jalview

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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
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 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-2464 fix cancel tree print behaviour

JAL-2388 Reinstated original overview checks for annotation display

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    /src/jalview/appletgui/OverviewPanel.java
Merge remote-tracking branch 'origin/bug/JAL-2436featureRendererThreading' into develop

Conflicts:

src/jalview/appletgui/OverviewPanel.java

src/jalview/gui/OverviewPanel.java

Merge remote-tracking branch 'origin/develop' into bug/JAL-2436featureRendererThreading

Conflicts:

src/jalview/appletgui/OverviewPanel.java

src/jalview/gui/OverviewPanel.java

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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/gui/OverviewPanel.java
JAL-2311 suppress autocalc'd annotation to isolate the 'real' failure

JAL-2307 Fixed SiftsClient unit test

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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-2306 assert no DAS sources

JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures

JAL-2243 update discovered features on opening structure in Chimera

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    /src/jalview/gui/ChimeraViewFrame.java
JAL-2438 check for null FeatureRenderer

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
Merge branch 'features/JAL-2388OverviewWindow' into develop

Merge branch 'bug/JAL-2421overviewboxflicker' into develop

JAL-2388 Comment typo

JAL-2388 ViewportRanges unit test

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    /test/jalview/viewmodel/ViewportRangesTest.java
JAL-2437 Synchronization corrections and unit tests

JAL-2388 Renamed column and row subtraction functions

Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop

JAL-1933 refactor parameter for code clarity

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    /src/jalview/analysis/AAFrequency.java
JAL-2388 Applied ViewportRanges to code

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/IdCanvas.java
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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/appletgui/SeqPanel.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
  1. … 12 more files in changeset.
JAL-2388 Renamed viewport position props to viewport ranges

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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/viewmodel/ViewportRanges.java
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    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2388 Unit test update

JAL-2388 Applet update for overview panel

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    /src/jalview/appletgui/OverviewPanel.java
JAL-2439 Out-by-one in setting endRes/endSeq

JAL-2388 Unit tests and tidies

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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/gui/OverviewPanel.java
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    /test/jalview/viewmodel/OverviewDimensionsTest.java