jalview

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JAL-3762 check for !args || args=="" before overwriting

JAL-3762 more typo fixing :q

JAL-3762 syntax error typo

JAL-3762 check if Info.args already defined before overwriting it with URL args. Also stashes URL args at Info.urlargs

JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

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    /utils/eclipse/org.eclipse.jdt.ui.prefs
JAL-3210 try adding setup method to unit test failing on server...

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    /test/jalview/gui/SeqCanvasTest.java
JAL-1889 corrected wait for consensus to be calculated

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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/gui/AlignViewportTest.java
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    /test/jalview/gui/AlignmentPanelTest.java
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    /test/jalview/schemes/PIDColourSchemeTest.java
JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies

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    /src/jalview/io/AnnotationFile.java
JAL-3602 Added configuration for enforced use of UTF-8 for creating the core js files and also in the closure-compiler.

added .gitignore paths

I need these until I fully grasp the ways that gradle works.

JAL-3587 Load Project bug

Fixed 2019.01.24 in Applet branch.

commit db8caac49ea663fbc2b8b78f7eb2e6ae893f40da

didn't have a JAL number. My mistake.

JAL-3583 remove debug logging, Javadoc added

JAL-3583 consistent last[Formatted]Tooltip, show once only per residue

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    /src/jalview/gui/AnnotationPanel.java
JAL-3587 save and reload project file fix

    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core-j11.jar
JAL-3253 SwingJS upgrade including J11 transpiler 3.2.9.v1f

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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3253 merge of new SwingJS api

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    /src/swingjs/api/JSUtilI.java
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    /src/swingjs/api/js/HTML5Applet.java
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 'task/JAL-3577_Jalview_Test_installers' into develop

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

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

JAL-3407 redact java 8 incompatible type inference

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