_j2sclasslist.txt

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JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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JAL-3690 Let's enable web services (seriously this time)

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JAL-3690 Web services and interactive workers somewhat working.

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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.

SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

- required transpiler fixes and redesign of final variables for stream

objects

- required redesign of $init$ and $static$ to exactly reproduce the full

class loading sequence of (1) method definition with default static

values, (2) superclass-sequenced initialization of static fields (3)

superclass-sequenced initialization of static fields, (4)

superclass-sequenced constructor initialization, in that order, able to

handle any complex situation

-includes fixes for JLabelUI HTML label wrapping issues

  1. … 22 more files in changeset.
JAL-3210 new transpiler fixes problem that it could have a null-pointer exception for comparison to history, where, apparently, IProject.getProject().getLocation() is null.

  1. … 10 more files in changeset.
Commit 113cc13-2019.09.28 with added transparency fix

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Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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JAL-3210 Moving j2s components around

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JAL-3210 Moving j2s components around

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JAL-3437 JVP reading broken in JS

updated SwingJS-site.zip

transpiler update just involves enhanced j2s.compiler.mode=debug option

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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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JAL-3422 JAL-3253-applet

SwingJS-site.zip fix for FontChooser combobox missing all text and

dropdown.

  1. … 5 more files in changeset.
JAL-3346 JAL-3253-applet JS Code issue 131 Carried forward - no mouseExited in ScalePanel on mouse drag out and right over SeqPanel border

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JAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip

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new _j2sclasslist.txt for tab-focus

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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.

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError. Also possible dependency on order of classloading if one class's static codes reference...

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError.
Also possible dependency on order of classloading if one class's static codes references another's.
Maybe move back to inside constructor?
In fact, was there any need to change this class from the 'standard' singleton pattern, if we don't want it "per applet"?

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.

Too much change around ASequenceFetcher, DbRoot etc to be able to review from the diffs. They seem to work when testing! (The code here may now be overcomplicated for the simplified (post-DAS) world.)

Too much change around ASequenceFetcher, DbRoot etc to be able to review from the diffs. They seem to work when testing!
(The code here may now be overcomplicated for the simplified (post-DAS) world.)

So what if anything used to access this? Why I hate public fields!

So what if anything used to access this? Why I hate public fields!

Could write file.contains("/") rather than file.indexOf('/') >= 0, for simplicity and readability. This is buggy - also in the original. Fetching from URL "https://www.ebi.ac.uk/Tools/dbfetch/dbfet...

Could write file.contains("/") rather than file.indexOf('/') >= 0, for simplicity and readability.
This is buggy - also in the original. Fetching from URL "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/1a70/pdb" results in file.substring(52, 18).
Issue JAL-3272 raised for that.