public class PCAModel
{
+ /*
+ * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
+ * for pairwise scoring; 2.10.2 uses gap score (last column) in
+ * score matrix (JAL-2397)
+ * Set this flag to true (via Groovy) for 2.10.1 behaviour
+ */
+ private static boolean scoreGapAsAny = false;
public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
boolean nucleotide2)
public void run()
{
-
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+ char gapChar = scoreGapAsAny ? (nucleotide ? 'N' : 'X') : ' ';
+ String[] sequenceStrings = seqstrings.getSequenceStrings(gapChar);
+ pca = new PCA(sequenceStrings, nucleotide,
score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
ii++;
}
- double[][] comps = new double[ii][ii];
-
- for (int i = 0; i < ii; i++)
- {
- if (pca.getEigenvalue(i) > 1e-4)
- {
- comps[i] = pca.component(i);
- }
- }
-
- top = pca.getM().rows - 1;
+ int height = pca.getHeight();
+ // top = pca.getM().height() - 1;
+ top = height - 1;
points = new Vector<SequencePoint>();
float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
- for (int i = 0; i < pca.getM().rows; i++)
+ for (int i = 0; i < height; i++)
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
points.addElement(sp);
}
-
}
public void updateRc(RotatableCanvasI rc)
{
- rc.setPoints(points, pca.getM().rows);
+ rc.setPoints(points, pca.getHeight());
}
public boolean isNucleotide()
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
- for (int i = 0; i < pca.getM().rows; i++)
+ for (int i = 0; i < pca.getHeight(); i++)
{
- ((SequencePoint) points.elementAt(i)).coord = scores[i];
+ points.elementAt(i).coord = scores[i];
}
}