jalview

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JAL-3253

sets setting for "unlikely argument type for collection" to warning; I

have set my workspace to error, but clearly it had not been like that,

because it found three errors. But now setting it to warning so that it

is not bothering me.

JAL-3592 logic question

JAL 3591 simple coding error in appletgui/SeqPanel

merge from develop: the fixy bit

merge from develop: the rest of the changes

merge from develop: Most of the changes

JAL-3589 (old Platform) fix for Jalvew-JS/develop only.

JAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility

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

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    /utils/install4j/DMG_background_image_creation_README.md
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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_layers-NON-RELEASE.svg
Merge branch 'bug/JAL-247autoIdWidthSeqMarker' into develop

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

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

    • binary
    /utils/install4j/DS_Store-DEVELOP
    • binary
    /utils/install4j/DS_Store-NON-RELEASE
    • binary
    /utils/install4j/jalview_dmg_background-DEVELOP.png
    • binary
    /utils/install4j/jalview_dmg_background-NON-RELEASE.png
    • binary
    /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.