2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.datamodel.*;
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23 import jalview.gui.*;
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27 import java.net.URL;
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29 import org.biojava.dasobert.das.FeatureThread;
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30 import org.biojava.dasobert.dasregistry.Das1Source;
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31 import org.biojava.dasobert.eventmodel.FeatureEvent;
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32 import org.biojava.dasobert.eventmodel.FeatureListener;
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33 import org.biojava.dasobert.dasregistry.DasSource;
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35 import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
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36 import org.biojava.dasobert.dasregistry.Das1Source;
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37 import org.biojava.dasobert.dasregistry.DasSource;
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38 import org.biojava.dasobert.das2.Das2Source;
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39 import org.biojava.dasobert.das2.DasSourceConverter;
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42 import jalview.bin.Cache;
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49 * @version $Revision$
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51 public class DasSequenceFeatureFetcher implements Runnable
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53 final AlignmentI dataset;
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54 final AlignFrame af;
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55 StringBuffer sbuffer = new StringBuffer();
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60 * Creates a new SequenceFeatureFetcher object.
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62 * @param align DOCUMENT ME!
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63 * @param ap DOCUMENT ME!
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65 public DasSequenceFeatureFetcher(AlignmentI align,
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68 this.dataset = align.getDataset();
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71 Thread thread = new Thread(this);
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75 * creates a jalview sequence feature from a das feature document
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77 * @return sequence feature object created using dasfeature information
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79 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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83 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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85 qName.equals("TYPE") ||
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86 qName.equals("START") ||
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87 qName.equals("END") ||
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88 qName.equals("NOTE") ||
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89 qName.equals("LINK") ||
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90 qName.equals("SCORE")
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92 String desc = new String();
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93 if (dasfeature.containsKey("NOTE"))
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94 desc+=(String) dasfeature.get("NOTE");
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97 int start = 0, end = 0;
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100 try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
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101 catch( Exception ex){}
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102 try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
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103 catch (Exception ex){}
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104 try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
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105 catch (Exception ex){}
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108 SequenceFeature f = new SequenceFeature(
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109 (String) dasfeature.get("TYPE"),
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116 if (dasfeature.containsKey("LINK"))
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118 f.addLink(f.getType()+" "+f.begin+"_"+f.end
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119 +"|"+ dasfeature.get("LINK"));
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121 // (String) dasfeature.get("ID"),
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122 //// (String) dasfeature.get("METHOD"),
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123 // (String) dasfeature.get("SCORE"),
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127 // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);
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130 catch (Exception e) {
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131 e.printStackTrace();
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132 Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
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137 * fetch and add das features to a sequence using the given source URL and Id to create a feature request
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142 protected void createFeatureFetcher(final Sequence seq,
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143 final String sourceUrl,
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147 /// fetch DAS features
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148 final Das1Source source = new Das1Source();
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149 source.setUrl(sourceUrl);
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150 source.setNickname(nickname);
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153 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
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155 if (id != null && id.length() > 0)
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157 FeatureThread fetcher = new FeatureThread(id
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158 // + ":" + seq.getStart() + "," +seq.getEnd()
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161 fetcher.addFeatureListener(new FeatureListener()
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163 public void comeBackLater(FeatureEvent e)
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165 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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166 " asked us to come back in " + e.getComeBackLater() +
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170 public void newFeatures(FeatureEvent e)
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172 Das1Source ds = e.getDasSource();
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174 Map[] features = e.getFeatures();
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175 // add features to sequence
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176 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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177 features.length + " features");
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179 if (features.length > 0)
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181 for (int i = 0; i < features.length; i++)
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183 SequenceFeature f = newSequenceFeature(features[i],
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184 source.getNickname());
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186 seq.addSequenceFeature(f);
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194 //NOTE alignPanel listener will be called after the previous
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195 //anonymous listener!!!
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196 fetcher.addFeatureListener(af);
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202 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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206 long startTime = System.currentTimeMillis();
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207 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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209 DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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211 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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212 StringTokenizer st = new StringTokenizer(active, "\t");
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213 Vector selectedSources = new Vector();
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215 while (st.hasMoreTokens())
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217 token = st.nextToken();
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218 for(int i=0; i<sources.length; i++)
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220 if(sources[i].getNickname().equals(token))
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222 selectedSources.addElement(sources[i]);
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229 if(selectedSources == null || selectedSources.size()==0)
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231 System.out.println("No DAS Sources active");
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232 af.setProgressBar("No DAS Sources Active", startTime);
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239 Vector sequences = dataset.getSequences();
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240 while (seqIndex < sequences.size())
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242 Sequence sequence = (Sequence) sequences.get(seqIndex);
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243 Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
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245 jalview.datamodel.DBRefSource.PDB,
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246 jalview.datamodel.DBRefSource.UNIPROT});
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248 for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
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250 DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
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252 if (uprefs != null)
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254 // we know the id for this entry, so don't note its ID in the unknownSequences list
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255 for (int j = 0; j < uprefs.size(); j++)
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258 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
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259 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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260 for (int l=0; l<cs.length; l++)
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262 if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
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265 Cache.log.debug("Launched fetcher for coordinate system " +
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269 createFeatureFetcher(sequence,
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270 dasSource.getUrl(),
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271 ( (DBRefEntry) uprefs.get(j)).
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273 dasSource.getNickname());
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281 // try and use the name as the sequence id
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282 if (sequence.getName().indexOf("|") > -1)
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284 id = sequence.getName().substring(
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285 sequence.getName().lastIndexOf("|") + 1);
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289 id = sequence.getName();
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293 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
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294 createFeatureFetcher(sequence,
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295 dasSource.getUrl(),
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297 dasSource.getNickname());
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305 catch (Exception ex)
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307 ex.printStackTrace();
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310 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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314 public static DasSource[] getDASSources()
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316 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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318 String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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319 "http://www.spice-3d.org/dasregistry/das1/sources"
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324 URL url = new URL(registryURL);
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326 DasSource[] sources = reader.readDasSource(url);
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328 List das1sources = new ArrayList();
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329 for (int i = 0; i < sources.length; i++)
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331 DasSource ds = sources[i];
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332 if (ds instanceof Das2Source)
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334 Das2Source d2s = (Das2Source) ds;
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335 if (d2s.hasDas1Capabilities())
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337 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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338 das1sources.add(d1s);
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342 else if (ds instanceof Das1Source)
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344 das1sources.add( (Das1Source) ds);
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348 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
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350 catch (Exception ex)
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352 ex.printStackTrace();
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