2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
24 import javax.swing.*;
\r
26 import org.biojava.dasobert.das.*;
\r
27 import org.biojava.dasobert.das2.*;
\r
28 import org.biojava.dasobert.das2.io.*;
\r
29 import org.biojava.dasobert.dasregistry.*;
\r
30 import org.biojava.dasobert.eventmodel.*;
\r
31 import jalview.bin.Cache;
\r
32 import jalview.datamodel.*;
\r
33 import jalview.gui.*;
\r
39 * @version $Revision$
\r
41 public class DasSequenceFeatureFetcher
\r
43 SequenceI[] sequences;
\r
45 FeatureSettings fsettings;
\r
46 StringBuffer sbuffer = new StringBuffer();
\r
47 Vector selectedSources;
\r
48 boolean cancelled = false;
\r
53 * Creates a new SequenceFeatureFetcher object.
\r
56 * @param align DOCUMENT ME!
\r
57 * @param ap DOCUMENT ME!
\r
59 public DasSequenceFeatureFetcher(SequenceI[] sequences,
\r
60 FeatureSettings fsettings,
\r
61 Vector selectedSources)
\r
63 this.selectedSources = selectedSources;
\r
64 this.sequences = sequences;
\r
65 this.af = fsettings.af;
\r
66 this.fsettings = fsettings;
\r
68 int uniprotCount = 0;
\r
69 for (int i = 0; i < selectedSources.size(); i++)
\r
71 DasSource source = (DasSource) selectedSources.elementAt(i);
\r
72 DasCoordinateSystem[] coords = source.getCoordinateSystem();
\r
73 for (int c = 0; c < coords.length; c++)
\r
75 if (coords[c].getName().indexOf("UniProt") > -1)
\r
84 for (int i = 0; i < sequences.length; i++)
\r
86 DBRefEntry[] dbref = sequences[i].getDBRef();
\r
89 for (int j = 0; j < dbref.length; j++)
\r
91 if (dbref[j].getSource()
\r
92 .equals(jalview.datamodel.DBRefSource.UNIPROT))
\r
101 if (refCount < sequences.length && uniprotCount > 0)
\r
104 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
105 "Do you want Jalview to find\n"
\r
106 + "Uniprot Accession ids for given sequence names?",
\r
107 "Find Uniprot Accession Ids",
\r
108 JOptionPane.YES_NO_OPTION,
\r
109 JOptionPane.QUESTION_MESSAGE);
\r
111 if (reply == JOptionPane.YES_OPTION)
\r
113 Thread thread = new Thread(new FetchDBRefs());
\r
129 implements Runnable
\r
134 af.getViewport().getAlignment(), af).fetchDBRefs(true);
\r
140 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
\r
142 void startFetching()
\r
145 startTime = System.currentTimeMillis();
\r
146 af.setProgressBar("Fetching DAS Sequence Features", startTime);
\r
148 DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
\r
150 if (selectedSources == null || selectedSources.size() == 0)
\r
152 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
\r
154 StringTokenizer st = new StringTokenizer(active, "\t");
\r
155 Vector selectedSources = new Vector();
\r
157 while (st.hasMoreTokens())
\r
159 token = st.nextToken();
\r
160 for (int i = 0; i < sources.length; i++)
\r
162 if (sources[i].getNickname().equals(token))
\r
164 selectedSources.addElement(sources[i]);
\r
171 if (selectedSources == null || selectedSources.size() == 0)
\r
173 System.out.println("No DAS Sources active");
\r
174 af.setProgressBar("No DAS Sources Active", startTime);
\r
178 sourcesRemaining = selectedSources.size();
\r
179 //Now sending requests one at a time to each server
\r
180 for (int sourceIndex = 0;
\r
181 sourceIndex < selectedSources.size()
\r
185 DasSource dasSource = (DasSource) selectedSources.elementAt(
\r
188 nextSequence(dasSource, sequences[0]);
\r
192 public void cancel()
\r
194 af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
\r
198 int sourcesRemaining = 0;
\r
199 void responseComplete(DasSource dasSource, SequenceI seq)
\r
203 for (int seqIndex = 0;
\r
204 seqIndex < sequences.length - 1
\r
205 && !cancelled; seqIndex++)
\r
207 if (sequences[seqIndex] == seq)
\r
209 nextSequence(dasSource, sequences[++seqIndex]);
\r
215 sourcesRemaining--;
\r
217 if (sourcesRemaining == 0)
\r
219 af.setProgressBar("DAS Feature Fetching Complete", startTime);
\r
221 if (af.featureSettings != null)
\r
223 af.featureSettings.setTableData();
\r
226 fsettings.complete();
\r
231 void featuresAdded(SequenceI seq)
\r
233 af.getFeatureRenderer().featuresAdded();
\r
235 int start = af.getViewport().getStartSeq();
\r
236 int end = af.getViewport().getEndSeq();
\r
238 for (index = start; index < end; index++)
\r
241 af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
\r
243 af.alignPanel.paintAlignment(true);
\r
249 void nextSequence(DasSource dasSource, SequenceI seq)
\r
251 DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
\r
254 // jalview.datamodel.DBRefSource.PDB,
\r
255 jalview.datamodel.DBRefSource.UNIPROT
\r
258 if (uprefs != null)
\r
260 // we know the id for this entry, so don't note its ID in the unknownSequences list
\r
261 // for (int j = 0; j < uprefs.length; j++)
\r
263 // Will have to pass any mapping information to the fetcher
\r
264 //- the start/end for the DBRefEntry may not be the same as the sequence's start/end
\r
265 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
\r
268 // for (int l = 0; l < cs.length; l++)
\r
271 if (jalview.util.DBRefUtils
\r
272 .isDasCoordinateSystem(cs[0].getName(), uprefs[0]))
\r
274 Cache.log.debug("Launched fetcher for coordinate system " +
\r
277 createFeatureFetcher(seq,
\r
279 uprefs[0].getAccessionId());
\r
288 // try and use the name as the sequence id
\r
289 if (seq.getName().indexOf("|") > -1)
\r
291 id = seq.getName().substring(
\r
292 seq.getName().lastIndexOf("|") + 1);
\r
296 id = seq.getName();
\r
300 // Should try to call a general feature fetcher that
\r
301 // queries many sources with name to discover applicable ID references
\r
302 createFeatureFetcher(seq,
\r
311 * fetch and add das features to a sequence using the given source URL and Id to create a feature request
\r
316 protected void createFeatureFetcher(final SequenceI seq,
\r
317 final DasSource dasSource,
\r
321 /// fetch DAS features
\r
322 final Das1Source source = new Das1Source();
\r
323 source.setUrl(dasSource.getUrl());
\r
324 source.setNickname(dasSource.getNickname());
\r
326 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
\r
327 dasSource.getUrl());
\r
329 if (id != null && id.length() > 0)
\r
331 FeatureThread fetcher = new FeatureThread(id
\r
332 // + ":" + start + "," + end,
\r
335 fetcher.addFeatureListener(new FeatureListener()
\r
337 public void comeBackLater(FeatureEvent e)
\r
339 responseComplete(dasSource, seq);
\r
340 Cache.log.debug("das source " + e.getDasSource().getNickname() +
\r
341 " asked us to come back in " + e.getComeBackLater() +
\r
345 public void newFeatures(FeatureEvent e)
\r
348 Das1Source ds = e.getDasSource();
\r
350 Map[] features = e.getFeatures();
\r
351 // add features to sequence
\r
352 Cache.log.debug("das source " + ds.getUrl() + " returned " +
\r
353 features.length + " features");
\r
355 if (features.length > 0)
\r
357 for (int i = 0; i < features.length; i++)
\r
359 SequenceFeature f = newSequenceFeature(features[i],
\r
360 source.getNickname());
\r
362 seq.addSequenceFeature(f);
\r
365 featuresAdded(seq);
\r
369 // System.out.println("No features found for " + seq.getName()
\r
370 // + " from: " + e.getDasSource().getNickname());
\r
372 responseComplete(dasSource, seq);
\r
384 * creates a jalview sequence feature from a das feature document
\r
385 * @param dasfeature
\r
386 * @return sequence feature object created using dasfeature information
\r
388 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
\r
393 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
\r
395 qName.equals("TYPE") ||
\r
396 qName.equals("START") ||
\r
397 qName.equals("END") ||
\r
398 qName.equals("NOTE") ||
\r
399 qName.equals("LINK") ||
\r
400 qName.equals("SCORE")
\r
402 String desc = new String();
\r
403 if (dasfeature.containsKey("NOTE"))
\r
405 desc += (String) dasfeature.get("NOTE");
\r
408 int start = 0, end = 0;
\r
413 start = Integer.parseInt(dasfeature.get("START").toString());
\r
415 catch (Exception ex)
\r
419 end = Integer.parseInt(dasfeature.get("END").toString());
\r
421 catch (Exception ex)
\r
425 score = Integer.parseInt(dasfeature.get("SCORE").toString());
\r
427 catch (Exception ex)
\r
430 SequenceFeature f = new SequenceFeature(
\r
431 (String) dasfeature.get("TYPE"),
\r
438 if (dasfeature.containsKey("LINK"))
\r
440 f.addLink(f.getType() + " " + f.begin + "_" + f.end
\r
441 + "|" + dasfeature.get("LINK"));
\r
446 catch (Exception e)
\r
448 System.out.println("ERRR " + e);
\r
449 e.printStackTrace();
\r
450 System.out.println("############");
\r
451 Cache.log.debug("Failed to parse " + dasfeature.toString(), e);
\r
456 public static DasSource[] getDASSources()
\r
458 DasSourceReaderImpl reader = new DasSourceReaderImpl();
\r
460 String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
\r
461 DasSourceBrowser.DEFAULT_REGISTRY
\r
466 URL url = new URL(registryURL);
\r
468 DasSource[] sources = reader.readDasSource(url);
\r
470 List das1sources = new ArrayList();
\r
471 for (int i = 0; i < sources.length; i++)
\r
473 DasSource ds = sources[i];
\r
474 if (ds instanceof Das2Source)
\r
476 Das2Source d2s = (Das2Source) ds;
\r
477 if (d2s.hasDas1Capabilities())
\r
479 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
\r
480 das1sources.add(d1s);
\r
484 else if (ds instanceof Das1Source)
\r
486 das1sources.add( (Das1Source) ds);
\r
490 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
\r
492 catch (Exception ex)
\r
494 ex.printStackTrace();
\r