- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
+ {
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ if (annotation.isRNA())
+ {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ }
+ else
+ {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+ : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ }
+ else
+ {
+ //
+ return Color.white;
+ }