import jalview.io.SequenceAnnotationReport;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueColourScheme;
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
- ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
if (sg.cs != null && sg.cs.conservationApplied())
{
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup()
.getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
-
sg.cs.setConservation(c);
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
SliderPanel.showConservationSlider();
}
else
AnnotationColourGradient.NO_THRESHOLD);
acg.setPredefinedColours(true);
- sg.cs = acg;
+ sg.setColourScheme(acg);
refresh();
}
/*
* switch to the chosen colour scheme (or null for None)
*/
- sg.cs = ColourSchemes.getInstance().getColourScheme(colourSchemeName,
- sg, ap.av.getHiddenRepSequences());
- if (sg.cs instanceof Blosum62ColourScheme
- || sg.cs instanceof PIDColourScheme)
+ ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
+ colourSchemeName, sg, ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),