jalview

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JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling

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    /utils/install4j/DS_Store-DEVELOP
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    /utils/install4j/DS_Store-NON-RELEASE
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    /utils/install4j/jalview_dmg_background-DEVELOP.png
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    /utils/install4j/jalview_dmg_background-NON-RELEASE.png
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    /utils/install4j/jalview_dmg_background-TEST.png
JAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for RELEASE channel only and Examples folder in Jalview Programme Group in Windows.

Merge branch 'develop' into releases/Release_2_11_1_Branch

JAL-3407 redact java 8 incompatible type inference

Merge branch 'develop' into releases/Release_2_11_1_Branch

JAL-3407 updated release date to Thursday 9th April, and release notes for JAL-3577 JAL-3581 JAL-3571

JAL-3581 no hidden sequence marker if hidden markers not shown

JAL-3581 no hidden sequence marker if hidden markers not shown

JAL-3577 Moved application Categories for freedesktop menus into correct place in install4j

Merge branch 'develop' into Jalview-JS/develop

Conflicts:

build.gradle

src/jalview/gui/SeqPanel.java

build.gradle and gradle.properties changes in develop ignored

JAL-3577 removed debugging

Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop

JAL-3577 Added existing and new Application IDs for Windows. Fixed Desktop shortcut and Menu entry.

JAL-3579 no Feature Editor if features not shown

Merge branch 'develop' into releases/Release_2_11_1_Branch

JAL-3577 Changed shortName to INTERNAL_ID

JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'

JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'

JAL-3253 JAL-3032 upgrade to SwingJS-3.2.9.v1e complete 2/2

- random tests failing can be ignored (just thread timing issues)

(AlignmentPanelTest and SeqCanvasTest). Problem is clearly from

concurrent thread interference not likely to affect standard

operation.

- branch can be deleted after merging.

JAL-3253 JAL-3032 upgrade to SwingJS-3.2.9.v1e complete

- random tests failing can be ignored (just thread timing issues)

(AlignmentPanelTest and SeqCanvasTest). Problem is clearly from

concurrent thread interference not likely to affect standard

operation.

- branch can be deleted after merging.

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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3253 JAL-3260 SwingJS-3.2.9.v1e and tests

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    /src/jalview/gui/AlignmentPanel.java
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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3577 Added DS_Store for Test release to look like proper installer

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    /utils/install4j/DS_Store-TEST-RELEASE
JAL-3577 Added a jalviewt scheme ONLY to TEST-RELEASE and TEST-LOCAL channels so that a test jvl can be made to ONLY open in the Test installation

JAL-3577 cleaned up old DMG files. Added NON-RELEASE DMG files. Changed how Jalview name propogates through install4j -- now dynamically created depending on the CHANNEL

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    /utils/install4j/DMG_background_image_creation_README.md
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    /utils/install4j/DMG_creation_README.md
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    /utils/install4j/DS_Store-NON-RELEASE
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    /utils/install4j/jalview_dmg_background-NON-RELEASE.png
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    /utils/install4j/jalview_dmg_background-NON-RELEASE.svg
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    /utils/install4j/jalview_dmg_background_blur_72dpi.png
  1. … 4 more files in changeset.
JAL-3577 First attempt at new folder names

Merge branch 'develop' into releases/Release_2_11_1_Branch

JAL-3572 Added getdown Implementation-Version to getdown jars META-INF/MANIFEST.MF

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    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
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    /getdown/lib/getdown-launcher-local.jar
Merge branch 'improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file' into develop

JAL-3438 Added spotless task to use the utils/eclipse/JalviewCodeStyle.xml to reformat all .java source files

JAL-3225 tasks to create extra desired settings for eclipse

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    /utils/eclipse/org.eclipse.jdt.groovy.core.prefs
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    /utils/eclipse/org.eclipse.jdt.ui.prefs