dgit.raspbian.org Git - ncbi-blast+.git/commit

author	Andreas Tille <tille@debian.org>
	Tue, 12 Apr 2016 12:52:30 +0000 (14:52 +0200)
committer	Andreas Tille <tille@debian.org>
	Tue, 12 Apr 2016 12:52:30 +0000 (14:52 +0200)
commit	35cc89086e8448b35b6cb59f82bc35cb6f9240b3
tree	27f737f12c41b09755f15364bde31a4012166903	tree \| snapshot
parent	03c4257c90dabff2b5ffe63c03acfee26e2eebc5	commit \| diff

Imported Upstream version 2.3.0

1371 files changed:

c++/compilers/cygwin/build.sh		diff \| blob \| history
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c++/include/algo/blast/api/bl2seq.hpp		diff \| blob \| history
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c++/include/algo/blast/api/blast_options_builder.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_options_handle.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_prot_options.hpp		diff \| blob \| history
c++/include/algo/blast/api/local_db_adapter.hpp		diff \| blob \| history
c++/include/algo/blast/api/psiblast_options.hpp		diff \| blob \| history
c++/include/algo/blast/api/remote_blast.hpp		diff \| blob \| history
c++/include/algo/blast/api/search_strategy.hpp		diff \| blob \| history
c++/include/algo/blast/api/seqsrc_multiseq.hpp		diff \| blob \| history
c++/include/algo/blast/api/tblastn_options.hpp		diff \| blob \| history
c++/include/algo/blast/api/traceback_stage.hpp		diff \| blob \| history
c++/include/algo/blast/api/uniform_search.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_args.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_input_aux.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/cmdline_flags.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/deltablast_args.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/psiblast_args.hpp		diff \| blob \| history
c++/include/algo/blast/core/blast_hits.h		diff \| blob \| history
c++/include/algo/blast/core/blast_message.h		diff \| blob \| history
c++/include/algo/blast/core/blast_options.h		diff \| blob \| history
c++/include/algo/blast/core/blast_stat.h		diff \| blob \| history
c++/include/algo/blast/format/blast_format.hpp		diff \| blob \| history
c++/include/algo/blast/format/blastfmtutil.hpp		diff \| blob \| history
c++/include/algo/blast/format/blastxml2_format.hpp		diff \| blob \| history
c++/include/algo/blast/format/data4xml2format.hpp		diff \| blob \| history
c++/include/algo/blast/format/sam.hpp	[new file with mode: 0644]	blob
c++/include/algo/dustmask/symdust.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_istat.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_istat_ascii.hpp		diff \| blob \| history
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c++/include/algo/winmask/seq_masker_istat_factory.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_istat_oascii.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_istat_obinary.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_ostat.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_ostat_ascii.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_ostat_bin.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_ostat_opt.hpp		diff \| blob \| history
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c++/include/algo/winmask/seq_masker_version.hpp	[new file with mode: 0644]	blob
c++/include/algo/winmask/seq_masker_window.hpp		diff \| blob \| history
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c++/include/common/ncbi_export.h		diff \| blob \| history
c++/include/common/ncbi_package_ver.h		diff \| blob \| history
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c++/include/common/ncbiconf_impl.h		diff \| blob \| history
c++/include/common/test_assert_impl.h		diff \| blob \| history
c++/include/connect/error_codes.hpp		diff \| blob \| history
c++/include/connect/impl/server_connection.hpp		diff \| blob \| history
c++/include/connect/ncbi_buffer.h		diff \| blob \| history
c++/include/connect/ncbi_conn_reader_writer.hpp		diff \| blob \| history
c++/include/connect/ncbi_conn_stream.hpp		diff \| blob \| history
c++/include/connect/ncbi_connection.h		diff \| blob \| history
c++/include/connect/ncbi_connutil.h		diff \| blob \| history
c++/include/connect/ncbi_http_connector.h		diff \| blob \| history
c++/include/connect/ncbi_http_session.hpp		diff \| blob \| history
c++/include/connect/ncbi_namedpipe.hpp		diff \| blob \| history
c++/include/connect/ncbi_namedpipe_connector.hpp		diff \| blob \| history
c++/include/connect/ncbi_pipe.hpp		diff \| blob \| history
c++/include/connect/ncbi_pipe_connector.hpp		diff \| blob \| history
c++/include/connect/ncbi_sendmail.h		diff \| blob \| history
c++/include/connect/ncbi_server_info.h		diff \| blob \| history
c++/include/connect/ncbi_service.h		diff \| blob \| history
c++/include/connect/ncbi_service_connector.h		diff \| blob \| history
c++/include/connect/ncbi_socket.h		diff \| blob \| history
c++/include/connect/ncbi_socket.hpp		diff \| blob \| history
c++/include/connect/ncbi_types.h		diff \| blob \| history
c++/include/connect/ncbi_util.h		diff \| blob \| history
c++/include/connect/services/clparser.hpp		diff \| blob \| history
c++/include/connect/services/compound_id.hpp		diff \| blob \| history
c++/include/connect/services/grid_client.hpp		diff \| blob \| history
c++/include/connect/services/grid_globals.hpp		diff \| blob \| history
c++/include/connect/services/grid_worker.hpp		diff \| blob \| history
c++/include/connect/services/grid_worker_app.hpp		diff \| blob \| history
c++/include/connect/services/named_parameters.hpp		diff \| blob \| history
c++/include/connect/services/netcache_admin.hpp		diff \| blob \| history
c++/include/connect/services/netcache_api.hpp		diff \| blob \| history
c++/include/connect/services/netcomponent.hpp		diff \| blob \| history
c++/include/connect/services/neticache_client.hpp		diff \| blob \| history
c++/include/connect/services/netschedule_api.hpp		diff \| blob \| history
c++/include/connect/services/netservice_api.hpp		diff \| blob \| history
c++/include/connect/services/netstorage.hpp		diff \| blob \| history
c++/include/connect/services/netstorage_impl.hpp		diff \| blob \| history
c++/include/connect/services/srv_connections.hpp		diff \| blob \| history
c++/include/connect/threaded_server.hpp		diff \| blob \| history
c++/include/corelib/env_reg.hpp		diff \| blob \| history
c++/include/corelib/error_codes.hpp		diff \| blob \| history
c++/include/corelib/expr.hpp		diff \| blob \| history
c++/include/corelib/guard.hpp		diff \| blob \| history
c++/include/corelib/hash_impl/stlp_defs.hpp		diff \| blob \| history
c++/include/corelib/impl/listener_stack.hpp	[new file with mode: 0644]	blob
c++/include/corelib/impl/ncbi_atomic_defs.h		diff \| blob \| history
c++/include/corelib/impl/ncbi_panfs.h		diff \| blob \| history
c++/include/corelib/impl/ncbi_param_impl.hpp		diff \| blob \| history
c++/include/corelib/impl/rwstreambuf.hpp		diff \| blob \| history
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c++/include/corelib/impl/stringutf8_deprecated.inl		diff \| blob \| history
c++/include/corelib/metareg.hpp		diff \| blob \| history
c++/include/corelib/ncbi_autoinit.hpp		diff \| blob \| history
c++/include/corelib/ncbi_config.hpp		diff \| blob \| history
c++/include/corelib/ncbi_cookies.hpp		diff \| blob \| history
c++/include/corelib/ncbi_limits.hpp		diff \| blob \| history
c++/include/corelib/ncbi_message.hpp	[new file with mode: 0644]	blob
c++/include/corelib/ncbi_os_mswin.hpp		diff \| blob \| history
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c++/include/corelib/ncbi_process.hpp		diff \| blob \| history
c++/include/corelib/ncbi_url.hpp		diff \| blob \| history
c++/include/corelib/ncbiapp.hpp		diff \| blob \| history
c++/include/corelib/ncbiargs.hpp		diff \| blob \| history
c++/include/corelib/ncbicntr.hpp		diff \| blob \| history
c++/include/corelib/ncbictype.hpp	[new file with mode: 0644]	blob
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c++/include/corelib/ncbidiag.inl		diff \| blob \| history
c++/include/corelib/ncbienv.hpp		diff \| blob \| history
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c++/include/corelib/ncbimtx.inl		diff \| blob \| history
c++/include/corelib/ncbiobj.hpp		diff \| blob \| history
c++/include/corelib/ncbireg.hpp		diff \| blob \| history
c++/include/corelib/ncbistl.hpp		diff \| blob \| history
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c++/include/corelib/perf_log.hpp		diff \| blob \| history
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c++/include/dbapi/error_codes.hpp		diff \| blob \| history
c++/include/dbapi/variant.hpp		diff \| blob \| history
c++/include/html/htmlhelper.hpp		diff \| blob \| history
c++/include/ncbi_pch.hpp		diff \| blob \| history
c++/include/ncbi_source_ver.h		diff \| blob \| history
c++/include/ncbiconf.h		diff \| blob \| history
c++/include/objects/biblio/Auth_list.hpp		diff \| blob \| history
c++/include/objects/blast/names.hpp		diff \| blob \| history
c++/include/objects/blastdb/defline_extra.hpp		diff \| blob \| history
c++/include/objects/general/Dbtag.hpp		diff \| blob \| history
c++/include/objects/general/Object_id.hpp		diff \| blob \| history
c++/include/objects/general/User_object.hpp		diff \| blob \| history
c++/include/objects/genomecoll/GCClient_GetAssemblyReques.hpp	[changed mode: 0644->0755]	diff \| blob \| history
c++/include/objects/genomecoll/GC_Assembly.hpp		diff \| blob \| history
c++/include/objects/genomecoll/GC_Sequence.hpp		diff \| blob \| history
c++/include/objects/genomecoll/cached_assembly.hpp	[new file with mode: 0644]	blob
c++/include/objects/genomecoll/genomic_collections_cli.hpp		diff \| blob \| history
c++/include/objects/macro/Search_func.hpp		diff \| blob \| history
c++/include/objects/macro/String_constraint.hpp		diff \| blob \| history
c++/include/objects/macro/Suspect_rule_set.hpp		diff \| blob \| history
c++/include/objects/macro/Word_substitution.hpp		diff \| blob \| history
c++/include/objects/misc/error_codes.hpp		diff \| blob \| history
c++/include/objects/pub/Pub.hpp		diff \| blob \| history
c++/include/objects/pub/Pub_equiv.hpp		diff \| blob \| history
c++/include/objects/seq/Bioseq.hpp		diff \| blob \| history
c++/include/objects/seq/Seq_descr.hpp		diff \| blob \| history
c++/include/objects/seq/annot_mapper_exception.hpp		diff \| blob \| history
c++/include/objects/seq/seq_align_mapper_base.hpp		diff \| blob \| history
c++/include/objects/seq/seq_id_handle.hpp		diff \| blob \| history
c++/include/objects/seq/seq_loc_mapper_base.hpp		diff \| blob \| history
c++/include/objects/seqalign/Dense_diag.hpp		diff \| blob \| history
c++/include/objects/seqfeat/BioSource.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Gb_qual.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Gene_ref.hpp		diff \| blob \| history
c++/include/objects/seqfeat/ISeq_feat.hpp		diff \| blob \| history
c++/include/objects/seqfeat/OrgMod.hpp		diff \| blob \| history
c++/include/objects/seqfeat/OrgName.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Org_ref.hpp		diff \| blob \| history
c++/include/objects/seqfeat/PCRPrimerSeq.hpp		diff \| blob \| history
c++/include/objects/seqfeat/RNA_ref.hpp		diff \| blob \| history
c++/include/objects/seqfeat/SeqFeatData.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Seq_feat.hpp		diff \| blob \| history
c++/include/objects/seqfeat/SubSource.hpp		diff \| blob \| history
c++/include/objects/seqloc/Seq_id.hpp		diff \| blob \| history
c++/include/objects/seqloc/Seq_loc.hpp		diff \| blob \| history
c++/include/objects/seqtable/Scaled_int_multi_data.hpp		diff \| blob \| history
c++/include/objects/seqtable/Scaled_real_multi_data.hpp		diff \| blob \| history
c++/include/objects/seqtable/SeqTable_column.hpp		diff \| blob \| history
c++/include/objects/seqtable/SeqTable_multi_data.hpp		diff \| blob \| history
c++/include/objects/seqtable/SeqTable_single_data.hpp	[new file with mode: 0644]	blob
c++/include/objects/seqtable/Seq_table.hpp		diff \| blob \| history
c++/include/objects/seqtable/impl/delta_cache.hpp		diff \| blob \| history
c++/include/objects/seqtable/seq_table_exception.hpp		diff \| blob \| history
c++/include/objects/taxon1/Taxon2_data.hpp	[new file with mode: 0644]	blob
c++/include/objects/taxon3/cached_taxon3.hpp	[new file with mode: 0755]	blob
c++/include/objects/taxon3/itaxon3.hpp	[new file with mode: 0644]	blob
c++/include/objects/taxon3/taxon3.hpp		diff \| blob \| history
c++/include/objects/trackmgr/gridrpcclient.hpp		diff \| blob \| history
c++/include/objects/valerr/ValidErrItem.hpp		diff \| blob \| history
c++/include/objects/valerr/ValidError.hpp		diff \| blob \| history
c++/include/objmgr/bioseq_handle.hpp		diff \| blob \| history
c++/include/objmgr/bioseq_set_handle.hpp		diff \| blob \| history
c++/include/objmgr/data_loader.hpp		diff \| blob \| history
c++/include/objmgr/gc_assembly_parser.hpp		diff \| blob \| history
c++/include/objmgr/graph_ci.hpp		diff \| blob \| history
c++/include/objmgr/impl/annot_collector.hpp		diff \| blob \| history
c++/include/objmgr/impl/annot_type_index.hpp		diff \| blob \| history
c++/include/objmgr/impl/bioseq_base_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/data_source.hpp		diff \| blob \| history
c++/include/objmgr/impl/handle_range_map.hpp		diff \| blob \| history
c++/include/objmgr/impl/scope_impl.hpp		diff \| blob \| history
c++/include/objmgr/impl/scope_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_annot_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_table_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_table_setter.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_table_setters.hpp		diff \| blob \| history
c++/include/objmgr/impl/snp_annot_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/synonyms.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_assigner.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_split_info.hpp		diff \| blob \| history
c++/include/objmgr/object_manager.hpp		diff \| blob \| history
c++/include/objmgr/objmgr_exception.hpp		diff \| blob \| history
c++/include/objmgr/scope.hpp		diff \| blob \| history
c++/include/objmgr/seq_entry_ci.hpp		diff \| blob \| history
c++/include/objmgr/seq_feat_handle.hpp		diff \| blob \| history
c++/include/objmgr/seq_loc_mapper.hpp		diff \| blob \| history
c++/include/objmgr/table_field.hpp		diff \| blob \| history
c++/include/objmgr/util/create_defline.hpp		diff \| blob \| history
c++/include/objmgr/util/feature.hpp		diff \| blob \| history
c++/include/objmgr/util/obj_sniff.hpp		diff \| blob \| history
c++/include/objmgr/util/objutil.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/seq_loc_util.hpp		diff \| blob \| history
c++/include/objmgr/util/sequence.hpp		diff \| blob \| history
c++/include/objtools/align_format/align_format_util.hpp		diff \| blob \| history
c++/include/objtools/align_format/format_flags.hpp		diff \| blob \| history
c++/include/objtools/align_format/seqalignfilter.hpp		diff \| blob \| history
c++/include/objtools/align_format/tabular.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/aln_converters.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/seqids_extractor.hpp		diff \| blob \| history
c++/include/objtools/blast/blastdb_format/blastdb_seqid.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/seqdb.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/seqdbexpert.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/build_db.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/multisource_util.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/writedb.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/writedb_files.hpp		diff \| blob \| history
c++/include/objtools/blast/services/blast_services.hpp		diff \| blob \| history
c++/include/objtools/cleanup/cleanup.hpp		diff \| blob \| history
c++/include/objtools/cleanup/cleanup_change.hpp		diff \| blob \| history
c++/include/objtools/cleanup/newcleanup.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/cache/writer_cache.hpp		diff \| blob \| history
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c++/include/objtools/data_loaders/genbank/gbloader_params.h		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/id1/reader_id1.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp		diff \| blob \| history
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