package jalview.analysis;
import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.BinarySequence;
import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
import jalview.math.Matrix;
-import jalview.schemes.ResidueProperties;
import java.io.PrintStream;
String sm = s_m;
if (sm != null)
{
- smtrx = ResidueProperties.getScoreMatrix(sm);
+ smtrx = (ScoreMatrix) ScoreModels.getInstance().forName(sm);
}
if (smtrx == null)
{
// either we were given a non-existent score matrix or a scoremodel that
// isn't based on a pairwise symbol score matrix
- smtrx = ResidueProperties.getScoreMatrix(sm = (nucleotides ? "DNA"
- : "BLOSUM62"));
+ smtrx = (ScoreMatrix) ScoreModels.getInstance().forName(
+ sm = (nucleotides ? "DNA" : "BLOSUM62"));
}
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");