[med-svn] [ncbi-blast+] branch upstream updated (e874c97 -> 74e6c3d)
Aaron M. Ucko
ucko at moszumanska.debian.org
Thu Aug 4 02:29:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
ucko pushed a change to branch upstream
in repository ncbi-blast+.
from e874c97 Imported Upstream version 2.3.0
new c943f55 Imported Upstream version 2.4.0
new 74e6c3d Imported Upstream version 2.4.0
The 2 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:
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c++/include/corelib/ncbireg.hpp | 35 +-
c++/include/corelib/ncbistr.hpp | 1110 +++---
c++/include/corelib/ncbistr_util.hpp | 69 +-
c++/include/corelib/ncbitime.hpp | 7 +-
c++/include/corelib/plugin_manager.hpp | 4 +-
c++/include/corelib/request_ctx.hpp | 177 +-
c++/include/corelib/tempstr.hpp | 148 +-
c++/include/corelib/test_boost.hpp | 210 +-
c++/include/corelib/test_mt.hpp | 25 +-
c++/include/corelib/version.hpp | 40 +-
c++/include/dbapi/dbapi.hpp | 22 +-
c++/include/dbapi/driver/dbapi_conn_factory.hpp | 2 +-
c++/include/dbapi/driver/dbapi_driver_conn_mgr.hpp | 20 +-
c++/include/dbapi/driver/dbapi_driver_convert.hpp | 8 +-
c++/include/dbapi/driver/dbapi_object_convert.hpp | 5 +-
c++/include/dbapi/driver/dbapi_svc_mapper.hpp | 31 +-
c++/include/dbapi/driver/drivers.hpp | 4 +-
c++/include/dbapi/driver/impl/dbapi_impl_cmd.hpp | 6 +-
.../dbapi/driver/impl/dbapi_impl_connection.hpp | 19 +-
.../dbapi/driver/impl/dbapi_impl_context.hpp | 15 +-
.../dbapi/driver/impl/dbapi_impl_result.hpp | 13 +-
c++/include/dbapi/driver/interfaces.hpp | 72 +-
c++/include/dbapi/driver/odbc/interfaces.hpp | 33 +-
c++/include/dbapi/driver/odbc/unix_odbc/odbcinst.h | 217 +-
c++/include/dbapi/driver/odbc/unix_odbc/sql.h | 28 +-
c++/include/dbapi/driver/odbc/unix_odbc/sqlext.h | 175 +-
c++/include/dbapi/driver/odbc/unix_odbc/sqlspi.h | 173 +
c++/include/dbapi/driver/odbc/unix_odbc/sqltypes.h | 106 +-
c++/include/dbapi/driver/odbc/unix_odbc/sqlucode.h | 4 +-
.../dbapi/driver/odbc/unix_odbc/unixodbc_conf.h | 7 +
c++/include/dbapi/driver/public.hpp | 65 +-
c++/include/dbapi/driver/types.hpp | 111 +-
c++/include/dbapi/driver/util/blobstore.hpp | 34 +-
c++/include/dbapi/driver/util/parameters.hpp | 4 +-
c++/include/dbapi/error_codes.hpp | 5 +-
c++/include/dbapi/variant.hpp | 33 +-
c++/include/ncbi_pch.hpp | 2 +-
c++/include/ncbi_source_ver.h | 2 +-
c++/include/ncbiconf.h | 2 +-
c++/include/objects/entrez2/Entrez2_id_list.hpp | 5 +-
c++/include/objects/entrez2/entrez2_client.hpp | 67 +-
c++/include/objects/general/Dbtag.hpp | 7 +-
c++/include/objects/general/User_field.hpp | 256 +-
c++/include/objects/general/User_object.hpp | 35 +-
.../genomecoll/GCClient_GetAssemblyReques.hpp | 3 +-
c++/include/objects/genomecoll/GC_Sequence.hpp | 2 +-
.../objects/genomecoll/genomic_collections_cli.hpp | 55 +-
.../{seq/Seq_gap.hpp => id2/id2_client.hpp} | 60 +-
.../id2/id2processor.hpp} | 59 +-
.../id2/id2processor_interface.hpp} | 39 +-
c++/include/objects/macro/String_constraint.hpp | 4 +-
c++/include/objects/misc/error_codes.hpp | 2 +-
c++/include/objects/seq/Bioseq.hpp | 4 +-
c++/include/objects/seq/Seq_gap.hpp | 38 +-
c++/include/objects/seq/Seq_inst.hpp | 5 +-
c++/include/objects/seq/seq_loc_mapper_base.hpp | 55 +-
c++/include/objects/seq/sofa_map.hpp | 6 +-
c++/include/objects/seqalign/Dense_diag.hpp | 2 +-
c++/include/objects/seqfeat/BioSource.hpp | 4 +-
c++/include/objects/seqfeat/Gb_qual.hpp | 22 +-
c++/include/objects/seqfeat/Prot_ref.hpp | 5 +-
c++/include/objects/seqfeat/RNA_ref.hpp | 4 +-
c++/include/objects/seqfeat/SeqFeatData.hpp | 2 +-
c++/include/objects/seqfeat/Seq_feat.hpp | 13 +-
c++/include/objects/seqfeat/SubSource.hpp | 15 +-
.../objects/seqfeat/{RNA_ref.hpp => Trna_ext.hpp} | 40 +-
c++/include/objects/seqfeat/seqfeat_macros.hpp | 22 +-
c++/include/objects/seqloc/Seq_id.hpp | 18 +-
c++/include/objects/seqloc/Seq_loc.hpp | 11 +-
c++/include/objects/taxon1/taxon1.hpp | 108 +-
c++/include/objects/taxon3/cached_taxon3.hpp | 2 +-
c++/include/objects/taxon3/itaxon3.hpp | 2 +-
c++/include/objects/taxon3/taxon3.hpp | 2 +-
c++/include/objects/trackmgr/TMgr_IdentityId.hpp | 3 +-
c++/include/objects/trackmgr/blast_client.hpp | 8 +-
...rvalue_client.hpp => createtrackset_client.hpp} | 41 +-
.../objects/trackmgr/createusertrack_client.hpp | 8 +-
.../objects/trackmgr/displaytrack_client.hpp | 8 +-
c++/include/objects/trackmgr/gridrpcclient.hpp | 40 +-
.../objects/trackmgr/item_resolver_client.hpp | 8 +-
.../objects/trackmgr/removeusertrack_client.hpp | 8 +-
..._client.hpp => supported_assemblies_client.hpp} | 43 +-
.../objects/trackmgr/switch_context_client.hpp | 8 +-
.../objects/trackmgr/track_attrvalue_client.hpp | 8 +-
c++/include/objects/trackmgr/trackmgr_client.hpp | 22 +-
...ck_attrvalue_client.hpp => trackset_client.hpp} | 41 +-
c++/include/objects/valerr/ValidErrItem.hpp | 2 +-
c++/include/objects/valid/Comment_rule.hpp | 10 +-
c++/include/objmgr/annot_selector.hpp | 10 +-
c++/include/objmgr/bioseq_handle.hpp | 15 +-
c++/include/objmgr/data_loader.hpp | 82 +-
c++/include/objmgr/error_codes.hpp | 3 +-
c++/include/objmgr/gc_assembly_parser.hpp | 2 +-
c++/include/objmgr/impl/annot_collector.hpp | 18 +-
c++/include/objmgr/impl/bioseq_info.hpp | 4 +-
c++/include/objmgr/impl/data_source.hpp | 24 +-
c++/include/objmgr/impl/handle_range_map.hpp | 2 +-
c++/include/objmgr/impl/scope_impl.hpp | 43 +-
c++/include/objmgr/impl/seq_annot_info.hpp | 7 +-
c++/include/objmgr/impl/seq_id_sort.hpp | 131 +
c++/include/objmgr/impl/seq_loc_cvt.hpp | 36 +-
c++/include/objmgr/impl/snp_annot_info.hpp | 46 +-
.../genbank => objmgr}/impl/split_parser.hpp | 4 +-
c++/include/objmgr/impl/tse_assigner.hpp | 2 +-
c++/include/objmgr/impl/tse_split_info.hpp | 2 +-
c++/include/objmgr/object_manager.hpp | 7 +-
c++/include/objmgr/objmgr_exception.hpp | 6 +-
c++/include/objmgr/scope.hpp | 221 +-
c++/include/objmgr/seq_entry_ci.hpp | 2 +-
c++/include/objmgr/seq_feat_handle.hpp | 4 +-
c++/include/objmgr/seq_loc_mapper.hpp | 2 +-
c++/include/objmgr/seq_map.hpp | 5 +-
c++/include/objmgr/seq_map_ci.hpp | 16 +-
c++/include/objmgr/util/create_defline.hpp | 10 +-
c++/include/objmgr/util/feature.hpp | 44 +-
c++/include/objmgr/util/objutil.hpp | 2 +-
c++/include/objmgr/util/sequence.hpp | 31 +-
.../objtools/align_format/align_format_util.hpp | 77 +-
c++/include/objtools/align_format/format_flags.hpp | 19 +-
.../objtools/align_format/seqalignfilter.hpp | 2 +-
c++/include/objtools/align_format/tabular.hpp | 17 +-
c++/include/objtools/align_format/taxFormat.hpp | 296 ++
c++/include/objtools/alnmgr/pairwise_aln.hpp | 20 +-
c++/include/objtools/alnmgr/sparse_aln.hpp | 3 +-
.../blast/blastdb_format/blastdb_seqid.hpp | 14 +-
.../blast/seqdb_reader/impl/seqdbatlas.hpp | 24 +-
.../blast/seqdb_reader/impl/seqdbgeneral.hpp | 2 +-
.../objtools/blast/seqdb_reader/impl/seqdbisam.hpp | 4 +-
.../objtools/blast/seqdb_reader/impl/seqdbvol.hpp | 2 +-
.../objtools/blast/seqdb_reader/seqdbcommon.hpp | 8 +-
.../objtools/blast/seqdb_reader/seqdbexpert.hpp | 2 +-
.../objtools/blast/seqdb_writer/build_db.hpp | 35 +-
.../blast/seqdb_writer/multisource_util.hpp | 7 +-
.../objtools/blast/seqdb_writer/writedb.hpp | 2 +-
c++/include/objtools/cleanup/cleanup.hpp | 199 +-
c++/include/objtools/cleanup/newcleanup.hpp | 2 -
.../data_loaders/genbank/cache/reader_cache.hpp | 10 +-
.../data_loaders/genbank/cache/writer_cache.hpp | 20 +-
.../objtools/data_loaders/genbank/gbloader.hpp | 20 +-
.../data_loaders/genbank/gbloader_params.h | 2 +-
.../genbank/gicache/reader_gicache.hpp | 5 +-
.../data_loaders/genbank/impl/dispatcher.hpp | 28 +-
.../data_loaders/genbank/impl/info_cache.hpp | 88 +-
.../data_loaders/genbank/impl/processors.hpp | 5 +-
.../data_loaders/genbank/impl/reader_id1_base.hpp | 4 +-
.../data_loaders/genbank/impl/reader_id2_base.hpp | 40 +-
.../data_loaders/genbank/impl/request_result.hpp | 437 ++-
.../data_loaders/genbank/impl/statistics.hpp | 4 +-
.../objtools/data_loaders/genbank/reader.hpp | 54 +-
.../data_loaders/genbank/reader_interface.hpp | 4 +-
.../objtools/data_loaders/genbank/writer.hpp | 10 +-
.../data_loaders/genbank/writer_interface.hpp | 4 +-
c++/include/objtools/data_loaders/loaders.hpp | 2 +-
c++/include/objtools/edit/autodef.hpp | 17 +-
.../objtools/edit/autodef_feature_clause.hpp | 4 +-
.../objtools/edit/autodef_feature_clause_base.hpp | 12 +-
c++/include/objtools/edit/autodef_mod_combo.hpp | 7 +-
c++/include/objtools/edit/autodef_options.hpp | 31 +-
c++/include/objtools/edit/cds_fix.hpp | 15 +-
c++/include/objtools/edit/feattable_edit.hpp | 11 +-
c++/include/objtools/edit/loc_edit.hpp | 5 +-
c++/include/objtools/edit/parse_text_options.hpp | 2 +-
.../publication_edit.hpp} | 50 +-
c++/include/objtools/edit/rna_edit.hpp | 2 +-
c++/include/objtools/edit/seq_entry_edit.hpp | 18 +-
c++/include/objtools/edit/source_edit.hpp | 2 +-
c++/include/objtools/edit/struc_comm_field.hpp | 44 +-
c++/include/objtools/error_codes.hpp | 4 +-
c++/include/objtools/format/cigar_formatter.hpp | 2 +-
c++/include/objtools/format/context.hpp | 15 +-
c++/include/objtools/format/flat_file_config.hpp | 8 +-
.../objtools/format/flat_file_generator.hpp | 2 +-
c++/include/objtools/format/gather_items.hpp | 3 +-
c++/include/objtools/format/genbank_gather.hpp | 3 +-
c++/include/objtools/format/items/comment_item.hpp | 3 +-
c++/include/objtools/format/items/gene_finder.hpp | 4 +-
c++/include/objtools/format/items/tsa_item.hpp | 7 +-
c++/include/objtools/format/sam_formatter.hpp | 2 +-
c++/include/objtools/readers/bed_reader.hpp | 2 +-
c++/include/objtools/readers/error_container.hpp | 2 +-
c++/include/objtools/readers/fasta.hpp | 35 +-
c++/include/objtools/readers/gff2_data.hpp | 13 +-
c++/include/objtools/readers/gff2_reader.hpp | 12 +-
c++/include/objtools/readers/gff3_reader.hpp | 9 +-
c++/include/objtools/readers/gtf_reader.hpp | 7 +-
c++/include/objtools/readers/gvf_reader.hpp | 3 +-
c++/include/objtools/readers/idmapper.hpp | 2 +-
c++/include/objtools/readers/line_error.hpp | 2 +-
c++/include/objtools/readers/message_listener.hpp | 2 +-
c++/include/objtools/readers/microarray_reader.hpp | 2 +-
c++/include/objtools/readers/reader_base.hpp | 2 +-
c++/include/objtools/readers/readfeat.hpp | 6 +-
c++/include/objtools/readers/rm_reader.hpp | 2 +-
c++/include/objtools/readers/source_mod_parser.hpp | 7 +-
c++/include/objtools/readers/ucscregion_reader.hpp | 2 +-
c++/include/objtools/readers/vcf_reader.hpp | 2 +-
c++/include/objtools/readers/wiggle_reader.hpp | 2 +-
c++/include/serial/enumvalues.hpp | 2 +-
c++/include/serial/impl/choice.hpp | 4 +-
c++/include/serial/impl/classinfohelper.hpp | 5 +-
c++/include/serial/impl/memberlist.hpp | 2 +-
c++/include/serial/impl/stltypes.hpp | 2 +-
c++/include/serial/objistrasn.hpp | 3 +-
c++/include/serial/objistrjson.hpp | 2 +-
c++/include/serial/objostr.hpp | 24 +-
c++/include/serial/objostrjson.hpp | 2 +-
c++/include/serial/rpcbase.hpp | 181 +-
c++/include/serial/rpcbase_impl.hpp | 170 +
c++/include/serial/serialimpl.hpp | 2 +-
c++/include/serial/serialutil.hpp | 2 +-
c++/include/util/bitset/bm.h | 4 +-
c++/include/util/bitset/bmalloc.h | 6 +-
c++/include/util/bitset/bmblocks.h | 6 +-
c++/include/util/bitset/bmconst.h | 9 +-
c++/include/util/bitset/bmfunc.h | 27 +-
c++/include/util/bitset/bmutil.h | 26 +-
c++/include/util/bitset/encoding.h | 4 +-
c++/include/util/cache/icache_cf.hpp | 4 +-
c++/include/util/file_manifest.hpp | 238 ++
c++/include/util/format_guess.hpp | 4 +-
c++/include/util/id_mux.hpp | 4 +-
c++/include/util/line_reader.hpp | 34 +-
c++/include/util/ncbi_cache.hpp | 20 +-
c++/include/util/range_coll.hpp | 4 +-
c++/include/util/resize_iter.hpp | 18 +-
c++/include/util/retry_ctx.hpp | 4 +-
c++/include/util/stream_source.hpp | 236 ++
c++/include/util/sync_queue.hpp | 673 ++--
c++/include/util/thread_pool_old.hpp | 8 +-
c++/include/util/transmissionrw.hpp | 8 +-
c++/include/util/value_convert.hpp | 241 +-
c++/include/util/value_convert_policy.hpp | 415 +-
c++/scripts/common/add_vdb.sh | 15 +-
c++/scripts/common/check/check_add.sh | 11 +-
c++/scripts/common/check/check_exec.sh | 6 +-
c++/scripts/common/check/check_exec_test.sh | 6 +-
c++/scripts/common/check/check_make_cfg.sh | 16 +-
c++/scripts/common/check/check_make_unix.sh | 25 +-
.../common/check/inspxe-suppressions/_vs.sup | 37 +
c++/scripts/common/check/inspxe.sh | 2 +-
c++/scripts/common/check/valgrind.supp | 37 +-
c++/scripts/common/common.sh | 2 +-
c++/scripts/common/impl/generate_all_objects.sh | 6 +-
c++/scripts/common/impl/install.sh | 2 +-
c++/scripts/common/impl/run_with_lock.sh | 2 +-
c++/scripts/common/new_project.wsf | 2 +-
c++/scripts/common/project_utilits.js | 22 +-
c++/scripts/projects/blast/Manifest | 8 +-
c++/scripts/projects/blast/components.link | 17 +-
.../projects/blast/post_build/blast_utils.py | 75 +-
.../projects/blast/post_build/make_installers.py | 27 +-
.../projects/blast/post_build/rpm/make_rpm.py | 37 +-
.../projects/blast/post_build/rpm/ncbi-blast.spec | 44 +
c++/scripts/projects/blast/post_build/rpm/test.sh | 13 +
.../projects/blast/post_build/win/make_win.py | 9 +-
c++/scripts/projects/corelib/Manifest | 4 +-
c++/scripts/projects/datatool/ChangeLog | 10 +
c++/scripts/projects/datatool/Manifest | 4 +-
c++/scripts/projects/datatool/components.link | 4 +-
c++/scripts/projects/dispatcher/Manifest | 4 +-
c++/scripts/projects/grid/ChangeLog | 219 --
c++/scripts/projects/grid/LICENSE | 19 -
c++/scripts/projects/grid/Manifest | 55 -
c++/scripts/projects/grid/README | 66 -
c++/scripts/projects/grid/components.link | 5 -
c++/scripts/projects/grid/project.lst | 24 -
c++/scripts/projects/igblast/Manifest | 13 +-
c++/scripts/projects/igblast/README | 13 +-
c++/scripts/projects/igblast/components.link | 17 +-
.../projects/igblast/post_build/blast_utils.py | 60 +-
.../ncbi-igblast.pmdoc/01_stage-contents.xml | 1 -
.../macosx/ncbi-igblast.pmdoc/01_stage.xml | 1 -
.../post_build/macosx/ncbi-igblast.pmdoc/index.xml | 1 -
.../igblast/post_build/macosx/ncbi-igblast.sh | 153 +-
.../igblast/post_build/macosx/ncbi_igblast | 1 -
.../projects/igblast/post_build/make_installers.py | 25 +-
.../projects/igblast/post_build/rpm/make_rpm.py | 38 +-
.../projects/igblast/post_build/win/make_win.py | 13 +-
c++/scripts/projects/ncbi_applog/ChangeLog | 49 +-
c++/scripts/projects/ncbi_applog/Manifest | 4 +-
c++/scripts/projects/ncbi_applog/README | 2 +-
c++/scripts/projects/ncbi_gui_base.lst | 2 +
c++/scripts/projects/netcache/ChangeLog | 25 +
c++/scripts/projects/netschedule/ChangeLog | 27 +
c++/scripts/projects/netschedule/components.link | 6 +-
c++/scripts/projects/netstorage/ChangeLog | 5 +
c++/scripts/projects/netstorage/components.link | 8 +-
c++/scripts/projects/netstorage/project.lst | 11 +
c++/scripts/projects/netstorage_gc/project.lst | 3 +-
.../projects/project_tree_builder/ChangeLog | 3 +
c++/scripts/projects/project_tree_builder/Manifest | 5 +-
.../projects/project_tree_builder/components.link | 4 +-
c++/scripts/projects/public/Manifest | 21 +-
c++/scripts/projects/public/components.link | 23 +-
.../public/tagprecommit/use_embedded_ptb.py | 32 +
c++/scripts/projects/python_ncbi_dbapi/ChangeLog | 3 +
.../python_ncbi_dbapi/post_build/post_build.py | 4 +-
c++/scripts/projects/python_ncbi_dbapi/project.lst | 4 +-
c++/scripts/projects/xmlwrapp/Manifest | 13 +-
c++/src/Makefile.in | 2 +-
c++/src/algo/Makefile.in | 2 +-
c++/src/algo/blast/api/bl2seq.cpp | 2 +-
c++/src/algo/blast/api/blast_objmgr_tools.cpp | 71 +-
c++/src/algo/blast/api/blast_options_builder.cpp | 4 +-
c++/src/algo/blast/api/blast_results.cpp | 9 +-
c++/src/algo/blast/api/blast_seqalign.cpp | 23 +-
c++/src/algo/blast/api/blast_setup_cxx.cpp | 12 +-
c++/src/algo/blast/api/dust_filter.cpp | 5 +-
c++/src/algo/blast/api/local_blast.cpp | 6 +-
c++/src/algo/blast/api/local_db_adapter.cpp | 2 +-
c++/src/algo/blast/api/msa_pssm_input.cpp | 2 +-
c++/src/algo/blast/api/prelim_stage.cpp | 2 +-
c++/src/algo/blast/api/psiblast_aux_priv.cpp | 4 +-
c++/src/algo/blast/api/remote_blast.cpp | 52 +-
c++/src/algo/blast/api/remote_search.cpp | 2 +-
c++/src/algo/blast/api/search_strategy.cpp | 2 +-
c++/src/algo/blast/api/seqinfosrc_bioseq.hpp | 9 +-
c++/src/algo/blast/api/seqsrc_multiseq.cpp | 2 +-
c++/src/algo/blast/api/seqsrc_seqdb.cpp | 2 +-
c++/src/algo/blast/api/uniform_search.cpp | 2 +-
c++/src/algo/blast/api/version.cpp | 16 +-
c++/src/algo/blast/blastinput/blast_args.cpp | 22 +-
.../algo/blast/blastinput/blast_fasta_input.cpp | 15 +-
c++/src/algo/blast/blastinput/blast_input_aux.cpp | 8 +-
c++/src/algo/blast/blastinput/blastn_args.cpp | 4 +-
c++/src/algo/blast/blastinput/cmdline_flags.cpp | 6 +-
c++/src/algo/blast/blastinput/deltablast_args.cpp | 4 +-
c++/src/algo/blast/blastinput/psiblast_args.cpp | 4 +-
.../unit_test/blast_scope_src_unit_test.cpp | 7 +-
.../blastinput/unit_test/blastinput_unit_test.cpp | 52 +-
.../blast/blastinput/unit_test/data/localid.txt | 9 +
.../composition_adjustment.c | 12 +-
.../blast/composition_adjustment/redo_alignment.c | 209 +-
c++/src/algo/blast/core/Makefile.blast.lib | 9 +-
c++/src/algo/blast/core/Makefile.blast.lib.unix | 7 +-
c++/src/algo/blast/core/blast_engine.c | 8 +-
c++/src/algo/blast/core/blast_gapalign.c | 4 +-
c++/src/algo/blast/core/blast_hits.c | 695 ++--
c++/src/algo/blast/core/blast_hspstream_mt_utils.c | 16 +-
c++/src/algo/blast/core/blast_hspstream_mt_utils.h | 13 +-
c++/src/algo/blast/core/blast_kappa.c | 1459 +++++--
c++/src/algo/blast/core/blast_options.c | 28 +-
c++/src/algo/blast/core/blast_seg.c | 4 +-
c++/src/algo/blast/core/blast_setup.c | 7 +-
c++/src/algo/blast/core/blast_stat.c | 563 +--
c++/src/algo/blast/core/blast_traceback.c | 448 ++-
c++/src/algo/blast/core/blast_traceback_mt_priv.c | 46 +-
c++/src/algo/blast/core/blast_util.c | 4 +-
c++/src/algo/blast/core/boost_erf.c | 256 ++
.../main.cpp => algo/blast/core/boost_erf.h} | 28 +-
c++/src/algo/blast/core/greedy_align.c | 6 +-
c++/src/algo/blast/dbindex/makeindex/main.cpp | 4 +-
.../algo/blast/format/Makefile.xblastformat.lib | 2 +-
c++/src/algo/blast/format/blast_format.cpp | 64 +-
c++/src/algo/blast/format/blastfmtutil.cpp | 4 +-
c++/src/algo/blast/format/blastxml2_format.cpp | 2 +-
c++/src/algo/blast/format/data4xml2format.cpp | 2 +-
c++/src/algo/blast/igblast/igblast.cpp | 171 +-
c++/src/algo/blast/unit_tests/api/Makefile.in | 7 +-
.../unit_tests/api/Makefile.stat_unit_test.app | 15 +
.../algo/blast/unit_tests/api/bl2seq_unit_test.cpp | 6 +-
.../blast/unit_tests/api/blastengine_unit_test.cpp | 14 +-
.../blast/unit_tests/api/blastextend_unit_test.cpp | 6 +-
.../blast/unit_tests/api/blastfilter_unit_test.cpp | 22 +-
.../blast/unit_tests/api/blasthits_unit_test.cpp | 6 +-
.../blast/unit_tests/api/blastsetup_unit_test.cpp | 15 +-
c++/src/algo/blast/unit_tests/api/data/biased.fsa | 0
.../blast/unit_tests/api/data/msa.clustalw.txt | 0
.../algo/blast/unit_tests/api/delta_unit_test.cpp | 28 +-
.../blast/unit_tests/api/psiblast_unit_test.cpp | 18 +-
.../api/pssmenginefreqratios_unit_test.cpp | 4 +-
.../unit_tests/api/redoalignment_unit_test.cpp | 10 +-
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.../Entrez2_id_list.cpp => seqfeat/Trna_ext.cpp} | 85 +-
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c++/src/objmgr/data_source.cpp | 49 +-
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c++/src/objmgr/handle_range_map.cpp | 2 +-
c++/src/objmgr/objmgr_exception.cpp | 4 +-
c++/src/objmgr/scope.cpp | 134 +-
c++/src/objmgr/scope_impl.cpp | 708 ++--
c++/src/objmgr/scope_info.cpp | 2 +-
c++/src/objmgr/seq_annot_info.cpp | 66 +-
c++/src/objmgr/seq_entry_ci.cpp | 2 +-
c++/src/objmgr/seq_feat_handle.cpp | 12 +-
c++/src/objmgr/seq_id_sort.cpp | 164 +
c++/src/objmgr/seq_loc_cvt.cpp | 348 +-
c++/src/objmgr/seq_loc_mapper.cpp | 2 +-
c++/src/objmgr/seq_map.cpp | 11 +-
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c++/src/objmgr/seq_table_info.cpp | 4 +-
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c++/src/objmgr/tse_assigner.cpp | 2 +-
c++/src/objmgr/tse_info.cpp | 2 +-
c++/src/objmgr/tse_split_info.cpp | 2 +-
c++/src/objmgr/util/Makefile.util.lib | 2 +-
c++/src/objmgr/util/create_defline.cpp | 132 +-
c++/src/objmgr/util/feature.cpp | 199 +-
c++/src/objmgr/util/objutil.cpp | 87 +-
c++/src/objmgr/util/seq_loc_util.cpp | 11 +-
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c++/src/objtools/Makefile.in | 2 +-
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c++/src/objtools/align_format/format_flags.cpp | 19 +-
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c++/src/objtools/align_format/tabular.cpp | 299 +-
c++/src/objtools/align_format/taxFormat.cpp | 966 +++++
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.../unit_test/data/in_showalign_use_this_gi.asn | 0
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c++/src/objtools/alnmgr/aln_builders.cpp | 15 +-
c++/src/objtools/alnmgr/alnsegments.cpp | 21 +-
c++/src/objtools/alnmgr/pairwise_aln.cpp | 50 +-
c++/src/objtools/alnmgr/score_builder_base.cpp | 2 +-
c++/src/objtools/alnmgr/sparse_aln.cpp | 191 +-
c++/src/objtools/alnmgr/sparse_ci.cpp | 31 +-
.../blast/blastdb_format/blastdb_dataextract.cpp | 4 +-
.../unit_test/seq_writer_unit_test.cpp | 8 +-
.../gene_info_reader/demo/gene_info_reader_app.cpp | 4 +-
c++/src/objtools/blast/seqdb_reader/seqdb.cpp | 8 +-
c++/src/objtools/blast/seqdb_reader/seqdbalias.cpp | 10 +-
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.../objtools/blast/seqdb_reader/seqdbgimask.cpp | 4 +-
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c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp | 4 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +-
c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp | 6 +-
c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp | 18 +-
.../blast/seqdb_reader/test/seqdb_perf.cpp | 6 +-
.../objtools/blast/seqdb_writer/build-alias-index | 2 +-
c++/src/objtools/blast/seqdb_writer/build_db.cpp | 60 +-
.../blast/seqdb_writer/multisource_util.cpp | 9 +-
c++/src/objtools/blast/seqdb_writer/taxid_set.cpp | 21 +-
.../seqdb_writer/unit_test/criteria_unit_test.cpp | 2 +-
.../seqdb_writer/unit_test/data/rabbit_mrna.fsa | 7 +-
.../unit_test/data/rabbit_taxidmap.txt | 4 +
.../seqdb_writer/unit_test/writedb_unit_test.cpp | 191 +-
c++/src/objtools/blast/seqdb_writer/writedb.cpp | 4 +-
.../blast/seqdb_writer/writedb_convert.cpp | 6 +-
.../objtools/blast/seqdb_writer/writedb_gimask.cpp | 4 +-
.../objtools/blast/seqdb_writer/writedb_gimask.hpp | 2 +-
.../objtools/blast/seqdb_writer/writedb_impl.cpp | 16 +-
.../objtools/blast/seqdb_writer/writedb_impl.hpp | 2 +-
.../objtools/blast/seqdb_writer/writedb_isam.cpp | 4 +-
.../objtools/blast/seqdb_writer/writedb_volume.cpp | 15 +-
.../objtools/blast/seqdb_writer/writedb_volume.hpp | 2 +-
c++/src/objtools/cleanup/Makefile.cleanup.lib | 2 +-
c++/src/objtools/cleanup/autogenerated_cleanup.cpp | 50 +-
c++/src/objtools/cleanup/autogenerated_cleanup.hpp | 4 +-
c++/src/objtools/cleanup/autogenerated_cleanup.txt | 6 +-
.../cleanup/autogenerated_extended_cleanup.cpp | 96 +-
.../cleanup/autogenerated_extended_cleanup.hpp | 13 +-
.../cleanup/autogenerated_extended_cleanup.txt | 67 +-
c++/src/objtools/cleanup/cleanup.cpp | 2533 ++++++++++--
c++/src/objtools/cleanup/cleanup_utils.cpp | 4 +-
c++/src/objtools/cleanup/cleanup_utils.hpp | 2 +-
c++/src/objtools/cleanup/newcleanupp.cpp | 4127 +++++++++++++++-----
c++/src/objtools/cleanup/newcleanupp.hpp | 131 +-
c++/src/objtools/data_loaders/Makefile.in | 4 +-
.../data_loaders/genbank/Makefile.ncbi_xreader.lib | 4 +-
.../data_loaders/genbank/cache/reader_cache.cpp | 188 +-
.../data_loaders/genbank/cache/writer_cache.cpp | 95 +-
.../objtools/data_loaders/genbank/dispatcher.cpp | 519 ++-
c++/src/objtools/data_loaders/genbank/gbloader.cpp | 188 +-
.../gicache/Makefile.ncbi_xreader_gicache.lib | 4 +-
.../data_loaders/genbank/gicache/gicache.c | 237 +-
.../data_loaders/genbank/gicache/gicache_cxx.cpp} | 44 +-
.../genbank/gicache/reader_gicache.cpp | 7 +-
.../data_loaders/genbank/id1/reader_id1.cpp | 26 +-
.../objtools/data_loaders/genbank/info_cache.cpp | 8 +-
.../objtools/data_loaders/genbank/processors.cpp | 105 +-
c++/src/objtools/data_loaders/genbank/reader.cpp | 277 +-
.../data_loaders/genbank/reader_id1_base.cpp | 9 +-
.../data_loaders/genbank/reader_id2_base.cpp | 810 +++-
.../objtools/data_loaders/genbank/reader_snp.cpp | 125 +-
.../data_loaders/genbank/request_result.cpp | 471 ++-
c++/src/objtools/edit/Makefile.edit.lib | 4 +-
c++/src/objtools/edit/autodef.cpp | 242 +-
.../objtools/edit/autodef_available_modifier.cpp | 11 +-
c++/src/objtools/edit/autodef_feature_clause.cpp | 106 +-
.../objtools/edit/autodef_feature_clause_base.cpp | 111 +-
c++/src/objtools/edit/autodef_mod_combo.cpp | 222 +-
c++/src/objtools/edit/autodef_options.cpp | 75 +-
c++/src/objtools/edit/capitalization_string.cpp | 5 +-
c++/src/objtools/edit/cds_fix.cpp | 45 +-
c++/src/objtools/edit/feattable_edit.cpp | 182 +-
c++/src/objtools/edit/field_handler.cpp | 8 +-
c++/src/objtools/edit/loc_edit.cpp | 18 +-
c++/src/objtools/edit/parse_text_options.cpp | 2 +-
c++/src/objtools/edit/publication_edit.cpp | 156 +
c++/src/objtools/edit/remote_updater.cpp | 117 +-
c++/src/objtools/edit/seq_entry_edit.cpp | 343 +-
c++/src/objtools/edit/seqid_guesser.cpp | 2 +-
c++/src/objtools/edit/struc_comm_field.cpp | 193 +-
c++/src/objtools/format/Makefile.xformat.lib | 2 +-
c++/src/objtools/format/accession_item.cpp | 2 +-
c++/src/objtools/format/cigar_formatter.cpp | 2 +-
c++/src/objtools/format/comment_item.cpp | 68 +-
c++/src/objtools/format/context.cpp | 24 +-
c++/src/objtools/format/ctrl_items.cpp | 2 +-
c++/src/objtools/format/dbsource_item.cpp | 2 +-
c++/src/objtools/format/defline_item.cpp | 2 +-
c++/src/objtools/format/embl_formatter.cpp | 2 +-
c++/src/objtools/format/feature_item.cpp | 120 +-
c++/src/objtools/format/flat_file_config.cpp | 6 +-
c++/src/objtools/format/flat_file_generator.cpp | 141 +-
c++/src/objtools/format/flat_seqloc.cpp | 66 +-
c++/src/objtools/format/gather_items.cpp | 52 +-
c++/src/objtools/format/gbseq_formatter.cpp | 2 +-
c++/src/objtools/format/genbank_formatter.cpp | 47 +-
c++/src/objtools/format/genbank_gather.cpp | 48 +-
c++/src/objtools/format/gene_finder.cpp | 27 +-
c++/src/objtools/format/genome_project_item.cpp | 2 +-
c++/src/objtools/format/gff_gather.cpp | 2 +-
c++/src/objtools/format/inst_info_map.cpp | 203 +-
c++/src/objtools/format/inst_info_map.hpp | 10 +-
c++/src/objtools/format/item_formatter.cpp | 3 +-
c++/src/objtools/format/keywords_item.cpp | 14 +-
c++/src/objtools/format/locus_item.cpp | 16 +-
c++/src/objtools/format/primary_item.cpp | 2 +-
c++/src/objtools/format/qualifiers.cpp | 10 +-
c++/src/objtools/format/reference_item.cpp | 2 +-
c++/src/objtools/format/sam_formatter.cpp | 2 +-
c++/src/objtools/format/source_item.cpp | 2 +-
c++/src/objtools/readers/bed_reader.cpp | 12 +-
c++/src/objtools/readers/fasta.cpp | 49 +-
c++/src/objtools/readers/format_guess_ex.cpp | 2 +-
c++/src/objtools/readers/gff2_data.cpp | 181 +-
c++/src/objtools/readers/gff2_reader.cpp | 81 +-
c++/src/objtools/readers/gff3_reader.cpp | 284 +-
c++/src/objtools/readers/gff3_sofa.cpp | 6 +-
c++/src/objtools/readers/gff_reader.cpp | 4 +-
c++/src/objtools/readers/gtf_reader.cpp | 164 +-
c++/src/objtools/readers/gvf_reader.cpp | 15 +-
c++/src/objtools/readers/idmapper.cpp | 2 +-
c++/src/objtools/readers/idmapper_builtin.cpp | 2 +-
c++/src/objtools/readers/idmapper_config.cpp | 7 +-
c++/src/objtools/readers/microarray_reader.cpp | 4 +-
c++/src/objtools/readers/phrap.cpp | 7 +-
c++/src/objtools/readers/read_util.cpp | 10 +-
c++/src/objtools/readers/reader_base.cpp | 4 +-
c++/src/objtools/readers/readfeat.cpp | 170 +-
c++/src/objtools/readers/rm_reader.cpp | 2 +-
c++/src/objtools/readers/source_mod_parser.cpp | 64 +-
c++/src/objtools/readers/ucscregion_reader.cpp | 2 +-
c++/src/objtools/readers/vcf_reader.cpp | 24 +-
c++/src/objtools/readers/wiggle_reader.cpp | 11 +-
c++/src/serial/Makefile.serial.lib | 2 +-
c++/src/serial/choice.cpp | 6 +-
c++/src/serial/classinfo.cpp | 4 +-
c++/src/serial/datatool/blocktype.cpp | 12 +-
c++/src/serial/datatool/choicestr.cpp | 4 +-
c++/src/serial/datatool/comments.cpp | 32 +-
c++/src/serial/datatool/comments.hpp | 5 +-
c++/src/serial/datatool/datatool.cpp | 6 +-
c++/src/serial/datatool/enumstr.cpp | 2 +-
c++/src/serial/datatool/enumtype.cpp | 31 +-
c++/src/serial/datatool/enumtype.hpp | 2 +-
c++/src/serial/datatool/filecode.cpp | 4 +-
c++/src/serial/datatool/generate.cpp | 6 +-
c++/src/serial/datatool/module.cpp | 4 +-
c++/src/serial/datatool/reftype.cpp | 8 +-
c++/src/serial/datatool/rpcgen.cpp | 4 +-
c++/src/serial/datatool/statictype.cpp | 40 +-
c++/src/serial/datatool/statictype.hpp | 10 +-
c++/src/serial/datatool/testdata/res/set.ent.3 | 482 +++
.../serial/datatool/traversal_spec_file_parser.cpp | 12 +-
c++/src/serial/datatool/unitype.cpp | 18 +-
c++/src/serial/datatool/xsdparser.cpp | 9 +-
c++/src/serial/enumerated.cpp | 2 +-
c++/src/serial/member.cpp | 15 +-
c++/src/serial/memberlist.cpp | 2 +-
c++/src/serial/objistrasn.cpp | 8 +-
c++/src/serial/objistrjson.cpp | 2 +-
c++/src/serial/objostr.cpp | 8 +-
c++/src/serial/objostrasn.cpp | 4 +-
c++/src/serial/objostrasnb.cpp | 31 +-
c++/src/serial/objostrjson.cpp | 4 +-
c++/src/serial/objostrxml.cpp | 2 +-
c++/src/serial/objstack.cpp | 2 +-
c++/src/serial/pathhook.cpp | 2 +-
c++/src/serial/rpcbase.cpp | 46 +-
c++/src/util/Makefile.util.lib | 4 +-
c++/src/util/checksum.cpp | 4 +-
c++/src/util/compress/api/archive.cpp | 6 +-
c++/src/util/compress/api/compress.cpp | 7 +-
c++/src/util/compress/api/streambuf.cpp | 4 +-
c++/src/util/compress/api/tar.cpp | 13 +-
c++/src/util/compress/api/zlib.cpp | 4 +-
c++/src/util/creaders/alnread.c | 128 +-
c++/src/util/ddump_viewer.cpp | 8 +-
c++/src/util/dictionary_util.cpp | 31 +-
c++/src/util/file_manifest.cpp | 165 +
c++/src/util/format_guess.cpp | 153 +-
c++/src/util/itree.cpp | 4 +-
c++/src/util/line_reader.cpp | 158 +-
c++/src/util/retry_ctx.cpp | 26 +-
c++/src/util/scheduler.cpp | 7 +-
c++/src/util/sequtil/sequtil_convert_imp.cpp | 118 +-
c++/src/util/sequtil/sequtil_convert_imp.hpp | 25 +-
c++/src/util/sequtil/sequtil_manip.cpp | 52 +-
c++/src/util/sequtil/sequtil_shared.hpp | 4 +-
c++/src/util/smalldns.cpp | 4 +-
c++/src/util/strbuffer.cpp | 74 +-
c++/src/util/stream_source.cpp | 394 ++
c++/src/util/strsearch.cpp | 8 +-
c++/src/util/table_printer.cpp | 9 +-
c++/src/util/tables/raw_scoremat.c | 8 +-
c++/src/util/thread_pool.cpp | 41 +-
c++/src/util/transmissionrw.cpp | 79 +-
c++/src/util/utf8.cpp | 4 +-
c++/src/util/util_misc.cpp | 5 +-
c++/src/util/uttp.cpp | 10 +-
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