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 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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34 seqPanel = new SeqPanel (av, this);
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35 idPanel = new IdPanel (av, this);
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37 scalePanel = new ScalePanel(av, this);
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39 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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40 idwidthAdjuster = new IdwidthAdjuster(this);
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41 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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43 annotationPanel = new AnnotationPanel(this);
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44 alabels = new AnnotationLabels(this);
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46 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
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47 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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48 annotationScroller.setViewportView(annotationPanel);
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49 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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51 Dimension d = calculateIdWidth();
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52 d.setSize( d.width+4, d.height);
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53 idPanel.idCanvas.setPreferredSize( d );
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54 hscrollFillerPanel.setPreferredSize( d );
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56 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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57 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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60 if(seqPanel.seqCanvas.getWidth()==0)
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61 javax.swing.SwingUtilities.invokeLater(new Runnable()
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65 setScrollValues(0,0);
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66 Dimension d = calculateIdWidth();
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67 d.setSize( d.width+4, d.height);
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68 idPanel.idCanvas.setPreferredSize( d );
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74 hscroll.addAdjustmentListener(this);
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75 vscroll.addAdjustmentListener(this);
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77 addComponentListener(new ComponentAdapter()
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79 public void componentResized(ComponentEvent evt)
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86 addKeyListener(new KeyAdapter()
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88 public void keyPressed(KeyEvent evt)
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90 switch(evt.getKeyCode())
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92 case 27: // escape key
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93 av.setSelectionGroup(null);
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97 if(evt.isControlDown())
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98 alignFrame.cut_actionPerformed(null);
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100 case KeyEvent.VK_C:
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101 if(evt.isControlDown())
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102 alignFrame.copy_actionPerformed(null);
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104 case KeyEvent.VK_V:
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105 if(evt.isControlDown())
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106 alignFrame.paste(true);
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108 case KeyEvent.VK_A:
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109 if(evt.isControlDown())
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110 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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112 case KeyEvent.VK_DOWN:
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113 alignFrame.moveSelectedSequences(false);
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115 case KeyEvent.VK_UP:
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116 alignFrame.moveSelectedSequences(true);
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118 case KeyEvent.VK_F:
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119 if(evt.isControlDown())
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120 alignFrame.findMenuItem_actionPerformed(null);
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127 Dimension calculateIdWidth()
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129 Graphics g = this.getGraphics();
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132 javax.swing.JFrame f = new javax.swing.JFrame();
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134 g = f.getGraphics();
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137 FontMetrics fm = g.getFontMetrics(av.font);
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138 AlignmentI al = av.getAlignment();
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143 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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145 SequenceI s = al.getSequenceAt(i);
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146 if(av.getShowFullId())
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147 id = s.getDisplayId();
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151 if (fm.stringWidth(id) > idWidth)
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152 idWidth = fm.stringWidth(id);
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156 return new Dimension(idWidth, 12);
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160 public void highlightSearchResults(int [] results)
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162 seqPanel.seqCanvas.highlightSearchResults( results );
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164 // do we need to scroll the panel?
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165 if(results!=null && (av.getStartSeq()>results[0]
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166 || av.getEndSeq()<results[0]
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167 || av.getStartRes()>results[1]
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168 || av.getEndRes()<results[2]))
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169 setScrollValues(results[1], results[0]);
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175 public OverviewPanel getOverviewPanel()
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177 return overviewPanel;
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180 public void setOverviewPanel(OverviewPanel op)
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182 overviewPanel = op;
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186 public void setAnnotationVisible(boolean b)
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188 annotationSpaceFillerHolder.setVisible(b);
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189 annotationScroller.setVisible(b);
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190 javax.swing.SwingUtilities.invokeLater(new Runnable()
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201 public void setWrapAlignment(boolean wrap)
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203 scalePanelHolder.setVisible(!wrap);
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204 hscroll.setVisible(!wrap);
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205 idwidthAdjuster.setVisible(!wrap);
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207 av.setShowAnnotation(!wrap);
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208 annotationScroller.setVisible(!wrap);
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209 annotationSpaceFillerHolder.setVisible(!wrap);
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210 idSpaceFillerPanel1.setVisible(!wrap);
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217 public void setColourScheme()
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219 ColourSchemeI cs = av.getGlobalColourScheme();
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221 if(av.getConservationSelected())
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224 Alignment al = (Alignment)av.getAlignment();
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225 Conservation c = new Conservation("All",
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226 ResidueProperties.propHash, 3, al.getSequences(), 0,
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230 c.verdict(false, 100);
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231 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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233 av.setGlobalColourScheme( ccs );
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241 public void RefreshPanels()
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246 Dimension d = idPanel.idCanvas.getPreferredSize();
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247 idPanelHolder.setPreferredSize(d);
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248 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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250 if (av.getWrapAlignment())
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252 int max = av.alignment.getWidth() /
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253 (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
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254 vscroll.setValues(0, 1, 0, max);
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258 if (overviewPanel != null)
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259 overviewPanel.updateOverviewImage();
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260 setScrollValues(av.getStartRes(), av.getStartSeq());
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270 // return value is true if the scroll is valid
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271 public boolean scrollUp(boolean up)
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275 if(vscroll.getValue()<1)
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277 vscroll.setValue(vscroll.getValue() - 1);
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281 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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283 vscroll.setValue(vscroll.getValue() + 1);
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288 public boolean scrollRight(boolean right)
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292 if(hscroll.getValue()<1)
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294 hscroll.setValue(hscroll.getValue() - 1);
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298 if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
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300 hscroll.setValue(hscroll.getValue() + 1);
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307 public void setScrollValues(int x, int y)
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309 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
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310 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
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312 if(hextent > av.alignment.getWidth())
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313 hextent = av.alignment.getWidth();
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314 if(vextent > av.alignment.getHeight())
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315 vextent = av.alignment.getHeight();
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317 if(hextent+x > av.getAlignment().getWidth())
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318 x = av.getAlignment().getWidth()- hextent;
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320 if(vextent+y > av.getAlignment().getHeight())
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321 y = av.getAlignment().getHeight() - vextent;
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329 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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330 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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335 public void adjustmentValueChanged(AdjustmentEvent evt)
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337 int oldX = av.getStartRes();
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338 int oldY = av.getStartSeq();
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340 if (evt.getSource() == hscroll)
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342 int x = hscroll.getValue();
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344 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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347 if (evt.getSource() == vscroll)
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349 int offy = vscroll.getValue();
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350 if (av.getWrapAlignment())
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352 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
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356 av.setStartSeq(offy);
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357 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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362 if(overviewPanel!=null)
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363 overviewPanel.setBoxPosition();
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365 if(av.getWrapAlignment())
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369 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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370 av.getStartSeq() - oldY);
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371 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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372 scalePanel.repaint();
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373 if (av.getShowAnnotation())
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374 annotationPanel.fastPaint(av.getStartRes() - oldX);
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379 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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381 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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383 int pwidth = (int) pf.getImageableWidth();
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384 int pheight = (int) pf.getImageableHeight();
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386 if (av.getWrapAlignment())
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387 return printWrappedAlignment(pg, pwidth,pheight, pi);
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389 return printUnwrapped(pg,pwidth, pheight,pi);
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392 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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395 int idWidth = calculateIdWidth().width + 4;
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398 pg.setColor(Color.white);
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399 pg.fillRect(0,0,pwidth, pheight);
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400 pg.setFont( av.getFont() );
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402 ////////////////////////////////////
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403 /// How many sequences and residues can we fit on a printable page?
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404 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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405 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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406 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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407 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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409 if (pi >= pagesWide*pagesHigh)
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410 return Printable.NO_SUCH_PAGE;
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412 /////////////////////////////
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413 /// Only print these sequences and residues on this page
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414 int startRes, endRes, startSeq, endSeq;
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415 startRes = (pi % pagesWide) * totalRes;
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416 endRes = startRes + totalRes-1;
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417 if(endRes>av.getAlignment().getWidth())
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418 endRes = av.getAlignment().getWidth();
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420 startSeq = (pi / pagesWide) * totalSeq;
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421 endSeq = startSeq + totalSeq;
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422 if(endSeq > av.getAlignment().getHeight())
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423 endSeq = av.getAlignment().getHeight();
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428 pg.translate(idWidth,0);
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429 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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431 pg.translate(-idWidth, 30);
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434 Color currentColor=null;
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435 Color currentTextColor=null;
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436 for(int i=startSeq; i<endSeq; i++)
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438 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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440 currentColor = Color.gray;
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441 currentTextColor = Color.black;
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445 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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446 currentTextColor = Color.black;
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449 pg.setColor(currentColor);
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450 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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452 av.getCharHeight());
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454 pg.setColor(currentTextColor);
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456 String string = av.getAlignment().getSequenceAt(i).getName();
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457 if(av.getShowFullId())
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458 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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460 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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461 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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464 // draw main sequence panel
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465 pg.translate(idWidth,0);
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466 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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469 if(av.getShowAnnotation())
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471 pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
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472 alabels.drawComponent((Graphics2D)pg);
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473 pg.translate(idWidth,0);
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474 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
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477 return Printable.PAGE_EXISTS;
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481 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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484 int idWidth = calculateIdWidth().width+4;
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486 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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487 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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490 pg.setColor(Color.white);
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491 pg.fillRect(0,0,pwidth, pheight);
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492 pg.setFont( av.getFont() );
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494 ////////////////////////////////////
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495 /// How many sequences and residues can we fit on a printable page?
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496 AlignmentI da = av.alignment;
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497 int endy = da.getHeight();
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498 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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499 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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501 int noChunksOnPage = pheight / chunkHeight;
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502 int totalChunks = da.getWidth() / chunkWidth;
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504 if ( pi*noChunksOnPage > totalChunks )
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505 return Printable.NO_SUCH_PAGE;
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509 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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511 int row = pi*noChunksOnPage;
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512 pg.setColor(Color.black);
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513 for(int ypos=2*av.charHeight;
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514 ypos <= pheight && row*chunkWidth<da.getWidth();
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515 ypos += chunkHeight, row++ )
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517 for (int i = 0; i < endy; i++)
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519 SequenceI s = da.getSequenceAt(i);
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520 String string = s.getName();
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521 if (av.getShowFullId())
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522 string = s.getDisplayId();
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524 pg.drawString(string, 0,
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525 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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526 av.charHeight - (av.charHeight / 5));
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530 // draw main sequence panel
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531 pg.translate(idWidth,0);
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532 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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535 return Printable.PAGE_EXISTS;
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540 public void makeEPS()
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542 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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543 int width = seqPanel.getWidth() + idPanel.getWidth();
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545 if (!av.getWrapAlignment())
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547 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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548 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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550 if(av.getShowAnnotation())
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552 height += annotationPanel.getPreferredSize().height;
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557 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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558 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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559 chooser.setFileView(new jalview.io.JalviewFileView());
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560 chooser.setDialogTitle("Create EPS file from alignment");
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561 chooser.setToolTipText("Save");
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563 int value = chooser.showSaveDialog(this);
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564 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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567 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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568 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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569 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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571 if (av.getWrapAlignment())
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572 printWrappedAlignment(pg, width, height, 0);
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574 printUnwrapped(pg, width, height, 0);
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580 catch (Exception ex)
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582 ex.printStackTrace();
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586 public void makePNG()
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588 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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589 int width = seqPanel.getWidth() + idPanel.getWidth();
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591 if (!av.getWrapAlignment())
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593 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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594 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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597 if(av.getShowAnnotation())
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599 height += annotationPanel.getPreferredSize().height;
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603 System.out.println(width +" "+height);
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607 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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608 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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609 chooser.setFileView(new jalview.io.JalviewFileView());
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610 chooser.setDialogTitle("Create EPS file from alignment");
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611 chooser.setToolTipText("Save");
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613 int value = chooser.showSaveDialog(this);
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614 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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617 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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618 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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620 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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621 Graphics png = bi.getGraphics();
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624 if (av.getWrapAlignment())
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625 printWrappedAlignment(png, width, height, 0);
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627 printUnwrapped(png, width, height, 0);
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629 ImageIO.write(bi, "png", out);
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632 catch (Exception ex)
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634 ex.printStackTrace();
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