Imported Upstream version 2.4.0
authorAaron M. Ucko <ucko@debian.org>
Wed, 3 Aug 2016 15:06:19 +0000 (11:06 -0400)
committerAaron M. Ucko <ucko@debian.org>
Wed, 3 Aug 2016 15:06:19 +0000 (11:06 -0400)
commitc943f5523f1ffa749c97d9323fe7416eb1f35438
treeda19966bf860b33bad344aa27f7cd450cb19fbdd
parente874c978c2adaedf31265c1ae6deda9bb61ee8d2
Imported Upstream version 2.4.0
1312 files changed:
c++/compilers/msvc1000_prj/Makefile.WinMain.app.msvc [deleted file]
c++/compilers/msvc1000_prj/Makefile.wxWidgets.app.msvc [deleted file]
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c++/compilers/msvc1000_prj/configure.bat [deleted file]
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c++/compilers/msvc1000_prj/dll/build/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/msvc1000_prj/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/msvc1000_prj/dll/build/UtilityProjects/configure._ [deleted file]
c++/compilers/msvc1000_prj/dll/build/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/msvc1000_prj/dll/build/all.bat [deleted file]
c++/compilers/msvc1000_prj/dll/build/all_gbench.bat [deleted file]
c++/compilers/msvc1000_prj/dll/build/all_gui.bat [deleted file]
c++/compilers/msvc1000_prj/dll/build/all_ncbi.bat [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/UtilityProjects/configure._ [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/configure_prebuild.bat [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/gbench_install/gbench-install.vcxproj [deleted file]
c++/compilers/msvc1000_prj/dll/build/gbench/ncbi_gbench.sln [deleted file]
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c++/compilers/msvc1000_prj/dll/build/gui/ncbi_gui_dll.sln [deleted file]
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c++/include/algo/blast/api/blast_seqinfosrc.hpp
c++/include/algo/blast/api/local_db_adapter.hpp
c++/include/algo/blast/api/psiblast_options.hpp
c++/include/algo/blast/api/remote_blast.hpp
c++/include/algo/blast/api/search_strategy.hpp
c++/include/algo/blast/api/seqinfosrc_seqdb.hpp
c++/include/algo/blast/api/seqinfosrc_seqvec.hpp
c++/include/algo/blast/api/seqsrc_multiseq.hpp
c++/include/algo/blast/api/tblastn_options.hpp
c++/include/algo/blast/api/uniform_search.hpp
c++/include/algo/blast/blastinput/blast_args.hpp
c++/include/algo/blast/blastinput/blast_input_aux.hpp
c++/include/algo/blast/blastinput/cmdline_flags.hpp
c++/include/algo/blast/blastinput/deltablast_args.hpp
c++/include/algo/blast/blastinput/psiblast_args.hpp
c++/include/algo/blast/composition_adjustment/composition_adjustment.h
c++/include/algo/blast/core/blast_kappa.h
c++/include/algo/blast/core/blast_stat.h
c++/include/algo/blast/format/blast_format.hpp
c++/include/algo/blast/format/blastfmtutil.hpp
c++/include/algo/blast/format/blastxml2_format.hpp
c++/include/algo/blast/format/data4xml2format.hpp
c++/include/algo/blast/igblast/igblast.hpp
c++/include/algo/dustmask/symdust.hpp
c++/include/cgi/cgi_serial.hpp
c++/include/cgi/cgi_session.hpp
c++/include/cgi/cgiapp.hpp
c++/include/cgi/error_codes.hpp
c++/include/cgi/ncbicgi.hpp
c++/include/cgi/ncbicgir.hpp
c++/include/common/boost_skew_guard.hpp [new file with mode: 0644]
c++/include/common/config/ncbiconf_msvc.h
c++/include/common/config/ncbiconf_universal.h
c++/include/common/config/ncbiconf_xcode.h
c++/include/common/ncbi_export.h
c++/include/common/ncbi_package_ver.h
c++/include/common/ncbi_source_ver.h
c++/include/common/ncbiconf_impl.h
c++/include/connect/ncbi_buffer.h
c++/include/connect/ncbi_conn_exception.hpp
c++/include/connect/ncbi_conn_reader_writer.hpp
c++/include/connect/ncbi_conn_stream.hpp
c++/include/connect/ncbi_connection.h
c++/include/connect/ncbi_connutil.h
c++/include/connect/ncbi_core_cxx.hpp
c++/include/connect/ncbi_http_connector.h
c++/include/connect/ncbi_http_session.hpp
c++/include/connect/ncbi_lbos.hpp [new file with mode: 0755]
c++/include/connect/ncbi_pipe.hpp
c++/include/connect/ncbi_service.h
c++/include/connect/ncbi_socket.h
c++/include/connect/ncbi_util.h
c++/include/connect/server_monitor.hpp
c++/include/connect/services/grid_client.hpp
c++/include/connect/services/grid_rw_impl.hpp
c++/include/connect/services/grid_worker.hpp
c++/include/connect/services/grid_worker_app.hpp
c++/include/connect/services/impl/neticache_client_int.hpp [new file with mode: 0644]
c++/include/connect/services/impl/netschedule_api_int.hpp [new file with mode: 0644]
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c++/include/connect/services/json_over_uttp.hpp
c++/include/connect/services/netcache_api.hpp
c++/include/connect/services/netcache_api_expt.hpp
c++/include/connect/services/netcomponent.hpp
c++/include/connect/services/neticache_client.hpp
c++/include/connect/services/netschedule_api.hpp
c++/include/connect/services/netservice_api.hpp
c++/include/connect/services/netstorage.hpp
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c++/include/connect/services/netstorage_impl.hpp
c++/include/connect/services/ns_output_parser.hpp
c++/include/connect/services/remote_app.hpp
c++/include/connect/services/srv_connections.hpp
c++/include/corelib/ddumpable.hpp
c++/include/corelib/env_reg.hpp
c++/include/corelib/error_codes.hpp
c++/include/corelib/impl/listener_stack.hpp
c++/include/corelib/impl/ncbi_atomic_defs.h
c++/include/corelib/impl/stringutf8_deprecated.hpp
c++/include/corelib/impl/stringutf8_deprecated.inl
c++/include/corelib/metareg.hpp
c++/include/corelib/ncbi_autoinit.hpp
c++/include/corelib/ncbi_bswap.hpp
c++/include/corelib/ncbi_config.hpp
c++/include/corelib/ncbi_limits.h
c++/include/corelib/ncbi_message.hpp
c++/include/corelib/ncbi_os_mswin.hpp
c++/include/corelib/ncbi_process.hpp
c++/include/corelib/ncbi_safe_static.hpp
c++/include/corelib/ncbi_url.hpp
c++/include/corelib/ncbiapp.hpp
c++/include/corelib/ncbiargs.hpp
c++/include/corelib/ncbidbg.hpp
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c++/include/corelib/ncbiexpt.hpp
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c++/include/corelib/ncbimisc.hpp
c++/include/corelib/ncbimtx.hpp
c++/include/corelib/ncbireg.hpp
c++/include/corelib/ncbistr.hpp
c++/include/corelib/ncbistr_util.hpp
c++/include/corelib/ncbitime.hpp
c++/include/corelib/plugin_manager.hpp
c++/include/corelib/request_ctx.hpp
c++/include/corelib/tempstr.hpp
c++/include/corelib/test_boost.hpp
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c++/include/corelib/version.hpp
c++/include/dbapi/dbapi.hpp
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c++/include/dbapi/driver/dbapi_object_convert.hpp
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c++/include/ncbi_source_ver.h
c++/include/ncbiconf.h
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c++/include/objmgr/scope.hpp
c++/include/objmgr/seq_entry_ci.hpp
c++/include/objmgr/seq_feat_handle.hpp
c++/include/objmgr/seq_loc_mapper.hpp
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c++/include/objmgr/util/create_defline.hpp
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c++/include/objtools/align_format/align_format_util.hpp
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c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
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c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp
c++/include/objtools/blast/seqdb_writer/build_db.hpp
c++/include/objtools/blast/seqdb_writer/multisource_util.hpp
c++/include/objtools/blast/seqdb_writer/writedb.hpp
c++/include/objtools/cleanup/cleanup.hpp
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c++/include/objtools/data_loaders/genbank/gbloader_params.h
c++/include/objtools/data_loaders/genbank/gicache/reader_gicache.hpp
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c++/src/objtools/blast/seqdb_reader/seqdbexpert.cpp
c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp
c++/src/objtools/blast/seqdb_reader/seqdbgimask.cpp
c++/src/objtools/blast/seqdb_reader/seqdbgimask.hpp
c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp
c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp
c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp
c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
c++/src/objtools/blast/seqdb_writer/build-alias-index
c++/src/objtools/blast/seqdb_writer/build_db.cpp
c++/src/objtools/blast/seqdb_writer/multisource_util.cpp
c++/src/objtools/blast/seqdb_writer/taxid_set.cpp
c++/src/objtools/blast/seqdb_writer/unit_test/criteria_unit_test.cpp
c++/src/objtools/blast/seqdb_writer/unit_test/data/rabbit_mrna.fsa
c++/src/objtools/blast/seqdb_writer/unit_test/data/rabbit_taxidmap.txt [new file with mode: 0644]
c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp
c++/src/objtools/blast/seqdb_writer/writedb.cpp
c++/src/objtools/blast/seqdb_writer/writedb_convert.cpp
c++/src/objtools/blast/seqdb_writer/writedb_gimask.cpp
c++/src/objtools/blast/seqdb_writer/writedb_gimask.hpp
c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp
c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp
c++/src/objtools/blast/seqdb_writer/writedb_isam.cpp
c++/src/objtools/blast/seqdb_writer/writedb_volume.cpp
c++/src/objtools/blast/seqdb_writer/writedb_volume.hpp
c++/src/objtools/cleanup/Makefile.cleanup.lib
c++/src/objtools/cleanup/autogenerated_cleanup.cpp
c++/src/objtools/cleanup/autogenerated_cleanup.hpp
c++/src/objtools/cleanup/autogenerated_cleanup.txt
c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp
c++/src/objtools/cleanup/autogenerated_extended_cleanup.hpp
c++/src/objtools/cleanup/autogenerated_extended_cleanup.txt
c++/src/objtools/cleanup/cleanup.cpp
c++/src/objtools/cleanup/cleanup_utils.cpp
c++/src/objtools/cleanup/cleanup_utils.hpp
c++/src/objtools/cleanup/newcleanupp.cpp
c++/src/objtools/cleanup/newcleanupp.hpp
c++/src/objtools/data_loaders/Makefile.in
c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
c++/src/objtools/data_loaders/genbank/cache/reader_cache.cpp
c++/src/objtools/data_loaders/genbank/cache/writer_cache.cpp
c++/src/objtools/data_loaders/genbank/dispatcher.cpp
c++/src/objtools/data_loaders/genbank/gbloader.cpp
c++/src/objtools/data_loaders/genbank/gicache/Makefile.ncbi_xreader_gicache.lib
c++/src/objtools/data_loaders/genbank/gicache/gicache.c
c++/src/objtools/data_loaders/genbank/gicache/gicache_cxx.cpp [new file with mode: 0644]
c++/src/objtools/data_loaders/genbank/gicache/reader_gicache.cpp
c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp
c++/src/objtools/data_loaders/genbank/info_cache.cpp
c++/src/objtools/data_loaders/genbank/processors.cpp
c++/src/objtools/data_loaders/genbank/reader.cpp
c++/src/objtools/data_loaders/genbank/reader_id1_base.cpp
c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp
c++/src/objtools/data_loaders/genbank/reader_snp.cpp
c++/src/objtools/data_loaders/genbank/request_result.cpp
c++/src/objtools/data_loaders/genbank/split_parser.cpp [deleted file]
c++/src/objtools/edit/Makefile.edit.lib
c++/src/objtools/edit/autodef.cpp
c++/src/objtools/edit/autodef_available_modifier.cpp
c++/src/objtools/edit/autodef_feature_clause.cpp
c++/src/objtools/edit/autodef_feature_clause_base.cpp
c++/src/objtools/edit/autodef_mod_combo.cpp
c++/src/objtools/edit/autodef_options.cpp
c++/src/objtools/edit/capitalization_string.cpp
c++/src/objtools/edit/cds_fix.cpp
c++/src/objtools/edit/feattable_edit.cpp
c++/src/objtools/edit/field_handler.cpp
c++/src/objtools/edit/loc_edit.cpp
c++/src/objtools/edit/parse_text_options.cpp
c++/src/objtools/edit/publication_edit.cpp [new file with mode: 0644]
c++/src/objtools/edit/remote_updater.cpp
c++/src/objtools/edit/seq_entry_edit.cpp
c++/src/objtools/edit/seqid_guesser.cpp
c++/src/objtools/edit/struc_comm_field.cpp
c++/src/objtools/format/Makefile.xformat.lib
c++/src/objtools/format/accession_item.cpp
c++/src/objtools/format/cigar_formatter.cpp
c++/src/objtools/format/comment_item.cpp
c++/src/objtools/format/context.cpp
c++/src/objtools/format/ctrl_items.cpp
c++/src/objtools/format/dbsource_item.cpp
c++/src/objtools/format/defline_item.cpp
c++/src/objtools/format/embl_formatter.cpp
c++/src/objtools/format/feature_item.cpp
c++/src/objtools/format/flat_file_config.cpp
c++/src/objtools/format/flat_file_generator.cpp
c++/src/objtools/format/flat_seqloc.cpp
c++/src/objtools/format/gather_items.cpp
c++/src/objtools/format/gbseq_formatter.cpp
c++/src/objtools/format/genbank_formatter.cpp
c++/src/objtools/format/genbank_gather.cpp
c++/src/objtools/format/gene_finder.cpp
c++/src/objtools/format/genome_project_item.cpp
c++/src/objtools/format/gff_gather.cpp
c++/src/objtools/format/inst_info_map.cpp
c++/src/objtools/format/inst_info_map.hpp
c++/src/objtools/format/item_formatter.cpp
c++/src/objtools/format/keywords_item.cpp
c++/src/objtools/format/locus_item.cpp
c++/src/objtools/format/primary_item.cpp
c++/src/objtools/format/qualifiers.cpp
c++/src/objtools/format/reference_item.cpp
c++/src/objtools/format/sam_formatter.cpp
c++/src/objtools/format/source_item.cpp
c++/src/objtools/readers/bed_reader.cpp
c++/src/objtools/readers/fasta.cpp
c++/src/objtools/readers/format_guess_ex.cpp
c++/src/objtools/readers/gff2_data.cpp
c++/src/objtools/readers/gff2_reader.cpp
c++/src/objtools/readers/gff3_reader.cpp
c++/src/objtools/readers/gff3_sofa.cpp
c++/src/objtools/readers/gff_reader.cpp
c++/src/objtools/readers/gtf_reader.cpp
c++/src/objtools/readers/gvf_reader.cpp
c++/src/objtools/readers/idmapper.cpp
c++/src/objtools/readers/idmapper_builtin.cpp
c++/src/objtools/readers/idmapper_config.cpp
c++/src/objtools/readers/microarray_reader.cpp
c++/src/objtools/readers/phrap.cpp
c++/src/objtools/readers/read_util.cpp
c++/src/objtools/readers/reader_base.cpp
c++/src/objtools/readers/readfeat.cpp
c++/src/objtools/readers/rm_reader.cpp
c++/src/objtools/readers/source_mod_parser.cpp
c++/src/objtools/readers/ucscregion_reader.cpp
c++/src/objtools/readers/vcf_reader.cpp
c++/src/objtools/readers/wiggle_reader.cpp
c++/src/serial/Makefile.serial.lib
c++/src/serial/choice.cpp
c++/src/serial/classinfo.cpp
c++/src/serial/datatool/blocktype.cpp
c++/src/serial/datatool/choicestr.cpp
c++/src/serial/datatool/comments.cpp
c++/src/serial/datatool/comments.hpp
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c++/src/serial/datatool/enumtype.cpp
c++/src/serial/datatool/enumtype.hpp
c++/src/serial/datatool/filecode.cpp
c++/src/serial/datatool/generate.cpp
c++/src/serial/datatool/module.cpp
c++/src/serial/datatool/reftype.cpp
c++/src/serial/datatool/rpcgen.cpp
c++/src/serial/datatool/statictype.cpp
c++/src/serial/datatool/statictype.hpp
c++/src/serial/datatool/testdata/res/set.ent.3 [new file with mode: 0644]
c++/src/serial/datatool/traversal_spec_file_parser.cpp
c++/src/serial/datatool/unitype.cpp
c++/src/serial/datatool/xsdparser.cpp
c++/src/serial/enumerated.cpp
c++/src/serial/member.cpp
c++/src/serial/memberlist.cpp
c++/src/serial/objistrasn.cpp
c++/src/serial/objistrjson.cpp
c++/src/serial/objostr.cpp
c++/src/serial/objostrasn.cpp
c++/src/serial/objostrasnb.cpp
c++/src/serial/objostrjson.cpp
c++/src/serial/objostrxml.cpp
c++/src/serial/objstack.cpp
c++/src/serial/pathhook.cpp
c++/src/serial/rpcbase.cpp
c++/src/util/Makefile.util.lib
c++/src/util/checksum.cpp
c++/src/util/compress/api/archive.cpp
c++/src/util/compress/api/compress.cpp
c++/src/util/compress/api/streambuf.cpp
c++/src/util/compress/api/tar.cpp
c++/src/util/compress/api/zlib.cpp
c++/src/util/creaders/alnread.c
c++/src/util/ddump_viewer.cpp
c++/src/util/dictionary_util.cpp
c++/src/util/file_manifest.cpp [new file with mode: 0644]
c++/src/util/format_guess.cpp
c++/src/util/itree.cpp
c++/src/util/line_reader.cpp
c++/src/util/retry_ctx.cpp
c++/src/util/scheduler.cpp
c++/src/util/sequtil/sequtil_convert_imp.cpp
c++/src/util/sequtil/sequtil_convert_imp.hpp
c++/src/util/sequtil/sequtil_manip.cpp
c++/src/util/sequtil/sequtil_shared.hpp
c++/src/util/smalldns.cpp
c++/src/util/strbuffer.cpp
c++/src/util/stream_source.cpp [new file with mode: 0644]
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c++/src/util/tables/raw_scoremat.c
c++/src/util/thread_pool.cpp
c++/src/util/transmissionrw.cpp
c++/src/util/utf8.cpp
c++/src/util/util_misc.cpp
c++/src/util/uttp.cpp