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 // System.out.println(evt.getKeyCode()); log.
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80 switch(evt.getKeyCode())
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82 case 27: // escape key
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83 av.setSelectionGroup(null);
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84 alignFrame.alignPanel.repaint();
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87 if(evt.isControlDown())
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88 alignFrame.cut_actionPerformed(null);
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91 if(evt.isControlDown())
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92 alignFrame.copy_actionPerformed(null);
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95 if(evt.isControlDown())
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96 alignFrame.paste(true);
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99 if(evt.isControlDown())
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100 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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102 case KeyEvent.VK_DOWN:
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103 alignFrame.moveSelectedSequences(false);
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105 case KeyEvent.VK_UP:
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106 alignFrame.moveSelectedSequences(true);
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108 case KeyEvent.VK_F:
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109 if(evt.isControlDown())
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110 alignFrame.findMenuItem_actionPerformed(null);
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116 public void fontChanged()
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118 // set idCanvas bufferedImage to null
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119 // to prevent drawing old image
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120 FontMetrics fm = getFontMetrics(av.getFont());
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122 scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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123 idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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125 annotationPanel.adjustPanelHeight();
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126 annotationPanel.repaint();
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127 Dimension d = calculateIdWidth();
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128 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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129 idPanel.idCanvas.setSize(d);
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130 hscrollFillerPanel.setSize(d);
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135 public void setIdWidth(int w, int h)
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137 idPanel.idCanvas.setSize(w,h);
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138 idPanelHolder.setSize(w,idPanelHolder.getSize().height);
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139 alabels.setSize(w,alabels.getSize().height);
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142 Dimension calculateIdWidth()
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144 Frame frame = new Frame();
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146 Graphics g = frame.getGraphics();
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149 Frame f = new Frame();
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151 g = f.getGraphics();
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154 FontMetrics fm = g.getFontMetrics(av.font);
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155 AlignmentI al = av.getAlignment();
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160 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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162 SequenceI s = al.getSequenceAt(i);
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163 if(av.getShowFullId())
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164 id = s.getDisplayId();
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168 if (fm.stringWidth(id) > idWidth)
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169 idWidth = fm.stringWidth(id);
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173 // Also check annotation label widths
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175 if(al.getAlignmentAnnotation()!=null)
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177 fm = g.getFontMetrics(frame.getFont());
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178 while (i < al.getAlignmentAnnotation().length)
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180 String label = al.getAlignmentAnnotation()[i].label;
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181 if (fm.stringWidth(label) > idWidth)
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182 idWidth = fm.stringWidth(label);
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187 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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191 public void highlightSearchResults(int [] results)
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193 seqPanel.seqCanvas.highlightSearchResults( results );
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195 // do we need to scroll the panel?
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198 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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199 int start = seq.findIndex( results[1] )-1;
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200 int end = seq.findIndex( results[2] )-1;
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201 if( av.getStartRes() > start
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202 || av.getEndRes() < end
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203 || (av.getStartSeq() > results[0]
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204 || av.getEndSeq() < results[0]))
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205 setScrollValues(start, results[0]);
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211 public OverviewPanel getOverviewPanel()
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213 return overviewPanel;
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216 public void setOverviewPanel(OverviewPanel op)
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218 overviewPanel = op;
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222 public void setAnnotationVisible(boolean b)
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224 annotationSpaceFillerHolder.setVisible(b);
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225 annotationScroller.setVisible(b);
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231 public void setWrapAlignment(boolean wrap)
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233 scalePanelHolder.setVisible(!wrap);
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234 hscroll.setVisible(!wrap);
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235 idwidthAdjuster.setVisible(!wrap);
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237 av.setShowAnnotation(!wrap);
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238 annotationScroller.setVisible(!wrap);
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239 annotationSpaceFillerHolder.setVisible(!wrap);
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240 idSpaceFillerPanel1.setVisible(!wrap);
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248 public void setColourScheme()
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250 ColourSchemeI cs = av.getGlobalColourScheme();
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252 if(av.getConservationSelected())
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255 Alignment al = (Alignment)av.getAlignment();
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256 Conservation c = new Conservation("All",
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257 ResidueProperties.propHash, 3, al.getSequences(), 0,
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261 c.verdict(false, av.ConsPercGaps);
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262 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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264 av.setGlobalColourScheme( ccs );
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275 // return value is true if the scroll is valid
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276 public boolean scrollUp(boolean up)
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280 if(vscroll.getValue()<1)
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283 vscroll.setValue(vscroll.getValue() - 1);
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287 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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290 vscroll.setValue(vscroll.getValue() + 1);
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296 public boolean scrollRight(boolean right)
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301 if (hscroll.getValue() < 1)
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304 hscroll.setValue(hscroll.getValue() - 1);
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308 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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311 hscroll.setValue(hscroll.getValue() + 1);
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318 public void setScrollValues(int x, int y)
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323 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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325 hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;
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326 vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;
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328 if(hextent > av.alignment.getWidth())
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329 hextent = av.alignment.getWidth();
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330 if(vextent > av.alignment.getHeight())
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331 vextent = av.alignment.getHeight();
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333 if(hextent+x > av.getAlignment().getWidth())
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334 x = av.getAlignment().getWidth()- hextent;
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336 if(vextent+y > av.getAlignment().getHeight())
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337 y = av.getAlignment().getHeight() - vextent;
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346 int endSeq = y + vextent;
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347 if(endSeq>av.alignment.getHeight())
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348 endSeq = av.alignment.getHeight();
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351 av.setEndSeq( endSeq );
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352 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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353 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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358 public void adjustmentValueChanged(AdjustmentEvent evt)
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360 int oldX = av.getStartRes();
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361 int oldY = av.getStartSeq();
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363 if (evt.getSource() == hscroll)
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365 int x = hscroll.getValue();
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367 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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370 if (evt.getSource() == vscroll)
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372 int offy = vscroll.getValue();
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373 if (av.getWrapAlignment())
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375 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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376 av.setStartRes( vscroll.getValue() * rowSize );
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377 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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381 av.setStartSeq(offy);
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382 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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386 if(overviewPanel!=null)
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387 overviewPanel.setBoxPosition();
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389 if(av.getWrapAlignment() || !fastPaint)
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393 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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394 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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395 av.getStartSeq() - oldY);
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397 scalePanel.repaint();
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398 if (av.getShowAnnotation())
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399 annotationPanel.fastPaint(av.getStartRes() - oldX);
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404 public void update(Graphics g)
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410 public void paint(Graphics g)
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412 Dimension d = idPanel.idCanvas.getSize();
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413 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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414 annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
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415 alabels.setSize(d.width,annotationPanel.getSize().height);
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418 idPanel.idCanvas.repaint();
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419 seqPanel.seqCanvas.repaint();
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420 scalePanel.repaint();
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421 annotationPanel.repaint();
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424 if (av.getWrapAlignment())
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426 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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427 vscroll.setMaximum(max);
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428 vscroll.setUnitIncrement(1);
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429 vscroll.setVisibleAmount(1);
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433 setScrollValues(av.getStartRes(), av.getStartSeq());
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