- helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils
- .generateRandomColor(Color.white));
- }
+ 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());
+
+ 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());
+ }