jalview

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JAL-2447 EXPERIMENTAL preference (option in Tools menu)

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    /src/jalview/gui/ChimeraViewFrame.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2482 bug fix

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2482 unit test for bug fix

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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-2489 JAL-2371 reinstate calls to ColourSchemeProperty.getColourName() to handle null case

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    /examples/testdata/example_annot_file.jva
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    /src/jalview/io/AnnotationFile.java
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    /test/jalview/io/AnnotationFileIOTest.java
Merge remote-tracking branch 'origin/bug/JAL-2479unitteststoNetworkGroup' into develop

Merge branch 'features/JAL-1933_occupancy' into develop

JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default (allows jalview.gui.AnnotationChooserTest to pass)

JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default

Merge branch 'features/JAL-1933_occupancy' into develop

JAL-1933 don't show occupancy row when testing conservation thread runs even when only quality calculation is enabled in preferences (JAL-1306)

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    /test/jalview/gui/AlignViewportTest.java
Merge branch 'features/JAL-1933_occupancy' into develop

JAL-1933 applet doc for showOccupancy parameter

JAL-1933 desktop documentation for show occupancy preference

JAL-1933 use constant for preference token

Merge branch 'features/JAL-1933_occupancy' into develop

JAL-1933 consensus calculation doesn’t depend on occupancy row being materialised

JAL-1933 desktop preferences for occupancy

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    /src/jalview/jbgui/GPreferences.java
JAL-1933 action and label for occupancy

JAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting

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    /test/jalview/gui/AlignViewportTest.java
JAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY .jalview_properties setting

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    /src/jalview/appletgui/AlignViewport.java
JAL-1933 only create and add occupancy row to alignment view if showOccupancy viewport attribute is set

JAL-2494 fix: updated behaviour for SequenceGroup.findAnnotations

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2494 fixed behaviour for null parameters in line with test

JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations

JAL-2494 test to cover AnnotatedCollectionI.findAnnotations

Merge branch 'features/JAL-1933_occupancy' into develop

JAL-2432 desktop: filter/select columns by threshold as a percentage

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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationRowFilter.java
JAL-1933 JAL-2432 code tidy

JAL-2432 left justify value shown after adjusting threshold slider