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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66 Font font = new Font("SansSerif", Font.PLAIN, 10);
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67 AlignmentI alignment;
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68 ColumnSelection colSel = new ColumnSelection();
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71 NJTree currentTree = null;
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72 boolean scaleAboveWrapped = false;
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73 boolean scaleLeftWrapped = true;
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74 boolean scaleRightWrapped = true;
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76 /** DOCUMENT ME!! */
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77 public Vector vconsensus;
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78 AlignmentAnnotation consensus;
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79 AlignmentAnnotation conservation;
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80 AlignmentAnnotation quality;
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82 /** DOCUMENT ME!! */
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83 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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85 // JBPNote Prolly only need this in the applet version.
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86 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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88 boolean ignoreGapsInConsensusCalculation = false;
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91 * Creates a new AlignViewport object.
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93 * @param al DOCUMENT ME!
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95 public AlignViewport(AlignmentI al)
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99 this.endRes = al.getWidth() - 1;
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101 this.endSeq = al.getHeight() - 1;
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103 updateFromPreferences();
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109 public void updateFromPreferences()
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111 showFullId = Cache.getDefault("SHOW_FULL_ID", true);
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112 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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113 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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115 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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116 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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118 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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119 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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120 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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124 if (fontStyle.equals("bold"))
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128 else if (fontStyle.equals("italic"))
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133 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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136 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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139 // We must set conservation and consensus before setting colour,
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140 // as Blosum and Clustal require this to be done
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141 updateConservation();
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144 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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146 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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147 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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149 if (globalColourScheme instanceof UserColourScheme)
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151 globalColourScheme = UserDefinedColours.loadDefaultColours();
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152 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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155 if (globalColourScheme != null)
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157 globalColourScheme.setConsensus(vconsensus);
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167 * @param b DOCUMENT ME!
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169 public void showSequenceFeatures(boolean b)
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171 showSequenceFeatures = b;
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177 public void updateConservation()
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179 Conservation cons = new jalview.analysis.Conservation("All",
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180 jalview.schemes.ResidueProperties.propHash, 3,
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181 alignment.getSequences(), 0, alignment.getWidth() - 1);
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183 cons.verdict(false, ConsPercGaps);
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184 cons.findQuality();
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186 int alWidth = alignment.getWidth();
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187 Annotation[] annotations = new Annotation[alWidth];
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188 Annotation[] qannotations = new Annotation[alWidth];
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189 String sequence = cons.getConsSequence().getSequence();
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199 maxR = 1.0f - minR;
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200 maxG = 0.9f - minG;
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201 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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205 float qmin = cons.qualityRange[0].floatValue();
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206 float qmax = cons.qualityRange[1].floatValue();
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208 for (int i = 0; i < alWidth; i++)
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214 value = Integer.parseInt(sequence.charAt(i) + "");
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216 catch (Exception ex)
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218 if (sequence.charAt(i) == '*')
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223 if (sequence.charAt(i) == '+')
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229 float vprop = value - min;
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231 annotations[i] = new Annotation(sequence.charAt(i) + "",
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232 String.valueOf(value), ' ', value,
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233 new Color(minR + (maxR * vprop), minG + (maxG * vprop),
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234 minB + (maxB * vprop)));
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237 value = ((Double) cons.quality.get(i)).floatValue();
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238 vprop = value - qmin;
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240 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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242 new Color(minR + (maxR * vprop), minG + (maxG * vprop),
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243 minB + (maxB * vprop)));
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246 if (conservation == null)
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248 conservation = new AlignmentAnnotation("Conservation",
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249 "Conservation of total alignment less than " +
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250 ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(),
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251 11f, // cons.qualityRange[1].floatValue()
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254 if (showConservation)
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256 alignment.addAnnotation(conservation);
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259 quality = new AlignmentAnnotation("Quality",
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260 "Alignment Quality based on Blosum62 scores", qannotations,
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261 cons.qualityRange[0].floatValue(),
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262 cons.qualityRange[1].floatValue(), 1);
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266 alignment.addAnnotation(quality);
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271 conservation.annotations = annotations;
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272 quality.annotations = qannotations;
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273 quality.graphMax = cons.qualityRange[1].floatValue();
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280 public void updateConsensus()
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282 Annotation[] annotations = new Annotation[alignment.getWidth()];
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284 // this routine prevents vconsensus becoming a new object each time
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285 // consenus is calculated. Important for speed of Blosum62
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286 // and PID colouring of alignment
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287 if (vconsensus == null)
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289 vconsensus = alignment.getAAFrequency();
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293 Vector temp = alignment.getAAFrequency();
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294 vconsensus.clear();
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296 Enumeration e = temp.elements();
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298 while (e.hasMoreElements())
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300 vconsensus.add(e.nextElement());
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304 Hashtable hash = null;
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306 for (int i = 0; i < alignment.getWidth(); i++)
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308 hash = (Hashtable) vconsensus.elementAt(i);
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311 if(ignoreGapsInConsensusCalculation)
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312 value = ((Float)hash.get("pid_nogaps")).floatValue();
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314 value = ((Float)hash.get("pid_gaps")).floatValue();
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316 String maxRes = hash.get("maxResidue").toString();
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317 String mouseOver = hash.get("maxResidue")+" ";
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319 if (maxRes.length() > 1)
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321 mouseOver = "[" + maxRes + "] ";
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325 mouseOver += ((int) value + "%");
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326 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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329 if (consensus == null)
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331 consensus = new AlignmentAnnotation("Consensus", "PID",
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332 annotations, 0f, 100f, 1);
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336 alignment.addAnnotation(consensus);
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341 consensus.annotations = annotations;
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344 if(globalColourScheme!=null)
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345 globalColourScheme.setConsensus(vconsensus);
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351 * @return DOCUMENT ME!
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353 public SequenceGroup getSelectionGroup()
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355 return selectionGroup;
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361 * @param sg DOCUMENT ME!
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363 public void setSelectionGroup(SequenceGroup sg)
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365 selectionGroup = sg;
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371 * @return DOCUMENT ME!
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373 public boolean getConservationSelected()
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375 return conservationColourSelected;
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381 * @param b DOCUMENT ME!
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383 public void setConservationSelected(boolean b)
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385 conservationColourSelected = b;
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391 * @return DOCUMENT ME!
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393 public boolean getAbovePIDThreshold()
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395 return abovePIDThreshold;
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401 * @param b DOCUMENT ME!
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403 public void setAbovePIDThreshold(boolean b)
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405 abovePIDThreshold = b;
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411 * @return DOCUMENT ME!
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413 public int getStartRes()
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421 * @return DOCUMENT ME!
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423 public int getEndRes()
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431 * @return DOCUMENT ME!
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433 public int getStartSeq()
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441 * @param cs DOCUMENT ME!
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443 public void setGlobalColourScheme(ColourSchemeI cs)
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445 globalColourScheme = cs;
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451 * @return DOCUMENT ME!
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453 public ColourSchemeI getGlobalColourScheme()
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455 return globalColourScheme;
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461 * @param res DOCUMENT ME!
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463 public void setStartRes(int res)
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465 this.startRes = res;
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471 * @param seq DOCUMENT ME!
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473 public void setStartSeq(int seq)
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475 this.startSeq = seq;
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481 * @param res DOCUMENT ME!
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483 public void setEndRes(int res)
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485 if (res > (alignment.getWidth() - 1))
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487 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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488 res = alignment.getWidth() - 1;
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502 * @param seq DOCUMENT ME!
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504 public void setEndSeq(int seq)
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506 if (seq > alignment.getHeight())
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508 seq = alignment.getHeight();
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522 * @return DOCUMENT ME!
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524 public int getEndSeq()
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532 * @param f DOCUMENT ME!
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534 public void setFont(Font f)
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538 Container c = new Container();
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540 java.awt.FontMetrics fm = c.getFontMetrics(font);
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541 setCharHeight(fm.getHeight());
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542 setCharWidth(fm.charWidth('M'));
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548 * @return DOCUMENT ME!
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550 public Font getFont()
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558 * @param w DOCUMENT ME!
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560 public void setCharWidth(int w)
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562 this.charWidth = w;
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568 * @return DOCUMENT ME!
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570 public int getCharWidth()
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578 * @param h DOCUMENT ME!
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580 public void setCharHeight(int h)
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582 this.charHeight = h;
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588 * @return DOCUMENT ME!
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590 public int getCharHeight()
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598 * @param w DOCUMENT ME!
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600 public void setChunkWidth(int w)
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602 this.chunkWidth = w;
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608 * @return DOCUMENT ME!
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610 public int getChunkWidth()
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618 * @param h DOCUMENT ME!
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620 public void setChunkHeight(int h)
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622 this.chunkHeight = h;
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628 * @return DOCUMENT ME!
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630 public int getChunkHeight()
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632 return chunkHeight;
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638 * @return DOCUMENT ME!
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640 public AlignmentI getAlignment()
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648 * @param align DOCUMENT ME!
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650 public void setAlignment(AlignmentI align)
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652 this.alignment = align;
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658 * @param state DOCUMENT ME!
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660 public void setWrapAlignment(boolean state)
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662 wrapAlignment = state;
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668 * @param state DOCUMENT ME!
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670 public void setShowText(boolean state)
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678 * @param state DOCUMENT ME!
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680 public void setRenderGaps(boolean state)
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682 renderGaps = state;
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688 * @return DOCUMENT ME!
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690 public boolean getColourText()
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692 return showColourText;
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698 * @param state DOCUMENT ME!
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700 public void setColourText(boolean state)
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702 showColourText = state;
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708 * @param state DOCUMENT ME!
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710 public void setShowBoxes(boolean state)
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718 * @return DOCUMENT ME!
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720 public boolean getWrapAlignment()
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722 return wrapAlignment;
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728 * @return DOCUMENT ME!
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730 public boolean getShowText()
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738 * @return DOCUMENT ME!
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740 public boolean getShowBoxes()
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748 * @return DOCUMENT ME!
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750 public char getGapCharacter()
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752 return getAlignment().getGapCharacter();
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758 * @param gap DOCUMENT ME!
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760 public void setGapCharacter(char gap)
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762 if (getAlignment() != null)
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764 getAlignment().setGapCharacter(gap);
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771 * @param thresh DOCUMENT ME!
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773 public void setThreshold(int thresh)
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775 threshold = thresh;
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781 * @return DOCUMENT ME!
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783 public int getThreshold()
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791 * @param inc DOCUMENT ME!
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793 public void setIncrement(int inc)
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801 * @return DOCUMENT ME!
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803 public int getIncrement()
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811 * @param y DOCUMENT ME!
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813 * @return DOCUMENT ME!
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815 public int getIndex(int y)
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818 int starty = getStartSeq();
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819 int endy = getEndSeq();
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821 for (int i = starty; i <= endy; i++)
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823 if ((i < alignment.getHeight()) &&
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824 (alignment.getSequenceAt(i) != null))
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826 int y2 = y1 + getCharHeight();
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828 if ((y >= y1) && (y <= y2))
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847 * @return DOCUMENT ME!
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849 public ColumnSelection getColumnSelection()
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858 * @param tree DOCUMENT ME!
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860 public void setCurrentTree(NJTree tree)
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862 currentTree = tree;
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868 * @return DOCUMENT ME!
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870 public NJTree getCurrentTree()
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872 return currentTree;
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878 * @param b DOCUMENT ME!
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880 public void setColourAppliesToAllGroups(boolean b)
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882 colourAppliesToAllGroups = b;
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888 * @return DOCUMENT ME!
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890 public boolean getColourAppliesToAllGroups()
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892 return colourAppliesToAllGroups;
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898 * @return DOCUMENT ME!
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900 public boolean getShowFullId()
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908 * @param b DOCUMENT ME!
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910 public void setShowFullId(boolean b)
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918 * @return DOCUMENT ME!
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920 public boolean getShowAnnotation()
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922 return showAnnotation;
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928 * @param b DOCUMENT ME!
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930 public void setShowAnnotation(boolean b)
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932 showAnnotation = b;
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938 * @return DOCUMENT ME!
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940 public boolean getScaleAboveWrapped()
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942 return scaleAboveWrapped;
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948 * @return DOCUMENT ME!
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950 public boolean getScaleLeftWrapped()
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952 return scaleLeftWrapped;
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958 * @return DOCUMENT ME!
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960 public boolean getScaleRightWrapped()
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962 return scaleRightWrapped;
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968 * @param b DOCUMENT ME!
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970 public void setScaleAboveWrapped(boolean b)
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972 scaleAboveWrapped = b;
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978 * @param b DOCUMENT ME!
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980 public void setScaleLeftWrapped(boolean b)
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982 scaleLeftWrapped = b;
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988 * @param b DOCUMENT ME!
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990 public void setScaleRightWrapped(boolean b)
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992 scaleRightWrapped = b;
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996 * Property change listener for changes in alignment
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998 * @param listener DOCUMENT ME!
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1000 public void addPropertyChangeListener(
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1001 java.beans.PropertyChangeListener listener)
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1003 changeSupport.addPropertyChangeListener(listener);
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1009 * @param listener DOCUMENT ME!
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1011 public void removePropertyChangeListener(
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1012 java.beans.PropertyChangeListener listener)
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1014 changeSupport.removePropertyChangeListener(listener);
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1018 * Property change listener for changes in alignment
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1020 * @param prop DOCUMENT ME!
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1021 * @param oldvalue DOCUMENT ME!
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1022 * @param newvalue DOCUMENT ME!
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1024 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1026 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1029 public void setIgnoreGapsConsensus(boolean b)
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1031 ignoreGapsInConsensusCalculation = b;
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1032 updateConsensus();
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1033 if(globalColourScheme!=null)
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1035 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1040 public boolean getIgnoreGapsConsensus()
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1042 return ignoreGapsInConsensusCalculation;
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