jalview

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JAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a cleanup

fix for JAL-2419 - don’t trash the current selection

JAL-2374 don’t search twice for containing group to assign to stretchGroup

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    /src/jalview/appletgui/SeqPanel.java
JAL-2374 tests for SequenceGroup.contains

JAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’

JAL-2374 new contains methods for seq and seq,apos

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignment, not share the same dataset sequence

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    /src/jalview/datamodel/AlignmentI.java
JAL-2371 small move of code, typo correction

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    /src/jalview/renderer/ResidueShader.java
Merge branch 'features/JAL-2316' into develop

Merge branch 'develop' into features/JAL-2316

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    /resources/lang/Messages_es.properties
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    • +18
    /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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    • +16
    /src/jalview/datamodel/SequenceGroup.java
JAL-2405 set initial selection group alignment context

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    • +22
    /test/jalview/gui/AlignViewportTest.java
JAL-2405 enable nucleotide/peptide colour schemes in applet menus

    • -1
    • +18
    /src/jalview/appletgui/APopupMenu.java
    • -0
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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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    • +1
    /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.