+ this.av = av;\r
+\r
+ if ((av.getSelectionGroup() != null) &&\r
+ (av.getSelectionGroup().getSize() > 3))\r
+ {\r
+ s = new Sequence[av.getSelectionGroup().getSize()];\r
+\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
+ s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ }\r
+ }\r
+\r
+ if (s == null)\r
+ {\r
+ s = new Sequence[av.getAlignment().getHeight()];\r
+\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ s[i] = av.getAlignment().getSequenceAt(i);\r
+ }\r
+ }\r
+\r
+ //////////////////////This part was done in PCATHread originally. Is it too slow???\r
+ pca = new PCA(s);\r
+ pca.run();\r
+\r
+ // Now find the component coordinates\r
+ int ii = 0;\r
+\r
+ while ((ii < s.length) && (s[ii] != null))\r
+ {\r
+ ii++;\r
+ }\r
+\r
+ double[][] comps = new double[ii][ii];\r
+\r
+ for (int i = 0; i < ii; i++)\r
+ {\r
+ if (pca.getEigenvalue(i) > 1e-4)\r
+ {\r
+ comps[i] = pca.component(i);\r
+ }\r
+ }\r
+\r
+ //////////////////\r
+ xCombobox.setSelectedIndex(0);\r
+ yCombobox.setSelectedIndex(1);\r
+ zCombobox.setSelectedIndex(2);\r
+\r
+ top = pca.getM().rows - 1;\r
+\r
+ Vector points = new Vector();\r
+ float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
+\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
+ {\r
+ SequencePoint sp = new SequencePoint(s[i], scores[i]);\r
+ points.addElement(sp);\r
+ }\r
+\r
+ rc = new RotatableCanvas(av, points, pca.getM().rows);\r
+\r
+ //rc.printPoints();\r
+ add(rc, BorderLayout.CENTER);\r