- Update biology/biojava to 1.30

- Install javadoc and example files
- Assign maintainership to submitter

PR:		ports/73391
Submitted by:	Cheng-Dae Choe
Add. reviewing:	hq@

3 files changed, 255 insertions, 613 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 8fbbe1f10f72..6d8895aa7238 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -6,54 +6,67 @@
 #
 
 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
+RUN_DEPENDS=	${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
+		${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp
 
-JDK_VERSION=	1.2.2
-JAVAVERSION=	linux-sun-jdk${JDK_VERSION}
-JAVADIR=	${PREFIX}/${JAVAVERSION}
-JAVA_COMPILE=	${JAVADIR}/bin/javac
-JAVA_COMMAND=	${JAVADIR}/bin/java
+USE_JAVA=	yes
+JAVA_VERSION=	1.3+
+USE_ANT=	yes
 
-do-build:
-	@(cd ${WRKSRC}; \
-		${JAVA_COMPILE} build/Builder.java; \
-		${SETENV} PATH=${PATH}:${JAVADIR}/bin \
-		${JAVA_COMMAND} build.Builder all;)
+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 --git a/biology/biojava/distinfo b/biology/biojava/distinfo
index ed6ef693b033..e57b6152ff68 100644
--- a/biology/biojava/distinfo
+++ b/biology/biojava/distinfo
@@ -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 --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist
index 1daa6eec24aa..bd91873e4870 100644
--- a/biology/biojava/pkg-plist
+++ b/biology/biojava/pkg-plist
@@ -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
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-%%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