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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

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-3446 AppletParams

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    ./JalviewJS-startupParams.xlsx
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JAL-3446 reorganized JalviewJSApp (accidentally put that in jalview/api) and fixes for 2-applet example

- API.md

- follows commit 01717e2 (missing JAL-3446 tag)

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JAL-3446 JavaScript interface

- testing with two apps on a page

- now requires Jalview1.getApp().xxxx, not just Jalview1.app, because a

call is needed to ensure that ThreadGroup is set correctly.

- still working on this...

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    ./JalviewJS-startupParams.md
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JAL-3446 adds Jmol viewer embedding.

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JAL-3379 JalviewJS-API specs - preliminary

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    ./JalviewJS-API.md
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JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

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    ./releaseprocess.html