2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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48 AlignmentView seqstrings;
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52 * Creates a new PCAPanel object.
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54 * @param av DOCUMENT ME!
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55 * @param s DOCUMENT ME!
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57 public PCAPanel(AlignmentPanel ap)
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62 boolean sameLength = true;
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64 seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
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65 if(av.getSelectionGroup()==null)
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67 seqs = av.alignment.getSequencesArray();
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71 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
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73 SeqCigar sq[]=seqstrings.getSequences();
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74 int length = sq[0].getWidth();
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76 for (int i = 0; i < seqs.length; i++)
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78 if (sq[i].getWidth() != length)
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87 JOptionPane.showMessageDialog(Desktop.desktop,
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88 "The sequences must be aligned before calculating PCA.\n" +
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89 "Try using the Pad function in the edit menu,\n" +
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90 "or one of the multiple sequence alignment web services.",
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91 "Sequences not aligned",
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92 JOptionPane.WARNING_MESSAGE);
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98 Desktop.addInternalFrame(this, "Principal component analysis",
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103 PaintRefresher.Register(this, av.getSequenceSetId());
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105 rc = new RotatableCanvas(ap);
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106 this.getContentPane().add(rc, BorderLayout.CENTER);
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107 Thread worker = new Thread(this);
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111 public void bgcolour_actionPerformed(ActionEvent e)
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113 Color col = JColorChooser.showDialog(this, "Select Background Colour",
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130 pca = new PCA(seqstrings.getSequenceStrings(' '));
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133 // Now find the component coordinates
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136 while ( (ii < seqs.length) && (seqs[ii] != null))
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141 double[][] comps = new double[ii][ii];
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143 for (int i = 0; i < ii; i++)
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145 if (pca.getEigenvalue(i) > 1e-4)
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147 comps[i] = pca.component(i);
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152 xCombobox.setSelectedIndex(0);
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153 yCombobox.setSelectedIndex(1);
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154 zCombobox.setSelectedIndex(2);
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156 top = pca.getM().rows - 1;
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158 Vector points = new Vector();
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159 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
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161 for (int i = 0; i < pca.getM().rows; i++)
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163 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
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164 points.addElement(sp);
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167 rc.setPoints(points, pca.getM().rows);
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170 addKeyListener(rc);
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173 catch(OutOfMemoryError er)
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174 { JOptionPane.showInternalMessageDialog(Desktop.desktop,
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175 "Out of memory calculating PCA!!"
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177 "\nSee help files for increasing Java Virtual Machine memory."
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179 JOptionPane.WARNING_MESSAGE);
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180 System.out.println("PCAPanel: "+er);
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190 void doDimensionChange()
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197 int dim1 = top - xCombobox.getSelectedIndex();
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198 int dim2 = top - yCombobox.getSelectedIndex();
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199 int dim3 = top - zCombobox.getSelectedIndex();
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201 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
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203 for (int i = 0; i < pca.getM().rows; i++)
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205 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
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209 rc.rotmat.setIdentity();
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211 rc.paint(rc.getGraphics());
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217 * @param e DOCUMENT ME!
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219 protected void xCombobox_actionPerformed(ActionEvent e)
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221 doDimensionChange();
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227 * @param e DOCUMENT ME!
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229 protected void yCombobox_actionPerformed(ActionEvent e)
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231 doDimensionChange();
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237 * @param e DOCUMENT ME!
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239 protected void zCombobox_actionPerformed(ActionEvent e)
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241 doDimensionChange();
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245 public void outputValues_actionPerformed(ActionEvent e)
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247 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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248 Desktop.addInternalFrame(cap, "PCA details", 500,
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251 cap.setText(pca.getDetails());
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254 public void showLabels_actionPerformed(ActionEvent e)
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256 rc.showLabels(showLabels.getState());
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259 public void print_actionPerformed(ActionEvent e)
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261 PCAPrinter printer = new PCAPrinter();
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265 public void originalSeqData_actionPerformed(ActionEvent e)
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267 // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows
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268 if (seqstrings==null)
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270 jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
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273 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
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274 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
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275 // or create a selection box around columns in alignment view
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276 // test Alignment(SeqCigar[])
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277 Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
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278 getGapCharacter());
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281 if (alAndColsel != null && alAndColsel[0]!=null)
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283 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
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285 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
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286 Alignment dataset = av.getAlignment().getDataset();
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287 if (dataset != null)
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289 al.setDataset(dataset);
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294 // make a new frame!
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295 AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
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296 AlignFrame.DEFAULT_WIDTH,
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297 AlignFrame.DEFAULT_HEIGHT
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300 //>>>This is a fix for the moment, until a better solution is found!!<<<
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301 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
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303 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
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306 Desktop.addInternalFrame(af, "Original Data for " + this.title,
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307 AlignFrame.DEFAULT_WIDTH,
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308 AlignFrame.DEFAULT_HEIGHT);
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311 /* CutAndPasteTransfer cap = new CutAndPasteTransfer();
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312 for (int i = 0; i < seqs.length; i++)
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314 cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
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315 seqs[i].getName()));
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316 cap.appendText(" " + seqstrings[i] + "\n");
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320 Desktop.addInternalFrame(cap, "Original Data",
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327 class PCAPrinter extends Thread implements Printable
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331 PrinterJob printJob = PrinterJob.getPrinterJob();
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332 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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334 printJob.setPrintable(this, pf);
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336 if (printJob.printDialog())
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342 catch (Exception PrintException)
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344 PrintException.printStackTrace();
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349 public int print(Graphics pg, PageFormat pf, int pi)
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350 throws PrinterException
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352 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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354 rc.drawBackground(pg, rc.bgColour);
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356 if (rc.drawAxes == true)
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362 return Printable.PAGE_EXISTS;
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364 return Printable.NO_SUCH_PAGE;
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373 * @param e DOCUMENT ME!
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375 public void eps_actionPerformed(ActionEvent e)
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377 makePCAImage(jalview.util.ImageMaker.EPS);
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383 * @param e DOCUMENT ME!
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385 public void png_actionPerformed(ActionEvent e)
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387 makePCAImage(jalview.util.ImageMaker.PNG);
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390 void makePCAImage(int type)
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392 int width = rc.getWidth();
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393 int height = rc.getHeight();
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395 jalview.util.ImageMaker im;
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397 if(type == jalview.util.ImageMaker.PNG)
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398 im = new jalview.util.ImageMaker(this,
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399 jalview.util.ImageMaker.PNG,
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400 "Make PNG image from PCA",
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404 im = new jalview.util.ImageMaker(this,
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405 jalview.util.ImageMaker.EPS,
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406 "Make EPS file from PCA",
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408 null, this.getTitle());
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410 if(im.getGraphics()!=null)
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412 rc.drawBackground(im.getGraphics(), Color.black);
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413 rc.drawScene(im.getGraphics());
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414 if (rc.drawAxes == true)
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416 rc.drawAxes(im.getGraphics());
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423 public void viewMenu_menuSelected()
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425 buildAssociatedViewMenu();
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429 void buildAssociatedViewMenu()
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431 AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
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432 if(aps.length==1 && rc.av ==aps[0].av)
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434 associateViewsMenu.setVisible(false);
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438 associateViewsMenu.setVisible(true);
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440 if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
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442 viewMenu.insertSeparator(viewMenu.getItemCount()-1);
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445 associateViewsMenu.removeAll();
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448 JRadioButtonMenuItem item;
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449 ButtonGroup buttonGroup = new ButtonGroup();
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450 int i, iSize = aps.length;
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451 final PCAPanel thisPCAPanel = this;
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452 for(i=0; i<iSize; i++)
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454 final AlignmentPanel ap = aps[i];
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455 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==rc.av );
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456 buttonGroup.add(item);
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457 item.addActionListener(new ActionListener()
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459 public void actionPerformed(ActionEvent evt)
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461 rc.applyToAllViews = false;
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464 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
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468 associateViewsMenu.add(item);
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471 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
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473 buttonGroup.add(itemf);
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475 itemf.setSelected(rc.applyToAllViews);
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476 itemf.addActionListener(new ActionListener()
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478 public void actionPerformed(ActionEvent evt)
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480 rc.applyToAllViews = itemf.isSelected();
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483 associateViewsMenu.add(itemf);
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