4 files changed, 29 insertions, 281 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 1af1f69a9832..a643d7a9f671 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -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}
-
-.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
+PORTEXAMPLES=	demos
+EXTRACT_CMD=	jar -xvf ${_DISTDIR}/${DISTFILES}
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
 
-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
 
diff --git a/biology/biojava/distinfo b/biology/biojava/distinfo
index ca1c5c4fb11d..23d4682f33e7 100644
--- a/biology/biojava/distinfo
+++ b/biology/biojava/distinfo
@@ -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 --git a/biology/biojava/files/patch-build.xml b/biology/biojava/files/patch-build.xml
deleted file mode 100644
index ef7a6cb0b5d4..000000000000
--- a/biology/biojava/files/patch-build.xml
+++ /dev/null
@@ -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 --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist
index e3823c52a54b..6e7694ed71dc 100644
--- a/biology/biojava/pkg-plist
+++ b/biology/biojava/pkg-plist
@@ -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