2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.analysis.AnnotationSorter;
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24 import jalview.api.AlignViewportI;
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25 import jalview.api.AlignmentViewPanel;
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26 import jalview.bin.JalviewLite;
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27 import jalview.datamodel.AlignmentI;
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28 import jalview.datamodel.SearchResults;
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29 import jalview.datamodel.SequenceI;
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30 import jalview.structure.StructureSelectionManager;
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32 import java.awt.BorderLayout;
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33 import java.awt.Color;
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34 import java.awt.Dimension;
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35 import java.awt.FontMetrics;
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36 import java.awt.Graphics;
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37 import java.awt.event.AdjustmentEvent;
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38 import java.awt.event.AdjustmentListener;
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39 import java.awt.event.ComponentAdapter;
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40 import java.awt.event.ComponentEvent;
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41 import java.util.List;
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43 import javax.swing.JPanel;
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44 import javax.swing.JFrame;
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45 import javax.swing.JScrollBar;
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47 public class AlignmentPanel extends JPanel implements AdjustmentListener,
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51 public AlignViewport av;
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53 OverviewPanel overviewPanel;
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59 IdwidthAdjuster idwidthAdjuster;
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61 public AlignFrame alignFrame;
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63 ScalePanel scalePanel;
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65 AnnotationPanel annotationPanel;
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67 AnnotationLabels alabels;
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69 // this value is set false when selection area being dragged
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70 boolean fastPaint = true;
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72 public void finalize()
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77 seqPanelHolder = null;
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78 sequenceHolderPanel = null;
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80 scalePanelHolder = null;
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81 annotationPanel = null;
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82 annotationPanelHolder = null;
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83 annotationSpaceFillerHolder = null;
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86 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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91 } catch (Exception e)
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93 e.printStackTrace();
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98 seqPanel = new SeqPanel(av, this);
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99 idPanel = new IdPanel(av, this);
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100 scalePanel = new ScalePanel(av, this);
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101 idwidthAdjuster = new IdwidthAdjuster(this);
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102 annotationPanel = new AnnotationPanel(this);
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103 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
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105 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
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106 alabels = new AnnotationLabels(this);
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108 setAnnotationVisible(av.isShowAnnotation());
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110 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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111 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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112 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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113 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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114 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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117 setScrollValues(0, 0);
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119 apvscroll.addAdjustmentListener(this);
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120 hscroll.addAdjustmentListener(this);
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121 vscroll.addAdjustmentListener(this);
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123 addComponentListener(new ComponentAdapter()
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125 public void componentResized(ComponentEvent evt)
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127 setScrollValues(av.getStartRes(), av.getStartSeq());
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128 if (getSize().height > 0
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129 && annotationPanelHolder.getSize().height > 0)
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131 validateAnnotationDimensions(false);
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138 Dimension d = calculateIdWidth();
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139 idPanel.idCanvas.setSize(d);
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141 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
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143 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
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144 annotationSpaceFillerHolder.setSize(d.width,
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145 annotationPanel.getSize().height);
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146 alabels.setSize(d.width, annotationPanel.getSize().height);
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147 final AlignmentPanel ap = this;
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148 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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150 public void propertyChange(java.beans.PropertyChangeEvent evt)
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152 if (evt.getPropertyName().equals("alignment"))
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154 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
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155 alignmentChanged();
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162 public AlignViewportI getAlignViewport()
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166 public SequenceRenderer getSequenceRenderer()
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168 return seqPanel.seqCanvas.sr;
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171 public jalview.api.FeatureRenderer getFeatureRenderer()
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173 return seqPanel.seqCanvas.fr;
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176 public jalview.api.FeatureRenderer cloneFeatureRenderer()
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178 FeatureRenderer nfr = new FeatureRenderer(av);
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179 nfr.transferSettings(seqPanel.seqCanvas.fr);
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182 public void alignmentChanged()
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184 av.alignmentChanged(this);
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186 if (overviewPanel != null)
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188 overviewPanel.updateOverviewImage();
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191 alignFrame.updateEditMenuBar();
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196 public void fontChanged()
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198 // set idCanvas bufferedImage to null
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199 // to prevent drawing old image
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200 idPanel.idCanvas.image = null;
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201 FontMetrics fm = getFontMetrics(av.getFont());
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203 scalePanel.setSize(new Dimension(10, av.getCharHeight()
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204 + fm.getDescent()));
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205 idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
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206 + fm.getDescent()));
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207 av.updateSequenceIdColours();
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208 annotationPanel.image = null;
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209 int ap = annotationPanel.adjustPanelHeight(false);
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210 Dimension d = calculateIdWidth();
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211 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
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212 alabels.setSize(d.width + 4, ap);
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214 idPanel.idCanvas.setSize(d);
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215 hscrollFillerPanel.setSize(d);
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217 validateAnnotationDimensions(false);
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218 annotationPanel.repaint();
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222 if (overviewPanel != null)
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224 overviewPanel.updateOverviewImage();
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228 public void setIdWidth(int w, int h)
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230 idPanel.idCanvas.setSize(w, h);
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231 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
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232 annotationSpaceFillerHolder.setSize(w,
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233 annotationSpaceFillerHolder.getSize().height);
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234 alabels.setSize(w, alabels.getSize().height);
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238 Dimension calculateIdWidth()
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240 if (av.nullFrame == null)
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242 av.nullFrame = new JFrame();
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243 av.nullFrame.addNotify();
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246 Graphics g = av.nullFrame.getGraphics();
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248 FontMetrics fm = g.getFontMetrics(av.font);
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249 AlignmentI al = av.getAlignment();
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254 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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256 SequenceI s = al.getSequenceAt(i);
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257 id = s.getDisplayId(av.getShowJVSuffix());
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259 if (fm.stringWidth(id) > idWidth)
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261 idWidth = fm.stringWidth(id);
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266 // Also check annotation label widths
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268 if (al.getAlignmentAnnotation() != null)
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270 fm = g.getFontMetrics(av.nullFrame.getFont());
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271 while (i < al.getAlignmentAnnotation().length)
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273 String label = al.getAlignmentAnnotation()[i].label;
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274 if (fm.stringWidth(label) > idWidth)
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276 idWidth = fm.stringWidth(label);
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282 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
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286 * Highlight the given results on the alignment.
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289 public void highlightSearchResults(SearchResults results)
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291 scrollToPosition(results);
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292 seqPanel.seqCanvas.highlightSearchResults(results);
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296 * scroll the view to show the position of the highlighted region in results
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297 * (if any) and redraw the overview
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300 * @return false if results were not found
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302 public boolean scrollToPosition(SearchResults results)
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304 return scrollToPosition(results, true);
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308 * scroll the view to show the position of the highlighted region in results
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312 * @param redrawOverview
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313 * - when set, the overview will be recalculated (takes longer)
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314 * @return false if results were not found
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316 public boolean scrollToPosition(SearchResults results,
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317 boolean redrawOverview)
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319 return scrollToPosition(results, redrawOverview, false);
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323 * scroll the view to show the position of the highlighted region in results
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327 * @param redrawOverview
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328 * - when set, the overview will be recalculated (takes longer)
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329 * @return false if results were not found
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331 public boolean scrollToPosition(SearchResults results,
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332 boolean redrawOverview, boolean centre)
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334 // do we need to scroll the panel?
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335 if (results != null && results.getSize() > 0)
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337 AlignmentI alignment = av.getAlignment();
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338 int seqIndex = alignment.findIndex(results);
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339 if (seqIndex == -1)
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343 SequenceI seq = alignment.getSequenceAt(seqIndex);
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344 int[] r = results.getResults(seq, 0, alignment.getWidth());
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347 if (JalviewLite.debug)
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350 .println("DEBUG: scroll didn't happen - results not within alignment : "
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351 + seq.getStart() + "," + seq.getEnd());
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355 if (JalviewLite.debug)
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359 * System.out.println("DEBUG: scroll: start=" + r[0] +
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360 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
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361 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
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362 * " hextent=" + hextent);
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369 * To centre results, scroll to positions half the visible width
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370 * left/right of the start/end positions
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374 int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
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375 start = Math.max(start - offset, 0);
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376 end = Math.min(end + offset, seq.getEnd() - 1);
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383 if (end == seq.getEnd())
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387 return scrollTo(start, end, seqIndex, false, redrawOverview);
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392 public boolean scrollTo(int ostart, int end, int seqIndex,
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393 boolean scrollToNearest, boolean redrawOverview)
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395 int startv, endv, starts, ends, width;
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398 if (av.hasHiddenColumns())
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400 start = av.getColumnSelection().findColumnPosition(ostart);
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401 end = av.getColumnSelection().findColumnPosition(end);
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404 if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
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406 // don't scroll - position isn't visible
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415 if (!av.getWrapAlignment())
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418 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
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419 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
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420 * setScrollValues(start - 1, seqIndex); } else if ((endv =
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421 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
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422 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
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423 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
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424 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
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425 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
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428 // below is scrolling logic up to Jalview 2.8.2
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429 // if ((av.getStartRes() > end)
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430 // || (av.getEndRes() < start)
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431 // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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433 // if (start > av.getAlignment().getWidth() - hextent)
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435 // start = av.getAlignment().getWidth() - hextent;
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442 // if (seqIndex > av.getAlignment().getHeight() - vextent)
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444 // seqIndex = av.getAlignment().getHeight() - vextent;
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445 // if (seqIndex < 0)
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450 // setScrollValues(start, seqIndex);
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452 // logic copied from jalview.gui.AlignmentPanel:
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453 if ((startv = av.getStartRes()) >= start)
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456 * Scroll left to make start of search results visible
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458 setScrollValues(start - 1, seqIndex);
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460 else if ((endv = av.getEndRes()) <= end)
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463 * Scroll right to make end of search results visible
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465 setScrollValues(startv + 1 + end - endv, seqIndex);
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467 else if ((starts = av.getStartSeq()) > seqIndex)
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470 * Scroll up to make start of search results visible
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472 setScrollValues(av.getStartRes(), seqIndex);
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474 else if ((ends = av.getEndSeq()) <= seqIndex)
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477 * Scroll down to make end of search results visible
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479 setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
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482 * Else results are already visible - no need to scroll
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487 scrollToWrappedVisible(start);
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489 if (redrawOverview && overviewPanel != null)
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491 overviewPanel.setBoxPosition();
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493 paintAlignment(redrawOverview);
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497 void scrollToWrappedVisible(int res)
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499 int cwidth = seqPanel.seqCanvas
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500 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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501 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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503 vscroll.setValue(res / cwidth);
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504 av.startRes = vscroll.getValue() * cwidth;
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508 public OverviewPanel getOverviewPanel()
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510 return overviewPanel;
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513 public void setOverviewPanel(OverviewPanel op)
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515 overviewPanel = op;
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518 public void setAnnotationVisible(boolean b)
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520 if (!av.getWrapAlignment())
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522 annotationSpaceFillerHolder.setVisible(b);
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523 annotationPanelHolder.setVisible(b);
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527 annotationSpaceFillerHolder.setVisible(false);
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528 annotationPanelHolder.setVisible(false);
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535 * automatically adjust annotation panel height for new annotation whilst
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536 * ensuring the alignment is still visible.
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538 public void adjustAnnotationHeight()
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540 // TODO: display vertical annotation scrollbar if necessary
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541 // this is called after loading new annotation onto alignment
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542 if (alignFrame.getSize().height == 0)
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545 .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
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548 validateAnnotationDimensions(true);
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549 apvscroll.addNotify();
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550 hscroll.addNotify();
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552 paintAlignment(true);
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556 * Calculate the annotation dimensions and refresh slider values accordingly.
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557 * Need to do repaints/notifys afterwards.
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559 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
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561 int rowHeight = av.getCharHeight();
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562 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
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563 int annotationHeight = av.calcPanelHeight();
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565 int mheight = annotationHeight;
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566 Dimension d = sequenceHolderPanel.getSize();
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568 int availableHeight = d.height - scalePanelHolder.getHeight();
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570 if (adjustPanelHeight)
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573 * If not enough vertical space, maximize annotation height while keeping
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574 * at least two rows of alignment visible
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576 if (annotationHeight + alignmentHeight > availableHeight)
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578 annotationHeight = Math.min(annotationHeight, availableHeight - 2
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584 // maintain same window layout whilst updating sliders
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585 annotationHeight = annotationPanelHolder.getSize().height;
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588 if (availableHeight - annotationHeight < 5)
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590 annotationHeight = availableHeight;
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593 annotationPanel.setSize(new Dimension(d.width, annotationHeight));
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594 annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
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595 // seqPanelHolder.setSize(d.width, seqandannot - height);
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597 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
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599 Dimension e = idPanel.getSize();
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600 alabels.setSize(new Dimension(e.width, annotationHeight));
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601 annotationSpaceFillerHolder.setSize(new Dimension(e.width,
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602 annotationHeight));
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604 int s = apvscroll.getValue();
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605 if (s > mheight - annotationHeight)
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609 apvscroll.setValues(s, annotationHeight, 0, mheight);
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610 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
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611 alabels.setScrollOffset(apvscroll.getValue(), false);
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614 public void setWrapAlignment(boolean wrap)
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618 scalePanelHolder.setVisible(!wrap);
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620 hscroll.setVisible(!wrap);
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621 idwidthAdjuster.setVisible(!wrap);
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625 annotationPanelHolder.setVisible(false);
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626 annotationSpaceFillerHolder.setVisible(false);
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628 else if (av.isShowAnnotation())
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630 annotationPanelHolder.setVisible(true);
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631 annotationSpaceFillerHolder.setVisible(true);
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634 idSpaceFillerPanel1.setVisible(!wrap);
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636 fontChanged(); // This is so that the scalePanel is resized correctly
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639 sequenceHolderPanel.validate();
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648 // return value is true if the scroll is valid
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649 public boolean scrollUp(boolean up)
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653 if (vscroll.getValue() < 1)
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657 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
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661 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
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665 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
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672 public boolean scrollRight(boolean right)
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676 if (hscroll.getValue() < 1)
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680 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
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684 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
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688 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
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695 public void setScrollValues(int x, int y)
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697 int width = av.getAlignment().getWidth();
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698 int height = av.getAlignment().getHeight();
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700 if (av.hasHiddenColumns())
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702 width = av.getColumnSelection().findColumnPosition(width);
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710 hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
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711 vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
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713 if (hextent > width)
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718 if (vextent > height)
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723 if ((hextent + x) > width)
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725 System.err.println("hextent was " + hextent + " and x was " + x);
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727 x = width - hextent;
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730 if ((vextent + y) > height)
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732 y = height - vextent;
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742 System.err.println("x was " + x);
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748 int endSeq = y + vextent;
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749 if (endSeq > av.getAlignment().getHeight())
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751 endSeq = av.getAlignment().getHeight();
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754 av.setEndSeq(endSeq);
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756 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
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757 .getCharWidth())) - 1);
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759 hscroll.setValues(x, hextent, 0, width);
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760 vscroll.setValues(y, vextent, 0, height);
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762 if (overviewPanel != null)
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764 overviewPanel.setBoxPosition();
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766 sendViewPosition();
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770 public void adjustmentValueChanged(AdjustmentEvent evt)
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772 int oldX = av.getStartRes();
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773 int oldY = av.getStartSeq();
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775 if (evt == null || evt.getSource() == apvscroll)
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777 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
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778 alabels.setScrollOffset(apvscroll.getValue(), false);
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779 // annotationPanel.image=null;
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780 // alabels.image=null;
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781 // alabels.repaint();
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782 // annotationPanel.repaint();
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784 if (evt == null || evt.getSource() == hscroll)
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786 int x = hscroll.getValue();
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788 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
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789 / av.getCharWidth() - 1);
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792 if (evt == null || evt.getSource() == vscroll)
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794 int offy = vscroll.getValue();
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795 if (av.getWrapAlignment())
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797 int rowSize = seqPanel.seqCanvas
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798 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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799 av.setStartRes(vscroll.getValue() * rowSize);
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800 av.setEndRes((vscroll.getValue() + 1) * rowSize);
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804 av.setStartSeq(offy);
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805 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
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806 / av.getCharHeight());
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810 if (overviewPanel != null)
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812 overviewPanel.setBoxPosition();
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815 int scrollX = av.startRes - oldX;
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816 int scrollY = av.startSeq - oldY;
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818 if (av.getWrapAlignment() || !fastPaint || av.MAC)
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824 // Make sure we're not trying to draw a panel
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825 // larger than the visible window
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826 if (scrollX > av.endRes - av.startRes)
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828 scrollX = av.endRes - av.startRes;
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830 else if (scrollX < av.startRes - av.endRes)
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832 scrollX = av.startRes - av.endRes;
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835 idPanel.idCanvas.fastPaint(scrollY);
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836 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
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838 scalePanel.repaint();
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839 if (av.isShowAnnotation())
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841 annotationPanel.fastPaint(av.getStartRes() - oldX);
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844 sendViewPosition();
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847 * If there is one, scroll the (Protein/cDNA) complementary alignment to
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848 * match, unless we are ourselves doing that.
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850 if (isFollowingComplementScroll())
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852 setFollowingComplementScroll(false);
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856 AlignmentPanel ap = getComplementPanel();
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857 av.scrollComplementaryAlignment(ap);
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863 * A helper method to return the AlignmentPanel in the other (complementary)
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864 * half of a SplitFrame view. Returns null if not in a SplitFrame.
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868 private AlignmentPanel getComplementPanel()
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870 AlignmentPanel ap = null;
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871 if (alignFrame != null)
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873 SplitFrame sf = alignFrame.getSplitFrame();
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876 AlignFrame other = sf.getComplement(alignFrame);
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879 ap = other.alignPanel;
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887 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
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888 * The aim is to keep the two alignments 'lined up' on their centre columns.
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891 * holds mapped region(s) of this alignment that we are scrolling
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892 * 'to'; may be modified for sequence offset by this method
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894 * the number of visible sequences to show above the mapped region
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896 protected void scrollToCentre(SearchResults sr, int seqOffset)
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899 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
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900 * mapped), we can make the scroll-to location a sequence above the one
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903 SequenceI mappedTo = sr.getResultSequence(0);
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904 List<SequenceI> seqs = av.getAlignment().getSequences();
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907 * This is like AlignmentI.findIndex(seq) but here we are matching the
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908 * dataset sequence not the aligned sequence
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910 int sequenceIndex = 0;
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911 boolean matched = false;
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912 for (SequenceI seq : seqs)
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914 if (mappedTo == seq.getDatasetSequence())
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923 return; // failsafe, shouldn't happen
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925 sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
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926 sr.getResults().get(0)
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927 .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
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930 * Scroll to position but centring the target residue. Also set a state flag
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931 * to prevent adjustmentValueChanged performing this recursively.
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933 setFollowingComplementScroll(true);
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934 scrollToPosition(sr, true, true);
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937 private void sendViewPosition()
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939 StructureSelectionManager.getStructureSelectionManager(av.applet)
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940 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
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945 * Repaint the alignment and annotations, and, optionally, any overview window
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947 public void paintAlignment(boolean updateOverview)
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949 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
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950 av.isShowAutocalculatedAbove());
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951 sorter.sort(getAlignment().getAlignmentAnnotation(),
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952 av.getSortAnnotationsBy());
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955 if (updateOverview)
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957 StructureSelectionManager.getStructureSelectionManager(av.applet)
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958 .sequenceColoursChanged(this);
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960 if (overviewPanel != null)
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962 overviewPanel.updateOverviewImage();
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967 public void update(Graphics g)
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972 public void paint(Graphics g)
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975 Dimension d = idPanel.idCanvas.getSize();
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976 final int canvasHeight = seqPanel.seqCanvas.getSize().height;
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977 if (canvasHeight != d.height)
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979 idPanel.idCanvas.setSize(d.width, canvasHeight);
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982 if (av.getWrapAlignment())
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984 int maxwidth = av.getAlignment().getWidth();
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986 if (av.hasHiddenColumns())
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988 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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991 int canvasWidth = seqPanel.seqCanvas
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992 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
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994 if (canvasWidth > 0)
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996 int max = maxwidth / canvasWidth;
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997 vscroll.setMaximum(1 + max);
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998 vscroll.setUnitIncrement(1);
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999 vscroll.setVisibleAmount(1);
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1004 setScrollValues(av.getStartRes(), av.getStartSeq());
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1007 seqPanel.seqCanvas.repaint();
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1008 idPanel.idCanvas.repaint();
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1009 if (!av.getWrapAlignment())
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1011 if (av.isShowAnnotation())
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1013 alabels.repaint();
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1014 annotationPanel.repaint();
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1016 scalePanel.repaint();
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1021 protected JPanel sequenceHolderPanel = new JPanel();
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1023 protected JScrollBar vscroll = new JScrollBar();
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1025 protected JScrollBar hscroll = new JScrollBar();
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1027 protected JPanel seqPanelHolder = new JPanel();
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1029 protected JPanel scalePanelHolder = new JPanel();
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1031 protected JPanel idPanelHolder = new JPanel();
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1033 protected JPanel idSpaceFillerPanel1 = new JPanel();
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1035 public JPanel annotationSpaceFillerHolder = new JPanel();
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1037 protected JPanel hscrollFillerPanel = new JPanel();
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1039 JPanel annotationPanelHolder = new JPanel();
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1041 protected JScrollBar apvscroll = new JScrollBar();
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1044 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
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1045 * true, suppresses invoking the same method recursively.
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1047 private boolean followingComplementScroll;
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1049 private void jbInit() throws Exception
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1051 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
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1052 this.setLayout(new BorderLayout());
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1054 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
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1055 sequenceHolderPanel.setLayout(new BorderLayout());
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1056 seqPanelHolder.setLayout(new BorderLayout());
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1057 scalePanelHolder.setBackground(Color.white);
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1059 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
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1060 scalePanelHolder.setLayout(new BorderLayout());
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1061 idPanelHolder.setLayout(new BorderLayout());
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1062 idSpaceFillerPanel1.setBackground(Color.white);
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1064 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
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1065 idSpaceFillerPanel1.setLayout(new BorderLayout());
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1066 annotationSpaceFillerHolder.setBackground(Color.white);
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1068 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
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1069 annotationSpaceFillerHolder.setLayout(new BorderLayout());
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1070 hscroll.setOrientation(JScrollBar.HORIZONTAL);
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1072 JPanel hscrollHolder = new JPanel();
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1073 hscrollHolder.setLayout(new BorderLayout());
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1074 hscrollFillerPanel.setBackground(Color.white);
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1075 apvscroll.setOrientation(JScrollBar.VERTICAL);
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1076 apvscroll.setVisible(true);
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1077 apvscroll.addAdjustmentListener(this);
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1079 annotationPanelHolder.setBackground(Color.white);
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1080 annotationPanelHolder.setLayout(new BorderLayout());
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1081 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
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1082 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
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1083 hscrollHolder.setBackground(Color.white);
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1085 // annotationScroller.setPreferredSize(new Dimension(10, 80));
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1086 // this.setPreferredSize(new Dimension(220, 166));
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1087 seqPanelHolder.setBackground(Color.white);
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1088 idPanelHolder.setBackground(Color.white);
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1089 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
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1090 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
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1091 seqPanelHolder.add(vscroll, BorderLayout.EAST);
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1093 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
\r
1094 this.add(idPanelHolder, BorderLayout.WEST);
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1095 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
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1096 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
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1097 this.add(hscrollHolder, BorderLayout.SOUTH);
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1098 hscrollHolder.add(hscroll, BorderLayout.CENTER);
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1099 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
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1100 this.add(sequenceHolderPanel, BorderLayout.CENTER);
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1104 * hides or shows dynamic annotation rows based on groups and av state flags
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1106 public void updateAnnotation()
\r
1108 updateAnnotation(false);
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1111 public void updateAnnotation(boolean applyGlobalSettings)
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1113 updateAnnotation(applyGlobalSettings, false);
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1116 public void updateAnnotation(boolean applyGlobalSettings,
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1117 boolean preserveNewGroupSettings)
\r
1119 av.updateGroupAnnotationSettings(applyGlobalSettings,
\r
1120 preserveNewGroupSettings);
\r
1121 adjustAnnotationHeight();
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1125 public AlignmentI getAlignment()
\r
1127 return av.getAlignment();
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1131 public String getViewName()
\r
1137 public StructureSelectionManager getStructureSelectionManager()
\r
1139 return StructureSelectionManager
\r
1140 .getStructureSelectionManager(av.applet);
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1144 public void raiseOOMWarning(String string, OutOfMemoryError error)
\r
1147 System.err.println("Out of memory whilst '" + string + "'");
\r
1148 error.printStackTrace();
\r
1152 * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
\r
1156 protected void setFollowingComplementScroll(boolean b)
\r
1158 this.followingComplementScroll = b;
\r
1161 protected boolean isFollowingComplementScroll()
\r
1163 return this.followingComplementScroll;
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