Initial import of artemis 4.0

Artemis is a  DNA sequence viewer and annotation tool.

PR: 32914
Submitted by: Camson <chuynh@biolateral.com.au>

5 files changed, 1528 insertions, 0 deletions

diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile
new file mode 100644
index 0000000..58af9be
--- /dev/null
+++ b/biology/artemis/Makefile
@@ -0,0 +1,33 @@
+# New ports collection makefile for:	artemis
+# Date created:				10 Nov 2001
+# Whom:					camson@bilateral.com.au
+#
+# $FreeBSD$
+#
+
+PORTNAME=	artemis
+PORTVERSION=	4.0
+CATEGORIES=	biology
+MASTER_SITES=	http://www.sanger.ac.uk/Software/Artemis/v4/
+DISTNAME=	artemis_compiled_v4
+
+MAINTAINER=	chuynh@biolateral.com.au
+
+RUN_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/jdk13
+
+WRKSRC=		${WRKDIR}/${PORTNAME}
+
+JDK_VERSION=	1.3.1
+JDK_DIR=	${PREFIX}/jdk${JDK_VERSION}
+JAVA_COMMAND=	${JDK_DIR}/bin/java
+
+NO_BUILD=	yes
+
+do-install:
+	@${MKDIR} ${PREFIX}/${PORTNAME}-${PORTVERSION}
+	@${TAR} -C ${WRKSRC} -cf- . | ${TAR} -C ${PREFIX}/${PORTNAME}-${PORTVERSION} -xpf-
+	@${LN} -s ${PREFIX}/${PORTNAME}-${PORTVERSION}/art ${PREFIX}/bin/art
+
+PLIST_SUB=	PORTVERSION="${PORTVERSION}"
+
+.include <bsd.port.mk>
diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo
new file mode 100644
index 0000000..dfad7f9
--- /dev/null
+++ b/biology/artemis/distinfo
@@ -0,0 +1 @@
+MD5 (artemis_compiled_v4.tar.gz) = e970b57e993a6b6d254ae70f83e1304e
diff --git a/biology/artemis/pkg-comment b/biology/artemis/pkg-comment
new file mode 100644
index 0000000..26b8a15
--- /dev/null
+++ b/biology/artemis/pkg-comment
@@ -0,0 +1 @@
+A DNA sequence viewer and annotation tool
diff --git a/biology/artemis/pkg-descr b/biology/artemis/pkg-descr
new file mode 100644
index 0000000..7aed26f
--- /dev/null
+++ b/biology/artemis/pkg-descr
@@ -0,0 +1,7 @@
+Artemis is a DNA sequence viewer and annotation tool that allows visualisation
+of sequence features and the results of analyses within the context of the
+sequence, and its six-frame translation.  Artemis is written in Java, reads
+EMBL or GENBANK format sequences and feature tables, and can work on sequences
+of any size.
+
+WWW:  http://www.sanger.ac.uk/Software/Artemis/manual
diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist
new file mode 100644
index 0000000..03ec13e
--- /dev/null
+++ b/biology/artemis/pkg-plist
@@ -0,0 +1,1486 @@
+artemis-4.0/CVS/Root
+artemis-4.0/CVS/Repository
+artemis-4.0/CVS/Entries
+artemis-4.0/.cvsignore
+artemis-4.0/AppGlobal.java
+artemis-4.0/COPYING
+artemis-4.0/COPYING.JacORB
+artemis-4.0/CorbaApplet.java
+artemis-4.0/Diana.java
+artemis-4.0/INSTALL
+artemis-4.0/Makefile
+artemis-4.0/README
+artemis-4.0/art
+artemis-4.0/art.bat
+artemis-4.0/mart
+artemis-4.0/results_to_netscape
+artemis-4.0/run_blast
+artemis-4.0/run_blastn
+artemis-4.0/run_blastp
+artemis-4.0/run_blastx
+artemis-4.0/run_fasta
+artemis-4.0/run_hth
+artemis-4.0/run_jalview
+artemis-4.0/run_sigcleave
+artemis-4.0/run_tblastn
+artemis-4.0/run_tblastx
+artemis-4.0/META-INF/CVS/Root
+artemis-4.0/META-INF/CVS/Repository
+artemis-4.0/META-INF/CVS/Entries
+artemis-4.0/META-INF/MANIFEST.MF
+artemis-4.0/collections/CVS/Root
+artemis-4.0/collections/CVS/Repository
+artemis-4.0/collections/CVS/Entries
+artemis-4.0/collections/ArrayEnumeration.java
+artemis-4.0/collections/Assertable.java
+artemis-4.0/collections/Bag.java
+artemis-4.0/collections/BinaryFunction.java
+artemis-4.0/collections/CEImpl.java
+artemis-4.0/collections/CLCell.java
+artemis-4.0/collections/CLEnumeration.java
+artemis-4.0/collections/Cell.java
+artemis-4.0/collections/CheckedBag.java
+artemis-4.0/collections/CheckedCollection.java
+artemis-4.0/collections/CheckedMap.java
+artemis-4.0/collections/CheckedSeq.java
+artemis-4.0/collections/CheckedSet.java
+artemis-4.0/collections/Keyed.java
+artemis-4.0/collections/CircularList.java
+artemis-4.0/collections/Collection.java
+artemis-4.0/collections/CollectionEnumeration.java
+artemis-4.0/collections/Comparator.java
+artemis-4.0/collections/Dynarray.java
+artemis-4.0/collections/CorruptedEnumerationException.java
+artemis-4.0/collections/DAEnumeration.java
+artemis-4.0/collections/DefaultComparator.java
+artemis-4.0/collections/DefaultImplementations.java
+artemis-4.0/collections/ElementSortedCollection.java
+artemis-4.0/collections/FilteringEnumeration.java
+artemis-4.0/collections/Function.java
+artemis-4.0/collections/HTEnumeration.java
+artemis-4.0/collections/HTPairEnumeration.java
+artemis-4.0/collections/HashTableParams.java
+artemis-4.0/collections/HashedMap.java
+artemis-4.0/collections/HashedSet.java
+artemis-4.0/collections/IllegalElementException.java
+artemis-4.0/collections/Immutable.java
+artemis-4.0/collections/ImplementationCheckable.java
+artemis-4.0/collections/IncrBag.java
+artemis-4.0/collections/ImplementationError.java
+artemis-4.0/collections/IncrCollectionEnumeration.java
+artemis-4.0/collections/IncrImpl.java
+artemis-4.0/collections/IncrMap.java
+artemis-4.0/collections/IncrSeq.java
+artemis-4.0/collections/IncrSet.java
+artemis-4.0/collections/InterleavingEnumeration.java
+artemis-4.0/collections/KeySortedCollection.java
+artemis-4.0/collections/LBEnumeration.java
+artemis-4.0/collections/LLCell.java
+artemis-4.0/collections/LLCellEnumeration.java
+artemis-4.0/collections/LLMap.java
+artemis-4.0/collections/LLPair.java
+artemis-4.0/collections/LLPairEnumeration.java
+artemis-4.0/collections/LinkedBuffer.java
+artemis-4.0/collections/LinkedList.java
+artemis-4.0/collections/Map.java
+artemis-4.0/collections/MappingEnumeration.java
+artemis-4.0/collections/Pair.java
+artemis-4.0/collections/Predicate.java
+artemis-4.0/collections/Procedure.java
+artemis-4.0/collections/RBCell.java
+artemis-4.0/collections/RBCellEnumeration.java
+artemis-4.0/collections/RBMap.java
+artemis-4.0/collections/RBPair.java
+artemis-4.0/collections/RBPairEnumeration.java
+artemis-4.0/collections/RBTree.java
+artemis-4.0/collections/Seq.java
+artemis-4.0/collections/Set.java
+artemis-4.0/collections/SimpleTest.java
+artemis-4.0/collections/SortableCollection.java
+artemis-4.0/collections/UpdatableBag.java
+artemis-4.0/collections/UpdatableBagImpl.java
+artemis-4.0/collections/UpdatableCollection.java
+artemis-4.0/collections/UpdatableImpl.java
+artemis-4.0/collections/UpdatableMap.java
+artemis-4.0/collections/UpdatableMapImpl.java
+artemis-4.0/collections/javaMake
+artemis-4.0/collections/UpdatableSeq.java
+artemis-4.0/collections/UpdatableSeqImpl.java
+artemis-4.0/collections/UpdatableSet.java
+artemis-4.0/collections/UpdatableSetImpl.java
+artemis-4.0/collections/collections_Dynarray.h
+artemis-4.0/collections/Dynarray.class
+artemis-4.0/collections/UpdatableSeqImpl.class
+artemis-4.0/collections/UpdatableSeq.class
+artemis-4.0/collections/SortableCollection.class
+artemis-4.0/collections/Seq.class
+artemis-4.0/collections/UpdatableImpl.class
+artemis-4.0/collections/UpdatableCollection.class
+artemis-4.0/collections/IllegalElementException.class
+artemis-4.0/collections/CorruptedEnumerationException.class
+artemis-4.0/collections/ImplementationError.class
+artemis-4.0/collections/Collection.class
+artemis-4.0/collections/Assertable.class
+artemis-4.0/collections/ImplementationCheckable.class
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+artemis-4.0/corba/nsdb.idl
+artemis-4.0/corba/nsdb_write.idl
+artemis-4.0/corba/seqdb.idl
+artemis-4.0/corba/types.idl
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+artemis-4.0/diana/AlignMatch.java
+artemis-4.0/diana/AlignMatchVector.java
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+artemis-4.0/diana/ChangeListener.java
+artemis-4.0/diana/ClipBoard.java
+artemis-4.0/diana/ComparisonData.java
+artemis-4.0/diana/ComparisonDataFactory.java
+artemis-4.0/diana/ComparisonDataParseException.java
+artemis-4.0/diana/Entry.java
+artemis-4.0/diana/EntryChangeEvent.java
+artemis-4.0/diana/EntryChangeListener.java
+artemis-4.0/diana/EntryGroup.java
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+artemis-4.0/diana/plot/Codon12CorrelationAlgorithm.java
+artemis-4.0/diana/plot/CodonUsageAlgorithm.java
+artemis-4.0/diana/plot/CodonUsageFormatException.java
+artemis-4.0/diana/plot/CodonUsageWeight.java
+artemis-4.0/diana/plot/CodonWeight.java
+artemis-4.0/diana/plot/CoilFeatureAlgorithm.java
+artemis-4.0/diana/plot/HydroAlgorithm.java
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+artemis-4.0/diana/MSPcrunchComparisonData.java
+artemis-4.0/diana/MUMmerComparisonData.java
+artemis-4.0/diana/Options.java
+artemis-4.0/diana/Selectable.java
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+artemis-4.0/diana/SelectionChangeListener.java
+artemis-4.0/diana/helix.gif
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+artemis-4.0/Diana.class
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+@dirrm artemis-4.0/META-INF
+@dirrm artemis-4.0/collections/CVS
+@dirrm artemis-4.0/collections
+@dirrm artemis-4.0/corba/CVS
+@dirrm artemis-4.0/corba
+@dirrm artemis-4.0/diana/CVS
+@dirrm artemis-4.0/diana/plot/CVS
+@dirrm artemis-4.0/diana/plot
+@dirrm artemis-4.0/diana/components/CVS
+@dirrm artemis-4.0/diana/components
+@dirrm artemis-4.0/diana/sequence/CVS
+@dirrm artemis-4.0/diana/sequence
+@dirrm artemis-4.0/diana
+@dirrm artemis-4.0/docs/CVS
+@dirrm artemis-4.0/docs
+@dirrm artemis-4.0/embl/CVS
+@dirrm artemis-4.0/embl
+@dirrm artemis-4.0/etc/CVS
+@dirrm artemis-4.0/etc
+@dirrm artemis-4.0/lib/CVS
+@dirrm artemis-4.0/lib
+@dirrm artemis-4.0/uk/CVS
+@dirrm artemis-4.0/uk/ac/sanger/CVS
+@dirrm artemis-4.0/uk/ac/sanger/pathogens/CVS
+@dirrm artemis-4.0/uk/ac/sanger/pathogens/embl/CVS
+@dirrm artemis-4.0/uk/ac/sanger/pathogens/embl
+@dirrm artemis-4.0/uk/ac/sanger/pathogens
+@dirrm artemis-4.0/uk/ac/CVS
+@dirrm artemis-4.0/uk/ac/sanger
+@dirrm artemis-4.0/uk/ac
+@dirrm artemis-4.0/uk
+@dirrm artemis-4.0/type
+@dirrm artemis-4.0/nsdb/LocationPackage
+@dirrm artemis-4.0/nsdb/NucFeaturePackage
+@dirrm artemis-4.0/nsdb/EmblPackage
+@dirrm artemis-4.0/nsdb
+@dirrm artemis-4.0/seqdb
+@dirrm artemis-4.0/Ensembl/artemis
+@dirrm artemis-4.0/Ensembl
+@dirrm artemis-4.0/CVS
+@dirrm artemis-4.0