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.analysis.*;
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26 import jalview.datamodel.*;
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27 import jalview.jbappletgui.*;
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28 import jalview.schemes.*;
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30 public class AlignmentPanel
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31 extends GAlignmentPanel implements AdjustmentListener
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35 OverviewPanel overviewPanel;
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38 IdwidthAdjuster idwidthAdjuster;
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39 public AlignFrame alignFrame;
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40 ScalePanel scalePanel;
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41 AnnotationPanel annotationPanel;
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42 AnnotationLabels alabels;
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44 // this value is set false when selection area being dragged
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45 boolean fastPaint = true;
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47 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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51 seqPanel = new SeqPanel(av, this);
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52 idPanel = new IdPanel(av, this);
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53 scalePanel = new ScalePanel(av, this);
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54 idwidthAdjuster = new IdwidthAdjuster(this);
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55 annotationPanel = new AnnotationPanel(this);
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56 alabels = new AnnotationLabels(this);
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58 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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59 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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60 annotationScroller.add(annotationPanel);
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61 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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62 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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63 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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66 setScrollValues(0, 0);
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68 hscroll.addAdjustmentListener(this);
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69 vscroll.addAdjustmentListener(this);
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71 seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());
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72 idPanel.idCanvas.addKeyListener(new MyKeyAdapter());
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74 addComponentListener(new ComponentAdapter()
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76 public void componentResized(ComponentEvent evt)
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78 setScrollValues(av.getStartRes(), av.getStartSeq());
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83 Dimension d = calculateIdWidth();
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84 idPanel.idCanvas.setSize(d);
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86 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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87 annotationScroller.setSize(annotationPanel.getSize());
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89 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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90 annotationSpaceFillerHolder.setSize(d.width,
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91 annotationPanel.getSize().height);
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92 alabels.setSize(d.width, annotationPanel.getSize().height);
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99 public void keyPressed(KeyEvent evt)
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101 // System.out.println(evt.getKeyCode()); log.
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102 switch (evt.getKeyCode())
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104 case 27: // escape key
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105 av.setSelectionGroup(null);
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106 alignFrame.alignPanel.repaint();
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108 case KeyEvent.VK_X:
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109 if (evt.isControlDown())
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111 alignFrame.cut_actionPerformed(null);
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114 case KeyEvent.VK_C:
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115 if (evt.isControlDown())
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117 alignFrame.copy_actionPerformed(null);
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120 case KeyEvent.VK_V:
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121 if (evt.isControlDown())
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123 alignFrame.paste(true);
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126 case KeyEvent.VK_A:
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127 if (evt.isControlDown())
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129 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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132 case KeyEvent.VK_DOWN:
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133 alignFrame.moveSelectedSequences(false);
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135 case KeyEvent.VK_UP:
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136 alignFrame.moveSelectedSequences(true);
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138 case KeyEvent.VK_F:
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139 if (evt.isControlDown())
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141 alignFrame.findMenuItem_actionPerformed(null);
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148 public void fontChanged()
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150 // set idCanvas bufferedImage to null
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151 // to prevent drawing old image
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152 FontMetrics fm = getFontMetrics(av.getFont());
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154 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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155 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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157 annotationPanel.adjustPanelHeight();
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158 annotationPanel.repaint();
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159 Dimension d = calculateIdWidth();
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160 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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161 idPanel.idCanvas.setSize(d);
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162 hscrollFillerPanel.setSize(d);
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167 public void setIdWidth(int w, int h)
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169 idPanel.idCanvas.setSize(w, h);
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170 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
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171 alabels.setSize(w, alabels.getSize().height);
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175 Dimension calculateIdWidth()
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177 Frame frame = new Frame();
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179 Graphics g = frame.getGraphics();
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182 Frame f = new Frame();
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184 g = f.getGraphics();
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187 FontMetrics fm = g.getFontMetrics(av.font);
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188 AlignmentI al = av.getAlignment();
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193 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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195 SequenceI s = al.getSequenceAt(i);
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196 if (av.getShowFullId())
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198 id = s.getDisplayId();
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205 if (fm.stringWidth(id) > idWidth)
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207 idWidth = fm.stringWidth(id);
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212 // Also check annotation label widths
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214 if (al.getAlignmentAnnotation() != null)
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216 fm = g.getFontMetrics(frame.getFont());
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217 while (i < al.getAlignmentAnnotation().length)
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219 String label = al.getAlignmentAnnotation()[i].label;
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220 if (fm.stringWidth(label) > idWidth)
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222 idWidth = fm.stringWidth(label);
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228 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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231 public void highlightSearchResults(int[] results)
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233 seqPanel.seqCanvas.highlightSearchResults(results);
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235 // do we need to scroll the panel?
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236 if (results != null)
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238 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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239 int start = seq.findIndex(results[1]) - 1;
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240 int end = seq.findIndex(results[2]) - 1;
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241 if (av.getStartRes() > start
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242 || av.getEndRes() < end
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243 || (av.getStartSeq() > results[0]
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244 || av.getEndSeq() < results[0]))
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246 setScrollValues(start, results[0]);
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252 public OverviewPanel getOverviewPanel()
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254 return overviewPanel;
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257 public void setOverviewPanel(OverviewPanel op)
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259 overviewPanel = op;
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262 public void setAnnotationVisible(boolean b)
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264 annotationSpaceFillerHolder.setVisible(b);
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265 annotationScroller.setVisible(b);
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270 public void setWrapAlignment(boolean wrap)
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272 scalePanelHolder.setVisible(!wrap);
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273 hscroll.setVisible(!wrap);
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274 idwidthAdjuster.setVisible(!wrap);
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276 av.setShowAnnotation(!wrap);
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277 annotationScroller.setVisible(!wrap);
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278 annotationSpaceFillerHolder.setVisible(!wrap);
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279 idSpaceFillerPanel1.setVisible(!wrap);
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286 public void setColourScheme()
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288 ColourSchemeI cs = av.getGlobalColourScheme();
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290 if (av.getConservationSelected())
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293 Alignment al = (Alignment) av.getAlignment();
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294 Conservation c = new Conservation("All",
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295 ResidueProperties.propHash, 3,
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296 al.getSequences(), 0,
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300 c.verdict(false, av.ConsPercGaps);
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301 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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303 av.setGlobalColourScheme(ccs);
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313 // return value is true if the scroll is valid
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314 public boolean scrollUp(boolean up)
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318 if (vscroll.getValue() < 1)
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323 vscroll.setValue(vscroll.getValue() - 1);
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327 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
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332 vscroll.setValue(vscroll.getValue() + 1);
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338 public boolean scrollRight(boolean right)
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343 if (hscroll.getValue() < 1)
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348 hscroll.setValue(hscroll.getValue() - 1);
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352 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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357 hscroll.setValue(hscroll.getValue() + 1);
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363 public void setScrollValues(int x, int y)
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368 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
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370 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
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371 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
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373 if (hextent > av.alignment.getWidth())
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375 hextent = av.alignment.getWidth();
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377 if (vextent > av.alignment.getHeight())
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379 vextent = av.alignment.getHeight();
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382 if (hextent + x > av.getAlignment().getWidth())
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384 x = av.getAlignment().getWidth() - hextent;
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387 if (vextent + y > av.getAlignment().getHeight())
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389 y = av.getAlignment().getHeight() - vextent;
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402 int endSeq = y + vextent;
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403 if (endSeq > av.alignment.getHeight())
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405 endSeq = av.alignment.getHeight();
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408 av.setEndSeq(endSeq);
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409 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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410 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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414 public void adjustmentValueChanged(AdjustmentEvent evt)
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416 int oldX = av.getStartRes();
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417 int oldY = av.getStartSeq();
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419 if (evt.getSource() == hscroll)
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421 int x = hscroll.getValue();
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423 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
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427 if (evt.getSource() == vscroll)
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429 int offy = vscroll.getValue();
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430 if (av.getWrapAlignment())
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432 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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433 seqCanvas.getSize().width);
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434 av.setStartRes(vscroll.getValue() * rowSize);
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435 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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439 av.setStartSeq(offy);
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440 av.setEndSeq(offy +
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441 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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445 if (overviewPanel != null)
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447 overviewPanel.setBoxPosition();
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450 if (av.getWrapAlignment() || !fastPaint)
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456 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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457 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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458 av.getStartSeq() - oldY);
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460 scalePanel.repaint();
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461 if (av.getShowAnnotation())
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463 annotationPanel.fastPaint(av.getStartRes() - oldX);
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469 public void update(Graphics g)
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474 public void paint(Graphics g)
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476 Dimension d = idPanel.idCanvas.getSize();
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477 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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478 annotationSpaceFillerHolder.setSize(d.width,
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479 annotationPanel.getSize().height);
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480 alabels.setSize(d.width, annotationPanel.getSize().height);
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483 idPanel.idCanvas.repaint();
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484 seqPanel.seqCanvas.repaint();
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485 scalePanel.repaint();
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486 annotationPanel.repaint();
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488 if (av.getWrapAlignment())
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490 int max = av.alignment.getWidth() /
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491 seqPanel.seqCanvas.
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492 getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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493 vscroll.setMaximum(max);
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494 vscroll.setUnitIncrement(1);
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495 vscroll.setVisibleAmount(1);
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499 setScrollValues(av.getStartRes(), av.getStartSeq());
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