Date: Tue, 1 Jan 2019 19:55:44 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r488931 - in head/biology/ncbi-blast+: . files Message-ID: <201901011955.x01JtiXk026960@repo.freebsd.org>
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Author: jwb Date: Tue Jan 1 19:55:44 2019 New Revision: 488931 URL: https://svnweb.freebsd.org/changeset/ports/488931 Log: biology/ncbi-blast+: Upgrade to 2.8.1 Remove hacks that are no longer needed New patch for endian.h location Approved by: jrm (mentor, implicit) Added: head/biology/ncbi-blast+/files/patch-src_util_checksum_farmhash_farmhash.h (contents, props changed) Modified: head/biology/ncbi-blast+/Makefile head/biology/ncbi-blast+/distinfo head/biology/ncbi-blast+/pkg-plist Modified: head/biology/ncbi-blast+/Makefile ============================================================================== --- head/biology/ncbi-blast+/Makefile Tue Jan 1 19:54:38 2019 (r488930) +++ head/biology/ncbi-blast+/Makefile Tue Jan 1 19:55:44 2019 (r488931) @@ -1,8 +1,7 @@ # $FreeBSD$ PORTNAME= ncbi-blast+ -DISTVERSION= 2.7.1 -PORTREVISION= 2 +DISTVERSION= 2.8.1 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ @@ -33,33 +32,21 @@ LIB_DEPENDS= libpcre.so:devel/pcre \ RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils USES= compiler:openmp gmake shebangfix perl5 python +USE_LDCONFIG= yes + SHEBANG_FILES= src/app/blast/legacy_blast.pl \ src/app/blast/update_blastdb.pl \ - src/app/winmasker/windowmasker_2.2.22_adapter.py -USE_LDCONFIG= yes + src/app/winmasker/windowmasker_2.2.22_adapter.py \ + src/app/blast/get_species_taxids.sh GNU_CONFIGURE= yes -# The test for amq can hang, but amq is not needed so just avoid the test -CONFIGURE_ENV= ncbi_cv_prog_amq_w=no - # configure chooses /usr/local/bin/ar with no flags # FreeBSD boost port flagged by configure as untested version # --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do # a postinstall mv. -CONFIGURE_ARGS+= AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++ +CONFIGURE_ARGS= AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++ WRKSRC_SUBDIR= c++ - -MAKE_JOBS_UNSAFE= yes - -# Fix "undefined _ThreadRuneLocale" error on 10.0 -# Fix unknown options in configure -post-patch: - @${REINPLACE_CMD} \ - -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \ - -e '/--infodir=DIR/d' \ - -e '/--mandir=DIR/d' \ - ${WRKSRC}/src/build-system/configure post-install: @${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra Modified: head/biology/ncbi-blast+/distinfo ============================================================================== --- head/biology/ncbi-blast+/distinfo Tue Jan 1 19:54:38 2019 (r488930) +++ head/biology/ncbi-blast+/distinfo Tue Jan 1 19:55:44 2019 (r488931) @@ -1,3 +1,3 @@ -TIMESTAMP = 1518995346 -SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca -SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 +TIMESTAMP = 1545573763 +SHA256 (ncbi-blast-2.8.1+-src.tar.gz) = e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f +SIZE (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 Added: head/biology/ncbi-blast+/files/patch-src_util_checksum_farmhash_farmhash.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-blast+/files/patch-src_util_checksum_farmhash_farmhash.h Tue Jan 1 19:55:44 2019 (r488931) @@ -0,0 +1,25 @@ +--- src/util/checksum/farmhash/farmhash.h.orig 2018-09-26 07:38:06 UTC ++++ src/util/checksum/farmhash/farmhash.h 2018-12-23 07:48:41 UTC +@@ -305,15 +305,18 @@ inline uint128_t Fingerprint128(const Str& s) { + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif +-#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) +- #include <endian.h> // libc6-dev, GLIBC ++#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) ++ #include <sys/endian.h> + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif + #endif +-#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) +- #include <sys/endian.h> ++// __GNUC__ actually does not imply the location of endian.h. It could ++// be set on any system running GCC. I'm wondering why this was added ++// Working around breakage for BSD systems by checking for BSD first. ++#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) ++ #include <endian.h> // libc6-dev, GLIBC + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN Modified: head/biology/ncbi-blast+/pkg-plist ============================================================================== --- head/biology/ncbi-blast+/pkg-plist Tue Jan 1 19:54:38 2019 (r488930) +++ head/biology/ncbi-blast+/pkg-plist Tue Jan 1 19:55:44 2019 (r488931) @@ -1,5 +1,6 @@ bin/blast_formatter bin/blastdb_aliastool +bin/blastdb_convert bin/blastdbcheck bin/blastdbcmd bin/blastdbcp @@ -12,7 +13,9 @@ bin/deltablast bin/dustmasker bin/gc_cli bin/gene_info_reader +bin/get_species_taxids.sh bin/legacy_blast.pl +bin/lmdbxx_sample bin/makeblastdb bin/makembindex bin/makeprofiledb @@ -257,10 +260,12 @@ include/ncbi-tools++/cgi/ref_args.hpp include/ncbi-tools++/cgi/user_agent.hpp include/ncbi-tools++/common/boost_skew_guard.hpp include/ncbi-tools++/common/config/ncbiconf_msvc.h +include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in include/ncbi-tools++/common/config/ncbiconf_universal.h include/ncbi-tools++/common/config/ncbiconf_xcode.h include/ncbi-tools++/common/header_template.hpp include/ncbi-tools++/common/metamodules_doxygen.h +include/ncbi-tools++/common/ncbi_build_info.h include/ncbi-tools++/common/ncbi_build_ver.h include/ncbi-tools++/common/ncbi_build_ver.h.in include/ncbi-tools++/common/ncbi_build_ver.h.last @@ -268,6 +273,7 @@ include/ncbi-tools++/common/ncbi_export.h include/ncbi-tools++/common/ncbi_package_ver.h include/ncbi-tools++/common/ncbi_pch_impl.hpp include/ncbi-tools++/common/ncbi_skew_guard.h +include/ncbi-tools++/common/ncbi_source_ver.cmake_nodep include/ncbi-tools++/common/ncbi_source_ver.h include/ncbi-tools++/common/ncbiconf_impl.h include/ncbi-tools++/common/test_assert.h @@ -312,6 +318,7 @@ include/ncbi-tools++/connect/ncbi_sendmail.h include/ncbi-tools++/connect/ncbi_server_info.h include/ncbi-tools++/connect/ncbi_service.h include/ncbi-tools++/connect/ncbi_service_connector.h +include/ncbi-tools++/connect/ncbi_service_cxx.hpp include/ncbi-tools++/connect/ncbi_socket.h include/ncbi-tools++/connect/ncbi_socket.hpp include/ncbi-tools++/connect/ncbi_socket_connector.h @@ -334,6 +341,7 @@ include/ncbi-tools++/connect/services/grid_globals.hpp include/ncbi-tools++/connect/services/grid_rw_impl.hpp include/ncbi-tools++/connect/services/grid_worker.hpp include/ncbi-tools++/connect/services/grid_worker_app.hpp +include/ncbi-tools++/connect/services/impl/netcache_api_int.hpp include/ncbi-tools++/connect/services/impl/neticache_client_int.hpp include/ncbi-tools++/connect/services/impl/netschedule_api_int.hpp include/ncbi-tools++/connect/services/impl/netstorage_impl.hpp @@ -399,6 +407,7 @@ include/ncbi-tools++/corelib/ncbi_base64.h include/ncbi-tools++/corelib/ncbi_bswap.hpp include/ncbi-tools++/corelib/ncbi_config.hpp include/ncbi-tools++/corelib/ncbi_cookies.hpp +include/ncbi-tools++/corelib/ncbi_fast.hpp include/ncbi-tools++/corelib/ncbi_limits.h include/ncbi-tools++/corelib/ncbi_limits.hpp include/ncbi-tools++/corelib/ncbi_mask.hpp @@ -530,10 +539,14 @@ include/ncbi-tools++/ncbi_random_macro.h include/ncbi-tools++/ncbi_source_ver.h include/ncbi-tools++/ncbiconf.h include/ncbi-tools++/ncbiconf_unix.h +include/ncbi-tools++/objects/access/.cvsignore +include/ncbi-tools++/objects/access/.gitignore include/ncbi-tools++/objects/access/Link_set.hpp include/ncbi-tools++/objects/access/Link_set_.hpp include/ncbi-tools++/objects/access/NCBI_Access_module.hpp include/ncbi-tools++/objects/access/access__.hpp +include/ncbi-tools++/objects/biblio/.cvsignore +include/ncbi-tools++/objects/biblio/.gitignore include/ncbi-tools++/objects/biblio/Affil.hpp include/ncbi-tools++/objects/biblio/Affil_.hpp include/ncbi-tools++/objects/biblio/ArticleId.hpp @@ -596,6 +609,8 @@ include/ncbi-tools++/objects/biblio/Title_.hpp include/ncbi-tools++/objects/biblio/biblio__.hpp include/ncbi-tools++/objects/biblio/biblio_macros.hpp include/ncbi-tools++/objects/biblio/citation_base.hpp +include/ncbi-tools++/objects/biotree/.cvsignore +include/ncbi-tools++/objects/biotree/.gitignore include/ncbi-tools++/objects/biotree/BioTreeContainer.hpp include/ncbi-tools++/objects/biotree/BioTreeContainer_.hpp include/ncbi-tools++/objects/biotree/DistanceMatrix.hpp @@ -614,6 +629,8 @@ include/ncbi-tools++/objects/biotree/NodeSet.hpp include/ncbi-tools++/objects/biotree/NodeSet_.hpp include/ncbi-tools++/objects/biotree/Node_.hpp include/ncbi-tools++/objects/biotree/biotree__.hpp +include/ncbi-tools++/objects/blast/.cvsignore +include/ncbi-tools++/objects/blast/.gitignore include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply.hpp include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply_.hpp include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reque.hpp @@ -743,6 +760,8 @@ include/ncbi-tools++/objects/blast/blast__.hpp include/ncbi-tools++/objects/blast/blastclient.hpp include/ncbi-tools++/objects/blast/blastclient_.hpp include/ncbi-tools++/objects/blast/names.hpp +include/ncbi-tools++/objects/blastdb/.cvsignore +include/ncbi-tools++/objects/blastdb/.gitignore include/ncbi-tools++/objects/blastdb/Blast_db_mask_info.hpp include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp include/ncbi-tools++/objects/blastdb/Blast_def_line.hpp @@ -756,6 +775,8 @@ include/ncbi-tools++/objects/blastdb/Blast_mask_list_. include/ncbi-tools++/objects/blastdb/NCBI_BlastDL_module.hpp include/ncbi-tools++/objects/blastdb/blastdb__.hpp include/ncbi-tools++/objects/blastdb/defline_extra.hpp +include/ncbi-tools++/objects/blastxml/.cvsignore +include/ncbi-tools++/objects/blastxml/.gitignore include/ncbi-tools++/objects/blastxml/BlastOutput.hpp include/ncbi-tools++/objects/blastxml/BlastOutput_.hpp include/ncbi-tools++/objects/blastxml/Hit.hpp @@ -770,6 +791,8 @@ include/ncbi-tools++/objects/blastxml/Parameters_.hpp include/ncbi-tools++/objects/blastxml/Statistics.hpp include/ncbi-tools++/objects/blastxml/Statistics_.hpp include/ncbi-tools++/objects/blastxml/blastxml__.hpp +include/ncbi-tools++/objects/blastxml2/.cvsignore +include/ncbi-tools++/objects/blastxml2/.gitignore include/ncbi-tools++/objects/blastxml2/BlastOutput2.hpp include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp @@ -800,6 +823,8 @@ include/ncbi-tools++/objects/blastxml2/Statistics_.hpp include/ncbi-tools++/objects/blastxml2/Target.hpp include/ncbi-tools++/objects/blastxml2/Target_.hpp include/ncbi-tools++/objects/blastxml2/blastxml2__.hpp +include/ncbi-tools++/objects/cdd/.cvsignore +include/ncbi-tools++/objects/cdd/.gitignore include/ncbi-tools++/objects/cdd/Algorithm_type.hpp include/ncbi-tools++/objects/cdd/Algorithm_type_.hpp include/ncbi-tools++/objects/cdd/Align_annot.hpp @@ -868,6 +893,8 @@ include/ncbi-tools++/objects/cdd/Update_align_.hpp include/ncbi-tools++/objects/cdd/Update_comment.hpp include/ncbi-tools++/objects/cdd/Update_comment_.hpp include/ncbi-tools++/objects/cdd/cdd__.hpp +include/ncbi-tools++/objects/cn3d/.cvsignore +include/ncbi-tools++/objects/cn3d/.gitignore include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix.hpp include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix_.hpp include/ncbi-tools++/objects/cn3d/Cn3d_backbone_label_style.hpp @@ -910,12 +937,16 @@ include/ncbi-tools++/objects/cn3d/Cn3d_view_settings.h include/ncbi-tools++/objects/cn3d/Cn3d_view_settings_.hpp include/ncbi-tools++/objects/cn3d/NCBI_Cn3d_module.hpp include/ncbi-tools++/objects/cn3d/cn3d__.hpp +include/ncbi-tools++/objects/coords/.cvsignore +include/ncbi-tools++/objects/coords/.gitignore include/ncbi-tools++/objects/coords/HGVS_Coordinate.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set_.hpp include/ncbi-tools++/objects/coords/NCBI_HGVSCoordinate_module.hpp include/ncbi-tools++/objects/coords/objcoords__.hpp +include/ncbi-tools++/objects/docsum/.cvsignore +include/ncbi-tools++/objects/docsum/.gitignore include/ncbi-tools++/objects/docsum/Assay.hpp include/ncbi-tools++/objects/docsum/Assay_.hpp include/ncbi-tools++/objects/docsum/Assembly.hpp @@ -942,6 +973,8 @@ include/ncbi-tools++/objects/docsum/Rs_.hpp include/ncbi-tools++/objects/docsum/Ss.hpp include/ncbi-tools++/objects/docsum/Ss_.hpp include/ncbi-tools++/objects/docsum/docsum__.hpp +include/ncbi-tools++/objects/entrez2/.cvsignore +include/ncbi-tools++/objects/entrez2/.gitignore include/ncbi-tools++/objects/entrez2/E2Reply.hpp include/ncbi-tools++/objects/entrez2/E2Reply_.hpp include/ncbi-tools++/objects/entrez2/E2Request.hpp @@ -1020,6 +1053,8 @@ include/ncbi-tools++/objects/entrez2/NCBI_Entrez2_modu include/ncbi-tools++/objects/entrez2/entrez2__.hpp include/ncbi-tools++/objects/entrez2/entrez2_client.hpp include/ncbi-tools++/objects/entrez2/entrez2_client_.hpp +include/ncbi-tools++/objects/entrezgene/.cvsignore +include/ncbi-tools++/objects/entrezgene/.gitignore include/ncbi-tools++/objects/entrezgene/Entrezgene.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_Set.hpp @@ -1038,6 +1073,8 @@ include/ncbi-tools++/objects/entrezgene/Other_source_. include/ncbi-tools++/objects/entrezgene/Xtra_Terms.hpp include/ncbi-tools++/objects/entrezgene/Xtra_Terms_.hpp include/ncbi-tools++/objects/entrezgene/entrezgene__.hpp +include/ncbi-tools++/objects/featdef/.cvsignore +include/ncbi-tools++/objects/featdef/.gitignore include/ncbi-tools++/objects/featdef/FeatDef.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet_.hpp @@ -1052,6 +1089,8 @@ include/ncbi-tools++/objects/featdef/FeatMolType.hpp include/ncbi-tools++/objects/featdef/FeatMolType_.hpp include/ncbi-tools++/objects/featdef/NCBI_FeatDef_module.hpp include/ncbi-tools++/objects/featdef/featdef__.hpp +include/ncbi-tools++/objects/gbproj/.cvsignore +include/ncbi-tools++/objects/gbproj/.gitignore include/ncbi-tools++/objects/gbproj/AbstractProjectItem.hpp include/ncbi-tools++/objects/gbproj/AbstractProjectItem_.hpp include/ncbi-tools++/objects/gbproj/DummyObsoleteType.hpp @@ -1082,6 +1121,8 @@ include/ncbi-tools++/objects/gbproj/ViewMemento_.hpp include/ncbi-tools++/objects/gbproj/gbproj__.hpp include/ncbi-tools++/objects/gbproj/gbproj_export.h include/ncbi-tools++/objects/gbproj/igbproject.hpp +include/ncbi-tools++/objects/gbseq/.cvsignore +include/ncbi-tools++/objects/gbseq/.gitignore include/ncbi-tools++/objects/gbseq/GBAltSeqData.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqData_.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqItem.hpp @@ -1120,6 +1161,8 @@ include/ncbi-tools++/objects/gbseq/GBXref.hpp include/ncbi-tools++/objects/gbseq/GBXref_.hpp include/ncbi-tools++/objects/gbseq/NCBI_GBSeq_module.hpp include/ncbi-tools++/objects/gbseq/gbseq__.hpp +include/ncbi-tools++/objects/general/.cvsignore +include/ncbi-tools++/objects/general/.gitignore include/ncbi-tools++/objects/general/Date.hpp include/ncbi-tools++/objects/general/Date_.hpp include/ncbi-tools++/objects/general/Date_std.hpp @@ -1143,6 +1186,8 @@ include/ncbi-tools++/objects/general/general__.hpp include/ncbi-tools++/objects/general/general_exception.hpp include/ncbi-tools++/objects/general/general_macros.hpp include/ncbi-tools++/objects/general/uoconv.hpp +include/ncbi-tools++/objects/genesbyloc/.cvsignore +include/ncbi-tools++/objects/genesbyloc/.gitignore include/ncbi-tools++/objects/genesbyloc/GBL_Data.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Data_.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Gene.hpp @@ -1151,6 +1196,8 @@ include/ncbi-tools++/objects/genesbyloc/GBL_Reply.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Reply_.hpp include/ncbi-tools++/objects/genesbyloc/NCBI_GenesByLoc_module.hpp include/ncbi-tools++/objects/genesbyloc/genesbyloc__.hpp +include/ncbi-tools++/objects/genomecoll/.cvsignore +include/ncbi-tools++/objects/genomecoll/.gitignore include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp @@ -1161,28 +1208,20 @@ include/ncbi-tools++/objects/genomecoll/GCClient_Assem include/ncbi-tools++/objects/genomecoll/GCClient_AssemblyInfo_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI.hpp include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl.hpp include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_Error.hpp include/ncbi-tools++/objects/genomecoll/GCClient_Error_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo.hpp include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo_.hpp +include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx.hpp +include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx_.hpp include/ncbi-tools++/objects/genomecoll/GC_Assemblies.hpp include/ncbi-tools++/objects/genomecoll/GC_Assemblies_.hpp include/ncbi-tools++/objects/genomecoll/GC_Assembly.hpp @@ -1228,6 +1267,8 @@ include/ncbi-tools++/objects/genomecoll/gencoll_client include/ncbi-tools++/objects/genomecoll/genome_collection__.hpp include/ncbi-tools++/objects/genomecoll/genomic_collections_cli.hpp include/ncbi-tools++/objects/genomecoll/genomic_collections_cli_.hpp +include/ncbi-tools++/objects/homologene/.cvsignore +include/ncbi-tools++/objects/homologene/.gitignore include/ncbi-tools++/objects/homologene/HG_Alignment.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet_.hpp @@ -1256,6 +1297,8 @@ include/ncbi-tools++/objects/homologene/HG_Stats.hpp include/ncbi-tools++/objects/homologene/HG_Stats_.hpp include/ncbi-tools++/objects/homologene/HomoloGene_module.hpp include/ncbi-tools++/objects/homologene/homologene__.hpp +include/ncbi-tools++/objects/id1/.cvsignore +include/ncbi-tools++/objects/id1/.gitignore include/ncbi-tools++/objects/id1/Entry_complexities.hpp include/ncbi-tools++/objects/id1/Entry_complexities_.hpp include/ncbi-tools++/objects/id1/ID1SeqEntry_info.hpp @@ -1276,6 +1319,8 @@ include/ncbi-tools++/objects/id1/NCBI_ID1Access_module include/ncbi-tools++/objects/id1/id1__.hpp include/ncbi-tools++/objects/id1/id1_client.hpp include/ncbi-tools++/objects/id1/id1_client_.hpp +include/ncbi-tools++/objects/id2/.cvsignore +include/ncbi-tools++/objects/id2/.gitignore include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk.hpp include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk_.hpp include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Split_Info.hpp @@ -1336,6 +1381,8 @@ include/ncbi-tools++/objects/id2/id2_client.hpp include/ncbi-tools++/objects/id2/id2_client_.hpp include/ncbi-tools++/objects/id2/id2processor.hpp include/ncbi-tools++/objects/id2/id2processor_interface.hpp +include/ncbi-tools++/objects/insdseq/.cvsignore +include/ncbi-tools++/objects/insdseq/.gitignore include/ncbi-tools++/objects/insdseq/INSDAltSeqData.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqItem.hpp @@ -1374,6 +1421,8 @@ include/ncbi-tools++/objects/insdseq/INSDXref.hpp include/ncbi-tools++/objects/insdseq/INSDXref_.hpp include/ncbi-tools++/objects/insdseq/INSD_INSDSeq_module.hpp include/ncbi-tools++/objects/insdseq/insdseq__.hpp +include/ncbi-tools++/objects/macro/.cvsignore +include/ncbi-tools++/objects/macro/.gitignore include/ncbi-tools++/objects/macro/AECRParse_action.hpp include/ncbi-tools++/objects/macro/AECRParse_action_.hpp include/ncbi-tools++/objects/macro/AECR_action.hpp @@ -1734,12 +1783,16 @@ include/ncbi-tools++/objects/macro/Word_substitution_s include/ncbi-tools++/objects/macro/Xref_type.hpp include/ncbi-tools++/objects/macro/Xref_type_.hpp include/ncbi-tools++/objects/macro/macro__.hpp +include/ncbi-tools++/objects/medlars/.cvsignore +include/ncbi-tools++/objects/medlars/.gitignore include/ncbi-tools++/objects/medlars/Medlars_entry.hpp include/ncbi-tools++/objects/medlars/Medlars_entry_.hpp include/ncbi-tools++/objects/medlars/Medlars_record.hpp include/ncbi-tools++/objects/medlars/Medlars_record_.hpp include/ncbi-tools++/objects/medlars/NCBI_Medlars_module.hpp include/ncbi-tools++/objects/medlars/medlars__.hpp +include/ncbi-tools++/objects/medline/.cvsignore +include/ncbi-tools++/objects/medline/.gitignore include/ncbi-tools++/objects/medline/DocRef.hpp include/ncbi-tools++/objects/medline/DocRef_.hpp include/ncbi-tools++/objects/medline/Medline_entry.hpp @@ -1756,6 +1809,8 @@ include/ncbi-tools++/objects/medline/Medline_si.hpp include/ncbi-tools++/objects/medline/Medline_si_.hpp include/ncbi-tools++/objects/medline/NCBI_Medline_module.hpp include/ncbi-tools++/objects/medline/medline__.hpp +include/ncbi-tools++/objects/mim/.cvsignore +include/ncbi-tools++/objects/mim/.gitignore include/ncbi-tools++/objects/mim/Mim_allelic_variant.hpp include/ncbi-tools++/objects/mim/Mim_allelic_variant_.hpp include/ncbi-tools++/objects/mim/Mim_author.hpp @@ -1787,6 +1842,8 @@ include/ncbi-tools++/objects/mim/mim__.hpp include/ncbi-tools++/objects/misc/error_codes.hpp include/ncbi-tools++/objects/misc/sequence_macros.hpp include/ncbi-tools++/objects/misc/sequence_util_macros.hpp +include/ncbi-tools++/objects/mla/.cvsignore +include/ncbi-tools++/objects/mla/.gitignore include/ncbi-tools++/objects/mla/Error_val.hpp include/ncbi-tools++/objects/mla/Error_val_.hpp include/ncbi-tools++/objects/mla/Mla_back.hpp @@ -1803,6 +1860,8 @@ include/ncbi-tools++/objects/mla/Title_type_.hpp include/ncbi-tools++/objects/mla/mla__.hpp include/ncbi-tools++/objects/mla/mla_client.hpp include/ncbi-tools++/objects/mla/mla_client_.hpp +include/ncbi-tools++/objects/mmdb1/.cvsignore +include/ncbi-tools++/objects/mmdb1/.gitignore include/ncbi-tools++/objects/mmdb1/Atom.hpp include/ncbi-tools++/objects/mmdb1/Atom_.hpp include/ncbi-tools++/objects/mmdb1/Atom_id.hpp @@ -1864,6 +1923,8 @@ include/ncbi-tools++/objects/mmdb1/Residue_graph_pntr_ include/ncbi-tools++/objects/mmdb1/Residue_id.hpp include/ncbi-tools++/objects/mmdb1/Residue_id_.hpp include/ncbi-tools++/objects/mmdb1/mmdb1__.hpp +include/ncbi-tools++/objects/mmdb2/.cvsignore +include/ncbi-tools++/objects/mmdb2/.gitignore include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp @@ -1910,6 +1971,8 @@ include/ncbi-tools++/objects/mmdb2/T_mesh_.hpp include/ncbi-tools++/objects/mmdb2/Triangles.hpp include/ncbi-tools++/objects/mmdb2/Triangles_.hpp include/ncbi-tools++/objects/mmdb2/mmdb2__.hpp +include/ncbi-tools++/objects/mmdb3/.cvsignore +include/ncbi-tools++/objects/mmdb3/.gitignore include/ncbi-tools++/objects/mmdb3/Align_stats.hpp include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp @@ -1986,6 +2049,8 @@ include/ncbi-tools++/objects/mmdb3/Trans_matrix_.hpp include/ncbi-tools++/objects/mmdb3/Transform.hpp include/ncbi-tools++/objects/mmdb3/Transform_.hpp include/ncbi-tools++/objects/mmdb3/mmdb3__.hpp +include/ncbi-tools++/objects/ncbimime/.cvsignore +include/ncbi-tools++/objects/ncbimime/.gitignore include/ncbi-tools++/objects/ncbimime/Biostruc_align.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_seq.hpp @@ -2006,6 +2071,8 @@ include/ncbi-tools++/objects/ncbimime/NCBI_Mime_module include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1.hpp include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1_.hpp include/ncbi-tools++/objects/ncbimime/ncbimime__.hpp +include/ncbi-tools++/objects/objprt/.cvsignore +include/ncbi-tools++/objects/objprt/.gitignore include/ncbi-tools++/objects/objprt/NCBI_ObjPrt_module.hpp include/ncbi-tools++/objects/objprt/PrintForm.hpp include/ncbi-tools++/objects/objprt/PrintFormBlock.hpp @@ -2028,6 +2095,8 @@ include/ncbi-tools++/objects/objprt/TemplateName_.hpp include/ncbi-tools++/objects/objprt/UserFormat.hpp include/ncbi-tools++/objects/objprt/UserFormat_.hpp include/ncbi-tools++/objects/objprt/objprt__.hpp +include/ncbi-tools++/objects/omssa/.cvsignore +include/ncbi-tools++/objects/omssa/.gitignore include/ncbi-tools++/objects/omssa/MSBioseq.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet_.hpp @@ -2114,6 +2183,8 @@ include/ncbi-tools++/objects/omssa/NameValue.hpp include/ncbi-tools++/objects/omssa/NameValue_.hpp include/ncbi-tools++/objects/omssa/OMSSA_module.hpp include/ncbi-tools++/objects/omssa/omssa__.hpp +include/ncbi-tools++/objects/pcassay/.cvsignore +include/ncbi-tools++/objects/pcassay/.gitignore include/ncbi-tools++/objects/pcassay/NCBI_PCAssay_module.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef_.hpp @@ -2148,6 +2219,8 @@ include/ncbi-tools++/objects/pcassay/PC_RealMinMax_.hp include/ncbi-tools++/objects/pcassay/PC_ResultType.hpp include/ncbi-tools++/objects/pcassay/PC_ResultType_.hpp include/ncbi-tools++/objects/pcassay/pcassay__.hpp +include/ncbi-tools++/objects/pcsubstance/.cvsignore +include/ncbi-tools++/objects/pcsubstance/.gitignore include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt_.hpp @@ -2224,6 +2297,8 @@ include/ncbi-tools++/objects/pcsubstance/PC_Urn_.hpp include/ncbi-tools++/objects/pcsubstance/PC_XRefData.hpp include/ncbi-tools++/objects/pcsubstance/PC_XRefData_.hpp include/ncbi-tools++/objects/pcsubstance/pcsubstance__.hpp +include/ncbi-tools++/objects/proj/.cvsignore +include/ncbi-tools++/objects/proj/.gitignore include/ncbi-tools++/objects/proj/NCBI_Project_module.hpp include/ncbi-tools++/objects/proj/Projdesc.hpp include/ncbi-tools++/objects/proj/Projdesc_.hpp @@ -2236,6 +2311,8 @@ include/ncbi-tools++/objects/proj/Project_id_.hpp include/ncbi-tools++/objects/proj/Project_item.hpp include/ncbi-tools++/objects/proj/Project_item_.hpp include/ncbi-tools++/objects/proj/proj__.hpp +include/ncbi-tools++/objects/pub/.cvsignore +include/ncbi-tools++/objects/pub/.gitignore include/ncbi-tools++/objects/pub/NCBI_Pub_module.hpp include/ncbi-tools++/objects/pub/Pub.hpp include/ncbi-tools++/objects/pub/Pub_.hpp @@ -2245,12 +2322,16 @@ include/ncbi-tools++/objects/pub/Pub_set.hpp include/ncbi-tools++/objects/pub/Pub_set_.hpp include/ncbi-tools++/objects/pub/pub__.hpp include/ncbi-tools++/objects/pub/pub_macros.hpp +include/ncbi-tools++/objects/pubmed/.cvsignore +include/ncbi-tools++/objects/pubmed/.gitignore include/ncbi-tools++/objects/pubmed/NCBI_PubMed_module.hpp include/ncbi-tools++/objects/pubmed/Pubmed_entry.hpp include/ncbi-tools++/objects/pubmed/Pubmed_entry_.hpp include/ncbi-tools++/objects/pubmed/Pubmed_url.hpp include/ncbi-tools++/objects/pubmed/Pubmed_url_.hpp include/ncbi-tools++/objects/pubmed/pubmed__.hpp +include/ncbi-tools++/objects/remap/.cvsignore +include/ncbi-tools++/objects/remap/.gitignore include/ncbi-tools++/objects/remap/NCBI_Remap_module.hpp include/ncbi-tools++/objects/remap/RMReply.hpp include/ncbi-tools++/objects/remap/RMReply_.hpp @@ -2271,6 +2352,8 @@ include/ncbi-tools++/objects/remap/Remap_result_.hpp include/ncbi-tools++/objects/remap/remap__.hpp include/ncbi-tools++/objects/remap/remap_client.hpp include/ncbi-tools++/objects/remap/remap_client_.hpp +include/ncbi-tools++/objects/scoremat/.cvsignore +include/ncbi-tools++/objects/scoremat/.gitignore include/ncbi-tools++/objects/scoremat/BlockProperty.hpp include/ncbi-tools++/objects/scoremat/BlockProperty_.hpp include/ncbi-tools++/objects/scoremat/CoreBlock.hpp @@ -2297,6 +2380,8 @@ include/ncbi-tools++/objects/scoremat/Site_annot_.hpp include/ncbi-tools++/objects/scoremat/Site_annot_set.hpp include/ncbi-tools++/objects/scoremat/Site_annot_set_.hpp include/ncbi-tools++/objects/scoremat/scoremat__.hpp +include/ncbi-tools++/objects/seq/.cvsignore +include/ncbi-tools++/objects/seq/.gitignore include/ncbi-tools++/objects/seq/Align_def.hpp include/ncbi-tools++/objects/seq/Align_def_.hpp include/ncbi-tools++/objects/seq/Annot_descr.hpp @@ -2398,6 +2483,8 @@ include/ncbi-tools++/objects/seq/seqport_util.hpp include/ncbi-tools++/objects/seq/so_map.hpp include/ncbi-tools++/objects/seq/sofa_map.hpp include/ncbi-tools++/objects/seq/sofa_type.hpp +include/ncbi-tools++/objects/seqalign/.cvsignore +include/ncbi-tools++/objects/seqalign/.gitignore include/ncbi-tools++/objects/seqalign/Dense_diag.hpp include/ncbi-tools++/objects/seqalign/Dense_diag_.hpp include/ncbi-tools++/objects/seqalign/Dense_seg.hpp @@ -2438,6 +2525,8 @@ include/ncbi-tools++/objects/seqalign/Std_seg_.hpp include/ncbi-tools++/objects/seqalign/seqalign__.hpp include/ncbi-tools++/objects/seqalign/seqalign_exception.hpp include/ncbi-tools++/objects/seqalign/seqalign_macros.hpp +include/ncbi-tools++/objects/seqblock/.cvsignore +include/ncbi-tools++/objects/seqblock/.gitignore include/ncbi-tools++/objects/seqblock/EMBL_General_module.hpp include/ncbi-tools++/objects/seqblock/EMBL_block.hpp include/ncbi-tools++/objects/seqblock/EMBL_block_.hpp @@ -2466,6 +2555,8 @@ include/ncbi-tools++/objects/seqblock/SP_block.hpp include/ncbi-tools++/objects/seqblock/SP_block_.hpp include/ncbi-tools++/objects/seqblock/seqblock__.hpp include/ncbi-tools++/objects/seqblock/seqblock_macros.hpp +include/ncbi-tools++/objects/seqcode/.cvsignore +include/ncbi-tools++/objects/seqcode/.gitignore include/ncbi-tools++/objects/seqcode/NCBI_SeqCode_module.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set_.hpp @@ -2476,6 +2567,8 @@ include/ncbi-tools++/objects/seqcode/Seq_code_type_.hp include/ncbi-tools++/objects/seqcode/Seq_map_table.hpp include/ncbi-tools++/objects/seqcode/Seq_map_table_.hpp include/ncbi-tools++/objects/seqcode/seqcode__.hpp +include/ncbi-tools++/objects/seqedit/.cvsignore +include/ncbi-tools++/objects/seqedit/.gitignore include/ncbi-tools++/objects/seqedit/NCBI_SeqEdit_module.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_.hpp @@ -2524,6 +2617,8 @@ include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_SetDe include/ncbi-tools++/objects/seqedit/SeqEdit_Id.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Id_.hpp include/ncbi-tools++/objects/seqedit/seqedit__.hpp +include/ncbi-tools++/objects/seqfeat/.cvsignore +include/ncbi-tools++/objects/seqfeat/.gitignore include/ncbi-tools++/objects/seqfeat/BinomialOrgName.hpp include/ncbi-tools++/objects/seqfeat/BinomialOrgName_.hpp include/ncbi-tools++/objects/seqfeat/BioSource.hpp @@ -2644,6 +2739,8 @@ include/ncbi-tools++/objects/seqfeat/Variation_ref.hpp include/ncbi-tools++/objects/seqfeat/Variation_ref_.hpp include/ncbi-tools++/objects/seqfeat/seqfeat__.hpp include/ncbi-tools++/objects/seqfeat/seqfeat_macros.hpp +include/ncbi-tools++/objects/seqloc/.cvsignore +include/ncbi-tools++/objects/seqloc/.gitignore include/ncbi-tools++/objects/seqloc/Giimport_id.hpp include/ncbi-tools++/objects/seqloc/Giimport_id_.hpp include/ncbi-tools++/objects/seqloc/NCBI_Seqloc_module.hpp @@ -2679,6 +2776,8 @@ include/ncbi-tools++/objects/seqloc/Textseq_id.hpp include/ncbi-tools++/objects/seqloc/Textseq_id_.hpp include/ncbi-tools++/objects/seqloc/seqloc__.hpp include/ncbi-tools++/objects/seqloc/seqloc_macros.hpp +include/ncbi-tools++/objects/seqres/.cvsignore +include/ncbi-tools++/objects/seqres/.gitignore include/ncbi-tools++/objects/seqres/Byte_graph.hpp include/ncbi-tools++/objects/seqres/Byte_graph_.hpp include/ncbi-tools++/objects/seqres/Int_graph.hpp @@ -2689,6 +2788,8 @@ include/ncbi-tools++/objects/seqres/Real_graph_.hpp include/ncbi-tools++/objects/seqres/Seq_graph.hpp include/ncbi-tools++/objects/seqres/Seq_graph_.hpp include/ncbi-tools++/objects/seqres/seqres__.hpp +include/ncbi-tools++/objects/seqset/.cvsignore +include/ncbi-tools++/objects/seqset/.gitignore include/ncbi-tools++/objects/seqset/Bioseq_set.hpp include/ncbi-tools++/objects/seqset/Bioseq_set_.hpp include/ncbi-tools++/objects/seqset/NCBI_Seqset_module.hpp @@ -2698,6 +2799,8 @@ include/ncbi-tools++/objects/seqset/gb_release_file.hp include/ncbi-tools++/objects/seqset/seqset__.hpp include/ncbi-tools++/objects/seqset/seqset_exception.hpp include/ncbi-tools++/objects/seqset/seqset_macros.hpp +include/ncbi-tools++/objects/seqsplit/.cvsignore +include/ncbi-tools++/objects/seqsplit/.gitignore include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids_.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Info.hpp @@ -2754,6 +2857,8 @@ include/ncbi-tools++/objects/seqsplit/ID2S_Split_Info. include/ncbi-tools++/objects/seqsplit/ID2S_Split_Info_.hpp include/ncbi-tools++/objects/seqsplit/NCBI_Seq_split_module.hpp include/ncbi-tools++/objects/seqsplit/seqsplit__.hpp +include/ncbi-tools++/objects/seqtable/.cvsignore +include/ncbi-tools++/objects/seqtable/.gitignore include/ncbi-tools++/objects/seqtable/BVector_data.hpp include/ncbi-tools++/objects/seqtable/BVector_data_.hpp include/ncbi-tools++/objects/seqtable/CommonBytes_table.hpp @@ -2780,6 +2885,8 @@ include/ncbi-tools++/objects/seqtable/Seq_table_.hpp include/ncbi-tools++/objects/seqtable/impl/delta_cache.hpp include/ncbi-tools++/objects/seqtable/seq_table_exception.hpp include/ncbi-tools++/objects/seqtable/seqtable__.hpp +include/ncbi-tools++/objects/seqtest/.cvsignore +include/ncbi-tools++/objects/seqtest/.gitignore include/ncbi-tools++/objects/seqtest/NCBI_SeqTest_module.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults_.hpp @@ -2788,6 +2895,8 @@ include/ncbi-tools++/objects/seqtest/Seq_test_result_. include/ncbi-tools++/objects/seqtest/Seq_test_result_set.hpp include/ncbi-tools++/objects/seqtest/Seq_test_result_set_.hpp include/ncbi-tools++/objects/seqtest/seqtest__.hpp +include/ncbi-tools++/objects/submit/.cvsignore +include/ncbi-tools++/objects/submit/.gitignore include/ncbi-tools++/objects/submit/Contact_info.hpp include/ncbi-tools++/objects/submit/Contact_info_.hpp include/ncbi-tools++/objects/submit/NCBI_Submit_module.hpp @@ -2797,6 +2906,8 @@ include/ncbi-tools++/objects/submit/Submit_block.hpp include/ncbi-tools++/objects/submit/Submit_block_.hpp include/ncbi-tools++/objects/submit/submit__.hpp include/ncbi-tools++/objects/submit/submit_macros.hpp +include/ncbi-tools++/objects/taxon1/.cvsignore +include/ncbi-tools++/objects/taxon1/.gitignore include/ncbi-tools++/objects/taxon1/NCBI_Taxon1_module.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data_.hpp @@ -2812,8 +2923,11 @@ include/ncbi-tools++/objects/taxon1/Taxon1_resp.hpp include/ncbi-tools++/objects/taxon1/Taxon1_resp_.hpp include/ncbi-tools++/objects/taxon1/Taxon2_data.hpp include/ncbi-tools++/objects/taxon1/Taxon2_data_.hpp +include/ncbi-tools++/objects/taxon1/local_taxon.hpp include/ncbi-tools++/objects/taxon1/taxon1.hpp include/ncbi-tools++/objects/taxon1/taxon1__.hpp +include/ncbi-tools++/objects/taxon3/.cvsignore +include/ncbi-tools++/objects/taxon3/.gitignore include/ncbi-tools++/objects/taxon3/NCBI_Taxon3_module.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt_.hpp @@ -2837,12 +2951,16 @@ include/ncbi-tools++/objects/taxon3/cached_taxon3.hpp include/ncbi-tools++/objects/taxon3/itaxon3.hpp include/ncbi-tools++/objects/taxon3/taxon3.hpp include/ncbi-tools++/objects/taxon3/taxon3__.hpp +include/ncbi-tools++/objects/tinyseq/.cvsignore +include/ncbi-tools++/objects/tinyseq/.gitignore include/ncbi-tools++/objects/tinyseq/NCBI_TSeq_module.hpp include/ncbi-tools++/objects/tinyseq/TSeq.hpp include/ncbi-tools++/objects/tinyseq/TSeqSet.hpp include/ncbi-tools++/objects/tinyseq/TSeqSet_.hpp include/ncbi-tools++/objects/tinyseq/TSeq_.hpp include/ncbi-tools++/objects/tinyseq/tinyseq__.hpp +include/ncbi-tools++/objects/trackmgr/.cvsignore +include/ncbi-tools++/objects/trackmgr/.gitignore include/ncbi-tools++/objects/trackmgr/NCBI_TrackManager_module.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel_.hpp @@ -2874,6 +2992,10 @@ include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDReq include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDRequest_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetRequest.hpp @@ -2884,6 +3006,8 @@ include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserT include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_DHubId.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_DHubId_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DatasetItem.hpp @@ -2900,6 +3024,10 @@ include/ncbi-tools++/objects/trackmgr/TMgr_DisplayTrac include/ncbi-tools++/objects/trackmgr/TMgr_DisplayTrack_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext.hpp include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_Hub.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_Hub_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Identity.hpp include/ncbi-tools++/objects/trackmgr/TMgr_IdentityId.hpp include/ncbi-tools++/objects/trackmgr/TMgr_IdentityIdType.hpp @@ -2924,6 +3052,8 @@ include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserT include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReques_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Reply.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Reply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Request.hpp @@ -2940,6 +3070,8 @@ include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextReq.hpp @@ -2966,9 +3098,12 @@ include/ncbi-tools++/objects/trackmgr/TMgr_TrackSetTyp include/ncbi-tools++/objects/trackmgr/TMgr_TrackSet_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat.hpp include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest_.hpp include/ncbi-tools++/objects/trackmgr/blast_client.hpp +include/ncbi-tools++/objects/trackmgr/createremotetrack_client.hpp include/ncbi-tools++/objects/trackmgr/createtrackset_client.hpp include/ncbi-tools++/objects/trackmgr/createusertrack_client.hpp include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp @@ -2984,12 +3119,16 @@ include/ncbi-tools++/objects/trackmgr/trackmgr_client. include/ncbi-tools++/objects/trackmgr/trackmgr_client_.hpp include/ncbi-tools++/objects/trackmgr/trackmgr_export.h include/ncbi-tools++/objects/trackmgr/trackset_client.hpp +include/ncbi-tools++/objects/valerr/.cvsignore +include/ncbi-tools++/objects/valerr/.gitignore include/ncbi-tools++/objects/valerr/NCBI_ValErrors_module.hpp include/ncbi-tools++/objects/valerr/ValidErrItem.hpp include/ncbi-tools++/objects/valerr/ValidErrItem_.hpp include/ncbi-tools++/objects/valerr/ValidError.hpp include/ncbi-tools++/objects/valerr/ValidError_.hpp include/ncbi-tools++/objects/valerr/valerr__.hpp +include/ncbi-tools++/objects/valid/.cvsignore +include/ncbi-tools++/objects/valid/.gitignore include/ncbi-tools++/objects/valid/Comment_rule.hpp include/ncbi-tools++/objects/valid/Comment_rule_.hpp include/ncbi-tools++/objects/valid/Comment_set.hpp @@ -3008,6 +3147,8 @@ include/ncbi-tools++/objects/valid/Phrase_list_.hpp include/ncbi-tools++/objects/valid/Severity_level.hpp include/ncbi-tools++/objects/valid/Severity_level_.hpp include/ncbi-tools++/objects/valid/valid__.hpp +include/ncbi-tools++/objects/variation/.cvsignore +include/ncbi-tools++/objects/variation/.gitignore include/ncbi-tools++/objects/variation/NCBI_VariationPackage_module.hpp include/ncbi-tools++/objects/variation/VariantPlacement.hpp include/ncbi-tools++/objects/variation/VariantPlacement_.hpp @@ -3018,6 +3159,32 @@ include/ncbi-tools++/objects/variation/VariationMethod include/ncbi-tools++/objects/variation/VariationMethod_.hpp include/ncbi-tools++/objects/variation/Variation_.hpp include/ncbi-tools++/objects/variation/variation__.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.cvsignore +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.gitignore +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/NCBI_search_by_rsid_module.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/search_by_rsid__.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.cvsignore +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.gitignore +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/NCBI_dbsnp_tooltips_module.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/dbsnp_tooltip_service__.hpp +include/ncbi-tools++/objects/varrep/.cvsignore +include/ncbi-tools++/objects/varrep/.gitignore include/ncbi-tools++/objects/varrep/AaInterval.hpp include/ncbi-tools++/objects/varrep/AaInterval_.hpp include/ncbi-tools++/objects/varrep/AaLocation.hpp @@ -3265,6 +3432,8 @@ include/ncbi-tools++/objtools/blast/gene_info_reader/f include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info_reader.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/column_reader.hpp +include/ncbi-tools++/objtools/blast/seqdb_reader/impl/lmdb++.h +include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbcol.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbfile.hpp @@ -3276,9 +3445,11 @@ include/ncbi-tools++/objtools/blast/seqdb_reader/seqdb include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbblob.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbcommon.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbexpert.hpp +include/ncbi-tools++/objtools/blast/seqdb_reader/seqidlist_reader.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/build_db.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/impl/criteria.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/multisource_util.hpp +include/ncbi-tools++/objtools/blast/seqdb_writer/seqidlist_writer.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/taxid_set.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_convert.hpp @@ -3286,8 +3457,10 @@ include/ncbi-tools++/objtools/blast/seqdb_writer/write include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_files.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_general.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_isam.hpp +include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_lmdb.hpp include/ncbi-tools++/objtools/blast/services/blast_services.hpp include/ncbi-tools++/objtools/cleanup/autogenerated_cleanup.hpp +include/ncbi-tools++/objtools/cleanup/capitalization_string.hpp include/ncbi-tools++/objtools/cleanup/cleanup.hpp include/ncbi-tools++/objtools/cleanup/cleanup_change.hpp include/ncbi-tools++/objtools/cleanup/newcleanup.hpp @@ -3340,6 +3513,7 @@ include/ncbi-tools++/objtools/data_loaders/genbank/seq include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp include/ncbi-tools++/objtools/data_loaders/loaders.hpp +include/ncbi-tools++/objtools/edit/apply_mods.hpp include/ncbi-tools++/objtools/edit/apply_object.hpp include/ncbi-tools++/objtools/edit/autodef.hpp include/ncbi-tools++/objtools/edit/autodef_options.hpp @@ -3348,8 +3522,11 @@ include/ncbi-tools++/objtools/edit/autodef_with_tax.hp include/ncbi-tools++/objtools/edit/capitalization_string.hpp include/ncbi-tools++/objtools/edit/cds_fix.hpp include/ncbi-tools++/objtools/edit/dblink_field.hpp +include/ncbi-tools++/objtools/edit/edit_error.hpp include/ncbi-tools++/objtools/edit/edit_exception.hpp +include/ncbi-tools++/objtools/edit/external_annots.hpp include/ncbi-tools++/objtools/edit/feattable_edit.hpp +include/ncbi-tools++/objtools/edit/feature_propagate.hpp include/ncbi-tools++/objtools/edit/field_handler.hpp include/ncbi-tools++/objtools/edit/gap_trim.hpp include/ncbi-tools++/objtools/edit/gaps_edit.hpp @@ -3369,6 +3546,7 @@ include/ncbi-tools++/objtools/edit/source_edit.hpp include/ncbi-tools++/objtools/edit/string_constraint.hpp include/ncbi-tools++/objtools/edit/struc_comm_field.hpp include/ncbi-tools++/objtools/edit/text_desc_field.hpp +include/ncbi-tools++/objtools/edit/text_object_description.hpp include/ncbi-tools++/objtools/error_codes.hpp include/ncbi-tools++/objtools/format/cigar_formatter.hpp include/ncbi-tools++/objtools/format/context.hpp @@ -3423,6 +3601,8 @@ include/ncbi-tools++/objtools/format/items/wgs_item.hp include/ncbi-tools++/objtools/format/ostream_text_ostream.hpp include/ncbi-tools++/objtools/format/sam_formatter.hpp include/ncbi-tools++/objtools/format/text_ostream.hpp +include/ncbi-tools++/objtools/logging/listener.hpp +include/ncbi-tools++/objtools/logging/message.hpp include/ncbi-tools++/objtools/readers/agp_converter.hpp include/ncbi-tools++/objtools/readers/agp_read.hpp include/ncbi-tools++/objtools/readers/agp_seq_entry.hpp @@ -3580,8 +3760,11 @@ include/ncbi-tools++/util/bitset/bitset_pool.hpp include/ncbi-tools++/util/bitset/bm.h include/ncbi-tools++/util/bitset/bmalgo.h include/ncbi-tools++/util/bitset/bmalgo_impl.h +include/ncbi-tools++/util/bitset/bmalgo_similarity.h include/ncbi-tools++/util/bitset/bmalloc.h +include/ncbi-tools++/util/bitset/bmavx2.h include/ncbi-tools++/util/bitset/bmblocks.h +include/ncbi-tools++/util/bitset/bmbuffer.h include/ncbi-tools++/util/bitset/bmconst.h include/ncbi-tools++/util/bitset/bmdbg.h include/ncbi-tools++/util/bitset/bmdef.h @@ -3590,12 +3773,16 @@ include/ncbi-tools++/util/bitset/bmfwd.h include/ncbi-tools++/util/bitset/bmgamma.h include/ncbi-tools++/util/bitset/bmrandom.h include/ncbi-tools++/util/bitset/bmserial.h +include/ncbi-tools++/util/bitset/bmsimd.h include/ncbi-tools++/util/bitset/bmsparsevec.h include/ncbi-tools++/util/bitset/bmsparsevec_algo.h +include/ncbi-tools++/util/bitset/bmsparsevec_compr.h include/ncbi-tools++/util/bitset/bmsparsevec_serial.h +include/ncbi-tools++/util/bitset/bmsparsevec_util.h include/ncbi-tools++/util/bitset/bmsse2.h include/ncbi-tools++/util/bitset/bmsse4.h include/ncbi-tools++/util/bitset/bmsse_util.h +include/ncbi-tools++/util/bitset/bmtimer.h include/ncbi-tools++/util/bitset/bmtrans.h include/ncbi-tools++/util/bitset/bmundef.h include/ncbi-tools++/util/bitset/bmutil.h @@ -3608,6 +3795,7 @@ include/ncbi-tools++/util/bitset/ncbi_bitset_util.hpp include/ncbi-tools++/util/bitset/readme include/ncbi-tools++/util/buffer_writer.hpp include/ncbi-tools++/util/bytesrc.hpp +include/ncbi-tools++/util/cache/cache_async.hpp include/ncbi-tools++/util/cache/cache_ref.hpp include/ncbi-tools++/util/cache/icache.hpp include/ncbi-tools++/util/cache/icache_cf.hpp @@ -3649,6 +3837,8 @@ include/ncbi-tools++/util/lightstr.hpp include/ncbi-tools++/util/limited_size_map.hpp include/ncbi-tools++/util/line_reader.hpp include/ncbi-tools++/util/linkedset.hpp +include/ncbi-tools++/util/lmdb/lmdb.h +include/ncbi-tools++/util/lmdbxx/lmdb++.h include/ncbi-tools++/util/lock_vector.hpp include/ncbi-tools++/util/logrotate.hpp include/ncbi-tools++/util/mask_regexp.hpp @@ -3658,6 +3848,7 @@ include/ncbi-tools++/util/math/promote.hpp include/ncbi-tools++/util/md5.hpp include/ncbi-tools++/util/miscmath.h include/ncbi-tools++/util/multi_writer.hpp +include/ncbi-tools++/util/multipattern_search.hpp include/ncbi-tools++/util/mutex_pool.hpp include/ncbi-tools++/util/ncbi_cache.hpp include/ncbi-tools++/util/ncbi_table.hpp @@ -3766,6 +3957,8 @@ lib/ncbi-tools++/libdbapi.a lib/ncbi-tools++/libdbapi_driver-dll.so lib/ncbi-tools++/libdbapi_driver-static.a lib/ncbi-tools++/libdbapi_driver.a +lib/ncbi-tools++/libdbsnp_tooltip_service-static.a +lib/ncbi-tools++/libdbsnp_tooltip_service.a lib/ncbi-tools++/libdocsum-static.a lib/ncbi-tools++/libdocsum.a lib/ncbi-tools++/libentrez2-static.a @@ -3806,6 +3999,8 @@ lib/ncbi-tools++/libigblast-static.a lib/ncbi-tools++/libigblast.a lib/ncbi-tools++/libinsdseq-static.a lib/ncbi-tools++/libinsdseq.a +lib/ncbi-tools++/liblocal_taxon-static.a +lib/ncbi-tools++/liblocal_taxon.a lib/ncbi-tools++/libmacro-static.a lib/ncbi-tools++/libmacro.a lib/ncbi-tools++/libmedlars-static.a @@ -3876,6 +4071,8 @@ lib/ncbi-tools++/libremapcli-static.a lib/ncbi-tools++/libremapcli.a lib/ncbi-tools++/libscoremat-static.a lib/ncbi-tools++/libscoremat.a +lib/ncbi-tools++/libsearchbyrsid-static.a +lib/ncbi-tools++/libsearchbyrsid.a lib/ncbi-tools++/libseq-static.a lib/ncbi-tools++/libseq.a lib/ncbi-tools++/libseqcode-static.a @@ -3956,6 +4153,8 @@ lib/ncbi-tools++/libxformat-static.a lib/ncbi-tools++/libxformat.a lib/ncbi-tools++/libxhtml-static.a lib/ncbi-tools++/libxhtml.a +lib/ncbi-tools++/libxlogging-static.a +lib/ncbi-tools++/libxlogging.a lib/ncbi-tools++/libxncbi-static.a lib/ncbi-tools++/libxncbi.a lib/ncbi-tools++/libxnetblast-static.a @@ -3986,3 +4185,4 @@ lib/ncbi-tools++/libxutil-static.a lib/ncbi-tools++/libxutil.a lib/ncbi-tools++/libxxconnect-static.a lib/ncbi-tools++/libxxconnect.a +@dir include/ncbi-tools++/objtools/data_loaders/genbank/psg
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