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 SequenceI [] sequences;
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55 StringBuffer sbuffer = new StringBuffer();
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56 Vector selectedSources;
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59 int threadsRunning = 0;
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63 * Creates a new SequenceFeatureFetcher object.
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66 * @param align DOCUMENT ME!
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67 * @param ap DOCUMENT ME!
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69 public DasSequenceFeatureFetcher(SequenceI [] sequences,
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71 Vector selectedSources)
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73 this.selectedSources = selectedSources;
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74 this.sequences = sequences;
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77 Thread thread = new Thread(this);
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81 * creates a jalview sequence feature from a das feature document
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83 * @return sequence feature object created using dasfeature information
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85 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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89 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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91 qName.equals("TYPE") ||
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92 qName.equals("START") ||
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93 qName.equals("END") ||
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94 qName.equals("NOTE") ||
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95 qName.equals("LINK") ||
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96 qName.equals("SCORE")
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98 String desc = new String();
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99 if (dasfeature.containsKey("NOTE"))
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100 desc+=(String) dasfeature.get("NOTE");
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103 int start = 0, end = 0;
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106 try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
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107 catch( Exception ex){}
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108 try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
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109 catch (Exception ex){}
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110 try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
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111 catch (Exception ex){}
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114 SequenceFeature f = new SequenceFeature(
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115 (String) dasfeature.get("TYPE"),
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122 if (dasfeature.containsKey("LINK"))
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124 f.addLink(f.getType()+" "+f.begin+"_"+f.end
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125 +"|"+ dasfeature.get("LINK"));
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127 // (String) dasfeature.get("ID"),
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128 //// (String) dasfeature.get("METHOD"),
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129 // (String) dasfeature.get("SCORE"),
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133 // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);
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136 catch (Exception e) {
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137 e.printStackTrace();
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138 Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
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143 * fetch and add das features to a sequence using the given source URL and Id to create a feature request
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148 protected void createFeatureFetcher(final SequenceI seq,
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149 final String sourceUrl,
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153 /// fetch DAS features
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154 final Das1Source source = new Das1Source();
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155 source.setUrl(sourceUrl);
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156 source.setNickname(nickname);
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159 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
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161 if (id != null && id.length() > 0)
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163 setThreadsRunning(+1);
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165 FeatureThread fetcher = new FeatureThread(id
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166 + ":" + seq.getStart() + "," +seq.getEnd()
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169 fetcher.addFeatureListener(new FeatureListener()
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171 public void comeBackLater(FeatureEvent e)
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173 setThreadsRunning(-1);
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174 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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175 " asked us to come back in " + e.getComeBackLater() +
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179 public void newFeatures(FeatureEvent e)
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181 setThreadsRunning(-1);
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182 Das1Source ds = e.getDasSource();
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184 Map[] features = e.getFeatures();
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185 // add features to sequence
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186 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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187 features.length + " features");
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189 if (features.length > 0)
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191 for (int i = 0; i < features.length; i++)
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193 SequenceFeature f = newSequenceFeature(features[i],
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194 source.getNickname());
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196 seq.addSequenceFeature(f);
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201 System.out.println("No features found for sequence " +seq.getName()
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202 +" from: "+ e.getDasSource().getNickname());
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210 //NOTE alignPanel listener will be called after the previous
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211 //anonymous listener!!!
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212 fetcher.addFeatureListener(af);
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218 synchronized void setThreadsRunning(int i)
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220 threadsRunning += i;
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221 if(threadsRunning<1)
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222 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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226 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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230 startTime = System.currentTimeMillis();
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231 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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233 DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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235 if(selectedSources==null || selectedSources.size()==0)
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237 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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238 StringTokenizer st = new StringTokenizer(active, "\t");
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239 Vector selectedSources = new Vector();
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241 while (st.hasMoreTokens())
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243 token = st.nextToken();
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244 for (int i = 0; i < sources.length; i++)
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246 if (sources[i].getNickname().equals(token))
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248 selectedSources.addElement(sources[i]);
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255 if(selectedSources == null || selectedSources.size()==0)
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257 System.out.println("No DAS Sources active");
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258 af.setProgressBar("No DAS Sources Active", startTime);
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265 while (seqIndex < sequences.length)
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267 Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
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269 jalview.datamodel.DBRefSource.PDB,
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270 jalview.datamodel.DBRefSource.UNIPROT});
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272 for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
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274 DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
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276 if (uprefs != null)
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278 // we know the id for this entry, so don't note its ID in the unknownSequences list
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279 for (int j = 0; j < uprefs.size(); j++)
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282 // 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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283 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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284 for (int l=0; l<cs.length; l++)
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286 if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
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289 Cache.log.debug("Launched fetcher for coordinate system " +
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293 createFeatureFetcher(sequences[seqIndex],
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294 dasSource.getUrl(),
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295 ( (DBRefEntry) uprefs.get(j)).
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297 dasSource.getNickname());
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305 // try and use the name as the sequence id
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306 if (sequences[seqIndex].getName().indexOf("|") > -1)
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308 id = sequences[seqIndex].getName().substring(
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309 sequences[seqIndex].getName().lastIndexOf("|") + 1);
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313 id = sequences[seqIndex].getName();
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317 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
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318 createFeatureFetcher(sequences[seqIndex],
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319 dasSource.getUrl(),
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321 dasSource.getNickname());
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329 catch (Exception ex)
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331 ex.printStackTrace();
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336 public static DasSource[] getDASSources()
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338 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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340 String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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341 "http://www.spice-3d.org/dasregistry/das1/sources"
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346 URL url = new URL(registryURL);
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348 DasSource[] sources = reader.readDasSource(url);
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350 List das1sources = new ArrayList();
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351 for (int i = 0; i < sources.length; i++)
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353 DasSource ds = sources[i];
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354 if (ds instanceof Das2Source)
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356 Das2Source d2s = (Das2Source) ds;
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357 if (d2s.hasDas1Capabilities())
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359 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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360 das1sources.add(d1s);
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364 else if (ds instanceof Das1Source)
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366 das1sources.add( (Das1Source) ds);
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370 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
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372 catch (Exception ex)
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374 ex.printStackTrace();
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