June 2009 Commit Log

Commit Logs

Number of Commits:: 86
Number of Active Developers:: 1

jprocter 2009-06-24 09:31 #86

ensure annotation row height is honoured for new VAMSAS annotation

4 lines of code changed in:

src/jalview/io: VamsasAppDatastore.java (+4)

jprocter 2009-06-24 09:28 #85

all alignment sequences associated with a dataset sequence must have start-end updated (and any mappings adjusted - see TODO)

0 lines of code changed in:

src/jalview/ws: DBRefFetcher.java (changed)

jprocter 2009-06-24 09:24 #84

can use whitespace, comma or semicolon to separate IDs

4 lines of code changed in:

src/jalview/gui: SequenceFetcher.java (+4 -2)

jprocter 2009-06-24 09:24 #83

fix to cope with EMBL records containing a CDS fragment (proper start/end codon positioning and trimming)

90 lines of code changed in:

src/jalview/datamodel/xdb/embl: EmblEntry.java (+90 -31)

jprocter 2009-06-24 09:22 #82

take the average of the three consecutive codon sites when translating annotation row scores from cDNA to protein.

0 lines of code changed in:

src/jalview/analysis: Dna.java (changed)

jprocter 2009-06-19 11:11 #81

implementation error warning todo

3 lines of code changed in:

src/jalview/io/vamsas: Rangetype.java (+3)

jprocter 2009-06-19 11:10 #80

debug and cyclefix for dbrefs with embedded sequences

45 lines of code changed in:

src/jalview/io/vamsas: Dbref.java (+45 -24)

jprocter 2009-06-19 11:09 #79

javadoc and datastoreitem registry support for binding/rebinding methods

21 lines of code changed in:

src/jalview/io/vamsas: DatastoreItem.java (+21 -3)

jprocter 2009-06-19 11:09 #78

more efficient synchronized methods

39 lines of code changed in:

src/jalview/io/vamsas: DatastoreRegistry.java (+39 -40)

jprocter 2009-06-19 11:01 #77

bugfix mapped reference transfer and made picr ID retrieval optional

0 lines of code changed in:

src/jalview/ws: DBRefFetcher.java (changed)

jprocter 2009-06-19 10:59 #76

selection handler and sender bugfix

4 lines of code changed in:

src/jalview/gui: VamsasApplication.java (+4 -17)

jprocter 2009-06-19 10:58 #75

todo

2 lines of code changed in:

src/jalview/gui: SeqPanel.java (+2 -1)

jprocter 2009-06-19 10:58 #74

selections sent when mouse is released (drags on ID panel)

3 lines of code changed in:

src/jalview/gui: IdPanel.java (+3 -4)

jprocter 2009-06-19 10:57 #73

progress bars (still need to be threaded properly) and URI drag'n'dropping

27 lines of code changed in:

src/jalview/gui: Desktop.java (+27 -6)

jprocter 2009-06-19 10:56 #72

smoother scroll-to-position action

12 lines of code changed in:

src/jalview/gui: AlignmentPanel.java (+12 -4)

jprocter 2009-06-19 10:55 #71

drag'n'drop a URL on to an alignment

17 lines of code changed in:

src/jalview/gui: AlignFrame.java (+17 -8)

jprocter 2009-06-19 10:54 #70

parent db references and mappings added to retrieved sequences, debugging of codon_start>1 for coding region and stop codon inclusion/exclusion detection

77 lines of code changed in:

src/jalview/datamodel/xdb/embl: EmblEntry.java (+77 -38)

jprocter 2009-06-19 10:53 #69

intersect did not intersect (used in selection listener)

16 lines of code changed in:

src/jalview/datamodel: SequenceGroup.java (+16 -9)

jprocter 2009-06-19 10:49 #68

regex validator for uniprot

3 lines of code changed in:

src/jalview/ws/dbsources: Uniprot.java (+3 -2)

jprocter 2009-06-19 10:49 #67

usepicr config property

3 lines of code changed in:

src/jalview/bin: Cache.java (+3 -1)

jprocter 2009-06-19 10:48 #66

debug

0 lines of code changed in:

src/jalview/analysis: CrossRef.java (changed)

jprocter 2009-06-19 10:41 #65

debug comments

5 lines of code changed in:

src/jalview/util: DBRefUtils.java (+5 -3)

jprocter 2009-06-19 10:40 #64

new coverage comparison - no test case in main method yet

17 lines of code changed in:

src/jalview/util: MapList.java (+17)

jprocter 2009-06-12 17:02 #63

updated Iclientfactory interface, XMl viewer tests - not properly released source yet...

0 lines of code changed in:

lib: vamsas-client.jar (changed)

jprocter 2009-06-12 16:57 #62

synching of all db references and sequence features

0 lines of code changed in:

src/jalview/io/vamsas: Datasetsequence.java (changed)

jprocter 2009-06-12 16:57 #61

prevent dbref->map->to->datasetsequence->dbref-> type cycles

6 lines of code changed in:

src/jalview/io/vamsas: Dbref.java (+6 -3)

jprocter 2009-06-12 16:56 #60

reinstate links on features

0 lines of code changed in:

src/jalview/io/vamsas: Sequencefeature.java (changed)

jprocter 2009-06-12 16:55 #59

datastore registration and class cast exception fix

19 lines of code changed in:

src/jalview/io/vamsas: DatastoreItem.java (+19 -3)

jprocter 2009-06-12 16:54 #58

prevent and keep track of which objects handling element/jv obj synchronizations.

160 lines of code changed in:

src/jalview/io/vamsas: DatastoreRegistry.java (new 160)

jprocter 2009-06-12 16:54 #57

numerous bugfixs (tree panel synchs) and DatastoreRegistry clas.

30 lines of code changed in:

src/jalview/io: VamsasAppDatastore.java (+30 -6)

jprocter 2009-06-12 16:51 #56

methods for importing anonymous vamsas documents into explicitly named sessions (e.g. temp file from URL). Suppress implementation Error messages if session update fails on first update.

39 lines of code changed in:

src/jalview/gui: VamsasApplication.java (+39 -9)

jprocter 2009-06-12 16:49 #55

nullpointer bugfix (possibly not needed - was an error in closing of alignment panels)

2 lines of code changed in:

src/jalview/gui: SequenceRenderer.java (+2 -1)

jprocter 2009-06-12 16:49 #54

recover pdb from jalview-xml in vamsas doc

16 lines of code changed in:

src/jalview/gui: Jalview2XML.java (+16 -8)

jprocter 2009-06-12 16:48 #53

send selection on drag over sequence ids

8 lines of code changed in:

src/jalview/gui: IdPanel.java (+8 -3)

jprocter 2009-06-12 16:47 #52

retrieve and init vamsas session from vdoc at URL

67 lines of code changed in:

src/jalview/bin: Jalview.java (+14 -9)
src/jalview/gui: Desktop.java (+53 -2)

jprocter 2009-06-12 16:46 #51

reinstated blind querying of datasources. Transfer references to alignment from Map.To sequences on retrieved entries (e.g. protein product from EMBLCDS record)

0 lines of code changed in:

src/jalview/ws: DBRefFetcher.java (changed)

jprocter 2009-06-12 16:43 #50

more ID validation

0 lines of code changed in:

src/jalview/ws/dbsources: EmblCdsSouce.java (changed), EmblSource.java (changed)

jprocter 2009-06-12 16:43 #49

javadoc

0 lines of code changed in:

src/jalview/util: UrlLink.java (changed)

jprocter 2009-06-10 13:04 #48

com.boxysystems.jgogleanalytics is now an optional dependency

171 lines of code changed in:

src/jalview/bin: Cache.java (+171 -97)

jprocter 2009-06-09 16:16 #47

fix null pointer when new view is created then closed after a vamsas sync of stored views

240 lines of code changed in:

src/jalview/gui: AlignFrame.java (+240 -176)

jprocter 2009-06-09 16:14 #46

fix null pointer when new view created on alignment with existing sequence mappings (cDNA list is null)

9 lines of code changed in:

src/jalview/io: VamsasAppDatastore.java (+9 -3)

jprocter 2009-06-08 15:38 #45

use structured UA naming for googleanalytics client

0 lines of code changed in:

lib: JGoogleAnalytics-0.2.1-SNAPSHOT.jar (changed)

jprocter 2009-06-08 15:07 #44

upgrade to simple vamsas client version 0.2 (not runtime compatible)

0 lines of code changed in:

lib: vamsas-client.jar (changed)

jprocter 2009-06-08 15:06 #43

trial of jGA with proper useragent info

0 lines of code changed in:

lib: JGoogleAnalytics-0.2.1-SNAPSHOT.jar (new), JGoogleAnalytics_0.2.jar (del)

jprocter 2009-06-08 12:20 #42

*experimental use of picr* apply gpl development license

0 lines of code changed in:

src/jalview/ws: DBRefFetcher.java (changed)

jprocter 2009-06-08 12:19 #41

clargs documentation, new vamsas session import and join args. apply gpl development license

59 lines of code changed in:

src/jalview/bin: Jalview.java (+59 -6)

jprocter 2009-06-08 12:18 #40

refactored public methods for non-interactive import and initiation of vamsas sessions. apply gpl development license

130 lines of code changed in:

src/jalview/gui: Desktop.java (+130 -67)

jprocter 2009-06-08 12:17 #39

refactored for non-interactive import and initiation of sessions. apply gpl development license

157 lines of code changed in:

src/jalview/gui: VamsasApplication.java (+157 -88)

jprocter 2009-06-08 12:14 #38

sequence scores only shown if they vary. shift stops tooltip moving with mouse pointer. bugfix selection sharing. apply gpl development license

28 lines of code changed in:

src/jalview/gui: SeqPanel.java (+28 -14)

jprocter 2009-06-08 12:11 #37

debug messages and graceful recovery when structure state is corrupted. apply gpl development license

48 lines of code changed in:

src/jalview/gui: Jalview2XML.java (+48 -9)

jprocter 2009-06-08 12:10 #36

better thread safety for tooltip. apply gpl development license

6 lines of code changed in:

src/jalview/gui: IdPanel.java (+6 -5)

jprocter 2009-06-08 12:08 #35

ensure listeners are deregistered when panel is closed. apply gpl development license

9 lines of code changed in:

src/jalview/gui: AlignFrame.java (+9 -16)

jprocter 2009-06-08 12:08 #34

ensure listeners are deregistered when panel is closed. Fix a scrolling bug and apply gpl development license

30 lines of code changed in:

src/jalview/gui: AlignmentPanel.java (+30 -5)

jprocter 2009-06-08 12:00 #33

ga tracker option and apply gpl development license

11 lines of code changed in:

src/jalview/bin: Cache.java (+11 -6)

jprocter 2009-06-08 11:56 #32

apply gpl development license

178 lines of code changed in:

src/jalview/bin: JalviewLite.java (+3 -3)
src/jalview/datamodel: AlignedCodonFrame.java (changed), Alignment.java (+2 -2), AlignmentAnnotation.java (+3 -3), AlignmentI.java (+2 -2), AlignmentOrder.java (+2 -2), AlignmentView.java (changed), Annotation.java (+3 -3), BinaryNode.java (+3 -3), BinarySequence.java (+3 -3), CigarArray.java (changed), CigarBase.java (changed), CigarCigar.java (changed), CigarSimple.java (changed), ColumnSelection.java (changed), DBRefEntry.java (+2 -2), DBRefSource.java (changed), FeatureProperties.java (changed), GraphLine.java (+2 -2), HiddenSequences.java (+2 -2), Mapping.java (+2 -2), NodeTransformI.java (+16 -1), PDBEntry.java (+2 -2), Provenance.java (+2 -2), ProvenanceEntry.java (+2 -2), SearchResults.java (+2 -2), SeqCigar.java (+2 -2), Sequence.java (+3 -3), SequenceFeature.java (+3 -3), SequenceGroup.java (+3 -3), SequenceI.java (+3 -3), SequenceNode.java (+3 -3), SequencePoint.java (+3 -3), UniprotEntry.java (+2 -2), UniprotFile.java (+2 -2), UniprotProteinName.java (changed), UniprotSequence.java (+2 -2)
src/jalview/gui: AlignViewport.java (+3 -3), AnnotationColourChooser.java (+2 -2), AnnotationExporter.java (changed), AnnotationLabels.java (+3 -3), AnnotationPanel.java (+3 -3), AppJmol.java (+2 -2), CutAndPasteTransfer.java (+3 -3), DasSourceBrowser.java (changed), EPSOptions.java (+2 -2), EditNameDialog.java (+2 -2), FeatureColourChooser.java (+2 -2), FeatureRenderer.java (+3 -3), FeatureSettings.java (+2 -2), Finder.java (+3 -3), FontChooser.java (+3 -3), IProgressIndicator.java (changed), IProgressIndicatorHandler.java (changed), IdCanvas.java (+3 -3), IdwidthAdjuster.java (+3 -3), Jalview2XML_V1.java (changed), OOMWarning.java (changed), OverviewPanel.java (+3 -3), PCAPanel.java (+3 -3), PaintRefresher.java (+3 -3), PairwiseAlignPanel.java (+3 -3), PopupMenu.java (+3 -3), Preferences.java (+3 -3), RedundancyPanel.java (+3 -3), RotatableCanvas.java (+3 -3), ScalePanel.java (+3 -3), ScriptWindow.java (+2 -2), SeqCanvas.java (+3 -3), SequenceFetcher.java (+2 -2), SequenceRenderer.java (+3 -3), SliderPanel.java (+3 -3), SplashScreen.java (+3 -3), TextColourChooser.java (+2 -2), TreeCanvas.java (+3 -3), TreePanel.java (+4 -4), UserDefinedColours.java (+3 -3), UserQuestionnaireCheck.java (+2 -2), WebserviceInfo.java (+3 -3)

jprocter 2009-06-08 11:53 #31

minor optimization. apply gpl development license

9 lines of code changed in:

src/jalview/io: VamsasAppDatastore.java (+9 -7)

jprocter 2009-06-08 11:46 #30

apply gpl development license

146 lines of code changed in:

src/jalview/io: AMSAFile.java (+2 -2), AlignFile.java (+3 -3), AnnotationFile.java (changed), AppletFormatAdapter.java (+3 -3), BLCFile.java (+3 -3), ClansFile.java (changed), ClustalFile.java (+2 -2), DBRefFile.java (changed), FastaFile.java (+3 -3), FeaturesFile.java (changed), FileLoader.java (+2 -2), FileParse.java (+2 -2), FormatAdapter.java (+3 -3), HTMLOutput.java (+2 -2), IdentifyFile.java (+3 -3), JPredFile.java (+3 -3), JalviewFileChooser.java (+2 -2), JalviewFileFilter.java (+2 -2), JalviewFileView.java (+2 -2), JnetAnnotationMaker.java (+2 -2), MSFfile.java (+3 -3), MatrixFile.java (changed), ModellerDescription.java (+2 -2), NewickFile.java (+3 -3), PIRFile.java (+2 -2), PfamFile.java (+2 -2), PileUpfile.java (+2 -2), StockholmFile.java (changed), WSWUBlastClient.java (+3 -3)
src/jalview/io/vamsas: Datasetsequence.java (changed), DatastoreItem.java (+2 -2), Dbref.java (+2 -2), LocalDocSyncObject.java (+2 -2), Rangetype.java (+2 -2), Sequencefeature.java (changed), Sequencemapping.java (+2 -2), Tree.java (+2 -2)
src/jalview/jbgui: GAlignFrame.java (+2 -2), GAlignmentPanel.java (+2 -2), GCutAndPasteTransfer.java (+3 -3), GDasSourceBrowser.java (changed), GDesktop.java (+3 -3), GFinder.java (+2 -2), GFontChooser.java (+3 -3), GPCAPanel.java (+2 -2), GPairwiseAlignPanel.java (+3 -3), GPreferences.java (+3 -3), GSequenceLink.java (+2 -2), GSliderPanel.java (+3 -3), GStructureViewer.java (+2 -2), GTreePanel.java (+2 -2), GUserDefinedColours.java (+3 -3), GWebserviceInfo.java (+3 -3)
src/jalview/math: Matrix.java (+3 -3), RotatableMatrix.java (+3 -3)
src/jalview/schemabinding/version2: AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+17 -6), SequenceType.java (changed), Setting.java (changed), StructureState.java (+17 -6), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)
src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2009-06-08 11:40 #29

apply gpl development license

158 lines of code changed in:

src/MCview: AppletPDBCanvas.java (+2 -2), AppletPDBViewer.java (+2 -2), Atom.java (+2 -2), Bond.java (+2 -2), MCMatrix.java (+2 -2), PDBCanvas.java (+2 -2), PDBChain.java (+6 -3), PDBViewer.java (+2 -2), Residue.java (+2 -2), Zsort.java (+2 -2)
src/jalview/schemes: AnnotationColourGradient.java (+2 -2), Blosum62ColourScheme.java (+2 -2), BuriedColourScheme.java (+3 -3), ClustalxColourScheme.java (+2 -2), ColourSchemeI.java (+2 -2), ColourSchemeProperty.java (+3 -3), Consensus.java (+2 -2), GraduatedColor.java (+16 -1), HelixColourScheme.java (+2 -2), HydrophobicColourScheme.java (+3 -3), NucleotideColourScheme.java (+3 -3), PIDColourScheme.java (+2 -2), ResidueColourScheme.java (+3 -3), ResidueProperties.java (+2 -2), ScoreColourScheme.java (+3 -3), ScoreMatrix.java (changed), StrandColourScheme.java (+3 -3), TaylorColourScheme.java (+2 -2), TurnColourScheme.java (+3 -3), UserColourScheme.java (+2 -2), ZappoColourScheme.java (+3 -3)
src/jalview/structure: SelectionListener.java (+16 -1), SelectionSource.java (+18), SequenceListener.java (+2 -2), StructureListener.java (+2 -2), StructureMapping.java (+2 -2), StructureSelectionManager.java (+2 -2), VamsasListener.java (changed)
src/jalview/util: BrowserLauncher.java (+2 -2), Comparison.java (+3 -3), DBRefUtils.java (+2 -2), Format.java (+3 -3), ImageMaker.java (+2 -2), MapList.java (+2 -2), Platform.java (changed), QuickSort.java (+2 -2), ShiftList.java (changed), TableSorter.java (changed), UrlLink.java (changed), jarInputStreamProvider.java (changed)
src/jalview/ws: DasSequenceFeatureFetcher.java (changed), Discoverer.java (+2 -2), JPredClient.java (+2 -2), JPredThread.java (changed), MsaWSClient.java (+3 -3), MsaWSThread.java (changed), SeqSearchWSClient.java (changed), SeqSearchWSThread.java (changed), SequenceFetcher.java (changed), WSClient.java (+2 -2), WSClientI.java (+2 -2), WSThread.java (changed)
src/jalview/ws/dbsources: DasSequenceSource.java (changed), EbiFileRetrievedProxy.java (changed), EmblCdsSouce.java (changed), EmblSource.java (changed), EmblXmlSource.java (changed), GeneDbSource.java (changed), Pdb.java (changed), Pfam.java (changed), PfamFull.java (changed), PfamSeed.java (changed), Uniprot.java (+2 -2), UnprotName.java (changed)
src/jalview/ws/dbsources/das: DasSequenceSourceListener.java (changed)
src/jalview/ws/ebi: EBIFetchClient.java (changed)
src/jalview/ws/seqfetcher: ASequenceFetcher.java (changed), DbSourceProxy.java (changed), DbSourceProxyImpl.java (changed)

jprocter 2009-06-08 11:40 #28

patch for wierd format header lines and apply gpl development license

11 lines of code changed in:

src/MCview: PDBfile.java (+11 -4)

jprocter 2009-06-08 11:38 #27

apply gpl development license

119 lines of code changed in:

src/uk/ac/ebi/picr/model: CrossReference.java (changed), CrossReference_Helper.java (changed), UPEntry.java (changed), UPEntry_Helper.java (changed)
src/uk/ac/ebi/www: Data.java (+17 -6), InputParams.java (+17 -6), WSFile.java (+17 -6), WSWUBlast.java (+17 -6), WSWUBlastService.java (+17 -6), WSWUBlastServiceLocator.java (+17 -6), WSWUBlastSoapBindingStub.java (+17 -6)
src/uk/ac/ebi/www/picr/AccessionMappingService: AccessionMapperBindingStub.java (changed), AccessionMapperInterface.java (changed), AccessionMapperService.java (changed), AccessionMapperServiceLocator.java (changed)

jprocter 2009-06-08 11:32 #26

apply gpl development license

658 lines of code changed in:

help: helpTOC.xml (+18)
src/ext/vamsas: IRegistry.java (+2 -2), IRegistryService.java (+2 -2), IRegistryServiceLocator.java (+2 -2), Jpred.java (+2 -2), JpredService.java (+2 -2), JpredServiceLocator.java (+2 -2), JpredSoapBindingStub.java (+2 -2), MuscleWS.java (+2 -2), MuscleWSService.java (+2 -2), MuscleWSServiceLocator.java (+2 -2), MuscleWSSoapBindingStub.java (+2 -2), RegistryServiceSoapBindingStub.java (+2 -2), SeqSearchI.java (changed), SeqSearchServiceLocator.java (changed), SeqSearchServiceService.java (changed), SeqSearchServiceSoapBindingStub.java (changed), ServiceHandle.java (+2 -2), ServiceHandles.java (+2 -2)
src/jalview/analysis: AAFrequency.java (+3 -3), AlignSeq.java (+3 -3), AlignmentSorter.java (+2 -2), Conservation.java (+3 -3), CrossRef.java (changed), Dna.java (changed), Finder.java (+2 -2), NJTree.java (+4 -4), PCA.java (+3 -3), ParseProperties.java (+2 -2), SeqsetUtils.java (+2 -2), SequenceIdMatcher.java (+2 -2)
src/jalview/appletgui: APopupMenu.java (+2 -2), AlignFrame.java (+2 -2), AlignViewport.java (+2 -2), AlignmentPanel.java (+2 -2), AnnotationColourChooser.java (+2 -2), AnnotationLabels.java (+2 -2), AnnotationPanel.java (+2 -2), AppletJmol.java (+2 -2), CutAndPasteTransfer.java (+2 -2), EditNameDialog.java (+2 -2), EmbmenuFrame.java (changed), FeatureColourChooser.java (+2 -2), FeatureRenderer.java (+3 -3), FeatureSettings.java (+2 -2), Finder.java (+2 -2), FontChooser.java (+2 -2), IdCanvas.java (+2 -2), IdPanel.java (+2 -2), IdwidthAdjuster.java (+2 -2), JVDialog.java (+2 -2), OverviewPanel.java (+2 -2), PCAPanel.java (+2 -2), PaintRefresher.java (+3 -3), PairwiseAlignPanel.java (+2 -2), RedundancyPanel.java (+2 -2), RotatableCanvas.java (+2 -2), ScalePanel.java (+2 -2), SeqCanvas.java (+2 -2), SeqPanel.java (+2 -2), SequenceRenderer.java (+2 -2), SliderPanel.java (+2 -2), Tooltip.java (changed), TreeCanvas.java (+2 -2), TreePanel.java (+2 -2), UserDefinedColours.java (+2 -2)
src/jalview/binding: Alignment.java (+17 -6), Annotation.java (+17 -6), AnnotationElement.java (+17 -6), Colour.java (+17 -6), Feature.java (+17 -6), FeatureSettings.java (+17 -6), Features.java (+17 -6), JGroup.java (+17 -6), JSeq.java (+17 -6), JalviewModel.java (+17 -6), JalviewModelSequence.java (+17 -6), JalviewUserColours.java (+17 -6), Pdbentry.java (+17 -6), PdbentryItem.java (+17 -6), Pdbids.java (+17 -6), Property.java (+17 -6), Sequence.java (+17 -6), SequenceSet.java (+17 -6), SequenceType.java (+17 -6), Setting.java (+17 -6), Tree.java (+17 -6), UserColourScheme.java (+17 -6), UserColours.java (+17 -6), VAMSAS.java (+17 -6), VamsasModel.java (+17 -6), Viewport.java (+17 -6)
src/jalview/commands: ChangeCaseCommand.java (+2 -2), CommandI.java (+2 -2), EditCommand.java (+2 -2), OrderCommand.java (+2 -2), RemoveGapColCommand.java (+2 -2), RemoveGapsCommand.java (+2 -2), SlideSequencesCommand.java (+2 -2), TrimRegionCommand.java (+2 -2)
src/jalview/datamodel/xdb/embl: BasePosition.java (+2 -2), EmblEntry.java (+2 -2), EmblError.java (+2 -2), EmblFeature.java (+2 -2), EmblFeatureLocElement.java (+2 -2), EmblFeatureLocations.java (+2 -2), EmblFile.java (+2 -2), EmblSequence.java (+2 -2), Qualifier.java (+2 -2)
src/vamsas: IMsaWS.java (+2 -2)
src/vamsas/objects/simple: Alignment.java (+2 -2), Alignment_Helper.java (+2 -2), JpredResult.java (+2 -2), JpredResult_Helper.java (+2 -2), MsaResult.java (+2 -2), MsaResult_Helper.java (+2 -2), Msfalignment.java (+2 -2), Msfalignment_Helper.java (+2 -2), Object.java (+2 -2), Object_Helper.java (+2 -2), Result.java (+2 -2), Result_Helper.java (+2 -2), Secstructpred.java (+2 -2), Secstructpred_Helper.java (+2 -2), SeqSearchResult.java (changed), SeqSearchResult_Helper.java (changed), Sequence.java (+2 -2), SequenceSet.java (+2 -2), SequenceSet_Helper.java (+2 -2), Sequence_Helper.java (+2 -2), WsJobId.java (+2 -2), WsJobId_Helper.java (+2 -2)

jprocter 2009-06-08 11:31 #25

ga in 2.4.0b2 release

30 lines of code changed in:

help/html: releases.html (+30 -1)

jprocter 2009-06-08 11:31 #24

nousagestats cli

8 lines of code changed in:

help/html/features: clarguments.html (+8 -2)

jprocter 2009-06-08 11:30 #23

apply gpl development license

20 lines of code changed in:

utils: help2Website.java (+2 -2)
utils/InstallAnywhere: jalview_buildinstaller.xml (+18)

jprocter 2009-06-08 11:29 #22

apply gpl development license and new donotobfuscate flag

19 lines of code changed in:

build.xml (+19)

jprocter 2009-06-08 11:29 #21

apply gpl development license

90 lines of code changed in:

resources: embl_mapping.xml (changed), uniprot_mapping.xml (+18)
schemas: JalviewUserColours.xsd (+34 -15), castor-mapping.xsd (changed), jalview.xsd (+19), jalviewJvV1.xsd (changed), vamsas.xsd (+19), vamsasJvV1.xsd (changed)

jprocter 2009-06-04 10:11 #20

full reference added.

1 lines of code changed in:

help/html: index.html (+1 -1)

jprocter 2009-06-04 10:08 #19

spelling

1 lines of code changed in:

help/html/vamsas: index.html (+1 -1)

jprocter 2009-06-04 09:38 #18

script goes at beginning of body to allow linkthrus to be embedded.

5 lines of code changed in:

utils: patchGt.pl (+5 -3)

jprocter 2009-06-02 13:20 #17

update minor version of release branch

0 lines of code changed in:

RELEASE (changed)

jprocter 2009-06-01 16:54 #16

graduated feature colour documentation

47 lines of code changed in:

help/html/features: featuresFormat.html (+47 -19)

jprocter 2009-06-01 16:54 #15

GA appender script

50 lines of code changed in:

utils: patchGt.pl (new 50)

jprocter 2009-06-01 16:54 #14

google tracking for index document

3 lines of code changed in:

utils: help2Website.java (+3 -2)

jprocter 2009-06-01 16:53 #13

more graduated feature support

6 lines of code changed in:

src/jalview/gui: AlignFrame.java (+6 -1)

jprocter 2009-06-01 16:53 #12

properly export graduated colour features

0 lines of code changed in:

src/jalview/gui: AnnotationExporter.java (changed)

jprocter 2009-06-01 16:52 #11

prototype function for relabelling treenodes with different accession/labels

60 lines of code changed in:

src/jalview/gui: TreePanel.java (+60 -2)

jprocter 2009-06-01 16:51 #10

better tooltip placement in alignment window

36 lines of code changed in:

src/jalview/gui: SeqPanel.java (+36 -28)

jprocter 2009-06-01 16:51 #9

more graduated feature support

72 lines of code changed in:

src/jalview/gui: FeatureColourChooser.java (+26 -4), FeatureRenderer.java (+46 -9)

jprocter 2009-06-01 16:48 #8

added graduated colourscheme support for feature file

43 lines of code changed in:

src/jalview/io: FeaturesFile.java (changed)
src/jalview/schemes: GraduatedColor.java (+43 -10)

jprocter 2009-06-01 16:47 #7

better decoupling of data loading routines for AJAX

27 lines of code changed in:

src/jalview/bin: JalviewLite.java (+27 -21)

jprocter 2009-06-01 16:46 #6

first experiment with GA application use tracking

45 lines of code changed in:

lib: JGoogleAnalytics_0.2.jar (new)
src/jalview/bin: Cache.java (+37 -2), Jalview.java (+8 -1)

jprocter 2009-06-01 16:45 #5

look in database references for more ID strings to match against node labels

14 lines of code changed in:

src/jalview/analysis: SequenceIdMatcher.java (+14)

jprocter 2009-06-01 16:45 #4

apply method for a NodeTransform to nodes in a tree

25 lines of code changed in:

src/jalview/analysis: NJTree.java (+12 -3)
src/jalview/datamodel: NodeTransformI.java (new 13)

jprocter 2009-06-01 16:45 #3

javadoc

8 lines of code changed in:

src/jalview/datamodel: BinaryNode.java (+8 -11)

jprocter 2009-06-01 16:44 #2

only make a link menu when there are links

28 lines of code changed in:

src/jalview/appletgui: APopupMenu.java (+28 -24)

jprocter 2009-06-01 16:44 #1

maxcolour is default colour for no-score features

2 lines of code changed in:

src/jalview/appletgui: FeatureRenderer.java (+2 -2)

May 2009 »

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