+ rc.setPoints(points, pca.getM().rows);\r
+ rc.repaint();\r
+\r
+ addKeyListener(rc);\r
+\r
+ }\r
+ catch (OutOfMemoryError er)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calculating PCA!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("PCAPanel: " + er);\r
+ System.gc();\r
+\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void doDimensionChange()\r
+ {\r
+ if (top == 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int dim1 = top - xCombobox.getSelectedIndex();\r
+ int dim2 = top - yCombobox.getSelectedIndex();\r
+ int dim3 = top - zCombobox.getSelectedIndex();\r
+\r
+ float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);\r
+\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
+ {\r
+ ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
+ }\r
+\r
+ rc.img = null;\r
+ rc.rotmat.setIdentity();\r
+ rc.initAxes();\r
+ rc.paint(rc.getGraphics());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void xCombobox_actionPerformed(ActionEvent e)\r
+ {\r
+ doDimensionChange();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void yCombobox_actionPerformed(ActionEvent e)\r
+ {\r
+ doDimensionChange();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void zCombobox_actionPerformed(ActionEvent e)\r
+ {\r
+ doDimensionChange();\r
+ }\r
+\r
+ public void outputValues_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap, "PCA details", 500,\r
+ 500);\r
+\r
+ cap.setText(pca.getDetails());\r
+ }\r
+\r
+ public void showLabels_actionPerformed(ActionEvent e)\r
+ {\r
+ rc.showLabels(showLabels.getState());\r
+ }\r
+\r
+ public void print_actionPerformed(ActionEvent e)\r
+ {\r
+ PCAPrinter printer = new PCAPrinter();\r
+ printer.start();\r
+ }\r
+\r
+ public void originalSeqData_actionPerformed(ActionEvent e)\r
+ {\r
+ // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows\r
+ if (seqstrings == null)\r
+ {\r
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+ return;\r
+ }\r
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+ // or create a selection box around columns in alignment view\r
+ // test Alignment(SeqCigar[])\r
+ Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
+ getGapCharacter());\r
+\r
+ if (alAndColsel != null && alAndColsel[0] != null)\r
+ {\r
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
+\r
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+ Alignment dataset = av.getAlignment().getDataset();\r
+ if (dataset != null)\r
+ {\r
+ al.setDataset(dataset);\r