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Merge branch 'develop' into features/JAL-2316

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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/APopupMenu.java
JAL-2401 tweaked button text, added Spanish

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    /resources/lang/Messages_es.properties
JAL-2401 change 'Lower Case Colour' to checkbox with tooltip

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    /src/jalview/gui/UserDefinedColours.java
JAL-2371 no test for lower case consensus as not expected or handled

JAL-2371 ensure some colour scheme (may be None) is set on startup

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    /src/jalview/gui/AlignViewport.java
JAL-2371 skip upper-casing consensus as it already is

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    /src/jalview/schemes/PIDColourScheme.java
JAL-2405 check for circular reference in SequenceGroup.context

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2405 set initial selection group alignment context

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    /test/jalview/gui/AlignViewportTest.java
JAL-2405 enable nucleotide/peptide colour schemes in applet menus

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
JAL-2316 tidying preferences help page

JAL-2316 tidied up documentation for Links tab

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    /help/html/features/preferences.html
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    /help/html/webServices/urllinks.html
JAL-2405 set context on selection group for tailored colour options

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    /src/jalview/appletgui/APopupMenu.java

changeset discussion

  1. Jim Procter: Mungo Carstairs suggest you check whether the context is already set for the selection group - if not, then set it to...
  2. Mungo Carstairs: done
JAL-2401 fix for NPE on selectedButtons, tweak for button appearance

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    /src/jalview/gui/UserDefinedColours.java
Merge remote-tracking branch 'origin/develop' into features/JAL-2316

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/APopupMenu.java
JAL-2366 updated default URL to www.jalview.org/services/identifiers

Merge branch 'features/JAL-2371collectionColourScheme' into develop

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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/jbgui/GUserDefinedColours.java
JAL-2401 Lower Case Colour toggleable, help text added

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    /src/jalview/gui/UserDefinedColours.java
JAL-2371 (slight!) simplification of isApplicableTo()

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    /src/jalview/schemes/ResidueColourScheme.java
JAL-2383 and Spanish!

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    /resources/lang/Messages_es.properties
JAL-2371 commented code removed only

JAL-2371 rename global/viewportColourScheme to residueShading

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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/TreeCanvas.java
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    /src/jalview/gui/SequenceRenderer.java
  1. … 6 more files in changeset.
JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some JAL-2371 tidying

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/SliderPanel.java
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    /src/jalview/gui/SliderPanel.java
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    /src/jalview/renderer/ResidueShader.java
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    /src/jalview/schemes/PIDColourScheme.java
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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/gui/AlignViewportTest.java
  1. … 5 more files in changeset.
JAL-2371 CollectionColourScheme renamed ResidueShader and moved to jalview.renderer

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/SliderPanel.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/gui/SequenceRenderer.java
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    /src/jalview/renderer/ResidueShader.java
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    /src/jalview/renderer/ResidueShaderI.java
  1. … 6 more files in changeset.
JAL-2099 belated unit test

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    /test/jalview/renderer/ScaleRendererTest.java
JAL-2360 JAL-2371 updates from review CR-JAL-1

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    /src/jalview/datamodel/SequenceGroup.java
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    /test/jalview/io/AnnotationFileIOTest.java
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    /test/jalview/util/ColorUtilsTest.java
JAL-2366 Removed unneeded setEnabled calls

JAL-2360 corrected comment

JAL-2360 C is Pink with consensus > 85% (not 100%)

Merge remote-tracking branch 'origin/develop' into features/JAL-2316

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    /src/jalview/appletgui/APopupMenu.java
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme

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    /src/jalview/gui/UserDefinedColours.java