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 // The following vector holds the features which are
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78 // currently visible, in the correct order or rendering
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79 Hashtable featuresDisplayed = null;
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82 /** DOCUMENT ME!! */
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83 public Vector vconsensus;
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84 AlignmentAnnotation consensus;
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85 AlignmentAnnotation conservation;
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86 AlignmentAnnotation quality;
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88 /** DOCUMENT ME!! */
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89 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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91 // JBPNote Prolly only need this in the applet version.
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92 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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94 boolean ignoreGapsInConsensusCalculation = false;
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96 boolean isDataset = false;
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98 boolean antiAlias = false;
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101 public AlignViewport(AlignmentI al, boolean dataset)
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103 isDataset = dataset;
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108 * Creates a new AlignViewport object.
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110 * @param al DOCUMENT ME!
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112 public AlignViewport(AlignmentI al)
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121 this.endRes = alignment.getWidth() - 1;
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123 this.endSeq = alignment.getHeight() - 1;
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125 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
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127 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
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128 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
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129 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
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131 showQuality = Cache.getDefault("SHOW_QUALITY", true);
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132 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
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134 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
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135 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
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136 String fontSize = Cache.getDefault("FONT_SIZE", "10");
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140 if (fontStyle.equals("bold"))
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144 else if (fontStyle.equals("italic"))
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149 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
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152 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
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155 // We must set conservation and consensus before setting colour,
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156 // as Blosum and Clustal require this to be done
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157 if(vconsensus==null && !isDataset)
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159 updateConservation();
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163 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
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165 globalColourScheme = ColourSchemeProperty.getColour(alignment,
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166 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
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168 if (globalColourScheme instanceof UserColourScheme)
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170 globalColourScheme = UserDefinedColours.loadDefaultColours();
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171 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
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174 if (globalColourScheme != null)
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176 globalColourScheme.setConsensus(vconsensus);
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186 * @param b DOCUMENT ME!
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188 public void setShowSequenceFeatures(boolean b)
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190 showSequenceFeatures = b;
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193 public boolean getShowSequenceFeatures()
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195 return showSequenceFeatures;
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201 public void updateConservation()
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203 if(alignment.isNucleotide())
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207 Conservation cons = new jalview.analysis.Conservation("All",
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208 jalview.schemes.ResidueProperties.propHash, 3,
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209 alignment.getSequences(), 0, alignment.getWidth() - 1);
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211 cons.verdict(false, ConsPercGaps);
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212 cons.findQuality();
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214 int alWidth = alignment.getWidth();
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215 Annotation[] annotations = new Annotation[alWidth];
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216 Annotation[] qannotations = new Annotation[alWidth];
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217 String sequence = cons.getConsSequence().getSequence();
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227 maxR = 1.0f - minR;
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228 maxG = 0.9f - minG;
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229 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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233 float qmin = cons.qualityRange[0].floatValue();
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234 float qmax = cons.qualityRange[1].floatValue();
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236 for (int i = 0; i < alWidth; i++)
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242 value = Integer.parseInt(sequence.charAt(i) + "");
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244 catch (Exception ex)
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246 if (sequence.charAt(i) == '*')
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251 if (sequence.charAt(i) == '+')
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257 float vprop = value - min;
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259 annotations[i] = new Annotation(sequence.charAt(i) + "",
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260 String.valueOf(value), ' ', value,
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261 new Color(minR + (maxR * vprop),
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262 minG + (maxG * vprop),
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263 minB + (maxB * vprop)));
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266 value = ( (Double) cons.quality.get(i)).floatValue();
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267 vprop = value - qmin;
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269 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
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271 new Color(minR + (maxR * vprop),
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272 minG + (maxG * vprop),
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273 minB + (maxB * vprop)));
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276 if (conservation == null)
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278 conservation = new AlignmentAnnotation("Conservation",
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279 "Conservation of total alignment less than " +
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280 ConsPercGaps + "% gaps",
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281 annotations, 0f, // cons.qualityRange[0].floatValue(),
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282 11f, // cons.qualityRange[1].floatValue()
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283 AlignmentAnnotation.BAR_GRAPH);
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285 if (showConservation)
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287 alignment.addAnnotation(conservation);
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290 quality = new AlignmentAnnotation("Quality",
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291 "Alignment Quality based on Blosum62 scores",
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293 cons.qualityRange[0].floatValue(),
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294 cons.qualityRange[1].floatValue(),
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295 AlignmentAnnotation.BAR_GRAPH);
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299 alignment.addAnnotation(quality);
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304 conservation.annotations = annotations;
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305 quality.annotations = qannotations;
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306 quality.graphMax = cons.qualityRange[1].floatValue();
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309 catch (OutOfMemoryError error)
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311 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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312 "Out of memory calculating conservation!!"
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314 "\nSee help files for increasing Java Virtual Machine memory."
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316 javax.swing.JOptionPane.WARNING_MESSAGE);
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317 System.out.println("Conservation calculation: " + error);
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326 public void updateConsensus()
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329 Annotation[] annotations = new Annotation[alignment.getWidth()];
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331 // this routine prevents vconsensus becoming a new object each time
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332 // consenus is calculated. Important for speed of Blosum62
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333 // and PID colouring of alignment
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334 if (vconsensus == null)
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336 vconsensus = alignment.getAAFrequency();
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340 Vector temp = alignment.getAAFrequency();
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341 vconsensus.clear();
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343 Enumeration e = temp.elements();
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345 while (e.hasMoreElements())
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347 vconsensus.add(e.nextElement());
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351 Hashtable hash = null;
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353 for (int i = 0; i < alignment.getWidth(); i++)
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355 hash = (Hashtable) vconsensus.elementAt(i);
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358 if (ignoreGapsInConsensusCalculation)
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359 value = ( (Float) hash.get("pid_nogaps")).floatValue();
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361 value = ( (Float) hash.get("pid_gaps")).floatValue();
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363 String maxRes = hash.get("maxResidue").toString();
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364 String mouseOver = hash.get("maxResidue") + " ";
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366 if (maxRes.length() > 1)
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368 mouseOver = "[" + maxRes + "] ";
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372 mouseOver += ( (int) value + "%");
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373 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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376 if (consensus == null)
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378 consensus = new AlignmentAnnotation("Consensus", "PID",
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379 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
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383 alignment.addAnnotation(consensus);
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388 consensus.annotations = annotations;
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391 if (globalColourScheme != null)
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392 globalColourScheme.setConsensus(vconsensus);
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394 }catch(OutOfMemoryError error)
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396 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
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397 "Out of memory calculating consensus!!"
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399 "\nSee help files for increasing Java Virtual Machine memory."
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401 javax.swing.JOptionPane.WARNING_MESSAGE);
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402 System.out.println("Consensus calculation: " + error);
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411 * @return DOCUMENT ME!
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413 public SequenceGroup getSelectionGroup()
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415 return selectionGroup;
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421 * @param sg DOCUMENT ME!
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423 public void setSelectionGroup(SequenceGroup sg)
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425 selectionGroup = sg;
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431 * @return DOCUMENT ME!
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433 public boolean getConservationSelected()
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435 return conservationColourSelected;
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441 * @param b DOCUMENT ME!
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443 public void setConservationSelected(boolean b)
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445 conservationColourSelected = b;
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451 * @return DOCUMENT ME!
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453 public boolean getAbovePIDThreshold()
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455 return abovePIDThreshold;
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461 * @param b DOCUMENT ME!
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463 public void setAbovePIDThreshold(boolean b)
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465 abovePIDThreshold = b;
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471 * @return DOCUMENT ME!
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473 public int getStartRes()
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481 * @return DOCUMENT ME!
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483 public int getEndRes()
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491 * @return DOCUMENT ME!
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493 public int getStartSeq()
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501 * @param cs DOCUMENT ME!
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503 public void setGlobalColourScheme(ColourSchemeI cs)
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505 globalColourScheme = cs;
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511 * @return DOCUMENT ME!
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513 public ColourSchemeI getGlobalColourScheme()
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515 return globalColourScheme;
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521 * @param res DOCUMENT ME!
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523 public void setStartRes(int res)
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525 this.startRes = res;
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531 * @param seq DOCUMENT ME!
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533 public void setStartSeq(int seq)
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535 this.startSeq = seq;
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541 * @param res DOCUMENT ME!
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543 public void setEndRes(int res)
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545 if (res > (alignment.getWidth() - 1))
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547 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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548 res = alignment.getWidth() - 1;
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562 * @param seq DOCUMENT ME!
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564 public void setEndSeq(int seq)
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566 if (seq > alignment.getHeight())
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568 seq = alignment.getHeight();
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582 * @return DOCUMENT ME!
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584 public int getEndSeq()
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592 * @param f DOCUMENT ME!
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594 public void setFont(Font f)
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598 Container c = new Container();
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600 java.awt.FontMetrics fm = c.getFontMetrics(font);
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601 setCharHeight(fm.getHeight());
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602 setCharWidth(fm.charWidth('M'));
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608 * @return DOCUMENT ME!
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610 public Font getFont()
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618 * @param w DOCUMENT ME!
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620 public void setCharWidth(int w)
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622 this.charWidth = w;
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628 * @return DOCUMENT ME!
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630 public int getCharWidth()
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638 * @param h DOCUMENT ME!
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640 public void setCharHeight(int h)
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642 this.charHeight = h;
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648 * @return DOCUMENT ME!
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650 public int getCharHeight()
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658 * @param w DOCUMENT ME!
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660 public void setWrappedWidth(int w)
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662 this.wrappedWidth = w;
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668 * @return DOCUMENT ME!
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670 public int getWrappedWidth()
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672 return wrappedWidth;
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679 * @return DOCUMENT ME!
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681 public AlignmentI getAlignment()
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689 * @param align DOCUMENT ME!
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691 public void setAlignment(AlignmentI align)
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693 this.alignment = align;
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699 * @param state DOCUMENT ME!
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701 public void setWrapAlignment(boolean state)
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703 wrapAlignment = state;
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709 * @param state DOCUMENT ME!
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711 public void setShowText(boolean state)
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719 * @param state DOCUMENT ME!
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721 public void setRenderGaps(boolean state)
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723 renderGaps = state;
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729 * @return DOCUMENT ME!
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731 public boolean getColourText()
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733 return showColourText;
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739 * @param state DOCUMENT ME!
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741 public void setColourText(boolean state)
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743 showColourText = state;
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749 * @param state DOCUMENT ME!
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751 public void setShowBoxes(boolean state)
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759 * @return DOCUMENT ME!
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761 public boolean getWrapAlignment()
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763 return wrapAlignment;
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769 * @return DOCUMENT ME!
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771 public boolean getShowText()
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779 * @return DOCUMENT ME!
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781 public boolean getShowBoxes()
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789 * @return DOCUMENT ME!
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791 public char getGapCharacter()
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793 return getAlignment().getGapCharacter();
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799 * @param gap DOCUMENT ME!
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801 public void setGapCharacter(char gap)
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803 if (getAlignment() != null)
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805 getAlignment().setGapCharacter(gap);
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812 * @param thresh DOCUMENT ME!
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814 public void setThreshold(int thresh)
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816 threshold = thresh;
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822 * @return DOCUMENT ME!
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824 public int getThreshold()
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832 * @param inc DOCUMENT ME!
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834 public void setIncrement(int inc)
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842 * @return DOCUMENT ME!
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844 public int getIncrement()
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852 * @param y DOCUMENT ME!
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854 * @return DOCUMENT ME!
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856 public int getIndex(int y)
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859 int starty = getStartSeq();
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860 int endy = getEndSeq();
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862 for (int i = starty; i <= endy; i++)
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864 if ((i < alignment.getHeight()) &&
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865 (alignment.getSequenceAt(i) != null))
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867 int y2 = y1 + getCharHeight();
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869 if ((y >= y1) && (y <= y2))
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888 * @return DOCUMENT ME!
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890 public ColumnSelection getColumnSelection()
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899 * @param tree DOCUMENT ME!
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901 public void setCurrentTree(NJTree tree)
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903 currentTree = tree;
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909 * @return DOCUMENT ME!
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911 public NJTree getCurrentTree()
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913 return currentTree;
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919 * @param b DOCUMENT ME!
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921 public void setColourAppliesToAllGroups(boolean b)
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923 colourAppliesToAllGroups = b;
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929 * @return DOCUMENT ME!
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931 public boolean getColourAppliesToAllGroups()
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933 return colourAppliesToAllGroups;
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939 * @return DOCUMENT ME!
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941 public boolean getShowJVSuffix()
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943 return showJVSuffix;
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949 * @param b DOCUMENT ME!
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951 public void setShowJVSuffix(boolean b)
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960 * @return DOCUMENT ME!
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962 public boolean getShowAnnotation()
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964 return showAnnotation;
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970 * @param b DOCUMENT ME!
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972 public void setShowAnnotation(boolean b)
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974 showAnnotation = b;
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980 * @return DOCUMENT ME!
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982 public boolean getScaleAboveWrapped()
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984 return scaleAboveWrapped;
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990 * @return DOCUMENT ME!
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992 public boolean getScaleLeftWrapped()
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994 return scaleLeftWrapped;
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1000 * @return DOCUMENT ME!
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1002 public boolean getScaleRightWrapped()
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1004 return scaleRightWrapped;
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1010 * @param b DOCUMENT ME!
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1012 public void setScaleAboveWrapped(boolean b)
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1014 scaleAboveWrapped = b;
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1020 * @param b DOCUMENT ME!
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1022 public void setScaleLeftWrapped(boolean b)
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1024 scaleLeftWrapped = b;
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1030 * @param b DOCUMENT ME!
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1032 public void setScaleRightWrapped(boolean b)
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1034 scaleRightWrapped = b;
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1038 * Property change listener for changes in alignment
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1040 * @param listener DOCUMENT ME!
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1042 public void addPropertyChangeListener(
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1043 java.beans.PropertyChangeListener listener)
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1045 changeSupport.addPropertyChangeListener(listener);
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1051 * @param listener DOCUMENT ME!
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1053 public void removePropertyChangeListener(
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1054 java.beans.PropertyChangeListener listener)
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1056 changeSupport.removePropertyChangeListener(listener);
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1060 * Property change listener for changes in alignment
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1062 * @param prop DOCUMENT ME!
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1063 * @param oldvalue DOCUMENT ME!
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1064 * @param newvalue DOCUMENT ME!
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1066 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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1068 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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1071 public void setIgnoreGapsConsensus(boolean b)
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1073 ignoreGapsInConsensusCalculation = b;
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1074 updateConsensus();
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1075 if(globalColourScheme!=null)
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1077 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
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1081 public boolean getIgnoreGapsConsensus()
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1083 return ignoreGapsInConsensusCalculation;
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1086 public void setDataset(boolean b)
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1091 public boolean isDataset()
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1096 public void hideSequence(SequenceI seq)
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1098 alignment.getHiddenSequences().hideSequence(seq);
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1099 hasHiddenRows = true;
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1102 public void showSequence(int index)
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1104 alignment.getHiddenSequences().showSequence(index);
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1106 if(alignment.getHiddenSequences().getSize()<1)
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1107 hasHiddenRows = false;
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1110 public int adjustForHiddenSeqs(int alignmentIndex)
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1112 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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