/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
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();
+ }
+
+ private long lastrefresh = -1;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < this.annotation._rnasecstr.length; x++)
+ public void refresh()
+ {
+ if (lastrefresh != annotation._rnasecstr.hashCode()
+ && annotation.isValidStruc())
{
+ annotation.getRNAStruc();
+ lastrefresh = annotation._rnasecstr.hashCode();
+ numHelix = 0;
+ positionsToHelix = new Hashtable();
+
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < this.annotation._rnasecstr.length; x++)
+ {
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
- this.annotation._rnasecstr[x].getFeatureGroup());
- positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
- this.annotation._rnasecstr[x].getFeatureGroup());
+ positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
+ this.annotation._rnasecstr[x].getFeatureGroup());
+ positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
+ this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
- {
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
- }
+ if (Integer.parseInt(this.annotation._rnasecstr[x]
+ .getFeatureGroup()) > numHelix)
+ {
+ numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
+ .getFeatureGroup());
+ }
- }
+ }
- // Generate random colors and store
- for (int j = 0; j <= numHelix; j++)
- {
- helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils
- .generateRandomColor(Color.white));
+ // Generate random colors and store
+ for (int j = 0; j <= numHelix; j++)
+ {
+ if (!helixcolorhash.containsKey(Integer.toString(j)))
+ {
+ helixcolorhash.put(Integer.toString(j),
+ jalview.util.ColorUtils.generateRandomColor(Color.white));
+ }
+ }
}
-
}
/**
*
* @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;
String currentHelix = null;
currentHelix = (String) positionsToHelix.get(j);