3 import jalview.jbgui.GAlignmentPanel;
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4 import jalview.schemes.*;
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5 import jalview.analysis.*;
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6 import jalview.datamodel.*;
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8 import java.awt.event.*;
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9 import java.awt.print.*;
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11 import java.awt.image.*;
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12 import org.jibble.epsgraphics.*;
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13 import javax.imageio.*;
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17 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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21 OverviewPanel overviewPanel;
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24 IdwidthAdjuster idwidthAdjuster;
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25 public AlignFrame alignFrame;
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26 ScalePanel scalePanel;
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27 AnnotationPanel annotationPanel;
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28 AnnotationLabels alabels;
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30 // this value is set false when selection area being dragged
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31 boolean fastPaint = true;
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33 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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37 seqPanel = new SeqPanel (av, this);
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38 idPanel = new IdPanel (av, this);
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40 scalePanel = new ScalePanel(av, this);
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42 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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43 idwidthAdjuster = new IdwidthAdjuster(this);
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44 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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46 annotationPanel = new AnnotationPanel(this);
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47 alabels = new AnnotationLabels(this);
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49 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
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50 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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51 annotationScroller.setViewportView(annotationPanel);
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52 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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54 Dimension d = calculateIdWidth();
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55 d.setSize( d.width+4, d.height);
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56 idPanel.idCanvas.setPreferredSize( d );
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57 hscrollFillerPanel.setPreferredSize( d );
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59 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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60 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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63 if(seqPanel.seqCanvas.getWidth()==0)
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64 javax.swing.SwingUtilities.invokeLater(new Runnable()
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68 setScrollValues(0,0);
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69 Dimension d = calculateIdWidth();
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70 d.setSize( d.width+4, d.height);
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71 idPanel.idCanvas.setPreferredSize( d );
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77 hscroll.addAdjustmentListener(this);
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78 vscroll.addAdjustmentListener(this);
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80 addComponentListener(new ComponentAdapter()
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82 public void componentResized(ComponentEvent evt)
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89 addKeyListener(new KeyAdapter()
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91 public void keyPressed(KeyEvent evt)
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93 switch(evt.getKeyCode())
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95 case 27: // escape key
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96 av.setSelectionGroup(null);
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100 if(evt.isControlDown())
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101 alignFrame.cut_actionPerformed(null);
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103 case KeyEvent.VK_C:
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104 if(evt.isControlDown())
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105 alignFrame.copy_actionPerformed(null);
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107 case KeyEvent.VK_V:
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108 if(evt.isControlDown())
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109 alignFrame.paste(true);
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111 case KeyEvent.VK_A:
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112 if(evt.isControlDown())
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113 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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115 case KeyEvent.VK_DOWN:
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116 alignFrame.moveSelectedSequences(false);
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118 case KeyEvent.VK_UP:
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119 alignFrame.moveSelectedSequences(true);
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121 case KeyEvent.VK_F:
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122 if(evt.isControlDown())
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123 alignFrame.findMenuItem_actionPerformed(null);
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130 Dimension calculateIdWidth()
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132 Graphics g = this.getGraphics();
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135 javax.swing.JFrame f = new javax.swing.JFrame();
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137 g = f.getGraphics();
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140 FontMetrics fm = g.getFontMetrics(av.font);
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141 AlignmentI al = av.getAlignment();
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146 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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148 SequenceI s = al.getSequenceAt(i);
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149 if(av.getShowFullId())
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150 id = s.getDisplayId();
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154 if (fm.stringWidth(id) > idWidth)
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155 idWidth = fm.stringWidth(id);
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159 // Also check annotation label widths
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161 if(al.getAlignmentAnnotation()!=null)
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163 fm = g.getFontMetrics(alabels.getFont());
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164 while (i < al.getAlignmentAnnotation().length)
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166 String label = al.getAlignmentAnnotation()[i].label;
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167 if (fm.stringWidth(label) > idWidth)
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168 idWidth = fm.stringWidth(label);
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173 return new Dimension(idWidth, 12);
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177 public void highlightSearchResults(int [] results)
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179 seqPanel.seqCanvas.highlightSearchResults( results );
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181 // do we need to scroll the panel?
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182 if(results!=null && (av.getStartSeq()>results[0]
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183 || av.getEndSeq()<results[0]
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184 || av.getStartRes()>results[1]
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185 || av.getEndRes()<results[2]))
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186 setScrollValues(results[1], results[0]);
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192 public OverviewPanel getOverviewPanel()
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194 return overviewPanel;
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197 public void setOverviewPanel(OverviewPanel op)
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199 overviewPanel = op;
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203 public void setAnnotationVisible(boolean b)
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205 annotationSpaceFillerHolder.setVisible(b);
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206 annotationScroller.setVisible(b);
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207 javax.swing.SwingUtilities.invokeLater(new Runnable()
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218 public void setWrapAlignment(boolean wrap)
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220 scalePanelHolder.setVisible(!wrap);
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221 hscroll.setVisible(!wrap);
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222 idwidthAdjuster.setVisible(!wrap);
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224 av.setShowAnnotation(!wrap);
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225 annotationScroller.setVisible(!wrap);
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226 annotationSpaceFillerHolder.setVisible(!wrap);
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227 idSpaceFillerPanel1.setVisible(!wrap);
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228 javax.swing.SwingUtilities.invokeLater(new Runnable()
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239 public void setColourScheme()
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241 ColourSchemeI cs = av.getGlobalColourScheme();
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243 if(av.getConservationSelected())
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246 Alignment al = (Alignment)av.getAlignment();
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247 Conservation c = new Conservation("All",
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248 ResidueProperties.propHash, 3, al.getSequences(), 0,
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252 c.verdict(false, 100);
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253 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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255 av.setGlobalColourScheme( ccs );
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263 public void RefreshPanels()
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268 Dimension d = idPanel.idCanvas.getPreferredSize();
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269 idPanelHolder.setPreferredSize(d);
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270 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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272 if (av.getWrapAlignment())
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274 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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275 vscroll.setValues(0, 1, 0, max);
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279 if (overviewPanel != null)
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280 overviewPanel.updateOverviewImage();
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281 setScrollValues(av.getStartRes(), av.getStartSeq());
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291 // return value is true if the scroll is valid
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292 public boolean scrollUp(boolean up)
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296 if(vscroll.getValue()<1)
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299 vscroll.setValue(vscroll.getValue() - 1);
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303 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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306 vscroll.setValue(vscroll.getValue() + 1);
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312 public boolean scrollRight(boolean right)
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317 if (hscroll.getValue() < 1)
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320 hscroll.setValue(hscroll.getValue() - 1);
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324 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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327 hscroll.setValue(hscroll.getValue() + 1);
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334 public void setScrollValues(int x, int y)
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336 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
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337 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
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339 if(hextent > av.alignment.getWidth())
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340 hextent = av.alignment.getWidth();
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341 if(vextent > av.alignment.getHeight())
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342 vextent = av.alignment.getHeight();
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344 if(hextent+x > av.getAlignment().getWidth())
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345 x = av.getAlignment().getWidth()- hextent;
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347 if(vextent+y > av.getAlignment().getHeight())
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348 y = av.getAlignment().getHeight() - vextent;
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356 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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357 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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362 public void adjustmentValueChanged(AdjustmentEvent evt)
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364 int oldX = av.getStartRes();
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365 int oldY = av.getStartSeq();
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367 if (evt.getSource() == hscroll)
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369 int x = hscroll.getValue();
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371 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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374 if (evt.getSource() == vscroll)
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376 int offy = vscroll.getValue();
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377 if (av.getWrapAlignment())
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379 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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380 av.setStartRes( vscroll.getValue() * rowSize );
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381 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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385 av.setStartSeq(offy);
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386 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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391 if(overviewPanel!=null)
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392 overviewPanel.setBoxPosition();
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394 if(av.getWrapAlignment() || !fastPaint)
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398 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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399 av.getStartSeq() - oldY);
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400 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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401 scalePanel.repaint();
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402 if (av.getShowAnnotation())
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403 annotationPanel.fastPaint(av.getStartRes() - oldX);
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408 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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410 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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412 int pwidth = (int) pf.getImageableWidth();
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413 int pheight = (int) pf.getImageableHeight();
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415 if (av.getWrapAlignment())
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416 return printWrappedAlignment(pg, pwidth,pheight, pi);
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418 return printUnwrapped(pg,pwidth, pheight,pi);
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421 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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424 int idWidth = calculateIdWidth().width + 4;
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427 pg.setColor(Color.white);
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428 pg.fillRect(0,0,pwidth, pheight);
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429 pg.setFont( av.getFont() );
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431 ////////////////////////////////////
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432 /// How many sequences and residues can we fit on a printable page?
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433 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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434 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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435 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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436 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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438 if (pi >= pagesWide*pagesHigh)
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439 return Printable.NO_SUCH_PAGE;
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441 /////////////////////////////
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442 /// Only print these sequences and residues on this page
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443 int startRes, endRes, startSeq, endSeq;
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444 startRes = (pi % pagesWide) * totalRes;
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445 endRes = startRes + totalRes-1;
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446 if(endRes>av.getAlignment().getWidth())
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447 endRes = av.getAlignment().getWidth();
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449 startSeq = (pi / pagesWide) * totalSeq;
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450 endSeq = startSeq + totalSeq;
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451 if(endSeq > av.getAlignment().getHeight())
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452 endSeq = av.getAlignment().getHeight();
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457 pg.translate(idWidth,0);
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458 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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460 pg.translate(-idWidth, 30);
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463 Color currentColor=null;
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464 Color currentTextColor=null;
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465 for(int i=startSeq; i<endSeq; i++)
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467 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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469 currentColor = Color.gray;
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470 currentTextColor = Color.black;
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474 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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475 currentTextColor = Color.black;
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478 pg.setColor(currentColor);
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479 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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481 av.getCharHeight());
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483 pg.setColor(currentTextColor);
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485 String string = av.getAlignment().getSequenceAt(i).getName();
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486 if(av.getShowFullId())
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487 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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489 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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490 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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493 // draw main sequence panel
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494 pg.translate(idWidth,0);
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495 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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498 if(av.getShowAnnotation())
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500 pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
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501 alabels.drawComponent((Graphics2D)pg);
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502 pg.translate(idWidth,0);
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503 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
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506 return Printable.PAGE_EXISTS;
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510 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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513 int idWidth = calculateIdWidth().width+4;
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515 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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516 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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519 pg.setColor(Color.white);
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520 pg.fillRect(0,0,pwidth, pheight);
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521 pg.setFont( av.getFont() );
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523 ////////////////////////////////////
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524 /// How many sequences and residues can we fit on a printable page?
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525 AlignmentI da = av.alignment;
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526 int endy = da.getHeight();
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527 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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528 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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530 int noChunksOnPage = pheight / chunkHeight;
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531 int totalChunks = da.getWidth() / chunkWidth;
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533 if ( pi*noChunksOnPage > totalChunks )
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534 return Printable.NO_SUCH_PAGE;
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538 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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540 pg.setColor(Color.black);
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542 int rowSize = av.getEndRes() - av.getStartRes();
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543 // Draw the rest of the panels
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545 for(int ypos=2*av.charHeight, row=av.getEndRes(); row<av.alignment.getWidth();
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546 ypos += av.chunkHeight, row+=rowSize )
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548 for (int i = 0; i < endy; i++)
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550 SequenceI s = da.getSequenceAt(i);
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551 String string = s.getName();
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552 if (av.getShowFullId())
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553 string = s.getDisplayId();
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555 pg.drawString(string, 0,
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556 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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557 av.charHeight - (av.charHeight / 5));
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561 // draw main sequence panel
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562 pg.translate(idWidth,0);
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563 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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566 return Printable.PAGE_EXISTS;
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571 public void makeEPS()
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573 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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574 int width = seqPanel.getWidth() + idPanel.getWidth();
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576 if (!av.getWrapAlignment())
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578 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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579 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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581 if(av.getShowAnnotation())
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583 height += annotationPanel.getPreferredSize().height;
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588 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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589 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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590 chooser.setFileView(new jalview.io.JalviewFileView());
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591 chooser.setDialogTitle("Create EPS file from alignment");
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592 chooser.setToolTipText("Save");
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594 int value = chooser.showSaveDialog(this);
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595 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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598 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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599 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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600 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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602 if (av.getWrapAlignment())
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603 printWrappedAlignment(pg, width, height, 0);
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605 printUnwrapped(pg, width, height, 0);
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611 catch (Exception ex)
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613 ex.printStackTrace();
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617 public void makePNG()
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619 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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620 int width = seqPanel.getWidth() + idPanel.getWidth();
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622 if (!av.getWrapAlignment())
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624 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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625 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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628 if(av.getShowAnnotation())
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630 height += annotationPanel.getPreferredSize().height;
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634 System.out.println(width +" "+height);
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638 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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639 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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640 chooser.setFileView(new jalview.io.JalviewFileView());
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641 chooser.setDialogTitle("Create EPS file from alignment");
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642 chooser.setToolTipText("Save");
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644 int value = chooser.showSaveDialog(this);
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645 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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648 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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649 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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651 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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652 Graphics png = bi.getGraphics();
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655 if (av.getWrapAlignment())
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656 printWrappedAlignment(png, width, height, 0);
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658 printUnwrapped(png, width, height, 0);
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660 ImageIO.write(bi, "png", out);
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663 catch (Exception ex)
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665 ex.printStackTrace();
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