+ 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
+ }\r
+\r
+ if (true)\r
+ {\r
+ // make a new frame!\r
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT\r
+ );\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ // msaorder);\r
+\r
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+ /* CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
+ seqs[i].getName()));\r
+ cap.appendText(" " + seqstrings[i] + "\n");\r
+\r
+ }\r
+\r
+ Desktop.addInternalFrame(cap, "Original Data",\r
+ 400, 400);\r
+ */\r
+ }\r
+\r
+ class PCAPrinter\r
+ extends Thread implements Printable\r
+ {\r
+ public void run()\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+\r
+ printJob.setPrintable(this, pf);\r
+\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r