Merge branch 'develop' into Jalview-JS/develop

Activity

CR-JAL-222 2

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    Details

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    Participant Role Time Spent Comments Latest Comment
    Author 6m 1 Let's say we have a number of unknown arguments. Then, I ...
    Reviewer - 0% reviewed 7m 1 I don't really know what you've commented on here Bob! th...
    Reviewer - 0% reviewed      
    Total   13m 2  
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    Objectives

    8521:
    Merge branch 'develop' into Jalview-JS/develop
    Conflicts:
    .gitignore
    build.gradle
    gradle.properties
    src/jalview/gui/AlignFrame.java
    src/jalview/gui/Desktop.java
    src/jalview/gui/FeatureSettings.java
    src/jalview/gui/JvSwingUtils.java
    src/jalview/util/MessageManager.java
    test/jalview/gui/AlignmentPanelTest.java
    test/jalview/gui/JvSwingUtilsTest.java
    test/jalview/gui/PopupMenuTest.java
    utils/eclipse/org.eclipse.jdt.core.jalview.prefs

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Bob Hanson

    Let's say we have a number of unknown arguments. Then, I believe, for every t...

    Let's say we have a number of unknown arguments. Then, I believe, for every two unknown arguments, this code will write (over?) the alignment file that was just loaded. And then, if there is still one more argument left, it will notify us of that one last argument. Am I reading that correctly? I'm going to make this Java-only and instead break if an output format was not identified. I don't know what the plan should be for Java. (I just deleted 30 identical files because I had a pile of unknown parameters.)

    [What does "[ ] Defect" mean, below in this form?]

    Jim Procter

    I don't really know what you've commented on here Bob! the 'defect' is an ind...

    I don't really know what you've commented on here Bob! the 'defect' is an indication that this comment needs to be addressed (somehow) by the recipient of your review.

    I think you might be talking about the argsParser here... which is uniquely Jalview-esque, and really designed for Jalview's use as a command line tool. The basic reason for separating the Javascript 'main' and Java 'main' is exactly for this reason - to allow us to exclude functionality not relevant for Javascript use of Jalview.

    /src/jalview/bin/Jalview.java Changed

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