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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53 e.printStackTrace();
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56 if(System.getProperty("os.name").startsWith("Mac"))
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61 seqPanel = new SeqPanel(av, this);
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62 idPanel = new IdPanel(av, this);
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63 scalePanel = new ScalePanel(av, this);
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64 idwidthAdjuster = new IdwidthAdjuster(this);
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65 annotationPanel = new AnnotationPanel(this);
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66 alabels = new AnnotationLabels(this);
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68 setAnnotationVisible(av.showAnnotation);
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70 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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71 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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72 annotationScroller.add(annotationPanel);
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73 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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74 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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75 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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78 setScrollValues(0, 0);
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80 hscroll.addAdjustmentListener(this);
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81 vscroll.addAdjustmentListener(this);
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83 addComponentListener(new ComponentAdapter()
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85 public void componentResized(ComponentEvent evt)
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87 setScrollValues(av.getStartRes(), av.getStartSeq());
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92 Dimension d = calculateIdWidth();
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93 idPanel.idCanvas.setSize(d);
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95 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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96 annotationScroller.setSize(annotationPanel.getSize());
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98 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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99 annotationSpaceFillerHolder.setSize(d.width,
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100 annotationPanel.getSize().height);
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101 alabels.setSize(d.width, annotationPanel.getSize().height);
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106 public void fontChanged()
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108 // set idCanvas bufferedImage to null
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109 // to prevent drawing old image
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110 idPanel.idCanvas.image =null;
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111 FontMetrics fm = getFontMetrics(av.getFont());
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113 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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114 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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116 int ap = annotationPanel.adjustPanelHeight();
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117 annotationPanel.repaint();
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118 Dimension d = calculateIdWidth();
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119 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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120 alabels.setSize(d.width+4, ap );
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121 idPanel.idCanvas.setSize(d);
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122 hscrollFillerPanel.setSize(d);
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127 if(overviewPanel!=null)
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128 overviewPanel.updateOverviewImage();
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131 public void setIdWidth(int w, int h)
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133 idPanel.idCanvas.setSize(w, h);
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134 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
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135 alabels.setSize(w, alabels.getSize().height);
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139 Dimension calculateIdWidth()
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141 Frame frame = new Frame();
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143 Graphics g = frame.getGraphics();
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146 Frame f = new Frame();
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148 g = f.getGraphics();
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151 FontMetrics fm = g.getFontMetrics(av.font);
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152 AlignmentI al = av.getAlignment();
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157 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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159 SequenceI s = al.getSequenceAt(i);
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160 id = s.getDisplayId(av.getShowJVSuffix());
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162 if (fm.stringWidth(id) > idWidth)
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164 idWidth = fm.stringWidth(id);
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169 // Also check annotation label widths
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171 if (al.getAlignmentAnnotation() != null)
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173 fm = g.getFontMetrics(frame.getFont());
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174 while (i < al.getAlignmentAnnotation().length)
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176 String label = al.getAlignmentAnnotation()[i].label;
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177 if (fm.stringWidth(label) > idWidth)
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179 idWidth = fm.stringWidth(label);
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185 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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188 public void highlightSearchResults(int[] results)
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190 seqPanel.seqCanvas.highlightSearchResults(results);
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192 // do we need to scroll the panel?
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193 if (results != null)
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195 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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196 int start = seq.findIndex(results[1]) - 1;
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197 int end = seq.findIndex(results[2]) - 1;
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199 if(!av.wrapAlignment)
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201 if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
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202 ( (av.getStartSeq() > results[0]) ||
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203 (av.getEndSeq() < results[0])))
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205 int newy = results[0];
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206 if(start > av.alignment.getWidth() - hextent)
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208 start = av.alignment.getWidth() - hextent;
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212 if(newy > av.alignment.getHeight() - vextent)
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214 newy = av.alignment.getHeight() - vextent;
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218 setScrollValues(start, newy);
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223 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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224 if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
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227 vscroll.setValue(start / cwidth);
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228 av.startRes = vscroll.getValue() * cwidth;
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236 public OverviewPanel getOverviewPanel()
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238 return overviewPanel;
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241 public void setOverviewPanel(OverviewPanel op)
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243 overviewPanel = op;
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246 public void setAnnotationVisible(boolean b)
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248 if (!av.wrapAlignment)
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250 annotationSpaceFillerHolder.setVisible(b);
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251 annotationScroller.setVisible(b);
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257 public void setWrapAlignment(boolean wrap)
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260 scalePanelHolder.setVisible(!wrap);
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263 hscroll.setVisible(!wrap);
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264 idwidthAdjuster.setVisible(!wrap);
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268 annotationScroller.setVisible(false);
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269 annotationSpaceFillerHolder.setVisible(false);
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271 else if (av.showAnnotation)
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273 annotationScroller.setVisible(true);
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274 annotationSpaceFillerHolder.setVisible(true);
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278 idSpaceFillerPanel1.setVisible(!wrap);
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280 fontChanged();//This is so that the scalePanel is resized correctly
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291 // return value is true if the scroll is valid
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292 public boolean scrollUp(boolean up)
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296 if (vscroll.getValue() < 1)
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301 vscroll.setValue(vscroll.getValue() - 1);
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305 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
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310 vscroll.setValue(vscroll.getValue() + 1);
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316 public boolean scrollRight(boolean right)
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321 if (hscroll.getValue() < 1)
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326 hscroll.setValue(hscroll.getValue() - 1);
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330 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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335 hscroll.setValue(hscroll.getValue() + 1);
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341 public void setScrollValues(int x, int y)
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346 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
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348 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
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349 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
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351 if (hextent > av.alignment.getWidth())
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353 hextent = av.alignment.getWidth();
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355 if (vextent > av.alignment.getHeight())
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357 vextent = av.alignment.getHeight();
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360 if (hextent + x > av.getAlignment().getWidth())
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362 x = av.getAlignment().getWidth() - hextent;
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365 if (vextent + y > av.getAlignment().getHeight())
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367 y = av.getAlignment().getHeight() - vextent;
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380 int endSeq = y + vextent;
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381 if (endSeq > av.alignment.getHeight())
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383 endSeq = av.alignment.getHeight();
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386 av.setEndSeq(endSeq);
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387 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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388 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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392 public void adjustmentValueChanged(AdjustmentEvent evt)
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394 int oldX = av.getStartRes();
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395 int oldY = av.getStartSeq();
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397 if (evt==null || evt.getSource() == hscroll)
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399 int x = hscroll.getValue();
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401 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
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405 if (evt==null || evt.getSource() == vscroll)
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407 int offy = vscroll.getValue();
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408 if (av.getWrapAlignment())
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410 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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411 seqCanvas.getSize().width);
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412 av.setStartRes(vscroll.getValue() * rowSize);
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413 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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417 av.setStartSeq(offy);
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418 av.setEndSeq(offy +
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419 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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423 if (overviewPanel != null)
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425 overviewPanel.setBoxPosition();
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428 int scrollX = av.startRes - oldX;
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429 int scrollY = av.startSeq - oldY;
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431 if (av.getWrapAlignment() || !fastPaint || MAC)
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435 else if(!seqPanel.seqCanvas.fastPaint)
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437 // Make sure we're not trying to draw a panel
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438 // larger than the visible window
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439 if(scrollX>av.endRes-av.startRes)
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440 scrollX = av.endRes-av.startRes;
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441 else if(scrollX<av.startRes-av.endRes)
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442 scrollX = av.startRes - av.endRes;
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444 idPanel.idCanvas.fastPaint(scrollY);
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445 seqPanel.seqCanvas.fastPaint(scrollX,
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448 scalePanel.repaint();
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449 if (av.getShowAnnotation())
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451 annotationPanel.fastPaint(av.getStartRes() - oldX);
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457 public void update(Graphics g)
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462 public void paint(Graphics g)
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464 Dimension d = idPanel.idCanvas.getSize();
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465 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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466 annotationSpaceFillerHolder.setSize(d.width,
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467 annotationPanel.getSize().height);
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469 alabels.setSize(d.width, annotationPanel.getSize().height);
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471 if (av.getWrapAlignment())
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473 int max = av.alignment.getWidth() /
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474 seqPanel.seqCanvas.
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475 getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
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476 vscroll.setMaximum(max);
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477 vscroll.setUnitIncrement(1);
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478 vscroll.setVisibleAmount(1);
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482 setScrollValues(av.getStartRes(), av.getStartSeq());
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487 seqPanel.seqCanvas.repaint();
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488 scalePanel.repaint();
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489 annotationPanel.repaint();
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490 idPanel.idCanvas.repaint();
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492 if (getBounds() == g.getClipBounds())
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494 if (overviewPanel != null)
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495 overviewPanel.updateOverviewImage();
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500 protected Panel sequenceHolderPanel = new Panel();
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501 protected Scrollbar vscroll = new Scrollbar();
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502 protected Scrollbar hscroll = new Scrollbar();
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503 protected Panel seqPanelHolder = new Panel();
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504 BorderLayout borderLayout1 = new BorderLayout();
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505 BorderLayout borderLayout3 = new BorderLayout();
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506 protected Panel scalePanelHolder = new Panel();
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507 protected Panel idPanelHolder = new Panel();
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508 BorderLayout borderLayout5 = new BorderLayout();
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509 protected Panel idSpaceFillerPanel1 = new Panel();
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510 public Panel annotationSpaceFillerHolder = new Panel();
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511 BorderLayout borderLayout6 = new BorderLayout();
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512 BorderLayout borderLayout7 = new BorderLayout();
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513 Panel hscrollHolder = new Panel();
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514 BorderLayout borderLayout10 = new BorderLayout();
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515 protected Panel hscrollFillerPanel = new Panel();
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516 BorderLayout borderLayout11 = new BorderLayout();
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517 public Panel annotationScroller = new Panel();
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518 BorderLayout borderLayout4 = new BorderLayout();
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519 BorderLayout borderLayout2 = new BorderLayout();
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521 private void jbInit() throws Exception {
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522 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
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523 this.setLayout(borderLayout7);
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525 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
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526 sequenceHolderPanel.setLayout(borderLayout3);
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527 seqPanelHolder.setLayout(borderLayout1);
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528 scalePanelHolder.setBackground(Color.white);
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530 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
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531 scalePanelHolder.setLayout(borderLayout6);
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532 idPanelHolder.setLayout(borderLayout5);
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533 idSpaceFillerPanel1.setBackground(Color.white);
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535 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
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536 idSpaceFillerPanel1.setLayout(borderLayout11);
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537 annotationSpaceFillerHolder.setBackground(Color.white);
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539 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
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540 annotationSpaceFillerHolder.setLayout(borderLayout4);
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541 hscroll.setOrientation(Scrollbar.HORIZONTAL);
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542 hscrollHolder.setLayout(borderLayout10);
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543 hscrollFillerPanel.setBackground(Color.white);
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545 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
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546 hscrollHolder.setBackground(Color.white);
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548 // annotationScroller.setPreferredSize(new Dimension(10, 80));
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549 // this.setPreferredSize(new Dimension(220, 166));
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550 seqPanelHolder.setBackground(Color.white);
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551 idPanelHolder.setBackground(Color.white);
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552 annotationScroller.setLayout(borderLayout2);
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553 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
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554 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
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555 seqPanelHolder.add(vscroll, BorderLayout.EAST);
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556 sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
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558 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
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559 this.add(idPanelHolder, BorderLayout.WEST);
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560 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
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561 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
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562 this.add(hscrollHolder, BorderLayout.SOUTH);
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563 hscrollHolder.add(hscroll, BorderLayout.CENTER);
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564 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
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565 this.add(sequenceHolderPanel, BorderLayout.CENTER);
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