Attachment 47941 Details for Bug 73391 – file.diff

[patch] file.diff

file.diff (text/plain), 56.49 KB, created by Choe, Cheng-Dae on 2004-11-01 19:50:21 UTC

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Creator: Choe, Cheng-Dae

Created: 2004-11-01 19:50:21 UTC

Size: 56.49 KB

patch

obsolete

>diff -ruN biojava.orig/Makefile biojava/Makefile
>--- biojava.orig/Makefile	Sun Nov  2 11:48:04 2003
>+++ biojava/Makefile	Tue Nov  2 04:41:14 2004
>@@ -6,54 +6,68 @@
> #
> 
> PORTNAME=	biojava
>-PORTVERSION=	1.01
>+PORTVERSION=	1.30
> CATEGORIES=	biology java
> MASTER_SITES=	http://www.biojava.org/download/source/
> 
>-MAINTAINER=	ports@FreeBSD.org
>+MAINTAINER=	whitekid@gmail.com
> COMMENT=	Open-source java tools for processing biological data
> 
>-BUILD_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/linux-sun-jdk12
>-
>-JDK_VERSION=	1.2.2
>-JAVAVERSION=	linux-sun-jdk${JDK_VERSION}
>-JAVADIR=	${PREFIX}/${JAVAVERSION}
>-JAVA_COMPILE=	${JAVADIR}/bin/javac
>-JAVA_COMMAND=	${JAVADIR}/bin/java
>-
>-do-build:
>-	@(cd ${WRKSRC}; \
>-		${JAVA_COMPILE} build/Builder.java; \
>-		${SETENV} PATH=${PATH}:${JAVADIR}/bin \
>-		${JAVA_COMMAND} build.Builder all;)
>+BUILD_DEPENDS=	${LOCALBASE}/bin/ant:${PORTSDIR}/devel/apache-ant
>+RUN_DEPENDS=	${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
>+		${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp
>+
>+USE_JAVA=	yes
>+JDK_VERSION=	1.3+
>+USE_ANT=	yes
>+
>+JARFILES=	biojava.jar bytecode.jar
>+PORTDOCS=	api
>+SAMPLES=	demos demos-1.4 demos-obsolete
> 
>+post-build:
> .if !defined(NOPORTDOCS)
>-	@(cd ${WRKSRC}; ${SETENV} PATH=${PATH}:${JAVADIR}/bin \
>-	${JAVA_COMMAND} build.Builder docs;)
>+	@${ECHO_MSG} -n ">> Build javadocs..."
>+	@cd ${WRKSRC} && ant javadocs
> .endif
> 
>+# from textproc/xerces-j
> do-install:
>-	@(cd ${WRKSRC}; \
>-		${MKDIR} ${PREFIX}/share/java/classes/; \
>-		${CP} ${WRKSRC}/biojava.jar ${PREFIX}/share/java/classes/; \
>-		${CP} ${WRKSRC}/xml.jar ${PREFIX}/share/java/classes/; \
>-		${MKDIR} ${PREFIX}/share/java/${PKGNAME}/; \
>-		${CP} -R README LICENSE ${PREFIX}/share/java/${PKGNAME}/; \
>-		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)
>-
>+	@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."
>+	@${MKDIR} ${JAVAJARDIR}
>+.for JARFILE in ${JARFILES}
>+	@cd ${WRKSRC}/ant-build && ${INSTALL_DATA} ${JARFILE} ${JAVAJARDIR}/${JARFILE}
>+	@${ECHO_MSG} -n " ${JARFILE}"
>+.endfor
>+	@${ECHO_MSG} " [ DONE ]"
> .if !defined(NOPORTDOCS)
>-	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/doc/${PKGNAME})
>-.endif)
>+	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."
>+	@${MKDIR} ${DOCSDIR}
>+	@${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR}
>+	@${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
>+	@cd ${WRKSRC}/ant-build/docs && \
>+		${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}/{}" \;
>+	@${ECHO_MSG} " [ DONE ]"
>+.endif
> 
> post-install:
> .if !defined(BATCH)
> 	@${ECHO_MSG} ""
>-	@${ECHO_MSG} "Libraries installed at: ${PREFIX}/share/java/classes/"
>+	@${ECHO_MSG} "Libraries installed at: ${JAVAJARDIR}"
> 	@${ECHO_MSG} "You should edit your CLASSPATH to include the jar files"
> 	@${ECHO_MSG} "in this directory."
> 	@${ECHO_MSG} ""
> 	@${ECHO_MSG} "Docs and demos are installed in:"
>-	@${ECHO_MSG} "${PREFIX}/share/java/${PKGNAME}"
>+	@${ECHO_MSG} "${DOCSDIR}"
> 	@${ECHO_MSG} ""
> .endif
> 
>diff -ruN biojava.orig/distinfo biojava/distinfo
>--- biojava.orig/distinfo	Wed Jan 28 05:51:05 2004
>+++ biojava/distinfo	Tue Nov  2 00:54:42 2004
>@@ -1,2 +1,2 @@
>-MD5 (biojava-1.01.tar.gz) = c4f3e397ff5f5f3b71da6c3e7b68b9b9
>-SIZE (biojava-1.01.tar.gz) = 787008
>+MD5 (biojava-1.30.tar.gz) = 68a70c9aaa06b935b86f9883bfbffd99
>+SIZE (biojava-1.30.tar.gz) = 9227361
>diff -ruN biojava.orig/pkg-plist biojava/pkg-plist
>--- biojava.orig/pkg-plist	Wed Oct 22 18:29:53 2003
>+++ biojava/pkg-plist	Tue Nov  2 03:25:14 2004
>@@ -1,585 +1,214 @@
>+%%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/xml.jar
>-share/java/biojava-1.01/LICENSE
>-share/java/biojava-1.01/README
>-share/java/biojava-1.01/demos/acedb/AceTreeView.java
>-share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java
>-share/java/biojava-1.01/demos/acedb/AceClient.java
>-share/java/biojava-1.01/demos/acedb/SequenceFetch.java
>-share/java/biojava-1.01/demos/gff/GFFFilter.java
>-share/java/biojava-1.01/demos/gff/EmblToGffFasta.java
>-share/java/biojava-1.01/demos/gff/GFFToFeatures.java
>-share/java/biojava-1.01/demos/gff/varC4-2.gff
>-share/java/biojava-1.01/demos/gff/AL121903.embl
>-share/java/biojava-1.01/demos/seq/db/AddFilesToIndex.java
>-share/java/biojava-1.01/demos/seq/db/CreateIndex.java
>-share/java/biojava-1.01/demos/seq/db/FetchSequence.java
>-share/java/biojava-1.01/demos/seq/db/ListSeqsInIndex.java
>-share/java/biojava-1.01/demos/seq/TestGenbank.java
>-share/java/biojava-1.01/demos/seq/AL121903.genbank
>-share/java/biojava-1.01/demos/seq/TestTranslation.java
>-share/java/biojava-1.01/demos/seq/TestEmbl.java
>-share/java/biojava-1.01/demos/seq/AL121903.embl
>-share/java/biojava-1.01/demos/dist/TestDistribution.java
>-share/java/biojava-1.01/demos/dp/PairwiseAlignment.java
>-share/java/biojava-1.01/demos/dp/fake.fasta
>-share/java/biojava-1.01/demos/dp/ViterbiAlign.java
>-share/java/biojava-1.01/demos/dp/package.html
>-share/java/biojava-1.01/demos/dp/SearchProfile.java
>-share/java/biojava-1.01/demos/dp/fakepromoter.xml
>-share/java/biojava-1.01/demos/dp/Dice.java
>-share/java/biojava-1.01/demos/BioCorba/CorbaDBServer.java
>-share/java/biojava-1.01/demos/BioCorba/ChrI.prom.fasta
>-share/java/biojava-1.01/demos/BioCorba/CorbaDBClient.java
>-share/java/biojava-1.01/demos/files/AL121903.embl
>-share/java/biojava-1.01/demos/files/test.hmm
>-share/java/biojava-1.01/demos/files/out.gff
>-share/java/biojava-1.01/demos/files/AL121903.genbank
>-share/java/biojava-1.01/demos/files/ChrI.prom.fasta
>-share/java/biojava-1.01/demos/files/fakepromoter.xml
>-share/java/biojava-1.01/demos/files/scoptest.fa
>-share/java/biojava-1.01/demos/files/varC4-2.gff
>-share/java/biojava-1.01/demos/files/varC4-2.dna
>-share/java/biojava-1.01/demos/files/fake.fasta
>-share/java/biojava-1.01/demos/symbol/TestAmbiguity.java
>-share/java/biojava-1.01/demos/symbol/TestSimpleAlignment.java
>-share/java/biojava-1.01/demos/symbol/Tools.java
>-share/java/biojava-1.01/demos/symbol/TestOrderNSymbolList.java
>-share/java/biojava-1.01/demos/symbol/TestGappedSymbolList.java
>-share/java/biojava-1.01/demos/symbol/TestWindowedSymbolList.java
>-share/java/biojava-1.01/demos/seqviewer/test.fa
>-share/java/biojava-1.01/demos/seqviewer/EmblViewer.java
>-share/java/biojava-1.01/demos/seqviewer/TestSequencePanel.java
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/UnknownHolder.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-tree.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-frame.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_Unknown_Operations.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/Unknown.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_Unknown_Tie.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_UnknownImplBase.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_UnknownStub.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/UnknownHelper.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-summary.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-summary.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-tree.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-frame.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/SocketDriver.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/SocketResultSet.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticStringValue.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/package-tree.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/package-frame.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceNode.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceObject.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceSet.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticDateValue.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticFloatValue.html
>-%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticIntValue.html
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>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/gui/sequence
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/gui
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/dist
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/search
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq/db
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq/io
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/symbol
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats/svm
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils/contract
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils/xml
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01
>+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

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Attachments on bug 73391: 47941