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 showJVSuffix = true;
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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 isDataset = false;
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92 public AlignViewport(AlignmentI al, boolean dataset)
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94 isDataset = dataset;
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99 * Creates a new AlignViewport object.
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101 * @param al DOCUMENT ME!
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103 public AlignViewport(AlignmentI al)
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112 this.endRes = alignment.getWidth() - 1;
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114 this.endSeq = alignment.getHeight() - 1;
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116 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
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117 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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118 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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120 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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121 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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123 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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124 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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125 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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129 if (fontStyle.equals("bold"))
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133 else if (fontStyle.equals("italic"))
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138 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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141 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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144 // We must set conservation and consensus before setting colour,
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145 // as Blosum and Clustal require this to be done
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146 if(vconsensus==null && !isDataset)
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148 updateConservation();
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152 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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154 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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155 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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157 if (globalColourScheme instanceof UserColourScheme)
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159 globalColourScheme = UserDefinedColours.loadDefaultColours();
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160 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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163 if (globalColourScheme != null)
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165 globalColourScheme.setConsensus(vconsensus);
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175 * @param b DOCUMENT ME!
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177 public void showSequenceFeatures(boolean b)
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179 showSequenceFeatures = b;
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185 public void updateConservation()
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187 if(alignment.isNucleotide())
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191 Conservation cons = new jalview.analysis.Conservation("All",
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192 jalview.schemes.ResidueProperties.propHash, 3,
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193 alignment.getSequences(), 0, alignment.getWidth() - 1);
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195 cons.verdict(false, ConsPercGaps);
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196 cons.findQuality();
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198 int alWidth = alignment.getWidth();
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199 Annotation[] annotations = new Annotation[alWidth];
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200 Annotation[] qannotations = new Annotation[alWidth];
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201 String sequence = cons.getConsSequence().getSequence();
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211 maxR = 1.0f - minR;
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212 maxG = 0.9f - minG;
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213 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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217 float qmin = cons.qualityRange[0].floatValue();
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218 float qmax = cons.qualityRange[1].floatValue();
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220 for (int i = 0; i < alWidth; i++)
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226 value = Integer.parseInt(sequence.charAt(i) + "");
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228 catch (Exception ex)
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230 if (sequence.charAt(i) == '*')
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235 if (sequence.charAt(i) == '+')
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241 float vprop = value - min;
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243 annotations[i] = new Annotation(sequence.charAt(i) + "",
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244 String.valueOf(value), ' ', value,
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245 new Color(minR + (maxR * vprop),
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246 minG + (maxG * vprop),
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247 minB + (maxB * vprop)));
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250 value = ( (Double) cons.quality.get(i)).floatValue();
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251 vprop = value - qmin;
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253 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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255 new Color(minR + (maxR * vprop),
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256 minG + (maxG * vprop),
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257 minB + (maxB * vprop)));
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260 if (conservation == null)
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262 conservation = new AlignmentAnnotation("Conservation",
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263 "Conservation of total alignment less than " +
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264 ConsPercGaps + "% gaps",
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265 annotations, 0f, // cons.qualityRange[0].floatValue(),
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266 11f, // cons.qualityRange[1].floatValue()
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269 if (showConservation)
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271 alignment.addAnnotation(conservation);
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274 quality = new AlignmentAnnotation("Quality",
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275 "Alignment Quality based on Blosum62 scores",
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277 cons.qualityRange[0].floatValue(),
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278 cons.qualityRange[1].floatValue(),
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283 alignment.addAnnotation(quality);
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288 conservation.annotations = annotations;
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289 quality.annotations = qannotations;
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290 quality.graphMax = cons.qualityRange[1].floatValue();
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293 catch (OutOfMemoryError error)
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295 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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296 "Out of memory calculating conservation!!"
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298 "\nSee help files for increasing Java Virtual Machine memory."
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300 javax.swing.JOptionPane.WARNING_MESSAGE);
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301 System.out.println("Conservation calculation: " + error);
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310 public void updateConsensus()
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313 Annotation[] annotations = new Annotation[alignment.getWidth()];
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315 // this routine prevents vconsensus becoming a new object each time
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316 // consenus is calculated. Important for speed of Blosum62
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317 // and PID colouring of alignment
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318 if (vconsensus == null)
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320 vconsensus = alignment.getAAFrequency();
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324 Vector temp = alignment.getAAFrequency();
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325 vconsensus.clear();
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327 Enumeration e = temp.elements();
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329 while (e.hasMoreElements())
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331 vconsensus.add(e.nextElement());
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335 Hashtable hash = null;
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337 for (int i = 0; i < alignment.getWidth(); i++)
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339 hash = (Hashtable) vconsensus.elementAt(i);
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342 if (ignoreGapsInConsensusCalculation)
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343 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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345 value = ( (Float) hash.get("pid_gaps")).floatValue();
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347 String maxRes = hash.get("maxResidue").toString();
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348 String mouseOver = hash.get("maxResidue") + " ";
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350 if (maxRes.length() > 1)
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352 mouseOver = "[" + maxRes + "] ";
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356 mouseOver += ( (int) value + "%");
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357 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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360 if (consensus == null)
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362 consensus = new AlignmentAnnotation("Consensus", "PID",
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363 annotations, 0f, 100f, 1);
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367 alignment.addAnnotation(consensus);
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372 consensus.annotations = annotations;
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375 if (globalColourScheme != null)
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376 globalColourScheme.setConsensus(vconsensus);
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378 }catch(OutOfMemoryError error)
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380 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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381 "Out of memory calculating consensus!!"
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383 "\nSee help files for increasing Java Virtual Machine memory."
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385 javax.swing.JOptionPane.WARNING_MESSAGE);
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386 System.out.println("Consensus calculation: " + error);
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395 * @return DOCUMENT ME!
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397 public SequenceGroup getSelectionGroup()
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399 return selectionGroup;
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405 * @param sg DOCUMENT ME!
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407 public void setSelectionGroup(SequenceGroup sg)
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409 selectionGroup = sg;
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415 * @return DOCUMENT ME!
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417 public boolean getConservationSelected()
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419 return conservationColourSelected;
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425 * @param b DOCUMENT ME!
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427 public void setConservationSelected(boolean b)
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429 conservationColourSelected = b;
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435 * @return DOCUMENT ME!
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437 public boolean getAbovePIDThreshold()
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439 return abovePIDThreshold;
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445 * @param b DOCUMENT ME!
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447 public void setAbovePIDThreshold(boolean b)
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449 abovePIDThreshold = b;
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455 * @return DOCUMENT ME!
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457 public int getStartRes()
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465 * @return DOCUMENT ME!
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467 public int getEndRes()
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475 * @return DOCUMENT ME!
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477 public int getStartSeq()
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485 * @param cs DOCUMENT ME!
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487 public void setGlobalColourScheme(ColourSchemeI cs)
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489 globalColourScheme = cs;
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495 * @return DOCUMENT ME!
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497 public ColourSchemeI getGlobalColourScheme()
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499 return globalColourScheme;
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505 * @param res DOCUMENT ME!
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507 public void setStartRes(int res)
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509 this.startRes = res;
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515 * @param seq DOCUMENT ME!
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517 public void setStartSeq(int seq)
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519 this.startSeq = seq;
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525 * @param res DOCUMENT ME!
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527 public void setEndRes(int res)
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529 if (res > (alignment.getWidth() - 1))
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531 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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532 res = alignment.getWidth() - 1;
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546 * @param seq DOCUMENT ME!
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548 public void setEndSeq(int seq)
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550 if (seq > alignment.getHeight())
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552 seq = alignment.getHeight();
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566 * @return DOCUMENT ME!
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568 public int getEndSeq()
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576 * @param f DOCUMENT ME!
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578 public void setFont(Font f)
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582 Container c = new Container();
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584 java.awt.FontMetrics fm = c.getFontMetrics(font);
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585 setCharHeight(fm.getHeight());
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586 setCharWidth(fm.charWidth('M'));
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592 * @return DOCUMENT ME!
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594 public Font getFont()
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602 * @param w DOCUMENT ME!
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604 public void setCharWidth(int w)
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606 this.charWidth = w;
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612 * @return DOCUMENT ME!
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614 public int getCharWidth()
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622 * @param h DOCUMENT ME!
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624 public void setCharHeight(int h)
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626 this.charHeight = h;
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632 * @return DOCUMENT ME!
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634 public int getCharHeight()
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642 * @param w DOCUMENT ME!
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644 public void setWrappedWidth(int w)
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646 this.wrappedWidth = w;
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652 * @return DOCUMENT ME!
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654 public int getWrappedWidth()
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656 return wrappedWidth;
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663 * @return DOCUMENT ME!
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665 public AlignmentI getAlignment()
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673 * @param align DOCUMENT ME!
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675 public void setAlignment(AlignmentI align)
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677 this.alignment = align;
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683 * @param state DOCUMENT ME!
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685 public void setWrapAlignment(boolean state)
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687 wrapAlignment = state;
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693 * @param state DOCUMENT ME!
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695 public void setShowText(boolean state)
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703 * @param state DOCUMENT ME!
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705 public void setRenderGaps(boolean state)
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707 renderGaps = state;
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713 * @return DOCUMENT ME!
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715 public boolean getColourText()
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717 return showColourText;
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723 * @param state DOCUMENT ME!
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725 public void setColourText(boolean state)
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727 showColourText = state;
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733 * @param state DOCUMENT ME!
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735 public void setShowBoxes(boolean state)
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743 * @return DOCUMENT ME!
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745 public boolean getWrapAlignment()
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747 return wrapAlignment;
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753 * @return DOCUMENT ME!
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755 public boolean getShowText()
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763 * @return DOCUMENT ME!
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765 public boolean getShowBoxes()
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773 * @return DOCUMENT ME!
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775 public char getGapCharacter()
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777 return getAlignment().getGapCharacter();
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783 * @param gap DOCUMENT ME!
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785 public void setGapCharacter(char gap)
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787 if (getAlignment() != null)
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789 getAlignment().setGapCharacter(gap);
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796 * @param thresh DOCUMENT ME!
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798 public void setThreshold(int thresh)
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800 threshold = thresh;
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806 * @return DOCUMENT ME!
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808 public int getThreshold()
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816 * @param inc DOCUMENT ME!
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818 public void setIncrement(int inc)
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826 * @return DOCUMENT ME!
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828 public int getIncrement()
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836 * @param y DOCUMENT ME!
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838 * @return DOCUMENT ME!
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840 public int getIndex(int y)
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843 int starty = getStartSeq();
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844 int endy = getEndSeq();
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846 for (int i = starty; i <= endy; i++)
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848 if ((i < alignment.getHeight()) &&
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849 (alignment.getSequenceAt(i) != null))
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851 int y2 = y1 + getCharHeight();
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853 if ((y >= y1) && (y <= y2))
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872 * @return DOCUMENT ME!
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874 public ColumnSelection getColumnSelection()
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883 * @param tree DOCUMENT ME!
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885 public void setCurrentTree(NJTree tree)
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887 currentTree = tree;
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893 * @return DOCUMENT ME!
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895 public NJTree getCurrentTree()
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897 return currentTree;
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903 * @param b DOCUMENT ME!
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905 public void setColourAppliesToAllGroups(boolean b)
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907 colourAppliesToAllGroups = b;
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913 * @return DOCUMENT ME!
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915 public boolean getColourAppliesToAllGroups()
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917 return colourAppliesToAllGroups;
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923 * @return DOCUMENT ME!
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925 public boolean getShowJVSuffix()
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927 return showJVSuffix;
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933 * @param b DOCUMENT ME!
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935 public void setShowJVSuffix(boolean b)
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944 * @return DOCUMENT ME!
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946 public boolean getShowAnnotation()
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948 return showAnnotation;
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954 * @param b DOCUMENT ME!
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956 public void setShowAnnotation(boolean b)
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958 showAnnotation = b;
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964 * @return DOCUMENT ME!
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966 public boolean getScaleAboveWrapped()
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968 return scaleAboveWrapped;
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974 * @return DOCUMENT ME!
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976 public boolean getScaleLeftWrapped()
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978 return scaleLeftWrapped;
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984 * @return DOCUMENT ME!
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986 public boolean getScaleRightWrapped()
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988 return scaleRightWrapped;
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994 * @param b DOCUMENT ME!
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996 public void setScaleAboveWrapped(boolean b)
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998 scaleAboveWrapped = b;
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1004 * @param b DOCUMENT ME!
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1006 public void setScaleLeftWrapped(boolean b)
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1008 scaleLeftWrapped = b;
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1014 * @param b DOCUMENT ME!
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1016 public void setScaleRightWrapped(boolean b)
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1018 scaleRightWrapped = b;
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1022 * Property change listener for changes in alignment
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1024 * @param listener DOCUMENT ME!
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1026 public void addPropertyChangeListener(
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1027 java.beans.PropertyChangeListener listener)
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1029 changeSupport.addPropertyChangeListener(listener);
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1035 * @param listener DOCUMENT ME!
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1037 public void removePropertyChangeListener(
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1038 java.beans.PropertyChangeListener listener)
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1040 changeSupport.removePropertyChangeListener(listener);
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1044 * Property change listener for changes in alignment
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1046 * @param prop DOCUMENT ME!
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1047 * @param oldvalue DOCUMENT ME!
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1048 * @param newvalue DOCUMENT ME!
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1050 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1052 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1055 public void setIgnoreGapsConsensus(boolean b)
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1057 ignoreGapsInConsensusCalculation = b;
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1058 updateConsensus();
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1059 if(globalColourScheme!=null)
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1061 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1066 public boolean getIgnoreGapsConsensus()
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1068 return ignoreGapsInConsensusCalculation;
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1071 public void setDataset(boolean b)
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1076 public boolean isDataset()
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