Attachment 95627 Details for Bug 134056 – file.diff

[patch] file.diff

file.diff (text/plain), 17.75 KB, created by wenheping on 2009-04-28 01:40:02 UTC

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Creator: wenheping

Created: 2009-04-28 01:40:02 UTC

Size: 17.75 KB

patch

obsolete

>diff -urN biojava/Makefile biojava.new/Makefile
>--- biojava/Makefile	2008-12-09 19:02:56.000000000 +0800
>+++ biojava.new/Makefile	2009-04-28 15:39:07.000000000 +0800
>@@ -2,67 +2,38 @@
> # Date created:	15 September 2000
> # Whom:		FreeBSD Bio porters (bio@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=	1.7
> 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}
>-
>-.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}
>+PORTEXAMPLES=	demos
>+EXTRACT_CMD=	jar -xvf ${_DISTDIR}/${DISTFILES}
>+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
>+
>+do-extract:
>+	@${RM} -rf ${WRKDIR}
>+	@${MKDIR} ${WRKDIR}
>+	@cd ${WRKDIR} && ${EXTRACT_CMD}
> 
> .if !defined(WITHOUT_TESTS)
> regression-test:
>@@ -70,7 +41,6 @@
> 		${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
> .endif
> 
>-# from textproc/xerces-j
> do-install:
> 	@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."
> 	@${MKDIR} ${JAVAJARDIR}
>@@ -79,21 +49,24 @@
> 	@${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
> 
>diff -urN biojava/distinfo biojava.new/distinfo
>--- biojava/distinfo	2007-03-27 16:01:54.000000000 +0800
>+++ biojava.new/distinfo	2009-04-24 16:29:18.000000000 +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-1.7-all.jar) = aedb49b6600430bc2b80090536c6ebff
>+SHA256 (biojava-1.7-all.jar) = 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f
>+SIZE (biojava-1.7-all.jar) = 28062592
>diff -urN 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 -urN biojava/pkg-plist biojava.new/pkg-plist
>--- biojava/pkg-plist	2006-11-22 06:35:28.000000000 +0800
>+++ biojava.new/pkg-plist	2009-04-28 14:32:03.000000000 +0800
>@@ -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

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Attachments on bug 134056: 95627