*/
package jalview.schemes;
-import jalview.datamodel.ProfileI;
+import jalview.datamodel.AnnotatedCollectionI;
+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
{
}
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
{
+ /*
+ * make everything uppercase; note this does nothing (fast)
+ * if consensusResidue is already uppercase
+ */
+ consensusResidue = consensusResidue.toUpperCase();
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
- if (consensus == null || consensus.get(j) == null)
- {
- return Color.white;
- }
-
- if ((threshold != 0) && !aboveThreshold(c, j))
+ if (consensusResidue == null)
{
return Color.white;
}
- Color currentColour = Color.white;
-
- double sc = 0;
-
+ Color colour = Color.white;
/*
* test whether this is the consensus (or joint consensus) residue
*/
- ProfileI profile = consensus.get(j);
- boolean matchesConsensus = profile.getModalResidue().contains(
+ boolean matchesConsensus = consensusResidue.contains(
String.valueOf(c));
if (matchesConsensus)
{
- sc = profile.getPercentageIdentity(ignoreGaps);
-
if (!Comparison.isGap(c))
{
for (int i = 0; i < thresholds.length; i++)
{
- if (sc > thresholds[i])
+ if (pid > thresholds[i])
{
- currentColour = pidColours[i];
+ colour = pidColours[i];
break;
}
}
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
@Override
{
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;
+ }
}