2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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24 import javax.swing.*;
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26 import org.biojava.dasobert.das.*;
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27 import org.biojava.dasobert.das2.*;
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28 import org.biojava.dasobert.das2.io.*;
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29 import org.biojava.dasobert.dasregistry.*;
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30 import org.biojava.dasobert.eventmodel.*;
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31 import jalview.bin.Cache;
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32 import jalview.datamodel.*;
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33 import jalview.gui.*;
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39 * @version $Revision$
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41 public class DasSequenceFeatureFetcher
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43 SequenceI[] sequences;
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45 FeatureSettings fsettings;
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46 StringBuffer sbuffer = new StringBuffer();
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47 Vector selectedSources;
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48 boolean cancelled = false;
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53 * Creates a new SequenceFeatureFetcher object.
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56 * @param align DOCUMENT ME!
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57 * @param ap DOCUMENT ME!
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59 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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60 FeatureSettings fsettings,
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61 Vector selectedSources)
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63 this.selectedSources = selectedSources;
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64 this.sequences = sequences;
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65 this.af = fsettings.af;
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66 this.fsettings = fsettings;
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68 int uniprotCount = 0;
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69 for (int i = 0; i < selectedSources.size(); i++)
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71 DasSource source = (DasSource) selectedSources.elementAt(i);
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72 DasCoordinateSystem[] coords = source.getCoordinateSystem();
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73 for (int c = 0; c < coords.length; c++)
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75 if (coords[c].getName().indexOf("UniProt") > -1)
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84 for (int i = 0; i < sequences.length; i++)
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86 DBRefEntry[] dbref = sequences[i].getDBRef();
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89 for (int j = 0; j < dbref.length; j++)
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91 if (dbref[j].getSource()
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92 .equals(jalview.datamodel.DBRefSource.UNIPROT))
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101 if (refCount < sequences.length && uniprotCount > 0)
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104 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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105 "Do you want Jalview to find\n"
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106 + "Uniprot Accession ids for given sequence names?",
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107 "Find Uniprot Accession Ids",
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108 JOptionPane.YES_NO_OPTION,
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109 JOptionPane.QUESTION_MESSAGE);
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111 if (reply == JOptionPane.YES_OPTION)
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113 Thread thread = new Thread(new FetchDBRefs());
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129 implements Runnable
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134 af.getViewport().getAlignment(), af).fetchDBRefs(true);
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141 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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143 void startFetching()
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146 startTime = System.currentTimeMillis();
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147 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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149 DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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151 if (selectedSources == null || selectedSources.size() == 0)
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153 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
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155 StringTokenizer st = new StringTokenizer(active, "\t");
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156 Vector selectedSources = new Vector();
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158 while (st.hasMoreTokens())
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160 token = st.nextToken();
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161 for (int i = 0; i < sources.length; i++)
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163 if (sources[i].getNickname().equals(token))
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165 selectedSources.addElement(sources[i]);
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172 if (selectedSources == null || selectedSources.size() == 0)
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174 System.out.println("No DAS Sources active");
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175 af.setProgressBar("No DAS Sources Active", startTime);
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179 sourcesRemaining = selectedSources.size();
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180 //Now sending requests one at a time to each server
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181 for (int sourceIndex = 0;
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182 sourceIndex < selectedSources.size()
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186 DasSource dasSource = (DasSource) selectedSources.elementAt(
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189 nextSequence(dasSource, sequences[0]);
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193 public void cancel()
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195 af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
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199 int sourcesRemaining=0;
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200 void responseComplete(DasSource dasSource, SequenceI seq)
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204 for (int seqIndex = 0;
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205 seqIndex < sequences.length-1
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206 && !cancelled; seqIndex++)
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208 if (sequences[seqIndex] == seq)
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210 nextSequence(dasSource, sequences[++seqIndex]);
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216 sourcesRemaining --;
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218 if(sourcesRemaining==0)
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220 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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222 if(af.featureSettings!=null)
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224 af.featureSettings.setTableData();
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227 fsettings.complete();
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232 void featuresAdded(SequenceI seq)
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234 af.getFeatureRenderer().featuresAdded();
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236 int start = af.getViewport().getStartSeq();
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237 int end = af.getViewport().getEndSeq();
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239 for(index=start; index<end; index++)
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242 af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
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244 af.alignPanel.paintAlignment(true);
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251 void nextSequence(DasSource dasSource, SequenceI seq)
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253 DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
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256 // jalview.datamodel.DBRefSource.PDB,
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257 jalview.datamodel.DBRefSource.UNIPROT,
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258 // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources
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260 // TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs
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262 boolean dasCoordSysFound = false;
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264 if (uprefs != null)
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266 // do any of these ids match the source's coordinate system ?
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267 for (int j = 0; j < uprefs.length; j++)
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269 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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271 for(int csIndex=0; csIndex<cs.length; csIndex++)
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273 if (cs.length > 0 && jalview.util.DBRefUtils
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274 .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))
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276 Cache.log.debug("Launched fetcher for coordinate system " +
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278 // Will have to pass any mapping information to the fetcher
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279 //- the start/end for the DBRefEntry may not be the same as the sequence's start/end
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281 System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)
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282 + " " + dasSource.getUrl());
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284 dasCoordSysFound = false;
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285 createFeatureFetcher(seq,
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288 break; // only do this for one reference - assume same source will send same features for all IDs
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291 System.out.println("IGNORE " + cs[csIndex].getName());
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296 if(!dasCoordSysFound)
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299 // try and use the name as the sequence id
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300 if (seq.getName().indexOf("|") > -1)
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302 id = seq.getName().substring(
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303 seq.getName().lastIndexOf("|") + 1);
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307 id = seq.getName();
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311 // Should try to call a general feature fetcher that
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312 // queries many sources with name to discover applicable ID references
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313 createFeatureFetcher(seq,
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323 * fetch and add das features to a sequence using the given source URL and compatible DbRef id.
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324 * new features are mapped using the DbRef mapping to the local coordinate system.
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329 protected void createFeatureFetcher(final SequenceI seq, final DasSource dasSource,
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330 final DBRefEntry dbref) {
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333 /// fetch DAS features
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334 final Das1Source source = new Das1Source();
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335 source.setUrl(dasSource.getUrl());
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336 source.setNickname(dasSource.getNickname());
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337 if (dbref==null || dbref.getAccessionId()==null || dbref.getAccessionId().length()<1)
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341 Cache.log.debug("new Das Feature Fetcher for " + dbref.getSource()+":"+dbref.getAccessionId() + " querying " +
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342 dasSource.getUrl());
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343 FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()
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344 // + ":" + start + "," + end,
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347 fetcher.addFeatureListener(new FeatureListener()
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349 public void comeBackLater(FeatureEvent e)
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351 responseComplete(dasSource, seq);
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352 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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353 " asked us to come back in " + e.getComeBackLater() +
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357 public void newFeatures(FeatureEvent e)
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360 Das1Source ds = e.getDasSource();
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362 Map[] features = e.getFeatures();
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363 // add features to sequence
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364 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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365 features.length + " features");
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367 if (features.length > 0)
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369 for (int i = 0; i < features.length; i++)
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371 SequenceFeature f = newSequenceFeature(features[i],
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372 source.getNickname());
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373 if (dbref.getMap()!=null && f.getBegin()>0 && f.getEnd()>0) {
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374 Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());
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375 SequenceFeature vf[] = dbref.getMap().locateFeature(f);
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377 for (int v=0;v<vf.length;v++)
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379 Cache.log.debug("mapping to "+v+": "+vf[v].getBegin()+" - "+vf[v].getEnd());
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380 seq.addSequenceFeature(vf[v]);
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384 seq.addSequenceFeature(f);
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388 featuresAdded(seq);
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392 // System.out.println("No features found for " + seq.getName()
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393 // + " from: " + e.getDasSource().getNickname());
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395 responseComplete(dasSource, seq);
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404 protected void createFeatureFetcher(final SequenceI seq,
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405 final DasSource dasSource,
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409 /// fetch DAS features
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410 final Das1Source source = new Das1Source();
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411 source.setUrl(dasSource.getUrl());
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412 source.setNickname(dasSource.getNickname());
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414 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
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415 dasSource.getUrl());
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417 if (id != null && id.length() > 0)
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419 FeatureThread fetcher = new FeatureThread(id
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420 // + ":" + start + "," + end,
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423 fetcher.addFeatureListener(new FeatureListener()
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425 public void comeBackLater(FeatureEvent e)
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427 responseComplete(dasSource, seq);
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428 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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429 " asked us to come back in " + e.getComeBackLater() +
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433 public void newFeatures(FeatureEvent e)
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436 Das1Source ds = e.getDasSource();
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438 Map[] features = e.getFeatures();
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439 // add features to sequence
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440 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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441 features.length + " features");
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443 if (features.length > 0)
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445 for (int i = 0; i < features.length; i++)
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447 SequenceFeature f = newSequenceFeature(features[i],
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448 source.getNickname());
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450 seq.addSequenceFeature(f);
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453 featuresAdded(seq);
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457 // System.out.println("No features found for " + seq.getName()
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458 // + " from: " + e.getDasSource().getNickname());
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460 responseComplete(dasSource, seq);
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472 * creates a jalview sequence feature from a das feature document
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473 * @param dasfeature
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474 * @return sequence feature object created using dasfeature information
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476 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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481 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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483 qName.equals("TYPE") ||
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484 qName.equals("START") ||
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485 qName.equals("END") ||
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486 qName.equals("NOTE") ||
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487 qName.equals("LINK") ||
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488 qName.equals("SCORE")
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490 String desc = new String();
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491 if (dasfeature.containsKey("NOTE"))
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493 desc += (String) dasfeature.get("NOTE");
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496 int start = 0, end = 0;
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501 start = Integer.parseInt(dasfeature.get("START").toString());
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503 catch (Exception ex)
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507 end = Integer.parseInt(dasfeature.get("END").toString());
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509 catch (Exception ex)
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513 score = Integer.parseInt(dasfeature.get("SCORE").toString());
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515 catch (Exception ex)
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518 SequenceFeature f = new SequenceFeature(
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519 (String) dasfeature.get("TYPE"),
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526 if (dasfeature.containsKey("LINK"))
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528 f.addLink(f.getType() + " " + f.begin + "_" + f.end
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529 + "|" + dasfeature.get("LINK"));
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534 catch (Exception e)
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536 System.out.println("ERRR " + e);
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537 e.printStackTrace();
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538 System.out.println("############");
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539 Cache.log.debug("Failed to parse " + dasfeature.toString(), e);
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544 public static DasSource[] getDASSources()
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546 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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548 String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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549 DasSourceBrowser.DEFAULT_REGISTRY
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554 URL url = new URL(registryURL);
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556 DasSource[] sources = reader.readDasSource(url);
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558 List das1sources = new ArrayList();
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559 for (int i = 0; i < sources.length; i++)
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561 DasSource ds = sources[i];
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562 if (ds instanceof Das2Source)
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564 Das2Source d2s = (Das2Source) ds;
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565 if (d2s.hasDas1Capabilities())
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567 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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568 das1sources.add(d1s);
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572 else if (ds instanceof Das1Source)
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574 das1sources.add( (Das1Source) ds);
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578 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
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580 catch (Exception ex)
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582 ex.printStackTrace();
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