Date: Sun, 22 Oct 2006 22:07:14 +0200 (CEST) From: Thierry Thomas <thierry@pompo.net> To: FreeBSD-gnats-submit@FreeBSD.org Cc: "Choe, Cheng-Dae" <whitekid@gmail.com> Subject: ports/104685: biology/biojava: upgrade to 1.5-beta and unbreak. Message-ID: <20061022200714.C195611457@graf.pompo.net> Resent-Message-ID: <200610222010.k9MKAGxL043009@freefall.freebsd.org>
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>Number: 104685 >Category: ports >Synopsis: biology/biojava: upgrade to 1.5-beta and unbreak. >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Sun Oct 22 20:10:16 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Thierry Thomas >Release: FreeBSD 6.2-PRERELEASE i386 >Organization: Kabbale Eros >Environment: System: FreeBSD graf.pompo.net 6.2-PRERELEASE FreeBSD 6.2-PRERELEASE #0: Sun Oct 1 18:37:56 CEST 2006 thierry@graf.pompo.net:/usr/obj/usr/src/sys/GRAF060511 i386 >Description: biology/biojava is marked BROKEN and DEPRECATED. The attached patch upgrades it to the latest version and fixes the build problem. Since I'm there, I have added a regression-tests target and fixed plist for WITHOUT_SAMPLES. >How-To-Repeat: See logs on pointyhat. E.g. http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/e.5.2006092519/biojava-1.30.log >Fix: Please apply the following patch: --- biojava.diff begins here --- diff -urN biology/biojava.orig/Makefile biology/biojava/Makefile --- biology/biojava.orig/Makefile Sat Sep 9 15:49:14 2006 +++ biology/biojava/Makefile Sun Oct 22 17:09:37 2006 @@ -6,32 +6,62 @@ # PORTNAME= biojava -PORTVERSION= 1.30 +DISTVERSION= 1.5-beta +PORTEPOCH= 1 CATEGORIES= biology java -MASTER_SITES= http://www.biojava.org/download/source/ +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} MAINTAINER= whitekid@gmail.com COMMENT= Open-source java tools for processing biological data -RUN_DEPENDS= ${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \ - ${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp +BUILD_DEPENDS= ${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \ + ${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \ + ${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool +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 -BROKEN= Does not compile -DEPRECATED= ${BROKEN} -EXPIRATION_DATE=2006-12-01 +.if !defined(WITHOUT_TESTS) +BUILD_DEPENDS+= ${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit +.endif USE_JAVA= yes -JAVA_VERSION= 1.3+ +JAVA_VERSION= 1.4+ USE_ANT= yes +MAKE_ENV= CLASSPATH="${JAVALIBDIR}" +ALL_TARGET= compile-apps + +PLIST_SUB+= VER=${DISTVERSION} -JARFILES= biojava.jar bytecode.jar -PORTDOCS= api -SAMPLES= demos demos-1.4 demos-obsolete +JARFILES= apps-${DISTVERSION}.jar biojava.jar bytecode.jar +PORTDOCS= biojava +SAMPLES= demos -post-build: .if !defined(NOPORTDOCS) - @${ECHO_MSG} -n ">> Build javadocs..." - @cd ${WRKSRC} && ant javadocs +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} + +.if !defined(WITHOUT_TESTS) +regression-test: + @(cd ${BUILD_WRKSRC}; \ + ${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests) .endif # from textproc/xerces-j @@ -53,7 +83,6 @@ ${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} && \ diff -urN biology/biojava.orig/distinfo biology/biojava/distinfo --- biology/biojava.orig/distinfo Tue Jan 31 20:44:46 2006 +++ biology/biojava/distinfo Sun Oct 22 11:45:35 2006 @@ -1,3 +1,6 @@ -MD5 (biojava-1.30.tar.gz) = 68a70c9aaa06b935b86f9883bfbffd99 -SHA256 (biojava-1.30.tar.gz) = c08a0c2f4b35eab056968f6d8f8d575fb4cd5172ee9bf9cbda0a60e408214f72 -SIZE (biojava-1.30.tar.gz) = 9227361 +MD5 (biojava-1.5-beta.tar.gz) = 8dc7307d9dc4bc9dd9222dfaaee5d047 +SHA256 (biojava-1.5-beta.tar.gz) = a8e0ba3a393bc70606bf7393255077b32bd1c1980f5daeec07c7362f0d2985e1 +SIZE (biojava-1.5-beta.tar.gz) = 15777707 +MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37 +SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f +SIZE (bytecode.jar) = 93463 diff -urN biology/biojava.orig/files/patch-build.xml biology/biojava/files/patch-build.xml --- biology/biojava.orig/files/patch-build.xml Thu Jan 1 01:00:00 1970 +++ biology/biojava/files/patch-build.xml Sun Oct 22 14:08:39 2006 @@ -0,0 +1,11 @@ +--- build.xml.orig Thu Sep 7 11:18:13 2006 ++++ build.xml Sun Oct 22 12:43:18 2006 +@@ -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 biology/biojava.orig/pkg-plist biology/biojava/pkg-plist --- biology/biojava.orig/pkg-plist Mon Nov 22 16:47:58 2004 +++ biology/biojava/pkg-plist Sun Oct 22 17:19:46 2006 @@ -1,214 +1,215 @@ %%PORTDOCS%%%%DOCSDIR%%/LICENSE %%PORTDOCS%%%%DOCSDIR%%/README -share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTableCompact.java -share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTableLarge.java -share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTable.java -share/examples/biojava/demos-1.4/ssaha/CreateEmblHashTable.java -share/examples/biojava/demos-1.4/ssaha/CreateEmblHashTableLarge.java -share/examples/biojava/demos-1.4/ssaha/ResultPrinter.java -share/examples/biojava/demos-1.4/ssaha/SSAHA.java -share/examples/biojava/demos-1.4/ssaha/SSAHALarge.java -share/examples/biojava/demos-1.4/ssaha/SSAHASeq.java -share/examples/biojava/demos-1.4/ssaha/SSAHASeqLarge.java -share/examples/biojava/demos-1.4/unigene/CreateUnigeneFlat.java -share/examples/biojava/demos-1.4/unigene/ParseLibInfo.java -share/examples/biojava/demos-1.4/unigene/ParseUnigene.java -share/examples/biojava/demos-1.4/unigene/SearchUnigeneFlat.java -share/examples/biojava/demos-obsolete/bioseqdb/UploadSwissprot.java -share/examples/biojava/demos-obsolete/search/FastaSearchParse.java -share/examples/biojava/demos-obsolete/seq/TestSwissprotOrg.java -share/examples/biojava/demos-obsolete/symbol/TestPackedSymbolList.java -share/examples/biojava/demos/CircLocTest/CircularLocationTester.java -share/examples/biojava/demos/CircLocTest/TestFrame.java -share/examples/biojava/demos/ListChangeTypes.java -share/examples/biojava/demos/RFetch.java -share/examples/biojava/demos/biosql/DummyFromGFF.java -share/examples/biojava/demos/biosql/LargeSequenceTest.java -share/examples/biojava/demos/biosql/SeqDumper.java -share/examples/biojava/demos/biosql/SeqEMBL.java -share/examples/biojava/demos/biosql/SeqGFF.java -share/examples/biojava/demos/biosql/SequenceTest.java -share/examples/biojava/demos/biosql/UploadFlat.java -share/examples/biojava/demos/das/TestDAS.java -share/examples/biojava/demos/das/TestDASG.java -share/examples/biojava/demos/das/TestDASH.java -share/examples/biojava/demos/das/TestDSN.java -share/examples/biojava/demos/dist/TestDistribution.java -share/examples/biojava/demos/dist/TestOrderNAlphabet.java -share/examples/biojava/demos/dist/TestOrderNDistribution.java -share/examples/biojava/demos/dist/Tools.java -share/examples/biojava/demos/dp/Dice.java -share/examples/biojava/demos/dp/PairwiseAlignment.java -share/examples/biojava/demos/dp/SearchProfile.java -share/examples/biojava/demos/dp/ViterbiAlign.java -share/examples/biojava/demos/dp/fake.fasta -share/examples/biojava/demos/dp/fakepromoter.xml -share/examples/biojava/demos/dp/package.html -share/examples/biojava/demos/eventbasedparsing/Blast2HTML.java -share/examples/biojava/demos/eventbasedparsing/BlastLike2XML.java -share/examples/biojava/demos/eventbasedparsing/Fasta2XML.java -share/examples/biojava/demos/eventbasedparsing/Pdb2XML.java -share/examples/biojava/demos/eventbasedparsing/TutorialEx1.java -share/examples/biojava/demos/eventbasedparsing/TutorialEx1Handler.java -share/examples/biojava/demos/eventbasedparsing/stylesheets/copyall.xsl -share/examples/biojava/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl -share/examples/biojava/demos/files/AL121903.embl -share/examples/biojava/demos/files/AL121903.genbank -share/examples/biojava/demos/files/ChrI.prom.fasta -share/examples/biojava/demos/files/GCG/blast.report -share/examples/biojava/demos/files/clustal/keratin.aln -share/examples/biojava/demos/files/fake.fasta -share/examples/biojava/demos/files/fakepromoter.xml -share/examples/biojava/demos/files/fp_demo.db -share/examples/biojava/demos/files/fp_demo.m10 -share/examples/biojava/demos/files/fp_queries.db -share/examples/biojava/demos/files/hmmer/plus_tot.out -share/examples/biojava/demos/files/ncbiblast/Massive.out -share/examples/biojava/demos/files/ncbiblast/ReadMe -share/examples/biojava/demos/files/ncbiblast/blastn.out -share/examples/biojava/demos/files/ncbiblast/blastp.out -share/examples/biojava/demos/files/ncbiblast/blastx.out -share/examples/biojava/demos/files/ncbiblast/shortBlastn.out -share/examples/biojava/demos/files/ncbiblast/tblastn.out -share/examples/biojava/demos/files/ncbiblast/tblastx.out -share/examples/biojava/demos/files/ncbiblast/unsuppVersionBlastn.out -share/examples/biojava/demos/files/out.gff -share/examples/biojava/demos/files/pdb/12E8.pdb -share/examples/biojava/demos/files/pdb/hgh_ori.pdb -share/examples/biojava/demos/files/pdb/hmga_1.pdb -share/examples/biojava/demos/files/pdb/tnf.pdb -share/examples/biojava/demos/files/scoptest.fa -share/examples/biojava/demos/files/test.hmm -share/examples/biojava/demos/files/varC4-2.dna -share/examples/biojava/demos/files/varC4-2.gff -share/examples/biojava/demos/files/wublast/blastn.out -share/examples/biojava/demos/files/wublast/blastp.out -share/examples/biojava/demos/files/wublast/blastx.out -share/examples/biojava/demos/files/wublast/sh_blastn.out -share/examples/biojava/demos/files/wublast/sh_blastp.out -share/examples/biojava/demos/files/wublast/sh_blastx.out -share/examples/biojava/demos/files/wublast/sh_tblastx.out -share/examples/biojava/demos/files/wublast/tblastn.out -share/examples/biojava/demos/files/wublast/tblastx.out -share/examples/biojava/demos/game/AE002734.game -share/examples/biojava/demos/game/README.txt -share/examples/biojava/demos/game/SeqIOTatler.java -share/examples/biojava/demos/game/TestGAME.java -share/examples/biojava/demos/gff/AL121903.embl -share/examples/biojava/demos/gff/EmblToGffFasta.java -share/examples/biojava/demos/gff/GFFCompare.java -share/examples/biojava/demos/gff/GFFFilter.java -share/examples/biojava/demos/gff/GFFMask.java -share/examples/biojava/demos/gff/GFFToFeatures.java -share/examples/biojava/demos/gff/GenbankToGffFasta.java -share/examples/biojava/demos/gff/SwissprotToGffFasta.java -share/examples/biojava/demos/gff/XFF2GFF.java -share/examples/biojava/demos/gff/varC4-2.gff -share/examples/biojava/demos/indexing/CreateFAIndex.java -share/examples/biojava/demos/indexing/CreateIndex.java -share/examples/biojava/demos/indexing/CreateSPIndex.java -share/examples/biojava/demos/indexing/ListIDs.java -share/examples/biojava/demos/indexing/ReadRaw.java -share/examples/biojava/demos/indexing/ReadRawSecondary.java -share/examples/biojava/demos/nativeapps/BlastLike2XML.java -share/examples/biojava/demos/nativeapps/Pdb2XML.java -share/examples/biojava/demos/prot/TestDigestIO.java -share/examples/biojava/demos/ragbag/README -share/examples/biojava/demos/ragbag/SequenceDumper.java -share/examples/biojava/demos/ragbag/TestRagbagAssembly.java -share/examples/biojava/demos/ragbag/embldir.tgz -share/examples/biojava/demos/ragbag/seqdir.tgz -share/examples/biojava/demos/ragbag/testfeature.game -share/examples/biojava/demos/ragbag/virtdir.tgz -share/examples/biojava/demos/search/IndexFastaDB.java -share/examples/biojava/demos/seq/AL121903.embl -share/examples/biojava/demos/seq/AL121903.genbank -share/examples/biojava/demos/seq/FetchSeq.java -share/examples/biojava/demos/seq/GCContent.java -share/examples/biojava/demos/seq/MotifFinder2.java -share/examples/biojava/demos/seq/ReverseComplement.java -share/examples/biojava/demos/seq/SimpleAssemblyTest.java -share/examples/biojava/demos/seq/TestEmbl.java -share/examples/biojava/demos/seq/TestEmbl2.java -share/examples/biojava/demos/seq/TestGenbank.java -share/examples/biojava/demos/seq/TestRefSeqPrt.java -share/examples/biojava/demos/seq/TestSubSequence.java -share/examples/biojava/demos/seq/TestSwissprot.java -share/examples/biojava/demos/seq/TestTranslation.java -share/examples/biojava/demos/seq/db/AddFilesToIndex.java -share/examples/biojava/demos/seq/db/CreateIndex.java -share/examples/biojava/demos/seq/db/FetchSequence.java -share/examples/biojava/demos/seq/db/ListSeqsInIndex.java -share/examples/biojava/demos/seq/utrs.fa -share/examples/biojava/demos/seqviewer/BeadDemo.java -share/examples/biojava/demos/seqviewer/EmblViewer.java -share/examples/biojava/demos/seqviewer/EmblViewer2.java -share/examples/biojava/demos/seqviewer/FastBeadDemo.java -share/examples/biojava/demos/seqviewer/TraceViewer.java -share/examples/biojava/demos/seqviewer/test.fa -share/examples/biojava/demos/ssbind/AlignmentBuilder.java -share/examples/biojava/demos/ssbind/CountHits.java -share/examples/biojava/demos/ssbind/CountSubHits.java -share/examples/biojava/demos/ssbind/Echoer.java -share/examples/biojava/demos/ssbind/FilterByValue.java -share/examples/biojava/demos/ssbind/ListQueries.java -share/examples/biojava/demos/ssbind/ListSubjects.java -share/examples/biojava/demos/ssbind/ProcessBlastReport.java -share/examples/biojava/demos/ssbind/PropertyEchoer.java -share/examples/biojava/demos/ssbind/SubHitBuilder.java -share/examples/biojava/demos/ssbind/SubHitFilter.java -share/examples/biojava/demos/symbol/MatrixValue.java -share/examples/biojava/demos/symbol/PatternDemo.java -share/examples/biojava/demos/symbol/TestAlphabetIndexers.java -share/examples/biojava/demos/symbol/TestAmbiguity.java -share/examples/biojava/demos/symbol/TestGappedSymbolList.java -share/examples/biojava/demos/symbol/TestIndexedIntegers.java -share/examples/biojava/demos/symbol/TestLocation.java -share/examples/biojava/demos/symbol/TestOrderNSymbolList.java -share/examples/biojava/demos/symbol/TestSimpleAlignment.java -share/examples/biojava/demos/symbol/TestWindowedSymbolList.java -share/examples/biojava/demos/symbol/Tools.java -share/examples/biojava/demos/symbol/WindowCount.java -share/examples/biojava/demos/tagvalue/ParseEmbl.java -share/examples/biojava/demos/tagvalue/ParseSwissprot.java -share/examples/biojava/demos/xff/TestXFFStreaming.java -share/java/classes/biojava.jar -share/java/classes/bytecode.jar -@dirrm share/examples/biojava/demos/xff -@dirrm share/examples/biojava/demos/tagvalue -@dirrm share/examples/biojava/demos/symbol -@dirrm share/examples/biojava/demos/ssbind -@dirrm share/examples/biojava/demos/seqviewer -@dirrm share/examples/biojava/demos/seq/db -@dirrm share/examples/biojava/demos/seq -@dirrm share/examples/biojava/demos/search -@dirrm share/examples/biojava/demos/ragbag -@dirrm share/examples/biojava/demos/prot -@dirrm share/examples/biojava/demos/nativeapps -@dirrm share/examples/biojava/demos/indexing -@dirrm share/examples/biojava/demos/gff -@dirrm share/examples/biojava/demos/game -@dirrm share/examples/biojava/demos/files/wublast -@dirrm share/examples/biojava/demos/files/pdb -@dirrm share/examples/biojava/demos/files/ncbiblast -@dirrm share/examples/biojava/demos/files/hmmer -@dirrm share/examples/biojava/demos/files/clustal -@dirrm share/examples/biojava/demos/files/GCG -@dirrm share/examples/biojava/demos/files -@dirrm share/examples/biojava/demos/eventbasedparsing/stylesheets -@dirrm share/examples/biojava/demos/eventbasedparsing -@dirrm share/examples/biojava/demos/dp -@dirrm share/examples/biojava/demos/dist -@dirrm share/examples/biojava/demos/das -@dirrm share/examples/biojava/demos/biosql -@dirrm share/examples/biojava/demos/CircLocTest -@dirrm share/examples/biojava/demos-obsolete/symbol -@dirrm share/examples/biojava/demos-obsolete/seq -@dirrm share/examples/biojava/demos-obsolete/search -@dirrm share/examples/biojava/demos-obsolete/bioseqdb -@dirrm share/examples/biojava/demos-obsolete -@dirrm share/examples/biojava/demos-1.4/unigene -@dirrm share/examples/biojava/demos-1.4/ssaha -@dirrm share/examples/biojava/demos-1.4 -@dirrm share/examples/biojava/demos -@dirrm share/examples/biojava +%%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%% --- biojava.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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