AlignViewport av;
+ AlignmentView seqstrings;
+
SequenceI[] seqs;
- AlignmentView seqstrings;
+
+ /**
+ * use the identity matrix for calculating similarity between sequences.
+ */
+ private boolean useidentity=false;
+
public PCAPanel(AlignViewport av)
{
this.av = av;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ useidentity=av.getAlignment().isNucleotide();
if (av.getSelectionGroup() == null)
{
seqs = av.getAlignment().getSequencesArray();
*/
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '));
+ pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
pca.run();
// Now find the component coordinates