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biology/ncbi-blast+: Upgrade to 2.8.1

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Remove hacks that are no longer needed
New patch for endian.h location

Approved by:    jrm (mentor, implicit)
This commit is contained in:
Jason W. Bacon 2019-01-01 19:55:44 +00:00
parent 70ae0602af
commit 6a0e6d81f2
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=488931
4 changed files with 244 additions and 32 deletions
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25
biology/ncbi-blast+/Makefile
View file

@ -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+/${PORTVERSION}/
@ -33,34 +32,22 @@ LIB_DEPENDS= libpcre.so:devel/pcre \
RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils
USES= compiler:openmp gmake shebangfix perl5 python
USE_LDCONFIG= yes
SHEBANG_FILES= src/app/blast/legacy_blast.pl \
src/app/blast/update_blastdb.pl \
src/app/winmasker/windowmasker_2.2.22_adapter.py
USE_LDCONFIG= yes
src/app/winmasker/windowmasker_2.2.22_adapter.py \
src/app/blast/get_species_taxids.sh
GNU_CONFIGURE= yes
# The test for amq can hang, but amq is not needed so just avoid the test
CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
# configure chooses /usr/local/bin/ar with no flags
# FreeBSD boost port flagged by configure as untested version
# --libdir=${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
@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11

6
biology/ncbi-blast+/distinfo
View file

@ -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

25
biology/ncbi-blast+/files/patch-src_util_checksum_farmhash_farmhash.h Normal file
View file

@ -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

220
biology/ncbi-blast+/pkg-plist
View file

@ -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_.hpp
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.hpp
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_module.hpp
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_.hpp
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_AssemblyInfo.hpp
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__.hpp
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.hpp
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_set_.hpp
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_.hpp
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.hpp
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_.hpp
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_.hpp
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_SetDescr_.hpp
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.hpp
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.hpp
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_.hpp
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_BlastRIDRequest.hpp
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_CreateUserTrackReply.hpp
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_DisplayTrackRequest_.hpp
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_RemoveUserTrackReques.hpp
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_TrackSetType_.hpp
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.hpp
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.hpp
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/file_utils.hpp
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.hpp
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/writedb_error.hpp
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/seqref.hpp
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.hpp
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.hpp
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