template.html

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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
updated template.html

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Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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JAL-3210 Moving j2s components around

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JAL-3210 Moving j2s components around

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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menu update; popup not functioning, though?? Working fine in test suite. Will test.

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JAL-3032 JTable work; JSUtil.jQuery object; drag-drop; reflect.Constructor; adds core:"NONE" to {project}/template.html

fixes drag-drop for first call in Firefox/win

fixes java.lang.reflect.Constructor for Integer

Remove the core:"NONE" if you do not want to see all the core files

separately.

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Bob first commit JAL-3032

- jalview/bin/cache.java

propsAreReadable true for JS

authordetails, builddetails "xxx" for JS for now

- org.apache.log4j -> jalview.javascript.log4j (minimal)

- jalview/util/MessageManager switch to org.apache.log4j

JavaScript Status:

jalview.io.FileFormatException: Failed to read data from source: CANNOT

ACCESS DATA AT URL 'http://www.jalview.org/examples/uniref50.fa'

((intermediate value).toBIS$O is not a function

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