- pca = new PCA(seqstrings.getSequenceStrings(' '));\r
- pca.run();\r
-\r
- // Now find the component coordinates\r
- int ii = 0;\r
-\r
- while ((ii < seqs.length) && (seqs[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.select(0);\r
- yCombobox.select(1);\r
- zCombobox.select(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(seqs[i], scores[i]);\r
- points.addElement(sp);\r
- }\r
-\r
- rc.setPoints(points, pca.getM().rows);\r
- rc.repaint();\r
- seqs = null;\r
- this.repaint();\r
+ pca = new PCA(seqstrings.getSequenceStrings(' '));\r
+ pca.run();\r
+\r
+ // Now find the component coordinates\r
+ int ii = 0;\r
+\r
+ while ( (ii < seqs.length) && (seqs[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.select(0);\r
+ yCombobox.select(1);\r
+ zCombobox.select(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(seqs[i], scores[i]);\r
+ points.addElement(sp);\r
+ }\r
+\r
+ rc.setPoints(points, pca.getM().rows);\r
+ rc.repaint();\r
+ seqs = null;\r
+ this.repaint();\r