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Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work! Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this m...

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work!
Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this method seems to be trying to do two different things.

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called). So what is it there for?

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called).
So what is it there for?

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Needs proper Javadoc

Needs proper Javadoc

JAL-3446 unused imports removed

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Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide...

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide documentation.
e.g. http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=doc/JalviewJS-startupParams.md;h=9ff33529b2dbc2da34d2a573ccf5d042194fbb0d;hb=refs/heads/Jalview-JS/develop

Due to the number of changes this is likely to be a 'best efforts' review.

Due to the number of changes this is likely to be a 'best efforts' review.

Commits to JS-develop from 2nd to 25th June 2020
Commits to JS-develop from 2nd to 25th June 2020
Minor updates

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JAL-3446 minor SwingJS-site.zip fixes; Assets.

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AsyncSwingWorker setpaused adjustment

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    ./async/AsyncSwingWorker.java
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JAL-3446 AsyncSwingWorker upgrade

swingjs/api, javajs/async

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    • +594
    ./async/Assets.java
    • -0
    • +189
    ./async/Async.java
    • -0
    • +67
    ./async/AsyncColorChooser.java
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    • +282
    ./async/AsyncDialog.java
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    • +217
    ./async/AsyncFileChooser.java
    • -0
    • +385
    ./async/AsyncSwingWorker.java
    • -0
    • +651
    ./async/SwingJSUtils.java
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updated AsyncSwingWorker

Adding SwingJS interface and utility classes

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    ./async/Assets.java
    • -0
    • +189
    ./async/Async.java
    • -0
    • +67
    ./async/AsyncColorChooser.java
    • -0
    • +282
    ./async/AsyncDialog.java
    • -0
    • +217
    ./async/AsyncFileChooser.java
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    • +358
    ./async/AsyncSwingWorker.java
    • -0
    • +651
    ./async/SwingJSUtils.java
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JAL-3026 moves javajs to srcjars

- important because Java is using older code from the Jmol jar file

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    • +0
    ./api/GenericBinaryDocumentReader.java
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update of javajs package; adds org.apache.harmony, org.xml.sax.helpers

File format identified as Fasta

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JAL-3026 adding javajs package

adding a general utility package for Java or JavaScript.

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    ./J2SRequireImport.java
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    ./api/EigenInterface.java
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    ./api/GenericBinaryDocument.java
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    ./api/GenericBinaryDocumentReader.java
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    ./api/GenericCifDataParser.java
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    ./api/GenericColor.java
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    ./api/GenericImageDialog.java
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    ./api/GenericImageEncoder.java
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    ./api/GenericLineReader.java
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    ./api/GenericOutputChannel.java
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    ./api/GenericZipInputStream.java
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    • +45
    ./api/GenericZipTools.java
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JAL-1807 first version showing alignment; off-screen images working); mouse-action roughed in; no threads;

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    ./J2SRequireImport.java
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    ./api/EigenInterface.java
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    ./api/EventManager.java
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    • +23
    ./api/FontManager.java
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    • +53
    ./api/GenericBinaryDocument.java
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    • +45
    ./api/GenericCifDataParser.java
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    • +19
    ./api/GenericColor.java
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    • +15
    ./api/GenericFileInterface.java
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    • +9
    ./api/GenericImageDialog.java
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    ./api/GenericImageEncoder.java
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    • +5
    ./api/GenericLineReader.java
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    • +18
    ./api/GenericMenuInterface.java
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    ./api/GenericMouseInterface.java
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JAL-1807 Bob's first commit -- Applet loaded; needs image

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    ./J2SRequireImport.java
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    ./api/EigenInterface.java
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    • +16
    ./api/EventManager.java
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    • +23
    ./api/FontManager.java
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    • +53
    ./api/GenericBinaryDocument.java
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    • +45
    ./api/GenericCifDataParser.java
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    • +19
    ./api/GenericColor.java
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    • +15
    ./api/GenericFileInterface.java
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    • +9
    ./api/GenericImageDialog.java
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    • +12
    ./api/GenericImageEncoder.java
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    • +5
    ./api/GenericLineReader.java
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    • +18
    ./api/GenericMenuInterface.java
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    • +13
    ./api/GenericMouseInterface.java
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