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.SwingUtilities.invokeLater(new Runnable()
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324 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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325 "Out of memory calculating conservation!!"
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327 "\nSee help files for increasing Java Virtual Machine memory."
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329 javax.swing.JOptionPane.WARNING_MESSAGE);
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333 System.out.println("Conservation calculation: " + error);
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342 public void updateConsensus()
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345 Annotation[] annotations = new Annotation[alignment.getWidth()];
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347 // this routine prevents vconsensus becoming a new object each time
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348 // consenus is calculated. Important for speed of Blosum62
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349 // and PID colouring of alignment
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350 if (vconsensus == null)
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352 vconsensus = alignment.getAAFrequency();
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356 Vector temp = alignment.getAAFrequency();
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357 vconsensus.clear();
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359 Enumeration e = temp.elements();
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361 while (e.hasMoreElements())
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363 vconsensus.add(e.nextElement());
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367 Hashtable hash = null;
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369 for (int i = 0; i < alignment.getWidth(); i++)
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371 hash = (Hashtable) vconsensus.elementAt(i);
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374 if (ignoreGapsInConsensusCalculation)
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375 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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377 value = ( (Float) hash.get("pid_gaps")).floatValue();
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379 String maxRes = hash.get("maxResidue").toString();
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380 String mouseOver = hash.get("maxResidue") + " ";
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382 if (maxRes.length() > 1)
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384 mouseOver = "[" + maxRes + "] ";
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388 mouseOver += ( (int) value + "%");
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389 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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392 if (consensus == null)
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394 consensus = new AlignmentAnnotation("Consensus", "PID",
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395 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
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399 alignment.addAnnotation(consensus);
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404 consensus.annotations = annotations;
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407 if (globalColourScheme != null)
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408 globalColourScheme.setConsensus(vconsensus);
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410 }catch(OutOfMemoryError error)
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412 javax.swing.SwingUtilities.invokeLater(new Runnable()
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416 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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417 "Out of memory calc45ulating consensus!!"
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419 "\nSee help files for increasing Java Virtual Machine memory."
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421 javax.swing.JOptionPane.WARNING_MESSAGE);
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426 System.out.println("Consensus calculation: " + error);
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435 * @return DOCUMENT ME!
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437 public SequenceGroup getSelectionGroup()
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439 return selectionGroup;
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445 * @param sg DOCUMENT ME!
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447 public void setSelectionGroup(SequenceGroup sg)
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449 selectionGroup = sg;
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455 * @return DOCUMENT ME!
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457 public boolean getConservationSelected()
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459 return conservationColourSelected;
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465 * @param b DOCUMENT ME!
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467 public void setConservationSelected(boolean b)
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469 conservationColourSelected = b;
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475 * @return DOCUMENT ME!
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477 public boolean getAbovePIDThreshold()
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479 return abovePIDThreshold;
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485 * @param b DOCUMENT ME!
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487 public void setAbovePIDThreshold(boolean b)
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489 abovePIDThreshold = b;
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495 * @return DOCUMENT ME!
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497 public int getStartRes()
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505 * @return DOCUMENT ME!
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507 public int getEndRes()
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515 * @return DOCUMENT ME!
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517 public int getStartSeq()
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525 * @param cs DOCUMENT ME!
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527 public void setGlobalColourScheme(ColourSchemeI cs)
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529 globalColourScheme = cs;
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535 * @return DOCUMENT ME!
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537 public ColourSchemeI getGlobalColourScheme()
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539 return globalColourScheme;
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545 * @param res DOCUMENT ME!
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547 public void setStartRes(int res)
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549 this.startRes = res;
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555 * @param seq DOCUMENT ME!
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557 public void setStartSeq(int seq)
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559 this.startSeq = seq;
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565 * @param res DOCUMENT ME!
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567 public void setEndRes(int res)
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569 if (res > (alignment.getWidth() - 1))
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571 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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572 res = alignment.getWidth() - 1;
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586 * @param seq DOCUMENT ME!
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588 public void setEndSeq(int seq)
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590 if (seq > alignment.getHeight())
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592 seq = alignment.getHeight();
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606 * @return DOCUMENT ME!
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608 public int getEndSeq()
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616 * @param f DOCUMENT ME!
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618 public void setFont(Font f)
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622 Container c = new Container();
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624 java.awt.FontMetrics fm = c.getFontMetrics(font);
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625 setCharHeight(fm.getHeight());
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626 setCharWidth(fm.charWidth('M'));
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632 * @return DOCUMENT ME!
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634 public Font getFont()
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642 * @param w DOCUMENT ME!
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644 public void setCharWidth(int w)
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646 this.charWidth = w;
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652 * @return DOCUMENT ME!
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654 public int getCharWidth()
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662 * @param h DOCUMENT ME!
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664 public void setCharHeight(int h)
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666 this.charHeight = h;
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672 * @return DOCUMENT ME!
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674 public int getCharHeight()
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682 * @param w DOCUMENT ME!
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684 public void setWrappedWidth(int w)
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686 this.wrappedWidth = w;
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692 * @return DOCUMENT ME!
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694 public int getWrappedWidth()
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696 return wrappedWidth;
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703 * @return DOCUMENT ME!
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705 public AlignmentI getAlignment()
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713 * @param align DOCUMENT ME!
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715 public void setAlignment(AlignmentI align)
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717 this.alignment = align;
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723 * @param state DOCUMENT ME!
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725 public void setWrapAlignment(boolean state)
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727 wrapAlignment = state;
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733 * @param state DOCUMENT ME!
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735 public void setShowText(boolean state)
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743 * @param state DOCUMENT ME!
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745 public void setRenderGaps(boolean state)
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747 renderGaps = state;
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753 * @return DOCUMENT ME!
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755 public boolean getColourText()
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757 return showColourText;
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763 * @param state DOCUMENT ME!
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765 public void setColourText(boolean state)
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767 showColourText = state;
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773 * @param state DOCUMENT ME!
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775 public void setShowBoxes(boolean state)
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783 * @return DOCUMENT ME!
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785 public boolean getWrapAlignment()
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787 return wrapAlignment;
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793 * @return DOCUMENT ME!
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795 public boolean getShowText()
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803 * @return DOCUMENT ME!
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805 public boolean getShowBoxes()
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813 * @return DOCUMENT ME!
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815 public char getGapCharacter()
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817 return getAlignment().getGapCharacter();
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823 * @param gap DOCUMENT ME!
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825 public void setGapCharacter(char gap)
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827 if (getAlignment() != null)
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829 getAlignment().setGapCharacter(gap);
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836 * @param thresh DOCUMENT ME!
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838 public void setThreshold(int thresh)
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840 threshold = thresh;
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846 * @return DOCUMENT ME!
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848 public int getThreshold()
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856 * @param inc DOCUMENT ME!
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858 public void setIncrement(int inc)
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866 * @return DOCUMENT ME!
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868 public int getIncrement()
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876 * @param y DOCUMENT ME!
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878 * @return DOCUMENT ME!
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880 public int getIndex(int y)
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883 int starty = getStartSeq();
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884 int endy = getEndSeq();
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886 for (int i = starty; i <= endy; i++)
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888 if ((i < alignment.getHeight()) &&
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889 (alignment.getSequenceAt(i) != null))
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891 int y2 = y1 + getCharHeight();
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893 if ((y >= y1) && (y <= y2))
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912 * @return DOCUMENT ME!
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914 public ColumnSelection getColumnSelection()
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923 * @param tree DOCUMENT ME!
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925 public void setCurrentTree(NJTree tree)
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927 currentTree = tree;
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933 * @return DOCUMENT ME!
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935 public NJTree getCurrentTree()
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937 return currentTree;
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943 * @param b DOCUMENT ME!
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945 public void setColourAppliesToAllGroups(boolean b)
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947 colourAppliesToAllGroups = b;
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953 * @return DOCUMENT ME!
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955 public boolean getColourAppliesToAllGroups()
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957 return colourAppliesToAllGroups;
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963 * @return DOCUMENT ME!
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965 public boolean getShowJVSuffix()
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967 return showJVSuffix;
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973 * @param b DOCUMENT ME!
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975 public void setShowJVSuffix(boolean b)
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984 * @return DOCUMENT ME!
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986 public boolean getShowAnnotation()
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988 return showAnnotation;
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994 * @param b DOCUMENT ME!
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996 public void setShowAnnotation(boolean b)
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998 showAnnotation = b;
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1004 * @return DOCUMENT ME!
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1006 public boolean getScaleAboveWrapped()
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1008 return scaleAboveWrapped;
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1014 * @return DOCUMENT ME!
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1016 public boolean getScaleLeftWrapped()
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1018 return scaleLeftWrapped;
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1024 * @return DOCUMENT ME!
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1026 public boolean getScaleRightWrapped()
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1028 return scaleRightWrapped;
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1034 * @param b DOCUMENT ME!
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1036 public void setScaleAboveWrapped(boolean b)
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1038 scaleAboveWrapped = b;
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1044 * @param b DOCUMENT ME!
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1046 public void setScaleLeftWrapped(boolean b)
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1048 scaleLeftWrapped = b;
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1054 * @param b DOCUMENT ME!
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1056 public void setScaleRightWrapped(boolean b)
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1058 scaleRightWrapped = b;
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1062 * Property change listener for changes in alignment
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1064 * @param listener DOCUMENT ME!
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1066 public void addPropertyChangeListener(
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1067 java.beans.PropertyChangeListener listener)
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1069 changeSupport.addPropertyChangeListener(listener);
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1075 * @param listener DOCUMENT ME!
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1077 public void removePropertyChangeListener(
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1078 java.beans.PropertyChangeListener listener)
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1080 changeSupport.removePropertyChangeListener(listener);
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1084 * Property change listener for changes in alignment
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1086 * @param prop DOCUMENT ME!
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1087 * @param oldvalue DOCUMENT ME!
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1088 * @param newvalue DOCUMENT ME!
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1090 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1092 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1095 public void setIgnoreGapsConsensus(boolean b)
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1097 ignoreGapsInConsensusCalculation = b;
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1098 updateConsensus();
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1099 if(globalColourScheme!=null)
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1101 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1105 public boolean getIgnoreGapsConsensus()
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1107 return ignoreGapsInConsensusCalculation;
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1110 public void setDataset(boolean b)
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1115 public boolean isDataset()
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1120 public void hideSequence(SequenceI seq)
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1122 alignment.getHiddenSequences().hideSequence(seq);
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1123 hasHiddenRows = true;
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1126 public void showSequence(int index)
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1128 alignment.getHiddenSequences().showSequence(index);
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1130 if(alignment.getHiddenSequences().getSize()<1)
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1131 hasHiddenRows = false;
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1134 public int adjustForHiddenSeqs(int alignmentIndex)
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1136 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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