Initial import of biology/biojava

PR:		21678
Submitted by:	Brad Chapman <chapmanb@arches.uga.edu>

6 files changed, 661 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 61cb362..c4b9f79 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -2,6 +2,7 @@
 #
 
     SUBDIR += babel
+    SUBDIR += biojava
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += deft
diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
new file mode 100644
index 0000000..76fe2ff
--- /dev/null
+++ b/biology/biojava/Makefile
@@ -0,0 +1,59 @@
+# New ports collection makefile for: biojava
+# Date created:	15 September 2000
+# Whom:		FreeBSD Bio porters (bio@freebsd.net)
+#
+# $FreeBSD$
+#
+
+PORTNAME=	biojava
+PORTVERSION=	1.01
+CATEGORIES=	biology java
+MASTER_SITES=	ftp://ftp.biojava.org/pub/biojava/source/
+
+MAINTAINER=	bio@freebsd.net
+
+BUILD_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/linux-jdk
+
+JDK_VERSION=	1.2.2
+JAVAVERSION=	linux-jdk${JDK_VERSION}
+JAVADIR=	${PREFIX}/${JAVAVERSION}
+JAVA_COMPILE=	${JAVADIR}/bin/javac
+JAVA_COMMAND=	${JAVADIR}/bin/java
+
+do-build:
+	@(cd ${WRKSRC}; \
+		${JAVA_COMPILE} build/Builder.java; \
+		${SETENV} PATH=${PATH}:${JAVADIR}/bin \
+		${JAVA_COMMAND} build.Builder all;)
+
+.if !defined(NOPORTDOCS)
+	@(cd ${WRKSRC}; ${SETENV} PATH=${PATH}:${JAVADIR}/bin \
+	${JAVA_COMMAND} build.Builder docs;)
+.endif
+
+do-install:
+	@(cd ${WRKSRC}; \
+		${MKDIR} ${PREFIX}/share/java/classes/; \
+		${CP} ${WRKSRC}/biojava.jar ${PREFIX}/share/java/classes/; \
+		${CP} ${WRKSRC}/xml.jar ${PREFIX}/share/java/classes/; \
+		${MKDIR} ${PREFIX}/share/java/${PKGNAME}/; \
+		${CP} -R README LICENSE ${PREFIX}/share/java/${PKGNAME}/; \
+		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)
+
+.if !defined(NOPORTDOCS)
+	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/java/${PKGNAME})
+.endif)
+
+post-install:
+.if !defined(BATCH)
+	@${ECHO_MSG} ""
+	@${ECHO_MSG} "Libraries installed at: ${PREFIX}/share/java/classes/"
+	@${ECHO_MSG} "You should edit your CLASSPATH to include the jar files"
+	@${ECHO_MSG} "in this directory."
+	@${ECHO_MSG} ""
+	@${ECHO_MSG} "Docs and demos are installed in:"
+	@${ECHO_MSG} "${PREFIX}/share/java/${PKGNAME}"
+	@${ECHO_MSG} ""
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/biojava/distinfo b/biology/biojava/distinfo
new file mode 100644
index 0000000..12cfd53
--- /dev/null
+++ b/biology/biojava/distinfo
@@ -0,0 +1 @@
+MD5 (biojava-1.01.tar.gz) = c4f3e397ff5f5f3b71da6c3e7b68b9b9
diff --git a/biology/biojava/pkg-comment b/biology/biojava/pkg-comment
new file mode 100644
index 0000000..bb2f70c
--- /dev/null
+++ b/biology/biojava/pkg-comment
@@ -0,0 +1 @@
+Open-source java tools for processing biological data
diff --git a/biology/biojava/pkg-descr b/biology/biojava/pkg-descr
new file mode 100644
index 0000000..6f23cb08e
--- /dev/null
+++ b/biology/biojava/pkg-descr
@@ -0,0 +1,11 @@
+The BioJava Project is an open-source project dedicated to providing Java
+tools for processing biological data. This will include objects for
+manipulating sequences, file parsers, CORBA interoperability, access to
+ACeDB, dynamic programming, and simple statistical routines. 
+
+The BioJava library is useful for automating those daily and mundane
+bioinformatics tasks. As the library matures, the BioJava libraries will
+provide a foundation upon which both free software and commercial packages
+can be developed.
+
+WWW: http://www.biojava.org
diff --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist
new file mode 100644
index 0000000..c0c4de8
--- /dev/null
+++ b/biology/biojava/pkg-plist
@@ -0,0 +1,588 @@
+share/java/classes/biojava.jar
+share/java/classes/xml.jar
+share/java/biojava-1.01/LICENSE
+share/java/biojava-1.01/README
+share/java/biojava-1.01/demos/acedb/AceTreeView.java
+share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java
+share/java/biojava-1.01/demos/acedb/AceClient.java
+share/java/biojava-1.01/demos/acedb/SequenceFetch.java
+share/java/biojava-1.01/demos/gff/GFFFilter.java
+share/java/biojava-1.01/demos/gff/EmblToGffFasta.java
+share/java/biojava-1.01/demos/gff/GFFToFeatures.java
+share/java/biojava-1.01/demos/gff/varC4-2.gff
+share/java/biojava-1.01/demos/gff/AL121903.embl
+share/java/biojava-1.01/demos/seq/db/AddFilesToIndex.java
+share/java/biojava-1.01/demos/seq/db/CreateIndex.java
+share/java/biojava-1.01/demos/seq/db/FetchSequence.java
+share/java/biojava-1.01/demos/seq/db/ListSeqsInIndex.java
+share/java/biojava-1.01/demos/seq/TestGenbank.java
+share/java/biojava-1.01/demos/seq/AL121903.genbank
+share/java/biojava-1.01/demos/seq/TestTranslation.java
+share/java/biojava-1.01/demos/seq/TestEmbl.java
+share/java/biojava-1.01/demos/seq/AL121903.embl
+share/java/biojava-1.01/demos/dist/TestDistribution.java
+share/java/biojava-1.01/demos/dp/PairwiseAlignment.java
+share/java/biojava-1.01/demos/dp/fake.fasta
+share/java/biojava-1.01/demos/dp/ViterbiAlign.java
+share/java/biojava-1.01/demos/dp/package.html
+share/java/biojava-1.01/demos/dp/SearchProfile.java
+share/java/biojava-1.01/demos/dp/fakepromoter.xml
+share/java/biojava-1.01/demos/dp/Dice.java
+share/java/biojava-1.01/demos/BioCorba/CorbaDBServer.java
+share/java/biojava-1.01/demos/BioCorba/ChrI.prom.fasta
+share/java/biojava-1.01/demos/BioCorba/CorbaDBClient.java
+share/java/biojava-1.01/demos/files/AL121903.embl
+share/java/biojava-1.01/demos/files/test.hmm
+share/java/biojava-1.01/demos/files/out.gff
+share/java/biojava-1.01/demos/files/AL121903.genbank
+share/java/biojava-1.01/demos/files/ChrI.prom.fasta
+share/java/biojava-1.01/demos/files/fakepromoter.xml
+share/java/biojava-1.01/demos/files/scoptest.fa
+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
+share/java/biojava-1.01/docs/api/GNOME/UnknownHolder.html
+share/java/biojava-1.01/docs/api/GNOME/package-tree.html
+share/java/biojava-1.01/docs/api/GNOME/package-frame.html
+share/java/biojava-1.01/docs/api/GNOME/_Unknown_Operations.html
+share/java/biojava-1.01/docs/api/GNOME/Unknown.html
+share/java/biojava-1.01/docs/api/GNOME/_Unknown_Tie.html
+share/java/biojava-1.01/docs/api/GNOME/_UnknownImplBase.html
+share/java/biojava-1.01/docs/api/GNOME/_UnknownStub.html
+share/java/biojava-1.01/docs/api/GNOME/UnknownHelper.html
+share/java/biojava-1.01/docs/api/GNOME/package-summary.html
+share/java/biojava-1.01/docs/api/org/acedb/socket/package-summary.html
+share/java/biojava-1.01/docs/api/org/acedb/socket/package-tree.html
+share/java/biojava-1.01/docs/api/org/acedb/socket/package-frame.html
+share/java/biojava-1.01/docs/api/org/acedb/socket/SocketDriver.html
+share/java/biojava-1.01/docs/api/org/acedb/socket/SocketResultSet.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticStringValue.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-tree.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-frame.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceNode.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceObject.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceSet.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticDateValue.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticFloatValue.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticIntValue.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelInclude.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelNode.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelReference.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelType.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticReference.html
+share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-summary.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/package-summary.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/package-tree.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/package-frame.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/AceAnnotation.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequence.html
+share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequenceDB.html
+share/java/biojava-1.01/docs/api/org/acedb/AceElement.html
+share/java/biojava-1.01/docs/api/org/acedb/AceNode.html
+share/java/biojava-1.01/docs/api/org/acedb/AceObject.html
+share/java/biojava-1.01/docs/api/org/acedb/AceSet.html
+share/java/biojava-1.01/docs/api/org/acedb/AceValue.html
+share/java/biojava-1.01/docs/api/org/acedb/Connection.html
+share/java/biojava-1.01/docs/api/org/acedb/Database.html
+share/java/biojava-1.01/docs/api/org/acedb/DateValue.html
+share/java/biojava-1.01/docs/api/org/acedb/Driver.html
+share/java/biojava-1.01/docs/api/org/acedb/FloatValue.html
+share/java/biojava-1.01/docs/api/org/acedb/IntValue.html
+share/java/biojava-1.01/docs/api/org/acedb/ModelInclude.html
+share/java/biojava-1.01/docs/api/org/acedb/ModelNode.html
+share/java/biojava-1.01/docs/api/org/acedb/ModelReference.html
+share/java/biojava-1.01/docs/api/org/acedb/ModelType.html
+share/java/biojava-1.01/docs/api/org/acedb/Reference.html
+share/java/biojava-1.01/docs/api/org/acedb/StringValue.html
+share/java/biojava-1.01/docs/api/org/acedb/Ace.html
+share/java/biojava-1.01/docs/api/org/acedb/AcePerlParser.html
+share/java/biojava-1.01/docs/api/org/acedb/AceURL.html
+share/java/biojava-1.01/docs/api/org/acedb/AceUtils.html
+share/java/biojava-1.01/docs/api/org/acedb/Handler.html
+share/java/biojava-1.01/docs/api/org/acedb/AceException.html
+share/java/biojava-1.01/docs/api/org/acedb/AceURLException.html
+share/java/biojava-1.01/docs/api/org/acedb/package-summary.html
+share/java/biojava-1.01/docs/api/org/acedb/AceError.html
+share/java/biojava-1.01/docs/api/org/acedb/package-tree.html
+share/java/biojava-1.01/docs/api/org/acedb/package-frame.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcess.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-tree.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-frame.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Operations.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeq.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeq.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDB.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIterator.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/Seq.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDB.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeature.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIterator.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Tie.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqImplBase.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqStub.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSet.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqType.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHelper.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHolder.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStream.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRange.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLarge.html
+share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/IgnoreRecordException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFDocumentHandler.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFErrorHandler.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecord.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecordFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFEntrySet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFFilterer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFWriter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/SequencesAsGFF.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/SimpleGFFRecord.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/program/Meme.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelVetoException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/DotState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/DPMatrix.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/EmissionState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/MarkovModel.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelInState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/State.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/StatePath.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/StoppingCriteria.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/Trainable.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/TrainingAlgorithm.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/TransitionListener.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/TransitionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/WeightMatrix.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/DP.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/AbstractTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/BaumWelchSampler.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/BaumWelchTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/DP.ReverseIterator.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/DPFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/MagicalState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelChangeEvent.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelView.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ModelView.ViewTransitionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/PairDPMatrix.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/PairwiseDP.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/ProfileHMM.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleDotState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleEmissionState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleMarkovModel.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleModelInState.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/Transition.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleModelTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleStatePath.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleTransitionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/SimpleWeightMatrix.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/TrainerTransition.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/TransitionEvent.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/WeightMatrixAnnotator.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/WMAsMM.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/XmlMarkovModel.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/IllegalTransitionException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dp/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/FeatureRenderer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/SequenceRenderer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/BasicFeatureRenderer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/LogoPainter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/SymbolStyle.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/BarLogoPainter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/DistributionLogo.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/DNAStyle.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/PlainStyle.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/SequencePanel.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/SequencePanel.Border.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/SimpleSymbolStyle.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/gui/TextLogoPainter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/UniformDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/Distribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/DistributionFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/DistributionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/DistributionTrainerContext.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/AbstractDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/ComplementaryDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/DNADistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/GapDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/IgnoreCountsTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/PairDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/SimpleDistribution.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/SimpleDistributionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/SimpleDistributionTrainerContext.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/dist/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SeqSimilaritySearcher.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SeqSimilaritySearchHit.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SeqSimilaritySearchResult.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SeqSimilaritySearchSubHit.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/search/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/IDMaker.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/SequenceDB.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/SequenceDBInstallation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/AnnotatedSequenceDB.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/CachingSequenceDB.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/HashSequenceDB.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/IDMaker.ByName.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/IDMaker.ByURN.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/IndexedSequenceDB.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/StreamWriter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/AlignmentFormat.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/FastaDescriptionReader.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/FeatureBuilder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/SequenceFormat.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/DefaultDescriptionReader.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/EmblFormat.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/FastaFormat.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/GenbankFormat.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/SimpleFeatureBuilder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/StreamReader.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/StreamReader.Context.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/Feature.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureRealizer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/RealizingFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/Sequence.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SequenceAnnotator.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SequenceFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SequenceIterator.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/StrandedFeature.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/AbstractFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/DNATools.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/Feature.Template.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.AcceptAllFilter.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.And.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.BySource.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.ByType.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.Not.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.Or.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/GeneticCode.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/MergeFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/ProteinTools.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SimpleFeatureHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SimpleFeatureRealizer.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SimpleSequence.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/SimpleSequenceFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/StrandedFeature.Strand.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/StrandedFeature.Template.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/ViewSequence.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/seq/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/IllegalSymbolException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Alignment.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Alphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AtomicSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/CrossProductAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/CrossProductSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/FiniteAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Location.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Symbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SymbolParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/TranslationTable.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AbstractAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AbstractSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AllTokensAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Alphabet.EmptyAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AlphabetManager.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/AlphabetManager.ListWrapper.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/CompoundLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/CrossProductSymbolNameParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/DoubleAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/FixedWidthParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/GappedSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/IntegerAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Location.EmptyLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/Location.LocationComparator.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/NameParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/OrderNSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/PointLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/RangeLocation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/ReverseSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleAlignment.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleAtomicSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleSymbol.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SimpleTranslationTable.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SingletonAlphabet.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SuffixTree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SuffixTree.SuffixNode.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/SymbolList.EmptySymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/TokenParser.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/TranslatedSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/WindowedSymbolList.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/IllegalAlphabetException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/symbol/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/SimpleAnnotation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/BioException.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/BioError.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/Annotatable.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/Annotation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/Annotation.EmptyAnnotation.html
+share/java/biojava-1.01/docs/api/org/biojava/bio/OverlayAnnotation.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SymbolListAdapter.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/AnonymousSeqImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/FeatureAdapter.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/PrimarySeqDBImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/PrimarySeqImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/PrimarySeqIteratorImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SeqDBImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SeqFeatureImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SeqFeatureIteratorImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SeqImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SequenceAdapter.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SequenceDBAdapter.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/SequenceIteratorAdapter.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME/UnknownImpl.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/TrainRegression.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.DepthScaler.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/ClassifierExample.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/Classify.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SVM_Light.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/Train.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/ItemValue.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SVMClassifierModel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SVMKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SVMTarget.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/TrainingContext.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/TrainingListener.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/AbstractSVMClassifierModel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/AbstractSVMTarget.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/CachingKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/DiagonalAddKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/DiagonalCachingKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/LinearKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/ListSumKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SMOTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/NestedKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/NormalizingKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/PolynomialKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/RadialBaseKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SigmoidKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SimpleItemValue.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SimpleSVMClassifierModel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SimpleSVMTarget.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SMORegressionTrainer.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SparseVector.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SparseVector.NormalizingKernel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/SVMRegressionModel.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/stats/svm/TrainingEvent.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/Contract.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/AssertionFailedException.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/PostconditionNotMetException.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/contract/PreconditionNotMetException.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/package-tree.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/XMLPeerFactory.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/XMLDispatcher.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/xml/XMLPeerBuilder.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/package-frame.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/ObjectUtil.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/StaticMemberPlaceHolder.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/TypedProperties.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/package-summary.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/ParserException.html
+share/java/biojava-1.01/docs/api/org/biojava/utils/package-tree.html
+share/java/biojava-1.01/docs/api/deprecated-list.html
+share/java/biojava-1.01/docs/api/allclasses-frame.html
+share/java/biojava-1.01/docs/api/index.html
+share/java/biojava-1.01/docs/api/packages.html
+share/java/biojava-1.01/docs/api/overview-summary.html
+share/java/biojava-1.01/docs/api/overview-frame.html
+share/java/biojava-1.01/docs/api/serialized-form.html
+share/java/biojava-1.01/docs/api/package-list
+share/java/biojava-1.01/docs/api/help-doc.html
+share/java/biojava-1.01/docs/api/overview-tree.html
+share/java/biojava-1.01/docs/api/stylesheet.css
+share/java/biojava-1.01/docs/api/index-all.html
+@dirrm share/java/classes
+@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
+@dirrm share/java/biojava-1.01/docs/api/GNOME
+@dirrm share/java/biojava-1.01/docs/api/org/acedb/socket
+@dirrm share/java/biojava-1.01/docs/api/org/acedb/staticobj
+@dirrm share/java/biojava-1.01/docs/api/org/acedb/seq
+@dirrm share/java/biojava-1.01/docs/api/org/acedb
+@dirrm share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore
+@dirrm share/java/biojava-1.01/docs/api/org/Biocorba
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/program
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/dp
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/gui
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/dist
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/search
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/symbol
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats/svm
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils/contract
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils/xml
+@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils
+@dirrm share/java/biojava-1.01/docs/api/org/biojava
+@dirrm share/java/biojava-1.01/docs/api/org
+@dirrm share/java/biojava-1.01/docs/api
+@dirrm share/java/biojava-1.01/docs
+@dirrm share/java/biojava-1.01
+@dirrm share/java