diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/artemis/Makefile | 2 | ||||
| -rw-r--r-- | biology/artemis/distinfo | 4 | ||||
| -rw-r--r-- | biology/artemis/pkg-plist | 201 |
3 files changed, 160 insertions, 47 deletions
diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile index 427e2a0a6668..b924100f1c28 100644 --- a/biology/artemis/Makefile +++ b/biology/artemis/Makefile @@ -6,7 +6,7 @@ # PORTNAME= artemis -PORTVERSION= 6 +PORTVERSION= 7 CATEGORIES= biology java MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/ DISTNAME= artemis_compiled_v${PORTVERSION} diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo index b5e7602972da..902cf64a4c4a 100644 --- a/biology/artemis/distinfo +++ b/biology/artemis/distinfo @@ -1,2 +1,2 @@ -MD5 (artemis_compiled_v6.tar.gz) = 5ebd3db7edbb74eab5a84df9c693d4e1 -SIZE (artemis_compiled_v6.tar.gz) = 3947732 +MD5 (artemis_compiled_v7.tar.gz) = 1830af32fb1010fadd7cb7f79e32a428 +SIZE (artemis_compiled_v7.tar.gz) = 4055112 diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist index b4c61867305d..77ffc075d8ef 100644 --- a/biology/artemis/pkg-plist +++ b/biology/artemis/pkg-plist @@ -7,6 +7,7 @@ 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%%/etc/af063097.embl artemis-%%PORTVERSION%%/etc/af063097.fasta artemis-%%PORTVERSION%%/etc/af063097_v_b132222.crunch @@ -17,12 +18,12 @@ artemis-%%PORTVERSION%%/etc/c1215.blastn.tab artemis-%%PORTVERSION%%/etc/c1215.embl artemis-%%PORTVERSION%%/etc/c1215.genbank artemis-%%PORTVERSION%%/etc/c1215.seq -artemis-%%PORTVERSION%%/etc/feature_keys +artemis-%%PORTVERSION%%/etc/run_blastn +artemis-%%PORTVERSION%%/etc/go_associations.pl artemis-%%PORTVERSION%%/etc/options artemis-%%PORTVERSION%%/etc/pombe.usage -artemis-%%PORTVERSION%%/etc/qualifier_types -artemis-%%PORTVERSION%%/etc/results_to_netscape -artemis-%%PORTVERSION%%/etc/run_blastn +artemis-%%PORTVERSION%%/etc/feature_keys +artemis-%%PORTVERSION%%/etc/run_fasta.orig artemis-%%PORTVERSION%%/etc/run_blastp artemis-%%PORTVERSION%%/etc/run_blastx artemis-%%PORTVERSION%%/etc/run_clustalx @@ -35,6 +36,20 @@ 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 @@ -120,6 +135,8 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Navigator.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PlotMouseListener.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintACT.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcher.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcherEvent.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcherListener.java @@ -133,13 +150,14 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChangeListener.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreScrollbar.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SearchResultViewer.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SegmentBorder.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionInfoDisplay.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionMenu.java -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionViewer.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SequenceViewer.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/StickyFileChooser.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SwingWorker.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/TaskViewerFrame.java @@ -156,11 +174,10 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/YesNoDialog.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisMain.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$6.class @@ -171,9 +188,9 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$10.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Splash.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEditVector.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$1.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$5.class @@ -188,7 +205,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager$15.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileManager.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProgressThread.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$3.class @@ -203,6 +219,9 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$11.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$12.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$14.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$15.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit$16.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryEdit.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/LogViewer$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/LogViewer.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileTree$1.class @@ -224,7 +243,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureDisplay$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureDisplay$7.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureDisplay.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupPanel$1.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CanvasPanel$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupPanel.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/CanvasPanel.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/DisplayComponent.class @@ -232,29 +250,31 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/DisplayAdjustmentListene artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/BasePlotGroup.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureList$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureList$2.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureList$3.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureList$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureList.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionInfoDisplay$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionInfoDisplay.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileViewer$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileViewer$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileViewer$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileViewer.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileNode.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SegmentBorder.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/BasePlot$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/BasePlot.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$2.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$5.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$7.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$8.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Plot$9.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PlotMouseListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ReadFeaturesActionListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryActionListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SaveEntryActionListener.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MessageDialog.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SaveEntryAsActionListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SaveEntryAsEMBLActionListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SaveEntryAsGenbankActionListener.class @@ -263,6 +283,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SaveEntryAsSubmissionAct artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MessageDialog$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MessageDialog$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MessageDialog$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MessageDialog.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Utilities.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryFileDialog$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryFileDialog$2.class @@ -273,8 +294,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SwingWorker$ThreadVar.cl artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SwingWorker$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SwingWorker$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SwingWorker.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionInfoDisplay$1.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionInfoDisplay.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/YesNoDialog$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/YesNoDialog$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/YesNoDialog.class @@ -317,6 +336,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupMenu$7.class @@ -337,8 +357,8 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$15.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$16.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$1SelectListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$17.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$1SelectListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$18.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$19.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectMenu$20.class @@ -353,7 +373,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu$7.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu$8.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu$9.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu$10.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GotoMenu.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EditMenu$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EditMenu$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EditMenu$3.class @@ -435,6 +454,16 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GraphMenu$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GraphMenu$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GraphMenu$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/GraphMenu.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$5.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$6.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$7.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$8.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis$9.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintArtemis.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay$3.class @@ -455,8 +484,8 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$15.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$16.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$14.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/KeyChoice.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$17.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/KeyChoice.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$18.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$19.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$20.class @@ -466,6 +495,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$23.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$24.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$25.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$26.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$27.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$2.class @@ -479,13 +509,17 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$9.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$10.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$11.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$12.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$13.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$15.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$14.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$16.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$17.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$18.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit$19.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureEdit.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierChoice.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierTextArea.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProgressThread.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FileDialogEntrySource.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/DbfetchEntrySource.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EMBLCorbaEntrySource.class @@ -500,10 +534,10 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/InputStreamProgressDialo artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/InputStreamProgressDialog.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionViewer$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/SelectionViewer.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureListFrame.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureListFrame$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureListFrame$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureListFrame$3.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeatureListFrame.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/KeyChooser$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/KeyChooser$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/KeyChooser.class @@ -539,6 +573,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$7.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$8.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$9.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$10.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$11.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$12.class @@ -546,7 +581,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$15.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector$16.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/Selector.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ChoiceFrame$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ChoiceFrame$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ChoiceFrame$3.class @@ -569,7 +603,6 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryHeaderEdit$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/EntryHeaderEdit.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierEditor$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierEditor$2.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierEditor$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierEditor$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/QualifierEditor$5.class @@ -590,11 +623,9 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$4.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreChanger$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ScoreScrollbar.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ArtemisCheckboxMenuItem.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcher.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcherListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ProcessWatcherEvent.class @@ -602,6 +633,8 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ListDialog$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ListDialog$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ListDialog.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePlot.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ActMain.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$1.class @@ -615,10 +648,13 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$8.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$9.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$10.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$11.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintACT.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$12.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$15.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$16.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator$17.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/MultiComparator.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$2.class @@ -628,17 +664,19 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$6.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$7.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$8.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$9.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$10.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$12.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$11.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$9.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$13.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$14.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$12.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$15.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$16.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$14.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$17.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$18.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/TextFieldSink.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$19.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$20.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer$ColorChooserShades.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentViewer.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignmentEvent.class @@ -654,6 +692,9 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ComparatorDialog$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ComparatorDialog$4.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ComparatorDialog$5.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/ComparatorDialog.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintACT$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintACT$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/PrintACT$3.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer$2.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer$3.class @@ -669,6 +710,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer$12.clas artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer$13.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/AlignMatchViewer.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/TextFieldSink$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/TextFieldSink.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/BioJavaEntrySource.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Action.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/ActionController.java @@ -787,11 +829,11 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/Qualifier.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/Range.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/InvalidRelationException.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/Entry.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/LocationParseException.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/ReadFormatException.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/RangeVector.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/LocationParseNode.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/EMBLObject.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/RangeVector.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/LocationParseException.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/ReadFormatException.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/LocationLexer$TokenEnumeration.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/LocationLexer.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/FeatureEnumeration.class @@ -845,6 +887,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/GFFMisc.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/StreamQualifier.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/ReadOnlyEmblStreamFeature.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/StreamFeatureTable.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/GenbankDocumentEntry.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/GenbankStreamSequence.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io/FeatureComparator.class @@ -917,6 +960,7 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/SSAHAComparisonData.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CVS/Root artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CVS/Repository artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CVS/Entries +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$1.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/Annotation.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BrowserControl.java @@ -924,13 +968,64 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CommonMenu.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/EvidenceViewer.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ExternalApplication.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/FastaListener.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/FastaTextPane.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/HitInfo.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MouseOverButton.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MultiLineToolTipUI.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/PlafMacros.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ScrollPanel.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ScrollPanel.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$5.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$6.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$7.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$8.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane$winExit.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BigPane.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataViewInternalFrame$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataViewInternalFrame$TabChangeListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataViewInternalFrame$ActiveJSplitPane.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataViewInternalFrame.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/Annotation$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/Annotation$PopupListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/Annotation.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MultiLineToolTipUI$MyToolTip.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MultiLineToolTipUI$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MultiLineToolTipUI.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/HitInfo.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/EvidenceViewer$MouseClickListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/EvidenceViewer.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CommonMenu$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/CommonMenu.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/FastaTextPane$GetzThread.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/FastaTextPane.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/FastaListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$5.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$6.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer$PopupListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DBViewer.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/MouseOverButton.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$1.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$2.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$3.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$4.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$5.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane$6.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/DataCollectionPane.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/BrowserControl.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/PlafMacros.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ExternalApplication$StdoutHandler.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ExternalApplication$StderrHandler.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor/ExternalApplication.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Selectable.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Selection.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/SelectionChangeEvent.java @@ -948,12 +1043,16 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ATDeviationAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/Algorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/BaseAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CSCSAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CodonUsageFormatException.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CodonUsageWeight.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CodonWeight.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CumulativeATSkewAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CumulativeGCSkewAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/EntropyAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/FeatureAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java @@ -961,8 +1060,13 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/HydroAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ICDIAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/MRIAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/NcAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/PositionalAsymmetryAlgorithm.java +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ScaledChiAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/BaseAlgorithm.class @@ -976,6 +1080,15 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ATDeviationAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CumulativeATSkewAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/EntropyAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CumulativeGCSkewAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/PositionalAsymmetryAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ScaledChiAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CSCSAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/MRIAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/NcAlgorithm.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/ICDIAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/CodonUsageFormatException.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/UserDataAlgorithm.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot/FeatureAlgorithm.class @@ -1002,9 +1115,9 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/SequenceChangeEvent.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/SequenceChangeListener.java artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/SequenceChangeListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/MarkerChangeListener.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/AminoAcidSequence.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/MarkerChangeEvent.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/SequenceChangeEvent.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/AminoAcidSequence.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/Strand.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/Bases.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence/NoSequenceException.class @@ -1058,11 +1171,11 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeatureVector.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Feature.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/EntryChangeListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Selectable.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/EntryChangeEvent.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Entry$FeatureEnumerator.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/Entry.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeatureChangeListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeatureSegmentVector.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/EntryChangeEvent.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeatureSegment.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/LastSegmentException.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeatureEnumeration.class @@ -1108,8 +1221,8 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeaturePredicateConjunction.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/FeaturePatternPredicate.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/AlignMatch.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/ComparisonDataFactory.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/AlignmentSelectionChangeListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/AlignMatchVector.class +artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/AlignmentSelectionChangeListener.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/AlignmentSelectionChangeEvent.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/MSPcrunchComparisonData.class artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/SimpleComparisonData.class @@ -1476,6 +1589,10 @@ 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 @@ -1496,12 +1613,8 @@ bin/art @dirrm artemis-%%PORTVERSION%%/uk/ac/sanger @dirrm artemis-%%PORTVERSION%%/uk/ac @dirrm artemis-%%PORTVERSION%%/uk -@dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage -@dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage -@dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage -@dirrm artemis-%%PORTVERSION%%/nsdb -@dirrm artemis-%%PORTVERSION%%/type @dirrm artemis-%%PORTVERSION%%/seqdb +@dirrm artemis-%%PORTVERSION%%/type @dirrm artemis-%%PORTVERSION%%/lib/CVS @dirrm artemis-%%PORTVERSION%%/lib @dirrm artemis-%%PORTVERSION%% |