*/
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 (ann.isRNA())
{
- result = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ result = ColourSchemes.getInstance().rnaHelices[(int) aj.value];
}
else
{