*/
package jalview.schemes;
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.PairwiseScoreModelI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
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()
public Color findColour(char res, int j, SequenceI seq,
String consensusResidue, float pid)
{
- PairwiseSeqScoreModel sm = ScoreModels.getInstance().getBlosum62();
+ PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
/*
* compare as upper case; note consensusResidue is
for (char consensus : consensusResidue.toCharArray())
{
score += sm.getPairwiseScore(consensus, res);
- // score += ResidueProperties.getBLOSUM62(consensus, res);
}
if (score > 0)