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.gui;
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21 import jalview.analysis.*;
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23 import jalview.bin.*;
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25 import jalview.datamodel.*;
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27 import jalview.schemes.*;
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38 * @version $Revision$
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40 public class AlignViewport
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46 boolean showFullId = false;
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47 boolean showText = true;
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48 boolean showColourText = false;
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49 boolean showBoxes = true;
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50 boolean wrapAlignment = false;
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51 boolean renderGaps = true;
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52 boolean showSequenceFeatures = false;
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53 boolean showAnnotation = true;
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54 boolean showConservation = true;
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55 boolean showQuality = true;
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56 boolean showIdentity = true;
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57 boolean colourAppliesToAllGroups = true;
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58 ColourSchemeI globalColourScheme = null;
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59 boolean conservationColourSelected = false;
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60 boolean abovePIDThreshold = false;
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61 SequenceGroup selectionGroup;
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65 Font font = new Font("SansSerif", Font.PLAIN, 10);
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66 AlignmentI alignment;
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67 ColumnSelection colSel = new ColumnSelection();
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70 NJTree currentTree = null;
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71 boolean scaleAboveWrapped = false;
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72 boolean scaleLeftWrapped = true;
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73 boolean scaleRightWrapped = true;
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75 /** DOCUMENT ME!! */
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76 public Vector vconsensus;
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77 AlignmentAnnotation consensus;
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78 AlignmentAnnotation conservation;
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79 AlignmentAnnotation quality;
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81 /** DOCUMENT ME!! */
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82 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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84 // JBPNote Prolly only need this in the applet version.
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85 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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87 boolean ignoreGapsInConsensusCalculation = false;
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89 boolean showTranslation = false;
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91 boolean isDataset = false;
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94 * Creates a new AlignViewport object.
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96 * @param al DOCUMENT ME!
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98 public AlignViewport(AlignmentI al)
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102 this.endRes = al.getWidth() - 1;
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104 this.endSeq = al.getHeight() - 1;
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107 showFullId = Cache.getDefault("SHOW_FULL_ID", true);
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108 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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109 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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111 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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112 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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114 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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115 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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116 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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120 if (fontStyle.equals("bold"))
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124 else if (fontStyle.equals("italic"))
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129 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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132 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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135 // We must set conservation and consensus before setting colour,
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136 // as Blosum and Clustal require this to be done
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137 if(vconsensus==null)
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139 updateConservation();
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143 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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145 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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146 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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148 if (globalColourScheme instanceof UserColourScheme)
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150 globalColourScheme = UserDefinedColours.loadDefaultColours();
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151 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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154 if (globalColourScheme != null)
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156 globalColourScheme.setConsensus(vconsensus);
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166 * @param b DOCUMENT ME!
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168 public void showSequenceFeatures(boolean b)
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170 showSequenceFeatures = b;
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176 public void updateConservation()
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178 if(alignment.isNucleotide())
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182 Conservation cons = new jalview.analysis.Conservation("All",
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183 jalview.schemes.ResidueProperties.propHash, 3,
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184 alignment.getSequences(), 0, alignment.getWidth() - 1);
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186 cons.verdict(false, ConsPercGaps);
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187 cons.findQuality();
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189 int alWidth = alignment.getWidth();
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190 Annotation[] annotations = new Annotation[alWidth];
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191 Annotation[] qannotations = new Annotation[alWidth];
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192 String sequence = cons.getConsSequence().getSequence();
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202 maxR = 1.0f - minR;
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203 maxG = 0.9f - minG;
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204 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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208 float qmin = cons.qualityRange[0].floatValue();
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209 float qmax = cons.qualityRange[1].floatValue();
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211 for (int i = 0; i < alWidth; i++)
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217 value = Integer.parseInt(sequence.charAt(i) + "");
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219 catch (Exception ex)
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221 if (sequence.charAt(i) == '*')
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226 if (sequence.charAt(i) == '+')
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232 float vprop = value - min;
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234 annotations[i] = new Annotation(sequence.charAt(i) + "",
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235 String.valueOf(value), ' ', value,
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236 new Color(minR + (maxR * vprop),
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237 minG + (maxG * vprop),
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238 minB + (maxB * vprop)));
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241 value = ( (Double) cons.quality.get(i)).floatValue();
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242 vprop = value - qmin;
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244 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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246 new Color(minR + (maxR * vprop),
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247 minG + (maxG * vprop),
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248 minB + (maxB * vprop)));
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251 if (conservation == null)
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253 conservation = new AlignmentAnnotation("Conservation",
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254 "Conservation of total alignment less than " +
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255 ConsPercGaps + "% gaps",
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256 annotations, 0f, // cons.qualityRange[0].floatValue(),
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257 11f, // cons.qualityRange[1].floatValue()
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260 if (showConservation)
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262 alignment.addAnnotation(conservation);
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265 quality = new AlignmentAnnotation("Quality",
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266 "Alignment Quality based on Blosum62 scores",
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268 cons.qualityRange[0].floatValue(),
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269 cons.qualityRange[1].floatValue(),
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274 alignment.addAnnotation(quality);
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279 conservation.annotations = annotations;
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280 quality.annotations = qannotations;
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281 quality.graphMax = cons.qualityRange[1].floatValue();
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284 catch (OutOfMemoryError error)
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286 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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287 "Out of memory calculating conservation!!"
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289 "\nSee help files for increasing Java Virtual Machine memory."
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291 javax.swing.JOptionPane.WARNING_MESSAGE);
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292 System.out.println("Conservation calculation: " + error);
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301 public void updateConsensus()
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304 Annotation[] annotations = new Annotation[alignment.getWidth()];
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306 // this routine prevents vconsensus becoming a new object each time
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307 // consenus is calculated. Important for speed of Blosum62
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308 // and PID colouring of alignment
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309 if (vconsensus == null)
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311 vconsensus = alignment.getAAFrequency();
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315 Vector temp = alignment.getAAFrequency();
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316 vconsensus.clear();
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318 Enumeration e = temp.elements();
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320 while (e.hasMoreElements())
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322 vconsensus.add(e.nextElement());
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326 Hashtable hash = null;
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328 for (int i = 0; i < alignment.getWidth(); i++)
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330 hash = (Hashtable) vconsensus.elementAt(i);
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333 if (ignoreGapsInConsensusCalculation)
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334 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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336 value = ( (Float) hash.get("pid_gaps")).floatValue();
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338 String maxRes = hash.get("maxResidue").toString();
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339 String mouseOver = hash.get("maxResidue") + " ";
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341 if (maxRes.length() > 1)
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343 mouseOver = "[" + maxRes + "] ";
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347 mouseOver += ( (int) value + "%");
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348 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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351 if (consensus == null)
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353 consensus = new AlignmentAnnotation("Consensus", "PID",
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354 annotations, 0f, 100f, 1);
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358 alignment.addAnnotation(consensus);
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363 consensus.annotations = annotations;
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366 if (globalColourScheme != null)
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367 globalColourScheme.setConsensus(vconsensus);
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369 }catch(OutOfMemoryError error)
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371 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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372 "Out of memory calculating consensus!!"
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374 "\nSee help files for increasing Java Virtual Machine memory."
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376 javax.swing.JOptionPane.WARNING_MESSAGE);
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377 System.out.println("Consensus calculation: " + error);
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386 * @return DOCUMENT ME!
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388 public SequenceGroup getSelectionGroup()
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390 return selectionGroup;
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396 * @param sg DOCUMENT ME!
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398 public void setSelectionGroup(SequenceGroup sg)
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400 selectionGroup = sg;
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406 * @return DOCUMENT ME!
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408 public boolean getConservationSelected()
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410 return conservationColourSelected;
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416 * @param b DOCUMENT ME!
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418 public void setConservationSelected(boolean b)
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420 conservationColourSelected = b;
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426 * @return DOCUMENT ME!
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428 public boolean getAbovePIDThreshold()
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430 return abovePIDThreshold;
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436 * @param b DOCUMENT ME!
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438 public void setAbovePIDThreshold(boolean b)
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440 abovePIDThreshold = b;
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446 * @return DOCUMENT ME!
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448 public int getStartRes()
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456 * @return DOCUMENT ME!
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458 public int getEndRes()
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466 * @return DOCUMENT ME!
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468 public int getStartSeq()
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476 * @param cs DOCUMENT ME!
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478 public void setGlobalColourScheme(ColourSchemeI cs)
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480 globalColourScheme = cs;
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486 * @return DOCUMENT ME!
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488 public ColourSchemeI getGlobalColourScheme()
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490 return globalColourScheme;
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496 * @param res DOCUMENT ME!
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498 public void setStartRes(int res)
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500 this.startRes = res;
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506 * @param seq DOCUMENT ME!
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508 public void setStartSeq(int seq)
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510 this.startSeq = seq;
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516 * @param res DOCUMENT ME!
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518 public void setEndRes(int res)
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520 if (res > (alignment.getWidth() - 1))
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522 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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523 res = alignment.getWidth() - 1;
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537 * @param seq DOCUMENT ME!
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539 public void setEndSeq(int seq)
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541 if (seq > alignment.getHeight())
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543 seq = alignment.getHeight();
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557 * @return DOCUMENT ME!
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559 public int getEndSeq()
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567 * @param f DOCUMENT ME!
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569 public void setFont(Font f)
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573 Container c = new Container();
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575 java.awt.FontMetrics fm = c.getFontMetrics(font);
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576 setCharHeight(fm.getHeight());
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577 setCharWidth(fm.charWidth('M'));
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583 * @return DOCUMENT ME!
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585 public Font getFont()
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593 * @param w DOCUMENT ME!
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595 public void setCharWidth(int w)
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597 this.charWidth = w;
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603 * @return DOCUMENT ME!
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605 public int getCharWidth()
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613 * @param h DOCUMENT ME!
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615 public void setCharHeight(int h)
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617 this.charHeight = h;
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623 * @return DOCUMENT ME!
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625 public int getCharHeight()
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633 * @param w DOCUMENT ME!
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635 public void setWrappedWidth(int w)
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637 this.wrappedWidth = w;
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643 * @return DOCUMENT ME!
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645 public int getWrappedWidth()
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647 return wrappedWidth;
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654 * @return DOCUMENT ME!
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656 public AlignmentI getAlignment()
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664 * @param align DOCUMENT ME!
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666 public void setAlignment(AlignmentI align)
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668 this.alignment = align;
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674 * @param state DOCUMENT ME!
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676 public void setWrapAlignment(boolean state)
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678 wrapAlignment = state;
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684 * @param state DOCUMENT ME!
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686 public void setShowText(boolean state)
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694 * @param state DOCUMENT ME!
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696 public void setRenderGaps(boolean state)
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698 renderGaps = state;
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704 * @return DOCUMENT ME!
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706 public boolean getColourText()
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708 return showColourText;
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714 * @param state DOCUMENT ME!
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716 public void setColourText(boolean state)
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718 showColourText = state;
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724 * @param state DOCUMENT ME!
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726 public void setShowBoxes(boolean state)
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734 * @return DOCUMENT ME!
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736 public boolean getWrapAlignment()
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738 return wrapAlignment;
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744 * @return DOCUMENT ME!
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746 public boolean getShowText()
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754 * @return DOCUMENT ME!
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756 public boolean getShowBoxes()
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764 * @return DOCUMENT ME!
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766 public char getGapCharacter()
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768 return getAlignment().getGapCharacter();
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774 * @param gap DOCUMENT ME!
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776 public void setGapCharacter(char gap)
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778 if (getAlignment() != null)
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780 getAlignment().setGapCharacter(gap);
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787 * @param thresh DOCUMENT ME!
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789 public void setThreshold(int thresh)
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791 threshold = thresh;
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797 * @return DOCUMENT ME!
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799 public int getThreshold()
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807 * @param inc DOCUMENT ME!
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809 public void setIncrement(int inc)
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817 * @return DOCUMENT ME!
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819 public int getIncrement()
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827 * @param y DOCUMENT ME!
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829 * @return DOCUMENT ME!
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831 public int getIndex(int y)
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834 int starty = getStartSeq();
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835 int endy = getEndSeq();
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837 for (int i = starty; i <= endy; i++)
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839 if ((i < alignment.getHeight()) &&
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840 (alignment.getSequenceAt(i) != null))
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842 int y2 = y1 + getCharHeight();
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844 if ((y >= y1) && (y <= y2))
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863 * @return DOCUMENT ME!
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865 public ColumnSelection getColumnSelection()
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874 * @param tree DOCUMENT ME!
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876 public void setCurrentTree(NJTree tree)
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878 currentTree = tree;
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884 * @return DOCUMENT ME!
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886 public NJTree getCurrentTree()
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888 return currentTree;
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894 * @param b DOCUMENT ME!
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896 public void setColourAppliesToAllGroups(boolean b)
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898 colourAppliesToAllGroups = b;
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904 * @return DOCUMENT ME!
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906 public boolean getColourAppliesToAllGroups()
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908 return colourAppliesToAllGroups;
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914 * @return DOCUMENT ME!
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916 public boolean getShowFullId()
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924 * @param b DOCUMENT ME!
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926 public void setShowFullId(boolean b)
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934 * @return DOCUMENT ME!
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936 public boolean getShowAnnotation()
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938 return showAnnotation;
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944 * @param b DOCUMENT ME!
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946 public void setShowAnnotation(boolean b)
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948 showAnnotation = b;
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954 * @return DOCUMENT ME!
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956 public boolean getScaleAboveWrapped()
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958 return scaleAboveWrapped;
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964 * @return DOCUMENT ME!
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966 public boolean getScaleLeftWrapped()
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968 return scaleLeftWrapped;
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974 * @return DOCUMENT ME!
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976 public boolean getScaleRightWrapped()
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978 return scaleRightWrapped;
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984 * @param b DOCUMENT ME!
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986 public void setScaleAboveWrapped(boolean b)
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988 scaleAboveWrapped = b;
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994 * @param b DOCUMENT ME!
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996 public void setScaleLeftWrapped(boolean b)
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998 scaleLeftWrapped = b;
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1004 * @param b DOCUMENT ME!
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1006 public void setScaleRightWrapped(boolean b)
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1008 scaleRightWrapped = b;
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1012 * Property change listener for changes in alignment
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1014 * @param listener DOCUMENT ME!
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1016 public void addPropertyChangeListener(
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1017 java.beans.PropertyChangeListener listener)
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1019 changeSupport.addPropertyChangeListener(listener);
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1025 * @param listener DOCUMENT ME!
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1027 public void removePropertyChangeListener(
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1028 java.beans.PropertyChangeListener listener)
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1030 changeSupport.removePropertyChangeListener(listener);
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1034 * Property change listener for changes in alignment
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1036 * @param prop DOCUMENT ME!
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1037 * @param oldvalue DOCUMENT ME!
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1038 * @param newvalue DOCUMENT ME!
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1040 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1042 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1045 public void setIgnoreGapsConsensus(boolean b)
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1047 ignoreGapsInConsensusCalculation = b;
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1048 updateConsensus();
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1049 if(globalColourScheme!=null)
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1051 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1056 public boolean getIgnoreGapsConsensus()
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1058 return ignoreGapsInConsensusCalculation;
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1061 public void showTranslation(boolean b)
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1063 this.showTranslation = b;
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1066 public boolean getShowTranslation()
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1068 return showTranslation;
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1071 public void setDataset(boolean b)
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1076 public boolean isDataset()
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