JAL-281: Load tree from URL

Activity

CR-JAL-147 29

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    Participant Role Time Spent Comments Latest Comment
    Author 2m    
    Reviewer - Complete 1h 4m 29 This introduces a Swing dependency here, not sure this is...
    Total   1h 5m 29  
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    Objectives

    There is no Load Tree from URL dialog box.

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Mungo Carstairs

    Something has changed (got worse!) in the file browser - not quite sure what,...

    Something has changed (got worse!) in the file browser - not quite sure what, but can't see all files or navigate directories.

    Mungo Carstairs

    Package naming: I don't think you need a jalview.ext.treeviewer package. jalv...

    Package naming:
    I don't think you need a jalview.ext.treeviewer package.
    jalview.ext.* is for classes that import from (depend on) a third party library - none of these do.
    Suggest they are distributed between:
    jalview.gui (classes that use awt / swing) (assuming there are no appletgui versions planned)
    jalview.datamodel.tree (datamodel classes!)
    jalview.io (TreeParserI)
    jalview.analysis (classes that operate on datamodels but have no gui component)

    I'd suggest also moving jalview.ext.archaeopteryx into jalview.ext.forester since the dependency is just on forester.jar.
    You can still have put these in a sub-package if you want.

    Depending how it ends up, updates to import-control.xml will be needed so that checkstyle rules pass.

    Mungo Carstairs

    All classes and methods should have Javadoc (especially interfaces) - except ...

    All classes and methods should have Javadoc (especially interfaces) - except trivial getter/setter methods.

    Mungo Carstairs

    Will need unit test coverage for new classes - currently none for ext/archaeo...

    Will need unit test coverage for new classes - currently none for ext/archaeopteryx or ext/forester

    /forester/.../archaeopteryx/Archaeopteryx.java Changed
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    /forester/.../archaeopteryx/MainPanel.java Changed
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    /forester/.../archaeopteryx/TreePanel.java Changed
    /resources/lang/Messages.properties Changed 4
    /src/jalview/.../archaeopteryx/AptxInit.java Changed 7
    /src/.../archaeopteryx/AptxTreeBuilder.java Changed 2
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    /src/.../archaeopteryx/JalviewBinding.java Changed 6
    /src/.../archaeopteryx/LoadedTreeAssociation.java Changed
    /src/jalview/.../archaeopteryx/TreeParser.java Deleted
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    /src/jalview/.../io/ForesterParser.java Added
    /src/jalview/.../io/ForesterReader.java Deleted
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    /src/jalview/.../forester/io/NexusParser.java Deleted
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    /src/jalview/.../io/PhyloXMLParser.java Deleted
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    /src/jalview/.../forester/io/TreeParser.java Deleted
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    /src/jalview/.../io/UtilityMethods.java Added 1
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    /src/jalview/.../forester/UtilityMethods.java Deleted
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    /src/.../treeviewer/ExternalTreeBuilderI.java Changed
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    /src/.../treeviewer/ExternalTreeParserI.java Changed
    /src/jalview/.../treeviewer/TreeParserI.java Changed
    /src/jalview/gui/AlignFrame.java Changed
    /src/jalview/gui/Desktop.java Changed
    /src/jalview/io/FileFormat.java Changed 2
    /src/jalview/io/FileFormatI.java Changed
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    /src/jalview/io/FileLoader.java Changed
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    /src/jalview/io/IdentifyFile.java Changed 1
    /src/jalview/jbgui/GAlignFrame.java Changed 1
    /src/jalview/util/MappingUtils.java Changed 1
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