*/
public PCA(String[] s, boolean nucleotides)
{
+ this(s, nucleotides, null);
+ }
+ public PCA(String[] s, boolean nucleotides, String s_m)
+ {
BinarySequence[] bs = new BinarySequence[s.length];
int ii = 0;
BinarySequence[] bs2 = new BinarySequence[s.length];
ii = 0;
-
- String sm = nucleotides ? "DNA" : "BLOSUM62";
- ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm);
+ ScoreMatrix smtrx = null;
+ String sm=s_m;
+ if (sm!=null)
+ {
+ smtrx = ResidueProperties.getScoreMatrix(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"));
+ }
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");
while ((ii < s.length) && (s[ii] != null))