ports/76219: [ update ] biology/artemis to v6
Fernan Aguero
fernan at iib.unsam.edu.ar
Thu Jan 13 19:40:30 UTC 2005
>Number: 76219
>Category: ports
>Synopsis: [ update ] biology/artemis to v6
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Thu Jan 13 19:40:29 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 4.10-RELEASE i386
>Organization:
IIB-UNSAM
>Environment:
FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan at pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386
>Description:
Artemis is now at v6, this is the first release of Artemis/ACT
to use java2. These patches bring the port to the latest
version.
Please note that:
* I changed the way the JAVA stuff was dealt with to comply with
the way it is described in bsd.java.mk
* PORTVERSION is now used in the pkg-plist
* the port now installs an executable named 'act' which is
currently also installed by biology/act. The port biology/act
is thus now made redundant with this update of artemis, and
thus it is asked to be removed in a separate PR.
Also, I have updated the pkg-descr to reflect the inclusion of
act in this port.
* I have already tried to contact the maintainer, but I'm
getting bounces with the address published in the Makefile
(chuynh at biolateral.com.au). I'm sending a copy to this address
anyway.
>How-To-Repeat:
>Fix:
--- artemis.diff begins here ---
diff -ruN /usr/ports/biology/artemis/Makefile artemis/Makefile
--- /usr/ports/biology/artemis/Makefile Sat Feb 7 01:04:33 2004
+++ artemis/Makefile Thu Jan 13 10:53:23 2005
@@ -6,30 +6,27 @@
#
PORTNAME= artemis
-PORTVERSION= 4.0
-PORTREVISION= 1
+PORTVERSION= 6
CATEGORIES= biology
-MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v4/
-DISTNAME= artemis_compiled_v4
+MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/
+DISTNAME= artemis_compiled_v${PORTVERSION}
MAINTAINER= chuynh at biolateral.com.au
COMMENT= A DNA sequence viewer and annotation tool
-RUN_DEPENDS= ${JAVA_COMMAND}:${PORTSDIR}/java/jdk13
-
WRKSRC= ${WRKDIR}/${PORTNAME}
-JDK_VERSION= 1.3.1
-JDK_DIR= ${PREFIX}/jdk${JDK_VERSION}
-JAVA_COMMAND= ${JDK_DIR}/bin/java
+USE_JAVA= yes
+JAVA_VERSION= 1.4+
+JAVA_RUN= yes
NO_BUILD= yes
+PLIST_SUB= PORTVERSION="${PORTVERSION}"
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}"
+ @${LN} -s ${PREFIX}/${PORTNAME}-${PORTVERSION}/act ${PREFIX}/bin/act
.include <bsd.port.mk>
diff -ruN /usr/ports/biology/artemis/distinfo artemis/distinfo
--- /usr/ports/biology/artemis/distinfo Sat Apr 3 01:03:35 2004
+++ artemis/distinfo Tue Jan 11 15:32:32 2005
@@ -1,2 +1,2 @@
-MD5 (artemis_compiled_v4.tar.gz) = e970b57e993a6b6d254ae70f83e1304e
-SIZE (artemis_compiled_v4.tar.gz) = 4773345
+MD5 (artemis_compiled_v6.tar.gz) = 5ebd3db7edbb74eab5a84df9c693d4e1
+SIZE (artemis_compiled_v6.tar.gz) = 3947732
diff -ruN /usr/ports/biology/artemis/pkg-descr artemis/pkg-descr
--- /usr/ports/biology/artemis/pkg-descr Sat Dec 22 11:39:40 2001
+++ artemis/pkg-descr Thu Jan 13 10:55:11 2005
@@ -1,7 +1,13 @@
-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.
+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
+ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based
+on Artemis. It can open two or more sequences (and their
+annotations/features) together with their comparisons (usually the
+result of running blastn or tblastx searches).
+
+WWW: http://www.sanger.ac.uk/Software/Artemis/manual
+WWW: http://www.sanger.ac.uk/Software/ACT/manual
diff -ruN /usr/ports/biology/artemis/pkg-plist artemis/pkg-plist
--- /usr/ports/biology/artemis/pkg-plist Sat Dec 22 11:39:40 2001
+++ artemis/pkg-plist Tue Jan 11 15:51:20 2005
@@ -1,1486 +1,1507 @@
-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
-artemis-4.0/collections/Comparator.class
-artemis-4.0/collections/Predicate.class
-artemis-4.0/collections/CollectionEnumeration.class
-artemis-4.0/collections/DAEnumeration.class
-artemis-4.0/collections/CEImpl.class
-artemis-4.0/collections/KeySortedCollection.class
-artemis-4.0/collections/Map.class
-artemis-4.0/collections/ElementSortedCollection.class
-artemis-4.0/collections/Bag.class
-artemis-4.0/collections/Set.class
-artemis-4.0/collections/RBTree.class
-artemis-4.0/collections/UpdatableBagImpl.class
-artemis-4.0/collections/UpdatableBag.class
-artemis-4.0/collections/RBCell.class
-artemis-4.0/collections/Cell.class
-artemis-4.0/collections/DefaultComparator.class
-artemis-4.0/collections/RBCellEnumeration.class
-artemis-4.0/collections/Keyed.class
-artemis-4.0/corba/CVS/Root
-artemis-4.0/corba/CVS/Repository
-artemis-4.0/corba/CVS/Entries
-artemis-4.0/corba/apollo.idl
-artemis-4.0/corba/ensembl.idl
-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
-artemis-4.0/diana/CVS/Root
-artemis-4.0/diana/CVS/Repository
-artemis-4.0/diana/CVS/Entries
-artemis-4.0/diana/AlignMatch.java
-artemis-4.0/diana/AlignMatchVector.java
-artemis-4.0/diana/ChangeEvent.java
-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
-artemis-4.0/diana/EntryGroupChangeEvent.java
-artemis-4.0/diana/EntryGroupChangeListener.java
-artemis-4.0/diana/EntrySource.java
-artemis-4.0/diana/plot/CVS/Root
-artemis-4.0/diana/plot/CVS/Repository
-artemis-4.0/diana/plot/CVS/Entries
-artemis-4.0/diana/plot/AGWindowAlgorithm.java
-artemis-4.0/diana/plot/ATDeviationAlgorithm.java
-artemis-4.0/diana/plot/Algorithm.java
-artemis-4.0/diana/plot/BaseAlgorithm.java
-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
-artemis-4.0/diana/plot/FeatureAlgorithm.java
-artemis-4.0/diana/plot/GCDeviationAlgorithm.java
-artemis-4.0/diana/plot/GCFrameAlgorithm.java
-artemis-4.0/diana/plot/GCSDWindowAlgorithm.java
-artemis-4.0/diana/plot/GCWindowAlgorithm.java
-artemis-4.0/diana/plot/HydrophilicityAlgorithm.java
-artemis-4.0/diana/plot/HydrophobicityAlgorithm.java
-artemis-4.0/diana/plot/UserDataAlgorithm.java
-artemis-4.0/diana/plot/CodonUsageAlgorithm.class
-artemis-4.0/diana/plot/BaseAlgorithm.class
-artemis-4.0/diana/plot/Algorithm.class
-artemis-4.0/diana/plot/UserDataAlgorithm.class
-artemis-4.0/diana/plot/CodonUsageWeight.class
-artemis-4.0/diana/plot/CodonWeight.class
-artemis-4.0/diana/plot/GCWindowAlgorithm.class
-artemis-4.0/diana/plot/GCSDWindowAlgorithm.class
-artemis-4.0/diana/plot/AGWindowAlgorithm.class
-artemis-4.0/diana/plot/GCFrameAlgorithm.class
-artemis-4.0/diana/plot/Codon12CorrelationAlgorithm.class
-artemis-4.0/diana/plot/GCDeviationAlgorithm.class
-artemis-4.0/diana/plot/ATDeviationAlgorithm.class
-artemis-4.0/diana/plot/CodonUsageFormatException.class
-artemis-4.0/diana/plot/FeatureAlgorithm.class
-artemis-4.0/diana/plot/HydroAlgorithm.class
-artemis-4.0/diana/plot/HydrophobicityAlgorithm.class
-artemis-4.0/diana/plot/HydrophilicityAlgorithm.class
-artemis-4.0/diana/plot/CoilFeatureAlgorithm.class
-artemis-4.0/diana/EntrySourceVector.java
-artemis-4.0/diana/EntryVector.java
-artemis-4.0/diana/ExternalApplication.java
-artemis-4.0/diana/ExternalProgram.java
-artemis-4.0/diana/ExternalProgramException.java
-artemis-4.0/diana/ExternalProgramVector.java
-artemis-4.0/diana/ExternalSearchProgram.java
-artemis-4.0/diana/Feature.java
-artemis-4.0/diana/FeatureChangeEvent.java
-artemis-4.0/diana/FeatureChangeListener.java
-artemis-4.0/diana/FeatureEnumeration.java
-artemis-4.0/diana/FeatureFromVectorPredicate.java
-artemis-4.0/diana/FeatureKeyPredicate.java
-artemis-4.0/diana/FeatureKeyQualifierPredicate.java
-artemis-4.0/diana/FeatureSegment.java
-artemis-4.0/diana/FeaturePredicate.java
-artemis-4.0/diana/FeatureSegmentVector.java
-artemis-4.0/diana/FeatureVector.java
-artemis-4.0/diana/FilteredEntryGroup.java
-artemis-4.0/diana/GotoEvent.java
-artemis-4.0/diana/GotoEventSource.java
-artemis-4.0/diana/GotoListener.java
-artemis-4.0/diana/LastSegmentException.java
-artemis-4.0/diana/Logger.java
-artemis-4.0/diana/MSPcrunchComparisonData.java
-artemis-4.0/diana/MUMmerComparisonData.java
-artemis-4.0/diana/Options.java
-artemis-4.0/diana/Selectable.java
-artemis-4.0/diana/Selection.java
-artemis-4.0/diana/SelectionChangeEvent.java
-artemis-4.0/diana/SelectionChangeListener.java
-artemis-4.0/diana/helix.gif
-artemis-4.0/diana/SimpleComparisonData.java
-artemis-4.0/diana/SimpleEntryGroup.java
-artemis-4.0/diana/SimpleGotoEventSource.java
-artemis-4.0/diana/sanger-centre.gif
-artemis-4.0/diana/components/CVS/Root
-artemis-4.0/diana/components/CVS/Repository
-artemis-4.0/diana/components/CVS/Entries
-artemis-4.0/diana/components/ActMain.java
-artemis-4.0/diana/components/AddMenu.java
-artemis-4.0/diana/components/AlignmentViewer.java
-artemis-4.0/diana/components/ArtemisMain.java
-artemis-4.0/diana/components/BasePlot.java
-artemis-4.0/diana/components/BasePlotGroup.java
-artemis-4.0/diana/components/CanvasPanel.java
-artemis-4.0/diana/components/Comparator.java
-artemis-4.0/diana/components/ComparatorDialog.java
-artemis-4.0/diana/components/CorbaEntrySource.java
-artemis-4.0/diana/components/DisplayAdjustmentEvent.java
-artemis-4.0/diana/components/DisplayAdjustmentListener.java
-artemis-4.0/diana/components/DisplayComponent.java
-artemis-4.0/diana/components/EMBLCorbaEntrySource.java
-artemis-4.0/diana/components/EditMenu.java
-artemis-4.0/diana/components/EnsemblEntrySource.java
-artemis-4.0/diana/components/EntryActionListener.java
-artemis-4.0/diana/components/EntryEdit.java
-artemis-4.0/diana/components/EntryEditVector.java
-artemis-4.0/diana/components/EntryFileDialog.java
-artemis-4.0/diana/components/EntryGroupDisplay.java
-artemis-4.0/diana/components/EntryGroupInfoDisplay.java
-artemis-4.0/diana/components/EntryGroupMenu.java
-artemis-4.0/diana/components/EntryGroupPanel.java
-artemis-4.0/diana/components/EntryHeaderEdit.java
-artemis-4.0/diana/components/ExternalProgramOptions.java
-artemis-4.0/diana/components/FeatureAminoAcidViewer.java
-artemis-4.0/diana/components/FeatureBaseViewer.java
-artemis-4.0/diana/components/FeatureDisplay.java
-artemis-4.0/diana/components/FeatureDisplayOwner.java
-artemis-4.0/diana/components/FeatureEdit.java
-artemis-4.0/diana/components/FeatureInfo.java
-artemis-4.0/diana/components/FeatureList.java
-artemis-4.0/diana/components/FeatureListFrame.java
-artemis-4.0/diana/components/FeaturePlot.java
-artemis-4.0/diana/components/FeaturePlotGroup.java
-artemis-4.0/diana/components/FeaturePopup.java
-artemis-4.0/diana/components/FeatureViewer.java
-artemis-4.0/diana/components/FileDialogEntrySource.java
-artemis-4.0/diana/components/FileViewer.java
-artemis-4.0/diana/components/GotoMenu.java
-artemis-4.0/diana/components/KeyChoice.java
-artemis-4.0/diana/components/KeyChooser.java
-artemis-4.0/diana/components/ListDialog.java
-artemis-4.0/diana/components/LogViewer.java
-artemis-4.0/diana/components/MarkerRangeRequester.java
-artemis-4.0/diana/components/MarkerRangeRequesterEvent.java
-artemis-4.0/diana/components/MarkerRangeRequesterListener.java
-artemis-4.0/diana/components/MessageDialog.java
-artemis-4.0/diana/components/MessageFrame.java
-artemis-4.0/diana/components/Navigator.java
-artemis-4.0/diana/components/Plot.java
-artemis-4.0/diana/components/PlotMouseListener.java
-artemis-4.0/diana/components/ProcessWatcher.java
-artemis-4.0/diana/components/ProcessWatcherEvent.java
-artemis-4.0/diana/components/ProcessWatcherListener.java
-artemis-4.0/diana/components/QualifierChoice.java
-artemis-4.0/diana/components/RawFeatureEdit.java
-artemis-4.0/diana/components/RunMenu.java
-artemis-4.0/diana/components/ScoreChangeEvent.java
-artemis-4.0/diana/components/ScoreChangeListener.java
-artemis-4.0/diana/components/ScoreChanger.java
-artemis-4.0/diana/components/ScoreScrollbar.java
-artemis-4.0/diana/components/SearchResultViewer.java
-artemis-4.0/diana/components/SelectMenu.java
-artemis-4.0/diana/components/SelectionInfoDisplay.java
-artemis-4.0/diana/components/SelectionMenu.java
-artemis-4.0/diana/components/SelectionViewer.java
-artemis-4.0/diana/components/Selector.java
-artemis-4.0/diana/components/SequenceViewer.java
-artemis-4.0/diana/components/Splash.java
-artemis-4.0/diana/components/TextDialog.java
-artemis-4.0/diana/components/TextRequester.java
-artemis-4.0/diana/components/TextRequesterEvent.java
-artemis-4.0/diana/components/TextRequesterListener.java
-artemis-4.0/diana/components/ViewMenu.java
-artemis-4.0/diana/components/WritableEMBLCorbaEntrySource.java
-artemis-4.0/diana/components/WriteMenu.java
-artemis-4.0/diana/components/Plot.class
-artemis-4.0/diana/components/YesNoDialog.java
-artemis-4.0/diana/components/ArtemisMain.class
-artemis-4.0/diana/components/ArtemisMain$1.class
-artemis-4.0/diana/components/ArtemisMain$2.class
-artemis-4.0/diana/components/ArtemisMain$3.class
-artemis-4.0/diana/components/ArtemisMain$4.class
-artemis-4.0/diana/components/ArtemisMain$5.class
-artemis-4.0/diana/components/ArtemisMain$6.class
-artemis-4.0/diana/components/Splash.class
-artemis-4.0/diana/components/Splash$1.class
-artemis-4.0/diana/components/Splash$2.class
-artemis-4.0/diana/components/Splash$3.class
-artemis-4.0/diana/components/EntryEditVector.class
-artemis-4.0/diana/components/LogViewer.class
-artemis-4.0/diana/components/LogViewer$1.class
-artemis-4.0/diana/components/EntryEdit.class
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+artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.java
+artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHolder.java
+artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHolder.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHelper.java
+artemis-%%PORTVERSION%%/nsdb/datestamp_tHelper.java
+artemis-%%PORTVERSION%%/nsdb/DatestampHelper.java
+artemis-%%PORTVERSION%%/nsdb/DatestampHolder.java
+artemis-%%PORTVERSION%%/nsdb/Datestamp.java
+artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.java
+artemis-%%PORTVERSION%%/nsdb/EntryStatsHolder.java
+artemis-%%PORTVERSION%%/nsdb/EntryStats.java
+artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.java
+artemis-%%PORTVERSION%%/nsdb/ServerInfoHolder.java
+artemis-%%PORTVERSION%%/nsdb/ServerInfo.java
+artemis-%%PORTVERSION%%/nsdb/_EmblWriterStub.java
+artemis-%%PORTVERSION%%/nsdb/EmblWriterHolder.java
+artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.java
+artemis-%%PORTVERSION%%/nsdb/EmblWriter.java
+artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.java
+artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.java
+artemis-%%PORTVERSION%%/nsdb/InvalidKeyHolder.java
+artemis-%%PORTVERSION%%/nsdb/InvalidKey.java
+artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.java
+artemis-%%PORTVERSION%%/nsdb/CommitFailedHolder.java
+artemis-%%PORTVERSION%%/nsdb/CommitFailed.java
+artemis-%%PORTVERSION%%/nsdb/_EmblSeqWriterStub.java
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHolder.java
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.java
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.java
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.java
+artemis-%%PORTVERSION%%/nsdb/_NucFeatureWriterStub.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHolder.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.java
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.java
+artemis-%%PORTVERSION%%/nsdb/Embl.class
+artemis-%%PORTVERSION%%/nsdb/EmblOperations.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeq.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeqOperations.class
+artemis-%%PORTVERSION%%/nsdb/NucSeqOperations.class
+artemis-%%PORTVERSION%%/nsdb/EntryInfoOperations.class
+artemis-%%PORTVERSION%%/nsdb/NucSeq.class
+artemis-%%PORTVERSION%%/nsdb/EntryInfo.class
+artemis-%%PORTVERSION%%/nsdb/NucFeature.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureOperations.class
+artemis-%%PORTVERSION%%/nsdb/Location.class
+artemis-%%PORTVERSION%%/nsdb/LocationOperations.class
+artemis-%%PORTVERSION%%/nsdb/InexactLocation.class
+artemis-%%PORTVERSION%%/nsdb/FeatureLocation.class
+artemis-%%PORTVERSION%%/nsdb/FeatureLocationOperations.class
+artemis-%%PORTVERSION%%/nsdb/EntryStats.class
+artemis-%%PORTVERSION%%/nsdb/ServerInfo.class
+artemis-%%PORTVERSION%%/nsdb/EmblWriter.class
+artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.class
+artemis-%%PORTVERSION%%/nsdb/Datestamp.class
+artemis-%%PORTVERSION%%/nsdb/InvalidKey.class
+artemis-%%PORTVERSION%%/nsdb/LocationParse.class
+artemis-%%PORTVERSION%%/nsdb/OutOfDate.class
+artemis-%%PORTVERSION%%/nsdb/QualifierParse.class
+artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.class
+artemis-%%PORTVERSION%%/nsdb/ReadOnlyException.class
+artemis-%%PORTVERSION%%/nsdb/CommitFailed.class
+artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.class
+artemis-%%PORTVERSION%%/nsdb/EmblHelper.class
+artemis-%%PORTVERSION%%/nsdb/InexactLocationHelper.class
+artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.class
+artemis-%%PORTVERSION%%/nsdb/LocationParseHelper.class
+artemis-%%PORTVERSION%%/nsdb/QualifierParseHelper.class
+artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.class
+artemis-%%PORTVERSION%%/nsdb/OutOfDateHelper.class
+artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHelper.class
+artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.class
+artemis-%%PORTVERSION%%/nsdb/_EmblWriterStub.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.class
+artemis-%%PORTVERSION%%/nsdb/_EmblStub.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.class
+artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.class
+artemis-%%PORTVERSION%%/nsdb/EmblSeqHelper.class
+artemis-%%PORTVERSION%%/nsdb/_EmblSeqWriterStub.class
+artemis-%%PORTVERSION%%/nsdb/_NucFeatureWriterStub.class
+artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.class
+artemis-%%PORTVERSION%%/nsdb/_EmblSeqStub.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureHelper.class
+artemis-%%PORTVERSION%%/nsdb/NucFeatureListHelper.class
+artemis-%%PORTVERSION%%/nsdb/DatestampHelper.class
+artemis-%%PORTVERSION%%/nsdb/LocationHelper.class
+artemis-%%PORTVERSION%%/nsdb/FeatureLocationHelper.class
+artemis-%%PORTVERSION%%/nsdb/datestamp_tHelper.class
+artemis-%%PORTVERSION%%/nsdb/_NucFeatureStub.class
+artemis-%%PORTVERSION%%/nsdb/_LocationStub.class
+artemis-%%PORTVERSION%%/nsdb/_FeatureLocationStub.class
+artemis-%%PORTVERSION%%/type/stringListHolder.java
+artemis-%%PORTVERSION%%/type/stringListHelper.java
+artemis-%%PORTVERSION%%/type/longListHolder.java
+artemis-%%PORTVERSION%%/type/longListHelper.java
+artemis-%%PORTVERSION%%/type/ulongListHolder.java
+artemis-%%PORTVERSION%%/type/ulongListHelper.java
+artemis-%%PORTVERSION%%/type/NoResultHelper.java
+artemis-%%PORTVERSION%%/type/NoResultHolder.java
+artemis-%%PORTVERSION%%/type/NoResult.java
+artemis-%%PORTVERSION%%/type/NoWritePermissionHelper.java
+artemis-%%PORTVERSION%%/type/NoWritePermissionHolder.java
+artemis-%%PORTVERSION%%/type/NoWritePermission.java
+artemis-%%PORTVERSION%%/type/InvalidRelationHelper.java
+artemis-%%PORTVERSION%%/type/InvalidRelationHolder.java
+artemis-%%PORTVERSION%%/type/InvalidRelation.java
+artemis-%%PORTVERSION%%/type/IndexOutOfRangeHelper.java
+artemis-%%PORTVERSION%%/type/IndexOutOfRangeHolder.java
+artemis-%%PORTVERSION%%/type/IndexOutOfRange.java
+artemis-%%PORTVERSION%%/type/InvalidArgumentValueHelper.java
+artemis-%%PORTVERSION%%/type/InvalidArgumentValueHolder.java
+artemis-%%PORTVERSION%%/type/InvalidArgumentValue.java
+artemis-%%PORTVERSION%%/type/ParseErrorHelper.java
+artemis-%%PORTVERSION%%/type/ParseErrorHolder.java
+artemis-%%PORTVERSION%%/type/ParseError.java
+artemis-%%PORTVERSION%%/type/DateHelper.java
+artemis-%%PORTVERSION%%/type/DateHolder.java
+artemis-%%PORTVERSION%%/type/Date.java
+artemis-%%PORTVERSION%%/type/DateListHolder.java
+artemis-%%PORTVERSION%%/type/DateListHelper.java
+artemis-%%PORTVERSION%%/type/PersonHelper.java
+artemis-%%PORTVERSION%%/type/PersonHolder.java
+artemis-%%PORTVERSION%%/type/Person.java
+artemis-%%PORTVERSION%%/type/PersonListHolder.java
+artemis-%%PORTVERSION%%/type/PersonListHelper.java
+artemis-%%PORTVERSION%%/type/RevisionHelper.java
+artemis-%%PORTVERSION%%/type/RevisionHolder.java
+artemis-%%PORTVERSION%%/type/Revision.java
+artemis-%%PORTVERSION%%/type/RevisionListHolder.java
+artemis-%%PORTVERSION%%/type/RevisionListHelper.java
+artemis-%%PORTVERSION%%/type/DbXrefHelper.java
+artemis-%%PORTVERSION%%/type/DbXrefHolder.java
+artemis-%%PORTVERSION%%/type/DbXref.java
+artemis-%%PORTVERSION%%/type/DbXrefListHolder.java
+artemis-%%PORTVERSION%%/type/DbXrefListHelper.java
+artemis-%%PORTVERSION%%/type/AminoAcidHelper.java
+artemis-%%PORTVERSION%%/type/AminoAcidHolder.java
+artemis-%%PORTVERSION%%/type/AminoAcid.java
+artemis-%%PORTVERSION%%/type/AminoAcidListHolder.java
+artemis-%%PORTVERSION%%/type/AminoAcidListHelper.java
+artemis-%%PORTVERSION%%/type/CodonTranslationHelper.java
+artemis-%%PORTVERSION%%/type/CodonTranslationHolder.java
+artemis-%%PORTVERSION%%/type/CodonTranslation.java
+artemis-%%PORTVERSION%%/type/CodonTranslationListHolder.java
+artemis-%%PORTVERSION%%/type/CodonTranslationListHelper.java
+artemis-%%PORTVERSION%%/type/AntiCodonHelper.java
+artemis-%%PORTVERSION%%/type/AntiCodonHolder.java
+artemis-%%PORTVERSION%%/type/AntiCodon.java
+artemis-%%PORTVERSION%%/type/AntiCodonListHolder.java
+artemis-%%PORTVERSION%%/type/AntiCodonListHelper.java
+artemis-%%PORTVERSION%%/type/TranslationExceptionHelper.java
+artemis-%%PORTVERSION%%/type/TranslationExceptionHolder.java
+artemis-%%PORTVERSION%%/type/TranslationException.java
+artemis-%%PORTVERSION%%/type/RepeatUnit.java
+artemis-%%PORTVERSION%%/type/Exact_ftc.java
+artemis-%%PORTVERSION%%/type/TranslationExceptionListHolder.java
+artemis-%%PORTVERSION%%/type/TranslationExceptionListHelper.java
+artemis-%%PORTVERSION%%/type/SpliceConsensusHelper.java
+artemis-%%PORTVERSION%%/type/SpliceConsensusHolder.java
+artemis-%%PORTVERSION%%/type/SpliceConsensus.java
+artemis-%%PORTVERSION%%/type/SpliceConsensusListHolder.java
+artemis-%%PORTVERSION%%/type/SpliceConsensusListHelper.java
+artemis-%%PORTVERSION%%/type/RepeatUnitHelper.java
+artemis-%%PORTVERSION%%/type/RepeatUnitHolder.java
+artemis-%%PORTVERSION%%/type/RepeatUnitListHolder.java
+artemis-%%PORTVERSION%%/type/RepeatUnitListHelper.java
+artemis-%%PORTVERSION%%/type/FuzzyTypeCodeHelper.java
+artemis-%%PORTVERSION%%/type/In_ftc.java
+artemis-%%PORTVERSION%%/type/Between_ftc.java
+artemis-%%PORTVERSION%%/type/Fuzzy.java
+artemis-%%PORTVERSION%%/type/Less_ftc.java
+artemis-%%PORTVERSION%%/type/Greater_ftc.java
+artemis-%%PORTVERSION%%/type/FuzzyHelper.java
+artemis-%%PORTVERSION%%/type/FuzzyHolder.java
+artemis-%%PORTVERSION%%/type/FuzzyListHolder.java
+artemis-%%PORTVERSION%%/type/FuzzyListHelper.java
+artemis-%%PORTVERSION%%/type/NoResult.class
+artemis-%%PORTVERSION%%/type/InvalidRelation.class
+artemis-%%PORTVERSION%%/type/DbXref.class
+artemis-%%PORTVERSION%%/type/InvalidArgumentValue.class
+artemis-%%PORTVERSION%%/type/IndexOutOfRange.class
+artemis-%%PORTVERSION%%/type/Revision.class
+artemis-%%PORTVERSION%%/type/Date.class
+artemis-%%PORTVERSION%%/type/Fuzzy.class
+artemis-%%PORTVERSION%%/type/TranslationException.class
+artemis-%%PORTVERSION%%/type/CodonTranslation.class
+artemis-%%PORTVERSION%%/type/AntiCodon.class
+artemis-%%PORTVERSION%%/type/SpliceConsensus.class
+artemis-%%PORTVERSION%%/type/RepeatUnit.class
+artemis-%%PORTVERSION%%/type/AminoAcid.class
+artemis-%%PORTVERSION%%/type/NoResultHelper.class
+artemis-%%PORTVERSION%%/type/InvalidRelationHelper.class
+artemis-%%PORTVERSION%%/type/InvalidArgumentValueHelper.class
+artemis-%%PORTVERSION%%/type/IndexOutOfRangeHelper.class
+artemis-%%PORTVERSION%%/type/stringListHelper.class
+artemis-%%PORTVERSION%%/type/DbXrefListHelper.class
+artemis-%%PORTVERSION%%/type/RevisionListHelper.class
+artemis-%%PORTVERSION%%/type/DbXrefHelper.class
+artemis-%%PORTVERSION%%/type/RevisionHelper.class
+artemis-%%PORTVERSION%%/type/DateHelper.class
+artemis-%%PORTVERSION%%/type/TranslationExceptionHelper.class
+artemis-%%PORTVERSION%%/type/CodonTranslationHelper.class
+artemis-%%PORTVERSION%%/type/AntiCodonHelper.class
+artemis-%%PORTVERSION%%/type/RepeatUnitHelper.class
+artemis-%%PORTVERSION%%/type/SpliceConsensusHelper.class
+artemis-%%PORTVERSION%%/type/AminoAcidHelper.class
+artemis-%%PORTVERSION%%/type/FuzzyHelper.class
+artemis-%%PORTVERSION%%/type/FuzzyTypeCodeHelper.class
+artemis-%%PORTVERSION%%/seqdb/_BioSeqStub.java
+artemis-%%PORTVERSION%%/seqdb/BioSeqHolder.java
+artemis-%%PORTVERSION%%/seqdb/BioSeqHelper.java
+artemis-%%PORTVERSION%%/seqdb/BioSeq.java
+artemis-%%PORTVERSION%%/seqdb/BioSeqOperations.java
+artemis-%%PORTVERSION%%/seqdb/_FeatureStub.java
+artemis-%%PORTVERSION%%/seqdb/FeatureHolder.java
+artemis-%%PORTVERSION%%/seqdb/FeatureHelper.java
+artemis-%%PORTVERSION%%/seqdb/Feature.java
+artemis-%%PORTVERSION%%/seqdb/FeatureOperations.java
+artemis-%%PORTVERSION%%/seqdb/_SeqInfoStub.java
+artemis-%%PORTVERSION%%/seqdb/SeqInfoHolder.java
+artemis-%%PORTVERSION%%/seqdb/SeqInfoHelper.java
+artemis-%%PORTVERSION%%/seqdb/SeqInfo.java
+artemis-%%PORTVERSION%%/seqdb/SeqInfoOperations.java
+artemis-%%PORTVERSION%%/seqdb/BioSeqOperations.class
+artemis-%%PORTVERSION%%/seqdb/SeqInfoOperations.class
+artemis-%%PORTVERSION%%/seqdb/BioSeq.class
+artemis-%%PORTVERSION%%/seqdb/SeqInfo.class
+artemis-%%PORTVERSION%%/seqdb/FeatureOperations.class
+artemis-%%PORTVERSION%%/seqdb/Feature.class
+artemis-%%PORTVERSION%%/lib/CVS/Root
+artemis-%%PORTVERSION%%/lib/CVS/Repository
+artemis-%%PORTVERSION%%/lib/CVS/Entries
+artemis-%%PORTVERSION%%/lib/LICENSE.Apache
+artemis-%%PORTVERSION%%/lib/README
+artemis-%%PORTVERSION%%/lib/biojava.jar
+artemis-%%PORTVERSION%%/lib/jakarta-regexp-1.2.jar
+artemis-%%PORTVERSION%%/lib/jemAlign.jar
+artemis-%%PORTVERSION%%/lib/jobcontrol.jar
+bin/act
bin/art
- at dirrm artemis-4.0/META-INF/CVS
- at dirrm artemis-4.0/META-INF
- at dirrm artemis-4.0/collections/CVS
- at dirrm artemis-4.0/collections
- at dirrm artemis-4.0/corba/CVS
- at dirrm artemis-4.0/corba
- at dirrm artemis-4.0/diana/CVS
- at dirrm artemis-4.0/diana/plot/CVS
- at dirrm artemis-4.0/diana/plot
- at dirrm artemis-4.0/diana/components/CVS
- at dirrm artemis-4.0/diana/components
- at dirrm artemis-4.0/diana/sequence/CVS
- at dirrm artemis-4.0/diana/sequence
- at dirrm artemis-4.0/diana
- at dirrm artemis-4.0/docs/CVS
- at dirrm artemis-4.0/docs
- at dirrm artemis-4.0/embl/CVS
- at dirrm artemis-4.0/embl
- at dirrm artemis-4.0/etc/CVS
- at dirrm artemis-4.0/etc
- at dirrm artemis-4.0/lib/CVS
- at dirrm artemis-4.0/lib
- at dirrm artemis-4.0/uk/CVS
- at dirrm artemis-4.0/uk/ac/sanger/CVS
- at dirrm artemis-4.0/uk/ac/sanger/pathogens/CVS
- at dirrm artemis-4.0/uk/ac/sanger/pathogens/embl/CVS
- at dirrm artemis-4.0/uk/ac/sanger/pathogens/embl
- at dirrm artemis-4.0/uk/ac/sanger/pathogens
- at dirrm artemis-4.0/uk/ac/CVS
- at dirrm artemis-4.0/uk/ac/sanger
- at dirrm artemis-4.0/uk/ac
- at dirrm artemis-4.0/uk
- at dirrm artemis-4.0/type
- at dirrm artemis-4.0/nsdb/LocationPackage
- at dirrm artemis-4.0/nsdb/NucFeaturePackage
- at dirrm artemis-4.0/nsdb/EmblPackage
- at dirrm artemis-4.0/nsdb
- at dirrm artemis-4.0/seqdb
- at dirrm artemis-4.0/Ensembl/artemis
- at dirrm artemis-4.0/Ensembl
- at dirrm artemis-4.0/CVS
- at dirrm artemis-4.0
+ at dirrm artemis-%%PORTVERSION%%/images
+ at dirrm artemis-%%PORTVERSION%%/etc/CVS
+ at dirrm artemis-%%PORTVERSION%%/etc
+ at dirrm artemis-%%PORTVERSION%%/uk/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/CVS
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis
+ at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger
+ at dirrm artemis-%%PORTVERSION%%/uk/ac
+ at dirrm artemis-%%PORTVERSION%%/uk
+ at dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage
+ at dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage
+ at dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage
+ at dirrm artemis-%%PORTVERSION%%/nsdb
+ at dirrm artemis-%%PORTVERSION%%/type
+ at dirrm artemis-%%PORTVERSION%%/seqdb
+ at dirrm artemis-%%PORTVERSION%%/lib/CVS
+ at dirrm artemis-%%PORTVERSION%%/lib
+ at dirrm artemis-%%PORTVERSION%%
--- artemis.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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