2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.appletgui;
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21 import jalview.datamodel.*;
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24 import java.awt.event.*;
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27 public class FeatureSettings extends Panel implements ItemListener,
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28 MouseListener, MouseMotionListener
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35 Panel featurePanel = new Panel();
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36 ScrollPane scrollPane;
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37 boolean alignmentHasFeatures = false;
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39 public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
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43 fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
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47 this.setLayout(new BorderLayout());
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48 scrollPane = new ScrollPane();
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49 scrollPane.add(featurePanel);
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50 if (alignmentHasFeatures)
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51 add(scrollPane, BorderLayout.CENTER);
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53 if(groupPanel!=null)
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55 groupPanel.setLayout(
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56 new GridLayout( fr.featureGroups.size() / 4 + 1, 4));
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57 groupPanel.validate();
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59 add(groupPanel, BorderLayout.NORTH);
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61 frame = new Frame();
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63 int height = featurePanel.getComponentCount()*50 +30;
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65 height = Math.max(100, height);
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66 height = Math.min(400, height);
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68 jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,
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72 public void paint(Graphics g)
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74 g.setColor(Color.black);
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75 g.drawString("No Features added to this alignment!!", 10, 20);
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80 alignmentHasFeatures = false;
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82 if(fr.featureGroups==null)
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83 fr.featureGroups = new Hashtable();
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85 Vector allFeatures = new Vector();
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86 Vector allGroups = new Vector();
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87 SequenceFeature[] tmpfeatures;
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91 for (int i = 0; i < av.alignment.getHeight(); i++)
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93 if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
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96 alignmentHasFeatures = true;
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98 tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
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100 while (index < tmpfeatures.length)
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102 if(tmpfeatures[index].getFeatureGroup()!=null)
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104 group = tmpfeatures[index].featureGroup;
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105 if(!allGroups.contains(group))
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107 allGroups.addElement(group);
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109 boolean visible = true;
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110 if (fr.featureGroups.containsKey(group))
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112 visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
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115 fr.featureGroups.put(group, new Boolean(visible));
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117 if (groupPanel == null)
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119 groupPanel = new Panel();
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122 Checkbox check = new Checkbox(group, visible);
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123 check.setFont(new Font("Serif", Font.BOLD, 12));
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124 check.addItemListener(this);
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125 groupPanel.add(check);
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129 if (!allFeatures.contains(tmpfeatures[index].getType()))
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131 allFeatures.addElement(tmpfeatures[index].getType());
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140 //This routine adds and removes checkboxes depending on
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141 //Group selection states
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142 void resetTable(boolean groupsChanged)
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144 SequenceFeature [] tmpfeatures;
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145 String group=null, type;
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146 Vector visibleChecks = new Vector();
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148 for (int i = 0; i < av.alignment.getHeight(); i++)
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150 if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
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153 tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
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155 while (index < tmpfeatures.length)
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157 group = tmpfeatures[index].featureGroup;
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159 if (group==null || fr.featureGroups.get(group)==null ||
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160 ((Boolean) fr.featureGroups.get(group)).booleanValue())
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162 type = tmpfeatures[index].getType();
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163 if(!visibleChecks.contains(type) )
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165 visibleChecks.addElement(type);
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173 int cSize = featurePanel.getComponentCount();
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175 //This will remove any checkboxes which shouldn't be
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177 for (int i = 0; i < cSize; i++)
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179 comps = featurePanel.getComponents();
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180 check = (Checkbox) comps[i];
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181 if (!visibleChecks.contains(check.getLabel()))
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183 featurePanel.remove(i);
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189 if(fr.renderOrder!=null)
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191 //First add the checks in the previous render order,
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192 //in case the window has been closed and reopened
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193 for(int ro=fr.renderOrder.length-1; ro>-1; ro--)
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195 String item = fr.renderOrder[ro];
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197 if(!visibleChecks.contains(item))
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200 visibleChecks.removeElement(item);
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202 addCheck(false, item);
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206 // now add checkboxes which should be visible,
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207 // if they have not already been added
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208 Enumeration en = visibleChecks.elements();
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209 while(en.hasMoreElements())
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211 addCheck(groupsChanged, en.nextElement().toString());
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215 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5));
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216 featurePanel.validate();
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219 if(scrollPane!=null)
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220 scrollPane.validate();
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222 itemStateChanged(null);
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225 void addCheck(boolean groupsChanged, String type)
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228 Component [] comps = featurePanel.getComponents();
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231 for (int i = 0; i < featurePanel.getComponentCount(); i++)
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233 check = (Checkbox) comps[i];
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234 if (check.getLabel().equals(type))
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243 boolean selected = false;
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244 if (groupsChanged || av.featuresDisplayed.containsKey(type))
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249 check = new Checkbox(type, selected);
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250 check.addMouseListener(this);
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251 check.addMouseMotionListener(this);
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252 check.setBackground(fr.getColour(type));
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253 check.addItemListener(this);
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254 featurePanel.add(check);
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258 public void itemStateChanged(ItemEvent evt)
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262 //Is the source a top level featureGroup?
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263 Checkbox source = (Checkbox) evt.getSource();
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264 if (fr.featureGroups.containsKey(source.getLabel()))
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266 fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
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267 ap.seqPanel.seqCanvas.repaint();
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268 if (ap.overviewPanel != null)
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269 ap.overviewPanel.updateOverviewImage();
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276 Component[] comps = featurePanel.getComponents();
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277 int cSize = comps.length;
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279 Object[][] tmp = new Object[cSize][3];
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281 for (int i = 0; i < cSize; i++)
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283 Checkbox check = (Checkbox) comps[i];
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284 tmp[tmpSize][0] = check.getLabel();
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285 tmp[tmpSize][1] = fr.getColour(check.getLabel());
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286 tmp[tmpSize][2] = new Boolean(check.getState());
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290 Object[][]data = new Object[tmpSize][3];
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291 System.arraycopy(tmp, 0, data,0, tmpSize);
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293 fr.setFeaturePriority(data);
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294 ap.seqPanel.seqCanvas.repaint();
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295 if (ap.overviewPanel != null)
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296 ap.overviewPanel.updateOverviewImage();
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299 Checkbox selectedCheck;
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300 boolean dragging = false;
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302 public void mousePressed(MouseEvent evt)
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304 selectedCheck = (Checkbox)evt.getSource();
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307 public void mouseDragged(MouseEvent evt)
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312 public void mouseReleased(MouseEvent evt)
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314 Component comp = null;
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315 Checkbox target = null;
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317 int height = evt.getY()+evt.getComponent().getLocation().y;
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319 if(height > this.getSize().height)
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321 comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
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323 else if(height < 0)
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325 comp = featurePanel.getComponent(0);
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329 comp = featurePanel.getComponentAt(evt.getX(),
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331 evt.getComponent().getLocation().y);
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334 if(comp!=null && comp instanceof Checkbox)
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335 target = (Checkbox)comp;
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337 if ( selectedCheck != null
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339 && selectedCheck != target)
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341 int targetIndex = -1;
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342 for(int i=0; i<featurePanel.getComponentCount(); i++)
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344 if(target==featurePanel.getComponent(i))
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345 { targetIndex = i; break; }
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348 featurePanel.remove(selectedCheck);
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349 featurePanel.add(selectedCheck, targetIndex);
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350 featurePanel.validate();
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351 itemStateChanged(null);
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355 public void setUserColour(String feature, Color col)
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357 fr.setColour(feature, col);
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358 featurePanel.removeAll();
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363 public void mouseEntered(MouseEvent evt){}
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364 public void mouseExited(MouseEvent evt){}
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365 public void mouseClicked(MouseEvent evt)
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367 Checkbox check = (Checkbox) evt.getSource();
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368 if(evt.getClickCount()>1)
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370 new UserDefinedColours(this, check.getLabel(),
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371 fr.getColour(check.getLabel()));
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374 public void mouseMoved(MouseEvent evt){}
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