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 61cb3623c851..c4b9f79e75f6 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 000000000000..76fe2ff54f1e
--- /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 000000000000..12cfd5369ece
--- /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 000000000000..bb2f70c7749d
--- /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 000000000000..6f23cb08e8c1
--- /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 000000000000..c0c4de8b8630
--- /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
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