* @return DOCUMENT ME!
*/
@Override
- public Color findColour(char c, int j, SequenceI seq) {
+ public Color findColourSeq(char c, int j, SequenceI seq) {
Color currentColour = Color.white;
AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
.get(seq) : this.annotation);
if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
&& aj.secondaryStructure != '-') {
if (colourScheme != null) {
- currentColour = colourScheme.findColour(c, j, seq);
+ currentColour = colourScheme.findColourSeq(c, j, seq);
} else {
if (annotation.isRNA()) {
currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
}
} else if (noGradient) {
if (colourScheme != null) {
- currentColour = colourScheme.findColour(c, j, seq);
+ currentColour = colourScheme.findColourSeq(c, j, seq);
} else {
if (aj.colour != null) {
currentColour = aj.colour;