jalview

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JAL-1933 JAL-2501 i18n for all auto calculated descriptions

JAL-1933 show occupancy in tooltip for row

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    /src/jalview/analysis/AAFrequency.java
JAL-2432 honour percentage checkbox when entering values in text box

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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationRowFilter.java
JAL-2432 applet: only enable percent checkbox when threshold is active

JAL-2432 percentage checkbox follows threshold value field

JAL-2432 recover state for ‘display percentage’ checkbox

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    /src/jalview/gui/AnnotationColumnChooser.java
JAL-2432 simplify code

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    /src/jalview/gui/AnnotationColumnChooser.java
JAL-1933 Spanish for Occupancy

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    /resources/lang/Messages_es.properties
Merge branch 'bug/JAL-2424getVisibleContigs' into develop

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