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.services.das.registry.DasRegistryAxisClient;
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34 import org.biojava.services.das.registry.DasSource;
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37 import jalview.bin.Cache;
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45 * @version $Revision$
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47 public class DasSequenceFeatureFetcher implements Runnable
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49 final AlignmentI dataset;
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50 final AlignmentPanel ap;
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51 StringBuffer sbuffer = new StringBuffer();
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56 * Creates a new SequenceFeatureFetcher object.
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58 * @param align DOCUMENT ME!
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59 * @param ap DOCUMENT ME!
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61 public DasSequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
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63 this.dataset = align.getDataset();
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66 Thread thread = new Thread(this);
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70 * creates a jalview sequence feature from a das feature document
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72 * @return sequence feature object created using dasfeature information
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74 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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78 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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80 qName.equals("TYPE") ||
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81 qName.equals("START") ||
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82 qName.equals("END") ||
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83 qName.equals("NOTE") ||
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84 qName.equals("LINK") ||
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85 qName.equals("SCORE")
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87 String desc = new String();
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88 if (dasfeature.containsKey("NOTE"))
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89 desc+=(String) dasfeature.get("NOTE");
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92 int start = 0, end = 0;
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95 try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
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96 catch( Exception ex){}
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97 try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
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98 catch (Exception ex){}
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99 try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
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100 catch (Exception ex){}
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103 SequenceFeature f = new SequenceFeature(
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104 (String) dasfeature.get("TYPE"),
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111 if (dasfeature.containsKey("LINK"))
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113 f.addLink(f.getType()+" "+f.begin+"_"+f.end
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114 +"|"+ dasfeature.get("LINK"));
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116 // (String) dasfeature.get("ID"),
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117 //// (String) dasfeature.get("METHOD"),
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118 // (String) dasfeature.get("SCORE"),
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122 // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);
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125 catch (Exception e) {
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126 e.printStackTrace();
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127 Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
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132 * fetch and add das features to a sequence using the given source URL and Id to create a feature request
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137 protected void createFeatureFetcher(final Sequence seq,
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138 final String sourceUrl,
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142 /// fetch DAS features
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143 final Das1Source source = new Das1Source();
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144 source.setUrl(sourceUrl);
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145 source.setNickname(nickname);
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148 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
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150 if (id != null && id.length() > 0)
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152 FeatureThread fetcher = new FeatureThread(id + ":" + seq.getStart() + "," +seq.getEnd()
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155 fetcher.addFeatureListener(new FeatureListener()
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157 public void comeBackLater(FeatureEvent e)
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159 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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160 " asked us to come back in " + e.getComeBackLater() +
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164 public void newFeatures(FeatureEvent e)
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166 Das1Source ds = e.getDasSource();
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168 Map[] features = e.getFeatures();
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169 // add features to sequence
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170 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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171 features.length + " features");
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174 if (features.length > 0)
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176 for (int i = 0; i < features.length; i++)
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179 SequenceFeature f = newSequenceFeature(features[i],
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180 source.getNickname());
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182 if (seq.sequenceFeatures != null)
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184 for (int j = 0; (f != null) && j < seq.sequenceFeatures.length;
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187 if (seq.sequenceFeatures[j].equals(f))
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195 seq.addSequenceFeature(f);
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205 //NOTE alignPanel listener will be called after the previous
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206 //anonymous listener!!!
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207 fetcher.addFeatureListener(ap);
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213 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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217 DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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219 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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220 StringTokenizer st = new StringTokenizer(active, "\t");
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221 Vector selectedSources = new Vector();
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223 while (st.hasMoreTokens())
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225 token = st.nextToken();
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226 for(int i=0; i<sources.length; i++)
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228 if(sources[i].getNickname().equals(token))
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230 selectedSources.addElement(sources[i]);
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235 // DasSource test = new DasSource();
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236 // test.setUrl("http://localhost:8080/das/gffdb/");
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237 //test.setNickname("Trixkid");
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238 // selectedSources.addElement(test);
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241 if(selectedSources == null || selectedSources.size()==0)
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243 System.out.println("No DAS Sources active");
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250 Vector sequences = dataset.getSequences();
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251 while (seqIndex < sequences.size())
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253 Sequence sequence = (Sequence) sequences.get(seqIndex);
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254 Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
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256 jalview.datamodel.DBRefSource.PDB,
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257 jalview.datamodel.DBRefSource.UNIPROT});
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259 for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
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261 DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
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263 if (uprefs != null)
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265 // we know the id for this entry, so don't note its ID in the unknownSequences list
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266 for (int j = 0, k = uprefs.size(); j < k; j++)
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268 // 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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269 org.biojava.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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270 for (int l=0; l<cs.length; l++) {
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271 if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
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274 Cache.log.debug("Launched fetcher for coordinate system " +
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276 createFeatureFetcher(sequence,
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277 dasSource.getUrl(),
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278 ( (DBRefEntry) uprefs.get(j)).
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280 dasSource.getNickname());
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288 // try and use the name as the sequence id
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289 if (sequence.getName().indexOf("|") > -1)
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291 id = sequence.getName().substring(
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292 sequence.getName().lastIndexOf("|") + 1);
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296 id = sequence.getName();
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300 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
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301 createFeatureFetcher(sequence,
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302 dasSource.getUrl(),
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304 dasSource.getNickname());
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312 catch (Exception ex)
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314 ex.printStackTrace();
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319 public static DasSource[] getDASSources()
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323 String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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324 "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");
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327 URL url = new URL(registryURL);
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329 DasRegistryAxisClient client = new DasRegistryAxisClient(url);
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331 DasSource[] services = client.listServices();
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335 catch (Exception ex)
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337 ex.printStackTrace();
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