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.io.FileOutputStream;
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33 import org.jibble.epsgraphics.EpsGraphics2D;
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34 import javax.imageio.ImageIO;
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35 import java.awt.image.BufferedImage;
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36 import java.awt.print.*;
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43 * @version $Revision$
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45 public class PCAPanel extends GPCAPanel implements Runnable
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54 * Creates a new PCAPanel object.
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56 * @param av DOCUMENT ME!
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57 * @param s DOCUMENT ME!
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59 public PCAPanel(AlignViewport av)
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63 boolean sameLength = true;
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65 if ((av.getSelectionGroup() != null) &&
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66 (av.getSelectionGroup().getSize() > 3))
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68 seqs = new Sequence[av.getSelectionGroup().getSize()];
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69 int length = av.getSelectionGroup().getSequenceAt(0).getLength();
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70 for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
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72 seqs[i] = av.getSelectionGroup().getSequenceAt(i);
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73 if(seqs[i].getLength()!=length)
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82 seqs = new Sequence[av.getAlignment().getHeight()];
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83 int length = av.alignment.getSequenceAt(0).getLength();
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85 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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87 seqs[i] = av.getAlignment().getSequenceAt(i);
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88 if(seqs[i].getLength()!=length)
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99 JOptionPane.showMessageDialog(Desktop.desktop,
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100 "The sequences must be aligned before calculating PCA.\n" +
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101 "Try using the Pad function in the edit menu,\n" +
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102 "or one of the multiple sequence alignment web services.",
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103 "Sequences not aligned",
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104 JOptionPane.WARNING_MESSAGE);
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110 Desktop.addInternalFrame(this, "Principal component analysis",
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114 rc = new RotatableCanvas(av);
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115 this.getContentPane().add(rc, BorderLayout.CENTER);
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116 Thread worker = new Thread(this);
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120 public void bgcolour_actionPerformed(ActionEvent e)
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122 Color col = JColorChooser.showDialog(this, "Select Background Colour",
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139 pca = new PCA(seqs);
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142 // Now find the component coordinates
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145 while ( (ii < seqs.length) && (seqs[ii] != null))
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150 double[][] comps = new double[ii][ii];
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152 for (int i = 0; i < ii; i++)
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154 if (pca.getEigenvalue(i) > 1e-4)
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156 comps[i] = pca.component(i);
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161 xCombobox.setSelectedIndex(0);
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162 yCombobox.setSelectedIndex(1);
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163 zCombobox.setSelectedIndex(2);
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165 top = pca.getM().rows - 1;
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167 Vector points = new Vector();
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168 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
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170 for (int i = 0; i < pca.getM().rows; i++)
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172 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
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173 points.addElement(sp);
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176 rc.setPoints(points, pca.getM().rows);
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180 catch(OutOfMemoryError er)
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181 { JOptionPane.showInternalMessageDialog(Desktop.desktop,
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182 "Out of memory calculating PCA!!"
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184 "\nSee help files for increasing Java Virtual Machine memory."
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186 JOptionPane.WARNING_MESSAGE);
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187 System.out.println("PCAPanel: "+er);
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197 void doDimensionChange()
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204 int dim1 = top - xCombobox.getSelectedIndex();
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205 int dim2 = top - yCombobox.getSelectedIndex();
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206 int dim3 = top - zCombobox.getSelectedIndex();
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208 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
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210 for (int i = 0; i < pca.getM().rows; i++)
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212 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
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216 rc.rotmat.setIdentity();
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218 rc.paint(rc.getGraphics());
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224 * @param e DOCUMENT ME!
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226 protected void xCombobox_actionPerformed(ActionEvent e)
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228 doDimensionChange();
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234 * @param e DOCUMENT ME!
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236 protected void yCombobox_actionPerformed(ActionEvent e)
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238 doDimensionChange();
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244 * @param e DOCUMENT ME!
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246 protected void zCombobox_actionPerformed(ActionEvent e)
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248 doDimensionChange();
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252 public void outputValues_actionPerformed(ActionEvent e)
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254 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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255 Desktop.addInternalFrame(cap, "PCA details", 500,
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258 cap.setText(pca.getDetails());
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261 public void showLabels_actionPerformed(ActionEvent e)
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263 rc.showLabels(showLabels.getState());
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266 public void print_actionPerformed(ActionEvent e)
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268 PCAPrinter printer = new PCAPrinter();
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273 class PCAPrinter extends Thread implements Printable
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277 PrinterJob printJob = PrinterJob.getPrinterJob();
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278 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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280 printJob.setPrintable(this, pf);
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282 if (printJob.printDialog())
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288 catch (Exception PrintException)
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290 PrintException.printStackTrace();
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295 public int print(Graphics pg, PageFormat pf, int pi)
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296 throws PrinterException
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298 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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300 rc.drawBackground(pg, rc.bgColour);
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302 if (rc.drawAxes == true)
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308 return Printable.PAGE_EXISTS;
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310 return Printable.NO_SUCH_PAGE;
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320 * @param e DOCUMENT ME!
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322 public void eps_actionPerformed(ActionEvent e)
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324 boolean accurateText = true;
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326 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
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327 "Prompt each time");
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329 // If we need to prompt, and if the GUI is visible then
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330 // Prompt for EPS rendering style
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331 if (renderStyle.equalsIgnoreCase("Prompt each time")
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333 (System.getProperty("java.awt.headless") != null
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334 && System.getProperty("java.awt.headless").equals("true")))
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336 EPSOptions eps = new EPSOptions();
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337 renderStyle = eps.getValue();
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339 if (renderStyle == null || eps.cancelled)
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344 if (renderStyle.equalsIgnoreCase("text"))
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346 accurateText = false;
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349 int width = rc.getWidth();
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350 int height = rc.getHeight();
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354 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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355 jalview.bin.Cache.getProperty(
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356 "LAST_DIRECTORY"), new String[]
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359 {"Encapsulated Postscript"},
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360 "Encapsulated Postscript");
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361 chooser.setFileView(new jalview.io.JalviewFileView());
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362 chooser.setDialogTitle("Create EPS file from PCA");
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363 chooser.setToolTipText("Save");
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365 int value = chooser.showSaveDialog(this);
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367 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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372 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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373 chooser.getSelectedFile().getParent());
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375 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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376 EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,
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379 pg.setAccurateTextMode(accurateText);
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381 rc.drawBackground(pg, rc.bgColour);
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384 if (rc.drawAxes == true)
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393 catch (Exception ex)
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395 ex.printStackTrace();
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402 * @param e DOCUMENT ME!
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404 public void png_actionPerformed(ActionEvent e)
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406 int width = rc.getWidth();
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407 int height = rc.getHeight();
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411 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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412 jalview.bin.Cache.getProperty(
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413 "LAST_DIRECTORY"), new String[]
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416 {"Portable network graphics"},
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417 "Portable network graphics");
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419 chooser.setFileView(new jalview.io.JalviewFileView());
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420 chooser.setDialogTitle("Create PNG image from PCA");
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421 chooser.setToolTipText("Save");
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423 int value = chooser.showSaveDialog(this);
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425 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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430 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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431 chooser.getSelectedFile().getParent());
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433 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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435 BufferedImage bi = new BufferedImage(width, height,
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436 BufferedImage.TYPE_INT_RGB);
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437 Graphics big = bi.getGraphics();
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439 big.drawImage(rc.img,0,0,this);
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441 ImageIO.write(bi, "png", out);
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444 catch (Exception ex)
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446 ex.printStackTrace();
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