public class RNAHelicesColour extends ResidueColourScheme
{
-
/**
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
{
super(ResidueProperties.nucleotideIndex);
this.annotation = annotation;
+ ColourSchemeProperty.resetRnaHelicesShading();
refresh();
}
public RNAHelicesColour(AnnotatedCollectionI alignment)
{
super(ResidueProperties.nucleotideIndex);
+ ColourSchemeProperty.resetRnaHelicesShading();
alignmentChanged(alignment, null);
}
// This loop will find the first rna structure annotation by which to colour
// the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ if (annotations == null)
+ {
+ return;
+ }
for (int i = 0; i < annotations.length; i++)
{