jalview

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JAL-3289 Ehancements to ARCHIVE building and script to show how to batch build and rsync the archived versions

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    /utils/archive_building.sh
JAL-3289 ARCHIVE now implemented (requires a compiled -PARCHIVEDIST=/path/to/old/jalview/dist). Improved delete file values in uninstaller. Added an ARCHIVELOCAL channel type for testing.

JAL-3289 implemented CHANNEL=LOCAL,RELEASE,TEST-RELEASE,SCRATCHH-...,DEVELOP,ARCHIVE. Added fallback install/getdown-launcher.jar and added to classpath in install4j_template.install4j

JAL-3330 merge styles onto originating view after fetching database references

JAL-3330 dbreffetcher: record any feature display models associated with sources that provide sequences

JAL-3330 merge styles onto originating views when show cross-refs performed (should really do this for all views involving dataset).

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    /src/jalview/gui/CrossRefAction.java
JAL-3330 mergeFeatureStyles - needs test coverage

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/gui/AlignViewport.java
JAL-3322 improve visibility of versioning of launcher

JAL-3111 formatting

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    /help/help/html/features/featuresettings.html
JAL-3111 JAL-2069 JAL-2808 documentation for feature filters and enhanced feature colours. Revised feature settings documentation for legibility.

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    /help/help/html/features/featureDisplaySettings.png
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    /help/help/html/features/featureSettings.gif
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    /help/help/html/features/featureSettings.png
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    /help/help/html/features/featureschemes.html
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    /help/help/html/features/featuresettings.html
JAL-3289 Start looking at automating location in appbase more sensibly

JAL-3328 improvement to the EQinvoke code

JAL-3328 Made choice of invokeLater or invokeAndWait configurable

JAL-3111 added Colour By ID and an overview of Jalview’s alignment colouring capabilities

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    /help/help/html/colourSchemes/index.html
JAL-3328 JAL-3300 changed invokeLaters to invokeAndWaits for more visible progress

JAL-3328 Getdown version number, changed to 1.8.3-1.0_JVL

JAL-3328 Improved progress bar. Higher-res file icons. Splashscreen visibile for slightly longer (now at least 7 seconds).

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    /resources/images/jalview_logo_background_getdown-progress.png
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    /resources/images/jalview_logo_background_getdown-progress3-0.png
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    /resources/images/jalview_logo_background_getdown-progress3-1.png
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    /resources/images/jalview_logo_background_getdown-progress3.png
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    /resources/images/jalview_logo_background_getdown-progress3.xcf
JAL-3322 Adding a configurable getdown version number display (above appbase) to getdown splashscreen

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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
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    /getdown/lib/getdown-core.jar
Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility

merging in develop

JAL-3111 last final release date for 2.11.0 !

JAL-3111 2.11 improvement JAL-3205 JAL-3203 Post-hoc documentation of known defects not listed in earlier versions.

JAL-3322 New progress bar. Added option to report appbase in launcher window. Added ui.keep_on_top option for getdown window. Added a launch.jvl file. Added build_properties as a resource and build_properties.install at installation time (only)

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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
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    /resources/images/jalview_logo_background_getdown-progress-TEST2.png
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    /resources/images/jalview_logo_background_getdown-progress.png
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    /resources/images/jalview_logo_background_getdown-progress3.png
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    /resources/images/jalview_logo_background_getdown-progress4.png
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    /resources/images/jalview_logo_background_getdown_instant-640x480.png
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    /resources/images/jalview_logo_background_getdown_instant-640x480.xcf
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Merge branch 'develop' into bug/JAL-2934proportionalScrolling

JAL-3111 JAL-1424 release notes

JAL-3111 JAL-3130 JAL-3235 Java 11 specific known defects in 2.11

JAL-3323 Improved macOS Old Jalview Uninstaller

Merge branch 'develop' into releases/Release_2_11_Branch