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JAL-3904 failing test

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

  1. … 100 more files in changeset.
JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

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JAL-2422 updated unit test for ChimeraX command change

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    ./rbvi/chimera/ChimeraXCommandsTest.java
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.

JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3390: Option to hide unmapped residues in structure viewer
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

JAL-3390 improved 'hide chain' commands

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/pymol/PymolCommands.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/ChimeraXCommands.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/structure/StructureCommandsBase.java

src/jalview/structure/StructureCommandsI.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/pymol/PymolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
  1. … 11 more files in changeset.
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-3518 pull up [get|list]ResidueAttributes to StructureCommandsI

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
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JAL-3518 separation of ChimeraXManager, pull up of closeViewer etc

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
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JAL-3390 unit tests and command and menu refinements

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    ./jmol/JalviewJmolBindingTest.java
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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
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    ./rbvi/chimera/JalviewChimeraBindingTest.java
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JAL-3390 obsolete classes/methods removed

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

gradle.properties

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/structures/JalviewStructureDisplayI.java

src/jalview/appletgui/AppletJmol.java

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/rbvi/chimera/AtomSpecModel.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AppJmol.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/gui/StructureViewerBase.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/jmol/JmolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/structures/models/AAStructureBindingModelTest.java

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    ./jmol/JmolCommandsTest.java
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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/JalviewChimeraBindingTest.java
  1. … 21 more files in changeset.
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

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    ./rbvi/chimera/ChimeraCommandsTest.java
  1. … 18 more files in changeset.
JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

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    ./rbvi/chimera/JalviewChimeraView.java
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JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

  1. … 17 more files in changeset.
JAL-3518 test result corrected

JAL-3518 add alwaysRun = true [sigh]

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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
JAL-3518 more test coverage for structure commands

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    ./pymol/PymolCommandsTest.java
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    ./rbvi/chimera/ChimeraCommandsTest.java
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    ./rbvi/chimera/ChimeraXCommandsTest.java
  1. … 3 more files in changeset.