1. Jalview Code Reviews

CR-JAL-17

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closed on 04 Oct 17
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JAL-2388: Option to exclude hidden regions in overview window

Activity

CR-JAL-17 24

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    Details

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    Participant Role Time Spent Comments Latest Comment
    Kira Mourão
    		Author 1h 26m 8 I think the argument is a relic from when I still had Col...
    Jim Procter
    Reviewer completed
    		Reviewer - Complete 1h 55m 13 prolly need to document why this hashCode method has an a...
    Total   3h 21m 24  
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    Objectives

    1. Overview panel refactoring, simplification, and bug fixing for 2.10.2.
    2. Extension for JAL-2388 (currently for 2.10.3):The overview panel should provide an option that allows hidden regions to be excluded (ie just a birds-eye version of the linked alignment view), rather than showing them as greyed-out regions.

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    There are no general comments on this review.
    /examples/bigal.fa Deleted 2
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    /help/html/features/overview.html Changed
    /help/help.jhm Changed
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    /help/helpTOC.xml Changed
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    /resources/lang/Messages.properties Changed
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    /resources/lang/Messages_es.properties Changed
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    /src/jalview/api/AlignViewportI.java Changed
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    /src/.../api/AlignmentColsCollectionI.java Added
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    /src/.../api/AlignmentRowsCollectionI.java Added
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    /src/jalview/api/ComplexAlignFile.java Changed
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    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/appletgui/AlignViewport.java Changed
    /src/jalview/appletgui/AlignmentPanel.java Changed
    /src/.../appletgui/AnnotationColumnChooser.java Changed
    /src/.../appletgui/AnnotationLabels.java Changed
    /src/.../appletgui/AnnotationPanel.java Changed
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    /src/.../appletgui/CutAndPasteTransfer.java Changed
    /src/jalview/appletgui/IdCanvas.java Changed 2
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    /src/jalview/appletgui/IdPanel.java Changed
    /src/jalview/appletgui/OverviewCanvas.java Added
    /src/jalview/appletgui/OverviewPanel.java Changed
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    /src/jalview/appletgui/PCAPanel.java Changed
    /src/jalview/appletgui/ScalePanel.java Changed
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    /src/jalview/appletgui/SeqCanvas.java Changed
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    /src/jalview/appletgui/SeqPanel.java Changed
    /src/jalview/appletgui/TreePanel.java Changed
    /src/jalview/bin/JalviewLite.java Changed
    /src/jalview/datamodel/Alignment.java Changed 5
    /src/.../datamodel/AlignmentAnnotation.java Changed
    /src/.../datamodel/AlignmentColsCollection.java Deleted
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    /src/jalview/datamodel/AlignmentI.java Changed
    /src/.../datamodel/AlignmentRowsCollection.java Deleted
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    /src/jalview/datamodel/AlignmentView.java Changed
    /src/.../datamodel/AllColsCollection.java Added
    /src/.../datamodel/AllColsIterator.java Added
    /src/.../datamodel/AllRowsCollection.java Added
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    /src/.../datamodel/AllRowsIterator.java Added
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    /src/jalview/datamodel/CigarArray.java Changed
    /src/.../datamodel/ColumnSelection.java Changed 1
    /src/jalview/datamodel/HiddenColumns.java Added 2
    /src/.../datamodel/HiddenSequences.java Changed 1
    /src/jalview/datamodel/SeqCigar.java Changed
    /src/.../datamodel/VisibleColsCollection.java Added
    /src/.../datamodel/VisibleColsIterator.java Added
    /src/.../datamodel/VisibleRowsCollection.java Added
    /src/.../datamodel/VisibleRowsIterator.java Added
    /src/jalview/.../jmol/JalviewJmolBinding.java Changed
    /src/jalview/ext/jmol/JmolCommands.java Changed
    /src/jalview/.../chimera/ChimeraCommands.java Changed
    /src/.../chimera/JalviewChimeraBinding.java Changed
    /src/jalview/gui/AlignFrame.java Changed
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    /src/jalview/gui/AlignViewport.java Changed
    /src/jalview/gui/AlignmentPanel.java Changed
    /src/.../gui/AnnotationColumnChooser.java Changed
    /src/jalview/gui/AnnotationLabels.java Changed
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    /src/jalview/gui/AppVarna.java Changed
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    /src/jalview/gui/IdPanel.java Changed
    /src/jalview/gui/Jalview2XML.java Changed
    /src/jalview/gui/Jalview2XML_V1.java Changed