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JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references

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    ./debian/debian/icons/128x128/apps/jalview-icon.png
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    ./debian/debian/icons/16x16/apps/jalview-icon.png
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    ./debian/debian/icons/16x16/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/22x22/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/24x24/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/256x256/apps/jalview-icon.png
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    ./debian/debian/icons/32x32/apps/jalview-icon.png
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    ./debian/debian/icons/32x32/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/48x48/apps/jalview-icon.png
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    ./debian/debian/icons/48x48/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/512x512/apps/jalview-icon.png
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    ./debian/debian/icons/512x512/mimetypes/x-jalview-file.png
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    ./debian/debian/icons/64x64/apps/jalview-icon.png
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    ./debian/debian/jalview-mime.xml
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    ./debian/file_associations_template-shared-mime-info.xml
JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg

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    ./debian/debian/wrappers/jalview
JAL-3815 default /etc/jalview_properties under utils/debian

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    ./debian/etc/jalview_properties
JAL-3251 debian build using maven, simplified build.gradle not needed

JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian

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    ./debian/build.gradle.debian
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JAL-3521 Updating file opening marker to %u

JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    ./debian/debian/jalview-file.png
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    ./debian/debian/jalview-icon.png
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    ./debian/debian/jalview-mailcap
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    ./debian/debian/jalview-mime.xml
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    ./debian/debian/jalview.desktop
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    ./debian/file_associations_template-mailcap.txt
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    ./debian/file_associations_template-shared-mime-info.xml
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    ./debian/mime_types_for_debian.pl
Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agree this is just touching on a much bigger task. However... The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview...

Agree this is just touching on a much bigger task.
However...
The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly u...

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS,...

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS, so probably not a dealbreaker. Do you agree ?

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
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.

JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3390: Option to hide unmapped residues in structure viewer
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-3541 Helpers for running tests, and other commands headlessly

JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

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    ./clover/lib/clover-ant-4.4.1.jar
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JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar

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    ./install4j/install4j8_template.install4j
JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list

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    ./install4j/install4j8_template.install4j
JAL-3577 improvement to non-release DMG background and source SVG. Updated docs on image specification/creation.

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    ./install4j/DMG_background_image_creation_README.md
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    ./install4j/jalview_dmg_background-NON-RELEASE.png
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    ./install4j/jalview_dmg_background-NON-RELEASE.svg
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    ./install4j/jalview_dmg_background_blur_layers-NON-RELEASE.svg
JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling

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    ./install4j/DS_Store-DEVELOP
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    ./install4j/install4j8_template.install4j
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    ./install4j/jalview_dmg_background-DEVELOP.png
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    ./install4j/jalview_dmg_background-NON-RELEASE.png
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    ./install4j/jalview_dmg_background-TEST.png
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