*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
+import java.util.Map;
public class PIDColourScheme extends ResidueColourScheme
{
c -= ('a' - 'A');
}
- if (consensus == null || j >= consensus.length || consensus[j] == null)
+ if (consensus == null || consensus.get(j) == null)
{
return Color.white;
}
double sc = 0;
- if (consensus.length <= j)
- {
- return Color.white;
- }
- if (consensus[j].getMaxCount() > 0) //!= -1)
- //&& consensus[j].contains(String.valueOf(c)))
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ ProfileI profile = consensus.get(j);
+ boolean matchesConsensus = profile.getModalResidue().contains(
+ String.valueOf(c));
+ if (matchesConsensus)
{
- sc = consensus[j].getPercentageIdentity(ignoreGaps);
+ sc = profile.getPercentageIdentity(ignoreGaps);
- if (!jalview.util.Comparison.isGap(c))
+ if (!Comparison.isGap(c))
{
for (int i = 0; i < thresholds.length; i++)
{
if (sc > thresholds[i])
{
currentColour = pidColours[i];
-
break;
}
}
return currentColour;
}
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PID.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new PIDColourScheme();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}