2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.analysis.*;
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23 import jalview.bin.*;
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25 import jalview.datamodel.*;
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27 import jalview.schemes.*;
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38 * @version $Revision$
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40 public class AlignViewport
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46 boolean showJVSuffix = true;
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47 boolean showText = true;
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48 boolean showColourText = false;
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49 boolean showBoxes = true;
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50 boolean wrapAlignment = false;
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51 boolean renderGaps = true;
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52 boolean showSequenceFeatures = false;
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53 boolean showAnnotation = true;
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54 boolean showConservation = true;
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55 boolean showQuality = true;
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56 boolean showIdentity = true;
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57 boolean colourAppliesToAllGroups = true;
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58 ColourSchemeI globalColourScheme = null;
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59 boolean conservationColourSelected = false;
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60 boolean abovePIDThreshold = false;
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61 SequenceGroup selectionGroup;
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65 Font font = new Font("SansSerif", Font.PLAIN, 10);
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66 AlignmentI alignment;
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67 ColumnSelection colSel = new ColumnSelection();
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70 NJTree currentTree = null;
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71 boolean scaleAboveWrapped = false;
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72 boolean scaleLeftWrapped = true;
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73 boolean scaleRightWrapped = true;
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74 boolean hasHiddenColumns = false;
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75 boolean hasHiddenRows = false;
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77 boolean cursorMode = false;
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79 // The following vector holds the features which are
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80 // currently visible, in the correct order or rendering
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81 Hashtable featuresDisplayed = null;
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84 /** DOCUMENT ME!! */
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85 public Vector vconsensus;
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86 AlignmentAnnotation consensus;
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87 AlignmentAnnotation conservation;
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88 AlignmentAnnotation quality;
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90 /** DOCUMENT ME!! */
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91 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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93 // JBPNote Prolly only need this in the applet version.
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94 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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96 boolean ignoreGapsInConsensusCalculation = false;
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98 boolean isDataset = false;
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100 boolean antiAlias = false;
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103 public AlignViewport(AlignmentI al, boolean dataset)
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105 isDataset = dataset;
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110 * Creates a new AlignViewport object.
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112 * @param al DOCUMENT ME!
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114 public AlignViewport(AlignmentI al)
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123 this.endRes = alignment.getWidth() - 1;
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125 this.endSeq = alignment.getHeight() - 1;
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127 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
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129 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
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130 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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131 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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133 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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134 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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136 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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137 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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138 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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142 if (fontStyle.equals("bold"))
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146 else if (fontStyle.equals("italic"))
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151 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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154 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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157 // We must set conservation and consensus before setting colour,
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158 // as Blosum and Clustal require this to be done
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159 if(vconsensus==null && !isDataset)
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161 updateConservation();
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165 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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167 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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168 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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170 if (globalColourScheme instanceof UserColourScheme)
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172 globalColourScheme = UserDefinedColours.loadDefaultColours();
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173 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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176 if (globalColourScheme != null)
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178 globalColourScheme.setConsensus(vconsensus);
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188 * @param b DOCUMENT ME!
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190 public void setShowSequenceFeatures(boolean b)
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192 showSequenceFeatures = b;
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195 public boolean getShowSequenceFeatures()
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197 return showSequenceFeatures;
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203 public void updateConservation()
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205 if(alignment.isNucleotide())
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209 Conservation cons = new jalview.analysis.Conservation("All",
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210 jalview.schemes.ResidueProperties.propHash, 3,
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211 alignment.getSequences(), 0, alignment.getWidth() - 1);
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213 cons.verdict(false, ConsPercGaps);
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214 cons.findQuality();
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216 int alWidth = alignment.getWidth();
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217 Annotation[] annotations = new Annotation[alWidth];
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218 Annotation[] qannotations = new Annotation[alWidth];
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219 String sequence = cons.getConsSequence().getSequence();
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229 maxR = 1.0f - minR;
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230 maxG = 0.9f - minG;
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231 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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235 float qmin = cons.qualityRange[0].floatValue();
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236 float qmax = cons.qualityRange[1].floatValue();
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238 for (int i = 0; i < alWidth; i++)
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244 value = Integer.parseInt(sequence.charAt(i) + "");
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246 catch (Exception ex)
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248 if (sequence.charAt(i) == '*')
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253 if (sequence.charAt(i) == '+')
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259 float vprop = value - min;
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261 annotations[i] = new Annotation(sequence.charAt(i) + "",
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262 String.valueOf(value), ' ', value,
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263 new Color(minR + (maxR * vprop),
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264 minG + (maxG * vprop),
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265 minB + (maxB * vprop)));
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268 value = ( (Double) cons.quality.get(i)).floatValue();
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269 vprop = value - qmin;
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271 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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273 new Color(minR + (maxR * vprop),
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274 minG + (maxG * vprop),
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275 minB + (maxB * vprop)));
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278 if (conservation == null)
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280 conservation = new AlignmentAnnotation("Conservation",
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281 "Conservation of total alignment less than " +
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282 ConsPercGaps + "% gaps",
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283 annotations, 0f, // cons.qualityRange[0].floatValue(),
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284 11f, // cons.qualityRange[1].floatValue()
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285 AlignmentAnnotation.BAR_GRAPH);
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287 if (showConservation)
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289 alignment.addAnnotation(conservation);
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292 quality = new AlignmentAnnotation("Quality",
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293 "Alignment Quality based on Blosum62 scores",
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295 cons.qualityRange[0].floatValue(),
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296 cons.qualityRange[1].floatValue(),
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297 AlignmentAnnotation.BAR_GRAPH);
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301 alignment.addAnnotation(quality);
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306 conservation.annotations = annotations;
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307 quality.annotations = qannotations;
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308 quality.graphMax = cons.qualityRange[1].floatValue();
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311 catch (OutOfMemoryError error)
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313 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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314 "Out of memory calculating conservation!!"
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316 "\nSee help files for increasing Java Virtual Machine memory."
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318 javax.swing.JOptionPane.WARNING_MESSAGE);
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319 System.out.println("Conservation calculation: " + error);
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328 public void updateConsensus()
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331 Annotation[] annotations = new Annotation[alignment.getWidth()];
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333 // this routine prevents vconsensus becoming a new object each time
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334 // consenus is calculated. Important for speed of Blosum62
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335 // and PID colouring of alignment
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336 if (vconsensus == null)
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338 vconsensus = alignment.getAAFrequency();
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342 Vector temp = alignment.getAAFrequency();
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343 vconsensus.clear();
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345 Enumeration e = temp.elements();
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347 while (e.hasMoreElements())
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349 vconsensus.add(e.nextElement());
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353 Hashtable hash = null;
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355 for (int i = 0; i < alignment.getWidth(); i++)
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357 hash = (Hashtable) vconsensus.elementAt(i);
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360 if (ignoreGapsInConsensusCalculation)
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361 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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363 value = ( (Float) hash.get("pid_gaps")).floatValue();
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365 String maxRes = hash.get("maxResidue").toString();
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366 String mouseOver = hash.get("maxResidue") + " ";
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368 if (maxRes.length() > 1)
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370 mouseOver = "[" + maxRes + "] ";
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374 mouseOver += ( (int) value + "%");
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375 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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378 if (consensus == null)
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380 consensus = new AlignmentAnnotation("Consensus", "PID",
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381 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
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385 alignment.addAnnotation(consensus);
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390 consensus.annotations = annotations;
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393 if (globalColourScheme != null)
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394 globalColourScheme.setConsensus(vconsensus);
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396 }catch(OutOfMemoryError error)
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398 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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399 "Out of memory calculating consensus!!"
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401 "\nSee help files for increasing Java Virtual Machine memory."
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403 javax.swing.JOptionPane.WARNING_MESSAGE);
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404 System.out.println("Consensus calculation: " + error);
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413 * @return DOCUMENT ME!
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415 public SequenceGroup getSelectionGroup()
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417 return selectionGroup;
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423 * @param sg DOCUMENT ME!
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425 public void setSelectionGroup(SequenceGroup sg)
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427 selectionGroup = sg;
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433 * @return DOCUMENT ME!
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435 public boolean getConservationSelected()
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437 return conservationColourSelected;
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443 * @param b DOCUMENT ME!
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445 public void setConservationSelected(boolean b)
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447 conservationColourSelected = b;
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453 * @return DOCUMENT ME!
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455 public boolean getAbovePIDThreshold()
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457 return abovePIDThreshold;
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463 * @param b DOCUMENT ME!
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465 public void setAbovePIDThreshold(boolean b)
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467 abovePIDThreshold = b;
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473 * @return DOCUMENT ME!
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475 public int getStartRes()
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483 * @return DOCUMENT ME!
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485 public int getEndRes()
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493 * @return DOCUMENT ME!
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495 public int getStartSeq()
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503 * @param cs DOCUMENT ME!
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505 public void setGlobalColourScheme(ColourSchemeI cs)
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507 globalColourScheme = cs;
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513 * @return DOCUMENT ME!
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515 public ColourSchemeI getGlobalColourScheme()
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517 return globalColourScheme;
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523 * @param res DOCUMENT ME!
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525 public void setStartRes(int res)
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527 this.startRes = res;
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533 * @param seq DOCUMENT ME!
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535 public void setStartSeq(int seq)
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537 this.startSeq = seq;
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543 * @param res DOCUMENT ME!
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545 public void setEndRes(int res)
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547 if (res > (alignment.getWidth() - 1))
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549 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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550 res = alignment.getWidth() - 1;
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564 * @param seq DOCUMENT ME!
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566 public void setEndSeq(int seq)
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568 if (seq > alignment.getHeight())
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570 seq = alignment.getHeight();
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584 * @return DOCUMENT ME!
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586 public int getEndSeq()
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594 * @param f DOCUMENT ME!
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596 public void setFont(Font f)
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600 Container c = new Container();
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602 java.awt.FontMetrics fm = c.getFontMetrics(font);
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603 setCharHeight(fm.getHeight());
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604 setCharWidth(fm.charWidth('M'));
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610 * @return DOCUMENT ME!
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612 public Font getFont()
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620 * @param w DOCUMENT ME!
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622 public void setCharWidth(int w)
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624 this.charWidth = w;
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630 * @return DOCUMENT ME!
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632 public int getCharWidth()
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640 * @param h DOCUMENT ME!
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642 public void setCharHeight(int h)
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644 this.charHeight = h;
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650 * @return DOCUMENT ME!
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652 public int getCharHeight()
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660 * @param w DOCUMENT ME!
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662 public void setWrappedWidth(int w)
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664 this.wrappedWidth = w;
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670 * @return DOCUMENT ME!
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672 public int getWrappedWidth()
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674 return wrappedWidth;
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681 * @return DOCUMENT ME!
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683 public AlignmentI getAlignment()
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691 * @param align DOCUMENT ME!
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693 public void setAlignment(AlignmentI align)
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695 this.alignment = align;
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701 * @param state DOCUMENT ME!
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703 public void setWrapAlignment(boolean state)
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705 wrapAlignment = state;
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711 * @param state DOCUMENT ME!
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713 public void setShowText(boolean state)
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721 * @param state DOCUMENT ME!
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723 public void setRenderGaps(boolean state)
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725 renderGaps = state;
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731 * @return DOCUMENT ME!
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733 public boolean getColourText()
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735 return showColourText;
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741 * @param state DOCUMENT ME!
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743 public void setColourText(boolean state)
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745 showColourText = state;
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751 * @param state DOCUMENT ME!
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753 public void setShowBoxes(boolean state)
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761 * @return DOCUMENT ME!
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763 public boolean getWrapAlignment()
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765 return wrapAlignment;
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771 * @return DOCUMENT ME!
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773 public boolean getShowText()
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781 * @return DOCUMENT ME!
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783 public boolean getShowBoxes()
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791 * @return DOCUMENT ME!
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793 public char getGapCharacter()
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795 return getAlignment().getGapCharacter();
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801 * @param gap DOCUMENT ME!
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803 public void setGapCharacter(char gap)
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805 if (getAlignment() != null)
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807 getAlignment().setGapCharacter(gap);
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814 * @param thresh DOCUMENT ME!
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816 public void setThreshold(int thresh)
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818 threshold = thresh;
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824 * @return DOCUMENT ME!
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826 public int getThreshold()
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834 * @param inc DOCUMENT ME!
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836 public void setIncrement(int inc)
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844 * @return DOCUMENT ME!
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846 public int getIncrement()
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854 * @param y DOCUMENT ME!
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856 * @return DOCUMENT ME!
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858 public int getIndex(int y)
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861 int starty = getStartSeq();
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862 int endy = getEndSeq();
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864 for (int i = starty; i <= endy; i++)
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866 if ((i < alignment.getHeight()) &&
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867 (alignment.getSequenceAt(i) != null))
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869 int y2 = y1 + getCharHeight();
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871 if ((y >= y1) && (y <= y2))
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890 * @return DOCUMENT ME!
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892 public ColumnSelection getColumnSelection()
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901 * @param tree DOCUMENT ME!
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903 public void setCurrentTree(NJTree tree)
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905 currentTree = tree;
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911 * @return DOCUMENT ME!
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913 public NJTree getCurrentTree()
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915 return currentTree;
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921 * @param b DOCUMENT ME!
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923 public void setColourAppliesToAllGroups(boolean b)
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925 colourAppliesToAllGroups = b;
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931 * @return DOCUMENT ME!
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933 public boolean getColourAppliesToAllGroups()
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935 return colourAppliesToAllGroups;
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941 * @return DOCUMENT ME!
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943 public boolean getShowJVSuffix()
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945 return showJVSuffix;
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951 * @param b DOCUMENT ME!
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953 public void setShowJVSuffix(boolean b)
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962 * @return DOCUMENT ME!
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964 public boolean getShowAnnotation()
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966 return showAnnotation;
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972 * @param b DOCUMENT ME!
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974 public void setShowAnnotation(boolean b)
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976 showAnnotation = b;
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982 * @return DOCUMENT ME!
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984 public boolean getScaleAboveWrapped()
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986 return scaleAboveWrapped;
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992 * @return DOCUMENT ME!
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994 public boolean getScaleLeftWrapped()
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996 return scaleLeftWrapped;
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1002 * @return DOCUMENT ME!
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1004 public boolean getScaleRightWrapped()
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1006 return scaleRightWrapped;
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1012 * @param b DOCUMENT ME!
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1014 public void setScaleAboveWrapped(boolean b)
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1016 scaleAboveWrapped = b;
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1022 * @param b DOCUMENT ME!
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1024 public void setScaleLeftWrapped(boolean b)
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1026 scaleLeftWrapped = b;
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1032 * @param b DOCUMENT ME!
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1034 public void setScaleRightWrapped(boolean b)
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1036 scaleRightWrapped = b;
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1040 * Property change listener for changes in alignment
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1042 * @param listener DOCUMENT ME!
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1044 public void addPropertyChangeListener(
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1045 java.beans.PropertyChangeListener listener)
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1047 changeSupport.addPropertyChangeListener(listener);
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1053 * @param listener DOCUMENT ME!
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1055 public void removePropertyChangeListener(
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1056 java.beans.PropertyChangeListener listener)
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1058 changeSupport.removePropertyChangeListener(listener);
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1062 * Property change listener for changes in alignment
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1064 * @param prop DOCUMENT ME!
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1065 * @param oldvalue DOCUMENT ME!
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1066 * @param newvalue DOCUMENT ME!
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1068 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1070 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1073 public void setIgnoreGapsConsensus(boolean b)
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1075 ignoreGapsInConsensusCalculation = b;
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1076 updateConsensus();
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1077 if(globalColourScheme!=null)
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1079 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1083 public boolean getIgnoreGapsConsensus()
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1085 return ignoreGapsInConsensusCalculation;
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1088 public void setDataset(boolean b)
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1093 public boolean isDataset()
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1098 public void hideSequence(SequenceI seq)
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1100 alignment.getHiddenSequences().hideSequence(seq);
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1101 hasHiddenRows = true;
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1104 public void showSequence(int index)
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1106 alignment.getHiddenSequences().showSequence(index);
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1108 if(alignment.getHiddenSequences().getSize()<1)
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1109 hasHiddenRows = false;
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1112 public int adjustForHiddenSeqs(int alignmentIndex)
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1114 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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