ports/129521: [Update]biology/biojava:update to 1.6.1
Wen Heping
wenheping at gmail.com
Tue Dec 9 12:50:05 UTC 2008
>Number: 129521
>Category: ports
>Synopsis: [Update]biology/biojava:update to 1.6.1
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Tue Dec 09 12:50:04 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator: Wen Heping
>Release: FreeBSD 8.0-CURRENT i386
>Organization:
ChangAn Midlle School
>Environment:
System: FreeBSD 8.0-CURRENT #0: Sun Sep 21 18:56:51 HKT 2008
root at fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC
>Description:
update to 1.6.1 from 1.5beta2
take over maintainership
>How-To-Repeat:
>Fix:
--- biojava161.diff.txt begins here ---
diff -curN biojava/Makefile biojava.new/Makefile
--- biojava/Makefile 2008-12-09 19:02:56.000000000 +0800
+++ biojava.new/Makefile 2008-12-10 01:06:28.000000000 +0800
@@ -2,67 +2,48 @@
# Date created: 15 September 2000
# Whom: FreeBSD Bio porters (bio at freebsd.net)
#
-# $FreeBSD: ports/biology/biojava/Makefile,v 1.17 2008/12/08 06:43:45 linimon Exp $
+# $FreeBSD: ports/biology/biojava/Makefile,v 1.16 2008/06/06 13:08:28 edwin Exp $
#
PORTNAME= biojava
-DISTVERSION= 1.5-beta2
-PORTREVISION= 2
+DISTVERSION= 1.6.1
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/bj16/all/
+DISTFILES= ${PORTNAME}-${DISTVERSION}-all
+EXTRACT_SUFX= .jar
-MAINTAINER= ports at FreeBSD.org
+MAINTAINER= wenheping at 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
-
USE_JAVA= yes
JAVA_VERSION= 1.5+
USE_ANT= yes
MAKE_ENV= CLASSPATH="${JAVALIBDIR}"
-ALL_TARGET= compile-apps
-
-PLIST_SUB+= VER=${DISTVERSION}
+ALL_TARGET= package-biojava
-JARFILES= apps-${DISTVERSION}.jar biojava.jar bytecode.jar
-PORTDOCS= biojava
+BIO_DIRS= META-INF doc manifest resources \
+ selfSignedCertificate src tests
+BIO_FILES= LICENSE README README.biosql \
+ build.xml bytecode.jar commons-cli.jar \
+ commons-collections-2.1.jar commons-dbcp-1.1.jar \
+ commons-pool-1.1.jar jgrapht-jdk1.5.jar junit-4.4.jar
+JARFILES= biojava.jar bytecode.jar
SAMPLES= demos
-WRKSRC=${WRKDIR}
.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}
+ ${MKDIR} ${WRKSRC}
+ ${MKDIR} ${WRKSRC}/demos
+.for f in ${BIO_FILES}
+ @cd ${WRKDIR} && ${MV} ${f} ${WRKSRC}/
+.endfor
+.for d in ${BIO_DIRS}
+ @cd ${WRKDIR} && ${MV} ${d} ${WRKSRC}/
+.endfor
.if !defined(WITHOUT_TESTS)
regression-test:
@@ -70,7 +51,6 @@
${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
.endif
-# from textproc/xerces-j
do-install:
@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."
@${MKDIR} ${JAVAJARDIR}
@@ -79,21 +59,13 @@
@${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 && \
- ${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}/{}" \;
+ @cd ${WRKSRC}/ant-build/docs && ${COPYTREE_SHARE} . ${DOCSDIR}
@${ECHO_MSG} " [ DONE ]"
.endif
diff -curN biojava/distinfo biojava.new/distinfo
--- biojava/distinfo 2007-03-27 16:01:54.000000000 +0800
+++ biojava.new/distinfo 2008-12-10 00:07:04.000000000 +0800
@@ -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-1.6.1-all) = fbc68c5ba5cd47816165aa6f701b44cf
+SHA256 (biojava-1.6.1-all) = d1be9cfb766317d87f63e111ea1c698b0624ec21ec267fa8d3933b7b66398a50
+SIZE (biojava-1.6.1-all) = 18014639
diff -curN biojava/files/patch-build.xml biojava.new/files/patch-build.xml
--- biojava/files/patch-build.xml 2007-03-27 16:01:54.000000000 +0800
+++ biojava.new/files/patch-build.xml 1970-01-01 08:00:00.000000000 +0800
@@ -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" />
-
diff -curN biojava/pkg-plist biojava.new/pkg-plist
--- biojava/pkg-plist 2006-11-22 06:35:28.000000000 +0800
+++ biojava.new/pkg-plist 2008-12-10 01:05:48.000000000 +0800
@@ -1,215 +1,3828 @@
-%%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
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+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/ontology
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/stats/svm/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/stats/svm/tools/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/stats/svm/tools
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/stats/svm
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/stats
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/automata/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/automata
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/cache/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/cache
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/candy/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/candy
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/io/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/io
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/lsid/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/lsid
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/math/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/math
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/net/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/net
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/process/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/process
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/regex/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/regex
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/stax/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/stax
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/walker/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/walker
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/xml/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils/xml
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava/utils
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojava
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db/biosql/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db/biosql
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db/ncbi/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db/ncbi
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/db
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/io/nexus/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/io/nexus
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/io/phylip/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/io/phylip
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo/io
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/phylo
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/seq/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/seq/io/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/seq/io
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/seq
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/taxa/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/taxa/io/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/taxa/io
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio/taxa
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/bio
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/exception/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/exception
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/functions/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/functions
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/impl/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/impl
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/util/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga/util
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ga
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ontology/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/ontology
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/utils/class-use
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax/utils
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org/biojavax
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/org
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava/resources
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/biojava
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/check/biojava
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/check
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/demos
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tests
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
--- biojava161.diff.txt ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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