Date: Tue, 28 Apr 2009 00:38:01 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/134056: [Update]biology/biojava:update to 1.7.0 Message-ID: <200904280038.n3S0c1XA076739@www.freebsd.org> Resent-Message-ID: <200904280040.n3S0e2bT097553@freefall.freebsd.org>
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>Number: 134056 >Category: ports >Synopsis: [Update]biology/biojava:update to 1.7.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Tue Apr 28 00:40:02 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Wen Heping >Release: FreeBSD 8.0-Current >Organization: ChangAn Middle School >Environment: FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #4: Fri Apr 10 16:36:28 HKT 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/wen1 i386 >Description: update to 1.7.0 from 1.5beta2 and take maintainership >How-To-Repeat: >Fix: Patch attached with submission follows: diff -urN biojava/Makefile biojava.new/Makefile --- biojava/Makefile 2008-12-09 19:02:56.000000000 +0800 +++ biojava.new/Makefile 2009-04-28 15:39:07.000000000 +0800 @@ -2,67 +2,38 @@ # Date created: 15 September 2000 # Whom: FreeBSD Bio porters (bio@freebsd.net) # -# $FreeBSD: ports/biology/biojava/Makefile,v 1.17 2008/12/08 06:43:45 linimon Exp $ +# $FreeBSD: ports/biology/biojava/Makefile,v 1.16 2008/06/06 13:08:28 edwin Exp $ # PORTNAME= biojava -DISTVERSION= 1.5-beta2 -PORTREVISION= 2 +DISTVERSION= 1.7 PORTEPOCH= 1 CATEGORIES= biology java -MASTER_SITES= http://www.biojava.org/download/bj15b/all/:source \ - http://www.biojava.org/download/bj15b/bin/:bin -DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:source \ - bytecode.jar:bin -EXTRACT_ONLY= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX} +MASTER_SITES= http://www.biojava.org/download/bj17/all/ +DISTNAME= ${PORTNAME}-${DISTVERSION}-all +EXTRACT_SUFX= .jar -MAINTAINER= ports@FreeBSD.org +MAINTAINER= wenheping@gmail.com COMMENT= Open-source java tools for processing biological data -BUILD_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \ - ${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \ - ${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \ - ${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \ - ${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \ - ${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \ - ${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections -RUN_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \ - ${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \ - ${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \ - ${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \ - ${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \ - ${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \ - ${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections - -.if !defined(WITHOUT_TESTS) -BUILD_DEPENDS+= ${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit -.endif +EXTRACT_DEPENDS+= jar:${PORTSDIR}/java/diablo-jdk16 USE_JAVA= yes JAVA_VERSION= 1.5+ USE_ANT= yes MAKE_ENV= CLASSPATH="${JAVALIBDIR}" -ALL_TARGET= compile-apps +ALL_TARGET= package-biojava -PLIST_SUB+= VER=${DISTVERSION} - -JARFILES= apps-${DISTVERSION}.jar biojava.jar bytecode.jar +JARFILES= biojava.jar bytecode.jar PORTDOCS= biojava -SAMPLES= demos -WRKSRC=${WRKDIR} - -.if !defined(NOPORTDOCS) -ALL_TARGET+= javadocs-biojava -.endif -.if !defined(WITHOUT_SAMPLES) -ALL_TARGET+= compile-demos -PLIST_SUB+= INSTEX="" -.else -PLIST_SUB+= INSTEX="@comment " -.endif - -post-extract: - ${CP} ${_DISTDIR}/bytecode.jar ${WRKSRC} +PORTEXAMPLES= demos +EXTRACT_CMD= jar -xvf ${_DISTDIR}/${DISTFILES} +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} + +do-extract: + @${RM} -rf ${WRKDIR} + @${MKDIR} ${WRKDIR} + @cd ${WRKDIR} && ${EXTRACT_CMD} .if !defined(WITHOUT_TESTS) regression-test: @@ -70,7 +41,6 @@ ${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests) .endif -# from textproc/xerces-j do-install: @${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..." @${MKDIR} ${JAVAJARDIR} @@ -79,21 +49,24 @@ @${ECHO_MSG} -n " ${JARFILE}" .endfor @${ECHO_MSG} " [ DONE ]" + .if !defined(NOPORTDOCS) @${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..." @${MKDIR} ${DOCSDIR} @${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR} @${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} - @cd ${WRKSRC}/ant-build/docs && \ + @cd ${WRKSRC}/doc && \ ${FIND} ${PORTDOCS} -type d -exec ${MKDIR} "${DOCSDIR}/{}" \; && \ ${FIND} ${PORTDOCS} -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \; @${ECHO_MSG} " [ DONE ]" .endif -.if !defined(WITHOUT_SAMPLES) - @${ECHO_MSG} -n ">> Installing demos in ${EXAMPLESDIR}..." - cd ${WRKSRC} && \ - ${FIND} ${SAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \ - ${FIND} ${SAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \; + +.if !defined(NOPORTEXAMPLES) + @${ECHO_MSG} -n ">> Installing examples in ${EXAMPLESDIR}..." + @${MKDIR} ${EXAMPLESDIR} + cd ${WRKSRC}/doc && \ + ${FIND} ${PORTEXAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \ + ${FIND} ${PORTEXAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \; @${ECHO_MSG} " [ DONE ]" .endif diff -urN biojava/distinfo biojava.new/distinfo --- biojava/distinfo 2007-03-27 16:01:54.000000000 +0800 +++ biojava.new/distinfo 2009-04-24 16:29:18.000000000 +0800 @@ -1,6 +1,3 @@ -MD5 (biojava-1.5-beta2.tar.gz) = 904e9a5600102a9a5238b87868e3f09f -SHA256 (biojava-1.5-beta2.tar.gz) = f2912bc90d4b9c01ac24e9db9718203af01b098538020989d4519cfabd901208 -SIZE (biojava-1.5-beta2.tar.gz) = 28767548 -MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37 -SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f -SIZE (bytecode.jar) = 93463 +MD5 (biojava-1.7-all.jar) = aedb49b6600430bc2b80090536c6ebff +SHA256 (biojava-1.7-all.jar) = 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f +SIZE (biojava-1.7-all.jar) = 28062592 diff -urN biojava/files/patch-build.xml biojava.new/files/patch-build.xml --- biojava/files/patch-build.xml 2007-03-27 16:01:54.000000000 +0800 +++ biojava.new/files/patch-build.xml 1970-01-01 08:00:00.000000000 +0800 @@ -1,11 +0,0 @@ ---- build.xml.orig Fri Dec 29 14:12:28 2006 -+++ build.xml Wed Mar 21 16:14:38 2007 -@@ -49,7 +49,7 @@ - - <property name="build.compiler" value="javac1.4" /> - -- <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-dbcp-1.1.jar:commons-pool-1.1.jar:hsqldb.jar" /> -+ <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-dbcp.jar:commons-pool.jar:hsqldb.jar" /> - - <property name="ant-tasks.path" value="ant-lib/sablecc.jar:ant-lib/anttask.jar" /> - diff -urN biojava/pkg-plist biojava.new/pkg-plist --- biojava/pkg-plist 2006-11-22 06:35:28.000000000 +0800 +++ biojava.new/pkg-plist 2009-04-28 14:32:03.000000000 +0800 @@ -1,215 +1,4 @@ -%%PORTDOCS%%%%DOCSDIR%%/LICENSE -%%PORTDOCS%%%%DOCSDIR%%/README -%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/CircularLocationTester.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/TestFrame.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ListChangeTypes.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/RFetch.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/annodb/CreateIndexDB.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/DummyFromGFF.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/LargeSequenceTest.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqDumper.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqEMBL.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqGFF.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SequenceTest.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/UploadFlat.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/BlastParser.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/input.xml -%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDAS.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASG.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASH.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDSN.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestDistribution.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNAlphabet.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNDistribution.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/Tools.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/Dice.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PairwiseAlignment.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PatternFinder.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/SearchProfile.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/ViterbiAlign.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fake.fasta -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fakepromoter.xml -%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/package.html -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Blast2HTML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/BlastLike2XML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Fasta2XML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Pdb2XML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1Handler.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/copyall.xsl -%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ACTN_HUMAN.uniprot -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AF438419.embl -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.embl -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.genbank -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ChrI.prom.fasta -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/GCG/blast.report -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/NP_001307.gp -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/clustal/keratin.aln -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fake.fasta -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fakepromoter.xml -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.db -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.m10 -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_queries.db -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/hmmer/plus_tot.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/Massive.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/ReadMe -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastp.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/shortBlastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/tblastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/tblastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/unsuppVersionBlastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/out.gff -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/12E8.pdb -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hgh_ori.pdb -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hmga_1.pdb -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/tnf.pdb -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/scoptest.fa -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/test.hmm -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.dna -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.gff -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastp.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastp.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_tblastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastn.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastx.out -%%INSTEX%%%%EXAMPLESDIR%%/demos/game/AE002734.game -%%INSTEX%%%%EXAMPLESDIR%%/demos/game/README.txt -%%INSTEX%%%%EXAMPLESDIR%%/demos/game/SeqIOTatler.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/game/TestGAME.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/AL121903.embl -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/EmblToGffFasta.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFCompare.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFFilter.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFMask.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFToFeatures.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GenbankToGffFasta.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/SwissprotToGffFasta.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/XFF2GFF.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/varC4-2.gff -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateFAIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateSPIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ListIDs.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRaw.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRawSecondary.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/BlastLike2XML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/Pdb2XML.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/process/ProcessToolsTest.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/prot/TestDigestIO.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/search/IndexFastaDB.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.embl -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.genbank -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/FetchSeq.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/GCContent.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/MotifFinder2.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/ReverseComplement.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/SimpleAssemblyTest.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl2.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestGenbank.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestRefSeqPrt.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSubSequence.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSwissprot.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestTranslation.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/UniProtDemo.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/AddFilesToIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/CreateIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/FetchSequence.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/ListSeqsInIndex.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/utrs.fa -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/BeadDemo.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/CircularEmblViewer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer2.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/FastBeadDemo.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/GappedViewer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/TraceViewer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/test.fa -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTable.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableCompact.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableLarge.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTable.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTableLarge.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/ResultPrinter.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHA.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHALarge.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeq.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeqLarge.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/AlignmentBuilder.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountHits.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountSubHits.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/Echoer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/FilterByValue.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListQueries.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListSubjects.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ProcessBlastReport.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/PropertyEchoer.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitBuilder.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitFilter.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/MatrixValue.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/PatternDemo.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAlphabetIndexers.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAmbiguity.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestGappedSymbolList.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestIndexedIntegers.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestLocation.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestOrderNSymbolList.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestSimpleAlignment.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestWindowedSymbolList.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/Tools.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/WindowCount.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Grep.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Index.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Parse.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseEmbl.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseSwissprot.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/PrintFormat.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/CreateUnigeneFlat.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseLibInfo.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseUnigene.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/SearchUnigeneFlat.java -%%INSTEX%%%%EXAMPLESDIR%%/demos/xff/TestXFFStreaming.java -%%JAVAJARDIR%%/apps-%%VER%%.jar %%JAVAJARDIR%%/biojava.jar %%JAVAJARDIR%%/bytecode.jar -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/xff -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/unigene -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/tagvalue -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/symbol -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssbind -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssaha -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seqviewer -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq/db -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/search -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/prot -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/process -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/nativeapps -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/indexing -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/gff -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/game -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/wublast -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/pdb -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/ncbiblast -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/hmmer -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/clustal -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/GCG -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dp -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dist -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/das -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/blastxml -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/biosql -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/annodb -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/CircLocTest -%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos -%%INSTEX%%@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%%%DOCSDIR%%/LICENSE +%%PORTDOCS%%%%DOCSDIR%%/README >Release-Note: >Audit-Trail: >Unformatted:
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