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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56 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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57 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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59 setScrollValues(0, 0);
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61 hscroll.addAdjustmentListener(this);
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62 vscroll.addAdjustmentListener(this);
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65 addKeyListener(new KeyAdapter()
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67 public void keyPressed(KeyEvent evt)
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69 switch(evt.getKeyCode())
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71 case 27: // escape key
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72 av.setSelectionGroup(null);
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76 if(evt.isControlDown())
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77 alignFrame.cut_actionPerformed(null);
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80 if(evt.isControlDown())
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81 alignFrame.copy_actionPerformed(null);
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84 if(evt.isControlDown())
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85 alignFrame.paste(true);
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88 if(evt.isControlDown())
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89 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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91 case KeyEvent.VK_DOWN:
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92 alignFrame.moveSelectedSequences(false);
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94 case KeyEvent.VK_UP:
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95 alignFrame.moveSelectedSequences(true);
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98 if(evt.isControlDown())
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99 alignFrame.findMenuItem_actionPerformed(null);
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106 public void fontChanged()
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108 // set idCanvas bufferedImage to null
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109 // to prevent drawing old image
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110 idPanel.idCanvas.gg = null;
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111 annotationPanel.adjustPanelHeight();
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112 Dimension d = calculateIdWidth();
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113 d.setSize(d.width + 4, d.height);
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114 idPanel.idCanvas.setPreferredSize(d);
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115 hscrollFillerPanel.setPreferredSize(d);
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120 Dimension calculateIdWidth()
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122 Graphics g = this.getGraphics();
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125 javax.swing.JFrame f = new javax.swing.JFrame();
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127 g = f.getGraphics();
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130 FontMetrics fm = g.getFontMetrics(av.font);
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131 AlignmentI al = av.getAlignment();
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136 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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138 SequenceI s = al.getSequenceAt(i);
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139 if(av.getShowFullId())
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140 id = s.getDisplayId();
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144 if (fm.stringWidth(id) > idWidth)
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145 idWidth = fm.stringWidth(id);
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149 // Also check annotation label widths
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151 if(al.getAlignmentAnnotation()!=null)
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153 fm = g.getFontMetrics(alabels.getFont());
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154 while (i < al.getAlignmentAnnotation().length)
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156 String label = al.getAlignmentAnnotation()[i].label;
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157 if (fm.stringWidth(label) > idWidth)
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158 idWidth = fm.stringWidth(label);
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163 return new Dimension(idWidth, 12);
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167 public void highlightSearchResults(int [] results)
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169 seqPanel.seqCanvas.highlightSearchResults( results );
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171 // do we need to scroll the panel?
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172 if(results!=null && (av.getStartSeq()>results[0]
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173 || av.getEndSeq()<results[0]
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174 || av.getStartRes()>results[1]
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175 || av.getEndRes()<results[2]))
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176 setScrollValues(results[1], results[0]);
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182 public OverviewPanel getOverviewPanel()
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184 return overviewPanel;
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187 public void setOverviewPanel(OverviewPanel op)
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189 overviewPanel = op;
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193 public void setAnnotationVisible(boolean b)
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195 annotationSpaceFillerHolder.setVisible(b);
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196 annotationScroller.setVisible(b);
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200 public void setWrapAlignment(boolean wrap)
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202 scalePanelHolder.setVisible(!wrap);
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203 hscroll.setVisible(!wrap);
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204 idwidthAdjuster.setVisible(!wrap);
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206 av.setShowAnnotation(!wrap);
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207 annotationScroller.setVisible(!wrap);
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208 annotationSpaceFillerHolder.setVisible(!wrap);
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209 idSpaceFillerPanel1.setVisible(!wrap);
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216 public void setColourScheme()
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218 ColourSchemeI cs = av.getGlobalColourScheme();
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220 if(av.getConservationSelected())
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223 Alignment al = (Alignment)av.getAlignment();
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224 Conservation c = new Conservation("All",
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225 ResidueProperties.propHash, 3, al.getSequences(), 0,
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229 c.verdict(false, av.ConsPercGaps);
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230 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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232 av.setGlobalColourScheme( ccs );
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243 // return value is true if the scroll is valid
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244 public boolean scrollUp(boolean up)
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248 if(vscroll.getValue()<1)
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251 vscroll.setValue(vscroll.getValue() - 1);
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255 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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258 vscroll.setValue(vscroll.getValue() + 1);
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264 public boolean scrollRight(boolean right)
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269 if (hscroll.getValue() < 1)
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272 hscroll.setValue(hscroll.getValue() - 1);
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276 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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279 hscroll.setValue(hscroll.getValue() + 1);
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286 public void setScrollValues(int x, int y)
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288 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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290 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
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291 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
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293 if(hextent > av.alignment.getWidth())
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294 hextent = av.alignment.getWidth();
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295 if(vextent > av.alignment.getHeight())
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296 vextent = av.alignment.getHeight();
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298 if(hextent+x > av.getAlignment().getWidth())
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299 x = av.getAlignment().getWidth()- hextent;
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301 if(vextent+y > av.getAlignment().getHeight())
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302 y = av.getAlignment().getHeight() - vextent;
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310 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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311 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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318 public void adjustmentValueChanged(AdjustmentEvent evt)
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320 int oldX = av.getStartRes();
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321 int oldY = av.getStartSeq();
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323 if (evt.getSource() == hscroll)
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325 int x = hscroll.getValue();
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327 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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330 if (evt.getSource() == vscroll)
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332 int offy = vscroll.getValue();
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333 if (av.getWrapAlignment())
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335 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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336 av.setStartRes( vscroll.getValue() * rowSize );
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337 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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341 av.setStartSeq(offy);
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342 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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346 if(overviewPanel!=null)
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347 overviewPanel.setBoxPosition();
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349 if(av.getWrapAlignment() || !fastPaint)
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353 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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354 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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355 av.getStartSeq() - oldY);
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357 scalePanel.repaint();
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358 if (av.getShowAnnotation())
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359 annotationPanel.fastPaint(av.getStartRes() - oldX);
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365 public void paintComponent(Graphics g)
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368 Dimension d = idPanel.idCanvas.getPreferredSize();
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369 idPanelHolder.setPreferredSize(d);
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370 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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373 if (av.getWrapAlignment())
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375 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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376 vscroll.setMaximum(max);
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377 vscroll.setUnitIncrement(1);
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378 vscroll.setVisibleAmount(1);
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382 if (overviewPanel != null)
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383 overviewPanel.updateOverviewImage();
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384 setScrollValues(av.getStartRes(), av.getStartSeq());
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391 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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393 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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395 int pwidth = (int) pf.getImageableWidth();
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396 int pheight = (int) pf.getImageableHeight();
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398 if (av.getWrapAlignment())
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399 return printWrappedAlignment(pg, pwidth,pheight, pi);
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401 return printUnwrapped(pg,pwidth, pheight,pi);
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404 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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407 int idWidth = calculateIdWidth().width + 4;
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410 pg.setColor(Color.white);
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411 pg.fillRect(0,0,pwidth, pheight);
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412 pg.setFont( av.getFont() );
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414 ////////////////////////////////////
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415 /// How many sequences and residues can we fit on a printable page?
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416 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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417 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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418 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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419 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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421 if (pi >= pagesWide*pagesHigh)
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422 return Printable.NO_SUCH_PAGE;
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424 /////////////////////////////
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425 /// Only print these sequences and residues on this page
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426 int startRes, endRes, startSeq, endSeq;
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427 startRes = (pi % pagesWide) * totalRes;
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428 endRes = startRes + totalRes-1;
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429 if(endRes>av.getAlignment().getWidth())
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430 endRes = av.getAlignment().getWidth();
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432 startSeq = (pi / pagesWide) * totalSeq;
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433 endSeq = startSeq + totalSeq;
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434 if(endSeq > av.getAlignment().getHeight())
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435 endSeq = av.getAlignment().getHeight();
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440 pg.translate(idWidth,0);
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441 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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443 pg.translate(-idWidth, 30);
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446 Color currentColor=null;
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447 Color currentTextColor=null;
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448 for(int i=startSeq; i<endSeq; i++)
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450 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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452 currentColor = Color.gray;
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453 currentTextColor = Color.black;
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457 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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458 currentTextColor = Color.black;
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461 pg.setColor(currentColor);
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462 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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464 av.getCharHeight());
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466 pg.setColor(currentTextColor);
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468 String string = av.getAlignment().getSequenceAt(i).getName();
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469 if(av.getShowFullId())
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470 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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472 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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473 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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476 // draw main sequence panel
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477 pg.translate(idWidth,0);
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478 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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481 if(av.getShowAnnotation())
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483 pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
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484 alabels.drawComponent((Graphics2D)pg);
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485 pg.translate(idWidth,0);
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486 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
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489 return Printable.PAGE_EXISTS;
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493 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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496 int idWidth = calculateIdWidth().width+4;
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498 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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499 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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502 pg.setColor(Color.white);
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503 pg.fillRect(0,0,pwidth, pheight);
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504 pg.setFont( av.getFont() );
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506 ////////////////////////////////////
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507 /// How many sequences and residues can we fit on a printable page?
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508 AlignmentI da = av.alignment;
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509 int endy = da.getHeight();
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510 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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511 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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513 int noChunksOnPage = pheight / chunkHeight;
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514 int totalChunks = da.getWidth() / chunkWidth;
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516 if ( pi*noChunksOnPage > totalChunks )
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517 return Printable.NO_SUCH_PAGE;
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521 // pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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523 pg.setColor(Color.black);
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525 int rowSize = av.getEndRes() - av.getStartRes();
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526 for(int ypos=2*av.charHeight, row=av.getEndRes()-rowSize;
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527 ypos <= pheight && row<av.alignment.getWidth();
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528 ypos += av.chunkHeight, row+=rowSize )
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530 for (int i = 0; i < endy; i++)
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532 SequenceI s = da.getSequenceAt(i);
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533 String string = s.getName();
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534 if (av.getShowFullId())
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535 string = s.getDisplayId();
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537 pg.drawString(string, 0,
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538 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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539 av.charHeight - (av.charHeight / 5));
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543 // draw main sequence panel
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544 pg.translate(idWidth,0);
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545 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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548 return Printable.PAGE_EXISTS;
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553 public void makeEPS()
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555 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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556 int width = seqPanel.getWidth() + idPanel.getWidth();
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558 if (!av.getWrapAlignment())
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560 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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561 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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563 if(av.getShowAnnotation())
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565 height += annotationPanel.getPreferredSize().height;
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570 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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571 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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572 chooser.setFileView(new jalview.io.JalviewFileView());
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573 chooser.setDialogTitle("Create EPS file from alignment");
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574 chooser.setToolTipText("Save");
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576 int value = chooser.showSaveDialog(this);
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577 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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580 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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581 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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582 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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584 if (av.getWrapAlignment())
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585 printWrappedAlignment(pg, width, height, 0);
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587 printUnwrapped(pg, width, height, 0);
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593 catch (Exception ex)
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595 ex.printStackTrace();
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599 public void makePNG()
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601 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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602 int width = seqPanel.getWidth() + idPanel.getWidth();
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604 if (!av.getWrapAlignment())
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606 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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607 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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610 if(av.getShowAnnotation())
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612 height += annotationPanel.getPreferredSize().height;
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619 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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620 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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621 chooser.setFileView(new jalview.io.JalviewFileView());
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622 chooser.setDialogTitle("Create EPS file from alignment");
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623 chooser.setToolTipText("Save");
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625 int value = chooser.showSaveDialog(this);
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626 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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629 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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630 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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632 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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633 Graphics2D png = (Graphics2D)bi.getGraphics();
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635 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
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637 if (av.getWrapAlignment())
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638 printWrappedAlignment(png, width, height, 0);
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640 printUnwrapped(png, width, height, 0);
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642 ImageIO.write(bi, "png", out);
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645 catch (Exception ex)
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647 ex.printStackTrace();
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