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 = Cache.getDefault("SHOW_FULL_ID", true);
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110 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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111 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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113 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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114 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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116 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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117 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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118 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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122 if (fontStyle.equals("bold"))
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126 else if (fontStyle.equals("italic"))
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131 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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134 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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137 // We must set conservation and consensus before setting colour,
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138 // as Blosum and Clustal require this to be done
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139 updateConservation();
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142 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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144 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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145 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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147 if (globalColourScheme instanceof UserColourScheme)
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149 globalColourScheme = UserDefinedColours.loadDefaultColours();
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152 if (globalColourScheme != null)
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154 globalColourScheme.setConsensus(vconsensus);
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164 * @param b DOCUMENT ME!
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166 public void showSequenceFeatures(boolean b)
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168 showSequenceFeatures = b;
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174 public void updateConservation()
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176 Conservation cons = new jalview.analysis.Conservation("All",
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177 jalview.schemes.ResidueProperties.propHash, 3,
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178 alignment.getSequences(), 0, alignment.getWidth() - 1);
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180 cons.verdict(false, ConsPercGaps);
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181 cons.findQuality();
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183 int alWidth = alignment.getWidth();
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184 Annotation[] annotations = new Annotation[alWidth];
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185 Annotation[] qannotations = new Annotation[alWidth];
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186 String sequence = cons.getConsSequence().getSequence();
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196 maxR = 1.0f - minR;
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197 maxG = 0.9f - minG;
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198 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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202 float qmin = cons.qualityRange[0].floatValue();
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203 float qmax = cons.qualityRange[1].floatValue();
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205 for (int i = 0; i < alWidth; i++)
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211 value = Integer.parseInt(sequence.charAt(i) + "");
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213 catch (Exception ex)
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215 if (sequence.charAt(i) == '*')
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220 if (sequence.charAt(i) == '+')
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226 float vprop = value - min;
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228 annotations[i] = new Annotation(sequence.charAt(i) + "",
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229 String.valueOf(value), ' ', value,
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230 new Color(minR + (maxR * vprop), minG + (maxG * vprop),
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231 minB + (maxB * vprop)));
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234 value = ((Double) cons.quality.get(i)).floatValue();
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235 vprop = value - qmin;
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237 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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239 new Color(minR + (maxR * vprop), minG + (maxG * vprop),
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240 minB + (maxB * vprop)));
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243 if (conservation == null)
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245 conservation = new AlignmentAnnotation("Conservation",
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246 "Conservation of total alignment less than " +
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247 ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(),
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248 11f, // cons.qualityRange[1].floatValue()
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251 if (showConservation)
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253 alignment.addAnnotation(conservation);
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256 quality = new AlignmentAnnotation("Quality",
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257 "Alignment Quality based on Blosum62 scores", qannotations,
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258 cons.qualityRange[0].floatValue(),
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259 cons.qualityRange[1].floatValue(), 1);
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263 alignment.addAnnotation(quality);
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268 conservation.annotations = annotations;
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269 quality.annotations = qannotations;
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270 quality.graphMax = cons.qualityRange[1].floatValue();
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277 public void updateConsensus()
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279 Annotation[] annotations = new Annotation[alignment.getWidth()];
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281 // this routine prevents vconsensus becoming a new object each time
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282 // consenus is calculated. Important for speed of Blosum62
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283 // and PID colouring of alignment
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284 if (vconsensus == null)
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286 vconsensus = alignment.getAAFrequency();
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290 Vector temp = alignment.getAAFrequency();
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291 vconsensus.clear();
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293 Enumeration e = temp.elements();
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295 while (e.hasMoreElements())
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297 vconsensus.add(e.nextElement());
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301 Hashtable hash = null;
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303 for (int i = 0; i < alignment.getWidth(); i++)
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305 hash = (Hashtable) vconsensus.elementAt(i);
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307 float value = Float.parseFloat(hash.get("maxCount").toString());
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308 value /= Float.parseFloat(hash.get("size").toString());
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312 String maxRes = hash.get("maxResidue") + " ";
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313 String mouseOver = hash.get("maxResidue") + " ";
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315 if (maxRes.length() > 2)
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317 mouseOver = "[" + maxRes + "] ";
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321 mouseOver += ((int) value + "%");
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322 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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325 if (consensus == null)
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327 consensus = new AlignmentAnnotation("Consensus", "PID",
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328 annotations, 0f, 100f, 1);
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332 alignment.addAnnotation(consensus);
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337 consensus.annotations = annotations;
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344 * @return DOCUMENT ME!
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346 public SequenceGroup getSelectionGroup()
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348 return selectionGroup;
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354 * @param sg DOCUMENT ME!
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356 public void setSelectionGroup(SequenceGroup sg)
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358 selectionGroup = sg;
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364 * @return DOCUMENT ME!
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366 public boolean getConservationSelected()
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368 return conservationColourSelected;
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374 * @param b DOCUMENT ME!
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376 public void setConservationSelected(boolean b)
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378 conservationColourSelected = b;
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384 * @return DOCUMENT ME!
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386 public boolean getAbovePIDThreshold()
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388 return abovePIDThreshold;
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394 * @param b DOCUMENT ME!
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396 public void setAbovePIDThreshold(boolean b)
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398 abovePIDThreshold = b;
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404 * @return DOCUMENT ME!
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406 public int getStartRes()
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414 * @return DOCUMENT ME!
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416 public int getEndRes()
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424 * @return DOCUMENT ME!
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426 public int getStartSeq()
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434 * @param cs DOCUMENT ME!
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436 public void setGlobalColourScheme(ColourSchemeI cs)
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438 globalColourScheme = cs;
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444 * @return DOCUMENT ME!
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446 public ColourSchemeI getGlobalColourScheme()
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448 return globalColourScheme;
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454 * @param res DOCUMENT ME!
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456 public void setStartRes(int res)
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458 this.startRes = res;
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464 * @param seq DOCUMENT ME!
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466 public void setStartSeq(int seq)
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468 this.startSeq = seq;
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474 * @param res DOCUMENT ME!
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476 public void setEndRes(int res)
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478 if (res > (alignment.getWidth() - 1))
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480 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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481 res = alignment.getWidth() - 1;
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495 * @param seq DOCUMENT ME!
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497 public void setEndSeq(int seq)
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499 if (seq > alignment.getHeight())
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501 seq = alignment.getHeight();
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515 * @return DOCUMENT ME!
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517 public int getEndSeq()
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525 * @param f DOCUMENT ME!
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527 public void setFont(Font f)
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531 Container c = new Container();
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533 java.awt.FontMetrics fm = c.getFontMetrics(font);
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534 setCharHeight(fm.getHeight());
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535 setCharWidth(fm.charWidth('M'));
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541 * @return DOCUMENT ME!
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543 public Font getFont()
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551 * @param w DOCUMENT ME!
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553 public void setCharWidth(int w)
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555 this.charWidth = w;
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561 * @return DOCUMENT ME!
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563 public int getCharWidth()
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571 * @param h DOCUMENT ME!
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573 public void setCharHeight(int h)
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575 this.charHeight = h;
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581 * @return DOCUMENT ME!
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583 public int getCharHeight()
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591 * @param w DOCUMENT ME!
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593 public void setChunkWidth(int w)
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595 this.chunkWidth = w;
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601 * @return DOCUMENT ME!
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603 public int getChunkWidth()
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611 * @param h DOCUMENT ME!
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613 public void setChunkHeight(int h)
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615 this.chunkHeight = h;
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621 * @return DOCUMENT ME!
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623 public int getChunkHeight()
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625 return chunkHeight;
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631 * @return DOCUMENT ME!
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633 public AlignmentI getAlignment()
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641 * @param align DOCUMENT ME!
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643 public void setAlignment(AlignmentI align)
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645 this.alignment = align;
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651 * @param state DOCUMENT ME!
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653 public void setWrapAlignment(boolean state)
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655 wrapAlignment = state;
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661 * @param state DOCUMENT ME!
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663 public void setShowText(boolean state)
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671 * @param state DOCUMENT ME!
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673 public void setRenderGaps(boolean state)
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675 renderGaps = state;
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681 * @return DOCUMENT ME!
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683 public boolean getColourText()
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685 return showColourText;
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691 * @param state DOCUMENT ME!
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693 public void setColourText(boolean state)
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695 showColourText = state;
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701 * @param state DOCUMENT ME!
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703 public void setShowBoxes(boolean state)
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711 * @return DOCUMENT ME!
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713 public boolean getWrapAlignment()
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715 return wrapAlignment;
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721 * @return DOCUMENT ME!
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723 public boolean getShowText()
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731 * @return DOCUMENT ME!
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733 public boolean getShowBoxes()
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741 * @return DOCUMENT ME!
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743 public char getGapCharacter()
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745 return getAlignment().getGapCharacter();
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751 * @param gap DOCUMENT ME!
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753 public void setGapCharacter(char gap)
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755 if (getAlignment() != null)
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757 getAlignment().setGapCharacter(gap);
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764 * @param thresh DOCUMENT ME!
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766 public void setThreshold(int thresh)
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768 threshold = thresh;
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774 * @return DOCUMENT ME!
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776 public int getThreshold()
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784 * @param inc DOCUMENT ME!
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786 public void setIncrement(int inc)
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794 * @return DOCUMENT ME!
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796 public int getIncrement()
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804 * @param y DOCUMENT ME!
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806 * @return DOCUMENT ME!
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808 public int getIndex(int y)
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811 int starty = getStartSeq();
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812 int endy = getEndSeq();
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814 for (int i = starty; i <= endy; i++)
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816 if ((i < alignment.getHeight()) &&
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817 (alignment.getSequenceAt(i) != null))
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819 int y2 = y1 + getCharHeight();
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821 if ((y >= y1) && (y <= y2))
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840 * @return DOCUMENT ME!
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842 public ColumnSelection getColumnSelection()
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850 * @param height DOCUMENT ME!
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852 public void resetSeqLimits(int height)
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854 setEndSeq(height / getCharHeight());
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860 * @param tree DOCUMENT ME!
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862 public void setCurrentTree(NJTree tree)
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864 currentTree = tree;
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870 * @return DOCUMENT ME!
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872 public NJTree getCurrentTree()
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874 return currentTree;
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880 * @param b DOCUMENT ME!
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882 public void setColourAppliesToAllGroups(boolean b)
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884 colourAppliesToAllGroups = b;
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890 * @return DOCUMENT ME!
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892 public boolean getColourAppliesToAllGroups()
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894 return colourAppliesToAllGroups;
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900 * @return DOCUMENT ME!
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902 public boolean getShowFullId()
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910 * @param b DOCUMENT ME!
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912 public void setShowFullId(boolean b)
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920 * @return DOCUMENT ME!
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922 public boolean getShowAnnotation()
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924 return showAnnotation;
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930 * @param b DOCUMENT ME!
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932 public void setShowAnnotation(boolean b)
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934 showAnnotation = b;
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940 * @return DOCUMENT ME!
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942 public boolean getScaleAboveWrapped()
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944 return scaleAboveWrapped;
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950 * @return DOCUMENT ME!
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952 public boolean getScaleLeftWrapped()
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954 return scaleLeftWrapped;
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960 * @return DOCUMENT ME!
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962 public boolean getScaleRightWrapped()
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964 return scaleRightWrapped;
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970 * @param b DOCUMENT ME!
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972 public void setScaleAboveWrapped(boolean b)
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974 scaleAboveWrapped = b;
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980 * @param b DOCUMENT ME!
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982 public void setScaleLeftWrapped(boolean b)
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984 scaleLeftWrapped = b;
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990 * @param b DOCUMENT ME!
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992 public void setScaleRightWrapped(boolean b)
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994 scaleRightWrapped = b;
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1000 * @param listener DOCUMENT ME!
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1002 public void addPropertyChangeListener(
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1003 java.beans.PropertyChangeListener listener)
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1005 changeSupport.addPropertyChangeListener(listener);
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1011 * @param listener DOCUMENT ME!
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1013 public void removePropertyChangeListener(
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1014 java.beans.PropertyChangeListener listener)
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1016 changeSupport.removePropertyChangeListener(listener);
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1022 * @param prop DOCUMENT ME!
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1023 * @param oldvalue DOCUMENT ME!
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1024 * @param newvalue DOCUMENT ME!
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1026 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1028 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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