{
public static final String NONE = "None";
+ /*
+ * lookup up by character value e.g. 'G' to the colors array index
+ * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
+ */
final int[] symbolIndex;
boolean conservationColouring = false;
+ /*
+ * colour for residue characters as indexed by symbolIndex
+ */
Color[] colors = null;
int threshold = 0;