diff options
| author | rafan <rafan@FreeBSD.org> | 2007-07-08 19:47:58 +0800 |
|---|---|---|
| committer | rafan <rafan@FreeBSD.org> | 2007-07-08 19:47:58 +0800 |
| commit | a759261773699ff59190c2c8635bef4b3f866474 (patch) | |
| tree | 597189ab13531ed27e565b9f5e49f9091c06784d /biology | |
| parent | 86814340533ff7f3064fb839871869c994c6fb27 (diff) | |
| download | freebsd-ports-gnome-a759261773699ff59190c2c8635bef4b3f866474.tar.gz freebsd-ports-gnome-a759261773699ff59190c2c8635bef4b3f866474.tar.zst freebsd-ports-gnome-a759261773699ff59190c2c8635bef4b3f866474.zip | |
- Update to version 9
- Don't install CVS directories which are going to be removed
in next release
PR: ports/113831
Submitted by: Thomas Abthorpe <thomas at goodking.ca>
Approved by: maintainer timeout (20 days)
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/artemis/Makefile | 13 | ||||
| -rw-r--r-- | biology/artemis/distinfo | 6 | ||||
| -rw-r--r-- | biology/artemis/pkg-plist | 2799 |
3 files changed, 1505 insertions, 1313 deletions
diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile index a9a88d12d447..05b63cc70e57 100644 --- a/biology/artemis/Makefile +++ b/biology/artemis/Makefile @@ -6,17 +6,15 @@ # PORTNAME= artemis -PORTVERSION= 7 -PORTREVISION= 2 +PORTVERSION= 9 CATEGORIES= biology java -MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/ -DISTNAME= artemis_compiled_v${PORTVERSION}_${PORTREVISION} +MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/ \ + ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/v${PORTVERSION}/ +DISTNAME= artemis_compiled_v${PORTVERSION} MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A DNA sequence viewer and annotation tool -BROKEN= Unfetchable - WRKSRC= ${WRKDIR}/${PORTNAME} USE_JAVA= yes @@ -25,6 +23,9 @@ JAVA_VERSION= 1.4+ NO_BUILD= yes PLIST_SUB= PORTVERSION="${PORTVERSION}" +post-extract: + @${FIND} ${WRKSRC} -type d -name CVS -exec ${RM} -rf {} + + do-install: @${MKDIR} ${PREFIX}/${PORTNAME}-${PORTVERSION} @${TAR} -C ${WRKSRC} -cf- . | ${TAR} -C ${PREFIX}/${PORTNAME}-${PORTVERSION} -xpf- diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo index 3355a8ea32d4..eefdf600aed0 100644 --- a/biology/artemis/distinfo +++ b/biology/artemis/distinfo @@ -1,3 +1,3 @@ -MD5 (artemis_compiled_v7_2.tar.gz) = f81f52a99a7c7b40c2a5289e71e0ea03 -SHA256 (artemis_compiled_v7_2.tar.gz) = d770c48464be5903107379775765883f7827833be7339d90d3dc8e1430c0646e -SIZE (artemis_compiled_v7_2.tar.gz) = 4055125 +MD5 (artemis_compiled_v9.tar.gz) = b644bf8447534973d9e3cca4e632ee3a +SHA256 (artemis_compiled_v9.tar.gz) = ec61fdb7915322b5d6c8ac53aa3576cfe1a5042cc3c738e168306fdbaf4bcbe5 +SIZE (artemis_compiled_v9.tar.gz) = 6310269 diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist index 77ffc075d8ef..175c8b5f4f3e 100644 --- a/biology/artemis/pkg-plist +++ b/biology/artemis/pkg-plist @@ -1,13 +1,25 @@ -artemis-%%PORTVERSION%%/images/icon.gif -artemis-%%PORTVERSION%%/images/helix.gif -artemis-%%PORTVERSION%%/images/sanger-centre.gif artemis-%%PORTVERSION%%/README artemis-%%PORTVERSION%%/act artemis-%%PORTVERSION%%/art -artemis-%%PORTVERSION%%/etc/CVS/Root -artemis-%%PORTVERSION%%/etc/CVS/Repository -artemis-%%PORTVERSION%%/etc/CVS/Entries -artemis-%%PORTVERSION%%/etc/test.genbank +artemis-%%PORTVERSION%%/artemis_sqlmap/Analysis.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/AnalysisFeature.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/CvTerm.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Db.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/DbXRef.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Feature.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTerm.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermDbXRef.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermProp.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermPub.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureDbXRef.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureLoc.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureProp.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureRelationship.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Organism.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Pub.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Synonym.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.properties +artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.xml artemis-%%PORTVERSION%%/etc/af063097.embl artemis-%%PORTVERSION%%/etc/af063097.fasta artemis-%%PORTVERSION%%/etc/af063097_v_b132222.crunch @@ -18,17 +30,27 @@ artemis-%%PORTVERSION%%/etc/c1215.blastn.tab artemis-%%PORTVERSION%%/etc/c1215.embl artemis-%%PORTVERSION%%/etc/c1215.genbank artemis-%%PORTVERSION%%/etc/c1215.seq -artemis-%%PORTVERSION%%/etc/run_blastn +artemis-%%PORTVERSION%%/etc/feature_keys +artemis-%%PORTVERSION%%/etc/feature_keys_gff artemis-%%PORTVERSION%%/etc/go_associations.pl +artemis-%%PORTVERSION%%/etc/log4j.properties artemis-%%PORTVERSION%%/etc/options artemis-%%PORTVERSION%%/etc/pombe.usage -artemis-%%PORTVERSION%%/etc/feature_keys -artemis-%%PORTVERSION%%/etc/run_fasta.orig +artemis-%%PORTVERSION%%/etc/qualifier_types +artemis-%%PORTVERSION%%/etc/qualifier_types_gff +artemis-%%PORTVERSION%%/etc/results_to_netscape +artemis-%%PORTVERSION%%/etc/run_blastn +artemis-%%PORTVERSION%%/etc/run_blastn.sanger artemis-%%PORTVERSION%%/etc/run_blastp +artemis-%%PORTVERSION%%/etc/run_blastp.sanger artemis-%%PORTVERSION%%/etc/run_blastx +artemis-%%PORTVERSION%%/etc/run_blastx.sanger artemis-%%PORTVERSION%%/etc/run_clustalx +artemis-%%PORTVERSION%%/etc/run_clustalx.sanger artemis-%%PORTVERSION%%/etc/run_fasta +artemis-%%PORTVERSION%%/etc/run_fasta.sanger artemis-%%PORTVERSION%%/etc/run_fastx +artemis-%%PORTVERSION%%/etc/run_fastx.sanger artemis-%%PORTVERSION%%/etc/run_hth artemis-%%PORTVERSION%%/etc/run_jalview artemis-%%PORTVERSION%%/etc/run_pepstats @@ -36,276 +58,1146 @@ artemis-%%PORTVERSION%%/etc/run_sigcleave artemis-%%PORTVERSION%%/etc/run_smart artemis-%%PORTVERSION%%/etc/run_tblastn artemis-%%PORTVERSION%%/etc/run_tblastx -artemis-%%PORTVERSION%%/etc/test2.genbank -artemis-%%PORTVERSION%%/etc/run_jalview_n -artemis-%%PORTVERSION%%/etc/results_to_netscape_new -artemis-%%PORTVERSION%%/etc/results_to_netscape -artemis-%%PORTVERSION%%/etc/options_n -artemis-%%PORTVERSION%%/etc/feature_keys_o -artemis-%%PORTVERSION%%/etc/qualifier_types_o -artemis-%%PORTVERSION%%/etc/qualifier_types -artemis-%%PORTVERSION%%/etc/run_blastn.sanger -artemis-%%PORTVERSION%%/etc/run_blastp.sanger -artemis-%%PORTVERSION%%/etc/run_blastx.sanger -artemis-%%PORTVERSION%%/etc/run_clustalx.sanger -artemis-%%PORTVERSION%%/etc/run_fasta.sanger -artemis-%%PORTVERSION%%/etc/run_fastx.sanger -artemis-%%PORTVERSION%%/uk/CVS/Root -artemis-%%PORTVERSION%%/uk/CVS/Repository -artemis-%%PORTVERSION%%/uk/CVS/Entries -artemis-%%PORTVERSION%%/uk/CVS/Entries.Log -artemis-%%PORTVERSION%%/uk/ac/CVS/Root -artemis-%%PORTVERSION%%/uk/ac/CVS/Repository -artemis-%%PORTVERSION%%/uk/ac/CVS/Entries -artemis-%%PORTVERSION%%/uk/ac/CVS/Entries.Log -artemis-%%PORTVERSION%%/uk/ac/sanger/CVS/Root -artemis-%%PORTVERSION%%/uk/ac/sanger/CVS/Repository -artemis-%%PORTVERSION%%/uk/ac/sanger/CVS/Entries -artemis-%%PORTVERSION%%/uk/ac/sanger/CVS/Entries.Log -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS/Root -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS/Repository -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS/Entries -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS/Entries.Log -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CVS/Root -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CVS/Repository -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CVS/Entries -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$1.class +artemis-%%PORTVERSION%%/images/helix.gif +artemis-%%PORTVERSION%%/images/icon.gif +artemis-%%PORTVERSION%%/images/sanger-centre.gif +artemis-%%PORTVERSION%%/lib/LICENSE.Apache +artemis-%%PORTVERSION%%/lib/LICENSE.JDBC +artemis-%%PORTVERSION%%/lib/README +artemis-%%PORTVERSION%%/lib/biojava.jar +artemis-%%PORTVERSION%%/lib/chado-14-interface.jar +artemis-%%PORTVERSION%%/lib/ibatis/README +artemis-%%PORTVERSION%%/lib/ibatis/cglib-nodep-2.2_beta1.jar +artemis-%%PORTVERSION%%/lib/ibatis/ibatis-2.3.0.677.jar +artemis-%%PORTVERSION%%/lib/ibatis/license.txt +artemis-%%PORTVERSION%%/lib/ibatis/log4j-1.2.14.jar +artemis-%%PORTVERSION%%/lib/j2ssh/COMMONS.LICENSE +artemis-%%PORTVERSION%%/lib/j2ssh/J2SSH.LICENSE +artemis-%%PORTVERSION%%/lib/j2ssh/README +artemis-%%PORTVERSION%%/lib/j2ssh/commons-logging.jar +artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh-artemis-plugin.jar +artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh-core.jar +artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh.properties +artemis-%%PORTVERSION%%/lib/jakarta-regexp-1.2.jar +artemis-%%PORTVERSION%%/lib/jemAlign.jar +artemis-%%PORTVERSION%%/lib/jobcontrol.jar +artemis-%%PORTVERSION%%/lib/macos.jar +artemis-%%PORTVERSION%%/lib/postgresql-8.1-407.jdbc2ee.jar +artemis-%%PORTVERSION%%/lib/retrotranslator-runtime-1.1.0.jar +artemis-%%PORTVERSION%%/nsdb/CommitFailed.class +artemis-%%PORTVERSION%%/nsdb/CommitFailed.java +artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.class +artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.java +artemis-%%PORTVERSION%%/nsdb/CommitFailedHolder.java +artemis-%%PORTVERSION%%/nsdb/Datestamp.class +artemis-%%PORTVERSION%%/nsdb/Datestamp.java +artemis-%%PORTVERSION%%/nsdb/DatestampHelper.class +artemis-%%PORTVERSION%%/nsdb/DatestampHelper.java +artemis-%%PORTVERSION%%/nsdb/DatestampHolder.java +artemis-%%PORTVERSION%%/nsdb/Embl.class +artemis-%%PORTVERSION%%/nsdb/Embl.java +artemis-%%PORTVERSION%%/nsdb/EmblHelper.class +artemis-%%PORTVERSION%%/nsdb/EmblHelper.java +artemis-%%PORTVERSION%%/nsdb/EmblHolder.java +artemis-%%PORTVERSION%%/nsdb/EmblOperations.class +artemis-%%PORTVERSION%%/nsdb/EmblOperations.java +artemis-%%PORTVERSION%%/nsdb/EmblPackage/Superceded.class +artemis-%%PORTVERSION%%/nsdb/EmblPackage/Superceded.java +artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHelper.class +artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHelper.java +artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHolder.java +artemis-%%PORTVERSION%%/nsdb/EmblSeq.class +artemis-%%PORTVERSION%%/nsdb/EmblSeq.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqHelper.class +artemis-%%PORTVERSION%%/nsdb/EmblSeqHelper.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqHolder.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqOperations.class +artemis-%%PORTVERSION%%/nsdb/EmblSeqOperations.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.class +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.class +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHolder.java +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.class +artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.java +artemis-%%PORTVERSION%%/nsdb/EmblWriter.class +artemis-%%PORTVERSION%%/nsdb/EmblWriter.java +artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.class +artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.java +artemis-%%PORTVERSION%%/nsdb/EmblWriterHolder.java +artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.class +artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.java +artemis-%%PORTVERSION%%/nsdb/EntryInfo.class +artemis-%%PORTVERSION%%/nsdb/EntryInfo.java +artemis-%%PORTVERSION%%/nsdb/EntryInfoHelper.java +artemis-%%PORTVERSION%%/nsdb/EntryInfoHolder.java +artemis-%%PORTVERSION%%/nsdb/EntryInfoListHelper.java +artemis-%%PORTVERSION%%/nsdb/EntryInfoListHolder.java +artemis-%%PORTVERSION%%/nsdb/EntryInfoOperations.class +artemis-%%PORTVERSION%%/nsdb/EntryInfoOperations.java +artemis-%%PORTVERSION%%/nsdb/EntryStats.class +artemis-%%PORTVERSION%%/nsdb/EntryStats.java +artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.class +artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.java +artemis-%%PORTVERSION%%/nsdb/EntryStatsHolder.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocation.class +artemis-%%PORTVERSION%%/nsdb/FeatureLocation.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocationHelper.class +artemis-%%PORTVERSION%%/nsdb/FeatureLocationHelper.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocationHolder.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocationListHelper.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocationListHolder.java +artemis-%%PORTVERSION%%/nsdb/FeatureLocationOperations.class +artemis-%%PORTVERSION%%/nsdb/FeatureLocationOperations.java +artemis-%%PORTVERSION%%/nsdb/InexactLocation.class +artemis-%%PORTVERSION%%/nsdb/InexactLocation.java +artemis-%%PORTVERSION%%/nsdb/InexactLocationHelper.class +artemis-%%PORTVERSION%%/nsdb/InexactLocationHelper.java +artemis-%%PORTVERSION%%/nsdb/InexactLocationHolder.java +artemis-%%PORTVERSION%%/nsdb/InvalidKey.class +artemis-%%PORTVERSION%%/nsdb/InvalidKey.java +artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.class +artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.java +artemis-%%PORTVERSION%%/nsdb/InvalidKeyHolder.java +artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.class +artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.java +artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.class +artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.java +artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHolder.java +artemis-%%PORTVERSION%%/nsdb/Location.class +artemis-%%PORTVERSION%%/nsdb/Location.java +artemis-%%PORTVERSION%%/nsdb/LocationHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationListHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationListHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationOperations.class +artemis-%%PORTVERSION%%/nsdb/LocationOperations.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocGapHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocGapHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocNodeTypeCodeHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocNodeTypeCodeHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperator.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperator.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocPhysicalSegmentHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocPhysicalSegmentHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegment.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegment.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_u.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_u.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHolder.java +artemis-%%PORTVERSION%%/nsdb/LocationParse.class +artemis-%%PORTVERSION%%/nsdb/LocationParse.java +artemis-%%PORTVERSION%%/nsdb/LocationParseHelper.class +artemis-%%PORTVERSION%%/nsdb/LocationParseHelper.java +artemis-%%PORTVERSION%%/nsdb/LocationParseHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeature.class +artemis-%%PORTVERSION%%/nsdb/NucFeature.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureListHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureListHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureListHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureOperations.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureOperations.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/Qualifier.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/Qualifier.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierTypeCodeHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierTypeCodeHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_u.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_u.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHelper.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHolder.java +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.class +artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.java +artemis-%%PORTVERSION%%/nsdb/NucSeq.class +artemis-%%PORTVERSION%%/nsdb/NucSeq.java +artemis-%%PORTVERSION%%/nsdb/NucSeqHelper.java +artemis-%%PORTVERSION%%/nsdb/NucSeqHolder.java +artemis-%%PORTVERSION%%/nsdb/NucSeqListHelper.java +artemis-%%PORTVERSION%%/nsdb/NucSeqListHolder.java +artemis-%%PORTVERSION%%/nsdb/NucSeqOperations.class +artemis-%%PORTVERSION%%/nsdb/NucSeqOperations.java +artemis-%%PORTVERSION%%/nsdb/OutOfDate.class +artemis-%%PORTVERSION%%/nsdb/OutOfDate.java +artemis-%%PORTVERSION%%/nsdb/OutOfDateHelper.class +artemis-%%PORTVERSION%%/nsdb/OutOfDateHelper.java +artemis-%%PORTVERSION%%/nsdb/OutOfDateHolder.java +artemis-%%PORTVERSION%%/nsdb/QualifierParse.class +artemis-%%PORTVERSION%%/nsdb/QualifierParse.java +artemis-%%PORTVERSION%%/nsdb/QualifierParseHelper.class +artemis-%%PORTVERSION%%/nsdb/QualifierParseHelper.java +artemis-%%PORTVERSION%%/nsdb/QualifierParseHolder.java +artemis-%%PORTVERSION%%/nsdb/ReadOnlyException.class +artemis-%%PORTVERSION%%/nsdb/ReadOnlyException.java +artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHelper.class +artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHelper.java +artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHolder.java +artemis-%%PORTVERSION%%/nsdb/ServerInfo.class +artemis-%%PORTVERSION%%/nsdb/ServerInfo.java +artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.class +artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.java +artemis-%%PORTVERSION%%/nsdb/ServerInfoHolder.java +artemis-%%PORTVERSION%%/nsdb/_EmblSeqStub.class +artemis-%%PORTVERSION%%/nsdb/_EmblSeqStub.java +artemis-%%PORTVERSION%%/nsdb/_EmblSeqWriterStub.class +artemis-%%PORTVERSION%%/nsdb/_EmblSeqWriterStub.java +artemis-%%PORTVERSION%%/nsdb/_EmblStub.class +artemis-%%PORTVERSION%%/nsdb/_EmblStub.java +artemis-%%PORTVERSION%%/nsdb/_EmblWriterStub.class +artemis-%%PORTVERSION%%/nsdb/_EmblWriterStub.java +artemis-%%PORTVERSION%%/nsdb/_EntryInfoStub.java +artemis-%%PORTVERSION%%/nsdb/_FeatureLocationStub.class +artemis-%%PORTVERSION%%/nsdb/_FeatureLocationStub.java +artemis-%%PORTVERSION%%/nsdb/_LocationStub.class +artemis-%%PORTVERSION%%/nsdb/_LocationStub.java +artemis-%%PORTVERSION%%/nsdb/_NucFeatureStub.class +artemis-%%PORTVERSION%%/nsdb/_NucFeatureStub.java +artemis-%%PORTVERSION%%/nsdb/_NucFeatureWriterStub.class +artemis-%%PORTVERSION%%/nsdb/_NucFeatureWriterStub.java +artemis-%%PORTVERSION%%/nsdb/_NucSeqStub.java 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artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$11.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$12.class @@ -316,6 +1208,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$16.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$17.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$18.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$19.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$20.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$21.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$22.class @@ -326,112 +1219,23 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$26.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ViewMenu$27.class 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-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 +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/WorkingGZIPInputStream.java bin/act bin/art -@dirrm artemis-%%PORTVERSION%%/images -@dirrm artemis-%%PORTVERSION%%/etc/CVS -@dirrm artemis-%%PORTVERSION%%/etc -@dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage -@dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage -@dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage -@dirrm artemis-%%PORTVERSION%%/nsdb -@dirrm artemis-%%PORTVERSION%%/uk/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/CVS +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/ibatis +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/j2ssh @dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CVS @dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/CVS -@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/gff +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/cv +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/filetree +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/database +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components +@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/chado @dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis @dirrm artemis-%%PORTVERSION%%/uk/ac/sanger @dirrm artemis-%%PORTVERSION%%/uk/ac @dirrm artemis-%%PORTVERSION%%/uk -@dirrm artemis-%%PORTVERSION%%/seqdb @dirrm artemis-%%PORTVERSION%%/type -@dirrm artemis-%%PORTVERSION%%/lib/CVS +@dirrm artemis-%%PORTVERSION%%/seqdb +@dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage +@dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage +@dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage +@dirrm artemis-%%PORTVERSION%%/nsdb +@dirrm artemis-%%PORTVERSION%%/lib/j2ssh +@dirrm artemis-%%PORTVERSION%%/lib/ibatis @dirrm artemis-%%PORTVERSION%%/lib +@dirrm artemis-%%PORTVERSION%%/images +@dirrm artemis-%%PORTVERSION%%/etc +@dirrm artemis-%%PORTVERSION%%/artemis_sqlmap @dirrm artemis-%%PORTVERSION%% |