2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 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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55 private void debug(String mesg)
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60 private void debug(String mesg, Exception e)
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62 if (Cache.log != null)
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64 Cache.log.debug(mesg, e);
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68 System.err.println(mesg);
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71 e.printStackTrace();
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79 * Creates a new SequenceFeatureFetcher object. Uses default
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86 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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87 FeatureSettings fsettings, Vector selectedSources)
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89 this(sequences, fsettings, selectedSources, true, true);
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92 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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93 FeatureSettings fsettings, Vector selectedSources,
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94 boolean checkDbrefs, boolean promptFetchDbrefs)
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96 this.selectedSources = selectedSources;
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97 this.sequences = sequences;
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98 if (fsettings != null)
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100 this.fsettings = fsettings;
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101 this.af = fsettings.af;
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102 af.getViewport().setShowSequenceFeatures(true);
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104 int uniprotCount = 0;
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105 for (int i = 0; i < selectedSources.size(); i++)
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107 DasSource source = (DasSource) selectedSources.elementAt(i);
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108 DasCoordinateSystem[] coords = source.getCoordinateSystem();
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109 for (int c = 0; c < coords.length; c++)
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111 // TODO: match UniProt coord system canonically (?) - does
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112 // UniProt==uniprot==UNIPROT ?
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113 if (coords[c].getName().indexOf("UniProt") > -1)
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122 for (int i = 0; i < sequences.length; i++)
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124 DBRefEntry[] dbref = sequences[i].getDBRef();
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127 for (int j = 0; j < dbref.length; j++)
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129 if (dbref[j].getSource().equals(
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130 jalview.datamodel.DBRefSource.UNIPROT))
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139 if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
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142 int reply = JOptionPane.YES_OPTION;
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143 if (promptFetchDbrefs)
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145 reply = JOptionPane
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146 .showInternalConfirmDialog(
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148 "Do you want Jalview to find\n"
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149 + "Uniprot Accession ids for given sequence names?",
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150 "Find Uniprot Accession Ids",
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151 JOptionPane.YES_NO_OPTION,
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152 JOptionPane.QUESTION_MESSAGE);
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155 if (reply == JOptionPane.YES_OPTION)
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157 Thread thread = new Thread(new FetchDBRefs());
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172 class FetchDBRefs implements Runnable
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176 new DBRefFetcher(sequences, af).fetchDBRefs(true);
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182 * Spawns a number of dasobert Fetcher threads to add features to sequences in
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185 void startFetching()
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188 startTime = System.currentTimeMillis();
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191 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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194 DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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196 if (selectedSources == null || selectedSources.size() == 0)
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198 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
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200 StringTokenizer st = new StringTokenizer(active, "\t");
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201 Vector selectedSources = new Vector();
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203 while (st.hasMoreTokens())
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205 token = st.nextToken();
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206 for (int i = 0; i < sources.length; i++)
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208 if (sources[i].getNickname().equals(token))
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210 selectedSources.addElement(sources[i]);
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217 if (selectedSources == null || selectedSources.size() == 0)
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219 System.out.println("No DAS Sources active");
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221 setGuiNoDassourceActive();
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225 sourcesRemaining = selectedSources.size();
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226 // Now sending requests one at a time to each server
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227 for (int sourceIndex = 0; sourceIndex < selectedSources.size()
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228 && !cancelled; sourceIndex++)
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230 DasSource dasSource = (DasSource) selectedSources
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231 .elementAt(sourceIndex);
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233 nextSequence(dasSource, sequences[0]);
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237 private void setGuiNoDassourceActive()
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242 af.setProgressBar("No DAS Sources Active", startTime);
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244 if (getFeatSettings() != null)
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246 fsettings.noDasSourceActive();
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251 * Update our fsettings dialog reference if we didn't have one when we were
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252 * first initialised.
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254 * @return fsettings
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256 private FeatureSettings getFeatSettings()
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258 if (fsettings == null)
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262 fsettings = af.featureSettings;
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268 public void cancel()
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272 af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
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277 int sourcesRemaining = 0;
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279 void responseComplete(DasSource dasSource, SequenceI seq)
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283 for (int seqIndex = 0; seqIndex < sequences.length - 1 && !cancelled; seqIndex++)
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285 if (sequences[seqIndex] == seq)
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287 nextSequence(dasSource, sequences[++seqIndex]);
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293 sourcesRemaining--;
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295 if (sourcesRemaining == 0)
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297 System.err.println("Fetching Complete.");
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298 setGuiFetchComplete();
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303 private void setGuiFetchComplete()
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308 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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311 if (af != null && af.featureSettings != null)
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313 af.featureSettings.setTableData();
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316 if (getFeatSettings() != null)
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318 fsettings.complete();
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322 void featuresAdded(SequenceI seq)
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326 // no gui to update with features.
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329 af.getFeatureRenderer().featuresAdded();
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331 int start = af.getViewport().getStartSeq();
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332 int end = af.getViewport().getEndSeq();
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334 for (index = start; index < end; index++)
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336 if (seq == af.getViewport().getAlignment().getSequenceAt(index)
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337 .getDatasetSequence())
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339 af.alignPanel.paintAlignment(true);
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345 void nextSequence(DasSource dasSource, SequenceI seq)
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349 DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
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350 seq.getDBRef(), new String[]
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352 // jalview.datamodel.DBRefSource.PDB,
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353 jalview.datamodel.DBRefSource.UNIPROT,
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354 // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
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357 // TODO: minimal list of DAS queries to make by querying with untyped ID if
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358 // distinct from any typed IDs
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360 boolean dasCoordSysFound = false;
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362 if (uprefs != null)
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364 // do any of these ids match the source's coordinate system ?
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365 for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
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367 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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369 for (int csIndex = 0; csIndex < cs.length && !dasCoordSysFound; csIndex++)
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372 && jalview.util.DBRefUtils.isDasCoordinateSystem(
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373 cs[csIndex].getName(), uprefs[j]))
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375 debug("Launched fetcher for coordinate system "
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376 + cs[0].getName());
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377 // Will have to pass any mapping information to the fetcher
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378 // - the start/end for the DBRefEntry may not be the same as the
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379 // sequence's start/end
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381 System.out.println(seq.getName() + " "
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382 + (seq.getDatasetSequence() == null) + " "
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383 + dasSource.getUrl());
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385 dasCoordSysFound = true; // break's out of the loop
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386 createFeatureFetcher(seq, dasSource, uprefs[j]);
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389 System.out.println("IGNORE " + cs[csIndex].getName());
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394 if (!dasCoordSysFound)
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397 // try and use the name as the sequence id
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398 if (seq.getName().indexOf("|") > -1)
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400 id = seq.getName().substring(seq.getName().lastIndexOf("|") + 1);
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401 if (id.trim().length() < 4)
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403 // hack - we regard a significant ID as being at least 4
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404 // non-whitespace characters
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405 id = seq.getName().substring(0, seq.getName().lastIndexOf("|"));
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406 if (id.indexOf("|") > -1)
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408 id = id.substring(id.lastIndexOf("|") + 1);
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414 id = seq.getName();
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418 // Should try to call a general feature fetcher that
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419 // queries many sources with name to discover applicable ID references
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420 createFeatureFetcher(seq, dasSource, id);
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427 * fetch and add das features to a sequence using the given source URL and
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428 * compatible DbRef id. new features are mapped using the DbRef mapping to the
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429 * local coordinate system.
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435 protected void createFeatureFetcher(final SequenceI seq,
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436 final DasSource dasSource, final DBRefEntry dbref)
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440 // / fetch DAS features
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441 final Das1Source source = new Das1Source();
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442 source.setUrl(dasSource.getUrl());
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443 source.setNickname(dasSource.getNickname());
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444 if (dbref == null || dbref.getAccessionId() == null
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445 || dbref.getAccessionId().length() < 1)
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447 responseComplete(dasSource, seq); // reduce thread count anyhow
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450 debug("new Das Feature Fetcher for " + dbref.getSource() + ":"
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451 + dbref.getAccessionId() + " querying " + dasSource.getUrl());
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452 FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()
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453 // + ":" + start + "," + end,
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456 fetcher.addFeatureListener(new FeatureListener()
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458 public void comeBackLater(FeatureEvent e)
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460 responseComplete(dasSource, seq);
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461 debug("das source " + e.getSource().getNickname()
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462 + " asked us to come back in " + e.getComeBackLater()
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466 public void newFeatures(FeatureEvent e)
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469 Das1Source ds = e.getSource();
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471 Map[] features = e.getFeatures();
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472 // add features to sequence
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473 debug("das source " + ds.getUrl() + " returned " + features.length
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476 if (features.length > 0)
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478 for (int i = 0; i < features.length; i++)
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480 SequenceFeature f = newSequenceFeature(features[i], source
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482 if (dbref.getMap() != null && f.getBegin() > 0
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485 debug("mapping from " + f.getBegin() + " - " + f.getEnd());
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486 SequenceFeature vf[] = null;
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490 vf = dbref.getMap().locateFeature(f);
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491 } catch (Exception ex)
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494 .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");
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495 Cache.log.info("Mapping feature from " + f.getBegin()
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496 + " to " + f.getEnd() + " in dbref "
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497 + dbref.getAccessionId() + " in "
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498 + dbref.getSource());
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499 Cache.log.info("using das Source " + ds.getUrl());
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500 Cache.log.info("Exception", ex);
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505 for (int v = 0; v < vf.length; v++)
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507 debug("mapping to " + v + ": " + vf[v].getBegin() + " - "
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509 seq.addSequenceFeature(vf[v]);
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515 seq.addSequenceFeature(f);
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519 featuresAdded(seq);
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523 // System.out.println("No features found for " + seq.getName()
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524 // + " from: " + e.getDasSource().getNickname());
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526 responseComplete(dasSource, seq);
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536 protected void createFeatureFetcher(final SequenceI seq,
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537 final DasSource dasSource, String id)
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540 // / fetch DAS features
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541 final Das1Source source = new Das1Source();
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542 source.setUrl(dasSource.getUrl());
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543 source.setNickname(dasSource.getNickname());
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549 if (id != null && id.length() > 0)
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551 debug("new Das Feature Fetcher for " + id + " querying "
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552 + dasSource.getUrl());
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553 FeatureThread fetcher = new FeatureThread(id
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554 // + ":" + start + "," + end,
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557 fetcher.addFeatureListener(new FeatureListener()
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559 public void comeBackLater(FeatureEvent e)
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561 responseComplete(dasSource, seq);
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562 debug("das source " + e.getSource().getNickname()
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563 + " asked us to come back in " + e.getComeBackLater()
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567 public void newFeatures(FeatureEvent e)
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570 Das1Source ds = e.getSource();
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572 Map[] features = e.getFeatures();
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573 // add features to sequence
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574 debug("das source " + ds.getUrl() + " returned "
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575 + features.length + " features");
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577 if (features.length > 0)
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579 for (int i = 0; i < features.length; i++)
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581 SequenceFeature f = newSequenceFeature(features[i], source
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584 seq.addSequenceFeature(f);
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587 featuresAdded(seq);
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591 // System.out.println("No features found for " + seq.getName()
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592 // + " from: " + e.getDasSource().getNickname());
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594 responseComplete(dasSource, seq);
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605 // invalid fetch - indicate it is finished.
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606 debug("Skipping empty ID for querying " + dasSource.getUrl());
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607 responseComplete(dasSource, seq);
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612 * creates a jalview sequence feature from a das feature document
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614 * @param dasfeature
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615 * @return sequence feature object created using dasfeature information
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617 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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619 if (dasfeature == null)
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626 * Different qNames for a DAS Feature - are string keys to the HashMaps in
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627 * features "METHOD") || qName.equals("TYPE") || qName.equals("START") ||
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628 * qName.equals("END") || qName.equals("NOTE") || qName.equals("LINK") ||
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629 * qName.equals("SCORE")
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631 String desc = new String();
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632 if (dasfeature.containsKey("NOTE"))
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634 desc += (String) dasfeature.get("NOTE");
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637 int start = 0, end = 0;
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642 start = Integer.parseInt(dasfeature.get("START").toString());
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643 } catch (Exception ex)
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648 end = Integer.parseInt(dasfeature.get("END").toString());
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649 } catch (Exception ex)
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654 score = Integer.parseInt(dasfeature.get("SCORE").toString());
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655 } catch (Exception ex)
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659 SequenceFeature f = new SequenceFeature((String) dasfeature
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660 .get("TYPE"), desc, start, end, score, nickname);
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662 if (dasfeature.containsKey("LINK"))
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664 f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"
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665 + dasfeature.get("LINK"));
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669 } catch (Exception e)
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671 System.out.println("ERRR " + e);
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672 e.printStackTrace();
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673 System.out.println("############");
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674 debug("Failed to parse " + dasfeature.toString(), e);
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680 * query the default DAS Source Registry for sources. Uses value of jalview
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681 * property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that
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684 * @return list of sources
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686 public static DasSource[] getDASSources()
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689 String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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690 DasSourceBrowser.DEFAULT_REGISTRY);
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691 return getDASSources(registryURL);
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695 * query the given URL for DasSources.
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697 * @param registryURL
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698 * return sources from registryURL
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700 public static DasSource[] getDASSources(String registryURL)
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702 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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706 URL url = new URL(registryURL);
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708 DasSource[] sources = reader.readDasSource(url);
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710 List das1sources = new ArrayList();
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711 for (int i = 0; i < sources.length; i++)
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713 DasSource ds = sources[i];
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714 if (ds instanceof Das2Source)
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716 Das2Source d2s = (Das2Source) ds;
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717 if (d2s.hasDas1Capabilities())
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719 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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720 das1sources.add(d1s);
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724 else if (ds instanceof Das1Source)
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726 das1sources.add((Das1Source) ds);
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730 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources
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732 } catch (Exception ex)
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734 ex.printStackTrace();
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