2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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45 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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53 e.printStackTrace();
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59 seqPanel = new SeqPanel(av, this);
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60 idPanel = new IdPanel(av, this);
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61 scalePanel = new ScalePanel(av, this);
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62 idwidthAdjuster = new IdwidthAdjuster(this);
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63 annotationPanel = new AnnotationPanel(this);
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65 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
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67 alabels = new AnnotationLabels(this);
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69 setAnnotationVisible(av.showAnnotation);
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71 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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72 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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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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97 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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98 annotationSpaceFillerHolder.setSize(d.width,
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99 annotationPanel.getSize().height);
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100 alabels.setSize(d.width, annotationPanel.getSize().height);
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105 public void fontChanged()
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107 // set idCanvas bufferedImage to null
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108 // to prevent drawing old image
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109 idPanel.idCanvas.image = null;
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110 FontMetrics fm = getFontMetrics(av.getFont());
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112 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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113 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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115 annotationPanel.image = null;
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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 if (av.nullFrame == null)
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143 av.nullFrame = new Frame();
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144 av.nullFrame.addNotify();
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147 Graphics g = av.nullFrame.getGraphics();
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149 FontMetrics fm = g.getFontMetrics(av.font);
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150 AlignmentI al = av.getAlignment();
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155 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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157 SequenceI s = al.getSequenceAt(i);
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158 id = s.getDisplayId(av.getShowJVSuffix());
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160 if (fm.stringWidth(id) > idWidth)
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162 idWidth = fm.stringWidth(id);
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167 // Also check annotation label widths
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169 if (al.getAlignmentAnnotation() != null)
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171 fm = g.getFontMetrics(av.nullFrame.getFont());
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172 while (i < al.getAlignmentAnnotation().length)
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174 String label = al.getAlignmentAnnotation()[i].label;
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175 if (fm.stringWidth(label) > idWidth)
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177 idWidth = fm.stringWidth(label);
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183 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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186 public void highlightSearchResults(SearchResults results)
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188 seqPanel.seqCanvas.highlightSearchResults(results);
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190 // do we need to scroll the panel?
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191 if (results != null)
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193 SequenceI seq = results.getResultSequence(0);
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194 int seqIndex = av.alignment.findIndex(seq);
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195 int start = seq.findIndex(results.getResultStart(0)) - 1;
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196 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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198 if(!av.wrapAlignment)
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200 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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201 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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203 if (start > av.alignment.getWidth() - hextent)
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205 start = av.alignment.getWidth() - hextent;
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209 if (seqIndex > av.alignment.getHeight() - vextent)
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211 seqIndex = av.alignment.getHeight() - vextent;
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215 setScrollValues(start, seqIndex);
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220 scrollToWrappedVisible(start);
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227 void scrollToWrappedVisible(int res)
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229 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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230 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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232 vscroll.setValue(res / cwidth);
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233 av.startRes = vscroll.getValue() * cwidth;
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238 public OverviewPanel getOverviewPanel()
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240 return overviewPanel;
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243 public void setOverviewPanel(OverviewPanel op)
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245 overviewPanel = op;
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248 public void setAnnotationVisible(boolean b)
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250 if (!av.wrapAlignment)
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252 annotationSpaceFillerHolder.setVisible(b);
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253 annotationPanel.setVisible(b);
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259 public void setWrapAlignment(boolean wrap)
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262 scalePanelHolder.setVisible(!wrap);
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265 hscroll.setVisible(!wrap);
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266 idwidthAdjuster.setVisible(!wrap);
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270 annotationPanel.setVisible(false);
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271 annotationSpaceFillerHolder.setVisible(false);
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273 else if (av.showAnnotation)
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275 annotationPanel.setVisible(true);
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276 annotationSpaceFillerHolder.setVisible(true);
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280 idSpaceFillerPanel1.setVisible(!wrap);
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282 fontChanged();//This is so that the scalePanel is resized correctly
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293 // return value is true if the scroll is valid
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294 public boolean scrollUp(boolean up)
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298 if (vscroll.getValue() < 1)
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302 setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
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306 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
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310 setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
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317 public boolean scrollRight(boolean right)
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321 if (hscroll.getValue() < 1)
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325 setScrollValues(hscroll.getValue()-1, vscroll.getValue());
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329 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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333 setScrollValues(hscroll.getValue()+1, vscroll.getValue());
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340 public void setScrollValues(int x, int y)
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342 int width = av.alignment.getWidth();
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343 int height = av.alignment.getHeight();
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345 if(av.hasHiddenColumns)
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346 width = av.getColumnSelection().findColumnPosition(width);
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351 av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);
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353 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
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354 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
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356 if (hextent > width)
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361 if (vextent > height)
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366 if ( (hextent + x) > width)
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368 x = width - hextent;
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371 if ( (vextent + y) > height)
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373 y = height - vextent;
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386 int endSeq = y + vextent;
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387 if (endSeq > av.alignment.getHeight())
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389 endSeq = av.alignment.getHeight();
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392 av.setEndSeq(endSeq);
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393 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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394 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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396 if(overviewPanel!=null)
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397 overviewPanel.setBoxPosition();
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401 public void adjustmentValueChanged(AdjustmentEvent evt)
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403 int oldX = av.getStartRes();
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404 int oldY = av.getStartSeq();
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407 if (evt==null || evt.getSource() == hscroll)
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409 int x = hscroll.getValue();
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411 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
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416 if (evt==null || evt.getSource() == vscroll)
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418 int offy = vscroll.getValue();
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419 if (av.getWrapAlignment())
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421 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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422 seqCanvas.getSize().width);
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423 av.setStartRes(vscroll.getValue() * rowSize);
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424 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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428 av.setStartSeq(offy);
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429 av.setEndSeq(offy +
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430 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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434 if (overviewPanel != null)
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436 overviewPanel.setBoxPosition();
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439 int scrollX = av.startRes - oldX;
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440 int scrollY = av.startSeq - oldY;
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442 if (av.getWrapAlignment() || !fastPaint || av.MAC)
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448 // Make sure we're not trying to draw a panel
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449 // larger than the visible window
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450 if(scrollX>av.endRes-av.startRes)
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452 scrollX = av.endRes - av.startRes;
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454 else if(scrollX<av.startRes-av.endRes)
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455 scrollX = av.startRes - av.endRes;
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457 idPanel.idCanvas.fastPaint(scrollY);
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458 seqPanel.seqCanvas.fastPaint(scrollX,
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461 scalePanel.repaint();
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462 if (av.getShowAnnotation())
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464 annotationPanel.fastPaint(av.getStartRes() - oldX);
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470 public void update(Graphics g)
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475 public void paint(Graphics g)
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478 Dimension d = idPanel.idCanvas.getSize();
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479 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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480 annotationSpaceFillerHolder.setSize(d.width,
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481 annotationPanel.getSize().height);
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483 alabels.setSize(d.width, annotationPanel.getSize().height);
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485 if (av.getWrapAlignment())
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487 int maxwidth = av.alignment.getWidth();
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489 if (av.hasHiddenColumns)
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490 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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492 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
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493 (seqPanel.seqCanvas.getSize().width);
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497 int max = maxwidth / canvasWidth;
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498 vscroll.setMaximum(max);
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499 vscroll.setUnitIncrement(1);
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500 vscroll.setVisibleAmount(1);
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505 setScrollValues(av.getStartRes(), av.getStartSeq());
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510 seqPanel.seqCanvas.repaint();
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511 scalePanel.repaint();
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512 annotationPanel.repaint();
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513 idPanel.idCanvas.repaint();
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515 if (getBounds() == g.getClipBounds())
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517 if (overviewPanel != null)
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518 overviewPanel.updateOverviewImage();
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523 protected Panel sequenceHolderPanel = new Panel();
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524 protected Scrollbar vscroll = new Scrollbar();
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525 protected Scrollbar hscroll = new Scrollbar();
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526 protected Panel seqPanelHolder = new Panel();
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527 BorderLayout borderLayout1 = new BorderLayout();
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528 BorderLayout borderLayout3 = new BorderLayout();
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529 protected Panel scalePanelHolder = new Panel();
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530 protected Panel idPanelHolder = new Panel();
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531 BorderLayout borderLayout5 = new BorderLayout();
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532 protected Panel idSpaceFillerPanel1 = new Panel();
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533 public Panel annotationSpaceFillerHolder = new Panel();
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534 BorderLayout borderLayout6 = new BorderLayout();
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535 BorderLayout borderLayout7 = new BorderLayout();
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536 Panel hscrollHolder = new Panel();
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537 BorderLayout borderLayout10 = new BorderLayout();
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538 protected Panel hscrollFillerPanel = new Panel();
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539 BorderLayout borderLayout11 = new BorderLayout();
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540 BorderLayout borderLayout4 = new BorderLayout();
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541 BorderLayout borderLayout2 = new BorderLayout();
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543 private void jbInit() throws Exception {
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544 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
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545 this.setLayout(borderLayout7);
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547 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
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548 sequenceHolderPanel.setLayout(borderLayout3);
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549 seqPanelHolder.setLayout(borderLayout1);
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550 scalePanelHolder.setBackground(Color.white);
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552 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
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553 scalePanelHolder.setLayout(borderLayout6);
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554 idPanelHolder.setLayout(borderLayout5);
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555 idSpaceFillerPanel1.setBackground(Color.white);
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557 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
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558 idSpaceFillerPanel1.setLayout(borderLayout11);
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559 annotationSpaceFillerHolder.setBackground(Color.white);
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561 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
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562 annotationSpaceFillerHolder.setLayout(borderLayout4);
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563 hscroll.setOrientation(Scrollbar.HORIZONTAL);
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564 hscrollHolder.setLayout(borderLayout10);
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565 hscrollFillerPanel.setBackground(Color.white);
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567 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
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568 hscrollHolder.setBackground(Color.white);
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570 // annotationScroller.setPreferredSize(new Dimension(10, 80));
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571 // this.setPreferredSize(new Dimension(220, 166));
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572 seqPanelHolder.setBackground(Color.white);
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573 idPanelHolder.setBackground(Color.white);
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574 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
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575 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
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576 seqPanelHolder.add(vscroll, BorderLayout.EAST);
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578 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
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579 this.add(idPanelHolder, BorderLayout.WEST);
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580 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
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581 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
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582 this.add(hscrollHolder, BorderLayout.SOUTH);
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583 hscrollHolder.add(hscroll, BorderLayout.CENTER);
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584 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
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585 this.add(sequenceHolderPanel, BorderLayout.CENTER);
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