CR-JAL-1 JAL-2362 corrected lookup of residue colour

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JAL-2362 corrected lookup of residue colour

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General Comments 1
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Number of files included: 127

jalview 0
- Folder examples 0
  - Folder groovy 0
    - File colourSchemes.groovy 8 Remove
  - File appletParameters.html 0 Remove
- Folder help/html 0
  - Folder colourSchemes 0
    - File clustal.html 7 Remove
  - Folder io 0
    - File tcoffeescores.html 0 Remove
- Folder resources/lang 0
  - File Messages.properties 0 Remove
  - File Messages_es.properties 0 Remove
- Folder src 0
  - Folder MCview 0
    - File AppletPDBViewer.java 0 Remove
    - File PDBChain.java 0 Remove
    - File PDBViewer.java 0 Remove
  - Folder jalview 0
    - Folder analysis 0
      - File AlignmentUtils.java 0 Remove
      - File Conservation.java 0 Remove
    - Folder api 0
      - File AlignViewportI.java 2 Remove
    - Folder appletgui 0
      - 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
    - Folder bin 0
      - File Cache.java 2 Remove
      - File Jalview.java 0 Remove
      - File JalviewLite.java 0 Remove
    - Folder datamodel 0
      - 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
    - Folder ext 0
      - Folder jmol 0
        
        File JalviewJmolBinding.java 0 Remove
      - Folder rbvi/chimera 0
        
        File ChimeraCommands.java 0 Remove
        
        File JalviewChimeraBinding.java 0 Remove
    - Folder gui 0
      - 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
    - Folder io 0
      - File AnnotationFile.java 0 Remove
      - File FeaturesFile.java 0 Remove
      - File JSONFile.java 2 Remove
      - File TCoffeeScoreFile.java 0 Remove
    - Folder jbgui 0
      - File GAlignFrame.java 6 Remove
      - File GStructureViewer.java 0 Remove
      - File GUserDefinedColours.java 0 Remove
    - Folder renderer 0
      - File AnnotationRenderer.java 3 Remove
      - File ResidueShader.java 3 Remove
      - File ResidueShaderI.java 0 Remove
    - Folder schemes 0
      - 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
    - Folder structures/models 0
      - File AAStructureBindingModel.java 0 Remove
    - Folder util 0
      - File ColorUtils.java 0 Remove
      - File MappingUtils.java 0 Remove
      - File ParseHtmlBodyAndLinks.java 0 Remove
    - Folder viewmodel 0
      - Folder seqfeatures 0
        
        File FeatureRendererModel.java 0 Remove
      - File AlignmentViewport.java 2 Remove
    - Folder workers 0
      - File ConsensusThread.java 0 Remove
    - Folder ws/jws2 0
      - File AADisorderClient.java 0 Remove
- Folder test/jalview 0
  - Folder datamodel 0
    - File AlignmentTest.java 0 Remove
    - File SequenceGroupTest.java 0 Remove
  - Folder ext/rbvi/chimera 0
    - File ChimeraCommandsTest.java 0 Remove
  - Folder gui 0
    - File AlignFrameTest.java 0 Remove
    - File AlignViewportTest.java 0 Remove
    - File PopupMenuTest.java 0 Remove
  - Folder io 0
    - 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
  - Folder renderer 0
    - File ResidueShaderTest.java 0 Remove
    - File ScaleRendererTest.java 0 Remove
  - Folder schemes 0
    - 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
  - Folder structures/models 0
    - File AAStructureBindingModelTest.java 0 Remove
  - Folder util 0
    - File ColorUtilsTest.java 2 Remove

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Participant	Role	Time Spent	Comments	Latest Comment
Mungo Carstairs	Author	3h 50m	39	The problem with the suggestions is for group colouring -...
Jim Procter	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:
JAL-2360

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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

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Issues Raised From Comments

Key	Summary	State	Assignee
JAL-2395
JAL-2410
JAL-2415
JAL-2407
JAL-2394
JAL-2396

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General Comments

Jim Procter

I think this is very nearly ready to merge to develop. A couple of ambiguitie...

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).

20 Jan 17

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JAL-2362 corrected lookup of residue colour

CR-JAL-1 94

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Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Jim Procter