- Upgrade to the latest beta and unbreak;

- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:		ports/104685
Approved by:	maintainer's time-out (1 month)

4 files changed, 274 insertions, 230 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 0a401afb8f79..3317cbcad715 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -6,32 +6,62 @@
 #
 
 PORTNAME=	biojava
-PORTVERSION=	1.30
+DISTVERSION=	1.5-beta
+PORTEPOCH=	1
 CATEGORIES=	biology java
-MASTER_SITES=	http://www.biojava.org/download/source/
+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}
 
 MAINTAINER=	whitekid@gmail.com
 COMMENT=	Open-source java tools for processing biological data
 
-RUN_DEPENDS=	${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \
-		${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp
+BUILD_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \
+		${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \
+		${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool
+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
 
-BROKEN=		Does not compile
-DEPRECATED=	${BROKEN}
-EXPIRATION_DATE=2006-12-01
+.if !defined(WITHOUT_TESTS)
+BUILD_DEPENDS+=	${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit
+.endif
 
 USE_JAVA=	yes
-JAVA_VERSION=	1.3+
+JAVA_VERSION=	1.4+
 USE_ANT=	yes
+MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"
+ALL_TARGET=	compile-apps
+
+PLIST_SUB+=	VER=${DISTVERSION}
 
-JARFILES=	biojava.jar bytecode.jar
-PORTDOCS=	api
-SAMPLES=	demos demos-1.4 demos-obsolete
+JARFILES=	apps-${DISTVERSION}.jar biojava.jar bytecode.jar
+PORTDOCS=	biojava
+SAMPLES=	demos
 
-post-build:
 .if !defined(NOPORTDOCS)
-	@${ECHO_MSG} -n ">> Build javadocs..."
-	@cd ${WRKSRC} && ant javadocs
+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}
+
+.if !defined(WITHOUT_TESTS)
+regression-test:
+	@(cd ${BUILD_WRKSRC}; \
+		${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
 .endif
 
 # from textproc/xerces-j
@@ -53,7 +83,6 @@ do-install:
 		${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} && \
diff --git a/biology/biojava/distinfo b/biology/biojava/distinfo
index 61c2384a1558..000afa26d21a 100644
--- a/biology/biojava/distinfo
+++ b/biology/biojava/distinfo
@@ -1,3 +1,6 @@
-MD5 (biojava-1.30.tar.gz) = 68a70c9aaa06b935b86f9883bfbffd99
-SHA256 (biojava-1.30.tar.gz) = c08a0c2f4b35eab056968f6d8f8d575fb4cd5172ee9bf9cbda0a60e408214f72
-SIZE (biojava-1.30.tar.gz) = 9227361
+MD5 (biojava-1.5-beta.tar.gz) = 8dc7307d9dc4bc9dd9222dfaaee5d047
+SHA256 (biojava-1.5-beta.tar.gz) = a8e0ba3a393bc70606bf7393255077b32bd1c1980f5daeec07c7362f0d2985e1
+SIZE (biojava-1.5-beta.tar.gz) = 15777707
+MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37
+SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f
+SIZE (bytecode.jar) = 93463
diff --git a/biology/biojava/files/patch-build.xml b/biology/biojava/files/patch-build.xml
new file mode 100644
index 000000000000..abce6b625052
--- /dev/null
+++ b/biology/biojava/files/patch-build.xml
@@ -0,0 +1,11 @@
+--- build.xml.orig	Thu Sep  7 11:18:13 2006
++++ build.xml	Sun Oct 22 12:43:18 2006
+@@ -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 bd91873e4870..e3823c52a54b 100644
--- a/biology/biojava/pkg-plist
+++ b/biology/biojava/pkg-plist
@@ -1,214 +1,215 @@
 %%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/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
+%%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
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