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

  1. … 98 more files in changeset.
JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency/per sequence annotation score encoding

WIP
WIP
JAL-3788 synchronize concurrent findColour() and alignmentChanged()

JAL-3788 synchronize concurrent findColour() and alignmentChanged()

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
JAL-3665 sequences shaded according to emmission probability of first aligned hmm at each column

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

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

JAL-3446 from JAL-3253 ApplicationSingletonProvider StructureSelectionManager and others

  1. … 24 more files in changeset.
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

  1. … 74 more files in changeset.
Couldn't you just move fr.featuresAdded() to here ?

Couldn't you just move fr.featuresAdded() to here ?

if this is public, there's a risk of recursive notifications. Probably want the 'firing' state conditional moved to here.

if this is public, there's a risk of recursive notifications. Probably want the 'firing' state conditional moved to here.

The semantics are unclear for isFeatureDisplayed .. e.g. if isFeatureDisplayed==false then does the caller then have to call isFeatureHidden to check visiblity ?

The semantics are unclear for isFeatureDisplayed .. e.g. if isFeatureDisplayed==false then does the caller then have to call isFeatureHidden to check visiblity ?

JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB
JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB
JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB

  1. … 10 more files in changeset.
JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB - resolved conflicts for 2.11.2

  1. … 10 more files in changeset.