this.annotation = annotation;
refresh();
}
+
public RNAHelicesColour(AnnotatedCollectionI alignment)
{
super(ResidueProperties.nucleotideIndex);
{
// This loop will find the first rna structure annotation by which to colour
- // the sequences.
+ // the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
- for (int i = 0; i < annotations.length; i++) {
-
- // is this a sensible way of determining type of annotation?
- if (annotations[i].getRNAStruc() != null) {
- annotation = annotations[i];
- break;
- }
+ for (int i = 0; i < annotations.length; i++)
+ {
+
+ // is this a sensible way of determining type of annotation?
+ if (annotations[i].getRNAStruc() != null)
+ {
+ annotation = annotations[i];
+ break;
+ }
}
refresh();
}
+
private long lastrefresh = -1;
public void refresh()
{
-
- if (annotation!=null && ((annotation._rnasecstr == null
- || lastrefresh != annotation._rnasecstr.hashCode())
- && annotation.isValidStruc()))
+
+ if (annotation != null
+ && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
+ .hashCode()) && annotation.isValidStruc()))
{
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();