpp
@@ -1,4 +1,4 @@
-/* $Id: bioseq_handle.cpp 197252 2010-07-14 20:38:30Z vasilche $
+/* $Id: bioseq_handle.cpp 474909 2015-08-03 10:48:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -761,6 +761,7 @@ void CBioseq_EditHandle::x_Detach(void) const
void CBioseq_EditHandle::ResetId(void) const
{
+ CScope_Impl::TConfWriteLockGuard guard(x_GetScopeImpl().m_ConfLock);
CCommandProcessor processor(x_GetScopeImpl());
processor.run(new CResetIds_EditCommand(*this));
}
@@ -768,19 +769,17 @@ void CBioseq_EditHandle::ResetId(void) const
bool CBioseq_EditHandle::AddId(const CSeq_id_Handle& id) const
{
- typedef CAddId_EditCommand TCommand;
+ CScope_Impl::TConfWriteLockGuard guard(x_GetScopeImpl().m_ConfLock);
CCommandProcessor processor(x_GetScopeImpl());
- return processor.run(new TCommand(*this,id));
- // return x_GetScopeInfo().AddId(id);
+ return processor.run(new CAddId_EditCommand(*this,id));
}
bool CBioseq_EditHandle::RemoveId(const CSeq_id_Handle& id) const
{
- typedef CRemoveId_EditCommand TCommand;
+ CScope_Impl::TConfWriteLockGuard guard(x_GetScopeImpl().m_ConfLock);
CCommandProcessor processor(x_GetScopeImpl());
- return processor.run(new TCommand(*this,id));
- // return x_GetScopeInfo().RemoveId(id);
+ return processor.run(new CRemoveId_EditCommand(*this,id));
}
diff --git a/c++/src/objmgr/bioseq_info.cpp b/c++/src/objmgr/bioseq_info.cpp
index bb1fee8..22c3619 100644
--- a/c++/src/objmgr/bioseq_info.cpp
+++ b/c++/src/objmgr/bioseq_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: bioseq_info.cpp 448092 2014-10-02 14:57:52Z ivanov $
+/* $Id: bioseq_info.cpp 444528 2014-08-25 18:33:18Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/bioseq_set_handle.cpp b/c++/src/objmgr/bioseq_set_handle.cpp
index 4f13552..69713e6 100644
--- a/c++/src/objmgr/bioseq_set_handle.cpp
+++ b/c++/src/objmgr/bioseq_set_handle.cpp
@@ -1,4 +1,4 @@
-/* $Id: bioseq_set_handle.cpp 444889 2014-08-28 17:54:38Z ivanov $
+/* $Id: bioseq_set_handle.cpp 444685 2014-08-27 13:07:18Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/data_loader.cpp b/c++/src/objmgr/data_loader.cpp
index 6bff1cd..9d66c1f 100644
--- a/c++/src/objmgr/data_loader.cpp
+++ b/c++/src/objmgr/data_loader.cpp
@@ -1,4 +1,4 @@
-/* $Id: data_loader.cpp 428346 2014-03-03 17:35:59Z vasilche $
+/* $Id: data_loader.cpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -317,6 +317,12 @@ int CDataLoader::GetSequenceState(const CSeq_id_Handle& idh)
}
+int CDataLoader::GetSequenceHash(const CSeq_id_Handle& idh)
+{
+ return 0;
+}
+
+
void CDataLoader::GetAccVers(const TIds& ids, TLoaded& loaded, TIds& ret)
{
size_t count = ids.size();
@@ -474,6 +480,12 @@ void CDataLoader::GetSequenceStates(const TIds& ids, TLoaded& loaded,
}
+void CDataLoader::GetSequenceHashes(const TIds& ids, TLoaded& loaded,
+ TSequenceHashes& ret)
+{
+}
+
+
void CDataLoader::GetBlobs(TTSE_LockSets& tse_sets)
{
NON_CONST_ITERATE(TTSE_LockSets, tse_set, tse_sets) {
diff --git a/c++/src/objmgr/data_source.cpp b/c++/src/objmgr/data_source.cpp
index 2987ba7..46a8510 100644
--- a/c++/src/objmgr/data_source.cpp
+++ b/c++/src/objmgr/data_source.cpp
@@ -1,4 +1,4 @@
-/* $Id: data_source.cpp 464548 2015-04-10 15:31:29Z vasilche $
+/* $Id: data_source.cpp 467006 2015-05-08 11:59:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -125,6 +125,15 @@ CDataSource::~CDataSource(void)
}
+void CDataSource::RevokeDataLoader(void)
+{
+ if ( m_Loader ) {
+ TMainLock::TWriteLockGuard guard(m_DSMainLock);
+ m_Loader = null;
+ }
+}
+
+
void CDataSource::DropAllTSEs(void)
{
// Lock indexes
@@ -147,8 +156,8 @@ void CDataSource::DropAllTSEs(void)
TCacheLock::TWriteLockGuard guard2(m_DSCacheLock);
// check if any TSE is locked by user
ITERATE ( TBlob_Map, it, m_Blob_Map ) {
- int lock_counter = it->second->m_LockCounter.Get();
- int used_counter = m_StaticBlobs.FindLock(it->second)? 1: 0;
+ CAtomicCounter::TValue lock_counter = it->second->m_LockCounter.Get();
+ CAtomicCounter::TValue used_counter = m_StaticBlobs.FindLock(it->second)? 1: 0;
if ( lock_counter != used_counter ) {
ERR_POST_X(1, "CDataSource::DropAllTSEs: tse is locked");
}
@@ -897,10 +906,13 @@ void CDataSource::GetTSESetWithOrphanAnnots(const TSeq_idSet& ids,
void CDataSource::GetTSESetWithBioseqAnnots(const CBioseq_Info& bioseq,
const TTSE_Lock& tse,
TTSE_LockMatchSet& ret,
- const SAnnotSelector* sel)
+ const SAnnotSelector* sel,
+ bool external_only)
{
- // always add bioseq annotations
- x_AddTSEBioseqAnnots(ret, bioseq, tse);
+ if ( !external_only ) {
+ // add bioseq annotations
+ x_AddTSEBioseqAnnots(ret, bioseq, tse);
+ }
if ( m_Loader ) {
// with loader installed we look only in TSE with bioseq,
@@ -1483,6 +1495,21 @@ void CDataSource::GetSequenceStates(const TIds& ids, TLoaded& loaded,
}
+int CDataSource::GetSequenceHash(const CSeq_id_Handle& idh)
+{
+ return m_Loader? m_Loader->GetSequenceHash(idh): 0;
+}
+
+
+void CDataSource::GetSequenceHashes(const TIds& ids, TLoaded& loaded,
+ TSequenceHashes& ret)
+{
+ if ( m_Loader ) {
+ m_Loader->GetSequenceHashes(ids, loaded, ret);
+ }
+}
+
+
void CDataSource::GetBlobs(TSeqMatchMap& match_map)
{
if ( match_map.empty() ) {
diff --git a/c++/src/objmgr/gc_assembly_parser.cpp b/c++/src/objmgr/gc_assembly_parser.cpp
index 497bec9..03138db 100644
--- a/c++/src/objmgr/gc_assembly_parser.cpp
+++ b/c++/src/objmgr/gc_assembly_parser.cpp
@@ -1,4 +1,4 @@
-/* $Id: gc_assembly_parser.cpp 427871 2014-02-25 18:00:57Z grichenk $
+/* $Id: gc_assembly_parser.cpp 479618 2015-09-22 15:42:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -289,13 +289,7 @@ void CGC_Assembly_Parser::x_ParseGCSequence(const CGC_Sequence& gc_seq,
}
// Create virtual bioseq and use it to initialize the mapper
- if ( gc_seq.IsSetStructure() ) {
- x_AddBioseq(entry, synonyms, &gc_seq.GetStructure());
- }
- else {
- // Create literal sequence
- x_AddBioseq(entry, synonyms, NULL);
- }
+ x_AddBioseq(entry, synonyms, gc_seq);
if ( !parent_seq ) {
// Save top-level sequences.
m_TopSeqs.insert(CSeq_id_Handle::GetHandle(*id));
@@ -323,9 +317,9 @@ void CGC_Assembly_Parser::x_ParseGCSequence(const CGC_Sequence& gc_seq,
}
-void CGC_Assembly_Parser::x_AddBioseq(CRef<CSeq_entry> parent_entry,
- const TSeqIds& synonyms,
- const CDelta_ext* delta)
+void CGC_Assembly_Parser::x_AddBioseq(CRef<CSeq_entry> parent_entry,
+ const TSeqIds& synonyms,
+ const CGC_Sequence& gc_seq)
{
CRef<CBioseq> bioseq(new CBioseq);
ITERATE(TSeqIds, syn, synonyms) {
@@ -341,12 +335,15 @@ void CGC_Assembly_Parser::x_AddBioseq(CRef<CSeq_entry> parent_entry,
}
bioseq->SetInst().SetMol(CSeq_inst::eMol_na);
- if ( delta ) {
+ if ( gc_seq.CanGetLength() ) {
+ bioseq->SetInst().SetLength(gc_seq.GetLength());
+ }
+ if ( gc_seq.IsSetStructure() ) {
// Create delta sequence
bioseq->SetInst().SetRepr(CSeq_inst::eRepr_delta);
// const_cast should be safe here - we are not going to modify data
bioseq->SetInst().SetExt().SetDelta(
- const_cast<CDelta_ext&>(*delta));
+ const_cast<CDelta_ext&>(gc_seq.GetStructure()));
}
else {
// Create virtual bioseq without length/data.
diff --git a/c++/src/objmgr/handle_range_map.cpp b/c++/src/objmgr/handle_range_map.cpp
index 1a748f9..ef9b1b4 100644
--- a/c++/src/objmgr/handle_range_map.cpp
+++ b/c++/src/objmgr/handle_range_map.cpp
@@ -1,4 +1,4 @@
-/* $Id: handle_range_map.cpp 448088 2014-10-02 14:56:47Z ivanov $
+/* $Id: handle_range_map.cpp 472372 2015-07-09 14:14:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -84,9 +84,11 @@ void CHandleRangeMap::clear(void)
}
-void CHandleRangeMap::AddLocation(const CSeq_loc& loc)
+void CHandleRangeMap::AddLocation(const CSeq_loc& loc,
+ ETransSplicing trans_splcing)
{
SAddState state;
+ state.m_TransSplicing = trans_splcing;
AddLocation(loc, state);
}
@@ -206,6 +208,7 @@ void CHandleRangeMap::AddRange(const CSeq_id_Handle& h,
const TRange& range, ENa_strand strand)
{
SAddState state;
+ state.m_TransSplicing = eNoTransSplicing;
AddRange(h, range, strand, state);
}
@@ -214,6 +217,7 @@ void CHandleRangeMap::AddRange(const CSeq_id& id,
const TRange& range, ENa_strand strand)
{
SAddState state;
+ state.m_TransSplicing = eNoTransSplicing;
AddRange(id, range, strand, state);
}
@@ -230,6 +234,7 @@ void CHandleRangeMap::AddRange(const CSeq_id& id,
TSeqPos from, TSeqPos to, ENa_strand strand)
{
SAddState state;
+ state.m_TransSplicing = eNoTransSplicing;
AddRange(id, from, to, strand, state);
}
@@ -240,7 +245,8 @@ void CHandleRangeMap::AddRange(const CSeq_id_Handle& h,
SAddState& state)
{
CHandleRange& hr = m_LocMap[h];
- if ( state.m_PrevId && h && state.m_PrevId != h ) {
+ if ( state.m_TransSplicing == eNoTransSplicing &&
+ state.m_PrevId && h && state.m_PrevId != h ) {
m_LocMap[state.m_PrevId].m_MoreAfter = true;
hr.m_MoreBefore = true;
if ( m_MasterSeq ) {
diff --git a/c++/src/objmgr/object_manager.cpp b/c++/src/objmgr/object_manager.cpp
index af79dae..f7d4d8e 100644
--- a/c++/src/objmgr/object_manager.cpp
+++ b/c++/src/objmgr/object_manager.cpp
@@ -1,4 +1,4 @@
-/* $Id: object_manager.cpp 448567 2014-10-07 16:45:01Z ivanov $
+/* $Id: object_manager.cpp 467023 2015-05-08 14:53:15Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -230,6 +230,39 @@ bool CObjectManager::RevokeDataLoader(const string& loader_name)
}
+void CObjectManager::RevokeAllDataLoaders(void)
+{
+ TWriteLockGuard guard(m_OM_Lock);
+ NON_CONST_ITERATE ( TMapToSource, iter, m_mapToSource ) {
+ iter->second->RevokeDataLoader();
+ }
+ m_mapToSource.clear();
+ m_mapNameToLoader.clear();
+ m_setDefaultSource.clear();
+}
+
+
+CObjectManager::IDataLoaderFilter::~IDataLoaderFilter()
+{
+}
+
+
+void CObjectManager::RevokeDataLoaders(IDataLoaderFilter& filter)
+{
+ TWriteLockGuard guard(m_OM_Lock);
+ ERASE_ITERATE ( TMapToSource, iter, m_mapToSource ) {
+ TDataSourceLock source = iter->second;
+ CDataLoader* loader = source->GetDataLoader();
+ if ( loader && filter.IsDataLoaderMatches(*loader) ) {
+ m_mapNameToLoader.erase(loader->GetName());
+ m_mapToSource.erase(loader);
+ m_setDefaultSource.erase(source);
+ source->RevokeDataLoader();
+ }
+ }
+}
+
+
CObjectManager::TDataSourceLock
CObjectManager::x_RevokeDataLoader(CDataLoader* loader)
{
diff --git a/c++/src/objmgr/scope.cpp b/c++/src/objmgr/scope.cpp
index 4157e15..4567235 100644
--- a/c++/src/objmgr/scope.cpp
+++ b/c++/src/objmgr/scope.cpp
@@ -1,4 +1,4 @@
-/* $Id: scope.cpp 428346 2014-03-03 17:35:59Z vasilche $
+/* $Id: scope.cpp 445270 2014-09-03 13:27:28Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -787,7 +787,7 @@ void CScope::GetSequenceStates(TSequenceStates* results,
{
if ( !results ) {
NCBI_THROW(CCoreException, eNullPtr,
- "CScope::GetSequenceTypes: null results pointer");
+ "CScope::GetSequenceStates: null results pointer");
}
return m_Impl->GetSequenceStates(*results, ids, force_load == eForceLoad);
}
@@ -802,5 +802,36 @@ CScope::TSequenceStates CScope::GetSequenceStates(const TSeq_id_Handles& ids,
}
+CScope::TSequenceHash CScope::GetSequenceHash(const CSeq_id& id)
+{
+ return GetSequenceHash(CSeq_id_Handle::GetHandle(id));
+}
+
+
+CScope::TSequenceHash CScope::GetSequenceHash(const CSeq_id_Handle& id)
+{
+ return m_Impl->GetSequenceHash(id);
+}
+
+
+void CScope::GetSequenceHashes(TSequenceHashes* results,
+ const TSeq_id_Handles& ids)
+{
+ if ( !results ) {
+ NCBI_THROW(CCoreException, eNullPtr,
+ "CScope::GetSequenceHashes: null results pointer");
+ }
+ return m_Impl->GetSequenceHashes(*results, ids);
+}
+
+
+CScope::TSequenceHashes CScope::GetSequenceHashes(const TSeq_id_Handles& ids)
+{
+ TSequenceHashes results;
+ GetSequenceHashes(&results, ids);
+ return results;
+}
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objmgr/scope_impl.cpp b/c++/src/objmgr/scope_impl.cpp
index adf5b13..c1782b1 100644
--- a/c++/src/objmgr/scope_impl.cpp
+++ b/c++/src/objmgr/scope_impl.cpp
@@ -1,4 +1,4 @@
-/* $Id: scope_impl.cpp 447986 2014-10-01 19:13:09Z vasilche $
+/* $Id: scope_impl.cpp 474909 2015-08-03 10:48:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,6 +80,17 @@
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
+
+NCBI_PARAM_DECL(bool, OBJMGR, KEEP_EXTERNAL_FOR_EDIT);
+NCBI_PARAM_DEF(bool, OBJMGR, KEEP_EXTERNAL_FOR_EDIT, false);
+
+static bool sx_KeepExternalAnnotsForEdit(void)
+{
+ static CSafeStatic<NCBI_PARAM_TYPE(OBJMGR, KEEP_EXTERNAL_FOR_EDIT)> sx_Value;
+ return sx_Value->Get();
+}
+
+
#define EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
/////////////////////////////////////////////////////////////////////////////
@@ -934,23 +945,23 @@ void CScope_Impl::x_ClearCacheOnNewData(const TIds& seq_ids,
while ( it1 != seq_ids.end() && it2 != m_Seq_idMap.end() ) {
if ( *it1 < it2->first ) {
++it1;
+ continue;
}
else if ( it2->first < *it1 ) {
++it2;
+ continue;
}
- else {
- if ( it2->second.m_Bioseq_Info ) {
- conflict_id = &*it1;
- CBioseq_ScopeInfo& binfo = *it2->second.m_Bioseq_Info;
- if ( !binfo.HasBioseq() ) {
- // try to resolve again
- binfo.m_SynCache.Reset(); // break circular link
- it2->second.m_Bioseq_Info.Reset();
- }
+ if ( it2->second.m_Bioseq_Info ) {
+ CBioseq_ScopeInfo& binfo = *it2->second.m_Bioseq_Info;
+ if ( !binfo.HasBioseq() ) {
+ // try to resolve again
+ binfo.m_SynCache.Reset(); // break circular link
+ it2->second.m_Bioseq_Info.Reset();
}
- ++it1;
- ++it2;
+ conflict_id = &*it1;
}
+ ++it1;
+ ++it2;
}
}
else if ( add_count < old_count ) {
@@ -959,27 +970,31 @@ void CScope_Impl::x_ClearCacheOnNewData(const TIds& seq_ids,
TSeq_idMap::iterator it2 = m_Seq_idMap.find(*it1);
if ( it2 != m_Seq_idMap.end() &&
it2->second.m_Bioseq_Info ) {
- conflict_id = &*it1;
CBioseq_ScopeInfo& binfo = *it2->second.m_Bioseq_Info;
if ( !binfo.HasBioseq() ) {
// try to resolve again
binfo.m_SynCache.Reset(); // break circular link
it2->second.m_Bioseq_Info.Reset();
}
+ conflict_id = &*it1;
}
}
}
else {
// lookup in add
NON_CONST_ITERATE ( TSeq_idMap, it2, m_Seq_idMap ) {
- if ( it2->second.m_Bioseq_Info &&
- binary_search(seq_ids.begin(), seq_ids.end(), it2->first) ) {
- conflict_id = &it2->first;
- CBioseq_ScopeInfo& binfo = *it2->second.m_Bioseq_Info;
- if ( !binfo.HasBioseq() ) {
- // try to resolve again
- binfo.m_SynCache.Reset(); // break circular link
- it2->second.m_Bioseq_Info.Reset();
+ if ( it2->second.m_Bioseq_Info ) {
+ TIds::const_iterator it1 = lower_bound(seq_ids.begin(),
+ seq_ids.end(),
+ it2->first);
+ if ( it1 != seq_ids.end() ) {
+ CBioseq_ScopeInfo& binfo = *it2->second.m_Bioseq_Info;
+ if ( !binfo.HasBioseq() ) {
+ // try to resolve again
+ binfo.m_SynCache.Reset(); // break circular link
+ it2->second.m_Bioseq_Info.Reset();
+ }
+ conflict_id = &*it1;
}
}
}
@@ -1088,6 +1103,41 @@ void CScope_Impl::x_ClearCacheOnRemoveData(const CTSE_Info* old_tse)
}
+void CScope_Impl::x_ClearCacheOnRemoveSeqId(const CSeq_id_Handle& id,
+ CBioseq_ScopeInfo& seq)
+{
+ if ( id ) {
+ // clear erased id
+ TSeq_idMap::iterator it = m_Seq_idMap.find(id);
+ if ( it != m_Seq_idMap.end() &&
+ &*it->second.m_Bioseq_Info == &seq ) {
+ m_Seq_idMap.erase(it);
+ }
+ }
+ else {
+ // clear all ids
+ ITERATE ( TIds, id_it, seq.GetIds() ) {
+ TSeq_idMap::iterator it = m_Seq_idMap.find(*id_it);
+ if ( it != m_Seq_idMap.end() &&
+ &*it->second.m_Bioseq_Info == &seq ) {
+ m_Seq_idMap.erase(it);
+ }
+ }
+ }
+ if ( seq.m_SynCache ) {
+ // clear synonyms
+ ITERATE ( CSynonymsSet, id_it, *seq.m_SynCache ) {
+ TSeq_idMap::iterator it = m_Seq_idMap.find(*id_it);
+ if ( it != m_Seq_idMap.end() &&
+ &*it->second.m_Bioseq_Info == &seq ) {
+ m_Seq_idMap.erase(it);
+ }
+ }
+ seq.m_SynCache.Reset();
+ }
+}
+
+
void CScope_Impl::x_ClearCacheOnRemoveAnnot(const CTSE_Info& old_tse)
{
// Clear annot cache
@@ -1816,33 +1866,36 @@ CTSE_Handle CScope_Impl::GetEditHandle(const CTSE_Handle& handle)
return handle;
}
CTSE_ScopeInfo& scope_info = handle.x_GetScopeInfo();
- CRef<CDataSource_ScopeInfo> old_ds(&scope_info.GetDSInfo());
- CRef<CDataSource_ScopeInfo> new_ds =
- GetEditDataSource(*old_ds, &scope_info);
+ CRef<CDataSource_ScopeInfo> old_ds_info(&scope_info.GetDSInfo());
+ CRef<CDataSource_ScopeInfo> new_ds_info =
+ GetEditDataSource(*old_ds_info, &scope_info);
// load all missing information if split
//scope_info.m_TSE_Lock->GetCompleteSeq_entry();
CRef<CTSE_Info> old_tse(const_cast<CTSE_Info*>(&*scope_info.m_TSE_Lock));
CRef<CTSE_Info> new_tse(new CTSE_Info(scope_info.m_TSE_Lock));
- CTSE_Lock new_tse_lock = new_ds->GetDataSource().AddStaticTSE(new_tse);
- scope_info.SetEditTSE(new_tse_lock, *new_ds,
- new_tse_lock->m_BaseTSE->m_ObjectCopyMap);
- const_cast<CTSE_Info&>(*new_tse_lock).m_BaseTSE->m_ObjectCopyMap.clear();
+ CTSE_Lock new_tse_lock =
+ new_ds_info->GetDataSource().AddStaticTSE(new_tse);
+ scope_info.SetEditTSE(new_tse_lock, *new_ds_info);
_ASSERT(handle.CanBeEdited());
- _ASSERT(!old_ds->CanBeEdited());
+ _ASSERT(!old_ds_info->CanBeEdited());
- CRef<CDataSource> ds(&old_ds->GetDataSource());
- if ( ds->GetSharedObject() ) {
+ // remove or mask original TSE
+ CRef<CDataSource> old_ds(&old_ds_info->GetDataSource());
+ if ( old_ds->GetSharedObject() ) {
// remove old shared object
- _ASSERT(!ds->GetDataLoader());
- _VERIFY(m_setDataSrc.Erase(*old_ds));
- _VERIFY(m_DSMap.erase(ds));
- ds.Reset();
- old_ds->DetachScope();
- }
- else if ( old_ds->IsConst() ) {
- _ASSERT(!ds->GetDataLoader());
+ _ASSERT(!old_ds->GetDataLoader());
+ _VERIFY(m_setDataSrc.Erase(*old_ds_info));
+ _VERIFY(m_DSMap.erase(old_ds));
+ old_ds.Reset();
+ old_ds_info->DetachScope();
+ }
+ else if ( old_ds_info->IsConst() ) {
+ _ASSERT(!old_ds->GetDataLoader());
const_cast<CTSE_Info&>(*new_tse_lock).m_BaseTSE.reset();
- _VERIFY(ds->DropStaticTSE(*old_tse));
+ _VERIFY(old_ds->DropStaticTSE(*old_tse));
+ }
+ else {
+ scope_info.ReplaceTSE(*old_tse);
}
return handle;
}
@@ -2114,36 +2167,10 @@ void CScope_Impl::GetTSESetWithAnnots(const CSeq_id_Handle& idh,
CRef<CBioseq_ScopeInfo> binfo =
x_InitBioseq_Info(info, CScope::eGetBioseq_All, seq_match);
if ( binfo->HasBioseq() ) {
- CInitGuard init(binfo->m_BioseqAnnotRef_Info, m_MutexPool);
- if ( init ) {
- CRef<CBioseq_ScopeInfo::TTSE_MatchSetObject> match
- (new CBioseq_ScopeInfo::TTSE_MatchSetObject);
- x_GetTSESetWithBioseqAnnots(lock, match->GetData(), *binfo, 0);
- binfo->m_BioseqAnnotRef_Info = match;
- }
- else {
- x_LockMatchSet(lock, *binfo->m_BioseqAnnotRef_Info);
- }
-#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
- if ( binfo->x_GetTSE_ScopeInfo().CanBeEdited() ) {
- x_GetTSESetWithBioseqAnnots(lock, *binfo, 0);
- return;
- }
-#endif
+ x_GetTSESetWithAnnots(lock, *binfo);
}
else {
- CInitGuard init(info.second.m_AllAnnotRef_Info, m_MutexPool);
- if ( init ) {
- CRef<CBioseq_ScopeInfo::TTSE_MatchSetObject> match
- (new CBioseq_ScopeInfo::TTSE_MatchSetObject);
- CSeq_id_Handle::TMatches ids;
- idh.GetReverseMatchingHandles(ids);
- x_GetTSESetWithOrphanAnnots(lock, match->GetData(), ids, 0, 0);
- info.second.m_AllAnnotRef_Info = match;
- }
- else {
- x_LockMatchSet(lock, *info.second.m_AllAnnotRef_Info);
- }
+ x_GetTSESetWithAnnots(lock, info);
}
}}
}
@@ -2158,23 +2185,7 @@ void CScope_Impl::GetTSESetWithAnnots(const CBioseq_Handle& bh,
(&const_cast<CBioseq_ScopeInfo&>(bh.x_GetScopeInfo()));
_ASSERT(binfo->HasBioseq());
-
- CInitGuard init(binfo->m_BioseqAnnotRef_Info, m_MutexPool);
- if ( init ) {
- CRef<CBioseq_ScopeInfo::TTSE_MatchSetObject> match
- (new CBioseq_ScopeInfo::TTSE_MatchSetObject);
- x_GetTSESetWithBioseqAnnots(lock, match->GetData(), *binfo, 0);
- binfo->m_BioseqAnnotRef_Info = match;
- }
- else {
- x_LockMatchSet(lock, *binfo->m_BioseqAnnotRef_Info);
- }
-#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
- if ( binfo->x_GetTSE_ScopeInfo().CanBeEdited() ) {
- x_GetTSESetWithBioseqAnnots(lock, *binfo, 0);
- return;
- }
-#endif
+ x_GetTSESetWithAnnots(lock, *binfo);
}
}
@@ -2188,19 +2199,11 @@ void CScope_Impl::GetTSESetWithAnnots(const CSeq_id_Handle& idh,
SSeqMatch_Scope seq_match;
CRef<CBioseq_ScopeInfo> binfo =
x_InitBioseq_Info(info, CScope::eGetBioseq_All, seq_match);
- TTSE_MatchSet match;
if ( binfo->HasBioseq() ) {
- x_GetTSESetWithBioseqAnnots(lock, match, *binfo, &sel);
-#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
- if ( binfo->x_GetTSE_ScopeInfo().CanBeEdited() ) {
- x_GetTSESetWithBioseqAnnots(lock, *binfo, &sel);
- }
-#endif
+ x_GetTSESetWithAnnots(lock, 0, *binfo, &sel);
}
else {
- CSeq_id_Handle::TMatches ids;
- idh.GetReverseMatchingHandles(ids);
- x_GetTSESetWithOrphanAnnots(lock, match, ids, 0, &sel);
+ x_GetTSESetWithAnnots(lock, 0, info, &sel);
}
}
@@ -2215,47 +2218,130 @@ void CScope_Impl::GetTSESetWithAnnots(const CBioseq_Handle& bh,
(&const_cast<CBioseq_ScopeInfo&>(bh.x_GetScopeInfo()));
_ASSERT(binfo->HasBioseq());
-
- TTSE_MatchSet match;
- x_GetTSESetWithBioseqAnnots(lock, match, *binfo, &sel);
+ x_GetTSESetWithAnnots(lock, 0, *binfo, &sel);
+ }
+}
+
+
+void CScope_Impl::x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ CBioseq_ScopeInfo& binfo)
+{
+ if ( binfo.x_GetTSE_ScopeInfo().CanBeEdited() ) {
+ // do not use cached TSE set for modified sequences
+ x_GetTSESetWithAnnots(lock, 0, binfo, 0);
+ return;
+ }
+
+ CInitGuard init(binfo.m_BioseqAnnotRef_Info, m_MutexPool);
+ if ( init ) {
+ CRef<CBioseq_ScopeInfo::TTSE_MatchSetObject> match
+ (new CBioseq_ScopeInfo::TTSE_MatchSetObject);
+ x_GetTSESetWithAnnots(lock, &match->GetData(), binfo);
+ binfo.m_BioseqAnnotRef_Info = match;
+ }
+ else {
+ x_LockMatchSet(lock, *binfo.m_BioseqAnnotRef_Info);
#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
- if ( binfo->x_GetTSE_ScopeInfo().CanBeEdited() ) {
- x_GetTSESetWithBioseqAnnots(lock, *binfo, &sel);
+ if ( binfo.x_GetTSE_ScopeInfo().CanBeEdited() ) {
+ x_GetTSESetWithBioseqAnnots(lock, binfo, 0);
+ return;
}
#endif
}
}
+void CScope_Impl::x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TSeq_idMapValue& info)
+{
+ CInitGuard init(info.second.m_AllAnnotRef_Info, m_MutexPool);
+ if ( init ) {
+ CRef<CBioseq_ScopeInfo::TTSE_MatchSetObject> match
+ (new CBioseq_ScopeInfo::TTSE_MatchSetObject);
+ x_GetTSESetWithAnnots(lock, &match->GetData(), info);
+ info.second.m_AllAnnotRef_Info = match;
+ }
+ else {
+ x_LockMatchSet(lock, *info.second.m_AllAnnotRef_Info);
+ }
+}
+
+
+void CScope_Impl::x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TTSE_MatchSet* save_match,
+ CBioseq_ScopeInfo& binfo,
+ const SAnnotSelector* sel)
+{
+ x_GetTSESetWithBioseqAnnots(lock, save_match, binfo, sel);
+#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
+ if ( binfo.x_GetTSE_ScopeInfo().CanBeEdited() ) {
+ x_GetTSESetWithBioseqAnnots(lock, binfo, sel);
+ }
+#endif
+}
+
+
+void CScope_Impl::x_GetTSESetWithAnnots(TTSE_LockMatchSet& lock,
+ TTSE_MatchSet* save_match,
+ TSeq_idMapValue& info,
+ const SAnnotSelector* sel)
+{
+ CSeq_id_Handle::TMatches ids;
+ info.first.GetReverseMatchingHandles(ids);
+ x_GetTSESetWithOrphanAnnots(lock, save_match, ids, 0, sel);
+}
+
+
void CScope_Impl::x_AddTSESetWithAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
const TTSE_LockMatchSet_DS& add,
CDataSource_ScopeInfo& ds_info)
{
-/*
- ITERATE( TTSE_LockMatchSet_DS, it, add ) {
- CTSE_Handle tse(*x_GetTSE_Lock(it->first, ds_info));
- CTSE_ScopeInfo& tse_info = tse.x_GetScopeInfo();
- match[Ref(&tse_info)].insert(it->second.begin(), it->second.end());
- lock[tse].insert(it->second.begin(), it->second.end());
+ lock.reserve(lock.size()+add.size());
+ if ( save_match ) {
+ save_match->reserve(save_match->size()+add.size());
}
-*/
- lock.reserve(add.size());
ITERATE( TTSE_LockMatchSet_DS, it, add ) {
- CTSE_Handle tse(*x_GetTSE_Lock(it->first, ds_info));
+ TTSE_Lock tse_lock = x_GetTSE_Lock(it->first, ds_info);
+ if ( !tse_lock ) {
+ continue;
+ }
+ CTSE_Handle tse(*tse_lock);
CTSE_ScopeInfo& tse_info = tse.x_GetScopeInfo();
- match.push_back(TTSE_MatchSet::value_type(Ref(&tse_info), it->second));
+ if ( save_match ) {
+ save_match->push_back(TTSE_MatchSet::value_type(Ref(&tse_info),
+ it->second));
+ }
lock.push_back(pair<CTSE_Handle, CSeq_id_Handle>(tse, it->second));
}
}
+void CScope_Impl::x_LockMatchSet(TTSE_LockMatchSet& lock,
+ const TTSE_MatchSet& match)
+{
+ size_t size = match.size();
+ lock.resize(size);
+ for ( size_t i = 0; i < size; ++i ) {
+ lock[i].first = *x_GetTSE_Lock(*match[i].first);
+ lock[i].second = match[i].second;
+ }
+}
+
+
void CScope_Impl::x_GetTSESetWithOrphanAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
const TSeq_idSet& ids,
- CDataSource_ScopeInfo* excl_ds,
+ CBioseq_ScopeInfo* binfo,
const SAnnotSelector* sel)
{
+ TBioseq_Lock bioseq;
+ CDataSource_ScopeInfo* excl_ds = 0;
+ if ( binfo ) {
+ bioseq = binfo->GetLock(null);
+ excl_ds = &binfo->x_GetTSE_ScopeInfo().GetDSInfo();
+ }
+
for (CPriority_I it(m_setDataSrc); it; ++it) {
CPrefetchManager::IsActive();
if ( &*it == excl_ds ) {
@@ -2264,20 +2350,26 @@ void CScope_Impl::x_GetTSESetWithOrphanAnnots(TTSE_LockMatchSet& lock,
}
CDataSource& ds = it->GetDataSource();
TTSE_LockMatchSet_DS ds_lock;
- ds.GetTSESetWithOrphanAnnots(ids, ds_lock, sel);
- x_AddTSESetWithAnnots(lock, match, ds_lock, *it);
+ if ( excl_ds && it->m_EditDS == excl_ds &&
+ sx_KeepExternalAnnotsForEdit() ) {
+ // add external annotations for edited sequences
+ ds.GetTSESetWithExternalAnnots(bioseq->GetObjectInfo(),
+ binfo->x_GetTSE_ScopeInfo().m_TSE_Lock,
+ ds_lock, sel);
+ }
+ else {
+ ds.GetTSESetWithOrphanAnnots(ids, ds_lock, sel);
+ }
+ x_AddTSESetWithAnnots(lock, save_match, ds_lock, *it);
}
}
void CScope_Impl::x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
- TTSE_MatchSet& match,
+ TTSE_MatchSet* save_match,
CBioseq_ScopeInfo& binfo,
const SAnnotSelector* sel)
{
- CDataSource_ScopeInfo& ds_info = binfo.x_GetTSE_ScopeInfo().GetDSInfo();
- CDataSource& ds = ds_info.GetDataSource();
-
if ( m_setDataSrc.HasSeveralNodes() ) {
// orphan annotations on all synonyms of Bioseq
TSeq_idSet ids;
@@ -2288,7 +2380,7 @@ void CScope_Impl::x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
ids.insert(syns->GetSeq_id_Handle(syn_it));
}
// add orphan annots
- x_GetTSESetWithOrphanAnnots(lock, match, ids, &ds_info, sel);
+ x_GetTSESetWithOrphanAnnots(lock, save_match, ids, &binfo, sel);
}
#ifdef EXCLUDE_EDITED_BIOSEQ_ANNOT_SET
@@ -2297,14 +2389,20 @@ void CScope_Impl::x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
#endif
CPrefetchManager::IsActive();
+
+ CDataSource_ScopeInfo& ds_info = binfo.x_GetTSE_ScopeInfo().GetDSInfo();
+
// datasource annotations on all ids of Bioseq
// add external annots
TBioseq_Lock bioseq = binfo.GetLock(null);
TTSE_LockMatchSet_DS ds_lock;
- ds.GetTSESetWithBioseqAnnots(bioseq->GetObjectInfo(),
- bioseq->x_GetTSE_ScopeInfo().m_TSE_Lock,
- ds_lock, sel);
- x_AddTSESetWithAnnots(lock, match, ds_lock, ds_info);
+ ds_info.GetDataSource()
+ .GetTSESetWithBioseqAnnots(bioseq->GetObjectInfo(),
+ bioseq->x_GetTSE_ScopeInfo().m_TSE_Lock,
+ ds_lock, sel);
+ x_AddTSESetWithAnnots(lock, save_match, ds_lock, ds_info);
+ sort(lock.begin(), lock.end());
+ lock.erase(unique(lock.begin(), lock.end()), lock.end());
}
@@ -2313,33 +2411,21 @@ void CScope_Impl::x_GetTSESetWithBioseqAnnots(TTSE_LockMatchSet& lock,
const SAnnotSelector* sel)
{
CDataSource_ScopeInfo& ds_info = binfo.x_GetTSE_ScopeInfo().GetDSInfo();
- CDataSource& ds = ds_info.GetDataSource();
+
// datasource annotations on all ids of Bioseq
// add external annots
TBioseq_Lock bioseq = binfo.GetLock(null);
TTSE_LockMatchSet_DS ds_lock;
- ds.GetTSESetWithBioseqAnnots(bioseq->GetObjectInfo(),
- bioseq->x_GetTSE_ScopeInfo().m_TSE_Lock,
- ds_lock, sel);
- CBioseq_ScopeInfo::TTSE_MatchSet match;
- x_AddTSESetWithAnnots(lock, match, ds_lock, ds_info);
+ ds_info.GetDataSource()
+ .GetTSESetWithBioseqAnnots(bioseq->GetObjectInfo(),
+ bioseq->x_GetTSE_ScopeInfo().m_TSE_Lock,
+ ds_lock, sel);
+ x_AddTSESetWithAnnots(lock, 0, ds_lock, ds_info);
sort(lock.begin(), lock.end());
lock.erase(unique(lock.begin(), lock.end()), lock.end());
}
-void CScope_Impl::x_LockMatchSet(TTSE_LockMatchSet& lock,
- const TTSE_MatchSet& match)
-{
- size_t size = match.size();
- lock.resize(size);
- for ( size_t i = 0; i < size; ++i ) {
- lock[i].first = *x_GetTSE_Lock(*match[i].first);
- lock[i].second = match[i].second;
- }
-}
-
-
void CScope_Impl::RemoveFromHistory(CTSE_Handle tse)
{
TConfWriteLockGuard guard(m_ConfLock);
@@ -2629,7 +2715,7 @@ void CScope_Impl::x_AddSynonym(const CSeq_id_Handle& idh,
if ( x_InitBioseq_Info(seq_id_info, info) ) {
// the same bioseq - add synonym
if ( !syn_set.ContainsSynonym(seq_id_info.first) ) {
- syn_set.AddSynonym(&seq_id_info);
+ syn_set.AddSynonym(seq_id_info.first);
}
}
else {
@@ -3256,5 +3342,40 @@ void CScope_Impl::GetSequenceStates(TSequenceStates& ret,
}
+int CScope_Impl::GetSequenceHash(const CSeq_id_Handle& idh)
+{
+ TConfReadLockGuard rguard(m_ConfLock);
+ // Unknown bioseq, try to find in data sources
+ for (CPriority_I it(m_setDataSrc); it; ++it) {
+ CPrefetchManager::IsActive();
+ int hash = it->GetDataSource().GetSequenceHash(idh);
+ if ( hash != 0 ) {
+ return hash;
+ }
+ }
+ return 0;
+}
+
+
+void CScope_Impl::GetSequenceHashes(TSequenceStates& ret,
+ const TIds& ids)
+{
+ size_t count = ids.size(), remaining = count;
+ ret.assign(count, 0);
+ vector<bool> loaded(count);
+
+ TConfReadLockGuard rguard(m_ConfLock);
+ // Unknown bioseq, try to find in data sources
+ for (CPriority_I it(m_setDataSrc); it; ++it) {
+ if ( !remaining ) {
+ break;
+ }
+ CPrefetchManager::IsActive();
+ it->GetDataSource().GetSequenceHashes(ids, loaded, ret);
+ remaining = sx_CountFalse(loaded);
+ }
+}
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objmgr/scope_info.cpp b/c++/src/objmgr/scope_info.cpp
index 2cc2abd..0efdd71 100644
--- a/c++/src/objmgr/scope_info.cpp
+++ b/c++/src/objmgr/scope_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: scope_info.cpp 448567 2014-10-07 16:45:01Z ivanov $
+/* $Id: scope_info.cpp 474909 2015-08-03 10:48:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -271,6 +271,9 @@ CDataSource_ScopeInfo::GetTSE_Lock(const CTSE_Lock& lock)
{
CTSE_ScopeUserLock ret;
_ASSERT(lock);
+ if ( m_EditDS && TSEIsReplaced(lock->GetBlobId()) ) {
+ return ret;
+ }
TTSE_ScopeInfo info;
{{
TTSE_InfoMapMutex::TWriteLockGuard guard(m_TSE_InfoMapMutex);
@@ -492,6 +495,7 @@ void CDataSource_ScopeInfo::RemoveFromHistory(CTSE_ScopeInfo& tse,
if ( tse.CanBeUnloaded() ) {
x_UnindexTSE(tse);
}
+ tse.RestoreReplacedTSE();
_VERIFY(m_TSE_InfoMap.erase(tse.GetBlobId()));
tse.m_TSE_LockCounter.Add(1); // to prevent storing into m_TSE_UnlockQueue
// remove TSE lock completely
@@ -701,6 +705,9 @@ SSeqMatch_Scope CDataSource_ScopeInfo::x_FindBestTSE(const CSeq_id_Handle& idh)
ITERATE ( CDataSource::TSeqMatches, it, matches ) {
SSeqMatch_Scope nxt;
x_SetMatch(nxt, *it);
+ if ( !nxt ) {
+ continue;
+ }
if ( !ret || x_IsBetter(idh, *nxt.m_TSE_Lock, *ret.m_TSE_Lock) ) {
ret = nxt;
}
@@ -749,8 +756,13 @@ void CDataSource_ScopeInfo::x_SetMatch(SSeqMatch_Scope& match,
void CDataSource_ScopeInfo::x_SetMatch(SSeqMatch_Scope& match,
const SSeqMatch_DS& ds_match)
{
- match.m_Seq_id = ds_match.m_Seq_id;
match.m_TSE_Lock = GetTSE_Lock(ds_match.m_TSE_Lock);
+ if ( !match.m_TSE_Lock ) {
+ match.m_Seq_id.Reset();
+ match.m_Bioseq.Reset();
+ return;
+ }
+ match.m_Seq_id = ds_match.m_Seq_id;
match.m_Bioseq = ds_match.m_Bioseq;
_ASSERT(match.m_Seq_id);
_ASSERT(match.m_Bioseq);
@@ -780,6 +792,9 @@ void CDataSource_ScopeInfo::GetBlobs(TSeqMatchMap& match_map)
SSeqMatch_Scope& scope_match = match_map[ds_match->first];
scope_match = x_GetSeqMatch(ds_match->first);
x_SetMatch(scope_match, ds_match->second);
+ if ( !scope_match ) {
+ match_map.erase(ds_match->first);
+ }
}
}
@@ -791,17 +806,26 @@ bool CDataSource_ScopeInfo::TSEIsInQueue(const CTSE_ScopeInfo& tse) const
}
+bool CDataSource_ScopeInfo::TSEIsReplaced(const TBlobId& blob_id) const
+{
+ if ( m_EditDS ) {
+ return m_EditDS->TSEIsReplaced(blob_id);
+ }
+ return m_ReplacedTSEs.find(blob_id) != m_ReplacedTSEs.end();
+}
+
+
/////////////////////////////////////////////////////////////////////////////
// CTSE_ScopeInfo
/////////////////////////////////////////////////////////////////////////////
CTSE_ScopeInfo::SUnloadedInfo::SUnloadedInfo(const CTSE_Lock& tse_lock)
- : m_Loader(tse_lock->GetDataSource().GetDataLoader()),
+ : m_Source(&tse_lock->GetDataSource()),
m_BlobId(tse_lock->GetBlobId()),
m_BlobOrder(tse_lock->GetBlobOrder())
{
- _ASSERT(m_Loader);
+ _ASSERT(m_Source);
_ASSERT(m_BlobId);
// copy all bioseq ids
tse_lock->GetBioseqsIds(m_BioseqsIds);
@@ -810,9 +834,9 @@ CTSE_ScopeInfo::SUnloadedInfo::SUnloadedInfo(const CTSE_Lock& tse_lock)
CTSE_Lock CTSE_ScopeInfo::SUnloadedInfo::LockTSE(void)
{
- _ASSERT(m_Loader);
+ _ASSERT(m_Source);
_ASSERT(m_BlobId);
- return m_Loader->GetBlobById(m_BlobId);
+ return m_Source->GetDataLoader()->GetBlobById(m_BlobId);
}
@@ -1027,8 +1051,7 @@ void CTSE_ScopeInfo::DropTSE_Lock(void)
void CTSE_ScopeInfo::SetEditTSE(const CTSE_Lock& new_tse_lock,
- CDataSource_ScopeInfo& new_ds,
- const TEditInfoMap& edit_map)
+ CDataSource_ScopeInfo& new_ds)
{
_ASSERT(!CanBeEdited());
_ASSERT(new_ds.CanBeEdited());
@@ -1054,6 +1077,7 @@ void CTSE_ScopeInfo::SetEditTSE(const CTSE_Lock& new_tse_lock,
}
// convert scope info map
+ const TEditInfoMap& edit_map = new_tse_lock->m_BaseTSE->m_ObjectCopyMap;
NON_CONST_ITERATE ( TScopeInfoMap, it, old_map ) {
CConstRef<CObject> old_obj(it->first);
_ASSERT(old_obj);
@@ -1081,6 +1105,31 @@ void CTSE_ScopeInfo::SetEditTSE(const CTSE_Lock& new_tse_lock,
_ASSERT(&GetDSInfo() == &new_ds);
_ASSERT(m_TSE_Lock == new_tse_lock);
+
+ const_cast<CTSE_Info&>(*new_tse_lock).m_BaseTSE->m_ObjectCopyMap.clear();
+}
+
+
+void CTSE_ScopeInfo::RestoreReplacedTSE(void)
+{
+ if ( m_ReplacedTSE ) {
+ _ASSERT(m_DS_Info);
+ m_DS_Info->m_ReplacedTSEs.erase(m_ReplacedTSE);
+ m_ReplacedTSE = TBlobId();
+ }
+}
+
+
+void CTSE_ScopeInfo::ReplaceTSE(const CTSE_Info& old_tse)
+{
+ RestoreReplacedTSE();
+ _ASSERT(m_DS_Info);
+ m_ReplacedTSE = old_tse.GetBlobId();
+ if ( !m_DS_Info->m_ReplacedTSEs.insert(m_ReplacedTSE).second ) {
+ m_ReplacedTSE = TBlobId();
+ ERR_POST("CTSE_ScopeInfo::ReplaceTSE("<<
+ old_tse.GetDescription()<<"): already replaced");
+ }
}
@@ -1812,6 +1861,7 @@ void CBioseq_ScopeInfo::ResetId(void)
{
_ASSERT(HasObject());
const_cast<CBioseq_Info&>(GetObjectInfo()).ResetId();
+ x_GetScopeImpl().x_ClearCacheOnRemoveSeqId(CSeq_id_Handle(), *this);
ITERATE ( TIds, it, GetIds() ) {
x_GetTSE_ScopeInfo().x_UnindexBioseq(*it, this);
}
@@ -1841,8 +1891,9 @@ bool CBioseq_ScopeInfo::RemoveId(const CSeq_id_Handle& id)
}
TIds::iterator it = find(m_Ids.begin(), m_Ids.end(), id);
_ASSERT(it != m_Ids.end());
- m_Ids.erase(it);
+ x_GetScopeImpl().x_ClearCacheOnRemoveSeqId(id, *this);
x_GetTSE_ScopeInfo().x_UnindexBioseq(id, this);
+ m_Ids.erase(it);
return true;
}
@@ -1875,20 +1926,14 @@ CSynonymsSet::~CSynonymsSet(void)
CSeq_id_Handle CSynonymsSet::GetSeq_id_Handle(const const_iterator& iter)
{
- return (*iter)->first;
-}
-
-
-CBioseq_Handle CSynonymsSet::GetBioseqHandle(const const_iterator& iter)
-{
- return CBioseq_Handle((*iter)->first, *(*iter)->second.m_Bioseq_Info);
+ return *iter;
}
bool CSynonymsSet::ContainsSynonym(const CSeq_id_Handle& id) const
{
ITERATE ( TIdSet, iter, m_IdSet ) {
- if ( (*iter)->first == id ) {
+ if ( *iter == id ) {
return true;
}
}
@@ -1896,10 +1941,10 @@ bool CSynonymsSet::ContainsSynonym(const CSeq_id_Handle& id) const
}
-void CSynonymsSet::AddSynonym(const value_type& syn)
+void CSynonymsSet::AddSynonym(const CSeq_id_Handle& id)
{
- _ASSERT(!ContainsSynonym(syn->first));
- m_IdSet.push_back(syn);
+ _ASSERT(!ContainsSynonym(id));
+ m_IdSet.push_back(id);
}
diff --git a/c++/src/objmgr/seq_annot_handle.cpp b/c++/src/objmgr/seq_annot_handle.cpp
index d3faf0f..ec1ba0a 100644
--- a/c++/src/objmgr/seq_annot_handle.cpp
+++ b/c++/src/objmgr/seq_annot_handle.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_annot_handle.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: seq_annot_handle.cpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_annot_info.cpp b/c++/src/objmgr/seq_annot_info.cpp
index 0b0703e..762dca8 100644
--- a/c++/src/objmgr/seq_annot_info.cpp
+++ b/c++/src/objmgr/seq_annot_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_annot_info.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: seq_annot_info.cpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_entry_ci.cpp b/c++/src/objmgr/seq_entry_ci.cpp
index a1a08c4..ef29ef7 100644
--- a/c++/src/objmgr/seq_entry_ci.cpp
+++ b/c++/src/objmgr/seq_entry_ci.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_entry_ci.cpp 393194 2013-03-22 15:49:03Z kornbluh $
+/* $Id: seq_entry_ci.cpp 485120 2015-11-18 19:39:01Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -88,7 +88,7 @@ CSeq_entry_CI& CSeq_entry_CI::operator =(const CSeq_entry_CI& iter)
{
if (this != &iter) {
m_Parent = iter.m_Parent;
- m_Iterator = iter.m_Iterator;
+ m_Index = iter.m_Index;
m_Current = iter.m_Current;
m_Flags = iter.m_Flags;
m_Filter = iter.m_Filter;
@@ -104,7 +104,7 @@ void CSeq_entry_CI::x_Initialize(const CBioseq_set_Handle& seqset)
{
if ( seqset ) {
m_Parent = seqset;
- m_Iterator = seqset.x_GetInfo().GetSeq_set().begin();
+ m_Index = 0;
x_SetCurrentEntry();
while ((*this) && !x_ValidType()) {
x_Next();
@@ -115,13 +115,16 @@ void CSeq_entry_CI::x_Initialize(const CBioseq_set_Handle& seqset)
void CSeq_entry_CI::x_SetCurrentEntry(void)
{
- if ( m_Parent && m_Iterator != m_Parent.x_GetInfo().GetSeq_set().end() ) {
- m_Current = CSeq_entry_Handle(**m_Iterator,
- m_Parent.GetTSE_Handle());
- }
- else {
- m_Current.Reset();
+ if ( m_Parent ) {
+ const vector< CRef<CSeq_entry_Info> >& entries =
+ m_Parent.x_GetInfo().GetSeq_set();
+ if ( m_Index < entries.size() ) {
+ m_Current = CSeq_entry_Handle(*entries[m_Index],
+ m_Parent.GetTSE_Handle());
+ return;
+ }
}
+ m_Current.Reset();
}
@@ -190,10 +193,10 @@ void CSeq_entry_CI::x_Next(void)
}
}
- // "if m_Parent" is really just a proxy for seeing if m_Iterator is valid,
+ // "if m_Parent" is really just a proxy for seeing if m_Index is valid,
// otherwise incrementing is undefined
if( m_Parent ) {
- ++m_Iterator;
+ ++m_Index;
}
x_SetCurrentEntry();
}
diff --git a/c++/src/objmgr/seq_feat_handle.cpp b/c++/src/objmgr/seq_feat_handle.cpp
index 3f99d93..3d17e4c 100644
--- a/c++/src/objmgr/seq_feat_handle.cpp
+++ b/c++/src/objmgr/seq_feat_handle.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_feat_handle.cpp 459296 2015-02-17 18:12:39Z ivanov $
+/* $Id: seq_feat_handle.cpp 458821 2015-02-10 17:18:44Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_loc_cvt.cpp b/c++/src/objmgr/seq_loc_cvt.cpp
index 682a1d4..b65b1a1 100644
--- a/c++/src/objmgr/seq_loc_cvt.cpp
+++ b/c++/src/objmgr/seq_loc_cvt.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_loc_cvt.cpp 448094 2014-10-02 14:58:37Z ivanov $
+/* $Id: seq_loc_cvt.cpp 444530 2014-08-25 18:34:06Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_loc_mapper.cpp b/c++/src/objmgr/seq_loc_mapper.cpp
index f0f5a2b..64d4dbc 100644
--- a/c++/src/objmgr/seq_loc_mapper.cpp
+++ b/c++/src/objmgr/seq_loc_mapper.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_loc_mapper.cpp 425911 2014-02-04 17:57:38Z grichenk $
+/* $Id: seq_loc_mapper.cpp 479618 2015-09-22 15:42:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -718,16 +718,14 @@ void CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(CSeqMap_CI seg_it,
CBioseq_Handle
-CSeq_loc_Mapper::x_AddVirtualBioseq(const TSynonyms& synonyms,
- const CDelta_ext* delta)
+CSeq_loc_Mapper::x_AddVirtualBioseq(const TSynonyms& synonyms,
+ const CGC_Sequence& gc_seq)
{
CRef<CBioseq> bioseq(new CBioseq);
ITERATE(IMapper_Sequence_Info::TSynonyms, syn, synonyms) {
- if (!delta ) {
- CBioseq_Handle h = m_Scope.GetScope().GetBioseqHandle(*syn);
- if ( h ) {
- return h;
- }
+ CBioseq_Handle h = m_Scope.GetScope().GetBioseqHandle(*syn);
+ if ( h ) {
+ return h;
}
CRef<CSeq_id> syn_id(new CSeq_id);
syn_id->Assign(*syn->GetSeqId());
@@ -735,17 +733,12 @@ CSeq_loc_Mapper::x_AddVirtualBioseq(const TSynonyms& synonyms,
}
bioseq->SetInst().SetMol(CSeq_inst::eMol_na);
- if ( delta ) {
- // Create delta sequence
- bioseq->SetInst().SetRepr(CSeq_inst::eRepr_delta);
- // const_cast should be safe here - we are not going to modify data
- bioseq->SetInst().SetExt().SetDelta(
- const_cast<CDelta_ext&>(*delta));
- }
- else {
- // Create virtual bioseq without length/data.
- bioseq->SetInst().SetRepr(CSeq_inst::eRepr_virtual);
+ if ( gc_seq.CanGetLength() ) {
+ bioseq->SetInst().SetLength(gc_seq.GetLength());
}
+
+ // Create virtual bioseq without length/data.
+ bioseq->SetInst().SetRepr(CSeq_inst::eRepr_virtual);
return m_Scope.GetScope().AddBioseq(*bioseq);
}
@@ -951,10 +944,15 @@ void CSeq_loc_Mapper::x_InitGCSequence(const CGC_Sequence& gc_seq,
break;
}
}
- x_AddVirtualBioseq(synonyms);
+ CBioseq_Handle h = x_AddVirtualBioseq(synonyms, gc_seq);
+ TSeqPos hlen = kInvalidSeqPos;
+ if (h && h.CanGetInst_Length()) {
+ hlen = h.GetInst_Length();
+ }
x_AddConversion(gc_seq.GetSeq_id(), 0, eNa_strand_unknown,
- *dst_id, 0, eNa_strand_unknown, TRange::GetWholeLength(),
- false, 0, kInvalidSeqPos, kInvalidSeqPos, kInvalidSeqPos );
+ *dst_id, 0, eNa_strand_unknown,
+ hlen != kInvalidSeqPos ? hlen : TRange::GetWholeLength(),
+ false, 0, hlen, hlen, hlen);
}
else if (to_alias == eGCA_UCSC || to_alias == eGCA_Refseq) {
TSynonyms synonyms;
@@ -963,7 +961,6 @@ void CSeq_loc_Mapper::x_InitGCSequence(const CGC_Sequence& gc_seq,
// check for UCSC random chromosomes.
if ( x_IsUCSCRandomChr(gc_seq, chr_id, synonyms) ) {
_ASSERT(chr_id);
- x_AddVirtualBioseq(synonyms);
// Use structure (delta-seq) to initialize the mapper.
// Here we use just one level of the delta and parse it
@@ -1005,6 +1002,7 @@ void CSeq_loc_Mapper::x_InitGCSequence(const CGC_Sequence& gc_seq,
}
}
}
+ x_AddVirtualBioseq(synonyms, gc_seq);
}
}
}
diff --git a/c++/src/objmgr/seq_map_ci.cpp b/c++/src/objmgr/seq_map_ci.cpp
index 3254610..a561fc4 100644
--- a/c++/src/objmgr/seq_map_ci.cpp
+++ b/c++/src/objmgr/seq_map_ci.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_map_ci.cpp 448095 2014-10-02 14:58:56Z ivanov $
+/* $Id: seq_map_ci.cpp 444531 2014-08-25 18:34:39Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_map_switch.cpp b/c++/src/objmgr/seq_map_switch.cpp
index b07b7c0..0870b73 100644
--- a/c++/src/objmgr/seq_map_switch.cpp
+++ b/c++/src/objmgr/seq_map_switch.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_map_switch.cpp 447993 2014-10-01 19:18:13Z vasilche $
+/* $Id: seq_map_switch.cpp 444133 2014-08-21 16:53:43Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/seq_table_info.cpp b/c++/src/objmgr/seq_table_info.cpp
index 4dd9bb8..b888006 100644
--- a/c++/src/objmgr/seq_table_info.cpp
+++ b/c++/src/objmgr/seq_table_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_table_info.cpp 397774 2013-04-30 17:47:53Z grichenk $
+/* $Id: seq_table_info.cpp 469241 2015-06-02 18:43:04Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,28 +70,6 @@ bool CSeqTableColumnInfo::x_ThrowUnsetValue(void) const
}
-bool CSeqTableColumnInfo::GetString(size_t row, string& v, bool force) const
-{
- const string* ptr = GetStringPtr(row, force);
- if ( !ptr ) {
- return false;
- }
- v = *ptr;
- return true;
-}
-
-
-bool CSeqTableColumnInfo::GetBytes(size_t row, vector<char>& v, bool force) const
-{
- const vector<char>* ptr = GetBytesPtr(row, force);
- if ( !ptr ) {
- return false;
- }
- v = *ptr;
- return true;
-}
-
-
const string* CSeqTableColumnInfo::GetStringPtr(size_t row,
bool force) const
{
@@ -140,10 +118,13 @@ void CSeqTableColumnInfo::UpdateSeq_loc(CSeq_loc& loc,
const CSeqTable_single_data& data,
const CSeqTableSetLocField& setter) const
{
- switch ( data.Which() ) {
+ switch ( data.GetValueType() ) {
case CSeqTable_single_data::e_Int:
setter.SetInt(loc, data.GetInt());
return;
+ case CSeqTable_single_data::e_Int8:
+ setter.SetInt8(loc, data.GetInt8());
+ return;
case CSeqTable_single_data::e_Real:
setter.SetReal(loc, data.GetReal());
return;
@@ -161,10 +142,16 @@ void CSeqTableColumnInfo::UpdateSeq_feat(CSeq_feat& feat,
const CSeqTable_single_data& data,
const CSeqTableSetFeatField& setter) const
{
- switch ( data.Which() ) {
+ switch ( data.GetValueType() ) {
+ case CSeqTable_single_data::e_Bit:
+ setter.SetInt(feat, data.GetBit());
+ return;
case CSeqTable_single_data::e_Int:
setter.SetInt(feat, data.GetInt());
return;
+ case CSeqTable_single_data::e_Int8:
+ setter.SetInt8(feat, data.GetInt8());
+ return;
case CSeqTable_single_data::e_Real:
setter.SetReal(feat, data.GetReal());
return;
@@ -186,43 +173,34 @@ bool CSeqTableColumnInfo::UpdateSeq_loc(CSeq_loc& loc,
size_t index,
const CSeqTableSetLocField& setter) const
{
- switch ( data.Which() ) {
+ switch ( data.GetValueType() ) {
case CSeqTable_multi_data::e_Int:
- if ( index < data.GetInt().size() ) {
- setter.SetInt(loc, data.GetInt()[index]);
+ int value_int;
+ if ( data.TryGetValue(index, value_int) ) {
+ setter.SetInt(loc, value_int);
return true;
}
break;
- case CSeqTable_multi_data::e_Real:
- if ( index < data.GetReal().size() ) {
- setter.SetReal(loc, data.GetReal()[index]);
+ case CSeqTable_multi_data::e_Int8:
+ Int8 value_int8;
+ if ( data.TryGetValue(index, value_int8) ) {
+ setter.SetInt8(loc, value_int8);
return true;
}
break;
- case CSeqTable_multi_data::e_String:
- if ( index < data.GetString().size() ) {
- setter.SetString(loc, data.GetString()[index]);
+ case CSeqTable_multi_data::e_Real:
+ double value_real;
+ if ( data.TryGetValue(index, value_real) ) {
+ setter.SetReal(loc, value_real);
return true;
}
break;
- case CSeqTable_multi_data::e_Common_string:
- {{
- const CCommonString_table& common = data.GetCommon_string();
- const CCommonString_table::TIndexes& indexes = common.GetIndexes();
- if ( index < indexes.size() ) {
- const CCommonString_table::TStrings& strings = common.GetStrings();
- size_t string_index = indexes[index];
- if ( string_index < strings.size() ) {
- setter.SetString(loc, strings[string_index]);
- return true;
- }
- else {
- ERR_POST_X(3, "Bad common string index");
- return false;
- }
+ case CSeqTable_multi_data::e_String:
+ if ( const string* ptr = data.GetStringPtr(index) ) {
+ setter.SetString(loc, *ptr);
+ return true;
}
break;
- }}
default:
ERR_POST_X(4, "Bad field data type: "<<data.Which());
return true;
@@ -236,67 +214,40 @@ bool CSeqTableColumnInfo::UpdateSeq_feat(CSeq_feat& feat,
size_t index,
const CSeqTableSetFeatField& setter) const
{
- switch ( data.Which() ) {
+ switch ( data.GetValueType() ) {
case CSeqTable_multi_data::e_Int:
- if ( index < data.GetInt().size() ) {
- setter.SetInt(feat, data.GetInt()[index]);
+ int value_int;
+ if ( data.TryGetValue(index, value_int) ) {
+ setter.SetInt(feat, value_int);
+ return true;
+ }
+ break;
+ case CSeqTable_multi_data::e_Int8:
+ Int8 value_int8;
+ if ( data.TryGetValue(index, value_int8) ) {
+ setter.SetInt8(feat, value_int8);
return true;
}
break;
case CSeqTable_multi_data::e_Real:
- if ( index < data.GetReal().size() ) {
- setter.SetReal(feat, data.GetReal()[index]);
+ double value_real;
+ if ( data.TryGetValue(index, value_real) ) {
+ setter.SetReal(feat, value_real);
return true;
}
break;
case CSeqTable_multi_data::e_String:
- if ( index < data.GetString().size() ) {
- setter.SetString(feat, data.GetString()[index]);
+ if ( const string* ptr = data.GetStringPtr(index) ) {
+ setter.SetString(feat, *ptr);
return true;
}
break;
case CSeqTable_multi_data::e_Bytes:
- if ( index < data.GetBytes().size() ) {
- setter.SetBytes(feat, *data.GetBytes()[index]);
+ if ( const vector<char>* ptr = data.GetBytesPtr(index) ) {
+ setter.SetBytes(feat, *ptr);
return true;
}
break;
- case CSeqTable_multi_data::e_Common_string:
- {{
- const CCommonString_table& common = data.GetCommon_string();
- const CCommonString_table::TIndexes& indexes = common.GetIndexes();
- if ( index < indexes.size() ) {
- const CCommonString_table::TStrings& strings = common.GetStrings();
- size_t string_index = indexes[index];
- if ( string_index < strings.size() ) {
- setter.SetString(feat, strings[string_index]);
- return true;
- }
- else {
- ERR_POST_X(5, "Bad common string index");
- return false;
- }
- }
- break;
- }}
- case CSeqTable_multi_data::e_Common_bytes:
- {{
- const CCommonBytes_table& common = data.GetCommon_bytes();
- const CCommonBytes_table::TIndexes& indexes = common.GetIndexes();
- if ( index < indexes.size() ) {
- const CCommonBytes_table::TBytes& bytes = common.GetBytes();
- size_t bytes_index = indexes[index];
- if ( bytes_index < bytes.size() ) {
- setter.SetBytes(feat, *bytes[bytes_index]);
- return true;
- }
- else {
- ERR_POST_X(6, "Bad common bytes index");
- return false;
- }
- }
- break;
- }}
default:
ERR_POST_X(7, "Bad field data type: "<<data.Which());
return true;
@@ -525,9 +476,9 @@ void CSeqTableLocColumns::ParseDefaults(void)
}
if ( m_Gi ) {
if ( m_Gi->IsSetDefault() ) {
- m_DefaultIdHandle =
- CSeq_id_Handle::GetGiHandle(
- GI_FROM(CSeqTable_single_data::TInt, m_Gi->GetDefault().GetInt()));
+ TIntId gi;
+ m_Gi->GetDefault().GetValue(gi);
+ m_DefaultIdHandle = CSeq_id_Handle::GetGiHandle(gi);
}
}
@@ -592,9 +543,9 @@ CSeq_id_Handle CSeqTableLocColumns::GetIdHandle(size_t row) const
else {
_ASSERT(!m_Gi->IsSetSparse());
if ( m_Gi->IsSetData() ) {
- int gi;
- if ( m_Gi.GetInt(row, gi) ) {
- return CSeq_id_Handle::GetGiHandle(GI_FROM(int, gi));
+ TIntId gi;
+ if ( m_Gi.GetValue(row, gi) ) {
+ return CSeq_id_Handle::GetGiHandle(gi);
}
}
}
@@ -607,12 +558,12 @@ CRange<TSeqPos> CSeqTableLocColumns::GetRange(size_t row) const
_ASSERT(!m_Loc);
_ASSERT(m_From);
int from;
- if ( !m_From || !m_From.GetInt(row, from) ) {
+ if ( !m_From || !m_From.GetValue(row, from) ) {
return CRange<TSeqPos>::GetWhole();
}
int to = from;
if ( m_To ) {
- m_To.GetInt(row, to);
+ m_To.GetValue(row, to);
}
return CRange<TSeqPos>(from, to);
}
@@ -623,7 +574,7 @@ ENa_strand CSeqTableLocColumns::GetStrand(size_t row) const
_ASSERT(!m_Loc);
int strand = eNa_strand_unknown;
if ( m_Strand ) {
- m_Strand.GetInt(row, strand);
+ m_Strand.GetValue(row, strand);
}
return ENa_strand(strand);
}
@@ -651,13 +602,13 @@ void CSeqTableLocColumns::UpdateSeq_loc(size_t row,
}
else {
_ASSERT(m_Gi);
- int igi = 0;
- m_Gi.GetInt(row, igi);
- gi = GI_FROM(int, igi);
+ TIntId igi = 0;
+ m_Gi.GetValue(row, igi);
+ gi = igi;
}
int from = 0;
- if ( !m_From || !m_From.GetInt(row, from) ) {
+ if ( !m_From || !m_From.GetValue(row, from) ) {
// whole
if ( id ) {
loc.SetWhole(const_cast<CSeq_id&>(*id));
@@ -669,11 +620,11 @@ void CSeqTableLocColumns::UpdateSeq_loc(size_t row,
else {
int strand = -1;
if ( m_Strand ) {
- m_Strand.GetInt(row, strand);
+ m_Strand.GetValue(row, strand);
}
int to = 0;
- if ( !m_To || !m_To.GetInt(row, to) ) {
+ if ( !m_To || !m_To.GetValue(row, to) ) {
// point
if ( !seq_pnt ) {
seq_pnt = new CSeq_point();
@@ -986,7 +937,7 @@ void CSeqTableInfo::UpdateSeq_feat(size_t row,
}
if ( m_Partial ) {
bool val = false;
- if ( m_Partial.GetBool(row, val) ) {
+ if ( m_Partial.GetValue(row, val) ) {
feat.SetPartial(val);
}
}
diff --git a/c++/src/objmgr/seq_table_setters.cpp b/c++/src/objmgr/seq_table_setters.cpp
index f725982..4013db3 100644
--- a/c++/src/objmgr/seq_table_setters.cpp
+++ b/c++/src/objmgr/seq_table_setters.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_table_setters.cpp 197444 2010-07-16 18:05:11Z vasilche $
+/* $Id: seq_table_setters.cpp 458003 2015-01-29 19:47:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -60,6 +60,13 @@ void CSeqTableSetFeatField::SetInt(CSeq_feat& feat, int value) const
}
+void CSeqTableSetFeatField::SetInt8(CSeq_feat& feat, Int8 value) const
+{
+ NCBI_THROW_FMT(CAnnotException, eOtherError,
+ "Incompatible Seq-feat field value: "<<value);
+}
+
+
void CSeqTableSetFeatField::SetReal(CSeq_feat& feat, double value) const
{
NCBI_THROW_FMT(CAnnotException, eOtherError,
@@ -94,6 +101,13 @@ void CSeqTableSetLocField::SetInt(CSeq_loc& loc, int value) const
}
+void CSeqTableSetLocField::SetInt8(CSeq_loc& loc, Int8 value) const
+{
+ NCBI_THROW_FMT(CAnnotException, eOtherError,
+ "Incompatible Seq-loc field value: "<<value);
+}
+
+
void CSeqTableSetLocField::SetReal(CSeq_loc& loc, double value) const
{
NCBI_THROW_FMT(CAnnotException, eOtherError,
@@ -208,6 +222,13 @@ void CSeqTableSetExt::SetInt(CSeq_feat& feat, int value) const
}
+void CSeqTableSetExt::SetInt8(CSeq_feat& feat, Int8 value) const
+{
+ // TODO: Int8 in User-field
+ x_SetField(feat).SetData().SetInt(value);
+}
+
+
void CSeqTableSetExt::SetReal(CSeq_feat& feat, double value) const
{
x_SetField(feat).SetData().SetReal(value);
@@ -235,6 +256,15 @@ void CSeqTableSetDbxref::SetInt(CSeq_feat& feat, int value) const
}
+void CSeqTableSetDbxref::SetInt8(CSeq_feat& feat, Int8 value) const
+{
+ CRef<CDbtag> dbtag(new CDbtag);
+ dbtag->SetDb(name);
+ dbtag->SetTag().SetId8(value);
+ feat.SetDbxref().push_back(dbtag);
+}
+
+
void CSeqTableSetDbxref::SetString(CSeq_feat& feat, const string& value) const
{
CRef<CDbtag> dbtag(new CDbtag);
@@ -250,6 +280,12 @@ void CSeqTableSetExtType::SetInt(CSeq_feat& feat, int value) const
}
+void CSeqTableSetExtType::SetInt8(CSeq_feat& feat, Int8 value) const
+{
+ feat.SetExt().SetType().SetId8(value);
+}
+
+
void CSeqTableSetExtType::SetString(CSeq_feat& feat, const string& value) const
{
feat.SetExt().SetType().SetStr(value);
@@ -413,6 +449,24 @@ void CSeqTableSetAnyObjField::SetObjectField(CObjectInfo obj,
void CSeqTableSetAnyObjField::SetObjectField(CObjectInfo obj,
+ Int8 value) const
+{
+ ITERATE ( TNexters, it, m_Nexters ) {
+ obj = (*it)->GetNextObject(obj);
+ }
+ if ( !m_SetUserField.empty() ) {
+ CUser_field* field = CType<CUser_field>::Get(obj);
+ field->SetLabel().SetStr(m_SetUserField);
+ // TODO: Int8 in User-field
+ field->SetData().SetInt(int(value));
+ }
+ else if ( m_SetFinalObject ) {
+ obj.GetPrimitiveTypeInfo()->SetValueInt8(obj.GetObjectPtr(), value);
+ }
+}
+
+
+void CSeqTableSetAnyObjField::SetObjectField(CObjectInfo obj,
double value) const
{
ITERATE ( TNexters, it, m_Nexters ) {
@@ -475,6 +529,12 @@ void CSeqTableSetAnyLocField::SetInt(CSeq_loc& obj, int value) const
}
+void CSeqTableSetAnyLocField::SetInt8(CSeq_loc& obj, Int8 value) const
+{
+ SetObjectField(CObjectInfo(&obj, obj.GetTypeInfo()), value);
+}
+
+
void CSeqTableSetAnyLocField::SetReal(CSeq_loc& obj, double value) const
{
SetObjectField(CObjectInfo(&obj, obj.GetTypeInfo()), value);
@@ -505,6 +565,12 @@ void CSeqTableSetAnyFeatField::SetInt(CSeq_feat& obj, int value) const
}
+void CSeqTableSetAnyFeatField::SetInt8(CSeq_feat& obj, Int8 value) const
+{
+ SetObjectField(CObjectInfo(&obj, obj.GetTypeInfo()), value);
+}
+
+
void CSeqTableSetAnyFeatField::SetReal(CSeq_feat& obj, double value) const
{
SetObjectField(CObjectInfo(&obj, obj.GetTypeInfo()), value);
diff --git a/c++/src/objmgr/seq_vector.cpp b/c++/src/objmgr/seq_vector.cpp
index 5cfd227..bca8f40 100644
--- a/c++/src/objmgr/seq_vector.cpp
+++ b/c++/src/objmgr/seq_vector.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_vector.cpp 429217 2014-03-12 16:29:48Z vasilche $
+/* $Id: seq_vector.cpp 465024 2015-04-16 13:13:41Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -556,6 +556,9 @@ void x_Append2To2(string& dst, char& dst_c, TSeqPos dst_pos,
// that the next dst_pos is aligned to 4.
TSeqPos chunk = min(count, TSeqPos(kBufferSize-(dst_pos&3)));
copy_2bit(buffer, chunk, src, src_pos);
+ // Array buffer[] is properly initialized in copy_2bit()
+ // but Clang static analyzer fails to notice it
+ // and issues false warning inside x_Append8To2() call.
x_Append8To2(dst, dst_c, dst_pos, buffer, chunk);
dst_pos += chunk;
src_pos += chunk;
@@ -576,7 +579,8 @@ void x_Append2To2(string& dst, char& dst_c, TSeqPos dst_pos,
dst += c;
dst_c = 0;
src_pos += add;
- dst_pos += add;
+ // Dead increment: dst_pos is not used anymore
+ //dst_pos += add;
count -= add;
}
_ASSERT(!(src_pos&3));
diff --git a/c++/src/objmgr/snp_annot_info.cpp b/c++/src/objmgr/snp_annot_info.cpp
index c5cdb95..ee21288 100644
--- a/c++/src/objmgr/snp_annot_info.cpp
+++ b/c++/src/objmgr/snp_annot_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: snp_annot_info.cpp 406810 2013-07-16 15:03:16Z vasilche $
+/* $Id: snp_annot_info.cpp 468372 2015-05-22 12:15:20Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -768,13 +768,13 @@ void SSNP_Info::UpdateSeq_feat(CRef<CSeq_feat>& feat_ref,
/////////////////////////////////////////////////////////////////////////////
CSeq_annot_SNP_Info::CSeq_annot_SNP_Info(void)
- : m_Gi(-1)
+ : m_Gi(INVALID_GI)
{
}
CSeq_annot_SNP_Info::CSeq_annot_SNP_Info(CSeq_annot& annot)
- : m_Gi(-1), m_Seq_annot(&annot)
+ : m_Gi(INVALID_GI), m_Seq_annot(&annot)
{
}
@@ -1028,6 +1028,14 @@ void CSeq_annot_SNP_Info::x_SetGi(TGi gi)
}
+void CSeq_annot_SNP_Info::SetGi(TGi gi)
+{
+ m_Gi = gi;
+ m_Seq_id.Reset(new CSeq_id);
+ m_Seq_id->SetGi(gi);
+}
+
+
void CSeq_annot_SNP_Info::x_FinishParsing(void)
{
// we don't need index maps anymore
diff --git a/c++/src/objmgr/split/blob_splitter_impl.cpp b/c++/src/objmgr/split/blob_splitter_impl.cpp
index 6e6dbe5..a107ddb 100644
--- a/c++/src/objmgr/split/blob_splitter_impl.cpp
+++ b/c++/src/objmgr/split/blob_splitter_impl.cpp
@@ -1,4 +1,4 @@
-/* $Id: blob_splitter_impl.cpp 448098 2014-10-02 14:59:57Z ivanov $
+/* $Id: blob_splitter_impl.cpp 444534 2014-08-25 18:35:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/split/blob_splitter_maker.cpp b/c++/src/objmgr/split/blob_splitter_maker.cpp
index b211f63..673e6dc 100644
--- a/c++/src/objmgr/split/blob_splitter_maker.cpp
+++ b/c++/src/objmgr/split/blob_splitter_maker.cpp
@@ -1,4 +1,4 @@
-/* $Id: blob_splitter_maker.cpp 397774 2013-04-30 17:47:53Z grichenk $
+/* $Id: blob_splitter_maker.cpp 457860 2015-01-28 20:06:17Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -436,16 +436,16 @@ namespace {
};
#endif
- typedef set<TGi> TGiSet;
+ typedef set<TIntId> TGiSet;
typedef set<CSeq_id_Handle> TIdSet;
template<class Func>
void ForEachGiRange(const TGiSet& gis, Func func)
{
- TGi gi_start = ZERO_GI;
+ TIntId gi_start = ZERO_GI;
int gi_count = 0;
ITERATE ( TGiSet, it, gis ) {
- if ( gi_count == 0 || *it != GI_FROM(TIntId, GI_TO(TIntId, gi_start) + gi_count) ) {
+ if ( gi_count == 0 || *it != gi_start + gi_count ) {
if ( gi_count > 0 ) {
func(gi_start, gi_count);
}
@@ -556,7 +556,7 @@ namespace {
enum { SEPARATE = 3 };
- void operator()(TGi start, int count) const
+ void operator()(TIntId start, int count) const
{
_ASSERT(count > 0);
if ( count <= SEPARATE ) {
@@ -651,7 +651,7 @@ namespace {
TIdSet id_set;
ITERATE ( set<CSeq_id_Handle>, it, ids ) {
if ( it->IsGi() ) {
- gi_set.insert(GI_TO(TGiSet::value_type, it->GetGi()));
+ gi_set.insert(it->GetGi());
}
else {
id_set.insert(it->GetSeqId());
diff --git a/c++/src/objmgr/split/blob_splitter_parser.cpp b/c++/src/objmgr/split/blob_splitter_parser.cpp
index aa72089..08b37d4 100644
--- a/c++/src/objmgr/split/blob_splitter_parser.cpp
+++ b/c++/src/objmgr/split/blob_splitter_parser.cpp
@@ -1,4 +1,4 @@
-/* $Id: blob_splitter_parser.cpp 448097 2014-10-02 14:59:35Z ivanov $
+/* $Id: blob_splitter_parser.cpp 444533 2014-08-25 18:35:34Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/split/id_range.cpp b/c++/src/objmgr/split/id_range.cpp
index ad7ec9b..9531d90 100644
--- a/c++/src/objmgr/split/id_range.cpp
+++ b/c++/src/objmgr/split/id_range.cpp
@@ -1,4 +1,4 @@
-/* $Id: id_range.cpp 408908 2013-08-02 18:30:22Z vasilche $
+/* $Id: id_range.cpp 460165 2015-02-25 15:37:24Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -258,11 +258,10 @@ void CSeqsRange::Add(const CDense_diag& diag,
dim = min(dim, diag.GetStarts().size());
}
TSeqPos len = diag.GetLen();
- CDense_diag::TStarts::const_iterator it_start = diag.GetStarts().begin();
- ITERATE ( CDense_diag::TIds, it_id, diag.GetIds() ) {
- CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(**it_id);
- m_Ranges[idh].Add(*it_start, *it_start + len);
- ++it_start;
+ for ( size_t i = 0; i < dim; ++i ) {
+ CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*diag.GetIds()[i]);
+ TSeqPos start = diag.GetStarts()[i];
+ m_Ranges[idh].Add(start, start + len);
}
}
diff --git a/c++/src/objmgr/split/size.cpp b/c++/src/objmgr/split/size.cpp
index 64c092c..f6aa816 100644
--- a/c++/src/objmgr/split/size.cpp
+++ b/c++/src/objmgr/split/size.cpp
@@ -1,4 +1,4 @@
-/* $Id: size.cpp 448096 2014-10-02 14:59:14Z ivanov $
+/* $Id: size.cpp 444532 2014-08-25 18:35:16Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/table_field.cpp b/c++/src/objmgr/table_field.cpp
index 0df2f23..c07e62d 100644
--- a/c++/src/objmgr/table_field.cpp
+++ b/c++/src/objmgr/table_field.cpp
@@ -1,4 +1,4 @@
-/* $Id: table_field.cpp 363564 2012-05-17 15:41:58Z vasilche $
+/* $Id: table_field.cpp 458003 2015-01-29 19:47:52Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -95,22 +95,6 @@ CTableFieldHandle_Base::x_FindColumn(const CSeq_annot_Info& annot) const
}
-inline
-const CSeqTable_column*
-CTableFieldHandle_Base::x_FindColumn(const CSeq_annot_Handle& annot) const
-{
- return x_FindColumn(annot.x_GetInfo());
-}
-
-
-inline
-const CSeqTable_column*
-CTableFieldHandle_Base::x_FindColumn(const CFeat_CI& feat_ci) const
-{
- return x_FindColumn(feat_ci.Get().GetSeq_annot_Info());
-}
-
-
const CSeqTable_column&
CTableFieldHandle_Base::x_GetColumn(const CSeq_annot_Info& annot) const
{
@@ -131,162 +115,6 @@ CTableFieldHandle_Base::x_GetColumn(const CSeq_annot_Info& annot) const
}
-inline
-const CSeqTable_column&
-CTableFieldHandle_Base::x_GetColumn(const CSeq_annot_Handle& annot) const
-{
- return x_GetColumn(annot.x_GetInfo());
-}
-
-
-inline
-const CSeqTable_column&
-CTableFieldHandle_Base::x_GetColumn(const CFeat_CI& feat_ci) const
-{
- return x_GetColumn(feat_ci.Get().GetSeq_annot_Info());
-}
-
-
-inline
-size_t CTableFieldHandle_Base::x_GetRow(const CFeat_CI& feat_ci) const
-{
- return feat_ci.Get().GetAnnotIndex();
-}
-
-
-bool CTableFieldHandle_Base::IsSet(const CFeat_CI& feat_ci) const
-{
- return x_GetColumn(feat_ci).IsSet(x_GetRow(feat_ci));
-}
-
-
-bool CTableFieldHandle_Base::IsSet(const CSeq_annot_Handle& annot,
- size_t row) const
-{
- return x_GetColumn(annot).IsSet(row);
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CFeat_CI& feat_ci,
- bool& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(feat_ci) ) {
- return column->TryGetBool(x_GetRow(feat_ci), v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CFeat_CI& feat_ci,
- bool& v) const
-{
- if ( !TryGet(feat_ci, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CFeat_CI& feat_ci,
- int& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(feat_ci) ) {
- return column->TryGetInt(x_GetRow(feat_ci), v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CFeat_CI& feat_ci,
- int& v) const
-{
- if ( !TryGet(feat_ci, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CSeq_annot_Handle& annot,
- size_t row,
- bool& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(annot) ) {
- return column->TryGetBool(row, v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CSeq_annot_Handle& annot,
- size_t row,
- bool& v) const
-{
- if ( !TryGet(annot, row, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CSeq_annot_Handle& annot,
- size_t row,
- int& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(annot) ) {
- return column->TryGetInt(row, v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CSeq_annot_Handle& annot,
- size_t row,
- int& v) const
-{
- if ( !TryGet(annot, row, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CFeat_CI& feat_ci,
- double& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(feat_ci) ) {
- return column->TryGetReal(x_GetRow(feat_ci), v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CFeat_CI& feat_ci,
- double& v) const
-{
- if ( !TryGet(feat_ci, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
-bool CTableFieldHandle_Base::TryGet(const CSeq_annot_Handle& annot,
- size_t row,
- double& v) const
-{
- if ( const CSeqTable_column* column = x_FindColumn(annot) ) {
- return column->TryGetReal(row, v);
- }
- return false;
-}
-
-
-void CTableFieldHandle_Base::Get(const CSeq_annot_Handle& annot,
- size_t row,
- double& v) const
-{
- if ( !TryGet(annot, row, v) ) {
- x_ThrowUnsetValue();
- }
-}
-
-
const string*
CTableFieldHandle_Base::GetPtr(const CFeat_CI& feat_ci,
const string* /*dummy*/,
@@ -303,29 +131,6 @@ CTableFieldHandle_Base::GetPtr(const CFeat_CI& feat_ci,
}
-bool CTableFieldHandle_Base::TryGet(const CFeat_CI& feat_ci,
- string& v) const
-{
- const string* ptr = 0;
- ptr = GetPtr(feat_ci, ptr, false);
- if ( ptr ) {
- v = *ptr;
- return true;
- }
- else {
- return false;
- }
-}
-
-
-void CTableFieldHandle_Base::Get(const CFeat_CI& feat_ci,
- string& v) const
-{
- const string* ptr = 0;
- v = *GetPtr(feat_ci, ptr, true);
-}
-
-
const string*
CTableFieldHandle_Base::GetPtr(const CSeq_annot_Handle& annot,
size_t row,
@@ -343,31 +148,6 @@ CTableFieldHandle_Base::GetPtr(const CSeq_annot_Handle& annot,
}
-bool CTableFieldHandle_Base::TryGet(const CSeq_annot_Handle& annot,
- size_t row,
- string& v) const
-{
- const string* ptr = 0;
- ptr = GetPtr(annot, row, ptr, false);
- if ( ptr ) {
- v = *ptr;
- return true;
- }
- else {
- return false;
- }
-}
-
-
-void CTableFieldHandle_Base::Get(const CSeq_annot_Handle& annot,
- size_t row,
- string& v) const
-{
- const string* ptr = 0;
- v = *GetPtr(annot, row, ptr, true);
-}
-
-
const vector<char>*
CTableFieldHandle_Base::GetPtr(const CFeat_CI& feat_ci,
const vector<char>* /*dummy*/,
@@ -384,29 +164,6 @@ CTableFieldHandle_Base::GetPtr(const CFeat_CI& feat_ci,
}
-bool CTableFieldHandle_Base::TryGet(const CFeat_CI& feat_ci,
- vector<char>& v) const
-{
- const vector<char>* ptr = 0;
- ptr = GetPtr(feat_ci, ptr, false);
- if ( ptr ) {
- v = *ptr;
- return true;
- }
- else {
- return false;
- }
-}
-
-
-void CTableFieldHandle_Base::Get(const CFeat_CI& feat_ci,
- vector<char>& v) const
-{
- const vector<char>* ptr = 0;
- v = *GetPtr(feat_ci, ptr, true);
-}
-
-
const vector<char>*
CTableFieldHandle_Base::GetPtr(const CSeq_annot_Handle& annot,
size_t row,
@@ -424,31 +181,6 @@ CTableFieldHandle_Base::GetPtr(const CSeq_annot_Handle& annot,
}
-bool CTableFieldHandle_Base::TryGet(const CSeq_annot_Handle& annot,
- size_t row,
- vector<char>& v) const
-{
- const vector<char>* ptr = 0;
- ptr = GetPtr(annot, row, ptr, false);
- if ( ptr ) {
- v = *ptr;
- return true;
- }
- else {
- return false;
- }
-}
-
-
-void CTableFieldHandle_Base::Get(const CSeq_annot_Handle& annot,
- size_t row,
- vector<char>& v) const
-{
- const vector<char>* ptr = 0;
- v = *GetPtr(annot, row, ptr, true);
-}
-
-
bool CTableFieldHandle_Base::x_ThrowUnsetValue(void) const
{
NCBI_THROW(CAnnotException, eOtherError,
diff --git a/c++/src/objmgr/tse_assigner.cpp b/c++/src/objmgr/tse_assigner.cpp
index 5ba99db..3a39846 100644
--- a/c++/src/objmgr/tse_assigner.cpp
+++ b/c++/src/objmgr/tse_assigner.cpp
@@ -1,4 +1,4 @@
-/* $Id: tse_assigner.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: tse_assigner.cpp 485121 2015-11-18 19:39:49Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -183,7 +183,7 @@ void CTSE_Default_Assigner::LoadDescr(CTSE_Info& tse,
void CTSE_Default_Assigner::LoadAnnot(CTSE_Info& tse,
const TPlace& place,
CRef<CSeq_annot> annot,
- TIntId chunk_id)
+ int chunk_id)
{
CRef<CSeq_annot_Info> annot_info;
{{
diff --git a/c++/src/objmgr/tse_chunk_info.cpp b/c++/src/objmgr/tse_chunk_info.cpp
index 37d5023..48fce87 100644
--- a/c++/src/objmgr/tse_chunk_info.cpp
+++ b/c++/src/objmgr/tse_chunk_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: tse_chunk_info.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: tse_chunk_info.cpp 465027 2015-04-16 13:18:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/tse_info.cpp b/c++/src/objmgr/tse_info.cpp
index da7cc0d..352c824 100644
--- a/c++/src/objmgr/tse_info.cpp
+++ b/c++/src/objmgr/tse_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: tse_info.cpp 440696 2014-07-16 15:33:15Z vasilche $
+/* $Id: tse_info.cpp 469738 2015-06-08 16:26:44Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -558,6 +558,9 @@ void CTSE_Info::x_DSDetachContents(CDataSource& ds)
ds.x_UnindexSeqTSE(it->first, this);
}
ds.x_UnindexAnnotTSEs(this);
+ if ( m_Split ) {
+ m_Split->x_DSDetach(ds);
+ }
TParent::x_DSDetachContents(ds);
m_DataSource = 0;
}
diff --git a/c++/src/objmgr/tse_split_info.cpp b/c++/src/objmgr/tse_split_info.cpp
index 3cc24b1..4e9468f 100644
--- a/c++/src/objmgr/tse_split_info.cpp
+++ b/c++/src/objmgr/tse_split_info.cpp
@@ -1,4 +1,4 @@
-/* $Id: tse_split_info.cpp 465051 2015-04-16 15:16:32Z vasilche $
+/* $Id: tse_split_info.cpp 472380 2015-07-09 14:16:30Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,7 +59,8 @@ BEGIN_SCOPE(objects)
CTSE_Split_Info::CTSE_Split_Info(void)
- : m_BlobVersion(-1),
+ : m_DataLoader(0),
+ m_BlobVersion(-1),
m_SplitVersion(-1),
m_BioseqChunkId(-1),
m_SeqIdToChunksSorted(false),
@@ -68,13 +69,14 @@ CTSE_Split_Info::CTSE_Split_Info(void)
}
CTSE_Split_Info::CTSE_Split_Info(TBlobId blob_id, TBlobVersion blob_ver)
- : m_BlobId(blob_id),
+ : m_DataLoader(0),
+ m_BlobId(blob_id),
m_BlobVersion(blob_ver),
m_SplitVersion(-1),
m_BioseqChunkId(-1),
m_SeqIdToChunksSorted(false),
m_ContainsBioseqs(false)
-{
+{
}
@@ -112,15 +114,24 @@ CRef<ITSE_Assigner> CTSE_Split_Info::GetAssigner(const CTSE_Info& tse)
return CRef<ITSE_Assigner>();
}
+
void CTSE_Split_Info::x_DSAttach(CDataSource& ds)
{
- if ( !m_DataLoader ) {
- m_DataLoader = ds.GetDataLoader();
+ if ( !m_DataLoader && ds.GetDataLoader() ) {
+ m_DataLoader = &ds;
_ASSERT(m_DataLoader);
}
}
+void CTSE_Split_Info::x_DSDetach(CDataSource& ds)
+{
+ if ( m_DataLoader == &ds ) {
+ m_DataLoader = 0;
+ }
+}
+
+
// identification
CTSE_Split_Info::TBlobId CTSE_Split_Info::GetBlobId(void) const
{
@@ -158,7 +169,10 @@ CInitMutexPool& CTSE_Split_Info::GetMutexPool(void)
CDataLoader& CTSE_Split_Info::GetDataLoader(void) const
{
- return m_DataLoader.GetNCObject();
+ _ASSERT(m_DataLoader);
+ CDataLoader* loader = m_DataLoader->GetDataLoader();
+ _ASSERT(loader);
+ return *loader;
}
@@ -483,7 +497,7 @@ void CTSE_Split_Info::x_LoadDescr(const TPlace& place,
void CTSE_Split_Info::x_LoadAnnot(const TPlace& place,
const CSeq_annot& annot,
- TIntId chunk_id)
+ int chunk_id)
{
CRef<CSeq_annot> add;
NON_CONST_ITERATE ( TTSE_Set, it, m_TSE_Set ) {
diff --git a/c++/src/objmgr/util/Makefile.util.lib b/c++/src/objmgr/util/Makefile.util.lib
index e2c75b3..df273ad 100644
--- a/c++/src/objmgr/util/Makefile.util.lib
+++ b/c++/src/objmgr/util/Makefile.util.lib
@@ -1,13 +1,16 @@
-# $Id: Makefile.util.lib 427420 2014-02-20 13:35:49Z gouriano $
+# $Id: Makefile.util.lib 474406 2015-07-28 18:14:17Z ivanov $
# Build library "xobjutil"
###############################
ASN_DEP = submit
-SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
+SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci \
+ objutil
LIB = xobjutil
+DLL_LIB = $(SOBJMGR_LIBS)
+
WATCHERS = ucko vasilche kornbluh
diff --git a/c++/src/objmgr/util/create_defline.cpp b/c++/src/objmgr/util/create_defline.cpp
index 224953e..de3644c 100644
--- a/c++/src/objmgr/util/create_defline.cpp
+++ b/c++/src/objmgr/util/create_defline.cpp
@@ -140,6 +140,111 @@ CFeat_CI Itr(Var, Sel)
#define FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE(Itr, Var, Sel) \
for (SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR(Itr, Var, Sel); Itr; ++Itr)
+// Copied from CleanAndCompress in objtools/format/utils.cpp
+
+// two-bytes combinations we're looking to clean
+#define twochars(a,b) Uint2((a) << 8 | (b))
+#define twocommas twochars(',',',')
+#define twospaces twochars(' ',' ')
+#define space_comma twochars(' ',',')
+#define space_bracket twochars(' ',')')
+#define bracket_space twochars('(',' ')
+#define space_semicolon twochars(' ',';')
+#define comma_space twochars(',',' ')
+#define semicolon_space twochars(';',' ')
+
+void x_CleanAndCompress(string& dest, const CTempString& instr)
+{
+ size_t left = instr.size();
+ // this is the input stream
+ const char* in = instr.data();
+
+ // skip front white spaces
+ while (left && *in == ' ')
+ {
+ in++;
+ left--;
+ }
+ // forget end white spaces
+ while (left && in[left - 1] == ' ')
+ {
+ left--;
+ }
+
+ dest.resize(left);
+
+ if (left < 1) return;
+
+ // this is where we write result
+ char* out = (char*)dest.c_str();
+
+ char curr = *in++; // initialize with first character
+ left--;
+
+ char next = 0;
+ Uint2 two_chars = curr; // this is two bytes storage where we see current and previous symbols
+
+ while (left > 0) {
+ next = *in++;
+
+ two_chars = (two_chars << 8) | next;
+
+ switch (two_chars)
+ {
+ case twocommas: // replace double commas with comma+space
+ *out++ = curr;
+ next = ' ';
+ break;
+ case twospaces: // skip multispaces (only print last one)
+ break;
+ case bracket_space: // skip space after bracket
+ next = curr;
+ two_chars = curr;
+ break;
+ case space_bracket: // skip space before bracket
+ break;
+ case space_comma:
+ case space_semicolon: // swap characters
+ *out++ = next;
+ next = curr;
+ two_chars = curr;
+ break;
+ case comma_space:
+ *out++ = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ',') {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ case semicolon_space:
+ *out++ = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ';') {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ default:
+ *out++ = curr;
+ break;
+ }
+
+ curr = next;
+ left--;
+ }
+
+ if (curr > 0 && curr != ' ') {
+ *out++ = curr;
+ }
+
+ dest.resize(out - dest.c_str());
+}
+
static const char* x_OrganelleName (
TBIOSOURCE_GENOME genome,
bool has_plasmid,
@@ -259,6 +364,7 @@ void CDeflineGenerator::x_SetFlags (
m_AllProtNames = (flags & fAllProteinNames) != 0;
m_LocalAnnotsOnly = (flags & fLocalAnnotsOnly) != 0;
m_GpipeMode = (flags & fGpipeMode) != 0;
+ m_OmitTaxonomicName = (flags & fOmitTaxonomicName) != 0;
// reset member variables to cleared state
m_IsNA = false;
@@ -307,11 +413,14 @@ void CDeflineGenerator::x_SetFlags (
m_TPAExp = false;
m_TPAInf = false;
m_TPAReasm = false;
+ m_Unordered = false;
m_PDBCompound.clear();
m_Source.Reset();
m_Taxname.clear();
+ m_Genus.clear();
+ m_Species.clear();
m_Multispecies = false;
m_Genome = NCBI_GENOME(unknown);
m_IsPlasmid = false;
@@ -649,23 +758,32 @@ void CDeflineGenerator::x_SetFlags (
}
}
- if (keywords != NULL && (m_HTGTech || m_ThirdParty)) {
+ if (keywords != NULL) {
FOR_EACH_STRING_IN_LIST (kw_itr, *keywords) {
- const string& str = *kw_itr;
- if (NStr::EqualNocase (str, "HTGS_DRAFT")) {
- m_HTGSDraft = true;
- } else if (NStr::EqualNocase (str, "HTGS_CANCELLED")) {
- m_HTGSCancelled = true;
- } else if (NStr::EqualNocase (str, "HTGS_POOLED_MULTICLONE")) {
- m_HTGSPooled = true;
- } else if (NStr::EqualNocase (str, "TPA:experimental")) {
- m_TPAExp = true;
- } else if (NStr::EqualNocase (str, "TPA:inferential")) {
- m_TPAInf = true;
- } else if (NStr::EqualNocase (str, "TPA:reassembly")) {
- m_TPAReasm = true;
- } else if (NStr::EqualNocase (str, "TPA:assembly")) {
- m_TPAReasm = true;
+ const string& clause = *kw_itr;
+ list<string> kywds;
+ NStr::Split( clause, ";", kywds );
+ FOR_EACH_STRING_IN_LIST ( k_itr, kywds ) {
+ const string& str = *k_itr;
+ if (NStr::EqualNocase (str, "UNORDERED")) {
+ m_Unordered = true;
+ }
+ if ((! m_HTGTech) && (! m_ThirdParty)) continue;
+ if (NStr::EqualNocase (str, "HTGS_DRAFT")) {
+ m_HTGSDraft = true;
+ } else if (NStr::EqualNocase (str, "HTGS_CANCELLED")) {
+ m_HTGSCancelled = true;
+ } else if (NStr::EqualNocase (str, "HTGS_POOLED_MULTICLONE")) {
+ m_HTGSPooled = true;
+ } else if (NStr::EqualNocase (str, "TPA:experimental")) {
+ m_TPAExp = true;
+ } else if (NStr::EqualNocase (str, "TPA:inferential")) {
+ m_TPAInf = true;
+ } else if (NStr::EqualNocase (str, "TPA:reassembly")) {
+ m_TPAReasm = true;
+ } else if (NStr::EqualNocase (str, "TPA:assembly")) {
+ m_TPAReasm = true;
+ }
}
}
}
@@ -737,7 +855,15 @@ void CDeflineGenerator::x_SetBioSrc (
const COrgName& onp = m_Source->GetOrgname();
if (onp.IsSetName()) {
const COrgName::TName& nam = onp.GetName();
- if (nam.IsPartial()) {
+ if (nam.IsBinomial()) {
+ const CBinomialOrgName& bon = nam.GetBinomial();
+ if (bon.IsSetGenus()) {
+ m_Genus = bon.GetGenus();
+ }
+ if (bon.IsSetSpecies()) {
+ m_Species = bon.GetSpecies();
+ }
+ } else if (nam.IsPartial()) {
const CPartialOrgName& pon = nam.GetPartial();
if (pon.IsSet()) {
const CPartialOrgName::Tdata& tx = pon.Get();
@@ -1015,15 +1141,15 @@ void CDeflineGenerator::x_SetTitleFromNC (void)
joiner.Add(pls_pfx).Add(m_Plasmid).Add(seq_tag);
} else if ( ! m_Organelle.empty() ) {
if ( m_Chromosome.empty() ) {
- switch (m_Genome) {
- case NCBI_GENOME(mitochondrion):
- case NCBI_GENOME(chloroplast):
- case NCBI_GENOME(kinetoplast):
- case NCBI_GENOME(plastid):
- case NCBI_GENOME(apicoplast):
- joiner.Add(" ").Add(m_Organelle);
- break;
- }
+ switch (m_Genome) {
+ case NCBI_GENOME(mitochondrion):
+ case NCBI_GENOME(chloroplast):
+ case NCBI_GENOME(kinetoplast):
+ case NCBI_GENOME(plastid):
+ case NCBI_GENOME(apicoplast):
+ joiner.Add(" ").Add(m_Organelle);
+ break;
+ }
joiner.Add(gen_tag);
} else if (m_IsChromosome) {
joiner.Add(" chromosome ").Add(m_Chromosome).Add(seq_tag);
@@ -1475,28 +1601,51 @@ static const char* s_proteinOrganellePrefix [] = {
"",
"",
"chloroplast",
- "",
- "",
+ "chromoplast",
+ "kinetoplast",
"mitochondrion",
+ "plastid",
+ "macronuclear",
"",
+ "plasmid",
"",
"",
+ "cyanelle",
"",
"",
+ "nucleomorph",
+ "apicoplast",
+ "leucoplast",
+ "protoplast",
+ "endogenous virus",
+ "hydrogenosome",
"",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- ""
+ "chromatophore"
};
+static string s_RemoveBracketedOrgFromEnd (string str, string taxname)
+
+{
+ string final;
+ if (str.empty()) return str;
+ if (taxname.empty()) return str;
+ SIZE_TYPE taxlen = taxname.length();
+ int len = str.length();
+ if (len < 5) return str;
+ if (str [len - 1] != ']') return str;
+ SIZE_TYPE cp = NStr::Find(str, "[", 0, NPOS, NStr::eLast);
+ if (cp == NPOS) return str;
+ string suffix = str.substr(cp+1);
+ if (NStr::StartsWith(suffix, "NAD")) return str;
+ if (suffix.length() != taxlen + 1) return str;
+ if (NStr::StartsWith(suffix, taxname)) {
+ str.erase (cp);
+ x_CleanAndCompress(final, str);
+
+ }
+ return final;
+}
+
void CDeflineGenerator::x_SetTitleFromProtein (
const CBioseq_Handle& bsh
)
@@ -1537,8 +1686,9 @@ void CDeflineGenerator::x_SetTitleFromProtein (
const char* prefix = "";
FOR_EACH_NAME_ON_PROT (prp_itr, prp) {
const string& str = *prp_itr;
+ string trimmed = s_RemoveBracketedOrgFromEnd (str, m_Taxname);
m_MainTitle += prefix;
- m_MainTitle += str;
+ m_MainTitle += trimmed;
if (! m_AllProtNames) {
break;
}
@@ -1552,6 +1702,30 @@ void CDeflineGenerator::x_SetTitleFromProtein (
m_MainTitle.erase (pos + 1);
}
+ int offset = 0;
+ int delta = 0;
+ string comma = "";
+ string isoform = "";
+ if (NStr::StartsWith (m_MainTitle, "hypothetical protein")) {
+ offset = 20;
+ } else if (NStr::StartsWith (m_MainTitle, "uncharacterized protein")) {
+ offset = 23;
+ }
+ if (offset > 0 && offset < m_MainTitle.length()) {
+ if (m_MainTitle [offset] == ',' && m_MainTitle [offset + 1] == ' ') {
+ comma = ", isoform ";
+ delta = 2;
+ }
+ if (m_MainTitle [offset] == ' ') {
+ comma = " isoform ";
+ delta = 1;
+ }
+ if (NStr::StartsWith (m_MainTitle.substr (offset + delta), "isoform ")) {
+ isoform = m_MainTitle.substr (offset + delta + 8);
+ // !!! check for single alphanumeric string
+ m_MainTitle.erase (offset);
+ }
+ }
if ((NStr::EqualNocase (m_MainTitle, "hypothetical protein") ||
NStr::EqualNocase (m_MainTitle, "uncharacterized protein"))
&& !m_LocalAnnotsOnly ) {
@@ -1563,7 +1737,7 @@ void CDeflineGenerator::x_SetTitleFromProtein (
}
}
if (! locus_tag.empty()) {
- m_MainTitle += " " + string(locus_tag);
+ m_MainTitle += " " + string(locus_tag) + string(comma) + string(isoform);
}
}
}
@@ -1643,6 +1817,8 @@ void CDeflineGenerator::x_SetTitleFromProtein (
m_MainTitle += ", partial";
}
+ if (m_OmitTaxonomicName) return;
+
CTempString taxname = m_Taxname;
if (m_Genome >= NCBI_GENOME(chloroplast) && m_Genome <= NCBI_GENOME(chromatophore)) {
@@ -1927,11 +2103,14 @@ void CDeflineGenerator::x_SetSuffix (
case NCBI_TECH(htgs_1):
case NCBI_TECH(htgs_2):
{
- if (m_HTGSDraft && m_MainTitle.find ("WORKING DRAFT") == NPOS) {
- type = ", WORKING DRAFT SEQUENCE";
- } else if ( !m_HTGSDraft && !m_HTGSCancelled &&
- m_MainTitle.find ("SEQUENCING IN") == NPOS) {
- type = ", *** SEQUENCING IN PROGRESS ***";
+ if (m_HTGSDraft) {
+ if (m_MainTitle.find ("WORKING DRAFT") == NPOS) {
+ type = ", WORKING DRAFT SEQUENCE";
+ }
+ } else if (!m_HTGSCancelled) {
+ if (m_MainTitle.find ("SEQUENCING IN") == NPOS) {
+ type = ", *** SEQUENCING IN PROGRESS ***";
+ }
}
string un;
@@ -2026,8 +2205,16 @@ void CDeflineGenerator::x_SetSuffix (
break;
}
- /*
- */
+ if (m_Unordered && m_IsDelta) {
+ unsigned int num_gaps = 0;
+ for (CSeqMap_CI it (bsh, CSeqMap::fFindGap); it; ++it) {
+ ++num_gaps;
+ }
+ if (num_gaps > 0) {
+ type += (", " + NStr::IntToString (num_gaps + 1)
+ + " unordered pieces");
+ }
+ }
suffix = type + comp;
}
@@ -2040,6 +2227,7 @@ static inline void s_TrimMainTitle (string& str)
}
}
+/*
// Strips all spaces in string in following manner. If the function
// meets several spaces (spaces and tabs) in succession it replaces them
// with one space. Strips all spaces after '(' and before ( ')' or ',' ).
@@ -2070,6 +2258,30 @@ static void x_CompressRunsOfSpaces (string& str)
}
str.erase(new_str, str.end());
}
+*/
+
+static size_t s_TitleEndsInOrganism (
+ string& title,
+ CTempString taxname
+)
+
+{
+ size_t pos;
+ int len1, len2, idx;
+
+ len1 = title.length();
+ len2 = taxname.length();
+
+ idx = len1 - len2 - 3;
+ if (len1 > len2 + 4 && title [idx] == ' ' && title [idx + 1] == '[' && title [len1 - 1] == ']') {
+ pos = NStr::FindNoCase(title, taxname, 0, NPOS, NStr::eLast);
+ if (pos == idx + 2) {
+ return pos - 1;
+ }
+ }
+
+ return NPOS;
+}
void CDeflineGenerator::x_AdjustProteinTitleSuffix (
const CBioseq_Handle& bsh
@@ -2077,8 +2289,8 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
{
CBioSource::TGenome genome;
- size_t pos;
- int len;
+ size_t pos, tpos = NPOS, opos = NPOS;
+ int len1, len2;
bool partial = false;
CConstRef<CBioSource> src;
@@ -2090,6 +2302,21 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
if (m_Source->IsSetGenome()) {
m_Genome = m_Source->GetGenome();
}
+ if (m_Source->IsSetOrgname()) {
+ const COrgName& onp = m_Source->GetOrgname();
+ if (onp.IsSetName()) {
+ const COrgName::TName& nam = onp.GetName();
+ if (nam.IsBinomial()) {
+ const CBinomialOrgName& bon = nam.GetBinomial();
+ if (bon.IsSetGenus()) {
+ m_Genus = bon.GetGenus();
+ }
+ if (bon.IsSetSpecies()) {
+ m_Species = bon.GetSpecies();
+ }
+ }
+ }
+ }
switch (m_MICompleteness) {
case NCBI_COMPLETENESS(partial):
@@ -2104,24 +2331,41 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
s_TrimMainTitle (m_MainTitle);
- len = m_MainTitle.length();
-
- // remove [taxname]
- if (len > 2 && m_MainTitle [len - 1] == ']') {
- pos = NStr::FindNoCase(m_MainTitle, "][", 0, NPOS, NStr::eLast);
- if (pos != NPOS) {
- m_MainTitle.erase (pos + 1);
- }
- pos = m_MainTitle.find_last_of ("[");
- if (pos != NPOS) {
- m_MainTitle.erase (pos);
+ len1 = m_MainTitle.length();
+ len2 = m_Taxname.length();
+
+ // find [taxname]
+
+ if (len1 > len2 + 4) {
+ tpos = s_TitleEndsInOrganism(m_MainTitle, m_Taxname);
+ if (tpos == NPOS) {
+ string binomial = m_Genus;
+ binomial += " ";
+ binomial += m_Species;
+ tpos = s_TitleEndsInOrganism(m_MainTitle, binomial);
+ if (tpos == NPOS) {
+ if (m_IsCrossKingdom) {
+ pos = NStr::FindNoCase(m_MainTitle, "][", 0, NPOS, NStr::eLast);
+ if (pos != NPOS) {
+ m_MainTitle.erase (pos + 1);
+ s_TrimMainTitle (m_MainTitle);
+ tpos = s_TitleEndsInOrganism(m_MainTitle, m_Taxname);
+ }
+ }
+ }
}
- s_TrimMainTitle (m_MainTitle);
- len = m_MainTitle.length();
}
- // remove (organelle)
- if (len > 2 && m_MainTitle [len - 1] == ')') {
+ /* do not change unless [genus species] was at the end */
+ if (tpos == NPOS) return;
+
+ m_MainTitle.erase (tpos);
+ s_TrimMainTitle (m_MainTitle);
+ len1 = m_MainTitle.length();
+
+ // find (organelle)
+
+ if (len1 > 2 && m_MainTitle [len1 - 1] == ')') {
pos = m_MainTitle.find_last_of ("(");
if (pos != NPOS) {
for ( genome = NCBI_GENOME(chloroplast); genome <= NCBI_GENOME(chromatophore); genome++ ) {
@@ -2129,14 +2373,20 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
if ( ! str.empty() ) {
string paren = "(" + str + ")";
if (NStr::EndsWith (m_MainTitle, paren )) {
- m_MainTitle.erase (pos);
+ opos = pos;
break;
}
}
}
}
s_TrimMainTitle (m_MainTitle);
- len = m_MainTitle.length();
+ len1 = m_MainTitle.length();
+ }
+
+ if (opos != NPOS) {
+ m_MainTitle.erase (opos);
+ s_TrimMainTitle (m_MainTitle);
+ len1 = m_MainTitle.length();
}
if ( NStr::EndsWith (m_MainTitle, ", partial")) {
@@ -2150,6 +2400,8 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
m_MainTitle += ", partial";
}
+ if (m_OmitTaxonomicName) return;
+
CTempString taxname = m_Taxname;
if (m_Genome >= NCBI_GENOME(chloroplast) && m_Genome <= NCBI_GENOME(chromatophore)) {
@@ -2175,7 +2427,6 @@ void CDeflineGenerator::x_AdjustProteinTitleSuffix (
}
}
-
if (m_IsCrossKingdom && ! m_FirstSuperKingdom.empty() && ! m_SecondSuperKingdom.empty()) {
m_MainTitle += " [" + string(m_FirstSuperKingdom) + "][" + string(m_SecondSuperKingdom) + "]";
} else if (! taxname.empty() /* && m_MainTitle.find(taxname) == NPOS */) {
@@ -2204,6 +2455,7 @@ string CDeflineGenerator::GenerateDefline (
string prefix; // from a small set of compile-time constants
string suffix;
+ string final;
// set flags from record components
x_SetFlags (bsh, flags);
@@ -2282,11 +2534,13 @@ string CDeflineGenerator::GenerateDefline (
// strip leading spaces remaining after removal of old TPA or TSA prefixes
m_MainTitle.erase (0, m_MainTitle.find_first_not_of (' '));
+ CStringUTF8 decoded = NStr::HtmlDecode (m_MainTitle);
+
// strip trailing commas, semicolons, and spaces (period may be an sp.
// species)
- size_t pos = m_MainTitle.find_last_not_of (",;~ ");
+ size_t pos = decoded.find_last_not_of (",;~ ");
if (pos != NPOS) {
- m_MainTitle.erase (pos + 1);
+ decoded.erase (pos + 1);
}
// calculate prefix
@@ -2296,19 +2550,9 @@ string CDeflineGenerator::GenerateDefline (
x_SetSuffix (suffix, bsh);
// produce final result
- string final = prefix + m_MainTitle + suffix;
-
- pos = final.find (" ,");
- if (pos != NPOS) {
- final [pos] = ',';
- final [pos+1] = ' ';
- }
- pos = final.find (",,");
- if (pos != NPOS) {
- final [pos+1] = ' ';
- }
+ string penult = prefix + decoded + suffix;
- x_CompressRunsOfSpaces (final);
+ x_CleanAndCompress (final, penult);
if (! m_IsPDB && ! m_IsPatent && ! m_IsAA && ! m_IsSeg) {
if (!final.empty() && islower ((unsigned char) final[0]) && capitalize) {
diff --git a/c++/src/objmgr/util/feature.cpp b/c++/src/objmgr/util/feature.cpp
index 56c77cd..4929bb7 100644
--- a/c++/src/objmgr/util/feature.cpp
+++ b/c++/src/objmgr/util/feature.cpp
@@ -1,4 +1,4 @@
-/* $Id: feature.cpp 468841 2015-05-28 18:44:43Z ivanov $
+/* $Id: feature.cpp 480957 2015-10-06 12:01:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,6 +56,7 @@
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Feat_id.hpp>
+#include <objects/seqfeat/Variation_ref.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/seqport_util.hpp>
@@ -65,6 +66,8 @@
#include <objects/seq/NCBI8aa.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Heterogen.hpp>
+#include <objects/seq/Seqdesc.hpp>
+#include <objects/seq/Seq_descr.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_loc_mix.hpp>
@@ -80,6 +83,7 @@
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
+#include <objmgr/annot_ci.hpp>
#include <algorithm>
@@ -98,8 +102,13 @@ void s_GetTypeLabel(const CSeq_feat& feat, string* label, TFeatLabelFlags flags)
CSeqFeatData::ESubtype idx = feat.GetData().GetSubtype();
if ( idx != CSeqFeatData::eSubtype_bad ) {
tlabel = feat.GetData().GetKey();
- if (feat.GetData().IsImp() && tlabel != "CDS") {
- tlabel = "[" + tlabel + "]";
+ if (feat.GetData().IsImp()) {
+ if ( tlabel == "variation" ) {
+ tlabel = "Variation";
+ }
+ else if ( tlabel != "CDS") {
+ tlabel = "[" + tlabel + "]";
+ }
} else if ((flags & fFGL_NoComments) == 0 && feat.GetData().IsRegion()
&& feat.GetData().GetRegion() == "Domain"
&& feat.IsSetComment() ) {
@@ -384,6 +393,26 @@ static void s_GetRnaRefLabel
}
+static void s_GetVariationDbtagLabel(string* tlabel,
+ TFeatLabelFlags /*flags*/,
+ const CDbtag& dbtag)
+{
+ if ( dbtag.GetDb() == "dbSNP" ) {
+ if ( !tlabel->empty() ) {
+ *tlabel += ", ";
+ }
+ const CObject_id& tag = dbtag.GetTag();
+ if ( tag.IsId() ) {
+ *tlabel += "rs";
+ *tlabel += NStr::NumericToString(tag.GetId());
+ }
+ else {
+ *tlabel += tag.GetStr();
+ }
+ }
+}
+
+
// Appends a label to tlabel for a CImp_feat. A return value of true indicates
// that the label was created for a CImp_feat key = "Site-ref"
inline
@@ -408,6 +437,14 @@ static bool s_GetImpLabel
feat.GetCit().GetLabel(tlabel);
return true;
}
+ }
+ else if (NStr::EqualNocase(key, "variation")) {
+ if ( feat.IsSetDbxref() ) {
+ ITERATE( CSeq_feat::TDbxref, it, feat.GetDbxref() ) {
+ s_GetVariationDbtagLabel(tlabel, flags, **it);
+ }
+ return false;
+ }
// else if the key is not Site-ref
} else if ((flags & fFGL_Type) == 0) {
// If the key is CDS
@@ -504,6 +541,31 @@ static bool s_GetImpLabel
}
+// Appends a label to tlabel for a CImp_feat. A return value of true indicates
+// that the label was created for a CImp_feat key = "Site-ref"
+static void s_GetVariationLabel(const CSeq_feat& feat,
+ string* tlabel,
+ TFeatLabelFlags flags,
+ const string* /*type_label*/)
+{
+ // Return if tlablel does not exist or feature data is not Imp-feat
+ if (!tlabel || !feat.GetData().IsVariation()) {
+ return;
+ }
+
+ const CVariation_ref& var = feat.GetData().GetVariation();
+ if ( var.IsSetId() ) {
+ s_GetVariationDbtagLabel(tlabel, flags, var.GetId());
+ }
+ if ( var.IsSetName() ) {
+ if ( !tlabel->empty() ) {
+ *tlabel += ", ";
+ }
+ *tlabel += var.GetName();
+ }
+}
+
+
// Return a label based on the content of the feature
void s_GetContentLabel
(const CSeq_feat& feat,
@@ -621,6 +683,9 @@ void s_GetContentLabel
tlabel += str;
}}
break;
+ case CSeqFeatData::e_Variation:
+ s_GetVariationLabel(feat, &tlabel, flags, type_label);
+ break;
default:
break;
}
@@ -1790,6 +1855,17 @@ CFeatTree::CFeatInfo& CFeatTree::x_GetInfo(const CSeq_feat_Handle& feat)
}
+const CMappedFeat& CFeatTree::GetMappedFeat(const CSeq_feat_Handle& feat) const
+{
+ TInfoMap::const_iterator it = m_InfoMap.find(feat);
+ if ( it == m_InfoMap.end() ) {
+ NCBI_THROW(CObjMgrException, eFindFailed,
+ "CFeatTree: feature not found");
+ }
+ return it->second.m_Feat;
+}
+
+
CFeatTree::CFeatInfo* CFeatTree::x_FindInfo(const CSeq_feat_Handle& feat)
{
TInfoMap::iterator it = m_InfoMap.find(feat);
@@ -3154,6 +3230,329 @@ void ReassignFeatureIds(const CSeq_annot_EditHandle& annot)
}
+static CRef<CSeq_loc> s_MakePointForLocationStop (const CSeq_loc& loc)
+{
+ CRef<CSeq_loc> stop(new CSeq_loc());
+
+ for ( CSeq_loc_CI citer (loc); citer; ++citer ) {
+ stop->SetPnt().SetId().Assign(citer.GetSeq_id());
+ }
+ stop->SetPnt().SetPoint(loc.GetStop(eExtreme_Biological));
+ return stop;
+}
+
+ELocationInFrame IsLocationInFrame (const CSeq_feat_Handle& cds, const CSeq_loc& loc)
+{
+ TSeqPos pos1 = sequence::LocationOffset(cds.GetLocation(), loc, sequence::eOffset_FromStart);
+ bool pos1_not_in = false;
+ if (pos1 == ((TSeqPos)-1)) {
+ pos1_not_in = true;
+ }
+ CRef<CSeq_loc> tmp = s_MakePointForLocationStop(loc);
+ TSeqPos pos2 = sequence::LocationOffset(cds.GetLocation(), *tmp, sequence::eOffset_FromStart);
+ bool pos2_not_in = false;
+ if (pos2 == ((TSeqPos)-1)) {
+ pos2_not_in = true;
+ }
+ if (pos1_not_in && pos2_not_in) {
+ return eLocationInFrame_NotIn;
+ }
+
+ unsigned int frame = 0;
+ if (cds.IsSetData() && cds.GetData().IsCdregion()) {
+ const CCdregion& cdr = cds.GetData().GetCdregion();
+ switch (cdr.GetFrame()) {
+ case CCdregion::eFrame_not_set:
+ case CCdregion::eFrame_one:
+ frame = 0;
+ break;
+ case CCdregion::eFrame_two:
+ frame = 1;
+ break;
+ case CCdregion::eFrame_three:
+ frame = 2;
+ break;
+ }
+ }
+ // note - have to add 3 to prevent negative result from subtraction
+ TSeqPos mod1 = (pos1 + 3 - frame) %3;
+ TSeqPos mod2 = (pos2 + 3 - frame) %3;
+
+ if ( mod1 != 0 && loc.IsPartialStart(eExtreme_Biological)
+ && cds.GetLocation().IsPartialStart(eExtreme_Biological)
+ && pos1 == 0) {
+ mod1 = 0;
+ } else if (pos1 < frame) {
+ // start is out of frame - it's before the coding region begins
+ mod1 = 1;
+ }
+
+ TSeqPos cds_len = sequence::GetLength (cds.GetLocation(), &(cds.GetScope()));
+
+ if ( mod2 != 0 && loc.IsPartialStop(eExtreme_Biological)
+ && cds.GetLocation().IsPartialStop(eExtreme_Biological)
+ && pos2 == cds_len) {
+ mod2 = 0;
+ } else if (pos2 <= frame) {
+ // stop is out of frame - it's before the coding region begins
+ mod2 = 1;
+ }
+ if (pos2 > cds_len) {
+ // stop is out of frame - it's after the coding region ends
+ mod2 = 1;
+ }
+
+ if (loc.IsPartialStart(eExtreme_Biological)) {
+ mod1 = 0;
+ }
+ if (loc.IsPartialStop(eExtreme_Biological)) {
+ mod2 = 2;
+ }
+
+ if ( (mod1 != 0) && (mod2 != 2) ) {
+ return eLocationInFrame_BadStartAndStop;
+ } else if (mod1 != 0) {
+ return eLocationInFrame_BadStart;
+ } else if (mod2 != 2) {
+ return eLocationInFrame_BadStop;
+ } else {
+ return eLocationInFrame_InFrame;
+ }
+}
+
+
+bool PromoteCDSToNucProtSet(objects::CSeq_feat_Handle& orig_feat)
+{
+ // only move coding regions to nuc-prot set
+ if (!orig_feat.IsSetData() || !orig_feat.GetData().IsCdregion()) {
+ return false;
+ }
+ // don't move if pseudo
+ if (orig_feat.IsSetPseudo() && orig_feat.GetPseudo()) {
+ return false;
+ }
+ CBioseq_Handle nuc_bsh = orig_feat.GetScope().GetBioseqHandle(orig_feat.GetLocation());
+ if (!nuc_bsh) {
+ return false;
+ }
+
+ // This is necessary, to make sure that we are in "editing mode"
+ const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot();
+ CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle();
+
+ CSeq_feat_EditHandle feh(orig_feat);
+ CSeq_entry_Handle parent_entry = feh.GetAnnot().GetParentEntry();
+
+ bool rval = false;
+
+ if (parent_entry.IsSet()
+ && parent_entry.GetSet().IsSetClass()
+ && parent_entry.GetSet().GetClass() == CBioseq_set::eClass_nuc_prot) {
+ // already on nuc-prot set, leave it alone
+ } else {
+ CBioseq_set_Handle nuc_parent = parent_entry.GetParentBioseq_set();
+ if (nuc_parent && nuc_parent.IsSetClass() && nuc_parent.GetClass() == CBioseq_set::eClass_nuc_prot) {
+ CSeq_annot_Handle ftable;
+ CSeq_entry_Handle parent_seh = nuc_parent.GetParentEntry();
+ CSeq_annot_CI annot_ci(parent_seh, CSeq_annot_CI::eSearch_entry);
+ for (; annot_ci; ++annot_ci) {
+ if ((*annot_ci).IsFtable()) {
+ ftable = *annot_ci;
+ break;
+ }
+ }
+
+ if (!ftable) {
+ CRef<CSeq_annot> new_annot(new CSeq_annot());
+ new_annot->SetData().SetFtable();
+ CSeq_entry_EditHandle eh = parent_seh.GetEditHandle();
+ ftable = eh.AttachAnnot(*new_annot);
+ }
+
+ CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle();
+ CSeq_annot_EditHandle new_annot = ftable.GetEditHandle();
+ orig_feat = new_annot.TakeFeat(feh);
+ const list< CRef< CSeq_feat > > &feat_list = old_annot.GetSeq_annotCore()->GetData().GetFtable();
+ if (feat_list.empty())
+ {
+ old_annot.Remove();
+ }
+ rval = true;
+ }
+ }
+ return rval;
+}
+
+// A function to ensure that Seq-feat.partial is set if either end of the
+// feature is partial, and clear if neither end of the feature is partial
+bool AdjustFeaturePartialFlagForLocation(CSeq_feat& new_feat)
+{
+ bool any_change = false;
+ bool partial5 = new_feat.GetLocation().IsPartialStart(eExtreme_Biological);
+ bool partial3 = new_feat.GetLocation().IsPartialStop(eExtreme_Biological);
+ bool should_be_partial = partial5 || partial3;
+ bool is_partial = false;
+ if (new_feat.IsSetPartial() && new_feat.GetPartial()) {
+ is_partial = true;
+ }
+ if (should_be_partial && !is_partial) {
+ new_feat.SetPartial(true);
+ any_change = true;
+ }
+ else if (!should_be_partial && is_partial) {
+ new_feat.ResetPartial();
+ any_change = true;
+ }
+ return any_change;
+}
+
+
+// A function to change an existing MolInfo to match a coding region
+bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat& new_prot, const CSeq_feat& cds)
+{
+ bool any_change = false;
+ bool partial5 = cds.GetLocation().IsPartialStart(eExtreme_Biological);
+ bool partial3 = cds.GetLocation().IsPartialStop(eExtreme_Biological);
+ bool prot_5 = new_prot.GetLocation().IsPartialStart(eExtreme_Biological);
+ bool prot_3 = new_prot.GetLocation().IsPartialStop(eExtreme_Biological);
+ if ((partial5 && !prot_5) || (!partial5 && prot_5)
+ || (partial3 && !prot_3) || (!partial3 && prot_3)) {
+ new_prot.SetLocation().SetPartialStart(partial5, eExtreme_Biological);
+ new_prot.SetLocation().SetPartialStop(partial3, eExtreme_Biological);
+ any_change = true;
+ }
+ any_change |= AdjustFeaturePartialFlagForLocation(new_prot);
+ return any_change;
+}
+
+// A function to change an existing MolInfo to match a coding region
+bool AdjustProteinMolInfoToMatchCDS(CMolInfo& molinfo, const CSeq_feat& cds)
+{
+ bool rval = false;
+ if (!molinfo.IsSetBiomol() || molinfo.GetBiomol() != CMolInfo::eBiomol_peptide) {
+ molinfo.SetBiomol(CMolInfo::eBiomol_peptide);
+ rval = true;
+ }
+
+ bool partial5 = cds.GetLocation().IsPartialStart(eExtreme_Biological);
+ bool partial3 = cds.GetLocation().IsPartialStop(eExtreme_Biological);
+ CMolInfo::ECompleteness completeness = CMolInfo::eCompleteness_complete;
+ if (partial5 && partial3) {
+ completeness = CMolInfo::eCompleteness_no_ends;
+ }
+ else if (partial5) {
+ completeness = CMolInfo::eCompleteness_no_left;
+ }
+ else if (partial3) {
+ completeness = CMolInfo::eCompleteness_no_right;
+ }
+ if (!molinfo.IsSetCompleteness() || molinfo.GetCompleteness() != completeness) {
+ molinfo.SetCompleteness(completeness);
+ rval = true;
+ }
+ return rval;
+}
+
+// A function to make all of the necessary related changes to
+// a Seq-entry after the partialness of a coding region has been
+// changed.
+bool AdjustForCDSPartials(const CSeq_feat& cds, CSeq_entry_Handle seh)
+{
+ bool any_change = false;
+
+ if (!cds.IsSetProduct() || !seh) {
+ return any_change;
+ }
+
+ // find Bioseq for product
+ CBioseq_Handle product = seh.GetScope().GetBioseqHandle(cds.GetProduct());
+ if (!product) {
+ return any_change;
+ }
+
+ // adjust protein feature
+ CFeat_CI f(product, SAnnotSelector(CSeqFeatData::eSubtype_prot));
+ if (f) {
+ // This is necessary, to make sure that we are in "editing mode"
+ const CSeq_annot_Handle& annot_handle = f->GetAnnot();
+ CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle();
+ CSeq_feat_EditHandle feh(*f);
+ CRef<CSeq_feat> new_feat(new CSeq_feat());
+ new_feat->Assign(*(f->GetSeq_feat()));
+ if (AdjustProteinFeaturePartialsToMatchCDS(*new_feat, cds)) {
+ feh.Replace(*new_feat);
+ any_change = true;
+ }
+ }
+
+ // change or create molinfo on protein bioseq
+ bool found = false;
+ CBioseq_EditHandle beh = product.GetEditHandle();
+
+ NON_CONST_ITERATE(CBioseq::TDescr::Tdata, it, beh.SetDescr().Set()) {
+ if ((*it)->IsMolinfo()) {
+ any_change |= AdjustProteinMolInfoToMatchCDS((*it)->SetMolinfo(), cds);
+ found = true;
+ }
+ }
+ if (!found) {
+ CRef<objects::CSeqdesc> new_molinfo_desc(new CSeqdesc);
+ AdjustProteinMolInfoToMatchCDS(new_molinfo_desc->SetMolinfo(), cds);
+ beh.SetDescr().Set().push_back(new_molinfo_desc);
+ any_change = true;
+ }
+
+ return any_change;
+}
+
+
+bool RetranslateCDS(const CSeq_feat& cds, CScope& scope)
+{
+ // feature must be cds and already have product
+ if (!cds.IsSetData() || !cds.GetData().IsCdregion() || !cds.IsSetProduct()) {
+ return false;
+ }
+
+ // Use Cdregion.Product to get handle to protein bioseq
+ CBioseq_Handle prot_bsh = scope.GetBioseqHandle(cds.GetProduct());
+
+ // Should be a protein!
+ if (!prot_bsh || !prot_bsh.IsProtein())
+ {
+ return false;
+ }
+
+ CBioseq_EditHandle peh = prot_bsh.GetEditHandle();
+ CRef<CBioseq> new_protein = CSeqTranslator::TranslateToProtein(cds, scope);
+ if (new_protein && new_protein->IsSetInst()) {
+ CRef<CSeq_inst> new_inst(new CSeq_inst());
+ new_inst->Assign(new_protein->GetInst());
+ peh.SetInst(*new_inst);
+ }
+
+ // If protein feature exists, update location
+ CFeat_CI f(prot_bsh, SAnnotSelector(CSeqFeatData::eSubtype_prot));
+ if (f) {
+ // This is necessary, to make sure that we are in "editing mode"
+ const CSeq_annot_Handle& annot_handle = f->GetAnnot();
+ CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle();
+ CSeq_feat_EditHandle feh(*f);
+ CRef<CSeq_feat> new_feat(new CSeq_feat());
+ new_feat->Assign(*(f->GetSeq_feat()));
+ if (new_feat->CanGetLocation() &&
+ new_feat->GetLocation().IsInt() &&
+ new_feat->GetLocation().GetInt().CanGetTo())
+ {
+ new_feat->SetLocation().SetInt().SetTo(
+ new_protein->GetLength() - 1);
+ feh.Replace(*new_feat);
+ }
+ }
+
+ AdjustForCDSPartials(cds, peh.GetSeq_entry_Handle());
+ return true;
+}
+
bool sFeatureGetChildrenOfSubtype(
CMappedFeat mf,
diff --git a/c++/src/objmgr/util/obj_sniff.cpp b/c++/src/objmgr/util/obj_sniff.cpp
index e121369..1364221 100644
--- a/c++/src/objmgr/util/obj_sniff.cpp
+++ b/c++/src/objmgr/util/obj_sniff.cpp
@@ -1,4 +1,4 @@
-/* $Id: obj_sniff.cpp 462547 2015-03-19 14:01:05Z vasilche $
+/* $Id: obj_sniff.cpp 464944 2015-04-15 15:49:50Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -214,15 +214,7 @@ bool CObjectsSniffer::x_TryReadObject(CObjectIStream& input,
x_ReadObject(input, object_info);
return true;
}
- catch ( CEofException& /*rethrown*/ ) {
- // no more objects
- throw;
- }
- catch ( bad_alloc& /*rethrown*/ ) {
- // no more memory
- throw;
- }
- catch ( exception& /*ignored*/ ) {
+ catch ( CSerialException& /*ignored*/ ) {
input.SetStreamPos(m_StreamPos);
Reset();
return false;
diff --git a/c++/src/objtools/format/utils.cpp b/c++/src/objmgr/util/objutil.cpp
similarity index 72%
rename from c++/src/objtools/format/utils.cpp
rename to c++/src/objmgr/util/objutil.cpp
index d984513..3d7b893 100644
--- a/c++/src/objtools/format/utils.cpp
+++ b/c++/src/objmgr/util/objutil.cpp
@@ -1,4 +1,4 @@
-/* $Id: utils.cpp 443816 2014-08-19 18:05:17Z ivanov $
+/* $Id: objutil.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,7 +55,7 @@
#include <objmgr/util/sequence.hpp>
#include <objects/general/general_macros.hpp>
#include <algorithm>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -131,7 +131,21 @@ bool IsPartOfUrl(
}
return false; /* never found the terminating '/' */
-};
+};
+
+static bool s_RunOfStars(string& s, SIZE_TYPE start, SIZE_TYPE length)
+{
+ SIZE_TYPE max = start + 66;
+ if (max >= length) {
+ return false;
+ }
+ for (SIZE_TYPE i = start; i < max; i++) {
+ if (s[i] != '*') {
+ return false;
+ }
+ }
+ return true;
+}
void ExpandTildes(string& s, ETildeStyle style)
{
@@ -203,6 +217,10 @@ void ExpandTildes(string& s, ETildeStyle style)
result += "\n";
}
start = tilde + 1;
+ if (s[start] == ' ' && s_RunOfStars(s, start+1, length)) {
+ start++;
+ result += '\n';
+ }
break;
default: // just keep it, for lack of better ideas
@@ -346,16 +364,13 @@ void AddPeriod(string& str)
}
-void TrimSpaces(string& str, int indent)
+void TrimSpaces(string& str, size_t indent)
{
- if (str.empty() || str.length() <= (size_t)indent) {
+ if (str.empty() || str.length() <= indent) {
return;
}
- if (indent < 0) {
- indent = 0;
- }
- int end = str.length() - 1;
+ size_t end = str.length() - 1;
while (end >= indent && isspace((unsigned char) str[end])) {
end--;
}
@@ -380,7 +395,7 @@ public:
// If trim_beginning, strips all spaces and unprintables from beginning of string.
// If trim_end, strips all spaces and unprintables from end of string.
// returns the string you gave it.
-string &CompressSpaces( string& str, const bool trim_beginning, const bool trim_end )
+string& CompressSpaces( string& str, const bool trim_beginning, const bool trim_end )
{
if( str.empty() ) {
return str;
@@ -610,6 +625,399 @@ bool TrimSpacesAndJunkFromEnds(string& str, bool allow_ellipsis)
return changed;
}
+// this is copy-pasted method and optimized to use CTempString
+void TrimSpacesAndJunkFromEnds(string& result, const CTempString& str, bool allow_ellipsis)
+{
+ // TODO: This commented out code represents how ellipsis trimming
+ // should work. However, for compatibility with C, we're using a
+ // (in my opinion) suboptimal algorithm. We can switch over later.
+
+ //if (str.empty()) {
+ // return;
+ //}
+
+ //size_t strlen = str.length();
+ //size_t begin = 0;
+
+ //// trim unprintable characters (and space) off the beginning
+ //while (begin != strlen) {
+ // unsigned char ch = str[begin];
+ // if (ch > ' ') {
+ // break;
+ // } else {
+ // ++begin;
+ // }
+ //}
+
+ //// we're done if we trimmed the string to nothing
+ //if (begin == strlen) {
+ // str.erase();
+ // return;
+ //}
+
+ //// trim junk off the end (while we're at it, record whether we're chopping off a period)
+ //size_t end = strlen - 1;
+ //bool has_period = false;
+ //while (end > begin) {
+ // unsigned char ch = str[end];
+ // if (ch <= ' ' || ch == '.' || ch == ',' || ch == '~' || ch == ';') {
+ // has_period = (has_period || ch == '.');
+ // --end;
+ // } else {
+ // break;
+ // }
+ //}
+
+ //// check whether we're about to chop off an ellipsis, so we remember to add it back
+ //// TODO: There's got to be a more efficient way of doing this
+ //const bool weChoppedOffAnEllipsis = ( NPOS != NStr::Find(str, "...", end) );
+
+ //// do the actual chopping here
+ //str = str.substr( begin, end + 1 );
+
+ //// restore chopped off ellipsis or period, if any
+ //if ( allow_ellipsis && weChoppedOffAnEllipsis ) {
+ // str += "...";
+ //} else if (has_period) {
+ // // re-add any periods if we had one before
+ // str += '.';
+ //}
+
+ // This is based on the C function TrimSpacesAndJunkFromEnds.
+ // Although it's updated to use iterators and such and to
+ // return whether it changed the string, it should
+ // have the same output, except:
+ // - We do NOT chop off a semicolon if we determine that it's
+ // part of an HTML escape char (e.g. "&bgr;" ).
+ // - There are some changes in how tildes are handled;
+ // this algo is less likely to remove them.
+
+ if (str.empty()) {
+ result.clear();
+ return;
+ }
+
+ // make start_of_junk_pos hold the beginning of the "junk" at the end
+ // (where junk is defined as one of several characters)
+ // while we're at it, also check if the junk contains a tilde and/or period
+ bool isPeriod = false;
+ bool isTilde = false;
+ size_t start_of_junk_pos = 0;
+ for (size_t len = str.length(); len && start_of_junk_pos == 0; len--)
+ {
+ char ch = str[len-1];
+ if (ch <= ' ') ch = ' ';
+ switch (ch)
+ {
+ case '.':
+ isPeriod = true;
+ break;
+ case '~':
+ isTilde = true;
+ break;
+ case ';':
+ case ',':
+ case ' ':
+ break;
+ default:
+ // found non-junk character. Last junk character is just after this
+ start_of_junk_pos = len;
+ break;
+ }
+ }
+
+ // check for ';' that's part of an HTML escape char like "&bgr;" and
+ // skip over it (i.e., don't remove it) if so
+ if (start_of_junk_pos < str.length() && str[start_of_junk_pos] == ';') {
+ // we assume no HTML escape char will be longer than this
+ static const int kMaxCharsToLookAt = 20;
+
+ // go backwards, looking for the ampersand
+ int amp_iter = (start_of_junk_pos - 1);
+ for (; amp_iter >= 0 && ((start_of_junk_pos - amp_iter) < kMaxCharsToLookAt); --amp_iter) {
+ const char ch = str[amp_iter];
+ if (isalnum(ch) || ch == '#') {
+ // just keep going
+ }
+ else if (ch == '&') {
+ // The semicolon ends an HTML escape character, so we skip it
+ ++start_of_junk_pos;
+ break;
+ }
+ else {
+ // The semicolon does NOT end an HTML escape character, so we might remove it
+ break;
+ }
+ }
+ }
+
+ // holds the suffix to add after we remove the junk
+ CTempString suffix; // by default, just remove junk
+
+ // if there's junk, chop it off (but leave period/tildes/ellipsis as appropriate)
+ if (start_of_junk_pos < str.length()) {
+
+ const int chars_in_junk = (str.length() - start_of_junk_pos);
+ _ASSERT(chars_in_junk >= 1);
+
+ // allow one period at end
+ if (isPeriod) {
+ // check if we should put an ellipsis, or just a period
+ const bool putEllipsis = (allow_ellipsis && (chars_in_junk >= 3) &&
+ str[start_of_junk_pos + 1] == '.' && str[start_of_junk_pos + 2] == '.');
+
+ suffix = (putEllipsis ? "..." : ".");
+ }
+ else if (isTilde) {
+ // allow tilde(s)
+ // (This should work on single- AND double-tildes because
+ // we don't know whether or not tilde-expansion was called before this
+ // point )
+ if (str[start_of_junk_pos] == '~') {
+ const bool doubleTilde = ((chars_in_junk >= 2) && str[start_of_junk_pos + 1] == '~');
+ suffix = (doubleTilde ? "~~" : "~");
+ }
+ }
+ }
+ const char* ptr = str.data();
+ size_t len = start_of_junk_pos;
+ while (len && *ptr <= ' ')
+ {
+ len--; ptr++;
+ }
+ result.reserve(len + suffix.length());
+ result.assign(ptr, len);
+ result.append(suffix.data(), suffix.length());
+}
+
+// two-bytes combinations we're looking to clean
+#define twochars(a,b) Uint2((a) << 8 | (b))
+#define twocommas twochars(',',',')
+#define twospaces twochars(' ',' ')
+#define twosemicolons twochars(';',';')
+#define space_comma twochars(' ',',')
+#define space_bracket twochars(' ',')')
+#define bracket_space twochars('(',' ')
+#define space_semicolon twochars(' ',';')
+#define comma_space twochars(',',' ')
+#define semicolon_space twochars(';',' ')
+
+void CleanAndCompress(string& dest, const CTempString& instr)
+{
+ size_t left = instr.size();
+ // this is the input stream
+ const char* in = instr.data();
+
+ // skip front white spaces
+ while (left && *in == ' ')
+ {
+ in++;
+ left--;
+ }
+ // forget end white spaces
+ while (left && in[left - 1] == ' ')
+ {
+ left--;
+ }
+
+ dest.resize(left);
+
+ if (left < 1) return;
+
+ // this is where we write result
+ char* out = (char*)dest.c_str();
+
+ char curr = *in++; // initialize with first character
+ left--;
+
+ char next = 0;
+ Uint2 two_chars = curr; // this is two bytes storage where we see current and previous symbols
+
+ while (left > 0) {
+ next = *in++;
+
+ two_chars = (two_chars << 8) | next;
+
+ switch (two_chars)
+ {
+ case twocommas: // replace double commas with comma+space
+ *out++ = curr;
+ next = ' ';
+ break;
+ case twospaces: // skip multiple spaces (only print last one)
+ break;
+ case twosemicolons: // skip multiple semicolons (only print last one)
+ break;
+ case bracket_space: // skip space after bracket
+ next = curr;
+ two_chars = curr;
+ break;
+ case space_bracket: // skip space before bracket
+ break;
+ case space_comma:
+ *out++ = next;
+ next = curr;
+ *out++ = ' ';
+ while ((next == ' ' || next == ',') && left > 0) {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ case space_semicolon:
+ *out++ = next;
+ next = curr;
+ *out++ = ' ';
+ while ((next == ' ' || next == ';') && left > 0) {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ case comma_space:
+ *out++ = curr;
+ *out++ = ' ';
+ while ((next == ' ' || next == ',') && left > 0) {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ case semicolon_space:
+ *out++ = curr;
+ *out++ = ' ';
+ while ((next == ' ' || next == ';') && left > 0) {
+ next = *in;
+ in++;
+ left--;
+ }
+ two_chars = next;
+ break;
+ default:
+ *out++ = curr;
+ break;
+ }
+
+ curr = next;
+ if (left > 0) {
+ left--;
+ }
+ }
+
+ if (curr > 0 && curr != ' ') {
+ *out++ = curr;
+ }
+
+ dest.resize(out - dest.c_str());
+}
+
+#if 0
+struct CleanAndCompress_unit_test
+{
+ CleanAndCompress_unit_test()
+ {
+ test("C( )C");
+ test("xx,,xx");
+ test("xx,, xx");
+ test("xx,, xx");
+ test(" xx xx ");
+ test("xx , xx");
+ test("xx , xx");
+ test("xx(xx)");
+ test("xx( xx )");
+ }
+ void test(char* s)
+ {
+ string str;
+ CleanAndCompress(str, s);
+ cout << s << "--->" << str << '.' << endl;
+ }
+};
+
+CleanAndCompress_unit_test t;
+#endif
+
+
+/*
+void CleanAndCompress (string& str)
+{
+ if (str.empty()) {
+ return;
+ }
+
+ size_t pos = str.find (" ,");
+ if (pos != NPOS) {
+ str [pos] = ',';
+ str [pos+1] = ' ';
+ }
+ pos = str.find (",,");
+ if (pos != NPOS) {
+ str [pos+1] = ' ';
+ }
+ pos = str.find (" ;");
+ if (pos != NPOS) {
+ str [pos] = ';';
+ str [pos+1] = ' ';
+ }
+ pos = str.find ("( ");
+ if (pos != NPOS) {
+ str [pos] = ' ';
+ str [pos+1] = '(';
+ }
+ pos = str.find (" )");
+ if (pos != NPOS) {
+ str [pos] = ')';
+ str [pos+1] = ' ';
+ }
+
+ string::iterator end = str.end();
+ string::iterator it = str.begin();
+ string::iterator new_str = it;
+ while (it != end) {
+ *new_str++ = *it;
+ if ( (*it == ' ') || (*it == '\t') || (*it == '(') ) {
+ for (++it; (it != end) && (*it == ' ' || *it == '\t'); ++it) continue;
+ if ((it != end) && (*it == ')' || *it == ',') ) {
+ // this "if" protects against the case "(...bunch of spaces and tabs...)".
+ // Otherwise, the first '(' is unintentionally erased
+ if( *(new_str - 1) != '(' ) {
+ --new_str;
+ }
+ }
+ } else {
+ ++it;
+ }
+ }
+ str.erase(new_str, str.end());
+}
+*/
+
+
+#if 0
+struct CJunkUnitTest
+{
+ void test(CTempString v, bool a_e)
+ {
+ string res(v);
+ TrimSpacesAndJunkFromEnds(res, a_e);
+ TrimSpacesAndJunkFromEnds(res, v, a_e);
+ }
+ CJunkUnitTest()
+ {
+ test(" .", true);
+ test(" aaa bbb.....", true);
+ test(" aaa bbb.....", false);
+ test(" aaa bbb~~~~~", true);
+ test(" aaa bbb,,,,,", true);
+ test(" aaa bbb;;;;;;", true);
+ }
+};
+
+static CJunkUnitTest c;
+#endif
static bool s_IsWholeWord(const string& str, size_t pos)
{
@@ -878,10 +1286,11 @@ void GetDeltaSeqSummary(const CBioseq_Handle& seq, SDeltaSeqSummary& summary)
const CDelta_seq::TLiteral& lit = (*curr)->GetLiteral();
size_t lit_len = lit.CanGetLength() ? lit.GetLength() : 0;
len += lit_len;
- if ( lit.CanGetSeq_data() ) {
+ if ( lit.CanGetSeq_data() && lit.GetSeq_data().Which() != CSeq_data::e_Gap ) {
temp.residues += lit_len;
while ( next != end && (*next)->IsLiteral() &&
- (*next)->GetLiteral().CanGetSeq_data() ) {
+ (*next)->GetLiteral().CanGetSeq_data() &&
+ (*next)->GetLiteral().GetSeq_data().Which() != CSeq_data::e_Gap ) {
const CDelta_seq::TLiteral& next_lit = (*next)->GetLiteral();
size_t next_len = next_lit.CanGetLength() ?
next_lit.GetLength() : 0;
@@ -1204,99 +1613,73 @@ EResolveOrder GetResolveOrder(CScope& scope,
// Link locations:
// ============================================================================
const string strLinkBaseNuc(
- "http://www.ncbi.nlm.nih.gov/nuccore/" );
+ "https://www.ncbi.nlm.nih.gov/nuccore/" );
const string strLinkBaseProt(
- "http://www.ncbi.nlm.nih.gov/protein/" );
+ "https://www.ncbi.nlm.nih.gov/protein/" );
const string strLinkBaseEntrezViewer(
- "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" );
+ "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" ); // https forwarded to http
const string strLinkBaseTaxonomy(
- "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?" );
+ "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?" );
const string strLinkBaseTransTable(
- "http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG" );
+ "https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG" );
const string strLinkBasePubmed(
- "http://www.ncbi.nlm.nih.gov/pubmed/" );
+ "https://www.ncbi.nlm.nih.gov/pubmed/" );
const string strLinkBaseExpasy(
- "http://www.expasy.org/enzyme/" );
+ "http://www.expasy.org/enzyme/" ); // not government site
const string strLinkBaseNucSearch(
- "http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&term=" );
+ "https://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&term=" );
const string strLinkBaseGenomePrj(
- "http://www.ncbi.nlm.nih.gov/bioproject/" );
+ "https://www.ncbi.nlm.nih.gov/bioproject/" );
const string strLinkBaseLatLon(
- "http://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html" );
+ "https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html" );
const string strLinkBaseGeneOntology (
- "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&depth=1&query=GO:" );
+ "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&depth=1&query=GO:" ); // not government site
const string strLinkBaseGeneOntologyRef (
- "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:" );
+ "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:" ); // not government site
const string strLinkBaseUSPTO(
"http://patft.uspto.gov/netacgi/nph-Parser?patentnumber=" );
const string strDocLink(
- "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" );
-
-bool ConvertQuotesNotInHTMLTags( string &str )
-{
- bool changes_made = false;
-
- bool in_tag = false;
- size_t idx = 0;
- for( ; idx < str.length(); ++idx ) {
- switch( str[idx] ) {
- case '<':
- // heuristic
- in_tag = true;
- break;
- case '>':
- in_tag = false;
- break;
- case '"':
- if( ! in_tag ) {
- str[idx] = '\'';
- changes_made = true;
- }
- break;
- }
- }
-
- return changes_made;
-}
-
-// make sure we're not "double-sanitizing"
-// (e.g. ">" to ">")
-// ============================================================================
-static bool
-s_ShouldWeEscapeAmpersand(
- string::const_iterator str_iter, // yes, COPY not reference
- const string::const_iterator &str_iter_end )
-// ============================================================================
-{
- _ASSERT(*str_iter == '&');
-
- // This is a long-winded way of checking if str_iter
- // is at ">", "<", """ or "&"
- // I'm concerned about regexes being too slow.
-
- ++str_iter;
- if( str_iter != str_iter_end ) {
- switch( *str_iter ) {
+ "https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" );
+
+namespace {
+ // make sure we're not "double-sanitizing"
+ // (e.g. ">" to ">")
+ // ============================================================================
+ template<typename _T>
+ bool s_ShouldWeEscapeAmpersand(
+ _T str_iter, // yes, COPY not reference
+ const _T &str_iter_end)
+ // ============================================================================
+ {
+ _ASSERT(*str_iter == '&');
+
+ // This is a long-winded way of checking if str_iter
+ // is at ">", "<", """ or "&"
+ // I'm concerned about regexes being too slow.
+
+ ++str_iter;
+ if (str_iter != str_iter_end) {
+ switch (*str_iter) {
case 'g':
case 'l':
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 't' ) {
+ if (str_iter != str_iter_end && *str_iter == 't') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == ';' ) {
+ if (str_iter != str_iter_end && *str_iter == ';') {
return false;
}
}
break;
case 'a':
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 'm' ) {
+ if (str_iter != str_iter_end && *str_iter == 'm') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 'p' ) {
+ if (str_iter != str_iter_end && *str_iter == 'p') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == ';' ) {
+ if (str_iter != str_iter_end && *str_iter == ';') {
return false;
}
}
@@ -1304,13 +1687,13 @@ s_ShouldWeEscapeAmpersand(
break;
case 'q':
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 'u' ) {
+ if (str_iter != str_iter_end && *str_iter == 'u') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 'o' ) {
+ if (str_iter != str_iter_end && *str_iter == 'o') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == 't' ) {
+ if (str_iter != str_iter_end && *str_iter == 't') {
++str_iter;
- if( str_iter != str_iter_end && *str_iter == ';' ) {
+ if (str_iter != str_iter_end && *str_iter == ';') {
return false;
}
}
@@ -1319,79 +1702,117 @@ s_ShouldWeEscapeAmpersand(
break;
default:
return true;
+ }
}
+ return true;
}
- return true;
-}
-// see if the '<' opens an HTML tag (currently we
-// only check for a few kinds of tags )
-// ============================================================================
-static bool
-s_IsTagStart(
- const string::const_iterator &str_iter,
- const string::const_iterator &str_iter_end )
-// ============================================================================
-{
- static const string possible_tag_starts[] = {
- "<a href=",
- "<acronym title",
- "</a>",
- "</acronym"
- };
- static const size_t num_possible_tag_starts =
- (sizeof(possible_tag_starts) / sizeof(possible_tag_starts[0]));
-
- // check every string it might start with
- for( int possible_str_idx = 0; possible_str_idx < num_possible_tag_starts; ++possible_str_idx ) {
- const string &expected_str = possible_tag_starts[possible_str_idx];
-
- string::size_type idx = 0;
- string::const_iterator check_str_iter = str_iter;
- for( ; check_str_iter != str_iter_end && idx < expected_str.length(); ++idx, ++check_str_iter ) {
- if( *check_str_iter != expected_str[idx] ) {
- break;
+ // see if the '<' opens an HTML tag (currently we
+ // only check for a few kinds of tags )
+ // ============================================================================
+ template<typename _T>
+ bool s_IsTagStart(
+ const _T &str_iter,
+ const _T &str_iter_end)
+ // ============================================================================
+ {
+ static const string possible_tag_starts[] = {
+ "<a href=",
+ "<acronym title",
+ "</a>",
+ "</acronym"
+ };
+ static const size_t num_possible_tag_starts =
+ (sizeof(possible_tag_starts) / sizeof(possible_tag_starts[0]));
+
+ // check every string it might start with
+ for (int possible_str_idx = 0; possible_str_idx < num_possible_tag_starts; ++possible_str_idx) {
+ const string &expected_str = possible_tag_starts[possible_str_idx];
+
+ string::size_type idx = 0;
+ _T check_str_iter = str_iter;
+ for (; check_str_iter != str_iter_end && idx < expected_str.length(); ++idx, ++check_str_iter) {
+ if (*check_str_iter != expected_str[idx]) {
+ break;
+ }
+ }
+
+ if (idx == expected_str.length()) {
+ return true;
}
}
- if( idx == expected_str.length() ) {
- return true;
+ // we're in a tag if we matched the whole expected_str
+ return false;
+ }
+
+}
+
+bool ConvertQuotesNotInHTMLTags(string &str)
+{
+ bool changes_made = false;
+
+ bool in_tag = false;
+ size_t idx = 0;
+ for (; idx < str.length(); ++idx) {
+ switch (str[idx]) {
+ case '<':
+ // heuristic
+ in_tag = true;
+ break;
+ case '>':
+ in_tag = false;
+ break;
+ case '"':
+ if (!in_tag) {
+ str[idx] = '\'';
+ changes_made = true;
+ }
+ break;
}
}
- // we're in a tag if we matched the whole expected_str
- return false;
+ return changes_made;
}
+
// ============================================================================
-void
-TryToSanitizeHtml( string &str )
-// ============================================================================
+void TryToSanitizeHtml(string &str)
{
string result;
-
// The "* 1.1" should keep up efficient in most cases since data tends not to have
// too many characters that need escaping.
- result.reserve( 1 + (int)( str.length() * 1.1 ) );
+ result.reserve(1 + (int)(str.length() * 1.1));
+ TryToSanitizeHtml(result, str);
+
+ // swap is faster than assignment
+ str.swap(result);
+}
+
+void TryToSanitizeHtml(std::string &result, const CTempString& str)
+// ============================================================================
+{
+ result.clear();
// we only sanitize when we're not in an url
bool in_html_tag = false;
- ITERATE( string, str_iter, str ) {
+ ITERATE(CTempString, str_iter, str) {
// see if we're entering an HTML tag
- if( ! in_html_tag && *str_iter =='<' && s_IsTagStart(str_iter, str.end()) ) {
+ if (!in_html_tag && *str_iter == '<' && s_IsTagStart(str_iter, str.end())) {
in_html_tag = true;
}
// now that we know whether we're in a tag,
// process characters appropriately.
- if( in_html_tag ) {
- switch( *str_iter ) {
+ if (in_html_tag) {
+ switch (*str_iter) {
case '&':
// make sure we're not "double-sanitizing"
// (e.g. ">" to ">")
- if( s_ShouldWeEscapeAmpersand(str_iter, str.end()) ) {
+ if (s_ShouldWeEscapeAmpersand(str_iter, str.end())) {
result += "&";
- } else {
+ }
+ else {
result += '&';
}
break;
@@ -1399,8 +1820,9 @@ TryToSanitizeHtml( string &str )
result += *str_iter;
break;
}
- } else {
- switch( *str_iter ) {
+ }
+ else {
+ switch (*str_iter) {
case '<':
result += "<";
break;
@@ -1414,15 +1836,12 @@ TryToSanitizeHtml( string &str )
}
// see if we're exiting an HTML tag
- if( in_html_tag && *str_iter == '>' ) {
+ if (in_html_tag && *str_iter == '>') {
// tag is closed now
// (Note: does this consider cases where '>' is in quotes?)
in_html_tag = false;
}
}
-
- // swap is faster than assignment
- str.swap( result );
}
void
diff --git a/c++/src/objmgr/util/seq_loc_util.cpp b/c++/src/objmgr/util/seq_loc_util.cpp
index 56daaeb..3623e56 100644
--- a/c++/src/objmgr/util/seq_loc_util.cpp
+++ b/c++/src/objmgr/util/seq_loc_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_loc_util.cpp 448101 2014-10-02 15:01:06Z ivanov $
+/* $Id: seq_loc_util.cpp 472370 2015-07-09 14:13:36Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -73,11 +73,15 @@ TSeqPos GetLength(const CSeq_id& id, CScope* scope)
if ( !scope ) {
return numeric_limits<TSeqPos>::max();
}
+#if 0
CBioseq_Handle hnd = scope->GetBioseqHandle(id);
if ( !hnd ) {
return numeric_limits<TSeqPos>::max();
}
return hnd.GetBioseqLength();
+#else
+ return scope->GetSequenceLength(id);
+#endif
}
@@ -430,7 +434,6 @@ static ENa_strand s_GetStrand(const CSeq_loc& loc)
strand_set = true;
} else if (strand == eNa_strand_plus &&
istrand == eNa_strand_unknown) {
- istrand = eNa_strand_plus;
strand_set = true;
} else if (!strand_set) {
strand = istrand;
@@ -455,7 +458,6 @@ static ENa_strand s_GetStrand(const CSeq_loc& loc)
strand_set = true;
} else if (strand == eNa_strand_plus &&
istrand == eNa_strand_unknown) {
- istrand = eNa_strand_plus;
strand_set = true;
} else if (!strand_set) {
strand = istrand;
@@ -1025,12 +1027,12 @@ void s_SeqLocToRangeInfoMap(const CSeq_loc& loc,
}
-ECompare Compare(const CSeq_loc& me,
- const CSeq_loc& you,
- CScope* scope)
+ECompare s_CompareOverlapping(const CSeq_loc& me,
+ const CSeq_loc& you,
+ TSynMap& syns,
+ CScope* scope)
{
TRangeInfoMap me_infos, you_infos;
- TSynMap syns;
s_SeqLocToRangeInfoMap(me, me_infos, syns, scope);
s_SeqLocToRangeInfoMap(you, you_infos, syns, scope);
@@ -1142,6 +1144,94 @@ ECompare Compare(const CSeq_loc& me,
}
+bool s_CheckAbutting(const CSeq_loc& loc1,
+ const CSeq_loc& loc2,
+ TSynMap& syns,
+ CScope* scope,
+ ESeqLocExtremes ext)
+{
+ // Compare biological end of loc1 and start of loc2.
+ // If not abutting, use Compare.
+ CSeq_loc_CI it1_last(loc1,
+ CSeq_loc_CI::eEmpty_Allow,
+ ext == eExtreme_Positional ?
+ CSeq_loc_CI::eOrder_Positional : CSeq_loc_CI::eOrder_Biological);
+ it1_last.SetPos(it1_last.GetSize() - 1);
+ CSeq_loc_CI it2_first(loc2,
+ CSeq_loc_CI::eEmpty_Allow,
+ ext == eExtreme_Positional ?
+ CSeq_loc_CI::eOrder_Positional : CSeq_loc_CI::eOrder_Biological);
+
+ CSeq_id_Handle id1_last = s_GetSynHandle(it1_last.GetSeq_id_Handle(), syns, scope);
+ CSeq_id_Handle id2_first = s_GetSynHandle(it2_first.GetSeq_id_Handle(), syns, scope);
+
+ // Empty and whole locations can not abut.
+ if (it1_last.IsEmpty() || it2_first.IsEmpty() ||
+ it1_last.IsWhole() || it2_first.IsWhole() ||
+ id1_last != id2_first) {
+ return false;
+ }
+
+ if (ext == eExtreme_Positional) {
+ return it1_last.GetRange().GetToOpen() == it2_first.GetRange().GetFrom();
+ }
+
+ // Plus strand
+ if (!IsReverse(it1_last.GetStrand()) &&
+ !IsReverse(it2_first.GetStrand()) &&
+ it1_last.GetRange().GetToOpen() == it2_first.GetRange().GetFrom()) {
+ return true;
+ }
+ // Minus strand
+ if (IsReverse(it1_last.GetStrand()) &&
+ IsReverse(it2_first.GetStrand()) &&
+ it1_last.GetRange().GetFrom() == it2_first.GetRange().GetToOpen()) {
+ return true;
+ }
+
+ return false;
+}
+
+
+ECompare Compare(const CSeq_loc& me,
+ const CSeq_loc& you,
+ CScope* scope)
+{
+ TSynMap syns;
+ return s_CompareOverlapping(me, you, syns, scope);
+}
+
+
+ECompare Compare(const CSeq_loc& loc1,
+ const CSeq_loc& loc2,
+ CScope* scope,
+ TCompareFlags flags)
+{
+ TSynMap syns;
+
+ bool abut = false;
+ ECompare ret = eNoOverlap;
+
+ if (flags & fCompareAbutting) {
+ abut = s_CheckAbutting(loc1, loc2, syns, scope,
+ (flags & fComparePositional)
+ ? eExtreme_Positional : eExtreme_Biological);
+ }
+ if (flags & fCompareOverlapping) {
+ ret = s_CompareOverlapping(loc1, loc2, syns, scope);
+ }
+ if ( abut ) {
+ if (ret == eNoOverlap) {
+ ret = eAbutting;
+ }
+ else {
+ ret = eAbutAndOverlap;
+ }
+ }
+ return ret;
+}
+
+
/////////////////////////////////////////////////////////////////////
//
// Implementation of TestForOverlap()
@@ -1766,7 +1856,8 @@ Int8 s_TestForOverlapEx(const CSeq_loc& loc1,
"Multi-bioseq locations are disabled by the flags.");
}
// Multi-id locations - no circular_len allowed
- if (circular_len != kInvalidSeqPos) {
+ if ( circular_len != kInvalidSeqPos &&
+ type != eOverlap_Subset ) {
NCBI_THROW(CObjmgrUtilException, eBadLocation,
"Circular bioseq length can not be specified "
"for multi-bioseq locations.");
diff --git a/c++/src/objmgr/util/seqtitle.cpp b/c++/src/objmgr/util/seqtitle.cpp
index b2883c7..d98eb05 100644
--- a/c++/src/objmgr/util/seqtitle.cpp
+++ b/c++/src/objmgr/util/seqtitle.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqtitle.cpp 447991 2014-10-01 19:16:50Z vasilche $
+/* $Id: seqtitle.cpp 444132 2014-08-21 16:49:43Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objmgr/util/sequence.cpp b/c++/src/objmgr/util/sequence.cpp
index 76bcaa7..45d2df0 100644
--- a/c++/src/objmgr/util/sequence.cpp
+++ b/c++/src/objmgr/util/sequence.cpp
@@ -1,4 +1,4 @@
-/* $Id: sequence.cpp 459979 2015-02-24 14:53:16Z ivanov $
+/* $Id: sequence.cpp 481919 2015-10-19 13:24:11Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -133,6 +133,16 @@ static string s_GetFastaTitle(const CBioseq& bs,
}
}
+const CBioSource* GetBioSource(const CBioseq& bioseq)
+{
+ ITERATE(CBioseq::TDescr::Tdata, it, bioseq.GetDescr().Get())
+ {
+ if ((**it).IsSource())
+ return &(**it).GetSource();
+ }
+
+ return NULL;
+}
const CBioSource* GetBioSource(const CBioseq_Handle& handle)
{
@@ -192,6 +202,17 @@ int GetTaxId(const CBioseq_Handle& handle)
}
+const CMolInfo* GetMolInfo(const CBioseq& bioseq)
+{
+ ITERATE(CBioseq::TDescr::Tdata, it, bioseq.GetDescr().Get())
+ {
+ if ((**it).IsMolinfo())
+ return &(**it).GetMolinfo();
+ }
+ return NULL;
+}
+
+
const CMolInfo* GetMolInfo(const CBioseq_Handle& handle)
{
CSeqdesc_CI desc_iter(handle, CSeqdesc::e_Molinfo);
@@ -521,14 +542,22 @@ TGi GetGiForAccession(const string& acc, CScope& scope, EGetIdType flags)
{
// Clear throw-on-error flag
EGetIdType get_id_flags = (flags & eGetId_VerifyId) | eGetId_ForceGi;
- CSeq_id acc_id(acc);
- // Get gi only if acc a real accession.
- if ( acc_id.GetTextseq_Id() ) {
- CSeq_id_Handle idh = GetId(acc_id, scope, get_id_flags);
- if ( idh.IsGi() ) {
- return idh.GetGi();
+ try {
+ CSeq_id acc_id(acc);
+ // Get gi only if acc a real accession.
+ if ( acc_id.GetTextseq_Id() ) {
+ CSeq_id_Handle idh = GetId(acc_id, scope, get_id_flags);
+ if ( idh.IsGi() ) {
+ return idh.GetGi();
+ }
}
}
+ catch (exception& e) {
+ if ( (flags & eGetId_ThrowOnError) != 0 ) {
+ throw e;
+ }
+ return ZERO_GI;
+ }
if ( (flags & eGetId_ThrowOnError) != 0 ) {
NCBI_THROW(CSeqIdFromHandleException, eRequestedIdNotFound,
"sequence::GetGiForAccession(): invalid seq-id type");
@@ -794,7 +823,8 @@ public:
const CSeq_loc &loc2 = gene2.second->GetLocation();
// If genes are at identical positions, we fall back on the label
- if( sequence::Compare( loc1, loc2, scope ) == sequence::eSame ) {
+ if( sequence::Compare(loc1, loc2, scope, sequence::fCompareOverlapping ) ==
+ sequence::eSame) {
if( gene1.second->IsSetData() && gene1.second->GetData().IsGene() &&
gene2.second->IsSetData() && gene2.second->GetData().IsGene() )
{
@@ -1819,7 +1849,8 @@ void GetMrnasForGene(const CSeq_feat& gene_feat, CScope& scope,
ECompare comp = sequence::Compare(gene_feat.GetLocation(),
feat_it->GetLocation(),
- &scope);
+ &scope,
+ sequence::fCompareOverlapping);
if (comp != eSame && comp != eContains) {
continue;
}
@@ -1865,7 +1896,8 @@ void GetMrnasForGene(const CSeq_feat& gene_feat, CScope& scope,
ECompare comp = sequence::Compare(gene_feat.GetLocation(),
feat_it->GetLocation(),
- &scope);
+ &scope,
+ sequence::fCompareOverlapping);
if (comp != eSame && comp != eContains) {
continue;
}
@@ -2255,7 +2287,11 @@ CBioseq_Handle GetNucleotideParent(const CBioseq_Handle& bsh)
CBioseq_Handle ret;
if ( sfp ) {
- ret = bsh.GetScope().GetBioseqHandle(sfp->GetLocation());
+ try {
+ ret = bsh.GetScope().GetBioseqHandle(sfp->GetLocation());
+ } catch(...) {
+ // may fail due to trans-splicing, e.g., on small-genome set
+ }
}
return ret;
}
diff --git a/c++/src/objmgr/util/weight.cpp b/c++/src/objmgr/util/weight.cpp
index e921f09..82a712a 100644
--- a/c++/src/objmgr/util/weight.cpp
+++ b/c++/src/objmgr/util/weight.cpp
@@ -1,4 +1,4 @@
-/* $Id: weight.cpp 448099 2014-10-02 15:00:23Z ivanov $
+/* $Id: weight.cpp 444535 2014-08-25 18:36:18Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/Makefile.in b/c++/src/objtools/Makefile.in
index b00ff4e..71e8c5e 100644
--- a/c++/src/objtools/Makefile.in
+++ b/c++/src/objtools/Makefile.in
@@ -1,11 +1,11 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
# Meta-makefile("objtools" project)
#################################
REQUIRES = objects
-SUB_PROJ = unit_test_util readers blast lds lds2 data_loaders simple \
+SUB_PROJ = unit_test_util readers blast lds2 data_loaders simple \
alnmgr cddalignview test manip cleanup format edit validator \
asniotest align seqmasks_io eutils \
align_format snputil uudutil variation writers
diff --git a/c++/src/objtools/align_format/align_format_util.cpp b/c++/src/objtools/align_format/align_format_util.cpp
index 1a67de1..20bfe79 100644
--- a/c++/src/objtools/align_format/align_format_util.cpp
+++ b/c++/src/objtools/align_format/align_format_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: align_format_util.cpp 465078 2015-04-16 17:36:39Z ivanov $
+/* $Id: align_format_util.cpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: align_format_util.cpp 465078 2015-04-16 17:36:39Z ivanov $";
+static char const rcsid[] = "$Id: align_format_util.cpp 482732 2015-10-26 16:31:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -112,9 +112,10 @@ s_GetBlastScore(const container& scoreList,
list<TGi>& use_this_gi,
int& comp_adj_method)
{
+ const string k_GiPrefix = "gi:";
bool hasScore = false;
ITERATE (typename container, iter, scoreList) {
- const CObject_id& id=(*iter)->GetId();
+ const CObject_id& id=(*iter)->GetId();
if (id.IsStr()) {
if (id.GetStr()=="score"){
score = (*iter)->GetValue().GetInt();
@@ -131,8 +132,13 @@ s_GetBlastScore(const container& scoreList,
num_ident = (*iter)->GetValue().GetInt();
} else if (id.GetStr()=="comp_adjustment_method") {
comp_adj_method = (*iter)->GetValue().GetInt();
+ }
+ else if(NStr::StartsWith(id.GetStr(),k_GiPrefix)) { //will be used when switch to 64bit GIs
+ string strGi = NStr::Replace(id.GetStr(),k_GiPrefix,"");
+ TGi gi = NStr::StringToInt8(strGi);
+ use_this_gi.push_back(gi);
}
- }
+ }
}
return hasScore;
@@ -277,6 +283,25 @@ s_FillDbInfoLocally(const string& dbname,
return true;
}
+void
+CAlignFormatUtil::FillScanModeBlastDbInfo(vector<CAlignFormatUtil::SDbInfo>& retval,
+ bool is_protein, int numSeqs, Int8 numLetters, string& tag)
+{
+ retval.clear();
+ CAlignFormatUtil::SDbInfo info;
+ info.is_protein = is_protein;
+ if (tag == "")
+ info.definition = string("User specified sequence set.");
+ else
+ {
+ info.definition = string("User specified sequence set ") +
+ string("(Input: ") + tag + string(").");
+ }
+ info.number_seqs = numSeqs;
+ info.total_length = numLetters;
+ retval.push_back(info);
+}
+
void
CAlignFormatUtil::GetBlastDbInfo(vector<CAlignFormatUtil::SDbInfo>& retval,
const string& blastdb_names, bool is_protein,
@@ -323,11 +348,11 @@ CAlignFormatUtil::GetBlastDbInfo(vector<CAlignFormatUtil::SDbInfo>& retval,
return;
}
else{
- vector<string> dbs;
- NStr::Tokenize(blastdb_names, " \n\t", dbs);
+ vector<CTempString> dbs;
+ SeqDB_SplitQuoted(blastdb_names, dbs, true);
retval.reserve(dbs.size());
- ITERATE(vector<string>, i, dbs) {
+ ITERATE(vector<CTempString>, i, dbs) {
CAlignFormatUtil::SDbInfo info;
info.is_protein = is_protein;
bool success = false;
@@ -1524,8 +1549,8 @@ map < string, CRef<CSeq_align_set> > CAlignFormatUtil::HspListToHitMap(vector
if(previous_id.Empty() || !cur_id.Match(*previous_id)) {
if(count >= seqIdList.size()) {
break;
- }
- string idString = cur_id.AsFastaString();
+ }
+ string idString = NStr::TruncateSpaces(cur_id.AsFastaString());
if(hitsMap.find(idString) != hitsMap.end()) {
temp = new CSeq_align_set;
temp->Set().push_back(*iter);
@@ -2333,8 +2358,9 @@ void s_AddOtherRelatedInfoLinks(const list< CRef< CBlast_def_line > > &bdl,
wid->GetLabel(&label, CSeq_id::eContent);
string url_link = kIdenticalProteinsUrl;
string lnk_displ = "Identical Proteins";
- url_link = s_MapLinkoutGenParam(url_link,rid,NStr::IntToString(gi),for_alignment, cur_align,label,lnk_displ);
+ url_link = s_MapLinkoutGenParam(url_link,rid,NStr::NumericToString(gi),for_alignment, cur_align,label,lnk_displ);
url_link = CAlignFormatUtil::MapTemplate(kIdenticalProteinsDispl,"lnk",url_link);
+ url_link = CAlignFormatUtil::MapTemplate(url_link,"label",label);
linkout_list.push_back(url_link);
}
}
@@ -2952,7 +2978,7 @@ CAlignFormatUtil::GetAsciiProteinMatrix(const char* matrix_name,
}
-string CAlignFormatUtil::MapTemplate(string inpString,string tmplParamName,int templParamVal)
+string CAlignFormatUtil::MapTemplate(string inpString,string tmplParamName,Int8 templParamVal)
{
string outString;
string tmplParam = "<@" + tmplParamName + "@>";
@@ -2980,7 +3006,7 @@ static string s_MapCommonUrlParams(string urlTemplate, CAlignFormatUtil::SSeqURL
}
string logstr_location = (seqUrlInfo->isAlignLink) ? "align" : "top";
string url_link = CAlignFormatUtil::MapTemplate(urlTemplate,"db",db);
- url_link = CAlignFormatUtil::MapTemplate(url_link,"gi",GI_TO(int, seqUrlInfo->gi));
+ url_link = CAlignFormatUtil::MapTemplate(url_link,"gi",seqUrlInfo->gi);
url_link = CAlignFormatUtil::MapTemplate(url_link,"log",logstr_moltype + logstr_location);
url_link = CAlignFormatUtil::MapTemplate(url_link,"blast_rank",seqUrlInfo->blast_rank);
url_link = CAlignFormatUtil::MapTemplate(url_link,"rid",seqUrlInfo->rid);
@@ -3006,7 +3032,7 @@ static string s_MapURLLink(string urlTemplate, CAlignFormatUtil::SSeqURLInfo *se
-static bool s_IsWGSPattern(string &wgsAccession)
+bool CAlignFormatUtil::IsWGSPattern(string &wgsAccession)
{
//const string kWgsAccessionPattern = "^[A-Z]{4}[0-9]{8,10}(\.[0-9]+){0,1}$"; //example AUXO013124042 or AUXO013124042.1
const unsigned int kWgsProjLength = 4;
@@ -3047,7 +3073,7 @@ static bool s_IsWGSPattern(string &wgsAccession)
bool CAlignFormatUtil::IsWGSAccession(string &wgsAccession, string &wgsProjName)
{
const unsigned int kWgsProgNameLength = 6;
- bool isWGS = s_IsWGSPattern(wgsAccession);
+ bool isWGS = IsWGSPattern(wgsAccession);
if(isWGS) {
wgsProjName = wgsAccession.substr(0,kWgsProgNameLength);
}
@@ -3214,7 +3240,7 @@ string CAlignFormatUtil::GetFullIDLink(SSeqURLInfo *seqUrlInfo,const CBioseq::TI
seqLink = CAlignFormatUtil::MapTemplate(linkTmpl,"url",linkURL);
seqLink = CAlignFormatUtil::MapTemplate(seqLink,"rid",seqUrlInfo->rid);
seqLink = CAlignFormatUtil::MapTemplate(seqLink,"seqid",seqUrlInfo->accession);
- seqLink = CAlignFormatUtil::MapTemplate(seqLink,"gi",GI_TO(int, seqUrlInfo->gi));
+ seqLink = CAlignFormatUtil::MapTemplate(seqLink,"gi",seqUrlInfo->gi);
seqLink = CAlignFormatUtil::MapTemplate(seqLink,"target","EntrezView");
if(seqUrlInfo->addCssInfo) {
seqLink = CAlignFormatUtil::MapTemplate(seqLink,"defline",NStr::JavaScriptEncode(seqUrlInfo->defline));
@@ -3277,7 +3303,7 @@ string CAlignFormatUtil::GetGraphiscLink(SSeqURLInfo *seqUrlInfo,
linkUrl = CAlignFormatUtil::MapTemplate(linkUrl,"seqViewerParams",seqViewerParams);
linkUrl = CAlignFormatUtil::MapTemplate(linkUrl,"dbtype",dbtype);
- linkUrl = CAlignFormatUtil::MapTemplate(linkUrl,"gi",GI_TO(int, seqUrlInfo->gi));
+ linkUrl = CAlignFormatUtil::MapTemplate(linkUrl,"gi",seqUrlInfo->gi);
string linkTitle = "Show alignment to <@seqid@> in <@custom_report_type@>";
string link_loc;
if(!hspRange) {
@@ -3629,9 +3655,12 @@ s_GetBlastScore(const container& scoreList,
int& sum_n,
list<TGi>& use_this_gi)
{
+ const string k_GiPrefix = "gi:";
bool hasScore = false;
+
+
ITERATE (typename container, iter, scoreList) {
- const CObject_id& id=(*iter)->GetId();
+ const CObject_id& id=(*iter)->GetId();
if (id.IsStr()) {
hasScore = true;
if (id.GetStr()=="seq_evalue") {
@@ -3655,7 +3684,12 @@ s_GetBlastScore(const container& scoreList,
} else if (id.GetStr()=="sum_n"){
sum_n = (*iter)->GetValue().GetInt();
}
- }
+ else if(NStr::StartsWith(id.GetStr(),k_GiPrefix)) { //will be used when switch to 64bit GIs
+ string strGi = NStr::Replace(id.GetStr(),k_GiPrefix,"");
+ TGi gi = NStr::StringToInt8(strGi);
+ use_this_gi.push_back(gi);
+ }
+ }
}
return hasScore;
}
@@ -3766,5 +3800,77 @@ CRef<CSeq_id> CAlignFormatUtil::GetDisplayIds(const CBioseq_Handle& handle,
return wid;
}
+static inline CRange<TSeqPos> & s_FixMinusStrandRange(CRange<TSeqPos> & rng)
+{
+ if(rng.GetFrom() > rng.GetTo()){
+ rng.Set(rng.GetTo(), rng.GetFrom());
+ }
+ //cerr << "Query Rng: " << rng.GetFrom() << "-" << rng.GetTo() << endl;
+ return rng;
+}
+
+int CAlignFormatUtil::GetUniqSeqCoverage(CSeq_align_set & alnset)
+{
+ if(alnset.IsEmpty())
+ return 0;
+
+ bool isDenDiag = (alnset.Get().front()->GetSegs().Which() == CSeq_align::C_Segs::e_Dendiag) ?
+ true : false;
+
+ list<CRef<CSeq_align> >::iterator mItr=alnset.Set().begin();
+ CRangeCollection<TSeqPos> subj_rng_coll((*mItr)->GetSeqRange(1));
+ CRange<TSeqPos> q_rng((*mItr)->GetSeqRange(0));
+ /*
+ cerr << MSerial_AsnText << **mItr;
+ cerr << (*mItr)->GetSeqRange(0).GetFrom() << endl;
+ cerr << (*mItr)->GetSeqRange(0).GetTo() << endl;
+ cerr << (*mItr)->GetSeqRange(0).GetToOpen() << endl;
+ cerr << (*mItr)->GetSeqRange(1).GetFrom() << endl;
+ cerr << (*mItr)->GetSeqRange(1).GetTo() << endl;
+ cerr << (*mItr)->GetSeqRange(1).GetToOpen() << endl;
+ */
+ CRangeCollection<TSeqPos> query_rng_coll(s_FixMinusStrandRange(q_rng));
+ ++mItr;
+ for(;mItr != alnset.Set().end(); ++mItr) {
+ const CRange<TSeqPos> align_subj_rng((*mItr)->GetSeqRange(1));
+ // subject range should always be on the positive strand
+ ASSERT(align_subj_rng.GetTo() > align_subj_rng.GetFrom());
+ CRangeCollection<TSeqPos> coll(align_subj_rng);
+ coll.Subtract(subj_rng_coll);
+
+ if (coll.empty())
+ continue;
+
+ if(coll[0] == align_subj_rng) {
+ CRange<TSeqPos> query_rng ((*mItr)->GetSeqRange(0));
+ //cerr << "Subj Rng :" << align_subj_rng.GetFrom() << "-" << align_subj_rng.GetTo() << endl;
+ query_rng_coll += s_FixMinusStrandRange(query_rng);
+ subj_rng_coll += align_subj_rng;
+ }
+ else {
+ ITERATE (CRangeCollection<TSeqPos>, uItr, coll) {
+ CRange<TSeqPos> query_rng;
+ const CRange<TSeqPos> & subj_rng = (*uItr);
+ CRef<CSeq_align> densegAln
+ = isDenDiag ? CAlignFormatUtil::CreateDensegFromDendiag(**mItr) : (*mItr);
+
+ CAlnMap map(densegAln->GetSegs().GetDenseg());
+ TSignedSeqPos subj_aln_start = map.GetAlnPosFromSeqPos(1,subj_rng.GetFrom());
+ TSignedSeqPos subj_aln_end = map.GetAlnPosFromSeqPos(1,subj_rng.GetTo());
+ query_rng.SetFrom(map.GetSeqPosFromAlnPos(0,subj_aln_start));
+ query_rng.SetTo(map.GetSeqPosFromAlnPos(0,subj_aln_end));
+
+ //cerr << "Subj Rng :" << subj_rng.GetFrom() << "-" << subj_rng.GetTo() << endl;
+ query_rng_coll += s_FixMinusStrandRange(query_rng);
+ subj_rng_coll += subj_rng;
+ }
+ }
+ }
+
+ return query_rng_coll.GetCoveredLength();
+}
+
+
+
END_SCOPE(align_format)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/align_format/format_flags.cpp b/c++/src/objtools/align_format/format_flags.cpp
index 8524119..115e6de 100644
--- a/c++/src/objtools/align_format/format_flags.cpp
+++ b/c++/src/objtools/align_format/format_flags.cpp
@@ -1,4 +1,4 @@
-/* $Id: format_flags.cpp 439436 2014-06-30 13:51:29Z fongah2 $
+/* $Id: format_flags.cpp 485058 2015-11-18 16:06:47Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,7 +40,7 @@ string kDfltArgTabularOutputFmt =
"evalue bitscore";
const string kDfltArgTabularOutputFmtTag("std");
-const size_t kNumTabularOutputFormatSpecifiers = 44;
+const size_t kNumTabularOutputFormatSpecifiers = 45;
const SFormatSpec sc_FormatSpecifiers[kNumTabularOutputFormatSpecifiers] = {
SFormatSpec("qseqid",
"Query Seq-id",
@@ -173,7 +173,10 @@ const SFormatSpec sc_FormatSpecifiers[kNumTabularOutputFormatSpecifiers] = {
eQueryCovSubject),
SFormatSpec("qcovhsp",
"Query Coverage Per HSP",
- eQueryCovSeqalign)
+ eQueryCovSeqalign),
+ SFormatSpec("qcovus",
+ "Query Coverage Per Unique Subject (blastn only)",
+ eQueryCovUniqSubject),
};
string DescribeTabularOutputFormatSpecifiers(bool is_igblast)
@@ -205,5 +208,23 @@ const string kArgProduceHtml("html");
const bool kDfltArgProduceHtml = false;
const size_t kDfltLineLength = 60;
+const size_t kNumSAMOutputFormatSpecifiers = 1;
+const SSAMFormatSpec sc_SAMFormatSpecifiers[kNumSAMOutputFormatSpecifiers] = {
+ SSAMFormatSpec("SQ",
+ "Include Sequence Data",
+ eSAM_SeqData)
+};
+
+string DescribeSAMOutputFormatSpecifiers()
+{
+ ostringstream os;
+ for (size_t i =0; i < kNumSAMOutputFormatSpecifiers; i++) {
+ os << "\t" << setw(10) << sc_SAMFormatSpecifiers[i].name << " means ";
+ os << sc_SAMFormatSpecifiers[i].description << "\n";
+ }
+
+ return os.str();
+}
+
END_SCOPE(align_format)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/align_format/seqalignfilter.cpp b/c++/src/objtools/align_format/seqalignfilter.cpp
index 6769f08..45f2b32 100644
--- a/c++/src/objtools/align_format/seqalignfilter.cpp
+++ b/c++/src/objtools/align_format/seqalignfilter.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqalignfilter.cpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: seqalignfilter.cpp 482389 2015-10-22 16:36:32Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
///
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqalignfilter.cpp 399305 2013-05-13 19:13:43Z grichenk $";
+static char const rcsid[] = "$Id: seqalignfilter.cpp 482389 2015-10-22 16:36:32Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -109,7 +109,7 @@ void CSeqAlignFilter::FilterByGiListFromFile(const CSeq_align_set& full_aln,
id_aligned_seq = &((*iter)->GetSeq_id(1));
TGi gi = id_aligned_seq->GetGi();
- if (seqdb_gis->FindGi(GI_TO(int, gi))) {
+ if (seqdb_gis->FindGi(gi)) {
filtered_aln.Set().push_back(*iter);
}
}
@@ -206,7 +206,7 @@ void CSeqAlignFilter::FilterBySeqDB(const CSeq_align_set& full_aln,
// get the corresponding oid from the db (!!! can we rely on this? !!!)
int oid_aligned_seq = -1;
- db->GiToOid(GI_TO(int, gi_aligned_seq), oid_aligned_seq);
+ db->GiToOid(gi_aligned_seq, oid_aligned_seq);
// retrieve the filtered list of gi's corresponding to this oid
vector<TGi> vec_gis_from_DB;
@@ -527,18 +527,18 @@ void CSeqAlignFilter::ReadGiList(const string& fname, list<TGi>& list_gis, bool
CRef<CSeqDBFileGiList> seqdb_gis;
seqdb_gis = new CSeqDBFileGiList(fname);
- vector<int> vec_gis;
+ vector<TGi> vec_gis;
seqdb_gis->GetGiList(vec_gis);
if (sorted)
sort(vec_gis.begin(), vec_gis.end());
list_gis.clear();
- for (vector<int>::iterator it = vec_gis.begin(); it != vec_gis.end(); it++)
- list_gis.push_back(GI_FROM(int, *it));
+ for (vector<TGi>::iterator it = vec_gis.begin(); it != vec_gis.end(); it++)
+ list_gis.push_back(*it);
}
-void CSeqAlignFilter::ReadGiVector(const string& fname, vector<int>& vec_gis, bool sorted)
+void CSeqAlignFilter::ReadGiVector(const string& fname, vector<TGi>& vec_gis, bool sorted)
{
CRef<CSeqDBFileGiList> seqdb_gis;
seqdb_gis = new CSeqDBFileGiList(fname);
diff --git a/c++/src/objtools/align_format/showalign.cpp b/c++/src/objtools/align_format/showalign.cpp
index d11843b..08c7ff1 100644
--- a/c++/src/objtools/align_format/showalign.cpp
+++ b/c++/src/objtools/align_format/showalign.cpp
@@ -1,4 +1,4 @@
-/* $Id: showalign.cpp 446202 2014-09-12 13:54:22Z ivanov $
+/* $Id: showalign.cpp 482385 2015-10-22 16:34:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: showalign.cpp 446202 2014-09-12 13:54:22Z ivanov $";
+static char const rcsid[] = "$Id: showalign.cpp 482385 2015-10-22 16:34:42Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -2347,9 +2347,12 @@ CDisplaySeqalign::x_PrintDefLine(const CBioseq_Handle& bsp_handle,SAlnInfo* aln_
if(m_AlignOption&eShowGi && alnDispParams->gi > ZERO_GI){
out<<"gi|"<<alnDispParams->gi<<"|";
}
- if(!(alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID")
- != string::npos)){
- alnDispParams->seqID->WriteAsFasta(out);
+ if(!((alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID") != string::npos) ||
+ alnDispParams->seqID->AsFastaString().find("lcl|Subject_") != string::npos)){
+ if (strncmp(alnDispParams->seqID->AsFastaString().c_str(), "lcl|", 4) == 0)
+ out << alnDispParams->label;
+ else
+ alnDispParams->seqID->WriteAsFasta(out);
}
if(m_AlignOption&eHtml){
if(alnDispParams->id_url != NcbiEmptyString){
@@ -2419,8 +2422,8 @@ CDisplaySeqalign::x_PrintDefLine(const CBioseq_Handle& bsp_handle,SAlnInfo* aln_
if(m_AlignOption&eShowGi && alnDispParams->gi > ZERO_GI){
out<<"gi|"<<alnDispParams->gi<<"|";
}
- if(!(alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID")
- != string::npos)){
+ if(!(alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID") != string::npos) ||
+ alnDispParams->seqID->AsFastaString().find("lcl|Subject_") != string::npos){
if (strncmp(alnDispParams->seqID->AsFastaString().c_str(), "lcl|", 4) == 0) {
out << alnDispParams->label;
}
@@ -2459,6 +2462,7 @@ CDisplaySeqalign::x_PrintDefLine(const CBioseq_Handle& bsp_handle,SAlnInfo* aln_
}
out<<"\n";
isFirst = false;
+ delete alnDispParams;
}
}
if(m_AlignOption&eHtml && bMultipleDeflines) {
@@ -3489,8 +3493,8 @@ void CDisplaySeqalign::x_DisplayBl2SeqLink(CNcbiOstream& out)
TGi query_gi = FindGi(query_handle.GetBioseqCore()->GetId());
TGi subject_gi = FindGi(subject_handle.GetBioseqCore()->GetId());
- string url_link = CAlignFormatUtil::MapTemplate(kBl2seqUrl,"query",GI_TO(int, query_gi));
- url_link = CAlignFormatUtil::MapTemplate(url_link,"subject",GI_TO(int, subject_gi));
+ string url_link = CAlignFormatUtil::MapTemplate(kBl2seqUrl,"query",query_gi);
+ url_link = CAlignFormatUtil::MapTemplate(url_link,"subject",subject_gi);
out << url_link << "\n";
}
@@ -3695,7 +3699,8 @@ CDisplaySeqalign::x_MapDefLine(SAlnDispParams *alnDispParams,bool isFirst, bool
string alnGi = (m_AlignOption&eShowGi && alnDispParams->gi > ZERO_GI) ?
"gi|" + NStr::NumericToString(alnDispParams->gi) + "|" : "";
string seqid;
- if(!(alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID") != string::npos)){
+ if(!(alnDispParams->seqID->AsFastaString().find("gnl|BL_ORD_ID") != string::npos) ||
+ alnDispParams->seqID->AsFastaString().find("lcl|Subject_") != string::npos){
seqid = alnDispParams->seqID->AsFastaString();
}
@@ -3797,7 +3802,8 @@ CDisplaySeqalign::x_InitDefLinesHeader(const CBioseq_Handle& bsp_handle,SAlnInfo
//This should probably change on dispId
m_CurrAlnAccession = alnDispParams->seqID->AsFastaString();
- if(m_CurrAlnAccession.find("gnl|BL_ORD_ID") != string::npos){
+ if(m_CurrAlnAccession.find("gnl|BL_ORD_ID") != string::npos ||
+ m_CurrAlnAccession.find("lcl|Subject_") != string::npos){
///Get first token of the title
vector <string> parts;
NStr::Tokenize(alnDispParams->title," ",parts);
@@ -3817,13 +3823,19 @@ CDisplaySeqalign::x_InitDefLinesHeader(const CBioseq_Handle& bsp_handle,SAlnInfo
}
else {
deflines += alnDefLine; //this contains all deflines except the first one
- }
-
- isFirst = false;
- delete alnDispParams;
+ }
+ if(isFirst) {
+ isFirst = false;
+ }
+ if(m_AlignTemplates->alnTitlesTmpl.empty() && !firstDefline.empty()) {
+ m_NumBlastDefLines = 1;
+ break;
+ }
+
+ delete alnDispParams;
}
}
- m_NumBlastDefLines = numBdl;
+ m_NumBlastDefLines = numBdl;
}
if(m_NumBlastDefLines == 1) {
deflines = firstDefline;
@@ -4119,7 +4131,7 @@ static string s_MapFeatureURL(string viewerURL,
string rid)
{
string url_link = CAlignFormatUtil::MapTemplate(viewerURL,"db",db);
- url_link = CAlignFormatUtil::MapTemplate(url_link,"gi",GI_TO(int, subject_gi));
+ url_link = CAlignFormatUtil::MapTemplate(url_link,"gi",subject_gi);
url_link = CAlignFormatUtil::MapTemplate(url_link,"rid",rid);
url_link = CAlignFormatUtil::MapTemplate(url_link,"from",fromRange);
url_link = CAlignFormatUtil::MapTemplate(url_link,"to",toRange);
diff --git a/c++/src/objtools/align_format/showdefline.cpp b/c++/src/objtools/align_format/showdefline.cpp
index ab0483b..246098d 100644
--- a/c++/src/objtools/align_format/showdefline.cpp
+++ b/c++/src/objtools/align_format/showdefline.cpp
@@ -1,4 +1,4 @@
-/* $Id: showdefline.cpp 446202 2014-09-12 13:54:22Z ivanov $
+/* $Id: showdefline.cpp 481975 2015-10-19 16:59:30Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: showdefline.cpp 446202 2014-09-12 13:54:22Z ivanov $";
+static char const rcsid[] = "$Id: showdefline.cpp 481975 2015-10-19 16:59:30Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -118,7 +118,8 @@ I\" VALUE = \"%d\">";
static const string kPsiblastCheckbox = "<INPUT TYPE=\"checkbox\" NAME=\"ch\
ecked_GI\" VALUE=\"%d\"> ";
-
+//Max length of title string for the the link
+static const int kMaxDescrLength = 4096;
string
CShowBlastDefline::GetSeqIdListString(const list<CRef<objects::CSeq_id> >& id,
@@ -187,9 +188,10 @@ CShowBlastDefline::GetSeqIdList(const objects::CBioseq_Handle& bh,
CRef<CSeq_id> next_seqid(new CSeq_id());
string id_token = NcbiEmptyString;
- if ((*itr)->IsGeneral() &&
+ if (((*itr)->IsGeneral() &&
(*itr)->AsFastaString().find("gnl|BL_ORD_ID")
- != string::npos) {
+ != string::npos) ||
+ (*itr)->AsFastaString().find("lcl|Subject_") != string::npos) {
vector<string> title_tokens;
id_token =
NStr::Tokenize(sequence::CDeflineGenerator().GenerateDefline(bh), " ", title_tokens)[0];
@@ -268,6 +270,17 @@ CShowBlastDefline::GetBioseqHandleDeflineAndId(const CBioseq_Handle& handle,
}
}
+static void s_LimitDescrLength(string &descr)
+{
+ if(descr.length() > kMaxDescrLength) {
+ size_t end = NStr::Find(descr," ",0,kMaxDescrLength,NStr::eLast);
+ if(end != NPOS) {
+ descr = descr.substr(0,end);
+ descr += "...";
+ }
+ }
+}
+
void CShowBlastDefline::x_FillDeflineAndId(const CBioseq_Handle& handle,
const CSeq_id& aln_id,
list<TGi>& use_this_gi,
@@ -441,6 +454,9 @@ void CShowBlastDefline::x_FillDeflineAndId(const CBioseq_Handle& handle,
" " +
(*iter)->GetTitle();
}
+ if(sdl->fullDefline.length() > kMaxDescrLength) {
+ break;
+ }
}
}
}
@@ -448,7 +464,6 @@ void CShowBlastDefline::x_FillDeflineAndId(const CBioseq_Handle& handle,
}
}
-
//Constructor
CShowBlastDefline::CShowBlastDefline(const CSeq_align_set& seqalign,
CScope& scope,
@@ -721,7 +736,8 @@ void CShowBlastDefline::x_DisplayDefline(CNcbiOstream & out)
}
}
if(!sdl->id.Empty()){
- if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos)){
+ if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
+ sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)){
string idStr = sdl->id->AsFastaString();
if (strncmp(idStr.c_str(), "lcl|", 4) == 0) {
idStr = sdl->id->AsFastaString().substr(4);
@@ -1146,8 +1162,8 @@ void CShowBlastDefline::x_DisplayDeflineTableBody(CNcbiOstream & out)
}
}
if(!sdl->id.Empty()){
- if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID")
- != string::npos)){
+ if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
+ sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)){
string id_str;
sdl->id->GetLabel(&id_str, CSeq_id::eContent);
out << id_str;
@@ -1467,24 +1483,15 @@ string CShowBlastDefline::x_FormatSeqSetHeaders(int isGenomicSeq, bool formatHea
return subHeader;
}
-static void s_LimitDescrLength(string &descr)
-{
- const int kMaxDescrLength = 4096;
- if(descr.length() > kMaxDescrLength) {
- size_t end = NStr::Find(descr," ",0,kMaxDescrLength,NStr::eLast);
- if(end != NPOS) {
- descr = descr.substr(0,end);
- descr += "...";
- }
- }
-}
+
string CShowBlastDefline::x_FormatDeflineTableLine(SDeflineInfo* sdl,SScoreInfo* iter,bool &first_new)
{
string defLine = ((sdl->gi > ZERO_GI) && ((m_Option & eCheckboxChecked) || (m_Option & eCheckbox))) ? x_FormatPsi(sdl, first_new) : m_DeflineTemplates->defLineTmpl;
string dflGi = (m_Option & eShowGi) && (sdl->gi > ZERO_GI) ? "gi|" + NStr::NumericToString(sdl->gi) + "|" : "";
string seqid;
if(!sdl->id.Empty()){
- if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos)){
+ if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
+ sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)) {
sdl->id->GetLabel(&seqid, CSeq_id::eContent);
}
}
@@ -1523,12 +1530,13 @@ string CShowBlastDefline::x_FormatDeflineTableLine(SDeflineInfo* sdl,SScoreInfo*
string accession;
sdl->id->GetLabel(& deflId, CSeq_id::eContent);
deflFrmID = CAlignFormatUtil::GetLabel(sdl->id);//Just accession without db part like GNOMON: or ti:
- deflFastaSeq = sdl->id->AsFastaString();
+ //deflFastaSeq = sdl->id->AsFastaString();
+ deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
}
else {
deflFrmID = deflId = NStr::NumericToString(sdl->gi);
deflFastaSeq = "gi|" + NStr::NumericToString(sdl->gi);
- deflFastaSeq = sdl->alnIDFasta;
+ deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
deflAccs = sdl->id->AsFastaString();
}
diff --git a/c++/src/objtools/align_format/tabular.cpp b/c++/src/objtools/align_format/tabular.cpp
index 9b724cc..d910079 100644
--- a/c++/src/objtools/align_format/tabular.cpp
+++ b/c++/src/objtools/align_format/tabular.cpp
@@ -1,4 +1,4 @@
-/* $Id: tabular.cpp 446201 2014-09-12 13:53:23Z ivanov $
+/* $Id: tabular.cpp 482732 2015-10-26 16:31:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
/// One line is printed for each alignment with tab-delimited fielalnVec.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: tabular.cpp 446201 2014-09-12 13:53:23Z ivanov $";
+static char const rcsid[] = "$Id: tabular.cpp 482732 2015-10-26 16:31:57Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -154,6 +154,8 @@ CBlastTabularInfo::CBlastTabularInfo(CNcbiOstream& ostr, const string& format,
SetNoFetch(false);
m_QueryCovSubject.first = NA;
m_QueryCovSubject.second = -1;
+ m_QueryCovUniqSubject.first = NA;
+ m_QueryCovUniqSubject.second = -1;
m_QueryGeneticCode = 1;
m_DbGeneticCode = 1;
@@ -407,6 +409,14 @@ void CBlastTabularInfo::x_PrintSubjectCoverage(void)
m_Ostream << NStr::IntToString(m_QueryCovSubject.second);
}
+void CBlastTabularInfo::x_PrintUniqSubjectCoverage(void)
+{
+ if(m_QueryCovUniqSubject.second < 0)
+ m_Ostream << NA;
+ else
+ m_Ostream << NStr::IntToString(m_QueryCovUniqSubject.second);
+}
+
void CBlastTabularInfo::x_PrintSeqalignCoverage(void)
{
if(m_QueryCovSeqalign < 0)
@@ -614,7 +624,21 @@ void CBlastTabularInfo::x_SetQueryCovSubject(const CSeq_align & align)
m_QueryCovSubject.first = NA;
m_QueryCovSubject.second = pct;
}
+}
+void CBlastTabularInfo::x_SetQueryCovUniqSubject(const CSeq_align & align)
+{
+ int pct=-1;
+ if(align.GetNamedScore("uniq_seq_percent_coverage", pct))
+ {
+ m_QueryCovUniqSubject.first = align.GetSeq_id(1).AsFastaString();
+ m_QueryCovUniqSubject.second = pct;
+ }
+ else if(align.GetSeq_id(1).AsFastaString() != m_QueryCovUniqSubject.first)
+ {
+ m_QueryCovUniqSubject.first = NA;
+ m_QueryCovUniqSubject.second = pct;
+ }
}
void CBlastTabularInfo::x_SetQueryCovSeqalign(const CSeq_align & align, int query_len)
@@ -687,6 +711,9 @@ int CBlastTabularInfo::SetFields(const CSeq_align& align,
if (x_IsFieldRequested(eQueryCovSubject))
x_SetQueryCovSubject(align);
+ if (x_IsFieldRequested(eQueryCovUniqSubject))
+ x_SetQueryCovUniqSubject(align);
+
// Extract the full list of subject ids
bool setSubjectIds = (x_IsFieldRequested(eSubjectAllSeqIds) ||
x_IsFieldRequested(eSubjectAllGis) ||
@@ -1068,6 +1095,8 @@ void CBlastTabularInfo::x_PrintFieldNames()
m_Ostream << "subject strand"; break;
case eQueryCovSubject:
m_Ostream << "% query coverage per subject"; break;
+ case eQueryCovUniqSubject:
+ m_Ostream << "% query coverage per uniq subject"; break;
case eQueryCovSeqalign:
m_Ostream << "% query coverage per hsp"; break;
default:
@@ -1148,6 +1177,10 @@ CBlastTabularInfo::SetScores(int score, double bit_score, double evalue)
m_Score = score;
CAlignFormatUtil::GetScoreString(evalue, bit_score, 0, score, m_Evalue,
m_BitScore, total_bit_string, raw_score_string);
+
+ if ((evalue >= 1.0e-180) && (evalue < 0.0009)){
+ m_Evalue = NStr::DoubleToString(evalue, 2, NStr::fDoubleScientific);
+ }
}
void
@@ -1310,6 +1343,8 @@ CBlastTabularInfo::x_PrintField(ETabularField field)
x_PrintSubjectStrand(); break;
case eQueryCovSubject:
x_PrintSubjectCoverage(); break;
+ case eQueryCovUniqSubject:
+ x_PrintUniqSubjectCoverage(); break;
case eQueryCovSeqalign:
x_PrintSeqalignCoverage(); break;
default:
@@ -1459,6 +1494,7 @@ void CIgBlastTabularInfo::SetIgAnnotation(const CRef<blast::CIgAnnotation> &anno
}
//stop codon anywhere between start of V and end of J
+ //This checks for stop codon between start of top matched V and and end of top matched J only
if (annot->m_FrameInfo[0] >= 0) {
int v_start = annot->m_FrameInfo[0];
int v_j_length = max(max(annot->m_GeneInfo[5], annot->m_GeneInfo[3]), annot->m_GeneInfo[1]) - annot->m_FrameInfo[0];
diff --git a/c++/src/objtools/align_format/unit_test/Makefile.align_format_unit_test.app b/c++/src/objtools/align_format/unit_test/Makefile.align_format_unit_test.app
index a9d8d04..5c5a934 100644
--- a/c++/src/objtools/align_format/unit_test/Makefile.align_format_unit_test.app
+++ b/c++/src/objtools/align_format/unit_test/Makefile.align_format_unit_test.app
@@ -1,4 +1,4 @@
-# $Id: Makefile.align_format_unit_test.app 398472 2013-05-06 19:02:03Z kornbluh $
+# $Id: Makefile.align_format_unit_test.app 451547 2014-11-07 14:32:47Z boratyng $
APP = align_format_unit_test
SRC = showdefline_unit_test showalign_unit_test blast_test_util \
@@ -16,7 +16,7 @@ LIB = $(LIB_:%=%$(STATIC))
LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
CHECK_CMD = align_format_unit_test
-CHECK_COPY = data
+CHECK_COPY = data align_format_unit_test.ini
CHECK_REQUIRES = in-house-resources
REQUIRES = Boost.Test.Included
diff --git a/c++/src/objtools/align_format/unit_test/align_format_unit_test.ini b/c++/src/objtools/align_format/unit_test/align_format_unit_test.ini
new file mode 100644
index 0000000..ce1ab88
--- /dev/null
+++ b/c++/src/objtools/align_format/unit_test/align_format_unit_test.ini
@@ -0,0 +1,5 @@
+# $Id: align_format_unit_test.ini 454298 2014-12-12 16:09:18Z vakatov $
+
+[UNITTESTS_DISABLE]
+; Temporarily disabled. Will need to be revisited eventually.
+TestRejectNexusWithNoAlignType = OS_MacOSX && COMPILER_Clang && BUILD_Release
diff --git a/c++/src/objtools/align_format/unit_test/aln_printer_unit_test.cpp b/c++/src/objtools/align_format/unit_test/aln_printer_unit_test.cpp
index 1cbbdd4..47c0f8d 100644
--- a/c++/src/objtools/align_format/unit_test/aln_printer_unit_test.cpp
+++ b/c++/src/objtools/align_format/unit_test/aln_printer_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: aln_printer_unit_test.cpp 439322 2014-06-27 15:47:21Z gotvyans $
+/* $Id: aln_printer_unit_test.cpp 482959 2015-10-27 18:45:46Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,39 +58,94 @@ USING_SCOPE(align_format);
using namespace TestUtil;
-// Read sequences from fasta file and add them to scope
-static CRef<CScope> CreateScope(const string& filename);
+class CAlnPrinterFixture
+{
+public:
+ CRef<CObjectManager> m_Objmgr;
+ CRef<CScope> m_Scope;
+ string kNuclSeqs;
+ string kProtSeqs;
+
+ void x_InitScope(void)
+ {
+ m_Objmgr = CObjectManager::GetInstance();
+ m_Scope.Reset(new CScope(*m_Objmgr));
+ }
+ void x_LoadSequences(const string& filename, bool parse_id)
+ {
+ CNcbiIfstream instream(filename.c_str());
+ BOOST_REQUIRE(instream);
-BOOST_AUTO_TEST_SUITE(aln_printer)
+ CStreamLineReader line_reader(instream);
+ CFastaReader::TFlags flags = 0;
+ if (!parse_id) {
+ flags |= CFastaReader::fNoParseID;
+ }
-// input file names
-const string protein_seqalign = "data/multialign.asn";
-const string nucleotide_seqalign = "data/multialign_nucleotide.asn";
-const string nucleotide_seqs = "data/nucleotide.fa";
+ CFastaReader fasta_reader(line_reader, flags);
+ fasta_reader.IgnoreProblem(
+ ILineError::eProblem_ModifierFoundButNoneExpected);
+ while (!line_reader.AtEOF()) {
-string PrintAlignment(CMultiAlnPrinter::EFormat format,
- const string& seqalign_file,
- const string& fasta_file = "",
- CMultiAlnPrinter::EAlignType type
- = CMultiAlnPrinter::eNotSet)
-{
- CRef<CScope> scope = CreateScope(fasta_file);
+ CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
+
+ if (entry == 0) {
+ NCBI_THROW(CObjReaderException, eInvalid,
+ "Could not retrieve seq entry");
+ }
+ m_Scope->AddTopLevelSeqEntry(*entry);
+ CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
+ }
+ }
+
+
+ CAlnPrinterFixture(void)
+ {
+ kNuclSeqs = "data/nucleotide.fa";
+ kProtSeqs = "data/protein.fa";
+
+ x_InitScope();
+ x_LoadSequences(kNuclSeqs, false);
+ x_LoadSequences(kProtSeqs, true);
+ }
+
+
+ ~CAlnPrinterFixture()
+ {
+ m_Scope.Reset();
+ m_Objmgr.Reset();
+ }
+
+ // Print alignment for a given Seq-align
+ string PrintAlignment(CMultiAlnPrinter::EFormat format,
+ const string& seqalign_file,
+ CMultiAlnPrinter::EAlignType type
+ = CMultiAlnPrinter::eNotSet)
+ {
+ CSeq_align seqalign;
+ CNcbiIfstream istr(seqalign_file.c_str());
+ istr >> MSerial_AsnText >> seqalign;
- CSeq_align seqalign;
- CNcbiIfstream istr(seqalign_file.c_str());
- istr >> MSerial_AsnText >> seqalign;
+ CMultiAlnPrinter printer(seqalign, *m_Scope, type);
+ printer.SetWidth(80);
+ printer.SetFormat(format);
+
+ CNcbiOstrstream output_stream;
+ printer.Print(output_stream);
+ string output = CNcbiOstrstreamToString(output_stream);
+
+ return output;
+ }
- CMultiAlnPrinter printer(seqalign, *scope, type);
- printer.SetWidth(80);
- printer.SetFormat(format);
+};
- CNcbiOstrstream output_stream;
- printer.Print(output_stream);
- string output = CNcbiOstrstreamToString(output_stream);
+BOOST_FIXTURE_TEST_SUITE(aln_printer, CAlnPrinterFixture)
+
+// input file names
+const string protein_seqalign = "data/multialign.asn";
+const string nucleotide_seqalign = "data/multialign_nucleotide.asn";
- return output;
-}
BOOST_AUTO_TEST_CASE(TestFastaPlusGaps)
{
@@ -110,7 +165,7 @@ BOOST_AUTO_TEST_CASE(TestFastaPlusGaps)
// Test nucleotide
output = PrintAlignment(CMultiAlnPrinter::eFastaPlusGaps,
- nucleotide_seqalign, nucleotide_seqs);
+ nucleotide_seqalign);
BOOST_REQUIRE(output.find(">lcl|1 gi|405832|gb|U00001.1|HSCDC27 Human "
"homologue of S. pombe nuc2+ and A. nidulans "
@@ -144,7 +199,7 @@ BOOST_AUTO_TEST_CASE(TestClustalW)
// Test nucleotide
output = PrintAlignment(CMultiAlnPrinter::eClustal,
- nucleotide_seqalign, nucleotide_seqs);
+ nucleotide_seqalign);
BOOST_REQUIRE(output.find("lcl|2 ------CCGCTACAGG"
"GGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGA"
@@ -179,7 +234,7 @@ BOOST_AUTO_TEST_CASE(TestPhylipSequential)
// Test nucleotide
output = PrintAlignment(CMultiAlnPrinter::ePhylipSequential,
- nucleotide_seqalign, nucleotide_seqs);
+ nucleotide_seqalign);
BOOST_REQUIRE(output.find(" 10 2634") != NPOS);
@@ -213,7 +268,7 @@ BOOST_AUTO_TEST_CASE(TestPhylipInterleaved)
// Test nucleotide
output = PrintAlignment(CMultiAlnPrinter::ePhylipInterleaved,
- nucleotide_seqalign, nucleotide_seqs);
+ nucleotide_seqalign);
BOOST_REQUIRE(output.find(" 10 2634") != NPOS);
@@ -230,7 +285,7 @@ BOOST_AUTO_TEST_CASE(TestNexus)
{
// Test protein
string output = PrintAlignment(CMultiAlnPrinter::eNexus,
- protein_seqalign, "",
+ protein_seqalign,
CMultiAlnPrinter::eProtein);
BOOST_REQUIRE(output.find("#NEXUS") != NPOS);
@@ -262,7 +317,7 @@ BOOST_AUTO_TEST_CASE(TestNexus)
// Test nucleotide
output = PrintAlignment(CMultiAlnPrinter::eNexus,
- nucleotide_seqalign, nucleotide_seqs,
+ nucleotide_seqalign,
CMultiAlnPrinter::eNucleotide);
BOOST_REQUIRE(output.find("#NEXUS") != NPOS);
@@ -292,46 +347,10 @@ BOOST_AUTO_TEST_CASE(TestRejectNexusWithNoAlignType)
// verify that formatting nexus alignment with m_AlignType == eNotSet
// throws the exception
BOOST_REQUIRE_THROW(PrintAlignment(CMultiAlnPrinter::eNexus,
- protein_seqalign, "",
+ protein_seqalign,
CMultiAlnPrinter::eNotSet),
CException);
}
BOOST_AUTO_TEST_SUITE_END()
-
-CRef<CScope> CreateScope(const string& filename)
-{
- const string kDbName("prot_dbs");
- const CBlastDbDataLoader::EDbType kDbType(CBlastDbDataLoader::eProtein);
- TestUtil::CBlastOM tmp_data_loader(kDbName, kDbType, CBlastOM::eLocal);
- CRef<CScope> scope = tmp_data_loader.NewScope();
-
- if (filename == "") {
- return scope;
- }
-
- CNcbiIfstream instream(filename.c_str());
- BOOST_REQUIRE(instream);
-
- CStreamLineReader line_reader(instream);
- CFastaReader fasta_reader(line_reader,
- CFastaReader::fAssumeProt |
- CFastaReader::fForceType |
- CFastaReader::fNoParseID);
-
- while (!line_reader.AtEOF()) {
-
- CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
-
- if (entry == 0) {
- NCBI_THROW(CObjReaderException, eInvalid,
- "Could not retrieve seq entry");
- }
- scope->AddTopLevelSeqEntry(*entry);
- CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
- }
-
- return scope;
-}
-
diff --git a/c++/src/objtools/align_format/unit_test/data/in_showalign_use_this_gi.asn b/c++/src/objtools/align_format/unit_test/data/in_showalign_use_this_gi.asn
new file mode 100755
index 0000000..1c523ac
--- /dev/null
+++ b/c++/src/objtools/align_format/unit_test/data/in_showalign_use_this_gi.asn
@@ -0,0 +1,985 @@
+Seq-annot ::= {
+ desc {
+ user {
+ type str "Hist Seqalign",
+ data {
+ {
+ label str "Hist Seqalign",
+ data bool TRUE
+ }
+ }
+ },
+ user {
+ type str "Blast Type",
+ data {
+ {
+ label str "psiblast",
+ data int 10
+ }
+ }
+ },
+ user {
+ type str "Blast Database Title",
+ data {
+ {
+ label str "All non-redundant GenBank CDS
+ translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS
+ projects",
+ data bool FALSE
+ }
+ }
+ }
+ },
+ data align {
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 1237
+ },
+ {
+ id str "blast_score",
+ value int 1237
+ },
+ {
+ id str "e_value",
+ value real { 811021147991027, 10, -186 }
+ },
+ {
+ id str "bit_score",
+ value real { 48110010768981, 10, -11 }
+ },
+ {
+ id str "num_ident",
+ value int 232
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:129295",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 232
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 1, 10, 0 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 811021147991027, 10, -186 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 48110010768981, 10, -11 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 48110010768981, 10, -11 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 100
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 129295
+ },
+ starts {
+ 0,
+ 0
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 1228
+ },
+ {
+ id str "blast_score",
+ value int 1228
+ },
+ {
+ id str "e_value",
+ value real { 48986488021524, 10, -181 }
+ },
+ {
+ id str "bit_score",
+ value real { 477633311506554, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 229
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:448824824",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 230
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 987068965517241, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 48986488021524, 10, -181 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 477633311506554, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 477633311506554, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 99
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 448824824
+ },
+ starts {
+ 0,
+ 156
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 1226
+ },
+ {
+ id str "blast_score",
+ value int 1226
+ },
+ {
+ id str "e_value",
+ value real { 170841590304487, 10, -181 }
+ },
+ {
+ id str "bit_score",
+ value real { 476862912354719, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 229
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:510032768",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 230
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 987068965517241, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 170841590304487, 10, -181 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 476862912354719, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 476862912354719, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 99
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 510032768
+ },
+ starts {
+ 0,
+ 170
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 1133
+ },
+ {
+ id str "blast_score",
+ value int 1133
+ },
+ {
+ id str "e_value",
+ value real { 237944940659373, 10, -167 }
+ },
+ {
+ id str "bit_score",
+ value real { 441039351794405, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 211
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:733881413",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 224
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 90948275862069, 10, -14 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 237944940659373, 10, -167 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 441039351794405, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 441039351794405, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 91
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 733881413
+ },
+ starts {
+ 0,
+ 170
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 990
+ },
+ {
+ id str "blast_score",
+ value int 990
+ },
+ {
+ id str "e_value",
+ value real { 656868398284742, 10, -146 }
+ },
+ {
+ id str "bit_score",
+ value real { 385955812438224, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 181
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:385145541",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 207
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 780172413793103, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 656868398284742, 10, -146 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 385955812438224, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 385955812438224, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 78
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 385145541
+ },
+ starts {
+ 0,
+ 156
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 985
+ },
+ {
+ id str "blast_score",
+ value int 985
+ },
+ {
+ id str "e_value",
+ value real { 30817206154261, 10, -144 }
+ },
+ {
+ id str "bit_score",
+ value real { 384029814558637, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 180
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:129296",
+ value int 0
+ },
+ {
+ id str "gi:212900",
+ value int 0
+ },
+ {
+ id str "gi:71897377",
+ value int 0
+ },
+ {
+ id str "gi:385145537",
+ value int 0
+ },
+ {
+ id str "gi:385145539",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 207
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 775862068965517, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 30817206154261, 10, -144 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 384029814558637, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 384029814558637, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 78
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 71897377
+ },
+ starts {
+ 0,
+ 156
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 977
+ },
+ {
+ id str "blast_score",
+ value int 977
+ },
+ {
+ id str "e_value",
+ value real { 588602003232089, 10, -144 }
+ },
+ {
+ id str "bit_score",
+ value real { 380948217951298, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 178
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:733881415",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 209
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 767241379310345, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 588602003232089, 10, -144 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 380948217951298, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 380948217951298, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 77
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 733881415
+ },
+ starts {
+ 0,
+ 156
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 958
+ },
+ {
+ id str "blast_score",
+ value int 958
+ },
+ {
+ id str "e_value",
+ value real { 17920560600765, 10, -142 }
+ },
+ {
+ id str "bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 175
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:697456700",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 214
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 754310344827586, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 17920560600765, 10, -142 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 75
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 697456700
+ },
+ starts {
+ 0,
+ 0
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 958
+ },
+ {
+ id str "blast_score",
+ value int 958
+ },
+ {
+ id str "e_value",
+ value real { 232892966327255, 10, -143 }
+ },
+ {
+ id str "bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 174
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:677552130",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 211
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 75, 10, -2 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 232892966327255, 10, -143 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 373629426008868, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 75
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 677552130
+ },
+ starts {
+ 0,
+ 0
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 955
+ },
+ {
+ id str "blast_score",
+ value int 955
+ },
+ {
+ id str "e_value",
+ value real { 62217975104378, 10, -142 }
+ },
+ {
+ id str "bit_score",
+ value real { 372473827281116, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 175
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "gi:679011882",
+ value int 0
+ },
+ {
+ id str "num_positives",
+ value int 211
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 1, 10, 2 }
+ },
+ {
+ id str "pc_ident",
+ value real { 754310344827586, 10, -15 }
+ },
+ {
+ id str "seq_evalue",
+ value real { 62217975104378, 10, -142 }
+ },
+ {
+ id str "seq_bit_score",
+ value real { 372473827281116, 10, -12 }
+ },
+ {
+ id str "seq_total_bit_score",
+ value real { 372473827281116, 10, -12 }
+ },
+ {
+ id str "seq_percent_coverage",
+ value int 100
+ },
+ {
+ id str "seq_percent_identity",
+ value int 75
+ },
+ {
+ id str "seq_hspnum",
+ value int 1
+ },
+ {
+ id str "seq_align_totlen",
+ value real { 232, 10, 0 }
+ }
+ },
+ segs denseg {
+ dim 2,
+ numseg 1,
+ ids {
+ gi 129295,
+ gi 679011882
+ },
+ starts {
+ 0,
+ 0
+ },
+ lens {
+ 232
+ },
+ strands {
+ unknown,
+ unknown
+ }
+ }
+ }
+ }
+}
+
+
+
+
diff --git a/c++/src/objtools/align_format/unit_test/data/protein.fa b/c++/src/objtools/align_format/unit_test/data/protein.fa
new file mode 100755
index 0000000..49e846d
--- /dev/null
+++ b/c++/src/objtools/align_format/unit_test/data/protein.fa
@@ -0,0 +1,862 @@
+>gi|129295|sp|P01013.1|OVALX_CHICK RecName: Full=Ovalbumin-related protein X; AltName: Full=Gene X protein
+QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
+KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
+VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
+FLFLIKHNPTNTIVYFGRYWSP
+
+>gi|217968049|ref|YP_002353555.1| Non-specific serine/threonine protein kinase [Dictyoglomus turgidum DSM 6724]
+MKNTTKIFVLLILLIFSFALAENVDKNLLTIAKGNNLFGLNLYQKLTIKEGGNIFISPYSISSALAMTYA
+GASGNTKKQMSEVLYFNLPDDELHFAFSKLNSILNTPKSDFQLAIANSLWGQINYPFQEDFLDLVKKYYS
+AGFNLVDFVDEINREKARNEINKWVEDRTNQKIRELIHKEDLNPMTRLVLVNAIYFKGKWKYTFNKEETR
+EMPFFLNENKTLKVSMMHQINEFNYYEDKNLQAIELPYSGNELSMVVILPKERNLSKIEKNLTYDMLNSI
+SRSMEKEKVDLYIPRFKIEKRYILNEALMKLGMTDAFIDMLADFSGMTGDKDLYISKVIHQSFIEVNEEG
+TEAAAATAVIMSGKSIGLGPKVFKADHPFLFFIIHKPTNTILFMGRFIEP
+
+>gi|223938552|ref|ZP_03630444.1| proteinase inhibitor I4 serpin [Pedosphaera parvula Ellin514]
+MPGEEEHFAYRPVMDPINLTTNMKNAFKSLFNVLVTTGALIMALPIKAESTNNVPKLVQGNNTFAFDLYS
+RVNAGKENENLCFSPYSISTCLAMTYAGARGETELQMAKALHFTTNQAQLHAGFATLQKQLNEAEKQQGI
+KLNVANALWAQQGHPFLPAFLQIAQQNYDARVNQVDFRTQSESARKEINDWVSKKTNGKIEEIIPSGALD
+AMTKLVLVNAIYFKGQWATQFNKSRTAPADFSISSSQKVQAQLMNLKSRFKFADRGNFQLLEMPYKGNEL
+SMVVLLPKEVEGTQKLESMLHPKELSDWLSQAASPEVNVFLPKFKINAGFELGQPLAAMGMTDAFTAKAD
+FSGMDGTRDLFISSVIHKAFVEVNEEGTEAAAATGITMSRTAAVHAPPTFRADHPFLFLIRDMKSGSILF
+MGRVTDPTK
+
+>gi|206901590|ref|YP_002251376.1| leukocyte elastase inhibitor [Dictyoglomus thermophilum H-6-12]
+MKLLIRIYILAFLLIIISFSFAEGIDNNLLTIAKGNNIFGLDLYQILTAKEDGNIFISPYSISSALAMTY
+AGANGNTKKQMAEVLYFNLPDNELHSAFSKLNSIFNAPKNDFQLAIANSLWGQINYPFREDFIELVKKYY
+SAGFNLVDFVNDLNREKARNEINKWVEDRTNQKIKELIQKGDLTSLTRLVLVNAIYFKGKWKYTFNKKET
+KEIPFFVDEKRTSKVPMMHQVNDFNYYEDKDLQAIELPYSGDELSMIVILPKERTLSKLEKNLNYTLLDK
+ISTNMAKEKIEVYFPKFKIEKRYILNEPLIKLGMSDAFDDMLADFSGMTGSRDLYISKVIHQSFIEVNEE
+GTEAAAATAVIMSGKSISLGPKIFKADHPFLFFIIHKPTNTILFMGRFIEP
+
+>gi|157364681|ref|YP_001471448.1| proteinase inhibitor I4 serpin [Thermotoga lettingae TMO]
+MKKVFLTAFLTGFILIGFGIVQDSSNLFGVDLYKVLSEKPGNIFFSPFSISSALAMTYIGADSDTAQQMK
+NVLHFDLDDETLLSNFSQLTTSLNQSNENYQLSVANSMWLQEGYPFLKEFVEQIQKYYQSWINYVDFANH
+KDEAREKINEWIEAKTNNKIRDLIKPDDIDSLTRLVLTNAIYFKGLWLNPFDPSSTRKESFHISKNEEKE
+VDMMFKNITANYTEDSLVQVLELPYAKNKISMIIVLPKEDKDLSQIEKNISLDLFKKWRSNLKPTEVNVH
+IPKFKTECRFNLKRTLMSMGIVDAFTDEADFSKMDGTKMLKIKDVIHQSFIEVYEEGTQAAAATATIVNI
+KMAPKKPVEFRADRPFIFFIYDSTYDLILFMGRLINP
+
+>gi|124002812|ref|ZP_01687664.1| scca2/scca1 fusion protein isoform 1 [Microscilla marina ATCC 23134]
+MLLGLLAFNTQAQNSQNSPTVKGSNQFALELYKKLSSNPQKNVFVSPYSISSALAMTYAGAKGSTAQEIA
+NALHLPKNSVHQDFKNLNTHLNQLNTKGLQLSVANALWSEKSQKFLKAYLGLTQSCYRAKVKRLDFKQQP
+EKSRLIINKWVEDKTQRKIKNLIPKGIINQTTRLVLTNAIYFKGQWKYKFKKSQTRKMDFIAGKQKISDV
+KFMQMQRKFKYAETESLQVIELPYASQKVSMVVLLPKDINGIAKLEASLTAESYQKLMDRLFYTQVKLSL
+PKFKMTLNVKLKNVLKTMGMQQAFGNTADFSGMTGNKSLKISEVVHKAFVEVSEKGTEAAAATAVVVRTK
+SASAHRPVKPKVFRADHPFIFMIKDNTTGSILFMGKLANPK
+
+>gi|223938550|ref|ZP_03630442.1| proteinase inhibitor I4 serpin [Pedosphaera parvula Ellin514]
+MSMYKNLTLLGILTGVMFASVPVKSETTNAIPELVQENNAFALELYGKLKSKEGNLFFSPYSVSTCLGMA
+YAGARGETEKQMAKTLHFSTNQAALHTGFGELQKELNKKPGVTLKVANALLAQKGMPFSKEFLDCLNKTY
+QADAMRFDFGTQAQLASDELNGWVAKKTEGRIQTILQPEALDRAVALVLVNAVYFKGAWATPFSKEVTMP
+NPFYFGKKGSVTAQMMYQQEHFDYYENPKLKALKLPYAGRKLSMVILLPSARDGLPDLESFITTQSLSSW
+ISQMHDQEVAIQLPKFKMDEEFDLNSTLGEMGLHDAFCSKADFRGMMSSGELHLSKVLHKSFVEVNETET
+EAAAVTMAGVAFGNTGKPGPKGFFADHPFLFVIRDNGTGSILFMGRVMDPMK
+
+>gi|162451149|ref|YP_001613516.1| serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member [Sorangium cellulosum So ce56]
+MARPISFFTTALCTLLGLGCQARDGAPPAAPAPSASWCGPADCGPLSVPVCDDGSSGAPQCVRAQNGACQ
+WVRVCQGPEPAAGTATPGPSEPATPDAQQADPPPAPALADTNAAFAQRLYGKLAATKDKLFFSPASISTA
+LAMTYAGARGETAAQMAKTLEFTLPPEALHPAFGGLLKELALATGPKGPELRIANRLWGQAGLPIEPAFQ
+STTQQHYGAGIELVDFKGGSEPARGRINQWVEQQTNGKIKDLMPAGSITGLTRLVLTNAVYFKGKWATPF
+DKQATKNEPFTVKPGTAPAVPMMRKTLQAGFGKTADASVLELAYEAQSPERRLAMVVVLPAQVDGLAKVE
+QRLAAGELKAYVEALQPARVDVALPRFKMTAELELSSTLSALGMPLAFDDKKADFTGITRAEPLFISQVR
+HKAFVEVNEEGTEAAAATGVVMTTRSAPAQPQVFRADHPFVFLIRDVATGTVLFLGRVTDPR
+
+>gi|189500654|ref|YP_001960124.1| proteinase inhibitor I4 serpin [Chlorobium phaeobacteroides BS1]
+MRIIIYNRLIPAAMYTRKALHLIPPLFLLMALFSFSQPAAPGKTEKPEPMQSTEAEKRENTAFALDLYHT
+IGKSTKGNIFFSPYSISSALSMTLSGAAGTTARQMGDMLYAPEDLQRYHHTRASREAEISSIAKKGSVTL
+ETANGLFPQKGYELSKTFVQELLTVYRSTLTPVDYRADTEKARKTINRWAEQRTRNTIRELIQPGILNTL
+SRLTLVNAIYFKGNWKKAFAESETTAADFYTDKSSTSTVSMMHQENTFPYTLSDSLQILELPYSGEDISM
+LVLLPEKNKGLAGLEADLTAEKLSLWTDSLKPQKVRVFLPKFTMSSTLRLDDSLKKLGMTDAFDPGRADF
+SPMTVNKDKLFIGAVVHKAFVDINETGTEASAATGVVVGLTSAVQAPTPVFRADHPFLVLIRSNRSGSIL
+FMGRVSEPDND
+
+>gi|223937479|ref|ZP_03629383.1| proteinase inhibitor I4 serpin [Pedosphaera parvula Ellin514]
+MRRGGMSLFWLVLALCGCNSPGPVTITPLPSGNAKVGLLLIPETDPLSTNAPTVYRAPVPYADLKPLVKG
+NTAFALELYAKVRSGEGNLAFSPYSISAAVGMTYAGARGETAIQIQQALHFPQNETNLPALFAQFDRTLQ
+TAQSVGGAQLNIANSLWPQKQYRFRPEFLELLKVNYRATITPLDYGREPEKAIRTINQWVDENTRHKIPE
+IVGPGDLNASTRMVLVNAIYFKGLWNTPFQESATRQDKFHVNAQRMLTVPFMNREGSFKYGENAQAKVLV
+IPYREHQFEMVLVLPQKQDGIAQLESTLNVTNLTAWTSVTEGQDVIVTVPKFKMSTGLGLTQTLQALGMR
+DAFDPGRADFSGMDGNPHYLYLSDAVHKAFIEVNEKGTEAAAATGMMVPMMGMAMEPPPKPREFRADHPF
+LFLIRESSTGCILFMGRVMEPGGN
+
+>gi|153868784|ref|ZP_01998527.1| Proteinase inhibitor I4, serpin [Beggiatoa sp. PS]
+MIKKIVIFLVTLIVLLGLHNCVENPVVSDSKAVTKTNDVEEETLPSKQPIATPIANQQNLATAAINAFAT
+KLYAQLSQQSGNLFLSPYSVSTALTMIYAGAKGETKLQMARALQFNTNQHIQHGFRELQKSFNNEDSSYQ
+LSIANGIWVQKRMTLFAEFMETLYDFYGIVARTADFENATEIARRSINAVIAKQTHGKIQDLLMPSLLSP
+ETRLVLTNAIYFKGKWQNPFLPEETQDMIFIKSDNSQIEVPTMYQKGEFGLWENEDVQLIELPYQTSQKN
+AELSMVILLPRKHENFAVVEQQLSDYLQKNSHDPSEVAVYLPKFKTESAFSLQEPLQTLGMTDAFDSTKA
+NLSGITEENIIISAVEHKAFIEVNEEGTEAAAATTVIASRGRATVFRANHPFIFWIKDNQSGTILFLGRL
+MNPTF
+
+>gi|153872807|ref|ZP_02001593.1| Proteinase inhibitor I4, serpin [Beggiatoa sp. PS]
+MVEGNTTFALDLYEQLRKDKGNLFFSPYSLSTALAMTYAGARGNTEKQMSQALHFPPNQIQLHPAFFHLQ
+QQINASQTENEAVELRIANALWSQKGYELVADFKNALTNYYQTKSQPVDFEKATETARQTINHWVEKQTN
+DKIQELLKRGVINRLTRLVLVNAIYFKGNWAMPFDSNKTKMEPFWNAPNSSANVPMMNQKNYFGYAENYN
+FQILELPYAAQQVNHLDISYDDNNLSMIVLLPRHRDGLSQLENSLNPTSLAEGIKKLQWQKVNVSFPKFK
+MNTGFELSKLLSKMGMPDAFNDRKADFSGMDGTKELSLTSVIHQAFVEVNEKGTEAAAATAVLVGTRGLP
+PPTPEFRADHPFIFFIRHNSSGSILFMGRVVNP
+
+>gi|223938554|ref|ZP_03630446.1| proteinase inhibitor I4 serpin [Pedosphaera parvula Ellin514]
+MAYAGAHGETERQIAQVLHFNSDQSKLHSLFGELQKKLTSAEQQKGIDLHMANILWTQKGHPFLPSFLEH
+ATNYETSIKQVDFATQSEAARQQINGWAGQQTRGTITNILAEGELDSLTSLVLVNVLYLNSHWEVPFDAK
+ETKTAAFHLADGRTKDVQMMHQKNKHRYHFFEDDTVQLVELSYTNYKLSMLILLPKDVNGLAKLEAAVNT
+KSLSKWEHDAEYLEVELFLPRFKFESGLELAPELKKLGIMDAFTGVANFSGIDGTKMLRISTALHKSFVK
+VDEQGTEASFITRLAYTAQSMVEHVGPAILRADHPFIFLVRDCGTGSILFMGRVMDPGN
+
+>gi|124002813|ref|ZP_01687665.1| scca2/scca1 fusion protein isoform 1 [Microscilla marina ATCC 23134]
+MTLLLCLLCVSLQAQLLPNNPTVQGNTRFALQLYKQLSKASHQTQDNNVFVSPYSISSALAMTYAGAKGS
+TAQQMAHTLHFSPKSLDKDYQFLNHHFNHLNSKGLQLSIVNAIWGEKSKKFQPSFLKLNHTYYQAKLGKL
+DFKNQPKKSRIVINQWVAKKTQDKIKNLIPSGMISGNTRMVLTNAIYFQGKWKLRFDKSNTRKMNFIAHK
+ITYPDIKFMHITNSIKYTENAILQAIELPYAGDKVSTVVLLPKHKNGLYQVEQWLTSKTYQALTTSLFHT
+KVILHLPKFKMTKNVPLKNALKALGMRIPFTKQADFSKIMQSESLVISEVVHKAFIEVSEKGTEAAAATA
+VIMSRPRSTSYNPEQPIPPKIFKADHPFMFIIKDNTTGSILFIGRLITPKQAI
+
+>gi|188997322|ref|YP_001931573.1| proteinase inhibitor I4 serpin [Sulfurihydrogenibium sp. YO3AOP1]
+MKKLVNILLMVLVIFFCNVAMADTDKDLKVVSQGINKFSFDLYKKLKDKNKEENLFYSPASISIALAMTY
+AGARGNTEKQMANVLNFTLPQDRLHPAYSKLIENLKSNKDYELNIANALWLQKDYKYLQEFLNTMEKYYK
+GGFNEADYITNPEGARIKINDWVSRETKEKIKDILNPKDITSLTRLVLTNAIYFKGKWQTEFNKMATRDE
+DFYLINGQKTKVKMMYQKNTFNYYENDDLQLLEISYKGNKISMVIILPKVGKFKTVENMMDEKKLQEWLK
+NATETKVEAYIPRFKFTQRFDLSKNLSDMGMKDAFDEVEADFSGINGEKNDLYISKVIHKAFVEVNEEGT
+EAAAATAVVLDTKALIEEPVFKADHPFIFLIRDKETGSILFMGRVMDPNKE
+
+>gi|189346873|ref|YP_001943402.1| proteinase inhibitor I4 serpin [Chlorobium limicola DSM 245]
+MPTTDTHEKHNFPMNNTIALLSLLGVMLTAPLSGASGATGLPENHAASPEAQNELAVDLYRNLAVTGKNL
+FFSPSSIETALSMTMSGARNRTERQMADVMHVGPDAMERHHAGLASFEKQLESIQKKGKVTIASSNSIWP
+QKNYPLAPSWLAQLKRYYGTSVTPVDYIHETEKARIAINRRVEKDTKNRIRELLKPGILDPLTRLALVNA
+VYFKGDWEHPFNENNTVASPFYIRQGTTGKAPLMRQSASFGYGDHDGVQVLELPYAGKKLSMIVVLPKER
+FGLEALEKTLTPKQFALWTANLSERKIEALLPKFRTTSAFRLDETLRHMGMTDAFDRNLADFSGMVSNSD
+KLYIGAVVHKAFVDVGEKGTEAAAATAVVMQLRSAMPMPVPVFKADHPFLFAIRENSTGRILFMGRISDP
+ADNG
+
+>gi|223938551|ref|ZP_03630443.1| proteinase inhibitor I4 serpin [Pedosphaera parvula Ellin514]
+MYKNLTLLGILTGLMFASLPIKSEPTNAVPDLVRGNNAFAFDLYGKLKSRDGNLFFSPLSISTSLGMAYA
+GARGETEKQMAQTLHFGTNQNQLHAQFSQLLSDFDEKGLEKLLRNSTPEDAQIANAIYVQKGQPLSQGFQ
+NIVTQSYHAFVKQVDFRTEKVSACKEINEWVSDKTSGKIREIVQPRDLDDLTQIALVNTVHFKGGWMFRF
+YPASTTQQPFTIAQGESKDVRMMHKNEGFPYYQDEDLQATELFYTEGQFSMLILLPRKQDGLKALEAKLS
+AETLMHLTSGMRGRHVDVFIPKFKLSFGAELSECLKTMGMQKAFSAHDADFSGMDGARDLHISAVFHKAV
+ADVNEDGTEAAASSVHMMSNGMDLDPPPTFRADHPFIFLIRERKSGSILFMGRVIDPTK
+
+>gi|209524126|ref|ZP_03272677.1| proteinase inhibitor I4 serpin [Arthrospira maxima CS-328]
+MSKFSAWGRRNGSLLASLLLLWGVGLPVITQAVGNSSESNSYQIARVDNNAIVNQNNQFAIDLYNQLQRE
+ISGNLFFSPYSLSTAMAMTYEGSRNQTAIQISQVFHFPQPPGSLYPEFTSLLNDIKSRNSSQLYLVNRLW
+GQSGYRFQEPFLQITKNHYNAQLNQVDFMGDHEKSRQIINDWVSQETNHKITDLIPPGILDRLTRLILTN
+AVYFSGDWLSPFPEKYTQDGIFNLPSGETISVPMMHHPNVSISYHSLPEVQIIELPYSDGNLSMIILLPA
+EGTDLPTFAQNMTIANFQNWLHRLEYVNLEIWLPKFNFSSSFNLKSTLSYMGMESAFTETADFSGISSEK
+PFFLYDVVHQAFVNVDEKGTEASAATGVIVGSRSSIRDRIHINRPFMFIIRELDSGTILFMGSVVNPLEQ
+
+>gi|115378735|ref|ZP_01465881.1| serpin [Stigmatella aurantiaca DW4/3-1]
+MTSSRRWLVPLFTAAMALAHCADAEKQEQEQEQEQEQPRTESPDGTNAPGEYVSSGKERVTSPNVPSQDI
+AALVTGNTDFGASLYRKIAKPGENLFFSPFSISQALSMVYTGARGNTEAEMAETLHFSLPQARLHPAANA
+LNLKLQAQAEETVGGVGTPTFLRLVNATWSQQGFSFEPAFLDVLALHYGNGMRVVDFSTQASAIRDGINT
+WVKDQTEGRIQDLLPPDGVNRNTRLLLVNALYFKGAWASPFAPQATQNAPFYLLNGGTQQVQMMNRTGSV
+EYMQGEGFEAVGLPYQKNTYRMLLIVPQQGRFAEIESRLSAGFLSEIRGALVNRFVALGFPRFQVEKSFS
+LADSLQALGMTDAFSEWANFSGLTTQEALAIARVEHKAFVAVDEKGTEAAAATAVIVAPPSVPEPLTVNR
+PFLFLIEDKETKTVLFLGRFVKP
+
+>gi|162452372|ref|YP_001614739.1| serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member [Sorangium cellulosum So ce56]
+MPQWANPVPAIAGAAPVVITSARAAISAGVDEAGALGTSAAVPGPMRYCRIFSVFIPLSVLLAGCSSGGT
+GEDPVPSPSGCSDPETPGCVLTSEKQRILAPSVPDADREALADGNTAFALDLYGKLGAEPGNIFYSPHSV
+SSALAMTYAGARTETEAEMASALRFTLPQERLHPAFNALDLALESRGEVAEGQDGEGFQLNIANALWGQV
+GYPFLPSFLDVLAENYGAGMNLLDFGQTSEARQIINGWVAERTEDRIKDLLPEGSISGGTRLVLTNAIYF
+NAAWKFPFKEEDTAPGDFTLPDGSTVSVPMMAATSEVRYGEGDGYAALEMPYDGDELAMVLVLPSDIEAF
+EDGLDGARLDGVLGSLEPRNVTIGLPKFKVESTFDLIPPLMDLGMTAAFGAADFSGIDGQRSLSISAVVH
+KAFVSVNEAGTEAAAATAVALDESGPPEPAAIRFDRPFFFFIRDNATSAILFVGRVADPSA
+
+>gi|86609234|ref|YP_477996.1| peptidase inhibitor [Synechococcus sp. JA-2-3B'a(2-13)]
+MKDLFNRSLVSRIPLLALLGLLSLGLWPTHGMGSRSQETPVRIPFEPTVTYGEGYGEKTVAQQAQSRFAL
+KLFDHLLRQQPQENLFFSPLSIRLALSMLYNGASGETQTAMAEVLEAQDLSLNELNWSNAQMVGWLAEGS
+PAGGPVQVQTANGLWVDQTLTLQPQFLQALATYYQAVVNRVNLGSRQTVNQINGWVAERTQGKINRIVDR
+LSREDLMVLLNAIYFKGEWTQPFDPERTQTQPFTRLDGRRVRVPMMVQSGRYDYLETEQLQVVSLPYGEG
+ELEMLILLPKKGVDLESLRAELSPETWQEWTGSLRPRAGSVRIPRFELAYETDLTSVLQQLGLGVAFSNR
+ADFSQMTPEPARISKVLHKAAIEVNEEGSEAAAATGVIVSRTAVDRQEPFQFVADRPFWFAIVASGSGGN
+PAAQTVLFMGSLVDPE
+
+>gi|196255895|ref|ZP_03154433.1| proteinase inhibitor I4 serpin [Cyanothece sp. PCC 7822]
+MIKTKGLLSALSDTKIKEKAVFATTSLTLLLFISGWLAQYSSDALEFVANPQATYRFHAFMPSLKQLNPQ
+QQLIEANTQFGLNLFQTLVTEDPNQNVFVSPTSVAIALSMVLQGTDGKTQQQMLSTLGYENLNLKQINMA
+NLTLLKTLQTENSQIEVALANALYAREGVSFRHQFLKDNEQYYHAQITSLNFSSPQAPGIINRWTKEHTN
+GKIDQIITRIDPSEVLILINAIYFKGIWKTEFAQKQTKEEPFYLPNGQTKQQPLMSGTGKYQYYENEEFQ
+AVNLPYGDGRLSMYVFLPRTNSNLTKFLNQVTAENWTQWTGKFNVQEGSLKIPRFKLEYDTNLKETLSAL
+GMESLFRQANFSQMTSSPVVINEVKHKTFIEVNEKGTEAAGVTSIGVRGTSTAGTFSMTVNRPFFCAIRD
+NQTGTILFMGAIVDPKQ
+
+>gi|46446353|ref|YP_007718.1| serine protease [Candidatus Protochlamydia amoebophila UWE25]
+MKYMRVSIFLLISMMSYLFSQEQEILTNAKVSTEDQHFNIVVDGNNRFAFALLQHLNKQYKGNIVCSSYS
+IASGLSRLALGAKGTTLNQIRQILNYPMSFNPLIGSLDQFFVTIPKEKNGSQVFLANSVWLQKDVSVIPA
+YQYAYKKNFFSELQKINFKENSVNSLKEINDWTLKQTNNRIHNIVSPQAFSENNQFILTTSFYLKGTWGK
+MFPVGQTTHKPFYINSSQVRQVDMMHTLGQYPILITEKLTMIEIPYLTQEGTTPDFSLVILLPKEQMGWQ
+TILEELNLENWKNWTKNLIPQSIKLSLPRFRIEQKLQLNSVLQAMGAKELFTPQADLTGITREKLQLNHA
+IHKTLIHVAEEGSDSKAWGVNMEEPEDSSLQELLIDHPFFFLIIERSTHSVLSIGRVLQP
+
+>gi|119510570|ref|ZP_01629700.1| Proteinase inhibitor I4, serpin [Nodularia spumigena CCY9414]
+MNRQKLSGVEKKFLQRRYGVSLGRRYVLAAASVVLFGVLGCSQVSGNTNSLTQSEQPYSETRLPKKTLIS
+DAKLVDANNKFGFKLFSEIWKNHSSQDNIFVSPSSVAIALAMVYNGASGSTQQAMAKTLELQGMSLPEIN
+SAYATLKELLENPDPQVQLTIANSLWANQEATLQPNFLQSTQDFYKAKVTNLDFKDAASANTINEWVKDS
+TRGKINKIVEKIEPDQVLFLINAIYFKGKWSNQFDKSQTAKHPFTSISGEQKQHPMMSQTGEYRYYENDQ
+FQAVSLPYGEDGKVSFYIFLPKEESNLQTFSENLNFDNWEKWLSQFRNRDGFIRLPRFKTDYDVTLNDAL
+KALGMAEAFTNQANFSGMGKNLKISEVKHKTFVEVNEEGTEAAAATSVGMVPTSFREKPEPFRMIVDRPF
+FSVIRDNQTGSILFMGSITDPQ
+
+>gi|37521539|ref|NP_924916.1| serine protease inhibitor [Gloeobacter violaceus PCC 7421]
+MKNDAPGRPFRRSTLLRWGLALALFGSGVLRAGAQEKSAVKMLSDAQTRFGLQLFAALHNKAADQNVVIS
+PLSIALALTMAYNGAGGSTRTAMAQTLALDGLDEDAINQGSADLATALQKTPKTSRVLIANSLWSQKGIT
+LQPAFIRTAEQYFQAQVEALNFAEPRSAERINRWVAEKTENKIDQIVSPGALRDALVVLMNAVYFKADWQ
+EAFEKSATRERPFKLGSGWQKNHPLMAKQGRFDYYETDEFQAVRLPYKDDFLGMYVFLPKADPAAFYRQL
+TAENWQQWLGPRTFARRPGELVLPRFQVRYEAQLKQTLSALGMGIAFTGRADFTRMVREPALISEVIHKT
+FVDVNEEGTEAAAATGVIVARTSAVATPPFRMVVDRPFFFAIQDNRTGTLLFAGAIADPMG
+
+>gi|57234981|ref|YP_180970.1| serine protease inhibitor family protein [Dehalococcoides mccartyi 195]
+MKTKLALSLLAVVSLFTFTACAGGVSAEELKSDKDRILSPNVSQQNLNTQVQANNDLAFKLYRYLKGTEE
+GNFFYSPFSISIALAMTYAGADTATKTEMQNTLNYLLPDADLHAFFNFIDQELNKREAQAKEADEGTFEL
+KLVNAIWGQKDYTFLSDFLDTLAQNYGAGLRVLDFAANSEEARKVINDWVSDATKDKIKDLIPADGIDAT
+TRLVLTNAIYFNAAWAAPFDEENTQSGLFYLQNGTSVNVQMLRQIENHGYYSGDDFQAVELAYAGNGLSM
+VIILPDEGKFAQVEDALSGQMLAEILSSIKSNQINLSLPKFSFESKFTLKDALSSLGMPTAFGSQADFSK
+MDGGYNLMIGDVFHKSFISVSEDGTEAAAATAVSMNLTSAPTELVTLSIDRAFIFCIVDMATGTTLFTGR
+VIDPTA
+
+>gi|255037413|ref|YP_003088034.1| proteinase inhibitor I4 serpin [Dyadobacter fermentans DSM 18053]
+MLFGCTNDDVNPGNEVNPVAIPASVSNGTTSFAFDFIHALQGTQPADDNLFVSPLSLHMALGMLLNGAEK
+ETAQEIQKGLKMDAVALSELNAAYEALINDLPVADSKVSLGLANSVWYKNNFSVEADFRSVLKNSFESEI
+IGLPFDDAAKSRINKWASDKTNGKIEKVIDQISPNHVMFLLNALYFKGDWQSRFDANKTQDAPFQLAGGQ
+SKNVKMMYVSSDFKTGAGSNYDAVQLPYANGQFNMTLLIPRGQNTVNQVLNGVTGEGWTELNSKMAVRGV
+TVGLPKFTLKYTAQLKETLTNLGIRKVFSEGADLGKINKANNLFVDFVKQDAYLGIDEQGTEAAALTTIG
+VGVTSAGPEPPRFICDRPFALVISENTSNTILFVGRINNPESK
+
+>gi|186681975|ref|YP_001865171.1| proteinase inhibitor I4 serpin [Nostoc punctiforme PCC 73102]
+MNRQKFSDAKENFLQRRYGVSLGRRYALAAASVVLFSVLGCSQVESNKSALAQSSLPQPETPLQKKTLNP
+DTRIVESSNKFGFKLFSEVLKDDKGENNIFISPSSIAIALAMTYNGASGSTQQAMAKTLELQGINLPEIN
+SSYAAVLKQLLENPDAKVQLSIANSLWANQDVSFAPDFLKRTQDFYQAKVSNLNFKDAAASNIINNWVKE
+NTKGKITKIVESIEPYQVLFLINAIYFKGNWSNEFDKSQTAQYPFYVTSSRRKQHPMMSQEGDYRYYESK
+EFQAVSLPYGKDGKISFYIFLPKQSSNLKAFYQNLNVENWEKWMTQFNKQKGFIRLPRFKTDYEVTLNDA
+LKNLGMEEAFSNKANFSGMGKNFAISQVKHKTFLEVNEEGTEAAAATSVGIVATSLRDEPEPFRMIVDRP
+FFCAIRDNQTGNVLFMGSIIDPQ
+
+>gi|86604957|ref|YP_473720.1| peptidase inhibitor [Synechococcus sp. JA-3-3Ab]
+MKDLFNRSLVSRIPLLALLSLLSLGLWPTHGMGSRSQETPVRIPFEPTVTYGEGYGEEAVAQQAQSRFAL
+KLFDRLLQQQPQENLFFSPLSIHLALSMLYNGAAGETQAAMAEVLEAQDLSLHELNWTNAQMARWLVERS
+QAEGPIQVQIANGLWVDQTLTLRPPFLQALATYYQAVANRVELGSRQTVQAINRWVAERTQGQIDRIVDR
+LSREDRLVLLNAIYFKGEWTQPFDPALTEPQPFTRPDGRRVQVLLMAQSGRYGYRETEQLQVVRLPYGEG
+ELAMVILLPKPGVSLEALRQELSPETWQEWTGSLPTRPGSLRLPKFKLAYETDLVPALQQLGLGIAFSRR
+ADFSQMTPEPTQVSRVLHKAAIEVDEKGSGAAAATGVIVSRTASDRQEPFQFVADRPFWFAIVASGANRE
+AQTVLFMGSVVNPK
+
+>gi|220907243|ref|YP_002482554.1| proteinase inhibitor I4 serpin [Cyanothece sp. PCC 7425]
+MNNAKTPGIVAIVTLGLTLSAILGSWLQERSWSQDLLAQAGSIMHSVVAQMPQNSNPNIKINPQILSAQT
+RFSLKLFQAISQQNQGKNVLISPTSIALALSMTYNGAVGETQQAMAKAMELQGITLADLNRANADLKAVL
+QNPDPKVQLAIANSLWARQDFTLKPNFIQLNRQFYGAEVTNLNFTDANAVNRINGWVSQNTRGKITQIVD
+RIQPDDVLFLINAIYFKGAWSQPFDPKATQNKPFYRAQGDNRPVPMMSLQEDLSYLSTEQFQAVSLPYGD
+KKRMRMDIFLPHKSSNLTSFTKTLTVQNWQNWLKQFSTREVALQFPRFKVEYGTELKPVLSSLGMGVAFT
+HQANFANLSPQPTLISQVKHKTFVEVNEEGTEAAAATSVGIMVTSARIPVEMVVDRPFFYAIRDEQTGAI
+LFMGTMTNP
+
+>gi|163811955|ref|ZP_02203636.1| proteinase inhibitor I4, serpin [Dehalococcoides sp. VS]
+MKTKIALSLLAVVSLFTFTACAGGVSAEELKSDKDRLVNPNVSQQSLNTQVQANNDLAFKLYRYLKGTEE
+GNFFYSPFSISIALAMTYAGADTATKTEMQNTLNYLLPDADLHAFFNFIDQELYKREAQAKEADEGTFEL
+KLVNAIWGQKDYTFLSDFLDTLAQNYGAGLRVLDFAANSEEARKVINDWVSDATKDKITDLIPADGIDAT
+TRLVLTNAIYFNAAWAAPFDEENTQSGLFYLQNGTSVNVQMLRQIENHGYYSGDDFQAVELAYAGNGLSM
+VIILPDEGKFAQVEDALSGQMLAKILSSIKSNQINLSLPKFSFESKFTLKDALSSLGMPTAFGSQADFSK
+MDGGYNLMIGDVFHKSFISVSEDGTEAAAATAVSMNLTSAPTELVTLSIDRAFIFCIVDMATGTTLFTGR
+VIDPTA
+
+>gi|162449537|ref|YP_001611904.1| serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member [Sorangium cellulosum So ce56]
+MRRPPIPVVLLPFSLLCAGCSSGGAEPEARPSPSGCADPGTAGCVVTSDRQRARAPRVPEADARELALGN
+TAFALELYRRIGAAPGNLFCSPYSVSSALAMTAAGARGETAEQMARALRFTLPEARLHPAFNALDLALAR
+RGEGAEGQGGKGFRLHVANAIWGQIGSAFEPSFLDVLAESYGAGLHVVDFVQAPDEARKIINGWVAERTE
+GRIKDILPEGALGPSTRLVLTNAIYFNAAWQLPFKEEETTPESFTLADGSTVSVPMMTNHAQVRYGEGGG
+YEALELPYDGGELSMVLVLPSELGGFEAGLDRERLEGVLASLGSRSVTMALPRFKIASTLDLARPLADLG
+MPAAFSERADFSGIDGQGGLFITDVLHEAFVSVNEAGTEAAAATAVVIGETSAPEPATIRFDRPFLFVIR
+DRATSAILFVGRVADPSR
+
+>gi|125973785|ref|YP_001037695.1| proteinase inhibitor I4, serpin [Ruminiclostridium thermocellum ATCC 27405]
+MKRTACAVLCIFVLTFLFSGCSREKKVFDELKLDTELEKKNTEFCFDIFSKLNEEDYNKNIFISPLSIST
+VLSMTVQGAGTTTKDGMLKALKYDGMDLDKINESYRYILDYLSKTDKTIELEINNSIWIREGKQIKKDFI
+DINKDVYNAYVTELDFSSPNAADRINKWISDSTKKKITDIIDSPIPENTAMFLINAIYFKGDWAEKFKKQ
+DTFTAKFQSGNGQTKEVMMMERKDTIEYGAKEDFKVVRLPYGKGTTSMYCVLPAKDVSINDFIKTLDVNK
+WEEIKNSISKAENVTLNIPRFKIAYGTKELRDCLIAMGMEEAFTERADFSGISEGLLFIDSVIHKAIIEV
+NEDGSTAAGSTVVRMIDGAAIGEPLSFIADRPFLFFITEDVTGTILFMGKLYDCEKY
+
+>gi|196252898|ref|ZP_03151545.1| proteinase inhibitor I4 serpin [Clostridium thermocellum JW20]
+MSNGTLFHYLRQKASEDKSDGGGENEKNSLRSFMHICFNIFIFRVFKGKKVFDELKLDTELEKKNTEFCF
+DIFSKLNEEDYNKNIFISPLSISTVLSMTVQGAGTTTKDGMLKALKYDGMDLDKINESYRYILDYLSKTD
+KTIELEINNSIWIREGKQIKKDFIDINKDVYNAYVTELDFSSPNAADRINKWISDSTKKKITDIIDSPIP
+ENTAMFLINAIYFKGDWAEKFKKQDTFTAKFQSGNGQTKEVMMMERKDTIEYGAKEDFKVVRLPYGKGTT
+SMYCVLPAKDVSINDFIKTLDVNKWEEIKNSISKAENVTLNIPRFKIAYGTKELRDCLIAMGMEEAFTER
+ADFSGISEGLLFIDSVIHKAIIEVNEDGSTAAGSTVVRMIDGAAIGEPLSFIADRPFLFFITEDVTGTIL
+FMGKLYDCEKY
+
+>gi|134098090|ref|YP_001103751.1| serine protease inhibitor serpin-like protein [Saccharopolyspora erythraea NRRL 2338]
+MSEHLDFSLSLHKHLAPPPEQPFCWSPYSVASALGLVTAAVGGSTRDELAAALRIGPDDLGGLLDLLAGS
+AELGGTGRSGEEPVLAVANTLWAYDDLLVHESFLRELKSWPGSDVRTAPFRERPETARQLINSDVEETTR
+GLIPELLPEGSVDPETVAALVNALYLRTSWQEAFDDKATAPRVFHAPRGDRDVPTMHVTRRFGYAAAGGW
+QAVTIPAAGGVDGVVLLPDEGLDQAEPALDADRLESLLSSAEQQRVELLLPKFDVRGAAELQRPLGALGV
+RTVFTPGADFSPLTDRTLRVSTVVHRSVLRVDENGLEGAAATAAMMRLTAIVREEEPIRVEVDRPFLFLV
+RHRKTGAVYFLARVVDPA
+
+>gi|160882350|ref|ZP_02063353.1| hypothetical protein BACOVA_00298 [Bacteroides ovatus ATCC 8483]
+MFKKEIILGILCLFAACHSNDEIIEEQESPKNEQQEPKARVDIILSHEEQAMSESTNDFAFQLFKQVCVS
+ENRKTNIFISPFSVSLCLSMSANGANGNTLTEIKKVLGFSSSSMDEVNTYNQKLMSSLLNIDNTTQIGIA
+NSVWINQGFVVKNTFIDINKLKYNAWVESLDFSSASAIATINAWCARNTENRLVDIMDEISPEARLILIN
+ALYFKGKWTNPFSKEVTKNDFFTNIDGEQVKVDMMCQEESFRCMNNEKFAIAEFPYGNEAFSMVVVLPVE
+NSSLEESLLWLSNDAWKQCETQMSYQKLQVKMPKFSFKYQKPLNSDMSVLGMKDAFILGLADFRNISASE
+NLYLSSLEQFTYLEVNEEGTESAAITTEVPATSTGDDKDIIHFFMDRPFIFMIKEKSTGLILFMGQVTKL
+
+>gi|196228114|ref|ZP_03126981.1| proteinase inhibitor I4 serpin [Chthoniobacter flavus Ellin428]
+MKTSLLLLLSISALLMNVQAADSKIASGTVNALGVDLYHAQAHGDGNLLLSPYSIQSALAMTYAGAAGDT
+QAEMQRVLHFPADDNALHESFSVLGQALAQTAKKTVDRIAESKKYGGPSTPIEFDLANRLFAQRGYDFRP
+SFLDLVKERYGAELEQMDYKTDPEGARKTINQWVEKQTKEKIRDLIPAGAIKHDARLTLVNALYLRAPWS
+DEFNAKATTKEKFLVHGRESAEVPMMQKESHCGYARREGFQIVTRPYVGGELQFVILLPDDPAGLAAMEK
+QLTPKLIEDCAHLSSQKVILHLPKFRLEPPTIPLGEDLKALGMKTAFDDPKGSANFDRMAPRRPNDYLYI
+SAVLHKTYLALDENGTEAAAATAVVVAAGMAMIKQPPPVEVRVDHPFLFMIQHVPSGACIFIGRVTDPR
+
+>gi|153007013|ref|YP_001381338.1| proteinase inhibitor I4 serpin [Anaeromyxobacter sp. Fw109-5]
+MSPSRAAVLVLATLTLVPACGNGSGSEPPPAAPGERVGSTSARVTAPAPAEDLAAAVAGNGALALDLYRV
+LSLEAEENLFFSPQSIAFALSMTYPGAAGETAAAFERTLHVSIPEPDYHRAMNDLDRQLRSRGAGAKAAD
+GQPFRLRLVNQLFAQRGFAFEPPFLDVLAQEYGADVRLLDFASAPEPSRGAINGWVAQETEDRILDLLPQ
+GTITTDTRAVLVNAIYFNAAWAKPFDPALTRDREFTLLDGSRVAVPTMSSADLAARAAQVDGVEVVELPY
+DGGELSMLLLVPPSGALAALEQALTPERLAEYVAALRAEHLALTLPRFEVRSSLALKPPLAALGLEVAFS
+ELADLSRMSSQADLLVSDVVHQAFVKVNEAGTEAAAATAVIIGVTSMPTIRPVAIDRPFLFVVRDDATGA
+LVFVGRVTRP
+
+>gi|160889214|ref|ZP_02070217.1| hypothetical protein BACUNI_01635 [Bacteroides uniformis ATCC 8492]
+MLKKTITALSLLCILAACQSDDNSSPQPKPRKDIALTRAEQEMMDLGTDFAFRFFNQVCKTEVEKPNLFI
+SPLSASLCLSMIANGALGNTLSEMTDVLGFSGYSLEEMNNYNKKLVEALLDLDNTTQLGIANSIWIKKGF
+GVHDDFVSVNKKMYDAQVQELDFASPKAPDIINGWCAGKTNNCIPKVLNEIPETARLYLLNALYFKGIWK
+NQFKKSDTAEEAFTNADGSKSTVHMMNLRDERFNYAENEYFSMAELPYGNEAFSMVVLLPAEGKSLDECL
+PQLNDERWGEWNSSLSSSALNLKLPRFEMEYDKELIDDMMAMGMQEAFTPSADFSGMADEDLFISLLQQF
+TYVKVNEEGTEAAAVTVGGMDVAAPGPSTVIPFYVDRPFIFLIKEKSTGVILFMGKVTKL
+
+>gi|153954385|ref|YP_001395150.1| protease inhibitor [Clostridium kluyveri DSM 555]
+MLNKSKRKKIVPLFFLMLFMTTYTHFTPVIHADSDEKSQITQLEAKQNISTMKTWTIKFRTPVDENSLFI
+NVKGSQGNFINVKISTDSSGKYVYVDPPEEGYKIGQTYYLNISKDIVFKEPGRSLKNDIQMKFTTNDIGT
+INIDETTSIITANNTFAFNLMKNLISEDNTENMIISPLSISSILAMTQNGAAEETKQEMLNCMGLKNISD
+SDINKQYYSLLDYYNNLKSTDLKMANSIWTNKQIALNSDFKDTAEKYYASDASSEDFEDADTLVKINKWV
+NNHTEGQIKKILDSIDKDTGAILINSLYFKGKWEDQFSTGNTKKEDFTLSNGNKLNIDTMQNTSYVNYLE
+GPNFQAISLPYYDNMEMDIFLPNKDVSINDFTKSITKEKFDTWINNFKSTYVLQQIPKFKMYYDVDLNDT
+LKALGMDKAFNSKEANFTKLITNTITSQESLYINKIKHKAYISVDEQGTEAAAATAVIMNPTSAPPGNPI
+YFKANRPFFFIIRDTKTGAISFMGKLDNPNASDTEPTN
+
+>gi|83816001|ref|YP_446447.1| serpin (serine proteinase inhibitor) [Salinibacter ruber DSM 13855]
+MFFGLGCDSTGPEDAADAPPPRPLTAAEDQVVDADNAFGLTLLRSTVDTEGTSKNVFLSPISVSMALGMT
+LNGARGETRSGMKAALEKQDLSPTDINDAYRGLIDLLEGLDPNVEVALANSIWYREGLPVKQAFIDTNRA
+HFDAEVEALDFADPSASDRINGWVNDQTRGNIEKIVPSQIPSNPVMYLINAIYFNGPWRDQFDPSNTAPE
+PFHRGDGSTVSVPMMEKTKNVVHPTYQAEQFRAVDIAYGDSLYSMTVLLPHEDASVQSVVDSLDTETWTE
+MTSGLSPQSLSRLKMPRFTLRYGKTLNDVLKDLGMGVAFTGRANFRGIADLSLAIDKANHKTFLRVDEEG
+TEASAATSVEIEPISSAPPSFVVDQPFVVAIREHHSGTSLFLGTIMDPTAG
+
+>gi|256670770|ref|ZP_05481723.1| serine protease inhibitor serpin-like protein [Streptomyces sp. AA4]
+MALDSHLTFTLALHGATAPPGSDACFSPYSAASALGLAEQAARGRTAEELAAVLGRDQSGLLHAAAELGD
+GAQLAVANTLWAADGITVEDNFQAALVRWPGGKAETVPFETDPEGARRRINDDVDQTTHGLIPELLPEGA
+IHPHTRASLVNALYLKTAWRRPFPEHATADADFHTPDGVRPVPTMHLDESVGYAHENGWQVVRLAAEGGV
+ETVILLPDGDLESAEAALDAQSLRALVESPKQHKIRLALPKISLDVRADLERALQGLGVRELFTDDADLT
+GLTPDRPLWVDSILHQAVLRLDEQGLEGAAATAIQMRTMSLISGEPLEVRVDRPFLLLVRHAETGAVYFF
+ARVVRPA
+
+>gi|240172431|ref|ZP_04751090.1| serine protease inhibitor family protein [Mycobacterium kansasii ATCC 12478]
+MKRLTRCFRVGFHGVIAACVVFAGAVGCGGDRNHVQSTPGPTSAPVARSNLPYDNTPDVAPAEEQRFVDA
+TNGFGLDLFRRMSAASEKNLVFSPLSLSVALSMAYAGAAGDTAAEMKTVLRDPFGNDSYYRAMNQLLLDL
+RSRNRAAISAEDPRSIELAMVDAVWLQRGLSVRAPFLDILATQYDAGVRLADFKGNPDGERVAINDFAGD
+ATKGQIKDLIPPGAIDDLTRMVLLNAAYLKASWERPFSKEDTRDGSFRLTPQSAVTVPMMHQVTGAMRYA
+AGSNFQAVELPYLGGDLKMLIVLPAEGELQAVRNSMDDAWFRTVAFADTAVSLSLPKFRISWGPEEFKET
+LAAMGMPRAFDENRADFSNVTTDEKLHIPHLLQKAFVGIDESGTEAAAVTPGLGGGLGSPERVAVDHPFL
+FAIVDKTGAVVFAGQVMDPR
+
+>gi|171915216|ref|ZP_02930686.1| proteinase inhibitor I4, serpin [Verrucomicrobium spinosum DSM 4136]
+MKVCSLWRAGWWALALLVAAAPGAMWAETDRAVGAQASNVLAFKLAPALQTMPENYVMCPYALHRVLSLV
+LEGAEGKTREELAQLLGWKADFATRSAAIKELGTALGRSAGEGAVTIDSSLNLLVRNRVRLEDSFLDLAQ
+DTYGVTPMVLKSDDPANAVEGVNELISRGTRGRITNLVPPGGLGADNVLTLVSTLFFKGAWSERFPAEKT
+VQRPFWVPSARTDKQVKMMRKTGDLRHASMKAGGYGLLELPMGARSQDFCMLILLPDAQDGLPAVEKALT
+QAGLEEAIGKLDSARVTVHLPRFSFSLGGDFTMLLKALGAGRVIAPGDAELGPMSRTVPLRLSALYKETT
+VDVNETGAEAASAVAMAAGPFSSGAPNAEAPKPPVMFIANHPFLFFIRHQPSGLILVMGRVDNP
+
+>gi|229870584|ref|ZP_04490178.1| serine protease inhibitor [Spirosoma linguale DSM 74]
+MKTTLFSTVSAAVTGILLTAVSCNTSTVTPTPGTTAELRVSAPFVNQTTQFAFDLAKQVNAQDGPAKNVF
+ISPLSLHMALGMILNGANGQTAQEIQKTLKLDAQTLAEANTTYQNLMANLPGVDPKVTMRLANSVWYRNT
+FTVETAFQDLLKQTFSADISAQDFNNPATVGTINSWASQKTNGKIPKVIDQIQPDNVLFLMNALYFKGDW
+TTRFDAAKTTDSPFTLVSDAQTTVRMMRLNTQLNHASRPGYSAFELPYGAGNYVMTVLLPTSNTTADALI
+NNLNSDEWALLQKDMTKSLFDIGLPKFTVNYEAKLNNVLSTLGMPTAFTDRADFTKINAKGGLLLSFVKQ
+NTFVAVDETGTEAAAVTTDGISTTSVQMPTLCDRPFVFVIHEKTSGTVLFVGKIADPTKTNA
+
+>gi|256375408|ref|YP_003099068.1| proteinase inhibitor I4 serpin [Actinosynnema mirum DSM 43827]
+MRDRGHLTFALALHDALAPDRARPACWSPYSVAGALGLLAEAGRGPTRDEVLALLGPGGPELVRGTGVGA
+PAEFAVANTLWAADDLPLVEGFLRGLADWPGGAARSAPFAADPEGARALINADVAKTTRDLVPQLLRSGS
+VRADTVSVLVNALYLKTAWVTAFPERATADRPFHTPSGTRPVPTMRVTANARHAARAGWQAVALPAEGGV
+ELVVLLPDGGLGALDGVPEVLDGLEHRRVDLSLPRARLEFSALLGGALRGLGVRSVFGSGADLTALSPDP
+RLVVGEVVHEAVLRVDEQGLEGAAATAVLVRAAAFRPAPEPLVVRVDRPHLLLVRHARTGAVFFLAQVVS
+P
+
+>gi|256389336|ref|YP_003110900.1| proteinase inhibitor I4 serpin [Catenulispora acidiphila DSM 44928]
+MPRKQIAAITAASLAALTACSSSGSSSSAGGSLVRVNAARATVGQADLSAASAGVNAFGVDVFHSVADGD
+EGNVMISPTSLATVLTMLLPGAKGQTEAQMAKALHTTMTADQFADALGALDSATVQRELADKAELQQYDT
+VWTQKGYDIQPSYLQTLASAFDAGVRETDFTNSESARQTINKTVEDQTNGLIKDLFGPGSISPATRLALT
+DSLYLKAKWADAFAKSATSDKPFHLTNGSTANVPTMGKEHSFAYAHGADWQYAELPYQQDHLAMGILLPA
+SGSFDTFRKSLTGDSLATMTASATPSPVDLELPKFTFDTSRDLKSPLESLGMQTVFDPNSADLSGVPAKP
+ESLFVGAVVQKTHVAVDEDGTTAAAASGVTVVAGAAPQQSPPAEMHVDRPFLFLIRDTVTGQILFLGQVS
+DPRG
+
+>gi|224536165|ref|ZP_03676704.1| hypothetical protein BACCELL_01031 [Bacteroides cellulosilyticus DSM 14838]
+MLMLKKTIAALSLLSILAACQNDENPSQPEPKPRQDINLTRAEQEFMDKGTDFAFRFFDQVCSTEKEKPN
+VFVSPLSASLCLSMITNGATDNTLAEMQDVLGFPANTFSLDDLNNYNQKLTSALLDLDNTTQLGIANSIW
+IEEGFKVYDSFVDVNKKMYDAQVQELDFTSPTAKDVINQWCATQTNNCIKEVIQEIPADARMYLINALYF
+KGIWKSQFDKSATGQDNFTNVDGSQQKVAMMNQTATFNYTQTDDFSIAELPYGNEAFSMVILLPSGDKTL
+DESLPSLNYENWKQWSKNMVGKELQIKLPRFKVEYDKELEEDMIAMGMKDAFDAYKAKFANMSGAELYIG
+LLQQFTYINVDEEGTEAAAVTVGGMFDNAVGFPSPVPFFVNRPFAFMVKEKSTGAILFMGKITEL
+
+>gi|147668783|ref|YP_001213601.1| proteinase inhibitor I4, serpin [Dehalococcoides mccartyi BAV1]
+MKIKHLFSLLAVASLFTLTACSGGVSAEELKSDKDRIANPNISQQDANIQAEANNDFAFKLYHFLKGTEE
+GNFFYSPFSISIALAMTYAGADTTTKTEMQNTLNYLLPDANLHAFFNFIDQELNKRESQAEEADAGTFEL
+KLVNAIWGQKNYTFLSDFLDTLAQNYGAGLRVLDFAASSEDARRVINDWVSEATKDKIKDLIPSDGIDST
+TRLVLTNAIYFNAAWAAPFEEEDTQNGLFYLQNGSSVSVQMMHQSEGHGYYNGDDFQAVELAYAGNSLSM
+VIILPDEGKFGQVEDALSGQMLTGILASIKYNQINLSLPKFSFESEFALKDALSALGMPTAFSGQADFSK
+MDGGYNLMIGDVFHKSFISVSEAGTEAAAATAVTMNLTSAPAEPVTLSIDRAFIFCIVDMATGTTLFTGR
+VLNPGA
+
+>gi|17228273|ref|NP_484821.1| hypothetical protein all0778 [Nostoc sp. PCC 7120]
+MPDTKIVDANNKFGFKLFSEIAKQDGNAKNISVSPTSVAIALAMTYNGASGSTQKAMAKTLELQGISLPE
+LNSGYASLNKLLQNPGENVQLTIANSLWVNQDVSLRPDFVQTTRDFYQAKVTNLDFQNVTAVNTINSWVQ
+ENTKGKIDKIVDNIEPNQALFLINAIYFNGKWSNAFDKSQTTPQTFYTASGQQKQHPMMSQTGEYRYYET
+PQFQSVSLPYGQDGKVSLYIFLPTKNSNLKAFSQNLNAENWEKWMPQFRNREGSIRLPRFQTDYDITLND
+ALKSLGMAEAFSNKANFSGIGDNLTISQVRHKTVIEVNEEGTEASAATSVGMVATSLREPQQPFKMIVDR
+PFFYAIRDNQSKNILFMGAVVEPN
+
+>gi|108762275|ref|YP_632451.1| serpin (serine proteinase inhibitor) family protein [Myxococcus xanthus DK 1622]
+MVVPRIQVVACCTAALLFAGCESTLCGSEPPTADASCLPPELEQAPGEYVASSAPRDGAPTIDEELAAFV
+SGNTSLGVALYQRAIQEKQNLFFSPYSVTQALSTVYAGARGNTEAQMAQALRFSLSQSRHHPTANALERA
+LAKPASPPPASGTPPTFHSLNSAWGQQGMTFHDGFLDTLARHYGAGMRLMDFENDAAGARAEINRWVEVN
+TRDRIQDLVNEESLPNATRLMLINAVYFKGAWSWPFREQGTRNAAFRALDGTSHQVPTMSGGRGQYMEGD
+GFEAVTLDYAGGTFRMVLVVPEWERFEEVESRLSPAFFKDVRARLENHQIDIQLPRFQIESELPLIPALQ
+ALGMEDAFTEGADFSAISPTKLRIATVNHKAFVAVNELGTEAAAATAVGMVPVSLPKPIHVNRPFIFVIE
+HVATQNVLFLGRFVKP
+
+>gi|73748140|ref|YP_307379.1| serine protease inhibitor family protein [Dehalococcoides mccartyi CBDB1]
+MKIKHVFSLLAVASLFTLTACSGGVSAEELKSDKDRIANPNISQQDANIQAEANNDFAFKLYHFLKGTEE
+GNFFYSPFSISIALAMTYAGADTTTKTEMQNTLNYLLPDANLHAFFNFIDQELNKRESQAEEADAGTFEL
+KLVNAIWGQKNYTFLSDFLDTLAQNYGAGLRVLDFAASSEDARRVINDWVSEATKDKIKDLIPSDGIDST
+TRLVLTNAIYFNAAWAAPFEEENTQNGLFYLQNGSSVSVQMMHQSEGHGYYNGDDFQAVELAYAGNSLSM
+VIILPDEGKFGQVEDALSGQMLTGILASIKYNQINLSLPKFSFESEFALKDALSALGMPTAFSGQADFSK
+MDGGYNLMIGDVFHKSFISVSEAGTEAAAATAVTMNLTSAPAEPVTLSIDRAFIFCIVDMATGTTLFTGR
+VLNPGA
+
+>gi|75910869|ref|YP_325165.1| proteinase inhibitor I4 serpin [Anabaena variabilis ATCC 29413]
+MNRQKFSGVKDSFLQRRYAVSLGRRYVLAAASVVLFSVLGCSQVNPDTSALAQTGVSPAESSLQKKTVVP
+DTKIVDANNKFGFKLFSEIAKEDGNAKNISVSPTSVAIALAMTYNGASGSTQKAMAKTLELQGISLPELN
+SAYASLNKLLQNPGENVQLTIANSLWANQDVSLRPDFLQTTRDFYQARVTNLDFKNVAAVNTINSWVKEN
+TKGKIDKIVDNIEPNQALFLINAIYFNGKWSSAFDKSQTTPQTFYTASGQQKQHPMMSQTGEYRYYETPQ
+FQSVSLPYGQDGKVSLYIFLPTKNSNLKAFYQNLNAENWETWMPQFRNREGSIRLPRFQTNYDITLNDAL
+KSLGMAEAFSDKANFSGIGDNLTISQVRHKTVIDVNEEGTEASAATSVGMVATSLREPQQPFKMIVDRPF
+FYAIRDNQSKNILFMGAVVEPT
+
+>gi|52078754|ref|YP_077545.1| proteinase inhibititor I4, serpin [Bacillus licheniformis DSM 13 = ATCC 14580]
+MKSKWSAMVVIAGLLLLAGCGALKEADPPRGRSAQKTEASFSEAEQRFALALFQDMIKEEGSRKNIFLSP
+YSIQQALLMTANGAAGDSRKELLSTLHLSQADMASINGISKSVNRSLETLPHGEFSSANSIWTKRELKES
+FQDAIKGLGDAYQLQIDPNRATEEINSWVKKKTKDRIDQIVDKVSSNTIAYIINAVYFKESWKHPFDPHM
+TAEQPFYSADGSAKKHPMMTQTNRFPYLENEHFQAVKLPFQDEGLSLAVFLPKKAANLEQLLTGMTHDQW
+RALQKGWTMKQVELKLPRFSFQTDYMLNEPLKRLGMKNVFSSANFSNMFTGHGAAQINKVRHKTFIKVDE
+AGTEASAATAVEIIESAPVPEVTMTADHPFYFAIVDEASGMILFLGSVAEPKDD
+
+>gi|125972714|ref|YP_001036624.1| proteinase inhibitor I4, serpin [Ruminiclostridium thermocellum ATCC 27405]
+MQKKLICFLVFALLSSFLFVGNSFADGNWKTYYELYPDPVVTDTSAVIRFKIIKVKIDDYITMPGYVYDV
+EYWKTDEPSNVMHSYNILWGESSKQISEGISEVVYRTELTGLEPNTEYTYKIYGQMPIRNKEGTPETITF
+KTLPKKLVYGELNGDGKINSSDLNMMKRYLLRLIDGLNDTACADLNGDGKINSSDYSILKRYLLRMIDKF
+PVEKEEKNEGVSENFIRGNSNFAFNIFKEINKDEQGKNVFISPFGISTALSMVYQGAKSDTREEMAKVLG
+YEGLDIEEVNKSYKYLLQYFNGLDNDTKIKSSNSIWMNSLHGNAIKEDFISTNKDVFDALAETRDFSDKG
+VVDEINDWISKATEGQIDKMLSEIDMDMLAYIISALYFKGTWTEEFDIEKTVSVPFASEDGGADHVMMMR
+KELCTIEFGEGDGYKAVRLPYGDGEMAMYCILPDEDTSINDFIQKLDLSMWEKIKNSITKRENGTIYLPR
+FKMEYAKGESGSIMESLKALGMKKAFEEDADLSGMTEADAFISDVLHKAVVEVNEKGTEASGVVVIPIAP
+TSIAPGPKFIANRPFAFVIADEKYDTILFMGKLCDGGLIN
+
+>gi|162456736|ref|YP_001619103.1| serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member [Sorangium cellulosum So ce56]
+MDGARAGSGLRQGLLCQNGPAVRRMSWFGGAPRAAARSLRAVRLGNTRARDRGRRGTADAGPGGMQRTIR
+TCAPLLVLSLAAILGCETSTDSNRNPDTGGEECSDSDSAICVIASDKQRISSPDVPPEDKTALVSGNSAF
+ALDLYQELRQEPGNVFYSPYSISTALAMTWAGAKGGTETAMADTLRFDLGQDRLHPAFNWIDQELESRGQ
+GAQGADGEGFRLNVVNALWGQNGYSFETPFLDTLGLHYGAGMRVVDFVGHRQESVDLINGWVSDQTEGKI
+EKLVPVDAITAETVLVLTNAIYFNAAWRTPFEPTATADGAFETVDGTEVTVPLMRGSLEMPYAEGDGYQA
+VAMPYDGDELSMVIILPAKGTLDAFEASLDAAKVDSIAGAMSEHLVDTTMPRFKFEYELSLKKTLEAMGM
+EIAFTPGVADFTGINSSGQPYIQDVIHKAFVGVNEAGTEAAAATAVIVGDESAPQPASLALVNPFLFLIR
+DNATGSILFVGRVADPSAS
+
+>gi|162449834|ref|YP_001612201.1| alpha-1-antitrypsin-like protein CM55-MS [Sorangium cellulosum So ce56]
+MRTATLLTAVGLSALVGCSSGRGGNAGGGGSGQGGGGSVEAPVECFEVKPGCVVPSEVTRIENPDVSAED
+RGSLSRNNASFALDLGRALHSSTTNVVYAPFSISTALAMTYAGARTTTEQAMAAAMRFELPQERLHPAFN
+HVDLQLRKHAEEGGFRLHTANGIWAQIDVPLEKPFLNVLGESYGAHVRLADFVTATKEAEGLINAWVSHR
+TEGKIPKLLDEDVTPETVAVLVNAVYFHAQWKTAFVKDATQPGTFLRGDGSSVTAQMMNGRHQGSYGDGD
+GWEAVGIPYAGSAVSMFLVLPAKGTTDAFEESLDGAALEAIIDSTYQQPVDITMPKFSFGTSTSLKGALM
+DLGMEVAFGDEADFTGIVAGMKLWIHEVIHAARIDVDEAGTEAAGSTGVILNSSGSGLPAAPAAIVLDRP
+FFFFIRDASTQAILFAGRVNDPTAR
+
+>gi|51894163|ref|YP_076854.1| serine proteinase inhibitor [Symbiobacterium thermophilum IAM 14863]
+MDPNLASAADRFGIRLLQEVHRERGAGNLFLSPASAQIILSLAANGARGETREEMLEAMGYGDMDLGAVN
+RAIADLRGILAHPGAGVELTAANAVWHQKGMTVAPAFREVAVQQYGAQVRETTFGEPASAEAINRWVSDQ
+TRGRIPQLVEGTRPDDVMWLVNVLYFKGAWQKPFDPARTYDRPFHLPDGGTAEVPFMHQTAVFGYLAEDG
+LVGVRLPYGEGDLALYAFMPDEWEGFVEGLTPERYAGWVERMGRQEIRLAFPKIRLTDRAELADPLAAMG
+MERAFTPGRADLGGLFEGSRELFISRVIQKTFLEINEEGTEAAAATGVAVTVTSAPAGQPPEVVLDKPFL
+LAIRDDRTGVTLFLGAIADPS
+
+>gi|209526029|ref|ZP_03274562.1| proteinase inhibitor I4 serpin [Arthrospira maxima CS-328]
+MKKLWANSCQYIGLLIATAVMVAVSGWAVDQIPDSHLTSDLSAHQTTENMRINYQVAAAYTGFAFKLFDH
+VYQHQSQENIFISPASITNAMAMTYNGAAGTTQEAIAETLQVQGISLAELNQANLALNNSISAINQDVQI
+NIANSLWLHESAFFLPDFLDRVNQFYQAKLTAVDFSSPDTPSQINDWVKQETNGKIAQIVQTIPNQTILY
+LINAIYFKGRWSEQFDEERTESQPFTLIDGSQKIHPLMFKFGNYLYLENSDFQGISIPYGDDARFSLYVF
+LPRENVSIDRFYTRLNATQWEEWINQMRSRPGSLRLPRFKLEYEVGLNDSLKSMGMDIAFHPNQADFSNM
+TLDNNVRISEVKHKTFVEVNEEGTEAAAVTSVTILSESTPSITEPFSMVVNRPFFVAIRDNQTRTILFMG
+SIVDPEL
+
+>gi|67922196|ref|ZP_00515710.1| Proteinase inhibitor I4, serpin [Crocosphaera watsonii WH 8501]
+MRTLKNTKAALSFLSILCCLSGLIAVSKTDMTAIFKDVKGLREVSPRIVFPQRTLQERHLVDAQVRFGFK
+LFSTLTKSQKNENILISPTSIALTLSMLYNGATGTTQKEIAQGLALRNINANTLNRANQTLYNDLNTHGL
+YNSLIVTNSLWAKEGFSFRYQFRKNSRKYYQAKISNLDFSSSEAGGIMNRWVKEETQGQVRKIMDSTQAD
+DVLFLINTATFQGLWEMGFDRDLTRDKPFYLKNQSVKNYPFMSRKGTYKYLETPQLQAAELPYANGRFSL
+YLFLPKPESDLPTILEEITAKKSRKLLSKFRKRQGVLELPRSQLKDELNLTNALKELGYSTMFDPDKAEF
+SQLSSHPTYISGMKHQTILVINEEGVTSPPEDDLLIKKASMDNTKEEFSLTIDRPFLSIIRDNDTGNVLF
+MGMIYEP
+
+>gi|240168538|ref|ZP_04747197.1| serine protease inhibitor family protein [Mycobacterium kansasii ATCC 12478]
+MIAAAVVFASALGCGGDRNRAQSTPGPTPAPVTRSSLPYDNTPDVAPADEQRFVNATNGFGLDVFRRMSA
+ASAKNLVFSPLSLSVALSMAYAGAAGDTAAQMKTVLRDPFGNDSYYRAMNQLLLDLRSRNRAAISAEDPR
+SIELAMVDAVWLQRGLTVRAPFLDILATQYDAGAHLGDFKGNPDGERVTIDNFASDATKGQIKDLIPPGA
+IDDLTRMVLLNAAYLKASWESPFPKERTADGSFRVTPQSAVTVPMMHKARVLRYVAASNFQAVELPYVGE
+DLNMLIVLPAEGQLQAVRNSMDDAWFRDLAFVQGPVDLSLPKFRISWGPEEFKETLAAMGMPRAFDEKQG
+DFSHITTDEQLKITHVLQKAFVGIDEFGTEAAAVSTVIGGGFGPVEEVTVDHPFLFAIVDKTGAVVFAGQ
+VMDPR
+
+>gi|150389934|ref|YP_001319983.1| proteinase inhibitor I4 serpin [Alkaliphilus metalliredigens QYMF]
+MIKRTAIVLLTALLLISTTGCGSLFNTVTVHEYNEDKVASSVMEGNNQFAWDIFKELNQEDSGESIFISP
+LSISTALSMTYQGAEGTTKDGMAEGLRYQGIDMEVLNESYRELLKYMNNMDQGIELNIANSIWAREGGGF
+KEAFLDINQDVFDAYVTELDFSKADSADKINGWIEDATEGKIEEMIQGPISSNVLMYLINAIYFKGSWTV
+PFEEAQTFDGEFFTEDGDVNDIKMMRRNGKVAYGDGVDFTAVKLPYGNESTSMYVILPEENTSINDFIGS
+MDHKKWNEIREGISSQKDVELQIPKFELEYGIKELNNSLANLGMGEAFGPAADFSKIREGIFISEVLHKA
+VIEVNEEGSEAAAATVVVMTESAMADPLSFVANRPFMFVIANDESDTILFMGKLSGIN
+
+>gi|51894162|ref|YP_076853.1| serine proteinase inhibitor [Symbiobacterium thermophilum IAM 14863]
+MTGCGSPGLASPPPRPDAVDPALSEAADRFGIELLRAVYDQRPDANLLLSPASAWVILSLAANGARGETQ
+REMLAALGYGDAEMGAVNAHMRDVWGIMANPGRGVKLTAANAVWHHRDFAVVPAFREVAAKQYGAEVFGT
+TFGRPEAAAAINRWVARRTRDRITDLIDRTYAEQRMALVNALHFKGEWQEPFDPDRTEPGPFRRPDGSEV
+QVEFMHQTETFGYLAEEGLVGVRMPYGEGDVALYAFMPDEWDGFVVGLTPERFRGWIDALAETRIRLAMP
+KVRFTDRHDLSEALQALGMERAFDDRRADFGGLLVTDEPLYIGAVIQKTFLEINEEGTEAAAATVVGITA
+GAAPPPQPPEVVLDRPFLLAIRDDRTGMTLFLGAVVNP
+
+>gi|188585351|ref|YP_001916896.1| proteinase inhibitor I4 serpin [Natranaerobius thermophilus JW/NM-WN-LF]
+MISPISVNYALYMTYSGADGETKEEMETALKLNGLDSEELNEQMHHLANYLEYGGVDLQIANSIWGRKNR
+VEFLDTFQDDMKDYYNARMEELDFNDPEASDTINNWVAENTEDKIEEMVPDNIPNGVLVYLINAIYFNGN
+WDIPFPEENTREDTFITEKGEERTVDMMSISEEEFSYLENNLFQAVALPYEDESYQMTLYLPQEENSLED
+FYNEMNSQNWKKWQKEFMDLEGEVKLPKFKMEYEIELNDVLKDMGMETPFEDADLSKMFHQSQGIYISEV
+LHKSFIEVDEKGTEAAAATSVAVEEAASMHEFQIEFNRPFFYAIENTEVDTILFMGVVHDPTLD
+
+>gi|23100626|ref|NP_694093.1| serine proteinase inhibitor [Oceanobacillus iheyensis HTE831]
+MTEVSEASNLLAFQSIQSLDPNREGNVFVSPTSYWLAMAMVYNGANGDTRSEMDQALQLQGINVEDFNRQ
+NAALMEHFTSVSDEDVELSIANSIWLNQDYEFLDTFHQSVTDTYEAELAPLTTPERINEWVSNQTNGKIK
+DIIKQIDPEHVAILVNATYFNGAWTYPFDENNTQERTFYKEDNSSVDVPFMALNEELPYVQTDQMQAVSL
+PYGENEDMQMELFLPNENIEMNDFLEGFTLENWQEWRDSMETQKGNLRMPKFSLEYETELQNFFQSLGMQ
+QAFDAQKADFSNMIDQEQIGDLYIDKIVHKTFLDVDEEGTEAAGATSVEMKTTSIEIGESFDMEINRPFL
+LTISDKETDSILFMGMIHEPTSVD
+
+>gi|223466033|ref|ZP_03617569.1| hypothetical protein PREVCOP_03074 [Prevotella copri DSM 18205]
+MNKKVFSAAILASAAMAMTSCSSSKNAQNESATKAEKITEAEAARLSADEEMDESYLILSEAQQNIVKKN
+NDFAFRLYQQISGMDSEVVSPMSIAYLMGMLANGADGKTQQEILKAIGCEGVSVKELNDCYKALMLSAGK
+LDKQTTVNIANFIAINKNFTLNSDFARTVADSYQAGVESMDFTNSKSAARINDWCKKQTKGMIPSIIDQV
+DPAAVSYLLNAIYFNGIWQEKFDAKNTRLENFSGYTRDIKKVNMMHQNKKFAYTENDMLQAVELPYGNGS
+YQMTVLLPKAGKSISEVMKEMDADKLQKLSNDMDRCQVDLKFPKFTTEMDLSLNQIISKLGAPSIFQPGT
+ADFSRFANGSFYVSKMLQKAKIEVSERGTKAAAVTAAVMLTSLGPHEMKRVEFHANRPFVYFITERNSGA
+ILFMGQFLGE
+
+>gi|126660474|ref|ZP_01731582.1| Proteinase inhibitor I4, serpin [Cyanothece sp. CCY0110]
+MRGLHEVSPRMIFPQPTLQEKQLVDAQVEFGFKLFSTLTKNQKPQNIFISPTSIALTLSMLYNGATGTTQ
+KEIARGLSFHDISVDTLNRGNQMLQHDLNSHPSYGSLAITHSLWAREGFSFRYQFLKDSRSYYQAQITNL
+DFASSEAQGIMNRWITEETQGEIQTIVDSTQADDVLFLINTASFQGFWKTGFDRNLIKDKPFYITDTSVK
+IFPFMSREGIYNFLETPQLKAIELPYDNDRFSLYLFLPKPEYNLSKMVEKLTAEKLSKLLSKFRKTQALL
+ELPRFRLNYEVDLTESLKSLGFSTMFDPAKAEFSELSSHPTYVNGLKHQTLLVLDEQGIKPATPNNFVVE
+TASVDNVVEKSSFIVDRPFFSIIRDNQTGNILFMGVIVEP
+
+>gi|257055420|ref|YP_003133252.1| serine protease inhibitor [Saccharomonospora viridis DSM 43017]
+MPERDAVQAHLNFALAVHRASGSPNGNACFSPYSVAGALGLVTRAARGETASQPAALLAGAPERVSEQAD
+LLRAAAVLDAPARGQDEPTLAVSNTLWVWRRLEVKPGFTDVVAEWPSGAVATAPFVEDPEAARTTINADV
+ARTTRDLIPELLLPGTIGGDTVAGLVSALYLKVAWTNPFRDTDTVEDDFHTPTGVVRVPMMRQAERLGYA
+RHAGWQLVDLPAVGGVSASVLLPDRPLVEAEPELDAATVDALLNARREAMVRLTMPRLSLDVRCPLKDTL
+NSLGVRTMFTPTADFGELSDDPRLLVSDVLHQSVLRLDENGLEGAAATAAMMRLVSAPAGEPVTVEVNRP
+FLLLVRHRASGAVYFLARVTEPWSR
+
+>gi|218438979|ref|YP_002377308.1| proteinase inhibitor I4 serpin [Cyanothece sp. PCC 7424]
+MIKSKGLLSALSDIKIKEKAVFVTTSLTLLFISGWLAQYSSNAFEFVATSQVTYPFYALMPSLKQTNSQQ
+QLLEANTLFGLRLFQTLVSEDPNQNVFVSPPSVAIALSILMQGANGKTREEMVSTLGYEELNVKEIHTTH
+QILLNSLQQDNPNLDIALANALYARDGISFRHQFLKDNELYYQSQITNLNFASPQAAGIINRWTREHTQG
+KIDQIVPHINPKDTLIVVNAIYFKGMWKHKFDRQQTKNQPFYLPNGKTKQYPLMSGKGKYQYYENEQFQA
+VNLPYGDERFSLYIFLPKSGSNLSSLLSQLTFQRWNEWIQEFNVKQGSLQIPRFTIEYESNLKQALSTLG
+MKSIFSQGDFSNMTSSAVVVNEIKHKTLVEVKEEGIEPPSSTSPEVEGKNTFTMIVNRPFFCAIRDQEKG
+IVLFMGAIVDPN
+
+>gi|255528220|ref|ZP_05395041.1| proteinase inhibitor I4 serpin [Clostridium carboxidivorans P7]
+MKNKLLIAIIFSAFLLIAPSVKAANYTDYQTVDKNKTWTIVFNGNVGFDDVTKQAITVTDSNGNPVNVSI
+QSGTDSKTVIVTAPQEGYTSGESYILNIGTKVHSNKGKALKKEYKLHFNIENDTDTMPIKTIDINEDSSV
+IQGNNNFAFNLMKQLTNKDKDKNIIISPLSISTILAETQNGANGQTKDEILNAIGLKNIDDKSINEQYYN
+TLNYYNSLNYMSSNSARLRVADSIWVNKNLSLTKSFVDTSKKYYNSEVNSVDFGAPDTVGTINQWVDKNT
+DGQIKKAINNIDESEKAILVNAISFKGAWENEFYPNNTKQEDFTLSSGEKVKIDTMQSTITNSYLKEDNF
+QAVRLPYYGGLEMDLFLPDRAVSVNDFMKEATKENFDKWLKEFSVADVNMKIPKFKLEYEEDNMKDVLKN
+LGMQQAFDPEKSSLDGISKSTFISDIIHKTCISVDEKGTEAAAITVEIACGSPAPVEHEKVDFVVDRPFV
+FAIRDCKTGAVIFIGKVENPRG
+
+>gi|192810220|ref|ZP_03038893.1| proteinase inhibitor I4 serpin [Geobacillus sp. Y412MC10]
+MRKKKILTGLCLLVGLTACAQDSGIQPGESQGIMHKQTKVKELSAQERKEVLGKVNAGMVKAQNDFGLRL
+HQALSDNPEYTSDNLIISPYSITQALALAYNGTAGDTAAEMADMLGWRGMNDAGINEGNRQLRSLLENGG
+GVVLNVANSVWHRPGLKLKEAYAEAVKDSYGAEVRETDLQQEDAMHEINQWVKDKTSGMIPKIYHEPPGG
+VAVLINAIYFNGGWTDEFDPANTVDEEFTLTDGTTQQVPMMKREDRYSYKEGESWQAIRIPYGDGRMHML
+VILPKESSTIDKLHRQLWKDASVWKGDYSFETVQLSLPKFKAEQSFELPDALKSLGMVKAFDAAEADFSK
+MAEQGDGFWIDHVTHQTIVDVSEKGTKAAAVTAVGITESAEPTEPIAMNINRPFFFAIEDRDTGAWLFMG
+SVLKP
+
+>gi|229206007|ref|ZP_04332464.1| serine protease inhibitor [Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111]
+MRLLTRRRTLAVEEGRSVRWRPDAGAESEQEPMQTSTSPRRDHLEFAAALDRVLTRQGESHVWSPHSVGT
+VLALLATGARERTLAELEALLGADVRGQLEALDAAVAAEPGLDLASLNGLYVPADLEVLPGFTSRVRERA
+GAEVEHADFEHDSEGVRSRVNARVAEVTRGLIEELLPAGSVHPGVRLLLVNALWVKLAWPDPFDPARTRD
+RPFHAPSGRRKVPTMHRSARLPHARARGWSMVSLEGDHGLTLDVLLPDERSAAPAPVTADALADLYAHRS
+SQQVDLALPRFEVETDTSLLEPLAALGVRDLATDEARFDGISPEPLRADEILHQSVLRVDEKGAEGAAAT
+AVMMLRAAAVAPRPVAFTVDRPFVFVLRRGGAVLFLGRVTDPVDPGPAS
+
+>gi|255531798|ref|YP_003092170.1| proteinase inhibitor I4 serpin [Pedobacter heparinus DSM 2366]
+MKKNYKLRLVVAVLMCVATSCKKGNKTPDTGKDLILTEREQQKAEADNAFTLKLFKEIIAKPLAGKNLML
+SPLSVSIALGMTSNGSSGTTLEAIRNTMEFKDFTEAEINSYYHKIATELPQLDPKASLKIANSIWYRNTF
+TTLPAFLNVNRDNYNAAVEGLDFANPAAKDKINNWVNNSTNGKIPTIIDAIGSDMVMYLINAVYFKSDWK
+YKFDKDKTAKSDFNLDANNKVQTDFMVAKATVNHLRSEEAYIYELPYGNEKYSMVIALPATNTNIAEFVA
+SVSPAKWKGWMAGLQKTGVEIKMPRFKFSYSSILNDQLTNLGMGIAFGKTGAADFSRMSAAGLQINEVKH
+KTFVEVNESGTEAAAVTSVGMELTSVQEPAPVLINRPFVFVIREMKTGLILFTGIVNNPLLDN
+
+>gi|162453653|ref|YP_001616020.1| hypothetical protein sce5377 [Sorangium cellulosum So ce56]
+MRTSIVLATVLMSALAGCSSNDGGGTGGGGPDQGEGGSGQGGGGGAVECFEKKAGCVLPSDAARIESPVV
+SEEDRVLLARNNASFALDLGRAIPSENGNLVYSPYSISTALAMTYAGARTTTEQAMAATMRFELPQERLH
+PAFNYVDLELRKRAEGSSNVEGGGFRLHTANAIWSQIDLGLEQPFLKVLGENYGARVRLADFSVPDEAES
+LINAWVKDQTEGMIPQLLNKNVTPETLLVLTNAIYFDAAWHTPFSESATKPGAFQRGDGTSVTAQMMHGT
+QPETRYGAGDGWEAVEIPYAGTPVSMFLVLPAEGNADALAESLDGAALETIIASTQSRSVDITMPKFSLD
+TSASLKKALVDLGMGAAFGPSADFSGLIPGGGVQIQDVIHKAVIDVDEAGTEAAAATAVLIAATGAGFFP
+EPAEIVLDRPFFFFISDLPTGALLFAGRVNDPTAH
+
+>gi|196251708|ref|ZP_03150375.1| proteinase inhibitor I4 serpin [Clostridium thermocellum JW20]
+MLPGFALLSSFLLVGNSFAANWYTYYELYPDPVVTDTSAVIRFKLTTEKIDDYITMPGYIYEFRYWKVDE
+PSKVKSVSIGLYVNEVQTVELTDLEPNTEYECKVWGQIYTSDKEGTPKTITFKTLPKKGDLNGDAKINST
+DLNMMKRYLLQMIDRFGVDDESCADLNGDGKITSSDYNLLKRYILHLIDKFPIGNDETDEGINDDFNNET
+DEGINDGFNDETDEDINDSFIEANSKFAFDIFKQISKDEQGKNVFISPFGISMALSMVYQGAESDTREEM
+AKVLGYEGLDIEEVNKSYKLLLKYFNELIGNVKLKNSNSIWKNSLKGDVIKEDFISVNKDVFNALVETRD
+FSDESVVDKINNWISDATEGKVKKALNAVNPDELLYIISALYFNGAWKEEFEFDINDTTMSTFKSEDGST
+DYVMMMRKSYNNWVGVMEFGKGDGYSAIRLPYGNGEMAMYCILPDEDISINDFIQNLDVSLWNEIKNSIR
+KTLQGLICLPRFKIEYFKDGNGSIKESLKALGLEKVFSLAEADLTGMSETNAYVSDVLHKAVVEVNEKGT
+EASSSVVVIPVPGFGTRSEFIADRPFVFIIADEKYDTILFMGKLAKGELIN
+
+>gi|125972715|ref|YP_001036625.1| proteinase inhibitor I4, serpin [Ruminiclostridium thermocellum ATCC 27405]
+MLPGFALLSSFLLVGNSFAANWYTYYELYPDPVVTDTSAVIRFKLTTEKIDDYITMPGYIYEFRYWKVDE
+PSKVKSVSIGLYVNEVQTVELTDLEPNTEYECKVWGQIYTSNKEGTPKTITFKTLPKKGDLNGDAKINST
+DLNMMKRYLLQMIDRFGVDDESCADLNGDGKITSSDYNLLKRYILHLIDKFPIGNDETDEGINDGFNDET
+DEDINDSFIEANSKFAFDIFKQISKDEQGKNVFISPFGISMALSMVYQGAESDTREEMAKVLGYEGLDIE
+EVNKSYKLLLKYFNELIGNVKLKNSNSIWKNSLKGDVIKEDFISVNKDVFNALVETRDFSDESVVDKINN
+WISDATEGKVKKALNAVNPDELLYIISALYFNGAWKEEFEFDINDTTMSTFKSEDGSTDYVMMMRKSYNN
+WVGVMEFGKGDGYSAIRLPYGNGEMAMYCILPDEDISINDFIQNLDVSLWNEIKNSIRKTLQGLICLPRF
+KIEYFKDGNGSIKESLKALGLEKVFSLAEADLTGMSETNAYVSDVLHKAVVEVNEKGTEASSSVVVIPVP
+GFGTRSEFIADRPFVFIIADEKYDTILFMGKLAKGELIN
+
+>gi|172036032|ref|YP_001802533.1| proteinase inhibitor I4 serpin [Cyanothece sp. ATCC 51142]
+MVMRTLKMTKATVGFLSICCLGGLIAISKTYLSNVFTDVRGLQEVSPRMIFPQPTLQERQLVDAQVQFGF
+KLFSTLTKSQKNENIFICPTSLALTLSMLYNGATGITQTEIARGLGFNDISANTLNRANQTLKQDLNSHD
+FYRYLTMTNSLWAREGFSFRYQFLKDSRSYYQAKITNLDFASSEARGIMNRWVTEETQGQIQEIMDHTQA
+DDVLFLINTASFQGVWETGFDRNSMEDKPFHLIDQSVKTYPFISRYGTYNYLETSQIKGVEIPYENGRFS
+LYLFLSKPENNLTQIVQELTAKKLSKLLSKFQETNLLLELPRFTLNYEVDLTESLKKLGFSTMFDSGKAQ
+FSELSSHPTYVNGIKHQTTLVINEQGVKQTPQKNLVVKATSVNNVTEQMSFTADRPFFSLIRDNETGNIL
+FMGMIFEP
+
+>gi|225022888|ref|ZP_03712080.1| hypothetical protein CORMATOL_02934 [Corynebacterium matruchotii ATCC 33806]
+MTLADDALNGDFTPIDGDQSDLMTIGFSLVGSPNTTAGSDNLPAKPNTVVSPVGAAAAAGVIAEGAANGT
+TKIDPKQLQPAWTMWHPWAGPPAATPQDIPVIAAVARLLAAPEVPIKPAYRDTIAGWDVPIETGAITQEN
+LDDWVNKSTAGLVNKSGIDATRGDINFVLQNAITFAARWRERFNANKTRQSQFTKTTGETIMVDMMWLSR
+TTAPYTVSDGWRGVRLDYTDGELAAFVLIPDADPGQVTPTMLKQAVSQLCRPNETTGLVRVGLPKLRLTT
+KKDLIPFLQYLGLAGNIDLPTMTNANPVDITQAVQQAIMLVDEEGTVASAVTEVGGLAGAAPGTIPEQPI
+DIIADRPFYLVIGDVETGTPLFLSRISDPAA
+
+>gi|149922543|ref|ZP_01910973.1| serine protease inhibitor family protein [Plesiocystis pacifica SIR-1]
+MIEWEPPRHIRGMTSSKLLFPRRFALAAFALTALTLPAVACTEAGEEEEGVDDVGDDDGDDDEGEMELWE
+SVHSELDYDDQPDADEVERLDLAMDQLALGLDLYHYMGEGAFEGQNVVNSPVSIQTAFGMLYGATEGVTK
+TQMESTLHFTLGEERQHVAMNWQHLQLASREMPKLESEFANEDPVILGTANRAWINEARSEELIPDFLDL
+LAVHYDTGVYLADFNSNADGERIAINGWVADRTHGLVQDLIPVIPDGSSMVLVNTLYLKAPWATPFEEFA
+TQTASFTLLDGSTRDVQMMQQYAMNGYYGEGEGYAAVGVPLRGNSLELALVLPEDLASFEAGLDAETLGG
+ILEGMDYATIDTSMPRFELRAKASLKQALTDLGMPAAFDNGEDFTGVLTNGMGPIFDVIHEAVILTDEGG
+IEAAAATAIVQDEGGGGELEPEYTFVADKPFVVVVYDRPSRTPLFVGRVVDPGAGD
+
+>gi|23100627|ref|NP_694094.1| serine proteinase inhibitor [Oceanobacillus iheyensis HTE831]
+MKKCFLIIPILGLFLLFSACGTDDNSVTGGNSTSDNPPTTKIDTSVLVNDANQASNHLGFQALQRLEGND
+EDNIFVSPLSIWLAVSMAYNGANGDTKDEMTNALQPENIDLQTLNEHNGTMMDQLNQHDDVELNILNSIW
+LDPEFTFLEDFEHQVTESYNPELGPLTTKEPMNEWVSEKTNGKITDLIEKVDDDHVAFLLNATYFNGNWK
+YPFDENNTQDGLFHLDESSTTEVPFMSLDEELPYWETDEFQSVALPYGEEGNIQMEIFLPNENIELQEFV
+NKLTLEDWQNWRESMQETVGSLKMPKFSLEYESELQDFFQVLGMEKAFEEKEADFTNMIDPAQLRGNLYI
+SKIMHKTFLEVDVRGTEAAGATSVEMKEESAVVSPAPFDMEINRPFLLTISDKETDSILFMGMIHEPTST
+
+>gi|119961090|ref|YP_946526.1| serpin (serine proteinase inhibitor) family protein [Arthrobacter aurescens TC1]
+MNRVRKATTLIAAAALVSGSATISACAPQPADVGLLTADGVTRVSVQTADYSAQLEAFNASARKLGVTLL
+ADGGDSGSGNVVSSPASLLIALSMLRSGASGVTAAEMDSVLGLPAEGRDEAMNALLASLEKFDGDPGSVD
+EENPPQKPVMHAANGLFVDKGVPTGEAFLTTLGKHFGTGVYPVNFRDEAVTKPAIDQWVSKNTGGRIKEA
+PAQYSPDNTFSLLNALYFAAAWQAPFDANDTADSPFTKAGGEVINVPSMHSSLTMAYAEAPGWKAVDLPY
+AEGFVMRLILPDGGASGPDGPAAVSAEVLADVARELSGAQQDMVHISMPKWDHKTTFELRKVFETLGLKD
+MLATSTDFDSIQQGMKLTQAAQAANITVAEKGTIASAVTQINAEASSAMVPERKIILDHPFHYQIVHSET
+GMPLFTEWVADPR
+
+>gi|162453652|ref|YP_001616019.1| serine protease inhibitor [Sorangium cellulosum So ce56]
+MAQAHRPLSHDSPPTAFPSSLSGSACGSSWHSLSLIPPAARGSSGQSRVFSRGGALAWCLQSASAMRTTI
+LLATMLMSALVGCSSAQGGGTGGGGPGQGEGGSDQGGGGGDSPEAPVECFEKKAGCVLPSGAARIESPDV
+SEEDQALLARNNASFALDLGRAISSANGNGNVVYSPYSISTALAMTYAGARTTTEQAMAAAMRFELPQER
+LHPAFNYVDLELHKRAEGSSNVEGGGFRLHTANAIWSHVDLTLEQPFLTVLGESYGARVRLADFDAPEEA
+EGLINAWVKDQTEGMIPNLLNGSVTQETRVVLTNAIYFDAAWHTPFNEGATKPGEFQRGDGTSVTAQMMH
+GTRETRYGAGDGWEAVEIPYAGTPVSMFLVLPAEGNADALAESLDGEGLETIIASTQSRSVDITMPKFSF
+GTGASLKKALVDLGMSVAFGDSADFSGIRKGGGLYIQDVIHKAVIGVDEAGTEAAAATAVLVAESSAAAG
+IFLEPVAIVLDRPFFFFISDLPTKALLFAGRVNDPTAQ
+
+>gi|163813927|ref|ZP_02205321.1| hypothetical protein COPEUT_00080 [Coprococcus eutactus ATCC 27759]
+MKKRITALLLSACICAGLAGCGTNTPGNNPGHTKPDSSVTSLTDNISVTPVKTDITSFDQLKNGINEFSM
+NMYSALPADKNIFYSPYSIASALSMLDVGADGATKKELENALGITDLDEWNDEMKAYLSKDWSQNTFVNT
+ANSVWMNKDTSWSADIEKDFLTPAKDYYSGEVYEADFNGQPDKVVQNVNNWVSTNTNKMIPEILKEIPGG
+TVMMLINAVYFEGKWDTPFTEDKTFQSSFYGTDKESVVDMMHLYGEHFTYMDNGEIKGITLPYDGDNVVM
+KVFMPTADDGDINELFDKLSNEEKQKLIDSLDNANNVEIDTLQLPKFTDEQSIDGLDEILQNMGIRSAYS
+DSADFSKIADGIAVSSVNHRAKVIVDENGTKAAAETDIMVKETAMMPSEETYNFIVDKPFVYVIEDQSTG
+MILFMGRVNSL
+
+>gi|239626096|ref|ZP_04669127.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
+MAAVFCGAVFLGGCAGTGSASVKAPAPKTVNYKADDYDSWNELMQENQISDSFKDALEQFAFQSGSRVLR
+EGHGNVNYSPLSLYYALAMAGCGADGETAAQIMDSLGVQDQSQLSGQCRKLYQWFYYDGQHRKSRNQEYK
+EGDDSSIELANSLWISNQLKLKKDYRKMAAAQFFASSYQVDFTSREAGIQMGKWISQETDGVMQPELQLP
+SDTMMAILNTLYFYGGWKGAFSVAETADDNFTKTDGSQVTCSFMNRVDNSGRFRKGAYCTVSALATGNNC
+SMVFLLPDQGHSVDEFLNTPEQLETSMDTDYRKWKSGKVTWKVPKFSFGSTFELTGLLQDMGVEKMFVPK
+AEFSKISESPLFVTNVIQETHMGIDEKGVEGAAYTMIVLEEAGIFMSEEKLEADMILDRPFIYGIQDNRT
+GTWLFLGVCRNPADRQ
+
+>gi|160894943|ref|ZP_02075717.1| hypothetical protein CLOL250_02493 [Clostridium sp. L2-50]
+MLVLFISNHERNGGFFMNKQIISLLLGACLCTSLAGCGNADNNGGSVTKQKLLASKELGSDIAVGAKPAP
+VDSYEELKNGVNNFAFDLYDALPKDSNCFYSPYSISSALSMLDQGAGGETKTELESTLGIKDLSTWNTEM
+QSYLNKDWSKQTYVNTANSIWMTTGKDWASNISDDFLLPAKTYYHGEIYEADFTDHADQVVKDVNNWVNE
+HTNQMIPSIMNELPTNTVMMLINAVYFEGKWQTPFTEDNTYDDTFHGTSGDSTVPMMHLYDERFSYADNG
+SIKGIVLPYDGDSVVMKVFLPSKEGDTITNLFDALSSDEKQALIDSLDNADSPEIETIQLPKFTDEQSIN
+GLDDILNRLGIRSAYAFADFSKIADGIAVSSVSHKAKVIVDENGTKAAAETDIIIKETAMMPPEETYNFI
+VDQPFVYVIEDQDTGMILFMGRVNDL
+
+>gi|37521415|ref|NP_924792.1| serine protease inhibitor [Gloeobacter violaceus PCC 7421]
+MADRVEVPTFIQMREANWRFGFKLLSLINEAPLRANRERSPLAVERNVLLSPLGLGITLGRLLPSLSETA
+QRAVASSLEWPNDGLIEPQSATALLAAQLTGADPQVQPVHAGLYWVEPGTPVKLGRDLSGNRVLESAFQD
+GAAPPEINRWIAAATGGQIGEALIPGPRRPGPLVVVDATVFEGIWSRAFNPQSSLQAPFTLLDGKQTTVW
+QMSRTGSFRYYETPGFQAVQLPFGGDGEWSMAVFVPAAGVPLRSFVRNLSDEKWRLWFEQFRMRDGSVTL
+PRLRLRYGQDLRRALRALGMRSAFTRSEGEESLGEAGLLIDAVDHQTAFTVSETGLTRPSAATGGERFAL
+PLRPGETPFTFSADRPFMFAVVNTYSGFVAMLGTVIDPTQP
+
+>gi|252127031|ref|ZP_04836974.1| putative proteinase inhibitor I4, serpin [Corynebacterium matruchotii ATCC 14266]
+MNRRRFLALFALTPGLATCTTSKTPTTTTMTPTFSFPTPTNTPEPPEPPIVLADDALNGDFTPIDGDQSD
+LMTIGFSLLGSPNTTAGSDNLPAKPNTVVSPVGAAAAAGVIAEGAANGTTKIDPKQLQPAWTMWHPWAGP
+PATTPQDIPVIAAVARLLVTPEVPIKPAYRDTIAGWDVPIETGAITQENLDDWVTKSTAGLVNKSGIDVT
+RGDINFVLQNAITFAARWRERFSINKTRQSRFTKTTGETIMVDMMWLSRITAPYTVSDGWRGVRLDYTDG
+QLAAFVLIPDADPGQVTPTMLKQAVSQLCRPNETTGLVRVGLPKLRLTTKKDLIPFLQYLGLAGTIDLPT
+MTNVNPVDITQAVQQAIMLVDEEGTVASAVTEVGGLAGAAPGTIPEQPIDIIADRPFYLVIGDVATGTPL
+FLSRISDPAA
+
+>gi|255690366|ref|ZP_05414041.1| peptidase inhibitor, I4 family [Bacteroides finegoldii DSM 17565]
+MKSFLLFATGISLCILISCQQTLSHKPFVELSSLELSEEEMPMVSISNDFACSFFQKMNEQEKGQSFFIS
+PLSAQFNLGMLANGAAGKTLEEIASVLSVSKSKPSLANNYFLKLISNLPRLDSTTVFQSANSIWIHDKSP
+VKDSFQQINQQYFLAEIQNLDFSEPKSTGIINRWAKEQTQGRIPHILDQAQGNCILINTLFFKGGWIFPF
+DPAETRQEYFYPVGGKKHPVSMMHLSDQWFAFHKAELFEMATLPYGNDSYAMTVILPKKGVSIDSCIDTF
+SEANWKAWLSASDSISCMLDLKLPSIKLDYKSDIIPTFQKMGIHDAFNENCADFSRMTDIPAHISEIEQF
+TRLEVTETGTVAAAATIANVVFESSIVPEITPYPFHVNRPFLLVIHENKTGLILFMGKMMDIL
+
+>gi|226225628|ref|YP_002759734.1| hypothetical protein GAU_0222 [Gemmatimonas aurantiaca T-27]
+MTGAGESEVGRETELPPRPDPAMSNLLSRSALIGALLLAACSEGTGPGDAGNTPVDSLTALPRALTAVER
+EGIQANNSFALHLLRTTASSRSGNVLLSPLSVSFALGMTMNGAGGETLAEMNRTLGWGTRTRAETNVAYR
+DLRTMLPTLDNSTTIRIANGLWVRQPLVIDTGFLREAQTFFNAPAQSLRTSQIMYDSVNVWGNRHTDGMI
+PRVLQEPPREDLAMLLANAVYFSGTWRDKFDPAKTTPMPFTLASGTQVSHPMMQRAGDFNVYQNSQLMAA
+ELLYGNAAYSMVVIAPASGTAAALAARLDSATYATIVQGLRKSDDRSMIFLPRFKVAGSLELSPELKAMG
+MPRAFTTAAEFPRLVNARTMLDFVQHSVALEVDERGSRAAAVTVVGVVPVSAPPSYQFNRPFVFFIRERL
+SGTILFTGVVNDPRQ
+
+>gi|20807990|ref|NP_623161.1| serine protease inhibitor [Caldanaerobacter subterraneus subsp. tengcongensis MB4]
+MMIPELKKLFTAILSITIFIGALINITACSFSTSKVQAANLMDRIKANPVSEKNIDEKFIYNTADFSIEL
+FKNSIDDKENSLISPLSAMLALAMTANGADNETLAQMEKALGKDISIEDLNKYLYTYMKKLPNEEKSKLT
+IANSIWFKENDFMPSKDFLQIIADYYKADIFKAAFDSSTVSDINNWVKSKTNGMIDKILNKIDPEDVMYL
+INAVAFDAEWETVYEKASVHEDIFTDVYGNRQKVEFMNSEENLYIEEENAVGFVKPYAKNHYSFVAILPD
+ENISVNEYIKTLTGQKFIDLIKNAKITLVRASLPKFKYEYTIKMNETLESLGMTDAFLPDKADFSKLGKS
+DIGNLYISEVLHKTFISVDELGTKAGAVTSVDITAAGIPVNFKTVKLNRPFIFAIIDNSTNLPIFIGTVL
+SLK
+
+>gi|150261378|pdb|2PEF|A Chain A, Crystal Structure Of A Thermophilic Serpin, Tengpin, In The Latent State
+MEKNIDEKFIYNTADFSIELFKNSIDDKENSLISPLSAMLALAMTANGADNETLAQMEKALGKDISIEDL
+NKYLYTYMKKLPNEEKSKLTIANSIWFKENDFMPSKDFLQIIADYYKADIFKAAFDSSTVSDINNWVKSK
+TNGMIDKILNKIDPEDVMYLINAVAFDAEWETVYEKASVHEDIFTDVYGNRQKVEFMNSEENLYIEEENA
+VGFVKPYAKNHYSFVAILPDENISVNEYIKTLTGQKFIDLIKNAKITLVRASLPKFKYEYTIKMNETLES
+LGMTDAFLPDKADFSKLGKSDIGNLYISEVLHKTFISVDELGTKAGAVTSVDITAAGIPVNFKTVKLNRP
+FIFAIIDNSTNLPIFIGTVLSLK
+
+>gi|225378784|ref|ZP_03756005.1| hypothetical protein ROSEINA2194_04454 [Roseburia inulinivorans DSM 16841]
+MKRKLVTILIGCMTLGLFGCGSGLSDTTKRLTPQQSEDSEQNADHTGNEDQQAEADTTEKKAEDDSTETS
+FGYQYRYCQFALNLLQQTYEDGKNEMISPLSVLTALTMTENGAKGDTLSQMEQVLSDGTPVGQQGRELSS
+YMKKLADTENAHLNIANSIWLKDADTLHVENDFLSENSKLFDAEIYQAPFDEHTLKDINTWVSQKTEKMI
+PEILEKIEDNSVMYLINAIAFDAKWQSPYEKEDVESGTFTSENGAQQTVDMMYSTEAYYLEDDSTTGFIR
+PYEDGYSFMALLPKEGISIEDYISHLSAEKLIGLVENASTDYEVDAAIPKFKSEYSIELKDTLQNMGMTD
+AFDEEQADFRGIGTSDNGNIYINMVLHKTYIEVDEQGTKAGASTVVGMVESMSLYEPEIKTVHLDRPFVY
+AIIDTETQMPIFLGVTESVEE
+
+>gi|164519546|pdb|2VH4|A Chain A, Structure Of A Loop C-sheet Serpin Polymer
+DRIKANPVSEKNIDEKFIYNTADFSIELFKNSIDDKENSLISPLSAMLALAMTANGADNETLAQMEKALG
+KDISIEDLNKYLYTYMKKLPNEEKSKLTIANSIWFKENDFMPSKDFLQIIADYYKADIFKAAFDSSTVSD
+INNWVKSKTNGMIDKILNKIDPEDVMYLINAVAFDAEWETVYEKASVHEDIFTDVYGNRQKVEFMNSEEN
+LYIEEENAIGFVKPYAKNHYSFVAILPDENISVNEYIKTLTGQKFIDLIKNAKITLVRASLPKFKYEYTI
+KMNETLESLGMTDAFLPDKADFSKLGKSDIGNLYISEVLHKTFISVDELGTKAGAVTSVDITAAGIPVNF
+KTVKLNRPFIFAIIDNSTNLPIFIGTVLSLK
+
+>gi|252118898|ref|ZP_04833261.1| serine proteinase inhibitor [Prevotella melaninogenica ATCC 25845]
+MTKKLLYVPILLLLVCCTQSKKTLHILEKTAQKTTTSSQLTLEDAAKKAKLDYVLSEEETKFVSSSNMFS
+LKLFQLLAKKNSKESIVLSPMAVIYSLDMINNGANGKTQEVISKALGYTADDLDAINSLNRTMLIGQRKE
+ETNVDNESMGYMITANFLMLHEQTKLLPDFQEALEHYYFTNIIDSANTPKGKESANKLCKTITKGEIQSL
+PINLTGPRAAQLINAVTLKTAWTLPFDKDITKPMPFFTEDGKSKQVNMMSNYDTMQKYQGYTTKDYQVLR
+MPLENGFSLYAVLPLKKNNLQDVIRKLTIKELHKISQNTKAYDYVNVLFPRFTISANIPMKQLYGEMGLG
+NLFSREADFGKMSTQPLAVDDVFQQINMNINEEGISAKVIQVMLFAKLSAMDSSSTFTFKADHPFLYYIL
+DKYNNICFIGKYMG
+
+>gi|150261376|pdb|2PEE|A Chain A, Crystal Structure Of A Thermophilic Serpin, Tengpin, In The Native State
+VQAANLMDRIKANPVSEKNIDEKFIYNTADFSIELFKNSIDDKENSLISPLSAMLALAMTANGADNETLA
+QMEKALGKDISIEDLNKYLYTYMKKLPNEEKSKLTIANSIWFKENDFMPSKDFLQIIADYYKADIFKAAF
+DSSTVSDINNWVKSKTNGMIDKILNKIDPEDVMYLINAVAFDAEWETVYEKASVHEDIFTDVYGNRQKVE
+FMNSEENLYIEEENAIGFVKPYAKNHYSFVAILPDENISVNEYIKTLTGQKFIDLIKNAKITLVRASLPK
+FKYEYTIKMNETLESLGMTDAFLPDKADFSKLGKSDIGNLYISEVLHKTFISVDELGTKAGAVTSVDITA
+AGIPVNFKTVKLNRPFIFAIIDNSTNLPIFIGTVLSL
+
+>gi|254478519|ref|ZP_05091894.1| serine proteinase inhibitor [Carboxydibrachium pacificum DSM 12653]
+MMIPELKKLFTAILSITIFIGALINITACSFSTSKVQAANLMDGIKANPVSEKNIDEKFIYNTADFSIEL
+FKNSTDDKENSLISPLSAMLALAMTANGADNETLAQMEKALEKDISIEDLNKYLYTYMKKLPNEEKSKLT
+IANSIWFKENDFMPSKDFLQIIADYYKADIFKAAFDSSTVSDINNWVKSKTNGMIDKILNKIDPEDVMYL
+INAVAFDAEWETVYEKASVHEDIFTDVYGNRQKVEFMNSEENLYIEEENAVGFVKPYAKNHYSFVAILPD
+ENIFVNEYIKTLTGQKFIDLIKNAKITLVRASLPKFKYEYTIKMNETLESLGMTDAFLPDKADFSKLGKS
+DIGNLYISEVLHKTFISVDELGTKAGAVTSVDITAAGIPVNFKTVKLNRPFIFAIIDNSTNLPIFIGTVL
+SLK
+
+>gi|224026921|ref|ZP_03645287.1| hypothetical protein BACCOPRO_03680 [Bacteroides coprophilus DSM 18228]
+MSKFERFLKGSIMKTKLYFLTPLLLFALSACNSDDPSSSETDVPAAKERQDIPLTRSETQLADHTLDFSL
+ALLRQASLQEAGKNMLVSPLGTAALLNLMANGAESHTADELYAVLSPSGVSAGELNDFFSKLNTWLPELD
+NTTSLAQAYSLWMDDQFTVHSGYTDVAQSVLGADVRQLDFQNTQSQQQLYDWCSEKTEGCIREIDCPLAD
+AQLVMLHTLYFKGAWTDKFDPAQTRTETFRGNLREVAVPMMHDRQRAGYAATESFTAVSLPYGNEAYSML
+LVLPAAGTDMAQAGRALADGAWKELTSRLYGAQVDLKLPKFELAYDTSLIEMLQEMGIHDAFSGEADFSG
+LTPDPLYFNVFKQQSVLRVDERGTEAASVTWAGLDTSLPEGGEEPVAAVTFDRPFYFFIQEKSTGLMLFM
+GKVEELNPE
+
+>gi|116669158|ref|YP_830091.1| proteinase inhibitor I4 serpin [Arthrobacter sp. FB24]
+MKTHRVARIATAGALAALTACSASSPELLKADGVERISVDGAAYAAELRSFRASALGLGEALLADGGDGS
+KGNVVSSPGSLLIALAMLRAGASGETAAEMDSVLKLPAEHRDEAMNALLSSLGKFDGDPGSVDEDNPPRK
+PVMHAANGLFVDKDVPTGDAFLETLARHYGTGVYPVDFSNEAATKPAIDAWVNRNTGGRIKEAPAKYDRD
+NTFSLLNSLYFASAWRAPFDPNDTSDLPFTTAAGEKIDAPAMHNELEMKYAEGAGWQGVDLPYADGFVMR
+LVLPGTGVPGAGTGAGSPVFGAERLTDIADAFDRAPLETVQIQLPRWDHKCSFDLRKVFESLGLRKTLTT
+TEDFNNIQPGMMITQAAQAANITVAEKGTVAAAVTQINGAVTSAPPQPERTITFDRPFHYQIVHVETGLP
+LFMGTVADPRS
+
+>gi|182417681|ref|ZP_02949000.1| putative serine protease inhibitor [Clostridium butyricum 5521]
+MNRKKISIILSGIMGIMTLLPSSVYGTSNNGWEKINGSWYYYENGNSISGWKYDHENWYYLNDDGSMAKG
+WNLIDNQWYYLQNNGAMKTGWFNDNNTWYYLNSNGSMAHDTVIDGYTLNSKGVYIDNKSDDKEENKKNYT
+FTEGLGKFCLDSGAMILANEDKNLNTSYSTLSFYMALAVLSEGSDNNTKTEIINALNVNDEEKLSEECRK
+LYEKESFDSKYGKCTLADSVWIDDDNNDVKFNEDTLKKIENDYNAGIFKGDLQSFNTAKDISNWLLQHTG
+GLLGGNPSDFISDEGAVMNIINSVYFKDKWADVFDRNLTEEKDFCLSDGSKVKSDFMSNSIYSKIYESNN
+GYKSSSLKFENGNEMMFILPDKGTSVYDIINDKNKFNEALNSLSDKNVTMEDVYYKVPKFKVSSKLDLNN
+CAKTLGLGNIFDGKTADFSKFSEKGGLAVSSISQEATVSIDEDGGEAAAYTEIEMDGCAYYPEAKSYDMT
+LDRPFIFAITDKDNTPLFLGVINNPTV
+
+>gi|241667095|ref|YP_002985179.1| proteinase inhibitor I4 serpin (plasmid) [Rhizobium leguminosarum bv. trifolii WSM1325]
+MPKSTLLAGLAAFLMTLAPSAHAGNSGDSKAMLAAQAGLAAELIDRTLAKEGAANIMVSPASLAAALGLA
+SLGASDEGKASIAKGLGFGGEVKGPEAVLDAIYQVKPAAADAPLTAAVAIVFDDKLVLVPDALSMLARHR
+IKPSIEDLDGPKSVEHINGWVSQATRGAIPVILDSPPGGGFVSLGALSFKARWKTSFEKESPASPFQRPD
+GSTISVPMMHLAGDGQRFRSDEKFSAVDLAYAGESYSMVVVAARSGKGVGGADLKTLASWLQGEKFEAAK
+GEIFLPRFSLNDGRDLMPILNAMGVAPEKAKDAGFPGFTKENIRLSRVLQKTMIKVDENGTEAAAATAVI
+TERSIDPKLVRVVADARFAFALRDTKTGLLLAAGLIGDPLLAGE
+
diff --git a/c++/src/objtools/align_format/unit_test/data/tabular_seqalignset_2.asn b/c++/src/objtools/align_format/unit_test/data/tabular_seqalignset_2.asn
index c30fba9..1b0b665 100644
--- a/c++/src/objtools/align_format/unit_test/data/tabular_seqalignset_2.asn
+++ b/c++/src/objtools/align_format/unit_test/data/tabular_seqalignset_2.asn
@@ -5,19 +5,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 130
+ value int 1371
+ },
+ {
+ id str "blast_score",
+ value int 1371
},
{
id str "e_value",
- value real { 127374482117249, 10, -22 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 546841771492999, 10, -13 }
+ value real { 532716850862735, 10, -12 }
},
{
id str "num_ident",
- value int 23
+ value int 270
},
{
id str "comp_adjustment_method",
@@ -25,28 +29,32 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 28
+ value int 275
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 282168494516451, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 357477583
+ gi 444,
+ gi 803030749
},
loc {
int {
- from 3,
- to 92,
+ from 2,
+ to 835,
strand plus,
- id gi 176224
+ id gi 444
},
int {
- from 37,
- to 66,
+ from 31,
+ to 308,
strand unknown,
- id gi 357477583
+ id gi 803030749
}
}
}
@@ -58,19 +66,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 80
+ value int 1354
+ },
+ {
+ id str "blast_score",
+ value int 1354
},
{
id str "e_value",
- value real { 806046844642502, 10, -16 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 354241983534323, 10, -13 }
+ value real { 52616845807214, 10, -11 }
},
{
id str "num_ident",
- value int 16
+ value int 268
},
{
id str "comp_adjustment_method",
@@ -78,28 +90,32 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 22
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 255528521
+ gi 444,
+ gi 27806577
},
loc {
int {
- from 39,
- to 119,
+ from 32,
+ to 835,
strand plus,
- id gi 176224
+ id gi 444
},
int {
- from 15,
- to 41,
+ from 0,
+ to 267,
strand unknown,
- id gi 255528521
+ id gi 27806577
}
}
}
@@ -111,19 +127,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 72
+ value int 1344
+ },
+ {
+ id str "blast_score",
+ value int 1344
},
{
id str "e_value",
- value real { 112243344912913, 10, -14 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 323426017460934, 10, -13 }
+ value real { 522316462312967, 10, -12 }
},
{
id str "num_ident",
- value int 13
+ value int 266
},
{
id str "comp_adjustment_method",
@@ -131,28 +151,32 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 13
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 134093252
+ gi 444,
+ gi 555955787
},
loc {
int {
- from 2,
- to 40,
- strand minus,
- id gi 176224
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
},
int {
from 0,
- to 12,
+ to 267,
strand unknown,
- id gi 134093252
+ id gi 555955787
}
}
}
@@ -164,48 +188,56 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 77
+ value int 1344
+ },
+ {
+ id str "blast_score",
+ value int 1344
},
{
id str "e_value",
- value real { 122816470766249, 10, -14 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 342685996256802, 10, -13 }
+ value real { 522316462312967, 10, -12 }
},
{
id str "num_ident",
- value int 12
+ value int 265
},
{
id str "comp_adjustment_method",
- value int 1
+ value int 2
},
{
id str "num_positives",
- value int 12
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 357459873
+ gi 444,
+ gi 300669780
},
loc {
int {
- from 2,
- to 40,
- strand minus,
- id gi 176224
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
},
int {
from 0,
- to 12,
+ to 267,
strand unknown,
- id gi 357459873
+ id gi 300669780
}
}
}
@@ -217,19 +249,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 72
+ value int 1340
+ },
+ {
+ id str "blast_score",
+ value int 1340
},
{
id str "e_value",
- value real { 549758256062729, 10, -14 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 323426017460934, 10, -13 }
+ value real { 520775664009297, 10, -12 }
},
{
id str "num_ident",
- value int 13
+ value int 265
},
{
id str "comp_adjustment_method",
@@ -237,28 +273,32 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 13
+ value int 267
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 358349383
+ gi 444,
+ gi 742093586
},
loc {
int {
- from 2,
- to 40,
- strand minus,
- id gi 176224
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
},
int {
from 0,
- to 12,
+ to 267,
strand unknown,
- id gi 358349383
+ id gi 742093586
}
}
}
@@ -270,19 +310,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 72
+ value int 1340
+ },
+ {
+ id str "blast_score",
+ value int 1340
},
{
id str "e_value",
- value real { 564998523124157, 10, -14 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 323426017460934, 10, -13 }
+ value real { 520775664009297, 10, -12 }
},
{
id str "num_ident",
- value int 13
+ value int 264
},
{
id str "comp_adjustment_method",
@@ -290,28 +334,93 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 13
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 357467743
+ gi 444,
+ gi 84993680
},
loc {
int {
- from 2,
- to 40,
- strand minus,
- id gi 176224
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
+ },
+ int {
+ from 0,
+ to 267,
+ strand unknown,
+ id gi 84993680
+ }
+ }
+ }
+ }
+ },
+ {
+ type partial,
+ dim 2,
+ score {
+ {
+ id str "score",
+ value int 1335
+ },
+ {
+ id str "blast_score",
+ value int 1335
+ },
+ {
+ id str "e_value",
+ value real { 0, 10, 0 }
+ },
+ {
+ id str "bit_score",
+ value real { 518849666129711, 10, -12 }
+ },
+ {
+ id str "num_ident",
+ value int 263
+ },
+ {
+ id str "comp_adjustment_method",
+ value int 2
+ },
+ {
+ id str "num_positives",
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
+ }
+ },
+ segs std {
+ {
+ dim 2,
+ ids {
+ gi 444,
+ gi 594064064
+ },
+ loc {
+ int {
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
},
int {
from 0,
- to 12,
+ to 267,
strand unknown,
- id gi 357467743
+ id gi 594064064
}
}
}
@@ -323,19 +432,23 @@ Seq-align-set ::= {
score {
{
id str "score",
- value int 69
+ value int 1330
+ },
+ {
+ id str "blast_score",
+ value int 1330
},
{
id str "e_value",
- value real { 880944988228886, 10, -14 }
+ value real { 0, 10, 0 }
},
{
id str "bit_score",
- value real { 311870030183414, 10, -13 }
+ value real { 516923668250124, 10, -12 }
},
{
id str "num_ident",
- value int 17
+ value int 262
},
{
id str "comp_adjustment_method",
@@ -343,28 +456,32 @@ Seq-align-set ::= {
},
{
id str "num_positives",
- value int 22
+ value int 268
+ },
+ {
+ id str "hsp_percent_coverage",
+ value real { 272198404785643, 10, -13 }
}
},
segs std {
{
dim 2,
ids {
- gi 176224,
- gi 167044667
+ gi 444,
+ gi 595763446
},
loc {
int {
- from 3,
- to 116,
- strand minus,
- id gi 176224
+ from 32,
+ to 835,
+ strand plus,
+ id gi 444
},
int {
- from 28,
- to 65,
+ from 0,
+ to 267,
strand unknown,
- id gi 167044667
+ id gi 595763446
}
}
}
diff --git a/c++/src/objtools/align_format/unit_test/showalign_unit_test.cpp b/c++/src/objtools/align_format/unit_test/showalign_unit_test.cpp
index 4cf208a..6142845 100644
--- a/c++/src/objtools/align_format/unit_test/showalign_unit_test.cpp
+++ b/c++/src/objtools/align_format/unit_test/showalign_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: showalign_unit_test.cpp 435003 2014-05-13 15:08:30Z ucko $
+/* $Id: showalign_unit_test.cpp 482386 2015-10-22 16:35:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,6 +80,39 @@ const int kPerformanceTimeout = 30;
#endif
BOOST_AUTO_TEST_CASE_TIMEOUT(TestPerformance, kPerformanceTimeout);
+BOOST_AUTO_TEST_CASE(TestTGIConversion)
+{
+ const string seqAlignFileName_in = "data/in_showalign_use_this_gi.asn";
+ CRef<CSeq_annot> san(new CSeq_annot);
+
+ ifstream in(seqAlignFileName_in.c_str());
+ in >> MSerial_AsnText >> *san;
+ in.close();
+
+ CRef<CSeq_align_set> fileSeqAlignSet(new CSeq_align_set);
+ fileSeqAlignSet->Set() = san->GetData().GetAlign();
+
+ const string kDbName("nr");
+ const CBlastDbDataLoader::EDbType kDbType(CBlastDbDataLoader::eProtein);
+ TestUtil::CBlastOM tmp_data_loader(kDbName, kDbType, CBlastOM::eLocal);
+ CRef<CScope> scope = tmp_data_loader.NewScope();
+
+ CDisplaySeqalign ds(*fileSeqAlignSet, *scope);
+ ds.SetDbName(kDbName);
+ ds.SetDbType((kDbType == CBlastDbDataLoader::eProtein));
+ int flags = CDisplaySeqalign::eShowBlastInfo |
+ CDisplaySeqalign::eShowGi |
+ CDisplaySeqalign::eShowBlastStyleId;
+ ds.SetAlignOption(flags);
+ ds.SetSeqLocChar(CDisplaySeqalign::eLowerCase);
+ CNcbiOstrstream output_stream;
+ ds.DisplaySeqalign(output_stream);
+ string output = CNcbiOstrstreamToString(output_stream);
+ BOOST_REQUIRE(output.find("gi|212900|gb|AAA68886.1| ") != NPOS);
+ BOOST_REQUIRE(output.find("gi|385145537|dbj|BAM13277.1|") != NPOS);
+ BOOST_REQUIRE(output.find("gi|385145539|dbj|BAM13278.1|") != NPOS);
+}
+
bool TestSimpleAlignment(CBlastOM::ELocation location)
{
const string seqAlignFileName_in = "data/blastn.vs.ecoli.asn";
@@ -108,10 +141,10 @@ bool TestSimpleAlignment(CBlastOM::ELocation location)
ds.SetSeqLocChar(CDisplaySeqalign::eLowerCase);
CNcbiOstrstream output_stream;
ds.DisplaySeqalign(output_stream);
- string output = CNcbiOstrstreamToString(output_stream);
+ string output = CNcbiOstrstreamToString(output_stream);
BOOST_REQUIRE(output.find(">gi|1788470|gb|AE000304.1|AE000304 ") != NPOS);
- BOOST_REQUIRE(output.find("Escherichia coli K-12 MG1655 section 1 of 400 of ") != NPOS ||
- output.find("Escherichia coli K12 MG1655 section 1 of 400 of ") != NPOS);
+ BOOST_REQUIRE(output.find("Escherichia coli K-12 MG1655 section 9 of 400 of ") != NPOS ||
+ output.find("Escherichia coli K12 MG1655 section 9 of 400 of ") != NPOS);
BOOST_REQUIRE(output.find("Sbjct 259 GCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC 294") != NPOS);
BOOST_REQUIRE(output.find("Length=11852") != NPOS);
BOOST_REQUIRE(output.find("Query 5636 GTAGG-CAGGATAAGGCGTTCACGCCGCATCCGGCA 5670") != NPOS);
@@ -122,6 +155,7 @@ bool TestSimpleAlignment(CBlastOM::ELocation location)
return true;
}
+
// Note: this essentially disables the performance tests for the automated
// toolkit builds, which implies that the BLAST team should be running these
// themselves (CVSROOT/individual/camacho/scripts/autobuild.pl should do this)
@@ -131,7 +165,7 @@ NCBITEST_AUTO_INIT()
.Get("NCBI_AUTOMATED_BUILD") == "1") {
// Suppress timeout
typedef SNcbiTestTCTimeout<BOOST_AUTO_TC_UNIQUE_ID(TestPerformance)> TTimeout;
- TTimeout new_timeout(kMax_Int);
+ static TTimeout new_timeout(kMax_Int);
}
}
diff --git a/c++/src/objtools/align_format/unit_test/showdefline_unit_test.cpp b/c++/src/objtools/align_format/unit_test/showdefline_unit_test.cpp
index 62594af..1030240 100644
--- a/c++/src/objtools/align_format/unit_test/showdefline_unit_test.cpp
+++ b/c++/src/objtools/align_format/unit_test/showdefline_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: showdefline_unit_test.cpp 457064 2015-01-20 15:09:15Z ivanov $
+/* $Id: showdefline_unit_test.cpp 482729 2015-10-26 16:30:38Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -122,8 +122,8 @@ struct CShowBlastDeflineTest : public CShowBlastDefline {
string bit_string[] = {"503", "502"};
int sum_n[] = {1, 1};
- string id_url[] = {"<a title=\"Show report for NP_569083.1\" href=\"http://www.ncbi.nlm.nih.gov/nucleotide/18426812?report=genbank&log$=nucltop&blast_rank=1&RID=\" >",
- "<a title=\"Show report for NP_031424.1\" href=\"http://www.ncbi.nlm.nih.gov/nucleotide/6680636?report=genbank&log$=nucltop&blast_rank=1&RID=\" >"};
+ string id_url[] = {"<a title=\"Show report for NP_569083.1\" href=\"//www.ncbi.nlm.nih.gov/nucleotide/18426812?report=genbank&log$=nucltop&blast_rank=1&RID=\" >",
+ "<a title=\"Show report for NP_031424.1\" href=\"//www.ncbi.nlm.nih.gov/nucleotide/6680636?report=genbank&log$=nucltop&blast_rank=1&RID=\" >"};
string score_url[] = {"<a href=#18426812>", "<a href=#6680636>"};
bool is_new[] = {false, false};
bool was_checked[] = {false, false};
diff --git a/c++/src/objtools/align_format/unit_test/tabularinof_unit_test.cpp b/c++/src/objtools/align_format/unit_test/tabularinof_unit_test.cpp
index 6557df4..92b04fc 100644
--- a/c++/src/objtools/align_format/unit_test/tabularinof_unit_test.cpp
+++ b/c++/src/objtools/align_format/unit_test/tabularinof_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: tabularinof_unit_test.cpp 439260 2014-06-26 20:17:50Z camacho $
+/* $Id: tabularinof_unit_test.cpp 482737 2015-10-26 16:33:40Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -96,8 +96,8 @@ BOOST_AUTO_TEST_CASE(StandardOutput) {
string output = CNcbiOstrstreamToString(output_stream);
- BOOST_REQUIRE(output.find("gi|1786181|gb|AE000111.1|AE000111 gi|1786181|gb|AE000111.1|AE000111 100.00 10596 0 0 1 10596") != NPOS);
- BOOST_REQUIRE(output.find("gi|1786181|gb|AE000111.1|AE000111 gi|1787084|gb|AE000188.1|AE000188 97.06 34 1 0 5567 5600 1088") != NPOS);
+ BOOST_REQUIRE(output.find("gi|1786181|gb|AE000111.1|AE000111 gi|1786181|gb|AE000111.1|AE000111 100.000 10596 0 0 1 10596") != NPOS);
+ BOOST_REQUIRE(output.find("gi|1786181|gb|AE000111.1|AE000111 gi|1787084|gb|AE000188.1|AE000188 97.059 34 1 0 5567 5600 1088") != NPOS);
BOOST_REQUIRE(output.find("# BLAST processed 1 queries") != NPOS);
}
@@ -163,9 +163,9 @@ BOOST_AUTO_TEST_CASE(QueryAccSubjectAccIdentScoreOutput) {
// First result should be "gi|1786181|gb|AE000111.1|AE000111 gi|1786181|gb|AE000111.1|AE000111 1.957e+04".
// but some windows binaires print the bit score as 1.957e+004. Hence, we drop the exponent.
- BOOST_REQUIRE(output.find("AE000111 AE000111 100.00 19568") != NPOS);
- BOOST_REQUIRE(output.find("AE000111 AE000310 94.59 56.5") != NPOS);
- BOOST_REQUIRE(output.find("AE000111 AE000509 80.51 76.8") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000111 100.000 19568") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000310 94.595 56.5") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000509 80.508 76.8") != NPOS);
}
BOOST_AUTO_TEST_CASE(QueryAccSubjectAccIdentBTOPOutput) {
@@ -195,10 +195,10 @@ BOOST_AUTO_TEST_CASE(QueryAccSubjectAccIdentBTOPOutput) {
string output = CNcbiOstrstreamToString(output_stream);
- BOOST_REQUIRE(output.find("AE000111 AE000111 10596 100.00 10596") != NPOS);
- BOOST_REQUIRE(output.find("AE000111 AE000447 57 89.41 15T-TA2TA2-T6AG8CT1GT4CA10AC28") != NPOS);
- BOOST_REQUIRE(output.find("AE000111 AE000116 48 98.04 12GA38") != NPOS);
- BOOST_REQUIRE(output.find("AE000111 AE000183 36 82.02 14G-TATGAG2-A3-G4-C1A-4-AGA3C-6CATATC7C-1-C28") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000111 10596 100.000 10596") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000447 57 89.412 15T-TA2TA2-T6AG8CT1GT4CA10AC28") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000116 48 98.039 12GA38") != NPOS);
+ BOOST_REQUIRE(output.find("AE000111 AE000183 36 82.022 14G-TATGAG2-A3-G4-C1A-4-AGA3C-6CATATC7C-1-C28") != NPOS);
}
BOOST_AUTO_TEST_CASE(TaxonomyOutput) {
@@ -225,13 +225,24 @@ BOOST_AUTO_TEST_CASE(TaxonomyOutput) {
ctab.SetFields(**iter, *scope);
ctab.Print();
}
+ const string ref[8] = {
+ "9940 Ovis aries sheep even-toed ungulates Eukaryota",
+ "9913 Bos taurus cattle even-toed ungulates Eukaryota",
+ "72004 Bos mutus Bos mutus even-toed ungulates Eukaryota",
+ "9970 Syncerus caffer African buffalo even-toed ungulates Eukaryota",
+ "43346 Bison bison bison Bison bison bison even-toed ungulates Eukaryota",
+ "346063 Bubalus carabanensis carabao even-toed ungulates Eukaryota",
+ "89462;365610 Bubalus bubalis;Bubalus bubalis x Bubalus carabanensis water buffalo;Bubalus bubalis x Bubalus carabanensis even-toed ungulates Eukaryota",
+ "89462 Bubalus bubalis water buffalo even-toed ungulates Eukaryota"
+ };
string output = CNcbiOstrstreamToString(output_stream);
+ vector<string> results;
+ NStr::Tokenize(output, "\n", results);
- BOOST_REQUIRE(output.find("M10360 XP_003609077 3880 Medicago truncatula barrel medic eudicots Eukaryota") != NPOS);
- BOOST_REQUIRE(output.find("M10360 ZP_05395304 536227 Clostridium carboxidivorans P7 Clostridium carboxidivorans P7 firmicutes Bacteria") != NPOS);
- BOOST_REQUIRE(output.find("M10360 YP_001109553 3694 Populus trichocarpa black cottonwood eudicots Eukaryota") != NPOS);
- BOOST_REQUIRE(output.find("M10360 ABZ09338 455551 uncultured marine microorganism HF4000_APKG7H23 uncultured marine microorganism HF4000_APKG7H23 N/A N/A") != NPOS);
+ for(unsigned int i=0; i < 8; i++) {
+ BOOST_REQUIRE(results[i].find(ref[i]) != NPOS);
+ }
}
BOOST_AUTO_TEST_CASE(SubjectTitlesOutput) {
@@ -260,14 +271,22 @@ BOOST_AUTO_TEST_CASE(SubjectTitlesOutput) {
ctab.Print();
}
- string output = CNcbiOstrstreamToString(output_stream);
+ const string ref[8] = {
+ "X12497 XP_012015192 PREDICTED: interleukin-1 alpha isoform X1 [Ovis aries]",
+ "X12497 NP_776517 interleukin-1 alpha precursor [Bos taurus]",
+ "X12497 XP_005890049 PREDICTED: interleukin-1 alpha [Bos mutus]",
+ "X12497 BAJ11606 interleukin 1 alpha [Syncerus caffer]",
+ "X12497 XP_010832415 PREDICTED: interleukin-1 alpha [Bison bison bison]",
+ "X12497 BAE76004 Interleukin-1 alpha [Bubalus carabanensis]",
+ "X12497 XP_006056051 PREDICTED: interleukin-1 alpha [Bubalus bubalis]",
+ "X12497 NP_001277833 interleukin 1, alpha [Bubalus bubalis]"};
+ string output = CNcbiOstrstreamToString(output_stream);
vector<string> results;
NStr::Tokenize(output, "\n", results);
- BOOST_REQUIRE(results[0].find("hypothetical protein MTR_4g111700 [Medicago truncatula]") != NPOS);
- BOOST_REQUIRE(results[3].find("Glycerophosphodiesterase-like protein [Medicago truncatula]") != NPOS);
- BOOST_REQUIRE(results[4].find("Cell wall-associated hydrolase [Medicago truncatula]") != NPOS);
- BOOST_REQUIRE(results[6].find("hypothetical protein ALOHA_HF4000APKG7H23ctg3g3 [uncultured marine microorganism HF4000_APKG7H23]") != NPOS);
+ for(unsigned int i=0; i < 8; i++) {
+ BOOST_REQUIRE(results[i].find(ref[i]) != NPOS);
+ }
}
{
@@ -281,20 +300,20 @@ BOOST_AUTO_TEST_CASE(SubjectTitlesOutput) {
}
string output = CNcbiOstrstreamToString(output_stream);
+ const string ref[8] = {
+ "PREDICTED: interleukin-1 alpha isoform X1 [Ovis aries]",
+ "interleukin-1 alpha precursor [Bos taurus]<>RecName: Full=Interleukin-1 alpha; Short=IL-1 alpha; Flags: Precursor<>pre-interleukin-1 alpha [Bos taurus]<>interleukin 1-alpha [Bos taurus]<>interleukin-1 alpha precursor [Bos taurus]<>TPA: interleukin-1 alpha precursor [Bos taurus]",
+ "PREDICTED: interleukin-1 alpha [Bos mutus]<>Interleukin-1 alpha [Bos mutus]",
+ "interleukin 1 alpha [Syncerus caffer]",
+ "PREDICTED: interleukin-1 alpha [Bison bison bison]",
+ "Interleukin-1 alpha [Bubalus carabanensis]",
+ "PREDICTED: interleukin-1 alpha [Bubalus bubalis]<>interleukin-1 alpha [Bubalus bubalis]<>Interleukin-1 alpha [Bubalus bubalis x Bubalus carabanensis]",
+ "interleukin 1, alpha [Bubalus bubalis]<>Interleukin-1 alpha [Bubalus bubalis]"};
vector<string> results;
NStr::Tokenize(output, "\n", results);
- string ref_0 = "hypothetical protein MTR_4g111700 [Medicago truncatula]<>" \
- "hypothetical protein MTR_4g112050 [Medicago truncatula]<>" \
- "hypothetical protein MTR_4g111700 [Medicago truncatula]";
- string ref_2 = "hypothetical protein Poptr_cp075 [Populus trichocarpa]<>hypothetical protein " \
- "Poptr_cp088 [Populus trichocarpa]<>hypothetical protein Poptr_cp075 [Populus " \
- "trichocarpa]<>hypothetical protein Poptr_cp088 [Populus trichocarpa]";
- string ref_6 = "hypothetical protein ALOHA_HF4000APKG7H23ctg3g3 [uncultured marine " \
- "microorganism HF4000_APKG7H23]";
-
- BOOST_REQUIRE(results[0].find(ref_0) != NPOS);
- BOOST_REQUIRE(results[2].find(ref_2) != NPOS);
- BOOST_REQUIRE(results[6].find(ref_6) != NPOS);
+ for(unsigned int i=0; i < 8; i++) {
+ BOOST_REQUIRE(results[i].find(ref[i]) != NPOS);
+ }
}
}
diff --git a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
index 3d25f46..fac02e9 100644
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.alnmgr.lib 427429 2014-02-20 13:41:40Z gouriano $
+# $Id: Makefile.alnmgr.lib 468535 2015-05-26 13:23:32Z ucko $
# Build library "xalnmgr"
#################################
@@ -10,6 +10,8 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \
alnsegments alnseq alnvec alnvec_iterator alnvecprint \
pairwise_aln sparse_aln sparse_ci alntext score_builder_base
+DLL_LIB = tables
+
WATCHERS = todorov dicuccio grichenk
diff --git a/c++/src/objtools/alnmgr/aln_builders.cpp b/c++/src/objtools/alnmgr/aln_builders.cpp
index 1df8985..fc12934 100644
--- a/c++/src/objtools/alnmgr/aln_builders.cpp
+++ b/c++/src/objtools/alnmgr/aln_builders.cpp
@@ -1,4 +1,4 @@
-/* $Id: aln_builders.cpp 377671 2012-10-15 15:57:48Z grichenk $
+/* $Id: aln_builders.cpp 464814 2015-04-14 16:29:46Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -548,7 +548,6 @@ BuildAln(TAnchoredAlnVec& in_alns,
{
// Types
typedef CAnchoredAln::TDim TDim;
- typedef CAnchoredAln::TPairwiseAlnVector TPairwiseAlnVector;
AutoPtr<TAnchoredAlnVec> adj_alns;
diff --git a/c++/src/objtools/alnmgr/alnmap.cpp b/c++/src/objtools/alnmgr/alnmap.cpp
index 3a1ae60..cf90588 100644
--- a/c++/src/objtools/alnmgr/alnmap.cpp
+++ b/c++/src/objtools/alnmgr/alnmap.cpp
@@ -1,4 +1,4 @@
-/* $Id: alnmap.cpp 425593 2014-01-30 20:25:36Z grichenk $
+/* $Id: alnmap.cpp 461118 2015-03-06 13:29:39Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1448,7 +1448,6 @@ CRef<CSeq_align> CAlnMap::CreateAlignFromRange(
if (seg_flag == eSegment_Trim) {
from_trim = aln_from - aln_seg_from;
len -= from_trim;
- aln_seg_from = aln_from;
}
}
// Check trimming of the last segment
@@ -1460,7 +1459,6 @@ CRef<CSeq_align> CAlnMap::CreateAlignFromRange(
}
if (seg_flag == eSegment_Trim) {
len -= aln_seg_to - aln_to;
- aln_seg_to = aln_to;
}
}
}
diff --git a/c++/src/objtools/alnmgr/alnmerger.cpp b/c++/src/objtools/alnmgr/alnmerger.cpp
index 54a2869..d57ade0 100644
--- a/c++/src/objtools/alnmgr/alnmerger.cpp
+++ b/c++/src/objtools/alnmgr/alnmerger.cpp
@@ -1,4 +1,4 @@
-/* $Id: alnmerger.cpp 454401 2014-12-15 14:50:17Z ivanov $
+/* $Id: alnmerger.cpp 453123 2014-12-01 15:13:46Z chetvern $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/alnmgr/alntext.cpp b/c++/src/objtools/alnmgr/alntext.cpp
index fbd242b..9eb5f0b 100644
--- a/c++/src/objtools/alnmgr/alntext.cpp
+++ b/c++/src/objtools/alnmgr/alntext.cpp
@@ -1,5 +1,5 @@
/*
-* $Id: alntext.cpp 423161 2013-12-31 18:32:31Z kiryutin $
+* $Id: alntext.cpp 452731 2014-11-24 17:25:20Z vasilche $
*
* =========================================================================
*
@@ -168,8 +168,8 @@ char CProteinAlignText::MatchChar(size_t i)
if(toupper(m_protein[i]) != 'X') {
if (m_translation[i] == m_protein[i]) {
m = MATCH_CHAR;
- } else if(m_matrix.s[(int)toupper(m_protein[i])]
- [(int)toupper(m_translation[i])] > 0)
+ } else if(m_matrix.s[toupper(m_protein[i])]
+ [toupper(m_translation[i])] > 0)
{
m = POSIT_CHAR;
}
diff --git a/c++/src/objtools/alnmgr/score_builder_base.cpp b/c++/src/objtools/alnmgr/score_builder_base.cpp
index 60de7fb..bdf1226 100644
--- a/c++/src/objtools/alnmgr/score_builder_base.cpp
+++ b/c++/src/objtools/alnmgr/score_builder_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: score_builder_base.cpp 443231 2014-08-12 16:00:57Z chetvern $
+/* $Id: score_builder_base.cpp 474108 2015-07-24 21:16:50Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -94,10 +94,22 @@ static void s_GetNucIdentityMismatch(const vector<string>& data,
int* identities,
int* mismatches)
{
- for (size_t a = 0; a < data[0].size(); ++a) {
+ if ( data.empty() ) {
+ return;
+ }
+ size_t rows = data.size();
+ size_t size = data[0].size();
+ for (size_t i = 1; i < rows; ++i ) {
+ if ( data[i].size() != size ) {
+ NCBI_THROW(CSeqalignException, eInvalidInputData,
+ "Rows have different lengths");
+ }
+ }
+ for (size_t a = 0; a < size; ++a) {
bool is_mismatch = false;
- for (size_t b = 1; b < data.size(); ++b) {
- if (data[b][a] != data[0][a]) {
+ char c = data[0][a];
+ for (size_t b = 1; b < rows; ++b) {
+ if (data[b][a] != c) {
is_mismatch = true;
break;
}
@@ -517,7 +529,7 @@ static bool s_IsProteinToGenomic(CScope& scope,
return false;
}
const CSeq_id& id1 = align.GetSeq_id(1);
- return s_SequenceIsProtein(scope, id0);
+ return s_SequenceIsProtein(scope, id1);
}
@@ -970,15 +982,15 @@ string GetAcceptor(const objects::CSpliced_exon& exon) {
//returns true for GT/AG, GC/AG AND AT/AC
bool IsConsSplice(const string& donor, const string acc) {
if(donor.length()<2 || acc.length()<2) return false;
- if(toupper(acc.c_str()[0]) != 'A') return false;
- switch(toupper(acc.c_str()[1])) {
+ if(toupper(Uchar(acc.c_str()[0])) != 'A') return false;
+ switch(toupper(Uchar(acc.c_str()[1]))) {
case 'C':
- if( toupper(donor.c_str()[0] == 'A') && toupper(donor.c_str()[1] == 'T') ) return true;
+ if( toupper(Uchar(donor.c_str()[0])) == 'A' && toupper(Uchar(donor.c_str()[1])) == 'T' ) return true;
else return false;
break;
case 'G':
- if( toupper(donor.c_str()[0] == 'G') ) {
- char don2 = toupper(donor.c_str()[1]);
+ if( toupper(Uchar(donor.c_str()[0])) == 'G' ) {
+ char don2 = toupper(Uchar(donor.c_str()[1]));
if(don2 == 'T' || don2 == 'C') return true;
}
return false;
diff --git a/c++/src/objtools/blast/blastdb_format/blastdb_dataextract.cpp b/c++/src/objtools/blast/blastdb_format/blastdb_dataextract.cpp
index 301b655..36fea28 100644
--- a/c++/src/objtools/blast/blastdb_format/blastdb_dataextract.cpp
+++ b/c++/src/objtools/blast/blastdb_format/blastdb_dataextract.cpp
@@ -1,4 +1,4 @@
-/* $Id: blastdb_dataextract.cpp 446244 2014-09-12 17:41:03Z ivanov $
+/* $Id: blastdb_dataextract.cpp 479602 2015-09-22 14:27:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blastdb_dataextract.cpp 446244 2014-09-12 17:41:03Z ivanov $";
+static char const rcsid[] = "$Id: blastdb_dataextract.cpp 479602 2015-09-22 14:27:21Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -44,6 +44,8 @@ static char const rcsid[] = "$Id: blastdb_dataextract.cpp 446244 2014-09-12 17:4
#include <corelib/ncbiutil.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <util/checksum.hpp>
+#include <objmgr/object_manager.hpp>
+#include <objmgr/scope.hpp>
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
@@ -112,7 +114,7 @@ void CBlastDBExtractor::SetSeqId(const CBlastDBSeqId &id, bool get_data) {
if (get_data) {
m_Bioseq.Reset(m_BlastDb.GetBioseq(m_Oid, target_gi, target_seq_id));
}
- else if (m_Gi <= 0)
+ else if (m_Gi <= ZERO_GI)
{ // If no GI, then all the Gi2XMaps will fail.
m_Bioseq.Reset(m_BlastDb.GetBioseqNoData(m_Oid, target_gi, target_seq_id));
}
@@ -144,11 +146,11 @@ string CBlastDBExtractor::ExtractPig() {
string CBlastDBExtractor::ExtractGi() {
x_SetGi();
- return (m_Gi ? NStr::IntToString(m_Gi) : NOT_AVAILABLE);
+ return (m_Gi != ZERO_GI ? NStr::NumericToString(m_Gi) : NOT_AVAILABLE);
}
void CBlastDBExtractor::x_SetGi() {
- if (m_Gi) return;
+ if (m_Gi != ZERO_GI) return;
ITERATE(list<CRef<CSeq_id> >, itr, m_Bioseq->GetId()) {
if ((*itr)->IsGi()) {
m_Gi = (*itr)->GetGi();
@@ -320,7 +322,7 @@ void CBlastDBExtractor::x_SetGi2TitleMap()
}
string CBlastDBExtractor::ExtractAccession() {
- if (m_Gi)
+ if (m_Gi != ZERO_GI)
{
x_SetGi2AccMap();
return m_Gi2AccMap.second[m_Gi];
@@ -336,7 +338,7 @@ string CBlastDBExtractor::ExtractAccession() {
}
string CBlastDBExtractor::ExtractSeqId() {
- if (m_Gi)
+ if (m_Gi != ZERO_GI)
{
x_SetGi2SeqIdMap();
return m_Gi2SeqIdMap.second[m_Gi];
@@ -356,7 +358,7 @@ string CBlastDBExtractor::ExtractSeqId() {
}
string CBlastDBExtractor::ExtractTitle() {
- if (m_Gi)
+ if (m_Gi != ZERO_GI)
{
x_SetGi2TitleMap();
return m_Gi2TitleMap.second[m_Gi];
@@ -615,6 +617,16 @@ static void s_ReplaceCtrlAsInTitle(CRef<CBioseq> bioseq)
}
}
+static string s_GetTitle(CConstRef<CBioseq> bioseq)
+{
+ ITERATE(CSeq_descr::Tdata, desc, bioseq->GetDescr().Get()) {
+ if ((*desc)->Which() == CSeqdesc::e_Title) {
+ return (*desc)->GetTitle();
+ }
+ }
+ return string();
+}
+
string CBlastDBExtractor::ExtractFasta(const CBlastDBSeqId &id) {
stringstream out("");
@@ -643,7 +655,6 @@ string CBlastDBExtractor::ExtractFasta(const CBlastDBSeqId &id) {
fasta.SetFlag(CFastaOstream::fSuppressRange);
}
}
-
// Handle any requests for masked FASTA
static const CFastaOstream::EMaskType kMaskType = CFastaOstream::eSoftMask;
CSeqDB::TSequenceRanges masked_ranges;
@@ -657,7 +668,18 @@ string CBlastDBExtractor::ExtractFasta(const CBlastDBSeqId &id) {
fasta.SetMask(kMaskType, masks);
}
- try { fasta.Write(*m_Bioseq, range); }
+ try {
+ if (seqid->IsLocal())
+ {
+ string lcl_tmp = seqid->AsFastaString();
+ lcl_tmp = lcl_tmp.erase(0, 4);
+ out << ">" << lcl_tmp << " " << s_GetTitle(m_Bioseq) << '\n';
+ CScope scope(*CObjectManager::GetInstance());
+ fasta.WriteSequence(scope.AddBioseq(*m_Bioseq), range);
+ }
+ else
+ fasta.Write(*m_Bioseq, range);
+ }
catch (const CObjmgrUtilException& e) {
if (e.GetErrCode() == CObjmgrUtilException::eBadLocation) {
NCBI_THROW(CInvalidDataException, eInvalidRange,
@@ -671,7 +693,7 @@ int CBlastDBExtractor::x_ExtractTaxId()
{
x_SetGi();
- if (m_Gi) {
+ if (m_Gi != ZERO_GI) {
if (m_Gi2TaxidMap.first != m_Oid)
{
m_Gi2TaxidMap.first = m_Oid;
@@ -689,7 +711,7 @@ void CBlastDBExtractor::x_ExtractLeafTaxIds(set<int>& taxids)
{
x_SetGi();
- if (m_Gi) {
+ if (m_Gi != ZERO_GI) {
if (m_Gi2TaxidSetMap.first != m_Oid)
{
m_Gi2TaxidSetMap.first = m_Oid;
diff --git a/c++/src/objtools/blast/blastdb_format/seq_writer.cpp b/c++/src/objtools/blast/blastdb_format/seq_writer.cpp
index 64acf1b..a9e2381 100644
--- a/c++/src/objtools/blast/blastdb_format/seq_writer.cpp
+++ b/c++/src/objtools/blast/blastdb_format/seq_writer.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_writer.cpp 446244 2014-09-12 17:41:03Z ivanov $
+/* $Id: seq_writer.cpp 445606 2014-09-05 13:00:52Z madden $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
- "$Id: seq_writer.cpp 446244 2014-09-12 17:41:03Z ivanov $";
+ "$Id: seq_writer.cpp 445606 2014-09-05 13:00:52Z madden $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
diff --git a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
index fe5f2d7..c46a572 100644
--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.seqdb.lib 428664 2014-03-06 15:07:06Z fongah2 $
+# $Id: Makefile.seqdb.lib 468761 2015-05-27 20:14:39Z ucko $
ASN_DEP = blastdb
@@ -23,6 +23,7 @@ seqdbgimask \
seqdbobj
LIB = seqdb
+DLL_LIB = blastdb $(SOBJMGR_LIBS)
CFLAGS = $(FAST_CFLAGS)
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
diff --git a/c++/src/objtools/blast/seqdb_reader/demo/seqdb_demo.cpp b/c++/src/objtools/blast/seqdb_reader/demo/seqdb_demo.cpp
index 02810ff..9bd7cba 100644
--- a/c++/src/objtools/blast/seqdb_reader/demo/seqdb_demo.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/demo/seqdb_demo.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdb_demo.cpp 161402 2009-05-27 17:35:47Z camacho $
+/* $Id: seqdb_demo.cpp 468781 2015-05-28 12:51:59Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,7 +71,7 @@ public:
{
CSeqDB nr("nr", CSeqDB::eProtein);
- int gi(129295);
+ TGi gi = GI_CONST(129295);
int oid(0);
if (nr.GiToOid(gi, oid)) {
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdb.cpp b/c++/src/objtools/blast/seqdb_reader/seqdb.cpp
index 309145d..3d32d46 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdb.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdb.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdb.cpp 453781 2014-12-08 15:31:31Z ivanov $
+/* $Id: seqdb.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Implementation for the CSeqDB class, the top level class for SeqDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdb.cpp 453781 2014-12-08 15:31:31Z ivanov $";
+static char const rcsid[] = "$Id: seqdb.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -324,6 +324,28 @@ CSeqDB::CSeqDB()
m_Impl->Verify();
}
+void CSeqDB::SetMmapStrategy(
+ EMmapFileTypes filetype,
+ EMmapStrategies strategy
+)
+{
+ // If this construct looks odd, it's a Perl-ish technique,
+ // chaining the ternary ?: operator.
+ // Read it as
+ // thing = (if this) then that
+ // else (if this) then that
+ // else that
+ EMemoryAdvise st =
+ (strategy == eMmap_Sequential) ? eMADV_Sequential
+ : (strategy == eMmap_WillNeed) ? eMADV_WillNeed
+ : eMADV_Normal;
+ if (filetype == eMmap_IndexFile) {
+ CRegionMap::SetMmapStrategy_Index(st);
+ } else if (filetype == eMmap_SequenceFile) {
+ CRegionMap::SetMmapStrategy_Sequence(st);
+ }
+}
+
int CSeqDB::GetSeqLength(int oid) const
{
m_Impl->Verify();
@@ -366,11 +388,19 @@ CSeqDB::ESeqType CSeqDB::GetSequenceType() const
}
void CSeqDB::GetTaxIDs(int oid,
- map<int, int> & gi_to_taxid,
+ map<TGi, int> & gi_to_taxid,
bool persist) const
{
m_Impl->Verify();
- m_Impl->GetTaxIDs(oid, gi_to_taxid, persist);
+ typedef map<TGi, int> TmpMap;
+ TmpMap gi_to_taxid_tmp;
+ m_Impl->GetTaxIDs(oid, gi_to_taxid_tmp, persist);
+ if ( !persist ) {
+ gi_to_taxid.clear();
+ }
+ ITERATE ( TmpMap, it, gi_to_taxid_tmp ) {
+ gi_to_taxid[it->first] = it->second;
+ }
m_Impl->Verify();
}
@@ -385,12 +415,20 @@ void CSeqDB::GetTaxIDs(int oid,
void CSeqDB::GetLeafTaxIDs(
int oid,
- map<int, set<int> >& gi_to_taxid_set,
+ map<TGi, set<int> >& gi_to_taxid_set,
bool persist
) const
{
m_Impl->Verify();
- m_Impl->GetLeafTaxIDs(oid, gi_to_taxid_set, persist);
+ typedef map<TGi, set<int> > TmpMap;
+ TmpMap gi_to_taxid_set_tmp;
+ m_Impl->GetLeafTaxIDs(oid, gi_to_taxid_set_tmp, persist);
+ if ( !persist ) {
+ gi_to_taxid_set.clear();
+ }
+ ITERATE ( TmpMap, it, gi_to_taxid_set_tmp ) {
+ gi_to_taxid_set[it->first] = it->second;
+ }
m_Impl->Verify();
}
@@ -406,7 +444,7 @@ void CSeqDB::GetLeafTaxIDs(
}
CRef<CBioseq>
-CSeqDB::GetBioseq(int oid, int target_gi, const CSeq_id * target_id) const
+CSeqDB::GetBioseq(int oid, TGi target_gi, const CSeq_id * target_id) const
{
m_Impl->Verify();
CRef<CBioseq> rv = m_Impl->GetBioseq(oid, target_gi, target_id, true);
@@ -416,7 +454,7 @@ CSeqDB::GetBioseq(int oid, int target_gi, const CSeq_id * target_id) const
}
CRef<CBioseq>
-CSeqDB::GetBioseqNoData(int oid, int target_gi, const CSeq_id * target_id) const
+CSeqDB::GetBioseqNoData(int oid, TGi target_gi, const CSeq_id * target_id) const
{
m_Impl->Verify();
CRef<CBioseq> rv = m_Impl->GetBioseq(oid, target_gi, target_id, false);
@@ -660,7 +698,7 @@ list< CRef<CSeq_id> > CSeqDB::GetSeqIDs(int oid) const
return rv;
}
-int CSeqDB::GetSeqGI(int oid) const
+TGi CSeqDB::GetSeqGI(int oid) const
{
return m_Impl->GetSeqGI(oid);
}
@@ -692,7 +730,7 @@ bool CSeqDB::TiToOid(Int8 ti, int & oid) const
return rv;
}
-bool CSeqDB::GiToOid(int gi, int & oid) const
+bool CSeqDB::GiToOid(TGi gi, int & oid) const
{
m_Impl->Verify();
bool rv = m_Impl->GiToOid(gi, oid);
@@ -701,16 +739,18 @@ bool CSeqDB::GiToOid(int gi, int & oid) const
return rv;
}
-bool CSeqDB::OidToGi(int oid, int & gi) const
+bool CSeqDB::OidToGi(int oid, TGi & gi) const
{
m_Impl->Verify();
- bool rv = m_Impl->OidToGi(oid, gi);
+ TGi gi_tmp;
+ bool rv = m_Impl->OidToGi(oid, gi_tmp);
+ gi = gi_tmp;
m_Impl->Verify();
return rv;
}
-bool CSeqDB::PigToGi(int pig, int & gi) const
+bool CSeqDB::PigToGi(int pig, TGi & gi) const
{
m_Impl->Verify();
bool rv = false;
@@ -718,14 +758,16 @@ bool CSeqDB::PigToGi(int pig, int & gi) const
int oid(0);
if (m_Impl->PigToOid(pig, oid)) {
- rv = m_Impl->OidToGi(oid, gi);
+ TGi gi_tmp;
+ rv = m_Impl->OidToGi(oid, gi_tmp);
+ gi = gi_tmp;
}
m_Impl->Verify();
return rv;
}
-bool CSeqDB::GiToPig(int gi, int & pig) const
+bool CSeqDB::GiToPig(TGi gi, int & pig) const
{
m_Impl->Verify();
bool rv = false;
@@ -753,14 +795,14 @@ void CSeqDB::AccessionToOids(const string & acc, vector<int> & oids) const
if (oids.empty()) {
try {
- int gi = NStr::StringToInt(acc, NStr::fConvErr_NoThrow);
+ TGi gi = GI_FROM(
+ TIntId,
+ NStr::StringToNumeric<TIntId>(acc, NStr::fConvErr_NoThrow)
+ );
int oid(-1);
- if (gi > 0 && GiToOid(gi, oid)) {
- int oid0 = oid;
- if (m_Impl->CheckOrFindOID(oid) && (oid==oid0)) {
+ if (gi > ZERO_GI && m_Impl->GiToOidwFilterCheck(gi, oid)) {
oids.push_back(oid);
- }
}
}
catch(...) {
@@ -866,7 +908,7 @@ CSeqDBIter & CSeqDBIter::operator++()
}
CRef<CBioseq>
-CSeqDB::GiToBioseq(int gi) const
+CSeqDB::GiToBioseq(TGi gi) const
{
m_Impl->Verify();
@@ -891,7 +933,7 @@ CSeqDB::PigToBioseq(int pig) const
CRef<CBioseq> bs;
if (m_Impl->PigToOid(pig, oid)) {
- bs = m_Impl->GetBioseq(oid, 0, NULL, true);
+ bs = m_Impl->GetBioseq(oid, ZERO_GI, NULL, true);
}
m_Impl->Verify();
@@ -910,7 +952,7 @@ CSeqDB::SeqidToBioseq(const CSeq_id & seqid) const
m_Impl->SeqidToOids(seqid, oids, false);
if (! oids.empty()) {
- bs = m_Impl->GetBioseq(oids[0], 0, &seqid, true);
+ bs = m_Impl->GetBioseq(oids[0], ZERO_GI, &seqid, true);
}
m_Impl->Verify();
@@ -949,7 +991,7 @@ CSeqDB::FindVolumePaths(vector<string> & paths, bool recursive) const
}
void
-CSeqDB::GetGis(int oid, vector<int> & gis, bool append) const
+CSeqDB::GetGis(int oid, vector<TGi> & gis, bool append) const
{
m_Impl->Verify();
@@ -965,7 +1007,7 @@ CSeqDB::GetGis(int oid, vector<int> & gis, bool append) const
ITERATE(list< CRef<CSeq_id> >, seqid, seqids) {
if ((**seqid).IsGi()) {
- gis.push_back(GI_TO(int, (**seqid).GetGi()));
+ gis.push_back((**seqid).GetGi());
}
}
@@ -1234,6 +1276,11 @@ string CSeqDB::GenerateSearchPath()
return CSeqDBAtlas::GenerateSearchPath();
}
+void CSeqDB::SetVolsMemBit(int mbit)
+{
+ m_Impl->SetVolsMemBit(mbit);
+}
+
/// Functor class for FindFilesInDir
class CBlastDbFinder {
public:
@@ -1446,6 +1493,7 @@ CWgsDbTrimmer::x_ExtractOriginalWgsDbs()
CWgsDbTrimmer::CWgsDbTrimmer(const string& wgs_db_list)
: m_OrigWgsList(wgs_db_list)
{
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if (app) {
m_Path = app->GetEnvironment().Get("WGS_GILIST_DIR");
@@ -1467,7 +1515,7 @@ CWgsDbTrimmer::x_ReadGiListsForDbs()
CNcbiOstrstream oss;
oss << m_Path << "/" << CDirEntry(*wgs_db_name).GetName() << kExtn;
string fname = CNcbiOstrstreamToString(oss);
- vector<int> gis;
+ vector<TGi> gis;
try {
bool in_order = false;
SeqDB_ReadGiList(fname, gis, &in_order);
@@ -1475,7 +1523,11 @@ CWgsDbTrimmer::x_ReadGiListsForDbs()
sort(gis.begin(), gis.end());
}
} catch (...) {} // if there's no GI list, save it
- retval[*wgs_db_name] = gis;
+ vector<TGi>& dst = retval[*wgs_db_name];
+ dst.clear();
+ ITERATE ( vector<TGi>, it, gis ) {
+ dst.push_back(*it);
+ }
_TRACE("Read " << gis.size() << " from " << fname);
}
}
@@ -1496,8 +1548,8 @@ string CWgsDbTrimmer::GetDbList()
}
NON_CONST_ITERATE(TGiLists, gis4wgs_db, wgs_gi_lists) {
const string& wgs_db_name = gis4wgs_db->first;
- const vector<int>& wgs_gis = gis4wgs_db->second;
- if (find(wgs_gis.begin(), wgs_gis.end(), GI_TO(int, *gi)) != wgs_gis.end()) {
+ const vector<TGi>& wgs_gis = gis4wgs_db->second;
+ if (find(wgs_gis.begin(), wgs_gis.end(), *gi) != wgs_gis.end()) {
trimmed_wgs_dbs.insert(wgs_db_name);
wgs_gi_lists.erase(wgs_db_name);
break;
@@ -1506,7 +1558,7 @@ string CWgsDbTrimmer::GetDbList()
}
ITERATE(TGiLists, gis4wgs_db, wgs_gi_lists) {
const string& wgs_db_name = gis4wgs_db->first;
- const vector<int>& wgs_gis = gis4wgs_db->second;
+ const vector<TGi>& wgs_gis = gis4wgs_db->second;
if (wgs_gis.empty()) {
trimmed_wgs_dbs.insert(wgs_db_name);
}
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp
index 59220f6..b1fca52 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbatlas.cpp 463520 2015-03-30 13:36:55Z ivanov $
+/* $Id: seqdbatlas.cpp 463291 2015-03-26 14:57:38Z rackerst $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// classes, which provide control of a set of memory mappings.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbatlas.cpp 463520 2015-03-30 13:36:55Z ivanov $";
+static char const rcsid[] = "$Id: seqdbatlas.cpp 463291 2015-03-26 14:57:38Z rackerst $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -1141,6 +1141,10 @@ void CRegionMap::Show()
}
}
+EMemoryAdvise CRegionMap::sm_MmapStrategy_Index = eMADV_Normal;
+
+EMemoryAdvise CRegionMap::sm_MmapStrategy_Sequence = eMADV_Normal;
+
CRegionMap::CRegionMap(const string * fname, int fid, TIndx begin, TIndx end)
: m_Data (0),
m_MemFile (0),
@@ -1201,16 +1205,27 @@ bool CRegionMap::MapMmap(CSeqDBAtlas * atlas)
}
m_Data = (const char*) m_MemFile->Map(m_Begin, m_End - m_Begin);
-/*
+
string last2 = m_Fname->substr(m_Fname->length() - 2);
- if (last2 == "in" || last2 == "sq") {
+ EMemoryAdvise strategy = eMADV_Normal;
+ if (last2 == "in") {
+ strategy = sm_MmapStrategy_Index;
+ } else if (last2 == "sq") {
+ strategy = sm_MmapStrategy_Sequence;
+ }
+
+ // If "normal" is set, don't call MemoryAdvise at all. We cannot
+ // guarantee that a call to MemoryAdvise with eMADV_Normal gives
+ // identical behavior to not calling MemoryAdvise in the first
+ // place, even if eMADV_Normal is the default.
+ if (strategy != eMADV_Normal) {
MemoryAdvise(
(void*) m_Data,
(unsigned long) (m_End - m_Begin),
- eMADV_WillNeed
+ strategy
);
}
-*/
+
}
catch(std::bad_alloc&) {
expt = "\nstd::bad_alloc.";
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbcommon.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbcommon.cpp
index d0f2bda..ffbddc3 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbcommon.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbcommon.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbcommon.cpp 433068 2014-04-22 16:33:04Z rackerst $
+/* $Id: seqdbcommon.cpp 484800 2015-11-16 15:18:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Definitions of various helper functions for SeqDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbcommon.cpp 433068 2014-04-22 16:33:04Z rackerst $";
+static char const rcsid[] = "$Id: seqdbcommon.cpp 484800 2015-11-16 15:18:00Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -645,21 +645,21 @@ void CSeqDBGiList::InsureOrder(ESortOrder order)
}
-bool CSeqDBGiList::FindGi(int gi) const
+bool CSeqDBGiList::FindGi(TGi gi) const
{
int oid(0), index(0);
return (const_cast<CSeqDBGiList *>(this))->GiToOid(gi, oid, index);
}
-bool CSeqDBGiList::GiToOid(int gi, int & oid)
+bool CSeqDBGiList::GiToOid(TGi gi, int & oid)
{
int index(0);
return GiToOid(gi, oid, index);
}
-bool CSeqDBGiList::GiToOid(int gi, int & oid, int & index)
+bool CSeqDBGiList::GiToOid(TGi gi, int & oid, int & index)
{
InsureOrder(eGi); // would assert be better?
@@ -667,7 +667,7 @@ bool CSeqDBGiList::GiToOid(int gi, int & oid, int & index)
while(b < e) {
int m = (b + e)/2;
- int m_gi = m_GisOids[m].gi;
+ TGi m_gi = m_GisOids[m].gi;
if (m_gi < gi) {
b = m + 1;
@@ -685,21 +685,21 @@ bool CSeqDBGiList::GiToOid(int gi, int & oid, int & index)
}
-bool CSeqDBGiList::FindTi(Int8 ti) const
+bool CSeqDBGiList::FindTi(TTi ti) const
{
int oid(0), index(0);
return (const_cast<CSeqDBGiList *>(this))->TiToOid(ti, oid, index);
}
-bool CSeqDBGiList::TiToOid(Int8 ti, int & oid)
+bool CSeqDBGiList::TiToOid(TTi ti, int & oid)
{
int index(0);
return TiToOid(ti, oid, index);
}
-bool CSeqDBGiList::TiToOid(Int8 ti, int & oid, int & index)
+bool CSeqDBGiList::TiToOid(TTi ti, int & oid, int & index)
{
InsureOrder(eGi); // would assert be better?
@@ -707,7 +707,7 @@ bool CSeqDBGiList::TiToOid(Int8 ti, int & oid, int & index)
while(b < e) {
int m = (b + e)/2;
- Int8 m_ti = m_TisOids[m].ti;
+ TTi m_ti = m_TisOids[m].ti;
if (m_ti < ti) {
b = m + 1;
@@ -762,7 +762,7 @@ bool CSeqDBGiList::SiToOid(const string &si, int & oid, int & index)
}
void
-CSeqDBGiList::GetGiList(vector<int>& gis) const
+CSeqDBGiList::GetGiList(vector<TGi>& gis) const
{
gis.clear();
gis.reserve(GetNumGis());
@@ -774,7 +774,7 @@ CSeqDBGiList::GetGiList(vector<int>& gis) const
void
-CSeqDBGiList::GetTiList(vector<Int8>& tis) const
+CSeqDBGiList::GetTiList(vector<TTi>& tis) const
{
tis.clear();
tis.reserve(GetNumTis());
@@ -785,7 +785,7 @@ CSeqDBGiList::GetTiList(vector<Int8>& tis) const
}
-void SeqDB_ReadBinaryGiList(const string & fname, vector<int> & gis)
+void SeqDB_ReadBinaryGiList(const string & fname, vector<TGi> & gis)
{
CMemoryFile mfile(SeqDB_MakeOSPath(fname));
@@ -807,7 +807,7 @@ void SeqDB_ReadBinaryGiList(const string & fname, vector<int> & gis)
gis.reserve(num_gis);
for(Int4 * elem = beginp + 2; elem < endp; elem ++) {
- gis.push_back((int) SeqDB_GetStdOrd(elem));
+ gis.push_back(GI_FROM(Int4, SeqDB_GetStdOrd(elem)));
}
}
@@ -884,12 +884,12 @@ void SeqDB_ReadMemoryGiList(const char * fbeginp,
gis.reserve(num_gis);
if (in_order) {
- int prev_gi =0;
+ TGi prev_gi = ZERO_GI;
bool in_gi_order = true;
Int4 * elem = bbeginp + 2;
while(elem < bendp) {
- int this_gi = (int) SeqDB_GetStdOrd(elem);
+ TGi this_gi = GI_FROM(Int4, SeqDB_GetStdOrd(elem));
gis.push_back(this_gi);
if (prev_gi > this_gi) {
@@ -901,13 +901,13 @@ void SeqDB_ReadMemoryGiList(const char * fbeginp,
}
while(elem < bendp) {
- gis.push_back((int) SeqDB_GetStdOrd(elem++));
+ gis.push_back(GI_FROM(Int4, SeqDB_GetStdOrd(elem++)));
}
*in_order = in_gi_order;
} else {
for(Int4 * elem = bbeginp + 2; elem < bendp; elem ++) {
- gis.push_back((int) SeqDB_GetStdOrd(elem));
+ gis.push_back(GI_FROM(Int4, SeqDB_GetStdOrd(elem)));
}
}
} else {
@@ -970,7 +970,7 @@ void SeqDB_ReadMemoryGiList(const char * fbeginp,
case '\r':
// Skip blank lines or comments by ignoring zero.
if (elem != 0) {
- gis.push_back(elem);
+ gis.push_back(GI_FROM(Uint4, elem));
}
elem = 0;
continue;
@@ -1283,10 +1283,10 @@ void SeqDB_ReadMemoryMixList(const char * fbeginp,
sis.push_back(NStr::ToLower(str_id));
}
else if (eTiId == id_type) {
- tis.push_back(num_id);
+ tis.push_back((TTi) num_id);
}
else if (eGiId == id_type) {
- gis.push_back(num_id);
+ gis.push_back(GI_FROM(Int8, num_id));
}
else {
cerr << "WARNING: " << acc
@@ -1361,7 +1361,7 @@ void SeqDB_ReadMixList(const string & fname, vector<CSeqDBGiList::SGiOid> & gis,
SeqDB_ReadMemoryMixList(fbeginp, fendp, gis, tis, sis, in_order);
}
-void SeqDB_ReadGiList(const string & fname, vector<int> & gis, bool * in_order)
+void SeqDB_ReadGiList(const string & fname, vector<TGi> & gis, bool * in_order)
{
typedef vector<CSeqDBGiList::SGiOid> TPairList;
@@ -1386,7 +1386,7 @@ void SeqDB_ReadSiList(const string & fname, vector<CSeqDBGiList::SSiOid> & sis,
SeqDB_ReadMemorySiList(fbeginp, fendp, sis, in_order);
}
-bool CSeqDBNegativeList::FindGi(int gi)
+bool CSeqDBNegativeList::FindGi(TGi gi)
{
InsureOrder();
@@ -1394,7 +1394,7 @@ bool CSeqDBNegativeList::FindGi(int gi)
while(b < e) {
int m = (b + e)/2;
- int m_gi = m_Gis[m];
+ TGi m_gi = m_Gis[m];
if (m_gi < gi) {
b = m + 1;
@@ -1409,7 +1409,7 @@ bool CSeqDBNegativeList::FindGi(int gi)
}
-bool CSeqDBNegativeList::FindTi(Int8 ti)
+bool CSeqDBNegativeList::FindTi(TTi ti)
{
InsureOrder();
@@ -1417,7 +1417,7 @@ bool CSeqDBNegativeList::FindTi(Int8 ti)
while(b < e) {
int m = (b + e)/2;
- Int8 m_ti = m_Tis[m];
+ TTi m_ti = m_Tis[m];
if (m_ti < ti) {
b = m + 1;
@@ -1442,7 +1442,7 @@ bool CSeqDBNegativeList::FindId(const CSeq_id & id, bool & match_type)
{
if (id.IsGi()) {
match_type = true;
- return FindGi(GI_TO(int, id.GetGi()));
+ return FindGi(id.GetGi());
} else if (id.IsGeneral() && id.GetGeneral().GetDb() == "ti") {
match_type = true;
const CObject_id & obj = id.GetGeneral().GetTag();
@@ -1462,13 +1462,13 @@ bool CSeqDBNegativeList::FindId(const CSeq_id & id, bool & match_type)
bool CSeqDBGiList::FindId(const CSeq_id & id)
{
if (id.IsGi()) {
- return FindGi(GI_TO(int, id.GetGi()));
+ return FindGi(id.GetGi());
} else if (id.IsGeneral() && id.GetGeneral().GetDb() == "ti") {
const CObject_id & obj = id.GetGeneral().GetTag();
- Int8 ti = (obj.IsId()
- ? obj.GetId()
- : NStr::StringToInt8(obj.GetStr()));
+ TTi ti = (obj.IsId()
+ ? (TTi) obj.GetId()
+ : (TTi) NStr::StringToInt8(obj.GetStr()));
return FindTi(ti);
} else {
@@ -1560,11 +1560,12 @@ void SeqDB_CombineAndQuote(const vector<string> & dbs,
void SeqDB_SplitQuoted(const string & dbname,
- vector<CTempString> & dbs)
+ vector<CTempString> & dbs,
+ bool keep_quote)
{
vector<CSeqDB_Substring> subs;
- SeqDB_SplitQuoted(dbname, subs);
+ SeqDB_SplitQuoted(dbname, subs, keep_quote);
dbs.resize(0);
dbs.reserve(subs.size());
@@ -1577,7 +1578,8 @@ void SeqDB_SplitQuoted(const string & dbname,
void SeqDB_SplitQuoted(const string & dbname,
- vector<CSeqDB_Substring> & dbs)
+ vector<CSeqDB_Substring> & dbs,
+ bool keep_quote)
{
// split names
@@ -1593,6 +1595,7 @@ void SeqDB_SplitQuoted(const string & dbname,
// Quoted mode sees '"' as the only actionable token.
if (ch == '"') {
if (begin < i) {
+ if(keep_quote) i++;
dbs.push_back(CSeqDB_Substring(sp + begin, sp + i));
}
begin = i + 1;
@@ -1610,7 +1613,7 @@ void SeqDB_SplitQuoted(const string & dbname,
if (begin < i) {
dbs.push_back(CSeqDB_Substring(sp + begin, sp + i));
}
- begin = i + 1;
+ begin = keep_quote ? i : i + 1;
quoted = true;
}
}
@@ -1622,7 +1625,7 @@ void SeqDB_SplitQuoted(const string & dbname,
}
-CIntersectionGiList::CIntersectionGiList(CSeqDBGiList & gilist, vector<int> & gis)
+CIntersectionGiList::CIntersectionGiList(CSeqDBGiList & gilist, vector<TGi> & gis)
{
_ASSERT(this != & gilist);
@@ -1635,8 +1638,8 @@ CIntersectionGiList::CIntersectionGiList(CSeqDBGiList & gilist, vector<int> & gi
int gis_n = (int) gis.size();
while(list_i < list_n && gis_i < gis_n) {
- int L = gilist.GetGiOid(list_i).gi;
- int G = gis[gis_i];
+ TGi L = gilist.GetGiOid(list_i).gi;
+ TGi G = gis[gis_i];
if (L < G) {
list_i ++;
@@ -1658,7 +1661,7 @@ CIntersectionGiList::CIntersectionGiList(CSeqDBGiList & gilist, vector<int> & gi
}
-CIntersectionGiList::CIntersectionGiList(CSeqDBNegativeList & neg_gilist, vector<int> & gis)
+CIntersectionGiList::CIntersectionGiList(CSeqDBNegativeList & neg_gilist, vector<TGi> & gis)
{
neg_gilist.InsureOrder();
sort(gis.begin(), gis.end());
@@ -1669,8 +1672,8 @@ CIntersectionGiList::CIntersectionGiList(CSeqDBNegativeList & neg_gilist, vector
int gis_n = (int) gis.size();
while(list_i < list_n && gis_i < gis_n) {
- int L = neg_gilist.GetGi(list_i);
- int G = gis[gis_i];
+ TGi L = neg_gilist.GetGi(list_i);
+ TGi G = gis[gis_i];
if (L < G) {
list_i ++;
@@ -1685,7 +1688,7 @@ CIntersectionGiList::CIntersectionGiList(CSeqDBNegativeList & neg_gilist, vector
list_i++;
- int last_gi = gis[gis_i];
+ TGi last_gi = gis[gis_i];
do { gis_i++; } while (gis_i < gis_n && gis[gis_i] == last_gi);
}
@@ -1698,7 +1701,7 @@ CIntersectionGiList::CIntersectionGiList(CSeqDBNegativeList & neg_gilist, vector
}
-CSeqDBIdSet::CSeqDBIdSet(const vector<int> & ids, EIdType t, bool positive)
+CSeqDBIdSet::CSeqDBIdSet(const vector<Int4> & ids, EIdType t, bool positive)
: m_Positive(positive), m_IdType(t), m_Ids(new CSeqDBIdSet_Vector(ids))
{
x_SortAndUnique(m_Ids->Set());
@@ -1710,6 +1713,20 @@ CSeqDBIdSet::CSeqDBIdSet(const vector<Int8> & ids, EIdType t, bool positive)
x_SortAndUnique(m_Ids->Set());
}
+CSeqDBIdSet::CSeqDBIdSet(const vector<Uint8> & ids, EIdType t, bool positive)
+ : m_Positive(positive), m_IdType(t), m_Ids(new CSeqDBIdSet_Vector(ids))
+{
+ x_SortAndUnique(m_Ids->Set());
+}
+
+#ifdef NCBI_STRICT_GI
+CSeqDBIdSet::CSeqDBIdSet(const vector<TGi> & ids, EIdType t, bool positive)
+ : m_Positive(positive), m_IdType(t), m_Ids(new CSeqDBIdSet_Vector(ids))
+{
+ x_SortAndUnique(m_Ids->Set());
+}
+#endif
+
void CSeqDBIdSet::x_SortAndUnique(vector<Int8> & ids)
{
sort(ids.begin(), ids.end());
@@ -1873,7 +1890,7 @@ x_BooleanSetOperation(EOperation op,
}
void CSeqDBIdSet::Compute(EOperation op,
- const vector<int> & ids,
+ const vector<Int4> & ids,
bool positive)
{
CRef<CSeqDBIdSet_Vector> result(new CSeqDBIdSet_Vector);
@@ -1919,6 +1936,29 @@ void CSeqDBIdSet::Compute(EOperation op,
m_Ids = result;
}
+void CSeqDBIdSet::Compute(EOperation op,
+ const vector<Uint8> & ids,
+ bool positive)
+{
+ CRef<CSeqDBIdSet_Vector> result(new CSeqDBIdSet_Vector);
+
+ CRef<CSeqDBIdSet_Vector> B(new CSeqDBIdSet_Vector(ids));
+ x_SortAndUnique(B->Set());
+
+ bool result_pos(true);
+
+ x_BooleanSetOperation(op,
+ m_Ids->Set(),
+ m_Positive,
+ B->Set(),
+ positive,
+ result->Set(),
+ result_pos);
+
+ m_Positive = result_pos;
+ m_Ids = result;
+}
+
void CSeqDBIdSet::Compute(EOperation op, const CSeqDBIdSet & ids)
{
if (m_IdType != ids.m_IdType ) {
@@ -1963,7 +2003,7 @@ CRef<CSeqDBGiList> CSeqDBIdSet::GetPositiveList()
ITERATE(vector<Int8>, iter, m_Ids->Set()) {
_ASSERT(((*iter) >> 32) == 0);
- ids->AddGi((int)*iter);
+ ids->AddGi(GI_FROM(Int8, *iter));
}
}
@@ -1991,7 +2031,7 @@ CRef<CSeqDBNegativeList> CSeqDBIdSet::GetNegativeList()
ITERATE(vector<Int8>, iter, m_Ids->Set()) {
_ASSERT(((*iter) >> 32) == 0);
- ids->AddGi((int)*iter);
+ ids->AddGi(GI_FROM(Int8, *iter));
}
}
@@ -2034,7 +2074,7 @@ ESeqDBIdType SeqDB_SimplifySeqid(CSeq_id & bestid,
switch(bestid.Which()) {
case CSeq_id::e_Gi:
simpler = true;
- num_id = bestid.GetGi();
+ num_id = GI_TO(Int8, bestid.GetGi());
result = eGiId;
break;
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbexpert.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbexpert.cpp
index 8a0176a..11bc02c 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbexpert.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbexpert.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbexpert.cpp 151315 2009-02-03 18:13:26Z camacho $
+/* $Id: seqdbexpert.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Implementation for the CSeqDBExpert class.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbexpert.cpp 151315 2009-02-03 18:13:26Z camacho $";
+static char const rcsid[] = "$Id: seqdbexpert.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -76,8 +76,8 @@ void CSeqDBExpert::GetRawSeqAndAmbig(int oid,
m_Impl->Verify();
}
-void CSeqDBExpert::GetGiBounds(int * low_id,
- int * high_id,
+void CSeqDBExpert::GetGiBounds(TGi * low_id,
+ TGi * high_id,
int * count)
{
m_Impl->Verify();
@@ -113,7 +113,7 @@ unsigned CSeqDBExpert::GetSequenceHash(int oid)
m_Impl->Verify();
unsigned h = m_Impl->GetSequenceHash(oid);
m_Impl->Verify();
-
+
return h;
}
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp
index d5a20a4..eb857a9 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbgilistset.cpp 255926 2011-03-01 13:20:37Z maning $
+/* $Id: seqdbgilistset.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// interface for all functionality of one database volume.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbgilistset.cpp 255926 2011-03-01 13:20:37Z maning $";
+static char const rcsid[] = "$Id: seqdbgilistset.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -51,10 +51,10 @@ struct SSeqDB_IndexCountPair {
public:
/// Index of the volume in the volume set.
int m_Index;
-
+
/// Number of OIDs associated with this volume.
int m_Count;
-
+
/// Less than operator, where elements with larger allows sorting.
/// Elements are sorted by number of OIDs in descending order.
/// @param rhs
@@ -67,7 +67,7 @@ public:
/// CSeqDBNodeIdList
-///
+///
/// This class defines a simple CSeqDBGiList subclass which is read
/// from a gi list file using the CSeqDBAtlas. It uses the atlas for
/// file access and registers the memory used by the vector with the
@@ -95,16 +95,16 @@ public:
: m_VectorMemory(atlas)
{
CSeqDBAtlas::TIndx file_size(0);
-
+
CSeqDBMemLease memlease(atlas);
atlas.GetFile(memlease, fname.GetPathS(), file_size, locked);
-
+
const char * fbeginp = memlease.GetPtr(0);
const char * fendp = fbeginp + (int)file_size;
-
+
try {
bool in_order = false;
-
+
switch(list_type) {
case CSeqDBGiListSet::eGiList:
SeqDB_ReadMemoryGiList(fbeginp, fendp, m_GisOids, & in_order);
@@ -115,7 +115,7 @@ public:
case CSeqDBGiListSet::eSiList:
SeqDB_ReadMemorySiList(fbeginp, fendp, m_SisOids, & in_order);
}
-
+
if (in_order) {
m_CurrentOrder = eGi;
}
@@ -124,22 +124,22 @@ public:
memlease.Clear();
throw;
}
-
+
memlease.Clear();
-
+
int vector_size =
(int(m_GisOids.size() * sizeof(m_GisOids[0])) +
int(m_TisOids.size() * sizeof(m_TisOids[0])));
-
+
atlas.RegisterExternal(m_VectorMemory, vector_size, locked);
// TODO m_VectorMemory for seqid_list
}
-
+
/// Destructor
virtual ~CSeqDBNodeFileIdList()
{
}
-
+
private:
/// Memory associated with the m_GisOids vector.
CSeqDBMemReg m_VectorMemory;
@@ -156,49 +156,49 @@ CSeqDBGiListSet::CSeqDBGiListSet(CSeqDBAtlas & atlas,
m_NegativeList (neg_list)
{
_ASSERT(user_list.Empty() || neg_list.Empty());
-
+
if (m_UserList.NotEmpty() && m_UserList->NotEmpty()) {
typedef SSeqDB_IndexCountPair TIndexCount;
vector<TIndexCount> OidsPerVolume;
-
+
// Build a list of volumes sorted by OID count.
-
+
for(int i = 0; i < volset.GetNumVols(); i++) {
const CSeqDBVolEntry * vol = volset.GetVolEntry(i);
-
+
TIndexCount vol_oids;
vol_oids.m_Index = i;
vol_oids.m_Count = vol->OIDEnd() - vol->OIDStart();
-
+
OidsPerVolume.push_back(vol_oids);
}
-
+
// The largest volumes should be used first, to minimize the
// number of failed GI->OID conversion attempts. Searching input
// GIs against larger volumes first should eliminate most of the
// GIs by the time smaller volumes are searched, thus reducing the
// total number of lookups.
-
+
std::sort(OidsPerVolume.begin(), OidsPerVolume.end());
-
+
for(int i = 0; i < (int)OidsPerVolume.size(); i++) {
int vol_idx = OidsPerVolume[i].m_Index;
-
+
const CSeqDBVolEntry * vol = volset.GetVolEntry(vol_idx);
-
+
// Note: The implied ISAM lookups will sort by GI/TI.
-
+
vol->Vol()->IdsToOids(*m_UserList, locked);
}
} else if (m_NegativeList.NotEmpty() && m_NegativeList->NotEmpty()) {
// We don't bother to sort these since every ISAM mapping must
// be examined for the negative ID list case.
-
+
for(int i = 0; i < volset.GetNumVols(); i++) {
const CSeqDBVolEntry * vol = volset.GetVolEntry(i);
-
+
// Note: The implied ISAM lookups will sort by GI/TI.
-
+
vol->Vol()->IdsToOids(*m_NegativeList, locked);
}
}
@@ -214,37 +214,37 @@ CSeqDBGiListSet::GetNodeIdList(const CSeqDB_Path & filename,
// subtract pseudo allocations from the memory bound; this would
// allow GI list vectors to share the memory bound with memory
// mapped file ranges.
-
+
m_Atlas.Lock(locked);
-
+
// Seperate indices are used for TIs and GIs. (Attempting to use
// the same file for both should also produce an error when the
// binary file is read, as the magic number is different.)
- TNodeListMap& map_ref = (list_type == eGiList) ? m_GINodeListMap :
+ TNodeListMap& map_ref = (list_type == eGiList) ? m_GINodeListMap :
((list_type == eTiList) ? m_TINodeListMap : m_SINodeListMap);
CRef<CSeqDBGiList> gilist = map_ref[filename.GetPathS()];
-
+
if (gilist.Empty()) {
gilist.Reset(new CSeqDBNodeFileIdList(m_Atlas,
filename,
list_type,
locked));
-
+
if (m_UserList.NotEmpty()) {
// Note: translates the GIs and TIs, but ignores Seq-ids.
x_TranslateFromUserList(*gilist);
}
-
+
map_ref[filename.GetPathS()] = gilist;
}
-
+
// Note: in pure-GI mode, it might be more efficient (in some
// cases) to translate all sub-lists, then translate the main list
// in terms of those, rather than the other way round. It might
// be a good idea to investigate this -- it should only be done if
// the sub-lists are (collectively) smaller than the user list.
-
+
// If there are Seq-ids, we need to translate all GI lists from
// the volume data, because some of the Seq-ids may refer to the
// same sequences as GIs in those lists. More sophisticated
@@ -253,32 +253,32 @@ CSeqDBGiListSet::GetNodeIdList(const CSeqDB_Path & filename,
// where GIs are available for all sequences), then we would be
// able to continue processing as if the User GI list were
// strictly GI based.
-
+
// The ideal solution might be to build a conceptual map of all
// data sources and estimate the time needed for different
// techniques. This has not been done.
-
+
bool mixed_ids = m_UserList.Empty() || (!! m_UserList->GetNumSis());
-
+
if (! mixed_ids) {
if ((m_UserList->GetNumTis() && gilist->GetNumGis()) ||
(m_UserList->GetNumGis() && gilist->GetNumTis())) {
-
+
mixed_ids = true;
}
}
-
+
if (m_UserList.Empty() || mixed_ids) {
volp->IdsToOids(*gilist, locked);
}
-
+
// If there is a volume GI list, it will also be attached to the
// volume, and replaces the user GI list attachment (if there was
// one). There can be one user GI list or multiple volume GI
// lists for each volume.
-
+
volp->AttachVolumeGiList(gilist);
-
+
return gilist;
}
@@ -286,22 +286,22 @@ void CSeqDBGiListSet::x_TranslateGisFromUserList(CSeqDBGiList & gilist)
{
CSeqDBGiList & source = *m_UserList;
CSeqDBGiList & target = gilist;
-
+
source.InsureOrder(CSeqDBGiList::eGi);
target.InsureOrder(CSeqDBGiList::eGi);
-
+
int source_num = source.GetNumGis();
int target_num = target.GetNumGis();
-
+
int source_index = 0;
int target_index = 0;
-
+
while(source_index < source_num && target_index < target_num) {
- int source_gi = source.GetGiOid(source_index).gi;
- int target_gi = target.GetGiOid(target_index).gi;
-
+ TGi source_gi = source.GetGiOid(source_index).gi;
+ TGi target_gi = target.GetGiOid(target_index).gi;
+
// Match; translate if needed
-
+
if (source_gi == target_gi) {
if (target.GetGiOid(target_index).oid == -1) {
target.SetGiTranslation(target_index, source.GetGiOid(source_index).oid);
@@ -310,11 +310,11 @@ void CSeqDBGiListSet::x_TranslateGisFromUserList(CSeqDBGiList & gilist)
source_index++;
} else if (source_gi > target_gi) {
target_index ++;
-
+
// Search target using expanding jumps
int jump = 2;
int test = target_index + jump;
-
+
while(test < target_num && target.GetGiOid(test).gi < source_gi) {
target_index = test;
jump *= 2;
@@ -322,11 +322,11 @@ void CSeqDBGiListSet::x_TranslateGisFromUserList(CSeqDBGiList & gilist)
}
} else /* source_gi < target_gi */ {
source_index ++;
-
+
// Search source using expanding jumps
int jump = 2;
int test = source_index + jump;
-
+
while(test < source_num && source.GetGiOid(test).gi < target_gi) {
source_index = test;
jump *= 2;
@@ -340,54 +340,54 @@ void CSeqDBGiListSet::x_TranslateTisFromUserList(CSeqDBGiList & gilist)
{
CSeqDBGiList & source = *m_UserList;
CSeqDBGiList & target = gilist;
-
+
source.InsureOrder(CSeqDBGiList::eGi);
target.InsureOrder(CSeqDBGiList::eGi);
-
+
int source_num = source.GetNumTis();
int target_num = target.GetNumTis();
-
+
int source_index = 0;
int target_index = 0;
-
+
while(source_index < source_num && target_index < target_num) {
Int8 source_ti = source.GetTiOid(source_index).ti;
Int8 target_ti = target.GetTiOid(target_index).ti;
-
+
// Match; translate if needed
-
+
if (source_ti == target_ti) {
if (target.GetTiOid(target_index).oid == -1) {
target.SetTiTranslation(target_index,
source.GetTiOid(source_index).oid);
}
-
+
target_index++;
source_index++;
} else if (source_ti > target_ti) {
target_index ++;
-
+
// Search target using expanding jumps
int jump = 2;
int test = target_index + jump;
-
+
while(test < target_num &&
target.GetTiOid(test).ti < source_ti) {
-
+
target_index = test;
jump *= 2;
test = target_index + jump;
}
} else /* source_ti < target_ti */ {
source_index ++;
-
+
// Search source using expanding jumps
int jump = 2;
int test = source_index + jump;
-
+
while(test < source_num &&
source.GetTiOid(test).ti < target_ti) {
-
+
source_index = test;
jump *= 2;
test = source_index + jump;
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbgimask.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbgimask.cpp
index e8d9cc6..e4cc75a 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbgimask.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbgimask.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbgimask.cpp 311249 2011-07-11 14:12:16Z camacho $
+/* $Id: seqdbgimask.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// which support read operations on Gi based BlastDB masks.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbgimask.cpp 311249 2011-07-11 14:12:16Z camacho $";
+static char const rcsid[] = "$Id: seqdbgimask.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -50,15 +50,15 @@ CSeqDBGiMask::CSeqDBGiMask(CSeqDBAtlas & atlas,
const vector <string> & mask_name)
: m_Atlas (atlas),
m_MaskNames (mask_name),
- m_AlgoId (-1),
+ m_AlgoId (-1),
m_IndexFile (m_Atlas),
m_IndexLease (m_Atlas),
m_OffsetFile (m_Atlas),
m_OffsetLease (m_Atlas)
{ }
-const string &
-CSeqDBGiMask::GetDesc(int algo_id,
+const string &
+CSeqDBGiMask::GetDesc(int algo_id,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
@@ -66,19 +66,19 @@ CSeqDBGiMask::GetDesc(int algo_id,
return m_Desc;
}
-void
+void
CSeqDBGiMask::GetMaskData(int algo_id,
- int gi,
+ TGi gi,
CSeqDB::TSequenceRanges &ranges,
CSeqDBLockHold &locked)
{
- m_Atlas.Lock(locked);
+ m_Atlas.Lock(locked);
x_Open(algo_id, locked);
int page, vol, off;
- if (s_BinarySearch(m_GiIndex, m_NumIndex, gi, page)) {
+ if (s_BinarySearch(m_GiIndex, m_NumIndex, GI_TO(int, gi), page)) {
vol = m_GiIndex[m_NumIndex + page * 2];
off = m_GiIndex[m_NumIndex + page * 2 + 1];
} else {
@@ -94,8 +94,8 @@ CSeqDBGiMask::GetMaskData(int algo_id,
const Int4 * offset = (const Int4 *)
m_OffsetFile.GetRegion(m_OffsetLease, begin, end, locked);
- if (!s_BinarySearch(offset, pagesize, gi, page)) return;
-
+ if (!s_BinarySearch(offset, pagesize, GI_TO(int, gi), page)) return;
+
vol = offset[pagesize + page * 2];
off = offset[pagesize + page * 2 + 1];
}
@@ -117,7 +117,7 @@ CSeqDBGiMask::GetMaskData(int algo_id,
}
void CSeqDBGiMask::x_Open(Int4 algo_id,
- CSeqDBLockHold & locked)
+ CSeqDBLockHold & locked)
{
if (algo_id == m_AlgoId) {
return;
@@ -137,14 +137,14 @@ void CSeqDBGiMask::x_Open(Int4 algo_id,
}
m_Atlas.Lock(locked);
-
+
try {
CSeqDB_Path fn_i(SeqDB_ResolveDbPath(m_MaskNames[algo_id] + ext_i));
CSeqDB_Path fn_o(SeqDB_ResolveDbPath(m_MaskNames[algo_id] + ext_o));
bool found_i = m_IndexFile.Open(fn_i, locked);
bool found_o = m_OffsetFile.Open(fn_o, locked);
-
+
if (! (found_i && found_o)) {
NCBI_THROW(CSeqDBException, eFileErr,
"Could not open gi-mask index files.");
@@ -176,7 +176,7 @@ void CSeqDBGiMask::x_Open(Int4 algo_id,
}
}
}
-
+
}
catch(...) {
m_AlgoId = -1;
@@ -200,22 +200,22 @@ void CSeqDBGiMask::s_GetFileRange(TIndx begin,
void CSeqDBGiMask::x_ReadFields(CSeqDBLockHold & locked)
{
const int kFixedFieldBytes = 32;
-
+
m_Atlas.Lock(locked);
-
+
// First, get the 32 bytes of fields that we know exist.
-
+
CBlastDbBlob header;
s_GetFileRange(0, kFixedFieldBytes, m_IndexFile, m_IndexLease, header, locked);
-
+
int fmt_version = header.ReadInt4();
-
+
if (fmt_version != 1) {
NCBI_THROW(CSeqDBException,
eFileErr,
"Gi-mask file uses unknown format_version.");
}
-
+
m_NumVols = header.ReadInt4();
m_GiSize = header.ReadInt4();
m_OffsetSize = header.ReadInt4();
@@ -225,32 +225,32 @@ void CSeqDBGiMask::x_ReadFields(CSeqDBLockHold & locked)
m_NumGi = header.ReadInt4();
m_IndexStart = header.ReadInt4();
-
+
SEQDB_FILE_ASSERT(m_IndexStart >= 0);
SEQDB_FILE_ASSERT(m_IndexFile.GetFileLength() >= m_IndexStart);
-
+
// Now we know how long the header actually is, so expand the blob
// to reference the whole thing. (The memory lease should already
// hold the data, so this will just adjust a few integer fields.)
-
+
s_GetFileRange(0, m_IndexStart, m_IndexFile, m_IndexLease, header, locked);
-
+
// Get string type header fields.
-
+
m_Desc = header.ReadString (kStringFmt);
m_Date = header.ReadString (kStringFmt);
SEQDB_FILE_ASSERT(m_Desc.size());
SEQDB_FILE_ASSERT(m_Date.size());
-
+
// Map the index file
TIndx begin = m_IndexStart;
TIndx end = begin + m_NumIndex * (m_GiSize + m_OffsetSize);
- m_GiIndex = (const Int4 *)
+ m_GiIndex = (const Int4 *)
m_IndexFile.GetRegion(m_IndexLease, begin, end, locked);
}
-// TODO: if gi becomes 8-bytes long, this may better be implemented as
+// TODO: if gi becomes 8-bytes long, this may better be implemented as
// a template function
bool
CSeqDBGiMask::s_BinarySearch(const int *keys,
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbgimask.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbgimask.hpp
index d316c3b..aa054ec 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbgimask.hpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbgimask.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS_SEQDB__SEQDBGIMASK_HPP
#define OBJTOOLS_READERS_SEQDB__SEQDBGIMASK_HPP
-/* $Id: seqdbgimask.hpp 315260 2011-07-22 13:48:03Z camacho $
+/* $Id: seqdbgimask.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,20 +51,20 @@ USING_SCOPE(objects);
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// CSeqDBGiMask class.
-///
+///
/// This code supports Gi-based database masks
class CSeqDBGiMask : public CObject {
public:
/// Constructor.
- ///
+ ///
/// @param atlas
/// The atlas layer managing memory lease [in]
/// @param mask_name
/// The names of the mask files. [in]
CSeqDBGiMask(CSeqDBAtlas & atlas,
const vector <string> & mask_name);
-
+
/// Destructor.
~CSeqDBGiMask() {
m_IndexLease.Clear();
@@ -75,7 +75,7 @@ public:
delete m_DataLease[i];
}
};
-
+
/// Get the mask description for algo id
/// @param algo_id The chosen algo id [in]
/// @param locked
@@ -90,7 +90,7 @@ public:
/// @param locked
/// The lock holder object for this thread (or NULL). [in]
void GetMaskData(int algo_id,
- int gi,
+ TGi gi,
CSeqDB::TSequenceRanges &ranges,
CSeqDBLockHold &locked);
@@ -121,12 +121,12 @@ public:
/// Get the mask algorithsm name for a numeric id
/// @param algo_id The algorithm id [in]
- /// @return the algorithm name
+ /// @return the algorithm name
const string & GetAlgorithmName(int algo_id) const {
x_VerifyAlgorithmId(algo_id);
return m_MaskNames[algo_id];
}
-
+
/// Get the names of available mask algorithms as string
string GetAvailableAlgorithmNames() const {
CNcbiOstrstream retval;
@@ -140,7 +140,7 @@ public:
<< setw(40) << left << m_MaskNames[id] << endl;
}
return CNcbiOstrstreamToString(retval);
- }
+ }
private:
/// Sgring format used by gi mask files
@@ -149,13 +149,13 @@ private:
/// File offset type.
typedef CSeqDBAtlas::TIndx TIndx;
-
+
/// Prevent copy construction.
CSeqDBGiMask(const CSeqDBGiMask&);
-
+
/// Prevent copy assignment.
CSeqDBGiMask& operator=(CSeqDBGiMask&);
-
+
/// Open file for a chosen algo_id
/// @param algo_id The chosen algo_id [in]
/// @param locked The lock holder object for this thread. [in]
@@ -176,7 +176,7 @@ private:
CNcbiOstrstreamToString(oss));
}
}
-
+
/// Get a range of the index or data file.
///
/// A range of file is acquired and returned in the provided blob.
@@ -193,14 +193,14 @@ private:
CSeqDBMemLease & lease,
CBlastDbBlob & blob,
CSeqDBLockHold & locked);
-
+
/// Binary search for value associated with a key
///
/// @param keys The (sorted) key array [in]
/// @param n Number of keys [in]
/// @param key The key to search for [in]
/// @param idx The index to the key array where key is found. [out]
- /// @return TRUE if the key is found
+ /// @return TRUE if the key is found
static bool s_BinarySearch(const int *keys,
const int n,
const int key,
@@ -208,13 +208,13 @@ private:
/// Reference to the atlas.
CSeqDBAtlas & m_Atlas;
-
+
/// The set of gi masks found in alias description
const vector<string> m_MaskNames;
/// The current used mask id
Int4 m_AlgoId;
-
+
/// Index file.
CSeqDBRawFile m_IndexFile;
@@ -229,13 +229,13 @@ private:
/// Number of data volumes
Int4 m_NumVols;
-
+
/// Data file.
vector<CSeqDBRawFile *> m_DataFile;
-
+
/// Data file lease.
vector<CSeqDBMemLease *> m_DataLease;
-
+
/// GI size
Int4 m_GiSize;
@@ -244,25 +244,25 @@ private:
/// Page size
Int4 m_PageSize;
-
+
/// Number of Gi indices
Int4 m_NumIndex;
/// Number of Gis
Int4 m_NumGi;
-
+
/// Mapped Gi index
- const Int4 *m_GiIndex;
+ const Int4 *m_GiIndex;
/// Start offset (in the index file) of the offset array.
Int4 m_IndexStart;
-
+
/// The description about the masking algo
string m_Desc;
-
+
/// The create date of the GI mask
string m_Date;
-
+
};
#endif
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp
index 5acae2f..9f7a80c 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbimpl.cpp 453781 2014-12-08 15:31:31Z ivanov $
+/* $Id: seqdbimpl.cpp 484800 2015-11-16 15:18:00Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// layer for SeqDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbimpl.cpp 453781 2014-12-08 15:31:31Z ivanov $";
+static char const rcsid[] = "$Id: seqdbimpl.cpp 484800 2015-11-16 15:18:00Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -455,7 +455,7 @@ int CSeqDBImpl::GetSeqLengthApprox(int oid) const
}
void CSeqDBImpl::GetTaxIDs(int oid,
- map<int, int> & gi_to_taxid,
+ map<TGi, int> & gi_to_taxid,
bool persist)
{
CSeqDBLockHold locked(m_Atlas);
@@ -484,7 +484,7 @@ void CSeqDBImpl::GetTaxIDs(int oid,
continue;
}
- gi_to_taxid[GI_TO(int, (**seqid).GetGi())] = (*defline)->GetTaxid();
+ gi_to_taxid[(**seqid).GetGi()] = (*defline)->GetTaxid();
}
}
}
@@ -517,7 +517,7 @@ void CSeqDBImpl::GetTaxIDs(int oid,
void CSeqDBImpl::GetLeafTaxIDs(
int oid,
- map<int, set<int> >& gi_to_taxid_set,
+ map<TGi, set<int> >& gi_to_taxid_set,
bool persist
)
{
@@ -544,7 +544,7 @@ void CSeqDBImpl::GetLeafTaxIDs(
}
CBlast_def_line::TTaxIds taxids = (*defline)->GetLeafTaxIds();
- gi_to_taxid_set[GI_TO(int, (**seqid).GetGi())].insert(
+ gi_to_taxid_set[(**seqid).GetGi()].insert(
taxids.begin(), taxids.end()
);
}
@@ -596,7 +596,7 @@ void CSeqDBImpl::GetLeafTaxIDs(
}
CRef<CBioseq>
-CSeqDBImpl::GetBioseq(int oid, int target_gi, const CSeq_id * target_seq_id, bool seqdata)
+CSeqDBImpl::GetBioseq(int oid, TGi target_gi, const CSeq_id * target_seq_id, bool seqdata)
{
CHECK_MARKER();
@@ -817,7 +817,7 @@ list< CRef<CSeq_id> > CSeqDBImpl::GetSeqIDs(int oid)
NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound);
}
-int CSeqDBImpl::GetSeqGI(int oid)
+TGi CSeqDBImpl::GetSeqGI(int oid)
{
CHECK_MARKER();
CSeqDBLockHold locked(m_Atlas);
@@ -891,7 +891,7 @@ int CSeqDBImpl::x_GetNumSeqs() const
return (int) rv;
}
-int CSeqDBImpl::x_GetSeqGI(int oid, CSeqDBLockHold & locked)
+TGi CSeqDBImpl::x_GetSeqGI(int oid, CSeqDBLockHold & locked)
{
CHECK_MARKER();
@@ -904,18 +904,18 @@ int CSeqDBImpl::x_GetSeqGI(int oid, CSeqDBLockHold & locked)
int vol_oid = 0;
if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) {
// Try lookup *.nxg first
- int gi = vol->GetSeqGI(vol_oid, locked);
- if (gi>=0) return gi;
+ TGi gi = vol->GetSeqGI(vol_oid, locked);
+ if (gi>=ZERO_GI) return gi;
// Fall back to parsing deflines
list< CRef<CSeq_id> > ids =
vol->GetSeqIDs(vol_oid, locked);
ITERATE(list< CRef<CSeq_id> >, id, ids) {
if ((**id).IsGi()) {
- return GI_TO(int, (**id).GetGi());
+ return (**id).GetGi();
}
}
// No GI found
- return -1;
+ return INVALID_GI;
}
NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound);
@@ -1170,7 +1170,7 @@ bool CSeqDBImpl::TiToOid(Int8 ti, int & oid)
return false;
}
-bool CSeqDBImpl::GiToOid(int gi, int & oid) const
+bool CSeqDBImpl::GiToOid(TGi gi, int & oid) const
{
CHECK_MARKER();
CSeqDBLockHold locked(m_Atlas);
@@ -1201,7 +1201,25 @@ bool CSeqDBImpl::GiToOid(int gi, int & oid) const
return false;
}
-bool CSeqDBImpl::OidToGi(int oid, int & gi)
+bool CSeqDBImpl::GiToOidwFilterCheck(TGi gi, int & oid)
+{
+ CHECK_MARKER();
+ CSeqDBLockHold locked(m_Atlas);
+
+ for(int i = 0; i < m_VolSet.GetNumVols(); i++) {
+ oid =-1;
+ if (m_VolSet.GetVol(i)->GiToOid(gi, oid, locked)) {
+ oid += m_VolSet.GetVolOIDStart(i);
+ int oid0 = oid;
+ if (CheckOrFindOID(oid) && (oid==oid0)) {
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
+bool CSeqDBImpl::OidToGi(int oid, TGi & gi)
{
CHECK_MARKER();
CSeqDBLockHold locked(m_Atlas);
@@ -1594,8 +1612,8 @@ inline void s_AccumulateMinMaxCount(TId low_in,
}
}
-void CSeqDBImpl::GetGiBounds(int * low_id,
- int * high_id,
+void CSeqDBImpl::GetGiBounds(TGi * low_id,
+ TGi * high_id,
int * count)
{
CSeqDBLockHold locked(m_Atlas);
@@ -1603,7 +1621,8 @@ void CSeqDBImpl::GetGiBounds(int * low_id,
bool found = false;
for(int i = 0; i < m_VolSet.GetNumVols(); i++) {
- int vlow(0), vhigh(0), vcount(0);
+ TGi vlow(ZERO_GI), vhigh(ZERO_GI);
+ int vcount(0);
m_VolSet.GetVol(i)->GetGiBounds(vlow, vhigh, vcount, locked);
@@ -1788,21 +1807,21 @@ CSeqDBIdSet CSeqDBImpl::GetIdSet()
// lists that specify filtering using CSeq-id objects.
if (m_UserGiList->GetNumGis()) {
- vector<int> gis;
+ vector<TGi> gis;
m_UserGiList->GetGiList(gis);
CSeqDBIdSet new_ids(gis, CSeqDBIdSet::eGi);
m_IdSet = new_ids;
} else if (m_UserGiList->GetNumTis()) {
- vector<Int8> tis;
+ vector<TTi> tis;
m_UserGiList->GetTiList(tis);
CSeqDBIdSet new_ids(tis, CSeqDBIdSet::eTi);
m_IdSet = new_ids;
}
} else if (! m_NegativeList.Empty()) {
- const vector<int> & ngis = m_NegativeList->GetGiList();
- const vector<Int8> & ntis = m_NegativeList->GetTiList();
+ const vector<TGi> & ngis = m_NegativeList->GetGiList();
+ const vector<TTi> & ntis = m_NegativeList->GetTiList();
if (! ngis.empty()) {
CSeqDBIdSet new_ids(ngis, CSeqDBIdSet::eGi, false);
@@ -2488,5 +2507,13 @@ int CSeqDBImpl::x_GetCacheID(CSeqDBLockHold &locked) const
return retval;
}
+void CSeqDBImpl::SetVolsMemBit(int mbit)
+{
+ int nvols = m_VolSet.GetNumVols();
+ for (int vol = 0; vol < nvols; ++vol) {
+ m_VolSet.GetVolNonConst(vol)->SetMemBit(mbit);
+ }
+}
+
END_NCBI_SCOPE
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
index 6d3f303..3c9dc77 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP
#define OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP
-/* $Id: seqdbimpl.hpp 453781 2014-12-08 15:31:31Z ivanov $
+/* $Id: seqdbimpl.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -294,7 +294,7 @@ public:
/// @param persist
/// If false, the map will be cleared before adding new entries.
void GetTaxIDs(int oid,
- map<int, int> & gi_to_taxid,
+ map<TGi, int> & gi_to_taxid,
bool persist);
/// Get taxids for an OID.
@@ -334,7 +334,7 @@ public:
/// If false, the map will be cleared before adding new entries.
void GetLeafTaxIDs(
int oid,
- map<int, set<int> >& gi_to_taxid_set,
+ map<TGi, set<int> >& gi_to_taxid_set,
bool persist
);
@@ -378,7 +378,7 @@ public:
/// @return
/// A CBioseq object corresponding to the sequence.
CRef<CBioseq> GetBioseq(int oid,
- int target_gi,
+ TGi target_gi,
const CSeq_id * target_seq_id,
bool seqdata);
@@ -478,7 +478,7 @@ public:
/// The oid of the sequence.
/// @return
/// GI or -1.
- int GetSeqGI(int oid);
+ TGi GetSeqGI(int oid);
/// Returns the database title.
///
@@ -669,10 +669,14 @@ public:
bool TiToOid(Int8 ti, int & oid);
/// Translate a GI to an OID.
- bool GiToOid(int gi, int & oid) const;
+ bool GiToOid(TGi gi, int & oid) const;
+
+ /// GiToOis is meant to simply return oid for a gi if one exisits
+ /// This method finds the oid and checks if the oid is being filtered or not.
+ bool GiToOidwFilterCheck(TGi gi, int & oid);
/// Translate a GI to an OID.
- bool OidToGi(int oid, int & gi);
+ bool OidToGi(int oid, TGi & gi);
/// Find OIDs matching the specified string.
void AccessionToOids(const string & acc,
@@ -859,7 +863,7 @@ public:
/// @param low_id Lowest GI value in database. [out]
/// @param high_id Highest GI value in database. [out]
/// @param count Number of GI values in database. [out]
- void GetGiBounds(int * low_id, int * high_id, int * count);
+ void GetGiBounds(TGi * low_id, TGi * high_id, int * count);
/// Get PIG Bounds.
///
@@ -1105,6 +1109,9 @@ public:
return m_Atlas.GetSliceSize();
}
+ /// Set the membership bit of all volumes
+ void SetVolsMemBit(int mbit);
+
private:
CLASS_MARKER_FIELD("IMPL")
@@ -1217,7 +1224,7 @@ private:
/// The lock hold object for this thread.
/// @return
/// GI or -1.
- int x_GetSeqGI(int oid, CSeqDBLockHold & locked);
+ TGi x_GetSeqGI(int oid, CSeqDBLockHold & locked);
/// Compute totals via iteration
///
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp
index 52440a3..1c1fc69 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbisam.cpp 454101 2014-12-10 20:04:18Z ivanov $
+/* $Id: seqdbisam.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// index of some particular kind of identifiers.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbisam.cpp 454101 2014-12-10 20:04:18Z ivanov $";
+static char const rcsid[] = "$Id: seqdbisam.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -65,66 +65,66 @@ CSeqDBIsam::x_InitSearch(CSeqDBLockHold & locked)
{
if(m_Initialized == true)
return eNoError;
-
+
TIndx info_needed = 10 * sizeof(Int4);
-
+
m_Atlas.Lock(locked);
-
+
bool found_index_file =
m_Atlas.GetFileSize(m_IndexFname, m_IndexFileLength, locked);
-
+
if ((! found_index_file) || (m_IndexFileLength < info_needed)) {
return eWrongFile;
}
-
+
m_Atlas.GetRegion(m_IndexLease, m_IndexFname, 0, info_needed);
-
+
Int4 * FileInfo = (Int4*) m_IndexLease.GetPtr(0);
-
+
// Check for consistence of files and parameters
-
+
Int4 Version = SeqDB_GetStdOrd(& FileInfo[0]);
-
+
if (Version != ISAM_VERSION)
return eBadVersion;
-
+
Int4 IsamType = SeqDB_GetStdOrd(& FileInfo[1]);
-
+
if (IsamType == eNumericLongId && m_Type == eNumeric) {
m_LongId = true;
m_TermSize = 12;
IsamType = eNumeric;
}
-
+
if (IsamType != m_Type)
return eBadType;
-
+
m_NumTerms = SeqDB_GetStdOrd(& FileInfo[3]);
m_NumSamples = SeqDB_GetStdOrd(& FileInfo[4]);
m_PageSize = SeqDB_GetStdOrd(& FileInfo[5]);
m_MaxLineSize = SeqDB_GetStdOrd(& FileInfo[6]);
-
- if(m_PageSize != MEMORY_ONLY_PAGE_SIZE) {
+
+ if(m_PageSize != MEMORY_ONLY_PAGE_SIZE) {
// Special case of memory-only index
m_DataFileLength = SeqDB_GetStdOrd(& FileInfo[2]);
-
+
TIndx disk_file_length(0);
bool found_data_file =
m_Atlas.GetFileSize(m_DataFname, disk_file_length, locked);
-
+
if ((! found_data_file) || (m_DataFileLength != disk_file_length)) {
return eWrongFile;
}
}
-
+
// This space reserved for future use
-
+
m_IdxOption = SeqDB_GetStdOrd(& FileInfo[7]);
-
+
m_KeySampleOffset = (9 * sizeof(Int4));
-
+
m_Initialized = true;
-
+
return eNoError;
}
@@ -132,20 +132,20 @@ Int4 CSeqDBIsam::x_GetPageNumElements(Int4 sample_num,
Int4 * start)
{
Int4 num_elements(0);
-
+
*start = sample_num * m_PageSize;
-
+
if (sample_num + 1 == m_NumSamples) {
num_elements = m_NumTerms - *start;
} else {
num_elements = m_PageSize;
}
-
+
return num_elements;
}
CSeqDBIsam::EErrorCode
-CSeqDBIsam::x_SearchIndexNumeric(Int8 Number,
+CSeqDBIsam::x_SearchIndexNumeric(Int8 Number,
int * Data,
Uint4 * Index,
Int4 & SampleNum,
@@ -153,86 +153,86 @@ CSeqDBIsam::x_SearchIndexNumeric(Int8 Number,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
done = true;
return error;
}
}
-
+
if (x_OutOfBounds(Number, locked)) {
done = true;
return eNotFound;
}
-
+
_ASSERT(m_Type != eNumericNoData);
-
+
// Search the sample file.
-
+
Int4 Start (0);
Int4 Stop (m_NumSamples - 1);
-
+
while(Stop >= Start) {
SampleNum = ((Uint4)(Stop + Start)) >> 1;
-
+
TIndx offset_begin = m_KeySampleOffset + (m_TermSize * SampleNum);
TIndx offset_end = offset_begin + m_TermSize;
-
+
m_Atlas.Lock(locked);
-
+
if (! m_IndexLease.Contains(offset_begin, offset_end)) {
m_Atlas.GetRegion(m_IndexLease,
m_IndexFname,
offset_begin,
offset_end);
}
-
+
const void* keydatap(0);
-
+
Int8 Key(0);
-
+
keydatap = m_IndexLease.GetPtr(offset_begin);
Key = x_GetNumericKey (keydatap);
-
+
// If this is an exact match, return the master term number.
-
+
if (Key == Number) {
if (Data != NULL) {
*Data = x_GetNumericData(keydatap);
}
-
+
if (Index != NULL)
*Index = SampleNum * m_PageSize;
-
+
done = true;
return eNoError;
}
-
+
// Otherwise, search for the next sample.
-
+
if ( Number < Key )
Stop = --SampleNum;
else
Start = SampleNum +1;
}
-
+
// If the term is out of range altogether, report not finding it.
-
+
if ( (SampleNum < 0) || (SampleNum >= m_NumSamples)) {
-
+
if (Data != NULL)
*Data = eNotFound;
-
+
if(Index != NULL)
*Index = eNotFound;
-
+
done = true;
return eNotFound;
}
-
+
done = false;
return eNoError;
}
@@ -245,75 +245,75 @@ CSeqDBIsam::x_SearchNegativeMulti(int vol_start,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
// Most ordinary errors (missing IDs for example) are
// ignored for "multi" mode searches. But if a GI list is
// specified, and cannot be interpreted, it is an error.
-
+
NCBI_THROW(CSeqDBException,
eArgErr,
"Error: Unable to use ISAM index in batch mode.");
}
}
-
+
m_Atlas.Lock(locked);
-
+
// We can use Parabolic Binary Search for the negative GI list but
// not for the ISAM file data, because in the negative ID list
// case, every line of the ISAM data must be looked at.
-
+
_ASSERT(m_Type != eNumericNoData);
-
+
//......................................................................
//
// Translate the entire Gi List.
//
//......................................................................
-
+
int gilist_size = use_tis ? ids.GetNumTis() : ids.GetNumGis();
-
+
int gilist_index = 0;
-
+
int sample_index(0);
const void * data_page (0);
-
+
while(sample_index < m_NumSamples) {
int start = 0, num_elements = 0;
-
+
x_MapDataPage(sample_index,
start,
num_elements,
& data_page,
locked);
-
+
for(int i = 0; i < num_elements; i++) {
Int8 isam_key(0);
int isam_data(0);
-
+
// 1. Get the ID+OID from the data page.
-
+
x_GetDataElement(data_page,
i,
isam_key,
isam_data);
-
+
// 2. Look for it in the negative id list.
-
+
bool found = false;
-
+
if (gilist_index < gilist_size) {
found = x_FindInNegativeList(ids,
gilist_index,
isam_key,
use_tis);
}
-
+
// 3. If not found, add the OID to the negative ID list.
-
+
if (isam_data < vol_end) {
if (found) {
// OID is found, but may not be included yet.
@@ -324,11 +324,11 @@ CSeqDBIsam::x_SearchNegativeMulti(int vol_start,
}
}
}
-
+
// Move to next data page. Note that for a negative ID list
// processing, we don't actually fetch any samples, because
// every ID->OID line needs to be examined anyway.
-
+
sample_index ++;
}
}
@@ -343,41 +343,41 @@ CSeqDBIsam::x_SearchDataNumeric(Int8 Number,
{
// Load the appropriate page of numbers into memory.
_ASSERT(m_Type != eNumericNoData);
-
+
Int4 Start(0);
Int4 NumElements = x_GetPageNumElements(SampleNum, & Start);
-
+
Int4 first = Start;
Int4 last = Start + NumElements - 1;
-
+
const void * KeyDataPage = NULL;
const void * KeyDataPageStart = NULL;
-
+
TIndx offset_begin = Start * m_TermSize;
TIndx offset_end = offset_begin + m_TermSize * NumElements;
-
+
m_Atlas.Lock(locked);
-
+
if (! m_DataLease.Contains(offset_begin, offset_end)) {
m_Atlas.GetRegion(m_DataLease,
m_DataFname,
offset_begin,
offset_end);
}
-
+
KeyDataPageStart = m_DataLease.GetPtr(offset_begin);
-
+
KeyDataPage = (char *)KeyDataPageStart - Start * m_TermSize;
-
+
bool found (false);
Int4 current (0);
-
+
// Search the page for the number.
while (first <= last) {
current = (first+last)/2;
-
+
Int8 Key = x_GetNumericKey((char *)KeyDataPage + current * m_TermSize);
-
+
if (Key > Number) {
last = --current;
} else if (Key < Number) {
@@ -387,31 +387,31 @@ CSeqDBIsam::x_SearchDataNumeric(Int8 Number,
break;
}
}
-
+
if (found == false) {
if (Data != NULL)
*Data = eNotFound;
-
+
if(Index != NULL)
*Index = eNotFound;
-
+
return eNotFound;
}
-
+
if (Data != NULL) {
*Data = x_GetNumericData((char *)KeyDataPage + current * m_TermSize);
}
-
+
if(Index != NULL)
*Index = Start + current;
-
+
return eNoError;
}
// ------------------------NumericSearch--------------------------
// Purpose: Main search function of Numeric ISAM
-//
+//
// Parameters: Key - interer to search
// Data - returned value (for NIASM with data)
// Index - internal index in database
@@ -420,21 +420,21 @@ CSeqDBIsam::x_SearchDataNumeric(Int8 Number,
// ----------------------------------------------------------------
CSeqDBIsam::EErrorCode
-CSeqDBIsam::x_NumericSearch(Int8 Number,
+CSeqDBIsam::x_NumericSearch(Int8 Number,
int * Data,
Uint4 * Index,
CSeqDBLockHold & locked)
{
bool done (false);
Int4 SampleNum (0);
-
+
EErrorCode error =
x_SearchIndexNumeric(Number, Data, Index, SampleNum, done, locked);
-
+
if (! done) {
error = x_SearchDataNumeric(Number, Data, Index, SampleNum, locked);
}
-
+
return error;
}
@@ -448,44 +448,44 @@ int CSeqDBIsam::x_DiffCharLease(const string & term_in,
CSeqDBLockHold & locked)
{
int result(-1);
-
+
m_Atlas.Lock(locked);
-
+
// Add one to term_end to insure we don't consider "AA" and "AAB"
// as equal.
-
+
TIndx offset_begin = KeyOffset;
TIndx term_end = KeyOffset + term_in.size() + 1;
TIndx map_end = term_end + at_least;
-
+
if (map_end > file_length) {
map_end = file_length;
-
+
if (term_end > map_end) {
term_end = map_end;
result = int(file_length - offset_begin);
}
}
-
+
if (! lease.Contains(offset_begin, map_end)) {
m_Atlas.GetRegion( lease,
file_name,
offset_begin,
term_end );
}
-
+
const char * file_data = lease.GetPtr(offset_begin);
-
+
Int4 dc_result =
x_DiffChar(term_in,
file_data,
file_data + term_in.size() + 1,
ignore_case);
-
+
if (dc_result != -1) {
result = dc_result;
}
-
+
return dc_result;
}
@@ -525,41 +525,41 @@ Int4 CSeqDBIsam::x_DiffChar(const string & term_in,
{
int result(-1);
int i(0);
-
+
const char * file_data = begin;
int bytes = int(end - begin);
-
+
for(i = 0; (i < bytes) && i < (int) term_in.size(); i++) {
char ch1 = term_in[i];
char ch2 = file_data[i];
-
+
if (ch1 != ch2) {
ch1 = s_SeqDBIsam_NullifyEOLs(ch1);
ch2 = s_SeqDBIsam_NullifyEOLs(ch2);
-
+
if (ignore_case) {
ch1 = toupper((unsigned char) ch1);
ch2 = toupper((unsigned char) ch2);
}
-
+
if (ch1 != ch2) {
break;
}
}
}
-
+
const char * p = file_data + i;
-
+
while((p < end) && ((*p) == ' ')) {
p++;
}
-
+
if (((p == end) || ENDS_ISAM_KEY(*p)) && (i == (int) term_in.size())) {
result = -1;
} else {
result = i;
}
-
+
return result;
}
@@ -572,47 +572,47 @@ void CSeqDBIsam::x_ExtractPageData(const string & term_in,
vector<string> & data_out)
{
// Collect all 'good' data from the page.
-
+
bool ignore_case = true;
-
+
Uint4 TermNum(0);
-
+
const char * indexp(beginp);
bool found_match(false);
-
+
while (indexp < endp) {
Int4 Diff = x_DiffChar(term_in,
indexp,
endp,
ignore_case);
-
+
if (Diff == -1) { // Complete match
found_match = true;
-
+
x_ExtractData(indexp,
endp,
keys_out,
data_out);
-
+
indices_out.push_back(page_index + TermNum);
} else {
// If we found a match, but the current term doesn't
// match, then we are past the set of matching entries.
-
+
if (found_match) {
break;
}
}
-
+
// Skip remainder of term, and any nulls after it.
-
+
while((indexp < endp) && s_SeqDBIsam_NullifyEOLs(*indexp)) {
indexp++;
}
while((indexp < endp) && (! s_SeqDBIsam_NullifyEOLs(*indexp))) {
indexp++;
}
-
+
TermNum++;
}
}
@@ -627,20 +627,20 @@ void CSeqDBIsam::x_ExtractAllData(const string & term_in,
// The object at sample_index is known to match; we will iterate
// over the surrounding values to see if they match as well. No
// assumptions about how many keys can match are made here.
-
+
bool ignore_case = true;
-
+
int pre_amt = 1;
int post_amt = 1;
-
+
bool done_b(false), done_e(false);
-
+
const char * beginp(0);
const char * endp(0);
-
+
TIndx beg_off(0);
TIndx end_off(0);
-
+
while(! (done_b && done_e)) {
if (sample_index < pre_amt) {
beg_off = 0;
@@ -648,42 +648,42 @@ void CSeqDBIsam::x_ExtractAllData(const string & term_in,
} else {
beg_off = sample_index - pre_amt;
}
-
+
if ((m_NumSamples - sample_index) < post_amt) {
end_off = m_NumSamples;
done_e = true;
} else {
end_off = sample_index + post_amt;
}
-
+
x_LoadPage(beg_off, end_off, & beginp, & endp, locked);
-
+
if (! done_b) {
Int4 diff_begin = x_DiffChar(term_in,
beginp,
endp,
ignore_case);
-
+
if (diff_begin != -1) {
done_b = true;
} else {
pre_amt ++;
}
}
-
+
if (! done_e) {
const char * last_term(0);
const char * p(endp-1);
-
+
// Skip over any non-terminating junk at the end
-
+
enum { eEndNulls, eLastTerm } search_stage = eEndNulls;
-
+
while(p > beginp) {
bool terminal = (0 == s_SeqDBIsam_NullifyEOLs(*p));
-
+
if (search_stage == eEndNulls) {
- if (! terminal) {
+ if (! terminal) {
search_stage = eLastTerm;
}
} else {
@@ -692,19 +692,19 @@ void CSeqDBIsam::x_ExtractAllData(const string & term_in,
break;
}
}
-
+
p--;
}
-
+
if (! last_term) {
last_term = beginp;
}
-
+
Int4 diff_end = x_DiffChar(term_in,
last_term,
endp,
ignore_case);
-
+
if (diff_end != -1) {
done_e = true;
} else {
@@ -712,7 +712,7 @@ void CSeqDBIsam::x_ExtractAllData(const string & term_in,
}
}
}
-
+
x_ExtractPageData(term_in,
m_PageSize * beg_off,
beginp,
@@ -729,7 +729,7 @@ void CSeqDBIsam::x_ExtractData(const char * key_start,
{
const char * data_ptr(0);
const char * p(key_start);
-
+
while(p < map_end) {
switch(s_SeqDBIsam_NullifyEOLs(*p)) {
case 0:
@@ -741,10 +741,10 @@ void CSeqDBIsam::x_ExtractData(const char * key_start,
data_out.push_back("");
}
return;
-
+
case ISAM_DATA_CHAR:
data_ptr = p;
-
+
default:
p++;
}
@@ -758,18 +758,18 @@ CSeqDBIsam::x_GetIndexKeyOffset(TIndx sample_offset,
{
TIndx offset_begin = sample_offset + (sample_num * sizeof(Uint4));
TIndx offset_end = offset_begin + sizeof(Uint4);
-
+
m_Atlas.Lock(locked);
-
+
if (! m_IndexLease.Contains(offset_begin, offset_end)) {
m_Atlas.GetRegion(m_IndexLease,
m_IndexFname,
offset_begin,
offset_end);
}
-
+
Int4 * key_offset_addr = (Int4 *) m_IndexLease.GetPtr(offset_begin);
-
+
return SeqDB_GetStdOrd(key_offset_addr);
}
@@ -781,19 +781,19 @@ CSeqDBIsam::x_GetIndexString(TIndx key_offset,
CSeqDBLockHold & locked)
{
TIndx offset_end = key_offset + length;
-
+
m_Atlas.Lock(locked);
-
+
if (! m_IndexLease.Contains(key_offset, offset_end)) {
m_Atlas.GetRegion(m_IndexLease,
m_IndexFname,
key_offset,
offset_end);
}
-
+
const char * key_offset_addr =
(const char *) m_IndexLease.GetPtr(key_offset);
-
+
if (trim_to_null) {
for(int i = 0; i<length; i++) {
if (! key_offset_addr[i]) {
@@ -802,7 +802,7 @@ CSeqDBIsam::x_GetIndexString(TIndx key_offset,
}
}
}
-
+
str.assign(key_offset_addr, length);
}
@@ -819,31 +819,31 @@ int CSeqDBIsam::x_DiffSample(const string & term_in,
// b. Address this number into SamplePos (indexlease)
// c. Swap this number to compute Key offset.
// d. Add to beginning of file to get key data pointer.
-
+
bool ignore_case(true);
-
+
TIndx SampleOffset(m_KeySampleOffset);
-
+
if(m_PageSize != MEMORY_ONLY_PAGE_SIZE) {
SampleOffset += (m_NumSamples + 1) * sizeof(Uint4);
}
-
+
TIndx offset_begin = SampleOffset + (SampleNum * sizeof(Uint4));
TIndx offset_end = offset_begin + sizeof(Uint4);
-
+
m_Atlas.Lock(locked);
-
+
if (! m_IndexLease.Contains(offset_begin, offset_end)) {
m_Atlas.GetRegion(m_IndexLease,
m_IndexFname,
offset_begin,
offset_end);
}
-
+
KeyOffset = SeqDB_GetStdOrd((Int4*) m_IndexLease.GetPtr(offset_begin));
-
+
Uint4 max_lines_2 = m_MaxLineSize * 2;
-
+
return x_DiffCharLease(term_in,
m_IndexLease,
m_IndexFname,
@@ -861,27 +861,27 @@ void CSeqDBIsam::x_LoadPage(TIndx SampleNum1,
CSeqDBLockHold & locked)
{
// Load the appropriate page of terms into memory.
-
+
_ASSERT(SampleNum2 > SampleNum1);
-
+
TIndx begin_offset = m_KeySampleOffset + SampleNum1 * sizeof(Uint4);
TIndx end_offset = m_KeySampleOffset + (SampleNum2 + 1) * sizeof(Uint4);
-
+
m_Atlas.Lock(locked);
-
+
if (! m_IndexLease.Contains(begin_offset, end_offset)) {
m_Atlas.GetRegion(m_IndexLease, m_IndexFname, begin_offset, end_offset);
}
-
+
Uint4 * key_offsets((Uint4*) m_IndexLease.GetPtr(begin_offset));
-
+
Uint4 key_off1 = SeqDB_GetStdOrd(& key_offsets[0]);
Uint4 key_off2 = SeqDB_GetStdOrd(& key_offsets[SampleNum2 - SampleNum1]);
-
+
if (! m_DataLease.Contains(key_off1, key_off2)) {
m_Atlas.GetRegion(m_DataLease, m_DataFname, key_off1, key_off2);
}
-
+
*beginp = (const char *) m_DataLease.GetPtr(key_off1);
*endp = (const char *) m_DataLease.GetPtr(key_off2);
}
@@ -889,7 +889,7 @@ void CSeqDBIsam::x_LoadPage(TIndx SampleNum1,
// ------------------------StringSearch--------------------------
// Purpose: Main search function of string search.
-//
+//
// Parameters: Key - interer to search
// Data - returned value
// Index - internal index in database
@@ -906,63 +906,63 @@ CSeqDBIsam::x_StringSearch(const string & term_in,
{
// These are always false; They may relate to the prior find_one /
// expand_to_many method of getting multiple OIDs.
-
+
bool short_match(false);
bool follow_match(false);
-
+
size_t preexisting_data_count = values_out.size();
-
+
if (m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
return error;
}
}
-
+
if (x_OutOfBounds(term_in, locked)) {
return eNotFound;
}
-
+
// We will set this option to avoid more complications
bool ignore_case = true;
-
+
// search the sample file first
-
+
TIndx Start(0);
TIndx Stop(m_NumSamples - 1);
-
+
int Length = (int) term_in.size();
-
+
TIndx SampleOffset(m_KeySampleOffset);
-
+
if(m_PageSize != MEMORY_ONLY_PAGE_SIZE) {
SampleOffset += (m_NumSamples + 1) * sizeof(Uint4);
}
-
+
int found_short(-1);
-
+
string short_term;
int SampleNum(-1);
-
+
while(Stop >= Start) {
SampleNum = ((Uint4)(Stop + Start)) >> 1;
-
+
TIndx KeyOffset(0);
-
+
int diff = x_DiffSample(term_in, SampleNum, KeyOffset, locked);
-
+
// If this is an exact match, return the master term number.
-
+
const char * KeyData = m_IndexLease.GetPtr(KeyOffset);
TIndx BytesToEnd = m_IndexFileLength - KeyOffset;
-
+
Uint4 max_lines_2 = m_MaxLineSize * 2;
-
+
if (BytesToEnd > (TIndx) max_lines_2) {
BytesToEnd = max_lines_2;
}
-
+
if (diff == -1) {
x_ExtractAllData(term_in,
SampleNum,
@@ -970,26 +970,26 @@ CSeqDBIsam::x_StringSearch(const string & term_in,
terms_out,
values_out,
locked);
-
+
return eNoError;
}
-
+
// If the key is a superset of the sample term, backup until
// just before the term.
-
+
if (short_match && (diff >= Length)) {
if (SampleNum > 0)
SampleNum--;
-
+
while(SampleNum > 0) {
TIndx key_offset =
x_GetIndexKeyOffset(SampleOffset,
SampleNum,
locked);
-
+
string prefix;
x_GetIndexString(key_offset, Length, prefix, false, locked);
-
+
if (ignore_case) {
if (NStr::CompareNocase(prefix, term_in) != 0) {
break;
@@ -999,33 +999,33 @@ CSeqDBIsam::x_StringSearch(const string & term_in,
break;
}
}
-
+
SampleNum--;
}
-
+
found_short = SampleNum + 1;
-
+
TIndx key_offset =
x_GetIndexKeyOffset(SampleOffset,
SampleNum + 1,
locked);
-
+
string prefix;
x_GetIndexString(key_offset, max_lines_2, short_term, true, locked);
-
+
break;
} else {
// If preceding is desired, note the key.
-
+
if (follow_match) {
found_short = SampleNum;
-
+
x_GetIndexString(KeyOffset, max_lines_2, short_term, true, locked);
}
}
-
+
// Otherwise, search for the next sample.
-
+
if (ignore_case
? tolower((unsigned char) term_in[diff]) < tolower((unsigned char) KeyData[diff])
: term_in[diff] < KeyData[diff]) {
@@ -1034,23 +1034,23 @@ CSeqDBIsam::x_StringSearch(const string & term_in,
Start = SampleNum + 1;
}
}
-
-
+
+
// If the term is out of range altogether, report not finding it.
-
+
if ( (SampleNum < 0) || (SampleNum >= m_NumSamples)) {
return eNotFound;
}
-
+
// Load the appropriate page of terms into memory.
-
+
const char * beginp(0);
const char * endp(0);
-
+
x_LoadPage(SampleNum, SampleNum + 1, & beginp, & endp, locked);
-
+
// Search the page for the term.
-
+
x_ExtractPageData(term_in,
m_PageSize * SampleNum,
beginp,
@@ -1058,15 +1058,15 @@ CSeqDBIsam::x_StringSearch(const string & term_in,
indices_out,
terms_out,
values_out);
-
+
// For now the short and follow logic is not implemented.
-
+
EErrorCode rv(eNoError);
-
+
if (preexisting_data_count == values_out.size()) {
rv = eNotFound;
}
-
+
return rv;
}
@@ -1095,39 +1095,39 @@ CSeqDBIsam::CSeqDBIsam(CSeqDBAtlas & atlas,
m_TermSize (8)
{
// These are the types that readdb.c seems to use.
-
+
switch(ident_type) {
case eGiId:
case ePigId:
case eTiId:
m_Type = eNumeric;
break;
-
+
case eStringId:
case eHashId:
m_Type = eString;
break;
-
+
default:
NCBI_THROW(CSeqDBException,
eArgErr,
"Error: ident type argument not valid");
}
-
+
x_MakeFilenames(dbname,
prot_nucl,
file_ext_char,
m_IndexFname,
m_DataFname);
-
+
if (! (CFile(m_IndexFname).Exists() &&
CFile(m_DataFname).Exists()) ) {
-
+
string msg("Error: Could not open input file (");
msg += m_IndexFname + "/" + m_DataFname + ")";
NCBI_THROW(CSeqDBException, eFileErr, msg);
}
-
+
if(m_Type == eNumeric) {
m_PageSize = DEFAULT_NISAM_SIZE;
} else {
@@ -1144,20 +1144,20 @@ void CSeqDBIsam::x_MakeFilenames(const string & dbname,
if (dbname.empty() ||
(! isalpha((unsigned char) prot_nucl)) ||
(! isalpha((unsigned char) file_ext_char))) {
-
+
NCBI_THROW(CSeqDBException,
eArgErr,
"Error: argument not valid");
}
-
+
index_name.reserve(dbname.size() + 4);
data_name.reserve(dbname.size() + 4);
-
+
index_name = dbname;
index_name += '.';
index_name += prot_nucl;
index_name += file_ext_char;
-
+
data_name = index_name;
index_name += 'i';
data_name += 'd';
@@ -1169,7 +1169,7 @@ bool CSeqDBIsam::IndexExists(const string & dbname,
{
string iname, dname;
x_MakeFilenames(dbname, prot_nucl, file_ext_char, iname, dname);
-
+
return CFile(iname).Exists() && CFile(dname).Exists();
}
@@ -1192,13 +1192,13 @@ bool CSeqDBIsam::x_IdentToOid(Int8 ident, TOid & oid, CSeqDBLockHold & locked)
{
EErrorCode err =
x_NumericSearch(ident, & oid, 0, locked);
-
+
if (err == eNoError) {
return true;
}
-
+
oid = -1u; /* NCBI_FAKE_WARNING */
-
+
return false;
}
@@ -1210,28 +1210,28 @@ void CSeqDBIsam::StringToOids(const string & acc,
{
bool strip_version = version_check;
version_check = false;
-
+
_ASSERT(m_IdentType == eStringId);
-
+
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
if (eNoError != x_InitSearch(locked)) {
return;
}
}
-
+
bool found = false;
-
+
string accession(string("gb|") + acc + "|");
string locus_str(string("gb||") + acc);
-
+
EErrorCode err = eNoError;
-
+
vector<string> keys_out;
vector<string> data_out;
vector<TIndx> indices_out;
-
+
if (! adjusted) {
if ((err = x_StringSearch(accession,
keys_out,
@@ -1240,11 +1240,11 @@ void CSeqDBIsam::StringToOids(const string & acc,
locked)) < 0) {
return;
}
-
+
if (err == eNoError) {
found = true;
}
-
+
if ((! found) &&
(err = x_StringSearch(locus_str,
keys_out,
@@ -1253,36 +1253,36 @@ void CSeqDBIsam::StringToOids(const string & acc,
locked)) < 0) {
return;
}
-
+
if (err != eNotFound) {
found = true;
}
}
-
+
if ((! found) &&
(err = x_StringSearch(acc,
keys_out,
data_out,
indices_out,
locked)) < 0) {
-
+
return;
}
-
+
if (err != eNotFound) {
found = true;
}
-
+
if ((! found) && strip_version) {
size_t pos = acc.find(".");
-
+
bool is_version = false;
-
+
if (pos != string::npos) {
int ver_len = acc.size() - pos - 1;
-
+
is_version = (ver_len <= 3 && ver_len >= 1);
-
+
for(size_t vp = pos+1; vp < acc.size(); vp++) {
if (! isdigit(acc[vp])) {
is_version = false;
@@ -1290,44 +1290,44 @@ void CSeqDBIsam::StringToOids(const string & acc,
}
}
}
-
+
if (is_version) {
string nover(acc, 0, pos);
-
+
err = x_StringSearch(nover,
keys_out,
data_out,
indices_out,
locked);
-
+
if (data_out.size()) {
version_check = true;
}
-
+
if (err < 0) {
return;
}
}
}
-
+
if (err != eNotFound) {
found = true;
}
-
+
if (! found) {
// Use CSeq_id to parse the id string and build a replacement,
// FASTA type string. This allows some IDs, such as PDBs with
// chains, such as '1qcfA' to be parsed.
-
+
string id;
-
+
try {
CSeq_id seqid(acc, CSeq_id::fParse_RawText | CSeq_id::fParse_AnyLocal);
id = seqid.AsFastaString();
}
catch(CSeqIdException &) {
}
-
+
if (id.size() &&
((err = x_StringSearch(id,
keys_out,
@@ -1337,11 +1337,11 @@ void CSeqDBIsam::StringToOids(const string & acc,
return;
}
}
-
+
if (err != eNotFound) {
found = true;
}
-
+
if (found) {
ITERATE(vector<string>, iter, data_out) {
oids.push_back(atoi((*iter).c_str()));
@@ -1366,10 +1366,10 @@ void CSeqDBIsam::IdsToOids(int vol_start,
{
// The vol_start parameter is needed because translations in the
// GI list should refer to global OIDs, not per-volume OIDs.
-
+
switch (m_IdentType) {
case eGiId:
- x_TranslateGiList<int>(vol_start, ids, locked);
+ x_TranslateGiList<TGi>(vol_start, ids, locked);
break;
case eTiId:
@@ -1380,7 +1380,7 @@ void CSeqDBIsam::IdsToOids(int vol_start,
x_TranslateGiList<string>(vol_start, ids, locked);
break;
- default:
+ default:
NCBI_THROW(CSeqDBException,
eArgErr,
"Error: Wrong type of idlist specified.");
@@ -1394,12 +1394,12 @@ void CSeqDBIsam::IdsToOids(int vol_start,
{
// The vol_start parameter is needed because translations in the
// GI list should refer to global OIDs, not per-volume OIDs.
-
+
_ASSERT(m_IdentType == eGiId || m_IdentType == eTiId);
-
+
m_Atlas.Lock(locked);
ids.InsureOrder();
-
+
if ((m_IdentType == eGiId) && ids.GetNumGis()) {
x_SearchNegativeMulti(vol_start,
vol_end,
@@ -1407,7 +1407,7 @@ void CSeqDBIsam::IdsToOids(int vol_start,
false,
locked);
}
-
+
if ((m_IdentType == eTiId) && ids.GetNumTis()) {
x_SearchNegativeMulti(vol_start,
vol_end,
@@ -1421,100 +1421,100 @@ void CSeqDBIsam::x_FindIndexBounds(CSeqDBLockHold & locked)
{
Int4 Start (0);
Int4 Stop (m_NumSamples - 1);
-
+
m_Atlas.Lock(locked);
-
+
if (m_Type == eNumeric) {
//
// Get first key from data file
-
+
int num_elements(0);
int start(0);
const void * data_page(0);
-
+
x_MapDataPage(Start,
start,
num_elements,
& data_page,
locked);
-
+
_ASSERT(num_elements);
-
+
int elem_index = 0;
-
+
Int8 data_gi(0);
int data_oid(-1);
-
+
x_GetDataElement(data_page,
elem_index,
data_gi,
data_oid);
-
+
m_FirstKey.SetNumeric(data_gi);
-
-
+
+
//
// Get last key from data file
-
+
x_MapDataPage(Stop,
start,
num_elements,
& data_page,
locked);
-
+
_ASSERT(num_elements);
-
+
elem_index = num_elements - 1;
-
+
x_GetDataElement(data_page,
elem_index,
data_gi,
data_oid);
-
+
m_LastKey.SetNumeric(data_gi);
} else {
//
// Load the appropriate page of terms into memory.
-
+
const char * beginp(0);
const char * endp(0);
-
+
//
// Load the first page
-
+
x_LoadPage(Start, Start + 1, & beginp, & endp, locked);
-
+
// Get first term
-
+
vector<string> keys_out;
vector<string> data_out; // not used
-
+
x_ExtractData(beginp,
endp,
keys_out,
data_out);
-
+
x_Lower(keys_out.front());
m_FirstKey.SetString(keys_out.front());
-
-
+
+
//
// Load the last page
-
+
x_LoadPage(Stop, Stop + 1, & beginp, & endp, locked);
-
+
// Advance to last item
-
+
const char * lastp(0);
const char * indexp(beginp);
-
+
while (indexp < endp) {
// Remember our new "last term" value.
-
+
lastp = indexp;
-
+
// Skip remainder of term, and any nulls after it.
-
+
while((indexp < endp) && s_SeqDBIsam_NullifyEOLs(*indexp)) {
indexp++;
}
@@ -1522,19 +1522,19 @@ void CSeqDBIsam::x_FindIndexBounds(CSeqDBLockHold & locked)
indexp++;
}
}
-
+
// Get the last key
-
+
_ASSERT(lastp);
-
+
keys_out.clear();
data_out.clear();
-
+
x_ExtractData(lastp,
endp,
keys_out,
data_out);
-
+
x_Lower(keys_out.front());
m_LastKey.SetString(keys_out.front());
}
@@ -1545,21 +1545,21 @@ bool CSeqDBIsam::x_OutOfBounds(Int8 key, CSeqDBLockHold & locked)
if (! m_FirstKey.IsSet()) {
x_FindIndexBounds(locked);
}
-
+
if (! (m_FirstKey.IsSet() && m_LastKey.IsSet())) {
return false;
}
-
+
_ASSERT(m_Type == eNumeric);
-
+
if (m_FirstKey.OutsideFirstBound(key)) {
return true;
}
-
+
if (m_LastKey.OutsideLastBound(key)) {
return true;
}
-
+
return false;
}
@@ -1568,23 +1568,23 @@ bool CSeqDBIsam::x_OutOfBounds(string key, CSeqDBLockHold & locked)
if (! m_FirstKey.IsSet()) {
x_FindIndexBounds(locked);
}
-
+
if (! (m_FirstKey.IsSet() && m_LastKey.IsSet())) {
return false;
}
-
+
_ASSERT(m_Type == eString);
-
+
x_Lower(key);
-
+
if (m_FirstKey.OutsideFirstBound(key)) {
return true;
}
-
+
if (m_LastKey.OutsideLastBound(key)) {
return true;
}
-
+
return false;
}
@@ -1594,20 +1594,20 @@ void CSeqDBIsam::GetIdBounds(Int8 & low_id,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
count = 0;
return;
}
}
-
+
if (! (m_FirstKey.IsSet() && m_LastKey.IsSet())) {
x_FindIndexBounds(locked);
}
-
+
low_id = m_FirstKey.GetNumeric();
high_id = m_LastKey.GetNumeric();
count = m_NumTerms;
@@ -1619,20 +1619,20 @@ void CSeqDBIsam::GetIdBounds(string & low_id,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
EErrorCode error = x_InitSearch(locked);
-
+
if(error != eNoError) {
count = 0;
return;
}
}
-
+
if (! (m_FirstKey.IsSet() && m_LastKey.IsSet())) {
x_FindIndexBounds(locked);
}
-
+
low_id = m_FirstKey.GetString();
high_id = m_LastKey.GetString();
count = m_NumTerms;
@@ -1643,25 +1643,25 @@ void CSeqDBIsam::HashToOids(unsigned hash,
CSeqDBLockHold & locked)
{
_ASSERT(m_IdentType == eHashId);
-
+
m_Atlas.Lock(locked);
-
+
if(m_Initialized == false) {
if (eNoError != x_InitSearch(locked)) {
return;
}
}
-
+
bool found = false;
-
+
string key(NStr::UIntToString(hash));
-
+
EErrorCode err = eNoError;
-
+
vector<string> keys_out;
vector<string> data_out;
vector<TIndx> indices_out;
-
+
if ((err = x_StringSearch(key,
keys_out,
data_out,
@@ -1669,11 +1669,11 @@ void CSeqDBIsam::HashToOids(unsigned hash,
locked)) < 0) {
return;
}
-
+
if (err != eNotFound) {
found = true;
}
-
+
if (found) {
ITERATE(vector<string>, iter, data_out) {
oids.push_back(atoi(iter->c_str()));
diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp b/c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp
index 5b4aa59..c21bff1 100644
--- a/c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdbvol.cpp 435003 2014-05-13 15:08:30Z ucko $
+/* $Id: seqdbvol.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// interface for all functionality of one database volume.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqdbvol.cpp 435003 2014-05-13 15:08:30Z ucko $";
+static char const rcsid[] = "$Id: seqdbvol.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -53,8 +53,8 @@ static char const rcsid[] = "$Id: seqdbvol.cpp 435003 2014-05-13 15:08:30Z ucko
BEGIN_NCBI_SCOPE
-int CSeqDBGiIndex::GetSeqGI(TOid oid,
- CSeqDBLockHold & locked)
+TGi CSeqDBGiIndex::GetSeqGI(TOid oid,
+ CSeqDBLockHold & locked)
{
const char* data(0);
@@ -68,11 +68,11 @@ int CSeqDBGiIndex::GetSeqGI(TOid oid,
m_NumOIDs = (Int4) SeqDB_GetStdOrd((Int4 *) (data+12));
}
- if (oid >= m_NumOIDs || oid < 0) return -1;
-
+ if (oid >= m_NumOIDs || oid < 0) return INVALID_GI;
+
TIndx offset = oid * m_Size + 32;
data = m_Lease.GetPtr(offset);
- return (TGi) SeqDB_GetStdOrd((TGi *) data);
+ return GI_FROM(Int4, SeqDB_GetStdOrd((Int4 *) data));
}
CSeqDBVol::CSeqDBVol(CSeqDBAtlas & atlas,
@@ -106,11 +106,11 @@ CSeqDBVol::CSeqDBVol(CSeqDBAtlas & atlas,
if (neg_list) {
m_NegativeList.Reset(neg_list);
}
-
+
m_Idx.Reset(new CSeqDBIdxFile(atlas, name, prot_nucl, locked));
-
+
m_VolEnd = m_VolStart + m_Idx->GetNumOIDs();
-
+
// To allow for empty volumes, we must tolerate the absence of all
// files other than the index file.
}
@@ -119,7 +119,7 @@ void
CSeqDBVol::OpenSeqFile(CSeqDBLockHold & locked) const{
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
}
-
+
void
CSeqDBVol::x_OpenSeqFile(CSeqDBLockHold & locked) const {
m_Atlas.Lock(locked);
@@ -128,8 +128,8 @@ CSeqDBVol::x_OpenSeqFile(CSeqDBLockHold & locked) const {
}
m_SeqFileOpened = true;
}
-
-void
+
+void
CSeqDBVol::x_OpenHdrFile(CSeqDBLockHold & locked) const {
m_Atlas.Lock(locked);
if (!m_HdrFileOpened && m_Idx->GetNumOIDs() != 0) {
@@ -141,7 +141,7 @@ CSeqDBVol::x_OpenHdrFile(CSeqDBLockHold & locked) const {
void
CSeqDBVol::x_OpenPigFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_PigFileOpened &&
+ if (!m_PigFileOpened &&
CSeqDBIsam::IndexExists(m_VolName, (m_IsAA?'p':'n'), 'p') &&
m_Idx->GetNumOIDs() != 0) {
m_IsamPig =
@@ -153,11 +153,11 @@ CSeqDBVol::x_OpenPigFile(CSeqDBLockHold & locked) const{
}
m_PigFileOpened = true;
}
-
-void
+
+void
CSeqDBVol::x_OpenGiFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_GiFileOpened &&
+ if (!m_GiFileOpened &&
CSeqDBIsam::IndexExists(m_VolName, (m_IsAA?'p':'n'), 'n') &&
m_Idx->GetNumOIDs() != 0) {
m_IsamGi =
@@ -169,11 +169,11 @@ CSeqDBVol::x_OpenGiFile(CSeqDBLockHold & locked) const{
}
m_GiFileOpened = true;
}
-
+
void
CSeqDBVol::x_OpenStrFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_StrFileOpened &&
+ if (!m_StrFileOpened &&
CSeqDBIsam::IndexExists(m_VolName, (m_IsAA?'p':'n'), 's') &&
m_Idx->GetNumOIDs() != 0) {
m_IsamStr =
@@ -185,11 +185,11 @@ CSeqDBVol::x_OpenStrFile(CSeqDBLockHold & locked) const{
}
m_StrFileOpened = true;
}
-
+
void
CSeqDBVol::x_OpenTiFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_TiFileOpened &&
+ if (!m_TiFileOpened &&
CSeqDBIsam::IndexExists(m_VolName, (m_IsAA?'p':'n'), 't') &&
m_Idx->GetNumOIDs() != 0) {
m_IsamTi =
@@ -201,11 +201,11 @@ CSeqDBVol::x_OpenTiFile(CSeqDBLockHold & locked) const{
}
m_TiFileOpened = true;
}
-
+
void
CSeqDBVol::x_OpenHashFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_HashFileOpened &&
+ if (!m_HashFileOpened &&
CSeqDBIsam::IndexExists(m_VolName, (m_IsAA?'p':'n'), 'h') &&
m_Idx->GetNumOIDs() != 0) {
m_IsamHash =
@@ -217,11 +217,11 @@ CSeqDBVol::x_OpenHashFile(CSeqDBLockHold & locked) const{
}
m_HashFileOpened = true;
}
-
+
void
CSeqDBVol::x_OpenOidFile(CSeqDBLockHold & locked) const{
m_Atlas.Lock(locked);
- if (!m_OidFileOpened &&
+ if (!m_OidFileOpened &&
CSeqDBGiIndex::IndexExists(m_VolName, (m_IsAA?'p':'n')) &&
m_Idx->GetNumOIDs() != 0) {
m_GiIndex =
@@ -231,7 +231,7 @@ CSeqDBVol::x_OpenOidFile(CSeqDBLockHold & locked) const{
}
m_OidFileOpened = true;
}
-
+
char CSeqDBVol::GetSeqType() const
{
return x_GetSeqType();
@@ -246,12 +246,12 @@ int CSeqDBVol::GetSeqLengthProt(int oid, CSeqDBLockHold & locked) const
{
TIndx start_offset = 0;
TIndx end_offset = 0;
-
+
m_Atlas.Lock(locked);
m_Idx->GetSeqStartEnd(oid, start_offset, end_offset);
-
+
_ASSERT('p' == m_Idx->GetSeqType());
-
+
// Subtract one, for the inter-sequence null.
return int(end_offset - start_offset - 1);
}
@@ -262,23 +262,23 @@ int CSeqDBVol::GetSeqLengthExact(int oid, CSeqDBLockHold & locked) const
{
TIndx start_offset = 0;
TIndx end_offset = 0;
-
+
m_Atlas.Lock(locked);
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
m_Idx->GetSeqStartEnd(oid, start_offset, end_offset);
-
+
_ASSERT(m_Idx->GetSeqType() == 'n');
-
+
int whole_bytes = int(end_offset - start_offset - 1);
-
+
// The last byte is partially full; the last two bits of
// the last byte store the number of nucleotides in the
// last byte (0 to 3).
-
+
char amb_char = 0;
-
+
m_Seq->ReadBytes(& amb_char, end_offset - 1, end_offset);
-
+
int remainder = amb_char & 3;
return (whole_bytes * 4) + remainder;
}
@@ -287,20 +287,20 @@ int CSeqDBVol::GetSeqLengthApprox(int oid, CSeqDBLockHold & locked) const
{
TIndx start_offset = 0;
TIndx end_offset = 0;
-
+
m_Atlas.Lock(locked);
m_Idx->GetSeqStartEnd(oid, start_offset, end_offset);
-
+
_ASSERT(m_Idx->GetSeqType() == 'n');
-
+
int whole_bytes = int(end_offset - start_offset - 1);
-
+
// Same principle as below - but use lower bits of oid
// instead of fetching the actual last byte. this should
// correct for bias, unless sequence length modulo 4 has a
// significant statistical bias, which seems unlikely to
// me.
-
+
return (whole_bytes * 4) + (oid & 0x03);
}
@@ -319,24 +319,24 @@ s_SeqDBMapNA2ToNA4Setup()
{
vector<Uint1> translated;
translated.resize(512);
-
+
Uint1 convert[16] = { 0x11, 0x12, 0x14, 0x18,
0x21, 0x22, 0x24, 0x28,
0x41, 0x42, 0x44, 0x48,
0x81, 0x82, 0x84, 0x88 };
-
+
Int2 pair1 = 0;
Int2 pair2 = 0;
-
+
for(pair1 = 0; pair1 < 16; pair1++) {
for(pair2 = 0; pair2 < 16; pair2++) {
Int2 index = (pair1 * 16 + pair2) * 2;
-
+
translated[index] = convert[pair1];
translated[index+1] = convert[pair2];
}
}
-
+
return translated;
}
@@ -358,38 +358,38 @@ s_SeqDBMapNA2ToNA4(const char * buf2bit,
int base_length)
{
static vector<Uint1> expanded = s_SeqDBMapNA2ToNA4Setup();
-
+
int estimated_length = (base_length + 1)/2;
int bytes = 0;
-
+
buf4bit.resize(estimated_length);
-
+
int inp_chars = base_length/4;
-
+
for(int i=0; i<inp_chars; i++) {
Uint4 inp_char = (buf2bit[i] & 0xFF);
-
+
buf4bit[bytes] = expanded[ (inp_char*2) ];
buf4bit[bytes+1] = expanded[ (inp_char*2) + 1 ];
bytes += 2;
}
-
+
int bases_remain = base_length - (inp_chars*4);
-
+
if (bases_remain) {
Uint1 remainder_bits = 2 * bases_remain;
Uint1 remainder_mask = (0xFF << (8 - remainder_bits)) & 0xFF;
Uint4 last_masked = buf2bit[inp_chars] & remainder_mask;
-
+
buf4bit[bytes++] = expanded[ (last_masked*2) ];
-
+
if (bases_remain > 2) {
buf4bit[bytes ++] = expanded[ (last_masked*2)+1 ];
}
}
-
+
buf4bit.resize(bytes);
-
+
_ASSERT(estimated_length == (int)buf4bit.size());
}
@@ -408,22 +408,22 @@ s_SeqDBMapNA2ToNA8Setup()
{
// Builds a table; each two bit slice holds 0,1,2 or 3. These are
// converted to whole bytes containing 1,2,4, or 8, respectively.
-
+
vector<Uint1> translated;
translated.reserve(1024);
-
+
for(int i = 0; i<256; i++) {
int p1 = (i >> 6) & 0x3;
int p2 = (i >> 4) & 0x3;
int p3 = (i >> 2) & 0x3;
int p4 = i & 0x3;
-
+
translated.push_back(1 << p1);
translated.push_back(1 << p2);
translated.push_back(1 << p3);
translated.push_back(1 << p4);
}
-
+
return translated;
}
@@ -453,81 +453,81 @@ s_SeqDBMapNA2ToNA8(const char * buf2bit,
// to write correctly. It represents a pointer into the input
// data and is maintained to point at the next unused byte of
// input data.
-
+
static vector<Uint1> expanded = s_SeqDBMapNA2ToNA8Setup();
-
+
int pos = range.begin;
-
+
int input_chars_begin = range.begin / 4;
int input_chars_end = (range.end + 3) / 4;
-
+
int whole_chars_begin = (range.begin + 3) / 4;
int whole_chars_end = range.end / 4;
-
+
int p = input_chars_begin;
-
+
if (p < whole_chars_begin) {
Int4 table_offset = (buf2bit[input_chars_begin] & 0xFF) * 4;
-
+
int endpt = (input_chars_begin + 1) * 4;
-
+
if (endpt > range.end) {
endpt = range.end;
}
-
+
for(int k = range.begin; k < endpt; k++) {
switch(k & 0x3) {
case 0:
_ASSERT(0);
break;
-
+
case 1:
buf8bit[pos++] = expanded[ table_offset + 1 ];
break;
-
+
case 2:
buf8bit[pos++] = expanded[ table_offset + 2 ];
break;
-
+
case 3:
buf8bit[pos++] = expanded[ table_offset + 3 ];
break;
}
}
-
+
p ++;
}
-
+
// In a nucleotide search, this loop is probably a noticeable time
// consumer, at least relative to the CSeqDB universe. Each input
// byte is used to look up a 4 byte output translation. That four
// byte section is copied to the output vector. By pre-processing
// the arithmetic in the ~Setup() function, we can just pull bytes
// from a vector.
-
+
p = whole_chars_begin;
-
+
while(p < whole_chars_end) {
Int4 table_offset = (buf2bit[p] & 0xFF) * 4;
-
+
buf8bit[pos++] = expanded[ table_offset ];
buf8bit[pos++] = expanded[ table_offset + 1 ];
buf8bit[pos++] = expanded[ table_offset + 2 ];
buf8bit[pos++] = expanded[ table_offset + 3 ];
p++;
}
-
+
if (p < input_chars_end) {
Int4 table_offset = (buf2bit[p] & 0xFF) * 4;
-
+
int remains = (range.end & 0x3);
_ASSERT(remains);
-
+
buf8bit[pos++] = expanded[ table_offset ];
-
+
if (remains > 1) {
buf8bit[pos++] = expanded[ table_offset + 1 ];
-
+
if (remains > 2) {
buf8bit[pos++] = expanded[ table_offset + 2 ];
}
@@ -565,10 +565,10 @@ unsigned SeqDB_ncbina8_to_blastna8[] = {
/// @param range
/// The range of opearation. [in]
static void
-s_SeqDBMapNcbiNA8ToBlastNA8(char * buf,
+s_SeqDBMapNcbiNA8ToBlastNA8(char * buf,
const SSeqDBSlice & range)
{
- for(int i = range.begin; i < range.end; i++)
+ for(int i = range.begin; i < range.end; i++)
buf[i] = SeqDB_ncbina8_to_blastna8[ buf[i] & 0xF ];
}
@@ -677,46 +677,46 @@ static void
s_SeqDBRebuildDNA_NA4(vector<char> & buf4bit,
const vector<Int4> & amb_chars)
{
- if (amb_chars.empty())
+ if (amb_chars.empty())
return;
-
+
// Number of ambiguities.
Uint4 amb_num = amb_chars[0];
-
+
// The new format is indicated by setting the highest order bit in
// the LENGTH field. Either all ambiguities for this sequence
// will use the new format, or all will use the old format.
-
+
bool new_format = (amb_num & 0x80000000) != 0;
-
+
if (new_format) {
amb_num &= 0x7FFFFFFF;
}
-
+
for(Uint4 i=1; i < amb_num+1; i++) {
Int4 row_len = 0;
Int4 position = 0;
Uint1 char_r = 0;
-
+
if (new_format) {
char_r = s_ResVal (amb_chars, i);
- row_len = s_ResLenNew(amb_chars, i);
+ row_len = s_ResLenNew(amb_chars, i);
position = s_ResPosNew(amb_chars, i);
} else {
char_r = s_ResVal (amb_chars, i);
- row_len = s_ResLenOld(amb_chars, i);
+ row_len = s_ResLenOld(amb_chars, i);
position = s_ResPosOld(amb_chars, i);
}
-
+
Int4 pos = position / 2;
Int4 rem = position & 1; /* 0 or 1 */
Uint1 char_l = char_r << 4;
-
+
Int4 j;
Int4 index = pos;
-
+
// This could be made slightly faster for long runs.
-
+
for(j = 0; j <= row_len; j++) {
if (!rem) {
buf4bit[index] = (buf4bit[index] & 0x0F) + char_l;
@@ -727,7 +727,7 @@ s_SeqDBRebuildDNA_NA4(vector<char> & buf4bit,
index++;
}
}
-
+
if (new_format) // for new format we have 8 bytes for each element.
i++;
}
@@ -754,36 +754,36 @@ s_SeqDBRebuildDNA_NA8(char * seq,
const SSeqDBSlice & region)
{
if (amb_chars.empty() || !seq ) return;
-
+
Uint4 amb_num = amb_chars[0];
-
+
/* Check if highest order bit set. */
bool new_format = (amb_num & 0x80000000) != 0;
-
+
if (new_format) amb_num &= 0x7FFFFFFF;
-
+
for(Uint4 i = 1; i < amb_num+1; i++) {
Int4 row_len = 0;
Int4 position = 0;
Uint1 trans_ch = 0;
-
+
if (new_format) {
trans_ch = s_ResVal (amb_chars, i);
- row_len = s_ResLenNew(amb_chars, i) + 1;
+ row_len = s_ResLenNew(amb_chars, i) + 1;
position = s_ResPosNew(amb_chars, i);
} else {
trans_ch = s_ResVal (amb_chars, i);
- row_len = s_ResLenOld(amb_chars, i) + 1;
+ row_len = s_ResLenOld(amb_chars, i) + 1;
position = s_ResPosOld(amb_chars, i);
}
-
+
if (new_format) ++i;
-
+
if (position + row_len <= region.begin || position >= region.end)
continue;
- for (int j = 0; j < row_len; ++j, ++position)
- if ( position >= region.begin && position < region.end)
+ for (int j = 0; j < row_len; ++j, ++position)
+ if ( position >= region.begin && position < region.end)
seq[position] = trans_ch;
}
}
@@ -807,19 +807,19 @@ s_SeqDBWriteSeqDataProt(CSeq_inst & seqinst,
{
// stuff - ncbistdaa
// mol = aa
-
+
// This possibly/probably copies several times.
// 1. One copy into stdaa_data.
// 2. Second copy into NCBIstdaa.
// 3. Third copy into seqdata.
-
+
vector<char> aa_data;
aa_data.resize(length);
-
+
for(int i = 0; i < length; i++) {
aa_data[i] = seq_buffer[i];
}
-
+
seqinst.SetSeq_data().SetNcbistdaa().Set().swap(aa_data);
seqinst.SetMol(CSeq_inst::eMol_aa);
}
@@ -844,18 +844,18 @@ s_SeqDBWriteSeqDataNucl(CSeq_inst & seqinst,
{
int whole_bytes = length / 4;
int partial_byte = ((length & 0x3) != 0) ? 1 : 0;
-
+
vector<char> na_data;
na_data.resize(whole_bytes + partial_byte);
-
+
for(int i = 0; i<whole_bytes; i++) {
na_data[i] = seq_buffer[i];
}
-
+
if (partial_byte) {
na_data[whole_bytes] = seq_buffer[whole_bytes] & (0xFF - 0x03);
}
-
+
seqinst.SetSeq_data().SetNcbi2na().Set().swap(na_data);
seqinst.SetMol(CSeq_inst::eMol_na);
}
@@ -884,7 +884,7 @@ s_SeqDBWriteSeqDataNucl(CSeq_inst & seqinst,
vector<char> buffer_4na;
s_SeqDBMapNA2ToNA4(seq_buffer, buffer_4na, length); // length is not /4 here
s_SeqDBRebuildDNA_NA4(buffer_4na, amb_chars);
-
+
seqinst.SetSeq_data().SetNcbi4na().Set().swap(buffer_4na);
seqinst.SetMol(CSeq_inst::eMol_na);
}
@@ -902,36 +902,36 @@ static void
s_GetBioseqTitle(CRef<CBlast_def_line_set> deflines, string & title)
{
title.erase();
-
+
string seqid_str;
-
- typedef list< CRef<CBlast_def_line> >::const_iterator TDefIt;
+
+ typedef list< CRef<CBlast_def_line> >::const_iterator TDefIt;
typedef list< CRef<CSeq_id > >::const_iterator TSeqIt;
-
+
const list< CRef<CBlast_def_line> > & dl = deflines->Get();
-
+
bool first_defline(true);
-
+
for(TDefIt iter = dl.begin(); iter != dl.end(); iter++) {
ostringstream oss;
-
+
const CBlast_def_line & defline = **iter;
-
+
if (! title.empty()) {
//oss << "\1";
oss << " ";
}
-
+
bool wrote_seqids(false);
-
+
if ((!first_defline) && defline.CanGetSeqid()) {
const list< CRef<CSeq_id > > & sl = defline.GetSeqid();
-
+
bool first_seqid(true);
-
+
// First should look like: "<title>"
// Others should look like: " ><seqid>|<seqid>|<seqid><title>"
-
+
// Should this be two sections not one loop?
for (TSeqIt seqit = sl.begin(); seqit != sl.end(); seqit++) {
@@ -940,24 +940,24 @@ s_GetBioseqTitle(CRef<CBlast_def_line_set> deflines, string & title)
} else {
oss << "|";
}
-
+
(*seqit)->WriteAsFasta(oss);
-
+
first_seqid = false;
wrote_seqids = true;
}
}
-
+
// Omit seqids from first defline
first_defline = false;
-
+
if (defline.CanGetTitle()) {
if (wrote_seqids) {
oss << " ";
}
oss << defline.GetTitle();
}
-
+
title += oss.str();
}
}
@@ -977,125 +977,132 @@ static bool
s_SeqDB_SeqIdIn(const list< CRef< CSeq_id > > & seqids, const CSeq_id & target)
{
typedef list< CRef<CSeq_id> > TSeqidList;
-
+
ITERATE(TSeqidList, iter, seqids) {
CSeq_id::E_SIC rv = (**iter).Compare(target);
-
+
switch(rv) {
case CSeq_id::e_YES:
return true;
-
+
case CSeq_id::e_NO:
return false;
-
+
default:
break;
}
}
-
+
return false;
}
CRef<CBlast_def_line_set>
CSeqDBVol::x_GetTaxDefline(int oid,
- int preferred_gi,
+ TGi preferred_gi,
+ const CSeq_id * preferred_seqid,
CSeqDBLockHold & locked)
{
typedef list< CRef<CBlast_def_line> > TBDLL;
typedef TBDLL::iterator TBDLLIter;
typedef TBDLL::const_iterator TBDLLConstIter;
-
+
// 1. read a defline set w/ gethdr, filtering by membership bit.
-
+
CRef<CBlast_def_line_set> BDLS =
x_GetFilteredHeader(oid, NULL, locked);
-
+
// 2. if there is a preferred gi, bump it to the top.
-
- if (preferred_gi != 0) {
+
+ if (preferred_gi || preferred_seqid) {
CRef<CBlast_def_line_set> new_bdls(new CBlast_def_line_set);
-
- CSeq_id seqid(CSeq_id::e_Gi, preferred_gi);
-
+
+ CRef<const CSeq_id> seqid;
+ if (preferred_gi) {
+ seqid.Reset(new CSeq_id(CSeq_id::e_Gi, GI_TO(TIntId, preferred_gi)));
+ } else {
+ seqid.Reset(preferred_seqid);
+ }
+
bool found = false;
-
+
ITERATE(list< CRef<CBlast_def_line> >, iter, BDLS->Get()) {
- if ((! found) && s_SeqDB_SeqIdIn((**iter).GetSeqid(), seqid)) {
+ if ((! found) && s_SeqDB_SeqIdIn((**iter).GetSeqid(), *seqid)) {
found = true;
new_bdls->Set().push_front(*iter);
} else {
new_bdls->Set().push_back(*iter);
}
}
-
+
return new_bdls;
}
-
+
return BDLS;
}
list< CRef<CSeqdesc> >
CSeqDBVol::x_GetTaxonomy(int oid,
- int preferred_gi,
+ TGi preferred_gi,
+ const CSeq_id * preferred_seqid,
CRef<CSeqDBTaxInfo> tax_info,
CSeqDBLockHold & locked)
{
const bool provide_new_taxonomy_info = true;
const bool use_taxinfo_cache = true;
-
+
const char * TAX_ORGREF_DB_NAME = "taxon";
-
+
list< CRef<CSeqdesc> > taxonomy;
-
+
CRef<CBlast_def_line_set> bdls =
- x_GetTaxDefline(oid, preferred_gi, locked);
-
+ x_GetTaxDefline(oid, preferred_gi, preferred_seqid, locked);
+
if (bdls.Empty()) {
return taxonomy;
}
-
+
typedef list< CRef<CBlast_def_line> > TBDLL;
typedef TBDLL::iterator TBDLLIter;
typedef TBDLL::const_iterator TBDLLConstIter;
-
+
const TBDLL & dl = bdls->Get();
-
+
// Lock for sake of tax cache
-
+
m_Atlas.Lock(locked);
-
+
for(TBDLLConstIter iter = dl.begin(); iter != dl.end(); iter ++) {
int taxid = 0;
-
+
if ((*iter)->CanGetTaxid()) {
taxid = (*iter)->GetTaxid();
}
if (taxid <= 0) {
continue;
}
-
+
bool have_org_desc = false;
-
+
if (use_taxinfo_cache && m_TaxCache.Lookup(taxid).NotEmpty()) {
have_org_desc = true;
}
-
+
SSeqDBTaxInfo tnames(taxid);
-
+
if (tax_info.Empty()) {
continue;
}
-
+
bool found_taxid_in_taxonomy_blastdb = true;
-
+
if ((! have_org_desc) && provide_new_taxonomy_info) {
try {
found_taxid_in_taxonomy_blastdb = tax_info->GetTaxNames(taxid, tnames, locked);
} catch (CSeqDBException &) {
found_taxid_in_taxonomy_blastdb = false;
- }
+ }
}
-
+
if (provide_new_taxonomy_info) {
if (have_org_desc) {
taxonomy.push_back(m_TaxCache.Lookup(taxid));
@@ -1103,33 +1110,33 @@ CSeqDBVol::x_GetTaxonomy(int oid,
CRef<CDbtag> org_tag(new CDbtag);
org_tag->SetDb(TAX_ORGREF_DB_NAME);
org_tag->SetTag().SetId(taxid);
-
+
CRef<COrg_ref> org(new COrg_ref);
if (found_taxid_in_taxonomy_blastdb) {
org->SetTaxname().swap(tnames.scientific_name);
org->SetCommon().swap(tnames.common_name);
}
org->SetDb().push_back(org_tag);
-
+
CRef<CBioSource> source;
source.Reset(new CBioSource);
source->SetOrg(*org);
-
+
CRef<CSeqdesc> desc(new CSeqdesc);
desc->SetSource(*source);
-
+
taxonomy.push_back(desc);
-
+
if (use_taxinfo_cache) {
m_TaxCache.Lookup(taxid) = desc;
}
}
}
}
-
+
return taxonomy;
}
-
+
/// Efficiently decode a Blast-def-line-set from binary ASN.1.
/// @param oss Octet string sequence of binary ASN.1 data.
/// @param bdls Blast def line set decoded from oss.
@@ -1137,34 +1144,34 @@ static CRef<CBlast_def_line_set>
s_OssToDefline(const CUser_field::TData::TOss & oss)
{
typedef const CUser_field::TData::TOss TOss;
-
+
const char * data = NULL;
size_t size = 0;
string temp;
-
+
if (oss.size() == 1) {
// In the single-element case, no copies are needed.
-
+
const vector<char> & v = *oss.front();
data = & v[0];
size = v.size();
} else {
// Determine the octet string length and do one allocation.
-
+
ITERATE (TOss, iter1, oss) {
size += (**iter1).size();
}
-
+
temp.reserve(size);
-
+
ITERATE (TOss, iter3, oss) {
// 23.2.4[1] "The elements of a vector are stored contiguously".
temp.append(& (**iter3)[0], (*iter3)->size());
}
-
+
data = & temp[0];
}
-
+
CObjectIStreamAsnBinary inpstr(data, size);
CRef<CBlast_def_line_set> retval(new CBlast_def_line_set);
inpstr >> *retval;
@@ -1200,11 +1207,11 @@ s_ExtractBlastDefline(const T& bioseq)
return failure;
}
-CRef<CBlast_def_line_set>
+CRef<CBlast_def_line_set>
CSeqDB::ExtractBlastDefline(const CBioseq_Handle & handle)
{ return s_ExtractBlastDefline(handle); }
-CRef<CBlast_def_line_set>
+CRef<CBlast_def_line_set>
CSeqDB::ExtractBlastDefline(const CBioseq & bioseq)
{ return s_ExtractBlastDefline(bioseq); }
@@ -1213,41 +1220,41 @@ CSeqDBVol::x_GetAsnDefline(int oid,
CSeqDBLockHold & locked) const
{
CRef<CSeqdesc> asndef;
-
+
vector<char> hdr_data;
x_GetFilteredBinaryHeader(oid, hdr_data, locked);
-
+
if (! hdr_data.empty()) {
CRef<CUser_object> uobj(new CUser_object);
-
+
CRef<CObject_id> uo_oi(new CObject_id);
uo_oi->SetStr(kAsnDeflineObjLabel);
uobj->SetType(*uo_oi);
-
+
CRef<CUser_field> uf(new CUser_field);
-
+
CRef<CObject_id> uf_oi(new CObject_id);
uf_oi->SetStr(kAsnDeflineObjLabel);
uf->SetLabel(*uf_oi);
-
+
vector< vector<char>* > & strs = uf->SetData().SetOss();
uf->SetNum(1);
-
+
strs.push_back(new vector<char>);
strs[0]->swap(hdr_data);
-
+
uobj->SetData().push_back(uf);
-
+
asndef = new CSeqdesc;
asndef->SetUser(*uobj);
}
-
+
return asndef;
}
CRef<CBioseq>
CSeqDBVol::GetBioseq(int oid,
- int target_gi,
+ TGi target_gi,
const CSeq_id * target_seq_id,
CRef<CSeqDBTaxInfo> tax_info,
bool seqdata,
@@ -1255,39 +1262,39 @@ CSeqDBVol::GetBioseq(int oid,
{
typedef list< CRef<CBlast_def_line> > TDeflines;
CRef<CBioseq> null_result;
-
+
CRef<CBlast_def_line> defline;
list< CRef< CSeq_id > > seqids;
-
+
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
// Get the defline set; but do not modify the object returned by
// GetFilteredHeader, since that object lives in the cache.
-
+
CRef<CBlast_def_line_set> orig_deflines =
x_GetFilteredHeader(oid, NULL, locked);
-
+
CRef<CBlast_def_line_set> defline_set;
-
- if (target_gi || target_seq_id ) {
+
+ if ((target_gi != ZERO_GI) || target_seq_id) {
defline_set.Reset(new CBlast_def_line_set);
-
+
CRef<const CSeq_id > seqid;
- if (target_gi) {
- seqid.Reset(new CSeq_id(CSeq_id::e_Gi, target_gi));
+ if (target_gi != ZERO_GI) {
+ seqid.Reset(new CSeq_id(CSeq_id::e_Gi, GI_TO(TIntId, target_gi)));
} else {
seqid.Reset(target_seq_id);
}
-
+
CRef<CBlast_def_line> filt_dl;
-
+
ITERATE(TDeflines, iter, orig_deflines->Get()) {
if (s_SeqDB_SeqIdIn((**iter).GetSeqid(), *seqid)) {
filt_dl = *iter;
break;
}
}
-
+
if (filt_dl.Empty()) {
NCBI_THROW(CSeqDBException, eArgErr,
"Error: oid headers do not contain target gi/seq_id.");
@@ -1296,34 +1303,34 @@ CSeqDBVol::GetBioseq(int oid,
}
} else {
defline_set = orig_deflines;
- }
-
+ }
+
if (defline_set.Empty() ||
(! defline_set->CanGet()) ||
(0 == defline_set->Get().size())) {
return null_result;
}
-
+
defline = defline_set->Get().front();
if (! defline->CanGetSeqid()) {
return null_result;
}
seqids = defline->GetSeqid();
-
+
// Get length & sequence.
-
+
CRef<CBioseq> bioseq(new CBioseq);
-
+
bool is_prot = (x_GetSeqType() == 'p');
-
+
if (seqdata) {
const char * seq_buffer = 0;
int length = x_GetSequence(oid, & seq_buffer, false, locked, false);
-
+
if (length < 1) {
return null_result;
}
-
+
// If protein, we set bsp->mol = Seq_mol_aa, seq_data_type =
// Seq_code_ncbistdaa; then we write the buffer into the byte
// store (or equivalent).
@@ -1333,17 +1340,17 @@ CSeqDBVol::GetBioseq(int oid,
// b. If there are any, convert sequence to 4 byte rep.
// c. Otherwise write to a byte store.
// d. Set mol = Seq_mol_na;
-
+
CSeq_inst & seqinst = bioseq->SetInst();
-
+
if (is_prot) {
s_SeqDBWriteSeqDataProt(seqinst, seq_buffer, length);
} else {
// nucl
vector<Int4> ambchars;
-
+
x_GetAmbChar(oid, ambchars, locked);
-
+
if (ambchars.empty()) {
// keep as 2 bit
s_SeqDBWriteSeqDataNucl(seqinst, seq_buffer, length);
@@ -1351,63 +1358,63 @@ CSeqDBVol::GetBioseq(int oid,
// translate to 4 bit
s_SeqDBWriteSeqDataNucl(seqinst, seq_buffer, length, ambchars);
}
-
+
// mol = na
seqinst.SetMol(CSeq_inst::eMol_na);
}
-
+
if (seq_buffer) {
seq_buffer = 0;
}
-
+
// Set the length and repr (== raw).
-
+
seqinst.SetLength(length);
seqinst.SetRepr(CSeq_inst::eRepr_raw);
} else {
CSeq_inst & seqinst = bioseq->SetInst();
seqinst.SetRepr(CSeq_inst::eRepr_not_set);
-
+
bioseq->SetInst().SetMol(is_prot
? CSeq_inst::eMol_aa
: CSeq_inst::eMol_na);
}
-
+
// Set the id (Seq_id)
-
+
bioseq->SetId().swap(seqids);
-
+
// If the format is binary, we get the defline and chain it onto
// the bsp->desc list; then we read and append taxonomy names to
// the list (x_GetTaxonomy()).
-
+
if (defline_set.NotEmpty()) {
// Convert defline to string.
-
+
string description;
-
+
s_GetBioseqTitle(defline_set, description);
-
+
CRef<CSeqdesc> desc1(new CSeqdesc);
desc1->SetTitle().swap(description);
-
+
CRef<CSeqdesc> desc2( x_GetAsnDefline(oid, locked) );
-
+
CSeq_descr & seq_desc_set = bioseq->SetDescr();
seq_desc_set.Set().push_back(desc1);
-
+
if (! desc2.Empty()) {
seq_desc_set.Set().push_back(desc2);
}
}
-
+
list< CRef<CSeqdesc> > tax =
- x_GetTaxonomy(oid, target_gi, tax_info, locked);
-
+ x_GetTaxonomy(oid, target_gi, target_seq_id, tax_info, locked);
+
ITERATE(list< CRef<CSeqdesc> >, iter, tax) {
bioseq->SetDescr().Set().push_back(*iter);
}
-
+
return bioseq;
}
@@ -1418,25 +1425,25 @@ char * CSeqDBVol::x_AllocType(size_t length,
// Allocation using the atlas is not intended for the end user.
// 16 bytes are added as insurance against potential off-by-one or
// off-by-a-few errors.
-
+
length += 16;
-
+
char * retval = 0;
-
+
switch(alloc_type) {
case eMalloc:
retval = (char*) malloc(length);
break;
-
+
case eNew:
retval = new char[length];
break;
-
+
case eAtlas:
default:
retval = m_Atlas.Alloc(length + 16, locked, false);
}
-
+
return retval;
}
@@ -1451,7 +1458,7 @@ int CSeqDBVol::GetAmbigSeq(int oid,
char * buf1 = 0;
int baselen =
x_GetAmbigSeq(oid, & buf1, nucl_code, alloc_type, region, masks, locked);
-
+
*buffer = buf1;
return baselen;
}
@@ -1493,7 +1500,7 @@ int CSeqDBVol::x_GetAmbigSeq(int oid,
// Note the use of the third argument of x_GetSequence() to manage
// the lifetime of the acquired region. Specifying false for that
// argument ties the lifetime to the CSeqDBSeqFile's memory lease.
-
+
const char * tmp(0);
int base_length = x_GetSequence(oid,
&tmp,
@@ -1503,7 +1510,7 @@ int CSeqDBVol::x_GetAmbigSeq(int oid,
if (region && region->end > base_length )
NCBI_THROW(CSeqDBException, eFileErr, "Error: region beyond sequence range.");
-
+
SSeqDBSlice range = region ? (*region) : SSeqDBSlice(0, base_length);
base_length = range.end - range.begin;
@@ -1523,28 +1530,28 @@ int CSeqDBVol::x_GetAmbigSeq(int oid,
bool sentinel = (nucl_code == kSeqDBNuclBlastNA8);
*buffer = x_AllocType(base_length + (sentinel ? 2 : 0), alloc_type, locked);
char *seq = *buffer - range.begin + (sentinel ? 1 : 0);
-
+
// Get ambiguity characters.
-
+
vector<Int4> ambchars;
x_GetAmbChar(oid, ambchars, locked);
-
+
// Determine if we want to filter by offset ranges. This
// is only done if:
//
// 1. No range is specified by the user.
// 2. We have cached ranges.
-
+
TRangeCache::iterator rciter = m_RangeCache.find(oid);
bool use_range_set = true;
- if (region
- || rciter == m_RangeCache.end()
- || rciter->second->GetRanges().empty()
- || CSeqDBRangeList::ImmediateLength() >= base_length)
+ if (region
+ || rciter == m_RangeCache.end()
+ || rciter->second->GetRanges().empty()
+ || CSeqDBRangeList::ImmediateLength() >= base_length)
use_range_set = false;
if (! use_range_set) {
-
+
s_SeqDBMapNA2ToNA8(tmp, seq, range);
s_SeqDBRebuildDNA_NA8(seq, ambchars, range);
s_SeqDBMaskSequence(seq, masks, (char)14, range);
@@ -1554,32 +1561,32 @@ int CSeqDBVol::x_GetAmbigSeq(int oid,
_ASSERT (!region);
const TRangeList & range_set = rciter->second->GetRanges();
-
+
// Place 'fence' sentinel bytes around each range; this is done
// before any of the range data is mapped so that the range data
// is free to replace the sentinel bytes if needed; that would
// only happen if range_set are adjacent or overlapping.
-
+
ITERATE(TRangeVector, riter, range_set) {
int begin(riter->first);
int end(riter->second);
-
+
if (begin) seq[begin - 1] = (char) FENCE_SENTRY;
if (end < base_length) seq[end] = (char) FENCE_SENTRY;
}
-
+
ITERATE(TRangeVector, riter, range_set) {
- SSeqDBSlice slice(max(0, riter->first),
+ SSeqDBSlice slice(max(0, riter->first),
min(range.end, riter->second));
-
+
s_SeqDBMapNA2ToNA8(tmp, seq, slice);
s_SeqDBRebuildDNA_NA8(seq, ambchars, slice);
s_SeqDBMaskSequence(seq, masks, (char)14, slice);
if (sentinel) s_SeqDBMapNcbiNA8ToBlastNA8(seq, slice);
}
}
-
+
// Put back the sentinel at last
if (sentinel) {
(*buffer)[0] = (char)15;
@@ -1589,7 +1596,7 @@ int CSeqDBVol::x_GetAmbigSeq(int oid,
// Clear the masks after consumption
if (masks) masks->clear();
-
+
return base_length;
}
@@ -1598,55 +1605,55 @@ void SeqDB_UnpackAmbiguities(const CTempString & sequence,
string & result)
{
result.resize(0);
-
+
// The code in this block is derived from GetBioseq() and
// s_SeqDBWriteSeqDataNucl().
-
+
// Get the length and the (probably mmapped) data.
-
+
if (sequence.length() == 0) {
NCBI_THROW(CSeqDBException, eFileErr,
"Error: packed sequence data is not valid.");
}
-
+
const char * seq_buffer = sequence.data();
-
+
int whole_bytes = sequence.length() - 1;
int remainder = sequence[whole_bytes] & 3;
int base_length = (whole_bytes * 4) + remainder;
-
+
if (base_length == 0) {
return;
}
-
+
// Get ambiguity characters.
-
+
vector<Int4> ambchars;
ambchars.reserve(ambiguities.length()/4);
-
+
for(size_t i = 0; i < ambiguities.length(); i+=4) {
Int4 A = SeqDB_GetStdOrd((int*) (ambiguities.data() + i));
ambchars.push_back(A);
}
-
+
// Combine and translate to 4 bits-per-character encoding.
-
+
char * buffer_na8 = (char*) malloc(base_length);
-
+
try {
SSeqDBSlice range(0, base_length);
-
+
s_SeqDBMapNA2ToNA8(seq_buffer, buffer_na8, range);
-
+
s_SeqDBRebuildDNA_NA8(buffer_na8, ambchars, range);
}
catch(...) {
free(buffer_na8);
throw;
}
-
+
result.assign(buffer_na8, base_length);
-
+
free(buffer_na8);
}
@@ -1660,30 +1667,30 @@ int CSeqDBVol::x_GetSequence(int oid,
{
TIndx start_offset = 0;
TIndx end_offset = 0;
-
+
int length = -1;
-
+
m_Atlas.Lock(locked);
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
-
+
if (oid >= m_Idx->GetNumOIDs()) return -1;
m_Idx->GetSeqStartEnd(oid, start_offset, end_offset);
char seqtype = m_Idx->GetSeqType();
-
+
if ('p' == seqtype) {
// Subtract one, for the inter-sequence null.
-
+
end_offset --;
-
+
length = int(end_offset - start_offset);
-
+
// Although we subtracted one above to get the correct length,
// we expand the range here by one byte in both directions.
// The normal consumer of this data relies on them, and can
// walk off memory if a sequence ends on a slice boundary.
-
+
*buffer = m_Seq->GetRegion(start_offset-1,
end_offset+1,
keep,
@@ -1696,22 +1703,22 @@ int CSeqDBVol::x_GetSequence(int oid,
// The last byte is partially full; the last two bits of the
// last byte store the number of nucleotides in the last byte
// (0 to 3).
-
+
// 'Hold' is used if we are going to fetch another kind of
// data after this data, but before we are done actually using
// this data. If can_release is true, we will return after
// this. If keep is true, we don't need hold because keep
// will already have preserved the region.
-
+
bool hold = ! (keep || can_release);
-
+
*buffer = m_Seq->GetRegion(start_offset,
end_offset,
keep,
hold,
locked,
in_lease);
-
+
if (! (*buffer)) return -1;
// If we are returning a hold on the sequence (keep), and the
@@ -1720,20 +1727,20 @@ int CSeqDBVol::x_GetSequence(int oid,
// the underlying data). This will allow the following data
// access to occur outside of the locked duration - lowering
// contention in the nucleotide case.
-
+
/* do not release the lock since we may be getting more...
if (keep && can_release) {
m_Atlas.Unlock(locked);
}*/
-
+
int whole_bytes = int(end_offset - start_offset - 1);
-
+
char last_char = (*buffer)[whole_bytes];
-
+
int remainder = last_char & 3;
length = (whole_bytes * 4) + remainder;
}
-
+
return length;
}
@@ -1741,33 +1748,33 @@ list< CRef<CSeq_id> > CSeqDBVol::GetSeqIDs(int oid,
CSeqDBLockHold & locked) const
{
list< CRef< CSeq_id > > seqids;
-
+
CRef<CBlast_def_line_set> defline_set =
x_GetFilteredHeader(oid, NULL, locked);
-
+
if ((! defline_set.Empty()) && defline_set->CanGet()) {
ITERATE(list< CRef<CBlast_def_line> >, defline, defline_set->Get()) {
if (! (*defline)->CanGetSeqid()) {
continue;
}
-
+
ITERATE(list< CRef<CSeq_id> >, seqid, (*defline)->GetSeqid()) {
seqids.push_back(*seqid);
}
}
}
-
+
return seqids;
}
-int CSeqDBVol::GetSeqGI(int oid,
- CSeqDBLockHold & locked) const
+TGi CSeqDBVol::GetSeqGI(int oid,
+ CSeqDBLockHold & locked) const
{
if (!m_OidFileOpened) x_OpenOidFile(locked);
if (!m_GiIndex.Empty()) {
return m_GiIndex->GetSeqGI(oid, locked);
}
- return -1;
+ return INVALID_GI;
}
Uint8 CSeqDBVol::GetVolumeLength() const
@@ -1789,71 +1796,71 @@ CSeqDBVol::x_GetFilteredHeader(int oid,
{
typedef list< CRef<CBlast_def_line> > TBDLL;
typedef TBDLL::iterator TBDLLIter;
-
+
m_Atlas.Lock(locked);
-
+
TDeflineCacheItem & cached = m_DeflineCache.Lookup(oid);
-
+
if (cached.first.NotEmpty()) {
if (changed) {
*changed = cached.second;
}
-
+
return cached.first;
}
-
+
bool asn_changed = false;
-
+
CRef<CBlast_def_line_set> BDLS =
x_GetHdrAsn1(oid, true, & asn_changed, locked);
-
+
bool id_filter = x_HaveIdFilter();
-
+
if (id_filter || m_MemBit) {
// Create the memberships mask (should this be fixed to allow
// membership bits greater than 32?)
-
+
TBDLL & dl = BDLS->Set();
-
+
for(TBDLLIter iter = dl.begin(); iter != dl.end(); ) {
const CBlast_def_line & defline = **iter;
-
+
bool have_memb = true;
-
+
if (m_MemBit) {
have_memb =
defline.CanGetMemberships() &&
defline.IsSetMemberships() &&
(! defline.GetMemberships().empty());
-
+
if (have_memb) {
int bits = defline.GetMemberships().front();
int memb_mask = 0x1 << (m_MemBit-1);
-
+
if ((bits & memb_mask) == 0) {
have_memb = false;
}
}
}
-
+
// Here we must pass both the user-gi and volume-gi test,
// for each defline, but not necessarily for each Seq-id.
-
+
if (have_memb && id_filter && defline.CanGetSeqid()) {
have_memb = false;
-
+
bool have_user = false, have_volume = false;
-
+
ITERATE(list< CRef<CSeq_id> >, seqid, defline.GetSeqid()) {
x_FilterHasId(**seqid, have_user, have_volume);
-
+
if (have_user && have_volume)
break;
}
-
+
have_memb = have_user && have_volume;
}
-
+
if (! have_memb) {
TBDLLIter eraseme = iter++;
dl.erase(eraseme);
@@ -1871,7 +1878,7 @@ CSeqDBVol::x_GetFilteredHeader(int oid,
cached.first = BDLS;
cached.second = asn_changed;
}
-
+
return BDLS;
}
@@ -1882,33 +1889,33 @@ CSeqDBVol::x_GetHdrAsn1(int oid,
CSeqDBLockHold & locked) const
{
CRef<CBlast_def_line_set> bdls;
-
+
CTempString raw_data = x_GetHdrAsn1Binary(oid, locked);
-
+
if (! raw_data.size()) {
return bdls;
}
-
+
// Now create an ASN.1 object from the memory chunk provided here.
-
+
CObjectIStreamAsnBinary inpstr(raw_data.data(), raw_data.size());
-
+
bdls.Reset(new objects::CBlast_def_line_set);
-
+
inpstr >> *bdls;
-
+
if (adjust_oids && bdls.NotEmpty() && m_VolStart) {
NON_CONST_ITERATE(list< CRef<CBlast_def_line> >, dl, bdls->Set()) {
if (! (**dl).CanGetSeqid()) {
continue;
}
-
+
NON_CONST_ITERATE(list< CRef<CSeq_id> >, id, (*dl)->SetSeqid()) {
CSeq_id & seqid = **id;
-
+
if (seqid.Which() == CSeq_id::e_General) {
CDbtag & dbt = seqid.SetGeneral();
-
+
if (dbt.GetDb() == "BL_ORD_ID") {
int vol_oid = dbt.GetTag().GetId();
dbt.SetTag().SetId(m_VolStart + vol_oid);
@@ -1920,7 +1927,7 @@ CSeqDBVol::x_GetHdrAsn1(int oid,
}
}
}
-
+
return bdls;
}
@@ -1929,15 +1936,15 @@ CSeqDBVol::x_GetHdrAsn1Binary(int oid, CSeqDBLockHold & locked) const
{
TIndx hdr_start = 0;
TIndx hdr_end = 0;
-
+
m_Atlas.Lock(locked);
-
+
if (!m_HdrFileOpened) x_OpenHdrFile(locked);
m_Idx->GetHdrStartEnd(oid, hdr_start, hdr_end);
-
+
const char * asn_region = m_Hdr->GetRegion(hdr_start, hdr_end, locked);
-
+
return CTempString(asn_region, hdr_end - hdr_start);
}
@@ -1949,19 +1956,19 @@ CSeqDBVol::x_GetFilteredBinaryHeader(int oid,
// This method's client is GetBioseq() and related methods. That
// code needs filtered ASN.1 headers; eliminating the fetching of
// filtered data here is not necessary (the cache will hit.)
-
+
// If the data changed after deserialization, we need to serialize
// the modified version. If not, we can just copy the binary data
// from disk.
-
+
bool changed = false;
-
+
CRef<CBlast_def_line_set> dls =
x_GetFilteredHeader(oid, & changed, locked);
-
+
if (changed) {
CNcbiOstrstream asndata;
-
+
{{
CObjectOStreamAsnBinary outpstr(asndata);
outpstr << *dls;
@@ -1980,36 +1987,36 @@ void CSeqDBVol::x_GetAmbChar(int oid,
{
TIndx start_offset = 0;
TIndx end_offset = 0;
-
+
m_Atlas.Lock(locked);
-
+
bool ok = m_Idx->GetAmbStartEnd(oid, start_offset, end_offset);
-
+
if (! ok) {
NCBI_THROW(CSeqDBException, eFileErr,
"File error: could not get ambiguity data.");
}
-
+
int length = int(end_offset - start_offset);
-
+
if (length) {
int total = length / 4;
-
+
// 'hold' should be false here because we only need the data
// for the duration of this function.
-
+
Int4 * buffer =
(Int4*) m_Seq->GetRegion(start_offset,
start_offset + (total * 4),
false,
false,
locked);
-
+
// This is probably unnecessary
total &= 0x7FFFFFFF;
-
+
ambchars.resize(total);
-
+
for(int i = 0; i<total; i++) {
ambchars[i] = SeqDB_GetStdOrd((const int *)(& buffer[i]));
}
@@ -2049,30 +2056,30 @@ bool CSeqDBVol::PigToOid(int pig, int & oid, CSeqDBLockHold & locked) const
if (m_IsamPig.Empty()) {
return false;
}
-
+
return m_IsamPig->PigToOid(pig, oid, locked);
}
bool CSeqDBVol::GetPig(int oid, int & pig, CSeqDBLockHold & locked) const
{
pig = -1;
-
+
CRef<CBlast_def_line_set> BDLS = x_GetHdrAsn1(oid, false, NULL, locked);
-
+
if (BDLS.Empty() || (! BDLS->IsSet())) {
return false;
}
-
+
typedef list< CRef< CBlast_def_line > >::const_iterator TI1;
typedef list< int >::const_iterator TI2;
-
+
TI1 it1 = BDLS->Get().begin();
-
+
for(; it1 != BDLS->Get().end(); it1++) {
if ((*it1)->IsSetOther_info()) {
TI2 it2 = (*it1)->GetOther_info().begin();
TI2 it2end = (*it1)->GetOther_info().end();
-
+
for(; it2 != it2end; it2++) {
if (*it2 != -1) {
pig = *it2;
@@ -2081,7 +2088,7 @@ bool CSeqDBVol::GetPig(int oid, int & pig, CSeqDBLockHold & locked) const
}
}
}
-
+
return false;
}
@@ -2092,37 +2099,37 @@ bool CSeqDBVol::TiToOid(Int8 ti,
// Note: this is the (Int8 to int) interface layer; code below
// this point (in the call stack) uses int; code above this level,
// up to the user level, uses Int8.
-
+
if (!m_TiFileOpened) x_OpenTiFile(locked);
if (m_IsamTi.Empty()) {
// If the "nti/ntd" files become ubiquitous, this could be
// removed. For now, I will look up trace IDs in the string
// DB if the database in question does not have the Trace ID
// ISAM files. (The following could be made more efficient.)
-
+
CSeq_id seqid(string("gnl|ti|") + NStr::Int8ToString(ti));
vector<int> oids;
-
+
SeqidToOids(seqid, oids, locked);
-
+
if (oids.size()) {
oid = oids[0];
}
-
+
return ! oids.empty();
}
-
+
return m_IsamTi->IdToOid(ti, oid, locked);
}
-bool CSeqDBVol::GiToOid(int gi, int & oid, CSeqDBLockHold & locked) const
+bool CSeqDBVol::GiToOid(TGi gi, int & oid, CSeqDBLockHold & locked) const
{
if (!m_GiFileOpened) x_OpenGiFile(locked);
if (m_IsamGi.Empty()) {
return false;
}
-
- return m_IsamGi->IdToOid(gi, oid, locked);
+
+ return m_IsamGi->IdToOid(GI_TO(Int8, gi), oid, locked);
}
void CSeqDBVol::IdsToOids(CSeqDBGiList & ids,
@@ -2138,7 +2145,7 @@ void CSeqDBVol::IdsToOids(CSeqDBGiList & ids,
"GI list specified but no ISAM file found for GI in " + m_VolName);
}
}
-
+
if (ids.GetNumTis()) {
if (!m_TiFileOpened) x_OpenTiFile(locked);
if (m_IsamTi.NotEmpty()) {
@@ -2149,7 +2156,7 @@ void CSeqDBVol::IdsToOids(CSeqDBGiList & ids,
"TI list specified but no ISAM file found for TI in " + m_VolName);
}
}
-
+
if (ids.GetNumSis()) {
if (!m_StrFileOpened) x_OpenStrFile(locked);
if (m_IsamStr.NotEmpty()) {
@@ -2166,7 +2173,7 @@ void CSeqDBVol::IdsToOids(CSeqDBNegativeList & ids,
CSeqDBLockHold & locked) const
{
// Numeric translation is done in batch mode.
-
+
if (ids.GetNumGis()) {
if (!m_GiFileOpened) x_OpenGiFile(locked);
if (m_IsamGi.NotEmpty()) {
@@ -2177,7 +2184,7 @@ void CSeqDBVol::IdsToOids(CSeqDBNegativeList & ids,
"GI list specified but no ISAM file found for GI in " + m_VolName);
}
}
-
+
if (ids.GetNumTis()) {
if (!m_TiFileOpened) x_OpenTiFile(locked);
if (m_IsamTi.NotEmpty()) {
@@ -2191,46 +2198,46 @@ void CSeqDBVol::IdsToOids(CSeqDBNegativeList & ids,
}
bool CSeqDBVol::GetGi(int oid,
- int & gi,
+ TGi & gi,
CSeqDBLockHold & locked) const
{
- gi = -1;
-
+ gi = INVALID_GI;
+
if (!m_GiFileOpened) x_OpenGiFile(locked);
if (m_IsamGi.Empty()) {
return false;
}
-
+
CRef<CBlast_def_line_set> BDLS =
x_GetFilteredHeader(oid, NULL, locked);
-
+
if (BDLS.Empty() || (! BDLS->IsSet())) {
return false;
}
-
+
typedef list< CRef< CBlast_def_line > >::const_iterator TI1;
typedef list< CRef< CSeq_id > >::const_iterator TI2;
-
+
TI1 it1 = BDLS->Get().begin();
-
+
// Iterate over all blast def lines in the set
-
+
for(; it1 != BDLS->Get().end(); it1++) {
if ((*it1)->CanGetSeqid()) {
TI2 it2 = (*it1)->GetSeqid().begin();
TI2 it2end = (*it1)->GetSeqid().end();
-
+
// Iterate within each defline
-
+
for(; it2 != it2end; it2++) {
if ((*it2)->IsGi()) {
- gi = GI_TO(int, (*it2)->GetGi());
+ gi = (*it2)->GetGi();
return true;
}
}
}
}
-
+
return false;
}
@@ -2245,7 +2252,7 @@ void CSeqDBVol::x_StringToOids(const string & acc,
bool vcheck (false);
bool fits_in_four = (ident == -1) || ! (ident >> 32);
bool needs_four = true;
-
+
switch(id_type) {
case eStringId:
if (!m_StrFileOpened) x_OpenStrFile(locked);
@@ -2255,71 +2262,71 @@ void CSeqDBVol::x_StringToOids(const string & acc,
m_IsamStr->StringToOids(str_id, oids, simpler, vcheck, locked);
}
break;
-
+
case ePigId:
// Converted to PIG type.
if (!m_PigFileOpened) x_OpenPigFile(locked);
if (! m_IsamPig.Empty()) {
int oid(-1);
-
+
if (m_IsamPig->PigToOid((int) ident, oid, locked)) {
oids.push_back(oid);
}
}
break;
-
+
case eGiId:
// Converted to GI type.
if (!m_GiFileOpened) x_OpenGiFile(locked);
if (! m_IsamGi.Empty()) {
int oid(-1);
-
+
if (m_IsamGi->IdToOid(ident, oid, locked)) {
oids.push_back(oid);
}
}
break;
-
+
case eTiId:
// Converted to TI type.
if (!m_TiFileOpened) x_OpenTiFile(locked);
if (!m_StrFileOpened) x_OpenStrFile(locked);
if (! m_IsamTi.Empty()) {
int oid(-1);
-
+
if (m_IsamTi->IdToOid(ident, oid, locked)) {
oids.push_back(oid);
}
} else if (m_IsamStr) {
// Not every database with TIs has a TI index, so fall
// back to a string comparison if the first attempt fails.
- //
+ //
// 1. TI's don't have versions.
// 2. Specify "adjusted" as true, because lookup of
// "gb|.." and similar tricks are not needed for TIs.
-
+
m_IsamStr->StringToOids(acc, oids, true, vcheck, locked);
}
break;
-
+
case eOID:
// Converted to OID directly.
oids.push_back((int) ident);
break;
-
+
case eHashId:
_ASSERT(0);
NCBI_THROW(CSeqDBException,
eArgErr,
"Internal error: hashes are not Seq-ids.");
}
-
+
if ((! fits_in_four) && needs_four) {
NCBI_THROW(CSeqDBException,
eArgErr,
"ID overflows range of specified type.");
}
-
+
if (vcheck) {
x_CheckVersions(acc, oids, locked);
}
@@ -2332,53 +2339,53 @@ void CSeqDBVol::x_CheckVersions(const string & acc,
// If we resolved a string id by stripping the version off of the
// string, we need to check (for each OID) if the real ID had a
// matching version.
-
+
// This condition happens in two cases: where the database has a
// different version of the same ID, and in the case of sparse
// databases (which do not store the version). In the latter
// case, we may get a list of OIDs where some of the OIDs pass
// this test, and others fail.
-
+
size_t pos = acc.find(".");
_ASSERT(pos != acc.npos);
-
+
string ver_str(acc, pos+1, acc.size()-(pos+1));
int vernum = NStr::StringToInt(ver_str,
NStr::fConvErr_NoThrow |
NStr::fAllowTrailingSymbols);
-
+
string nover(acc, 0, pos);
-
+
size_t pos2(0);
while((pos2 = nover.find("|")) != nover.npos) {
nover.erase(0, pos2+1);
}
-
+
NON_CONST_ITERATE(vector<int>, iter, oids) {
list< CRef<CSeq_id> > ids =
GetSeqIDs(*iter, locked);
-
+
bool found = false;
-
+
ITERATE(list< CRef<CSeq_id> >, seqid, ids) {
const CTextseq_id * id = (*seqid)->GetTextseq_Id();
-
+
if (id &&
id->CanGetAccession() &&
id->GetAccession() == nover &&
id->CanGetVersion() &&
id->GetVersion() == vernum) {
-
+
found = true;
break;
}
}
-
+
if (! found) {
*iter = -1;
}
}
-
+
oids.erase(remove(oids.begin(), oids.end(), -1), oids.end());
}
@@ -2389,13 +2396,13 @@ void CSeqDBVol::AccessionToOids(const string & acc,
Int8 ident (-1);
string str_id;
bool simpler (false);
-
+
ESeqDBIdType id_type = SeqDB_SimplifyAccession(acc, ident, str_id, simpler);
x_StringToOids(acc, id_type, ident, str_id, simpler, oids, locked);
}
-
+
void CSeqDBVol::SeqidToOids(CSeq_id & seqid,
vector<int> & oids,
CSeqDBLockHold & locked) const
@@ -2403,9 +2410,9 @@ void CSeqDBVol::SeqidToOids(CSeq_id & seqid,
Int8 ident (-1);
string str_id;
bool simpler (false);
-
+
ESeqDBIdType id_type = SeqDB_SimplifySeqid(seqid, 0, ident, str_id, simpler);
-
+
x_StringToOids(seqid.AsFastaString(), id_type, ident, str_id, simpler, oids, locked);
}
@@ -2413,7 +2420,7 @@ void CSeqDBVol::SeqidToOids(CSeq_id & seqid,
void CSeqDBVol::UnLease()
{
m_Idx->UnLease();
-
+
if (m_Seq.NotEmpty()) {
m_Seq->UnLease();
}
@@ -2439,77 +2446,77 @@ int CSeqDBVol::GetOidAtOffset(int first_seq,
//
// 1. For protein, we subtract the oid to compensate for
// inter-sequence nulls.
- //
+ //
// 2. For nucleotide, the input value is 0..(num residues). We
// scale this value to the length of the byte data.
-
+
int vol_cnt = GetNumOIDs();
Uint8 vol_len = GetVolumeLength();
-
+
if (first_seq >= vol_cnt) {
NCBI_THROW(CSeqDBException,
eArgErr,
"OID not in valid range.");
}
-
+
if (residue >= vol_len) {
NCBI_THROW(CSeqDBException,
eArgErr,
"Residue offset not in valid range.");
}
-
+
if ('n' == m_Idx->GetSeqType()) {
// Input range is from 0 .. total_length
// Require range from 0 .. byte_length
-
+
Uint8 end_of_bytes = x_GetSeqResidueOffset(vol_cnt, locked);
-
+
double dresidue = (double(residue) * end_of_bytes) / vol_len;
-
+
if (dresidue < 0) {
residue = 0;
- } else {
+ } else {
residue = Uint8(dresidue);
-
+
if (residue > (end_of_bytes-1)) {
residue = end_of_bytes - 1;
}
}
}
-
+
// First seq limit handled right here.
// oid_end refers to first disincluded oid.
-
+
int oid_beg = first_seq;
int oid_end = vol_cnt-1;
-
+
// Residue limit we need to search for.
-
+
int oid_mid = (oid_beg + oid_end)/2;
-
+
while(oid_beg < oid_end) {
Uint8 offset = x_GetSeqResidueOffset(oid_mid, locked);
-
+
if ('p' == m_Idx->GetSeqType()) {
offset -= oid_mid;
}
-
+
if (offset >= residue) {
oid_end = oid_mid;
} else {
oid_beg = oid_mid + 1;
}
-
+
oid_mid = (oid_beg + oid_end)/2;
}
-
+
return oid_mid;
}
Uint8 CSeqDBVol::x_GetSeqResidueOffset(int oid, CSeqDBLockHold & locked) const
{
m_Atlas.Lock(locked);
-
+
TIndx start_offset = 0;
m_Idx->GetSeqStart(oid, start_offset);
return start_offset;
@@ -2522,38 +2529,38 @@ CSeqDBVol::GetSeqData(int oid,
CSeqDBLockHold & locked) const
{
// This design was part of the BlastDbDataLoader code.
-
+
m_Atlas.Lock(locked);
-
+
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
CRef<CSeq_data> seq_data(new CSeq_data);
-
+
if (m_IsAA) {
const char * buffer(0);
TSeqPos length(0);
-
+
length = x_GetSequence(oid, & buffer, false, locked, false);
-
+
if ((begin >= end) || (end > length)) {
NCBI_THROW(CSeqDBException,
eArgErr,
"Begin and end offsets are not valid.");
}
-
+
seq_data->SetNcbistdaa().Set().assign(buffer + begin, buffer + end);
} else {
// This code builds an array and packs the output in 4 bit
// format for NA. No attempt is made to find an optimal
// packing for the data.
-
+
int nucl_code(kSeqDBNuclNcbiNA8);
-
+
SSeqDBSlice slice(begin, end);
-
+
char * buffer(0);
TSeqPos length(0);
-
+
length = x_GetAmbigSeq(oid,
& buffer,
nucl_code,
@@ -2561,30 +2568,30 @@ CSeqDBVol::GetSeqData(int oid,
& slice,
NULL,
locked);
-
- // validity of begin, end, and length has already been checked by
+
+ // validity of begin, end, and length has already been checked by
// overloaded x_GetSequence()
// note: length has been redefined to be end - begin
vector<char> v4;
v4.reserve((length+1)/2);
-
+
// (this is an attempt to stop a warning message.)
TSeqPos length_whole = TSeqPos(length & (TSeqPos(0)-TSeqPos(2)));
-
+
for(TSeqPos i = 0; i < length_whole; i += 2) {
v4.push_back((buffer[i] << 4) | buffer[i+1]);
}
-
+
if (length_whole != length) {
_ASSERT((length_whole) == (length-1));
v4.push_back(buffer[length_whole] << 4);
}
-
+
seq_data->SetNcbi4na().Set().swap(v4);
delete [] buffer;
}
-
+
return seq_data;
}
@@ -2597,64 +2604,64 @@ CSeqDBVol::GetRawSeqAndAmbig(int oid,
{
if (seq_length)
*seq_length = 0;
-
+
if (amb_length)
*amb_length = 0;
-
+
if (buffer)
*buffer = 0;
-
+
TIndx start_S = 0;
TIndx end_S = 0;
TIndx start_A = 0;
TIndx end_A = 0;
TIndx map_begin = 0;
TIndx map_end = 0;
-
+
m_Atlas.Lock(locked);
if (!m_SeqFileOpened) x_OpenSeqFile(locked);
-
+
m_Idx->GetSeqStartEnd(oid, start_S, end_S);
bool amb_ok = true;
-
+
if (m_IsAA) {
// No ambiguities in protein dbs, but there is a NUL between
// sequences, so we subtract one to remove that.
-
+
end_A = start_A = --end_S;
-
+
_ASSERT(start_S > 0);
-
+
map_begin = start_S - 1;
map_end = end_A + 1;
} else {
amb_ok = m_Idx->GetAmbStartEnd(oid, start_A, end_A);
-
+
map_begin = start_S;
map_end = end_A;
}
-
+
int s_len = int(end_S - start_S);
int a_len = int(end_A - start_A);
-
+
if (! (s_len && amb_ok)) {
NCBI_THROW(CSeqDBException, eFileErr,
"File error: could not get sequence data.");
}
-
+
if (amb_length) {
*amb_length = a_len;
}
-
+
if (seq_length) {
*seq_length = s_len;
}
-
+
if (buffer) {
*buffer = m_Seq->GetRegion(map_begin, map_end, true, false, locked);
*buffer += (start_S - map_begin);
}
-
+
if (buffer && *buffer) {
if (! *seq_length) {
NCBI_THROW(CSeqDBException,
@@ -2678,23 +2685,25 @@ s_SeqDBFitsInFour(Int8 id)
}
}
-void CSeqDBVol::GetGiBounds(int & low_id,
- int & high_id,
+void CSeqDBVol::GetGiBounds(TGi & low_id,
+ TGi & high_id,
int & count,
CSeqDBLockHold & locked) const
{
m_Atlas.Lock(locked);
if (!m_GiFileOpened) x_OpenGiFile(locked);
- low_id = high_id = count = 0;
-
+ low_id = ZERO_GI;
+ high_id = ZERO_GI;
+ count = 0;
+
if (m_IsamGi.NotEmpty()) {
Int8 L(0), H(0);
-
+
m_IsamGi->GetIdBounds(L, H, count, locked);
-
- low_id = (int) L;
- high_id = (int) H;
-
+
+ low_id = GI_FROM(Int8, L);
+ high_id = GI_FROM(Int8, H);
+
s_SeqDBFitsInFour(L);
s_SeqDBFitsInFour(H);
}
@@ -2708,15 +2717,15 @@ void CSeqDBVol::GetPigBounds(int & low_id,
m_Atlas.Lock(locked);
if (!m_PigFileOpened) x_OpenPigFile(locked);
low_id = high_id = count = 0;
-
+
if (m_IsamPig.NotEmpty()) {
Int8 L(0), H(0);
-
+
m_IsamPig->GetIdBounds(L, H, count, locked);
-
+
low_id = (int) L;
high_id = (int) H;
-
+
s_SeqDBFitsInFour(L);
s_SeqDBFitsInFour(H);
}
@@ -2732,7 +2741,7 @@ void CSeqDBVol::GetStringBounds(string & low_id,
count = 0;
low_id.erase();
high_id.erase();
-
+
if (m_IsamStr.NotEmpty()) {
m_IsamStr->GetIdBounds(low_id, high_id, count, locked);
}
@@ -2745,49 +2754,49 @@ void CSeqDBVol::SetOffsetRanges(int oid,
CSeqDBLockHold & locked) const
{
m_Atlas.Lock(locked);
-
+
if (offset_ranges.empty() && (! cache_data) && (! append_ranges)) {
// Specifying no-cache plus an empty offset range list, means
// that we are clearing out this sequence. In this case, just
// free the relevant element and be done.
-
+
m_RangeCache.erase(oid);
return;
}
-
+
// This adds the range cache object to the map.
-
+
CRef<CSeqDBRangeList> & R = m_RangeCache[oid];
-
+
if (R.Empty() || R->GetRanges().empty()) {
// In this case, we are disabling caching, and no ranges
// exist. There is nothing to do, and no need to keep the
// element around, so once again we erase + exit.
-
+
if (offset_ranges.empty() && (! cache_data)) {
m_RangeCache.erase(oid);
return;
}
-
+
if (R.Empty()) {
R.Reset(new CSeqDBRangeList(m_Atlas));
}
}
-
+
// We should flush the sequence if:
//
// 1. We are not keeping the old ranges (1).
// 2. There are new ranges to add (2).
// 3. We are clearing the 'cache data' flag.
-
+
bool flush_sequence = ((! append_ranges) || // (1)
(! offset_ranges.empty()) || // (2)
(! cache_data)); // (3)
-
+
if (flush_sequence) {
R->FlushSequence();
}
-
+
R->SetRanges(offset_ranges, append_ranges, cache_data);
}
@@ -2806,7 +2815,7 @@ void CSeqDBRangeList::SetRanges(const TRangeList & offset_ranges,
} else {
m_Ranges = offset_ranges;
}
-
+
// Note that actual caching is not currently done.
m_CacheData = cache_data;
}
@@ -2817,18 +2826,18 @@ void CSeqDBVol::OptimizeGiLists() const
m_VolumeGiLists.empty() ||
m_UserGiList->GetNumSis() ||
m_UserGiList->GetNumTis()) {
-
+
return;
}
-
+
NON_CONST_ITERATE(TGiLists, gilist, m_VolumeGiLists) {
if ((**gilist).GetNumSis() != 0)
return;
-
+
if ((**gilist).GetNumTis() != 0)
return;
}
-
+
// If we have volume GI lists, and a user gi list, and neither of
// these uses Seq-ids, then we can detach the user gi list (from
// the volume) because it is redundant with the volume GI lists.
@@ -2837,7 +2846,7 @@ void CSeqDBVol::OptimizeGiLists() const
// each volume GI list is translated in terms of the user GI list,
// which means that only the intersection of the two lists is left
// in the volume GI list.
-
+
m_UserGiList.Reset();
}
@@ -2849,18 +2858,18 @@ void CSeqDBVol::HashToOids(unsigned hash,
// long term interest or whether standard databases will be built
// with these indices, but it should not cause any harm to support
// them for databases where the files do exist.
-
+
// Since it is normal for a hash lookup to fail (the user of this
// feature generally does not know if the sequence will be found),
// the lack of hash indexing is reported by throwing an exception.
-
+
if (!m_HashFileOpened) x_OpenHashFile(locked);
if (m_IsamHash.Empty()) {
NCBI_THROW(CSeqDBException,
eArgErr,
"Hash lookup requested but no hash ISAM file found.");
}
-
+
m_IsamHash->HashToOids(hash, oids, locked);
}
@@ -2873,15 +2882,15 @@ void CSeqDBVol::GetColumnBlob(int col_id,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if (! m_HaveColumns) {
x_OpenAllColumns(locked);
}
-
+
_ASSERT(col_id >= 0);
_ASSERT(col_id < (int)m_Columns.size());
_ASSERT(m_Columns[col_id].NotEmpty());
-
+
m_Columns[col_id]->GetBlob(oid, blob, keep, & locked);
}
@@ -2890,15 +2899,15 @@ CSeqDBVol::GetColumnMetaData(int col_id,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if (! m_HaveColumns) {
x_OpenAllColumns(locked);
}
-
+
_ASSERT(col_id >= 0);
_ASSERT(col_id < (int)m_Columns.size());
_ASSERT(m_Columns[col_id].NotEmpty());
-
+
return m_Columns[col_id]->GetMetaData();
}
@@ -2906,11 +2915,11 @@ void CSeqDBVol::ListColumns(set<string> & titles,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if (! m_HaveColumns) {
x_OpenAllColumns(locked);
}
-
+
ITERATE(vector< CRef<CSeqDBColumn> >, iter, m_Columns) {
titles.insert((**iter).GetTitle());
}
@@ -2919,28 +2928,28 @@ void CSeqDBVol::ListColumns(set<string> & titles,
void CSeqDBVol::x_OpenAllColumns(CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if (m_HaveColumns) {
return;
}
-
+
string alpha("abcdefghijklmnopqrstuvwxyz");
string ei("??a"), ed("??b"), ed2("??c");
-
+
ei[0] = ed[0] = ed2[0] = (m_IsAA ? 'p' : 'n');
-
+
map<string,int> unique_titles;
-
+
for(size_t i = 0; i < alpha.size(); i++) {
ei[1] = ed[1] = ed2[1] = alpha[i];
-
+
if (CSeqDBColumn::ColumnExists(m_VolName, ei, m_Atlas, locked)) {
bool big = CSeqDBColumn::ColumnExists(m_VolName, ed, m_Atlas, locked);
bool small = CSeqDBColumn::ColumnExists(m_VolName, ed2, m_Atlas, locked);
if ( ! (big || small)) continue;
-
+
CRef<CSeqDBColumn> col;
const Int2 bytetest = 0x0011;
@@ -2950,26 +2959,26 @@ void CSeqDBVol::x_OpenAllColumns(CSeqDBLockHold & locked)
} else {
col.Reset(new CSeqDBColumn(m_VolName, ei, ed, & locked));
}
-
+
string errmsg, errarg;
-
+
string title = col->GetTitle();
-
+
if (unique_titles[title]) {
errmsg = "duplicate column title";
errarg = title;
} else {
unique_titles[title] = 1;
}
-
+
int noidc(col->GetNumOIDs()), noidv(m_Idx->GetNumOIDs());
-
+
if (noidc != noidv) {
errmsg = "column has wrong #oids";
errarg = NStr::IntToString(noidc) + " vs "
+ NStr::IntToString(noidv);
}
-
+
if (errmsg.size()) {
if (errarg.size()) {
errmsg += string(" [") + errarg + "].";
@@ -2977,11 +2986,11 @@ void CSeqDBVol::x_OpenAllColumns(CSeqDBLockHold & locked)
NCBI_THROW(CSeqDBException, eFileErr,
string("Error: ") + errmsg);
}
-
+
m_Columns.push_back(col);
- }
+ }
}
-
+
m_HaveColumns = true;
}
@@ -2989,17 +2998,17 @@ int CSeqDBVol::GetColumnId(const string & title,
CSeqDBLockHold & locked)
{
m_Atlas.Lock(locked);
-
+
if (! m_HaveColumns) {
x_OpenAllColumns(locked);
}
-
+
for(size_t i = 0; i < m_Columns.size(); i++) {
if (m_Columns[i]->GetTitle() == title) {
return i;
}
}
-
+
return -1;
}
#endif
diff --git a/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp b/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
index 7d91938..30faa7a 100644
--- a/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
+++ b/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqdb_perf.cpp 429038 2014-03-10 21:34:26Z camacho $
+/* $Id: seqdb_perf.cpp 463291 2015-03-26 14:57:38Z rackerst $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,8 +32,8 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] =
- "$Id: seqdb_perf.cpp 429038 2014-03-10 21:34:26Z camacho $";
+static char const rcsid[] =
+ "$Id: seqdb_perf.cpp 463291 2015-03-26 14:57:38Z rackerst $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -87,7 +87,7 @@ private:
virtual void Init();
/** @inheritDoc */
virtual int Run();
-
+
typedef vector< CRef<CSeqDBExpert> > TDbHandles;
/// Handle to BLAST database
CRef<CSeqDBExpert> m_BlastDb;
@@ -112,7 +112,7 @@ private:
int x_ScanDatabase();
};
-void
+void
CSeqDBPerfApp::x_UpdateMemoryUsage(const int thread_id /* = 0 */)
{
SMemUsage mu;
@@ -121,7 +121,7 @@ CSeqDBPerfApp::x_UpdateMemoryUsage(const int thread_id /* = 0 */)
}
}
-void
+void
CSeqDBPerfApp::x_ReportMemUsage() const
{
SMemUsage total = std::accumulate(m_MemoryUsage.begin(),
@@ -144,7 +144,7 @@ CSeqDBPerfApp::x_ScanDatabase()
#pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
shared(oids2iterate) if(m_DbHandles.size() > 1)
- {
+ {
int thread_id = 0;
#ifdef _OPENMP
thread_id = omp_get_thread_num();
@@ -164,7 +164,7 @@ CSeqDBPerfApp::x_ScanDatabase()
}
for (int i = 0; i < seqlen; i++) {
char base = buffer[i];
- base = base; // dummy statement
+ (void)base; // pacify compiler warnings
}
if (m_DbIsProtein || kScanUncompressed) {
m_DbHandles[thread_id]->RetAmbigSeq(&buffer);
@@ -177,8 +177,8 @@ CSeqDBPerfApp::x_ScanDatabase()
sw.Stop();
Uint8 bases = static_cast<Uint8>(num_letters / sw.Elapsed());
- cout << "Scanning rate: "
- << NStr::NumericToString(bases, NStr::fWithCommas)
+ cout << "Scanning rate: "
+ << NStr::NumericToString(bases, NStr::fWithCommas)
<< " bases/second" << endl;
return 0;
}
@@ -191,6 +191,16 @@ CSeqDBPerfApp::x_InitApplicationData()
const CArgs& args = GetArgs();
const CSeqDB::ESeqType kSeqType = ParseMoleculeTypeString(args["dbtype"].AsString());
const string& kDbName(args["db"].AsString());
+
+ // To test the use of CSeqDB::SetMmapStrategy, uncomment one of the two
+ // pairs of statements below.
+
+// CSeqDB::SetMmapStrategy(CSeqDB::eMmap_IndexFile, CSeqDB::eMmap_Sequential);
+// CSeqDB::SetMmapStrategy(CSeqDB::eMmap_SequenceFile, CSeqDB::eMmap_Sequential);
+
+// CSeqDB::SetMmapStrategy(CSeqDB::eMmap_IndexFile, CSeqDB::eMmap_WillNeed);
+// CSeqDB::SetMmapStrategy(CSeqDB::eMmap_SequenceFile, CSeqDB::eMmap_WillNeed);
+
m_BlastDb.Reset(new CSeqDBExpert(kDbName, kSeqType));
m_DbIsProtein = static_cast<bool>(m_BlastDb->GetSequenceType() == CSeqDB::eProtein);
@@ -226,13 +236,13 @@ CSeqDBPerfApp::x_PrintBlastDatabaseInformation()
// Print basic database information
out << "Database: " << m_BlastDb->GetTitle() << endl
- << "\t" << NStr::IntToString(m_BlastDb->GetNumSeqs(), kFlags)
+ << "\t" << NStr::IntToString(m_BlastDb->GetNumSeqs(), kFlags)
<< " sequences; "
<< NStr::UInt8ToString(m_BlastDb->GetTotalLength(), kFlags)
<< " total " << kLetters << endl << endl
- << "Date: " << m_BlastDb->GetDate()
- << "\tLongest sequence: "
- << NStr::IntToString(m_BlastDb->GetMaxLength(), kFlags) << " "
+ << "Date: " << m_BlastDb->GetDate()
+ << "\tLongest sequence: "
+ << NStr::IntToString(m_BlastDb->GetMaxLength(), kFlags) << " "
<< kLetters << endl;
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
@@ -261,11 +271,11 @@ void CSeqDBPerfApp::Init()
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
- arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
+ arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"CSeqDB performance testing client");
arg_desc->SetCurrentGroup("BLAST database options");
- arg_desc->AddDefaultKey("db", "dbname", "BLAST database name",
+ arg_desc->AddDefaultKey("db", "dbname", "BLAST database name",
CArgDescriptions::eString, "nr");
arg_desc->AddDefaultKey("dbtype", "molecule_type",
@@ -275,21 +285,21 @@ void CSeqDBPerfApp::Init()
"nucl", "prot", "guess"));
arg_desc->SetCurrentGroup("Retrieval options");
- arg_desc->AddFlag("scan_uncompressed",
+ arg_desc->AddFlag("scan_uncompressed",
"Do a full database scan of uncompressed sequence data", true);
- arg_desc->AddFlag("scan_compressed",
+ arg_desc->AddFlag("scan_compressed",
"Do a full database scan of compressed sequence data", true);
- arg_desc->AddFlag("get_metadata",
+ arg_desc->AddFlag("get_metadata",
"Retrieve BLAST database metadata", true);
-
- arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
+
+ arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
"scan_uncompressed");
- arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
+ arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
+ "get_metadata");
+ arg_desc->SetDependency("scan_uncompressed", CArgDescriptions::eExcludes,
"get_metadata");
- arg_desc->SetDependency("scan_uncompressed", CArgDescriptions::eExcludes,
- "get_metadata");
- arg_desc->AddDefaultKey("num_threads", "number",
+ arg_desc->AddDefaultKey("num_threads", "number",
"Number of threads to use (requires OpenMP)",
CArgDescriptions::eInteger, "1");
arg_desc->SetConstraint("num_threads", new CArgAllow_Integers(0, kMax_Int));
@@ -297,7 +307,7 @@ void CSeqDBPerfApp::Init()
//arg_desc->SetDependency("one_db_handle", CArgDescriptions::eRequires, "num_threads");
arg_desc->SetCurrentGroup("Output configuration options");
- arg_desc->AddDefaultKey("out", "output_file", "Output file name",
+ arg_desc->AddDefaultKey("out", "output_file", "Output file name",
CArgDescriptions::eOutputFile, "-");
SetupArgDescriptions(arg_desc.release());
diff --git a/c++/src/objtools/blast/seqdb_writer/build-alias-index b/c++/src/objtools/blast/seqdb_writer/build-alias-index
index 1f64631..c02f683 100755
--- a/c++/src/objtools/blast/seqdb_writer/build-alias-index
+++ b/c++/src/objtools/blast/seqdb_writer/build-alias-index
@@ -3,7 +3,7 @@
# subdirectory
# Author: Kevin Bealer
# Original date: 10/21/2005
-# $URL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.2.31/c++/src/objtools/blast/seqdb_writer/build-alias-index $
+# $URL: https://svn.ncbi.nlm.nih.gov/repos/toolkit/release/blast/2.3.0/c++/src/objtools/blast/seqdb_writer/build-alias-index $
INDEX_NAME=index.alx
OUTNAME=index.alx.new
diff --git a/c++/src/objtools/blast/seqdb_writer/build_db.cpp b/c++/src/objtools/blast/seqdb_writer/build_db.cpp
index fb06b55..66a4b75 100644
--- a/c++/src/objtools/blast/seqdb_writer/build_db.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/build_db.cpp
@@ -1,4 +1,4 @@
-/* $Id: build_db.cpp 452854 2014-11-25 16:06:34Z ivanov $
+/* $Id: build_db.cpp 483266 2015-10-29 15:45:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -27,11 +27,11 @@
*
*/
-/** @file build_db.cpp
+/** @file build_db.cpp
Code to build a database given various sources of sequence data.
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: build_db.cpp 452854 2014-11-25 16:06:34Z ivanov $";
+static char const rcsid[] = "$Id: build_db.cpp 483266 2015-10-29 15:45:01Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -65,23 +65,23 @@ USING_SCOPE(objects);
int debug_mode = 0;
-void CBuildDatabase::x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, int & gi)
+void CBuildDatabase::x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, TGi & gi)
{
CScope::TIds ids = x_GetScope().GetIds(*seqid);
-
+
bool have_seqid = false;
bool have_gi = false;
-
- gi = 0;
-
+
+ gi = ZERO_GI;
+
ITERATE(CScope::TIds, iter, ids) {
CConstRef<CSeq_id> id = iter->GetSeqId();
if (debug_mode > 5)
m_LogFile << "Seq-id " << seqid->AsFastaString()
<< " contains id " << id->AsFastaString() << endl;
-
+
if (id->IsGi()) {
- if (gi > 0) {
+ if (gi > ZERO_GI) {
if (debug_mode > 5)
m_LogFile << "WARNING: multiple GIs discovered; gi[0] = "
<< gi << endl;
@@ -90,16 +90,16 @@ void CBuildDatabase::x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, int & gi)
m_LogFile << "Seq-id " << seqid->AsFastaString()
<< " resolved to "
<< id->GetGi() << endl;
- gi = GI_TO(int, id->GetGi());
+ gi = id->GetGi();
have_gi = true;
}
} else if ((! have_seqid) && (id->Which() == seqid->Which())) {
m_LogFile << "Remote: Resolving <" << seqid->AsFastaString()
<< "> to <" << id->AsFastaString() << ">" << endl;
-
+
if (id->GetTextseq_Id() == NULL ||
id->GetTextseq_Id()->IsSetVersion() == false) {
-
+
m_LogFile
<< "Warning: Resolution still does not provide version."
<< endl;
@@ -108,7 +108,7 @@ void CBuildDatabase::x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, int & gi)
have_seqid = true;
}
}
-
+
if (have_gi)
break;
}
@@ -119,7 +119,7 @@ void CBuildDatabase::x_ResolveRemoteId(CRef<objects::CSeq_id> & seqid, int & gi)
CRef<CInputGiList> CBuildDatabase::x_ResolveGis(const vector<string> & ids)
{
CRef<CInputGiList> gi_list(new CInputGiList);
-
+
ITERATE(vector<string>, id, ids) {
// There are three possibilities:
//
@@ -133,55 +133,55 @@ CRef<CInputGiList> CBuildDatabase::x_ResolveGis(const vector<string> & ids)
// A. Remote services are enabled.
// B. The Seq-id can have a version (only CTextseq_id types.)
// C. The version is not present.
-
- int gi(0);
+
+ TGi gi(ZERO_GI);
bool specific = false;
CRef<CSeq_id> seqid;
-
+
bool worked = CheckAccession(*id, gi, seqid, specific);
-
+
// If a source database is specified, try that as a backup
// resolution mechanism.
-
+
if (! worked) {
if (m_SourceDb.NotEmpty()) {
worked = x_ResolveFromSource(*id, seqid);
}
}
-
+
if (! worked) {
m_LogFile << "Did not recognize id: \"" << *id << "\"" << endl;
continue;
}
-
+
// 1. Numeric GI
-
- if (gi != 0) {
+
+ if (gi != ZERO_GI) {
if (debug_mode > 5)
m_LogFile << "Found numerical GI:" << gi << endl;
-
+
gi_list->AppendGi(gi);
continue;
}
-
+
// 2. Possible remote resolution. We look for a GI and if
// that is not found, try to find a Seq-id of the same type
// (but with a version).
-
+
if (m_UseRemote && (! specific)) {
x_ResolveRemoteId(seqid, gi);
-
- if (gi != 0) {
+
+ if (gi != ZERO_GI) {
gi_list->AppendGi(gi);
continue;
}
}
-
+
// 3. Just add the Seq-id as a Seq-id.
-
+
gi_list->AppendSi(*id);
}
-
+
return gi_list;
}
@@ -191,98 +191,98 @@ bool CBuildDatabase::x_ResolveFromSource(const string & acc,
if (m_SourceDb.Empty()) {
return false;
}
-
+
vector<int> oids;
m_SourceDb->AccessionToOids(acc, oids);
-
+
bool found(false), done(false);
-
+
ITERATE(vector<int>, oid, oids) {
list< CRef<CSeq_id> > ids = m_SourceDb->GetSeqIDs(*oid);
-
+
ITERATE(list< CRef<CSeq_id> >, seqid, ids) {
CRef<CSeq_id> s = *seqid;
-
+
string S = s->AsFastaString();
size_t pos = S.find(acc);
-
+
if (pos != string::npos) {
size_t endpos = pos + acc.size();
-
+
bool start_okay = (pos == 0 || S[pos-1] == '|');
bool end_okay = ((endpos == S.size()) ||
(S[endpos] == '.' ||
S[endpos] == '|'));
-
+
if (start_okay && end_okay) {
done = true;
}
-
+
if (done || (! found)) {
found = true;
id = s;
}
}
-
+
if (done)
break;
}
-
+
if (done)
break;
}
-
+
return found;
}
void CBuildDatabase::x_DupLocal()
{
TIdToBits bitset;
-
+
// Get sequence, deflines, ambiguities, and sometimes pigs. The
// simplest route (for WriteDB) is raw data + asn deflines, so we
// use that when possible.
-
+
CStopWatch sw(CStopWatch::eStart);
int count = 0;
-
+
for(int oid = 0; m_SourceDb->CheckOrFindOID(oid); oid++) {
// Raw data.
-
+
const char * buffer (0);
int slength(0);
int alength(0);
-
+
m_SourceDb->GetRawSeqAndAmbig(oid, & buffer, & slength, & alength);
-
+
CSequenceReturn seqret(*m_SourceDb, buffer);
-
+
CTempString sequence(buffer, slength);
CTempString ambig(buffer + slength, alength);
-
+
// Deflines
-
+
CRef<CBlast_def_line_set> headers = m_SourceDb->GetHdr(oid);
m_DeflineCount += headers->Get().size();
m_OIDCount ++;
-
+
x_SetLinkAndMbit(headers);
-
+
// Always include the taxid; although OPTIONAL, some programs
// expect it, since the C ASN.1 loaders always emit integers.
-
+
m_Taxids->FixTaxId(headers);
-
+
// Now, add the sequence to the WriteDB database.
-
+
m_OutputDb->AddSequence(sequence, ambig);
m_OutputDb->SetDeflines(*headers);
count ++;
}
-
+
if (count) {
double t = sw.Elapsed();
-
+
m_LogFile << "Duplication from source DB; duplicated "
<< count << " sequences in " << t << " seconds." << endl;
}
@@ -296,7 +296,7 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
! bs->GetInst().CanGetExt() || ! bs->GetInst().GetExt().IsDelta()) {
return bs;
}
-
+
if (bs->GetInst().CanGetMol() &&
!CSeq_inst::IsNa(bs->GetInst().GetMol())) {
CConstRef<CSeq_id> id = FindBestChoice(bs->GetId(), CSeq_id::BestRank);
@@ -308,23 +308,23 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
try {
const CDelta_ext & dext = bs->GetInst().GetExt().GetDelta();
-
+
if(dext.Get().front()->Which() != CDelta_seq::e_Literal)
return bs;
typedef list< CRef< CDelta_seq > > TItems;
-
+
// Don't really want to use na4, because a half byte at the
// end of a string would require that string to be manually
// adjusted before appending.
-
+
string seq8na;
if (bs->GetInst().CanGetLength()) {
seq8na.reserve(bs->GetInst().GetLength());
}
-
+
string na8;
-
+
ITERATE(TItems, item, dext.Get()) {
if(((**item).IsLoc()) && ((**item).GetLoc().IsNull())) {
seq8na.append(1, 0x0f);
@@ -342,7 +342,7 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
"Part of the delta sequence, including its length, is un-available.");
}
}
-
+
if (L.GetSeq_data().IsNcbi2na()) {
CSeqConvert::Convert(L.GetSeq_data().GetNcbi2na(),
CSeqUtil::e_Ncbi2na,
@@ -363,14 +363,14 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
NCBI_THROW(CMultisourceException, eArg,
"Unhandled type of sequence data encountered.");
}
-
+
seq8na += na8;
na8.resize(0);
}
-
+
// Now convert back to 4na, since WriteDB does not yet handle
// 8na sequences.
-
+
int length = seq8na.size();
vector<char> seq4na;
CSeqConvert::Convert(seq8na,
@@ -379,33 +379,33 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
length,
seq4na,
CSeqUtil::e_Ncbi4na);
-
+
// Copy the needed fields of the CBioseq (but remove the delta
// sequence) and add a Seq-data.
-
+
CRef<CBioseq> bs2(new CBioseq);
-
+
if (bs->IsSetId()) {
bs2->SetId() = bs->GetId();
}
-
+
if (bs->IsSetDescr()) {
bs2->SetDescr(const_cast<CSeq_descr&>(bs->GetDescr()));
}
-
+
CRef<CSeq_inst> inst(new CSeq_inst);
-
+
inst->SetSeq_data().SetNcbi4na().Set().swap(seq4na);
inst->SetMol(CSeq_inst::eMol_na);
inst->SetLength(length);
inst->SetRepr(CSeq_inst::eRepr_raw);
-
+
bs2->SetInst(*inst);
-
+
if (bs->IsSetAnnot()) {
bs2->SetAnnot() = bs->GetAnnot();
}
-
+
bs = bs2;
}
catch(CInvalidChoiceSelection &) {
@@ -413,7 +413,7 @@ static CConstRef<CBioseq> s_FixBioseqDeltas(CConstRef<objects::CBioseq> bs)
"Bioseq must have Seq-data or "
"Delta containing only literals.");
}
-
+
return bs;
}
@@ -432,32 +432,32 @@ void CBuildDatabase::x_EditHeaders(CRef<objects::CBlast_def_line_set> headers)
{
// Always include the taxid; although OPTIONAL, some programs
// expect it, since the C ASN.1 loaders always emit integers.
-
+
m_Taxids->FixTaxId(headers);
-
+
// Edit the linkouts
-
+
x_SetLinkAndMbit(headers);
}
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
void
-CBuildDatabase::x_AddMasksForSeqId(const list< CRef<CSeq_id> >& ids)
+CBuildDatabase::x_AddMasksForSeqId(const list< CRef<CSeq_id> >& ids)
{
if (m_MaskData.Empty()) {
return;
}
-
+
const CMaskedRangesVector& rng = m_MaskData->GetRanges(ids);
if (rng.empty()) {
return;
}
- vector <int> gis;
+ vector <TGi> gis;
ITERATE(list< CRef<CSeq_id> >, id, ids) {
if ((*id)->IsGi()) {
- gis.push_back(GI_TO(int, (*id)->GetGi()));
+ gis.push_back((*id)->GetGi());
}
}
m_OutputDb->SetMaskData(rng, gis);
@@ -471,9 +471,9 @@ bool CBuildDatabase::x_EditAndAddBioseq(CConstRef<objects::CBioseq> bs,
{
CRef<CBlast_def_line_set> headers =
CWriteDB::ExtractBioseqDeflines(*bs, m_ParseIDs);
-
+
x_EditHeaders(headers);
-
+
// Add the sequence
if (sv) {
m_OutputDb->AddSequence(*bs, *sv);
@@ -491,9 +491,9 @@ bool CBuildDatabase::x_EditAndAddBioseq(CConstRef<objects::CBioseq> bs,
if(add_pig) {
x_AddPig(headers);
}
-
+
m_OutputDb->SetDeflines(*headers);
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
const list< CRef<CSeq_id> > & ids = bs->GetId();
@@ -507,14 +507,14 @@ void CBuildDatabase::x_AddOneRemoteSequence(const objects::CSeq_id & seqid,
bool & error)
{
// Get handle and bioseq
-
+
CConstRef<CBioseq> bs;
CBioseq_Handle bsh;
-
+
try {
bsh = x_GetScope().GetBioseqHandle(seqid);
bs = bsh.GetCompleteBioseq();
-
+
if (debug_mode > 5) m_LogFile << MSerial_AsnText << *bs << endl;
}
catch (const CException & e) {
@@ -524,15 +524,15 @@ void CBuildDatabase::x_AddOneRemoteSequence(const objects::CSeq_id & seqid,
found_all = false;
error = true;
}
-
+
if (bsh.GetState() & CBioseq_Handle::fState_not_found) {
error = true;
}
-
-
+
+
CSeqVector sv(bsh);
-
+
if(!x_EditAndAddBioseq(bs, & sv))
error = true;
@@ -544,7 +544,7 @@ void CBuildDatabase::x_AddOneRemoteSequence(const objects::CSeq_id & seqid,
found_all = false;
return;
}
-
+
if (debug_mode > 5)
m_LogFile << "-- REMOTE: Found sequence "
<< seqid.AsFastaString() << endl;
@@ -554,28 +554,28 @@ bool CBuildDatabase::x_AddRemoteSequences(CInputGiList & gi_list)
{
CStopWatch sw(CStopWatch::eStart);
int count = 0;
-
+
bool found_all = true;
-
+
int num_gis = gi_list.GetNumGis();
int i = 0;
-
+
for(i = 0; i < num_gis; i++) {
if (m_Verbose)
- m_LogFile << "GI " << gi_list.GetKey<int>(i);
-
+ m_LogFile << "GI " << gi_list.GetKey<TGi>(i);
+
// We only need to fetch here for those cases where the SeqDB
// attempt could not translate the GI.
-
+
if (gi_list.GetGiOid(i).oid == -1) {
if (m_Verbose)
m_LogFile << " not found locally; adding remotely." << endl;
-
+
CRef<CSeq_id> id(new CSeq_id);
- id->SetGi(GI_FROM(int, gi_list.GetKey<int>(i)));
-
+ id->SetGi(gi_list.GetKey<TGi>(i));
+
bool error = false;
-
+
x_AddOneRemoteSequence(*id, found_all, error);
count++;
} else {
@@ -583,23 +583,23 @@ bool CBuildDatabase::x_AddRemoteSequences(CInputGiList & gi_list)
m_LogFile << " found locally; not adding remotely." << endl;
}
}
-
+
int num_seqids = gi_list.GetNumSis();
-
+
for(i = 0; i < num_seqids; i++) {
if (m_Verbose)
m_LogFile << "Seq-id "
<< gi_list.GetKey<string>(i);
-
+
// We only need to fetch here for those cases where the SeqDB
// attempt could not translate the GI.
-
+
if (gi_list.GetSiOid(i).oid == -1) {
if (m_Verbose)
m_LogFile << " not found locally; adding remotely." << endl;
-
+
bool error = false;
-
+
string acc = gi_list.GetKey<string>(i);
CRef<CSeq_id> id(new CSeq_id(acc));
x_AddOneRemoteSequence(*id, found_all, error);
@@ -609,14 +609,14 @@ bool CBuildDatabase::x_AddRemoteSequences(CInputGiList & gi_list)
m_LogFile << " found locally; not adding remotely." << endl;
}
}
-
+
if (count) {
double t = sw.Elapsed();
-
+
m_LogFile << "Adding sequences from remote source; added "
<< count << " sequences in " << t << " seconds." << endl;
}
-
+
return found_all;
}
@@ -624,42 +624,42 @@ bool
CBuildDatabase::x_ReportUnresolvedIds(const CInputGiList & gi_list) const
{
bool success = true;
-
+
int num_gis = gi_list.GetNumGis();
-
+
int unresolved = 0;
-
+
int i;
for(i = 0; i < num_gis; i++) {
// We only need to fetch here for those cases where the SeqDB
// attempt could not translate the GI.
-
+
if (gi_list.GetGiOid(i).oid == -1) {
if (m_Verbose)
- m_LogFile << "GI " << gi_list.GetKey<int>(i)
+ m_LogFile << "GI " << gi_list.GetKey<TGi>(i)
<< " was not resolvable." << endl;
-
+
success = false;
unresolved ++;
} else {
if (m_Verbose)
- m_LogFile << "GI " << gi_list.GetKey<int>(i)
+ m_LogFile << "GI " << gi_list.GetKey<TGi>(i)
<< " found locally." << endl;
}
}
-
+
int num_seqids = gi_list.GetNumSis();
-
+
for(i = 0; i < num_seqids; i++) {
// We only need to fetch here for those cases where the SeqDB
// attempt could not translate the GI.
-
+
if (gi_list.GetSiOid(i).oid == -1) {
if (m_Verbose)
m_LogFile << "Seq-id "
<< gi_list.GetKey<string>(i)
<< " was not resolvable." << endl;
-
+
unresolved ++;
success = false;
} else {
@@ -669,14 +669,14 @@ CBuildDatabase::x_ReportUnresolvedIds(const CInputGiList & gi_list) const
<< " found locally." << endl;
}
}
-
+
if (unresolved) {
m_LogFile << "Could not resolve " << unresolved << " IDs." << endl;
}
-
+
success = false;
unresolved ++;
-
+
return success;
}
@@ -685,11 +685,11 @@ public:
CFastaBioseqSource(CNcbiIstream & fasta_file,
bool is_protein,
bool parse_ids);
-
+
~CFastaBioseqSource();
-
+
virtual CConstRef<CBioseq> GetNext();
-
+
private:
CRef<ILineReader> m_LineReader;
CFastaReader* m_FastaReader;
@@ -701,19 +701,19 @@ CFastaBioseqSource::CFastaBioseqSource(CNcbiIstream & fasta_file,
: m_FastaReader(NULL)
{
m_LineReader.Reset(new CBufferedLineReader(fasta_file));
-
+
typedef CFastaReader::EFlags TFlags;
-
+
int iflags = CFastaReader::fAllSeqIds |
CFastaReader::fForceType;
-
+
if (is_protein) {
iflags |= CFastaReader::fAssumeProt;
} else {
iflags |= CFastaReader::fAssumeNuc;
iflags |= CFastaReader::fParseGaps;
}
-
+
if (parse_ids) {
iflags |= CFastaReader::fAllSeqIds | CFastaReader::fRequireID;
} else {
@@ -721,14 +721,15 @@ CFastaBioseqSource::CFastaBioseqSource(CNcbiIstream & fasta_file,
}
iflags |= CFastaReader::fQuickIDCheck;
-
+ iflags |= CFastaReader::fDisableNoResidues;
+
TFlags flags = (TFlags) iflags;
-
+
m_FastaReader = new CFastaReader(*m_LineReader, flags);
m_FastaReader->IgnoreProblem(ILineError::eProblem_ModifierFoundButNoneExpected);
m_FastaReader->IgnoreProblem(ILineError::eProblem_TooManyAmbiguousResidues);
m_FastaReader->IgnoreProblem(ILineError::eProblem_TooLong);
-
+
}
CFastaBioseqSource::~CFastaBioseqSource()
@@ -739,11 +740,11 @@ CFastaBioseqSource::~CFastaBioseqSource()
CConstRef<CBioseq> CFastaBioseqSource::GetNext()
{
CConstRef<CBioseq> rv;
-
+
if (m_LineReader.NotEmpty() && ! m_LineReader->AtEOF()) {
CRef<CSeq_entry> entry;
try { entry = m_FastaReader->ReadOneSeq(); }
- catch (const CObjReaderParseException& e) {
+ catch (const CObjReaderParseException& e) {
static const string kKeyword("m_Pos = ");
SIZE_TYPE start = NStr::Find(e.what(), kKeyword);
SIZE_TYPE end = NStr::Find(e.what(), ")", start);
@@ -759,31 +760,31 @@ CConstRef<CBioseq> CFastaBioseqSource::GetNext()
}
NCBI_THROW(CWriteDBException, eFileErr, msg);
}
-
+
if (entry.NotEmpty()) {
_ASSERT(entry->IsSeq());
rv.Reset(& entry->GetSeq());
}
}
-
+
// Any failure to read a Bioseq is considered an EOF.
-
+
if (rv.Empty()) {
m_LineReader.Reset();
}
-
+
return rv;
}
bool CBuildDatabase::AddSequences(IBioseqSource & src, bool add_pig)
{
bool found = false;
-
+
CStopWatch sw(CStopWatch::eStart);
int count = 0;
-
+
CConstRef<CBioseq> bs = src.GetNext();
-
+
while(bs.NotEmpty()) {
string bioseq_id("Unknown");
@@ -810,45 +811,45 @@ bool CBuildDatabase::AddSequences(IBioseqSource & src, bool add_pig)
m_LogFile << "Adding bioseq from fasta; first id is: '" << bioseq_id
<< "'" << endl;
}
-
+
// No linkouts or memberships here (yet).
found = true;
-
+
count++;
-
+
if (debug_mode > 5) m_LogFile << "-- FASTA: Found sequence." << endl;
-
+
bs = src.GetNext();
}
-
+
if (count) {
double t = sw.Elapsed();
-
+
m_LogFile << "Adding sequences from FASTA; added "
<< count << " sequences in " << t << " seconds." << endl;
}
-
+
return found;
}
bool CBuildDatabase::AddSequences(IRawSequenceSource & src)
{
CStopWatch sw(CStopWatch::eStart);
-
+
bool done = false;
bool rv = false;
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
// Get all column names.
-
+
vector<string> all_names;
map<int, int> in2out;
int mask_id = -1;
-
+
src.GetColumnNames(all_names);
-
+
for(int i = 0; i < (int) all_names.size(); i++) {
string name = all_names[i];
int in_id = src.GetColumnId(name);
@@ -859,99 +860,99 @@ bool CBuildDatabase::AddSequences(IRawSequenceSource & src)
continue;
}
int out_id = m_OutputDb->FindColumn(name);
-
+
if (out_id < 0) {
out_id = m_OutputDb->CreateUserColumn(name);
}
-
+
typedef map<string,string> StringPairMap;
const StringPairMap & meta = src.GetColumnMetaData(in_id);
-
+
ITERATE(StringPairMap, iter, meta) {
m_OutputDb->AddColumnMetaData(out_id, iter->first, iter->second);
}
-
+
in2out[in_id] = out_id;
}
-#endif
+#endif
// Copy all data.
-
+
vector<CTempString> column_blobs;
vector<int> column_ids;
-
+
int count = 0;
-
+
while(! done) {
CTempString sequence, ambiguities;
CRef<CBlast_def_line_set> deflines;
CMaskedRangesVector mask_data;
-
+
if (src.GetNext(sequence,
ambiguities,
deflines,
mask_data,
column_ids,
column_blobs)) {
-
+
// Copy data
-
+
_ASSERT(column_blobs.size() == column_ids.size());
-
+
if (sequence.empty()) {
NCBI_THROW(CMultisourceException, eArg,
"Error in raw data: no sequence");
}
-
+
if ((! ambiguities.empty()) && m_IsProtein) {
NCBI_THROW(CMultisourceException, eArg,
"Error in raw data: "
"protein db cannot with ambiguities");
}
-
+
if (deflines.Empty()) {
NCBI_THROW(CMultisourceException, eArg,
"Error in raw data: no headers provided");
}
-
+
x_EditHeaders(deflines);
-
+
m_OutputDb->AddSequence(sequence, ambiguities);
x_AddPig(deflines);
m_OutputDb->SetDeflines(*deflines);
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
for(int i = 0; i < (int)column_ids.size(); i++) {
int in_id = column_ids[i];
if (in_id == mask_id) continue;
-
+
if (column_blobs[i].size() == 0)
continue;
-
+
_ASSERT(in2out.find(in_id) != in2out.end());
-
+
int out_id = in2out[in_id];
-
+
CTempString blob_in = column_blobs[i];
CBlastDbBlob & blob_out = m_OutputDb->SetBlobData(out_id);
-
+
blob_out.Clear();
blob_out.WriteRaw(& blob_in.data()[0], blob_in.size());
}
// Don't forget about the IMaskDataSource!
- vector <int> gis; // GIs associated with this sequence
+ vector <TGi> gis; // GIs associated with this sequence
if (!mask_data.empty() || !m_MaskData.Empty()) {
ITERATE(CBlast_def_line_set::Tdata, defline, deflines->Get()) {
const list< CRef<CSeq_id> > & ids = (*defline)->GetSeqid();
ITERATE(list< CRef<CSeq_id> >, id, ids) {
if ((*id)->IsGi()) {
- gis.push_back(GI_TO(int, (*id)->GetGi()));
+ gis.push_back((*id)->GetGi());
}
}
if (!m_MaskData.Empty()) {
const CMaskedRangesVector rng = m_MaskData->GetRanges(ids);
if (!rng.empty()) {
- mask_data.insert(mask_data.end(), rng.begin(), rng.end());
+ mask_data.insert(mask_data.end(), rng.begin(), rng.end());
m_FoundMatchingMasks = true;
}
}
@@ -961,21 +962,21 @@ bool CBuildDatabase::AddSequences(IRawSequenceSource & src)
m_OutputDb->SetMaskData(mask_data, gis);
}
#endif
-
+
rv = true;
count ++;
} else {
done = true;
}
}
-
+
if (count) {
double t = sw.Elapsed();
-
+
m_LogFile << "Adding sequences from raw db source; added "
<< count << " sequences in " << t << " seconds." << endl;
}
-
+
return rv;
}
@@ -995,7 +996,7 @@ static void s_CreateDirectories(const string& dbname)
}
}
if (!d.CheckAccess(CDirEntry::fWrite)) {
- string msg("You do not have write permissions on '" +
+ string msg("You do not have write permissions on '" +
d.GetName() + "'");
NCBI_THROW(CMultisourceException, eOutputFileError, msg);
}
@@ -1023,28 +1024,28 @@ CBuildDatabase::CBuildDatabase(const string & dbname,
const string output_dbname = CDirEntry::CreateAbsolutePath(dbname);
m_LogFile << "\n\nBuilding a new DB, current time: "
<< CTime(CTime::eCurrent).AsString() << endl;
-
+
m_LogFile << "New DB name: " << output_dbname << endl;
m_LogFile << "New DB title: " << title << endl;
const string mol_type(is_protein ? "Protein" : "Nucleotide");
m_LogFile << "Sequence type: " << mol_type << endl;
if (DeleteBlastDb(output_dbname, ParseMoleculeTypeString(mol_type))) {
- m_LogFile << "Deleted existing " << mol_type
+ m_LogFile << "Deleted existing " << mol_type
<< " BLAST database named " << output_dbname << endl;
}
-
+
CWriteDB::ESeqType seqtype =
(is_protein ? CWriteDB::eProtein : CWriteDB::eNucleotide);
-
+
m_OutputDb.Reset(new CWriteDB(output_dbname,
seqtype,
title,
indexing,
m_ParseIDs,
use_gi_mask));
-
+
// Standard 1 GB limit
-
+
m_OutputDb->SetMaxFileSize(1000*1000*1000);
}
@@ -1071,23 +1072,23 @@ CBuildDatabase::CBuildDatabase(const string & dbname,
const string output_dbname = CDirEntry::CreateAbsolutePath(dbname);
m_LogFile << "\n\nBuilding a new DB, current time: "
<< CTime(CTime::eCurrent).AsString() << endl;
-
+
m_LogFile << "New DB name: " << output_dbname << endl;
m_LogFile << "New DB title: " << title << endl;
const string mol_type(is_protein ? "Protein" : "Nucleotide");
m_LogFile << "Sequence type: " << mol_type << endl;
if (DeleteBlastDb(output_dbname, ParseMoleculeTypeString(mol_type))) {
- m_LogFile << "Deleted existing " << mol_type
+ m_LogFile << "Deleted existing " << mol_type
<< " BLAST database named " << output_dbname << endl;
}
-
+
CWriteDB::ESeqType seqtype =
(is_protein ? CWriteDB::eProtein : CWriteDB::eNucleotide);
-
+
CWriteDB::EIndexType ix = (sparse
? CWriteDB::eSparseIndex
: CWriteDB::eDefault);
-
+
m_OutputDb.Reset(new CWriteDB(output_dbname,
seqtype,
title,
@@ -1096,7 +1097,7 @@ CBuildDatabase::CBuildDatabase(const string & dbname,
use_gi_mask));
// Standard 1 GB limit
-
+
m_OutputDb->SetMaxFileSize(1000*1000*1000);
}
@@ -1128,13 +1129,13 @@ CScope & CBuildDatabase::x_GetScope()
if (m_ObjMgr.Empty()) {
m_ObjMgr.Reset(CObjectManager::GetInstance());
}
-
+
m_Scope.Reset(new CScope(*m_ObjMgr));
-
+
// Add default loaders (GB loader in this demo) to the scope.
m_Scope->AddDefaults();
}
-
+
return *m_Scope;
}
@@ -1153,7 +1154,7 @@ void CBuildDatabase::SetSourceDb(const string & src_db_name)
m_IsProtein
? CSeqDB::eProtein
: CSeqDB::eNucleotide));
-
+
SetSourceDb(src_db);
}
@@ -1178,27 +1179,27 @@ CBuildDatabase::Build(const vector<string> & ids,
CNcbiIstream * fasta_file)
{
CStopWatch sw(CStopWatch::eStart);
-
+
StartBuild();
-
+
bool success = AddIds(ids);
-
+
if (success) {
success = AddFasta(*fasta_file);
}
-
+
bool success2 = EndBuild();
-
+
success = success || success2;
-
+
double t = sw.Elapsed();
-
+
m_LogFile << "Total sequences stored: " << m_OIDCount << endl;
m_LogFile << "Total deflines stored: " << m_DeflineCount << endl;
-
+
m_LogFile << "Total time to build database: "
<< t << " seconds.\n" << endl;
-
+
return success;
}
@@ -1208,22 +1209,22 @@ void CBuildDatabase::StartBuild()
bool CBuildDatabase::AddIds(const vector<string> & ids)
{
-
+
bool success = true;
-
+
// Resolve all ids to GIs, storing them in a GI list.
-
+
CRef<CInputGiList> gi_list;
-
+
if (m_SourceDb.NotEmpty() && ! ids.empty()) {
gi_list = x_ResolveGis(ids);
}
-
+
// Translate the GI list.
-
+
if (gi_list.NotEmpty() &&
(gi_list->GetNumGis() || gi_list->GetNumSis())) {
-
+
// The process of constructing a SeqDB object with a user GI
// list causes translation of the User GI list, and is the
// fastest way of performing such a translation in bulk. It
@@ -1236,28 +1237,28 @@ bool CBuildDatabase::AddIds(const vector<string> & ids)
// found using OID iteration over SeqDB, which produces a
// better ordering inasmuch as the reads from the source
// sequence data will be sequential on disk.
-
+
_ASSERT(m_SourceDb.NotEmpty());
-
+
CRef<CSeqDBExpert> filtered
(new CSeqDBExpert(m_SourceDb->GetDBNameList(),
m_SourceDb->GetSequenceType(),
&* gi_list));
-
+
m_SourceDb = filtered;
-
+
// Add all local database sequences to the output DB.
-
+
x_DupLocal();
-
+
if (m_Verbose) {
// Map oid to gi.
- map<int,int> seen_it;
-
+ map<int,TGi> seen_it;
+
for(int i = 0; i < gi_list->GetNumGis(); i++) {
int this_oid = gi_list->GetGiOid(i).oid;
- int this_gi = gi_list->GetGiOid(i).gi;
-
+ TGi this_gi = gi_list->GetGiOid(i).gi;
+
if (this_oid != -1) {
if (seen_it.find(this_oid) == seen_it.end()) {
seen_it[this_oid] = this_gi;
@@ -1271,7 +1272,7 @@ bool CBuildDatabase::AddIds(const vector<string> & ids)
}
}
}
-
+
if (gi_list.NotEmpty()) {
if (m_UseRemote) {
success = x_AddRemoteSequences(*gi_list);
@@ -1279,7 +1280,7 @@ bool CBuildDatabase::AddIds(const vector<string> & ids)
success = x_ReportUnresolvedIds(*gi_list);
}
}
-
+
return success;
}
@@ -1287,14 +1288,17 @@ bool CBuildDatabase::AddFasta(CNcbiIstream & fasta_file)
{
// Add any fasta sequences as well.
bool success = true;
-
+
if (fasta_file) {
CFastaBioseqSource fbs(fasta_file,
m_IsProtein,
m_ParseIDs);
-
+
try {
success = AddSequences(fbs);
+ if (success == false)
+ NCBI_THROW(CWriteDBException, eFileErr, "No sequences added");
+
}
catch (...) {
EndBuild(true);
@@ -1326,24 +1330,24 @@ bool CBuildDatabase::x_EndBuild(bool erase, const CException * close_exception)
vector<string> vols;
vector<string> files;
-
+
m_OutputDb->ListVolumes(vols);
m_OutputDb->ListFiles(files);
-
+
m_LogFile << endl;
-
+
_ASSERT(vols.empty() == files.empty());
-
+
if (vols.empty()) {
m_LogFile << "No volumes were created because no sequences were found."
<< endl;
-
+
success = false;
} else {
ITERATE(vector<string>, iterv, vols) {
m_LogFile << "volume: " << *iterv << endl;
}
-
+
m_LogFile << endl;
ITERATE(vector<string>, iterf, files) {
m_LogFile << "file: " << *iterf << endl;
@@ -1353,14 +1357,14 @@ bool CBuildDatabase::x_EndBuild(bool erase, const CException * close_exception)
}
}
}
-
+
m_LogFile << endl;
if (close_exception) {
NCBI_RETHROW(*close_exception, CWriteDBException, eArgErr,
"Can not close files.");
}
-
+
return success;
}
@@ -1374,28 +1378,28 @@ s_SetDeflineBits(objects::CBlast_def_line & defline,
{
bool found = false;
int value = 0;
-
+
ITERATE(vector<string>, key, keys) {
if (! key->size())
continue;
-
+
TIdToBits::iterator item = bitmap.find(*key);
-
+
if (item != bitmap.end()) {
found = true;
value |= item->second;
}
}
-
+
if (found) {
list<int> & linkv = (is_memb
? defline.SetMemberships()
: defline.SetLinks());
-
+
if (! keep_old) {
linkv.clear();
}
-
+
if (linkv.empty()) {
linkv.push_back(value);
} else {
@@ -1412,15 +1416,15 @@ s_SetDeflineBits(objects::CBlast_def_line & defline,
}
}
-void
+void
CBuildDatabase::x_SetLinkAndMbit(CRef<objects::CBlast_def_line_set> headers)
{
vector<string> keys;
-
+
NON_CONST_ITERATE(CBlast_def_line_set::Tdata, iter, headers->Set()) {
CBlast_def_line & defline = **iter;
GetDeflineKeys(defline, keys);
-
+
s_SetDeflineBits(defline, m_Id2Links, m_KeepLinks, false, keys);
s_SetDeflineBits(defline, m_Id2Mbits, m_KeepMbits, true, keys);
}
@@ -1432,7 +1436,7 @@ void CBuildDatabase::SetMaxFileSize(Uint8 max_file_size)
}
int
-CBuildDatabase::RegisterMaskingAlgorithm(EBlast_filter_program program,
+CBuildDatabase::RegisterMaskingAlgorithm(EBlast_filter_program program,
const string & options,
const string & name)
{
@@ -1445,7 +1449,7 @@ CBuildDatabase::RegisterMaskingAlgorithm(EBlast_filter_program program,
}
int
-CBuildDatabase::RegisterMaskingAlgorithm(const string & program,
+CBuildDatabase::RegisterMaskingAlgorithm(const string & program,
const string & description,
const string & options)
{
diff --git a/c++/src/objtools/blast/seqdb_writer/multisource_util.cpp b/c++/src/objtools/blast/seqdb_writer/multisource_util.cpp
index 253b570..c5bf046 100644
--- a/c++/src/objtools/blast/seqdb_writer/multisource_util.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/multisource_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: multisource_util.cpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: multisource_util.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: multisource_util.cpp 399305 2013-05-13 19:13:43Z grichenk $";
+static char const rcsid[] = "$Id: multisource_util.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -52,13 +52,13 @@ void ReadTextFile(CNcbiIstream & f,
// version might use string::swap() to avoid copying strings, but
// in the case of gcc, strings should be reference counted, so
// copying is already cheap.
-
+
lines.reserve(128);
-
+
while(f && (! f.eof())) {
string s;
NcbiGetlineEOL(f, s);
-
+
if (s.size()) {
lines.push_back(s);
}
@@ -73,10 +73,10 @@ void MapToLMBits(const TLinkoutMap & gilist, TIdToBits & id2links)
ITERATE(TLinkoutMap, iter1, gilist) {
int bitnum = iter1->first;
const vector<string> & v = iter1->second;
-
+
ITERATE(vector<string>, iter2, v) {
string key = AccessionToKey(*iter2);
-
+
if (key.size()) {
id2links[key] |= bitnum;
}
@@ -86,72 +86,72 @@ void MapToLMBits(const TLinkoutMap & gilist, TIdToBits & id2links)
string AccessionToKey(const string & acc)
{
- int gi(0);
+ TGi gi(ZERO_GI);
CRef<CSeq_id> seqid;
bool specific(false);
-
+
string str;
-
+
if (CheckAccession(acc, gi, seqid, specific)) {
if (seqid.Empty()) {
- if (gi != 0) {
+ if (gi != ZERO_GI) {
str = "gi|";
- str += NStr::IntToString(gi);
+ str += NStr::IntToString(GI_TO(int, gi));
}
} else {
GetSeqIdKey(*seqid, str);
}
}
-
+
return str;
}
bool CheckAccession(const string & acc,
- int & gi,
+ TGi & gi,
CRef<objects::CSeq_id> & seqid,
bool & specific)
{
specific = true;
- gi = 0;
+ gi = ZERO_GI;
seqid.Reset();
-
+
// Case 1: Numeric GI
-
+
bool digits = !! acc.size();
-
+
for(unsigned i = 0; i < acc.size(); i++) {
if (! isdigit(acc[i])) {
digits = false;
break;
}
}
-
+
if (digits) {
- gi = NStr::StringToInt(acc);
+ gi = GI_FROM(int, NStr::StringToInt(acc));
return true;
}
-
+
try {
seqid.Reset(new CSeq_id(acc));
}
catch(CException &) {
return false;
}
-
+
if (seqid->IsGi()) {
- gi = GI_TO(int, seqid->GetGi());
+ gi = seqid->GetGi();
seqid.Reset();
return true;
}
-
+
// Case 2: Other Seq-ids.
-
+
const CTextseq_id * tsi = seqid->GetTextseq_Id();
-
+
if (tsi != NULL) {
specific = tsi->IsSetVersion();
}
-
+
return true;
}
@@ -164,7 +164,7 @@ void GetDeflineKeys(const objects::CBlast_def_line & defline,
vector<string> & keys)
{
keys.clear();
-
+
ITERATE(CBlast_def_line::TSeqid, iter, defline.GetSeqid()) {
string key;
GetSeqIdKey(**iter, key);
diff --git a/c++/src/objtools/blast/seqdb_writer/unit_test/criteria_unit_test.cpp b/c++/src/objtools/blast/seqdb_writer/unit_test/criteria_unit_test.cpp
index cd6c8ab..a651677 100644
--- a/c++/src/objtools/blast/seqdb_writer/unit_test/criteria_unit_test.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/unit_test/criteria_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: criteria_unit_test.cpp 401964 2013-06-04 15:01:28Z camacho $
+/* $Id: criteria_unit_test.cpp 469956 2015-06-10 13:34:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
*
* ===========================================================================
*/
-
+#define NCBI_TEST_APPLICATION
#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
diff --git a/c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp b/c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp
index d6d6775..a5829f4 100644
--- a/c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_unit_test.cpp 437906 2014-06-11 13:50:58Z camacho $
+/* $Id: writedb_unit_test.cpp 480969 2015-10-06 12:05:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
* CWriteDB unit test.
*
*/
-
+#define NCBI_TEST_APPLICATION
#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/seqdbexpert.hpp>
@@ -67,21 +67,21 @@ s_FetchRawData(CSeqDBExpert & seqdb,
const char * buffer (0);
int slength(0);
int alength(0);
-
+
seqdb.GetRawSeqAndAmbig(oid, & buffer, & slength, & alength);
-
+
sequence.assign(buffer, slength);
ambig.assign(buffer + slength, alength);
-
+
seqdb.RetAmbigSeq(& buffer);
}
// Return a Seq-id built from the given int (gi).
-CRef<CSeq_id> s_GiToSeqId(int gi)
+CRef<CSeq_id> s_GiToSeqId(TGi gi)
{
CRef<CSeq_id> seqid(new CSeq_id(CSeq_id::e_Gi, gi));
-
+
return seqid;
}
@@ -91,7 +91,7 @@ CRef<CSeq_id> s_GiToSeqId(int gi)
CRef<CSeq_id> s_AccToSeqId(const char * acc)
{
CRef<CSeq_id> seqid(new CSeq_id(acc));
-
+
return seqid;
}
@@ -102,43 +102,43 @@ string s_HexDumpText(const string & raw,
int base)
{
BOOST_REQUIRE(layout.size());
-
+
string visible;
string tmp;
-
+
int layout_i = 0;
int width = 0;
-
+
for(int i = 0; i < (int)raw.size(); i += width) {
width = layout[layout_i];
BOOST_REQUIRE(width);
-
+
Uint8 mask = Uint8(Int8(-1));
mask >>= (64 - 8*width);
-
+
int left = raw.size() - i;
int width1 = (left < width) ? left : width;
-
+
string sub(raw, i, width1);
-
+
// Read a standard order value into x.
-
+
Uint8 x = 0;
-
+
for(int by = 0; by < (int)sub.size(); by++) {
x = (x << 8) + (sub[by] & 0xFF);
}
-
+
if (visible.size())
visible += " ";
-
+
tmp.resize(0);
NStr::UInt8ToString(tmp, x & mask, 0, base);
-
+
visible += tmp;
layout_i = (layout_i + 1) % layout.size();
}
-
+
return visible;
}
@@ -146,7 +146,7 @@ string s_HexDumpText(const string & raw, int per, int base)
{
vector<int> layout;
layout.push_back(per);
-
+
return s_HexDumpText(raw, layout, base);
}
@@ -157,21 +157,21 @@ string s_HexDumpFile(const string & fname,
int base)
{
ifstream f(fname.c_str());
-
+
string raw;
-
+
while(f && ! f.eof()) {
char buf[1024];
f.read(buf, 1024);
-
+
int amt = f.gcount();
-
+
if (! amt)
break;
-
+
raw.append(buf, amt);
}
-
+
return s_HexDumpText(raw, layout, base);
}
@@ -181,7 +181,7 @@ string s_HexDumpFile(const string & fname,
{
vector<int> layout;
layout.push_back(per);
-
+
return s_HexDumpFile(fname, layout, base);
}
@@ -193,7 +193,7 @@ typedef vector< CRef<CSeq_id> > TIdList;
class CNonException : exception {
public:
-
+
};
#define BOOST_REQUIRE_CUTPOINT(X) if (cutpoint == X) throw CNonException()
@@ -207,48 +207,48 @@ s_DupIdsBioseq(CWriteDB & w,
int cutpoint)
{
int count1 = 0;
-
+
ITERATE(TIdList, iter, ids) {
CRef<CSeq_id> seqid = *iter;
-
+
BOOST_REQUIRE(seqid.NotEmpty());
-
+
BOOST_REQUIRE_CUTPOINT(4);
-
+
int oid = -1;
bool found = s.SeqidToOid(*seqid, oid);
-
+
BOOST_REQUIRE(found);
-
+
CRef<CBioseq> bs;
-
+
BOOST_REQUIRE_CUTPOINT(5);
-
+
if (seqid->IsGi()) {
- bs = s.GetBioseq(oid, GI_TO(int, seqid->GetGi()));
+ bs = s.GetBioseq(oid, seqid->GetGi());
} else {
bs = s.GetBioseq(oid);
}
-
+
BOOST_REQUIRE_CUTPOINT(6);
-
+
CRef<CBlast_def_line_set> bdls = s.GetHdr(oid);
-
+
BOOST_REQUIRE(bs.NotEmpty());
BOOST_REQUIRE(bdls.NotEmpty());
-
+
BOOST_REQUIRE_CUTPOINT(7);
-
+
w.AddSequence(*bs);
w.SetDeflines(*bdls);
-
+
count1++;
BOOST_REQUIRE_CUTPOINT(8);
-
+
if (count1 > 3) {
BOOST_REQUIRE_CUTPOINT(9);
}
-
+
if (count1 > g_NuclJ_OidCount) {
BOOST_REQUIRE_CUTPOINT(10);
}
@@ -265,24 +265,24 @@ s_DupIdsRaw(CWriteDB & w,
const TIdList & ids)
{
bool is_nucl = seqdb.GetSequenceType() == CSeqDB::eNucleotide;
-
+
ITERATE(TIdList, iter, ids) {
CRef<CSeq_id> seqid = *iter;
-
+
int oid = -1;
bool found = seqdb.SeqidToOid(*seqid, oid);
-
+
BOOST_REQUIRE(found);
-
+
string seq, ambig;
-
+
s_FetchRawData(seqdb, oid, seq, ambig);
CRef<CBlast_def_line_set> bdls = seqdb.GetHdr(oid);
-
+
BOOST_REQUIRE(! seq.empty());
BOOST_REQUIRE(ambig.empty() || is_nucl);
BOOST_REQUIRE(bdls.NotEmpty());
-
+
w.AddSequence(seq, ambig);
w.SetDeflines(*bdls);
}
@@ -314,11 +314,11 @@ template<class ASNOBJ>
CRef<ASNOBJ> s_Duplicate(const ASNOBJ & a)
{
CRef<ASNOBJ> newobj(new ASNOBJ);
-
+
string s;
s_Stringify(a, s);
s_Unstringify(s, *newobj);
-
+
return newobj;
}
@@ -329,7 +329,7 @@ void s_CompareBioseqs(CBioseq & src, CBioseq & dst)
string s1, s2;
s_Stringify(src, s1);
s_Stringify(dst, s2);
-
+
BOOST_REQUIRE_EQUAL(s1, s2);
}
@@ -342,22 +342,23 @@ s_TestDatabase(CSeqDBExpert & src,
const string & title)
{
CSeqDBExpert dst(name, src.GetSequenceType());
-
+
for(int oid = 0; dst.CheckOrFindOID(oid); oid++) {
- int gi(0), src_oid(0);
-
+ TGi gi = ZERO_GI;
+ int src_oid(0);
+
bool rv1 = dst.OidToGi(oid, gi);
bool rv2 = src.GiToOid(gi, src_oid);
-
+
BOOST_REQUIRE(rv1);
BOOST_REQUIRE(rv2);
-
+
CRef<CBioseq> bss = src.GetBioseq(src_oid);
CRef<CBioseq> bsd = dst.GetBioseq(oid);
-
+
s_CompareBioseqs(*bss, *bsd);
}
-
+
BOOST_REQUIRE_EQUAL(dst.GetTitle(), title);
}
@@ -383,9 +384,9 @@ void s_RemoveFiles(const vector<string> & files)
void s_CheckSorted(const string & fname)
{
CNcbiIfstream file(fname.c_str());
-
+
string s, s2;
-
+
while(NcbiGetlineEOL(file, s)) {
if (s.size() == 0) break;
BOOST_REQUIRE(s2 <= s);
@@ -400,10 +401,10 @@ void s_CheckSorted(const string & fname)
string s_ExtractLast(const string & data, const string & delim)
{
size_t pos = data.rfind(delim);
-
+
if (pos == string::npos)
return "";
-
+
return string(data,
pos+delim.size(),
data.size()-(pos + delim.size()));
@@ -417,10 +418,10 @@ void s_CheckFiles(const vector<string> & files,
bool need_hash = false)
{
bool found_hash = false;
-
+
for(unsigned i = 0; i < files.size(); i++) {
string ext = s_ExtractLast(files[i], ".");
-
+
if (ext == "nsd" || ext == "psd") {
s_CheckSorted(files[i]);
}
@@ -429,7 +430,7 @@ void s_CheckFiles(const vector<string> & files,
found_hash = true;
}
}
-
+
if (need_hash) {
BOOST_REQUIRE(found_hash);
}
@@ -457,19 +458,19 @@ public:
CWrapperUpper()
{
}
-
+
~CWrapperUpper()
{
if (m_Db.NotEmpty()) {
s_WrapUpDb(*m_Db);
}
}
-
+
void SetDb(CWriteDB & db)
{
m_Db.Reset(& db);
}
-
+
private:
CRef<CWriteDB> m_Db;
};
@@ -488,7 +489,7 @@ s_DupSequencesTest(const TIdList & ids,
int cutpoint = 99)
{
CWrapperUpper wrap;
-
+
BOOST_REQUIRE_CUTPOINT(1);
// Ensure no strange files are left after text execution
@@ -499,44 +500,44 @@ s_DupSequencesTest(const TIdList & ids,
string fname(basename+string(ext[i]));
CFileDeleteAtExit::Add(fname);
}
-
+
CSeqDBExpert src(src_name, (is_protein
? CSeqDB::eProtein
: CSeqDB::eNucleotide));
-
+
vector<string> files;
-
+
CRef<CWriteDB> db;
-
+
BOOST_REQUIRE_CUTPOINT(2);
-
+
db.Reset(new CWriteDB(dst_name,
(is_protein
? CWriteDB::eProtein
: CWriteDB::eNucleotide),
title,
CWriteDB::eFullIndex));
-
+
wrap.SetDb(*db);
-
+
BOOST_REQUIRE_CUTPOINT(3);
-
+
if (raw_data) {
s_DupIdsRaw(*db, src, ids);
} else {
s_DupIdsBioseq(*db, src, ids, cutpoint);
}
-
+
BOOST_REQUIRE_CUTPOINT(10);
-
+
db->Close();
db->ListFiles(files);
db.Reset();
-
+
BOOST_REQUIRE_CUTPOINT(11);
-
+
s_TestDatabase(src, dst_name, title);
-
+
BOOST_REQUIRE_CUTPOINT(12);
}
@@ -564,9 +565,9 @@ static CRef<CScope> s_GetScope()
return scope;
}
-static void s_BuildIds(TIdList & ids, int * gis)
+static void s_BuildIds(TIdList & ids, TGi * gis)
{
- for(int * ptr = gis; *ptr; ptr ++) {
+ for(TGi * ptr = gis; *ptr; ptr ++) {
ids.push_back(s_GiToSeqId(*ptr));
}
}
@@ -581,26 +582,26 @@ static void s_BuildIds(TIdList & ids, const char ** gis)
CRef<CBioseq> s_FastaStringToBioseq(const string & str, bool protein)
{
istrstream istr(str.data(), str.size());
-
+
CRef<ILineReader> lr(new CStreamLineReader(istr));
-
+
typedef CFastaReader::EFlags TFlags;
-
+
TFlags flags = (TFlags) (CFastaReader::fAllSeqIds |
(protein
? CFastaReader::fAssumeProt
: CFastaReader::fAssumeNuc));
-
+
CFastaReader fr(*lr, flags);
-
+
BOOST_REQUIRE(! lr->AtEOF());
CRef<CSeq_entry> entry = fr.ReadOneSeq();
-
+
BOOST_REQUIRE(! entry.Empty());
BOOST_REQUIRE(entry->IsSeq());
-
+
CRef<CBioseq> bs(& entry->SetSeq());
-
+
return bs;
}
@@ -611,8 +612,8 @@ CRef<CBioseq> s_FastaStringToBioseq(const string & str, bool protein)
static void s_NuclBioseqDupSwitch(int cutpoint)
{
-
- int gis[] = {
+
+ TGi gis[] = {
78883515, 78883517, /*71143095,*/ 24431485, 19110479, 15054463,
15054465, 15054467, 15054469, 15054471, 19570808, 18916476,
1669608, 1669610, 1669612, 1669614, 1669616, 10944307,
@@ -623,12 +624,12 @@ static void s_NuclBioseqDupSwitch(int cutpoint)
21623739, 21623761, 38303844, 38197377, 56788779, 57032781,
57870443, 56789136, 0
};
-
+
TIdList ids;
s_BuildIds(ids, gis);
-
+
BOOST_REQUIRE_CUTPOINT(0);
-
+
const string srcname("nt");
const string dstname("w-nucl-bs");
const string title("bioseq nucleotide dup");
@@ -640,9 +641,9 @@ static void s_NuclBioseqDupSwitch(int cutpoint)
dstname,
title,
cutpoint);
-
+
BOOST_REQUIRE_CUTPOINT(13);
-
+
const string dstname2("w-nucl-raw");
const string title2("raw nucleotide dup");
s_DupSequencesTest(ids,
@@ -652,7 +653,7 @@ static void s_NuclBioseqDupSwitch(int cutpoint)
dstname2,
title2,
cutpoint);
-
+
BOOST_REQUIRE_CUTPOINT(14);
}
@@ -661,7 +662,7 @@ BOOST_AUTO_TEST_SUITE(writedb)
#if 0
BOOST_AUTO_TEST_CASE(NuclBioseqDupZ)
{
-
+
try {
s_NuclBioseqDupSwitch(0);
}
@@ -671,7 +672,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupZ)
BOOST_AUTO_TEST_CASE(NuclBioseqDupA)
{
-
+
try {
s_NuclBioseqDupSwitch(1);
}
@@ -681,7 +682,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupA)
BOOST_AUTO_TEST_CASE(NuclBioseqDupB)
{
-
+
try {
s_NuclBioseqDupSwitch(2);
}
@@ -691,7 +692,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupB)
BOOST_AUTO_TEST_CASE(NuclBioseqDupC)
{
-
+
try {
s_NuclBioseqDupSwitch(3);
}
@@ -701,7 +702,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupC)
BOOST_AUTO_TEST_CASE(NuclBioseqDupD)
{
-
+
try {
s_NuclBioseqDupSwitch(4);
}
@@ -711,7 +712,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupD)
BOOST_AUTO_TEST_CASE(NuclBioseqDupE)
{
-
+
try {
s_NuclBioseqDupSwitch(5);
}
@@ -721,7 +722,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupE)
BOOST_AUTO_TEST_CASE(NuclBioseqDupF)
{
-
+
try {
s_NuclBioseqDupSwitch(6);
}
@@ -731,7 +732,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupF)
BOOST_AUTO_TEST_CASE(NuclBioseqDupG)
{
-
+
try {
s_NuclBioseqDupSwitch(7);
}
@@ -741,7 +742,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupG)
BOOST_AUTO_TEST_CASE(NuclBioseqDupH)
{
-
+
try {
s_NuclBioseqDupSwitch(8);
}
@@ -752,7 +753,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupH)
BOOST_AUTO_TEST_CASE(NuclBioseqDupI)
{
-
+
try {
s_NuclBioseqDupSwitch(9);
}
@@ -762,9 +763,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupI)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ4)
{
-
+
g_NuclJ_OidCount = 4;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -774,9 +775,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ4)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ8)
{
-
+
g_NuclJ_OidCount = 8;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -786,9 +787,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ8)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ12)
{
-
+
g_NuclJ_OidCount = 12;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -798,9 +799,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ12)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ16)
{
-
+
g_NuclJ_OidCount = 16;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -810,9 +811,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ16)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ20)
{
-
+
g_NuclJ_OidCount = 20;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -822,9 +823,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ20)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ24)
{
-
+
g_NuclJ_OidCount = 24;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -834,9 +835,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ24)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ28)
{
-
+
g_NuclJ_OidCount = 28;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -846,9 +847,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ28)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ32)
{
-
+
g_NuclJ_OidCount = 32;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -858,9 +859,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ32)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ33)
{
-
+
g_NuclJ_OidCount = 33;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -870,9 +871,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ33)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ34)
{
-
+
g_NuclJ_OidCount = 34;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -882,9 +883,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ34)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ35)
{
-
+
g_NuclJ_OidCount = 35;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -894,9 +895,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ35)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ36)
{
-
+
g_NuclJ_OidCount = 36;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -906,9 +907,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ36)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ40)
{
-
+
g_NuclJ_OidCount = 40;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -918,9 +919,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ40)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ44)
{
-
+
g_NuclJ_OidCount = 44;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -930,9 +931,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ44)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ45)
{
-
+
g_NuclJ_OidCount = 45;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -942,9 +943,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ45)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ46)
{
-
+
g_NuclJ_OidCount = 46;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -954,9 +955,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ46)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ47)
{
-
+
g_NuclJ_OidCount = 47;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -966,9 +967,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ47)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ48)
{
-
+
g_NuclJ_OidCount = 48;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -978,9 +979,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ48)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ49)
{
-
+
g_NuclJ_OidCount = 49;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -990,9 +991,9 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ49)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ50)
{
-
+
g_NuclJ_OidCount = 50;
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -1002,7 +1003,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ50)
BOOST_AUTO_TEST_CASE(NuclBioseqDupJ)
{
-
+
try {
s_NuclBioseqDupSwitch(10);
}
@@ -1012,7 +1013,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupJ)
BOOST_AUTO_TEST_CASE(NuclBioseqDupK)
{
-
+
try {
s_NuclBioseqDupSwitch(11);
}
@@ -1023,7 +1024,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupK)
#if 0
BOOST_AUTO_TEST_CASE(NuclBioseqDupL)
{
-
+
try {
s_NuclBioseqDupSwitch(12);
}
@@ -1033,7 +1034,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupL)
BOOST_AUTO_TEST_CASE(NuclBioseqDupM)
{
-
+
try {
s_NuclBioseqDupSwitch(13);
}
@@ -1043,7 +1044,7 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupM)
BOOST_AUTO_TEST_CASE(NuclBioseqDupN)
{
-
+
try {
s_NuclBioseqDupSwitch(14);
}
@@ -1054,14 +1055,14 @@ BOOST_AUTO_TEST_CASE(NuclBioseqDupN)
BOOST_AUTO_TEST_CASE(NuclBioseqDup)
{
-
+
s_NuclBioseqDupSwitch(99);
}
BOOST_AUTO_TEST_CASE(ProtBioseqDup)
{
-
- int gis[] = {
+
+ TGi gis[] = {
1477444, 1669609, 1669611, 1669615, 1669617, 7544146,
22652804, /*1310870,*/ 3114354, 3891778, 3891779, 81294290,
81294330, 49089974, 62798905, 3041810, 7684357, 7684359,
@@ -1072,17 +1073,17 @@ BOOST_AUTO_TEST_CASE(ProtBioseqDup)
13365559, 8096667, 3721768, 9857600, 2190043, 3219276,
10799943, 10799945, 0
};
-
+
TIdList ids;
s_BuildIds(ids, gis);
-
+
s_DupSequencesTest(ids,
true,
false,
"nr",
"w-prot-bs",
"bioseq protein dup");
-
+
s_DupSequencesTest(ids,
true,
true,
@@ -1093,163 +1094,163 @@ BOOST_AUTO_TEST_CASE(ProtBioseqDup)
BOOST_AUTO_TEST_CASE(EmptyBioseq)
{
-
+
CWriteDB fails("failing-db",
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex);
-
+
CRef<CBioseq> bs(new CBioseq);
fails.AddSequence(*bs);
-
+
BOOST_REQUIRE_THROW(fails.Close(), CWriteDBException);
}
BOOST_AUTO_TEST_CASE(BioseqHandle)
{
-
+
CWriteDB db("from-loader",
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex);
-
+
CRef<CScope> scope = s_GetScope();
-
+
// Normal bioseq handle.
-
+
CRef<CSeq_id> id1(new CSeq_id("gi|129295"));
CBioseq_Handle bsh1 = scope->GetBioseqHandle(*id1);
db.AddSequence(bsh1);
-
+
// Clean up.
-
+
db.Close();
s_WrapUpDb(db);
}
BOOST_AUTO_TEST_CASE(BioseqHandleAndSeqVectorNonWriteDB)
{
-
+
// This is a modified version of the following test. The
// assumption is that some errors occur due to environmental
// factors. Hopefully this test will help to determine the
// library in which these intermittent errors occur.
-
+
CRef<CScope> scope = s_GetScope();
-
+
CRef<CSeq_id> id2(new CSeq_id("gi|129296"));
CBioseq_Handle bsh2 = scope->GetBioseqHandle(*id2);
CConstRef<CBioseq> bs1c = bsh2.GetCompleteBioseq();
CRef<CBioseq> bs1 = s_Duplicate(*bs1c);
CSeqVector sv(bsh2);
-
+
string bytes;
sv.GetSeqData(0, sv.size(), bytes);
-
+
BOOST_REQUIRE(bytes.size() == sv.size());
}
BOOST_AUTO_TEST_CASE(BioseqHandleAndSeqVector)
{
-
+
CRef<CScope> scope = s_GetScope();
-
+
// Bioseq + CSeqVector.
-
+
CRef<CSeq_id> id2(new CSeq_id("gi|129296"));
CBioseq_Handle bsh2 = scope->GetBioseqHandle(*id2);
CConstRef<CBioseq> bs1c = bsh2.GetCompleteBioseq();
-
+
CRef<CBioseq> bs1 = s_Duplicate(*bs1c);
CSeqVector sv(bsh2);
-
+
string bytes;
sv.GetSeqData(0, sv.size(), bytes);
}
BOOST_AUTO_TEST_CASE(BioseqHandleAndSeqVectorWriteDB)
{
-
+
CWriteDB db("from-loader",
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex);
-
+
CRef<CScope> scope = s_GetScope();
-
+
// Bioseq + CSeqVector.
-
+
CRef<CSeq_id> id2(new CSeq_id("gi|129296"));
CBioseq_Handle bsh2 = scope->GetBioseqHandle(*id2);
CConstRef<CBioseq> bs1c = bsh2.GetCompleteBioseq();
-
+
CRef<CBioseq> bs1 = s_Duplicate(*bs1c);
CSeqVector sv(bsh2);
-
+
// Make sure CSeqVector is exercised by removing the Seq-data.
-
+
bs1->SetInst().ResetSeq_data();
db.AddSequence(*bs1, sv);
-
+
// Clean up.
-
+
db.Close();
s_WrapUpDb(db);
}
BOOST_AUTO_TEST_CASE(SetPig)
{
-
+
string nm = "pigs";
vector<string> files;
-
+
{
CSeqDB nr("nr", CSeqDB::eProtein);
-
+
CWriteDB db(nm,
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex);
-
+
db.AddSequence(*nr.GiToBioseq(129295));
db.SetPig(101);
-
+
db.AddSequence(*nr.GiToBioseq(129296));
db.SetPig(102);
-
+
db.AddSequence(*nr.GiToBioseq(129297));
db.SetPig(103);
-
+
db.Close();
db.ListFiles(files);
}
-
+
CSeqDB db2(nm, CSeqDB::eProtein);
-
+
int oid = 0;
-
+
for(; db2.CheckOrFindOID(oid); oid++) {
int pig(0);
- vector<int> gis;
-
+ vector<TGi> gis;
+
bool rv1 = db2.OidToPig(oid, pig);
db2.GetGis(oid, gis, false);
-
+
bool found_gi = false;
for(unsigned i = 0; i < gis.size(); i++) {
- if (gis[i] == (129295 + oid)) {
+ if (gis[i] == 129295 + oid) {
found_gi = true;
}
}
-
+
BOOST_REQUIRE(rv1);
BOOST_REQUIRE(found_gi);
BOOST_REQUIRE_EQUAL(pig-oid, 101);
}
-
+
BOOST_REQUIRE_EQUAL(oid, 3);
-
+
s_WrapUpFiles(files);
}
@@ -1257,120 +1258,120 @@ BOOST_AUTO_TEST_CASE(SetPig)
BOOST_AUTO_TEST_CASE(MultiVolume)
{
-
+
CSeqDB nr("nr", CSeqDB::eProtein);
-
+
CWriteDB db("multivol",
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex);
-
+
db.SetMaxVolumeLetters(500);
-
+
int gis[] = { 129295, 129296, 129297, 129299, 0 };
-
+
Uint8 letter_count = 0;
-
+
for(int i = 0; gis[i]; i++) {
int oid(0);
nr.GiToOid(gis[i], oid);
-
+
db.AddSequence(*nr.GetBioseq(oid));
letter_count += nr.GetSeqLength(oid);
}
-
+
db.Close();
-
+
vector<string> v;
vector<string> f;
db.ListVolumes(v);
db.ListFiles(f);
-
+
BOOST_REQUIRE_EQUAL(3, (int) v.size());
BOOST_REQUIRE_EQUAL(v[0], string("multivol.00"));
BOOST_REQUIRE_EQUAL(v[1], string("multivol.01"));
BOOST_REQUIRE_EQUAL(v[2], string("multivol.02"));
-
+
BOOST_REQUIRE_EQUAL(25, (int) f.size());
-
+
// Check resulting db.
-
+
CRef<CSeqDB> seqdb(new CSeqDB("multivol", CSeqDB::eProtein));
-
+
int oids(0);
Uint8 letters(0);
-
+
seqdb->GetTotals(CSeqDB::eUnfilteredAll, & oids, & letters, false);
-
+
BOOST_REQUIRE_EQUAL(oids, 4);
BOOST_REQUIRE_EQUAL(letter_count, letters);
-
+
seqdb.Reset();
-
+
s_WrapUpFiles(f);
}
BOOST_AUTO_TEST_CASE(UsPatId)
{
-
+
CRef<CSeq_id> seqid(new CSeq_id("pat|us|123|456"));
vector<string> files;
-
+
{
CRef<CWriteDB> writedb
(new CWriteDB("uspatid",
CWriteDB::eProtein,
"patent id test",
CWriteDB::eFullIndex));
-
+
CSeqDB seqdb("nr", CSeqDB::eProtein);
-
+
CRef<CBioseq> bs = seqdb.GiToBioseq(129297);
-
+
CRef<CBlast_def_line_set> bdls(new CBlast_def_line_set);
CRef<CBlast_def_line> dl(new CBlast_def_line);
bdls->Set().push_back(dl);
-
+
dl->SetTitle("Some protein sequence");
dl->SetSeqid().push_back(seqid);
dl->SetTaxid(12345);
-
+
writedb->AddSequence(*bs);
writedb->SetDeflines(*bdls);
-
+
writedb->Close();
writedb->ListFiles(files);
BOOST_REQUIRE(files.size() != 0);
}
-
+
CSeqDB seqdb("uspatid", CSeqDB::eProtein);
int oid(-1);
bool found = seqdb.SeqidToOid(*seqid, oid);
-
+
BOOST_REQUIRE_EQUAL(found, true);
BOOST_REQUIRE_EQUAL(oid, 0);
-
+
s_WrapUpFiles(files);
}
BOOST_AUTO_TEST_CASE(IsamSorting)
{
-
+
// This checks whether the following IDs are fetchable from the
// given database. It will fail if either the production blast
// databases (i.e. found at $BLASTDB) are corrupted or if the
// newly produced database is corrupted. It will also fail if any
// of the IDs are legitimately missing (removed by the curators),
// in which case the given ID must be removed from the list.
-
+
// However, the selection of these specific IDs is not arbitrary;
// these are several sets of IDs which have a common 6 letter
// prefix. The test will not work correctly if these IDs are
// replaced with IDs that don't have this trait, if too many are
// removed, or if the IDs are put in sorted order.
-
+
// A null terminated array of NUL terminated strings.
-
+
const char* accs[] = {
/*"AAC76335.1",*/ "AAC77159.1", /*"AAA58145.1",*/ "AAC76880.1",
"AAC76230.1", "AAC76373.1", "AAC77137.1", "AAC76637.2",
@@ -1383,10 +1384,10 @@ BOOST_AUTO_TEST_CASE(IsamSorting)
"AAC76918.1", "AAC76727.1", /*"AAC76161.1",*/ "AAA57964.1",
"AAA24251.1", 0
};
-
+
TIdList ids;
s_BuildIds(ids, accs);
-
+
s_DupSequencesTest(ids,
true,
false,
@@ -1397,9 +1398,9 @@ BOOST_AUTO_TEST_CASE(IsamSorting)
BOOST_AUTO_TEST_CASE(DuplicateId)
{
-
- // This checks if duplicate IDs (AAC76373 and AAA58145) are found
-
+
+ // This checks if duplicate IDs (AAC76373 and AAA58145) are found
+
const char* accs[] = {
"AAC76335.1", "AAC77159.1", "AAA58145.1", "AAC76880.1",
"AAC76230.1", "AAC76373.1", "AAC77137.1", "AAC76637.2",
@@ -1412,10 +1413,10 @@ BOOST_AUTO_TEST_CASE(DuplicateId)
"AAC76918.1", "AAC76727.1", "AAC76161.1", "AAA57964.1",
"AAA24251.1", 0
};
-
+
TIdList ids;
s_BuildIds(ids, accs);
-
+
BOOST_REQUIRE_THROW(s_DupSequencesTest(ids,
true,
false,
@@ -1427,35 +1428,35 @@ BOOST_AUTO_TEST_CASE(DuplicateId)
BOOST_AUTO_TEST_CASE(HashToOid)
{
-
+
CSeqDBExpert nr("nr", CSeqDB::eProtein);
CSeqDBExpert nt("nt", CSeqDB::eNucleotide);
-
- int prot_gis[] = { 129295, 129296, 129297, 0 };
- int nucl_gis[] = { 555, 556, 405832, 0 };
-
+
+ TGi prot_gis[] = { 129295, 129296, 129297, 0 };
+ TGi nucl_gis[] = { 555, 556, 405832, 0 };
+
TIdList prot_ids, nucl_ids;
s_BuildIds(prot_ids, prot_gis);
s_BuildIds(nucl_ids, nucl_gis);
-
+
typedef CWriteDB::EIndexType TType;
-
+
TType itype = TType(CWriteDB::eFullWithTrace |
CWriteDB::eAddHash);
-
+
CRef<CWriteDB> prot(new CWriteDB("w-prot-hash",
CWriteDB::eProtein,
"test of hash ISAMs (P)",
itype));
-
+
CRef<CWriteDB> nucl(new CWriteDB("w-nucl-hash",
CWriteDB::eNucleotide,
"test of hash ISAMs (N)",
itype));
-
+
s_DupIdsBioseq(*prot, nr, prot_ids, 99);
s_DupIdsBioseq(*nucl, nt, nucl_ids, 99);
-
+
prot->Close();
nucl->Close();
@@ -1468,261 +1469,261 @@ BOOST_AUTO_TEST_CASE(MismatchedDb_Bioseq) // per SB-1330
vector<string> files;
string title = "pdb-id";
string I1("pdb|3E3Q|BB"), T1("Lower case chain b");
-
+
{
CRef<CWriteDB> wr(new CWriteDB(title,
CWriteDB::eNucleotide,
"title",
CWriteDB::eFullIndex));
-
+
// Build a multi-defline bioseq and read it with CFastaReader.
-
+
string str = ">" + I1 + " " + T1 + "\n" + "ELVISLIVES\n";
-
+
CRef<CBioseq> bs = s_FastaStringToBioseq(str, true);
-
+
BOOST_REQUIRE_THROW(wr->AddSequence(*bs), CWriteDBException);
wr->Close();
-
+
// Clean up.
-
+
wr->ListFiles(files);
}
-
+
s_RemoveFiles(files);
}
BOOST_AUTO_TEST_CASE(PDBIdLowerCase)
{
-
+
vector<string> files;
-
+
string title = "pdb-id";
-
+
string
I1("pdb|3E3Q|BB"), T1("Lower case chain b");
-
+
{
CRef<CWriteDB> wr(new CWriteDB(title,
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex));
-
+
// Build a multi-defline bioseq and read it with CFastaReader.
-
+
string str = ">" + I1 + " " + T1 + "\n" + "ELVISLIVES\n";
-
+
CRef<CBioseq> bs = s_FastaStringToBioseq(str, true);
-
+
wr->AddSequence(*bs);
wr->Close();
-
+
// Clean up.
-
+
wr->ListFiles(files);
}
-
+
{
CSeqDB rd("pdb-id", CSeqDB::eProtein);
BOOST_REQUIRE(rd.GetNumOIDs() == 1);
-
+
vector<int> oids;
rd.AccessionToOids("3e3q bb", oids);
-
+
BOOST_REQUIRE(oids.size() == 1);
BOOST_REQUIRE(oids[0] == 0);
oids.clear();
rd.AccessionToOids("3e3q b", oids);
-
+
BOOST_REQUIRE(oids.size() == 0);
}
-
+
s_WrapUpFiles(files);
}
BOOST_AUTO_TEST_CASE(FastaReaderBioseq)
{
-
+
vector<string> files;
-
+
string title = "from-fasta-reader";
-
+
string
I1("gi|123"), T1("One two three."),
I2("gi|124"), T2("One two four.");
-
+
{
CRef<CWriteDB> wr(new CWriteDB(title,
CWriteDB::eProtein,
"title",
CWriteDB::eFullIndex));
-
+
// Build a multi-defline bioseq and read it with CFastaReader.
-
+
string str =
">" + I1 + " " + T1 +
"\001" + I2 + " " + T2 + "\n" +
"ELVISLIVES\n";
-
+
CRef<CBioseq> bs = s_FastaStringToBioseq(str, true);
-
+
wr->AddSequence(*bs);
wr->Close();
-
+
// Clean up.
-
+
wr->ListFiles(files);
}
-
+
{
CSeqDB rd("from-fasta-reader", CSeqDB::eProtein);
BOOST_REQUIRE(rd.GetNumOIDs() == 1);
-
+
CRef<CBlast_def_line_set> bdls =
rd.GetHdr(0);
-
+
BOOST_REQUIRE(bdls->Get().size() == 2);
BOOST_REQUIRE(bdls->Get().front()->GetTitle() == T1);
BOOST_REQUIRE(bdls->Get().front()->GetSeqid().size() == 1);
BOOST_REQUIRE(bdls->Get().front()->GetSeqid().front()->AsFastaString() == I1);
-
+
BOOST_REQUIRE(bdls->Get().back()->GetTitle() == T2);
BOOST_REQUIRE(bdls->Get().back()->GetSeqid().size() == 1);
BOOST_REQUIRE(bdls->Get().back()->GetSeqid().front()->AsFastaString() == I2);
}
-
+
s_WrapUpFiles(files);
}
BOOST_AUTO_TEST_CASE(BinaryListBuilder)
{
-
+
string fn4("test4.til"), fn8("test8.til");
-
+
{
CBinaryListBuilder blb4(CBinaryListBuilder::eTi);
CBinaryListBuilder blb8(CBinaryListBuilder::eTi);
-
+
for(int i = 0; i<10; i++) {
blb4.AppendId(Int8(1) << (i*2));
blb8.AppendId(Int8(1) << (i*4));
}
-
+
blb4.Write(fn4);
blb8.Write(fn8);
}
-
+
string h4 = s_HexDumpFile(fn4, 4, 16);
string h8 = s_HexDumpFile(fn8, 4, 16);
-
+
// The FF...FD symbol indicates a 4 byte TI list; the FF..FC
// symbol is the eight byte version.
-
+
BOOST_REQUIRE(h4 ==
"FFFFFFFD A "
"1 4 10 40 100 "
"400 1000 4000 10000 40000");
-
+
BOOST_REQUIRE(h8 ==
"FFFFFFFC A "
"0 1 0 10 0 100 0 1000 0 10000 "
"0 100000 0 1000000 0 10000000 1 0 10 0");
-
+
CFile(fn4).Remove();
CFile(fn8).Remove();
}
BOOST_AUTO_TEST_CASE(FourAndEightByteTis)
{
-
+
typedef pair<string, string> TPair;
vector< TPair > ids48;
-
+
// Generate gnl|ti# IDs where # is 1234*2^N for db4, and
// 1234*1000^N for db8.
-
+
{
Int8 a4(1234), b4(2), a8(1234), b8(1000);
-
+
string prefix = "gnl|ti|";
-
+
for(int i = 0; i < 5; i++) {
TPair p;
p.first = prefix + NStr::Int8ToString(a4);
p.second = prefix + NStr::Int8ToString(a8);
-
+
ids48.push_back(p);
Int8 p4(a4), p8(a8);
-
+
a4 *= b4;
a8 *= b8;
-
+
// Check for overflow.
-
+
BOOST_REQUIRE(a4 > p4);
BOOST_REQUIRE(a8 > p8);
}
-
+
// Make sure we really do have 32 and 64 bit IDs.
-
+
BOOST_REQUIRE((a4 >> 32) == 0);
BOOST_REQUIRE((a8 >> 32) != 0);
}
-
+
string dbname4 = "test-db-short-tis";
string dbname8 = "test-db-long-tis";
-
+
CWriteDB db4(dbname4,
CWriteDB::eNucleotide,
dbname4 + " database.",
CWriteDB::eFullWithTrace);
-
+
CWriteDB db8(dbname8,
CWriteDB::eNucleotide,
dbname8 + " database.",
CWriteDB::eFullWithTrace);
-
+
string iupac = "GATTACA";
-
+
ITERATE(vector< TPair >, iter, ids48) {
string f4 = string(">") + iter->first + " test\n" + iupac + "\n";
string f8 = string(">") + iter->second + " test\n" + iupac + "\n";
-
+
db4.AddSequence( *s_FastaStringToBioseq(f4, false) );
db8.AddSequence( *s_FastaStringToBioseq(f8, false) );
}
-
+
db4.Close();
db8.Close();
-
+
// Use 4 byte dumps for the (mixed field width) index files.
-
+
string index4 = s_HexDumpFile(dbname4 + ".nti", 4, 16);
string index8 = s_HexDumpFile(dbname8 + ".nti", 4, 16);
-
+
string
i4("1 0 28 5 1 100 0 0 0 4D2 0 FFFFFFFF 0"),
i8("1 5 3C 5 1 100 0 0 0 0 4D2 0 FFFFFFFF FFFFFFFF 0"),
d4("1234 0 2468 1 4936 2 9872 3 19744 4"),
d8("1234 0 1234000 1 1234000000 2 1234000000000 3 1234000000000000 4");
-
+
BOOST_REQUIRE(index4 == i4);
BOOST_REQUIRE(index8 == i8);
-
+
vector<int> overlay;
overlay.push_back(8);
overlay.push_back(4);
-
+
// The 32-bit TI data file is uniformly 4 bytes. The 8 byte file
// alternates between 8 and 4 byte fields.
-
+
string data4 = s_HexDumpFile(dbname4 + ".ntd", 4, 10);
string data8 = s_HexDumpFile(dbname8 + ".ntd", overlay, 10);
-
+
s_WrapUpDb(db4);
s_WrapUpDb(db8);
-
+
BOOST_REQUIRE(data4 == d4);
BOOST_REQUIRE(data8 == d8);
}
@@ -1738,15 +1739,15 @@ void s_WrapUpColumn(CWriteDB_ColumnBuilder & cb)
BOOST_AUTO_TEST_CASE(UserDefinedColumns)
{
-
+
// Create and open the DBs and columns.
-
+
typedef map<string,string> TMeta;
TMeta meta_data;
meta_data["created-by"] = "unit test";
meta_data["purpose"] = "none";
meta_data["format"] = "text";
-
+
vector<string> column_data;
column_data.push_back("Groucho Marx");
column_data.push_back("Charlie Chaplain");
@@ -1755,52 +1756,52 @@ BOOST_AUTO_TEST_CASE(UserDefinedColumns)
column_data.push_back("Jackie Gleason");
column_data.push_back("Jerry Seinfeld");
column_data.back()[5] = (char) 0;
-
+
string fname("user-column");
string vname("user-column-db");
string title("comedy");
-
+
CSeqDB R("nr", CSeqDB::eProtein);
CWriteDB W(vname,
CWriteDB::eProtein,
"User defined column");
-
+
CWriteDB_ColumnBuilder CB(title, fname);
-
+
int col_id = W.CreateUserColumn(title);
-
+
ITERATE(TMeta, iter, meta_data) {
CB.AddMetaData(iter->first, iter->second);
W.AddColumnMetaData(col_id, iter->first, iter->second);
}
-
+
// Build database and column.
-
+
int i = 0;
-
+
ITERATE(vector<string>, iter, column_data) {
W.AddSequence(*R.GetBioseq(i++));
-
+
CBlastDbBlob & b1 = W.SetBlobData(col_id);
b1.WriteString(*iter, CBlastDbBlob::eNone);
-
+
CBlastDbBlob b2(*iter, false);
CB.AddBlob(b2);
}
-
+
// Close the DB and the column.
-
+
W.Close();
CB.Close();
-
+
// Test the resulting files.
-
+
// (Currently, the files created here are not tested. Instead,
// the SeqDB test uses copies of these files and tests the data
// integrity via the SeqDB functionality.)
-
+
// Clean up.
-
+
s_WrapUpColumn(CB);
s_WrapUpDb(W);
}
@@ -1831,7 +1832,7 @@ BOOST_AUTO_TEST_CASE(RegisterVariantsOfSameMaskingAlgorithm)
BOOST_REQUIRE_EQUAL(id1+1, id2);
}
-void
+void
RegisterTooManyVariantsOfSameMaskingAlgorithm
(EBlast_filter_program masking_algo,
size_t kMaxNumSupportedAlgorithmVariants)
@@ -1849,10 +1850,10 @@ RegisterTooManyVariantsOfSameMaskingAlgorithm
} else {
options.assign(NStr::SizetToString(i));
}
-
+
int algo_id = -1;
if (i >= kMaxNumSupportedAlgorithmVariants) {
- BOOST_REQUIRE_THROW(algo_id = registry.Add(masking_algo, options),
+ BOOST_REQUIRE_THROW(algo_id = registry.Add(masking_algo, options),
CWriteDBException);
} else {
algo_id = registry.Add(masking_algo, options);
@@ -1917,96 +1918,96 @@ BOOST_AUTO_TEST_CASE(RegisterTooManyVariantsOfOther)
BOOST_AUTO_TEST_CASE(MaskDataColumn)
{
-
+
CSeqDB R("nr", CSeqDB::eProtein);
CWriteDB W("mask-data-db", CWriteDB::eProtein, "Mask data test");
const int kNumSeqs = 10;
-
+
vector<int> oids;
int next_oid = 0;
-
+
// Get kNumSeqs sequences with length less than 1024
for(int i = 0; i < kNumSeqs; i++) {
int L = R.GetSeqLength(next_oid);
-
+
while(L < 1024) {
++next_oid;
L = R.GetSeqLength(next_oid);
}
-
+
oids.push_back(next_oid++);
}
-
+
int seg_id = W.RegisterMaskAlgorithm(eBlast_filter_program_seg);
-
- int repeat_id = W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
+
+ int repeat_id = W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
"-species Desmodus_rotundus");
-
+
// Populate it.
-
+
for(int i = 0; i < kNumSeqs; i++) {
int oid = oids[i];
W.AddSequence(*R.GetBioseq(oid));
-
+
CMaskedRangesVector ranges;
-
+
if (i & 1) {
ranges.push_back(SBlastDbMaskData());
ranges.back().algorithm_id = seg_id;
-
+
for(int j = 0; j < (i+5); j++) {
pair<TSeqPos, TSeqPos> rng;
rng.first = i * 13 + j * 7 + 2;
rng.second = rng.first + 3 + (i+j) % 11;
-
+
ranges.back().offsets.push_back(rng);
}
}
-
+
if (i & 2) {
ranges.push_back(SBlastDbMaskData());
ranges.back().algorithm_id = repeat_id;
-
+
for(int j = 0; j < (i+5); j++) {
pair<TSeqPos, TSeqPos> rng;
rng.first = i * 10 + j * 5 + 2;
rng.second = rng.first + 20;
-
+
ranges.back().offsets.push_back(rng);
}
}
-
+
// Set the mask data if either list above was used, or in some
// cases when neither is. (Calling SetMaskData() with an
// empty array should be the same as not calling it at all;
// this code tests that equivalence.)
-
- vector <int> gis;
+
+ vector <TGi> gis;
if (i & 7) {
W.SetMaskData(ranges, gis);
}
}
-
+
// Close the DB.
-
+
W.Close();
-
+
// Test the resulting files.
-
+
// (Currently, the files created here are not tested. Instead,
// the SeqDB test uses copies of these files and tests the data
// integrity via the SeqDB functionality.)
-
+
// Clean up.
-
+
s_WrapUpDb(W);
}
BOOST_AUTO_TEST_CASE(DuplicateAlgoId)
{
-
+
CWriteDB W("mask-data-db", CWriteDB::eProtein, "Mask data test");
-
+
(void)W.RegisterMaskAlgorithm(eBlast_filter_program_seg);
int seg_repeated_id;
BOOST_REQUIRE_THROW( seg_repeated_id =
@@ -2017,9 +2018,9 @@ BOOST_AUTO_TEST_CASE(DuplicateAlgoId)
BOOST_AUTO_TEST_CASE(TooManyAlgoId)
{
-
+
CWriteDB W("mask-data-db", CWriteDB::eProtein, "Mask data test");
-
+
EBlast_filter_program masking_algorithm = eBlast_filter_program_seg;
vector<int> algo_ids;
@@ -2030,7 +2031,7 @@ BOOST_AUTO_TEST_CASE(TooManyAlgoId)
string options( i == 0 ? "" : NStr::SizetToString(i));
int algo_id = -1;
if (i >= kMaxNumSupportedAlgorithmVariants) {
- BOOST_REQUIRE_THROW(
+ BOOST_REQUIRE_THROW(
algo_id = W.RegisterMaskAlgorithm(masking_algorithm, options),
CWriteDBException);
} else {
@@ -2050,39 +2051,39 @@ BOOST_AUTO_TEST_CASE(TooManyAlgoId)
BOOST_AUTO_TEST_CASE(UndefinedAlgoID)
{
-
+
CSeqDB R("nr", CSeqDB::eProtein);
CWriteDB W("mask-data-db", CWriteDB::eProtein, "Mask data test");
-
+
W.RegisterMaskAlgorithm(eBlast_filter_program_seg);
-
- W.RegisterMaskAlgorithm(eBlast_filter_program_seg,
+
+ W.RegisterMaskAlgorithm(eBlast_filter_program_seg,
"-species Aotus_vociferans");
-
- W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
+
+ W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
"-species Desmodus_rotundus");
-
+
// Populate it.
-
+
int oid = 0;
-
+
int L = R.GetSeqLength(oid);
W.AddSequence(*R.GetBioseq(oid));
-
+
CMaskedRangesVector ranges;
-
+
ranges.push_back(SBlastDbMaskData());
ranges.back().algorithm_id = (int)eBlast_filter_program_dust;
-
+
pair<TSeqPos, TSeqPos> rng;
rng.first = L/3;
rng.second = L;
-
+
ranges.back().offsets.push_back(rng);
-
- vector <int> gis;
+
+ vector <TGi> gis;
BOOST_REQUIRE_THROW(W.SetMaskData(ranges, gis), CWriteDBException);
-
+
W.Close();
s_WrapUpDb(W);
}
@@ -2091,35 +2092,35 @@ BOOST_AUTO_TEST_CASE(MaskDataBoundsError)
{
CSeqDB R("nr", CSeqDB::eProtein);
CWriteDB W("mask-data-db", CWriteDB::eProtein, "Mask data test");
-
+
W.RegisterMaskAlgorithm(eBlast_filter_program_seg);
-
- W.RegisterMaskAlgorithm(eBlast_filter_program_seg,
+
+ W.RegisterMaskAlgorithm(eBlast_filter_program_seg,
"-species Aotus_vociferans");
-
- W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
+
+ W.RegisterMaskAlgorithm(eBlast_filter_program_repeat,
"-species Desmodus_rotundus");
-
+
// Populate it.
-
+
int oid = 0;
-
+
int L = R.GetSeqLength(oid);
W.AddSequence(*R.GetBioseq(oid));
-
+
CMaskedRangesVector ranges;
-
+
ranges.push_back(SBlastDbMaskData());
ranges.back().algorithm_id = (int)eBlast_filter_program_dust;
-
+
pair<TSeqPos, TSeqPos> rng;
rng.first = L/3;
rng.second = L+1;
-
+
ranges.back().offsets.push_back(rng);
- vector <int> gis;
+ vector <TGi> gis;
BOOST_REQUIRE_THROW(W.SetMaskData(ranges,gis), CWriteDBException);
-
+
W.Close();
s_WrapUpDb(W);
}
@@ -2133,10 +2134,10 @@ struct SAliasFileData {
Value(const string& name) : m_Found(false), m_Name(name) {}
bool Found() const { return m_Found;}
string Get() const { return m_Value;}
- void Set(const string& v) {
+ void Set(const string& v) {
if ( !v.empty() ) {
- m_Value = v;
- m_Found = true;
+ m_Value = v;
+ m_Found = true;
}
}
string GetKey() const { return m_Name; }
@@ -2156,7 +2157,7 @@ struct SAliasFileData {
Value m_TiList;
Value m_SeqidList;
- SAliasFileData(const string& fname) :
+ SAliasFileData(const string& fname) :
m_Title("TITLE"), m_DbList("DBLIST"), m_NSeqs("NSEQ"),
m_Length("LENGTH"), m_FirstOid("FIRST_OID"), m_LastOid("LAST_OID"),
m_GiList("GILIST"), m_TiList("TILIST"), m_SeqidList("SEQIDLIST")
@@ -2200,7 +2201,7 @@ private:
}
if (NStr::Find(line, "Alias file created") != NPOS) {
// this should be enough granularity
- const string kCurrentYear =
+ const string kCurrentYear =
NStr::IntToString(CTime(CTime::eCurrent).Year());
BOOST_REQUIRE(NStr::Find(line, kCurrentYear) != NPOS);
}
@@ -2484,7 +2485,7 @@ BOOST_AUTO_TEST_CASE(InvalidAliasFileGeneration_NoGisInBlastDB)
CWriteDB_CreateAliasFile(kAliasFileName, kDbName, CWriteDB::eProtein,
kGiFileName, kTitle),
CSeqDBException);
-
+
kAliasFileName += ".pal";
CFileDeleteAtExit::Add(kAliasFileName);
@@ -2498,11 +2499,11 @@ BOOST_AUTO_TEST_CASE(CBuildDatabase_WriteToInvalidPathWindows)
const string kOutput("nul:");
CRef<CBuildDatabase> bd;
BOOST_REQUIRE_THROW(
- bd.Reset(new CBuildDatabase(kOutput, "foo", true,
+ bd.Reset(new CBuildDatabase(kOutput, "foo", true,
CWriteDB::eDefault, false, &log)),
CMultisourceException);
BOOST_REQUIRE(bd.Empty());
-/* temporarily disabled.
+/* temporarily disabled.
CFile f1(kOutput + ".pal"), f2(kOutput + ".pin");
BOOST_REQUIRE(f1.Exists() == false);
BOOST_REQUIRE(f2.Exists() == false);
@@ -2516,7 +2517,7 @@ BOOST_AUTO_TEST_CASE(CBuildDatabase_WriteToInvalidPathUnix)
const string kOutput("/dev/null");
CRef<CBuildDatabase> bd;
BOOST_REQUIRE_THROW(
- bd.Reset(new CBuildDatabase(kOutput, "foo", true,
+ bd.Reset(new CBuildDatabase(kOutput, "foo", true,
CWriteDB::eDefault, false, &log)),
CMultisourceException);
BOOST_REQUIRE(bd.Empty());
@@ -2531,10 +2532,10 @@ BOOST_AUTO_TEST_CASE(CWriteDB_SetTaxonomy)
CTaxIdSet tis(kTaxId);
const string kDbName("foo");
CWriteDB blastdb(kDbName, CWriteDB::eNucleotide, kDbName);
- const CFastaReader::TFlags flags =
+ const CFastaReader::TFlags flags =
CFastaReader::fAssumeNuc | CFastaReader::fAllSeqIds;
CFastaReader reader("data/rabbit_mrna.fsa", flags);
- set<int> gis;
+ set<TGi> gis;
while (!reader.AtEOF()) {
CRef<CSeq_entry> se = reader.ReadOneSeq();
BOOST_REQUIRE(se.NotEmpty());
@@ -2544,12 +2545,12 @@ BOOST_AUTO_TEST_CASE(CWriteDB_SetTaxonomy)
tis.FixTaxId(bds);
blastdb.AddSequence(*bs);
blastdb.SetDeflines(*bds);
- gis.insert(GI_TO(int, FindGi(bs->GetId())));
+ gis.insert(FindGi(bs->GetId()));
}
blastdb.Close();
CSeqDB db(kDbName, CSeqDB::eNucleotide);
- ITERATE(set<int>, gi, gis) {
+ ITERATE(set<TGi>, gi, gis) {
int oid = -1;
if (db.GiToOid(*gi, oid)) {
vector<int> taxids;
@@ -2571,7 +2572,7 @@ BOOST_AUTO_TEST_CASE(CBuildDatabase_TestDirectoryCreation)
CFileDeleteAtExit::Add("a");
CRef<CBuildDatabase> bd;
- bd.Reset(new CBuildDatabase(kOutput, "foo", true,
+ bd.Reset(new CBuildDatabase(kOutput, "foo", true,
CWriteDB::eNoIndex, false, &log));
//CWriteDB::eDefault, false, &cerr));
//CRef<CTaxIdSet> tid(new CTaxIdSet(9301));
@@ -2602,7 +2603,7 @@ BOOST_AUTO_TEST_CASE(CBuildDatabase_TestBasicDatabaseCreation)
CFileDeleteAtExit::Add("x.psq");
CRef<CBuildDatabase> bd;
- bd.Reset(new CBuildDatabase(kOutput, "foo", true,
+ bd.Reset(new CBuildDatabase(kOutput, "foo", true,
CWriteDB::eNoIndex, false, &log));
//CWriteDB::eDefault, false, &cerr));
//CRef<CTaxIdSet> tid(new CTaxIdSet(9301));
@@ -2636,12 +2637,12 @@ public:
}
m_entry->Parentize();
}
-
+
virtual CConstRef<CBioseq> GetNext()
{
CConstRef<CBioseq> rv;
-
+
if (m_Bioseq)
{
rv.Reset(&(*m_Bioseq));
@@ -2676,8 +2677,8 @@ BOOST_AUTO_TEST_CASE(CBuildDatabase_WGS_gap)
(CObjectIStream::Open(eSerial_AsnText, "data/AXBT01000003.asn"));
CRef<CSeq_entry> entry(new CSeq_entry);
*ois >> *entry;
- CSeqEntryGetSource seqentry_source(entry);
-
+ CSeqEntryGetSource seqentry_source(entry);
+
bool status = bd->AddSequences(seqentry_source);
BOOST_REQUIRE(status == true);
bd->EndBuild();
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb.cpp b/c++/src/objtools/blast/seqdb_writer/writedb.cpp
index 9e09cf4..6db3497 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb.cpp 437339 2014-06-05 13:54:41Z camacho $
+/* $Id: writedb.cpp 480972 2015-10-06 12:06:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Implementation for the CWriteDB class, the top level class for WriteDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb.cpp 437339 2014-06-05 13:54:41Z camacho $";
+static char const rcsid[] = "$Id: writedb.cpp 480972 2015-10-06 12:06:22Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -106,7 +106,7 @@ void CWriteDB::AddSequence(const CTempString & sequence,
{
string s(sequence.data(), sequence.length());
string a(ambig.data(), ambig.length());
-
+
m_Impl->AddSequence(s, a);
}
@@ -144,7 +144,7 @@ void CWriteDB::ListFiles(vector<string> & files)
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
int CWriteDB::
-RegisterMaskAlgorithm(EBlast_filter_program program,
+RegisterMaskAlgorithm(EBlast_filter_program program,
const string & options,
const string & name)
{
@@ -160,7 +160,7 @@ RegisterMaskAlgorithm(const string & id,
}
void CWriteDB::SetMaskData(const CMaskedRangesVector & ranges,
- const vector<int> & gis)
+ const vector<TGi> & gis)
{
m_Impl->SetMaskData(ranges, gis);
}
@@ -199,43 +199,43 @@ void CBinaryListBuilder::Write(const string & fname)
}
void CBinaryListBuilder::Write(CNcbiOstream& outp)
-{
+{
// Header; first check for 8 byte ids.
-
+
bool eight = false;
-
+
ITERATE(vector<Int8>, iter, m_Ids) {
Int8 id = *iter;
_ASSERT(id > 0);
-
+
if ((id >> 32) != 0) {
eight = true;
break;
}
}
-
+
Int4 magic = 0;
-
+
switch(m_IdType) {
case eGi:
magic = eight ? -2 : -1;
break;
-
+
case eTi:
magic = eight ? -4 : -3;
break;
-
+
default:
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Unsupported ID type specified.");
}
-
+
s_WriteInt4(outp, magic);
s_WriteInt4(outp, (int)m_Ids.size());
-
+
sort(m_Ids.begin(), m_Ids.end());
-
+
if (eight) {
ITERATE(vector<Int8>, iter, m_Ids) {
s_WriteInt8BE(outp, *iter);
@@ -250,7 +250,7 @@ void CBinaryListBuilder::Write(CNcbiOstream& outp)
/// Returns true if the BLAST DB exists, otherwise throws a CSeqDBException
/// @param dbname name of BLAST DB [in]
/// @param is_prot is the BLAST DB protein? [in]
-static bool
+static bool
s_DoesBlastDbExist(const string& dbname, bool is_protein)
{
char dbtype(is_protein ? 'p' : 'n');
@@ -309,13 +309,13 @@ s_PrintAliasFileCreationLog(const string& dbname,
num_seqs_in_gifile = gilist->Size();
} */
LOG_POST("Created " << (is_protein ? "protein " : "nucleotide ") <<
- dbname << " BLAST (alias) database with " << num_seqs_found
- << " sequences (out of " << num_seqs_in_gifile << " in "
- << gi_file_name << ", " << setprecision(0) << fixed <<
+ dbname << " BLAST (alias) database with " << num_seqs_found
+ << " sequences (out of " << num_seqs_in_gifile << " in "
+ << gi_file_name << ", " << setprecision(0) << fixed <<
(num_seqs_found*100.0/num_seqs_in_gifile) << "% found)");
} else {
LOG_POST("Created " << (is_protein ? "protein " : "nucleotide ") <<
- "BLAST (alias) database " << dbname << " with " <<
+ "BLAST (alias) database " << dbname << " with " <<
num_seqs_found << " sequences");
}
}
@@ -363,7 +363,7 @@ s_CreateAliasFilePriv(const string& file_name,
string fname = CNcbiOstrstreamToString(fnamestr);
ofstream out(fname.c_str());
- out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString()
+ out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString()
<< "\n#\n";
if ( !title.empty() ) {
@@ -376,7 +376,7 @@ s_CreateAliasFilePriv(const string& file_name,
out << "\n";
if ( !gi_file_name.empty() ) {
_ASSERT(alias_type != eNoAliasFilterType);
- out << s_AliasFileFilterTypeToString(alias_type) << " "
+ out << s_AliasFileFilterTypeToString(alias_type) << " "
<< gi_file_name << "\n";
} else if (oid_range) {
out << "FIRST_OID " << oid_range->GetFrom() << "\n"
@@ -433,7 +433,7 @@ void CWriteDB_CreateAliasFile(const string& file_name,
fname << file_name << (is_prot ? ".pal" : ".nal");
ofstream out(((string)CNcbiOstrstreamToString(fname)).c_str());
- out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString()
+ out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString()
<< "\n#\n";
if ( !title.empty() ) {
@@ -471,8 +471,8 @@ void CWriteDB_CreateAliasFile(const string& file_name,
eNoAliasFilterType, &oid_range);
}
-void
-CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
+void
+CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
bool delete_source_alias_files /* = false */)
{
if (alias_files.empty()) {
@@ -483,7 +483,7 @@ CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
ofstream out(kSeqDBGroupAliasFileName.c_str());
out << "# Alias file index for " << CDir::GetCwd() << endl;
- out << "# Generated on " << CTime(CTime::eCurrent).AsString() << " by "
+ out << "# Generated on " << CTime(CTime::eCurrent).AsString() << " by "
<< NCBI_CURRENT_FUNCTION << endl;
out << "#" << endl;
@@ -513,7 +513,7 @@ CWriteDB_ConsolidateAliasFiles(const list<string>& alias_files,
}
}
-void
+void
CWriteDB_ConsolidateAliasFiles(bool delete_source_alias_files /* = false */)
{
list<string> alias_files;
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_files.cpp b/c++/src/objtools/blast/seqdb_writer/writedb_files.cpp
index 67933e8..b5241fd 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_files.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_files.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_files.cpp 214595 2010-12-06 20:24:17Z maning $
+/* $Id: writedb_files.cpp 446663 2014-09-17 14:36:30Z rackerst $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// class for WriteDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb_files.cpp 214595 2010-12-06 20:24:17Z maning $";
+static char const rcsid[] = "$Id: writedb_files.cpp 446663 2014-09-17 14:36:30Z rackerst $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -113,16 +113,24 @@ CWriteDB_File::CWriteDB_File(const string & basename,
m_Offset (0),
m_MaxFileSize(max_file_size)
{
+ // Define number of usable bits in m_Offset,
+ // deducting one for the sign bit.
+ static const int MAX_OFFSET_BITS = (sizeof m_Offset * 8) - 1;
+ // Define maximum allowed max_file_size.
+ static const Uint8 MAX_FILE_SIZE = (1L << MAX_OFFSET_BITS) - 1L;
+
if (m_MaxFileSize == 0) {
m_MaxFileSize = x_DefaultByteLimit();
+ } else {
+ _ASSERT(max_file_size <= MAX_FILE_SIZE);
}
-
+
m_Nul.resize(1);
m_Nul[0] = (char) 0;
-
+
m_UseIndex = (index >= 0);
x_MakeFileName();
-
+
if (always_create) {
Create();
}
@@ -137,9 +145,16 @@ void CWriteDB_File::Create()
int CWriteDB_File::Write(const CTempString & data)
{
+ // Define number of usable bits in m_Offset,
+ // deducting one for the sign bit.
+ static const int MAX_OFFSET_BITS = (sizeof m_Offset * 8) - 1;
+ // Define maximum allowed max_file_size.
+ static const Uint8 MAX_OFFSET = (1L << MAX_OFFSET_BITS) - 1L;
+
_ASSERT(m_Created);
+ _ASSERT(((Uint8) m_Offset + data.length()) <= MAX_OFFSET);
m_RealFile.write(data.data(), data.length());
-
+
m_Offset += data.length();
return m_Offset;
}
@@ -147,12 +162,12 @@ int CWriteDB_File::Write(const CTempString & data)
string CWriteDB_File::MakeShortName(const string & base, int index)
{
ostringstream fns;
-
+
fns << base;
fns << ".";
fns << (index / 10);
fns << (index % 10);
-
+
return fns.str();
}
@@ -163,7 +178,7 @@ void CWriteDB_File::x_MakeFileName()
} else {
m_Fname = m_BaseName;
}
-
+
m_Fname += ".";
m_Fname += m_Extension;
}
@@ -179,11 +194,11 @@ void CWriteDB_File::Close()
void CWriteDB_File::RenameSingle()
{
_ASSERT(m_UseIndex == true);
-
+
string nm1 = m_Fname;
m_UseIndex = false;
x_MakeFileName();
-
+
CDirEntry fn1(nm1);
fn1.Rename(m_Fname, CDirEntry::fRF_Overwrite);
}
@@ -208,16 +223,16 @@ CWriteDB_IndexFile::CWriteDB_IndexFile(const string & dbname,
m_MaxLength (0)
{
// Compute index overhead, rounding up.
-
+
m_Overhead = x_Overhead(title, date);
m_Overhead = s_RoundUp(m_Overhead, 8);
m_DataSize = m_Overhead;
-
+
// The '1' added to the sequence offset array refers to the fact
// that sequence files contain an initial NUL byte. This seems to
// be for the benefit of the protein database scanning code, but
// it is also done for nucleotide databases.
-
+
m_Hdr.push_back(0);
m_Seq.push_back(1);
}
@@ -231,26 +246,26 @@ int CWriteDB_IndexFile::x_Overhead(const string & T,
void CWriteDB_IndexFile::x_Flush()
{
_ASSERT(m_Created);
-
+
int format_version = 4;
int seq_type = (m_Protein ? 1 : 0);
-
+
// Pad the date string (see comments at top.)
-
+
string pad_date = m_Date;
int count = 0;
-
+
while(x_Overhead(m_Title, pad_date) & 0x7) {
pad_date.append(m_Nul);
if (count != -1) {
_ASSERT(count++ < 8);
}
}
-
+
// Write header
-
+
ostream & F = m_RealFile;
-
+
s_WriteInt4 (F, format_version);
s_WriteInt4 (F, seq_type);
s_WriteString(F, m_Title);
@@ -258,20 +273,20 @@ void CWriteDB_IndexFile::x_Flush()
s_WriteInt4 (F, m_OIDs);
s_WriteInt8LE(F, m_Letters);
s_WriteInt4 (F, m_MaxLength);
-
+
for(unsigned i = 0; i < m_Hdr.size(); i++) {
s_WriteInt4(F, m_Hdr[i]);
}
-
+
for(unsigned i = 0; i < m_Seq.size(); i++) {
s_WriteInt4(F, m_Seq[i]);
}
-
+
// Should loop m_OID times, or not at all.
for(unsigned i = 0; i < m_Amb.size(); i++) {
s_WriteInt4(F, m_Amb[i]);
}
-
+
// This extra index is added here because formatdb adds it. SeqDB
// depends on its existence, but I don't think anyone reads (or
// needs) the data. The last offset in the ambiguity column
@@ -279,7 +294,7 @@ void CWriteDB_IndexFile::x_Flush()
// to the last offset in the sequence column. But the last
// sequence offset is not really a sequence start, it is the
// 'extra' offset used by sequence length computations.
-
+
if (m_Amb.size()) {
s_WriteInt4(F, m_Seq.back());
}
@@ -321,7 +336,7 @@ CWriteDB_SequenceFile::CWriteDB_SequenceFile(const string & dbname,
// The first null written here is for nucleotide sequences.
// It doesn't seem necessary, but formatdb provides it, so I
// will too.
-
+
WriteWithNull(string());
}
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_gimask.cpp b/c++/src/objtools/blast/seqdb_writer/writedb_gimask.cpp
index 14e4de9..b265bcd 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_gimask.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_gimask.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_gimask.cpp 177347 2009-11-30 18:43:57Z maning $
+/* $Id: writedb_gimask.cpp 480969 2015-10-06 12:05:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Implementation for the CWriteDB_GiMask and related classes.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb_gimask.cpp 177347 2009-11-30 18:43:57Z maning $";
+static char const rcsid[] = "$Id: writedb_gimask.cpp 480969 2015-10-06 12:05:12Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -72,7 +72,7 @@ void CWriteDB_GiMask::ListFiles(vector<string> & files) const
files.push_back(m_DFile_LE->GetFilename());
}
-void CWriteDB_GiMask::AddGiMask(const vector<int> & GIs,
+void CWriteDB_GiMask::AddGiMask(const vector<TGi> & GIs,
const TPairVector & mask)
{
if (!m_DFile->CanFit(mask.size())) {
@@ -87,8 +87,8 @@ void CWriteDB_GiMask::AddGiMask(const vector<int> & GIs,
m_DFile->WriteMask(mask);
m_DFile_LE->WriteMask(mask);
- ITERATE(vector<int>, gi, GIs) {
- m_GiOffset.push_back(pair<int, TOffset> (*gi, offset));
+ ITERATE(vector<TGi>, gi, GIs) {
+ m_GiOffset.push_back(pair<TGi, TOffset> (*gi, offset));
}
}
@@ -131,7 +131,7 @@ CWriteDB_GiMaskOffset(const string & maskname,
const string & extn,
Uint8 max_file_size,
bool le)
- : CWriteDB_File (maskname, extn, -1, max_file_size, false),
+ : CWriteDB_File (maskname, extn, -1, max_file_size, false),
m_UseLE (le)
{ }
@@ -139,14 +139,25 @@ void CWriteDB_GiMaskOffset::AddGIs(const TGiOffset & gi_offset)
{
CBlastDbBlob gis(kPageSize * kGISize);
CBlastDbBlob offsets(kPageSize * kOffsetSize);
-
+
if ( ! m_Created) {
Create();
}
int i = 0;
ITERATE(TGiOffset, iter, gi_offset) {
- if (m_UseLE ) {
+#ifdef NCBI_INT8_GI
+ if (m_UseLE) {
+ gis.WriteInt4_LE(GI_TO(int, iter->first));
+ offsets.WriteInt4_LE(iter->second.first);
+ offsets.WriteInt4_LE(iter->second.second);
+ } else {
+ gis.WriteInt4(GI_TO(int, iter->first));
+ offsets.WriteInt4(iter->second.first);
+ offsets.WriteInt4(iter->second.second);
+ }
+#else
+ if (m_UseLE) {
gis.WriteInt4_LE(iter->first);
offsets.WriteInt4_LE(iter->second.first);
offsets.WriteInt4_LE(iter->second.second);
@@ -155,9 +166,10 @@ void CWriteDB_GiMaskOffset::AddGIs(const TGiOffset & gi_offset)
offsets.WriteInt4(iter->second.first);
offsets.WriteInt4(iter->second.second);
}
-
+#endif
+
++i;
-
+
if (i== kPageSize) {
Write(gis.Str());
Write(offsets.Str());
@@ -190,7 +202,7 @@ CWriteDB_GiMaskIndex(const string & maskname,
m_Date = CTime(CTime::eCurrent).AsString();
}
-void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
+void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
int num_vols)
{
m_NumGIs = gi_offset.size();
@@ -198,7 +210,7 @@ void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
CBlastDbBlob gis(m_NumIndex * kGISize);
CBlastDbBlob offsets(m_NumIndex * kOffsetSize);
-
+
if ( ! m_Created) {
Create();
}
@@ -213,7 +225,18 @@ void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
}
++i;
-
+
+#ifdef NCBI_INT8_GI
+ if (m_UseLE ) {
+ gis.WriteInt4_LE(GI_TO(int, iter->first));
+ offsets.WriteInt4_LE(iter->second.first);
+ offsets.WriteInt4_LE(iter->second.second);
+ } else {
+ gis.WriteInt4(GI_TO(int, iter->first));
+ offsets.WriteInt4(iter->second.first);
+ offsets.WriteInt4(iter->second.second);
+ }
+#else
if (m_UseLE ) {
gis.WriteInt4_LE(iter->first);
offsets.WriteInt4_LE(iter->second.first);
@@ -223,6 +246,7 @@ void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
offsets.WriteInt4(iter->second.first);
offsets.WriteInt4(iter->second.second);
}
+#endif
++m_NumIndex;
}
@@ -234,7 +258,7 @@ void CWriteDB_GiMaskIndex::AddGIs(const TGiOffset & gi_offset,
void CWriteDB_GiMaskIndex::x_BuildHeaderFields(int num_vols)
{
const int kFormatVersion = 1; // SeqDB has one of these.
-
+
CBlastDbBlob header;
header.WriteInt4(kFormatVersion);
@@ -252,7 +276,7 @@ void CWriteDB_GiMaskIndex::x_BuildHeaderFields(int num_vols)
Int4 size = header.GetWriteOffset();
header.WriteInt4(size, 28);
- Write(header.Str());
+ Write(header.Str());
}
// CWriteDB_GiMaskData
@@ -270,7 +294,7 @@ CWriteDB_GiMaskData::CWriteDB_GiMaskData(const string & maskname,
void CWriteDB_GiMaskData::WriteMask(const TPairVector & mask)
{
-
+
if (! mask.size()) return;
if (! m_Created) Create();
@@ -291,7 +315,7 @@ void CWriteDB_GiMaskData::WriteMask(const TPairVector & mask)
}
}
- Write(data.Str());
+ Write(data.Str());
m_DataLength += (1+2*mask.size()) * 4;
}
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_gimask.hpp b/c++/src/objtools/blast/seqdb_writer/writedb_gimask.hpp
index 162d5e6..3ae9d13 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_gimask.hpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_gimask.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_GIMASK_HPP
#define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_GIMASK_HPP
-/* $Id: writedb_gimask.hpp 200354 2010-08-06 17:58:25Z camacho $
+/* $Id: writedb_gimask.hpp 480969 2015-10-06 12:05:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
/// Code for gi-based database mask file construction.
///
/// Defines classes:
-/// CWriteDB_GiMaskIndex, CWriteDB_GiMaskOffset, CWriteDB_GiMaskData,
+/// CWriteDB_GiMaskIndex, CWriteDB_GiMaskOffset, CWriteDB_GiMaskData,
/// and CWriteDB_GiMask
///
/// Implemented for: UNIX, MS-Windows
@@ -50,7 +50,7 @@ USING_SCOPE(objects);
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// CWriteDB_GiMaskData class
-///
+///
/// Manufacture gi based mask data files from input data.
class CWriteDB_GiMaskData : public CWriteDB_File {
@@ -69,10 +69,10 @@ public:
int index,
Uint8 max_file_size,
bool le = false);
-
+
/// Destructor.
~CWriteDB_GiMaskData() { };
-
+
/// Write a new data blob.
/// @param mask Mask data to write.
void WriteMask(const TPairVector & mask);
@@ -85,11 +85,11 @@ public:
/// Get current index/offset pair
/// @return The current volume index and offset in byte
- TOffset GetOffset() const
+ TOffset GetOffset() const
{
return pair<int, int>(m_Index, m_DataLength);
}
-
+
/// Tests whether there is room for another batch
/// @param the number of masks to be added. [in]
/// @return Return TRUE if masks can fit into the volume.
@@ -107,21 +107,21 @@ private:
/// Current index
int m_Index;
-
+
/// Flush any stored data.
void x_Flush() { };
};
/// CWriteDB_GiMaskOffset class
-///
+///
/// Manufacture gi based mask offset files from input data.
class CWriteDB_GiMaskOffset : public CWriteDB_File {
public:
typedef pair<int, int> TOffset;
- typedef vector< pair<int, TOffset> > TGiOffset;
-
+ typedef vector< pair<TGi, TOffset> > TGiOffset;
+
/// Constructor for gimask offset file.
///
/// @param maskname Database name (same for all volumes).
@@ -132,7 +132,7 @@ public:
const string & extn,
Uint8 max_file_size,
bool le = false);
-
+
/// Destructor.
~CWriteDB_GiMaskOffset() {};
@@ -140,26 +140,26 @@ public:
///
/// @param gi_offset GI->offset array [in]
void AddGIs(const TGiOffset &gi_offset);
-
+
protected:
- /// Size of a GI
+ /// Size of a GI
static const int kGISize = 4;
/// Size of offset entry
static const int kOffsetSize = 8;
-
+
/// Page size
static const int kPageSize = 512;
/// Flush offset data in preparation for Close().
void x_Flush() { };
-
+
/// Use little endian?
bool m_UseLE;
};
/// CWriteDB_GiMaskIndex class
-///
+///
/// Manufacture gimask index files from input data.
class CWriteDB_GiMaskIndex : public CWriteDB_GiMaskOffset {
@@ -168,7 +168,7 @@ public:
///
/// @param maskname Database name (same for all volumes).
/// @param extn File extension to use for index file.
- /// @param desc Description of the mask algo
+ /// @param desc Description of the mask algo
/// @param max_file_size Maximum size in bytes for component files.
/// @param le Use little endian format
CWriteDB_GiMaskIndex(const string & maskname,
@@ -176,7 +176,7 @@ public:
const string & desc,
Uint8 max_file_size,
bool le = false);
-
+
/// Destructor.
~CWriteDB_GiMaskIndex() {};
@@ -185,21 +185,21 @@ public:
/// @param gi_offset GI->offset array [in]
/// @param num_vols Number of volumes [in]
void AddGIs(const TGiOffset &gi_offset, int num_vols);
-
+
private:
/// String format used by gimask files.
static const CBlastDbBlob::EStringFormat
kStringFmt = CBlastDbBlob::eSizeVar;
-
+
/// Build fixed length header fields.
void x_BuildHeaderFields(int num_vols);
-
+
/// Creation timestamp for this gimask.
string m_Date;
-
+
/// Description of this gimask.
string m_Desc;
-
+
/// Number of GIs
Int4 m_NumGIs;
@@ -219,7 +219,7 @@ class CWriteDB_GiMask : public CObject {
public:
typedef vector< pair<TSeqPos, TSeqPos> > TPairVector;
typedef pair<int, int> TOffset;
- typedef vector< pair<int, TOffset> > TGiOffset;
+ typedef vector< pair<TGi, TOffset> > TGiOffset;
/// Construct WriteDB style database gimask.
/// @param maskname Name of the mask data
@@ -227,13 +227,13 @@ public:
CWriteDB_GiMask(const string & maskname,
const string & desc,
Uint8 max_file_size);
-
+
/// Destructor.
~CWriteDB_GiMask() {};
-
+
/// Flush data to disk and close all associated files.
void Close();
-
+
/// List Filenames
///
/// Returns a list of the files constructed by this class; the
@@ -246,17 +246,17 @@ public:
void ListFiles(vector<string> & files) const;
/// Get Mask Name
- ///
+ ///
/// Returns the name of the mask
const string & GetName() const {
return m_MaskName;
}
-
+
/// Add a mask data for a sequence represented by a set of GIs.
///
/// @param GIs The GIs of the sequence
/// @param masks The masks represented as ranges
- void AddGiMask(const vector<int> & GIs,
+ void AddGiMask(const vector<TGi> & GIs,
const TPairVector & masks);
private:
@@ -270,7 +270,7 @@ private:
/// Offset file
CRef<CWriteDB_GiMaskOffset> m_OFile;
CRef<CWriteDB_GiMaskOffset> m_OFile_LE; // little endian
-
+
/// Index file
CRef<CWriteDB_GiMaskIndex> m_IFile;
CRef<CWriteDB_GiMaskIndex> m_IFile_LE; // little endian
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp b/c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp
index eb5781a..82d6750 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_impl.cpp 439070 2014-06-25 13:48:56Z fongah2 $
+/* $Id: writedb_impl.cpp 480972 2015-10-06 12:06:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// class for WriteDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb_impl.cpp 439070 2014-06-25 13:48:56Z fongah2 $";
+static char const rcsid[] = "$Id: writedb_impl.cpp 480972 2015-10-06 12:06:22Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -79,14 +79,14 @@ CWriteDB_Impl::CWriteDB_Impl(const string & dbname,
m_HaveSequence (false)
{
CTime now(CTime::eCurrent);
-
+
m_Date = now.AsString("b d, Y ");
string t = now.AsString("H:m P");
-
+
if (t[0] == '0') {
t.assign(t, 1, t.size() - 1);
}
-
+
m_Date += t;
}
@@ -111,11 +111,11 @@ void CWriteDB_Impl::x_ResetSequenceData()
m_Pig = 0;
m_Hash = 0;
m_SeqLength = 0;
-
+
m_Sequence.erase();
m_Ambig.erase();
m_BinHdr.erase();
-
+
NON_CONST_ITERATE(vector<int>, iter, m_HaveBlob) {
*iter = 0;
}
@@ -132,17 +132,17 @@ void CWriteDB_Impl::AddSequence(const CTempString & seq,
{
// Publish previous sequence (if any)
x_Publish();
-
+
// Blank slate for new sequence.
x_ResetSequenceData();
-
+
m_Sequence.assign(seq.data(), seq.length());
m_Ambig.assign(ambig.data(), ambig.length());
-
+
if (m_Indices & CWriteDB::eAddHash) {
x_ComputeHash(seq, ambig);
}
-
+
x_SetHaveSequence();
}
@@ -150,10 +150,10 @@ void CWriteDB_Impl::AddSequence(const CBioseq & bs)
{
// Publish previous sequence
x_Publish();
-
+
// Blank slate for new sequence.
x_ResetSequenceData();
-
+
m_Bioseq.Reset(& bs);
if (m_Bioseq->GetInst().CanGetMol() && (m_Bioseq->IsAa() != m_Protein)) {
CNcbiOstrstream msg;
@@ -162,11 +162,11 @@ void CWriteDB_Impl::AddSequence(const CBioseq & bs)
<< "); expected " << (m_Protein ? "protein" : "nucleotide");
NCBI_THROW(CWriteDBException, eArgErr, CNcbiOstrstreamToString(msg));
}
-
+
if (m_Indices & CWriteDB::eAddHash) {
x_ComputeHash(bs);
}
-
+
x_SetHaveSequence();
}
@@ -193,8 +193,8 @@ class CWriteDB_IsamKey {
CNcbiIfstream * source;
// constructor
- CWriteDB_IsamKey(const string &fn) {
- source = new CNcbiIfstream(fn.c_str(),
+ CWriteDB_IsamKey(const string &fn) {
+ source = new CNcbiIfstream(fn.c_str(),
IOS_BASE::in | IOS_BASE::binary);
key = x_GetNextKey();
};
@@ -252,11 +252,11 @@ CWriteDB_IsamKey<string>::x_GetNextKey() {
while (*p != 0x02) ++p;
string in(s, p);
- // check if the current key is PDB-like,
+ // check if the current key is PDB-like,
// if so, advance for the next
// PDB key must be [0-9]...
- if ( (in.size() == 4)
- && ((in[0] - '0') * (in[0] - '9') <= 0) ) {
+ if ( (in.size() == 4)
+ && ((in[0] - '0') * (in[0] - '9') <= 0) ) {
// probing the next key to make sure this is pdb id
char next_token[4];
@@ -272,60 +272,60 @@ CWriteDB_IsamKey<string>::x_GetNextKey() {
return in;
};
-/// Comparison function for set<CWriteDB_IsamKey<T> *>
-template <class T>
-struct CWriteDB_IsamKey_Compare {
- bool operator() (const CWriteDB_IsamKey<T> * lhs,
- const CWriteDB_IsamKey<T> * rhs) const {
- return (*lhs < *rhs);
- }
-};
-
-/// Check for duplicate ids across volumes
-template <class T>
-static void s_CheckDuplicateIds(set<CWriteDB_IsamKey<T> *,
- CWriteDB_IsamKey_Compare<T> > & keys) {
- while (!keys.empty()) {
- // pick the smallest key
- CWriteDB_IsamKey<T> * key = *(keys.begin());
-
- keys.erase(key);
-
- if (keys.empty()) {
- delete key;
- return;
- }
-
- const CWriteDB_IsamKey<T> * next = *(keys.begin());
- if (key->AdvanceKey(*next)) {
+/// Comparison function for set<CWriteDB_IsamKey<T> *>
+template <class T>
+struct CWriteDB_IsamKey_Compare {
+ bool operator() (const CWriteDB_IsamKey<T> * lhs,
+ const CWriteDB_IsamKey<T> * rhs) const {
+ return (*lhs < *rhs);
+ }
+};
+
+/// Check for duplicate ids across volumes
+template <class T>
+static void s_CheckDuplicateIds(set<CWriteDB_IsamKey<T> *,
+ CWriteDB_IsamKey_Compare<T> > & keys) {
+ while (!keys.empty()) {
+ // pick the smallest key
+ CWriteDB_IsamKey<T> * key = *(keys.begin());
+
+ keys.erase(key);
+
+ if (keys.empty()) {
+ delete key;
+ return;
+ }
+
+ const CWriteDB_IsamKey<T> * next = *(keys.begin());
+ if (key->AdvanceKey(*next)) {
if (keys.find(key) != keys.end()) {
CNcbiOstrstream msg;
msg << "Error: Duplicate seq_id <"
<< key->key
<< "> is found multiple times across volumes.";
NCBI_THROW(CWriteDBException, eArgErr, CNcbiOstrstreamToString(msg));
- }
- keys.insert(key);
- } else {
- delete key;
- }
- }
-};
+ }
+ keys.insert(key);
+ } else {
+ delete key;
+ }
+ }
+};
void CWriteDB_Impl::Close()
{
if (m_Closed)
return;
-
+
m_Closed = true;
-
+
x_Publish();
m_Sequence.erase();
m_Ambig.erase();
-
+
if (! m_Volume.Empty()) {
m_Volume->Close();
-
+
if (m_UseGiMask) {
for (unsigned int i=0; i<m_GiMasks.size(); ++i) {
m_GiMasks[i]->Close();
@@ -334,10 +334,10 @@ void CWriteDB_Impl::Close()
if (m_VolumeList.size() == 1) {
m_Volume->RenameSingle();
- }
+ }
// disable the check for duplicate ids across volumes
- /*
+ /*
else if (m_Indices != CWriteDB::eNoIndex) {
set<CWriteDB_IsamKey<string> *, CWriteDB_IsamKey_Compare<string> > sids;
ITERATE(vector< CRef<CWriteDB_Volume> >, iter, m_VolumeList) {
@@ -361,7 +361,7 @@ void CWriteDB_Impl::Close()
if (m_VolumeList.size() > 1 || m_UseGiMask) {
x_MakeAlias();
}
-
+
m_Volume.Reset();
}
}
@@ -378,13 +378,13 @@ void CWriteDB_Impl::x_MakeAlias()
for(unsigned i = 0; i < m_VolumeList.size(); i++) {
if (dblist.size())
dblist += " ";
-
+
dblist += CDirEntry(CWriteDB_File::MakeShortName(m_Dbname, i)).GetName();
}
} else {
dblist = m_Dbname;
}
-
+
string masklist("");
if (m_UseGiMask) {
for (unsigned i = 0; i < m_GiMasks.size(); i++) {
@@ -396,9 +396,9 @@ void CWriteDB_Impl::x_MakeAlias()
}
string nm = x_MakeAliasName();
-
+
ofstream alias(nm.c_str());
-
+
alias << "#\n# Alias file created: " << m_Date << "\n#\n"
<< "TITLE " << m_Title << "\n"
<< "DBLIST " << dblist << "\n";
@@ -414,25 +414,25 @@ void CWriteDB_Impl::x_GetBioseqBinaryHeader(const CBioseq & bioseq,
if (! bin_hdr.empty()) {
return;
}
-
+
if (! bioseq.CanGetDescr()) {
return;
}
-
+
// Getting the binary headers, when they exist, is probably faster
// than building new deflines from the 'visible' CBioseq parts.
-
+
vector< vector< char >* > bindata;
-
+
ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) {
if ((**iter).IsUser()) {
const CUser_object & uo = (**iter).GetUser();
const CObject_id & oi = uo.GetType();
-
+
if (oi.IsStr() && oi.GetStr() == kAsnDeflineObjLabel) {
if (uo.CanGetData()) {
const vector< CRef< CUser_field > > & D = uo.GetData();
-
+
if (D.size() &&
D[0].NotEmpty() &&
D[0]->CanGetLabel() &&
@@ -440,7 +440,7 @@ void CWriteDB_Impl::x_GetBioseqBinaryHeader(const CBioseq & bioseq,
D[0]->GetLabel().GetStr() == kAsnDeflineObjLabel &&
D[0]->CanGetData() &&
D[0]->GetData().IsOss()) {
-
+
bindata = D[0]->GetData().GetOss();
break;
}
@@ -448,11 +448,11 @@ void CWriteDB_Impl::x_GetBioseqBinaryHeader(const CBioseq & bioseq,
}
}
}
-
+
if (! bindata.empty()) {
if (bindata[0] && (! bindata[0]->empty())) {
vector<char> & b = *bindata[0];
-
+
bin_hdr.assign(& b[0], b.size());
}
}
@@ -475,29 +475,29 @@ s_CheckEmptyLists(CRef<CBlast_def_line_set> & deflines, bool owner)
{
CBlast_def_line_set * bdls = 0;
CConstRef<CBlast_def_line_set> here(&*deflines);
-
+
if (! owner) {
here = s_EditDeflineSet(here);
return;
}
-
+
bdls = const_cast<CBlast_def_line_set*>(here.GetPointer());
-
+
NON_CONST_ITERATE(list< CRef< CBlast_def_line > >, iter, bdls->Set()) {
CRef<CBlast_def_line> defline = *iter;
if (defline->CanGetMemberships() &&
defline->GetMemberships().size() == 0) {
-
+
defline->ResetMemberships();
}
-
+
if (defline->CanGetLinks() &&
defline->GetLinks().size() == 0) {
-
+
defline->ResetLinks();
}
}
-
+
deflines.Reset(bdls);
}
@@ -511,15 +511,15 @@ CWriteDB_Impl::x_BuildDeflinesFromBioseq(const CBioseq & bioseq
if (! (bioseq.CanGetDescr() && bioseq.CanGetId())) {
return;
}
-
+
vector<int> taxids;
string titles;
-
+
// Scan the CBioseq for taxids and the title string.
-
+
ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) {
const CSeqdesc & desc = **iter;
-
+
if (desc.IsTitle()) {
//defline->SetTitle((**iter)->GetTitle());
titles = (**iter).GetTitle();
@@ -537,12 +537,12 @@ CWriteDB_Impl::x_BuildDeflinesFromBioseq(const CBioseq & bioseq
ITERATE(vector< CRef< CDbtag > >,
dbiter,
org_pt->GetDb()) {
-
+
if ((**dbiter).CanGetDb() &&
(**dbiter).GetDb() == "taxon") {
-
+
const CObject_id & oi = (**dbiter).GetTag();
-
+
if (oi.IsId()) {
//defline->SetTaxid(oi.GetId());
taxids.push_back(oi.GetId());
@@ -552,48 +552,48 @@ CWriteDB_Impl::x_BuildDeflinesFromBioseq(const CBioseq & bioseq
}
}
}
-
+
// The bioseq has a field contianing the ids for the first
// defline. The title string contains the title for the first
// defline, plus all the other defline titles and ids. This code
// unpacks them and builds a normal blast defline set.
-
+
list< CRef<CSeq_id> > ids = bioseq.GetId();
-
+
unsigned taxid_i(0), mship_i(0), links_i(0);
bool used_pig(false);
-
+
// Build the deflines.
-
+
CRef<CBlast_def_line_set> bdls(new CBlast_def_line_set);
CRef<CBlast_def_line> defline;
-
+
while(! ids.empty()) {
defline.Reset(new CBlast_def_line);
-
+
defline->SetSeqid() = ids;
ids.clear();
-
+
/*
size_t pos = titles.find(" >");
string T;
-
+
if (pos != titles.npos) {
T.assign(titles, 0, pos);
titles.erase(0, pos + 2);
-
+
pos = titles.find(" ");
string nextid;
-
+
if (pos != titles.npos) {
nextid.assign(titles, 0, pos);
titles.erase(0, pos + 1);
} else {
nextid.swap(titles);
}
-
+
// Parse '|' seperated ids.
- if ( nextid.find('|') == NPOS
+ if ( nextid.find('|') == NPOS
|| !isalpha((unsigned char)(nextid[0]))) {
ids.push_back(CRef<CSeq_id> (new CSeq_id(CSeq_id::e_Local, nextid)));
} else {
@@ -609,25 +609,25 @@ CWriteDB_Impl::x_BuildDeflinesFromBioseq(const CBioseq & bioseq
if (taxid_i < taxids.size()) {
defline->SetTaxid(taxids[taxid_i++]);
}
-
+
if (mship_i < membbits.size()) {
const vector<int> & V = membbits[mship_i++];
defline->SetMemberships().assign(V.begin(), V.end());
}
-
+
if (links_i < linkouts.size()) {
const vector<int> & V = linkouts[mship_i++];
defline->SetLinks().assign(V.begin(), V.end());
}
-
+
if ((! used_pig) && pig) {
defline->SetOther_info().push_back(pig);
used_pig = true;
}
-
+
bdls->Set().push_back(defline);
}
-
+
s_CheckEmptyLists(bdls, true);
deflines = bdls;
}
@@ -637,10 +637,10 @@ x_SetDeflinesFromBinary(const string & bin_hdr,
CConstRef<CBlast_def_line_set> & deflines)
{
CRef<CBlast_def_line_set> bdls(new CBlast_def_line_set);
-
+
istringstream iss(bin_hdr);
iss >> MSerial_AsnBinary >> *bdls;
-
+
s_CheckEmptyLists(bdls, true);
deflines.Reset(&* bdls);
}
@@ -679,29 +679,29 @@ CWriteDB_Impl::x_ExtractDeflines(CConstRef<CBioseq> & bioseq,
bool parse_ids)
{
bool use_bin = (deflines.Empty() && pig == 0);
-
+
if (! bin_hdr.empty() && OID<0) {
return;
}
-
+
if (deflines.Empty()) {
// Use bioseq if deflines are not provided.
-
+
if (bioseq.Empty()) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Cannot find CBioseq or deflines.");
}
-
+
// CBioseq objects from SeqDB have binary headers embedded in
// them. If these are found, we try to use them. However,
// using binary headers may not help us much if we also want
// lists of sequence identifiers (for building ISAM files).
-
+
if (use_bin) {
x_GetBioseqBinaryHeader(*bioseq, bin_hdr);
}
-
+
if (bin_hdr.empty()) {
x_GetFastaReaderDeflines(*bioseq,
deflines,
@@ -711,7 +711,7 @@ CWriteDB_Impl::x_ExtractDeflines(CConstRef<CBioseq> & bioseq,
false,
parse_ids);
}
-
+
if(!s_UseFastaReaderDeflines(bioseq, deflines)) {
deflines.Reset();
}
@@ -724,37 +724,37 @@ CWriteDB_Impl::x_ExtractDeflines(CConstRef<CBioseq> & bioseq,
pig);
}
}
-
+
if (bin_hdr.empty() &&
(deflines.Empty() || deflines->Get().empty())) {
-
+
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: No deflines provided.");
}
-
+
if (pig != 0) {
const list<int> * L = 0;
-
+
if (deflines->Get().front()->CanGetOther_info()) {
L = & deflines->Get().front()->GetOther_info();
}
-
+
// If the pig does not agree with the current value, set the
// new value and force a rebuild of the binary headers. If
// there is more than one value in the list, leave the others
// in place.
-
+
if ((L == 0) || L->empty()) {
CRef<CBlast_def_line_set> bdls = s_EditDeflineSet(deflines);
bdls->Set().front()->SetOther_info().push_back(pig);
-
+
deflines.Reset(&* bdls);
bin_hdr.erase();
} else if (L->front() != pig) {
CRef<CBlast_def_line_set> bdls = s_EditDeflineSet(deflines);
bdls->Set().front()->SetOther_info().front() = pig;
-
+
deflines.Reset(&* bdls);
bin_hdr.erase();
}
@@ -767,21 +767,21 @@ CWriteDB_Impl::x_ExtractDeflines(CConstRef<CBioseq> & bioseq,
gnl_id->SetGeneral().SetTag().SetId(OID);
CRef<CBlast_def_line_set> bdls = s_EditDeflineSet(deflines);
bdls->Set().front()->SetSeqid().front() = gnl_id;
-
+
deflines.Reset(&* bdls);
}
-
+
if (bin_hdr.empty() || OID>=0) {
// Compress the deflines to binary.
-
+
ostringstream oss;
oss << MSerial_AsnBinary << *deflines;
bin_hdr = oss.str();
}
-
+
if (deflines.Empty() && (! bin_hdr.empty())) {
// Uncompress the deflines from binary.
-
+
x_SetDeflinesFromBinary(bin_hdr, deflines);
}
}
@@ -807,17 +807,17 @@ void CWriteDB_Impl::x_CookIds()
if (! m_Ids.empty()) {
return;
}
-
+
if (m_Deflines.Empty()) {
if (m_BinHdr.empty()) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Cannot find IDs or deflines.");
}
-
+
x_SetDeflinesFromBinary(m_BinHdr, m_Deflines);
}
-
+
ITERATE(list< CRef<CBlast_def_line> >, iter, m_Deflines->Get()) {
const list< CRef<CSeq_id> > & ids = (**iter).GetSeqid();
// m_Ids.insert(m_Ids.end(), ids.begin(), ids.end());
@@ -849,18 +849,18 @@ int CWriteDB_Impl::x_ComputeSeqLength()
} else if (! (m_Bioseq &&
m_Bioseq->CanGetInst() &&
m_Bioseq->GetInst().GetLength())) {
-
+
NCBI_THROW(CWriteDBException,
eArgErr,
"Need sequence data.");
}
-
+
if (m_Bioseq.NotEmpty()) {
const CSeq_inst & si = m_Bioseq->GetInst();
m_SeqLength = si.GetLength();
}
}
-
+
return m_SeqLength;
}
@@ -868,41 +868,41 @@ void CWriteDB_Impl::x_CookSequence()
{
if (! m_Sequence.empty())
return;
-
+
if (! (m_Bioseq.NotEmpty() && m_Bioseq->CanGetInst())) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Need sequence data.");
}
-
+
const CSeq_inst & si = m_Bioseq->GetInst();
-
+
if (m_Bioseq->GetInst().CanGetSeq_data()) {
const CSeq_data & sd = si.GetSeq_data();
-
+
string msg;
-
+
switch(sd.Which()) {
case CSeq_data::e_Ncbistdaa:
WriteDB_StdaaToBinary(si, m_Sequence);
break;
-
+
case CSeq_data::e_Ncbieaa:
WriteDB_EaaToBinary(si, m_Sequence);
break;
-
+
case CSeq_data::e_Iupacaa:
WriteDB_IupacaaToBinary(si, m_Sequence);
break;
-
+
case CSeq_data::e_Ncbi2na:
WriteDB_Ncbi2naToBinary(si, m_Sequence);
break;
-
+
case CSeq_data::e_Ncbi4na:
WriteDB_Ncbi4naToBinary(si, m_Sequence, m_Ambig);
break;
-
+
case CSeq_data::e_Iupacna:
WriteDB_IupacnaToBinary(si, m_Sequence, m_Ambig);
break;
@@ -912,42 +912,42 @@ void CWriteDB_Impl::x_CookSequence()
msg += NStr::IntToString((int) sd.Which());
msg += "].";
}
-
+
if (! msg.empty()) {
NCBI_THROW(CWriteDBException, eArgErr, msg);
}
} else {
int sz = m_SeqVector.size();
-
+
if (sz == 0) {
NCBI_THROW(CWriteDBException,
eArgErr,
"No sequence data in Bioseq, "
"and no Bioseq_Handle available.");
}
-
+
if (m_Protein) {
// I add one to the string length to allow the "i+1" in
// the loop to be done safely.
-
+
m_Sequence.reserve(sz);
m_SeqVector.GetSeqData(0, sz, m_Sequence);
} else {
// I add one to the string length to allow the "i+1" in the
// loop to be done safely.
-
+
string na8;
na8.reserve(sz + 1);
m_SeqVector.GetSeqData(0, sz, na8);
na8.resize(sz + 1);
-
+
string na4;
na4.resize((sz + 1) / 2);
-
+
for(int i = 0; i < sz; i += 2) {
na4[i/2] = (na8[i] << 4) + na8[i+1];
}
-
+
WriteDB_Ncbi4naToBinary(na4.data(),
(int) na4.size(),
(int) si.GetLength(),
@@ -966,16 +966,16 @@ void CWriteDB_Impl::x_CookData()
{
// We need sequence, ambiguity, and binary deflines. If any of
// these is missing, it is created from other data if possible.
-
+
// For now I am disabling binary headers, because in normal usage
// I would expect to see sequences from ID1 or similar, and the
// non-binary case is slightly more complex.
-
+
x_CookHeader();
x_CookIds();
x_CookSequence();
x_CookColumns();
-
+
if (m_Protein && m_MaskedLetters.size()) {
x_MaskSequence();
}
@@ -1002,15 +1002,15 @@ void CWriteDB_Impl::x_Publish()
{
// This test should fail only on the first call, or if an
// exception was thrown.
-
+
if (x_HaveSequence()) {
_ASSERT(! (m_Bioseq.Empty() && m_Sequence.empty()));
-
+
x_ClearHaveSequence();
} else {
return;
}
-
+
x_CookData();
bool done = false;
@@ -1025,14 +1025,14 @@ void CWriteDB_Impl::x_Publish()
m_Blobs,
m_MaskDataColumn);
}
-
+
if (! done) {
int index = (int) m_VolumeList.size();
-
+
if (m_Volume.NotEmpty()) {
m_Volume->Close();
}
-
+
{
m_Volume.Reset(new CWriteDB_Volume(m_Dbname,
m_Protein,
@@ -1042,15 +1042,15 @@ void CWriteDB_Impl::x_Publish()
m_MaxFileSize,
m_MaxVolumeLetters,
m_Indices));
-
+
m_VolumeList.push_back(m_Volume);
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
_ASSERT(m_Blobs.size() == m_ColumnTitles.size() * 2);
_ASSERT(m_Blobs.size() == m_ColumnMetas.size() * 2);
_ASSERT(m_Blobs.size() == m_HaveBlob.size() * 2);
-
+
for(size_t i = 0; i < m_ColumnTitles.size(); i++) {
m_Volume->CreateColumn(m_ColumnTitles[i],
m_ColumnMetas[i],
@@ -1062,7 +1062,7 @@ void CWriteDB_Impl::x_Publish()
// need to reset OID, hense recalculate the header and id
x_CookHeader();
x_CookIds();
-
+
done = m_Volume->WriteSequence(m_Sequence,
m_Ambig,
m_BinHdr,
@@ -1071,7 +1071,7 @@ void CWriteDB_Impl::x_Publish()
m_Hash,
m_Blobs,
m_MaskDataColumn);
-
+
if (! done) {
NCBI_THROW(CWriteDBException,
eArgErr,
@@ -1084,7 +1084,7 @@ void CWriteDB_Impl::SetDeflines(const CBlast_def_line_set & deflines)
{
CRef<CBlast_def_line_set>
bdls(const_cast<CBlast_def_line_set*>(& deflines));
-
+
s_CheckEmptyLists(bdls, true);
m_Deflines = bdls;
}
@@ -1096,7 +1096,7 @@ inline int s_AbsMax(int a, int b)
}
// Filtering data format on disk:
-//
+//
// Size of integer type for this blob (1, 2, or 4) (4 bytes).
//
// Array of filtering types:
@@ -1104,16 +1104,16 @@ inline int s_AbsMax(int a, int b)
// Array of offsets:
// Start Offset
// End Offset
-//
+//
// The isize is one of 1, 2, or 4, written in the first byte, and
// followed by 0, 1, or 3 NUL bytes to align the data offset to a
// multiple of `isize'.
-//
+//
// All other integer values in this array use isize bytes, including
// array counts and the `type' enumerations. After all the offset is
// written, the blob is aligned to a multiple of 4 using the `eSimple'
// method.
-//
+//
// Each array is an element count followed by that many elements.
#if 0
@@ -1148,27 +1148,27 @@ void s_WriteRanges(CBlastDbBlob & blob,
const TRanges & ranges)
{
typedef vector< pair<TSeqPos, TSeqPos> > TPairVector;
-
+
Int4 num_written = 0;
TWriteSize::WriteInt(blob, count);
-
+
for ( typename TRanges::const_iterator r1 = (ranges).begin(),
r1_end = (ranges).end();
r1 != r1_end;
++r1 ) {
-
+
if (r1->offsets.size()) {
num_written ++;
TWriteSize::WriteInt(blob, r1->algorithm_id);
TWriteSize::WriteInt(blob, r1->offsets.size());
-
+
ITERATE(TPairVector, r2, r1->offsets) {
TWriteSize::WriteInt(blob, r2->first);
TWriteSize::WriteInt(blob, r2->second);
}
}
}
-
+
_ASSERT(num_written == count);
}
@@ -1176,66 +1176,67 @@ void s_WriteRanges(CBlastDbBlob & blob,
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
+
void CWriteDB_Impl::SetMaskData(const CMaskedRangesVector & ranges,
- const vector <int> & gis)
+ const vector <TGi> & gis)
{
- // No GI is found for the sequence
+ // No GI is found for the sequence
// TODO should we generate a warning?
if (m_UseGiMask && !gis.size()) {
return;
}
TSeqPos seq_length = x_ComputeSeqLength();
-
+
// Check validity of data and determine maximum integer value
// stored here before writing anything. The best numeric_size
// will be selected; this numeric size is applied uniformly to all
// integers in this blob (except for the first one, which is the
// integer size itself, and which is always a single byte.)
-
+
typedef vector< pair<TSeqPos, TSeqPos> > TPairVector;
-
+
int range_list_count = 0;
int offset_pairs_count = 0;
-
-
+
+
ITERATE(CMaskedRangesVector, r1, ranges) {
if (r1->empty()) {
continue;
}
-
+
range_list_count ++;
offset_pairs_count += r1->offsets.size();
-
+
if ( !m_MaskAlgoRegistry.IsRegistered(r1->algorithm_id) ) {
string msg("Error: Algorithm IDs must be registered before use.");
msg += " Unknown algorithm ID = " +
NStr::IntToString((int)r1->algorithm_id);
NCBI_THROW(CWriteDBException, eArgErr, msg);
}
-
-
+
+
ITERATE(TPairVector, r2, r1->offsets) {
if ((r2->first > r2->second) ||
(r2->second > seq_length)) {
-
+
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Masked data offsets out of bounds.");
}
}
}
-
-
+
+
// We may be passed an empty list of ranges, or we might be passed
// several ranges whose lists of offsets are themself empty. No
// matter what is passed in, we should not emit empty lists and we
// should not emit any bytes at all if there are no elements.
-
+
if (offset_pairs_count == 0) {
return;
}
-
+
// Gi-based masks
if (m_UseGiMask) {
ITERATE(CMaskedRangesVector, r1, ranges) {
@@ -1245,25 +1246,25 @@ void CWriteDB_Impl::SetMaskData(const CMaskedRangesVector & ranges,
}
}
return;
- }
+ }
// OID-based masks
const int col_id = x_GetMaskDataColumnId();
CBlastDbBlob & blob = SetBlobData(col_id);
blob.Clear();
blob.WriteInt4(range_list_count);
-
+
CBlastDbBlob & blob2 = SetBlobData(col_id);
blob2.Clear();
blob2.WriteInt4(range_list_count);
-
+
ITERATE(CMaskedRangesVector, r1, ranges) {
if (r1->offsets.size()) {
blob.WriteInt4(r1->algorithm_id);
blob.WriteInt4(r1->offsets.size());
blob2.WriteInt4(r1->algorithm_id);
blob2.WriteInt4(r1->offsets.size());
-
+
ITERATE(TPairVector, r2, r1->offsets) {
blob.WriteInt4(r2->first);
blob.WriteInt4(r2->second);
@@ -1272,9 +1273,9 @@ void CWriteDB_Impl::SetMaskData(const CMaskedRangesVector & ranges,
}
}
}
-
+
blob.WritePadBytes(4, CBlastDbBlob::eSimple);
- blob2.WritePadBytes(4, CBlastDbBlob::eSimple);
+ blob2.WritePadBytes(4, CBlastDbBlob::eSimple);
}
static const string s_EscapeColon(const string &in) {
@@ -1283,19 +1284,19 @@ static const string s_EscapeColon(const string &in) {
}
int CWriteDB_Impl::
-RegisterMaskAlgorithm(EBlast_filter_program program,
+RegisterMaskAlgorithm(EBlast_filter_program program,
const string & options,
const string & name)
{
int algorithm_id = m_MaskAlgoRegistry.Add(program, options);
-
+
string key = NStr::IntToString(algorithm_id);
string value = NStr::IntToString((int)program) + ":" +
s_EscapeColon(options);
if (m_UseGiMask) {
m_MaskAlgoMap[algorithm_id] = m_GiMasks.size();
- m_GiMasks.push_back(CRef<CWriteDB_GiMask>
+ m_GiMasks.push_back(CRef<CWriteDB_GiMask>
(new CWriteDB_GiMask(name, value, m_MaxFileSize)));
} else {
m_ColumnMetas[x_GetMaskDataColumnId()][key] = value;
@@ -1312,8 +1313,8 @@ RegisterMaskAlgorithm(const string &id,
int algorithm_id = m_MaskAlgoRegistry.Add(id);
string key = NStr::IntToString(algorithm_id);
- string value = "100:" +
- s_EscapeColon(options) + ":" +
+ string value = "100:" +
+ s_EscapeColon(options) + ":" +
s_EscapeColon(id) + ":" +
s_EscapeColon(description);
@@ -1329,35 +1330,35 @@ int CWriteDB_Impl::FindColumn(const string & title) const
return i;
}
}
-
+
return -1;
}
int CWriteDB_Impl::CreateColumn(const string & title, bool mbo)
{
_ASSERT(FindColumn(title) == -1);
-
+
size_t col_id = m_Blobs.size() / 2;
-
+
_ASSERT(m_HaveBlob.size() == col_id);
_ASSERT(m_ColumnTitles.size() == col_id);
_ASSERT(m_ColumnMetas.size() == col_id);
-
+
CRef<CBlastDbBlob> new_blob(new CBlastDbBlob);
CRef<CBlastDbBlob> new_blob2(new CBlastDbBlob);
-
+
m_Blobs .push_back(new_blob);
m_Blobs .push_back(new_blob2);
m_HaveBlob .push_back(0);
m_ColumnTitles.push_back(title);
m_ColumnMetas .push_back(TColumnMeta());
-
+
if (m_Volume.NotEmpty()) {
size_t id2 = m_Volume->CreateColumn(title, m_ColumnMetas.back(), mbo);
_ASSERT(id2 == col_id);
(void)id2; // get rid of compiler warning
}
-
+
return col_id;
}
@@ -1369,9 +1370,9 @@ void CWriteDB_Impl::AddColumnMetaData(int col_id,
NCBI_THROW(CWriteDBException, eArgErr,
"Error: provided column ID is not valid");
}
-
+
m_ColumnMetas[col_id][key] = value;
-
+
if (m_Volume.NotEmpty()) {
m_Volume->AddColumnMetaData(col_id, key, value);
}
@@ -1383,17 +1384,17 @@ CBlastDbBlob & CWriteDB_Impl::SetBlobData(int col_id)
NCBI_THROW(CWriteDBException, eArgErr,
"Error: provided column ID is not valid");
}
-
+
if (m_HaveBlob[col_id] > 1) {
NCBI_THROW(CWriteDBException, eArgErr,
"Error: Already have blob for this sequence and column");
}
-
+
++m_HaveBlob[col_id];
-
+
// Blobs are reused to reduce buffer reallocation; a missing blob
// means the corresponding column does not exist.
-
+
return *m_Blobs[col_id * 2 + m_HaveBlob[col_id] - 1];
}
#endif
@@ -1417,43 +1418,43 @@ CRef<CBlast_def_line_set>
CWriteDB_Impl::ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids)
{
// Get information
-
+
CConstRef<CBlast_def_line_set> deflines;
string binary_header;
vector< vector<int> > v1, v2;
-
+
CConstRef<CBioseq> bsref(& bs);
x_ExtractDeflines(bsref, deflines, binary_header, v2, v2, 0, -1, parse_ids);
-
+
// Convert to return type
-
+
CRef<CBlast_def_line_set> bdls;
bdls.Reset(const_cast<CBlast_def_line_set*>(&*deflines));
-
+
return bdls;
}
void CWriteDB_Impl::SetMaskedLetters(const string & masked)
{
// Only supported for protein.
-
+
if (! m_Protein) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Nucleotide masking not supported.");
}
-
+
m_MaskedLetters = masked;
-
+
if (masked.empty()) {
vector<char> none;
m_MaskLookup.swap(none);
return;
}
-
+
// Convert set of masked letters to stdaa, use the result to build
// a lookup table.
-
+
string mask_bytes;
CSeqConvert::Convert(m_MaskedLetters,
CSeqUtil::e_Iupacaa,
@@ -1461,31 +1462,31 @@ void CWriteDB_Impl::SetMaskedLetters(const string & masked)
(int) m_MaskedLetters.size(),
mask_bytes,
CSeqUtil::e_Ncbistdaa);
-
+
_ASSERT(mask_bytes.size() == m_MaskedLetters.size());
-
+
// Build a table of character-to-bool.
// (Bool is represented by char 0 and 1.)
-
+
m_MaskLookup.resize(256, (char)0);
-
+
for (unsigned i = 0; i < mask_bytes.size(); i++) {
int ch = ((int) mask_bytes[i]) & 0xFF;
m_MaskLookup[ch] = (char)1;
}
-
+
// Convert the masking character - always 'X' - to stdaa.
-
+
if (m_MaskByte.empty()) {
string mask_byte = "X";
-
+
CSeqConvert::Convert(mask_byte,
CSeqUtil::e_Iupacaa,
0,
1,
m_MaskByte,
CSeqUtil::e_Ncbistdaa);
-
+
_ASSERT(m_MaskByte.size() == 1);
}
}
@@ -1493,7 +1494,7 @@ void CWriteDB_Impl::SetMaskedLetters(const string & masked)
void CWriteDB_Impl::ListVolumes(vector<string> & vols)
{
vols.clear();
-
+
ITERATE(vector< CRef<CWriteDB_Volume> >, iter, m_VolumeList) {
vols.push_back((**iter).GetVolumeName());
}
@@ -1502,11 +1503,11 @@ void CWriteDB_Impl::ListVolumes(vector<string> & vols)
void CWriteDB_Impl::ListFiles(vector<string> & files)
{
files.clear();
-
+
ITERATE(vector< CRef<CWriteDB_Volume> >, iter, m_VolumeList) {
(**iter).ListFiles(files);
}
-
+
if (m_VolumeList.size() > 1) {
files.push_back(x_MakeAliasName());
}
@@ -1558,51 +1559,51 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
if (! bioseq.CanGetDescr()) {
return;
}
-
+
string fasta;
-
+
// Scan the CBioseq for the CFastaReader user object.
-
+
ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) {
const CSeqdesc & desc = **iter;
-
+
if (desc.IsUser() &&
desc.GetUser().CanGetType() &&
desc.GetUser().GetType().IsStr() &&
desc.GetUser().GetType().GetStr() == "CFastaReader" &&
desc.GetUser().CanGetData()) {
-
+
const vector< CRef< CUser_field > > & D = desc.GetUser().GetData();
-
+
ITERATE(vector< CRef< CUser_field > >, iter, D) {
const CUser_field & f = **iter;
-
+
if (f.CanGetLabel() &&
f.GetLabel().IsStr() &&
f.GetLabel().GetStr() == "DefLine" &&
f.CanGetData() &&
f.GetData().IsStr()) {
-
+
fasta = NStr::ParseEscapes(f.GetData().GetStr());
break;
}
}
}
}
-
+
if (fasta.empty())
return;
-
+
// The bioseq has a field contianing the ids for the first
// defline. The title string contains the title for the first
// defline, plus all the other defline titles and ids. This code
// unpacks them and builds a normal blast defline set.
-
+
unsigned mship_i(0), links_i(0);
bool used_pig(false);
-
+
// Build the deflines.
-
+
CRef<CBlast_def_line_set> bdls(new CBlast_def_line_set);
CRef<CBlast_def_line> defline;
@@ -1612,7 +1613,7 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
CRef<CSeq_id> gnl_id(new CSeq_id());
gnl_id->SetGeneral().SetDb("BL_ORD_ID");
gnl_id->SetGeneral().SetTag().SetId(0); // will be filled later
-
+
// Build the local defline.
defline.Reset(new CBlast_def_line);
defline->SetSeqid().push_back(gnl_id);
@@ -1628,19 +1629,19 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
const vector<int> & V = membits[mship_i++];
defline->SetMemberships().assign(V.begin(), V.end());
}
-
+
if (links_i < linkout.size()) {
const vector<int> & V = linkout[mship_i++];
defline->SetLinks().assign(V.begin(), V.end());
}
-
+
if ((! used_pig) && pig) {
defline->SetOther_info().push_back(pig);
used_pig = true;
}
bdls->Set().push_back(defline);
-
+
} else {
int skip = 1;
@@ -1649,7 +1650,7 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
size_t pos_title = fasta.find(" ", skip);
size_t pos_next = fasta.find("\001", skip);
skip = 1;
-
+
if (pos_next == fasta.npos) {
if (accept_gt) {
pos_next = fasta.find(" >");
@@ -1659,7 +1660,7 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
// If there is a ^A, turn off GT checking.
accept_gt = false;
}
-
+
if (pos_next == fasta.npos) {
pos_next = fasta.size();
skip = 0;
@@ -1669,43 +1670,43 @@ x_GetFastaReaderDeflines(const CBioseq & bioseq,
// title field is missing
pos_title = pos_next;
}
-
+
string ids(fasta, id_start, pos_title - id_start);
if (pos_title == pos_next) pos_title--;
string title(fasta, pos_title + 1, pos_next-pos_title - 1);
string remaining(fasta, pos_next, fasta.size() - pos_next);
fasta.swap(remaining);
-
+
// Parse '|' seperated ids.
list< CRef<CSeq_id> > seqids;
- if ( ids.find('|') == NPOS
+ if ( ids.find('|') == NPOS
|| !isalpha((unsigned char)(ids[0]))) {
seqids.push_back(CRef<CSeq_id> (new CSeq_id(CSeq_id::e_Local, ids)));
} else {
CSeq_id::ParseFastaIds(seqids, ids);
}
-
+
// Build the actual defline.
-
+
defline.Reset(new CBlast_def_line);
defline->SetSeqid().swap(seqids);
defline->SetTitle(title);
-
+
if (mship_i < membits.size()) {
const vector<int> & V = membits[mship_i++];
defline->SetMemberships().assign(V.begin(), V.end());
}
-
+
if (links_i < linkout.size()) {
const vector<int> & V = linkout[mship_i++];
defline->SetLinks().assign(V.begin(), V.end());
}
-
+
if ((! used_pig) && pig) {
defline->SetOther_info().push_back(pig);
used_pig = true;
}
-
+
bdls->Set().push_back(defline);
}
}
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp b/c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp
index 45bf90a..10f3581 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_IMPL_HPP
#define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_IMPL_HPP
-/* $Id: writedb_impl.hpp 389699 2013-02-20 15:33:26Z maning $
+/* $Id: writedb_impl.hpp 480972 2015-10-06 12:06:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,16 +56,16 @@ BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
/// CWriteDB_Impl class
-///
+///
/// This manufactures blast database header files from input data.
class CWriteDB_Impl {
public:
/// Whether and what kind of indices to build.
typedef CWriteDB::EIndexType EIndexType;
-
+
// Setup and control
-
+
/// Constructor.
/// @param dbname Name of the database to create.
/// @param protein True for protein, false for nucleotide.
@@ -79,17 +79,17 @@ public:
EIndexType indices,
bool parse_ids,
bool use_gi_mask);
-
+
/// Destructor.
~CWriteDB_Impl();
-
+
/// Close the file and flush any remaining data to disk.
void Close();
-
+
// Sequence Data
-
+
/// Add a new sequence as raw sequence and ambiguity data.
- ///
+ ///
/// A new sequence record is started, and data from any previous
/// sequence is combined and written to disk. Each sequence needs
/// sequence data and header data. This method takes sequence
@@ -105,9 +105,9 @@ public:
/// @param ambiguities Ambiguity data in blast db disk format.
void AddSequence(const CTempString & sequence,
const CTempString & ambiguities);
-
+
/// Add a new sequence as a CBioseq.
- ///
+ ///
/// A new sequence record is started, and data from any previous
/// sequence is combined and written to disk. Each sequence needs
/// sequence data and header data. This method can extract both
@@ -123,9 +123,9 @@ public:
///
/// @param bs Bioseq containing sequence and header data.
void AddSequence(const CBioseq & bs);
-
+
/// Add a new sequence as a CBioseq_Handle.
- ///
+ ///
/// A new sequence record is started, and data from any previous
/// sequence is combined and written to disk. Each sequence needs
/// sequence data and header data. This method can extract both
@@ -134,12 +134,12 @@ public:
/// replace the header data from the CBioseq. (Note: objects
/// provided to WriteDB will be kept alive until the next
/// AddSequence call.)
- ///
+ ///
/// @param bsh Bioseq_Handle for sequence to add.
void AddSequence(const CBioseq_Handle & bsh);
-
+
/// Add a new sequence as a CBioseq_Handle.
- ///
+ ///
/// A new sequence record is started, and data from any previous
/// sequence is combined and written to disk. Each sequence needs
/// sequence data and header data. This method will extract
@@ -149,11 +149,11 @@ public:
/// header data is preferred, SetDeflines() can be called after
/// this method. (Note: objects provided to WriteDB will be kept
/// alive until the next AddSequence call.)
- ///
+ ///
/// @param bs Bioseq_Handle for header and sequence data.
/// @param sv CSeqVector for sequence data.
void AddSequence(const CBioseq & bs, CSeqVector & sv);
-
+
/// This method replaces any stored header data for the current
/// sequence with the provided CBlast_def_line_set. Header data
/// can be constructed directly by the caller, or extracted from
@@ -164,30 +164,30 @@ public:
///
/// @param deflines Header data for the most recent sequence.
void SetDeflines(const CBlast_def_line_set & deflines);
-
+
/// Set the PIG identifier of this sequence.
- ///
+ ///
/// For protein sequences, this sets the PIG identifier. PIG ids
/// are per-sequence, so it will only be attached to the first
/// defline in the set.
- ///
+ ///
/// @param pig PIG identifier as an integer.
void SetPig(int pig);
-
+
// Options
-
+
/// Set the maximum size for any file in the database.
- ///
+ ///
/// This method sets the maximum size for any file in a database
/// volume. If adding a sequence would cause any file in the
/// generated database to exceed this size, the current volume is
/// ended and a new volume is started. This is not a strict
/// limit, inasmuch as it always puts at least one sequence in
/// each volume regardless of that sequence's size.
- ///
+ ///
/// @param sz Maximum file size (in bytes).
void SetMaxFileSize(Uint8 sz);
-
+
/// Set the maximum letters in one volume.
///
/// This method sets the maximum number of sequence letters per
@@ -199,7 +199,7 @@ public:
///
/// @param sz Maximum sequence letters per volume.
void SetMaxVolumeLetters(Uint8 sz);
-
+
/// Extract deflines from a CBioseq.
///
/// Given a CBioseq, this method extracts and returns header info
@@ -216,18 +216,18 @@ public:
/// @return The blast defline set.
static CRef<CBlast_def_line_set>
ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids);
-
+
/// Set bases that should not be used in sequences.
- ///
+ ///
/// This method specifies nucelotide or protein bases that should
/// not be used in the resulting database. The bases in question
/// will be replaced with N (for nucleotide) or X (for protein).
/// The input data is expected to be specified in the appropriate
/// 'alphabetic' encoding (either IUPACAA and IUPACNA).
- ///
+ ///
/// @param masked
void SetMaskedLetters(const string & masked);
-
+
/// List Volumes
///
/// Returns the base names of all volumes constructed by this
@@ -237,7 +237,7 @@ public:
/// @param vols
/// The set of volumes produced by this class.
void ListVolumes(vector<string> & vols);
-
+
/// List Filenames
///
/// Returns a list of the files constructed by this class; the
@@ -247,7 +247,7 @@ public:
/// @param files
/// The set of resolved database path names.
void ListFiles(vector<string> & files);
-
+
/// Register a type of filtering data found in this database.
///
/// The BlastDb format supports storage of masking data (lists of
@@ -268,7 +268,7 @@ public:
int RegisterMaskAlgorithm(EBlast_filter_program program,
const string & options,
const string & name = "");
-
+
/// Register a type of filtering data found in this database.
///
/// The BlastDb format supports storage of masking data (lists of
@@ -289,17 +289,17 @@ public:
int RegisterMaskAlgorithm(const string & id,
const string & description,
const string & options);
-
+
/// Set filtering data for a sequence.
- ///
+ ///
/// This method specifies filtered regions for the sequence. Each
/// sequence can have filtering data from various algorithms.
- ///
+ ///
/// @param ranges Filtered ranges for this sequence and algorithm.
/// @param gis The GIs associated with this sequence
void SetMaskData(const CMaskedRangesVector & ranges,
- const vector <int> & gis);
-
+ const vector <TGi> & gis);
+
/// Set up a generic CWriteDB metadata column.
///
/// This method creates a column with the specified name (title).
@@ -314,7 +314,7 @@ public:
/// @param title Name identifying this column.
/// @return Column identifier (a positive integer).
int CreateColumn(const string & title, bool mbo=false);
-
+
/// Find an existing column.
///
/// This looks for an existing column with the specified title and
@@ -323,7 +323,7 @@ public:
/// @param title The column title to look for.
/// @return The column ID if this column title is already defined.
int FindColumn(const string & title) const;
-
+
/// Add meta data to a column.
///
/// In addition to normal blob data, database columns can store a
@@ -339,7 +339,7 @@ public:
void AddColumnMetaData(int col_id,
const string & key,
const string & value);
-
+
/// Get a blob to use for a given column letter.
///
/// To add data for a `blob' type column, this method should be
@@ -354,10 +354,10 @@ public:
/// @param col_id Indicates the column receiving the blob data.
/// @return The user data should be stored in this blob.
CBlastDbBlob & SetBlobData(int col_id);
-
+
private:
// Configuration
-
+
string m_Dbname; ///< Database base name.
bool m_Protein; ///< True if DB is protein.
string m_Title; ///< Title field of database.
@@ -373,57 +373,57 @@ private:
map<int, int> m_MaskAlgoMap; ///< Mapping from algo_id to gi-mask id
bool m_ParseIDs; ///< Generate ISAM files
bool m_UseGiMask; ///< Generate GI-based mask files
-
+
/// Column titles.
vector<string> m_ColumnTitles;
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Per-column metadata.
typedef CWriteDB_Column::TColumnMeta TColumnMeta;
-
+
/// Meta data for all columns.
vector< TColumnMeta > m_ColumnMetas;
/// Gi-based masks
vector< CRef<CWriteDB_GiMask> > m_GiMasks;
#endif
-
+
// Functions
-
+
/// Flush accumulated sequence data to volume.
void x_Publish();
-
+
/// Compute name of alias file produced.
string x_MakeAliasName();
-
+
/// Flush accumulated sequence data to volume.
void x_MakeAlias();
-
+
/// Clear sequence data from last sequence.
void x_ResetSequenceData();
-
+
/// Convert and compute final data formats.
void x_CookData();
-
+
/// Convert header data into usable forms.
void x_CookHeader();
-
+
/// Collect ids for ISAM files.
void x_CookIds();
-
+
/// Compute the length of the current sequence.
int x_ComputeSeqLength();
-
+
/// Convert sequence data into usable forms.
void x_CookSequence();
-
+
/// Prepare column data to be appended to disk.
void x_CookColumns();
-
+
/// Replace masked input letters with m_MaskByte value.
void x_MaskSequence();
-
+
/// Get binary version of deflines from 'user' data in Bioseq.
///
/// Some CBioseq objects (e.g. those from CSeqDB) have an ASN.1
@@ -436,7 +436,7 @@ private:
/// @param binhdr Header data as binary ASN.1. [out]
static void x_GetBioseqBinaryHeader(const CBioseq & bioseq,
string & binhdr);
-
+
/// Construct deflines from a CBioseq and other meta-data.
///
/// This method builds deflines from various data found in the
@@ -450,11 +450,11 @@ private:
/// @param pig PIG to attach to a protein sequence. [in]
static void
x_BuildDeflinesFromBioseq(const CBioseq & bioseq,
- CConstRef<CBlast_def_line_set> & deflines,
+ CConstRef<CBlast_def_line_set> & deflines,
const vector< vector<int> > & membits,
const vector< vector<int> > & linkout,
int pig);
-
+
/// Extract a defline set from a binary ASN.1 blob.
/// @param bin_hdr Binary ASN.1 encoding of defline set. [in]
/// @param deflines Defline set. [out]
@@ -486,16 +486,16 @@ private:
int pig,
bool accept_gt,
bool parse_ids);
-
+
/// Returns true if we have unwritten sequence data.
bool x_HaveSequence() const;
-
+
/// Records that we now have unwritten sequence data.
void x_SetHaveSequence();
-
+
/// Records that we no longer have unwritten sequence data.
void x_ClearHaveSequence();
-
+
/// Get deflines from a CBioseq and other meta-data.
///
/// This method extracts binary ASN.1 deflines from a CBioseq if
@@ -521,7 +521,7 @@ private:
int pig,
int OID=-1,
bool parse_ids=true);
-
+
/// Compute the hash of a (raw) sequence.
///
/// The hash of the provided sequence will be computed and
@@ -533,7 +533,7 @@ private:
/// @param ambiguities Nucleotide ambiguities are provided here. [in]
void x_ComputeHash(const CTempString & sequence,
const CTempString & ambiguities);
-
+
/// Compute the hash of a (Bioseq) sequence.
///
/// The hash of the provided sequence will be computed and
@@ -542,7 +542,7 @@ private:
///
/// @param sequence The sequence as a CBioseq. [in]
void x_ComputeHash(const CBioseq & sequence);
-
+
/// Get the mask data column id.
///
/// The mask data column is created if it does not exist, and its
@@ -550,66 +550,66 @@ private:
///
/// @return The column ID for the mask data column.
int x_GetMaskDataColumnId();
-
+
//
// Accumulated sequence data.
//
-
+
/// Bioseq object for next sequence to write.
CConstRef<CBioseq> m_Bioseq;
-
+
/// SeqVector for next sequence to write.
CSeqVector m_SeqVector;
-
+
/// Deflines to write as header.
CConstRef<CBlast_def_line_set> m_Deflines;
-
+
/// Ids for next sequence to write, for use during ISAM construction.
vector< CRef<CSeq_id> > m_Ids;
-
+
/// Linkout bits - outer vector is per-defline, inner is bits.
vector< vector<int> > m_Linkouts;
-
+
/// Membership bits - outer vector is per-defline, inner is bits.
vector< vector<int> > m_Memberships;
-
+
/// PIG to attach to headers for protein sequences.
int m_Pig;
-
+
/// Sequence hash for this sequence.
int m_Hash;
-
+
/// When a sequence is added, this will be populated with the length of that sequence.
int m_SeqLength;
-
+
/// True if we have a sequence to write.
bool m_HaveSequence;
-
+
// Cooked
-
+
/// Sequence data in format that will be written to disk.
string m_Sequence;
-
+
/// Ambiguities in format that will be written to disk.
string m_Ambig;
-
+
/// Binary header in format that will be written to disk.
string m_BinHdr;
-
+
// Volumes
-
+
/// This volume is currently accepting sequences.
CRef<CWriteDB_Volume> m_Volume;
-
+
/// List of all volumes so far, up to and including m_Volume.
vector< CRef<CWriteDB_Volume> > m_VolumeList;
-
+
/// Blob data for the current sequence, indexed by letter.
vector< CRef<CBlastDbBlob> > m_Blobs;
-
+
/// List of blob columns that are active for this sequence.
vector<int> m_HaveBlob;
-
+
/// Registry for masking algorithms in this database.
CMaskInfoRegistry m_MaskAlgoRegistry;
};
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_isam.cpp b/c++/src/objtools/blast/seqdb_writer/writedb_isam.cpp
index e13b1e8..15933d3 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_isam.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_isam.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_isam.cpp 290538 2011-05-20 15:06:54Z camacho $
+/* $Id: writedb_isam.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
/// Implementation for the CWriteDB_Isam and related classes.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb_isam.cpp 290538 2011-05-20 15:06:54Z camacho $";
+static char const rcsid[] = "$Id: writedb_isam.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -64,39 +64,39 @@ s_IsamExtension(EWriteDBIsamType itype,
bool is_index)
{
char type_ch = '?';
-
+
switch(itype) {
case ePig:
type_ch = 'p';
break;
-
+
case eGi:
type_ch = 'n';
break;
-
+
case eAcc:
type_ch = 's';
break;
-
+
case eTrace:
type_ch = 't';
break;
-
+
case eHash:
type_ch = 'h';
break;
-
+
default:
NCBI_THROW(CWriteDBException,
eArgErr,
"Not implemented.");
}
-
+
string extn("???");
extn[0] = protein ? 'p' : 'n';
extn[1] = type_ch;
extn[2] = is_index ? 'i' : 'd';
-
+
return extn;
}
@@ -112,7 +112,7 @@ CWriteDB_Isam::CWriteDB_Isam(EIsamType itype,
protein,
index,
max_file_size));
-
+
m_IFile.Reset(new CWriteDB_IsamIndex(itype,
dbname,
protein,
@@ -150,7 +150,7 @@ void CWriteDB_Isam::Close()
// Index must be closed first, because ISAM indices are built in
// memory until the volume is closed, and only then is anything
// written to disk.
-
+
m_IFile->Close();
m_DFile->Close();
}
@@ -186,7 +186,7 @@ CWriteDB_IsamIndex::CWriteDB_IsamIndex(EWriteDBIsamType itype,
// too. The index file can be larger than the data file, but only
// if there are less than (about) 9 entries; at that size I'm not
// concerned about the byte limits.
-
+
if (itype == eAcc || itype == eHash) {
// If there is a maximum string size it's something large like
// 4k per table line. In practice, string table rows tend to
@@ -200,7 +200,7 @@ CWriteDB_IsamIndex::CWriteDB_IsamIndex(EWriteDBIsamType itype,
// This is far more than any current sequence currently uses.
// If this is not enough, the max size limit may be violated
// (but see the last sentence of paragraph 1).
-
+
m_BytesPerElem = 1024;
m_PageSize = 64;
} else {
@@ -220,7 +220,7 @@ void CWriteDB_IsamIndex::x_WriteHeader()
int isam_type = 0;
int num_terms = 0;
int max_line_size = 0;
-
+
switch(m_Type) {
case eGi:
case ePig:
@@ -230,33 +230,33 @@ void CWriteDB_IsamIndex::x_WriteHeader()
num_terms = (int) m_NumberTable.size();
max_line_size = 0;
break;
-
+
case eAcc:
case eHash:
isam_type = eIsamStringType; // string w/ data
max_line_size = eMaxStringLine;
num_terms = m_StringSort.Size();
break;
-
+
default:
NCBI_THROW(CWriteDBException,
eArgErr,
"Unknown id type specified.");
}
-
+
int samples = s_DivideRoundUp(num_terms, m_PageSize);
-
+
// These should probably use be a WriteInt4 method which should be
// added to the CWriteDB_File class.
-
+
WriteInt4(isam_version);
WriteInt4(isam_type);
WriteInt4((int)m_DataFileSize);
-
+
WriteInt4(num_terms);
WriteInt4(samples);
WriteInt4(m_PageSize);
-
+
WriteInt4(max_line_size);
WriteInt4(m_Sparse ? 1 : 0);
WriteInt4(0);
@@ -265,128 +265,128 @@ void CWriteDB_IsamIndex::x_WriteHeader()
void CWriteDB_IsamIndex::x_FlushStringIndex()
{
_ASSERT(m_StringSort.Size());
-
+
// Note: This function can take a noticeable portion of the
// database dumping time. For some databases, the length of the
// data file for the string index competes with the sequence file
// to determine volumes seperation points.
-
+
// String ISAM files have four parts. First, the standard
// meta-data header. Then (at address 36), we have a table of
// page offsets. After this is a table of key offsets in the
// index file, then finally the list of keys.
-
+
int data_pos = 0;
unsigned count = m_StringSort.Size();
-
+
unsigned nsamples = s_DivideRoundUp(count, m_PageSize);
-
+
string key_buffer;
vector<int> key_off;
-
+
// Reserve enough room, throwing in some extra. Since we excerpt
// every 64th entry, dividing by 64 would be exactly balanced. To
// make reallocation rare, I divide by 63 instead, and throw in an
// extra 16 bytes.
-
+
key_buffer.reserve((int)(m_DataFileSize/63 + 16));
key_off.reserve(nsamples);
-
+
unsigned i(0);
-
+
string NUL("x");
NUL[0] = (char) 0;
-
+
int output_count = 0;
int index = 0;
-
+
m_StringSort.Sort();
CWriteDB_PackedSemiTree::Iterator iter = m_StringSort.Begin();
CWriteDB_PackedSemiTree::Iterator end_iter = m_StringSort.End();
-
+
string element, prev_elem;
-
+
// A string containing a NUL cannot possibly be valid, so I'm
// using one as the "not set yet" value.
-
+
element.resize(1);
element[0] = char(0);
-
+
while(iter != end_iter) {
prev_elem.swap(element);
iter.Get(element);
-
+
if (prev_elem == element) {
++iter;
continue;
}
-
+
// For each element whose index is a multiple of m_PageSize
// (starting with element zero), we add the record to the
// index file.
-
+
// The page offset table can be written as it comes in, but
// the key offsets and keys are not written until all the page
// offsets have been written, so they are accumulated in a
// vector (key_off) and string (key_buffer) respectively.
-
+
if ((output_count & (m_PageSize-1)) == 0) {
// Write the data file position to the index file.
-
+
WriteInt4(data_pos);
-
+
// Store the overall index file position where the key
// will be written.
-
+
key_off.push_back((int) key_buffer.size());
-
+
// Store the string record for the index file (but this
// string is NUL terminated, whereas the data file rows
// are line feed (aka newline) terminated.
-
+
key_buffer.append(element.data(), element.length()-1);
key_buffer.append(NUL);
}
output_count ++;
-
+
data_pos = m_DataFile->Write(element);
index ++;
-
+
++iter;
}
-
+
// Write the final data position.
-
+
WriteInt4(data_pos);
-
+
// Push back the final buffer offset.
-
+
key_off.push_back((int) key_buffer.size());
-
+
int key_off_start = eKeyOffset + (nsamples + 1) * 8;
-
+
// Write index file offsets of keys.
-
+
for(i = 0; i < key_off.size(); i++) {
WriteInt4(key_off[i] + key_off_start);
}
-
+
// Write buffer of keys.
-
+
Write(key_buffer);
}
void CWriteDB_IsamIndex::x_FlushNumericIndex()
{
_ASSERT(m_NumberTable.size());
-
+
int row_index = 0;
-
+
sort(m_NumberTable.begin(), m_NumberTable.end());
-
+
int count = (int) m_NumberTable.size();
-
+
const SIdOid * prevp = 0;
// Note: could strip out code for 8/4 detection; then reorder this
@@ -399,53 +399,53 @@ void CWriteDB_IsamIndex::x_FlushNumericIndex()
// at least TIs) are probably guaranteed not to exceed the limit;
// in any case a conservative estimate of 12 bytes per ID could be
// used for numeric or just for TI indices.
-
+
if (m_UseInt8) {
for(int i = 0; i < count; i++) {
const SIdOid & elem = m_NumberTable[i];
-
+
if (prevp && (*prevp == elem)) {
continue;
} else {
prevp = & elem;
}
-
+
if ((row_index & (m_PageSize-1)) == 0) {
WriteInt8(elem.id());
WriteInt4(elem.oid());
}
-
+
m_DataFile->WriteInt8(elem.id());
m_DataFile->WriteInt4(elem.oid());
row_index ++;
}
-
+
// 64 bit numeric files end in (max-uint8, 0).
-
+
WriteInt8(-1);
WriteInt4(0);
} else {
for(int i = 0; i < count; i++) {
const SIdOid & elem = m_NumberTable[i];
-
+
if (prevp && (*prevp == elem)) {
continue;
} else {
prevp = & elem;
}
-
+
if ((row_index & (m_PageSize-1)) == 0) {
WriteInt4(elem.id());
WriteInt4(elem.oid());
}
-
+
m_DataFile->WriteInt4(elem.id());
m_DataFile->WriteInt4(elem.oid());
row_index ++;
}
-
+
// 32 bit numeric files end in (max-uint4, 0).
-
+
WriteInt4(-1);
WriteInt4(0);
}
@@ -456,22 +456,22 @@ void CWriteDB_IsamIndex::x_Flush()
if (m_NumberTable.size() || m_StringSort.Size()) {
Create();
m_DataFile->Create();
-
+
// Step 1: Write header data.
x_WriteHeader();
-
+
// Step 2: Flush all data to the data file.
// A. Sort all entries up front with sort.
// B. Pick out periodic samples for the index, every 256 elements
// for numeric and every 64 for string.
-
+
if (m_Type == eAcc || m_Type == eHash) {
x_FlushStringIndex();
} else {
x_FlushNumericIndex();
}
}
-
+
x_Free();
}
@@ -501,7 +501,7 @@ void CWriteDB_IsamIndex::AddHash(int oid, int hash)
{
char buf[256];
int sz = sprintf(buf, "%u", (unsigned)hash);
-
+
x_AddStringData(oid, buf, sz);
}
@@ -509,9 +509,9 @@ void CWriteDB_IsamIndex::x_AddGis(int oid, const TIdList & idlist)
{
ITERATE(TIdList, iter, idlist) {
const CSeq_id & seqid = **iter;
-
+
if (seqid.IsGi()) {
- SIdOid row(seqid.GetGi(), oid);
+ SIdOid row(GI_TO(Int8, seqid.GetGi()), oid);
m_NumberTable.push_back(row);
m_DataFileSize += 8;
}
@@ -522,23 +522,23 @@ void CWriteDB_IsamIndex::x_AddTraceIds(int oid, const TIdList & idlist)
{
ITERATE(TIdList, iter, idlist) {
const CSeq_id & seqid = **iter;
-
+
if (seqid.IsGeneral() && seqid.GetGeneral().GetDb() == "ti") {
const CObject_id & obj = seqid.GetGeneral().GetTag();
-
+
Int8 id = (obj.IsId()
? obj.GetId()
: NStr::StringToInt8(obj.GetStr()));
-
+
SIdOid row(id, oid);
m_NumberTable.push_back(row);
-
+
if (m_UseInt8) {
m_DataFileSize += 12;
} else if (id >= kMax_Int) {
// Adjust the data file size to account for the
// already-stored IDs.
-
+
m_UseInt8 = true;
m_DataFileSize /= 8;
m_DataFileSize *= 12;
@@ -553,7 +553,7 @@ void CWriteDB_IsamIndex::x_AddTraceIds(int oid, const TIdList & idlist)
void CWriteDB_IsamIndex::x_AddStringIds(int oid, const TIdList & idlist)
{
// Build all sub-string objects and add those.
-
+
ITERATE(TIdList, iter, idlist) {
const CSeq_id & seqid = **iter;
@@ -561,19 +561,19 @@ void CWriteDB_IsamIndex::x_AddStringIds(int oid, const TIdList & idlist)
case CSeq_id::e_Gi:
break;
-
+
case CSeq_id::e_Pdb:
x_AddPdb(oid, seqid);
break;
-
+
case CSeq_id::e_Local:
x_AddLocal(oid, seqid);
break;
-
+
case CSeq_id::e_Patent:
x_AddPatent(oid, seqid);
break;
-
+
case CSeq_id::e_General:
if (! m_Sparse) {
x_AddStdString(oid, seqid.AsFastaString());
@@ -585,14 +585,14 @@ void CWriteDB_IsamIndex::x_AddStringIds(int oid, const TIdList & idlist)
break;
// default processing:
- default:
+ default:
{
const CTextseq_id * textid = seqid.GetTextseq_Id();
if (textid) {
x_AddTextId(oid, *textid);
} else {
string acc = seqid.AsFastaString();
- x_AddStringData(oid, acc.data(), acc.size());
+ x_AddStringData(oid, acc.data(), acc.size());
}
}
}
@@ -603,7 +603,7 @@ void CWriteDB_IsamIndex::x_AddLocal(int oid,
const CSeq_id & seqid)
{
const CObject_id & objid = seqid.GetLocal();
-
+
if (! m_Sparse) {
x_AddStdString(oid, seqid.AsFastaString());
}
@@ -624,7 +624,7 @@ void CWriteDB_IsamIndex::x_AddPdb(int oid,
const CSeq_id & seqid)
{
const CPDB_seq_id & pdb = seqid.GetPdb();
-
+
// Sparse mode:
//
// "102l"
@@ -636,7 +636,7 @@ void CWriteDB_IsamIndex::x_AddPdb(int oid,
// "102l "
// "102l| "
// "pdb|102l| "
-
+
CTempString mol;
if (pdb.CanGetMol()) {
mol = pdb.GetMol().Get();
@@ -653,19 +653,19 @@ void CWriteDB_IsamIndex::x_AddPdb(int oid,
if (! m_Sparse) {
x_AddStdString(oid, full_id);
}
-
+
string short_id(full_id, 4);
x_AddStdString(oid, short_id);
-
+
int len = short_id.size();
if (short_id[len-2] == '|') {
short_id[len-2] = ' ';
- } else {
+ } else {
// This is lower case chain encoding, i.e., xxxx|a -> xxxx|AA
_ASSERT(short_id[len-1] == short_id[len-2]);
_ASSERT(short_id[len-3] == '|');
short_id[len-3] = ' ';
- }
+ }
x_AddStdString(oid, short_id);
}
@@ -676,7 +676,7 @@ bool s_NoCaseEqual(CTempString & a, CTempString & b)
{
if (a.size() != b.size())
return false;
-
+
return 0 == NStr::strncasecmp(a.data(), b.data(), a.size());
}
@@ -684,32 +684,32 @@ void CWriteDB_IsamIndex::x_AddTextId(int oid,
const CTextseq_id & id)
{
CTempString acc, nm;
-
+
// Note: if there is no accession, the id will not be added to a
// sparse databases (even if there is a name).
-
+
if (id.CanGetAccession()) {
acc = id.GetAccession();
}
-
+
if (id.CanGetName()) {
nm = id.GetName();
}
-
+
if (! acc.empty()) {
x_AddStringData(oid, acc);
}
-
+
if (! m_Sparse) {
// Skip name if it is empty or if it is the same as 'acc' when
// case is ignored.
-
+
if (! (nm.empty() || s_NoCaseEqual(acc, nm))) {
x_AddStringData(oid, nm);
}
-
+
int ver = id.CanGetVersion() ? id.GetVersion() : 0;
-
+
if (ver && acc.size()) {
x_AddString(oid, acc, ver);
}
@@ -738,18 +738,18 @@ void CWriteDB_IsamIndex::x_AddStringData(int oid, const char * sbuf, int ssize)
// be used.
//
// 5. User would need to return strings they were done with.
-
+
char buf[256];
-
+
int sz = ssize;
memcpy(buf, sbuf, sz);
_ASSERT(sz);
-
+
// lowercase the 'key' portion
for(int i = 0; i < sz; i++) {
buf[i] = tolower(buf[i]);
}
-
+
buf[sz++] = (char) eKeyDelim;
sz += sprintf(buf + sz, "%d", oid);
buf[sz++] = (char) eRecordDelim;
@@ -759,7 +759,7 @@ void CWriteDB_IsamIndex::x_AddStringData(int oid, const char * sbuf, int ssize)
m_Oid = oid;
m_OidStringData.clear();
}
-
+
string tmp(buf, sz);
pair< set<string>::iterator, bool> rv = m_OidStringData.insert(tmp);
if (rv.second) {
@@ -771,14 +771,14 @@ void CWriteDB_IsamIndex::x_AddStringData(int oid, const char * sbuf, int ssize)
void CWriteDB_IsamIndex::x_AddString(int oid, const CTempString & acc, int ver)
{
_ASSERT(! m_Sparse);
-
+
if (acc.size() && ver) {
char buf[256];
memcpy(buf, acc.data(), acc.size());
-
+
int sz = acc.size();
sz += sprintf(buf + sz, ".%d", ver);
-
+
x_AddStringData(oid, buf, sz);
}
}
@@ -828,7 +828,7 @@ bool CWriteDB_IsamIndex::Empty() const
{
// Also test 'created' bit in case the file data has already
// been dumped and cleared.
-
+
return ! (m_StringSort.Size() ||
m_NumberTable.size() ||
m_Created);
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_volume.cpp b/c++/src/objtools/blast/seqdb_writer/writedb_volume.cpp
index 3b444a9..4b219a2 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_volume.cpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_volume.cpp
@@ -1,4 +1,4 @@
-/* $Id: writedb_volume.cpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: writedb_volume.cpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
/// class for WriteDB.
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: writedb_volume.cpp 399305 2013-05-13 19:13:43Z grichenk $";
+static char const rcsid[] = "$Id: writedb_volume.cpp 481616 2015-10-14 14:41:28Z ivanov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -63,29 +63,29 @@ CWriteDB_Volume::CWriteDB_Volume(const string & dbname,
m_Open (true)
{
m_VolName = CWriteDB_File::MakeShortName(m_DbName, m_Index);
-
+
m_Idx.Reset(new CWriteDB_IndexFile(dbname,
protein,
title,
date,
index,
max_file_size));
-
+
m_Hdr.Reset(new CWriteDB_HeaderFile(dbname,
protein,
index,
max_file_size));
-
+
m_Seq.Reset(new CWriteDB_SequenceFile(dbname,
protein,
index,
max_file_size,
max_letters));
-
+
if (m_Indices != CWriteDB::eNoIndex) {
bool sparse =
(m_Indices & CWriteDB::eSparseIndex) == CWriteDB::eSparseIndex;
-
+
if (m_Protein) {
m_PigIsam.Reset(new CWriteDB_Isam(ePig,
dbname,
@@ -94,21 +94,21 @@ CWriteDB_Volume::CWriteDB_Volume(const string & dbname,
max_file_size,
false));
}
-
+
m_GiIsam.Reset(new CWriteDB_Isam(eGi,
dbname,
protein,
index,
max_file_size,
false));
-
+
m_AccIsam.Reset(new CWriteDB_Isam(eAcc,
dbname,
protein,
index,
max_file_size,
sparse));
-
+
if (m_Indices & CWriteDB::eAddTrace) {
m_TraceIsam.Reset(new CWriteDB_Isam(eTrace,
dbname,
@@ -117,7 +117,7 @@ CWriteDB_Volume::CWriteDB_Volume(const string & dbname,
max_file_size,
false));
}
-
+
if (m_Indices & CWriteDB::eAddHash) {
m_HashIsam.Reset(new CWriteDB_Isam(eHash,
dbname,
@@ -131,7 +131,7 @@ CWriteDB_Volume::CWriteDB_Volume(const string & dbname,
protein,
index,
max_file_size));
-
+
}
}
@@ -153,69 +153,69 @@ bool CWriteDB_Volume::WriteSequence(const string & seq,
{
// Zero is a legal hash value, but we should not be computing the
// hash value if there is no corresponding ISAM file.
-
+
_ASSERT((! hash) || m_HashIsam.NotEmpty());
-
+
if (! (seq.size() && binhdr.size())) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Cannot find CBioseq or deflines.");
}
-
+
_ASSERT(m_Open);
-
+
int length = (m_Protein
? (int) seq.size()
: x_FindNuclLength(seq));
-
+
bool overfull = false;
-
+
if (! (m_Idx->CanFit() &&
m_Hdr->CanFit((int)binhdr.size()) &&
m_Seq->CanFit((int)(seq.size() + ambig.size()), length))) {
overfull = true;
}
-
+
if (m_Indices != CWriteDB::eNoIndex) {
int num = (int)idlist.size();
-
+
if (! (m_AccIsam->CanFit(num) &&
m_GiIsam->CanFit(num) &&
(m_TraceIsam.Empty() || m_TraceIsam->CanFit(num)))) {
overfull = true;
}
-
+
if (m_Protein && (! m_PigIsam->CanFit(1))) {
overfull = true;
}
-
+
if (m_HashIsam.NotEmpty() && (! m_HashIsam->CanFit(1))) {
overfull = true;
}
}
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
for(int blob_i = 0; blob_i < (int) blobs.size(); blob_i++) {
_ASSERT(blob_i / 2 < (int) m_Columns.size());
-
+
if (! m_Columns[blob_i / 2]->CanFit(blobs[blob_i]->Size())) {
overfull = true;
break;
}
}
#endif
-
+
// Exception - if volume has no data, ignore the file size limits;
// otherwise there would be either a hard failure or an infinite
// recursion of building empty volumes. Building a volume that's
// too big is considered preferable to either of these outcomes.
-
+
if (m_OID && overfull) {
return false;
}
-
+
// check the uniqueness of id
if (m_Indices != CWriteDB::eNoIndex) {
set<string>::size_type orig_size = m_IdSet.size();
@@ -238,9 +238,9 @@ bool CWriteDB_Volume::WriteSequence(const string & seq,
}
int off_hdr(0), off_seq(0), off_amb(0);
-
+
m_Hdr->AddSequence(binhdr, off_hdr);
-
+
if (m_Protein) {
m_Seq->AddSequence(seq, off_seq, length);
m_Idx->AddSequence((int) seq.size(), off_hdr, off_seq);
@@ -248,34 +248,34 @@ bool CWriteDB_Volume::WriteSequence(const string & seq,
m_Seq->AddSequence(seq, ambig, off_seq, off_amb, length);
m_Idx->AddSequence(length, off_hdr, off_seq, off_amb);
}
-
+
if (m_Indices != CWriteDB::eNoIndex) {
m_AccIsam->AddIds(m_OID, idlist);
m_GiIsam->AddIds(m_OID, idlist);
- Int4 gi = -1;
+ TGi gi = INVALID_GI;
ITERATE(TIdList, iter, idlist) {
const CSeq_id & seqid = **iter;
if (seqid.IsGi()) {
- gi = GI_TO(Int4, seqid.GetGi());
+ gi = seqid.GetGi();
break;
}
}
m_GiIndex->AddGi(gi);
-
+
if (m_Protein && pig) {
m_PigIsam->AddPig(m_OID, pig);
}
-
+
if (m_TraceIsam.NotEmpty()) {
m_TraceIsam->AddIds(m_OID, idlist);
}
-
+
if (m_HashIsam.NotEmpty()) {
m_HashIsam->AddHash(m_OID, hash);
}
}
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
for(int col_i = 0; col_i < (int)m_Columns.size(); col_i++) {
@@ -287,9 +287,9 @@ bool CWriteDB_Volume::WriteSequence(const string & seq,
}
}
#endif
-
+
m_OID ++;
-
+
return true;
}
@@ -297,7 +297,7 @@ int CWriteDB_Volume::x_FindNuclLength(const string & seq)
{
_ASSERT(! m_Protein);
_ASSERT(seq.size());
-
+
return WriteDB_FindSequenceLength(m_Protein, seq);
}
@@ -305,12 +305,12 @@ void CWriteDB_Volume::Close()
{
if (m_Open) {
m_Open = false;
-
+
// close each file.
m_Idx->Close();
m_Hdr->Close();
m_Seq->Close();
-
+
if (m_Indices != CWriteDB::eNoIndex) {
if (m_Protein) {
m_PigIsam->Close();
@@ -318,18 +318,18 @@ void CWriteDB_Volume::Close()
m_GiIsam->Close();
m_AccIsam->Close();
m_GiIndex->Close();
-
+
if (m_TraceIsam.NotEmpty()) {
m_TraceIsam->Close();
}
-
+
if (m_HashIsam.NotEmpty()) {
m_HashIsam->Close();
}
m_IdSet.clear();
}
}
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
NON_CONST_ITERATE(vector< CRef<CWriteDB_Column> >, iter, m_Columns) {
@@ -342,12 +342,12 @@ void CWriteDB_Volume::RenameSingle()
{
_ASSERT(! m_Open);
m_VolName = m_DbName;
-
+
// rename all files to 'single volume' notation.
m_Idx->RenameSingle();
m_Hdr->RenameSingle();
m_Seq->RenameSingle();
-
+
if (m_Indices != CWriteDB::eNoIndex) {
if (m_Protein) {
m_PigIsam->RenameSingle();
@@ -355,16 +355,16 @@ void CWriteDB_Volume::RenameSingle()
m_GiIsam->RenameSingle();
m_AccIsam->RenameSingle();
m_GiIndex->RenameSingle();
-
+
if (m_TraceIsam.NotEmpty()) {
m_TraceIsam->RenameSingle();
}
-
+
if (m_HashIsam.NotEmpty()) {
m_HashIsam->RenameSingle();
}
}
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
NON_CONST_ITERATE(vector< CRef<CWriteDB_Column> >, iter, m_Columns) {
@@ -378,27 +378,27 @@ void CWriteDB_Volume::ListFiles(vector<string> & files) const
files.push_back(m_Idx->GetFilename());
files.push_back(m_Hdr->GetFilename());
files.push_back(m_Seq->GetFilename());
-
+
if (m_AccIsam.NotEmpty()) {
m_AccIsam->ListFiles(files);
}
-
+
if (m_GiIsam.NotEmpty()) {
m_GiIsam->ListFiles(files);
}
-
+
if (m_PigIsam.NotEmpty()) {
m_PigIsam->ListFiles(files);
}
-
+
if (m_TraceIsam.NotEmpty()) {
m_TraceIsam->ListFiles(files);
}
-
+
if (m_HashIsam.NotEmpty()) {
m_HashIsam->ListFiles(files);
}
-
+
if (m_GiIndex.NotEmpty()) {
files.push_back(m_GiIndex->GetFilename());
}
@@ -418,24 +418,24 @@ int CWriteDB_Volume::CreateColumn(const string & title,
bool mbo)
{
int col_id = m_Columns.size();
-
+
string extn(m_Protein ? "p??" : "n??");
-
+
if (col_id >= 36) {
NCBI_THROW(CWriteDBException,
eArgErr,
"Error: Cannot have more than 36 columns.");
}
-
+
extn[1] = "abcdefghijklmnopqrstuvwxyz0123456789"[col_id];
-
+
string extn2 = extn;
string extn3 = extn;
-
+
extn[2] = 'a';
extn2[2] = 'b';
extn3[2] = 'c';
-
+
CRef<CWriteDB_Column> new_col
(new CWriteDB_Column(m_DbName,
extn,
@@ -450,19 +450,19 @@ int CWriteDB_Volume::CreateColumn(const string & title,
extn3,
m_Index,
max_sz);
-
+
// If the OID is not zero, then add all the blank records for the
// prior OIDs to the new column.
-
+
CBlastDbBlob blank;
-
+
for(int j = 0; j < m_OID; j++) {
if (mbo) new_col->AddBlob(blank, blank);
else new_col->AddBlob(blank);
}
-
+
m_Columns.push_back(new_col);
-
+
return col_id;
}
@@ -474,7 +474,7 @@ void CWriteDB_Volume::AddColumnMetaData(int col_id,
NCBI_THROW(CWriteDBException, eArgErr,
"Error: provided column ID is not valid");
}
-
+
m_Columns[col_id]->AddMetaData(key, value);
}
#endif
diff --git a/c++/src/objtools/blast/seqdb_writer/writedb_volume.hpp b/c++/src/objtools/blast/seqdb_writer/writedb_volume.hpp
index f35109d..f6137ca 100644
--- a/c++/src/objtools/blast/seqdb_writer/writedb_volume.hpp
+++ b/c++/src/objtools/blast/seqdb_writer/writedb_volume.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_VOLUME_HPP
#define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_VOLUME_HPP
-/* $Id: writedb_volume.hpp 364229 2012-05-23 18:15:34Z maning $
+/* $Id: writedb_volume.hpp 481616 2015-10-14 14:41:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -61,8 +61,8 @@ public:
: CWriteDB_File (dbname, (protein ? "pog" : "nog"), index, max_fsize, false){ }
~CWriteDB_GiIndex() { };
-
- void AddGi(Int4 gi) {
+
+ void AddGi(TGi gi) {
m_Gi.push_back(gi);
}
@@ -73,7 +73,7 @@ private:
if (! nGi) return;
- Create();
+ Create();
WriteInt4(kVersion);
WriteInt4(kFileType);
WriteInt4(kGiSize);
@@ -84,37 +84,37 @@ private:
}
for (Int4 i=0; i<nGi; i++) {
- WriteInt4(m_Gi[i]);
+ WriteInt4(GI_TO(Int4, m_Gi[i]));
}
- vector<Int4> tmp;
+ vector<TGi> tmp;
m_Gi.swap(tmp);
}
static const int kVersion = 1;
static const int kFileType = 0;
static const int kGiSize = 4;
- vector<Int4> m_Gi;
+ vector<TGi> m_Gi;
};
-
-
+
+
/// CWriteDB_Volume class
-///
+///
/// This manufactures a blast database volume from sequences.
class CWriteDB_Volume : public CObject {
public:
/// Whether and what kind of indices to build.
typedef CWriteDB::EIndexType EIndexType;
-
+
/// Type used for lists of identifiers.
typedef vector< CRef<CSeq_id> > TIdList;
-
+
/// Type used for lists of identifiers.
typedef vector< CRef<CBlastDbBlob> > TBlobList;
-
+
// Setup and control
-
+
/// Build a database volume.
///
/// @param dbname Base name of the database, such as 'nr'.
@@ -133,17 +133,17 @@ public:
Uint8 max_file_size,
Uint8 max_letters,
EIndexType indices);
-
+
/// Destructor.
///
/// The Close() method will be called if it has not already been.
~CWriteDB_Volume();
-
+
/// Add a sequence to this volume.
- ///
+ ///
/// The provided data represents all information for one
/// non-redundant sequence that will be added to this volume.
- ///
+ ///
/// @param seq Sequence data in format ncbi2na or ncbistdaa.
/// @param ambig Ambiguities (for protein this should be empty).
/// @param binhdr Binary headers (blast deflines in binary ASN.1).
@@ -158,16 +158,16 @@ public:
int hash,
const TBlobList & blobs,
int maskcol_id=-1);
-
+
/// Rename all volumes files to single-volume names.
- ///
+ ///
/// When volume component files are generated by WriteDB, the
/// volume names include a volume index. This method renames the
/// generated files for this volume to names that do not include
/// the volume index. This method should not be called until the
/// volume is Close()s.
void RenameSingle();
-
+
/// Close the volume.
///
/// This method finalizes and closes all files associated with
@@ -175,15 +175,15 @@ public:
/// indices and the index file (pin or nin) cannot be written
/// until all of the data has been seen.)
void Close();
-
+
/// Get the name of the volume.
- ///
+ ///
/// The volume name includes the path and version (if a version is
/// used) but does not include the extension. It is the name that
/// would be provided to SeqDB to open this volume. This method
/// should be called after RenameSingle() if that method is going
/// to be called.
- ///
+ ///
/// @return The volume name.
const string & GetVolumeName() const
{
@@ -192,23 +192,23 @@ public:
/// Get the current OID of the volume.
///
- /// The current OID is needed for generating BL_ORD_ID.
+ /// The current OID is needed for generating BL_ORD_ID.
///
/// @return the OID
const int & GetOID() const
{
- return m_OID;
+ return m_OID;
}
-
+
/// List all files associated with this volume.
/// @param files The filenames will be appended to this vector.
void ListFiles(vector<string> & files) const;
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Type used for database column meta-data.
typedef CWriteDB_Column::TColumnMeta TColumnMeta;
-
+
/// Create a new database column.
///
/// @param title The title of the new column.
@@ -219,7 +219,7 @@ public:
const TColumnMeta & meta,
Uint8 max_sz,
bool mbo = true);
-
+
/// Add meta data to a column.
///
/// In addition to normal blob data, database columns can store a
@@ -236,10 +236,10 @@ public:
const string & key,
const string & value);
#endif
-
+
private:
// Configuration.
-
+
string m_DbName; ///< Base name of the database.
string m_VolName; ///< Database name plus version (if used).
bool m_Protein; ///< True for protein; false for nucleotide.
@@ -248,25 +248,25 @@ private:
int m_Index; ///< Index of this volume (1 based).
EIndexType m_Indices; ///< Indices are sparse, full, or disabled.
Uint8 m_MaxFileSize; ///< Maximum size for any component file.
-
+
// Status.
-
+
int m_OID; ///< Next assigned OID.
bool m_Open; ///< True if user can still append sequences.
-
+
// Components
-
+
CRef<CWriteDB_IndexFile> m_Idx; ///< Index file (pin / nin).
CRef<CWriteDB_HeaderFile> m_Hdr; ///< Header file (phr / nhr).
CRef<CWriteDB_SequenceFile> m_Seq; ///< Sequence file (psq / nsq).
-
+
CRef<CWriteDB_Isam> m_AccIsam; ///< Accession index (psi+psd / nsi+nsd).
CRef<CWriteDB_Isam> m_GiIsam; ///< GI index (pni+pnd / nni+nnd).
CRef<CWriteDB_Isam> m_PigIsam; ///< PIG index (ppi+ppd, protein only).
CRef<CWriteDB_Isam> m_TraceIsam; ///< Trace ID index (pti+ptd or nti+ntd).
CRef<CWriteDB_Isam> m_HashIsam; ///< Hash index (phi+phd or nhi+nhd).
CRef<CWriteDB_GiIndex> m_GiIndex;///< OID->GI lookup (pgx or ngx).
-
+
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \
(!defined(NCBI_COMPILER_MIPSPRO)) )
/// Database columns.
@@ -275,9 +275,9 @@ private:
/// Included Seq_ids
set<string> m_IdSet;
-
+
// Functions
-
+
/// Compute base-length of compressed nucleotide sequence.
///
/// Nucleotide sequences stored on disk are packed 4 bases to a byte,
@@ -285,7 +285,7 @@ private:
/// data plus a 'remainder' value (from 0-3) that indicates how many of
/// the bases of the last byte are sequence data. This method finds the
/// exact length in bases for a nucleotide sequence packed in this way.
- ///
+ ///
/// @param seq Ncbi2na sequence with length remainder encoding.
/// @return Length in bases of actual sequence data in this sequence.
int x_FindNuclLength(const string & seq);
diff --git a/c++/src/objtools/blast/services/Makefile.blast_services.lib b/c++/src/objtools/blast/services/Makefile.blast_services.lib
index e53b598..b598c92 100644
--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.blast_services.lib 427429 2014-02-20 13:41:40Z gouriano $
+# $Id: Makefile.blast_services.lib 468535 2015-05-26 13:23:32Z ucko $
WATCHERS = madden camacho
@@ -8,6 +8,8 @@ SRC = blast_services
LIB = blast_services
+DLL_LIB = xnetblastcli xnetblast
+
CFLAGS = $(FAST_CFLAGS)
CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
CXXFLAGS = $(FAST_CXXFLAGS)
diff --git a/c++/src/objtools/blast/services/blast_services.cpp b/c++/src/objtools/blast/services/blast_services.cpp
index 8dd86ab..ed63345 100644
--- a/c++/src/objtools/blast/services/blast_services.cpp
+++ b/c++/src/objtools/blast/services/blast_services.cpp
@@ -1,4 +1,4 @@
-/* $Id: blast_services.cpp 465078 2015-04-16 17:36:39Z ivanov $
+/* $Id: blast_services.cpp 464987 2015-04-15 19:29:32Z merezhuk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/cleanup/autogenerated_cleanup.cpp b/c++/src/objtools/cleanup/autogenerated_cleanup.cpp
index 294134c..0bd65e6 100644
--- a/c++/src/objtools/cleanup/autogenerated_cleanup.cpp
+++ b/c++/src/objtools/cleanup/autogenerated_cleanup.cpp
@@ -1,4 +1,4 @@
-/* $Id: autogenerated_cleanup.cpp 404925 2013-06-27 18:47:47Z kornbluh $
+/* $Id: autogenerated_cleanup.cpp 477586 2015-08-31 17:42:50Z fukanchi $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,54 +39,9 @@
BEGIN_SCOPE(ncbi)
BEGIN_SCOPE(objects)
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( std::string & arg0 )
-{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_named_annot_track_ETC( CTextseq_id & arg0 )
-{ // type Sequence
- if( arg0.IsSetAccession() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAccession() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
- if( arg0.IsSetRelease() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRelease() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_named_annot_track_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( CTextseq_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_named_annot_track_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_ETC( CObject_id & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case CObject_id::e_Str:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStr() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( CObject_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_ETC( CDbtag & arg0 )
{ // type Sequence
m_NewCleanup.DbtagBC( arg0 );
- if( arg0.IsSetDb() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDb() );
- }
- if( arg0.IsSetTag() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetTag() );
- }
} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( CDbtag & arg0 )
@@ -94,76 +49,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_giim_ETC( CGiimport_id & arg0 )
-{ // type Sequence
- if( arg0.IsSetDb() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDb() );
- }
- if( arg0.IsSetRelease() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRelease() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_giim_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_ETC( CGiimport_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_giim_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_id_ETC( CId_pat::C_Id & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case CId_pat::C_Id::e_App_number:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetApp_number() );
- break;
- case CId_pat::C_Id::e_Number:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNumber() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_id_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_ETC( CId_pat & arg0 )
-{ // type Sequence
- if( arg0.IsSetCountry() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCountry() );
- }
- if( arg0.IsSetDoc_type() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDoc_type() );
- }
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_id_ETC( arg0.SetId() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC( CId_pat & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_ETC( CPatent_seq_id & arg0 )
-{ // type Sequence
- if( arg0.IsSetCit() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC( arg0.SetCit() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_ETC( CPatent_seq_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_mol_ETC( CPDB_mol_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_mol_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_std_ETC( CDate_std & arg0 )
{ // type Sequence
m_NewCleanup.x_DateStdBC( arg0 );
- if( arg0.IsSetSeason() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSeason() );
- }
} // end of x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_std_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_ETC( CDate_std & arg0 )
@@ -177,9 +65,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
case CDate::e_Std:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_ETC( arg0.SetStd() );
break;
- case CDate::e_Str:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStr() );
- break;
default:
break;
}
@@ -192,9 +77,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_ETC( CPDB_seq_id & arg0 )
{ // type Sequence
- if( arg0.IsSetMol() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_mol_ETC( arg0.SetMol() );
- }
if( arg0.IsSetRel() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetRel() );
}
@@ -209,57 +91,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
{ // type Choice
m_NewCleanup.SeqIdBC( arg0 );
switch( arg0.Which() ) {
- case CSeq_id::e_Ddbj:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetDdbj() );
- break;
- case CSeq_id::e_Embl:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetEmbl() );
- break;
- case CSeq_id::e_Genbank:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetGenbank() );
- break;
case CSeq_id::e_General:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetGeneral() );
break;
- case CSeq_id::e_Giim:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_ETC( arg0.SetGiim() );
- break;
- case CSeq_id::e_Gpipe:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetGpipe() );
- break;
- case CSeq_id::e_Local:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetLocal() );
- break;
- case CSeq_id::e_Named_annot_track:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetNamed_annot_track() );
- break;
- case CSeq_id::e_Other:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetOther() );
- break;
- case CSeq_id::e_Patent:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_ETC( arg0.SetPatent() );
- break;
case CSeq_id::e_Pdb:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_ETC( arg0.SetPdb() );
break;
- case CSeq_id::e_Pir:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetPir() );
- break;
- case CSeq_id::e_Prf:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetPrf() );
- break;
- case CSeq_id::e_Swissprot:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetSwissprot() );
- break;
- case CSeq_id::e_Tpd:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetTpd() );
- break;
- case CSeq_id::e_Tpe:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetTpe() );
- break;
- case CSeq_id::e_Tpg:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( arg0.SetTpg() );
- break;
default:
break;
}
@@ -323,12 +160,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_ids_E_E_ETC( CFeat_id & arg0 )
case CFeat_id::e_General:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetGeneral() );
break;
- case CFeat_id::e_Giim:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_ETC( arg0.SetGiim() );
- break;
- case CFeat_id::e_Local:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetLocal() );
- break;
default:
break;
}
@@ -402,7 +233,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_E1812_ETC( CSeq_loc & arg0 )
{ // type Choice
m_NewCleanup.SeqLocBC( arg0 );
- m_NewCleanup.ConvertSeqLocWholeToInt( arg0 );
+ m_NewCleanup.x_BothStrandBC( arg0 );
switch( arg0.Which() ) {
case CSeq_loc::e_Bond:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_bond_ETC( arg0.SetBond() );
@@ -480,15 +311,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data( Tcontainer_ncbi
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_object1818( CUser_object & arg0 )
{ // type Sequence
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetClass() );
- }
if( arg0.IsSetData() ) {
x_BasicCleanupSeqFeat_exts_E_E_data( arg0.SetData() );
}
- if( arg0.IsSetType() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetType() );
- }
} // end of x_BasicCleanupSeqFeat_exts_E_object1818
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data_object( CUser_object & arg0 )
@@ -498,15 +323,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data_object(
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E1817( CUser_object & arg0 )
{ // type Sequence
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetClass() );
- }
if( arg0.IsSetData() ) {
x_BasicCleanupSeqFeat_exts_E_E_data( arg0.SetData() );
}
- if( arg0.IsSetType() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetType() );
- }
} // end of x_BasicCleanupSeqFeat_exts_E_E1817
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data_objects_E( CUser_object & arg0 )
@@ -545,9 +364,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_ETC( CUser_f
if( arg0.IsSetData() ) {
x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data( arg0.SetData() );
}
- if( arg0.IsSetLabel() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetLabel() );
- }
} // end of x_BasicCleanupSeqFeat_exts_E_E_data_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_fields_E_ETC( CUser_field & arg0 )
@@ -565,15 +381,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_object1816_ETC( CUser_object & arg0 )
{ // type Sequence
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetClass() );
- }
if( arg0.IsSetData() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_fields_ETC( arg0.SetData() );
}
- if( arg0.IsSetType() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetType() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_object1816_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_E_ETC( CUser_object & arg0 )
@@ -589,34 +399,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC
-template< typename Tcontainer_ncbi_cref_cobject_id_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC( Tcontainer_ncbi_cref_cobject_id_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cobject_id_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_E_ETC( CScore & arg0 )
-{ // type Sequence
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetId() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_ETC( CScore & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cscore_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( Tcontainer_ncbi_cref_cscore_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cscore_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC
-
template< typename Tcontainer_ncbi_cref_cseq_id_ >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( Tcontainer_ncbi_cref_cseq_id_ & arg0 )
{ // type UniSequence
@@ -630,9 +412,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetIds() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetIds() );
}
- if( arg0.IsSetScores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_dendiag_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_dendiag_E_ETC( CDense_diag & arg0 )
@@ -653,9 +432,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetIds() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetIds() );
}
- if( arg0.IsSetScores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_denseg_denseg_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_denseg_ETC( CDense_seg & arg0 )
@@ -688,9 +464,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetIds() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetIds() );
}
- if( arg0.IsSetScores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_packed_packed_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_packed_ETC( CPacked_seg & arg0 )
@@ -706,9 +479,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetSecond_id() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetSecond_id() );
}
- if( arg0.IsSetSeg_scores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetSeg_scores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_rows_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_rows_E_ETC( CSparse_align & arg0 )
@@ -729,9 +499,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetMaster_id() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetMaster_id() );
}
- if( arg0.IsSetRow_scores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetRow_scores() );
- }
if( arg0.IsSetRows() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_rows_ETC( arg0.SetRows() );
}
@@ -742,33 +509,8 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_donor_after_exon_ETC( CSplice_site & arg0 )
-{ // type Sequence
- if( arg0.IsSetBases() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetBases() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_donor_after_exon_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_ETC( CSplice_site & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_donor_after_exon_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_scores_ETC( CScore_set & arg0 )
-{ // type Reference
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.Set() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_scores_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_ETC( CSpliced_exon & arg0 )
{ // type Sequence
- if( arg0.IsSetAcceptor_before_exon() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_ETC( arg0.SetAcceptor_before_exon() );
- }
- if( arg0.IsSetDonor_after_exon() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_ETC( arg0.SetDonor_after_exon() );
- }
if( arg0.IsSetExt() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC( arg0.SetExt() );
}
@@ -778,9 +520,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetProduct_id() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetProduct_id() );
}
- if( arg0.IsSetScores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_scores_ETC( arg0.SetScores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_ETC( CSpliced_exon & arg0 )
@@ -822,9 +561,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetLoc() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_equiv_ETC( arg0.SetLoc() );
}
- if( arg0.IsSetScores() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScores() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_std_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_std_E_ETC( CStd_seg & arg0 )
@@ -877,12 +613,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetExt() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC( arg0.SetExt() );
}
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC( arg0.SetId() );
- }
- if( arg0.IsSetScore() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScore() );
- }
if( arg0.IsSetSegs() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs( arg0.SetSegs() );
}
@@ -913,41 +643,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Postal_code );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Street );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Sub );
- if( arg0.IsSetAffil() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAffil() );
- }
- if( arg0.IsSetCity() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCity() );
- }
- if( arg0.IsSetCountry() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCountry() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
- if( arg0.IsSetEmail() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetEmail() );
- }
- if( arg0.IsSetFax() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFax() );
- }
- if( arg0.IsSetPhone() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPhone() );
- }
- if( arg0.IsSetPostal_code() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPostal_code() );
- }
- if( arg0.IsSetStreet() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStreet() );
- }
- if( arg0.IsSetSub() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSub() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_std_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_str_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
m_NewCleanup.x_CleanupStringMarkChanged( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_str_ETC
@@ -971,62 +670,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_ETC
-template< typename Tcontainer_std_string_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( Tcontainer_std_string_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_std_string_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( *iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_name_ETC( CName_std & arg0 )
-{ // type Sequence
- if( arg0.IsSetFirst() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFirst() );
- }
- if( arg0.IsSetFull() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFull() );
- }
- if( arg0.IsSetInitials() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetInitials() );
- }
- if( arg0.IsSetLast() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLast() );
- }
- if( arg0.IsSetMiddle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMiddle() );
- }
- if( arg0.IsSetSuffix() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSuffix() );
- }
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_name_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_ETC( CName_std & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_name_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_ETC( CPerson_id & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CPerson_id::e_Consortium:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetConsortium() );
- break;
case CPerson_id::e_Dbtag:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetDbtag() );
break;
- case CPerson_id::e_Ml:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMl() );
- break;
- case CPerson_id::e_Name:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_ETC( arg0.SetName() );
- break;
- case CPerson_id::e_Str:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStr() );
- break;
default:
break;
}
@@ -1063,15 +712,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_ETC( CAuth_list::C_Names & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CAuth_list::C_Names::e_Ml:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetMl() );
- break;
case CAuth_list::C_Names::e_Std:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_ETC( arg0.SetStd() );
break;
- case CAuth_list::C_Names::e_Str:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetStr() );
- break;
default:
break;
}
@@ -1092,60 +735,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC
-template< typename Tcontainer_ncbi_cref_c_e_c_e >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_E_ETC( Tcontainer_ncbi_cref_c_e_c_e & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case Tcontainer_ncbi_cref_c_e_c_e::e_Abr:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAbr() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Coden:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCoden() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Isbn:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIsbn() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Iso_jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIso_jta() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Issn:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIssn() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetJta() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Ml_jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMl_jta() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Name:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Trans:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTrans() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Tsub:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTsub() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_E_ETC
-
-template< typename Tcontainer_ncbi_cref_c_e_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_ETC( Tcontainer_ncbi_cref_c_e_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_c_e_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( CTitle & arg0 )
-{ // type Reference
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_ETC( arg0.Set() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_history_E_E_ETC( CPubStatusDate & arg0 )
{ // type Sequence
if( arg0.IsSetDate() ) {
@@ -1173,18 +762,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_retract_ETC( CCitRetract & arg0 )
-{ // type Sequence
- if( arg0.IsSetExp() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetExp() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_retract_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_ETC( CCitRetract & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_retract_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_ETC( CImprint & arg0 )
{ // type Sequence
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Issue );
@@ -1203,33 +780,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetHistory() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_ETC( arg0.SetHistory() );
}
- if( arg0.IsSetIssue() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIssue() );
- }
- if( arg0.IsSetLanguage() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLanguage() );
- }
- if( arg0.IsSetPages() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPages() );
- }
- if( arg0.IsSetPart_sup() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPart_sup() );
- }
- if( arg0.IsSetPart_supi() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPart_supi() );
- }
if( arg0.IsSetPub() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_ETC( arg0.SetPub() );
}
- if( arg0.IsSetRetract() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_ETC( arg0.SetRetract() );
- }
- if( arg0.IsSetSection() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSection() );
- }
- if( arg0.IsSetVolume() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVolume() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( CImprint & arg0 )
@@ -1242,15 +795,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetAuthors() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetAuthors() );
}
- if( arg0.IsSetColl() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( arg0.SetColl() );
- }
if( arg0.IsSetImp() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( arg0.SetImp() );
}
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( arg0.SetTitle() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_ETC( CCit_book & arg0 )
@@ -1263,9 +810,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetImp() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( arg0.SetImp() );
}
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( arg0.SetTitle() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_journal_journal_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_journal_ETC( CCit_jour & arg0 )
@@ -1278,9 +822,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetNumber() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNumber() );
- }
if( arg0.IsSetPlace() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_ETC( arg0.SetPlace() );
}
@@ -1323,44 +864,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_from_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_E_ETC( CDOI & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pii_ETC( CPII & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pii_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmcpid_ETC( CPmcPid & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmcpid_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmpid_ETC( CPmPid & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmpid_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_ETC( CArticleId & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CArticleId::e_Doi:
- x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_E_ETC( arg0.SetDoi() );
- break;
case CArticleId::e_Other:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetOther() );
break;
- case CArticleId::e_Pii:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pii_ETC( arg0.SetPii() );
- break;
- case CArticleId::e_Pmcpid:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmcpid_ETC( arg0.SetPmcpid() );
- break;
- case CArticleId::e_Pmpid:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmpid_ETC( arg0.SetPmpid() );
- break;
default:
break;
}
@@ -1388,7 +897,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_title_title_E_name_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_StripSpacesMarkChanged( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_title_title_E_name_ETC
@@ -1396,36 +904,9 @@ template< typename Tcontainer_ncbi_cref_c_e_c_e >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_title_title_E_ETC( Tcontainer_ncbi_cref_c_e_c_e & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case Tcontainer_ncbi_cref_c_e_c_e::e_Abr:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAbr() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Coden:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCoden() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Isbn:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIsbn() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Iso_jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIso_jta() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Issn:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIssn() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetJta() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Ml_jta:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMl_jta() );
- break;
case Tcontainer_ncbi_cref_c_e_c_e::e_Name:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_title_title_E_name_ETC( arg0.SetName() );
break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Trans:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTrans() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Tsub:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTsub() );
- break;
default:
break;
}
@@ -1491,144 +972,14 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_journal_ETC( Tcontaine
}
} // end of x_BasicCleanupSeqFeat_cit_cit_journal_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_E_ETC( CMedline_qual & arg0 )
-{ // type Sequence
- if( arg0.IsSetSubh() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSubh() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_ETC( CMedline_qual & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cmedline_qual_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_ETC( Tcontainer_ncbi_cref_cmedline_qual_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cmedline_qual_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_ETC( CMedline_mesh & arg0 )
-{ // type Sequence
- if( arg0.IsSetQual() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_ETC( arg0.SetQual() );
- }
- if( arg0.IsSetTerm() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTerm() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_ETC( CMedline_mesh & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cmedline_mesh_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_ETC( Tcontainer_ncbi_cref_cmedline_mesh_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cmedline_mesh_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_E_ETC( CMedline_field & arg0 )
-{ // type Sequence
- if( arg0.IsSetStr() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStr() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_ETC( CMedline_field & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cmedline_field_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_ETC( Tcontainer_ncbi_cref_cmedline_field_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cmedline_field_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_E_ETC( CMedline_rn & arg0 )
-{ // type Sequence
- if( arg0.IsSetCit() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCit() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_ETC( CMedline_rn & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cmedline_rn_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_ETC( Tcontainer_ncbi_cref_cmedline_rn_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cmedline_rn_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_E_ETC( CMedline_si & arg0 )
-{ // type Sequence
- if( arg0.IsSetCit() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCit() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_ETC( CMedline_si & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cmedline_si_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_ETC( Tcontainer_ncbi_cref_cmedline_si_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cmedline_si_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_ETC( CMedline_entry & arg0 )
{ // type Sequence
- if( arg0.IsSetAbstract() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAbstract() );
- }
if( arg0.IsSetCit() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_ETC( arg0.SetCit() );
}
if( arg0.IsSetEm() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetEm() );
}
- if( arg0.IsSetGene() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetGene() );
- }
- if( arg0.IsSetIdnum() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetIdnum() );
- }
- if( arg0.IsSetMesh() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_ETC( arg0.SetMesh() );
- }
- if( arg0.IsSetMlfield() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_ETC( arg0.SetMlfield() );
- }
- if( arg0.IsSetPub_type() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetPub_type() );
- }
- if( arg0.IsSetSubstance() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_ETC( arg0.SetSubstance() );
- }
- if( arg0.IsSetXref() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_ETC( arg0.SetXref() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_ETC( CMedline_entry & arg0 )
@@ -1646,15 +997,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_medline_ETC( Tcontaine
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_priority_E_E_ETC( CPatent_priority & arg0 )
{ // type Sequence
- if( arg0.IsSetCountry() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCountry() );
- }
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetNumber() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNumber() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_priority_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_priority_E_ETC( CPatent_priority & arg0 )
@@ -1672,15 +1017,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_ETC( CCit_pat & arg0 )
{ // type Sequence
- if( arg0.IsSetAbstract() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAbstract() );
- }
if( arg0.IsSetApp_date() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetApp_date() );
}
- if( arg0.IsSetApp_number() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetApp_number() );
- }
if( arg0.IsSetApplicants() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetApplicants() );
}
@@ -1688,29 +1027,14 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetAssignees() );
}
if( arg0.IsSetAuthors() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetAuthors() );
- }
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetClass() );
- }
- if( arg0.IsSetCountry() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCountry() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetAuthors() );
}
if( arg0.IsSetDate_issue() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate_issue() );
}
- if( arg0.IsSetDoc_type() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDoc_type() );
- }
- if( arg0.IsSetNumber() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNumber() );
- }
if( arg0.IsSetPriority() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_priority_ETC( arg0.SetPriority() );
}
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_ETC( CCit_pat & arg0 )
@@ -1759,27 +1083,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetAuthors() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( arg0.SetAuthors() );
}
- if( arg0.IsSetCit() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCit() );
- }
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetIssue() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIssue() );
- }
- if( arg0.IsSetJournal() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( arg0.SetJournal() );
- }
- if( arg0.IsSetPages() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPages() );
- }
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- }
- if( arg0.IsSetVolume() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVolume() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_gen_gen_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_gen_ETC( CCit_gen & arg0 )
@@ -1792,9 +1098,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetCit() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_ETC( arg0.SetCit() );
}
- if( arg0.IsSetMan_id() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMan_id() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_ETC( CCit_let & arg0 )
@@ -1815,9 +1118,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetDescr() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescr() );
- }
if( arg0.IsSetImp() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( arg0.SetImp() );
}
@@ -1861,9 +1161,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_pub_E_E_ETC( CPub & ar
// instead of int, but we can't tell where by looking at the .asn file.
x_BasicCleanupSeqFeat_cit_cit_pub_E_E_muid( *(int*)&arg0.SetMuid() );
break;
- case CPub::e_Pat_id:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC( arg0.SetPat_id() );
- break;
case CPub::e_Patent:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_ETC( arg0.SetPatent() );
break;
@@ -1935,6 +1232,11 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_comment_ETC( std::string & arg
m_NewCleanup.x_FixUpEllipsis( arg0 );
} // end of x_BasicCleanupSeqFeat_comment_ETC
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_TrimInternalSemicolonsMarkChanged( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC
+
template< typename Tcontainer_ncbi_cref_cdbtag_ >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( Tcontainer_ncbi_cref_cdbtag_ & arg0 )
{ // type UniSequence
@@ -1945,8 +1247,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_mod_E_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
- m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
+ m_NewCleanup.OrgrefModBC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_mod_E_ETC
template< typename Tcontainer_std_string_ >
@@ -1961,12 +1262,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
{ // type Sequence
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Attrib );
CLEAN_AND_COMPRESS_STRING_MEMBER_JUNK( arg0, Subname );
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetSubname() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSubname() );
- }
+ m_NewCleanup.x_OrgModBC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_E_ETC( COrgMod & arg0 )
@@ -1982,24 +1278,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_namedhybrid_ETC( CBinomialOrgName & arg0 )
-{ // type Sequence
- if( arg0.IsSetGenus() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetGenus() );
- }
- if( arg0.IsSetSpecies() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSpecies() );
- }
- if( arg0.IsSetSubspecies() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSubspecies() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_namedhybrid_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( CBinomialOrgName & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_namedhybrid_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E( COrgName & arg0 )
{ // type Reference
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC( arg0 );
@@ -2020,54 +1298,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_E_ETC( CTaxElement & arg0 )
-{ // type Sequence
- if( arg0.IsSetLevel() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLevel() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_ETC( CTaxElement & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_ETC
-
-template< typename Tcontainer_ncbi_cref_ctaxelement_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_ETC( Tcontainer_ncbi_cref_ctaxelement_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_ctaxelement_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_ETC( CPartialOrgName & arg0 )
-{ // type Reference
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_ETC( arg0.Set() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( COrgName::C_Name & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case COrgName::C_Name::e_Binomial:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( arg0.SetBinomial() );
- break;
case COrgName::C_Name::e_Hybrid:
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid( arg0.SetHybrid() );
break;
- case COrgName::C_Name::e_Namedhybrid:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( arg0.SetNamedhybrid() );
- break;
- case COrgName::C_Name::e_Partial:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_ETC( arg0.SetPartial() );
- break;
- case COrgName::C_Name::e_Virus:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVirus() );
- break;
default:
break;
}
@@ -2078,15 +1314,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
CLEAN_STRING_MEMBER( arg0, Attrib );
CLEAN_STRING_MEMBER( arg0, Div );
CLEAN_STRING_MEMBER( arg0, Lineage );
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
- if( arg0.IsSetLineage() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLineage() );
- }
if( arg0.IsSetMod() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC( arg0.SetMod() );
}
@@ -2118,21 +1345,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_orgname_name_ETC( COrgName::C_Name & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case COrgName::C_Name::e_Binomial:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( arg0.SetBinomial() );
- break;
case COrgName::C_Name::e_Hybrid:
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_orgname_name_hybrid_ETC( arg0.SetHybrid() );
break;
- case COrgName::C_Name::e_Namedhybrid:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( arg0.SetNamedhybrid() );
- break;
- case COrgName::C_Name::e_Partial:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_ETC( arg0.SetPartial() );
- break;
- case COrgName::C_Name::e_Virus:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVirus() );
- break;
default:
break;
}
@@ -2144,15 +1359,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_or
CLEAN_STRING_MEMBER( arg0, Div );
CLEAN_STRING_MEMBER( arg0, Lineage );
m_NewCleanup.x_CleanupOrgModAndSubSourceOther( arg0, *m_LastArg_x_BasicCleanupSeqFeat_data_data_biosrc_biosrc );
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
- if( arg0.IsSetLineage() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLineage() );
- }
if( arg0.IsSetMod() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC( arg0.SetMod() );
}
@@ -2170,10 +1376,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_or
{ // type Sequence
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Common );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Taxname );
- m_NewCleanup.x_GBQualToOrgRef( arg0, *m_LastArg_BasicCleanupSeqFeat );
m_NewCleanup.OrgrefBC( arg0 );
+ m_NewCleanup.x_GBQualToOrgRef( arg0, *m_LastArg_BasicCleanupSeqFeat );
if( arg0.IsSetCommon() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCommon() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( arg0.SetCommon() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
@@ -2184,12 +1390,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_or
if( arg0.IsSetOrgname() ) {
x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_org_orgname( arg0.SetOrgname() );
}
- if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSyn() );
- }
- if( arg0.IsSetTaxname() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxname() );
- }
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.x_PostOrgRef( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_org
@@ -2199,85 +1399,14 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org( C
x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_org( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_name_ETC( CPCRPrimerName & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_name_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_seq_ETC( CPCRPrimerSeq & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_seq_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_ETC( CPCRPrimer & arg0 )
-{ // type Sequence
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_name_ETC( arg0.SetName() );
- }
- if( arg0.IsSetSeq() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_seq_ETC( arg0.SetSeq() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_ETC( CPCRPrimer & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cpcrprimer_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_ETC( Tcontainer_ncbi_cref_cpcrprimer_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cpcrprimer_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_ETC( CPCRPrimerSet & arg0 )
-{ // type Reference
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_ETC( arg0.Set() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_ETC( CPCRReaction & arg0 )
-{ // type Sequence
- if( arg0.IsSetForward() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_ETC( arg0.SetForward() );
- }
- if( arg0.IsSetReverse() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_ETC( arg0.SetReverse() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_ETC( CPCRReaction & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cpcrreaction_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_ETC( Tcontainer_ncbi_cref_cpcrreaction_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cpcrreaction_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_ETC( CPCRReactionSet & arg0 )
{ // type Reference
m_NewCleanup.PCRReactionSetBC( arg0 );
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_ETC( arg0.Set() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_source_source_ETC( CSubSource & arg0 )
{ // type Sequence
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
+ m_NewCleanup.x_SubSourceBC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_source_source_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_source_ETC( CSubSource & arg0 )
@@ -2319,42 +1448,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_biosrc( CBioSource &
x_BasicCleanupSeqFeat_data_data_biosrc_biosrc( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_biosrc
-template< typename Tcontainer_ncbi_cref_c_e_c_e >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_E_ETC( Tcontainer_ncbi_cref_c_e_c_e & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case Tcontainer_ncbi_cref_c_e_c_e::e_Name:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Ncbieaa:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNcbieaa() );
- break;
- case Tcontainer_ncbi_cref_c_e_c_e::e_Sncbieaa:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSncbieaa() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_E_ETC
-
-template< typename Tcontainer_ncbi_cref_c_e_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_ETC( Tcontainer_ncbi_cref_c_e_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_c_e_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_ETC( CGenetic_code & arg0 )
-{ // type Reference
- if( arg0.IsSet() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_ETC( arg0.Set() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location1813_ETC( CSeq_loc & arg0 )
{ // type Choice
m_NewCleanup.SeqLocBC( arg0 );
+ m_NewCleanup.x_BothStrandBC( arg0 );
m_NewCleanup.ConvertSeqLocWholeToInt( arg0 );
switch( arg0.Which() ) {
case CSeq_loc::e_Bond:
@@ -2420,9 +1517,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cd
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_cdregion_cdregion( CCdregion & arg0 )
{ // type Sequence
m_NewCleanup.CdregionFeatBC( arg0, *m_LastArg_BasicCleanupSeqFeat );
- if( arg0.IsSetCode() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_ETC( arg0.SetCode() );
- }
if( arg0.IsSetCode_break() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_break_ETC( arg0.SetCode_break() );
}
@@ -2471,12 +1565,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone
if( arg0.IsSetClone_seq() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_ETC( arg0.SetClone_seq() );
}
- if( arg0.IsSetLibrary() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLibrary() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_ETC( CClone_ref & arg0 )
@@ -2484,23 +1572,22 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_ETC(
x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( std::string & arg0 )
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC
+
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
+ m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_formal_name_ETC( CGene_nomenclature & arg0 )
{ // type Sequence
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
if( arg0.IsSetSource() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetSource() );
}
- if( arg0.IsSetSymbol() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSymbol() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_formal_name_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_ETC( CGene_nomenclature & arg0 )
@@ -2508,13 +1595,26 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_formal_name_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_ETC
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
+ m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
+ m_NewCleanup.x_TrimInternalSemicolonsMarkChanged( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC
+
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_E_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
+ m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_E_ETC
+
template< typename Tcontainer_std_string_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( Tcontainer_std_string_ & arg0 )
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC( Tcontainer_std_string_ & arg0 )
{ // type UniSequence
NON_CONST_ITERATE( typename Tcontainer_std_string_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( *iter );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_E_ETC( *iter );
}
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_gene_gene( CGene_ref & arg0 )
{ // type Sequence
@@ -2523,30 +1623,31 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_gene_gene( CGene_ref
CLEAN_STRING_MEMBER( arg0, Locus );
CLEAN_STRING_MEMBER( arg0, Locus_tag );
CLEAN_STRING_MEMBER( arg0, Maploc );
+ CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Locus );
m_NewCleanup.GeneFeatBC( arg0, *m_LastArg_BasicCleanupSeqFeat );
if( arg0.IsSetAllele() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetAllele() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetAllele() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
}
if( arg0.IsSetDesc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetDesc() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC( arg0.SetDesc() );
}
if( arg0.IsSetFormal_name() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_ETC( arg0.SetFormal_name() );
}
if( arg0.IsSetLocus() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetLocus() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC( arg0.SetLocus() );
}
if( arg0.IsSetLocus_tag() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetLocus_tag() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetLocus_tag() );
}
if( arg0.IsSetMaploc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetMaploc() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetMaploc() );
}
if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( arg0.SetSyn() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC( arg0.SetSyn() );
}
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.GenerefBC( arg0 );
@@ -2557,25 +1658,11 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_gene( CGene_ref & ar
x_BasicCleanupSeqFeat_data_data_gene_gene( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_gene
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( CHeterogen & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( CImp_feat & arg0 )
{ // type Sequence
CLEAN_STRING_MEMBER( arg0, Descr );
CLEAN_STRING_MEMBER( arg0, Key );
CLEAN_STRING_MEMBER( arg0, Loc );
- if( arg0.IsSetDescr() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescr() );
- }
- if( arg0.IsSetKey() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetKey() );
- }
- if( arg0.IsSetLoc() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLoc() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC( CImp_feat & arg0 )
@@ -2583,30 +1670,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC( CI
x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_enum_ETC( CNum_enum & arg0 )
-{ // type Sequence
- if( arg0.IsSetNames() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetNames() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_enum_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_ETC( CNum_enum & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_enum_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_real_ETC( CNum_real & arg0 )
-{ // type Sequence
- if( arg0.IsSetUnits() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetUnits() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_real_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_ETC( CNum_real & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_real_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns1793_ETC( CSeq_align & arg0 )
{ // type Sequence
if( arg0.IsSetBounds() ) {
@@ -2615,12 +1678,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
if( arg0.IsSetExt() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC( arg0.SetExt() );
}
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC( arg0.SetId() );
- }
- if( arg0.IsSetScore() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( arg0.SetScore() );
- }
if( arg0.IsSetSegs() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs( arg0.SetSegs() );
}
@@ -2646,12 +1703,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ETC( CNumbering & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CNumbering::e_Enum:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_ETC( arg0.SetEnum() );
- break;
- case CNumbering::e_Real:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_ETC( arg0.SetReal() );
- break;
case CNumbering::e_Ref:
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ETC( arg0.SetRef() );
break;
@@ -2670,15 +1721,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
CLEAN_STRING_MEMBER( arg0, Attrib );
CLEAN_STRING_MEMBER( arg0, Div );
CLEAN_STRING_MEMBER( arg0, Lineage );
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
- if( arg0.IsSetLineage() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLineage() );
- }
if( arg0.IsSetMod() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC( arg0.SetMod() );
}
@@ -2696,10 +1738,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_org_org( COrg_ref &
{ // type Sequence
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Common );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Taxname );
- m_NewCleanup.x_GBQualToOrgRef( arg0, *m_LastArg_BasicCleanupSeqFeat );
m_NewCleanup.OrgrefBC( arg0 );
+ m_NewCleanup.x_GBQualToOrgRef( arg0, *m_LastArg_BasicCleanupSeqFeat );
if( arg0.IsSetCommon() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCommon() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( arg0.SetCommon() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
@@ -2710,12 +1752,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_org_org( COrg_ref &
if( arg0.IsSetOrgname() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_ETC( arg0.SetOrgname() );
}
- if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSyn() );
- }
- if( arg0.IsSetTaxname() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxname() );
- }
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.x_PostOrgRef( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_org_org
@@ -2725,20 +1761,29 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_org( COrg_ref & arg0
x_BasicCleanupSeqFeat_data_data_org_org( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_org
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.ProtActivityBC( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC
+
+template< typename Tcontainer_std_string_ >
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( Tcontainer_std_string_ & arg0 )
+{ // type UniSequence
+ NON_CONST_ITERATE( typename Tcontainer_std_string_, iter, arg0 ) {
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( *iter );
+ }
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_desc_ETC( std::string & arg0 )
{ // type Primitive
m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
- m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
- m_NewCleanup.x_RemoveFlankingQuotes( arg0 );
+ m_NewCleanup.x_TrimInternalSemicolonsMarkChanged( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_desc_ETC
template< typename Tcontainer_std_string_ >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ec_ETC( Tcontainer_std_string_ & arg0 )
{ // type UniSequence
m_NewCleanup.x_CleanupECNumberList( arg0 );
- NON_CONST_ITERATE( typename Tcontainer_std_string_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( *iter );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ec_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_E_ETC( std::string & arg0 )
@@ -2747,6 +1792,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
m_NewCleanup.x_RemoveFlankingQuotes( arg0 );
+ m_NewCleanup.ProtNameBC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_E_ETC
template< typename Tcontainer_std_string_ >
@@ -2759,7 +1805,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_prot_prot( CProt_ref & arg0 )
{ // type Sequence
- CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Desc );
m_NewCleanup.ProtFeatfBC( arg0, *m_LastArg_BasicCleanupSeqFeat );
m_NewCleanup.ProtrefBC( arg0 );
if( arg0.IsSetActivity() ) {
@@ -2777,8 +1822,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_prot_prot( CProt_ref
if( arg0.IsSetName() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_ETC( arg0.SetName() );
}
- CLEAN_STRING_LIST( arg0, Activity );
- CLEAN_STRING_LIST( arg0, Ec );
CLEAN_STRING_LIST( arg0, Name );
m_NewCleanup.PostProtFeatfBC( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_prot_prot
@@ -2833,9 +1876,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
case CPub::e_Medline:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_ETC( arg0.SetMedline() );
break;
- case CPub::e_Pat_id:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC( arg0.SetPat_id() );
- break;
case CPub::e_Patent:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_ETC( arg0.SetPatent() );
break;
@@ -2874,16 +1914,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_pub_pub_pub_ETC( CPu
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_pub_pub_ETC( CPubdesc & arg0 )
{ // type Sequence
if( arg0.IsSetComment() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetComment() );
- }
- if( arg0.IsSetFig() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFig() );
- }
- if( arg0.IsSetMaploc() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMaploc() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetComment() );
}
if( arg0.IsSetNum() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_ETC( arg0.SetNum() );
@@ -2891,9 +1922,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_pub_pub_ETC( CPubdes
if( arg0.IsSetPub() ) {
x_BasicCleanupSeqFeat_data_data_pub_pub_pub_ETC( arg0.SetPub() );
}
- if( arg0.IsSetSeq_raw() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSeq_raw() );
- }
m_NewCleanup.PubdescBC( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_pub_pub_ETC
@@ -2904,21 +1932,27 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_pub_ETC( CPubdesc &
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data_region_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
m_NewCleanup.x_CleanupStringMarkChanged( arg0 );
m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
+ m_NewCleanup.x_TrimInternalSemicolonsMarkChanged( arg0 );
} // end of x_BasicCleanupSeqFeat_data_data_region_ETC
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_product_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
+ m_NewCleanup.x_RemoveFlankingQuotes( arg0 );
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_product_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC( CRNA_qual & arg0 )
{ // type Sequence
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Qual );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Val );
if( arg0.IsSetQual() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetQual() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetQual() );
}
if( arg0.IsSetVal() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetVal() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetVal() );
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC
@@ -2947,10 +1981,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Class );
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Product );
if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetClass() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetClass() );
}
if( arg0.IsSetProduct() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_desc_ETC( arg0.SetProduct() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_product_ETC( arg0.SetProduct() );
}
if( arg0.IsSetQuals() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_ETC( arg0.SetQuals() );
@@ -3020,9 +2054,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rsite_rsite
case CRsite_ref::e_Db:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetDb() );
break;
- case CRsite_ref::e_Str:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStr() );
- break;
default:
break;
}
@@ -3045,29 +2076,30 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
CLEAN_STRING_MEMBER( arg0, Locus );
CLEAN_STRING_MEMBER( arg0, Locus_tag );
CLEAN_STRING_MEMBER( arg0, Maploc );
+ CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Locus );
if( arg0.IsSetAllele() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetAllele() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetAllele() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
}
if( arg0.IsSetDesc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetDesc() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC( arg0.SetDesc() );
}
if( arg0.IsSetFormal_name() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_ETC( arg0.SetFormal_name() );
}
if( arg0.IsSetLocus() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetLocus() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC( arg0.SetLocus() );
}
if( arg0.IsSetLocus_tag() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetLocus_tag() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetLocus_tag() );
}
if( arg0.IsSetMaploc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetMaploc() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetMaploc() );
}
if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( arg0.SetSyn() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC( arg0.SetSyn() );
}
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.GenerefBC( arg0 );
@@ -3088,7 +2120,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC( CProt_ref & arg0 )
{ // type Sequence
- CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Desc );
m_NewCleanup.ProtrefBC( arg0 );
if( arg0.IsSetActivity() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( arg0.SetActivity() );
@@ -3105,8 +2136,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
if( arg0.IsSetName() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_ETC( arg0.SetName() );
}
- CLEAN_STRING_LIST( arg0, Activity );
- CLEAN_STRING_LIST( arg0, Ec );
CLEAN_STRING_LIST( arg0, Name );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC
@@ -3129,7 +2158,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Taxname );
m_NewCleanup.OrgrefBC( arg0 );
if( arg0.IsSetCommon() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCommon() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( arg0.SetCommon() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
@@ -3140,12 +2169,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
if( arg0.IsSetOrgname() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_ETC( arg0.SetOrgname() );
}
- if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSyn() );
- }
- if( arg0.IsSetTaxname() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxname() );
- }
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.x_PostOrgRef( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_ETC
@@ -3157,27 +2180,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txin
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_ETC( CTxinit & arg0 )
{ // type Sequence
- if( arg0.IsSetExpression() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetExpression() );
- }
if( arg0.IsSetGene() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC( arg0.SetGene() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
if( arg0.IsSetProtein() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC( arg0.SetProtein() );
}
- if( arg0.IsSetRna() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetRna() );
- }
- if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSyn() );
- }
- if( arg0.IsSetTxdescr() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTxdescr() );
- }
if( arg0.IsSetTxorg() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_ETC( arg0.SetTxorg() );
}
@@ -3191,15 +2199,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_ETC(
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_ext_ext1769_ETC( CUser_object & arg0 )
{ // type Sequence
m_NewCleanup.UserObjectBC( arg0 );
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetClass() );
- }
if( arg0.IsSetData() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_fields_ETC( arg0.SetData() );
}
- if( arg0.IsSetType() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetType() );
- }
} // end of x_BasicCleanupSeqFeat_ext_ext1769_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_ext_ETC( CUser_object & arg0 )
@@ -3207,103 +2209,34 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_ext_ETC( CUser_object & arg0 )
x_BasicCleanupSeqFeat_ext_ext1769_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_ext_ETC
-template< typename Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence_c_loss_of_heterozygosity >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_loss_of_heterozygosity_ETC( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence_c_loss_of_heterozygosity & arg0 )
-{ // type Sequence
- if( arg0.IsSetReference() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetReference() );
- }
- if( arg0.IsSetTest() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTest() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_loss_of_heterozygosity_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_variation( CVariation_ref & arg0 )
{ // type Reference
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation1805_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_variation
template< typename Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_ETC( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence & arg0 )
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence::e_Loss_of_heterozygosity:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_loss_of_heterozygosity_ETC( arg0.SetLoss_of_heterozygosity() );
- break;
- case Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence::e_Note:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNote() );
- break;
case Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence::e_Variation:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_variation( arg0.SetVariation() );
break;
default:
break;
}
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_ETC
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E
template< typename Tcontainer_ncbi_cref_c_e_consequence_ >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence( Tcontainer_ncbi_cref_c_e_consequence_ & arg0 )
{ // type UniSequence
NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_c_e_consequence_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_ETC( **iter );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E( **iter );
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacaa_ETC( CIUPACaa & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacaa_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacna_ETC( CIUPACna & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacna_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ncbieaa_ETC( CNCBIeaa & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.Set() );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ncbieaa_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ETC( CSeq_data & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case CSeq_data::e_Iupacaa:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacaa_ETC( arg0.SetIupacaa() );
- break;
- case CSeq_data::e_Iupacna:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacna_ETC( arg0.SetIupacna() );
- break;
- case CSeq_data::e_Ncbieaa:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ncbieaa_ETC( arg0.SetNcbieaa() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_ETC( CSeq_data & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_ETC( CSeq_literal & arg0 )
-{ // type Sequence
- if( arg0.IsSetSeq_data() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_ETC( arg0.SetSeq_data() );
- }
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_ETC( CSeq_literal & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_ETC( CDelta_item::C_Seq & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CDelta_item::C_Seq::e_Literal:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_ETC( arg0.SetLiteral() );
- break;
case CDelta_item::C_Seq::e_Loc:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_ETC( arg0.SetLoc() );
break;
@@ -3346,12 +2279,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_phenotype_E_E_ETC( CPhenotype & arg0 )
{ // type Sequence
- if( arg0.IsSetSource() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSource() );
- }
- if( arg0.IsSetTerm() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTerm() );
- }
if( arg0.IsSetXref() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetXref() );
}
@@ -3373,9 +2300,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
template< typename Tcvariation_ref_container_ncbi_cref_c_e_somatic_origin_c_e_somatic_origin_c_condition >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_condition_ETC( Tcvariation_ref_container_ncbi_cref_c_e_somatic_origin_c_e_somatic_origin_c_condition & arg0 )
{ // type Sequence
- if( arg0.IsSetDescription() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescription() );
- }
if( arg0.IsSetObject_id() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetObject_id() );
}
@@ -3406,17 +2330,11 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_E
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence( arg0.SetConsequence() );
}
if( arg0.IsSetData() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_ETC( arg0.SetData() );
- }
- if( arg0.IsSetDescription() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescription() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data( arg0.SetData() );
}
if( arg0.IsSetId() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
if( arg0.IsSetOther_ids() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetOther_ids() );
}
@@ -3426,15 +2344,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_E
if( arg0.IsSetPhenotype() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_phenotype_ETC( arg0.SetPhenotype() );
}
- if( arg0.IsSetSample_id() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetSample_id() );
- }
if( arg0.IsSetSomatic_origin() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_ETC( arg0.SetSomatic_origin() );
}
- if( arg0.IsSetSynonyms() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSynonyms() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_E1804_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations_E( CVariation_ref & arg0 )
@@ -3450,32 +2362,26 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_ETC( CVariation_ref::C_Data::C_Set & arg0 )
-{ // type Sequence
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set( CVariation_ref::C_Data::C_Set & arg0 )
+{ // type Sequence
if( arg0.IsSetVariations() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations( arg0.SetVariations() );
}
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_ETC
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_ETC( CVariation_ref::C_Data & arg0 )
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data( CVariation_ref::C_Data & arg0 )
{ // type Choice
switch( arg0.Which() ) {
case CVariation_ref::C_Data::e_Instance:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_ETC( arg0.SetInstance() );
break;
- case CVariation_ref::C_Data::e_Note:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNote() );
- break;
case CVariation_ref::C_Data::e_Set:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_ETC( arg0.SetSet() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set( arg0.SetSet() );
break;
default:
break;
}
-} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_ETC
+} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation1805_ETC( CVariation_ref & arg0 )
{ // type Sequence
@@ -3483,17 +2389,11 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence( arg0.SetConsequence() );
}
if( arg0.IsSetData() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_ETC( arg0.SetData() );
- }
- if( arg0.IsSetDescription() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescription() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data( arg0.SetData() );
}
if( arg0.IsSetId() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
if( arg0.IsSetOther_ids() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetOther_ids() );
}
@@ -3503,15 +2403,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
if( arg0.IsSetPhenotype() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_phenotype_ETC( arg0.SetPhenotype() );
}
- if( arg0.IsSetSample_id() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetSample_id() );
- }
if( arg0.IsSetSomatic_origin() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_ETC( arg0.SetSomatic_origin() );
}
- if( arg0.IsSetSynonyms() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSynonyms() );
- }
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation1805_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_ETC( CVariation_ref & arg0 )
@@ -3534,15 +2428,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data_data( CSeqFeatData & arg0
case CSeqFeatData::e_Gene:
x_BasicCleanupSeqFeat_data_data_gene( arg0.SetGene() );
break;
- case CSeqFeatData::e_Het:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( arg0.SetHet() );
- break;
case CSeqFeatData::e_Imp:
x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC( arg0.SetImp() );
break;
- case CSeqFeatData::e_Non_std_residue:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNon_std_residue() );
- break;
case CSeqFeatData::e_Num:
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_ETC( arg0.SetNum() );
break;
@@ -3617,9 +2505,55 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_v
}
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_ETC
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_location1767_ETC( CSeq_loc & arg0 )
+{ // type Choice
+ m_NewCleanup.SeqLocBC( arg0 );
+ m_NewCleanup.ConvertSeqLocWholeToInt( arg0 );
+ switch( arg0.Which() ) {
+ case CSeq_loc::e_Bond:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_bond_ETC( arg0.SetBond() );
+ break;
+ case CSeq_loc::e_Empty:
+ x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetEmpty() );
+ break;
+ case CSeq_loc::e_Equiv:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_ETC( arg0.SetEquiv() );
+ break;
+ case CSeq_loc::e_Feat:
+ x_BasicCleanupSeqFeat_ids_E_ETC( arg0.SetFeat() );
+ break;
+ case CSeq_loc::e_Int:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_packed_int_packed_int_E_ETC( arg0.SetInt() );
+ break;
+ case CSeq_loc::e_Mix:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_mix_ETC( arg0.SetMix() );
+ break;
+ case CSeq_loc::e_Packed_int:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_packed_int_ETC( arg0.SetPacked_int() );
+ break;
+ case CSeq_loc::e_Packed_pnt:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_packed_pnt_ETC( arg0.SetPacked_pnt() );
+ break;
+ case CSeq_loc::e_Pnt:
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_bond_bond_b_ETC( arg0.SetPnt() );
+ break;
+ case CSeq_loc::e_Whole:
+ x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetWhole() );
+ break;
+ default:
+ break;
+ }
+} // end of x_BasicCleanupSeqFeat_location_location1767_ETC
+
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_location_ETC( CSeq_loc & arg0 )
+{ // type Reference
+ x_BasicCleanupSeqFeat_location_location1767_ETC( arg0 );
+} // end of x_BasicCleanupSeqFeat_location_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_product_product1765_ETC( CSeq_loc & arg0 )
{ // type Choice
m_NewCleanup.SeqLocBC( arg0 );
+ m_NewCleanup.x_BothStrandBC( arg0 );
switch( arg0.Which() ) {
case CSeq_loc::e_Bond:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_bond_ETC( arg0.SetBond() );
@@ -3661,92 +2595,17 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_product_ETC( CSeq_loc & arg0 )
x_BasicCleanupSeqFeat_product_product1765_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_product_ETC
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_qual_E_E_ETC( CGb_qual & arg0 )
-{ // type Sequence
- if( arg0.IsSetQual() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetQual() );
- }
- if( arg0.IsSetVal() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVal() );
- }
-} // end of x_BasicCleanupSeqFeat_qual_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_qual_E_ETC( CGb_qual & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_qual_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_qual_E_ETC
-
template< typename Tcontainer_ncbi_cref_cgb_qual_ >
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_qual_ETC( Tcontainer_ncbi_cref_cgb_qual_ & arg0 )
{ // type UniSequence
m_NewCleanup.x_ExpandCombinedQuals( arg0 );
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cgb_qual_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_qual_E_ETC( **iter );
- }
} // end of x_BasicCleanupSeqFeat_qual_ETC
-template< typename Tcontainer_cdoi_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_ETC( Tcontainer_cdoi_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_cdoi_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_E_ETC( *iter );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_experiment_E_E_ETC( CExperimentSupport & arg0 )
-{ // type Sequence
- if( arg0.IsSetDois() ) {
- x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_ETC( arg0.SetDois() );
- }
- if( arg0.IsSetExplanation() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetExplanation() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_experiment_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_experiment_E_ETC( CExperimentSupport & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_experiment_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_experiment_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cexperimentsupport_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_experiment_ETC( Tcontainer_ncbi_cref_cexperimentsupport_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cexperimentsupport_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_support_support_experiment_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_experiment_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_E_ETC( CProgram_id & arg0 )
-{ // type Sequence
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
- if( arg0.IsSetVersion() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetVersion() );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_ETC( CProgram_id & arg0 )
-{ // type Reference
- x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_E_ETC( arg0 );
-} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cprogram_id_ >
-void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_ETC( Tcontainer_ncbi_cref_cprogram_id_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cprogram_id_, iter, arg0 ) {
- x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_ETC( **iter );
- }
-} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_ETC( CEvidenceBasis & arg0 )
{ // type Sequence
if( arg0.IsSetAccessions() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetAccessions() );
}
- if( arg0.IsSetPrograms() ) {
- x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_ETC( arg0.SetPrograms() );
- }
} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_ETC( CEvidenceBasis & arg0 )
@@ -3759,12 +2618,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_
if( arg0.IsSetBasis() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_ETC( arg0.SetBasis() );
}
- if( arg0.IsSetDois() ) {
- x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_ETC( arg0.SetDois() );
- }
- if( arg0.IsSetOther_type() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetOther_type() );
- }
} // end of x_BasicCleanupSeqFeat_support_support_inference_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_ETC( CInferenceSupport & arg0 )
@@ -3811,9 +2664,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
if( arg0.IsSetIdentification() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetIdentification() );
}
- if( arg0.IsSetMethod() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMethod() );
- }
if( arg0.IsSetMrna() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_protein_ETC( arg0.SetMrna() );
}
@@ -3837,9 +2687,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_ETC( CSeqFeatSupport & arg0 )
{ // type Sequence
- if( arg0.IsSetExperiment() ) {
- x_BasicCleanupSeqFeat_support_support_experiment_ETC( arg0.SetExperiment() );
- }
if( arg0.IsSetInference() ) {
x_BasicCleanupSeqFeat_support_support_inference_ETC( arg0.SetInference() );
}
@@ -3853,21 +2700,17 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_ETC( CSeqFeatSupport &
x_BasicCleanupSeqFeat_support_support_ETC( arg0 );
} // end of x_BasicCleanupSeqFeat_support_ETC
+void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_title_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
+} // end of x_BasicCleanupSeqFeat_title_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799( COrgName & arg0 )
{ // type Sequence
CLEAN_STRING_MEMBER( arg0, Attrib );
CLEAN_STRING_MEMBER( arg0, Div );
CLEAN_STRING_MEMBER( arg0, Lineage );
m_NewCleanup.x_CleanupOrgModAndSubSourceOther( arg0, *m_LastArg_x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_ETC );
- if( arg0.IsSetAttrib() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAttrib() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
- if( arg0.IsSetLineage() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLineage() );
- }
if( arg0.IsSetMod() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC( arg0.SetMod() );
}
@@ -3887,7 +2730,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Taxname );
m_NewCleanup.OrgrefBC( arg0 );
if( arg0.IsSetCommon() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCommon() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( arg0.SetCommon() );
}
if( arg0.IsSetDb() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDb() );
@@ -3898,12 +2741,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_bios
if( arg0.IsSetOrgname() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname( arg0.SetOrgname() );
}
- if( arg0.IsSetSyn() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSyn() );
- }
- if( arg0.IsSetTaxname() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxname() );
- }
CLEAN_STRING_LIST( arg0, Syn );
m_NewCleanup.x_PostOrgRef( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org
@@ -3940,9 +2777,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC(
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_ETC( CCdregion & arg0 )
{ // type Sequence
- if( arg0.IsSetCode() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_ETC( arg0.SetCode() );
- }
if( arg0.IsSetCode_break() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_break_ETC( arg0.SetCode_break() );
}
@@ -3963,16 +2797,7 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_pub
void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_ETC( CPubdesc & arg0 )
{ // type Sequence
if( arg0.IsSetComment() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( arg0.SetComment() );
- }
- if( arg0.IsSetFig() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFig() );
- }
- if( arg0.IsSetMaploc() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMaploc() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
+ x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( arg0.SetComment() );
}
if( arg0.IsSetNum() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_ETC( arg0.SetNum() );
@@ -3980,9 +2805,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_ETC
if( arg0.IsSetPub() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_pub_pub_E_E_equiv_ETC( arg0.SetPub() );
}
- if( arg0.IsSetSeq_raw() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSeq_raw() );
- }
m_NewCleanup.PubdescBC( arg0 );
} // end of x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_ETC
@@ -4019,15 +2841,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_ETC( CSeqFe
case CSeqFeatData::e_Gene:
x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC( arg0.SetGene() );
break;
- case CSeqFeatData::e_Het:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( arg0.SetHet() );
- break;
case CSeqFeatData::e_Imp:
x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC( arg0.SetImp() );
break;
- case CSeqFeatData::e_Non_std_residue:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetNon_std_residue() );
- break;
case CSeqFeatData::e_Num:
x_BasicCleanupSeqFeat_xref_E_E_data_data_num_ETC( arg0.SetNum() );
break;
@@ -4040,9 +2856,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_ETC( CSeqFe
case CSeqFeatData::e_Pub:
x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_ETC( arg0.SetPub() );
break;
- case CSeqFeatData::e_Region:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRegion() );
- break;
case CSeqFeatData::e_Rna:
x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_ETC( arg0.SetRna() );
break;
@@ -4117,9 +2930,9 @@ void CAutogeneratedCleanup::BasicCleanupSeqFeat( CSeq_feat & arg0_raw )
CLEAN_STRING_MEMBER( arg0, Comment );
CLEAN_STRING_MEMBER( arg0, Except_text );
CLEAN_STRING_MEMBER( arg0, Title );
+ CLEAN_AND_COMPRESS_STRING_MEMBER( arg0, Comment );
m_NewCleanup.ImpFeatBC( arg0 );
m_NewCleanup.SeqfeatBC( arg0 );
- m_NewCleanup.x_MoveSeqfeatOrgToSourceOrg( arg0 );
if( arg0.IsSetCit() ) {
x_BasicCleanupSeqFeat_cit_ETC( arg0.SetCit() );
}
@@ -4132,9 +2945,6 @@ void CAutogeneratedCleanup::BasicCleanupSeqFeat( CSeq_feat & arg0_raw )
if( arg0.IsSetDbxref() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDbxref() );
}
- if( arg0.IsSetExcept_text() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetExcept_text() );
- }
if( arg0.IsSetExt() ) {
x_BasicCleanupSeqFeat_ext_ETC( arg0.SetExt() );
}
@@ -4148,7 +2958,7 @@ void CAutogeneratedCleanup::BasicCleanupSeqFeat( CSeq_feat & arg0_raw )
x_BasicCleanupSeqFeat_ids_ETC( arg0.SetIds() );
}
if( arg0.IsSetLocation() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_ETC( arg0.SetLocation() );
+ x_BasicCleanupSeqFeat_location_ETC( arg0.SetLocation() );
}
if( arg0.IsSetProduct() ) {
x_BasicCleanupSeqFeat_product_ETC( arg0.SetProduct() );
@@ -4160,7 +2970,7 @@ void CAutogeneratedCleanup::BasicCleanupSeqFeat( CSeq_feat & arg0_raw )
x_BasicCleanupSeqFeat_support_ETC( arg0.SetSupport() );
}
if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
+ x_BasicCleanupSeqFeat_title_ETC( arg0.SetTitle() );
}
if( arg0.IsSetXref() ) {
x_BasicCleanupSeqFeat_xref_ETC( arg0.SetXref() );
@@ -4191,21 +3001,9 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E_data_ftable( Tcontain
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_graph_E_E_ETC( CSeq_graph & arg0 )
{ // type Sequence
- if( arg0.IsSetComment() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetComment() );
- }
if( arg0.IsSetLoc() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_ETC( arg0.SetLoc() );
}
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- }
- if( arg0.IsSetTitle_x() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle_x() );
- }
- if( arg0.IsSetTitle_y() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle_y() );
- }
} // end of x_BasicCleanupBioseqSet_annot_E_E_data_graph_E_E_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_graph_E_ETC( CSeq_graph & arg0 )
@@ -4339,21 +3137,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq
x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_sparse_other_ETC( arg0 );
} // end of x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_ETC
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_header_ETC( CSeqTable_column_info & arg0 )
-{ // type Sequence
- if( arg0.IsSetField_name() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetField_name() );
- }
- if( arg0.IsSetTitle() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- }
-} // end of x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_header_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_ETC( CSeqTable_column_info & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_header_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_ETC( CSeqTable_column & arg0 )
{ // type Sequence
if( arg0.IsSetData() ) {
@@ -4362,9 +3145,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq
if( arg0.IsSetDefault() ) {
x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_ETC( arg0.SetDefault() );
}
- if( arg0.IsSetHeader() ) {
- x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_ETC( arg0.SetHeader() );
- }
if( arg0.IsSetSparse_other() ) {
x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_ETC( arg0.SetSparse_other() );
}
@@ -4439,15 +3219,9 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_desc_desc_E_E_ETC(
case CAnnotdesc::e_Align:
x_BasicCleanupBioseqSet_annot_E_E_desc_desc_E_E_align_ETC( arg0.SetAlign() );
break;
- case CAnnotdesc::e_Comment:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetComment() );
- break;
case CAnnotdesc::e_Create_date:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetCreate_date() );
break;
- case CAnnotdesc::e_Name:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- break;
case CAnnotdesc::e_Pub:
x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_ETC( arg0.SetPub() );
break;
@@ -4457,9 +3231,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_desc_desc_E_E_ETC(
case CAnnotdesc::e_Src:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_ETC( arg0.SetSrc() );
break;
- case CAnnotdesc::e_Title:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTitle() );
- break;
case CAnnotdesc::e_Update_date:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetUpdate_date() );
break;
@@ -4491,36 +3262,12 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_desc_ETC( CAnnot_d
}
} // end of x_BasicCleanupBioseqSet_annot_E_E_desc_ETC
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_other_ETC( CTextannot_id & arg0 )
-{ // type Sequence
- if( arg0.IsSetAccession() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetAccession() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
- if( arg0.IsSetRelease() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRelease() );
- }
-} // end of x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_other_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_ETC( CTextannot_id & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_other_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_id_E_E_ETC( CAnnot_id & arg0 )
{ // type Choice
switch( arg0.Which() ) {
case CAnnot_id::e_General:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetGeneral() );
break;
- case CAnnot_id::e_Local:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetLocal() );
- break;
- case CAnnot_id::e_Other:
- x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_ETC( arg0.SetOther() );
- break;
default:
break;
}
@@ -4550,9 +3297,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E( CSeq_annot & arg0 )
if( arg0.IsSetId() ) {
x_BasicCleanupBioseqSet_annot_E_E_id_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of x_BasicCleanupBioseq_annot_E_E
void CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E( CSeq_annot & arg0 )
@@ -4573,65 +3317,18 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_CleanupStringJunkMarkChanged( arg0 );
m_NewCleanup.x_RemoveSpacesBetweenTildesMarkChanged( arg0 );
+ m_NewCleanup.X_CommentTildeFixes( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_comment_ETC
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_dbname_ETC( CEMBL_dbname & arg0 )
-{ // type Choice
- switch( arg0.Which() ) {
- case CEMBL_dbname::e_Name:
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- break;
- default:
- break;
- }
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_dbname_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_ETC( CEMBL_dbname & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_dbname_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_ETC( CEMBL_xref & arg0 )
-{ // type Sequence
- if( arg0.IsSetDbname() ) {
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_ETC( arg0.SetDbname() );
- }
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC( arg0.SetId() );
- }
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_ETC( CEMBL_xref & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_ETC
-
-template< typename Tcontainer_ncbi_cref_cembl_xref_ >
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_ETC( Tcontainer_ncbi_cref_cembl_xref_ & arg0 )
-{ // type UniSequence
- NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cembl_xref_, iter, arg0 ) {
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_ETC( **iter );
- }
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_ETC( CEMBL_block & arg0 )
{ // type Sequence
m_NewCleanup.EMBLblockBC( arg0 );
if( arg0.IsSetCreation_date() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetCreation_date() );
}
- if( arg0.IsSetExtra_acc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetExtra_acc() );
- }
- if( arg0.IsSetKeywords() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetKeywords() );
- }
if( arg0.IsSetUpdate_date() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetUpdate_date() );
}
- if( arg0.IsSetXref() ) {
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_ETC( arg0.SetXref() );
- }
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_ETC( CEMBL_block & arg0 )
@@ -4639,32 +3336,19 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_ETC( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_ETC
+void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_origin_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.GBblockOriginBC( arg0 );
+} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_origin_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC( CGB_block & arg0 )
{ // type Sequence
m_NewCleanup.GBblockBC( arg0 );
- if( arg0.IsSetDate() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDate() );
- }
- if( arg0.IsSetDiv() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDiv() );
- }
if( arg0.IsSetEntry_date() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetEntry_date() );
}
- if( arg0.IsSetExtra_accessions() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetExtra_accessions() );
- }
- if( arg0.IsSetKeywords() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetKeywords() );
- }
if( arg0.IsSetOrigin() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetOrigin() );
- }
- if( arg0.IsSetSource() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSource() );
- }
- if( arg0.IsSetTaxonomy() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxonomy() );
+ x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_origin_ETC( arg0.SetOrigin() );
}
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC
@@ -4677,12 +3361,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E_molinfo_molinfo
{ // type Sequence
m_NewCleanup.MolInfoBC( arg0 );
m_NewCleanup.x_FixUnsetMolFromBiomol( arg0, *m_LastArg_BasicCleanupBioseq );
- if( arg0.IsSetGbmoltype() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetGbmoltype() );
- }
- if( arg0.IsSetTechexp() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTechexp() );
- }
} // end of x_BasicCleanupBioseq_descr_descr_E_E_molinfo_molinfo
void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E_molinfo( CMolInfo & arg0 )
@@ -4692,7 +3370,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E_molinfo( CMolIn
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_name_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_CleanupStringMarkChanged( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_name_ETC
@@ -4701,9 +3378,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetIds() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetIds() );
- }
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_pdb_replace_replace_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_pdb_replace_ETC( CPDB_replace & arg0 )
@@ -4713,24 +3387,12 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_pdb_ETC( CPDB_block & arg0 )
{ // type Sequence
- if( arg0.IsSetClass() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetClass() );
- }
- if( arg0.IsSetCompound() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetCompound() );
- }
if( arg0.IsSetDeposition() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDeposition() );
}
- if( arg0.IsSetExp_method() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetExp_method() );
- }
if( arg0.IsSetReplace() ) {
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_pdb_replace_ETC( arg0.SetReplace() );
}
- if( arg0.IsSetSource() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetSource() );
- }
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_pdb_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_ETC( CPDB_block & arg0 )
@@ -4740,42 +3402,9 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_pir_ETC( CPIR_block & arg0 )
{ // type Sequence
- if( arg0.IsSetCross_reference() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetCross_reference() );
- }
- if( arg0.IsSetDate() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDate() );
- }
- if( arg0.IsSetGenetic() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetGenetic() );
- }
- if( arg0.IsSetHost() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetHost() );
- }
- if( arg0.IsSetIncludes() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetIncludes() );
- }
- if( arg0.IsSetKeywords() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetKeywords() );
- }
- if( arg0.IsSetPlacement() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPlacement() );
- }
- if( arg0.IsSetSeq_raw() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSeq_raw() );
- }
if( arg0.IsSetSeqref() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetSeqref() );
}
- if( arg0.IsSetSource() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSource() );
- }
- if( arg0.IsSetSummary() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSummary() );
- }
- if( arg0.IsSetSuperfamily() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetSuperfamily() );
- }
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_pir_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_ETC( CPIR_block & arg0 )
@@ -4783,48 +3412,8 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_pir_ETC( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_ETC
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_extra_src_ETC( CPRF_ExtraSrc & arg0 )
-{ // type Sequence
- if( arg0.IsSetHost() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetHost() );
- }
- if( arg0.IsSetPart() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPart() );
- }
- if( arg0.IsSetState() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetState() );
- }
- if( arg0.IsSetStrain() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetStrain() );
- }
- if( arg0.IsSetTaxon() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTaxon() );
- }
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_extra_src_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_ETC( CPRF_ExtraSrc & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_extra_src_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_ETC( CPRF_block & arg0 )
-{ // type Sequence
- if( arg0.IsSetExtra_src() ) {
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_ETC( arg0.SetExtra_src() );
- }
- if( arg0.IsSetKeywords() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetKeywords() );
- }
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_ETC
-
-void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_ETC( CPRF_block & arg0 )
-{ // type Reference
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_ETC( arg0 );
-} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_ETC
-
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_region_ETC( std::string & arg0 )
{ // type Primitive
- m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
m_NewCleanup.x_CleanupStringMarkChanged( arg0 );
m_NewCleanup.x_ConvertDoubleQuotesMarkChanged( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_region_ETC
@@ -4840,15 +3429,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
if( arg0.IsSetDbref() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( arg0.SetDbref() );
}
- if( arg0.IsSetExtra_acc() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetExtra_acc() );
- }
- if( arg0.IsSetKeywords() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetKeywords() );
- }
- if( arg0.IsSetPlasnm() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetPlasnm() );
- }
if( arg0.IsSetSeqref() ) {
x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( arg0.SetSeqref() );
}
@@ -4862,9 +3442,15 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_de
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_sp_ETC( arg0 );
} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_ETC
+void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_title_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_DecodeXMLMarkChanged( arg0 );
+ m_NewCleanup.x_CompressStringSpacesMarkChanged( arg0 );
+ m_NewCleanup.x_CleanupStringMarkChanged( arg0 );
+} // end of x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_title_ETC
+
void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E( CSeqdesc & arg0 )
{ // type Choice
- m_NewCleanup.x_MoveSeqdescOrgToSourceOrg( arg0 );
switch( arg0.Which() ) {
case CSeqdesc::e_Comment:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_comment_ETC( arg0.SetComment() );
@@ -4881,9 +3467,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E( CSeqdesc & arg
case CSeqdesc::e_Genbank:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( arg0.SetGenbank() );
break;
- case CSeqdesc::e_Het:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( arg0.SetHet() );
- break;
case CSeqdesc::e_Maploc:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetMaploc() );
break;
@@ -4908,9 +3491,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E( CSeqdesc & arg
case CSeqdesc::e_Pir:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_ETC( arg0.SetPir() );
break;
- case CSeqdesc::e_Prf:
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_ETC( arg0.SetPrf() );
- break;
case CSeqdesc::e_Pub:
x_BasicCleanupSeqFeat_data_data_pub_ETC( arg0.SetPub() );
break;
@@ -4924,7 +3504,7 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr_E_E( CSeqdesc & arg
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_ETC( arg0.SetSp() );
break;
case CSeqdesc::e_Title:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_str_ETC( arg0.SetTitle() );
+ x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_title_ETC( arg0.SetTitle() );
break;
case CSeqdesc::e_Update_date:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetUpdate_date() );
@@ -4960,9 +3540,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_descr( CSeq_descr & arg0 )
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_inst_inst_ext_ext_delta_delta_E_E_ETC( CDelta_seq & arg0 )
{ // type Choice
switch( arg0.Which() ) {
- case CDelta_seq::e_Literal:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_ETC( arg0.SetLiteral() );
- break;
case CDelta_seq::e_Loc:
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_ETC( arg0.SetLoc() );
break;
@@ -5106,9 +3683,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseq_inst_inst( CSeq_inst & arg0 )
if( arg0.IsSetHist() ) {
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_inst_inst_hist_ETC( arg0.SetHist() );
}
- if( arg0.IsSetSeq_data() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_ETC( arg0.SetSeq_data() );
- }
m_LastArg_x_BasicCleanupBioseq_inst_inst = NULL;
} // end of x_BasicCleanupBioseq_inst_inst
@@ -5122,6 +3696,7 @@ void CAutogeneratedCleanup::BasicCleanupBioseq( CBioseq & arg0 )
{ // type Sequence
m_LastArg_BasicCleanupBioseq = &arg0;
+ m_NewCleanup.ProtSeqBC( arg0 );
if( arg0.IsSetAnnot() ) {
x_BasicCleanupBioseq_annot( arg0.SetAnnot() );
}
@@ -5135,6 +3710,7 @@ void CAutogeneratedCleanup::BasicCleanupBioseq( CBioseq & arg0 )
x_BasicCleanupBioseq_inst( arg0.SetInst() );
}
m_NewCleanup.x_AddPartialToProteinTitle( arg0 );
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
m_LastArg_BasicCleanupBioseq = NULL;
} // end of BasicCleanupBioseq
@@ -5194,9 +3770,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E_E( CSeq_annot
if( arg0.IsSetId() ) {
x_BasicCleanupBioseqSet_annot_E_E_id_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of x_BasicCleanupSeqEntry_set_set_annot_E_E
void CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E( CSeq_annot & arg0 )
@@ -5215,12 +3788,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot( Tcontainer_ncb
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_molinfo_molinfo_ETC( CMolInfo & arg0 )
{ // type Sequence
m_NewCleanup.MolInfoBC( arg0 );
- if( arg0.IsSetGbmoltype() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetGbmoltype() );
- }
- if( arg0.IsSetTechexp() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTechexp() );
- }
} // end of x_BasicCleanupBioseqSet_descr_descr_E_E_molinfo_molinfo_ETC
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_molinfo_ETC( CMolInfo & arg0 )
@@ -5230,7 +3797,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_molinfo_ETC(
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_ETC( CSeqdesc & arg0 )
{ // type Choice
- m_NewCleanup.x_MoveSeqdescOrgToSourceOrg( arg0 );
switch( arg0.Which() ) {
case CSeqdesc::e_Comment:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_comment_ETC( arg0.SetComment() );
@@ -5247,9 +3813,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_ETC( CSeqdes
case CSeqdesc::e_Genbank:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( arg0.SetGenbank() );
break;
- case CSeqdesc::e_Het:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( arg0.SetHet() );
- break;
case CSeqdesc::e_Maploc:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( arg0.SetMaploc() );
break;
@@ -5274,9 +3837,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_ETC( CSeqdes
case CSeqdesc::e_Pir:
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_ETC( arg0.SetPir() );
break;
- case CSeqdesc::e_Prf:
- x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_ETC( arg0.SetPrf() );
- break;
case CSeqdesc::e_Pub:
x_BasicCleanupSeqFeat_data_data_pub_ETC( arg0.SetPub() );
break;
@@ -5290,7 +3850,7 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_E_E_ETC( CSeqdes
x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_ETC( arg0.SetSp() );
break;
case CSeqdesc::e_Title:
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_str_ETC( arg0.SetTitle() );
+ x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_title_ETC( arg0.SetTitle() );
break;
case CSeqdesc::e_Update_date:
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetUpdate_date() );
@@ -5351,15 +3911,10 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_ETC( CBioseq_set & ar
if( arg0.IsSetDescr() ) {
x_BasicCleanupBioseqSet_descr_ETC( arg0.SetDescr() );
}
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetId() );
- }
- if( arg0.IsSetRelease() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRelease() );
- }
if( arg0.IsSetSeq_set() ) {
x_BasicCleanupSeqEntry_set_set_seq_set( arg0.SetSeq_set() );
}
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
} // end of x_BasicCleanupSeqEntry_set_set_ETC
void CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set( CBioseq_set & arg0 )
@@ -5434,9 +3989,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E_E( CSeq_annot
if( arg0.IsSetId() ) {
x_BasicCleanupBioseqSet_annot_E_E_id_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of x_BasicCleanupSeqSubmit_data_annots_E_E
void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E( CSeq_annot & arg0 )
@@ -5506,9 +4058,6 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub_sub_cit_cit( CCit_sub &
if( arg0.IsSetDate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetDate() );
}
- if( arg0.IsSetDescr() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetDescr() );
- }
if( arg0.IsSetImp() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( arg0.SetImp() );
}
@@ -5521,39 +4070,9 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub_sub_cit( CCit_sub & arg0
void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub_sub_contact_contact( CContact_info & arg0 )
{ // type Sequence
- if( arg0.IsSetAddress() ) {
- x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( arg0.SetAddress() );
- }
if( arg0.IsSetContact() ) {
x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_ETC( arg0.SetContact() );
}
- if( arg0.IsSetEmail() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetEmail() );
- }
- if( arg0.IsSetFax() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFax() );
- }
- if( arg0.IsSetFirst_name() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetFirst_name() );
- }
- if( arg0.IsSetLast_name() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetLast_name() );
- }
- if( arg0.IsSetMiddle_initial() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetMiddle_initial() );
- }
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
- if( arg0.IsSetOwner_id() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetOwner_id() );
- }
- if( arg0.IsSetPhone() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetPhone() );
- }
- if( arg0.IsSetTelex() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTelex() );
- }
} // end of x_BasicCleanupSeqSubmit_sub_sub_contact_contact
void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub_sub_contact( CContact_info & arg0 )
@@ -5566,21 +4085,12 @@ void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub_sub( CSubmit_block & arg
if( arg0.IsSetCit() ) {
x_BasicCleanupSeqSubmit_sub_sub_cit( arg0.SetCit() );
}
- if( arg0.IsSetComment() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetComment() );
- }
if( arg0.IsSetContact() ) {
x_BasicCleanupSeqSubmit_sub_sub_contact( arg0.SetContact() );
}
if( arg0.IsSetReldate() ) {
x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_ETC( arg0.SetReldate() );
}
- if( arg0.IsSetTool() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetTool() );
- }
- if( arg0.IsSetUser_tag() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetUser_tag() );
- }
} // end of x_BasicCleanupSeqSubmit_sub_sub
void CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_sub( CSubmit_block & arg0 )
@@ -5648,9 +4158,6 @@ void CAutogeneratedCleanup::BasicCleanupSeqAnnot( CSeq_annot & arg0 )
if( arg0.IsSetId() ) {
x_BasicCleanupBioseqSet_annot_E_E_id_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of BasicCleanupSeqAnnot
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_ftable_E( CSeq_feat & arg0 )
@@ -5703,9 +4210,6 @@ void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E( CSeq_annot & arg0
if( arg0.IsSetId() ) {
x_BasicCleanupBioseqSet_annot_E_E_id_ETC( arg0.SetId() );
}
- if( arg0.IsSetName() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetName() );
- }
} // end of x_BasicCleanupBioseqSet_annot_E_E
void CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E( CSeq_annot & arg0 )
@@ -5776,15 +4280,10 @@ void CAutogeneratedCleanup::BasicCleanupBioseqSet( CBioseq_set & arg0 )
if( arg0.IsSetDescr() ) {
x_BasicCleanupBioseqSet_descr_ETC( arg0.SetDescr() );
}
- if( arg0.IsSetId() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( arg0.SetId() );
- }
- if( arg0.IsSetRelease() ) {
- x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( arg0.SetRelease() );
- }
if( arg0.IsSetSeq_set() ) {
x_BasicCleanupBioseqSet_seq_set( arg0.SetSeq_set() );
}
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
} // end of BasicCleanupBioseqSet
diff --git a/c++/src/objtools/cleanup/autogenerated_cleanup.hpp b/c++/src/objtools/cleanup/autogenerated_cleanup.hpp
index 0bf2d45..49e17c1 100644
--- a/c++/src/objtools/cleanup/autogenerated_cleanup.hpp
+++ b/c++/src/objtools/cleanup/autogenerated_cleanup.hpp
@@ -1,7 +1,7 @@
#ifndef AUTOGENERATEDCLEANUP__HPP
#define AUTOGENERATEDCLEANUP__HPP
-/* $Id: autogenerated_cleanup.hpp 404925 2013-06-27 18:47:47Z kornbluh $
+/* $Id: autogenerated_cleanup.hpp 477586 2015-08-31 17:42:50Z fukanchi $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -41,12 +41,7 @@
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqloc/Seq_id.hpp>
-#include <objects/seqloc/Textseq_id.hpp>
#include <objects/general/Dbtag.hpp>
-#include <objects/general/Object_id.hpp>
-#include <objects/seqloc/Giimport_id.hpp>
-#include <objects/seqloc/Patent_seq_id.hpp>
-#include <objects/biblio/Id_pat.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Date_std.hpp>
@@ -58,7 +53,6 @@
#include <objects/seqloc/Packed_seqpnt.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
-#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
@@ -67,8 +61,6 @@
#include <objects/seqalign/Sparse_align.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
-#include <objects/seqalign/Splice_site.hpp>
-#include <objects/seqalign/Score_set.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/pub/Pub_set.hpp>
@@ -77,24 +69,17 @@
#include <objects/biblio/Affil.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/general/Person_id.hpp>
-#include <objects/general/Name_std.hpp>
#include <objects/biblio/Cit_book.hpp>
-#include <objects/biblio/Title.hpp>
#include <objects/biblio/Imprint.hpp>
#include <objects/biblio/PubStatusDateSet.hpp>
#include <objects/biblio/PubStatusDate.hpp>
-#include <objects/biblio/CitRetract.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/biblio/Cit_proc.hpp>
#include <objects/biblio/Meeting.hpp>
#include <objects/biblio/ArticleIdSet.hpp>
#include <objects/biblio/ArticleId.hpp>
+#include <objects/biblio/Title.hpp>
#include <objects/medline/Medline_entry.hpp>
-#include <objects/medline/Medline_mesh.hpp>
-#include <objects/medline/Medline_qual.hpp>
-#include <objects/medline/Medline_field.hpp>
-#include <objects/medline/Medline_rn.hpp>
-#include <objects/medline/Medline_si.hpp>
#include <objects/biblio/Cit_pat.hpp>
#include <objects/biblio/Patent_priority.hpp>
#include <objects/pub/Pub.hpp>
@@ -107,17 +92,9 @@
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
-#include <objects/seqfeat/BinomialOrgName.hpp>
#include <objects/seqfeat/MultiOrgName.hpp>
-#include <objects/seqfeat/PartialOrgName.hpp>
-#include <objects/seqfeat/TaxElement.hpp>
-#include <objects/seqfeat/PCRReactionSet.hpp>
-#include <objects/seqfeat/PCRReaction.hpp>
-#include <objects/seqfeat/PCRPrimerSet.hpp>
-#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Cdregion.hpp>
-#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/Clone_ref.hpp>
#include <objects/seqfeat/Clone_seq_set.hpp>
@@ -126,8 +103,6 @@
#include <objects/seqfeat/Gene_nomenclature.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seq/Numbering.hpp>
-#include <objects/seq/Num_enum.hpp>
-#include <objects/seq/Num_real.hpp>
#include <objects/seq/Num_ref.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seq/Pubdesc.hpp>
@@ -141,15 +116,10 @@
#include <objects/seqfeat/Variation_ref.hpp>
#include <objects/seqfeat/Variation_inst.hpp>
#include <objects/seqfeat/Delta_item.hpp>
-#include <objects/seq/Seq_literal.hpp>
-#include <objects/seq/Seq_data.hpp>
#include <objects/seqfeat/Phenotype.hpp>
-#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/SeqFeatSupport.hpp>
-#include <objects/seqfeat/ExperimentSupport.hpp>
#include <objects/seqfeat/InferenceSupport.hpp>
#include <objects/seqfeat/EvidenceBasis.hpp>
-#include <objects/seqfeat/Program_id.hpp>
#include <objects/seqfeat/ModelEvidenceSupport.hpp>
#include <objects/seqfeat/ModelEvidenceItem.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
@@ -160,24 +130,18 @@
#include <objects/seqtable/Scaled_int_multi_data.hpp>
#include <objects/seqtable/Scaled_real_multi_data.hpp>
#include <objects/seqtable/SeqTable_single_data.hpp>
-#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Align_def.hpp>
#include <objects/seq/Annot_id.hpp>
-#include <objects/seq/Textannot_id.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqblock/EMBL_block.hpp>
-#include <objects/seqblock/EMBL_xref.hpp>
-#include <objects/seqblock/EMBL_dbname.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seqblock/PDB_block.hpp>
#include <objects/seqblock/PDB_replace.hpp>
#include <objects/seqblock/PIR_block.hpp>
-#include <objects/seqblock/PRF_block.hpp>
-#include <objects/seqblock/PRF_ExtraSrc.hpp>
#include <objects/seqblock/SP_block.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_ext.hpp>
@@ -223,21 +187,8 @@ public:
void BasicCleanupSeqFeat( CSeq_feat & arg0_raw );
private:
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_str_ETC( std::string & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_named_annot_track_ETC( CTextseq_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_named_annot_track_ETC( CTextseq_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_tag_ETC( CObject_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_tag_ETC( CObject_id & arg0 );
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_E_ETC( CDbtag & arg0 );
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_E_ETC( CDbtag & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_giim_ETC( CGiimport_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_giim_ETC( CGiimport_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_id_ETC( CId_pat::C_Id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_cit_ETC( CId_pat & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_cit_ETC( CId_pat & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_patent_ETC( CPatent_seq_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_patent_ETC( CPatent_seq_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_mol_ETC( CPDB_mol_id & arg0 );
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_std_ETC( CDate_std & arg0 );
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_std_ETC( CDate_std & arg0 );
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_rel_rel_ETC( CDate & arg0 );
@@ -292,12 +243,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_E_ETC( CUser_object & arg0 );
template< typename Tcontainer_ncbi_cref_cuser_object_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC( Tcontainer_ncbi_cref_cuser_object_ & arg0 );
- template< typename Tcontainer_ncbi_cref_cobject_id_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_population_data_E_E_sample_ids_ETC( Tcontainer_ncbi_cref_cobject_id_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_E_ETC( CScore & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_E_ETC( CScore & arg0 );
- template< typename Tcontainer_ncbi_cref_cscore_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_row_scores_ETC( Tcontainer_ncbi_cref_cscore_ & arg0 );
template< typename Tcontainer_ncbi_cref_cseq_id_ >
void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC( Tcontainer_ncbi_cref_cseq_id_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_dendiag_E_E_ETC( CDense_diag & arg0 );
@@ -318,9 +263,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_rows_ETC( Tcontainer_ncbi_cref_csparse_align_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_ETC( CSparse_seg & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_ETC( CSparse_seg & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_donor_after_exon_ETC( CSplice_site & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_donor_after_exon_ETC( CSplice_site & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_scores_ETC( CScore_set & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_E_ETC( CSpliced_exon & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_E_ETC( CSpliced_exon & arg0 );
template< typename Tcontainer_ncbi_cref_cspliced_exon_ >
@@ -340,10 +282,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_num_num_ref_ref_aligns_ali
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_str_ETC( std::string & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_pub_ETC( CAffil & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_pub_ETC( CAffil & arg0 );
- template< typename Tcontainer_std_string_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_str_ETC( Tcontainer_std_string_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_name_ETC( CName_std & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_name_ETC( CName_std & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_name_ETC( CPerson_id & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_name_ETC( CPerson_id & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_E_E_ETC( CAuthor & arg0 );
@@ -353,18 +291,11 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_ma
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_ETC( CAuth_list::C_Names & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_ETC( CAuth_list & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_ETC( CAuth_list & arg0 );
- template< typename Tcontainer_ncbi_cref_c_e_c_e >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_E_ETC( Tcontainer_ncbi_cref_c_e_c_e & arg0 );
- template< typename Tcontainer_ncbi_cref_c_e_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_coll_ETC( Tcontainer_ncbi_cref_c_e_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_coll_ETC( CTitle & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_history_E_E_ETC( CPubStatusDate & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_history_E_ETC( CPubStatusDate & arg0 );
template< typename Tcontainer_ncbi_cref_cpubstatusdate_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_history_ETC( Tcontainer_ncbi_cref_cpubstatusdate_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_ETC( CPubStatusDateSet & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_retract_ETC( CCitRetract & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_retract_ETC( CCitRetract & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_ETC( CImprint & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_ETC( CImprint & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_ETC( CCit_book & arg0 );
@@ -376,10 +307,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_ma
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_proc_proc_ETC( CCit_proc & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_proc_ETC( CCit_proc & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_from_ETC( CCit_art::C_From & arg0 );
- void x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_E_ETC( CDOI & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pii_ETC( CPII & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmcpid_ETC( CPmcPid & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_pmpid_ETC( CPmPid & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_E_ETC( CArticleId & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_ids_ids_E_ETC( CArticleId & arg0 );
template< typename Tcontainer_ncbi_cref_carticleid_ >
@@ -399,26 +326,6 @@ void x_BasicCleanupSeqFeat_cit_cit_article_ETC( Tcontainer_ncbi_cref_ccit_art_ &
void x_BasicCleanupSeqFeat_cit_cit_book_ETC( Tcontainer_ncbi_cref_ccit_book_ & arg0 );
template< typename Tcontainer_ncbi_cref_ccit_jour_ >
void x_BasicCleanupSeqFeat_cit_cit_journal_ETC( Tcontainer_ncbi_cref_ccit_jour_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_E_ETC( CMedline_qual & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_E_ETC( CMedline_qual & arg0 );
- template< typename Tcontainer_ncbi_cref_cmedline_qual_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_qual_ETC( Tcontainer_ncbi_cref_cmedline_qual_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_E_ETC( CMedline_mesh & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_E_ETC( CMedline_mesh & arg0 );
- template< typename Tcontainer_ncbi_cref_cmedline_mesh_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mesh_ETC( Tcontainer_ncbi_cref_cmedline_mesh_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_E_ETC( CMedline_field & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_E_ETC( CMedline_field & arg0 );
- template< typename Tcontainer_ncbi_cref_cmedline_field_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_mlfield_ETC( Tcontainer_ncbi_cref_cmedline_field_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_E_ETC( CMedline_rn & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_E_ETC( CMedline_rn & arg0 );
- template< typename Tcontainer_ncbi_cref_cmedline_rn_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_substance_ETC( Tcontainer_ncbi_cref_cmedline_rn_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_E_ETC( CMedline_si & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_E_ETC( CMedline_si & arg0 );
- template< typename Tcontainer_ncbi_cref_cmedline_si_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_xref_ETC( Tcontainer_ncbi_cref_cmedline_si_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_medline_ETC( CMedline_entry & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_medline_ETC( CMedline_entry & arg0 );
template< typename Tcontainer_ncbi_cref_cmedline_entry_ >
@@ -451,6 +358,7 @@ void x_BasicCleanupSeqFeat_cit_cit_pub_ETC( Tcontainer_ncbi_cref_cpub_ & arg0 );
void x_BasicCleanupSeqFeat_cit_cit_ETC( CPub_set & arg0 );
void x_BasicCleanupSeqFeat_cit_ETC( CPub_set & arg0 );
void x_BasicCleanupSeqFeat_comment_ETC( std::string & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_common_ETC( std::string & arg0 );
template< typename Tcontainer_ncbi_cref_cdbtag_ >
void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_dbxref_ETC( Tcontainer_ncbi_cref_cdbtag_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_mod_E_ETC( std::string & arg0 );
@@ -460,17 +368,10 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_mod_ETC( Tco
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_E_ETC( COrgMod & arg0 );
template< typename Tcontainer_ncbi_cref_corgmod_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC( Tcontainer_ncbi_cref_corgmod_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_namedhybrid_ETC( CBinomialOrgName & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_namedhybrid_ETC( CBinomialOrgName & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E( COrgName & arg0 );
template< typename Tcontainer_ncbi_cref_corgname_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid( Tcontainer_ncbi_cref_corgname_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid( CMultiOrgName & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_E_ETC( CTaxElement & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_E_ETC( CTaxElement & arg0 );
- template< typename Tcontainer_ncbi_cref_ctaxelement_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_partial_ETC( Tcontainer_ncbi_cref_ctaxelement_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_partial_ETC( CPartialOrgName & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( COrgName::C_Name & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC( COrgName & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_orgname_name_hybrid_hybrid_E_ETC( COrgName & arg0 );
@@ -482,17 +383,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_
void x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_org_orgname( COrgName & arg0 );
void x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org_org( COrg_ref & arg0 );
void x_BasicCleanupSeqFeat_data_data_biosrc_biosrc_org( COrg_ref & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_name_ETC( CPCRPrimerName & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_seq_ETC( CPCRPrimerSeq & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_E_ETC( CPCRPrimer & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_E_ETC( CPCRPrimer & arg0 );
- template< typename Tcontainer_ncbi_cref_cpcrprimer_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_reverse_ETC( Tcontainer_ncbi_cref_cpcrprimer_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_reverse_ETC( CPCRPrimerSet & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_E_ETC( CPCRReaction & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_E_ETC( CPCRReaction & arg0 );
- template< typename Tcontainer_ncbi_cref_cpcrreaction_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_primers_ETC( Tcontainer_ncbi_cref_cpcrreaction_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_ETC( CPCRReactionSet & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_source_source_ETC( CSubSource & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_E_source_ETC( CSubSource & arg0 );
@@ -500,11 +390,6 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_pcr_primers_pcr_prim
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_subtype_ETC( Tcontainer_ncbi_cref_csubsource_ & arg0 );
void x_BasicCleanupSeqFeat_data_data_biosrc_biosrc( CBioSource & arg0 );
void x_BasicCleanupSeqFeat_data_data_biosrc( CBioSource & arg0 );
- template< typename Tcontainer_ncbi_cref_c_e_c_e >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_E_ETC( Tcontainer_ncbi_cref_c_e_c_e & arg0 );
- template< typename Tcontainer_ncbi_cref_c_e_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_code_ETC( Tcontainer_ncbi_cref_c_e_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_ETC( CGenetic_code & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location1813_ETC( CSeq_loc & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_ETC( CSeq_loc & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_break_E_E_ETC( CCode_break & arg0 );
@@ -520,20 +405,18 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_clone_seq_ET
void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_ETC( CClone_seq_set & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_ETC( CClone_ref & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_ETC( CClone_ref & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( std::string & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_tag_ETC( std::string & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_desc_ETC( std::string & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_formal_name_ETC( CGene_nomenclature & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_formal_name_ETC( CGene_nomenclature & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_locus_ETC( std::string & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_E_ETC( std::string & arg0 );
template< typename Tcontainer_std_string_ >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( Tcontainer_std_string_ & arg0 );
+void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC( Tcontainer_std_string_ & arg0 );
void x_BasicCleanupSeqFeat_data_data_gene_gene( CGene_ref & arg0 );
void x_BasicCleanupSeqFeat_data_data_gene( CGene_ref & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_het_ETC( CHeterogen & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( CImp_feat & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_imp_ETC( CImp_feat & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_enum_ETC( CNum_enum & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_enum_ETC( CNum_enum & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_real_ETC( CNum_real & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_real_ETC( CNum_real & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns1793_ETC( CSeq_align & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_ETC( CSeq_align & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_ETC( CNum_ref & arg0 );
@@ -544,6 +427,9 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_ETC( COrgName & arg0 );
void x_BasicCleanupSeqFeat_data_data_org_org( COrg_ref & arg0 );
void x_BasicCleanupSeqFeat_data_data_org( COrg_ref & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_E_ETC( std::string & arg0 );
+ template< typename Tcontainer_std_string_ >
+void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC( Tcontainer_std_string_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_desc_ETC( std::string & arg0 );
template< typename Tcontainer_std_string_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ec_ETC( Tcontainer_std_string_ & arg0 );
@@ -564,6 +450,7 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_pub_pub1778_ETC( Tcontaine
void x_BasicCleanupSeqFeat_data_data_pub_pub_ETC( CPubdesc & arg0 );
void x_BasicCleanupSeqFeat_data_data_pub_ETC( CPubdesc & arg0 );
void x_BasicCleanupSeqFeat_data_data_region_ETC( std::string & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_product_ETC( std::string & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_E_ETC( CRNA_qual & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_E_ETC( CRNA_qual & arg0 );
template< typename Tcontainer_ncbi_cref_crna_qual_ >
@@ -594,20 +481,11 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC( Tcontai
void x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_ETC( CTxinit & arg0 );
void x_BasicCleanupSeqFeat_ext_ext1769_ETC( CUser_object & arg0 );
void x_BasicCleanupSeqFeat_ext_ETC( CUser_object & arg0 );
- template< typename Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence_c_loss_of_heterozygosity >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_loss_of_heterozygosity_ETC( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence_c_loss_of_heterozygosity & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_variation( CVariation_ref & arg0 );
template< typename Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence >
-void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E_ETC( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence & arg0 );
+void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence_E( Tcvariation_ref_container_ncbi_cref_c_e_consequence_c_e_consequence & arg0 );
template< typename Tcontainer_ncbi_cref_c_e_consequence_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence( Tcontainer_ncbi_cref_c_e_consequence_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacaa_ETC( CIUPACaa & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_iupacna_ETC( CIUPACna & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ncbieaa_ETC( CNCBIeaa & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_seq_data_ETC( CSeq_data & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_seq_data_ETC( CSeq_data & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_literal_ETC( CSeq_literal & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_literal_ETC( CSeq_literal & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_seq_ETC( CDelta_item::C_Seq & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_E_ETC( CDelta_item & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_E_ETC( CDelta_item & arg0 );
@@ -629,8 +507,8 @@ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations_E( CVariation_ref & arg0 );
template< typename Tcontainer_ncbi_cref_cvariation_ref_ >
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations( Tcontainer_ncbi_cref_cvariation_ref_ & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_ETC( CVariation_ref::C_Data::C_Set & arg0 );
- void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_ETC( CVariation_ref::C_Data & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set( CVariation_ref::C_Data::C_Set & arg0 );
+ void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data( CVariation_ref::C_Data & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation1805_ETC( CVariation_ref & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_ETC( CVariation_ref & arg0 );
void x_BasicCleanupSeqFeat_data_data( CSeqFeatData & arg0 );
@@ -641,22 +519,12 @@ void x_BasicCleanupSeqFeat_exts( Tcontainer_ncbi_cref_cuser_object_ & arg0 );
template< typename Tcontainer_ncbi_cref_cfeat_id_ >
void x_BasicCleanupSeqFeat_ids_ETC( Tcontainer_ncbi_cref_cfeat_id_ & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_ETC( CSeq_loc_equiv & arg0 );
+ void x_BasicCleanupSeqFeat_location_location1767_ETC( CSeq_loc & arg0 );
+ void x_BasicCleanupSeqFeat_location_ETC( CSeq_loc & arg0 );
void x_BasicCleanupSeqFeat_product_product1765_ETC( CSeq_loc & arg0 );
void x_BasicCleanupSeqFeat_product_ETC( CSeq_loc & arg0 );
- void x_BasicCleanupSeqFeat_qual_E_E_ETC( CGb_qual & arg0 );
- void x_BasicCleanupSeqFeat_qual_E_ETC( CGb_qual & arg0 );
template< typename Tcontainer_ncbi_cref_cgb_qual_ >
void x_BasicCleanupSeqFeat_qual_ETC( Tcontainer_ncbi_cref_cgb_qual_ & arg0 );
- template< typename Tcontainer_cdoi_ >
-void x_BasicCleanupSeqFeat_support_support_inference_E_E_dois_ETC( Tcontainer_cdoi_ & arg0 );
- void x_BasicCleanupSeqFeat_support_support_experiment_E_E_ETC( CExperimentSupport & arg0 );
- void x_BasicCleanupSeqFeat_support_support_experiment_E_ETC( CExperimentSupport & arg0 );
- template< typename Tcontainer_ncbi_cref_cexperimentsupport_ >
-void x_BasicCleanupSeqFeat_support_support_experiment_ETC( Tcontainer_ncbi_cref_cexperimentsupport_ & arg0 );
- void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_E_ETC( CProgram_id & arg0 );
- void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_E_ETC( CProgram_id & arg0 );
- template< typename Tcontainer_ncbi_cref_cprogram_id_ >
-void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_programs_ETC( Tcontainer_ncbi_cref_cprogram_id_ & arg0 );
void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_ETC( CEvidenceBasis & arg0 );
void x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_ETC( CEvidenceBasis & arg0 );
void x_BasicCleanupSeqFeat_support_support_inference_E_E_ETC( CInferenceSupport & arg0 );
@@ -673,6 +541,7 @@ void x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_protein_ETC( Tcont
void x_BasicCleanupSeqFeat_support_support_model_evidence_ETC( Tcontainer_ncbi_cref_cmodelevidencesupport_ & arg0 );
void x_BasicCleanupSeqFeat_support_support_ETC( CSeqFeatSupport & arg0 );
void x_BasicCleanupSeqFeat_support_ETC( CSeqFeatSupport & arg0 );
+ void x_BasicCleanupSeqFeat_title_ETC( std::string & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799( COrgName & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname( COrgName & arg0 );
void x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org( COrg_ref & arg0 );
@@ -711,8 +580,6 @@ void x_BasicCleanupBioseqSet_annot_E_E_data_graph_ETC( Tcontainer_ncbi_cref_cseq
void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_data_ETC( CSeqTable_multi_data & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_sparse_other_ETC( CSeqTable_single_data & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_sparse_other_ETC( CSeqTable_single_data & arg0 );
- void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_header_ETC( CSeqTable_column_info & arg0 );
- void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_header_ETC( CSeqTable_column_info & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_E_ETC( CSeqTable_column & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_E_ETC( CSeqTable_column & arg0 );
template< typename Tcontainer_ncbi_cref_cseqtable_column_ >
@@ -727,8 +594,6 @@ void x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_ETC( Tco
template< typename Tcontainer_ncbi_cref_cannotdesc_ >
void x_BasicCleanupBioseqSet_annot_E_E_desc_desc_ETC( Tcontainer_ncbi_cref_cannotdesc_ & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_desc_ETC( CAnnot_descr & arg0 );
- void x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_other_ETC( CTextannot_id & arg0 );
- void x_BasicCleanupBioseqSet_annot_E_E_id_E_E_other_ETC( CTextannot_id & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_id_E_E_ETC( CAnnot_id & arg0 );
void x_BasicCleanupBioseqSet_annot_E_E_id_E_ETC( CAnnot_id & arg0 );
template< typename Tcontainer_ncbi_cref_cannot_id_ >
@@ -738,14 +603,9 @@ void x_BasicCleanupBioseqSet_annot_E_E_id_ETC( Tcontainer_ncbi_cref_cannot_id_ &
template< typename Tcontainer_ncbi_cref_cseq_annot_ >
void x_BasicCleanupBioseq_annot( Tcontainer_ncbi_cref_cseq_annot_ & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_comment_ETC( std::string & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_dbname_ETC( CEMBL_dbname & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_dbname_ETC( CEMBL_dbname & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_E_ETC( CEMBL_xref & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_E_ETC( CEMBL_xref & arg0 );
- template< typename Tcontainer_ncbi_cref_cembl_xref_ >
-void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_ETC( Tcontainer_ncbi_cref_cembl_xref_ & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_ETC( CEMBL_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_ETC( CEMBL_block & arg0 );
+ void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_origin_ETC( std::string & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC( CGB_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( CGB_block & arg0 );
void x_BasicCleanupBioseq_descr_descr_E_E_molinfo_molinfo( CMolInfo & arg0 );
@@ -757,13 +617,10 @@ void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_embl_embl_xref_
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pdb_ETC( CPDB_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_pir_ETC( CPIR_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_pir_ETC( CPIR_block & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_extra_src_ETC( CPRF_ExtraSrc & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_extra_src_ETC( CPRF_ExtraSrc & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_prf_ETC( CPRF_block & arg0 );
- void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_prf_ETC( CPRF_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_region_ETC( std::string & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_sp_ETC( CSP_block & arg0 );
void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_sp_ETC( CSP_block & arg0 );
+ void x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_title_ETC( std::string & arg0 );
void x_BasicCleanupBioseq_descr_descr_E_E( CSeqdesc & arg0 );
void x_BasicCleanupBioseq_descr_descr_E( CSeqdesc & arg0 );
template< typename Tcontainer_ncbi_cref_cseqdesc_ >
diff --git a/c++/src/objtools/cleanup/autogenerated_cleanup.sh b/c++/src/objtools/cleanup/autogenerated_cleanup.sh
new file mode 100755
index 0000000..cb45c4a
--- /dev/null
+++ b/c++/src/objtools/cleanup/autogenerated_cleanup.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+datatool -pch ncbi_pch.hpp -m ../../objects/seqset/seqset.asn -m ../../objects/general/general.asn -m ../../objects/seq/seq.asn -m ../../objects/seqloc/seqloc.asn -m ../../objects/seqfeat/seqfeat.asn -m ../../objects/seqblock/seqblock.asn -m ../../objects/seqalign/seqalign.asn -m ../../objects/pub/pub.asn -m ../../objects/biblio/biblio.asn -m ../../objects/seqres/seqres.asn -m ../../objects/seqtable/seqtable.asn -m ../../objects/medline/medline.asn -m ../../objects/submit/submit.asn [...]
+
diff --git a/c++/src/objtools/cleanup/autogenerated_cleanup.txt b/c++/src/objtools/cleanup/autogenerated_cleanup.txt
index 4bd3f7c..9941551 100644
--- a/c++/src/objtools/cleanup/autogenerated_cleanup.txt
+++ b/c++/src/objtools/cleanup/autogenerated_cleanup.txt
@@ -11,7 +11,7 @@
# Last known command-line used for this:
# (You would have to adjust the file names to fit your
# directory, of course )
-# datatool -pch ncbi_pch.hpp -m /home/kornbluh/c++.opt/src/objects/seqset/seqset.asn -m /home/kornbluh/c++.opt/src/objects/general/general.asn -m /home/kornbluh/c++.opt/src/objects/seq/seq.asn -m /home/kornbluh/c++.opt/src/objects/seqloc/seqloc.asn -m /home/kornbluh/c++.opt/src/objects/seqfeat/seqfeat.asn -m /home/kornbluh/c++.opt/src/objects/seqblock/seqblock.asn -m /home/kornbluh/c++.opt/src/objects/seqalign/seqalign.asn -m /home/kornbluh/c++.opt/src/objects/pub/pub.asn -m /home/ko [...]
+# datatool -pch ncbi_pch.hpp -m ../../objects/seqset/seqset.asn -m ../../objects/general/general.asn -m ../../objects/seq/seq.asn -m ../../objects/seqloc/seqloc.asn -m ../../objects/seqfeat/seqfeat.asn -m ../../objects/seqblock/seqblock.asn -m ../../objects/seqalign/seqalign.asn -m ../../objects/pub/pub.asn -m ../../objects/biblio/biblio.asn -m ../../objects/seqres/seqres.asn -m ../../objects/seqtable/seqtable.asn -m ../../objects/medline/medline.asn -m ../../objects/submit/submit.a [...]
# When browsing in a text-editor, perl-mode does a reasonable
# job of highlighting this file.
@@ -19,9 +19,8 @@
# Notice the hard-coded paths in here. It's likely that you'll want
# to change these to put the code into the right place in your own
# build directory.
-# ( TODO: Hard-coded paths are bad coding style. I should fix this when I get the chance. )
-output_header_file "/home/kornbluh/c++.opt/src/objtools/cleanup/autogenerated_cleanup.hpp"
-output_source_file "/home/kornbluh/c++.opt/src/objtools/cleanup/autogenerated_cleanup.cpp"
+output_header_file "./autogenerated_cleanup.hpp"
+output_source_file "./autogenerated_cleanup.cpp"
output_class_name ncbi::objects::CAutogeneratedCleanup
# The auto-generated class needs a pointer to the class containing all the cleanup functions
@@ -69,16 +68,24 @@ use m_NewCleanup.EnteringEntry { Seq-entry }
# Should be before other types of cleaning, since other cleaners
# might remove the ';' at the end of XML codes
use m_NewCleanup.x_DecodeXMLMarkChanged {
- std::string
+ Seq-feat.comment ,
+ Seq-feat.title ,
+ Gene-ref.locus ,
+ Gene-ref.syn.E ,
+ Prot-ref.name.E ,
+ Prot-ref.desc ,
+ RNA-ref.ext.name ,
+ Seqdesc.title ,
+ Seqdesc.comment ,
}
use m_NewCleanup.x_CompressStringSpacesMarkChanged {
Affil.str ,
- Org-ref.mod.E ,
Prot-ref.name.E ,
RNA-ref.ext.name ,
Seq-feat.data.region ,
Seqdesc.title ,
+ Gene-ref.desc ,
}
membermacro CLEAN_STRING_MEMBER {
@@ -132,11 +139,12 @@ membermacro CLEAN_AND_COMPRESS_STRING_MEMBER {
Org-ref.common ,
Org-ref.taxname ,
OrgMod.attrib ,
- Prot-ref.desc ,
RNA-gen.class ,
RNA-gen.product ,
RNA-gen.quals.E.qual ,
RNA-gen.quals.E.val ,
+ Seq-feat.comment ,
+ Gene-ref.locus ,
}
membermacro CLEAN_AND_COMPRESS_STRING_MEMBER_JUNK {
@@ -150,9 +158,6 @@ use m_NewCleanup.x_ConvertDoubleQuotesMarkChanged {
Gene-ref.locus-tag ,
Gene-ref.maploc ,
Gene-ref.syn.E ,
- Prot-ref.activity.E ,
- Prot-ref.desc ,
- Prot-ref.ec.E ,
Prot-ref.name.E ,
Pubdesc.comment ,
RNA-gen.class ,
@@ -164,13 +169,18 @@ use m_NewCleanup.x_ConvertDoubleQuotesMarkChanged {
Seq-feat.data.region ,
Seqdesc.region ,
}
+
+use m_NewCleanup.x_TrimInternalSemicolonsMarkChanged {
+ Org-ref.common ,
+ Gene-ref.locus ,
+ Seq-feat.data.region ,
+ Prot-ref.desc ,
+}
# These are POST in case substrings will be cleaned some way first
membermacro CLEAN_STRING_LIST {
POST Gene-ref.syn ,
POST Org-ref.syn ,
- POST Prot-ref.activity ,
- POST Prot-ref.ec ,
POST Prot-ref.name ,
}
@@ -182,7 +192,6 @@ use m_NewCleanup.x_RemoveFlankingQuotes {
RNA-ref.ext.name ,
RNA-gen.product ,
Prot-ref.name.E ,
- Prot-ref.desc
}
use m_NewCleanup.x_FixUpEllipsis {
@@ -193,16 +202,31 @@ use m_NewCleanup.x_RemoveSpacesBetweenTildesMarkChanged {
Seqdesc.comment
}
+use m_NewCleanup.X_CommentTildeFixes {
+ Seqdesc.comment
+}
+
use m_NewCleanup.SeqIdBC { Seq-id }
use m_NewCleanup.SeqLocBC { Seq-loc }
+use m_NewCleanup.x_BothStrandBC {
+ Seq-loc EXCEPT {
+ Seq-feat.location ,
+ }
+}
use m_NewCleanup.ConvertSeqLocWholeToInt {
- Seq-loc EXCEPT { product }
+ Seq-loc EXCEPT {
+ product ,
+ Seq-inst.ext.seg.E ,
+ Seq-loc.mix.E
+ }
}
use m_NewCleanup.SeqLocMixBC { Seq-loc.mix }
use m_NewCleanup.SeqsetBC { Bioseq-set }
+use m_NewCleanup.ProtSeqBC { Bioseq }
+
# This really works on the Imp-feat inside the Seq-feat, if any.
# It's here so we convert Seq-feat's imp to another type (e.g. cdregion)
# if necessary. And, we put it before SeqfeatBC, etc. so it happens
@@ -212,6 +236,9 @@ use m_NewCleanup.ImpFeatBC { Seq-feat }
use m_NewCleanup.SeqfeatBC { Seq-feat }
use m_NewCleanup.x_PostSeqFeat { POST Seq-feat }
+use m_NewCleanup.ProtNameBC { Prot-ref.name.E }
+use m_NewCleanup.ProtActivityBC { Prot-ref.activity.E }
+
# Seq-feat data stuff
use m_NewCleanup.GeneFeatBC { Seq-feat.data.gene AND Seq-feat }
use m_NewCleanup.GenerefBC { POST Gene-ref }
@@ -224,32 +251,33 @@ use m_NewCleanup.PubdescBC { POST Pubdesc }
use m_NewCleanup.SiteFeatBC { Seq-feat.data.site AND Seq-feat }
use m_NewCleanup.CdregionFeatBC { Seq-feat.data.cdregion AND Seq-feat }
+use m_NewCleanup.GBblockOriginBC { GB-block.origin }
use m_NewCleanup.GBblockBC { GB-block }
use m_NewCleanup.EMBLblockBC { EMBL-block }
-use m_NewCleanup.x_MoveSeqdescOrgToSourceOrg { Seqdesc }
-
# Biosource stuff
+use m_NewCleanup.x_SubSourceBC { SubSource }
+use m_NewCleanup.x_OrgModBC { OrgMod }
use m_NewCleanup.BiosourceFeatBC { POST Seq-feat.data.biosrc AND Seq-feat }
use m_NewCleanup.BiosourceBC { BioSource }
use m_NewCleanup.x_PostBiosource { POST BioSource }
use m_NewCleanup.x_ModernizePCRPrimers { POST BioSource }
use m_NewCleanup.PCRReactionSetBC { BioSource.pcr-primers }
-use m_NewCleanup.x_GBQualToOrgRef {
- Seq-feat.data.org AND Seq-feat ,
- Seq-feat.data.biosrc.org AND Seq-feat
-}
use m_NewCleanup.x_CleanupOrgModAndSubSourceOther { BioSource.org.orgname AND BioSource }
-use m_NewCleanup.x_MoveSeqfeatOrgToSourceOrg { Seq-feat }
-
use m_NewCleanup.x_CopyGBBlockDivToOrgnameDiv { Seq-entry }
use m_NewCleanup.x_ExpandCombinedQuals { Seq-feat.qual }
+use m_NewCleanup.OrgrefModBC { Org-ref.mod.E }
use m_NewCleanup.OrgrefBC { Org-ref }
use m_NewCleanup.x_PostOrgRef { POST Org-ref }
+use m_NewCleanup.x_GBQualToOrgRef {
+ Seq-feat.data.org AND Seq-feat ,
+ Seq-feat.data.biosrc.org AND Seq-feat
+}
+
use m_NewCleanup.x_DateStdBC { Date-std }
use m_NewCleanup.DbtagBC { Dbtag }
@@ -298,6 +326,12 @@ use m_NewCleanup.x_AuthListBCWithFixInitials {
Seq-submit.sub.cit.authors
}
+#remove empty descr set after other cleaning steps are done
+use m_NewCleanup.x_ClearEmptyDescr {
+ POST Bioseq-set,
+ POST Bioseq
+}
+
# Call LeavingEntry as late as possible, so keep this as close
# as possible to end of file.
# (Its partner function is EnteringEntry. See above.)
diff --git a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp
index b2573a8..5489bd1 100644
--- a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp
+++ b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp
@@ -1,4 +1,4 @@
-/* $Id: autogenerated_extended_cleanup.cpp 439484 2014-06-30 18:29:55Z bollin $
+/* $Id: autogenerated_extended_cleanup.cpp 485531 2015-11-23 16:16:33Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,9 +39,91 @@
BEGIN_SCOPE(ncbi)
BEGIN_SCOPE(objects)
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( std::string & arg0 )
+{ // type Primitive
+ m_NewCleanup.x_TrimInternalSemicolonsMarkChanged( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC( COrgName & arg0 )
+{ // type Sequence
+ if( arg0.IsSetAttrib() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetAttrib() );
+ }
+ if( arg0.IsSetLineage() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetLineage() );
+ }
+ if( arg0.IsSetName() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( arg0.SetName() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E( COrgName & arg0 )
+{ // type Reference
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E
+
+template< typename Tcontainer_ncbi_cref_corgname_ >
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid( Tcontainer_ncbi_cref_corgname_ & arg0 )
+{ // type UniSequence
+ NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_corgname_, iter, arg0 ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E( **iter );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid( CMultiOrgName & arg0 )
+{ // type Reference
+ if( arg0.IsSet() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid( arg0.Set() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( COrgName::C_Name & arg0 )
+{ // type Choice
+ switch( arg0.Which() ) {
+ case COrgName::C_Name::e_Hybrid:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid( arg0.SetHybrid() );
+ break;
+ default:
+ break;
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799_ETC( COrgName & arg0 )
+{ // type Sequence
+ if( arg0.IsSetAttrib() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetAttrib() );
+ }
+ if( arg0.IsSetLineage() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetLineage() );
+ }
+ if( arg0.IsSetName() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( arg0.SetName() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_ETC( COrgName & arg0 )
+{ // type Reference
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799_ETC( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_ETC( COrg_ref & arg0 )
+{ // type Sequence
+ if( arg0.IsSetOrgname() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_ETC( arg0.SetOrgname() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( COrg_ref & arg0 )
+{ // type Reference
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_ETC( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC
+
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_ETC( CBioSource & arg0 )
{ // type Sequence
m_NewCleanup.BioSourceEC( arg0 );
+ if( arg0.IsSetOrg() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( arg0.SetOrg() );
+ }
} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_ETC
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC( CBioSource & arg0 )
@@ -52,6 +134,12 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_data_data_gene_gene( CGene_ref & arg0 )
{ // type Sequence
m_NewCleanup.x_RemoveRedundantComment( arg0, *m_LastArg_ExtendedCleanupSeqFeat );
+ if( arg0.IsSetLocus_tag() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetLocus_tag() );
+ }
+ if( arg0.IsSetMaploc() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetMaploc() );
+ }
} // end of x_ExtendedCleanupSeqFeat_data_data_gene_gene
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_data_data_gene( CGene_ref & arg0 )
@@ -59,9 +147,25 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_data_data_gene( CGe
x_ExtendedCleanupSeqFeat_data_data_gene_gene( arg0 );
} // end of x_ExtendedCleanupSeqFeat_data_data_gene
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( CImp_feat & arg0 )
+{ // type Sequence
+ if( arg0.IsSetKey() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetKey() );
+ }
+ if( arg0.IsSetLoc() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetLoc() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_ETC( CImp_feat & arg0 )
+{ // type Reference
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_ETC
+
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC( CProt_ref & arg0 )
{ // type Sequence
m_NewCleanup.x_RemoveProtDescThatDupsProtName( arg0 );
+ m_NewCleanup.ProtRefEC( arg0 );
} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_ETC( CProt_ref & arg0 )
@@ -69,6 +173,29 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC( arg0 );
} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_ETC
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_ETC( CGene_ref & arg0 )
+{ // type Sequence
+ if( arg0.IsSetLocus_tag() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetLocus_tag() );
+ }
+ if( arg0.IsSetMaploc() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetMaploc() );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC( CGene_ref & arg0 )
+{ // type Reference
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_ETC( arg0 );
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC
+
+template< typename Tcontainer_ncbi_cref_cgene_ref_ >
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC( Tcontainer_ncbi_cref_cgene_ref_ & arg0 )
+{ // type UniSequence
+ NON_CONST_ITERATE( typename Tcontainer_ncbi_cref_cgene_ref_, iter, arg0 ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC( **iter );
+ }
+} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC
+
template< typename Tcontainer_ncbi_cref_cprot_ref_ >
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC( Tcontainer_ncbi_cref_cprot_ref_ & arg0 )
{ // type UniSequence
@@ -79,9 +206,15 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_ETC( CTxinit & arg0 )
{ // type Sequence
+ if( arg0.IsSetGene() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC( arg0.SetGene() );
+ }
if( arg0.IsSetProtein() ) {
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC( arg0.SetProtein() );
}
+ if( arg0.IsSetTxorg() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( arg0.SetTxorg() );
+ }
} // end of x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_ETC
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_ETC( CTxinit & arg0 )
@@ -98,6 +231,12 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_data_data( CSeqFeat
case CSeqFeatData::e_Gene:
x_ExtendedCleanupSeqFeat_data_data_gene( arg0.SetGene() );
break;
+ case CSeqFeatData::e_Imp:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_ETC( arg0.SetImp() );
+ break;
+ case CSeqFeatData::e_Org:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( arg0.SetOrg() );
+ break;
case CSeqFeatData::e_Prot:
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_ETC( arg0.SetProt() );
break;
@@ -120,6 +259,15 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_
case CSeqFeatData::e_Biosrc:
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC( arg0.SetBiosrc() );
break;
+ case CSeqFeatData::e_Gene:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC( arg0.SetGene() );
+ break;
+ case CSeqFeatData::e_Imp:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_ETC( arg0.SetImp() );
+ break;
+ case CSeqFeatData::e_Org:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( arg0.SetOrg() );
+ break;
case CSeqFeatData::e_Prot:
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_ETC( arg0.SetProt() );
break;
@@ -176,9 +324,15 @@ void CAutogeneratedExtendedCleanup::ExtendedCleanupSeqFeat( CSeq_feat & arg0_raw
m_LastArg_ExtendedCleanupSeqFeat = &arg0;
+ m_NewCleanup.CdRegionEC( arg0 );
+ m_NewCleanup.ResynchProteinPartials( arg0 );
+ m_NewCleanup.x_MoveSeqfeatOrgToSourceOrg( arg0 );
if( arg0.IsSetData() ) {
x_ExtendedCleanupSeqFeat_data( arg0.SetData() );
}
+ if( arg0.IsSetTitle() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetTitle() );
+ }
if( arg0.IsSetXref() ) {
x_ExtendedCleanupSeqFeat_xref_ETC( arg0.SetXref() );
}
@@ -237,9 +391,28 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseq_annot( Tcontainer_nc
}
} // end of x_ExtendedCleanupBioseq_annot
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC( CGB_block & arg0 )
+{ // type Sequence
+ if( arg0.IsSetOrigin() ) {
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( arg0.SetOrigin() );
+ }
+} // end of x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC
+
+void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( CGB_block & arg0 )
+{ // type Reference
+ x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC( arg0 );
+} // end of x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC
+
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_ETC( CSeqdesc & arg0 )
{ // type Choice
+ m_NewCleanup.x_MoveSeqdescOrgToSourceOrg( arg0 );
switch( arg0.Which() ) {
+ case CSeqdesc::e_Genbank:
+ x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( arg0.SetGenbank() );
+ break;
+ case CSeqdesc::e_Org:
+ x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( arg0.SetOrg() );
+ break;
case CSeqdesc::e_Source:
x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC( arg0.SetSource() );
break;
@@ -264,6 +437,8 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_s
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_ETC( CSeq_descr & arg0 )
{ // type Reference
m_NewCleanup.x_RemoveEmptyUserObject( arg0 );
+ m_NewCleanup.KeepLatestDateDesc( arg0 );
+ m_NewCleanup.x_CleanupGenbankBlock( arg0 );
if( arg0.IsSet() ) {
x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_ETC( arg0.Set() );
}
@@ -321,6 +496,8 @@ void CAutogeneratedExtendedCleanup::ExtendedCleanupBioseq( CBioseq & arg0 )
{ // type Sequence
m_NewCleanup.x_RemoveDupBioSource( arg0 );
m_NewCleanup.x_FixStructuredCommentKeywords( arg0 );
+ m_NewCleanup.CreateMissingMolInfo( arg0 );
+ m_NewCleanup.AddProteinTitles( arg0 );
m_NewCleanup.x_RemoveEmptyFeatureTables( arg0 );
if( arg0.IsSetAnnot() ) {
x_ExtendedCleanupBioseq_annot( arg0.SetAnnot() );
@@ -331,6 +508,8 @@ void CAutogeneratedExtendedCleanup::ExtendedCleanupBioseq( CBioseq & arg0 )
if( arg0.IsSetInst() ) {
x_ExtendedCleanupBioseq_inst( arg0.SetInst() );
}
+ m_NewCleanup.ResynchPeptidePartials( arg0 );
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
} // end of ExtendedCleanupBioseq
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_seq( CBioseq & arg0 )
@@ -368,6 +547,7 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_set_set_ETC( CBios
{ // type Sequence
m_NewCleanup.x_BioseqSetEC( arg0 );
m_NewCleanup.x_RemoveDupBioSource( arg0 );
+ m_NewCleanup.x_MoveCDSFromNucAnnotToSetAnnot( arg0 );
m_NewCleanup.x_RemoveEmptyFeatureTables( arg0 );
if( arg0.IsSetAnnot() ) {
x_ExtendedCleanupSeqEntry_set_set_annot( arg0.SetAnnot() );
@@ -378,6 +558,7 @@ void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_set_set_ETC( CBios
if( arg0.IsSetSeq_set() ) {
x_ExtendedCleanupSeqEntry_set_set_seq_set( arg0.SetSeq_set() );
}
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
} // end of x_ExtendedCleanupSeqEntry_set_set_ETC
void CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_set( CBioseq_set & arg0 )
@@ -502,6 +683,7 @@ void CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet( CBioseq_set & arg0
{ // type Sequence
m_NewCleanup.x_BioseqSetEC( arg0 );
m_NewCleanup.x_RemoveDupBioSource( arg0 );
+ m_NewCleanup.x_MoveCDSFromNucAnnotToSetAnnot( arg0 );
m_NewCleanup.x_RemoveEmptyFeatureTables( arg0 );
if( arg0.IsSetAnnot() ) {
x_ExtendedCleanupBioseqSet_annot( arg0.SetAnnot() );
@@ -512,6 +694,7 @@ void CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet( CBioseq_set & arg0
if( arg0.IsSetSeq_set() ) {
x_ExtendedCleanupBioseqSet_seq_set( arg0.SetSeq_set() );
}
+ m_NewCleanup.x_ClearEmptyDescr( arg0 );
} // end of ExtendedCleanupBioseqSet
diff --git a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.hpp b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.hpp
index dbe9e81..715ffad 100644
--- a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.hpp
+++ b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.hpp
@@ -1,7 +1,7 @@
#ifndef AUTOGENERATEDEXTENDEDCLEANUP__HPP
#define AUTOGENERATEDEXTENDEDCLEANUP__HPP
-/* $Id: autogenerated_extended_cleanup.hpp 439484 2014-06-30 18:29:55Z bollin $
+/* $Id: autogenerated_extended_cleanup.hpp 468920 2015-05-29 14:02:03Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,12 +39,17 @@
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/BioSource.hpp>
+#include <objects/seqfeat/Org_ref.hpp>
+#include <objects/seqfeat/OrgName.hpp>
+#include <objects/seqfeat/MultiOrgName.hpp>
#include <objects/seqfeat/Gene_ref.hpp>
+#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seqfeat/Txinit.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
+#include <objects/seqblock/GB_block.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Map_ext.hpp>
@@ -76,12 +81,29 @@ public:
void ExtendedCleanupSeqFeat( CSeq_feat & arg0_raw );
private:
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_lineage_ETC( std::string & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_E1798_ETC( COrgName & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid_E( COrgName & arg0 );
+ template< typename Tcontainer_ncbi_cref_corgname_ >
+void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid( Tcontainer_ncbi_cref_corgname_ & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid( CMultiOrgName & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name( COrgName::C_Name & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname1799_ETC( COrgName & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_ETC( COrgName & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_ETC( COrg_ref & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_ETC( COrg_ref & arg0 );
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_ETC( CBioSource & arg0 );
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_ETC( CBioSource & arg0 );
void x_ExtendedCleanupSeqFeat_data_data_gene_gene( CGene_ref & arg0 );
void x_ExtendedCleanupSeqFeat_data_data_gene( CGene_ref & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_imp_ETC( CImp_feat & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_imp_ETC( CImp_feat & arg0 );
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_ETC( CProt_ref & arg0 );
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_ETC( CProt_ref & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_ETC( CGene_ref & arg0 );
+ void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_ETC( CGene_ref & arg0 );
+ template< typename Tcontainer_ncbi_cref_cgene_ref_ >
+void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC( Tcontainer_ncbi_cref_cgene_ref_ & arg0 );
template< typename Tcontainer_ncbi_cref_cprot_ref_ >
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC( Tcontainer_ncbi_cref_cprot_ref_ & arg0 );
void x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_ETC( CTxinit & arg0 );
@@ -101,6 +123,8 @@ void x_ExtendedCleanupSeqAnnot_data_ftable( Tcontainer_ncbi_cref_cseq_feat_ & ar
void x_ExtendedCleanupBioseq_annot_E( CSeq_annot & arg0 );
template< typename Tcontainer_ncbi_cref_cseq_annot_ >
void x_ExtendedCleanupBioseq_annot( Tcontainer_ncbi_cref_cseq_annot_ & arg0 );
+ void x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_genbank_ETC( CGB_block & arg0 );
+ void x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_genbank_ETC( CGB_block & arg0 );
void x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_E_ETC( CSeqdesc & arg0 );
void x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_E_ETC( CSeqdesc & arg0 );
template< typename Tcontainer_ncbi_cref_cseqdesc_ >
diff --git a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.sh b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.sh
new file mode 100755
index 0000000..0dbcd6a
--- /dev/null
+++ b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+datatool -pch ncbi_pch.hpp -m ../../objects/seqset/seqset.asn -m ../../objects/general/general.asn -m ../../objects/seq/seq.asn -m ../../objects/seqloc/seqloc.asn -m ../../objects/seqfeat/seqfeat.asn -m ../../objects/seqblock/seqblock.asn -m ../../objects/seqalign/seqalign.asn -m ../../objects/pub/pub.asn -m ../../objects/biblio/biblio.asn -m ../../objects/seqres/seqres.asn -m ../../objects/seqtable/seqtable.asn -m ../../objects/medline/medline.asn -m ../../objects/submit/submit.asn [...]
+
diff --git a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.txt b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.txt
index 3998171..61b7788 100644
--- a/c++/src/objtools/cleanup/autogenerated_extended_cleanup.txt
+++ b/c++/src/objtools/cleanup/autogenerated_extended_cleanup.txt
@@ -49,6 +49,18 @@ deprecated {
# Don't forget: order matters!
+# some string cleanups that Basic does not do but extended does
+use m_NewCleanup.x_TrimInternalSemicolonsMarkChanged {
+ OrgName.attrib ,
+ OrgName.lineage ,
+ GB-block.origin ,
+ Gene-ref.maploc ,
+ Gene-ref.locus-tag ,
+ Seq-feat.title ,
+ Imp-feat.key ,
+ Imp-feat.loc ,
+}
+
use m_NewCleanup.x_BioseqSetEC
{
Bioseq-set
@@ -74,6 +86,11 @@ use m_NewCleanup.x_RemoveProtDescThatDupsProtName
Prot-ref
}
+use m_NewCleanup.ProtRefEC
+{
+ Prot-ref
+}
+
use m_NewCleanup.x_RemoveRedundantComment
{
Seq-feat.data.gene AND Seq-feat
@@ -85,6 +102,30 @@ use m_NewCleanup.x_RemoveEmptyUserObject
Bioseq-set.descr
}
+use m_NewCleanup.KeepLatestDateDesc
+{
+ Bioseq.descr,
+ Bioseq-set.descr
+}
+
+use m_NewCleanup.x_CleanupGenbankBlock
+{
+ Bioseq.descr,
+ Bioseq-set.descr
+}
+
+use m_NewCleanup.CdRegionEC { Seq-feat }
+
+use m_NewCleanup.CreateMissingMolInfo { Bioseq }
+
+use m_NewCleanup.ResynchProteinPartials { Seq-feat }
+use m_NewCleanup.ResynchPeptidePartials { POST Bioseq }
+
+use m_NewCleanup.AddProteinTitles { Bioseq }
+
+use m_NewCleanup.x_MoveSeqdescOrgToSourceOrg { Seqdesc }
+use m_NewCleanup.x_MoveSeqfeatOrgToSourceOrg { Seq-feat }
+
use m_NewCleanup.BioSourceEC { BioSource }
use m_NewCleanup.x_RemoveEmptyFeatures
@@ -92,10 +133,17 @@ use m_NewCleanup.x_RemoveEmptyFeatures
Seq-annot
}
+use m_NewCleanup.x_MoveCDSFromNucAnnotToSetAnnot { Bioseq-set }
+
use m_NewCleanup.x_RemoveEmptyFeatureTables
{
Bioseq,
Bioseq-set
}
+#remove empty descr set after other cleaning steps are done
+use m_NewCleanup.x_ClearEmptyDescr {
+ POST Bioseq-set,
+ POST Bioseq
+}
diff --git a/c++/src/objtools/cleanup/cleanup.cpp b/c++/src/objtools/cleanup/cleanup.cpp
index d2a71dd..e51ac9d 100644
--- a/c++/src/objtools/cleanup/cleanup.cpp
+++ b/c++/src/objtools/cleanup/cleanup.cpp
@@ -1,4 +1,4 @@
-/* $Id: cleanup.cpp 440441 2014-07-14 12:03:57Z bollin $
+/* $Id: cleanup.cpp 480959 2015-10-06 12:01:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -36,12 +36,22 @@
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
+#include <objects/seqset/seqset_macros.hpp>
+#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
+#include <objects/seqfeat/SeqFeatXref.hpp>
+#include <objects/general/Object_id.hpp>
+#include <objects/general/User_object.hpp>
#include <objects/submit/Seq_submit.hpp>
+#include <objects/taxon3/taxon3.hpp>
#include <objmgr/util/sequence.hpp>
+#include <objmgr/util/feature.hpp>
+#include <objmgr/seq_annot_ci.hpp>
+#include <objmgr/seqdesc_ci.hpp>
#include <objtools/cleanup/cleanup.hpp>
+#include <objtools/edit/cds_fix.hpp>
#include "newcleanupp.hpp"
@@ -398,11 +408,775 @@ const char* const CCleanupChange::sm_ChangeDesc[eNumberofChangeTypes + 1] = {
"Decode XML", // 90
"Remove Dup BioSource",
"Clean Org-ref",
+ "Trim Internal Semicolons",
// set when any other change is made.
"Change Other",
"Invalid Change Code"
};
+
+bool CCleanup::MoveProteinSpecificFeats(CSeq_entry_Handle seh)
+{
+ bool any_change = false;
+ SAnnotSelector sel(CSeqFeatData::e_Prot);
+ sel.IncludeFeatType(CSeqFeatData::e_Psec_str);
+ for (CFeat_CI prot_it(seh, sel); prot_it; ++prot_it) {
+ CBioseq_Handle parent_bsh = seh.GetScope().GetBioseqHandle(prot_it->GetLocation());
+
+ if (!parent_bsh) {
+ // protein feature is mispackaged
+ continue;
+ }
+ if (parent_bsh.IsAa()) {
+ // protein feature is already on protein sequence
+ continue;
+ }
+
+ CConstRef<CSeq_feat> cds = sequence::GetOverlappingCDS(prot_it->GetLocation(), seh.GetScope());
+ if (!cds || !cds->IsSetProduct()) {
+ // there is no overlapping coding region feature, so there is no appropriate
+ // protein sequence to move to
+ continue;
+ }
+
+ CSeq_feat_Handle cds_h = seh.GetScope().GetSeq_featHandle(*cds);
+ if (!cds_h) {
+ // can't get handle
+ continue;
+ }
+
+ if (feature::IsLocationInFrame(cds_h, prot_it->GetLocation()) != feature::eLocationInFrame_InFrame) {
+ // not in frame, can't convert
+ continue;
+ }
+
+ CConstRef<CSeq_feat> orig_feat = prot_it->GetSeq_feat();
+ CRef<CSeq_feat> new_feat(new CSeq_feat());
+ new_feat->Assign(*orig_feat);
+ CRef<CSeq_loc> new_loc;
+ CRef<CSeq_loc_Mapper> nuc2prot_mapper(
+ new CSeq_loc_Mapper(*cds, CSeq_loc_Mapper::eLocationToProduct, &seh.GetScope()) );
+ new_loc = nuc2prot_mapper->Map(orig_feat->GetLocation());
+ if (!new_loc || new_loc->GetId()->Equals(*(orig_feat->GetLocation().GetId()))) {
+ // unable to map to protein location
+ continue;
+ }
+ new_loc->GetStart(eExtreme_Biological);
+ new_loc->GetStop(eExtreme_Biological);
+
+ // change location to protein
+ new_feat->ResetLocation();
+ new_feat->SetLocation(*new_loc);
+
+ // remove the feature from the nuc bioseq
+ CSeq_feat_Handle fh = seh.GetScope().GetSeq_featHandle(*orig_feat);
+ CSeq_feat_EditHandle edh(fh);
+ edh.Remove();
+
+ CBioseq_Handle target_bsh = seh.GetScope().GetBioseqHandle(new_feat->GetLocation());
+ CBioseq_EditHandle eh = target_bsh.GetEditHandle();
+
+ // Find a feature table on the protein sequence to add the feature to.
+ CSeq_annot_Handle ftable;
+ CSeq_annot_CI annot_ci(target_bsh);
+ for (; annot_ci; ++annot_ci) {
+ if ((*annot_ci).IsFtable()) {
+ ftable = *annot_ci;
+ break;
+ }
+ }
+ // If there is no feature table present, make one
+ if (!ftable) {
+ CRef<CSeq_annot> new_annot(new CSeq_annot());
+ ftable = eh.AttachAnnot(*new_annot);
+ }
+
+ // add feature to the protein bioseq
+ CSeq_annot_EditHandle aeh(ftable);
+ aeh.AddFeat(*new_feat);
+ any_change = true;
+ }
+ return any_change;
+}
+
+
+bool CCleanup::IsGeneXrefUnnecessary(const CSeq_feat& sf, CScope& scope, const CGene_ref& gene_xref)
+{
+ if (gene_xref.IsSuppressed()) {
+ return false;
+ }
+ CConstRef<CSeq_feat> gene = sequence::GetOverlappingGene(sf.GetLocation(), scope);
+ if (!gene || !gene->IsSetData() || !gene->GetData().IsGene()) {
+ return false;
+ }
+
+ return gene->GetData().GetGene().RefersToSameGene(gene_xref);
+}
+
+
+bool CCleanup::RemoveUnnecessaryGeneXrefs(CSeq_feat& f, CScope& scope)
+{
+ if (!f.IsSetXref()) {
+ return false;
+ }
+ bool any_removed = false;
+ CSeq_feat::TXref::iterator xit = f.SetXref().begin();
+ while (xit != f.SetXref().end()) {
+ if ((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&
+ IsGeneXrefUnnecessary(f, scope, (*xit)->GetData().GetGene())) {
+ xit = f.SetXref().erase(xit);
+ any_removed = true;
+ } else {
+ ++xit;
+ }
+ }
+ if (any_removed) {
+ if (f.IsSetXref() && f.GetXref().empty()) {
+ f.ResetXref();
+ }
+ }
+ return any_removed;
+}
+
+
+bool CCleanup::RemoveUnnecessaryGeneXrefs(CSeq_entry_Handle seh)
+{
+ bool any_change = false;
+ CScope& scope = seh.GetScope();
+
+ for (CFeat_CI fi(seh); fi; ++fi) {
+ if (fi->IsSetXref()) {
+ CRef<CSeq_feat> new_feat(new CSeq_feat());
+ new_feat->Assign(*(fi->GetOriginalSeq_feat()));
+ bool any_removed = RemoveUnnecessaryGeneXrefs(*new_feat, scope);
+ if (any_removed) {
+ CSeq_feat_EditHandle edh(*fi);
+ edh.Replace(*new_feat);
+ any_change = true;
+ }
+ }
+ }
+
+ return any_change;
+}
+
+bool CCleanup::RemoveNonsuppressingGeneXrefs(CSeq_feat& f)
+{
+ if (!f.IsSetXref()) {
+ return false;
+ }
+ bool any_removed = false;
+ CSeq_feat::TXref::iterator xit = f.SetXref().begin();
+ while (xit != f.SetXref().end()) {
+ if ((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&
+ !(*xit)->GetData().GetGene().IsSuppressed()) {
+ xit = f.SetXref().erase(xit);
+ any_removed = true;
+ } else {
+ ++xit;
+ }
+ }
+ if (any_removed) {
+ if (f.IsSetXref() && f.GetXref().empty()) {
+ f.ResetXref();
+ }
+ }
+ return any_removed;
+}
+
+bool CCleanup::FindMatchingLocusGene(CSeq_feat& f, const CGene_ref& gene_xref, CBioseq_Handle bsh)
+{
+ bool match = false;
+ string locus1;
+ if (gene_xref.IsSetLocus())
+ locus1 = gene_xref.GetLocus();
+ for (CFeat_CI feat_ci(bsh, SAnnotSelector(CSeqFeatData::eSubtype_gene)); feat_ci; ++feat_ci)
+ {
+ string locus2;
+ if ( !f.Equals(*feat_ci->GetSeq_feat()) && feat_ci->GetSeq_feat()->IsSetData() && feat_ci->GetSeq_feat()->GetData().IsGene()
+ && feat_ci->GetSeq_feat()->GetData().GetGene().IsSetLocus())
+ {
+ locus2 = feat_ci->GetSeq_feat()->GetData().GetGene().GetLocus();
+ }
+ if (!locus1.empty() && !locus2.empty() && locus1 == locus2)
+ {
+ match = true;
+ break;
+ }
+ }
+ return match;
+}
+
+bool CCleanup::RemoveOrphanLocusGeneXrefs(CSeq_feat& f, CBioseq_Handle bsh)
+{
+ if (!f.IsSetXref()) {
+ return false;
+ }
+ bool any_removed = false;
+ CSeq_feat::TXref::iterator xit = f.SetXref().begin();
+ while (xit != f.SetXref().end()) {
+ if ((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&
+ !(*xit)->GetData().GetGene().IsSuppressed() && !FindMatchingLocusGene(f, (*xit)->GetData().GetGene(), bsh)) {
+ xit = f.SetXref().erase(xit);
+ any_removed = true;
+ } else {
+ ++xit;
+ }
+ }
+ if (any_removed) {
+ if (f.IsSetXref() && f.GetXref().empty()) {
+ f.ResetXref();
+ }
+ }
+ return any_removed;
+}
+
+bool CCleanup::FindMatchingLocus_tagGene(CSeq_feat& f, const CGene_ref& gene_xref, CBioseq_Handle bsh)
+{
+ bool match = false;
+ string locus_tag1;
+ if (gene_xref.IsSetLocus_tag())
+ locus_tag1 = gene_xref.GetLocus_tag();
+ for (CFeat_CI feat_ci(bsh, SAnnotSelector(CSeqFeatData::eSubtype_gene)); feat_ci; ++feat_ci)
+ {
+ string locus_tag2;
+ if ( !f.Equals(*feat_ci->GetSeq_feat()) && feat_ci->GetSeq_feat()->IsSetData() && feat_ci->GetSeq_feat()->GetData().IsGene()
+ && feat_ci->GetSeq_feat()->GetData().GetGene().IsSetLocus_tag())
+ {
+ locus_tag2 = feat_ci->GetSeq_feat()->GetData().GetGene().GetLocus_tag();
+ }
+ if (!locus_tag1.empty() && !locus_tag2.empty() && locus_tag1 == locus_tag2)
+ {
+ match = true;
+ break;
+ }
+ }
+ return match;
+}
+
+bool CCleanup::RemoveOrphanLocus_tagGeneXrefs(CSeq_feat& f, CBioseq_Handle bsh)
+{
+ if (!f.IsSetXref()) {
+ return false;
+ }
+ bool any_removed = false;
+ CSeq_feat::TXref::iterator xit = f.SetXref().begin();
+ while (xit != f.SetXref().end()) {
+ if ((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&
+ !(*xit)->GetData().GetGene().IsSuppressed() && !FindMatchingLocus_tagGene(f, (*xit)->GetData().GetGene(), bsh)) {
+ xit = f.SetXref().erase(xit);
+ any_removed = true;
+ } else {
+ ++xit;
+ }
+ }
+ if (any_removed) {
+ if (f.IsSetXref() && f.GetXref().empty()) {
+ f.ResetXref();
+ }
+ }
+ return any_removed;
+}
+
+
+bool CCleanup::SetMolinfoTech(CBioseq_Handle bsh, CMolInfo::ETech tech)
+{
+ CSeqdesc_CI di(bsh, CSeqdesc::e_Molinfo);
+ if (di) {
+ if (di->GetMolinfo().IsSetTech() && di->GetMolinfo().GetTech() == tech) {
+ // no change necessary
+ return false;
+ } else {
+ CSeqdesc* d = const_cast<CSeqdesc*>(&(*di));
+ d->SetMolinfo().SetTech(tech);
+ return true;
+ }
+ }
+ CRef<CSeqdesc> m(new CSeqdesc());
+ m->SetMolinfo().SetTech(tech);
+ if (bsh.IsSetInst() && bsh.GetInst().IsSetMol() && bsh.IsAa()) {
+ m->SetMolinfo().SetBiomol(CMolInfo::eBiomol_peptide);
+ }
+ CBioseq_EditHandle eh = bsh.GetEditHandle();
+ eh.AddSeqdesc(*m);
+ return true;
+}
+
+
+bool CCleanup::SetMolinfoBiomol(CBioseq_Handle bsh, CMolInfo::EBiomol biomol)
+{
+ CSeqdesc_CI di(bsh, CSeqdesc::e_Molinfo);
+ if (di) {
+ if (di->GetMolinfo().IsSetTech() && di->GetMolinfo().GetBiomol() == biomol) {
+ // no change necessary
+ return false;
+ } else {
+ CSeqdesc* d = const_cast<CSeqdesc*>(&(*di));
+ d->SetMolinfo().SetBiomol(biomol);
+ return true;
+ }
+ }
+ CRef<CSeqdesc> m(new CSeqdesc());
+ m->SetMolinfo().SetBiomol(biomol);
+ CBioseq_EditHandle eh = bsh.GetEditHandle();
+ eh.AddSeqdesc(*m);
+ return true;
+}
+
+
+bool CCleanup::AddMissingMolInfo(CBioseq& seq, bool is_product)
+{
+ if (!seq.IsSetInst() || !seq.GetInst().IsSetMol()) {
+ return false;
+ }
+ bool needs_molinfo = true;
+
+ if (seq.IsSetDescr()) {
+ NON_CONST_ITERATE(CBioseq::TDescr::Tdata, it, seq.SetDescr().Set()) {
+ if ((*it)->IsMolinfo()) {
+ needs_molinfo = false;
+ if (seq.IsAa() &&
+ (!(*it)->GetMolinfo().IsSetBiomol() ||
+ (*it)->GetMolinfo().GetBiomol() == CMolInfo::eBiomol_unknown)) {
+ (*it)->SetMolinfo().SetBiomol(CMolInfo::eBiomol_peptide);
+ }
+ }
+ }
+ }
+ if (needs_molinfo) {
+ if (seq.IsAa()) {
+ CRef<CSeqdesc> m(new CSeqdesc());
+ m->SetMolinfo().SetBiomol(CMolInfo::eBiomol_peptide);
+ if (is_product) {
+ m->SetMolinfo().SetTech(CMolInfo::eTech_concept_trans);
+ }
+ seq.SetDescr().Set().push_back(m);
+ } else if (seq.GetInst().GetMol() == CSeq_inst::eMol_rna && is_product) {
+ CRef<CSeqdesc> m(new CSeqdesc());
+ m->SetMolinfo().SetBiomol(CMolInfo::eBiomol_mRNA);
+ m->SetMolinfo().SetTech(CMolInfo::eTech_standard);
+ seq.SetDescr().Set().push_back(m);
+ }
+ }
+
+ return needs_molinfo;
+}
+
+
+bool CCleanup::AddProteinTitle(CBioseq_Handle bsh)
+{
+ if (!bsh.IsSetInst() || !bsh.GetInst().IsSetMol() || !bsh.IsAa()) {
+ return false;
+ }
+ if (bsh.IsSetId()) {
+ ITERATE(CBioseq_Handle::TId, it, bsh.GetId()) {
+ // do not add titles for sequences with certain IDs
+ switch (it->Which()) {
+ case CSeq_id::e_Pir:
+ case CSeq_id::e_Swissprot:
+ case CSeq_id::e_Patent:
+ case CSeq_id::e_Prf:
+ case CSeq_id::e_Pdb:
+ return false;
+ break;
+ default:
+ break;
+ }
+ }
+ }
+
+ string new_defline = sequence::CDeflineGenerator().GenerateDefline(bsh, sequence::CDeflineGenerator::fIgnoreExisting);
+ CSeqdesc_CI di(bsh, CSeqdesc::e_Title);
+ if (di) {
+ if (sequence::GetCDSForProduct(*(bsh.GetCompleteBioseq()), &(bsh.GetScope())) != NULL
+ && !NStr::Equal(di->GetTitle(), new_defline)) {
+ CSeqdesc* d = const_cast<CSeqdesc*>(&(*di));
+ d->SetTitle(new_defline);
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ CRef<CSeqdesc> t(new CSeqdesc());
+ t->SetTitle(sequence::CDeflineGenerator().GenerateDefline(bsh));
+ CBioseq_EditHandle eh = bsh.GetEditHandle();
+ eh.AddSeqdesc(*t);
+ return true;
+}
+
+
+bool CCleanup::RemoveNcbiCleanupObject(CSeq_entry &seq_entry)
+{
+ bool rval = false;
+ if (seq_entry.IsSetDescr()) {
+ CBioseq::TDescr::Tdata::iterator it = seq_entry.SetDescr().Set().begin();
+ while (it != seq_entry.SetDescr().Set().end()) {
+ if ((*it)->IsUser() && (*it)->GetUser().GetObjectType() == CUser_object::eObjectType_Cleanup){
+ it = seq_entry.SetDescr().Set().erase(it);
+ rval = true;
+ }
+ else {
+ ++it;
+ }
+ }
+ if (seq_entry.SetDescr().Set().empty()) {
+ if (seq_entry.IsSeq()) {
+ seq_entry.SetSeq().ResetDescr();
+ }
+ else if (seq_entry.IsSet()) {
+ seq_entry.SetSet().ResetDescr();
+ }
+ }
+ }
+ if (seq_entry.IsSet() && seq_entry.GetSet().IsSetSeq_set()) {
+ NON_CONST_ITERATE(CBioseq_set::TSeq_set, it, seq_entry.SetSet().SetSeq_set()) {
+ rval |= RemoveNcbiCleanupObject(**it);
+ }
+ }
+ return rval;
+}
+
+
+void GetSourceDescriptors(const CSeq_entry& se, vector<const CSeqdesc* >& src_descs)
+{
+ if (se.IsSetDescr()) {
+ ITERATE(CBioseq::TDescr::Tdata, it, se.GetDescr().Get()) {
+ if ((*it)->IsSource() && (*it)->GetSource().IsSetOrg()) {
+ src_descs.push_back(*it);
+ }
+ }
+ }
+
+ if (se.IsSet() && se.GetSet().IsSetSeq_set()) {
+ ITERATE(CBioseq_set::TSeq_set, it, se.GetSet().GetSeq_set()) {
+ GetSourceDescriptors(**it, src_descs);
+ }
+ }
+}
+
+
+bool CCleanup::TaxonomyLookup(CSeq_entry_Handle seh)
+{
+ bool any_changes = false;
+
+ vector<CRef<COrg_ref> > rq_list;
+ vector<const CSeqdesc* > src_descs;
+ vector<CConstRef<CSeq_feat> > src_feats;
+
+ GetSourceDescriptors(*(seh.GetCompleteSeq_entry()), src_descs);
+ vector<const CSeqdesc* >::iterator desc_it = src_descs.begin();
+ while (desc_it != src_descs.end()) {
+ // add org ref for descriptor to request list
+ CRef<COrg_ref> org(new COrg_ref());
+ org->Assign((*desc_it)->GetSource().GetOrg());
+ rq_list.push_back(org);
+
+ ++desc_it;
+ }
+
+ CFeat_CI feat(seh, SAnnotSelector(CSeqFeatData::e_Biosrc));
+ while (feat) {
+ if (feat->GetData().GetBiosrc().IsSetOrg()) {
+ // add org ref for feature to request list
+ CRef<COrg_ref> org(new COrg_ref());
+ org->Assign(feat->GetData().GetBiosrc().GetOrg());
+ rq_list.push_back(org);
+ // add feature to list
+ src_feats.push_back(feat->GetOriginalSeq_feat());
+ }
+ ++feat;
+ }
+
+ if (rq_list.size() > 0) {
+ CTaxon3 taxon3;
+ taxon3.Init();
+ CRef<CTaxon3_reply> reply = taxon3.SendOrgRefList(rq_list);
+ if (reply) {
+ CTaxon3_reply::TReply::const_iterator reply_it = reply->GetReply().begin();
+
+ // process descriptor responses
+ desc_it = src_descs.begin();
+
+ while (reply_it != reply->GetReply().end()
+ && desc_it != src_descs.end()) {
+ if ((*reply_it)->IsData() &&
+ !(*desc_it)->GetSource().GetOrg().Equals((*reply_it)->GetData().GetOrg())) {
+ any_changes = true;
+ CSeqdesc* desc = const_cast<CSeqdesc*>(*desc_it);
+ desc->SetSource().SetOrg().Assign((*reply_it)->GetData().GetOrg());
+ }
+ ++reply_it;
+ ++desc_it;
+ }
+
+ // process feature responses
+ vector<CConstRef<CSeq_feat> >::iterator feat_it = src_feats.begin();
+ while (reply_it != reply->GetReply().end()
+ && feat_it != src_feats.end()) {
+ if ((*reply_it)->IsData() &&
+ !(*feat_it)->GetData().GetBiosrc().GetOrg().Equals((*reply_it)->GetData().GetOrg())) {
+ any_changes = true;
+ CRef<CSeq_feat> new_feat(new CSeq_feat());
+ new_feat->Assign(**feat_it);
+ new_feat->SetData().SetBiosrc().SetOrg().Assign((*reply_it)->GetData().GetOrg());
+ CSeq_feat_Handle fh = seh.GetScope().GetSeq_featHandle(**feat_it);
+ CSeq_feat_EditHandle efh(fh);
+ efh.Replace(*new_feat);
+ }
+ ++reply_it;
+ ++feat_it;
+ }
+ }
+ }
+
+ return any_changes;
+}
+
+CRef<CSeq_entry> AddProtein(const CSeq_feat& cds, CScope& scope)
+{
+ CBioseq_Handle cds_bsh = scope.GetBioseqHandle(cds.GetLocation());
+ if (!cds_bsh) {
+ return CRef<CSeq_entry>(NULL);
+ }
+ CSeq_entry_Handle seh = cds_bsh.GetSeq_entry_Handle();
+ if (!seh) {
+ return CRef<CSeq_entry>(NULL);
+ }
+
+ CRef<CBioseq> new_product = CSeqTranslator::TranslateToProtein(cds, scope);
+ if (cds.IsSetProduct()) {
+ CRef<CSeq_id> prot_id(new CSeq_id());
+ prot_id->Assign(*(cds.GetProduct().GetId()));
+ new_product->SetId().push_back(prot_id);
+ }
+ CRef<CSeq_entry> prot_entry(new CSeq_entry());
+ prot_entry->SetSeq(*new_product);
+
+ CSeq_entry_EditHandle eh = seh.GetEditHandle();
+ if (!eh.IsSet()) {
+ CBioseq_set_Handle nuc_parent = eh.GetParentBioseq_set();
+ if (nuc_parent && nuc_parent.IsSetClass() && nuc_parent.GetClass() == objects::CBioseq_set::eClass_nuc_prot) {
+ eh = nuc_parent.GetParentEntry().GetEditHandle();
+ }
+ }
+ if (!eh.IsSet()) {
+ eh.ConvertSeqToSet();
+ // move all descriptors on nucleotide sequence except molinfo and title to set
+ eh.SetSet().SetClass(CBioseq_set::eClass_nuc_prot);
+ CConstRef<CBioseq_set> set = eh.GetSet().GetCompleteBioseq_set();
+ if (set && set->IsSetSeq_set()) {
+ CConstRef<CSeq_entry> nuc = set->GetSeq_set().front();
+ CSeq_entry_EditHandle neh = eh.GetScope().GetSeq_entryEditHandle(*nuc);
+ CBioseq_set::TDescr::Tdata::const_iterator it = nuc->GetDescr().Get().begin();
+ while (it != nuc->GetDescr().Get().end()) {
+ if (!(*it)->IsMolinfo() && !(*it)->IsTitle()) {
+ CRef<CSeqdesc> copy(new CSeqdesc());
+ copy->Assign(**it);
+ eh.AddSeqdesc(*copy);
+ neh.RemoveSeqdesc(**it);
+ if (nuc->IsSetDescr()) {
+ it = nuc->GetDescr().Get().begin();
+ }
+ else {
+ break;
+ }
+ }
+ else {
+ ++it;
+ }
+ }
+ }
+ }
+
+ CSeq_entry_EditHandle added = eh.AttachEntry(*prot_entry);
+ return prot_entry;
+}
+
+
+CRef<objects::CSeq_id> GetNewProteinId(objects::CSeq_entry_Handle seh, objects::CBioseq_Handle bsh)
+{
+ string id_base;
+ objects::CSeq_id_Handle hid;
+
+ ITERATE(objects::CBioseq_Handle::TId, it, bsh.GetId()) {
+ if (!hid || !it->IsBetter(hid)) {
+ hid = *it;
+ }
+ }
+
+ hid.GetSeqId()->GetLabel(&id_base, objects::CSeq_id::eContent);
+
+ int offset = 1;
+ string id_label = id_base + "_" + NStr::NumericToString(offset);
+ CRef<objects::CSeq_id> id(new objects::CSeq_id());
+ id->SetLocal().SetStr(id_label);
+ objects::CBioseq_Handle b_found = seh.GetBioseqHandle(*id);
+ while (b_found) {
+ offset++;
+ id_label = id_base + "_" + NStr::NumericToString(offset);
+ id->SetLocal().SetStr(id_label);
+ b_found = seh.GetBioseqHandle(*id);
+ }
+ return id;
+}
+
+
+bool CCleanup::WGSCleanup(CSeq_entry_Handle entry)
+{
+ bool any_changes = false;
+
+ SAnnotSelector sel(CSeqFeatData::e_Cdregion);
+ for (CFeat_CI cds_it(entry, sel); cds_it; ++cds_it) {
+ bool change_this_cds;
+ CRef<CSeq_feat> new_cds(new CSeq_feat());
+ new_cds->Assign(*(cds_it->GetSeq_feat()));
+
+ // set best frame
+ CCdregion::TFrame frame = CCdregion::eFrame_not_set;
+ if (new_cds->GetData().GetCdregion().IsSetFrame()) {
+ frame = new_cds->GetData().GetCdregion().GetFrame();
+ }
+ CCdregion::TFrame new_frame = CSeqTranslator::FindBestFrame(*new_cds, entry.GetScope());
+ if (frame != new_frame) {
+ new_cds->SetData().SetCdregion().SetFrame(new_frame);
+ change_this_cds = true;
+ frame = new_frame;
+ }
+
+ // set partials for frames
+ if (frame != CCdregion::eFrame_not_set && frame != CCdregion::eFrame_one &&
+ !new_cds->GetLocation().IsPartialStart(eExtreme_Biological)) {
+ new_cds->SetLocation().SetPartialStart(true, eExtreme_Biological);
+ change_this_cds = true;
+ }
+
+ // retranslate
+ if (new_cds->IsSetProduct() && entry.GetScope().GetBioseqHandle(new_cds->GetProduct())) {
+ any_changes |= feature::RetranslateCDS(*new_cds, entry.GetScope());
+ } else {
+ // need to set product if not set
+ if (!new_cds->IsSetProduct()) {
+ CRef<CSeq_id> new_id = GetNewProteinId(entry, entry.GetScope().GetBioseqHandle(new_cds->GetLocation()));
+ if (new_id) {
+ new_cds->SetProduct().SetWhole().Assign(*new_id);
+ change_this_cds = true;
+ }
+ }
+ if (new_cds->IsSetProduct()) {
+ CRef<CSeq_entry> prot = AddProtein(*new_cds, entry.GetScope());
+ if (prot) {
+ any_changes = true;
+ }
+ }
+ }
+
+ if (change_this_cds) {
+ CSeq_feat_EditHandle cds_h(*cds_it);
+ CRef<CSeq_feat> new_cds(new CSeq_feat());
+ new_cds->Assign(*(cds_it->GetSeq_feat()));
+
+ cds_h.Replace(*new_cds);
+ any_changes = true;
+ }
+
+ }
+
+ // SSEC
+ // remove protein titles
+ // add missing prot-refs
+ // CopyCDSproductToMrna
+ // instantiate protein titles
+ // ImposeCodingRegionPartials
+ // ResynchCodingRegionPartials
+ // ResynchMessengerRNAPartials
+ // ResynchProteinPartials
+ // InstantiateProteinTitles
+ NormalizeDescriptorOrder(entry);
+
+ return any_changes;
+}
+
+// maps the type of seqdesc to the order it should be in
+// (lowest to highest)
+typedef SStaticPair<CSeqdesc::E_Choice, int> TSeqdescOrderElem;
+static const TSeqdescOrderElem sc_seqdesc_order_map[] = {
+ // Note that ordering must match ordering
+ // in CSeqdesc::E_Choice
+ { CSeqdesc::e_Mol_type, 13 },
+ { CSeqdesc::e_Modif, 14 },
+ { CSeqdesc::e_Method, 15 },
+ { CSeqdesc::e_Name, 7 },
+ { CSeqdesc::e_Title, 1 },
+ { CSeqdesc::e_Org, 16 },
+ { CSeqdesc::e_Comment, 6 },
+ { CSeqdesc::e_Num, 11 },
+ { CSeqdesc::e_Maploc, 9 },
+ { CSeqdesc::e_Pir, 18 },
+ { CSeqdesc::e_Genbank, 22 },
+ { CSeqdesc::e_Pub, 5 },
+ { CSeqdesc::e_Region, 10 },
+ { CSeqdesc::e_User, 8 },
+ { CSeqdesc::e_Sp, 17 },
+ { CSeqdesc::e_Dbxref, 12 },
+ { CSeqdesc::e_Embl, 21 },
+ { CSeqdesc::e_Create_date, 24 },
+ { CSeqdesc::e_Update_date, 25 },
+ { CSeqdesc::e_Prf, 19 },
+ { CSeqdesc::e_Pdb, 20 },
+ { CSeqdesc::e_Het, 4 },
+ { CSeqdesc::e_Source, 2 },
+ { CSeqdesc::e_Molinfo, 3 },
+ { CSeqdesc::e_Modelev, 23 }
+};
+typedef CStaticPairArrayMap<CSeqdesc::E_Choice, int> TSeqdescOrderMap;
+DEFINE_STATIC_ARRAY_MAP(TSeqdescOrderMap, sc_SeqdescOrderMap, sc_seqdesc_order_map);
+
+static
+int s_SeqDescToOrdering(const CRef<CSeqdesc> &desc) {
+ // ordering assigned to unknown
+ const int unknown_seqdesc = (1 + sc_SeqdescOrderMap.size());
+
+ TSeqdescOrderMap::const_iterator find_iter = sc_SeqdescOrderMap.find(desc->Which());
+ if (find_iter == sc_SeqdescOrderMap.end()) {
+ return unknown_seqdesc;
+ }
+
+ return find_iter->second;
+}
+
+static
+bool s_SeqDescLessThan(const CRef<CSeqdesc> &desc1, const CRef<CSeqdesc> &desc2)
+{
+ return (s_SeqDescToOrdering(desc1) < s_SeqDescToOrdering(desc2));
+}
+
+bool CCleanup::NormalizeDescriptorOrder(CSeq_descr& descr)
+{
+ bool rval = false;
+ if (!seq_mac_is_sorted(descr.Set().begin(), descr.Set().end(), s_SeqDescLessThan)) {
+ descr.Set().sort(s_SeqDescLessThan);
+ rval = true;
+ }
+ return rval;
+}
+
+bool CCleanup::NormalizeDescriptorOrder(CSeq_entry_Handle seh)
+{
+ bool rval = false;
+
+ CSeq_entry_CI ci(seh);
+ while (ci) {
+ CSeq_entry_EditHandle edit(*ci);
+ if (edit.IsSetDescr()) {
+ rval |= NormalizeDescriptorOrder(edit.SetDescr());
+ }
+ ++ci;
+ }
+
+ return rval;
+}
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/cleanup/cleanup_utils.cpp b/c++/src/objtools/cleanup/cleanup_utils.cpp
index b6fa093..13703d8 100644
--- a/c++/src/objtools/cleanup/cleanup_utils.cpp
+++ b/c++/src/objtools/cleanup/cleanup_utils.cpp
@@ -1,4 +1,4 @@
-/* $Id: cleanup_utils.cpp 365885 2012-06-08 14:05:17Z kornbluh $
+/* $Id: cleanup_utils.cpp 480957 2015-10-06 12:01:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -98,23 +98,14 @@ string s_NormalizeSuffix( const string& raw_suffix )
//
// Note: (2008-02-13) Suffixes I..VI no longer have trailing periods.
//
- if ( raw_suffix == "1d" || raw_suffix == "1st" ) {
- return "I";
+ if ( raw_suffix == "1d" ) {
+ return "1st";
}
- if ( raw_suffix == "2d" || raw_suffix == "2nd" ) {
- return "II";
+ if ( raw_suffix == "2d" ) {
+ return "2nd";
}
- if ( raw_suffix == "3d" || raw_suffix == "3rd" ) {
- return "III";
- }
- if ( raw_suffix == "4th" ) {
- return "IV";
- }
- if ( raw_suffix == "5th" ) {
- return "V";
- }
- if ( raw_suffix == "6th" ) {
- return "VI";
+ if ( raw_suffix == "3d" ) {
+ return "3rd";
}
if ( raw_suffix == "Sr" ) {
return "Sr.";
@@ -193,26 +184,6 @@ void s_SplitMLAuthorName(string name, string& last, string& initials, string& su
// ------------------------------------------------------------------------
}
-bool CleanString(string& str, bool rm_trailing_period)
-{
- size_t orig_slen = str.size();
- NStr::TruncateSpacesInPlace(str, NStr::eTrunc_Begin);
- size_t slen = 0;
- while (!str.empty() && slen != str.size()) {
- slen = str.size();
- NStr::TruncateSpacesInPlace(str, NStr::eTrunc_End);
- RemoveTrailingJunk(str);
- if (rm_trailing_period) {
- RemoveTrailingPeriod(str);
- }
- }
- TrimInternalSemicolons(str);
- if (orig_slen != str.size()) {
- return true;
- }
- return false;
-}
-
bool CleanVisString( string &str )
{
bool changed = false;
@@ -282,7 +253,7 @@ bool CleanVisString( string &str )
}
}
-bool CleanVisStringJunk( string &str )
+bool CleanVisStringJunk( string &str, bool allow_ellipses )
{
// This is based on the C function TrimSpacesAndJunkFromEnds.
// Although it's updated to use iterators and such and to
@@ -334,14 +305,15 @@ bool CleanVisStringJunk( string &str )
// allow one period at end
if (isPeriod) {
suffix = ".";
+ if ( allow_ellipses && (chars_in_junk >= 3) &&
+ str[start_of_junk_pos+1] == '.' && str[start_of_junk_pos+2] == '.' ) {
+ suffix = "...";
+ }
} else if (isTilde ) {
- // allow tilde(s)
- // (This should work on single- AND double-tildes because
- // we don't know whether or not tilde-expansion was called before this
- // point )
+ // allow double tilde(s) at the end
if ( str[start_of_junk_pos] == '~' ) {
const bool doubleTilde = ( (chars_in_junk >= 2) && str[start_of_junk_pos+1] == '~' );
- suffix = ( doubleTilde ? "~~" : "~" );
+ suffix = ( doubleTilde ? "~~" : "" );
}
}
if( suffix[0] != '\0' ) {
@@ -369,77 +341,6 @@ bool CleanVisStringJunk( string &str )
return changed;
}
-bool CleanStringList(list< string >& string_list)
-{
- bool rval = false;
- list< string >::iterator it = string_list.begin();
-
- while (it != string_list.end()) {
- // trim leading spaces/unprintable characters, semicolons, and commas
- size_t start_junk_len = 0;
- const char *start = (*it).c_str();
- while (*start != 0 && (*start <= ' ' || *start == ';' || *start == ',')) {
- start_junk_len++;
- start++;
- }
- if (start_junk_len > 0) {
- (*it) = (*it).substr(start_junk_len);
- rval = true;
- }
-
- // trim trailing spaces/unprintable characters, commas.
- // trim trailing semicolons if they are not preceded by an ampersand
- // followed by characters greater than space
- size_t len_good = 0;
- size_t pos = 0;
- bool in_amp_phrase = false;
- const char *cp = (*it).c_str();
- while (*cp != 0) {
- if (*cp <= ' ' || *cp == ',') {
- // not ok for end
- in_amp_phrase = false;
- } else if (*cp == '&') {
- in_amp_phrase = true;
- } else if (*cp == ';') {
- // keep only if in ampersand phrase
- if (in_amp_phrase) {
- len_good = pos + 1;
- }
- in_amp_phrase = false;
- } else {
- len_good = pos + 1;
- }
- pos++;
- cp++;
- }
- if (len_good < (*it).length()) {
- (*it) = (*it).substr(0, len_good);
- rval = true;
- }
-
- if (NStr::IsBlank (*it)) {
- it = string_list.erase(it);
- } else {
- // keep in list if not a duplicate of previous item
- list< string >::iterator it2 = string_list.begin();
- bool found = false;
- while (it2 != it && !found) {
- if (NStr::EqualCase (*it, *it2)) {
- found = true;
- }
- ++it2;
- }
- if (found) {
- it = string_list.erase(it);
- rval = true;
- } else {
- ++it;
- }
- }
- }
- return rval;
-}
-
bool RemoveTrailingPeriod(string& str)
{
@@ -561,6 +462,248 @@ void TrimInternalSemicolons (string& str)
}
}
+#define twocommas ((',') << 8 | (','))
+#define twospaces ((' ') << 8 | (' '))
+#define twosemicolons ((';') << 8 | (';'))
+#define space_comma ((' ') << 8 | (','))
+#define space_bracket ((' ') << 8 | (')'))
+#define bracket_space (('(') << 8 | (' '))
+#define space_semicolon ((' ') << 8 | (';'))
+#define comma_space ((',') << 8 | (' '))
+#define semicolon_space ((';') << 8 | (' '))
+
+bool Asn2gnbkCompressSpaces(string& val)
+{
+ if (val.length() == 0) return false;
+
+ char * str = new char[sizeof(char) * (val.length() + 1)];
+ strcpy(str, val.c_str());
+
+ char ch;
+ char * dst;
+ char * ptr;
+
+ char curr;
+ char next;
+ char * in;
+ char * out;
+ unsigned short two_chars;
+
+
+ in = str;
+ out = str;
+
+ curr = *in;
+ in++;
+
+ next = 0;
+ two_chars = curr;
+
+ while (curr != '\0') {
+ next = *in;
+ in++;
+
+ two_chars = (two_chars << 8) | next;
+
+ if (two_chars == twocommas) {
+ *out++ = curr;
+ next = ' ';
+ }
+ else if (two_chars == twospaces) {
+ }
+ else if (two_chars == twosemicolons) {
+ }
+ else if (two_chars == bracket_space) {
+ next = curr;
+ two_chars = curr;
+ }
+ else if (two_chars == space_bracket) {
+ }
+ else if (two_chars == space_comma) {
+ *out++ = next;
+ next = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ',') {
+ next = *in;
+ in++;
+ }
+ two_chars = next;
+ }
+ else if (two_chars == space_semicolon) {
+ *out++ = next;
+ next = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ';') {
+ next = *in;
+ in++;
+ }
+ two_chars = next;
+ }
+ else if (two_chars == comma_space) {
+ *out++ = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ',') {
+ next = *in;
+ in++;
+ }
+ two_chars = next;
+ }
+ else if (two_chars == semicolon_space) {
+ *out++ = curr;
+ *out++ = ' ';
+ while (next == ' ' || next == ';') {
+ next = *in;
+ in++;
+ }
+ two_chars = next;
+ }
+ else {
+ *out++ = curr;
+ }
+
+ curr = next;
+ }
+
+ if (curr > 0 && curr != ' ') {
+ *out = curr;
+ out++;
+ }
+ *out = '\0';
+
+ /* TrimSpacesAroundString but allow leading/trailing tabs/newlines */
+
+ if (str != NULL && str[0] != '\0') {
+ dst = str;
+ ptr = str;
+ ch = *ptr;
+ while (ch != '\0' && ch == ' ') {
+ ptr++;
+ ch = *ptr;
+ }
+ while (ch != '\0') {
+ *dst = ch;
+ dst++;
+ ptr++;
+ ch = *ptr;
+ }
+ *dst = '\0';
+ dst = NULL;
+ ptr = str;
+ ch = *ptr;
+ while (ch != '\0') {
+ if (ch != ' ') {
+ dst = NULL;
+ }
+ else if (dst == NULL) {
+ dst = ptr;
+ }
+ ptr++;
+ ch = *ptr;
+ }
+ if (dst != NULL) {
+ *dst = '\0';
+ }
+ }
+ string new_val;
+ new_val = str;
+ delete[] str;
+
+ if (!NStr::Equal(val, new_val)) {
+#ifdef _DEBUG
+#if 0
+ printf("Use new string\n");
+#endif
+#endif
+ val = new_val;
+ return true;
+ }
+ else {
+ return false;
+ }
+}
+
+bool TrimSpacesSemicolonsAndCommas(string& val)
+{
+ if (val.length() == 0) return false;
+
+ char * str = new char[sizeof(char) * (val.length() + 1)];
+ strcpy(str, val.c_str());
+
+ char * amp;
+ unsigned char ch; /* to use 8bit characters in multibyte languages */
+ char * dst;
+ char * ptr;
+
+ dst = str;
+ ptr = str;
+ ch = *ptr;
+ if (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',')) {
+ while (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',')) {
+ ptr++;
+ ch = *ptr;
+ }
+ while (ch != '\0') {
+ *dst = ch;
+ dst++;
+ ptr++;
+ ch = *ptr;
+ }
+ *dst = '\0';
+ }
+ amp = NULL;
+ dst = NULL;
+ ptr = str;
+ ch = *ptr;
+ while (ch != '\0') {
+ if (ch == '&') {
+ amp = ptr;
+ dst = NULL;
+ }
+ else if (ch <= ' ') {
+ if (dst == NULL) {
+ dst = ptr;
+ }
+ amp = NULL;
+ }
+ else if (ch == ';') {
+ if (dst == NULL && amp == NULL) {
+ dst = ptr;
+ }
+ }
+ else if (ch == ',') {
+ if (dst == NULL) {
+ dst = ptr;
+ }
+ amp = NULL;
+ }
+ else {
+ dst = NULL;
+ }
+ ptr++;
+ ch = *ptr;
+ }
+ if (dst != NULL) {
+ *dst = '\0';
+ }
+
+ string new_val;
+ new_val = str;
+ delete[] str;
+
+ if (!NStr::Equal(val, new_val)) {
+#ifdef _DEBUG
+#if 0
+ printf("Use new string\n");
+#endif
+#endif
+ val = new_val;
+ return true;
+ }
+ else {
+ return false;
+ }
+}
+
bool OnlyPunctuation (string str)
{
@@ -918,7 +1061,7 @@ bool IsFeatureFullLength(const CSeq_feat& cf, CScope* scope)
// start at 0 and end at the end of the Bioseq.
CRef<CSeq_loc> whole_loc = MakeFullLengthLocation (cf.GetLocation(), scope);
- if (sequence::Compare(*whole_loc, cf.GetLocation(), scope) == sequence::eSame) {
+ if (sequence::Compare(*whole_loc, cf.GetLocation(), scope, sequence::fCompareOverlapping) == sequence::eSame) {
return true;
} else {
return false;
diff --git a/c++/src/objtools/cleanup/cleanup_utils.hpp b/c++/src/objtools/cleanup/cleanup_utils.hpp
index 10ff393..e8edb9e 100644
--- a/c++/src/objtools/cleanup/cleanup_utils.hpp
+++ b/c++/src/objtools/cleanup/cleanup_utils.hpp
@@ -1,7 +1,7 @@
#ifndef OBJECTS_GENERAL___CLEANUP_UTILS__HPP
#define OBJECTS_GENERAL___CLEANUP_UTILS__HPP
-/* $Id: cleanup_utils.hpp 365885 2012-06-08 14:05:17Z kornbluh $
+/* $Id: cleanup_utils.hpp 480957 2015-10-06 12:01:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -71,14 +71,9 @@ bool ConvertDoubleQuotes(string& str)
}
-/// truncate spaces and other trailing characters.
-bool CleanString(string& str, bool rm_trailing_period = false);
-
bool CleanVisString( string &str );
-bool CleanVisStringJunk( string &str );
-
-bool CleanStringList(list< string >& string_list);
+bool CleanVisStringJunk( string &str, bool allow_ellipses = false );
/// remove a trailing period,
bool RemoveTrailingPeriod(string& str);
@@ -94,6 +89,12 @@ bool RemoveSpacesBetweenTildes(string& str);
/// "a;;b" will become "a;b".
void TrimInternalSemicolons (string& str);
+/// weird space compression from C Toolkit
+bool Asn2gnbkCompressSpaces (string& val);
+
+// special trimming function from C Toolkit
+bool TrimSpacesSemicolonsAndCommas (string& val);
+
/// Change double to single quotes
bool CleanDoubleQuote(string& str);
@@ -105,26 +106,6 @@ bool RemoveSpaces(string& str);
/// convert medline names to standard names
CRef<CAuthor> ConvertMltoSTD(const string& token);
-/// clean a container of strings, remove blanks and repeats.
-template<typename C>
-bool CleanStringContainer(C& str_cont, bool rm_trailing_junk = false)
-{
- bool changed = false;
- typename C::iterator it = str_cont.begin();
- while (it != str_cont.end()) {
- if (CleanString(*it, rm_trailing_junk)) {
- changed = true;
- }
- if (NStr::IsBlank(*it)) {
- it = str_cont.erase(it);
- changed = true;
- } else {
- ++it;
- }
- }
- return changed;
-}
-
template<typename C>
bool CleanVisStringContainer(C& str_cont)
{
diff --git a/c++/src/objtools/cleanup/newcleanupp.cpp b/c++/src/objtools/cleanup/newcleanupp.cpp
index c332c76..30c531b 100644
--- a/c++/src/objtools/cleanup/newcleanupp.cpp
+++ b/c++/src/objtools/cleanup/newcleanupp.cpp
@@ -43,7 +43,10 @@
#include <objmgr/feat_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/scope.hpp>
+#include <objmgr/seq_vector.hpp>
#include <objmgr/util/seq_loc_util.hpp>
+#include <objmgr/util/feature.hpp>
+#include <objmgr/util/sequence.hpp>
#include <objtools/cleanup/cleanup_change.hpp>
#include <objtools/cleanup/cleanup.hpp>
@@ -679,6 +682,30 @@ void CNewCleanup_imp::x_RemoveSpacesBetweenTildesMarkChanged( std::string & str
}
}
+void CNewCleanup_imp::X_CommentTildeFixes(std::string & str)
+{
+/*
+#ifndef NCBI_OS_MSWIN
+ string orig = str;
+ NStr::ReplaceInPlace(str, "based on SOLiD3 (Applied Biosystems)~~", "based on SOLiD3 (Applied Biosystems)", false, false);
+ NStr::ReplaceInPlace(str, "Biological resourse center, NITE (NRBC)~~", "Biological resourse center, NITE (NRBC)", false, false);
+ NStr::ReplaceInPlace(str, "developmental01.html~~", "developmental01.html", false, false);
+ NStr::ReplaceInPlace(str, "http://bionano.toyo.ac.jp/~~", "http://bionano.toyo.ac.jp/", false, false);
+ NStr::ReplaceInPlace(str, "http://dictycdb1.biol.tsukuba.ac.jp/acytodb/~~", "http://dictycdb1.biol.tsukuba.ac.jp/acytodb/", false, false);
+ NStr::ReplaceInPlace(str, "http://egg.umh.es~~", "http://egg.umh.es", false, false);
+ NStr::ReplaceInPlace(str, "http://www.aist.go.jp/~~", "http://www.aist.go.jp/", false, false);
+ NStr::ReplaceInPlace(str, "http://www.bio.nite.go.jp/~~", "http://www.bio.nite.go.jp/", false, false);
+ NStr::ReplaceInPlace(str, "http://www.bio.nite.go.jp/ngac/e/~~", "http://www.bio.nite.go.jp/ngac/e/", false, false);
+ NStr::ReplaceInPlace(str, "http://www.brs.kyushu-u.ac.jp/~fcmic/~~", "http://www.brs.kyushu-u.ac.jp/~fcmic/", false, false);
+ NStr::ReplaceInPlace(str, "http://www.miyazaki-u.ac.jp/ir/english/index.html~~", "http://www.miyazaki-u.ac.jp/ir/english/index.html", false, false);
+ NStr::ReplaceInPlace(str, "URL:http://www.bio.nite.go.jp/ngac/e/~~", "URL:http://www.bio.nite.go.jp/ngac/e/", false, false);
+ if (!NStr::Equal(orig, str)) {
+ ChangeMade(CCleanupChange::eTrimSpaces);
+ }
+#endif //NCBI_OS_MSWIN
+*/
+}
+
void CNewCleanup_imp::x_TruncateSpacesMarkChanged( std::string & str )
{
const size_t old_str_size = str.length();
@@ -688,6 +715,15 @@ void CNewCleanup_imp::x_TruncateSpacesMarkChanged( std::string & str )
}
}
+void CNewCleanup_imp::x_TrimInternalSemicolonsMarkChanged( std::string & str )
+{
+ const size_t old_str_size = str.length();
+ TrimInternalSemicolons(str);
+ if( old_str_size != str.length() ) {
+ ChangeMade(CCleanupChange::eTrimInternalSemicolons);
+ }
+}
+
void CNewCleanup_imp::SeqsetBC (
CBioseq_set& bss
)
@@ -745,6 +781,101 @@ void CNewCleanup_imp::SeqsetBC (
}
}
+static CMolInfo::TCompleteness GetCompletenessFromFlags(bool partial5, bool partial3, bool partial)
+{
+ CMolInfo::TCompleteness comp = CMolInfo::eCompleteness_unknown;
+ if (partial5 && partial3) {
+ comp = CMolInfo::eCompleteness_no_ends;
+ } else if (partial5) {
+ comp = CMolInfo::eCompleteness_no_left;
+ } else if (partial3) {
+ comp = CMolInfo::eCompleteness_no_right;
+ } else if (partial) {
+ comp = CMolInfo::eCompleteness_partial;
+ }
+ return comp;
+}
+
+void CNewCleanup_imp::ProtSeqBC (CBioseq& bs)
+{
+ // Bail if not protein
+ if( ! FIELD_CHAIN_OF_2_IS_SET(bs, Inst, Mol) ||
+ bs.GetInst().GetMol() != NCBI_SEQMOL(aa) )
+ {
+ return;
+ }
+
+ // Bail if no GIBBSQ ID
+ if (!bs.IsSetId()) {
+ return;
+ }
+ bool has_gibbsq = false;
+ ITERATE(CBioseq::TId, id, bs.GetId()) {
+ if ((*id)->IsGibbsq()) {
+ has_gibbsq = true;
+ break;
+ }
+ }
+ if (!has_gibbsq) {
+ return;
+ }
+
+ CSeq_entry_Handle seh = m_Scope->GetSeq_entryHandle(*(bs.GetParentEntry()));
+
+ // Bail if no title or no partialness clues in title
+ CSeqdesc_CI title(seh, CSeqdesc::e_Title);
+ if (!title) {
+ return;
+ }
+ bool make_partial5 = false;
+ bool make_partial3 = false;
+ if (NStr::Find(title->GetTitle(), "{C-terminal}") != string::npos) {
+ make_partial5 = true;
+ }
+ if (NStr::Find(title->GetTitle(), "{N-terminal}") != string::npos) {
+ make_partial3 = true;
+ }
+ if (!make_partial5 && !make_partial3) {
+ return;
+ }
+
+ // Bail if no protein feature with missing partials
+ SAnnotSelector sel(CSeqFeatData::e_Prot);
+ CFeat_CI fi(seh, sel);
+
+ if (fi && fi->IsSetPartial() && fi->GetPartial()) {
+ const CSeq_feat& orig = *(fi->GetOriginalSeq_feat());
+ if (orig.IsSetLocation() &&
+ !orig.GetLocation().IsPartialStart(eExtreme_Biological) &&
+ !orig.GetLocation().IsPartialStop(eExtreme_Biological)) {
+ CSeq_feat_EditHandle edit_feature_handle(fi->GetSeq_feat_Handle());
+ CRef<CSeq_feat> replace(new CSeq_feat());
+ replace->Assign(orig);
+ if (make_partial5) {
+ replace->SetLocation().SetPartialStart(true, eExtreme_Biological);
+ }
+ if (make_partial3) {
+ replace->SetLocation().SetPartialStop(true, eExtreme_Biological);
+ }
+ edit_feature_handle.Replace(*replace);
+ ChangeMade(CCleanupChange::eChangeSeqloc);
+
+ if (bs.IsSetDescr()) {
+ CMolInfo::TCompleteness wanted = GetCompletenessFromFlags(make_partial5, make_partial3, true);
+ NON_CONST_ITERATE(CBioseq::TDescr::Tdata, ds, bs.SetDescr().Set()) {
+ if ((*ds)->IsMolinfo() &&
+ (!(*ds)->GetMolinfo().IsSetCompleteness() ||
+ (*ds)->GetMolinfo().GetCompleteness() != wanted)) {
+ (*ds)->SetMolinfo().SetCompleteness(wanted);
+ ChangeMade(CCleanupChange::eChangeMolInfo);
+ }
+ }
+ }
+ }
+ }
+}
+
+
void CNewCleanup_imp::SeqIdBC( CSeq_id &seq_id )
{
// try to find CObject_id in Seq-id for certain types
@@ -761,102 +892,6 @@ void CNewCleanup_imp::SeqIdBC( CSeq_id &seq_id )
x_TruncateSpacesMarkChanged( GET_MUTABLE(*pObjectId, Str) );
}
-typedef SStaticPair<const char*, TORGMOD_SUBTYPE> TOrgModElem;
-static const TOrgModElem sc_orgmod_map[] = {
- { "Acronym", NCBI_ORGMOD(acronym) },
- { "Anamorph", NCBI_ORGMOD(anamorph) },
- { "Authority", NCBI_ORGMOD(authority) },
- { "Bio-material", NCBI_ORGMOD(bio_material) },
- { "Biotype", NCBI_ORGMOD(biotype) },
- { "Biovar", NCBI_ORGMOD(biovar) },
- { "Breed", NCBI_ORGMOD(breed) },
- { "Chemovar", NCBI_ORGMOD(chemovar) },
- { "Common", NCBI_ORGMOD(common) },
- { "Cultivar", NCBI_ORGMOD(cultivar) },
- { "Culture-collection", NCBI_ORGMOD(culture_collection) },
- { "Ecotype", NCBI_ORGMOD(ecotype) },
- { "Forma", NCBI_ORGMOD(forma) },
- { "Forma-specialis", NCBI_ORGMOD(forma_specialis) },
- { "Group", NCBI_ORGMOD(group) },
- { "Host", NCBI_ORGMOD(nat_host) },
- { "Isolate", NCBI_ORGMOD(isolate) },
- { "Metagenome-source", NCBI_ORGMOD(metagenome_source) },
- { "Pathovar", NCBI_ORGMOD(pathovar) },
- { "Serogroup", NCBI_ORGMOD(serogroup) },
- { "Serotype", NCBI_ORGMOD(serotype) },
- { "Serovar", NCBI_ORGMOD(serovar) },
- { "Specimen-voucher", NCBI_ORGMOD(specimen_voucher) },
- { "Strain", NCBI_ORGMOD(strain) },
- { "Sub-species", NCBI_ORGMOD(sub_species) },
- { "Subgroup", NCBI_ORGMOD(subgroup) },
- { "Substrain", NCBI_ORGMOD(substrain) },
- { "Subtype", NCBI_ORGMOD(subtype) },
- { "Synonym", NCBI_ORGMOD(synonym) },
- { "Teleomorph", NCBI_ORGMOD(teleomorph) },
- { "Type", NCBI_ORGMOD(type) },
- { "Variety", NCBI_ORGMOD(variety) }
-};
-typedef CStaticArrayMap<string, TORGMOD_SUBTYPE, PNocase> TOrgModMap;
-DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TOrgModMap, sc_OrgModMap, sc_orgmod_map);
-
-static const TOrgModElem sc_orgmodalias_map[] = {
- { "nat-host", NCBI_ORGMOD(nat_host) },
- { "specific-host", NCBI_ORGMOD(nat_host) },
- { "sub-strain", NCBI_ORGMOD(substrain) },
- { "subspecies", NCBI_ORGMOD(sub_species) }
-};
-DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TOrgModMap, sc_OrgModAliasMap, sc_orgmodalias_map);
-
-typedef SStaticPair<const char*, TORGMOD_SUBTYPE> TSubsourceElem;
-static const TSubsourceElem sc_subsource_map[] = {
- { "Cell-line", NCBI_SUBSOURCE(cell_line) },
- { "Cell-type", NCBI_SUBSOURCE(cell_type) },
- { "Chromosome", NCBI_SUBSOURCE(chromosome) },
- { "Clone", NCBI_SUBSOURCE(clone) },
- { "Clone-lib", NCBI_SUBSOURCE(clone_lib) },
- { "Collected-by", NCBI_SUBSOURCE(collected_by) },
- { "Collection-date", NCBI_SUBSOURCE(collection_date) },
- { "Country", NCBI_SUBSOURCE(country) },
- { "Dev-stage", NCBI_SUBSOURCE(dev_stage) },
- { "Endogenous-virus-name", NCBI_SUBSOURCE(endogenous_virus_name) },
- { "Environmental-sample", NCBI_SUBSOURCE(environmental_sample) },
- { "Frequency", NCBI_SUBSOURCE(frequency) },
- { "Genotype", NCBI_SUBSOURCE(genotype) },
- { "Germline", NCBI_SUBSOURCE(germline) },
- { "Haplogroup", NCBI_SUBSOURCE(haplogroup) },
- { "Haplotype", NCBI_SUBSOURCE(haplotype) },
- { "Identified-by", NCBI_SUBSOURCE(identified_by) },
- { "Isolation-source", NCBI_SUBSOURCE(isolation_source) },
- { "Lab-host", NCBI_SUBSOURCE(lab_host) },
- { "Lat-Lon", NCBI_SUBSOURCE(lat_lon) },
- { "Linkage-group", NCBI_SUBSOURCE(linkage_group) },
- { "Map", NCBI_SUBSOURCE(map) },
- { "Mating-type", NCBI_SUBSOURCE(mating_type) },
- { "Metagenomic", NCBI_SUBSOURCE(metagenomic) },
- { "Plasmid-name", NCBI_SUBSOURCE(plasmid_name) },
- { "Pop-variant", NCBI_SUBSOURCE(pop_variant) },
- { "Rearranged", NCBI_SUBSOURCE(rearranged) },
- { "Segment", NCBI_SUBSOURCE(segment) },
- { "Sex", NCBI_SUBSOURCE(sex) },
- { "Subclone", NCBI_SUBSOURCE(subclone) },
- { "Tissue-lib", NCBI_SUBSOURCE(tissue_lib) },
- { "Tissue-type", NCBI_SUBSOURCE(tissue_type) },
- { "Transgenic", NCBI_SUBSOURCE(transgenic) }
-};
-typedef CStaticArrayMap<string, TSUBSOURCE_SUBTYPE, PNocase> TSubsourceMap;
-DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TSubsourceMap, sc_SubsourceMap, sc_subsource_map);
-
-static const TSubsourceElem sc_subsourcealias_map[] = {
- { "fwd-primer-name", NCBI_SUBSOURCE(fwd_primer_name) },
- { "fwd-primer-seq", NCBI_SUBSOURCE(fwd_primer_seq) },
- { "Lat-long", NCBI_SUBSOURCE(lat_lon) },
- { "Latitude-Longitude", NCBI_SUBSOURCE(lat_lon) },
- { "rev-primer-name", NCBI_SUBSOURCE(rev_primer_name) },
- { "rev-primer-seq", NCBI_SUBSOURCE(rev_primer_seq) },
- { "sub-clone", NCBI_SUBSOURCE(subclone) }
-};
-DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TSubsourceMap, sc_SubsourceAliasMap, sc_subsourcealias_map);
-
// change the target string by searching for the given search_pattern
// and replacing it with replacement up to max_replace times (0 means unlimited)
//
@@ -1077,6 +1112,15 @@ static bool s_AccessionEqual (
return false;
}
+
+void CNewCleanup_imp::GBblockOriginBC ( string& str )
+{
+ if (CleanVisStringJunk(str)) {
+ ChangeMade (CCleanupChange::eTrimSpaces);
+ }
+}
+
+
void CNewCleanup_imp::GBblockBC (
CGB_block& gbk
)
@@ -1094,16 +1138,30 @@ void CNewCleanup_imp::GBblockBC (
ChangeMade (CCleanupChange::eCleanQualifiers);
}
+ // split keywords at semicolons
+ if (gbk.IsSetKeywords()) {
+ CGB_block::TKeywords::iterator it = gbk.SetKeywords().begin();
+ while (it != gbk.SetKeywords().end()) {
+ vector<string> tokens;
+ NStr::Tokenize(*it, ";", tokens);
+ if (tokens.size() > 1) {
+ it = gbk.SetKeywords().erase(it);
+ gbk.SetKeywords().insert(it, tokens.begin(), tokens.end());
+ } else {
+ ++it;
+ }
+ }
+ }
+
CLEAN_STRING_LIST (gbk, Keywords);
- CCachedRegexp reassembly_regex = regexpCache.Get(
- "^tpa[:_]reassembly$",
- CRegexp::fCompile_ignore_case );
+ CCachedRegexp reassembly_regex
+ = regexpCache.Get("^tpa(?:_|[_:]re)assembly$",
+ CRegexp::fCompile_ignore_case);
EDIT_EACH_KEYWORD_ON_EMBLBLOCK(keyword_it, gbk) {
string & sKeyword = *keyword_it;
if( reassembly_regex->IsMatch(sKeyword) ) {
- // remove the "re" in "reassembly"
- sKeyword.erase(4, 2);
+ sKeyword = "TPA:assembly";
ChangeMade (CCleanupChange::eCleanQualifiers);
}
}
@@ -1119,7 +1177,6 @@ void CNewCleanup_imp::GBblockBC (
RESET_FIELD(gbk, Source);
ChangeMade(CCleanupChange::eRemoveQualifier);
}
- CLEAN_STRING_MEMBER_JUNK (gbk, Origin);
if( FIELD_EQUALS(gbk, Origin, ".") ) {
RESET_FIELD(gbk, Origin);
ChangeMade(CCleanupChange::eRemoveQualifier);
@@ -1203,84 +1260,89 @@ typename TSetType::const_iterator s_FindInSetAsPrefix( const string &str, const
return the_set.end();
}
+
// copy "str" because we're changing it anyway
// returns true if we found anything
static
bool s_StringHasOrgModPrefix(const string &str, string::size_type &out_val_start_pos, TORGMOD_SUBTYPE &out_subtype)
{
- bool found_something = false;
-
- TOrgModMap::const_iterator orgmod_it = s_FindInMapAsPrefix<TOrgModMap>( str, sc_OrgModMap );
- if( orgmod_it != sc_OrgModMap.end() && orgmod_it->second != NCBI_ORGMOD(nat_host) ) {
- out_val_start_pos = orgmod_it->first.length();
- out_subtype = orgmod_it->second;
- found_something = true;
- } else {
- TOrgModMap::const_iterator orgmodalias_it = s_FindInMapAsPrefix<TOrgModMap>( str, sc_OrgModAliasMap );
- if( orgmodalias_it != sc_OrgModAliasMap.end() && orgmodalias_it->second != NCBI_ORGMOD(nat_host) ) {
- out_val_start_pos = orgmodalias_it->first.length();
- out_subtype = orgmodalias_it->second;
- found_something = true;
- }
- }
-
- if( (! found_something) && ( str.find_first_of("-") != string::npos ) ) {
- string new_str = str;
- NStr::ReplaceInPlace( new_str, "-", "_" );
- return s_StringHasOrgModPrefix( new_str, out_val_start_pos, out_subtype );
- }
-
- if( found_something ) {
- // move out_val_start_pos to where the val begins, since we're probably on an equal sign or something
- out_val_start_pos = str.find_first_not_of("=: ", out_val_start_pos);
- if( string::npos == out_val_start_pos ) {
- out_val_start_pos = str.length();
+ SIZE_TYPE pos = str.find_first_of(": ="), pos2;
+ if (pos != 0 && pos != NPOS
+ && (pos2 = str.find_first_not_of(": =", pos)) != NPOS) {
+ try {
+ string val = str.substr(0, pos);
+ COrgMod::TSubtype subtype = COrgMod::GetSubtypeValue(val);
+ if ( !COrgMod::IsDiscouraged(subtype) ) {
+ out_subtype = subtype;
+ out_val_start_pos = pos2;
+ return true;
+ }
+ } catch (CSerialException&) {
}
}
-
- return found_something;
+ return false;
}
// returns true if we found anything
static
bool s_StringHasSubSourcePrefix(const string &str, string::size_type &out_val_start_pos, TSUBSOURCE_SUBTYPE &out_subtype)
{
- bool found_something = false;
-
- // We check alias before regular because regular contains "Lat-Lon" which is a strict prefix
- // of "Lat-Long" in alias.
- TOrgModMap::const_iterator subsrcalias_it = s_FindInMapAsPrefix<TSubsourceMap>( str, sc_SubsourceAliasMap );
- if( subsrcalias_it != sc_SubsourceAliasMap.end() ) {
- out_val_start_pos = subsrcalias_it->first.length();
- out_subtype = subsrcalias_it->second;
- found_something = true;
+ SIZE_TYPE pos = str.find_first_of(": ="), pos2;
+ if (pos != 0 && pos != NPOS
+ && (pos2 = str.find_first_not_of(": =", pos)) != NPOS) {
+ try {
+ string val = str.substr(0, pos);
+ CSubSource::TSubtype subtype;
+ if (NStr::EqualNocase(val, "Lat-long") || NStr::EqualNocase(val, "Latitude-Longitude")) {
+ subtype = CSubSource::eSubtype_lat_lon;
+ } else {
+ subtype = CSubSource::GetSubtypeValue(val);
+ }
+ if ( subtype == CSubSource::eSubtype_fwd_primer_name ||
+ subtype == CSubSource::eSubtype_fwd_primer_seq ||
+ subtype == CSubSource::eSubtype_rev_primer_name ||
+ subtype == CSubSource::eSubtype_rev_primer_seq ||
+ !CSubSource::IsDiscouraged(subtype) ) {
+ out_subtype = subtype;
+ out_val_start_pos = pos2;
+ return true;
+ }
+ } catch (CSerialException&) {
+ }
} else {
- TOrgModMap::const_iterator subsrc_it = s_FindInMapAsPrefix<TSubsourceMap>( str, sc_SubsourceMap );
- if( subsrc_it != sc_SubsourceMap.end() ) {
- out_val_start_pos = subsrc_it->first.length();
- out_subtype = subsrc_it->second;
- found_something = true;
+ // did not find delimiters
+ try {
+ CSubSource::TSubtype subtype = CSubSource::GetSubtypeValue(str);
+ if ( !CSubSource::IsDiscouraged(subtype) && CSubSource::NeedsNoText(subtype)) {
+ out_subtype = subtype;
+ out_val_start_pos = str.length();
+ return true;
+ }
+ } catch (CSerialException&) {
}
}
+ return false;
+}
- if( (! found_something) && ( str.find_first_of("-") != string::npos ) ) {
- string new_str = str;
- NStr::ReplaceInPlace( new_str, "-", "_" );
- return s_StringHasSubSourcePrefix( new_str, out_val_start_pos, out_subtype );
+static bool s_ValueOkForQual(const string& value)
+{
+ if (NStr::Find(value, ",") != string::npos) {
+ return false;
}
-
- if( found_something ) {
- // move out_val_start_pos to where the val begins, since we're probably on an equal sign or something
- out_val_start_pos = str.find_first_not_of("=: ", out_val_start_pos);
- if( string::npos == out_val_start_pos ) {
- out_val_start_pos = str.length();
+ size_t num_space = 0;
+ ITERATE(string, it, value) {
+ if (isspace(*it)) {
+ num_space++;
}
}
-
- return found_something;
+ if (num_space > 4) {
+ return false;
+ }
+ return true;
}
-static CSubSource* s_StringToSubSource (
+
+static CRef<CSubSource> s_StringToSubSource (
const string& str
)
@@ -1288,19 +1350,22 @@ static CSubSource* s_StringToSubSource (
string::size_type val_start_pos;
TSUBSOURCE_SUBTYPE subtype = -1;
if( ! s_StringHasSubSourcePrefix( str, val_start_pos, subtype ) ) {
- return NULL;
+ return CRef<CSubSource>(NULL);
}
// we should have split on something non-alphanumeric
// (equals sign, colon, or whatever)
if( (val_start_pos < 1) ||
( val_start_pos < str.length() && isalnum( str[val_start_pos-1] ) ) ) {
- return NULL;
+ return CRef<CSubSource>(NULL);
+ }
+
+ string value = str.substr(val_start_pos);
+ if (!s_ValueOkForQual(value)) {
+ return CRef<CSubSource>(NULL);
}
- CSubSource *result = new CSubSource;
- result->SetSubtype( subtype );
- result->SetName( str.substr(val_start_pos) );
+ CRef<CSubSource> result(new CSubSource(subtype, value));
return result;
}
@@ -1421,6 +1486,62 @@ void CNewCleanup_imp::BiosourceFeatBC (
RESET_FIELD(seqfeat, Comment);
ChangeMade ( CCleanupChange::eChangeComment );
}
+
+ // special orgmod cleanup just for features (yes, is stupid, but is what C toolkit does)
+ if (biosrc.IsSetOrg() && biosrc.GetOrg().IsSetMod()) {
+ EDIT_EACH_MOD_ON_ORGREF (it, biosrc.SetOrg()) {
+ if (x_CompressSpaces(*it)) {
+ ChangeMade ( CCleanupChange::eTrimSpaces );
+ }
+ }
+ }
+}
+
+static void s_CorrectTildes (
+ string& str
+)
+
+{
+#ifndef NCBI_OS_MSWIN
+ NStr::ReplaceInPlace (str, "were ~25 cm in height (~3 weeks)", "were ~~25 cm in height (~~3 weeks)");
+ NStr::ReplaceInPlace (str, "generally ~3 weeks", "generally ~~3 weeks");
+ NStr::ReplaceInPlace (str, "sequencing (~4 96-well plates)", "sequencing (~~4 96-well plates)");
+ NStr::ReplaceInPlace (str, "size distribution (~2 kb)", "size distribution (~~2 kb)");
+ NStr::ReplaceInPlace (str, "sequencing (~3 96-well plates)", "sequencing (~~3 96-well plates)");
+ NStr::ReplaceInPlace (str, "vector. 1~2 ul of ligated", "vector. 1~~2 ul of ligated");
+ /*
+ NStr::ReplaceInPlace (str, "Lambda FLC I.~Islet cells were provided", "Lambda FLC I.~~Islet cells were provided");
+ */
+ NStr::ReplaceInPlace (str, "different strains~of mice", "different strains of mice");
+ NStr::ReplaceInPlace (str, "oligo-dT-NotI primer~(5'-biotin", "oligo-dT-NotI primer (5'-biotin");
+ NStr::ReplaceInPlace (str, "sizes of 200~800 bp were purified", "sizes of 200~~800 bp were purified");
+ NStr::ReplaceInPlace (str, "Tween 20 (~50 ml per tree)", "Tween 20 (~~50 ml per tree)");
+ NStr::ReplaceInPlace (str, "the SMART approach (~http://www.evrogen.com", "the SMART approach (http://www.evrogen.com");
+ NStr::ReplaceInPlace (str, "the morning (~10 am) with", "the morning (~~10 am) with");
+ NStr::ReplaceInPlace (str, "(host) sequences (~10%)", "(host) sequences (~~10%)");
+ /*
+ NStr::ReplaceInPlace (str, "unidirectionally.~ High quality", "unidirectionally. High quality");
+ NStr::ReplaceInPlace (str, "onlysubmitted.~ Average", "onlysubmitted. Average");
+ */
+ NStr::ReplaceInPlace (str, "Plasmid; ~The F03-1270", "Plasmid; The F03-1270");
+ NStr::ReplaceInPlace (str, "using STS-PCR~from Eb", "using STS-PCR from Eb");
+ NStr::ReplaceInPlace (str, "specific to~the Eb", "specific to the Eb");
+ NStr::ReplaceInPlace (str, "side of insert); , M.F., Lennon", "side of insert); Bonaldo, M.F., Lennon");
+ NStr::ReplaceInPlace (str, "Uni-ZAP XR vector. 1~2 ul of", "Uni-ZAP XR vector. 1~~2 ul of");
+ NStr::ReplaceInPlace (str, "from diploid~Secale montanum", "from diploid Secale montanum");
+ NStr::ReplaceInPlace (str, "homology with~U43516,", "homology with U43516,");
+ /*
+ NStr::ReplaceInPlace (str, "from http//www.biobase.dk/~ddbase", "from http//www.biobase.dk/~~ddbase");
+ */
+ NStr::ReplaceInPlace (str, "plasmid; ~Assembled EST", "plasmid; Assembled EST");
+ NStr::ReplaceInPlace (str, "databases.~Different cDNA", "databases. Different cDNA");
+ NStr::ReplaceInPlace (str, "enzyme PstI.~DH5-alpha", "enzyme PstI. DH5-alpha");
+ NStr::ReplaceInPlace (str, "as they~were prepared", "as they were prepared");
+ NStr::ReplaceInPlace (str, "loci in~the genome", "loci in the genome");
+ NStr::ReplaceInPlace (str, "P{CaSpeR}Cp1~50C (FBti0004219)", "P{CaSpeR}Cp1~~50C (FBti0004219)");
+ NStr::ReplaceInPlace (str, "seedlings with 2~4 leaves", "seedlings with 2~~4 leaves");
+ NStr::ReplaceInPlace (str, "tween 20 (~50mLs per tree)", "tween 20 (~~50mLs per tree)");
+#endif //NCBI_OS_MSWIN
}
void CNewCleanup_imp::BiosourceBC (
@@ -1437,6 +1558,8 @@ void CNewCleanup_imp::BiosourceBC (
ChangeMade ( CCleanupChange::eChangeBioSourceOrigin );
}
+ // note - move this
+ x_ConvertOrgref_modToSubSource(biosrc);
// remove spaces and convert to lowercase in fwd_primer_seq and rev_primer_seq.
if( FIELD_IS_SET(biosrc, Subtype) ) {
@@ -1500,6 +1623,7 @@ void CNewCleanup_imp::BiosourceBC (
}
}
+ /*
if( chs == NCBI_SUBSOURCE(lat_lon) ) {
string &lat_lon = GET_MUTABLE(sbs, Name);
@@ -1513,6 +1637,7 @@ void CNewCleanup_imp::BiosourceBC (
ChangeMade(CCleanupChange::eCleanSubsource);
}
}
+ */
if ( chs == NCBI_SUBSOURCE(fwd_primer_seq) ||
chs == NCBI_SUBSOURCE(rev_primer_seq) )
@@ -1586,6 +1711,35 @@ void CNewCleanup_imp::BiosourceBC (
ChangeMade(CCleanupChange::eChangePCRPrimers);
}
}
+
+ // correct specific cases of inconsistently applied tildes
+ EDIT_EACH_ORGMOD_ON_BIOSOURCE(orgmod_it, biosrc) {
+ COrgMod & orgmod = **orgmod_it;
+
+ // we're only correcting tildes for the ones of type "other"
+ if( ! FIELD_EQUALS(orgmod, Subtype, NCBI_ORGMOD(other)) ||
+ ! FIELD_IS_SET(orgmod, Subname) )
+ {
+ continue;
+ }
+
+ string &subname = GET_MUTABLE (orgmod, Subname);
+ s_CorrectTildes(subname);
+ }
+
+ EDIT_EACH_SUBSOURCE_ON_BIOSOURCE( subsrc_iter, biosrc ) {
+ CSubSource &subsrc = **subsrc_iter;
+
+ // we're only correcting tildes for the ones of type "other"
+ if( ! FIELD_EQUALS(subsrc, Subtype, NCBI_SUBSOURCE(other) ) ||
+ ! FIELD_IS_SET(subsrc, Name) )
+ {
+ continue;
+ }
+
+ string &name = GET_MUTABLE(subsrc, Name);
+ s_CorrectTildes(name);
+ }
}
void CNewCleanup_imp::x_PostBiosource( CBioSource& biosrc )
@@ -1595,25 +1749,6 @@ void CNewCleanup_imp::x_PostBiosource( CBioSource& biosrc )
ChangeMade(CCleanupChange::eChangeBioSourceGenome);
}
- if (BIOSOURCE_HAS_ORGREF (biosrc)) {
- COrg_ref& org = GET_MUTABLE (biosrc, Org);
-
- // convert COrg_reg.TMod string to SubSource objects
- EDIT_EACH_MOD_ON_ORGREF (it, org) {
- string& str = *it;
- CRef<CSubSource> sbs (s_StringToSubSource (str));
- if (! sbs) continue;
- ADD_SUBSOURCE_TO_BIOSOURCE (biosrc, sbs);
- ERASE_MOD_ON_ORGREF (it, org);
- ChangeMade (CCleanupChange::eChangeSubsource);
- }
-
- if( MOD_ON_ORGREF_IS_EMPTY(org) ) {
- RESET_FIELD(org, Mod);
- ChangeMade (CCleanupChange::eRemoveOrgmod);
- }
- }
-
if (BIOSOURCE_HAS_SUBSOURCE (biosrc)) {
// remove plastid-name subsource if the value is the same as the biosource location
@@ -1677,7 +1812,31 @@ void CNewCleanup_imp::x_PostBiosource( CBioSource& biosrc )
}
}
-static COrgMod* s_StringToOrgMod (
+
+void CNewCleanup_imp::x_ConvertOrgref_modToSubSource( CBioSource& biosrc )
+{
+ if (BIOSOURCE_HAS_ORGREF (biosrc)) {
+ COrg_ref& org = GET_MUTABLE (biosrc, Org);
+
+ // convert COrg_reg.TMod string to SubSource objects
+ EDIT_EACH_MOD_ON_ORGREF (it, org) {
+ string str = *it;
+ NStr::TruncateSpacesInPlace(str);
+ CRef<CSubSource> sbs = s_StringToSubSource (str);
+ if (! sbs) continue;
+ ADD_SUBSOURCE_TO_BIOSOURCE (biosrc, sbs);
+ ERASE_MOD_ON_ORGREF (it, org);
+ ChangeMade (CCleanupChange::eChangeSubsource);
+ }
+
+ if( MOD_ON_ORGREF_IS_EMPTY(org) ) {
+ RESET_FIELD(org, Mod);
+ ChangeMade (CCleanupChange::eRemoveOrgmod);
+ }
+ }
+}
+
+static CRef<COrgMod> s_StringToOrgMod (
const string& str
)
@@ -1685,22 +1844,42 @@ static COrgMod* s_StringToOrgMod (
string::size_type val_start_pos;
TORGMOD_SUBTYPE subtype = -1;
if( ! s_StringHasOrgModPrefix( str, val_start_pos, subtype) ) {
- return NULL;
+ return CRef<COrgMod>(NULL);
}
// we should have split on something non-alphanumeric
// (equals sign, colon, or whatever)
if( (val_start_pos < 1) || isalnum( str[val_start_pos-1] ) ) {
- return NULL;
+ return CRef<COrgMod>(NULL);
}
- COrgMod *result = new COrgMod;
- result->SetSubtype( subtype );
- result->SetSubname( str.substr(val_start_pos) );
+ string value = str.substr(val_start_pos);
+ if (!s_ValueOkForQual(value)) {
+ return CRef<COrgMod>(NULL);
+ }
+
+ CRef<COrgMod> result(new COrgMod(subtype, value));
return result;
}
+void CNewCleanup_imp::x_ConvertOrgref_modToOrgMod(COrg_ref& org)
+{
+ EDIT_EACH_MOD_ON_ORGREF(it, org) {
+ string str = *it;
+ NStr::TruncateSpacesInPlace(str);
+ CRef<COrgMod> omd = s_StringToOrgMod(str);
+ if (!omd) continue;
+ ADD_ORGMOD_TO_ORGREF(org, omd);
+ ERASE_MOD_ON_ORGREF(it, org);
+ ChangeMade(CCleanupChange::eChangeOrgmod);
+ }
+ if (RAW_FIELD_IS_EMPTY(org, Mod)) {
+ RESET_FIELD(org, Mod);
+ ChangeMade(CCleanupChange::eChangeOrgmod);
+ }
+}
+
static bool s_DbtagIsBad (
CDbtag& dbt
)
@@ -1728,6 +1907,13 @@ static bool s_DbtagIsBad (
return false;
}
+void CNewCleanup_imp::OrgrefModBC (string& str)
+{
+ if (TrimSpacesSemicolonsAndCommas(str)) {
+ ChangeMade (CCleanupChange::eTrimSpaces);
+ }
+}
+
void CNewCleanup_imp::OrgrefBC (
COrg_ref& org
)
@@ -1735,21 +1921,9 @@ void CNewCleanup_imp::OrgrefBC (
{
CLEAN_STRING_MEMBER (org, Taxname);
CLEAN_STRING_MEMBER (org, Common);
- CLEAN_STRING_LIST (org, Mod);
CLEAN_STRING_LIST (org, Syn);
- EDIT_EACH_MOD_ON_ORGREF (it, org) {
- string& str = *it;
- CRef<COrgMod> omd (s_StringToOrgMod (str));
- if (! omd) continue;
- ADD_ORGMOD_TO_ORGREF (org, omd);
- ERASE_MOD_ON_ORGREF (it, org);
- ChangeMade (CCleanupChange::eChangeOrgmod);
- }
- if ( RAW_FIELD_IS_EMPTY(org, Mod) ) {
- RESET_FIELD (org, Mod);
- ChangeMade (CCleanupChange::eChangeOrgmod);
- }
+ x_ConvertOrgref_modToOrgMod(org);
if (FIELD_IS_SET (org, Orgname)) {
COrgName& onm = GET_MUTABLE (org, Orgname);
@@ -1839,7 +2013,6 @@ static bool s_OrgModCompare (
// Two OrgMod's are equal and duplicates if:
// they have the same subname and same subtype
-// or one has subtype 'other'.
static bool s_OrgModEqual (
const CRef<COrgMod>& om1,
@@ -1861,7 +2034,6 @@ static bool s_OrgModEqual (
TORGMOD_SUBTYPE chs1 = GET_FIELD (omd1, Subtype);
TORGMOD_SUBTYPE chs2 = GET_FIELD (omd2, Subtype);
if (chs1 == chs2) return true;
- if ( chs1 == NCBI_ORGMOD(other) || chs2 == NCBI_ORGMOD(other)) return true;
return false;
}
@@ -1884,30 +2056,6 @@ void CNewCleanup_imp::OrgnameBC (
}
}
- // special value fixes
- EDIT_EACH_ORGMOD_ON_ORGNAME (it, onm) {
- COrgMod& omd = **it;
- switch (omd.GetSubtype()) {
- case COrgMod::eSubtype_bio_material:
- if (COrgMod::FixStructuredVoucher(omd.SetSubname(), "b")) {
- ChangeMade (CCleanupChange::eChangeOrgmod);
- }
- break;
- case COrgMod::eSubtype_culture_collection:
- if (COrgMod::FixStructuredVoucher(omd.SetSubname(), "c")) {
- ChangeMade (CCleanupChange::eChangeOrgmod);
- }
- break;
- case COrgMod::eSubtype_specimen_voucher:
- if (COrgMod::FixStructuredVoucher(omd.SetSubname(), "s")) {
- ChangeMade (CCleanupChange::eChangeOrgmod);
- }
- break;
- default:
- break;
- }
- }
-
// erase structured notes that already match value
// (Note: This is O(N^2). Maybe worth converting to a faster algo?)
EDIT_EACH_ORGMOD_ON_ORGNAME (it, onm) {
@@ -1973,6 +2121,7 @@ void CNewCleanup_imp::OrgmodBC (
{
CLEAN_AND_COMPRESS_STRING_MEMBER (omd, Subname);
if (FIELD_IS_SET (omd, Subname)) {
+ x_TrimInternalSemicolonsMarkChanged( GET_MUTABLE(omd, Subname) );
x_RemoveFlankingQuotes( GET_MUTABLE(omd, Subname) );
}
@@ -1996,6 +2145,21 @@ void CNewCleanup_imp::OrgmodBC (
}
}
+bool s_IsAllDigits(const string& str)
+{
+ if (str.length() == 0) {
+ return false;
+ }
+ bool all_digits = true;
+ ITERATE(string, s, str) {
+ if (!isdigit(*s)) {
+ all_digits = false;
+ break;
+ }
+ }
+ return all_digits;
+}
+
void CNewCleanup_imp::DbtagBC (
CDbtag& dbtag
)
@@ -2007,7 +2171,17 @@ void CNewCleanup_imp::DbtagBC (
string& db = GET_MUTABLE (dbtag, Db);
if (NStr::IsBlank (db)) return;
- x_CleanupStringMarkChanged( db );
+ size_t len = db.length();
+ NStr::TruncateSpacesInPlace(db);
+ if (len != db.length()) {
+ ChangeMade(CCleanupChange::eTrimSpaces);
+ }
+
+ if (dbtag.GetTag().IsStr()) {
+ if (TrimSpacesSemicolonsAndCommas(dbtag.SetTag().SetStr())) {
+ ChangeMade(CCleanupChange::eTrimSpaces);
+ }
+ }
if (NStr::EqualNocase(db, "Swiss-Prot")
|| NStr::EqualNocase (db, "SWISSPROT")) {
@@ -2048,10 +2222,10 @@ void CNewCleanup_imp::DbtagBC (
} else if (NStr::Equal(db, "FlyBase")) {
db = "FLYBASE";
ChangeMade(CCleanupChange::eChangeDbxrefs);
- } else if (NStr::EqualNocase(db, "GreengenesID")) {
+ } else if (NStr::Equal(db, "GreengenesID")) {
db = "Greengenes";
ChangeMade(CCleanupChange::eChangeDbxrefs);
- } else if (NStr::EqualNocase(db, "HMPID")) {
+ } else if (NStr::Equal(db, "HMPID")) {
db = "HMP";
ChangeMade(CCleanupChange::eChangeDbxrefs);
}
@@ -2072,7 +2246,6 @@ void CNewCleanup_imp::DbtagBC (
string& str = GET_MUTABLE(oid, Str);
if (NStr::IsBlank (str)) return;
- x_CleanupStringMarkChanged( str );
db = dbtag.GetDb();
str = dbtag.GetTag().GetStr();
@@ -2085,14 +2258,14 @@ void CNewCleanup_imp::DbtagBC (
dbtag.SetTag().SetStr (dbtag.GetTag().GetStr().substr (4));
ChangeMade(CCleanupChange::eChangeDbxrefs);
*/
- } else if( NStr::StartsWith (str, "MGD:") ) {
- /*
- dbtag.SetTag().SetStr (dbtag.GetTag().GetStr().substr (4));
- ChangeMade(CCleanupChange::eChangeDbxrefs);
- */
- } else if( NStr::StartsWith( str, "J:", NStr::eNocase ) ) {
- dbtag.SetTag().SetStr("J");
+ }
+ else if (NStr::StartsWith(str, "MGD:")) {
+ dbtag.SetTag().SetStr("MGI:" + dbtag.GetTag().GetStr().substr(4));
ChangeMade(CCleanupChange::eChangeDbxrefs);
+ } else if (NStr::StartsWith(str, "J:")) {
+ if (s_IsAllDigits(str.substr(2))) {
+ dbtag.SetTag().SetStr("MGI:");
+ }
} else {
string newstr = "MGI:" + str;
dbtag.SetTag().SetStr(newstr);
@@ -2115,19 +2288,8 @@ void CNewCleanup_imp::DbtagBC (
}
}
- bool all_zero = true;
- FOR_EACH_CHAR_IN_STRING (it, str) {
- const char& ch = *it;
- if (isdigit((unsigned char)(ch))) {
- if (ch != '0') {
- all_zero = false;
- }
- } else if (!isspace((unsigned char)(ch))) {
- return;
- }
- }
-
- if (str[0] != '0' || all_zero) {
+ // convert to number if all digits
+ if (s_IsAllDigits(str) && !NStr::StartsWith(str, "0")) {
try {
// extract the part before the first space for conversion
string::size_type pos_of_first_space = 0;
@@ -2139,7 +2301,7 @@ void CNewCleanup_imp::DbtagBC (
// only convert str to int if it fits into the non-negative side
// of an int.
int value = NStr::StringToInt(sStrOfNum, NStr::fConvErr_NoThrow);
- if( value > 0 || (value == 0 && all_zero) ) {
+ if( value > 0) {
SET_FIELD ( oid, Id, NStr::StringToUInt(sStrOfNum) );
ChangeMade (CCleanupChange::eChangeDbxrefs);
}
@@ -2180,6 +2342,64 @@ static bool s_ShouldWeFixInitials(const CPub_equiv& equiv)
return !(has_art && has_id);
}
+static size_t s_PubPriority( CPub::E_Choice val)
+{
+ size_t priority = 0;
+ switch (val) {
+ case CPub::e_not_set:
+ priority = 0;
+ break;
+ case CPub::e_Gen:
+ priority = 3;
+ break;
+ case CPub::e_Sub:
+ priority = 4;
+ break;
+ case CPub::e_Medline:
+ priority = 13;
+ break;
+ case CPub::e_Muid:
+ priority = 2;
+ break;
+ case CPub::e_Article:
+ priority = 5;
+ break;
+ case CPub::e_Journal:
+ priority = 6;
+ break;
+ case CPub::e_Book:
+ priority = 7;
+ break;
+ case CPub::e_Proc:
+ priority = 8;
+ break;
+ case CPub::e_Patent:
+ priority = 9;
+ break;
+ case CPub::e_Pat_id:
+ priority = 10;
+ break;
+ case CPub::e_Man:
+ priority = 11;
+ break;
+ case CPub::e_Equiv:
+ priority = 12;
+ break;
+ case CPub::e_Pmid:
+ priority = 1;
+ break;
+ }
+ return priority;
+}
+
+inline
+static
+bool s_PubWhichCompare( CRef<CPub> pub1, CRef<CPub> pub2 ) {
+ size_t pr1 = s_PubPriority(pub1->Which());
+ size_t pr2 = s_PubPriority(pub2->Which());
+ return (pr1 < pr2);
+}
+
void CNewCleanup_imp::PubEquivBC (CPub_equiv& pub_equiv)
{
x_FlattenPubEquiv(pub_equiv);
@@ -2191,6 +2411,9 @@ void CNewCleanup_imp::PubEquivBC (CPub_equiv& pub_equiv)
CRef<CCit_art> last_article;
bool fix_initials = s_ShouldWeFixInitials(pub_equiv);
+
+ pub_equiv.Set().sort(s_PubWhichCompare);
+
EDIT_EACH_PUB_ON_PUBEQUIV(it, pub_equiv) {
CPub &pub = **it;
@@ -2294,7 +2517,7 @@ static bool s_IsEmpty(const CAuth_list::TAffil& affil)
static
bool s_IsEmpty( const CCit_gen &cg )
{
- return ( ! FIELD_IS_SET(cg, Cit) || GET_FIELD(cg, Cit).empty() ) &&
+ return ( ! FIELD_IS_SET(cg, Cit) ) &&
! FIELD_IS_SET(cg, Authors) &&
( ! FIELD_IS_SET(cg, Muid) || GET_FIELD(cg, Muid) <= 0 ) &&
! FIELD_IS_SET(cg, Journal) &&
@@ -2442,6 +2665,13 @@ CNewCleanup_imp::EAction CNewCleanup_imp::CitPatBC(CCit_pat& citpat, bool fix_in
AuthListBC( GET_MUTABLE(citpat, Assignees), fix_initials);
}
+ if ( FIELD_IS_SET(citpat, Country) ) {
+ if (NStr::Equal(citpat.GetCountry(), "USA")) {
+ citpat.SetCountry("US");
+ ChangeMade(CCleanupChange::eChangePublication);
+ }
+ }
+
return eAction_Nothing;
}
@@ -2642,6 +2872,24 @@ void CNewCleanup_imp::AffilBC( CAffil& af )
ChangeMade (CCleanupChange::eChangePublication);
}
}
+
+ if (std.CanGetCountry() ) {
+ if ( NStr::EqualNocase(std.GetCountry(), "USA") && ! NStr::EqualCase(std.GetCountry(), "USA") ) {
+ SET_FIELD( std, Country, "USA");
+ ChangeMade (CCleanupChange::eChangePublication);
+ }
+ }
+
+ if (std.CanGetSub() && std.CanGetCountry() ) {
+ if ( NStr::EqualCase(std.GetCountry(), "USA") ) {
+ string oldsub = std.GetSub();
+ string newsub = NStr::Replace(oldsub, ".", "");
+ if ( ! NStr::EqualNocase(oldsub, newsub) ) {
+ SET_FIELD( std, Sub, newsub);
+ ChangeMade (CCleanupChange::eChangePublication);
+ }
+ }
+ }
break;
}}
default:
@@ -2805,16 +3053,16 @@ void CNewCleanup_imp::ImpFeatBC( CSeq_feat& feat )
CSeqFeatData::ESubtype subtype = feat.GetData().GetSubtype();
if (CSeqFeatData::IsRegulatory(subtype)) {
string regulatory_class = CSeqFeatData::GetRegulatoryClass(subtype);
- if (!NStr::IsBlank(regulatory_class)) {
- SET_FIELD(imf, Key, "regulatory");
- ChangeMade(CCleanupChange::eChangeKeywords);
-
- CRef<CGb_qual> regulatory_class_qual( new CGb_qual );
- regulatory_class_qual->SetQual("regulatory_class");
+ SET_FIELD(imf, Key, "regulatory");
+ ChangeMade(CCleanupChange::eChangeKeywords);
+ CRef<CGb_qual> regulatory_class_qual( new CGb_qual );
+ regulatory_class_qual->SetQual("regulatory_class");
+ if (NStr::IsBlank(regulatory_class)) {
+ regulatory_class_qual->SetVal( "other" );
+ } else {
regulatory_class_qual->SetVal( regulatory_class );
-
- feat.SetQual().push_back( regulatory_class_qual );
}
+ feat.SetQual().push_back( regulatory_class_qual );
}
if( key == "repeat_region" && ! m_SeqEntryInfoStack.top().m_IsEmblOrDdbj ) {
@@ -2880,13 +3128,8 @@ void CNewCleanup_imp::ImpFeatBC( CSeq_feat& feat )
new_rna_ref->SetType( rna_ref_type );
feat.SetData().SetRna( *new_rna_ref );
ChangeMade(CCleanupChange::eAddRNAref);
-
- // autogenerated code won't traverse this.
- // Also we create a NEW CAutogeneratedCleanup because
- // CAutogeneratedCleanup is stateful and we don't
- // want to interfere with its state.
- CAutogeneratedCleanup auto_cleanup( *m_Scope, *this );
- auto_cleanup.BasicCleanupSeqFeat( feat );
+ x_CleanSeqFeatQuals(feat);
+ RnaFeatBC(feat.SetData().SetRna(), feat);
} else {
TPROTREF_PROCESSED processed = NCBI_PROTREF(not_set);
if ( key == "proprotein" || key == "preprotein" ) {
@@ -2907,13 +3150,7 @@ void CNewCleanup_imp::ImpFeatBC( CSeq_feat& feat )
new_prot_ref->SetProcessed( processed );
feat.SetData().SetProt( *new_prot_ref );
ChangeMade(CCleanupChange::eAddProtFeat);
-
- // autogenerated code won't traverse this.
- // Also we create a NEW CAutogeneratedCleanup because
- // CAutogeneratedCleanup is stateful and we don't
- // want to interfere with its state.
- CAutogeneratedCleanup auto_cleanup( *m_Scope, *this );
- auto_cleanup.BasicCleanupSeqFeat( feat );
+ x_CleanSeqFeatQuals(feat);
}
}
}
@@ -3012,13 +3249,7 @@ void CNewCleanup_imp::SeqLocBC( CSeq_loc &loc )
// change both and both-rev to plus and minus, respectively
if (pnt.CanGetStrand()) {
ENa_strand strand = pnt.GetStrand();
- if (strand == eNa_strand_both) {
- pnt.SetStrand(eNa_strand_plus);
- ChangeMade(CCleanupChange::eChangeStrand);
- } else if (strand == eNa_strand_both_rev) {
- pnt.SetStrand(eNa_strand_minus);
- ChangeMade(CCleanupChange::eChangeStrand);
- } else if( strand == eNa_strand_unknown ) {
+ if( strand == eNa_strand_unknown ) {
pnt.ResetStrand();
ChangeMade(CCleanupChange::eChangeStrand);
}
@@ -3099,6 +3330,7 @@ void CNewCleanup_imp::SeqLocBC( CSeq_loc &loc )
ChangeMade(CCleanupChange::eChangeStrand);
}
}
+
}
void CNewCleanup_imp::ConvertSeqLocWholeToInt( CSeq_loc &loc )
@@ -3241,7 +3473,15 @@ void CNewCleanup_imp::GBQualBC (
ChangeMade(CCleanupChange::eChangeQualifiers);
}
- CLEAN_STRING_MEMBER (gbq, Val);
+ if (FIELD_IS_SET (gbq, Val)) {
+ const string::size_type old_length = gbq.GetVal().length();
+ CleanVisString (gbq.SetVal());
+ TrimInternalSemicolons (gbq.SetVal());
+ x_CompressSpaces( gbq.SetVal() );
+ if (gbq.GetVal().length() != old_length) {
+ ChangeMade (CCleanupChange::eTrimSpaces);
+ }
+ }
if (FIELD_IS_SET (gbq, Val) && s_IsJustQuotes (GET_FIELD (gbq, Val))) {
SET_FIELD (gbq, Val, kEmptyStr);
ChangeMade (CCleanupChange::eCleanDoubleQuotes);
@@ -3257,6 +3497,7 @@ void CNewCleanup_imp::GBQualBC (
if (CGb_qual::CleanupRptUnitSeq(gbq.SetVal())) {
ChangeMade(CCleanupChange::eChangeQualifiers);
}
+ x_CleanupRptUnit(gbq);
} else if (NStr::EqualNocase(gbq.GetQual(), "rpt_unit_range")) {
if (CGb_qual::CleanupRptUnitRange(gbq.SetVal())) {
ChangeMade(CCleanupChange::eChangeQualifiers);
@@ -3269,7 +3510,7 @@ void CNewCleanup_imp::GBQualBC (
if (CGb_qual::CleanupReplace(gbq.SetVal())) {
ChangeMade(CCleanupChange::eChangeQualifiers);
}
- }
+ }
x_ChangeTransposonToMobileElement(gbq);
x_ChangeInsertionSeqToMobileElement(gbq);
@@ -3425,13 +3666,43 @@ const char *s_FindKeyFromFeatDefType( const CSeq_feat &feat )
return kFeatBad;
}
-static
-bool s_IsAllDigits( const string &str )
+
+static bool SetExceptFromGbqual(const CGb_qual& gb_qual, CSeq_feat& feat)
+{
+ bool rval = false;
+ if (!feat.IsSetExcept() || !feat.GetExcept()) {
+ feat.SetExcept(true);
+ rval = true;
+ }
+
+ if (!gb_qual.IsSetQual()) {
+ return rval;
+ }
+ if (feat.IsSetExcept_text() && !NStr::IsBlank(feat.GetExcept_text())) {
+ return rval;
+ }
+ // for whatever reason, C Toolkit only sets text if Gbqual was blank
+ if (gb_qual.IsSetVal() && !NStr::IsBlank(gb_qual.GetVal())) {
+ return rval;
+ }
+ string exc = gb_qual.GetQual();
+ NStr::ReplaceInPlace (exc, "-", " ");
+ NStr::ReplaceInPlace (exc, "_", " ");
+ feat.SetExcept_text(exc);
+ return true;
+}
+
+
+static bool s_StringsAreEquivalent(const string& str1, const string& str2)
{
- CCachedRegexp all_digits_regex = regexpCache.Get("^[0-9]+$");
- return all_digits_regex->IsMatch(str);
+ string s1 = NStr::Replace(str1, " ", "_");
+ NStr::ReplaceInPlace(s1, "-", "_");
+ string s2 = NStr::Replace(str2, " ", "_");
+ NStr::ReplaceInPlace(s2, "-", "_");
+ return NStr::EqualNocase(s1, s2);
}
+
CNewCleanup_imp::EAction CNewCleanup_imp::GBQualSeqFeatBC(CGb_qual& gb_qual, CSeq_feat& feat)
{
if( ! FIELD_IS_SET(feat, Data) ) {
@@ -3454,6 +3725,13 @@ CNewCleanup_imp::EAction CNewCleanup_imp::GBQualSeqFeatBC(CGb_qual& gb_qual, CSe
if (NStr::EqualNocase(qual, "cons_splice")) {
return eAction_Erase;
+ } else if (s_StringsAreEquivalent(qual, "ribosomal-slippage") ||
+ s_StringsAreEquivalent(qual, "trans-splicing") ||
+ s_StringsAreEquivalent(qual, "artificial-location")) {
+ if (SetExceptFromGbqual(gb_qual, feat)) {
+ ChangeMade (CCleanupChange::eChangeException);
+ }
+ return eAction_Erase;
} else if (NStr::EqualNocase(qual, "partial")) {
feat.SetPartial(true);
ChangeMade(CCleanupChange::eChangeQualifiers);
@@ -3508,12 +3786,25 @@ CNewCleanup_imp::EAction CNewCleanup_imp::GBQualSeqFeatBC(CGb_qual& gb_qual, CSe
ChangeMade(CCleanupChange::eChangeComment);
}
return eAction_Erase;
+ } else if (NStr::EqualNocase(qual, "regulatory_class")) {
+ string::size_type colon_pos = val.find_first_of(":");
+ if (colon_pos != string::npos && ! NStr::StartsWith (val, "other:")) {
+ string comment = val.substr( colon_pos + 1 );
+ val.resize( colon_pos );
+ if( GET_STRING_FLD_OR_BLANK(feat, Comment).empty() ) {
+ SET_FIELD(feat, Comment, comment );
+ } else {
+ GET_MUTABLE(feat, Comment) += "; " + comment;
+ }
+ ChangeMade(CCleanupChange::eChangeComment);
+ }
} else if (NStr::EqualNocase(qual, "db_xref")) {
string tag, db;
if (NStr::SplitInTwo(val, ":", db, tag)) {
CRef<CDbtag> dbp(new CDbtag);
dbp->SetDb(db);
dbp->SetTag().SetStr(tag);
+
feat.SetDbxref().push_back(dbp);
ChangeMade(CCleanupChange::eChangeDbxrefs);
return eAction_Erase; // mark qual for deletion
@@ -3555,7 +3846,7 @@ CNewCleanup_imp::EAction CNewCleanup_imp::GBQualSeqFeatBC(CGb_qual& gb_qual, CSe
if (!NStr::IsBlank(val)) {
CRef<CSeqFeatXref> xref(new CSeqFeatXref);
xref->SetData().SetGene().SetLocus(val);
- feat.SetXref().push_back(xref);
+ feat.SetXref().insert(feat.SetXref().begin(), xref);
ChangeMade(CCleanupChange::eCopyGeneXref);
return eAction_Erase; // mark qual for deletion
}
@@ -3775,6 +4066,10 @@ void s_ExpandThisQual(
CGb_qual& qual = **it;
string qual_type = qual.GetQual();
string& val = qual.SetVal();
+ if (NStr::Equal(val, "()")) {
+ val = "";
+ return;
+ }
if ( ! s_IsCompoundRptTypeValue( val ) ) {
//
// nothing to do ...
@@ -3878,17 +4173,6 @@ CNewCleanup_imp::x_GeneGBQualBC( CGene_ref& gene, const CGb_qual& gb_qual )
} else if (NStr::EqualNocase(qual, "gene_synonym")) {
change_made = true;
gene.SetSyn().push_back(val);
- } else if (NStr::EqualNocase(qual, "gene") ) {
- change_made = true;
- if ( ! gene.IsSetLocus() ) {
- gene.SetLocus(val);
- } else if (gene.GetLocus() != val) {
- CGene_ref::TSyn::const_iterator syn_it =
- find(gene.GetSyn().begin(), gene.GetSyn().end(), val);
- if (syn_it == gene.GetSyn().end()) {
- gene.SetSyn().push_back(val);
- }
- }
}
if (change_made) {
ChangeMade(CCleanupChange::eChangeQualifiers);
@@ -4155,6 +4439,15 @@ static CRef<CTrna_ext> s_ParseTRnaFromAnticodonString (const string &str, const
}
CRef<CSeq_loc> anticodon = ReadLocFromText (pos_str, feat.GetLocation().GetId(), scope);
if( anticodon ) {
+ CBioseq_Handle bsh = scope->GetBioseqHandle(*(feat.GetLocation().GetId()));
+ if (!bsh) {
+ trna.Reset(NULL);
+ return trna;
+ }
+ if (anticodon->GetStop(eExtreme_Positional) >= bsh.GetInst_Length()) {
+ trna.Reset(NULL);
+ return trna;
+ }
anticodon->SetStrand(eNa_strand_plus); // anticodon is always on plus strand
}
if (anticodon == NULL) {
@@ -4336,7 +4629,6 @@ char s_ParseSeqFeatTRnaString( const string &comment, bool *out_justTrnaText, st
}
if( curraa == 'A' && str.length() == 1 ) {
is_A = true;
- curraa = 0;
} else if (curraa != '\0') {
if (aa == '\0') {
aa = curraa;
@@ -4382,6 +4674,159 @@ char s_ParseSeqFeatTRnaString( const string &comment, bool *out_justTrnaText, st
}
+void CNewCleanup_imp::x_AddToComment(CSeq_feat& feat, const string& comment)
+{
+ if (!feat.IsSetComment()) {
+ feat.SetComment(comment);
+ }
+ else {
+ feat.SetComment() += "; " + comment;
+ }
+ ChangeMade(CCleanupChange::eChangeComment);
+}
+
+CNewCleanup_imp::EAction
+CNewCleanup_imp::x_HandleTrnaProductGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& product)
+{
+ CRNA_ref::TType& rna_type = rna.SetType();
+
+ if (rna_type != CRNA_ref::eType_tRNA &&
+ rna_type != CRNA_ref::eType_other &&
+ rna_type != CRNA_ref::eType_unknown) {
+ return eAction_Nothing;
+ }
+
+ if (rna_type == NCBI_RNAREF(tRNA) && rna.IsSetExt() && rna.GetExt().IsName()) {
+ string name = rna.GetExt().GetName();
+ bool justTrnaText = false;
+ string codon;
+ char aa = s_ParseSeqFeatTRnaString(name, &justTrnaText, codon, false);
+ if (aa != '\0') {
+ const bool is_fMet = (NStr::Find(name, "fMet") != NPOS);
+ CRNA_ref_Base::C_Ext::TTRNA &trp = rna.SetExt().SetTRNA();
+ trp.SetAa().SetNcbieaa(aa);
+ if (justTrnaText) {
+ copy(codon.begin(), codon.end(), back_inserter(trp.SetCodon()));
+ }
+ if (aa == 'M') {
+ if (is_fMet) {
+ x_AddToComment(feat, "fMet");
+ }
+ }
+ x_SeqFeatTRNABC(feat, trp);
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
+ }
+ if (rna_type == NCBI_RNAREF(tRNA) && !rna.IsSetExt()) {
+ // this part inserted from: AddQualifierToFeature (sfp, "product", gb_qual_val);
+ bool justTrnaText = false;
+ string codon;
+ char aa = s_ParseSeqFeatTRnaString(product, &justTrnaText, codon, false);
+ if (aa != '\0') {
+
+ CRNA_ref_Base::C_Ext::TTRNA& trna = rna.SetExt().SetTRNA();
+ trna.SetAa().SetNcbieaa(aa);
+
+ if (justTrnaText) {
+ copy(codon.begin(), codon.end(), back_inserter(trna.SetCodon()));
+ }
+ else {
+ x_AddToComment(feat, product);
+ }
+
+ if (aa == 'M') {
+ if (NStr::Find(product, "fMet") != NPOS) {
+ x_AddToComment(feat, "fMet");
+ }
+ }
+
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
+ else {
+ x_AddToComment(feat, product);
+ }
+ return eAction_Erase;
+ }
+ if (rna_type == NCBI_RNAREF(tRNA) && rna.IsSetExt() && rna.GetExt().IsTRNA()) {
+ CRNA_ref_Base::C_Ext::TTRNA& trp = rna.SetExt().SetTRNA();
+ if (trp.IsSetAa() && trp.GetAa().IsNcbieaa()) {
+ string ignored;
+ if (trp.GetAa().GetNcbieaa() == s_ParseSeqFeatTRnaString(product, NULL, ignored, false) &&
+ NStr::IsBlank(ignored)) {
+ } else {
+ x_AddToComment(feat, product);
+ }
+ return eAction_Erase;
+ }
+ }
+
+ if (rna.IsSetExt() && rna.GetExt().IsName() && NStr::Equal(rna.GetExt().GetName(), product)) {
+ return eAction_Erase;
+ }
+
+ return eAction_Nothing;
+}
+
+
+CNewCleanup_imp::EAction CNewCleanup_imp::x_HandleStandardNameRnaGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& standard_name)
+{
+ if (!rna.IsSetType()) {
+ return eAction_Nothing;
+ }
+ EAction rval = eAction_Nothing;
+
+ TRNAREF_TYPE rna_type = rna.GetType();
+ string previous_product = rna.GetRnaProductName();
+
+ switch (rna_type)
+ {
+ case CRNA_ref::eType_rRNA:
+ case CRNA_ref::eType_premsg:
+ /*
+ if (NStr::IsBlank(previous_product)) {
+ string remainder;
+ rna.SetRnaProductName(standard_name, remainder);
+ if (!NStr::IsBlank(remainder)) {
+ x_AddToComment(feat, remainder);
+ }
+ } else {
+ x_AddToComment(feat, standard_name);
+ }
+ rval = eAction_Erase;
+ */
+ break;
+ case CRNA_ref::eType_ncRNA:
+ /*
+ x_AddToComment(feat, standard_name);
+ rval = eAction_Erase;
+ */
+ break;
+ case CRNA_ref::eType_mRNA:
+ /*
+ if (NStr::IsBlank(standard_name)) {
+ if (!m_SeqEntryInfoStack.top().m_IsEmblOrDdbj) {
+ rval = eAction_Erase;
+ }
+ } else {
+ if (NStr::IsBlank(previous_product)) {
+ rna.SetExt().SetName(standard_name);
+ rval = eAction_Erase;
+ }
+ }
+ */
+ break;
+ case CRNA_ref::eType_tRNA:
+ /*
+ rval = x_HandleTrnaProductGBQual(feat, rna, standard_name);
+ */
+ break;
+ default:
+ break;
+ }
+ return rval;
+}
+
+
// homologous to C's HandledGBQualOnRNA.
// That func was copy-pasted, then translated into C++.
// Later we can go back and actually refactor the code
@@ -4389,21 +4834,26 @@ char s_ParseSeqFeatTRnaString( const string &comment, bool *out_justTrnaText, st
CNewCleanup_imp::EAction
CNewCleanup_imp::x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual& gb_qual)
{
- if( ! gb_qual.IsSetVal() ) {
+ if( ! gb_qual.IsSetVal()) {
return eAction_Nothing;
}
const string &gb_qual_qual = gb_qual.GetQual();
string &gb_qual_val = gb_qual.SetVal();
TRNAREF_TYPE& rna_type = rna.SetType();
- const bool is_std_name = NStr::EqualNocase( gb_qual_qual, "standard_name" );
- if (NStr::EqualNocase( gb_qual_qual, "product" ) ||
- (is_std_name && (! m_SeqEntryInfoStack.top().m_IsEmblOrDdbj) ))
+
+ if (NStr::EqualNocase(gb_qual_qual, "standard_name")) {
+ return x_HandleStandardNameRnaGBQual(feat, rna, gb_qual_val);
+ }
+ if (NStr::IsBlank(gb_qual_val)) {
+ return eAction_Nothing;
+ }
+
+ if (NStr::EqualNocase( gb_qual_qual, "product" ))
{
if (rna_type == NCBI_RNAREF(unknown)) {
rna_type = NCBI_RNAREF(other);
ChangeMade(CCleanupChange::eChangeRNAref);
}
- if (rna_type == NCBI_RNAREF(other) && is_std_name) return eAction_Nothing;
if ( rna.IsSetExt() && rna.GetExt().IsName() ) {
const string &name = rna.SetExt().SetName();
if ( name.empty() ) {
@@ -4411,91 +4861,10 @@ CNewCleanup_imp::x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual&
ChangeMade(CCleanupChange::eChangeRNAref);
}
}
- if ( rna.IsSetExt() && rna.GetExt().IsTRNA() ) {
- CRNA_ref_Base::C_Ext::TTRNA& trp = rna.SetExt().SetTRNA();
- if ( ! trp.IsSetAa() && ! trp.IsSetAnticodon() ) {
- if( ! trp.IsSetCodon() || trp.GetCodon().empty() ) {
- rna.ResetExt();
- ChangeMade(CCleanupChange::eChangeRNAref);
- }
- }
- }
- if (rna_type == NCBI_RNAREF(tRNA) && rna.IsSetExt() && rna.GetExt().IsName() ) {
- const string &name = rna.SetExt().SetName();
- bool justTrnaText = false;
- string codon;
- char aa = s_ParseSeqFeatTRnaString( name, &justTrnaText, codon, false );
- if (aa != '\0') {
- const bool is_fMet = ( NStr::Find(name, "fMet") != NPOS );
- CRNA_ref_Base::C_Ext::TTRNA &trp = rna.SetExt().SetTRNA();
- trp.SetAa().SetNcbieaa(aa);
- if (justTrnaText) {
- copy( codon.begin(), codon.end(), back_inserter(trp.SetCodon()) );
- }
- if (aa == 'M') {
- if (is_fMet) {
- if ( ! feat.IsSetComment() ) {
- feat.SetComment("fMet");
- } else {
- feat.SetComment() += "; fMet";
- }
- }
- }
- x_SeqFeatTRNABC(feat, trp);
- ChangeMade(CCleanupChange::eChangeRNAref);
- }
- }
- if (rna_type == NCBI_RNAREF(tRNA) && ! rna.IsSetExt() ) {
- // this part inserted from: AddQualifierToFeature (sfp, "product", gb_qual_val);
- bool justTrnaText = false;
- string codon;
- char aa = s_ParseSeqFeatTRnaString (gb_qual_val, &justTrnaText, codon, false);
- if (aa != '\0') {
-
- CRNA_ref_Base::C_Ext::TTRNA& trna = rna.SetExt().SetTRNA();
- trna.SetAa().SetNcbieaa(aa);
-
- if (justTrnaText) {
- copy( codon.begin(), codon.end(), back_inserter(trna.SetCodon()) );
- } else {
- if( ! feat.IsSetComment() ) {
- feat.SetComment(gb_qual_val);
- } else {
- feat.SetComment() += "; " + gb_qual_val;
- }
- }
-
- if (aa == 'M') {
- if( NStr::Find(gb_qual_val, "fMet") != NPOS ) {
- if ( ! feat.IsSetComment() ) {
- feat.SetComment("fMet");
- } else {
- feat.SetComment() += "; fMet";
- }
- }
- }
-
- ChangeMade(CCleanupChange::eChangeRNAref);
- } else {
- if ( ! feat.IsSetComment() ) {
- feat.SetComment(gb_qual_val);
- } else {
- feat.SetComment() += "; ";
- feat.SetComment() += gb_qual_val;
- }
- ChangeMade(CCleanupChange::eChangeComment);
- }
+ if (x_HandleTrnaProductGBQual(feat, rna, gb_qual_val) == eAction_Erase) {
return eAction_Erase;
}
- if (rna_type == NCBI_RNAREF(tRNA) && rna.IsSetExt() && rna.GetExt().IsTRNA() ) {
- CRNA_ref_Base::C_Ext::TTRNA& trp = rna.SetExt().SetTRNA();
- if ( trp.IsSetAa() && trp.GetAa().IsNcbieaa() ) {
- string ignored;
- if ( trp.GetAa().GetNcbieaa() == s_ParseSeqFeatTRnaString (gb_qual_val, NULL, ignored, false)) {
- return eAction_Erase;
- }
- }
- }
+
if( FIELD_IS_SET_AND_IS(rna, Ext, Gen) ) {
CRNA_gen & rna_gen = rna.SetExt().SetGen();
if( RAW_FIELD_IS_EMPTY_OR_UNSET(rna_gen, Product) ) {
@@ -4523,13 +4892,7 @@ CNewCleanup_imp::x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual&
return eAction_Nothing;
}
// subsequent /product now added to comment
- if ( ! feat.IsSetComment() ) {
- feat.SetComment( gb_qual_val );
- gb_qual.ResetVal();
- } else if ( NStr::Find(gb_qual_val, feat.GetComment()) == NPOS) {
- feat.SetComment() += "; ";
- feat.SetComment() += gb_qual_val;
- }
+ x_AddToComment(feat, gb_qual_val);
ChangeMade(CCleanupChange::eChangeComment);
return eAction_Erase;
}
@@ -4545,73 +4908,73 @@ CNewCleanup_imp::x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual&
return eAction_Erase;
}
} else if (NStr::EqualNocase(gb_qual_qual, "anticodon") ) {
- if (!rna.IsSetType()) {
- rna.SetType(CRNA_ref::eType_tRNA);
+ if (!rna.IsSetType() || rna.GetType() == CRNA_ref::eType_unknown) {
+ rna.SetType(CRNA_ref::eType_other);
ChangeMade(CCleanupChange::eChangeKeywords);
}
- _ASSERT(rna.IsSetType());
- CRNA_ref::TType type = rna.GetType();
- if (type == CRNA_ref::eType_unknown) {
- rna.SetType(CRNA_ref::eType_tRNA);
- ChangeMade(CCleanupChange::eChangeKeywords);
- } else if (type != CRNA_ref::eType_tRNA) {
+ if (rna.GetType() != CRNA_ref::eType_tRNA) {
return eAction_Nothing;
}
- if (!rna.IsSetExt()) {
- rna.SetExt().SetTRNA();
- ChangeMade(CCleanupChange::eChangeRNAref);
+
+ CRef<CTrna_ext> trna = s_ParseTRnaFromAnticodonString(gb_qual.GetVal(), feat, m_Scope);
+ if (!trna) {
+ return eAction_Nothing;
}
- if ( rna.IsSetExt() &&
- rna.GetExt().Which() == NCBI_RNAEXT(TRNA) ) {
-
- CRef<CTrna_ext> trna = s_ParseTRnaFromAnticodonString( gb_qual.GetVal(), feat, m_Scope );
- if( ! trna ) {
- return eAction_Nothing;
- }
- x_SeqFeatTRNABC( feat, *trna );
- if (trna->IsSetAa() || trna->IsSetAnticodon()) {
- // don't apply at all if there are conflicts
- bool apply_aa = false;
- bool apply_anticodon = false;
- bool ok_to_apply = true;
+ x_SeqFeatTRNABC( feat, *trna );
+ if (trna->IsSetAa() || trna->IsSetAnticodon()) {
+ // don't apply at all if there are conflicts
+ bool apply_aa = false;
+ bool apply_anticodon = false;
+ bool ok_to_apply = true;
- // look for conflict with aa
- if (trna->IsSetAa() ) {
- if (rna.GetExt().GetTRNA().IsSetAa() ) {
- if( rna.GetExt().GetTRNA().GetAa().IsIupacaa() ) {
+ // look for conflict with aa
+ if (!rna.IsSetExt() || !rna.GetExt().IsTRNA()) {
+ if (trna->IsSetAa()) {
+ apply_aa = true;
+ }
+ if (trna->IsSetAnticodon()) {
+ apply_anticodon = true;
+ }
+ }
+ else {
+ if (trna->IsSetAa()) {
+ if (rna.GetExt().GetTRNA().IsSetAa()) {
+ if (rna.GetExt().GetTRNA().GetAa().IsIupacaa()) {
if (trna->GetAa().GetIupacaa() != rna.GetExt().GetTRNA().GetAa().GetIupacaa()) {
ok_to_apply = false;
}
}
- } else {
+ }
+ else {
apply_aa = true;
}
}
// look for conflict with anticodon
if (trna->IsSetAnticodon()) {
if (rna.GetExt().GetTRNA().IsSetAnticodon()) {
- if (sequence::Compare(rna.GetExt().GetTRNA().GetAnticodon(), trna->GetAnticodon(), m_Scope) != sequence::eSame) {
+ if (sequence::Compare(rna.GetExt().GetTRNA().GetAnticodon(),
+ trna->GetAnticodon(), m_Scope, sequence::fCompareOverlapping) != sequence::eSame) {
ok_to_apply = false;
}
- } else {
+ }
+ else {
apply_anticodon = true;
}
}
-
- if (ok_to_apply) {
- if (apply_aa ) {
- rna.SetExt().SetTRNA().SetAa().SetIupacaa(trna->GetAa().GetNcbieaa());
- ChangeMade (CCleanupChange::eChange_tRna);
- }
- if (apply_anticodon) {
- CRef<CSeq_loc> anticodon(new CSeq_loc());
- anticodon->Add (trna->GetAnticodon());
- rna.SetExt().SetTRNA().SetAnticodon(*anticodon);
- ChangeMade (CCleanupChange::eChangeAnticodon);
- }
- return eAction_Erase;
+ }
+ if (ok_to_apply) {
+ if (apply_aa ) {
+ rna.SetExt().SetTRNA().SetAa().SetIupacaa(trna->GetAa().GetNcbieaa());
+ ChangeMade (CCleanupChange::eChange_tRna);
+ }
+ if (apply_anticodon) {
+ CRef<CSeq_loc> anticodon(new CSeq_loc());
+ anticodon->Add (trna->GetAnticodon());
+ rna.SetExt().SetTRNA().SetAnticodon(*anticodon);
+ ChangeMade (CCleanupChange::eChangeAnticodon);
}
+ return eAction_Erase;
}
}
}
@@ -4692,7 +5055,8 @@ CNewCleanup_imp::EAction CNewCleanup_imp::x_ParseCodeBreak(const CSeq_feat& feat
}
if (break_loc == NULL
- || (break_loc->IsInt() && sequence::Compare (*break_loc, feat.GetLocation(), m_Scope) != sequence::eContained )
+ || (break_loc->IsInt()
+ && sequence::Compare (*break_loc, feat.GetLocation(), m_Scope, sequence::fCompareOverlapping) != sequence::eContained )
|| (break_loc->IsInt() && sequence::GetLength(*break_loc, m_Scope) != 3)) {
return eAction_Nothing;
}
@@ -4923,6 +5287,8 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
}
string first_initials;
+ string sDot(".");
+ //string sSpace(" ");
// like in C: str = NameStdPtrToTabbedString (nsp, fixInitials);
{
if ( ! FIELD_IS_SET(name, Suffix) && FIELD_IS_SET(name, Initials) ) {
@@ -4930,7 +5296,7 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
}
TRUNCATE_SPACES(name, First);
if( FIELD_IS_SET(name, Initials) ) {
- NStr::ReplaceInPlace( GET_MUTABLE(name, Initials), ".", "" );
+ NStr::ReplaceInPlace( GET_MUTABLE(name, Initials), sDot, kEmptyStr);
NStr::TruncateSpacesInPlace( GET_MUTABLE(name, Initials), NStr::eTrunc_Begin );
}
if( FIELD_IS_SET(name, Last) ) {
@@ -4967,7 +5333,7 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
}
if( FIELD_IS_SET(name, First) ) {
- NStr::ReplaceInPlace( GET_MUTABLE(name, First), ".", "" );
+ NStr::ReplaceInPlace( GET_MUTABLE(name, First), sDot, kEmptyStr);
NStr::TruncateSpacesInPlace( GET_MUTABLE(name, First), NStr::eTrunc_Begin );
}
@@ -4994,7 +5360,7 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
}
if( FIELD_IS_SET(name, Suffix) ) {
- NStr::ReplaceInPlace( GET_MUTABLE(name, Suffix), ".", "" );
+ NStr::ReplaceInPlace( GET_MUTABLE(name, Suffix), sDot, kEmptyStr );
NStr::TruncateSpacesInPlace( GET_MUTABLE(name, Suffix), NStr::eTrunc_Begin );
}
@@ -5067,23 +5433,11 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
}
if( NStr::EqualNocase(suffix, "1d") ) {
- suffix = "I";
- } else if( NStr::EqualNocase(suffix, "1st") ) {
- suffix = "I";
+ suffix = "1st";
} else if( NStr::EqualNocase(suffix, "2d") ) {
- suffix = "II";
- } else if( NStr::EqualNocase(suffix, "2nd") ) {
- suffix = "II";
+ suffix = "2nd";
} else if( NStr::EqualNocase(suffix, "3d") ) {
- suffix = "III";
- } else if( NStr::EqualNocase(suffix, "3rd") ) {
- suffix = "III";
- } else if( NStr::EqualNocase(suffix, "4th") ) {
- suffix = "IV";
- } else if( NStr::EqualNocase(suffix, "5th") ) {
- suffix = "V";
- } else if( NStr::EqualNocase(suffix, "6th") ) {
- suffix = "VI";
+ suffix = "3rd";
} else if( NStr::EqualNocase(suffix, "Sr") ) {
suffix = "Sr.";
} else if( NStr::EqualNocase(suffix, "Jr") ) {
@@ -5101,6 +5455,15 @@ void CNewCleanup_imp::x_NameStdBC ( CName_std& name, bool fix_initials )
if ( FIELD_EQUALS(name, Middle, kEmptyStr) ) {
RESET_FIELD(name, Middle);
}
+
+ // side effect of C Toolkit converting to tabbed string and back
+ // is that some fields are removed
+ if ( name.IsSetFull()) {
+ name.ResetFull();
+ }
+ if (name.IsSetTitle()) {
+ name.ResetTitle();
+ }
}
if (upcaseinits && FIELD_IS_SET(name, Initials) ) {
@@ -5239,15 +5602,60 @@ void CNewCleanup_imp::x_SeqIntervalBC( CSeq_interval & seq_interval )
// change bad strand values.
if (seq_interval.CanGetStrand()) {
ENa_strand strand = seq_interval.GetStrand();
+ if (strand == eNa_strand_unknown ) {
+ seq_interval.ResetStrand();
+ ChangeMade(CCleanupChange::eChangeStrand);
+ }
+ }
+}
+
+void CNewCleanup_imp::x_BothStrandBC( CSeq_loc &loc )
+{
+ switch (loc.Which()) {
+ case CSeq_loc::e_Int :
+ x_BothStrandBC( GET_MUTABLE(loc, Int) );
+ break;
+ case CSeq_loc::e_Packed_int :
+ {
+ CSeq_loc::TPacked_int::Tdata& ints = loc.SetPacked_int().Set();
+ NON_CONST_ITERATE(CSeq_loc::TPacked_int::Tdata, interval_it, ints) {
+ x_BothStrandBC(**interval_it);
+ }
+ }
+ break;
+ case CSeq_loc::e_Pnt :
+ {
+ CSeq_loc::TPnt& pnt = loc.SetPnt();
+
+ // change both and both-rev to plus and minus, respectively
+ if (pnt.CanGetStrand()) {
+ ENa_strand strand = pnt.GetStrand();
+ if (strand == eNa_strand_both) {
+ pnt.SetStrand(eNa_strand_plus);
+ ChangeMade(CCleanupChange::eChangeStrand);
+ } else if (strand == eNa_strand_both_rev) {
+ pnt.SetStrand(eNa_strand_minus);
+ ChangeMade(CCleanupChange::eChangeStrand);
+ }
+ }
+ }
+ break;
+
+ default:
+ break;
+ }
+}
+
+void CNewCleanup_imp::x_BothStrandBC( CSeq_interval & seq_interval )
+{
+ if (seq_interval.CanGetStrand()) {
+ ENa_strand strand = seq_interval.GetStrand();
if (strand == eNa_strand_both) {
seq_interval.SetStrand(eNa_strand_plus);
ChangeMade(CCleanupChange::eChangeStrand);
} else if (strand == eNa_strand_both_rev) {
seq_interval.SetStrand(eNa_strand_minus);
ChangeMade(CCleanupChange::eChangeStrand);
- } else if (strand == eNa_strand_unknown ) {
- seq_interval.ResetStrand();
- ChangeMade(CCleanupChange::eChangeStrand);
}
}
}
@@ -5262,6 +5670,14 @@ void CNewCleanup_imp::x_SplitDbtag( CDbtag &dbt, vector< CRef< CDbtag > > & out_
return;
}
+ // check if we're trying to split something we shouldn't
+ if (dbt.IsSetDb()) {
+ string db = dbt.GetDb();
+ if (NStr::Equal(db, "MGD") || NStr::Equal(db, "MGI") || NStr::Equal(db, "HGNC")) {
+ return;
+ }
+ }
+
if ( m_SeqEntryInfoStack.top().m_IsEmblOrDdbj) {
return;
}
@@ -5271,16 +5687,6 @@ void CNewCleanup_imp::x_SplitDbtag( CDbtag &dbt, vector< CRef< CDbtag > > & out_
NStr::Tokenize( dbt.GetTag().GetStr(), ":", tags );
_ASSERT( tags.size() >= 2 );
- // check if we're trying to split something we shouldn't
- if( NStr::EqualNocase( tags.front(), "MGD" ) ||
- NStr::EqualNocase( tags.front(), "MGI" ) ||
- NStr::EqualNocase( tags.front(), "HGNC" ) ||
- NStr::EqualNocase( tags.front(), "RGD" ) ||
- NStr::EqualNocase( tags.front(), "J" ) )
- {
- return;
- }
-
// treat the CDbtag argument as the first of the new CDbtags
dbt.SetTag().SetStr( tags.front() );
vector<string>::const_iterator str_iter = tags.begin() + 1;
@@ -5454,16 +5860,16 @@ public:
const string &GetRevName() const { return m_Rev_name; }
bool operator <( const CPCRParsedSet &rhs ) {
- const int fwd_seq_comparison = NStr::CompareNocase( m_Fwd_seq, rhs.m_Fwd_seq );
- if( fwd_seq_comparison != 0 ) return fwd_seq_comparison;
- const int rev_seq_comparison = NStr::CompareNocase( m_Rev_seq, rhs.m_Rev_seq );
- if( rev_seq_comparison != 0 ) return rev_seq_comparison;
- const int fwd_name_comparison = NStr::CompareNocase( m_Fwd_name, rhs.m_Fwd_name );
- if( fwd_name_comparison != 0 ) return fwd_name_comparison;
- const int rev_name_comparison = NStr::CompareNocase( m_Rev_name, rhs.m_Rev_name );
- if( rev_name_comparison != 0 ) return rev_name_comparison;
+ if ( int diff = NStr::CompareNocase( m_Fwd_seq, rhs.m_Fwd_seq ) )
+ return diff < 0;
+ if ( int diff = NStr::CompareNocase( m_Rev_seq, rhs.m_Rev_seq ) )
+ return diff < 0;
+ if ( int diff = NStr::CompareNocase( m_Fwd_name, rhs.m_Fwd_name ) )
+ return diff < 0;
+ if ( int diff = NStr::CompareNocase( m_Rev_name, rhs.m_Rev_name ) )
+ return diff < 0;
// last resort
- return m_Original_order - rhs.m_Original_order;
+ return m_Original_order < rhs.m_Original_order;
}
private:
@@ -5471,12 +5877,12 @@ private:
string m_Rev_seq;
string m_Fwd_name;
string m_Rev_name;
- int m_Original_order;
+ CAtomicCounter::TValue m_Original_order;
- static CAtomicCounter_WithAutoInit ms_Next_original_order;
+ static CAtomicCounter ms_Next_original_order;
};
-CAtomicCounter_WithAutoInit CPCRParsedSet::ms_Next_original_order;
+CAtomicCounter CPCRParsedSet::ms_Next_original_order;
static
void s_ParsePCRSet( const CBioSource &biosrc, list<CPCRParsedSet> &out_pcr_set )
@@ -6012,6 +6418,30 @@ CNewCleanup_imp::x_OrgnameModBC( COrgName &orgname, const string &org_ref_common
}
}
+void CNewCleanup_imp::x_SubSourceBC(CSubSource & subsrc)
+{
+ if (!subsrc.IsSetSubtype() || !subsrc.IsSetName()) {
+ return;
+ }
+ string orig = subsrc.GetName();
+ subsrc.AutoFix();
+ if (!NStr::Equal(subsrc.GetName(), orig)) {
+ ChangeMade(CCleanupChange::eChangeSubsource);
+ }
+}
+
+void CNewCleanup_imp::x_OrgModBC(COrgMod & orgmod)
+{
+ if (!orgmod.IsSetSubtype() || !orgmod.IsSetSubname()) {
+ return;
+ }
+ string orig = orgmod.GetSubname();
+ orgmod.AutoFix();
+ if (!NStr::Equal(orgmod.GetSubname(), orig)) {
+ ChangeMade(CCleanupChange::eChangeOrgmod);
+ }
+}
+
void CNewCleanup_imp::x_FixUnsetMolFromBiomol( CMolInfo& molinfo, CBioseq &bioseq )
{
if( FIELD_IS_SET(molinfo, Biomol) )
@@ -6127,6 +6557,41 @@ static SIZE_TYPE s_TitleEndsInOrganism (
return answer;
}
+static void s_RemoveOrgFromEndOfProtein (CBioseq& seq, string taxname)
+
+{
+ if (taxname.empty()) return;
+ SIZE_TYPE taxlen = taxname.length();
+
+ EDIT_EACH_SEQANNOT_ON_BIOSEQ (annot_it, seq) {
+ CSeq_annot& annot = **annot_it;
+ if (! annot.IsFtable()) continue;
+ EDIT_EACH_FEATURE_ON_ANNOT (feat_it, annot) {
+ CSeq_feat& feat = **feat_it;
+ CSeqFeatData& data = feat.SetData();
+ if (! data.IsProt()) continue;
+ CProt_ref& prot_ref = data.SetProt();
+ EDIT_EACH_NAME_ON_PROTREF (it, prot_ref) {
+ string str = *it;
+ if (str.empty()) continue;
+ int len = str.length();
+ if (len < 5) continue;
+ if (str [len - 1] != ']') continue;
+ SIZE_TYPE cp = NStr::Find(str, "[", 0, NPOS, NStr::eLast);
+ if (cp == NPOS) continue;
+ string suffix = str.substr(cp+1);
+ if (NStr::StartsWith(suffix, "NAD")) continue;
+ if (suffix.length() != taxlen + 1) continue;
+ if (NStr::StartsWith(suffix, taxname)) {
+ str.erase (cp);
+ Asn2gnbkCompressSpaces(str);
+ *it = str;
+ }
+ }
+ }
+ }
+}
+
void CNewCleanup_imp::x_AddPartialToProteinTitle( CBioseq &bioseq )
{
// Bail if not protein
@@ -6185,10 +6650,6 @@ void CNewCleanup_imp::x_AddPartialToProteinTitle( CBioseq &bioseq )
psTitle = & GET_MUTABLE(descr, Title);
}
}
- // bail if no title
- if( (NULL == psTitle) || psTitle->empty() ) {
- return;
- }
// iterate Seqdescs from bottom to top
// accumulate seqdescs into here
@@ -6257,7 +6718,14 @@ void CNewCleanup_imp::x_AddPartialToProteinTitle( CBioseq &bioseq )
}
}
- // put title into a reference,
+ s_RemoveOrgFromEndOfProtein(bioseq, sTaxname);
+
+ // bail if no title
+ if( (NULL == psTitle) || psTitle->empty() ) {
+ return;
+ }
+
+ // put title into a reference,
// just because it's more convenient than a pointer
string & sTitle = *psTitle;
// remember original so we can see if we changed it
@@ -6521,17 +6989,6 @@ void CNewCleanup_imp::x_CleanupECNumber( string &ec_num )
const string::size_type original_ec_num_length = ec_num.length();
NStr::TruncateSpacesInPlace( ec_num );
- // remove any final periods
- string::size_type last_non_period = ec_num.find_last_not_of(".");
- if( last_non_period == string::npos ) {
- if( ! ec_num.empty() ) {
- ec_num.clear();
- ChangeMade(CCleanupChange::eCleanECNumber);
- }
- return;
- }
- ec_num.resize( last_non_period + 1 );
-
// remove any unnecessary "EC " prefix
s_RemoveInitial( ec_num, "EC ", NStr::eNocase );
s_RemoveInitial( ec_num, "EC:", NStr::eNocase );
@@ -6566,11 +7023,26 @@ void CNewCleanup_imp::x_CleanupECNumberList( CProt_ref::TEc & ec_num_list )
CProt_ref::TEc::iterator next_ec_num_iter = ec_num_iter;
++next_ec_num_iter;
ec_num_list.insert( next_ec_num_iter, new_ec_num );
+ ChangeMade(CCleanupChange::eCleanECNumber);
}
}
}
}
+void CNewCleanup_imp::x_CleanupECNumberListEC( CProt_ref::TEc & ec_num_list )
+{
+ // CProt_ref::TEc is a list, so the iterator stays valid even if we
+ // add new entries after the current one
+ NON_CONST_ITERATE( CProt_ref::TEc, ec_num_iter, ec_num_list ) {
+ string & ec_num = *ec_num_iter;
+ size_t tlen = ec_num.length();
+ CleanVisStringJunk (ec_num);
+ if(tlen != ec_num.length()) {
+ ChangeMade(CCleanupChange::eCleanECNumber);
+ }
+ }
+}
+
void CNewCleanup_imp::x_CleanupAndRepairInference( string &inference )
{
if( inference.empty() ) {
@@ -6921,15 +7393,6 @@ static bool s_GbQualCompare (
const string& ql1 = GET_FIELD (gbq1, Qual);
const string& ql2 = GET_FIELD (gbq2, Qual);
- // legal quals first
- const bool is_illegal1 = s_IsIllegalQual(ql1);
- const bool is_illegal2 = s_IsIllegalQual(ql2);
- if( is_illegal1 && ! is_illegal2 ) {
- return false;
- } else if( ! is_illegal1 && is_illegal2 ) {
- return true;
- }
-
int comp = s_CompareNoCaseCStyle(ql1, ql2);
if (comp < 0) return true;
if (comp > 0) return false;
@@ -6942,6 +7405,30 @@ static bool s_GbQualCompare (
return false;
}
+static bool s_GbQualCompareLegalFirst (
+ const CRef<CGb_qual>& gb1,
+ const CRef<CGb_qual>& gb2
+)
+
+{
+ const CGb_qual& gbq1 = *(gb1);
+ const CGb_qual& gbq2 = *(gb2);
+
+ const string& ql1 = GET_FIELD (gbq1, Qual);
+ const string& ql2 = GET_FIELD (gbq2, Qual);
+
+ // legal quals first
+ const bool is_illegal1 = s_IsIllegalQual(ql1);
+ const bool is_illegal2 = s_IsIllegalQual(ql2);
+ if( is_illegal1 && ! is_illegal2 ) {
+ return false;
+ } else if( ! is_illegal1 && is_illegal2 ) {
+ return true;
+ }
+
+ return s_GbQualCompare(gb1, gb2);
+}
+
static bool s_GbQualEqual (
const CRef<CGb_qual>& gb1,
const CRef<CGb_qual>& gb2
@@ -7024,35 +7511,52 @@ bool s_SeqLocAnyNull( const CSeq_loc & loc )
return false;
}
-void CNewCleanup_imp::SeqfeatBC (
- CSeq_feat& sf
-)
-
+void CNewCleanup_imp::x_CleanSeqFeatQuals(CSeq_feat& sf)
{
- // note - need to clean up GBQuals before dbxrefs, because they may be converted to populate other fields
-
- // sort/unique gbquals
+ // clean before uniquing
+ EDIT_EACH_GBQUAL_ON_SEQFEAT(gbq_it, sf) {
+ CGb_qual& gbq = **gbq_it;
+ GBQualBC(gbq);
+ }
- if (! GBQUAL_ON_SEQFEAT_IS_SORTED (sf, s_GbQualCompare)) {
- SORT_GBQUAL_ON_SEQFEAT (sf, s_GbQualCompare);
- ChangeMade (CCleanupChange::eCleanQualifiers);
+ // sort/unique gbquals, just alphabetically
+ if (!GBQUAL_ON_SEQFEAT_IS_SORTED(sf, s_GbQualCompare)) {
+ SORT_GBQUAL_ON_SEQFEAT(sf, s_GbQualCompare);
+ ChangeMade(CCleanupChange::eCleanQualifiers);
}
- if (! GBQUAL_ON_SEQFEAT_IS_UNIQUE (sf, s_GbQualEqual)) {
- UNIQUE_GBQUAL_ON_SEQFEAT (sf, s_GbQualEqual);
- ChangeMade (CCleanupChange::eRemoveQualifier);
+ if (!GBQUAL_ON_SEQFEAT_IS_UNIQUE(sf, s_GbQualEqual)) {
+ UNIQUE_GBQUAL_ON_SEQFEAT(sf, s_GbQualEqual);
+ ChangeMade(CCleanupChange::eRemoveQualifier);
}
- EDIT_EACH_GBQUAL_ON_SEQFEAT (gbq_it, sf) {
+ // move quals to other parts of the feature as appropriate
+ EDIT_EACH_GBQUAL_ON_SEQFEAT(gbq_it, sf) {
CGb_qual& gbq = **gbq_it;
- GBQualBC(gbq);
- if( GBQualSeqFeatBC(gbq, sf) == eAction_Erase )
+ if (GBQualSeqFeatBC(gbq, sf) == eAction_Erase)
{
- ERASE_GBQUAL_ON_SEQFEAT (gbq_it, sf);
- ChangeMade (CCleanupChange::eRemoveQualifier);
+ ERASE_GBQUAL_ON_SEQFEAT(gbq_it, sf);
+ ChangeMade(CCleanupChange::eRemoveQualifier);
}
}
+ // sort again, putting legal qualifiers first
+ if (!GBQUAL_ON_SEQFEAT_IS_SORTED(sf, s_GbQualCompareLegalFirst)) {
+ SORT_GBQUAL_ON_SEQFEAT(sf, s_GbQualCompareLegalFirst);
+ ChangeMade(CCleanupChange::eCleanQualifiers);
+ }
+
+ REMOVE_IF_EMPTY_GBQUAL_ON_SEQFEAT(sf);
+}
+
+void CNewCleanup_imp::SeqfeatBC (
+ CSeq_feat& sf
+)
+
+{
+ // note - need to clean up GBQuals before dbxrefs, because they may be converted to populate other fields
+ x_CleanSeqFeatQuals(sf);
+
CLEAN_STRING_MEMBER (sf, Title);
if( FIELD_EQUALS( sf, Except, false ) ) {
@@ -7083,13 +7587,25 @@ void CNewCleanup_imp::SeqfeatBC (
vector< CRef< CDbtag > > new_dbtags;
EDIT_EACH_DBXREF_ON_SEQFEAT (dbx_it, sf) {
CDbtag& dbt = **dbx_it;
+ DbtagBC(dbt);
x_SplitDbtag(dbt, new_dbtags );
}
if( ! new_dbtags.empty() ) {
copy( new_dbtags.begin(), new_dbtags.end(), back_inserter(sf.SetDbxref()) );
}
+ // sort dbxrefs
+ if (!DBXREF_ON_SEQFEAT_IS_SORTED(sf, s_DbtagCompare)) {
+ SORT_DBXREF_ON_SEQFEAT(sf, s_DbtagCompare);
+ ChangeMade(CCleanupChange::eCleanDbxrefs);
+ }
+
+
CALL_IF_SET( PubSetBC, sf, Cit );
+
+ if (!CSeqFeatData::AllowStrandBoth(sf.GetData().GetSubtype())) {
+ x_BothStrandBC(sf.SetLocation());
+ }
}
void CNewCleanup_imp::x_PostSeqFeat( CSeq_feat& sf )
@@ -7103,15 +7619,7 @@ void CNewCleanup_imp::x_PostSeqFeat( CSeq_feat& sf )
}
// sort/unique gbquals (yes, must do before *and* after )
- if (! GBQUAL_ON_SEQFEAT_IS_SORTED (sf, s_GbQualCompare)) {
- SORT_GBQUAL_ON_SEQFEAT (sf, s_GbQualCompare);
- ChangeMade (CCleanupChange::eCleanQualifiers);
- }
- if (! GBQUAL_ON_SEQFEAT_IS_UNIQUE (sf, s_GbQualEqual)) {
- UNIQUE_GBQUAL_ON_SEQFEAT (sf, s_GbQualEqual);
- ChangeMade (CCleanupChange::eRemoveQualifier);
- }
- REMOVE_IF_EMPTY_GBQUAL_ON_SEQFEAT(sf);
+ x_CleanSeqFeatQuals(sf);
EDIT_EACH_DBXREF_ON_SEQFEAT (dbx_it, sf) {
CDbtag& dbt = **dbx_it;
@@ -7265,7 +7773,7 @@ void CNewCleanup_imp::GenerefBC (
EDIT_EACH_SYNONYM_ON_GENEREF (syn_itr, gr) {
string& syn = *syn_itr;
- if (NStr::EqualNocase (locus, syn)) {
+ if (NStr::Equal (locus, syn)) {
ERASE_SYNONYM_ON_GENEREF (syn_itr, gr);
ChangeMade (CCleanupChange::eChangeGeneRef);
}
@@ -7522,6 +8030,26 @@ void CNewCleanup_imp::GeneFeatBC (
}
}
+void CNewCleanup_imp::ProtNameBC ( std::string & str )
+{
+ const string::size_type old_length = str.length();
+ CleanVisStringJunk (str, true);
+ TrimInternalSemicolons (str);
+ if (str.length() != old_length) {
+ ChangeMade (CCleanupChange::eChangeProtNames);
+ }
+}
+
+void CNewCleanup_imp::ProtActivityBC ( std::string & str )
+{
+ const string::size_type old_length = str.length();
+ CleanVisStringJunk (str, true);
+ TrimInternalSemicolons (str);
+ if (str.length() != old_length) {
+ ChangeMade (CCleanupChange::eTrimSpaces);
+ }
+}
+
void CNewCleanup_imp::ProtrefBC (
CProt_ref& prot_ref
)
@@ -7534,13 +8062,9 @@ void CNewCleanup_imp::ProtrefBC (
}
CLEAN_STRING_MEMBER (prot_ref, Desc);
- if (CleanStringList (GET_MUTABLE (prot_ref, Name))) {
- ChangeMade (CCleanupChange::eChangeProtNames);
- }
REMOVE_IF_EMPTY_NAME_ON_PROTREF(prot_ref);
- CLEAN_STRING_LIST_JUNK (prot_ref, Ec);
- CLEAN_STRING_LIST (prot_ref, Activity);
+ CLEAN_STRING_LIST (prot_ref, Ec);
UNIQUE_WITHOUT_SORT_ACTIVITY_ON_PROTREF( prot_ref, PNocase );
@@ -7775,11 +8299,33 @@ static const TInTrSpElem sc_its_map[] = {
typedef CStaticArrayMap<string, string, PNocase> TInTrSpMap;
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TInTrSpMap, sc_ITSMap, sc_its_map);
-void CNewCleanup_imp::x_TranslateITSName( string &in_out_name )
+
+bool CNewCleanup_imp::IsInternalTranscribedSpacer(const string& name)
+{
+ if (NStr::EqualNocase(name, "internal transcribed spacer 1") ||
+ NStr::EqualNocase(name, "internal transcribed spacer 2") ||
+ NStr::EqualNocase(name, "internal transcribed spacer 3")) {
+ return true;
+ }
+ return false;
+}
+
+
+bool CNewCleanup_imp::TranslateITSName( string &in_out_name )
{
TInTrSpMap::const_iterator its_iter = sc_ITSMap.find(in_out_name);
if( its_iter != sc_ITSMap.end() ) {
in_out_name = its_iter->second;
+ return true;
+ } else {
+ return false;
+ }
+}
+
+
+void CNewCleanup_imp::x_TranslateITSNameAndFlag( string &in_out_name )
+{
+ if (TranslateITSName( in_out_name )) {
ChangeMade(CCleanupChange::eChangeITS);
}
}
@@ -7949,7 +8495,7 @@ void CNewCleanup_imp::RnarefBC (
case CRNA_ref::eType_other:
case CRNA_ref::eType_miscRNA:
{{
- x_TranslateITSName(name);
+ x_TranslateITSNameAndFlag(name);
// convert to RNA-gen
string name_copy; // copy because name is about to be destroyed
@@ -7987,12 +8533,6 @@ void CNewCleanup_imp::RnarefBC (
REMOVE_IF_EMPTY_CODON_ON_TRNAEXT(tRNA);
- if (! FIELD_IS_SET (tRNA, Aa) &&
- ! FIELD_IS_SET (tRNA, Codon) &&
- ! FIELD_IS_SET (tRNA, Anticodon)) {
- RESET_FIELD (rr, Ext);
- ChangeMade(CCleanupChange::eChangeRNAref);
- }
}
break;
case NCBI_RNAEXT(Gen):
@@ -8161,6 +8701,8 @@ void CNewCleanup_imp::x_GBQualToOrgRef( COrg_ref &org, CSeq_feat &seqfeat )
return;
}
+ bool any_conversions = false;
+
EDIT_EACH_GBQUAL_ON_SEQFEAT( qual_iter, seqfeat ) {
CGb_qual &gb_qual = **qual_iter;
if( FIELD_IS_SET(gb_qual, Qual) && FIELD_IS_SET(gb_qual, Val) ) {
@@ -8168,34 +8710,30 @@ void CNewCleanup_imp::x_GBQualToOrgRef( COrg_ref &org, CSeq_feat &seqfeat )
const string &val = GET_FIELD(gb_qual, Val);
// determine whether we should convert this gbqual into an orgmod
- bool do_gbqual_to_orgmod = false;
- TOrgModMap::const_iterator orgmod_it = s_FindInMapAsPrefix<TOrgModMap>( qual, sc_OrgModMap );
- if( orgmod_it != sc_OrgModMap.end() && orgmod_it->second != NCBI_ORGMOD(nat_host) ) {
- do_gbqual_to_orgmod = true;
- }
- if( ! do_gbqual_to_orgmod ) {
- TOrgModMap::const_iterator orgmodalias_it = s_FindInMapAsPrefix<TOrgModMap>( qual, sc_OrgModAliasMap );
- if( orgmodalias_it != sc_OrgModAliasMap.end() && orgmodalias_it->second != NCBI_ORGMOD(nat_host) ) {
- do_gbqual_to_orgmod = true;
- }
- }
- if( ! do_gbqual_to_orgmod ) {
- if( s_FindInMapAsPrefix<TSubsourceMap>( qual, sc_SubsourceMap) != sc_SubsourceMap.end() ||
- s_FindInMapAsPrefix<TSubsourceMap>( qual, sc_SubsourceAliasMap) != sc_SubsourceAliasMap.end() )
- {
- do_gbqual_to_orgmod = true;
- }
- }
+ string mod_val = qual + "=" + val;
+ size_t val_pos;
+ COrgMod::TSubtype ost;
+ CSubSource::TSubtype sst;
+ bool do_gbqual_to_orgmod =
+ s_StringHasOrgModPrefix(mod_val, val_pos, ost) ||
+ s_StringHasSubSourcePrefix(mod_val, val_pos, sst);
// if required, do the conversion
if( do_gbqual_to_orgmod ) {
- org.SetMod().push_back( qual + "=" + val );
+ org.SetMod().push_back( mod_val );
ERASE_GBQUAL_ON_SEQFEAT( qual_iter, seqfeat );
ChangeMade(CCleanupChange::eAddOrgMod);
ChangeMade(CCleanupChange::eRemoveQualifier);
+ any_conversions = true;
}
}
}
+ if (any_conversions) {
+ if (seqfeat.GetData().IsBiosrc()) {
+ x_ConvertOrgref_modToSubSource(seqfeat.SetData().SetBiosrc());
+ x_ConvertOrgref_modToOrgMod(seqfeat.SetData().SetBiosrc().SetOrg());
+ }
+ }
}
void CNewCleanup_imp::x_MoveSeqdescOrgToSourceOrg( CSeqdesc &seqdesc )
@@ -8215,9 +8753,29 @@ void CNewCleanup_imp::x_MoveSeqfeatOrgToSourceOrg( CSeq_feat &seqfeat )
CRef <COrg_ref> org ( &GET_MUTABLE(seqfeat.SetData(), Org) );
seqfeat.SetData().SetBiosrc().SetOrg(*org);
ChangeMade (CCleanupChange::eConvertFeature);
+ x_ConvertOrgref_modToSubSource(seqfeat.SetData().SetBiosrc());
+ x_ConvertOrgref_modToOrgMod(seqfeat.SetData().SetBiosrc().SetOrg());
+ }
+}
+
+
+void CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot( CBioseq_set &set )
+{
+ if (set.IsSetClass() && set.GetClass() == CBioseq_set::eClass_nuc_prot) {
+ CSeq_entry_Handle seh = m_Scope->GetSeq_entryHandle(*(set.GetParentEntry()));
+ SAnnotSelector sel(CSeqFeatData::e_Cdregion);
+ CFeat_CI fi(seh, sel);
+ while (fi) {
+ CSeq_feat_Handle fh = fi->GetSeq_feat_Handle();
+ if (feature::PromoteCDSToNucProtSet(fh)) {
+ ChangeMade (CCleanupChange::eMoveFeat);
+ }
+ ++fi;
+ }
}
}
+
void CNewCleanup_imp::x_CleanupStringMarkChanged( std::string &str )
{
if (CleanVisString (str)) {
@@ -8232,11 +8790,11 @@ void CNewCleanup_imp::x_CleanupStringJunkMarkChanged( std::string &str )
}
}
+
+
bool CNewCleanup_imp::x_CompressSpaces( string &str )
{
- bool rval = s_RegexpReplace( str, " [ ]+", " " );
- rval |= s_RegexpReplace( str, " ,", "," );
- return rval;
+ return Asn2gnbkCompressSpaces(str);
}
void CNewCleanup_imp::x_CompressStringSpacesMarkChanged( std::string &str )
@@ -8258,71 +8816,317 @@ void CNewCleanup_imp::x_ConvertDoubleQuotesMarkChanged( std::string &str )
}
}
-static void
-s_AddStringToUserField( CSeqdesc_Base::TUser& user, const char* field, const char *str )
+void CNewCleanup_imp::x_AddNcbiCleanupObject( CSeq_entry &seq_entry )
+{
+ // remove from lower levels
+ if (seq_entry.IsSet() && seq_entry.GetSet().IsSetSeq_set()) {
+ NON_CONST_ITERATE(CBioseq_set::TSeq_set, it, seq_entry.SetSet().SetSeq_set()) {
+ CCleanup::RemoveNcbiCleanupObject(**it);
+ }
+ }
+
+ // update existing
+ if (seq_entry.IsSetDescr()) {
+ NON_CONST_ITERATE(CBioseq::TDescr::Tdata, it, seq_entry.SetDescr().Set()) {
+ if ((*it)->IsUser() && (*it)->GetUser().GetObjectType() == CUser_object::eObjectType_Cleanup) {
+ (*it)->SetUser().UpdateNcbiCleanup(NCBI_CLEANUP_VERSION);
+ ChangeMade(CCleanupChange::eAddNcbiCleanupObject);
+ return;
+ }
+ }
+ }
+ // create new
+ CRef<CSeqdesc> ncbi_cleanup_object( new CSeqdesc );
+ CSeqdesc_Base::TUser& user = ncbi_cleanup_object->SetUser();
+ user.UpdateNcbiCleanup(NCBI_CLEANUP_VERSION);
+ seq_entry.SetDescr().Set().push_back( ncbi_cleanup_object );
+
+ ChangeMade(CCleanupChange::eAddNcbiCleanupObject);
+}
+
+static
+string
+s_GetMiRNAProduct( const string &name )
+{
+ if ( NStr::StartsWith(name, "miRNA ") ) {
+ return name.substr(6);
+ } else if ( NStr::StartsWith(name, "microRNA ") ) {
+ return name.substr(9);
+ } else {
+ if ( NStr::EndsWith(name, " miRNA") &&
+ ! NStr::EndsWith(name, "precursor miRNA") )
+ {
+ return name.substr(0, name.length() - 6);
+ }
+ else if ( NStr::EndsWith( name, " microRNA") &&
+ ! NStr::EndsWith(name, "precursor microRNA") )
+ {
+ return name.substr(0, name.length() - 9 );
+ }
+ }
+ return kEmptyStr;
+}
+
+bool s_FixRNAOtherByName(CSeq_feat& feat)
+{
+ if (!feat.IsSetData() || !feat.GetData().IsRna()) {
+ return false;
+ }
+
+ CRNA_ref& rna = feat.SetData().SetRna();
+ if (!rna.IsSetType() ||
+ rna.GetType() != CRNA_ref::eType_other ||
+ !rna.IsSetExt() ||
+ !rna.GetExt().IsName()) {
+ return false;
+ }
+
+ string rna_name = rna.GetExt().GetName();
+
+ bool any_change = false;
+
+ string miRNAproduct;
+ if (s_IsNcrnaName(rna_name))
+ {
+ rna.SetType(CRNA_ref::eType_ncRNA);
+ rna.SetExt().SetGen().SetClass(rna_name);
+ any_change = true;
+ } else if (NStr::Equal(rna_name, "ncRNA")) {
+ rna.ResetExt();
+ rna.SetType(CRNA_ref::eType_ncRNA);
+ any_change = true;
+ } else if (!(miRNAproduct = s_GetMiRNAProduct(rna_name)).empty())
+ {
+ rna.SetType(CRNA_ref::eType_ncRNA);
+ rna.SetExt().SetGen().SetClass("miRNA");
+ rna.SetExt().SetGen().SetProduct(miRNAproduct);
+ any_change = true;
+ } else if (NStr::Equal(rna_name, "tmRNA")) {
+ rna.SetType(CRNA_ref::eType_tmRNA);
+ any_change = true;
+ } else if (NStr::Equal(rna_name, "misc_RNA")) {
+ string remainder;
+ rna.SetRnaProductName("", remainder);
+ any_change = true;
+ }
+ return any_change;
+}
+
+bool s_FixncRNA(CSeq_feat& feat)
{
- CRef< CUser_field > new_field( new CUser_field );
+ if (!feat.IsSetData() || !feat.GetData().IsRna()) {
+ return false;
+ }
+
+ bool any_change = false;
+ CRNA_ref& rna = feat.SetData().SetRna();
+ const CRNA_ref_Base::TType rna_type =
+ (rna.IsSetType() ? rna.GetType() : NCBI_RNAREF(unknown));
+
+ switch (rna_type) {
+ case CRNA_ref::eType_snRNA:
+ case CRNA_ref::eType_scRNA:
+ case CRNA_ref::eType_snoRNA:
+ {{
+
+ string rna_type_name = CRNA_ref::GetRnaTypeName(rna_type);
+ if (rna.IsSetExt() && rna.GetExt().IsName() &&
+ !NStr::EqualNocase(rna.GetExt().GetName(), rna_type_name))
+ {
+ string rna_product = rna.GetExt().GetName();
+ rna.SetExt().SetGen().SetProduct(rna_product);
+ }
+ rna.SetType(CRNA_ref::eType_ncRNA);
+ rna.SetExt().SetGen().SetClass(rna_type_name);
+ any_change = true;
+ break;
+ }}
+ default:
+ break;
+ }
+
+ if (feat.IsSetQual() &&
+ (rna_type == CRNA_ref::eType_ncRNA ||
+ rna_type == NCBI_RNAREF(other))) {
+ CSeq_feat::TQual::iterator qual_iter = feat.SetQual().begin();
+ while (qual_iter != feat.SetQual().end()) {
+ string &qual = (*qual_iter)->SetQual();
+ string &val = (*qual_iter)->SetVal();
+ if (qual == "ncRNA_class") {
+ string product = rna.GetRnaProductName();
+ rna.SetType(CRNA_ref::eType_ncRNA);
+ rna.SetExt().SetGen().SetClass(val);
+ if (!NStr::IsBlank(product)) {
+ string remainder;
+ rna.SetRnaProductName(product, remainder);
+ }
+ any_change = true;
+ qual_iter = feat.SetQual().erase(qual_iter);
+ }
+ else {
+ ++qual_iter;
+ }
+ }
+ if (feat.SetQual().empty()) {
+ feat.ResetQual();
+ }
+ }
+
+ if (rna_type == NCBI_RNAREF(ncRNA) && rna.IsSetExt() &&
+ rna.GetExt().IsGen() && rna.GetExt().GetGen().IsSetClass() &&
+ NStr::EqualNocase(rna.GetExt().GetGen().GetClass(), "antisense"))
+ {
+ rna.SetExt().SetGen().SetClass("antisense_RNA");
+ any_change = true;
+ }
+
+ if (rna_type == NCBI_RNAREF(ncRNA)) {
+ string product_name = rna.GetRnaProductName();
+ if (NStr::Equal(product_name, "ncRNA")) {
+ string remainder;
+ rna.SetRnaProductName("", remainder);
+ any_change = true;
+ }
+ }
+ return any_change;
+}
- new_field->SetLabel().SetStr( field );
- new_field->SetData().SetStr( CUtf8::AsUTF8(str, eEncoding_Ascii) );
+bool s_FixtmRNA(CSeq_feat& feat)
+{
+ if (!feat.IsSetData() || !feat.GetData().IsRna()) {
+ return false;
+ }
- user.SetData().push_back( new_field );
+ bool any_change = false;
+ CRNA_ref& rna = feat.SetData().SetRna();
+
+ CRNA_ref::TType rna_type = (rna.IsSetType() ? rna.GetType() : CRNA_ref::eType_unknown);
+
+ string product = rna.GetRnaProductName();
+
+ if (feat.IsSetQual() &&
+ (rna_type == CRNA_ref::eType_other ||
+ rna_type == CRNA_ref::eType_tmRNA ||
+ rna_type == CRNA_ref::eType_ncRNA)) {
+ CSeq_feat::TQual::iterator qual_iter = feat.SetQual().begin();
+ while (qual_iter != feat.SetQual().end()) {
+ string &qual = (*qual_iter)->SetQual();
+ string &val = (*qual_iter)->SetVal();
+ if (qual == "tag_peptide") {
+ if (rna_type == CRNA_ref::eType_other) {
+ rna.SetType(CRNA_ref::eType_tmRNA);
+ }
+ CRef<CRNA_qual> rna_qual(new CRNA_qual);
+ rna_qual->SetQual(qual);
+ rna_qual->SetVal(val);
+ rna.SetExt().SetGen().SetQuals().Set().push_back(rna_qual);
+ any_change = true;
+ qual_iter = feat.SetQual().erase(qual_iter);
+ } else if (qual == "ncRNA_class" && rna_type == CRNA_ref::eType_tmRNA) {
+ rna.SetExt().SetGen().SetClass(val);
+ any_change = true;
+ qual_iter = feat.SetQual().erase(qual_iter);
+ } else {
+ ++qual_iter;
+ }
+ }
+ if (feat.SetQual().empty()) {
+ feat.ResetQual();
+ }
+ }
+ if (any_change) {
+ string remainder;
+ rna.SetRnaProductName(product, remainder);
+ }
+ if (rna_type == NCBI_RNAREF(tmRNA)) {
+ string product_name = rna.GetRnaProductName();
+ if (NStr::Equal(product_name, "tmRNA")) {
+ string remainder;
+ rna.SetRnaProductName("", remainder);
+ any_change = true;
+ }
+ }
+ return any_change;
}
-static void
-s_AddIntegerToUserField
-( CSeqdesc_Base::TUser& user, const char* field, int num )
-{
- CRef< CUser_field > new_field( new CUser_field );
+bool CNewCleanup_imp::x_FixMiscRNA(CSeq_feat& feat)
+{
+ if (!feat.IsSetData() || !feat.GetData().IsRna()) {
+ return false;
+ }
+
+ bool any_change = false;
+ CRNA_ref& rna = feat.SetData().SetRna();
+ if (!rna.IsSetType() || (rna.GetType() != CRNA_ref::eType_other && rna.GetType() != CRNA_ref::eType_miscRNA)) {
+ return false;
+ }
+
+ if (rna.GetType() == CRNA_ref::eType_other) {
+ rna.SetType(CRNA_ref::eType_miscRNA);
+ any_change = true;
+ }
- new_field->SetLabel().SetStr( field );
- new_field->SetData().SetInt(num);
+ if (rna.IsSetExt() && rna.GetExt().IsName()) {
+ string rna_name = rna.SetExt().SetName();
+ if (rna_name != "ncRNA" &&
+ rna_name != "tmRNA" &&
+ rna_name != "misc_RNA")
+ {
+ rna.SetExt().SetGen().SetProduct(rna_name);
+ any_change = true;
+ }
+ }
- user.SetData().push_back( new_field );
+ if (feat.IsSetQual())
+ {
+ CSeq_feat::TQual::iterator qual_iter = feat.SetQual().begin();
+ while (qual_iter != feat.SetQual().end()) {
+ string &qual = (*qual_iter)->SetQual();
+ string &val = (*qual_iter)->SetVal();
+ if (qual == "product") {
+ // e.g. "its1" to "internal transcribed spacer 1"
+ CNewCleanup_imp::TranslateITSName(val);
+ rna.SetExt().SetGen().SetProduct(val);
+ any_change = true;
+ qual_iter = feat.SetQual().erase(qual_iter);
+ }
+ else {
+ ++qual_iter;
+ }
+ }
+ }
+ return any_change;
}
-void CNewCleanup_imp::x_AddNcbiCleanupObject( CSeq_entry &seq_entry )
-{
- CRef<CSeqdesc> ncbi_cleanup_object( new CSeqdesc );
- CSeqdesc_Base::TUser& user = ncbi_cleanup_object->SetUser();
- user.SetType().SetStr("NcbiCleanup");
+void CNewCleanup_imp::x_ModernizeRNAFeat(CSeq_feat& feat)
+{
+ if (!feat.IsSetData() || !feat.GetData().IsRna()) {
+ return;
+ }
- s_AddStringToUserField( user, "method", "ExtendedSeqEntryCleanup" );
- s_AddIntegerToUserField( user, "version", NCBI_CLEANUP_VERSION );
-
- // get current time
- CTime curr_time( CTime::eCurrent );
- s_AddIntegerToUserField( user, "month", curr_time.Month() );
- s_AddIntegerToUserField( user, "day", curr_time.Day() );
- s_AddIntegerToUserField( user, "year", curr_time.Year() );
+ if (s_FixRNAOtherByName(feat)) {
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
+ if (s_FixncRNA(feat)) {
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
+ if (s_FixtmRNA(feat)) {
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
+ if (x_FixMiscRNA(feat)) {
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
- seq_entry.SetDescr().Set().push_back( ncbi_cleanup_object );
- ChangeMade(CCleanupChange::eAddNcbiCleanupObject);
}
-static
-string
-s_GetMiRNAProduct( const string &name )
+static bool s_IsEmpty(const CTrna_ext& trna)
{
- if ( NStr::StartsWith(name, "miRNA ") ) {
- return name.substr(6);
- } else if ( NStr::StartsWith(name, "microRNA ") ) {
- return name.substr(9);
- } else {
- if ( NStr::EndsWith(name, " miRNA") &&
- ! NStr::EndsWith(name, "precursor miRNA") )
- {
- return name.substr(0, name.length() - 6);
- }
- else if ( NStr::EndsWith( name, " microRNA") &&
- ! NStr::EndsWith(name, "precursor microRNA") )
- {
- return name.substr(0, name.length() - 9 );
- }
- }
- return kEmptyStr;
+ if (trna.IsSetAa()) return false;
+ if (trna.IsSetCodon() && trna.GetCodon().size() > 0) return false;
+ if (trna.IsSetAnticodon()) return false;
+ return true;
}
void CNewCleanup_imp::RnaFeatBC (
@@ -8331,6 +9135,10 @@ void CNewCleanup_imp::RnaFeatBC (
)
{
+ if (!rna.IsSetType() || rna.GetType() == CRNA_ref::eType_unknown) {
+ rna.SetType(CRNA_ref::eType_other);
+ ChangeMade(CCleanupChange::eChangeRNAref);
+ }
// move rna.pseudo to feat.pseudo
if ( FIELD_IS_SET(rna, Pseudo) ) {
SET_FIELD(seq_feat, Pseudo, true);
@@ -8434,12 +9242,25 @@ void CNewCleanup_imp::RnaFeatBC (
if( FIELD_EQUALS( rna, Type, NCBI_RNAREF(other)) ||
FIELD_EQUALS( rna, Type, NCBI_RNAREF(miscRNA) ) )
{
- if( FIELD_IS_SET_AND_IS(rna, Ext, Name) ) {
- x_TranslateITSName( GET_MUTABLE(rna.SetExt(), Name) );
- } else if( FIELD_IS_SET(rna, Ext) && FIELD_IS( rna.GetExt(), Gen) &&
- FIELD_IS_SET(rna.GetExt().GetGen(), Product) )
- {
- x_TranslateITSName( rna.SetExt().SetGen().SetProduct() );
+
+ if ( !rna.IsSetExt()) {
+ if ( seq_feat.IsSetComment() &&
+ (IsInternalTranscribedSpacer(seq_feat.GetComment()) ||
+ TranslateITSName(seq_feat.SetComment()))) {
+ rna.SetExt().SetName(seq_feat.GetComment());
+ seq_feat.ResetComment();
+ ChangeMade(CCleanupChange::eChangeITS);
+ }
+ } else if (rna.GetExt().IsName()) {
+ if (IsInternalTranscribedSpacer(rna.GetExt().GetName()) ||
+ TranslateITSName(rna.SetExt().SetName())) {
+ rna.SetExt().SetName(rna.GetExt().GetName());
+ ChangeMade(CCleanupChange::eChangeITS);
+ }
+ } else if (rna.GetExt().IsGen() && rna.GetExt().GetGen().IsSetProduct()) {
+ if (TranslateITSName(rna.SetExt().SetGen().SetProduct())) {
+ ChangeMade(CCleanupChange::eChangeITS);
+ }
}
}
@@ -8505,150 +9326,17 @@ void CNewCleanup_imp::RnaFeatBC (
}
}
- // this part is like C's ConvertToNcRNA
- {
- const CRNA_ref_Base::TType rna_type =
- ( rna.IsSetType() ? rna.GetType() : NCBI_RNAREF(unknown) );
- if (rna_type == NCBI_RNAREF(snRNA) ||
- rna_type == NCBI_RNAREF(scRNA) ||
- rna_type == NCBI_RNAREF(snoRNA) )
- {
- if (rna_type == NCBI_RNAREF(snRNA)) {
- x_AddNonCopiedQual ( seq_feat.SetQual(), "ncRNA_class", "snRNA");
- } else if (rna_type == NCBI_RNAREF(scRNA)) {
- x_AddNonCopiedQual ( seq_feat.SetQual(), "ncRNA_class", "scRNA");
- } else if (rna_type == NCBI_RNAREF(snoRNA)) {
- x_AddNonCopiedQual ( seq_feat.SetQual(), "ncRNA_class", "snoRNA");
- }
- if ( rna.IsSetExt() && rna.GetExt().IsName() )
- {
- x_AddNonCopiedQual (seq_feat.SetQual(), "product", rna.GetExt().GetName().c_str() );
- }
- rna.SetExt().SetName("ncRNA");
- rna.SetType( NCBI_RNAREF(other) );
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- else if (rna_type == NCBI_RNAREF(other) && rna.IsSetExt() && rna.GetExt().IsName() )
- {
- string &rna_name = rna.SetExt().SetName();
- string miRNAproduct;
- if (s_IsNcrnaName(rna.GetExt().GetName()))
- {
- x_AddNonCopiedQual (seq_feat.SetQual(), "ncRNA_class", rna_name.c_str() );
- rna.SetExt().SetName("ncRNA");
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- else if ( ! (miRNAproduct = s_GetMiRNAProduct (rna_name)).empty() )
- {
- x_AddNonCopiedQual ( seq_feat.SetQual(), "ncRNA_class", "miRNA");
- rna_name = "ncRNA";
- x_AddNonCopiedQual ( seq_feat.SetQual(), "product", miRNAproduct.c_str() );
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- else if (
- rna_name != "ncRNA" &&
- rna_name != "tmRNA" &&
- rna_name != "misc_RNA" )
- {
- x_AddNonCopiedQual ( seq_feat.SetQual(), "product", rna_name.c_str() );
- rna_name = "misc_RNA";
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- }
- if (rna_type == NCBI_RNAREF(other) && ! rna.IsSetExt() ) {
- rna.SetExt().SetName( "misc_RNA" );
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- if (rna_type == NCBI_RNAREF(other) && rna.IsSetExt() && rna.GetExt().IsName() &&
- rna.GetExt().GetName() == "misc_RNA" )
- {
- NON_CONST_ITERATE( CSeq_feat::TQual, qual_iter, seq_feat.SetQual() ) {
- string &qual = (*qual_iter)->SetQual();
- if ( qual == "ncRNA_class" ) {
- rna.SetExt().SetName( "ncRNA" );
- ChangeMade( CCleanupChange::eChangeRNAref );
- } else if ( qual == "tag_peptide") {
- rna.SetExt().SetName( "tmRNA" );
- ChangeMade( CCleanupChange::eChangeRNAref );
- } else if ( qual == "product" ) {
- // e.g. "its1" to "internal transcribed spacer 1"
- x_TranslateITSName( (*qual_iter)->SetVal() );
- }
- }
- }
- }
-
- // This part is like C's FixncRNAClass
- {
- const CRNA_ref_Base::TType rna_type =
- ( rna.IsSetType() ? rna.GetType() : NCBI_RNAREF(unknown) );
- if( rna_type == NCBI_RNAREF(ncRNA) && rna.IsSetExt() &&
- rna.GetExt().IsGen() && rna.GetExt().GetGen().IsSetClass() &&
- NStr::EqualNocase( rna.GetExt().GetGen().GetClass(), "antisense") )
- {
- rna.SetExt().SetGen().SetClass("antisense_RNA");
- }
+ // if not tRNA and ext is tRNA and tRNA is empty, remove ext.tRNA
+ if (rna.IsSetType() &&
+ (rna.GetType() == CRNA_ref::eType_mRNA || rna.GetType() == CRNA_ref::eType_rRNA) &&
+ rna.IsSetExt() && rna.GetExt().IsTRNA() &&
+ s_IsEmpty(rna.GetExt().GetTRNA())) {
+ rna.ResetExt();
+ ChangeMade(CCleanupChange::eChangeRNAref);
}
- // this part is like C's ModernizeRNAFields
- const CRNA_ref_Base::TType rna_type =
- ( rna.IsSetType() ? rna.GetType() : NCBI_RNAREF(unknown) );
- if( rna_type == NCBI_RNAREF(other) && rna.IsSetExt() && rna.GetExt().IsName() )
- {
- const string &name = rna.GetExt().GetName();
- bool need_qual_cleanup = true;
- if( name == "ncRNA" ) {
- SET_FIELD(rna, Type, NCBI_RNAREF(ncRNA) );
- ChangeMade( CCleanupChange::eChangeRNAref );
- } else if( name == "tmRNA" ) {
- SET_FIELD(rna, Type, NCBI_RNAREF(tmRNA) );
- ChangeMade( CCleanupChange::eChangeRNAref );
- } else if( name == "misc_RNA" ) {
- SET_FIELD(rna, Type, NCBI_RNAREF(miscRNA) );
- ChangeMade( CCleanupChange::eChangeRNAref );
- } else {
- need_qual_cleanup = false;
- }
-
- if( need_qual_cleanup ) {
- const string name_copy = name; // we're about to destroy name
- CRNA_gen& rna_gen = rna.SetExt().SetGen();
-
- if( seq_feat.IsSetQual() ) {
- vector< CRef< CGb_qual > > new_qual_vec;
- vector< CRef< CGb_qual > > &qual_vec = GET_MUTABLE(seq_feat, Qual);
- NON_CONST_ITERATE( vector< CRef< CGb_qual > >, qual_iter, qual_vec ) {
- const string &qual = ( (*qual_iter)->IsSetQual() ? (*qual_iter)->GetQual() : kEmptyStr );
- const string &val = ( (*qual_iter)->IsSetVal() ? (*qual_iter)->GetVal() : kEmptyStr );
- if ( qual == "ncRNA_class" ) {
- rna_gen.SetClass( val );
- } else if (qual == "product") {
- rna_gen.SetProduct( val );
- } else if ( qual == "tag_peptide") {
- CRef<CRNA_qual> rna_qual( new CRNA_qual );
- rna_qual->SetQual( qual );
- rna_qual->SetVal( val );
-
- rna_gen.SetQuals().Set().push_back( rna_qual );
- } else {
- // keep this one
- new_qual_vec.push_back( *qual_iter );
- }
- }
-
- // update qual vec if changed
- if( new_qual_vec.empty() ) {
- seq_feat.ResetQual();
- ChangeMade( CCleanupChange::eRemoveQualifier );
- } else if( new_qual_vec.size() != qual_vec.size() ) {
- seq_feat.SetQual().swap( new_qual_vec );
- ChangeMade( CCleanupChange::eChangeQualifiers );
- }
- }
+ x_ModernizeRNAFeat(seq_feat);
- ChangeMade( CCleanupChange::eChangeRNAref );
- }
- }
}
class CCodeBreakCompare
@@ -8706,7 +9394,7 @@ public:
const CSeq_loc &loc1 = GET_FIELD(*break1, Loc);
const CSeq_loc &loc2 = GET_FIELD(*break2, Loc);
- if( sequence::eSame != sequence::Compare( loc1, loc2, &*m_Scope ) ) {
+ if( sequence::eSame != sequence::Compare(loc1, loc2, &*m_Scope, sequence::fCompareOverlapping) ) {
return false;
}
@@ -9068,6 +9756,7 @@ void CNewCleanup_imp::UserObjectBC( CUser_object &user_object )
SWITCH_ON_USERFIELD_CHOICE(user_field) {
case NCBI_USERFIELD(Str):
+ x_CompressStringSpacesMarkChanged( user_field.SetData().SetStr() );
x_CleanupStringMarkChanged( user_field.SetData().SetStr() );
break;
case NCBI_USERFIELD(Object):
@@ -9082,6 +9771,7 @@ void CNewCleanup_imp::UserObjectBC( CUser_object &user_object )
break;
case NCBI_USERFIELD(Strs):
NON_CONST_ITERATE( CUser_field::C_Data::TStrs, str_iter, user_field.SetData().SetStrs() ) {
+ x_CompressStringSpacesMarkChanged( *str_iter );
x_CleanupStringMarkChanged( *str_iter );
}
break;
@@ -9134,6 +9824,8 @@ public:
void CNewCleanup_imp::x_PCRPrimerSetBC( CPCRPrimerSet &primer_set )
{
+ CPCRPrimer *last = NULL;
+
EDIT_EACH_PCRPRIMER_IN_PCRPRIMERSET( primer_iter, primer_set ) {
CPCRPrimer &primer = **primer_iter;
@@ -9155,6 +9847,7 @@ void CNewCleanup_imp::x_PCRPrimerSetBC( CPCRPrimerSet &primer_set )
string &name = GET_MUTABLE(primer, Name).Set();
const string before = name;
x_CleanupStringMarkChanged(name);
+ x_CompressStringSpacesMarkChanged(name);
if( before != name ) {
ChangeMade(CCleanupChange::eChangePCRPrimers);
}
@@ -9164,9 +9857,30 @@ void CNewCleanup_imp::x_PCRPrimerSetBC( CPCRPrimerSet &primer_set )
}
}
+ if (last != NULL) {
+ CPCRPrimer &lastprimer = *last;
+ if (FIELD_IS_SET(lastprimer, Name) && FIELD_IS_SET(primer, Name)) {
+ string &name1 = GET_MUTABLE(lastprimer, Name).Set();
+ string &name2 = GET_MUTABLE(primer, Name).Set();
+ if (NStr::EqualNocase(name1, name2)) {
+ if (! FIELD_IS_SET(lastprimer, Seq)) {
+ SET_FIELD(lastprimer, Seq, GET_FIELD(primer, Seq) );
+ RESET_FIELD(primer, Name);
+ RESET_FIELD(primer, Seq);
+ ChangeMade(CCleanupChange::eChangePCRPrimers);
+ } else if (! FIELD_IS_SET(primer, Seq)) {
+ RESET_FIELD(primer, Name);
+ ChangeMade(CCleanupChange::eChangePCRPrimers);
+ }
+ }
+ }
+ }
+
if( ! FIELD_IS_SET(primer, Name) && ! FIELD_IS_SET(primer, Seq) ) {
ERASE_PCRPRIMER_IN_PCRPRIMERSET(primer_iter, primer_set);
ChangeMade(CCleanupChange::eChangePCRPrimers);
+ } else {
+ last = *primer_iter;
}
}
@@ -9312,6 +10026,22 @@ void CNewCleanup_imp::x_PostProcessing(void)
}
+void CNewCleanup_imp::x_ClearEmptyDescr( CBioseq_set& bioseq_set )
+{
+ if (bioseq_set.IsSetDescr() && bioseq_set.GetDescr().Get().empty()) {
+ bioseq_set.ResetDescr();
+ }
+}
+
+
+void CNewCleanup_imp::x_ClearEmptyDescr( CBioseq& bioseq )
+{
+ if (bioseq.IsSetDescr() && bioseq.GetDescr().Get().empty()) {
+ bioseq.ResetDescr();
+ }
+}
+
+
void CNewCleanup_imp::x_NotePubdescOrAnnotPubs(
const CPub_equiv &pub_equiv )
{
@@ -9539,64 +10269,11 @@ void CNewCleanup_imp::x_DecodeXMLMarkChanged( std::string & str )
}
}
-// maps the type of seqdesc to the order it should be in
-// (lowest to highest)
-typedef SStaticPair<CSeqdesc::E_Choice, int> TSeqdescOrderElem;
-static const TSeqdescOrderElem sc_seqdesc_order_map[] = {
- // Note that ordering must match ordering
- // in CSeqdesc::E_Choice
- { CSeqdesc::e_Mol_type, 13 },
- { CSeqdesc::e_Modif, 14 },
- { CSeqdesc::e_Method, 15 },
- { CSeqdesc::e_Name, 7 },
- { CSeqdesc::e_Title, 1 },
- { CSeqdesc::e_Org, 16 },
- { CSeqdesc::e_Comment, 6 },
- { CSeqdesc::e_Num, 11 },
- { CSeqdesc::e_Maploc, 9 },
- { CSeqdesc::e_Pir, 18 },
- { CSeqdesc::e_Genbank, 22 },
- { CSeqdesc::e_Pub, 5 },
- { CSeqdesc::e_Region, 10 },
- { CSeqdesc::e_User, 8 },
- { CSeqdesc::e_Sp, 17 },
- { CSeqdesc::e_Dbxref, 12 },
- { CSeqdesc::e_Embl, 21 },
- { CSeqdesc::e_Create_date, 24 },
- { CSeqdesc::e_Update_date, 25 },
- { CSeqdesc::e_Prf, 19 },
- { CSeqdesc::e_Pdb, 20 },
- { CSeqdesc::e_Het, 4 },
- { CSeqdesc::e_Source, 2 },
- { CSeqdesc::e_Molinfo, 3 },
- { CSeqdesc::e_Modelev, 23 }
-};
-typedef CStaticPairArrayMap<CSeqdesc::E_Choice, int> TSeqdescOrderMap;
-DEFINE_STATIC_ARRAY_MAP(TSeqdescOrderMap, sc_SeqdescOrderMap, sc_seqdesc_order_map);
-
-static
-int s_SeqDescToOrdering( const CRef<CSeqdesc> &desc ) {
- // ordering assigned to unknown
- const int unknown_seqdesc = (1 + sc_SeqdescOrderMap.size());
-
- TSeqdescOrderMap::const_iterator find_iter = sc_SeqdescOrderMap.find(desc->Which());
- if( find_iter == sc_SeqdescOrderMap.end() ) {
- return unknown_seqdesc;
- }
-
- return find_iter->second;
-}
-
-static
-bool s_SeqDescLessThan( const CRef<CSeqdesc> &desc1, const CRef<CSeqdesc> &desc2 )
-{
- return ( s_SeqDescToOrdering(desc1) < s_SeqDescToOrdering(desc2) );
-}
void CNewCleanup_imp::x_SortSeqDescs( CSeq_entry & seq_entry )
{
- if( ! SEQDESC_ON_SEQENTRY_IS_SORTED(seq_entry, s_SeqDescLessThan) ) {
- SORT_SEQDESC_ON_SEQENTRY(seq_entry, s_SeqDescLessThan);
+ if (seq_entry.IsSetDescr() &&
+ CCleanup::NormalizeDescriptorOrder(seq_entry.SetDescr())) {
ChangeMade( CCleanupChange::eMoveDescriptor );
}
}
@@ -9829,6 +10506,37 @@ void CNewCleanup_imp::x_RemoveEmptyUserObject( CSeq_descr & seq_descr )
}
}
+void CNewCleanup_imp::x_CleanupGenbankBlock( CSeq_descr & seq_descr )
+{
+ EDIT_EACH_SEQDESC_ON_SEQDESCR( descr_iter, seq_descr ) {
+ CSeqdesc &desc = **descr_iter;
+ if( ! FIELD_IS(desc, Genbank) ) {
+ continue;
+ }
+
+ CGB_block& gb = desc.SetGenbank();
+
+ if (gb.IsSetTaxonomy()) {
+ gb.ResetTaxonomy();
+ ChangeMade(CCleanupChange::eChangeOther);
+ }
+
+ // remove empty GenBank blocks
+ if (!gb.IsSetExtra_accessions() &&
+ !gb.IsSetSource() &&
+ !gb.IsSetKeywords() &&
+ !gb.IsSetOrigin() &&
+ !gb.IsSetDate() &&
+ !gb.IsSetEntry_date() &&
+ !gb.IsSetDiv()) {
+
+ ERASE_SEQDESC_ON_SEQDESCR(descr_iter, seq_descr);
+ ChangeMade(CCleanupChange::eRemoveDescriptor);
+ }
+ }
+
+}
+
bool CNewCleanup_imp::x_ShouldRemoveEmptyGene(CGene_ref& gene)
{
bool should_remove = false;
@@ -10113,14 +10821,7 @@ bool CNewCleanup_imp::x_IsDBLinkUserObj( const CSeqdesc & desc )
if( ! desc.IsUser() ) {
return false;
}
-
- const CUser_object & user_obj = desc.GetUser();
-
- if( ! FIELD_IS_SET_AND_IS(user_obj, Type, Str) ) {
- return false;
- }
-
- return ( user_obj.GetType().GetStr() == "DBLink" );
+ return (desc.GetUser().GetObjectType() == CUser_object::eObjectType_DBLink);
}
// neg for "<", 0 for "==", and pos for ">"
@@ -10141,7 +10842,7 @@ static int s_PcrPrimerSetCompare( const CPCRPrimerSet &s1, const CPCRPrimerSet &
// smaller first
if( primer_set_1.size() != primer_set_2.size() ) {
- return (primer_set_1.size() - primer_set_2.size());
+ return int(primer_set_1.size()) - int(primer_set_2.size());
}
// find so we can compare
@@ -10178,10 +10879,14 @@ public:
}
}
+ if( r1->IsSetReverse() != r2->IsSetReverse() ) {
+ // note where the "!" operator is and isn't
+ return ! r1->IsSetReverse() && r2->IsSetReverse();
+ }
if( ! r1->IsSetReverse() && ! r2->IsSetReverse() ) {
// note where the "!" operator is and isn't
return ! r1->IsSetReverse() && r2->IsSetReverse();
- }
+ }
return ( s_PcrPrimerSetCompare( r1->GetReverse(), r2->GetReverse() ) < 0 );
}
@@ -10232,6 +10937,269 @@ void CNewCleanup_imp::MolInfoBC( CMolInfo &molinfo )
}
}
+void CNewCleanup_imp::CreateMissingMolInfo( CBioseq& seq )
+{
+ if (seq.IsSetInst() && seq.GetInst().IsSetMol()) {
+ bool is_product = false;
+ CBioseq_Handle bsh = m_Scope->GetBioseqHandle(seq);
+ CBioseq_set_Handle p = bsh.GetParentBioseq_set();
+ if (p && p.IsSetClass() && p.GetClass() == CBioseq_set::eClass_nuc_prot) {
+ p = p.GetParentBioseq_set();
+ }
+ if (p && p.IsSetClass() && p.GetClass() == CBioseq_set::eClass_gen_prod_set) {
+ if (seq.IsAa() && sequence::GetCDSForProduct(seq, m_Scope) != NULL) {
+ is_product = true;
+ } else if (seq.GetInst().GetMol() == CSeq_inst::eMol_rna &&
+ sequence::GetmRNAForProduct(seq, m_Scope) != NULL) {
+ is_product = true;
+ }
+ }
+ if (CCleanup::AddMissingMolInfo(seq, is_product)) {
+ ChangeMade(CCleanupChange::eChangeMolInfo);
+ }
+ }
+}
+
+
+void CNewCleanup_imp::AddProteinTitles(CBioseq& seq)
+{
+ if (!(m_Options & CCleanup::eClean_NoProteinTitles)) {
+ CBioseq_Handle bsh = m_Scope->GetBioseqHandle(seq);
+ if (CCleanup::AddProteinTitle(bsh)) {
+ ChangeMade(CCleanupChange::eAddDescriptor);
+ }
+ }
+}
+
+
+void CNewCleanup_imp::ProtRefEC(CProt_ref& pr)
+{
+ if (pr.IsSetDesc()) {
+ string desc = pr.GetDesc();
+ TrimInternalSemicolons(desc);
+ if (!NStr::Equal(desc, pr.GetDesc())) {
+ pr.SetDesc(desc);
+ ChangeMade(CCleanupChange::eChangeOther);
+ }
+ }
+ if (pr.IsSetEc()) {
+ x_CleanupECNumberListEC(pr.SetEc());
+ }
+}
+
+
+void CNewCleanup_imp::CdRegionEC(CSeq_feat& sf)
+{
+ if (!sf.IsSetData() || !sf.GetData().IsCdregion()) {
+ return;
+ }
+
+ CCdregion& cdr = sf.SetData().SetCdregion();
+
+ if (cdr.IsSetConflict() &&
+ cdr.GetConflict() &&
+ sf.IsSetProduct()) {
+ CBioseq_Handle prot = m_Scope->GetBioseqHandle(sf.GetProduct());
+ string expected;
+ CSeqTranslator::Translate(sf, *m_Scope, expected, false);
+ CSeqVector vec(prot, CBioseq_Handle::eCoding_Iupac);
+ CSeqVector_CI vi = vec.begin();
+ string::iterator si = expected.begin();
+ while (vi != vec.end() && si != expected.end() && *vi == *si) {
+ ++vi;
+ ++si;
+ }
+ if (vi != vec.end() || si != expected.end()) {
+ if (CCleanup::SetMolinfoTech(prot, CMolInfo::eTech_concept_trans_a)) {
+ ChangeMade(CCleanupChange::eChangeMolInfo);
+ }
+ } else {
+ cdr.ResetConflict();
+ ChangeMade(CCleanupChange::eChangeOther);
+ }
+ }
+}
+
+
+void CNewCleanup_imp::ResynchProteinPartials ( CSeq_feat& feat )
+{
+ if (!feat.IsSetData() || !feat.GetData().IsProt()) {
+ return;
+ }
+
+ if (feat.GetData().GetProt().IsSetProcessed() &&
+ feat.GetData().GetProt().GetProcessed() != CProt_ref::eProcessed_not_set) {
+ // not a "real" protein feature
+ return;
+ }
+
+ CBioseq_Handle prot = m_Scope->GetBioseqHandle(feat.GetLocation());
+ if (!prot) {
+ return;
+ }
+
+ // set protein feature partial to match coding region partial
+ const CSeq_feat* cds = sequence::GetCDSForProduct(*(prot.GetCompleteBioseq()), m_Scope);
+ if (!cds) {
+ return;
+ }
+
+ bool cds_partial5 = cds->GetLocation().IsPartialStart(eExtreme_Biological);
+ bool cds_partial3 = cds->GetLocation().IsPartialStop(eExtreme_Biological);
+ bool prot_partial = feat.IsSetPartial() && feat.GetPartial();
+ bool new_prot_partial = cds_partial5 || cds_partial3;
+
+ if (cds_partial5 != feat.GetLocation().IsPartialStart(eExtreme_Biological)) {
+ feat.SetLocation().SetPartialStart(cds_partial5, eExtreme_Biological);
+ ChangeMade(CCleanupChange::eChangePartial);
+ }
+ if (cds_partial3 != feat.GetLocation().IsPartialStop(eExtreme_Biological)) {
+ feat.SetLocation().SetPartialStop(cds_partial3, eExtreme_Biological);
+ ChangeMade(CCleanupChange::eChangePartial);
+ }
+ if (prot_partial != new_prot_partial) {
+ feat.SetPartial(new_prot_partial);
+ ChangeMade(CCleanupChange::eChangePartial);
+ }
+}
+
+
+void CNewCleanup_imp::ResynchPeptidePartials (
+ CBioseq& seq
+)
+
+{
+ if (!seq.IsSetInst() || !seq.GetInst().IsSetMol() || !seq.IsAa()) {
+ return;
+ }
+ CBioseq_Handle bsh = m_Scope->GetBioseqHandle(seq);
+
+ // need to find best protein feature
+ SAnnotSelector sel( CSeqFeatData::eSubtype_prot );
+ CFeat_CI feat_ci( bsh, sel );
+ if (!feat_ci) {
+ // no protein feature;
+ return;
+ }
+ if (feat_ci->GetData().GetProt().IsSetProcessed() &&
+ feat_ci->GetData().GetProt().GetProcessed() != CProt_ref::eProcessed_not_set) {
+ // not a "real" protein feature
+ return;
+ }
+
+ bool partial5 = feat_ci->GetLocation().IsPartialStart(eExtreme_Biological);
+ bool partial3 = feat_ci->GetLocation().IsPartialStop(eExtreme_Biological);
+
+ CMolInfo::TCompleteness desired = GetCompletenessFromFlags(partial5, partial3, partial5 || partial3);
+
+ bool found = false;
+ bool changed = false;
+ if (seq.IsSetDescr()) {
+ NON_CONST_ITERATE(CBioseq::TDescr::Tdata, it, seq.SetDescr().Set()) {
+ if ((*it)->IsMolinfo()) {
+ if ((*it)->GetMolinfo().IsSetCompleteness()) {
+ if ((*it)->GetMolinfo().GetCompleteness() != desired) {
+ (*it)->SetMolinfo().SetCompleteness(desired);
+ ChangeMade(CCleanupChange::eChangeMolInfo);
+ changed = true;
+ }
+ } else if (desired != CMolInfo::eCompleteness_unknown) {
+ (*it)->SetMolinfo().SetCompleteness(desired);
+ ChangeMade(CCleanupChange::eChangeMolInfo);
+ changed = true;
+ }
+ found = true;
+ }
+ }
+ }
+ if (!found) {
+ // no molinfo descriptor found, need to make new one
+ CRef<CSeqdesc> new_desc(new CSeqdesc());
+ new_desc->SetMolinfo().SetBiomol(CMolInfo::eBiomol_peptide);
+ new_desc->SetMolinfo().SetCompleteness(desired);
+ new_desc->SetMolinfo().SetTech(CMolInfo::eTech_concept_trans_a);
+ seq.SetDescr().Set().push_back(new_desc);
+ ChangeMade(CCleanupChange::eAddDescriptor);
+ changed = true;
+ }
+
+ if (changed) {
+ x_AddPartialToProteinTitle(seq);
+ }
+}
+
+
+void CNewCleanup_imp::KeepLatestDateDesc(CSeq_descr & seq_descr)
+{
+ const CSeqdesc::TCreate_date * best_create_date = NULL;
+ const CSeqdesc::TUpdate_date * best_update_date = NULL;
+
+ bool do_continue = true;
+ bool delete_equal_create = false;
+ bool delete_equal_update = false;
+ while (do_continue) {
+ do_continue = false;
+ CBioseq::TDescr::Tdata::iterator it = seq_descr.Set().begin();
+ while (it != seq_descr.Set().end()) {
+ bool remove = false;
+ if ((*it)->IsCreate_date()) {
+ if (best_create_date == NULL) {
+ best_create_date = &((*it)->GetCreate_date());
+ delete_equal_create = true;
+ } else {
+ CDate::ECompare compare = best_create_date->Compare((*it)->GetCreate_date());
+ if (compare == CDate::eCompare_after) {
+ // previous date is later, get rid of this one
+ remove = true;
+ } else if (compare == CDate::eCompare_same) {
+ if (delete_equal_create) {
+ remove = true;
+ } else {
+ delete_equal_create = true;
+ }
+ } else {
+ best_create_date = &((*it)->GetCreate_date());
+ delete_equal_create = true;
+ // need to loop through again to get rid of earlier dates
+ do_continue = true;
+ }
+ }
+ } else if ((*it)->IsUpdate_date()) {
+ if (best_update_date == NULL) {
+ best_update_date = &((*it)->GetUpdate_date());
+ delete_equal_update = true;
+ } else {
+ CDate::ECompare compare = best_update_date->Compare((*it)->GetUpdate_date());
+ if (compare == CDate::eCompare_after) {
+ // previous date is later, get rid of this one
+ remove = true;
+ } else if (compare == CDate::eCompare_same) {
+ if (delete_equal_update) {
+ remove = true;
+ } else {
+ delete_equal_update = true;
+ }
+ } else {
+ best_update_date = &((*it)->GetUpdate_date());
+ delete_equal_update = true;
+ // need to loop through again to get rid of earlier dates
+ do_continue = true;
+ }
+ }
+ }
+ if (remove) {
+ it = seq_descr.Set().erase(it);
+ ChangeMade(CCleanupChange::eRemoveDescriptor);
+ } else {
+ ++it;
+ }
+ }
+ delete_equal_create = false;
+ delete_equal_update = false;
+ }
+}
+
+
void CNewCleanup_imp::ExtendedCleanupSeqEntry (
CSeq_entry& seq_entry
)
@@ -10246,7 +11214,7 @@ void CNewCleanup_imp::ExtendedCleanupSeqEntry (
CAutogeneratedExtendedCleanup auto_ext_cleanup( *m_Scope, *this );
auto_ext_cleanup.ExtendedCleanupSeqEntry( seq_entry );
-
+
// TODO: implement more of ExtendedCleanup
}
@@ -10257,6 +11225,12 @@ void CNewCleanup_imp::ExtendedCleanupSeqSubmit (
// extended cleanup includes basic cleanup
BasicCleanupSeqSubmit( ss );
+ if( ! (m_Options & CCleanup::eClean_NoNcbiUserObjects) && ss.IsEntrys() ) {
+ NON_CONST_ITERATE(CSeq_submit::TData::TEntrys, it, ss.SetData().SetEntrys()) {
+ x_AddNcbiCleanupObject(**it);
+ }
+ }
+
CAutogeneratedExtendedCleanup auto_ext_cleanup( *m_Scope, *this );
auto_ext_cleanup.ExtendedCleanupSeqSubmit( ss );
diff --git a/c++/src/objtools/cleanup/newcleanupp.hpp b/c++/src/objtools/cleanup/newcleanupp.hpp
index 8fecb09..f216e19 100644
--- a/c++/src/objtools/cleanup/newcleanupp.hpp
+++ b/c++/src/objtools/cleanup/newcleanupp.hpp
@@ -222,14 +222,17 @@ private:
void SubmitblockBC (CSubmit_block& sb);
void SeqsetBC (CBioseq_set& bss);
+ void ProtSeqBC (CBioseq& bs);
void SeqIdBC( CSeq_id &seq_id );
+ void GBblockOriginBC( string& str);
void GBblockBC (CGB_block& gbk);
void EMBLblockBC (CEMBL_block& emb);
void BiosourceFeatBC (CBioSource& biosrc, CSeq_feat & seqfeat);
void BiosourceBC (CBioSource& bsc);
+ void OrgrefModBC (string& str);
void OrgrefBC (COrg_ref& org);
void OrgnameBC (COrgName& onm, COrg_ref &org_ref);
void OrgmodBC (COrgMod& omd);
@@ -271,6 +274,8 @@ private:
void Except_textBC (string& except_text);
void GenerefBC (CGene_ref& gr);
+ void ProtNameBC ( std::string & str );
+ void ProtActivityBC ( std::string & str );
void ProtrefBC (CProt_ref& pr);
void RnarefBC (CRNA_ref& rr);
@@ -287,10 +292,20 @@ private:
void PCRReactionSetBC( CPCRReactionSet &pcr_reaction_set );
void MolInfoBC( CMolInfo &molinfo );
+ void CreateMissingMolInfo( CBioseq& seq );
+
+ static bool IsInternalTranscribedSpacer(const string& name);
+ static bool TranslateITSName( string &in_out_name );
// Extended Cleanup functions
void BioSourceEC ( CBioSource& biosrc );
+ void AddProteinTitles (CBioseq& seq);
+ void ProtRefEC( CProt_ref& pr);
+ void CdRegionEC( CSeq_feat& sf);
+ void ResynchProteinPartials ( CSeq_feat& feat );
+ void ResynchPeptidePartials( CBioseq& seq );
+ void KeepLatestDateDesc(CSeq_descr & seq_descr);
// void XxxxxxBC (Cxxxxx& xxx);
@@ -331,6 +346,7 @@ private:
};
// Gb_qual cleanup.
+ void x_CleanSeqFeatQuals(CSeq_feat& sf);
EAction GBQualSeqFeatBC(CGb_qual& gbq, CSeq_feat& seqfeat);
void x_AddNcbiCleanupObject( CSeq_entry &seq_entry );
@@ -348,10 +364,13 @@ private:
void x_ExpandCombinedQuals(CSeq_feat::TQual& quals);
EAction x_GeneGBQualBC( CGene_ref& gene, const CGb_qual& gb_qual );
EAction x_SeqFeatCDSGBQualBC(CSeq_feat& feat, CCdregion& cds, const CGb_qual& gb_qual);
+ EAction x_HandleTrnaProductGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& product);
+ EAction x_HandleStandardNameRnaGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& standard_name);
EAction x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual& gb_qual);
EAction x_ParseCodeBreak(const CSeq_feat& feat, CCdregion& cds, const string& str);
EAction x_ProtGBQualBC(CProt_ref& prot, const CGb_qual& gb_qual, EGBQualOpt opt );
void x_AddEnvSamplOrMetagenomic(CBioSource& biosrc);
+ void x_AddToComment(CSeq_feat& feat, const string& comment);
// publication-related cleanup
void x_FlattenPubEquiv(CPub_equiv& pe);
@@ -371,6 +390,8 @@ private:
void x_AddReplaceQual(CSeq_feat& feat, const string& str);
void x_SeqIntervalBC( CSeq_interval & seq_interval );
+ void x_BothStrandBC( CSeq_loc &loc );
+ void x_BothStrandBC( CSeq_interval & seq_interval );
void x_SplitDbtag( CDbtag &dbt, vector< CRef< CDbtag > > & out_new_dbtags );
@@ -383,6 +404,9 @@ private:
void x_OrgnameModBC( COrgName &orgname, const string &org_ref_common );
+ void x_SubSourceBC( CSubSource & subsrc );
+ void x_OrgModBC( COrgMod & orgmod );
+
void x_FixUnsetMolFromBiomol( CMolInfo& molinfo, CBioseq &bioseq );
void x_AddPartialToProteinTitle( CBioseq &bioseq );
@@ -395,6 +419,7 @@ private:
void x_CleanupECNumber( string &ec_num );
void x_CleanupECNumberList( CProt_ref::TEc & ec_num_list );
+ void x_CleanupECNumberListEC( CProt_ref::TEc & ec_num_list );
void x_CleanupAndRepairInference( string &inference );
@@ -419,6 +444,8 @@ private:
void x_MoveSeqdescOrgToSourceOrg( CSeqdesc &seqdesc );
void x_MoveSeqfeatOrgToSourceOrg( CSeq_feat &seqfeat );
+ void x_MoveCDSFromNucAnnotToSetAnnot( CBioseq_set &set );
+
// string cleanup funcs
void x_CleanupStringMarkChanged( std::string &str );
void x_CleanupStringJunkMarkChanged( std::string &str );
@@ -428,13 +455,17 @@ private:
void x_CompressStringSpacesMarkChanged( std::string &str );
void x_StripSpacesMarkChanged( std::string& str );
void x_RemoveSpacesBetweenTildesMarkChanged( std::string & str );
+ void X_CommentTildeFixes( std::string & str );
void x_TruncateSpacesMarkChanged( std::string & str );
+ void x_TrimInternalSemicolonsMarkChanged( std::string & str );
void x_PostSeqFeat( CSeq_feat& seq_feat );
void x_PostOrgRef( COrg_ref& org );
void x_PostBiosource( CBioSource& biosrc );
+ void x_ConvertOrgref_modToSubSource( CBioSource& biosrc );
+ void x_ConvertOrgref_modToOrgMod(COrg_ref& org);
- void x_TranslateITSName( string &in_out_name ) ;
+ void x_TranslateITSNameAndFlag( string &in_out_name ) ;
void x_PCRPrimerSetBC( CPCRPrimerSet &primer_set );
@@ -451,6 +482,10 @@ private:
// This function does that processing.
void x_PostProcessing(void);
+ // after cleaning bioseq and bioseq-set, need to clear empty descriptors
+ void x_ClearEmptyDescr( CBioseq_set& bioseq_set );
+ void x_ClearEmptyDescr( CBioseq& bioseq );
+
// functions that prepare for post-processing while traversing
void x_NotePubdescOrAnnotPubs( const CPub_equiv &pub_equiv );
void x_NotePubdescOrAnnotPubs_RecursionHelper(
@@ -473,6 +508,7 @@ private:
void x_RemoveRedundantComment( CGene_ref& gene, CSeq_feat& seq_feat );
void x_RemoveEmptyUserObject( CSeq_descr & seq_descr );
+ void x_CleanupGenbankBlock( CSeq_descr & seq_descr );
void x_RemoveEmptyFeatures( CSeq_annot & seq_annot );
void x_RemoveEmptyFeatureTables( list< CRef< CSeq_annot > > & annot_list);
void x_RemoveEmptyFeatureTables( CBioseq & bioseq );
@@ -487,6 +523,9 @@ private:
bool x_IsDBLinkUserObj( const CSeqdesc & desc );
+ bool x_FixMiscRNA(CSeq_feat& feat);
+ void x_ModernizeRNAFeat(CSeq_feat& feat);
+
protected:
// variables used for the whole cleaning process
diff --git a/c++/src/objtools/data_loaders/Makefile.in b/c++/src/objtools/data_loaders/Makefile.in
index 84ff6d2..0c02e0a 100644
--- a/c++/src/objtools/data_loaders/Makefile.in
+++ b/c++/src/objtools/data_loaders/Makefile.in
@@ -1,6 +1,6 @@
-# $Id: Makefile.in 469194 2015-06-02 14:03:42Z blastadm $
+# $Id: Makefile.in 485953 2015-11-30 17:53:34Z blastadm $
-SUB_PROJ = genbank lds lds2 blastdb cdd trace patcher
+SUB_PROJ = genbank lds2 blastdb cdd trace patcher
srcdir = @srcdir@
include @builddir@/Makefile.meta
diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
index e62bcc7..9b75e5a 100644
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
@@ -1,8 +1,10 @@
-# $Id: Makefile.ncbi_xloader_blastdb.lib 427429 2014-02-20 13:41:40Z gouriano $
+# $Id: Makefile.ncbi_xloader_blastdb.lib 468535 2015-05-26 13:23:32Z ucko $
LIB = ncbi_xloader_blastdb
SRC = bdbloader cached_sequence local_blastdb_adapter
+DLL_LIB = seqdb
+
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
ASN_DEP = blastdb seqset
diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
index fa80caf..7228f3e 100644
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
@@ -1,8 +1,10 @@
-# $Id: Makefile.ncbi_xloader_blastdb_rmt.lib 427429 2014-02-20 13:41:40Z gouriano $
+# $Id: Makefile.ncbi_xloader_blastdb_rmt.lib 468535 2015-05-26 13:23:32Z ucko $
LIB = ncbi_xloader_blastdb_rmt
SRC = bdbloader_rmt remote_blastdb_adapter
+DLL_LIB = blast_services
+
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
ASN_DEP = blastdb xnetblast
diff --git a/c++/src/objtools/data_loaders/blastdb/bdbloader.cpp b/c++/src/objtools/data_loaders/blastdb/bdbloader.cpp
index 2434343..631c64f 100644
--- a/c++/src/objtools/data_loaders/blastdb/bdbloader.cpp
+++ b/c++/src/objtools/data_loaders/blastdb/bdbloader.cpp
@@ -1,4 +1,4 @@
-/* $Id: bdbloader.cpp 368048 2012-07-02 13:25:25Z camacho $
+/* $Id: bdbloader.cpp 443376 2014-08-13 17:03:05Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
* ===========================================================================
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: bdbloader.cpp 368048 2012-07-02 13:25:25Z camacho $";
+static char const rcsid[] = "$Id: bdbloader.cpp 443376 2014-08-13 17:03:05Z vakatov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -451,10 +451,8 @@ CBlastDbDataLoader::GetBlobById(const TBlobId& blob_id)
void
-CBlastDbDataLoader::DebugDump(CDebugDumpContext ddc, unsigned int depth) const
+CBlastDbDataLoader::DebugDump(CDebugDumpContext ddc, unsigned int /*depth*/) const
{
- // dummy assignment to eliminate compiler and doxygen warnings
- depth = depth;
ddc.SetFrame("CBlastDbDataLoader");
DebugDumpValue(ddc,"m_DBName", m_DBName);
DebugDumpValue(ddc,"m_DBType", m_DBType);
diff --git a/c++/src/objtools/data_loaders/blastdb/bdbloader_rmt.cpp b/c++/src/objtools/data_loaders/blastdb/bdbloader_rmt.cpp
index 2625a24..c0bc6c9 100644
--- a/c++/src/objtools/data_loaders/blastdb/bdbloader_rmt.cpp
+++ b/c++/src/objtools/data_loaders/blastdb/bdbloader_rmt.cpp
@@ -1,4 +1,4 @@
-/* $Id: bdbloader_rmt.cpp 219674 2011-01-12 20:09:13Z vasilche $
+/* $Id: bdbloader_rmt.cpp 443376 2014-08-13 17:03:05Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@
* ===========================================================================
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: bdbloader_rmt.cpp 219674 2011-01-12 20:09:13Z vasilche $";
+static char const rcsid[] = "$Id: bdbloader_rmt.cpp 443376 2014-08-13 17:03:05Z vakatov $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -258,10 +258,8 @@ CRemoteBlastDbDataLoader::GetChunks(const TChunkSet& chunks_orig)
}
void
-CRemoteBlastDbDataLoader::DebugDump(CDebugDumpContext ddc, unsigned int depth) const
+CRemoteBlastDbDataLoader::DebugDump(CDebugDumpContext ddc, unsigned int /*depth*/) const
{
- // dummy assignment to eliminate compiler and doxygen warnings
- depth = depth;
ddc.SetFrame("CRemoteBlastDbDataLoader");
DebugDumpValue(ddc,"m_DBName", m_DBName);
DebugDumpValue(ddc,"m_DBType", m_DBType);
diff --git a/c++/src/objtools/data_loaders/blastdb/cached_sequence.cpp b/c++/src/objtools/data_loaders/blastdb/cached_sequence.cpp
index 9da692b..145a68d 100644
--- a/c++/src/objtools/data_loaders/blastdb/cached_sequence.cpp
+++ b/c++/src/objtools/data_loaders/blastdb/cached_sequence.cpp
@@ -1,4 +1,4 @@
-/* $Id: cached_sequence.cpp 401240 2013-05-29 14:08:40Z madden $
+/* $Id: cached_sequence.cpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
* Defines the CCachedSequence class
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: cached_sequence.cpp 401240 2013-05-29 14:08:40Z madden $";
+static char const rcsid[] = "$Id: cached_sequence.cpp 468783 2015-05-28 13:00:08Z vasilche $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -47,36 +47,6 @@ static char const rcsid[] = "$Id: cached_sequence.cpp 401240 2013-05-29 14:08:40
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
-static void
-s_ReplaceProvidedSeqIdsForRequestedSeqIds(const CSeq_id_Handle& idh, CBioseq&
- bioseq)
-{
- CRef<CBlast_def_line_set> deflines = CSeqDB::ExtractBlastDefline(bioseq);
- _ASSERT(deflines.NotEmpty());
-
- CRef<CBlast_def_line> target_defline;
- NON_CONST_ITERATE(CBlast_def_line_set::Tdata, one_defline,
- deflines->Set()) {
- if (! (*one_defline)->CanGetSeqid()) {
- continue;
- }
- NON_CONST_ITERATE(CBlast_def_line::TSeqid, seqid,
- (*one_defline)->SetSeqid()) {
- if ((*seqid)->Match(*idh.GetSeqId())) {
- target_defline = *one_defline;
- break;
- }
- }
- if (target_defline.NotEmpty()) {
- break;
- }
- }
-
- if (target_defline.NotEmpty()) {
- bioseq.SetId() = target_defline->SetSeqid();
- }
-}
-
CCachedSequence::CCachedSequence(IBlastDbAdapter& db,
const CSeq_id_Handle& idh,
int oid,
@@ -88,11 +58,9 @@ CCachedSequence::CCachedSequence(IBlastDbAdapter& db,
{
m_TSE.Reset();
m_Length = m_BlastDb.GetSeqLength(m_OID);
-
- CRef<CBioseq> bioseq(m_BlastDb.GetBioseqNoData(m_OID, 0, &*(m_SIH.GetSeqId())));
- s_ReplaceProvidedSeqIdsForRequestedSeqIds(m_SIH, *bioseq);
-
+ CRef<CBioseq> bioseq(m_BlastDb.GetBioseqNoData(m_OID, ZERO_GI, &*(m_SIH.GetSeqId())));
+
CConstRef<CSeq_id> first_id( bioseq->GetFirstId() );
_ASSERT(first_id);
if ( first_id ) {
diff --git a/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.cpp b/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.cpp
index b4fca3f..aeeefa2 100644
--- a/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.cpp
+++ b/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.cpp
@@ -1,4 +1,4 @@
-/* $Id: local_blastdb_adapter.cpp 401240 2013-05-29 14:08:40Z madden $
+/* $Id: local_blastdb_adapter.cpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
* Defines the CLocalBlastDbAdapter class
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: local_blastdb_adapter.cpp 401240 2013-05-29 14:08:40Z madden $";
+static char const rcsid[] = "$Id: local_blastdb_adapter.cpp 468783 2015-05-28 13:00:08Z vasilche $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -60,10 +60,10 @@ CLocalBlastDbAdapter::GetTaxId(const CSeq_id_Handle& idh)
if (id.NotEmpty()) {
int oid = 0;
if (SeqidToOid(*id, oid)) {
- map<int, int> gi_to_taxid;
+ map<TGi, int> gi_to_taxid;
m_SeqDB->GetTaxIDs(oid, gi_to_taxid);
if (idh.IsGi()) {
- retval = gi_to_taxid[GI_TO(int, idh.GetGi())];
+ retval = gi_to_taxid[idh.GetGi()];
} else {
retval = gi_to_taxid.begin()->second;
}
@@ -85,7 +85,7 @@ CLocalBlastDbAdapter::GetSeqIDs(int oid)
}
CRef<CBioseq>
-CLocalBlastDbAdapter::GetBioseqNoData(int oid, int target_gi /* = 0 */, const CSeq_id * target_id /* = NULL */)
+CLocalBlastDbAdapter::GetBioseqNoData(int oid, TGi target_gi /* = 0 */, const CSeq_id * target_id /* = NULL */)
{
return m_SeqDB->GetBioseqNoData(oid, target_gi, target_id);
}
diff --git a/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.hpp b/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.hpp
index 5824db0..9e7e6e1 100644
--- a/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.hpp
+++ b/c++/src/objtools/data_loaders/blastdb/local_blastdb_adapter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_DATA_LOADERS_BLASTDB___LOCAL_BLASTDB_ADAPTER__HPP
#define OBJTOOLS_DATA_LOADERS_BLASTDB___LOCAL_BLASTDB_ADAPTER__HPP
-/* $Id: local_blastdb_adapter.hpp 401240 2013-05-29 14:08:40Z madden $
+/* $Id: local_blastdb_adapter.hpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -63,7 +63,7 @@ public:
/** @inheritDoc */
virtual TSeqIdList GetSeqIDs(int oid);
/** @inheritDoc */
- virtual CRef<CBioseq> GetBioseqNoData(int oid, int target_gi = 0, const CSeq_id * target_id = NULL);
+ virtual CRef<CBioseq> GetBioseqNoData(int oid, TGi target_gi = ZERO_GI, const CSeq_id * target_id = NULL);
/** @inheritDoc */
virtual CRef<CSeq_data> GetSequence(int oid, int begin = 0, int end = 0);
/** @inheritDoc */
diff --git a/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.cpp b/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.cpp
index 60850da..c2e6dad 100644
--- a/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.cpp
+++ b/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.cpp
@@ -1,4 +1,4 @@
-/* $Id: remote_blastdb_adapter.cpp 435003 2014-05-13 15:08:30Z ucko $
+/* $Id: remote_blastdb_adapter.cpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
* Defines the CRemoteBlastDbAdapter class
*/
#ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: remote_blastdb_adapter.cpp 435003 2014-05-13 15:08:30Z ucko $";
+static char const rcsid[] = "$Id: remote_blastdb_adapter.cpp 468783 2015-05-28 13:00:08Z vasilche $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <ncbi_pch.hpp>
@@ -79,7 +79,7 @@ CRemoteBlastDbAdapter::GetSeqIDs(int oid)
}
CRef<CBioseq>
-CRemoteBlastDbAdapter::GetBioseqNoData(int oid, int /* target_gi = 0 */, const CSeq_id * target_id /* = NULL */)
+CRemoteBlastDbAdapter::GetBioseqNoData(int oid, TGi /* target_gi = 0 */, const CSeq_id * target_id /* = NULL */)
{
/// @todo FIXME we should do something with the target_gi
_ASSERT(m_Cache[oid].IsValid());
diff --git a/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.hpp b/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.hpp
index 36d0504..9b0baf1 100644
--- a/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.hpp
+++ b/c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.hpp
@@ -1,7 +1,7 @@
#ifndef OBJTOOLS_DATA_LOADERS_BLASTDB___REMOTE_BLASTDB_ADAPTER__HPP
#define OBJTOOLS_DATA_LOADERS_BLASTDB___REMOTE_BLASTDB_ADAPTER__HPP
-/* $Id: remote_blastdb_adapter.hpp 401240 2013-05-29 14:08:40Z madden $
+/* $Id: remote_blastdb_adapter.hpp 468783 2015-05-28 13:00:08Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -189,7 +189,7 @@ public:
/** @inheritDoc */
virtual TSeqIdList GetSeqIDs(int oid);
/** @inheritDoc */
- virtual CRef<CBioseq> GetBioseqNoData(int oid, int target_gi = 0, const CSeq_id * target_id = NULL);
+ virtual CRef<CBioseq> GetBioseqNoData(int oid, TGi target_gi = ZERO_GI, const CSeq_id * target_id = NULL);
/** @inheritDoc */
virtual CRef<CSeq_data> GetSequence(int oid, int begin = 0, int end = 0);
/// Batch-version of GetSequence
diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
index abe43c5..a14a005 100644
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.ncbi_xreader.lib 440703 2014-07-16 15:38:41Z vasilche $
+# $Id: Makefile.ncbi_xreader.lib 468607 2015-05-26 18:31:30Z ucko $
SRC = dispatcher reader writer processors \
reader_snp seqref blob_id split_parser request_result \
@@ -12,8 +12,7 @@ LIB = ncbi_xreader
LIB_OR_DLL = both
# Dependencies for shared library
-DLL_LIB =
-DLL_DLIB = $(GENBANK_READER_LDEP)
+DLL_LIB = $(GENBANK_READER_LDEP)
WATCHERS = vasilche
diff --git a/c++/src/objtools/data_loaders/genbank/cache/reader_cache.cpp b/c++/src/objtools/data_loaders/genbank/cache/reader_cache.cpp
index 3995421..6cc9f3d 100644
--- a/c++/src/objtools/data_loaders/genbank/cache/reader_cache.cpp
+++ b/c++/src/objtools/data_loaders/genbank/cache/reader_cache.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_cache.cpp 448568 2014-10-07 16:45:31Z ivanov $
+/* $Id: reader_cache.cpp 475255 2015-08-05 19:25:27Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -153,7 +153,7 @@ void SCacheInfo::GetBlob_idsSubkey(const SAnnotSelector* sel,
const char* SCacheInfo::GetGiSubkey(void)
{
- return "gi4";
+ return "gi8";
}
@@ -175,6 +175,12 @@ const char* SCacheInfo::GetTaxIdSubkey(void)
}
+const char* SCacheInfo::GetHashSubkey(void)
+{
+ return "hash";
+}
+
+
const char* SCacheInfo::GetSeq_idsSubkey(void)
{
return "ids4";
@@ -372,6 +378,12 @@ namespace {
{
return ParseUint4();
}
+ Int8 ParseInt8(void)
+ {
+ Int8 n = Int8(ParseInt4()) << 32;
+ n |= ParseUint4();
+ return n;
+ }
string ParseString(void);
string FullString(void);
@@ -678,7 +690,16 @@ bool CCacheReader::LoadSeq_idGi(CReaderRequestResult& result,
CConn conn(result, this);
CParseBuffer str(result, m_IdCache, GetIdKey(seq_id), GetGiSubkey());
if ( str.Found() ) {
- TGi gi = GI_FROM(Int4, str.ParseInt4());
+ Int8 gi_num = str.ParseInt8();
+#ifdef NCBI_INT8_GI
+ TGi gi = gi_num;
+#else
+ if ( gi_num != Int4(gi_num) ) {
+ NCBI_THROW(CLoaderException, eLoaderFailed,
+ "64-bit gi overflow");
+ }
+ TGi gi = Int4(gi_num);
+#endif
if ( str.Done() ) {
conn.Release();
lock.SetLoadedGi(gi, str.GetExpirationTime());
@@ -796,6 +817,35 @@ bool CCacheReader::LoadSeq_idTaxId(CReaderRequestResult& result,
}
+bool CCacheReader::LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id)
+{
+ if ( !m_IdCache ) {
+ return false;
+ }
+
+ CLoadLockHash lock(result, seq_id);
+ if ( lock.IsLoadedHash() ) {
+ return true;
+ }
+
+ CConn conn(result, this);
+ CParseBuffer str(result, m_IdCache, GetIdKey(seq_id), GetHashSubkey());
+ if ( !str.Found() ) {
+ conn.Release();
+ return false;
+ }
+ int hash = str.ParseInt4();
+ if ( !str.Done() ) {
+ conn.Release();
+ return false;
+ }
+ conn.Release();
+ lock.SetLoadedHash(hash, str.GetExpirationTime());
+ return true;
+}
+
+
bool CCacheReader::LoadAccVers(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TIds& ret)
{
@@ -1366,35 +1416,54 @@ GetCacheParamsCopy(const SCacheInfo::TParams* src_params,
}
static const SPluginParams::SDefaultValue s_DefaultParams[] = {
- { "path", ".genbank_cache" },
+ // common:
{ "keep_versions", "all" },
{ "write_sync", "no" },
+ // bdb:
+ { "path", ".genbank_cache" },
{ "mem_size", "20M" },
{ "log_file_max", "20M" },
{ "purge_batch_sleep", "500" }, // .5 sec
{ "purge_thread_delay", "3600" }, // 1 hour
{ "purge_clean_log", "16" },
+ // netcache:
+ { "connection_max_retries", "0" },
+ { "connection_timeout", "0.3" },
+ { "communication_timeout", "0.1" },
+ { "max_connection_pool_size", "30" },
+ { "max_find_lbname_retries", "2" },
+ { "retry_delay", "0.001" },
+
{ 0, 0 }
};
static const SPluginParams::SDefaultValue s_DefaultIdParams[] = {
+ // common:
{ "name", "ids" },
{ "timeout", "172800" }, // 2 days
{ "timestamp", "subkey check_expiration" /* purge_on_startup"*/ },
+ // bdb:
{ "page_size", "small" },
- { 0, 0}
+
+ { 0, 0 }
};
static const SPluginParams::SDefaultValue s_DefaultBlobParams[] = {
+ // common:
{ "name", "blobs" },
{ "timeout", "432000" }, // 5 days
{ "timestamp", "onread expire_not_used" /* purge_on_startup"*/ },
+
{ 0, 0 }
};
static const SPluginParams::SDefaultValue s_DefaultReaderParams[] = {
+ // bdb:
{ "purge_thread", "yes" },
+
{ 0, 0 }
};
static const SPluginParams::SDefaultValue s_DefaultWriterParams[] = {
+ // bdb:
{ "purge_thread", "no" },
+
{ 0, 0 }
};
diff --git a/c++/src/objtools/data_loaders/genbank/cache/writer_cache.cpp b/c++/src/objtools/data_loaders/genbank/cache/writer_cache.cpp
index e17aeb3..c6c29b5 100644
--- a/c++/src/objtools/data_loaders/genbank/cache/writer_cache.cpp
+++ b/c++/src/objtools/data_loaders/genbank/cache/writer_cache.cpp
@@ -1,4 +1,4 @@
-/* $Id: writer_cache.cpp 447937 2014-10-01 17:41:13Z vasilche $
+/* $Id: writer_cache.cpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -196,7 +196,7 @@ void CCacheWriter::SaveStringGi(CReaderRequestResult& result,
CLoadLockGi lock(result, seq_id);
if ( lock.IsLoadedGi() ) {
CStoreBuffer str;
- str.StoreInt4(GI_TO(Int4, lock.GetGi()));
+ str.StoreInt8(lock.GetGi());
x_WriteId(seq_id, GetGiSubkey(), str);
}
}
@@ -224,7 +224,7 @@ void CCacheWriter::SaveSeq_idGi(CReaderRequestResult& result,
CLoadLockGi lock(result, seq_id);
if ( lock.IsLoadedGi() ) {
CStoreBuffer str;
- str.StoreInt4(GI_TO(Int4, lock.GetGi()));
+ str.StoreInt8(lock.GetGi());
x_WriteId(GetIdKey(seq_id), GetGiSubkey(), str);
}
}
@@ -279,6 +279,22 @@ void CCacheWriter::SaveSeq_idTaxId(CReaderRequestResult& result,
}
+void CCacheWriter::SaveSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id)
+{
+ if( !m_IdCache) {
+ return;
+ }
+
+ CLoadLockHash lock(result, seq_id);
+ if ( lock.IsLoadedHash() ) {
+ CStoreBuffer str;
+ str.StoreInt4(lock.GetHash());
+ x_WriteId(GetIdKey(seq_id), GetHashSubkey(), str);
+ }
+}
+
+
void CCacheWriter::WriteSeq_ids(const string& key,
const CLoadLockSeqIds& lock)
{
diff --git a/c++/src/objtools/data_loaders/genbank/dispatcher.cpp b/c++/src/objtools/data_loaders/genbank/dispatcher.cpp
index 4f2118d..9a06567 100644
--- a/c++/src/objtools/data_loaders/genbank/dispatcher.cpp
+++ b/c++/src/objtools/data_loaders/genbank/dispatcher.cpp
@@ -1,4 +1,4 @@
-/* $Id: dispatcher.cpp 448568 2014-10-07 16:45:31Z ivanov $
+/* $Id: dispatcher.cpp 452490 2014-11-20 15:50:53Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -71,7 +71,8 @@ static CGBRequestStatistics sx_Statistics[CGBRequestStatistics::eStats_Count] =
CGBRequestStatistics("parsed", "blob data"),
CGBRequestStatistics("parsed", "SNP data"),
CGBRequestStatistics("parsed", "split data"),
- CGBRequestStatistics("parsed", "chunk data")
+ CGBRequestStatistics("parsed", "chunk data"),
+ CGBRequestStatistics("loaded", "sequence hash")
};
CGBRequestStatistics::CGBRequestStatistics(const char* action,
@@ -483,6 +484,49 @@ namespace {
TLock m_Lock;
};
+ class CCommandLoadSequenceHash : public CReadDispatcherCommand
+ {
+ public:
+ typedef CSeq_id_Handle TKey;
+ typedef CLoadLockHash TLock;
+ CCommandLoadSequenceHash(CReaderRequestResult& result,
+ const TKey& key)
+ : CReadDispatcherCommand(result),
+ m_Key(key), m_Lock(result, key)
+ {
+ }
+
+ bool IsDone(void)
+ {
+ return m_Lock.IsLoadedHash();
+ }
+ bool Execute(CReader& reader)
+ {
+ return reader.LoadSequenceHash(GetResult(), m_Key);
+ }
+ bool MayBeSkipped(void) const
+ {
+ return true;
+ }
+ string GetErrMsg(void) const
+ {
+ return "LoadSequenceHash("+m_Key.AsString()+"): "
+ "data not found";
+ }
+ CGBRequestStatistics::EStatType GetStatistics(void) const
+ {
+ return CGBRequestStatistics::eStat_Hash;
+ }
+ string GetStatisticsDescription(void) const
+ {
+ return "hash("+m_Key.AsString()+")";
+ }
+
+ private:
+ TKey m_Key;
+ TLock m_Lock;
+ };
+
bool s_Blob_idsLoaded(CLoadLockBlobIds& ids,
CReaderRequestResult& result,
const CSeq_id_Handle& seq_id)
@@ -723,6 +767,10 @@ namespace {
{
return reader.LoadTaxIds(GetResult(), m_Key, m_Loaded, m_Ret);
}
+ bool MayBeSkipped(void) const
+ {
+ return true;
+ }
string GetErrMsg(void) const
{
return "LoadTaxIds("+sx_DescribeUnloaded(m_Key, m_Loaded)+"): "
@@ -743,6 +791,51 @@ namespace {
TRet& m_Ret;
};
+ class CCommandLoadHashes : public CReadDispatcherCommand
+ {
+ public:
+ typedef vector<CSeq_id_Handle> TKey;
+ typedef vector<bool> TLoaded;
+ typedef vector<int> TRet;
+ CCommandLoadHashes(CReaderRequestResult& result,
+ const TKey& key, TLoaded& loaded, TRet& ret)
+ : CReadDispatcherCommand(result),
+ m_Key(key), m_Loaded(loaded), m_Ret(ret)
+ {
+ }
+
+ bool IsDone(void)
+ {
+ return sx_BulkIsDone(m_Key, m_Loaded);
+ }
+ bool Execute(CReader& reader)
+ {
+ return reader.LoadHashes(GetResult(), m_Key, m_Loaded, m_Ret);
+ }
+ bool MayBeSkipped(void) const
+ {
+ return true;
+ }
+ string GetErrMsg(void) const
+ {
+ return "LoadHashes("+sx_DescribeUnloaded(m_Key, m_Loaded)+"): "
+ "data not found";
+ }
+ CGBRequestStatistics::EStatType GetStatistics(void) const
+ {
+ return CGBRequestStatistics::eStat_Hash;
+ }
+ string GetStatisticsDescription(void) const
+ {
+ return "hashes("+sx_DescribeUnloaded(m_Key, m_Loaded)+")";
+ }
+
+ private:
+ const TKey& m_Key;
+ TLoaded& m_Loaded;
+ TRet& m_Ret;
+ };
+
class CCommandLoadStates : public CReadDispatcherCommand
{
public:
@@ -1366,6 +1459,14 @@ void CReadDispatcher::LoadSeq_idTaxId(CReaderRequestResult& result,
}
+void CReadDispatcher::LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id)
+{
+ CCommandLoadSequenceHash command(result, seq_id);
+ Process(command);
+}
+
+
void CReadDispatcher::LoadAccVers(CReaderRequestResult& result,
const TIds ids, TLoaded& loaded, TIds& ret)
{
@@ -1398,6 +1499,14 @@ void CReadDispatcher::LoadTaxIds(CReaderRequestResult& result,
}
+void CReadDispatcher::LoadHashes(CReaderRequestResult& result,
+ const TIds ids, TLoaded& loaded, THashes& ret)
+{
+ CCommandLoadHashes command(result, ids, loaded, ret);
+ Process(command);
+}
+
+
void CReadDispatcher::LoadStates(CReaderRequestResult& result,
const TIds ids, TLoaded& loaded, TStates& ret)
{
@@ -1504,9 +1613,12 @@ bool CReadDispatcher::SetBlobState(size_t i,
CFixedBlob_ids blob_ids = lock.GetBlob_ids();
ITERATE ( CFixedBlob_ids, it, blob_ids ) {
if ( it->Matches(fBlobHasCore, 0) ) {
- ret[i] = lock.GetState();
- loaded[i] = true;
- return true;
+ CFixedBlob_ids::TState state = lock.GetState();
+ if ( state != CFixedBlob_ids::kUnknownState ) {
+ ret[i] = lock.GetState();
+ loaded[i] = true;
+ return true;
+ }
}
}
if ( lock.GetState() & CBioseq_Handle::fState_no_data ) {
diff --git a/c++/src/objtools/data_loaders/genbank/gbloader.cpp b/c++/src/objtools/data_loaders/genbank/gbloader.cpp
index ef62f22..d0bc280 100644
--- a/c++/src/objtools/data_loaders/genbank/gbloader.cpp
+++ b/c++/src/objtools/data_loaders/genbank/gbloader.cpp
@@ -1,4 +1,4 @@
-/* $Id: gbloader.cpp 455763 2015-01-05 12:57:27Z vasilche $
+/* $Id: gbloader.cpp 475892 2015-08-12 18:52:12Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -448,6 +448,7 @@ void CGBDataLoader::x_CreateDriver(const CGBLoaderParams& params)
gb_params = GetLoaderParams(params.GetParamTree());
}
else {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
if ( app ) {
app_params.reset(CConfig::ConvertRegToTree(app->GetConfig()));
@@ -502,6 +503,22 @@ void CGBDataLoader::x_CreateDriver(const CGBLoaderParams& params)
}
}
}
+ m_AlwaysLoadNamedAcc = true;
+ if ( gb_params ) {
+ string param =
+ GetParam(gb_params, NCBI_GBLOADER_PARAM_ALWAYS_LOAD_NAMED_ACC);
+ if ( !param.empty() ) {
+ try {
+ m_AlwaysLoadNamedAcc = NStr::StringToBool(param);
+ }
+ catch ( CException& exc ) {
+ NCBI_RETHROW_FMT(exc, CLoaderException, eBadConfig,
+ "Bad value of parameter "
+ NCBI_GBLOADER_PARAM_ALWAYS_LOAD_NAMED_ACC
+ ": \""<<param<<"\"");
+ }
+ }
+ }
m_AddWGSMasterDescr = true;
if ( gb_params ) {
string param =
@@ -879,7 +896,10 @@ int CGBDataLoader::GetSequenceState(const CSeq_id_Handle& sih)
CFixedBlob_ids blob_ids = blobs.GetBlob_ids();
ITERATE ( CFixedBlob_ids, it, blob_ids ) {
if ( it->Matches(fBlobHasCore, 0) ) {
- return blob_ids.GetState();
+ CFixedBlob_ids::TState state = blob_ids.GetState();
+ if ( state != CFixedBlob_ids::kUnknownState ) {
+ return blob_ids.GetState();
+ }
}
}
return kNotFound;
@@ -1098,6 +1118,34 @@ void CGBDataLoader::GetSequenceStates(const TIds& ids, TLoaded& loaded,
}
+int CGBDataLoader::GetSequenceHash(const CSeq_id_Handle& sih)
+{
+ if ( CReadDispatcher::CannotProcess(sih) ) {
+ return 0;
+ }
+ CGBReaderRequestResult result(this, sih);
+ CLoadLockHash lock(result, sih);
+ if ( !lock.IsLoadedHash() ) {
+ m_Dispatcher->LoadSequenceHash(result, sih);
+ }
+ return lock.IsLoaded()? lock.GetHash(): 0;
+}
+
+
+void CGBDataLoader::GetSequenceHashes(const TIds& ids, TLoaded& loaded,
+ TSequenceHashes& ret)
+{
+ for ( size_t i = 0; i < ids.size(); ++i ) {
+ if ( loaded[i] || CReadDispatcher::CannotProcess(ids[i]) ) {
+ continue;
+ }
+ CGBReaderRequestResult result(this, ids[i]);
+ m_Dispatcher->LoadHashes(result, ids, loaded, ret);
+ return;
+ }
+}
+
+
CDataLoader::TBlobVersion CGBDataLoader::GetBlobVersion(const TBlobId& id)
{
const TRealBlobId& blob_id = GetRealBlobId(id);
@@ -1462,10 +1510,22 @@ CDataLoader::TTSE_LockSet
CGBDataLoader::GetOrphanAnnotRecords(const CSeq_id_Handle& idh,
const SAnnotSelector* sel)
{
- if ( !m_AlwaysLoadExternal ) {
+ bool load_external = m_AlwaysLoadExternal;
+ bool load_namedacc = m_AlwaysLoadNamedAcc &&
+ sel && sel->IsIncludedAnyNamedAnnotAccession();
+ if ( load_external || load_namedacc ) {
+ TBlobContentsMask mask = 0;
+ if ( load_external ) {
+ mask |= fBlobHasExtAnnot;
+ }
+ if ( load_namedacc ) {
+ mask |= fBlobHasNamedAnnot;
+ }
+ return x_GetRecords(idh, mask, sel);
+ }
+ else {
return CDataLoader::GetOrphanAnnotRecords(idh, sel);
}
- return GetExternalAnnotRecords(idh, sel);
}
diff --git a/c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp b/c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp
index 7ed486d..6348740 100644
--- a/c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp
+++ b/c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_id1.cpp 448568 2014-10-07 16:45:31Z ivanov $
+/* $Id: reader_id1.cpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -56,6 +56,7 @@
#include <serial/objistrasnb.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/serial.hpp>
+#include <serial/iterator.hpp>
#include <connect/ncbi_conn_stream.hpp>
#include <util/static_map.hpp>
@@ -307,7 +308,7 @@ bool CId1Reader::LoadSeq_idSeq_ids(CReaderRequestResult& result,
CConstRef<CSeq_id> id_ref = seq_id.GetSeqId();
const CDbtag& dbtag = id_ref->GetGeneral();
Int8 id;
- if ( dbtag.GetTag().GetIdType(id) == CObject_id::e_Id && id > 0 &&
+ if ( dbtag.GetTag().GetId8(id) && id > 0 &&
sc_SatMap.find(dbtag.GetDb().c_str()) != sc_SatMap.end() ) {
// only one source Seq-id and no synonyms
TSeqIds seq_ids;
@@ -384,8 +385,8 @@ bool CId1Reader::LoadGiSeq_ids(CReaderRequestResult& result,
bool CId1Reader::LoadSeq_idBlob_ids(CReaderRequestResult& result,
- const CSeq_id_Handle& seq_id,
- const SAnnotSelector* sel)
+ const CSeq_id_Handle& seq_id,
+ const SAnnotSelector* sel)
{
CLoadLockBlobIds ids(result, seq_id, sel);
if ( ids.IsLoaded() ) {
@@ -402,22 +403,25 @@ bool CId1Reader::LoadSeq_idBlob_ids(CReaderRequestResult& result,
if ( seq_id.Which() == CSeq_id::e_General ) {
CConstRef<CSeq_id> id_ref = seq_id.GetSeqId();
const CSeq_id& id = *id_ref;
- if ( id.GetGeneral().GetTag().IsId() ) {
+ Int8 num;
+ if ( id.GetGeneral().GetTag().GetId8(num) && num != 0 ) {
const CDbtag& dbtag = id.GetGeneral();
const string& db = dbtag.GetDb();
- int num = dbtag.GetTag().GetId();
- if ( num != 0 ) {
- TSatMap::const_iterator iter = sc_SatMap.find(db.c_str());
- if ( iter != sc_SatMap.end() ) {
- TBlobIds blob_ids;
- CRef<CBlob_id> blob_id(new CBlob_id);
- blob_id->SetSat(iter->second.first);
- blob_id->SetSatKey(num);
- blob_id->SetSubSat(iter->second.second);
- blob_ids.push_back(CBlob_Info(blob_id, fBlobHasAllLocal));
- ids.SetLoadedBlob_ids(CFixedBlob_ids(eTakeOwnership, blob_ids));
- return true;
+ TSatMap::const_iterator iter = sc_SatMap.find(db.c_str());
+ if ( iter != sc_SatMap.end() ) {
+ TBlobIds blob_ids;
+ CRef<CBlob_id> blob_id(new CBlob_id);
+ ESat sat = iter->second.first;
+ Int8 sat_key = num;
+ if ( sat == eSat_ANNOT_CDD || sat == eSat_ANNOT ) {
+ sat_key = CProcessor::ConvertGiFromOM(sat_key);
}
+ blob_id->SetSat(sat);
+ blob_id->SetSatKey(sat_key);
+ blob_id->SetSubSat(iter->second.second);
+ blob_ids.push_back(CBlob_Info(blob_id, fBlobHasAllLocal));
+ ids.SetLoadedBlob_ids(CFixedBlob_ids(eTakeOwnership, blob_ids));
+ return true;
}
}
}
@@ -443,8 +447,6 @@ bool CId1Reader::LoadSeq_idBlob_ids(CReaderRequestResult& result,
}
-const int kSat_BlobError = -1;
-
bool CId1Reader::LoadGiBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id)
{
@@ -527,7 +529,7 @@ bool CId1Reader::LoadGiBlob_ids(CReaderRequestResult& result,
ext_feat -= bit;
CRef<CBlob_id> blob_id(new CBlob_id);
blob_id->SetSat(GetAnnotSat(bit));
- blob_id->SetSatKey(gi);
+ blob_id->SetSatKey(CProcessor::ConvertGiFromOM(gi));
blob_id->SetSubSat(bit);
blob_ids.push_back(CBlob_Info(blob_id, fBlobHasExtAnnot));
}
@@ -600,7 +602,7 @@ void CId1Reader::GetBlobVersion(CReaderRequestResult& result,
CReader::TBlobVersion
CId1Reader::x_ResolveId(CReaderRequestResult& result,
CID1server_back& reply,
- const CID1server_request& request)
+ CID1server_request& request)
{
CConn conn(result, this);
x_SendRequest(conn, request);
@@ -706,8 +708,9 @@ void CId1Reader::x_SendRequest(const CBlob_id& blob_id, TConn conn)
void CId1Reader::x_SendRequest(TConn conn,
- const CID1server_request& request)
+ CID1server_request& request)
{
+ CProcessor::OffsetAllGisFromOM(Begin(request));
CConn_IOStream* stream = x_GetConnection(conn);
#ifdef GENBANK_ID1_RANDOM_FAILS
@@ -772,6 +775,7 @@ void CId1Reader::x_ReceiveReply(TConn conn,
s << " ID1server-back.";
}
}
+ CProcessor::OffsetAllGisToOM(Begin(reply));
}
END_SCOPE(objects)
diff --git a/c++/src/objtools/data_loaders/genbank/processors.cpp b/c++/src/objtools/data_loaders/genbank/processors.cpp
index e9a5f95..ddc4e0a 100644
--- a/c++/src/objtools/data_loaders/genbank/processors.cpp
+++ b/c++/src/objtools/data_loaders/genbank/processors.cpp
@@ -1,4 +1,4 @@
-/* $Id: processors.cpp 453538 2014-12-04 14:34:59Z vasilche $
+/* $Id: processors.cpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -48,9 +48,7 @@
#include <objects/id1/id1__.hpp>
#include <objects/id2/ID2_Reply_Data.hpp>
-#include <objects/seqsplit/ID2S_Split_Info.hpp>
-#include <objects/seqsplit/ID2S_Feat_type_Info.hpp>
-#include <objects/seqsplit/ID2S_Chunk.hpp>
+#include <objects/seqsplit/seqsplit__.hpp>
// for read hooks setup
#include <objects/general/general__.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
@@ -410,6 +408,193 @@ CWriter* CProcessor::GetWriter(const CReaderRequestResult& result) const
}
+NCBI_PARAM_DEF_EX(Int8, GENBANK, GI_OFFSET, 0,
+ eParam_NoThread, GENBANK_GI_OFFSET);
+
+
+TIntId CProcessor::GetGiOffset(void)
+{
+ static volatile TIntId gi_offset;
+ static volatile bool initialized;
+ if ( !initialized ) {
+ gi_offset = NCBI_PARAM_TYPE(GENBANK, GI_OFFSET)::GetDefault();
+ initialized = true;
+ }
+ return gi_offset;
+}
+
+
+bool CProcessor::OffsetId(CSeq_id& id, TIntId gi_offset)
+{
+ if ( !gi_offset ) {
+ return false;
+ }
+ if ( id.IsGi() ) {
+ if ( TGi gi = id.GetGi() ) {
+ id.SetGi(gi + gi_offset);
+ return true;
+ }
+ }
+ else if ( id.IsGeneral() ) {
+ CDbtag& dbtag = id.SetGeneral();
+ CObject_id& tag = dbtag.SetTag();
+ if ( tag.IsStr() &&
+ NStr::EqualNocase(dbtag.GetDb(), "NAnnot") ) {
+ // Named annotation virtual sequence id:
+ // gnl|NAnnot|12345:NA000012345.1
+ const string& s = tag.GetStr();
+ SIZE_TYPE sep = s.find(':');
+ Int8 id8;
+ if ( sep != NPOS &&
+ NStr::StringToNumeric(s, &id8, NStr::fConvErr_NoThrow) &&
+ id8 != 0 ) {
+ // offset only non-zero GIs
+ tag.SetStr(NStr::NumericToString(id8 + gi_offset) +
+ s.substr(sep));
+ return true;
+ }
+ }
+ else if ( NStr::StartsWith(dbtag.GetDb(), "ANNOT:", NStr::eNocase) ) {
+ // External annotation virtual sequence id:
+ // gnl|Annot:SNP|12345
+ CObject_id::TId8 id8 = 0;
+ if ( tag.GetId8(id8) &&
+ id8 != 0 ) {
+ // offset only non-zero GIs
+ tag.SetId8(id8 + gi_offset);
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
+
+bool CProcessor::OffsetId(CSeq_id_Handle& id, TIntId gi_offset)
+{
+ if ( !gi_offset ) {
+ return false;
+ }
+ if ( id.IsGi() ) {
+ if ( TGi gi = id.GetGi() ) {
+ id = CSeq_id_Handle::GetGiHandle(gi + gi_offset);
+ return true;
+ }
+ }
+ else if ( id.Which() == CSeq_id::e_General ) {
+ CRef<CSeq_id> seq_id(SerialClone(*id.GetSeqId()));
+ if ( OffsetId(*seq_id, gi_offset) ) {
+ id = CSeq_id_Handle::GetHandle(*seq_id);
+ return true;
+ }
+ }
+ return false;
+}
+
+
+void CProcessor::OffsetAllGis(CBeginInfo obj, TIntId gi_offset)
+{
+ if ( !gi_offset ) {
+ return;
+ }
+ for ( CTypeIterator<CSeq_id> it(obj); it; ++it ) {
+ OffsetId(*it, gi_offset);
+ }
+
+ // ID2
+ for ( CTypeIterator<CID1server_request> it(obj); it; ++it ) {
+ CID1server_request& req = *it;
+ switch ( req.Which() ) {
+ case CID1server_request::e_Getseqidsfromgi:
+ OffsetGi(req.SetGetseqidsfromgi(), gi_offset);
+ break;
+ case CID1server_request::e_Getgihist:
+ OffsetGi(req.SetGetgihist(), gi_offset);
+ break;
+ case CID1server_request::e_Getgirev:
+ OffsetGi(req.SetGetgirev(), gi_offset);
+ break;
+ case CID1server_request::e_Getgistate:
+ OffsetGi(req.SetGetgistate(), gi_offset);
+ break;
+ default:
+ break;
+ }
+ }
+ for ( CTypeIterator<CID1server_maxcomplex> it(obj); it; ++it ) {
+ OffsetGi(it->SetGi(), gi_offset);
+ }
+ for ( CTypeIterator<CID1server_back> it(obj); it; ++it ) {
+ CID1server_back& reply = *it;
+ if ( reply.IsGotgi() ) {
+ OffsetGi(reply.SetGotgi(), gi_offset);
+ }
+ }
+ for ( CTypeIterator<CID1blob_info> it(obj); it; ++it ) {
+ OffsetGi(it->SetGi(), gi_offset);
+ }
+
+ // ID2
+ for ( CTypeIterator<CID2S_Seq_loc> it(obj); it; ++it ) {
+ CID2S_Seq_loc& loc = *it;
+ if ( loc.IsWhole_gi() ) {
+ OffsetGi(loc.SetWhole_gi(), gi_offset);
+ }
+ }
+ for ( CTypeIterator<CID2S_Gi_Range> it(obj); it; ++it ) {
+ OffsetGi(it->SetStart(), gi_offset);
+ }
+ for ( CTypeIterator<CID2S_Gi_Interval> it(obj); it; ++it ) {
+ OffsetGi(it->SetGi(), gi_offset);
+ }
+ for ( CTypeIterator<CID2S_Gi_Ints> it(obj); it; ++it ) {
+ OffsetGi(it->SetGi(), gi_offset);
+ }
+ for ( CTypeIterator<CID2S_Bioseq_Ids> it(obj); it; ++it ) {
+ NON_CONST_ITERATE ( CID2S_Bioseq_Ids::Tdata, it2, it->Set() ) {
+ if ( (*it2)->IsGi() ) {
+ OffsetGi((*it2)->SetGi(), gi_offset);
+ }
+ }
+ }
+ for ( CTypeIterator<CID2S_Chunk_Data> it(obj); it; ++it ) {
+ if ( it->SetId().IsGi() ) {
+ OffsetGi(it->SetId().SetGi(), gi_offset);
+ }
+ }
+}
+
+
+void CProcessor::OffsetAllGis(CTSE_SetObjectInfo& set_info, TIntId gi_offset)
+{
+ if ( !gi_offset ) {
+ return;
+ }
+ NON_CONST_ITERATE ( CTSE_SetObjectInfo::TSeq_annot_InfoMap, it,
+ set_info.m_Seq_annot_InfoMap ) {
+ CSeq_annot_SNP_Info& snp_info = *it->second.m_SNP_annot_Info;
+ snp_info.SetGi(TIntId(snp_info.GetGi())+gi_offset);
+ }
+}
+
+
+void CProcessor::OffsetAllGisFromOM(CBeginInfo obj)
+{
+ OffsetAllGis(obj, -GetGiOffset());
+}
+
+
+void CProcessor::OffsetAllGisToOM(CBeginInfo obj, CTSE_SetObjectInfo* set_info)
+{
+ if ( TIntId gi_offset = GetGiOffset() ) {
+ OffsetAllGis(obj, gi_offset);
+ if ( set_info ) {
+ OffsetAllGis(*set_info, gi_offset);
+ }
+ }
+}
+
+
BEGIN_LOCAL_NAMESPACE;
@@ -770,6 +955,7 @@ void CProcessor_ID1::ProcessObjStream(CReaderRequestResult& result,
CLoadLockSetter setter(blob);
if ( !setter.IsLoaded() ) {
if ( entry.first ) {
+ OffsetAllGisToOM(*entry.first);
setter.SetSeq_entry(*entry.first);
}
setter.SetLoaded();
@@ -989,6 +1175,7 @@ void CProcessor_ID1_SNP::ProcessObjStream(CReaderRequestResult& result,
CLoadLockSetter setter(blob);
if ( !setter.IsLoaded() ) {
if ( entry.first ) {
+ OffsetAllGisToOM(*entry.first, &set_info);
setter.SetSeq_entry(*entry.first, &set_info);
}
setter.SetLoaded();
@@ -1079,6 +1266,7 @@ void CProcessor_SE::ProcessObjStream(CReaderRequestResult& result,
}}
+ OffsetAllGisToOM(*seq_entry);
setter.SetSeq_entry(*seq_entry);
if ( chunk_id == kMain_ChunkId &&
result.GetAddWGSMasterDescr() ) {
@@ -1204,6 +1392,7 @@ void CProcessor_SE_SNP::ProcessObjStream(CReaderRequestResult& result,
}
}
}}
+ OffsetAllGisToOM(*seq_entry, &set_info);
setter.SetSeq_entry(*seq_entry, &set_info);
setter.SetLoaded();
}
@@ -1481,6 +1670,7 @@ void CProcessor_St_SE_SNPT::ProcessStream(CReaderRequestResult& result,
if ( writer ) {
SaveSNPBlob(result, blob_id, chunk_id, writer, *seq_entry, blob_state, set_info);
}
+ OffsetAllGisToOM(*seq_entry, &set_info);
setter.SetSeq_entry(*seq_entry, &set_info);
setter.SetLoaded();
}
@@ -1609,6 +1799,7 @@ void CProcessor_ID2::ProcessData(CReaderRequestResult& result,
result.SetAndSaveBlobState(blob_id, blob_state);
CLoadLockSetter setter(blob);
if ( !setter.IsLoaded() ) {
+ OffsetAllGisToOM(*entry);
setter.SetSeq_entry(*entry);
if ( result.GetAddWGSMasterDescr() ) {
AddWGSMaster(setter);
@@ -1682,6 +1873,7 @@ void CProcessor_ID2::ProcessData(CReaderRequestResult& result,
if ( !setter.IsLoaded() ) {
CTSE_LoadLock& lock = setter.GetTSE_LoadLock();
lock->GetSplitInfo().SetSplitVersion(split_version);
+ OffsetAllGisToOM(*split_info);
CSplitParser::Attach(*lock, *split_info);
if ( result.GetAddWGSMasterDescr() ) {
AddWGSMaster(setter);
@@ -1729,6 +1921,7 @@ void CProcessor_ID2::ProcessData(CReaderRequestResult& result,
CReaderRequestResultRecursion r(result);
x_ReadData(data, Begin(*chunk), data_size);
+ OffsetAllGisToOM(*chunk);
CSplitParser::Load(setter.GetTSE_Chunk_Info(), *chunk);
LogStat(r, blob_id, chunk_id,
@@ -1906,7 +2099,7 @@ void CProcessor_ID2::x_ReadData(const CID2_Reply_Data& data,
in->SetSkipUnknownMembers(eSerialSkipUnknown_Yes);
in->SetSkipUnknownVariants(eSerialSkipUnknown_Yes);
in->Read(object);
- data_size += in->GetStreamPos();
+ data_size += size_t(in->GetStreamPos()); // in-memory size can't be bigger than size_t
}
@@ -2275,11 +2468,11 @@ void CProcessor_ExtAnnot::Process(CReaderRequestResult& result,
setter.GetTSE_LoadLock()->SetName(name);
}
- TGi gi = blob_id.GetSatKey();
+ TGi gi = ConvertGiToOM(blob_id.GetSatKey());
CSeq_id_Handle gih = CSeq_id_Handle::GetGiHandle(gi);
CSeq_id seq_id;
seq_id.SetGeneral().SetDb(db_name);
- seq_id.SetGeneral().SetTag().SetId(GI_TO(CObject_id::TId, gi));
+ seq_id.SetGeneral().SetTag().SetId8(gi);
CSeq_id_Handle seh = CSeq_id_Handle::GetHandle(seq_id);
CRef<CTSE_Chunk_Info> chunk(new CTSE_Chunk_Info(kDelayedMain_ChunkId));
diff --git a/c++/src/objtools/data_loaders/genbank/reader.cpp b/c++/src/objtools/data_loaders/genbank/reader.cpp
index c9d8734..eda9d2c 100644
--- a/c++/src/objtools/data_loaders/genbank/reader.cpp
+++ b/c++/src/objtools/data_loaders/genbank/reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader.cpp 448190 2014-10-02 20:01:18Z vasilche $
+/* $Id: reader.cpp 452490 2014-11-20 15:50:53Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -566,6 +566,16 @@ bool CReader::LoadSeq_idTaxId(CReaderRequestResult& result,
}
+bool CReader::LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id)
+{
+ if ( !result.IsLoadedHash(seq_id) ) {
+ result.SetLoadedHash(seq_id, 0);
+ }
+ return true;
+}
+
+
bool CReader::LoadAccVers(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TIds& ret)
{
@@ -650,6 +660,27 @@ bool CReader::LoadTaxIds(CReaderRequestResult& result,
}
+bool CReader::LoadHashes(CReaderRequestResult& result,
+ const TIds& ids, TLoaded& loaded, TTaxIds& ret)
+{
+ size_t count = ids.size();
+ for ( size_t i = 0; i < count; ++i ) {
+ if ( loaded[i] || CReadDispatcher::CannotProcess(ids[i]) ) {
+ continue;
+ }
+ CLoadLockHash lock(result, ids[i]);
+ if ( !lock.IsLoadedHash() ) {
+ m_Dispatcher->LoadSequenceHash(result, ids[i]);
+ }
+ if ( lock.IsLoadedHash() ) {
+ ret[i] = lock.GetHash();
+ loaded[i] = true;
+ }
+ }
+ return true;
+}
+
+
bool CReader::LoadStates(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TStates& ret)
{
@@ -665,6 +696,23 @@ bool CReader::LoadStates(CReaderRequestResult& result,
if ( lock.IsLoaded() ) {
CReadDispatcher::SetBlobState(i, result, ids, loaded, ret);
}
+ if ( loaded[i] ) {
+ continue;
+ }
+ CFixedBlob_ids blob_ids = lock.GetBlob_ids();
+ ITERATE ( CFixedBlob_ids, it, blob_ids ) {
+ if ( it->Matches(fBlobHasCore, 0) ) {
+ CLoadLockBlobState state_lock(result, *it->GetBlob_id());
+ if ( !state_lock.IsLoaded() ) {
+ m_Dispatcher->LoadBlobState(result, *it->GetBlob_id());
+ }
+ if ( state_lock.IsLoaded() ) {
+ ret[i] = state_lock.GetBlobState();
+ loaded[i] = true;
+ break;
+ }
+ }
+ }
}
return true;
}
@@ -1076,6 +1124,20 @@ void CReader::SetAndSaveSeq_idTaxId(CReaderRequestResult& result,
}
+void CReader::SetAndSaveSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id,
+ int hash,
+ ESave save) const
+{
+ if ( !result.SetLoadedHash(seq_id, hash) || save != eSave ) {
+ return;
+ }
+ if ( CWriter* writer = result.GetIdWriter() ) {
+ writer->SaveSequenceHash(result, seq_id);
+ }
+}
+
+
void CReader::SetAndSaveSeq_idBlob_ids(CReaderRequestResult& result,
const CSeq_id_Handle& seq_id,
const SAnnotSelector* sel,
diff --git a/c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp b/c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp
index fbc215e..6aa7e0f 100644
--- a/c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp
+++ b/c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_id2_base.cpp 463675 2015-03-31 18:23:39Z vasilche $
+/* $Id: reader_id2_base.cpp 469251 2015-06-02 19:33:36Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -370,6 +370,33 @@ bool CId2ReaderBase::LoadSeq_idTaxId(CReaderRequestResult& result,
}
+bool CId2ReaderBase::LoadSequenceHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& seq_id)
+{
+ if ( m_AvoidRequest & fAvoidRequest_for_SequenceHash ) {
+ return CReader::LoadSequenceHash(result, seq_id);
+ }
+
+ CLoadLockHash lock(result, seq_id);
+ if ( lock.IsLoadedHash() ) {
+ return true;
+ }
+ CID2_Request req;
+ CID2_Request::C_Request::TGet_seq_id& get_id =
+ req.SetRequest().SetGet_seq_id();
+ get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.GetSeqId());
+ get_id.SetSeq_id_type(CID2_Request_Get_Seq_id::eSeq_id_type_hash);
+ x_ProcessRequest(result, req, 0);
+
+ if ( !lock.IsLoadedHash() ) {
+ m_AvoidRequest |= fAvoidRequest_for_SequenceHash;
+ return true; // repeat
+ }
+
+ return true;
+}
+
+
bool CId2ReaderBase::LoadAccVers(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TIds& ret)
{
@@ -687,6 +714,86 @@ bool CId2ReaderBase::LoadTaxIds(CReaderRequestResult& result,
}
+bool CId2ReaderBase::LoadHashes(CReaderRequestResult& result,
+ const TIds& ids, TLoaded& loaded, THashes& ret)
+{
+ size_t max_request_size = GetMaxIdsRequestSize();
+ if ( max_request_size <= 1 ||
+ (m_AvoidRequest & fAvoidRequest_for_SequenceHash) ) {
+ return CReader::LoadHashes(result, ids, loaded, ret);
+ }
+
+ size_t count = ids.size();
+ CID2_Request_Packet packet;
+ size_t packet_start = 0;
+
+ for ( size_t i = 0; i < count; ++i ) {
+ if ( loaded[i] || CReadDispatcher::CannotProcess(ids[i]) ) {
+ continue;
+ }
+ if ( m_AvoidRequest & fAvoidRequest_for_SequenceHash ) {
+ return CReader::LoadHashes(result, ids, loaded, ret);
+ }
+ CLoadLockHash lock(result, ids[i]);
+ if ( lock.IsLoadedHash() ) {
+ ret[i] = lock.GetHash();
+ loaded[i] = true;
+ continue;
+ }
+
+ CRef<CID2_Request> req(new CID2_Request);
+ CID2_Request::C_Request::TGet_seq_id& get_id =
+ req->SetRequest().SetGet_seq_id();
+ get_id.SetSeq_id().SetSeq_id().Assign(*ids[i].GetSeqId());
+ get_id.SetSeq_id_type(CID2_Request_Get_Seq_id::eSeq_id_type_hash);
+ if ( packet.Set().empty() ) {
+ packet_start = i;
+ }
+ packet.Set().push_back(req);
+ if ( packet.Set().size() == max_request_size ) {
+ x_ProcessPacket(result, packet, 0);
+ size_t count = i+1;
+ for ( size_t i = packet_start; i < count; ++i ) {
+ if ( loaded[i] || CReadDispatcher::CannotProcess(ids[i]) ) {
+ continue;
+ }
+ CLoadLockHash lock(result, ids[i]);
+ if ( lock.IsLoadedHash() ) {
+ ret[i] = lock.GetHash();
+ loaded[i] = true;
+ continue;
+ }
+ else {
+ m_AvoidRequest |= fAvoidRequest_for_SequenceHash;
+ }
+ }
+ packet.Set().clear();
+ }
+ }
+
+ if ( !packet.Set().empty() ) {
+ x_ProcessPacket(result, packet, 0);
+
+ for ( size_t i = packet_start; i < count; ++i ) {
+ if ( loaded[i] || CReadDispatcher::CannotProcess(ids[i]) ) {
+ continue;
+ }
+ CLoadLockHash lock(result, ids[i]);
+ if ( lock.IsLoadedHash() ) {
+ ret[i] = lock.GetHash();
+ loaded[i] = true;
+ continue;
+ }
+ else {
+ m_AvoidRequest |= fAvoidRequest_for_SequenceHash;
+ }
+ }
+ }
+
+ return true;
+}
+
+
bool CId2ReaderBase::LoadStates(CReaderRequestResult& result,
const TIds& ids, TLoaded& loaded, TStates& ret)
{
@@ -1231,18 +1338,18 @@ void CId2ReaderBase::x_ProcessPacket(CReaderRequestResult& result,
// prepare serial nums and result state
int request_count = static_cast<int>(packet.Get().size());
- int end_serial_num = m_RequestSerialNumber.Add(request_count);
- if ( end_serial_num <= request_count ) {
+ int end_serial_num = static_cast<int>(m_RequestSerialNumber.Add(request_count));
+ while ( end_serial_num <= request_count ) {
// int overflow, adjust to 1
{{
DEFINE_STATIC_FAST_MUTEX(sx_Mutex);
CFastMutexGuard guard(sx_Mutex);
- int num = m_RequestSerialNumber.Get();
+ int num = static_cast<int>(m_RequestSerialNumber.Get());
if ( num <= request_count ) {
m_RequestSerialNumber.Set(1);
}
}}
- end_serial_num = m_RequestSerialNumber.Add(request_count);
+ end_serial_num = static_cast<int>(m_RequestSerialNumber.Add(request_count));
}
int start_serial_num = end_serial_num - request_count;
{{
@@ -1258,6 +1365,8 @@ void CId2ReaderBase::x_ProcessPacket(CReaderRequestResult& result,
CRef<CID2_Reply> reply;
try {
// send request
+
+ CProcessor::OffsetAllGisFromOM(packet);
{{
if ( GetDebugLevel() >= eTraceConn ) {
CDebugPrinter s(conn, "CId2Reader");
@@ -1348,6 +1457,7 @@ void CId2ReaderBase::x_ProcessPacket(CReaderRequestResult& result,
}
}
}
+ CProcessor::OffsetAllGisToOM(*reply);
int num = reply->GetSerial_number() - start_serial_num;
if ( reply->IsSetDiscard() ) {
// discard whole reply for now
@@ -1502,6 +1612,34 @@ void CId2ReaderBase::x_UpdateLoadedSet(CReaderRequestResult& result,
}
+inline void CId2ReaderBase::sx_CheckErrorFlag(const CID2_Error& error,
+ TErrorFlags& error_flags,
+ EErrorFlags test_flag,
+ const char* marker1,
+ const char* marker2)
+{
+ if ( !error.IsSetMessage() ) {
+ // no message to parse
+ return;
+ }
+ if ( error_flags & test_flag ) {
+ // already set
+ return;
+ }
+ SIZE_TYPE pos = NStr::FindNoCase(error.GetMessage(), marker1);
+ if ( pos == NPOS) {
+ // no marker
+ return;
+ }
+ if ( marker2 &&
+ NStr::FindNoCase(error.GetMessage(), marker2, pos) == NPOS ) {
+ // no second marker
+ return;
+ }
+ error_flags |= test_flag;
+}
+
+
CId2ReaderBase::TErrorFlags
CId2ReaderBase::x_GetError(CReaderRequestResult& result,
const CID2_Error& error)
@@ -1516,10 +1654,9 @@ CId2ReaderBase::x_GetError(CReaderRequestResult& result,
break;
case CID2_Error::eSeverity_failed_connection:
error_flags |= fError_bad_connection;
- if ( error.IsSetMessage() &&
- NStr::FindNoCase(error.GetMessage(), "timed") &&
- NStr::FindNoCase(error.GetMessage(), "out") ) {
- error_flags |= fError_inactivity_timeout;
+ if ( error.IsSetMessage() ) {
+ sx_CheckErrorFlag(error, error_flags,
+ fError_inactivity_timeout, "timed", "out");
}
break;
case CID2_Error::eSeverity_failed_server:
@@ -1554,22 +1691,16 @@ CId2ReaderBase::x_GetMessageError(const CID2_Error& error)
case CID2_Error::eSeverity_warning:
error_flags |= fError_warning;
if ( error.IsSetMessage() ) {
- if ( !(error_flags & fError_warning_dead) &&
- NStr::FindNoCase(error.GetMessage(), "obsolete") != NPOS ) {
- error_flags |= fError_warning_dead;
- }
- if ( !(error_flags & fError_suppressed_perm) &&
- NStr::FindNoCase(error.GetMessage(), "removed") != NPOS ) {
- error_flags |= fError_suppressed_perm;
- }
- if ( !(error_flags & fError_suppressed_perm) &&
- NStr::FindNoCase(error.GetMessage(), "suppressed") != NPOS ) {
- error_flags |= fError_suppressed_perm;
- }
- if ( !(error_flags & fError_suppressed_temp) &&
- NStr::FindNoCase(error.GetMessage(), "superseded") != NPOS ) {
- error_flags |= fError_suppressed_temp;
- }
+ sx_CheckErrorFlag(error, error_flags,
+ fError_warning_dead, "obsolete");
+ sx_CheckErrorFlag(error, error_flags,
+ fError_suppressed_perm, "removed");
+ sx_CheckErrorFlag(error, error_flags,
+ fError_suppressed_perm, "suppressed");
+ sx_CheckErrorFlag(error, error_flags,
+ fError_suppressed_perm, "superceded"); // temp?
+ sx_CheckErrorFlag(error, error_flags,
+ fError_suppressed_temp, "superseded"); // perm?
}
break;
case CID2_Error::eSeverity_failed_command:
@@ -1586,12 +1717,13 @@ CId2ReaderBase::x_GetMessageError(const CID2_Error& error)
break;
case CID2_Error::eSeverity_restricted_data:
error_flags |= fError_no_data;
- if ( error.IsSetMessage() &&
- (NStr::FindNoCase(error.GetMessage(), "withdrawn") != NPOS ||
- NStr::FindNoCase(error.GetMessage(), "removed") != NPOS) ) {
- error_flags |= fError_withdrawn;
+ if ( error.IsSetMessage() ) {
+ sx_CheckErrorFlag(error, error_flags,
+ fError_withdrawn, "withdrawn");
+ sx_CheckErrorFlag(error, error_flags,
+ fError_withdrawn, "removed");
}
- else {
+ if ( !(error_flags & fError_withdrawn) ) {
error_flags |= fError_restricted;
}
break;
@@ -1635,9 +1767,48 @@ CId2ReaderBase::x_GetMessageError(const CID2_Reply& reply)
CReader::TBlobState
-CId2ReaderBase::x_GetBlobState(const CID2_Reply& reply,
+CId2ReaderBase::x_GetBlobStateFromID2(const CBlob_id& blob_id,
+ SId2LoadedSet& loaded_set,
+ int id2_state)
+{
+ TBlobState blob_state = 0;
+ if ( id2_state & (1<<eID2_Blob_State_suppressed_temp) ) {
+ blob_state |= CBioseq_Handle::fState_suppress_temp;
+ }
+ if ( id2_state & (1<<eID2_Blob_State_suppressed) ) {
+ blob_state |= CBioseq_Handle::fState_suppress_perm;
+ }
+ if ( id2_state & (1<<eID2_Blob_State_dead) ) {
+ blob_state |= CBioseq_Handle::fState_dead;
+ }
+ if ( id2_state & (1<<eID2_Blob_State_protected) ) {
+ blob_state |= CBioseq_Handle::fState_confidential;
+ blob_state |= CBioseq_Handle::fState_no_data;
+ }
+ if ( id2_state & (1<<eID2_Blob_State_withdrawn) ) {
+ blob_state |= CBioseq_Handle::fState_withdrawn;
+ blob_state |= CBioseq_Handle::fState_no_data;
+ }
+ if ( blob_state ) {
+ loaded_set.m_BlobStates[blob_id] |= blob_state;
+ }
+ return blob_state;
+}
+
+
+
+CReader::TBlobState
+CId2ReaderBase::x_GetBlobState(const CBlob_id& blob_id,
+ SId2LoadedSet& loaded_set,
+ const CID2_Reply& reply,
TErrorFlags* errors_ptr)
{
+ SId2LoadedSet::TBlobStates::const_iterator it =
+ loaded_set.m_BlobStates.find(blob_id);
+ if ( it != loaded_set.m_BlobStates.end() ) {
+ return it->second;
+ }
+
TBlobState blob_state = 0;
TErrorFlags errors = x_GetMessageError(reply);
if ( errors_ptr ) {
@@ -1655,12 +1826,12 @@ CId2ReaderBase::x_GetBlobState(const CID2_Reply& reply,
if ( errors & fError_warning_dead ) {
blob_state |= CBioseq_Handle::fState_dead;
}
- if ( errors & fError_suppressed_temp ) {
- blob_state |= CBioseq_Handle::fState_suppress_temp;
- }
if ( errors & fError_suppressed_perm ) {
blob_state |= CBioseq_Handle::fState_suppress_perm;
}
+ else if ( errors & fError_suppressed_temp ) {
+ blob_state |= CBioseq_Handle::fState_suppress_temp;
+ }
return blob_state;
}
@@ -1827,6 +1998,9 @@ void CId2ReaderBase::x_ProcessGetSeqIdSeqId(
case CID2_Request_Get_Seq_id::eSeq_id_type_taxid:
SetAndSaveSeq_idTaxId(result, seq_id, -1);
break;
+ case CID2_Request_Get_Seq_id::eSeq_id_type_hash:
+ SetAndSaveSequenceHash(result, seq_id, 0);
+ break;
default:
break;
}
@@ -1908,6 +2082,25 @@ void CId2ReaderBase::x_ProcessGetSeqIdSeqId(
SetAndSaveSeq_idTaxId(result, seq_id, taxid, save);
break;
}}
+ case CID2_Request_Get_Seq_id::eSeq_id_type_hash:
+ {{
+ ESave save = eDoNotSave;
+ int hash = 0;
+ ITERATE ( CID2_Reply_Get_Seq_id::TSeq_id, it, reply.GetSeq_id() ) {
+ const CSeq_id& id = **it;
+ if ( id.IsGeneral() ) {
+ const CDbtag& dbtag = id.GetGeneral();
+ const CObject_id& obj_id = dbtag.GetTag();
+ if ( obj_id.IsId() && dbtag.GetDb() == "HASH" ) {
+ hash = obj_id.GetId();
+ save = eSave;
+ break;
+ }
+ }
+ }
+ SetAndSaveSequenceHash(result, seq_id, hash, save);
+ break;
+ }}
default:
// ???
break;
@@ -1923,8 +2116,17 @@ void CId2ReaderBase::x_ProcessGetBlobId(
{
const CSeq_id& seq_id = reply.GetSeq_id();
CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(seq_id);
- TErrorFlags errors;
- TBlobState blob_state = x_GetBlobState(main_reply, &errors);
+ const CID2_Blob_Id& src_blob_id = reply.GetBlob_id();
+ CBlob_id blob_id = GetBlobId(src_blob_id);
+ TErrorFlags errors = 0;
+ TBlobState blob_state;
+ if ( reply.IsSetBlob_state() ) {
+ blob_state = x_GetBlobStateFromID2(blob_id, loaded_set,
+ reply.GetBlob_state());
+ }
+ else {
+ blob_state = x_GetBlobState(blob_id, loaded_set, main_reply, &errors);
+ }
if ( blob_state & CBioseq_Handle::fState_no_data ) {
SetAndSaveNoSeq_idBlob_ids(result, idh, 0, blob_state);
return;
@@ -1935,8 +2137,6 @@ void CId2ReaderBase::x_ProcessGetBlobId(
SId2LoadedSet::TBlob_idsInfo& ids = loaded_set.m_Blob_ids[idh];
ids.first |= blob_state;
- const CID2_Blob_Id& src_blob_id = reply.GetBlob_id();
- CBlob_id blob_id = GetBlobId(src_blob_id);
if ( blob_state ) {
loaded_set.m_BlobStates[blob_id] |= blob_state;
}
@@ -2024,7 +2224,14 @@ void CId2ReaderBase::x_ProcessGetBlob(
SetAndSaveBlobVersion(result, blob_id, blob_version);
}
- TBlobState blob_state = x_GetBlobState(main_reply);
+ TBlobState blob_state;
+ if ( reply.IsSetBlob_state() ) {
+ blob_state = x_GetBlobStateFromID2(blob_id, loaded_set,
+ reply.GetBlob_state());
+ }
+ else {
+ blob_state = x_GetBlobState(blob_id, loaded_set, main_reply);
+ }
if ( blob_state & CBioseq_Handle::fState_no_data ) {
SetAndSaveNoBlob(result, blob_id, chunk_id, blob_state);
return;
@@ -2145,14 +2352,14 @@ void CId2ReaderBase::x_ProcessGetSplitInfo(
}
}
- TBlobState blob_state = x_GetBlobState(main_reply);
- {{
- SId2LoadedSet::TBlobStates::iterator iter =
- loaded_set.m_BlobStates.find(blob_id);
- if ( iter != loaded_set.m_BlobStates.end() ) {
- blob_state |= iter->second;
- }
- }}
+ TBlobState blob_state;
+ if ( reply.IsSetBlob_state() ) {
+ blob_state = x_GetBlobStateFromID2(blob_id, loaded_set,
+ reply.GetBlob_state());
+ }
+ else {
+ blob_state = x_GetBlobState(blob_id, loaded_set, main_reply);
+ }
if ( blob_state & CBioseq_Handle::fState_no_data ) {
SetAndSaveNoBlob(result, blob_id, chunk_id, blob_state);
return;
diff --git a/c++/src/objtools/data_loaders/genbank/reader_service.cpp b/c++/src/objtools/data_loaders/genbank/reader_service.cpp
index 3f00e2e..ad7d9c4 100644
--- a/c++/src/objtools/data_loaders/genbank/reader_service.cpp
+++ b/c++/src/objtools/data_loaders/genbank/reader_service.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_service.cpp 448568 2014-10-07 16:45:31Z ivanov $
+/* $Id: reader_service.cpp 446572 2014-09-16 19:05:59Z grichenk $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
diff --git a/c++/src/objtools/data_loaders/genbank/reader_snp.cpp b/c++/src/objtools/data_loaders/genbank/reader_snp.cpp
index 0e38852..469c3c0 100644
--- a/c++/src/objtools/data_loaders/genbank/reader_snp.cpp
+++ b/c++/src/objtools/data_loaders/genbank/reader_snp.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_snp.cpp 448568 2014-10-07 16:45:31Z ivanov $
+/* $Id: reader_snp.cpp 468616 2015-05-26 19:33:41Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -181,7 +181,7 @@ CSNP_Seq_feat_hook::~CSNP_Seq_feat_hook(void)
{
if ( CollectSNPStat() ) {
size_t total =
- accumulate(m_Count, m_Count+SSNP_Info::eSNP_Type_last, 0);
+ accumulate(m_Count, m_Count+SSNP_Info::eSNP_Type_last, size_t(0));
NcbiCout << "CSeq_annot_SNP_Info statistic (gi = " <<
m_Seq_annot_SNP_Info.GetGi() << "):\n";
for ( size_t i = 0; i < SSNP_Info::eSNP_Type_last; ++i ) {
@@ -194,7 +194,7 @@ CSNP_Seq_feat_hook::~CSNP_Seq_feat_hook(void)
NcbiCout << NcbiEndl;
total =
- accumulate(s_TotalCount, s_TotalCount+SSNP_Info::eSNP_Type_last,0);
+ accumulate(s_TotalCount, s_TotalCount+SSNP_Info::eSNP_Type_last,size_t(0));
NcbiCout << "cumulative CSeq_annot_SNP_Info statistic:\n";
for ( size_t i = 0; i < SSNP_Info::eSNP_Type_last; ++i ) {
NcbiCout <<
@@ -332,6 +332,51 @@ static unsigned read_unsigned(CNcbiIstream& stream,
}
+static void write_gi(CNcbiOstream& stream,
+ TGi gi,
+ const char* name)
+{
+ TIntId n = gi;
+ char c[8];
+ for ( int i = 7; i >= 0; --i ) {
+ c[i] = char(n);
+ n >>= 8;
+ }
+ stream.write(c, sizeof(c));
+}
+
+
+static TGi read_gi(CNcbiIstream& stream,
+ const char* name)
+{
+ char c[8];
+ stream.read(c, sizeof(c));
+ if ( !stream ) {
+ NCBI_THROW(CLoaderException, eLoaderFailed,
+ string("Cannot read ")+name);
+ }
+ TIntId n =
+ (Uint1(c[4])<<24) |
+ (Uint1(c[5])<<16) |
+ (Uint1(c[6])<< 8) |
+ (Uint1(c[7]) );
+ TIntId n2 =
+ (Uint1(c[0])<<24) |
+ (Uint1(c[1])<<16) |
+ (Uint1(c[2])<< 8) |
+ (Uint1(c[3]) );
+#ifdef NCBI_INT8_GI
+ n |= n2<<32;
+#else
+ if ( n2 != (n>>31) ) { // high 32-bits must be the same as sign bit
+ NCBI_THROW(CLoaderException, eLoaderFailed,
+ string("GI overflow ")+name);
+ }
+#endif
+ return n;
+}
+
+
static void write_size(CNcbiOstream& stream, size_t size)
{
// use ASN.1 binary like format
@@ -490,7 +535,7 @@ public:
}
-static const unsigned MAGIC = 0x12340007;
+static const unsigned MAGIC = 0x12340008;
void CSeq_annot_SNP_Info_Reader::Write(CNcbiOstream& stream,
const CConstObjectInfo& object,
@@ -600,7 +645,7 @@ void CSeq_annot_SNP_Info_Reader::x_Write(CNcbiOstream& stream,
{
// header
write_unsigned(stream, MAGIC, "SNP table magic number");
- write_unsigned(stream, GI_TO(unsigned, snp_info.GetGi()), "SNP table GI");
+ write_gi(stream, snp_info.GetGi(), "SNP table GI");
// strings
StoreIndexedStringsTo(stream, snp_info.m_Comments);
@@ -633,7 +678,7 @@ void CSeq_annot_SNP_Info_Reader::x_Read(CNcbiIstream& stream,
NCBI_THROW(CLoaderException, eLoaderFailed,
"Incompatible version of SNP table");
}
- snp_info.x_SetGi(GI_FROM(unsigned, read_unsigned(stream, "SNP table GI")));
+ snp_info.x_SetGi(read_gi(stream, "SNP table GI"));
// strings
LoadIndexedStringsFrom(stream,
diff --git a/c++/src/objtools/data_loaders/genbank/request_result.cpp b/c++/src/objtools/data_loaders/genbank/request_result.cpp
index 45cd39f..ef2e7d5 100644
--- a/c++/src/objtools/data_loaders/genbank/request_result.cpp
+++ b/c++/src/objtools/data_loaders/genbank/request_result.cpp
@@ -1,4 +1,4 @@
-/* $Id: request_result.cpp 440718 2014-07-16 16:14:09Z vasilche $
+/* $Id: request_result.cpp 468561 2015-05-26 15:57:12Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,21 +39,30 @@
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <corelib/ncbithr.hpp>
+#include <serial/iterator.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
using namespace GBL;
-static const CReaderRequestResult::TBlobState kBlobStateNotSet = -1;
static const CReaderRequestResult::TBlobVersion kBlobVersionNotSet = -1;
+NCBI_PARAM_DECL(int, GENBANK, TRACE_LOAD);
+NCBI_PARAM_DEF_EX(int, GENBANK, TRACE_LOAD, 0,
+ eParam_NoThread, GENBANK_TRACE_LOAD);
-static inline TThreadSystemID GetThreadId(void)
+
+static
+int s_GetLoadTraceLevel(void)
{
- TThreadSystemID thread_id = 0;
- CThread::GetSystemID(&thread_id);
- return thread_id;
+ static volatile int load_trace_level;
+ static volatile bool initialized;
+ if ( !initialized ) {
+ load_trace_level = NCBI_PARAM_TYPE(GENBANK, TRACE_LOAD)::GetDefault();
+ initialized = true;
+ }
+ return load_trace_level;
}
@@ -73,7 +82,7 @@ CFixedSeq_ids::CFixedSeq_ids(const TList& list, TState state)
m_Ref(new TObject(list))
{
if ( list.empty() ) {
- state |= CBioseq_Handle::fState_no_data;
+ m_State |= CBioseq_Handle::fState_no_data;
}
}
@@ -125,6 +134,20 @@ string CFixedSeq_ids::FindLabel(void) const
}
+CNcbiOstream& operator<<(CNcbiOstream& out, const CFixedSeq_ids& ids)
+{
+ const char* sep = "( ";
+ const char* end = "()";
+ ITERATE ( CFixedSeq_ids, it, ids ) {
+ out << sep << *it;
+ sep = ", ";
+ end = " )";
+ }
+ out << end;
+ return out;
+}
+
+
/////////////////////////////////////////////////////////////////////////////
// CFixedBlob_ids
/////////////////////////////////////////////////////////////////////////////
@@ -165,6 +188,20 @@ CFixedBlob_ids::CFixedBlob_ids(ENcbiOwnership ownership, TList& list,
}
+CNcbiOstream& operator<<(CNcbiOstream& out, const CFixedBlob_ids& ids)
+{
+ const char* sep = "( ";
+ const char* end = "()";
+ ITERATE ( CFixedBlob_ids, it, ids ) {
+ out << sep << it->GetBlob_id();
+ sep = ", ";
+ end = " )";
+ }
+ out << end;
+ return out;
+}
+
+
/////////////////////////////////////////////////////////////////////////////
// CBlob_Info
/////////////////////////////////////////////////////////////////////////////
@@ -404,6 +441,70 @@ void CLoadLockBlob::x_ObtainTSE_LoadLock(CReaderRequestResult& result)
/////////////////////////////////////////////////////////////////////////////
+BEGIN_LOCAL_NAMESPACE;
+
+struct SBlobId
+{
+ SBlobId(const CTSE_Info& tse)
+ : m_TSE(tse)
+ {
+ }
+
+ const CTSE_Info& m_TSE;
+};
+
+CNcbiOstream& operator<<(CNcbiOstream& out, const SBlobId& id)
+{
+ out << id.m_TSE.GetBlobId().ToString();
+ return out;
+}
+
+struct SChunkId
+{
+ SChunkId(const CTSE_Chunk_Info& chunk)
+ : m_Chunk(chunk)
+ {
+ }
+
+ const CTSE_Chunk_Info& m_Chunk;
+};
+
+CNcbiOstream& operator<<(CNcbiOstream& out, const SChunkId& id)
+{
+ out << id.m_Chunk.GetSplitInfo().GetBlobId().ToString()<<"."<<id.m_Chunk.GetChunkId();
+ return out;
+}
+
+struct SSeqIds
+{
+ SSeqIds(const CSeq_entry& entry)
+ : m_Entry(entry)
+ {
+ }
+
+ const CSeq_entry& m_Entry;
+};
+
+CNcbiOstream& operator<<(CNcbiOstream& out, const SSeqIds& ids)
+{
+ for ( CTypeConstIterator<CBioseq> it = Begin(ids.m_Entry); it; ++it ) {
+ const CBioseq& seq = *it;
+ const char* sep = "Bioseq( ";
+ const char* end = "Bioseq()";
+ ITERATE ( CBioseq::TId, it2, seq.GetId() ) {
+ out << sep << (*it2)->AsFastaString();
+ sep = ", ";
+ end = " )";
+ }
+ out << end;
+ break;
+ }
+ return out;
+}
+
+END_LOCAL_NAMESPACE;
+
+
CLoadLockSetter::CLoadLockSetter(CLoadLockBlob& lock)
{
x_Init(lock, lock.GetSelectedChunkId());
@@ -476,6 +577,9 @@ void CLoadLockSetter::SetLoaded(void)
{
_ASSERT(!IsLoaded());
if ( !m_Chunk ) {
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:"<<SBlobId(*m_TSE_LoadLock)<<" loaded");
+ }
m_TSE_LoadLock.SetLoaded();
TParent::SetLoaded(m_TSE_LoadLock);
CReaderRequestResult& result =
@@ -483,6 +587,11 @@ void CLoadLockSetter::SetLoaded(void)
result.x_AddTSE_LoadLock(m_TSE_LoadLock);
}
else {
+ if ( s_GetLoadTraceLevel() >= 2 ||
+ (s_GetLoadTraceLevel() >= 1 &&
+ m_Chunk->GetChunkId() >= kMasterWGS_ChunkId) ) {
+ LOG_POST(Info<<"GBLoader:"<<SChunkId(*m_Chunk)<<" loaded");
+ }
m_Chunk->SetLoaded();
}
}
@@ -548,9 +657,15 @@ void CLoadLockSetter::SetSeq_entry(CSeq_entry& entry,
{
_ASSERT(!IsLoaded());
if ( !m_Chunk ) {
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:"<<SBlobId(*m_TSE_LoadLock)<<" entry = "<<SSeqIds(entry));
+ }
m_TSE_LoadLock->SetSeq_entry(entry, set_info);
}
else {
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:"<<SChunkId(*m_Chunk)<<" entry = "<<SSeqIds(entry));
+ }
m_Chunk->x_LoadSeq_entry(entry, set_info);
}
}
@@ -755,6 +870,7 @@ CGBInfoManager::CGBInfoManager(size_t gc_size)
m_CacheStrGi(GetMainMutex(), gc_size),
m_CacheLabel(GetMainMutex(), gc_size),
m_CacheTaxId(GetMainMutex(), gc_size),
+ m_CacheHash(GetMainMutex(), gc_size),
m_CacheBlobIds(GetMainMutex(), gc_size),
m_CacheBlobState(GetMainMutex(), gc_size),
m_CacheBlobVersion(GetMainMutex(), gc_size),
@@ -769,7 +885,7 @@ CGBInfoManager::~CGBInfoManager(void)
CLoadLockSeqIds::CLoadLockSeqIds(CReaderRequestResult& result,
- const CSeq_id_Handle& id)
+ const CSeq_id_Handle& id)
: TParent(result.GetLoadLockSeqIds(id))
{
}
@@ -832,6 +948,13 @@ CLoadLockTaxId::CLoadLockTaxId(CReaderRequestResult& result,
}
+CLoadLockHash::CLoadLockHash(CReaderRequestResult& result,
+ const CSeq_id_Handle& id)
+ : TParent(result.GetLoadLockHash(id))
+{
+}
+
+
CLoadLockBlobIds::CLoadLockBlobIds(CReaderRequestResult& result,
const CSeq_id_Handle& id,
const SAnnotSelector* sel)
@@ -917,6 +1040,9 @@ bool
CReaderRequestResult::SetLoadedSeqIds(const CSeq_id_Handle& id,
const CFixedSeq_ids& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") seq_ids = "<<value);
+ }
return GetGBInfoManager().m_CacheSeqIds.SetLoaded(*this, id, value);
}
@@ -959,6 +1085,9 @@ bool
CReaderRequestResult::SetLoadedSeqIds(const string& id,
const CFixedSeq_ids& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:StrId("<<id<<") seq_ids = "<<value);
+ }
return GetGBInfoManager().m_CacheStrSeqIds.SetLoaded(*this, id, value);
}
@@ -971,6 +1100,9 @@ bool
CReaderRequestResult::SetLoadedSeqIds(const CSeq_id_Handle& id,
const CLoadLockSeqIds& ids)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") seq_ids = "<<ids.GetData());
+ }
CLoadLockSeqIds lock(*this, id);
return lock.SetLoadedSeq_ids(ids);
}
@@ -981,6 +1113,9 @@ CReaderRequestResult::SetLoadedBlobIds(const CSeq_id_Handle& id,
const SAnnotSelector* sel,
const CLoadLockBlobIds& ids)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") blob_ids = "<<ids.GetData());
+ }
CLoadLockBlobIds lock(*this, id, sel);
return lock.SetLoadedBlob_ids(ids);
}
@@ -1034,6 +1169,9 @@ bool
CReaderRequestResult::SetLoadedAcc(const CSeq_id_Handle& id,
const CSeq_id_Handle& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") acc = "<<value);
+ }
return GetGBInfoManager().m_CacheAcc.SetLoaded(*this, id, value);
}
@@ -1056,6 +1194,9 @@ bool CReaderRequestResult::SetLoadedAccFromSeqIds(const CSeq_id_Handle& id,
const CLoadLockSeqIds& ids)
{
CSeq_id_Handle acc = ids.GetSeq_ids().FindAccVer();
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") acc = "<<acc);
+ }
TExpirationTime exp_time = ids.GetExpirationTime();
return GetGBInfoManager().m_CacheAcc.SetLoaded(*this, id, acc, exp_time);
}
@@ -1069,6 +1210,9 @@ CReaderRequestResult::SetLoadedSeqIdsFromZeroGi(const CSeq_id_Handle& id,
const CLoadLockGi& gi_lock)
{
_ASSERT(gi_lock.IsLoadedGi() && gi_lock.GetGi() == ZERO_GI);
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") seq_ids = null");
+ }
CLoadLockSeqIds lock(*this, id);
TBlobState state = CBioseq_Handle::fState_no_data;
return lock.SetLoadedSeq_ids(CFixedSeq_ids(state),
@@ -1082,6 +1226,9 @@ CReaderRequestResult::SetLoadedBlobIdsFromZeroGi(const CSeq_id_Handle& id,
const CLoadLockGi& gi_lock)
{
_ASSERT(gi_lock.IsLoadedGi() && gi_lock.GetGi() == ZERO_GI);
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") blob_ids = null");
+ }
CLoadLockBlobIds lock(*this, id, sel);
TBlobState state = CBioseq_Handle::fState_no_data;
return lock.SetNoBlob_ids(state,
@@ -1104,6 +1251,9 @@ bool CReaderRequestResult::SetLoadedGiFromSeqIds(const CSeq_id_Handle& id,
const CLoadLockSeqIds& ids)
{
TGi gi = ids.GetSeq_ids().FindGi();
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") gi = "<<gi);
+ }
TExpirationTime exp_time = ids.GetExpirationTime();
return GetGBInfoManager().m_CacheGi.SetLoaded(*this, id, gi, exp_time);
}
@@ -1156,6 +1306,9 @@ bool
CReaderRequestResult::SetLoadedGi(const CSeq_id_Handle& id,
const TGi& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") gi = "<<value);
+ }
return GetGBInfoManager().m_CacheGi.SetLoaded(*this, id, value);
}
@@ -1207,6 +1360,9 @@ bool
CReaderRequestResult::SetLoadedGi(const string& id,
const TGi& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:StrId("<<id<<") gi = "<<value);
+ }
return GetGBInfoManager().m_CacheStrGi.SetLoaded(*this, id, value);
}
@@ -1229,6 +1385,9 @@ bool CReaderRequestResult::SetLoadedLabelFromSeqIds(const CSeq_id_Handle& id,
const CLoadLockSeqIds& ids)
{
string label = ids.GetSeq_ids().FindLabel();
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") label = "<<label);
+ }
TExpirationTime exp_time = ids.GetExpirationTime();
return GetGBInfoManager().m_CacheLabel.SetLoaded(*this, id, label, exp_time);
}
@@ -1272,6 +1431,9 @@ bool
CReaderRequestResult::SetLoadedLabel(const CSeq_id_Handle& id,
const string& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") label = "<<value);
+ }
return GetGBInfoManager().m_CacheLabel.SetLoaded(*this, id, value);
}
@@ -1314,11 +1476,59 @@ bool
CReaderRequestResult::SetLoadedTaxId(const CSeq_id_Handle& id,
const TTaxId& value)
{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") tax_id = "<<value);
+ }
return GetGBInfoManager().m_CacheTaxId.SetLoaded(*this, id, value);
}
/////////////////////////////////////////////////////////////////////////////
+// Seq-id -> Hash
+
+bool
+CReaderRequestResult::IsLoadedHash(const CSeq_id_Handle& id)
+{
+ return GetGBInfoManager().m_CacheHash.IsLoaded(*this, id);
+}
+
+
+bool
+CReaderRequestResult::MarkLoadingHash(const CSeq_id_Handle& id)
+{
+ return GetGBInfoManager().m_CacheHash.MarkLoading(*this, id);
+}
+
+
+CReaderRequestResult::TInfoLockHash
+CReaderRequestResult::GetLoadLockHash(const CSeq_id_Handle& id)
+{
+ // if connection is allocated we cannot wait for another lock because
+ // of possible deadlock.
+ EDoNotWait do_not_wait = m_AllocatedConnection? eDoNotWait: eAllowWaiting;
+ return GetGBInfoManager().m_CacheHash.GetLoadLock(*this, id, do_not_wait);
+}
+
+
+CReaderRequestResult::TInfoLockHash
+CReaderRequestResult::GetLoadedHash(const CSeq_id_Handle& id)
+{
+ return GetGBInfoManager().m_CacheHash.GetLoaded(*this, id);
+}
+
+
+bool
+CReaderRequestResult::SetLoadedHash(const CSeq_id_Handle& id,
+ const TSequenceHash& value)
+{
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") hash = "<<value);
+ }
+ return GetGBInfoManager().m_CacheHash.SetLoaded(*this, id, value);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////
// Seq-id -> BlobIds
bool
@@ -1366,7 +1576,9 @@ CReaderRequestResult::SetLoadedBlobIds(const CSeq_id_Handle& id,
const CFixedBlob_ids& value)
{
TKeyBlob_ids key = s_KeyBlobIds(id, sel);
- LOG_POST("SetLoadedBlobIds("<<id<<","<<key.second<<")");
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:SeqId("<<id<<") blob_ids("<<key.second<<") = "<<value);
+ }
return GetGBInfoManager().m_CacheBlobIds.SetLoaded(*this, key, value);
}
@@ -1398,6 +1610,9 @@ bool CReaderRequestResult::SetLoadedBlobState(const CBlob_id& blob_id,
blob_id,
state);
if ( changed ) {
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:"<<blob_id<<" state = "<<state);
+ }
// set to TSE_Info
CLoadLockBlob blob(*this, blob_id);
if ( blob.IsLoadedBlob() ) {
@@ -1453,6 +1668,9 @@ bool CReaderRequestResult::SetLoadedBlobVersion(const CBlob_id& blob_id,
blob_id,
version);
if ( changed ) {
+ if ( s_GetLoadTraceLevel() > 0 ) {
+ LOG_POST(Info<<"GBLoader:"<<blob_id<<" version = "<<version);
+ }
// set to TSE_Info
CLoadLockBlob blob(*this, blob_id);
if ( blob.IsLoadedBlob() ) {
diff --git a/c++/src/objtools/data_loaders/genbank/seqref.cpp b/c++/src/objtools/data_loaders/genbank/seqref.cpp
index e2ff08b..2ca4f90 100644
--- a/c++/src/objtools/data_loaders/genbank/seqref.cpp
+++ b/c++/src/objtools/data_loaders/genbank/seqref.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqref.cpp 440703 2014-07-16 15:38:41Z vasilche $
+/* $Id: seqref.cpp 468375 2015-05-22 13:03:02Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -35,7 +35,7 @@ BEGIN_SCOPE(objects)
CSeqref::CSeqref(void)
: m_Flags(fBlobHasAllLocal),
- m_Gi(0), m_Sat(0), m_SubSat(eSubSat_main), m_SatKey(0),
+ m_Gi(ZERO_GI), m_Sat(0), m_SubSat(eSubSat_main), m_SatKey(0),
m_Version(0)
{
}
diff --git a/c++/src/objtools/edit/Makefile.edit.lib b/c++/src/objtools/edit/Makefile.edit.lib
index d487464..888cb6c 100644
--- a/c++/src/objtools/edit/Makefile.edit.lib
+++ b/c++/src/objtools/edit/Makefile.edit.lib
@@ -1,22 +1,24 @@
-# $Id: Makefile.edit.lib 450054 2014-10-22 18:00:12Z ivanov $
+# $Id: Makefile.edit.lib 478650 2015-09-11 12:00:48Z ivanov $
# Build library "xobjedit"
###############################
SRC = gene_utils seq_entry_edit promote autodef_available_modifier autodef \
autodef_feature_clause_base autodef_feature_clause autodef_mod_combo \
- autodef_source_desc autodef_source_group \
+ autodef_source_desc autodef_source_group autodef_options \
field_handler apply_object string_constraint seqid_guesser dblink_field \
struc_comm_field text_desc_field gb_block_field \
link_cds_mrna cds_fix capitalization_string loc_edit mail_report \
feattable_edit gaps_edit source_edit rna_edit \
- remote_updater
+ remote_updater parse_text_options
LIB = xobjedit
+DLL_LIB = $(XFORMAT_LIBS) xregexp $(PCRE_LIB) $(SOBJMGR_LIBS)
+
ASN_DEP = seqset valid macro
-WATCHERS = bollin kornbluh gotvyans chenj
+WATCHERS = bollin kornbluh gotvyans
USES_LIBRARIES = \
diff --git a/c++/src/objtools/edit/apply_object.cpp b/c++/src/objtools/edit/apply_object.cpp
index 236c18a..596a275 100644
--- a/c++/src/objtools/edit/apply_object.cpp
+++ b/c++/src/objtools/edit/apply_object.cpp
@@ -1,4 +1,4 @@
-/* $Id: apply_object.cpp 447186 2014-09-23 14:45:51Z ivanov $
+/* $Id: apply_object.cpp 447037 2014-09-22 11:21:25Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/autodef.cpp b/c++/src/objtools/edit/autodef.cpp
index 59f7d44..9138944 100644
--- a/c++/src/objtools/edit/autodef.cpp
+++ b/c++/src/objtools/edit/autodef.cpp
@@ -1,4 +1,4 @@
-/* $Id: autodef.cpp 459546 2015-02-19 15:31:02Z ivanov $
+/* $Id: autodef.cpp 484817 2015-11-16 16:23:10Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,6 +42,7 @@
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Bioseq.hpp>
+#include <objects/seqblock/GB_block.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
@@ -59,26 +60,8 @@ BEGIN_SCOPE(objects)
CAutoDef::CAutoDef()
- : m_FeatureListType(eListAllFeatures),
- m_MiscFeatRule(eDelete),
- m_SpecifyNuclearProduct(false),
- m_ProductFlag(CBioSource::eGenome_unknown),
- m_AltSpliceFlag(false),
- m_SuppressAltSplicePhrase(false),
- m_SuppressLocusTags(false),
- m_GeneOppStrand(false),
- m_RemoveMobileElementAndInsertionSequenceSubfeatures(false),
- m_KeepExons(false),
- m_KeepIntrons(false),
- m_KeepPromoters(false),
- m_KeepLTRs(false),
- m_Keep3UTRs(false),
- m_Keep5UTRs(false),
- m_UseNcRNAComment(false),
- m_UseFakePromoters(false),
- m_Cancelled(false)
+ : m_Cancelled(false)
{
- m_SuppressedFeatures.clear();
}
@@ -309,78 +292,13 @@ string CAutoDef::GetOneSourceDescription(CBioseq_Handle bh)
}
return "";
}
-
-
-bool CAutoDef::x_AddIntergenicSpacerFeatures(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, CAutoDefFeatureClause_Base &main_clause, bool suppress_locus_tags)
-{
- CSeqFeatData::ESubtype subtype = cf.GetData().GetSubtype();
- if ((subtype != CSeqFeatData::eSubtype_misc_feature && subtype != CSeqFeatData::eSubtype_otherRNA)
- || !cf.CanGetComment()) {
- return false;
- }
- string comment = cf.GetComment();
-
- // get rid of any leading or trailing spaces
- NStr::TruncateSpacesInPlace(comment);
-
- // ignore anything after the first semicolon
- string::size_type pos = NStr::Find(comment, ";");
- if (pos != NCBI_NS_STD::string::npos) {
- comment = comment.substr(0, pos);
- }
-
- bool is_region = false;
-
- // ignore "contains " at beginning of comment
- if (NStr::StartsWith(comment, "contains ")) {
- comment = comment.substr(9);
- } else if (NStr::StartsWith (comment, "may contain ")) {
- comment = comment.substr(12);
- is_region = true;
- }
-
- vector<CAutoDefFeatureClause *> clause_list = GetIntergenicSpacerClauseList (comment, bh, cf, mapped_loc, suppress_locus_tags);
-
- if (clause_list.size() > 0) {
- if (is_region) {
- main_clause.AddSubclause (new CAutoDefParsedRegionClause (bh, cf, mapped_loc, comment));
- for (size_t i = 0; i < clause_list.size(); i++) {
- delete (clause_list[i]);
- }
- } else {
- for (size_t i = 0; i < clause_list.size(); i++) {
- main_clause.AddSubclause (clause_list[i]);
- }
- }
- return true;
- } else {
- return false;
- }
-}
// Some misc_RNA clauses have a comment that actually lists multiple
// features. These functions create a clause for each element in the
// comment.
-static string misc_words [] = {
- "internal transcribed spacer",
- "external transcribed spacer",
- "ribosomal RNA intergenic spacer",
- "ribosomal RNA",
- "intergenic spacer"
-};
-
-typedef enum {
- MISC_RNA_WORD_INTERNAL_SPACER = 0,
- MISC_RNA_WORD_EXTERNAL_SPACER,
- MISC_RNA_WORD_RNA_INTERGENIC_SPACER,
- MISC_RNA_WORD_RNA,
- MISC_RNA_WORD_INTERGENIC_SPACER,
- NUM_MISC_RNA_WORDS
-} MiscWord;
-
-bool CAutoDef::x_AddMiscRNAFeatures(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, CAutoDefFeatureClause_Base &main_clause, bool suppress_locus_tags)
+bool CAutoDef::x_AddMiscRNAFeatures(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, CAutoDefFeatureClause_Base &main_clause)
{
string comment = "";
string::size_type pos;
@@ -412,9 +330,6 @@ bool CAutoDef::x_AddMiscRNAFeatures(CBioseq_Handle bh, const CSeq_feat& cf, cons
return false;
}
- vector<CAutoDefFeatureClause *> clause_list;
- size_t j;
- bool bad_phrase = false;
bool is_region = false;
if (NStr::StartsWith (comment, "contains ")) {
@@ -423,92 +338,59 @@ bool CAutoDef::x_AddMiscRNAFeatures(CBioseq_Handle bh, const CSeq_feat& cf, cons
comment = comment.substr(12);
is_region = true;
}
-
-
- clause_list.clear();
- pos = NStr::Find (comment, " and ");
- // insert comma for parsing
- if (pos != NCBI_NS_STD::string::npos && pos > 0 && !NStr::StartsWith (comment.substr(pos - 1), ",")) {
- comment = comment.substr(0, pos) + "," + comment.substr(pos);
- }
- vector<string> parts;
- NStr::Tokenize(comment, ",", parts, NStr::eMergeDelims );
- if ( parts.empty() ) {
- return false;
+ pos = NStr::Find(comment, ";");
+ if (pos != string::npos) {
+ comment = comment.substr(0, pos);
}
- vector<unsigned int> types;
-
- for (j = 0; j < parts.size() && !bad_phrase; j++) {
- // clean up part name
- NStr::TruncateSpacesInPlace(parts[j]);
- if (NStr::StartsWith(parts[j], "and ")) {
- parts[j] = parts[j].substr(4);
- }
- // find first of the recognized words to occur in the string
- string::size_type first_word = NCBI_NS_STD::string::npos;
- unsigned int word_id = 0;
-
- for (unsigned int i = 0; i < NUM_MISC_RNA_WORDS && first_word == NCBI_NS_STD::string::npos; i++) {
- first_word = NStr::Find (parts[j], misc_words[i]);
- if (first_word != NCBI_NS_STD::string::npos) {
- word_id = i;
+ if (is_region) {
+ main_clause.AddSubclause(new CAutoDefParsedRegionClause(bh, cf, mapped_loc, comment));
+ } else {
+ vector<string> elements = CAutoDefFeatureClause_Base::GetMiscRNAElements(comment);
+ if (!elements.empty()) {
+ ITERATE(vector<string>, s, elements) {
+ CAutoDefParsedClause *new_clause = new CAutoDefParsedClause(bh, cf, mapped_loc,
+ (*s == elements.front()), (*s == elements.back()));
+ new_clause->SetMiscRNAWord(*s);
+ main_clause.AddSubclause(new_clause);
}
- }
- if (first_word == NCBI_NS_STD::string::npos) {
- bad_phrase = true;
- } else {
- types.push_back (word_id);
- }
- }
-
- if (!bad_phrase) {
- if (is_region) {
- clause_list.push_back (new CAutoDefParsedRegionClause(bh, cf, mapped_loc, comment));
} else {
- for (j = 0; j < parts.size(); j++) {
- // create a clause of the appropriate type
- CAutoDefParsedClause *new_clause = new CAutoDefParsedClause(bh, cf, mapped_loc, j == 0, j == parts.size() - 1);
- string description = "";
- if (types[j] == MISC_RNA_WORD_INTERNAL_SPACER
- || types[j] == MISC_RNA_WORD_EXTERNAL_SPACER
- || types[j] == MISC_RNA_WORD_RNA_INTERGENIC_SPACER
- || types[j] == MISC_RNA_WORD_INTERGENIC_SPACER) {
- if (NStr::StartsWith (parts[j], misc_words[types[j]])) {
- new_clause->SetTypewordFirst(true);
- description = parts[j].substr(misc_words[types[j]].length());
+ elements = CAutoDefFeatureClause_Base::GetTrnaIntergenicSpacerClausePhrases(comment);
+ if (!elements.empty()) {
+ ITERATE(vector<string>, s, elements) {
+ size_t pos = NStr::Find(*s, "intergenic spacer");
+ if (pos != string::npos) {
+ CAutoDefParsedIntergenicSpacerClause *spacer =
+ new CAutoDefParsedIntergenicSpacerClause(bh,
+ cf,
+ mapped_loc,
+ (*s),
+ (*s == elements.front()),
+ (*s == elements.back()));
+ main_clause.AddSubclause(spacer);
} else {
- new_clause->SetTypewordFirst(false);
- description = parts[j].substr(0, NStr::Find(parts[j], misc_words[types[j]]));
+ CAutoDefFeatureClause *gene = s_tRNAClauseFromNote(bh, cf, mapped_loc, *s, (*s == elements.front()), (*s == elements.back()));
+ main_clause.AddSubclause(gene);
}
- new_clause->SetTypeword(misc_words[types[j]]);
- } else if (types[j] == MISC_RNA_WORD_RNA) {
- description = parts[j];
- new_clause->SetTypeword("gene");
- new_clause->SetTypewordFirst(false);
}
- NStr::TruncateSpacesInPlace(description);
- new_clause->SetDescription(description);
-
- new_clause->SetSuppressLocusTag(suppress_locus_tags);
- clause_list.push_back (new_clause);
+ } else {
+ CAutoDefParsedIntergenicSpacerClause *spacer =
+ new CAutoDefParsedIntergenicSpacerClause(bh,
+ cf,
+ mapped_loc,
+ comment,
+ true,
+ true);
+ main_clause.AddSubclause(spacer);
}
}
}
-
- if (clause_list.size() > 0) {
- for (j = 0; j < clause_list.size(); j++) {
- main_clause.AddSubclause(clause_list[j]);
- }
- return true;
- } else {
- return false;
- }
+ return true;
}
-bool CAutoDef::x_AddtRNAAndOther(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, CAutoDefFeatureClause_Base &main_clause, bool suppress_locus_tags)
+bool CAutoDef::x_AddtRNAAndOther(CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, CAutoDefFeatureClause_Base &main_clause)
{
if (cf.GetData().GetSubtype() != CSeqFeatData::eSubtype_misc_feature ||
!cf.IsSetComment()) {
@@ -574,17 +456,17 @@ void CAutoDef::x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause,
}
// keep 5' UTRs only if lonely or requested
- if (!m_Keep5UTRs && !main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_5UTR)) {
+ if (!m_Options.GetKeep5UTRs() && !main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_5UTR)) {
main_clause->RemoveFeaturesByType(CSeqFeatData::eSubtype_5UTR);
}
// keep 3' UTRs only if lonely or requested
- if (!m_Keep3UTRs && !main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_3UTR)) {
+ if (!m_Options.GetKeep3UTRs() && !main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_3UTR)) {
main_clause->RemoveFeaturesByType(CSeqFeatData::eSubtype_3UTR);
}
// keep LTRs only if requested or lonely and not in parent
- if (!m_KeepLTRs) {
+ if (!m_Options.GetKeepLTRs()) {
if (main_clause->GetNumSubclauses() > 1
|| main_clause->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_LTR) {
main_clause->RemoveFeaturesByType(CSeqFeatData::eSubtype_LTR);
@@ -592,7 +474,7 @@ void CAutoDef::x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause,
}
// keep promoters only if requested or lonely and not in mRNA
- if (!m_KeepPromoters) {
+ if (!m_Options.GetKeepPromoters()) {
if (!main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_promoter)) {
main_clause->RemoveFeaturesByType(CSeqFeatData::eSubtype_promoter);
} else {
@@ -601,7 +483,7 @@ void CAutoDef::x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause,
}
// keep introns only if requested or lonely and not in mRNA
- if (!m_KeepIntrons) {
+ if (!m_Options.GetKeepIntrons()) {
if (!main_clause->IsFeatureTypeLonely(CSeqFeatData::eSubtype_intron)) {
main_clause->RemoveFeaturesByType(CSeqFeatData::eSubtype_intron);
} else {
@@ -610,16 +492,26 @@ void CAutoDef::x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause,
}
// keep exons only if requested or lonely or in mRNA or in partial CDS or on segment
- if (!m_KeepExons && !IsSegment(bh)) {
+ if (!m_Options.GetKeepExons() && !IsSegment(bh)) {
if (main_clause->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_exon) {
main_clause->RemoveUnwantedExons();
}
}
- // only keep bioseq precursor RNAs if lonely
- if (!main_clause->IsBioseqPrecursorRNA()) {
+ // only keep bioseq precursor RNAs if lonely or requested
+ if (!main_clause->IsBioseqPrecursorRNA() && !m_Options.GetKeepPrecursorRNA()) {
main_clause->RemoveBioseqPrecursorRNAs();
}
+
+ // keep uORFs if lonely or requested
+ if (!m_Options.GetKeepuORFs() && main_clause->GetNumSubclauses() > 1) {
+ main_clause->RemoveuORFs();
+ }
+
+ // remove "optional" mobile element features unless lonely or requested
+ if (!m_Options.GetKeepMobileElements() && main_clause->GetNumSubclauses() > 1) {
+ main_clause->RemoveOptionalMobileElements();
+ }
// delete subclauses at end, so that loneliness calculations will be correct
main_clause->RemoveDeletedSubclauses();
@@ -628,27 +520,23 @@ void CAutoDef::x_RemoveOptionalFeatures(CAutoDefFeatureClause_Base *main_clause,
bool CAutoDef::x_IsFeatureSuppressed(CSeqFeatData::ESubtype subtype)
{
- unsigned int feat_type = CSeqFeatData::GetTypeFromSubtype(subtype);
- ITERATE(TFeatTypeItemSet, it, m_SuppressedFeatures) {
- unsigned i_feat_type = it->GetType();
- if (i_feat_type == CSeqFeatData::e_not_set) {
- return true;
- } else if (feat_type != i_feat_type) {
- continue;
- }
- unsigned int i_subtype = it->GetSubtype();
- if (i_subtype == CSeqFeatData::eSubtype_any
- || i_subtype == subtype ) {
- return true;
- }
- }
- return false;
+ return m_Options.IsFeatureSuppressed(subtype);
}
void CAutoDef::SuppressFeature(objects::CFeatListItem feat)
{
- m_SuppressedFeatures.insert(feat);
+ if (feat.GetType() == CSeqFeatData::e_not_set) {
+ m_Options.SuppressAllFeatures();
+ } else {
+ m_Options.SuppressFeature((CSeqFeatData::ESubtype)(feat.GetSubtype()));
+ }
+}
+
+
+void CAutoDef::SuppressFeature(objects::CSeqFeatData::ESubtype subtype)
+{
+ m_Options.SuppressFeature(subtype);
}
@@ -767,7 +655,7 @@ bool s_HasPromoter(CBioseq_Handle bh)
string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
{
- CAutoDefFeatureClause_Base main_clause(m_SuppressLocusTags);
+ CAutoDefFeatureClause_Base main_clause;
CAutoDefFeatureClause *new_clause;
CRange<TSeqPos> range;
CBioseq_Handle master_bh = bh;
@@ -775,7 +663,7 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
GetMasterLocation(master_bh, range);
// if no promoter, and fake promoters are requested, create one
- if (m_UseFakePromoters && !s_HasPromoter(bh)) {
+ if (m_Options.GetUseFakePromoters() && !s_HasPromoter(bh)) {
CRef<CSeq_feat> fake_promoter(new CSeq_feat());
CRef<CSeq_loc> fake_promoter_loc(new CSeq_loc());
const CSeq_id* id = FindBestChoice(bh.GetBioseqCore()->GetId(), CSeq_id::BestRank);
@@ -814,8 +702,10 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
&& !x_IsFeatureSuppressed(cf.GetData().GetSubtype())) {
// some clauses can be created differently just knowing the subtype
- if (subtype == CSeqFeatData::eSubtype_ncRNA) {
- new_clause = new CAutoDefNcRNAClause(bh, cf, mapped_loc, m_UseNcRNAComment);
+ if (subtype == CSeqFeatData::eSubtype_gene) {
+ new_clause = new CAutoDefGeneClause(bh, cf, mapped_loc, m_Options.GetSuppressLocusTags());
+ } else if (subtype == CSeqFeatData::eSubtype_ncRNA) {
+ new_clause = new CAutoDefNcRNAClause(bh, cf, mapped_loc, m_Options.GetUseNcRNAComment());
} else if (subtype == CSeqFeatData::eSubtype_mobile_element) {
new_clause = new CAutoDefMobileElementClause(bh, cf, mapped_loc);
} else if (CAutoDefFeatureClause::IsSatellite(cf)) {
@@ -823,44 +713,42 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
} else if (subtype == CSeqFeatData::eSubtype_otherRNA
|| subtype == CSeqFeatData::eSubtype_misc_RNA
|| subtype == CSeqFeatData::eSubtype_rRNA) {
- if (!x_AddMiscRNAFeatures(bh, cf, mapped_loc, main_clause, m_SuppressLocusTags)) {
+ if (!x_AddMiscRNAFeatures(bh, cf, mapped_loc, main_clause)) {
new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
}
} else if (CAutoDefFeatureClause::IsPromoter(cf)) {
new_clause = new CAutoDefPromoterClause(bh, cf, mapped_loc);
- } else if (CAutoDefFeatureClause::IsIntergenicSpacer(cf)) {
- x_AddIntergenicSpacerFeatures(bh, cf, mapped_loc, main_clause, m_SuppressLocusTags);
} else if (CAutoDefFeatureClause::IsGeneCluster(cf)) {
new_clause = new CAutoDefGeneClusterClause(bh, cf, mapped_loc);
} else if (CAutoDefFeatureClause::IsControlRegion(cf)) {
new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
- } else {
- // misc-features may require more parsing
- if (subtype == CSeqFeatData::eSubtype_misc_feature) {
- if (!x_AddMiscRNAFeatures(bh, cf, mapped_loc, main_clause, m_SuppressLocusTags) &&
- !x_AddtRNAAndOther(bh, cf, mapped_loc, main_clause, m_SuppressLocusTags)) {
- new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
- if (m_MiscFeatRule == eDelete
- || (m_MiscFeatRule == eNoncodingProductFeat && !new_clause->IsNoncodingProductFeat())) {
- delete new_clause;
- new_clause = NULL;
- } else if (m_MiscFeatRule == eCommentFeat) {
- delete new_clause;
- new_clause = NULL;
- if (cf.CanGetComment() && ! NStr::IsBlank(cf.GetComment())) {
- new_clause = new CAutoDefMiscCommentClause(bh, cf, mapped_loc);
- }
- }
+ } else if ((subtype == CSeqFeatData::eSubtype_misc_feature || subtype == CSeqFeatData::eSubtype_otherRNA) &&
+ (x_AddMiscRNAFeatures(bh, cf, mapped_loc, main_clause) || x_AddtRNAAndOther(bh, cf, mapped_loc, main_clause))) {
+ // special misc_features and misc_RNA features
+ } else if (subtype == CSeqFeatData::eSubtype_misc_feature) {
+ // some misc-features may require more parsing
+ new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
+ if (m_Options.GetMiscFeatRule() == CAutoDefOptions::eDelete
+ || (m_Options.GetMiscFeatRule() == CAutoDefOptions::eNoncodingProductFeat && !new_clause->IsNoncodingProductFeat())) {
+ delete new_clause;
+ new_clause = NULL;
+ } else if (m_Options.GetMiscFeatRule() == CAutoDefOptions::eCommentFeat) {
+ delete new_clause;
+ new_clause = NULL;
+ if (cf.CanGetComment() && !NStr::IsBlank(cf.GetComment())) {
+ new_clause = new CAutoDefMiscCommentClause(bh, cf, mapped_loc);
}
- } else {
- new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
}
+ } else {
+ new_clause = new CAutoDefFeatureClause(bh, cf, mapped_loc);
}
- if (new_clause != NULL && new_clause->IsRecognizedFeature()) {
- new_clause->SetSuppressLocusTag(m_SuppressLocusTags);
- if (new_clause->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_exon) {
- new_clause->Label();
+ if (new_clause != NULL &&
+ (new_clause->IsRecognizedFeature() ||
+ (new_clause->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_repeat_region && m_Options.GetKeepRepeatRegion()))) {
+ if (new_clause->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_exon ||
+ new_clause->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_intron) {
+ new_clause->Label(m_Options.GetSuppressAlleles());
}
main_clause.AddSubclause(new_clause);
} else if (new_clause != NULL) {
@@ -875,29 +763,29 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
main_clause.RemoveDeletedSubclauses();
// Add mRNAs to other clauses
- main_clause.GroupmRNAs();
+ main_clause.GroupmRNAs(m_Options.GetSuppressAlleles());
main_clause.RemoveDeletedSubclauses();
// Add genes to clauses that need them for descriptions/products
- main_clause.GroupGenes();
+ main_clause.GroupGenes(m_Options.GetSuppressAlleles());
- main_clause.GroupSegmentedCDSs();
+ main_clause.GroupSegmentedCDSs(m_Options.GetSuppressAlleles());
main_clause.RemoveDeletedSubclauses();
// Group all features
- main_clause.GroupClauses(m_GeneOppStrand);
+ main_clause.GroupClauses(m_Options.GetGeneClusterOppStrand());
main_clause.RemoveDeletedSubclauses();
// now that features have been grouped, can expand lists of spliced exons
main_clause.ExpandExonLists();
// assign product names for features associated with genes that have products
- main_clause.AssignGeneProductNames(&main_clause);
+ main_clause.AssignGeneProductNames(&main_clause, m_Options.GetSuppressAlleles());
// reverse the order of clauses for minus-strand CDSfeatures
main_clause.ReverseCDSClauseLists();
- main_clause.Label();
+ main_clause.Label(m_Options.GetSuppressAlleles());
main_clause.CountUnknownGenes();
main_clause.RemoveDeletedSubclauses();
@@ -912,7 +800,7 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
main_clause.RemoveGenesMentionedElsewhere();
main_clause.RemoveDeletedSubclauses();
- if (m_RemoveMobileElementAndInsertionSequenceSubfeatures) {
+ if (m_Options.GetSuppressMobileElementSubfeatures()) {
main_clause.SuppressMobileElementAndInsertionSequenceSubfeatures();
}
@@ -921,22 +809,22 @@ string CAutoDef::x_GetFeatureClauses(CBioseq_Handle bh)
// information
main_clause.RemoveNonSegmentClauses(range);
- main_clause.Label();
+ main_clause.Label(m_Options.GetSuppressAlleles());
- if (!m_SuppressAltSplicePhrase) {
- main_clause.FindAltSplices();
+ if (!m_Options.GetSuppressFeatureAltSplice()) {
+ main_clause.FindAltSplices(m_Options.GetSuppressAlleles());
main_clause.RemoveDeletedSubclauses();
}
- main_clause.ConsolidateRepeatedClauses();
+ main_clause.ConsolidateRepeatedClauses(m_Options.GetSuppressAlleles());
main_clause.RemoveDeletedSubclauses();
main_clause.GroupConsecutiveExons(bh);
main_clause.RemoveDeletedSubclauses();
- main_clause.Label();
+ main_clause.Label(m_Options.GetSuppressAlleles());
- return main_clause.ListClauses(true, false);
+ return main_clause.ListClauses(true, false, m_Options.GetSuppressAlleles());
}
@@ -1041,10 +929,10 @@ string CAutoDef::x_GetFeatureClauseProductEnding(const string& feature_clauses,
bool pluralize = false;
unsigned int product_flag_to_use;
- if (m_SpecifyNuclearProduct) {
+ if (m_Options.GetSpecifyNuclearProduct()) {
product_flag_to_use = s_GetProductFlagFromCDSProductNames (bh);
} else {
- product_flag_to_use = m_ProductFlag;
+ product_flag_to_use = m_Options.GetProductFlag();
}
if (NStr::Find(feature_clauses, "genes") != NCBI_NS_STD::string::npos) {
pluralize = true;
@@ -1107,21 +995,21 @@ string CAutoDef::x_GetFeatureClauseProductEnding(const string& feature_clauses,
string CAutoDef::x_GetNonFeatureListEnding()
{
string end = "";
- switch (m_FeatureListType)
+ switch (m_Options.GetFeatureListType())
{
- case eCompleteSequence:
+ case CAutoDefOptions::eCompleteSequence:
end = ", complete sequence.";
break;
- case eCompleteGenome:
+ case CAutoDefOptions::eCompleteGenome:
end = ", complete genome.";
break;
- case ePartialSequence:
+ case CAutoDefOptions::ePartialSequence:
end = ", partial sequence.";
break;
- case ePartialGenome:
+ case CAutoDefOptions::ePartialGenome:
end = ", partial genome.";
break;
- case eSequence:
+ case CAutoDefOptions::eSequence:
end = " sequence.";
break;
default:
@@ -1131,13 +1019,40 @@ string CAutoDef::x_GetNonFeatureListEnding()
}
+bool IsBioseqmRNA(CBioseq_Handle bsh)
+{
+ bool is_mRNA = false;
+ for (CSeqdesc_CI desc(bsh, CSeqdesc::e_Molinfo); desc && !is_mRNA; ++desc) {
+ if (desc->GetMolinfo().CanGetBiomol()
+ && desc->GetMolinfo().GetBiomol() == CMolInfo::eBiomol_mRNA) {
+ is_mRNA = true;
+ }
+ }
+ return is_mRNA;
+}
+
+
+bool IsInGenProdSet(CBioseq_Handle bh)
+{
+ CBioseq_set_Handle parent = bh.GetParentBioseq_set();
+ while (parent) {
+ if (parent.IsSetClass() && parent.GetClass() == CBioseq_set::eClass_gen_prod_set) {
+ return true;
+ }
+ parent = parent.GetParentBioseq_set();
+ }
+ return false;
+}
+
+
string CAutoDef::GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_val)
{
string feature_clauses = "";
- if (m_FeatureListType == eListAllFeatures) {
+ if (m_Options.GetFeatureListType() == CAutoDefOptions::eListAllFeatures ||
+ (IsBioseqmRNA(bh) && IsInGenProdSet(bh))) {
feature_clauses = " " + x_GetFeatureClauses(bh);
string ending = x_GetFeatureClauseProductEnding(feature_clauses, bh);
- if (m_AltSpliceFlag) {
+ if (m_Options.GetAltSpliceFlag()) {
if (NStr::IsBlank(ending)) {
ending = "; alternatively spliced";
} else {
@@ -1153,7 +1068,7 @@ string CAutoDef::GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_
} else {
string organelle = "";
- if (m_FeatureListType != eSequence
+ if (m_Options.GetFeatureListType() != CAutoDefOptions::eSequence
|| genome_val == CBioSource::eGenome_apicoplast
|| genome_val == CBioSource::eGenome_chloroplast
|| genome_val == CBioSource::eGenome_kinetoplast
@@ -1164,7 +1079,7 @@ string CAutoDef::GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_
}
if (!NStr::IsBlank(organelle)) {
feature_clauses = " " + organelle;
- } else if (NStr::IsBlank(organelle) && m_FeatureListType == eSequence) {
+ } else if (NStr::IsBlank(organelle) && m_Options.GetFeatureListType() == CAutoDefOptions::eSequence) {
string biomol = "";
CSeqdesc_CI mi(bh, CSeqdesc::e_Molinfo);
if (mi && mi->GetMolinfo().IsSetBiomol()) {
@@ -1181,6 +1096,33 @@ string CAutoDef::GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_
}
+string CAutoDef::GetKeywordPrefix(CBioseq_Handle bh)
+{
+ string keyword = kEmptyStr;
+
+ CSeqdesc_CI gb(bh, CSeqdesc::e_Genbank);
+ if (gb) {
+ if (gb->GetGenbank().IsSetKeywords()) {
+ ITERATE(CGB_block::TKeywords, it, gb->GetGenbank().GetKeywords()) {
+ if (NStr::EqualNocase(*it, "TPA:inferential")) {
+ keyword = "TPA_inf: ";
+ break;
+ } else if (NStr::EqualNocase(*it, "TPA:experimental")) {
+ keyword = "TPA_exp: ";
+ break;
+ }
+ }
+ }
+ } else {
+ CSeqdesc_CI mi(bh, CSeqdesc::e_Molinfo);
+ if (mi && mi->GetMolinfo().IsSetTech() && mi->GetMolinfo().GetTech() == CMolInfo::eTech_tsa) {
+ keyword = "TSA: ";
+ }
+ }
+ return keyword;
+}
+
+
string CAutoDef::GetOneDefLine(CAutoDefModifierCombo *mod_combo, CBioseq_Handle bh)
{
// for protein sequences, use sequence::GetTitle
@@ -1192,6 +1134,7 @@ string CAutoDef::GetOneDefLine(CAutoDefModifierCombo *mod_combo, CBioseq_Handle
}
string org_desc = "Unknown organism";
unsigned int genome_val = CBioSource::eGenome_unknown;
+ mod_combo->InitOptions(m_Options);
for (CSeqdesc_CI dit(bh, CSeqdesc::e_Source); dit; ++dit) {
const CBioSource& bsrc = dit->GetSource();
@@ -1210,7 +1153,48 @@ string CAutoDef::GetOneDefLine(CAutoDefModifierCombo *mod_combo, CBioseq_Handle
org_desc = first_letter + remainder;
}
- return org_desc + feature_clauses;
+ string keyword = GetKeywordPrefix(bh);
+
+ return keyword + org_desc + feature_clauses;
+}
+
+
+// use internal settings to create mod combo
+string CAutoDef::GetOneDefLine(CBioseq_Handle bh)
+{
+ // for protein sequences, use sequence::GetTitle
+ if (bh.CanGetInst() && bh.GetInst().CanGetMol() && bh.GetInst().GetMol() == CSeq_inst::eMol_aa) {
+ return sequence::CDeflineGenerator()
+ .GenerateDefline(bh,
+ sequence::CDeflineGenerator::fIgnoreExisting |
+ sequence::CDeflineGenerator::fAllProteinNames);
+ }
+ string org_desc = "Unknown organism";
+ unsigned int genome_val = CBioSource::eGenome_unknown;
+
+ CAutoDefModifierCombo *mod_combo = GetEmptyCombo();
+ mod_combo->InitFromOptions(m_Options);
+
+ for (CSeqdesc_CI dit(bh, CSeqdesc::e_Source); dit; ++dit) {
+ const CBioSource& bsrc = dit->GetSource();
+ org_desc = mod_combo->GetSourceDescriptionString(bsrc);
+ if (bsrc.CanGetGenome()) {
+ genome_val = bsrc.GetGenome();
+ }
+ break;
+ }
+ string feature_clauses = GetOneFeatureClauseList(bh, genome_val);
+
+ if (org_desc.length() > 0 && isalpha(org_desc.c_str()[0])) {
+ string first_letter = org_desc.substr(0, 1);
+ string remainder = org_desc.substr(1);
+ NStr::ToUpper(first_letter);
+ org_desc = first_letter + remainder;
+ }
+
+ string keyword = GetKeywordPrefix(bh);
+
+ return keyword + org_desc + feature_clauses;
}
@@ -1300,5 +1284,56 @@ void CAutoDef::GetAvailableModifiers(CAutoDef::TAvailableModifierSet &mod_set)
}
+void CAutoDef::SetOptionsObject(const CUser_object& user)
+{
+ m_Options.InitFromUserObject(user);
+}
+
+
+bool CAutoDef::RegenerateDefLines(CSeq_entry_Handle se)
+{
+ bool any = false;
+ CBioseq_CI b_iter(se);
+ for (; b_iter; ++b_iter) {
+ if (b_iter->IsAa()) {
+ continue;
+ }
+ CSeqdesc_CI desc(*b_iter, CSeqdesc::e_User);
+ while (desc && desc->GetUser().GetObjectType() != CUser_object::eObjectType_AutodefOptions) {
+ ++desc;
+ }
+ if (desc) {
+ CAutoDef autodef;
+ autodef.SetOptionsObject(desc->GetUser());
+ CAutoDefModifierCombo mod_combo;
+ CAutoDefOptions options;
+ options.InitFromUserObject(desc->GetUser());
+ mod_combo.SetOptions(options);
+ string defline = autodef.GetOneDefLine(&mod_combo, *b_iter);
+
+ bool found_existing = false;
+ CBioseq_EditHandle beh(*b_iter);
+ NON_CONST_ITERATE(CBioseq_EditHandle::TDescr::Tdata, it, beh.SetDescr().Set()) {
+ if ((*it)->IsTitle()) {
+ if (!NStr::Equal((*it)->GetTitle(), defline)) {
+ (*it)->SetTitle(defline);
+ any = true;
+ }
+ found_existing = true;
+ break;
+ }
+ }
+ if (!found_existing) {
+ CRef<CSeqdesc> new_desc(new CSeqdesc());
+ new_desc->SetTitle(defline);
+ beh.SetDescr().Set().push_back(new_desc);
+ any = true;
+ }
+ }
+ }
+ return any;
+}
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/edit/autodef_available_modifier.cpp b/c++/src/objtools/edit/autodef_available_modifier.cpp
index 3f2677f..4310cb8 100644
--- a/c++/src/objtools/edit/autodef_available_modifier.cpp
+++ b/c++/src/objtools/edit/autodef_available_modifier.cpp
@@ -1,4 +1,4 @@
-/* $Id: autodef_available_modifier.cpp 459547 2015-02-19 15:31:32Z ivanov $
+/* $Id: autodef_available_modifier.cpp 459368 2015-02-18 14:46:24Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/autodef_feature_clause.cpp b/c++/src/objtools/edit/autodef_feature_clause.cpp
index bfaa29c..afe08be 100644
--- a/c++/src/objtools/edit/autodef_feature_clause.cpp
+++ b/c++/src/objtools/edit/autodef_feature_clause.cpp
@@ -1,4 +1,4 @@
-/* $Id: autodef_feature_clause.cpp 455172 2014-12-23 18:29:14Z ivanov $
+/* $Id: autodef_feature_clause.cpp 485525 2015-11-23 16:14:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -70,37 +70,20 @@ CAutoDefFeatureClause::CAutoDefFeatureClause(CBioseq_Handle bh, const CSeq_feat&
m_DescriptionChosen = false;
m_ProductName = "";
m_ProductNameChosen = false;
-
+
CSeqFeatData::ESubtype subtype = m_MainFeat.GetData().GetSubtype();
-
- if (subtype == CSeqFeatData::eSubtype_gene) {
- m_GeneName = x_GetGeneName(m_MainFeat.GetData().GetGene());
- if (m_MainFeat.GetData().GetGene().CanGetAllele()) {
- m_AlleleName = m_MainFeat.GetData().GetGene().GetAllele();
- if (!NStr::StartsWith(m_AlleleName, m_GeneName, NStr::eNocase)) {
- if (!NStr::StartsWith(m_AlleleName, "-")) {
- m_AlleleName = "-" + m_AlleleName;
- }
- m_AlleleName = m_GeneName + m_AlleleName;
- }
- }
- if (m_MainFeat.CanGetPseudo() && m_MainFeat.GetPseudo()) {
- m_GeneIsPseudo = true;
- }
- m_HasGene = true;
- }
-
+
m_ClauseLocation = new CSeq_loc();
m_ClauseLocation->Add(mapped_loc);
-
+
if (subtype == CSeqFeatData::eSubtype_operon || IsGeneCluster()) {
m_SuppressSubfeatures = true;
}
-
+
if (m_MainFeat.CanGetComment() && NStr::Find(m_MainFeat.GetComment(), "alternatively spliced") != NCBI_NS_STD::string::npos
&& (subtype == CSeqFeatData::eSubtype_cdregion
- || subtype == CSeqFeatData::eSubtype_exon
- || IsNoncodingProductFeat())) {
+ || subtype == CSeqFeatData::eSubtype_exon
+ || IsNoncodingProductFeat())) {
m_IsAltSpliced = true;
}
}
@@ -111,7 +94,7 @@ CAutoDefFeatureClause::~CAutoDefFeatureClause()
}
-CSeqFeatData::ESubtype CAutoDefFeatureClause::GetMainFeatureSubtype()
+CSeqFeatData::ESubtype CAutoDefFeatureClause::GetMainFeatureSubtype() const
{
return m_MainFeat.GetData().GetSubtype();
}
@@ -211,16 +194,17 @@ bool CAutoDefFeatureClause::IsRecognizedFeature()
|| subtype == CSeqFeatData::eSubtype_otherRNA
|| subtype == CSeqFeatData::eSubtype_misc_RNA
|| subtype == CSeqFeatData::eSubtype_ncRNA
+ || subtype == CSeqFeatData::eSubtype_preRNA
|| subtype == CSeqFeatData::eSubtype_D_loop
|| IsNoncodingProductFeat()
|| IsMobileElement()
|| IsInsertionSequence()
|| IsControlRegion()
- || IsIntergenicSpacer()
|| IsEndogenousVirusSourceFeature()
|| IsSatelliteClause()
|| IsPromoter()
- || IsGeneCluster()) {
+ || IsGeneCluster()
+ || GetClauseType() != eDefault) {
return true;
} else {
return false;
@@ -228,9 +212,9 @@ bool CAutoDefFeatureClause::IsRecognizedFeature()
}
-
void CAutoDefFeatureClause::x_SetBiomol()
{
+ m_Biomol = CMolInfo::eBiomol_genomic;
CSeqdesc_CI desc_iter(m_BH, CSeqdesc::e_Molinfo);
for ( ; desc_iter; ++desc_iter) {
if (desc_iter->GetMolinfo().IsSetBiomol()) {
@@ -245,15 +229,8 @@ bool CAutoDefFeatureClause::x_IsPseudo()
if (m_MainFeat.CanGetPseudo() && m_MainFeat.IsSetPseudo()) {
return true;
} else {
- CSeqFeatData::ESubtype subtype = m_MainFeat.GetData().GetSubtype();
- if (subtype == CSeqFeatData::eSubtype_gene) {
- const CGene_ref& gene = m_MainFeat.GetData().GetGene();
- if (gene.CanGetPseudo() && gene.IsSetPseudo()) {
- return true;
- }
- }
+ return false;
}
- return false;
}
@@ -306,6 +283,8 @@ bool CAutoDefFeatureClause::x_GetFeatureTypeWord(string &typeword)
typeword = "transposon";
return true;
}
+ typeword = "repeat region";
+ return true;
break;
case CSeqFeatData::eSubtype_misc_feature:
if (m_MainFeat.CanGetComment()) {
@@ -326,7 +305,7 @@ bool CAutoDefFeatureClause::x_GetFeatureTypeWord(string &typeword)
break;
}
- if (m_Biomol == CMolInfo::eBiomol_genomic) {
+ if (m_Biomol == CMolInfo::eBiomol_genomic || m_Biomol == CMolInfo::eBiomol_cRNA) {
if (x_IsPseudo()) {
typeword = "pseudogene";
return true;
@@ -351,9 +330,9 @@ bool CAutoDefFeatureClause::x_GetFeatureTypeWord(string &typeword)
return true;
} else if (m_Biomol == CMolInfo::eBiomol_pre_RNA) {
if (x_IsPseudo()) {
- typeword = "pseudogene precursor mRNA";
+ typeword = "pseudogene precursor RNA";
} else {
- typeword = "precursor mRNA";
+ typeword = "precursor RNA";
}
return true;
} else if (m_Biomol == CMolInfo::eBiomol_other_genetic) {
@@ -454,70 +433,54 @@ bool CAutoDefFeatureClause::IsNoncodingProductFeat()
return x_GetNoncodingProductFeatProduct(product_name);
}
+CAutoDefGeneClause::CAutoDefGeneClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, bool suppress_locus_tag)
+ : CAutoDefFeatureClause(bh, main_feat, mapped_loc)
+{
+ m_SuppressLocusTag = suppress_locus_tag;
+ m_GeneName = x_GetGeneName(m_MainFeat.GetData().GetGene(), suppress_locus_tag);
+ if (m_MainFeat.GetData().GetGene().CanGetAllele()) {
+ m_AlleleName = m_MainFeat.GetData().GetGene().GetAllele();
+ if (!NStr::StartsWith(m_AlleleName, m_GeneName, NStr::eNocase)) {
+ if (!NStr::StartsWith(m_AlleleName, "-")) {
+ m_AlleleName = "-" + m_AlleleName;
+ }
+ m_AlleleName = m_GeneName + m_AlleleName;
+ }
+ }
+ if (m_MainFeat.CanGetPseudo() && m_MainFeat.GetPseudo()) {
+ m_GeneIsPseudo = true;
+ }
+ m_HasGene = true;
+}
+
-string s_tRNAGeneFromProduct (string product)
+bool CAutoDefGeneClause::x_IsPseudo()
{
- string gene = "";
+ if (CAutoDefFeatureClause::x_IsPseudo()) {
+ return true;
+ }
+ const CGene_ref& gene = m_MainFeat.GetData().GetGene();
+ if (gene.CanGetPseudo() && gene.IsSetPseudo()) {
+ return true;
+ }
+ return false;
+}
- if (!NStr::StartsWith (product, "tRNA-")) {
- return "";
+/*
+*If the feature is a gene and has different strings in the description than
+* in the locus or locus tag, the description will be used as the product for
+* the gene.
+*/
+bool CAutoDefGeneClause::x_GetProductName(string &product_name)
+{
+ if (m_MainFeat.GetData().GetGene().CanGetDesc()
+ && !NStr::Equal(m_MainFeat.GetData().GetGene().GetDesc(),
+ m_GeneName)) {
+ product_name = m_MainFeat.GetData().GetGene().GetDesc();
+ return true;
+ } else {
+ return false;
}
- product = product.substr (5);
-
- if (NStr::EqualNocase (product, "Ala")) {
- gene = "trnA";
- } else if (NStr::EqualNocase (product, "Asx")) {
- gene = "trnB";
- } else if (NStr::EqualNocase (product, "Cys")) {
- gene = "trnC";
- } else if (NStr::EqualNocase (product, "Asp")) {
- gene = "trnD";
- } else if (NStr::EqualNocase (product, "Glu")) {
- gene = "trnE";
- } else if (NStr::EqualNocase (product, "Phe")) {
- gene = "trnF";
- } else if (NStr::EqualNocase (product, "Gly")) {
- gene = "trnG";
- } else if (NStr::EqualNocase (product, "His")) {
- gene = "trnH";
- } else if (NStr::EqualNocase (product, "Ile")) {
- gene = "trnI";
- } else if (NStr::EqualNocase (product, "Xle")) {
- gene = "trnJ";
- } else if (NStr::EqualNocase (product, "Lys")) {
- gene = "trnK";
- } else if (NStr::EqualNocase (product, "Leu")) {
- gene = "trnL";
- } else if (NStr::EqualNocase (product, "Met")) {
- gene = "trnM";
- } else if (NStr::EqualNocase (product, "Asn")) {
- gene = "trnN";
- } else if (NStr::EqualNocase (product, "Pyl")) {
- gene = "trnO";
- } else if (NStr::EqualNocase (product, "Pro")) {
- gene = "trnP";
- } else if (NStr::EqualNocase (product, "Gln")) {
- gene = "trnQ";
- } else if (NStr::EqualNocase (product, "Arg")) {
- gene = "trnR";
- } else if (NStr::EqualNocase (product, "Ser")) {
- gene = "trnS";
- } else if (NStr::EqualNocase (product, "Thr")) {
- gene = "trnT";
- } else if (NStr::EqualNocase (product, "Sec")) {
- gene = "trnU";
- } else if (NStr::EqualNocase (product, "Val")) {
- gene = "trnV";
- } else if (NStr::EqualNocase (product, "Trp")) {
- gene = "trnW";
- } else if (NStr::EqualNocase (product, "OTHER")) {
- gene = "trnX";
- } else if (NStr::EqualNocase (product, "Tyr")) {
- gene = "trnY";
- } else if (NStr::EqualNocase (product, "Glx")) {
- gene = "trnZ";
- }
- return gene;
}
@@ -539,14 +502,14 @@ bool CAutoDefParsedtRNAClause::ParseString(string comment, string& gene_name, st
product_name = comment;
} else {
/* if not tRNA, gene name is required */
- return NULL;
+ return false;
}
} else {
product_name = comment.substr(0, pos);
comment = comment.substr (pos + 1);
pos = NStr::Find(comment, ")");
if (pos == NCBI_NS_STD::string::npos) {
- return NULL;
+ return false;
}
gene_name = comment.substr (0, pos);
NStr::TruncateSpacesInPlace(gene_name);
@@ -594,191 +557,14 @@ CAutoDefParsedtRNAClause *s_tRNAClauseFromNote(CBioseq_Handle bh, const CSeq_fea
}
-const int kParsedTrnaGene = 1;
-const int kParsedTrnaSpacer = 2;
-
-vector<string> GetIntergenicSpacerClausePhrases(string comment)
-{
- vector<string> clause_list;
-
- clause_list.clear();
-
- if (NStr::StartsWith (comment, "contains ")) {
- comment = comment.substr (9);
- }
- if (NStr::StartsWith (comment, "may contain ")) {
- comment = comment.substr (12);
- }
- string::size_type pos = NStr::Find(comment, ";");
- if (pos != NCBI_NS_STD::string::npos) {
- comment = comment.substr(0, pos);
- }
-
- pos = NStr::Find (comment, " and ");
- // insert comma for parsing
- if (pos != NCBI_NS_STD::string::npos && pos > 0 && !NStr::StartsWith (comment.substr(pos - 1), ",")) {
- comment = comment.substr(0, pos) + "," + comment.substr(pos);
- }
-
- vector<string> parts;
- NStr::Tokenize(comment, ",", parts, NStr::eMergeDelims );
- if ( parts.empty() ) {
- return clause_list;
- }
-
- if (parts.size() == 1 && NStr::Find (parts[0], "intergenic spacer") != NCBI_NS_STD::string::npos) {
- clause_list.push_back (parts[0]);
- return clause_list;
- }
-
- bool bad_phrase = false;
- bool names_correct = true;
- int last_type = 0;
-
- string last_gene_name = "";
- string last_product = "";
-
- for (size_t j = 0; j < parts.size() && names_correct && !bad_phrase; j++) {
- NStr::TruncateSpacesInPlace(parts[j]);
- if (NStr::StartsWith (parts[j], "and ")) {
- parts[j] = parts[j].substr(4);
- }
- if (NStr::EndsWith (parts[j], " intergenic spacer")) {
- // must be a spacer
- string spacer_description = parts[j].substr(0, parts[j].length() - 18);
- clause_list.push_back(parts[j]);
- if (last_type == kParsedTrnaGene) {
- // spacer names and gene names must agree
- if (NStr::IsBlank (last_gene_name)) {
- last_gene_name = s_tRNAGeneFromProduct (last_product);
- }
- if (!NStr::StartsWith (spacer_description, last_gene_name + "-")) {
- names_correct = false;
- }
- }
- last_type = kParsedTrnaSpacer;
- } else {
- string gene_name = "";
- string product_name = "";
- if (!CAutoDefParsedtRNAClause::ParseString(parts[j], gene_name, product_name)) {
- bad_phrase = true;
- } else {
- // must alternate between genes and spacers
- if (last_type == kParsedTrnaSpacer) {
- // spacer names and gene names must agree
- if (NStr::IsBlank (gene_name)) {
- gene_name = s_tRNAGeneFromProduct (product_name);
- }
- if (!NStr::EndsWith (parts[j - 1], "-" + gene_name + " intergenic spacer")) {
- names_correct = false;
- }
- }
- clause_list.push_back (parts[j]);
- last_type = kParsedTrnaGene;
- last_gene_name = gene_name;
- last_product = product_name;
- }
- }
- }
- if (bad_phrase || !names_correct) {
- clause_list.clear();
- }
- return clause_list;
-}
-
-
-vector<CAutoDefFeatureClause *> GetIntergenicSpacerClauseList (string comment, CBioseq_Handle bh, const CSeq_feat& cf, const CSeq_loc& mapped_loc, bool suppress_locus_tags)
-{
- vector<CAutoDefFeatureClause *> clause_list;
-
- clause_list.clear();
-
- vector<string> parts = GetIntergenicSpacerClausePhrases(comment);
- if (parts.empty()) {
- return clause_list;
- }
-
- for (size_t j = 0; j < parts.size(); j++) {
- size_t pos = NStr::Find(parts[j], "intergenic spacer");
- if (pos != string::npos) {
- string spacer_description = parts[j].substr(0, pos);
- NStr::TruncateSpacesInPlace(spacer_description);
- CAutoDefFeatureClause *spacer =
- new CAutoDefParsedIntergenicSpacerClause(bh,
- cf,
- mapped_loc,
- spacer_description,
- j == 0,
- j == parts.size() - 1);
- clause_list.push_back (spacer);
- } else {
- CAutoDefFeatureClause *gene = s_tRNAClauseFromNote(bh, cf, mapped_loc, parts[j], j == 0, j == parts.size() - 1);
- clause_list.push_back(gene);
- }
- }
-
- return clause_list;
-}
-
-
-bool CAutoDefFeatureClause::IsIntergenicSpacer (const CSeq_feat& feat)
-{
- CSeqFeatData::ESubtype subtype = feat.GetData().GetSubtype();
- if ((subtype != CSeqFeatData::eSubtype_misc_feature && subtype != CSeqFeatData::eSubtype_otherRNA)
- || !feat.IsSetComment()) {
- return false;
- }
- string comment = feat.GetComment();
-
- vector<string> parts = GetIntergenicSpacerClausePhrases(comment);
- if (parts.size() > 0) {
- return true;
- } else {
- return false;
- }
-}
-
-
-bool CAutoDefFeatureClause::IsIntergenicSpacer()
-{
- CSeqFeatData::ESubtype subtype = m_MainFeat.GetData().GetSubtype();
- if ((subtype != CSeqFeatData::eSubtype_misc_feature && subtype != CSeqFeatData::eSubtype_otherRNA)
- || !m_MainFeat.CanGetComment()) {
- return false;
- }
- string comment = m_MainFeat.GetComment();
-
- if (NStr::StartsWith (comment, "contains ")) {
- comment = comment.substr (9);
- }
- if (NStr::StartsWith (comment, "may contain ")) {
- comment = comment.substr (12);
- }
- string::size_type pos = NStr::Find(comment, ";");
- if (pos != NCBI_NS_STD::string::npos) {
- comment = comment.substr(0, pos);
- }
-
-
- vector<CAutoDefFeatureClause *> clause_list = GetIntergenicSpacerClauseList (comment, m_BH, m_MainFeat, m_MainFeat.GetLocation(), true);
-
- if (clause_list.size() == 0) {
- return false;
- } else {
- for (size_t i = 0; i < clause_list.size(); i++) {
- delete (clause_list[i]);
- }
- return true;
- }
-}
-
-
-string CAutoDefFeatureClause::x_GetGeneName(const CGene_ref& gref)
+string CAutoDefFeatureClause::x_GetGeneName(const CGene_ref& gref, bool suppress_locus_tag) const
{
if (gref.IsSuppressed()) {
return "";
} else if (gref.CanGetLocus() && !NStr::IsBlank(gref.GetLocus())) {
return gref.GetLocus();
+ } else if (!suppress_locus_tag && gref.IsSetLocus_tag() && !NStr::IsBlank(gref.GetLocus_tag())) {
+ return gref.GetLocus_tag();
} else {
return "";
}
@@ -820,19 +606,10 @@ bool CAutoDefFeatureClause::x_GetProductName(string &product_name)
product_name = comment;
return true;
}
- } else if (subtype == CSeqFeatData::eSubtype_gene) {
- if (m_MainFeat.GetData().GetGene().CanGetDesc()
- && !NStr::Equal(m_MainFeat.GetData().GetGene().GetDesc(),
- m_GeneName)) {
- product_name = m_MainFeat.GetData().GetGene().GetDesc();
- return true;
- } else {
- return false;
- }
} else if (m_MainFeat.GetData().Which() == CSeqFeatData::e_Rna) {
if (subtype == CSeqFeatData::eSubtype_tRNA) {
string label;
-
+
feature::GetLabel(m_MainFeat, &label, feature::fFGL_Content);
if (NStr::Equal(label, "tRNA-Xxx")) {
label = "tRNA-OTHER";
@@ -844,7 +621,7 @@ bool CAutoDefFeatureClause::x_GetProductName(string &product_name)
} else {
product_name = m_MainFeat.GetNamedQual("product");
if (NStr::IsBlank(product_name)) {
- if (subtype == CSeqFeatData::eSubtype_otherRNA
+ if (subtype == CSeqFeatData::eSubtype_otherRNA
|| subtype == CSeqFeatData::eSubtype_misc_RNA) {
if (m_MainFeat.CanGetComment()) {
product_name = m_MainFeat.GetComment();
@@ -856,7 +633,7 @@ bool CAutoDefFeatureClause::x_GetProductName(string &product_name)
}
}
} else if (m_MainFeat.GetData().GetRna().IsSetExt()
- && m_MainFeat.GetData().GetRna().GetExt().Which() == CRNA_ref::C_Ext::e_Name) {
+ && m_MainFeat.GetData().GetRna().GetExt().Which() == CRNA_ref::C_Ext::e_Name) {
product_name = m_MainFeat.GetData().GetRna().GetExt().GetName();
}
}
@@ -955,14 +732,21 @@ bool CAutoDefFeatureClause::x_GetDescription(string &description)
} else {
return true;
}
- } else if (subtype == CSeqFeatData::eSubtype_repeat_region
- && NStr::Equal(m_Typeword, "endogenous virus")) {
- description = m_MainFeat.GetNamedQual("endogenous_virus");
- if (NStr::Equal(description, "unnamed")
- || NStr::IsBlank(description)) {
- description = "";
- return false;
+ } else if (subtype == CSeqFeatData::eSubtype_repeat_region) {
+ if (NStr::Equal(m_Typeword, "endogenous virus")) {
+ description = m_MainFeat.GetNamedQual("endogenous_virus");
+ if (NStr::Equal(description, "unnamed")
+ || NStr::IsBlank(description)) {
+ description = "";
+ return false;
+ } else {
+ return true;
+ }
} else {
+ description = m_MainFeat.GetNamedQual("rpt_family");
+ if (NStr::IsBlank(description) && m_MainFeat.IsSetComment()) {
+ description = m_MainFeat.GetComment();
+ }
return true;
}
} else if (subtype == CSeqFeatData::eSubtype_biosrc
@@ -989,7 +773,7 @@ bool CAutoDefFeatureClause::x_GetDescription(string &description)
} else if (subtype == CSeqFeatData::eSubtype_LTR) {
if (m_MainFeat.CanGetComment()) {
string comment = m_MainFeat.GetComment();
- if (NStr::StartsWith(comment,"LTR ")) {
+ if (NStr::StartsWith(comment, "LTR ")) {
comment = comment.substr(4);
} else if (NStr::EndsWith(comment, " LTR")) {
comment = comment.substr(0, comment.length() - 4);
@@ -1001,6 +785,9 @@ bool CAutoDefFeatureClause::x_GetDescription(string &description)
} else {
return true;
}
+ } else if (subtype == CSeqFeatData::eSubtype_operon) {
+ description = m_MainFeat.GetNamedQual("operon");
+ return true;
} else {
if (!m_ProductNameChosen) {
m_ProductNameChosen = x_GetProductName(m_ProductName);
@@ -1064,7 +851,7 @@ bool CAutoDefFeatureClause::IsPromoter(const CSeq_feat& feat)
* subfeatures of the clause, or the interval could be a combination of the
* last two items if the feature is a CDS.
*/
-bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval)
+bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval, bool suppress_allele)
{
unsigned int k;
@@ -1084,7 +871,8 @@ bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval)
|| subtype == CSeqFeatData::eSubtype_exon
|| subtype == CSeqFeatData::eSubtype_intron
|| subtype == CSeqFeatData::eSubtype_5UTR
- || subtype == CSeqFeatData::eSubtype_3UTR) {
+ || subtype == CSeqFeatData::eSubtype_3UTR
+ || (subtype == CSeqFeatData::eSubtype_repeat_region && !NStr::Equal(m_Typeword, "endogenous virus"))) {
return false;
}
@@ -1094,7 +882,7 @@ bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval)
// label subclauses
// check to see if 3'UTR is present, and whether there are any other features
for (k = 0; k < m_ClauseList.size(); k++) {
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(suppress_allele);
if (m_ClauseList[k]->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_3UTR && subtype == CSeqFeatData::eSubtype_cdregion) {
utr3 = m_ClauseList[k];
for (unsigned int j = k + 1; j < m_ClauseList.size(); j++) {
@@ -1113,7 +901,7 @@ bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval)
}
// create subclause list for interval
- interval += ListClauses(false, suppress_final_and);
+ interval += ListClauses(false, suppress_final_and, suppress_allele);
if (subtype == CSeqFeatData::eSubtype_cdregion && !m_ClauseInfoOnly) {
if (utr3 != NULL) {
@@ -1163,7 +951,7 @@ bool CAutoDefFeatureClause::x_GetGenericInterval (string &interval)
}
-void CAutoDefFeatureClause::Label()
+void CAutoDefFeatureClause::Label(bool suppress_allele)
{
if (!m_TypewordChosen) {
m_TypewordChosen = x_GetFeatureTypeWord(m_Typeword);
@@ -1177,14 +965,15 @@ void CAutoDefFeatureClause::Label()
m_DescriptionChosen = x_GetDescription(m_Description);
}
- x_GetGenericInterval (m_Interval);
+ x_GetGenericInterval (m_Interval, suppress_allele);
}
sequence::ECompare CAutoDefFeatureClause::CompareLocation(const CSeq_loc& loc)
{
- return sequence::Compare(loc, *m_ClauseLocation, &(m_BH.GetScope()));
+ return sequence::Compare(loc, *m_ClauseLocation, &(m_BH.GetScope()),
+ sequence::fCompareOverlapping);
}
@@ -1292,29 +1081,6 @@ bool CAutoDefFeatureClause::AddmRNA (CAutoDefFeatureClause_Base *mRNAClause)
}
-bool CAutoDefFeatureClause::x_MatchGene(const CGene_ref& gref)
-{
- if (!m_HasGene
- || !NStr::Equal(x_GetGeneName(gref), m_GeneName)) {
- return false;
- }
-
- if (NStr::IsBlank(m_AlleleName)) {
- if (gref.CanGetAllele() && !NStr::IsBlank(gref.GetAllele())) {
- return false;
- } else {
- return true;
- }
- } else {
- if (!gref.CanGetAllele() || !NStr::Equal(m_AlleleName, gref.GetAllele())) {
- return false;
- } else {
- return true;
- }
- }
-}
-
-
/* This function searches this list for clauses to which this gene should
* apply. This is not taken care of by the GroupAllClauses function
* because genes are added to clauses as a GeneRefPtr instead of as an
@@ -1322,7 +1088,7 @@ bool CAutoDefFeatureClause::x_MatchGene(const CGene_ref& gref)
* than one clause, while other features should really only belong to
* one clause.
*/
-bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause)
+bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele)
{
bool used_gene = false;
@@ -1332,9 +1098,6 @@ bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause)
CSeqFeatData::ESubtype subtype = GetMainFeatureSubtype ();
- sequence::ECompare loc_compare = gene_clause->CompareLocation(*m_ClauseLocation);
-
-
string noncoding_product_name;
// only add gene to certain other types of clauses
@@ -1356,8 +1119,10 @@ bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause)
// already assigned
} else {
// find overlapping gene for this feature
+ CAutoDefGeneClause *gene = dynamic_cast<CAutoDefGeneClause *>(gene_clause);
+ bool suppress_locus_tag = gene ? gene->GetSuppressLocusTag() : false;
CConstRef <CSeq_feat> gene_for_feat = edit::GetGeneForFeature(m_MainFeat, m_BH.GetScope());
- if (gene_for_feat && NStr::Equal(x_GetGeneName(gene_for_feat->GetData().GetGene()), gene_clause->GetGeneName())) {
+ if (gene_for_feat && NStr::Equal(x_GetGeneName(gene_for_feat->GetData().GetGene(), suppress_locus_tag), gene_clause->GetGeneName())) {
used_gene = true;
m_HasGene = true;
m_GeneName = gene_clause->GetGeneName();
@@ -1367,7 +1132,7 @@ bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause)
}
if (used_gene && ! m_ProductNameChosen) {
- Label();
+ Label(suppress_allele);
if (!m_ProductNameChosen) {
m_ProductNameChosen = true;
m_ProductName = gene_clause->GetProductName();
@@ -1375,7 +1140,7 @@ bool CAutoDefFeatureClause::AddGene (CAutoDefFeatureClause_Base *gene_clause)
}
if (used_gene) {
m_DescriptionChosen = false;
- Label();
+ Label(suppress_allele);
}
return used_gene;
@@ -1426,8 +1191,7 @@ bool CAutoDefFeatureClause::OkToGroupUnderByType(CAutoDefFeatureClause_Base *par
|| IsMobileElement()
|| IsNoncodingProductFeat()
|| subtype == CSeqFeatData::eSubtype_operon
- || IsGeneCluster()
- || IsIntergenicSpacer()) {
+ || IsGeneCluster()) {
if (parent_clause->IsMobileElement()
|| parent_clause->IsInsertionSequence()
|| parent_clause->IsEndogenousVirusSourceFeature()
@@ -1517,6 +1281,12 @@ bool CAutoDefFeatureClause::OkToGroupUnderByLocation(CAutoDefFeatureClause_Base
prev_stop = cds_stop;
++seq_loc_it;
}
+ // intron could also group with coding region if coding region is adjacent
+ if (intron_start > prev_stop && intron_start - 1 == prev_stop) {
+ return true;
+ } else if (prev_start > intron_stop && prev_start - 1 == intron_stop) {
+ return true;
+ }
}
}
@@ -1682,6 +1452,9 @@ CAutoDefMobileElementClause::CAutoDefMobileElementClause(CBioseq_Handle bh, cons
: CAutoDefFeatureClause(bh, main_feat, mapped_loc)
{
string mobile_element_name = m_MainFeat.GetNamedQual("mobile_element_type");
+ if (NStr::StartsWith(mobile_element_name, "other:")) {
+ mobile_element_name = mobile_element_name.substr(6);
+ }
bool found_keyword = false;
m_Pluralizable = true;
@@ -1755,10 +1528,23 @@ CAutoDefMobileElementClause::~CAutoDefMobileElementClause()
}
-void CAutoDefMobileElementClause::Label()
+void CAutoDefMobileElementClause::Label(bool suppress_allele)
{
m_DescriptionChosen = true;
- x_GetGenericInterval (m_Interval);
+ x_GetGenericInterval (m_Interval, suppress_allele);
+}
+
+
+bool CAutoDefMobileElementClause::IsOptional()
+{
+ if (NStr::Equal(m_Typeword, "SINE") ||
+ NStr::Equal(m_Typeword, "LINE") ||
+ NStr::Equal(m_Typeword, "MITE")) {
+ return true;
+ } else {
+ return false;
+ }
+
}
@@ -1783,7 +1569,11 @@ CAutoDefSatelliteClause::CAutoDefSatelliteClause(CBioseq_Handle bh, const CSeq_f
len = strlen (kMicrosatellite);
} else if (NStr::StartsWith (comment, kSatellite)) {
len = strlen (kSatellite);
- }
+ } else {
+ // use default label satellite
+ string prefix = kSatellite;
+ comment = prefix + " " + comment;
+ }
if (len > 0 && NStr::Equal(comment.substr(len, 1), ":")) {
comment = comment.substr (0, len) + " " + comment.substr (len + 1);
}
@@ -1800,10 +1590,10 @@ CAutoDefSatelliteClause::~CAutoDefSatelliteClause()
}
-void CAutoDefSatelliteClause::Label()
+void CAutoDefSatelliteClause::Label(bool suppress_allele)
{
m_DescriptionChosen = true;
- x_GetGenericInterval(m_Interval);
+ x_GetGenericInterval(m_Interval, suppress_allele);
}
@@ -1823,7 +1613,7 @@ CAutoDefPromoterClause::~CAutoDefPromoterClause()
}
-void CAutoDefPromoterClause::Label()
+void CAutoDefPromoterClause::Label(bool suppress_allele)
{
m_DescriptionChosen = true;
}
@@ -1840,7 +1630,7 @@ void CAutoDefPromoterClause::Label()
* "intergenic spacer".
*/
-void CAutoDefIntergenicSpacerClause::InitWithString (string comment)
+void CAutoDefIntergenicSpacerClause::InitWithString (string comment, bool suppress_allele)
{
m_Typeword = "intergenic spacer";
m_TypewordChosen = true;
@@ -1886,7 +1676,7 @@ void CAutoDefIntergenicSpacerClause::InitWithString (string comment)
m_ShowTypewordFirst = false;
}
}
- x_GetGenericInterval(m_Interval);
+ x_GetGenericInterval(m_Interval, suppress_allele);
}
}
@@ -1894,7 +1684,7 @@ void CAutoDefIntergenicSpacerClause::InitWithString (string comment)
CAutoDefIntergenicSpacerClause::CAutoDefIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat& main_feat, const CSeq_loc &mapped_loc, string comment)
: CAutoDefFeatureClause(bh, main_feat, mapped_loc)
{
- InitWithString (comment);
+ InitWithString (comment, true);
}
@@ -1910,7 +1700,7 @@ CAutoDefIntergenicSpacerClause::CAutoDefIntergenicSpacerClause(CBioseq_Handle bh
comment = comment.substr(0, pos);
}
- InitWithString (comment);
+ InitWithString (comment, true);
}
@@ -1919,26 +1709,37 @@ CAutoDefIntergenicSpacerClause::~CAutoDefIntergenicSpacerClause()
}
-void CAutoDefIntergenicSpacerClause::Label()
+void CAutoDefIntergenicSpacerClause::Label(bool suppress_allele)
{
m_DescriptionChosen = true;
}
CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc,
- string description, bool is_first, bool is_last)
+ const string& description, bool is_first, bool is_last)
: CAutoDefIntergenicSpacerClause(bh, main_feat, mapped_loc)
{
if (!NStr::IsBlank(description)) {
m_Description = description;
+ size_t pos = NStr::Find(m_Description, "intergenic spacer");
+ if (pos != string::npos) {
+ m_Description = m_Description.substr(0, pos);
+ NStr::TruncateSpacesInPlace(m_Description);
+ }
+ m_DescriptionChosen = true;
}
+ m_Typeword = "intergenic spacer";
+ m_TypewordChosen = true;
// adjust partialness of location
bool partial5 = m_ClauseLocation->IsPartialStart(eExtreme_Biological) && is_first;
bool partial3 = m_ClauseLocation->IsPartialStop(eExtreme_Biological) && is_last;
m_ClauseLocation->SetPartialStart(partial5, eExtreme_Biological);
m_ClauseLocation->SetPartialStop(partial3, eExtreme_Biological);
- x_GetGenericInterval(m_Interval);
+ x_GetGenericInterval(m_Interval, true);
+ if (NStr::EndsWith(description, " region")) {
+ MakeRegion();
+ }
}
@@ -1966,6 +1767,35 @@ CAutoDefParsedClause::~CAutoDefParsedClause()
{
}
+void CAutoDefParsedClause::SetMiscRNAWord(const string& phrase)
+{
+ ERnaMiscWord word_type = x_GetRnaMiscWordType(phrase);
+ if (word_type == eMiscRnaWordType_InternalSpacer ||
+ word_type == eMiscRnaWordType_ExternalSpacer ||
+ word_type == eMiscRnaWordType_RNAIntergenicSpacer ||
+ word_type == eMiscRnaWordType_IntergenicSpacer) {
+ const string& item_name = x_GetRnaMiscWord(word_type);
+ if (NStr::StartsWith(phrase, item_name)) {
+ SetTypewordFirst(true);
+ m_Description = phrase.substr(item_name.length());
+ } else {
+ SetTypewordFirst(false);
+ m_Description = phrase.substr(0, NStr::Find(phrase, item_name));
+ }
+ if (NStr::EndsWith(phrase, " region")) {
+ SetTypeword(item_name + " region");
+ } else {
+ SetTypeword(item_name);
+ }
+ } else if (word_type == eMiscRnaWordType_RNA) {
+ m_Description = phrase;
+ SetTypeword("gene");
+ SetTypewordFirst(false);
+ }
+ NStr::TruncateSpacesInPlace(m_Description);
+ m_DescriptionChosen = true;
+}
+
CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc,
string gene_name, string product_name,
@@ -2015,9 +1845,9 @@ CAutoDefGeneClusterClause::~CAutoDefGeneClusterClause()
}
-void CAutoDefGeneClusterClause::Label()
+void CAutoDefGeneClusterClause::Label(bool suppress_allele)
{
- x_GetGenericInterval(m_Interval);
+ x_GetGenericInterval(m_Interval, suppress_allele);
m_DescriptionChosen = true;
}
@@ -2050,7 +1880,7 @@ CAutoDefMiscCommentClause::~CAutoDefMiscCommentClause()
}
-void CAutoDefMiscCommentClause::Label()
+void CAutoDefMiscCommentClause::Label(bool suppress_allele)
{
m_DescriptionChosen = true;
}
@@ -2058,9 +1888,25 @@ void CAutoDefMiscCommentClause::Label()
CAutoDefParsedRegionClause::CAutoDefParsedRegionClause
(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string product)
- : CAutoDefFeatureClause(bh, main_feat, mapped_loc)
-{
- m_Description = product;
+: CAutoDefFeatureClause(bh, main_feat, mapped_loc)
+{
+ vector<string> elements = GetMiscRNAElements(product);
+ if (elements.empty()) {
+ m_Description = product;
+ } else {
+ ITERATE(vector<string>, it, elements) {
+ if (!NStr::IsBlank(m_Description)) {
+ m_Description += ", ";
+ if (*it == elements.back()) {
+ m_Description += "and ";
+ }
+ }
+ m_Description += *it;
+ if (NStr::Find(*it, "RNA") != string::npos && !NStr::EndsWith(*it, "gene") && !NStr::EndsWith(*it, "genes")) {
+ m_Description += " gene";
+ }
+ }
+ }
m_DescriptionChosen = true;
m_Typeword = "";
@@ -2074,7 +1920,7 @@ CAutoDefParsedRegionClause::~CAutoDefParsedRegionClause()
}
-void CAutoDefParsedRegionClause::Label()
+void CAutoDefParsedRegionClause::Label(bool suppress_allele)
{
}
@@ -2105,7 +1951,7 @@ CAutoDefFakePromoterClause::~CAutoDefFakePromoterClause()
}
-void CAutoDefFakePromoterClause::Label()
+void CAutoDefFakePromoterClause::Label(bool suppress_allele)
{
}
@@ -2141,6 +1987,17 @@ bool CAutoDefFakePromoterClause::OkToGroupUnderByType(CAutoDefFeatureClause_Base
return ok_to_group;
}
+CAutoDefFeatureClause::EClauseType CAutoDefFeatureClause::GetClauseType()
+{
+ CSeqFeatData::ESubtype subtype = GetMainFeatureSubtype();
+ if (subtype == CSeqFeatData::eSubtype_repeat_region) {
+ if (!NStr::IsBlank(m_MainFeat.GetNamedQual("endogenous_virus"))) {
+ return eEndogenousVirusRepeatRegion;
+ }
+ }
+ return eDefault;
+}
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/edit/autodef_feature_clause_base.cpp b/c++/src/objtools/edit/autodef_feature_clause_base.cpp
index e13d000..6191629 100644
--- a/c++/src/objtools/edit/autodef_feature_clause_base.cpp
+++ b/c++/src/objtools/edit/autodef_feature_clause_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: autodef_feature_clause_base.cpp 459369 2015-02-18 14:48:00Z ivanov $
+/* $Id: autodef_feature_clause_base.cpp 485525 2015-11-23 16:14:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,33 +59,18 @@ CAutoDefFeatureClause_Base::CAutoDefFeatureClause_Base() :
m_MakePlural(false),
m_IsUnknown(false),
m_ClauseInfoOnly(false),
- m_SuppressLocusTag(false),
m_SuppressSubfeatures(false),
m_DeleteMe(false)
{
}
-CAutoDefFeatureClause_Base::CAutoDefFeatureClause_Base(bool suppress_locus_tag) :
- m_GeneIsPseudo(false),
- m_IsAltSpliced(false),
- m_HasmRNA(false),
- m_HasGene(false),
- m_MakePlural(false),
- m_IsUnknown(false),
- m_ClauseInfoOnly(false),
- m_SuppressLocusTag(suppress_locus_tag),
- m_DeleteMe(false)
-{
-}
-
-
CAutoDefFeatureClause_Base::~CAutoDefFeatureClause_Base()
{
}
-CSeqFeatData::ESubtype CAutoDefFeatureClause_Base::GetMainFeatureSubtype()
+CSeqFeatData::ESubtype CAutoDefFeatureClause_Base::GetMainFeatureSubtype() const
{
if (m_ClauseList.size() == 1) {
return m_ClauseList[0]->GetMainFeatureSubtype();
@@ -95,6 +80,22 @@ CSeqFeatData::ESubtype CAutoDefFeatureClause_Base::GetMainFeatureSubtype()
}
+bool CAutoDefFeatureClause_Base::IsuORF(const string& product)
+{
+ // find uORF as whole word in product name
+ size_t pos = NStr::Find(product, "uORF");
+ if (pos != string::npos &&
+ (pos == 0 || isspace(product.c_str()[pos - 1])) &&
+ (pos == product.length() - 4 || isspace(product.c_str()[pos + 4]))) {
+ return true;
+ } else if (NStr::EndsWith(product, "leader peptide")) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+
void CAutoDefFeatureClause_Base::AddSubclause (CAutoDefFeatureClause_Base *subclause)
{
if (subclause) {
@@ -128,7 +129,7 @@ void CAutoDefFeatureClause_Base::SetAltSpliced(string splice_name)
}
-string CAutoDefFeatureClause_Base::PrintClause(bool print_typeword, bool typeword_is_plural)
+string CAutoDefFeatureClause_Base::PrintClause(bool print_typeword, bool typeword_is_plural, bool suppress_allele)
{
bool print_comma_between_description_and_typeword = false;
string clause_text;
@@ -220,6 +221,21 @@ bool CAutoDefFeatureClause_Base::IsGeneMentioned(CAutoDefFeatureClause_Base *gen
}
+bool CAutoDefFeatureClause_Base::IsUnattachedGene() const
+{
+ if (GetMainFeatureSubtype() != CSeqFeatData::eSubtype_gene) {
+ return false;
+ }
+
+ for (unsigned int j = 0; j < m_ClauseList.size(); j++) {
+ if (!m_ClauseList[j]->IsMarkedForDeletion()) {
+ return false;
+ }
+ }
+ return true;
+}
+
+
bool CAutoDefFeatureClause_Base::AddmRNA (CAutoDefFeatureClause_Base *mRNAClause)
{
bool retval = false;
@@ -230,25 +246,25 @@ bool CAutoDefFeatureClause_Base::AddmRNA (CAutoDefFeatureClause_Base *mRNAClause
}
-bool CAutoDefFeatureClause_Base::AddGene (CAutoDefFeatureClause_Base *gene_clause)
+bool CAutoDefFeatureClause_Base::AddGene (CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele)
{
bool retval = false;
for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
- retval |= m_ClauseList[k]->AddGene(gene_clause);
+ retval |= m_ClauseList[k]->AddGene(gene_clause, suppress_allele);
}
return retval;
}
-void CAutoDefFeatureClause_Base::Label()
+void CAutoDefFeatureClause_Base::Label(bool suppress_allele)
{
for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(suppress_allele);
}
}
// Grouping functions
-void CAutoDefFeatureClause_Base::GroupmRNAs()
+void CAutoDefFeatureClause_Base::GroupmRNAs(bool suppress_allele)
{
unsigned int k, j;
@@ -258,7 +274,7 @@ void CAutoDefFeatureClause_Base::GroupmRNAs()
|| m_ClauseList[k]->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_mRNA) {
continue;
}
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(suppress_allele);
bool mRNA_used = false;
for (j = 0; j < m_ClauseList.size() && !mRNA_used; j++) {
if (m_ClauseList[j]->IsMarkedForDeletion()
@@ -266,7 +282,7 @@ void CAutoDefFeatureClause_Base::GroupmRNAs()
|| m_ClauseList[j]->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_cdregion) {
continue;
} else {
- m_ClauseList[j]->Label();
+ m_ClauseList[j]->Label(suppress_allele);
mRNA_used |= m_ClauseList[j]->AddmRNA (m_ClauseList[k]);
}
}
@@ -277,7 +293,7 @@ void CAutoDefFeatureClause_Base::GroupmRNAs()
}
-void CAutoDefFeatureClause_Base::GroupGenes()
+void CAutoDefFeatureClause_Base::GroupGenes(bool suppress_allele)
{
unsigned int k, j;
@@ -293,7 +309,7 @@ void CAutoDefFeatureClause_Base::GroupGenes()
if (j == k || m_ClauseList[j]->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_gene) {
continue;
}
- used_gene |= m_ClauseList[j]->AddGene(m_ClauseList[k]);
+ used_gene |= m_ClauseList[j]->AddGene(m_ClauseList[k], suppress_allele);
}
}
}
@@ -305,10 +321,13 @@ void CAutoDefFeatureClause_Base::RemoveGenesMentionedElsewhere()
for (k = 0; k < m_ClauseList.size(); k++) {
if (m_ClauseList[k]->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_gene) {
- for (j = 0; j < m_ClauseList.size() && !m_ClauseList[k]->IsMarkedForDeletion(); j++) {
- if (j != k && !m_ClauseList[j]->IsMarkedForDeletion()
- && m_ClauseList[j]->IsGeneMentioned(m_ClauseList[k])) {
- m_ClauseList[k]->MarkForDeletion();
+ // only remove the gene if it has no subclauses not already marked for deletion
+ if (m_ClauseList[k]->IsUnattachedGene()) {
+ for (j = 0; j < m_ClauseList.size() && !m_ClauseList[k]->IsMarkedForDeletion(); j++) {
+ if (j != k && !m_ClauseList[j]->IsMarkedForDeletion()
+ && m_ClauseList[j]->IsGeneMentioned(m_ClauseList[k])) {
+ m_ClauseList[k]->MarkForDeletion();
+ }
}
}
} else {
@@ -319,7 +338,7 @@ void CAutoDefFeatureClause_Base::RemoveGenesMentionedElsewhere()
}
-string CAutoDefFeatureClause_Base::ListClauses(bool allow_semicolons, bool suppress_final_and)
+string CAutoDefFeatureClause_Base::ListClauses(bool allow_semicolons, bool suppress_final_and, bool suppress_allele)
{
if (m_ClauseList.size() < 1) {
return "";
@@ -533,7 +552,7 @@ string CAutoDefFeatureClause_Base::ListClauses(bool allow_semicolons, bool suppr
}
}
- string clause_text = m_ClauseList[k]->PrintClause(print_typeword, typeword_is_plural);
+ string clause_text = m_ClauseList[k]->PrintClause(print_typeword, typeword_is_plural, suppress_allele);
if (!NStr::IsBlank(clause_text)) {
if (!NStr::IsBlank(full_clause_list)) {
@@ -721,49 +740,85 @@ bool CAutoDefFeatureClause_Base::x_OkToConsolidate (unsigned int clause1, unsign
}
-void CAutoDefFeatureClause_Base::ConsolidateRepeatedClauses ()
+void CAutoDefFeatureClause_Base::Consolidate(CAutoDefFeatureClause_Base& other, bool suppress_allele)
+{
+ // Add subfeatures from new clause to last clause
+ TClauseList new_subfeatures;
+ new_subfeatures.clear();
+ other.TransferSubclauses(new_subfeatures);
+ for (unsigned int j = 0; j < new_subfeatures.size(); j++) {
+ AddSubclause(new_subfeatures[j]);
+ new_subfeatures[j] = NULL;
+ }
+ new_subfeatures.clear();
+
+ // Add new clause location to last clause
+ AddToLocation(other.GetLocation());
+ // if we have two clauses that are really identical instead of
+ // just sharing a "prefix", make the description plural
+ if (NStr::Equal(GetInterval(), other.GetInterval())) {
+ SetMakePlural();
+ }
+
+ // this will regenerate the interval
+ Label(suppress_allele);
+
+ // mark other clause for deletion
+ other.MarkForDeletion();
+}
+
+
+void CAutoDefFeatureClause_Base::x_RemoveNullClauses()
+{
+ TClauseList::iterator it = m_ClauseList.begin();
+ while (it != m_ClauseList.end()) {
+ if (*it == NULL) {
+ it = m_ClauseList.erase(it);
+ } else {
+ ++it;
+ }
+ }
+}
+
+
+void CAutoDefFeatureClause_Base::ConsolidateRepeatedClauses (bool suppress_allele)
{
if (m_ClauseList.size() < 2) {
return;
}
for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
- m_ClauseList[k]->ConsolidateRepeatedClauses();
- if (m_ClauseList[k]->IsMarkedForDeletion()) {
+ if (!m_ClauseList[k] || m_ClauseList[k]->IsMarkedForDeletion()) {
continue;
}
+ m_ClauseList[k]->ConsolidateRepeatedClauses(suppress_allele);
for (unsigned int n = k + 1; n < m_ClauseList.size(); n++) {
- if (m_ClauseList[n]->IsMarkedForDeletion()) {
+ if (!m_ClauseList[n] || m_ClauseList[n]->IsMarkedForDeletion()) {
continue;
}
if (x_OkToConsolidate(k, n)) {
- // Add subfeatures from new clause to last clause
- TClauseList new_subfeatures;
- new_subfeatures.clear();
- m_ClauseList[n]->TransferSubclauses(new_subfeatures);
- for (unsigned int j = 0; j < new_subfeatures.size(); j++) {
- m_ClauseList[k]->AddSubclause(new_subfeatures[j]);
- new_subfeatures[j] = NULL;
- }
- new_subfeatures.clear();
-
- // Add new clause location to last clause
- m_ClauseList[k]->AddToLocation(m_ClauseList[n]->GetLocation());
- // if we have two clauses that are really identical instead of
- // just sharing a "prefix", make the description plural
- if (NStr::Equal(m_ClauseList[k]->GetInterval(), m_ClauseList[n]->GetInterval())) {
+ CSeqFeatData::ESubtype subtypek = m_ClauseList[k]->GetMainFeatureSubtype();
+ CSeqFeatData::ESubtype subtypen = m_ClauseList[n]->GetMainFeatureSubtype();
+
+ if (subtypek == CSeqFeatData::eSubtype_gene) {
+ m_ClauseList[n]->Consolidate(*m_ClauseList[k], suppress_allele);
+ } else if (subtypen == CSeqFeatData::eSubtype_gene) {
+ m_ClauseList[k]->Consolidate(*m_ClauseList[n], suppress_allele);
+ } else {
+ m_ClauseList[k]->AddSubclause(m_ClauseList[n]);
+ m_ClauseList[k]->SuppressSubfeatures();
m_ClauseList[k]->SetMakePlural();
- }
-
- // this will regenerate the interval
- m_ClauseList[k]->Label();
-
- // mark new clause for deletion
- m_ClauseList[n]->MarkForDeletion();
+ m_ClauseList[n] = NULL;
+ }
+ } else {
+ // do not consolidate with non-consecutive clauses
+ break;
}
}
}
+ x_RemoveNullClauses();
+ Label(suppress_allele);
}
// These are words that are used to introduced the part of the protein
@@ -850,7 +905,7 @@ bool CAutoDefFeatureClause_Base::x_MeetAltSpliceRules (unsigned int clause1, uns
match_left_len--;
}
if (match_left_len == len1 && m_ClauseList[clause1]->IsAltSpliced()) {
- match_left_token = match_left_len;
+ // no adjustment
} else {
match_left_len = match_left_token;
}
@@ -868,7 +923,7 @@ bool CAutoDefFeatureClause_Base::x_MeetAltSpliceRules (unsigned int clause1, uns
}
if (match_right_len == len1 && m_ClauseList[clause1]->IsAltSpliced()) {
- match_right_token = match_right_len;
+ // no adjustment
} else {
match_right_len = match_right_token;
}
@@ -899,6 +954,7 @@ bool CAutoDefFeatureClause_Base::x_MeetAltSpliceRules (unsigned int clause1, uns
if (pos < splice_name.length()) {
temp_name += splice_name.substr(pos + unwanted_words[k].length());
}
+ splice_name = temp_name;
}
}
@@ -910,7 +966,7 @@ bool CAutoDefFeatureClause_Base::x_MeetAltSpliceRules (unsigned int clause1, uns
}
-void CAutoDefFeatureClause_Base::FindAltSplices()
+void CAutoDefFeatureClause_Base::FindAltSplices(bool suppress_allele)
{
unsigned int last_cds = m_ClauseList.size();
string splice_name;
@@ -919,7 +975,7 @@ void CAutoDefFeatureClause_Base::FindAltSplices()
if (m_ClauseList[k]->IsMarkedForDeletion()) {
continue;
}
- m_ClauseList[k]->FindAltSplices();
+ m_ClauseList[k]->FindAltSplices(suppress_allele);
if (m_ClauseList[k]->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_cdregion) {
if (x_MeetAltSpliceRules(last_cds, k, splice_name)) {
// set splice flag and product name for last cds
@@ -939,7 +995,7 @@ void CAutoDefFeatureClause_Base::FindAltSplices()
m_ClauseList[k]->MarkForDeletion();
//Label original
- m_ClauseList[last_cds]->Label();
+ m_ClauseList[last_cds]->Label(suppress_allele);
} else {
last_cds = k;
}
@@ -1059,7 +1115,7 @@ string CAutoDefFeatureClause_Base::FindGeneProductName(CAutoDefFeatureClause_Bas
}
-void CAutoDefFeatureClause_Base::AssignGeneProductNames(CAutoDefFeatureClause_Base *main_clause)
+void CAutoDefFeatureClause_Base::AssignGeneProductNames(CAutoDefFeatureClause_Base *main_clause, bool suppress_allele)
{
if (main_clause == NULL) {
return;
@@ -1069,7 +1125,7 @@ void CAutoDefFeatureClause_Base::AssignGeneProductNames(CAutoDefFeatureClause_Ba
string product_name = main_clause->FindGeneProductName(m_ClauseList[k]);
if (!NStr::IsBlank(product_name)) {
m_ClauseList[k]->SetProductName(product_name);
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(suppress_allele);
}
}
}
@@ -1085,7 +1141,7 @@ void CAutoDefFeatureClause_Base::SetProductName(string product_name)
void CAutoDefFeatureClause_Base::CountUnknownGenes()
{
- CAutoDefUnknownGeneList *unknown_list = new CAutoDefUnknownGeneList(m_SuppressLocusTag);
+ CAutoDefUnknownGeneList *unknown_list = new CAutoDefUnknownGeneList();
bool any_found = false;
for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
@@ -1146,7 +1202,7 @@ void CAutoDefFeatureClause_Base::GroupAltSplicedExons(CBioseq_Handle bh)
if (!found_any) {
continue;
}
- CAutoDefExonListClause *new_clause = new CAutoDefExonListClause (bh, m_SuppressLocusTag);
+ CAutoDefExonListClause *new_clause = new CAutoDefExonListClause (bh);
new_clause->AddSubclause(m_ClauseList[k]);
new_clause->AddSubclause(m_ClauseList[j]);
@@ -1228,7 +1284,7 @@ void CAutoDefFeatureClause_Base::GroupConsecutiveExons(CBioseq_Handle bh)
|| m_ClauseList[k]->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_exon) {
continue;
}
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(false);
string sequence = m_ClauseList[k]->GetDescription();
unsigned int seq_num = 0, next_num;
try {
@@ -1242,7 +1298,7 @@ void CAutoDefFeatureClause_Base::GroupConsecutiveExons(CBioseq_Handle bh)
while (j < m_ClauseList.size()) {
if (m_ClauseList[j] != NULL && !m_ClauseList[j]->IsMarkedForDeletion()) {
if (m_ClauseList[j]->GetMainFeatureSubtype() == CSeqFeatData::eSubtype_exon) {
- m_ClauseList[j]->Label();
+ m_ClauseList[j]->Label(false);
sequence = m_ClauseList[j]->GetDescription();
try {
next_num = NStr::StringToUInt (sequence);
@@ -1257,7 +1313,7 @@ void CAutoDefFeatureClause_Base::GroupConsecutiveExons(CBioseq_Handle bh)
}
if (next_num == seq_num + 1) {
if (new_clause == NULL) {
- new_clause = new CAutoDefExonListClause(bh, m_SuppressLocusTag);
+ new_clause = new CAutoDefExonListClause(bh);
new_clause->AddSubclause(m_ClauseList[k]);
last_new_clause = new_clause;
last_new_clause_position = k;
@@ -1283,7 +1339,7 @@ void CAutoDefFeatureClause_Base::GroupConsecutiveExons(CBioseq_Handle bh)
}
if (new_clause != NULL) {
m_ClauseList[k] = new_clause;
- new_clause->Label();
+ new_clause->Label(false);
}
}
if (last_new_clause != NULL) {
@@ -1314,7 +1370,7 @@ void CAutoDefFeatureClause_Base::GroupConsecutiveExons(CBioseq_Handle bh)
// This function should combine CDSs on a segmented set that do not have a joined location
// but are part of the same gene and have the same protein name.
-void CAutoDefFeatureClause_Base::GroupSegmentedCDSs ()
+void CAutoDefFeatureClause_Base::GroupSegmentedCDSs (bool suppress_allele)
{
if (m_ClauseList.size() > 1) {
for (unsigned int k = 0; k < m_ClauseList.size() - 1; k++) {
@@ -1323,14 +1379,14 @@ void CAutoDefFeatureClause_Base::GroupSegmentedCDSs ()
|| m_ClauseList[k]->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_cdregion) {
continue;
}
- m_ClauseList[k]->Label();
+ m_ClauseList[k]->Label(suppress_allele);
for (unsigned int j = k + 1; j < m_ClauseList.size(); j++) {
if (m_ClauseList[j] == NULL
|| m_ClauseList[j]->IsMarkedForDeletion()
|| m_ClauseList[j]->GetMainFeatureSubtype() != CSeqFeatData::eSubtype_cdregion) {
continue;
}
- m_ClauseList[j]->Label();
+ m_ClauseList[j]->Label(suppress_allele);
if (NStr::Equal(m_ClauseList[k]->GetProductName(), m_ClauseList[j]->GetProductName())
&& !NStr::IsBlank(m_ClauseList[k]->GetGeneName())
&& NStr::Equal(m_ClauseList[k]->GetGeneName(), m_ClauseList[j]->GetGeneName())
@@ -1359,7 +1415,7 @@ void CAutoDefFeatureClause_Base::GroupSegmentedCDSs ()
}
for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
if (m_ClauseList[k] != NULL && !m_ClauseList[k]->IsMarkedForDeletion()) {
- m_ClauseList[k]->GroupSegmentedCDSs();
+ m_ClauseList[k]->GroupSegmentedCDSs(suppress_allele);
}
}
}
@@ -1465,8 +1521,34 @@ void CAutoDefFeatureClause_Base::RemoveTransSplicedLeaders()
}
-CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(bool suppress_locus_tags)
- : CAutoDefFeatureClause_Base(suppress_locus_tags)
+void CAutoDefFeatureClause_Base::RemoveuORFs()
+{
+ for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
+ unsigned int subtype = m_ClauseList[k]->GetMainFeatureSubtype();
+ if (subtype == CSeqFeatData::eSubtype_cdregion &&
+ IsuORF(m_ClauseList[k]->GetProductName())) {
+ m_ClauseList[k]->MarkForDeletion();
+ } else {
+ m_ClauseList[k]->RemoveuORFs();
+ }
+ }
+}
+
+void CAutoDefFeatureClause_Base::RemoveOptionalMobileElements()
+{
+ for (unsigned int k = 0; k < m_ClauseList.size(); k++) {
+ CAutoDefMobileElementClause* clause = dynamic_cast<CAutoDefMobileElementClause *>(m_ClauseList[k]);
+ if (clause && clause->IsOptional()) {
+ m_ClauseList[k]->MarkForDeletion();
+ } else {
+ m_ClauseList[k]->RemoveOptionalMobileElements();
+ }
+ }
+}
+
+
+CAutoDefUnknownGeneList::CAutoDefUnknownGeneList()
+ : CAutoDefFeatureClause_Base()
{
m_Description = "unknown";
m_DescriptionChosen = true;
@@ -1481,7 +1563,7 @@ CAutoDefUnknownGeneList::~CAutoDefUnknownGeneList()
}
-void CAutoDefUnknownGeneList::Label()
+void CAutoDefUnknownGeneList::Label(bool suppress_allele)
{
if (m_ClauseList.size() > 1) {
m_MakePlural = true;
@@ -1491,8 +1573,8 @@ void CAutoDefUnknownGeneList::Label()
}
-CAutoDefExonListClause::CAutoDefExonListClause(CBioseq_Handle bh, bool suppress_locus_tags)
- : CAutoDefFeatureClause_Base(suppress_locus_tags),
+CAutoDefExonListClause::CAutoDefExonListClause(CBioseq_Handle bh)
+ : CAutoDefFeatureClause_Base(),
m_SuppressFinalAnd(false),
m_BH(bh)
{
@@ -1504,7 +1586,7 @@ CAutoDefExonListClause::CAutoDefExonListClause(CBioseq_Handle bh, bool suppress_
}
-CSeqFeatData::ESubtype CAutoDefExonListClause::GetMainFeatureSubtype()
+CSeqFeatData::ESubtype CAutoDefExonListClause::GetMainFeatureSubtype() const
{
return CSeqFeatData::eSubtype_exon;
}
@@ -1564,12 +1646,12 @@ void CAutoDefExonListClause::AddSubclause (CAutoDefFeatureClause_Base *subclause
}
-void CAutoDefExonListClause::Label()
+void CAutoDefExonListClause::Label(bool suppress_allele)
{
if (m_ClauseList.size() > 2) {
m_Description = m_ClauseList[0]->GetDescription() + " through " + m_ClauseList[m_ClauseList.size() - 1]->GetDescription();
} else {
- m_Description = ListClauses(false, m_SuppressFinalAnd);
+ m_Description = ListClauses(false, m_SuppressFinalAnd, suppress_allele);
if (NStr::StartsWith(m_Description, "exons")) {
m_Description = m_Description.substr(5);
} else if (NStr::StartsWith(m_Description, "exon")) {
@@ -1626,5 +1708,237 @@ bool CAutoDefExonListClause::OkToGroupUnderByType(CAutoDefFeatureClause_Base *pa
}
+// Some misc_RNA clauses have a comment that actually lists multiple
+// features. This function creates a list of each element in the
+// comment.
+static string kRNAMiscWords[] = {
+ "internal transcribed spacer",
+ "external transcribed spacer",
+ "ribosomal RNA intergenic spacer",
+ "ribosomal RNA",
+ "intergenic spacer"
+};
+
+CAutoDefFeatureClause_Base::ERnaMiscWord CAutoDefFeatureClause_Base::x_GetRnaMiscWordType(const string& phrase)
+{
+ // find first of the recognized words to occur in the string
+ for (size_t i = eMiscRnaWordType_InternalSpacer; i < eMiscRnaWordType_Unrecognized; i++) {
+ if (NStr::Find(phrase, kRNAMiscWords[i]) != string::npos) {
+ return (ERnaMiscWord)i;
+ }
+ }
+ return eMiscRnaWordType_Unrecognized;
+}
+
+const string& CAutoDefFeatureClause_Base::x_GetRnaMiscWord(ERnaMiscWord word_type)
+{
+ if (word_type == eMiscRnaWordType_Unrecognized) {
+ return kEmptyStr;
+ } else {
+ return kRNAMiscWords[word_type];
+ }
+}
+
+
+bool CAutoDefFeatureClause_Base::x_AddOneMiscWordElement(const string& phrase, vector<string>& elements)
+{
+ string val = phrase;
+ NStr::TruncateSpacesInPlace(val);
+ ERnaMiscWord word_type = x_GetRnaMiscWordType(val);
+ if (word_type == eMiscRnaWordType_Unrecognized) {
+ elements.clear();
+ return false;
+ } else {
+ elements.push_back(val);
+ return true;
+ }
+}
+
+
+vector<string> CAutoDefFeatureClause_Base::GetMiscRNAElements(const string& comment)
+{
+ vector<string> elements;
+ vector<string> parts;
+ NStr::Tokenize(comment, ",", parts, NStr::eMergeDelims);
+ if (parts.empty()) {
+ return elements;
+ }
+ ITERATE(vector<string>, it, parts) {
+ size_t pos = NStr::Find(*it, " and ");
+ if (pos == string::npos) {
+ if (!x_AddOneMiscWordElement(*it, elements)) {
+ break;
+ }
+ } else {
+ if (pos > 0) {
+ if (!x_AddOneMiscWordElement((*it).substr(0, pos), elements)) {
+ break;
+ }
+ }
+ if (!x_AddOneMiscWordElement((*it).substr(pos + 5), elements)) {
+ break;
+ }
+ }
+ }
+ return elements;
+}
+
+
+CAutoDefFeatureClause_Base::ETRNAIntergenicSpacerType CAutoDefFeatureClause_Base::x_GetTRNAIntergenicSpacerType(const string& phrase)
+{
+ string gene_name, product_name;
+ if (NStr::EndsWith(phrase, " intergenic spacer")) {
+ return eTRNAIntergenicSpacerType_Spacer;
+ } else if (CAutoDefParsedtRNAClause::ParseString(phrase, gene_name, product_name)) {
+ return eTRNAIntergenicSpacerType_Gene;
+ } else {
+ return eTRNAIntergenicSpacerType_Unrecognized;
+ }
+}
+
+
+string CAutoDefFeatureClause_Base::x_tRNAGeneFromProduct(const string& label)
+{
+ string gene = "";
+
+ if (!NStr::StartsWith(label, "tRNA-")) {
+ return kEmptyStr;
+ }
+ string product = label.substr(5);
+
+ if (NStr::EqualNocase(product, "Ala")) {
+ gene = "trnA";
+ } else if (NStr::EqualNocase(product, "Asx")) {
+ gene = "trnB";
+ } else if (NStr::EqualNocase(product, "Cys")) {
+ gene = "trnC";
+ } else if (NStr::EqualNocase(product, "Asp")) {
+ gene = "trnD";
+ } else if (NStr::EqualNocase(product, "Glu")) {
+ gene = "trnE";
+ } else if (NStr::EqualNocase(product, "Phe")) {
+ gene = "trnF";
+ } else if (NStr::EqualNocase(product, "Gly")) {
+ gene = "trnG";
+ } else if (NStr::EqualNocase(product, "His")) {
+ gene = "trnH";
+ } else if (NStr::EqualNocase(product, "Ile")) {
+ gene = "trnI";
+ } else if (NStr::EqualNocase(product, "Xle")) {
+ gene = "trnJ";
+ } else if (NStr::EqualNocase(product, "Lys")) {
+ gene = "trnK";
+ } else if (NStr::EqualNocase(product, "Leu")) {
+ gene = "trnL";
+ } else if (NStr::EqualNocase(product, "Met")) {
+ gene = "trnM";
+ } else if (NStr::EqualNocase(product, "Asn")) {
+ gene = "trnN";
+ } else if (NStr::EqualNocase(product, "Pyl")) {
+ gene = "trnO";
+ } else if (NStr::EqualNocase(product, "Pro")) {
+ gene = "trnP";
+ } else if (NStr::EqualNocase(product, "Gln")) {
+ gene = "trnQ";
+ } else if (NStr::EqualNocase(product, "Arg")) {
+ gene = "trnR";
+ } else if (NStr::EqualNocase(product, "Ser")) {
+ gene = "trnS";
+ } else if (NStr::EqualNocase(product, "Thr")) {
+ gene = "trnT";
+ } else if (NStr::EqualNocase(product, "Sec")) {
+ gene = "trnU";
+ } else if (NStr::EqualNocase(product, "Val")) {
+ gene = "trnV";
+ } else if (NStr::EqualNocase(product, "Trp")) {
+ gene = "trnW";
+ } else if (NStr::EqualNocase(product, "OTHER")) {
+ gene = "trnX";
+ } else if (NStr::EqualNocase(product, "Tyr")) {
+ gene = "trnY";
+ } else if (NStr::EqualNocase(product, "Glx")) {
+ gene = "trnZ";
+ }
+ return gene;
+}
+
+
+bool CAutoDefFeatureClause_Base::x_AddOnetRNAIntergenicSpacerElement(const string& phrase, vector<string>& elements)
+{
+ string val = phrase;
+ NStr::TruncateSpacesInPlace(val);
+
+ ETRNAIntergenicSpacerType word_type = x_GetTRNAIntergenicSpacerType(val);
+ if (word_type == eTRNAIntergenicSpacerType_Unrecognized) {
+ elements.clear();
+ return false;
+ }
+
+ if (elements.size() > 0) {
+ ETRNAIntergenicSpacerType previous_type = x_GetTRNAIntergenicSpacerType(elements.back());
+ if (word_type == previous_type) {
+ // element types must alternate
+ elements.clear();
+ return false;
+ }
+ if (word_type == eTRNAIntergenicSpacerType_Gene) {
+ // gene must match previous spacer
+ string gene_name, product_name;
+ CAutoDefParsedtRNAClause::ParseString(val, gene_name, product_name);
+ if (NStr::IsBlank(gene_name)) {
+ gene_name = x_tRNAGeneFromProduct(product_name);
+ }
+ if (!NStr::EndsWith(elements.back(), "-" + gene_name + " intergenic spacer")) {
+ elements.clear();
+ return false;
+ }
+ } else {
+ // spacer must match previous gene
+ string gene_name, product_name;
+ CAutoDefParsedtRNAClause::ParseString(elements.back(), gene_name, product_name);
+ if (NStr::IsBlank(gene_name)) {
+ gene_name = x_tRNAGeneFromProduct(product_name);
+ }
+ if (!NStr::StartsWith(val, gene_name + "-")) {
+ elements.clear();
+ return false;
+ }
+ }
+ }
+ elements.push_back(val);
+ return true;
+}
+
+
+vector<string> CAutoDefFeatureClause_Base::GetTrnaIntergenicSpacerClausePhrases(const string& comment)
+{
+ vector<string> elements;
+
+ vector<string> parts;
+ NStr::Tokenize(comment, ",", parts, NStr::eMergeDelims);
+ if (parts.empty()) {
+ return elements;
+ }
+
+ ITERATE(vector<string>, it, parts) {
+ size_t pos = NStr::Find(*it, " and ");
+ if (pos == string::npos) {
+ x_AddOnetRNAIntergenicSpacerElement(*it, elements);
+ } else {
+ if (pos > 0) {
+ if (!x_AddOnetRNAIntergenicSpacerElement((*it).substr(0, pos), elements)) {
+ break;
+ }
+ }
+ if (!x_AddOnetRNAIntergenicSpacerElement((*it).substr(pos + 5), elements)) {
+ break;
+ }
+ }
+ }
+ return elements;
+}
+
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/edit/autodef_mod_combo.cpp b/c++/src/objtools/edit/autodef_mod_combo.cpp
index a954383..e7d32c7 100644
--- a/c++/src/objtools/edit/autodef_mod_combo.cpp
+++ b/c++/src/objtools/edit/autodef_mod_combo.cpp
@@ -1,4 +1,4 @@
-/* $Id: autodef_mod_combo.cpp 459547 2015-02-19 15:31:32Z ivanov $
+/* $Id: autodef_mod_combo.cpp 484819 2015-11-16 16:23:56Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -49,15 +49,16 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
CAutoDefModifierCombo::CAutoDefModifierCombo() : m_UseModifierLabels(false),
- m_MaxModifiers(0),
+ m_MaxModifiers(-99),
+ m_AllowModAtEndOfTaxname(false),
m_KeepCountryText(false),
- m_ExcludeSpOrgs(false),
+ m_ExcludeSpOrgs(true),
m_ExcludeCfOrgs(false),
m_ExcludeNrOrgs(false),
m_ExcludeAffOrgs(false),
m_KeepParen(true),
m_KeepAfterSemicolon(false),
- m_HIVCloneIsolateRule(ePreferClone)
+ m_HIVCloneIsolateRule(CAutoDefOptions::eWantBoth)
{
m_SubSources.clear();
@@ -103,6 +104,7 @@ CAutoDefModifierCombo::CAutoDefModifierCombo(CAutoDefModifierCombo *orig)
m_KeepParen = orig->GetKeepParen();
m_KeepAfterSemicolon = orig->GetKeepAfterSemicolon();
m_HIVCloneIsolateRule = orig->GetHIVCloneIsolateRule();
+ m_AllowModAtEndOfTaxname = orig->GetAllowModAtEndOfTaxname();
m_MaxModifiers = orig->GetMaxModifiers();
}
@@ -115,6 +117,56 @@ CAutoDefModifierCombo::~CAutoDefModifierCombo()
}
+void CAutoDefModifierCombo::InitFromOptions(const CAutoDefOptions& options)
+{
+ m_UseModifierLabels = options.GetUseLabels();
+ m_MaxModifiers = options.GetMaxMods();
+ m_AllowModAtEndOfTaxname = options.GetAllowModAtEndOfTaxname();
+ m_KeepCountryText = options.GetIncludeCountryText();
+ m_ExcludeSpOrgs = options.GetDoNotApplyToSp();
+ m_ExcludeCfOrgs = options.GetDoNotApplyToCf();
+ m_ExcludeNrOrgs = options.GetDoNotApplyToNr();
+ m_ExcludeAffOrgs = options.GetDoNotApplyToAff();
+ m_KeepParen = options.GetLeaveParenthetical();
+ m_KeepAfterSemicolon = options.GetKeepAfterSemicolon();
+ m_HIVCloneIsolateRule = (CAutoDefOptions::EHIVCloneIsolateRule)(options.GetHIVRule());
+
+ const CAutoDefOptions::TSubSources& subsrcs = options.GetSubSources();
+ ITERATE(CAutoDefOptions::TSubSources, it, subsrcs) {
+ AddQual(false, *it, true);
+ }
+ const CAutoDefOptions::TOrgMods& orgmods = options.GetOrgMods();
+ ITERATE(CAutoDefOptions::TOrgMods, it, orgmods) {
+ AddQual(true, *it, true);
+ }
+}
+
+
+void CAutoDefModifierCombo::InitOptions(CAutoDefOptions& options) const
+{
+ options.SetUseLabels(m_UseModifierLabels);
+ options.SetMaxMods(m_MaxModifiers);
+ options.SetAllowModAtEndOfTaxname(m_AllowModAtEndOfTaxname);
+ options.SetIncludeCountryText(m_KeepCountryText);
+ options.SetDoNotApplyToSp(m_ExcludeSpOrgs);
+ options.SetDoNotApplyToCf(m_ExcludeCfOrgs);
+ options.SetDoNotApplyToNr(m_ExcludeNrOrgs);
+ options.SetDoNotApplyToAff(m_ExcludeAffOrgs);
+ options.SetLeaveParenthetical(m_KeepParen);
+ options.SetKeepAfterSemicolon(m_KeepAfterSemicolon);
+ options.SetHIVRule(m_HIVCloneIsolateRule);
+
+ // add subsources and orgmods
+ ITERATE(CAutoDefSourceDescription::TModifierVector, it, m_Modifiers) {
+ if (it->IsOrgMod()) {
+ options.AddOrgMod(it->GetSubtype());
+ } else {
+ options.AddSubSource(it->GetSubtype());
+ }
+ }
+}
+
+
unsigned int CAutoDefModifierCombo::GetNumGroups()
{
return m_GroupList.size();
@@ -351,6 +403,34 @@ void CAutoDefModifierCombo::x_CleanUpTaxName (string &tax_name)
}
}
+bool CAutoDefModifierCombo::x_BioSourceHasSubSrc(const CBioSource& src, CSubSource::ESubtype subtype)
+{
+ if (!src.IsSetSubtype()) {
+ return false;
+ }
+ ITERATE(CBioSource::TSubtype, it, src.GetSubtype()) {
+ if ((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {
+ return true;
+ }
+ }
+ return false;
+}
+
+
+bool CAutoDefModifierCombo::x_BioSourceHasOrgMod(const CBioSource& src, COrgMod::ESubtype subtype)
+{
+ if (!src.IsSetOrg() || !src.GetOrg().IsSetOrgname() || !src.GetOrg().GetOrgname().IsSetMod()) {
+ return false;
+ }
+ ITERATE(COrgName::TMod, it, src.GetOrg().GetOrgname().GetMod()) {
+ if ((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {
+ return true;
+ }
+ }
+ return false;
+
+}
+
bool CAutoDefModifierCombo::x_AddSubsourceString (string &source_description, const CBioSource& bsrc, CSubSource::ESubtype st)
{
@@ -391,6 +471,40 @@ bool CAutoDefModifierCombo::x_AddSubsourceString (string &source_description, co
return used;
}
+bool CAutoDefModifierCombo::IsModifierInString(const string& find_this, const string& find_in, bool ignore_at_end)
+{
+ size_t pos = NStr::Find(find_in, find_this);
+ if (pos == string::npos) {
+ return false;
+ }
+
+ bool keep_looking = false;
+ // need to make sure it's a whole word and not a partial match
+ if (pos != 0 && find_in.c_str()[pos - 1] != '(' && find_in.c_str()[pos - 1] != ' ') {
+ // not whole word
+ keep_looking = true;
+ } else if (find_in.c_str()[pos + find_this.length()] != ')' &&
+ find_in.c_str()[pos + find_this.length()] != ' ' &&
+ find_in.c_str()[pos + find_this.length()] != 0) {
+ // not whole word
+ keep_looking = true;
+ }
+
+ bool at_end = (pos == find_in.length() - find_this.length());
+
+ if (keep_looking) {
+ if (at_end) {
+ return false;
+ } else {
+ return IsModifierInString(find_this, find_in.substr(pos + 1), ignore_at_end);
+ }
+ } else if (at_end && ignore_at_end) {
+ return false;
+ } else {
+ return true;
+ }
+}
+
bool CAutoDefModifierCombo::x_AddOrgModString (string &source_description, const CBioSource& bsrc, COrgMod::ESubtype st)
{
@@ -420,8 +534,9 @@ bool CAutoDefModifierCombo::x_AddOrgModString (string &source_description, const
|| st == COrgMod::eSubtype_forma
|| st == COrgMod::eSubtype_forma_specialis
|| st == COrgMod::eSubtype_pathovar
- || st == COrgMod::eSubtype_specimen_voucher)
- && NStr::Find (bsrc.GetOrg().GetTaxname(), " " + val) != NCBI_NS_STD::string::npos) {
+ || st == COrgMod::eSubtype_specimen_voucher
+ || st == COrgMod::eSubtype_isolate)
+ && IsModifierInString(val, bsrc.GetOrg().GetTaxname(), m_AllowModAtEndOfTaxname)) {
// can't use this
} else {
source_description += x_GetOrgModLabel(st);
@@ -429,6 +544,7 @@ bool CAutoDefModifierCombo::x_AddOrgModString (string &source_description, const
source_description += " ";
source_description += val;
used = true;
+ break;
}
}
}
@@ -447,49 +563,47 @@ bool CAutoDefModifierCombo::HasTrickyHIV()
}
-unsigned int CAutoDefModifierCombo::x_AddHIVModifiers (string &source_description, const CBioSource& bsrc)
+void CAutoDefModifierCombo::x_AddHIVModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc)
{
- unsigned int mods_used = 0;
string clone_text = "";
string isolate_text = "";
bool src_has_clone = false;
bool src_has_isolate = false;
- if (!NStr::Equal (source_description, "HIV-1")
- && !NStr::Equal (source_description, "HIV-2")) {
- return mods_used;
+ if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetTaxname() ||
+ (!NStr::Equal(bsrc.GetOrg().GetTaxname(), "HIV-1") &&
+ !NStr::Equal(bsrc.GetOrg().GetTaxname(), "HIV-2"))) {
+ return;
}
-
- if (!HasSubSource (CSubSource::eSubtype_country)) {
- if (x_AddSubsourceString (source_description, bsrc, CSubSource::eSubtype_country)) {
- mods_used++;
- }
+
+ if (extra_subsrcs.find(CSubSource::eSubtype_country) == extra_subsrcs.end()) {
+ extra_subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_country, true));
}
-
- src_has_clone = x_AddSubsourceString(clone_text, bsrc, CSubSource::eSubtype_clone);
- src_has_isolate = x_AddOrgModString (isolate_text, bsrc, COrgMod::eSubtype_isolate);
-
+
+ src_has_clone = x_BioSourceHasSubSrc(bsrc, CSubSource::eSubtype_clone);
+ src_has_isolate = x_BioSourceHasOrgMod(bsrc, COrgMod::eSubtype_isolate);
+
if ((HasSubSource (CSubSource::eSubtype_clone) && src_has_clone)
|| (HasOrgMod (COrgMod::eSubtype_isolate) && src_has_isolate)) {
// no additional changes - isolate and clone rule taken care of
} else {
if ( ! HasOrgMod (COrgMod::eSubtype_isolate) && src_has_isolate
- && (m_HIVCloneIsolateRule == ePreferIsolate
- || m_HIVCloneIsolateRule == eWantBoth
+ && (m_HIVCloneIsolateRule == CAutoDefOptions::ePreferIsolate
+ || m_HIVCloneIsolateRule == CAutoDefOptions::eWantBoth
|| !src_has_clone)) {
- x_AddOrgModString (source_description, bsrc, COrgMod::eSubtype_isolate);
- mods_used++;
+ if (extra_orgmods.find(COrgMod::eSubtype_isolate) == extra_orgmods.end()) {
+ extra_orgmods.insert(TExtraOrgMod(COrgMod::eSubtype_isolate, true));
+ }
}
if (! HasSubSource(CSubSource::eSubtype_clone) && src_has_clone
- && (m_HIVCloneIsolateRule == ePreferClone
- || m_HIVCloneIsolateRule == eWantBoth
+ && (m_HIVCloneIsolateRule == CAutoDefOptions::ePreferClone
+ || m_HIVCloneIsolateRule == CAutoDefOptions::eWantBoth
|| !src_has_isolate)) {
- x_AddSubsourceString (source_description, bsrc, CSubSource::eSubtype_clone);
- mods_used++;
+ if (extra_subsrcs.find(CSubSource::eSubtype_clone) == extra_subsrcs.end()) {
+ extra_subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_clone, true));
+ }
}
}
-
- return mods_used;
}
@@ -504,21 +618,45 @@ bool CAutoDefModifierCombo::GetDefaultExcludeSp ()
}
-unsigned int CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers (string& description, const CBioSource& bsrc)
+void CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc)
{
- unsigned int num_added = 0;
+ if (extra_subsrcs.find(CSubSource::eSubtype_transgenic) == extra_subsrcs.end()) {
+ extra_subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_transgenic, true));
+ }
+
+ if (extra_subsrcs.find(CSubSource::eSubtype_plasmid_name) == extra_subsrcs.end()) {
+ extra_subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_plasmid_name, true));
+ }
- if (x_AddSubsourceString (description, bsrc, CSubSource::eSubtype_endogenous_virus_name)) {
- num_added++;
+ if (extra_subsrcs.find(CSubSource::eSubtype_endogenous_virus_name) == extra_subsrcs.end()) {
+ extra_subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_endogenous_virus_name, true));
}
- if (x_AddSubsourceString (description, bsrc, CSubSource::eSubtype_plasmid_name)) {
- num_added++;
+}
+
+
+bool CAutoDefModifierCombo::x_HasTypeStrainComment(const CBioSource& bsrc)
+{
+ if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetOrgname() || !bsrc.GetOrg().GetOrgname().IsSetMod()) {
+ return false;
}
- if (x_AddSubsourceString (description, bsrc, CSubSource::eSubtype_transgenic)) {
- num_added++;
+
+ ITERATE(COrgName::TMod, it, bsrc.GetOrg().GetOrgname().GetMod()) {
+ if ((*it)->IsSetSubtype() && (*it)->GetSubtype() == COrgMod::eSubtype_other &&
+ (*it)->IsSetSubname() && NStr::FindNoCase((*it)->GetSubname(), "type strain of") != string::npos) {
+ return true;
+ }
}
-
- return num_added;
+ return false;
+}
+
+
+void CAutoDefModifierCombo::x_AddTypeStrainModifiers(TExtraOrgMods& extra_orgmods, TExtraSubSrcs& extra_subsrcs, const CBioSource& bsrc)
+{
+ if (x_HasTypeStrainComment(bsrc)) {
+ if (extra_orgmods.find(COrgMod::eSubtype_strain) == extra_orgmods.end()) {
+ extra_orgmods.insert(TExtraOrgMod(COrgMod::eSubtype_strain, true));
+ }
+ }
}
@@ -534,132 +672,136 @@ static const SPreferredQual s_PreferredList[] = {
{ COrgMod::eSubtype_cultivar, true },
{ COrgMod::eSubtype_specimen_voucher, true },
{ COrgMod::eSubtype_ecotype, true },
- { COrgMod::eSubtype_type, true},
{ COrgMod::eSubtype_serotype, true},
- { COrgMod::eSubtype_authority, true},
{ COrgMod::eSubtype_breed, true},
- { COrgMod::eSubtype_acronym, true },
- { COrgMod::eSubtype_anamorph, true },
{ COrgMod::eSubtype_bio_material, true },
{ COrgMod::eSubtype_biotype, true },
{ COrgMod::eSubtype_biovar, true },
{ COrgMod::eSubtype_chemovar, true },
- { COrgMod::eSubtype_common, true },
{ COrgMod::eSubtype_culture_collection, true },
- { COrgMod::eSubtype_forma, true },
- { COrgMod::eSubtype_forma_specialis, true },
- { COrgMod::eSubtype_group, true },
- { COrgMod::eSubtype_nat_host, true },
- { COrgMod::eSubtype_other, true },
{ COrgMod::eSubtype_pathovar, true },
{ COrgMod::eSubtype_serogroup, true },
{ COrgMod::eSubtype_serovar, true },
- { COrgMod::eSubtype_subgroup, true },
- { COrgMod::eSubtype_sub_species, true },
{ COrgMod::eSubtype_substrain, true },
- { COrgMod::eSubtype_subtype, true },
- { COrgMod::eSubtype_synonym, true },
- { COrgMod::eSubtype_teleomorph, true },
- { COrgMod::eSubtype_type_material, true },
- { COrgMod::eSubtype_variety, true },
{ CSubSource::eSubtype_plasmid_name, false } ,
{ CSubSource::eSubtype_endogenous_virus_name, false } ,
{ CSubSource::eSubtype_clone, false } ,
{ CSubSource::eSubtype_haplotype, false } ,
- { CSubSource::eSubtype_altitude, false },
{ CSubSource::eSubtype_cell_line, false } ,
- { CSubSource::eSubtype_cell_type, false } ,
{ CSubSource::eSubtype_chromosome, false } ,
- { CSubSource::eSubtype_clone_lib, false } ,
- { CSubSource::eSubtype_collected_by, false } ,
- { CSubSource::eSubtype_collection_date, false } ,
{ CSubSource::eSubtype_country, false } ,
{ CSubSource::eSubtype_dev_stage, false } ,
- { CSubSource::eSubtype_environmental_sample, false } ,
- { CSubSource::eSubtype_frequency, false } ,
{ CSubSource::eSubtype_genotype, false } ,
- { CSubSource::eSubtype_germline, false } ,
{ CSubSource::eSubtype_haplogroup, false } ,
- { CSubSource::eSubtype_identified_by, false } ,
- { CSubSource::eSubtype_isolation_source, false } ,
- { CSubSource::eSubtype_lab_host, false } ,
- { CSubSource::eSubtype_lat_lon, false } ,
{ CSubSource::eSubtype_linkage_group, false } ,
{ CSubSource::eSubtype_map, false } ,
- { CSubSource::eSubtype_mating_type, false } ,
- { CSubSource::eSubtype_metagenomic, false } ,
- { CSubSource::eSubtype_other, false } ,
- { CSubSource::eSubtype_plastid_name, false } ,
{ CSubSource::eSubtype_pop_variant, false } ,
- { CSubSource::eSubtype_rearranged, false } ,
{ CSubSource::eSubtype_segment, false } ,
- { CSubSource::eSubtype_sex, false } ,
{ CSubSource::eSubtype_subclone, false } ,
- { CSubSource::eSubtype_tissue_lib, false } ,
- { CSubSource::eSubtype_tissue_type, false } ,
};
static const size_t kNumPreferred = sizeof(s_PreferredList) / sizeof (SPreferredQual);
+bool CAutoDefModifierCombo::IsModifierRequiredByDefault(bool is_orgmod, int subtype)
+{
+ bool rval = false;
+ if (is_orgmod) {
+ rval = false;
+ } else {
+ if (subtype == CSubSource::eSubtype_endogenous_virus_name ||
+ subtype == CSubSource::eSubtype_plasmid_name ||
+ subtype == CSubSource::eSubtype_transgenic) {
+ rval = true;
+ } else {
+ rval = false;
+ }
+ }
+ return rval;
+}
+
+
string CAutoDefModifierCombo::GetSourceDescriptionString (const CBioSource& bsrc)
{
unsigned int k;
string source_description = "";
- unsigned int mods_used = 0;
+ map<COrgMod::ESubtype, bool> orgmods;
+ map<CSubSource::ESubtype, bool> subsrcs;
+ bool no_extras = false;
/* start with tax name */
source_description += bsrc.GetOrg().GetTaxname();
x_CleanUpTaxName(source_description);
+ x_AddRequiredSubSourceModifiers(orgmods, subsrcs, bsrc);
+
+ x_AddHIVModifiers(orgmods, subsrcs, bsrc);
+ x_AddTypeStrainModifiers(orgmods, subsrcs, bsrc);
+
/* should this organism be excluded? */
if (m_ExcludeSpOrgs) {
string::size_type pos = NStr::Find(source_description, " sp. ");
if (pos != NCBI_NS_STD::string::npos
&& (pos < 2 || !NStr::StartsWith(source_description.substr(pos - 2), "f."))) {
- return source_description;
+ no_extras = true;
+ // but add plasmid name anyway
+ if (subsrcs.find(CSubSource::eSubtype_plasmid_name) == subsrcs.end()) {
+ subsrcs.insert(TExtraSubSrc(CSubSource::eSubtype_plasmid_name, true));
+ }
}
}
if (m_ExcludeCfOrgs) {
string::size_type pos = NStr::Find(source_description, " cf. ");
if (pos != NCBI_NS_STD::string::npos) {
- return source_description;
+ no_extras = true;
}
}
if (m_ExcludeNrOrgs) {
string::size_type pos = NStr::Find(source_description, " nr. ");
if (pos != NCBI_NS_STD::string::npos) {
- return source_description;
+ no_extras = true;
}
}
if (m_ExcludeAffOrgs) {
string::size_type pos = NStr::Find(source_description, " aff. ");
if (pos != NCBI_NS_STD::string::npos) {
- return source_description;
+ no_extras = true;
}
}
- mods_used += x_AddRequiredSubSourceModifiers(source_description, bsrc);
- mods_used += x_AddHIVModifiers (source_description, bsrc);
+ if (!no_extras) {
+ if (bsrc.CanGetOrigin() && bsrc.GetOrigin() == CBioSource::eOrigin_mut) {
+ source_description = "Mutant " + source_description;
+ }
- if (bsrc.CanGetOrigin() && bsrc.GetOrigin() == CBioSource::eOrigin_mut) {
- source_description = "Mutant " + source_description;
+ // add requested orgmods
+ for (unsigned int k = 0; k < m_OrgMods.size(); k++) {
+ if (orgmods.find(m_OrgMods[k]) == orgmods.end()) {
+ orgmods.insert(TExtraOrgMod(m_OrgMods[k], true));
+ }
+ }
+
+ // add requested subsources
+ for (unsigned int k = 0; k < m_SubSources.size(); k++) {
+ if (subsrcs.find(m_SubSources[k]) == subsrcs.end()) {
+ subsrcs.insert(TExtraSubSrc(m_SubSources[k], true));
+ }
+ }
}
+
for (k = 0; k < kNumPreferred; k++) {
if (s_PreferredList[k].is_orgmod) {
- if (HasOrgMod((COrgMod::ESubtype)s_PreferredList[k].subtype) &&
- x_AddOrgModString (source_description, bsrc, (COrgMod::ESubtype)s_PreferredList[k].subtype)) {
- mods_used++;
+ if (orgmods.find((COrgMod::ESubtype)s_PreferredList[k].subtype) != orgmods.end()) {
+ x_AddOrgModString(source_description, bsrc, (COrgMod::ESubtype)s_PreferredList[k].subtype);
}
} else {
- if (HasSubSource((CSubSource::ESubtype)s_PreferredList[k].subtype) &&
- x_AddSubsourceString(source_description, bsrc, (CSubSource::ESubtype)s_PreferredList[k].subtype)) {
- mods_used++;
+ if (subsrcs.find((CSubSource::ESubtype)s_PreferredList[k].subtype) != subsrcs.end()) {
+ x_AddSubsourceString(source_description, bsrc, (CSubSource::ESubtype)s_PreferredList[k].subtype);
}
}
}
diff --git a/c++/src/objtools/edit/autodef_options.cpp b/c++/src/objtools/edit/autodef_options.cpp
new file mode 100644
index 0000000..8de2f63
--- /dev/null
+++ b/c++/src/objtools/edit/autodef_options.cpp
@@ -0,0 +1,439 @@
+/* $Id: autodef_options.cpp 483235 2015-10-29 14:22:28Z ivanov $
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's official duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author: Colleen Bollin
+*
+* File Description:
+* Generate unique definition lines for a set of sequences using organism
+* descriptions and feature clauses.
+*/
+
+#include <ncbi_pch.hpp>
+#include <objtools/edit/autodef_options.hpp>
+#include <corelib/ncbimisc.hpp>
+
+#include <objects/seqfeat/BioSource.hpp>
+
+
+BEGIN_NCBI_SCOPE
+BEGIN_SCOPE(objects)
+
+
+CAutoDefOptions::CAutoDefOptions()
+{
+ x_Reset();
+}
+
+
+CRef<CUser_object> CAutoDefOptions::MakeUserObject() const
+{
+ CRef<CUser_object> user(new CUser_object());
+
+ user->SetObjectType(CUser_object::eObjectType_AutodefOptions);
+ user->SetClass("1.0");
+
+ for (unsigned int i = 0; i < eOptionFieldMax; i++) {
+ if (x_IsBoolean(i) && m_BooleanFlags[i]) {
+ CRef<CUser_field> field = x_MakeBooleanField(i);
+ user->SetData().push_back(field);
+ }
+ }
+
+ user->SetData().push_back(x_MakeMaxMods());
+ user->SetData().push_back(x_MakeFeatureListType());
+ user->SetData().push_back(x_MakeMiscFeatRule());
+ user->SetData().push_back(x_MakeHIVRule());
+ if (!GetSpecifyNuclearProduct()) {
+ user->SetData().push_back(x_MakeProductFlag());
+ }
+ x_MakeSuppressedFeatures(*user);
+ x_MakeModifierList(*user);
+
+ return user;
+}
+
+
+#define INITENUMFIELD(Fieldname) \
+ } else if (field_type == eOptionFieldType_##Fieldname) { \
+ if ((*it)->IsSetData() && (*it)->GetData().IsStr()) { \
+ m_##Fieldname = Get##Fieldname((*it)->GetData().GetStr()); \
+ }
+
+
+void CAutoDefOptions::InitFromUserObject(const CUser_object& obj)
+{
+ x_Reset();
+
+ ITERATE(CUser_object::TData, it, obj.GetData()) {
+ if ((*it)->IsSetLabel() && (*it)->GetLabel().IsStr()) {}
+ TFieldType field_type = GetFieldType((*it)->GetLabel().GetStr());
+ if (field_type != eOptionFieldType_Unknown) {
+ if (x_IsBoolean(field_type)) {
+ if ((*it)->IsSetData() && (*it)->GetData().IsBool() && (*it)->GetData().GetBool()) {
+ m_BooleanFlags[field_type] = true;
+ }
+ } else if (field_type == eOptionFieldType_ProductFlag) {
+ if ((*it)->IsSetData() && (*it)->GetData().IsStr()) {
+ m_ProductFlag = GetProductFlag((*it)->GetData().GetStr());
+ m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = false;
+ }
+ INITENUMFIELD(FeatureListType)
+ INITENUMFIELD(MiscFeatRule)
+ INITENUMFIELD(HIVRule)
+ }
+ else if (field_type == eOptionFieldType_SuppressedFeatures) {
+ x_SetSuppressedFeatures(**it);
+ } else if (field_type == eOptionFieldType_MaxMods) {
+ if ((*it)->IsSetData() && (*it)->GetData().IsInt()) {
+ m_MaxMods = (*it)->GetData().GetInt();
+ }
+ } else if (field_type == eOptionFieldType_ModifierList) {
+ x_SetModifierList(**it);
+ }
+ }
+ }
+}
+
+
+void CAutoDefOptions::x_Reset()
+{
+ m_FeatureListType = eListAllFeatures;
+ m_MiscFeatRule = eNoncodingProductFeat;
+ m_ProductFlag = CBioSource::eGenome_unknown;
+ m_HIVRule = eWantBoth;
+ m_MaxMods = -99;
+
+ ClearSuppressedFeatures();
+ ClearModifierList();
+
+ for (unsigned int i = 0; i < eOptionFieldMax; i++) {
+ m_BooleanFlags[i] = false;
+ }
+ m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = true;
+}
+
+
+typedef SStaticPair<const char *, unsigned int> TNameValPair;
+const TNameValPair sc_FieldTypes[] = {
+ { "AllowModAtEndOfTaxname", CAutoDefOptions::eOptionFieldType_AllowModAtEndOfTaxname },
+ { "AltSpliceFlag", CAutoDefOptions::eOptionFieldType_AltSpliceFlag },
+ { "DoNotApplyToAff", CAutoDefOptions::eOptionFieldType_DoNotApplyToAff },
+ { "DoNotApplyToCf", CAutoDefOptions::eOptionFieldType_DoNotApplyToCf },
+ { "DoNotApplyToNr", CAutoDefOptions::eOptionFieldType_DoNotApplyToNr },
+ { "DoNotApplyToSp", CAutoDefOptions::eOptionFieldType_DoNotApplyToSp },
+ { "FeatureListType", CAutoDefOptions::eOptionFieldType_FeatureListType },
+ { "GeneClusterOppStrand", CAutoDefOptions::eOptionFieldType_GeneClusterOppStrand },
+ { "HIVRule", CAutoDefOptions::eOptionFieldType_HIVRule },
+ { "IncludeCountryText", CAutoDefOptions::eOptionFieldType_IncludeCountryText },
+ { "Keep3UTRs", CAutoDefOptions::eOptionFieldType_Keep3UTRs },
+ { "Keep5UTRs", CAutoDefOptions::eOptionFieldType_Keep5UTRs },
+ { "KeepAfterSemicolon", CAutoDefOptions::eOptionFieldType_KeepAfterSemicolon },
+ { "KeepExons", CAutoDefOptions::eOptionFieldType_KeepExons },
+ { "KeepIntrons", CAutoDefOptions::eOptionFieldType_KeepIntrons },
+ { "KeepLTRs", CAutoDefOptions::eOptionFieldType_KeepLTRs },
+ { "KeepMobileElements", CAutoDefOptions::eOptionFieldType_KeepMobileElements },
+ { "KeepPrecursorRNA", CAutoDefOptions::eOptionFieldType_KeepPrecursorRNA },
+ { "KeepPromoters", CAutoDefOptions::eOptionFieldType_KeepPromoters },
+ { "KeepRepeatRegion", CAutoDefOptions::eOptionFieldType_KeepRepeatRegion },
+ { "KeepuORFs", CAutoDefOptions::eOptionFieldType_KeepuORFs },
+ { "LeaveParenthetical", CAutoDefOptions::eOptionFieldType_LeaveParenthetical },
+ { "MaxMods", CAutoDefOptions::eOptionFieldType_MaxMods },
+ { "MiscFeatRule", CAutoDefOptions::eOptionFieldType_MiscFeatRule },
+ { "ModifierList", CAutoDefOptions::eOptionFieldType_ModifierList },
+ { "ProductFlag", CAutoDefOptions::eOptionFieldType_ProductFlag },
+ { "SpecifyNuclearProduct", CAutoDefOptions::eOptionFieldType_SpecifyNuclearProduct },
+ { "SuppressAlleles", CAutoDefOptions::eOptionFieldType_SuppressAlleles },
+ { "SuppressedFeatures", CAutoDefOptions::eOptionFieldType_SuppressedFeatures },
+ { "SuppressFeatureAltSplice", CAutoDefOptions::eOptionFieldType_SuppressFeatureAltSplice },
+ { "SuppressLocusTags", CAutoDefOptions::eOptionFieldType_SuppressLocusTags },
+ { "SuppressMobileElementSubfeatures", CAutoDefOptions::eOptionFieldType_SuppressMobileElementSubfeatures },
+ { "UseFakePromoters", CAutoDefOptions::eOptionFieldType_UseFakePromoters },
+ { "UseLabels", CAutoDefOptions::eOptionFieldType_UseLabels },
+ { "UseNcRNAComment", CAutoDefOptions::eOptionFieldType_UseNcRNAComment }
+};
+
+typedef CStaticArrayMap<const char *, unsigned int, PNocase> TNameValPairMap;
+DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_FieldTypeStrsMap, sc_FieldTypes);
+
+const TNameValPair sc_FeatureListTypeStr[] = {
+ { "Complete Genome", CAutoDefOptions::eCompleteGenome },
+ { "Complete Sequence", CAutoDefOptions::eCompleteSequence },
+ { "List All Features", CAutoDefOptions::eListAllFeatures },
+ { "Partial Genome", CAutoDefOptions::ePartialGenome },
+ { "Partial Sequence", CAutoDefOptions::ePartialSequence },
+ { "Sequence", CAutoDefOptions::eSequence }
+};
+DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_FeatureListTypeStrsMap, sc_FeatureListTypeStr);
+
+const TNameValPair sc_MiscFeatRuleStr[] = {
+ { "CommentFeat", CAutoDefOptions::eCommentFeat },
+ { "Delete", CAutoDefOptions::eDelete },
+ { "NoncodingProductFeat", CAutoDefOptions::eNoncodingProductFeat }
+};
+DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_MiscFeatRuleStrsMap, sc_MiscFeatRuleStr);
+
+const TNameValPair sc_HIVRuleStr[] = {
+ { "PreferClone", CAutoDefOptions::ePreferClone },
+ { "PreferIsolate", CAutoDefOptions::ePreferIsolate },
+ { "WantBoth", CAutoDefOptions::eWantBoth }
+};
+DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_HIVRuleStrsMap, sc_HIVRuleStr);
+
+
+
+#define AUTODEFGETENUM(Fieldname, Map, Default) \
+string CAutoDefOptions::Get##Fieldname(unsigned int value) const \
+{ \
+ TNameValPairMap::const_iterator it = Map.begin(); \
+ while (it != Map.end()) { \
+ if (value == it->second) { \
+ return it->first; \
+ } \
+ ++it; \
+ } \
+ return kEmptyStr; \
+} \
+CAutoDefOptions::T##Fieldname CAutoDefOptions::Get##Fieldname(const string& value) const \
+{ \
+ TNameValPairMap::const_iterator it = Map.find(value.c_str()); \
+ if (it != Map.end()) { \
+ return it->second; \
+ } \
+ return Default; \
+}
+
+AUTODEFGETENUM(FieldType, sc_FieldTypeStrsMap, eOptionFieldType_Unknown)
+AUTODEFGETENUM(FeatureListType, sc_FeatureListTypeStrsMap, eListAllFeatures)
+AUTODEFGETENUM(MiscFeatRule, sc_MiscFeatRuleStrsMap, eNoncodingProductFeat);
+AUTODEFGETENUM(HIVRule, sc_HIVRuleStrsMap, eWantBoth);
+
+string CAutoDefOptions::GetProductFlag(CBioSource::TGenome value) const
+{
+ return CBioSource::GetOrganelleByGenome(value);
+}
+
+
+CBioSource::TGenome CAutoDefOptions::GetProductFlag(const string& value) const
+{
+ return CBioSource::GetGenomeByOrganelle(value);
+}
+
+
+bool CAutoDefOptions::x_IsBoolean(TFieldType field_type) const
+{
+ bool rval = true;
+ switch (field_type)
+ {
+ case eOptionFieldType_HIVRule:
+ case eOptionFieldType_FeatureListType:
+ case eOptionFieldType_MiscFeatRule:
+ case eOptionFieldType_ProductFlag:
+ case eOptionFieldType_SuppressedFeatures:
+ case eOptionFieldType_ModifierList:
+ case eOptionFieldType_MaxMods:
+ rval = false;
+ break;
+ default:
+ rval = true;
+ break;
+ }
+ return rval;
+}
+
+
+CRef<CUser_field> CAutoDefOptions::x_MakeBooleanField(TFieldType field_type) const
+{
+ CRef<CUser_field> field(new CUser_field());
+ field->SetLabel().SetStr(GetFieldType(field_type));
+ field->SetData().SetBool(true);
+ return field;
+}
+
+
+void CAutoDefOptions::SuppressAllFeatures()
+{
+ ClearSuppressedFeatures();
+ m_SuppressedFeatureSubtypes.push_back(CSeqFeatData::eSubtype_any);
+}
+
+
+bool CAutoDefOptions::IsFeatureSuppressed(CSeqFeatData::ESubtype subtype) const
+{
+ ITERATE(TSuppressedFeatureSubtypes, it, m_SuppressedFeatureSubtypes) {
+ if (subtype == *it || *it == CSeqFeatData::eSubtype_any) {
+ return true;
+ }
+ }
+ return false;
+}
+
+void CAutoDefOptions::SuppressFeature(CSeqFeatData::ESubtype subtype)
+{
+ m_SuppressedFeatureSubtypes.push_back(subtype);
+}
+
+
+void CAutoDefOptions::ClearSuppressedFeatures()
+{
+ m_SuppressedFeatureSubtypes.clear();
+}
+
+
+void CAutoDefOptions::x_MakeSuppressedFeatures(CUser_object& user) const
+{
+ if (m_SuppressedFeatureSubtypes.empty()) {
+ return;
+ }
+ CRef<CUser_field> field(new CUser_field());
+ field->SetLabel().SetStr(GetFieldType(eOptionFieldType_SuppressedFeatures));
+
+ ITERATE(TSuppressedFeatureSubtypes, it, m_SuppressedFeatureSubtypes) {
+ if (*it == CSeqFeatData::eSubtype_any) {
+ field->SetData().SetStr("All");
+ user.SetData().push_back(field);
+ return;
+ }
+ field->SetData().SetStrs().push_back(CSeqFeatData::SubtypeValueToName(*it));
+ }
+ user.SetData().push_back(field);
+}
+
+
+void CAutoDefOptions::x_SetSuppressedFeatures(const CUser_field& field)
+{
+ ClearSuppressedFeatures();
+
+ if (!field.IsSetData()) {
+ return;
+ }
+ if (field.GetData().IsStr() && NStr::EqualNocase(field.GetData().GetStr(), "All")) {
+ m_SuppressedFeatureSubtypes.push_back(CSeqFeatData::eSubtype_any);
+ return;
+ }
+
+ if (!field.GetData().IsStrs()){
+ return;
+ }
+
+ ITERATE(CUser_field::TData::TStrs, v, field.GetData().GetStrs()) {
+ CSeqFeatData::ESubtype val = CSeqFeatData::SubtypeNameToValue(*v);
+ if (val != CSeqFeatData::eSubtype_bad) {
+ m_SuppressedFeatureSubtypes.push_back(val);
+ }
+ }
+}
+
+
+void CAutoDefOptions::AddSubSource(CSubSource::TSubtype subtype)
+{
+ m_SubSources.push_back(subtype);
+}
+
+
+void CAutoDefOptions::AddOrgMod(COrgMod::TSubtype subtype)
+{
+ m_OrgMods.push_back(subtype);
+}
+
+
+void CAutoDefOptions::ClearModifierList()
+{
+ m_OrgMods.clear();
+ m_SubSources.clear();
+}
+
+
+const string kSubSources = "SubSources";
+const string kOrgMods = "OrgMods";
+
+void CAutoDefOptions::x_MakeModifierList(CUser_object& user) const
+{
+ CRef<CUser_field> field(new CUser_field());
+ field->SetLabel().SetStr(GetFieldType(eOptionFieldType_ModifierList));
+
+ if (!m_SubSources.empty()) {
+ CRef<CUser_field> subsources(new CUser_field());
+ subsources->SetLabel().SetStr(kSubSources);
+ ITERATE(TSubSources, it, m_SubSources) {
+ string val = CSubSource::GetSubtypeName(*it);
+ subsources->SetData().SetStrs().push_back(val);
+ }
+ field->SetData().SetFields().push_back(subsources);
+ }
+
+ if (!m_OrgMods.empty()) {
+ CRef<CUser_field> orgmods(new CUser_field());
+ orgmods->SetLabel().SetStr(kOrgMods);
+ ITERATE(TOrgMods, it, m_OrgMods) {
+ string val = COrgMod::GetSubtypeName(*it);
+ orgmods->SetData().SetStrs().push_back(val);
+ }
+ field->SetData().SetFields().push_back(orgmods);
+ }
+
+ if (field->IsSetData() && field->GetData().IsFields() && field->GetData().GetFields().size() > 0) {
+ user.SetData().push_back(field);
+ }
+}
+
+
+void CAutoDefOptions::x_SetModifierList(const CUser_field& field)
+{
+ ClearModifierList();
+
+ if (!field.IsSetData() || !field.GetData().IsFields()) {
+ return;
+ }
+
+ ITERATE(CUser_field::TData::TFields, it, field.GetData().GetFields()) {
+ if ((*it)->IsSetLabel() && (*it)->GetLabel().IsStr() &&
+ (*it)->IsSetData() && (*it)->GetData().IsStrs()) {
+ if (NStr::EqualNocase((*it)->GetLabel().GetStr(), kSubSources)) {
+ ITERATE(CUser_field::TData::TStrs, s, (*it)->GetData().GetStrs()) {
+ CSubSource::TSubtype subtype = CSubSource::GetSubtypeValue(*s);
+ m_SubSources.push_back(subtype);
+ }
+ } else if (NStr::EqualNocase((*it)->GetLabel().GetStr(), kOrgMods)) {
+ ITERATE(CUser_field::TData::TStrs, s, (*it)->GetData().GetStrs()) {
+ COrgMod::TSubtype subtype = COrgMod::GetSubtypeValue(*s);
+ m_OrgMods.push_back(subtype);
+ }
+ }
+ }
+ }
+}
+
+
+CRef<CUser_field> CAutoDefOptions::x_MakeMaxMods() const
+{
+ CRef<CUser_field> field(new CUser_field());
+ field->SetLabel().SetStr(GetFieldType(eOptionFieldType_MaxMods));
+ field->SetData().SetInt(m_MaxMods);
+ return field;
+}
+
+
+END_SCOPE(objects)
+END_NCBI_SCOPE
diff --git a/c++/src/objtools/edit/capitalization_string.cpp b/c++/src/objtools/edit/capitalization_string.cpp
index 969fcc8..1803153 100644
--- a/c++/src/objtools/edit/capitalization_string.cpp
+++ b/c++/src/objtools/edit/capitalization_string.cpp
@@ -1,4 +1,4 @@
-/* $Id: capitalization_string.cpp 458727 2015-02-09 16:40:15Z ivanov $
+/* $Id: capitalization_string.cpp 458478 2015-02-05 15:31:46Z filippov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/cds_fix.cpp b/c++/src/objtools/edit/cds_fix.cpp
index 60ba420..e3b69b8 100644
--- a/c++/src/objtools/edit/cds_fix.cpp
+++ b/c++/src/objtools/edit/cds_fix.cpp
@@ -1,4 +1,4 @@
-/* $Id: cds_fix.cpp 459885 2015-02-23 16:49:52Z ivanov $
+/* $Id: cds_fix.cpp 480562 2015-10-01 16:51:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -595,28 +595,64 @@ string s_GetmRNAName (const CSeq_feat& mrna)
}
}
+void s_AdjustForUTR_SingleSide(CSeq_loc& mrna_loc, const CSeq_loc &utr_loc, const CSeq_id &id)
+{
+ CRef<CSeq_loc> new_loc(new CSeq_loc);
+ new_loc->Assign(utr_loc);
+ new_loc->SetId(id);
+ CSeq_loc_I loc_it(*new_loc);
+ while(loc_it)
+ {
+ ++loc_it;
+ }
+ size_t pos = loc_it.GetPos();
+ if (pos > 0)
+ loc_it.SetPos(pos-1);
+ int utr_stop = loc_it.GetRange().GetTo();
+ CSeq_loc_CI old_loc_it(mrna_loc, CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional);
+ int cds_start = old_loc_it.GetRange().GetFrom();
+ int cds_stop = old_loc_it.GetRange().GetTo();
+ while (old_loc_it && cds_stop < utr_stop)
+ {
+ ++old_loc_it;
+ if (old_loc_it)
+ {
+ cds_start = old_loc_it.GetRange().GetFrom();
+ cds_stop = old_loc_it.GetRange().GetTo();
+ }
+ }
+
+ if (cds_start - utr_stop <= 2 && cds_stop >= utr_stop)
+ {
+ loc_it.SetTo(cds_stop);
+ if (old_loc_it)
+ ++old_loc_it;
+ }
+ ++loc_it;
+ while (old_loc_it)
+ {
+ loc_it.InsertInterval(id, old_loc_it.GetRange(), old_loc_it.GetStrand());
+ ++old_loc_it;
+ }
+ mrna_loc.Assign(*loc_it.MakeSeq_loc());
+}
void s_AdjustForUTR(const CSeq_feat& utr, int cd_start, int cd_stop, CSeq_loc& mrna_loc, bool& found5, bool& found3, CScope& scope)
{
- int utr_start = utr.GetLocation().GetStart(eExtreme_Positional);
- int utr_stop = utr.GetLocation().GetStop(eExtreme_Positional);
if ( utr.GetData().GetSubtype() == CSeqFeatData::eSubtype_5UTR )
{
found5 = true;
- if (abs(utr_stop - cd_start) <= 2)
- {
- mrna_loc.Assign(*SeqLocExtend(mrna_loc, utr_start, &scope));
- mrna_loc.SetPartialStart( utr.GetLocation().IsPartialStart(eExtreme_Positional), eExtreme_Positional );
- }
+ s_AdjustForUTR_SingleSide(mrna_loc, utr.GetLocation(), *mrna_loc.GetId());
+ mrna_loc.SetPartialStart( utr.GetLocation().IsPartialStart(eExtreme_Positional), eExtreme_Positional );
}
else if ( utr.GetData().GetSubtype() == CSeqFeatData::eSubtype_3UTR )
{
found3 = true;
- if ( abs(utr_start - cd_stop) <= 2)
- {
- mrna_loc.Assign(*SeqLocExtend(mrna_loc, utr_stop, &scope));
- mrna_loc.SetPartialStop( utr.GetLocation().IsPartialStop(eExtreme_Positional), eExtreme_Positional );
- }
+ CRef<CSeq_loc> new_loc(new CSeq_loc);
+ new_loc->Assign(utr.GetLocation());
+ s_AdjustForUTR_SingleSide(*new_loc, mrna_loc, *mrna_loc.GetId());
+ mrna_loc.Assign(*new_loc);
+ mrna_loc.SetPartialStop( utr.GetLocation().IsPartialStop(eExtreme_Positional), eExtreme_Positional );
}
}
@@ -1044,71 +1080,6 @@ void AdjustCDSFrameForStartChange(CCdregion& cds, int change)
}
-bool PromoteCDSToNucProtSet(objects::CSeq_feat_Handle& orig_feat)
-{
- // only move coding regions to nuc-prot set, and only do this if they
- // have a product that is "local"
- if (!orig_feat.IsSetData() || !orig_feat.GetData().IsCdregion()
- || !orig_feat.IsSetProduct()) {
- return false;
- }
- CBioseq_Handle nuc_bsh = orig_feat.GetScope().GetBioseqHandle(orig_feat.GetLocation());
- if (!nuc_bsh) {
- return false;
- }
- CBioseq_Handle p_bsh = orig_feat.GetScope().GetBioseqHandleFromTSE(*(orig_feat.GetProduct().GetId()), nuc_bsh);
- if (!p_bsh) {
- return false;
- }
-
- // This is necessary, to make sure that we are in "editing mode"
- const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot();
- CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle();
-
- CSeq_feat_EditHandle feh(orig_feat);
- CSeq_entry_Handle parent_entry = feh.GetAnnot().GetParentEntry();
-
- bool rval = false;
-
- if (parent_entry.IsSet()
- && parent_entry.GetSet().IsSetClass()
- && parent_entry.GetSet().GetClass() == CBioseq_set::eClass_nuc_prot) {
- // already on nuc-prot set, leave it alone
- } else {
- CBioseq_set_Handle nuc_parent = parent_entry.GetParentBioseq_set();
- if (nuc_parent && nuc_parent.IsSetClass() && nuc_parent.GetClass() == CBioseq_set::eClass_nuc_prot) {
- CSeq_annot_Handle ftable;
- CSeq_entry_Handle parent_seh = nuc_parent.GetParentEntry();
- CSeq_annot_CI annot_ci(parent_seh, CSeq_annot_CI::eSearch_entry);
- for (; annot_ci; ++annot_ci) {
- if ((*annot_ci).IsFtable()) {
- ftable = *annot_ci;
- break;
- }
- }
-
- if (!ftable) {
- CRef<CSeq_annot> new_annot(new CSeq_annot());
- new_annot->SetData().SetFtable();
- CSeq_entry_EditHandle eh = parent_seh.GetEditHandle();
- ftable = eh.AttachAnnot(*new_annot);
- }
-
- CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle();
- CSeq_annot_EditHandle new_annot = ftable.GetEditHandle();
- orig_feat = new_annot.TakeFeat(feh);
- const list< CRef< CSeq_feat > > &feat_list = old_annot.GetSeq_annotCore()->GetData().GetFtable();
- if (feat_list.empty())
- {
- old_annot.Remove();
- }
- rval = true;
- }
- }
- return rval;
-}
-
-
bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat)
{
CSeq_feat_EditHandle feh(orig_feat);
diff --git a/c++/src/objtools/edit/dblink_field.cpp b/c++/src/objtools/edit/dblink_field.cpp
index 66b6d9c..ca4c36f 100644
--- a/c++/src/objtools/edit/dblink_field.cpp
+++ b/c++/src/objtools/edit/dblink_field.cpp
@@ -1,4 +1,4 @@
-/* $Id: dblink_field.cpp 465911 2015-04-27 16:16:16Z ivanov $
+/* $Id: dblink_field.cpp 465633 2015-04-23 12:24:56Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/feattable_edit.cpp b/c++/src/objtools/edit/feattable_edit.cpp
index b91f06f..1ba2ce6 100644
--- a/c++/src/objtools/edit/feattable_edit.cpp
+++ b/c++/src/objtools/edit/feattable_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: feattable_edit.cpp 464927 2015-04-15 15:02:18Z ivanov $
+/* $Id: feattable_edit.cpp 478464 2015-09-09 15:29:44Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,7 @@
#include <objmgr/scope.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/sequence.hpp>
+#include <objmgr/util/feature.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/edit/loc_edit.hpp>
@@ -49,24 +50,38 @@ BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
BEGIN_SCOPE(edit)
+// ----------------------------------------------------------------------------
+CRef<CSeq_loc> sProductFromString(
+const string str)
+// ----------------------------------------------------------------------------
+{
+ CRef<CSeq_loc> pProduct(new CSeq_loc(CSeq_loc::e_Whole));
+ CRef<CSeq_id> pId(new CSeq_id(CSeq_id::e_Local, str));
+ pProduct->SetId(*pId);
+ return pProduct;
+}
+
// -------------------------------------------------------------------------
CFeatTableEdit::CFeatTableEdit(
CSeq_annot& annot,
- const string& locusTagPrefix,
- IMessageListener* pMessageListener):
-// -------------------------------------------------------------------------
+ const string& locusTagPrefix,
+ unsigned int locusTagNumber,
+ ILineErrorListener* pMessageListener) :
+ // -------------------------------------------------------------------------
mAnnot(annot),
mpMessageListener(pMessageListener),
mNextFeatId(1),
- mLocusTagNumber(1),
- mLocusTagPrefix(locusTagPrefix)
+ mLocusTagNumber(locusTagNumber),
+ mLocusTagPrefix(locusTagPrefix)
{
mpScope.Reset(new CScope(*CObjectManager::GetInstance()));
mpScope->AddDefaults();
mHandle = mpScope->AddSeq_annot(mAnnot);
mEditHandle = mpScope->GetEditHandle(mHandle);
+ mTree = feature::CFeatTree(mHandle);
};
+
// -------------------------------------------------------------------------
CFeatTableEdit::~CFeatTableEdit()
// -------------------------------------------------------------------------
@@ -108,16 +123,30 @@ void CFeatTableEdit::InferParentGenes()
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_mRNA);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
- const CSeq_feat& rna = it->GetOriginalFeature();
+ CMappedFeat rna = *it;
CRef<CSeq_feat> pGene = xMakeGeneForMrna(rna);
if (!pGene) {
+ if (!rna.IsSetPartial() || !rna.GetPartial()) {
+ continue;
+ }
+ CMappedFeat parentGene = feature::GetBestGeneForMrna(rna);
+ if (parentGene &&
+ !(parentGene.IsSetPartial() && parentGene.GetPartial())) {
+ CRef<CSeq_feat> pEditedGene(new CSeq_feat);
+ pEditedGene->Assign(parentGene.GetOriginalFeature());
+ pEditedGene->SetPartial(true);
+ CSeq_feat_EditHandle geneEh(
+ mpScope->GetObjectHandle(parentGene.GetOriginalFeature()));
+ geneEh.Replace(*pEditedGene);
+ }
continue;
}
//find proper name for gene
string geneId(xNextFeatId());
pGene->SetId().SetLocal().SetStr(geneId);
//add gene xref to rna
- CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(rna));
+ CSeq_feat_EditHandle feh(
+ mpScope->GetObjectHandle(rna.GetOriginalFeature()));
feh.AddFeatXref(geneId);
//add new gene to feature table
mEditHandle.AddFeat(*pGene);
@@ -128,6 +157,7 @@ void CFeatTableEdit::InferParentGenes()
void CFeatTableEdit::InferPartials()
// ----------------------------------------------------------------------------
{
+ bool infered(false);
edit::CLocationEditPolicy editPolicy(
edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,
edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,
@@ -142,13 +172,64 @@ void CFeatTableEdit::InferPartials()
const CSeq_feat& cds = it->GetOriginalFeature();
CRef<CSeq_feat> pEditedCds(new CSeq_feat);
pEditedCds->Assign(cds);
- editPolicy.ApplyPolicyToFeature(*pEditedCds, *mpScope);
- CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(cds));
- feh.Replace(*pEditedCds);
+ infered = editPolicy.ApplyPolicyToFeature(*pEditedCds, *mpScope);
+ if (!infered) {
+ continue;
+ }
+ CSeq_feat_EditHandle cdsEh(mpScope->GetObjectHandle(cds));
+ cdsEh.Replace(*pEditedCds);
+
+ // make sure the parent rna is partial as well
+ CMappedFeat parentRna = feature::GetBestMrnaForCds(*it, &mTree);
+ if (parentRna &&
+ !(parentRna.IsSetPartial() && parentRna.GetPartial())) {
+ CRef<CSeq_feat> pEditedRna(new CSeq_feat);
+ pEditedRna->Assign(parentRna.GetOriginalFeature());
+ pEditedRna->SetPartial(true);
+ CSeq_feat_EditHandle rnaEh(
+ mpScope->GetObjectHandle(parentRna.GetOriginalFeature()));
+ rnaEh.Replace(*pEditedRna);
+ }
+
+ // make sure the gene parent is partial as well
+ CMappedFeat parentGene = feature::GetBestGeneForCds(*it);
+ if (parentGene &&
+ !(parentGene.IsSetPartial() && parentGene.GetPartial())) {
+ CRef<CSeq_feat> pEditedGene(new CSeq_feat);
+ pEditedGene->Assign(parentGene.GetOriginalFeature());
+ pEditedGene->SetPartial(true);
+ CSeq_feat_EditHandle geneEh(
+ mpScope->GetObjectHandle(parentGene.GetOriginalFeature()));
+ geneEh.Replace(*pEditedGene);
+ }
}
}
// ----------------------------------------------------------------------------
+void CFeatTableEdit::SubmitFixProducts()
+// ----------------------------------------------------------------------------
+{
+ SAnnotSelector sel;
+ //sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_mRNA);
+ sel.IncludeFeatType(CSeqFeatData::e_Rna);
+ sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
+ for (CFeat_CI it(mHandle, sel); it; ++it){
+ CMappedFeat mf = *it;
+ //debug CSeqFeatData::ESubtype st = mf.GetFeatSubtype();
+ string product = mf.GetNamedQual("Product");
+ CRef<CSeq_feat> pEditedFeature(new CSeq_feat);
+ pEditedFeature->Assign(mf.GetOriginalFeature());
+ pEditedFeature->ResetProduct();
+ if (!product.empty()) {
+ pEditedFeature->AddQualifier("product", product);
+ pEditedFeature->RemoveQualifier("Product");
+ }
+ CSeq_feat_EditHandle feh(mf);
+ feh.Replace(*pEditedFeature);
+ }
+}
+
+// ----------------------------------------------------------------------------
void CFeatTableEdit::EliminateBadQualifiers()
// ----------------------------------------------------------------------------
{
@@ -156,6 +237,7 @@ void CFeatTableEdit::EliminateBadQualifiers()
CFeat_CI it(mHandle);
for ( ; it; ++it) {
+ CSeqFeatData::ESubtype subtype = it->GetData().GetSubtype();
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
(it)->GetOriginalFeature()));
const QUALS& quals = (*it).GetQual();
@@ -163,14 +245,20 @@ void CFeatTableEdit::EliminateBadQualifiers()
for (QUALS::const_iterator qual = quals.begin(); qual != quals.end();
++qual) {
string qualVal = (*qual)->GetQual();
- if (qualVal == "orig_transcript_id") {
+ if (qualVal == "transcript_id") {
continue;
}
- if (qualVal == "orig_protein_id") {
+ if (qualVal == "protein_id") {
+ continue;
+ }
+ if (qualVal == "Protein") {
+ continue;
+ }
+ if (qualVal == "protein") {
continue;
}
CSeqFeatData::EQualifier qualType = CSeqFeatData::GetQualifierType(qualVal);
- if (qualType == CSeqFeatData::eQual_bad) {
+ if (!CSeqFeatData::IsLegalQualifier(subtype, qualType)) {
badQuals.push_back(qualVal);
}
}
@@ -185,67 +273,90 @@ void CFeatTableEdit::EliminateBadQualifiers()
void CFeatTableEdit::GenerateProteinAndTranscriptIds()
// ----------------------------------------------------------------------------
{
- // that's for cds's.
- // scheme hinges on us generating locus tags, so if don't do that we should
- // not generate protein_ids and transcript_ids either.
- if (mLocusTagPrefix.empty()) {
- return;
- }
-
SAnnotSelector sel;
+ sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_mRNA);
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
- CFeat_CI it(mHandle, sel);
- for ( ; it; ++it) {
- const CSeq_feat& cds = it->GetOriginalFeature();
- string proteinId = xNextProteinId(cds);
- string transcriptId = xCurrentTranscriptId(cds);
- if (proteinId.empty()) {
- continue;
- }
- CRef<CSeq_feat> pEditedCds(new CSeq_feat);
- pEditedCds->Assign(cds);
- CRef<CGb_qual> pProteinId(new CGb_qual);
- pProteinId->SetQual("protein_id");
- pProteinId->SetVal(proteinId);
- pEditedCds->SetQual().push_back(pProteinId);
- CRef<CGb_qual> pTranscriptId(new CGb_qual);
- pTranscriptId->SetQual("transcript_id");
- pTranscriptId->SetVal(transcriptId);
- pEditedCds->SetQual().push_back(pTranscriptId);
- CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(cds));
- feh.Replace(*pEditedCds);
- }
+ for (CFeat_CI it(mHandle, sel); it; ++it){
+ CMappedFeat mf = *it;
+ xFeatureAddProteinId(mf);
+ xFeatureAddTranscriptId(mf);
+ }
}
// ----------------------------------------------------------------------------
-void CFeatTableEdit::GenerateOrigProteinAndOrigTranscriptIds()
+void CFeatTableEdit::xFeatureAddProteinId(
+ CMappedFeat mf)
// ----------------------------------------------------------------------------
{
- // that's for cds's.
- SAnnotSelector sel;
- sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
- CFeat_CI it(mHandle, sel);
- for ( ; it; ++it) {
- const CSeq_feat& cds = it->GetOriginalFeature();
- string proteinId = cds.GetNamedQual("protein_id");
- string transcriptId = cds.GetNamedQual("transcript_id");
- CConstRef<CSeq_feat> pParentRna = xGetMrnaParent(cds);
- if (!pParentRna) {
- continue;
- }
- CRef<CSeq_feat> pEditedRna(new CSeq_feat);
- pEditedRna->Assign(*pParentRna);
- CRef<CGb_qual> pOrigProteinId(new CGb_qual);
- pOrigProteinId->SetQual("orig_protein_id");
- pOrigProteinId->SetVal(proteinId);
- pEditedRna->SetQual().push_back(pOrigProteinId);
- CRef<CGb_qual> pOrigTranscriptId(new CGb_qual);
- pOrigTranscriptId->SetQual("orig_transcript_id");
- pOrigTranscriptId->SetVal(transcriptId);
- pEditedRna->SetQual().push_back(pOrigTranscriptId);
- CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(*pParentRna));
- feh.Replace(*pEditedRna);
- }
+ //mss-375:
+ // make sure we got a protein_id qualifier:
+ // if we already got one from the GFF then keep it
+ // otherwise if the parent/child got one then use that
+ // otherwise generate one based on the gene locustag
+
+ string protein_id = mf.GetNamedQual("protein_id");
+ if (!protein_id.empty()) {
+ return;
+ }
+ CMappedFeat associateFeat;
+
+ CSeqFeatData::ESubtype s = mf.GetFeatSubtype();
+ switch (mf.GetFeatSubtype()) {
+ default:
+ // we do this only for select feature types
+ return;
+ case CSeqFeatData::eSubtype_mRNA:
+ associateFeat = feature::GetBestCdsForMrna(mf, &mTree);
+ break;
+ case CSeqFeatData::eSubtype_cdregion:
+ associateFeat = feature::GetBestMrnaForCds(mf, &mTree);
+ break;
+ }
+ if (associateFeat) {
+ protein_id = associateFeat.GetNamedQual("protein_id");
+ }
+ if (protein_id.empty()) {
+ protein_id = xNextProteinId(mf);
+ }
+ xFeatureAddQualifier(mf, "protein_id", protein_id);
+}
+
+// ----------------------------------------------------------------------------
+void CFeatTableEdit::xFeatureAddTranscriptId(
+ CMappedFeat mf)
+ // ----------------------------------------------------------------------------
+{
+ //mss-375:
+ // make sure we got a transcript_id qualifier:
+ // if we already got one from the GFF then keep it
+ // otherwise if the parent/child got one then use that
+ // otherwise generate one based on the gene locustag
+
+ string transcript_id = mf.GetNamedQual("transcript_id");
+ if (!transcript_id.empty()) {
+ return;
+ }
+ CMappedFeat associateFeat;
+
+ CSeqFeatData::ESubtype s = mf.GetFeatSubtype();
+ switch (mf.GetFeatSubtype()) {
+ default:
+ // we do this only for select feature types
+ return;
+ case CSeqFeatData::eSubtype_mRNA:
+ associateFeat = feature::GetBestCdsForMrna(mf, &mTree);
+ break;
+ case CSeqFeatData::eSubtype_cdregion:
+ associateFeat = feature::GetBestMrnaForCds(mf, &mTree);
+ break;
+ }
+ if (associateFeat) {
+ transcript_id = associateFeat.GetNamedQual("transcript_id");
+ }
+ if (transcript_id.empty()) {
+ transcript_id = xNextTranscriptId(mf);
+ }
+ xFeatureAddQualifier(mf, "transcript_id", transcript_id);
}
// ----------------------------------------------------------------------------
@@ -292,20 +403,20 @@ void CFeatTableEdit::xGenerateLocusIdsRegenerate()
const CSeq_feat& f = mf.GetOriginalFeature();
CSeq_feat_EditHandle feh(mf);
- feh.RemoveQualifier("locus_tag");
- feh.RemoveQualifier("protein_id");
+ //feh.RemoveQualifier("locus_tag");
+ //feh.RemoveQualifier("protein_id");
feh.RemoveQualifier("orig_protein_id");
- feh.RemoveQualifier("transcript_id");
+ //feh.RemoveQualifier("transcript_id");
feh.RemoveQualifier("orig_transcript_id");
CSeqFeatData::ESubtype subtype = mf.GetFeatSubtype();
switch (subtype) {
case CSeqFeatData::eSubtype_mRNA: {
- string proteinId = xNextProteinId(f);
- feh.AddQualifier("protein_id", proteinId);
+ string proteinId = xNextProteinId(mf);
+ //feh.AddQualifier("protein_id", proteinId);
feh.AddQualifier("orig_protein_id", proteinId);
- string transcriptId = xNextTranscriptId(f);
- feh.AddQualifier("transcript_id", transcriptId);
+ string transcriptId = xNextTranscriptId(mf);
+ //feh.AddQualifier("transcript_id", transcriptId);
feh.AddQualifier("orig_transcript_id", transcriptId);
break;
}
@@ -322,11 +433,12 @@ void CFeatTableEdit::xGenerateLocusIdsRegenerate()
for (CFeat_CI it(mHandle, selCds); it; ++it) {
CMappedFeat mf = *it;
- const CSeq_feat& f = mf.GetOriginalFeature();
CSeq_feat_EditHandle feh(mf);
- string transcriptId = xCurrentTranscriptId(f);
- feh.AddQualifier("transcript_id", transcriptId);
+ CMappedFeat rna = feature::GetBestMrnaForCds(mf);
+ string transcriptId = rna.GetNamedQual("transcript_id");
feh.AddQualifier("orig_transcript_id", transcriptId);
+ string proteinId = rna.GetNamedQual("protein_id");
+ feh.AddQualifier("orig_protein_id", proteinId);
}
}
@@ -391,9 +503,12 @@ void CFeatTableEdit::GenerateLocusTags()
CFeat_CI itGenes(mHandle, selGenes);
for ( ; itGenes; ++itGenes) {
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
- (itGenes)->GetOriginalFeature()));
- feh.RemoveQualifier("locus_tag");
- feh.AddQualifier("locus_tag", xNextLocusTag());
+ itGenes->GetOriginalFeature()));
+ CRef<CSeq_feat> pEditedFeat(new CSeq_feat);
+ pEditedFeat->Assign(itGenes->GetOriginalFeature());
+ pEditedFeat->RemoveQualifier("locus_tag");
+ pEditedFeat->SetData().SetGene().SetLocus_tag(xNextLocusTag());
+ feh.Replace(*pEditedFeat);
}
SAnnotSelector selOther;
selOther.ExcludeFeatSubtype(CSeqFeatData::eSubtype_gene);
@@ -408,16 +523,28 @@ void CFeatTableEdit::GenerateLocusTags()
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
(itOther)->GetOriginalFeature()));
feh.RemoveQualifier("locus_tag");
- CConstRef<CSeq_feat> pGeneParent = xGetGeneParent(feat);
- if (!pGeneParent) {
- continue;
- }
- //string locusTag = pGeneParent->GetNamedQual("locus_tag");
- //feh.AddQualifier("locus_tag", locusTag);
}
}
// ----------------------------------------------------------------------------
+void CFeatTableEdit::xFeatureAddQualifier(
+ CMappedFeat mf,
+ const string& qualKey,
+ const string& qualVal)
+// ----------------------------------------------------------------------------
+{
+ const CSeq_feat& origFeat = mf.GetOriginalFeature();
+ CRef<CSeq_feat> pEditedFeat(new CSeq_feat);
+ pEditedFeat->Assign(origFeat);
+ CRef<CGb_qual> pQual(new CGb_qual);
+ pQual->SetQual(qualKey);
+ pQual->SetVal(qualVal);
+ pEditedFeat->SetQual().push_back(pQual);
+ CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(origFeat));
+ feh.Replace(*pEditedFeat);
+}
+
+// ----------------------------------------------------------------------------
string CFeatTableEdit::xNextFeatId()
// ----------------------------------------------------------------------------
{
@@ -447,15 +574,15 @@ string CFeatTableEdit::xNextLocusTag()
// ----------------------------------------------------------------------------
string CFeatTableEdit::xNextProteinId(
- const CSeq_feat& f)
+ const CMappedFeat& mf)
// ----------------------------------------------------------------------------
{
// format: mLocusTagPrefix|<locus tag of gene>[_numeric disambiguation]
- CConstRef<CSeq_feat> pGene = xGetGeneParent(f);
- if (!pGene) {
+ CMappedFeat parentGene = feature::GetBestGeneForFeat(mf, &mTree);
+ if (!parentGene) {
return "";
}
- string locusTag = pGene->GetData().GetGene().GetLocus_tag();
+ string locusTag = parentGene.GetData().GetGene().GetLocus_tag();
string disAmbig = "";
map<string, int>::iterator it = mMapProtIdCounts.find(locusTag);
if (it == mMapProtIdCounts.end()) {
@@ -470,15 +597,15 @@ string CFeatTableEdit::xNextProteinId(
// ----------------------------------------------------------------------------
string CFeatTableEdit::xNextTranscriptId(
- const CSeq_feat& cds)
+ const CMappedFeat& cds)
// ----------------------------------------------------------------------------
{
// format: mLocusTagPrefix|mrna.<locus tag of gene>[_numeric disambiguation]
- CConstRef<CSeq_feat> pGene = xGetGeneParent(cds);
- if (!pGene) {
+ CMappedFeat parentGene = feature::GetBestGeneForFeat(cds, &mTree);
+ if (!parentGene) {
return "";
}
- string locusTag = pGene->GetData().GetGene().GetLocus_tag();
+ string locusTag = parentGene.GetData().GetGene().GetLocus_tag();
string disAmbig = "";
map<string, int>::iterator it = mMapProtIdCounts.find(locusTag);
if (it != mMapProtIdCounts.end() && mMapProtIdCounts[locusTag] != 0) {
@@ -488,91 +615,19 @@ string CFeatTableEdit::xNextTranscriptId(
}
// ----------------------------------------------------------------------------
-string CFeatTableEdit::xCurrentTranscriptId(
- const CSeq_feat& f)
- // ----------------------------------------------------------------------------
-{
- CConstRef<CSeq_feat> pRna = xGetMrnaParent(f);
- if (!pRna) {
- return "";
- }
- string transcriptId = pRna->GetNamedQual("transcript_id");
- return transcriptId;
-}
-
-// ----------------------------------------------------------------------------
-CConstRef<CSeq_feat> CFeatTableEdit::xGetGeneParent(
- const CSeq_feat& feat)
-// ----------------------------------------------------------------------------
-{
- CConstRef<CSeq_feat> pGene;
- CSeq_feat_Handle sfh = mpScope->GetSeq_featHandle(feat);
- CSeq_annot_Handle sah = sfh.GetAnnot();
- if (!sah) {
- return pGene;
- }
-
- size_t bestLength(0);
- CFeat_CI findGene(sah, CSeqFeatData::eSubtype_gene);
- for ( ; findGene; ++findGene) {
- Int8 compare = sequence::TestForOverlap64(
- findGene->GetLocation(), feat.GetLocation(),
- sequence::eOverlap_Contained);
- if (compare == -1) {
- continue;
- }
- size_t currentLength = sequence::GetLength(findGene->GetLocation(), mpScope);
- if (!bestLength || currentLength > bestLength) {
- pGene.Reset(&(findGene->GetOriginalFeature()));
- bestLength = currentLength;
- }
- }
- return pGene;
-}
-
-// ----------------------------------------------------------------------------
-CConstRef<CSeq_feat> CFeatTableEdit::xGetMrnaParent(
- const CSeq_feat& feat)
-// ----------------------------------------------------------------------------
-{
- CConstRef<CSeq_feat> pMrna;
- CSeq_feat_Handle sfh = mpScope->GetSeq_featHandle(feat);
- CSeq_annot_Handle sah = sfh.GetAnnot();
- if (!sah) {
- return pMrna;
- }
-
- size_t bestLength(0);
- CFeat_CI findGene(sah, CSeqFeatData::eSubtype_mRNA);
- for ( ; findGene; ++findGene) {
- Int8 compare = sequence::TestForOverlap64(
- findGene->GetLocation(), feat.GetLocation(),
- sequence::eOverlap_Contained);
- if (compare == -1) {
- continue;
- }
- size_t currentLength = sequence::GetLength(findGene->GetLocation(), mpScope);
- if (!bestLength || currentLength > bestLength) {
- pMrna.Reset(&(findGene->GetOriginalFeature()));
- bestLength = currentLength;
- }
- }
- return pMrna;
-}
-
-// ----------------------------------------------------------------------------
CRef<CSeq_feat> CFeatTableEdit::xMakeGeneForMrna(
- const CSeq_feat& rna)
+ const CMappedFeat& rna)
// ----------------------------------------------------------------------------
{
CRef<CSeq_feat> pGene;
- CSeq_feat_Handle sfh = mpScope->GetSeq_featHandle(rna);
+ //const CSeq_loc& loc = rna.GetOriginalFeature().GetLocation();
+ CSeq_feat_Handle sfh = mpScope->GetSeq_featHandle(rna.GetOriginalFeature());
CSeq_annot_Handle sah = sfh.GetAnnot();
if (!sah) {
return pGene;
}
- CConstRef<CSeq_feat> pExistingGene = xGetGeneParent(rna);
- if (pExistingGene) {
+ CMappedFeat existingGene = feature::GetBestGeneForMrna(rna, &mTree);
+ if (existingGene) {
return pGene;
}
pGene.Reset(new CSeq_feat);
diff --git a/c++/src/objtools/edit/field_handler.cpp b/c++/src/objtools/edit/field_handler.cpp
index ed38c01..32ab4a5 100644
--- a/c++/src/objtools/edit/field_handler.cpp
+++ b/c++/src/objtools/edit/field_handler.cpp
@@ -1,4 +1,4 @@
-/* $Id: field_handler.cpp 453539 2014-12-04 14:50:14Z ivanov $
+/* $Id: field_handler.cpp 481033 2015-10-06 16:46:10Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,18 +51,23 @@ BEGIN_SCOPE(edit)
bool CFieldHandler::QualifierNamesAreEquivalent (string name1, string name2)
{
- // spaces and underscores do not count
+ // ignore protein at beginning
+ const string protein("protein");
+ if (NStr::StartsWith(name1, protein)) {
+ name1 = name1.substr(protein.length());
+ }
+ if (NStr::StartsWith(name2, protein)) {
+ name2 = name2.substr(protein.length());
+ }
+
+ // spaces, dashes, and underscores do not count
NStr::ReplaceInPlace (name1, " ", "");
NStr::ReplaceInPlace (name1, "_", "");
+ NStr::ReplaceInPlace (name1, "-", "");
NStr::ReplaceInPlace (name2, " ", "");
NStr::ReplaceInPlace (name2, "_", "");
- // ignore protein at beginning
- if (NStr::StartsWith(name1, "protein ")) {
- name1 = name1.substr(8);
- }
- if (NStr::StartsWith(name2, "protein ")) {
- name2 = name2.substr(8);
- }
+ NStr::ReplaceInPlace (name2, "-", "");
+
return NStr::EqualNocase(name1, name2);
}
diff --git a/c++/src/objtools/edit/gaps_edit.cpp b/c++/src/objtools/edit/gaps_edit.cpp
index ba58140..47882a0 100644
--- a/c++/src/objtools/edit/gaps_edit.cpp
+++ b/c++/src/objtools/edit/gaps_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: gaps_edit.cpp 458369 2015-02-04 15:31:06Z ivanov $
+/* $Id: gaps_edit.cpp 468747 2015-05-27 18:57:10Z gotvyans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -103,8 +103,8 @@ CRef<CDelta_seq> MakeGap(const CSeq_data& data, TSeqPos len, CDelta_ext& ext, T
if (gap_start+gap_length < decoded.length())
{
ext.AddAndSplit(
- CTempString(decoded, gap_start+gap_length, decoded.length()-gap_start-gap_length),
- CSeq_data::e_Iupacna, decoded.length()-gap_start-gap_length, true, true);
+ CTempString(decoded, gap_start+gap_length, TSeqPos(decoded.length())-gap_start-gap_length),
+ CSeq_data::e_Iupacna, TSeqPos(decoded.length())-gap_start-gap_length, true, true);
}
return CRef<CDelta_seq>(&gap);
@@ -215,7 +215,7 @@ CRef<CDelta_seq> MakeGap(CBioseq::TInst& inst, TSeqPos gap_start, TSeqPos gap_le
CRef<CDelta_seq>
CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos gap_length, CSeq_gap::EType gap_type,
- CLinkage_evidence::EType evidence)
+ const TEvidenceSet& evidences)
{
if (!bioseq.IsSetInst())
return CRef<CDelta_seq>();
@@ -226,12 +226,15 @@ CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos gap_length, C
CDelta_seq::TLiteral& lit = seq->SetLiteral();
lit.SetSeq_data().SetGap().SetType(gap_type);
- if (evidence >= 0)
+ if (evidences.size() > 0)
{
- CRef<CLinkage_evidence> le(new CLinkage_evidence);
- le->SetType(evidence);
lit.SetSeq_data().SetGap().SetLinkage_evidence().clear();
- lit.SetSeq_data().SetGap().SetLinkage_evidence().push_back(le);
+ ITERATE(TEvidenceSet, it, evidences)
+ {
+ CRef<CLinkage_evidence> le(new CLinkage_evidence);
+ le->SetType(*it);
+ lit.SetSeq_data().SetGap().SetLinkage_evidence().push_back(le);
+ }
lit.SetSeq_data().SetGap().SetLinkage(CSeq_gap::eLinkage_linked);
}
}
@@ -256,9 +259,9 @@ void CGapsEditor::ConvertNs2Gaps(const CSeq_data& data, TSeqPos len, CDelta_ext
if (end - start >= gap_min)
{
if (start > 0)
- ext.AddAndSplit(current, CSeq_data::e_Iupacna, start, false, true);
+ ext.AddAndSplit(current, CSeq_data::e_Iupacna, TSeqPos(start), false, true);
- CDelta_seq& gap = ext.AddLiteral(end-start);
+ CDelta_seq& gap = ext.AddLiteral(TSeqPos(end-start));
gap.SetLiteral().SetSeq_data().SetGap().SetType(CSeq_gap::eType_unknown);
current.assign(current.data(), end, current.length() - end);
end = 0;
@@ -266,7 +269,7 @@ void CGapsEditor::ConvertNs2Gaps(const CSeq_data& data, TSeqPos len, CDelta_ext
index = end;
}
if (current.length() > 0)
- ext.AddAndSplit(current, CSeq_data::e_Iupacna, current.length(), false, true);
+ ext.AddAndSplit(current, CSeq_data::e_Iupacna, TSeqPos(current.length()), false, true);
}
}
@@ -292,7 +295,7 @@ void CGapsEditor::ConvertNs2Gaps(CBioseq::TInst& inst, TSeqPos gap_min)
void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq,
TSeqPos gapNmin, TSeqPos gap_Unknown_length,
CSeq_gap::EType gap_type,
- CLinkage_evidence::EType evidence)
+ const TEvidenceSet& evidences)
{
if (bioseq.IsSetInst() && bioseq.GetInst().IsSetSeq_data() && !bioseq.GetInst().GetSeq_data().IsGap())
{
@@ -338,14 +341,17 @@ void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq,
{
lit.SetFuzz().SetLim(CInt_fuzz::eLim_unk);
}
- if (evidence >= 0)
+ if (evidences.size() > 0)
{
if (lit.IsSetSeq_data() && lit.GetSeq_data().IsGap() && lit.GetSeq_data().GetGap().GetLinkage_evidence().size() > 0)
continue;
- CRef<CLinkage_evidence> le(new CLinkage_evidence);
- le->SetType(evidence);
- lit.SetSeq_data().SetGap().SetLinkage_evidence().push_back(le);
+ ITERATE(TEvidenceSet, it, evidences)
+ {
+ CRef<CLinkage_evidence> le(new CLinkage_evidence);
+ le->SetType(*it);
+ lit.SetSeq_data().SetGap().SetLinkage_evidence().push_back(le);
+ }
lit.SetSeq_data().SetGap().SetLinkage(CSeq_gap::eLinkage_linked);
lit.SetSeq_data().SetGap().SetType(gap_type);
}
@@ -355,7 +361,7 @@ void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq,
void CGapsEditor::ConvertNs2Gaps(
objects::CSeq_entry& entry, TSeqPos gapNmin, TSeqPos gap_Unknown_length,
CSeq_gap::EType gap_type,
- CLinkage_evidence::EType evidence)
+ const TEvidenceSet& evidences)
{
if (gapNmin==0 && gap_Unknown_length > 0)
return;
@@ -364,13 +370,13 @@ void CGapsEditor::ConvertNs2Gaps(
{
case CSeq_entry::e_Seq:
{
- ConvertNs2Gaps(entry.SetSeq(), gapNmin, gap_Unknown_length, gap_type, evidence);
+ ConvertNs2Gaps(entry.SetSeq(), gapNmin, gap_Unknown_length, gap_type, evidences);
}
break;
case CSeq_entry::e_Set:
NON_CONST_ITERATE(CSeq_entry::TSet::TSeq_set, it, entry.SetSet().SetSeq_set())
{
- ConvertNs2Gaps(**it, gapNmin, gap_Unknown_length, gap_type, evidence);
+ ConvertNs2Gaps(**it, gapNmin, gap_Unknown_length, gap_type, evidences);
}
break;
default:
diff --git a/c++/src/objtools/edit/gene_utils.cpp b/c++/src/objtools/edit/gene_utils.cpp
index c4d6ab8..9b120f8 100644
--- a/c++/src/objtools/edit/gene_utils.cpp
+++ b/c++/src/objtools/edit/gene_utils.cpp
@@ -1,4 +1,4 @@
-/* $Id: gene_utils.cpp 452843 2014-11-25 15:31:38Z ivanov $
+/* $Id: gene_utils.cpp 452682 2014-11-24 13:03:23Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/link_cds_mrna.cpp b/c++/src/objtools/edit/link_cds_mrna.cpp
index 3d92bd6..ad7356f 100755
--- a/c++/src/objtools/edit/link_cds_mrna.cpp
+++ b/c++/src/objtools/edit/link_cds_mrna.cpp
@@ -1,4 +1,4 @@
-/* $Id: link_cds_mrna.cpp 446709 2014-09-17 17:37:40Z ivanov $
+/* $Id: link_cds_mrna.cpp 448677 2014-10-08 13:43:15Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -164,16 +164,15 @@ void xLinkCDSmRNAbyLabelAndLocation(CSeq_annot::C_Data::TFtable& ftable)
// is this the best?
// TODO: add choosing of the best mRNA*CDS combinations
// instead of getting the first one
- sequence::ECompare located = sequence::Compare(mrna->GetLocation(), cds->GetLocation(), 0);
+ sequence::ECompare located = sequence::Compare(mrna->GetLocation(),
+ cds->GetLocation(), 0, sequence::fCompareOverlapping);
switch (located)
{
case sequence::eContains: ///< First CSeq_loc contains second
case sequence::eSame: ///< CSeq_locs contain each other
best_fit = current;
break;
- case sequence::eContained: ///< First CSeq_loc contained by second
- case sequence::eNoOverlap: ///< CSeq_locs do not overlap
- case sequence::eOverlap: ///< CSeq_locs overlap
+ default:
break;
}
diff --git a/c++/src/objtools/edit/loc_edit.cpp b/c++/src/objtools/edit/loc_edit.cpp
index cda08e9..6828ddd 100644
--- a/c++/src/objtools/edit/loc_edit.cpp
+++ b/c++/src/objtools/edit/loc_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: loc_edit.cpp 446220 2014-09-12 15:25:03Z ivanov $
+/* $Id: loc_edit.cpp 472216 2015-07-08 13:39:11Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -421,7 +421,7 @@ bool CLocationEditPolicy::Interpret3Policy
}
break;
case ePartialPolicy_eClearForGoodEnd:
- if (orig_feat.GetLocation().IsPartialStart(eExtreme_Biological)
+ if (orig_feat.GetLocation().IsPartialStop(eExtreme_Biological)
&& orig_feat.GetData().IsCdregion()
&& bsh) {
string transl_prot;
@@ -533,7 +533,7 @@ bool CLocationEditPolicy::ApplyPolicyToFeature(CSeq_feat& feat, CScope& scope) c
case CLocationEditPolicy::eMergePolicy_SingleInterval:
{
CRef<CSeq_loc> new_loc = sequence::Seq_loc_Merge(feat.GetLocation(), CSeq_loc::fMerge_SingleRange, &scope);
- if (sequence::Compare(*new_loc, feat.GetLocation(), &scope) != sequence::eSame) {
+ if (sequence::Compare(*new_loc, feat.GetLocation(), &scope, sequence::fCompareOverlapping) != sequence::eSame) {
feat.SetLocation().Assign(*new_loc);
any_change = true;
}
diff --git a/c++/src/objtools/edit/parse_text_options.cpp b/c++/src/objtools/edit/parse_text_options.cpp
new file mode 100644
index 0000000..9892d13
--- /dev/null
+++ b/c++/src/objtools/edit/parse_text_options.cpp
@@ -0,0 +1,247 @@
+/* $Id: parse_text_options.cpp 477904 2015-09-02 15:51:03Z ivanov $
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's official duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author: Colleen Bollin, Andrea Asztalos
+*
+* File Description:
+*
+*/
+
+#include <ncbi_pch.hpp>
+#include <objtools/edit/parse_text_options.hpp>
+
+BEGIN_NCBI_SCOPE
+BEGIN_SCOPE(objects)
+BEGIN_SCOPE(edit)
+
+
+SIZE_TYPE FindWithOptions(const string& str, const string& pattern, SIZE_TYPE start_search, bool case_insensitive, bool whole_word)
+{
+ SIZE_TYPE pos = start_search;
+ NStr::ECase str_case = case_insensitive ? NStr::eNocase : NStr::eCase;
+
+ bool found = false;
+ while (pos != NPOS && !found) {
+ pos = NStr::Find(str, pattern, pos, NPOS, NStr::eFirst, str_case);
+ if (pos != NPOS) {
+ if (whole_word) {
+ bool whole_at_start = false;
+ if (pos == 0 || !isalpha(str.c_str()[pos - 1])) {
+ whole_at_start = true;
+ }
+ bool whole_at_end = false;
+ if (pos + pattern.length() == str.length() || !isalpha(str.c_str()[pos + pattern.length()])) {
+ whole_at_end = true;
+ }
+ if (whole_at_start && whole_at_end) {
+ found = true;
+ }
+ } else {
+ found = true;
+ }
+
+ if (!found) {
+ ++pos;
+ }
+ }
+ }
+ return pos;
+}
+
+
+void CParseTextMarker::SetText(const string& val)
+{
+ m_Text = val;
+ if (m_Text.empty()) {
+ m_MarkerType = eMarkerType_None;
+ } else {
+ m_MarkerType = eMarkerType_Text;
+ }
+}
+
+
+bool CParseTextMarker::FindInText(const string& val, size_t& pos, size_t& len, size_t start_search,
+ bool case_insensitive, bool whole_word) const
+{
+ bool found = false;
+
+ switch (m_MarkerType) {
+ case eMarkerType_None:
+ pos = 0;
+ if (start_search != 0)
+ pos = NPOS;
+ len = 0;
+ found = true;
+ break;
+ case eMarkerType_Text:
+ pos = FindWithOptions(val, m_Text, start_search, case_insensitive, whole_word);
+ if (pos != NPOS) {
+ len = m_Text.length();
+ found = true;
+ }
+ break;
+ case eMarkerType_Digits:
+ s_GetDigitsPosition(val, pos, len, start_search);
+ if (len > 0) {
+ found = true;
+ }
+ break;
+ case eMarkerType_Letters:
+ s_GetLettersPosition(val, pos, len, start_search);
+ if (len > 0) {
+ found = true;
+ }
+ break;
+ }
+ return found;
+}
+
+
+void CParseTextMarker::s_GetDigitsPosition(const string& str, size_t& pos, size_t& len, size_t start_search)
+{
+ pos = start_search;
+ string substr = str.substr(start_search);
+ const char *cp = substr.c_str();
+ while (*cp != 0 && !isdigit(*cp)) {
+ pos++;
+ cp++;
+ }
+ if (*cp != 0) {
+ len = 1;
+ cp++;
+ while (*cp != 0 && isdigit(*cp)) {
+ len++;
+ cp++;
+ }
+ }
+}
+
+
+void CParseTextMarker::s_GetLettersPosition(const string& str, size_t& pos, size_t& len, size_t start_search)
+{
+ pos = start_search;
+ string substr = str.substr(start_search);
+ const char *cp = substr.c_str();
+ while (*cp != 0 && !isalpha(*cp)) {
+ pos++;
+ cp++;
+ }
+ if (*cp != 0) {
+ len = 1;
+ cp++;
+ while (*cp != 0 && isalpha(*cp)) {
+ len++;
+ cp++;
+ }
+ }
+}
+
+void CParseTextMarker::Reset()
+{
+ m_MarkerType = eMarkerType_None;
+ m_Text.clear();
+}
+
+string CParseTextOptions::GetSelectedText(const string& input) const
+{
+ string rval = kEmptyStr;
+ size_t start_pos(0), start_len(0), stop_pos(0), stop_len(0);
+ if (m_StartMarker.FindInText(input, start_pos, start_len, 0, m_CaseInsensitive, m_WholeWord)
+ && m_StopMarker.FindInText(input, stop_pos, stop_len, start_pos + start_len, m_CaseInsensitive, m_WholeWord)) {
+ size_t sel_start = start_pos;
+ size_t sel_stop = stop_pos;
+ if (!m_IncludeStartMarker) {
+ sel_start += start_len;
+ }
+ if (m_IncludeStopMarker) {
+ sel_stop += stop_len;
+ }
+ if (sel_start == 0 && sel_stop == 0) {
+ sel_stop = NPOS;
+ }
+ rval = input.substr(sel_start, sel_stop - sel_start);
+ }
+
+ NStr::TruncateSpacesInPlace(rval);
+ return rval;
+}
+
+void CParseTextOptions::RemoveSelectedText(string& input, bool remove_first_only) const
+{
+ bool found = true;
+ size_t start_pos = 0;
+ while (found)
+ {
+ found = false;
+ size_t start_len(0), stop_pos(0), stop_len(0);
+ if (m_StartMarker.FindInText(input, start_pos, start_len, start_pos, m_CaseInsensitive, m_WholeWord)
+ && m_StopMarker.FindInText(input, stop_pos, stop_len, start_pos + start_len, m_CaseInsensitive, m_WholeWord)) {
+ size_t sel_start = start_pos;
+ size_t sel_stop = stop_pos;
+ if (!m_IncludeStartMarker && !m_RemoveBeforePattern) {
+ sel_start += start_len;
+ }
+ if (m_IncludeStopMarker || m_RemoveAfterPattern) {
+ sel_stop += stop_len;
+ }
+ string new_val = kEmptyStr;
+ if (sel_start > 0) {
+ new_val = input.substr(0, sel_start);
+ }
+ if (sel_stop > 0 && sel_stop < input.length() - 1) {
+ new_val += input.substr(sel_stop);
+ }
+ if (new_val != input)
+ {
+ found = true;
+ }
+ input = new_val;
+ }
+ if (remove_first_only)
+ {
+ found = false;
+ }
+ start_pos++;
+ }
+
+ NStr::TruncateSpacesInPlace(input);
+}
+
+void CParseTextOptions::Reset()
+{
+ m_StartMarker.Reset();
+ m_StopMarker.Reset();
+ m_IncludeStartMarker = false;
+ m_IncludeStopMarker = false;
+ m_RemoveFromParsed = false;
+ m_RemoveBeforePattern = false;
+ m_RemoveAfterPattern = false;
+ m_CaseInsensitive = false;
+ m_WholeWord = false;
+}
+
+END_SCOPE(edit)
+END_SCOPE(objects)
+END_NCBI_SCOPE
diff --git a/c++/src/objtools/edit/remote_updater.cpp b/c++/src/objtools/edit/remote_updater.cpp
index 8431175..e8e5d69 100644
--- a/c++/src/objtools/edit/remote_updater.cpp
+++ b/c++/src/objtools/edit/remote_updater.cpp
@@ -1,4 +1,4 @@
-/* $Id: remote_updater.cpp 458364 2015-02-04 15:29:09Z ivanov $
+/* $Id: remote_updater.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -142,7 +142,7 @@ public:
}
}
- CRef<COrg_ref> GetOrg(const COrg_ref& org, objects::IMessageListener* logger)
+ CRef<COrg_ref> GetOrg(const COrg_ref& org, objects::ILineErrorListener* logger)
{
CRef<COrg_ref> result;
CRef<CT3Reply> reply = GetOrgReply(org);
@@ -212,7 +212,7 @@ protected:
auto_ptr<CCachedReplyMap> m_cache;
};
-void CRemoteUpdater::UpdateOrgFromTaxon(objects::IMessageListener* logger, objects::CSeqdesc& obj)
+void CRemoteUpdater::UpdateOrgFromTaxon(objects::ILineErrorListener* logger, objects::CSeqdesc& obj)
{
if (obj.IsOrg())
{
@@ -225,7 +225,7 @@ void CRemoteUpdater::UpdateOrgFromTaxon(objects::IMessageListener* logger, objec
}
}
-void CRemoteUpdater::xUpdateOrgTaxname(objects::IMessageListener* logger, COrg_ref& org)
+void CRemoteUpdater::xUpdateOrgTaxname(objects::ILineErrorListener* logger, COrg_ref& org)
{
CMutexGuard guard(m_Mutex);
@@ -362,7 +362,7 @@ void CRemoteUpdater::xUpdatePubReferences(objects::CSeq_descr& seq_descr)
}
}
-void CRemoteUpdater::UpdateOrgFromTaxon(objects::IMessageListener* logger, objects::CSeq_entry& entry)
+void CRemoteUpdater::UpdateOrgFromTaxon(objects::ILineErrorListener* logger, objects::CSeq_entry& entry)
{
if (entry.IsSet())
{
@@ -390,7 +390,7 @@ void CRemoteUpdater::UpdateOrgFromTaxon(objects::IMessageListener* logger, objec
}
}
-void CRemoteUpdater::UpdateOrgFromTaxon(objects::IMessageListener* logger, objects::CSeq_entry_EditHandle& obj)
+void CRemoteUpdater::UpdateOrgFromTaxon(objects::ILineErrorListener* logger, objects::CSeq_entry_EditHandle& obj)
{
for (CBioseq_CI bioseq_it(obj); bioseq_it; ++bioseq_it)
{
diff --git a/c++/src/objtools/edit/rna_edit.cpp b/c++/src/objtools/edit/rna_edit.cpp
index 6a8904d..5e954ce 100755
--- a/c++/src/objtools/edit/rna_edit.cpp
+++ b/c++/src/objtools/edit/rna_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: rna_edit.cpp 460302 2015-02-26 12:24:48Z ivanov $
+/* $Id: rna_edit.cpp 460068 2015-02-24 19:12:10Z filippov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/seq_entry_edit.cpp b/c++/src/objtools/edit/seq_entry_edit.cpp
index c70cccb..3235b7b 100644
--- a/c++/src/objtools/edit/seq_entry_edit.cpp
+++ b/c++/src/objtools/edit/seq_entry_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: seq_entry_edit.cpp 457945 2015-01-29 16:10:58Z ivanov $
+/* $Id: seq_entry_edit.cpp 468566 2015-05-26 16:19:06Z filippov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1538,11 +1538,24 @@ void s_AddLiteral(CSeq_inst& inst, const string& element)
}
-void s_AddGap(CSeq_inst& inst, size_t n_len, bool is_unknown)
+void s_AddGap(CSeq_inst& inst, size_t n_len, bool is_unknown, bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkage_evidence = -1 )
{
CRef<CDelta_seq> gap(new CDelta_seq());
- gap->SetLiteral().SetSeq_data().SetGap();
- gap->SetLiteral().SetSeq_data().SetGap().SetType(CSeq_gap::eType_unknown);
+ if (is_assembly_gap)
+ {
+ gap->SetLiteral().SetSeq_data().SetGap();
+ gap->SetLiteral().SetSeq_data().SetGap().SetType(gap_type);
+ if (linkage >= 0)
+ {
+ gap->SetLiteral().SetSeq_data().SetGap().SetLinkage(linkage);
+ }
+ if (linkage_evidence >= 0)
+ {
+ CRef<CLinkage_evidence> link_ev(new CLinkage_evidence);
+ link_ev->SetType(linkage_evidence);
+ gap->SetLiteral().SetSeq_data().SetGap().SetLinkage_evidence().push_back(link_ev);
+ }
+ }
if (is_unknown) {
gap->SetLiteral().SetFuzz().SetLim(CInt_fuzz::eLim_unk);
}
@@ -1573,7 +1586,8 @@ void s_AddGap(CSeq_inst& inst, size_t n_len, bool is_unknown)
/// @return none
void ConvertRawToDeltaByNs(CSeq_inst& inst,
size_t min_unknown, int max_unknown,
- size_t min_known, int max_known)
+ size_t min_known, int max_known,
+ bool is_assembly_gap, int gap_type, int linkage, int linkage_evidence )
{
// can only convert if starting as raw
if (!inst.IsSetRepr() || inst.GetRepr() != CSeq_inst::eRepr_raw
@@ -1627,7 +1641,7 @@ void ConvertRawToDeltaByNs(CSeq_inst& inst,
element = element.substr(0, element.length() - n_len);
s_AddLiteral(inst, element);
}
- s_AddGap(inst, n_len, is_unknown);
+ s_AddGap(inst, n_len, is_unknown, is_assembly_gap, gap_type, linkage, linkage_evidence);
element = "";
}
n_len = 0;
@@ -1652,7 +1666,7 @@ void ConvertRawToDeltaByNs(CSeq_inst& inst,
element = element.substr(0, element.length() - n_len);
s_AddLiteral(inst, element);
}
- s_AddGap(inst, n_len, is_unknown);
+ s_AddGap(inst, n_len, is_unknown, is_assembly_gap, gap_type, linkage, linkage_evidence);
}
} else {
s_AddLiteral(inst, element);
@@ -1710,12 +1724,13 @@ TLocAdjustmentVector NormalizeUnknownLengthGaps(CSeq_inst& inst, size_t unknown_
void ConvertRawToDeltaByNs(CBioseq_Handle bsh,
size_t min_unknown, int max_unknown,
- size_t min_known, int max_known)
+ size_t min_known, int max_known,
+ bool is_assembly_gap, int gap_type, int linkage, int linkage_evidence )
{
CRef<CSeq_inst> inst(new CSeq_inst());
inst->Assign(bsh.GetInst());
- ConvertRawToDeltaByNs(*inst, min_unknown, max_unknown, min_known, max_known);
+ ConvertRawToDeltaByNs(*inst, min_unknown, max_unknown, min_known, max_known, is_assembly_gap, gap_type, linkage, linkage_evidence);
TLocAdjustmentVector changes = NormalizeUnknownLengthGaps(*inst);
CBioseq_EditHandle beh = bsh.GetEditHandle();
beh.SetInst(*inst);
@@ -1843,22 +1858,54 @@ void ResetLinkageEvidence(CSeq_ext& ext)
**** Trim functions
*******************************************************************************/
-/// Implementation detail: first trim all associated annotation, then
-/// trim sequence data
-void TrimSequenceAndAnnotation(CBioseq_Handle bsh,
- const TCuts& cuts,
- EInternalTrimType internal_cut_conversion)
+void s_BasicValidation(CBioseq_Handle bsh,
+ const TCuts& cuts)
{
// Should be a nuc!
if (!bsh.IsNucleotide()) {
- return;
+ NCBI_THROW(CEditException, eInvalid, "Bioseq is not a nucleotide.");
}
// Cannot get nuc sequence data
if (!bsh.CanGetInst()) {
- return;
+ NCBI_THROW(CEditException, eInvalid, "Cannot get sequence data for nucleotide.");
+ }
+
+ // Are the cuts within range of sequence length?
+ TSeqPos nuc_len = 0;
+ if (bsh.GetInst().CanGetLength()) {
+ nuc_len = bsh.GetInst().GetLength();
}
+ if (nuc_len <= 0) {
+ stringstream ss;
+ ss << "Nuc has invalid sequence length = " << nuc_len;
+ NCBI_THROW(CEditException, eInvalid, ss.str());
+ }
+
+ TCuts::const_iterator cit;
+ for (cit = cuts.begin(); cit != cuts.end(); ++cit) {
+ const TRange& cut = *cit;
+ TSeqPos cut_from = cut.GetFrom();
+ TSeqPos cut_to = cut.GetTo();
+ if (cut_from < 0 || cut_to < 0 || cut_from >= nuc_len || cut_to >= nuc_len) {
+ stringstream ss;
+ ss << "Cut location is invalid = [" << cut_from << " - " << cut_to << "]";
+ NCBI_THROW(CEditException, eInvalid, ss.str());
+ }
+ }
+}
+
+
+/// Implementation detail: first trim all associated annotation, then
+/// trim sequence data
+void TrimSequenceAndAnnotation(CBioseq_Handle bsh,
+ const TCuts& cuts,
+ EInternalTrimType internal_cut_conversion)
+{
+ // Check the input data for anomalies
+ s_BasicValidation(bsh, cuts);
+
// Sort the cuts
TCuts sorted_cuts;
GetSortedCuts(bsh, cuts, sorted_cuts, internal_cut_conversion);
@@ -1907,7 +1954,7 @@ void TrimSequenceAndAnnotation(CBioseq_Handle bsh,
{
// Get length of nuc sequence before trimming
TSeqPos original_nuc_len = 0;
- if (bsh.CanGetInst() && bsh.GetInst().CanGetLength()) {
+ if (bsh.GetInst().CanGetLength()) {
original_nuc_len = bsh.GetInst().GetLength();
}
AdjustCdregionFrame(original_nuc_len, copy_feat, sorted_cuts);
diff --git a/c++/src/objtools/edit/seqid_guesser.cpp b/c++/src/objtools/edit/seqid_guesser.cpp
index cd7dd76..a464594 100644
--- a/c++/src/objtools/edit/seqid_guesser.cpp
+++ b/c++/src/objtools/edit/seqid_guesser.cpp
@@ -1,4 +1,4 @@
-/* $Id: seqid_guesser.cpp 438363 2014-06-16 13:35:48Z bollin $
+/* $Id: seqid_guesser.cpp 482749 2015-10-26 17:01:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -82,6 +82,16 @@ CSeqIdGuesser::CSeqIdGuesser(CSeq_entry_Handle entry) : m_SeqEntry(entry)
// BankIt IDs can be specified with "BankIt" prefix
if (NStr::EqualNocase(dbtag.GetDb(), "BankIt")) {
x_AddIdString("BankIt" + tag_str, *id);
+ size_t pos = NStr::Find(tag_str, "/", 0, string::npos, NStr::eLast);
+ if (pos != string::npos) {
+ string file = tag_str.substr(0, pos);
+ x_AddIdString(file, *id);
+ x_AddIdString("BankIt" + file, *id);
+ string file_id = tag_str.substr(pos + 1);
+ if (!NStr::EqualNocase(file_id, local)) {
+ x_AddIdString(file_id, *id);
+ }
+ }
} else if (NStr::EqualNocase(dbtag.GetDb(), "NCBIFILE")) {
// File ID are usually a filename plus a slash plus the original local ID
// add the filename as its own identifier, but only add the local ID if it hasn't
@@ -151,6 +161,16 @@ vector<string> CSeqIdGuesser::GetIdStrings(CBioseq_Handle bsh)
// BankIt IDs can be specified with "BankIt" prefix
if (NStr::EqualNocase(dbtag.GetDb(), "BankIt")) {
id_str.push_back("BankIt" + tag_str);
+ size_t pos = NStr::Find(tag_str, "/", 0, string::npos, NStr::eLast);
+ if (pos != string::npos) {
+ string file = tag_str.substr(0, pos);
+ id_str.push_back(file);
+ id_str.push_back("BankIt" + file);
+ string file_id = tag_str.substr(pos + 1);
+ if (!NStr::EqualNocase(file_id, local)) {
+ id_str.push_back(file_id);
+ }
+ }
} else if (NStr::EqualNocase(dbtag.GetDb(), "NCBIFILE")) {
// File ID are usually a filename plus a slash plus the original local ID
// add the filename as its own identifier, but only add the local ID if it hasn't
diff --git a/c++/src/objtools/edit/source_edit.cpp b/c++/src/objtools/edit/source_edit.cpp
index 0940dca..0cb9148 100644
--- a/c++/src/objtools/edit/source_edit.cpp
+++ b/c++/src/objtools/edit/source_edit.cpp
@@ -1,4 +1,4 @@
-/* $Id: source_edit.cpp 453265 2014-12-02 15:21:28Z ivanov $
+/* $Id: source_edit.cpp 453178 2014-12-01 18:15:03Z bollin $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/edit/string_constraint.cpp b/c++/src/objtools/edit/string_constraint.cpp
index 5ea74ff..baab6ac 100644
--- a/c++/src/objtools/edit/string_constraint.cpp
+++ b/c++/src/objtools/edit/string_constraint.cpp
@@ -1,4 +1,4 @@
-/* $Id: string_constraint.cpp 460812 2015-03-03 16:57:06Z ivanov $
+/* $Id: string_constraint.cpp 460632 2015-03-02 14:41:06Z asztalos $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/format/Makefile.xformat.lib b/c++/src/objtools/format/Makefile.xformat.lib
index f33e5f7..6a2d1b3 100644
--- a/c++/src/objtools/format/Makefile.xformat.lib
+++ b/c++/src/objtools/format/Makefile.xformat.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.xformat.lib 440222 2014-07-10 15:17:10Z gouriano $
+# $Id: Makefile.xformat.lib 474406 2015-07-28 18:14:17Z ivanov $
# Build library "xformat"
###############################
@@ -10,14 +10,16 @@ SRC = accession_item basecount_item comment_item contig_item date_item \
dbsource_item defline_item feature_item genome_item ctrl_items \
keywords_item locus_item primary_item reference_item segment_item \
sequence_item source_item version_item wgs_item tsa_item flat_seqloc qualifiers \
- context utils gather_items embl_gather genbank_gather \
+ context gather_items embl_gather genbank_gather \
flat_file_generator item_formatter embl_formatter genbank_formatter \
format_item_ostream item_ostream ostream_text_ostream \
- gff_gather gff_formatter origin_item ftable_gather ftable_formatter \
- gbseq_formatter flat_file_config alignment_item gff3_formatter \
+ origin_item ftable_gather ftable_formatter \
+ gbseq_formatter flat_file_config alignment_item \
gap_item genome_project_item sam_formatter cigar_formatter \
gather_iter html_anchor_item inst_info_map gene_finder flat_qual_slots
+DLL_LIB = xalnmgr xconnect
+
WATCHERS = ludwigf dicuccio kornbluh
diff --git a/c++/src/objtools/format/accession_item.cpp b/c++/src/objtools/format/accession_item.cpp
index 37f3957..35df007 100644
--- a/c++/src/objtools/format/accession_item.cpp
+++ b/c++/src/objtools/format/accession_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: accession_item.cpp 445966 2014-09-10 13:01:50Z dicuccio $
+/* $Id: accession_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -44,7 +44,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/accession_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
#include <algorithm>
diff --git a/c++/src/objtools/format/cigar_formatter.cpp b/c++/src/objtools/format/cigar_formatter.cpp
index cb6003d..edb4989 100644
--- a/c++/src/objtools/format/cigar_formatter.cpp
+++ b/c++/src/objtools/format/cigar_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: cigar_formatter.cpp 457254 2015-01-21 18:33:24Z ivanov $
+/* $Id: cigar_formatter.cpp 484561 2015-11-12 17:46:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -166,9 +166,11 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
if ( !m_RefId ) {
m_RefId.Reset(&m_AlnMap->GetSeqId(m_RefRow));
+ AdjustSeqIdType(m_RefId);
}
if ( !m_TargetId ) {
m_TargetId.Reset(&m_AlnMap->GetSeqId(m_TargetRow));
+ AdjustSeqIdType(m_TargetId);
}
m_RefWidth =
@@ -192,6 +194,8 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
"and thus are not supported in current CIGAR output");
}
+ StartRow();
+
// HACK HACK HACK
// Is the following correct???
//
@@ -212,12 +216,14 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
// one of (1, 1) for nuc-nuc, (1, 3) for nuc-prot,
// (3, 1) for prot-nuc, and (3, 3) for prot-prot.
TSeqPos width = max(m_RefWidth, m_TargetWidth);
-
- for (CAlnMap::TNumchunk i0 = 0; i0 < m_AlnMap->GetNumSegs(); ++i0) {
- TRange ref_piece = m_AlnMap->GetRange(m_RefRow, i0);
- TRange tgt_piece = m_AlnMap->GetRange(m_TargetRow, i0);
- CAlnMap::TSegTypeFlags ref_flags = m_AlnMap->GetSegType(m_RefRow, i0);
- CAlnMap::TSegTypeFlags tgt_flags = m_AlnMap->GetSegType(m_TargetRow, i0);
+ CAlnMap::TNumchunk numseg = m_AlnMap->GetNumSegs();
+ for (CAlnMap::TNumchunk idx = 0; idx < numseg; ++idx) {
+ // If ref is on minus strand, revert the order of segments.
+ CAlnMap::TNumchunk seg = m_RefSign > 0 ? idx : numseg - idx - 1;
+ TRange ref_piece = m_AlnMap->GetRange(m_RefRow, seg);
+ TRange tgt_piece = m_AlnMap->GetRange(m_TargetRow, seg);
+ CAlnMap::TSegTypeFlags ref_flags = m_AlnMap->GetSegType(m_RefRow, seg);
+ CAlnMap::TSegTypeFlags tgt_flags = m_AlnMap->GetSegType(m_TargetRow, seg);
//The type and count are guaranteed set by one of the if/else cases below.
char type = 'X'; // Guaranteed set. Pacify compiler.
TSeqPos count = 0; // Guaranteed set. Pacify compiler.
@@ -229,7 +235,7 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
// on an aa boundary.
//
type = 'I';
- if (i0 == 0 && IsSetFlag(fCIGAR_GffForFlybase) && m_TargetWidth == 3) {
+ if (idx == 0 && IsSetFlag(fCIGAR_GffForFlybase) && m_TargetWidth == 3) {
// See comments about frame and phase, below.
m_Frame = tgt_piece.GetFrom() % m_TargetWidth;
}
@@ -244,7 +250,7 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
// TODO: Handle gap that does not start on an aa boundary.
//
type = 'D';
- if (i0 == 0 && IsSetFlag(fCIGAR_GffForFlybase) && m_RefWidth == 3) {
+ if (idx == 0 && IsSetFlag(fCIGAR_GffForFlybase) && m_RefWidth == 3) {
// See comments about frame and phase, below.
m_Frame = ref_piece.GetFrom() % m_RefWidth;
}
@@ -276,7 +282,7 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
"Frameshift(s) in Spliced-exon-chunk's diag "
"not supported in current CIGAR output");
}
- if (i0 == 0 && IsSetFlag(fCIGAR_GffForFlybase)) {
+ if (idx == 0 && IsSetFlag(fCIGAR_GffForFlybase)) {
// Semantics of the phase aren't defined in GFF3 for
// feature types other than a CDS, and this is an alignment.
//
@@ -339,15 +345,6 @@ void CCIGAR_Formatter::x_FormatLine(bool width_inverted)
}
}
CNcbiOstrstream aln_out;
- m_TargetId.Reset(&m_AlnMap->GetSeqId(m_TargetRow));
- if ( m_Scope ) {
- CSeq_id_Handle acc_id = sequence::GetId(
- *m_TargetId, *m_Scope, sequence::eGetId_ForceAcc);
- if ( acc_id ) {
- m_TargetId.Reset(acc_id.GetSeqId());
- }
- }
- StartRow();
AddSegment(cigar, m_LastType, last_count);
string cigar_string = CNcbiOstrstreamToString(cigar);
@@ -432,6 +429,7 @@ void CCIGAR_Formatter::x_FormatDensegRows(const CDense_seg& ds,
else {
_ASSERT(m_TargetRow >= 0);
m_TargetId.Reset(&m_AlnMap->GetSeqId(m_TargetRow));
+ AdjustSeqIdType(m_TargetId);
}
StartRows();
for (m_RefRow = 0; m_RefRow < m_AlnMap->GetNumRows(); ++m_RefRow) {
diff --git a/c++/src/objtools/format/comment_item.cpp b/c++/src/objtools/format/comment_item.cpp
index 4691f35..08f5ee8 100644
--- a/c++/src/objtools/format/comment_item.cpp
+++ b/c++/src/objtools/format/comment_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: comment_item.cpp 450153 2014-10-23 14:02:56Z ivanov $
+/* $Id: comment_item.cpp 478449 2015-09-09 15:23:58Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -40,6 +40,7 @@
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
+#include <objects/seq/seq_macros.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/SubSource.hpp>
@@ -50,6 +51,7 @@
#include <objects/general/Object_id.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Dbtag.hpp>
+#include <objects/general/general_macros.hpp>
#include <objects/misc/sequence_util_macros.hpp>
#include <objmgr/seqdesc_ci.hpp>
@@ -59,7 +61,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/comment_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -963,6 +965,32 @@ string CCommentItem::GetStringForMolinfo(const CMolInfo& mi, CBioseqContext& ctx
}
+string CCommentItem::GetStringForUnordered(CBioseqContext& ctx)
+{
+ SDeltaSeqSummary summary;
+ if (ctx.IsDelta()) {
+ GetDeltaSeqSummary(ctx.GetHandle(), summary);
+ }
+
+ CNcbiOstrstream text;
+
+ text << "* NOTE: This is a partial genome representation.";
+ if ( summary.num_gaps > 0 ) {
+ text << " It currently~* consists of " << (summary.num_gaps + 1) << " contigs. The true order of the pieces~"
+ << "* is not known and their order in this sequence record is~"
+ << "* arbitrary. Gaps between the contigs are represented as~"
+ << "* runs of N, but the exact sizes of the gaps are unknown.";
+ }
+ text << "~";
+
+ string comment = CNcbiOstrstreamToString(text);
+ ConvertQuotes(comment);
+ ncbi::objects::AddPeriod(comment);
+
+ return comment;
+}
+
+
string CCommentItem::GetStringForHTGS(CBioseqContext& ctx)
{
SDeltaSeqSummary summary;
@@ -1339,39 +1367,50 @@ string CCommentItem::GetStringForBaseMod(CBioseqContext& ctx)
return CNcbiOstrstreamToString(str);
}
- str << "There ";
- if ( numBases > 1 ) {
- str << "are ";
- } else {
- str << "is ";
- }
- str << numBases;
- str << " base modification file";
- if ( numBases > 1 ) {
- str << "s";
+ if( ! sm_FirstComment ) {
+ str << "\n";
}
- if( bHtml ) {
- string pfx = " (";
- string sfx = "";
- int j = 0;
- FOR_EACH_STRING_IN_VECTOR (itr, sBasemodURLs) {
- string url = *itr;
- if ( ! url.empty() ) {
- j++;
- str << pfx << "<a href=\"" << url << "\">" << j << "</a>";
- if ( numBases == 2 ) {
- pfx = " and ";
- } else if ( j == numBases - 1 ) {
- pfx = ", and ";
- } else {
- pfx = ", ";
+
+ if ( numBases == 1 ) {
+ str << "This genome has a ";
+ if( bHtml ) {
+ FOR_EACH_STRING_IN_VECTOR (itr, sBasemodURLs) {
+ string url = *itr;
+ if ( ! url.empty() ) {
+ str << "<a href=\"" << url << "\">" << "base modification file" << "</a>";
+ }
+ }
+ } else {
+ str << "base modification file";
+ }
+ str << " available.";
+ } else {
+ str << "There are ";
+ str << numBases;
+ str << " base modification files";
+ if( bHtml ) {
+ string pfx = " (";
+ string sfx = "";
+ int j = 0;
+ FOR_EACH_STRING_IN_VECTOR (itr, sBasemodURLs) {
+ string url = *itr;
+ if ( ! url.empty() ) {
+ j++;
+ str << pfx << "<a href=\"" << url << "\">" << j << "</a>";
+ if ( numBases == 2 ) {
+ pfx = " and ";
+ } else if ( j == numBases - 1 ) {
+ pfx = ", and ";
+ } else {
+ pfx = ", ";
+ }
+ sfx = ")";
}
- sfx = ")";
}
+ str << sfx;
}
- str << sfx;
+ str << " available for this genome.";
}
- str << " available for this genome";
return CNcbiOstrstreamToString(str);
}
@@ -1423,7 +1462,7 @@ void CCommentItem::x_GatherInfo(CBioseqContext& ctx)
// returns the data_str, but wrapped in appropriate <a href...>...</a> if applicable
static
-string s_HtmlizeStructuredCommentData( const bool is_html, const string &label_str, const string &data_str )
+string s_HtmlizeStructuredCommentData( const bool is_html, const string &label_str, const string &data_str, const char* provider )
{
if( ! is_html ) {
return data_str;
@@ -1436,16 +1475,16 @@ string s_HtmlizeStructuredCommentData( const bool is_html, const string &label_s
return CNcbiOstrstreamToString(result);
}
if ( label_str == "Annotation Software Version") {
- result << "<a href=\"http://www.ncbi.nlm.nih.gov/genome/annotation_euk/release_notes/#version"
+ result << "<a href=\"https://www.ncbi.nlm.nih.gov/genome/annotation_euk/release_notes/#version"
<< data_str
<< "\">" << data_str << "</a>";
return CNcbiOstrstreamToString(result);
- } else if ( label_str == "Annotation Version") {
+ } else if ( NStr::Equal (label_str, "Annotation Version") && NStr::Equal (provider, "NCBI") ) {
string fst;
string snd;
NStr::Replace( data_str, " Annotation Release ", "/", fst );
NStr::Replace( fst, " ", "_", snd );
- result << "<a href=\"http://www.ncbi.nlm.nih.gov/genome/annotation_euk/"
+ result << "<a href=\"https://www.ncbi.nlm.nih.gov/genome/annotation_euk/"
<< snd
<< "\">" << data_str << "</a>";
return CNcbiOstrstreamToString(result);
@@ -1471,6 +1510,7 @@ void s_GetStrForStructuredComment(
// default prefix and suffix
const char* prefix = "##Metadata-START##";
const char* suffix = "##Metadata-END##";
+ const char* provider = "";
bool fieldOverThreshold = false;
@@ -1487,6 +1527,9 @@ void s_GetStrForStructuredComment(
} else if( label == "StructuredCommentSuffix" ) {
suffix = (*it_for_len)->GetData().GetStr().c_str();
} else {
+ if ( label == "Annotation Provider" ) {
+ provider = (*it_for_len)->GetData().GetStr().c_str();
+ }
const string::size_type label_len = label.length();
if( (label_len > longest_label_len) && (label_len <= kFieldLenThreshold) ) {
longest_label_len = label_len;
@@ -1535,7 +1578,7 @@ void s_GetStrForStructuredComment(
next_line.resize( max( next_line.size(), longest_label_len), ' ' );
}
next_line.append( " :: " );
- next_line.append( s_HtmlizeStructuredCommentData( is_html, (*it)->GetLabel().GetStr(), (*it)->GetData().GetStr() ) );
+ next_line.append( s_HtmlizeStructuredCommentData( is_html, (*it)->GetLabel().GetStr(), (*it)->GetData().GetStr(), provider ) );
next_line.append( "\n" );
ExpandTildes(next_line, eTilde_comment);
@@ -1981,24 +2024,65 @@ CLocalIdComment::CLocalIdComment(const CObject_id& oid, CBioseqContext& ctx) :
}
-void CLocalIdComment::x_GatherInfo(CBioseqContext&)
+static string s_GetOriginalID (CBioseqContext& ctx)
+
+{
+ const CBioseq_Handle& bsh = ctx.GetHandle();
+ const CBioseq& seq = *bsh.GetCompleteBioseq();
+
+ FOR_EACH_SEQDESC_ON_BIOSEQ (it, seq) {
+ const CSeqdesc& desc = **it;
+ if (! desc.IsUser()) continue;
+ if (! desc.GetUser().IsSetType()) continue;
+ const CUser_object& usr = desc.GetUser();
+ const CObject_id& oi = usr.GetType();
+ if (! oi.IsStr()) continue;
+ const string& type = oi.GetStr();
+ if (! NStr::EqualNocase(type, "OrginalID") && ! NStr::EqualNocase(type, "OriginalID")) continue;
+ FOR_EACH_USERFIELD_ON_USEROBJECT (uitr, usr) {
+ const CUser_field& fld = **uitr;
+ if (FIELD_IS_SET_AND_IS(fld, Label, Str)) {
+ const string &label_str = GET_FIELD(fld.GetLabel(), Str);
+ if (! NStr::EqualNocase(label_str, "LocalId")) continue;
+ if (fld.IsSetData() && fld.GetData().IsStr()) {
+ return fld.GetData().GetStr();
+ }
+ }
+ }
+ }
+
+ return "";
+}
+
+
+void CLocalIdComment::x_GatherInfo(CBioseqContext& ctx)
{
CNcbiOstrstream msg;
- switch ( m_Oid->Which() ) {
- case CObject_id::e_Id:
- msg << "LocalID: " << m_Oid->GetId();
- break;
- case CObject_id::e_Str:
- if ( m_Oid->GetStr().length() < 1000 ) {
- msg << "LocalID: " << m_Oid->GetStr();
+ string orig_id = s_GetOriginalID (ctx);
+ if (!NStr::EqualNocase(orig_id, "")) {
+ if ( orig_id.length() < 1000 ) {
+ msg << "LocalID: " << orig_id;
} else {
msg << "LocalID string too large";
}
- break;
- default:
- break;
+ } else {
+ switch ( m_Oid->Which() ) {
+ case CObject_id::e_Id:
+ msg << "LocalID: " << m_Oid->GetId();
+ break;
+ case CObject_id::e_Str:
+ if ( m_Oid->GetStr().length() < 1000 ) {
+ msg << "LocalID: " << m_Oid->GetStr();
+ } else {
+ msg << "LocalID string too large";
+ }
+ break;
+ default:
+ break;
+ }
}
+
x_SetComment(CNcbiOstrstreamToString(msg));
}
diff --git a/c++/src/objtools/format/context.cpp b/c++/src/objtools/format/context.cpp
index 43f52df..6bbfde0 100644
--- a/c++/src/objtools/format/context.cpp
+++ b/c++/src/objtools/format/context.cpp
@@ -1,4 +1,4 @@
-/* $Id: context.cpp 462431 2015-03-18 17:23:52Z ivanov $
+/* $Id: context.cpp 468376 2015-05-22 13:03:34Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -111,7 +111,7 @@ CBioseqContext::CBioseqContext
m_IsTSA(false),
m_IsTSAMaster(false),
m_IsHup(false),
- m_Gi(0),
+ m_Gi(ZERO_GI),
m_ShowGBBSource(false),
m_PatSeqid(0),
m_HasOperon(false),
@@ -169,7 +169,7 @@ CBioseqContext::CBioseqContext
m_IsTSA(false),
m_IsTSAMaster(false),
m_IsHup(false),
- m_Gi(0),
+ m_Gi(ZERO_GI),
m_ShowGBBSource(false),
m_PatSeqid(0),
m_HasOperon(false),
@@ -449,7 +449,11 @@ void CBioseqContext::x_SetFiletrackURL(const CUser_object& uo)
CConstRef<CUser_field> pBaseModURLField = uo.GetFieldRef("BaseModification-FileTrackURL");
if ( pBaseModURLField) {
- if ( FIELD_IS_SET_AND_IS(*pBaseModURLField, Data, Strs) ) {
+ if ( FIELD_IS_SET_AND_IS(*pBaseModURLField, Data, Str) ) {
+ if ( ! pBaseModURLField->GetData().GetStr().empty() ) {
+ m_BasemodURLs.push_back(pBaseModURLField->GetData().GetStr());
+ }
+ } else if ( FIELD_IS_SET_AND_IS(*pBaseModURLField, Data, Strs) ) {
m_BasemodURLs = pBaseModURLField->GetData().GetStrs();
}
}
diff --git a/c++/src/objtools/format/ctrl_items.cpp b/c++/src/objtools/format/ctrl_items.cpp
index ad5b671..2901e7d 100644
--- a/c++/src/objtools/format/ctrl_items.cpp
+++ b/c++/src/objtools/format/ctrl_items.cpp
@@ -1,4 +1,4 @@
-/* $Id: ctrl_items.cpp 194363 2010-06-12 18:34:00Z dicuccio $
+/* $Id: ctrl_items.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,7 +56,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/ctrl_items.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/src/objtools/format/dbsource_item.cpp b/c++/src/objtools/format/dbsource_item.cpp
index 559519e..119eaef 100644
--- a/c++/src/objtools/format/dbsource_item.cpp
+++ b/c++/src/objtools/format/dbsource_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: dbsource_item.cpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: dbsource_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -59,7 +59,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/dbsource_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -446,7 +446,7 @@ void CDBSourceItem::x_AddSPBlock(CBioseqContext& ctx)
if (ctx.Config().DoHTML()) {
xrefs.push_back
("MIM <a href=\""
- "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=" + id
+ "https://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=" + id
+ "\">" + id + "</a>");
} else {
xrefs.push_back("MIM:" + id);
@@ -677,7 +677,7 @@ bool CDBSourceItem::x_ExtractLinkableSource(
string m_url;
bool m_must_be_all_digits;
} potentialPrefixes[] = {
- { "Mmdb_id:", "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=", true }
+ { "Mmdb_id:", "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=", true }
};
const static size_t numPotentialPrefixes = sizeof(potentialPrefixes)/sizeof(potentialPrefixes[0]);
diff --git a/c++/src/objtools/format/defline_item.cpp b/c++/src/objtools/format/defline_item.cpp
index 3095cc9..23b4e39 100644
--- a/c++/src/objtools/format/defline_item.cpp
+++ b/c++/src/objtools/format/defline_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: defline_item.cpp 210334 2010-11-03 14:56:15Z kornbluh $
+/* $Id: defline_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -39,7 +39,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/defline_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -80,7 +80,8 @@ void CDeflineItem::x_GatherInfo(CBioseqContext& ctx)
CConstRef<CBioseq> bioseq = ctx.GetHandle().GetBioseqCore();
CScope& scope = ctx.GetScope();
m_Defline = Defliner.GenerateDefline( *bioseq, scope );
- CompressSpaces( m_Defline );
+ // CompressSpaces( m_Defline );
+ CleanAndCompress (m_Defline, m_Defline.c_str());
ConvertQuotes(m_Defline);
AddPeriod(m_Defline);
}
diff --git a/c++/src/objtools/format/embl_formatter.cpp b/c++/src/objtools/format/embl_formatter.cpp
index 0408669..49d5521 100644
--- a/c++/src/objtools/format/embl_formatter.cpp
+++ b/c++/src/objtools/format/embl_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: embl_formatter.cpp 399305 2013-05-13 19:13:43Z grichenk $
+/* $Id: embl_formatter.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,7 +42,7 @@
#include <objtools/format/items/source_item.hpp>
#include <objtools/format/embl_formatter.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/src/objtools/format/feature_item.cpp b/c++/src/objtools/format/feature_item.cpp
index 0a10490..b26ebd8 100644
--- a/c++/src/objtools/format/feature_item.cpp
+++ b/c++/src/objtools/format/feature_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: feature_item.cpp 456879 2015-01-15 19:49:54Z ivanov $
+/* $Id: feature_item.cpp 481617 2015-10-14 14:42:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -107,7 +107,7 @@
#include <objtools/format/items/gene_finder.hpp>
#include <objtools/format/context.hpp>
#include <objtools/format/items/qualifiers.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
#include "inst_info_map.hpp"
// On Mac OS X 10.3, FixMath.h defines ff as a one-argument macro(!)
@@ -1057,6 +1057,7 @@ string CFeatureItem::GetKey(void) const
case CSeqFeatData::eSubtype_polyA_signal:
case CSeqFeatData::eSubtype_attenuator:
case CSeqFeatData::eSubtype_terminator:
+ case CSeqFeatData::eSubtype_misc_signal:
return "regulatory";
default:
break;
@@ -1186,6 +1187,9 @@ void CFeatureItem::x_AddQualsRegulatoryClass(
case CSeqFeatData::eSubtype_terminator:
x_AddQual(eFQ_regulatory_class, new CFlatStringQVal("terminator"));
break;
+ case CSeqFeatData::eSubtype_misc_signal:
+ x_AddQual(eFQ_regulatory_class, new CFlatStringQVal("other"));
+ break;
default:
break;
}
@@ -1213,47 +1217,35 @@ void CFeatureItem::x_AddQualPseudo(
{
switch (subtype) {
case CSeqFeatData::eSubtype_allele:
- case CSeqFeatData::eSubtype_attenuator:
- case CSeqFeatData::eSubtype_CAAT_signal:
case CSeqFeatData::eSubtype_conflict:
case CSeqFeatData::eSubtype_D_loop:
- case CSeqFeatData::eSubtype_enhancer:
- case CSeqFeatData::eSubtype_GC_signal:
case CSeqFeatData::eSubtype_iDNA:
case CSeqFeatData::eSubtype_LTR:
case CSeqFeatData::eSubtype_misc_binding:
case CSeqFeatData::eSubtype_misc_difference:
case CSeqFeatData::eSubtype_misc_recomb:
case CSeqFeatData::eSubtype_misc_RNA:
- case CSeqFeatData::eSubtype_misc_signal:
case CSeqFeatData::eSubtype_misc_structure:
case CSeqFeatData::eSubtype_modified_base:
case CSeqFeatData::eSubtype_mutation:
case CSeqFeatData::eSubtype_old_sequence:
- case CSeqFeatData::eSubtype_polyA_signal:
case CSeqFeatData::eSubtype_polyA_site:
case CSeqFeatData::eSubtype_precursor_RNA:
case CSeqFeatData::eSubtype_prim_transcript:
case CSeqFeatData::eSubtype_primer_bind:
case CSeqFeatData::eSubtype_protein_bind:
- case CSeqFeatData::eSubtype_RBS:
case CSeqFeatData::eSubtype_repeat_region:
case CSeqFeatData::eSubtype_repeat_unit:
case CSeqFeatData::eSubtype_rep_origin:
case CSeqFeatData::eSubtype_satellite:
case CSeqFeatData::eSubtype_stem_loop:
case CSeqFeatData::eSubtype_STS:
- case CSeqFeatData::eSubtype_TATA_signal:
- case CSeqFeatData::eSubtype_terminator:
case CSeqFeatData::eSubtype_unsure:
case CSeqFeatData::eSubtype_variation:
case CSeqFeatData::eSubtype_3clip:
case CSeqFeatData::eSubtype_3UTR:
case CSeqFeatData::eSubtype_5clip:
case CSeqFeatData::eSubtype_5UTR:
- case CSeqFeatData::eSubtype_10_signal:
- case CSeqFeatData::eSubtype_35_signal:
- case CSeqFeatData::eSubtype_regulatory:
return;
default:
break;
@@ -1647,13 +1639,45 @@ void CFeatureItem::x_AddQuals(
const CGene_ref* gene_ref = 0;
CConstRef<CSeq_feat> gene_feat;
+ const CGene_ref* feat_gene_xref = m_Feat.GetGeneXref();
+ bool suppressed = false;
const bool gene_forbidden_if_genbank =
( subtype == CSeqFeatData::eSubtype_repeat_region ||
subtype == CSeqFeatData::eSubtype_mobile_element ||
subtype == CSeqFeatData::eSubtype_centromere ||
subtype == CSeqFeatData::eSubtype_telomere );
- const CGene_ref* feat_gene_xref = m_Feat.GetGeneXref();
+
+ if ( type == CSeqFeatData::e_Gene ) {
+ } else if (subtype != CSeqFeatData::eSubtype_operon &&
+ subtype != CSeqFeatData::eSubtype_gap &&
+ (is_not_genbank || ! gene_forbidden_if_genbank)) {
+ if (feat_gene_xref) {
+ if (feat_gene_xref->IsSuppressed()) {
+ suppressed = true;
+ }
+ }
+ if (feat_gene_xref && ! suppressed &&
+ ! CGeneFinder::ResolveGeneXref(feat_gene_xref, ctx.GetTopLevelEntry())) {
+ gene_ref = feat_gene_xref;
+ } else if (! feat_gene_xref || ! suppressed) {
+ CMappedFeat mapped_gene = GetBestGeneForFeat (m_Feat, m_Feat_Tree);
+ if (mapped_gene && subtype != CSeqFeatData::eSubtype_primer_bind) {
+ gene_feat = &mapped_gene.GetOriginalFeature();
+ gene_ref = &gene_feat->GetData().GetGene();
+ } else {
+ // e.g., check sig_peptide for gene overlapping parent CDS
+ CSeq_feat_Handle parent_feat_handle;
+ if( parentFeatureItem ) {
+ parent_feat_handle = parentFeatureItem->GetFeat();
+ }
+ CGeneFinder::GetAssociatedGeneInfo( m_Feat, ctx, m_Loc, m_GeneRef, gene_ref,
+ gene_feat, parent_feat_handle );
+ }
+ }
+ }
+
+ /*
if ( feat_gene_xref && feat_gene_xref->IsSuppressed() ) {
// suppress gene by overlap
} else if ( type != CSeqFeatData::e_Gene &&
@@ -1662,7 +1686,7 @@ void CFeatureItem::x_AddQuals(
( ! gene_forbidden_if_genbank || is_not_genbank ) )
{
CMappedFeat mapped_gene = GetBestGeneForFeat (m_Feat, m_Feat_Tree);
- if (mapped_gene) {
+ if (mapped_gene && subtype != CSeqFeatData::eSubtype_primer_bind) {
gene_feat = &mapped_gene.GetOriginalFeature();
gene_ref = &gene_feat->GetData().GetGene();
} else {
@@ -1683,6 +1707,8 @@ void CFeatureItem::x_AddQuals(
gene_ref = feat_gene_xref;
}
}
+ */
+
bool pseudo = x_GetPseudo(gene_ref, gene_feat );
//
@@ -2068,7 +2094,7 @@ void CFeatureItem::x_AddQualTranslationTable(
if ( gcode == 1 || gcode == 255 ) {
return;
}
- if ( ctx.Config().IsFormatGBSeq() || gcode != 1 ) {
+ if ( ctx.Config().IsFormatGBSeq() || gcode > 1 ) {
x_AddQual(eFQ_transl_table, new CFlatIntQVal(gcode));
}
}
@@ -2118,14 +2144,18 @@ void CFeatureItem::x_AddQualProteinConflict(
static const string conflict_msg =
"Protein sequence is in conflict with the conceptual translation";
- if ( !ctx.IsProt() || !IsMappedFromCDNA() ) {
- bool has_prot = false;
- if ( m_Feat.IsSetProduct() && m_Feat.GetProduct().GetId() != 0 ) {
- has_prot = ( sequence::GetLength( m_Feat.GetProduct(), &ctx.GetScope() ) > 0 );
- }
- const bool conflict_set = ( cdr.IsSetConflict() && cdr.GetConflict() );
- if ( has_prot && conflict_set ) {
- x_AddQual( eFQ_prot_conflict, new CFlatStringQVal( conflict_msg ) );
+ const bool conflict_set = (cdr.IsSetConflict() && cdr.GetConflict());
+
+ if (conflict_set)
+ {
+ if (!ctx.IsProt() || !IsMappedFromCDNA()) {
+ bool has_prot = false;
+ if (m_Feat.IsSetProduct() && m_Feat.GetProduct().GetId() != 0) {
+ has_prot = (sequence::GetLength(m_Feat.GetProduct(), &ctx.GetScope()) > 0);
+ }
+ if (has_prot) {
+ x_AddQual(eFQ_prot_conflict, new CFlatStringQVal(conflict_msg));
+ }
}
}
}
@@ -2201,7 +2231,7 @@ void CFeatureItem::x_GetAssociatedProtInfo(
if ( protId ) {
if ( !cfg.AlwaysTranslateCDS() ) {
CScope::EGetBioseqFlag get_flag = CScope::eGetBioseq_Loaded;
- if ( cfg.ShowFarTranslations() || ctx.IsGED() ) {
+ if ( cfg.ShowFarTranslations() || ctx.IsGED() || ctx.IsRefSeq() ) {
get_flag = CScope::eGetBioseq_All;
}
protHandle = scope.GetBioseqHandle(*protId, get_flag);
@@ -3676,6 +3706,10 @@ void CFeatureItem::x_ImportQuals(
case eFQ_replace:
{{
string s(val);
+ if (string::npos == s.find_first_not_of("ACGTUacgtu")) {
+ NStr::ToLower(s);
+ NStr::ReplaceInPlace(s, "u", "t");
+ }
replace_quals.push_back(s);
}}
break;
@@ -4101,12 +4135,12 @@ void CFeatureItem::x_FormatNoteQuals(CFlatFeature& ff) const
void CFeatureItem::x_FormatQual
(EFeatureQualifier slot,
- const CTempString & name,
+ const char* name,
CFlatFeature::TQuals& qvec,
IFlatQVal::TFlags flags) const
{
- TQCI it = const_cast<const TQuals&>(m_Quals).LowerBound(slot);
- TQCI end = const_cast<const TQuals&>(m_Quals).end();
+ TQCI it = m_Quals.LowerBound(slot);
+ TQCI end = m_Quals.end();
while (it != end && it->first == slot) {
it->second->Format(qvec, name, *GetContext(), flags);
++it;
@@ -4122,8 +4156,8 @@ void CFeatureItem::x_FormatNoteQual
{
flags |= IFlatQVal::fIsNote;
- TQCI it = const_cast<const TQuals&>(m_Quals).LowerBound(slot);
- TQCI end = const_cast<const TQuals&>(m_Quals).end();
+ TQCI it = m_Quals.LowerBound(slot);
+ TQCI end = m_Quals.end();
while (it != end && it->first == slot) {
it->second->Format(qvec, name, *GetContext(), flags);
++it;
@@ -4141,8 +4175,8 @@ void CFeatureItem::x_FormatGOQualCombined
// copy all the given quals with that name since we need to sort them
vector<CConstRef<CFlatGoQVal> > goQuals;
- TQCI it = const_cast<const TQuals&>(m_Quals).LowerBound(slot);
- TQCI end = const_cast<const TQuals&>(m_Quals).end();
+ TQCI it = m_Quals.LowerBound(slot);
+ TQCI end = m_Quals.end();
while (it != end && it->first == slot) {
goQuals.push_back( CConstRef<CFlatGoQVal>( dynamic_cast<const CFlatGoQVal*>( it->second.GetNonNullPointer() ) ) );
++it;
@@ -4885,6 +4919,7 @@ void CFeatureItem::x_AddFTableRnaQuals(
if ( !feat.GetData().IsRna() ) {
return;
}
+ const CFlatFileConfig& cfg = GetContext()->Config();
const CSeqFeatData::TRna& rna = feat.GetData().GetRna();
if (rna.IsSetExt()) {
const CRNA_ref::TExt& ext = rna.GetExt();
@@ -4913,7 +4948,9 @@ void CFeatureItem::x_AddFTableRnaQuals(
} else if ( id->IsGeneral() ) {
id_str = id->AsFastaString();
}
- x_AddFTableQual("transcript_id", id_str);
+ if (! cfg.HideProteinID()) {
+ x_AddFTableQual("transcript_id", id_str);
+ }
}
}
}
@@ -4925,6 +4962,7 @@ void CFeatureItem::x_AddFTableCdregionQuals(
// ----------------------------------------------------------------------------
{
CBioseq_Handle prod;
+ const CFlatFileConfig& cfg = GetContext()->Config();
if ( feat.IsSetProduct() ) {
prod = ctx.GetScope().GetBioseqHandle(feat.GetProductId());
}
@@ -4980,7 +5018,9 @@ void CFeatureItem::x_AddFTableCdregionQuals(
} else if ( id->IsGi() ) {
id_str = id->AsFastaString();
}
- x_AddFTableQual("protein_id", id_str);
+ if (! cfg.HideProteinID()) {
+ x_AddFTableQual("protein_id", id_str);
+ }
}
}
@@ -5329,7 +5369,8 @@ static string s_GetSpecimenVoucherText(
void CSourceFeatureItem::x_AddQuals(const COrg_ref& org, CBioseqContext& ctx) const
{
- string taxname, common;
+ CTempString taxname;
+ CTempString common;
if ( org.IsSetTaxname() ) {
taxname = org.GetTaxname();
}
@@ -5346,7 +5387,7 @@ void CSourceFeatureItem::x_AddQuals(const COrg_ref& org, CBioseqContext& ctx) co
x_AddQual(eSQ_common_name, new CFlatStringQVal(common));
}
if ( org.IsSetOrgname() ) {
- set<string> ecotypesSeen; // holds the ones we've seen so don't show them again
+ set<CTempString> ecotypesSeen; // holds the ones we've seen so don't show them again
ecotypesSeen.insert(kEmptyStr); // empty string is always considered seen so we hide it
ITERATE (COrgName::TMod, it, org.GetOrgname().GetMod()) {
@@ -5665,6 +5706,34 @@ void CSourceFeatureItem::x_FormatGBNoteQuals(CFlatFeature& ff) const
}
+static bool s_IsExactAndNonExactMatchOnNoteQuals(CFlatFeature::TQuals& qvec, const string& str)
+{
+ if (qvec.empty()) {
+ return false;
+ }
+
+ int has_exact = 0;
+ int non_exact = 0;
+
+ CFlatFeature::TQuals::iterator it = qvec.begin();
+ while (it != qvec.end()) {
+ const string& val = (*it)->GetValue();
+ if (NStr::Find(val, str) != NPOS) {
+ if (NStr::Equal(val, str)) {
+ has_exact++;
+ } else {
+ non_exact++;
+ }
+ }
+ ++it;
+ }
+
+ if (has_exact == 1 && non_exact > 0) return true;
+ return false;
+}
+
+
+
void CSourceFeatureItem::x_FormatNoteQuals(CFlatFeature& ff) const
{
CFlatFeature::TQuals qvec;
@@ -5706,7 +5775,11 @@ void CSourceFeatureItem::x_FormatNoteQuals(CFlatFeature& ff) const
DO_NOTE(frequency);
}
- x_FormatNoteQual(eSQ_metagenome_source, "derived from metagenome", qvec);
+ if (s_IsExactAndNonExactMatchOnNoteQuals(qvec, "metagenomic")) {
+ x_FormatNoteQual(eSQ_metagenome_source, "metagenomic; derived from metagenome", qvec);
+ } else {
+ x_FormatNoteQual(eSQ_metagenome_source, "derived from metagenome", qvec);
+ }
DO_NOTE(genotype);
x_FormatNoteQual(eSQ_plastid_name, "plastid", qvec);
@@ -5791,12 +5864,12 @@ CSourceFeatureItem::CSourceFeatureItem
void CSourceFeatureItem::x_FormatQual
(ESourceQualifier slot,
- const string& name,
+ const CTempString& name,
CFlatFeature::TQuals& qvec,
IFlatQVal::TFlags flags) const
{
- TQCI it = const_cast<const TQuals&>(m_Quals).LowerBound(slot);
- TQCI end = const_cast<const TQuals&>(m_Quals).end();
+ TQCI it = m_Quals.LowerBound(slot);
+ TQCI end = m_Quals.end();
while (it != end && it->first == slot) {
const IFlatQVal* qual = it->second;
qual->Format(qvec, name, *GetContext(),
diff --git a/c++/src/objtools/format/flat_file_config.cpp b/c++/src/objtools/format/flat_file_config.cpp
index fc159f8..6700df2 100644
--- a/c++/src/objtools/format/flat_file_config.cpp
+++ b/c++/src/objtools/format/flat_file_config.cpp
@@ -1,4 +1,4 @@
-/* $Id: flat_file_config.cpp 452837 2014-11-25 15:29:23Z ivanov $
+/* $Id: flat_file_config.cpp 481617 2015-10-14 14:42:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -305,13 +305,13 @@ CFlatFileConfig::CFlatFileConfig(
TGenbankBlocks genbank_blocks,
CGenbankBlockCallback* pGenbankBlockCallback,
const ICanceled * pCanceledCallback,
- bool basicCleanup ) :
+ bool basicCleanup, TCustom custom ) :
m_Format(format), m_Mode(mode), m_Style(style), m_View(view),
m_Flags(flags), m_RefSeqConventions(false), m_GffOptions(gff_options),
m_fGenbankBlocks(genbank_blocks),
m_GenbankBlockCallback(pGenbankBlockCallback),
m_pCanceledCallback(pCanceledCallback),
- m_BasicCleanup(basicCleanup)
+ m_BasicCleanup(basicCleanup), m_Custom(custom)
{
// GFF/GFF3 and FTable always require master style
if (m_Format == eFormat_GFF || m_Format == eFormat_GFF3 ||
@@ -554,6 +554,13 @@ void CFlatFileConfig::AddArgumentDescriptions(CArgDescriptions& args)
CArgDescriptions::eInteger, "0");
+ // custom (default: 0)
+ arg_desc->AddDefaultKey("custom", "Custom",
+ "Custom flat file output bits. The value is the bitwise OR (logical addition) of:\n"
+ " 1 - hide protein_id and transcript_id",
+
+ CArgDescriptions::eInteger, "0");
+
arg_desc->AddOptionalKey("showblocks", "COMMA_SEPARATED_BLOCK_LIST",
"Use this to only show certain parts of the flatfile (e.g. '-showblocks locus,defline'). "
"These are all possible values for block names: " + NStr::Join(CFlatFileConfig::GetAllGenbankStrings(), ", "),
@@ -577,6 +584,9 @@ void CFlatFileConfig::AddArgumentDescriptions(CArgDescriptions& args)
arg_desc->AddFlag("resolve-all",
"Resolves all, e.g. for contigs.");
+ arg_desc->AddOptionalKey("depth", "Depth",
+ "Exploration depth", CArgDescriptions::eInteger);
+
arg_desc->AddFlag("show-flags",
"Describe the current flag set in ENUM terms");
@@ -774,6 +784,14 @@ CFlatFileConfig::EFlags x_GetFlags(const CArgs& args)
}
+CFlatFileConfig::ECustom x_GetCustom(const CArgs& args)
+{
+ int custom = args["custom"].AsInteger();
+
+ return (CFlatFileConfig::ECustom)custom;
+}
+
+
CFlatFileConfig::EView x_GetView(const CArgs& args)
{
const string& view = args["view"].AsString();
@@ -832,6 +850,7 @@ void CFlatFileConfig::FromArguments(const CArgs& args)
CFlatFileConfig::EView view = x_GetView(args);
CFlatFileConfig::EGffOptions gff_options = CFlatFileConfig::fGffGTFCompat;
CFlatFileConfig::TGenbankBlocks genbank_blocks = x_GetGenbankBlocks(args);
+ CFlatFileConfig::ECustom custom = x_GetCustom(args);
SetFormat(format);
SetMode(mode);
@@ -841,6 +860,7 @@ void CFlatFileConfig::FromArguments(const CArgs& args)
m_GffOptions = gff_options;
m_fGenbankBlocks = genbank_blocks;
m_BasicCleanup = args["cleanup"];
+ SetCustom(custom);
}
END_SCOPE(objects)
diff --git a/c++/src/objtools/format/flat_file_generator.cpp b/c++/src/objtools/format/flat_file_generator.cpp
index 44814f2..e9a4e17 100644
--- a/c++/src/objtools/format/flat_file_generator.cpp
+++ b/c++/src/objtools/format/flat_file_generator.cpp
@@ -1,4 +1,4 @@
-/* $Id: flat_file_generator.cpp 435165 2014-05-14 13:21:26Z gotvyans $
+/* $Id: flat_file_generator.cpp 481618 2015-10-14 14:42:22Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -80,8 +80,9 @@ CFlatFileGenerator::CFlatFileGenerator
CFlatFileConfig::TMode mode,
CFlatFileConfig::TStyle style,
CFlatFileConfig::TFlags flags,
- CFlatFileConfig::TView view) :
- m_Ctx(new CFlatFileContext(CFlatFileConfig(format, mode, style, flags, view)))
+ CFlatFileConfig::TView view,
+ CFlatFileConfig::TCustom custom) :
+ m_Ctx(new CFlatFileContext(CFlatFileConfig(format, mode, style, flags, view, custom)))
{
if ( !m_Ctx ) {
NCBI_THROW(CFlatException, eInternal, "Unable to initialize context");
@@ -103,6 +104,10 @@ SAnnotSelector& CFlatFileGenerator::SetAnnotSelector(void)
return m_Ctx->SetAnnotSelector();
}
+void CFlatFileGenerator::SetFeatTree(feature::CFeatTree* tree)
+{
+ m_Ctx->SetFeatTree(tree);
+}
// Generate a flat-file report for a Seq-entry
// (the other CFlatFileGenerator::Generate functions ultimately
diff --git a/c++/src/objtools/format/flat_qual_slots.cpp b/c++/src/objtools/format/flat_qual_slots.cpp
index 9b50bc3..dc2cce0 100644
--- a/c++/src/objtools/format/flat_qual_slots.cpp
+++ b/c++/src/objtools/format/flat_qual_slots.cpp
@@ -1,4 +1,4 @@
-/* $Id: flat_qual_slots.cpp 450158 2014-10-23 14:04:08Z ivanov $
+/* $Id: flat_qual_slots.cpp 449759 2014-10-20 19:44:53Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/format/flat_seqloc.cpp b/c++/src/objtools/format/flat_seqloc.cpp
index 6ace4c1..d77b266 100644
--- a/c++/src/objtools/format/flat_seqloc.cpp
+++ b/c++/src/objtools/format/flat_seqloc.cpp
@@ -1,4 +1,4 @@
-/* $Id: flat_seqloc.cpp 405740 2013-07-08 18:14:10Z kornbluh $
+/* $Id: flat_seqloc.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -47,7 +47,7 @@
#include <objtools/format/items/flat_seqloc.hpp>
#include <objtools/format/context.hpp>
#include <algorithm>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
diff --git a/c++/src/objtools/format/gather_items.cpp b/c++/src/objtools/format/gather_items.cpp
index e66db17..8d04f44 100644
--- a/c++/src/objtools/format/gather_items.cpp
+++ b/c++/src/objtools/format/gather_items.cpp
@@ -1,4 +1,4 @@
-/* $Id: gather_items.cpp 462431 2015-03-18 17:23:52Z ivanov $
+/* $Id: gather_items.cpp 478453 2015-09-09 15:25:04Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -101,12 +101,11 @@
#include <objtools/format/gather_iter.hpp>
#include <objtools/format/genbank_gather.hpp>
#include <objtools/format/embl_gather.hpp>
-#include <objtools/format/gff_gather.hpp>
#include <objtools/format/ftable_gather.hpp>
#include <objtools/format/feature_gather.hpp>
#include <objtools/format/context.hpp>
#include <objtools/error_codes.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
#include <connect/ncbi_socket.hpp>
@@ -185,10 +184,6 @@ CFlatGatherer* CFlatGatherer::New(CFlatFileConfig::TFormat format)
case CFlatFileConfig::eFormat_EMBL:
return new CEmblGatherer;
- case CFlatFileConfig::eFormat_GFF:
- case CFlatFileConfig::eFormat_GFF3:
- return new CGFFGatherer;
-
case CFlatFileConfig::eFormat_FTable:
return new CFtableGatherer;
@@ -223,7 +218,7 @@ void CFlatGatherer::Gather(CFlatFileContext& ctx, CFlatItemOStream& os) const
CConstRef<IFlatItem> item;
item.Reset( new CStartItem() );
os << item;
- x_GatherSeqEntry(ctx.GetEntry(), topLevelSeqEntryContext);
+ x_GatherSeqEntry(ctx, topLevelSeqEntryContext);
item.Reset( new CEndItem() );
os << item;
}
@@ -238,16 +233,19 @@ CFlatGatherer::~CFlatGatherer(void)
//
// Protected:
-void CFlatGatherer::x_GatherSeqEntry(const CSeq_entry_Handle& entry,
+void CFlatGatherer::x_GatherSeqEntry(CFlatFileContext& ctx,
CRef<CTopLevelSeqEntryContext> topLevelSeqEntryContext) const
{
- m_TopSEH = entry;
- CFeat_CI iter (m_TopSEH);
- m_Feat_Tree.Reset (new feature::CFeatTree (iter));
+ m_TopSEH = ctx.GetEntry();
+ m_Feat_Tree.Reset(ctx.GetFeatTree());
+ if (m_Feat_Tree.Empty()) {
+ CFeat_CI iter (m_TopSEH);
+ m_Feat_Tree.Reset (new feature::CFeatTree (iter));
+ }
// visit bioseqs in the entry (excluding segments)
- CGather_Iter seq_iter(entry, Config());
+ CGather_Iter seq_iter(m_TopSEH, Config());
CBioseq_Handle prev_seq;
CBioseq_Handle this_seq;
CBioseq_Handle next_seq;
@@ -774,7 +772,9 @@ void CFlatGatherer::x_GatherComments(void) const
// There are some comments that we want to know the existence of right away, but we don't
// want to add until later:
- CConstRef<CUser_object> firstGenAnnotSCAD = x_PrepareAnnotDescStrucComment(ctx);
+ // CConstRef<CUser_object> firstGenAnnotSCAD = x_PrepareAnnotDescStrucComment(ctx);
+
+ m_FirstGenAnnotSCAD = x_PrepareAnnotDescStrucComment(ctx);
x_UnverifiedComment(ctx);
@@ -782,9 +782,9 @@ void CFlatGatherer::x_GatherComments(void) const
// Gather comments related to the seq-id
x_IdComments(ctx,
- ( firstGenAnnotSCAD ? eGenomeAnnotComment_No : eGenomeAnnotComment_Yes ) );
+ ( m_FirstGenAnnotSCAD ? eGenomeAnnotComment_No : eGenomeAnnotComment_Yes ) );
x_RefSeqComments(ctx,
- ( firstGenAnnotSCAD ? eGenomeAnnotComment_No : eGenomeAnnotComment_Yes ) );
+ ( m_FirstGenAnnotSCAD ? eGenomeAnnotComment_No : eGenomeAnnotComment_Yes ) );
/*
if ( s_NsAreGaps(ctx.GetHandle(), ctx) ) {
@@ -796,6 +796,7 @@ void CFlatGatherer::x_GatherComments(void) const
x_RefSeqGenomeComments(ctx);
x_WGSComment(ctx);
x_TSAComment(ctx);
+ x_UnorderedComments(ctx);
if ( ctx.ShowGBBSource() ) {
x_GBBSourceComment(ctx);
}
@@ -803,18 +804,15 @@ void CFlatGatherer::x_GatherComments(void) const
x_MaplocComments(ctx);
x_RegionComments(ctx);
x_NameComments(ctx);
+ x_BasemodComment(ctx);
x_StructuredComments(ctx);
x_HTGSComments(ctx);
if( ctx.ShowAnnotCommentAsCOMMENT() ) {
x_AnnotComments(ctx);
}
- if( firstGenAnnotSCAD ) {
- x_AddComment(new CCommentItem(*firstGenAnnotSCAD, ctx));
- }
// x_FeatComments(ctx);
x_MapComment(ctx);
- x_BasemodComment(ctx);
x_RemoveDupComments();
x_RemoveExcessNewlines();
@@ -935,12 +933,12 @@ void CFlatGatherer::x_UnverifiedComment(CBioseqContext& ctx) const
static const string kUnverifiedPrefix = "GenBank staff is unable to verify ";
static const string kUnverifiedSuffix = " provided by the submitter.";
- typedef pair<CBioseqContext::TUnverified, const string> TUnverifiedElem;
+ typedef SStaticPair<CBioseqContext::TUnverified, const char*> TUnverifiedElem;
static const TUnverifiedElem sc_unverified_map[] = {
- TUnverifiedElem(CBioseqContext::fUnverified_Organism, "source organism"),
- TUnverifiedElem(CBioseqContext::fUnverified_SequenceOrAnnotation, "sequence and/or annotation")
+ { CBioseqContext::fUnverified_Organism, "source organism" },
+ { CBioseqContext::fUnverified_SequenceOrAnnotation, "sequence and/or annotation" }
};
- typedef CStaticArrayMap<CBioseqContext::TUnverified, const string> TUnverifiedMap;
+ typedef CStaticArrayMap<CBioseqContext::TUnverified, const char*> TUnverifiedMap;
DEFINE_STATIC_ARRAY_MAP(TUnverifiedMap, sc_UnverifiedMap, sc_unverified_map);
vector<string> arr_type_string;
@@ -1290,8 +1288,41 @@ void CFlatGatherer::x_NameComments(CBioseqContext& ctx) const
void CFlatGatherer::x_StructuredComments(CBioseqContext& ctx) const
{
for (CSeqdesc_CI it(ctx.GetHandle(), CSeqdesc::e_User); it; ++it) {
+ const CSeqdesc & desc = *it;
+ if (m_FirstGenAnnotSCAD && desc.IsUser()) {
+ const CUser_object& usr = desc.GetUser();
+ const CUser_object& fst = *m_FirstGenAnnotSCAD;
+ if (&usr == &fst) {
+ m_FirstGenAnnotSCAD.Reset();
+ }
+ }
x_AddComment(new CCommentItem(*it, ctx));
}
+ if ( m_FirstGenAnnotSCAD ) {
+ x_AddComment(new CCommentItem(*m_FirstGenAnnotSCAD, ctx));
+ }
+}
+
+void CFlatGatherer::x_UnorderedComments(CBioseqContext& ctx) const
+{
+ CSeqdesc_CI desc(ctx.GetHandle(), CSeqdesc::e_Genbank);
+ if ( !desc ) {
+ return;
+ }
+ const list<string>* keywords = NULL;
+ const CGB_block& gb = desc->GetGenbank();
+ if (gb.CanGetKeywords()) {
+ keywords = &(gb.GetKeywords());
+ if (keywords != NULL) {
+ ITERATE (list<string>, kwd, *keywords) {
+ if (NStr::EqualNocase (*kwd, "UNORDERED")) {
+ x_AddComment(new CCommentItem(
+ CCommentItem::GetStringForUnordered(ctx), ctx, &(*desc)));
+ return;
+ }
+ }
+ }
+ }
}
void CFlatGatherer::x_HTGSComments(CBioseqContext& ctx) const
@@ -1458,7 +1489,7 @@ void CFlatGatherer::x_FeatComments(CBioseqContext& ctx) const
for (CFeat_CI it(ctx.GetScope(), loc, CSeqFeatData::e_Comment);
it; ++it) {
- ECompare comp = Compare(it->GetLocation(), loc, scope);
+ ECompare comp = Compare(it->GetLocation(), loc, scope, fCompareOverlapping);
if ((comp == eSame) || (comp == eContains)) {
x_AddComment(new CCommentItem(it->GetOriginalFeature(), ctx));
@@ -2516,7 +2547,7 @@ void CFlatGatherer::x_GatherFeaturesOnLocation
CSeq_id seq_id;
seq_id.Assign( *ctx.GetHandle().GetSeqId() );
- const size_t new_len = sequence::GetLength( ctx.GetLocation(), &scope );
+ const TSeqPos new_len = sequence::GetLength( ctx.GetLocation(), &scope );
CSeq_loc old_loc;
old_loc.SetInt().SetId( seq_id );
@@ -2833,46 +2864,50 @@ void CFlatGatherer::x_GatherFeatures(void) const
feat_it = CFeat_CI(handle, sel);
}
if (feat_it) {
- CMappedFeat cds = *feat_it;
-
- // map CDS location to its location on the product
- CSeq_loc_Mapper mapper(*cds.GetOriginalSeq_feat(),
- CSeq_loc_Mapper::eLocationToProduct,
- &ctx.GetScope());
- mapper.SetFuzzOption( CSeq_loc_Mapper::fFuzzOption_CStyle | CSeq_loc_Mapper::fFuzzOption_RemoveLimTlOrTr );
- CRef<CSeq_loc> cds_prod = mapper.Map(cds.GetLocation());
- cds_prod = cds_prod->Merge( ( s_IsCircularTopology(ctx) ? CSeq_loc::fMerge_All : CSeq_loc::fSortAndMerge_All ), NULL );
-
- // it's a common case that we map one residue past the edge of the protein (e.g. NM_131089).
- // In that case, we shrink the cds's location back one residue.
- if( cds_prod->IsInt() && cds.GetProduct().IsWhole() ) {
- const CSeq_id *cds_prod_seq_id = cds.GetProduct().GetId();
- if( cds_prod_seq_id != NULL ) {
- CBioseq_Handle prod_bioseq_handle = ctx.GetScope().GetBioseqHandle( *cds_prod_seq_id );
- if( prod_bioseq_handle ) {
- const TSeqPos bioseq_len = prod_bioseq_handle.GetBioseqLength();
- if( cds_prod->GetInt().GetTo() >= bioseq_len ) {
- cds_prod->SetInt().SetTo( bioseq_len - 1 );
+ try {
+ CMappedFeat cds = *feat_it;
+
+ // map CDS location to its location on the product
+ CSeq_loc_Mapper mapper(*cds.GetOriginalSeq_feat(),
+ CSeq_loc_Mapper::eLocationToProduct,
+ &ctx.GetScope());
+ mapper.SetFuzzOption( CSeq_loc_Mapper::fFuzzOption_CStyle | CSeq_loc_Mapper::fFuzzOption_RemoveLimTlOrTr );
+ CRef<CSeq_loc> cds_prod = mapper.Map(cds.GetLocation());
+ cds_prod = cds_prod->Merge( ( s_IsCircularTopology(ctx) ? CSeq_loc::fMerge_All : CSeq_loc::fSortAndMerge_All ), NULL );
+
+ // it's a common case that we map one residue past the edge of the protein (e.g. NM_131089).
+ // In that case, we shrink the cds's location back one residue.
+ if( cds_prod->IsInt() && cds.GetProduct().IsWhole() ) {
+ const CSeq_id *cds_prod_seq_id = cds.GetProduct().GetId();
+ if( cds_prod_seq_id != NULL ) {
+ CBioseq_Handle prod_bioseq_handle = ctx.GetScope().GetBioseqHandle( *cds_prod_seq_id );
+ if( prod_bioseq_handle ) {
+ const TSeqPos bioseq_len = prod_bioseq_handle.GetBioseqLength();
+ if( cds_prod->GetInt().GetTo() >= bioseq_len ) {
+ cds_prod->SetInt().SetTo( bioseq_len - 1 );
+ }
}
}
}
- }
- // if there are any gaps in the location, we know that there was an issue with the mapping, so
- // we fall back on the product.
- if( s_ContainsGaps(*cds_prod) ) {
- cds_prod->Assign( cds.GetProduct() );
- }
+ // if there are any gaps in the location, we know that there was an issue with the mapping, so
+ // we fall back on the product.
+ if( s_ContainsGaps(*cds_prod) ) {
+ cds_prod->Assign( cds.GetProduct() );
+ }
- // remove fuzz
- cds_prod->SetPartialStart( false, eExtreme_Positional );
- cds_prod->SetPartialStop ( false, eExtreme_Positional );
+ // remove fuzz
+ cds_prod->SetPartialStart( false, eExtreme_Positional );
+ cds_prod->SetPartialStop ( false, eExtreme_Positional );
- item.Reset(
- x_NewFeatureItem(cds, ctx, &*cds_prod, m_Feat_Tree,
- CFeatureItem::eMapped_from_cdna) );
+ item.Reset(
+ x_NewFeatureItem(cds, ctx, &*cds_prod, m_Feat_Tree,
+ CFeatureItem::eMapped_from_cdna) );
- out << item;
+ out << item;
+ } catch (CAnnotMapperException& e) {
+ LOG_POST_X(2, Error << e );
+ }
}
// look for Prot features (only for RefSeq records or
@@ -2955,8 +2990,8 @@ void s_FixIntervalProtToCds(
// [3] Coordintates are relative to coding region + codon_start.
//
- size_t uRawFrom = srcInt.GetFrom() * 3;
- size_t uRawTo = srcInt.GetTo() * 3 + 2;
+ TSeqPos uRawFrom = srcInt.GetFrom() * 3;
+ TSeqPos uRawTo = srcInt.GetTo() * 3 + 2;
const CSeqFeatData::TCdregion& srcCdr = srcFeat.GetData().GetCdregion();
if ( srcInt.CanGetStrand() ) {
diff --git a/c++/src/objtools/format/gbseq_formatter.cpp b/c++/src/objtools/format/gbseq_formatter.cpp
index 14c2663..43c49aa 100644
--- a/c++/src/objtools/format/gbseq_formatter.cpp
+++ b/c++/src/objtools/format/gbseq_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: gbseq_formatter.cpp 440004 2014-07-08 17:42:12Z kans $
+/* $Id: gbseq_formatter.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -67,7 +67,7 @@
#include <objtools/format/items/segment_item.hpp>
#include <objtools/format/items/contig_item.hpp>
#include <objtools/format/items/genome_project_item.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -274,6 +274,8 @@ void CGBSeqFormatter::FormatLocus
CGBSeq::TMoltype sMolType = s_GBSeqMoltype(locus.GetBiomol());
if( ! sMolType.empty() ) {
m_GBSeq->SetMoltype(sMolType);
+ } else if (ctx.IsProt()) {
+ m_GBSeq->SetMoltype("AA");
}
CGBSeq::TStrandedness sStrandedness =
s_GBSeqStrandedness(locus.GetStrand(), locus.GetBiomol());
diff --git a/c++/src/objtools/format/genbank_formatter.cpp b/c++/src/objtools/format/genbank_formatter.cpp
index 3749c59..540ca0d 100644
--- a/c++/src/objtools/format/genbank_formatter.cpp
+++ b/c++/src/objtools/format/genbank_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: genbank_formatter.cpp 434574 2014-05-08 16:24:45Z vasilche $
+/* $Id: genbank_formatter.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -69,7 +69,7 @@
#include <objtools/format/items/html_anchor_item.hpp>
#include <objtools/format/context.hpp>
#include <objtools/format/ostream_text_ostream.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
#include <algorithm>
#include <stdio.h>
@@ -132,16 +132,24 @@ namespace {
virtual void AddParagraph(const list< string > &text, const CSerialObject *obj)
{
+ size_t add_size = m_block_text_str.size();
ITERATE(list<string>, line, text) {
- m_block_text_str += *line;
- m_block_text_str += '\n';
+ add_size += (line->size() + 1);
+ }
+ m_block_text_str.reserve(max(m_block_text_str.capacity(), add_size));
+ ITERATE(list<string>, line, text) {
+ AddLine(*line, obj, eAddNewline_Yes);
}
}
virtual void AddLine( const CTempString &line, const CSerialObject *obj,
EAddNewline add_newline )
{
- m_block_text_str += line;
+ m_block_text_str.reserve(max(m_block_text_str.capacity(),
+ m_block_text_str.length() +
+ line.size() +
+ (add_newline == eAddNewline_Yes?1:0) ) );
+ m_block_text_str.append(line.data(), line.size());
if( add_newline == eAddNewline_Yes ) {
m_block_text_str += '\n';
}
@@ -853,6 +861,9 @@ void CGenbankFormatter::x_Authors
string authors;
if (ref.IsSetAuthors()) {
CReferenceItem::FormatAuthors(ref.GetAuthors(), authors);
+ if (NStr::EqualNocase(authors, "?")) {
+ authors = ".";
+ }
}
if( authors.empty() ) {
if( NStr::IsBlank(ref.GetConsortium()) ) {
@@ -875,6 +886,7 @@ void CGenbankFormatter::x_Authors
if (!NStr::EndsWith(authors, '.')) {
authors += '.';
}
+ CleanAndCompress(authors, authors.c_str());
if( ref.GetContext()->Config().DoHTML() ) {
TryToSanitizeHtml( authors );
}
@@ -968,7 +980,7 @@ void CGenbankFormatter::x_Pubmed
string strPubmed = NStr::IntToString( ref.GetPMID() );
if ( ctx.Config().DoHTML() ) {
string strRaw = strPubmed;
- strPubmed = "<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/";
+ strPubmed = "<a href=\"https://www.ncbi.nlm.nih.gov/pubmed/";
strPubmed += strRaw;
strPubmed += "\">";
strPubmed += strRaw;
@@ -1139,9 +1151,10 @@ CGenbankFormatter::x_LocusHtmlPrefix( string &first_line, CBioseqContext& ctx )
first_line = CNcbiOstrstreamToString(result);
}
-string
+void
CGenbankFormatter::x_GetFeatureSpanAndScriptStart(
- const char * strKey,
+ IFlatTextOStream& text_os,
+ const CTempString& strKey,
const CSeq_loc &feat_loc,
CBioseqContext& ctx )
{
@@ -1176,7 +1189,8 @@ CGenbankFormatter::x_GetFeatureSpanAndScriptStart(
s_PrintLocAsJavascriptArray( ctx, pre_feature_html, feat_loc );
pre_feature_html << ");</script>";
- return CNcbiOstrstreamToString(pre_feature_html);
+ string temp = CNcbiOstrstreamToString(pre_feature_html);
+ text_os.AddLine(temp, 0, IFlatTextOStream::eAddNewline_No);
}
///////////////////////////////////////////////////////////////////////////
@@ -1318,7 +1332,7 @@ void CGenbankFormatter::FormatFeatHeader
// ============================================================================
bool s_GetFeatureKeyLinkLocation(
- CMappedFeat feat,
+ const CMappedFeat& feat,
TGi& iGi,
unsigned int& iFrom, // one based
unsigned int& iTo ) // one based
@@ -1347,17 +1361,18 @@ bool s_GetFeatureKeyLinkLocation(
}
// ============================================================================
-string s_GetLinkFeatureKey(
+bool s_GetLinkFeatureKey(
const CFeatureItemBase& item,
+ const CFlatFeature& feat,
+ const string& strRawKey,
+ string& strLink,
unsigned int uItemNumber = 0 )
// ============================================================================
{
- CConstRef<CFlatFeature> feat = item.Format();
- string strRawKey = feat->GetKey();
if ( strRawKey == "gap" || strRawKey == "assembly_gap" ||
strRawKey == "source" )
{
- return strRawKey;
+ return false;
}
TGi iGi = ZERO_GI;
@@ -1367,7 +1382,7 @@ string s_GetLinkFeatureKey(
iGi = item.GetContext()->GetGI();
}
if ( iFrom == 0 && iFrom == iTo ) {
- return strRawKey;
+ return false;
}
// check if this is a protein or nucleotide link
@@ -1386,38 +1401,135 @@ string s_GetLinkFeatureKey(
}
}}
- // link base
- string strLinkbase;
- if( is_prot ) {
- strLinkbase += strLinkBaseProt;
- } else {
- strLinkbase += strLinkBaseNuc;
- }
-
- // id
- string strId = NStr::NumericToString(iGi);
-
- // location
- string strLocation;
- if( item.GetFeat().GetLocation().IsInt() || item.GetFeat().GetLocation().IsPnt() ) {
- strLocation += "?from=";
- strLocation += NStr::IntToString( iFrom );
- strLocation += "&to=";
- strLocation += NStr::IntToString( iTo );
- } else if(strRawKey != "Precursor") {
- // TODO: this fails on URLs that require "?itemID=" (e.g. almost any, such as U54469)
- strLocation += "?itemid=TBD";
- }
-
// assembly of the actual string:
- string strLink = "<a href=\"";
- strLink += strLinkbase;
- strLink += strId;
- strLink += strLocation;
- strLink += "\">";
+ strLink.reserve(100); // euristical URL length
+
+ strLink = "<a href=\"";
+
+ // link base
+ if (is_prot) {
+ strLink += strLinkBaseProt;
+ }
+ else {
+ strLink += strLinkBaseNuc;
+ }
+ strLink += NStr::NumericToString(iGi);
+
+ // location
+ if (item.GetFeat().GetLocation().IsInt() || item.GetFeat().GetLocation().IsPnt()) {
+ strLink += "?from=";
+ strLink += NStr::IntToString(iFrom);
+ strLink += "&to=";
+ strLink += NStr::IntToString(iTo);
+ }
+ else if (strRawKey != "Precursor") {
+ // TODO: this fails on URLs that require "?itemID=" (e.g. almost any, such as U54469)
+ strLink += "?itemid=TBD";
+ }
+
+ strLink += "\">";
strLink += strRawKey;
strLink += "</a>";
- return strLink;
+ return true;
+}
+
+class CGenbankFormatterWrapDest : public NStr::IWrapDest
+{
+public:
+ CGenbankFormatterWrapDest(IFlatTextOStream& s) : m_text_os(s) {};
+ IFlatTextOStream& m_text_os;
+ virtual void Append(const string& s)
+ {
+ Append(CTempString(s));
+ }
+ virtual void Append(const CTempString& s)
+ {
+ m_text_os.AddLine(NStr::TruncateSpaces_Unsafe(s, NStr::eTrunc_End));
+ }
+};
+
+void CGenbankFormatter::x_SmartWrapQuals(const CFeatureItemBase& feat, const CFlatFeature& ff, IFlatTextOStream& text_os)
+{
+ // reuse some variable in the loop
+ string prefix1;
+ string value;
+ string sanitized;
+
+ const vector<CRef<CFormatQual> > & quals = ff.GetQuals();
+ bool bHtml = feat.GetContext()->Config().DoHTML();
+
+ ITERATE(vector<CRef<CFormatQual> >, it, quals) {
+ const string& qual = (*it)->GetName();
+ const string& prefix = GetFeatIndent();
+
+ prefix1 = prefix;
+
+ switch ((*it)->GetTrim()) {
+ case CFormatQual::eTrim_Normal:
+ TrimSpacesAndJunkFromEnds(value, (*it)->GetValue(), true);
+ break;
+ case CFormatQual::eTrim_WhitespaceOnly:
+ value = NStr::TruncateSpaces_Unsafe((*it)->GetValue());
+ break;
+ default:
+ value = (*it)->GetValue();
+ }
+
+ if (bHtml) {
+ TryToSanitizeHtml(sanitized, value);
+ }
+
+ switch ((*it)->GetStyle()) {
+ case CFormatQual::eEmpty:
+ prefix1 += '/';
+ value = qual;
+ break;
+ case CFormatQual::eQuoted:
+ if (bHtml) sanitized += '"'; else value += '"';
+ prefix1 += '/';
+ prefix1 += qual;
+ prefix1 += "=\"";
+ break;
+ case CFormatQual::eUnquoted:
+ prefix1 += '/';
+ prefix1 += qual;
+ prefix1 += '=';
+ break;
+ }
+ // Call NStr::Wrap directly to avoid unwanted line breaks right
+ // before the start of the value (in /translation, e.g.)
+#if 1
+ CGenbankFormatterWrapDest dest(text_os);
+ NStr::Wrap((bHtml) ? sanitized : value, GetWidth(), dest, SetWrapFlags(), &prefix, &prefix1);
+#else
+ NStr::Wrap((bHtml) ? sanitized : value, GetWidth(), l_new, SetWrapFlags(), prefix, prefix1);
+
+ if (l_new.size() > 1) {
+ const string &last_line = l_new.back();
+
+ list<string>::const_iterator end_iter = l_new.end();
+ end_iter--;
+ end_iter--;
+ const string &second_to_last_line = *end_iter;
+
+ if (NStr::TruncateSpaces(last_line) == "\"" && second_to_last_line.length() < GetWidth()) {
+ l_new.pop_back();
+ l_new.back() += "\"";
+ }
+ }
+ // Values of qualifiers coming down this path do not carry additional
+ // internal format (at least, they aren't supposed to). So we strip extra
+ // blanks from both the begin and the end of qualifier lines.
+ // (May have to be amended once sizeable numbers of violators are found
+ // in existing data).
+ NON_CONST_ITERATE(list<string>, it, l_new) {
+ //NStr::TruncateSpacesInPlace(*it, NStr::eTrunc_End);
+ text_os.AddLine(NStr::TruncateSpaces_Unsafe(*it, NStr::eTrunc_End));
+ }
+ //l.insert(l.end(), l_new.begin(), l_new.end());
+ //l_new.clear();
+#endif
+ }
}
// ============================================================================
@@ -1427,35 +1539,42 @@ void CGenbankFormatter::FormatFeature
// ============================================================================
{
CRef<IFlatTextOStream> p_text_os;
- IFlatTextOStream *ostrm = NULL;
- {
- // this works differently from the others because we have to check
- // the underlying type
- const CSourceFeatureItem *p_source_feature_item =
- dynamic_cast<const CSourceFeatureItem *>(&f);
- if( ostrm == NULL && p_source_feature_item ) {
- ostrm = &s_WrapOstreamIfCallbackExists(p_text_os, *p_source_feature_item, orig_text_os);
- }
- const CFeatureItem *p_feature_item =
- dynamic_cast<const CFeatureItem *>(&f);
- if( ostrm == NULL && p_feature_item ) {
- ostrm = &s_WrapOstreamIfCallbackExists(p_text_os, *p_feature_item, orig_text_os);
- }
- _ASSERT( ostrm != NULL );
+ IFlatTextOStream *text_os = NULL;
+ {
+ // this works differently from the others because we have to check
+ // the underlying type
+ const CSourceFeatureItem *p_source_feature_item =
+ dynamic_cast<const CSourceFeatureItem *>(&f);
+ if (p_source_feature_item) {
+ text_os = &s_WrapOstreamIfCallbackExists(p_text_os, *p_source_feature_item, orig_text_os);
+ }
+ else
+ {
+ const CFeatureItem *p_feature_item =
+ dynamic_cast<const CFeatureItem *>(&f);
+ if (text_os == NULL && p_feature_item) {
+ text_os = &s_WrapOstreamIfCallbackExists(p_text_os, *p_feature_item, orig_text_os);
+ }
+ }
+ _ASSERT(text_os != NULL);
}
- IFlatTextOStream & text_os = *ostrm;
bool bHtml = f.GetContext()->Config().DoHTML();
CConstRef<CFlatFeature> feat = f.Format();
- const vector<CRef<CFormatQual> > & quals = feat->GetQuals();
- list<string> l, l_new;
if ( feat->GetKey() != "source" ) {
++ m_uFeatureCount;
}
- string strKey = feat->GetKey();
+ const string& strKey = feat->GetKey();
+ // write <span...> and <script...> in HTML mode
+ if (bHtml && f.GetContext()->Config().IsModeEntrez() && f.GetContext()->Config().ShowSeqSpans()) {
+ x_GetFeatureSpanAndScriptStart(*text_os, strKey, f.GetLoc(), *f.GetContext());
+ }
+
+#if 1
+ list<string> l;
Wrap(l, strKey, feat->GetLoc().GetString(), eFeat );
// In HTML mode, if not taking a "slice" (i.e. -from and -to args )
@@ -1464,80 +1583,27 @@ void CGenbankFormatter::FormatFeature
// we will need to pad since the feature's key might be smaller than strDummy
// negative padding means we need to remove spaces.
// const int padding_needed = (int)strDummy.length() - (int)feat->GetKey().length();
- string strFeatKey = s_GetLinkFeatureKey( f, m_uFeatureCount );
- // strFeatKey += string( padding_needed, ' ' );
-
- NON_CONST_ITERATE( list<string>, it, l ) {
- // string::size_type dummy_loc = (*it).find(strDummy);
- NStr::ReplaceInPlace( *it, strKey, strFeatKey );
- }
+ string strFeatKey;
+ if (s_GetLinkFeatureKey(f, *feat, strKey, strFeatKey, m_uFeatureCount))
+ {
+ // strFeatKey += string( padding_needed, ' ' );
+ NON_CONST_ITERATE(list<string>, it, l) {
+ // string::size_type dummy_loc = (*it).find(strDummy);
+ NStr::ReplaceInPlace( *it, strKey, strFeatKey );
+ }
+ }
}
- // write <span...> and <script...> in HTML mode
- if( bHtml && f.GetContext()->Config().IsModeEntrez() && f.GetContext()->Config().ShowSeqSpans() ) {
- *l.begin() = x_GetFeatureSpanAndScriptStart(strKey.c_str(), f.GetLoc(), *f.GetContext() ) + *l.begin();
- }
-
- ITERATE (vector<CRef<CFormatQual> >, it, quals ) {
- string qual = '/' + (*it)->GetName(), value = (*it)->GetValue();
- switch ( (*it)->GetTrim() ) {
- case CFormatQual::eTrim_Normal:
- TrimSpacesAndJunkFromEnds( value, true );
- break;
- case CFormatQual::eTrim_WhitespaceOnly:
- NStr::TruncateSpacesInPlace( value );
- break;
- }
- if( bHtml ) {
- TryToSanitizeHtml( value );
- }
+#else
+#endif
- switch ((*it)->GetStyle()) {
- case CFormatQual::eEmpty:
- value = qual;
- qual.erase();
- break;
- case CFormatQual::eQuoted:
- qual += "=\""; value += '"';
- break;
- case CFormatQual::eUnquoted:
- qual += '=';
- break;
- }
- // Call NStr::Wrap directly to avoid unwanted line breaks right
- // before the start of the value (in /translation, e.g.)
- NStr::Wrap(value, GetWidth(), l_new, SetWrapFlags(), GetFeatIndent(),
- GetFeatIndent() + qual);
- if ( l_new.size() > 1 ) {
- const string &last_line = l_new.back();
-
- list<string>::const_iterator end_iter = l_new.end();
- end_iter--;
- end_iter--;
- const string &second_to_last_line = *end_iter;
-
- if( NStr::TruncateSpaces( last_line ) == "\"" && second_to_last_line.length() < GetWidth() ) {
- l_new.pop_back();
- l_new.back() += "\"";
- }
- }
- // Values of qualifiers coming down this path do not carry additional
- // internal format (at least, they aren't supposed to). So we strip extra
- // blanks from both the begin and the end of qualifier lines.
- // (May have to be amended once sizeable numbers of violators are found
- // in existing data).
- NON_CONST_ITERATE (list<string>, it, l_new) {
- NStr::TruncateSpacesInPlace( *it, NStr::eTrunc_End );
- }
- l.insert( l.end(), l_new.begin(), l_new.end() );
- l_new.clear();
- }
-
- text_os.AddParagraph(l, f.GetObject());
+ text_os->AddParagraph(l, f.GetObject());
+
+ x_SmartWrapQuals(f, *feat, *text_os);
if( bHtml && f.GetContext()->Config().IsModeEntrez() && f.GetContext()->Config().ShowSeqSpans() ) {
// close the <span...>, without an endline
- text_os.AddLine("</span>", 0, IFlatTextOStream::eAddNewline_No );
+ text_os->AddLine("</span>", 0, IFlatTextOStream::eAddNewline_No );
}
}
@@ -1956,7 +2022,7 @@ void CGenbankFormatter::FormatWGS
if( bHtml ) {
string link;
if( first_id_equals_second_id ) {
- link = "http://www.ncbi.nlm.nih.gov/nuccore/" + first_id;
+ link = "https://www.ncbi.nlm.nih.gov/nuccore/" + first_id;
} else {
string url_arg;
const bool bIsWGSProject = CWGSItem::eWGS_Projects == wgs.GetType();
@@ -1970,10 +2036,10 @@ void CGenbankFormatter::FormatWGS
} else {
url_arg = first_id.substr(0, 6);
}
- link = "http://www.ncbi.nlm.nih.gov/Traces/wgs?val=" +
+ link = "https://www.ncbi.nlm.nih.gov/Traces/wgs?val=" +
url_arg + ( bIsWGSProject ? "#contigs" : "#scaffolds" );
} else {
- link = "http://www.ncbi.nlm.nih.gov/nuccore?term=" + first_id + ":" + last_id + "[PACC]";
+ link = "https://www.ncbi.nlm.nih.gov/nuccore?term=" + first_id + ":" + last_id + "[PACC]";
}
}
wgs_line = "<a href=\"" + link + "\">" + wgs_line + "</a>";
@@ -2032,7 +2098,7 @@ void CGenbankFormatter::FormatTSA
}
TryToSanitizeHtml(tsa_master);
if( ! tsa_master.empty() ) {
- id_range = "<a href=\"http://www.ncbi.nlm.nih.gov/Traces/wgs?val=" + tsa_master + "\">" + id_range + "</a>";
+ id_range = "<a href=\"https://www.ncbi.nlm.nih.gov/Traces/wgs?val=" + tsa_master + "\">" + id_range + "</a>";
}
}
diff --git a/c++/src/objtools/format/gene_finder.cpp b/c++/src/objtools/format/gene_finder.cpp
index ad1347f..4eca430 100644
--- a/c++/src/objtools/format/gene_finder.cpp
+++ b/c++/src/objtools/format/gene_finder.cpp
@@ -1,4 +1,4 @@
-/* $Id: gene_finder.cpp 381432 2012-11-23 11:12:25Z kornbluh $
+/* $Id: gene_finder.cpp 481005 2015-10-06 14:22:12Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,7 +38,9 @@
#include <objtools/format/items/gene_finder.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Feat_id.hpp>
+#include <objmgr/blob_id.hpp>
#include <objmgr/object_manager.hpp>
+#include <objmgr/seq_map_ci.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
@@ -201,7 +203,7 @@ fGeneSearchLocOpt_RemoveFar :
sequence::ECompare piece_comparison = sequence::Compare(
*candidate_feat_loc_iter.GetRangeAsSeq_loc(),
*cleaned_loc_this_iteration,
- &*m_Scope );
+ &*m_Scope, sequence::fCompareOverlapping);
if( piece_comparison != sequence::eNoOverlap )
{
if( x_StrandsMatch( m_Loc_original_strand, candidate_feat_loc_iter.GetStrand() ) ) {
@@ -379,7 +381,7 @@ void CGeneFinder::GetAssociatedGeneInfo(
bool ownGeneIsOkay = false;
if( out_s_feat ) {
const CSeq_loc &gene_loc = out_s_feat->GetLocation();
- if( sequence::Compare(gene_loc, *feat_loc, &ctx.GetScope()) == sequence::eSame ) {
+ if( sequence::Compare(gene_loc, *feat_loc, &ctx.GetScope(), sequence::fCompareOverlapping) == sequence::eSame ) {
ownGeneIsOkay = true;
}
}
@@ -460,6 +462,14 @@ CSeq_feat_Handle CGeneFinder::ResolveGeneXref(
const CGene_ref *xref_g_ref,
const CSeq_entry_Handle &top_level_seq_entry )
{
+ // Allow locus to match locus-tag or vice versa, but favor proper
+ // locus-to-locus or tag-to-tag matches.
+ enum ERGX_MatchQuality {
+ eRGX_NoMatch,
+ eRGX_MatchedTagForLocus,
+ eRGX_MatchedLocusForTag,
+ eRGX_MatchedAsIs
+ };
CSeq_feat_Handle feat;
if( xref_g_ref == NULL ) {
@@ -467,16 +477,67 @@ CSeq_feat_Handle CGeneFinder::ResolveGeneXref(
}
if( top_level_seq_entry ) {
- const CTSE_Handle &tse_handle = top_level_seq_entry.GetTSE_Handle();
- if( tse_handle ) {
- CTSE_Handle::TSeq_feat_Handles possible_feats = tse_handle.GetGenesByRef(*xref_g_ref);
- if( possible_feats.empty() && xref_g_ref->IsSetLocus_tag() ) {
- possible_feats = tse_handle.GetGenesWithLocus( xref_g_ref->GetLocus_tag(), false );
- }
- if( possible_feats.empty() && xref_g_ref->IsSetLocus() ) {
- possible_feats = tse_handle.GetGenesWithLocus( xref_g_ref->GetLocus(), true );
+ CTSE_Handle::TSeq_feat_Handles possible_feats;
+ set<CTSE_Handle> tried;
+ SSeqMapSelector sel(CSeqMap::fFindAny, kMax_Auto);
+ ERGX_MatchQuality match_quality = eRGX_NoMatch;
+ bool found_near_match = false;
+ for (CBioseq_CI bs(top_level_seq_entry);
+ !found_near_match && bs;
+ ++bs) {
+ for (CSeqMap_CI it(*bs, sel); it; ++it) {
+ const CTSE_Handle& tse_handle = it.GetUsingTSE();
+ if (tried.find(tse_handle) != tried.end()) {
+ continue;
+ }
+ tried.insert(tse_handle);
+
+ ERGX_MatchQuality new_quality = eRGX_NoMatch;
+
+ CTSE_Handle::TSeq_feat_Handles new_possibilities
+ = tse_handle.GetGenesByRef(*xref_g_ref);
+ if ( !new_possibilities.empty() ) {
+ new_quality = eRGX_MatchedAsIs;
+ }
+ if (new_quality == eRGX_NoMatch
+ && match_quality <= eRGX_MatchedLocusForTag
+ && xref_g_ref->IsSetLocus_tag()) {
+ new_possibilities = tse_handle.GetGenesWithLocus
+ (xref_g_ref->GetLocus_tag(), false);
+ if ( !new_possibilities.empty() ) {
+ new_quality = eRGX_MatchedLocusForTag;
+ }
+ }
+ if (new_quality == eRGX_NoMatch
+ && match_quality <= eRGX_MatchedTagForLocus
+ && xref_g_ref->IsSetLocus()) {
+ new_possibilities = tse_handle.GetGenesWithLocus
+ (xref_g_ref->GetLocus(), true);
+ if ( !new_possibilities.empty() ) {
+ new_quality = eRGX_MatchedTagForLocus;
+ }
+ }
+
+ if (new_quality > match_quality) {
+ possible_feats = new_possibilities;
+ match_quality = new_quality;
+ } else if (new_quality == match_quality) {
+ possible_feats.insert(possible_feats.end(),
+ new_possibilities.begin(),
+ new_possibilities.end());
+ } else {
+ _ASSERT(new_quality == eRGX_NoMatch);
+ }
+
+ if (match_quality != eRGX_NoMatch
+ && tse_handle == top_level_seq_entry.GetTSE_Handle()) {
+ found_near_match = true;
+ break;
+ }
}
+ }
+ if (match_quality != eRGX_NoMatch) {
int best_score = INT_MAX;
NON_CONST_ITERATE( CTSE_Handle::TSeq_feat_Handles, feat_iter, possible_feats) {
CSeq_feat_Handle a_possible_feat = *feat_iter;
diff --git a/c++/src/objtools/format/genome_project_item.cpp b/c++/src/objtools/format/genome_project_item.cpp
index dc23e2a..a31795f 100644
--- a/c++/src/objtools/format/genome_project_item.cpp
+++ b/c++/src/objtools/format/genome_project_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: genome_project_item.cpp 443815 2014-08-19 18:04:50Z ivanov $
+/* $Id: genome_project_item.cpp 482361 2015-10-22 15:48:50Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,7 +42,7 @@
#include <objtools/format/items/genome_project_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
@@ -93,7 +93,7 @@ s_JoinLinkableStrs(const CUser_field_Base::C_Data::TStrs &strs,
if (NStr::StartsWith (id, "SRZ") ||
NStr::StartsWith (id, "DRZ") ||
NStr::StartsWith (id, "ERZ")) {
- url = "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis=";
+ url = "https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis=";
}
result << "<a href=\"" << url << id << "\">";
}
@@ -158,11 +158,11 @@ namespace {
// we skip numbers just to make it easier to insert things in between.
// the exact number used and the amount skipped doesn't matter, as long
// as the smallest is first, largest is last, etc.
- { "Assembly", 20 },
+ { "Assembly", 50 },
{ "BioProject", 10 },
- { "BioSample", 30 },
- { "ProbeDB", 40 },
- { "Sequence Read Archive", 50 },
+ { "BioSample", 20 },
+ { "ProbeDB", 30 },
+ { "Sequence Read Archive", 40 },
{ "Trace Assembly Archive", 60 }
};
typedef CStaticArrayMap<const char *, int, PNocase_CStr> TPrefixMap;
@@ -222,11 +222,11 @@ void CGenomeProjectItem::x_GatherInfo(CBioseqContext& ctx)
typedef SStaticPair<const char *, SDbLinkLabelInfo> TDbLinkLabelToInfo;
static const TDbLinkLabelToInfo kDbLinkLabelToInfo[] = {
- { "Assembly", { true, false, "http://www.ncbi.nlm.nih.gov/assembly/" } },
- { "BioProject", { true, false, "http://www.ncbi.nlm.nih.gov/bioproject/" } },
- { "BioSample", { true, false, "http://www.ncbi.nlm.nih.gov/biosample/" } },
+ { "Assembly", { true, false, "https://www.ncbi.nlm.nih.gov/assembly/" } },
+ { "BioProject", { true, false, "https://www.ncbi.nlm.nih.gov/bioproject/" } },
+ { "BioSample", { true, false, "https://www.ncbi.nlm.nih.gov/biosample/" } },
{ "ProbeDB", { true, false, "" } },
- { "Sequence Read Archive", { true, false, "http://www.ncbi.nlm.nih.gov/sra/" } },
+ { "Sequence Read Archive", { true, false, "https://www.ncbi.nlm.nih.gov/sra/" } },
{ "Trace Assembly Archive", { false, true, "" } }
};
typedef const CStaticPairArrayMap<const char *, SDbLinkLabelInfo, PNocase> TDbLinkLabelToInfoMap;
@@ -274,7 +274,7 @@ void CGenomeProjectItem::x_GatherInfo(CBioseqContext& ctx)
string alt_url;
if (NStr::Equal (label, "Sequence Read Archive")) {
- alt_url = "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis=";
+ alt_url = "https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis=";
}
string dblinkValue = s_JoinLinkableStrs(
*pStrs, dbLinkLabelInfo.url, alt_url, bHtml );
diff --git a/c++/src/objtools/format/gff_gather.cpp b/c++/src/objtools/format/gff_gather.cpp
index 54c8ae8..5b08af4 100644
--- a/c++/src/objtools/format/gff_gather.cpp
+++ b/c++/src/objtools/format/gff_gather.cpp
@@ -1,4 +1,4 @@
-/* $Id: gff_gather.cpp 179812 2009-12-31 14:04:25Z ludwigf $
+/* $Id: gff_gather.cpp 478453 2015-09-09 15:25:04Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -65,7 +65,7 @@ void CGFFGatherer::Gather(
CConstRef<IFlatItem> item;
item.Reset( new CStartItem(seh) );
os << item;
- x_GatherSeqEntry(ctx.GetEntry());
+ x_GatherSeqEntry(ctx);
item.Reset( new CEndItem() );
os << item;
}
diff --git a/c++/src/objtools/format/inst_info_map.cpp b/c++/src/objtools/format/inst_info_map.cpp
index 24d23ff..4733995 100644
--- a/c++/src/objtools/format/inst_info_map.cpp
+++ b/c++/src/objtools/format/inst_info_map.cpp
@@ -1,4 +1,4 @@
-/* $Id: inst_info_map.cpp 452834 2014-11-25 15:28:32Z ivanov $
+/* $Id: inst_info_map.cpp 451488 2014-11-06 20:12:57Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/format/item_formatter.cpp b/c++/src/objtools/format/item_formatter.cpp
index 01485b9..5112e7b 100644
--- a/c++/src/objtools/format/item_formatter.cpp
+++ b/c++/src/objtools/format/item_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: item_formatter.cpp 438410 2014-06-16 17:21:26Z kans $
+/* $Id: item_formatter.cpp 481007 2015-10-06 14:22:51Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -55,12 +55,11 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/genbank_formatter.hpp>
#include <objtools/format/embl_formatter.hpp>
-#include <objtools/format/gff3_formatter.hpp>
#include <objtools/format/ftable_formatter.hpp>
#include <objtools/format/gbseq_formatter.hpp>
#include <objtools/format/context.hpp>
#include <objtools/format/flat_expt.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -89,12 +88,6 @@ CFlatItemFormatter* CFlatItemFormatter::New(CFlatFileConfig::TFormat format)
case CFlatFileConfig::eFormat_EMBL:
return new CEmblFormatter;
- case CFlatFileConfig::eFormat_GFF:
- return new CGFFFormatter;
-
- case CFlatFileConfig::eFormat_GFF3:
- return new CGFF3_Formatter;
-
case CFlatFileConfig::eFormat_FTable:
return new CFtableFormatter;
@@ -872,7 +865,7 @@ static void s_FormatCitGen
if (gen.IsSetDate()) {
const CDate& date = gen.GetDate();
if (date.IsStr() ||
- date.IsStd() && date.GetStd().IsSetYear() && date.GetStd().GetYear() != 0) {
+ (date.IsStd() && date.GetStd().IsSetYear() && date.GetStd().GetYear() != 0)) {
gen.GetDate().GetDate(&year, "(%Y)");
}
}
@@ -1191,7 +1184,9 @@ static void s_FormatPatent
if (pat.IsSetAuthors() && pat.GetAuthors().IsSetAffil()) {
const CAffil& affil = pat.GetAuthors().GetAffil();
if (affil.IsStr() && !NStr::IsBlank(affil.GetStr())) {
- jour << '\n' << affil.GetStr();
+ string str = affil.GetStr();
+ CleanAndCompress (str, str.c_str());
+ jour << '\n' << str;
} else if (affil.IsStd()) {
const CAffil::TStd& std = affil.GetStd();
@@ -1292,6 +1287,7 @@ static void s_FormatPatent
}
journal = CNcbiOstrstreamToString(jour);
+ CleanAndCompress (journal, journal.c_str());
}
@@ -1393,6 +1389,7 @@ static void s_FormatJournal
}
string volume = imp.IsSetVolume() ? imp.GetVolume() : kEmptyStr;
+ TrimSpacesAndJunkFromEnds (volume, false);
if (!NStr::IsBlank(volume)) {
jour << ' ' << volume;
}
@@ -1518,6 +1515,7 @@ void CFlatItemFormatter::x_GetKeywords
}
ExpandTildes( keywords, eTilde_space );
+ CleanAndCompress (keywords, keywords.c_str());
Wrap(l, prefix, keywords);
}
diff --git a/c++/src/objtools/format/keywords_item.cpp b/c++/src/objtools/format/keywords_item.cpp
index ed12e42..799ebb5 100644
--- a/c++/src/objtools/format/keywords_item.cpp
+++ b/c++/src/objtools/format/keywords_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: keywords_item.cpp 462428 2015-03-18 17:21:39Z ivanov $
+/* $Id: keywords_item.cpp 468774 2015-05-28 01:25:57Z kans $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -247,12 +247,9 @@ void CKeywordsItem::x_GatherInfo(CBioseqContext& ctx)
}
// propagate TSA keyword from nuc to prot in same nuc-prot set
- if( ! is_tsa && ctx.IsProt() ) {
- CBioseq_set_Handle parent_bioseq_set =
- ctx.GetHandle().GetParentBioseq_set();
- if( parent_bioseq_set && parent_bioseq_set.CanGetLevel() &&
- parent_bioseq_set.GetLevel() == CBioseq_set::eClass_nuc_prot )
- {
+ if( ! is_tsa && ctx.IsProt() && ctx.IsInNucProt() ) {
+ CBioseq_set_Handle parent_bioseq_set = ctx.GetHandle().GetParentBioseq_set();
+ if( parent_bioseq_set ) {
CBioseq_CI bioseq_ci( parent_bioseq_set, CSeq_inst::eMol_na );
if( bioseq_ci ) {
CBioseq_Handle nuc = *bioseq_ci;
diff --git a/c++/src/objtools/format/locus_item.cpp b/c++/src/objtools/format/locus_item.cpp
index b7aae9b..8583a08 100644
--- a/c++/src/objtools/format/locus_item.cpp
+++ b/c++/src/objtools/format/locus_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: locus_item.cpp 457346 2015-01-22 14:34:47Z ivanov $
+/* $Id: locus_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -62,7 +62,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/locus_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -107,7 +107,7 @@ void CLocusItem::x_GatherInfo(CBioseqContext& ctx)
// NB: order of execution is important, as some values depend on others
x_SetName(ctx);
x_SetLength(ctx);
- x_SetBiomol(ctx); // must come befoer x_SetStrand
+ x_SetBiomol(ctx); // must come before x_SetStrand
x_SetStrand(ctx);
x_SetTopology(ctx);
x_SetDivision(ctx);
diff --git a/c++/src/objtools/format/primary_item.cpp b/c++/src/objtools/format/primary_item.cpp
index 2d4e378..f99c408 100644
--- a/c++/src/objtools/format/primary_item.cpp
+++ b/c++/src/objtools/format/primary_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: primary_item.cpp 400413 2013-05-21 12:32:09Z kornbluh $
+/* $Id: primary_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,7 +46,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/primary_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/src/objtools/format/qualifiers.cpp b/c++/src/objtools/format/qualifiers.cpp
index 11db666..d206fda 100644
--- a/c++/src/objtools/format/qualifiers.cpp
+++ b/c++/src/objtools/format/qualifiers.cpp
@@ -1,4 +1,4 @@
-/* $Id: qualifiers.cpp 462440 2015-03-18 17:42:04Z ivanov $
+/* $Id: qualifiers.cpp 483654 2015-11-03 12:42:05Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,7 @@
#include <objtools/format/items/qualifiers.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -71,53 +71,6 @@ static bool s_IsNote(IFlatQVal::TFlags flags, CBioseqContext& ctx)
return (flags & IFlatQVal::fIsNote) && !ctx.Config().IsModeDump();
}
-static void s_CleanAndCompress (string& str)
-{
- if (str.empty()) {
- return;
- }
-
- size_t pos = str.find (" ,");
- if (pos != NPOS) {
- str [pos] = ',';
- str [pos+1] = ' ';
- }
- pos = str.find (",,");
- if (pos != NPOS) {
- str [pos+1] = ' ';
- }
- pos = str.find ("( ");
- if (pos != NPOS) {
- str [pos] = ' ';
- str [pos+1] = '(';
- }
- pos = str.find (" )");
- if (pos != NPOS) {
- str [pos] = ')';
- str [pos+1] = ' ';
- }
-
- string::iterator end = str.end();
- string::iterator it = str.begin();
- string::iterator new_str = it;
- while (it != end) {
- *new_str++ = *it;
- if ( (*it == ' ') || (*it == '\t') || (*it == '(') ) {
- for (++it; (it != end) && (*it == ' ' || *it == '\t'); ++it) continue;
- if ((it != end) && (*it == ')' || *it == ',') ) {
- // this "if" protects against the case "(...bunch of spaces and tabs...)".
- // Otherwise, the first '(' is unintentionally erased
- if( *(new_str - 1) != '(' ) {
- --new_str;
- }
- }
- } else {
- ++it;
- }
- }
- str.erase(new_str, str.end());
-}
-
static bool s_StringIsJustQuotes(const string& str)
{
@@ -190,6 +143,7 @@ static string s_GetGOText(
go_text += *evidence;
}
} else {
+ bool add_dash = false;
if (go_id != NULL) {
go_text = string( "GO:" );
if( is_html ) {
@@ -199,15 +153,18 @@ static string s_GetGOText(
if( is_html ) {
go_text += "</a>";
}
+ add_dash = true;
} else {
go_text.clear();
}
if ( text_string != 0 && text_string->length() > 0 ) {
- go_text += string( " - " );
+ if (add_dash) {
+ go_text += string( " - " );
+ }
if( is_html && go_id != NULL ) {
go_text += "<a href=\"" + strLinkBaseGeneOntology + *go_id + "\">";
}
- // Yes, we have the dash here even if there's no go_id (compatibility with C)
+ // NO, we NO LONGER have the dash here even if there's no go_id (RETAIN compatibility with CHANGE in C)
go_text += *text_string;
if( is_html && go_id != NULL ) {
go_text += "</a>";
@@ -241,7 +198,7 @@ static string s_GetGOText(
go_text += "]";
}
}
- s_CleanAndCompress(go_text);
+ CleanAndCompress(go_text, go_text.c_str());
NStr::TruncateSpacesInPlace(go_text);
return go_text;
}
@@ -347,70 +304,67 @@ static bool s_AltitudeIsValid(const string & str )
}
}
- // should end with " m."
- return NStr::Equal(pch, " m.");
+ // should end with " m"
+ return NStr::Equal(pch, " m");
}
/////////////////////////////////////////////////////////////////////////////
// CFormatQual - low-level formatted qualifier
CFormatQual::CFormatQual
-(const string& name,
- const string& value,
- const string& prefix,
- const string& suffix,
+(const CTempString& name,
+ const CTempString& value,
+ const CTempString& prefix,
+ const CTempString& suffix,
TStyle style,
TFlags flags,
ETrim trim ) :
- m_Name(name), m_Value(value), m_Prefix(prefix), m_Suffix(suffix),
- m_Style(style), m_Flags(flags), m_Trim(trim), m_AddPeriod(false)
+ m_Name(name),
+ m_Prefix(prefix),
+ m_Suffix(suffix),
+ m_Style(style), m_Flags(flags), m_Trim(trim), m_AddPeriod(false)
{
- s_CleanAndCompress(m_Value);
- NStr::TruncateSpacesInPlace(m_Value, NStr::eTrunc_End);
+ CleanAndCompress(m_Value, value);
}
-CFormatQual::CFormatQual(const string& name, const string& value, TStyle style, TFlags flags, ETrim trim) :
- m_Name(name), m_Value(value), m_Prefix(" "), m_Suffix(kEmptyStr),
+CFormatQual::CFormatQual(const CTempString& name, const CTempString& value, TStyle style, TFlags flags, ETrim trim) :
+ m_Name(name),
+ m_Prefix(" "), m_Suffix(kEmptyStr),
m_Style(style), m_Flags(flags), m_Trim(trim), m_AddPeriod(false)
{
- s_CleanAndCompress(m_Value);
- NStr::TruncateSpacesInPlace(m_Value, NStr::eTrunc_End);
+ CleanAndCompress(m_Value, value);
}
// === CFlatStringQVal ======================================================
-CFlatStringQVal::CFlatStringQVal(const string& value, TStyle style, ETrim trim)
+CFlatStringQVal::CFlatStringQVal(const CTempString& value, TStyle style, ETrim trim)
: IFlatQVal(&kSpace, &kSemicolon),
- m_Value(value), m_Style(style), m_Trim(trim), m_AddPeriod(0)
+ m_Style(style), m_Trim(trim), m_AddPeriod(0)
{
- s_CleanAndCompress(m_Value);
- NStr::TruncateSpacesInPlace(m_Value);
+ CleanAndCompress(m_Value, value);
}
CFlatStringQVal::CFlatStringQVal
-(const string& value,
+(const CTempString& value,
const string& pfx,
const string& sfx,
TStyle style,
ETrim trim)
: IFlatQVal(&pfx, &sfx),
- m_Value(value),
m_Style(style), m_Trim(trim), m_AddPeriod(0)
{
- s_CleanAndCompress(m_Value);
- NStr::TruncateSpacesInPlace(m_Value);
+ CleanAndCompress(m_Value, value);
}
-CFlatStringQVal::CFlatStringQVal(const string& value,
+CFlatStringQVal::CFlatStringQVal(const CTempString& value,
ETrim trim )
: IFlatQVal(&kSpace, &kSemicolon),
- m_Value(value), m_Style(CFormatQual::eQuoted), m_Trim(trim), m_AddPeriod(0)
+ m_Style(CFormatQual::eQuoted), m_Trim(trim), m_AddPeriod(0)
{
- s_CleanAndCompress(m_Value);
- NStr::TruncateSpacesInPlace(m_Value);
+ CleanAndCompress(m_Value, value);
}
@@ -435,7 +389,7 @@ ETildeStyle s_TildeStyleFromName( const string &name )
}
}
-void CFlatStringQVal::Format(TFlatQuals& q, const string& name,
+void CFlatStringQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
bool bHtml = ctx.Config().DoHTML();
@@ -474,8 +428,9 @@ void CFlatStringQVal::Format(TFlatQuals& q, const string& name,
name == "metagenomic" );
const bool prependNewline = (flags & fPrependNewline) && ! q.empty();
- TFlatQual qual = x_AddFQ(q, (is_note ? "note" : name),
- ( prependNewline ? "\n" + m_Value : m_Value ),
+ TFlatQual qual = x_AddFQ(
+ q, (is_note ? "note" : name),
+ ( prependNewline ? CTempString("\n" + m_Value) : CTempString(m_Value) ),
( forceNoValue ? CFormatQual::eEmpty : m_Style ),
0, m_Trim );
@@ -490,7 +445,7 @@ void CFlatStringQVal::Format(TFlatQuals& q, const string& name,
void CFlatNumberQVal::Format
(TFlatQuals& quals,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
TFlags flags) const
{
@@ -517,7 +472,7 @@ void CFlatNumberQVal::Format
void CFlatBondQVal::Format
(TFlatQuals& quals,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
TFlags flags) const
{
@@ -533,7 +488,7 @@ void CFlatBondQVal::Format
void CFlatGeneQVal::Format
(TFlatQuals& quals,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
TFlags flags) const
{
@@ -545,7 +500,7 @@ void CFlatGeneQVal::Format
void CFlatSiteQVal::Format
(TFlatQuals& quals,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
TFlags flags) const
{
@@ -575,7 +530,7 @@ void CFlatSiteQVal::Format
void CFlatStringListQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -616,7 +571,7 @@ public:
void CFlatGeneSynonymsQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -646,7 +601,7 @@ void CFlatGeneSynonymsQVal::Format
// === CFlatCodeBreakQVal ===================================================
-void CFlatCodeBreakQVal::Format(TFlatQuals& q, const string& name,
+void CFlatCodeBreakQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags) const
{
static const char* kOTHER = "OTHER";
@@ -673,7 +628,7 @@ void CFlatCodeBreakQVal::Format(TFlatQuals& q, const string& name,
}
}
-void CFlatNomenclatureQVal::Format(TFlatQuals& q, const string& name,
+void CFlatNomenclatureQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags) const
{
if( m_Value.IsNull() ) {
@@ -736,7 +691,7 @@ CFlatCodonQVal::CFlatCodonQVal(unsigned int codon, unsigned char aa, bool is_asc
}
-void CFlatCodonQVal::Format(TFlatQuals& q, const string& name, CBioseqContext& ctx,
+void CFlatCodonQVal::Format(TFlatQuals& q, const CTempString& name, CBioseqContext& ctx,
IFlatQVal::TFlags) const
{
if ( !m_Checked ) {
@@ -754,7 +709,7 @@ CFlatExperimentQVal::CFlatExperimentQVal(
}
}
-void CFlatExperimentQVal::Format(TFlatQuals& q, const string& name,
+void CFlatExperimentQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext&, IFlatQVal::TFlags) const
{
x_AddFQ(q, name, m_str.c_str(), CFormatQual::eQuoted);
@@ -782,14 +737,14 @@ CFlatInferenceQVal::CFlatInferenceQVal( const string& gbValue ) :
}
-void CFlatInferenceQVal::Format(TFlatQuals& q, const string& name,
+void CFlatInferenceQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext&, IFlatQVal::TFlags) const
{
x_AddFQ(q, name, m_str, CFormatQual::eQuoted);
}
-void CFlatIllegalQVal::Format(TFlatQuals& q, const string&, CBioseqContext &ctx,
+void CFlatIllegalQVal::Format(TFlatQuals& q, const CTempString& name, CBioseqContext &ctx,
IFlatQVal::TFlags) const
{
// XXX - return if too strict
@@ -806,7 +761,7 @@ void CFlatIllegalQVal::Format(TFlatQuals& q, const string&, CBioseqContext &ctx,
}
-void CFlatMolTypeQVal::Format(TFlatQuals& q, const string& name,
+void CFlatMolTypeQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
const char* s = 0;
@@ -903,7 +858,7 @@ void CFlatMolTypeQVal::Format(TFlatQuals& q, const string& name,
}
}
-void CFlatOrgModQVal::Format(TFlatQuals& q, const string& name,
+void CFlatOrgModQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
TFlatQual qual;
@@ -913,7 +868,9 @@ void CFlatOrgModQVal::Format(TFlatQuals& q, const string& name,
subname = kEmptyStr;
}
ConvertQuotesNotInHTMLTags(subname);
- ExpandTildes(subname, ( (flags & IFlatQVal::fIsNote) != 0 ? eTilde_note : eTilde_space ) );
+ CleanAndCompress(subname, subname.c_str());
+ NStr::TruncateSpacesInPlace(subname);
+ ExpandTildes(subname, ( (flags & IFlatQVal::fIsNote) != 0 ? eTilde_tilde : eTilde_space ) );
if (s_IsNote(flags, ctx)) {
bool add_period = RemovePeriodFromEnd(subname, true);
@@ -928,7 +885,7 @@ void CFlatOrgModQVal::Format(TFlatQuals& q, const string& name,
m_Suffix = ( add_period ? &kEOL : &kSemicolonEOL );
qual = x_AddFQ(q, "note", subname);
} else {
- qual = x_AddFQ(q, "note", name + ": " + subname,
+ qual = x_AddFQ(q, "note", string(name) + ": " + subname,
CFormatQual::eQuoted, CFormatQual::fFlags_showEvenIfRedund );
}
if (add_period && qual) {
@@ -943,7 +900,7 @@ void CFlatOrgModQVal::Format(TFlatQuals& q, const string& name,
}
-void CFlatOrganelleQVal::Format(TFlatQuals& q, const string& name,
+void CFlatOrganelleQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext&, IFlatQVal::TFlags) const
{
const string& organelle
@@ -995,7 +952,7 @@ void CFlatOrganelleQVal::Format(TFlatQuals& q, const string& name,
}
-void CFlatPubSetQVal::Format(TFlatQuals& q, const string& name,
+void CFlatPubSetQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags) const
{
const bool bHtml = ctx.Config().DoHTML();
@@ -1037,31 +994,33 @@ void CFlatPubSetQVal::Format(TFlatQuals& q, const string& name,
// out of the pubs which are still unused, we may still be able to salvage some
// under certain conditions.
- if( ctx.IsRefSeq() && ! ctx.Config().IsModeRelease() ) {
+ string pubmed;
+ if (ctx.IsRefSeq() && !ctx.Config().IsModeRelease()) {
CPub_set_Base::TPub::iterator pub_iter = unusedPubs.begin();
- for( ; pub_iter != unusedPubs.end() ; ++pub_iter ) {
- if( (*pub_iter)->IsPmid() ) {
+ for (; pub_iter != unusedPubs.end(); ++pub_iter) {
+ if ((*pub_iter)->IsPmid()) {
const int pmid = (*pub_iter)->GetPmid().Get();
- CNcbiOstrstream pubmed;
- pubmed << "[PUBMED ";
- if( bHtml ) {
- pubmed << "<a href=\"" << strLinkBasePubmed << pmid << "\">";
+ pubmed = "[PUBMED ";
+ if (bHtml) {
+ pubmed += "<a href=\"";
+ pubmed += strLinkBasePubmed;
+ pubmed += NStr::NumericToString(pmid);
+ pubmed += "\">";
}
- pubmed << pmid;
- if( bHtml ) {
- pubmed << "</a>";
+ pubmed += pmid;
+ if (bHtml) {
+ pubmed += "</a>";
}
- pubmed << ']';
+ pubmed += ']';
- x_AddFQ(q, name, CNcbiOstrstreamToString(pubmed),
- CFormatQual::eUnquoted);
+ x_AddFQ(q, name, pubmed, CFormatQual::eUnquoted);
}
}
}
}
-void CFlatIntQVal::Format(TFlatQuals& q, const string& name,
+void CFlatIntQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, TFlags) const
{
bool bHtml = ctx.Config().DoHTML();
@@ -1080,7 +1039,7 @@ void CFlatIntQVal::Format(TFlatQuals& q, const string& name,
}
-void CFlatSeqIdQVal::Format(TFlatQuals& q, const string& name,
+void CFlatSeqIdQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags) const
{
bool bHtml = ctx.Config().DoHTML();
@@ -1195,7 +1154,7 @@ void s_HtmlizeLatLon( string &subname ) {
void CFlatSubSourcePrimer::Format(
TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -1262,7 +1221,7 @@ void CFlatSubSourcePrimer::Format(
}
}
-void CFlatSubSourceQVal::Format(TFlatQuals& q, const string& name,
+void CFlatSubSourceQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
TFlatQual qual;
@@ -1271,6 +1230,8 @@ void CFlatSubSourceQVal::Format(TFlatQuals& q, const string& name,
subname = kEmptyStr;
}
ConvertQuotes(subname);
+ CleanAndCompress(subname, subname.c_str());
+ NStr::TruncateSpacesInPlace(subname);
if (ctx.Config().DoHTML()) {
s_ConvertGtLt(subname);
}
@@ -1287,7 +1248,7 @@ void CFlatSubSourceQVal::Format(TFlatQuals& q, const string& name,
m_Suffix = ( add_period ? &kEOL : &kSemicolonEOL );
qual = x_AddFQ(q, "note", subname);
} else {
- qual = x_AddFQ(q, "note", name + ": " + subname);
+ qual = x_AddFQ(q, "note", string(name) + ": " + subname);
}
if (add_period && qual) {
qual->SetAddPeriod();
@@ -1339,33 +1300,33 @@ void CFlatSubSourceQVal::Format(TFlatQuals& q, const string& name,
struct SSortReferenceByName
{
- bool operator()(const CRef< CDbtag >& sfp1,
- const CRef< CDbtag >& sfp2)
- {
- if (NStr::CompareNocase(sfp1->GetDb().c_str(), sfp2->GetDb().c_str()) < 0)
- return true;
- else
- return false;
- }
+ bool operator()(const CDbtag* dbt1, const CDbtag* dbt2)
+ {
+ return (dbt1->Compare(*dbt2)<0);
+ }
};
-void CFlatXrefQVal::Format(TFlatQuals& q, const string& name,
+void CFlatXrefQVal::Format(TFlatQuals& q, const CTempString& name,
CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
// to avoid duplicates, keep track of ones we've already done
set<string> quals_already_done;
- vector< CRef< CDbtag > > temp(m_Value);
+ TXref temp(m_Value);
+
sort(temp.begin(), temp.end(), SSortReferenceByName());
- ITERATE (TXref, it, temp) {
+ string id;
+ string db_xref; db_xref.reserve(100);
+
+ ITERATE(TXref, it, temp) {
const CDbtag& dbt = **it;
if (!m_Quals.Empty() && x_XrefInGeneXref(dbt)) {
continue;
}
- CDbtag::TDb db = dbt.GetDb();
+ CTempString db = dbt.GetDb();
if (db == "PID" || db == "GI") {
continue;
}
@@ -1397,7 +1358,7 @@ void CFlatXrefQVal::Format(TFlatQuals& q, const string& name,
}
const CDbtag::TTag& tag = (*it)->GetTag();
- string id;
+ id.clear();
if (tag.IsId()) {
id = NStr::IntToString(tag.GetId());
} else if (tag.IsStr()) {
@@ -1434,24 +1395,24 @@ void CFlatXrefQVal::Format(TFlatQuals& q, const string& name,
}
}
- CNcbiOstrstream db_xref;
- db_xref << db << ':';
+ db_xref.clear();
+ db_xref.append(db.data(), db.length()).push_back(':');
+
if (ctx.Config().DoHTML()) {
string url = dbt.GetUrl( ctx.GetTaxname() );
if (!NStr::IsBlank(url)) {
- db_xref << "<a href=\"" << url << "\">" << id << "</a>";
+ db_xref.append("<a href=\"").append(url).append("\">").append(id).append("</a>");
} else {
- db_xref << id;
+ db_xref.append(id);
}
} else {
- db_xref << id;
+ db_xref.append(id);
}
// add quals not already done
- string db_xref_str = CNcbiOstrstreamToString(db_xref);
- if( quals_already_done.find(db_xref_str) == quals_already_done.end() ) {
- quals_already_done.insert( db_xref_str );
- x_AddFQ(q, name, db_xref_str);
+ if (quals_already_done.find(db_xref) == quals_already_done.end()) {
+ quals_already_done.insert(db_xref);
+ x_AddFQ(q, name, db_xref);
}
}
}
@@ -1526,7 +1487,7 @@ static size_t s_CountAccessions(const CUser_field& field)
void CFlatModelEvQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -1612,16 +1573,16 @@ void CFlatModelEvQVal::Format
}
prefix = ", ";
}
- if (num_prot > 0) {
- text << prefix << num_prot << " Protein";
- if (num_prot > 1) {
+ if (num_long_sra > 0) {
+ text << prefix << num_long_sra << " long SRA read";
+ if (num_long_sra > 1) {
text << 's';
}
prefix = ", ";
}
- if (num_long_sra > 0) {
- text << prefix << num_long_sra << " long SRA read";
- if (num_long_sra > 1) {
+ if (num_prot > 0) {
+ text << prefix << num_prot << " Protein";
+ if (num_prot > 1) {
text << 's';
}
prefix = ", ";
@@ -1646,13 +1607,13 @@ void CFlatModelEvQVal::Format
section_prefix = ", and ";
}
- x_AddFQ(q, name, CNcbiOstrstreamToString(text));
+ x_AddFQ(q, name, CNcbiOstrstreamToString(text).operator std::string());
}
void CFlatGoQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -1664,7 +1625,7 @@ void CFlatGoQVal::Format
static const string sfx = ";";
m_Prefix = &kEOL;
m_Suffix = &sfx;
- x_AddFQ(q, "note", name + ": " + s_GetGOText(*m_Value, is_ftable, is_html));
+ x_AddFQ(q, "note", string(name) + ": " + s_GetGOText(*m_Value, is_ftable, is_html));
} else {
x_AddFQ(q, name, s_GetGOText(*m_Value, is_ftable, is_html));
}
@@ -1715,7 +1676,7 @@ int CFlatGoQVal::GetPubmedId(void) const
void CFlatAnticodonQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -1725,34 +1686,38 @@ void CFlatAnticodonQVal::Format
string locationString = CFlatSeqLoc(*m_Anticodon, ctx).GetString();
- CNcbiOstrstream text;
- text << "(pos:" << locationString;
- text << ",aa:" << m_Aa;
+ string text;
+ text = "(pos:";
+ text += locationString;
+ text += ",aa:";
+ text += m_Aa;
CScope & scope = ctx.GetScope();
- if( sequence::GetLength(*m_Anticodon, &scope) == 3 ) { // "3" because 3 nucleotides to an amino acid (and thus anticodon sequence)
-
+ if (sequence::GetLength(*m_Anticodon, &scope) == 3) { // "3" because 3 nucleotides to an amino acid (and thus anticodon sequence)
+
try {
CSeqVector seq_vector(*m_Anticodon, scope, CBioseq_Handle::eCoding_Iupac);
- if( seq_vector.size() == 3 ) {
+ if (seq_vector.size() == 3) {
string seq("---");
seq_vector.GetSeqData(0, 3, seq);
NStr::ToLower(seq);
- text << ",seq:" << seq;
+ text += ",seq:";
+ text += seq;
}
- } catch(...) {
+ }
+ catch (...) {
// ignore any sort of error that occurs in this process
}
}
- text << ')' ;
+ text += ')';
- x_AddFQ(q, name, CNcbiOstrstreamToString(text), CFormatQual::eUnquoted);
+ x_AddFQ(q, name, text, CFormatQual::eUnquoted);
}
void CFlatTrnaCodonsQVal::Format
(TFlatQuals& q,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
IFlatQVal::TFlags flags) const
{
@@ -1783,7 +1748,7 @@ void CFlatTrnaCodonsQVal::Format
void CFlatProductNamesQVal::Format
(TFlatQuals& quals,
- const string& name,
+ const CTempString& name,
CBioseqContext& ctx,
TFlags flags) const
{
diff --git a/c++/src/objtools/format/reference_item.cpp b/c++/src/objtools/format/reference_item.cpp
index 89796c9..7ae5286 100644
--- a/c++/src/objtools/format/reference_item.cpp
+++ b/c++/src/objtools/format/reference_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: reference_item.cpp 450150 2014-10-23 14:01:55Z ivanov $
+/* $Id: reference_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -66,7 +66,7 @@
#include <objtools/format/formatter.hpp>
#include <objtools/format/items/reference_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
@@ -159,6 +159,7 @@ void CReferenceItem::FormatAffil(const CAffil& affil, string& result, bool gen_s
if (gen_sub) {
ConvertQuotes(result);
}
+ CleanAndCompress(result, result.c_str());
NStr::TruncateSpacesInPlace(result);
}
@@ -1124,7 +1125,6 @@ void CReferenceItem::GetAuthNames(const CAuth_list& alp, TStrList& authors)
authors.clear();
const CAuth_list::TNames& names = alp.GetNames();
- string name;
switch (names.Which()) {
case CAuth_list::TNames::e_Std:
ITERATE (CAuth_list::TNames::TStd, it, names.GetStd()) {
@@ -1133,9 +1133,9 @@ void CReferenceItem::GetAuthNames(const CAuth_list& alp, TStrList& authors)
}
const CPerson_id& pid = (*it)->GetName();
if (pid.IsName() || pid.IsMl() || pid.IsStr()) {
- name.erase();
+ authors.push_back(kEmptyStr);
+ string& name = authors.back();
pid.GetLabel(&name, CPerson_id::eGenbank);
- authors.push_back(name);
}
}
break;
diff --git a/c++/src/objtools/format/sam_formatter.cpp b/c++/src/objtools/format/sam_formatter.cpp
index 51bec6c..6b4f1bb 100644
--- a/c++/src/objtools/format/sam_formatter.cpp
+++ b/c++/src/objtools/format/sam_formatter.cpp
@@ -1,4 +1,4 @@
-/* $Id: sam_formatter.cpp 457255 2015-01-21 18:33:52Z ivanov $
+/* $Id: sam_formatter.cpp 485551 2015-11-23 18:31:26Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,9 +51,10 @@ class CSAM_CIGAR_Formatter : public CCIGAR_Formatter
{
public:
typedef CSAM_Formatter::TFlags TFlags;
- typedef list<string> TLines;
+ typedef CSAM_Formatter::CSAM_Headers THeaders;
+ typedef CSAM_Formatter::TLines TLines;
- CSAM_CIGAR_Formatter(TLines& header,
+ CSAM_CIGAR_Formatter(THeaders& headers,
TLines& body,
const CSeq_align& aln,
CScope& scope,
@@ -62,10 +63,16 @@ public:
protected:
virtual void StartAlignment(void);
+ virtual void StartRow(void)
+ {
+ m_NumDif = 0;
+ }
virtual void AddRow(const string& cigar);
virtual void AddSegment(CNcbiOstream& cigar,
char seg_type,
TSeqPos seg_len);
+ virtual void AdjustSeqIdType(CConstRef<CSeq_id>& id);
+
private:
enum EReadFlags {
fRead_Default = 0x0000,
@@ -73,11 +80,12 @@ private:
};
typedef unsigned int TReadFlags;
+ string x_GetSeqIdString(const CSeq_id& id, TFlags flags) const;
string x_GetRefIdString(void) const;
string x_GetTargetIdString(void) const;
TFlags m_Flags;
- TLines& m_Head;
+ THeaders& m_Head;
TLines& m_Rows;
int m_NumDif; // count differences
@@ -85,14 +93,14 @@ private:
};
-CSAM_CIGAR_Formatter::CSAM_CIGAR_Formatter(TLines& header,
+CSAM_CIGAR_Formatter::CSAM_CIGAR_Formatter(THeaders& headers,
TLines& body,
const CSeq_align& aln,
CScope& scope,
TFlags flags)
: CCIGAR_Formatter(aln, &scope),
m_Flags(flags),
- m_Head(header),
+ m_Head(headers),
m_Rows(body),
m_NumDif(0)
{
@@ -100,30 +108,45 @@ CSAM_CIGAR_Formatter::CSAM_CIGAR_Formatter(TLines& header,
inline
+string CSAM_CIGAR_Formatter::x_GetSeqIdString(const CSeq_id& id, TFlags flags) const
+{
+ return (flags & CSAM_Formatter::fSAM_PlainSeqIds) ?
+ id.GetSeqIdString(true) : id.AsFastaString();
+}
+
+
+inline
string CSAM_CIGAR_Formatter::x_GetRefIdString(void) const
{
- // ???
- return GetRefId().AsFastaString();
+ return x_GetSeqIdString(GetRefId(), m_Flags);
}
inline
string CSAM_CIGAR_Formatter::x_GetTargetIdString(void) const
{
- // ???
- return GetTargetId().AsFastaString();
+ return x_GetSeqIdString(GetTargetId(), m_Flags);
}
-void CSAM_CIGAR_Formatter::StartAlignment(void)
+void CSAM_CIGAR_Formatter::AdjustSeqIdType(CConstRef<CSeq_id>& id)
{
- // One header per file.
- if ( m_Head.empty() ) {
- m_Head.push_back("@HD\tVN:1.2\tGO:query");
+ CScope* scope = GetScope();
+ if ( !scope) return;
+ sequence::EGetIdType force_type = (m_Flags & CSAM_Formatter::fSAM_ForceGISeqIds) ?
+ sequence::eGetId_ForceGi : sequence::eGetId_ForceAcc;
+ CSeq_id_Handle forced_id = sequence::GetId(*id, *scope, force_type);
+ if (forced_id) {
+ id.Reset(forced_id.GetSeqId());
}
}
+void CSAM_CIGAR_Formatter::StartAlignment(void)
+{
+}
+
+
void CSAM_CIGAR_Formatter::AddSegment(CNcbiOstream& cigar,
char seg_type,
TSeqPos seg_len)
@@ -157,7 +180,8 @@ void CSAM_CIGAR_Formatter::AddRow(const string& cigar)
{
CBioseq_Handle refseq = GetScope()->GetBioseqHandle(GetRefId());
if (m_KnownRefSeqs.find(refseq) == m_KnownRefSeqs.end()) {
- m_Head.push_back("@SQ\tSN:" + x_GetRefIdString() +
+ m_Head.AddSequence(CSeq_id_Handle::GetHandle(GetRefId()),
+ "@SQ\tSN:" + x_GetRefIdString() +
"\tLN:" + NStr::UInt8ToString(refseq.GetBioseqLength()));
m_KnownRefSeqs.insert(refseq);
}
@@ -165,7 +189,7 @@ void CSAM_CIGAR_Formatter::AddRow(const string& cigar)
string id = x_GetTargetIdString();
TReadFlags flags = fRead_Default;
- if ( GetTargetSign() < 0 ) {
+ if ( GetTargetSign() != GetRefSign() ) {
flags |= fRead_Reverse;
}
@@ -173,25 +197,47 @@ void CSAM_CIGAR_Formatter::AddRow(const string& cigar)
const TRange& tgt_rg = GetTargetRange();
string clip_front, clip_back;
if (tgt_rg.GetFrom() > 0) {
- clip_front = NStr::UInt8ToString(tgt_rg.GetFrom()) + "H";
+ if(flags & fRead_Reverse) {
+ clip_back = NStr::UInt8ToString(tgt_rg.GetFrom()) + "H";
+ }
+ else {
+ clip_front = NStr::UInt8ToString(tgt_rg.GetFrom()) + "H";
+ }
}
- //string seq_data;
+ string seq_data = "*";
CBioseq_Handle h;
h = GetScope()->GetBioseqHandle(GetTargetId());
if ( h ) {
- //CSeqVector vect = h.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
- //vect.GetSeqData(tgt_rg.GetFrom(), tgt_rg.GetTo(), seq_data);
if ( TSeqPos(tgt_rg.GetToOpen()) < h.GetBioseqLength() ) {
- clip_back = NStr::UInt8ToString(
- h.GetBioseqLength() - tgt_rg.GetToOpen()) + "H";
+ if(flags & fRead_Reverse) {
+ clip_front = NStr::UInt8ToString(
+ h.GetBioseqLength() - tgt_rg.GetToOpen()) + "H";
+ }
+ else {
+ clip_back = NStr::UInt8ToString(
+ h.GetBioseqLength() - tgt_rg.GetToOpen()) + "H";
+ }
+ }
+ if (m_Flags & CSAM_Formatter::fSAM_SeqData) {
+ if(flags & fRead_Reverse) {
+ CSeqVector vect = h.GetSeqVector(
+ CBioseq_Handle::eCoding_Iupac, eNa_strand_minus);
+ vect.GetSeqData(h.GetBioseqLength() - tgt_rg.GetToOpen(),
+ h.GetBioseqLength() - tgt_rg.GetFrom(), seq_data);
+ }
+ else {
+ CSeqVector vect = h.GetSeqVector(
+ CBioseq_Handle::eCoding_Iupac, eNa_strand_plus);
+ vect.GetSeqData(tgt_rg.GetFrom(), tgt_rg.GetToOpen(), seq_data);
+ }
}
}
- /*
else {
- seq_data = string(tgt_rg.GetLength(), 'N'); // ???
+ if (m_Flags & CSAM_Formatter::fSAM_SeqData) {
+ seq_data = string(tgt_rg.GetLength(), 'N'); // ???
+ }
}
- */
// Add tags
string AS; // alignment score, int
@@ -245,7 +291,7 @@ void CSAM_CIGAR_Formatter::AddRow(const string& cigar)
"*\t" + // ??? mate reference sequence
"0\t" + // mate position, 1-based
"0\t" + // inferred insert size
- /*seq_data + */ "*\t" +
+ seq_data + "\t" +
"*" + // query quality
AS + EV + NM + PI + BS // tags
);
@@ -257,7 +303,9 @@ CSAM_Formatter::CSAM_Formatter(CNcbiOstream& out,
TFlags flags)
: m_Out(&out),
m_Scope(&scope),
- m_Flags(flags)
+ m_Flags(flags),
+ m_SO(eSO_Skip),
+ m_GO(eGO_Query)
{
}
@@ -308,19 +356,101 @@ CSAM_Formatter& CSAM_Formatter::Print(const CSeq_align_set& aln_set,
}
+void CSAM_Formatter::x_PrintSOTag(void) const
+{
+ switch ( m_SO ) {
+ case eSO_Unsorted:
+ *m_Out << "\tSO:unsorted";
+ break;
+ case eSO_QueryName:
+ *m_Out << "\tSO:queryname";
+ break;
+ case eSO_Coordinate:
+ *m_Out << "\tSO:coordinate";
+ break;
+ case eSO_User:
+ if ( !m_SO_Value.empty() ) {
+ *m_Out << "\tSO:" << m_SO_Value;
+ }
+ break;
+ default:
+ break;
+ }
+}
+
+
+void CSAM_Formatter::x_PrintGOTag(void) const
+{
+ switch ( m_GO ) {
+ case eGO_None:
+ *m_Out << "\tGO:none";
+ break;
+ case eGO_Query:
+ *m_Out << "\tGO:query";
+ break;
+ case eGO_Reference:
+ *m_Out << "\tGO:reference";
+ break;
+ case eGO_User:
+ if ( !m_GO_Value.empty() ) {
+ *m_Out << "\tGO:" << m_GO_Value;
+ }
+ break;
+ default:
+ break;
+ }
+}
+
+
void CSAM_Formatter::Flush(void)
{
if ( !m_Out ) return;
- ITERATE(TLines, it, m_Header) {
- *m_Out << *it << '\n';
+ // Headers
+ bool have_data = !m_Header.m_Data.empty() || !m_Body.empty();
+ if (have_data) {
+ *m_Out << "@HD\tVN:1.2";
+ x_PrintSOTag();
+ x_PrintGOTag();
+ *m_Out << '\n';
}
+ ITERATE(CSAM_Headers::TData, it, m_Header.m_Data) {
+ *m_Out << it->second << '\n';
+ }
+ if (have_data && !m_ProgramInfo.m_Id.empty()) {
+ *m_Out << "@PG\tID:" << m_ProgramInfo.m_Id;
+ if ( !m_ProgramInfo.m_Version.empty() ) {
+ *m_Out << "\tVN:" << m_ProgramInfo.m_Version;
+ }
+ if ( !m_ProgramInfo.m_CmdLine.empty() ) {
+ *m_Out << "\tCL:" << m_ProgramInfo.m_CmdLine;
+ }
+ if ( !m_ProgramInfo.m_Desc.empty() ) {
+ *m_Out << "\tDS:" << m_ProgramInfo.m_Desc;
+ }
+ if ( !m_ProgramInfo.m_Name.empty() ) {
+ *m_Out << "\tPN:" << m_ProgramInfo.m_Name;
+ }
+ *m_Out << '\n';
+ }
+
+ // Alignments
ITERATE(TLines, it, m_Body) {
*m_Out << *it << '\n';
}
- m_Header.clear();
+ m_Header.m_Data.clear();
m_Body.clear();
}
+void CSAM_Formatter::CSAM_Headers::AddSequence(CSeq_id_Handle id,
+ const string& line)
+{
+ ITERATE(TData, it, m_Data) {
+ if (it->first == id) return; // duplicate
+ }
+ m_Data.push_back(TData::value_type(id, line));
+}
+
+
END_SCOPE(objects)
END_NCBI_SCOPE
diff --git a/c++/src/objtools/format/source_item.cpp b/c++/src/objtools/format/source_item.cpp
index a707cd0..890c91a 100644
--- a/c++/src/objtools/format/source_item.cpp
+++ b/c++/src/objtools/format/source_item.cpp
@@ -1,4 +1,4 @@
-/* $Id: source_item.cpp 428492 2014-03-04 21:09:14Z kans $
+/* $Id: source_item.cpp 474406 2015-07-28 18:14:17Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -45,7 +45,7 @@
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/source_item.hpp>
#include <objtools/format/context.hpp>
-#include "utils.hpp"
+#include <objmgr/util/objutil.hpp>
BEGIN_NCBI_SCOPE
diff --git a/c++/src/objtools/readers/Makefile.xobjread.lib b/c++/src/objtools/readers/Makefile.xobjread.lib
index c37123d..dde090c 100644
--- a/c++/src/objtools/readers/Makefile.xobjread.lib
+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
@@ -1,9 +1,9 @@
-# $Id: Makefile.xobjread.lib 432807 2014-04-18 13:52:28Z gotvyans $
+# $Id: Makefile.xobjread.lib 468535 2015-05-26 13:23:32Z ucko $
WATCHERS = jcherry sapojnik bollin ludwigf ucko kornbluh gotvyans
-ASN_DEP = seq seqset
+ASN_DEP = submit
CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \
message_listener line_error
-DLL_LIB = creaders
+DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil
diff --git a/c++/src/objtools/readers/agp_util.cpp b/c++/src/objtools/readers/agp_util.cpp
index 47e2832..d09aa5a 100644
--- a/c++/src/objtools/readers/agp_util.cpp
+++ b/c++/src/objtools/readers/agp_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: agp_util.cpp 435421 2014-05-15 19:29:47Z ucko $
+/* $Id: agp_util.cpp 465403 2015-04-21 14:55:53Z sapojnik $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -112,7 +112,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
// Size for a gap of unknown length is not 100 bases. The International Sequence
// Database Collaboration uses a length of 100 bases for all gaps of unknown length.
"gap length (column 6) is not 100 for a gap of unknown size (an INSDC standard)",
- "component lines with the same component_id found on different scaffolds",
+ "same component_id found on different scaffolds",
/*
"component X is not used in full in a single-component scaffold",
"only a part of component X is included in a singleton scaffold",
@@ -145,7 +145,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
"all objects are singletons with component_beg=1",
"\"gnl|\" prefix in X is deprecated inside AGP files (no \"prefix|\" is best)",
- kEmptyCStr,
+ "component_id X is a not an accession, but is used with component_type other than W",
kEmptyCStr,
kEmptyCStr,
kEmptyCStr,
@@ -1160,9 +1160,12 @@ void CAgpErrEx::PrintAllMessages(CNcbiOstream& out)
out << "\n";
}
- out << "### Warnings ###\n";
+ out << "### Warnings (most are errors in -sub mode) ###\n";
for(int i=W_First; i<W_Last; i++) {
- out << GetPrintableCode(i) << "\t";
+ string lbl = GetPrintableCode(i);
+ string lbl_strict = GetPrintableCode(i, true);
+ if(lbl!=lbl_strict) lbl+="/"+lbl_strict;
+ out << lbl << "\t";
if(i==W_GapLineMissingCol9) {
out << GetMsg(i) << " (no longer reported)";
//out << " (only the total count is printed unless you specify: -only " << GetPrintableCode(i) << ")";
@@ -1186,15 +1189,20 @@ void CAgpErrEx::PrintAllMessages(CNcbiOstream& out)
out <<
"#\tErrors reported once at the end of validation:\n"
"#\tunable to determine a Taxid for the AGP (less than 80% of components have one common taxid)\n"
- "#\tcomponents with incorrect taxids\n";
+ "#\tcomponents with incorrect taxids\n"
+ "#Error with -sub, warning if no -sub option:\n"
+ "#\tcomponent name(s)/object name(s) in FASTA not found in AGP\n"
+ "#\tscaffold(s) not found in Chromosome from scaffold AGP\n"
+ ;
}
-string CAgpErrEx::GetPrintableCode(int code)
+string CAgpErrEx::GetPrintableCode(int code, bool strict)
{
string res =
(code<E_Last) ? "e" :
(code<W_Last) ? "w" :
(code<G_Last) ? "g" : "x";
+ if( res[0]=='w' && strict && !IsStrictModeWarning(code) ) res = "e";
if(code<10) res += "0";
res += NStr::IntToString(code);
return res;
@@ -1259,18 +1267,18 @@ void CAgpErrEx::PrintLineXml(CNcbiOstream& ostr,
void CAgpErrEx::PrintMessage(CNcbiOstream& ostr, int code,
const string& details)
{
- ostr<< "\t" << ErrorWarningOrNote(code)
+ ostr<< "\t" << ErrorWarningOrNoteEx(code)
<< (code <=E_LastToSkipLine ? ", line skipped" : "")
<< ": " << FormatMessage( GetMsg(code), details ) << "\n";
}
void CAgpErrEx::PrintMessageXml(CNcbiOstream& ostr, int code, const string& details, int appliesTo)
{
- ostr<< " <message severity=\"" << ErrorWarningOrNote(code) << "\"";
+ ostr<< " <message severity=\"" << ErrorWarningOrNoteEx(code) << "\"";
if(code <=E_LastToSkipLine) ostr << " line_skipped=\"1\"";
ostr<<">\n";
- ostr << " <code>" << GetPrintableCode(code) << "</code>\n";
+ ostr << " <code>" << GetPrintableCode(code, m_strict) << "</code>\n";
if(appliesTo & CAgpErr::fAtPpLine ) ostr << " <line_num>" << m_line_num_pp << "</line_num>\n";
if(appliesTo & CAgpErr::fAtPrevLine) ostr << " <line_num>" << m_line_num_prev << "</line_num>\n";
if(appliesTo & CAgpErr::fAtThisLine) ostr << " <line_num>current</line_num>\n";
@@ -1285,6 +1293,7 @@ void CAgpErrEx::PrintMessageXml(CNcbiOstream& ostr, int code, const string& deta
//// class CAgpErrEx - constructor
CAgpErrEx::CAgpErrEx(CNcbiOstream* out, bool use_xml, EOwnership eOwnsOut) :
m_use_xml(use_xml),
+ m_strict(false),
m_messages( new CNcbiOstrstream() ),
m_out(out)
{
@@ -1309,14 +1318,17 @@ CAgpErrEx::CAgpErrEx(CNcbiOstream* out, bool use_xml, EOwnership eOwnsOut) :
ResetTotals();
// errors that are "silenced" by default (only the count is printed)
- m_MustSkip[W_GapLineMissingCol9]=true;
+ m_MustSkip[W_GapLineMissingCol9]=1;
if(!use_xml) // perhaps, we should have a separate parameter for hiding these...
{
- m_MustSkip[W_ExtraTab ]=true;
- m_MustSkip[W_CompIsWgsTypeIsNot]=true;
- m_MustSkip[W_CompIsNotWgsTypeIs]=true;
- m_MustSkip[W_CompIsNotHtgTypeIs]=true;
- m_MustSkip[W_ShortGap ]=true;
+ m_MustSkip[W_ExtraTab ]=1;
+
+ // print the first 5 only
+ m_MustSkip[W_CompIsWgsTypeIsNot ]=5+1;
+ m_MustSkip[W_CompIsNotWgsTypeIs ]=5+1;
+ m_MustSkip[W_CompIsNotHtgTypeIs ]=5+1;
+ m_MustSkip[W_CompIsLocalTypeNotW]=5+1;
+ m_MustSkip[W_ShortGap ]=5+1;
}
// A "random check" to make sure enum and msg[] are not out of skew.
@@ -1342,6 +1354,13 @@ CAgpErrEx::CAgpErrEx(CNcbiOstream* out, bool use_xml, EOwnership eOwnsOut) :
//// class CAgpErrEx - non-static functions
+const char* CAgpErrEx::ErrorWarningOrNoteEx(int code)
+{
+ const char* t = ErrorWarningOrNote(code);
+ if(m_strict && t[0]=='W' && !IsStrictModeWarning(code) ) t = "ERROR";
+ return t;
+}
+
void CAgpErrEx::ResetTotals()
{
memset(m_MsgCount, 0, sizeof(m_MsgCount));
@@ -1351,10 +1370,12 @@ void CAgpErrEx::Msg(int code, const string& details, int appliesTo)
{
// Suppress some messages while still counting them
m_MsgCount[code]++;
- if( m_MustSkip[code]) {
+ if( m_MustSkip[code]==1) {
m_msg_skipped++;
return;
}
+ if( m_MustSkip[code]>1 ) m_MustSkip[code]--;
+
if( m_MaxRepeat>0 && m_MsgCount[code] > m_MaxRepeat) {
m_MaxRepeatTopped=true;
m_msg_skipped++;
@@ -1509,7 +1530,7 @@ string CAgpErrEx::SkipMsg(const string& str, bool skip_other)
// Error or warning codes, substrings of the messages.
res="";
for( int i=E_First; i<CODE_Last; i++ ) {
- bool matchesCode = ( str==GetPrintableCode(i) );
+ bool matchesCode = ( str==GetPrintableCode(i) || str==GetPrintableCode(i, true) );
if( matchesCode || NStr::Find(GetMsg(i), str) != NPOS) {
m_MustSkip[i] = !skip_other;
res += " ";
@@ -1527,12 +1548,20 @@ string CAgpErrEx::SkipMsg(const string& str, bool skip_other)
int CAgpErrEx::CountTotals(int from, int to)
{
int count=0;
+
+ // filtering by s_StrictModeWarningMask
+ bool strictModeErrors =false;
+ bool strictModeWarningsOnly=false;
+
if(to==E_First) {
//// One argument: count errors/warnings/genbank errors/given type
- if (from==E_Last) { from=E_First; to=E_Last; }
+ if (from==E_Last) { from=E_First; to=E_Last;
+ strictModeErrors=m_strict; // usual errors + an extra loop for warnings turned into errors
+ }
else if(from==W_Last) { from=W_First; to=W_Last;
// out of range warning
count = m_MsgCount[G_NsWithinCompSpan];
+ strictModeWarningsOnly=m_strict; // filter within the general loop
}
else if(from==G_Last) {
from=G_First; to=G_Last;
@@ -1544,7 +1573,12 @@ int CAgpErrEx::CountTotals(int from, int to)
}
for(int i=from; i<to; i++) {
- count += m_MsgCount[i];
+ if( !strictModeWarningsOnly || IsStrictModeWarning(i) ) count += m_MsgCount[i];
+ }
+ if(strictModeErrors) {
+ for(int i=W_First; i<W_Last; i++) {
+ if( !IsStrictModeWarning(i) ) count += m_MsgCount[i];
+ }
}
return count;
}
@@ -1566,7 +1600,7 @@ void CAgpErrEx::PrintMessageCounts(CNcbiOstream& ostr, int from, int to, bool re
for(int i=from; i<to; i++) {
if( m_MsgCount[i] ) {
ostr << "<msg_summary>\n";
- ostr << " <code>" << GetPrintableCode(i) << "</code>\n";
+ ostr << " <code>" << GetPrintableCode(i, m_strict) << "</code>\n";
ostr << " <text>" << NStr::XmlEncode(GetMsg(i)) << "</text>\n";
ostr << " <cnt>" << m_MsgCount[i] << "</cnt>\n";
ostr << "</msg_summary>\n";
@@ -1580,7 +1614,7 @@ void CAgpErrEx::PrintMessageCounts(CNcbiOstream& ostr, int from, int to, bool re
for(int i=from; i<to; i++) {
if( m_MsgCount[i] ) {
ostr<< setw(7) << m_MsgCount[i] << " "
- << GetPrintableCode(i) << " "
+ << GetPrintableCode(i, m_strict) << " "
<< GetMsg(i) << "\n";
}
// ouside of previous "if" because one hint may apply to one or more of several consequitive warnings
diff --git a/c++/src/objtools/readers/agp_validate_reader.cpp b/c++/src/objtools/readers/agp_validate_reader.cpp
index 0783079..e0a9c3a 100644
--- a/c++/src/objtools/readers/agp_validate_reader.cpp
+++ b/c++/src/objtools/readers/agp_validate_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: agp_validate_reader.cpp 440982 2014-07-18 16:44:52Z sapojnik $
+/* $Id: agp_validate_reader.cpp 465301 2015-04-20 16:41:10Z sapojnik $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -201,7 +201,7 @@ void CAgpValidateReader::OnGapOrComponent()
// check for W_BreakingGapSameCompId on the next row
m_prev_component_id=m_prev_row->GetComponentId();
}
- if(m_explicit_scaf && !m_is_chr) {
+ if((m_explicit_scaf||m_unplaced) && !m_is_chr) {
m_AgpErr->Msg(CAgpErrEx::E_ScafBreakingGap);
}
@@ -368,12 +368,14 @@ void CAgpValidateReader::OnGapOrComponent()
else if( div == CSeq_id::eAcc_htgs ) {
if(m_this_row->component_type == 'W') m_AgpErr->Msg(CAgpErr::W_CompIsNotWgsTypeIs);
}
- else {
+ else if( div != CSeq_id::eAcc_other // no further classification
+ ) {
if( string("ADF").find(m_this_row->component_type)!=NPOS ) m_AgpErr->Msg(CAgpErr::W_CompIsNotHtgTypeIs, m_this_row->GetComponentId());
}
}
else {
if( string("ADF").find(m_this_row->component_type)!=NPOS ) m_AgpErr->Msg(CAgpErr::W_CompIsNotHtgTypeIs, m_this_row->GetComponentId());
+ else if(m_this_row->component_type!='W') m_AgpErr->Msg( CAgpErr::W_CompIsLocalTypeNotW, m_this_row->GetComponentId() );
}
if( m_comp2len->size() ) {
@@ -837,11 +839,19 @@ void CAgpValidateReader::x_PrintGapCountsLine(XPrintTotalsItem& xprint, int gap_
void CAgpValidateReader::x_PrintTotals(CNcbiOstream& out, bool use_xml) // without comment counts
{
+ CIdsNotInAgp not_in_agp(*this);
+ string not_in_agp_msg = not_in_agp.CheckIds();
+
//// Counts of errors and warnings
int e_count=m_AgpErr->CountTotals(CAgpErrEx::E_Last);
// In case -fa or -len was used, add counts for G_InvalidCompId and G_CompEndGtLength.
e_count+=m_AgpErr->CountTotals(CAgpErrEx::G_Last);
int w_count=m_AgpErr->CountTotals(CAgpErrEx::W_Last);
+
+ if(not_in_agp_msg.size()) {
+ if(m_AgpErr->m_strict) e_count++; else w_count++;
+ }
+
if(e_count || w_count || m_ObjCount) {
if( m_ObjCount==0 && !m_AgpErr->m_MaxRepeatTopped &&
e_count==m_AgpErr->CountTotals(CAgpErrEx::E_NoValidLines)
@@ -892,6 +902,9 @@ void CAgpValidateReader::x_PrintTotals(CNcbiOstream& out, bool use_xml) // witho
// w: width for right alignment
int w = NStr::IntToString((unsigned)(m_CompId2Spans.size())).size(); // +1;
XPrintTotalsItem xprint(out, use_xml, w);
+ if(not_in_agp_msg.size() && !use_xml) {
+ out << " - - " << not_in_agp_msg << "\n";
+ }
xprint.line();
//// Prepare component/gap types and counts for later printing
@@ -1130,15 +1143,22 @@ void CAgpValidateReader::x_PrintTotals(CNcbiOstream& out, bool use_xml) // witho
}
}
if(use_xml) out << "</stats>\n";
+
+ /* This would print the message where it was previously.
+ (Could be moved up, if wanted...)
+ */
+
+ if(not_in_agp_msg.size()) {
+ if(use_xml) not_in_agp.PrintXml(out, not_in_agp_msg);
+ else not_in_agp.Print (out, not_in_agp_msg);
+ }
}
void CAgpValidateReader::PrintTotals(CNcbiOstream& out, bool use_xml)
{
x_PrintTotals(out, use_xml);
- if(m_comp2len->size()) {
- x_PrintIdsNotInAgp(out, use_xml);
- }
+ // if(m_comp2len->size()) x_PrintIdsNotInAgp(out, use_xml);
if(use_xml) {
if(m_CommentLineCount) out << " <CommentLineCount>" << m_CommentLineCount << "</CommentLineCount>\n";
@@ -1456,81 +1476,93 @@ bool CAgpValidateReader::x_PrintPatterns(
return mixedCategories||mixedPattern;
}
+void CAgpValidateReader::SetRowOutput(IAgpRowOutput* row_output)
+{
+ m_row_output = row_output;
+}
+
+/* An equivalent for the old functionality before splitting CheckIds() from Print()/PrintXml().
+void CAgpValidateReader::x_PrintIdsNotInAgp(CNcbiOstream& out, bool use_xml)
+{
+ CIdsNotInAgp not_in_agp(*this);
+ string msg = not_in_agp.CheckIds();
+ if(msg.size()) {
+ if(use_xml) not_in_agp.PrintXml(out, msg);
+ else not_in_agp.Print (out, msg);
+ }
+}
+*/
+
+//// class CAgpValidateReader::CIdsNotInAgp
// label = "component(s) from FASTA not found in AGP"
// label = "scaffold(s) not found in Chromosome from scaffold AGP"
// 2012/02/21: xml mode not tested since the current CGI has no info to provide this kind of validation
-void CAgpValidateReader::x_PrintIdsNotInAgp(CNcbiOstream& out, bool use_xml)
+string CAgpValidateReader::CIdsNotInAgp::CheckIds()
{
- CAccPatternCounter patterns;
- set<string> ids;
- int cnt=0;
-
- // ids in m_comp2len but not in m_CompId2Spans
- for(CMapCompLen::iterator it = m_comp2len->begin(); it != m_comp2len->end(); ++it) {
+ // ids in m_comp2len but not in m_CompId2Spans
+ for(CMapCompLen::iterator it = m_reader.m_comp2len->begin(); it != m_reader.m_comp2len->end(); ++it) {
string id;
- if(m_CheckObjLen) {
+ if(m_reader.m_CheckObjLen) {
// ids in m_comp2len but not in m_ObjIdSet
- TObjSet::iterator obj = m_ObjIdSet.find(it->first);
- if(obj==m_ObjIdSet.end()) {
+ TObjSet::iterator obj = m_reader.m_ObjIdSet.find(it->first);
+ if(obj==m_reader.m_ObjIdSet.end()) {
id=it->first;
}
}
else {
- TCompId2Spans::iterator spans = m_CompId2Spans.find(it->first);
- if(spans==m_CompId2Spans.end()) {
+ TCompId2Spans::iterator spans = m_reader.m_CompId2Spans.find(it->first);
+ if(spans==m_reader.m_CompId2Spans.end()) {
id=it->first;
}
}
if( id.size() &&
id.find("|") == NPOS // works only if AGP contains plain accessions...
) {
- patterns.AddName(it->first);
- ids.insert(it->first);
- cnt++;
+ m_patterns.AddName(it->first);
+ m_ids.insert(it->first);
+ m_cnt++;
}
}
- if(cnt>0) {
- string label =
- m_CheckObjLen ? "object name(s) in FASTA not found in AGP" :
- m_comp2len == &m_scaf2len ? "scaffold(s) not found in Chromosome from scaffold AGP":
- "component name(s) in FASTA not found in AGP";
+ if(m_cnt>0) return
+ m_reader.m_CheckObjLen ? "object name(s) in FASTA not found in AGP" :
+ m_reader.m_comp2len == &(m_reader.m_scaf2len) ? "scaffold(s) not found in Chromosome from scaffold AGP":
+ "component name(s) in FASTA not found in AGP";
+ return NcbiEmptyString; // OK
+}
- if(use_xml) {
- // print both patterns and ALL missing names
- label = label.substr(0, label.find(' '));
- out << "<MissingSeqNames level=\""+label+"\">\n";
- for(set<string>::iterator it = ids.begin(); it != ids.end(); ++it) {
- out << " <name>" << NStr::XmlEncode(*it) << "</name>\n";
- }
- }
- else {
- string tmp;
- NStr::Replace(label, "(s)", cnt==1 ? "" : "s", tmp);
- out << "\nWARNING -- " << cnt << " " << tmp << ": ";
- }
+void CAgpValidateReader::CIdsNotInAgp::Print(CNcbiOstream& out, const string& msg)
+{
+ string tmp, label=msg;
- if(!use_xml && cnt==1) {
- out << *(ids.begin()) << "\n";
- }
- else if(!use_xml && (cnt<m_AgpErr->m_MaxRepeat||m_AgpErr->m_MaxRepeat==0)) {
- out << "\n";
- for(set<string>::iterator it = ids.begin(); it != ids.end(); ++it) {
- out << " " << *it << "\n";
- }
- }
- else {
- x_PrintPatterns(patterns, NcbiEmptyString, 0, NULL, out, use_xml);
- }
- if(use_xml) {
- out << "</MissingSeqNames>\n";
+ NStr::Replace(label, "(s)", m_cnt==1 ? "" : "s", tmp);
+ out << "\n" << (m_reader.m_AgpErr->m_strict?"ERROR":"WARNING")
+ << " -- " << m_cnt << " " << tmp << ": ";
+
+ if(m_cnt==1) {
+ out << *(m_ids.begin()) << "\n";
+ }
+ else if(m_cnt<m_reader.m_AgpErr->m_MaxRepeat||m_reader.m_AgpErr->m_MaxRepeat==0) {
+ out << "\n";
+ for(set<string>::iterator it = m_ids.begin(); it != m_ids.end(); ++it) {
+ out << " " << *it << "\n";
}
}
+ else {
+ m_reader.x_PrintPatterns(m_patterns, NcbiEmptyString, 0, NULL, out, false);
+ }
}
-void CAgpValidateReader::SetRowOutput(IAgpRowOutput* row_output)
+void CAgpValidateReader::CIdsNotInAgp::PrintXml(CNcbiOstream& out, const string& msg)
{
- m_row_output = row_output;
+ // print both patterns and ALL missing names
+ string label = msg.substr(0, msg.find(' '));
+ out << "<MissingSeqNames level=\""+label+"\">\n";
+ for(set<string>::iterator it = m_ids.begin(); it != m_ids.end(); ++it) {
+ out << " <name>" << NStr::XmlEncode(*it) << "</name>\n";
+ }
+ m_reader.x_PrintPatterns(m_patterns, NcbiEmptyString, 0, NULL, out, true);
+ out << "</MissingSeqNames>\n";
}
//// class CValuesCount
diff --git a/c++/src/objtools/readers/bed_reader.cpp b/c++/src/objtools/readers/bed_reader.cpp
index 07059f3..14dc7ab 100644
--- a/c++/src/objtools/readers/bed_reader.cpp
+++ b/c++/src/objtools/readers/bed_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: bed_reader.cpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: bed_reader.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -122,7 +122,7 @@ CBedReader::~CBedReader()
CRef< CSeq_annot >
CBedReader::ReadSeqAnnot(
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -133,7 +133,7 @@ CBedReader::ReadSeqAnnot(
CRef< CSeq_annot >
CBedReader::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pEC )
+ ILineErrorListener* pEC )
// ----------------------------------------------------------------------------
{
const size_t MAX_RECORDS = 100000;
@@ -216,7 +216,7 @@ CBedReader::ReadSeqAnnot(
CRef< CSerialObject >
CBedReader::ReadObject(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CSerialObject> object(
@@ -228,7 +228,7 @@ CBedReader::ReadObject(
bool
CBedReader::xParseTrackLine(
const string& strLine,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if ( ! NStr::StartsWith( strLine, "track" ) ) {
@@ -280,7 +280,7 @@ bool CBedReader::xParseFeature(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
unsigned int featureCount,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
static int count = 0;
@@ -314,7 +314,7 @@ bool CBedReader::xParseFeatureThreeFeatFormat(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
unsigned int baseId,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if (!xAppendFeatureChrom(fields, annot, baseId, pEC)) {
@@ -336,7 +336,7 @@ bool CBedReader::xAppendFeatureChrom(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
unsigned int baseId,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CSeq_annot::C_Data::TFtable& ftable = annot->SetData().SetFtable();
@@ -363,7 +363,7 @@ bool CBedReader::xAppendFeatureThick(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
unsigned int baseId,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CSeq_annot::C_Data::TFtable& ftable = annot->SetData().SetFtable();
@@ -389,7 +389,7 @@ bool CBedReader::xAppendFeatureBlock(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
unsigned int baseId,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CSeq_annot::C_Data::TFtable& ftable = annot->SetData().SetFtable();
@@ -413,7 +413,7 @@ bool CBedReader::xAppendFeatureBlock(
bool CBedReader::xParseFeatureUserFormat(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
// assign
@@ -758,11 +758,13 @@ void CBedReader::xSetFeatureIdsBlock(
pXrefChrom->SetId(*pIdChrom);
feature->SetXref().push_back(pXrefChrom);
- CRef<CFeat_id> pIdBlock(new CFeat_id);
- pIdBlock->SetLocal().SetId(baseId+1);
- CRef<CSeqFeatXref> pXrefBlock(new CSeqFeatXref);
- pXrefBlock->SetId(*pIdBlock);
- feature->SetXref().push_back(pXrefBlock);
+ if (xContainsThickFeature(fields)) {
+ CRef<CFeat_id> pIdThick(new CFeat_id);
+ pIdThick->SetLocal().SetId(baseId+1);
+ CRef<CSeqFeatXref> pXrefBlock(new CSeqFeatXref);
+ pXrefBlock->SetId(*pIdThick);
+ feature->SetXref().push_back(pXrefBlock);
+ }
}
// ----------------------------------------------------------------------------
@@ -1008,7 +1010,7 @@ bool
CBedReader::ReadTrackData(
ILineReader& lr,
CRawBedTrack& rawdata,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if (m_CurBatchSize == m_MaxBatchSize) {
@@ -1037,7 +1039,7 @@ bool
CBedReader::xReadBedRecordRaw(
const string& line,
CRawBedRecord& record,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if (line == "browser" || NStr::StartsWith(line, "browser ")
@@ -1143,7 +1145,28 @@ CBedReader::xContainsThickFeature(
const vector<string>& fields) const
// ----------------------------------------------------------------------------
{
- return (fields.size() >= 8);
+ if (fields.size() < 8) {
+ return false;
+ }
+
+ int start = -1, from = -1, to = -1;
+ try {
+ start = NStr::StringToInt(fields[1]);
+ from = NStr::StringToInt(fields[6]);
+ to = NStr::StringToInt(fields[7]);
+ }
+ catch (std::exception&) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Error,
+ 0,
+ "Invalid data line: Bad \"Start/ThickStart/ThickStop\" values." ) );
+ pErr->Throw();
+ }
+ if (start == from && from == to) {
+ return false;
+ }
+ return true;
}
@@ -1162,7 +1185,7 @@ bool
CBedReader::xReadBedDataRaw(
ILineReader& lr,
CRawBedTrack& rawdata,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
rawdata.Reset();
diff --git a/c++/src/objtools/readers/cigar.cpp b/c++/src/objtools/readers/cigar.cpp
index a2d1444..c94a1c3 100644
--- a/c++/src/objtools/readers/cigar.cpp
+++ b/c++/src/objtools/readers/cigar.cpp
@@ -1,4 +1,4 @@
-/* $Id: cigar.cpp 142435 2008-10-06 20:26:37Z ucko $
+/* $Id: cigar.cpp 461118 2015-03-06 13:29:39Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -131,6 +131,7 @@ SCigarAlignment::EFormat SCigarAlignment::GuessFormat(const string& s,
case eLengthFirst:
case eLengthFirstIfAmbiguous:
result = eLengthFirst;
+ break;
case eOpFirst:
case eOpFirstIfAmbiguous:
result = eOpFirst;
diff --git a/c++/src/objtools/readers/fasta.cpp b/c++/src/objtools/readers/fasta.cpp
index c3cf096..e720dc7 100644
--- a/c++/src/objtools/readers/fasta.cpp
+++ b/c++/src/objtools/readers/fasta.cpp
@@ -1,4 +1,4 @@
-/* $Id: fasta.cpp 452767 2014-11-24 19:16:42Z ivanov $
+/* $Id: fasta.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -287,7 +287,7 @@ void CFastaReader::SetMinGaps(TSeqPos gapNmin, TSeqPos gap_Unknown_length)
}
inline
-void CFastaReader::CloseGap(bool atStartOfLine, IMessageListener * pMessageListener)
+void CFastaReader::CloseGap(bool atStartOfLine, ILineErrorListener * pMessageListener)
{
if (m_CurrentGapLength > 0) {
x_CloseGap(m_CurrentGapLength, atStartOfLine, pMessageListener);
@@ -296,7 +296,7 @@ void CFastaReader::CloseGap(bool atStartOfLine, IMessageListener * pMessageListe
}
CRef<CSerialObject>
-CFastaReader::ReadObject (ILineReader &lr, IMessageListener *pMessageListener)
+CFastaReader::ReadObject (ILineReader &lr, ILineErrorListener *pMessageListener)
{
CRef<CSerialObject> object(
ReadSeqEntry( lr, pMessageListener ).ReleaseOrNull() );
@@ -304,7 +304,7 @@ CFastaReader::ReadObject (ILineReader &lr, IMessageListener *pMessageListener)
}
CRef<CSeq_entry>
-CFastaReader::ReadSeqEntry (ILineReader &lr, IMessageListener *pMessageListener)
+CFastaReader::ReadSeqEntry (ILineReader &lr, ILineErrorListener *pMessageListener)
{
CRef<ILineReader> pTempLineReader( &lr );
CTempRefSwap<ILineReader> tempRefSwap(m_LineReader, pTempLineReader);
@@ -312,7 +312,7 @@ CFastaReader::ReadSeqEntry (ILineReader &lr, IMessageListener *pMessageListener)
return ReadSet(kMax_Int, pMessageListener);
}
-CRef<CSeq_entry> CFastaReader::ReadOneSeq(IMessageListener * pMessageListener)
+CRef<CSeq_entry> CFastaReader::ReadOneSeq(ILineErrorListener * pMessageListener)
{
m_CurrentSeq.Reset(new CBioseq);
// m_CurrentMask.Reset();
@@ -384,7 +384,7 @@ CRef<CSeq_entry> CFastaReader::ReadOneSeq(IMessageListener * pMessageListener)
}
c = line[0];
- if (c == '!' || c == '#') {
+ if (c == '!' || c == '#' || c == ';') {
// no content, just a comment or blank line
continue;
} else if (need_defline) {
@@ -435,7 +435,7 @@ CRef<CSeq_entry> CFastaReader::ReadOneSeq(IMessageListener * pMessageListener)
return entry;
}
-CRef<CSeq_entry> CFastaReader::x_ReadSegSet(IMessageListener * pMessageListener)
+CRef<CSeq_entry> CFastaReader::x_ReadSegSet(ILineErrorListener * pMessageListener)
{
CFlagGuard guard(m_Flags, GetFlags() | fInSegSet);
CRef<CSeq_entry> entry(new CSeq_entry), master(new CSeq_entry), parts;
@@ -491,7 +491,7 @@ CRef<CSeq_entry> CFastaReader::x_ReadSegSet(IMessageListener * pMessageListener)
return entry;
}
-CRef<CSeq_entry> CFastaReader::ReadSet(int max_seqs, IMessageListener * pMessageListener)
+CRef<CSeq_entry> CFastaReader::ReadSet(int max_seqs, ILineErrorListener * pMessageListener)
{
CRef<CSeq_entry> entry(new CSeq_entry);
if (TestFlag(fOneSeq)) {
@@ -534,7 +534,7 @@ void CFastaReader::SetIDGenerator(CSeqIdGenerator& gen)
m_IDGenerator.Reset(&gen);
}
-void CFastaReader::ParseDefLine(const TStr& s, IMessageListener * pMessageListener)
+void CFastaReader::ParseDefLine(const TStr& s, ILineErrorListener * pMessageListener)
{
size_t start = 1, pos, len = s.length(), range_len = 0, title_start;
TSeqPos range_start, range_end;
@@ -729,7 +729,7 @@ void CFastaReader::ParseDefLine(const TStr& s, IMessageListener * pMessageListen
}
bool CFastaReader::ParseIDs(
- const TStr& s, IMessageListener * pMessageListener)
+ const TStr& s, ILineErrorListener * pMessageListener)
{
// if user wants all ids to be purely local, no problem
if( m_iFlags & CReaderBase::fAllIdsAsLocal )
@@ -811,7 +811,7 @@ bool CFastaReader::ParseIDs(
size_t CFastaReader::ParseRange(
const TStr& s, TSeqPos& start, TSeqPos& end,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
bool on_start = false;
bool negative = false;
@@ -849,7 +849,7 @@ size_t CFastaReader::ParseRange(
}
void CFastaReader::ParseTitle(
- const SLineTextAndLoc & lineInfo, IMessageListener * pMessageListener)
+ const SLineTextAndLoc & lineInfo, ILineErrorListener * pMessageListener)
{
const static size_t kWarnTitleLength = 1000;
if( lineInfo.m_sLineText.length() > kWarnTitleLength ) {
@@ -894,7 +894,7 @@ void CFastaReader::GenerateID(void)
}
void CFastaReader::CheckDataLine(
- const TStr& s, IMessageListener * pMessageListener)
+ const TStr& s, ILineErrorListener * pMessageListener)
{
// make sure the first data line has at least SOME resemblance to
// actual sequence data.
@@ -950,7 +950,7 @@ void CFastaReader::CheckDataLine(
}
void CFastaReader::ParseDataLine(
- const TStr& s, IMessageListener * pMessageListener)
+ const TStr& s, ILineErrorListener * pMessageListener)
{
if( NStr::StartsWith(s, ">?") ) {
ParseGapLine(s, pMessageListener);
@@ -1072,7 +1072,7 @@ void CFastaReader::ParseDataLine(
}
void CFastaReader::x_CloseGap(
- TSeqPos len, bool atStartOfLine, IMessageListener * pMessageListener)
+ TSeqPos len, bool atStartOfLine, ILineErrorListener * pMessageListener)
{
_ASSERT(len > 0 && TestFlag(fParseGaps));
@@ -1142,7 +1142,7 @@ void CFastaReader::x_CloseMask(void)
}
bool CFastaReader::ParseGapLine(
- const TStr& line, IMessageListener * pMessageListener)
+ const TStr& line, ILineErrorListener * pMessageListener)
{
_ASSERT( NStr::StartsWith(line, ">?") );
@@ -1380,7 +1380,7 @@ bool CFastaReader::ParseGapLine(
return true;
}
-void CFastaReader::AssembleSeq(IMessageListener * pMessageListener)
+void CFastaReader::AssembleSeq(ILineErrorListener * pMessageListener)
{
CSeq_inst& inst = m_CurrentSeq->SetInst();
@@ -1547,7 +1547,7 @@ void CFastaReader::AssembleSeq(IMessageListener * pMessageListener)
}
}
-void CFastaReader::AssignMolType(IMessageListener * pMessageListener)
+void CFastaReader::AssignMolType(ILineErrorListener * pMessageListener)
{
CSeq_inst& inst = m_CurrentSeq->SetInst();
CSeq_inst::EMol default_mol;
@@ -1600,7 +1600,7 @@ bool
CFastaReader::CreateWarningsForSeqDataInTitle(
const TStr& sLineText,
TSeqPos iLineNum,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
bool bFoundProblem = false;
@@ -1661,7 +1661,7 @@ CFastaReader::CreateWarningsForSeqDataInTitle(
}
CRef<CSeq_entry> CFastaReader::ReadAlignedSet(
- int reference_row, IMessageListener * pMessageListener)
+ int reference_row, ILineErrorListener * pMessageListener)
{
TIds ids;
CRef<CSeq_entry> entry = x_ReadSeqsToAlign(ids, pMessageListener);
@@ -1686,7 +1686,7 @@ CRef<CSeq_entry> CFastaReader::ReadAlignedSet(
}
CRef<CSeq_entry> CFastaReader::x_ReadSeqsToAlign(TIds& ids,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
CRef<CSeq_entry> entry(new CSeq_entry);
vector<TSeqPos> lengths;
@@ -1865,7 +1865,7 @@ private:
CRef<CSeq_entry> ReadFasta(CNcbiIstream& in, TReadFastaFlags flags,
int* counter, vector<CConstRef<CSeq_loc> >* lcv,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
CRef<ILineReader> lr(ILineReader::New(in));
CFastaReader reader(*lr, flags);
@@ -1891,10 +1891,10 @@ public:
protected:
void ParseDefLine(const TStr& s,
- IMessageListener * pMessageListener);
+ ILineErrorListener * pMessageListener);
void ParseTitle(const SLineTextAndLoc & lineInfo,
- IMessageListener * pMessageListener = 0);
- void AssembleSeq(IMessageListener * pMessageListener);
+ ILineErrorListener * pMessageListener = 0);
+ void AssembleSeq(ILineErrorListener * pMessageListener);
private:
SFastaFileMap* m_Map;
@@ -1909,7 +1909,7 @@ CFastaMapper::CFastaMapper(ILineReader& reader, SFastaFileMap* fasta_map,
fasta_map->file_map.resize(0);
}
-void CFastaMapper::ParseDefLine(const TStr& s, IMessageListener * pMessageListener)
+void CFastaMapper::ParseDefLine(const TStr& s, ILineErrorListener * pMessageListener)
{
TParent::ParseDefLine(s, pMessageListener); // We still want the default behavior.
m_MapEntry.seq_id = GetIDs().front()->AsFastaString(); // XXX -- GetBestID?
@@ -1921,13 +1921,13 @@ void CFastaMapper::ParseDefLine(const TStr& s, IMessageListener * pMessageListen
}
void CFastaMapper::ParseTitle(const SLineTextAndLoc & s,
- IMessageListener * pMessageListener)
+ ILineErrorListener * pMessageListener)
{
TParent::ParseTitle(s, pMessageListener);
m_MapEntry.description = s.m_sLineText;
}
-void CFastaMapper::AssembleSeq(IMessageListener * pMessageListener)
+void CFastaMapper::AssembleSeq(ILineErrorListener * pMessageListener)
{
TParent::AssembleSeq(pMessageListener);
m_Map->file_map.push_back(m_MapEntry);
@@ -1979,7 +1979,7 @@ void ScanFastaFile(IFastaEntryScan* scanner,
void CFastaReader::x_ApplyAllMods(
CBioseq & bioseq,
TSeqPos iLineNum,
- IMessageListener * pMessageListener )
+ ILineErrorListener * pMessageListener )
{
// this is called even if there the user did not request
// mods to be added because we want to give a warning if there
@@ -2166,8 +2166,7 @@ CFastaReader::SGap::SGap(
{
}
-
-void CFastaReader::SetGapLinkageEvidence(CSeq_gap::EType type, CLinkage_evidence::EType evidence)
+void CFastaReader::SetGapLinkageEvidences(CSeq_gap::EType type, const set<int>& evidences)
{
if (type == -1)
m_gap_type.Release();
@@ -2175,12 +2174,14 @@ void CFastaReader::SetGapLinkageEvidence(CSeq_gap::EType type, CLinkage_evidence
m_gap_type.Reset(new SGap::TGapTypeObj(type));
m_gap_linkage_evidence.clear();
- if (evidence != -1)
- m_gap_linkage_evidence.insert(evidence);
+ ITERATE(set<int>, it, evidences)
+ {
+ m_gap_linkage_evidence.insert((CLinkage_evidence::EType)*it);
+ }
}
void CFastaReader::PostWarning(
- IMessageListener * pMessageListener,
+ ILineErrorListener * pMessageListener,
EDiagSev _eSeverity, size_t _uLineNum, CTempString _MessageStrmOps, CObjReaderParseException::EErrCode _eErrCode, ILineError::EProblem _eProblem, CTempString _sFeature, CTempString _sQualName, CTempString _sQualValue)
{
if (find(m_ignorable.begin(), m_ignorable.end(), _eProblem) != m_ignorable.end())
diff --git a/c++/src/objtools/readers/format_guess_ex.cpp b/c++/src/objtools/readers/format_guess_ex.cpp
index d41cb64..532499b 100644
--- a/c++/src/objtools/readers/format_guess_ex.cpp
+++ b/c++/src/objtools/readers/format_guess_ex.cpp
@@ -1,4 +1,4 @@
-/* $Id: format_guess_ex.cpp 436470 2014-05-28 16:25:19Z gotvyans $
+/* $Id: format_guess_ex.cpp 479675 2015-09-22 18:45:37Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -291,14 +291,14 @@ bool CFormatGuessEx::x_TryBed()
CBedReader Reader;
CStreamLineReader LineReader(m_LocalBuffer);
- vector<CRef<CSeq_annot> > LocalAnnots;
+ list<CRef<CSeq_annot> > LocalAnnots;
try {
Reader.ReadSeqAnnots(LocalAnnots, LineReader);
} catch(CException&) {
} catch(...) {
}
- ITERATE(vector<CRef<CSeq_annot> >, AnnotIter, LocalAnnots) {
+ ITERATE(list<CRef<CSeq_annot> >, AnnotIter, LocalAnnots) {
if(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&
(*AnnotIter)->GetData().IsFtable())
BedCount++;
@@ -360,16 +360,16 @@ bool CFormatGuessEx::x_TryGtf()
CGtfReader Reader(CGtfReader::fNewCode);
CStreamLineReader LineReader(m_LocalBuffer);
- vector<CRef<CSeq_annot> > LocalAnnots;
+ CGtfReader::TAnnots LocalAnnots;
try {
Reader.ReadSeqAnnotsNew(LocalAnnots, LineReader);
} catch(CException&) {
} catch(...) {
}
- ITERATE(vector<CRef<CSeq_annot> >, AnnotIter, LocalAnnots) {
- if(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&
- (*AnnotIter)->GetData().IsFtable())
+ ITERATE(CGtfReader::TAnnots, AnnotIter, LocalAnnots) {
+ if(!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
+ (**AnnotIter).GetData().IsFtable())
GtfCount++;
}
@@ -386,16 +386,16 @@ bool CFormatGuessEx::x_TryGff3()
CGff3Reader Reader(CGff3Reader::fNewCode);
CStreamLineReader LineReader(m_LocalBuffer);
- vector<CRef<CSeq_annot> > LocalAnnots;
+ CGff3Reader::TAnnots LocalAnnots;
try {
Reader.ReadSeqAnnotsNew(LocalAnnots, LineReader);
} catch(CException&) {
} catch(...) {
}
- ITERATE(vector<CRef<CSeq_annot> >, AnnotIter, LocalAnnots) {
- if(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&
- (*AnnotIter)->GetData().IsFtable())
+ ITERATE(CGff3Reader::TAnnots, AnnotIter, LocalAnnots) {
+ if (!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
+ (**AnnotIter).GetData().IsFtable())
Gff3Count++;
}
@@ -412,16 +412,16 @@ bool CFormatGuessEx::x_TryGff2()
CGff2Reader Reader(CGff2Reader::fNewCode);
CStreamLineReader LineReader(m_LocalBuffer);
- vector<CRef<CSeq_annot> > LocalAnnots;
+ CGff2Reader::TAnnots LocalAnnots;
try {
Reader.ReadSeqAnnotsNew(LocalAnnots, LineReader);
} catch(CException&) {
} catch(...) {
}
- ITERATE(vector<CRef<CSeq_annot> >, AnnotIter, LocalAnnots) {
- if(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&
- (*AnnotIter)->GetData().IsFtable())
+ ITERATE(CGff2Reader::TAnnots, AnnotIter, LocalAnnots) {
+ if (!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&
+ (**AnnotIter).IsFtable())
Gff2Count++;
}
diff --git a/c++/src/objtools/readers/gff2_data.cpp b/c++/src/objtools/readers/gff2_data.cpp
index 016dcda..a024df1 100644
--- a/c++/src/objtools/readers/gff2_data.cpp
+++ b/c++/src/objtools/readers/gff2_data.cpp
@@ -1,4 +1,4 @@
-/* $Id: gff2_data.cpp 464934 2015-04-15 15:05:28Z ivanov $
+/* $Id: gff2_data.cpp 479671 2015-09-22 18:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -180,21 +180,29 @@ CGff2Record::~CGff2Record()
delete m_pePhase;
};
+
+unsigned int CGff2Record::m_nextId(0);
+// -----------------------------------------------------------------------------
+unsigned int CGff2Record::NextId()
+// -----------------------------------------------------------------------------
+{
+ return ++m_nextId;
+}
+
// -----------------------------------------------------------------------------
-string CGff2Record::NextId()
+void CGff2Record::ResetId()
// -----------------------------------------------------------------------------
{
- static size_t nextId(0);
- return string("local-id:")+NStr::NumericToString(++nextId);
+ m_nextId = 0;
}
-void CGff2Record::TokenizeGFF(vector<CTempString>& columns, const CTempString& in_line)
+void CGff2Record::TokenizeGFF(vector<CTempStringEx>& columns, const CTempStringEx& in_line)
{
columns.clear();
columns.reserve(9);
size_t index;
// first try to split just using tabs
- NStr::Tokenize(in_line, "\t", columns, NStr::eMergeDelims);
+ NStr::Tokenize(in_line, "\t", columns, NStr::fSplit_MergeDelims);
if (columns.size() == 9)
return;
columns.clear();
@@ -204,17 +212,17 @@ void CGff2Record::TokenizeGFF(vector<CTempString>& columns, const CTempString& i
const CTempString digits("0123456789");
size_t current = 0;
- while (current != CTempString::npos && columns.size()<8 &&
- (index = in_line.find_first_of(space_tab_delim, current)) != CTempString::npos) {
- CTempString next = in_line.substr(current, index-current);
+ while (current != CTempStringEx::npos && columns.size()<8 &&
+ (index = in_line.find_first_of(space_tab_delim, current)) != CTempStringEx::npos) {
+ CTempStringEx next = in_line.substr(current, index-current);
current = in_line.find_first_not_of(space_tab_delim, index);
if (columns.size() == 5) {
// reminder:
// columns [3] and [4] are positions and must always be numeric
// column [5] is a score (floating point or "." if absent)
- bool isNumericCol3 = columns[3].find_first_not_of(digits) == CTempString::npos;
- bool isNumericCol4 = columns[4].find_first_not_of(digits) == CTempString::npos;
- bool isNumericNext = next.find_first_not_of(digits) == CTempString::npos;
+ bool isNumericCol3 = columns[3].find_first_not_of(digits) == CTempStringEx::npos;
+ bool isNumericCol4 = columns[4].find_first_not_of(digits) == CTempStringEx::npos;
+ bool isNumericNext = next.find_first_not_of(digits) == CTempStringEx::npos;
if (!isNumericCol3 && isNumericCol4 && isNumericNext) {
// merge col2 with col3 and shift subsequent columns
@@ -230,7 +238,7 @@ void CGff2Record::TokenizeGFF(vector<CTempString>& columns, const CTempString& i
}
columns.push_back(next);
}
- if (current != CTempString::npos)
+ if (current != CTempStringEx::npos)
columns.push_back(in_line.substr(current));
}
// ----------------------------------------------------------------------------
@@ -238,7 +246,7 @@ bool CGff2Record::AssignFromGff(
const string& strRawInput )
// ----------------------------------------------------------------------------
{
- vector< CTempString > columns;
+ vector< CTempStringEx > columns;
TokenizeGFF(columns, strRawInput);
if ( columns.size() < 9 ) {
@@ -252,11 +260,23 @@ bool CGff2Record::AssignFromGff(
}
// to do: more sanity checks
- m_strId = columns[0];
- m_strSource = columns[1];
- m_strType = columns[2];
- m_uSeqStart = NStr::StringToUInt( columns[3] ) - 1;
- m_uSeqStop = NStr::StringToUInt( columns[4] ) - 1;
+ columns[0].Copy(m_strId, 0, CTempString::npos);
+ columns[1].Copy(m_strSource, 0, CTempString::npos);
+ columns[2].Copy(m_strType, 0, CTempString::npos);
+
+ try {
+ m_uSeqStart = NStr::StringToUInt( columns[3] ) - 1;
+ m_uSeqStop = NStr::StringToUInt( columns[4] ) - 1;
+ }
+ catch (const CException&) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Error,
+ 0,
+ "Bad data line: Both \"start\" and \"stop\" must be positive integers.",
+ ILineError::eProblem_FeatureBadStartAndOrStop));
+ pErr->Throw();
+ }
if (m_uSeqStop < m_uSeqStart) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
@@ -272,37 +292,44 @@ bool CGff2Record::AssignFromGff(
m_pdScore = new double( NStr::StringToDouble( columns[5] ) );
}
- char strand = columns[6][0];
- switch (strand) {
+ enum ENa_strand strand;
+ switch (columns[6][0]) {
default:
- m_peStrand = new ENa_strand(objects::eNa_strand_unknown);
+ strand = objects::eNa_strand_unknown;
break;
case '+':
- m_peStrand = new ENa_strand(objects::eNa_strand_plus);
+ strand = objects::eNa_strand_plus;
break;
case '-':
- m_peStrand = new ENa_strand(objects::eNa_strand_minus);
+ strand = objects::eNa_strand_minus;
break;
case '.':
- m_peStrand = new ENa_strand(objects::eNa_strand_both);
+ strand = objects::eNa_strand_both;
break;
}
+ m_peStrand = new ENa_strand(strand);
+
+
+ enum CCdregion::EFrame frame = CCdregion::eFrame_not_set;
if ( columns[7] == "0" ) {
- m_pePhase = new TFrame( CCdregion::eFrame_one );
+ frame = CCdregion::eFrame_one;
}
else
if ( columns[7] == "1" ) {
- m_pePhase = new TFrame( CCdregion::eFrame_two );
+ frame = CCdregion::eFrame_two;
}
else
if ( columns[7] == "2" ) {
- m_pePhase = new TFrame( CCdregion::eFrame_three );
+ frame = CCdregion::eFrame_three;
}
- m_strAttributes = columns[8];
+ if (frame != CCdregion::eFrame_not_set)
+ m_pePhase = new TFrame(frame);
+
+ columns[8].Copy(m_strAttributes, 0, CTempString::npos);
- return x_AssignAttributesFromGff( m_strAttributes );
+ return x_AssignAttributesFromGff(columns[8]);
}
// ----------------------------------------------------------------------------
@@ -326,11 +353,12 @@ bool CGff2Record::GetAttribute(
list<string>& values ) const
// ----------------------------------------------------------------------------
{
- string strValues;
- if (!GetAttribute(strKey, strValues)) {
+ values.clear();
+ TAttrCit it = m_Attributes.find(strKey);
+ if (it == m_Attributes.end()) {
return false;
}
- NStr::Split(strValues, ",", values);
+ NStr::Split(it->second, ",", values);
return !values.empty();
}
@@ -351,14 +379,14 @@ CRef<CSeq_loc> CGff2Record::GetSeqLoc(
pLocation->SetInt().SetId(*GetSeqId(flags));
pLocation->SetInt().SetFrom(SeqStart());
pLocation->SetInt().SetTo(SeqStop());
- if (IsSetStrand()) {
+ if (IsSetStrand()) {
pLocation->SetInt().SetStrand(Strand());
- }
+ }
return pLocation;
-}
+ }
// ----------------------------------------------------------------------------
-string CGff2Record::x_NormalizedAttributeKey(
+string CGff2Record::xNormalizedAttributeKey(
const string& strRawKey )
// ----------------------------------------------------------------------------
{
@@ -367,7 +395,7 @@ string CGff2Record::x_NormalizedAttributeKey(
}
// ----------------------------------------------------------------------------
-string CGff2Record::x_NormalizedAttributeValue(
+string CGff2Record::xNormalizedAttributeValue(
const string& strRawValue )
// ----------------------------------------------------------------------------
{
@@ -383,28 +411,108 @@ string CGff2Record::x_NormalizedAttributeValue(
// ----------------------------------------------------------------------------
+CTempString x_GetNextAttribute(CTempString& input)
+{
+ CTempString result;
+ bool inQuotes = false;
+ size_t i = 0;
+ for (; i < input.length(); i++)
+ {
+ if (inQuotes) {
+ if (input[i] == '\"') {
+ inQuotes = false;
+ }
+ }
+ else { // not in quotes
+ if (input[i] == ';') {
+ result = NStr::TruncateSpaces_Unsafe(input.substr(0, i));
+ if (!result.empty())
+ {
+ input = input.substr(i+1);
+ return result;
+ }
+ }
+ else {
+ if (input[i] == '\"') {
+ inQuotes = true;
+ }
+ }
+ }
+ }
+ result = NStr::TruncateSpaces_Unsafe(input);
+ input.clear();
+ return result;
+}
+
+bool x_GetNextAttribute(CTempString& input, CTempString& key, CTempString& value)
+{
+ size_t semicolon = CTempString::npos;
+ size_t space = CTempString::npos;
+ size_t equal = CTempString::npos;
+
+ key.clear();
+ value.clear();
+
+ bool inQuotes = false;
+ size_t i = 0;
+ for (; i < input.length(); i++)
+ {
+ if (inQuotes) {
+ if (input[i] == '\"') {
+ inQuotes = false;
+ }
+ }
+ else { // not in quotes
+ switch (input[i])
+ {
+ case ';':
+ semicolon = i;
+ break;
+ case ' ':
+ if (space == CTempString::npos && equal == CTempString::npos)
+ space = i;
+ continue;
+ case '"':
+ inQuotes = true;
+ continue;
+ case '=':
+ if (equal == CTempString::npos)
+ equal = i;
+ continue;
+ default:
+ continue;
+ }
+ break;
+ }
+ }
+
+ if (semicolon == CTempString::npos)
+ semicolon = input.length();
+
+ if (equal == CTempString::npos)
+ equal = min(space, semicolon);
+
+ key = NStr::TruncateSpaces_Unsafe(input.substr(0, equal));
+ value = NStr::TruncateSpaces_Unsafe(input.substr(equal + 1, semicolon - equal - 1));
+
+ input = NStr::TruncateSpaces_Unsafe(input.substr(semicolon+1));
+
+ return !key.empty();
+}
+
bool CGff2Record::x_AssignAttributesFromGff(
const string& strRawAttributes )
// ----------------------------------------------------------------------------
{
m_Attributes.clear();
- vector< string > attributes;
- x_SplitGffAttributes(strRawAttributes, attributes);
- for ( size_t u=0; u < attributes.size(); ++u ) {
- string strKey;
- string strValue;
- if ( ! NStr::SplitInTwo( attributes[u], "=", strKey, strValue ) ) {
- if ( ! NStr::SplitInTwo( attributes[u], " ", strKey, strValue ) ) {
- m_Attributes[attributes[u]] = "";
- continue;
- }
- }
- if ( strKey.empty() && strValue.empty() ) {
- // Probably due to trailing "; ". Sequence Ontology generates such
- // things.
- continue;
- }
- m_Attributes[ strKey ] = strValue;
+ CTempString input(strRawAttributes);
+ CTempString next;
+ CTempString strKey;
+ CTempString strValue;
+
+ while (!input.empty() && x_GetNextAttribute(input, strKey, strValue))
+ {
+ m_Attributes[strKey] = strValue;
}
return true;
}
@@ -480,8 +588,14 @@ bool CGff2Record::UpdateFeature(
}
else {
// indicates the feature location is already under construction
- pFeature->SetLocation(*pFeature->SetLocation().Add(*pAddLoc, CSeq_loc::fSortAndMerge_All, 0));
- }
+ pFeature->SetLocation(*pFeature->SetLocation().Add(
+ *pAddLoc, CSeq_loc::fSortAndMerge_All, 0));
+ if (pFeature->GetLocation().IsInt()) {
+ CRef<CSeq_loc> pOld(new CSeq_loc);
+ pOld->Assign(pFeature->GetLocation());
+ pFeature->SetLocation().SetMix().AddSeqLoc(*pOld);
+ }
+ }
return true;
}
@@ -490,12 +604,12 @@ bool CGff2Record::x_MigrateId(
CRef<CSeq_feat> pFeature ) const
// ----------------------------------------------------------------------------
{
- string featIdStr;
- if (!GetAttribute("ID", featIdStr)) {
- featIdStr = NextId();
- }
+ unsigned int featId = NextId();
+// if (!GetAttribute("ID", featIdStr)) {
+// featIdStr = NextId();
+// }
CRef<CFeat_id> pFeatId(new CFeat_id);
- pFeatId->SetLocal().SetStr(featIdStr);
+ pFeatId->SetLocal().SetId(featId);
pFeature->SetId(*pFeatId);
return true;
}
@@ -544,7 +658,7 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("Note");
if (it != attrs_left.end()) {
- pFeature->SetComment(x_NormalizedAttributeValue(it->second));
+ pFeature->SetComment(xNormalizedAttributeValue(it->second));
attrs_left.erase(it);
}
@@ -554,7 +668,7 @@ bool CGff2Record::x_MigrateAttributes(
NStr::Tokenize(it->second, ",", dbxrefs, NStr::eMergeDelims);
for (vector<string>::iterator it1 = dbxrefs.begin(); it1 != dbxrefs.end();
++it1 ) {
- string dbtag = x_NormalizedAttributeValue(*it1);
+ string dbtag = xNormalizedAttributeValue(*it1);
pFeature->SetDbxref().push_back(CGff2Reader::x_ParseDbtag(dbtag));
}
attrs_left.erase(it);
@@ -573,15 +687,9 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("Name");
if (it != attrs_left.end()) {
if (0 == NStr::CompareNocase(Type(), "cds")) {
- CRef<CSeqFeatData> pData(new CSeqFeatData);
- pData->SetProt().SetName().push_back(it->second);
- CRef<CSeqFeatXref> pName(new CSeqFeatXref);
- pName->SetData(*pData);
- pFeature->SetXref().push_back(pName);
attrs_left.erase(it);
}
if (0 == NStr::CompareNocase(Type(), "mRNA")) {
- pFeature->SetData().SetRna().SetExt().SetName(it->second);
attrs_left.erase(it);
}
}
@@ -610,7 +718,8 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("description");
if (it != attrs_left.end()) {
if (pFeature->GetData().IsGene()) {
- pFeature->SetData().SetGene().SetDesc(it->second);
+ string description = xNormalizedAttributeValue(it->second);
+ pFeature->SetData().SetGene().SetDesc(description);
attrs_left.erase(it);
}
}
@@ -618,7 +727,7 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("exception");
if (it != attrs_left.end()) {
pFeature->SetExcept(true);
- pFeature->SetExcept_text(x_NormalizedAttributeValue(it->second));
+ pFeature->SetExcept_text(xNormalizedAttributeValue(it->second));
attrs_left.erase(it);
}
@@ -635,7 +744,7 @@ bool CGff2Record::x_MigrateAttributes(
if (it != attrs_left.end()) {
const string strExperimentDefault(
"experimental evidence, no additional details recorded" );
- string value = x_NormalizedAttributeValue(it->second);
+ string value = xNormalizedAttributeValue(it->second);
if (value == strExperimentDefault) {
pFeature->SetExp_ev(CSeq_feat::eExp_ev_experimental);
}
@@ -656,7 +765,20 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("gene");
if (it != attrs_left.end()) {
if (pFeature->GetData().IsGene()) {
- pFeature->SetData().SetGene().SetLocus(it->second);
+ list<string> geneValues;
+ NStr::Split(it->second, ",", geneValues);
+ string value;
+ list<string>::const_iterator cit = geneValues.begin();
+ if (cit != geneValues.end()) {
+ value = xNormalizedAttributeValue(*cit);
+ pFeature->SetData().SetGene().SetLocus(value);
+ cit++;
+ while (cit != geneValues.end()) {
+ value = xNormalizedAttributeValue(*cit);
+ pFeature->SetData().SetGene().SetSyn().push_back(value);
+ cit++;
+ }
+ }
attrs_left.erase(it);
}
}
@@ -677,7 +799,7 @@ bool CGff2Record::x_MigrateAttributes(
NStr::Tokenize(it->second, ",", synonyms, NStr::eMergeDelims);
for (vector<string>::iterator it1 = synonyms.begin(); it1 != synonyms.end();
++it1 ) {
- string synonym = x_NormalizedAttributeValue(*it1);
+ string synonym = xNormalizedAttributeValue(*it1);
pFeature->SetData().SetGene().SetSyn().push_back(synonym);
}
attrs_left.erase(it);
@@ -688,7 +810,7 @@ bool CGff2Record::x_MigrateAttributes(
if (it != attrs_left.end()) {
const string strInferenceDefault(
"non-experimental evidence, no additional details recorded" );
- string value = x_NormalizedAttributeValue(it->second);
+ string value = xNormalizedAttributeValue(it->second);
if (value == strInferenceDefault) {
pFeature->SetExp_ev(CSeq_feat::eExp_ev_not_experimental);
}
@@ -704,8 +826,8 @@ bool CGff2Record::x_MigrateAttributes(
it = attrs_left.find("locus_tag");
if (it != attrs_left.end()) {
if (pFeature->GetData().IsGene()) {
- pFeature->SetData().SetGene().SetLocus_tag(
- x_NormalizedAttributeValue(it->second));
+ string tag = xNormalizedAttributeValue(it->second);
+ pFeature->SetData().SetGene().SetLocus_tag(tag);
}
attrs_left.erase(it);
}
@@ -714,7 +836,7 @@ bool CGff2Record::x_MigrateAttributes(
if (it != attrs_left.end()) {
if (pFeature->GetData().IsGene()) {
pFeature->SetData().SetGene().SetMaploc(
- x_NormalizedAttributeValue(it->second));
+ xNormalizedAttributeValue(it->second));
}
}
@@ -722,7 +844,7 @@ bool CGff2Record::x_MigrateAttributes(
if (it != attrs_left.end()) {
if (pFeature->GetData().GetSubtype() == CSeqFeatData::eSubtype_ncRNA) {
pFeature->SetData().SetRna().SetExt().SetGen().SetClass(
- x_NormalizedAttributeValue(it->second));
+ xNormalizedAttributeValue(it->second));
}
attrs_left.erase(it);
}
@@ -741,9 +863,13 @@ bool CGff2Record::x_MigrateAttributes(
pLoc->SetId(*pId);
pFeature->SetProduct(*pLoc);
}
- attrs_left.erase(it);
+ xMigrateAttributeDefault(
+ attrs_left, "product", pFeature, "product", flags);
}
+ xMigrateAttributeDefault(
+ attrs_left, "Product", pFeature, "product", flags);
+
it = attrs_left.find("protein_id");
if (it != attrs_left.end()) {
string protId = it->second;
@@ -752,13 +878,8 @@ bool CGff2Record::x_MigrateAttributes(
pLoc->SetId(*pId);
pFeature->SetProduct(*pLoc);
- CRef<CGb_qual> pQual;
- pQual.Reset(new CGb_qual);
- pQual->SetQual("protein_id");
- pQual->SetVal(protId);
- pFeature->SetQual().push_back(pQual);
-
- attrs_left.erase(it);
+ this->xMigrateAttributeDefault(
+ attrs_left, "protein_id", pFeature, "protein_id", flags);
}
it = attrs_left.find("pseudo");
@@ -777,12 +898,8 @@ bool CGff2Record::x_MigrateAttributes(
pFeature->SetProduct(*pLoc);
}
// mss-362: turn transcript_id attributes into transcript_id quailifiers.
- CRef<CGb_qual> pQual;
- pQual.Reset(new CGb_qual);
- pQual->SetQual("transcript_id");
- pQual->SetVal(transcriptId);
- pFeature->SetQual().push_back(pQual);
- attrs_left.erase(it);
+ xMigrateAttributeSingle(
+ attrs_left, "transcript_id", pFeature, "transcript_id", flags);
}
it = attrs_left.find("transl_except");
@@ -793,7 +910,7 @@ bool CGff2Record::x_MigrateAttributes(
for (vector<string>::iterator it1 = codebreaks.begin();
it1 != codebreaks.end(); ++it1 ) {
CRef<CCode_break> pCodeBreak = s_StringToCodeBreak(
- x_NormalizedAttributeValue(*it1), *GetSeqId(flags), flags);
+ xNormalizedAttributeValue(*it1), *GetSeqId(flags), flags);
if (pCodeBreak) {
pFeature->SetData().SetCdregion().SetCode_break().push_back(
pCodeBreak);
@@ -825,16 +942,61 @@ bool CGff2Record::x_MigrateAttributes(
//
// Turn whatever is left into a gbqual:
//
- CRef<CGb_qual> pQual;
while (!attrs_left.empty()) {
- it = attrs_left.begin();
- string qual = it->first;
- pQual.Reset(new CGb_qual);
- pQual->SetQual(qual);
- pQual->SetVal(it->second);
- pFeature->SetQual().push_back(pQual);
- attrs_left.erase(it);
+ string key = attrs_left.begin()->first;
+ if (!xMigrateAttributeDefault(attrs_left, key, pFeature, key, flags)) {
+ return false;
+ }
+ }
+ return true;
+}
+
+// ----------------------------------------------------------------------------
+bool CGff2Record::xMigrateAttributeSingle(
+ TAttributes& attributes,
+ const string& attrKey,
+ CRef<CSeq_feat> pFeature,
+ const string& qualKey,
+ int flags)
+ // -----------------------------------------------------------------------------
+{
+ //retrieve GFF3 attribute as a single value,
+ // turn unescaped value into gbqual of the same key.
+
+ TAttributes::iterator it = attributes.find(attrKey);
+ if (it == attributes.end()) {
+ return true;
+ }
+ string value = xNormalizedAttributeValue(it->second);
+ pFeature->AddQualifier(qualKey, value);
+ attributes.erase(it);
+ return true;
+}
+
+// ----------------------------------------------------------------------------
+bool CGff2Record::xMigrateAttributeDefault(
+ TAttributes& attributes,
+ const string& attrKey,
+ CRef<CSeq_feat> pFeature,
+ const string& qualKey,
+ int flags)
+ // -----------------------------------------------------------------------------
+{
+ //split GFF3 multi-value into individual values, create a gbqual of the
+ // same key for each of the individual values.
+ //
+ TAttributes::iterator it = attributes.find(attrKey);
+ if (it == attributes.end()) {
+ return true;
+ }
+ list<string> values;
+ NStr::Split(it->second, ",", values);
+ for (list<string>::const_iterator cit = values.begin(); cit != values.end();
+ cit++) {
+ string value = xNormalizedAttributeValue(*cit);
+ pFeature->AddQualifier(qualKey, value);
}
+ attributes.erase(it);
return true;
}
@@ -972,7 +1134,7 @@ bool CGff2Record::x_MigrateAttributesSubSource(
}
CRef<CSubSource> pSubSource(new CSubSource);
pSubSource->SetSubtype(sit->second);
- pSubSource->SetName(ait->second);
+ pSubSource->SetName(xNormalizedAttributeValue(ait->second));
subType.push_back(pSubSource);
attrs_left.erase(ait);
}
diff --git a/c++/src/objtools/readers/gff2_reader.cpp b/c++/src/objtools/readers/gff2_reader.cpp
index 06a8de7..ad7926e 100644
--- a/c++/src/objtools/readers/gff2_reader.cpp
+++ b/c++/src/objtools/readers/gff2_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: gff2_reader.cpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: gff2_reader.cpp 479671 2015-09-22 18:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -85,6 +85,8 @@
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Score.hpp>
+#include <objmgr/feat_ci.hpp>
+
#include <objtools/readers/read_util.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/readers/line_error.hpp>
@@ -105,23 +107,21 @@ BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
// ----------------------------------------------------------------------------
-bool CGff2Reader::s_GetAnnotId(
- const CSeq_annot& annot,
- string& strId )
+const string* CGff2Reader::s_GetAnnotId(
+ const CSeq_annot& annot)
// ----------------------------------------------------------------------------
{
if ( ! annot.CanGetId() || annot.GetId().size() != 1 ) {
// internal error
- return false;
+ return 0;
}
CRef< CAnnot_id > pId = *( annot.GetId().begin() );
if ( ! pId->IsLocal() ) {
// internal error
- return false;
+ return 0;
}
- strId = pId->GetLocal().GetStr();
- return true;
+ return &pId->GetLocal().GetStr();
}
// ----------------------------------------------------------------------------
@@ -144,9 +144,9 @@ CGff2Reader::~CGff2Reader()
// ---------------------------------------------------------------------------
void
CGff2Reader::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnotList& annots,
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ---------------------------------------------------------------------------
{
xReadInit();
@@ -157,33 +157,34 @@ CGff2Reader::ReadSeqAnnots(
// ---------------------------------------------------------------------------
void
CGff2Reader::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnotList& annots,
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
if ( m_iFlags & fNewCode ) {
- return ReadSeqAnnotsNew( annots, lr, pMessageListener );
+ ReadSeqAnnotsNew(annots, lr, pMessageListener);
}
- CRef< CSeq_entry > entry = ReadSeqEntry( lr, pMessageListener );
- CTypeIterator<CSeq_annot> annot_iter( *entry );
- for ( ; annot_iter; ++annot_iter) {
- annots.push_back( CRef<CSeq_annot>( annot_iter.operator->() ) );
+ else {
+ CRef< CSeq_entry > entry = ReadSeqEntry(lr, pMessageListener);
+ CTypeIterator<CSeq_annot> annot_iter( *entry );
+ for (; annot_iter; ++annot_iter) {
+ annots.push_back(CRef<CSeq_annot>(annot_iter.operator->()));
+ }
}
}
// ---------------------------------------------------------------------------
void
CGff2Reader::ReadSeqAnnotsNew(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
ILineReader& lr,
- IMessageListener* pEC )
+ ILineErrorListener* pEC )
// ----------------------------------------------------------------------------
{
string line;
- //int linecount = 0;
while (xGetLine(lr, line)) {
if (IsCanceled()) {
AutoPtr<CObjReaderLineException> pErr(
@@ -217,8 +218,7 @@ CGff2Reader::ReadSeqAnnotsNew(
ProcessError(err, pEC);
}
}
- typedef vector< CRef<CSeq_annot> >::iterator ANNOTIT;
- for (ANNOTIT it = annots.begin(); it != annots.end(); ++it) {
+ for (TAnnots::iterator it = annots.begin(); it != annots.end(); ++it) {
try {
xAnnotPostProcess(*it);
}
@@ -233,18 +233,18 @@ CGff2Reader::ReadSeqAnnotsNew(
CRef< CSeq_entry >
CGff2Reader::ReadSeqEntry(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
- vector<CRef<CSeq_annot> > annots;
+ TAnnots annots;
ReadSeqAnnotsNew( annots, lr, pMessageListener );
CRef<CSeq_entry> pSeqEntry(new CSeq_entry());
pSeqEntry->SetSet();
- for (vector<CRef<CSeq_annot> >::iterator it = annots.begin();
+ for (TAnnots::iterator it = annots.begin();
it != annots.end(); ++it) {
CRef<CBioseq> pSeq( new CBioseq() );
pSeq->SetAnnot().push_back(*it);
@@ -264,7 +264,7 @@ CGff2Reader::ReadSeqEntry(
CRef< CSerialObject >
CGff2Reader::ReadObject(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CSerialObject> object(
@@ -313,7 +313,7 @@ bool CGff2Reader::x_ParseStructuredCommentGff(
bool CGff2Reader::x_ParseDataGff(
const string& strLine,
TAnnots& annots,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if ( CGff2Reader::IsAlignmentData(strLine) ) {
@@ -326,7 +326,7 @@ bool CGff2Reader::x_ParseDataGff(
bool CGff2Reader::x_ParseFeatureGff(
const string& strLine,
TAnnots& annots,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
//
@@ -343,6 +343,27 @@ bool CGff2Reader::x_ParseFeatureGff(
ProcessError(err, pEC);
return false;
}
+ if (pRecord->Type() == "protein") {
+ if (this->m_iFlags & CGff2Reader::fGenbankMode) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Fatal,
+ 0,
+ "Type \"protein\" in column 3 is not supported in -genbank mode.",
+ ILineError::eProblem_FeatureNameNotAllowed));
+ ProcessError(*pErr, pEC);
+ }
+ else {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Warning,
+ 0,
+ "Type \"protein\" in column 3 is not supported - ignored.",
+ ILineError::eProblem_FeatureNameNotAllowed));
+ ProcessError(*pErr, pEC);
+ }
+ return false;
+ }
//
// Search annots for a pre-existing annot pertaining to the same ID:
@@ -350,11 +371,11 @@ bool CGff2Reader::x_ParseFeatureGff(
TAnnotIt it = annots.begin();
for ( /*NOOP*/; it != annots.end(); ++it ) {
if (!(**it).IsFtable()) continue;
- string strAnnotId;
- if ( ! s_GetAnnotId( **it, strAnnotId ) ) {
+ const string* strAnnotId = s_GetAnnotId(**it);
+ if (strAnnotId == 0) {
return false;
}
- if ( pRecord->Id() == strAnnotId ) {
+ if ( pRecord->Id() == *strAnnotId ) {
break;
}
}
@@ -378,9 +399,9 @@ bool CGff2Reader::x_ParseFeatureGff(
if ( ! x_InitAnnot( *pRecord, pAnnot, pEC ) ) {
return false;
}
- annots.push_back( pAnnot );
+ annots.insert(annots.begin(), pAnnot );
}
-
+
return true;
};
@@ -405,11 +426,11 @@ bool CGff2Reader::x_ParseAlignmentGff(
TAnnotIt it = annots.begin();
for ( /*NOOP*/; it != annots.end(); ++it ) {
if (!(**it).IsAlign()) continue;
- string strAnnotId;
- if ( ! s_GetAnnotId( **it, strAnnotId ) ) {
+ const string* strAnnotId = s_GetAnnotId(**it);
+ if (!strAnnotId) {
return false;
}
- if ( pRecord->Id() == strAnnotId ) {
+ if ( pRecord->Id() == *strAnnotId ) {
break;
}
}
@@ -433,9 +454,9 @@ bool CGff2Reader::x_ParseAlignmentGff(
if ( ! x_InitAnnot( *pRecord, pAnnot ) ) {
return false;
}
- annots.push_back( pAnnot );
+ annots.insert(annots.begin(), pAnnot );
}
-
+
return true;
};
@@ -523,7 +544,7 @@ bool CGff2Reader::x_ParseTrackLineGff(
bool CGff2Reader::x_InitAnnot(
const CGff2Record& gff,
CRef< CSeq_annot > pAnnot,
- IMessageListener* pEC )
+ ILineErrorListener* pEC )
// ----------------------------------------------------------------------------
{
CRef< CAnnot_id > pAnnotId( new CAnnot_id );
@@ -562,7 +583,7 @@ bool CGff2Reader::x_InitAnnot(
bool CGff2Reader::x_UpdateAnnotFeature(
const CGff2Record& gff,
CRef< CSeq_annot > pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CRef< CSeq_feat > pFeature( new CSeq_feat );
@@ -1208,10 +1229,111 @@ bool CGff2Reader::xAnnotPostProcess(
CRef<CSeq_annot> pAnnot)
// ============================================================================
{
+ if (!xGenerateParentChildXrefs(pAnnot)) {
+ return false;
+ }
return true;
}
// ============================================================================
+bool CGff2Reader::xGenerateParentChildXrefs(
+ CRef<CSeq_annot> pAnnot)
+// ============================================================================
+{
+ typedef list<CRef<CSeq_feat> > FTABLE;
+ typedef list<string> PARENTS;
+
+ if (!(m_iFlags & CGff2Reader::fGenbankMode)) {
+ return true;
+ }
+ FTABLE& ftable = pAnnot->SetData().SetFtable();
+ for (FTABLE::iterator featIt = ftable.begin(); featIt != ftable.end(); ++featIt) {
+ CSeq_feat& feat = **featIt;
+ const string& parentStr = feat.GetNamedQual("Parent");
+ PARENTS parents;
+ NStr::Split(parentStr, ",", parents);
+ for (PARENTS::iterator parentIt = parents.begin(); parentIt != parents.end(); ++parentIt) {
+ const string& parent = *parentIt;
+ xSetAncestryLine(feat, parent);
+ }
+ }
+ return true;
+}
+
+// ============================================================================
+void CGff2Reader::xSetAncestryLine(
+ CSeq_feat& feat,
+ const string& directParentStr)
+// ============================================================================
+{
+ typedef list<string> PARENTS;
+
+ string ancestorStr(directParentStr);
+ CRef<CSeq_feat> pAncestor;
+ while (!ancestorStr.empty()) {
+ if (!x_GetFeatureById(ancestorStr, pAncestor)) {
+ return;
+ }
+ xSetAncestorXrefs(feat, *pAncestor);
+ ancestorStr = pAncestor->GetNamedQual("Parent");
+ PARENTS ancestors;
+ NStr::Split(ancestorStr, ",", ancestors);
+ for (PARENTS::iterator it = ancestors.begin(); it != ancestors.end(); ++it) {
+ const string& ancestorStr = *it;
+ xSetAncestryLine(feat, ancestorStr);
+ }
+ }
+}
+
+// ============================================================================
+bool sFeatureHasXref(
+ const CSeq_feat& feat,
+ const CFeat_id& featId)
+// ============================================================================
+{
+ typedef vector<CRef<CSeqFeatXref> > XREFS;
+ if (!feat.IsSetXref()) {
+ return false;
+ }
+ int xrefId = featId.GetLocal().GetId();
+ const XREFS& xrefs = feat.GetXref();
+ for (XREFS::const_iterator cit = xrefs.begin(); cit != xrefs.end(); ++cit) {
+ const CSeqFeatXref& ref = **cit;
+ int contentId = ref.GetId().GetLocal().GetId();
+ if (contentId == xrefId) {
+ return true;
+ }
+ }
+ return false;
+}
+
+// ============================================================================
+void CGff2Reader::xSetAncestorXrefs(
+ CSeq_feat& descendent,
+ CSeq_feat& ancestor)
+// ============================================================================
+{
+
+ //xref descendent->ancestor
+ if (!sFeatureHasXref(descendent, ancestor.GetId())) {
+ CRef<CFeat_id> pAncestorId(new CFeat_id);
+ pAncestorId->Assign(ancestor.GetId());
+ CRef<CSeqFeatXref> pAncestorXref(new CSeqFeatXref);
+ pAncestorXref->SetId(*pAncestorId);
+ descendent.SetXref().push_back(pAncestorXref);
+ }
+
+ //xref ancestor->descendent
+ if (!sFeatureHasXref(ancestor, descendent.GetId())) {
+ CRef<CFeat_id> pDescendentId(new CFeat_id);
+ pDescendentId->Assign(descendent.GetId());
+ CRef<CSeqFeatXref> pDescendentXref(new CSeqFeatXref);
+ pDescendentXref->SetId(*pDescendentId);
+ ancestor.SetXref().push_back(pDescendentXref);
+ }
+}
+
+// ============================================================================
bool CGff2Reader::xReadInit()
// ============================================================================
{
@@ -1226,7 +1348,7 @@ bool CGff2Reader::IsAlignmentData(
const string& line)
// ============================================================================
{
- vector<CTempString> columns;
+ vector<CTempStringEx> columns;
CGff2Record::TokenizeGFF(columns, line);
if (columns.size() < 9) {
return false;
diff --git a/c++/src/objtools/readers/gff3_reader.cpp b/c++/src/objtools/readers/gff3_reader.cpp
index d449cea..fcc786c 100644
--- a/c++/src/objtools/readers/gff3_reader.cpp
+++ b/c++/src/objtools/readers/gff3_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: gff3_reader.cpp 464928 2015-04-15 15:02:44Z ivanov $
+/* $Id: gff3_reader.cpp 484580 2015-11-12 19:14:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -114,7 +114,7 @@ string CGff3ReadRecord::x_NormalizedAttributeKey(
const string& strRawKey )
// ---------------------------------------------------------------------------
{
- string strKey = CGff2Record::x_NormalizedAttributeKey( strRawKey );
+ string strKey = CGff2Record::xNormalizedAttributeKey( strRawKey );
if ( 0 == NStr::CompareNocase( strRawKey, "ID" ) ) {
return "ID";
}
@@ -157,6 +157,7 @@ CGff3Reader::CGff3Reader(
// ----------------------------------------------------------------------------
CGff2Reader( uFlags, name, title )
{
+ CGff2Record::ResetId();
}
// ----------------------------------------------------------------------------
@@ -183,7 +184,7 @@ bool CGff3Reader::x_UpdateFeatureCds(
bool CGff3Reader::x_UpdateAnnotFeature(
const CGff2Record& record,
CRef< CSeq_annot > pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CRef< CSeq_feat > pFeature(new CSeq_feat);
@@ -206,18 +207,54 @@ bool CGff3Reader::x_UpdateAnnotFeature(
}
// ----------------------------------------------------------------------------
+void CGff3Reader::xVerifyExonLocation(
+ const string& mrnaId,
+ const CGff2Record& exon,
+ ILineErrorListener* pEC)
+// ----------------------------------------------------------------------------
+{
+ map<string,CRef<CSeq_interval> >::const_iterator cit = mMrnaLocs.find(mrnaId);
+ if (cit == mMrnaLocs.end()) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Error,
+ 0,
+ "Bad data line: Exon record referring to non-existing mRNA parent.",
+ ILineError::eProblem_FeatureBadStartAndOrStop));
+ ProcessError(*pErr, pEC);
+ return; // can not continue without cit being valid, regardless of ProcessError()
+ }
+ const CSeq_interval& containingInt = cit->second.GetObject();
+ const CRef<CSeq_loc> pContainedLoc = exon.GetSeqLoc(m_iFlags);
+ const CSeq_interval& containedInt = pContainedLoc->GetInt();
+ bool failed = (containedInt.GetFrom() < containingInt.GetFrom()) ||
+ (containedInt.GetTo() > containingInt.GetTo());
+ if (failed) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Error,
+ 0,
+ "Bad data line: Exon record that lies outside its parent location.",
+ ILineError::eProblem_FeatureBadStartAndOrStop));
+ ProcessError(*pErr, pEC);
+ }
+}
+
+// ----------------------------------------------------------------------------
bool CGff3Reader::xUpdateAnnotExon(
const CGff2Record& record,
CRef<CSeq_feat>,
CRef<CSeq_annot>,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
list<string> parents;
if (record.GetAttribute("Parent", parents)) {
for (list<string>::const_iterator it = parents.begin(); it != parents.end();
++it) {
- IdToFeatureMap::iterator fit = m_MapIdToFeature.find(*it);
+ const string& parentId = *it;
+ xVerifyExonLocation(parentId, record, pEC);
+ IdToFeatureMap::iterator fit = m_MapIdToFeature.find(parentId);
if (fit != m_MapIdToFeature.end()) {
if (!record.UpdateFeature(m_iFlags, fit->second)) {
return false;
@@ -233,17 +270,16 @@ bool CGff3Reader::xUpdateAnnotCds(
const CGff2Record& record,
CRef<CSeq_feat> pFeature,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if (!xVerifyCdsParents(record)) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
- eDiag_Fatal,
+ eDiag_Error,
0,
"Bad data line: CDS record with bad parent assignments.",
ILineError::eProblem_FeatureBadStartAndOrStop) );
- pErr->SetLineNumber(m_uLineNumber);
ProcessError(*pErr, pEC);
}
@@ -325,7 +361,6 @@ bool CGff3Reader::xUpdateAnnotCds(
0,
"Bad data line: CDS record with bad parent assignment.",
ILineError::eProblem_MissingContext) );
- pErr->SetLineNumber(m_uLineNumber);
ProcessError(*pErr, pEC);
}
if (m_iFlags & fGeneXrefs) {
@@ -336,7 +371,6 @@ bool CGff3Reader::xUpdateAnnotCds(
0,
"Bad data line: CDS record with bad parent assignment.",
ILineError::eProblem_MissingContext) );
- pErr->SetLineNumber(m_uLineNumber);
ProcessError(*pErr, pEC);
}
}
@@ -425,7 +459,7 @@ bool CGff3Reader::xUpdateAnnotGeneric(
const CGff2Record& record,
CRef<CSeq_feat> pFeature,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
string id;
@@ -454,7 +488,7 @@ bool CGff3Reader::xUpdateAnnotMrna(
const CGff2Record& record,
CRef<CSeq_feat> pFeature,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
string id;
@@ -468,6 +502,19 @@ bool CGff3Reader::xUpdateAnnotMrna(
if (!record.InitializeFeature(m_iFlags, pFeature)) {
return false;
}
+ CRef<CSeq_interval> mrnaLoc(new CSeq_interval);
+ CSeq_loc::E_Choice choice = pFeature->GetLocation().Which();
+ if (choice != CSeq_loc::e_Int) {
+ AutoPtr<CObjReaderLineException> pErr(
+ CObjReaderLineException::Create(
+ eDiag_Error,
+ 0,
+ "Internal error: Unexpected location type.",
+ ILineError::eProblem_BadFeatureInterval));
+ }
+ mrnaLoc->Assign(pFeature->GetLocation().GetInt());
+ mMrnaLocs[id] = mrnaLoc;
+
string parentsStr;
if ((m_iFlags & fGeneXrefs) && record.GetAttribute("Parent", parentsStr)) {
list<string> parents;
@@ -482,7 +529,6 @@ bool CGff3Reader::xUpdateAnnotMrna(
0,
"Bad data line: mRNA record with bad parent assignment.",
ILineError::eProblem_MissingContext) );
- pErr->SetLineNumber(m_uLineNumber);
ProcessError(*pErr, pEC);
}
}
@@ -503,7 +549,7 @@ bool CGff3Reader::xUpdateAnnotGene(
const CGff2Record& record,
CRef<CSeq_feat> pFeature,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
return xUpdateAnnotGeneric(record, pFeature, pAnnot, pEC);
diff --git a/c++/src/objtools/readers/gff_reader.cpp b/c++/src/objtools/readers/gff_reader.cpp
index 8e15769..c741b9b 100644
--- a/c++/src/objtools/readers/gff_reader.cpp
+++ b/c++/src/objtools/readers/gff_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: gff_reader.cpp 451795 2014-11-12 14:47:56Z ivanov $
+/* $Id: gff_reader.cpp 468563 2015-05-26 16:00:34Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1277,7 +1277,7 @@ CRef<CSeq_id> CGFFReader::x_ResolveNewSeqName(const string& name)
}
try {
CRef<CSeq_id> pId(new CSeq_id(name));
- if (!pId || (pId->IsGi() && pId->GetGi() < TGi(500)) ) {
+ if (!pId || (pId->IsGi() && pId->GetGi() < GI_CONST(500)) ) {
pId = new CSeq_id(CSeq_id::e_Local, name);
}
return pId;
diff --git a/c++/src/objtools/readers/gtf_reader.cpp b/c++/src/objtools/readers/gtf_reader.cpp
index c2c2f95..e3eab6e 100644
--- a/c++/src/objtools/readers/gtf_reader.cpp
+++ b/c++/src/objtools/readers/gtf_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: gtf_reader.cpp 456167 2015-01-08 15:37:20Z ivanov $
+/* $Id: gtf_reader.cpp 479671 2015-09-22 18:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -132,8 +132,8 @@ bool CGtfReadRecord::x_AssignAttributesFromGff(
return false;
}
}
- strKey = x_NormalizedAttributeKey( strKey );
- strValue = x_NormalizedAttributeValue( strValue );
+ strKey = xNormalizedAttributeKey( strKey );
+ strValue = xNormalizedAttributeValue( strValue );
if ( strKey.empty() && strValue.empty() ) {
// Probably due to trailing "; ". Sequence Ontology generates such
// things.
@@ -201,9 +201,9 @@ CGtfReader::~CGtfReader()
// ---------------------------------------------------------------------------
void
CGtfReader::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
ILineReader& lr,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -242,9 +242,9 @@ CGtfReader::ReadSeqAnnots(
// ---------------------------------------------------------------------------
void
CGtfReader::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ---------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -255,7 +255,7 @@ CGtfReader::ReadSeqAnnots(
bool CGtfReader::x_UpdateAnnotFeature(
const CGff2Record& gff,
CRef< CSeq_annot > pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CRef< CSeq_feat > pFeature( new CSeq_feat );
diff --git a/c++/src/objtools/readers/gvf_reader.cpp b/c++/src/objtools/readers/gvf_reader.cpp
index 156cbde..791e7c3 100644
--- a/c++/src/objtools/readers/gvf_reader.cpp
+++ b/c++/src/objtools/readers/gvf_reader.cpp
@@ -1,4 +1,4 @@
- /* $Id: gvf_reader.cpp 413973 2013-09-19 15:46:29Z kornbluh $
+ /* $Id: gvf_reader.cpp 479671 2015-09-22 18:44:45Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -150,7 +150,7 @@ bool CGvfReadRecord::x_AssignAttributesFromGff(
}
}
strKey = x_NormalizedAttributeKey( strKey );
- strValue = x_NormalizedAttributeValue( strValue );
+ strValue = xNormalizedAttributeValue( strValue );
if ( strKey.empty() && strValue.empty() ) {
// Probably due to trailing "; ". Sequence Ontology generates such
@@ -214,7 +214,7 @@ CGvfReader::~CGvfReader()
bool CGvfReader::x_ParseFeatureGff(
const string& strLine,
TAnnots& annots,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
//
@@ -254,7 +254,7 @@ CRef<CSeq_annot> CGvfReader::x_GetAnnotById(
}
}
CRef<CSeq_annot> pNewAnnot( new CSeq_annot );
- annots.push_back( pNewAnnot );
+ annots.insert(annots.begin(), pNewAnnot);
CRef< CAnnot_id > pAnnotId( new CAnnot_id );
pAnnotId->SetLocal().SetStr( strId );
@@ -289,7 +289,7 @@ CRef<CSeq_annot> CGvfReader::x_GetAnnotById(
bool CGvfReader::x_MergeRecord(
const CGvfReadRecord& record,
CRef< CSeq_annot > pAnnot,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if ( ! record.SanityCheck() ) {
@@ -984,7 +984,7 @@ bool CGvfReader::xVariationSetSnvs(
bool CGvfReader::x_FeatureSetExt(
const CGvfReadRecord& record,
CRef< CSeq_feat > pFeature,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ---------------------------------------------------------------------------
{
string strAttribute;
diff --git a/c++/src/objtools/readers/idmapper.cpp b/c++/src/objtools/readers/idmapper.cpp
index ead0a47..77ff6a7 100644
--- a/c++/src/objtools/readers/idmapper.cpp
+++ b/c++/src/objtools/readers/idmapper.cpp
@@ -1,4 +1,4 @@
-/* $Id: idmapper.cpp 432036 2014-04-09 17:27:03Z grichenk $
+/* $Id: idmapper.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -54,7 +54,7 @@ USING_SCOPE(objects);
CIdMapper::CIdMapper(const std::string& strContext,
bool bInvert,
- IMessageListener* pErrors)
+ ILineErrorListener* pErrors)
: m_strContext(strContext),
m_bInvert(bInvert),
m_pErrors( pErrors )
@@ -225,7 +225,7 @@ void CIdMapper::MapObject(CSerialObject& object)
// Composite mapper
-CAtomicCounter_WithAutoInit CIdMapperComposite::SNode::sm_Counter(0);
+CAtomicCounter CIdMapperComposite::SNode::sm_Counter;
void CIdMapperComposite::AddMapper(IIdMapper* mapper,
TPriority priority,
diff --git a/c++/src/objtools/readers/idmapper_builtin.cpp b/c++/src/objtools/readers/idmapper_builtin.cpp
index d065346..558a4f3 100644
--- a/c++/src/objtools/readers/idmapper_builtin.cpp
+++ b/c++/src/objtools/readers/idmapper_builtin.cpp
@@ -1,4 +1,4 @@
-/* $Id: idmapper_builtin.cpp 407582 2013-07-23 11:15:22Z kornbluh $
+/* $Id: idmapper_builtin.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@ extern const char* sc_BuiltinConfig;
CIdMapperBuiltin::CIdMapperBuiltin(const std::string& strContext,
bool bInvert,
- IMessageListener* pErrors)
+ ILineErrorListener* pErrors)
: CIdMapperConfig(strContext, bInvert, pErrors)
{
Initialize();
diff --git a/c++/src/objtools/readers/idmapper_config.cpp b/c++/src/objtools/readers/idmapper_config.cpp
index 6dcf4ec..0d56b1f 100644
--- a/c++/src/objtools/readers/idmapper_config.cpp
+++ b/c++/src/objtools/readers/idmapper_config.cpp
@@ -1,4 +1,4 @@
-/* $Id: idmapper_config.cpp 407582 2013-07-23 11:15:22Z kornbluh $
+/* $Id: idmapper_config.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,7 +48,7 @@ USING_SCOPE(objects);
CIdMapperConfig::CIdMapperConfig(CNcbiIstream& istr,
const std::string& strContext,
bool bInvert,
- IMessageListener* pErrors)
+ ILineErrorListener* pErrors)
: CIdMapper(strContext, bInvert, pErrors)
{
Initialize(istr);
@@ -57,7 +57,7 @@ CIdMapperConfig::CIdMapperConfig(CNcbiIstream& istr,
CIdMapperConfig::CIdMapperConfig(const std::string& strContext,
bool bInvert,
- IMessageListener* pErrors)
+ ILineErrorListener* pErrors)
: CIdMapper(strContext, bInvert, pErrors)
{
}
diff --git a/c++/src/objtools/readers/microarray_reader.cpp b/c++/src/objtools/readers/microarray_reader.cpp
index 1844478..d525a37 100644
--- a/c++/src/objtools/readers/microarray_reader.cpp
+++ b/c++/src/objtools/readers/microarray_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: microarray_reader.cpp 448857 2014-10-09 16:31:19Z ivanov $
+/* $Id: microarray_reader.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -101,8 +101,8 @@ CMicroArrayReader::CMicroArrayReader(
// ----------------------------------------------------------------------------
: CReaderBase(flags),
m_currentId(""),
- m_usescore(false),
- m_columncount(15)
+ m_columncount(15),
+ m_usescore(false)
{
}
@@ -116,7 +116,7 @@ CMicroArrayReader::~CMicroArrayReader()
CRef< CSerialObject >
CMicroArrayReader::ReadObject(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CSerialObject> object(
@@ -128,7 +128,7 @@ CMicroArrayReader::ReadObject(
CRef< CSeq_annot >
CMicroArrayReader::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
const int MAX_RECORDS = 100000;
@@ -207,7 +207,7 @@ CMicroArrayReader::ReadSeqAnnot(
bool CMicroArrayReader::xParseFeature(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
const size_t columncount = 15;
@@ -305,7 +305,7 @@ void CMicroArrayReader::xSetFeatureDisplayData(
// ----------------------------------------------------------------------------
bool CMicroArrayReader::xParseTrackLine(
const string& strLine,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
m_strExpNames = "";
diff --git a/c++/src/objtools/readers/read_util.cpp b/c++/src/objtools/readers/read_util.cpp
index a270a9a..6f0fe3a 100644
--- a/c++/src/objtools/readers/read_util.cpp
+++ b/c++/src/objtools/readers/read_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: read_util.cpp 443184 2014-08-12 12:26:11Z mcelhany $
+/* $Id: read_util.cpp 478458 2015-09-09 15:27:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -87,11 +87,13 @@ void CReadUtil::Tokenize(
// -----------------------------------------------------------------
CRef<CSeq_id> CReadUtil::AsSeqId(
- const string& rawId,
+ const string& givenId,
unsigned int flags,
bool localInts)
// -----------------------------------------------------------------
{
+ string rawId(NStr::URLDecode(givenId));
+
if (flags & CReaderBase::fAllIdsAsLocal) {
CRef<CSeq_id> pId(new CSeq_id);
if (string::npos == rawId.find_first_not_of("0987654321") &&
@@ -112,7 +114,7 @@ CRef<CSeq_id> CReadUtil::AsSeqId(
}
if (pId->IsGi()) {
if (flags & CReaderBase::fNumericIdsAsLocal ||
- pId->GetGi() < TGi(500)) {
+ pId->GetGi() < GI_CONST(500)) {
pId.Reset(new CSeq_id);
if (!localInts) {
pId->SetLocal().SetStr(rawId);
diff --git a/c++/src/objtools/readers/reader_base.cpp b/c++/src/objtools/readers/reader_base.cpp
index 9c13568..db928f5 100644
--- a/c++/src/objtools/readers/reader_base.cpp
+++ b/c++/src/objtools/readers/reader_base.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_base.cpp 463661 2015-03-31 17:11:17Z ivanov $
+/* $Id: reader_base.cpp 484580 2015-11-12 19:14:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -172,7 +172,7 @@ CReaderBase::~CReaderBase()
CRef< CSerialObject >
CReaderBase::ReadObject(
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -183,7 +183,7 @@ CReaderBase::ReadObject(
CRef< CSeq_annot >
CReaderBase::ReadSeqAnnot(
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -194,7 +194,7 @@ CReaderBase::ReadSeqAnnot(
CRef< CSeq_annot >
CReaderBase::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* )
+ ILineErrorListener* )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -204,9 +204,9 @@ CReaderBase::ReadSeqAnnot(
// ---------------------------------------------------------------------------
void
CReaderBase::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ---------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -216,9 +216,9 @@ CReaderBase::ReadSeqAnnots(
// ---------------------------------------------------------------------------
void
CReaderBase::ReadSeqAnnots(
- vector< CRef<CSeq_annot> >& annots,
+ TAnnots& annots,
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -234,7 +234,7 @@ CReaderBase::ReadSeqAnnots(
CRef< CSeq_entry >
CReaderBase::ReadSeqEntry(
CNcbiIstream& istr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CStreamLineReader lr( istr );
@@ -246,7 +246,7 @@ CReaderBase::ReadSeqEntry(
CRef< CSeq_entry >
CReaderBase::ReadSeqEntry(
ILineReader& lr,
- IMessageListener* )
+ ILineErrorListener* )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -257,7 +257,7 @@ CReaderBase::ReadSeqEntry(
void
CReaderBase::ProcessError(
CObjReaderLineException& err,
- IMessageListener* pContainer )
+ ILineErrorListener* pContainer )
// ----------------------------------------------------------------------------
{
err.SetLineNumber( m_uLineNumber );
@@ -267,7 +267,7 @@ CReaderBase::ProcessError(
if (!pContainer->PutError(err)) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
- eDiag_Fatal,
+ eDiag_Critical,
0,
"Error allowance exceeded",
ILineError::eProblem_GeneralParsingError) );
@@ -280,7 +280,7 @@ CReaderBase::ProcessError(
void
CReaderBase::ProcessWarning(
CObjReaderLineException& err,
- IMessageListener* pContainer )
+ ILineErrorListener* pContainer )
// ----------------------------------------------------------------------------
{
err.SetLineNumber( m_uLineNumber );
@@ -298,7 +298,7 @@ CReaderBase::ProcessWarning(
void
CReaderBase::ProcessError(
CLineError& err,
- IMessageListener* pContainer )
+ ILineErrorListener* pContainer )
// ----------------------------------------------------------------------------
{
if (!pContainer || !pContainer->PutError(err)) {
@@ -310,7 +310,7 @@ CReaderBase::ProcessError(
void
CReaderBase::ProcessWarning(
CLineError& err,
- IMessageListener* pContainer )
+ ILineErrorListener* pContainer )
// ----------------------------------------------------------------------------
{
if (!pContainer) {
@@ -327,7 +327,7 @@ CReaderBase::ProcessWarning(
void CReaderBase::xSetBrowserRegion(
const string& strRaw,
CAnnot_descr& desc,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
CRef<CSeq_loc> location( new CSeq_loc );
@@ -398,7 +398,7 @@ void CReaderBase::xSetBrowserRegion(
bool CReaderBase::xParseBrowserLine(
const string& strLine,
CRef<CSeq_annot>& annot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if ( ! NStr::StartsWith( strLine, "browser" ) ) {
@@ -465,7 +465,7 @@ void CReaderBase::xAssignTrackData(
// ----------------------------------------------------------------------------
bool CReaderBase::xParseTrackLine(
const string& strLine,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
vector<string> parts;
@@ -480,7 +480,7 @@ bool CReaderBase::xParseTrackLine(
// ----------------------------------------------------------------------------
bool CReaderBase::xParseBrowserLine(
const string& strLine,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
return true;
@@ -512,7 +512,7 @@ bool CReaderBase::xParseComment(
// ----------------------------------------------------------------------------
void CReaderBase::xAddConversionInfo(
CRef<CSeq_annot >& annot,
- IMessageListener *pMessageListener)
+ ILineErrorListener *pMessageListener)
// ----------------------------------------------------------------------------
{
if (!annot || !pMessageListener) {
@@ -534,7 +534,7 @@ void CReaderBase::xAddConversionInfo(
// ----------------------------------------------------------------------------
void CReaderBase::xAddConversionInfo(
CRef<CSeq_entry >& entry,
- IMessageListener *pMessageListener)
+ ILineErrorListener *pMessageListener)
// ----------------------------------------------------------------------------
{
if (!entry || !pMessageListener) {
@@ -547,7 +547,7 @@ void CReaderBase::xAddConversionInfo(
// ----------------------------------------------------------------------------
CRef<CUser_object> CReaderBase::xMakeAsnConversionInfo(
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CUser_object> conversioninfo(new CUser_object());
@@ -587,7 +587,7 @@ bool CReaderBase::xIsReportingProgress() const
// ----------------------------------------------------------------------------
void CReaderBase::xReportProgress(
- IMessageListener* pProgress)
+ ILineErrorListener* pProgress)
// ----------------------------------------------------------------------------
{
if (!xIsReportingProgress()) { // progress reports disabled
@@ -677,11 +677,13 @@ bool CReaderBase::xGetLine(
string& line)
// ----------------------------------------------------------------------------
{
+ CTempString temp;
while (!lr.AtEOF()) {
- line = *++lr;
+ temp = *++lr;
++m_uLineNumber;
- NStr::TruncateSpacesInPlace(line);
- if (!xIsCommentLine(line)) {
+ temp = NStr::TruncateSpaces_Unsafe(temp);
+ if (!xIsCommentLine(temp)) {
+ line = temp;
return true;
}
}
diff --git a/c++/src/objtools/readers/reader_data.cpp b/c++/src/objtools/readers/reader_data.cpp
index bae265f..aaa9f25 100644
--- a/c++/src/objtools/readers/reader_data.cpp
+++ b/c++/src/objtools/readers/reader_data.cpp
@@ -1,4 +1,4 @@
-/* $Id: reader_data.cpp 443186 2014-08-12 12:26:30Z mcelhany $
+/* $Id: reader_data.cpp 441980 2014-07-29 17:37:08Z ludwigf $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/readers/reader_data.hpp b/c++/src/objtools/readers/reader_data.hpp
index 686deb0..5933176 100644
--- a/c++/src/objtools/readers/reader_data.hpp
+++ b/c++/src/objtools/readers/reader_data.hpp
@@ -1,4 +1,4 @@
-/* $Id: reader_data.hpp 443186 2014-08-12 12:26:30Z mcelhany $
+/* $Id: reader_data.hpp 441980 2014-07-29 17:37:08Z ludwigf $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/objtools/readers/readfeat.cpp b/c++/src/objtools/readers/readfeat.cpp
index defa919..3cb8149 100644
--- a/c++/src/objtools/readers/readfeat.cpp
+++ b/c++/src/objtools/readers/readfeat.cpp
@@ -237,14 +237,14 @@ public:
const string& seqid,
const string& annotname,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter);
// create single feature from key
CRef<CSeq_feat> CreateSeqFeat (const string& feat,
CSeq_loc& location,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
unsigned int line,
const string &seq_id,
ITableFilter *filter);
@@ -255,7 +255,7 @@ public:
const string& qual,
const string& val,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
int line,
const string &seq_id );
@@ -276,35 +276,35 @@ private:
bool x_ParseFeatureTableLine (const string& line, Int4* startP, Int4* stopP,
bool* partial5P, bool* partial3P, bool* ispointP, bool* isminusP,
string& featP, string& qualP, string& valP, Int4 offset,
- IMessageListener *pMessageListener, int line_num, const string &seq_id );
+ ILineErrorListener *pMessageListener, int line_num, const string &seq_id );
bool x_IsWebComment(CTempString line);
bool x_AddIntervalToFeature (CTempString strFeatureName, CRef<CSeq_feat> sfp, CSeq_loc_mix& mix,
Int4 start, Int4 stop,
bool partial5, bool partial3, bool ispoint, bool isminus,
- IMessageListener *pMessageListener, int line_num, const string& seqid);
+ ILineErrorListener *pMessageListener, int line_num, const string& seqid);
bool x_AddQualifierToFeature (CRef<CSeq_feat> sfp,
const string &feat_name,
const string& qual, const string& val,
const CFeature_table_reader::TFlags flags,
- IMessageListener *pMessageListener, int line_num, const string &seq_id );
+ ILineErrorListener *pMessageListener, int line_num, const string &seq_id );
bool x_AddQualifierToGene (CSeqFeatData& sfdata,
EQual qtype, const string& val);
bool x_AddQualifierToCdregion (CRef<CSeq_feat> sfp, CSeqFeatData& sfdata,
EQual qtype, const string& val,
- IMessageListener *pMessageListener, int line_num, const string &seq_id );
+ ILineErrorListener *pMessageListener, int line_num, const string &seq_id );
bool x_AddQualifierToRna (CSeqFeatData& sfdata,
EQual qtype, const string& val,
- IMessageListener *pMessageListener, int line_num, const string &seq_id );
+ ILineErrorListener *pMessageListener, int line_num, const string &seq_id );
bool x_AddQualifierToImp (CRef<CSeq_feat> sfp, CSeqFeatData& sfdata,
EQual qtype, const string& qual, const string& val);
bool x_AddQualifierToBioSrc (CSeqFeatData& sfdata,
const string &feat_name,
EOrgRef rtype, const string& val,
- IMessageListener *pMessageListener, int line, const string &seq_id );
+ ILineErrorListener *pMessageListener, int line, const string &seq_id );
bool x_AddQualifierToBioSrc (CSeqFeatData& sfdata,
CSubSource::ESubtype stype, const string& val);
bool x_AddQualifierToBioSrc (CSeqFeatData& sfdata,
@@ -347,7 +347,7 @@ private:
CRef<CSeq_annot> sap,
TChoiceToFeatMap & choiceToFeatMap, // an input param, but might get more items added
const CFeature_table_reader::TFlags flags,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
const string& seqid );
bool x_StringIsJustQuotes (const string& str);
@@ -360,7 +360,7 @@ private:
long x_StringToLongNoThrow (
CTempString strToConvert,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
const std::string& strSeqId,
unsigned int uLine,
CTempString strFeatureName,
@@ -373,11 +373,11 @@ private:
const CFeature_table_reader::TFlags flags,
unsigned int line,
const string &seq_id,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter);
void x_ProcessMsg (
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ILineError::EProblem eProblem,
EDiagSev eSeverity,
const std::string& strSeqId,
@@ -821,7 +821,7 @@ bool CFeature_table_reader_imp::x_ParseFeatureTableLine (
string& valP,
Int4 offset,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line_num,
const string &seq_id
)
@@ -1088,7 +1088,7 @@ bool CFeature_table_reader_imp::x_AddQualifierToCdregion (
CRef<CSeq_feat> sfp,
CSeqFeatData& sfdata,
EQual qtype, const string& val,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line,
const string &seq_id
)
@@ -1350,7 +1350,7 @@ SIZE_TYPE CFeature_table_reader_imp::x_MatchingParenPos(
long CFeature_table_reader_imp::x_StringToLongNoThrow (
CTempString strToConvert,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
const std::string& strSeqId,
unsigned int uLine,
CTempString strFeatureName,
@@ -1400,7 +1400,7 @@ bool CFeature_table_reader_imp::x_AddQualifierToRna (
CSeqFeatData& sfdata,
EQual qtype,
const string& val,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line_num,
const string &seq_id
)
@@ -1632,7 +1632,7 @@ bool CFeature_table_reader_imp::x_AddQualifierToBioSrc (
const string &feat_name,
EOrgRef rtype,
const string& val,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line,
const string &seq_id
)
@@ -1862,7 +1862,7 @@ void CFeature_table_reader_imp::x_CreateGenesFromCDSs(
CRef<CSeq_annot> sap,
TChoiceToFeatMap & choiceToFeatMap,
const CFeature_table_reader::TFlags flags,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
const string& seq_id )
{
// load cds_equal_range to hold the CDSs
@@ -2072,7 +2072,7 @@ bool CFeature_table_reader_imp::x_AddQualifierToFeature (
const string& qual,
const string& val,
const CFeature_table_reader::TFlags flags,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line,
const string &seq_id
)
@@ -2450,7 +2450,7 @@ bool CFeature_table_reader_imp::x_AddIntervalToFeature(
bool partial3,
bool ispoint,
bool isminus,
- IMessageListener *pMessageListener,
+ ILineErrorListener *pMessageListener,
int line_num,
const string& seqid
)
@@ -2528,7 +2528,7 @@ bool CFeature_table_reader_imp::x_SetupSeqFeat (
const CFeature_table_reader::TFlags flags,
unsigned int line,
const std::string &seq_id,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
@@ -2613,8 +2613,15 @@ bool CFeature_table_reader_imp::x_SetupSeqFeat (
sfdata.SetSite (CSeqFeatData::eSite_other);
} else if (typ == CSeqFeatData::e_Prot ) {
CProt_ref &prot_ref = sfdata.SetProt();
- if( sbtyp == CSeqFeatData::eSubtype_mat_peptide_aa ) {
- prot_ref.SetProcessed( CProt_ref::eProcessed_mature );
+ switch (sbtyp) {
+ default:
+ break;
+ case CSeqFeatData::eSubtype_mat_peptide_aa:
+ prot_ref.SetProcessed(CProt_ref::eProcessed_mature);
+ break;
+ case CSeqFeatData::eSubtype_sig_peptide_aa:
+ prot_ref.SetProcessed(CProt_ref::eProcessed_signal_peptide);
+ break;
}
}
@@ -2662,7 +2669,7 @@ bool CFeature_table_reader_imp::x_SetupSeqFeat (
void CFeature_table_reader_imp::x_ProcessMsg(
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ILineError::EProblem eProblem,
EDiagSev eSeverity,
const std::string& strSeqId,
@@ -2704,7 +2711,7 @@ CRef<CSeq_annot> CFeature_table_reader_imp::ReadSequinFeatureTable (
const string& seqid,
const string& annotname,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -2978,7 +2985,7 @@ CRef<CSeq_feat> CFeature_table_reader_imp::CreateSeqFeat (
const string& feat,
CSeq_loc& location,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
unsigned int line,
const string &seq_id,
ITableFilter *filter
@@ -3014,7 +3021,7 @@ void CFeature_table_reader_imp::AddFeatQual (
const string& qual,
const string& val,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
int line,
const string &seq_id )
@@ -3104,7 +3111,7 @@ CFeature_table_reader::CFeature_table_reader(
CRef<CSerialObject>
CFeature_table_reader::ReadObject(
- ILineReader &lr, IMessageListener *pMessageListener)
+ ILineReader &lr, ILineErrorListener *pMessageListener)
{
CRef<CSerialObject> object(
ReadSeqAnnot( lr, pMessageListener ).ReleaseOrNull() );
@@ -3113,7 +3120,7 @@ CFeature_table_reader::ReadObject(
CRef<CSeq_annot>
CFeature_table_reader::ReadSeqAnnot(
- ILineReader &lr, IMessageListener *pMessageListener)
+ ILineReader &lr, ILineErrorListener *pMessageListener)
{
return ReadSequinFeatureTable(lr, 0, pMessageListener);
}
@@ -3123,7 +3130,7 @@ CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
const string& seqid,
const string& annotname,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3137,7 +3144,7 @@ CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
const string& seqid,
const string& annotname,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3174,7 +3181,7 @@ CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
CNcbiIstream& ifs,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3186,7 +3193,7 @@ CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
CRef<CSeq_annot> CFeature_table_reader::ReadSequinFeatureTable (
ILineReader& reader,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3212,7 +3219,7 @@ void CFeature_table_reader::ReadSequinFeatureTables(
CNcbiIstream& ifs,
CSeq_entry& entry,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3233,7 +3240,7 @@ void CFeature_table_reader::ReadSequinFeatureTables(
ILineReader& reader,
CSeq_entry& entry,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
ITableFilter *filter
)
{
@@ -3278,7 +3285,7 @@ CRef<CSeq_feat> CFeature_table_reader::CreateSeqFeat (
const string& feat,
CSeq_loc& location,
const TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
unsigned int line,
string *seq_id,
ITableFilter *filter
@@ -3296,7 +3303,7 @@ void CFeature_table_reader::AddFeatQual (
const string& qual,
const string& val,
const CFeature_table_reader::TFlags flags,
- IMessageListener* pMessageListener,
+ ILineErrorListener* pMessageListener,
int line,
const string &seq_id
)
diff --git a/c++/src/objtools/readers/rm_reader.cpp b/c++/src/objtools/readers/rm_reader.cpp
index 0b247e0..c212d58 100644
--- a/c++/src/objtools/readers/rm_reader.cpp
+++ b/c++/src/objtools/readers/rm_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: rm_reader.cpp 448854 2014-10-09 16:30:00Z ivanov $
+/* $Id: rm_reader.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -761,7 +761,7 @@ CRepeatMaskerReader::TConverter& CRepeatMaskerReader::SetConverter()
}
CRef<CSerialObject>
-CRepeatMaskerReader::ReadObject(ILineReader& lr, IMessageListener* pMessageListener)
+CRepeatMaskerReader::ReadObject(ILineReader& lr, ILineErrorListener* pMessageListener)
{
CRef<CSerialObject> object(
ReadSeqAnnot(lr, pMessageListener).ReleaseOrNull());
@@ -769,7 +769,7 @@ CRepeatMaskerReader::ReadObject(ILineReader& lr, IMessageListener* pMessageListe
}
CRef<CSeq_annot>
-CRepeatMaskerReader::ReadSeqAnnot(ILineReader& lr, IMessageListener* pMessageListener)
+CRepeatMaskerReader::ReadSeqAnnot(ILineReader& lr, ILineErrorListener* pMessageListener)
{
CRef<CSeq_annot> annot(new CSeq_annot);
// CRef<CAnnot_descr> desc(new CAnnot_descr);
diff --git a/c++/src/objtools/readers/source_mod_parser.cpp b/c++/src/objtools/readers/source_mod_parser.cpp
index 7250312..cf8a612 100644
--- a/c++/src/objtools/readers/source_mod_parser.cpp
+++ b/c++/src/objtools/readers/source_mod_parser.cpp
@@ -1,4 +1,4 @@
-/* $Id: source_mod_parser.cpp 459292 2015-02-17 18:10:31Z ivanov $
+/* $Id: source_mod_parser.cpp 478277 2015-09-08 14:32:41Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -88,38 +88,60 @@ const unsigned char CSourceModParser::kKeyCanonicalizationTable[257] =
"\xF0\xF1\xF2\xF3\xF4\xF5\xF6\xF7\xF8\xF9\xFA\xFB\xFC\xFD\xFE\xFF";
-template <typename T>
-inline
-T* LeaveAsIs(void)
-{
- return static_cast<T*>(NULL);
-}
-
template<class _T>
-class CAutoInitDesc: public CAutoAddDesc
+class CAutoInitDesc : protected CAutoAddDesc
{
public:
CAutoInitDesc(CSeq_descr& descr, CSeqdesc::E_Choice which);
+ CAutoInitDesc(CBioseq& bioseq, CSeqdesc::E_Choice which);
+ CAutoInitDesc(CBioseq_set& bioset, CSeqdesc::E_Choice which);
CAutoInitDesc(_T& obj);
_T* operator->();
_T& operator*();
protected:
_T* m_ptr;
void _getfromdesc();
+ mutable CRef<CBioseq> m_bioseq;
+ mutable CRef<CBioseq_set> m_bioset;
};
+CSafeStaticRef<CSeq_descr> fake_descr;
+
+template<class _T>
+inline
+CAutoInitDesc<_T>::CAutoInitDesc(CSeq_descr& descr, CSeqdesc::E_Choice which) :
+ CAutoAddDesc(descr, which),
+ m_ptr(0)
+{
+}
+
template<class _T>
inline
-CAutoInitDesc<_T>::CAutoInitDesc(CSeq_descr& descr, CSeqdesc::E_Choice which):
- CAutoAddDesc(descr, which), m_ptr(0)
+CAutoInitDesc<_T>::CAutoInitDesc(CBioseq& bioseq, CSeqdesc::E_Choice which) :
+ CAutoAddDesc(*fake_descr, which),
+ m_ptr(0),
+ m_bioseq(&bioseq)
{
+ m_descr.Reset();
+}
+
+template<class _T>
+inline
+CAutoInitDesc<_T>::CAutoInitDesc(CBioseq_set& bioset, CSeqdesc::E_Choice which) :
+ CAutoAddDesc(*fake_descr, which),
+ m_ptr(0),
+ m_bioset(&bioset)
+
+{
+ m_descr.Reset();
}
template<class _T>
inline
CAutoInitDesc<_T>::CAutoInitDesc(_T& obj):
- CAutoAddDesc(*(CSeq_descr*)0, CSeqdesc::e_not_set), m_ptr(&obj)
+ CAutoAddDesc(*fake_descr, CSeqdesc::e_not_set), m_ptr(&obj)
{
+ m_descr.Reset();
}
@@ -137,7 +159,15 @@ _T* CAutoInitDesc<_T>::operator->()
if (m_ptr == 0 &&
m_which != CSeqdesc::e_not_set)
{
- _getfromdesc();
+ if (m_descr.Empty())
+ {
+ if (!m_bioseq.Empty())
+ m_descr = &m_bioseq->SetDescr();
+ else
+ if (!m_bioset.Empty())
+ m_descr = &m_bioset->SetDescr();
+ }
+ _getfromdesc();
}
return m_ptr;
@@ -250,7 +280,7 @@ void CSourceModParser::ApplyAllMods(CBioseq& seq, CTempString organism, CConstRe
if( ! FIELD_CHAIN_OF_2_IS_SET(seq, Inst, Mol) || seq.IsNa() ) {
CAutoInitRef<CGene_ref> gene;
x_ApplyMods(gene);
- if (&gene.Get(LeaveAsIs<CGene_ref>) != NULL) {
+ if (gene.IsInitialized()) {
CRef<CSeq_feat> feat(new CSeq_feat);
feat->SetData().SetGene(*gene);
feat->SetLocation().Assign(*location);
@@ -264,7 +294,7 @@ void CSourceModParser::ApplyAllMods(CBioseq& seq, CTempString organism, CConstRe
if( ! FIELD_CHAIN_OF_2_IS_SET(seq, Inst, Mol) || seq.IsAa() ) {
CAutoInitRef<CProt_ref> prot;
x_ApplyMods(prot);
- if ( &prot.Get(LeaveAsIs<CProt_ref>) != NULL ) {
+ if ( prot.IsInitialized() ) {
CRef<CSeq_feat> feat(new CSeq_feat);
feat->SetData().SetProt(*prot);
feat->SetLocation().Assign(*location);
@@ -272,7 +302,7 @@ void CSourceModParser::ApplyAllMods(CBioseq& seq, CTempString organism, CConstRe
}
}
- if ( !had_ftable && &ftable.Get(LeaveAsIs<CSeq_annot>) != NULL ) {
+ if ( !had_ftable && ftable.IsInitialized() ) {
seq.SetAnnot().push_back(CRef<CSeq_annot>(&*ftable));
}
}
@@ -283,30 +313,46 @@ void CSourceModParser::ApplyAllMods(CBioseq& seq, CTempString organism, CConstRe
} else {
CAutoInitRef<CSeq_hist> hist;
x_ApplyMods(hist);
- if (&hist.Get(LeaveAsIs<CSeq_hist>) != NULL) {
+ if (hist.IsInitialized()) {
seq.SetInst().SetHist(*hist);
}
}
{{
- CAutoInitDesc<CBioSource> bsrc(seq.SetDescr(), CSeqdesc::e_Source);
- x_ApplyMods(bsrc, organism);
+ //CSeq_descr* descr = 0;
+ if (
+ seq.GetParentSet() && seq.GetParentSet()->IsSetClass() &&
+ seq.GetParentSet()->GetClass() == CBioseq_set::eClass_nuc_prot)
+ {
+ CBioseq_set& bioset = *(CBioseq_set*)(seq.GetParentSet().GetPointerOrNull());
+ //descr = &bioset.SetDescr();
+ CAutoInitDesc<CBioSource> bsrc(bioset, CSeqdesc::e_Source);
+ x_ApplyMods(bsrc, organism);
+ }
+ else
+ {
+ //descr = &seq.SetDescr();
+ CAutoInitDesc<CBioSource> bsrc(seq, CSeqdesc::e_Source);
+ x_ApplyMods(bsrc, organism);
+ }
+ //CAutoInitDesc<CBioSource> bsrc(*descr, CSeqdesc::e_Source);
+ //x_ApplyMods(bsrc, organism);
}}
{{
- CAutoInitDesc<CMolInfo> mi(seq.SetDescr(), CSeqdesc::e_Molinfo);
+ CAutoInitDesc<CMolInfo> mi(seq, CSeqdesc::e_Molinfo);
x_ApplyMods(mi);
}}
{{
- CAutoInitDesc<CGB_block> gbb(seq.SetDescr(), CSeqdesc::e_Genbank);
+ CAutoInitDesc<CGB_block> gbb(seq, CSeqdesc::e_Genbank);
x_ApplyMods(gbb);
}}
{{
CAutoInitRef<CUser_object> tpa;
x_ApplyTPAMods(tpa);
- if (&tpa.Get(LeaveAsIs<CUser_object>) != NULL) {
+ if (tpa.IsInitialized()) {
CRef<CSeqdesc> desc(new CSeqdesc);
desc->SetUser(*tpa);
seq.SetDescr().Set().push_back(desc);
@@ -316,7 +362,7 @@ void CSourceModParser::ApplyAllMods(CBioseq& seq, CTempString organism, CConstRe
{{
CAutoInitRef<CUser_object> gpdb;
x_ApplyGenomeProjectsDBMods(gpdb);
- if (&gpdb.Get(LeaveAsIs<CUser_object>) != NULL) {
+ if (gpdb.IsInitialized()) {
CRef<CSeqdesc> desc(new CSeqdesc);
desc->SetUser(*gpdb);
seq.SetDescr().Set().push_back(desc);
@@ -658,19 +704,20 @@ void CSourceModParser::x_ApplyMods(CAutoInitDesc<CBioSource>& bsrc,
++db_xref_iter ) {
CRef< CDbtag > new_db( new CDbtag );
- const string &db_xref_str = db_xref_iter->value;
- int colon_location = db_xref_str.find( ":" );
- if( colon_location == string::npos ) {
+ const CTempString db_xref_str = db_xref_iter->value;
+ CRef<CObject_id> object_id(new CObject_id);
+
+ size_t colon_location = db_xref_str.find(":");
+ if (colon_location == string::npos) {
// no colon: it's just tag, and db is unknown
- colon_location = -1; // we imagine the colon to be just before the start of the string
- new_db->SetDb( "?" );
+ new_db->SetDb() = "?";
+ db_xref_str.Copy(object_id->SetStr(), 0, CTempString::npos);
} else {
// there's a colon, so db and tag are both known
- new_db->SetDb( db_xref_str.substr( 0, colon_location ) );
+ db_xref_str.Copy(new_db->SetDb(), 0, colon_location);
+ db_xref_str.Copy(object_id->SetStr(), colon_location + 1, CTempString::npos);
}
- CRef<CObject_id> object_id( new CObject_id );
- object_id->SetStr( db_xref_str.substr( colon_location + 1 ) );
new_db->SetTag( *object_id );
bsrc->SetOrg().SetDb().push_back( new_db );
diff --git a/c++/src/objtools/readers/ucscregion_reader.cpp b/c++/src/objtools/readers/ucscregion_reader.cpp
index e9f2034..619f0f8 100644
--- a/c++/src/objtools/readers/ucscregion_reader.cpp
+++ b/c++/src/objtools/readers/ucscregion_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: ucscregion_reader.cpp 432807 2014-04-18 13:52:28Z gotvyans $
+/* $Id: ucscregion_reader.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -202,7 +202,7 @@ void CUCSCRegionReader::xSmartFieldSplit(vector<string>& fields, CTempString lin
bool CUCSCRegionReader::xParseFeature(
const vector<string>& fields,
CRef<CSeq_annot>& annot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
{
// assign
string str_line_number = NStr::IntToString(m_uLineNumber);
@@ -316,7 +316,7 @@ void CUCSCRegionReader::x_SetFeatureLocation(
}
// ----------------------------------------------------------------------------
-CRef<CSerialObject> CUCSCRegionReader::ReadObject(ILineReader& lr, IMessageListener* pErrors)
+CRef<CSerialObject> CUCSCRegionReader::ReadObject(ILineReader& lr, ILineErrorListener* pErrors)
{
CRef<CSeq_annot> annot = ReadSeqAnnot(lr, pErrors);
return CRef<CSerialObject>(annot);
@@ -324,7 +324,7 @@ CRef<CSerialObject> CUCSCRegionReader::ReadObject(ILineReader& lr, IMessageListe
// ----------------------------------------------------------------------------
CRef<CSeq_annot> CUCSCRegionReader::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pEC )
+ ILineErrorListener* pEC )
{
const size_t MAX_RECORDS = 100000;
diff --git a/c++/src/objtools/readers/vcf_reader.cpp b/c++/src/objtools/readers/vcf_reader.cpp
index adcfbe1..bf07c67 100644
--- a/c++/src/objtools/readers/vcf_reader.cpp
+++ b/c++/src/objtools/readers/vcf_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: vcf_reader.cpp 451795 2014-11-12 14:47:56Z ivanov $
+/* $Id: vcf_reader.cpp 481063 2015-10-06 17:15:25Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -185,7 +185,7 @@ CVcfReader::~CVcfReader()
CRef< CSeq_annot >
CVcfReader::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pEC )
+ ILineErrorListener* pEC )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -253,7 +253,7 @@ CVcfReader::ReadSeqAnnot(
CRef< CSerialObject >
CVcfReader::ReadObject(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CSerialObject> object(
@@ -266,7 +266,7 @@ bool
CVcfReader::xProcessMetaLine(
const string& line,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if ( ! NStr::StartsWith( line, "##" ) ) {
@@ -291,7 +291,7 @@ bool
CVcfReader::xProcessMetaLineInfo(
const string& line,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
const string prefix = "##INFO=<";
@@ -360,7 +360,7 @@ bool
CVcfReader::xProcessMetaLineFilter(
const string& line,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
const string prefix = "##FILTER=<";
@@ -409,7 +409,7 @@ bool
CVcfReader::xProcessMetaLineFormat(
const string& line,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
const string prefix = "##FORMAT=<";
@@ -531,7 +531,7 @@ bool
CVcfReader::xProcessDataLine(
const string& line,
CRef<CSeq_annot> pAnnot,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if ( NStr::StartsWith( line, "#" ) ) {
@@ -607,8 +607,23 @@ CVcfReader::xAssignVariationAlleleSet(
variants.push_back(pIdentity);
}
+ bool no_alt = true;
+ for (unsigned int i=0; i < data.m_Alt.size(); ++i) {
+ if (!NStr::Equal(data.m_Alt[i],".")) {
+ no_alt = false;
+ }
+ }
+ if (no_alt) {
+ instance.SetObservation() |= CVariation_inst::eObservation_variant;
+ return true;
+ }
+
+
//add additional variations, one for each alternative
for (unsigned int i=0; i < data.m_Alt.size(); ++i) {
+ if (NStr::Equal(data.m_Alt[i],".")) {
+ continue;
+ }
switch(data.m_SetType) {
default:
if (!xAssignVariantDelins(data, i, pFeature)) {
@@ -683,6 +698,20 @@ CVcfReader::xAssignVariantMnv(
}
// ----------------------------------------------------------------------------
+static void
+s_AddDeleteDeltaItem(
+ CVariation_inst& instance )
+{
+ CRef<CDelta_item> pItem(new CDelta_item);
+
+ pItem->SetSeq().SetThis();
+ instance.SetType(CVariation_inst::eType_del);
+ pItem->SetAction(CDelta_item::eAction_del_at);
+ instance.SetDelta().push_back(pItem);
+}
+
+
+// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDel(
const CVcfData& data,
@@ -698,10 +727,8 @@ CVcfReader::xAssignVariantDel(
//pVariant->SetData().SetNote("DEL");
pVariant->SetDeletion();
CVariation_inst& instance = pVariant->SetData().SetInstance();
- CRef<CDelta_item> pItem(new CDelta_item);
- pItem->SetAction(CDelta_item::eAction_del_at);
- pItem->SetSeq().SetThis();
- instance.SetDelta().push_back(pItem);
+ s_AddDeleteDeltaItem(instance);
+
}}
variants.push_back(pVariant);
return true;
@@ -735,6 +762,8 @@ CVcfReader::xAssignVariantIns(
return true;
}
+
+
// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDelins(
@@ -743,33 +772,41 @@ CVcfReader::xAssignVariantDelins(
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
+ string insertion(data.m_Alt[index]);
+
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
CRef<CVariation_ref> pVariant(new CVariation_ref);
- {{
- string insertion(data.m_Alt[index]);
- CRef<CSeq_literal> pLiteral(new CSeq_literal);
- pLiteral->SetSeq_data().SetIupacna().Set(insertion);
- pLiteral->SetLength(insertion.size());
- CRef<CDelta_item> pItem(new CDelta_item);
- pItem->SetSeq().SetLiteral(*pLiteral);
- CVariation_inst& instance = pVariant->SetData().SetInstance();
+ CVariation_inst& instance = pVariant->SetData().SetInstance();
+ // If it is a deletion, add Deleteion Delta-item and be done.
+ if (insertion.size() == 0) {
- //Let's try to smartly set the Type.
+ s_AddDeleteDeltaItem(instance);
+ variants.push_back(pVariant);
+ return true;
+ }
- if( data.m_Alt[index].size() == 1 && data.m_strRef.size() == 1) {
- instance.SetType(CVariation_inst::eType_snv);
- } else {
- instance.SetType(CVariation_inst::eType_delins);
- }
+ // Must be a SNV or delins
+ CRef<CSeq_literal> pLiteral(new CSeq_literal);
+ pLiteral->SetSeq_data().SetIupacna().Set(insertion);
+ pLiteral->SetLength(insertion.size());
+
+ CRef<CDelta_item> pItem(new CDelta_item);
+ pItem->SetSeq().SetLiteral(*pLiteral);
+ instance.SetDelta().push_back(pItem);
+ //Let's try to smartly set the Type.
+ if (insertion.size() == 1 && data.m_strRef.size() == 1) {
+ instance.SetType(CVariation_inst::eType_snv);
+ } else {
+ instance.SetType(CVariation_inst::eType_delins);
+ }
- instance.SetDelta().push_back(pItem);
- }}
variants.push_back(pVariant);
return true;
+
}
// ----------------------------------------------------------------------------
@@ -777,7 +814,7 @@ bool
CVcfReader::xParseData(
const string& line,
CVcfData& data,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
vector<string> columns;
@@ -907,7 +944,7 @@ CVcfReader::xParseData(
bool
CVcfReader::xNormalizeData(
CVcfData& data,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ---------------------------------------------------------------------------
{
// make sure none of the alternatives is equal to the reference:
@@ -1076,8 +1113,10 @@ CVcfReader::xProcessFilter(
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
- CSeq_feat::TExt& ext = pFeature->SetExt();
- ext.AddField( "filter", data.m_strFilter );
+ if(!NStr::Equal(data.m_strFilter,".")) {
+ CSeq_feat::TExt& ext = pFeature->SetExt();
+ ext.AddField( "filter", data.m_strFilter );
+ }
return true;
}
@@ -1086,7 +1125,7 @@ bool
CVcfReader::xProcessInfo(
CVcfData& data,
CRef<CSeq_feat> pFeature,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if (!xAssignVariantProps(data, pFeature, pEC)) {
@@ -1106,7 +1145,7 @@ CVcfReader::xProcessInfo(
infos.push_back( key );
}
else {
- string joined = NStr::Join( list<string>( value.begin(), value.end() ), ";" );
+ string joined = NStr::Join( list<string>( value.begin(), value.end() ), "," );
infos.push_back( key + "=" + joined );
}
}
@@ -1119,7 +1158,7 @@ bool
CVcfReader::xProcessTrackLine(
const string& strLine,
CRef< CSeq_annot >& current,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
if (!xIsTrackLine(strLine)) {
@@ -1224,7 +1263,7 @@ bool
CVcfReader::xAssignVariantProps(
CVcfData& data,
CRef<CSeq_feat> pFeat,
- IMessageListener* pEC)
+ ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
typedef CVariantProperties VP;
diff --git a/c++/src/objtools/readers/wiggle_reader.cpp b/c++/src/objtools/readers/wiggle_reader.cpp
index 86dde91..8148397 100644
--- a/c++/src/objtools/readers/wiggle_reader.cpp
+++ b/c++/src/objtools/readers/wiggle_reader.cpp
@@ -1,4 +1,4 @@
-/* $Id: wiggle_reader.cpp 458457 2015-02-05 13:19:52Z ivanov $
+/* $Id: wiggle_reader.cpp 477847 2015-09-02 13:12:31Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -141,7 +141,7 @@ CWiggleReader::~CWiggleReader()
CRef< CSerialObject >
CWiggleReader::ReadObject(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
CRef<CSerialObject> object(
@@ -153,7 +153,7 @@ CWiggleReader::ReadObject(
CRef<CSeq_annot>
CWiggleReader::ReadSeqAnnot(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
@@ -174,7 +174,7 @@ CWiggleReader::ReadSeqAnnot(
CRef<CSeq_annot>
CWiggleReader::xReadSeqAnnotGraph(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
m_ChromId.clear();
@@ -240,7 +240,7 @@ CWiggleReader::xReadSeqAnnotGraph(
CRef<CSeq_annot>
CWiggleReader::xReadSeqAnnotTable(
ILineReader& lr,
- IMessageListener* pMessageListener )
+ ILineErrorListener* pMessageListener )
// ----------------------------------------------------------------------------
{
m_ChromId.clear();
@@ -308,7 +308,7 @@ bool
CWiggleReader::ReadTrackData(
ILineReader& lr,
CRawWiggleTrack& rawdata,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
while (xGetLine(lr, m_CurLine)) {
@@ -336,7 +336,7 @@ bool
CWiggleReader::xReadFixedStepDataRaw(
ILineReader& lr,
CRawWiggleTrack& rawdata,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
rawdata.Reset();
@@ -365,7 +365,7 @@ bool
CWiggleReader::xReadVariableStepDataRaw(
ILineReader& lr,
CRawWiggleTrack& rawdata,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
rawdata.Reset();
@@ -751,7 +751,7 @@ inline bool CWiggleReader::xCommentLine(void) const
// ----------------------------------------------------------------------------
string CWiggleReader::xGetWord(
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
const char* ptr = m_CurLine.c_str();
@@ -777,7 +777,7 @@ string CWiggleReader::xGetWord(
// ----------------------------------------------------------------------------
string CWiggleReader::xGetParamName(
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
const char* ptr = m_CurLine.c_str();
@@ -804,7 +804,7 @@ string CWiggleReader::xGetParamName(
// ----------------------------------------------------------------------------
string CWiggleReader::xGetParamValue(
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
const char* ptr = m_CurLine.c_str();
@@ -832,7 +832,7 @@ string CWiggleReader::xGetParamValue(
// ----------------------------------------------------------------------------
void CWiggleReader::xGetPos(
TSeqPos& v,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
TSeqPos ret = 0;
@@ -922,7 +922,7 @@ bool CWiggleReader::xTryGetDoubleSimple(double& v)
// ----------------------------------------------------------------------------
bool CWiggleReader::xTryGetDouble(
double& v,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if ( xTryGetDoubleSimple(v) ) {
@@ -949,7 +949,7 @@ bool CWiggleReader::xTryGetDouble(
// ----------------------------------------------------------------------------
inline bool CWiggleReader::xTryGetPos(
TSeqPos& v,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
char c = m_CurLine.c_str()[0];
@@ -963,7 +963,7 @@ inline bool CWiggleReader::xTryGetPos(
// ----------------------------------------------------------------------------
inline void CWiggleReader::xGetDouble(
double& v,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if ( !xTryGetDouble(v, pMessageListener) ) {
@@ -1034,7 +1034,7 @@ void CWiggleReader::xSetChrom(
// ----------------------------------------------------------------------------
bool CWiggleReader::xProcessBrowserLine(
- IMessageListener* pMl)
+ ILineErrorListener* pMl)
// ----------------------------------------------------------------------------
{
if (!NStr::StartsWith(m_CurLine, "browser")) {
@@ -1046,7 +1046,7 @@ bool CWiggleReader::xProcessBrowserLine(
// ----------------------------------------------------------------------------
bool CWiggleReader::xParseTrackLine(
const string& line,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if (!xIsTrackLine(line)) {
@@ -1075,7 +1075,7 @@ bool CWiggleReader::xParseTrackLine(
// ----------------------------------------------------------------------------
void CWiggleReader::xGetFixedStepInfo(
SFixedStepInfo& fixedStepInfo,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if ( m_TrackType != eTrackType_wiggle_0 ) {
@@ -1147,7 +1147,7 @@ void CWiggleReader::xGetFixedStepInfo(
void CWiggleReader::xReadFixedStepData(
const SFixedStepInfo& fixedStepInfo,
ILineReader& lr,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
xSetChrom(fixedStepInfo.mChrom);
@@ -1168,7 +1168,7 @@ void CWiggleReader::xReadFixedStepData(
// ----------------------------------------------------------------------------
void CWiggleReader::xGetVarStepInfo(
SVarStepInfo& varStepInfo,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// ----------------------------------------------------------------------------
{
if ( m_TrackType != eTrackType_wiggle_0 ) {
@@ -1218,7 +1218,7 @@ void CWiggleReader::xGetVarStepInfo(
void CWiggleReader::xReadVariableStepData(
const SVarStepInfo& varStepInfo,
ILineReader& lr,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// =========================================================================
{
xSetChrom(varStepInfo.mChrom);
@@ -1240,7 +1240,7 @@ void CWiggleReader::xReadVariableStepData(
// =========================================================================
void CWiggleReader::xReadBedLine(
const string& chrom,
- IMessageListener* pMessageListener)
+ ILineErrorListener* pMessageListener)
// =========================================================================
{
if ( m_TrackType != eTrackType_bedGraph &&
diff --git a/c++/src/serial/Makefile.serial.lib b/c++/src/serial/Makefile.serial.lib
index 1734c56..c7ee512 100644
--- a/c++/src/serial/Makefile.serial.lib
+++ b/c++/src/serial/Makefile.serial.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.serial.lib 427416 2014-02-20 13:34:14Z gouriano $
+# $Id: Makefile.serial.lib 478544 2015-09-10 13:20:18Z ivanov $
# Build library "XSER"
#################################
@@ -14,10 +14,12 @@ SRC = \
exception objhook objlist objstack \
$(serial_ws50_rtti_kludge) \
objostrasn objistrasn objostrasnb objistrasnb objostrxml objistrxml \
- objostrjson objistrjson serializable serialobject pathhook
+ objostrjson objistrjson serializable serialobject pathhook rpcbase
LIB = xser
+DLL_LIB = xutil
+
WATCHERS = gouriano
diff --git a/c++/src/serial/choice.cpp b/c++/src/serial/choice.cpp
index ae1f445..d424227 100644
--- a/c++/src/serial/choice.cpp
+++ b/c++/src/serial/choice.cpp
@@ -1,4 +1,4 @@
-/* $Id: choice.cpp 418737 2013-11-19 18:50:38Z gouriano $
+/* $Id: choice.cpp 448624 2014-10-07 18:54:36Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -131,18 +131,26 @@ void CChoiceTypeInfo::InitChoiceTypeInfoFunctions(void)
SetCopyFunction(&TFunc::CopyChoiceDefault);
SetSkipFunction(&TFunc::SkipChoiceDefault);
m_SelectDelayFunction = 0;
+ m_AllowEmpty = false;
}
-CVariantInfo* CChoiceTypeInfo::AddVariant(const char* memberId,
- const void* memberPtr,
- const CTypeRef& memberType)
+void CChoiceTypeInfo::AdjustChoiceTypeInfoFunctions(void)
{
- if ( GetVariants().Size() == 1 &&
+ m_AllowEmpty = GetVariants().Size() == 0 || (
+ GetVariantInfo(kFirstMemberIndex)->GetId().HaveNoPrefix() &&
+ CItemsInfo::FindNextMandatory(this) == NULL);
+ if ( !m_AllowEmpty &&
!GetVariantInfo(kFirstMemberIndex)->GetId().IsAttlist() ) {
// simple
SetReadFunction(&TFunc::ReadChoiceSimple);
SetSkipFunction(&TFunc::SkipChoiceSimple);
}
+}
+
+CVariantInfo* CChoiceTypeInfo::AddVariant(const char* memberId,
+ const void* memberPtr,
+ const CTypeRef& memberType)
+{
CVariantInfo* variantInfo = new CVariantInfo(this, memberId,
TPointerOffsetType(memberPtr),
memberType);
@@ -154,12 +162,6 @@ CVariantInfo* CChoiceTypeInfo::AddVariant(const CMemberId& memberId,
const void* memberPtr,
const CTypeRef& memberType)
{
- if ( GetVariants().Size() == 1 &&
- !GetVariantInfo(kFirstMemberIndex)->GetId().IsAttlist() ) {
- // simple
- SetReadFunction(&TFunc::ReadChoiceSimple);
- SetSkipFunction(&TFunc::SkipChoiceSimple);
- }
CVariantInfo* variantInfo = new CVariantInfo(this, memberId,
TPointerOffsetType(memberPtr),
memberType);
@@ -360,7 +362,7 @@ void CChoiceTypeInfoFunctions::ReadChoiceDefault(CObjectIStream& in,
BEGIN_OBJECT_FRAME_OF(in, eFrameChoiceVariant);
TMemberIndex index = in.BeginChoiceVariant(choiceType);
if ( index == kInvalidMember ) {
- if (in.CanSkipUnknownVariants()) {
+ if (choiceType->MayBeEmpty() || in.CanSkipUnknownVariants()) {
in.SkipAnyContentVariant();
} else {
in.ThrowError(in.fFormatError, "choice variant id expected");
@@ -426,7 +428,7 @@ void CChoiceTypeInfoFunctions::WriteChoiceDefault(CObjectOStream& out,
index = choiceType->GetIndex(objectPtr);
if ( index == kInvalidMember ) {
- if (CItemsInfo::FindNextMandatory(objectType) != NULL) {
+ if (!choiceType->MayBeEmpty()) {
out.ThrowError(out.fInvalidData, "cannot write empty choice");
}
} else {
@@ -459,26 +461,40 @@ void CChoiceTypeInfoFunctions::SkipChoiceDefault(CObjectIStream& in,
in.BeginChoice(choiceType);
BEGIN_OBJECT_FRAME_OF(in, eFrameChoiceVariant);
TMemberIndex index = in.BeginChoiceVariant(choiceType);
- if ( index == kInvalidMember )
- in.ThrowError(in.fFormatError,"choice variant id expected");
- const CVariantInfo* variantInfo = choiceType->GetVariantInfo(index);
- if (variantInfo->GetId().IsAttlist()) {
- const CMemberInfo* memberInfo =
- dynamic_cast<const CMemberInfo*>(
- choiceType->GetVariants().GetItemInfo(index));
- memberInfo->SkipMember(in);
+ if ( index == kInvalidMember ) {
+ if (choiceType->MayBeEmpty() || in.CanSkipUnknownVariants()) {
+ in.SkipAnyContentVariant();
+ } else {
+ in.ThrowError(in.fFormatError, "choice variant id expected");
+ }
+ } else {
+ for (;;) {
+ const CVariantInfo* variantInfo = choiceType->GetVariantInfo(index);
+ if (variantInfo->GetId().IsAttlist()) {
+ const CMemberInfo* memberInfo =
+ dynamic_cast<const CMemberInfo*>(
+ choiceType->GetVariants().GetItemInfo(index));
+ memberInfo->SkipMember(in);
+ in.EndChoiceVariant();
+ index = in.BeginChoiceVariant(choiceType);
+ if ( index == kInvalidMember ) {
+ if (in.CanSkipUnknownVariants()) {
+ in.SkipAnyContentVariant();
+ break;
+ } else {
+ in.ThrowError(in.fFormatError, "choice variant id expected");
+ }
+ }
+ variantInfo = choiceType->GetVariantInfo(index);
+ }
+ in.SetTopMemberId(variantInfo->GetId());
+
+ variantInfo->SkipVariant(in);
in.EndChoiceVariant();
- index = in.BeginChoiceVariant(choiceType);
- if ( index == kInvalidMember )
- in.ThrowError(in.fFormatError,"choice variant id expected");
- variantInfo = choiceType->GetVariantInfo(index);
+ break;
+ }
}
- in.SetTopMemberId(variantInfo->GetId());
-
- variantInfo->SkipVariant(in);
-
- in.EndChoiceVariant();
END_OBJECT_FRAME_OF(in);
in.EndChoice();
END_OBJECT_FRAME_OF(in);
diff --git a/c++/src/serial/continfo.cpp b/c++/src/serial/continfo.cpp
index f21e1cf..602d54d 100644
--- a/c++/src/serial/continfo.cpp
+++ b/c++/src/serial/continfo.cpp
@@ -1,4 +1,4 @@
-/* $Id: continfo.cpp 412224 2013-09-05 15:30:00Z gouriano $
+/* $Id: continfo.cpp 463313 2015-03-26 17:05:21Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -207,29 +207,22 @@ CContainerTypeInfo::GetMayContainType(TTypeInfo type) const
void CContainerTypeInfo::Assign(TObjectPtr dst, TConstObjectPtr src,
ESerialRecursionMode how) const
{
- //SetDefault(dst); // clear destination container
if (how == eShallowChildless) {
+ SetDefault(dst); // clear destination container
return;
}
CIterator idst;
CConstIterator isrc;
bool old_element = InitIterator(idst,dst);
if ( InitIterator(isrc, src) ) {
+ TTypeInfo elementType = GetElementType();
do {
- if (GetElementType()->GetTypeFamily() == eTypeFamilyPointer) {
- const CPointerTypeInfo* pointerType =
- CTypeConverter<CPointerTypeInfo>::SafeCast(GetElementType());
- _ASSERT(pointerType->GetObjectPointer(GetElementPtr(isrc)));
- if ( !pointerType->GetObjectPointer(GetElementPtr(isrc)) ) {
- ERR_POST_X(2, Warning << " NULL pointer found in container: skipping");
- continue;
- }
- }
+ TConstObjectPtr elementPtr = GetElementPtr(isrc);
if (old_element) {
- GetElementType()->Assign(GetElementPtr(idst), GetElementPtr(isrc), how);
+ elementType->Assign(GetElementPtr(idst), elementPtr, how);
old_element = NextElement(idst);
} else {
- AddElement(dst, GetElementPtr(isrc), how);
+ AddElement(dst, elementPtr, how);
}
} while ( NextElement(isrc) );
}
diff --git a/c++/src/serial/datatool/aparser.cpp b/c++/src/serial/datatool/aparser.cpp
index f5f01ee..f4ebb2a 100644
--- a/c++/src/serial/datatool/aparser.cpp
+++ b/c++/src/serial/datatool/aparser.cpp
@@ -1,4 +1,4 @@
-/* $Id: aparser.cpp 122761 2008-03-25 16:45:09Z gouriano $
+/* $Id: aparser.cpp 466898 2015-05-07 13:36:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,7 +48,7 @@ AbstractParser::~AbstractParser(void)
string AbstractParser::GetLocation(void)
{
- return kEmptyStr;
+ return Lexer().GetName() + "(" + NStr::NumericToString(LastTokenLine()) + "):";
}
void AbstractParser::ParseError(const char* error, const char* expected,
@@ -56,16 +56,11 @@ void AbstractParser::ParseError(const char* error, const char* expected,
{
NCBI_THROW(CDatatoolException,eWrongInput,
GetLocation() +
- "LINE " + NStr::IntToString(token.GetLine()) +
+// " LINE " + NStr::IntToString(token.GetLine()) +
", TOKEN \"" + token.GetText() + "\": " + error +
(string(error).empty() ? "" : ": ") + expected + " expected");
}
-string AbstractParser::Location(void) const
-{
- return NStr::IntToString(LastTokenLine()) + ':';
-}
-
void AbstractParser::CopyLineComment(int line, CComments& comments,
int flags)
{
diff --git a/c++/src/serial/datatool/aparser.hpp b/c++/src/serial/datatool/aparser.hpp
index 731230f..7e776df 100644
--- a/c++/src/serial/datatool/aparser.hpp
+++ b/c++/src/serial/datatool/aparser.hpp
@@ -1,7 +1,7 @@
#ifndef ABSTRACT_PARSER_HPP
#define ABSTRACT_PARSER_HPP
-/* $Id: aparser.hpp 122761 2008-03-25 16:45:09Z gouriano $
+/* $Id: aparser.hpp 466898 2015-05-07 13:36:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -48,6 +48,7 @@ public:
virtual ~AbstractParser(void);
virtual string GetLocation(void);
+ NCBI_NORETURN
virtual void ParseError(const char* error, const char* expected,
const AbstractToken& token);
virtual void EndCommentBlock(void) {}
@@ -62,7 +63,6 @@ public:
ParseError("", expected);
}
- string Location(void) const;
AbstractLexer& Lexer(void)
{
diff --git a/c++/src/serial/datatool/blocktype.cpp b/c++/src/serial/datatool/blocktype.cpp
index 9dc50fb..e61e1c3 100644
--- a/c++/src/serial/datatool/blocktype.cpp
+++ b/c++/src/serial/datatool/blocktype.cpp
@@ -1,4 +1,4 @@
-/* $Id: blocktype.cpp 412225 2013-09-05 15:31:52Z gouriano $
+/* $Id: blocktype.cpp 455924 2015-01-06 14:35:19Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -719,11 +719,12 @@ AutoPtr<CTypeStrings> CDataContainerType::AddMembers(
bool delayed = GetBoolVar((*i)->GetName()+"._delay");
AutoPtr<CTypeStrings> memberType = (*i)->GetType()->GetFullCType();
+ string external_name = (*i)->GetName();
string member_name = (*i)->GetType()->DefClassMemberName();
if (member_name.empty()) {
- member_name = (*i)->GetName();
+ member_name = external_name;
}
- code->AddMember(member_name, memberType,
+ code->AddMember(external_name, member_name, memberType,
(*i)->GetType()->GetVar("_pointer"),
optional, defaultCode, delayed,
(*i)->GetType()->GetTag(),
diff --git a/c++/src/serial/datatool/choicestr.cpp b/c++/src/serial/datatool/choicestr.cpp
index 16b2690..8a6f83d 100644
--- a/c++/src/serial/datatool/choicestr.cpp
+++ b/c++/src/serial/datatool/choicestr.cpp
@@ -1,4 +1,4 @@
-/* $Id: choicestr.cpp 412225 2013-09-05 15:31:52Z gouriano $
+/* $Id: choicestr.cpp 461337 2015-03-09 18:00:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -77,26 +77,28 @@ CChoiceTypeStrings::~CChoiceTypeStrings(void)
{
}
-void CChoiceTypeStrings::AddVariant(const string& name,
+void CChoiceTypeStrings::AddVariant(const string& external_name,
+ const string& name,
const AutoPtr<CTypeStrings>& type,
bool delayed, bool in_union, int tag,
bool noPrefix, bool attlist, bool noTag,
bool simple, const CDataType* dataType,
const CComments& comments)
{
- m_Variants.push_back(SVariantInfo(name, type, delayed, in_union, tag,
+ m_Variants.push_back(SVariantInfo(external_name, name, type, delayed, in_union, tag,
noPrefix,attlist,noTag,simple,dataType,
comments));
}
-CChoiceTypeStrings::SVariantInfo::SVariantInfo(const string& name,
+CChoiceTypeStrings::SVariantInfo::SVariantInfo(const string& external_name,
+ const string& name,
const AutoPtr<CTypeStrings>& t,
bool del, bool in_un, int tag,
bool noPrefx, bool attlst,
bool noTg,bool simpl,
const CDataType* dataTp,
const CComments& commnts)
- : externalName(name), cName(Identifier(name)),
+ : externalName(external_name), cName(Identifier(name)),
type(t), delayed(del), in_union(in_un), memberTag(tag),
noPrefix(noPrefx), attlist(attlst), noTag(noTg), simple(simpl),
dataType(dataTp), comments(commnts)
@@ -1549,6 +1551,9 @@ void CChoiceTypeStrings::GenerateClassCode(CClassCode& code,
if ( i->delayed ) {
methods << "->SetDelayBuffer(MEMBER_PTR(m_delayBuffer))";
}
+ if (i->dataType && i->dataType->GetDataMember() && i->dataType->GetDataMember()->Optional()) {
+ methods << "->SetOptional()";
+ }
if (i->noPrefix) {
methods << "->SetNoPrefix()";
}
@@ -1569,15 +1574,18 @@ void CChoiceTypeStrings::GenerateClassCode(CClassCode& code,
methods << ")";
}
if (i->dataType) {
+ const CUniSequenceDataType* uniseq =
+ dynamic_cast<const CUniSequenceDataType*>(i->dataType);
const COctetStringDataType* octets =
dynamic_cast<const COctetStringDataType*>(i->dataType);
+ if (!octets && uniseq) {
+ octets = dynamic_cast<const COctetStringDataType*>(uniseq->GetElementType());
+ }
if (octets) {
if (octets->IsCompressed()) {
methods << "->SetCompressed()";
}
}
- const CUniSequenceDataType* uniseq =
- dynamic_cast<const CUniSequenceDataType*>(i->dataType);
if (uniseq && uniseq->IsNonEmpty()) {
methods << "->SetNonEmpty()";
}
diff --git a/c++/src/serial/datatool/choicestr.hpp b/c++/src/serial/datatool/choicestr.hpp
index f00e75b..3634718 100644
--- a/c++/src/serial/datatool/choicestr.hpp
+++ b/c++/src/serial/datatool/choicestr.hpp
@@ -1,7 +1,7 @@
#ifndef CHOICESTR_HPP
#define CHOICESTR_HPP
-/* $Id: choicestr.hpp 282780 2011-05-16 16:02:27Z gouriano $
+/* $Id: choicestr.hpp 455924 2015-01-06 14:35:19Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -66,7 +66,7 @@ public:
const CDataType* dataType;
CComments comments;
- SVariantInfo(const string& name, const AutoPtr<CTypeStrings>& type,
+ SVariantInfo(const string& external_name, const string& name, const AutoPtr<CTypeStrings>& type,
bool delayed, bool in_union,
int tag, bool noPrefx, bool attlst, bool noTg,
bool simpl, const CDataType* dataTp, const CComments& commnts);
@@ -83,7 +83,9 @@ public:
return m_HaveAssignment;
}
- void AddVariant(const string& name, const AutoPtr<CTypeStrings>& type,
+ void AddVariant(const string& external_name,
+ const string& name,
+ const AutoPtr<CTypeStrings>& type,
bool delayed, bool in_union, int tag,
bool noPrefix, bool attlist,
bool noTag, bool simple, const CDataType* dataType,
diff --git a/c++/src/serial/datatool/choicetype.cpp b/c++/src/serial/datatool/choicetype.cpp
index c992331..d5e50f2 100644
--- a/c++/src/serial/datatool/choicetype.cpp
+++ b/c++/src/serial/datatool/choicetype.cpp
@@ -1,4 +1,4 @@
-/* $Id: choicetype.cpp 412225 2013-09-05 15:31:52Z gouriano $
+/* $Id: choicetype.cpp 455924 2015-01-06 14:35:19Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -270,13 +270,14 @@ AutoPtr<CTypeStrings> CChoiceDataType::GetFullCType(void) const
code->SetObject(true);
ITERATE ( TMembers, i, GetMembers() ) {
AutoPtr<CTypeStrings> varType = (*i)->GetType()->GetFullCType();
+ string external_name = (*i)->GetName();
string member_name = (*i)->GetType()->DefClassMemberName();
if (member_name.empty()) {
- member_name = (*i)->GetName();
+ member_name = external_name;
}
bool delayed = GetBoolVar((*i)->GetName()+"._delay");
bool in_union = GetBoolVar((*i)->GetName()+"._in_union", true);
- code->AddVariant(member_name, varType, delayed, in_union,
+ code->AddVariant(external_name, member_name, varType, delayed, in_union,
(*i)->GetType()->GetTag(),
(*i)->NoPrefix(), (*i)->Attlist(), (*i)->Notag(),
(*i)->SimpleType(),(*i)->GetType(),
diff --git a/c++/src/serial/datatool/classstr.cpp b/c++/src/serial/datatool/classstr.cpp
index 056096f..bdc2ead 100644
--- a/c++/src/serial/datatool/classstr.cpp
+++ b/c++/src/serial/datatool/classstr.cpp
@@ -1,4 +1,4 @@
-/* $Id: classstr.cpp 412225 2013-09-05 15:31:52Z gouriano $
+/* $Id: classstr.cpp 461337 2015-03-09 18:00:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -103,7 +103,8 @@ bool CClassTypeStrings::x_IsUniSeq(TMembers::const_iterator i) const
return i->dataType && i->dataType->IsUniSeq();
}
-void CClassTypeStrings::AddMember(const string& name,
+void CClassTypeStrings::AddMember(const string& external_name,
+ const string& name,
const AutoPtr<CTypeStrings>& type,
const string& pointerType,
bool optional,
@@ -113,14 +114,15 @@ void CClassTypeStrings::AddMember(const string& name,
bool simple,const CDataType* dataType,
bool nonempty, const CComments& comments)
{
- m_Members.push_back(SMemberInfo(name, type,
+ m_Members.push_back(SMemberInfo(external_name, name, type,
pointerType,
optional, defaultValue,
delayed, tag, noPrefix,attlist,noTag,
simple,dataType,nonempty, comments));
}
-CClassTypeStrings::SMemberInfo::SMemberInfo(const string& name,
+CClassTypeStrings::SMemberInfo::SMemberInfo(const string& external_name,
+ const string& name,
const AutoPtr<CTypeStrings>& t,
const string& pType,
bool opt, const string& defValue,
@@ -128,7 +130,7 @@ CClassTypeStrings::SMemberInfo::SMemberInfo(const string& name,
bool attlst, bool noTg, bool simpl,
const CDataType* dataTp, bool nEmpty,
const CComments& commnts)
- : externalName(name), cName(Identifier(name)),
+ : externalName(external_name), cName(Identifier(name)),
mName("m_"+cName), tName('T'+cName),
type(t), ptrType(pType),
optional(opt), delayed(del), memberTag(tag),
@@ -169,7 +171,8 @@ CClassTypeStrings::SMemberInfo::SMemberInfo(const string& name,
ref = false;
}
else {
- _ASSERT("Unknown reference type: "+ref);
+ // Unknown reference type
+ _ASSERT(false);
}
if ( ref ) {
@@ -1427,8 +1430,13 @@ void CClassTypeStrings::GenerateClassCode(CClassCode& code,
methods << ")";
}
if (i->dataType) {
+ const CUniSequenceDataType* uniseq =
+ dynamic_cast<const CUniSequenceDataType*>(i->dataType);
const COctetStringDataType* octets =
dynamic_cast<const COctetStringDataType*>(i->dataType);
+ if (!octets && uniseq) {
+ octets = dynamic_cast<const COctetStringDataType*>(uniseq->GetElementType());
+ }
if (octets) {
if (octets->IsCompressed()) {
methods << "->SetCompressed()";
diff --git a/c++/src/serial/datatool/classstr.hpp b/c++/src/serial/datatool/classstr.hpp
index 60a8037..9aee72d 100644
--- a/c++/src/serial/datatool/classstr.hpp
+++ b/c++/src/serial/datatool/classstr.hpp
@@ -1,7 +1,7 @@
#ifndef CLASSSTR_HPP
#define CLASSSTR_HPP
-/* $Id: classstr.hpp 282780 2011-05-16 16:02:27Z gouriano $
+/* $Id: classstr.hpp 455924 2015-01-06 14:35:19Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -68,7 +68,9 @@ public:
const CDataType* dataType;
bool nonEmpty;
CComments comments;
- SMemberInfo(const string& name, const AutoPtr<CTypeStrings>& type,
+ SMemberInfo(const string& external_name,
+ const string& name,
+ const AutoPtr<CTypeStrings>& type,
const string& pointerType,
bool optional, const string& defaultValue,
bool delayed, int tag,
@@ -98,7 +100,8 @@ public:
void SetParentClass(const string& className, const CNamespace& ns,
const string& fileName);
- void AddMember(const string& name, const AutoPtr<CTypeStrings>& type,
+ void AddMember(const string& external_name, const string& name,
+ const AutoPtr<CTypeStrings>& type,
const string& pointerType,
bool optional, const string& defaultValue,
bool delayed, int tag,
@@ -106,7 +109,7 @@ public:
const CDataType* dataType, bool nonEmpty, const CComments& comments);
void AddMember(const AutoPtr<CTypeStrings>& type, int tag, bool nonEmpty, bool noPrefix)
{
- AddMember(NcbiEmptyString, type, NcbiEmptyString,
+ AddMember(NcbiEmptyString, NcbiEmptyString, type, NcbiEmptyString,
false, NcbiEmptyString, false, tag,
noPrefix,false,false,false,0,nonEmpty,CComments());
}
diff --git a/c++/src/serial/datatool/datatool.cpp b/c++/src/serial/datatool/datatool.cpp
index ac47a63..8572338 100644
--- a/c++/src/serial/datatool/datatool.cpp
+++ b/c++/src/serial/datatool/datatool.cpp
@@ -1,4 +1,4 @@
-/* $Id: datatool.cpp 428029 2014-02-26 19:29:54Z gouriano $
+/* $Id: datatool.cpp 471533 2015-06-29 11:41:42Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -88,7 +88,7 @@ int CDataTool::Run(void)
CDataTool::CDataTool(void)
{
- SetVersion( CVersionInfo(2,12,0) );
+ SetVersion( CVersionInfo(2,14,0) );
}
void CDataTool::Init(void)
@@ -815,11 +815,16 @@ string CDataTool::GetConfigValue(const string& section, const string& name) cons
return generator.GetConfig().Get(section,name);
}
+bool CDataTool::HasConfig(void) const
+{
+ return !generator.GetConfig().Empty();
+}
+
END_NCBI_SCOPE
int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
USING_NCBI_SCOPE;
CException::EnableBackgroundReporting(false);
- return CDataTool().AppMain(argc, argv, 0, eDS_Default, 0, _T_XSTRING("datatool"));
+ return CDataTool().AppMain(argc, argv, 0, eDS_Default, _T_XCSTRING(""), _T_XSTRING("datatool"));
}
diff --git a/c++/src/serial/datatool/datatool.hpp b/c++/src/serial/datatool/datatool.hpp
index 80ff68d..30b0b05 100644
--- a/c++/src/serial/datatool/datatool.hpp
+++ b/c++/src/serial/datatool/datatool.hpp
@@ -1,7 +1,7 @@
#ifndef DATATOOL__HPP
#define DATATOOL__HPP
-/* $Id: datatool.hpp 413435 2013-09-16 14:30:30Z gouriano $
+/* $Id: datatool.hpp 461580 2015-03-11 13:15:39Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,6 +51,7 @@ public:
int Run(void);
string GetConfigValue(const string& section, const string& name) const;
+ bool HasConfig(void) const;
private:
bool ProcessModules(void);
diff --git a/c++/src/serial/datatool/dtdparser.cpp b/c++/src/serial/datatool/dtdparser.cpp
index 443b0e1..ec62bc8 100644
--- a/c++/src/serial/datatool/dtdparser.cpp
+++ b/c++/src/serial/datatool/dtdparser.cpp
@@ -1,4 +1,4 @@
-/* $Id: dtdparser.cpp 432803 2014-04-18 13:00:20Z gouriano $
+/* $Id: dtdparser.cpp 466898 2015-05-07 13:36:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -119,10 +119,10 @@ void DTDParser::Module(
EndCommentBlock();
}
catch (CException& e) {
- NCBI_RETHROW_SAME(e,"DTDParser::BuildDocumentTree: failed");
+ NCBI_RETHROW_SAME(e, GetLocation() + " DTDParser::BuildDocumentTree: failed");
}
catch (exception& e) {
- ERR_POST_X(5, e.what());
+ ERR_POST_X(5, GetLocation() << e.what());
throw;
}
@@ -219,10 +219,10 @@ void DTDParser::SkipConditionalSection(void)
}
}
catch (CException& e) {
- NCBI_RETHROW_SAME(e,"DTDParser::BuildDocumentTree: failed");
+ NCBI_RETHROW_SAME(e, GetLocation() + "DTDParser::BuildDocumentTree: failed");
}
catch (exception& e) {
- ERR_POST_X(6, e.what());
+ ERR_POST_X(6, GetLocation() << e.what());
throw;
}
}
@@ -232,13 +232,15 @@ string DTDParser::GetLocation(void)
{
string loc;
list<string>::const_iterator i;
- for (i = m_StackLexerName.begin(); i != m_StackLexerName.end(); ++i) {
- if (i != m_StackLexerName.begin()) {
- loc += "/";
+ size_t len = m_StackLexerName.size();
+ if (len > 0) {
+ for (--len, i = m_StackLexerName.begin(); len > 0 && i != m_StackLexerName.end(); ++i) {
+ if (i != m_StackLexerName.begin()) {
+ loc += "/";
+ }
+ loc += *i;
}
- loc += *i;
}
- loc += ": ";
return loc + AbstractParser::GetLocation();
}
@@ -1129,9 +1131,20 @@ CDataType* DTDParser::x_Type(
AutoPtr<CDataValue> DTDParser::Value(const DTDElement& node)
{
- AutoPtr<CDataValue> value(x_Value(node));
- value->SetSourceLine(node.GetSourceLine());
- return value;
+ try {
+ AutoPtr<CDataValue> value(x_Value(node));
+ value->SetSourceLine(node.GetSourceLine());
+ return value;
+ }
+ catch (CException& e) {
+ NCBI_RETHROW_SAME(e,
+ string("Element: ") + node.GetName() +
+ ", type: " + node.GetTypeName() +
+ ", namespace: " + node.GetNamespaceName() +
+ ", on line: " + NStr::NumericToString(node.GetSourceLine()) +
+ ": failed to define default value");
+ }
+ return AutoPtr<CDataValue>();
}
AutoPtr<CDataValue> DTDParser::x_Value(const DTDElement& node)
@@ -1200,7 +1213,7 @@ CDataType* DTDParser::TypesBlock(
for (list<string>::const_iterator i= refs.begin(); i != refs.end(); ++i) {
if (*i == s_SpecialName) {
AutoPtr<CDataType> stype(new CStringDataType());
- AutoPtr<CDataMember> smember(new CDataMember("_CharData", stype));
+ AutoPtr<CDataMember> smember(new CDataMember("-CharData", stype));
smember->SetNotag();
smember->SetNoPrefix();
container->AddMember(smember);
@@ -1209,9 +1222,9 @@ CDataType* DTDParser::TypesBlock(
DTDElement& refNode = m_MapElement[*i];
if (refNode.GetName().empty()) {
if (refNode.GetType() == DTDElement::eAny) {
- refNode.SetName("_Any");
+ refNode.SetName("-Any");
} else {
- ERR_POST_X(7, Warning << "Element with no name: " << *i);
+ ERR_POST_X(7, Warning << GetLocation() << "Element with no name: " << *i);
refNode.SetName(*i);
}
}
diff --git a/c++/src/serial/datatool/enumstr.cpp b/c++/src/serial/datatool/enumstr.cpp
index ecbd3ef..5b96b33 100644
--- a/c++/src/serial/datatool/enumstr.cpp
+++ b/c++/src/serial/datatool/enumstr.cpp
@@ -1,4 +1,4 @@
-/* $Id: enumstr.cpp 413810 2013-09-18 15:28:07Z gouriano $
+/* $Id: enumstr.cpp 471532 2015-06-29 11:41:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -119,7 +119,7 @@ void CEnumTypeStrings::GenerateTypeCode(CClassContext& ctx) const
}
hpp << " {";
ITERATE ( TValues, i, m_Values ) {
- string id = Identifier( i->GetName(), false );
+ string id = Identifier( i->GetEnumId(), false );
hpp << "\n " << m_ValuesPrefix << id;
hpp << string( maxlen - i->GetName().size(),' ' ) << " = ";
hpp.width( maxwidth );
@@ -190,9 +190,15 @@ void CEnumTypeStrings::GenerateTypeCode(CClassContext& ctx) const
" SET_ENUM_BITSET;\n";
}
ITERATE ( TValues, i, m_Values ) {
- string id = Identifier(i->GetName(), false);
- cpp <<
- " ADD_ENUM_VALUE(\""<<i->GetName()<<"\", "<<m_ValuesPrefix<<id<<");\n";
+ string id = Identifier(i->GetEnumId(), false);
+ CEnumDataTypeValue::TValueFlags flags = i->GetFlags();
+ if (flags) {
+ cpp <<
+ " ADD_ENUM_VALUE_FLAGS(\""<<i->GetName()<<"\", "<<m_ValuesPrefix<<id<<", "<<flags<<");\n";
+ } else {
+ cpp <<
+ " ADD_ENUM_VALUE(\""<<i->GetName()<<"\", "<<m_ValuesPrefix<<id<<");\n";
+ }
}
cpp <<
"}\n"
diff --git a/c++/src/serial/datatool/enumtype.cpp b/c++/src/serial/datatool/enumtype.cpp
index bbae94c..9718da8 100644
--- a/c++/src/serial/datatool/enumtype.cpp
+++ b/c++/src/serial/datatool/enumtype.cpp
@@ -1,4 +1,4 @@
-/* $Id: enumtype.cpp 413810 2013-09-18 15:28:07Z gouriano $
+/* $Id: enumtype.cpp 471532 2015-06-29 11:41:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -314,7 +314,7 @@ bool CEnumDataType::CheckValue(const CDataValue& value) const
if ( i->GetValue() == intValue->GetValue() )
return true;
}
- value.Warning("illegal INTEGER value: " + intValue->GetValue(), 14);
+ value.Warning("illegal INTEGER value: " + NStr::NumericToString(intValue->GetValue()), 14);
return false;
}
@@ -430,6 +430,20 @@ AutoPtr<CTypeStrings> CEnumDataType::GetRefCType(void) const
AutoPtr<CTypeStrings> CEnumDataType::GetFullCType(void) const
{
+ ITERATE ( TValues, i, m_Values ) {
+ string id(Identifier( i->GetEnumId(), false ));
+ string value;
+ value = GetVar(id + "._hidename", false);
+ if (!value.empty()) {
+ if (NStr::StringToBool(value)) {
+ i->SetFlag(CEnumDataTypeValue::eHideName);
+ }
+ }
+ value = GetVar( id, false);
+ if (!value.empty()) {
+ i->SetEnumId(value);
+ }
+ }
// in case client wants std type instead of enum.
// I must be accurate here to not to mess with GetEnumCInfo()
string type = GetAndVerifyVar("_type");
diff --git a/c++/src/serial/datatool/enumtype.hpp b/c++/src/serial/datatool/enumtype.hpp
index 05823be..653bde2 100644
--- a/c++/src/serial/datatool/enumtype.hpp
+++ b/c++/src/serial/datatool/enumtype.hpp
@@ -1,7 +1,7 @@
#ifndef ENUMTYPE_HPP
#define ENUMTYPE_HPP
-/* $Id: enumtype.hpp 365689 2012-06-07 13:52:21Z gouriano $
+/* $Id: enumtype.hpp 471532 2015-06-29 11:41:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,7 +42,7 @@ class CEnumDataTypeValue
{
public:
CEnumDataTypeValue(const string& name, TEnumValueType value)
- : m_SourceLine(0), m_Name(name), m_Value(value)
+ : m_SourceLine(0), m_Name(name), m_Value(value), m_Flags(eNone), m_IdName(name)
{
}
@@ -71,11 +71,33 @@ public:
{
return m_SourceLine;
}
+
+ const string& GetEnumId(void) const {
+ return m_IdName;
+ }
+ void SetEnumId(const string& id) const {
+ m_IdName = id;
+ }
+
+ enum EValueFlags {
+ eNone = 0,
+ eHideName = 1
+ };
+ typedef unsigned int TValueFlags;
+
+ void SetFlag(EValueFlags flag) const {
+ m_Flags |= flag;
+ }
+ TValueFlags GetFlags(void) const {
+ return m_Flags;
+ }
private:
int m_SourceLine;
string m_Name;
TEnumValueType m_Value;
CComments m_Comments;
+ mutable TValueFlags m_Flags;
+ mutable string m_IdName;
};
class CEnumDataType : public CDataType
diff --git a/c++/src/serial/datatool/generate.cpp b/c++/src/serial/datatool/generate.cpp
index 7d69796..1a48560 100644
--- a/c++/src/serial/datatool/generate.cpp
+++ b/c++/src/serial/datatool/generate.cpp
@@ -1,4 +1,4 @@
-/* $Id: generate.cpp 435065 2014-05-13 18:28:20Z ucko $
+/* $Id: generate.cpp 452865 2014-11-25 17:18:48Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -790,7 +790,7 @@ void CCodeGenerator::GenerateModuleHPP(const string& path, list<string>& generat
}
isfound = true;
if ( !out.get() || !out->is_open() ) {
- if (isdigit((unsigned int)current_module[0])) {
+ if (isdigit((unsigned char)current_module[0])) {
current_module.insert(current_module.begin(),'x');
}
filename = Path(path, current_module + "_module.hpp");
@@ -875,7 +875,7 @@ void CCodeGenerator::GenerateModuleCPP(const string& path, list<string>& generat
}
isfound = true;
if ( !out.get() || !out->is_open()) {
- if (isdigit((unsigned int)current_module[0])) {
+ if (isdigit((unsigned char)current_module[0])) {
current_module.insert(current_module.begin(),'x');
}
filename = Path(path, current_module + "_module.cpp");
diff --git a/c++/src/serial/datatool/parser.cpp b/c++/src/serial/datatool/parser.cpp
index 9a79ff7..c46036a 100644
--- a/c++/src/serial/datatool/parser.cpp
+++ b/c++/src/serial/datatool/parser.cpp
@@ -1,4 +1,4 @@
-/* $Id: parser.cpp 412890 2013-09-11 14:05:41Z gouriano $
+/* $Id: parser.cpp 467208 2015-05-11 17:01:47Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -172,7 +172,7 @@ void ASNParser::ModuleBody(CDataTypeModule& module)
ModuleType(module, name);
break;
case T_DEFINE:
- ERR_POST_X(1, "LINE " << Location() <<
+ ERR_POST_X(1, GetLocation() <<
" type name omitted");
Consume();
ModuleType(module, "unnamed type");
@@ -180,16 +180,16 @@ void ASNParser::ModuleBody(CDataTypeModule& module)
case K_END:
return;
default:
- ERR_POST_X(2, "LINE " << Location() <<
+ ERR_POST_X(2, GetLocation() <<
" type definition expected");
return;
}
}
catch (CException& e) {
- NCBI_RETHROW_SAME(e,"ASNParser::ModuleBody: failed");
+ NCBI_RETHROW_SAME(e,GetLocation() + " ASNParser::ModuleBody: failed");
}
catch (exception& e) {
- ERR_POST_X(3, e.what());
+ ERR_POST_X(3, GetLocation() << e.what());
}
}
}
@@ -522,7 +522,7 @@ AutoPtr<CDataMember> ASNParser::NamedDataType(bool allowDefaults)
break;
case K_DEFAULT:
Consume();
- member->SetDefault(Value());
+ member->SetDefault(Value(type.get()));
break;
}
}
@@ -564,23 +564,32 @@ void ASNParser::TypeList(list<string>& ids)
} while ( ConsumeIfSymbol(',') );
}
-AutoPtr<CDataValue> ASNParser::Value(void)
+AutoPtr<CDataValue> ASNParser::Value(const CDataType* type)
{
int line = NextTokenLine();
- AutoPtr<CDataValue> value(x_Value());
- value->SetSourceLine(line);
- return value;
+ try {
+ AutoPtr<CDataValue> value(x_Value(type));
+ value->SetSourceLine(line);
+ return value;
+ }
+ catch (CException& e) {
+ NCBI_RETHROW_SAME(e, GetLocation() + " failed to parse value");
+ }
+ return AutoPtr<CDataValue>();
}
-AutoPtr<CDataValue> ASNParser::x_Value(void)
+AutoPtr<CDataValue> ASNParser::x_Value(const CDataType* type)
{
switch ( Next() ) {
default:
break;
case T_NUMBER:
+ if (type && NStr::Compare( type->GetASNKeyword(), "REAL") == 0) {
+ return AutoPtr<CDataValue>(new CDoubleDataValue(Double(T_NUMBER)));
+ }
return AutoPtr<CDataValue>(new CIntDataValue(Number()));
case T_DOUBLE:
- return AutoPtr<CDataValue>(new CDoubleDataValue(Double()));
+ return AutoPtr<CDataValue>(new CDoubleDataValue(Double(T_DOUBLE)));
case T_STRING:
return AutoPtr<CDataValue>(new CStringDataValue(String()));
case K_NULL:
@@ -598,7 +607,7 @@ AutoPtr<CDataValue> ASNParser::x_Value(void)
if ( CheckSymbols(',', '}') )
return AutoPtr<CDataValue>(new CIdDataValue(id));
else
- return AutoPtr<CDataValue>(new CNamedDataValue(id, Value()));
+ return AutoPtr<CDataValue>(new CNamedDataValue(id, Value(nullptr)));
}
case T_BINARY_STRING:
case T_HEXADECIMAL_STRING:
@@ -615,7 +624,7 @@ AutoPtr<CDataValue> ASNParser::x_Value(void)
AutoPtr<CBlockDataValue> b(new CBlockDataValue());
if ( !CheckSymbol('}') ) {
do {
- b->GetValues().push_back(Value());
+ b->GetValues().push_back(Value(nullptr));
} while ( ConsumeIfSymbol(',') );
}
ConsumeSymbol('}');
@@ -633,9 +642,9 @@ Int4 ASNParser::Number(void)
return NStr::StringToInt(ValueOf(T_NUMBER, "number"));
}
-double ASNParser::Double(void)
+double ASNParser::Double(TToken token)
{
- return NStr::StringToDouble(ValueOf(T_DOUBLE, "double"), NStr::fDecimalPosix);
+ return NStr::StringToDouble(ValueOf(token, "double"), NStr::fDecimalPosix);
}
const string& ASNParser::String(void)
diff --git a/c++/src/serial/datatool/parser.hpp b/c++/src/serial/datatool/parser.hpp
index 41c6289..a9285b4 100644
--- a/c++/src/serial/datatool/parser.hpp
+++ b/c++/src/serial/datatool/parser.hpp
@@ -1,7 +1,7 @@
#ifndef ASNPARSER_HPP
#define ASNPARSER_HPP
-/* $Id: parser.hpp 412890 2013-09-11 14:05:41Z gouriano $
+/* $Id: parser.hpp 467208 2015-05-11 17:01:47Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -84,10 +84,10 @@ public:
CEnumDataType* EnumeratedBlock(CEnumDataType* enumType);
CEnumDataTypeValue& EnumeratedValue(CEnumDataType& enumType);
void TypeList(list<string>& ids);
- AutoPtr<CDataValue> Value(void);
- AutoPtr<CDataValue> x_Value(void);
+ AutoPtr<CDataValue> Value(const CDataType* type);
+ AutoPtr<CDataValue> x_Value(const CDataType* type);
Int4 Number(void);
- double Double(void);
+ double Double(TToken token);
const string& String(void);
const string& Identifier(void);
const string& TypeReference(void);
diff --git a/c++/src/serial/datatool/srcutil.cpp b/c++/src/serial/datatool/srcutil.cpp
index 1fecbed..326bd04 100644
--- a/c++/src/serial/datatool/srcutil.cpp
+++ b/c++/src/serial/datatool/srcutil.cpp
@@ -1,4 +1,4 @@
-/* $Id: srcutil.cpp 179973 2010-01-05 15:39:42Z gouriano $
+/* $Id: srcutil.cpp 462658 2015-03-20 13:05:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,16 +46,26 @@ string Identifier(const string& typeName, bool capitalize)
if (isalnum((unsigned char)(*i))) {
s += capitalize? toupper((unsigned char)(*i)): *i;
} else {
- s += '_';
+ string ent(NStr::HtmlEntity((unsigned char)(*i)));
+ if (*i != '_' && !ent.empty()) {
+ s += ent;
+ } else {
+ s += '_';
+ }
}
while ( ++i != typeName.end() ) {
char c = *i;
if ( c == ':' ) {
continue;
}
- if ( c == '-' || c == '.' ) {
+ if ( c == '-' || c == '.' || c == '_') {
c = '_';
} else if (!isalnum((unsigned char)c)) {
+ string ent(NStr::HtmlEntity((unsigned char)(*i)));
+ if (!ent.empty()) {
+ s += ent;
+ continue;
+ }
c = '_';
}
s += c;
diff --git a/c++/src/serial/datatool/traversal_code_generator.cpp b/c++/src/serial/datatool/traversal_code_generator.cpp
index 59af9c8..69c4cee 100644
--- a/c++/src/serial/datatool/traversal_code_generator.cpp
+++ b/c++/src/serial/datatool/traversal_code_generator.cpp
@@ -1,4 +1,4 @@
-/* $Id: traversal_code_generator.cpp 444230 2014-08-22 12:39:00Z ivanov $
+/* $Id: traversal_code_generator.cpp 443700 2014-08-18 18:10:33Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/serial/datatool/type.cpp b/c++/src/serial/datatool/type.cpp
index a0f3c29..ad0c83e 100644
--- a/c++/src/serial/datatool/type.cpp
+++ b/c++/src/serial/datatool/type.cpp
@@ -1,4 +1,4 @@
-/* $Id: type.cpp 412776 2013-09-10 17:20:56Z gouriano $
+/* $Id: type.cpp 462658 2015-03-20 13:05:49Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -46,6 +46,7 @@
#include "enumtype.hpp"
#include "fileutil.hpp"
#include "srcutil.hpp"
+#include "datatool.hpp"
#include <serial/error_codes.hpp>
#include <algorithm>
@@ -334,6 +335,10 @@ bool CDataType::CheckType(void) const
const string CDataType::GetVar(const string& varName, int collect /*= 0*/) const
{
+ if ( !((CDataTool*)CNcbiApplication::Instance())->HasConfig() &&
+ !CNcbiApplication::Instance()->GetArgs()["ods"].HasValue()) {
+ return kEmptyStr;
+ }
const CDataType* parent = GetParentType();
if (collect >=0 && GetDataMember()) {
#if 0
diff --git a/c++/src/serial/datatool/unitype.cpp b/c++/src/serial/datatool/unitype.cpp
index dd905f3..aa5d514 100644
--- a/c++/src/serial/datatool/unitype.cpp
+++ b/c++/src/serial/datatool/unitype.cpp
@@ -1,4 +1,4 @@
-/* $Id: unitype.cpp 412225 2013-09-05 15:31:52Z gouriano $
+/* $Id: unitype.cpp 449690 2014-10-20 14:10:16Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -121,7 +121,9 @@ void CUniSequenceDataType::PrintXMLSchema(CNcbiOstream& out,
}
else if (typeContainer->GetMembers().size() == 2) {
hasAttlist = typeContainer->GetMembers().front().get()->Attlist();
- typeStatic = dynamic_cast<const CStaticDataType*>( typeContainer->GetMembers().back()->GetType() );
+ if (hasAttlist) {
+ typeStatic = dynamic_cast<const CStaticDataType*>( typeContainer->GetMembers().back()->GetType() );
+ }
}
}
diff --git a/c++/src/serial/datatool/wsdlparser.cpp b/c++/src/serial/datatool/wsdlparser.cpp
index 9bcc4d9..b721462 100644
--- a/c++/src/serial/datatool/wsdlparser.cpp
+++ b/c++/src/serial/datatool/wsdlparser.cpp
@@ -1,4 +1,4 @@
-/* $Id: wsdlparser.cpp 366263 2012-06-13 14:08:32Z gouriano $
+/* $Id: wsdlparser.cpp 466898 2015-05-07 13:36:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -286,7 +286,7 @@ void WSDLParser::ParseHeader(void)
;
tok = GetNextToken();
} else {
- ERR_POST_X(4, "LINE " << Location() << " XML declaration is missing");
+ ERR_POST_X(4, GetLocation() << " XML declaration is missing");
}
// schema
if (tok != K_DEFINITIONS) {
diff --git a/c++/src/serial/datatool/xsdlexer.cpp b/c++/src/serial/datatool/xsdlexer.cpp
index 6904dd3..3faaad4 100644
--- a/c++/src/serial/datatool/xsdlexer.cpp
+++ b/c++/src/serial/datatool/xsdlexer.cpp
@@ -1,4 +1,4 @@
-/* $Id: xsdlexer.cpp 191921 2010-05-18 15:56:37Z gouriano $
+/* $Id: xsdlexer.cpp 453174 2014-12-01 18:07:21Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -192,13 +192,19 @@ TToken XSDLexer::LookupLexeme(void)
char ctest = Char(sp_count);
if (!isspace((unsigned char)ctest)) {
if (ctest == '=') {
+ AddChars(sp_count-1);
space = false;
}
break;
}
}
}
- if (att && (c == cOpen)) {
+ if (att && !space && cOpen == '\0') {
+ if (c != '\"' && c != '\'') {
+ LexerError("No opening quote in attribute");
+ }
+ cOpen = c;
+ } else if (att && (c == cOpen)) {
AddChar();
if (strncmp(CurrentTokenStart(),"xmlns",5)==0) {
return K_XMLNS;
@@ -210,12 +216,10 @@ TToken XSDLexer::LookupLexeme(void)
}
}
if (c == '=') {
- att = true;
- AddChar();
- cOpen = c = Char();
- if (c != '\"' && c != '\'') {
- LexerError("No opening quote in attribute");
+ if (att) {
+ LexerError("Invalid format of an attribute");
}
+ att = true;
}
AddChar();
}
diff --git a/c++/src/serial/datatool/xsdparser.cpp b/c++/src/serial/datatool/xsdparser.cpp
index 95db5fe..7d5d3c9 100644
--- a/c++/src/serial/datatool/xsdparser.cpp
+++ b/c++/src/serial/datatool/xsdparser.cpp
@@ -1,4 +1,4 @@
-/* $Id: xsdparser.cpp 463777 2015-04-01 15:27:57Z ivanov $
+/* $Id: xsdparser.cpp 470480 2015-06-16 15:07:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -160,6 +160,7 @@ TToken XSDParser::GetNextToken(void)
ParseError("Unexpected data", "attribute (name=\"value\")");
}
NStr::TruncateSpacesInPlace(str1);
+ NStr::TruncateSpacesInPlace(data2);
// attribute
data = str1;
if (NStr::SplitInTwo(data, ":", str1, str2)) {
@@ -338,7 +339,7 @@ void XSDParser::ParseHeader()
tok = GetNextToken();
} else {
if (m_SrcType == eSchema) {
- ERR_POST_X(4, "LINE " << Location() << " XML declaration is missing");
+ ERR_POST_X(4, GetLocation() << " XML declaration is missing");
}
}
// schema
@@ -532,7 +533,7 @@ DTDElement::EOccurrence XSDParser::ParseMinOccurs( DTDElement::EOccurrence occNo
occNew = DTDElement::eZeroOrMore;
}
} else if (m > 1) {
- ERR_POST_X(8, Warning << "Unsupported element minOccurs= " << m);
+ ERR_POST_X(8, Warning << GetLocation() << "Unsupported element minOccurs= " << m);
occNew = DTDElement::eOneOrMore;
}
}
@@ -546,7 +547,7 @@ DTDElement::EOccurrence XSDParser::ParseMaxOccurs( DTDElement::EOccurrence occNo
int m = IsValue("unbounded") ? -1 : NStr::StringToInt(m_Value);
if (m == -1 || m > 1) {
if (m > 1) {
- ERR_POST_X(8, Warning << "Unsupported element maxOccurs= " << m);
+ ERR_POST_X(8, Warning << GetLocation() << "Unsupported element maxOccurs= " << m);
}
if (occNow == DTDElement::eOne) {
occNew = DTDElement::eOneOrMore;
@@ -1036,6 +1037,7 @@ void XSDParser::ParseAny(DTDElement& node)
void XSDParser::ParseUnion(DTDElement& node)
{
ERR_POST_X(9, Warning
+ << GetLocation()
<< "Unsupported element type: union; in node "
<< node.GetName());
node.SetType(DTDElement::eString);
@@ -1050,6 +1052,7 @@ void XSDParser::ParseUnion(DTDElement& node)
void XSDParser::ParseList(DTDElement& node)
{
ERR_POST_X(10, Warning
+ << GetLocation()
<< "Unsupported element type: list; in node "
<< node.GetName());
node.SetType(DTDElement::eString);
@@ -1191,6 +1194,7 @@ void XSDParser::ParseEnumeration(DTDAttribute& att)
void XSDParser::ParseUnion(DTDAttribute& att)
{
ERR_POST_X(9, Warning
+ << GetLocation()
<< "Unsupported attribute type: union; in attribute "
<< att.GetName());
att.SetType(DTDAttribute::eString);
@@ -1204,6 +1208,7 @@ void XSDParser::ParseUnion(DTDAttribute& att)
void XSDParser::ParseList(DTDAttribute& att)
{
ERR_POST_X(10, Warning
+ << GetLocation()
<< "Unsupported attribute type: list; in attribute "
<< att.GetName());
att.SetType(DTDAttribute::eString);
@@ -1251,7 +1256,7 @@ string XSDParser::CreateEntityId(
break;
}
if (prefix) {
- if (m_PrefixToNamespace.find(*prefix) == m_PrefixToNamespace.end()) {
+ if (m_PrefixToNamespace.find(*prefix) == m_PrefixToNamespace.end() && !prefix->empty()) {
string msg("Namespace prefix not defined: ");
msg += *prefix;
ParseError(msg.c_str(), "namespace declaration");
@@ -1439,6 +1444,8 @@ void XSDParser::ProcessNamedTypes(void)
}
}
processed.insert(i->second.GetName() + i->second.GetNamespaceName());
+ } else {
+ node.SetTypeIfUnknown(node.GetContent().empty() ? DTDElement::eEmpty : DTDElement::eString);
}
}
} while (found);
@@ -1459,9 +1466,7 @@ void XSDParser::ProcessNamedTypes(void)
found = true;
PushEntityLexer(a->GetTypeName());
ParseContent(*a);
- if (a->GetType() == DTDAttribute::eUnknown) {
- a->SetType(DTDAttribute::eString);
- }
+ a->SetTypeIfUnknown(DTDAttribute::eString);
} else if ( a->GetType() == DTDAttribute::eUnknownGroup) {
found = true;
PushEntityLexer(a->GetTypeName());
@@ -1469,6 +1474,8 @@ void XSDParser::ProcessNamedTypes(void)
ParseAttributeGroupRef(node);
break;
}
+ } else {
+ a->SetTypeIfUnknown(DTDAttribute::eString);
}
}
}
diff --git a/c++/src/serial/enumerated.cpp b/c++/src/serial/enumerated.cpp
index f458d1a..557c798 100644
--- a/c++/src/serial/enumerated.cpp
+++ b/c++/src/serial/enumerated.cpp
@@ -1,4 +1,4 @@
-/* $Id: enumerated.cpp 413810 2013-09-18 15:28:07Z gouriano $
+/* $Id: enumerated.cpp 471532 2015-06-29 11:41:24Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -75,7 +75,7 @@ const string& CEnumeratedTypeValues::GetModuleName(void) const
void CEnumeratedTypeValues::SetModuleName(const string& name)
{
if ( !m_ModuleName.empty() )
- NCBI_THROW(CSerialException,eFail,"cannot change module name");
+ NCBI_THROW(CSerialException,eFail,"cannot change module name: " + m_ModuleName + " to " + name);
m_ModuleName = name;
}
@@ -92,7 +92,7 @@ const string& CEnumeratedTypeValues::GetInternalModuleName(void) const
void CEnumeratedTypeValues::SetInternalName(const string& name)
{
if ( IsInternal() || !m_Name.empty() || !m_ModuleName.empty() )
- NCBI_THROW(CSerialException,eFail, "cannot change (internal) name");
+ NCBI_THROW(CSerialException,eFail, "cannot change (internal) name to " + name);
m_IsInternal = true;
m_Name = name;
}
@@ -117,7 +117,7 @@ TEnumValueType CEnumeratedTypeValues::FindValue(const CTempString& name) const
i = m.find(name_alt);
if ( i == m.end() ) {
NCBI_THROW(CSerialException,eInvalidData,
- "invalid value of enumerated type");
+ "invalid value of enumerated type: " + string(name));
}
}
return i->second;
@@ -140,12 +140,21 @@ const string& CEnumeratedTypeValues::FindName(TEnumValueType value,
}
else {
NCBI_THROW(CSerialException,eInvalidData,
- "invalid value of enumerated type");
+ "invalid value of enumerated type: " + NStr::NumericToString(value));
}
}
return *i->second;
}
+const string& CEnumeratedTypeValues::FindNameEx(TEnumValueType value,
+ bool allowBadValue) const
+{
+ if ((GetValueFlags(value) & eHideName) != 0) {
+ return kEmptyStr;
+ }
+ return FindName( value, allowBadValue);
+}
+
string CEnumeratedTypeValues::GetDisplayName(TEnumValueType value) const
{
string res;
@@ -178,17 +187,27 @@ string CEnumeratedTypeValues::GetDisplayName(TEnumValueType value) const
return res;
}
-void CEnumeratedTypeValues::AddValue(const string& name, TEnumValueType value)
+void CEnumeratedTypeValues::AddValue(const string& name,
+ TEnumValueType value, TValueFlags flags)
{
if ( name.empty() ) {
NCBI_THROW(CSerialException,eInvalidData,
"empty enum value name");
}
m_Values.push_back(make_pair(name, value));
+ m_ValueFlags[value] = flags;
m_ValueToName.reset(0);
m_NameToValue.reset(0);
}
+
+CEnumeratedTypeValues::TValueFlags
+CEnumeratedTypeValues::GetValueFlags(TEnumValueType value) const
+{
+ map<TEnumValueType, TValueFlags>::const_iterator i = m_ValueFlags.find(value);
+ return i != m_ValueFlags.end() ? i->second : eNone;
+}
+
DEFINE_STATIC_FAST_MUTEX(s_EnumValuesMutex);
const CEnumeratedTypeValues::TValueToName&
@@ -224,7 +243,7 @@ CEnumeratedTypeValues::NameToValue(void) const
m->insert(TNameToValue::value_type(s, i->second));
if ( !p.second ) {
NCBI_THROW(CSerialException,eInvalidData,
- "duplicate enum value name");
+ "duplicate enum value name: " + s);
}
}
m_NameToValue = keep;
@@ -233,9 +252,10 @@ CEnumeratedTypeValues::NameToValue(void) const
return *m;
}
-void CEnumeratedTypeValues::AddValue(const char* name, TEnumValueType value)
+void CEnumeratedTypeValues::AddValue(const char* name,
+ TEnumValueType value, TValueFlags flags)
{
- AddValue(string(name), value);
+ AddValue(string(name), value, flags);
}
CEnumeratedTypeInfo::CEnumeratedTypeInfo(size_t size,
diff --git a/c++/src/serial/exception.cpp b/c++/src/serial/exception.cpp
index aab520a..903a7d8 100644
--- a/c++/src/serial/exception.cpp
+++ b/c++/src/serial/exception.cpp
@@ -1,4 +1,4 @@
-/* $Id: exception.cpp 448169 2014-10-02 18:07:36Z vasilche $
+/* $Id: exception.cpp 457136 2015-01-20 19:45:17Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -122,8 +122,7 @@ CInvalidChoiceSelection::CInvalidChoiceSelection(
size_t currentIndex, size_t mustBeIndex,
const char* const names[], size_t namesCount,
EDiagSev severity)
- : CSerialException(diag_info, 0,
- (CSerialException::EErrCode) CException::eInvalid,"")
+ : CSerialException(diag_info, 0, "", severity, 0)
{
CNcbiOstrstream msg;
const CChoiceTypeInfo* type = 0;
@@ -152,8 +151,7 @@ CInvalidChoiceSelection::CInvalidChoiceSelection(
size_t currentIndex, size_t mustBeIndex,
const char* const names[], size_t namesCount,
EDiagSev severity)
- : CSerialException(diag_info, 0,
- (CSerialException::EErrCode) CException::eInvalid,"")
+ : CSerialException(diag_info, 0, "", severity, 0)
{
x_Init(diag_info,
string("Invalid choice selection: ")+
@@ -168,8 +166,7 @@ CInvalidChoiceSelection::CInvalidChoiceSelection(
size_t currentIndex, size_t mustBeIndex,
const char* const names[], size_t namesCount,
EDiagSev severity)
- : CSerialException(CDiagCompileInfo(file, line), 0,
- (CSerialException::EErrCode) CException::eInvalid,"")
+ : CSerialException(CDiagCompileInfo(file, line), 0, "", severity, 0)
{
x_Init(CDiagCompileInfo(file, line),
string("Invalid choice selection: ")+
@@ -183,8 +180,7 @@ CInvalidChoiceSelection::CInvalidChoiceSelection(
size_t currentIndex, size_t mustBeIndex,
const char* const names[], size_t namesCount,
EDiagSev severity)
- : CSerialException(CDiagCompileInfo("unknown", 0), 0,
- (CSerialException::EErrCode) CException::eInvalid,"")
+ : CSerialException(CDiagCompileInfo("unknown", 0), 0, "", severity, 0)
{
x_Init(CDiagCompileInfo("unknown", 0),
string("Invalid choice selection: ")+
diff --git a/c++/src/serial/item.cpp b/c++/src/serial/item.cpp
index dec06da..9caf2f2 100644
--- a/c++/src/serial/item.cpp
+++ b/c++/src/serial/item.cpp
@@ -1,4 +1,4 @@
-/* $Id: item.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: item.cpp 448671 2014-10-08 13:11:24Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -37,25 +37,29 @@ BEGIN_NCBI_SCOPE
CItemInfo::CItemInfo(const CMemberId& id,
TPointerOffsetType offset, TTypeInfo type)
- : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type), m_NonEmpty(false)
+ : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type),
+ m_NonEmpty(false), m_Optional(false)
{
}
CItemInfo::CItemInfo(const CMemberId& id,
TPointerOffsetType offset, const CTypeRef& type)
- : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type), m_NonEmpty(false)
+ : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type),
+ m_NonEmpty(false), m_Optional(false)
{
}
CItemInfo::CItemInfo(const char* id,
TPointerOffsetType offset, TTypeInfo type)
- : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type), m_NonEmpty(false)
+ : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type),
+ m_NonEmpty(false), m_Optional(false)
{
}
CItemInfo::CItemInfo(const char* id,
TPointerOffsetType offset, const CTypeRef& type)
- : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type), m_NonEmpty(false)
+ : m_Id(id), m_Index(kInvalidMember), m_Offset(offset), m_Type(type),
+ m_NonEmpty(false), m_Optional(false)
{
}
diff --git a/c++/src/serial/member.cpp b/c++/src/serial/member.cpp
index ba9510d..598aa99 100644
--- a/c++/src/serial/member.cpp
+++ b/c++/src/serial/member.cpp
@@ -1,4 +1,4 @@
-/* $Id: member.cpp 406812 2013-07-16 15:03:55Z vasilche $
+/* $Id: member.cpp 450827 2014-10-30 18:38:02Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -171,7 +171,7 @@ CMemberInfo::CMemberInfo(const CClassTypeInfoBase* classType,
const CMemberId& id, TPointerOffsetType offset,
const CTypeRef& type)
: CParent(id, offset, type),
- m_ClassType(classType), m_Optional(false), m_Default(0),
+ m_ClassType(classType), m_Default(0),
m_SetFlagOffset(eNoOffset), m_BitSetMask(0),
m_DelayOffset(eNoOffset),
m_GetConstFunction(&TFunc::GetConstSimpleMember),
@@ -196,7 +196,7 @@ CMemberInfo::CMemberInfo(const CClassTypeInfoBase* classType,
const CMemberId& id, TPointerOffsetType offset,
TTypeInfo type)
: CParent(id, offset, type),
- m_ClassType(classType), m_Optional(false), m_Default(0),
+ m_ClassType(classType), m_Default(0),
m_SetFlagOffset(eNoOffset), m_BitSetMask(0),
m_DelayOffset(eNoOffset),
m_GetConstFunction(&TFunc::GetConstSimpleMember),
@@ -221,7 +221,7 @@ CMemberInfo::CMemberInfo(const CClassTypeInfoBase* classType,
const char* id, TPointerOffsetType offset,
const CTypeRef& type)
: CParent(id, offset, type),
- m_ClassType(classType), m_Optional(false), m_Default(0),
+ m_ClassType(classType), m_Default(0),
m_SetFlagOffset(eNoOffset), m_BitSetMask(0),
m_DelayOffset(eNoOffset),
m_GetConstFunction(&TFunc::GetConstSimpleMember),
@@ -246,7 +246,7 @@ CMemberInfo::CMemberInfo(const CClassTypeInfoBase* classType,
const char* id, TPointerOffsetType offset,
TTypeInfo type)
: CParent(id, offset, type),
- m_ClassType(classType), m_Optional(false), m_Default(0),
+ m_ClassType(classType), m_Default(0),
m_SetFlagOffset(eNoOffset), m_BitSetMask(0),
m_DelayOffset(eNoOffset),
m_GetConstFunction(&TFunc::GetConstSimpleMember),
@@ -291,6 +291,7 @@ bool NCBI_XSERIAL_EXPORT EnabledDelayBuffers(void)
};
static State state = eUnset;
if ( state == eUnset ) {
+ CMutexGuard guard(CNcbiApplication::GetInstanceMutex());
CNcbiApplication* app = CNcbiApplication::Instance();
string value;
if ( app ) {
diff --git a/c++/src/serial/memberlist.cpp b/c++/src/serial/memberlist.cpp
index 8c614ac..6e96019 100644
--- a/c++/src/serial/memberlist.cpp
+++ b/c++/src/serial/memberlist.cpp
@@ -1,4 +1,4 @@
-/* $Id: memberlist.cpp 418737 2013-11-19 18:50:38Z gouriano $
+/* $Id: memberlist.cpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -248,7 +248,8 @@ TMemberIndex CItemsInfo::Find(const CTempString& name) const
return i->second;
}
-TMemberIndex CItemsInfo::FindDeep(const CTempString& name, bool search_attlist) const
+TMemberIndex CItemsInfo::FindDeep(const CTempString& name, bool search_attlist,
+ const CClassTypeInfoBase** pclassInfo) const
{
TMemberIndex ind = Find(name);
if (ind != kInvalidMember) {
@@ -265,6 +266,9 @@ TMemberIndex CItemsInfo::FindDeep(const CTempString& name, bool search_attlist)
if (classType) {
if (classType->GetItems().FindDeep(name, search_attlist)
!= kInvalidMember) {
+ if (pclassInfo) {
+ *pclassInfo = classType;
+ }
return *item;
}
}
@@ -298,12 +302,16 @@ const CTypeInfo* CItemsInfo::FindRealTypeInfo(const CTypeInfo* info)
const CItemInfo* CItemsInfo::FindNextMandatory(const CItemInfo* info)
{
- if (!info->GetId().HasNotag()) {
+ if (!info->GetId().HasNotag() && !info->GetId().IsAttlist()) {
+#if 0
const CMemberInfo* mem = dynamic_cast<const CMemberInfo*>(info);
if (mem && mem->Optional()) {
return 0;
}
return info;
+#else
+ return info->Optional() ? 0 : info;
+#endif
}
return FindNextMandatory(info->GetTypeInfo());
}
@@ -361,7 +369,7 @@ TMemberIndex CItemsInfo::FindEmpty(void) const
{
for (CIterator item(*this); item.Valid(); ++item) {
const CItemInfo* info = GetItemInfo(item);
- if (info->GetId().IsAttlist()) {
+ if (info->NonEmpty() || info->GetId().IsAttlist()) {
continue;
}
const CTypeInfo* type;
diff --git a/c++/src/serial/objistr.cpp b/c++/src/serial/objistr.cpp
index c4ad328..f88acc5 100644
--- a/c++/src/serial/objistr.cpp
+++ b/c++/src/serial/objistr.cpp
@@ -1,4 +1,4 @@
-/* $Id: objistr.cpp 448569 2014-10-07 16:45:47Z ivanov $
+/* $Id: objistr.cpp 446573 2014-09-16 19:07:04Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/serial/objistrasn.cpp b/c++/src/serial/objistrasn.cpp
index 7208438..b16fe6a 100644
--- a/c++/src/serial/objistrasn.cpp
+++ b/c++/src/serial/objistrasn.cpp
@@ -1,4 +1,4 @@
-/* $Id: objistrasn.cpp 448592 2014-10-07 16:55:18Z ivanov $
+/* $Id: objistrasn.cpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -625,7 +625,7 @@ void CObjectIStreamAsn::ReadBitString(CBitString& obj)
obj.reserve(obj.size());
#else
obj.resize(0);
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
ReadCompressedBitString(obj);
return;
}
@@ -1214,6 +1214,7 @@ bool CObjectIStreamAsn::BeginContainerElement(TTypeInfo /*elementType*/)
void CObjectIStreamAsn::ReadContainer(const CContainerTypeInfo* contType,
TObjectPtr contPtr)
{
+ BEGIN_OBJECT_FRAME2(eFrameArray, contType);
StartBlock();
BEGIN_OBJECT_FRAME(eFrameArrayElement);
@@ -1237,10 +1238,12 @@ void CObjectIStreamAsn::ReadContainer(const CContainerTypeInfo* contType,
END_OBJECT_FRAME();
EndBlock();
+ END_OBJECT_FRAME();
}
void CObjectIStreamAsn::SkipContainer(const CContainerTypeInfo* contType)
{
+ BEGIN_OBJECT_FRAME2(eFrameArray, contType);
StartBlock();
TTypeInfo elementType = contType->GetElementType();
@@ -1253,6 +1256,7 @@ void CObjectIStreamAsn::SkipContainer(const CContainerTypeInfo* contType)
END_OBJECT_FRAME();
EndBlock();
+ END_OBJECT_FRAME();
}
#endif
diff --git a/c++/src/serial/objistrasnb.cpp b/c++/src/serial/objistrasnb.cpp
index 13da512..1765c97 100644
--- a/c++/src/serial/objistrasnb.cpp
+++ b/c++/src/serial/objistrasnb.cpp
@@ -1,4 +1,4 @@
-/* $Id: objistrasnb.cpp 448596 2014-10-07 16:57:02Z ivanov $
+/* $Id: objistrasnb.cpp 461337 2015-03-09 18:00:58Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -142,6 +142,9 @@ void CObjectIStreamAsnBinary::ResetThisState(void)
void CObjectIStreamAsnBinary::ResetState(void)
{
CObjectIStream::ResetState();
+ if (GetStackDepth() > 1) {
+ return;
+ }
ResetThisState();
}
@@ -171,7 +174,7 @@ CObjectIStreamAsnBinary::PeekLongTag(void)
void CObjectIStreamAsnBinary::UnexpectedTagClassByte(TByte first_tag_byte,
TByte expected_class_byte)
{
- ThrowError(fFormatError, "unexpected tag class/constructed: " +
+ ThrowError(fFormatError, "unexpected tag: " +
TagToString(first_tag_byte) + ", should be " +
TagToString(expected_class_byte));
}
@@ -208,7 +211,7 @@ void CObjectIStreamAsnBinary::UnexpectedTagValue(ETagClass tag_class,
} else if (tag_class == ePrivate) {
s += "Private ";
}
- s += NStr::NumericToString(tag_got) + " expected: " +
+ s += NStr::NumericToString(tag_got) + ", expected: " +
NStr::NumericToString(tag_expected);
ThrowError(fFormatError, s);
}
@@ -323,11 +326,13 @@ string CObjectIStreamAsnBinary::TagToString(TByte byte)
case eContextSpecific: cls = "contextspecific/";break;
case ePrivate: cls = "private/"; break;
}
+ string str(cls);
switch (byte & eTagConstructedMask) {
default:
case ePrimitive: con = ""; break;
case eConstructed: con = "constructed/"; break;
}
+ str += con;
if ((byte & eTagClassMask) == eUniversal) {
const char *v;
switch (byte & eTagValueMask) {
@@ -359,9 +364,11 @@ string CObjectIStreamAsnBinary::TagToString(TByte byte)
case eObjectReference: v= "ObjectReference"; break;
default: v= "unknown"; break;
}
- return string(cls) + con + v + " (" + NStr::IntToString(byte) + ")";
+ str += v;
+ } else {
+ str += NStr::NumericToString((byte & eTagValueMask));
}
- return string(cls) + con + NStr::NumericToString((byte & eTagValueMask));
+ return str += " (" + NStr::NumericToString(byte) + ")";
}
void CObjectIStreamAsnBinary::UnexpectedSysTagByte(TByte tag_byte)
@@ -1704,7 +1711,7 @@ void CObjectIStreamAsnBinary::ReadBitString(CBitString& obj)
{
obj.clear();
#if !BITSTRING_AS_VECTOR
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
ReadCompressedBitString(obj);
return;
}
diff --git a/c++/src/serial/objistrjson.cpp b/c++/src/serial/objistrjson.cpp
index 97b1504..f9dcb28 100644
--- a/c++/src/serial/objistrjson.cpp
+++ b/c++/src/serial/objistrjson.cpp
@@ -1,4 +1,4 @@
-/* $Id: objistrjson.cpp 448588 2014-10-07 16:53:42Z ivanov $
+/* $Id: objistrjson.cpp 481917 2015-10-19 13:23:10Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -51,12 +51,26 @@ CObjectIStreamJson::CObjectIStreamJson(void)
m_FileHeader(false),
m_BlockStart(false),
m_ExpectValue(false),
+ m_GotNameless(false),
m_Closing(0),
m_StringEncoding( eEncoding_Unknown ),
m_BinaryFormat(eDefault)
{
}
+CObjectIStreamJson::CObjectIStreamJson(CNcbiIstream& in, EOwnership deleteIn)
+ : CObjectIStream(eSerial_Json),
+ m_FileHeader(false),
+ m_BlockStart(false),
+ m_ExpectValue(false),
+ m_GotNameless(false),
+ m_Closing(0),
+ m_StringEncoding( eEncoding_Unknown ),
+ m_BinaryFormat(eDefault)
+{
+ Open(in, deleteIn);
+}
+
CObjectIStreamJson::~CObjectIStreamJson(void)
{
}
@@ -64,6 +78,9 @@ CObjectIStreamJson::~CObjectIStreamJson(void)
void CObjectIStreamJson::ResetState(void)
{
CObjectIStream::ResetState();
+ if (GetStackDepth() > 1) {
+ return;
+ }
m_LastTag.clear();
m_RejectedTag.clear();
}
@@ -583,7 +600,7 @@ void CObjectIStreamJson::ReadBitString(CBitString& obj)
#if BITSTRING_AS_VECTOR
ThrowError(fNotImplemented, "Not Implemented");
#else
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
ThrowError(fNotImplemented, "Not Implemented");
return;
}
@@ -677,6 +694,7 @@ void CObjectIStreamJson::BeginClass(const CClassTypeInfo* classInfo)
void CObjectIStreamJson::EndClass(void)
{
+ m_GotNameless = false;
EndBlock((GetStackDepth() > 1 && FetchFrameFromTop(1).GetNotag()) ? 0 : '}');
}
@@ -729,9 +747,38 @@ TMemberIndex CObjectIStreamJson::FindDeep(
TMemberIndex CObjectIStreamJson::BeginClassMember(const CClassTypeInfo* classType)
{
- if ( !NextElement() )
+ TMemberIndex first = classType->GetMembers().FirstIndex();
+ TMemberIndex last = classType->GetMembers().LastIndex();
+
+ if ( !NextElement() ) {
+ if (!m_GotNameless &&
+ classType->GetMemberInfo(last)->GetId().HasNotag() &&
+ classType->GetMemberInfo(last)->GetTypeInfo()->GetTypeFamily() == eTypeFamilyPrimitive) {
+ TopFrame().SetNotag();
+ m_GotNameless = true;
+ return last;
+ }
return kInvalidMember;
+ }
+ m_GotNameless = false;
+
+ char c = PeekChar();
+ if (m_RejectedTag.empty() && (c == '[' || c == '{')) {
+ for (TMemberIndex i = first; i <= last; ++i) {
+ if (classType->GetMemberInfo(i)->GetId().HasNotag()) {
+ TopFrame().SetNotag();
+ return i;
+ }
+ }
+ }
string tagName = ReadKey();
+
+ if (tagName[0] == '#') {
+ tagName = tagName.substr(1);
+ TopFrame().SetNotag();
+ m_GotNameless = true;
+ }
+
bool deep = false;
TMemberIndex ind = FindDeep(classType->GetMembers(), tagName, deep);
/*
@@ -916,7 +963,7 @@ size_t CObjectIStreamJson::ReadBytes(
if (m_BinaryFormat != CObjectIStreamJson::eDefault) {
return ReadCustomBytes(block,dst,length);
}
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
return ReadBase64Bytes( block, dst, length );
}
return ReadHexBytes( block, dst, length );
diff --git a/c++/src/serial/objistrxml.cpp b/c++/src/serial/objistrxml.cpp
index 973bdbf..0cc55e6 100644
--- a/c++/src/serial/objistrxml.cpp
+++ b/c++/src/serial/objistrxml.cpp
@@ -1,4 +1,4 @@
-/* $Id: objistrxml.cpp 448598 2014-10-07 16:57:50Z ivanov $
+/* $Id: objistrxml.cpp 461579 2015-03-11 13:12:43Z gouriano $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -65,6 +65,18 @@ CObjectIStreamXml::CObjectIStreamXml(void)
m_Utf8Pos = m_Utf8Buf.begin();
}
+CObjectIStreamXml::CObjectIStreamXml(CNcbiIstream& in, EOwnership deleteIn)
+ : CObjectIStream(eSerial_Xml),
+ m_TagState(eTagOutside), m_Attlist(false),
+ m_StdXml(false), m_Doctype_found(false), m_IsNil(false),
+ m_Encoding( eEncoding_Unknown ),
+ m_StringEncoding( eEncoding_Unknown ),
+ m_SkipNextTag(false)
+{
+ m_Utf8Pos = m_Utf8Buf.begin();
+ Open(in, deleteIn);
+}
+
CObjectIStreamXml::~CObjectIStreamXml(void)
{
}
@@ -72,6 +84,9 @@ CObjectIStreamXml::~CObjectIStreamXml(void)
void CObjectIStreamXml::ResetState(void)
{
CObjectIStream::ResetState();
+ if (GetStackDepth() > 1) {
+ return;
+ }
m_TagState = eTagOutside;
m_LastTag.clear();
m_RejectedTag.clear();
@@ -580,7 +595,7 @@ string CObjectIStreamXml::ReadFileHeader(void)
CTempString tagName = ReadName(m_Input.PeekChar());
if ( tagName == "DOCTYPE" ) {
m_Doctype_found = true;
- CTempString docType = ReadName(SkipWS());
+ ReadName(SkipWS());
// skip the rest of !DOCTYPE
for ( ;; ) {
char c = SkipWS();
@@ -1091,10 +1106,15 @@ void CObjectIStreamXml::ReadAnyContentObject(CAnyContentObject& obj)
bool CObjectIStreamXml::SkipAnyContent(void)
{
- if (ThisTagIsSelfClosed()) {
+ if (SelfClosedTag() || ThisTagIsSelfClosed()) {
//EndSelfClosedTag();
return true;
}
+ if ( m_Attlist && InsideOpeningTag() ) {
+ ReadUndefinedAttributes();
+ m_Attlist = true;
+ return true;
+ }
while (!NextTagIsClosing()) {
while (NextIsTag()) {
string tagName = ReadName(BeginOpeningTag());
@@ -1145,7 +1165,7 @@ void CObjectIStreamXml::ReadBitString(CBitString& obj)
if (EndOpeningTagSelfClosed()) {
return;
}
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
ReadCompressedBitString(obj);
return;
}
@@ -2330,7 +2350,13 @@ TMemberIndex CObjectIStreamXml::BeginChoiceVariant(const CChoiceTypeInfo* choice
}
}
m_Attlist = false;
+ if ( SelfClosedTag() ) {
+ return kInvalidMember;
+ }
if ( NextTagIsClosing() ) {
+ if (choiceType->MayBeEmpty()) {
+ return kInvalidMember;
+ }
TMemberIndex ind = choiceType->GetVariants().FindEmpty();
if (ind != kInvalidMember) {
TopFrame().SetNotag();
@@ -2454,7 +2480,7 @@ size_t CObjectIStreamXml::ReadBytes(ByteBlock& block,
char* dst, size_t length)
{
size_t count = 0;
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
bool end_of_data = false;
const size_t chunk_in = 80;
char src_buf[chunk_in];
diff --git a/c++/src/serial/objlist.cpp b/c++/src/serial/objlist.cpp
index c5a504e..ad2e58c 100644
--- a/c++/src/serial/objlist.cpp
+++ b/c++/src/serial/objlist.cpp
@@ -1,4 +1,4 @@
-/* $Id: objlist.cpp 103491 2007-05-04 17:18:18Z kazimird $
+/* $Id: objlist.cpp 450705 2014-10-29 19:41:05Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -62,11 +62,13 @@ void CWriteObjectList::RegisterObject(TTypeInfo typeInfo)
m_Objects.push_back(CWriteObjectInfo(typeInfo, NextObjectIndex()));
}
+#if _DEBUG
static inline
TConstObjectPtr EndOf(TConstObjectPtr objectPtr, TTypeInfo objectType)
{
return CRawPointer::Add(objectPtr, TPointerOffsetType(objectType->GetSize()));
}
+#endif
const CWriteObjectInfo*
CWriteObjectList::RegisterObject(TConstObjectPtr object, TTypeInfo typeInfo)
diff --git a/c++/src/serial/objostr.cpp b/c++/src/serial/objostr.cpp
index 7febef1..1173c87 100644
--- a/c++/src/serial/objostr.cpp
+++ b/c++/src/serial/objostr.cpp
@@ -1,4 +1,4 @@
-/* $Id: objostr.cpp 448569 2014-10-07 16:45:47Z ivanov $
+/* $Id: objostr.cpp 463313 2015-03-26 17:05:21Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -125,8 +125,9 @@ CObjectOStream* CObjectOStream::Open(ESerialDataFormat format,
CObjectOStream* CObjectOStream::Open(ESerialDataFormat format,
CNcbiOstream& outStream,
- bool deleteStream)
+ bool bdeleteStream)
{
+ EOwnership deleteStream = bdeleteStream ? eTakeOwnership : eNoOwnership;
switch ( format ) {
case eSerial_AsnText:
return OpenObjectOStreamAsn(outStream, deleteStream);
@@ -145,11 +146,10 @@ CObjectOStream* CObjectOStream::Open(ESerialDataFormat format,
CObjectOStream* CObjectOStream::Open(ESerialDataFormat format,
CNcbiOstream& outStream,
- EOwnership edeleteStream,
+ EOwnership deleteStream,
TSerial_Format_Flags formatFlags)
{
CObjectOStream* os = NULL;
- bool deleteStream = edeleteStream == eTakeOwnership;
switch ( format ) {
case eSerial_AsnText:
os = OpenObjectOStreamAsn(outStream, deleteStream);
@@ -287,8 +287,8 @@ EFixNonPrint CObjectOStream::x_GetFixCharsMethodDefault(void) const
/////////////////////////////////////////////////////////////////////////////
CObjectOStream::CObjectOStream(ESerialDataFormat format,
- CNcbiOstream& out, bool deleteOut)
- : m_Output(out, deleteOut), m_Fail(fNoError), m_Flags(fFlagNone),
+ CNcbiOstream& out, EOwnership edeleteOut)
+ : m_Output(out, edeleteOut == eTakeOwnership), m_Fail(fNoError), m_Flags(fFlagNone),
m_Separator(""), m_AutoSeparator(false),
m_DataFormat(format),
m_WriteNamedIntegersByValue(false),
@@ -795,10 +795,23 @@ void CObjectOStream::WriteContainer(const CContainerTypeInfo* cType,
TTypeInfo elementType = cType->GetElementType();
BEGIN_OBJECT_FRAME2(eFrameArrayElement, elementType);
+ const CPointerTypeInfo* pointerType =
+ dynamic_cast<const CPointerTypeInfo*>(elementType);
do {
+ TConstObjectPtr elementPtr = cType->GetElementPtr(i);
+ if ( pointerType &&
+ !pointerType->GetObjectPointer(elementPtr) ) {
+ if ( GetVerifyData() == eSerialVerifyData_Yes ) {
+ ThrowError(fUnassigned,
+ "NULL element while writing container "+
+ cType->GetName());
+ }
+ continue;
+ }
+
BeginContainerElement(elementType);
- WriteObject(cType->GetElementPtr(i), elementType);
+ WriteObject(elementPtr, elementType);
EndContainerElement();
} while ( cType->NextElement(i) );
@@ -1010,35 +1023,48 @@ void CObjectOStream::CopyChoice(const CChoiceTypeInfo* choiceType,
BEGIN_OBJECT_2FRAMES_OF(copier, eFrameChoiceVariant);
TMemberIndex index = copier.In().BeginChoiceVariant(choiceType);
if ( index == kInvalidMember ) {
- copier.ThrowError(CObjectIStream::fFormatError,
- "choice variant id expected");
- }
-
- const CVariantInfo* variantInfo = choiceType->GetVariantInfo(index);
- if (variantInfo->GetId().IsAttlist()) {
- const CMemberInfo* memberInfo =
- dynamic_cast<const CMemberInfo*>(
- choiceType->GetVariants().GetItemInfo(index));
- BeginClassMember(memberInfo->GetId());
- memberInfo->CopyMember(copier);
- EndClassMember();
- copier.In().EndChoiceVariant();
- index = copier.In().BeginChoiceVariant(choiceType);
- if ( index == kInvalidMember )
+ if (choiceType->MayBeEmpty() || copier.In().CanSkipUnknownVariants()) {
+ copier.In().SkipAnyContentVariant();
+ } else {
copier.ThrowError(CObjectIStream::fFormatError,
- "choice variant id expected");
- variantInfo = choiceType->GetVariantInfo(index);
- }
- copier.In().SetTopMemberId(variantInfo->GetId());
- copier.Out().SetTopMemberId(variantInfo->GetId());
- copier.SetPathHooks(copier.Out(), true);
- BeginChoiceVariant(choiceType, variantInfo->GetId());
+ "choice variant id expected");
+ }
+ } else {
+ for (;;) {
+ const CVariantInfo* variantInfo = choiceType->GetVariantInfo(index);
+ if (variantInfo->GetId().IsAttlist()) {
+ const CMemberInfo* memberInfo =
+ dynamic_cast<const CMemberInfo*>(
+ choiceType->GetVariants().GetItemInfo(index));
+ BeginClassMember(memberInfo->GetId());
+ memberInfo->CopyMember(copier);
+ EndClassMember();
+ copier.In().EndChoiceVariant();
+ index = copier.In().BeginChoiceVariant(choiceType);
+ if ( index == kInvalidMember ) {
+ if (copier.In().CanSkipUnknownVariants()) {
+ copier.In().SkipAnyContentVariant();
+ break;
+ } else {
+ copier.ThrowError(CObjectIStream::fFormatError,
+ "choice variant id expected");
+ }
+ }
+ variantInfo = choiceType->GetVariantInfo(index);
+ }
+ copier.In().SetTopMemberId(variantInfo->GetId());
+ copier.Out().SetTopMemberId(variantInfo->GetId());
+ copier.SetPathHooks(copier.Out(), true);
+ BeginChoiceVariant(choiceType, variantInfo->GetId());
- variantInfo->CopyVariant(copier);
+ variantInfo->CopyVariant(copier);
- EndChoiceVariant();
- copier.SetPathHooks(copier.Out(), false);
- copier.In().EndChoiceVariant();
+ EndChoiceVariant();
+ copier.SetPathHooks(copier.Out(), false);
+ copier.In().EndChoiceVariant();
+ break;
+ }
+ }
END_OBJECT_2FRAMES_OF(copier);
copier.In().EndChoice();
EndChoice();
diff --git a/c++/src/serial/objostrasn.cpp b/c++/src/serial/objostrasn.cpp
index 7cd67eb..73312eb 100644
--- a/c++/src/serial/objostrasn.cpp
+++ b/c++/src/serial/objostrasn.cpp
@@ -1,4 +1,4 @@
-/* $Id: objostrasn.cpp 448578 2014-10-07 16:49:58Z ivanov $
+/* $Id: objostrasn.cpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -56,7 +56,7 @@
BEGIN_NCBI_SCOPE
CObjectOStream* CObjectOStream::OpenObjectOStreamAsn(CNcbiOstream& out,
- bool deleteOut)
+ EOwnership deleteOut)
{
return new CObjectOStreamAsn(out, deleteOut);
}
@@ -74,6 +74,17 @@ CObjectOStreamAsn::CObjectOStreamAsn(CNcbiOstream& out,
CObjectOStreamAsn::CObjectOStreamAsn(CNcbiOstream& out,
bool deleteOut,
EFixNonPrint how)
+ : CObjectOStream(eSerial_AsnText, out, deleteOut ? eTakeOwnership : eNoOwnership)
+{
+ FixNonPrint(how);
+ m_Output.SetBackLimit(80);
+ SetSeparator("\n");
+ SetAutoSeparator(true);
+}
+
+CObjectOStreamAsn::CObjectOStreamAsn(CNcbiOstream& out,
+ EOwnership deleteOut,
+ EFixNonPrint how)
: CObjectOStream(eSerial_AsnText, out, deleteOut)
{
FixNonPrint(how);
@@ -116,14 +127,14 @@ void CObjectOStreamAsn::WriteEnum(
void CObjectOStreamAsn::WriteEnum(const CEnumeratedTypeValues& values,
TEnumValueType value)
{
- WriteEnum(values,value,values.FindName(value, values.IsInteger()));
+ WriteEnum(values,value,values.FindNameEx(value, values.IsInteger()));
}
void CObjectOStreamAsn::CopyEnum(const CEnumeratedTypeValues& values,
CObjectIStream& in)
{
TEnumValueType value = in.ReadEnum(values);
- WriteEnum(values, value, values.FindName(value, values.IsInteger()));
+ WriteEnum(values, value, values.FindNameEx(value, values.IsInteger()));
}
void CObjectOStreamAsn::WriteBool(bool data)
@@ -307,7 +318,7 @@ void CObjectOStreamAsn::WriteBitString(const CBitString& obj)
}
}
#else
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
bm::word_t* tmp_block = obj.allocate_tempblock();
CBitString::statistics st;
obj.calc_stat(&st);
@@ -510,20 +521,23 @@ void CObjectOStreamAsn::WriteContainer(const CContainerTypeInfo* cType,
TTypeInfo elementType = cType->GetElementType();
BEGIN_OBJECT_FRAME2(eFrameArrayElement, elementType);
+ const CPointerTypeInfo* pointerType =
+ dynamic_cast<const CPointerTypeInfo*>(elementType);
do {
- if (elementType->GetTypeFamily() == eTypeFamilyPointer) {
- const CPointerTypeInfo* pointerType =
- CTypeConverter<CPointerTypeInfo>::SafeCast(elementType);
- _ASSERT(pointerType->GetObjectPointer(cType->GetElementPtr(i)));
- if ( !pointerType->GetObjectPointer(cType->GetElementPtr(i)) ) {
- ERR_POST_X(8, Warning << " NULL pointer found in container: skipping");
- continue;
+ TConstObjectPtr elementPtr = cType->GetElementPtr(i);
+ if ( pointerType &&
+ !pointerType->GetObjectPointer(elementPtr) ) {
+ if ( GetVerifyData() == eSerialVerifyData_Yes ) {
+ ThrowError(fUnassigned,
+ "NULL element while writing container "+
+ cType->GetName());
}
+ continue;
}
NextElement();
- WriteObject(cType->GetElementPtr(i), elementType);
+ WriteObject(elementPtr, elementType);
} while ( cType->NextElement(i) );
@@ -601,6 +615,7 @@ void CObjectOStreamAsn::BeginClassMember(const CMemberId& id)
void CObjectOStreamAsn::WriteClass(const CClassTypeInfo* classType,
TConstObjectPtr classPtr)
{
+ BEGIN_OBJECT_FRAME2(eFrameClass, classType);
StartBlock();
for ( CClassTypeInfo::CIterator i(classType); i.Valid(); ++i ) {
@@ -608,6 +623,7 @@ void CObjectOStreamAsn::WriteClass(const CClassTypeInfo* classType,
}
EndBlock();
+ END_OBJECT_FRAME();
}
void CObjectOStreamAsn::WriteClassMember(const CMemberId& memberId,
diff --git a/c++/src/serial/objostrasnb.cpp b/c++/src/serial/objostrasnb.cpp
index cbbc395..0698ade 100644
--- a/c++/src/serial/objostrasnb.cpp
+++ b/c++/src/serial/objostrasnb.cpp
@@ -1,4 +1,4 @@
-/* $Id: objostrasnb.cpp 448578 2014-10-07 16:49:58Z ivanov $
+/* $Id: objostrasnb.cpp 463313 2015-03-26 17:05:21Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -64,7 +64,7 @@ BEGIN_NCBI_SCOPE
CObjectOStream* CObjectOStream::OpenObjectOStreamAsnBinary(CNcbiOstream& out,
- bool deleteOut)
+ EOwnership deleteOut)
{
return new CObjectOStreamAsnBinary(out, deleteOut);
}
@@ -85,6 +85,20 @@ CObjectOStreamAsnBinary::CObjectOStreamAsnBinary(CNcbiOstream& out,
CObjectOStreamAsnBinary::CObjectOStreamAsnBinary(CNcbiOstream& out,
bool deleteOut,
EFixNonPrint how)
+ : CObjectOStream(eSerial_AsnBinary, out, deleteOut ? eTakeOwnership : eNoOwnership),
+ m_CStyleBigInt(false), m_SkipNextTag(false), m_AutomaticTagging(true)
+{
+ FixNonPrint(how);
+#if CHECK_OUTSTREAM_INTEGRITY
+ m_CurrentPosition = 0;
+ m_CurrentTagState = eTagStart;
+ m_CurrentTagLimit = 0;
+#endif
+}
+
+CObjectOStreamAsnBinary::CObjectOStreamAsnBinary(CNcbiOstream& out,
+ EOwnership deleteOut,
+ EFixNonPrint how)
: CObjectOStream(eSerial_AsnBinary, out, deleteOut),
m_CStyleBigInt(false), m_SkipNextTag(false), m_AutomaticTagging(true)
{
@@ -439,7 +453,7 @@ void CObjectOStreamAsnBinary::WriteBitString(const CBitString& obj)
#if BITSTRING_AS_VECTOR
bool compressed = false;
#else
- bool compressed = TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed();
+ bool compressed = IsCompressed();
#endif
char* buf=0;
unsigned int len = obj.size();
@@ -1140,17 +1154,21 @@ void CObjectOStreamAsnBinary::WriteContainer(const CContainerTypeInfo* cType,
TTypeInfo elementType = cType->GetElementType();
BEGIN_OBJECT_FRAME2(eFrameArrayElement, elementType);
+ const CPointerTypeInfo* pointerType =
+ dynamic_cast<const CPointerTypeInfo*>(elementType);
do {
- if (elementType->GetTypeFamily() == eTypeFamilyPointer) {
- const CPointerTypeInfo* pointerType =
- CTypeConverter<CPointerTypeInfo>::SafeCast(elementType);
- _ASSERT(pointerType->GetObjectPointer(cType->GetElementPtr(i)));
- if ( !pointerType->GetObjectPointer(cType->GetElementPtr(i)) ) {
- ERR_POST_X(10, Warning << " NULL pointer found in container: skipping");
- continue;
+ TConstObjectPtr elementPtr = cType->GetElementPtr(i);
+ if ( pointerType &&
+ !pointerType->GetObjectPointer(elementPtr) ) {
+ if ( GetVerifyData() == eSerialVerifyData_Yes ) {
+ ThrowError(fUnassigned,
+ "NULL element while writing container "+
+ cType->GetName());
}
+ continue;
}
- WriteObject(cType->GetElementPtr(i), elementType);
+
+ WriteObject(elementPtr, elementType);
} while ( cType->NextElement(i) );
diff --git a/c++/src/serial/objostrjson.cpp b/c++/src/serial/objostrjson.cpp
index 58c1a3b..852a30b 100644
--- a/c++/src/serial/objostrjson.cpp
+++ b/c++/src/serial/objostrjson.cpp
@@ -1,4 +1,4 @@
-/* $Id: objostrjson.cpp 448082 2014-10-02 14:54:45Z ivanov $
+/* $Id: objostrjson.cpp 481916 2015-10-19 13:22:37Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,7 +58,7 @@ BEGIN_NCBI_SCOPE
CObjectOStream* CObjectOStream::OpenObjectOStreamJson(CNcbiOstream& out,
- bool deleteOut)
+ EOwnership deleteOut)
{
return new CObjectOStreamJson(out, deleteOut);
}
@@ -66,6 +66,17 @@ CObjectOStream* CObjectOStream::OpenObjectOStreamJson(CNcbiOstream& out,
CObjectOStreamJson::CObjectOStreamJson(CNcbiOstream& out, bool deleteOut)
+ : CObjectOStream(eSerial_Json, out, deleteOut ? eTakeOwnership : eNoOwnership),
+ m_BlockStart(false),
+ m_ExpectValue(false),
+ m_StringEncoding(eEncoding_Unknown),
+ m_BinaryFormat(eDefault),
+ m_WrapAt(0)
+{
+ m_WriteNamedIntegersByValue = true;
+}
+
+CObjectOStreamJson::CObjectOStreamJson(CNcbiOstream& out, EOwnership deleteOut)
: CObjectOStream(eSerial_Json, out, deleteOut),
m_BlockStart(false),
m_ExpectValue(false),
@@ -73,6 +84,7 @@ CObjectOStreamJson::CObjectOStreamJson(CNcbiOstream& out, bool deleteOut)
m_BinaryFormat(eDefault),
m_WrapAt(0)
{
+ m_WriteNamedIntegersByValue = true;
}
CObjectOStreamJson::~CObjectOStreamJson(void)
@@ -258,6 +270,9 @@ void CObjectOStreamJson::WriteOther(TConstObjectPtr /*object*/, TTypeInfo /*type
void CObjectOStreamJson::WriteNull(void)
{
+ if (!m_ExpectValue && !m_SkippedMemberId.empty()) {
+ m_SkippedMemberId.erase();
+ }
if (m_ExpectValue) {
WriteKeywordValue("null");
}
@@ -318,7 +333,7 @@ void CObjectOStreamJson::WriteBitString(const CBitString& obj)
m_Output.PutChar(ToHex[data]);
}
#else
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
bm::word_t* tmp_block = obj.allocate_tempblock();
CBitString::statistics st;
obj.calc_stat(&st);
@@ -353,14 +368,14 @@ void CObjectOStreamJson::WriteEnum(const CEnumeratedTypeValues& values,
string value_str;
if (values.IsInteger()) {
value_str = NStr::IntToString(value);
- const string& name = values.FindName(value, values.IsInteger());
+ const string& name = values.FindNameEx(value, values.IsInteger());
if (name.empty() || GetWriteNamedIntegersByValue()) {
WriteKeywordValue(value_str);
} else {
WriteValue(name);
}
} else {
- value_str = values.FindName(value, values.IsInteger());
+ value_str = values.FindNameEx(value, values.IsInteger());
WriteValue(value_str);
}
}
@@ -514,7 +529,7 @@ void CObjectOStreamJson::WriteBytes(const ByteBlock& block,
WriteCustomBytes(bytes,length);
return;
}
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
WriteBase64Bytes(bytes,length);
return;
}
@@ -710,26 +725,30 @@ void CObjectOStreamJson::WriteKey(const string& key)
NameSeparator();
}
-void CObjectOStreamJson::WriteValue(const string& value, EStringType type)
+void CObjectOStreamJson::BeginValue(void)
{
if (!m_ExpectValue && !m_SkippedMemberId.empty()) {
WriteSkippedMember();
}
+}
+
+void CObjectOStreamJson::WriteValue(const string& value, EStringType type)
+{
+ BeginValue();
x_WriteString(value,type);
m_ExpectValue = false;
}
void CObjectOStreamJson::WriteKeywordValue(const string& value)
{
+ BeginValue();
m_Output.PutString(value);
m_ExpectValue = false;
}
void CObjectOStreamJson::StartBlock(void)
{
- if (!m_ExpectValue && !m_SkippedMemberId.empty()) {
- WriteSkippedMember();
- }
+ BeginValue();
m_Output.PutChar('{');
m_Output.IncIndentLevel();
m_BlockStart = true;
@@ -758,9 +777,7 @@ void CObjectOStreamJson::NextElement(void)
void CObjectOStreamJson::BeginArray(void)
{
- if (!m_ExpectValue && !m_SkippedMemberId.empty()) {
- WriteSkippedMember();
- }
+ BeginValue();
m_Output.PutChar('[');
m_Output.IncIndentLevel();
m_BlockStart = true;
diff --git a/c++/src/serial/objostrxml.cpp b/c++/src/serial/objostrxml.cpp
index 03dfd95..801ab68 100644
--- a/c++/src/serial/objostrxml.cpp
+++ b/c++/src/serial/objostrxml.cpp
@@ -1,4 +1,4 @@
-/* $Id: objostrxml.cpp 448082 2014-10-02 14:54:45Z ivanov $
+/* $Id: objostrxml.cpp 471531 2015-06-29 11:40:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -58,7 +58,7 @@
BEGIN_NCBI_SCOPE
CObjectOStream* CObjectOStream::OpenObjectOStreamXml(CNcbiOstream& out,
- bool deleteOut)
+ EOwnership deleteOut)
{
return new CObjectOStreamXml(out, deleteOut);
}
@@ -71,6 +71,22 @@ const char* s_SchemaInstanceNamespace = "http://www.w3.org/2001/XMLSchema-instan
CObjectOStreamXml::CObjectOStreamXml(CNcbiOstream& out, bool deleteOut)
+ : CObjectOStream(eSerial_Xml, out, deleteOut ? eTakeOwnership : eNoOwnership),
+ m_LastTagAction(eTagClose), m_EndTag(true),
+ m_UseDefaultDTDFilePrefix( true),
+ m_UsePublicId( true),
+ m_Attlist( false), m_StdXml( false), m_EnforcedStdXml( false),
+ m_RealFmt( eRealScientificFormat ),
+ m_Encoding( eEncoding_Unknown ), m_StringEncoding( eEncoding_Unknown ),
+ m_UseXmlDecl(true),
+ m_UseSchemaRef( false ), m_UseSchemaLoc( true ), m_UseDTDRef( true ),
+ m_DefaultSchemaNamespace( sm_DefaultSchemaNamespace ),
+ m_SkipIndent( false ), m_SkipNextTag(false)
+{
+ m_Output.SetBackLimit(1);
+}
+
+CObjectOStreamXml::CObjectOStreamXml(CNcbiOstream& out, EOwnership deleteOut)
: CObjectOStream(eSerial_Xml, out, deleteOut),
m_LastTagAction(eTagClose), m_EndTag(true),
m_UseDefaultDTDFilePrefix( true),
@@ -451,14 +467,14 @@ void CObjectOStreamXml::WriteEnum(const CEnumeratedTypeValues& values,
void CObjectOStreamXml::WriteEnum(const CEnumeratedTypeValues& values,
TEnumValueType value)
{
- WriteEnum(values, value, values.FindName(value, values.IsInteger()));
+ WriteEnum(values, value, values.FindNameEx(value, values.IsInteger()));
}
void CObjectOStreamXml::CopyEnum(const CEnumeratedTypeValues& values,
CObjectIStream& in)
{
TEnumValueType value = in.ReadEnum(values);
- WriteEnum(values, value, values.FindName(value, values.IsInteger()));
+ WriteEnum(values, value, values.FindNameEx(value, values.IsInteger()));
}
void CObjectOStreamXml::WriteEscapedChar(char c)
@@ -832,7 +848,7 @@ void CObjectOStreamXml::WriteBitString(const CBitString& obj)
m_Output.PutChar(ToHex[data]);
}
#else
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
bm::word_t* tmp_block = obj.allocate_tempblock();
CBitString::statistics st;
obj.calc_stat(&st);
@@ -1205,18 +1221,22 @@ void CObjectOStreamXml::WriteContainerContents(const CContainerTypeInfo* cType,
CContainerTypeInfo::CConstIterator i;
if ( WillHaveName(elementType) ) {
if ( cType->InitIterator(i, containerPtr) ) {
+
+ const CPointerTypeInfo* pointerType =
+ dynamic_cast<const CPointerTypeInfo*>(elementType);
do {
- if (elementType->GetTypeFamily() == eTypeFamilyPointer) {
- const CPointerTypeInfo* pointerType =
- CTypeConverter<CPointerTypeInfo>::SafeCast(elementType);
- _ASSERT(pointerType->GetObjectPointer(cType->GetElementPtr(i)));
- if ( !pointerType->GetObjectPointer(cType->GetElementPtr(i)) ) {
- ERR_POST_X(11, Warning << " NULL pointer found in container: skipping");
- continue;
+ TConstObjectPtr elementPtr = cType->GetElementPtr(i);
+ if ( pointerType &&
+ !pointerType->GetObjectPointer(elementPtr) ) {
+ if ( GetVerifyData() == eSerialVerifyData_Yes ) {
+ ThrowError(fUnassigned,
+ "NULL element while writing container "+
+ cType->GetName());
}
+ continue;
}
- WriteObject(cType->GetElementPtr(i), elementType);
+ WriteObject(elementPtr, elementType);
} while ( cType->NextElement(i) );
}
@@ -1225,9 +1245,23 @@ void CObjectOStreamXml::WriteContainerContents(const CContainerTypeInfo* cType,
BEGIN_OBJECT_FRAME2(eFrameArrayElement, elementType);
if ( cType->InitIterator(i, containerPtr) ) {
+
+ const CPointerTypeInfo* pointerType =
+ dynamic_cast<const CPointerTypeInfo*>(elementType);
do {
+ TConstObjectPtr elementPtr = cType->GetElementPtr(i);
+ if ( pointerType &&
+ !pointerType->GetObjectPointer(elementPtr) ) {
+ if ( GetVerifyData() == eSerialVerifyData_Yes ) {
+ ThrowError(fUnassigned,
+ "NULL element while writing container "+
+ cType->GetName());
+ }
+ continue;
+ }
+
BeginArrayElement(elementType);
- WriteObject(cType->GetElementPtr(i), elementType);
+ WriteObject(elementPtr, elementType);
EndArrayElement();
} while ( cType->NextElement(i) );
} else {
@@ -1607,7 +1641,7 @@ static const char* const HEX = "0123456789ABCDEF";
void CObjectOStreamXml::WriteBytes(const ByteBlock& ,
const char* bytes, size_t length)
{
- if (TopFrame().HasMemberId() && TopFrame().GetMemberId().IsCompressed()) {
+ if (IsCompressed()) {
WriteBase64Bytes(bytes,length);
return;
}
diff --git a/c++/src/serial/objstack.cpp b/c++/src/serial/objstack.cpp
index a66a0b1..7cd9264 100644
--- a/c++/src/serial/objstack.cpp
+++ b/c++/src/serial/objstack.cpp
@@ -1,4 +1,4 @@
-/* $Id: objstack.cpp 421693 2013-12-13 14:11:00Z gouriano $
+/* $Id: objstack.cpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -179,6 +179,18 @@ bool CObjectStack::IsNsQualified(void)
return true;
}
+bool CObjectStack::IsCompressed(void) const
+{
+ size_t i, count = GetStackDepth();
+ for (i=0; i<count; ++i) {
+ const CObjectStack::TFrame& frame = FetchFrameFromTop(i);
+ if (frame.HasMemberId()) {
+ return frame.GetMemberId().IsCompressed();
+ }
+ }
+ return false;
+}
+
void CObjectStack::x_PushStackPath(void)
{
if (!m_WatchPathHooks) {
@@ -186,6 +198,8 @@ void CObjectStack::x_PushStackPath(void)
return;
}
if (!m_PathValid) {
+ GetStackPath();
+#if 0
for ( size_t i = 1; i < GetStackDepth(); ++i ) {
const TFrame& frame = FetchFrameFromTop(i);
if (frame.HasTypeInfo()) {
@@ -194,6 +208,7 @@ void CObjectStack::x_PushStackPath(void)
break;
}
}
+#endif
}
const CMemberId& mem_id = TopFrame().GetMemberId();
if (mem_id.HasNotag() || mem_id.IsAttlist()) {
diff --git a/c++/src/serial/pack_string.cpp b/c++/src/serial/pack_string.cpp
index a52d099..c0a16b5 100644
--- a/c++/src/serial/pack_string.cpp
+++ b/c++/src/serial/pack_string.cpp
@@ -1,4 +1,4 @@
-/* $Id: pack_string.cpp 130314 2008-06-09 19:19:52Z vasilche $
+/* $Id: pack_string.cpp 450690 2014-10-29 19:01:34Z vasilche $
* ===========================================================================
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
@@ -42,7 +42,7 @@ static const size_t kDefaultLengthLimit = 32;
static const size_t kDefaultCountLimit = 32;
CPackString::CPackString(void)
- : m_LengthLimit(kDefaultCountLimit), m_CountLimit(kDefaultCountLimit),
+ : m_LengthLimit(kDefaultLengthLimit), m_CountLimit(kDefaultCountLimit),
m_Skipped(0), m_CompressedIn(0),
m_CompressedOut(0)
{
diff --git a/c++/src/serial/pathhook.cpp b/c++/src/serial/pathhook.cpp
index 371899a..9c4c962 100644
--- a/c++/src/serial/pathhook.cpp
+++ b/c++/src/serial/pathhook.cpp
@@ -1,4 +1,4 @@
-/* $Id: pathhook.cpp 432412 2014-04-14 12:45:58Z gouriano $
+/* $Id: pathhook.cpp 483285 2015-10-29 18:05:21Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -284,7 +284,8 @@ CItemInfo* CStreamPathHookBase::FindItem(const CObjectStack& stk)
dynamic_cast<const CClassTypeInfoBase*>(frame.GetTypeInfo());
if (classInfo) {
const string& name(stk.TopFrame().GetMemberId().GetName());
- return (classInfo->GetItems().Find(name) != kInvalidMember) ?
+ TMemberIndex ind = classInfo->GetItems().FindDeep(name,true,&classInfo);
+ return (ind != kInvalidMember) ?
const_cast<CItemInfo*>(classInfo->GetItemInfo(name)) : 0;
}
break;
diff --git a/c++/src/serial/rpcbase.cpp b/c++/src/serial/rpcbase.cpp
new file mode 100644
index 0000000..7e74bc1
--- /dev/null
+++ b/c++/src/serial/rpcbase.cpp
@@ -0,0 +1,335 @@
+/* $Id: rpcbase.cpp 483519 2015-11-02 14:44:04Z ivanov $
+* ===========================================================================
+*
+* PUBLIC DOMAIN NOTICE
+* National Center for Biotechnology Information
+*
+* This software/database is a "United States Government Work" under the
+* terms of the United States Copyright Act. It was written as part of
+* the author's official duties as a United States Government employee and
+* thus cannot be copyrighted. This software/database is freely available
+* to the public for use. The National Library of Medicine and the U.S.
+* Government have not placed any restriction on its use or reproduction.
+*
+* Although all reasonable efforts have been taken to ensure the accuracy
+* and reliability of the software and data, the NLM and the U.S.
+* Government do not and cannot warrant the performance or results that
+* may be obtained by using this software or data. The NLM and the U.S.
+* Government disclaim all warranties, express or implied, including
+* warranties of performance, merchantability or fitness for any particular
+* purpose.
+*
+* Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author: Aleksey Grichenko
+*
+* File Description:
+* CRPCClient helpers
+*/
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbistr.hpp>
+#include <corelib/ncbi_cookies.hpp>
+#include <serial/rpcbase.hpp>
+
+BEGIN_NCBI_SCOPE
+
+
+// HTTP headers controlling retries.
+
+// Stop retries if set, value describes the reason.
+const char* kRetryStop = "X-NCBI-Retry-Stop";
+// Override retries delay. Use min of the header and m_RetryDelay.
+const char* kRetryDelay = "X-NCBI-Retry-Delay";
+// Add args to the request when sending next retry.
+const char* kRetryArgs = "X-NCBI-Retry-Args";
+// Use the specified URL for the next retry.
+const char* kRetryURL = "X-NCBI-Retry-URL";
+// Use different content when sending retry. The values are described below.
+const char* kRetryContent = "X-NCBI-Retry-Content";
+// Send no content whith the next retry.
+const char* kRetryContent_no_content = "no_content";
+// Send content from the last response when retrying.
+const char* kRetryContent_from_response = "from_response";
+// Send content following the prefix (URL-encoded).
+const char* kRetryContent_content = "content:";
+
+
+CRPCClient_Base::CRPCClient_Base(const string& service,
+ ESerialDataFormat format,
+ unsigned int retry_limit)
+ : m_Format(format),
+ m_RetryCount(0),
+ m_RecursionCount(0),
+ m_Service(service),
+ m_Timeout(kDefaultTimeout),
+ m_RetryLimit(retry_limit)
+{
+}
+
+
+CRPCClient_Base::~CRPCClient_Base(void)
+{
+ Disconnect();
+ if ( !sx_IsSpecial(m_Timeout) ) {
+ delete const_cast<STimeout*>(m_Timeout);
+ }
+}
+
+
+void CRPCClient_Base::Connect(void)
+{
+ // Do not connect from recursive requests - this must be done
+ // by the main request only.
+ if (m_RecursionCount > 1) return;
+
+ if (m_Stream.get() && m_Stream->good()) {
+ return; // already connected
+ }
+ CMutexGuard LOCK(m_Mutex);
+ // repeat test with mutex held to avoid races
+ if (m_Stream.get() && m_Stream->good()) {
+ return; // already connected
+ }
+ x_Connect();
+ m_RetryCtx.ResetNeedReconnect();
+}
+
+
+void CRPCClient_Base::Disconnect(void)
+{
+ CMutexGuard LOCK(m_Mutex);
+ if ( !m_Stream.get() || !m_Stream->good() ) {
+ // not connected -- don't call x_Disconnect, which might
+ // temporarily reconnect to send a fini!
+ return;
+ }
+ x_Disconnect();
+}
+
+
+void CRPCClient_Base::Reset(void)
+{
+ CMutexGuard LOCK(m_Mutex);
+ if (m_Stream.get() && m_Stream->good()) {
+ x_Disconnect();
+ }
+ x_Connect();
+}
+
+
+void CRPCClient_Base::SetAffinity(const string& affinity)
+{
+ if (m_Affinity != affinity) {
+ if (m_RecursionCount > 1) {
+ ERR_POST("Affinity can not be changed on a recursive request");
+ return;
+ }
+ Disconnect();
+ m_Affinity = affinity;
+ }
+}
+
+
+void CRPCClient_Base::x_Disconnect(void)
+{
+ m_In.reset();
+ m_Out.reset();
+ m_Stream.reset();
+}
+
+
+void CRPCClient_Base::x_SetStream(CNcbiIostream* stream)
+{
+ m_In .reset();
+ m_Out.reset();
+ m_Stream.reset(stream);
+ m_In .reset(CObjectIStream::Open(m_Format, *stream));
+ m_Out.reset(CObjectOStream::Open(m_Format, *stream));
+}
+
+
+class CCounterGuard
+{
+public:
+ CCounterGuard(int* counter)
+ : m_Counter(*counter)
+ {
+
+ m_Counter++;
+ }
+
+ ~CCounterGuard(void)
+ {
+ m_Counter--;
+ }
+
+private:
+ int& m_Counter;
+};
+
+void CRPCClient_Base::x_Ask(const CSerialObject& request, CSerialObject& reply)
+{
+ CMutexGuard LOCK(m_Mutex);
+ if (m_RecursionCount == 0) {
+ m_RetryCount = 0;
+ }
+ // Recursion counter needs to be decremented on both success and failure.
+ CCounterGuard recursion_guard(&m_RecursionCount);
+
+ // Reset headers from previous requests if any.
+ m_RetryCtx.Reset();
+ double max_span = m_RetryDelay.GetAsDouble()*m_RetryLimit;
+ double span = max_span;
+ bool limit_by_time = !m_RetryDelay.IsEmpty();
+ // Retry context can be either the default one (m_RetryCtx), or provided
+ // through an exception.
+ for (;;) {
+ try {
+ SetAffinity(x_GetAffinity(request));
+ Connect(); // No-op if already connected
+ if ( m_RetryCtx.IsSetContentOverride() ) {
+ if (m_RetryCtx.GetContentOverride() != CHttpRetryContext::eNoContent &&
+ m_RetryCtx.IsSetContent() ) {
+ *m_Stream << m_RetryCtx.GetContent();
+ }
+ }
+ else {
+ // by default re-send the original request
+ x_WriteRequest(*m_Out, request);
+ }
+ m_Stream->peek(); // send data, read response headers
+ if (m_RetryCtx.IsSetContentOverride() &&
+ m_RetryCtx.GetContentOverride() == CHttpRetryContext::eFromResponse) {
+ // store response content to send it with the next retry
+ CNcbiOstrstream buf;
+ NcbiStreamCopy(buf, *m_Stream);
+ m_RetryCtx.SetContent(CNcbiOstrstreamToString(buf));
+ }
+ else {
+ // read normal response
+ x_ReadReply(*m_In, reply);
+ }
+ // If reading reply succeeded and no retry was requested by the server, break.
+ if ( !m_RetryCtx.GetNeedRetry() ) {
+ break;
+ }
+ } catch (CException& e) {
+ // Some exceptions tend to correspond to transient glitches;
+ // the remainder, however, may as well get propagated immediately.
+ CRPCClientException* rpc_ex = dynamic_cast<CRPCClientException*>(&e);
+ if (rpc_ex && rpc_ex->GetErrCode() == CRPCClientException::eRetry) {
+ if ( rpc_ex->IsSetRetryContext() ) {
+ // Save information to the local retry context and proceed.
+ m_RetryCtx = rpc_ex->GetRetryContext();
+ }
+ // proceed to retry
+ }
+ else if ( !dynamic_cast<CSerialException*>(&e)
+ && !dynamic_cast<CIOException*>(&e) ) {
+ // Not a retry related exception, abort.
+ throw;
+ }
+ }
+ // No retries for recursive requests (e.g. AskInit called by Connect).
+ // Exit immediately, do not reset retry context - it may be used by
+ // the main request's retry loop.
+ if (m_RecursionCount > 1) return;
+
+ // Retry request on exception or on explicit retry request from the server.
+
+ // If using time limit, allow to make more than m_RetryLimit attempts
+ // if the server has set shorter delay.
+ if ((!limit_by_time && ++m_RetryCount >= m_RetryLimit) ||
+ !x_ShouldRetry(m_RetryCount)) {
+ NCBI_THROW(CRPCClientException, eFailed,
+ "Failed to receive reply after " +
+ NStr::NumericToString(m_RetryCount) + " tries");
+ }
+ if ( m_RetryCtx.IsSetStop() ) {
+ NCBI_THROW(CRPCClientException, eFailed,
+ "Retrying request stopped by the server: " +
+ m_RetryCtx.GetStopReason());
+ }
+ CTimeSpan delay = x_GetRetryDelay(span);
+ if ( !delay.IsEmpty() ) {
+ SleepSec(delay.GetCompleteSeconds());
+ SleepMicroSec(delay.GetNanoSecondsAfterSecond() / 1000);
+ span -= delay.GetAsDouble();
+ if (limit_by_time && span <= 0) {
+ NCBI_THROW(CRPCClientException, eFailed,
+ "Failed to receive reply in " +
+ CTimeSpan(max_span).AsSmartString());
+ }
+ }
+ // Do not try to force reconnect in recursive calls.
+ if ( !(m_RetryCount & 1) || m_RetryCtx.NeedReconnect() ) {
+ // reset on every other attempt in case we're out of sync
+ try {
+ Reset();
+ } STD_CATCH_ALL_XX(Serial_RPCClient, 1 ,"CRPCClient_Base::Reset()");
+ }
+ }
+ // Reset retry context when done.
+ m_RetryCtx.Reset();
+}
+
+
+bool CRPCClient_Base::x_ShouldRetry(unsigned int tries)
+{
+ _TRACE("CRPCClient_Base::x_ShouldRetry: retrying after " << tries
+ << " failures");
+ return true;
+}
+
+
+CTimeSpan CRPCClient_Base::x_GetRetryDelay(double max_delay) const
+{
+ // If not set by the server, use local delay.
+ if ( !m_RetryCtx.IsSetDelay() ) {
+ return m_RetryDelay;
+ }
+ // If local delay is not zero, we have to limit total retries time to max_delay.
+ if (!m_RetryDelay.IsEmpty() &&
+ m_RetryCtx.GetDelay().GetAsDouble() > max_delay) {
+ return CTimeSpan(max_delay);
+ }
+ return m_RetryCtx.GetDelay();
+}
+
+
+EHTTP_HeaderParse
+CRPCClient_Base::sx_ParseHeader(const char* http_header,
+ void* user_data,
+ int server_error)
+{
+ if ( !user_data ) return eHTTP_HeaderContinue;
+ CHttpRetryContext* retry_ctx = reinterpret_cast<CHttpRetryContext*>(user_data);
+ _ASSERT(retry_ctx);
+ retry_ctx->ParseHeader(http_header);
+
+ // Always read response body - normal content or error.
+ return eHTTP_HeaderContinue;
+}
+
+
+bool CRPCClient_Base::sx_IsSpecial(const STimeout* timeout)
+{
+ return timeout == kDefaultTimeout || timeout == kInfiniteTimeout;
+}
+
+
+const char* CRPCClientException::GetErrCodeString(void) const
+{
+ switch (GetErrCode()) {
+ case eRetry: return "eRetry";
+ case eFailed: return "eFailed";
+ case eOther: return "eOther";
+ default: return CException::GetErrCodeString();
+ }
+}
+
+
+END_NCBI_SCOPE
diff --git a/c++/src/util/Makefile.util.lib b/c++/src/util/Makefile.util.lib
index 4b54f67..9709e9d 100644
--- a/c++/src/util/Makefile.util.lib
+++ b/c++/src/util/Makefile.util.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.util.lib 448239 2014-10-03 14:17:45Z kazimird $
+# $Id: Makefile.util.lib 483516 2015-11-02 14:43:15Z ivanov $
SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \
thread_pool_old ddump_viewer strsearch logrotate \
@@ -7,7 +7,7 @@ SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \
transmissionrw miscmath mutex_pool ncbi_cache line_reader \
util_exception uttp multi_writer itransaction thread_pool \
thread_pool_ctrl scheduler distribution rangelist util_misc \
- histogram_binning table_printer
+ histogram_binning table_printer retry_ctx
LIB = xutil
PROJ_TAG = core
diff --git a/c++/src/util/checksum.cpp b/c++/src/util/checksum.cpp
index e05dba0..29554e4 100644
--- a/c++/src/util/checksum.cpp
+++ b/c++/src/util/checksum.cpp
@@ -1,4 +1,4 @@
-/* $Id: checksum.cpp 448175 2014-10-02 18:33:47Z vasilche $
+/* $Id: checksum.cpp 462148 2015-03-16 19:31:40Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,12 +31,42 @@
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
+#include <corelib/ncbifile.hpp>
#include <util/checksum.hpp>
+#define USE_CRC32C_INTEL // try to use Intel CRC32C instructions
+
+#ifdef USE_CRC32C_INTEL
+# undef USE_CRC32C_INTEL // we'll define it again where available
+# if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_ICC)
+# if defined(__x86_64__) || defined(__i386__)
+# ifdef HAVE_CPUID_H
+# include <cpuid.h>
+# endif
+# define USE_CRC32C_INTEL
+# endif
+# if defined(__x86_64__)
+# define HAVE_CRC32C_64
+# endif
+# elif defined(NCBI_COMPILER_MSVC)
+# if defined(_M_X64) || defined(_M_IX86)
+# include <intrin.h>
+# define USE_CRC32C_INTEL
+# endif
+# if defined(_M_X64)
+# define HAVE_CRC32C_64
+# endif
+# endif
+#endif
BEGIN_NCBI_SCOPE
+static const size_t kCRC32Size = 256;
+typedef Uint4 TCRC32Table[kCRC32Size];
+
+// Defines
+#define TABLES_COUNT 8
#define NCBI_USE_PRECOMPILED_CRC32_TABLES 1
// sx_Start must begin with "/* O" (see ValidChecksumLine() in checksum.hpp)
@@ -45,64 +75,39 @@ static const char sx_End[] = " */";
static const char sx_LineCount[] = "lines: ";
static const char sx_CharCount[] = "chars: ";
+// Forward declarations
+
#ifdef NCBI_USE_PRECOMPILED_CRC32_TABLES
-inline void s_InitTableCRC32() {}
-inline void s_InitTableCRC32ZIP() {}
+ static inline void s_InitTableCRC32Forward() {}
+ static inline void s_InitTableCRC32Reverse() {}
+ static inline void s_InitTableCRC32CReverse() {}
#else
-static Uint4 s_CalcByteCRC32(size_t byte);
-static Uint4 s_CalcByteCRC32ZIP(size_t byte);
-static void s_FillMultiBitsCRC(Uint4* table, size_t size);
-static void s_InitTableCRC32();
-static void s_InitTableCRC32ZIP();
+ static void s_InitTableCRC32Forward();
+ static void s_InitTableCRC32Reverse();
+ static void s_InitTableCRC32CReverse();
#endif //NCBI_USE_PRECOMPILED_CRC32_TABLES
-static Uint4 s_UpdateCRC32(Uint4 checksum, const char* str, size_t length);
-static Uint4 s_UpdateCRC32ZIP(Uint4 checksum, const char* str, size_t length);
-static Uint4 s_UpdateAdler32(Uint4 sum, const char* data, size_t len);
-static void s_PrintTable(CNcbiOstream& out, const char* name,
- const Uint4* table, size_t size);
+
+#ifdef USE_CRC32C_INTEL
+ static bool s_IsCRC32CIntelEnabled(void);
+#endif
CChecksum::CChecksum(EMethod method)
- : m_LineCount(0), m_CharCount(0), m_Method(method)
+ : m_Method(eNone)
{
- switch ( GetMethod() ) {
- case eCRC32:
- s_InitTableCRC32();
- m_Checksum.m_CRC32 = 0;
- break;
- case eCRC32ZIP:
- case eCRC32INSD:
- s_InitTableCRC32ZIP();
- m_Checksum.m_CRC32 = ~0;
- break;
- case eMD5:
- m_Checksum.m_MD5 = new CMD5;
- break;
- case eAdler32:
- m_Checksum.m_CRC32 = 1;
- break;
- default:
- break;
- }
+ Reset(method);
}
CChecksum::CChecksum(const CChecksum& cks)
- : m_LineCount(cks.m_LineCount), m_CharCount(cks.m_CharCount),
+ : m_LineCount(cks.m_LineCount),
+ m_CharCount(cks.m_CharCount),
m_Method(cks.m_Method)
{
- switch ( GetMethod() ) {
- case eCRC32:
- case eCRC32ZIP:
- case eCRC32INSD:
- case eAdler32:
- m_Checksum.m_CRC32 = cks.m_Checksum.m_CRC32;
- break;
- case eMD5:
+ if ( GetMethod() == eMD5 ) {
m_Checksum.m_MD5 = new CMD5(*cks.m_Checksum.m_MD5);
- break;
- default:
- break;
+ } else {
+ m_Checksum.m_CRC32 = cks.m_Checksum.m_CRC32;
}
}
@@ -115,13 +120,9 @@ CChecksum::~CChecksum()
void CChecksum::x_Free(void)
{
- switch ( GetMethod() ) {
- case eMD5:
+ if ( GetMethod() == eMD5 ) {
delete m_Checksum.m_MD5;
- m_Checksum.m_MD5 = 0;
- break;
- default:
- break;
+ m_Checksum.m_MD5 = NULL;
}
}
@@ -134,18 +135,10 @@ CChecksum& CChecksum::operator= (const CChecksum& cks)
m_CharCount = cks.m_CharCount;
m_Method = cks.m_Method;
- switch ( GetMethod() ) {
- case eCRC32:
- case eCRC32ZIP:
- case eCRC32INSD:
- case eAdler32:
- m_Checksum.m_CRC32 = cks.m_Checksum.m_CRC32;
- break;
- case eMD5:
+ if ( GetMethod() == eMD5 ) {
m_Checksum.m_MD5 = new CMD5(*cks.m_Checksum.m_MD5);
- break;
- default:
- break;
+ } else {
+ m_Checksum.m_CRC32 = cks.m_Checksum.m_CRC32;
}
return *this;
}
@@ -163,11 +156,23 @@ void CChecksum::Reset(EMethod method)
switch ( GetMethod() ) {
case eCRC32:
+ case eCRC32CKSUM:
m_Checksum.m_CRC32 = 0;
+ s_InitTableCRC32Forward();
break;
case eCRC32ZIP:
case eCRC32INSD:
m_Checksum.m_CRC32 = ~0;
+ s_InitTableCRC32Reverse();
+ break;
+ case eCRC32C:
+ m_Checksum.m_CRC32 = ~0;
+#ifdef USE_CRC32C_INTEL
+ if ( s_IsCRC32CIntelEnabled() ) {
+ break;
+ }
+#endif
+ s_InitTableCRC32CReverse();
break;
case eMD5:
m_Checksum.m_MD5 = new CMD5;
@@ -181,15 +186,39 @@ void CChecksum::Reset(EMethod method)
}
+size_t CChecksum::GetChecksumSize(void) const
+{
+ switch ( GetMethod() ) {
+ case eMD5: return 16;
+ case eNone: return 0;
+ default: return 4;
+ }
+}
+
+
Uint4 CChecksum::GetChecksum(void) const
{
switch ( GetMethod() ) {
case eCRC32:
return m_Checksum.m_CRC32;
+ case eCRC32CKSUM:
+ {
+ // POSIX checksum includes length of data
+ char extra_bytes[8];
+ size_t extra_len = 0;
+ for ( size_t len = m_CharCount; len; len >>= 8 ) {
+ extra_bytes[extra_len++] = len & 0xff;
+ }
+ CChecksum extra(*this);
+ extra.AddChars(extra_bytes, extra_len);
+ return ~extra.m_Checksum.m_CRC32;
+ }
case eCRC32ZIP:
return ~m_Checksum.m_CRC32;
case eCRC32INSD:
return m_Checksum.m_CRC32;
+ case eCRC32C:
+ return ~m_Checksum.m_CRC32;
case eAdler32:
return m_Checksum.m_CRC32;
default:
@@ -204,9 +233,9 @@ CNcbiOstream& CChecksum::WriteChecksum(CNcbiOstream& out) const
if (!Valid() || !out.good()) {
return out;
}
- out << sx_Start <<
- sx_LineCount << m_LineCount << ", " <<
- sx_CharCount << m_CharCount << ", ";
+ out << sx_Start
+ << sx_LineCount << m_LineCount << ", "
+ << sx_CharCount << m_CharCount << ", ";
WriteChecksumData(out);
return out << sx_End << '\n';
}
@@ -227,44 +256,56 @@ bool CChecksum::ValidChecksumLineLong(const char* line, size_t length) const
}
-CNcbiOstream& CChecksum::WriteChecksumData(CNcbiOstream& out) const
+string CChecksum::GetHexSum(void) const
{
switch ( GetMethod() ) {
- case eCRC32:
- case eCRC32ZIP:
- case eCRC32INSD:
- return out << "CRC32: " << hex << setprecision(8)
- << GetChecksum();
case eMD5:
- return out << "MD5: " << m_Checksum.m_MD5->GetHexSum();
- case eAdler32:
- return out << "Adler32: " << hex << setprecision(8)
- << GetChecksum();
+ return m_Checksum.m_MD5->GetHexSum();
+ case eNone:
+ return kEmptyStr;
default:
- return out << "none";
+ return NStr::NumericToString(GetChecksum(), 0, 16);
}
}
-void CChecksum::x_Update(const char* str, size_t count)
+CNcbiOstream& CChecksum::WriteHexSum(CNcbiOstream& out) const
+{
+ if ( GetMethod() == eMD5 ) {
+ out << m_Checksum.m_MD5->GetHexSum();
+ } else {
+ IOS_BASE::fmtflags flags = out.setf(IOS_BASE::hex, IOS_BASE::basefield);
+ out << setprecision(8) << GetChecksum();
+ out.flags(flags);
+ }
+ return out;
+}
+
+
+CNcbiOstream& CChecksum::WriteChecksumData(CNcbiOstream& out) const
{
switch ( GetMethod() ) {
case eCRC32:
- m_Checksum.m_CRC32 = s_UpdateCRC32(m_Checksum.m_CRC32, str, count);
- break;
case eCRC32ZIP:
case eCRC32INSD:
- m_Checksum.m_CRC32 = s_UpdateCRC32ZIP(m_Checksum.m_CRC32, str, count);
- break;
- case eAdler32:
- m_Checksum.m_CRC32 = s_UpdateAdler32(m_Checksum.m_CRC32, str, count);
+ case eCRC32CKSUM:
+ case eCRC32C:
+ out << "CRC32: ";
+ WriteHexSum(out);
break;
case eMD5:
- m_Checksum.m_MD5->Update(str, count);
+ out << "MD5: ";
+ WriteHexSum(out);
+ break;
+ case eAdler32:
+ out << "Adler32: ";
+ WriteHexSum(out);
break;
default:
+ out << "none";
break;
}
+ return out;
}
@@ -276,203 +317,145 @@ void CChecksum::NextLine(void)
}
-CChecksum ComputeFileChecksum(const string& path, CChecksum::EMethod method)
+void CChecksum::AddFile(const string& file_path)
{
- CNcbiIfstream input(path.c_str(), IOS_BASE::in | IOS_BASE::binary);
- CChecksum cks(method);
- return ComputeFileChecksum(path, cks);
+ CFileIO f;
+ try {
+ f.Open(file_path, CFileIO::eOpen, CFileIO::eRead);
+ CChecksum tmp(*this);
+ size_t n;
+ char buf[1024 * 8];
+ while ((n = f.Read(buf, sizeof(buf))) > 0) {
+ tmp.AddChars(buf, n);
+ }
+ f.Close();
+ *this = tmp;
+ }
+ catch (CFileException& e) {
+ f.Close();
+ NCBI_RETHROW(e, CChecksumException, eFileIO,
+ "Error add checksum for file: " + file_path);
+ throw;
+ }
}
-CChecksum& ComputeFileChecksum(const string& path, CChecksum& checksum)
+void CChecksum::AddStream(CNcbiIstream& is)
+{
+ if ( is.eof() ) {
+ return;
+ }
+ if ( !is.good() ) {
+ NCBI_THROW(CChecksumException, eStreamIO,
+ "Input stream is not good()");
+ return;
+ }
+ CChecksum tmp(*this);
+
+ while ( !is.eof() ) {
+ char buf[1024 * 8];
+ is.read(buf, sizeof(buf));
+ size_t n = (size_t)is.gcount();
+ if (n) {
+ tmp.AddChars(buf, n);
+ } else {
+ if (is.fail() && !is.eof()) {
+ NCBI_THROW(CChecksumException, eStreamIO,
+ "Error reading from input stream");
+ return;
+ }
+ }
+ }
+ *this = tmp;
+}
+
+
+// @deprecated
+CChecksum& ComputeFileChecksum_deprecated(const string& path, CChecksum& checksum)
{
- CNcbiIfstream input(path.c_str(), IOS_BASE::in | IOS_BASE::binary);
- if ( !input.is_open() ) {
+ CNcbiIfstream is(path.c_str(), IOS_BASE::in | IOS_BASE::binary);
+ if ( !is.is_open() ) {
return checksum;
}
- while ( !input.eof() ) {
- char buf[1024*4];
- input.read(buf, sizeof(buf));
- size_t count = (size_t)input.gcount();
+ while ( !is.eof() ) {
+ char buf[1024*8];
+ is.read(buf, sizeof(buf));
+ size_t count = (size_t)is.gcount();
if ( count ) {
checksum.AddChars(buf, count);
}
}
- input.close();
+ is.close();
return checksum;
}
+// @deprecated
+CChecksum ComputeFileChecksum(const string& path, CChecksum::EMethod method)
+{
+ CChecksum cks(method);
+ return ComputeFileChecksum_deprecated(path, cks);
+}
+
+// @deprecated
+CChecksum& ComputeFileChecksum(const string& path, CChecksum& checksum)
+{
+ return ComputeFileChecksum_deprecated(path, checksum);
+}
+
+// @deprecated
+Uint4 ComputeFileCRC32(const string& path)
+{
+ CChecksum cks(CChecksum::eCRC32);
+ return ComputeFileChecksum_deprecated(path, cks).GetChecksum();
+}
+
void CChecksum::InitTables(void)
{
- s_InitTableCRC32();
- s_InitTableCRC32ZIP();
+ s_InitTableCRC32Forward();
+ s_InitTableCRC32Reverse();
+ s_InitTableCRC32CReverse();
}
-static void s_PrintTable(CNcbiOstream& out, const char* name,
- const Uint4* table, size_t size)
+template<size_t kCRC32Tables>
+static inline
+void s_PrintTable(CNcbiOstream& out, const char* name,
+ const TCRC32Table (&table)[kCRC32Tables])
{
const size_t kLineSize = 4;
- out << "static Uint4 " << name << "[" << size << "] = {";
- for ( size_t i = 0; i < size; ++i ) {
- if ( i != 0 ) {
+ out << "static const TCRC32Table " << name << "["<<kCRC32Tables<<"] = {";
+ for ( size_t k = 0; k < kCRC32Tables; ++k ) {
+ if ( k ) {
out << ',';
}
- if ( i % kLineSize == 0 ) {
- out << "\n ";
- }
- else {
- out << ' ';
+ out << "\n {";
+ for ( size_t i = 0; i < kCRC32Size; ++i ) {
+ if ( i != 0 ) {
+ out << ',';
+ }
+ if ( i % kLineSize == 0 ) {
+ out << "\n ";
+ } else {
+ out << ' ';
+ }
+ out << "0x" << hex << setw(8) << setfill('0') << table[k][i];
}
- out << "0x" << hex << setw(8) << setfill('0') << table[i];
+ out << "\n }";
}
out << dec << "\n};\n" << endl;
}
-static const size_t kCRC32Size = 256;
-
#ifdef NCBI_USE_PRECOMPILED_CRC32_TABLES
-static Uint4 s_CRC32Table[kCRC32Size] = {
- 0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9,
- 0x130476dc, 0x17c56b6b, 0x1a864db2, 0x1e475005,
- 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61,
- 0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd,
- 0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9,
- 0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75,
- 0x6a1936c8, 0x6ed82b7f, 0x639b0da6, 0x675a1011,
- 0x791d4014, 0x7ddc5da3, 0x709f7b7a, 0x745e66cd,
- 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
- 0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5,
- 0xbe2b5b58, 0xbaea46ef, 0xb7a96036, 0xb3687d81,
- 0xad2f2d84, 0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d,
- 0xd4326d90, 0xd0f37027, 0xddb056fe, 0xd9714b49,
- 0xc7361b4c, 0xc3f706fb, 0xceb42022, 0xca753d95,
- 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
- 0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d,
- 0x34867077, 0x30476dc0, 0x3d044b19, 0x39c556ae,
- 0x278206ab, 0x23431b1c, 0x2e003dc5, 0x2ac12072,
- 0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16,
- 0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca,
- 0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde,
- 0x6b93dddb, 0x6f52c06c, 0x6211e6b5, 0x66d0fb02,
- 0x5e9f46bf, 0x5a5e5b08, 0x571d7dd1, 0x53dc6066,
- 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
- 0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e,
- 0xbfa1b04b, 0xbb60adfc, 0xb6238b25, 0xb2e29692,
- 0x8aad2b2f, 0x8e6c3698, 0x832f1041, 0x87ee0df6,
- 0x99a95df3, 0x9d684044, 0x902b669d, 0x94ea7b2a,
- 0xe0b41de7, 0xe4750050, 0xe9362689, 0xedf73b3e,
- 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
- 0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686,
- 0xd5b88683, 0xd1799b34, 0xdc3abded, 0xd8fba05a,
- 0x690ce0ee, 0x6dcdfd59, 0x608edb80, 0x644fc637,
- 0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb,
- 0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f,
- 0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53,
- 0x251d3b9e, 0x21dc2629, 0x2c9f00f0, 0x285e1d47,
- 0x36194d42, 0x32d850f5, 0x3f9b762c, 0x3b5a6b9b,
- 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
- 0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623,
- 0xf12f560e, 0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7,
- 0xe22b20d2, 0xe6ea3d65, 0xeba91bbc, 0xef68060b,
- 0xd727bbb6, 0xd3e6a601, 0xdea580d8, 0xda649d6f,
- 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604, 0xc960ebb3,
- 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
- 0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b,
- 0x9b3660c6, 0x9ff77d71, 0x92b45ba8, 0x9675461f,
- 0x8832161a, 0x8cf30bad, 0x81b02d74, 0x857130c3,
- 0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640,
- 0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c,
- 0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8,
- 0x68860bfd, 0x6c47164a, 0x61043093, 0x65c52d24,
- 0x119b4be9, 0x155a565e, 0x18197087, 0x1cd86d30,
- 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
- 0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088,
- 0x2497d08d, 0x2056cd3a, 0x2d15ebe3, 0x29d4f654,
- 0xc5a92679, 0xc1683bce, 0xcc2b1d17, 0xc8ea00a0,
- 0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb, 0xdbee767c,
- 0xe3a1cbc1, 0xe760d676, 0xea23f0af, 0xeee2ed18,
- 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
- 0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0,
- 0x9abc8bd5, 0x9e7d9662, 0x933eb0bb, 0x97ffad0c,
- 0xafb010b1, 0xab710d06, 0xa6322bdf, 0xa2f33668,
- 0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4
-};
-
-static Uint4 s_CRC32ZIPTable[kCRC32Size] = {
- 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba,
- 0x076dc419, 0x706af48f, 0xe963a535, 0x9e6495a3,
- 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,
- 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91,
- 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de,
- 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7,
- 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec,
- 0x14015c4f, 0x63066cd9, 0xfa0f3d63, 0x8d080df5,
- 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172,
- 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b,
- 0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940,
- 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59,
- 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116,
- 0x21b4f4b5, 0x56b3c423, 0xcfba9599, 0xb8bda50f,
- 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
- 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d,
- 0x76dc4190, 0x01db7106, 0x98d220bc, 0xefd5102a,
- 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433,
- 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818,
- 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01,
- 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e,
- 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457,
- 0x65b0d9c6, 0x12b7e950, 0x8bbeb8ea, 0xfcb9887c,
- 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65,
- 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2,
- 0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb,
- 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0,
- 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9,
- 0x5005713c, 0x270241aa, 0xbe0b1010, 0xc90c2086,
- 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
- 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4,
- 0x59b33d17, 0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad,
- 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a,
- 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683,
- 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8,
- 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1,
- 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe,
- 0xf762575d, 0x806567cb, 0x196c3671, 0x6e6b06e7,
- 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc,
- 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5,
- 0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252,
- 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b,
- 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60,
- 0xdf60efc3, 0xa867df55, 0x316e8eef, 0x4669be79,
- 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
- 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f,
- 0xc5ba3bbe, 0xb2bd0b28, 0x2bb45a92, 0x5cb36a04,
- 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d,
- 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a,
- 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713,
- 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38,
- 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21,
- 0x86d3d2d4, 0xf1d4e242, 0x68ddb3f8, 0x1fda836e,
- 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777,
- 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c,
- 0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45,
- 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2,
- 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db,
- 0xaed16a4a, 0xd9d65adc, 0x40df0b66, 0x37d83bf0,
- 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
- 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6,
- 0xbad03605, 0xcdd70693, 0x54de5729, 0x23d967bf,
- 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94,
- 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d
-};
+# include "crc32tables.c"
#else
-static Uint4 s_CRC32Table[kCRC32Size];
-static Uint4 s_CRC32ZIPTable[kCRC32Size];
+static TCRC32Table s_CRC32TableForward[TABLES_COUNT];
+static TCRC32Table s_CRC32TableReverse[TABLES_COUNT];
+static TCRC32Table s_CRC32CTableReverse[TABLES_COUNT];
/////////////////////////////////////////////////////////////////////////////
// Implementation of CRC32 algorithm.
@@ -484,7 +467,9 @@ static Uint4 s_CRC32ZIPTable[kCRC32Size];
// The polynomial used is
// x^32+x^26+x^23+x^22+x^16+x^12+x^11+x^10+x^8+x^7+x^5+x^4+x^2+x^1+x^0
#define CRC32_POLYNOMIAL 0x04c11db7
-#define CRC32ZIP_POLYNOMIAL 0xedb88320
+// CRC32C (Castagnoli) polynomial is
+// x^32+x^28+x^27+x^26+x^25+x^23+x^22+x^20+x^19+x^18+x^14+x^13+x^11+x^10+x^9+x^8+x^6+x^0
+#define CRC32C_POLYNOMIAL 0x1edc6f41
// CRC32 is linear meaning that for any texts t1 & t2:
// CRC32[t1 XOR t2] = CRC32[t1] XOR CRC32[t2].
@@ -498,12 +483,13 @@ static Uint4 s_CRC32ZIPTable[kCRC32Size];
// s_FillMultiBitsCRC().
-Uint4 s_CalcByteCRC32(size_t byte)
+static inline
+Uint4 s_CalcByteCRC32Forward(size_t byte, Uint4 polynomial)
{
Uint4 byteCRC = byte << 24;
for ( int j = 0; j < 8; ++j ) {
if ( byteCRC & 0x80000000L )
- byteCRC = (byteCRC << 1) ^ CRC32_POLYNOMIAL;
+ byteCRC = (byteCRC << 1) ^ polynomial;
else
byteCRC = (byteCRC << 1);
}
@@ -511,12 +497,13 @@ Uint4 s_CalcByteCRC32(size_t byte)
}
-Uint4 s_CalcByteCRC32ZIP(size_t byte)
+static inline
+Uint4 s_CalcByteCRC32Reverse(size_t byte, Uint4 reversed_polynomial)
{
Uint4 byteCRC = byte;
for ( int j = 0; j < 8; ++j ) {
if ( byteCRC & 1 )
- byteCRC = (byteCRC >> 1) ^ CRC32ZIP_POLYNOMIAL;
+ byteCRC = (byteCRC >> 1) ^ reversed_polynomial;
else
byteCRC = (byteCRC >> 1);
}
@@ -524,11 +511,12 @@ Uint4 s_CalcByteCRC32ZIP(size_t byte)
}
+static inline
void s_FillMultiBitsCRC(Uint4* table, size_t size)
{
// Preconditions:
// Entries at one-bit indexes (1<<k), are calculated.
- for ( size_t i = 0; i < size; ++i ) { // order is significant
+ for ( size_t i = 1; i < size; ++i ) { // order is significant
// Split bits of i into two parts:
// lobit contains lowest bit set, or zero if no bits are set,
// hibits contains all other bits.
@@ -558,58 +546,512 @@ void s_FillMultiBitsCRC(Uint4* table, size_t size)
}
-void s_InitTableCRC32(void)
+template<size_t kCRC32Tables>
+static inline
+void s_InitTableCRC32Forward(TCRC32Table (&table)[kCRC32Tables],
+ Uint4 polynomial)
{
// check the last element to make sure we minimize chances of races
// in MT programs.
- if ( s_CRC32Table[kCRC32Size-1] == 0 ) {
- // Initialize CRC32 for bytes with only one bit set
- for ( size_t i = 1; i < kCRC32Size; i <<= 1 ) {
- s_CRC32Table[i] = s_CalcByteCRC32(i);
+ if ( table[kCRC32Tables-1][kCRC32Size-1] ) {
+ return;
+ }
+ // Initialize CRC32 for bytes with only one bit set
+ for ( size_t i = 1; i < kCRC32Size; i <<= 1 ) {
+ table[0][i] = s_CalcByteCRC32Forward(i, polynomial);
+ }
+ // Fill the rest of the main table
+ s_FillMultiBitsCRC(table[0], kCRC32Size);
+ // Fill secondary tables
+ for ( size_t k = 1; k < kCRC32Tables; ++k ) {
+ for ( size_t i = 0; i < kCRC32Size; ++i ) {
+ Uint4 checksum = table[k-1][i];
+ checksum = (checksum << 8) ^ table[0][checksum >> 24];
+ table[k][i] = checksum;
}
- // Fill the rest of table
- s_FillMultiBitsCRC(s_CRC32Table, kCRC32Size);
}
}
-void s_InitTableCRC32ZIP(void)
+template<size_t kCRC32Tables>
+static inline
+void s_InitTableCRC32Reverse(TCRC32Table (&table)[kCRC32Tables],
+ Uint4 polynomial)
{
+ Uint4 reversed_polynomial = 0;
+ for ( size_t i = 0; i < 32; ++i ) {
+ reversed_polynomial = (reversed_polynomial << 1)|(polynomial & 1);
+ polynomial >>= 1;
+ }
// check the last element to make sure we minimize chances of races
// in MT programs.
- if ( s_CRC32ZIPTable[kCRC32Size-1] == 0 ) {
- // Initialize CRC32 for bytes with only one bit set
- for ( size_t i = 1; i < kCRC32Size; i <<= 1 ) {
- s_CRC32ZIPTable[i] = s_CalcByteCRC32ZIP(i);
+ if ( table[kCRC32Tables-1][kCRC32Size-1] ) {
+ return;
+ }
+ // Initialize CRC32 for bytes with only one bit set
+ for ( size_t i = 1; i < kCRC32Size; i <<= 1 ) {
+ table[0][i] = s_CalcByteCRC32Reverse(i, reversed_polynomial);
+ }
+ // Fill the rest of the table
+ s_FillMultiBitsCRC(table[0], kCRC32Size);
+ // Fill secondary tables
+ for ( size_t k = 1; k < kCRC32Tables; ++k ) {
+ for ( size_t i = 0; i < kCRC32Size; ++i ) {
+ Uint4 checksum = table[k-1][i];
+ checksum = (checksum >> 8) ^ table[0][checksum & 0xff];
+ table[k][i] = checksum;
}
- // Fill the rest of table
- s_FillMultiBitsCRC(s_CRC32ZIPTable, kCRC32Size);
}
}
+
+void s_InitTableCRC32Forward(void)
+{
+ s_InitTableCRC32Forward(s_CRC32TableForward, CRC32_POLYNOMIAL);
+}
+
+
+void s_InitTableCRC32Reverse(void)
+{
+ s_InitTableCRC32Reverse(s_CRC32TableReverse, CRC32_POLYNOMIAL);
+}
+
+
+void s_InitTableCRC32CReverse(void)
+{
+ s_InitTableCRC32Reverse(s_CRC32CTableReverse, CRC32C_POLYNOMIAL);
+}
+
+
#endif //NCBI_USE_PRECOMPILED_CRC32_TABLES
-Uint4 s_UpdateCRC32(Uint4 checksum, const char *str, size_t count)
+#define s_UpdateCRC32Forward_1(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint1*)(str) ^ ((crc) >> 24); \
+ (crc) = ((crc) << 8) ^ (table)[0][v]; \
+ } while(0)
+
+#define s_UpdateCRC32Forward_2(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint2*)(str); \
+ /* index bytes are in wrong order */ \
+ (crc) = ((crc) << 16) ^ \
+ (table)[0][(((crc)>>16)^(v>>8)) & 0xff] ^ \
+ (table)[1][(((crc)>>24)^(v )) & 0xff]; \
+ } while(0)
+
+#define s_UpdateCRC32Forward_4(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint4*)(str); \
+ /* index bytes are in wrong order */ \
+ (crc) = \
+ (table)[0][(((crc) )^(v>>24)) & 0xff] ^ \
+ (table)[1][(((crc)>> 8)^(v>>16)) & 0xff] ^ \
+ (table)[2][(((crc)>>16)^(v>> 8)) & 0xff] ^ \
+ (table)[3][(((crc)>>24)^(v )) & 0xff]; \
+ } while(0)
+
+#define s_UpdateCRC32Forward_8(crc, str, table) \
+ do { \
+ Uint4 v0 = ((const Uint4*)(str))[0]; \
+ Uint4 v1 = ((const Uint4*)(str))[1]; \
+ /* index bytes are in wrong order */ \
+ (crc) = \
+ (table)[0][( (v1>>24)) ] ^ \
+ (table)[1][( (v1>>16)) & 0xff] ^ \
+ (table)[2][( (v1>> 8)) & 0xff] ^ \
+ (table)[3][( (v1 )) & 0xff] ^ \
+ (table)[4][(((crc) )^(v0>>24)) & 0xff] ^ \
+ (table)[5][(((crc)>> 8)^(v0>>16)) & 0xff] ^ \
+ (table)[6][(((crc)>>16)^(v0>> 8)) & 0xff] ^ \
+ (table)[7][(((crc)>>24)^(v0 )) & 0xff]; \
+ } while(0)
+
+
+#define s_UpdateCRC32Reverse_1(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint1*)(str); \
+ v ^= (crc); \
+ (crc) = ((crc) >> 8) ^ \
+ (table)[0][v & 0xff]; \
+ } while(0)
+
+#define s_UpdateCRC32Reverse_2(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint2*)(str); \
+ v ^= (crc); \
+ (crc) = ((crc) >> 16) ^ \
+ (table)[1][(v ) & 0xff] ^ \
+ (table)[0][(v>>8) & 0xff]; \
+ } while(0)
+
+#define s_UpdateCRC32Reverse_4(crc, str, table) \
+ do { \
+ Uint4 v = *(const Uint4*)(str); \
+ v ^= (crc); \
+ (crc) = \
+ (table)[3][(v ) & 0xff] ^ \
+ (table)[2][(v>> 8) & 0xff] ^ \
+ (table)[1][(v>>16) & 0xff] ^ \
+ (table)[0][(v>>24) ]; \
+ } while(0)
+
+#define s_UpdateCRC32Reverse_8(crc, str, table) \
+ do { \
+ Uint4 v0 = ((const Uint4*)(str))[0]; \
+ Uint4 v1 = ((const Uint4*)(str))[1]; \
+ v0 ^= (crc); \
+ (crc) = \
+ (table)[7][(v0 ) & 0xff] ^ \
+ (table)[6][(v0>> 8) & 0xff] ^ \
+ (table)[5][(v0>>16) & 0xff] ^ \
+ (table)[4][(v0>>24) ] ^ \
+ (table)[3][(v1 ) & 0xff] ^ \
+ (table)[2][(v1>> 8) & 0xff] ^ \
+ (table)[1][(v1>>16) & 0xff] ^ \
+ (table)[0][(v1>>24) ]; \
+ } while(0)
+
+
+template<size_t kCRC32Tables>
+static inline
+Uint4 s_UpdateCRC32Forward(Uint4 checksum, const char *str, size_t count,
+ const TCRC32Table (&table)[kCRC32Tables])
{
- for ( size_t j = 0; j < count; ++j ) {
- size_t tableIndex = ((checksum >> 24) ^ *str++) & 0xff;
- checksum = (checksum << 8) ^ s_CRC32Table[tableIndex];
+#if TABLES_COUNT >= 2
+ if ( (uintptr_t(str)&1) && count >= 1 ) {
+ s_UpdateCRC32Forward_1(checksum, str, table);
+ count -= 1;
+ str += 1;
+ }
+# if TABLES_COUNT >= 4
+ if ( (uintptr_t(str)&2) && count >= 2 ) {
+ s_UpdateCRC32Forward_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# if TABLES_COUNT >= 8
+ while ( count >= 8 ) {
+ s_UpdateCRC32Forward_8(checksum, str, table);
+ count -= 8;
+ str += 8;
}
+ if ( count >= 4 ) {
+ s_UpdateCRC32Forward_4(checksum, str, table);
+ count -= 4;
+ str += 4;
+ }
+# else // < 8
+ while ( count >= 4 ) {
+ s_UpdateCRC32Forward_4(checksum, str, table);
+ count -= 4;
+ str += 4;
+ }
+# endif // done 4
+ if ( count >= 2 ) {
+ s_UpdateCRC32Forward_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# else // < 4
+ while ( count >= 2 ) {
+ s_UpdateCRC32Forward_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# endif // done 2
+ if ( count ) {
+ s_UpdateCRC32Forward_1(checksum, str, table);
+ }
+#else // < 2
+ while ( count ) {
+ s_UpdateCRC32Forward_1(checksum, str, table);
+ count -= 1;
+ str += 1;
+ }
+#endif // done 1
return checksum;
}
-Uint4 s_UpdateCRC32ZIP(Uint4 checksum, const char *str, size_t count)
+template<size_t kCRC32Tables>
+static inline
+Uint4 s_UpdateCRC32Reverse(Uint4 checksum, const char *str, size_t count,
+ const TCRC32Table (&table)[kCRC32Tables])
{
- for ( size_t j = 0; j < count; ++j ) {
- size_t tableIndex = (checksum ^ *str++) & 0xff;
- checksum = (checksum >> 8) ^ s_CRC32ZIPTable[tableIndex];
+#if TABLES_COUNT >= 2
+ if ( (uintptr_t(str)&1) && count >= 1 ) {
+ s_UpdateCRC32Reverse_1(checksum, str, table);
+ count -= 1;
+ str += 1;
+ }
+# if TABLES_COUNT >= 4
+ if ( (uintptr_t(str)&2) && count >= 2 ) {
+ s_UpdateCRC32Reverse_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# if TABLES_COUNT >= 8
+ while ( count >= 8 ) {
+ s_UpdateCRC32Reverse_8(checksum, str, table);
+ count -= 8;
+ str += 8;
}
+ if ( count >= 4 ) {
+ s_UpdateCRC32Reverse_4(checksum, str, table);
+ count -= 4;
+ str += 4;
+ }
+# else // < 8
+ while ( count >= 4 ) {
+ s_UpdateCRC32Reverse_4(checksum, str, table);
+ count -= 4;
+ str += 4;
+ }
+# endif // done 4
+ if ( count >= 2 ) {
+ s_UpdateCRC32Reverse_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# else // < 4
+ while ( count >= 2 ) {
+ s_UpdateCRC32Reverse_2(checksum, str, table);
+ count -= 2;
+ str += 2;
+ }
+# endif // done 2
+ if ( count ) {
+ s_UpdateCRC32Reverse_1(checksum, str, table);
+ }
+#else // < 2
+ while ( count ) {
+ s_UpdateCRC32Reverse_1(checksum, str, table);
+ count -= 1;
+ str += 1;
+ }
+#endif // done 1
return checksum;
}
+#ifdef USE_CRC32C_INTEL
+
+#if !defined(NCBI_COMPILER_MSVC) && !defined(bit_SSE4_2)
+// our Darwin GCC doesn't have cpuid.h :(
+// we have to reimplement cpuid functionality, luckily it's not too big
+static inline
+void call_cpuid(unsigned level,
+ unsigned* a, unsigned* b, unsigned* c, unsigned* d)
+{
+#if defined(__i386__) && defined(__PIC__)
+ // ebx may be the PIC register and some old GCC versions fail to take care
+ __asm__("xchgl %%ebx, %k1;"
+ "cpuid;"
+ "xchgl %%ebx, %k1;"
+ : "=a" (*a), "=&r" (*b), "=c" (*c), "=d" (*d)
+ : "0" (level));
+#elif defined(__x86_64__) && defined(__PIC__)
+ // rbx may be the PIC register and some old GCC versions fail to take care
+ __asm__("xchgq %%rbx, %q1;"
+ "cpuid;"
+ "xchgq %%rbx, %q1;"
+ : "=a" (*a), "=&r" (*b), "=c" (*c), "=d" (*d)
+ : "0" (level));
+#else
+ __asm__("cpuid"
+ : "=a" (*a), "=b" (*b), "=c" (*c), "=d" (*d)
+ : "0" (level));
+#endif
+}
+static inline
+unsigned get_cpuid_max(unsigned extended)
+{
+ unsigned a, b, c, d;
+#ifdef __i386__
+ // on 32-bit processors we test special flag to check CPUID support
+ const unsigned HAS_CPUID_FLAG = 0x00200000;
+ __asm__(
+ "pushfl;"
+ "pushfl;"
+ "popl %0;"
+ "movl %0, %1;"
+ "xorl %2, %0;"
+ "pushl %0;"
+ "popfl;"
+ "pushfl;"
+ "popl %0;"
+ "popfl;"
+ : "=&r" (a), "=&r" (b)
+ : "i" (HAS_CPUID_FLAG));
+ if ( !((a ^ b) & HAS_CPUID_FLAG) )
+ return 0;
+#endif
+ call_cpuid(extended, &a, &b, &c, &d);
+ return a;
+}
+static inline
+bool get_cpuid(unsigned level,
+ unsigned *a, unsigned *b, unsigned *c, unsigned *d)
+{
+ if ( get_cpuid_max(level & 0x80000000) < level) {
+ return false;
+ }
+ call_cpuid (level, a, b, c, d);
+ return true;
+}
+# define __get_cpuid get_cpuid
+# define bit_SSE4_2 (1<<20)
+#endif
+
+bool s_IsCRC32CIntelEnabled(void)
+{
+ static volatile bool enabled, initialized;
+ if ( !initialized ) {
+#ifdef NCBI_COMPILER_MSVC
+ int a[4];
+ __cpuid(a, 0);
+ if ( a[0] >= 1 ) {
+ __cpuid(a, 1);
+ enabled = (a[2] & (1<<20)) != 0;
+ }
+#else
+ unsigned a, b, c, d;
+ enabled = __get_cpuid(1, &a, &b, &c, &d) && (c & bit_SSE4_2);
+#endif
+ initialized = true;
+ }
+ return enabled;
+}
+
+static inline
+Uint4 s_CRC32C(Uint4 checksum, const char* data)
+{
+#ifdef NCBI_COMPILER_MSVC
+ return _mm_crc32_u8(checksum, *data);
+#else
+ // We cannot rely on _mm_crc32_u8() as it's available only when
+ // -msse4_2 compiler option is specified.
+ __asm__("crc32b %1, %0"
+ : "+r" (checksum)
+ : "m" (*data));
+ return checksum;
+#endif
+}
+
+static inline
+Uint4 s_CRC32C(Uint4 checksum, const Uint2* data)
+{
+#ifdef NCBI_COMPILER_MSVC
+ return _mm_crc32_u16(checksum, *data);
+#else
+ // We cannot rely on _mm_crc32_u16() as it's available only when
+ // -msse4_2 compiler option is specified.
+ __asm__("crc32w %1, %0"
+ : "+r" (checksum)
+ : "m" (*data));
+ return checksum;
+#endif
+}
+
+static inline
+Uint4 s_CRC32C(Uint4 checksum, const Uint4* data)
+{
+#ifdef NCBI_COMPILER_MSVC
+ return _mm_crc32_u32(checksum, *data);
+#else
+ // We cannot rely on _mm_crc32_u32() as it's available only when
+ // -msse4_2 compiler option is specified.
+ __asm__("crc32l %1, %0"
+ : "+r" (checksum)
+ : "m" (*data));
+ return checksum;
+#endif
+}
+
+#ifdef HAVE_CRC32C_64
+static inline
+Uint8 s_CRC32C(Uint8 checksum, const Uint8* data)
+{
+#ifdef NCBI_COMPILER_MSVC
+ return _mm_crc32_u64(checksum, *data);
+#else
+ // We cannot rely on _mm_crc32_u64() as it's available only when
+ // -msse4_2 compiler option is specified.
+ __asm__("crc32q %1, %0"
+ : "+r" (checksum)
+ : "m" (*data));
+#endif
+ return checksum;
+}
+#endif // HAVE_CRC32C_64
+
+static inline
+Uint4 s_UpdateCRC32CIntel(Uint4 checksum, const char *str, size_t count)
+{
+ // Newer Intel CPUs with SSE 4.2 have instructions for CRC32C polynomial.
+ // Since byte order is little-endian on Intel there is no need to bswap.
+
+ // Align buffer
+ if ( (uintptr_t(str)&1) && count >= 1 ) {
+ checksum = s_CRC32C(checksum, str);
+ count -= 1;
+ str += 1;
+ }
+ if ( (uintptr_t(str)&2) && count >= 2 ) {
+ checksum = s_CRC32C(checksum, (const Uint2*)str);
+ count -= 2;
+ str += 2;
+ }
+#ifdef HAVE_CRC32C_64
+ // Main loop processes by 8 bytes
+ if ( count >= 4 ) {
+ if ( (uintptr_t(str)&4) ) {
+ checksum = s_CRC32C(checksum, (const Uint4*)str);
+ count -= 4;
+ str += 4;
+ }
+ Uint8 crc = checksum;
+ while ( count >= 8 ) {
+ crc = s_CRC32C(crc, (const Uint8*)str);
+ count -= 8;
+ str += 8;
+ }
+ checksum = Uint4(crc);
+ if ( count >= 4 ) {
+ checksum = s_CRC32C(checksum, (const Uint4*)str);
+ count -= 4;
+ str += 4;
+ }
+ }
+#else
+ // Main loop processes by 4 bytes
+ while ( count >= 4 ) {
+ checksum = s_CRC32C(checksum, (const Uint4*)str);
+ count -= 4;
+ str += 4;
+ }
+#endif
+ // Process remainder smaller than 8 bytes
+ if ( count >= 2 ) {
+ checksum = s_CRC32C(checksum, (const Uint2*)str);
+ count -= 2;
+ str += 2;
+ }
+ if ( count >= 1 ) {
+ checksum = s_CRC32C(checksum, str);
+ //last count and str updates aren't necessary
+ //count -= 1;
+ //str += 1;
+ }
+ return checksum;
+}
+
+#endif //USE_CRC32C_INTEL
+
+
+static inline
Uint4 s_UpdateAdler32(Uint4 sum, const char* data, size_t len)
{
const Uint4 MOD_ADLER = 65521;
@@ -630,8 +1072,7 @@ Uint4 s_UpdateAdler32(Uint4 sum, const char* data, size_t len)
b += a += Uint1(data[3]);
data += 4;
}
- }
- else {
+ } else {
for ( size_t i = len >> 2; i; --i ) {
b += a += Uint1(data[0]);
b += a += Uint1(data[1]);
@@ -659,13 +1100,68 @@ Uint4 s_UpdateAdler32(Uint4 sum, const char* data, size_t len)
void CChecksum::PrintTables(CNcbiOstream& out)
{
InitTables();
- s_PrintTable(out, "s_CRC32Table", s_CRC32Table, kCRC32Size);
- s_PrintTable(out, "s_CRC32ZIPTable", s_CRC32ZIPTable, kCRC32Size);
+ s_PrintTable(out, "s_CRC32TableForward", s_CRC32TableForward);
+ s_PrintTable(out, "s_CRC32TableReverse", s_CRC32TableReverse);
+ s_PrintTable(out, "s_CRC32CTableReverse", s_CRC32CTableReverse);
+}
+
+
+void CChecksum::x_Update(const char* str, size_t count)
+{
+ switch ( GetMethod() ) {
+ case eCRC32:
+ case eCRC32CKSUM:
+ m_Checksum.m_CRC32 =
+ s_UpdateCRC32Forward(m_Checksum.m_CRC32, str, count, s_CRC32TableForward);
+ break;
+ case eCRC32ZIP:
+ case eCRC32INSD:
+ m_Checksum.m_CRC32 =
+ s_UpdateCRC32Reverse(m_Checksum.m_CRC32, str, count, s_CRC32TableReverse);
+ break;
+ case eCRC32C:
+#ifdef USE_CRC32C_INTEL
+ if ( s_IsCRC32CIntelEnabled() ) {
+ m_Checksum.m_CRC32 =
+ s_UpdateCRC32CIntel(m_Checksum.m_CRC32, str, count);
+ break;
+ }
+#endif
+ m_Checksum.m_CRC32 =
+ s_UpdateCRC32Reverse(m_Checksum.m_CRC32, str, count, s_CRC32CTableReverse);
+ break;
+ case eAdler32:
+ m_Checksum.m_CRC32 = s_UpdateAdler32(m_Checksum.m_CRC32, str, count);
+ break;
+ case eMD5:
+ m_Checksum.m_MD5->Update(str, count);
+ break;
+ default:
+ break;
+ }
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+//
+// CChecksumException
+//
+
+const char* CChecksumException::GetErrCodeString(void) const
+{
+ switch (GetErrCode()) {
+ case eStreamIO: return "eStreamError";
+ case eFileIO: return "eFileError";
+ default: return CException::GetErrCodeString();
+ }
}
/////////////////////////////////////////////////////////////////////////////
+//
// CChecksumStreamWriter
+//
CChecksumStreamWriter::CChecksumStreamWriter(CChecksum::EMethod method)
: m_Checksum(method)
diff --git a/c++/src/util/compress/api/archive_zip.cpp b/c++/src/util/compress/api/archive_zip.cpp
index 205e1df..0ede917 100644
--- a/c++/src/util/compress/api/archive_zip.cpp
+++ b/c++/src/util/compress/api/archive_zip.cpp
@@ -1,4 +1,4 @@
-/* $Id: archive_zip.cpp 430126 2014-03-24 12:25:47Z ivanov $
+/* $Id: archive_zip.cpp 447940 2014-10-01 17:43:28Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -220,6 +220,10 @@ size_t CArchiveZip::GetNumEntries(void)
_ASSERT(m_Mode == eRead);
ZIP_CHECK;
mz_uint n = mz_zip_reader_get_num_files(ZIP_HANDLE);
+ // TODO: remove with zip64 support added to miniz
+ if (n == 65535) {
+ ZIP_THROW(eUnsupported, "Too many files in the archive");
+ }
return n;
}
@@ -447,6 +451,14 @@ void CArchiveZip::TestEntry(const CArchiveEntryInfo& info)
void CArchiveZip::AddEntryFromFileSystem(const CArchiveEntryInfo& info,
const string& src_path, ELevel level)
{
+ // TODO: remove with zip64 support added to miniz
+ {{
+ mz_uint n = mz_zip_reader_get_num_files(ZIP_HANDLE);
+ if (n >= 65534) {
+ ZIP_THROW(eAppend, "Too many files in the archive");
+ }
+ }}
+
const string& comment = info.m_Comment;
mz_uint16 comment_size = (mz_uint16)comment.size();
mz_bool status;
@@ -471,6 +483,14 @@ void CArchiveZip::AddEntryFromFileSystem(const CArchiveEntryInfo& info,
void CArchiveZip::AddEntryFromMemory(const CArchiveEntryInfo& info,
void* buf, size_t size, ELevel level)
{
+ // TODO: remove with zip64 support added to miniz
+ {{
+ mz_uint n = mz_zip_reader_get_num_files(ZIP_HANDLE);
+ if (n >= 65534) {
+ ZIP_THROW(eAppend, "Too many files in the archive");
+ }
+ }}
+
const string& comment = info.m_Comment;
mz_uint16 comment_size = (mz_uint16)comment.size();
mz_bool status;
diff --git a/c++/src/util/compress/api/archive_zip.hpp b/c++/src/util/compress/api/archive_zip.hpp
index 399e61e..1f2d89e 100644
--- a/c++/src/util/compress/api/archive_zip.hpp
+++ b/c++/src/util/compress/api/archive_zip.hpp
@@ -1,7 +1,7 @@
#ifndef UTIL_COMPRESS__ARCHIVE_ZIP__HPP
#define UTIL_COMPRESS__ARCHIVE_ZIP__HPP
-/* $Id: archive_zip.hpp 393401 2013-03-25 16:10:35Z ivanov $
+/* $Id: archive_zip.hpp 448156 2014-10-02 17:22:01Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -31,6 +31,12 @@
* File Description:
* Compression archive API - ZIP file support.
*
+ * Implementation based on 'miniz' v1.16 r1:
+ * https://code.google.com/p/miniz/
+ *
+ * It support zip32 implementation only, no zip64 support yet. The number
+ * of files in the archive limited to 65535.
+ *
*/
/// @file archive_.hpp
diff --git a/c++/src/util/compress/api/miniz/miniz.c b/c++/src/util/compress/api/miniz/miniz.c
index 58a96ea..8042593 100644
--- a/c++/src/util/compress/api/miniz/miniz.c
+++ b/c++/src/util/compress/api/miniz/miniz.c
@@ -1,33 +1,69 @@
-/* miniz.c v1.14 - public domain deflate/inflate, zlib-subset, ZIP reading/writing/appending, PNG writing
+/* miniz.c v1.16 beta r1 - public domain deflate/inflate, zlib-subset, ZIP reading/writing/appending, PNG writing
See "unlicense" statement at the end of this file.
- Rich Geldreich <richgel99 at gmail.com>, last updated May 20, 2012
+ Rich Geldreich <richgel99 at gmail.com>, last updated Oct. 13, 2013
Implements RFC 1950: http://www.ietf.org/rfc/rfc1950.txt and RFC 1951: http://www.ietf.org/rfc/rfc1951.txt
Most API's defined in miniz.c are optional. For example, to disable the archive related functions just define
MINIZ_NO_ARCHIVE_APIS, or to get rid of all stdio usage define MINIZ_NO_STDIO (see the list below for more macros).
* Change History
+ 10/19/13 v1.16 beta r1 - Two key inflator-only robustness and streaming related changes. Also merged in tdefl_compressor_alloc(), tdefl_compressor_free() helpers to make script bindings easier for rustyzip.
+ - The inflator coroutine func. is subtle and complex so I'm being cautious about this release. I would greatly appreciate any help with testing or any feedback.
+ I feel good about these changes, and they've been through several hours of automated testing, but they will probably not fix anything for the majority of prev. users so I'm
+ going to mark this release as beta for a few weeks and continue testing it at work/home on various things.
+ - The inflator in raw (non-zlib) mode is now usable on gzip or similiar data streams that have a bunch of bytes following the raw deflate data (problem discovered by rustyzip author williamw520).
+ This version should *never* read beyond the last byte of the raw deflate data independent of how many bytes you pass into the input buffer. This issue was caused by the various Huffman bitbuffer lookahead optimizations, and
+ would not be an issue if the caller knew and enforced the precise size of the raw compressed data *or* if the compressed data was in zlib format (i.e. always followed by the byte aligned zlib adler32).
+ So in other words, you can now call the inflator on deflate streams that are followed by arbitrary amounts of data and it's guaranteed that decompression will stop exactly on the last byte.
+ - The inflator now has a new failure status: TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS (-4). Previously, if the inflator was starved of bytes and could not make progress (because the input buffer was empty and the
+ caller did not set the TINFL_FLAG_HAS_MORE_INPUT flag - say on truncated or corrupted compressed data stream) it would append all 0's to the input and try to soldier on.
+ This is scary, because in the worst case, I believe it was possible for the prev. inflator to start outputting large amounts of literal data. If the caller didn't know when to stop accepting output
+ (because it didn't know how much uncompressed data was expected, or didn't enforce a sane maximum) it could continue forever. v1.16 cannot fall into this failure mode, instead it'll return
+ TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS immediately if it needs 1 or more bytes to make progress, the input buf is empty, and the caller has indicated that no more input is available. This is a "soft"
+ failure, so you can call the inflator again with more input and it will try to continue, or you can give up and fail. This could be very useful in network streaming scenarios.
+ - Added documentation to all the tinfl return status codes, fixed miniz_tester so it accepts double minus params for Linux, tweaked example1.c, added a simple "follower bytes" test to miniz_tester.cpp.
+ 10/13/13 v1.15 r4 - Interim bugfix release while I work on the next major release with Zip64 support (almost there!):
+ - Critical fix for the MZ_ZIP_FLAG_DO_NOT_SORT_CENTRAL_DIRECTORY bug (thanks kahmyong.moon at hp.com) which could cause locate files to not find files. This bug
+ would only have occured in earlier versions if you explicitly used this flag, OR if you used mz_zip_extract_archive_file_to_heap() or mz_zip_add_mem_to_archive_file_in_place()
+ (which used this flag). If you can't switch to v1.15 but want to fix this bug, just remove the uses of this flag from both helper funcs (and of course don't use the flag).
+ - Bugfix in mz_zip_reader_extract_to_mem_no_alloc() from kymoon when pUser_read_buf is not NULL and compressed size is > uncompressed size
+ - Fixing mz_zip_reader_extract_*() funcs so they don't try to extract compressed data from directory entries, to account for weird zipfiles which contain zero-size compressed data on dir entries.
+ Hopefully this fix won't cause any issues on weird zip archives, because it assumes the low 16-bits of zip external attributes are DOS attributes (which I believe they always are in practice).
+ - Fixing mz_zip_reader_is_file_a_directory() so it doesn't check the internal attributes, just the filename and external attributes
+ - mz_zip_reader_init_file() - missing MZ_FCLOSE() call if the seek failed
+ - Added cmake support for Linux builds which builds all the examples, tested with clang v3.3 and gcc v4.6.
+ - Clang fix for tdefl_write_image_to_png_file_in_memory() from toffaletti
+ - Merged MZ_FORCEINLINE fix from hdeanclark
+ - Fix <time.h> include before config #ifdef, thanks emil.brink
+ - Added tdefl_write_image_to_png_file_in_memory_ex(): supports Y flipping (super useful for OpenGL apps), and explicit control over the compression level (so you can
+ set it to 1 for real-time compression).
+ - Merged in some compiler fixes from paulharris's github repro.
+ - Retested this build under Windows (VS 2010, including static analysis), tcc 0.9.26, gcc v4.6 and clang v3.3.
+ - Added example6.c, which dumps an image of the mandelbrot set to a PNG file.
+ - Modified example2 to help test the MZ_ZIP_FLAG_DO_NOT_SORT_CENTRAL_DIRECTORY flag more.
+ - In r3: Bugfix to mz_zip_writer_add_file() found during merge: Fix possible src file fclose() leak if alignment bytes+local header file write faiiled
+ - In r4: Minor bugfix to mz_zip_writer_add_from_zip_reader(): Was pushing the wrong central dir header offset, appears harmless in this release, but it became a problem in the zip64 branch
5/20/12 v1.14 - MinGW32/64 GCC 4.6.1 compiler fixes: added MZ_FORCEINLINE, #include <time.h> (thanks fermtect).
5/19/12 v1.13 - From jason at cornsyrup.org and kelwert at mtu.edu - Fix mz_crc32() so it doesn't compute the wrong CRC-32's when mz_ulong is 64-bit.
- Temporarily/locally slammed in "typedef unsigned long mz_ulong" and re-ran a randomized regression test on ~500k files.
- Eliminated a bunch of warnings when compiling with GCC 32-bit/64.
- Ran all examples, miniz.c, and tinfl.c through MSVC 2008's /analyze (static analysis) option and fixed all warnings (except for the silly
- "Use of the comma-operator in a tested expression.." analysis warning, which I purposely use to work around a MSVC compiler warning).
- Created 32-bit and 64-bit Codeblocks projects/workspace. Built and tested Linux executables. The codeblocks workspace is compatible with Linux+Win32/x64.
- Added miniz_tester solution/project, which is a useful little app derived from LZHAM's tester app that I use as part of the regression test.
- Ran miniz.c and tinfl.c through another series of regression testing on ~500,000 files and archives.
- Modified example5.c so it purposely disables a bunch of high-level functionality (MINIZ_NO_STDIO, etc.). (Thanks to corysama for the MINIZ_NO_STDIO bug report.)
- Fix ftell() usage in examples so they exit with an error on files which are too large (a limitation of the examples, not miniz itself).
+ - Temporarily/locally slammed in "typedef unsigned long mz_ulong" and re-ran a randomized regression test on ~500k files.
+ - Eliminated a bunch of warnings when compiling with GCC 32-bit/64.
+ - Ran all examples, miniz.c, and tinfl.c through MSVC 2008's /analyze (static analysis) option and fixed all warnings (except for the silly
+ "Use of the comma-operator in a tested expression.." analysis warning, which I purposely use to work around a MSVC compiler warning).
+ - Created 32-bit and 64-bit Codeblocks projects/workspace. Built and tested Linux executables. The codeblocks workspace is compatible with Linux+Win32/x64.
+ - Added miniz_tester solution/project, which is a useful little app derived from LZHAM's tester app that I use as part of the regression test.
+ - Ran miniz.c and tinfl.c through another series of regression testing on ~500,000 files and archives.
+ - Modified example5.c so it purposely disables a bunch of high-level functionality (MINIZ_NO_STDIO, etc.). (Thanks to corysama for the MINIZ_NO_STDIO bug report.)
+ - Fix ftell() usage in examples so they exit with an error on files which are too large (a limitation of the examples, not miniz itself).
4/12/12 v1.12 - More comments, added low-level example5.c, fixed a couple minor level_and_flags issues in the archive API's.
level_and_flags can now be set to MZ_DEFAULT_COMPRESSION. Thanks to Bruce Dawson <bruced at valvesoftware.com> for the feedback/bug report.
5/28/11 v1.11 - Added statement from unlicense.org
5/27/11 v1.10 - Substantial compressor optimizations:
- Level 1 is now ~4x faster than before. The L1 compressor's throughput now varies between 70-110MB/sec. on a
- Core i7 (actual throughput varies depending on the type of data, and x64 vs. x86).
- Improved baseline L2-L9 compression perf. Also, greatly improved compression perf. issues on some file types.
- Refactored the compression code for better readability and maintainability.
- Added level 10 compression level (L10 has slightly better ratio than level 9, but could have a potentially large
- drop in throughput on some files).
+ - Level 1 is now ~4x faster than before. The L1 compressor's throughput now varies between 70-110MB/sec. on a
+ - Core i7 (actual throughput varies depending on the type of data, and x64 vs. x86).
+ - Improved baseline L2-L9 compression perf. Also, greatly improved compression perf. issues on some file types.
+ - Refactored the compression code for better readability and maintainability.
+ - Added level 10 compression level (L10 has slightly better ratio than level 9, but could have a potentially large
+ drop in throughput on some files).
5/15/11 v1.09 - Initial stable release.
* Low-level Deflate/Inflate implementation notes:
@@ -129,6 +165,10 @@
#define MINIZ_USE_UNALIGNED_LOADS_AND_STORES 1
#define MINIZ_LITTLE_ENDIAN 1
#define MINIZ_HAS_64BIT_REGISTERS 1
+
+ * On platforms using glibc, Be sure to "#define _LARGEFILE64_SOURCE 1" before including miniz.c to ensure miniz
+ uses the 64-bit variants: fopen64(), stat64(), etc. Otherwise you won't be able to process large files
+ (i.e. 32-bit stat() fails for me on files > 0x7FFFFFFF bytes).
*/
#ifndef MINIZ_HEADER_INCLUDED
@@ -136,10 +176,6 @@
#include <stdlib.h>
-#if !defined(MINIZ_NO_TIME) && !defined(MINIZ_NO_ARCHIVE_APIS)
-#include <time.h>
-#endif
-
// Defines to completely disable specific portions of miniz.c:
// If all macros here are defined the only functionality remaining will be CRC-32, adler-32, tinfl, and tdefl.
@@ -147,7 +183,8 @@
//#define MINIZ_NO_STDIO
// If MINIZ_NO_TIME is specified then the ZIP archive functions will not be able to get the current time, or
-// get/set file times.
+// get/set file times, and the C run-time funcs that get/set times won't be called.
+// The current downside is the times written to your archives will be from 1979.
//#define MINIZ_NO_TIME
// Define MINIZ_NO_ARCHIVE_APIS to disable all ZIP archive API's.
@@ -157,7 +194,7 @@
//#define MINIZ_NO_ARCHIVE_WRITING_APIS
// Define MINIZ_NO_ZLIB_APIS to remove all ZLIB-style compression/decompression API's.
-// #define MINIZ_NO_ZLIB_APIS
+//#define MINIZ_NO_ZLIB_APIS
// Define MINIZ_NO_ZLIB_COMPATIBLE_NAME to disable zlib names, to prevent conflicts against stock zlib.
//#define MINIZ_NO_ZLIB_COMPATIBLE_NAMES
@@ -168,6 +205,15 @@
// functions (such as tdefl_compress_mem_to_heap() and tinfl_decompress_mem_to_heap()) won't work.
//#define MINIZ_NO_MALLOC
+#if defined(__TINYC__) && (defined(__linux) || defined(__linux__))
+ // TODO: Work around "error: include file 'sys\utime.h' when compiling with tcc on Linux
+ #define MINIZ_NO_TIME
+#endif
+
+#if !defined(MINIZ_NO_TIME) && !defined(MINIZ_NO_ARCHIVE_APIS)
+ #include <time.h>
+#endif
+
#if defined(_M_IX86) || defined(_M_X64) || defined(__i386__) || defined(__i386) || defined(__i486__) || defined(__i486) || defined(i386) || defined(__ia64__) || defined(__x86_64__)
// MINIZ_X86_OR_X64_CPU is only used to help set the below macros.
#define MINIZ_X86_OR_X64_CPU 1
@@ -197,11 +243,8 @@ extern "C" {
// For more compatibility with zlib, miniz.c uses unsigned long for some parameters/struct members. Beware: mz_ulong can be either 32 or 64-bits!
typedef unsigned long mz_ulong;
-// Heap allocation callbacks.
-// Note that mz_alloc_func parameter types purpsosely differ from zlib's: items/size is size_t, not unsigned long.
-typedef void *(*mz_alloc_func)(void *opaque, size_t items, size_t size);
-typedef void (*mz_free_func)(void *opaque, void *address);
-typedef void *(*mz_realloc_func)(void *opaque, void *address, size_t items, size_t size);
+// mz_free() internally uses the MZ_FREE() macro (which by default calls free() unless you've modified the MZ_MALLOC macro) to release a block allocated from the heap.
+void mz_free(void *p);
#define MZ_ADLER32_INIT (1)
// mz_adler32() returns the initial adler-32 value to use when called with ptr==NULL.
@@ -219,11 +262,18 @@ enum { MZ_DEFAULT_STRATEGY = 0, MZ_FILTERED = 1, MZ_HUFFMAN_ONLY = 2, MZ_RLE = 3
#ifndef MINIZ_NO_ZLIB_APIS
-#define MZ_VERSION "9.1.14"
-#define MZ_VERNUM 0x91E0
+// Heap allocation callbacks.
+// Note that mz_alloc_func parameter types purpsosely differ from zlib's: items/size is size_t, not unsigned long.
+typedef void *(*mz_alloc_func)(void *opaque, size_t items, size_t size);
+typedef void (*mz_free_func)(void *opaque, void *address);
+typedef void *(*mz_realloc_func)(void *opaque, void *address, size_t items, size_t size);
+
+// TODO: I can't encode "1.16" here, argh
+#define MZ_VERSION "9.1.15"
+#define MZ_VERNUM 0x91F0
#define MZ_VER_MAJOR 9
#define MZ_VER_MINOR 1
-#define MZ_VER_REVISION 14
+#define MZ_VER_REVISION 15
#define MZ_VER_SUBREVISION 0
// Flush values. For typical usage you only need MZ_NO_FLUSH and MZ_FINISH. The other values are for advanced use (refer to the zlib docs).
@@ -444,7 +494,7 @@ typedef int mz_bool;
#define MZ_FALSE (0)
#define MZ_TRUE (1)
-// Works around MSVC's spammy "warning C4127: conditional expression is constant" message.
+// An attempt to work around MSVC's spammy "warning C4127: conditional expression is constant" message.
#ifdef _MSC_VER
#define MZ_MACRO_END while (0, 0)
#else
@@ -498,7 +548,7 @@ typedef enum
MZ_ZIP_MODE_WRITING_HAS_BEEN_FINALIZED = 3
} mz_zip_mode;
-typedef struct
+typedef struct mz_zip_archive_tag
{
mz_uint64 m_archive_size;
mz_uint64 m_central_directory_file_ofs;
@@ -666,7 +716,7 @@ enum
// On return:
// Function returns a pointer to the decompressed data, or NULL on failure.
// *pOut_len will be set to the decompressed data's size, which could be larger than src_buf_len on uncompressible data.
-// The caller must free() the returned block when it's no longer needed.
+// The caller must call mz_free() on the returned block when it's no longer needed.
void *tinfl_decompress_mem_to_heap(const void *pSrc_buf, size_t src_buf_len, size_t *pOut_len, int flags);
// tinfl_decompress_mem_to_mem() decompresses a block in memory to another block in memory.
@@ -687,12 +737,37 @@ struct tinfl_decompressor_tag; typedef struct tinfl_decompressor_tag tinfl_decom
// Return status.
typedef enum
{
+ // This flags indicates the inflator needs 1 or more input bytes to make forward progress, but the caller is indicating that no more are available. The compressed data
+ // is probably corrupted. If you call the inflator again with more bytes it'll try to continue processing the input but this is a BAD sign (either the data is corrupted or you called it incorrectly).
+ // If you call it again with no input you'll just get TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS again.
+ TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS = -4,
+
+ // This flag indicates that one or more of the input parameters was obviously bogus. (You can try calling it again, but if you get this error the calling code is wrong.)
TINFL_STATUS_BAD_PARAM = -3,
+
+ // This flags indicate the inflator is finished but the adler32 check of the uncompressed data didn't match. If you call it again it'll return TINFL_STATUS_DONE.
TINFL_STATUS_ADLER32_MISMATCH = -2,
+
+ // This flags indicate the inflator has somehow failed (bad code, corrupted input, etc.). If you call it again without resetting via tinfl_init() it it'll just keep on returning the same status failure code.
TINFL_STATUS_FAILED = -1,
+
+ // Any status code less than TINFL_STATUS_DONE must indicate a failure.
+
+ // This flag indicates the inflator has returned every byte of uncompressed data that it can, has consumed every byte that it needed, has successfully reached the end of the deflate stream, and
+ // if zlib headers and adler32 checking enabled that it has successfully checked the uncompressed data's adler32. If you call it again you'll just get TINFL_STATUS_DONE over and over again.
TINFL_STATUS_DONE = 0,
+
+ // This flag indicates the inflator MUST have more input data (even 1 byte) before it can make any more forward progress, or you need to clear the TINFL_FLAG_HAS_MORE_INPUT
+ // flag on the next call if you don't have any more source data. If the source data was somehow corrupted it's also possible (but unlikely) for the inflator to keep on demanding input to
+ // proceed, so be sure to properly set the TINFL_FLAG_HAS_MORE_INPUT flag.
TINFL_STATUS_NEEDS_MORE_INPUT = 1,
+
+ // This flag indicates the inflator definitely has 1 or more bytes of uncompressed data available, but it cannot write this data into the output buffer.
+ // Note if the source compressed data was corrupted it's possible for the inflator to return a lot of uncompressed data to the caller. I've been assuming you know how much uncompressed data to expect
+ // (either exact or worst case) and will stop calling the inflator and fail after receiving too much. In pure streaming scenarios where you have no idea how many bytes to expect this may not be possible
+ // so I may need to add some code to address this.
TINFL_STATUS_HAS_MORE_OUTPUT = 2
+
} tinfl_status;
// Initializes the decompressor to its initial state.
@@ -757,6 +832,7 @@ enum
// TDEFL_FILTER_MATCHES: Discards matches <= 5 chars if enabled.
// TDEFL_FORCE_ALL_STATIC_BLOCKS: Disable usage of optimized Huffman tables.
// TDEFL_FORCE_ALL_RAW_BLOCKS: Only use raw (uncompressed) deflate blocks.
+// The low 12 bits are reserved to control the max # of hash probes per dictionary lookup (see TDEFL_MAX_PROBES_MASK).
enum
{
TDEFL_WRITE_ZLIB_HEADER = 0x01000,
@@ -786,11 +862,15 @@ size_t tdefl_compress_mem_to_mem(void *pOut_buf, size_t out_buf_len, const void
// Compresses an image to a compressed PNG file in memory.
// On entry:
-// pImage, w, h, and num_chans describe the image to compress. num_chans may be 1, 2, 3, or 4.
+// pImage, w, h, and num_chans describe the image to compress. num_chans may be 1, 2, 3, or 4.
+// The image pitch in bytes per scanline will be w*num_chans. The leftmost pixel on the top scanline is stored first in memory.
+// level may range from [0,10], use MZ_NO_COMPRESSION, MZ_BEST_SPEED, MZ_BEST_COMPRESSION, etc. or a decent default is MZ_DEFAULT_LEVEL
+// If flip is true, the image will be flipped on the Y axis (useful for OpenGL apps).
// On return:
// Function returns a pointer to the compressed data, or NULL on failure.
// *pLen_out will be set to the size of the PNG image file.
-// The caller must free() the returned heap block (which will typically be larger than *pLen_out) when it's no longer needed.
+// The caller must mz_free() the returned heap block (which will typically be larger than *pLen_out) when it's no longer needed.
+void *tdefl_write_image_to_png_file_in_memory_ex(const void *pImage, int w, int h, int num_chans, size_t *pLen_out, mz_uint level, mz_bool flip);
void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h, int num_chans, size_t *pLen_out);
// Output stream interface. The compressor uses this interface to write compressed data. It'll typically be called TDEFL_OUT_BUF_SIZE at a time.
@@ -880,6 +960,14 @@ mz_uint32 tdefl_get_adler32(tdefl_compressor *d);
mz_uint tdefl_create_comp_flags_from_zip_params(int level, int window_bits, int strategy);
#endif // #ifndef MINIZ_NO_ZLIB_APIS
+// Allocate the tdefl_compressor and tinfl_decompressor structures in C so that
+// non-C language bindings to tdefl_ and tinfl_ API don't need to worry about
+// structure size and allocation mechanism.
+tdefl_compressor *tdefl_compressor_alloc();
+void tdefl_compressor_free(tdefl_compressor *pComp);
+tinfl_decompressor *tinfl_decompressor_alloc();
+void tinfl_decompressor_free(tinfl_decompressor *pDecomp);
+
#ifdef __cplusplus
}
#endif
@@ -924,7 +1012,7 @@ typedef unsigned char mz_validate_uint64[sizeof(mz_uint64)==8 ? 1 : -1];
#ifdef _MSC_VER
#define MZ_FORCEINLINE __forceinline
#elif defined(__GNUC__)
- #define MZ_FORCEINLINE __attribute__((__always_inline__))
+ #define MZ_FORCEINLINE inline __attribute__((__always_inline__))
#else
#define MZ_FORCEINLINE inline
#endif
@@ -961,6 +1049,11 @@ mz_ulong mz_crc32(mz_ulong crc, const mz_uint8 *ptr, size_t buf_len)
return ~crcu32;
}
+void mz_free(void *p)
+{
+ MZ_FREE(p);
+}
+
#ifndef MINIZ_NO_ZLIB_APIS
static void *def_alloc_func(void *opaque, size_t items, size_t size) { (void)opaque, (void)items, (void)size; return MZ_MALLOC(items * size); }
@@ -1321,23 +1414,10 @@ const char *mz_error(int err)
#define TINFL_CR_RETURN_FOREVER(state_index, result) do { for ( ; ; ) { TINFL_CR_RETURN(state_index, result); } } MZ_MACRO_END
#define TINFL_CR_FINISH }
-// TODO: If the caller has indicated that there's no more input, and we attempt to read beyond the input buf, then something is wrong with the input because the inflator never
-// reads ahead more than it needs to. Currently TINFL_GET_BYTE() pads the end of the stream with 0's in this scenario.
#define TINFL_GET_BYTE(state_index, c) do { \
- if (pIn_buf_cur >= pIn_buf_end) { \
- for ( ; ; ) { \
- if (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) { \
- TINFL_CR_RETURN(state_index, TINFL_STATUS_NEEDS_MORE_INPUT); \
- if (pIn_buf_cur < pIn_buf_end) { \
- c = *pIn_buf_cur++; \
- break; \
- } \
- } else { \
- c = 0; \
- break; \
- } \
- } \
- } else c = *pIn_buf_cur++; } MZ_MACRO_END
+ while (pIn_buf_cur >= pIn_buf_end) { \
+ TINFL_CR_RETURN(state_index, (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) ? TINFL_STATUS_NEEDS_MORE_INPUT : TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS); \
+ } c = *pIn_buf_cur++; } MZ_MACRO_END
#define TINFL_NEED_BITS(state_index, n) do { mz_uint c; TINFL_GET_BYTE(state_index, c); bit_buf |= (((tinfl_bit_buf_t)c) << num_bits); num_bits += 8; } while (num_bits < (mz_uint)(n))
#define TINFL_SKIP_BITS(state_index, n) do { if (num_bits < (mz_uint)(n)) { TINFL_NEED_BITS(state_index, n); } bit_buf >>= (n); num_bits -= (n); } MZ_MACRO_END
@@ -1366,6 +1446,8 @@ const char *mz_error(int err)
// beyond the final byte of the deflate stream. (In other words, when this macro wants to read another byte from the input, it REALLY needs another byte in order to fully
// decode the next Huffman code.) Handling this properly is particularly important on raw deflate (non-zlib) streams, which aren't followed by a byte aligned adler-32.
// The slow path is only executed at the very end of the input buffer.
+// v1.16: The original macro handled the case at the very end of the passed-in input buffer, but we also need to handle the case where the user passes in 1+zillion bytes
+// following the deflate data and our non-conservative read-ahead path won't kick in here on this code. This is much trickier.
#define TINFL_HUFF_DECODE(state_index, sym, pHuff) do { \
int temp; mz_uint code_len, c; \
if (num_bits < 15) { \
@@ -1430,14 +1512,7 @@ tinfl_status tinfl_decompress(tinfl_decompressor *r, const mz_uint8 *pIn_buf_nex
size_t n; while (pOut_buf_cur >= pOut_buf_end) { TINFL_CR_RETURN(9, TINFL_STATUS_HAS_MORE_OUTPUT); }
while (pIn_buf_cur >= pIn_buf_end)
{
- if (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT)
- {
- TINFL_CR_RETURN(38, TINFL_STATUS_NEEDS_MORE_INPUT);
- }
- else
- {
- TINFL_CR_RETURN_FOREVER(40, TINFL_STATUS_FAILED);
- }
+ TINFL_CR_RETURN(38, (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) ? TINFL_STATUS_NEEDS_MORE_INPUT : TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS);
}
n = MZ_MIN(MZ_MIN((size_t)(pOut_buf_end - pOut_buf_cur), (size_t)(pIn_buf_end - pIn_buf_cur)), counter);
TINFL_MEMCPY(pOut_buf_cur, pIn_buf_cur, n); pIn_buf_cur += n; pOut_buf_cur += n; counter -= (mz_uint)n;
@@ -1624,15 +1699,27 @@ tinfl_status tinfl_decompress(tinfl_decompressor *r, const mz_uint8 *pIn_buf_nex
}
}
} while (!(r->m_final & 1));
+
+ // Ensure byte alignment and put back any bytes from the bitbuf if we've looked ahead too far on gzip, or other Deflate streams followed by arbitrary data.
+ // I'm being super conservative here. A number of simplifications can be made to the byte alignment part, and the Adler32 check shouldn't ever need to worry about reading from the bitbuf now.
+ TINFL_SKIP_BITS(32, num_bits & 7);
+ while ((pIn_buf_cur > pIn_buf_next) && (num_bits >= 8)) { --pIn_buf_cur; num_bits -= 8; } bit_buf &= (tinfl_bit_buf_t)((1ULL << num_bits) - 1ULL);
+ MZ_ASSERT(!num_bits); // if this assert fires then we've read beyond the end of non-deflate/zlib streams with following data (such as gzip streams).
+
if (decomp_flags & TINFL_FLAG_PARSE_ZLIB_HEADER)
{
- TINFL_SKIP_BITS(32, num_bits & 7); for (counter = 0; counter < 4; ++counter) { mz_uint s; if (num_bits) TINFL_GET_BITS(41, s, 8); else TINFL_GET_BYTE(42, s); r->m_z_adler32 = (r->m_z_adler32 << 8) | s; }
+ for (counter = 0; counter < 4; ++counter) { mz_uint s; if (num_bits) TINFL_GET_BITS(41, s, 8); else TINFL_GET_BYTE(42, s); r->m_z_adler32 = (r->m_z_adler32 << 8) | s; }
}
TINFL_CR_RETURN_FOREVER(34, TINFL_STATUS_DONE);
+
TINFL_CR_FINISH
common_exit:
- r->m_num_bits = num_bits; r->m_bit_buf = bit_buf; r->m_dist = dist; r->m_counter = counter; r->m_num_extra = num_extra; r->m_dist_from_out_buf_start = dist_from_out_buf_start;
+ // As long as we aren't telling the caller that we NEED more input to make forward progress:
+ // Put back any bytes from the bitbuf in case we've looked ahead too far on gzip, or other Deflate streams followed by arbitrary data.
+ // We need to be very careful here to NOT push back any bytes we definitely know we need to make forward progress, though, or we'll lock the caller up into an inf loop.
+ if ((status != TINFL_STATUS_NEEDS_MORE_INPUT) && (status != TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS)) { while ((pIn_buf_cur > pIn_buf_next) && (num_bits >= 8)) { --pIn_buf_cur; num_bits -= 8; } }
+ r->m_num_bits = num_bits; r->m_bit_buf = bit_buf & (tinfl_bit_buf_t)((1ULL << num_bits) - 1ULL); r->m_dist = dist; r->m_counter = counter; r->m_num_extra = num_extra; r->m_dist_from_out_buf_start = dist_from_out_buf_start;
*pIn_buf_size = pIn_buf_cur - pIn_buf_next; *pOut_buf_size = pOut_buf_cur - pOut_buf_next;
if ((decomp_flags & (TINFL_FLAG_PARSE_ZLIB_HEADER | TINFL_FLAG_COMPUTE_ADLER32)) && (status >= 0))
{
@@ -2754,22 +2841,26 @@ mz_uint tdefl_create_comp_flags_from_zip_params(int level, int window_bits, int
// Simple PNG writer function by Alex Evans, 2011. Released into the public domain: https://gist.github.com/908299, more context at
// http://altdevblogaday.org/2011/04/06/a-smaller-jpg-encoder/.
-void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h, int num_chans, size_t *pLen_out)
+// This is actually a modification of Alex's original code so PNG files generated by this function pass pngcheck.
+void *tdefl_write_image_to_png_file_in_memory_ex(const void *pImage, int w, int h, int num_chans, size_t *pLen_out, mz_uint level, mz_bool flip)
{
+ // Using a local copy of this array here in case MINIZ_NO_ZLIB_APIS was defined.
+ static const mz_uint s_tdefl_png_num_probes[11] = { 0, 1, 6, 32, 16, 32, 128, 256, 512, 768, 1500 };
tdefl_compressor *pComp = (tdefl_compressor *)MZ_MALLOC(sizeof(tdefl_compressor)); tdefl_output_buffer out_buf; int i, bpl = w * num_chans, y, z; mz_uint32 c; *pLen_out = 0;
if (!pComp) return NULL;
MZ_CLEAR_OBJ(out_buf); out_buf.m_expandable = MZ_TRUE; out_buf.m_capacity = 57+MZ_MAX(64, (1+bpl)*h); if (NULL == (out_buf.m_pBuf = (mz_uint8*)MZ_MALLOC(out_buf.m_capacity))) { MZ_FREE(pComp); return NULL; }
// write dummy header
for (z = 41; z; --z) tdefl_output_buffer_putter(&z, 1, &out_buf);
// compress image data
- tdefl_init(pComp, tdefl_output_buffer_putter, &out_buf, TDEFL_DEFAULT_MAX_PROBES | TDEFL_WRITE_ZLIB_HEADER);
- for (y = 0; y < h; ++y) { tdefl_compress_buffer(pComp, &z, 1, TDEFL_NO_FLUSH); tdefl_compress_buffer(pComp, (mz_uint8*)pImage + y * bpl, bpl, TDEFL_NO_FLUSH); }
+ tdefl_init(pComp, tdefl_output_buffer_putter, &out_buf, s_tdefl_png_num_probes[MZ_MIN(10, level)] | TDEFL_WRITE_ZLIB_HEADER);
+ for (y = 0; y < h; ++y) { tdefl_compress_buffer(pComp, &z, 1, TDEFL_NO_FLUSH); tdefl_compress_buffer(pComp, (mz_uint8*)pImage + (flip ? (h - 1 - y) : y) * bpl, bpl, TDEFL_NO_FLUSH); }
if (tdefl_compress_buffer(pComp, NULL, 0, TDEFL_FINISH) != TDEFL_STATUS_DONE) { MZ_FREE(pComp); MZ_FREE(out_buf.m_pBuf); return NULL; }
// write real header
*pLen_out = out_buf.m_size-41;
{
+ static const mz_uint8 chans[] = {0x00, 0x00, 0x04, 0x02, 0x06};
mz_uint8 pnghdr[41]={0x89,0x50,0x4e,0x47,0x0d,0x0a,0x1a,0x0a,0x00,0x00,0x00,0x0d,0x49,0x48,0x44,0x52,
- 0,0,(mz_uint8)(w>>8),(mz_uint8)w,0,0,(mz_uint8)(h>>8),(mz_uint8)h,8,(mz_uint8)("\0\0\04\02\06"[num_chans]),0,0,0,0,0,0,0,
+ 0,0,(mz_uint8)(w>>8),(mz_uint8)w,0,0,(mz_uint8)(h>>8),(mz_uint8)h,8,chans[num_chans],0,0,0,0,0,0,0,
(mz_uint8)(*pLen_out>>24),(mz_uint8)(*pLen_out>>16),(mz_uint8)(*pLen_out>>8),(mz_uint8)*pLen_out,0x49,0x44,0x41,0x54};
c=(mz_uint32)mz_crc32(MZ_CRC32_INIT,pnghdr+12,17); for (i=0; i<4; ++i, c<<=8) ((mz_uint8*)(pnghdr+29))[i]=(mz_uint8)(c>>24);
memcpy(out_buf.m_pBuf, pnghdr, 41);
@@ -2781,6 +2872,38 @@ void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h,
*pLen_out += 57; MZ_FREE(pComp); return out_buf.m_pBuf;
}
+void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h, int num_chans, size_t *pLen_out)
+{
+ // Level 6 corresponds to TDEFL_DEFAULT_MAX_PROBES or MZ_DEFAULT_LEVEL (but we can't depend on MZ_DEFAULT_LEVEL being available in case the zlib API's where #defined out)
+ return tdefl_write_image_to_png_file_in_memory_ex(pImage, w, h, num_chans, pLen_out, 6, MZ_FALSE);
+}
+
+// Allocate the tdefl_compressor and tinfl_decompressor structures in C so that
+// non-C language bindings to tdefL_ and tinfl_ API don't need to worry about
+// structure size and allocation mechanism.
+tdefl_compressor *tdefl_compressor_alloc()
+{
+ return (tdefl_compressor *)MZ_MALLOC(sizeof(tdefl_compressor));
+}
+
+void tdefl_compressor_free(tdefl_compressor* pComp)
+{
+ MZ_FREE(pComp);
+}
+
+tinfl_decompressor *tinfl_decompressor_alloc()
+{
+ tinfl_decompressor *pDecomp = (tinfl_decompressor *)MZ_MALLOC(sizeof(tinfl_decompressor));
+ if (pDecomp)
+ tinfl_init(pDecomp);
+ return pDecomp;
+}
+
+void tinfl_decompressor_free(tinfl_decompressor *pDecomp)
+{
+ MZ_FREE(pDecomp);
+}
+
#ifdef _MSC_VER
#pragma warning (pop)
#endif
@@ -2794,10 +2917,26 @@ void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h,
#else
#include <stdio.h>
#include <sys/stat.h>
+
#if defined(_MSC_VER) || defined(__MINGW64__)
- #include <sys/utime.h>
+ static FILE *mz_fopen(const char *pFilename, const char *pMode)
+ {
+ FILE* pFile = NULL;
+ fopen_s(&pFile, pFilename, pMode);
+ return pFile;
+ }
+ static FILE *mz_freopen(const char *pPath, const char *pMode, FILE *pStream)
+ {
+ FILE* pFile = NULL;
+ if (freopen_s(&pFile, pPath, pMode, pStream))
+ return NULL;
+ return pFile;
+ }
+ #ifndef MINIZ_NO_TIME
+ #include <sys/utime.h>
+ #endif
#define MZ_FILE FILE
- #define MZ_FOPEN fopen
+ #define MZ_FOPEN mz_fopen
#define MZ_FCLOSE fclose
#define MZ_FREAD fread
#define MZ_FWRITE fwrite
@@ -2806,12 +2945,14 @@ void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h,
#define MZ_FILE_STAT_STRUCT _stat
#define MZ_FILE_STAT _stat
#define MZ_FFLUSH fflush
- #define MZ_FREOPEN freopen
+ #define MZ_FREOPEN mz_freopen
#define MZ_DELETE_FILE remove
#elif defined(__MINGW32__)
- #include <sys/utime.h>
+ #ifndef MINIZ_NO_TIME
+ #include <sys/utime.h>
+ #endif
#define MZ_FILE FILE
- #define MZ_FOPEN fopen
+ #define MZ_FOPEN(f, m) fopen(f, m)
#define MZ_FCLOSE fclose
#define MZ_FREAD fread
#define MZ_FWRITE fwrite
@@ -2820,12 +2961,46 @@ void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h,
#define MZ_FILE_STAT_STRUCT _stat
#define MZ_FILE_STAT _stat
#define MZ_FFLUSH fflush
- #define MZ_FREOPEN freopen
+ #define MZ_FREOPEN(f, m, s) freopen(f, m, s)
+ #define MZ_DELETE_FILE remove
+ #elif defined(__TINYC__)
+ #ifndef MINIZ_NO_TIME
+ #include <sys/utime.h>
+ #endif
+ #define MZ_FILE FILE
+ #define MZ_FOPEN(f, m) fopen(f, m)
+ #define MZ_FCLOSE fclose
+ #define MZ_FREAD fread
+ #define MZ_FWRITE fwrite
+ #define MZ_FTELL64 ftell
+ #define MZ_FSEEK64 fseek
+ #define MZ_FILE_STAT_STRUCT stat
+ #define MZ_FILE_STAT stat
+ #define MZ_FFLUSH fflush
+ #define MZ_FREOPEN(f, m, s) freopen(f, m, s)
+ #define MZ_DELETE_FILE remove
+ #elif defined(__GNUC__) && _LARGEFILE64_SOURCE
+ #ifndef MINIZ_NO_TIME
+ #include <utime.h>
+ #endif
+ #define MZ_FILE FILE
+ #define MZ_FOPEN(f, m) fopen64(f, m)
+ #define MZ_FCLOSE fclose
+ #define MZ_FREAD fread
+ #define MZ_FWRITE fwrite
+ #define MZ_FTELL64 ftello64
+ #define MZ_FSEEK64 fseeko64
+ #define MZ_FILE_STAT_STRUCT stat64
+ #define MZ_FILE_STAT stat64
+ #define MZ_FFLUSH fflush
+ #define MZ_FREOPEN(p, m, s) freopen64(p, m, s)
#define MZ_DELETE_FILE remove
#else
- #include <utime.h>
+ #ifndef MINIZ_NO_TIME
+ #include <utime.h>
+ #endif
#define MZ_FILE FILE
- #define MZ_FOPEN fopen
+ #define MZ_FOPEN(f, m) fopen(f, m)
#define MZ_FCLOSE fclose
#define MZ_FREAD fread
#define MZ_FWRITE fwrite
@@ -2834,7 +3009,7 @@ void *tdefl_write_image_to_png_file_in_memory(const void *pImage, int w, int h,
#define MZ_FILE_STAT_STRUCT stat
#define MZ_FILE_STAT stat
#define MZ_FFLUSH fflush
- #define MZ_FREOPEN freopen
+ #define MZ_FREOPEN(f, m, s) freopen(f, m, s)
#define MZ_DELETE_FILE remove
#endif // #ifdef _MSC_VER
#endif // #ifdef MINIZ_NO_STDIO
@@ -2934,7 +3109,18 @@ static time_t mz_zip_dos_to_time_t(int dos_time, int dos_date)
static void mz_zip_time_to_dos_time(time_t time, mz_uint16 *pDOS_time, mz_uint16 *pDOS_date)
{
+#ifdef _MSC_VER
+ struct tm tm_struct;
+ struct tm *tm = &tm_struct;
+ errno_t err = localtime_s(tm, &time);
+ if (err)
+ {
+ *pDOS_date = 0; *pDOS_time = 0;
+ return;
+ }
+#else
struct tm *tm = localtime(&time);
+#endif
*pDOS_time = (mz_uint16)(((tm->tm_hour) << 11) + ((tm->tm_min) << 5) + ((tm->tm_sec) >> 1));
*pDOS_date = (mz_uint16)(((tm->tm_year + 1900 - 1980) << 9) + ((tm->tm_mon + 1) << 5) + tm->tm_mday);
}
@@ -2946,23 +3132,23 @@ static mz_bool mz_zip_get_file_modified_time(const char *pFilename, mz_uint16 *p
#ifdef MINIZ_NO_TIME
(void)pFilename; *pDOS_date = *pDOS_time = 0;
#else
- struct MZ_FILE_STAT_STRUCT file_stat; if (MZ_FILE_STAT(pFilename, &file_stat) != 0) return MZ_FALSE;
+ struct MZ_FILE_STAT_STRUCT file_stat;
+ // On Linux with x86 glibc, this call will fail on large files (>= 0x80000000 bytes) unless you compiled with _LARGEFILE64_SOURCE. Argh.
+ if (MZ_FILE_STAT(pFilename, &file_stat) != 0)
+ return MZ_FALSE;
mz_zip_time_to_dos_time(file_stat.st_mtime, pDOS_time, pDOS_date);
#endif // #ifdef MINIZ_NO_TIME
return MZ_TRUE;
}
+#ifndef MINIZ_NO_TIME
static mz_bool mz_zip_set_file_times(const char *pFilename, time_t access_time, time_t modified_time)
{
-#ifndef MINIZ_NO_TIME
struct utimbuf t; t.actime = access_time; t.modtime = modified_time;
return !utime(pFilename, &t);
-#else
- pFilename, access_time, modified_time;
- return MZ_TRUE;
-#endif // #ifndef MINIZ_NO_TIME
}
-#endif
+#endif // #ifndef MINIZ_NO_TIME
+#endif // #ifndef MINIZ_NO_STDIO
static mz_bool mz_zip_reader_init_internal(mz_zip_archive *pZip, mz_uint32 flags)
{
@@ -3056,6 +3242,7 @@ static mz_bool mz_zip_reader_read_central_dir(mz_zip_archive *pZip, mz_uint32 fl
mz_int64 cur_file_ofs;
const mz_uint8 *p;
mz_uint32 buf_u32[4096 / sizeof(mz_uint32)]; mz_uint8 *pBuf = (mz_uint8 *)buf_u32;
+ mz_bool sort_central_dir = ((flags & MZ_ZIP_FLAG_DO_NOT_SORT_CENTRAL_DIRECTORY) == 0);
// Basic sanity checks - reject files which are too small, and check the first 4 bytes of the file to make sure a local header is there.
if (pZip->m_archive_size < MZ_ZIP_END_OF_CENTRAL_DIR_HEADER_SIZE)
return MZ_FALSE;
@@ -3102,11 +3289,18 @@ static mz_bool mz_zip_reader_read_central_dir(mz_zip_archive *pZip, mz_uint32 fl
if (pZip->m_total_files)
{
mz_uint i, n;
+
// Read the entire central directory into a heap block, and allocate another heap block to hold the unsorted central dir file record offsets, and another to hold the sorted indices.
if ((!mz_zip_array_resize(pZip, &pZip->m_pState->m_central_dir, cdir_size, MZ_FALSE)) ||
- (!mz_zip_array_resize(pZip, &pZip->m_pState->m_central_dir_offsets, pZip->m_total_files, MZ_FALSE)) ||
- (!mz_zip_array_resize(pZip, &pZip->m_pState->m_sorted_central_dir_offsets, pZip->m_total_files, MZ_FALSE)))
+ (!mz_zip_array_resize(pZip, &pZip->m_pState->m_central_dir_offsets, pZip->m_total_files, MZ_FALSE)))
return MZ_FALSE;
+
+ if (sort_central_dir)
+ {
+ if (!mz_zip_array_resize(pZip, &pZip->m_pState->m_sorted_central_dir_offsets, pZip->m_total_files, MZ_FALSE))
+ return MZ_FALSE;
+ }
+
if (pZip->m_pRead(pZip->m_pIO_opaque, cdir_ofs, pZip->m_pState->m_central_dir.m_p, cdir_size) != cdir_size)
return MZ_FALSE;
@@ -3118,7 +3312,8 @@ static mz_bool mz_zip_reader_read_central_dir(mz_zip_archive *pZip, mz_uint32 fl
if ((n < MZ_ZIP_CENTRAL_DIR_HEADER_SIZE) || (MZ_READ_LE32(p) != MZ_ZIP_CENTRAL_DIR_HEADER_SIG))
return MZ_FALSE;
MZ_ZIP_ARRAY_ELEMENT(&pZip->m_pState->m_central_dir_offsets, mz_uint32, i) = (mz_uint32)(p - (const mz_uint8 *)pZip->m_pState->m_central_dir.m_p);
- MZ_ZIP_ARRAY_ELEMENT(&pZip->m_pState->m_sorted_central_dir_offsets, mz_uint32, i) = i;
+ if (sort_central_dir)
+ MZ_ZIP_ARRAY_ELEMENT(&pZip->m_pState->m_sorted_central_dir_offsets, mz_uint32, i) = i;
comp_size = MZ_READ_LE32(p + MZ_ZIP_CDH_COMPRESSED_SIZE_OFS);
decomp_size = MZ_READ_LE32(p + MZ_ZIP_CDH_DECOMPRESSED_SIZE_OFS);
if (((!MZ_READ_LE32(p + MZ_ZIP_CDH_METHOD_OFS)) && (decomp_size != comp_size)) || (decomp_size && !comp_size) || (decomp_size == 0xFFFFFFFF) || (comp_size == 0xFFFFFFFF))
@@ -3134,7 +3329,7 @@ static mz_bool mz_zip_reader_read_central_dir(mz_zip_archive *pZip, mz_uint32 fl
}
}
- if ((flags & MZ_ZIP_FLAG_DO_NOT_SORT_CENTRAL_DIRECTORY) == 0)
+ if (sort_central_dir)
mz_zip_reader_sort_central_dir_offsets_by_filename(pZip);
return MZ_TRUE;
@@ -3170,7 +3365,11 @@ mz_bool mz_zip_reader_init_mem(mz_zip_archive *pZip, const void *pMem, size_t si
pZip->m_archive_size = size;
pZip->m_pRead = mz_zip_mem_read_func;
pZip->m_pIO_opaque = pZip;
+#ifdef __cplusplus
+ pZip->m_pState->m_pMem = const_cast<void *>(pMem);
+#else
pZip->m_pState->m_pMem = (void *)pMem;
+#endif
pZip->m_pState->m_mem_size = size;
if (!mz_zip_reader_read_central_dir(pZip, flags))
{
@@ -3197,7 +3396,10 @@ mz_bool mz_zip_reader_init_file(mz_zip_archive *pZip, const char *pFilename, mz_
if (!pFile)
return MZ_FALSE;
if (MZ_FSEEK64(pFile, 0, SEEK_END))
+ {
+ MZ_FCLOSE(pFile);
return MZ_FALSE;
+ }
file_size = MZ_FTELL64(pFile);
if (!mz_zip_reader_init_internal(pZip, flags))
{
@@ -3241,16 +3443,12 @@ mz_bool mz_zip_reader_is_file_encrypted(mz_zip_archive *pZip, mz_uint file_index
mz_bool mz_zip_reader_is_file_a_directory(mz_zip_archive *pZip, mz_uint file_index)
{
- mz_uint filename_len, internal_attr, external_attr;
+ mz_uint filename_len, external_attr;
const mz_uint8 *p = mz_zip_reader_get_cdh(pZip, file_index);
if (!p)
return MZ_FALSE;
- internal_attr = MZ_READ_LE16(p + MZ_ZIP_CDH_INTERNAL_ATTR_OFS);
- external_attr = MZ_READ_LE32(p + MZ_ZIP_CDH_EXTERNAL_ATTR_OFS);
- if ((!internal_attr) && ((external_attr & 0x10) != 0))
- return MZ_TRUE;
-
+ // First see if the filename ends with a '/' character.
filename_len = MZ_READ_LE16(p + MZ_ZIP_CDH_FILENAME_LEN_OFS);
if (filename_len)
{
@@ -3258,6 +3456,13 @@ mz_bool mz_zip_reader_is_file_a_directory(mz_zip_archive *pZip, mz_uint file_ind
return MZ_TRUE;
}
+ // Bugfix: This code was also checking if the internal attribute was non-zero, which wasn't correct.
+ // Most/all zip writers (hopefully) set DOS file/directory attributes in the low 16-bits, so check for the DOS directory flag and ignore the source OS ID in the created by field.
+ // FIXME: Remove this check? Is it necessary - we already check the filename.
+ external_attr = MZ_READ_LE32(p + MZ_ZIP_CDH_EXTERNAL_ATTR_OFS);
+ if ((external_attr & 0x10) != 0)
+ return MZ_TRUE;
+
return MZ_FALSE;
}
@@ -3365,7 +3570,7 @@ int mz_zip_reader_locate_file(mz_zip_archive *pZip, const char *pName, const cha
mz_uint file_index; size_t name_len, comment_len;
if ((!pZip) || (!pZip->m_pState) || (!pName) || (pZip->m_zip_mode != MZ_ZIP_MODE_READING))
return -1;
- if (((flags & (MZ_ZIP_FLAG_IGNORE_PATH | MZ_ZIP_FLAG_CASE_SENSITIVE)) == 0) && (!pComment) && (pZip->m_pState->m_sorted_central_dir_offsets.m_p))
+ if (((flags & (MZ_ZIP_FLAG_IGNORE_PATH | MZ_ZIP_FLAG_CASE_SENSITIVE)) == 0) && (!pComment) && (pZip->m_pState->m_sorted_central_dir_offsets.m_size))
return mz_zip_reader_locate_file_binary_search(pZip, pName);
name_len = strlen(pName); if (name_len > 0xFFFF) return -1;
comment_len = pComment ? strlen(pComment) : 0; if (comment_len > 0xFFFF) return -1;
@@ -3415,9 +3620,15 @@ mz_bool mz_zip_reader_extract_to_mem_no_alloc(mz_zip_archive *pZip, mz_uint file
if (!mz_zip_reader_file_stat(pZip, file_index, &file_stat))
return MZ_FALSE;
+ // Empty file, or a directory (but not always a directory - I've seen odd zips with directories that have compressed data which inflates to 0 bytes)
if (!file_stat.m_comp_size)
return MZ_TRUE;
+ // Entry is a subdirectory (I've seen old zips with dir entries which have compressed deflate data which inflates to 0 bytes, but these entries claim to uncompress to 512 bytes in the headers).
+ // I'm torn how to handle this case - should it fail instead?
+ if (mz_zip_reader_is_file_a_directory(pZip, file_index))
+ return MZ_TRUE;
+
// Encryption and patch files are not supported.
if (file_stat.m_bit_flag & (1 | 32))
return MZ_FALSE;
@@ -3468,7 +3679,7 @@ mz_bool mz_zip_reader_extract_to_mem_no_alloc(mz_zip_archive *pZip, mz_uint file
pRead_buf = (mz_uint8 *)pUser_read_buf;
read_buf_size = user_read_buf_size;
read_buf_avail = 0;
- comp_remaining = file_stat.m_uncomp_size;
+ comp_remaining = file_stat.m_comp_size;
}
else
{
@@ -3595,9 +3806,15 @@ mz_bool mz_zip_reader_extract_to_callback(mz_zip_archive *pZip, mz_uint file_ind
if (!mz_zip_reader_file_stat(pZip, file_index, &file_stat))
return MZ_FALSE;
+ // Empty file, or a directory (but not always a directory - I've seen odd zips with directories that have compressed data which inflates to 0 bytes)
if (!file_stat.m_comp_size)
return MZ_TRUE;
+ // Entry is a subdirectory (I've seen old zips with dir entries which have compressed deflate data which inflates to 0 bytes, but these entries claim to uncompress to 512 bytes in the headers).
+ // I'm torn how to handle this case - should it fail instead?
+ if (mz_zip_reader_is_file_a_directory(pZip, file_index))
+ return MZ_TRUE;
+
// Encryption and patch files are not supported.
if (file_stat.m_bit_flag & (1 | 32))
return MZ_FALSE;
@@ -4294,7 +4511,7 @@ mz_bool mz_zip_writer_add_file(mz_zip_archive *pZip, const char *pArchive_name,
if (!mz_zip_get_file_modified_time(pSrc_filename, &dos_time, &dos_date))
return MZ_FALSE;
-
+
pSrc_file = MZ_FOPEN(pSrc_filename, "rb");
if (!pSrc_file)
return MZ_FALSE;
@@ -4312,7 +4529,10 @@ mz_bool mz_zip_writer_add_file(mz_zip_archive *pZip, const char *pArchive_name,
level = 0;
if (!mz_zip_writer_write_zeros(pZip, cur_archive_file_ofs, num_alignment_padding_bytes + sizeof(local_dir_header)))
+ {
+ MZ_FCLOSE(pSrc_file);
return MZ_FALSE;
+ }
local_dir_header_ofs += num_alignment_padding_bytes;
if (pZip->m_file_offset_alignment) { MZ_ASSERT((local_dir_header_ofs & (pZip->m_file_offset_alignment - 1)) == 0); }
cur_archive_file_ofs += num_alignment_padding_bytes + sizeof(local_dir_header);
@@ -4547,7 +4767,7 @@ mz_bool mz_zip_writer_add_from_zip_reader(mz_zip_archive *pZip, mz_zip_archive *
if (pState->m_central_dir.m_size > 0xFFFFFFFF)
return MZ_FALSE;
- n = (mz_uint32)pState->m_central_dir.m_size;
+ n = (mz_uint32)orig_central_dir_size;
if (!mz_zip_array_push_back(pZip, &pState->m_central_dir_offsets, &n, 1))
{
mz_zip_array_resize(pZip, &pState->m_central_dir, orig_central_dir_size, MZ_FALSE);
diff --git a/c++/src/util/compress/api/miniz/tinfl.c b/c++/src/util/compress/api/miniz/tinfl.c
index a17a156..88fb8e8 100644
--- a/c++/src/util/compress/api/miniz/tinfl.c
+++ b/c++/src/util/compress/api/miniz/tinfl.c
@@ -1,9 +1,10 @@
-/* tinfl.c v1.11 - public domain inflate with zlib header parsing/adler32 checking (inflate-only subset of miniz.c)
+/* tinfl.c v1.16 beta - public domain inflate with zlib header parsing/adler32 checking (inflate-only subset of miniz.c)
See "unlicense" statement at the end of this file.
- Rich Geldreich <richgel99 at gmail.com>, last updated May 20, 2011
- Implements RFC 1950: http://www.ietf.org/rfc/rfc1950.txt and RFC 1951: http://www.ietf.org/rfc/rfc1951.txt
+ Rich Geldreich <richgel99 at gmail.com>, last updated Oct. 19, 2013
+ Implements the decompression side of RFC 1950: http://www.ietf.org/rfc/rfc1950.txt and RFC 1951: http://www.ietf.org/rfc/rfc1951.txt
- The entire decompressor coroutine is implemented in tinfl_decompress(). The other functions are optional high-level helpers.
+ There entire decompressor coroutine function is implemented in a *single* C function: tinfl_decompress().
+ All other C functions in this file are optional high-level usage examples.
*/
#ifndef TINFL_HEADER_INCLUDED
#define TINFL_HEADER_INCLUDED
@@ -77,12 +78,37 @@ struct tinfl_decompressor_tag; typedef struct tinfl_decompressor_tag tinfl_decom
// Return status.
typedef enum
{
+ // This flags indicates the inflator needs 1 or more input bytes to make forward progress, but the caller is indicating that no more are available. The compressed data
+ // is probably corrupted. If you call the inflator again with more bytes it'll try to continue processing the input but this is a BAD sign (either the data is corrupted or you called it incorrectly).
+ // If you call it again with no input you'll just get TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS again.
+ TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS = -4,
+
+ // This flag indicates that one or more of the input parameters was obviously bogus. (You can try calling it again, but if you get this error the calling code is wrong.)
TINFL_STATUS_BAD_PARAM = -3,
+
+ // This flags indicate the inflator is finished but the adler32 check of the uncompressed data didn't match. If you call it again it'll return TINFL_STATUS_DONE.
TINFL_STATUS_ADLER32_MISMATCH = -2,
+
+ // This flags indicate the inflator has somehow failed (bad code, corrupted input, etc.). If you call it again without resetting via tinfl_init() it it'll just keep on returning the same status failure code.
TINFL_STATUS_FAILED = -1,
+
+ // Any status code less than TINFL_STATUS_DONE must indicate a failure.
+
+ // This flag indicates the inflator has returned every byte of uncompressed data that it can, has consumed every byte that it needed, has successfully reached the end of the deflate stream, and
+ // if zlib headers and adler32 checking enabled that it has successfully checked the uncompressed data's adler32. If you call it again you'll just get TINFL_STATUS_DONE over and over again.
TINFL_STATUS_DONE = 0,
+
+ // This flag indicates the inflator MUST have more input data (even 1 byte) before it can make any more forward progress, or you need to clear the TINFL_FLAG_HAS_MORE_INPUT
+ // flag on the next call if you don't have any more source data. If the source data was somehow corrupted it's also possible (but unlikely) for the inflator to keep on demanding input to
+ // proceed, so be sure to properly set the TINFL_FLAG_HAS_MORE_INPUT flag.
TINFL_STATUS_NEEDS_MORE_INPUT = 1,
+
+ // This flag indicates the inflator definitely has 1 or more bytes of uncompressed data available, but it cannot write this data into the output buffer.
+ // Note if the source compressed data was corrupted it's possible for the inflator to return a lot of uncompressed data to the caller. I've been assuming you know how much uncompressed data to expect
+ // (either exact or worst case) and will stop calling the inflator and fail after receiving too much. In pure streaming scenarios where you have no idea how many bytes to expect this may not be possible
+ // so I may need to add some code to address this.
TINFL_STATUS_HAS_MORE_OUTPUT = 2
+
} tinfl_status;
// Initializes the decompressor to its initial state.
@@ -138,7 +164,7 @@ struct tinfl_decompressor_tag
// MZ_MALLOC, etc. are only used by the optional high-level helper functions.
#ifdef MINIZ_NO_MALLOC
#define MZ_MALLOC(x) NULL
- #define MZ_FREE(x) x, ((void)0)
+ #define MZ_FREE(x) (void)x, ((void)0)
#define MZ_REALLOC(p, x) NULL
#else
#define MZ_MALLOC(x) malloc(x)
@@ -166,23 +192,10 @@ struct tinfl_decompressor_tag
#define TINFL_CR_RETURN_FOREVER(state_index, result) do { for ( ; ; ) { TINFL_CR_RETURN(state_index, result); } } MZ_MACRO_END
#define TINFL_CR_FINISH }
-// TODO: If the caller has indicated that there's no more input, and we attempt to read beyond the input buf, then something is wrong with the input because the inflator never
-// reads ahead more than it needs to. Currently TINFL_GET_BYTE() pads the end of the stream with 0's in this scenario.
#define TINFL_GET_BYTE(state_index, c) do { \
- if (pIn_buf_cur >= pIn_buf_end) { \
- for ( ; ; ) { \
- if (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) { \
- TINFL_CR_RETURN(state_index, TINFL_STATUS_NEEDS_MORE_INPUT); \
- if (pIn_buf_cur < pIn_buf_end) { \
- c = *pIn_buf_cur++; \
- break; \
- } \
- } else { \
- c = 0; \
- break; \
- } \
- } \
- } else c = *pIn_buf_cur++; } MZ_MACRO_END
+ while (pIn_buf_cur >= pIn_buf_end) { \
+ TINFL_CR_RETURN(state_index, (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) ? TINFL_STATUS_NEEDS_MORE_INPUT : TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS); \
+ } c = *pIn_buf_cur++; } MZ_MACRO_END
#define TINFL_NEED_BITS(state_index, n) do { mz_uint c; TINFL_GET_BYTE(state_index, c); bit_buf |= (((tinfl_bit_buf_t)c) << num_bits); num_bits += 8; } while (num_bits < (mz_uint)(n))
#define TINFL_SKIP_BITS(state_index, n) do { if (num_bits < (mz_uint)(n)) { TINFL_NEED_BITS(state_index, n); } bit_buf >>= (n); num_bits -= (n); } MZ_MACRO_END
@@ -211,6 +224,8 @@ struct tinfl_decompressor_tag
// beyond the final byte of the deflate stream. (In other words, when this macro wants to read another byte from the input, it REALLY needs another byte in order to fully
// decode the next Huffman code.) Handling this properly is particularly important on raw deflate (non-zlib) streams, which aren't followed by a byte aligned adler-32.
// The slow path is only executed at the very end of the input buffer.
+// v1.16: The original macro handled the case at the very end of the passed-in input buffer, but we also need to handle the case where the user passes in 1+zillion bytes
+// following the deflate data and our non-conservative read-ahead path won't kick in here on this code. This is much trickier.
#define TINFL_HUFF_DECODE(state_index, sym, pHuff) do { \
int temp; mz_uint code_len, c; \
if (num_bits < 15) { \
@@ -275,14 +290,7 @@ tinfl_status tinfl_decompress(tinfl_decompressor *r, const mz_uint8 *pIn_buf_nex
size_t n; while (pOut_buf_cur >= pOut_buf_end) { TINFL_CR_RETURN(9, TINFL_STATUS_HAS_MORE_OUTPUT); }
while (pIn_buf_cur >= pIn_buf_end)
{
- if (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT)
- {
- TINFL_CR_RETURN(38, TINFL_STATUS_NEEDS_MORE_INPUT);
- }
- else
- {
- TINFL_CR_RETURN_FOREVER(40, TINFL_STATUS_FAILED);
- }
+ TINFL_CR_RETURN(38, (decomp_flags & TINFL_FLAG_HAS_MORE_INPUT) ? TINFL_STATUS_NEEDS_MORE_INPUT : TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS);
}
n = MZ_MIN(MZ_MIN((size_t)(pOut_buf_end - pOut_buf_cur), (size_t)(pIn_buf_end - pIn_buf_cur)), counter);
TINFL_MEMCPY(pOut_buf_cur, pIn_buf_cur, n); pIn_buf_cur += n; pOut_buf_cur += n; counter -= (mz_uint)n;
@@ -469,15 +477,27 @@ tinfl_status tinfl_decompress(tinfl_decompressor *r, const mz_uint8 *pIn_buf_nex
}
}
} while (!(r->m_final & 1));
+
+ // Ensure byte alignment and put back any bytes from the bitbuf if we've looked ahead too far on gzip, or other Deflate streams followed by arbitrary data.
+ // I'm being super conservative here. A number of simplifications can be made to the byte alignment part, and the Adler32 check shouldn't ever need to worry about reading from the bitbuf now.
+ TINFL_SKIP_BITS(32, num_bits & 7);
+ while ((pIn_buf_cur > pIn_buf_next) && (num_bits >= 8)) { --pIn_buf_cur; num_bits -= 8; } bit_buf &= (tinfl_bit_buf_t)((1ULL << num_bits) - 1ULL);
+ //MZ_ASSERT(!num_bits); // if this assert fires then we've read beyond the end of non-deflate/zlib streams with following data (such as gzip streams).
+
if (decomp_flags & TINFL_FLAG_PARSE_ZLIB_HEADER)
{
- TINFL_SKIP_BITS(32, num_bits & 7); for (counter = 0; counter < 4; ++counter) { mz_uint s; if (num_bits) TINFL_GET_BITS(41, s, 8); else TINFL_GET_BYTE(42, s); r->m_z_adler32 = (r->m_z_adler32 << 8) | s; }
+ for (counter = 0; counter < 4; ++counter) { mz_uint s; if (num_bits) TINFL_GET_BITS(41, s, 8); else TINFL_GET_BYTE(42, s); r->m_z_adler32 = (r->m_z_adler32 << 8) | s; }
}
TINFL_CR_RETURN_FOREVER(34, TINFL_STATUS_DONE);
+
TINFL_CR_FINISH
common_exit:
- r->m_num_bits = num_bits; r->m_bit_buf = bit_buf; r->m_dist = dist; r->m_counter = counter; r->m_num_extra = num_extra; r->m_dist_from_out_buf_start = dist_from_out_buf_start;
+ // As long as we aren't telling the caller that we NEED more input to make forward progress:
+ // Put back any bytes from the bitbuf in case we've looked ahead too far on gzip, or other Deflate streams followed by arbitrary data.
+ // We need to be very careful here to NOT push back any bytes we definitely know we need to make forward progress, though, or we'll lock the caller up into an inf loop.
+ if ((status != TINFL_STATUS_NEEDS_MORE_INPUT) && (status != TINFL_STATUS_FAILED_CANNOT_MAKE_PROGRESS)) { while ((pIn_buf_cur > pIn_buf_next) && (num_bits >= 8)) { --pIn_buf_cur; num_bits -= 8; } }
+ r->m_num_bits = num_bits; r->m_bit_buf = bit_buf & (tinfl_bit_buf_t)((1ULL << num_bits) - 1ULL); r->m_dist = dist; r->m_counter = counter; r->m_num_extra = num_extra; r->m_dist_from_out_buf_start = dist_from_out_buf_start;
*pIn_buf_size = pIn_buf_cur - pIn_buf_next; *pOut_buf_size = pOut_buf_cur - pOut_buf_next;
if ((decomp_flags & (TINFL_FLAG_PARSE_ZLIB_HEADER | TINFL_FLAG_COMPUTE_ADLER32)) && (status >= 0))
{
diff --git a/c++/src/util/compress/api/tar.cpp b/c++/src/util/compress/api/tar.cpp
index 683ee2e..385adfe 100644
--- a/c++/src/util/compress/api/tar.cpp
+++ b/c++/src/util/compress/api/tar.cpp
@@ -1,4 +1,4 @@
-/* $Id: tar.cpp 425992 2014-02-05 04:01:25Z lavr $
+/* $Id: tar.cpp 463379 2015-03-26 21:18:59Z lavr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1387,6 +1387,7 @@ bool CTar::x_Flush(bool no_throw)
&& !m_Bad == !m_BufferPos);
}
}
+ m_ZeroBlockCount = zbc;
}
_ASSERT(!OFFSET_OF(m_BufferPos));
@@ -1542,12 +1543,12 @@ void CTar::x_Open(EAction action)
_ASSERT(m_OpenMode > eWO && action != eCreate);
if (m_Bad) {
TAR_THROW(this, eOpen,
- "Archive is in bad state");
+ "Archive file is in bad state");
}
if (action != eAppend && action != eInternal) {
m_BufferPos = 0;
m_StreamPos = 0;
- m_FileStream->seekg(0, IOS_BASE::beg);
+ m_FileStream->seekg(0);
}
}
}
@@ -2673,12 +2674,12 @@ void CTar::x_Backspace(EAction action)
m_StreamPos -= gap;
CT_POS_TYPE rec = (CT_OFF_TYPE)(m_StreamPos / m_BufferSize);
size_t off = (size_t) (m_StreamPos % m_BufferSize);
- size_t temp = BLOCK_SIZE;
if (m_BufferPos == 0) {
m_BufferPos += m_BufferSize;
}
if (gap > m_BufferPos) {
m_BufferPos = 0;
+ size_t temp = BLOCK_SIZE;
// Re-fetch the entire record
if (!m_FileStream->seekg(rec * m_BufferSize)
// NB: successful positioning guarantees the stream was !fail(),
@@ -2688,7 +2689,7 @@ void CTar::x_Backspace(EAction action)
TAR_POST(65, Error,
"Archive backspace error in record reget");
s_SetStateSafe(m_Stream, NcbiBadbit);
- temp = 0;
+ return;
}
m_BufferPos = off;
} else {
@@ -2696,11 +2697,15 @@ void CTar::x_Backspace(EAction action)
}
_ASSERT(!OFFSET_OF(m_BufferPos) && m_BufferPos < m_BufferSize);
- // Always set put position here
- if (!m_FileStream->seekp(rec * m_BufferSize) && temp) {
+ // Always reset the put position there
+#if defined(_LIBCPP_VERSION) && _LIBCPP_VERSION <= 1101
+ m_FileStream->clear(); // This is to only work around a bug
+#endif //_LIBCPP_VERSION
+ if (!m_FileStream->seekp(rec * m_BufferSize)) {
TAR_POST(80, Error,
"Archive backspace error in record reset");
s_SetStateSafe(m_Stream, NcbiBadbit);
+ return;
}
m_ZeroBlockCount = 0;
}
@@ -3455,22 +3460,23 @@ void CTar::x_RestoreAttrs(const CTarEntryInfo& info,
}
-static string s_BaseDir(const string& dirname)
+static string s_ToFilesystemPath(const string& base_dir, const string& name)
{
- string retval = CDirEntry::AddTrailingPathSeparator(dirname);
-#ifdef NCBI_OS_MSWIN
- // Replace backslashes with forward slashes
- NStr::ReplaceInPlace(retval, "\\", "/");
-#endif //NCBI_OS_MSWIN
- return retval;
+ string path(base_dir.empty() || CDirEntry::IsAbsolutePath(name)
+ ? name : CDirEntry::ConcatPath(base_dir, name));
+ return CDirEntry::NormalizePath(path);
}
-static string s_ToFilesystemPath(const string& base_dir, const string& name)
+static string s_BaseDir(const string& dirname)
{
- string path(CDirEntry::IsAbsolutePath(name) || base_dir.empty()
- ? name : CDirEntry::ConcatPath(base_dir, name));
- return CDirEntry::NormalizePath(path);
+ string path = s_ToFilesystemPath(kEmptyStr, dirname);
+ path += CDirEntry::GetPathSeparator();
+#ifdef NCBI_OS_MSWIN
+ // Replace backslashes with forward slashes
+ NStr::ReplaceInPlace(path, "\\", "/");
+#endif //NCBI_OS_MSWIN
+ return path;
}
@@ -3917,7 +3923,7 @@ void CTar::SetMask(CMask* mask, EOwnership own,
void CTar::SetBaseDir(const string& dirname)
{
string dir = s_BaseDir(dirname);
- dir.swap(m_BaseDir);
+ m_BaseDir.swap(dir);
}
@@ -3926,7 +3932,7 @@ Uint8 CTar::EstimateArchiveSize(const TFiles& files,
const string& base_dir)
{
const size_t buffer_size = SIZE_OF(blocking_factor);
- string basedir = s_BaseDir(base_dir);
+ string prefix = s_BaseDir(base_dir);
Uint8 result = 0;
ITERATE(TFiles, f, files) {
@@ -3934,8 +3940,8 @@ Uint8 CTar::EstimateArchiveSize(const TFiles& files,
result += BLOCK_SIZE/*header*/ + ALIGN_SIZE(f->second);
// Count in the long name (if any)
- string path = s_ToFilesystemPath(basedir, f->first);
- string name = s_ToArchiveName(basedir, path);
+ string path = s_ToFilesystemPath(prefix, f->first);
+ string name = s_ToArchiveName (prefix, path);
size_t namelen = name.size() + 1;
if (namelen > sizeof(((SHeader*) 0)->name)) {
result += BLOCK_SIZE/*long name header*/ + ALIGN_SIZE(namelen);
@@ -4055,6 +4061,13 @@ ERW_Result CTarReader::PendingCount(size_t* count)
if (m_Tar->m_BufferPos) {
avail += m_Tar->m_BufferSize - m_Tar->m_BufferPos;
}
+ if (!avail && m_Tar->m_Stream.good()) {
+ // NB: good() subsumes there's streambuf (bad() otherwise)
+ streamsize sb_avail = m_Tar->m_Stream.rdbuf()->in_avail();
+ if (sb_avail != -1) {
+ avail = (size_t) sb_avail;
+ }
+ }
*count = avail > left ? (size_t) left : avail;
return eRW_Success;
}
diff --git a/c++/src/util/compress/api/zlib.cpp b/c++/src/util/compress/api/zlib.cpp
index 78d2b2d..4bc0185 100644
--- a/c++/src/util/compress/api/zlib.cpp
+++ b/c++/src/util/compress/api/zlib.cpp
@@ -1,4 +1,4 @@
-/* $Id: zlib.cpp 430126 2014-03-24 12:25:47Z ivanov $
+/* $Id: zlib.cpp 460187 2015-02-25 16:32:09Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -1350,7 +1350,7 @@ CCompressionProcessor::EStatus CZipDecompressor::Process(
m_Cache.erase(0, total);
out_size -= total;
}
- if (x_in_len && out_size) {
+ if (x_in_buf && x_in_len && out_size) {
size_t n = min(x_in_len, out_size);
memcpy(out_buf + total, x_in_buf, n);
total += n;
diff --git a/c++/src/util/compress/zlib/ChangeLog b/c++/src/util/compress/zlib/ChangeLog
index 9b8dae6..b43d09c 100644
--- a/c++/src/util/compress/zlib/ChangeLog
+++ b/c++/src/util/compress/zlib/ChangeLog
@@ -1216,7 +1216,7 @@ Changes in 1.0.6 (19 Jan 1998)
- use _fdopen instead of fdopen for MSC >= 6.0 (Thomas Fanslau)
- added makelcc.bat for lcc-win32 (Tom St Denis)
- in Makefile.dj2, use copy and del instead of install and rm (Frank Donahoe)
-- Avoid expanded $Id: ChangeLog 444753 2014-08-27 18:08:04Z ivanov $. Use "rcs -kb" or "cvs admin -kb" to avoid Id expansion.
+- Avoid expanded $Id: ChangeLog 444593 2014-08-26 12:32:08Z ivanov $. Use "rcs -kb" or "cvs admin -kb" to avoid Id expansion.
- check for unistd.h in configure (for off_t)
- remove useless check parameter in inflate_blocks_free
- avoid useless assignment of s->check to itself in inflate_blocks_new
diff --git a/c++/src/util/compress/zlib/Makefile.zlib.lib b/c++/src/util/compress/zlib/Makefile.zlib.lib
index bbc046a..0287463 100644
--- a/c++/src/util/compress/zlib/Makefile.zlib.lib
+++ b/c++/src/util/compress/zlib/Makefile.zlib.lib
@@ -1,4 +1,4 @@
-# $Id: Makefile.zlib.lib 444753 2014-08-27 18:08:04Z ivanov $
+# $Id: Makefile.zlib.lib 444593 2014-08-26 12:32:08Z ivanov $
SRC = adler32 crc32 deflate infback inffast inflate inftrees trees zutil \
ncbi_z_compress uncompr gzclose gzlib gzread gzwrite
diff --git a/c++/src/util/compress/zlib/adler32.c b/c++/src/util/compress/zlib/adler32.c
index 00e357a..42a1dba 100644
--- a/c++/src/util/compress/zlib/adler32.c
+++ b/c++/src/util/compress/zlib/adler32.c
@@ -3,7 +3,7 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
-/* @(#) $Id: adler32.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: adler32.c 444593 2014-08-26 12:32:08Z ivanov $ */
#include "zutil.h"
diff --git a/c++/src/util/compress/zlib/compress.c b/c++/src/util/compress/zlib/compress.c
index a67b5e4..bdcb1fc 100644
--- a/c++/src/util/compress/zlib/compress.c
+++ b/c++/src/util/compress/zlib/compress.c
@@ -3,7 +3,7 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
-/* @(#) $Id: compress.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: compress.c 444593 2014-08-26 12:32:08Z ivanov $ */
#define ZLIB_INTERNAL
#include "zlib.h"
diff --git a/c++/src/util/compress/zlib/crc32.c b/c++/src/util/compress/zlib/crc32.c
index c4f833f..61f2595 100644
--- a/c++/src/util/compress/zlib/crc32.c
+++ b/c++/src/util/compress/zlib/crc32.c
@@ -9,7 +9,7 @@
* factor of two increase in speed on a Power PC G4 (PPC7455) using gcc -O3.
*/
-/* @(#) $Id: crc32.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: crc32.c 444593 2014-08-26 12:32:08Z ivanov $ */
/*
Note on the use of DYNAMIC_CRC_TABLE: there is no mutex or semaphore
diff --git a/c++/src/util/compress/zlib/deflate.c b/c++/src/util/compress/zlib/deflate.c
index 725ea36..1c652ae 100644
--- a/c++/src/util/compress/zlib/deflate.c
+++ b/c++/src/util/compress/zlib/deflate.c
@@ -47,7 +47,7 @@
*
*/
-/* @(#) $Id: deflate.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: deflate.c 444593 2014-08-26 12:32:08Z ivanov $ */
#include "deflate.h"
diff --git a/c++/src/util/compress/zlib/deflate.h b/c++/src/util/compress/zlib/deflate.h
index 79b8393..250841a 100644
--- a/c++/src/util/compress/zlib/deflate.h
+++ b/c++/src/util/compress/zlib/deflate.h
@@ -8,7 +8,7 @@
subject to change. Applications should only use zlib.h.
*/
-/* @(#) $Id: deflate.h 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: deflate.h 444593 2014-08-26 12:32:08Z ivanov $ */
#ifndef DEFLATE_H
#define DEFLATE_H
diff --git a/c++/src/util/compress/zlib/trees.c b/c++/src/util/compress/zlib/trees.c
index 6d8e13d..d156ed3 100644
--- a/c++/src/util/compress/zlib/trees.c
+++ b/c++/src/util/compress/zlib/trees.c
@@ -30,7 +30,7 @@
* Addison-Wesley, 1983. ISBN 0-201-06672-6.
*/
-/* @(#) $Id: trees.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: trees.c 444593 2014-08-26 12:32:08Z ivanov $ */
/* #define GEN_TREES_H */
diff --git a/c++/src/util/compress/zlib/uncompr.c b/c++/src/util/compress/zlib/uncompr.c
index e778ec6..99d25d2 100644
--- a/c++/src/util/compress/zlib/uncompr.c
+++ b/c++/src/util/compress/zlib/uncompr.c
@@ -3,7 +3,7 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
-/* @(#) $Id: uncompr.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: uncompr.c 444593 2014-08-26 12:32:08Z ivanov $ */
#define ZLIB_INTERNAL
#include "zlib.h"
diff --git a/c++/src/util/compress/zlib/zutil.c b/c++/src/util/compress/zlib/zutil.c
index 317549c..1a1fdb4 100644
--- a/c++/src/util/compress/zlib/zutil.c
+++ b/c++/src/util/compress/zlib/zutil.c
@@ -3,7 +3,7 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
-/* @(#) $Id: zutil.c 444753 2014-08-27 18:08:04Z ivanov $ */
+/* @(#) $Id: zutil.c 444593 2014-08-26 12:32:08Z ivanov $ */
#include "zutil.h"
#ifndef Z_SOLO
diff --git a/c++/src/util/crc32tables.c b/c++/src/util/crc32tables.c
new file mode 100644
index 0000000..883032c
--- /dev/null
+++ b/c++/src/util/crc32tables.c
@@ -0,0 +1,1598 @@
+static const TCRC32Table s_CRC32TableForward[TABLES_COUNT] = {
+ {
+ 0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9,
+ 0x130476dc, 0x17c56b6b, 0x1a864db2, 0x1e475005,
+ 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61,
+ 0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd,
+ 0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9,
+ 0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75,
+ 0x6a1936c8, 0x6ed82b7f, 0x639b0da6, 0x675a1011,
+ 0x791d4014, 0x7ddc5da3, 0x709f7b7a, 0x745e66cd,
+ 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
+ 0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5,
+ 0xbe2b5b58, 0xbaea46ef, 0xb7a96036, 0xb3687d81,
+ 0xad2f2d84, 0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d,
+ 0xd4326d90, 0xd0f37027, 0xddb056fe, 0xd9714b49,
+ 0xc7361b4c, 0xc3f706fb, 0xceb42022, 0xca753d95,
+ 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
+ 0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d,
+ 0x34867077, 0x30476dc0, 0x3d044b19, 0x39c556ae,
+ 0x278206ab, 0x23431b1c, 0x2e003dc5, 0x2ac12072,
+ 0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16,
+ 0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca,
+ 0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde,
+ 0x6b93dddb, 0x6f52c06c, 0x6211e6b5, 0x66d0fb02,
+ 0x5e9f46bf, 0x5a5e5b08, 0x571d7dd1, 0x53dc6066,
+ 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
+ 0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e,
+ 0xbfa1b04b, 0xbb60adfc, 0xb6238b25, 0xb2e29692,
+ 0x8aad2b2f, 0x8e6c3698, 0x832f1041, 0x87ee0df6,
+ 0x99a95df3, 0x9d684044, 0x902b669d, 0x94ea7b2a,
+ 0xe0b41de7, 0xe4750050, 0xe9362689, 0xedf73b3e,
+ 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
+ 0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686,
+ 0xd5b88683, 0xd1799b34, 0xdc3abded, 0xd8fba05a,
+ 0x690ce0ee, 0x6dcdfd59, 0x608edb80, 0x644fc637,
+ 0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb,
+ 0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f,
+ 0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53,
+ 0x251d3b9e, 0x21dc2629, 0x2c9f00f0, 0x285e1d47,
+ 0x36194d42, 0x32d850f5, 0x3f9b762c, 0x3b5a6b9b,
+ 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
+ 0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623,
+ 0xf12f560e, 0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7,
+ 0xe22b20d2, 0xe6ea3d65, 0xeba91bbc, 0xef68060b,
+ 0xd727bbb6, 0xd3e6a601, 0xdea580d8, 0xda649d6f,
+ 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604, 0xc960ebb3,
+ 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
+ 0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b,
+ 0x9b3660c6, 0x9ff77d71, 0x92b45ba8, 0x9675461f,
+ 0x8832161a, 0x8cf30bad, 0x81b02d74, 0x857130c3,
+ 0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640,
+ 0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c,
+ 0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8,
+ 0x68860bfd, 0x6c47164a, 0x61043093, 0x65c52d24,
+ 0x119b4be9, 0x155a565e, 0x18197087, 0x1cd86d30,
+ 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
+ 0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088,
+ 0x2497d08d, 0x2056cd3a, 0x2d15ebe3, 0x29d4f654,
+ 0xc5a92679, 0xc1683bce, 0xcc2b1d17, 0xc8ea00a0,
+ 0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb, 0xdbee767c,
+ 0xe3a1cbc1, 0xe760d676, 0xea23f0af, 0xeee2ed18,
+ 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
+ 0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0,
+ 0x9abc8bd5, 0x9e7d9662, 0x933eb0bb, 0x97ffad0c,
+ 0xafb010b1, 0xab710d06, 0xa6322bdf, 0xa2f33668,
+ 0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4
+ },
+ {
+ 0x00000000, 0xd219c1dc, 0xa0f29e0f, 0x72eb5fd3,
+ 0x452421a9, 0x973de075, 0xe5d6bfa6, 0x37cf7e7a,
+ 0x8a484352, 0x5851828e, 0x2abadd5d, 0xf8a31c81,
+ 0xcf6c62fb, 0x1d75a327, 0x6f9efcf4, 0xbd873d28,
+ 0x10519b13, 0xc2485acf, 0xb0a3051c, 0x62bac4c0,
+ 0x5575baba, 0x876c7b66, 0xf58724b5, 0x279ee569,
+ 0x9a19d841, 0x4800199d, 0x3aeb464e, 0xe8f28792,
+ 0xdf3df9e8, 0x0d243834, 0x7fcf67e7, 0xadd6a63b,
+ 0x20a33626, 0xf2baf7fa, 0x8051a829, 0x524869f5,
+ 0x6587178f, 0xb79ed653, 0xc5758980, 0x176c485c,
+ 0xaaeb7574, 0x78f2b4a8, 0x0a19eb7b, 0xd8002aa7,
+ 0xefcf54dd, 0x3dd69501, 0x4f3dcad2, 0x9d240b0e,
+ 0x30f2ad35, 0xe2eb6ce9, 0x9000333a, 0x4219f2e6,
+ 0x75d68c9c, 0xa7cf4d40, 0xd5241293, 0x073dd34f,
+ 0xbabaee67, 0x68a32fbb, 0x1a487068, 0xc851b1b4,
+ 0xff9ecfce, 0x2d870e12, 0x5f6c51c1, 0x8d75901d,
+ 0x41466c4c, 0x935fad90, 0xe1b4f243, 0x33ad339f,
+ 0x04624de5, 0xd67b8c39, 0xa490d3ea, 0x76891236,
+ 0xcb0e2f1e, 0x1917eec2, 0x6bfcb111, 0xb9e570cd,
+ 0x8e2a0eb7, 0x5c33cf6b, 0x2ed890b8, 0xfcc15164,
+ 0x5117f75f, 0x830e3683, 0xf1e56950, 0x23fca88c,
+ 0x1433d6f6, 0xc62a172a, 0xb4c148f9, 0x66d88925,
+ 0xdb5fb40d, 0x094675d1, 0x7bad2a02, 0xa9b4ebde,
+ 0x9e7b95a4, 0x4c625478, 0x3e890bab, 0xec90ca77,
+ 0x61e55a6a, 0xb3fc9bb6, 0xc117c465, 0x130e05b9,
+ 0x24c17bc3, 0xf6d8ba1f, 0x8433e5cc, 0x562a2410,
+ 0xebad1938, 0x39b4d8e4, 0x4b5f8737, 0x994646eb,
+ 0xae893891, 0x7c90f94d, 0x0e7ba69e, 0xdc626742,
+ 0x71b4c179, 0xa3ad00a5, 0xd1465f76, 0x035f9eaa,
+ 0x3490e0d0, 0xe689210c, 0x94627edf, 0x467bbf03,
+ 0xfbfc822b, 0x29e543f7, 0x5b0e1c24, 0x8917ddf8,
+ 0xbed8a382, 0x6cc1625e, 0x1e2a3d8d, 0xcc33fc51,
+ 0x828cd898, 0x50951944, 0x227e4697, 0xf067874b,
+ 0xc7a8f931, 0x15b138ed, 0x675a673e, 0xb543a6e2,
+ 0x08c49bca, 0xdadd5a16, 0xa83605c5, 0x7a2fc419,
+ 0x4de0ba63, 0x9ff97bbf, 0xed12246c, 0x3f0be5b0,
+ 0x92dd438b, 0x40c48257, 0x322fdd84, 0xe0361c58,
+ 0xd7f96222, 0x05e0a3fe, 0x770bfc2d, 0xa5123df1,
+ 0x189500d9, 0xca8cc105, 0xb8679ed6, 0x6a7e5f0a,
+ 0x5db12170, 0x8fa8e0ac, 0xfd43bf7f, 0x2f5a7ea3,
+ 0xa22feebe, 0x70362f62, 0x02dd70b1, 0xd0c4b16d,
+ 0xe70bcf17, 0x35120ecb, 0x47f95118, 0x95e090c4,
+ 0x2867adec, 0xfa7e6c30, 0x889533e3, 0x5a8cf23f,
+ 0x6d438c45, 0xbf5a4d99, 0xcdb1124a, 0x1fa8d396,
+ 0xb27e75ad, 0x6067b471, 0x128ceba2, 0xc0952a7e,
+ 0xf75a5404, 0x254395d8, 0x57a8ca0b, 0x85b10bd7,
+ 0x383636ff, 0xea2ff723, 0x98c4a8f0, 0x4add692c,
+ 0x7d121756, 0xaf0bd68a, 0xdde08959, 0x0ff94885,
+ 0xc3cab4d4, 0x11d37508, 0x63382adb, 0xb121eb07,
+ 0x86ee957d, 0x54f754a1, 0x261c0b72, 0xf405caae,
+ 0x4982f786, 0x9b9b365a, 0xe9706989, 0x3b69a855,
+ 0x0ca6d62f, 0xdebf17f3, 0xac544820, 0x7e4d89fc,
+ 0xd39b2fc7, 0x0182ee1b, 0x7369b1c8, 0xa1707014,
+ 0x96bf0e6e, 0x44a6cfb2, 0x364d9061, 0xe45451bd,
+ 0x59d36c95, 0x8bcaad49, 0xf921f29a, 0x2b383346,
+ 0x1cf74d3c, 0xceee8ce0, 0xbc05d333, 0x6e1c12ef,
+ 0xe36982f2, 0x3170432e, 0x439b1cfd, 0x9182dd21,
+ 0xa64da35b, 0x74546287, 0x06bf3d54, 0xd4a6fc88,
+ 0x6921c1a0, 0xbb38007c, 0xc9d35faf, 0x1bca9e73,
+ 0x2c05e009, 0xfe1c21d5, 0x8cf77e06, 0x5eeebfda,
+ 0xf33819e1, 0x2121d83d, 0x53ca87ee, 0x81d34632,
+ 0xb61c3848, 0x6405f994, 0x16eea647, 0xc4f7679b,
+ 0x79705ab3, 0xab699b6f, 0xd982c4bc, 0x0b9b0560,
+ 0x3c547b1a, 0xee4dbac6, 0x9ca6e515, 0x4ebf24c9
+ },
+ {
+ 0x00000000, 0x01d8ac87, 0x03b1590e, 0x0269f589,
+ 0x0762b21c, 0x06ba1e9b, 0x04d3eb12, 0x050b4795,
+ 0x0ec56438, 0x0f1dc8bf, 0x0d743d36, 0x0cac91b1,
+ 0x09a7d624, 0x087f7aa3, 0x0a168f2a, 0x0bce23ad,
+ 0x1d8ac870, 0x1c5264f7, 0x1e3b917e, 0x1fe33df9,
+ 0x1ae87a6c, 0x1b30d6eb, 0x19592362, 0x18818fe5,
+ 0x134fac48, 0x129700cf, 0x10fef546, 0x112659c1,
+ 0x142d1e54, 0x15f5b2d3, 0x179c475a, 0x1644ebdd,
+ 0x3b1590e0, 0x3acd3c67, 0x38a4c9ee, 0x397c6569,
+ 0x3c7722fc, 0x3daf8e7b, 0x3fc67bf2, 0x3e1ed775,
+ 0x35d0f4d8, 0x3408585f, 0x3661add6, 0x37b90151,
+ 0x32b246c4, 0x336aea43, 0x31031fca, 0x30dbb34d,
+ 0x269f5890, 0x2747f417, 0x252e019e, 0x24f6ad19,
+ 0x21fdea8c, 0x2025460b, 0x224cb382, 0x23941f05,
+ 0x285a3ca8, 0x2982902f, 0x2beb65a6, 0x2a33c921,
+ 0x2f388eb4, 0x2ee02233, 0x2c89d7ba, 0x2d517b3d,
+ 0x762b21c0, 0x77f38d47, 0x759a78ce, 0x7442d449,
+ 0x714993dc, 0x70913f5b, 0x72f8cad2, 0x73206655,
+ 0x78ee45f8, 0x7936e97f, 0x7b5f1cf6, 0x7a87b071,
+ 0x7f8cf7e4, 0x7e545b63, 0x7c3daeea, 0x7de5026d,
+ 0x6ba1e9b0, 0x6a794537, 0x6810b0be, 0x69c81c39,
+ 0x6cc35bac, 0x6d1bf72b, 0x6f7202a2, 0x6eaaae25,
+ 0x65648d88, 0x64bc210f, 0x66d5d486, 0x670d7801,
+ 0x62063f94, 0x63de9313, 0x61b7669a, 0x606fca1d,
+ 0x4d3eb120, 0x4ce61da7, 0x4e8fe82e, 0x4f5744a9,
+ 0x4a5c033c, 0x4b84afbb, 0x49ed5a32, 0x4835f6b5,
+ 0x43fbd518, 0x4223799f, 0x404a8c16, 0x41922091,
+ 0x44996704, 0x4541cb83, 0x47283e0a, 0x46f0928d,
+ 0x50b47950, 0x516cd5d7, 0x5305205e, 0x52dd8cd9,
+ 0x57d6cb4c, 0x560e67cb, 0x54679242, 0x55bf3ec5,
+ 0x5e711d68, 0x5fa9b1ef, 0x5dc04466, 0x5c18e8e1,
+ 0x5913af74, 0x58cb03f3, 0x5aa2f67a, 0x5b7a5afd,
+ 0xec564380, 0xed8eef07, 0xefe71a8e, 0xee3fb609,
+ 0xeb34f19c, 0xeaec5d1b, 0xe885a892, 0xe95d0415,
+ 0xe29327b8, 0xe34b8b3f, 0xe1227eb6, 0xe0fad231,
+ 0xe5f195a4, 0xe4293923, 0xe640ccaa, 0xe798602d,
+ 0xf1dc8bf0, 0xf0042777, 0xf26dd2fe, 0xf3b57e79,
+ 0xf6be39ec, 0xf766956b, 0xf50f60e2, 0xf4d7cc65,
+ 0xff19efc8, 0xfec1434f, 0xfca8b6c6, 0xfd701a41,
+ 0xf87b5dd4, 0xf9a3f153, 0xfbca04da, 0xfa12a85d,
+ 0xd743d360, 0xd69b7fe7, 0xd4f28a6e, 0xd52a26e9,
+ 0xd021617c, 0xd1f9cdfb, 0xd3903872, 0xd24894f5,
+ 0xd986b758, 0xd85e1bdf, 0xda37ee56, 0xdbef42d1,
+ 0xdee40544, 0xdf3ca9c3, 0xdd555c4a, 0xdc8df0cd,
+ 0xcac91b10, 0xcb11b797, 0xc978421e, 0xc8a0ee99,
+ 0xcdaba90c, 0xcc73058b, 0xce1af002, 0xcfc25c85,
+ 0xc40c7f28, 0xc5d4d3af, 0xc7bd2626, 0xc6658aa1,
+ 0xc36ecd34, 0xc2b661b3, 0xc0df943a, 0xc10738bd,
+ 0x9a7d6240, 0x9ba5cec7, 0x99cc3b4e, 0x981497c9,
+ 0x9d1fd05c, 0x9cc77cdb, 0x9eae8952, 0x9f7625d5,
+ 0x94b80678, 0x9560aaff, 0x97095f76, 0x96d1f3f1,
+ 0x93dab464, 0x920218e3, 0x906bed6a, 0x91b341ed,
+ 0x87f7aa30, 0x862f06b7, 0x8446f33e, 0x859e5fb9,
+ 0x8095182c, 0x814db4ab, 0x83244122, 0x82fceda5,
+ 0x8932ce08, 0x88ea628f, 0x8a839706, 0x8b5b3b81,
+ 0x8e507c14, 0x8f88d093, 0x8de1251a, 0x8c39899d,
+ 0xa168f2a0, 0xa0b05e27, 0xa2d9abae, 0xa3010729,
+ 0xa60a40bc, 0xa7d2ec3b, 0xa5bb19b2, 0xa463b535,
+ 0xafad9698, 0xae753a1f, 0xac1ccf96, 0xadc46311,
+ 0xa8cf2484, 0xa9178803, 0xab7e7d8a, 0xaaa6d10d,
+ 0xbce23ad0, 0xbd3a9657, 0xbf5363de, 0xbe8bcf59,
+ 0xbb8088cc, 0xba58244b, 0xb831d1c2, 0xb9e97d45,
+ 0xb2275ee8, 0xb3fff26f, 0xb19607e6, 0xb04eab61,
+ 0xb545ecf4, 0xb49d4073, 0xb6f4b5fa, 0xb72c197d
+ },
+ {
+ 0x00000000, 0xdc6d9ab7, 0xbc1a28d9, 0x6077b26e,
+ 0x7cf54c05, 0xa098d6b2, 0xc0ef64dc, 0x1c82fe6b,
+ 0xf9ea980a, 0x258702bd, 0x45f0b0d3, 0x999d2a64,
+ 0x851fd40f, 0x59724eb8, 0x3905fcd6, 0xe5686661,
+ 0xf7142da3, 0x2b79b714, 0x4b0e057a, 0x97639fcd,
+ 0x8be161a6, 0x578cfb11, 0x37fb497f, 0xeb96d3c8,
+ 0x0efeb5a9, 0xd2932f1e, 0xb2e49d70, 0x6e8907c7,
+ 0x720bf9ac, 0xae66631b, 0xce11d175, 0x127c4bc2,
+ 0xeae946f1, 0x3684dc46, 0x56f36e28, 0x8a9ef49f,
+ 0x961c0af4, 0x4a719043, 0x2a06222d, 0xf66bb89a,
+ 0x1303defb, 0xcf6e444c, 0xaf19f622, 0x73746c95,
+ 0x6ff692fe, 0xb39b0849, 0xd3ecba27, 0x0f812090,
+ 0x1dfd6b52, 0xc190f1e5, 0xa1e7438b, 0x7d8ad93c,
+ 0x61082757, 0xbd65bde0, 0xdd120f8e, 0x017f9539,
+ 0xe417f358, 0x387a69ef, 0x580ddb81, 0x84604136,
+ 0x98e2bf5d, 0x448f25ea, 0x24f89784, 0xf8950d33,
+ 0xd1139055, 0x0d7e0ae2, 0x6d09b88c, 0xb164223b,
+ 0xade6dc50, 0x718b46e7, 0x11fcf489, 0xcd916e3e,
+ 0x28f9085f, 0xf49492e8, 0x94e32086, 0x488eba31,
+ 0x540c445a, 0x8861deed, 0xe8166c83, 0x347bf634,
+ 0x2607bdf6, 0xfa6a2741, 0x9a1d952f, 0x46700f98,
+ 0x5af2f1f3, 0x869f6b44, 0xe6e8d92a, 0x3a85439d,
+ 0xdfed25fc, 0x0380bf4b, 0x63f70d25, 0xbf9a9792,
+ 0xa31869f9, 0x7f75f34e, 0x1f024120, 0xc36fdb97,
+ 0x3bfad6a4, 0xe7974c13, 0x87e0fe7d, 0x5b8d64ca,
+ 0x470f9aa1, 0x9b620016, 0xfb15b278, 0x277828cf,
+ 0xc2104eae, 0x1e7dd419, 0x7e0a6677, 0xa267fcc0,
+ 0xbee502ab, 0x6288981c, 0x02ff2a72, 0xde92b0c5,
+ 0xcceefb07, 0x108361b0, 0x70f4d3de, 0xac994969,
+ 0xb01bb702, 0x6c762db5, 0x0c019fdb, 0xd06c056c,
+ 0x3504630d, 0xe969f9ba, 0x891e4bd4, 0x5573d163,
+ 0x49f12f08, 0x959cb5bf, 0xf5eb07d1, 0x29869d66,
+ 0xa6e63d1d, 0x7a8ba7aa, 0x1afc15c4, 0xc6918f73,
+ 0xda137118, 0x067eebaf, 0x660959c1, 0xba64c376,
+ 0x5f0ca517, 0x83613fa0, 0xe3168dce, 0x3f7b1779,
+ 0x23f9e912, 0xff9473a5, 0x9fe3c1cb, 0x438e5b7c,
+ 0x51f210be, 0x8d9f8a09, 0xede83867, 0x3185a2d0,
+ 0x2d075cbb, 0xf16ac60c, 0x911d7462, 0x4d70eed5,
+ 0xa81888b4, 0x74751203, 0x1402a06d, 0xc86f3ada,
+ 0xd4edc4b1, 0x08805e06, 0x68f7ec68, 0xb49a76df,
+ 0x4c0f7bec, 0x9062e15b, 0xf0155335, 0x2c78c982,
+ 0x30fa37e9, 0xec97ad5e, 0x8ce01f30, 0x508d8587,
+ 0xb5e5e3e6, 0x69887951, 0x09ffcb3f, 0xd5925188,
+ 0xc910afe3, 0x157d3554, 0x750a873a, 0xa9671d8d,
+ 0xbb1b564f, 0x6776ccf8, 0x07017e96, 0xdb6ce421,
+ 0xc7ee1a4a, 0x1b8380fd, 0x7bf43293, 0xa799a824,
+ 0x42f1ce45, 0x9e9c54f2, 0xfeebe69c, 0x22867c2b,
+ 0x3e048240, 0xe26918f7, 0x821eaa99, 0x5e73302e,
+ 0x77f5ad48, 0xab9837ff, 0xcbef8591, 0x17821f26,
+ 0x0b00e14d, 0xd76d7bfa, 0xb71ac994, 0x6b775323,
+ 0x8e1f3542, 0x5272aff5, 0x32051d9b, 0xee68872c,
+ 0xf2ea7947, 0x2e87e3f0, 0x4ef0519e, 0x929dcb29,
+ 0x80e180eb, 0x5c8c1a5c, 0x3cfba832, 0xe0963285,
+ 0xfc14ccee, 0x20795659, 0x400ee437, 0x9c637e80,
+ 0x790b18e1, 0xa5668256, 0xc5113038, 0x197caa8f,
+ 0x05fe54e4, 0xd993ce53, 0xb9e47c3d, 0x6589e68a,
+ 0x9d1cebb9, 0x4171710e, 0x2106c360, 0xfd6b59d7,
+ 0xe1e9a7bc, 0x3d843d0b, 0x5df38f65, 0x819e15d2,
+ 0x64f673b3, 0xb89be904, 0xd8ec5b6a, 0x0481c1dd,
+ 0x18033fb6, 0xc46ea501, 0xa419176f, 0x78748dd8,
+ 0x6a08c61a, 0xb6655cad, 0xd612eec3, 0x0a7f7474,
+ 0x16fd8a1f, 0xca9010a8, 0xaae7a2c6, 0x768a3871,
+ 0x93e25e10, 0x4f8fc4a7, 0x2ff876c9, 0xf395ec7e,
+ 0xef171215, 0x337a88a2, 0x530d3acc, 0x8f60a07b
+ }
+#if TABLES_COUNT >= 8
+ , {
+ 0x00000000, 0x490d678d, 0x921acf1a, 0xdb17a897,
+ 0x20f48383, 0x69f9e40e, 0xb2ee4c99, 0xfbe32b14,
+ 0x41e90706, 0x08e4608b, 0xd3f3c81c, 0x9afeaf91,
+ 0x611d8485, 0x2810e308, 0xf3074b9f, 0xba0a2c12,
+ 0x83d20e0c, 0xcadf6981, 0x11c8c116, 0x58c5a69b,
+ 0xa3268d8f, 0xea2bea02, 0x313c4295, 0x78312518,
+ 0xc23b090a, 0x8b366e87, 0x5021c610, 0x192ca19d,
+ 0xe2cf8a89, 0xabc2ed04, 0x70d54593, 0x39d8221e,
+ 0x036501af, 0x4a686622, 0x917fceb5, 0xd872a938,
+ 0x2391822c, 0x6a9ce5a1, 0xb18b4d36, 0xf8862abb,
+ 0x428c06a9, 0x0b816124, 0xd096c9b3, 0x999bae3e,
+ 0x6278852a, 0x2b75e2a7, 0xf0624a30, 0xb96f2dbd,
+ 0x80b70fa3, 0xc9ba682e, 0x12adc0b9, 0x5ba0a734,
+ 0xa0438c20, 0xe94eebad, 0x3259433a, 0x7b5424b7,
+ 0xc15e08a5, 0x88536f28, 0x5344c7bf, 0x1a49a032,
+ 0xe1aa8b26, 0xa8a7ecab, 0x73b0443c, 0x3abd23b1,
+ 0x06ca035e, 0x4fc764d3, 0x94d0cc44, 0xddddabc9,
+ 0x263e80dd, 0x6f33e750, 0xb4244fc7, 0xfd29284a,
+ 0x47230458, 0x0e2e63d5, 0xd539cb42, 0x9c34accf,
+ 0x67d787db, 0x2edae056, 0xf5cd48c1, 0xbcc02f4c,
+ 0x85180d52, 0xcc156adf, 0x1702c248, 0x5e0fa5c5,
+ 0xa5ec8ed1, 0xece1e95c, 0x37f641cb, 0x7efb2646,
+ 0xc4f10a54, 0x8dfc6dd9, 0x56ebc54e, 0x1fe6a2c3,
+ 0xe40589d7, 0xad08ee5a, 0x761f46cd, 0x3f122140,
+ 0x05af02f1, 0x4ca2657c, 0x97b5cdeb, 0xdeb8aa66,
+ 0x255b8172, 0x6c56e6ff, 0xb7414e68, 0xfe4c29e5,
+ 0x444605f7, 0x0d4b627a, 0xd65ccaed, 0x9f51ad60,
+ 0x64b28674, 0x2dbfe1f9, 0xf6a8496e, 0xbfa52ee3,
+ 0x867d0cfd, 0xcf706b70, 0x1467c3e7, 0x5d6aa46a,
+ 0xa6898f7e, 0xef84e8f3, 0x34934064, 0x7d9e27e9,
+ 0xc7940bfb, 0x8e996c76, 0x558ec4e1, 0x1c83a36c,
+ 0xe7608878, 0xae6deff5, 0x757a4762, 0x3c7720ef,
+ 0x0d9406bc, 0x44996131, 0x9f8ec9a6, 0xd683ae2b,
+ 0x2d60853f, 0x646de2b2, 0xbf7a4a25, 0xf6772da8,
+ 0x4c7d01ba, 0x05706637, 0xde67cea0, 0x976aa92d,
+ 0x6c898239, 0x2584e5b4, 0xfe934d23, 0xb79e2aae,
+ 0x8e4608b0, 0xc74b6f3d, 0x1c5cc7aa, 0x5551a027,
+ 0xaeb28b33, 0xe7bfecbe, 0x3ca84429, 0x75a523a4,
+ 0xcfaf0fb6, 0x86a2683b, 0x5db5c0ac, 0x14b8a721,
+ 0xef5b8c35, 0xa656ebb8, 0x7d41432f, 0x344c24a2,
+ 0x0ef10713, 0x47fc609e, 0x9cebc809, 0xd5e6af84,
+ 0x2e058490, 0x6708e31d, 0xbc1f4b8a, 0xf5122c07,
+ 0x4f180015, 0x06156798, 0xdd02cf0f, 0x940fa882,
+ 0x6fec8396, 0x26e1e41b, 0xfdf64c8c, 0xb4fb2b01,
+ 0x8d23091f, 0xc42e6e92, 0x1f39c605, 0x5634a188,
+ 0xadd78a9c, 0xe4daed11, 0x3fcd4586, 0x76c0220b,
+ 0xccca0e19, 0x85c76994, 0x5ed0c103, 0x17dda68e,
+ 0xec3e8d9a, 0xa533ea17, 0x7e244280, 0x3729250d,
+ 0x0b5e05e2, 0x4253626f, 0x9944caf8, 0xd049ad75,
+ 0x2baa8661, 0x62a7e1ec, 0xb9b0497b, 0xf0bd2ef6,
+ 0x4ab702e4, 0x03ba6569, 0xd8adcdfe, 0x91a0aa73,
+ 0x6a438167, 0x234ee6ea, 0xf8594e7d, 0xb15429f0,
+ 0x888c0bee, 0xc1816c63, 0x1a96c4f4, 0x539ba379,
+ 0xa878886d, 0xe175efe0, 0x3a624777, 0x736f20fa,
+ 0xc9650ce8, 0x80686b65, 0x5b7fc3f2, 0x1272a47f,
+ 0xe9918f6b, 0xa09ce8e6, 0x7b8b4071, 0x328627fc,
+ 0x083b044d, 0x413663c0, 0x9a21cb57, 0xd32cacda,
+ 0x28cf87ce, 0x61c2e043, 0xbad548d4, 0xf3d82f59,
+ 0x49d2034b, 0x00df64c6, 0xdbc8cc51, 0x92c5abdc,
+ 0x692680c8, 0x202be745, 0xfb3c4fd2, 0xb231285f,
+ 0x8be90a41, 0xc2e46dcc, 0x19f3c55b, 0x50fea2d6,
+ 0xab1d89c2, 0xe210ee4f, 0x390746d8, 0x700a2155,
+ 0xca000d47, 0x830d6aca, 0x581ac25d, 0x1117a5d0,
+ 0xeaf48ec4, 0xa3f9e949, 0x78ee41de, 0x31e32653
+ },
+ {
+ 0x00000000, 0x1b280d78, 0x36501af0, 0x2d781788,
+ 0x6ca035e0, 0x77883898, 0x5af02f10, 0x41d82268,
+ 0xd9406bc0, 0xc26866b8, 0xef107130, 0xf4387c48,
+ 0xb5e05e20, 0xaec85358, 0x83b044d0, 0x989849a8,
+ 0xb641ca37, 0xad69c74f, 0x8011d0c7, 0x9b39ddbf,
+ 0xdae1ffd7, 0xc1c9f2af, 0xecb1e527, 0xf799e85f,
+ 0x6f01a1f7, 0x7429ac8f, 0x5951bb07, 0x4279b67f,
+ 0x03a19417, 0x1889996f, 0x35f18ee7, 0x2ed9839f,
+ 0x684289d9, 0x736a84a1, 0x5e129329, 0x453a9e51,
+ 0x04e2bc39, 0x1fcab141, 0x32b2a6c9, 0x299aabb1,
+ 0xb102e219, 0xaa2aef61, 0x8752f8e9, 0x9c7af591,
+ 0xdda2d7f9, 0xc68ada81, 0xebf2cd09, 0xf0dac071,
+ 0xde0343ee, 0xc52b4e96, 0xe853591e, 0xf37b5466,
+ 0xb2a3760e, 0xa98b7b76, 0x84f36cfe, 0x9fdb6186,
+ 0x0743282e, 0x1c6b2556, 0x311332de, 0x2a3b3fa6,
+ 0x6be31dce, 0x70cb10b6, 0x5db3073e, 0x469b0a46,
+ 0xd08513b2, 0xcbad1eca, 0xe6d50942, 0xfdfd043a,
+ 0xbc252652, 0xa70d2b2a, 0x8a753ca2, 0x915d31da,
+ 0x09c57872, 0x12ed750a, 0x3f956282, 0x24bd6ffa,
+ 0x65654d92, 0x7e4d40ea, 0x53355762, 0x481d5a1a,
+ 0x66c4d985, 0x7decd4fd, 0x5094c375, 0x4bbcce0d,
+ 0x0a64ec65, 0x114ce11d, 0x3c34f695, 0x271cfbed,
+ 0xbf84b245, 0xa4acbf3d, 0x89d4a8b5, 0x92fca5cd,
+ 0xd32487a5, 0xc80c8add, 0xe5749d55, 0xfe5c902d,
+ 0xb8c79a6b, 0xa3ef9713, 0x8e97809b, 0x95bf8de3,
+ 0xd467af8b, 0xcf4fa2f3, 0xe237b57b, 0xf91fb803,
+ 0x6187f1ab, 0x7aaffcd3, 0x57d7eb5b, 0x4cffe623,
+ 0x0d27c44b, 0x160fc933, 0x3b77debb, 0x205fd3c3,
+ 0x0e86505c, 0x15ae5d24, 0x38d64aac, 0x23fe47d4,
+ 0x622665bc, 0x790e68c4, 0x54767f4c, 0x4f5e7234,
+ 0xd7c63b9c, 0xccee36e4, 0xe196216c, 0xfabe2c14,
+ 0xbb660e7c, 0xa04e0304, 0x8d36148c, 0x961e19f4,
+ 0xa5cb3ad3, 0xbee337ab, 0x939b2023, 0x88b32d5b,
+ 0xc96b0f33, 0xd243024b, 0xff3b15c3, 0xe41318bb,
+ 0x7c8b5113, 0x67a35c6b, 0x4adb4be3, 0x51f3469b,
+ 0x102b64f3, 0x0b03698b, 0x267b7e03, 0x3d53737b,
+ 0x138af0e4, 0x08a2fd9c, 0x25daea14, 0x3ef2e76c,
+ 0x7f2ac504, 0x6402c87c, 0x497adff4, 0x5252d28c,
+ 0xcaca9b24, 0xd1e2965c, 0xfc9a81d4, 0xe7b28cac,
+ 0xa66aaec4, 0xbd42a3bc, 0x903ab434, 0x8b12b94c,
+ 0xcd89b30a, 0xd6a1be72, 0xfbd9a9fa, 0xe0f1a482,
+ 0xa12986ea, 0xba018b92, 0x97799c1a, 0x8c519162,
+ 0x14c9d8ca, 0x0fe1d5b2, 0x2299c23a, 0x39b1cf42,
+ 0x7869ed2a, 0x6341e052, 0x4e39f7da, 0x5511faa2,
+ 0x7bc8793d, 0x60e07445, 0x4d9863cd, 0x56b06eb5,
+ 0x17684cdd, 0x0c4041a5, 0x2138562d, 0x3a105b55,
+ 0xa28812fd, 0xb9a01f85, 0x94d8080d, 0x8ff00575,
+ 0xce28271d, 0xd5002a65, 0xf8783ded, 0xe3503095,
+ 0x754e2961, 0x6e662419, 0x431e3391, 0x58363ee9,
+ 0x19ee1c81, 0x02c611f9, 0x2fbe0671, 0x34960b09,
+ 0xac0e42a1, 0xb7264fd9, 0x9a5e5851, 0x81765529,
+ 0xc0ae7741, 0xdb867a39, 0xf6fe6db1, 0xedd660c9,
+ 0xc30fe356, 0xd827ee2e, 0xf55ff9a6, 0xee77f4de,
+ 0xafafd6b6, 0xb487dbce, 0x99ffcc46, 0x82d7c13e,
+ 0x1a4f8896, 0x016785ee, 0x2c1f9266, 0x37379f1e,
+ 0x76efbd76, 0x6dc7b00e, 0x40bfa786, 0x5b97aafe,
+ 0x1d0ca0b8, 0x0624adc0, 0x2b5cba48, 0x3074b730,
+ 0x71ac9558, 0x6a849820, 0x47fc8fa8, 0x5cd482d0,
+ 0xc44ccb78, 0xdf64c600, 0xf21cd188, 0xe934dcf0,
+ 0xa8ecfe98, 0xb3c4f3e0, 0x9ebce468, 0x8594e910,
+ 0xab4d6a8f, 0xb06567f7, 0x9d1d707f, 0x86357d07,
+ 0xc7ed5f6f, 0xdcc55217, 0xf1bd459f, 0xea9548e7,
+ 0x720d014f, 0x69250c37, 0x445d1bbf, 0x5f7516c7,
+ 0x1ead34af, 0x058539d7, 0x28fd2e5f, 0x33d52327
+ },
+ {
+ 0x00000000, 0x4f576811, 0x9eaed022, 0xd1f9b833,
+ 0x399cbdf3, 0x76cbd5e2, 0xa7326dd1, 0xe86505c0,
+ 0x73397be6, 0x3c6e13f7, 0xed97abc4, 0xa2c0c3d5,
+ 0x4aa5c615, 0x05f2ae04, 0xd40b1637, 0x9b5c7e26,
+ 0xe672f7cc, 0xa9259fdd, 0x78dc27ee, 0x378b4fff,
+ 0xdfee4a3f, 0x90b9222e, 0x41409a1d, 0x0e17f20c,
+ 0x954b8c2a, 0xda1ce43b, 0x0be55c08, 0x44b23419,
+ 0xacd731d9, 0xe38059c8, 0x3279e1fb, 0x7d2e89ea,
+ 0xc824f22f, 0x87739a3e, 0x568a220d, 0x19dd4a1c,
+ 0xf1b84fdc, 0xbeef27cd, 0x6f169ffe, 0x2041f7ef,
+ 0xbb1d89c9, 0xf44ae1d8, 0x25b359eb, 0x6ae431fa,
+ 0x8281343a, 0xcdd65c2b, 0x1c2fe418, 0x53788c09,
+ 0x2e5605e3, 0x61016df2, 0xb0f8d5c1, 0xffafbdd0,
+ 0x17cab810, 0x589dd001, 0x89646832, 0xc6330023,
+ 0x5d6f7e05, 0x12381614, 0xc3c1ae27, 0x8c96c636,
+ 0x64f3c3f6, 0x2ba4abe7, 0xfa5d13d4, 0xb50a7bc5,
+ 0x9488f9e9, 0xdbdf91f8, 0x0a2629cb, 0x457141da,
+ 0xad14441a, 0xe2432c0b, 0x33ba9438, 0x7cedfc29,
+ 0xe7b1820f, 0xa8e6ea1e, 0x791f522d, 0x36483a3c,
+ 0xde2d3ffc, 0x917a57ed, 0x4083efde, 0x0fd487cf,
+ 0x72fa0e25, 0x3dad6634, 0xec54de07, 0xa303b616,
+ 0x4b66b3d6, 0x0431dbc7, 0xd5c863f4, 0x9a9f0be5,
+ 0x01c375c3, 0x4e941dd2, 0x9f6da5e1, 0xd03acdf0,
+ 0x385fc830, 0x7708a021, 0xa6f11812, 0xe9a67003,
+ 0x5cac0bc6, 0x13fb63d7, 0xc202dbe4, 0x8d55b3f5,
+ 0x6530b635, 0x2a67de24, 0xfb9e6617, 0xb4c90e06,
+ 0x2f957020, 0x60c21831, 0xb13ba002, 0xfe6cc813,
+ 0x1609cdd3, 0x595ea5c2, 0x88a71df1, 0xc7f075e0,
+ 0xbadefc0a, 0xf589941b, 0x24702c28, 0x6b274439,
+ 0x834241f9, 0xcc1529e8, 0x1dec91db, 0x52bbf9ca,
+ 0xc9e787ec, 0x86b0effd, 0x574957ce, 0x181e3fdf,
+ 0xf07b3a1f, 0xbf2c520e, 0x6ed5ea3d, 0x2182822c,
+ 0x2dd0ee65, 0x62878674, 0xb37e3e47, 0xfc295656,
+ 0x144c5396, 0x5b1b3b87, 0x8ae283b4, 0xc5b5eba5,
+ 0x5ee99583, 0x11befd92, 0xc04745a1, 0x8f102db0,
+ 0x67752870, 0x28224061, 0xf9dbf852, 0xb68c9043,
+ 0xcba219a9, 0x84f571b8, 0x550cc98b, 0x1a5ba19a,
+ 0xf23ea45a, 0xbd69cc4b, 0x6c907478, 0x23c71c69,
+ 0xb89b624f, 0xf7cc0a5e, 0x2635b26d, 0x6962da7c,
+ 0x8107dfbc, 0xce50b7ad, 0x1fa90f9e, 0x50fe678f,
+ 0xe5f41c4a, 0xaaa3745b, 0x7b5acc68, 0x340da479,
+ 0xdc68a1b9, 0x933fc9a8, 0x42c6719b, 0x0d91198a,
+ 0x96cd67ac, 0xd99a0fbd, 0x0863b78e, 0x4734df9f,
+ 0xaf51da5f, 0xe006b24e, 0x31ff0a7d, 0x7ea8626c,
+ 0x0386eb86, 0x4cd18397, 0x9d283ba4, 0xd27f53b5,
+ 0x3a1a5675, 0x754d3e64, 0xa4b48657, 0xebe3ee46,
+ 0x70bf9060, 0x3fe8f871, 0xee114042, 0xa1462853,
+ 0x49232d93, 0x06744582, 0xd78dfdb1, 0x98da95a0,
+ 0xb958178c, 0xf60f7f9d, 0x27f6c7ae, 0x68a1afbf,
+ 0x80c4aa7f, 0xcf93c26e, 0x1e6a7a5d, 0x513d124c,
+ 0xca616c6a, 0x8536047b, 0x54cfbc48, 0x1b98d459,
+ 0xf3fdd199, 0xbcaab988, 0x6d5301bb, 0x220469aa,
+ 0x5f2ae040, 0x107d8851, 0xc1843062, 0x8ed35873,
+ 0x66b65db3, 0x29e135a2, 0xf8188d91, 0xb74fe580,
+ 0x2c139ba6, 0x6344f3b7, 0xb2bd4b84, 0xfdea2395,
+ 0x158f2655, 0x5ad84e44, 0x8b21f677, 0xc4769e66,
+ 0x717ce5a3, 0x3e2b8db2, 0xefd23581, 0xa0855d90,
+ 0x48e05850, 0x07b73041, 0xd64e8872, 0x9919e063,
+ 0x02459e45, 0x4d12f654, 0x9ceb4e67, 0xd3bc2676,
+ 0x3bd923b6, 0x748e4ba7, 0xa577f394, 0xea209b85,
+ 0x970e126f, 0xd8597a7e, 0x09a0c24d, 0x46f7aa5c,
+ 0xae92af9c, 0xe1c5c78d, 0x303c7fbe, 0x7f6b17af,
+ 0xe4376989, 0xab600198, 0x7a99b9ab, 0x35ced1ba,
+ 0xddabd47a, 0x92fcbc6b, 0x43050458, 0x0c526c49
+ },
+ {
+ 0x00000000, 0x5ba1dcca, 0xb743b994, 0xece2655e,
+ 0x6a466e9f, 0x31e7b255, 0xdd05d70b, 0x86a40bc1,
+ 0xd48cdd3e, 0x8f2d01f4, 0x63cf64aa, 0x386eb860,
+ 0xbecab3a1, 0xe56b6f6b, 0x09890a35, 0x5228d6ff,
+ 0xadd8a7cb, 0xf6797b01, 0x1a9b1e5f, 0x413ac295,
+ 0xc79ec954, 0x9c3f159e, 0x70dd70c0, 0x2b7cac0a,
+ 0x79547af5, 0x22f5a63f, 0xce17c361, 0x95b61fab,
+ 0x1312146a, 0x48b3c8a0, 0xa451adfe, 0xfff07134,
+ 0x5f705221, 0x04d18eeb, 0xe833ebb5, 0xb392377f,
+ 0x35363cbe, 0x6e97e074, 0x8275852a, 0xd9d459e0,
+ 0x8bfc8f1f, 0xd05d53d5, 0x3cbf368b, 0x671eea41,
+ 0xe1bae180, 0xba1b3d4a, 0x56f95814, 0x0d5884de,
+ 0xf2a8f5ea, 0xa9092920, 0x45eb4c7e, 0x1e4a90b4,
+ 0x98ee9b75, 0xc34f47bf, 0x2fad22e1, 0x740cfe2b,
+ 0x262428d4, 0x7d85f41e, 0x91679140, 0xcac64d8a,
+ 0x4c62464b, 0x17c39a81, 0xfb21ffdf, 0xa0802315,
+ 0xbee0a442, 0xe5417888, 0x09a31dd6, 0x5202c11c,
+ 0xd4a6cadd, 0x8f071617, 0x63e57349, 0x3844af83,
+ 0x6a6c797c, 0x31cda5b6, 0xdd2fc0e8, 0x868e1c22,
+ 0x002a17e3, 0x5b8bcb29, 0xb769ae77, 0xecc872bd,
+ 0x13380389, 0x4899df43, 0xa47bba1d, 0xffda66d7,
+ 0x797e6d16, 0x22dfb1dc, 0xce3dd482, 0x959c0848,
+ 0xc7b4deb7, 0x9c15027d, 0x70f76723, 0x2b56bbe9,
+ 0xadf2b028, 0xf6536ce2, 0x1ab109bc, 0x4110d576,
+ 0xe190f663, 0xba312aa9, 0x56d34ff7, 0x0d72933d,
+ 0x8bd698fc, 0xd0774436, 0x3c952168, 0x6734fda2,
+ 0x351c2b5d, 0x6ebdf797, 0x825f92c9, 0xd9fe4e03,
+ 0x5f5a45c2, 0x04fb9908, 0xe819fc56, 0xb3b8209c,
+ 0x4c4851a8, 0x17e98d62, 0xfb0be83c, 0xa0aa34f6,
+ 0x260e3f37, 0x7dafe3fd, 0x914d86a3, 0xcaec5a69,
+ 0x98c48c96, 0xc365505c, 0x2f873502, 0x7426e9c8,
+ 0xf282e209, 0xa9233ec3, 0x45c15b9d, 0x1e608757,
+ 0x79005533, 0x22a189f9, 0xce43eca7, 0x95e2306d,
+ 0x13463bac, 0x48e7e766, 0xa4058238, 0xffa45ef2,
+ 0xad8c880d, 0xf62d54c7, 0x1acf3199, 0x416eed53,
+ 0xc7cae692, 0x9c6b3a58, 0x70895f06, 0x2b2883cc,
+ 0xd4d8f2f8, 0x8f792e32, 0x639b4b6c, 0x383a97a6,
+ 0xbe9e9c67, 0xe53f40ad, 0x09dd25f3, 0x527cf939,
+ 0x00542fc6, 0x5bf5f30c, 0xb7179652, 0xecb64a98,
+ 0x6a124159, 0x31b39d93, 0xdd51f8cd, 0x86f02407,
+ 0x26700712, 0x7dd1dbd8, 0x9133be86, 0xca92624c,
+ 0x4c36698d, 0x1797b547, 0xfb75d019, 0xa0d40cd3,
+ 0xf2fcda2c, 0xa95d06e6, 0x45bf63b8, 0x1e1ebf72,
+ 0x98bab4b3, 0xc31b6879, 0x2ff90d27, 0x7458d1ed,
+ 0x8ba8a0d9, 0xd0097c13, 0x3ceb194d, 0x674ac587,
+ 0xe1eece46, 0xba4f128c, 0x56ad77d2, 0x0d0cab18,
+ 0x5f247de7, 0x0485a12d, 0xe867c473, 0xb3c618b9,
+ 0x35621378, 0x6ec3cfb2, 0x8221aaec, 0xd9807626,
+ 0xc7e0f171, 0x9c412dbb, 0x70a348e5, 0x2b02942f,
+ 0xada69fee, 0xf6074324, 0x1ae5267a, 0x4144fab0,
+ 0x136c2c4f, 0x48cdf085, 0xa42f95db, 0xff8e4911,
+ 0x792a42d0, 0x228b9e1a, 0xce69fb44, 0x95c8278e,
+ 0x6a3856ba, 0x31998a70, 0xdd7bef2e, 0x86da33e4,
+ 0x007e3825, 0x5bdfe4ef, 0xb73d81b1, 0xec9c5d7b,
+ 0xbeb48b84, 0xe515574e, 0x09f73210, 0x5256eeda,
+ 0xd4f2e51b, 0x8f5339d1, 0x63b15c8f, 0x38108045,
+ 0x9890a350, 0xc3317f9a, 0x2fd31ac4, 0x7472c60e,
+ 0xf2d6cdcf, 0xa9771105, 0x4595745b, 0x1e34a891,
+ 0x4c1c7e6e, 0x17bda2a4, 0xfb5fc7fa, 0xa0fe1b30,
+ 0x265a10f1, 0x7dfbcc3b, 0x9119a965, 0xcab875af,
+ 0x3548049b, 0x6ee9d851, 0x820bbd0f, 0xd9aa61c5,
+ 0x5f0e6a04, 0x04afb6ce, 0xe84dd390, 0xb3ec0f5a,
+ 0xe1c4d9a5, 0xba65056f, 0x56876031, 0x0d26bcfb,
+ 0x8b82b73a, 0xd0236bf0, 0x3cc10eae, 0x6760d264
+ }
+#endif
+};
+
+static const TCRC32Table s_CRC32TableReverse[TABLES_COUNT] = {
+ {
+ 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba,
+ 0x076dc419, 0x706af48f, 0xe963a535, 0x9e6495a3,
+ 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,
+ 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91,
+ 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de,
+ 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7,
+ 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec,
+ 0x14015c4f, 0x63066cd9, 0xfa0f3d63, 0x8d080df5,
+ 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172,
+ 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b,
+ 0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940,
+ 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59,
+ 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116,
+ 0x21b4f4b5, 0x56b3c423, 0xcfba9599, 0xb8bda50f,
+ 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
+ 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d,
+ 0x76dc4190, 0x01db7106, 0x98d220bc, 0xefd5102a,
+ 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433,
+ 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818,
+ 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01,
+ 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e,
+ 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457,
+ 0x65b0d9c6, 0x12b7e950, 0x8bbeb8ea, 0xfcb9887c,
+ 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65,
+ 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2,
+ 0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb,
+ 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0,
+ 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9,
+ 0x5005713c, 0x270241aa, 0xbe0b1010, 0xc90c2086,
+ 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
+ 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4,
+ 0x59b33d17, 0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad,
+ 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a,
+ 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683,
+ 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8,
+ 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1,
+ 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe,
+ 0xf762575d, 0x806567cb, 0x196c3671, 0x6e6b06e7,
+ 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc,
+ 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5,
+ 0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252,
+ 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b,
+ 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60,
+ 0xdf60efc3, 0xa867df55, 0x316e8eef, 0x4669be79,
+ 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
+ 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f,
+ 0xc5ba3bbe, 0xb2bd0b28, 0x2bb45a92, 0x5cb36a04,
+ 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d,
+ 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a,
+ 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713,
+ 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38,
+ 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21,
+ 0x86d3d2d4, 0xf1d4e242, 0x68ddb3f8, 0x1fda836e,
+ 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777,
+ 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c,
+ 0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45,
+ 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2,
+ 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db,
+ 0xaed16a4a, 0xd9d65adc, 0x40df0b66, 0x37d83bf0,
+ 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
+ 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6,
+ 0xbad03605, 0xcdd70693, 0x54de5729, 0x23d967bf,
+ 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94,
+ 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d
+ },
+ {
+ 0x00000000, 0x191b3141, 0x32366282, 0x2b2d53c3,
+ 0x646cc504, 0x7d77f445, 0x565aa786, 0x4f4196c7,
+ 0xc8d98a08, 0xd1c2bb49, 0xfaefe88a, 0xe3f4d9cb,
+ 0xacb54f0c, 0xb5ae7e4d, 0x9e832d8e, 0x87981ccf,
+ 0x4ac21251, 0x53d92310, 0x78f470d3, 0x61ef4192,
+ 0x2eaed755, 0x37b5e614, 0x1c98b5d7, 0x05838496,
+ 0x821b9859, 0x9b00a918, 0xb02dfadb, 0xa936cb9a,
+ 0xe6775d5d, 0xff6c6c1c, 0xd4413fdf, 0xcd5a0e9e,
+ 0x958424a2, 0x8c9f15e3, 0xa7b24620, 0xbea97761,
+ 0xf1e8e1a6, 0xe8f3d0e7, 0xc3de8324, 0xdac5b265,
+ 0x5d5daeaa, 0x44469feb, 0x6f6bcc28, 0x7670fd69,
+ 0x39316bae, 0x202a5aef, 0x0b07092c, 0x121c386d,
+ 0xdf4636f3, 0xc65d07b2, 0xed705471, 0xf46b6530,
+ 0xbb2af3f7, 0xa231c2b6, 0x891c9175, 0x9007a034,
+ 0x179fbcfb, 0x0e848dba, 0x25a9de79, 0x3cb2ef38,
+ 0x73f379ff, 0x6ae848be, 0x41c51b7d, 0x58de2a3c,
+ 0xf0794f05, 0xe9627e44, 0xc24f2d87, 0xdb541cc6,
+ 0x94158a01, 0x8d0ebb40, 0xa623e883, 0xbf38d9c2,
+ 0x38a0c50d, 0x21bbf44c, 0x0a96a78f, 0x138d96ce,
+ 0x5ccc0009, 0x45d73148, 0x6efa628b, 0x77e153ca,
+ 0xbabb5d54, 0xa3a06c15, 0x888d3fd6, 0x91960e97,
+ 0xded79850, 0xc7cca911, 0xece1fad2, 0xf5facb93,
+ 0x7262d75c, 0x6b79e61d, 0x4054b5de, 0x594f849f,
+ 0x160e1258, 0x0f152319, 0x243870da, 0x3d23419b,
+ 0x65fd6ba7, 0x7ce65ae6, 0x57cb0925, 0x4ed03864,
+ 0x0191aea3, 0x188a9fe2, 0x33a7cc21, 0x2abcfd60,
+ 0xad24e1af, 0xb43fd0ee, 0x9f12832d, 0x8609b26c,
+ 0xc94824ab, 0xd05315ea, 0xfb7e4629, 0xe2657768,
+ 0x2f3f79f6, 0x362448b7, 0x1d091b74, 0x04122a35,
+ 0x4b53bcf2, 0x52488db3, 0x7965de70, 0x607eef31,
+ 0xe7e6f3fe, 0xfefdc2bf, 0xd5d0917c, 0xcccba03d,
+ 0x838a36fa, 0x9a9107bb, 0xb1bc5478, 0xa8a76539,
+ 0x3b83984b, 0x2298a90a, 0x09b5fac9, 0x10aecb88,
+ 0x5fef5d4f, 0x46f46c0e, 0x6dd93fcd, 0x74c20e8c,
+ 0xf35a1243, 0xea412302, 0xc16c70c1, 0xd8774180,
+ 0x9736d747, 0x8e2de606, 0xa500b5c5, 0xbc1b8484,
+ 0x71418a1a, 0x685abb5b, 0x4377e898, 0x5a6cd9d9,
+ 0x152d4f1e, 0x0c367e5f, 0x271b2d9c, 0x3e001cdd,
+ 0xb9980012, 0xa0833153, 0x8bae6290, 0x92b553d1,
+ 0xddf4c516, 0xc4eff457, 0xefc2a794, 0xf6d996d5,
+ 0xae07bce9, 0xb71c8da8, 0x9c31de6b, 0x852aef2a,
+ 0xca6b79ed, 0xd37048ac, 0xf85d1b6f, 0xe1462a2e,
+ 0x66de36e1, 0x7fc507a0, 0x54e85463, 0x4df36522,
+ 0x02b2f3e5, 0x1ba9c2a4, 0x30849167, 0x299fa026,
+ 0xe4c5aeb8, 0xfdde9ff9, 0xd6f3cc3a, 0xcfe8fd7b,
+ 0x80a96bbc, 0x99b25afd, 0xb29f093e, 0xab84387f,
+ 0x2c1c24b0, 0x350715f1, 0x1e2a4632, 0x07317773,
+ 0x4870e1b4, 0x516bd0f5, 0x7a468336, 0x635db277,
+ 0xcbfad74e, 0xd2e1e60f, 0xf9ccb5cc, 0xe0d7848d,
+ 0xaf96124a, 0xb68d230b, 0x9da070c8, 0x84bb4189,
+ 0x03235d46, 0x1a386c07, 0x31153fc4, 0x280e0e85,
+ 0x674f9842, 0x7e54a903, 0x5579fac0, 0x4c62cb81,
+ 0x8138c51f, 0x9823f45e, 0xb30ea79d, 0xaa1596dc,
+ 0xe554001b, 0xfc4f315a, 0xd7626299, 0xce7953d8,
+ 0x49e14f17, 0x50fa7e56, 0x7bd72d95, 0x62cc1cd4,
+ 0x2d8d8a13, 0x3496bb52, 0x1fbbe891, 0x06a0d9d0,
+ 0x5e7ef3ec, 0x4765c2ad, 0x6c48916e, 0x7553a02f,
+ 0x3a1236e8, 0x230907a9, 0x0824546a, 0x113f652b,
+ 0x96a779e4, 0x8fbc48a5, 0xa4911b66, 0xbd8a2a27,
+ 0xf2cbbce0, 0xebd08da1, 0xc0fdde62, 0xd9e6ef23,
+ 0x14bce1bd, 0x0da7d0fc, 0x268a833f, 0x3f91b27e,
+ 0x70d024b9, 0x69cb15f8, 0x42e6463b, 0x5bfd777a,
+ 0xdc656bb5, 0xc57e5af4, 0xee530937, 0xf7483876,
+ 0xb809aeb1, 0xa1129ff0, 0x8a3fcc33, 0x9324fd72
+ },
+ {
+ 0x00000000, 0x01c26a37, 0x0384d46e, 0x0246be59,
+ 0x0709a8dc, 0x06cbc2eb, 0x048d7cb2, 0x054f1685,
+ 0x0e1351b8, 0x0fd13b8f, 0x0d9785d6, 0x0c55efe1,
+ 0x091af964, 0x08d89353, 0x0a9e2d0a, 0x0b5c473d,
+ 0x1c26a370, 0x1de4c947, 0x1fa2771e, 0x1e601d29,
+ 0x1b2f0bac, 0x1aed619b, 0x18abdfc2, 0x1969b5f5,
+ 0x1235f2c8, 0x13f798ff, 0x11b126a6, 0x10734c91,
+ 0x153c5a14, 0x14fe3023, 0x16b88e7a, 0x177ae44d,
+ 0x384d46e0, 0x398f2cd7, 0x3bc9928e, 0x3a0bf8b9,
+ 0x3f44ee3c, 0x3e86840b, 0x3cc03a52, 0x3d025065,
+ 0x365e1758, 0x379c7d6f, 0x35dac336, 0x3418a901,
+ 0x3157bf84, 0x3095d5b3, 0x32d36bea, 0x331101dd,
+ 0x246be590, 0x25a98fa7, 0x27ef31fe, 0x262d5bc9,
+ 0x23624d4c, 0x22a0277b, 0x20e69922, 0x2124f315,
+ 0x2a78b428, 0x2bbade1f, 0x29fc6046, 0x283e0a71,
+ 0x2d711cf4, 0x2cb376c3, 0x2ef5c89a, 0x2f37a2ad,
+ 0x709a8dc0, 0x7158e7f7, 0x731e59ae, 0x72dc3399,
+ 0x7793251c, 0x76514f2b, 0x7417f172, 0x75d59b45,
+ 0x7e89dc78, 0x7f4bb64f, 0x7d0d0816, 0x7ccf6221,
+ 0x798074a4, 0x78421e93, 0x7a04a0ca, 0x7bc6cafd,
+ 0x6cbc2eb0, 0x6d7e4487, 0x6f38fade, 0x6efa90e9,
+ 0x6bb5866c, 0x6a77ec5b, 0x68315202, 0x69f33835,
+ 0x62af7f08, 0x636d153f, 0x612bab66, 0x60e9c151,
+ 0x65a6d7d4, 0x6464bde3, 0x662203ba, 0x67e0698d,
+ 0x48d7cb20, 0x4915a117, 0x4b531f4e, 0x4a917579,
+ 0x4fde63fc, 0x4e1c09cb, 0x4c5ab792, 0x4d98dda5,
+ 0x46c49a98, 0x4706f0af, 0x45404ef6, 0x448224c1,
+ 0x41cd3244, 0x400f5873, 0x4249e62a, 0x438b8c1d,
+ 0x54f16850, 0x55330267, 0x5775bc3e, 0x56b7d609,
+ 0x53f8c08c, 0x523aaabb, 0x507c14e2, 0x51be7ed5,
+ 0x5ae239e8, 0x5b2053df, 0x5966ed86, 0x58a487b1,
+ 0x5deb9134, 0x5c29fb03, 0x5e6f455a, 0x5fad2f6d,
+ 0xe1351b80, 0xe0f771b7, 0xe2b1cfee, 0xe373a5d9,
+ 0xe63cb35c, 0xe7fed96b, 0xe5b86732, 0xe47a0d05,
+ 0xef264a38, 0xeee4200f, 0xeca29e56, 0xed60f461,
+ 0xe82fe2e4, 0xe9ed88d3, 0xebab368a, 0xea695cbd,
+ 0xfd13b8f0, 0xfcd1d2c7, 0xfe976c9e, 0xff5506a9,
+ 0xfa1a102c, 0xfbd87a1b, 0xf99ec442, 0xf85cae75,
+ 0xf300e948, 0xf2c2837f, 0xf0843d26, 0xf1465711,
+ 0xf4094194, 0xf5cb2ba3, 0xf78d95fa, 0xf64fffcd,
+ 0xd9785d60, 0xd8ba3757, 0xdafc890e, 0xdb3ee339,
+ 0xde71f5bc, 0xdfb39f8b, 0xddf521d2, 0xdc374be5,
+ 0xd76b0cd8, 0xd6a966ef, 0xd4efd8b6, 0xd52db281,
+ 0xd062a404, 0xd1a0ce33, 0xd3e6706a, 0xd2241a5d,
+ 0xc55efe10, 0xc49c9427, 0xc6da2a7e, 0xc7184049,
+ 0xc25756cc, 0xc3953cfb, 0xc1d382a2, 0xc011e895,
+ 0xcb4dafa8, 0xca8fc59f, 0xc8c97bc6, 0xc90b11f1,
+ 0xcc440774, 0xcd866d43, 0xcfc0d31a, 0xce02b92d,
+ 0x91af9640, 0x906dfc77, 0x922b422e, 0x93e92819,
+ 0x96a63e9c, 0x976454ab, 0x9522eaf2, 0x94e080c5,
+ 0x9fbcc7f8, 0x9e7eadcf, 0x9c381396, 0x9dfa79a1,
+ 0x98b56f24, 0x99770513, 0x9b31bb4a, 0x9af3d17d,
+ 0x8d893530, 0x8c4b5f07, 0x8e0de15e, 0x8fcf8b69,
+ 0x8a809dec, 0x8b42f7db, 0x89044982, 0x88c623b5,
+ 0x839a6488, 0x82580ebf, 0x801eb0e6, 0x81dcdad1,
+ 0x8493cc54, 0x8551a663, 0x8717183a, 0x86d5720d,
+ 0xa9e2d0a0, 0xa820ba97, 0xaa6604ce, 0xaba46ef9,
+ 0xaeeb787c, 0xaf29124b, 0xad6fac12, 0xacadc625,
+ 0xa7f18118, 0xa633eb2f, 0xa4755576, 0xa5b73f41,
+ 0xa0f829c4, 0xa13a43f3, 0xa37cfdaa, 0xa2be979d,
+ 0xb5c473d0, 0xb40619e7, 0xb640a7be, 0xb782cd89,
+ 0xb2cddb0c, 0xb30fb13b, 0xb1490f62, 0xb08b6555,
+ 0xbbd72268, 0xba15485f, 0xb853f606, 0xb9919c31,
+ 0xbcde8ab4, 0xbd1ce083, 0xbf5a5eda, 0xbe9834ed
+ },
+ {
+ 0x00000000, 0xb8bc6765, 0xaa09c88b, 0x12b5afee,
+ 0x8f629757, 0x37def032, 0x256b5fdc, 0x9dd738b9,
+ 0xc5b428ef, 0x7d084f8a, 0x6fbde064, 0xd7018701,
+ 0x4ad6bfb8, 0xf26ad8dd, 0xe0df7733, 0x58631056,
+ 0x5019579f, 0xe8a530fa, 0xfa109f14, 0x42acf871,
+ 0xdf7bc0c8, 0x67c7a7ad, 0x75720843, 0xcdce6f26,
+ 0x95ad7f70, 0x2d111815, 0x3fa4b7fb, 0x8718d09e,
+ 0x1acfe827, 0xa2738f42, 0xb0c620ac, 0x087a47c9,
+ 0xa032af3e, 0x188ec85b, 0x0a3b67b5, 0xb28700d0,
+ 0x2f503869, 0x97ec5f0c, 0x8559f0e2, 0x3de59787,
+ 0x658687d1, 0xdd3ae0b4, 0xcf8f4f5a, 0x7733283f,
+ 0xeae41086, 0x525877e3, 0x40edd80d, 0xf851bf68,
+ 0xf02bf8a1, 0x48979fc4, 0x5a22302a, 0xe29e574f,
+ 0x7f496ff6, 0xc7f50893, 0xd540a77d, 0x6dfcc018,
+ 0x359fd04e, 0x8d23b72b, 0x9f9618c5, 0x272a7fa0,
+ 0xbafd4719, 0x0241207c, 0x10f48f92, 0xa848e8f7,
+ 0x9b14583d, 0x23a83f58, 0x311d90b6, 0x89a1f7d3,
+ 0x1476cf6a, 0xaccaa80f, 0xbe7f07e1, 0x06c36084,
+ 0x5ea070d2, 0xe61c17b7, 0xf4a9b859, 0x4c15df3c,
+ 0xd1c2e785, 0x697e80e0, 0x7bcb2f0e, 0xc377486b,
+ 0xcb0d0fa2, 0x73b168c7, 0x6104c729, 0xd9b8a04c,
+ 0x446f98f5, 0xfcd3ff90, 0xee66507e, 0x56da371b,
+ 0x0eb9274d, 0xb6054028, 0xa4b0efc6, 0x1c0c88a3,
+ 0x81dbb01a, 0x3967d77f, 0x2bd27891, 0x936e1ff4,
+ 0x3b26f703, 0x839a9066, 0x912f3f88, 0x299358ed,
+ 0xb4446054, 0x0cf80731, 0x1e4da8df, 0xa6f1cfba,
+ 0xfe92dfec, 0x462eb889, 0x549b1767, 0xec277002,
+ 0x71f048bb, 0xc94c2fde, 0xdbf98030, 0x6345e755,
+ 0x6b3fa09c, 0xd383c7f9, 0xc1366817, 0x798a0f72,
+ 0xe45d37cb, 0x5ce150ae, 0x4e54ff40, 0xf6e89825,
+ 0xae8b8873, 0x1637ef16, 0x048240f8, 0xbc3e279d,
+ 0x21e91f24, 0x99557841, 0x8be0d7af, 0x335cb0ca,
+ 0xed59b63b, 0x55e5d15e, 0x47507eb0, 0xffec19d5,
+ 0x623b216c, 0xda874609, 0xc832e9e7, 0x708e8e82,
+ 0x28ed9ed4, 0x9051f9b1, 0x82e4565f, 0x3a58313a,
+ 0xa78f0983, 0x1f336ee6, 0x0d86c108, 0xb53aa66d,
+ 0xbd40e1a4, 0x05fc86c1, 0x1749292f, 0xaff54e4a,
+ 0x322276f3, 0x8a9e1196, 0x982bbe78, 0x2097d91d,
+ 0x78f4c94b, 0xc048ae2e, 0xd2fd01c0, 0x6a4166a5,
+ 0xf7965e1c, 0x4f2a3979, 0x5d9f9697, 0xe523f1f2,
+ 0x4d6b1905, 0xf5d77e60, 0xe762d18e, 0x5fdeb6eb,
+ 0xc2098e52, 0x7ab5e937, 0x680046d9, 0xd0bc21bc,
+ 0x88df31ea, 0x3063568f, 0x22d6f961, 0x9a6a9e04,
+ 0x07bda6bd, 0xbf01c1d8, 0xadb46e36, 0x15080953,
+ 0x1d724e9a, 0xa5ce29ff, 0xb77b8611, 0x0fc7e174,
+ 0x9210d9cd, 0x2aacbea8, 0x38191146, 0x80a57623,
+ 0xd8c66675, 0x607a0110, 0x72cfaefe, 0xca73c99b,
+ 0x57a4f122, 0xef189647, 0xfdad39a9, 0x45115ecc,
+ 0x764dee06, 0xcef18963, 0xdc44268d, 0x64f841e8,
+ 0xf92f7951, 0x41931e34, 0x5326b1da, 0xeb9ad6bf,
+ 0xb3f9c6e9, 0x0b45a18c, 0x19f00e62, 0xa14c6907,
+ 0x3c9b51be, 0x842736db, 0x96929935, 0x2e2efe50,
+ 0x2654b999, 0x9ee8defc, 0x8c5d7112, 0x34e11677,
+ 0xa9362ece, 0x118a49ab, 0x033fe645, 0xbb838120,
+ 0xe3e09176, 0x5b5cf613, 0x49e959fd, 0xf1553e98,
+ 0x6c820621, 0xd43e6144, 0xc68bceaa, 0x7e37a9cf,
+ 0xd67f4138, 0x6ec3265d, 0x7c7689b3, 0xc4caeed6,
+ 0x591dd66f, 0xe1a1b10a, 0xf3141ee4, 0x4ba87981,
+ 0x13cb69d7, 0xab770eb2, 0xb9c2a15c, 0x017ec639,
+ 0x9ca9fe80, 0x241599e5, 0x36a0360b, 0x8e1c516e,
+ 0x866616a7, 0x3eda71c2, 0x2c6fde2c, 0x94d3b949,
+ 0x090481f0, 0xb1b8e695, 0xa30d497b, 0x1bb12e1e,
+ 0x43d23e48, 0xfb6e592d, 0xe9dbf6c3, 0x516791a6,
+ 0xccb0a91f, 0x740cce7a, 0x66b96194, 0xde0506f1
+ }
+#if TABLES_COUNT >= 8
+ , {
+ 0x00000000, 0x3d6029b0, 0x7ac05360, 0x47a07ad0,
+ 0xf580a6c0, 0xc8e08f70, 0x8f40f5a0, 0xb220dc10,
+ 0x30704bc1, 0x0d106271, 0x4ab018a1, 0x77d03111,
+ 0xc5f0ed01, 0xf890c4b1, 0xbf30be61, 0x825097d1,
+ 0x60e09782, 0x5d80be32, 0x1a20c4e2, 0x2740ed52,
+ 0x95603142, 0xa80018f2, 0xefa06222, 0xd2c04b92,
+ 0x5090dc43, 0x6df0f5f3, 0x2a508f23, 0x1730a693,
+ 0xa5107a83, 0x98705333, 0xdfd029e3, 0xe2b00053,
+ 0xc1c12f04, 0xfca106b4, 0xbb017c64, 0x866155d4,
+ 0x344189c4, 0x0921a074, 0x4e81daa4, 0x73e1f314,
+ 0xf1b164c5, 0xccd14d75, 0x8b7137a5, 0xb6111e15,
+ 0x0431c205, 0x3951ebb5, 0x7ef19165, 0x4391b8d5,
+ 0xa121b886, 0x9c419136, 0xdbe1ebe6, 0xe681c256,
+ 0x54a11e46, 0x69c137f6, 0x2e614d26, 0x13016496,
+ 0x9151f347, 0xac31daf7, 0xeb91a027, 0xd6f18997,
+ 0x64d15587, 0x59b17c37, 0x1e1106e7, 0x23712f57,
+ 0x58f35849, 0x659371f9, 0x22330b29, 0x1f532299,
+ 0xad73fe89, 0x9013d739, 0xd7b3ade9, 0xead38459,
+ 0x68831388, 0x55e33a38, 0x124340e8, 0x2f236958,
+ 0x9d03b548, 0xa0639cf8, 0xe7c3e628, 0xdaa3cf98,
+ 0x3813cfcb, 0x0573e67b, 0x42d39cab, 0x7fb3b51b,
+ 0xcd93690b, 0xf0f340bb, 0xb7533a6b, 0x8a3313db,
+ 0x0863840a, 0x3503adba, 0x72a3d76a, 0x4fc3feda,
+ 0xfde322ca, 0xc0830b7a, 0x872371aa, 0xba43581a,
+ 0x9932774d, 0xa4525efd, 0xe3f2242d, 0xde920d9d,
+ 0x6cb2d18d, 0x51d2f83d, 0x167282ed, 0x2b12ab5d,
+ 0xa9423c8c, 0x9422153c, 0xd3826fec, 0xeee2465c,
+ 0x5cc29a4c, 0x61a2b3fc, 0x2602c92c, 0x1b62e09c,
+ 0xf9d2e0cf, 0xc4b2c97f, 0x8312b3af, 0xbe729a1f,
+ 0x0c52460f, 0x31326fbf, 0x7692156f, 0x4bf23cdf,
+ 0xc9a2ab0e, 0xf4c282be, 0xb362f86e, 0x8e02d1de,
+ 0x3c220dce, 0x0142247e, 0x46e25eae, 0x7b82771e,
+ 0xb1e6b092, 0x8c869922, 0xcb26e3f2, 0xf646ca42,
+ 0x44661652, 0x79063fe2, 0x3ea64532, 0x03c66c82,
+ 0x8196fb53, 0xbcf6d2e3, 0xfb56a833, 0xc6368183,
+ 0x74165d93, 0x49767423, 0x0ed60ef3, 0x33b62743,
+ 0xd1062710, 0xec660ea0, 0xabc67470, 0x96a65dc0,
+ 0x248681d0, 0x19e6a860, 0x5e46d2b0, 0x6326fb00,
+ 0xe1766cd1, 0xdc164561, 0x9bb63fb1, 0xa6d61601,
+ 0x14f6ca11, 0x2996e3a1, 0x6e369971, 0x5356b0c1,
+ 0x70279f96, 0x4d47b626, 0x0ae7ccf6, 0x3787e546,
+ 0x85a73956, 0xb8c710e6, 0xff676a36, 0xc2074386,
+ 0x4057d457, 0x7d37fde7, 0x3a978737, 0x07f7ae87,
+ 0xb5d77297, 0x88b75b27, 0xcf1721f7, 0xf2770847,
+ 0x10c70814, 0x2da721a4, 0x6a075b74, 0x576772c4,
+ 0xe547aed4, 0xd8278764, 0x9f87fdb4, 0xa2e7d404,
+ 0x20b743d5, 0x1dd76a65, 0x5a7710b5, 0x67173905,
+ 0xd537e515, 0xe857cca5, 0xaff7b675, 0x92979fc5,
+ 0xe915e8db, 0xd475c16b, 0x93d5bbbb, 0xaeb5920b,
+ 0x1c954e1b, 0x21f567ab, 0x66551d7b, 0x5b3534cb,
+ 0xd965a31a, 0xe4058aaa, 0xa3a5f07a, 0x9ec5d9ca,
+ 0x2ce505da, 0x11852c6a, 0x562556ba, 0x6b457f0a,
+ 0x89f57f59, 0xb49556e9, 0xf3352c39, 0xce550589,
+ 0x7c75d999, 0x4115f029, 0x06b58af9, 0x3bd5a349,
+ 0xb9853498, 0x84e51d28, 0xc34567f8, 0xfe254e48,
+ 0x4c059258, 0x7165bbe8, 0x36c5c138, 0x0ba5e888,
+ 0x28d4c7df, 0x15b4ee6f, 0x521494bf, 0x6f74bd0f,
+ 0xdd54611f, 0xe03448af, 0xa794327f, 0x9af41bcf,
+ 0x18a48c1e, 0x25c4a5ae, 0x6264df7e, 0x5f04f6ce,
+ 0xed242ade, 0xd044036e, 0x97e479be, 0xaa84500e,
+ 0x4834505d, 0x755479ed, 0x32f4033d, 0x0f942a8d,
+ 0xbdb4f69d, 0x80d4df2d, 0xc774a5fd, 0xfa148c4d,
+ 0x78441b9c, 0x4524322c, 0x028448fc, 0x3fe4614c,
+ 0x8dc4bd5c, 0xb0a494ec, 0xf704ee3c, 0xca64c78c
+ },
+ {
+ 0x00000000, 0xcb5cd3a5, 0x4dc8a10b, 0x869472ae,
+ 0x9b914216, 0x50cd91b3, 0xd659e31d, 0x1d0530b8,
+ 0xec53826d, 0x270f51c8, 0xa19b2366, 0x6ac7f0c3,
+ 0x77c2c07b, 0xbc9e13de, 0x3a0a6170, 0xf156b2d5,
+ 0x03d6029b, 0xc88ad13e, 0x4e1ea390, 0x85427035,
+ 0x9847408d, 0x531b9328, 0xd58fe186, 0x1ed33223,
+ 0xef8580f6, 0x24d95353, 0xa24d21fd, 0x6911f258,
+ 0x7414c2e0, 0xbf481145, 0x39dc63eb, 0xf280b04e,
+ 0x07ac0536, 0xccf0d693, 0x4a64a43d, 0x81387798,
+ 0x9c3d4720, 0x57619485, 0xd1f5e62b, 0x1aa9358e,
+ 0xebff875b, 0x20a354fe, 0xa6372650, 0x6d6bf5f5,
+ 0x706ec54d, 0xbb3216e8, 0x3da66446, 0xf6fab7e3,
+ 0x047a07ad, 0xcf26d408, 0x49b2a6a6, 0x82ee7503,
+ 0x9feb45bb, 0x54b7961e, 0xd223e4b0, 0x197f3715,
+ 0xe82985c0, 0x23755665, 0xa5e124cb, 0x6ebdf76e,
+ 0x73b8c7d6, 0xb8e41473, 0x3e7066dd, 0xf52cb578,
+ 0x0f580a6c, 0xc404d9c9, 0x4290ab67, 0x89cc78c2,
+ 0x94c9487a, 0x5f959bdf, 0xd901e971, 0x125d3ad4,
+ 0xe30b8801, 0x28575ba4, 0xaec3290a, 0x659ffaaf,
+ 0x789aca17, 0xb3c619b2, 0x35526b1c, 0xfe0eb8b9,
+ 0x0c8e08f7, 0xc7d2db52, 0x4146a9fc, 0x8a1a7a59,
+ 0x971f4ae1, 0x5c439944, 0xdad7ebea, 0x118b384f,
+ 0xe0dd8a9a, 0x2b81593f, 0xad152b91, 0x6649f834,
+ 0x7b4cc88c, 0xb0101b29, 0x36846987, 0xfdd8ba22,
+ 0x08f40f5a, 0xc3a8dcff, 0x453cae51, 0x8e607df4,
+ 0x93654d4c, 0x58399ee9, 0xdeadec47, 0x15f13fe2,
+ 0xe4a78d37, 0x2ffb5e92, 0xa96f2c3c, 0x6233ff99,
+ 0x7f36cf21, 0xb46a1c84, 0x32fe6e2a, 0xf9a2bd8f,
+ 0x0b220dc1, 0xc07ede64, 0x46eaacca, 0x8db67f6f,
+ 0x90b34fd7, 0x5bef9c72, 0xdd7beedc, 0x16273d79,
+ 0xe7718fac, 0x2c2d5c09, 0xaab92ea7, 0x61e5fd02,
+ 0x7ce0cdba, 0xb7bc1e1f, 0x31286cb1, 0xfa74bf14,
+ 0x1eb014d8, 0xd5ecc77d, 0x5378b5d3, 0x98246676,
+ 0x852156ce, 0x4e7d856b, 0xc8e9f7c5, 0x03b52460,
+ 0xf2e396b5, 0x39bf4510, 0xbf2b37be, 0x7477e41b,
+ 0x6972d4a3, 0xa22e0706, 0x24ba75a8, 0xefe6a60d,
+ 0x1d661643, 0xd63ac5e6, 0x50aeb748, 0x9bf264ed,
+ 0x86f75455, 0x4dab87f0, 0xcb3ff55e, 0x006326fb,
+ 0xf135942e, 0x3a69478b, 0xbcfd3525, 0x77a1e680,
+ 0x6aa4d638, 0xa1f8059d, 0x276c7733, 0xec30a496,
+ 0x191c11ee, 0xd240c24b, 0x54d4b0e5, 0x9f886340,
+ 0x828d53f8, 0x49d1805d, 0xcf45f2f3, 0x04192156,
+ 0xf54f9383, 0x3e134026, 0xb8873288, 0x73dbe12d,
+ 0x6eded195, 0xa5820230, 0x2316709e, 0xe84aa33b,
+ 0x1aca1375, 0xd196c0d0, 0x5702b27e, 0x9c5e61db,
+ 0x815b5163, 0x4a0782c6, 0xcc93f068, 0x07cf23cd,
+ 0xf6999118, 0x3dc542bd, 0xbb513013, 0x700de3b6,
+ 0x6d08d30e, 0xa65400ab, 0x20c07205, 0xeb9ca1a0,
+ 0x11e81eb4, 0xdab4cd11, 0x5c20bfbf, 0x977c6c1a,
+ 0x8a795ca2, 0x41258f07, 0xc7b1fda9, 0x0ced2e0c,
+ 0xfdbb9cd9, 0x36e74f7c, 0xb0733dd2, 0x7b2fee77,
+ 0x662adecf, 0xad760d6a, 0x2be27fc4, 0xe0beac61,
+ 0x123e1c2f, 0xd962cf8a, 0x5ff6bd24, 0x94aa6e81,
+ 0x89af5e39, 0x42f38d9c, 0xc467ff32, 0x0f3b2c97,
+ 0xfe6d9e42, 0x35314de7, 0xb3a53f49, 0x78f9ecec,
+ 0x65fcdc54, 0xaea00ff1, 0x28347d5f, 0xe368aefa,
+ 0x16441b82, 0xdd18c827, 0x5b8cba89, 0x90d0692c,
+ 0x8dd55994, 0x46898a31, 0xc01df89f, 0x0b412b3a,
+ 0xfa1799ef, 0x314b4a4a, 0xb7df38e4, 0x7c83eb41,
+ 0x6186dbf9, 0xaada085c, 0x2c4e7af2, 0xe712a957,
+ 0x15921919, 0xdececabc, 0x585ab812, 0x93066bb7,
+ 0x8e035b0f, 0x455f88aa, 0xc3cbfa04, 0x089729a1,
+ 0xf9c19b74, 0x329d48d1, 0xb4093a7f, 0x7f55e9da,
+ 0x6250d962, 0xa90c0ac7, 0x2f987869, 0xe4c4abcc
+ },
+ {
+ 0x00000000, 0xa6770bb4, 0x979f1129, 0x31e81a9d,
+ 0xf44f2413, 0x52382fa7, 0x63d0353a, 0xc5a73e8e,
+ 0x33ef4e67, 0x959845d3, 0xa4705f4e, 0x020754fa,
+ 0xc7a06a74, 0x61d761c0, 0x503f7b5d, 0xf64870e9,
+ 0x67de9cce, 0xc1a9977a, 0xf0418de7, 0x56368653,
+ 0x9391b8dd, 0x35e6b369, 0x040ea9f4, 0xa279a240,
+ 0x5431d2a9, 0xf246d91d, 0xc3aec380, 0x65d9c834,
+ 0xa07ef6ba, 0x0609fd0e, 0x37e1e793, 0x9196ec27,
+ 0xcfbd399c, 0x69ca3228, 0x582228b5, 0xfe552301,
+ 0x3bf21d8f, 0x9d85163b, 0xac6d0ca6, 0x0a1a0712,
+ 0xfc5277fb, 0x5a257c4f, 0x6bcd66d2, 0xcdba6d66,
+ 0x081d53e8, 0xae6a585c, 0x9f8242c1, 0x39f54975,
+ 0xa863a552, 0x0e14aee6, 0x3ffcb47b, 0x998bbfcf,
+ 0x5c2c8141, 0xfa5b8af5, 0xcbb39068, 0x6dc49bdc,
+ 0x9b8ceb35, 0x3dfbe081, 0x0c13fa1c, 0xaa64f1a8,
+ 0x6fc3cf26, 0xc9b4c492, 0xf85cde0f, 0x5e2bd5bb,
+ 0x440b7579, 0xe27c7ecd, 0xd3946450, 0x75e36fe4,
+ 0xb044516a, 0x16335ade, 0x27db4043, 0x81ac4bf7,
+ 0x77e43b1e, 0xd19330aa, 0xe07b2a37, 0x460c2183,
+ 0x83ab1f0d, 0x25dc14b9, 0x14340e24, 0xb2430590,
+ 0x23d5e9b7, 0x85a2e203, 0xb44af89e, 0x123df32a,
+ 0xd79acda4, 0x71edc610, 0x4005dc8d, 0xe672d739,
+ 0x103aa7d0, 0xb64dac64, 0x87a5b6f9, 0x21d2bd4d,
+ 0xe47583c3, 0x42028877, 0x73ea92ea, 0xd59d995e,
+ 0x8bb64ce5, 0x2dc14751, 0x1c295dcc, 0xba5e5678,
+ 0x7ff968f6, 0xd98e6342, 0xe86679df, 0x4e11726b,
+ 0xb8590282, 0x1e2e0936, 0x2fc613ab, 0x89b1181f,
+ 0x4c162691, 0xea612d25, 0xdb8937b8, 0x7dfe3c0c,
+ 0xec68d02b, 0x4a1fdb9f, 0x7bf7c102, 0xdd80cab6,
+ 0x1827f438, 0xbe50ff8c, 0x8fb8e511, 0x29cfeea5,
+ 0xdf879e4c, 0x79f095f8, 0x48188f65, 0xee6f84d1,
+ 0x2bc8ba5f, 0x8dbfb1eb, 0xbc57ab76, 0x1a20a0c2,
+ 0x8816eaf2, 0x2e61e146, 0x1f89fbdb, 0xb9fef06f,
+ 0x7c59cee1, 0xda2ec555, 0xebc6dfc8, 0x4db1d47c,
+ 0xbbf9a495, 0x1d8eaf21, 0x2c66b5bc, 0x8a11be08,
+ 0x4fb68086, 0xe9c18b32, 0xd82991af, 0x7e5e9a1b,
+ 0xefc8763c, 0x49bf7d88, 0x78576715, 0xde206ca1,
+ 0x1b87522f, 0xbdf0599b, 0x8c184306, 0x2a6f48b2,
+ 0xdc27385b, 0x7a5033ef, 0x4bb82972, 0xedcf22c6,
+ 0x28681c48, 0x8e1f17fc, 0xbff70d61, 0x198006d5,
+ 0x47abd36e, 0xe1dcd8da, 0xd034c247, 0x7643c9f3,
+ 0xb3e4f77d, 0x1593fcc9, 0x247be654, 0x820cede0,
+ 0x74449d09, 0xd23396bd, 0xe3db8c20, 0x45ac8794,
+ 0x800bb91a, 0x267cb2ae, 0x1794a833, 0xb1e3a387,
+ 0x20754fa0, 0x86024414, 0xb7ea5e89, 0x119d553d,
+ 0xd43a6bb3, 0x724d6007, 0x43a57a9a, 0xe5d2712e,
+ 0x139a01c7, 0xb5ed0a73, 0x840510ee, 0x22721b5a,
+ 0xe7d525d4, 0x41a22e60, 0x704a34fd, 0xd63d3f49,
+ 0xcc1d9f8b, 0x6a6a943f, 0x5b828ea2, 0xfdf58516,
+ 0x3852bb98, 0x9e25b02c, 0xafcdaab1, 0x09baa105,
+ 0xfff2d1ec, 0x5985da58, 0x686dc0c5, 0xce1acb71,
+ 0x0bbdf5ff, 0xadcafe4b, 0x9c22e4d6, 0x3a55ef62,
+ 0xabc30345, 0x0db408f1, 0x3c5c126c, 0x9a2b19d8,
+ 0x5f8c2756, 0xf9fb2ce2, 0xc813367f, 0x6e643dcb,
+ 0x982c4d22, 0x3e5b4696, 0x0fb35c0b, 0xa9c457bf,
+ 0x6c636931, 0xca146285, 0xfbfc7818, 0x5d8b73ac,
+ 0x03a0a617, 0xa5d7ada3, 0x943fb73e, 0x3248bc8a,
+ 0xf7ef8204, 0x519889b0, 0x6070932d, 0xc6079899,
+ 0x304fe870, 0x9638e3c4, 0xa7d0f959, 0x01a7f2ed,
+ 0xc400cc63, 0x6277c7d7, 0x539fdd4a, 0xf5e8d6fe,
+ 0x647e3ad9, 0xc209316d, 0xf3e12bf0, 0x55962044,
+ 0x90311eca, 0x3646157e, 0x07ae0fe3, 0xa1d90457,
+ 0x579174be, 0xf1e67f0a, 0xc00e6597, 0x66796e23,
+ 0xa3de50ad, 0x05a95b19, 0x34414184, 0x92364a30
+ },
+ {
+ 0x00000000, 0xccaa009e, 0x4225077d, 0x8e8f07e3,
+ 0x844a0efa, 0x48e00e64, 0xc66f0987, 0x0ac50919,
+ 0xd3e51bb5, 0x1f4f1b2b, 0x91c01cc8, 0x5d6a1c56,
+ 0x57af154f, 0x9b0515d1, 0x158a1232, 0xd92012ac,
+ 0x7cbb312b, 0xb01131b5, 0x3e9e3656, 0xf23436c8,
+ 0xf8f13fd1, 0x345b3f4f, 0xbad438ac, 0x767e3832,
+ 0xaf5e2a9e, 0x63f42a00, 0xed7b2de3, 0x21d12d7d,
+ 0x2b142464, 0xe7be24fa, 0x69312319, 0xa59b2387,
+ 0xf9766256, 0x35dc62c8, 0xbb53652b, 0x77f965b5,
+ 0x7d3c6cac, 0xb1966c32, 0x3f196bd1, 0xf3b36b4f,
+ 0x2a9379e3, 0xe639797d, 0x68b67e9e, 0xa41c7e00,
+ 0xaed97719, 0x62737787, 0xecfc7064, 0x205670fa,
+ 0x85cd537d, 0x496753e3, 0xc7e85400, 0x0b42549e,
+ 0x01875d87, 0xcd2d5d19, 0x43a25afa, 0x8f085a64,
+ 0x562848c8, 0x9a824856, 0x140d4fb5, 0xd8a74f2b,
+ 0xd2624632, 0x1ec846ac, 0x9047414f, 0x5ced41d1,
+ 0x299dc2ed, 0xe537c273, 0x6bb8c590, 0xa712c50e,
+ 0xadd7cc17, 0x617dcc89, 0xeff2cb6a, 0x2358cbf4,
+ 0xfa78d958, 0x36d2d9c6, 0xb85dde25, 0x74f7debb,
+ 0x7e32d7a2, 0xb298d73c, 0x3c17d0df, 0xf0bdd041,
+ 0x5526f3c6, 0x998cf358, 0x1703f4bb, 0xdba9f425,
+ 0xd16cfd3c, 0x1dc6fda2, 0x9349fa41, 0x5fe3fadf,
+ 0x86c3e873, 0x4a69e8ed, 0xc4e6ef0e, 0x084cef90,
+ 0x0289e689, 0xce23e617, 0x40ace1f4, 0x8c06e16a,
+ 0xd0eba0bb, 0x1c41a025, 0x92cea7c6, 0x5e64a758,
+ 0x54a1ae41, 0x980baedf, 0x1684a93c, 0xda2ea9a2,
+ 0x030ebb0e, 0xcfa4bb90, 0x412bbc73, 0x8d81bced,
+ 0x8744b5f4, 0x4beeb56a, 0xc561b289, 0x09cbb217,
+ 0xac509190, 0x60fa910e, 0xee7596ed, 0x22df9673,
+ 0x281a9f6a, 0xe4b09ff4, 0x6a3f9817, 0xa6959889,
+ 0x7fb58a25, 0xb31f8abb, 0x3d908d58, 0xf13a8dc6,
+ 0xfbff84df, 0x37558441, 0xb9da83a2, 0x7570833c,
+ 0x533b85da, 0x9f918544, 0x111e82a7, 0xddb48239,
+ 0xd7718b20, 0x1bdb8bbe, 0x95548c5d, 0x59fe8cc3,
+ 0x80de9e6f, 0x4c749ef1, 0xc2fb9912, 0x0e51998c,
+ 0x04949095, 0xc83e900b, 0x46b197e8, 0x8a1b9776,
+ 0x2f80b4f1, 0xe32ab46f, 0x6da5b38c, 0xa10fb312,
+ 0xabcaba0b, 0x6760ba95, 0xe9efbd76, 0x2545bde8,
+ 0xfc65af44, 0x30cfafda, 0xbe40a839, 0x72eaa8a7,
+ 0x782fa1be, 0xb485a120, 0x3a0aa6c3, 0xf6a0a65d,
+ 0xaa4de78c, 0x66e7e712, 0xe868e0f1, 0x24c2e06f,
+ 0x2e07e976, 0xe2ade9e8, 0x6c22ee0b, 0xa088ee95,
+ 0x79a8fc39, 0xb502fca7, 0x3b8dfb44, 0xf727fbda,
+ 0xfde2f2c3, 0x3148f25d, 0xbfc7f5be, 0x736df520,
+ 0xd6f6d6a7, 0x1a5cd639, 0x94d3d1da, 0x5879d144,
+ 0x52bcd85d, 0x9e16d8c3, 0x1099df20, 0xdc33dfbe,
+ 0x0513cd12, 0xc9b9cd8c, 0x4736ca6f, 0x8b9ccaf1,
+ 0x8159c3e8, 0x4df3c376, 0xc37cc495, 0x0fd6c40b,
+ 0x7aa64737, 0xb60c47a9, 0x3883404a, 0xf42940d4,
+ 0xfeec49cd, 0x32464953, 0xbcc94eb0, 0x70634e2e,
+ 0xa9435c82, 0x65e95c1c, 0xeb665bff, 0x27cc5b61,
+ 0x2d095278, 0xe1a352e6, 0x6f2c5505, 0xa386559b,
+ 0x061d761c, 0xcab77682, 0x44387161, 0x889271ff,
+ 0x825778e6, 0x4efd7878, 0xc0727f9b, 0x0cd87f05,
+ 0xd5f86da9, 0x19526d37, 0x97dd6ad4, 0x5b776a4a,
+ 0x51b26353, 0x9d1863cd, 0x1397642e, 0xdf3d64b0,
+ 0x83d02561, 0x4f7a25ff, 0xc1f5221c, 0x0d5f2282,
+ 0x079a2b9b, 0xcb302b05, 0x45bf2ce6, 0x89152c78,
+ 0x50353ed4, 0x9c9f3e4a, 0x121039a9, 0xdeba3937,
+ 0xd47f302e, 0x18d530b0, 0x965a3753, 0x5af037cd,
+ 0xff6b144a, 0x33c114d4, 0xbd4e1337, 0x71e413a9,
+ 0x7b211ab0, 0xb78b1a2e, 0x39041dcd, 0xf5ae1d53,
+ 0x2c8e0fff, 0xe0240f61, 0x6eab0882, 0xa201081c,
+ 0xa8c40105, 0x646e019b, 0xeae10678, 0x264b06e6
+ }
+#endif
+};
+
+static const TCRC32Table s_CRC32CTableReverse[TABLES_COUNT] = {
+ {
+ 0x00000000, 0xf26b8303, 0xe13b70f7, 0x1350f3f4,
+ 0xc79a971f, 0x35f1141c, 0x26a1e7e8, 0xd4ca64eb,
+ 0x8ad958cf, 0x78b2dbcc, 0x6be22838, 0x9989ab3b,
+ 0x4d43cfd0, 0xbf284cd3, 0xac78bf27, 0x5e133c24,
+ 0x105ec76f, 0xe235446c, 0xf165b798, 0x030e349b,
+ 0xd7c45070, 0x25afd373, 0x36ff2087, 0xc494a384,
+ 0x9a879fa0, 0x68ec1ca3, 0x7bbcef57, 0x89d76c54,
+ 0x5d1d08bf, 0xaf768bbc, 0xbc267848, 0x4e4dfb4b,
+ 0x20bd8ede, 0xd2d60ddd, 0xc186fe29, 0x33ed7d2a,
+ 0xe72719c1, 0x154c9ac2, 0x061c6936, 0xf477ea35,
+ 0xaa64d611, 0x580f5512, 0x4b5fa6e6, 0xb93425e5,
+ 0x6dfe410e, 0x9f95c20d, 0x8cc531f9, 0x7eaeb2fa,
+ 0x30e349b1, 0xc288cab2, 0xd1d83946, 0x23b3ba45,
+ 0xf779deae, 0x05125dad, 0x1642ae59, 0xe4292d5a,
+ 0xba3a117e, 0x4851927d, 0x5b016189, 0xa96ae28a,
+ 0x7da08661, 0x8fcb0562, 0x9c9bf696, 0x6ef07595,
+ 0x417b1dbc, 0xb3109ebf, 0xa0406d4b, 0x522bee48,
+ 0x86e18aa3, 0x748a09a0, 0x67dafa54, 0x95b17957,
+ 0xcba24573, 0x39c9c670, 0x2a993584, 0xd8f2b687,
+ 0x0c38d26c, 0xfe53516f, 0xed03a29b, 0x1f682198,
+ 0x5125dad3, 0xa34e59d0, 0xb01eaa24, 0x42752927,
+ 0x96bf4dcc, 0x64d4cecf, 0x77843d3b, 0x85efbe38,
+ 0xdbfc821c, 0x2997011f, 0x3ac7f2eb, 0xc8ac71e8,
+ 0x1c661503, 0xee0d9600, 0xfd5d65f4, 0x0f36e6f7,
+ 0x61c69362, 0x93ad1061, 0x80fde395, 0x72966096,
+ 0xa65c047d, 0x5437877e, 0x4767748a, 0xb50cf789,
+ 0xeb1fcbad, 0x197448ae, 0x0a24bb5a, 0xf84f3859,
+ 0x2c855cb2, 0xdeeedfb1, 0xcdbe2c45, 0x3fd5af46,
+ 0x7198540d, 0x83f3d70e, 0x90a324fa, 0x62c8a7f9,
+ 0xb602c312, 0x44694011, 0x5739b3e5, 0xa55230e6,
+ 0xfb410cc2, 0x092a8fc1, 0x1a7a7c35, 0xe811ff36,
+ 0x3cdb9bdd, 0xceb018de, 0xdde0eb2a, 0x2f8b6829,
+ 0x82f63b78, 0x709db87b, 0x63cd4b8f, 0x91a6c88c,
+ 0x456cac67, 0xb7072f64, 0xa457dc90, 0x563c5f93,
+ 0x082f63b7, 0xfa44e0b4, 0xe9141340, 0x1b7f9043,
+ 0xcfb5f4a8, 0x3dde77ab, 0x2e8e845f, 0xdce5075c,
+ 0x92a8fc17, 0x60c37f14, 0x73938ce0, 0x81f80fe3,
+ 0x55326b08, 0xa759e80b, 0xb4091bff, 0x466298fc,
+ 0x1871a4d8, 0xea1a27db, 0xf94ad42f, 0x0b21572c,
+ 0xdfeb33c7, 0x2d80b0c4, 0x3ed04330, 0xccbbc033,
+ 0xa24bb5a6, 0x502036a5, 0x4370c551, 0xb11b4652,
+ 0x65d122b9, 0x97baa1ba, 0x84ea524e, 0x7681d14d,
+ 0x2892ed69, 0xdaf96e6a, 0xc9a99d9e, 0x3bc21e9d,
+ 0xef087a76, 0x1d63f975, 0x0e330a81, 0xfc588982,
+ 0xb21572c9, 0x407ef1ca, 0x532e023e, 0xa145813d,
+ 0x758fe5d6, 0x87e466d5, 0x94b49521, 0x66df1622,
+ 0x38cc2a06, 0xcaa7a905, 0xd9f75af1, 0x2b9cd9f2,
+ 0xff56bd19, 0x0d3d3e1a, 0x1e6dcdee, 0xec064eed,
+ 0xc38d26c4, 0x31e6a5c7, 0x22b65633, 0xd0ddd530,
+ 0x0417b1db, 0xf67c32d8, 0xe52cc12c, 0x1747422f,
+ 0x49547e0b, 0xbb3ffd08, 0xa86f0efc, 0x5a048dff,
+ 0x8ecee914, 0x7ca56a17, 0x6ff599e3, 0x9d9e1ae0,
+ 0xd3d3e1ab, 0x21b862a8, 0x32e8915c, 0xc083125f,
+ 0x144976b4, 0xe622f5b7, 0xf5720643, 0x07198540,
+ 0x590ab964, 0xab613a67, 0xb831c993, 0x4a5a4a90,
+ 0x9e902e7b, 0x6cfbad78, 0x7fab5e8c, 0x8dc0dd8f,
+ 0xe330a81a, 0x115b2b19, 0x020bd8ed, 0xf0605bee,
+ 0x24aa3f05, 0xd6c1bc06, 0xc5914ff2, 0x37faccf1,
+ 0x69e9f0d5, 0x9b8273d6, 0x88d28022, 0x7ab90321,
+ 0xae7367ca, 0x5c18e4c9, 0x4f48173d, 0xbd23943e,
+ 0xf36e6f75, 0x0105ec76, 0x12551f82, 0xe03e9c81,
+ 0x34f4f86a, 0xc69f7b69, 0xd5cf889d, 0x27a40b9e,
+ 0x79b737ba, 0x8bdcb4b9, 0x988c474d, 0x6ae7c44e,
+ 0xbe2da0a5, 0x4c4623a6, 0x5f16d052, 0xad7d5351
+ },
+ {
+ 0x00000000, 0x13a29877, 0x274530ee, 0x34e7a899,
+ 0x4e8a61dc, 0x5d28f9ab, 0x69cf5132, 0x7a6dc945,
+ 0x9d14c3b8, 0x8eb65bcf, 0xba51f356, 0xa9f36b21,
+ 0xd39ea264, 0xc03c3a13, 0xf4db928a, 0xe7790afd,
+ 0x3fc5f181, 0x2c6769f6, 0x1880c16f, 0x0b225918,
+ 0x714f905d, 0x62ed082a, 0x560aa0b3, 0x45a838c4,
+ 0xa2d13239, 0xb173aa4e, 0x859402d7, 0x96369aa0,
+ 0xec5b53e5, 0xfff9cb92, 0xcb1e630b, 0xd8bcfb7c,
+ 0x7f8be302, 0x6c297b75, 0x58ced3ec, 0x4b6c4b9b,
+ 0x310182de, 0x22a31aa9, 0x1644b230, 0x05e62a47,
+ 0xe29f20ba, 0xf13db8cd, 0xc5da1054, 0xd6788823,
+ 0xac154166, 0xbfb7d911, 0x8b507188, 0x98f2e9ff,
+ 0x404e1283, 0x53ec8af4, 0x670b226d, 0x74a9ba1a,
+ 0x0ec4735f, 0x1d66eb28, 0x298143b1, 0x3a23dbc6,
+ 0xdd5ad13b, 0xcef8494c, 0xfa1fe1d5, 0xe9bd79a2,
+ 0x93d0b0e7, 0x80722890, 0xb4958009, 0xa737187e,
+ 0xff17c604, 0xecb55e73, 0xd852f6ea, 0xcbf06e9d,
+ 0xb19da7d8, 0xa23f3faf, 0x96d89736, 0x857a0f41,
+ 0x620305bc, 0x71a19dcb, 0x45463552, 0x56e4ad25,
+ 0x2c896460, 0x3f2bfc17, 0x0bcc548e, 0x186eccf9,
+ 0xc0d23785, 0xd370aff2, 0xe797076b, 0xf4359f1c,
+ 0x8e585659, 0x9dface2e, 0xa91d66b7, 0xbabffec0,
+ 0x5dc6f43d, 0x4e646c4a, 0x7a83c4d3, 0x69215ca4,
+ 0x134c95e1, 0x00ee0d96, 0x3409a50f, 0x27ab3d78,
+ 0x809c2506, 0x933ebd71, 0xa7d915e8, 0xb47b8d9f,
+ 0xce1644da, 0xddb4dcad, 0xe9537434, 0xfaf1ec43,
+ 0x1d88e6be, 0x0e2a7ec9, 0x3acdd650, 0x296f4e27,
+ 0x53028762, 0x40a01f15, 0x7447b78c, 0x67e52ffb,
+ 0xbf59d487, 0xacfb4cf0, 0x981ce469, 0x8bbe7c1e,
+ 0xf1d3b55b, 0xe2712d2c, 0xd69685b5, 0xc5341dc2,
+ 0x224d173f, 0x31ef8f48, 0x050827d1, 0x16aabfa6,
+ 0x6cc776e3, 0x7f65ee94, 0x4b82460d, 0x5820de7a,
+ 0xfbc3faf9, 0xe861628e, 0xdc86ca17, 0xcf245260,
+ 0xb5499b25, 0xa6eb0352, 0x920cabcb, 0x81ae33bc,
+ 0x66d73941, 0x7575a136, 0x419209af, 0x523091d8,
+ 0x285d589d, 0x3bffc0ea, 0x0f186873, 0x1cbaf004,
+ 0xc4060b78, 0xd7a4930f, 0xe3433b96, 0xf0e1a3e1,
+ 0x8a8c6aa4, 0x992ef2d3, 0xadc95a4a, 0xbe6bc23d,
+ 0x5912c8c0, 0x4ab050b7, 0x7e57f82e, 0x6df56059,
+ 0x1798a91c, 0x043a316b, 0x30dd99f2, 0x237f0185,
+ 0x844819fb, 0x97ea818c, 0xa30d2915, 0xb0afb162,
+ 0xcac27827, 0xd960e050, 0xed8748c9, 0xfe25d0be,
+ 0x195cda43, 0x0afe4234, 0x3e19eaad, 0x2dbb72da,
+ 0x57d6bb9f, 0x447423e8, 0x70938b71, 0x63311306,
+ 0xbb8de87a, 0xa82f700d, 0x9cc8d894, 0x8f6a40e3,
+ 0xf50789a6, 0xe6a511d1, 0xd242b948, 0xc1e0213f,
+ 0x26992bc2, 0x353bb3b5, 0x01dc1b2c, 0x127e835b,
+ 0x68134a1e, 0x7bb1d269, 0x4f567af0, 0x5cf4e287,
+ 0x04d43cfd, 0x1776a48a, 0x23910c13, 0x30339464,
+ 0x4a5e5d21, 0x59fcc556, 0x6d1b6dcf, 0x7eb9f5b8,
+ 0x99c0ff45, 0x8a626732, 0xbe85cfab, 0xad2757dc,
+ 0xd74a9e99, 0xc4e806ee, 0xf00fae77, 0xe3ad3600,
+ 0x3b11cd7c, 0x28b3550b, 0x1c54fd92, 0x0ff665e5,
+ 0x759baca0, 0x663934d7, 0x52de9c4e, 0x417c0439,
+ 0xa6050ec4, 0xb5a796b3, 0x81403e2a, 0x92e2a65d,
+ 0xe88f6f18, 0xfb2df76f, 0xcfca5ff6, 0xdc68c781,
+ 0x7b5fdfff, 0x68fd4788, 0x5c1aef11, 0x4fb87766,
+ 0x35d5be23, 0x26772654, 0x12908ecd, 0x013216ba,
+ 0xe64b1c47, 0xf5e98430, 0xc10e2ca9, 0xd2acb4de,
+ 0xa8c17d9b, 0xbb63e5ec, 0x8f844d75, 0x9c26d502,
+ 0x449a2e7e, 0x5738b609, 0x63df1e90, 0x707d86e7,
+ 0x0a104fa2, 0x19b2d7d5, 0x2d557f4c, 0x3ef7e73b,
+ 0xd98eedc6, 0xca2c75b1, 0xfecbdd28, 0xed69455f,
+ 0x97048c1a, 0x84a6146d, 0xb041bcf4, 0xa3e32483
+ },
+ {
+ 0x00000000, 0xa541927e, 0x4f6f520d, 0xea2ec073,
+ 0x9edea41a, 0x3b9f3664, 0xd1b1f617, 0x74f06469,
+ 0x38513ec5, 0x9d10acbb, 0x773e6cc8, 0xd27ffeb6,
+ 0xa68f9adf, 0x03ce08a1, 0xe9e0c8d2, 0x4ca15aac,
+ 0x70a27d8a, 0xd5e3eff4, 0x3fcd2f87, 0x9a8cbdf9,
+ 0xee7cd990, 0x4b3d4bee, 0xa1138b9d, 0x045219e3,
+ 0x48f3434f, 0xedb2d131, 0x079c1142, 0xa2dd833c,
+ 0xd62de755, 0x736c752b, 0x9942b558, 0x3c032726,
+ 0xe144fb14, 0x4405696a, 0xae2ba919, 0x0b6a3b67,
+ 0x7f9a5f0e, 0xdadbcd70, 0x30f50d03, 0x95b49f7d,
+ 0xd915c5d1, 0x7c5457af, 0x967a97dc, 0x333b05a2,
+ 0x47cb61cb, 0xe28af3b5, 0x08a433c6, 0xade5a1b8,
+ 0x91e6869e, 0x34a714e0, 0xde89d493, 0x7bc846ed,
+ 0x0f382284, 0xaa79b0fa, 0x40577089, 0xe516e2f7,
+ 0xa9b7b85b, 0x0cf62a25, 0xe6d8ea56, 0x43997828,
+ 0x37691c41, 0x92288e3f, 0x78064e4c, 0xdd47dc32,
+ 0xc76580d9, 0x622412a7, 0x880ad2d4, 0x2d4b40aa,
+ 0x59bb24c3, 0xfcfab6bd, 0x16d476ce, 0xb395e4b0,
+ 0xff34be1c, 0x5a752c62, 0xb05bec11, 0x151a7e6f,
+ 0x61ea1a06, 0xc4ab8878, 0x2e85480b, 0x8bc4da75,
+ 0xb7c7fd53, 0x12866f2d, 0xf8a8af5e, 0x5de93d20,
+ 0x29195949, 0x8c58cb37, 0x66760b44, 0xc337993a,
+ 0x8f96c396, 0x2ad751e8, 0xc0f9919b, 0x65b803e5,
+ 0x1148678c, 0xb409f5f2, 0x5e273581, 0xfb66a7ff,
+ 0x26217bcd, 0x8360e9b3, 0x694e29c0, 0xcc0fbbbe,
+ 0xb8ffdfd7, 0x1dbe4da9, 0xf7908dda, 0x52d11fa4,
+ 0x1e704508, 0xbb31d776, 0x511f1705, 0xf45e857b,
+ 0x80aee112, 0x25ef736c, 0xcfc1b31f, 0x6a802161,
+ 0x56830647, 0xf3c29439, 0x19ec544a, 0xbcadc634,
+ 0xc85da25d, 0x6d1c3023, 0x8732f050, 0x2273622e,
+ 0x6ed23882, 0xcb93aafc, 0x21bd6a8f, 0x84fcf8f1,
+ 0xf00c9c98, 0x554d0ee6, 0xbf63ce95, 0x1a225ceb,
+ 0x8b277743, 0x2e66e53d, 0xc448254e, 0x6109b730,
+ 0x15f9d359, 0xb0b84127, 0x5a968154, 0xffd7132a,
+ 0xb3764986, 0x1637dbf8, 0xfc191b8b, 0x595889f5,
+ 0x2da8ed9c, 0x88e97fe2, 0x62c7bf91, 0xc7862def,
+ 0xfb850ac9, 0x5ec498b7, 0xb4ea58c4, 0x11abcaba,
+ 0x655baed3, 0xc01a3cad, 0x2a34fcde, 0x8f756ea0,
+ 0xc3d4340c, 0x6695a672, 0x8cbb6601, 0x29faf47f,
+ 0x5d0a9016, 0xf84b0268, 0x1265c21b, 0xb7245065,
+ 0x6a638c57, 0xcf221e29, 0x250cde5a, 0x804d4c24,
+ 0xf4bd284d, 0x51fcba33, 0xbbd27a40, 0x1e93e83e,
+ 0x5232b292, 0xf77320ec, 0x1d5de09f, 0xb81c72e1,
+ 0xccec1688, 0x69ad84f6, 0x83834485, 0x26c2d6fb,
+ 0x1ac1f1dd, 0xbf8063a3, 0x55aea3d0, 0xf0ef31ae,
+ 0x841f55c7, 0x215ec7b9, 0xcb7007ca, 0x6e3195b4,
+ 0x2290cf18, 0x87d15d66, 0x6dff9d15, 0xc8be0f6b,
+ 0xbc4e6b02, 0x190ff97c, 0xf321390f, 0x5660ab71,
+ 0x4c42f79a, 0xe90365e4, 0x032da597, 0xa66c37e9,
+ 0xd29c5380, 0x77ddc1fe, 0x9df3018d, 0x38b293f3,
+ 0x7413c95f, 0xd1525b21, 0x3b7c9b52, 0x9e3d092c,
+ 0xeacd6d45, 0x4f8cff3b, 0xa5a23f48, 0x00e3ad36,
+ 0x3ce08a10, 0x99a1186e, 0x738fd81d, 0xd6ce4a63,
+ 0xa23e2e0a, 0x077fbc74, 0xed517c07, 0x4810ee79,
+ 0x04b1b4d5, 0xa1f026ab, 0x4bdee6d8, 0xee9f74a6,
+ 0x9a6f10cf, 0x3f2e82b1, 0xd50042c2, 0x7041d0bc,
+ 0xad060c8e, 0x08479ef0, 0xe2695e83, 0x4728ccfd,
+ 0x33d8a894, 0x96993aea, 0x7cb7fa99, 0xd9f668e7,
+ 0x9557324b, 0x3016a035, 0xda386046, 0x7f79f238,
+ 0x0b899651, 0xaec8042f, 0x44e6c45c, 0xe1a75622,
+ 0xdda47104, 0x78e5e37a, 0x92cb2309, 0x378ab177,
+ 0x437ad51e, 0xe63b4760, 0x0c158713, 0xa954156d,
+ 0xe5f54fc1, 0x40b4ddbf, 0xaa9a1dcc, 0x0fdb8fb2,
+ 0x7b2bebdb, 0xde6a79a5, 0x3444b9d6, 0x91052ba8
+ },
+ {
+ 0x00000000, 0xdd45aab8, 0xbf672381, 0x62228939,
+ 0x7b2231f3, 0xa6679b4b, 0xc4451272, 0x1900b8ca,
+ 0xf64463e6, 0x2b01c95e, 0x49234067, 0x9466eadf,
+ 0x8d665215, 0x5023f8ad, 0x32017194, 0xef44db2c,
+ 0xe964b13d, 0x34211b85, 0x560392bc, 0x8b463804,
+ 0x924680ce, 0x4f032a76, 0x2d21a34f, 0xf06409f7,
+ 0x1f20d2db, 0xc2657863, 0xa047f15a, 0x7d025be2,
+ 0x6402e328, 0xb9474990, 0xdb65c0a9, 0x06206a11,
+ 0xd725148b, 0x0a60be33, 0x6842370a, 0xb5079db2,
+ 0xac072578, 0x71428fc0, 0x136006f9, 0xce25ac41,
+ 0x2161776d, 0xfc24ddd5, 0x9e0654ec, 0x4343fe54,
+ 0x5a43469e, 0x8706ec26, 0xe524651f, 0x3861cfa7,
+ 0x3e41a5b6, 0xe3040f0e, 0x81268637, 0x5c632c8f,
+ 0x45639445, 0x98263efd, 0xfa04b7c4, 0x27411d7c,
+ 0xc805c650, 0x15406ce8, 0x7762e5d1, 0xaa274f69,
+ 0xb327f7a3, 0x6e625d1b, 0x0c40d422, 0xd1057e9a,
+ 0xaba65fe7, 0x76e3f55f, 0x14c17c66, 0xc984d6de,
+ 0xd0846e14, 0x0dc1c4ac, 0x6fe34d95, 0xb2a6e72d,
+ 0x5de23c01, 0x80a796b9, 0xe2851f80, 0x3fc0b538,
+ 0x26c00df2, 0xfb85a74a, 0x99a72e73, 0x44e284cb,
+ 0x42c2eeda, 0x9f874462, 0xfda5cd5b, 0x20e067e3,
+ 0x39e0df29, 0xe4a57591, 0x8687fca8, 0x5bc25610,
+ 0xb4868d3c, 0x69c32784, 0x0be1aebd, 0xd6a40405,
+ 0xcfa4bccf, 0x12e11677, 0x70c39f4e, 0xad8635f6,
+ 0x7c834b6c, 0xa1c6e1d4, 0xc3e468ed, 0x1ea1c255,
+ 0x07a17a9f, 0xdae4d027, 0xb8c6591e, 0x6583f3a6,
+ 0x8ac7288a, 0x57828232, 0x35a00b0b, 0xe8e5a1b3,
+ 0xf1e51979, 0x2ca0b3c1, 0x4e823af8, 0x93c79040,
+ 0x95e7fa51, 0x48a250e9, 0x2a80d9d0, 0xf7c57368,
+ 0xeec5cba2, 0x3380611a, 0x51a2e823, 0x8ce7429b,
+ 0x63a399b7, 0xbee6330f, 0xdcc4ba36, 0x0181108e,
+ 0x1881a844, 0xc5c402fc, 0xa7e68bc5, 0x7aa3217d,
+ 0x52a0c93f, 0x8fe56387, 0xedc7eabe, 0x30824006,
+ 0x2982f8cc, 0xf4c75274, 0x96e5db4d, 0x4ba071f5,
+ 0xa4e4aad9, 0x79a10061, 0x1b838958, 0xc6c623e0,
+ 0xdfc69b2a, 0x02833192, 0x60a1b8ab, 0xbde41213,
+ 0xbbc47802, 0x6681d2ba, 0x04a35b83, 0xd9e6f13b,
+ 0xc0e649f1, 0x1da3e349, 0x7f816a70, 0xa2c4c0c8,
+ 0x4d801be4, 0x90c5b15c, 0xf2e73865, 0x2fa292dd,
+ 0x36a22a17, 0xebe780af, 0x89c50996, 0x5480a32e,
+ 0x8585ddb4, 0x58c0770c, 0x3ae2fe35, 0xe7a7548d,
+ 0xfea7ec47, 0x23e246ff, 0x41c0cfc6, 0x9c85657e,
+ 0x73c1be52, 0xae8414ea, 0xcca69dd3, 0x11e3376b,
+ 0x08e38fa1, 0xd5a62519, 0xb784ac20, 0x6ac10698,
+ 0x6ce16c89, 0xb1a4c631, 0xd3864f08, 0x0ec3e5b0,
+ 0x17c35d7a, 0xca86f7c2, 0xa8a47efb, 0x75e1d443,
+ 0x9aa50f6f, 0x47e0a5d7, 0x25c22cee, 0xf8878656,
+ 0xe1873e9c, 0x3cc29424, 0x5ee01d1d, 0x83a5b7a5,
+ 0xf90696d8, 0x24433c60, 0x4661b559, 0x9b241fe1,
+ 0x8224a72b, 0x5f610d93, 0x3d4384aa, 0xe0062e12,
+ 0x0f42f53e, 0xd2075f86, 0xb025d6bf, 0x6d607c07,
+ 0x7460c4cd, 0xa9256e75, 0xcb07e74c, 0x16424df4,
+ 0x106227e5, 0xcd278d5d, 0xaf050464, 0x7240aedc,
+ 0x6b401616, 0xb605bcae, 0xd4273597, 0x09629f2f,
+ 0xe6264403, 0x3b63eebb, 0x59416782, 0x8404cd3a,
+ 0x9d0475f0, 0x4041df48, 0x22635671, 0xff26fcc9,
+ 0x2e238253, 0xf36628eb, 0x9144a1d2, 0x4c010b6a,
+ 0x5501b3a0, 0x88441918, 0xea669021, 0x37233a99,
+ 0xd867e1b5, 0x05224b0d, 0x6700c234, 0xba45688c,
+ 0xa345d046, 0x7e007afe, 0x1c22f3c7, 0xc167597f,
+ 0xc747336e, 0x1a0299d6, 0x782010ef, 0xa565ba57,
+ 0xbc65029d, 0x6120a825, 0x0302211c, 0xde478ba4,
+ 0x31035088, 0xec46fa30, 0x8e647309, 0x5321d9b1,
+ 0x4a21617b, 0x9764cbc3, 0xf54642fa, 0x2803e842
+ }
+#if TABLES_COUNT >= 8
+ , {
+ 0x00000000, 0x38116fac, 0x7022df58, 0x4833b0f4,
+ 0xe045beb0, 0xd854d11c, 0x906761e8, 0xa8760e44,
+ 0xc5670b91, 0xfd76643d, 0xb545d4c9, 0x8d54bb65,
+ 0x2522b521, 0x1d33da8d, 0x55006a79, 0x6d1105d5,
+ 0x8f2261d3, 0xb7330e7f, 0xff00be8b, 0xc711d127,
+ 0x6f67df63, 0x5776b0cf, 0x1f45003b, 0x27546f97,
+ 0x4a456a42, 0x725405ee, 0x3a67b51a, 0x0276dab6,
+ 0xaa00d4f2, 0x9211bb5e, 0xda220baa, 0xe2336406,
+ 0x1ba8b557, 0x23b9dafb, 0x6b8a6a0f, 0x539b05a3,
+ 0xfbed0be7, 0xc3fc644b, 0x8bcfd4bf, 0xb3debb13,
+ 0xdecfbec6, 0xe6ded16a, 0xaeed619e, 0x96fc0e32,
+ 0x3e8a0076, 0x069b6fda, 0x4ea8df2e, 0x76b9b082,
+ 0x948ad484, 0xac9bbb28, 0xe4a80bdc, 0xdcb96470,
+ 0x74cf6a34, 0x4cde0598, 0x04edb56c, 0x3cfcdac0,
+ 0x51eddf15, 0x69fcb0b9, 0x21cf004d, 0x19de6fe1,
+ 0xb1a861a5, 0x89b90e09, 0xc18abefd, 0xf99bd151,
+ 0x37516aae, 0x0f400502, 0x4773b5f6, 0x7f62da5a,
+ 0xd714d41e, 0xef05bbb2, 0xa7360b46, 0x9f2764ea,
+ 0xf236613f, 0xca270e93, 0x8214be67, 0xba05d1cb,
+ 0x1273df8f, 0x2a62b023, 0x625100d7, 0x5a406f7b,
+ 0xb8730b7d, 0x806264d1, 0xc851d425, 0xf040bb89,
+ 0x5836b5cd, 0x6027da61, 0x28146a95, 0x10050539,
+ 0x7d1400ec, 0x45056f40, 0x0d36dfb4, 0x3527b018,
+ 0x9d51be5c, 0xa540d1f0, 0xed736104, 0xd5620ea8,
+ 0x2cf9dff9, 0x14e8b055, 0x5cdb00a1, 0x64ca6f0d,
+ 0xccbc6149, 0xf4ad0ee5, 0xbc9ebe11, 0x848fd1bd,
+ 0xe99ed468, 0xd18fbbc4, 0x99bc0b30, 0xa1ad649c,
+ 0x09db6ad8, 0x31ca0574, 0x79f9b580, 0x41e8da2c,
+ 0xa3dbbe2a, 0x9bcad186, 0xd3f96172, 0xebe80ede,
+ 0x439e009a, 0x7b8f6f36, 0x33bcdfc2, 0x0badb06e,
+ 0x66bcb5bb, 0x5eadda17, 0x169e6ae3, 0x2e8f054f,
+ 0x86f90b0b, 0xbee864a7, 0xf6dbd453, 0xcecabbff,
+ 0x6ea2d55c, 0x56b3baf0, 0x1e800a04, 0x269165a8,
+ 0x8ee76bec, 0xb6f60440, 0xfec5b4b4, 0xc6d4db18,
+ 0xabc5decd, 0x93d4b161, 0xdbe70195, 0xe3f66e39,
+ 0x4b80607d, 0x73910fd1, 0x3ba2bf25, 0x03b3d089,
+ 0xe180b48f, 0xd991db23, 0x91a26bd7, 0xa9b3047b,
+ 0x01c50a3f, 0x39d46593, 0x71e7d567, 0x49f6bacb,
+ 0x24e7bf1e, 0x1cf6d0b2, 0x54c56046, 0x6cd40fea,
+ 0xc4a201ae, 0xfcb36e02, 0xb480def6, 0x8c91b15a,
+ 0x750a600b, 0x4d1b0fa7, 0x0528bf53, 0x3d39d0ff,
+ 0x954fdebb, 0xad5eb117, 0xe56d01e3, 0xdd7c6e4f,
+ 0xb06d6b9a, 0x887c0436, 0xc04fb4c2, 0xf85edb6e,
+ 0x5028d52a, 0x6839ba86, 0x200a0a72, 0x181b65de,
+ 0xfa2801d8, 0xc2396e74, 0x8a0ade80, 0xb21bb12c,
+ 0x1a6dbf68, 0x227cd0c4, 0x6a4f6030, 0x525e0f9c,
+ 0x3f4f0a49, 0x075e65e5, 0x4f6dd511, 0x777cbabd,
+ 0xdf0ab4f9, 0xe71bdb55, 0xaf286ba1, 0x9739040d,
+ 0x59f3bff2, 0x61e2d05e, 0x29d160aa, 0x11c00f06,
+ 0xb9b60142, 0x81a76eee, 0xc994de1a, 0xf185b1b6,
+ 0x9c94b463, 0xa485dbcf, 0xecb66b3b, 0xd4a70497,
+ 0x7cd10ad3, 0x44c0657f, 0x0cf3d58b, 0x34e2ba27,
+ 0xd6d1de21, 0xeec0b18d, 0xa6f30179, 0x9ee26ed5,
+ 0x36946091, 0x0e850f3d, 0x46b6bfc9, 0x7ea7d065,
+ 0x13b6d5b0, 0x2ba7ba1c, 0x63940ae8, 0x5b856544,
+ 0xf3f36b00, 0xcbe204ac, 0x83d1b458, 0xbbc0dbf4,
+ 0x425b0aa5, 0x7a4a6509, 0x3279d5fd, 0x0a68ba51,
+ 0xa21eb415, 0x9a0fdbb9, 0xd23c6b4d, 0xea2d04e1,
+ 0x873c0134, 0xbf2d6e98, 0xf71ede6c, 0xcf0fb1c0,
+ 0x6779bf84, 0x5f68d028, 0x175b60dc, 0x2f4a0f70,
+ 0xcd796b76, 0xf56804da, 0xbd5bb42e, 0x854adb82,
+ 0x2d3cd5c6, 0x152dba6a, 0x5d1e0a9e, 0x650f6532,
+ 0x081e60e7, 0x300f0f4b, 0x783cbfbf, 0x402dd013,
+ 0xe85bde57, 0xd04ab1fb, 0x9879010f, 0xa0686ea3
+ },
+ {
+ 0x00000000, 0xef306b19, 0xdb8ca0c3, 0x34bccbda,
+ 0xb2f53777, 0x5dc55c6e, 0x697997b4, 0x8649fcad,
+ 0x6006181f, 0x8f367306, 0xbb8ab8dc, 0x54bad3c5,
+ 0xd2f32f68, 0x3dc34471, 0x097f8fab, 0xe64fe4b2,
+ 0xc00c303e, 0x2f3c5b27, 0x1b8090fd, 0xf4b0fbe4,
+ 0x72f90749, 0x9dc96c50, 0xa975a78a, 0x4645cc93,
+ 0xa00a2821, 0x4f3a4338, 0x7b8688e2, 0x94b6e3fb,
+ 0x12ff1f56, 0xfdcf744f, 0xc973bf95, 0x2643d48c,
+ 0x85f4168d, 0x6ac47d94, 0x5e78b64e, 0xb148dd57,
+ 0x370121fa, 0xd8314ae3, 0xec8d8139, 0x03bdea20,
+ 0xe5f20e92, 0x0ac2658b, 0x3e7eae51, 0xd14ec548,
+ 0x570739e5, 0xb83752fc, 0x8c8b9926, 0x63bbf23f,
+ 0x45f826b3, 0xaac84daa, 0x9e748670, 0x7144ed69,
+ 0xf70d11c4, 0x183d7add, 0x2c81b107, 0xc3b1da1e,
+ 0x25fe3eac, 0xcace55b5, 0xfe729e6f, 0x1142f576,
+ 0x970b09db, 0x783b62c2, 0x4c87a918, 0xa3b7c201,
+ 0x0e045beb, 0xe13430f2, 0xd588fb28, 0x3ab89031,
+ 0xbcf16c9c, 0x53c10785, 0x677dcc5f, 0x884da746,
+ 0x6e0243f4, 0x813228ed, 0xb58ee337, 0x5abe882e,
+ 0xdcf77483, 0x33c71f9a, 0x077bd440, 0xe84bbf59,
+ 0xce086bd5, 0x213800cc, 0x1584cb16, 0xfab4a00f,
+ 0x7cfd5ca2, 0x93cd37bb, 0xa771fc61, 0x48419778,
+ 0xae0e73ca, 0x413e18d3, 0x7582d309, 0x9ab2b810,
+ 0x1cfb44bd, 0xf3cb2fa4, 0xc777e47e, 0x28478f67,
+ 0x8bf04d66, 0x64c0267f, 0x507ceda5, 0xbf4c86bc,
+ 0x39057a11, 0xd6351108, 0xe289dad2, 0x0db9b1cb,
+ 0xebf65579, 0x04c63e60, 0x307af5ba, 0xdf4a9ea3,
+ 0x5903620e, 0xb6330917, 0x828fc2cd, 0x6dbfa9d4,
+ 0x4bfc7d58, 0xa4cc1641, 0x9070dd9b, 0x7f40b682,
+ 0xf9094a2f, 0x16392136, 0x2285eaec, 0xcdb581f5,
+ 0x2bfa6547, 0xc4ca0e5e, 0xf076c584, 0x1f46ae9d,
+ 0x990f5230, 0x763f3929, 0x4283f2f3, 0xadb399ea,
+ 0x1c08b7d6, 0xf338dccf, 0xc7841715, 0x28b47c0c,
+ 0xaefd80a1, 0x41cdebb8, 0x75712062, 0x9a414b7b,
+ 0x7c0eafc9, 0x933ec4d0, 0xa7820f0a, 0x48b26413,
+ 0xcefb98be, 0x21cbf3a7, 0x1577387d, 0xfa475364,
+ 0xdc0487e8, 0x3334ecf1, 0x0788272b, 0xe8b84c32,
+ 0x6ef1b09f, 0x81c1db86, 0xb57d105c, 0x5a4d7b45,
+ 0xbc029ff7, 0x5332f4ee, 0x678e3f34, 0x88be542d,
+ 0x0ef7a880, 0xe1c7c399, 0xd57b0843, 0x3a4b635a,
+ 0x99fca15b, 0x76ccca42, 0x42700198, 0xad406a81,
+ 0x2b09962c, 0xc439fd35, 0xf08536ef, 0x1fb55df6,
+ 0xf9fab944, 0x16cad25d, 0x22761987, 0xcd46729e,
+ 0x4b0f8e33, 0xa43fe52a, 0x90832ef0, 0x7fb345e9,
+ 0x59f09165, 0xb6c0fa7c, 0x827c31a6, 0x6d4c5abf,
+ 0xeb05a612, 0x0435cd0b, 0x308906d1, 0xdfb96dc8,
+ 0x39f6897a, 0xd6c6e263, 0xe27a29b9, 0x0d4a42a0,
+ 0x8b03be0d, 0x6433d514, 0x508f1ece, 0xbfbf75d7,
+ 0x120cec3d, 0xfd3c8724, 0xc9804cfe, 0x26b027e7,
+ 0xa0f9db4a, 0x4fc9b053, 0x7b757b89, 0x94451090,
+ 0x720af422, 0x9d3a9f3b, 0xa98654e1, 0x46b63ff8,
+ 0xc0ffc355, 0x2fcfa84c, 0x1b736396, 0xf443088f,
+ 0xd200dc03, 0x3d30b71a, 0x098c7cc0, 0xe6bc17d9,
+ 0x60f5eb74, 0x8fc5806d, 0xbb794bb7, 0x544920ae,
+ 0xb206c41c, 0x5d36af05, 0x698a64df, 0x86ba0fc6,
+ 0x00f3f36b, 0xefc39872, 0xdb7f53a8, 0x344f38b1,
+ 0x97f8fab0, 0x78c891a9, 0x4c745a73, 0xa344316a,
+ 0x250dcdc7, 0xca3da6de, 0xfe816d04, 0x11b1061d,
+ 0xf7fee2af, 0x18ce89b6, 0x2c72426c, 0xc3422975,
+ 0x450bd5d8, 0xaa3bbec1, 0x9e87751b, 0x71b71e02,
+ 0x57f4ca8e, 0xb8c4a197, 0x8c786a4d, 0x63480154,
+ 0xe501fdf9, 0x0a3196e0, 0x3e8d5d3a, 0xd1bd3623,
+ 0x37f2d291, 0xd8c2b988, 0xec7e7252, 0x034e194b,
+ 0x8507e5e6, 0x6a378eff, 0x5e8b4525, 0xb1bb2e3c
+ },
+ {
+ 0x00000000, 0x68032cc8, 0xd0065990, 0xb8057558,
+ 0xa5e0c5d1, 0xcde3e919, 0x75e69c41, 0x1de5b089,
+ 0x4e2dfd53, 0x262ed19b, 0x9e2ba4c3, 0xf628880b,
+ 0xebcd3882, 0x83ce144a, 0x3bcb6112, 0x53c84dda,
+ 0x9c5bfaa6, 0xf458d66e, 0x4c5da336, 0x245e8ffe,
+ 0x39bb3f77, 0x51b813bf, 0xe9bd66e7, 0x81be4a2f,
+ 0xd27607f5, 0xba752b3d, 0x02705e65, 0x6a7372ad,
+ 0x7796c224, 0x1f95eeec, 0xa7909bb4, 0xcf93b77c,
+ 0x3d5b83bd, 0x5558af75, 0xed5dda2d, 0x855ef6e5,
+ 0x98bb466c, 0xf0b86aa4, 0x48bd1ffc, 0x20be3334,
+ 0x73767eee, 0x1b755226, 0xa370277e, 0xcb730bb6,
+ 0xd696bb3f, 0xbe9597f7, 0x0690e2af, 0x6e93ce67,
+ 0xa100791b, 0xc90355d3, 0x7106208b, 0x19050c43,
+ 0x04e0bcca, 0x6ce39002, 0xd4e6e55a, 0xbce5c992,
+ 0xef2d8448, 0x872ea880, 0x3f2bddd8, 0x5728f110,
+ 0x4acd4199, 0x22ce6d51, 0x9acb1809, 0xf2c834c1,
+ 0x7ab7077a, 0x12b42bb2, 0xaab15eea, 0xc2b27222,
+ 0xdf57c2ab, 0xb754ee63, 0x0f519b3b, 0x6752b7f3,
+ 0x349afa29, 0x5c99d6e1, 0xe49ca3b9, 0x8c9f8f71,
+ 0x917a3ff8, 0xf9791330, 0x417c6668, 0x297f4aa0,
+ 0xe6ecfddc, 0x8eefd114, 0x36eaa44c, 0x5ee98884,
+ 0x430c380d, 0x2b0f14c5, 0x930a619d, 0xfb094d55,
+ 0xa8c1008f, 0xc0c22c47, 0x78c7591f, 0x10c475d7,
+ 0x0d21c55e, 0x6522e996, 0xdd279cce, 0xb524b006,
+ 0x47ec84c7, 0x2fefa80f, 0x97eadd57, 0xffe9f19f,
+ 0xe20c4116, 0x8a0f6dde, 0x320a1886, 0x5a09344e,
+ 0x09c17994, 0x61c2555c, 0xd9c72004, 0xb1c40ccc,
+ 0xac21bc45, 0xc422908d, 0x7c27e5d5, 0x1424c91d,
+ 0xdbb77e61, 0xb3b452a9, 0x0bb127f1, 0x63b20b39,
+ 0x7e57bbb0, 0x16549778, 0xae51e220, 0xc652cee8,
+ 0x959a8332, 0xfd99affa, 0x459cdaa2, 0x2d9ff66a,
+ 0x307a46e3, 0x58796a2b, 0xe07c1f73, 0x887f33bb,
+ 0xf56e0ef4, 0x9d6d223c, 0x25685764, 0x4d6b7bac,
+ 0x508ecb25, 0x388de7ed, 0x808892b5, 0xe88bbe7d,
+ 0xbb43f3a7, 0xd340df6f, 0x6b45aa37, 0x034686ff,
+ 0x1ea33676, 0x76a01abe, 0xcea56fe6, 0xa6a6432e,
+ 0x6935f452, 0x0136d89a, 0xb933adc2, 0xd130810a,
+ 0xccd53183, 0xa4d61d4b, 0x1cd36813, 0x74d044db,
+ 0x27180901, 0x4f1b25c9, 0xf71e5091, 0x9f1d7c59,
+ 0x82f8ccd0, 0xeafbe018, 0x52fe9540, 0x3afdb988,
+ 0xc8358d49, 0xa036a181, 0x1833d4d9, 0x7030f811,
+ 0x6dd54898, 0x05d66450, 0xbdd31108, 0xd5d03dc0,
+ 0x8618701a, 0xee1b5cd2, 0x561e298a, 0x3e1d0542,
+ 0x23f8b5cb, 0x4bfb9903, 0xf3feec5b, 0x9bfdc093,
+ 0x546e77ef, 0x3c6d5b27, 0x84682e7f, 0xec6b02b7,
+ 0xf18eb23e, 0x998d9ef6, 0x2188ebae, 0x498bc766,
+ 0x1a438abc, 0x7240a674, 0xca45d32c, 0xa246ffe4,
+ 0xbfa34f6d, 0xd7a063a5, 0x6fa516fd, 0x07a63a35,
+ 0x8fd9098e, 0xe7da2546, 0x5fdf501e, 0x37dc7cd6,
+ 0x2a39cc5f, 0x423ae097, 0xfa3f95cf, 0x923cb907,
+ 0xc1f4f4dd, 0xa9f7d815, 0x11f2ad4d, 0x79f18185,
+ 0x6414310c, 0x0c171dc4, 0xb412689c, 0xdc114454,
+ 0x1382f328, 0x7b81dfe0, 0xc384aab8, 0xab878670,
+ 0xb66236f9, 0xde611a31, 0x66646f69, 0x0e6743a1,
+ 0x5daf0e7b, 0x35ac22b3, 0x8da957eb, 0xe5aa7b23,
+ 0xf84fcbaa, 0x904ce762, 0x2849923a, 0x404abef2,
+ 0xb2828a33, 0xda81a6fb, 0x6284d3a3, 0x0a87ff6b,
+ 0x17624fe2, 0x7f61632a, 0xc7641672, 0xaf673aba,
+ 0xfcaf7760, 0x94ac5ba8, 0x2ca92ef0, 0x44aa0238,
+ 0x594fb2b1, 0x314c9e79, 0x8949eb21, 0xe14ac7e9,
+ 0x2ed97095, 0x46da5c5d, 0xfedf2905, 0x96dc05cd,
+ 0x8b39b544, 0xe33a998c, 0x5b3fecd4, 0x333cc01c,
+ 0x60f48dc6, 0x08f7a10e, 0xb0f2d456, 0xd8f1f89e,
+ 0xc5144817, 0xad1764df, 0x15121187, 0x7d113d4f
+ },
+ {
+ 0x00000000, 0x493c7d27, 0x9278fa4e, 0xdb448769,
+ 0x211d826d, 0x6821ff4a, 0xb3657823, 0xfa590504,
+ 0x423b04da, 0x0b0779fd, 0xd043fe94, 0x997f83b3,
+ 0x632686b7, 0x2a1afb90, 0xf15e7cf9, 0xb86201de,
+ 0x847609b4, 0xcd4a7493, 0x160ef3fa, 0x5f328edd,
+ 0xa56b8bd9, 0xec57f6fe, 0x37137197, 0x7e2f0cb0,
+ 0xc64d0d6e, 0x8f717049, 0x5435f720, 0x1d098a07,
+ 0xe7508f03, 0xae6cf224, 0x7528754d, 0x3c14086a,
+ 0x0d006599, 0x443c18be, 0x9f789fd7, 0xd644e2f0,
+ 0x2c1de7f4, 0x65219ad3, 0xbe651dba, 0xf759609d,
+ 0x4f3b6143, 0x06071c64, 0xdd439b0d, 0x947fe62a,
+ 0x6e26e32e, 0x271a9e09, 0xfc5e1960, 0xb5626447,
+ 0x89766c2d, 0xc04a110a, 0x1b0e9663, 0x5232eb44,
+ 0xa86bee40, 0xe1579367, 0x3a13140e, 0x732f6929,
+ 0xcb4d68f7, 0x827115d0, 0x593592b9, 0x1009ef9e,
+ 0xea50ea9a, 0xa36c97bd, 0x782810d4, 0x31146df3,
+ 0x1a00cb32, 0x533cb615, 0x8878317c, 0xc1444c5b,
+ 0x3b1d495f, 0x72213478, 0xa965b311, 0xe059ce36,
+ 0x583bcfe8, 0x1107b2cf, 0xca4335a6, 0x837f4881,
+ 0x79264d85, 0x301a30a2, 0xeb5eb7cb, 0xa262caec,
+ 0x9e76c286, 0xd74abfa1, 0x0c0e38c8, 0x453245ef,
+ 0xbf6b40eb, 0xf6573dcc, 0x2d13baa5, 0x642fc782,
+ 0xdc4dc65c, 0x9571bb7b, 0x4e353c12, 0x07094135,
+ 0xfd504431, 0xb46c3916, 0x6f28be7f, 0x2614c358,
+ 0x1700aeab, 0x5e3cd38c, 0x857854e5, 0xcc4429c2,
+ 0x361d2cc6, 0x7f2151e1, 0xa465d688, 0xed59abaf,
+ 0x553baa71, 0x1c07d756, 0xc743503f, 0x8e7f2d18,
+ 0x7426281c, 0x3d1a553b, 0xe65ed252, 0xaf62af75,
+ 0x9376a71f, 0xda4ada38, 0x010e5d51, 0x48322076,
+ 0xb26b2572, 0xfb575855, 0x2013df3c, 0x692fa21b,
+ 0xd14da3c5, 0x9871dee2, 0x4335598b, 0x0a0924ac,
+ 0xf05021a8, 0xb96c5c8f, 0x6228dbe6, 0x2b14a6c1,
+ 0x34019664, 0x7d3deb43, 0xa6796c2a, 0xef45110d,
+ 0x151c1409, 0x5c20692e, 0x8764ee47, 0xce589360,
+ 0x763a92be, 0x3f06ef99, 0xe44268f0, 0xad7e15d7,
+ 0x572710d3, 0x1e1b6df4, 0xc55fea9d, 0x8c6397ba,
+ 0xb0779fd0, 0xf94be2f7, 0x220f659e, 0x6b3318b9,
+ 0x916a1dbd, 0xd856609a, 0x0312e7f3, 0x4a2e9ad4,
+ 0xf24c9b0a, 0xbb70e62d, 0x60346144, 0x29081c63,
+ 0xd3511967, 0x9a6d6440, 0x4129e329, 0x08159e0e,
+ 0x3901f3fd, 0x703d8eda, 0xab7909b3, 0xe2457494,
+ 0x181c7190, 0x51200cb7, 0x8a648bde, 0xc358f6f9,
+ 0x7b3af727, 0x32068a00, 0xe9420d69, 0xa07e704e,
+ 0x5a27754a, 0x131b086d, 0xc85f8f04, 0x8163f223,
+ 0xbd77fa49, 0xf44b876e, 0x2f0f0007, 0x66337d20,
+ 0x9c6a7824, 0xd5560503, 0x0e12826a, 0x472eff4d,
+ 0xff4cfe93, 0xb67083b4, 0x6d3404dd, 0x240879fa,
+ 0xde517cfe, 0x976d01d9, 0x4c2986b0, 0x0515fb97,
+ 0x2e015d56, 0x673d2071, 0xbc79a718, 0xf545da3f,
+ 0x0f1cdf3b, 0x4620a21c, 0x9d642575, 0xd4585852,
+ 0x6c3a598c, 0x250624ab, 0xfe42a3c2, 0xb77edee5,
+ 0x4d27dbe1, 0x041ba6c6, 0xdf5f21af, 0x96635c88,
+ 0xaa7754e2, 0xe34b29c5, 0x380faeac, 0x7133d38b,
+ 0x8b6ad68f, 0xc256aba8, 0x19122cc1, 0x502e51e6,
+ 0xe84c5038, 0xa1702d1f, 0x7a34aa76, 0x3308d751,
+ 0xc951d255, 0x806daf72, 0x5b29281b, 0x1215553c,
+ 0x230138cf, 0x6a3d45e8, 0xb179c281, 0xf845bfa6,
+ 0x021cbaa2, 0x4b20c785, 0x906440ec, 0xd9583dcb,
+ 0x613a3c15, 0x28064132, 0xf342c65b, 0xba7ebb7c,
+ 0x4027be78, 0x091bc35f, 0xd25f4436, 0x9b633911,
+ 0xa777317b, 0xee4b4c5c, 0x350fcb35, 0x7c33b612,
+ 0x866ab316, 0xcf56ce31, 0x14124958, 0x5d2e347f,
+ 0xe54c35a1, 0xac704886, 0x7734cfef, 0x3e08b2c8,
+ 0xc451b7cc, 0x8d6dcaeb, 0x56294d82, 0x1f1530a5
+ }
+#endif
+};
diff --git a/c++/src/util/creaders/alnread.c b/c++/src/util/creaders/alnread.c
index f808b48..682b26e 100644
--- a/c++/src/util/creaders/alnread.c
+++ b/c++/src/util/creaders/alnread.c
@@ -1,5 +1,5 @@
/*
- * $Id: alnread.c 430866 2014-03-29 22:08:47Z lavr $
+ * $Id: alnread.c 463944 2015-04-02 14:59:37Z bollin $
*
* ===========================================================================
*
@@ -136,7 +136,7 @@ typedef struct SAlignFileRaw {
static EBool s_AfrpInitLineData(
SAlignRawFilePtr afrp, FReadLineFunction readfunc, void* pfile);
static void s_AfrpProcessFastaGap(
- SAlignRawFilePtr afrp, SLengthListPtr patterns, char* plinestr, int overall_line_count);
+ SAlignRawFilePtr afrp, SLengthListPtr * patterns, EBool * last_line_was_marked_id, char* plinestr, int overall_line_count);
/* These functions are used for storing and transmitting information
* about errors encountered while reading the alignment data.
@@ -1460,7 +1460,9 @@ static int s_CountSequencesInBracketedComment (TBracketedCommentListPtr comment)
}
/* Last line must be right bracket on a line by itself */
/* First line must be left bracket on a line by itself */
- if (lip->data[0] != ']' || strspn (lip->data + 1, " \t\r\n") != strlen (lip->data + 1))
+ if (lip != NULL &&
+ lip->data != NULL &&
+ (lip->data[0] != ']' || strspn (lip->data + 1, " \t\r\n") != strlen (lip->data + 1)))
{
return 0;
}
@@ -2725,7 +2727,9 @@ static void s_RemoveOrganismCommentFromLine (char * string)
TCommentLocPtr clp;
while ((clp = s_FindOrganismComment (string)) != NULL) {
- strcpy (clp->start, clp->end + 1);
+ if (clp->end != NULL) {
+ strcpy (clp->start, clp->end + 1);
+ }
s_CommentLocFree (clp);
}
}
@@ -2850,7 +2854,7 @@ static void s_AddDeflineFromOrganismLine
defline_num ++;
}
- if (defline_num == org_num) {
+ if (defline_num == org_num && lip != NULL) {
/* if previous defline is empty, replace with new defline */
if (strlen (lip->data) == 0)
{
@@ -3425,6 +3429,9 @@ s_FindInterleavedBlocks
size_list = s_AddSizeInfo (size_list, llp->num_appearances);
}
}
+ if (size_list == NULL) {
+ return;
+ }
best_ptr = s_GetMostPopularSizeInfo (size_list);
if (best_ptr != NULL
&& (best_ptr->num_appearances > 1 ||
@@ -3532,17 +3539,28 @@ s_AfrpInitLineData(
static void
s_AfrpProcessFastaGap(
SAlignRawFilePtr afrp,
- SLengthListPtr patterns,
+ SLengthListPtr * patterns,
+ EBool * last_line_was_marked_id,
char* linestr,
int overall_line_count)
{
- static EBool last_line_was_marked_id = eFalse;
- static SLengthListPtr last_pattern = NULL;
-
TIntLinkPtr new_offset = NULL;
SLengthListPtr this_pattern = NULL;
int len = 0;
char* cp;
+ SLengthListPtr last_pattern;
+
+ if (patterns == NULL || last_line_was_marked_id == NULL) {
+ return;
+ }
+ last_pattern = *patterns;
+
+ /* find last pattern in list */
+ if (last_pattern != NULL) {
+ while (last_pattern->next != NULL) {
+ last_pattern = last_pattern->next;
+ }
+ }
/* ID line
*/
@@ -3551,7 +3569,7 @@ s_AfrpProcessFastaGap(
* NEXUS file. If there is no sequence data between
* the lines, don't process this file for marked IDs.
*/
- if (last_line_was_marked_id)
+ if (*last_line_was_marked_id)
{
afrp->marked_ids = eFalse;
// eFormat = ALNFMT_UNKNOWN;
@@ -3564,13 +3582,13 @@ s_AfrpProcessFastaGap(
new_offset = s_IntLinkNew (overall_line_count + 1,
afrp->offset_list);
if (afrp->offset_list == NULL) afrp->offset_list = new_offset;
- last_line_was_marked_id = eTrue;
+ *last_line_was_marked_id = eTrue;
return;
}
/* Data line
*/
- last_line_was_marked_id = eFalse;
+ *last_line_was_marked_id = eFalse;
/* add to length list for interleaved block search */
len = strcspn (linestr, " \t\r");
if (len > 0) {
@@ -3589,14 +3607,12 @@ s_AfrpProcessFastaGap(
}
if (last_pattern == NULL) {
- patterns = this_pattern;
- last_pattern = this_pattern;
+ *patterns = this_pattern;
} else if (s_DoLengthPatternsMatch (last_pattern, this_pattern)) {
last_pattern->num_appearances ++;
s_LengthListFree (this_pattern);
} else {
last_pattern->next = this_pattern;
- last_pattern = this_pattern;
}
}
@@ -3650,7 +3666,7 @@ s_ReadAlignFileRaw
s_ReadOrgNamesFromText (linestring, overall_line_count, afrp);
if (*pformat == ALNFMT_FASTAGAP) {
- s_AfrpProcessFastaGap(afrp, pattern_list, linestring, overall_line_count);
+ s_AfrpProcessFastaGap(afrp, & pattern_list, & last_line_was_marked_id, linestring, overall_line_count);
continue;
}
/* we want to remove the comment from the line for the purpose
@@ -3745,7 +3761,7 @@ s_ReadAlignFileRaw
else
{
*pformat = ALNFMT_FASTAGAP;
- s_AfrpProcessFastaGap(afrp, pattern_list, linestring, overall_line_count);
+ s_AfrpProcessFastaGap(afrp, & pattern_list, & last_line_was_marked_id, linestring, overall_line_count);
continue;
}
new_offset = s_IntLinkNew (overall_line_count + 1,
@@ -3993,7 +4009,6 @@ s_ProcessBlockLines
int len;
int line_number;
EBool this_block_has_ids;
- int pos;
TAlignRawSeqPtr arsp;
this_block_has_ids = s_DoesBlockHaveIds (afrp, lines, num_lines_in_block);
@@ -4005,7 +4020,6 @@ s_ProcessBlockLines
{
linestring = lip->data;
if (linestring != NULL) {
- pos = 0;
if (this_block_has_ids) {
len = strcspn (linestring, " \t\r");
if (first_block && len == strlen (linestring)) {
@@ -4022,10 +4036,9 @@ s_ProcessBlockLines
strncpy (this_id, linestring, len);
this_id [len] = 0;
cp = linestring + len;
- pos += len;
len = strspn (cp, " \t\r");
cp += len;
- pos += len;
+
/* Check for duplicate IDs in the first block */
if (first_block)
{
@@ -4156,7 +4169,6 @@ s_CreateSequencesBasedOnTokenPatterns
line_counter = 0;
lip = token_list;
- offset_ptr = offset_list;
curr_seg = 0;
for (offset_ptr = offset_list;
@@ -4252,7 +4264,7 @@ s_CreateAnchorPatternForMarkedIDs
TLineInfoPtr lip;
int curr_seg;
- if (afrp == NULL) {
+ if (afrp == NULL || afrp->num_segments < 1) {
return NULL;
}
@@ -4304,6 +4316,7 @@ s_CreateAnchorPatternForMarkedIDs
s_LengthListFree (list [curr_seg]);
}
free (list);
+ free (best);
return NULL;
}
this_pattern->num_appearances = 1;
@@ -4354,6 +4367,11 @@ s_CreateAnchorPatternForMarkedIDs
}
}
+ /* free list. note that all of the elements of list that are not pointed to by best
+ have already been freed*/
+ free (list);
+
+
for (curr_seg = 0; curr_seg < afrp->num_segments; curr_seg ++)
{
if (best[curr_seg] == NULL)
@@ -4362,6 +4380,7 @@ s_CreateAnchorPatternForMarkedIDs
{
s_LengthListFree (best [curr_seg]);
}
+ free (best);
return NULL;
}
}
@@ -5096,7 +5115,7 @@ s_CountCharactersBetweenOffsets
if (lip == NULL || line_diff == distance) {
return 0;
}
- num_starts = 1;
+
list = lip->next;
start_of_unknown = line_diff;
@@ -5250,7 +5269,7 @@ static void s_InsertNewOffsets
/* if we have room for one more sequence, or even most of one more sequence, add it */
if (lip != NULL && ! s_SkippableString (lip->data)) {
- splice_offset = s_IntLinkNew (line_diff + prev_offset->ival, prev_offset);
+ s_IntLinkNew (line_diff + prev_offset->ival, prev_offset);
}
}
@@ -5307,6 +5326,7 @@ static void s_ProcessAlignFileRawByLengthPattern (SAlignRawFilePtr afrp)
anchorpattern [0] = s_FindMostPopularPattern (list->lengthrepeats);
anchorpattern [1] = NULL;
if (anchorpattern [0] == NULL || anchorpattern[0]->lengthrepeats == NULL) {
+ s_LengthListFree (list);
return;
}
@@ -5669,6 +5689,7 @@ s_FindBadDataCharsInSequence
}
if (! found_middle_start) {
+ s_LineInfoReaderFree (lirp);
if (num_segments > 1)
{
return eFalse;
@@ -5677,7 +5698,6 @@ s_FindBadDataCharsInSequence
{
s_ReportMissingSequenceData (arsp->id,
report_error, report_error_userdata);
- s_LineInfoReaderFree (lirp);
return eTrue;
}
@@ -5809,11 +5829,13 @@ static EBool s_AreOrganismsUnique (SAlignRawFilePtr afrp)
}
if (lip != NULL && lip != this_org) {
are_unique = eFalse;
- s_ReportRepeatedOrganismName (arsp->id, this_org->line_num,
- lip->line_num,
- this_org->data,
- afrp->report_error,
- afrp->report_error_userdata);
+ if (arsp != NULL && arsp->id != NULL) {
+ s_ReportRepeatedOrganismName (arsp->id, this_org->line_num,
+ lip->line_num,
+ this_org->data,
+ afrp->report_error,
+ afrp->report_error_userdata);
+ }
}
}
return are_unique;
@@ -5836,7 +5858,8 @@ s_ConvertDataToOutput
TLineInfoPtr lip;
int curr_seg;
- if (afrp == NULL || sip == NULL || afrp->sequences == NULL) {
+ if (afrp == NULL || sip == NULL || afrp->sequences == NULL ||
+ afrp->num_segments < 1) {
return NULL;
}
afp = AlignmentFileNew ();
@@ -5863,17 +5886,32 @@ s_ConvertDataToOutput
s_AreOrganismsUnique (afrp);
}
+ // allocate memory to store sequence strings
afp->sequences = (char **)malloc (afp->num_sequences
* sizeof (char *));
if (afp->sequences == NULL) {
AlignmentFileFree (afp);
return NULL;
}
+ // initialize afp->sequences, in case AlignmentFileFree must be called
+ // before real data can be added
+ for (index = 0; index < afp->num_sequences; index++) {
+ afp->sequences[index] = NULL;
+ }
+
+ // allocate memory to store sequence IDs
afp->ids = (char **)malloc (afp->num_sequences * sizeof (char *));
if (afp->ids == NULL) {
AlignmentFileFree (afp);
return NULL;
}
+ // initialize afp->ids, in case AlignmentFileFree must be called
+ // before real data can be added
+ for (index = 0; index < afp->num_sequences; index++) {
+ afp->ids[index] = NULL;
+ }
+
+ // allocate memory to store organism names
if (afp->num_organisms > 0) {
afp->organisms = (char **) malloc (afp->num_organisms
* sizeof (char *));
@@ -5882,6 +5920,13 @@ s_ConvertDataToOutput
return NULL;
}
}
+ // initialize afp->organisms, in case AlignmentFileFree must be called
+ // before real data can be added
+ for (index = 0; index < afp->num_organisms; index++) {
+ afp->organisms[index] = NULL;
+ }
+
+ // allocate memory to store definition lines
if (afp->num_deflines > 0) {
afp->deflines = (char **)malloc (afp->num_deflines
* sizeof (char *));
diff --git a/c++/src/util/dictionary_util.cpp b/c++/src/util/dictionary_util.cpp
index 87758ff..57353ac 100644
--- a/c++/src/util/dictionary_util.cpp
+++ b/c++/src/util/dictionary_util.cpp
@@ -1,4 +1,4 @@
-/* $Id: dictionary_util.cpp 458469 2015-02-05 14:52:54Z ivanov $
+/* $Id: dictionary_util.cpp 464904 2015-04-15 14:26:24Z kotliaro $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -76,9 +76,12 @@ void CDictionaryUtil::GetMetaphone(const string& in, string* out,
break;
case 'b':
- if (remaining != 0 || *(iter - 1) != 'm') {
+ if (remaining != 0 ||
+ !prev_len ||
+ *(iter - 1) != 'm') {
*out += 'p';
}
+
break;
case 'f':
@@ -275,8 +278,8 @@ void CDictionaryUtil::GetMetaphone(const string& in, string* out,
case 'w':
if ( !prev_len ) {
- if (*(iter + 1) == 'h' ||
- *(iter + 1) == 'r') {
+ if (remaining && ( *(iter + 1) == 'h' ||
+ *(iter + 1) == 'r') ) {
*out += *(iter + 1);
++iter;
break;
@@ -476,15 +479,17 @@ size_t CDictionaryUtil::GetEditDistance(const string& str1,
const string* short_str = &str1;
const string* long_str = &str2;
- if (str2.length() < str1.length()) {
+ if (long_str->size() < short_str->size()) {
swap(short_str, long_str);
}
+ size_t short_size = short_str->size();
+ size_t long_size = long_str->size();
size_t* row0_ptr = buf0;
size_t* row1_ptr = buf1;
- if (short_str->size() > kMaxMetaphoneStack) {
- row0.resize(short_str->size() + 1);
- row1.resize(short_str->size() + 1);
+ if (short_size > kMaxMetaphoneStack) {
+ row0.resize(short_size + 1);
+ row1.resize(short_size + 1);
row0_ptr = &row0[0];
row1_ptr = &row1[0];
}
@@ -493,17 +498,17 @@ size_t CDictionaryUtil::GetEditDistance(const string& str1,
size_t j;
//cout << " ";
- for (i = 0; i < short_str->size() + 1; ++i) {
+ for (i = 0; i <= short_size; ++i) {
//cout << (*short_str)[i] << " ";
row0_ptr[i] = i;
row1_ptr[i] = i;
}
//cout << endl;
- for (i = 0; i < long_str->size(); ++i) {
+ for (i = 0; i < long_size; ++i) {
row1_ptr[0] = i + 1;
//cout << (*long_str)[i] << " ";
- for (j = 0; j < short_str->size(); ++j) {
+ for (j = 0; j < short_size; ++j) {
int c0 = tolower((unsigned char) (*short_str)[j]);
int c1 = tolower((unsigned char) (*long_str)[i]);
size_t cost = (c0 == c1 ? 0 : 1);
@@ -518,7 +523,7 @@ size_t CDictionaryUtil::GetEditDistance(const string& str1,
swap(row0_ptr, row1_ptr);
}
- return row0_ptr[short_str->size()];
+ return row0_ptr[short_size];
}}
}
diff --git a/c++/src/util/distribution.cpp b/c++/src/util/distribution.cpp
index 03832da..3727aa6 100644
--- a/c++/src/util/distribution.cpp
+++ b/c++/src/util/distribution.cpp
@@ -1,4 +1,4 @@
-/* $Id: distribution.cpp 448239 2014-10-03 14:17:45Z kazimird $
+/* $Id: distribution.cpp 448236 2014-10-03 14:05:43Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/format_guess.cpp b/c++/src/util/format_guess.cpp
index dd9ebd9..80cc7dc 100644
--- a/c++/src/util/format_guess.cpp
+++ b/c++/src/util/format_guess.cpp
@@ -1,4 +1,4 @@
-/* $Id: format_guess.cpp 464933 2015-04-15 15:04:44Z ivanov $
+/* $Id: format_guess.cpp 479107 2015-09-16 15:58:57Z ivanov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -65,11 +65,15 @@ static unsigned char symbol_type_table[256];
// ----------------------------------------------------------------------------
static bool s_IsTokenPosInt(
const string& strToken )
+ // ----------------------------------------------------------------------------
{
size_t tokenSize = strToken.size();
if (tokenSize == 0) {
return false;
}
+ if (tokenSize == 1 && strToken[0] == '0') {
+ return true;
+ }
if (strToken[0] < '1' || '9' < strToken[0]) {
return false;
}
@@ -86,7 +90,7 @@ static bool s_IsTokenInteger(
const string& strToken )
// ----------------------------------------------------------------------------
{
- if ( ! strToken.empty() && strToken[0] == '-' ) {
+ if ( ! strToken.empty() && (strToken[0] == '-' || strToken[0] == '+')) {
return s_IsTokenPosInt( strToken.substr( 1 ) );
}
return s_IsTokenPosInt( strToken );
@@ -101,7 +105,10 @@ static bool s_IsTokenDouble(
if ( token.size() > 1 && token[0] == '-' ) {
token[0] = '1';
}
- return s_IsTokenPosInt( token );
+ if (token.size() > 1 && token[0] == '0') {
+ token[0] = '1';
+ }
+ return s_IsTokenPosInt(token);
}
// ----------------------------------------------------------------------------
@@ -161,9 +168,9 @@ CFormatGuess::s_CheckOrder[] =
eSra,
eRmo,
eVcf,
- eGtf,
eGvf,
eGff3,
+ eGtf,
eGff2,
eGlimmer3,
eAgp,
@@ -200,9 +207,9 @@ const char* const CFormatGuess::sm_FormatNames[CFormatGuess::eFormat_max] = {
"AGP",
"XML",
"WIGGLE",
- "Newick",
"BED",
"BED15",
+ "Newick",
"alignment",
"distance matrix",
"flat-file sequence",
@@ -528,6 +535,7 @@ CFormatGuess::Initialize()
m_iStatsCountAlNumChars = 0;
m_iStatsCountDnaChars = 0;
m_iStatsCountAaChars = 0;
+ m_iStatsCountBraces = 0;
}
// ----------------------------------------------------------------------------
@@ -600,6 +608,7 @@ CFormatGuess::EnsureStats()
// from the DNA alphabet
// m_iStatsCountAaChars: number of characters counted in m_iStatsCountData
// from the AA alphabet
+ // m_iStatsCountBraces: Opening { and closing } braces
//
while ( ! TestBuffer.fail() ) {
NcbiGetlineEOL( TestBuffer, strLine );
@@ -617,6 +626,9 @@ CFormatGuess::EnsureStats()
if ( type & (fAlpha | fDigit | fSpace) ) {
++m_iStatsCountAlNumChars;
}
+ else if (c == '{' || c == '}') {
+ ++m_iStatsCountBraces;
+ }
if ( !is_header ) {
if ( !(type & fSpace) ) {
++m_iStatsCountData;
@@ -769,6 +781,9 @@ CFormatGuess::TestFormatGff3(
// Make sure to ignore any UCSC track and browser lines prior to the
// start of data
//
+ if (!uGffLineCount && NStr::StartsWith(*it, "##gff-version 3")) {
+ return true;
+ }
if ( it->empty() || (*it)[0] == '#' ) {
continue;
}
@@ -1137,7 +1152,8 @@ CFormatGuess::TestFormatAlignment(
// Don't skip though if file is very short - add up to 3, 1 for each line
// over 5:
for (size_t i=5; i<7; ++i)
- if (m_TestLines.size() > i) ++iter;
+ if (m_TestLines.size() > i)
+ ++iter;
/// determine the number of observed columns
size_t ncols = 0;
@@ -1186,6 +1202,9 @@ CFormatGuess::TestFormatTable(
if ( ! EnsureTestBuffer() || ! EnsureSplitLines() ) {
return false;
}
+ if ( ! IsAsciiText()) {//gp-13007: "table" means "ascii table"
+ return false;
+ }
//
// NOTE 1:
@@ -1221,6 +1240,21 @@ CFormatGuess::TestFormatTable(
}
// -----------------------------------------------------------------------------
+void SkipCommentAndBlank(CTempString &text)
+{
+ const CTempString COMMENT_SYMBOLS(";#!");
+ const CTempString NEW_LINE_SYMBOLS("\r\n");
+ while (true) {
+ text = NStr::TruncateSpaces_Unsafe(text, NStr::eTrunc_Begin);
+ if ( COMMENT_SYMBOLS.find(text[0]) != CTempString::npos ) {
+ CTempString::size_type pos = text.find_first_of(NEW_LINE_SYMBOLS, 1);
+ text = text.substr(pos);
+ } else {
+ break;
+ }
+ }
+}
+
bool
CFormatGuess::TestFormatFasta(
EMode /* not used */ )
@@ -1230,7 +1264,9 @@ CFormatGuess::TestFormatFasta(
}
// reject obvious misfits:
- if ( m_iTestDataSize == 0 || m_pTestBuffer[0] != '>' ) {
+ CTempString header(m_pTestBuffer, m_iTestDataSize);
+ SkipCommentAndBlank(header);
+ if ( m_iTestDataSize == 0 || header.length() == 0 || header[0] != '>' ) {
return false;
}
if ( m_iStatsCountData == 0 ) {
@@ -1276,7 +1312,7 @@ CFormatGuess::TestFormatTextAsn(
// at least 80% text-ish,
// "::=" as the 2nd field of the first non-blank non comment line.
//
- double dAlNumFraction = (double)m_iStatsCountAlNumChars / m_iTestDataSize;
+ double dAlNumFraction = (double)(m_iStatsCountAlNumChars+m_iStatsCountBraces) / m_iTestDataSize;
if ( dAlNumFraction < 0.80 ) {
return false;
}
@@ -2182,14 +2218,14 @@ bool CFormatGuess::IsLineGff3(
}
if ( tokens.size() >= 9 && tokens[8].size() > 1) {
const string& col9 = tokens[8];
- if ( NPOS == NStr::FindNoCase(col9, "ID") &&
- NPOS == NStr::FindNoCase(col9, "Parent") &&
- NPOS == NStr::FindNoCase(col9, "Target") &&
- NPOS == NStr::FindNoCase(col9, "Name") &&
- NPOS == NStr::FindNoCase(col9, "Alias") &&
- NPOS == NStr::FindNoCase(col9, "Note") &&
- NPOS == NStr::FindNoCase(col9, "Dbxref") &&
- NPOS == NStr::FindNoCase(col9, "Xref") ) {
+ if ( NPOS == NStr::Find(col9, "ID") &&
+ NPOS == NStr::Find(col9, "Parent") &&
+ NPOS == NStr::Find(col9, "Target") &&
+ NPOS == NStr::Find(col9, "Name") &&
+ NPOS == NStr::Find(col9, "Alias") &&
+ NPOS == NStr::Find(col9, "Note") &&
+ NPOS == NStr::Find(col9, "Dbxref") &&
+ NPOS == NStr::Find(col9, "Xref") ) {
return false;
}
}
diff --git a/c++/src/util/md5.cpp b/c++/src/util/md5.cpp
index 10ecdb4..7e3c53f 100644
--- a/c++/src/util/md5.cpp
+++ b/c++/src/util/md5.cpp
@@ -1,4 +1,4 @@
-/* $Id: md5.cpp 339430 2011-09-28 19:07:14Z vasilche $
+/* $Id: md5.cpp 450819 2014-10-30 18:10:49Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -38,7 +38,7 @@
BEGIN_NCBI_SCOPE
-// Note: this code is harmless on little-endian machines.
+#ifdef WORDS_BIGENDIAN
inline
static void s_ByteReverse(unsigned char* buf, size_t longs)
{
@@ -50,6 +50,7 @@ static void s_ByteReverse(unsigned char* buf, size_t longs)
buf += 4;
} while (--longs);
}
+#endif
// Start MD5 accumulation. Set bit count to 0 and buffer to mysterious
@@ -168,8 +169,9 @@ void CMD5::Finalize(unsigned char digest[16])
string CMD5::GetHexSum(unsigned char digest[16])
{
CNcbiOstrstream oss;
+ oss << hex << setfill('0');
for (size_t i = 0; i < 16; ++i) {
- oss << hex << setw(2) << setfill('0') << (int)digest[i];
+ oss << setw(2) << (int)digest[i];
}
return CNcbiOstrstreamToString(oss);
}
diff --git a/c++/src/util/random_gen.cpp b/c++/src/util/random_gen.cpp
index 2efc191..9722747 100644
--- a/c++/src/util/random_gen.cpp
+++ b/c++/src/util/random_gen.cpp
@@ -1,4 +1,4 @@
-/* $Id: random_gen.cpp 415954 2013-10-22 18:58:45Z satskyse $
+/* $Id: random_gen.cpp 459009 2015-02-12 15:18:36Z sadyrovr $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -328,4 +328,28 @@ CRandom::TValue CRandom::x_GetSysRand32Bits(void) const
}
+Uint8 CRandom::GetRandIndexUint8(Uint8 size)
+{
+ if ( size <= kMax_UI4 ) {
+ return GetRandIndex(Uint4(size));
+ }
+
+ if ( (size & (size-1)) == 0 ) { // only one bit set - power of 2
+ // get high bits via multiplication - it's faster than division
+ Uint8 bits = GetRandUint8();
+ while ( size <<= 1 ) {
+ bits >>= 1;
+ }
+ return bits;
+ }
+
+ Uint8 bits, r;
+ do {
+ bits = GetRandUint8();
+ r = bits % size;
+ } while ( bits > r - size ); // 64-bit overflow is intentional
+ return r;
+}
+
+
END_NCBI_SCOPE
diff --git a/c++/src/util/rangelist.cpp b/c++/src/util/rangelist.cpp
index 432c965..5f43660 100644
--- a/c++/src/util/rangelist.cpp
+++ b/c++/src/util/rangelist.cpp
@@ -1,4 +1,4 @@
-/* $Id: rangelist.cpp 448243 2014-10-03 14:19:30Z kazimird $
+/* $Id: rangelist.cpp 448238 2014-10-03 14:16:50Z kazimird $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/regexp/pcretest.c b/c++/src/util/regexp/pcretest.c
index 79218a2..92616fb 100644
--- a/c++/src/util/regexp/pcretest.c
+++ b/c++/src/util/regexp/pcretest.c
@@ -250,7 +250,7 @@ for (;;)
/* Read the next line by normal means, prompting if the file is stdin. */
{
- if (f == stdin) printf(prompt);
+ if (f == stdin) fputs(prompt, f);
if (fgets((char *)here, rlen, f) == NULL)
return (here == start)? NULL : start;
}
diff --git a/c++/src/util/regexp/test_pcre.sh b/c++/src/util/regexp/test_pcre.sh
index 592da9e..ef84d59 100755
--- a/c++/src/util/regexp/test_pcre.sh
+++ b/c++/src/util/regexp/test_pcre.sh
@@ -21,7 +21,7 @@ case "`uname -s`" in
diff testdata/wintestoutput3 $out || errcode=3
;;
- FreeBSD )
+ FreeBSD | Darwin )
# Do not run test2 on FreeBSD.
# Some parts of test 2 can exceed available memory in some configurations.
;;
diff --git a/c++/src/util/retry_ctx.cpp b/c++/src/util/retry_ctx.cpp
new file mode 100644
index 0000000..a0b2139
--- /dev/null
+++ b/c++/src/util/retry_ctx.cpp
@@ -0,0 +1,165 @@
+/* $Id: retry_ctx.cpp 483516 2015-11-02 14:43:15Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Aleksey Grichenko
+ *
+ * File Description:
+ * CRetryContext implementation.
+ *
+ * ===========================================================================
+ */
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbi_cookies.hpp>
+#include <util/retry_ctx.hpp>
+
+BEGIN_NCBI_SCOPE
+
+
+const char* CHttpRetryContext::kHeader_Stop = "X-NCBI-Retry-Stop";
+const char* CHttpRetryContext::kHeader_Delay = "X-NCBI-Retry-Delay";
+const char* CHttpRetryContext::kHeader_Args = "X-NCBI-Retry-Args";
+const char* CHttpRetryContext::kHeader_Url = "X-NCBI-Retry-URL";
+const char* CHttpRetryContext::kHeader_Content = "X-NCBI-Retry-Content";
+const char* CHttpRetryContext::kContent_None = "no_content";
+const char* CHttpRetryContext::kContent_FromResponse = "from_response";
+const char* CHttpRetryContext::kContent_Value = "content:";
+
+
+CHttpRetryContext::CHttpRetryContext(const CRetryContext& ctx)
+{
+ *this = ctx;
+}
+
+
+CHttpRetryContext& CHttpRetryContext::operator=(const CRetryContext& ctx)
+{
+ if (&ctx != this) {
+ // Copy parent's data, ignore any extras.
+ CRetryContext::operator=(ctx);
+ }
+ return *this;
+}
+
+
+void CHttpRetryContext::ParseHeader(const char* http_header)
+{
+ list<string> lines;
+ NStr::Split(http_header, HTTP_EOL, lines);
+
+ SetContentOverride(eNot_set);
+ ResetContent();
+ ResetNeedRetry();
+
+ string name, value;
+ ITERATE(list<string>, line, lines) {
+ size_t delim = line->find(':');
+ if (delim == NPOS || delim < 1) {
+ // skip lines without delimiter - can be HTTP status or
+ // something else.
+ continue;
+ }
+ name = line->substr(0, delim);
+ value = line->substr(delim + 1);
+ NStr::TruncateSpacesInPlace(value, NStr::eTrunc_Both);
+
+ if ( NStr::EqualNocase(name, kHeader_Stop) ) {
+ SetStop(value);
+ }
+ if ( NStr::EqualNocase(name, kHeader_Delay) ) {
+ double val = NStr::StringToDouble(value);
+ if (errno == 0) {
+ SetDelay(val);
+ }
+ SetNeedRetry(); // Even if the value was wrong.
+ }
+ if ( NStr::EqualNocase(name, kHeader_Args) ) {
+ SetArgs(value);
+ SetNeedReconnect();
+ SetNeedRetry();
+ }
+ if ( NStr::EqualNocase(name, kHeader_Url) ) {
+ SetUrl(value);
+ SetNeedReconnect();
+ SetNeedRetry();
+ }
+ if ( NStr::EqualNocase(name, kHeader_Content) ) {
+ string content = value;
+ if ( NStr::EqualNocase(content, kContent_None) ) {
+ SetContentOverride(eNoContent);
+ }
+ else if ( NStr::EqualNocase(content, kContent_FromResponse) ) {
+ SetContentOverride(eFromResponse);
+ }
+ else if ( NStr::StartsWith(content, kContent_Value, NStr::eNocase) ) {
+ SetContentOverride(eData);
+ SetContent(NStr::URLDecode(content.substr(strlen(kContent_Value))));
+ }
+ SetNeedRetry();
+ }
+ }
+}
+
+
+void CHttpRetryContext::GetValues(TValues& values) const
+{
+ values.clear();
+ if ( IsSetStop() ) {
+ values[kHeader_Stop] = GetStopReason();
+ }
+ if ( IsSetDelay() ) {
+ values[kHeader_Delay] = NStr::NumericToString(GetDelay().GetAsDouble());
+ }
+ if ( IsSetArgs() ) {
+ values[kHeader_Args] = GetArgs();
+ }
+ if ( IsSetUrl() ) {
+ values[kHeader_Url] = GetUrl();
+ }
+ if ( IsSetContentOverride() ) {
+ switch ( GetContentOverride() ) {
+ case eNoContent:
+ values[kHeader_Content] = kContent_None;
+ break;
+ case eFromResponse:
+ values[kHeader_Content] = kContent_FromResponse;
+ break;
+ case eData:
+ {
+ string value = kContent_Value;
+ if ( IsSetContent() ) {
+ value += NStr::URLEncode(GetContent());
+ }
+ values[kHeader_Content] = value;
+ break;
+ }
+ default:
+ break;
+ }
+ }
+}
+
+
+END_NCBI_SCOPE
diff --git a/c++/src/util/sequtil/Makefile.sequtil.lib b/c++/src/util/sequtil/Makefile.sequtil.lib
index e104852..2190e28 100644
--- a/c++/src/util/sequtil/Makefile.sequtil.lib
+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
@@ -1,9 +1,9 @@
-# $Id: Makefile.sequtil.lib 420255 2013-12-03 17:28:10Z gouriano $
+# $Id: Makefile.sequtil.lib 443775 2014-08-19 15:14:56Z vakatov $
LIB = sequtil
SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-WATCHERS = shomrat
+WATCHERS = grichenk ucko
USES_LIBRARIES = \
diff --git a/c++/src/util/sequtil/sequtil_convert.cpp b/c++/src/util/sequtil/sequtil_convert.cpp
index b7d5c39..11c23bb 100644
--- a/c++/src/util/sequtil/sequtil_convert.cpp
+++ b/c++/src/util/sequtil/sequtil_convert.cpp
@@ -1,4 +1,4 @@
-/* $Id: sequtil_convert.cpp 444998 2014-08-29 14:53:16Z ivanov $
+/* $Id: sequtil_convert.cpp 444660 2014-08-26 20:15:25Z ucko $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/sequtil/sequtil_convert_imp.cpp b/c++/src/util/sequtil/sequtil_convert_imp.cpp
index f2ef1ee..c3fe0c3 100644
--- a/c++/src/util/sequtil/sequtil_convert_imp.cpp
+++ b/c++/src/util/sequtil/sequtil_convert_imp.cpp
@@ -1,4 +1,4 @@
-/* $Id: sequtil_convert_imp.cpp 446394 2014-09-15 17:57:40Z ivanov $
+/* $Id: sequtil_convert_imp.cpp 443752 2014-08-19 12:38:37Z grichenk $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/strbuffer.cpp b/c++/src/util/strbuffer.cpp
index a309d19..41ae634 100644
--- a/c++/src/util/strbuffer.cpp
+++ b/c++/src/util/strbuffer.cpp
@@ -1,4 +1,4 @@
-/* $Id: strbuffer.cpp 355801 2012-03-08 16:20:00Z ivanovp $
+/* $Id: strbuffer.cpp 465289 2015-04-20 15:17:20Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -78,10 +78,7 @@ CIStreamBuffer::~CIStreamBuffer(void)
try {
Close();
}
- catch ( exception& exc ) {
- ERR_POST_X(1, Warning <<
- "~CIStreamBuffer: exception while closing: " << exc.what());
- }
+ NCBI_CATCH_X(1, "~CIStreamBuffer: exception while closing");
if ( m_BufferSize ) {
delete[] m_Buffer;
}
@@ -737,22 +734,51 @@ COStreamBuffer::~COStreamBuffer(void)
try {
Close();
}
- catch ( exception& exc ) {
- ERR_POST_X(2, Warning <<
- "~COStreamBuffer: exception while closing: " << exc.what());
+ NCBI_CATCH_X(2, "~COStreamBuffer: exception while closing");
+ if ( m_DeleteOutput ) {
+ try {
+ delete &m_Output;
+ }
+ NCBI_CATCH_X(2, "~COStreamBuffer: exception deleting output stream");
+ m_DeleteOutput = false;
}
delete[] m_Buffer;
}
+BEGIN_LOCAL_NAMESPACE;
+
+struct STemporarilyClearStreamState
+{
+ STemporarilyClearStreamState(ios& stream)
+ : m_Stream(stream),
+ m_State(stream.rdstate())
+ {
+ m_Stream.clear();
+ }
+ ~STemporarilyClearStreamState()
+ {
+ m_Stream.setstate(m_State);
+ }
+
+ ios& m_Stream;
+ IOS_BASE::iostate m_State;
+};
+
+END_LOCAL_NAMESPACE;
+
+
void COStreamBuffer::Close(void)
{
if ( m_Output ) {
- FlushBuffer();
if ( m_DeleteOutput ) {
Flush();
delete &m_Output;
m_DeleteOutput = false;
}
+ else {
+ STemporarilyClearStreamState state(m_Output);
+ FlushBuffer();
+ }
}
m_Error = 0;
m_IndentLevel = 0;
@@ -808,19 +834,11 @@ void COStreamBuffer::FlushBuffer(bool fullBuffer)
void COStreamBuffer::Flush(void)
THROWS1((CIOException))
{
+ STemporarilyClearStreamState state(m_Output);
FlushBuffer();
- IOS_BASE::iostate state = m_Output.rdstate();
- m_Output.clear();
- try {
- if ( !m_Output.flush() ) {
- NCBI_THROW(CIOException,eFlush,"COStreamBuffer::Flush: failed");
- }
- }
- catch (...) {
- m_Output.clear(state);
- throw;
+ if ( !m_Output.flush() ) {
+ NCBI_THROW(CIOException,eFlush,"COStreamBuffer::Flush: failed");
}
- m_Output.clear(state);
}
diff --git a/c++/src/util/strsearch.cpp b/c++/src/util/strsearch.cpp
index fec19ba..c726488 100644
--- a/c++/src/util/strsearch.cpp
+++ b/c++/src/util/strsearch.cpp
@@ -1,4 +1,4 @@
-/* $Id: strsearch.cpp 459982 2015-02-24 14:54:35Z ivanov $
+/* $Id: strsearch.cpp 462120 2015-03-16 18:27:48Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -127,13 +127,11 @@ void CBoyerMooreMatcher::AddDelimiters(char ch)
if (m_WholeWord == 0) {
m_WholeWord = eWholeWordMatch;
}
- m_WordDelimiters[ch] = true;
+ m_WordDelimiters[(unsigned char)ch] = true;
if (m_CaseSensitive == NStr::eNocase) {
- ch = toupper((unsigned char) ch);
+ m_WordDelimiters[toupper((unsigned char) ch)] = true;
}
-
- m_WordDelimiters[ch] = true;
}
void CBoyerMooreMatcher::InitCommonDelimiters()
@@ -171,7 +169,7 @@ void CBoyerMooreMatcher::x_InitPattern(void)
// compute right-most occurrence
for ( int j = 0; j < (int)m_PatLen - 1; ++j ) {
/* int lo = */
- m_LastOccurrence[(int)m_Pattern[j]] = m_PatLen - j - 1;
+ m_LastOccurrence[(unsigned char)m_Pattern[j]] = m_PatLen - j - 1;
}
}
@@ -188,23 +186,21 @@ SIZE_TYPE CBoyerMooreMatcher::Search(const char* text,
while (shift + m_PatLen <= text_len) {
int j = (int)m_PatLen - 1;
- for(char text_char = text[shift + j];
- j >= 0 && m_Pattern[j]==(text_char=text[shift + j]);
- --j) {}
+ for( ; j >= 0 && m_Pattern[j]==text[shift + j]; --j )
+ {}
if ( (j == -1) && IsWholeWord(text, shift, text_len) ) {
return shift;
} else {
- shift += (unsigned int)m_LastOccurrence[text[shift + (int)m_PatLen - 1]];
+ shift += (unsigned int)m_LastOccurrence[(unsigned char)text[shift + (int)m_PatLen - 1]];
}
}
} else { // case insensitive NStr::eNocase
while (shift + m_PatLen <= text_len) {
int j = (int)m_PatLen - 1;
- for(char text_char = toupper((unsigned char) text[shift + j]);
- j >= 0 && m_Pattern[j]==(text_char=toupper((unsigned char) text[shift + j]));
- --j) {}
+ for( ; j >= 0 && m_Pattern[j]==char(toupper((unsigned char) text[shift + j])); --j )
+ {}
if ( (j == -1) && IsWholeWord(text, shift, text_len) ) {
return shift;
@@ -238,14 +234,14 @@ bool CBoyerMooreMatcher::IsWholeWord(const char* text,
// check on the left
if (m_WholeWord & ePrefixMatch) {
left = (pos == 0) ||
- ((pos > 0) && m_WordDelimiters[text[pos - 1]]);
+ ((pos > 0) && m_WordDelimiters[(unsigned char)text[pos - 1]]);
}
// check on the right
if (m_WholeWord & eSuffixMatch) {
pos += (unsigned int)m_PatLen;
right = (pos == text_len) ||
- ((pos < text_len) && m_WordDelimiters[text[pos]]);
+ ((pos < text_len) && m_WordDelimiters[(unsigned char)text[pos]]);
}
diff --git a/c++/src/util/tables/raw_scoremat.c b/c++/src/util/tables/raw_scoremat.c
index 06fb17a..757a8c1 100644
--- a/c++/src/util/tables/raw_scoremat.c
+++ b/c++/src/util/tables/raw_scoremat.c
@@ -1,4 +1,4 @@
-/* $Id: raw_scoremat.c 459038 2015-02-12 17:28:36Z ivanov $
+/* $Id: raw_scoremat.c 458581 2015-02-06 15:18:12Z boratyng $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/tables/sm_identity.c b/c++/src/util/tables/sm_identity.c
index 7673dae..ea27ca3 100644
--- a/c++/src/util/tables/sm_identity.c
+++ b/c++/src/util/tables/sm_identity.c
@@ -1,4 +1,4 @@
-/* $Id: sm_identity.c 459038 2015-02-12 17:28:36Z ivanov $
+/* $Id: sm_identity.c 458581 2015-02-06 15:18:12Z boratyng $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/thread_pool_old.cpp b/c++/src/util/thread_pool_old.cpp
index 06df4aa..3cefabe 100644
--- a/c++/src/util/thread_pool_old.cpp
+++ b/c++/src/util/thread_pool_old.cpp
@@ -1,4 +1,4 @@
-/* $Id: thread_pool_old.cpp 448084 2014-10-02 14:55:06Z ivanov $
+/* $Id: thread_pool_old.cpp 444514 2014-08-25 17:30:00Z vasilche $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
diff --git a/c++/src/util/unicode.cpp b/c++/src/util/unicode.cpp
index f69d581..7be7f41 100644
--- a/c++/src/util/unicode.cpp
+++ b/c++/src/util/unicode.cpp
@@ -1,4 +1,4 @@
-/* $Id: unicode.cpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: unicode.cpp 459667 2015-02-20 16:49:22Z gouriano $
* ==========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -110,7 +110,7 @@ static string s_FindUnicodeToAscii(void)
return g_FindDataFile("unicode_to_ascii.txt");
}
NCBI_PARAM_DECL(string, NCBI, UnicodeToAscii);
-NCBI_PARAM_DEF_WITH_INIT (string, NCBI, UnicodeToAscii, kEmptyStr, s_FindUnicodeToAscii);
+NCBI_PARAM_DEF_WITH_INIT (string, NCBI, UnicodeToAscii, "", s_FindUnicodeToAscii);
/////////////////////////////////////////////////////////////////////////////
// CUnicodeToAsciiTranslation helper class
@@ -201,7 +201,14 @@ void CUnicodeToAsciiTranslation::x_Initialize(const string& name)
++poolpos;
}
}
- m_pool = (char*)realloc( m_pool, poolpos);
+ if (poolpos == 0) {
+ ERR_POST_X(1, "UnicodeToAscii table is empty: " << name);
+ free(m_pool);
+ m_pool = nullptr;
+ return;
+ } else {
+ m_pool = (char*)realloc( m_pool, poolpos);
+ }
// create translation table
map<TUnicode, size_t>::const_iterator symend = symbolToOffset.end();
diff --git a/c++/src/util/util_misc.cpp b/c++/src/util/util_misc.cpp
index 3cf9ba1..13c6488 100644
--- a/c++/src/util/util_misc.cpp
+++ b/c++/src/util/util_misc.cpp
@@ -1,4 +1,4 @@
-/* $Id: util_misc.cpp 403742 2013-06-18 15:26:09Z grichenk $
+/* $Id: util_misc.cpp 447439 2014-09-25 17:52:46Z vakatov $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -126,11 +126,11 @@ string g_GetPasswordFromConsole(const string& prompt)
NCBI_PARAM_DECL (string, NCBI, DataPath);
-NCBI_PARAM_DEF_EX(string, NCBI, DataPath, kEmptyStr, 0, NCBI_DATA_PATH);
+NCBI_PARAM_DEF_EX(string, NCBI, DataPath, "", 0, NCBI_DATA_PATH);
typedef NCBI_PARAM_TYPE(NCBI, DataPath) TNCBIDataPath;
NCBI_PARAM_DECL(string, NCBI, Data);
-NCBI_PARAM_DEF (string, NCBI, Data, kEmptyStr);
+NCBI_PARAM_DEF (string, NCBI, Data, "");
typedef NCBI_PARAM_TYPE(NCBI, Data) TNCBIDataDir;
typedef vector<string> TIgnoreDataFiles;
diff --git a/c++/src/util/xregexp/Makefile.in b/c++/src/util/xregexp/Makefile.in
index a5715ab..aa7994b 100644
--- a/c++/src/util/xregexp/Makefile.in
+++ b/c++/src/util/xregexp/Makefile.in
@@ -1,6 +1,6 @@
-# $Id: Makefile.in 173670 2009-10-20 15:45:31Z gouriano $
+# $Id: Makefile.in 467289 2015-05-12 16:23:41Z ivanov $
-LIB_PROJ = xregexp
+LIB_PROJ = xregexp xregexp_template_tester
PROJ_TAG = core
srcdir = @srcdir@
diff --git a/c++/src/util/xregexp/Makefile.xregexp.lib b/c++/src/util/xregexp/Makefile.xregexp.lib
index 4f42724..b4c3386 100644
--- a/c++/src/util/xregexp/Makefile.xregexp.lib
+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
@@ -1,7 +1,6 @@
-# $Id: Makefile.xregexp.lib 427415 2014-02-20 13:33:40Z gouriano $
+# $Id: Makefile.xregexp.lib 467289 2015-05-12 16:23:41Z ivanov $
SRC = regexp arg_regexp mask_regexp
-
LIB = xregexp
CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
@@ -9,8 +8,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
DLL_LIB = $(PCRE_LIB)
LIBS = $(PCRE_LIBS)
-WATCHERS = ivanov
-
-
USES_LIBRARIES = \
$(PCRE_LIB) $(PCRE_LIBS) xncbi
+
+WATCHERS = ivanov
diff --git a/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
new file mode 100644
index 0000000..ad57796
--- /dev/null
+++ b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
@@ -0,0 +1,14 @@
+# $Id: Makefile.xregexp_template_tester.lib 467289 2015-05-12 16:23:41Z ivanov $
+
+SRC = regexp_template_tester
+LIB = xregexp_template_tester
+
+DLL_LIB = $(PCRE_LIB)
+LIBS = $(PCRE_LIBS)
+
+USES_LIBRARIES = \
+ xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi
+
+PROJ_TAG = test
+
+WATCHERS = ivanov
diff --git a/c++/src/util/xregexp/regexp_template_tester.cpp b/c++/src/util/xregexp/regexp_template_tester.cpp
new file mode 100644
index 0000000..9ef205b
--- /dev/null
+++ b/c++/src/util/xregexp/regexp_template_tester.cpp
@@ -0,0 +1,710 @@
+/*$Id: regexp_template_tester.cpp 467289 2015-05-12 16:23:41Z ivanov $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the author's official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author: Vladimir Ivanov
+ *
+ * File Description:
+ * Regexp template tester based on the Perl Compatible Regular
+ * Expression (pcre) library. Allow to test delimited text data
+ * against template with regular expression rules.
+ *
+ */
+
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbifile.hpp>
+#include <corelib/tempstr.hpp>
+#include <util/xregexp/regexp.hpp>
+#include <util/xregexp/regexp_template_tester.hpp>
+
+
+BEGIN_NCBI_SCOPE
+
+
+//////////////////////////////////////////////////////////////////////////////
+//
+// Macros for throwing an exceptions on error
+//
+
+#define FILE_NAME(name) \
+ (name.empty() ? string("(stream)") : name)
+
+#define ERROR_FILE(errcode, message, file) \
+ NCBI_THROW(CRegexpTemplateTesterException, errcode, \
+ FILE_NAME(file) + " -- " + message)
+
+#define ERROR_TEMPLATE(errcode, message) \
+ NCBI_THROW(CRegexpTemplateTesterException, errcode, "\n" + \
+ FILE_NAME(m_FileName) + "(" + \
+ NStr::NumericToString(m_FileLineNum) + ")\n" + \
+ FILE_NAME(m_TemplateName) + "(" + \
+ NStr::NumericToString(m_TemplateLineNum) + ")\n-- " + \
+ message)
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CRegexpTemplateTester --
+///
+
+
+CRegexpTemplateTester::CRegexpTemplateTester(TFlags flags)
+ : m_Flags(flags),
+ m_VarStart("${"),
+ m_VarEnd("}"),
+ m_OpStart("#"),
+ m_CommentStart("//"),
+ m_EOLs("\r\n")
+{
+ x_Reset();
+}
+
+
+void CRegexpTemplateTester::x_Reset()
+{
+ // File/template
+ m_FileName.clear();
+ m_FileLineNum = 0;
+ m_TemplateName.clear();
+ m_TemplateLineNum = 0;
+
+ // Variables
+ m_Vars.clear();
+
+ // Cached line
+ m_FileLine.clear();
+ m_ReprocessFileLine = false;
+}
+
+
+void CRegexpTemplateTester::SetVarScope(string& start, string& end)
+{
+ m_VarStart = start;
+ m_VarEnd = end;
+}
+
+
+void CRegexpTemplateTester::SetCommentStart(string& str)
+{
+ m_CommentStart = str;
+}
+
+
+void CRegexpTemplateTester::SetCommandStart(string& str)
+{
+ m_OpStart = str;
+}
+
+
+void CRegexpTemplateTester::SetDelimiters(string& str)
+{
+ m_EOLs = str;
+}
+
+
+string CRegexpTemplateTester::GetVar(const string& name) const
+{
+ TVarMap::const_iterator var = m_Vars.find(name);
+ if (var == m_Vars.end()) {
+ ERROR_TEMPLATE(eVarNotFound, string("variable '") + name + "' is not defined");
+ }
+ return var->second;
+}
+
+
+const CRegexpTemplateTester::TVarMap& CRegexpTemplateTester::GetVars(void) const
+{
+ return m_Vars;
+}
+
+
+void CRegexpTemplateTester::PrintVar(const string& name) const
+{
+ string value = GetVar(name);
+ cout << name << " = " << NStr::PrintableString(value) << endl;
+}
+
+
+void CRegexpTemplateTester::PrintVars(void) const
+{
+ ITERATE(TVarMap, it, m_Vars) {
+ cout << it->first << " = " << NStr::PrintableString(it->second) << endl;
+ }
+}
+
+
+void CRegexpTemplateTester::Compare(const string& file_path, const string& template_path)
+{
+ x_Reset();
+ m_FileName = file_path;
+ m_TemplateName = template_path;
+
+ CNcbiIfstream file_stm(file_path.c_str());
+ if (!file_stm.good()) {
+ ERROR_FILE(eOpenFile, "cannot open file", file_path);
+ }
+ CNcbiIfstream template_stm(template_path.c_str());
+ if (!template_stm.good()) {
+ ERROR_FILE(eOpenFile, "cannot open file", template_path);
+ }
+ // Compare
+ if ( x_Compare(file_stm, template_stm) == eStop ) {
+ return;
+ }
+ // Compare number of lines in both files
+ if (x_GetLine(file_stm, eFile)) {
+ ERROR_TEMPLATE(eMismatchLength, "file/template length mismatch");
+ }
+ return;
+}
+
+
+void CRegexpTemplateTester::Compare(istream& file_stm, istream& template_stm)
+{
+ x_Reset();
+ if (x_Compare(file_stm, template_stm) == eStop) {
+ return;
+ }
+ // Compare number of lines in both streams
+ if (x_GetLine(file_stm, eFile)) {
+ ERROR_TEMPLATE(eMismatchLength, "stream/template length mismatch");
+ }
+ return;
+}
+
+
+CRegexpTemplateTester::EResult CRegexpTemplateTester::x_Compare(istream& file_stm, istream& template_stm)
+{
+ while (x_GetLine(template_stm, eTemplate))
+ {
+ CTempString str(m_TemplateLine);
+
+ // Comment line
+ if (NStr::StartsWith(str, m_CommentStart)) {
+ continue;
+ }
+ // Operations
+ if (NStr::StartsWith(str, m_OpStart)) {
+ str = NStr::TruncateSpaces_Unsafe(str.substr(m_OpStart.length()));
+
+ // stop
+ if (str == "stop") {
+ return eStop;
+ }
+ // set var=value
+ if (NStr::StartsWith(str, "set ")) {
+ x_Op_Set(str);
+ continue;
+ }
+ // echo <string>
+ if (NStr::StartsWith(str, "echo ")) {
+ x_Op_Echo(str);
+ continue;
+ }
+ // test <expression>
+ if (NStr::StartsWith(str, "test ")) {
+ x_Op_Test(str);
+ continue;
+ }
+ // include <path>
+ if (NStr::StartsWith(str, "include ")) {
+ x_Op_Include(str, file_stm);
+ continue;
+ }
+ // skip <expression>
+ if (NStr::StartsWith(str, "skip ")) {
+ x_Op_Skip(str, file_stm);
+ continue;
+ }
+ SIZE_TYPE len = str.find(' ');
+ ERROR_TEMPLATE(eOpUnknown, "unknown operation '" + string(str.substr(0, len)) + "'");
+ // unreachable
+ }
+
+ if (!m_ReprocessFileLine) {
+ // Get next line from the file
+ if (!x_GetLine(file_stm, eFile)) {
+ ERROR_TEMPLATE(eMismatchLength, "file/template length mismatch");
+ }
+ ++m_FileLineNum;
+ }
+ m_ReprocessFileLine = false;
+
+ // Compare
+ x_CompareLines(m_FileLine, str);
+ }
+ return eTemplateEOF;
+}
+
+
+istream& CRegexpTemplateTester::x_GetLine(istream& is, ESource src)
+{
+ string* str = NULL;
+ SIZE_TYPE* num = NULL;
+ bool skip_empty = false;;
+
+ switch(src) {
+ case eFile:
+ str = &m_FileLine;
+ num = &m_FileLineNum;
+ skip_empty = (m_Flags & fSkipEmptySourceLines) > 0;
+ break;
+ case eTemplate:
+ str = &m_TemplateLine;
+ num = &m_TemplateLineNum;
+ skip_empty = (m_Flags & fSkipEmptyTemplateLines) > 0;
+ break;
+ default:
+ _TROUBLE;
+ }
+
+ while (NcbiGetline(is, *str, m_EOLs)) {
+ (*num)++;
+ if (!skip_empty || !str->empty()) {
+ break;
+ }
+ }
+ return is;
+}
+
+
+void CRegexpTemplateTester::x_CompareLines(CTempString file_line, CTempString template_line)
+{
+ // Check template line on variables and substitute
+
+ // Substitute known variables (constants) with values
+ string s = x_SubstituteVars(template_line, NULL);
+ // Now, replace inline variable definitions with regexp counterparts
+ TVarList inline_vars;
+ s = x_SubstituteVars(s, &inline_vars);
+
+ // Compare lines
+
+ CRegexp re(s);
+ if ( !re.IsMatch(file_line) ) {
+ ERROR_TEMPLATE(eMismatchContent, "content mismatch");
+ }
+ if ( inline_vars.size() != (SIZE_TYPE)(re.NumFound()-1) ) {
+ ERROR_TEMPLATE(eMismatchContent, "cannot match all variables");
+ }
+ // Convert sub-patterns to variables
+ int i = 1;
+ ITERATE(TVarList, it, inline_vars) {
+ m_Vars[*it] = re.GetSub(file_line, i++);
+ }
+ return;
+}
+
+
+SIZE_TYPE CRegexpTemplateTester::x_ParseVar(CTempString str, SIZE_TYPE pos) const
+{
+ SIZE_TYPE len = str.length();
+ pos += m_VarStart.length();
+ if (pos >= len) {
+ return NPOS;
+ }
+
+ int counter = 1;
+
+ for (; pos <= len - m_VarEnd.length(); pos++) {
+ if (NStr::CompareCase(str, pos, m_VarStart.length(), m_VarStart) == 0) {
+ counter++;
+ } else
+ if (NStr::CompareCase(str, pos, m_VarEnd.length(), m_VarEnd) == 0) {
+ counter--;
+ }
+ if (counter == 0) {
+ return pos;
+ }
+ }
+ return NPOS;
+}
+
+
+SIZE_TYPE CRegexpTemplateTester::x_ParseVarName(CTempString str, SIZE_TYPE pos) const
+{
+ SIZE_TYPE len = str.length();
+ if (pos >= len) {
+ return NPOS;
+ }
+ _ASSERT(!isspace((unsigned char)str[pos]));
+ if (!isalpha((unsigned char)str[pos])) {
+ ERROR_TEMPLATE(eVarErr, "variable name should start with alphabetic symbol");
+ }
+ SIZE_TYPE start = pos;
+ ++pos;
+ while (pos < len &&
+ (isalnum((unsigned char)str[pos]) || str[pos] == '-' || str[pos] == '_') ) ++pos;
+ return pos - start;
+}
+
+
+string CRegexpTemplateTester::x_SubstituteVars(CTempString str, TVarList* inline_vars) const
+{
+ SIZE_TYPE start = NStr::Find(str, m_VarStart);
+ if (start == NPOS) {
+ return str;
+ }
+ string out;
+ bool out_have_value = false; // allow to process empty variables
+ SIZE_TYPE last = 0;
+ do {
+ SIZE_TYPE end = x_ParseVar(str, start);
+ if (end == NPOS || end == start) {
+ ERROR_TEMPLATE(eVarErr, "cannot find closing tag for variable definition");
+ }
+ // Get variable definition
+ CTempString vdef = str.substr(start + m_VarStart.length(),
+ end - start - m_VarStart.length());
+
+ // If variable definition looks like like "var=value", replace it with
+ // regexp sub-pattern "(value)" and add "var" to 'inline_vars' list.
+ // Otherwise, just substitute variable with its value.
+
+ SIZE_TYPE eqpos = vdef.find('=');
+
+ if (inline_vars || (!inline_vars && eqpos == NPOS)) {
+ // Append string before variable definition
+ if (start - last) {
+ out.append(str.data() + last, start - last);
+ out_have_value = true;
+ }
+ last = end + m_VarEnd.length();
+ }
+ if (eqpos == NPOS) {
+ // Replace variable with its value
+ string s = x_SubstituteVars(vdef, NULL);
+ out.append(GetVar(s));
+ out_have_value = true;
+ } else
+
+ if (inline_vars) {
+ // Get variable name
+ SIZE_TYPE n = x_ParseVarName(vdef, 0);
+ CTempString inline_name = vdef.substr(0, n);
+ if ( !n || (inline_name.length() != eqpos)) {
+ ERROR_TEMPLATE(eVarErr, "wrong variable definition");
+ }
+ CTempString inline_val = vdef.substr(eqpos + 1);
+ if (inline_val.empty()) {
+ ERROR_TEMPLATE(eVarErr, "variable definition cannot have empty value");
+ }
+ string s = x_SubstituteVars(inline_val, NULL);
+ // Replace with subpattern
+ out.append("(" + s + ")");
+ out_have_value = true;
+ inline_vars->push_back(inline_name);
+ }
+ // Find next variable
+ start = NStr::Find(str, m_VarStart, end + m_VarEnd.length());
+ }
+ while ( start != NPOS );
+
+ if (out.empty() && !out_have_value) {
+ return str;
+ }
+ // append string tail
+ if (last < str.length()) {
+ out.append(str.data() + last, str.length() - last);
+ }
+ // return result
+ return out;
+}
+
+
+// Skip white spaces
+#define SKIP_SPACES \
+ while (i < len && isspace((unsigned char)str[i])) ++i
+
+
+void CRegexpTemplateTester::x_Op_Set(CTempString str)
+{
+ SIZE_TYPE len = str.length();
+ SIZE_TYPE i = 4; // length of "set "
+ _ASSERT(i < len);
+
+ SKIP_SPACES;
+ SIZE_TYPE n = x_ParseVarName(str, i);
+ if ( !n ) {
+ ERROR_TEMPLATE(eOpErr, "SET: variable not specified");
+ }
+ string name = str.substr(i, n);
+ i += n;
+ if (str[i] != '=') {
+ ERROR_TEMPLATE(eOpErr, "SET: no assignment operator");
+ }
+ if (i >= len) {
+ ERROR_TEMPLATE(eOpErr, "SET: variable cannot have empty value");
+ }
+ // Substitute all variables with its values
+ m_Vars[name] = x_SubstituteVars(str.substr(++i), NULL);
+}
+
+
+void CRegexpTemplateTester::x_Op_Echo(CTempString str)
+{
+ SIZE_TYPE len = str.length();
+ SIZE_TYPE i = 5; // length of "echo "
+ SKIP_SPACES;
+ string s = x_SubstituteVars(str.substr(i), NULL);
+ cout << s << endl;
+}
+
+
+void CRegexpTemplateTester::x_Op_Test(CTempString str)
+{
+ enum ETestOp {
+ eEqual,
+ eNotEqual,
+ eMatch,
+ eNotMatch
+ };
+ SIZE_TYPE len = str.length();
+ SIZE_TYPE i = 5; // length of "test "
+ _ASSERT(i < len);
+
+ SKIP_SPACES;
+
+ ETestOp op;
+ SIZE_TYPE pop;
+
+ if ((pop = NStr::Find(str, "==", i)) != NPOS) {
+ op = eEqual;
+ } else
+ if ((pop = NStr::Find(str, "!=", i)) != NPOS) {
+ op = eNotEqual;
+ } else
+ if ((pop = NStr::Find(str, "=~", i)) != NPOS) {
+ op = eMatch;
+ } else
+ if ((pop = NStr::Find(str, "!~", i)) != NPOS) {
+ op = eNotMatch;
+ } else {
+ ERROR_TEMPLATE(eOpErr, "TEST: no comparison operator");
+ }
+ string sop = str.substr(pop, 2);
+ string s1 = x_SubstituteVars(str.substr(i, pop - i), NULL);
+ string s2 = x_SubstituteVars(str.substr(pop+2), NULL);
+
+ bool res;
+ switch (op) {
+ case eEqual:
+ res = (s1 == s2);
+ break;
+ case eNotEqual:
+ res = (s1 != s2);
+ break;
+ case eMatch:
+ case eNotMatch:
+ {{
+ CRegexp re(s2);
+ if (re.IsMatch(s1)) {
+ res = (op == eMatch);
+ } else {
+ res = (op == eNotMatch);
+ }
+ }}
+ break;
+ }
+ if (!res) {
+ ERROR_TEMPLATE(eOpTest, "TEST: result of comparison is FALSE: '" +
+ NStr::PrintableString(s1) + "' " + sop + " '" +
+ NStr::PrintableString(s2) + "'");
+ }
+ return;
+}
+
+
+void CRegexpTemplateTester::x_Op_Include(CTempString str, istream& file_stm)
+{
+ SIZE_TYPE len = str.length();
+ SIZE_TYPE i = 8; // length of "include "
+ _ASSERT(i < len);
+
+ SKIP_SPACES;
+
+ string path;
+ CFile::SplitPath(m_TemplateName, &path);
+ path = CFile::ConcatPath(path, str.substr(i));
+
+ CNcbiIfstream template_stm(path.c_str());
+ if (!template_stm.good()) {
+ ERROR_TEMPLATE(eOpErr, "INCLUDE: cannot open file: " + path);
+ }
+
+ // Save context for current template
+ string saved_name = m_TemplateName;
+ SIZE_TYPE saved_line = m_TemplateLineNum;
+
+ // Reset
+ m_TemplateName = path;
+ m_TemplateLineNum = 0;
+
+ // Continue comparing
+ x_Compare(file_stm, template_stm);
+
+ // Restore saved context
+ m_TemplateName = saved_name;
+ m_TemplateLineNum = saved_line;
+
+ return;
+}
+
+
+void CRegexpTemplateTester::x_Op_Skip(CTempString str, istream& file_stm)
+{
+ enum ESkipOp {
+ eNumber,
+ eWhile,
+ eUntil
+ };
+ SIZE_TYPE len = str.length();
+ SIZE_TYPE i = 5; // length of "skip "
+ _ASSERT(i < len);
+
+ SKIP_SPACES;
+ CTempString op_str = str.substr(i);
+ CTempString op_name;
+
+ ESkipOp op;
+ SIZE_TYPE op_num = 0;
+ CTempString re_str;
+
+ if (NStr::StartsWith(op_str, "while")) {
+ // # skip while <regexp>
+ op = eWhile;
+ op_name = op_str.substr(0, 5);
+ i += 5;
+ if (str[i] == ' ') {
+ SKIP_SPACES;
+ re_str = str.substr(i);
+ }
+ }
+ else
+ if (NStr::StartsWith(op_str, "until")) {
+ // # skip until <regexp>
+ op = eUntil;
+ op_name = op_str.substr(0, 5);
+ i += 5;
+ if (str[i] == ' ') {
+ SKIP_SPACES;
+ re_str = str.substr(i);
+ }
+ }
+ else {
+ // # skip <num>
+ op = eNumber;
+ try {
+ op_num = NStr::StringToNumeric<SIZE_TYPE>(op_str);
+ }
+ catch (CStringException&) {}
+ if (!op_num) {
+ ERROR_TEMPLATE(eOpErr, "SKIP: expected number of lines");
+ }
+ }
+
+ AutoPtr<CRegexp> re;
+ string re_pattern;
+
+ if (op == eWhile || op == eUntil) {
+ re_pattern = x_SubstituteVars(re_str, NULL);
+ if (re_str.empty()) {
+ ERROR_TEMPLATE(eOpErr, "SKIP: expected regular expression after '" +
+ (string)op_name + "'");
+ }
+ re.reset(new CRegexp(re_pattern));
+ }
+
+ // Skip lines in the input data
+
+ SIZE_TYPE num_lines = 0;
+ bool matched = false;
+
+ while (x_GetLine(file_stm, eFile))
+ {
+ ++num_lines;
+
+ if (op == eNumber) {
+ if (num_lines == op_num) {
+ break;
+ }
+ } else {
+ matched = re->IsMatch(m_FileLine);
+ if (op == eWhile) {
+ // revert
+ matched = !matched;
+ }
+ if (matched) {
+ break;
+ }
+ }
+ }
+
+ // Check that we skipped all requested number of lines or
+ // found the line matched (or not) to the regular expression.
+ if (op == eNumber) {
+ if (num_lines != op_num) {
+ ERROR_TEMPLATE(eMismatchLength, "SKIP: unable to skip " +
+ NStr::NumericToString(num_lines ) + " lines");
+ }
+ } else {
+ if (!matched) {
+ ERROR_TEMPLATE(eMismatchLength, "SKIP: unable to skip " +
+ (string)op_name + " '" +
+ NStr::PrintableString(re_pattern) + "'");
+ }
+ // For the while/until cases we should be able to process current
+ // 'stopper' file line also, it can be compared with the next template
+ // 'data' line.
+ m_ReprocessFileLine = true;
+ }
+ return;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// CRegexpTemplateTesterException --
+///
+
+const char* CRegexpTemplateTesterException::GetErrCodeString(void) const
+{
+ switch (GetErrCode()) {
+ case eOpenFile: return "eOpenFile";
+ case eMismatchLength: return "eMismatchLength";
+ case eMismatchContent: return "eMismatchContent";
+ case eVarNotFound: return "eVarNotFound";
+ case eVarErr: return "eVarErr";
+ case eOpUnknown: return "eOpUnknown";
+ case eOpErr: return "eOpErr";
+ case eOpTest: return "eOpTest";
+ default: return CException::GetErrCodeString();
+ }
+}
+
+
+END_NCBI_SCOPE
--
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