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  1. Jalview
  2. JAL-2952

Exceptions raised when shading sequences with negative values from 3D structure annotation

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.4
    • Component/s: analysis, renderer, Structures
    • Labels:
      None
    • Environment:
      Java version: 1.8.0_144
      x86_64 Mac OS X 10.10.5

      Description

      Originally noticed with attached PDB file (generated with CONSURF).
      1. Ensure 'Add temperature factor' is enabled and load attached pdb file
      2. Select Colour->By Annotation, and temperature factor.
      3. change the min-colour for the colour gradient to white.
      4. Attempt to hit OK.

      Exception raised is:
      Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Color parameter outside of expected range: Green Blue
      at java.awt.Color.testColorValueRange(Color.java:310)
      at java.awt.Color.<init>(Color.java:395)
      at java.awt.Color.<init>(Color.java:369)
      at jalview.schemes.AnnotationColourGradient.shadeCalculation(AnnotationColourGradient.java:442)
      at jalview.schemes.AnnotationColourGradient.findColour(AnnotationColourGradient.java:390)
      at jalview.schemes.ResidueColourScheme.findColour(ResidueColourScheme.java:120)
      at jalview.renderer.ResidueShader.findColour(ResidueShader.java:251)
      at jalview.renderer.ResidueColourFinder.getBoxColour(ResidueColourFinder.java:151)
      at jalview.gui.SequenceRenderer.drawBoxes(SequenceRenderer.java:197)
      at jalview.gui.SequenceRenderer.drawSequence(SequenceRenderer.java:132)
      at jalview.gui.SeqCanvas.draw(SeqCanvas.java:1114)
      at jalview.gui.SeqCanvas.drawPanel(SeqCanvas.java:1030)
      at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:412)

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            Assignee:
            gmungoc Mungo Carstairs
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated:
              Resolved: