Date: Tue, 27 Mar 2018 18:04:21 +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: r465726 - in head/biology/ncbi-blast+: . files Message-ID: <201803271804.w2RI4Lgb080523@repo.freebsd.org>
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Author: jwb Date: Tue Mar 27 18:04:21 2018 New Revision: 465726 URL: https://svnweb.freebsd.org/changeset/ports/465726 Log: biology/ncbi-blast+: Upgrade to 2.7.1 Patch Makefile.in.top to cleanly support DESTDIR Also resolves 225002, conflict with libproj PR: 226037 Reported by: wen Reviewed by: mat rene Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14854 Modified: head/biology/ncbi-blast+/Makefile head/biology/ncbi-blast+/distinfo head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top head/biology/ncbi-blast+/files/patch-src_build-system_configure head/biology/ncbi-blast+/pkg-descr head/biology/ncbi-blast+/pkg-plist Modified: head/biology/ncbi-blast+/Makefile ============================================================================== --- head/biology/ncbi-blast+/Makefile Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/Makefile Tue Mar 27 18:04:21 2018 (r465726) @@ -1,12 +1,10 @@ # $FreeBSD$ -PORTNAME= blast+ -PORTVERSION= 2.5.0 -PORTREVISION= 3 -CATEGORIES= biology -MASTER_SITES= http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \ - http://acadix.biz/Ports/distfiles/ -PKGNAMEPREFIX= ncbi- +PORTNAME= ncbi-blast+ +DISTVERSION= 2.7.1 +CATEGORIES= biology perl5 python +MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ + https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ DISTNAME= ncbi-blast-${PORTVERSION}+-src MAINTAINER= jwb@FreeBSD.org @@ -15,43 +13,55 @@ COMMENT= NCBI implementation of Basic Local Alignment LICENSE= PD LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE -LIB_DEPENDS= libpcre.so:devel/pcre +LIB_DEPENDS= libpcre.so:devel/pcre \ + liblmdb.so:databases/lmdb \ + liblzo2.so:archivers/lzo2 \ + libgnutls.so:security/gnutls \ + libtspi.so:security/trousers \ + libgmp.so:math/gmp \ + libidn2.so:dns/libidn2 \ + libnettle.so:security/nettle \ + libhogweed.so:security/nettle \ + libtasn1.so:security/libtasn1 \ + libp11-kit.so:security/p11-kit \ + libgcrypt.so:security/libgcrypt \ + libgpg-error.so:security/libgpg-error \ + libsqlite3.so:databases/sqlite3 RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils -WRKSRC= ${WRKDIR}/${DISTNAME}/c++ - -GNU_CONFIGURE= yes -USES= gmake shebangfix perl5 python +USES= compiler:openmp gmake shebangfix perl5 python SHEBANG_FILES= src/app/blast/legacy_blast.pl \ src/app/blast/update_blastdb.pl \ src/app/winmasker/windowmasker_2.2.22_adapter.py - -MAKE_JOBS_UNSAFE= yes - -# Requires openmp -USE_GCC= yes USE_LDCONFIG= yes +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 -CONFIGURE_ARGS+=AR="ar cr" --without-boost +# --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++ +WRKSRC_SUBDIR= c++ + +MAKE_JOBS_UNSAFE= yes + # Fix "undefined _ThreadRuneLocale" error on 10.0 # Fix unknown options in configure -# Add staging support to configure-generated Makefile post-patch: - ${REINPLACE_CMD} \ + @${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 - ${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \ - ${WRKSRC}/src/build-system/Makefile.in.top post-install: - ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so + @${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra + @${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11 + @${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so .include <bsd.port.mk> Modified: head/biology/ncbi-blast+/distinfo ============================================================================== --- head/biology/ncbi-blast+/distinfo Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/distinfo Tue Mar 27 18:04:21 2018 (r465726) @@ -1,3 +1,3 @@ -TIMESTAMP = 1480648908 -SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54 -SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544 +TIMESTAMP = 1518995346 +SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca +SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 Modified: head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top ============================================================================== --- head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top Tue Mar 27 18:04:21 2018 (r465726) @@ -1,11 +1,32 @@ ---- src/build-system/Makefile.in.top.orig 2014-11-13 01:41:55.000000000 +0900 -+++ src/build-system/Makefile.in.top 2016-12-02 16:39:58.415910000 +0900 -@@ -51,7 +51,7 @@ +--- src/build-system/Makefile.in.top.orig 2018-03-27 03:40:40 UTC ++++ src/build-system/Makefile.in.top +@@ -37,21 +37,21 @@ check: $(PROJECTS) + fi + + install-toolkit: +- -$(RMDIR) $(pincludedir) +- $(INSTALL) -d $(bindir) $(libdir) $(pincludedir) +- $(INSTALL) $(lbindir)/* $(bindir) +- $(INSTALL) -m 644 $(llibdir)/*.* $(libdir) ++ -$(RMDIR) $(DESTDIR)$(pincludedir) ++ $(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir) ++ $(INSTALL) $(lbindir)/* $(DESTDIR)$(bindir) ++ $(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir) + if test -d $(llibdir)/ncbi; then \ +- cp -pPR $(llibdir)/ncbi $(libdir)/; \ ++ cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \ + fi +- -rm -f $(libdir)/lib*-static.a +- cd $(libdir) && \ ++ -rm -f $(DESTDIR)$(libdir)/lib*-static.a ++ cd $(DESTDIR)$(libdir) && \ + for x in *.a; do \ + $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \ done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ cd $(incdir) && find * | cpio -pd $(pincludedir) + for d in $(includedir0) $(incdir); do \ + cd $$d && find * -name .svn -prune -o -print | \ +- cpio -pd $(pincludedir) ; \ ++ cpio -pd $(DESTDIR)$(pincludedir) ; \ + done ## set up appropriate build and status directories somewhere under $(libdir)? - install-gbench: Modified: head/biology/ncbi-blast+/files/patch-src_build-system_configure ============================================================================== --- head/biology/ncbi-blast+/files/patch-src_build-system_configure Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/files/patch-src_build-system_configure Tue Mar 27 18:04:21 2018 (r465726) @@ -1,11 +1,30 @@ ---- src/build-system/configure.orig 2016-09-09 21:04:16.000000000 +0900 -+++ src/build-system/configure 2016-12-02 15:04:04.258800000 +0900 -@@ -1715,7 +1715,7 @@ - | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \ - | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \ +--- src/build-system/configure.orig 2017-10-18 15:21:39 UTC ++++ src/build-system/configure +@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \ + | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \ + | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | --with-runpath=* | --with-relative-runpath=* \ + | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \ | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \ +@@ -1828,9 +1828,7 @@ Fine tuning of the installation director + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] + --datadir=DIR read-only architecture-independent data [DATAROOTDIR] +- --infodir=DIR info documentation [DATAROOTDIR/info] + --localedir=DIR locale-dependent data [DATAROOTDIR/locale] +- --mandir=DIR man documentation [DATAROOTDIR/man] + --docdir=DIR documentation root [DATAROOTDIR/doc/ncbi-tools--] + --htmldir=DIR html documentation [DOCDIR] + --dvidir=DIR dvi documentation [DOCDIR] +@@ -8086,7 +8084,7 @@ case "$host_os:$compiler" in + esac + + if test "$with_mt" != "no" ; then +- CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE" ++ CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL" + LIBS="$LIBS $THREAD_LIBS" + case "$host_os:$compiler" in + solaris2.??:* | solaris*:GCC | *:Compaq | irix* | aix* | darwin* | cygwin*) Modified: head/biology/ncbi-blast+/pkg-descr ============================================================================== --- head/biology/ncbi-blast+/pkg-descr Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/pkg-descr Tue Mar 27 18:04:21 2018 (r465726) @@ -1,8 +1,7 @@ -The Basic Local Alignment Search Tool (BLAST) finds regions of local -similarity between sequences. The program compares nucleotide or protein -sequences to sequence databases and calculates the statistical -significance of matches. BLAST can be used to infer functional and -evolutionary relationships between sequences as well as help identify -members of gene families. +The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity +between sequences. The program compares nucleotide or protein sequences to +sequence databases and calculates the statistical significance of matches. +BLAST can be used to infer functional and evolutionary relationships between +sequences as well as help identify members of gene families. WWW: http://blast.ncbi.nlm.nih.gov Modified: head/biology/ncbi-blast+/pkg-plist ============================================================================== --- head/biology/ncbi-blast+/pkg-plist Tue Mar 27 17:45:30 2018 (r465725) +++ head/biology/ncbi-blast+/pkg-plist Tue Mar 27 18:04:21 2018 (r465726) @@ -10,6 +10,7 @@ bin/convert2blastmask bin/datatool bin/deltablast bin/dustmasker +bin/gc_cli bin/gene_info_reader bin/legacy_blast.pl bin/makeblastdb @@ -45,6 +46,7 @@ include/ncbi-tools++/algo/blast/api/blast_rps_options. include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp include/ncbi-tools++/algo/blast/api/blast_types.hpp +include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp include/ncbi-tools++/algo/blast/api/blastx_options.hpp include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp include/ncbi-tools++/algo/blast/api/deltablast.hpp @@ -105,6 +107,7 @@ include/ncbi-tools++/algo/blast/blastinput/cmdline_fla include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp +include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp @@ -175,12 +178,14 @@ include/ncbi-tools++/algo/blast/core/pattern.h include/ncbi-tools++/algo/blast/core/phi_extend.h include/ncbi-tools++/algo/blast/core/phi_gapalign.h include/ncbi-tools++/algo/blast/core/phi_lookup.h +include/ncbi-tools++/algo/blast/core/spliced_hits.h include/ncbi-tools++/algo/blast/core/split_query.h include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp +include/ncbi-tools++/algo/blast/format/blast_async_format.hpp include/ncbi-tools++/algo/blast/format/blast_format.hpp include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp @@ -191,6 +196,13 @@ include/ncbi-tools++/algo/blast/format/data4xmlformat. include/ncbi-tools++/algo/blast/format/sam.hpp include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp include/ncbi-tools++/algo/blast/igblast/igblast.hpp +include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp +include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp +include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp +include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp +include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp +include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp +include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp include/ncbi-tools++/algo/dustmask/sdust.tex include/ncbi-tools++/algo/dustmask/symdust.hpp include/ncbi-tools++/algo/segmask/segmask.hpp @@ -284,7 +296,11 @@ include/ncbi-tools++/connect/ncbi_heapmgr.h include/ncbi-tools++/connect/ncbi_host_info.h include/ncbi-tools++/connect/ncbi_http_connector.h include/ncbi-tools++/connect/ncbi_http_session.hpp +include/ncbi-tools++/connect/ncbi_iprange.h +include/ncbi-tools++/connect/ncbi_ipv6.h include/ncbi-tools++/connect/ncbi_lbos.hpp +include/ncbi-tools++/connect/ncbi_localip.h +include/ncbi-tools++/connect/ncbi_mbedtls.h include/ncbi-tools++/connect/ncbi_memory_connector.h include/ncbi-tools++/connect/ncbi_misc.hpp include/ncbi-tools++/connect/ncbi_monkey.hpp @@ -301,6 +317,7 @@ include/ncbi-tools++/connect/ncbi_socket.hpp include/ncbi-tools++/connect/ncbi_socket_connector.h include/ncbi-tools++/connect/ncbi_socket_unix.h include/ncbi-tools++/connect/ncbi_socket_unix.hpp +include/ncbi-tools++/connect/ncbi_tls.h include/ncbi-tools++/connect/ncbi_types.h include/ncbi-tools++/connect/ncbi_userhost.hpp include/ncbi-tools++/connect/ncbi_util.h @@ -327,6 +344,7 @@ include/ncbi-tools++/connect/services/netcache_admin.h include/ncbi-tools++/connect/services/netcache_api.hpp include/ncbi-tools++/connect/services/netcache_api_expt.hpp include/ncbi-tools++/connect/services/netcache_key.hpp +include/ncbi-tools++/connect/services/netcache_search.hpp include/ncbi-tools++/connect/services/netcomponent.hpp include/ncbi-tools++/connect/services/neticache_client.hpp include/ncbi-tools++/connect/services/netschedule_api.hpp @@ -337,7 +355,6 @@ include/ncbi-tools++/connect/services/netservice_api_e include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp include/ncbi-tools++/connect/services/netstorage.hpp include/ncbi-tools++/connect/services/netstorage_ft.hpp -include/ncbi-tools++/connect/services/netstorage_impl.hpp include/ncbi-tools++/connect/services/ns_client_factory.hpp include/ncbi-tools++/connect/services/ns_job_serializer.hpp include/ncbi-tools++/connect/services/ns_output_parser.hpp @@ -446,10 +463,13 @@ include/ncbi-tools++/corelib/resource_info.hpp include/ncbi-tools++/corelib/rwstream.hpp include/ncbi-tools++/corelib/stream_utils.hpp include/ncbi-tools++/corelib/syslog.hpp +include/ncbi-tools++/corelib/teamcity_messages.h include/ncbi-tools++/corelib/tempstr.hpp include/ncbi-tools++/corelib/test_boost.hpp include/ncbi-tools++/corelib/test_mt.hpp include/ncbi-tools++/corelib/version.hpp +include/ncbi-tools++/db/error_codes.hpp +include/ncbi-tools++/db/sqlite/sqlitewrapp.hpp include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp include/ncbi-tools++/dbapi/dbapi.hpp include/ncbi-tools++/dbapi/dbapi_variant_convert.hpp @@ -506,15 +526,14 @@ include/ncbi-tools++/html/selection.hpp include/ncbi-tools++/html/writer_htmlenc.hpp include/ncbi-tools++/misc/error_codes.hpp include/ncbi-tools++/ncbi_pch.hpp +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/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/Affil.hpp include/ncbi-tools++/objects/biblio/Affil_.hpp include/ncbi-tools++/objects/biblio/ArticleId.hpp @@ -577,7 +596,6 @@ 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/BioTreeContainer.hpp include/ncbi-tools++/objects/biotree/BioTreeContainer_.hpp include/ncbi-tools++/objects/biotree/DistanceMatrix.hpp @@ -596,8 +614,6 @@ 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/.cvsignore.extra 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 @@ -727,7 +743,6 @@ 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/Blast_db_mask_info.hpp include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp include/ncbi-tools++/objects/blastdb/Blast_def_line.hpp @@ -741,7 +756,6 @@ 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/BlastOutput.hpp include/ncbi-tools++/objects/blastxml/BlastOutput_.hpp include/ncbi-tools++/objects/blastxml/Hit.hpp @@ -756,7 +770,6 @@ 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/BlastOutput2.hpp include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp @@ -787,7 +800,6 @@ 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/Algorithm_type.hpp include/ncbi-tools++/objects/cdd/Algorithm_type_.hpp include/ncbi-tools++/objects/cdd/Align_annot.hpp @@ -856,7 +868,6 @@ 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/Cn3d_GL_matrix.hpp include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix_.hpp include/ncbi-tools++/objects/cn3d/Cn3d_backbone_label_style.hpp @@ -899,14 +910,12 @@ 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/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/Assay.hpp include/ncbi-tools++/objects/docsum/Assay_.hpp include/ncbi-tools++/objects/docsum/Assembly.hpp @@ -933,8 +942,6 @@ 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/.cvsignore.extra include/ncbi-tools++/objects/entrez2/E2Reply.hpp include/ncbi-tools++/objects/entrez2/E2Reply_.hpp include/ncbi-tools++/objects/entrez2/E2Request.hpp @@ -1013,7 +1020,6 @@ 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/Entrezgene.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_Set.hpp @@ -1032,7 +1038,6 @@ 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/FeatDef.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet_.hpp @@ -1047,7 +1052,6 @@ 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/AbstractProjectItem.hpp include/ncbi-tools++/objects/gbproj/AbstractProjectItem_.hpp include/ncbi-tools++/objects/gbproj/DummyObsoleteType.hpp @@ -1078,7 +1082,6 @@ 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/GBAltSeqData.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqData_.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqItem.hpp @@ -1117,7 +1120,6 @@ 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/Date.hpp include/ncbi-tools++/objects/general/Date_.hpp include/ncbi-tools++/objects/general/Date_std.hpp @@ -1141,7 +1143,6 @@ 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/GBL_Data.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Data_.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Gene.hpp @@ -1150,8 +1151,6 @@ 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/.cvsignore.extra include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp @@ -1229,7 +1228,6 @@ 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/HG_Alignment.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet_.hpp @@ -1258,8 +1256,6 @@ 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/.cvsignore.extra include/ncbi-tools++/objects/id1/Entry_complexities.hpp include/ncbi-tools++/objects/id1/Entry_complexities_.hpp include/ncbi-tools++/objects/id1/ID1SeqEntry_info.hpp @@ -1280,7 +1276,6 @@ 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/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 @@ -1341,7 +1336,6 @@ 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/INSDAltSeqData.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqItem.hpp @@ -1380,7 +1374,6 @@ 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/AECRParse_action.hpp include/ncbi-tools++/objects/macro/AECRParse_action_.hpp include/ncbi-tools++/objects/macro/AECR_action.hpp @@ -1741,14 +1734,12 @@ 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/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/DocRef.hpp include/ncbi-tools++/objects/medline/DocRef_.hpp include/ncbi-tools++/objects/medline/Medline_entry.hpp @@ -1765,7 +1756,6 @@ 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/Mim_allelic_variant.hpp include/ncbi-tools++/objects/mim/Mim_allelic_variant_.hpp include/ncbi-tools++/objects/mim/Mim_author.hpp @@ -1797,8 +1787,6 @@ 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/.cvsignore.extra include/ncbi-tools++/objects/mla/Error_val.hpp include/ncbi-tools++/objects/mla/Error_val_.hpp include/ncbi-tools++/objects/mla/Mla_back.hpp @@ -1815,7 +1803,6 @@ 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/Atom.hpp include/ncbi-tools++/objects/mmdb1/Atom_.hpp include/ncbi-tools++/objects/mmdb1/Atom_id.hpp @@ -1877,7 +1864,6 @@ 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/Alternate_conformation_id.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp @@ -1924,7 +1910,6 @@ 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/Align_stats.hpp include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp @@ -2001,7 +1986,6 @@ 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/Biostruc_align.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_seq.hpp @@ -2022,7 +2006,6 @@ 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/NCBI_ObjPrt_module.hpp include/ncbi-tools++/objects/objprt/PrintForm.hpp include/ncbi-tools++/objects/objprt/PrintFormBlock.hpp @@ -2045,7 +2028,6 @@ 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/MSBioseq.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet_.hpp @@ -2132,7 +2114,6 @@ 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/NCBI_PCAssay_module.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef_.hpp @@ -2167,7 +2148,6 @@ 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/NCBI_PCSubstance_module.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt_.hpp @@ -2244,7 +2224,6 @@ 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/NCBI_Project_module.hpp include/ncbi-tools++/objects/proj/Projdesc.hpp include/ncbi-tools++/objects/proj/Projdesc_.hpp @@ -2257,7 +2236,6 @@ 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/NCBI_Pub_module.hpp include/ncbi-tools++/objects/pub/Pub.hpp include/ncbi-tools++/objects/pub/Pub_.hpp @@ -2267,15 +2245,12 @@ 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/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/.cvsignore.extra include/ncbi-tools++/objects/remap/NCBI_Remap_module.hpp include/ncbi-tools++/objects/remap/RMReply.hpp include/ncbi-tools++/objects/remap/RMReply_.hpp @@ -2296,7 +2271,6 @@ 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/BlockProperty.hpp include/ncbi-tools++/objects/scoremat/BlockProperty_.hpp include/ncbi-tools++/objects/scoremat/CoreBlock.hpp @@ -2323,7 +2297,6 @@ 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/Align_def.hpp include/ncbi-tools++/objects/seq/Align_def_.hpp include/ncbi-tools++/objects/seq/Annot_descr.hpp @@ -2422,9 +2395,9 @@ include/ncbi-tools++/objects/seq/seq_loc_reverse_compl include/ncbi-tools++/objects/seq/seq_macros.hpp include/ncbi-tools++/objects/seq/seqlocinfo.hpp 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/Dense_diag.hpp include/ncbi-tools++/objects/seqalign/Dense_diag_.hpp include/ncbi-tools++/objects/seqalign/Dense_seg.hpp @@ -2465,7 +2438,6 @@ 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/EMBL_General_module.hpp include/ncbi-tools++/objects/seqblock/EMBL_block.hpp include/ncbi-tools++/objects/seqblock/EMBL_block_.hpp @@ -2494,7 +2466,6 @@ 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/NCBI_SeqCode_module.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set_.hpp @@ -2505,7 +2476,6 @@ 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/NCBI_SeqEdit_module.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_.hpp @@ -2554,7 +2524,6 @@ 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/BinomialOrgName.hpp include/ncbi-tools++/objects/seqfeat/BinomialOrgName_.hpp include/ncbi-tools++/objects/seqfeat/BioSource.hpp @@ -2675,7 +2644,6 @@ 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/Giimport_id.hpp include/ncbi-tools++/objects/seqloc/Giimport_id_.hpp include/ncbi-tools++/objects/seqloc/NCBI_Seqloc_module.hpp @@ -2711,7 +2679,6 @@ 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/Byte_graph.hpp include/ncbi-tools++/objects/seqres/Byte_graph_.hpp include/ncbi-tools++/objects/seqres/Int_graph.hpp @@ -2722,7 +2689,6 @@ 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/Bioseq_set.hpp include/ncbi-tools++/objects/seqset/Bioseq_set_.hpp include/ncbi-tools++/objects/seqset/NCBI_Seqset_module.hpp @@ -2732,7 +2698,6 @@ 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/ID2S_Bioseq_Ids.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids_.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Info.hpp @@ -2789,7 +2754,6 @@ 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/BVector_data.hpp include/ncbi-tools++/objects/seqtable/BVector_data_.hpp include/ncbi-tools++/objects/seqtable/CommonBytes_table.hpp @@ -2816,7 +2780,6 @@ 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/NCBI_SeqTest_module.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults_.hpp @@ -2825,7 +2788,6 @@ 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/Contact_info.hpp include/ncbi-tools++/objects/submit/Contact_info_.hpp include/ncbi-tools++/objects/submit/NCBI_Submit_module.hpp @@ -2835,7 +2797,6 @@ 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/NCBI_Taxon1_module.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data_.hpp @@ -2853,7 +2814,6 @@ include/ncbi-tools++/objects/taxon1/Taxon2_data.hpp include/ncbi-tools++/objects/taxon1/Taxon2_data_.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/NCBI_Taxon3_module.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt_.hpp @@ -2877,14 +2837,12 @@ 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/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/NCBI_TrackManager_module.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel_.hpp @@ -2974,6 +2932,10 @@ include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTra include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp @@ -3012,6 +2974,7 @@ include/ncbi-tools++/objects/trackmgr/createusertrack_ include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp +include/ncbi-tools++/objects/trackmgr/primary_snp.hpp include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp @@ -3021,14 +2984,12 @@ 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/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/Comment_rule.hpp include/ncbi-tools++/objects/valid/Comment_rule_.hpp include/ncbi-tools++/objects/valid/Comment_set.hpp @@ -3047,7 +3008,6 @@ 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/NCBI_VariationPackage_module.hpp include/ncbi-tools++/objects/variation/VariantPlacement.hpp include/ncbi-tools++/objects/variation/VariantPlacement_.hpp @@ -3058,7 +3018,6 @@ 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/varrep/.cvsignore include/ncbi-tools++/objects/varrep/AaInterval.hpp include/ncbi-tools++/objects/varrep/AaInterval_.hpp include/ncbi-tools++/objects/varrep/AaLocation.hpp @@ -3237,8 +3196,18 @@ include/ncbi-tools++/objmgr/split/split_exceptions.hpp include/ncbi-tools++/objmgr/table_field.hpp include/ncbi-tools++/objmgr/tse_handle.hpp include/ncbi-tools++/objmgr/unsupp_editsaver.hpp +include/ncbi-tools++/objmgr/util/autodef.hpp +include/ncbi-tools++/objmgr/util/autodef_available_modifier.hpp +include/ncbi-tools++/objmgr/util/autodef_feature_clause.hpp +include/ncbi-tools++/objmgr/util/autodef_feature_clause_base.hpp +include/ncbi-tools++/objmgr/util/autodef_mod_combo.hpp +include/ncbi-tools++/objmgr/util/autodef_options.hpp +include/ncbi-tools++/objmgr/util/autodef_source_desc.hpp +include/ncbi-tools++/objmgr/util/autodef_source_group.hpp include/ncbi-tools++/objmgr/util/create_defline.hpp include/ncbi-tools++/objmgr/util/feature.hpp +include/ncbi-tools++/objmgr/util/feature_edit.hpp +include/ncbi-tools++/objmgr/util/indexer.hpp include/ncbi-tools++/objmgr/util/obj_sniff.hpp include/ncbi-tools++/objmgr/util/objutil.hpp include/ncbi-tools++/objmgr/util/seq_align_util.hpp @@ -3290,6 +3259,7 @@ include/ncbi-tools++/objtools/blast/blastdb_format/bla include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_formatter.hpp include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp +include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp @@ -3372,19 +3342,16 @@ include/ncbi-tools++/objtools/data_loaders/genbank/wri include/ncbi-tools++/objtools/data_loaders/loaders.hpp include/ncbi-tools++/objtools/edit/apply_object.hpp include/ncbi-tools++/objtools/edit/autodef.hpp -include/ncbi-tools++/objtools/edit/autodef_available_modifier.hpp -include/ncbi-tools++/objtools/edit/autodef_feature_clause.hpp -include/ncbi-tools++/objtools/edit/autodef_feature_clause_base.hpp -include/ncbi-tools++/objtools/edit/autodef_mod_combo.hpp include/ncbi-tools++/objtools/edit/autodef_options.hpp include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp -include/ncbi-tools++/objtools/edit/autodef_source_group.hpp +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_exception.hpp include/ncbi-tools++/objtools/edit/feattable_edit.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 include/ncbi-tools++/objtools/edit/gb_block_field.hpp include/ncbi-tools++/objtools/edit/gene_utils.hpp @@ -3420,9 +3387,6 @@ include/ncbi-tools++/objtools/format/gather_iter.hpp include/ncbi-tools++/objtools/format/gbseq_formatter.hpp include/ncbi-tools++/objtools/format/genbank_formatter.hpp include/ncbi-tools++/objtools/format/genbank_gather.hpp -include/ncbi-tools++/objtools/format/gff3_formatter.hpp -include/ncbi-tools++/objtools/format/gff_formatter.hpp -include/ncbi-tools++/objtools/format/gff_gather.hpp include/ncbi-tools++/objtools/format/item_formatter.hpp include/ncbi-tools++/objtools/format/item_ostream.hpp include/ncbi-tools++/objtools/format/items/accession_item.hpp @@ -3470,6 +3434,7 @@ include/ncbi-tools++/objtools/readers/cigar.hpp include/ncbi-tools++/objtools/readers/error_container.hpp include/ncbi-tools++/objtools/readers/fasta.hpp include/ncbi-tools++/objtools/readers/fasta_exception.hpp +include/ncbi-tools++/objtools/readers/fasta_reader_utils.hpp include/ncbi-tools++/objtools/readers/featuredump.hpp include/ncbi-tools++/objtools/readers/format_guess_ex.hpp include/ncbi-tools++/objtools/readers/getfeature.hpp @@ -3495,6 +3460,7 @@ include/ncbi-tools++/objtools/readers/readfeat.hpp include/ncbi-tools++/objtools/readers/rm_reader.hpp include/ncbi-tools++/objtools/readers/source_mod_parser.hpp include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp +include/ncbi-tools++/objtools/readers/struct_cmt_reader.hpp include/ncbi-tools++/objtools/readers/table_filter.hpp include/ncbi-tools++/objtools/readers/track_data.hpp include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp @@ -3624,6 +3590,9 @@ 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/bmsparsevec.h +include/ncbi-tools++/util/bitset/bmsparsevec_algo.h +include/ncbi-tools++/util/bitset/bmsparsevec_serial.h include/ncbi-tools++/util/bitset/bmsse2.h include/ncbi-tools++/util/bitset/bmsse4.h include/ncbi-tools++/util/bitset/bmsse_util.h @@ -3709,6 +3678,14 @@ include/ncbi-tools++/util/request_control.hpp include/ncbi-tools++/util/resize_iter.hpp include/ncbi-tools++/util/resource_pool.hpp include/ncbi-tools++/util/retry_ctx.hpp +include/ncbi-tools++/util/row_reader.hpp +include/ncbi-tools++/util/row_reader.inl +include/ncbi-tools++/util/row_reader_base.hpp +include/ncbi-tools++/util/row_reader_char_delimited.hpp +include/ncbi-tools++/util/row_reader_excel_csv.hpp +include/ncbi-tools++/util/row_reader_iana_csv.hpp +include/ncbi-tools++/util/row_reader_iana_tsv.hpp +include/ncbi-tools++/util/row_reader_ncbi_tsv.hpp include/ncbi-tools++/util/scheduler.hpp include/ncbi-tools++/util/sequtil/sequtil.hpp include/ncbi-tools++/util/sequtil/sequtil_convert.hpp @@ -3748,258 +3725,264 @@ include/ncbi-tools++/util/xregexp/arg_regexp.hpp include/ncbi-tools++/util/xregexp/mask_regexp.hpp include/ncbi-tools++/util/xregexp/regexp.hpp include/ncbi-tools++/util/xregexp/regexp_template_tester.hpp -lib/libaccess-static.a -lib/libaccess.a -lib/libalign_format-static.a -lib/libalign_format.a -lib/libbiblio-static.a -lib/libbiblio.a -lib/libbiotree-static.a -lib/libbiotree.a -lib/libblast-static.a -lib/libblast.a -lib/libblast_app_util-static.a -lib/libblast_app_util.a -lib/libblast_services-static.a -lib/libblast_services.a -lib/libblastdb-static.a -lib/libblastdb.a -lib/libblastdb_format-static.a -lib/libblastdb_format.a -lib/libblastinput-static.a -lib/libblastinput.a -lib/libblastxml-static.a -lib/libblastxml.a -lib/libblastxml2-static.a -lib/libblastxml2.a -lib/libcdd-static.a -lib/libcdd.a -lib/libcn3d-static.a -lib/libcn3d.a -lib/libcomposition_adjustment-static.a -lib/libcomposition_adjustment.a -lib/libconnect-static.a -lib/libconnect.a -lib/libconnssl-static.a -lib/libconnssl.a -lib/libcreaders-static.a -lib/libcreaders.a -lib/libdbapi-static.a -lib/libdbapi.a -lib/libdbapi_driver-dll.so -lib/libdbapi_driver-static.a -lib/libdbapi_driver.a -lib/libdocsum-static.a -lib/libdocsum.a -lib/libentrez2-static.a -lib/libentrez2.a -lib/libentrez2cli-static.a -lib/libentrez2cli.a -lib/libentrezgene-static.a -lib/libentrezgene.a -lib/libfeatdef-static.a -lib/libfeatdef.a -lib/libgbproj-static.a -lib/libgbproj.a -lib/libgbseq-static.a -lib/libgbseq.a -lib/libgencoll_client-static.a -lib/libgencoll_client.a -lib/libgene_info-static.a -lib/libgene_info.a -lib/libgeneral-static.a -lib/libgeneral.a -lib/libgenesbyloc-static.a -lib/libgenesbyloc.a -lib/libgenome_collection-static.a -lib/libgenome_collection.a -lib/libhomologene-static.a -lib/libhomologene.a -lib/libid1-static.a -lib/libid1.a -lib/libid1cli-static.a -lib/libid1cli.a -lib/libid2-static.a -lib/libid2.a *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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