*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
getColourScheme(), aboveAnnotationThreshold);
if (annotation.isRNA())
{
// reset colour palette
- ColourSchemeProperty.resetRnaHelicesShading();
- ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ ColourSchemes.resetRnaHelicesShading();
+ ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
}
}
}
if (rna)
{
- ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
}
}
}
if (annotationThreshold != null)
{
if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
- && aj.value < annotationThreshold.value)
+ && aj.value <= annotationThreshold.value)
|| (aboveAnnotationThreshold == BELOW_THRESHOLD
- && aj.value > annotationThreshold.value))
+ && aj.value >= annotationThreshold.value))
{
return Color.white;
}
{
if (ann.isRNA())
{
- result = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ result = ColourSchemes.getInstance().rnaHelices[(int) aj.value];
}
else
{
@Override
public String getSchemeName()
{
- return "Annotation";
+ return ANNOTATION_COLOUR;
}
@Override