2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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20 package jalview.appletgui;
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26 import jalview.analysis.*;
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27 import jalview.bin.*;
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28 import jalview.datamodel.*;
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29 import jalview.schemes.*;
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31 public class AlignViewport
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40 boolean cursorMode = false;
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42 boolean showJVSuffix = true;
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43 boolean showText = true;
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44 boolean showColourText = false;
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45 boolean showBoxes = true;
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46 boolean wrapAlignment = false;
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47 boolean renderGaps = true;
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48 boolean showSequenceFeatures = false;
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49 boolean showAnnotation = true;
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50 boolean showConservation = true;
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51 boolean showQuality = true;
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52 boolean showConsensus = true;
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53 boolean upperCasebold = false;
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55 boolean colourAppliesToAllGroups = true;
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56 ColourSchemeI globalColourScheme = null;
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57 boolean conservationColourSelected = false;
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58 boolean abovePIDThreshold = false;
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60 SequenceGroup selectionGroup;
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66 Font font = new Font("SansSerif", Font.PLAIN, 10);
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67 boolean validCharWidth = true;
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68 AlignmentI alignment;
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70 ColumnSelection colSel = new ColumnSelection();
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75 NJTree currentTree = null;
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77 boolean scaleAboveWrapped = true;
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78 boolean scaleLeftWrapped = true;
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79 boolean scaleRightWrapped = true;
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81 // The following vector holds the features which are
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82 // currently visible, in the correct order or rendering
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83 public Hashtable featuresDisplayed;
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85 boolean hasHiddenColumns = false;
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86 boolean hasHiddenRows = false;
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87 boolean showHiddenMarkers = true;
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90 public Hashtable [] hconsensus;
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91 AlignmentAnnotation consensus;
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92 AlignmentAnnotation conservation;
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93 AlignmentAnnotation quality;
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95 boolean autocalculateConsensus = true;
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97 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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99 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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101 boolean ignoreGapsInConsensusCalculation = false;
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103 jalview.bin.JalviewLite applet;
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105 Hashtable sequenceColours;
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107 boolean MAC = false;
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109 Stack historyList = new Stack();
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110 Stack redoList = new Stack();
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112 String sequenceSetID;
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114 public AlignViewport(AlignmentI al, JalviewLite applet)
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116 this.applet = applet;
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119 this.endRes = al.getWidth() - 1;
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121 this.endSeq = al.getHeight() - 1;
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124 if(System.getProperty("os.name").startsWith("Mac"))
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127 if (applet != null)
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129 String param = applet.getParameter("showFullId");
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132 showJVSuffix = Boolean.valueOf(param).booleanValue();
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135 param = applet.getParameter("showAnnotation");
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138 showAnnotation = Boolean.valueOf(param).booleanValue();
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141 param = applet.getParameter("showConservation");
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144 showConservation = Boolean.valueOf(param).booleanValue();
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147 param = applet.getParameter("showQuality");
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150 showQuality = Boolean.valueOf(param).booleanValue();
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153 param = applet.getParameter("showConsensus");
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156 showConsensus = Boolean.valueOf(param).booleanValue();
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159 param = applet.getParameter("upperCase");
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162 if(param.equalsIgnoreCase("bold"))
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163 upperCasebold = true;
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168 if (applet != null)
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170 String colour = applet.getParameter("defaultColour");
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174 colour = applet.getParameter("userDefinedColour");
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176 colour = "User Defined";
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181 globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
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182 if (globalColourScheme != null)
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184 globalColourScheme.setConsensus(hconsensus);
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188 if(applet.getParameter("userDefinedColour")!=null)
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190 ((UserColourScheme)globalColourScheme).parseAppletParameter(
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191 applet.getParameter("userDefinedColour"));
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194 if(hconsensus==null)
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196 if(!alignment.isNucleotide())
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198 conservation = new AlignmentAnnotation("Conservation",
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199 "Conservation of total alignment less than " +
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200 ConsPercGaps + "% gaps",
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201 new Annotation[1], 0f,
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203 AlignmentAnnotation.BAR_GRAPH);
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204 conservation.hasText = true;
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207 if (showConservation)
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209 alignment.addAnnotation(conservation);
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214 quality = new AlignmentAnnotation("Quality",
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215 "Alignment Quality based on Blosum62 scores",
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219 AlignmentAnnotation.BAR_GRAPH);
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220 quality.hasText = true;
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222 alignment.addAnnotation(quality);
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226 consensus = new AlignmentAnnotation("Consensus", "PID",
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227 new Annotation[1], 0f, 100f,
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228 AlignmentAnnotation.BAR_GRAPH);
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229 consensus.hasText = true;
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233 alignment.addAnnotation(consensus);
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239 public void showSequenceFeatures(boolean b)
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241 showSequenceFeatures = b;
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244 public boolean getShowSequenceFeatures()
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246 return showSequenceFeatures;
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250 class ConservationThread extends Thread
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253 public ConservationThread(AlignmentPanel ap)
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262 updatingConservation = true;
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264 while (UPDATING_CONSERVATION)
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274 catch (Exception ex)
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276 ex.printStackTrace();
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280 UPDATING_CONSERVATION = true;
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283 int alWidth = alignment.getWidth();
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287 Conservation cons = new jalview.analysis.Conservation("All",
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288 jalview.schemes.ResidueProperties.propHash, 3,
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289 alignment.getSequences(), 0, alWidth -1);
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292 cons.verdict(false, ConsPercGaps);
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296 cons.findQuality();
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299 String sequence = cons.getConsSequence().getSequence();
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309 maxR = 1.0f - minR;
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310 maxG = 0.9f - minG;
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311 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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320 conservation.annotations = new Annotation[alWidth];
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324 quality.graphMax = cons.qualityRange[1].floatValue();
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325 quality.annotations = new Annotation[alWidth];
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326 qmin = cons.qualityRange[0].floatValue();
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327 qmax = cons.qualityRange[1].floatValue();
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330 for (int i = 0; i < alWidth; i++)
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334 c = sequence.charAt(i);
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336 if (Character.isDigit(c))
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337 value = (int) (c - '0');
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343 float vprop = value - min;
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345 conservation.annotations[i] =
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346 new Annotation(String.valueOf(c),
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347 String.valueOf(value), ' ', value,
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348 new Color(minR + (maxR * vprop),
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349 minG + (maxG * vprop),
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350 minB + (maxB * vprop)));
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355 value = ( (Double) cons.quality.elementAt(i)).floatValue();
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356 vprop = value - qmin;
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358 quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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360 new Color(minR + (maxR * vprop),
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361 minG + (maxG * vprop),
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362 minB + (maxB * vprop)));
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366 catch (OutOfMemoryError error)
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368 System.out.println("Out of memory calculating conservation!!");
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369 conservation = null;
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374 UPDATING_CONSERVATION = false;
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375 updatingConservation = false;
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386 ConservationThread conservationThread;
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388 ConsensusThread consensusThread;
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390 boolean consUpdateNeeded = false;
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392 static boolean UPDATING_CONSENSUS = false;
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394 static boolean UPDATING_CONSERVATION = false;
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396 boolean updatingConsensus = false;
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398 boolean updatingConservation = false;
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403 public void updateConservation(final AlignmentPanel ap)
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405 if (alignment.isNucleotide() || conservation==null)
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408 conservationThread = new ConservationThread(ap);
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409 conservationThread.start();
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415 public void updateConsensus(final AlignmentPanel ap)
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417 consensusThread = new ConsensusThread(ap);
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418 consensusThread.start();
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422 class ConsensusThread extends Thread
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425 public ConsensusThread(AlignmentPanel ap)
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431 updatingConsensus = true;
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432 while (UPDATING_CONSENSUS)
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443 catch (Exception ex)
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445 ex.printStackTrace();
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450 UPDATING_CONSENSUS = true;
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454 int aWidth = alignment.getWidth();
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458 consensus.annotations = null;
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459 consensus.annotations = new Annotation[aWidth];
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462 hconsensus = new Hashtable[aWidth];
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463 AAFrequency.calculate(alignment.getSequencesArray(),
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465 alignment.getWidth(),
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468 for (int i = 0; i < aWidth; i++)
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471 if (ignoreGapsInConsensusCalculation)
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472 value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
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475 value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
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478 String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
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479 String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
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481 if (maxRes.length() > 1)
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483 mouseOver = "[" + maxRes + "] ";
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487 mouseOver += ( (int) value + "%");
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488 consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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492 if (globalColourScheme != null)
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493 globalColourScheme.setConsensus(hconsensus);
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496 catch (OutOfMemoryError error)
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498 alignment.deleteAnnotation(consensus);
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502 System.out.println("Out of memory calculating consensus!!");
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505 UPDATING_CONSENSUS = false;
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506 updatingConsensus = false;
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516 * get the consensus sequence as displayed under the PID consensus annotation row.
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517 * @return consensus sequence as a new sequence object
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520 * get the consensus sequence as displayed under the PID consensus annotation row.
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521 * @return consensus sequence as a new sequence object
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523 public SequenceI getConsensusSeq()
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525 if (consensus==null)
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527 StringBuffer seqs=new StringBuffer();
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528 for (int i=0; i<consensus.annotations.length; i++) {
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529 if (consensus.annotations[i]!=null) {
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530 if (consensus.annotations[i].description.charAt(0) == '[')
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531 seqs.append(consensus.annotations[i].description.charAt(1));
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533 seqs.append(consensus.annotations[i].displayCharacter);
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536 SequenceI sq = new Sequence("Consensus", seqs.toString());
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537 sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
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540 public SequenceGroup getSelectionGroup()
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542 return selectionGroup;
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545 public void setSelectionGroup(SequenceGroup sg)
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547 selectionGroup = sg;
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550 public boolean getConservationSelected()
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552 return conservationColourSelected;
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555 public void setConservationSelected(boolean b)
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557 conservationColourSelected = b;
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560 public boolean getAbovePIDThreshold()
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562 return abovePIDThreshold;
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565 public void setAbovePIDThreshold(boolean b)
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567 abovePIDThreshold = b;
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570 public int getStartRes()
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575 public int getEndRes()
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580 public int getStartSeq()
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585 public void setGlobalColourScheme(ColourSchemeI cs)
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587 globalColourScheme = cs;
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590 public ColourSchemeI getGlobalColourScheme()
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592 return globalColourScheme;
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595 public void setStartRes(int res)
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597 this.startRes = res;
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600 public void setStartSeq(int seq)
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602 this.startSeq = seq;
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605 public void setEndRes(int res)
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607 if (res > alignment.getWidth() - 1)
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609 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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610 res = alignment.getWidth() - 1;
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619 public void setEndSeq(int seq)
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621 if (seq > alignment.getHeight())
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623 seq = alignment.getHeight();
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632 public int getEndSeq()
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637 java.awt.Frame nullFrame;
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638 public void setFont(Font f)
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641 if(nullFrame == null)
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643 nullFrame = new java.awt.Frame();
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644 nullFrame.addNotify();
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647 java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
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648 setCharHeight(fm.getHeight());
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649 charWidth = fm.charWidth('M');
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653 Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
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654 fm = nullFrame.getGraphics().getFontMetrics(f2);
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655 charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
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659 public Font getFont()
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664 public int getCharWidth()
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669 public void setCharHeight(int h)
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671 this.charHeight = h;
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674 public int getCharHeight()
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679 public void setWrappedWidth(int w)
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681 this.wrappedWidth = w;
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684 public int getwrappedWidth()
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686 return wrappedWidth;
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689 public AlignmentI getAlignment()
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694 public void setAlignment(AlignmentI align)
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696 this.alignment = align;
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699 public void setWrapAlignment(boolean state)
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701 wrapAlignment = state;
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704 public void setShowText(boolean state)
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709 public void setRenderGaps(boolean state)
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711 renderGaps = state;
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714 public boolean getColourText()
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716 return showColourText;
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719 public void setColourText(boolean state)
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721 showColourText = state;
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724 public void setShowBoxes(boolean state)
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729 public boolean getWrapAlignment()
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731 return wrapAlignment;
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734 public boolean getShowText()
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739 public boolean getShowBoxes()
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744 public char getGapCharacter()
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746 return getAlignment().getGapCharacter();
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749 public void setGapCharacter(char gap)
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751 if (getAlignment() != null)
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753 getAlignment().setGapCharacter(gap);
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757 public void setThreshold(int thresh)
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759 threshold = thresh;
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762 public int getThreshold()
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767 public void setIncrement(int inc)
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772 public int getIncrement()
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777 public void setHiddenColumns(ColumnSelection colsel)
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779 this.colSel = colsel;
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780 if(colSel.getHiddenColumns()!=null)
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781 hasHiddenColumns = true;
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784 public ColumnSelection getColumnSelection()
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789 public void resetSeqLimits(int height)
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791 setEndSeq(height / getCharHeight());
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794 public void setCurrentTree(NJTree tree)
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796 currentTree = tree;
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799 public NJTree getCurrentTree()
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801 return currentTree;
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804 public void setColourAppliesToAllGroups(boolean b)
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806 colourAppliesToAllGroups = b;
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809 public boolean getColourAppliesToAllGroups()
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811 return colourAppliesToAllGroups;
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814 public boolean getShowJVSuffix()
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816 return showJVSuffix;
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819 public void setShowJVSuffix(boolean b)
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824 public boolean getShowAnnotation()
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826 return showAnnotation;
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829 public void setShowAnnotation(boolean b)
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831 showAnnotation = b;
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834 public boolean getScaleAboveWrapped()
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836 return scaleAboveWrapped;
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839 public boolean getScaleLeftWrapped()
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841 return scaleLeftWrapped;
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844 public boolean getScaleRightWrapped()
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846 return scaleRightWrapped;
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849 public void setScaleAboveWrapped(boolean b)
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851 scaleAboveWrapped = b;
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854 public void setScaleLeftWrapped(boolean b)
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856 scaleLeftWrapped = b;
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859 public void setScaleRightWrapped(boolean b)
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861 scaleRightWrapped = b;
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864 public void setIgnoreGapsConsensus(boolean b)
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866 ignoreGapsInConsensusCalculation = b;
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867 updateConsensus(null);
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868 if (globalColourScheme!=null)
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870 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
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871 ignoreGapsInConsensusCalculation);
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877 * Property change listener for changes in alignment
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879 * @param listener DOCUMENT ME!
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881 public void addPropertyChangeListener(
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882 java.beans.PropertyChangeListener listener)
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884 changeSupport.addPropertyChangeListener(listener);
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890 * @param listener DOCUMENT ME!
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892 public void removePropertyChangeListener(
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893 java.beans.PropertyChangeListener listener)
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895 changeSupport.removePropertyChangeListener(listener);
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899 * Property change listener for changes in alignment
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901 * @param prop DOCUMENT ME!
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902 * @param oldvalue DOCUMENT ME!
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903 * @param newvalue DOCUMENT ME!
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905 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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907 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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912 public boolean getIgnoreGapsConsensus()
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914 return ignoreGapsInConsensusCalculation;
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916 public void hideSelectedColumns()
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918 if (colSel.size() < 1)
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921 colSel.hideSelectedColumns();
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922 setSelectionGroup(null);
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924 hasHiddenColumns = true;
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927 public void invertColumnSelection()
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930 for (int i = 0; i < alignment.getWidth(); i++)
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934 if (colSel.contains(column))
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935 colSel.removeElement(column);
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937 colSel.addElement(column);
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943 public void hideColumns(int start, int end)
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946 colSel.hideColumns(start);
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948 colSel.hideColumns(start, end);
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950 hasHiddenColumns = true;
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953 public void hideAllSelectedSeqs()
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955 if (selectionGroup == null)
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958 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
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960 hideSequence(seqs);
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962 setSelectionGroup(null);
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965 public void hideSequence(SequenceI [] seq)
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969 for (int i = 0; i < seq.length; i++)
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970 alignment.getHiddenSequences().hideSequence(seq[i]);
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972 hasHiddenRows = true;
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973 firePropertyChange("alignment", null, alignment.getSequences());
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977 public void showColumn(int col)
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979 colSel.revealHiddenColumns(col);
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980 if(colSel.getHiddenColumns()==null)
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981 hasHiddenColumns = false;
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984 public void showAllHiddenColumns()
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986 colSel.revealAllHiddenColumns();
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987 hasHiddenColumns = false;
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990 public void showAllHiddenSeqs()
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992 if(alignment.getHiddenSequences().getSize()>0)
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994 if(selectionGroup==null)
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996 selectionGroup = new SequenceGroup();
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997 selectionGroup.setEndRes(alignment.getWidth()-1);
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999 Vector tmp = alignment.getHiddenSequences().showAll();
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1000 for(int t=0; t<tmp.size(); t++)
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1002 selectionGroup.addSequence(
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1003 (SequenceI)tmp.elementAt(t), false
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1006 firePropertyChange("alignment", null, alignment.getSequences());
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1007 hasHiddenRows = false;
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1011 public int adjustForHiddenSeqs(int alignmentIndex)
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1013 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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1017 * This method returns the a new SequenceI [] with
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1018 * the selection sequence and start and end points adjusted
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1019 * @return String[]
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1021 public SequenceI[] getSelectionAsNewSequence()
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1023 SequenceI[] sequences;
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1025 if (selectionGroup == null)
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1026 sequences = alignment.getSequencesArray();
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1028 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
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1034 * This method returns the visible alignment as text, as
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1035 * seen on the GUI, ie if columns are hidden they will not
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1036 * be returned in the result.
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1037 * Use this for calculating trees, PCA, redundancy etc on views
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1038 * which contain hidden columns.
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1039 * @return String[]
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1041 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
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1043 CigarArray selection=null;
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1044 SequenceI [] seqs= null;
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1046 int start = 0, end = 0;
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1047 if(selectedRegionOnly && selectionGroup!=null)
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1049 iSize = selectionGroup.getSize(false);
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1050 seqs = selectionGroup.getSequencesInOrder(alignment);
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1051 start = selectionGroup.getStartRes();
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1052 end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
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1056 iSize = alignment.getHeight();
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1057 seqs = alignment.getSequencesArray();
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1058 end = alignment.getWidth()-1;
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1060 SeqCigar[] selseqs = new SeqCigar[iSize];
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1061 for(i=0; i<iSize; i++)
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1063 selseqs[i] = new SeqCigar(seqs[i], start, end);
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1065 selection=new CigarArray(selseqs);
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1066 // now construct the CigarArray operations
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1067 if (hasHiddenColumns) {
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1068 Vector regions = colSel.getHiddenColumns();
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1070 int hideStart, hideEnd;
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1072 for (int j = 0; last<end & j < regions.size(); j++)
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1074 region = (int[]) regions.elementAt(j);
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1075 hideStart = region[0];
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1076 hideEnd = region[1];
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1077 // edit hidden regions to selection range
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1078 if(hideStart<last) {
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1079 if (hideEnd > last)
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1086 if (hideStart>end)
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1092 if (hideStart>hideEnd)
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1095 * form operations...
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1097 if (last<hideStart)
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1098 selection.addOperation(CigarArray.M, hideStart-last);
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1099 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
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1102 // Final match if necessary.
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1104 selection.addOperation(CigarArray.M, end-last+1);
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1106 selection.addOperation(CigarArray.M, end-start+1);
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1111 * return a compact representation of the current alignment selection to
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1112 * pass to an analysis function
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1113 * @param selectedOnly boolean true to just return the selected view
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1114 * @return AlignmentView
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1116 jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
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1118 // this is here because the AlignmentView constructor modifies the CigarArray
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1119 // object. Refactoring of Cigar and alignment view representation should
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1120 // be done to remove redundancy.
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1121 CigarArray aligview = getViewAsCigars(selectedOnly);
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1122 if (aligview!=null) {
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1123 return new AlignmentView(aligview,
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1124 (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
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1129 * This method returns the visible alignment as text, as
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1130 * seen on the GUI, ie if columns are hidden they will not
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1131 * be returned in the result.
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1132 * Use this for calculating trees, PCA, redundancy etc on views
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1133 * which contain hidden columns.
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1134 * @return String[]
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1136 public String [] getViewAsString(boolean selectedRegionOnly)
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1138 String [] selection = null;
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1139 SequenceI [] seqs= null;
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1141 int start = 0, end = 0;
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1142 if(selectedRegionOnly && selectionGroup!=null)
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1144 iSize = selectionGroup.getSize(false);
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1145 seqs = selectionGroup.getSequencesInOrder(alignment);
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1146 start = selectionGroup.getStartRes();
\r
1147 end = selectionGroup.getEndRes()+1;
\r
1151 iSize = alignment.getHeight();
\r
1152 seqs = alignment.getSequencesArray();
\r
1153 end = alignment.getWidth();
\r
1156 selection = new String[iSize];
\r
1159 for(i=0; i<iSize; i++)
\r
1161 if (hasHiddenColumns)
\r
1163 StringBuffer visibleSeq = new StringBuffer();
\r
1164 Vector regions = colSel.getHiddenColumns();
\r
1166 int blockStart = start, blockEnd=end;
\r
1168 int hideStart, hideEnd;
\r
1170 for (int j = 0; j < regions.size(); j++)
\r
1172 region = (int[]) regions.elementAt(j);
\r
1173 hideStart = region[0];
\r
1174 hideEnd = region[1];
\r
1176 if(hideStart < start)
\r
1181 blockStart = Math.min(blockStart, hideEnd+1);
\r
1182 blockEnd = Math.min(blockEnd, hideStart);
\r
1184 if(blockStart>blockEnd)
\r
1190 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
\r
1192 blockStart = hideEnd+1;
\r
1196 if(end>blockStart)
\r
1197 visibleSeq.append(seqs[i].getSequence(blockStart, end));
\r
1199 selection[i] = visibleSeq.toString();
\r
1203 selection[i] = seqs[i].getSequence(start, end);
\r
1210 public boolean getShowHiddenMarkers()
\r
1212 return showHiddenMarkers;
\r
1215 public void setShowHiddenMarkers(boolean show)
\r
1217 showHiddenMarkers = show;
\r
1220 public Color getSequenceColour(SequenceI seq)
\r
1222 if (sequenceColours == null || !sequenceColours.containsKey(seq))
\r
1223 return Color.white;
\r
1225 return (Color) sequenceColours.get(seq);
\r
1228 public void setSequenceColour(SequenceI seq, Color col)
\r
1230 if (sequenceColours == null)
\r
1231 sequenceColours = new Hashtable();
\r
1234 sequenceColours.remove(seq);
\r
1236 sequenceColours.put(seq, col);
\r
1239 public String getSequenceSetId()
\r
1241 if (sequenceSetID == null)
\r
1242 sequenceSetID = alignment.hashCode() + "";
\r
1244 return sequenceSetID;
\r
1247 public void alignmentChanged(AlignmentPanel ap)
\r
1249 alignment.padGaps();
\r
1251 if (hconsensus != null && autocalculateConsensus)
\r
1253 updateConsensus(ap);
\r
1254 updateConservation(ap);
\r
1257 //Reset endRes of groups if beyond alignment width
\r
1258 int alWidth = alignment.getWidth();
\r
1259 Vector groups = alignment.getGroups();
\r
1262 for(int i=0; i<groups.size(); i++)
\r
1264 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
\r
1265 if(sg.getEndRes()>alWidth)
\r
1266 sg.setEndRes(alWidth-1);
\r
1270 if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
\r
1271 selectionGroup.setEndRes(alWidth-1);
\r
1273 resetAllColourSchemes();
\r
1275 alignment.adjustSequenceAnnotations();
\r
1278 void resetAllColourSchemes()
\r
1280 ColourSchemeI cs = globalColourScheme;
\r
1283 if (cs instanceof ClustalxColourScheme)
\r
1285 ( (ClustalxColourScheme) cs).
\r
1286 resetClustalX(alignment.getSequences(),
\r
1287 alignment.getWidth());
\r
1290 cs.setConsensus(hconsensus);
\r
1291 if (cs.conservationApplied())
\r
1293 Alignment al = (Alignment) alignment;
\r
1294 Conservation c = new Conservation("All",
\r
1295 ResidueProperties.propHash, 3,
\r
1296 al.getSequences(), 0,
\r
1297 al.getWidth() - 1);
\r
1299 c.verdict(false, ConsPercGaps);
\r
1301 cs.setConservation(c);
\r
1305 int s, sSize = alignment.getGroups().size();
\r
1306 for(s=0; s<sSize; s++)
\r
1308 SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
\r
1309 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1311 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1312 sg.getSequences(true), sg.getWidth());
\r
1314 sg.recalcConservation();
\r