CR-JAL-1 94
- Details
- Objectives
- General Comments 1
- Unresolved
- Resolved
- Number of files included: 127
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jalview
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examples
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groovy
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- File colourSchemes.groovy 8 Remove
- File appletParameters.html 0 Remove
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groovy
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help/html
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colourSchemes
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- File clustal.html 7 Remove
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io
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- File tcoffeescores.html 0 Remove
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colourSchemes
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resources/lang
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- File Messages.properties 0 Remove
- File Messages_es.properties 0 Remove
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src
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MCview
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- File AppletPDBViewer.java 0 Remove
- File PDBChain.java 0 Remove
- File PDBViewer.java 0 Remove
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jalview
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analysis
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- File AlignmentUtils.java 0 Remove
- File Conservation.java 0 Remove
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api
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- File AlignViewportI.java 2 Remove
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appletgui
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- File APopupMenu.java 0 Remove
- File AlignFrame.java 0 Remove
- File AlignViewport.java 0 Remove
- File AnnotationColourChooser.java 0 Remove
- File AppletJmol.java 0 Remove
- File FeatureRenderer.java 0 Remove
- File SeqPanel.java 0 Remove
- File SequenceRenderer.java 0 Remove
- File SliderPanel.java 3 Remove
- File TreeCanvas.java 3 Remove
- File UserDefinedColours.java 0 Remove
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bin
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- File Cache.java 2 Remove
- File Jalview.java 0 Remove
- File JalviewLite.java 0 Remove
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datamodel
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- File Alignment.java 2 Remove
- File AlignmentI.java 0 Remove
- File AnnotatedCollectionI.java 0 Remove
- File SequenceCollectionI.java 0 Remove
- File SequenceGroup.java 16 Remove
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ext
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jmol
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- File JalviewJmolBinding.java 0 Remove
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rbvi/chimera
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- File ChimeraCommands.java 0 Remove
- File JalviewChimeraBinding.java 0 Remove
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jmol
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gui
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- File AlignFrame.java 1 Remove
- File AlignViewport.java 2 Remove
- File AnnotationColourChooser.java 0 Remove
- File AnnotationRowFilter.java 0 Remove
- File AppJmol.java 0 Remove
- File ChimeraViewFrame.java 0 Remove
- File ColourMenuHelper.java 1 Remove
- File FeatureRenderer.java 0 Remove
- File Jalview2XML.java 0 Remove
- File Jalview2XML_V1.java 0 Remove
- File JalviewChimeraBindingModel.java 0 Remove
- File PCAPanel.java 0 Remove
- File PopupMenu.java 0 Remove
- File Preferences.java 0 Remove
- File SeqPanel.java 0 Remove
- File SequenceRenderer.java 0 Remove
- File SliderPanel.java 0 Remove
- File StructureViewerBase.java 0 Remove
- File TreeCanvas.java 0 Remove
- File UserDefinedColours.java 2 Remove
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io
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- File AnnotationFile.java 0 Remove
- File FeaturesFile.java 0 Remove
- File JSONFile.java 2 Remove
- File TCoffeeScoreFile.java 0 Remove
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jbgui
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- File GAlignFrame.java 6 Remove
- File GStructureViewer.java 0 Remove
- File GUserDefinedColours.java 0 Remove
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renderer
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- File AnnotationRenderer.java 3 Remove
- File ResidueShader.java 3 Remove
- File ResidueShaderI.java 0 Remove
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schemes
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- File AnnotationColourGradient.java 0 Remove
- File Blosum62ColourScheme.java 3 Remove
- File BuriedColourScheme.java 0 Remove
- File ClustalxColourScheme.java 0 Remove
- File CollectionColourScheme.java 2 Remove
- File CollectionColourSchemeI.java 0 Remove
- File ColourSchemeI.java 2 Remove
- File ColourSchemeProperty.java 3 Remove
- File ColourSchemes.java 0 Remove
- File CovariationColourScheme.java 1 Remove
- File FeatureColour.java 3 Remove
- File FollowerColourScheme.java 0 Remove
- File HelixColourScheme.java 0 Remove
- File HydrophobicColourScheme.java 0 Remove
- File JalviewColourScheme.java 0 Remove
- File NucleotideColourScheme.java 0 Remove
- File PIDColourScheme.java 5 Remove
- File PurinePyrimidineColourScheme.java 0 Remove
- File RNAHelicesColour.java 1 Remove
- File RNAHelicesColourChooser.java 0 Remove
- File RNAInteractionColourScheme.java 0 Remove
- File ResidueColourScheme.java 0 Remove
- File ResidueProperties.java 0 Remove
- File ScoreColourScheme.java 0 Remove
- File StrandColourScheme.java 0 Remove
- File TCoffeeColourScheme.java 0 Remove
- File TaylorColourScheme.java 0 Remove
- File TurnColourScheme.java 0 Remove
- File UserColourScheme.java 2 Remove
- File ZappoColourScheme.java 0 Remove
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structures/models
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- File AAStructureBindingModel.java 0 Remove
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util
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- File ColorUtils.java 0 Remove
- File MappingUtils.java 0 Remove
- File ParseHtmlBodyAndLinks.java 0 Remove
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viewmodel
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seqfeatures
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- File FeatureRendererModel.java 0 Remove
- File AlignmentViewport.java 2 Remove
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seqfeatures
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workers
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- File ConsensusThread.java 0 Remove
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ws/jws2
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- File AADisorderClient.java 0 Remove
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analysis
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MCview
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test/jalview
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datamodel
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- File AlignmentTest.java 0 Remove
- File SequenceGroupTest.java 0 Remove
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ext/rbvi/chimera
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- File ChimeraCommandsTest.java 0 Remove
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gui
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- File AlignFrameTest.java 0 Remove
- File AlignViewportTest.java 0 Remove
- File PopupMenuTest.java 0 Remove
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io
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- File AnnotationFileIOTest.java 0 Remove
- File FileFormatsTest.java 0 Remove
- File JSONFileTest.java 0 Remove
- File Jalview2xmlTests.java 0 Remove
- File JalviewFileViewTest.java 0 Remove
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renderer
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- File ResidueShaderTest.java 0 Remove
- File ScaleRendererTest.java 0 Remove
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schemes
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- File Blosum62ColourSchemeTest.java 0 Remove
- File ClustalxColourSchemeTest.java 0 Remove
- File CollectionColourSchemeTest.java 0 Remove
- File ColourSchemePropertyTest.java 0 Remove
- File ColourSchemesTest.java 2 Remove
- File FeatureColourTest.java 0 Remove
- File JalviewColourSchemeTest.java 0 Remove
- File PIDColourSchemeTest.java 0 Remove
- File ResidueColourSchemeTest.java 2 Remove
- File UserColourSchemeTest.java 0 Remove
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structures/models
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- File AAStructureBindingModelTest.java 0 Remove
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util
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- File ColorUtilsTest.java 2 Remove
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datamodel
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examples
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Participant | Role | Time Spent | Comments | Latest Comment |
---|---|---|---|---|
Author | 3h 50m | 39 | The problem with the suggestions is for group colouring -... | |
Reviewer - Complete | 7h 40m | 55 (3 defects) | I think you're trying to incorporate logic that already h... | |
Total | 11h 30m | 94 (3 defects) |
- Linked Issue:
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Objectives
- JAL-2362 corrected lookup of residue colour
- JAL-2362 return correct lower-case colour; Javadoc; unit test
- JAL-1544 backgroud -> background
- JAL-2361 use consistent colour names on menus
- JAL-2360 simplify nucleotide flag, remove setter
- JAL-2361 extract methods to (re-)build colour menu
- JAL-2361 adding items to applet colour menus, TCoffee colour to desktop popup menu, extracted PopupMenu.buildColourMenu()
- JAL-2360 code formatting only and if-else changed to switch
- JAL-2365 test for lightgray, darkgray not lightGray, darkGray
- JAL-1544 JAL-2360 reformatted help page a bit nicer + spelling fix
- JAL-2360 added check for null annotations array
- JAL-2360 test added
- JAL-1354 use i18n text for expected value
- JAL-2360 refactoring for JalviewColourScheme enum, ColourSchemeI.getSchemeName(), isApplicableTo()
- JAL-1705 JAL-98 use SortedMap as more accurate type than Map
- JAL-2360 getColour() renamed to getColourScheme(), handling of "None" corrected, tests added
- JAL-2360 added UserColourScheme.toAppletParameter+test, hid parseAppletParameter()
- JAL-2360 report line number when threshold cannot be parsed as a value
- JAL-2361 select colour menu item by matching its name to colour scheme name
- JAL-2360 amended toAppletParameter() for reproducible behaviour
- JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu construction and actions done dynamically
- JAL-2360 testRegisterColourScheme to demonstrate a 'plug-in' scheme
- JAL-2360 Javadoc and test cases for findAnnotation
- JAL-2360 tidy spelling and file contents order only
- JAL-2360 fix incorrect action on Cancel user defined colour for group
- JAL-1421 add types to Map
- JAL-2361 Blosum is enabled for peptide
- JAL-2360 no RNAHelices colouring for groups
- JAL-2360 tidy up, simplify isApplicableTo test
- JAL-2360 comment only
- JAL-2360 ColourMenuHelper now builds and selects items in colour menu for align frame and popup menus
- JAL-2360 added a table to show score colours
- JAL-2360 simplified code to create a new colour scheme
- JAL-2360 set new/loaded colour scheme name correctly
- JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods and fields removed, more methods pulled up
- JAL-2360 fix bug that prematurely created a SequenceGroup
- JAL-2120 JAL-2360 remove obsolete PDBViewer
- JAL-2360 removed UserDefinedColours.userColourSchemes
- JAL-2371 CollectionColourScheme wraps ColourSchemeI
- JAL-2630 first pass groovy colour scheme (with slight refactoring)
- JAL-2371 tests added
- Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/gui/PopupMenu.java - Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
Conflicts:
src/jalview/appletgui/APopupMenu.java - Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
- JAL-2371 add test for toggling ignore gaps with PID colour scheme
- JAL-2360 findColour() with no args removed from ColourSchemeI
- Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
- Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
- JAL-2371 correct Clustal, Blosum, PID colouring of consensus logo
- JAL-2371 slight simplification of findColour overrides
Branches in review
Repository | Branch to review | Branched from |
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/examples/groovy/colourSchemes.groovy
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/examples/appletParameters.html
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/help/html/colourSchemes/clustal.html
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/help/html/io/tcoffeescores.html
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/resources/lang/Messages.properties
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/resources/lang/Messages_es.properties
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/src/MCview/AppletPDBViewer.java
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/src/MCview/PDBChain.java
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/src/MCview/PDBViewer.java
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/src/jalview/analysis/AlignmentUtils.java
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/src/jalview/analysis/Conservation.java
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/src/jalview/api/AlignViewportI.java
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/src/jalview/appletgui/APopupMenu.java
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/src/jalview/appletgui/AlignFrame.java
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/src/jalview/appletgui/AlignViewport.java
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/src/.../appletgui/AnnotationColourChooser.java
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/src/jalview/appletgui/AppletJmol.java
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/src/.../appletgui/FeatureRenderer.java
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/src/jalview/appletgui/SeqPanel.java
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/src/.../appletgui/SequenceRenderer.java
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/src/jalview/appletgui/SliderPanel.java
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/src/jalview/appletgui/TreeCanvas.java
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/src/.../appletgui/UserDefinedColours.java
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/src/jalview/bin/Cache.java
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/src/jalview/bin/Jalview.java
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/src/jalview/bin/JalviewLite.java
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/src/jalview/datamodel/Alignment.java
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/src/jalview/datamodel/AlignmentI.java
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/src/.../datamodel/AnnotatedCollectionI.java
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/src/.../datamodel/SequenceCollectionI.java
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/src/jalview/datamodel/SequenceGroup.java
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/src/jalview/.../jmol/JalviewJmolBinding.java
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/src/jalview/.../chimera/ChimeraCommands.java
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/src/.../chimera/JalviewChimeraBinding.java
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/src/jalview/gui/AlignFrame.java
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/src/jalview/gui/AlignViewport.java
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/src/.../gui/AnnotationColourChooser.java
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/src/jalview/gui/AnnotationRowFilter.java
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/src/jalview/gui/AppJmol.java
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/src/jalview/gui/ChimeraViewFrame.java
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/src/jalview/gui/ColourMenuHelper.java
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/src/jalview/gui/FeatureRenderer.java
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I think this is very nearly ready to merge to develop. A couple of ambiguities regarding the class/interface architecture that might be worth revising before the merge, but otherwise the patch looks to maintain functionality (and, of course, fix several bugs).