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JAL-3746 update the example corefile for jalviewjs

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

WIP
WIP
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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_jvjmol.txt

JAL-3664 support for user.home, user.dir, user

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    • +232
    ./_j2sclasslist_jmol.txt
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JAL-3210 multiple core templates. work in progress

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JAL-3210 Test with coreall.z.js

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Revert "JAL-3210 merging in Jalview-JS/develop"

This reverts commit 9499aed89323b8f53689d6428ffc9b32250eae6c, reversing

changes made to fb616bbaa70ca0f8bbae7e076f3c403a737205a9.

Still not working right in Eclipse

  1. … 6 more files in changeset.
Revert "JAL-3210 work in progress on closures"

This reverts commit 581fcc0aab400bcdd52f5c0ec64f34a8fd5e786a.

Seems to have broken development in Eclipse IDE. Reverting.

  1. … 4 more files in changeset.
JAL-3210 work in progress on closures

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    • +1183
    ./jvexamplefile.txt
  1. … 4 more files in changeset.