PORTVERSION=	1.01

PORTVERSION=	1.30

MAINTAINER=	ports@FreeBSD.org

MAINTAINER=	whitekid@gmail.com

BUILD_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/linux-sun-jdk12

BUILD_DEPENDS=	${LOCALBASE}/bin/ant:${PORTSDIR}/devel/apache-ant

RUN_DEPENDS=	${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \

JDK_VERSION=	1.2.2

		${JAVAJARDIR:S,^${PREFIX},${LOCALBASE},}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp

JAVAVERSION=	linux-sun-jdk${JDK_VERSION}

JAVADIR=	${PREFIX}/${JAVAVERSION}

USE_JAVA=	yes

JAVA_COMPILE=	${JAVADIR}/bin/javac

JDK_VERSION=	1.3+

JAVA_COMMAND=	${JAVADIR}/bin/java

USE_ANT=	yes

do-build:

JARFILES=	biojava.jar bytecode.jar

	@(cd ${WRKSRC}; \

PORTDOCS=	api

		${JAVA_COMPILE} build/Builder.java; \

SAMPLES=	demos demos-1.4 demos-obsolete

		${SETENV} PATH=${PATH}:${JAVADIR}/bin \

		${JAVA_COMMAND} build.Builder all;)

	@(cd ${WRKSRC}; ${SETENV} PATH=${PATH}:${JAVADIR}/bin \

	@${ECHO_MSG} -n ">> Build javadocs..."

	${JAVA_COMMAND} build.Builder docs;)

	@cd ${WRKSRC} && ant javadocs

	@(cd ${WRKSRC}; \

	@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."

		${MKDIR} ${PREFIX}/share/java/classes/; \

	@${MKDIR} ${JAVAJARDIR}

		${CP} ${WRKSRC}/biojava.jar ${PREFIX}/share/java/classes/; \

.for JARFILE in ${JARFILES}

		${CP} ${WRKSRC}/xml.jar ${PREFIX}/share/java/classes/; \

	@cd ${WRKSRC}/ant-build && ${INSTALL_DATA} ${JARFILE} ${JAVAJARDIR}/${JARFILE}

		${MKDIR} ${PREFIX}/share/java/${PKGNAME}/; \

	@${ECHO_MSG} -n " ${JARFILE}"

		${CP} -R README LICENSE ${PREFIX}/share/java/${PKGNAME}/; \

.endfor

		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)

	@${ECHO_MSG} " [ DONE ]"

	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/doc/${PKGNAME})

	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."

.endif)

	@${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}/{}" \;

	@${ECHO_MSG} " [ DONE ]"

.endif

	@${ECHO_MSG} "Libraries installed at: ${PREFIX}/share/java/classes/"

	@${ECHO_MSG} "Libraries installed at: ${JAVAJARDIR}"

	@${ECHO_MSG} "${PREFIX}/share/java/${PKGNAME}"

	@${ECHO_MSG} "${DOCSDIR}"

MD5 (biojava-1.01.tar.gz) = c4f3e397ff5f5f3b71da6c3e7b68b9b9

MD5 (biojava-1.30.tar.gz) = 68a70c9aaa06b935b86f9883bfbffd99

SIZE (biojava-1.01.tar.gz) = 787008

SIZE (biojava-1.30.tar.gz) = 9227361

share/java/classes/xml.jar

share/java/classes/bytecode.jar

share/java/biojava-1.01/LICENSE

@dirrm share/examples/biojava/demos/xff

share/java/biojava-1.01/README

@dirrm share/examples/biojava/demos/tagvalue

share/java/biojava-1.01/demos/acedb/AceTreeView.java

@dirrm share/examples/biojava/demos/symbol

share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java

@dirrm share/examples/biojava/demos/ssbind

share/java/biojava-1.01/demos/acedb/AceClient.java

@dirrm share/examples/biojava/demos/seqviewer

share/java/biojava-1.01/demos/acedb/SequenceFetch.java

@dirrm share/examples/biojava/demos/seq/db

share/java/biojava-1.01/demos/gff/GFFFilter.java

@dirrm share/examples/biojava/demos/seq

share/java/biojava-1.01/demos/gff/EmblToGffFasta.java

@dirrm share/examples/biojava/demos/search

share/java/biojava-1.01/demos/gff/GFFToFeatures.java

@dirrm share/examples/biojava/demos/ragbag

share/java/biojava-1.01/demos/gff/varC4-2.gff

@dirrm share/examples/biojava/demos/prot

share/java/biojava-1.01/demos/gff/AL121903.embl

@dirrm share/examples/biojava/demos/nativeapps

share/java/biojava-1.01/demos/seq/db/AddFilesToIndex.java

@dirrm share/examples/biojava/demos/indexing

share/java/biojava-1.01/demos/seq/db/CreateIndex.java

@dirrm share/examples/biojava/demos/gff

share/java/biojava-1.01/demos/seq/db/FetchSequence.java

@dirrm share/examples/biojava/demos/game

share/java/biojava-1.01/demos/seq/db/ListSeqsInIndex.java

@dirrm share/examples/biojava/demos/files/wublast

share/java/biojava-1.01/demos/seq/TestGenbank.java

@dirrm share/examples/biojava/demos/files/pdb

share/java/biojava-1.01/demos/seq/AL121903.genbank

@dirrm share/examples/biojava/demos/files/ncbiblast

share/java/biojava-1.01/demos/seq/TestTranslation.java

@dirrm share/examples/biojava/demos/files/hmmer

share/java/biojava-1.01/demos/seq/TestEmbl.java

@dirrm share/examples/biojava/demos/files/clustal

share/java/biojava-1.01/demos/seq/AL121903.embl

@dirrm share/examples/biojava/demos/files/GCG

share/java/biojava-1.01/demos/dist/TestDistribution.java

@dirrm share/examples/biojava/demos/files

share/java/biojava-1.01/demos/dp/PairwiseAlignment.java

@dirrm share/examples/biojava/demos/eventbasedparsing/stylesheets

share/java/biojava-1.01/demos/dp/fake.fasta

@dirrm share/examples/biojava/demos/eventbasedparsing

share/java/biojava-1.01/demos/dp/ViterbiAlign.java

@dirrm share/examples/biojava/demos/dp

share/java/biojava-1.01/demos/dp/package.html

@dirrm share/examples/biojava/demos/dist

share/java/biojava-1.01/demos/dp/SearchProfile.java

@dirrm share/examples/biojava/demos/das

share/java/biojava-1.01/demos/dp/fakepromoter.xml

@dirrm share/examples/biojava/demos/biosql

share/java/biojava-1.01/demos/dp/Dice.java

@dirrm share/examples/biojava/demos/CircLocTest

share/java/biojava-1.01/demos/BioCorba/CorbaDBServer.java

@dirrm share/examples/biojava/demos-obsolete/symbol

share/java/biojava-1.01/demos/BioCorba/ChrI.prom.fasta

@dirrm share/examples/biojava/demos-obsolete/seq

share/java/biojava-1.01/demos/BioCorba/CorbaDBClient.java

@dirrm share/examples/biojava/demos-obsolete/search

share/java/biojava-1.01/demos/files/AL121903.embl

@dirrm share/examples/biojava/demos-obsolete/bioseqdb

share/java/biojava-1.01/demos/files/test.hmm

@dirrm share/examples/biojava/demos-obsolete

share/java/biojava-1.01/demos/files/out.gff

@dirrm share/examples/biojava/demos-1.4/unigene

share/java/biojava-1.01/demos/files/AL121903.genbank

@dirrm share/examples/biojava/demos-1.4/ssaha

share/java/biojava-1.01/demos/files/ChrI.prom.fasta

@dirrm share/examples/biojava/demos-1.4

share/java/biojava-1.01/demos/files/fakepromoter.xml

@dirrm share/examples/biojava/demos

share/java/biojava-1.01/demos/files/scoptest.fa

@dirrm share/examples/biojava

share/java/biojava-1.01/demos/files/varC4-2.gff

share/java/biojava-1.01/demos/files/varC4-2.dna

share/java/biojava-1.01/demos/files/fake.fasta

share/java/biojava-1.01/demos/symbol/TestAmbiguity.java

share/java/biojava-1.01/demos/symbol/TestSimpleAlignment.java

share/java/biojava-1.01/demos/symbol/Tools.java

share/java/biojava-1.01/demos/symbol/TestOrderNSymbolList.java

share/java/biojava-1.01/demos/symbol/TestGappedSymbolList.java

share/java/biojava-1.01/demos/symbol/TestWindowedSymbolList.java

share/java/biojava-1.01/demos/seqviewer/test.fa

share/java/biojava-1.01/demos/seqviewer/EmblViewer.java

share/java/biojava-1.01/demos/seqviewer/TestSequencePanel.java

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/UnknownHolder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_Unknown_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/Unknown.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_Unknown_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_UnknownImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/_UnknownStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/UnknownHelper.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/GNOME/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/SocketDriver.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/socket/SocketResultSet.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticStringValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceNode.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceObject.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticAceSet.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticDateValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticFloatValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticIntValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticModelInclude.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticModelNode.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticModelReference.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticModelType.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/StaticReference.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/staticobj/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/AceAnnotation.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/AceSequence.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/seq/AceSequenceDB.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceElement.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceNode.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceObject.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceSet.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Connection.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Database.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/DateValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Driver.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/FloatValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/IntValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/ModelInclude.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/ModelNode.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/ModelReference.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/ModelType.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Reference.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/StringValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Ace.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AcePerlParser.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceURL.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceUtils.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/Handler.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceURLException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/AceError.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/acedb/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/UnableToProcess.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_AnonymousSeq_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeq_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqDB_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_Seq_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqDB_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeature_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Operations.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/AnonymousSeq.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/PrimarySeq.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/PrimarySeqDB.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/PrimarySeqIterator.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/Seq.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/SeqDB.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/SeqFeature.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/SeqFeatureIterator.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_AnonymousSeq_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_AnonymousSeqImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_AnonymousSeqStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeq_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqDB_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqDBImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqDBStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_PrimarySeqIteratorImplBase.html

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%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqDBImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqDBStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeature_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Tie.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureIteratorImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureIteratorStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqFeatureStub.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqImplBase.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/_SeqStub.html

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%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/AnonymousSeqHolder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/EndOfStreamHelper.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/EndOfStreamHolder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/NameValueSet.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/NameValueSetHelper.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/NameValueSetHolder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore/NameValueSetListHelper.html

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%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SeqFeatureImpl.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SeqFeatureIteratorImpl.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SeqImpl.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SequenceAdapter.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SequenceDBAdapter.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/SequenceIteratorAdapter.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME/UnknownImpl.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/TrainRegression.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.DepthScaler.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/ClassifierExample.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/Classify.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SVM_Light.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/Train.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/ItemValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SVMClassifierModel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SVMKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SVMTarget.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/TrainingContext.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/TrainingListener.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/AbstractSVMClassifierModel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/AbstractSVMTarget.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/CachingKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/DiagonalAddKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/DiagonalCachingKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/LinearKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/ListSumKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SMOTrainer.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/NestedKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/NormalizingKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/PolynomialKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/RadialBaseKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SigmoidKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SimpleItemValue.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SimpleSVMClassifierModel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SimpleSVMTarget.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SMORegressionTrainer.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SparseVector.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SparseVector.NormalizingKernel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/SVMRegressionModel.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/stats/svm/TrainingEvent.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/Contract.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/AssertionFailedException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/PostconditionNotMetException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/contract/PreconditionNotMetException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/XMLPeerFactory.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/XMLDispatcher.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/xml/XMLPeerBuilder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/package-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/ObjectUtil.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/StaticMemberPlaceHolder.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/TypedProperties.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/package-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/ParserException.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/org/biojava/utils/package-tree.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/deprecated-list.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/allclasses-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/index.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/packages.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/overview-summary.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/overview-frame.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/serialized-form.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/package-list

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/help-doc.html

%%PORTDOCS%%%%DOCSDIR%%-1.01/api/overview-tree.html

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%%PORTDOCS%%%%DOCSDIR%%-1.01/api/index-all.html

@dirrm share/java/biojava-1.01/demos/acedb

@dirrm share/java/biojava-1.01/demos/gff

@dirrm share/java/biojava-1.01/demos/seq/db

@dirrm share/java/biojava-1.01/demos/seq

@dirrm share/java/biojava-1.01/demos/dist

@dirrm share/java/biojava-1.01/demos/dp

@dirrm share/java/biojava-1.01/demos/BioCorba

@dirrm share/java/biojava-1.01/demos/files

@dirrm share/java/biojava-1.01/demos/symbol

@dirrm share/java/biojava-1.01/demos/seqviewer

@dirrm share/java/biojava-1.01/demos

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/GNOME

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/acedb/socket

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/acedb/staticobj

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/acedb/seq

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/acedb

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/Biocorba/Seqcore

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/Biocorba

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/program/gff

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/program

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/dp

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/gui/sequence

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/gui

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/dist

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/search

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq/db

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq/io

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/seq

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio/symbol

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bio

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba/Seqcore

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/Biocorba

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge/GNOME

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/bridge

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats/svm/tools

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats/svm

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/stats

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils/contract

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils/xml

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava/utils

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org/biojava

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api/org

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01/api

%%PORTDOCS%%@dirrm %%DOCSDIR%%-1.01