2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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
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28 extends Panel implements AdjustmentListener
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32 OverviewPanel overviewPanel;
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35 IdwidthAdjuster idwidthAdjuster;
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36 public AlignFrame alignFrame;
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37 ScalePanel scalePanel;
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38 AnnotationPanel annotationPanel;
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39 AnnotationLabels alabels;
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41 // this value is set false when selection area being dragged
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42 boolean fastPaint = true;
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44 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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52 e.printStackTrace();
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57 seqPanel = new SeqPanel(av, this);
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58 idPanel = new IdPanel(av, this);
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59 scalePanel = new ScalePanel(av, this);
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60 idwidthAdjuster = new IdwidthAdjuster(this);
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61 annotationPanel = new AnnotationPanel(this);
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63 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
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65 alabels = new AnnotationLabels(this);
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67 setAnnotationVisible(av.showAnnotation);
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69 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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70 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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71 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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72 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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73 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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76 setScrollValues(0, 0);
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78 hscroll.addAdjustmentListener(this);
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79 vscroll.addAdjustmentListener(this);
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81 addComponentListener(new ComponentAdapter()
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83 public void componentResized(ComponentEvent evt)
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85 setScrollValues(av.getStartRes(), av.getStartSeq());
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90 Dimension d = calculateIdWidth();
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91 idPanel.idCanvas.setSize(d);
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93 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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95 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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96 annotationSpaceFillerHolder.setSize(d.width,
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97 annotationPanel.getSize().height);
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98 alabels.setSize(d.width, annotationPanel.getSize().height);
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100 final AlignmentPanel ap = this;
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101 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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103 public void propertyChange(java.beans.PropertyChangeEvent evt)
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105 if (evt.getPropertyName().equals("alignment"))
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107 PaintRefresher.Refresh(ap,
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108 av.getSequenceSetId(),
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111 alignmentChanged();
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118 public void alignmentChanged()
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120 av.alignmentChanged(this);
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122 if (overviewPanel != null)
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124 overviewPanel.updateOverviewImage();
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127 alignFrame.updateEditMenuBar();
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132 public void fontChanged()
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134 // set idCanvas bufferedImage to null
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135 // to prevent drawing old image
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136 idPanel.idCanvas.image = null;
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137 FontMetrics fm = getFontMetrics(av.getFont());
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139 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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140 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
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142 annotationPanel.image = null;
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143 int ap = annotationPanel.adjustPanelHeight();
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144 annotationPanel.repaint();
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145 Dimension d = calculateIdWidth();
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146 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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147 alabels.setSize(d.width + 4, ap);
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148 idPanel.idCanvas.setSize(d);
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149 hscrollFillerPanel.setSize(d);
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154 if (overviewPanel != null)
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156 overviewPanel.updateOverviewImage();
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160 public void setIdWidth(int w, int h)
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162 idPanel.idCanvas.setSize(w, h);
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163 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
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164 alabels.setSize(w, alabels.getSize().height);
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168 Dimension calculateIdWidth()
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170 if (av.nullFrame == null)
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172 av.nullFrame = new Frame();
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173 av.nullFrame.addNotify();
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176 Graphics g = av.nullFrame.getGraphics();
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178 FontMetrics fm = g.getFontMetrics(av.font);
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179 AlignmentI al = av.getAlignment();
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184 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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186 SequenceI s = al.getSequenceAt(i);
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187 id = s.getDisplayId(av.getShowJVSuffix());
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189 if (fm.stringWidth(id) > idWidth)
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191 idWidth = fm.stringWidth(id);
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196 // Also check annotation label widths
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198 if (al.getAlignmentAnnotation() != null)
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200 fm = g.getFontMetrics(av.nullFrame.getFont());
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201 while (i < al.getAlignmentAnnotation().length)
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203 String label = al.getAlignmentAnnotation()[i].label;
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204 if (fm.stringWidth(label) > idWidth)
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206 idWidth = fm.stringWidth(label);
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212 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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215 public void highlightSearchResults(SearchResults results)
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217 seqPanel.seqCanvas.highlightSearchResults(results);
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219 // do we need to scroll the panel?
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220 if (results != null)
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222 SequenceI seq = results.getResultSequence(0);
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223 int seqIndex = av.alignment.findIndex(seq);
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224 int start = seq.findIndex(results.getResultStart(0)) - 1;
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225 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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227 if (!av.wrapAlignment)
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229 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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230 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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232 if (start > av.alignment.getWidth() - hextent)
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234 start = av.alignment.getWidth() - hextent;
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240 if (seqIndex > av.alignment.getHeight() - vextent)
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242 seqIndex = av.alignment.getHeight() - vextent;
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248 setScrollValues(start, seqIndex);
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253 scrollToWrappedVisible(start);
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260 void scrollToWrappedVisible(int res)
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262 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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264 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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266 vscroll.setValue(res / cwidth);
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267 av.startRes = vscroll.getValue() * cwidth;
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271 public OverviewPanel getOverviewPanel()
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273 return overviewPanel;
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276 public void setOverviewPanel(OverviewPanel op)
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278 overviewPanel = op;
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281 public void setAnnotationVisible(boolean b)
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283 if (!av.wrapAlignment)
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285 annotationSpaceFillerHolder.setVisible(b);
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286 annotationPanel.setVisible(b);
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292 public void setWrapAlignment(boolean wrap)
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296 scalePanelHolder.setVisible(!wrap);
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298 hscroll.setVisible(!wrap);
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299 idwidthAdjuster.setVisible(!wrap);
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303 annotationPanel.setVisible(false);
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304 annotationSpaceFillerHolder.setVisible(false);
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306 else if (av.showAnnotation)
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308 annotationPanel.setVisible(true);
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309 annotationSpaceFillerHolder.setVisible(true);
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312 idSpaceFillerPanel1.setVisible(!wrap);
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314 fontChanged(); //This is so that the scalePanel is resized correctly
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324 // return value is true if the scroll is valid
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325 public boolean scrollUp(boolean up)
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329 if (vscroll.getValue() < 1)
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333 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
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337 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
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341 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
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348 public boolean scrollRight(boolean right)
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352 if (hscroll.getValue() < 1)
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356 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
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360 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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364 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
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371 public void setScrollValues(int x, int y)
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373 int width = av.alignment.getWidth();
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374 int height = av.alignment.getHeight();
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376 if (av.hasHiddenColumns)
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378 width = av.getColumnSelection().findColumnPosition(width);
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382 av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
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384 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
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385 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
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387 if (hextent > width)
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392 if (vextent > height)
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397 if ( (hextent + x) > width)
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399 x = width - hextent;
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402 if ( (vextent + y) > height)
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404 y = height - vextent;
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419 int endSeq = y + vextent;
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420 if (endSeq > av.alignment.getHeight())
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422 endSeq = av.alignment.getHeight();
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425 av.setEndSeq(endSeq);
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426 hscroll.setValues(x, hextent, 0, width);
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427 vscroll.setValues(y, vextent, 0, height);
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429 if (overviewPanel != null)
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431 overviewPanel.setBoxPosition();
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436 public void adjustmentValueChanged(AdjustmentEvent evt)
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438 int oldX = av.getStartRes();
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439 int oldY = av.getStartSeq();
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441 if (evt == null || evt.getSource() == hscroll)
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443 int x = hscroll.getValue();
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445 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
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449 if (evt == null || evt.getSource() == vscroll)
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451 int offy = vscroll.getValue();
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452 if (av.getWrapAlignment())
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454 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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455 seqCanvas.getSize().width);
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456 av.setStartRes(vscroll.getValue() * rowSize);
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457 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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461 av.setStartSeq(offy);
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462 av.setEndSeq(offy +
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463 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
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467 if (overviewPanel != null)
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469 overviewPanel.setBoxPosition();
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472 int scrollX = av.startRes - oldX;
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473 int scrollY = av.startSeq - oldY;
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475 if (av.getWrapAlignment() || !fastPaint || av.MAC)
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481 // Make sure we're not trying to draw a panel
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482 // larger than the visible window
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483 if (scrollX > av.endRes - av.startRes)
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485 scrollX = av.endRes - av.startRes;
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487 else if (scrollX < av.startRes - av.endRes)
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489 scrollX = av.startRes - av.endRes;
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492 idPanel.idCanvas.fastPaint(scrollY);
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493 seqPanel.seqCanvas.fastPaint(scrollX,
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496 scalePanel.repaint();
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497 if (av.getShowAnnotation())
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499 annotationPanel.fastPaint(av.getStartRes() - oldX);
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505 public void update(Graphics g)
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510 public void paint(Graphics g)
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513 Dimension d = idPanel.idCanvas.getSize();
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514 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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515 annotationSpaceFillerHolder.setSize(d.width,
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516 annotationPanel.getSize().height);
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518 alabels.setSize(d.width, annotationPanel.getSize().height);
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520 if (av.getWrapAlignment())
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522 int maxwidth = av.alignment.getWidth();
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524 if (av.hasHiddenColumns)
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526 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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529 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
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530 (seqPanel.seqCanvas.getSize().width);
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532 if (canvasWidth > 0)
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534 int max = maxwidth / canvasWidth;
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535 vscroll.setMaximum(max);
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536 vscroll.setUnitIncrement(1);
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537 vscroll.setVisibleAmount(1);
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542 setScrollValues(av.getStartRes(), av.getStartSeq());
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547 seqPanel.seqCanvas.repaint();
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548 scalePanel.repaint();
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549 annotationPanel.repaint();
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550 idPanel.idCanvas.repaint();
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552 if (getBounds() == g.getClipBounds())
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554 if (overviewPanel != null)
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556 overviewPanel.updateOverviewImage();
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562 protected Panel sequenceHolderPanel = new Panel();
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563 protected Scrollbar vscroll = new Scrollbar();
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564 protected Scrollbar hscroll = new Scrollbar();
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565 protected Panel seqPanelHolder = new Panel();
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566 BorderLayout borderLayout1 = new BorderLayout();
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567 BorderLayout borderLayout3 = new BorderLayout();
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568 protected Panel scalePanelHolder = new Panel();
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569 protected Panel idPanelHolder = new Panel();
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570 BorderLayout borderLayout5 = new BorderLayout();
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571 protected Panel idSpaceFillerPanel1 = new Panel();
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572 public Panel annotationSpaceFillerHolder = new Panel();
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573 BorderLayout borderLayout6 = new BorderLayout();
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574 BorderLayout borderLayout7 = new BorderLayout();
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575 Panel hscrollHolder = new Panel();
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576 BorderLayout borderLayout10 = new BorderLayout();
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577 protected Panel hscrollFillerPanel = new Panel();
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578 BorderLayout borderLayout11 = new BorderLayout();
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579 BorderLayout borderLayout4 = new BorderLayout();
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580 BorderLayout borderLayout2 = new BorderLayout();
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582 private void jbInit()
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585 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
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586 this.setLayout(borderLayout7);
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588 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
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589 sequenceHolderPanel.setLayout(borderLayout3);
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590 seqPanelHolder.setLayout(borderLayout1);
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591 scalePanelHolder.setBackground(Color.white);
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593 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
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594 scalePanelHolder.setLayout(borderLayout6);
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595 idPanelHolder.setLayout(borderLayout5);
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596 idSpaceFillerPanel1.setBackground(Color.white);
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598 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
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599 idSpaceFillerPanel1.setLayout(borderLayout11);
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600 annotationSpaceFillerHolder.setBackground(Color.white);
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602 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
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603 annotationSpaceFillerHolder.setLayout(borderLayout4);
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604 hscroll.setOrientation(Scrollbar.HORIZONTAL);
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605 hscrollHolder.setLayout(borderLayout10);
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606 hscrollFillerPanel.setBackground(Color.white);
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608 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
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609 hscrollHolder.setBackground(Color.white);
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611 // annotationScroller.setPreferredSize(new Dimension(10, 80));
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612 // this.setPreferredSize(new Dimension(220, 166));
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613 seqPanelHolder.setBackground(Color.white);
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614 idPanelHolder.setBackground(Color.white);
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615 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
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616 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
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617 seqPanelHolder.add(vscroll, BorderLayout.EAST);
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619 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
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620 this.add(idPanelHolder, BorderLayout.WEST);
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621 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
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622 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
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623 this.add(hscrollHolder, BorderLayout.SOUTH);
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624 hscrollHolder.add(hscroll, BorderLayout.CENTER);
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625 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
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626 this.add(sequenceHolderPanel, BorderLayout.CENTER);
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