/*\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
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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.datamodel.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbgui.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
+import java.awt.print.*;\r
+import javax.swing.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
\r
-public class PCAPanel extends GPCAPanel implements Runnable\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class PCAPanel\r
+ extends GPCAPanel implements Runnable\r
{\r
PCA pca;\r
int top;\r
RotatableCanvas rc;\r
+ AlignmentPanel ap;\r
AlignViewport av;\r
+ AlignmentView seqstrings;\r
+ SequenceI[] seqs;\r
\r
- public void run()\r
+ /**\r
+ * Creates a new PCAPanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ */\r
+ public PCAPanel(AlignmentPanel ap)\r
{\r
- // do stuff\r
- }\r
+ this.av = ap.av;\r
+ this.ap = ap;\r
\r
- public PCAPanel(AlignViewport av, SequenceI[] s) {\r
+ boolean sameLength = true;\r
\r
- this.av = av;\r
- if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3)\r
+ seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);\r
+ if (av.getSelectionGroup() == null)\r
+ {\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
{\r
- s = new Sequence[av.getSelectionGroup().getSize()];\r
- for(int i=0; i<s.length; i++)\r
- s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
}\r
+ SeqCigar sq[] = seqstrings.getSequences();\r
+ int length = sq[0].getWidth();\r
\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (sq[i].getWidth() != length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
+ }\r
\r
- if(s==null)\r
+ if (!sameLength)\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
- }\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
+ Desktop.addInternalFrame(this, "Principal component analysis",\r
+ 400, 400);\r
\r
-//////////////////////This part was done in PCATHread originally. Is it too slow???\r
- pca = new PCA(s);\r
- pca.run();\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
\r
- // Now find the component coordinates\r
- int ii=0;\r
- while (ii < s.length && s[ii] != null)\r
+ rc = new RotatableCanvas(ap);\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
{\r
- ii++;\r
+ rc.bgColour = col;\r
}\r
+ rc.repaint();\r
+ }\r
\r
- double[][] comps = new double[ii][ii];\r
-\r
- for (int i=0; i < ii; i++ )\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ try\r
{\r
- if (pca.getEigenvalue(i) > 1e-4)\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
- comps[i] = pca.component(i);\r
+ ii++;\r
}\r
- }\r
\r
- //////////////////\r
+ double[][] comps = new double[ii][ii];\r
\r
- xCombobox.setSelectedIndex(0);\r
- yCombobox.setSelectedIndex(1);\r
- zCombobox.setSelectedIndex(2);\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
- top = pca.getM().rows-1;\r
+ //////////////////\r
+ xCombobox.setSelectedIndex(0);\r
+ yCombobox.setSelectedIndex(1);\r
+ zCombobox.setSelectedIndex(2);\r
\r
- Vector points = new Vector();\r
- float[][] scores = pca.getComponents(top-1,top-2,top-3,100);\r
+ top = pca.getM().rows - 1;\r
\r
- for (int i =0; i < pca.getM().rows; i++ )\r
- {\r
- SequencePoint sp = new SequencePoint(s[i],scores[i]);\r
- points.addElement(sp);\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 = new RotatableCanvas(av,points,pca.getM().rows);\r
+ rc.setPoints(points, pca.getM().rows);\r
+ rc.repaint();\r
\r
- //rc.printPoints();\r
+ addKeyListener(rc);\r
\r
- add(rc, BorderLayout.CENTER);\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
+ 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
- for (int i=0; i < pca.getM().rows; i++) {\r
- ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];\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.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
+ {\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
+ {\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\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
+ {\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
+ }\r
+ else\r
+ {\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
+\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
+ public void viewMenu_menuSelected()\r
+ {\r
+ buildAssociatedViewMenu();\r
+ }\r
+\r
+ void buildAssociatedViewMenu()\r
+ {\r
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.\r
+ getSequenceSetId());\r
+ if (aps.length == 1 && rc.av == aps[0].av)\r
+ {\r
+ associateViewsMenu.setVisible(false);\r
+ return;\r
+ }\r
+\r
+ associateViewsMenu.setVisible(true);\r
+\r
+ if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))\r
+ {\r
+ viewMenu.insertSeparator(viewMenu.getItemCount() - 1);\r
+ }\r
+\r
+ associateViewsMenu.removeAll();\r
+\r
+ JRadioButtonMenuItem item;\r
+ ButtonGroup buttonGroup = new ButtonGroup();\r
+ int i, iSize = aps.length;\r
+ final PCAPanel thisPCAPanel = this;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ final AlignmentPanel ap = aps[i];\r
+ item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);\r
+ buttonGroup.add(item);\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ rc.applyToAllViews = false;\r
+ rc.av = ap.av;\r
+ rc.ap = ap;\r
+ PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());\r
+ }\r
+ });\r
+\r
+ associateViewsMenu.add(item);\r
+ }\r
+\r
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");\r
+\r
+ buttonGroup.add(itemf);\r
+\r
+ itemf.setSelected(rc.applyToAllViews);\r
+ itemf.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ rc.applyToAllViews = itemf.isSelected();\r
+ }\r
+ });\r
+ associateViewsMenu.add(itemf);\r
+\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff