JAL-2362 corrected lookup of residue colour

Activity

CR-JAL-1 94

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    Details

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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)  
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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).

    /examples/groovy/colourSchemes.groovy Added 8
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    /examples/appletParameters.html Changed
    /help/html/colourSchemes/clustal.html Changed 7
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    /help/html/io/tcoffeescores.html Changed
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    /resources/lang/Messages.properties Changed
    /resources/lang/Messages_es.properties Changed
    /src/MCview/AppletPDBViewer.java Changed
    /src/MCview/PDBChain.java Changed
    /src/MCview/PDBViewer.java Deleted
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    /src/jalview/analysis/AlignmentUtils.java Changed
    /src/jalview/analysis/Conservation.java Changed
    /src/jalview/api/AlignViewportI.java Changed 2
    /src/jalview/appletgui/APopupMenu.java Changed
    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/appletgui/AlignViewport.java Changed
    /src/.../appletgui/AnnotationColourChooser.java Changed
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    /src/jalview/appletgui/AppletJmol.java Changed
    /src/.../appletgui/FeatureRenderer.java Changed
    /src/jalview/appletgui/SeqPanel.java Changed
    /src/.../appletgui/SequenceRenderer.java Changed
    /src/jalview/appletgui/SliderPanel.java Changed 3
    /src/jalview/appletgui/TreeCanvas.java Changed 3
    /src/.../appletgui/UserDefinedColours.java Changed
    /src/jalview/bin/Cache.java Changed 2
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    /src/jalview/bin/Jalview.java Changed
    /src/jalview/bin/JalviewLite.java Changed
    /src/jalview/datamodel/Alignment.java Changed 2
    /src/jalview/datamodel/AlignmentI.java Changed
    /src/.../datamodel/AnnotatedCollectionI.java Changed
    /src/.../datamodel/SequenceCollectionI.java Changed
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    /src/jalview/datamodel/SequenceGroup.java Changed 16
    /src/jalview/.../jmol/JalviewJmolBinding.java Changed
    /src/jalview/.../chimera/ChimeraCommands.java Changed
    /src/.../chimera/JalviewChimeraBinding.java Changed
    /src/jalview/gui/AlignFrame.java Changed 1
    /src/jalview/gui/AlignViewport.java Changed 2
    /src/.../gui/AnnotationColourChooser.java Changed
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    /src/jalview/gui/AnnotationRowFilter.java Changed
    /src/jalview/gui/AppJmol.java Changed
    /src/jalview/gui/ChimeraViewFrame.java Changed
    /src/jalview/gui/ColourMenuHelper.java Added 1
    /src/jalview/gui/FeatureRenderer.java Changed