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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47 FeatureSettings fsettings;
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49 StringBuffer sbuffer = new StringBuffer();
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51 Vector selectedSources;
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53 boolean cancelled = false;
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54 private void debug(String mesg)
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58 private void debug(String mesg, Exception e)
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60 if (Cache.log!=null)
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62 Cache.log.debug(mesg, e);
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64 System.err.println(mesg);
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67 e.printStackTrace();
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74 * Creates a new SequenceFeatureFetcher object.
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77 * @param align DOCUMENT ME!
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78 * @param ap DOCUMENT ME!
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80 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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81 FeatureSettings fsettings, Vector selectedSources)
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83 this(sequences, fsettings, selectedSources, true, true);
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85 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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86 FeatureSettings fsettings, Vector selectedSources, boolean checkDbrefs, boolean promptFetchDbrefs)
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88 this.selectedSources = selectedSources;
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89 this.sequences = sequences;
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90 if (fsettings!=null)
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92 this.fsettings = fsettings;
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93 this.af = fsettings.af;
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94 af.getViewport().setShowSequenceFeatures(true);
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96 int uniprotCount = 0;
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97 for (int i = 0; i < selectedSources.size(); i++)
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99 DasSource source = (DasSource) selectedSources.elementAt(i);
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100 DasCoordinateSystem[] coords = source.getCoordinateSystem();
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101 for (int c = 0; c < coords.length; c++)
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103 // TODO: match UniProt coord system canonically (?) - does UniProt==uniprot==UNIPROT ?
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104 if (coords[c].getName().indexOf("UniProt") > -1)
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113 for (int i = 0; i < sequences.length; i++)
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115 DBRefEntry[] dbref = sequences[i].getDBRef();
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118 for (int j = 0; j < dbref.length; j++)
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120 if (dbref[j].getSource().equals(
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121 jalview.datamodel.DBRefSource.UNIPROT))
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130 if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
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133 int reply = JOptionPane.YES_OPTION;
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134 if (promptFetchDbrefs)
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136 reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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137 "Do you want Jalview to find\n"
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138 + "Uniprot Accession ids for given sequence names?",
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139 "Find Uniprot Accession Ids", JOptionPane.YES_NO_OPTION,
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140 JOptionPane.QUESTION_MESSAGE);
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144 if (reply == JOptionPane.YES_OPTION)
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146 Thread thread = new Thread(new FetchDBRefs());
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161 class FetchDBRefs implements Runnable
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165 new DBRefFetcher(sequences, af).fetchDBRefs(true);
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171 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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173 void startFetching()
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176 startTime = System.currentTimeMillis();
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179 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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182 DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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184 if (selectedSources == null || selectedSources.size() == 0)
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186 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
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188 StringTokenizer st = new StringTokenizer(active, "\t");
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189 Vector selectedSources = new Vector();
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191 while (st.hasMoreTokens())
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193 token = st.nextToken();
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194 for (int i = 0; i < sources.length; i++)
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196 if (sources[i].getNickname().equals(token))
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198 selectedSources.addElement(sources[i]);
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205 if (selectedSources == null || selectedSources.size() == 0)
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207 System.out.println("No DAS Sources active");
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209 setGuiNoDassourceActive();
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213 sourcesRemaining = selectedSources.size();
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214 //Now sending requests one at a time to each server
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215 for (int sourceIndex = 0; sourceIndex < selectedSources.size()
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216 && !cancelled; sourceIndex++)
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218 DasSource dasSource = (DasSource) selectedSources
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219 .elementAt(sourceIndex);
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221 nextSequence(dasSource, sequences[0]);
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225 private void setGuiNoDassourceActive()
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230 af.setProgressBar("No DAS Sources Active", startTime);
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232 if (getFeatSettings()!=null)
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234 fsettings.noDasSourceActive();
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239 * Update our fsettings dialog reference if we didn't have one when we were first initialised.
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240 * @return fsettings
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242 private FeatureSettings getFeatSettings()
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244 if (fsettings == null)
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248 fsettings = af.featureSettings;
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254 public void cancel()
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258 af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
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263 int sourcesRemaining = 0;
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265 void responseComplete(DasSource dasSource, SequenceI seq)
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269 for (int seqIndex = 0; seqIndex < sequences.length - 1 && !cancelled; seqIndex++)
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271 if (sequences[seqIndex] == seq)
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273 nextSequence(dasSource, sequences[++seqIndex]);
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279 sourcesRemaining--;
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281 if (sourcesRemaining == 0)
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283 System.err.println("Fetching Complete.");
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284 setGuiFetchComplete();
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289 private void setGuiFetchComplete()
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294 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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297 if (af != null && af.featureSettings != null)
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299 af.featureSettings.setTableData();
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302 if (getFeatSettings() != null)
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304 fsettings.complete();
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308 void featuresAdded(SequenceI seq)
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312 // no gui to update with features.
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315 af.getFeatureRenderer().featuresAdded();
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317 int start = af.getViewport().getStartSeq();
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318 int end = af.getViewport().getEndSeq();
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320 for (index = start; index < end; index++)
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322 if (seq == af.getViewport().getAlignment().getSequenceAt(index)
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323 .getDatasetSequence())
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325 af.alignPanel.paintAlignment(true);
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331 void nextSequence(DasSource dasSource, SequenceI seq)
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335 DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
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336 seq.getDBRef(), new String[]
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338 // jalview.datamodel.DBRefSource.PDB,
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339 jalview.datamodel.DBRefSource.UNIPROT,
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340 // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources
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342 // TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs
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344 boolean dasCoordSysFound = false;
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346 if (uprefs != null)
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348 // do any of these ids match the source's coordinate system ?
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349 for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
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351 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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353 for (int csIndex = 0; csIndex < cs.length && !dasCoordSysFound; csIndex++)
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356 && jalview.util.DBRefUtils.isDasCoordinateSystem(
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357 cs[csIndex].getName(), uprefs[j]))
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359 debug("Launched fetcher for coordinate system "
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360 + cs[0].getName());
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361 // Will have to pass any mapping information to the fetcher
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362 //- the start/end for the DBRefEntry may not be the same as the sequence's start/end
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364 System.out.println(seq.getName() + " "
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365 + (seq.getDatasetSequence() == null) + " "
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366 + dasSource.getUrl());
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368 dasCoordSysFound = true; // break's out of the loop
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369 createFeatureFetcher(seq, dasSource, uprefs[j]);
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372 System.out.println("IGNORE " + cs[csIndex].getName());
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377 if (!dasCoordSysFound)
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380 // try and use the name as the sequence id
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381 if (seq.getName().indexOf("|") > -1)
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383 id = seq.getName().substring(seq.getName().lastIndexOf("|") + 1);
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384 if (id.trim().length()<4)
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386 // hack - we regard a significant ID as being at least 4 non-whitespace characters
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387 id = seq.getName().substring(0, seq.getName().lastIndexOf("|"));
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388 if (id.indexOf("|")>-1)
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390 id = id.substring(id.lastIndexOf("|")+1);
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396 id = seq.getName();
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400 // Should try to call a general feature fetcher that
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401 // queries many sources with name to discover applicable ID references
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402 createFeatureFetcher(seq, dasSource, id);
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409 * fetch and add das features to a sequence using the given source URL and compatible DbRef id.
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410 * new features are mapped using the DbRef mapping to the local coordinate system.
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415 protected void createFeatureFetcher(final SequenceI seq,
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416 final DasSource dasSource, final DBRefEntry dbref)
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420 /// fetch DAS features
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421 final Das1Source source = new Das1Source();
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422 source.setUrl(dasSource.getUrl());
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423 source.setNickname(dasSource.getNickname());
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424 if (dbref == null || dbref.getAccessionId() == null
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425 || dbref.getAccessionId().length() < 1)
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427 responseComplete(dasSource, seq); // reduce thread count anyhow
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430 debug("new Das Feature Fetcher for " + dbref.getSource()
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431 + ":" + dbref.getAccessionId() + " querying "
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432 + dasSource.getUrl());
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433 FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()
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434 // + ":" + start + "," + end,
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437 fetcher.addFeatureListener(new FeatureListener()
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439 public void comeBackLater(FeatureEvent e)
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441 responseComplete(dasSource, seq);
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442 debug("das source " + e.getSource().getNickname()
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443 + " asked us to come back in " + e.getComeBackLater()
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447 public void newFeatures(FeatureEvent e)
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450 Das1Source ds = e.getSource();
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452 Map[] features = e.getFeatures();
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453 // add features to sequence
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454 debug("das source " + ds.getUrl() + " returned "
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455 + features.length + " features");
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457 if (features.length > 0)
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459 for (int i = 0; i < features.length; i++)
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461 SequenceFeature f = newSequenceFeature(features[i], source
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463 if (dbref.getMap() != null && f.getBegin() > 0
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466 debug("mapping from " + f.getBegin() + " - "
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468 SequenceFeature vf[] = null;
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472 vf = dbref.getMap().locateFeature(f);
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473 } catch (Exception ex)
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476 .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");
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477 Cache.log.info("Mapping feature from " + f.getBegin()
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478 + " to " + f.getEnd() + " in dbref "
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479 + dbref.getAccessionId() + " in "
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480 + dbref.getSource());
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481 Cache.log.info("using das Source " + ds.getUrl());
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482 Cache.log.info("Exception", ex);
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487 for (int v = 0; v < vf.length; v++)
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489 debug("mapping to " + v + ": "
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490 + vf[v].getBegin() + " - " + vf[v].getEnd());
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491 seq.addSequenceFeature(vf[v]);
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497 seq.addSequenceFeature(f);
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501 featuresAdded(seq);
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505 // System.out.println("No features found for " + seq.getName()
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506 // + " from: " + e.getDasSource().getNickname());
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508 responseComplete(dasSource, seq);
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518 protected void createFeatureFetcher(final SequenceI seq,
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519 final DasSource dasSource, String id)
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522 /// fetch DAS features
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523 final Das1Source source = new Das1Source();
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524 source.setUrl(dasSource.getUrl());
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525 source.setNickname(dasSource.getNickname());
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531 if (id != null && id.length() > 0)
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533 debug("new Das Feature Fetcher for " + id + " querying "
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534 + dasSource.getUrl());
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535 FeatureThread fetcher = new FeatureThread(id
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536 // + ":" + start + "," + end,
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539 fetcher.addFeatureListener(new FeatureListener()
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541 public void comeBackLater(FeatureEvent e)
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543 responseComplete(dasSource, seq);
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544 debug("das source " + e.getSource().getNickname()
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545 + " asked us to come back in " + e.getComeBackLater()
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549 public void newFeatures(FeatureEvent e)
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552 Das1Source ds = e.getSource();
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554 Map[] features = e.getFeatures();
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555 // add features to sequence
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556 debug("das source " + ds.getUrl() + " returned "
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557 + features.length + " features");
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559 if (features.length > 0)
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561 for (int i = 0; i < features.length; i++)
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563 SequenceFeature f = newSequenceFeature(features[i], source
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566 seq.addSequenceFeature(f);
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569 featuresAdded(seq);
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573 // System.out.println("No features found for " + seq.getName()
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574 // + " from: " + e.getDasSource().getNickname());
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576 responseComplete(dasSource, seq);
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585 // invalid fetch - indicate it is finished.
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586 debug("Skipping empty ID for querying "
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587 + dasSource.getUrl());
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588 responseComplete(dasSource, seq);
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593 * creates a jalview sequence feature from a das feature document
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594 * @param dasfeature
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595 * @return sequence feature object created using dasfeature information
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597 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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599 if (dasfeature == null)
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606 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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608 qName.equals("TYPE") ||
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609 qName.equals("START") ||
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610 qName.equals("END") ||
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611 qName.equals("NOTE") ||
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612 qName.equals("LINK") ||
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613 qName.equals("SCORE")
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615 String desc = new String();
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616 if (dasfeature.containsKey("NOTE"))
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618 desc += (String) dasfeature.get("NOTE");
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621 int start = 0, end = 0;
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626 start = Integer.parseInt(dasfeature.get("START").toString());
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627 } catch (Exception ex)
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632 end = Integer.parseInt(dasfeature.get("END").toString());
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633 } catch (Exception ex)
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638 score = Integer.parseInt(dasfeature.get("SCORE").toString());
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639 } catch (Exception ex)
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643 SequenceFeature f = new SequenceFeature((String) dasfeature
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644 .get("TYPE"), desc, start, end, score, nickname);
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646 if (dasfeature.containsKey("LINK"))
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648 f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"
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649 + dasfeature.get("LINK"));
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653 } catch (Exception e)
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655 System.out.println("ERRR " + e);
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656 e.printStackTrace();
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657 System.out.println("############");
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658 debug("Failed to parse " + dasfeature.toString(), e);
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663 * query the default DAS Source Registry for sources.
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664 * Uses value of jalview property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that doesn't exist.
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665 * @return list of sources
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667 public static DasSource[] getDASSources()
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670 String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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671 DasSourceBrowser.DEFAULT_REGISTRY);
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672 return getDASSources(registryURL);
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675 * query the given URL for DasSources.
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676 * @param registryURL
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677 * return sources from registryURL
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679 public static DasSource[] getDASSources(String registryURL)
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681 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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685 URL url = new URL(registryURL);
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687 DasSource[] sources = reader.readDasSource(url);
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689 List das1sources = new ArrayList();
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690 for (int i = 0; i < sources.length; i++)
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692 DasSource ds = sources[i];
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693 if (ds instanceof Das2Source)
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695 Das2Source d2s = (Das2Source) ds;
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696 if (d2s.hasDas1Capabilities())
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698 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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699 das1sources.add(d1s);
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703 else if (ds instanceof Das1Source)
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705 das1sources.add((Das1Source) ds);
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709 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources
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711 } catch (Exception ex)
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713 ex.printStackTrace();
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