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- Update to 1.7

Browse source 
- Pass maintainership to submitter

PR:		134056
Submitted by:	Wen Heping <wenheping@gmail.com>
This commit is contained in:
Martin Wilke 2009-05-01 09:33:42 +00:00
parent e1e806faac
commit 8fd8309d5d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=233032
4 changed files with 29 additions and 281 deletions
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75
biology/biojava/Makefile
View file

@ -6,63 +6,34 @@
#
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}
PORTEXAMPLES= demos
EXTRACT_CMD= jar -xvf ${_DISTDIR}/${DISTFILES}
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
.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 ${WRKSRC}
do-extract:
@${RM} -rf ${WRKDIR}
@${MKDIR} ${WRKDIR}
@cd ${WRKDIR} && ${EXTRACT_CMD}
.if !defined(WITHOUT_TESTS)
regression-test:
@ -70,7 +41,6 @@ regression-test:
${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
.endif
# from textproc/xerces-j
do-install:
@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."
@${MKDIR} ${JAVAJARDIR}
@ -79,21 +49,24 @@ do-install:
@${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

9
biology/biojava/distinfo
View file

@ -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

11
biology/biojava/files/patch-build.xml
View file

@ -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" />

215
biology/biojava/pkg-plist
View file

@ -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