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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23 import java.awt.event.*;
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25 import jalview.datamodel.*;
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27 public class AlignmentPanel extends Panel implements AdjustmentListener
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31 OverviewPanel overviewPanel;
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34 IdwidthAdjuster idwidthAdjuster;
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35 public AlignFrame alignFrame;
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36 ScalePanel scalePanel;
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37 AnnotationPanel annotationPanel;
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38 AnnotationLabels alabels;
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40 // this value is set false when selection area being dragged
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41 boolean fastPaint = true;
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43 boolean MAC = false;
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45 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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47 this.addKeyListener(new KeyAdapter()
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49 public void keyPressed(KeyEvent ke)
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51 System.out.println("Align Panel "+ke);
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61 e.printStackTrace();
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64 if(System.getProperty("os.name").startsWith("Mac"))
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69 seqPanel = new SeqPanel(av, this);
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70 idPanel = new IdPanel(av, this);
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71 scalePanel = new ScalePanel(av, this);
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72 idwidthAdjuster = new IdwidthAdjuster(this);
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73 annotationPanel = new AnnotationPanel(this);
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74 alabels = new AnnotationLabels(this);
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76 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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77 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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78 annotationScroller.add(annotationPanel);
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79 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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80 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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81 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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84 setScrollValues(0, 0);
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86 hscroll.addAdjustmentListener(this);
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87 vscroll.addAdjustmentListener(this);
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89 addComponentListener(new ComponentAdapter()
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91 public void componentResized(ComponentEvent evt)
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93 setScrollValues(av.getStartRes(), av.getStartSeq());
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98 Dimension d = calculateIdWidth();
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99 idPanel.idCanvas.setSize(d);
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101 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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102 annotationScroller.setSize(annotationPanel.getSize());
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104 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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105 annotationSpaceFillerHolder.setSize(d.width,
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106 annotationPanel.getSize().height);
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107 alabels.setSize(d.width, annotationPanel.getSize().height);
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112 public void fontChanged()
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114 // set idCanvas bufferedImage to null
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115 // to prevent drawing old image
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116 FontMetrics fm = getFontMetrics(av.getFont());
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118 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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119 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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121 annotationPanel.adjustPanelHeight();
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122 annotationPanel.repaint();
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123 Dimension d = calculateIdWidth();
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124 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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125 idPanel.idCanvas.setSize(d);
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126 hscrollFillerPanel.setSize(d);
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130 if(overviewPanel!=null)
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131 overviewPanel.updateOverviewImage();
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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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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 id = s.getDisplayId(av.getShowJVSuffix());
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165 if (fm.stringWidth(id) > idWidth)
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167 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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182 idWidth = fm.stringWidth(label);
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188 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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196 if (results != null)
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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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206 setScrollValues(start, results[0]);
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212 public OverviewPanel getOverviewPanel()
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214 return overviewPanel;
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217 public void setOverviewPanel(OverviewPanel op)
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219 overviewPanel = op;
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222 public void setAnnotationVisible(boolean b)
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224 if (!av.wrapAlignment)
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226 annotationSpaceFillerHolder.setVisible(b);
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227 annotationScroller.setVisible(b);
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233 public void setWrapAlignment(boolean wrap)
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236 scalePanelHolder.setVisible(!wrap);
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237 hscroll.setVisible(!wrap);
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238 idwidthAdjuster.setVisible(!wrap);
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242 annotationScroller.setVisible(false);
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243 annotationSpaceFillerHolder.setVisible(false);
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245 else if (av.showAnnotation)
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247 annotationScroller.setVisible(true);
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248 annotationSpaceFillerHolder.setVisible(true);
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251 idSpaceFillerPanel1.setVisible(!wrap);
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262 // return value is true if the scroll is valid
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263 public boolean scrollUp(boolean up)
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267 if (vscroll.getValue() < 1)
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272 vscroll.setValue(vscroll.getValue() - 1);
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276 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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297 hscroll.setValue(hscroll.getValue() - 1);
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301 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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306 hscroll.setValue(hscroll.getValue() + 1);
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312 public void setScrollValues(int x, int y)
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317 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
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319 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
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320 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
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322 if (hextent > av.alignment.getWidth())
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324 hextent = av.alignment.getWidth();
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326 if (vextent > av.alignment.getHeight())
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328 vextent = av.alignment.getHeight();
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331 if (hextent + x > av.getAlignment().getWidth())
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333 x = av.getAlignment().getWidth() - hextent;
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336 if (vextent + y > av.getAlignment().getHeight())
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338 y = av.getAlignment().getHeight() - vextent;
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351 int endSeq = y + vextent;
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352 if (endSeq > av.alignment.getHeight())
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354 endSeq = av.alignment.getHeight();
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357 av.setEndSeq(endSeq);
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358 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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359 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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363 public void adjustmentValueChanged(AdjustmentEvent evt)
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365 int oldX = av.getStartRes();
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366 int oldY = av.getStartSeq();
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368 if (evt.getSource() == hscroll)
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370 int x = hscroll.getValue();
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372 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
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376 if (evt.getSource() == vscroll)
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378 int offy = vscroll.getValue();
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379 if (av.getWrapAlignment())
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381 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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382 seqCanvas.getSize().width);
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383 av.setStartRes(vscroll.getValue() * rowSize);
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384 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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388 av.setStartSeq(offy);
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389 av.setEndSeq(offy +
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390 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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394 if (overviewPanel != null)
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396 overviewPanel.setBoxPosition();
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399 if (av.getWrapAlignment() || !fastPaint || MAC)
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405 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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406 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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407 av.getStartSeq() - oldY);
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409 scalePanel.repaint();
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410 if (av.getShowAnnotation())
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412 annotationPanel.fastPaint(av.getStartRes() - oldX);
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418 public void update(Graphics g)
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423 public void paint(Graphics g)
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425 Dimension d = idPanel.idCanvas.getSize();
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426 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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427 annotationSpaceFillerHolder.setSize(d.width,
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428 annotationPanel.getSize().height);
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430 alabels.setSize(d.width, annotationPanel.getSize().height);
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432 if (av.getWrapAlignment())
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434 int max = av.alignment.getWidth() /
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435 seqPanel.seqCanvas.
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436 getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
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437 vscroll.setMaximum(max);
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438 vscroll.setUnitIncrement(1);
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439 vscroll.setVisibleAmount(1);
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443 setScrollValues(av.getStartRes(), av.getStartSeq());
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448 seqPanel.seqCanvas.repaint();
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449 scalePanel.repaint();
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450 annotationPanel.repaint();
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451 idPanel.idCanvas.repaint();
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453 if (getBounds() == g.getClipBounds())
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455 if (overviewPanel != null)
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456 overviewPanel.updateOverviewImage();
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461 protected Panel sequenceHolderPanel = new Panel();
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462 protected Scrollbar vscroll = new Scrollbar();
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463 protected Scrollbar hscroll = new Scrollbar();
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464 protected Panel seqPanelHolder = new Panel();
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465 BorderLayout borderLayout1 = new BorderLayout();
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466 BorderLayout borderLayout3 = new BorderLayout();
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467 protected Panel scalePanelHolder = new Panel();
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468 protected Panel idPanelHolder = new Panel();
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469 BorderLayout borderLayout5 = new BorderLayout();
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470 protected Panel idSpaceFillerPanel1 = new Panel();
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471 public Panel annotationSpaceFillerHolder = new Panel();
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472 BorderLayout borderLayout6 = new BorderLayout();
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473 BorderLayout borderLayout7 = new BorderLayout();
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474 Panel hscrollHolder = new Panel();
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475 BorderLayout borderLayout10 = new BorderLayout();
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476 protected Panel hscrollFillerPanel = new Panel();
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477 BorderLayout borderLayout11 = new BorderLayout();
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478 public Panel annotationScroller = new Panel();
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479 BorderLayout borderLayout4 = new BorderLayout();
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480 BorderLayout borderLayout2 = new BorderLayout();
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482 private void jbInit() throws Exception {
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483 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
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484 this.setLayout(borderLayout7);
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486 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
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487 sequenceHolderPanel.setLayout(borderLayout3);
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488 seqPanelHolder.setLayout(borderLayout1);
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489 scalePanelHolder.setBackground(Color.white);
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491 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
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492 scalePanelHolder.setLayout(borderLayout6);
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493 idPanelHolder.setLayout(borderLayout5);
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494 idSpaceFillerPanel1.setBackground(Color.white);
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496 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
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497 idSpaceFillerPanel1.setLayout(borderLayout11);
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498 annotationSpaceFillerHolder.setBackground(Color.white);
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500 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
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501 annotationSpaceFillerHolder.setLayout(borderLayout4);
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502 hscroll.setOrientation(Scrollbar.HORIZONTAL);
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503 hscrollHolder.setLayout(borderLayout10);
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504 hscrollFillerPanel.setBackground(Color.white);
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506 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
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507 hscrollHolder.setBackground(Color.white);
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509 // annotationScroller.setPreferredSize(new Dimension(10, 80));
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510 // this.setPreferredSize(new Dimension(220, 166));
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511 seqPanelHolder.setBackground(Color.white);
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512 idPanelHolder.setBackground(Color.white);
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513 annotationScroller.setLayout(borderLayout2);
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514 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
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515 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
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516 seqPanelHolder.add(vscroll, BorderLayout.EAST);
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517 sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
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519 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
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520 this.add(idPanelHolder, BorderLayout.WEST);
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521 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
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522 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
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523 this.add(hscrollHolder, BorderLayout.SOUTH);
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524 hscrollHolder.add(hscroll, BorderLayout.CENTER);
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525 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
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526 this.add(sequenceHolderPanel, BorderLayout.CENTER);
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