*/
package jalview.schemes;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.PairwiseScoreModelI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public Color findColour(char res, int j, SequenceI seq,
String consensusResidue, float pid)
{
+ PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
+
/*
- * compare as upper case; note toUpperCase does nothing
- * if the string is already uppercase
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
*/
- consensusResidue = consensusResidue.toUpperCase();
if ('a' <= res && res <= 'z')
{
res -= ('a' - 'A');
}
else
{
- int c = 0;
+ float score = 0;
for (char consensus : consensusResidue.toCharArray())
{
- c += ResidueProperties.getBLOSUM62(consensus, res);
+ score += sm.getPairwiseScore(consensus, res);
}
- if (c > 0)
+ if (score > 0)
{
colour = LIGHT_BLUE;
}