public class Blosum62ColourScheme extends ResidueColourScheme
{
+ private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+ private static final Color DARK_BLUE = new Color(154, 154, 255);
+
public Blosum62ColourScheme()
{
super();
res -= ('a' - 'A');
}
- if (consensus == null || j >= consensus.length || consensus[j] == null
+ if (consensus == null || consensus.get(j) == null
|| (threshold != 0 && !aboveThreshold(res, j)))
{
return Color.white;
if (!Comparison.isGap(res))
{
- String max = consensus[j].getModalResidue();
+ /*
+ * test if this is the consensus (or joint consensus) residue
+ */
+ String max = consensus.get(j).getModalResidue();
if (max.indexOf(res) > -1)
{
- // TODO use a constant here?
- currentColour = new Color(154, 154, 255);
+ currentColour = DARK_BLUE;
}
else
{
if (c > 0)
{
- // TODO use a constant here?
- currentColour = new Color(204, 204, 255);
+ currentColour = LIGHT_BLUE;
}
else
{