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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14 import javax.swing.*;
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18 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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22 OverviewPanel overviewPanel;
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25 IdwidthAdjuster idwidthAdjuster;
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26 public AlignFrame alignFrame;
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27 ScalePanel scalePanel;
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28 AnnotationPanel annotationPanel;
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29 AnnotationLabels alabels;
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31 // this value is set false when selection area being dragged
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32 boolean fastPaint = true;
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34 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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38 seqPanel = new SeqPanel (av, this);
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39 idPanel = new IdPanel (av, this);
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41 scalePanel = new ScalePanel(av, this);
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43 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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44 idwidthAdjuster = new IdwidthAdjuster(this);
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45 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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47 annotationPanel = new AnnotationPanel(this);
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48 alabels = new AnnotationLabels(this);
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50 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
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51 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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52 annotationScroller.setViewportView(annotationPanel);
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53 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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57 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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58 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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60 setScrollValues(0, 0);
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62 hscroll.addAdjustmentListener(this);
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63 vscroll.addAdjustmentListener(this);
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66 addKeyListener(new KeyAdapter()
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68 public void keyPressed(KeyEvent evt)
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70 switch(evt.getKeyCode())
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72 case 27: // escape key
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73 av.setSelectionGroup(null);
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77 case KeyEvent.VK_DOWN:
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78 alignFrame.moveSelectedSequences(false);
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80 case KeyEvent.VK_UP:
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81 alignFrame.moveSelectedSequences(true);
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88 public void fontChanged()
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90 // set idCanvas bufferedImage to null
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91 // to prevent drawing old image
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92 FontMetrics fm = getFontMetrics(av.getFont());
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94 scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
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95 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
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97 idPanel.idCanvas.gg = null;
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98 annotationPanel.adjustPanelHeight();
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99 Dimension d = calculateIdWidth();
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100 d.setSize(d.width + 4, d.height);
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101 idPanel.idCanvas.setPreferredSize(d);
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102 hscrollFillerPanel.setPreferredSize(d);
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107 Dimension calculateIdWidth()
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109 Graphics g = this.getGraphics();
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112 javax.swing.JFrame f = new javax.swing.JFrame();
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114 g = f.getGraphics();
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117 FontMetrics fm = g.getFontMetrics(av.font);
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118 AlignmentI al = av.getAlignment();
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123 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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125 SequenceI s = al.getSequenceAt(i);
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126 if(av.getShowFullId())
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127 id = s.getDisplayId();
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131 if (fm.stringWidth(id) > idWidth)
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132 idWidth = fm.stringWidth(id);
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136 // Also check annotation label widths
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138 if(al.getAlignmentAnnotation()!=null)
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140 fm = g.getFontMetrics(alabels.getFont());
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141 while (i < al.getAlignmentAnnotation().length)
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143 String label = al.getAlignmentAnnotation()[i].label;
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144 if (fm.stringWidth(label) > idWidth)
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145 idWidth = fm.stringWidth(label);
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150 return new Dimension(idWidth, 12);
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154 public void highlightSearchResults(int [] results)
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156 seqPanel.seqCanvas.highlightSearchResults( results );
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158 // do we need to scroll the panel?
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159 if(results!=null && (av.getStartSeq()>results[0]
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160 || av.getEndSeq()<results[0]
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161 || av.getStartRes()>results[1]
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162 || av.getEndRes()<results[2]))
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163 setScrollValues(results[1], results[0]);
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169 public OverviewPanel getOverviewPanel()
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171 return overviewPanel;
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174 public void setOverviewPanel(OverviewPanel op)
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176 overviewPanel = op;
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180 public void setAnnotationVisible(boolean b)
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182 annotationSpaceFillerHolder.setVisible(b);
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183 annotationScroller.setVisible(b);
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187 public void setWrapAlignment(boolean wrap)
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189 scalePanelHolder.setVisible(!wrap);
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190 hscroll.setVisible(!wrap);
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191 idwidthAdjuster.setVisible(!wrap);
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193 av.setShowAnnotation(!wrap);
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194 annotationScroller.setVisible(!wrap);
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195 annotationSpaceFillerHolder.setVisible(!wrap);
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196 idSpaceFillerPanel1.setVisible(!wrap);
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203 public void setColourScheme()
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205 ColourSchemeI cs = av.getGlobalColourScheme();
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207 if(av.getConservationSelected())
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210 Alignment al = (Alignment)av.getAlignment();
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211 Conservation c = new Conservation("All",
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212 ResidueProperties.propHash, 3, al.getSequences(), 0,
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216 c.verdict(false, av.ConsPercGaps);
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217 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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219 av.setGlobalColourScheme( ccs );
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230 // return value is true if the scroll is valid
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231 public boolean scrollUp(boolean up)
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235 if(vscroll.getValue()<1)
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238 vscroll.setValue(vscroll.getValue() - 1);
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242 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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245 vscroll.setValue(vscroll.getValue() + 1);
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251 public boolean scrollRight(boolean right)
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256 if (hscroll.getValue() < 1)
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259 hscroll.setValue(hscroll.getValue() - 1);
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263 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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266 hscroll.setValue(hscroll.getValue() + 1);
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273 public void setScrollValues(int x, int y)
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275 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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277 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
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278 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
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280 if(hextent > av.alignment.getWidth())
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281 hextent = av.alignment.getWidth();
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282 if(vextent > av.alignment.getHeight())
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283 vextent = av.alignment.getHeight();
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285 if(hextent+x > av.getAlignment().getWidth())
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286 x = av.getAlignment().getWidth()- hextent;
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288 if(vextent+y > av.getAlignment().getHeight())
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289 y = av.getAlignment().getHeight() - vextent;
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297 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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298 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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305 public void adjustmentValueChanged(AdjustmentEvent evt)
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307 int oldX = av.getStartRes();
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308 int oldY = av.getStartSeq();
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310 if (evt.getSource() == hscroll)
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312 int x = hscroll.getValue();
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314 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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317 if (evt.getSource() == vscroll)
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319 int offy = vscroll.getValue();
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320 if (av.getWrapAlignment())
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322 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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323 av.setStartRes( vscroll.getValue() * rowSize );
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324 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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328 av.setStartSeq(offy);
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329 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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333 if(overviewPanel!=null)
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334 overviewPanel.setBoxPosition();
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336 if(av.getWrapAlignment() || !fastPaint)
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340 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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341 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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342 av.getStartSeq() - oldY);
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344 scalePanel.repaint();
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345 if (av.getShowAnnotation())
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346 annotationPanel.fastPaint(av.getStartRes() - oldX);
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352 public void paintComponent(Graphics g)
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355 Dimension d = idPanel.idCanvas.getPreferredSize();
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356 idPanelHolder.setPreferredSize(d);
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357 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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360 if (av.getWrapAlignment())
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362 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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363 vscroll.setMaximum(max);
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364 vscroll.setUnitIncrement(1);
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365 vscroll.setVisibleAmount(1);
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369 setScrollValues(av.getStartRes(), av.getStartSeq());
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376 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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378 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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380 int pwidth = (int) pf.getImageableWidth();
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381 int pheight = (int) pf.getImageableHeight();
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383 if (av.getWrapAlignment())
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384 return printWrappedAlignment(pg, pwidth,pheight, pi);
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386 return printUnwrapped(pg,pwidth, pheight,pi);
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389 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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392 int idWidth = calculateIdWidth().width + 4;
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393 FontMetrics fm = getFontMetrics(av.getFont());
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394 int scaleHeight = av.charHeight + fm.getDescent();
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396 pg.setColor(Color.white);
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397 pg.fillRect(0, 0, pwidth, pheight);
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398 pg.setFont(av.getFont());
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400 ////////////////////////////////////
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401 /// How many sequences and residues can we fit on a printable page?
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402 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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404 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;
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406 int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
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408 /////////////////////////////
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409 /// Only print these sequences and residues on this page
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410 int startRes, endRes, startSeq, endSeq;
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411 startRes = (pi % pagesWide) * totalRes;
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412 endRes = startRes + totalRes - 1;
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413 if (endRes > av.getAlignment().getWidth()-1)
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414 endRes = av.getAlignment().getWidth()-1;
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416 startSeq = (pi / pagesWide) * totalSeq;
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417 endSeq = startSeq + totalSeq;
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418 if (endSeq > av.getAlignment().getHeight())
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419 endSeq = av.getAlignment().getHeight();
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421 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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423 if (av.showAnnotation)
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424 pagesHigh += annotationPanel.getHeight();
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426 pagesHigh /= pheight;
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428 if (pi >= pagesWide * pagesHigh)
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429 return Printable.NO_SUCH_PAGE;
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432 pg.translate(idWidth, 0);
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433 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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434 pg.translate( -idWidth, scaleHeight);
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437 Color currentColor = null;
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438 Color currentTextColor = null;
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439 for (int i = startSeq; i < endSeq; i++)
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441 if (av.getSelectionGroup() != null &&
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442 av.getSelectionGroup().sequences.
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443 contains(av.getAlignment().getSequenceAt(i)))
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445 currentColor = Color.gray;
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446 currentTextColor = Color.black;
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450 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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451 currentTextColor = Color.black;
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454 pg.setColor(currentColor);
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456 jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
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457 av.getCharHeight()),
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459 av.getCharHeight());
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461 pg.setColor(currentTextColor);
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463 String string = av.getAlignment().getSequenceAt(i).getName();
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464 if (av.getShowFullId())
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465 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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467 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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468 (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
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469 (av.getCharHeight() / 5));
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472 // draw main sequence panel
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473 pg.translate(idWidth, 0);
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474 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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475 startRes, startSeq, 0);
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478 if (av.showAnnotation && endSeq == av.alignment.getHeight())
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480 pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
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481 alabels.drawComponent( (Graphics2D) pg);
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482 pg.translate(idWidth, 0);
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483 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);
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486 return Printable.PAGE_EXISTS;
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491 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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493 int idWidth = calculateIdWidth().width + 4;
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495 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
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496 int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
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497 ( (av.alignment.getWidth()
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498 / resWidth) + 1) * av.charHeight;
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501 pg.setColor(Color.white);
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502 pg.fillRect(0, 0, pwidth, pheight);
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503 pg.setFont(av.getFont());
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507 pg.setColor(Color.black);
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509 pg.translate(0, -pi * pheight);
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511 pg.setClip(0,pi*pheight,pwidth, pheight);
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513 int ypos = 2 * av.charHeight;
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516 for (int i = 0; i < av.alignment.getHeight(); i++)
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518 SequenceI s = av.alignment.getSequenceAt(i);
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519 String string = s.getName();
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520 if (av.getShowFullId())
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521 string = s.getDisplayId();
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523 pg.drawString(string, 0,
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524 AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
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526 av.charHeight - (av.charHeight / 5));
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530 ypos += (av.alignment.getHeight() + 2) * av.charHeight;
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533 while (ypos < totalHeight);
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535 pg.translate(idWidth, 0);
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537 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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539 if (pi * pheight < totalHeight)
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540 return Printable.PAGE_EXISTS;
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542 return Printable.NO_SUCH_PAGE;
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549 public void makeEPS()
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551 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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552 int width = seqPanel.getWidth() + idPanel.getWidth();
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554 if (!av.getWrapAlignment())
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556 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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557 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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559 if(av.getShowAnnotation())
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561 height += annotationPanel.getPreferredSize().height;
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566 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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567 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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568 chooser.setFileView(new jalview.io.JalviewFileView());
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569 chooser.setDialogTitle("Create EPS file from alignment");
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570 chooser.setToolTipText("Save");
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572 int value = chooser.showSaveDialog(this);
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573 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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576 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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577 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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578 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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580 if (av.getWrapAlignment())
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581 printWrappedAlignment(pg, width, height, 0);
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583 printUnwrapped(pg, width, height, 0);
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589 catch (Exception ex)
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591 ex.printStackTrace();
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595 public void makePNG()
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597 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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598 int width = seqPanel.getWidth() + idPanel.getWidth();
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600 if (!av.getWrapAlignment())
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602 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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603 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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606 if(av.getShowAnnotation())
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608 height += annotationPanel.getPreferredSize().height;
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615 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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616 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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617 chooser.setFileView(new jalview.io.JalviewFileView());
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618 chooser.setDialogTitle("Create EPS file from alignment");
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619 chooser.setToolTipText("Save");
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621 int value = chooser.showSaveDialog(this);
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622 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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625 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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626 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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628 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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629 Graphics2D png = (Graphics2D)bi.getGraphics();
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631 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
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633 if (av.getWrapAlignment())
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634 printWrappedAlignment(png, width, height, 0);
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636 printUnwrapped(png, width, height, 0);
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638 ImageIO.write(bi, "png", out);
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641 catch (Exception ex)
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643 ex.printStackTrace();
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649 class Preview extends JFrame
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652 public Preview(Image image)
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654 setResizable(true);
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655 setSize(image.getWidth(this), image.getHeight(this));
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657 getContentPane().setLayout(new BorderLayout());
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658 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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664 class PreviewPanel extends JPanel
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667 public PreviewPanel(Image image)
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669 this.image = image;
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671 public void paintComponent(Graphics g)
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674 g.drawImage(image,0,0,this);
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676 System.out.println("image is null");
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