import java.awt.event.*;\r
\r
import java.util.*;\r
-import javax.swing.JOptionPane;\r
+import javax.swing.*;\r
+import java.awt.print.*;\r
\r
\r
/**\r
int top;\r
RotatableCanvas rc;\r
AlignViewport av;\r
- SequenceI [] seqs;\r
+ String [] seqstrings;\r
+ SequenceI [] seqs;\r
\r
/**\r
* Creates a new PCAPanel object.\r
* @param av DOCUMENT ME!\r
* @param s DOCUMENT ME!\r
*/\r
- public PCAPanel(AlignViewport av, SequenceI[] s)\r
+ public PCAPanel(AlignViewport av)\r
{\r
this.av = av;\r
\r
- if ((av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
- {\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
+ boolean sameLength = true;\r
+\r
+ seqstrings = av.getSelectionAsString();\r
\r
- for (int i = 0; i < s.length; i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
+ if (av.getSelectionGroup() == null)\r
+ {\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
}\r
\r
- if (s == null)\r
+ int length = seqs[0].getLength();\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
{\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
+ if (seqs[i].getLength() != length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
+ }\r
\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
+ if (!sameLength)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The sequences must be aligned before calculating PCA.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
}\r
\r
\r
+ Desktop.addInternalFrame(this, "Principal component analysis",\r
+ 400, 400);\r
+\r
+\r
rc = new RotatableCanvas(av);\r
- add(rc, BorderLayout.CENTER);\r
+ this.getContentPane().add(rc, BorderLayout.CENTER);\r
Thread worker = new Thread(this);\r
worker.start();\r
}\r
\r
+ public void bgcolour_actionPerformed(ActionEvent e)\r
+ {\r
+ Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
+ rc.bgColour);\r
+\r
+ if(col!=null)\r
+ rc.bgColour = col;\r
+ rc.repaint();\r
+ }\r
+\r
+\r
\r
\r
/**\r
public void run()\r
{\r
try{\r
- pca = new PCA(seqs);\r
+ pca = new PCA(seqstrings);\r
pca.run();\r
\r
// Now find the component coordinates\r
\r
rc.setPoints(points, pca.getM().rows);\r
rc.repaint();\r
- seqs = null;\r
}\r
catch(OutOfMemoryError er)\r
{ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
, "Out of memory",\r
JOptionPane.WARNING_MESSAGE);\r
System.out.println("PCAPanel: "+er);\r
+ System.gc();\r
\r
}\r
\r
{\r
doDimensionChange();\r
}\r
-}\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
+ 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
+\r
+\r
+ class PCAPrinter 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
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
+ {\r
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
+\r
+ rc.drawBackground(pg, rc.bgColour);\r
+ rc.drawScene(pg);\r
+ if (rc.drawAxes == true)\r
+ {\r
+ rc.drawAxes(pg);\r
+ }\r
+\r
+ if (pi == 0)\r
+ return Printable.PAGE_EXISTS;\r
+ else\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void eps_actionPerformed(ActionEvent e)\r
+ {\r
+ makePCAImage(jalview.util.ImageMaker.EPS);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void png_actionPerformed(ActionEvent e)\r
+ {\r
+ makePCAImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePCAImage(int type)\r
+ {\r
+ int width = rc.getWidth();\r
+ int height = rc.getHeight();\r
+\r
+ jalview.util.ImageMaker im;\r
+\r
+ if(type == jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from PCA",\r
+ width, height,\r
+ null, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from PCA",\r
+ width, height,\r
+ null, this.getTitle());\r
+\r
+ if(im.getGraphics()!=null)\r
+ {\r
+ rc.drawBackground(im.getGraphics(), Color.black);\r
+ rc.drawScene(im.getGraphics());\r
+ if (rc.drawAxes == true)\r
+ {\r
+ rc.drawAxes(im.getGraphics());\r
+ }\r
+ im.writeImage();\r
+ }\r
+ }\r
+ }\r
git://source.jalview.org / jalview.git / blobdiff