2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.jbgui.*;
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28 import java.awt.event.*;
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31 import javax.swing.*;
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32 import java.awt.print.*;
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39 * @version $Revision$
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41 public class PCAPanel extends GPCAPanel implements Runnable
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50 * Creates a new PCAPanel object.
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52 * @param av DOCUMENT ME!
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53 * @param s DOCUMENT ME!
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55 public PCAPanel(AlignViewport av)
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59 boolean sameLength = true;
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61 if ((av.getSelectionGroup() != null) &&
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62 (av.getSelectionGroup().getSize() > 3))
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64 seqs = new Sequence[av.getSelectionGroup().getSize()];
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65 int length = av.getSelectionGroup().getSequenceAt(0).getLength();
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66 for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
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68 seqs[i] = av.getSelectionGroup().getSequenceAt(i);
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69 if(seqs[i].getLength()!=length)
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78 seqs = new Sequence[av.getAlignment().getHeight()];
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79 int length = av.alignment.getSequenceAt(0).getLength();
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81 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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83 seqs[i] = av.getAlignment().getSequenceAt(i);
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84 if(seqs[i].getLength()!=length)
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95 JOptionPane.showMessageDialog(Desktop.desktop,
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96 "The sequences must be aligned before calculating PCA.\n" +
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97 "Try using the Pad function in the edit menu,\n" +
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98 "or one of the multiple sequence alignment web services.",
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99 "Sequences not aligned",
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100 JOptionPane.WARNING_MESSAGE);
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106 Desktop.addInternalFrame(this, "Principal component analysis",
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110 rc = new RotatableCanvas(av);
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111 this.getContentPane().add(rc, BorderLayout.CENTER);
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112 Thread worker = new Thread(this);
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116 public void bgcolour_actionPerformed(ActionEvent e)
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118 Color col = JColorChooser.showDialog(this, "Select Background Colour",
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135 pca = new PCA(seqs);
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138 // Now find the component coordinates
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141 while ( (ii < seqs.length) && (seqs[ii] != null))
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146 double[][] comps = new double[ii][ii];
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148 for (int i = 0; i < ii; i++)
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150 if (pca.getEigenvalue(i) > 1e-4)
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152 comps[i] = pca.component(i);
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157 xCombobox.setSelectedIndex(0);
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158 yCombobox.setSelectedIndex(1);
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159 zCombobox.setSelectedIndex(2);
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161 top = pca.getM().rows - 1;
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163 Vector points = new Vector();
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164 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
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166 for (int i = 0; i < pca.getM().rows; i++)
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168 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
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169 points.addElement(sp);
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172 rc.setPoints(points, pca.getM().rows);
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176 catch(OutOfMemoryError er)
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177 { JOptionPane.showInternalMessageDialog(Desktop.desktop,
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178 "Out of memory calculating PCA!!"
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180 "\nSee help files for increasing Java Virtual Machine memory."
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182 JOptionPane.WARNING_MESSAGE);
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183 System.out.println("PCAPanel: "+er);
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193 void doDimensionChange()
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200 int dim1 = top - xCombobox.getSelectedIndex();
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201 int dim2 = top - yCombobox.getSelectedIndex();
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202 int dim3 = top - zCombobox.getSelectedIndex();
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204 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
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206 for (int i = 0; i < pca.getM().rows; i++)
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208 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
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212 rc.rotmat.setIdentity();
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214 rc.paint(rc.getGraphics());
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220 * @param e DOCUMENT ME!
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222 protected void xCombobox_actionPerformed(ActionEvent e)
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224 doDimensionChange();
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230 * @param e DOCUMENT ME!
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232 protected void yCombobox_actionPerformed(ActionEvent e)
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234 doDimensionChange();
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240 * @param e DOCUMENT ME!
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242 protected void zCombobox_actionPerformed(ActionEvent e)
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244 doDimensionChange();
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248 public void outputValues_actionPerformed(ActionEvent e)
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250 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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251 Desktop.addInternalFrame(cap, "PCA details", 500,
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254 cap.setText(pca.getDetails());
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257 public void showLabels_actionPerformed(ActionEvent e)
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259 rc.showLabels(showLabels.getState());
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262 public void print_actionPerformed(ActionEvent e)
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264 PCAPrinter printer = new PCAPrinter();
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269 class PCAPrinter extends Thread implements Printable
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273 PrinterJob printJob = PrinterJob.getPrinterJob();
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274 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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276 printJob.setPrintable(this, pf);
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278 if (printJob.printDialog())
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284 catch (Exception PrintException)
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286 PrintException.printStackTrace();
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291 public int print(Graphics pg, PageFormat pf, int pi)
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292 throws PrinterException
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294 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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296 rc.drawBackground(pg, rc.bgColour);
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298 if (rc.drawAxes == true)
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304 return Printable.PAGE_EXISTS;
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306 return Printable.NO_SUCH_PAGE;
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315 * @param e DOCUMENT ME!
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317 public void eps_actionPerformed(ActionEvent e)
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319 makePCAImage(jalview.util.ImageMaker.EPS);
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325 * @param e DOCUMENT ME!
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327 public void png_actionPerformed(ActionEvent e)
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329 makePCAImage(jalview.util.ImageMaker.PNG);
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332 void makePCAImage(int type)
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334 int width = rc.getWidth();
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335 int height = rc.getHeight();
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337 jalview.util.ImageMaker im;
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339 if(type == jalview.util.ImageMaker.PNG)
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340 im = new jalview.util.ImageMaker(this,
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341 jalview.util.ImageMaker.PNG,
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342 "Make PNG image from PCA",
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346 im = new jalview.util.ImageMaker(this,
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347 jalview.util.ImageMaker.EPS,
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348 "Make EPS file from PCA",
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350 null, this.getTitle());
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352 if(im.getGraphics()!=null)
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354 rc.drawBackground(im.getGraphics(), Color.black);
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355 rc.drawScene(im.getGraphics());
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356 if (rc.drawAxes == true)
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358 rc.drawAxes(im.getGraphics());
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