1 package jalview.appletgui;
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3 import jalview.jbappletgui.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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10 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
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14 OverviewPanel overviewPanel;
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17 IdwidthAdjuster idwidthAdjuster;
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18 public AlignFrame alignFrame;
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19 ScalePanel scalePanel;
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20 AnnotationPanel annotationPanel;
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21 AnnotationLabels alabels;
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23 // this value is set false when selection area being dragged
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24 boolean fastPaint = true;
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26 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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30 seqPanel = new SeqPanel (av, this);
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31 idPanel = new IdPanel (av, this);
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32 scalePanel = new ScalePanel(av, this);
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33 idwidthAdjuster = new IdwidthAdjuster(this);
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34 annotationPanel = new AnnotationPanel(this);
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35 alabels = new AnnotationLabels(this);
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38 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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39 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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40 annotationScroller.add(annotationPanel);
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41 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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42 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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43 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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46 setScrollValues(0, 0);
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48 hscroll.addAdjustmentListener(this);
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49 vscroll.addAdjustmentListener(this);
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51 seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );
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52 idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );
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54 addComponentListener(new ComponentAdapter()
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56 public void componentResized(ComponentEvent evt)
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58 setScrollValues(av.getStartRes(), av.getStartSeq());
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63 Dimension d = calculateIdWidth();
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64 idPanel.idCanvas.setSize(d);
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66 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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67 annotationScroller.setSize(annotationPanel.getSize());
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69 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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70 annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
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71 alabels.setSize(d.width,annotationPanel.getSize().height);
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75 class MyKeyAdapter extends KeyAdapter
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77 public void keyPressed(KeyEvent evt)
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79 switch(evt.getKeyCode())
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81 case 27: // escape key
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82 av.setSelectionGroup(null);
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83 alignFrame.alignPanel.repaint();
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86 if(evt.isControlDown())
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87 alignFrame.cut_actionPerformed(null);
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90 if(evt.isControlDown())
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91 alignFrame.copy_actionPerformed(null);
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94 if(evt.isControlDown())
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95 alignFrame.paste(true);
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98 if(evt.isControlDown())
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99 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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101 case KeyEvent.VK_DOWN:
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102 alignFrame.moveSelectedSequences(false);
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104 case KeyEvent.VK_UP:
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105 alignFrame.moveSelectedSequences(true);
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107 case KeyEvent.VK_F:
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108 if(evt.isControlDown())
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109 alignFrame.findMenuItem_actionPerformed(null);
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115 public void fontChanged()
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117 // set idCanvas bufferedImage to null
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118 // to prevent drawing old image
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119 FontMetrics fm = getFontMetrics(av.getFont());
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121 scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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122 idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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124 annotationPanel.adjustPanelHeight();
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125 annotationPanel.repaint();
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126 Dimension d = calculateIdWidth();
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127 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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128 idPanel.idCanvas.setSize(d);
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129 hscrollFillerPanel.setSize(d);
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134 public void setIdWidth(int w, int h)
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136 idPanel.idCanvas.setSize(w,h);
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137 idPanelHolder.setSize(w,idPanelHolder.getSize().height);
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138 alabels.setSize(w,alabels.getSize().height);
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141 Dimension calculateIdWidth()
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143 Frame frame = new Frame();
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145 Graphics g = frame.getGraphics();
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148 Frame f = new Frame();
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150 g = f.getGraphics();
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153 FontMetrics fm = g.getFontMetrics(av.font);
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154 AlignmentI al = av.getAlignment();
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159 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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161 SequenceI s = al.getSequenceAt(i);
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162 if(av.getShowFullId())
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163 id = s.getDisplayId();
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167 if (fm.stringWidth(id) > idWidth)
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168 idWidth = fm.stringWidth(id);
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172 // Also check annotation label widths
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174 if(al.getAlignmentAnnotation()!=null)
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176 fm = g.getFontMetrics(frame.getFont());
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177 while (i < al.getAlignmentAnnotation().length)
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179 String label = al.getAlignmentAnnotation()[i].label;
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180 if (fm.stringWidth(label) > idWidth)
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181 idWidth = fm.stringWidth(label);
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186 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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190 public void highlightSearchResults(int [] results)
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192 seqPanel.seqCanvas.highlightSearchResults( results );
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194 // do we need to scroll the panel?
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195 if(results!=null && (av.getStartSeq()>results[0]
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196 || av.getEndSeq()<results[0]
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197 || av.getStartRes()>results[1]
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198 || av.getEndRes()<results[2]))
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199 setScrollValues(results[1], results[0]);
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205 public OverviewPanel getOverviewPanel()
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207 return overviewPanel;
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210 public void setOverviewPanel(OverviewPanel op)
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212 overviewPanel = op;
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216 public void setAnnotationVisible(boolean b)
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218 annotationSpaceFillerHolder.setVisible(b);
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219 annotationScroller.setVisible(b);
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223 public void setWrapAlignment(boolean wrap)
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225 scalePanelHolder.setVisible(!wrap);
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226 hscroll.setVisible(!wrap);
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227 idwidthAdjuster.setVisible(!wrap);
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229 av.setShowAnnotation(!wrap);
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230 annotationScroller.setVisible(!wrap);
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231 annotationSpaceFillerHolder.setVisible(!wrap);
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232 idSpaceFillerPanel1.setVisible(!wrap);
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239 public void setColourScheme()
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241 ColourSchemeI cs = av.getGlobalColourScheme();
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243 if(av.getConservationSelected())
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246 Alignment al = (Alignment)av.getAlignment();
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247 Conservation c = new Conservation("All",
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248 ResidueProperties.propHash, 3, al.getSequences(), 0,
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252 c.verdict(false, av.ConsPercGaps);
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253 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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255 av.setGlobalColourScheme( ccs );
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266 // return value is true if the scroll is valid
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267 public boolean scrollUp(boolean up)
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271 if(vscroll.getValue()<1)
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274 vscroll.setValue(vscroll.getValue() - 1);
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278 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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281 vscroll.setValue(vscroll.getValue() + 1);
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287 public boolean scrollRight(boolean right)
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292 if (hscroll.getValue() < 1)
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295 hscroll.setValue(hscroll.getValue() - 1);
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299 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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302 hscroll.setValue(hscroll.getValue() + 1);
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309 public void setScrollValues(int x, int y)
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314 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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316 hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;
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317 vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;
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319 if(hextent > av.alignment.getWidth())
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320 hextent = av.alignment.getWidth();
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321 if(vextent > av.alignment.getHeight())
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322 vextent = av.alignment.getHeight();
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324 if(hextent+x > av.getAlignment().getWidth())
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325 x = av.getAlignment().getWidth()- hextent;
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327 if(vextent+y > av.getAlignment().getHeight())
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328 y = av.getAlignment().getHeight() - vextent;
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337 int endSeq = y + vextent;
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338 if(endSeq>av.alignment.getHeight())
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339 endSeq = av.alignment.getHeight();
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342 av.setEndSeq( endSeq );
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343 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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344 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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349 public void adjustmentValueChanged(AdjustmentEvent evt)
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351 int oldX = av.getStartRes();
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352 int oldY = av.getStartSeq();
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354 if (evt.getSource() == hscroll)
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356 int x = hscroll.getValue();
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358 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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361 if (evt.getSource() == vscroll)
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363 int offy = vscroll.getValue();
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364 if (av.getWrapAlignment())
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366 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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367 av.setStartRes( vscroll.getValue() * rowSize );
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368 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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372 av.setStartSeq(offy);
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373 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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377 if(overviewPanel!=null)
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378 overviewPanel.setBoxPosition();
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380 if(av.getWrapAlignment() || !fastPaint)
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384 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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385 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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386 av.getStartSeq() - oldY);
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388 scalePanel.repaint();
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389 if (av.getShowAnnotation())
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390 annotationPanel.fastPaint(av.getStartRes() - oldX);
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395 public void update(Graphics g)
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401 public void paint(Graphics g)
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403 Dimension d = idPanel.idCanvas.getSize();
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404 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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405 annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
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406 alabels.setSize(d.width,annotationPanel.getSize().height);
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409 idPanel.idCanvas.repaint();
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410 seqPanel.seqCanvas.repaint();
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411 scalePanel.repaint();
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412 annotationPanel.repaint();
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415 if (av.getWrapAlignment())
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417 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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418 vscroll.setMaximum(max);
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419 vscroll.setUnitIncrement(1);
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420 vscroll.setVisibleAmount(1);
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424 setScrollValues(av.getStartRes(), av.getStartSeq());
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