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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62 javax.swing.SwingUtilities.invokeLater(new Runnable()
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67 setScrollValues(0,0);
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68 Dimension d = calculateIdWidth();
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69 d.setSize( d.width+4, d.height);
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70 idPanel.idCanvas.setPreferredSize( d );
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76 hscroll.addAdjustmentListener(this);
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77 vscroll.addAdjustmentListener(this);
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79 addComponentListener(new ComponentAdapter()
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81 public void componentResized(ComponentEvent evt)
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88 addKeyListener(new KeyAdapter()
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90 public void keyPressed(KeyEvent evt)
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92 switch(evt.getKeyCode())
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94 case 27: // escape key
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95 av.setSelectionGroup(null);
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99 if(evt.isControlDown())
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100 alignFrame.cut_actionPerformed(null);
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102 case KeyEvent.VK_C:
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103 if(evt.isControlDown())
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104 alignFrame.copy_actionPerformed(null);
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106 case KeyEvent.VK_V:
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107 if(evt.isControlDown())
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108 alignFrame.paste(true);
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110 case KeyEvent.VK_A:
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111 if(evt.isControlDown())
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112 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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114 case KeyEvent.VK_DOWN:
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115 alignFrame.moveSelectedSequences(false);
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117 case KeyEvent.VK_UP:
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118 alignFrame.moveSelectedSequences(true);
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120 case KeyEvent.VK_F:
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121 if(evt.isControlDown())
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122 alignFrame.findMenuItem_actionPerformed(null);
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129 Dimension calculateIdWidth()
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131 Graphics g = this.getGraphics();
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134 javax.swing.JFrame f = new javax.swing.JFrame();
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136 g = f.getGraphics();
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139 FontMetrics fm = g.getFontMetrics(av.font);
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140 AlignmentI al = av.getAlignment();
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145 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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147 SequenceI s = al.getSequenceAt(i);
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148 if(av.getShowFullId())
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149 id = s.getDisplayId();
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153 if (fm.stringWidth(id) > idWidth)
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154 idWidth = fm.stringWidth(id);
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158 // Also check annotation label widths
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160 if(al.getAlignmentAnnotation()!=null)
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162 fm = g.getFontMetrics(alabels.getFont());
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163 while (i < al.getAlignmentAnnotation().length)
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165 String label = al.getAlignmentAnnotation()[i].label;
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166 if (fm.stringWidth(label) > idWidth)
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167 idWidth = fm.stringWidth(label);
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172 return new Dimension(idWidth, 12);
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176 public void highlightSearchResults(int [] results)
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178 seqPanel.seqCanvas.highlightSearchResults( results );
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180 // do we need to scroll the panel?
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181 if(results!=null && (av.getStartSeq()>results[0]
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182 || av.getEndSeq()<results[0]
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183 || av.getStartRes()>results[1]
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184 || av.getEndRes()<results[2]))
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185 setScrollValues(results[1], results[0]);
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191 public OverviewPanel getOverviewPanel()
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193 return overviewPanel;
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196 public void setOverviewPanel(OverviewPanel op)
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198 overviewPanel = op;
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202 public void setAnnotationVisible(boolean b)
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204 annotationSpaceFillerHolder.setVisible(b);
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205 annotationScroller.setVisible(b);
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206 javax.swing.SwingUtilities.invokeLater(new Runnable()
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217 public void setWrapAlignment(boolean wrap)
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219 scalePanelHolder.setVisible(!wrap);
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220 hscroll.setVisible(!wrap);
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221 idwidthAdjuster.setVisible(!wrap);
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223 av.setShowAnnotation(!wrap);
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224 annotationScroller.setVisible(!wrap);
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225 annotationSpaceFillerHolder.setVisible(!wrap);
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226 idSpaceFillerPanel1.setVisible(!wrap);
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227 javax.swing.SwingUtilities.invokeLater(new Runnable()
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238 public void setColourScheme()
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240 ColourSchemeI cs = av.getGlobalColourScheme();
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242 if(av.getConservationSelected())
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245 Alignment al = (Alignment)av.getAlignment();
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246 Conservation c = new Conservation("All",
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247 ResidueProperties.propHash, 3, al.getSequences(), 0,
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251 c.verdict(false, av.ConsPercGaps);
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252 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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254 av.setGlobalColourScheme( ccs );
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262 public void RefreshPanels()
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265 Dimension d = idPanel.idCanvas.getPreferredSize();
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266 idPanelHolder.setPreferredSize(d);
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267 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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269 if (av.getWrapAlignment())
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271 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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272 vscroll.setValues(0, 1, 0, max);
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276 if (overviewPanel != null)
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277 overviewPanel.updateOverviewImage();
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278 setScrollValues(av.getStartRes(), av.getStartSeq());
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289 // return value is true if the scroll is valid
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290 public boolean scrollUp(boolean up)
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294 if(vscroll.getValue()<1)
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297 vscroll.setValue(vscroll.getValue() - 1);
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301 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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304 vscroll.setValue(vscroll.getValue() + 1);
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310 public boolean scrollRight(boolean right)
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315 if (hscroll.getValue() < 1)
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318 hscroll.setValue(hscroll.getValue() - 1);
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322 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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325 hscroll.setValue(hscroll.getValue() + 1);
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332 public void setScrollValues(int x, int y)
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334 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
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335 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
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337 if(hextent > av.alignment.getWidth())
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338 hextent = av.alignment.getWidth();
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339 if(vextent > av.alignment.getHeight())
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340 vextent = av.alignment.getHeight();
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342 if(hextent+x > av.getAlignment().getWidth())
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343 x = av.getAlignment().getWidth()- hextent;
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345 if(vextent+y > av.getAlignment().getHeight())
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346 y = av.getAlignment().getHeight() - vextent;
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354 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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355 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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360 public void adjustmentValueChanged(AdjustmentEvent evt)
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362 int oldX = av.getStartRes();
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363 int oldY = av.getStartSeq();
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365 if (evt.getSource() == hscroll)
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367 int x = hscroll.getValue();
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369 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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372 if (evt.getSource() == vscroll)
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374 int offy = vscroll.getValue();
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375 if (av.getWrapAlignment())
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377 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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378 av.setStartRes( vscroll.getValue() * rowSize );
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379 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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383 av.setStartSeq(offy);
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384 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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389 if(overviewPanel!=null)
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390 overviewPanel.setBoxPosition();
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392 if(av.getWrapAlignment() || !fastPaint)
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396 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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397 av.getStartSeq() - oldY);
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398 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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399 scalePanel.repaint();
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400 if (av.getShowAnnotation())
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401 annotationPanel.fastPaint(av.getStartRes() - oldX);
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406 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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408 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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410 int pwidth = (int) pf.getImageableWidth();
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411 int pheight = (int) pf.getImageableHeight();
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413 if (av.getWrapAlignment())
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414 return printWrappedAlignment(pg, pwidth,pheight, pi);
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416 return printUnwrapped(pg,pwidth, pheight,pi);
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419 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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422 int idWidth = calculateIdWidth().width + 4;
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425 pg.setColor(Color.white);
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426 pg.fillRect(0,0,pwidth, pheight);
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427 pg.setFont( av.getFont() );
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429 ////////////////////////////////////
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430 /// How many sequences and residues can we fit on a printable page?
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431 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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432 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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433 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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434 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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436 if (pi >= pagesWide*pagesHigh)
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437 return Printable.NO_SUCH_PAGE;
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439 /////////////////////////////
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440 /// Only print these sequences and residues on this page
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441 int startRes, endRes, startSeq, endSeq;
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442 startRes = (pi % pagesWide) * totalRes;
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443 endRes = startRes + totalRes-1;
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444 if(endRes>av.getAlignment().getWidth())
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445 endRes = av.getAlignment().getWidth();
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447 startSeq = (pi / pagesWide) * totalSeq;
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448 endSeq = startSeq + totalSeq;
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449 if(endSeq > av.getAlignment().getHeight())
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450 endSeq = av.getAlignment().getHeight();
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455 pg.translate(idWidth,0);
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456 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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458 pg.translate(-idWidth, 30);
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461 Color currentColor=null;
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462 Color currentTextColor=null;
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463 for(int i=startSeq; i<endSeq; i++)
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465 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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467 currentColor = Color.gray;
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468 currentTextColor = Color.black;
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472 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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473 currentTextColor = Color.black;
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476 pg.setColor(currentColor);
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477 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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479 av.getCharHeight());
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481 pg.setColor(currentTextColor);
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483 String string = av.getAlignment().getSequenceAt(i).getName();
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484 if(av.getShowFullId())
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485 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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487 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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488 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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491 // draw main sequence panel
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492 pg.translate(idWidth,0);
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493 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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496 if(av.getShowAnnotation())
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498 pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
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499 alabels.drawComponent((Graphics2D)pg);
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500 pg.translate(idWidth,0);
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501 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
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504 return Printable.PAGE_EXISTS;
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508 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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511 int idWidth = calculateIdWidth().width+4;
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513 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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514 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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517 pg.setColor(Color.white);
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518 pg.fillRect(0,0,pwidth, pheight);
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519 pg.setFont( av.getFont() );
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521 ////////////////////////////////////
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522 /// How many sequences and residues can we fit on a printable page?
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523 AlignmentI da = av.alignment;
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524 int endy = da.getHeight();
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525 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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526 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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528 int noChunksOnPage = pheight / chunkHeight;
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529 int totalChunks = da.getWidth() / chunkWidth;
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531 if ( pi*noChunksOnPage > totalChunks )
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532 return Printable.NO_SUCH_PAGE;
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536 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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538 pg.setColor(Color.black);
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540 int rowSize = av.getEndRes() - av.getStartRes();
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541 // Draw the rest of the panels
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543 for(int ypos=2*av.charHeight, row=av.getEndRes(); row<av.alignment.getWidth();
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544 ypos += av.chunkHeight, row+=rowSize )
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546 for (int i = 0; i < endy; i++)
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548 SequenceI s = da.getSequenceAt(i);
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549 String string = s.getName();
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550 if (av.getShowFullId())
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551 string = s.getDisplayId();
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553 pg.drawString(string, 0,
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554 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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555 av.charHeight - (av.charHeight / 5));
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559 // draw main sequence panel
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560 pg.translate(idWidth,0);
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561 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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564 return Printable.PAGE_EXISTS;
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569 public void makeEPS()
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571 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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572 int width = seqPanel.getWidth() + idPanel.getWidth();
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574 if (!av.getWrapAlignment())
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576 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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577 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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579 if(av.getShowAnnotation())
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581 height += annotationPanel.getPreferredSize().height;
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586 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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587 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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588 chooser.setFileView(new jalview.io.JalviewFileView());
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589 chooser.setDialogTitle("Create EPS file from alignment");
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590 chooser.setToolTipText("Save");
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592 int value = chooser.showSaveDialog(this);
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593 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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596 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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597 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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598 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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600 if (av.getWrapAlignment())
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601 printWrappedAlignment(pg, width, height, 0);
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603 printUnwrapped(pg, width, height, 0);
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609 catch (Exception ex)
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611 ex.printStackTrace();
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615 public void makePNG()
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617 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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618 int width = seqPanel.getWidth() + idPanel.getWidth();
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620 if (!av.getWrapAlignment())
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622 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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623 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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626 if(av.getShowAnnotation())
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628 height += annotationPanel.getPreferredSize().height;
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632 System.out.println(width +" "+height);
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636 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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637 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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638 chooser.setFileView(new jalview.io.JalviewFileView());
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639 chooser.setDialogTitle("Create EPS file from alignment");
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640 chooser.setToolTipText("Save");
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642 int value = chooser.showSaveDialog(this);
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643 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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646 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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647 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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649 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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650 Graphics png = bi.getGraphics();
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653 if (av.getWrapAlignment())
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654 printWrappedAlignment(png, width, height, 0);
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656 printUnwrapped(png, width, height, 0);
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658 ImageIO.write(bi, "png", out);
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661 catch (Exception ex)
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663 ex.printStackTrace();
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