2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.jbappletgui.GAlignmentPanel;
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23 import jalview.schemes.*;
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24 import jalview.analysis.*;
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25 import jalview.datamodel.*;
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27 import java.awt.event.*;
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29 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
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33 OverviewPanel overviewPanel;
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36 IdwidthAdjuster idwidthAdjuster;
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37 public AlignFrame alignFrame;
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38 ScalePanel scalePanel;
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39 AnnotationPanel annotationPanel;
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40 AnnotationLabels alabels;
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42 // this value is set false when selection area being dragged
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43 boolean fastPaint = true;
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45 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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49 seqPanel = new SeqPanel (av, this);
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50 idPanel = new IdPanel (av, this);
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51 scalePanel = new ScalePanel(av, this);
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52 idwidthAdjuster = new IdwidthAdjuster(this);
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53 annotationPanel = new AnnotationPanel(this);
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54 alabels = new AnnotationLabels(this);
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57 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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58 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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59 annotationScroller.add(annotationPanel);
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60 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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61 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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62 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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65 setScrollValues(0, 0);
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67 hscroll.addAdjustmentListener(this);
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68 vscroll.addAdjustmentListener(this);
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70 seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );
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71 idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );
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73 addComponentListener(new ComponentAdapter()
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75 public void componentResized(ComponentEvent evt)
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77 setScrollValues(av.getStartRes(), av.getStartSeq());
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82 Dimension d = calculateIdWidth();
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83 idPanel.idCanvas.setSize(d);
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85 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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86 annotationScroller.setSize(annotationPanel.getSize());
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88 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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89 annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
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90 alabels.setSize(d.width,annotationPanel.getSize().height);
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94 class MyKeyAdapter extends KeyAdapter
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96 public void keyPressed(KeyEvent evt)
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98 // System.out.println(evt.getKeyCode()); log.
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99 switch(evt.getKeyCode())
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101 case 27: // escape key
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102 av.setSelectionGroup(null);
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103 alignFrame.alignPanel.repaint();
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105 case KeyEvent.VK_X:
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106 if(evt.isControlDown())
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107 alignFrame.cut_actionPerformed(null);
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109 case KeyEvent.VK_C:
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110 if(evt.isControlDown())
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111 alignFrame.copy_actionPerformed(null);
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113 case KeyEvent.VK_V:
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114 if(evt.isControlDown())
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115 alignFrame.paste(true);
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117 case KeyEvent.VK_A:
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118 if(evt.isControlDown())
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119 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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121 case KeyEvent.VK_DOWN:
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122 alignFrame.moveSelectedSequences(false);
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124 case KeyEvent.VK_UP:
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125 alignFrame.moveSelectedSequences(true);
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127 case KeyEvent.VK_F:
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128 if(evt.isControlDown())
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129 alignFrame.findMenuItem_actionPerformed(null);
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135 public void fontChanged()
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137 // set idCanvas bufferedImage to null
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138 // to prevent drawing old image
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139 FontMetrics fm = getFontMetrics(av.getFont());
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141 scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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142 idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
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144 annotationPanel.adjustPanelHeight();
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145 annotationPanel.repaint();
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146 Dimension d = calculateIdWidth();
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147 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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148 idPanel.idCanvas.setSize(d);
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149 hscrollFillerPanel.setSize(d);
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154 public void setIdWidth(int w, int h)
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156 idPanel.idCanvas.setSize(w,h);
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157 idPanelHolder.setSize(w,idPanelHolder.getSize().height);
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158 alabels.setSize(w,alabels.getSize().height);
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161 Dimension calculateIdWidth()
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163 Frame frame = new Frame();
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165 Graphics g = frame.getGraphics();
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168 Frame f = new Frame();
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170 g = f.getGraphics();
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173 FontMetrics fm = g.getFontMetrics(av.font);
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174 AlignmentI al = av.getAlignment();
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179 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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181 SequenceI s = al.getSequenceAt(i);
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182 if(av.getShowFullId())
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183 id = s.getDisplayId();
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187 if (fm.stringWidth(id) > idWidth)
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188 idWidth = fm.stringWidth(id);
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192 // Also check annotation label widths
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194 if(al.getAlignmentAnnotation()!=null)
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196 fm = g.getFontMetrics(frame.getFont());
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197 while (i < al.getAlignmentAnnotation().length)
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199 String label = al.getAlignmentAnnotation()[i].label;
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200 if (fm.stringWidth(label) > idWidth)
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201 idWidth = fm.stringWidth(label);
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206 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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210 public void highlightSearchResults(int [] results)
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212 seqPanel.seqCanvas.highlightSearchResults( results );
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214 // do we need to scroll the panel?
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217 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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218 int start = seq.findIndex( results[1] )-1;
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219 int end = seq.findIndex( results[2] )-1;
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220 if( av.getStartRes() > start
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221 || av.getEndRes() < end
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222 || (av.getStartSeq() > results[0]
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223 || av.getEndSeq() < results[0]))
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224 setScrollValues(start, results[0]);
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230 public OverviewPanel getOverviewPanel()
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232 return overviewPanel;
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235 public void setOverviewPanel(OverviewPanel op)
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237 overviewPanel = op;
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241 public void setAnnotationVisible(boolean b)
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243 annotationSpaceFillerHolder.setVisible(b);
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244 annotationScroller.setVisible(b);
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250 public void setWrapAlignment(boolean wrap)
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252 scalePanelHolder.setVisible(!wrap);
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253 hscroll.setVisible(!wrap);
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254 idwidthAdjuster.setVisible(!wrap);
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256 av.setShowAnnotation(!wrap);
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257 annotationScroller.setVisible(!wrap);
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258 annotationSpaceFillerHolder.setVisible(!wrap);
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259 idSpaceFillerPanel1.setVisible(!wrap);
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267 public void setColourScheme()
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269 ColourSchemeI cs = av.getGlobalColourScheme();
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271 if(av.getConservationSelected())
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274 Alignment al = (Alignment)av.getAlignment();
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275 Conservation c = new Conservation("All",
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276 ResidueProperties.propHash, 3, al.getSequences(), 0,
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280 c.verdict(false, av.ConsPercGaps);
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281 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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283 av.setGlobalColourScheme( ccs );
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294 // return value is true if the scroll is valid
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295 public boolean scrollUp(boolean up)
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299 if(vscroll.getValue()<1)
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302 vscroll.setValue(vscroll.getValue() - 1);
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306 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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309 vscroll.setValue(vscroll.getValue() + 1);
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315 public boolean scrollRight(boolean right)
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320 if (hscroll.getValue() < 1)
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323 hscroll.setValue(hscroll.getValue() - 1);
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327 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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330 hscroll.setValue(hscroll.getValue() + 1);
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337 public void setScrollValues(int x, int y)
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342 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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344 hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;
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345 vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;
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347 if(hextent > av.alignment.getWidth())
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348 hextent = av.alignment.getWidth();
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349 if(vextent > av.alignment.getHeight())
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350 vextent = av.alignment.getHeight();
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352 if(hextent+x > av.getAlignment().getWidth())
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353 x = av.getAlignment().getWidth()- hextent;
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355 if(vextent+y > av.getAlignment().getHeight())
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356 y = av.getAlignment().getHeight() - vextent;
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365 int endSeq = y + vextent;
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366 if(endSeq>av.alignment.getHeight())
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367 endSeq = av.alignment.getHeight();
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370 av.setEndSeq( endSeq );
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371 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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372 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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377 public void adjustmentValueChanged(AdjustmentEvent evt)
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379 int oldX = av.getStartRes();
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380 int oldY = av.getStartSeq();
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382 if (evt.getSource() == hscroll)
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384 int x = hscroll.getValue();
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386 av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
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389 if (evt.getSource() == vscroll)
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391 int offy = vscroll.getValue();
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392 if (av.getWrapAlignment())
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394 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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395 av.setStartRes( vscroll.getValue() * rowSize );
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396 av.setEndRes( (vscroll.getValue()+1) * rowSize );
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400 av.setStartSeq(offy);
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401 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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405 if(overviewPanel!=null)
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406 overviewPanel.setBoxPosition();
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408 if(av.getWrapAlignment() || !fastPaint)
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412 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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413 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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414 av.getStartSeq() - oldY);
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416 scalePanel.repaint();
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417 if (av.getShowAnnotation())
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418 annotationPanel.fastPaint(av.getStartRes() - oldX);
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423 public void update(Graphics g)
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429 public void paint(Graphics g)
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431 Dimension d = idPanel.idCanvas.getSize();
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432 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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433 annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
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434 alabels.setSize(d.width,annotationPanel.getSize().height);
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437 idPanel.idCanvas.repaint();
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438 seqPanel.seqCanvas.repaint();
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439 scalePanel.repaint();
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440 annotationPanel.repaint();
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443 if (av.getWrapAlignment())
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445 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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446 vscroll.setMaximum(max);
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447 vscroll.setUnitIncrement(1);
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448 vscroll.setVisibleAmount(1);
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452 setScrollValues(av.getStartRes(), av.getStartSeq());
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