+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
-import jalview.analysis.PCA;\r
+\r
import jalview.jbgui.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import java.util.*;\r
+import javax.swing.*;\r
+import java.io.FileOutputStream;\r
+import org.jibble.epsgraphics.EpsGraphics2D;\r
+import javax.imageio.ImageIO;\r
+import java.awt.image.BufferedImage;\r
+import java.awt.print.*;\r
\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class PCAPanel extends GPCAPanel implements Runnable\r
{\r
- PCA pca;\r
- int top;\r
- RotatableCanvas rc;\r
- AlignViewport av;\r
-\r
- public void run()\r
- {\r
- // do stuff\r
- }\r
+ PCA pca;\r
+ int top;\r
+ RotatableCanvas rc;\r
+ AlignViewport av;\r
+ SequenceI [] seqs;\r
+\r
+ /**\r
+ * Creates a new PCAPanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ */\r
+ public PCAPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+\r
+ boolean sameLength = true;\r
+\r
+ if ((av.getSelectionGroup() != null) &&\r
+ (av.getSelectionGroup().getSize() > 3))\r
+ {\r
+ seqs = new Sequence[av.getSelectionGroup().getSize()];\r
+ int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
+ for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
+ {\r
+ seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ if(seqs[i].getLength()!=length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ seqs = new Sequence[av.getAlignment().getHeight()];\r
+ int length = av.alignment.getSequenceAt(0).getLength();\r
+\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ seqs[i] = av.getAlignment().getSequenceAt(i);\r
+ if(seqs[i].getLength()!=length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
+\r
+ }\r
+ }\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
+ 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
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ try{\r
+ pca = new PCA(seqs);\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.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(seqs[i], scores[i]);\r
+ points.addElement(sp);\r
+ }\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 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
- public PCAPanel(AlignViewport av, SequenceI[] s) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void yCombobox_actionPerformed(ActionEvent e)\r
+ {\r
+ doDimensionChange();\r
+ }\r
\r
- this.av = av;\r
- if(av.getSelection().size()>3)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void zCombobox_actionPerformed(ActionEvent e)\r
{\r
- s = new Sequence[av.getSelection().size()];\r
- for(int i=0; i<s.length; i++)\r
- s[i] = av.getSelection().sequenceAt(i);\r
+ doDimensionChange();\r
}\r
\r
\r
- if(s==null)\r
+ public void outputValues_actionPerformed(ActionEvent e)\r
{\r
- s = new Sequence[av.getAlignment().getHeight()];\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- s[i] = av.getAlignment().getSequenceAt(i);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap, "PCA details", 500,\r
+ 500);\r
+\r
+ cap.setText(pca.getDetails());\r
}\r
\r
-//////////////////////This part was done in PCATHread originally. Is it too slow???\r
- pca = new PCA(s);\r
- pca.run();\r
+ public void showLabels_actionPerformed(ActionEvent e)\r
+ {\r
+ rc.showLabels(showLabels.getState());\r
+ }\r
\r
- // Now find the component coordinates\r
- int ii=0;\r
- while (ii < s.length && s[ii] != null)\r
+ public void print_actionPerformed(ActionEvent e)\r
{\r
- ii++;\r
+ PCAPrinter printer = new PCAPrinter();\r
+ printer.start();\r
}\r
\r
- double[][] comps = new double[ii][ii];\r
\r
- for (int i=0; i < ii; i++ )\r
+ class PCAPrinter extends Thread implements Printable\r
{\r
- if (pca.getEigenvalue(i) > 1e-4)\r
+ public void run()\r
{\r
- comps[i] = pca.component(i);\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
\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
- xCombobox.setSelectedIndex(0);\r
- yCombobox.setSelectedIndex(1);\r
- zCombobox.setSelectedIndex(2);\r
+ if (pi == 0)\r
+ return Printable.PAGE_EXISTS;\r
+ else\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
+ }\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void eps_actionPerformed(ActionEvent e)\r
{\r
- SequencePoint sp = new SequencePoint(s[i],scores[i]);\r
- points.addElement(sp);\r
- }\r
+ boolean accurateText = true;\r
+\r
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
+ "Prompt each time");\r
\r
- rc = new RotatableCanvas(av,points,pca.getM().rows);\r
+ // If we need to prompt, and if the GUI is visible then\r
+ // Prompt for EPS rendering style\r
+ if (renderStyle.equalsIgnoreCase("Prompt each time")\r
+ && !\r
+ (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true")))\r
+ {\r
+ EPSOptions eps = new EPSOptions();\r
+ renderStyle = eps.getValue();\r
\r
- //rc.printPoints();\r
+ if (renderStyle == null || eps.cancelled)\r
+ return;\r
\r
- add(rc, BorderLayout.CENTER);\r
- }\r
+ }\r
+\r
+ if (renderStyle.equalsIgnoreCase("text"))\r
+ {\r
+ accurateText = false;\r
+ }\r
+\r
+ int width = rc.getWidth();\r
+ int height = rc.getHeight();\r
+\r
+ try\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create EPS file from PCA");\r
+ chooser.setToolTipText("Save");\r
\r
+ int value = chooser.showSaveDialog(this);\r
\r
- void doDimensionChange()\r
- {\r
- if(top==0)\r
- return;\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
\r
- int dim1 = top - xCombobox.getSelectedIndex();\r
- int dim2 = top - yCombobox.getSelectedIndex();\r
- int dim3 = top - zCombobox.getSelectedIndex();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- float[][] scores = pca.getComponents(dim1,dim2,dim3,100);\r
- for (int i=0; i < pca.getM().rows; i++) {\r
- ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,\r
+ height);\r
+\r
+ pg.setAccurateTextMode(accurateText);\r
+\r
+ rc.drawBackground(pg, rc.bgColour);\r
+ rc.drawScene(pg);\r
+\r
+ if (rc.drawAxes == true)\r
+ {\r
+ rc.drawAxes(pg);\r
+ }\r
+\r
+\r
+ pg.flush();\r
+ pg.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
- rc.img = null;\r
- rc.rotmat.setIdentity();\r
- rc.initAxes();\r
- rc.paint(rc.getGraphics());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void png_actionPerformed(ActionEvent e)\r
+ {\r
+ int width = rc.getWidth();\r
+ int height = rc.getHeight();\r
\r
- protected void xCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
+ try\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "Portable network graphics");\r
\r
- protected void yCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create PNG image from PCA");\r
+ chooser.setToolTipText("Save");\r
\r
- protected void zCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics big = bi.getGraphics();\r
+\r
+ big.drawImage(rc.img,0,0,this);\r
\r
-}\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ }\r
git://source.jalview.org / jalview.git / blobdiff