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JAL-3438 spotless for 2.11.2.0

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    ./DisorderAnnotExportImport.java
  1. … 658 more files in changeset.
JAL-3438 - all src and test run through spotless..

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    ./DisorderAnnotExportImport.java
  1. … 665 more files in changeset.
JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

Conflicts:

src/jalview/bin/Jalview.java

  1. … 97 more files in changeset.
JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

  1. … 101 more files in changeset.
JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

WIP
WIP
JAL-3690 refactoring web-services discovery

  1. … 9 more files in changeset.
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
I suggest we close this. It's all ancient history now.

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

JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.

- integrated changes from 0b573ed (gmungoc)

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startDiscoverer should not return Thread because Discoverer's internal implementation may spawn more threads or use a thread pool. Returned thread is not a reliable indicator whether the discoverer...

startDiscoverer should not return Thread because Discoverer's internal implementation may spawn more threads or use a thread pool. Returned thread is not a reliable indicator whether the discoverer is still running. isRunning() should be used instead. The return type was kept for compatibility with Jws2Discoverer and other classes relying on it.

Adding the same change listener over and over by the Desktop class may cause events to be received multiple times. PropertyChangeListener uses an array internally and doesn't check for repeated lis...

Adding the same change listener over and over by the Desktop class may cause events to be received multiple times. PropertyChangeListener uses an array internally and doesn't check for repeated listeners.

How about adding WSDiscoverer.isEnabled()

How about adding WSDiscoverer.isEnabled()

JAL-3515 Extract core WSDiscoverer methods to a separate interface
JAL-3515 Extract core WSDiscoverer methods to a separate interface
JAL-3515 Extract core WSDiscoverer methods to a separate interface

Creating WSDiscovererI interface helps to separating exposed methods from internal implementation details of Jws2Discoverer and implements the same functionality in SlivkaWSDiscoverer

  1. … 6 more files in changeset.
JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.

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JAL-3070 jaba/slivka independent tests for disorder and AACon services

JAL-3070 test jabaws and slivka AACon service functionality

JAL-3070 basic AACon service functionality test

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    ./AAConAnnotAndSettingsIO.java