ports/73391: [Maintainer update] update biology/biojava to 1.30
Choe, Cheng-Dae
whitekid at gmail.com
Mon Nov 1 19:50:22 UTC 2004
>Number: 73391
>Category: ports
>Synopsis: [Maintainer update] update biology/biojava to 1.30
>Confidential: no
>Severity: non-critical
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Mon Nov 01 19:50:21 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator: "Choe, Cheng-Dae"
>Release: FreeBSD 5.3-STABLE i386
>Organization:
>Environment:
System: FreeBSD comdongin.com 5.3-STABLE FreeBSD 5.3-STABLE #0: Fri Oct 29 05:53:59 KST 2004 root at comdongin.com:/usr/obj/data/src/sys/CDI i386
>Description:
- Update biology/biojava to 1.30
- Update maintainer to me
- Build with apache-ant
- Install javadoc and example files
But it has some todo.
If biojava compiled with jdk1.4, it produce demo-1.4 directory. but this pr don't consider this. When it ccompiled with jdk1.3 or below, just ignore demo-1.4.
>How-To-Repeat:
N/A
>Fix:
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 at FreeBSD.org
+MAINTAINER= whitekid at 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
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-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
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-share/java/biojava-1.01/demos/dp/fakepromoter.xml
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-share/java/biojava-1.01/demos/files/fake.fasta
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-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
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-share/java/biojava-1.01/demos/seqviewer/TestSequencePanel.java
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- at dirrm share/java/biojava-1.01/demos/acedb
- at dirrm share/java/biojava-1.01/demos/gff
- at dirrm share/java/biojava-1.01/demos/seq/db
- at dirrm share/java/biojava-1.01/demos/seq
- at dirrm share/java/biojava-1.01/demos/dist
- at dirrm share/java/biojava-1.01/demos/dp
- at dirrm share/java/biojava-1.01/demos/BioCorba
- at dirrm share/java/biojava-1.01/demos/files
- at dirrm share/java/biojava-1.01/demos/symbol
- at dirrm share/java/biojava-1.01/demos/seqviewer
- at dirrm share/java/biojava-1.01/demos
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-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/program/gff
-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/program
-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/dp
-%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/gui/sequence
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-%%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
+ at dirrm share/examples/biojava/demos/xff
+ at dirrm share/examples/biojava/demos/tagvalue
+ at dirrm share/examples/biojava/demos/symbol
+ at dirrm share/examples/biojava/demos/ssbind
+ at dirrm share/examples/biojava/demos/seqviewer
+ at dirrm share/examples/biojava/demos/seq/db
+ at dirrm share/examples/biojava/demos/seq
+ at dirrm share/examples/biojava/demos/search
+ at dirrm share/examples/biojava/demos/ragbag
+ at dirrm share/examples/biojava/demos/prot
+ at dirrm share/examples/biojava/demos/nativeapps
+ at dirrm share/examples/biojava/demos/indexing
+ at dirrm share/examples/biojava/demos/gff
+ at dirrm share/examples/biojava/demos/game
+ at dirrm share/examples/biojava/demos/files/wublast
+ at dirrm share/examples/biojava/demos/files/pdb
+ at dirrm share/examples/biojava/demos/files/ncbiblast
+ at dirrm share/examples/biojava/demos/files/hmmer
+ at dirrm share/examples/biojava/demos/files/clustal
+ at dirrm share/examples/biojava/demos/files/GCG
+ at dirrm share/examples/biojava/demos/files
+ at dirrm share/examples/biojava/demos/eventbasedparsing/stylesheets
+ at dirrm share/examples/biojava/demos/eventbasedparsing
+ at dirrm share/examples/biojava/demos/dp
+ at dirrm share/examples/biojava/demos/dist
+ at dirrm share/examples/biojava/demos/das
+ at dirrm share/examples/biojava/demos/biosql
+ at dirrm share/examples/biojava/demos/CircLocTest
+ at dirrm share/examples/biojava/demos-obsolete/symbol
+ at dirrm share/examples/biojava/demos-obsolete/seq
+ at dirrm share/examples/biojava/demos-obsolete/search
+ at dirrm share/examples/biojava/demos-obsolete/bioseqdb
+ at dirrm share/examples/biojava/demos-obsolete
+ at dirrm share/examples/biojava/demos-1.4/unigene
+ at dirrm share/examples/biojava/demos-1.4/ssaha
+ at dirrm share/examples/biojava/demos-1.4
+ at dirrm share/examples/biojava/demos
+ at dirrm share/examples/biojava
>Release-Note:
>Audit-Trail:
>Unformatted:
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