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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89 * Creates a new AlignViewport object.
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91 * @param al DOCUMENT ME!
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93 public AlignViewport(AlignmentI al)
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97 this.endRes = al.getWidth() - 1;
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99 this.endSeq = al.getHeight() - 1;
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101 updateFromPreferences();
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107 public void updateFromPreferences()
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109 showFullId = Preferences.showFullId;
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110 showAnnotation = Preferences.showAnnotation;
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111 showConservation = Preferences.showConservation;
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112 showQuality = Preferences.showQuality;
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113 showIdentity = Preferences.showIdentity;
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114 showFullId = Preferences.showFullId;
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116 String fontName = Preferences.fontName;
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117 String fontStyle = Preferences.fontStyle;
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118 String fontSize = Cache.getProperty("FONT_SIZE");
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120 if ((fontName != null) && (fontStyle != null) && (fontSize != null))
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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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140 alignment.setGapCharacter(Preferences.gapSymbol);
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142 // We must set conservation and consensus before setting colour,
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143 // as Blosum and Clustal require this to be done
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144 updateConservation();
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147 if (Preferences.defaultColour != null)
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149 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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150 Preferences.defaultColour);
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152 if (globalColourScheme instanceof UserColourScheme)
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154 globalColourScheme = UserDefinedColours.loadDefaultColours();
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157 if (globalColourScheme != null)
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159 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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310 float value = Float.parseFloat(hash.get("maxCount").toString());
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311 value /= Float.parseFloat(hash.get("size").toString());
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315 String maxRes = hash.get("maxResidue") + " ";
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316 String mouseOver = hash.get("maxResidue") + " ";
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318 if (maxRes.length() > 2)
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320 mouseOver = "[" + maxRes + "] ";
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324 mouseOver += ((int) value + "%");
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325 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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328 if (consensus == null)
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330 consensus = new AlignmentAnnotation("Consensus", "PID",
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331 annotations, 0f, 100f, 1);
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335 alignment.addAnnotation(consensus);
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340 consensus.annotations = annotations;
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347 * @return DOCUMENT ME!
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349 public SequenceGroup getSelectionGroup()
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351 return selectionGroup;
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357 * @param sg DOCUMENT ME!
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359 public void setSelectionGroup(SequenceGroup sg)
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361 selectionGroup = sg;
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367 * @return DOCUMENT ME!
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369 public boolean getConservationSelected()
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371 return conservationColourSelected;
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377 * @param b DOCUMENT ME!
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379 public void setConservationSelected(boolean b)
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381 conservationColourSelected = b;
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387 * @return DOCUMENT ME!
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389 public boolean getAbovePIDThreshold()
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391 return abovePIDThreshold;
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397 * @param b DOCUMENT ME!
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399 public void setAbovePIDThreshold(boolean b)
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401 abovePIDThreshold = b;
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407 * @return DOCUMENT ME!
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409 public int getStartRes()
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417 * @return DOCUMENT ME!
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419 public int getEndRes()
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427 * @return DOCUMENT ME!
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429 public int getStartSeq()
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437 * @param cs DOCUMENT ME!
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439 public void setGlobalColourScheme(ColourSchemeI cs)
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441 globalColourScheme = cs;
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447 * @return DOCUMENT ME!
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449 public ColourSchemeI getGlobalColourScheme()
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451 return globalColourScheme;
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457 * @param res DOCUMENT ME!
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459 public void setStartRes(int res)
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461 this.startRes = res;
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467 * @param seq DOCUMENT ME!
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469 public void setStartSeq(int seq)
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471 this.startSeq = seq;
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477 * @param res DOCUMENT ME!
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479 public void setEndRes(int res)
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481 if (res > (alignment.getWidth() - 1))
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483 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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484 res = alignment.getWidth() - 1;
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498 * @param seq DOCUMENT ME!
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500 public void setEndSeq(int seq)
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502 if (seq > alignment.getHeight())
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504 seq = alignment.getHeight();
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518 * @return DOCUMENT ME!
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520 public int getEndSeq()
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528 * @param f DOCUMENT ME!
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530 public void setFont(Font f)
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534 Container c = new Container();
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536 java.awt.FontMetrics fm = c.getFontMetrics(font);
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537 setCharHeight(fm.getHeight());
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538 setCharWidth(fm.charWidth('M'));
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544 * @return DOCUMENT ME!
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546 public Font getFont()
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554 * @param w DOCUMENT ME!
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556 public void setCharWidth(int w)
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558 this.charWidth = w;
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564 * @return DOCUMENT ME!
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566 public int getCharWidth()
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574 * @param h DOCUMENT ME!
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576 public void setCharHeight(int h)
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578 this.charHeight = h;
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584 * @return DOCUMENT ME!
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586 public int getCharHeight()
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594 * @param w DOCUMENT ME!
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596 public void setChunkWidth(int w)
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598 this.chunkWidth = w;
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604 * @return DOCUMENT ME!
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606 public int getChunkWidth()
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614 * @param h DOCUMENT ME!
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616 public void setChunkHeight(int h)
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618 this.chunkHeight = h;
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624 * @return DOCUMENT ME!
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626 public int getChunkHeight()
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628 return chunkHeight;
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634 * @return DOCUMENT ME!
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636 public AlignmentI getAlignment()
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644 * @param align DOCUMENT ME!
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646 public void setAlignment(AlignmentI align)
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648 this.alignment = align;
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654 * @param state DOCUMENT ME!
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656 public void setWrapAlignment(boolean state)
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658 wrapAlignment = state;
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664 * @param state DOCUMENT ME!
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666 public void setShowText(boolean state)
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674 * @param state DOCUMENT ME!
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676 public void setRenderGaps(boolean state)
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678 renderGaps = state;
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684 * @return DOCUMENT ME!
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686 public boolean getColourText()
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688 return showColourText;
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694 * @param state DOCUMENT ME!
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696 public void setColourText(boolean state)
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698 showColourText = state;
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704 * @param state DOCUMENT ME!
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706 public void setShowBoxes(boolean state)
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714 * @return DOCUMENT ME!
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716 public boolean getWrapAlignment()
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718 return wrapAlignment;
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724 * @return DOCUMENT ME!
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726 public boolean getShowText()
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734 * @return DOCUMENT ME!
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736 public boolean getShowBoxes()
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744 * @return DOCUMENT ME!
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746 public char getGapCharacter()
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748 return getAlignment().getGapCharacter();
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754 * @param gap DOCUMENT ME!
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756 public void setGapCharacter(char gap)
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758 if (getAlignment() != null)
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760 getAlignment().setGapCharacter(gap);
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767 * @param thresh DOCUMENT ME!
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769 public void setThreshold(int thresh)
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771 threshold = thresh;
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777 * @return DOCUMENT ME!
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779 public int getThreshold()
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787 * @param inc DOCUMENT ME!
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789 public void setIncrement(int inc)
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797 * @return DOCUMENT ME!
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799 public int getIncrement()
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807 * @param y DOCUMENT ME!
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809 * @return DOCUMENT ME!
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811 public int getIndex(int y)
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814 int starty = getStartSeq();
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815 int endy = getEndSeq();
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817 for (int i = starty; i <= endy; i++)
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819 if ((i < alignment.getHeight()) &&
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820 (alignment.getSequenceAt(i) != null))
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822 int y2 = y1 + getCharHeight();
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824 if ((y >= y1) && (y <= y2))
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843 * @return DOCUMENT ME!
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845 public ColumnSelection getColumnSelection()
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853 * @param height DOCUMENT ME!
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855 public void resetSeqLimits(int height)
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857 setEndSeq(height / getCharHeight());
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863 * @param tree DOCUMENT ME!
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865 public void setCurrentTree(NJTree tree)
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867 currentTree = tree;
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873 * @return DOCUMENT ME!
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875 public NJTree getCurrentTree()
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877 return currentTree;
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883 * @param b DOCUMENT ME!
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885 public void setColourAppliesToAllGroups(boolean b)
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887 colourAppliesToAllGroups = b;
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893 * @return DOCUMENT ME!
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895 public boolean getColourAppliesToAllGroups()
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897 return colourAppliesToAllGroups;
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903 * @return DOCUMENT ME!
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905 public boolean getShowFullId()
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913 * @param b DOCUMENT ME!
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915 public void setShowFullId(boolean b)
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923 * @return DOCUMENT ME!
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925 public boolean getShowAnnotation()
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927 return showAnnotation;
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933 * @param b DOCUMENT ME!
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935 public void setShowAnnotation(boolean b)
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937 showAnnotation = b;
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943 * @return DOCUMENT ME!
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945 public boolean getScaleAboveWrapped()
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947 return scaleAboveWrapped;
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953 * @return DOCUMENT ME!
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955 public boolean getScaleLeftWrapped()
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957 return scaleLeftWrapped;
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963 * @return DOCUMENT ME!
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965 public boolean getScaleRightWrapped()
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967 return scaleRightWrapped;
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973 * @param b DOCUMENT ME!
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975 public void setScaleAboveWrapped(boolean b)
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977 scaleAboveWrapped = b;
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983 * @param b DOCUMENT ME!
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985 public void setScaleLeftWrapped(boolean b)
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987 scaleLeftWrapped = b;
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993 * @param b DOCUMENT ME!
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995 public void setScaleRightWrapped(boolean b)
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997 scaleRightWrapped = b;
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1003 * @param listener DOCUMENT ME!
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1005 public void addPropertyChangeListener(
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1006 java.beans.PropertyChangeListener listener)
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1008 changeSupport.addPropertyChangeListener(listener);
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1014 * @param listener DOCUMENT ME!
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1016 public void removePropertyChangeListener(
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1017 java.beans.PropertyChangeListener listener)
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1019 changeSupport.removePropertyChangeListener(listener);
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1025 * @param prop DOCUMENT ME!
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1026 * @param oldvalue DOCUMENT ME!
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1027 * @param newvalue DOCUMENT ME!
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1029 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1031 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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