February 2007 Commit Log

Number of Commits:

70

Number of Active Developers:

3

andrew 2007-02-27 13:43 #70

Uncomment graphics 2d bit

3 lines of code changed in:

• src/jalview/appletgui: FeatureRenderer.java (+3 -3)

andrew 2007-02-27 13:39 #69

Launch applet jmol

41 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+41 -13)

andrew 2007-02-27 13:39 #68

Use paintAlignment

688 lines of code changed in:

• src/jalview/appletgui: APopupMenu.java (+3 -7), AlignFrame.java (+129 -29), AlignViewport.java (+5 -5), AlignmentPanel.java (+27 -10), AnnotationColourChooser.java (+13 -5), AnnotationLabels.java (+2 -2), CutAndPasteTransfer.java (+18 -4), FeatureSettings.java (+1 -1), FontChooser.java (+1 -1), IdPanel.java (+3 -3), OverviewPanel.java (+1 -10), RedundancyPanel.java (+1 -1), ScalePanel.java (+7 -7), SeqCanvas.java (-10), SeqPanel.java (+70 -22), SliderPanel.java (+1 -4), UserDefinedColours.java (+3 -4)
• src/jalview/gui: AlignFrame.java (+165 -48), AlignViewport.java (+51 -6), AlignmentPanel.java (+17 -72), AnnotationColourChooser.java (+10 -3), AnnotationLabels.java (+3 -3), AnnotationPanel.java (+4 -4), FeatureSettings.java (+3 -3), FontChooser.java (+3 -3), IdPanel.java (+19 -5), IdwidthAdjuster.java (+2 -2), OverviewPanel.java (+1 -10), PopupMenu.java (+32 -47), RedundancyPanel.java (+2 -2), ScalePanel.java (+8 -8), SeqCanvas.java (+1 -11), SeqPanel.java (+66 -40), SliderPanel.java (+10 -2), TextColourChooser.java (+3 -3), UserDefinedColours.java (+3 -3)

andrew 2007-02-27 13:38 #67

check conservation length

6 lines of code changed in:

• src/jalview/schemes: ResidueColourScheme.java (+6 -4)

andrew 2007-02-27 13:38 #66

Structure listener

510 lines of code changed in:

• src/jalview/structure: SequenceListener.java (new 30), StructureListener.java (new 30), StructureMapping.java (new 100), StructureSelectionManager.java (new 350)

andrew 2007-02-27 13:37 #65

Use paintAlignment

2 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed), WSWUBlastClient.java (+2 -2)

andrew 2007-02-27 13:37 #64

remove p+3 < query.length

2 lines of code changed in:

• src/jalview/io: EBIFetchClient.java (+2 -26)

andrew 2007-02-27 13:36 #63

No longer use ref to seqcanvas for painting

1445 lines of code changed in:

• src/MCview: AppletPDBCanvas.java (+1156 -1100), AppletPDBViewer.java (+43 -93), PDBCanvas.java (+3 -4), PDBViewer.java (+243 -6)

andrew 2007-02-27 13:30 #62

blank space for chain name if empty

3 lines of code changed in:

• src/MCview: PDBChain.java (+3 -3)

andrew 2007-02-27 13:28 #61

keep record of atomIndeX

4 lines of code changed in:

• src/MCview: Atom.java (+4 -1)

andrew 2007-02-27 13:27 #60

jmol added

2087 lines of code changed in:

• src/jalview/appletgui: AppletJmol.java (new 590)
• src/jalview/commands: SlideSequencesCommand.java (new 93)
• src/jalview/gui: AppJMol.java (new 665), ScriptWindow.java (new 619)
• src/jalview/jbgui: GStructureViewer.java (new 120)

andrew 2007-02-27 13:26 #59

jmol

0 lines of code changed in:

• lib: jmol.jar (new)

amwaterhouse 2007-02-12 14:48 #58

version 3.7

0 lines of code changed in:

• utils: proguard.jar (changed)

andrew 2007-02-12 12:43 #57

date added

1 lines of code changed in:

• help/html: releases.html (+1 -1)

andrew 2007-02-12 12:10 #56

>0 rather than -1 check

2 lines of code changed in:

• src/MCview: PDBCanvas.java (+2 -2)

jprocter 2007-02-12 10:05 #55

tranfer pdbresno features to dataset sequence.

1 lines of code changed in:

• src/MCview: PDBCanvas.java (+1 -1)

andrew 2007-02-12 09:44 #54

Reload jar files

4 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+4 -1)

andrew 2007-02-12 09:44 #53

Hashtable for previously loaded pdb files

10 lines of code changed in:

• src/jalview/gui: Jalview2XML.java (+10 -2)

andrew 2007-02-12 09:43 #52

Make checkbox bigger for text on mac

3 lines of code changed in:

• src/jalview/jbgui: GPreferences.java (+3 -2)

jprocter 2007-02-09 18:02 #51

running jalview from the command line.

117 lines of code changed in:

• help/html/features: clarguments.html (new 82), commandline.html (new 35)

jprocter 2007-02-09 18:00 #50

added command line help documentation and preferences help to
contents. Documented SHOW_OVERVIEW property in preferences.

17 lines of code changed in:

• help: help.jhm (+2), helpTOC.xml (+5 -1)
• help/html: releases.html (+6 -1), whatsNew.html (+1)
• help/html/features: preferences.html (+3)

jprocter 2007-02-09 17:50 #49

added 'show overview' preference.

20 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+6 -1), Preferences.java (+5 -2)
• src/jalview/jbgui: GPreferences.java (+9 -1)

jprocter 2007-02-08 15:30 #48

fix on newquestionaire notification bug (again)

0 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (-4)

andrew 2007-02-07 16:03 #47

formatted

1947 lines of code changed in:

• src/com/stevesoft/pat: Regex.java (+1947 -1347)

andrew 2007-02-07 15:46 #46

restore unformatted state

1347 lines of code changed in:

• src/com/stevesoft/pat: Regex.java (+1347 -1943)

andrew 2007-02-07 15:11 #45

Formatting

0 lines of code changed in:

• src/org/biojava/dasobert/das2/io: DAS2SourceHandler.java (changed), DasSourceReader.java (changed), DasSourceReaderImpl.java (changed)

andrew 2007-02-07 15:05 #44

Formatting

34086 lines of code changed in:

• src/com/stevesoft/pat: AmpersandRule.java (+18 -9), Any.java (+42 -15), BackG.java (+35 -15), BackMatch.java (+45 -21), BackRefRule.java (+24 -9), Backup.java (+38 -13), BasicStringBufferLike.java (+8 -4), Bits.java (+2948 -2923), Boundary.java (+80 -39), Bracket.java (+70 -31), CaseMgr.java (+4366 -1496), ChangeRule.java (+36 -11), CodeRule.java (+21 -10), Ctrl.java (+262 -260), Custom.java (+44 -26), CustomEndpoint.java (+31 -15), DirFileRegex.java (+18 -6), DotMulti.java (+186 -106), End.java (+53 -25), FastBracket.java (+231 -166), FastMulti.java (+152 -92), FileRegex.java (+243 -165), Group.java (+60 -27), LeftRule.java (+16 -7), Multi.java (+66 -41), MultiMin.java (+9 -5), Multi_stage2.java (+137 -84), NoPattern.java (+23 -9), NonDirFileRegex.java (+18 -6), NotImplementedError.java (+7 -4), NullPattern.java (+26 -10), NullRule.java (+15 -6), Or.java (+111 -65), OrMark.java (+57 -35), PartialBuffer.java (+39 -16), Pattern.java (+263 -176), PatternSub.java (+6 -4), PopRule.java (+12 -5), Prop.java (+55 -34), Pthings.java (+23 -21), PushRule.java (+33 -8), RBuffer.java (+26 -13), Range.java (+84 -47), RegOpt.java (+432 -298), RegRes.java (+262 -150), RegSyntax.java (+12 -7), RegSyntaxError.java (+21 -8), Regex.java (+1944 -1348), RegexReader.java (+179 -102), RegexTokenizer.java (+146 -95), RegexWriter.java (+200 -138), ReplaceRule.java (+368 -225), Replacer.java (+323 -225), RightRule.java (+16 -9), Rthings.java (+39 -31), RuleHolder.java (+32 -10), Skip.java (+168 -107), Skip2.java (+39 -22), SkipBMH.java (+247 -159), Skipped.java (+40 -13), SpecialRule.java (+8 -3), Start.java (+45 -18), StrPos.java (+163 -104), StringBufferLike.java (+64 -38), StringLike.java (+25 -18), StringRule.java (+24 -9), SubMark.java (+19 -10), TransPat.java (+30 -24), Transformer.java (+185 -120), UniValidator.java (+14 -5), Validator.java (+59 -47), WantMoreTextReplaceRule.java (+15 -6), lookAhead.java (+87 -34), oneChar.java (+61 -34), parsePerl.java (+362 -249), patInf.java (+7 -2), patInt.java (+158 -75)
• src/com/stevesoft/pat/wrap: CharArrayBufferWrap.java (+27 -12), CharArrayWrap.java (+58 -23), RandomAccessFileWrap.java (+150 -93), StringBufferWrap.java (+18 -7), StringWrap.java (+43 -19), WriterWrap.java (+27 -13)
• src/jalview/gui: SeqPanel.java (+1268 -1169), SequenceFetcher.java (+181 -131), SequenceRenderer.java (+329 -316), SliderPanel.java (+268 -269), SplashScreen.java (+128 -123), TextColourChooser.java (+30 -25), TreeCanvas.java (+21 -15), TreePanel.java (+507 -494), UserDefinedColours.java (+718 -651), UserQuestionnaireCheck.java (+134 -95), VamsasClient.java (+106 -55), WebserviceInfo.java (+431 -389)
• src/jalview/io: AMSAFile.java (+72 -61), AlignFile.java (+159 -161), AnnotationFile.java (changed), AppletFormatAdapter.java (+225 -219), BLCFile.java (+170 -168), ClustalFile.java (+8 -4), DBRefFetcher.java (changed), DasSequenceFeatureFetcher.java (changed), EBIFetchClient.java (+245 -222), FastaFile.java (+170 -162), FeaturesFile.java (changed), FileLoader.java (+120 -118), FileParse.java (+2 -2), FormatAdapter.java (+102 -103), HTMLOutput.java (+116 -108), IdentifyFile.java (+142 -144), JPredFile.java (+303 -295), JalviewFileChooser.java (+21 -27), JalviewFileFilter.java (+2 -2), JalviewFileView.java (+1 -1), JnetAnnotationMaker.java (+57 -40), MSFfile.java (+320 -317), ModellerDescription.java (+17 -17), NewickFile.java (+750 -741), PIRFile.java (+72 -66), PfamFile.java (+7 -6), PileUpfile.java (+28 -27), StockholmFile.java (changed), VamsasDatastore.java (+664 -334), WSWUBlastClient.java (+240 -242)
• src/jalview/jbgui: GAlignFrame.java (+62 -59), GAlignmentPanel.java (+1 -1), GCutAndPasteTransfer.java (+147 -148), GDasSourceBrowser.java (changed), GDesktop.java (+240 -236), GFinder.java (+18 -13), GFontChooser.java (+176 -178), GPCAPanel.java (+2 -4), GPairwiseAlignPanel.java (+70 -70), GPreferences.java (+218 -214), GSequenceLink.java (+26 -31), GSliderPanel.java (+150 -150), GTreePanel.java (+2 -3), GUserDefinedColours.java (+146 -146), GWebserviceInfo.java (+87 -86)
• src/jalview/math: Matrix.java (+719 -720), RotatableMatrix.java (+232 -233)
• src/jalview/schemabinding/version2: Annotation.java (changed), AnnotationColours.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElement.java (changed), AnnotationElementDescriptor.java (changed), Colour.java (changed), ColourDescriptor.java (changed), DBRef.java (changed), DBRefDescriptor.java (changed), Feature.java (changed), FeatureDescriptor.java (changed), FeatureSettings.java (changed), FeatureSettingsDescriptor.java (changed), Features.java (changed), FeaturesDescriptor.java (changed), HiddenColumns.java (changed), HiddenColumnsDescriptor.java (changed), JGroup.java (changed), JGroupDescriptor.java (changed), JSeq.java (changed), JSeqDescriptor.java (changed), JalviewModel.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequence.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColours.java (changed), JalviewUserColoursDescriptor.java (changed), OtherData.java (changed), OtherDataDescriptor.java (changed), Pdbentry.java (changed), PdbentryDescriptor.java (changed), PdbentryItem.java (changed), PdbentryItemDescriptor.java (changed), Pdbids.java (changed), PdbidsDescriptor.java (changed), Property.java (changed), PropertyDescriptor.java (changed), Sequence.java (changed), SequenceDescriptor.java (changed), SequenceSet.java (changed), SequenceSetDescriptor.java (changed), SequenceType.java (changed), SequenceTypeDescriptor.java (changed), Setting.java (changed), SettingDescriptor.java (changed), ThresholdLine.java (changed), ThresholdLineDescriptor.java (changed), Tree.java (changed), TreeDescriptor.java (changed), UserColourScheme.java (changed), UserColourSchemeDescriptor.java (changed), UserColours.java (changed), UserColoursDescriptor.java (changed), VAMSAS.java (changed), VAMSASDescriptor.java (changed), VamsasModel.java (changed), VamsasModelDescriptor.java (changed), Viewport.java (changed), ViewportDescriptor.java (changed)
• src/jalview/schemes: AnnotationColourGradient.java (+158 -141), Blosum62ColourScheme.java (+11 -9), BuriedColourScheme.java (+39 -39), ClustalxColourScheme.java (+12 -11), ColourSchemeI.java (+2 -3), ColourSchemeProperty.java (+361 -333), Consensus.java (+1 -1), HelixColourScheme.java (+1 -1), HydrophobicColourScheme.java (+39 -39), NucleotideColourScheme.java (+68 -66), PIDColourScheme.java (+21 -16), ResidueColourScheme.java (+213 -207), ResidueProperties.java (+26 -18), ScoreColourScheme.java (+96 -94), ScoreMatrix.java (changed), StrandColourScheme.java (+39 -39), TaylorColourScheme.java (+1 -1), TurnColourScheme.java (+39 -39), UserColourScheme.java (+59 -38), ZappoColourScheme.java (+27 -27)
• src/jalview/util: BrowserLauncher.java (+5 -2), Comparison.java (+33 -29), DBRefUtils.java (+50 -37), Format.java (+732 -724), ImageMaker.java (+30 -25), MapList.java (+283 -168), QuickSort.java (+1 -1), ShiftList.java (changed), TableSorter.java (changed)
• src/jalview/ws: Discoverer.java (+85 -56), JPredClient.java (+79 -53), JPredThread.java (changed), MsaWSClient.java (+40 -34), MsaWSThread.java (changed), WSClient.java (+6 -6), WSClientI.java (+12 -10), WSThread.java (changed)
• src/org/biojava/dasobert/das: DAS_FeatureRetrieve.java (changed), DAS_Feature_Handler.java (changed), FeatureThread.java (changed)
• src/org/biojava/dasobert/das2: Das2Capability.java (changed), Das2CapabilityImpl.java (changed), Das2Source.java (changed), Das2SourceImpl.java (changed), DasSourceConverter.java (changed)
• src/org/biojava/dasobert/dasregistry: Das1Source.java (changed), Das2Validator.java (changed), DasCoordSysComparator.java (changed), DasCoordinateSystem.java (changed), DasSource.java (changed), DasSourceComparator.java (changed)
• src/org/biojava/dasobert/eventmodel: FeatureEvent.java (changed), FeatureListener.java (changed), ObjectListener.java (changed), SequenceEvent.java (changed), SequenceListener.java (changed)
• src/org/jibble/epsgraphics: EpsDocument.java (+245 -214), EpsException.java (+20 -17), EpsGraphics2D.java (+1383 -1282)
• src/uk/ac/ebi/www: Data.java (+135 -106), InputParams.java (+441 -362), WSFile.java (+135 -106), WSWUBlast.java (+24 -8), WSWUBlastService.java (+8 -4), WSWUBlastServiceLocator.java (+115 -82), WSWUBlastSoapBindingStub.java (+484 -311)
• src/vamsas/objects/simple: Alignment.java (+174 -153), Alignment_Helper.java (+79 -72), JpredResult.java (+111 -92), JpredResult_Helper.java (+52 -43), MsaResult.java (+89 -76), MsaResult_Helper.java (+67 -60), Msfalignment.java (+111 -92), Msfalignment_Helper.java (+52 -43), Object.java (+63 -53), Object_Helper.java (+55 -49), Result.java (+331 -313), Result_Helper.java (+106 -88), Secstructpred.java (+81 -63), Secstructpred_Helper.java (+46 -38), Sequence.java (+111 -92), SequenceSet.java (+97 -81), SequenceSet_Helper.java (+67 -60), Sequence_Helper.java (+52 -43), WsJobId.java (+126 -110), WsJobId_Helper.java (+73 -66)

andrew 2007-02-07 15:00 #43

Formatting

28368 lines of code changed in:

• src/ext/vamsas: IRegistry.java (+5 -2), IRegistryService.java (+8 -4), IRegistryServiceLocator.java (+170 -125), Jpred.java (+14 -5), JpredService.java (+8 -4), JpredServiceLocator.java (+169 -125), JpredSoapBindingStub.java (+374 -278), MuscleWS.java (+29 -27), MuscleWSService.java (+25 -23), MuscleWSServiceLocator.java (+197 -157), MuscleWSSoapBindingStub.java (+439 -363), RegistryServiceSoapBindingStub.java (+206 -158), ServiceHandle.java (+237 -206), ServiceHandles.java (+137 -110)
• src/jalview/analysis: AAFrequency.java (+112 -106), AlignSeq.java (+767 -758), AlignmentSorter.java (+395 -392), Conservation.java (+450 -446), Finder.java (+289 -254), NJTree.java (+1051 -1032), PCA.java (+217 -219), SeqsetUtils.java (+82 -46), SequenceIdMatcher.java (+52 -32)
• src/jalview/appletgui: APopupMenu.java (+199 -115), AlignFrame.java (+1001 -775), AlignViewport.java (+257 -163), AlignmentPanel.java (+103 -91), AnnotationColourChooser.java (+62 -32), AnnotationLabels.java (+64 -47), AnnotationPanel.java (+381 -340), CutAndPasteTransfer.java (+99 -63), EditNameDialog.java (+13 -8), FeatureRenderer.java (+317 -284), FeatureSettings.java (+230 -193), Finder.java (+80 -66), FontChooser.java (+68 -58), IdCanvas.java (+68 -53), IdPanel.java (+30 -18), IdwidthAdjuster.java (+1 -1), OverviewPanel.java (+82 -63), PCAPanel.java (+71 -66), PaintRefresher.java (+153 -128), PairwiseAlignPanel.java (+25 -18), RedundancyPanel.java (+140 -122), RotatableCanvas.java (+44 -41), ScalePanel.java (+76 -50), SeqCanvas.java (+432 -399), SeqPanel.java (+873 -777), SequenceRenderer.java (+40 -35), SliderPanel.java (+66 -51), Tooltip.java (changed), TreeCanvas.java (+77 -70), TreePanel.java (+86 -69), UserDefinedColours.java (+144 -112)
• src/jalview/bin: Cache.java (+243 -233), Jalview.java (+314 -300), JalviewLite.java (+449 -413)
• src/jalview/commands: ChangeCaseCommand.java (+17 -6), CommandI.java (+5 -5), EditCommand.java (+218 -174), OrderCommand.java (+40 -40), RemoveGapColCommand.java (+15 -12), RemoveGapsCommand.java (+27 -19), TrimRegionCommand.java (+41 -26)
• src/jalview/datamodel: Alignment.java (+510 -483), AlignmentAnnotation.java (+266 -253), AlignmentI.java (+221 -228), AlignmentOrder.java (+256 -215), AlignmentView.java (changed), Annotation.java (+63 -64), BinaryNode.java (+251 -251), BinarySequence.java (+145 -140), CigarArray.java (changed), CigarBase.java (changed), CigarCigar.java (changed), CigarSimple.java (changed), ColumnSelection.java (changed), DBRefEntry.java (+10 -4), DBRefSource.java (changed), GraphLine.java (+31 -27), HiddenSequences.java (+92 -60), PDBEntry.java (+21 -9), Provenance.java (+10 -7), ProvenanceEntry.java (+26 -15), SearchResults.java (+59 -42), SeqCigar.java (+92 -60), Sequence.java (+110 -81), SequenceFeature.java (+254 -226), SequenceGroup.java (+484 -470), SequenceI.java (+236 -239), SequenceNode.java (+114 -114), SequencePoint.java (+13 -13), UniprotEntry.java (+21 -21), UniprotFile.java (+11 -8), UniprotProteinName.java (changed), UniprotSequence.java (+9 -5)
• src/jalview/gui: AlignFrame.java (+754 -668), AlignViewport.java (+1489 -1403), AlignmentPanel.java (+157 -117), AnnotationColourChooser.java (+64 -32), AnnotationExporter.java (changed), AnnotationLabels.java (+564 -525), AnnotationPanel.java (+1073 -1013), CutAndPasteTransfer.java (+176 -172), DasSourceBrowser.java (changed), Desktop.java (+751 -684), EPSOptions.java (+11 -6), EditNameDialog.java (+11 -9), FeatureRenderer.java (+605 -550), FeatureSettings.java (+439 -392), Finder.java (+173 -171), FontChooser.java (+192 -192), IdCanvas.java (+369 -341), IdPanel.java (+315 -310), IdwidthAdjuster.java (+129 -130), Jalview2XML.java (+1380 -1339), Jalview2XML_V1.java (changed), OverviewPanel.java (+344 -341), PCAPanel.java (+358 -361), PaintRefresher.java (+160 -135), PairwiseAlignPanel.java (+106 -108), PopupMenu.java (+937 -908), Preferences.java (+422 -351), RedundancyPanel.java (+254 -245), RotatableCanvas.java (+613 -615), ScalePanel.java (+358 -329), SeqCanvas.java (+745 -717)
• src/vamsas: IMsaWS.java (+30 -27)

andrew 2007-02-07 14:59 #42

formatting

2938 lines of code changed in:

• src/MCview: AppletPDBCanvas.java (+884 -787), AppletPDBViewer.java (+226 -192), Atom.java (+58 -56), Bond.java (+46 -44), MCMatrix.java (+167 -148), PDBCanvas.java (+825 -749), PDBChain.java (+342 -288), PDBViewer.java (+129 -117), PDBfile.java (+154 -129), Residue.java (+41 -40), Zsort.java (+66 -54)

andrew 2007-02-07 14:28 #41

Extend annotation if too short

10 lines of code changed in:

• src/jalview/gui: AnnotationPanel.java (+10 -1)

andrew 2007-02-07 11:29 #40

reload, just close this frame and open a new one

8 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+8 -21)

andrew 2007-02-07 10:38 #39

2.2.1 changes

3 lines of code changed in:

• help: help.jhm (-1), helpTOC.xml (+3 -8)

andrew 2007-02-07 10:38 #38

removed

0 lines of code changed in:

• help/html/features: reloadSave.html (del)

jprocter 2007-02-06 17:29 #37

hardwired default user questionnaire url and by default will always check for a questionnaire when running with gui.

17 lines of code changed in:

• src/jalview/bin: Jalview.java (+17 -10)

jprocter 2007-02-06 17:27 #36

more bugfixes.

17 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (+17 -15)

amwaterhouse 2007-02-06 17:20 #35

2.2.1 updates

406 lines of code changed in:

• help/html: releases.html (+256 -246), whatsNew.html (+25 -50)
• help/html/features: annotationsFormat.html (+125 -82)

amwaterhouse 2007-02-06 15:52 #34

Dont add null description to tooltip

12 lines of code changed in:

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

amwaterhouse 2007-02-06 15:51 #33

Applet params cant read tab character

1 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+1 -29)

amwaterhouse 2007-02-06 15:51 #32

Allow for frame insets

18 lines of code changed in:

• src/jalview/appletgui: EditNameDialog.java (+18 -5)

amwaterhouse 2007-02-06 15:50 #31

Format label

2 lines of code changed in:

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

jprocter 2007-02-06 15:05 #30

debug log message

1 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (+1)

jprocter 2007-02-05 17:36 #29

simplified and refactored along with cgi-script.

48 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (+48 -74)

andrew 2007-02-05 16:11 #28

Alignment editing columns 0 and 1 fixed

6 lines of code changed in:

• src/jalview/commands: EditCommand.java (+6 -3)

jprocter 2007-02-05 14:46 #27

command line hook for questionnaire url argument.

364 lines of code changed in:

• src/jalview/bin: Jalview.java (+354 -346)
• src/jalview/gui: Desktop.java (+10 -2)

jprocter 2007-02-05 14:44 #26

kkv change

128 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (+128 -128)

jprocter 2007-02-05 14:44 #25

client side machinery for user questionnaire responses

128 lines of code changed in:

• src/jalview/gui: UserQuestionnaireCheck.java (new 128)

andrew 2007-02-05 14:40 #24

Fixed bug in trim right annotation adjust

51 lines of code changed in:

• src/jalview/commands: EditCommand.java (+51 -7)

andrew 2007-02-05 11:58 #23

stop flickering annotationPanel

10 lines of code changed in:

• src/jalview/appletgui: AnnotationPanel.java (+10 -3)

andrew 2007-02-05 11:46 #22

Fixed bug in trim right annotation adjust

7 lines of code changed in:

• src/jalview/commands: EditCommand.java (+7 -2)

andrew 2007-02-05 10:57 #21

image is panel size

3 lines of code changed in:

• src/jalview/appletgui: AnnotationPanel.java (+3 -2)

andrew 2007-02-05 10:57 #20

applet can define groups as parameters

34 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+34 -6)
• src/jalview/io: AnnotationFile.java (changed)

andrew 2007-02-02 17:35 #19

Dont add group if seqs not found

0 lines of code changed in:

• src/jalview/io: AnnotationFile.java (changed)

andrew 2007-02-02 17:34 #18

getWidth -1 for trim right

1 lines of code changed in:

• src/jalview/commands: TrimRegionCommand.java (+1 -1)

andrew 2007-02-02 17:34 #17

check annotation size when cutting

9 lines of code changed in:

• src/jalview/commands: EditCommand.java (+9 -6)

andrew 2007-02-02 17:17 #16

annotation might have been deleted

3 lines of code changed in:

• src/jalview/gui: AnnotationLabels.java (+3 -2)

andrew 2007-02-02 17:17 #15

catch control down before editing null pointer

14 lines of code changed in:

• src/jalview/appletgui: SeqPanel.java (+7)
• src/jalview/gui: SeqPanel.java (+7 -1)

andrew 2007-02-02 11:44 #14

22 = scrollbar and insets widthcvs diff gui/AlignmentPanel.java

7 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+7 -4)

andrew 2007-02-02 11:39 #13

Must allow for scollbar and frame insets when getting headless width

9 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+9 -6)

andrew 2007-02-02 11:38 #12

LookandFeel must be set in headless state as window sizes will be affected

20 lines of code changed in:

• src/jalview/bin: Jalview.java (+20 -19)

andrew 2007-02-01 18:35 #11

removed deprecated bits

6 lines of code changed in:

• src/jalview/appletgui: AlignFrame.java (+3 -3)
• src/jalview/bin: JalviewLite.java (+3 -3)

andrew 2007-02-01 18:02 #10

find colours uncommented

15 lines of code changed in:

• src/MCview: PDBChain.java (+15 -18)

andrew 2007-02-01 17:05 #9

sequence.getStart() in findTrueIndex

2 lines of code changed in:

• src/MCview: PDBCanvas.java (+2 -2)

andrew 2007-02-01 14:07 #8

get fontmetrics from pg

4 lines of code changed in:

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

andrew 2007-02-01 14:07 #7

Dont add null tooltip

3 lines of code changed in:

• src/jalview/gui: AnnotationPanel.java (+3 -2)

andrew 2007-02-01 14:07 #6

New description

2 lines of code changed in:

• src/jalview/gui: AnnotationLabels.java (+2 -2)

andrew 2007-02-01 12:49 #5

tooltips

7 lines of code changed in:

• src/jalview/gui: SeqPanel.java (+7 -3)

andrew 2007-02-01 12:40 #4

set description for groups

2 lines of code changed in:

• src/jalview/gui: PopupMenu.java (+2 -2)

andrew 2007-02-01 12:37 #3

Doesnt move with mouse, friendlier for mac users

0 lines of code changed in:

• src/jalview/appletgui: Tooltip.java (changed)

andrew 2007-02-01 12:36 #2

Dont repaint tooltip

4 lines of code changed in:

• src/jalview/appletgui: IdPanel.java (-3), SeqPanel.java (+4 -3)

andrew 2007-02-01 12:36 #1

One class for edit name/description

305 lines of code changed in:

• src/jalview/appletgui: APopupMenu.java (+32 -48), AnnotationLabels.java (+10 -52), EditNameDialog.java (new 93)
• src/jalview/gui: AnnotationLabels.java (+12 -29), EditNameDialog.java (new 78), PopupMenu.java (+80 -96)

January 2007 »