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JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars

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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

  1. … 102 more files in changeset.
JAL-3810 - Add trace method to javascript implementation of Logger

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

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
Refactoring of Jalview, JalviewAppLoader, JalviewApp, various applet-related interfaces

- makes JalviewJSApp the JavaScript interface "app" class

- removes JS interface from Jalview

- removes JalviewAppLoader and associated duplication of classes

- adds JavaScript selection and "oninit" listeners (untested)

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    ./MouseOverStructureListener.java
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I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

Gitter comment 2020.05.28 Cache.log.err(msg) not appearing

Gitter comment 2020.05.28 Cache.log.err(msg) not appearing

temp push

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JAL-2422 pull-up refactoring of structure commands (continued)

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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

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    ./MouseOverStructureListener.java
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I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit ...

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit with the issue.

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./MouseOverStructureListener.java
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JAL-3269 ready for testing embedded interface

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Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

Deferred to JAL-3265

Deferred to JAL-3265

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test). Now throws NullPointerException but coded only to expect SiftsException. Traced to uninitialized field DBRefEntry.ucv...

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test).
Now throws NullPointerException but coded only to expect SiftsException.
Traced to uninitialized field DBRefEntry.ucversion. Initialising this to "" (like version) resolves this.