2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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24 import jalview.analysis.*;
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25 import jalview.datamodel.*;
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26 import jalview.schemes.*;
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28 public class AnnotationFile
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30 StringBuffer text = new StringBuffer("JALVIEW_ANNOTATION\n"
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31 + "# Created: " + new java.util.Date() + "\n\n");
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34 * convenience method for pre-2.4 feature files which have no view, hidden
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35 * columns or hidden row keywords.
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37 * @param annotations
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40 * @return feature file as a string.
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42 public String printAnnotations(AlignmentAnnotation[] annotations,
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43 Vector groups, Hashtable properties)
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45 return printAnnotations(annotations, groups, properties, null);
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50 * hold all the information about a particular view definition read from or
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51 * written out in an annotations file.
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53 public class ViewDef
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55 public String viewname;
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57 public HiddenSequences hidseqs;
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59 public ColumnSelection hiddencols;
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61 public Vector visibleGroups;
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63 public Hashtable hiddenRepSeqs;
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65 public ViewDef(String viewname, HiddenSequences hidseqs,
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66 ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
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68 this.viewname = viewname;
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69 this.hidseqs = hidseqs;
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70 this.hiddencols = hiddencols;
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71 this.hiddenRepSeqs = hiddenRepSeqs;
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76 * Prepare an annotation file given a set of annotations, groups, alignment
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77 * properties and views.
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79 * @param annotations
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83 * @return annotation file
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85 public String printAnnotations(AlignmentAnnotation[] annotations,
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86 Vector groups, Hashtable properties, ViewDef[] views)
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88 // TODO: resolve views issue : annotationFile could contain visible region,
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89 // or full data + hidden region specifications for a view.
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90 if (annotations != null)
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92 boolean oneColour = true;
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93 AlignmentAnnotation row;
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95 SequenceI refSeq = null;
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96 SequenceGroup refGroup = null;
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98 StringBuffer colours = new StringBuffer();
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99 StringBuffer graphLine = new StringBuffer();
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100 StringBuffer rowprops = new StringBuffer();
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101 Hashtable graphGroup = new Hashtable();
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103 java.awt.Color color;
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105 for (int i = 0; i < annotations.length; i++)
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107 row = annotations[i];
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109 if (!row.visible && !row.hasScore())
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117 if (row.sequenceRef == null)
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119 if (refSeq != null)
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121 text.append("\nSEQUENCE_REF\tALIGNMENT\n");
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129 if (refSeq == null || refSeq != row.sequenceRef)
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131 refSeq = row.sequenceRef;
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132 text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
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135 // mark any group references for the row
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136 if (row.groupRef == null)
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139 if (refGroup != null)
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141 text.append("\nGROUP_REF\tALIGNMENT\n");
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148 if (refGroup == null || refGroup != row.groupRef)
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150 refGroup = row.groupRef;
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151 text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");
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155 boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
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156 // lookahead to check what the annotation row object actually contains.
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157 for (int j = 0; row.annotations != null
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158 && j < row.annotations.length
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159 && (!hasGlyphs || !hasLabels || !hasValues); j++)
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161 if (row.annotations[j] != null)
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163 hasLabels |= (row.annotations[j].displayCharacter != null
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164 && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
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166 hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
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167 hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
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170 hasText |= (row.annotations[j].description != null && row.annotations[j].description
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175 if (row.graph == AlignmentAnnotation.NO_GRAPH)
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177 text.append("NO_GRAPH\t");
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178 hasValues = false; // only secondary structure
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179 // hasLabels = false; // and annotation description string.
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183 if (row.graph == AlignmentAnnotation.BAR_GRAPH)
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185 text.append("BAR_GRAPH\t");
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186 hasGlyphs = false; // no secondary structure
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189 else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
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191 hasGlyphs = false; // no secondary structure
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192 text.append("LINE_GRAPH\t");
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195 if (row.getThreshold() != null)
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198 .append("GRAPHLINE\t"
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201 + row.getThreshold().value
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203 + row.getThreshold().label
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205 + jalview.util.Format.getHexString(row
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206 .getThreshold().colour) + "\n");
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209 if (row.graphGroup > -1)
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211 String key = String.valueOf(row.graphGroup);
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212 if (graphGroup.containsKey(key))
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214 graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
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218 graphGroup.put(key, row.label);
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223 text.append(row.label + "\t");
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224 if (row.description != null)
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226 text.append(row.description + "\t");
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228 for (int j = 0; row.annotations != null
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229 && j < row.annotations.length; j++)
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232 && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
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237 if (row.annotations[j] != null)
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240 if (hasGlyphs) // could be also hasGlyphs || ...
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243 text.append(comma);
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244 if (row.annotations[j].secondaryStructure != ' ')
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246 // only write out the field if its not whitespace.
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247 text.append(row.annotations[j].secondaryStructure);
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253 if (row.annotations[j].value != Float.NaN)
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255 text.append(comma + row.annotations[j].value);
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259 System.err.println("Skipping NaN - not valid value.");
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260 text.append(comma + 0f);// row.annotations[j].value);
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266 // TODO: labels are emitted after values for bar graphs.
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267 if // empty labels are allowed, so
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268 (row.annotations[j].displayCharacter != null
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269 && row.annotations[j].displayCharacter.length() > 0
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270 && !row.annotations[j].displayCharacter.equals(" "))
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272 text.append(comma + row.annotations[j].displayCharacter);
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278 if (row.annotations[j].description != null
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279 && row.annotations[j].description.length() > 0
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280 && !row.annotations[j].description
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281 .equals(row.annotations[j].displayCharacter))
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283 text.append(comma + row.annotations[j].description);
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287 if (color != null && !color.equals(row.annotations[j].colour))
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292 color = row.annotations[j].colour;
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294 if (row.annotations[j].colour != null
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295 && row.annotations[j].colour != java.awt.Color.black)
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299 + jalview.util.Format
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300 .getHexString(row.annotations[j].colour)
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308 if (row.hasScore())
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309 text.append("\t" + row.score);
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313 if (color != null && color != java.awt.Color.black && oneColour)
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315 colours.append("COLOUR\t" + row.label + "\t"
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316 + jalview.util.Format.getHexString(color) + "\n");
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318 if (row.scaleColLabel || row.showAllColLabels
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319 || row.centreColLabels)
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321 rowprops.append("ROWPROPERTIES\t" + row.label);
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322 rowprops.append("\tscaletofit=" + row.scaleColLabel);
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323 rowprops.append("\tshowalllabs=" + row.showAllColLabels);
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324 rowprops.append("\tcentrelabs=" + row.centreColLabels);
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325 rowprops.append("\n");
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331 text.append(colours.toString());
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332 text.append(graphLine.toString());
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333 if (graphGroup.size() > 0)
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335 text.append("COMBINE\t");
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336 Enumeration en = graphGroup.elements();
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337 while (en.hasMoreElements())
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339 text.append(en.nextElement() + "\n");
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342 text.append(rowprops.toString());
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345 if (groups != null)
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347 printGroups(groups);
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350 if (properties != null)
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352 text.append("\n\nALIGNMENT");
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353 Enumeration en = properties.keys();
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354 while (en.hasMoreElements())
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356 String key = en.nextElement().toString();
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357 text.append("\t" + key + "=" + properties.get(key));
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359 // TODO: output alignment visualization settings here if required
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363 return text.toString();
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366 public void printGroups(Vector sequenceGroups)
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369 SequenceI seqrep = null;
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370 for (int i = 0; i < sequenceGroups.size(); i++)
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372 sg = (SequenceGroup) sequenceGroups.elementAt(i);
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373 if (!sg.hasSeqrep())
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375 text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
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376 + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
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382 seqrep = sg.getSeqrep();
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383 text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");
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384 text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
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385 + (seqrep.findPosition(sg.getStartRes())) + "\t"
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386 + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");
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388 for (int s = 0; s < sg.getSize(); s++)
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390 text.append(sg.getSequenceAt(s).getName() + "\t");
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393 text.append("\nPROPERTIES\t" + sg.getName() + "\t");
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395 if (sg.getDescription() != null)
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397 text.append("description=" + sg.getDescription() + "\t");
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401 text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)
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403 if (sg.cs.getThreshold() != 0)
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405 text.append("pidThreshold=" + sg.cs.getThreshold());
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407 if (sg.cs.conservationApplied())
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409 text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
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412 text.append("outlineColour="
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413 + jalview.util.Format.getHexString(sg.getOutlineColour())
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416 text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
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417 text.append("displayText=" + sg.getDisplayText() + "\t");
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418 text.append("colourText=" + sg.getColourText() + "\t");
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419 text.append("showUnconserved=" + sg.getShowNonconserved() + "\t");
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420 if (sg.textColour != java.awt.Color.black)
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422 text.append("textCol1="
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423 + jalview.util.Format.getHexString(sg.textColour) + "\t");
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425 if (sg.textColour2 != java.awt.Color.white)
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427 text.append("textCol2="
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428 + jalview.util.Format.getHexString(sg.textColour2) + "\t");
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430 if (sg.thresholdTextColour != 0)
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432 text.append("textColThreshold=" + sg.thresholdTextColour + "\t");
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434 if (sg.idColour != null)
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436 text.append("idColour="
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437 + jalview.util.Format.getHexString(sg.idColour) + "\t");
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439 if (sg.isHidereps())
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441 text.append("hide=true\t");
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443 if (sg.isHideCols())
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445 text.append("hidecols=true\t");
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447 if (seqrep != null)
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449 // terminate the last line and clear the sequence ref for the group
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450 text.append("\nSEQUENCE_REF");
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452 text.append("\n\n");
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457 SequenceI refSeq = null;
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459 String refSeqId = null;
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461 public boolean readAnnotationFile(AlignmentI al, String file,
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464 BufferedReader in = null;
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467 if (protocol.equals(AppletFormatAdapter.FILE))
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469 in = new BufferedReader(new FileReader(file));
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471 else if (protocol.equals(AppletFormatAdapter.URL))
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473 URL url = new URL(file);
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474 in = new BufferedReader(new InputStreamReader(url.openStream()));
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476 else if (protocol.equals(AppletFormatAdapter.PASTE))
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478 in = new BufferedReader(new StringReader(file));
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480 else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
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482 java.io.InputStream is = getClass().getResourceAsStream("/" + file);
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485 in = new BufferedReader(new java.io.InputStreamReader(is));
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490 return parseAnnotationFrom(al, in);
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493 } catch (Exception ex)
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495 ex.printStackTrace();
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496 System.out.println("Problem reading annotation file: " + ex);
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502 public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
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505 boolean modified=false;
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506 String groupRef = null;
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507 Hashtable groupRefRows = new Hashtable();
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509 Hashtable autoAnnots = new Hashtable();
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511 String line, label, description, token;
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512 int graphStyle, index;
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513 int refSeqIndex = 1;
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514 int existingAnnotations = 0;
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515 // when true - will add new rows regardless of whether they are duplicate
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516 // auto-annotation like consensus or conservation graphs
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517 boolean overrideAutoAnnot = false;
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518 if (al.getAlignmentAnnotation() != null)
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520 existingAnnotations = al.getAlignmentAnnotation().length;
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521 if (existingAnnotations > 0)
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523 AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
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524 for (int aai = 0; aai < aa.length; aai++)
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526 if (aa[aai].autoCalculated)
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528 // make a note of the name and description
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530 .put(autoAnnotsKey(aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef==null ? null : aa[aai].groupRef.getName())
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538 int alWidth = al.getWidth();
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540 StringTokenizer st;
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541 Annotation[] annotations;
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542 AlignmentAnnotation annotation = null;
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544 // First confirm this is an Annotation file
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545 boolean jvAnnotationFile = false;
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546 while ((line = in.readLine()) != null)
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548 if (line.indexOf("#") == 0)
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553 if (line.indexOf("JALVIEW_ANNOTATION") > -1)
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555 jvAnnotationFile = true;
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560 if (!jvAnnotationFile)
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566 while ((line = in.readLine()) != null)
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568 if (line.indexOf("#") == 0
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569 || line.indexOf("JALVIEW_ANNOTATION") > -1
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570 || line.length() == 0)
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575 st = new StringTokenizer(line, "\t");
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576 token = st.nextToken();
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577 if (token.equalsIgnoreCase("COLOUR"))
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579 // TODO: use graduated colour def'n here too
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580 colourAnnotations(al, st.nextToken(), st.nextToken());
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581 modified=true;continue;
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584 else if (token.equalsIgnoreCase("COMBINE"))
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586 combineAnnotations(al, st);
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587 modified=true;continue;
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589 else if (token.equalsIgnoreCase("ROWPROPERTIES"))
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591 addRowProperties(al, st);
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592 modified=true;continue;
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594 else if (token.equalsIgnoreCase("GRAPHLINE"))
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601 else if (token.equalsIgnoreCase("SEQUENCE_REF"))
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603 if (st.hasMoreTokens())
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605 refSeq = al.findName(refSeqId = st.nextToken());
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606 if (refSeq == null)
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612 refSeqIndex = Integer.parseInt(st.nextToken());
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613 if (refSeqIndex < 1)
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617 .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
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619 } catch (Exception ex)
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631 else if (token.equalsIgnoreCase("GROUP_REF"))
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633 // Group references could be forward or backwards, so they are
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634 // resolved after the whole file is read in
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636 if (st.hasMoreTokens())
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638 groupRef = st.nextToken();
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639 if (groupRef.length() < 1)
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641 groupRef = null; // empty string
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645 if (groupRefRows.get(groupRef) == null)
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647 groupRefRows.put(groupRef, new Vector());
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653 else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
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659 else if (token.equalsIgnoreCase("PROPERTIES"))
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661 addProperties(al, st);
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662 modified=true; continue;
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665 else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
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667 setBelowAlignment(al, st);
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668 modified=true;continue;
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670 else if (token.equalsIgnoreCase("ALIGNMENT"))
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672 addAlignmentDetails(al, st);
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673 modified=true;continue;
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676 // Parse out the annotation row
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677 graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
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678 label = st.nextToken();
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681 annotations = new Annotation[alWidth];
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682 description = null;
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683 float score = Float.NaN;
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685 if (st.hasMoreTokens())
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687 line = st.nextToken();
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689 if (line.indexOf("|") == -1)
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691 description = line;
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692 if (st.hasMoreTokens())
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693 line = st.nextToken();
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696 if (st.hasMoreTokens())
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698 // This must be the score
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699 score = Float.valueOf(st.nextToken()).floatValue();
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702 st = new StringTokenizer(line, "|", true);
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704 boolean emptyColumn = true;
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705 boolean onlyOneElement = (st.countTokens() == 1);
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707 while (st.hasMoreElements() && index < alWidth)
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709 token = st.nextToken().trim();
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711 if (onlyOneElement)
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715 score = Float.valueOf(token).floatValue();
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717 } catch (NumberFormatException ex)
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722 if (token.equals("|"))
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729 emptyColumn = true;
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733 annotations[index++] = parseAnnotation(token, graphStyle);
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734 emptyColumn = false;
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740 annotation = new AlignmentAnnotation(label, description,
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741 (index == 0) ? null : annotations, 0, 0, graphStyle);
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743 annotation.score = score;
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744 if (!overrideAutoAnnot
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746 .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
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748 // skip - we've already got an automatic annotation of this type.
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751 // otherwise add it!
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752 if (refSeq != null)
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755 annotation.belowAlignment = false;
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756 // make a copy of refSeq so we can find other matches in the alignment
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757 SequenceI referedSeq = refSeq;
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760 // copy before we do any mapping business.
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761 // TODO: verify that undo/redo with 1:many sequence associated
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762 // annotations can be undone correctly
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763 AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
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765 .createSequenceMapping(referedSeq, refSeqIndex, false);
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766 annotation.adjustForAlignment();
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767 referedSeq.addAlignmentAnnotation(annotation);
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768 al.addAnnotation(annotation);
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769 al.setAnnotationIndex(annotation,
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770 al.getAlignmentAnnotation().length
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771 - existingAnnotations - 1);
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772 if (groupRef != null)
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774 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
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776 // and recover our virgin copy to use again if necessary.
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779 } while (refSeqId != null
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780 && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
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784 al.addAnnotation(annotation);
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785 al.setAnnotationIndex(annotation,
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786 al.getAlignmentAnnotation().length - existingAnnotations
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788 if (groupRef != null)
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790 ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
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793 // and set modification flag
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796 // Finally, resolve the groupRefs
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797 Enumeration en = groupRefRows.keys();
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798 SequenceGroup theGroup = null;
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800 while (en.hasMoreElements())
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802 groupRef = (String) en.nextElement();
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803 boolean matched = false;
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804 // Resolve group: TODO: add a getGroupByName method to alignments
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805 Vector grps = al.getGroups();
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806 for (int g = 0, gSize = grps.size(); g < gSize; g++)
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808 theGroup = (SequenceGroup) grps.elementAt(g);
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809 if (theGroup.getName().equals(groupRef))
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813 // TODO: specify and implement duplication of alignment annotation
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814 // for multiple group references.
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816 .println("Ignoring 1:many group reference mappings for group name '"
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822 Vector rowset = (Vector) groupRefRows.get(groupRef);
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823 if (rowset != null && rowset.size() > 0)
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825 AlignmentAnnotation alan = null;
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826 for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
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828 alan = (AlignmentAnnotation) rowset.elementAt(elm);
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829 alan.groupRef = theGroup;
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835 ((Vector) groupRefRows.get(groupRef)).removeAllElements();
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841 private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef)
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843 return annotation.graph
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847 + annotation.description
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849 + (refSeq != null ? refSeq
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850 .getDisplayId(true) : "");
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853 Annotation parseAnnotation(String string, int graphStyle)
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855 boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
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864 String desc = null, displayChar = null;
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865 char ss = ' '; // secondaryStructure
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867 boolean parsedValue = false, dcset = false;
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869 // find colour here
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870 java.awt.Color colour = null;
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871 int i = string.indexOf("[");
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872 int j = string.indexOf("]");
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873 if (i > -1 && j > -1)
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875 UserColourScheme ucs = new UserColourScheme();
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877 colour = ucs.getColourFromString(string.substring(i + 1, j));
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878 if (i > 0 && string.charAt(i - 1) == ',')
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880 // clip the preceding comma as well
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883 string = string.substring(0, i) + string.substring(j + 1);
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886 StringTokenizer st = new StringTokenizer(string, ",", true);
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888 boolean seenContent = false;
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890 while (st.hasMoreTokens())
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893 token = st.nextToken().trim();
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894 if (token.equals(","))
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896 if (!seenContent && parsedValue && !dcset)
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898 // allow the value below the bar/line to be empty
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902 seenContent = false;
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907 seenContent = true;
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914 displayChar = token;
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916 value = new Float(token).floatValue();
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917 parsedValue = true;
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919 } catch (NumberFormatException ex)
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925 if (token.length() == 1)
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927 displayChar = token;
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931 && (token.equals("H") || token.equals("E") || token
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934 // Either this character represents a helix or sheet
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935 // or an integer which can be displayed
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936 ss = token.charAt(0);
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937 if (displayChar.equals(token.substring(0, 1)))
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942 else if (desc == null || (parsedValue && pass > 2))
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948 // if (!dcset && string.charAt(string.length() - 1) == ',')
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950 // displayChar = " "; // empty display char symbol.
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952 if (displayChar != null && desc != null && desc.length() == 1)
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954 if (displayChar.length() > 1)
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956 // switch desc and displayChar - legacy support
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957 String tmp = displayChar;
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958 displayChar = desc;
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963 if (displayChar.equals(desc))
\r
965 // duplicate label - hangover from the 'robust parser' above
\r
970 Annotation anot = new Annotation(displayChar, desc, ss, value);
\r
972 anot.colour = colour;
\r
977 void colourAnnotations(AlignmentI al, String label, String colour)
\r
979 UserColourScheme ucs = new UserColourScheme(colour);
\r
980 Annotation[] annotations;
\r
981 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
983 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
\r
985 annotations = al.getAlignmentAnnotation()[i].annotations;
\r
986 for (int j = 0; j < annotations.length; j++)
\r
988 if (annotations[j] != null)
\r
990 annotations[j].colour = ucs.findColour('A');
\r
997 void combineAnnotations(AlignmentI al, StringTokenizer st)
\r
999 int graphGroup = -1;
\r
1000 String group = st.nextToken();
\r
1001 // First make sure we are not overwriting the graphIndex
\r
1002 if (al.getAlignmentAnnotation() != null)
\r
1004 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
1006 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
\r
1008 graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
\r
1009 al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
\r
1014 // Now update groups
\r
1015 while (st.hasMoreTokens())
\r
1017 group = st.nextToken();
\r
1018 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
1020 if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
\r
1022 al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
\r
1031 .println("Couldn't combine annotations. None are added to alignment yet!");
\r
1035 void addLine(AlignmentI al, StringTokenizer st)
\r
1037 String group = st.nextToken();
\r
1038 AlignmentAnnotation annotation = null, alannot[] = al
\r
1039 .getAlignmentAnnotation();
\r
1040 if (alannot != null)
\r
1042 for (int i = 0; i < alannot.length; i++)
\r
1044 if (alannot[i].label.equalsIgnoreCase(group))
\r
1046 annotation = alannot[i];
\r
1051 if (annotation == null)
\r
1055 float value = new Float(st.nextToken()).floatValue();
\r
1056 String label = st.hasMoreTokens() ? st.nextToken() : null;
\r
1057 java.awt.Color colour = null;
\r
1058 if (st.hasMoreTokens())
\r
1060 UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
1061 colour = ucs.findColour('A');
\r
1064 annotation.setThreshold(new GraphLine(value, label, colour));
\r
1067 void addGroup(AlignmentI al, StringTokenizer st)
\r
1069 SequenceGroup sg = new SequenceGroup();
\r
1070 sg.setName(st.nextToken());
\r
1074 rng = st.nextToken();
\r
1075 if (rng.length() > 0 && !rng.startsWith("*"))
\r
1077 sg.setStartRes(Integer.parseInt(rng) - 1);
\r
1081 sg.setStartRes(0);
\r
1083 rng = st.nextToken();
\r
1084 if (rng.length() > 0 && !rng.startsWith("*"))
\r
1086 sg.setEndRes(Integer.parseInt(rng) - 1);
\r
1090 sg.setEndRes(al.getWidth() - 1);
\r
1092 } catch (Exception e)
\r
1095 .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
\r
1096 + rng + "' - assuming alignment width for group.");
\r
1097 // assume group is full width
\r
1098 sg.setStartRes(0);
\r
1099 sg.setEndRes(al.getWidth() - 1);
\r
1102 String index = st.nextToken();
\r
1103 if (index.equals("-1"))
\r
1105 while (st.hasMoreElements())
\r
1107 sg.addSequence(al.findName(st.nextToken()), false);
\r
1112 StringTokenizer st2 = new StringTokenizer(index, ",");
\r
1114 while (st2.hasMoreTokens())
\r
1116 String tmp = st2.nextToken();
\r
1117 if (tmp.equals("*"))
\r
1119 for (int i = 0; i < al.getHeight(); i++)
\r
1121 sg.addSequence(al.getSequenceAt(i), false);
\r
1124 else if (tmp.indexOf("-") >= 0)
\r
1126 StringTokenizer st3 = new StringTokenizer(tmp, "-");
\r
1128 int start = (Integer.parseInt(st3.nextToken()));
\r
1129 int end = (Integer.parseInt(st3.nextToken()));
\r
1133 for (int i = start; i <= end; i++)
\r
1135 sg.addSequence(al.getSequenceAt(i - 1), false);
\r
1141 sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
\r
1146 if (refSeq != null)
\r
1148 sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
\r
1149 sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
\r
1150 sg.setSeqrep(refSeq);
\r
1153 if (sg.getSize() > 0)
\r
1159 void addRowProperties(AlignmentI al, StringTokenizer st)
\r
1161 String label = st.nextToken(), keyValue, key, value;
\r
1162 boolean scaletofit = false, centerlab = false, showalllabs = false;
\r
1163 while (st.hasMoreTokens())
\r
1165 keyValue = st.nextToken();
\r
1166 key = keyValue.substring(0, keyValue.indexOf("="));
\r
1167 value = keyValue.substring(keyValue.indexOf("=") + 1);
\r
1168 if (key.equalsIgnoreCase("scaletofit"))
\r
1170 scaletofit = Boolean.valueOf(value).booleanValue();
\r
1172 if (key.equalsIgnoreCase("showalllabs"))
\r
1174 showalllabs = Boolean.valueOf(value).booleanValue();
\r
1176 if (key.equalsIgnoreCase("centrelabs"))
\r
1178 centerlab = Boolean.valueOf(value).booleanValue();
\r
1180 AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
\r
1183 for (int i = 0; i < alr.length; i++)
\r
1185 if (alr[i].label.equalsIgnoreCase(label))
\r
1187 alr[i].centreColLabels = centerlab;
\r
1188 alr[i].scaleColLabel = scaletofit;
\r
1189 alr[i].showAllColLabels = showalllabs;
\r
1196 void addProperties(AlignmentI al, StringTokenizer st)
\r
1199 // So far we have only added groups to the annotationHash,
\r
1200 // the idea is in the future properties can be added to
\r
1201 // alignments, other annotations etc
\r
1202 if (al.getGroups() == null)
\r
1206 SequenceGroup sg = null;
\r
1208 String name = st.nextToken();
\r
1210 Vector groups = al.getGroups();
\r
1211 for (int i = 0; i < groups.size(); i++)
\r
1213 sg = (SequenceGroup) groups.elementAt(i);
\r
1214 if (sg.getName().equals(name))
\r
1226 String keyValue, key, value;
\r
1227 ColourSchemeI def = sg.cs;
\r
1229 while (st.hasMoreTokens())
\r
1231 keyValue = st.nextToken();
\r
1232 key = keyValue.substring(0, keyValue.indexOf("="));
\r
1233 value = keyValue.substring(keyValue.indexOf("=") + 1);
\r
1235 if (key.equalsIgnoreCase("description"))
\r
1237 sg.setDescription(value);
\r
1239 else if (key.equalsIgnoreCase("colour"))
\r
1241 sg.cs = ColourSchemeProperty.getColour(al, value);
\r
1243 else if (key.equalsIgnoreCase("pidThreshold"))
\r
1245 sg.cs.setThreshold(Integer.parseInt(value), true);
\r
1248 else if (key.equalsIgnoreCase("consThreshold"))
\r
1250 sg.cs.setConservationInc(Integer.parseInt(value));
\r
1251 Conservation c = new Conservation("Group",
\r
1252 ResidueProperties.propHash, 3, sg.getSequences(null),
\r
1253 sg.getStartRes(), sg.getEndRes() + 1);
\r
1256 c.verdict(false, 25);
\r
1258 sg.cs.setConservation(c);
\r
1261 else if (key.equalsIgnoreCase("outlineColour"))
\r
1263 sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
\r
1265 else if (key.equalsIgnoreCase("displayBoxes"))
\r
1267 sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
\r
1269 else if (key.equalsIgnoreCase("showUnconserved"))
\r
1271 sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
\r
1273 else if (key.equalsIgnoreCase("displayText"))
\r
1275 sg.setDisplayText(Boolean.valueOf(value).booleanValue());
\r
1277 else if (key.equalsIgnoreCase("colourText"))
\r
1279 sg.setColourText(Boolean.valueOf(value).booleanValue());
\r
1281 else if (key.equalsIgnoreCase("textCol1"))
\r
1283 sg.textColour = new UserColourScheme(value).findColour('A');
\r
1285 else if (key.equalsIgnoreCase("textCol2"))
\r
1287 sg.textColour2 = new UserColourScheme(value).findColour('A');
\r
1289 else if (key.equalsIgnoreCase("textColThreshold"))
\r
1291 sg.thresholdTextColour = Integer.parseInt(value);
\r
1293 else if (key.equalsIgnoreCase("idColour"))
\r
1295 // consider warning if colour doesn't resolve to a real colour
\r
1296 sg.setIdColour((def = new UserColourScheme(value))
\r
1297 .findColour('A'));
\r
1299 else if (key.equalsIgnoreCase("hide"))
\r
1301 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
\r
1302 sg.setHidereps(true);
\r
1304 else if (key.equalsIgnoreCase("hidecols"))
\r
1306 // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
\r
1307 sg.setHideCols(true);
\r
1309 sg.recalcConservation();
\r
1311 if (sg.cs == null)
\r
1318 void setBelowAlignment(AlignmentI al, StringTokenizer st)
\r
1321 AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
\r
1325 .print("Warning - no annotation to set below for sequence associated annotation:");
\r
1327 while (st.hasMoreTokens())
\r
1329 token = st.nextToken();
\r
1332 System.err.print(" " + token);
\r
1336 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
\r
1338 aa = al.getAlignmentAnnotation()[i];
\r
1339 if (aa.sequenceRef == refSeq && aa.label.equals(token))
\r
1341 aa.belowAlignment = true;
\r
1348 System.err.print("\n");
\r
1352 void addAlignmentDetails(AlignmentI al, StringTokenizer st)
\r
1354 String keyValue, key, value;
\r
1355 while (st.hasMoreTokens())
\r
1357 keyValue = st.nextToken();
\r
1358 key = keyValue.substring(0, keyValue.indexOf("="));
\r
1359 value = keyValue.substring(keyValue.indexOf("=") + 1);
\r
1360 al.setProperty(key, value);
\r
1365 * Write annotations as a CSV file of the form 'label, value, value, ...' for
\r
1368 * @param annotations
\r
1369 * @return CSV file as a string.
\r
1371 public String printCSVAnnotations(AlignmentAnnotation[] annotations)
\r
1373 StringBuffer sp = new StringBuffer();
\r
1374 for (int i = 0; i < annotations.length; i++)
\r
1376 String atos = annotations[i].toString();
\r
1380 int cp = atos.indexOf("\n", p);
\r
1381 sp.append(annotations[i].label);
\r
1385 sp.append(atos.substring(p, cp + 1));
\r
1389 sp.append(atos.substring(p));
\r
1395 return sp.toString();
\r