/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.viewmodel;
-import java.util.Vector;
-
import jalview.analysis.PCA;
+import jalview.api.RotatableCanvasI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
public class PCAModel
{
public void run()
{
-
pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
score_matrix);
pca.setJvCalcMode(jvCalcMode);
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;
+ top = pca.getM().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 < pca.getM().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.getM().height());
}
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.getM().height(); i++)
{
- ((SequencePoint) points.elementAt(i)).coord = scores[i];
+ points.elementAt(i).coord = scores[i];
}
}