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JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

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JAL-3753 put resources in gradle run and test path

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JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

  1. … 45 more files in changeset.
JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

  1. … 45 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 see...

updated template.html

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Bob's gitignore addition

/build-site.xml

/buildcore.xml

/j11lib/intervalstore-v1.0.jar

added .gitignore paths

I need these until I fully grasp the ways that gradle works.

JAL-3225 This one file needed for project if git clean -dfx run

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JAL-3225 This one file needed for project if git clean -dfx run

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JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

  1. … 6 more files in changeset.
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

  1. … 6 more files in changeset.
JAL-3248 Added instructions for downloading and configuring as gradle project in Eclipse only, i.e. no command line tools needed

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JAL-3559 temporary branch adding JS files complete

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JAL-3521 Ignore quilt dir /.pc

JAL-3449 Fixed Info.plist file insertion. Simplified install4j conf filename

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JAL-3449 Using .gitignore from Jalview-JS/develop

JAL-3210 need this .gitignore addition for the new location of .build_properties

JAL-3210 .build_properties now created in /resources, which is found in Eclipse/buildship classpath. Does not affect jar build

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JAL-3210 Fixed jalviewjs dependencies. Changed linkCheck to tee output to .out file. Tidying jalviewjs paths.

  1. … 3 more files in changeset.