- if (view.getAnnotationColours().getColourScheme().equals(
- "None"))
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours().
- getMinColour()),
- new java.awt.Color(view.getAnnotationColours().
- getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme().
- startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view.getAnnotationColours().
- getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
- else
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
- view.getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
-
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg
- = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
-
- if(sg.cs == null)
- continue;
-
-
- /* if (view.getAnnotationColours().getColourScheme().equals("None"))
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours().
- getMinColour()),
- new java.awt.Color(view.getAnnotationColours().
- getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else*/
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs,
- view.getAnnotationColours().getAboveThreshold()
- );
- }