*/
package jalview.schemes;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
+import jalview.api.analysis.PairwiseScoreModelI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
-import java.util.Map;
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()
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new Blosum62ColourScheme();
}
public Color findColour(char res, int j, SequenceI seq,
String consensusResidue, float pid)
{
+ PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
+
/*
* compare as upper case; note consensusResidue is
* always computed as uppercase
for (char consensus : consensusResidue.toCharArray())
{
- score += ResidueProperties.getBLOSUM62(consensus, res);
+ score += sm.getPairwiseScore(consensus, res);
}
if (score > 0)