/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import java.util.Hashtable;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
/**
* Looks at the information computed from an RNA Stockholm format file on the
*/
public RNAHelicesColour(AlignmentAnnotation annotation)
{
+ super(ResidueProperties.nucleotideIndex);
this.annotation = annotation;
refresh();
}
public void refresh()
{
- if (lastrefresh != annotation._rnasecstr.hashCode() && annotation.isValidStruc())
+ if (lastrefresh != annotation._rnasecstr.hashCode()
+ && annotation.isValidStruc())
{
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
*
* @return color in RGB
*/
+ @Override
public Color findColour(char c)
{
return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
*
* @return Color in RGB
*/
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
refresh();
Color currentColour = Color.white;