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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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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74 boolean hasHiddenColumns = false;
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75 boolean hasHiddenRows = false;
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77 boolean cursorMode = false;
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79 // The following vector holds the features which are
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80 // currently visible, in the correct order or rendering
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81 Hashtable featuresDisplayed = null;
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84 /** DOCUMENT ME!! */
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85 public Vector vconsensus;
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86 AlignmentAnnotation consensus;
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87 AlignmentAnnotation conservation;
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88 AlignmentAnnotation quality;
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89 boolean autoCalculateConsensus = true;
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91 /** DOCUMENT ME!! */
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92 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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94 // JBPNote Prolly only need this in the applet version.
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95 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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97 boolean ignoreGapsInConsensusCalculation = false;
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99 boolean isDataset = false;
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101 boolean antiAlias = false;
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103 boolean padGaps = false;
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106 public AlignViewport(AlignmentI al, boolean dataset)
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108 isDataset = dataset;
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113 * Creates a new AlignViewport object.
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115 * @param al DOCUMENT ME!
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117 public AlignViewport(AlignmentI al)
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126 this.endRes = alignment.getWidth() - 1;
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128 this.endSeq = alignment.getHeight() - 1;
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130 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
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132 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
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133 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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134 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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136 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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137 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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139 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
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141 padGaps = Cache.getDefault("PAD_GAPS", false);
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143 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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144 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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145 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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149 if (fontStyle.equals("bold"))
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153 else if (fontStyle.equals("italic"))
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158 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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161 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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164 // We must set conservation and consensus before setting colour,
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165 // as Blosum and Clustal require this to be done
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166 if(vconsensus==null && !isDataset)
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168 updateConservation();
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172 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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174 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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175 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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177 if (globalColourScheme instanceof UserColourScheme)
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179 globalColourScheme = UserDefinedColours.loadDefaultColours();
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180 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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183 if (globalColourScheme != null)
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185 globalColourScheme.setConsensus(vconsensus);
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195 * @param b DOCUMENT ME!
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197 public void setShowSequenceFeatures(boolean b)
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199 showSequenceFeatures = b;
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202 public boolean getShowSequenceFeatures()
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204 return showSequenceFeatures;
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210 public void updateConservation()
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212 if(alignment.isNucleotide())
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216 Conservation cons = new jalview.analysis.Conservation("All",
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217 jalview.schemes.ResidueProperties.propHash, 3,
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218 alignment.getSequences(), 0, alignment.getWidth() - 1);
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220 cons.verdict(false, ConsPercGaps);
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221 cons.findQuality();
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223 int alWidth = alignment.getWidth();
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224 Annotation[] annotations = new Annotation[alWidth];
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225 Annotation[] qannotations = new Annotation[alWidth];
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226 String sequence = cons.getConsSequence().getSequence();
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236 maxR = 1.0f - minR;
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237 maxG = 0.9f - minG;
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238 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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242 float qmin = cons.qualityRange[0].floatValue();
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243 float qmax = cons.qualityRange[1].floatValue();
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245 for (int i = 0; i < alWidth; i++)
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251 value = Integer.parseInt(sequence.charAt(i) + "");
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253 catch (Exception ex)
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255 if (sequence.charAt(i) == '*')
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260 if (sequence.charAt(i) == '+')
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266 float vprop = value - min;
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268 annotations[i] = new Annotation(sequence.charAt(i) + "",
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269 String.valueOf(value), ' ', value,
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270 new Color(minR + (maxR * vprop),
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271 minG + (maxG * vprop),
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272 minB + (maxB * vprop)));
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275 value = ( (Double) cons.quality.get(i)).floatValue();
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276 vprop = value - qmin;
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278 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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280 new Color(minR + (maxR * vprop),
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281 minG + (maxG * vprop),
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282 minB + (maxB * vprop)));
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285 if (conservation == null)
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287 conservation = new AlignmentAnnotation("Conservation",
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288 "Conservation of total alignment less than " +
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289 ConsPercGaps + "% gaps",
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290 annotations, 0f, // cons.qualityRange[0].floatValue(),
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291 11f, // cons.qualityRange[1].floatValue()
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292 AlignmentAnnotation.BAR_GRAPH);
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294 if (showConservation)
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296 alignment.addAnnotation(conservation);
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299 quality = new AlignmentAnnotation("Quality",
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300 "Alignment Quality based on Blosum62 scores",
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302 cons.qualityRange[0].floatValue(),
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303 cons.qualityRange[1].floatValue(),
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304 AlignmentAnnotation.BAR_GRAPH);
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308 alignment.addAnnotation(quality);
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313 conservation.annotations = annotations;
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314 quality.annotations = qannotations;
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315 quality.graphMax = cons.qualityRange[1].floatValue();
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318 catch (OutOfMemoryError error)
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320 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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321 "Out of memory calculating conservation!!"
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323 "\nSee help files for increasing Java Virtual Machine memory."
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325 javax.swing.JOptionPane.WARNING_MESSAGE);
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326 System.out.println("Conservation calculation: " + error);
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335 public void updateConsensus()
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338 Annotation[] annotations = new Annotation[alignment.getWidth()];
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340 // this routine prevents vconsensus becoming a new object each time
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341 // consenus is calculated. Important for speed of Blosum62
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342 // and PID colouring of alignment
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343 if (vconsensus == null)
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345 vconsensus = alignment.getAAFrequency();
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349 Vector temp = alignment.getAAFrequency();
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350 vconsensus.clear();
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352 Enumeration e = temp.elements();
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354 while (e.hasMoreElements())
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356 vconsensus.add(e.nextElement());
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360 Hashtable hash = null;
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362 for (int i = 0; i < alignment.getWidth(); i++)
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364 hash = (Hashtable) vconsensus.elementAt(i);
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367 if (ignoreGapsInConsensusCalculation)
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368 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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370 value = ( (Float) hash.get("pid_gaps")).floatValue();
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372 String maxRes = hash.get("maxResidue").toString();
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373 String mouseOver = hash.get("maxResidue") + " ";
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375 if (maxRes.length() > 1)
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377 mouseOver = "[" + maxRes + "] ";
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381 mouseOver += ( (int) value + "%");
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382 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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385 if (consensus == null)
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387 consensus = new AlignmentAnnotation("Consensus", "PID",
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388 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
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392 alignment.addAnnotation(consensus);
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397 consensus.annotations = annotations;
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400 if (globalColourScheme != null)
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401 globalColourScheme.setConsensus(vconsensus);
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403 }catch(OutOfMemoryError error)
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405 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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406 "Out of memory calculating consensus!!"
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408 "\nSee help files for increasing Java Virtual Machine memory."
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410 javax.swing.JOptionPane.WARNING_MESSAGE);
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411 System.out.println("Consensus calculation: " + error);
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420 * @return DOCUMENT ME!
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422 public SequenceGroup getSelectionGroup()
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424 return selectionGroup;
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430 * @param sg DOCUMENT ME!
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432 public void setSelectionGroup(SequenceGroup sg)
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434 selectionGroup = sg;
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440 * @return DOCUMENT ME!
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442 public boolean getConservationSelected()
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444 return conservationColourSelected;
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450 * @param b DOCUMENT ME!
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452 public void setConservationSelected(boolean b)
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454 conservationColourSelected = b;
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460 * @return DOCUMENT ME!
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462 public boolean getAbovePIDThreshold()
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464 return abovePIDThreshold;
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470 * @param b DOCUMENT ME!
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472 public void setAbovePIDThreshold(boolean b)
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474 abovePIDThreshold = b;
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480 * @return DOCUMENT ME!
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482 public int getStartRes()
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490 * @return DOCUMENT ME!
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492 public int getEndRes()
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500 * @return DOCUMENT ME!
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502 public int getStartSeq()
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510 * @param cs DOCUMENT ME!
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512 public void setGlobalColourScheme(ColourSchemeI cs)
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514 globalColourScheme = cs;
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520 * @return DOCUMENT ME!
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522 public ColourSchemeI getGlobalColourScheme()
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524 return globalColourScheme;
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530 * @param res DOCUMENT ME!
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532 public void setStartRes(int res)
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534 this.startRes = res;
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540 * @param seq DOCUMENT ME!
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542 public void setStartSeq(int seq)
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544 this.startSeq = seq;
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550 * @param res DOCUMENT ME!
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552 public void setEndRes(int res)
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554 if (res > (alignment.getWidth() - 1))
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556 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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557 res = alignment.getWidth() - 1;
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571 * @param seq DOCUMENT ME!
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573 public void setEndSeq(int seq)
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575 if (seq > alignment.getHeight())
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577 seq = alignment.getHeight();
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591 * @return DOCUMENT ME!
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593 public int getEndSeq()
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601 * @param f DOCUMENT ME!
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603 public void setFont(Font f)
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607 Container c = new Container();
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609 java.awt.FontMetrics fm = c.getFontMetrics(font);
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610 setCharHeight(fm.getHeight());
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611 setCharWidth(fm.charWidth('M'));
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617 * @return DOCUMENT ME!
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619 public Font getFont()
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627 * @param w DOCUMENT ME!
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629 public void setCharWidth(int w)
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631 this.charWidth = w;
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637 * @return DOCUMENT ME!
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639 public int getCharWidth()
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647 * @param h DOCUMENT ME!
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649 public void setCharHeight(int h)
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651 this.charHeight = h;
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657 * @return DOCUMENT ME!
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659 public int getCharHeight()
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667 * @param w DOCUMENT ME!
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669 public void setWrappedWidth(int w)
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671 this.wrappedWidth = w;
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677 * @return DOCUMENT ME!
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679 public int getWrappedWidth()
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681 return wrappedWidth;
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688 * @return DOCUMENT ME!
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690 public AlignmentI getAlignment()
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698 * @param align DOCUMENT ME!
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700 public void setAlignment(AlignmentI align)
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702 this.alignment = align;
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708 * @param state DOCUMENT ME!
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710 public void setWrapAlignment(boolean state)
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712 wrapAlignment = state;
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718 * @param state DOCUMENT ME!
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720 public void setShowText(boolean state)
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728 * @param state DOCUMENT ME!
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730 public void setRenderGaps(boolean state)
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732 renderGaps = state;
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738 * @return DOCUMENT ME!
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740 public boolean getColourText()
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742 return showColourText;
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748 * @param state DOCUMENT ME!
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750 public void setColourText(boolean state)
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752 showColourText = state;
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758 * @param state DOCUMENT ME!
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760 public void setShowBoxes(boolean state)
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768 * @return DOCUMENT ME!
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770 public boolean getWrapAlignment()
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772 return wrapAlignment;
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778 * @return DOCUMENT ME!
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780 public boolean getShowText()
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788 * @return DOCUMENT ME!
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790 public boolean getShowBoxes()
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798 * @return DOCUMENT ME!
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800 public char getGapCharacter()
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802 return getAlignment().getGapCharacter();
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808 * @param gap DOCUMENT ME!
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810 public void setGapCharacter(char gap)
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812 if (getAlignment() != null)
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814 getAlignment().setGapCharacter(gap);
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821 * @param thresh DOCUMENT ME!
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823 public void setThreshold(int thresh)
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825 threshold = thresh;
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831 * @return DOCUMENT ME!
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833 public int getThreshold()
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841 * @param inc DOCUMENT ME!
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843 public void setIncrement(int inc)
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851 * @return DOCUMENT ME!
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853 public int getIncrement()
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861 * @param y DOCUMENT ME!
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863 * @return DOCUMENT ME!
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865 public int getIndex(int y)
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868 int starty = getStartSeq();
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869 int endy = getEndSeq();
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871 for (int i = starty; i <= endy; i++)
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873 if ((i < alignment.getHeight()) &&
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874 (alignment.getSequenceAt(i) != null))
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876 int y2 = y1 + getCharHeight();
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878 if ((y >= y1) && (y <= y2))
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897 * @return DOCUMENT ME!
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899 public ColumnSelection getColumnSelection()
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908 * @param tree DOCUMENT ME!
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910 public void setCurrentTree(NJTree tree)
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912 currentTree = tree;
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918 * @return DOCUMENT ME!
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920 public NJTree getCurrentTree()
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922 return currentTree;
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928 * @param b DOCUMENT ME!
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930 public void setColourAppliesToAllGroups(boolean b)
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932 colourAppliesToAllGroups = b;
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938 * @return DOCUMENT ME!
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940 public boolean getColourAppliesToAllGroups()
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942 return colourAppliesToAllGroups;
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948 * @return DOCUMENT ME!
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950 public boolean getShowJVSuffix()
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952 return showJVSuffix;
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958 * @param b DOCUMENT ME!
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960 public void setShowJVSuffix(boolean b)
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969 * @return DOCUMENT ME!
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971 public boolean getShowAnnotation()
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973 return showAnnotation;
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979 * @param b DOCUMENT ME!
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981 public void setShowAnnotation(boolean b)
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983 showAnnotation = b;
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989 * @return DOCUMENT ME!
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991 public boolean getScaleAboveWrapped()
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993 return scaleAboveWrapped;
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999 * @return DOCUMENT ME!
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1001 public boolean getScaleLeftWrapped()
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1003 return scaleLeftWrapped;
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1009 * @return DOCUMENT ME!
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1011 public boolean getScaleRightWrapped()
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1013 return scaleRightWrapped;
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1019 * @param b DOCUMENT ME!
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1021 public void setScaleAboveWrapped(boolean b)
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1023 scaleAboveWrapped = b;
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1029 * @param b DOCUMENT ME!
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1031 public void setScaleLeftWrapped(boolean b)
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1033 scaleLeftWrapped = b;
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1039 * @param b DOCUMENT ME!
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1041 public void setScaleRightWrapped(boolean b)
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1043 scaleRightWrapped = b;
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1047 * Property change listener for changes in alignment
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1049 * @param listener DOCUMENT ME!
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1051 public void addPropertyChangeListener(
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1052 java.beans.PropertyChangeListener listener)
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1054 changeSupport.addPropertyChangeListener(listener);
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1060 * @param listener DOCUMENT ME!
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1062 public void removePropertyChangeListener(
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1063 java.beans.PropertyChangeListener listener)
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1065 changeSupport.removePropertyChangeListener(listener);
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1069 * Property change listener for changes in alignment
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1071 * @param prop DOCUMENT ME!
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1072 * @param oldvalue DOCUMENT ME!
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1073 * @param newvalue DOCUMENT ME!
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1075 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1077 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1080 public void setIgnoreGapsConsensus(boolean b)
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1082 ignoreGapsInConsensusCalculation = b;
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1083 updateConsensus();
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1084 if(globalColourScheme!=null)
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1086 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1090 public boolean getIgnoreGapsConsensus()
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1092 return ignoreGapsInConsensusCalculation;
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1095 public void setDataset(boolean b)
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1100 public boolean isDataset()
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1105 public void hideSequence(SequenceI seq)
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1107 alignment.getHiddenSequences().hideSequence(seq);
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1108 hasHiddenRows = true;
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1111 public void showSequence(int index)
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1113 alignment.getHiddenSequences().showSequence(index);
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1115 if(alignment.getHiddenSequences().getSize()<1)
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1116 hasHiddenRows = false;
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1119 public int adjustForHiddenSeqs(int alignmentIndex)
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1121 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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