[med-svn] [ncbi-blast+] branch upstream updated (03c4257 -> 35cc890)
Andreas Tille
tille at debian.org
Tue Apr 12 14:08:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository ncbi-blast+.
from 03c4257 Imported Upstream version 2.2.31
new 35cc890 Imported Upstream version 2.3.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +-
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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 +
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.../unit_test/data/in_showalign_use_this_gi.asn | 985 +
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.../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 +-
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c++/src/objtools/blast/seqdb_reader/seqdb.cpp | 112 +-
c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp | 27 +-
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c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 25 +-
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c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp | 1095 +-
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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 +-
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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 +-
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.../objtools/blast/seqdb_writer/writedb_impl.cpp | 529 +-
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.../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 +-
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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 +-
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c++/src/objtools/edit/autodef_feature_clause.cpp | 579 +-
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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(-)
create mode 100755 c++/compilers/xcode30_prj/xcodebuild.sh
copy c++/include/{objects/seqtable/seq_table_exception.hpp => algo/blast/format/sam.hpp} (58%)
copy c++/include/{cgi/error_codes.hpp => algo/winmask/seq_masker_version.hpp} (52%)
copy c++/{src/app/winmasker/win_mask_app.hpp => include/corelib/impl/listener_stack.hpp} (56%)
create mode 100644 c++/include/corelib/ncbi_message.hpp
create mode 100644 c++/include/corelib/ncbictype.hpp
mode change 100644 => 100755 c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp
copy c++/{src/util/distribution.cpp => include/objects/genomecoll/cached_assembly.hpp} (64%)
create mode 100644 c++/include/objects/seqtable/SeqTable_single_data.hpp
copy c++/include/objects/{biblio/Auth_list.hpp => taxon1/Taxon2_data.hpp} (56%)
copy c++/include/objects/taxon3/{taxon3.hpp => cached_taxon3.hpp} (58%)
mode change 100644 => 100755
copy c++/include/objects/taxon3/{taxon3.hpp => itaxon3.hpp} (70%)
rename c++/{src/objtools/format/utils.hpp => include/objmgr/util/objutil.hpp} (92%)
create mode 100644 c++/include/objtools/edit/autodef_options.hpp
create mode 100644 c++/include/objtools/edit/parse_text_options.hpp
create mode 100644 c++/include/util/retry_ctx.hpp
create mode 100644 c++/include/util/xregexp/regexp_template_tester.hpp
create mode 100755 c++/scripts/common/add_vdb.sh
delete mode 100755 c++/scripts/projects/python_ncbi_dbapi/post_build/build_tarball.sh
create mode 100644 c++/src/algo/blast/format/sam.cpp
copy c++/{include/common/ncbi_source_ver.h => src/algo/winmask/seq_masker_istat.cpp} (85%)
create mode 100755 c++/src/app/winmasker/windowmasker_counts_adapter.py
create mode 100644 c++/src/build-system/Makefile.compress_tests
copy c++/src/{objects/seqtable/Scaled_int_multi_data.cpp => corelib/guard.cpp} (72%)
create mode 100644 c++/src/corelib/ncbi_message.cpp
mode change 100644 => 100755 c++/src/objects/genomecoll/GCClient_GetAssemblyReques.cpp
create mode 100644 c++/src/objects/genomecoll/cached_assembly.cpp
create mode 100644 c++/src/objects/seqtable/SeqTable_single_data.cpp
create mode 100644 c++/src/objects/taxon1/Taxon2_data.cpp
create mode 100755 c++/src/objects/taxon3/cached_taxon3.cpp
rename c++/src/{objtools/format/utils.cpp => objmgr/util/objutil.cpp} (72%)
create mode 100644 c++/src/objtools/align_format/unit_test/align_format_unit_test.ini
create mode 100755 c++/src/objtools/align_format/unit_test/data/in_showalign_use_this_gi.asn
create mode 100755 c++/src/objtools/align_format/unit_test/data/protein.fa
create mode 100755 c++/src/objtools/cleanup/autogenerated_cleanup.sh
create mode 100755 c++/src/objtools/cleanup/autogenerated_extended_cleanup.sh
create mode 100644 c++/src/objtools/edit/autodef_options.cpp
create mode 100644 c++/src/objtools/edit/parse_text_options.cpp
create mode 100644 c++/src/serial/rpcbase.cpp
create mode 100644 c++/src/util/crc32tables.c
create mode 100644 c++/src/util/retry_ctx.cpp
create mode 100644 c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
create mode 100644 c++/src/util/xregexp/regexp_template_tester.cpp
--
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