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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54 boolean colourAppliesToAllGroups = true;
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55 ColourSchemeI globalColourScheme = null;
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56 boolean conservationColourSelected = false;
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57 boolean abovePIDThreshold = false;
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59 SequenceGroup selectionGroup;
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65 Font font = new Font("SansSerif", Font.PLAIN, 10);
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66 boolean validCharWidth = true;
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67 AlignmentI alignment;
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69 ColumnSelection colSel = new ColumnSelection();
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74 NJTree currentTree = null;
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76 boolean scaleAboveWrapped = true;
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77 boolean scaleLeftWrapped = true;
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78 boolean scaleRightWrapped = true;
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80 // The following vector holds the features which are
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81 // currently visible, in the correct order or rendering
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82 Hashtable featuresDisplayed;
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84 boolean hasHiddenColumns = false;
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85 boolean hasHiddenRows = false;
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86 boolean showHiddenMarkers = true;
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89 public Vector vconsensus;
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90 AlignmentAnnotation consensus;
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91 AlignmentAnnotation conservation;
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92 AlignmentAnnotation quality;
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94 boolean autocalculateConsensus = true;
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96 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
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98 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
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100 boolean ignoreGapsInConsensusCalculation = false;
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102 jalview.bin.JalviewLite applet;
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104 boolean MAC = false;
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106 public AlignViewport(AlignmentI al, JalviewLite applet)
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108 this.applet = applet;
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111 this.endRes = al.getWidth() - 1;
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113 this.endSeq = al.getHeight() - 1;
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116 if(System.getProperty("os.name").startsWith("Mac"))
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119 if (applet != null)
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121 String param = applet.getParameter("showFullId");
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124 showJVSuffix = Boolean.valueOf(param).booleanValue();
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127 param = applet.getParameter("showAnnotation");
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130 showAnnotation = Boolean.valueOf(param).booleanValue();
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133 param = applet.getParameter("showConservation");
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136 showConservation = Boolean.valueOf(param).booleanValue();
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139 param = applet.getParameter("showQuality");
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142 showQuality = Boolean.valueOf(param).booleanValue();
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145 param = applet.getParameter("showConsensus");
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148 showConsensus = Boolean.valueOf(param).booleanValue();
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151 // We must set conservation and consensus before setting colour,
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152 // as Blosum and Clustal require this to be done
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153 updateConservation();
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157 if (applet != null)
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159 String colour = applet.getParameter("defaultColour");
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163 colour = applet.getParameter("userDefinedColour");
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165 colour = "User Defined";
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170 globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
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171 if (globalColourScheme != null)
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173 globalColourScheme.setConsensus(vconsensus);
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177 if(applet.getParameter("userDefinedColour")!=null)
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179 ((UserColourScheme)globalColourScheme).parseAppletParameter(
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180 applet.getParameter("userDefinedColour"));
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187 public void showSequenceFeatures(boolean b)
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189 showSequenceFeatures = b;
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192 public boolean getShowSequenceFeatures()
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194 return showSequenceFeatures;
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198 public void updateConservation()
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200 if(alignment.isNucleotide())
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203 Conservation cons = new jalview.analysis.Conservation("All",
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204 jalview.schemes.ResidueProperties.propHash, 3,
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205 alignment.getSequences(), 0,
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206 alignment.getWidth() - 1);
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208 cons.verdict(false, ConsPercGaps);
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209 cons.findQuality();
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210 int alWidth = alignment.getWidth();
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211 Annotation[] annotations = new Annotation[alWidth];
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212 Annotation[] qannotations = new Annotation[alWidth];
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213 String sequence = cons.getConsSequence().getSequence();
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214 float minR, minG, minB, maxR, maxG, maxB;
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218 maxR = 1.0f - minR;
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219 maxG = 0.9f - minG;
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220 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
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223 float qmin = cons.qualityRange[0].floatValue();
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224 float qmax = cons.qualityRange[1].floatValue();
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226 for (int i = 0; i < alWidth; i++)
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231 value = Integer.parseInt(sequence.charAt(i) + "");
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233 catch (Exception ex)
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235 if (sequence.charAt(i) == '*')
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239 if (sequence.charAt(i) == '+')
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244 float vprop = value - min;
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247 annotations[i] = new Annotation(sequence.charAt(i) + "",
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249 new Color(minR + maxR * vprop,
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250 minG + maxG * vprop,
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251 minB + maxB * vprop));
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253 value = ( (Double) cons.quality.elementAt(i)).floatValue();
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254 vprop = value - qmin;
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256 qannotations[i] = new Annotation(" ",
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257 String.valueOf(value), ' ', value,
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259 Color(minR + maxR * vprop,
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260 minG + maxG * vprop,
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261 minB + maxB * vprop));
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264 if (conservation == null)
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266 conservation = new AlignmentAnnotation("Conservation",
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267 "Conservation of total alignment less than " +
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268 ConsPercGaps + "% gaps",
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270 0f, // cons.qualityRange[0].floatValue(),
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271 11f, // cons.qualityRange[1].floatValue()
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272 AlignmentAnnotation.BAR_GRAPH);
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273 if (showConservation)
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275 alignment.addAnnotation(conservation);
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277 quality = new AlignmentAnnotation("Quality",
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278 "Alignment Quality based on Blosum62 scores",
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280 cons.qualityRange[0].floatValue(),
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281 cons.qualityRange[1].floatValue(),
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282 AlignmentAnnotation.BAR_GRAPH);
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285 alignment.addAnnotation(quality);
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290 conservation.annotations = annotations;
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291 quality.annotations = qannotations;
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292 quality.graphMax = cons.qualityRange[1].floatValue();
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297 public void updateConsensus()
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299 Annotation[] annotations = new Annotation[alignment.getWidth()];
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301 // this routine prevents vconsensus becoming a new object each time
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302 // consenus is calculated. Important for speed of Blosum62
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303 // and PID colouring of alignment
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304 if (vconsensus == null)
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306 vconsensus = alignment.getAAFrequency();
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310 Vector temp = alignment.getAAFrequency();
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311 vconsensus.removeAllElements();
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312 Enumeration e = temp.elements();
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313 while (e.hasMoreElements())
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315 vconsensus.addElement(e.nextElement());
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318 Hashtable hash = null;
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319 for (int i = 0; i < alignment.getWidth(); i++)
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321 hash = (Hashtable) vconsensus.elementAt(i);
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323 if(ignoreGapsInConsensusCalculation)
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324 value = ((Float)hash.get("pid_nogaps")).floatValue();
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326 value = ((Float)hash.get("pid_gaps")).floatValue();
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328 String maxRes = hash.get("maxResidue").toString();
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329 String mouseOver = hash.get("maxResidue") + " ";
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330 if (maxRes.length() > 1)
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332 mouseOver = "[" + maxRes + "] ";
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337 mouseOver += (int) value + "%";
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338 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
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342 if (consensus == null)
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344 consensus = new AlignmentAnnotation("Consensus",
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345 "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
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348 alignment.addAnnotation(consensus);
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353 consensus.annotations = annotations;
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356 if(globalColourScheme!=null)
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357 globalColourScheme.setConsensus(vconsensus);
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361 public SequenceGroup getSelectionGroup()
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363 return selectionGroup;
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366 public void setSelectionGroup(SequenceGroup sg)
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368 selectionGroup = sg;
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371 public boolean getConservationSelected()
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373 return conservationColourSelected;
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376 public void setConservationSelected(boolean b)
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378 conservationColourSelected = b;
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381 public boolean getAbovePIDThreshold()
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383 return abovePIDThreshold;
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386 public void setAbovePIDThreshold(boolean b)
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388 abovePIDThreshold = b;
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391 public int getStartRes()
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396 public int getEndRes()
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401 public int getStartSeq()
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406 public void setGlobalColourScheme(ColourSchemeI cs)
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408 globalColourScheme = cs;
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411 public ColourSchemeI getGlobalColourScheme()
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413 return globalColourScheme;
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416 public void setStartRes(int res)
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418 this.startRes = res;
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421 public void setStartSeq(int seq)
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423 this.startSeq = seq;
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426 public void setEndRes(int res)
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428 if (res > alignment.getWidth() - 1)
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430 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
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431 res = alignment.getWidth() - 1;
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440 public void setEndSeq(int seq)
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442 if (seq > alignment.getHeight())
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444 seq = alignment.getHeight();
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453 public int getEndSeq()
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458 java.awt.Frame nullFrame;
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459 public void setFont(Font f)
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462 if(nullFrame == null)
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464 nullFrame = new java.awt.Frame();
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465 nullFrame.addNotify();
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468 java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
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469 setCharHeight(fm.getHeight());
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470 charWidth = fm.charWidth('M');
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473 public Font getFont()
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478 public int getCharWidth()
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483 public void setCharHeight(int h)
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485 this.charHeight = h;
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488 public int getCharHeight()
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493 public void setWrappedWidth(int w)
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495 this.wrappedWidth = w;
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498 public int getwrappedWidth()
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500 return wrappedWidth;
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503 public AlignmentI getAlignment()
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508 public void setAlignment(AlignmentI align)
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510 this.alignment = align;
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513 public void setWrapAlignment(boolean state)
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515 wrapAlignment = state;
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518 public void setShowText(boolean state)
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523 public void setRenderGaps(boolean state)
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525 renderGaps = state;
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528 public boolean getColourText()
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530 return showColourText;
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533 public void setColourText(boolean state)
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535 showColourText = state;
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538 public void setShowBoxes(boolean state)
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543 public boolean getWrapAlignment()
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545 return wrapAlignment;
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548 public boolean getShowText()
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553 public boolean getShowBoxes()
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558 public char getGapCharacter()
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560 return getAlignment().getGapCharacter();
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563 public void setGapCharacter(char gap)
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565 if (getAlignment() != null)
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567 getAlignment().setGapCharacter(gap);
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571 public void setThreshold(int thresh)
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573 threshold = thresh;
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576 public int getThreshold()
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581 public void setIncrement(int inc)
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586 public int getIncrement()
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591 public void setHiddenColumns(ColumnSelection colsel)
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593 this.colSel = colsel;
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594 if(colSel.getHiddenColumns()!=null)
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595 hasHiddenColumns = true;
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598 public ColumnSelection getColumnSelection()
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603 public void resetSeqLimits(int height)
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605 setEndSeq(height / getCharHeight());
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608 public void setCurrentTree(NJTree tree)
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610 currentTree = tree;
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613 public NJTree getCurrentTree()
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615 return currentTree;
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618 public void setColourAppliesToAllGroups(boolean b)
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620 colourAppliesToAllGroups = b;
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623 public boolean getColourAppliesToAllGroups()
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625 return colourAppliesToAllGroups;
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628 public boolean getShowJVSuffix()
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630 return showJVSuffix;
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633 public void setShowJVSuffix(boolean b)
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638 public boolean getShowAnnotation()
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640 return showAnnotation;
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643 public void setShowAnnotation(boolean b)
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645 showAnnotation = b;
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648 public boolean getScaleAboveWrapped()
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650 return scaleAboveWrapped;
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653 public boolean getScaleLeftWrapped()
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655 return scaleLeftWrapped;
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658 public boolean getScaleRightWrapped()
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660 return scaleRightWrapped;
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663 public void setScaleAboveWrapped(boolean b)
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665 scaleAboveWrapped = b;
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668 public void setScaleLeftWrapped(boolean b)
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670 scaleLeftWrapped = b;
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673 public void setScaleRightWrapped(boolean b)
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675 scaleRightWrapped = b;
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678 public void setIgnoreGapsConsensus(boolean b)
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680 ignoreGapsInConsensusCalculation = b;
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682 if (globalColourScheme!=null)
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684 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
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685 ignoreGapsInConsensusCalculation);
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691 * Property change listener for changes in alignment
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693 * @param listener DOCUMENT ME!
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695 public void addPropertyChangeListener(
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696 java.beans.PropertyChangeListener listener)
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698 changeSupport.addPropertyChangeListener(listener);
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704 * @param listener DOCUMENT ME!
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706 public void removePropertyChangeListener(
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707 java.beans.PropertyChangeListener listener)
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709 changeSupport.removePropertyChangeListener(listener);
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713 * Property change listener for changes in alignment
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715 * @param prop DOCUMENT ME!
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716 * @param oldvalue DOCUMENT ME!
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717 * @param newvalue DOCUMENT ME!
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719 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
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721 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
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726 public boolean getIgnoreGapsConsensus()
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728 return ignoreGapsInConsensusCalculation;
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730 public void hideSelectedColumns()
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732 if (colSel.size() < 1)
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735 colSel.hideSelectedColumns();
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736 setSelectionGroup(null);
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738 hasHiddenColumns = true;
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741 public void invertColumnSelection()
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744 for (int i = 0; i < alignment.getWidth(); i++)
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748 if (colSel.contains(column))
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749 colSel.removeElement(column);
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751 colSel.addElement(column);
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757 public void hideColumns(int start, int end)
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760 colSel.hideColumns(start);
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762 colSel.hideColumns(start, end);
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764 hasHiddenColumns = true;
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767 public void hideSequence(SequenceI seq)
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771 alignment.getHiddenSequences().hideSequence(seq);
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772 hasHiddenRows = true;
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773 firePropertyChange("alignment", null, alignment.getSequences());
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777 public void hideAllSelectedSeqs()
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779 if (selectionGroup == null)
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782 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
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784 for (int i = 0; i < seqs.length; i++)
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786 alignment.getHiddenSequences().hideSequence(seqs[i]);
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788 firePropertyChange("alignment", null, alignment.getSequences());
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789 hasHiddenRows = true;
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790 setSelectionGroup(null);
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793 public void showColumn(int col)
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795 colSel.revealHiddenColumns(col);
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796 if(colSel.getHiddenColumns()==null)
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797 hasHiddenColumns = false;
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800 public void showAllHiddenColumns()
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802 colSel.revealAllHiddenColumns();
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803 hasHiddenColumns = false;
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806 public void showAllHiddenSeqs()
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808 if(alignment.getHiddenSequences().getSize()>0)
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810 if(selectionGroup==null)
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812 selectionGroup = new SequenceGroup();
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813 selectionGroup.setEndRes(alignment.getWidth()-1);
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815 Vector tmp = alignment.getHiddenSequences().showAll();
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816 for(int t=0; t<tmp.size(); t++)
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818 selectionGroup.addSequence(
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819 (SequenceI)tmp.elementAt(t), false
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822 firePropertyChange("alignment", null, alignment.getSequences());
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823 hasHiddenRows = false;
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827 public int adjustForHiddenSeqs(int alignmentIndex)
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829 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
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833 * This method returns the a new SequenceI [] with
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834 * the selection sequence and start and end points adjusted
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837 public SequenceI[] getSelectionAsNewSequence()
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839 SequenceI[] sequences;
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841 if (selectionGroup == null)
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842 sequences = alignment.getSequencesArray();
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844 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
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850 * This method returns the visible alignment as text, as
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851 * seen on the GUI, ie if columns are hidden they will not
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852 * be returned in the result.
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853 * Use this for calculating trees, PCA, redundancy etc on views
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854 * which contain hidden columns.
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857 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
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859 CigarArray selection=null;
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860 SequenceI [] seqs= null;
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862 int start = 0, end = 0;
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863 if(selectedRegionOnly && selectionGroup!=null)
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865 iSize = selectionGroup.getSize(false);
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866 seqs = selectionGroup.getSequencesInOrder(alignment);
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867 start = selectionGroup.getStartRes();
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868 end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
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872 iSize = alignment.getHeight();
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873 seqs = alignment.getSequencesArray();
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874 end = alignment.getWidth()-1;
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876 SeqCigar[] selseqs = new SeqCigar[iSize];
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877 for(i=0; i<iSize; i++)
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879 selseqs[i] = new SeqCigar(seqs[i], start, end);
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881 selection=new CigarArray(selseqs);
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882 // now construct the CigarArray operations
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883 if (hasHiddenColumns) {
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884 Vector regions = colSel.getHiddenColumns();
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886 int hideStart, hideEnd;
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888 for (int j = 0; last<end & j < regions.size(); j++)
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890 region = (int[]) regions.elementAt(j);
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891 hideStart = region[0];
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892 hideEnd = region[1];
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893 // edit hidden regions to selection range
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894 if(hideStart<last) {
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895 if (hideEnd > last)
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908 if (hideStart>hideEnd)
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911 * form operations...
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913 if (last<hideStart)
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914 selection.addOperation(CigarArray.M, hideStart-last);
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915 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
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918 // Final match if necessary.
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920 selection.addOperation(CigarArray.M, end-last);
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922 selection.addOperation(CigarArray.M, end-start);
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927 * return a compact representation of the current alignment selection to
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928 * pass to an analysis function
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929 * @param selectedOnly boolean true to just return the selected view
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930 * @return AlignmentView
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932 jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
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934 // this is here because the AlignmentView constructor modifies the CigarArray
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935 // object. Refactoring of Cigar and alignment view representation should
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936 // be done to remove redundancy.
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937 CigarArray aligview = getViewAsCigars(selectedOnly);
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938 if (aligview!=null)
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939 return new AlignmentView(aligview);
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943 * This method returns the visible alignment as text, as
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944 * seen on the GUI, ie if columns are hidden they will not
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945 * be returned in the result.
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946 * Use this for calculating trees, PCA, redundancy etc on views
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947 * which contain hidden columns.
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950 public String [] getViewAsString(boolean selectedRegionOnly)
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952 String [] selection = null;
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953 SequenceI [] seqs= null;
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955 int start = 0, end = 0;
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956 if(selectedRegionOnly && selectionGroup!=null)
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958 iSize = selectionGroup.getSize(false);
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959 seqs = selectionGroup.getSequencesInOrder(alignment);
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960 start = selectionGroup.getStartRes();
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961 end = selectionGroup.getEndRes()+1;
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965 iSize = alignment.getHeight();
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966 seqs = alignment.getSequencesArray();
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967 end = alignment.getWidth();
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970 selection = new String[iSize];
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973 for(i=0; i<iSize; i++)
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975 if (hasHiddenColumns)
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977 StringBuffer visibleSeq = new StringBuffer();
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978 Vector regions = colSel.getHiddenColumns();
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980 int blockStart = start, blockEnd=end;
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982 int hideStart, hideEnd;
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984 for (int j = 0; j < regions.size(); j++)
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986 region = (int[]) regions.elementAt(j);
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987 hideStart = region[0];
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988 hideEnd = region[1];
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990 if(hideStart < start)
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995 blockStart = Math.min(blockStart, hideEnd+1);
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996 blockEnd = Math.min(blockEnd, hideStart);
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998 if(blockStart>blockEnd)
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1004 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
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1006 blockStart = hideEnd+1;
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1010 if(end>blockStart)
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1011 visibleSeq.append(seqs[i].getSequence(blockStart, end));
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1013 selection[i] = visibleSeq.toString();
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1017 selection[i] = seqs[i].getSequence(start, end);
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1024 public boolean getShowHiddenMarkers()
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1026 return showHiddenMarkers;
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1029 public void setShowHiddenMarkers(boolean show)
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1031 showHiddenMarkers = show;
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