jalview

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JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

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    /utils/jalviewjs/_j2sclasslist.txt
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    /utils/jalviewjs/classlists/_jvjmol.txt
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    /utils/jalviewjs/classlists/jalview.txt
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    /utils/jalviewjs/classlists/jvjmol.txt
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    /utils/jalviewjs/classlists/stevesoft.txt
JAL-3446 breaking change redacted

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3445 BSML BBB file format.

- merge of BSML test branch.

- includes BSMLFileTest

- preliminary; does not read complement

- See Jalview-JS/develop/temp/bbb.dtd.pdf

JAL-3653 SwingJS support for indeterminate JProgressBar

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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3487 Splash screen

- cleaner code, more comments

- adds SwingJS support for 1-ms image finalization

(using JSToolkit.dispatch instead of invokeLater

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    /src/jalview/gui/SplashScreen.java
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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3487 Splash screen

- JS now uses StateMachine

- simple example of how StateMachine works.

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    /src/jalview/gui/SplashScreen.java
Merge branch 'Jalview-JS/develop.JAL-3445-BSML-reader' into Jalview-JS/develop

minor changes

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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /test/jalview/gui/JvSwingUtilsTest.java
JAL-3446 SwingJS update

-fixes desktop frame not taking focus when clicked, so not processing

menu shortcuts

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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3664 shortcuts in Desktop not working from AlignFrame

- missing test for JInternalFrame in JComponent.processKeyBindings

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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3446 fixing a bad merge, sorry

JAL-3446 separated out potential exceptions for simplified key mask operation

JAL-3446 removing mouse button test debug

SwingJS upgrade fixes AlignmentPanel keyPressed not called

- ContentPane was getting the message, not JInternalFrame

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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3446 from applet -- reload; also fixes some repaint issues

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationPanel.java
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    /src/jalview/gui/PaintRefresher.java
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    /src/jalview/io/VamsasAppDatastore.java
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/util/jarInputStreamProvider.java
JAL-3624 code tidy

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    /test/jalview/util/PlatformTest.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-3624 unneeded import removed

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    /src/jalview/ws/sifts/SiftsSettings.java
JAL-3446 separated out potential exceptions for simplified key mask operation

JAL-3446 misplaced } removed drop and window listeners from JS

JAL-3446 no need for SHIFT_DOWN or ALT_DOWN masks

First try at merging didn't go so well.

Merge branch 'Jalview-JS/develop.JAL-3446.ctrlDown' into Jalview-JS/develop

Conflicts:

src/jalview/bin/JalviewJS2.java

src/jalview/gui/Desktop.java

src/jalview/util/Platform.java

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    /src/jalview/jbgui/GAlignFrame.java
JAL-3446, JAL-3647 after first successful test run; removing debug messages

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    /src/jalview/gui/AlignmentPanel.java
Bamboo #36 checking component sizes

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    /test/jalview/gui/SeqCanvasTest.java
Bamboo text #35 - simpler logic; avoids impossible repaint, validation?

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    /src/jalview/gui/AlignmentPanel.java
Bamboo test #3 The problem is not threading. It is feedback from ViewportRanges to AlignmentPanel from trying to set the ranges to invalid values.

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    /src/jalview/gui/AlignmentPanel.java
Bamboo test - setting method priorities

Bamboo test 2 -- threads and stacktrace

So close! Bamboo test