jalview

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JAL-2314 made non-test method non-public

Merge branch 'develop' into bug/JAL-2314

Merge branch 'develop' into bug/JAL-2461

JAL-2405 additional checks for circular reference in context or dataset

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2472 PrivilegedAccessor added

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    /test/junit/extensions/PA.java
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    /test/junit/extensions/PrivilegedAccessor.java
Merge branch 'develop' into bug/JAL-2431splitFrameNewView

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
JAL-2430 code tidy, unit test for Jmol hidden column colours

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    /src/jalview/ext/jmol/JmolCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
Merge branch 'develop' into bug/JAL-1608createGroups

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    /resources/lang/Messages_es.properties
JAL-1608 leave Create Group, Remove Group menu items enabled

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    /src/jalview/jbgui/GAlignFrame.java
JAL-2401 code and help tidy for review comments

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    /src/jalview/gui/UserDefinedColours.java
JAL-2401 don't apply lower case colour to upper case

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    /src/jalview/gui/UserDefinedColours.java
Merge branch 'develop' into bug/JAL-2399textColour

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
JAL-2346 JAL-1933 test updated to include Occupancy

JAL-2346 always run setup!

JAL-2346 more test coverage for AnnotationColourGradient

Merge branch 'develop' into bug/JAL-2346annotationChoice

Conflicts:

src/jalview/gui/AnnotationRowFilter.java

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    /src/jalview/gui/AnnotationRowFilter.java
Merge branch 'develop' into bug/JAL-1608createGroups

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/gui/AlignFrame.java
JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes.ColourSchemes to jalview.schemes.ColourSchemeLoader

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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/schemes/ColourSchemeLoader.java
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    /src/jalview/schemes/ColourSchemes.java
Merge remote-tracking branch 'origin/develop' into bug/JAL-2314

JAL-2314 Tidy up

JAL-2314 Fixes to DisorderAnnotExportImport test

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

JAL-2388 unit test initialisation fix for running full suite

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-2314 Tweaks to stop thread sync issues

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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-2464 fix cancel tree print behaviour

JAL-2464 fix cancel tree print behaviour

JAL-2314 Tidies

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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-2314 Re-annotated unit tests using Jws2Discoverer

JAL-2461 Removed DAS error stack trace, updated message

JAL-2388 Reinstated original overview checks for annotation display

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    /src/jalview/appletgui/OverviewPanel.java