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JAL-3851 merged to develop 2022-03-22

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    ./api_specification.md
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JAL-3393 Updated DS_Store files, script and doc

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JAL-3393 updated Jalview Test DMG background image

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    ./README-DMG_background_image_creation.md
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JAL-3393 improved flexibility of script and updated doc

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JAL-3393 Made an all-in-one script to create the DS_Store from scratch (has to be run on a mac desktop, it incorporates the AppleScript Finder adjustments). Updated docs. Updated the release DMG background image with the script. Changed install4j9 to put the background image as .background/background.png.

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Merge branch 'master' into releases/Release_2_11_2_Branch

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JAL-3393 Added version number to DMG Volume name. New jalview_dmg_DS_Store and documentation about it

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JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

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    ./README-DMG_background_image_creation.md
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    ./README-DMG_creation.md
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    ./README_convert_PNG_to_ICNS_and_ICO
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JAL-3851 api_specification.md in progress

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    ./api_specification.md
JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

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JAL-3248 Archived old README. Added new README to point user to doc/building.md

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    ./old_ant_build_README
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JAL-3816 bump version number and cut release notes

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JAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST

JAL-3594 Changed building.md to reflect change of name of channel_properties to channel.props

JAL-3594 Documentation added to building.md for using the utils/channels/... folders

JAL-3690 update to swingjs patch 3.2.9

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JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

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JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.

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