Embarrassingly long overdue update to 0.7.0, including optional support for

GUI (Tk) and CORBA extensions.

3 files changed, 300 insertions, 66 deletions

diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 302592a9a251..59fb85f02cfb 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -6,78 +6,166 @@
 #
 
 PORTNAME=	bioperl
-PORTVERSION=	0.6.2
+PORTVERSION=	0.7.0
 CATEGORIES=	biology perl5
-MASTER_SITES=	ftp://bio.perl.org/pub/DIST/ \
-		http://bio.perl.org/Core/Latest/ \
+MASTER_SITES=	ftp://bioperl.org/pub/DIST/ \
+		http://bioperl.org/Core/Latest/ \
 		${MASTER_SITE_PERL_CPAN}
-MASTER_SITE_SUBDIR=Bio
+MASTER_SITE_SUBDIR=	Bio
 PKGNAMEPREFIX=	p5-
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
 
-MAINTAINER=	johann@egenetics.com
+MAINTAINER=	wjv@FreeBSD.org
 
-BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
 
 PERL_CONFIGURE=	YES
 
-MAN3=		Bio::Annotation.3 Bio::Annotation::Comment.3 \
-		Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
-		Bio::DB::Ace.3 Bio::DB::GenBank.3 Bio::DB::GenPept.3 \
-		Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 \
-		Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
-		Bio::Index::EMBL.3 Bio::Index::Fasta.3 \
-		Bio::Index::SwissPfam.3 Bio::LocatableSeq.3 \
-		Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
-		Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \
-		Bio::Root::IOManager.3 Bio::Root::Object.3 \
-		Bio::Root::RootI.3 Bio::Root::Utilities.3 \
-		Bio::Root::Vector.3 Bio::Root::Xref.3 \
-		Bio::Search::Hit::Fasta.3 Bio::Search::Hit::HitI.3 \
-		Bio::Search::Processor.3 Bio::Search::Processor::Fasta.3 \
-		Bio::Search::Processor::ProcessorI.3 \
-		Bio::Search::Result::Fasta.3 \
-		Bio::Search::Result::ResultI.3 Bio::SearchDist.3 \
-		Bio::Seq.3 Bio::SeqFeature::FeaturePair.3 \
-		Bio::SeqFeature::Generic.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
-		Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \
-		Bio::SeqIO::MultiFile.3 Bio::SeqIO::embl.3 \
-		Bio::SeqIO::fasta.3 Bio::SeqIO::gcg.3 \
-		Bio::SeqIO::genbank.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
-		Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SimpleAlign.3 \
-		Bio::Species.3 Bio::Tools::AlignFactory.3 \
-		Bio::Tools::Blast.3 Bio::Tools::Blast::HSP.3 \
-		Bio::Tools::Blast::HTML.3 \
-		Bio::Tools::Blast::Run::LocalBlast.3 \
-		Bio::Tools::Blast::Run::Webblast.3 \
-		Bio::Tools::Blast::Sbjct.3 Bio::Tools::CodonTable.3 \
-		Bio::Tools::Fasta.3 Bio::Tools::HMMER::Domain.3 \
-		Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
-		Bio::Tools::IUPAC.3 Bio::Tools::RestrictionEnzyme.3 \
-		Bio::Tools::SeqAnal.3 Bio::Tools::SeqPattern.3 \
-		Bio::Tools::SeqStats.3 Bio::Tools::SeqWords.3 \
-		Bio::Tools::Sigcleave.3 Bio::Tools::WWW.3 \
-		Bio::Tools::pSW.3 Bio::UnivAln.3 \
-		bioback.3 biodesign.3 bioperl.3 biostart.3
-MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
+.if defined(WITH_CORBA)
+WITH_CORBA_CLIENT=	YES
+WITH_CORBA_SERVER=	YES
+.endif
 
+EXT_VERSION=	0.6
+CORBA_CLIENT_VERSION=	0.2
+CORBA_SERVER_VERSION=	0.2
+GUI_VERSION=	0.7
+DISTFILES+=	bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
 EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
 
+.if defined(WITH_CORBA_CLIENT)
+BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+.endif
+.if defined(WITH_CORBA_SERVER)
+BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+.endif
+.if defined(WITH_GUI)
+RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
+.endif
+
+.for ext in CORBA_CLIENT CORBA_SERVER GUI
+.if defined(WITH_${ext})
+EXTLIST+=	${ext}
+DISTFILES+=	bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX}
+${ext}_WRKSRC=	${WRKDIR}/bioperl-${ext:L:S/_/-/}
+PLIST_${ext}=	""
+.else
+PLIST_${ext}=	"@comment "
+.endif
+PLIST_SUB+=	PLIST_${ext}=${PLIST_${ext}}
+.endfor
+
+MAN3=		Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
+		Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
+		Bio::AlignIO::mase.3 Bio::AlignIO::msf.3 Bio::AlignIO::pfam.3 \
+		Bio::AlignIO::prodom.3 Bio::AlignIO::selex.3 \
+		Bio::AlignIO::stockholm.3 Bio::DB::GDB.3 \
+		Bio::DB::NCBIHelper.3 Bio::DB::SwissProt.3 \
+		Bio::DB::UpdateableSeqI.3 Bio::DB::WebDBSeqI.3 \
+		Bio::DBLinkContainerI.3 Bio::Factory::DriverFactory.3 \
+		Bio::Factory::SeqAnalysisParserFactory.3 \
+		Bio::Factory::SeqAnalysisParserFactoryI.3 \
+		Bio::Index::GenBank.3 Bio::Index::Swissprot.3 \
+		Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \
+		Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \
+		Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \
+		Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \
+		Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \
+		Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \
+		Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \
+		Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \
+		Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \
+		Bio::LiveSeq::Translation.3 \
+		Bio::Location::AvWithinCoordPolicy.3 \
+		Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
+		Bio::Location::FuzzyLocationI.3 \
+		Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \
+		Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \
+		Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \
+		Bio::Root::IO.3 Bio::Seq::LargePrimarySeq.3 \
+		Bio::Seq::LargeSeq.3 Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
+		Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Gene::Exon.3 \
+		Bio::SeqFeature::Gene::ExonI.3 \
+		Bio::SeqFeature::Gene::GeneStructure.3 \
+		Bio::SeqFeature::Gene::GeneStructureI.3 \
+		Bio::SeqFeature::Gene::Transcript.3 \
+		Bio::SeqFeature::Gene::TranscriptI.3 \
+		Bio::SeqFeature::Similarity.3 \
+		Bio::SeqFeature::SimilarityPair.3 Bio::SeqIO::ace.3 \
+		Bio::SeqIO::game.3 Bio::SeqIO::largefasta.3 Bio::SeqUtils.3 \
+		Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
+		Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
+		Bio::Tools::BPpsilite.3 Bio::Tools::ESTScan.3 \
+		Bio::Tools::GFF.3 Bio::Tools::Genscan.3 Bio::Tools::MZEF.3 \
+		Bio::Tools::OddCodes.3 Bio::Tools::Prediction::Exon.3 \
+		Bio::Tools::Prediction::Gene.3 \
+		Bio::Tools::Run::Alignment::Clustalw.3 \
+		Bio::Tools::Run::Alignment::TCoffee.3 \
+		Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::Sim4::Exon.3 \
+		Bio::Tools::Sim4::Results.3 Bio::Variation::AAChange.3 \
+		Bio::Variation::AAReverseMutate.3 Bio::Variation::Allele.3 \
+		Bio::Variation::DNAMutation.3 Bio::Variation::IO.3 \
+		Bio::Variation::IO::flat.3 Bio::Variation::IO::xml.3 \
+		Bio::Variation::RNAChange.3 Bio::Variation::SeqDiff.3 \
+		Bio::Variation::VariantI.3 bptutorial.3
+.if defined(WITH_CORBA_CLIENT)
+MAN3+=		Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \
+		Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \
+		Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \
+		Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3
+.endif
+.if defined(WITH_CORBA_SERVER)
+MAN3+=		Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
+		Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \
+		Bio::CorbaServer::PrimarySeqDB.3 \
+		Bio::CorbaServer::PrimarySeqIterator.3 \
+		Bio::CorbaServer::PrimarySeqVector.3 \
+		Bio::CorbaServer::Seq.3 \
+		Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \
+		Bio::CorbaServer::SeqFeatureIterator.3 \
+		Bio::CorbaServer::SeqFeatureVector.3 \
+		Bio::CorbaServer::Server.3
+.endif
+.if defined(WITH_GUI)
+MAN3+=		Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
+.endif
+MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
+
 post-configure:
-	@ (cd ${EXT_WRKSRC} && \
+	@ cd ${EXT_WRKSRC} && \
 	  ${SETENV} ${CONFIGURE_ENV} \
-	  ${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
+	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
+
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && \
+	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
+.endfor
 
 post-build:
-	@ (cd ${EXT_WRKSRC} && \
-	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
+	@ cd ${EXT_WRKSRC} && \
+	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \
+	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
+.endfor
 
 post-install:
-	@ (cd ${EXT_WRKSRC} && \
+	@ cd ${EXT_WRKSRC} && \
+	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
+	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && \
 	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
-	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
+	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
+.endfor
 
 .include <bsd.port.mk>
diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo
index 2d04f782e757..d21690e7523e 100644
--- a/biology/p5-bioperl/distinfo
+++ b/biology/p5-bioperl/distinfo
@@ -1,2 +1,5 @@
-MD5 (bioperl-0.6.2.tar.gz) = 26330f4f0c1e08a4f5cbcbe8b05b72f1
+MD5 (bioperl-0.7.0.tar.gz) = 10b4d196346495fdd6f4337bac115776
 MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240
+MD5 (bioperl-corba-client-0.2.tar.gz) = 9635488e779d771bc5f976bf56826590
+MD5 (bioperl-corba-server-0.2.tar.gz) = d5e3353ed6c8717de06e0db8f5bbc0f5
+MD5 (bioperl-gui-0.7.tar.gz) = 07b50934c5dc8fcbbb89d2d35c758dea
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index 1ac85ff54cd3..30fa55f0a56b 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,62 +1,166 @@
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Base.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Client.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/ORB.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/PrimarySeq.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Seq.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/SeqFeature.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/DB/Biocorba.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/SeqIO/biocorba.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/AnonymousSeq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Base.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/BioEnv.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqDB.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqIterator.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqVector.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Seq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqDB.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeature.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureIterator.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureVector.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Server.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/AnnotMap.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/BioTkPerl8_1.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/GO_Browser.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/HitDisplay.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/README
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/SeqCanvas.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/Tkpsh.pl
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Map.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_SeqSubs.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Sequence.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Utilities.pm
+%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/bl2seq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/clustalw.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/mase.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/msf.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/pfam.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/prodom.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/selex.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/stockholm.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GDB.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/NCBIHelper.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SwissProt.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/UpdateableSeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/WebDBSeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DBLinkContainerI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/DriverFactory.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactory.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/GenBank.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Swissprot.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/AARange.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Chain.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/ChainI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/DNA.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Exon.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Gene.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/BioPerl.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/Loader.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/SRS.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Intron.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutation.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutator.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Prim_Transcript.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Range.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Region.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Unit.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/SeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Transcript.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Translation.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/AvWithinCoordPolicy.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/CoordinatePolicyI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Fuzzy.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/FuzzyLocationI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/NarrowestCoordPolicy.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Simple.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Split.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/SplitLocationI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/WidestCoordPolicy.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LocationI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IO.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargePrimarySeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargeSeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqAnalysisParserI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Exon.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/ExonI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructure.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructureI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Transcript.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/TranscriptI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Similarity.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/SimilarityPair.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/ace.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/featureHandler.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/idHandler.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/seqHandler.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/largefasta.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqUtils.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AnalysisResult.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPbl2seq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/HSP.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Iteration.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Sbjct.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPpsilite.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
@@ -68,38 +172,77 @@ lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/ESTScan.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/GFF.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Genscan.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/MZEF.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/OddCodes.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Exon.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Gene.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/Clustalw.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/TCoffee.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/StandAloneBlast.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAChange.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAReverseMutate.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/Allele.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/DNAMutation.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/flat.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/xml.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/README
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/RNAChange.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/SeqDiff.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/VariantI.pm
 lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
 lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
 lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
 lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
+lib/perl5/site_perl/%%PERL_VER%%/bptutorial.pl
+%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk
+%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/Bio/Tk
+%%PLIST_CORBA_SERVER%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaServer
+%%PLIST_CORBA_CLIENT%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaClient
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Location
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext