jalviewjs

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JAL-3746 update the example corefile for jalviewjs

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    ./classlists/jvexamplefile.txt
JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to 14.31.54 and SwingJS to 3.3.1

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JAL-3848 update jalview core with slivka classes, example file import and structure view

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    ./classlists/jalview.txt
JAL-3848 Update slivka client javajs library.

JAL-3848 j2s 3.2.10-v1 slivka-java-client jslib

JAL-3848 nominal build of slivka 0.8 compatible java client library

WIP
WIP
JAL-3690 Fix typo in enum name in slivka client.

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JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

JAL-3690 disable proxy server for JalviewJS

JAL-3690 Let's enable web services (seriously this time)

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JAL-3690 Web services and interactive workers somewhat working.

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    ./libjs/slivka-client-site.zip
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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-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

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    ./classlists/jvexamplefile.txt
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    ./classlists/jvjmol.txt
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    ./classlists/stevesoft.txt
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JAL-3446 rearranged parameters for JalviewJS API methods

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    ./site-resources/_jalview_embedded_example1.html
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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    ./site-resources/_jalview_bin_JalviewJS_core.html
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    ./site-resources/_jalview_embedded_example1.html
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    ./site-resources/_jalview_embedded_example2.html
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    ./site-resources/jalview_bin_JalviewJS_core.html
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    ./site-resources/jalview_embedded_example1.html
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reorganized JalviewJSApp (accidentally put that in jalview/api) and fixes for 2-applet example

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    ./site-resources/_jalview_bin_JalviewJS_core.html
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    ./site-resources/_jalview_embedded_example1.html
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    ./site-resources/_jalview_embedded_example2.html
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    ./site-resources/jalview_bin_JalviewJS_core.html
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    ./site-resources/jalview_embedded_example1.html
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JAL-3446 adds Jmol viewer embedding.

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    ./site-resources/jalview_embedded_example1.html