diff options
| author | Daichi GOTO <daichi@FreeBSD.org> | 2003-06-23 13:37:39 +0000 |
|---|---|---|
| committer | Daichi GOTO <daichi@FreeBSD.org> | 2003-06-23 13:37:39 +0000 |
| commit | 262d632dae42d1475e6a654fb57aa5eb699e2865 (patch) | |
| tree | 921d1a4dd1f9bb678849bccd180f1d05384defd5 /biology | |
| parent | 11da343a7fab22a280e4bf323c2bc1d52dd3906d (diff) | |
| download | ports-262d632dae42d1475e6a654fb57aa5eb699e2865.tar.gz ports-262d632dae42d1475e6a654fb57aa5eb699e2865.zip | |
Notes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/act/Makefile | 10 | ||||
| -rw-r--r-- | biology/act/distinfo | 2 | ||||
| -rw-r--r-- | biology/act/pkg-plist | 2579 |
3 files changed, 1603 insertions, 988 deletions
diff --git a/biology/act/Makefile b/biology/act/Makefile index d19ea54476f1..5146c497584c 100644 --- a/biology/act/Makefile +++ b/biology/act/Makefile @@ -1,15 +1,15 @@ # New ports collection makefile for: artemis -# Date created: 11 Mar 2002 -# Whom: chuynh@bilateral.com.au +# Date created: 10 Mar 2003 +# Whom: fernan@iib.unsam.edu.ar # # $FreeBSD$ # PORTNAME= act -PORTVERSION= 1.0 +PORTVERSION= 2.0 CATEGORIES= biology -MASTER_SITES= http://www.sanger.ac.uk/Software/ACT/v1/ -DISTNAME= act_compiled_v1 +MASTER_SITES= http://www.sanger.ac.uk/Software/ACT/v2/ +DISTNAME= act_compiled_v2 MAINTAINER= chuynh@biolateral.com.au COMMENT= A DNA sequence comparison viewer based on Artemis diff --git a/biology/act/distinfo b/biology/act/distinfo index 48b31986c4a9..8095e70cb564 100644 --- a/biology/act/distinfo +++ b/biology/act/distinfo @@ -1 +1 @@ -MD5 (act_compiled_v1.tar.gz) = 30e263c6507007d866a24b59c0767d77 +MD5 (act_compiled_v2.tar.gz) = 7029fb9ac1beb63679a41cfea788e4f5 diff --git a/biology/act/pkg-plist b/biology/act/pkg-plist index 46e5a821c9db..bfa40bc00500 100644 --- a/biology/act/pkg-plist +++ b/biology/act/pkg-plist @@ -1,983 +1,1598 @@ -act-1.0/CVS/Root -act-1.0/CVS/Repository -act-1.0/CVS/Entries -act-1.0/.cvsignore -act-1.0/AppGlobal.java -act-1.0/Dad.java -act-1.0/Makefile -act-1.0/act -act-1.0/META-INF/CVS/Root -act-1.0/META-INF/CVS/Repository -act-1.0/META-INF/CVS/Entries -act-1.0/META-INF/MANIFEST.MF -act-1.0/uk/CVS/Root -act-1.0/uk/CVS/Repository -act-1.0/uk/CVS/Entries -act-1.0/uk/ac/CVS/Root -act-1.0/uk/ac/CVS/Repository -act-1.0/uk/ac/CVS/Entries -act-1.0/uk/ac/sanger/CVS/Root -act-1.0/uk/ac/sanger/CVS/Repository -act-1.0/uk/ac/sanger/CVS/Entries -act-1.0/uk/ac/sanger/pathogens/CVS/Root -act-1.0/uk/ac/sanger/pathogens/CVS/Repository -act-1.0/uk/ac/sanger/pathogens/CVS/Entries -act-1.0/uk/ac/sanger/pathogens/Document.java -act-1.0/uk/ac/sanger/pathogens/FastVector.java -act-1.0/uk/ac/sanger/pathogens/FileDocument.java -act-1.0/uk/ac/sanger/pathogens/FileProgressDocument.java -act-1.0/uk/ac/sanger/pathogens/InputStreamProgressEvent.java -act-1.0/uk/ac/sanger/pathogens/InputStreamProgressListener.java -act-1.0/uk/ac/sanger/pathogens/OutOfRangeException.java -act-1.0/uk/ac/sanger/pathogens/ProgressInputStream.java -act-1.0/uk/ac/sanger/pathogens/ReadOnlyException.java -act-1.0/uk/ac/sanger/pathogens/StringVector.java -act-1.0/uk/ac/sanger/pathogens/URLDocument.java -act-1.0/uk/ac/sanger/pathogens/embl/CVS/Root -act-1.0/uk/ac/sanger/pathogens/embl/CVS/Repository -act-1.0/uk/ac/sanger/pathogens/embl/CVS/Entries -act-1.0/uk/ac/sanger/pathogens/embl/BetweenRange.java -act-1.0/uk/ac/sanger/pathogens/embl/ComparableFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/CorbaEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/CorbaFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/CorbaSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/DateStampFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryAutosaveThread.java -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryFactory.java -act-1.0/uk/ac/sanger/pathogens/embl/DocumentFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/EMBLObject.java -act-1.0/uk/ac/sanger/pathogens/embl/Entry.java -act-1.0/uk/ac/sanger/pathogens/embl/EmblDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/EmblMisc.java -act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/EntryInformation.java -act-1.0/uk/ac/sanger/pathogens/embl/EntryInformationException.java -act-1.0/uk/ac/sanger/pathogens/embl/FastaStreamSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/Feature.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureComparator.java -act-1.0/uk/ac/sanger/pathogens/embl/Key.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureEnumeration.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureHeader.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureTable.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureTree.java -act-1.0/uk/ac/sanger/pathogens/embl/FeatureVector.java -act-1.0/uk/ac/sanger/pathogens/embl/FuzzyRange.java -act-1.0/uk/ac/sanger/pathogens/embl/GFFDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/GFFMisc.java -act-1.0/uk/ac/sanger/pathogens/embl/GFFEntryInformation.java -act-1.0/uk/ac/sanger/pathogens/embl/GFFStreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/GenbankDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/GenbankMisc.java -act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/InvalidKeyException.java -act-1.0/uk/ac/sanger/pathogens/embl/InvalidQualifierException.java -act-1.0/uk/ac/sanger/pathogens/embl/InvalidRelationException.java -act-1.0/uk/ac/sanger/pathogens/embl/KeyVector.java -act-1.0/uk/ac/sanger/pathogens/embl/LineGroup.java -act-1.0/uk/ac/sanger/pathogens/embl/LineGroupVector.java -act-1.0/uk/ac/sanger/pathogens/embl/LinePushBackReader.java -act-1.0/uk/ac/sanger/pathogens/embl/Location.java -act-1.0/uk/ac/sanger/pathogens/embl/LocationLexer.java -act-1.0/uk/ac/sanger/pathogens/embl/Qualifier.java -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseException.java -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNode.java -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNodeVector.java -act-1.0/uk/ac/sanger/pathogens/embl/LowerInteger.java -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchEntryInformation.java -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchStreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/MiscLineGroup.java -act-1.0/uk/ac/sanger/pathogens/embl/OutOfDateException.java -act-1.0/uk/ac/sanger/pathogens/embl/PublicDBDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/PublicDBStreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/PushBackException.java -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfo.java -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoException.java -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoVector.java -act-1.0/uk/ac/sanger/pathogens/embl/QualifierParseException.java -act-1.0/uk/ac/sanger/pathogens/embl/QualifierVector.java -act-1.0/uk/ac/sanger/pathogens/embl/RWCorbaEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/RWCorbaFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/Range.java -act-1.0/uk/ac/sanger/pathogens/embl/RangeVector.java -act-1.0/uk/ac/sanger/pathogens/embl/RawStreamSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/ReadFormatException.java -act-1.0/uk/ac/sanger/pathogens/embl/ReadOnlyEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/Sequence.java -act-1.0/uk/ac/sanger/pathogens/embl/SimpleDocumentEntry.java -act-1.0/uk/ac/sanger/pathogens/embl/SimpleDocumentFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/SimpleEntryInformation.java -act-1.0/uk/ac/sanger/pathogens/embl/StreamFeature.java -act-1.0/uk/ac/sanger/pathogens/embl/StreamFeatureTable.java -act-1.0/uk/ac/sanger/pathogens/embl/StreamQualifier.java -act-1.0/uk/ac/sanger/pathogens/embl/StreamSequence.java -act-1.0/uk/ac/sanger/pathogens/embl/StreamSequenceFactory.java -act-1.0/uk/ac/sanger/pathogens/embl/UpperInteger.java -act-1.0/uk/ac/sanger/pathogens/embl/embl.example -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoVector.class -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoException.class -act-1.0/uk/ac/sanger/pathogens/embl/EntryInformation.class -act-1.0/uk/ac/sanger/pathogens/embl/EntryInformationException.class -act-1.0/uk/ac/sanger/pathogens/embl/ReadFormatException.class -act-1.0/uk/ac/sanger/pathogens/embl/InvalidRelationException.class -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryFactory.class -act-1.0/uk/ac/sanger/pathogens/embl/SimpleEntryInformation.class -act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfo.class -act-1.0/uk/ac/sanger/pathogens/embl/Key.class -act-1.0/uk/ac/sanger/pathogens/embl/KeyVector.class -act-1.0/uk/ac/sanger/pathogens/embl/Qualifier.class -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/Entry.class -act-1.0/uk/ac/sanger/pathogens/embl/EmblDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/PublicDBDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/SimpleDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/SimpleDocumentEntry$1.class -act-1.0/uk/ac/sanger/pathogens/embl/LineGroup.class -act-1.0/uk/ac/sanger/pathogens/embl/EMBLObject.class -act-1.0/uk/ac/sanger/pathogens/embl/LinePushBackReader.class -act-1.0/uk/ac/sanger/pathogens/embl/PushBackException.class -act-1.0/uk/ac/sanger/pathogens/embl/StreamSequenceFactory.class -act-1.0/uk/ac/sanger/pathogens/embl/StreamSequence.class -act-1.0/uk/ac/sanger/pathogens/embl/Sequence.class -act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/PublicDBStreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/SimpleDocumentFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/DocumentFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/Feature.class -act-1.0/uk/ac/sanger/pathogens/embl/StreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/ComparableFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/QualifierParseException.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureHeader.class -act-1.0/uk/ac/sanger/pathogens/embl/EmblMisc.class -act-1.0/uk/ac/sanger/pathogens/embl/MiscLineGroup.class -act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/GFFStreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchStreamFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/GenbankMisc.class -act-1.0/uk/ac/sanger/pathogens/embl/GFFMisc.class -act-1.0/uk/ac/sanger/pathogens/embl/GFFDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/GenbankDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchDocumentEntry.class -act-1.0/uk/ac/sanger/pathogens/embl/InvalidKeyException.class -act-1.0/uk/ac/sanger/pathogens/embl/InvalidQualifierException.class -act-1.0/uk/ac/sanger/pathogens/embl/Range.class -act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamSequence.class -act-1.0/uk/ac/sanger/pathogens/embl/RangeVector.class -act-1.0/uk/ac/sanger/pathogens/embl/Location.class -act-1.0/uk/ac/sanger/pathogens/embl/LocationLexer.class -act-1.0/uk/ac/sanger/pathogens/embl/LocationLexer$TokenEnumeration.class -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseException.class -act-1.0/uk/ac/sanger/pathogens/embl/QualifierVector.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureEnumeration.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureVector.class -act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamSequence.class -act-1.0/uk/ac/sanger/pathogens/embl/LineGroupVector.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureTable.class -act-1.0/uk/ac/sanger/pathogens/embl/RawStreamSequence.class -act-1.0/uk/ac/sanger/pathogens/embl/FastaStreamSequence.class -act-1.0/uk/ac/sanger/pathogens/embl/StreamFeatureTable.class -act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryAutosaveThread.class -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNode.class -act-1.0/uk/ac/sanger/pathogens/embl/StreamQualifier.class -act-1.0/uk/ac/sanger/pathogens/embl/GFFEntryInformation.class -act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchEntryInformation.class -act-1.0/uk/ac/sanger/pathogens/embl/LowerInteger.class -act-1.0/uk/ac/sanger/pathogens/embl/UpperInteger.class -act-1.0/uk/ac/sanger/pathogens/embl/FuzzyRange.class -act-1.0/uk/ac/sanger/pathogens/embl/OutOfDateException.class -act-1.0/uk/ac/sanger/pathogens/embl/DateStampFeature.class -act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNodeVector.class -act-1.0/uk/ac/sanger/pathogens/embl/BetweenRange.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureTree.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureTree$FeatureEnumerator.class -act-1.0/uk/ac/sanger/pathogens/embl/FeatureComparator.class -act-1.0/uk/ac/sanger/pathogens/OutOfRangeException.class -act-1.0/uk/ac/sanger/pathogens/StringVector.class -act-1.0/uk/ac/sanger/pathogens/StringVector$1.class -act-1.0/uk/ac/sanger/pathogens/ReadOnlyException.class -act-1.0/uk/ac/sanger/pathogens/Document.class -act-1.0/uk/ac/sanger/pathogens/InputStreamProgressListener.class -act-1.0/uk/ac/sanger/pathogens/FileDocument.class -act-1.0/uk/ac/sanger/pathogens/InputStreamProgressEvent.class -act-1.0/uk/ac/sanger/pathogens/FileProgressDocument.class -act-1.0/uk/ac/sanger/pathogens/FastVector.class -act-1.0/uk/ac/sanger/pathogens/ProgressInputStream.class -act-1.0/diana/CVS/Root -act-1.0/diana/CVS/Repository -act-1.0/diana/CVS/Entries -act-1.0/diana/AlignMatch.java -act-1.0/diana/AlignMatchVector.java -act-1.0/diana/ChangeEvent.java -act-1.0/diana/ChangeListener.java -act-1.0/diana/ClipBoard.java -act-1.0/diana/ComparisonData.java -act-1.0/diana/ComparisonDataFactory.java -act-1.0/diana/ComparisonDataParseException.java -act-1.0/diana/Entry.java -act-1.0/diana/EntryChangeEvent.java -act-1.0/diana/EntryChangeListener.java -act-1.0/diana/EntryGroup.java -act-1.0/diana/EntryGroupChangeEvent.java -act-1.0/diana/EntryGroupChangeListener.java -act-1.0/diana/EntrySource.java -act-1.0/diana/plot/CVS/Root -act-1.0/diana/plot/CVS/Repository -act-1.0/diana/plot/CVS/Entries -act-1.0/diana/plot/AGWindowAlgorithm.java -act-1.0/diana/plot/ATDeviationAlgorithm.java -act-1.0/diana/plot/Algorithm.java -act-1.0/diana/plot/BaseAlgorithm.java -act-1.0/diana/plot/Codon12CorrelationAlgorithm.java -act-1.0/diana/plot/CodonUsageAlgorithm.java -act-1.0/diana/plot/CodonUsageFormatException.java -act-1.0/diana/plot/CodonUsageWeight.java -act-1.0/diana/plot/CodonWeight.java -act-1.0/diana/plot/CoilFeatureAlgorithm.java -act-1.0/diana/plot/HydroAlgorithm.java -act-1.0/diana/plot/FeatureAlgorithm.java -act-1.0/diana/plot/GCDeviationAlgorithm.java -act-1.0/diana/plot/GCFrameAlgorithm.java -act-1.0/diana/plot/GCSDWindowAlgorithm.java -act-1.0/diana/plot/GCWindowAlgorithm.java -act-1.0/diana/plot/HydrophilicityAlgorithm.java -act-1.0/diana/plot/HydrophobicityAlgorithm.java -act-1.0/diana/plot/UserDataAlgorithm.java -act-1.0/diana/plot/BaseAlgorithm.class -act-1.0/diana/plot/Algorithm.class -act-1.0/diana/plot/Codon12CorrelationAlgorithm.class -act-1.0/diana/plot/GCWindowAlgorithm.class -act-1.0/diana/plot/GCSDWindowAlgorithm.class -act-1.0/diana/plot/AGWindowAlgorithm.class -act-1.0/diana/plot/GCFrameAlgorithm.class -act-1.0/diana/plot/GCDeviationAlgorithm.class -act-1.0/diana/plot/ATDeviationAlgorithm.class -act-1.0/diana/plot/UserDataAlgorithm.class -act-1.0/diana/plot/CodonUsageAlgorithm.class -act-1.0/diana/plot/CodonUsageWeight.class -act-1.0/diana/plot/CodonWeight.class -act-1.0/diana/plot/FeatureAlgorithm.class -act-1.0/diana/plot/HydrophobicityAlgorithm.class -act-1.0/diana/plot/HydroAlgorithm.class -act-1.0/diana/plot/HydrophilicityAlgorithm.class -act-1.0/diana/plot/CoilFeatureAlgorithm.class -act-1.0/diana/plot/CodonUsageFormatException.class -act-1.0/diana/EntrySourceVector.java -act-1.0/diana/EntryVector.java -act-1.0/diana/ExternalApplication.java -act-1.0/diana/ExternalProgram.java -act-1.0/diana/ExternalProgramException.java -act-1.0/diana/ExternalProgramVector.java -act-1.0/diana/ExternalSearchProgram.java -act-1.0/diana/Feature.java -act-1.0/diana/FeatureChangeEvent.java -act-1.0/diana/FeatureChangeListener.java -act-1.0/diana/FeatureEnumeration.java -act-1.0/diana/FeatureFromVectorPredicate.java -act-1.0/diana/FeatureKeyPredicate.java -act-1.0/diana/FeatureKeyQualifierPredicate.java -act-1.0/diana/FeatureSegment.java -act-1.0/diana/FeaturePredicate.java -act-1.0/diana/FeatureSegmentVector.java -act-1.0/diana/FeatureVector.java -act-1.0/diana/FilteredEntryGroup.java -act-1.0/diana/GotoEvent.java -act-1.0/diana/GotoEventSource.java -act-1.0/diana/GotoListener.java -act-1.0/diana/LastSegmentException.java -act-1.0/diana/Logger.java -act-1.0/diana/MSPcrunchComparisonData.java -act-1.0/diana/MUMmerComparisonData.java -act-1.0/diana/Options.java -act-1.0/diana/Selectable.java -act-1.0/diana/Selection.java -act-1.0/diana/SelectionChangeEvent.java -act-1.0/diana/SelectionChangeListener.java -act-1.0/diana/helix.gif -act-1.0/diana/SimpleComparisonData.java -act-1.0/diana/SimpleEntryGroup.java -act-1.0/diana/SimpleGotoEventSource.java -act-1.0/diana/sanger-centre.gif -act-1.0/diana/components/CVS/Root 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