2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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20 import jalview.bin.Cache;
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21 import jalview.datamodel.DBRefEntry;
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22 import jalview.datamodel.SequenceFeature;
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23 import jalview.datamodel.SequenceI;
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24 import jalview.gui.AlignFrame;
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25 import jalview.gui.Desktop;
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26 import jalview.gui.FeatureSettings;
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27 import jalview.util.UrlLink;
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28 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
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29 import jalview.ws.dbsources.das.api.jalviewSourceI;
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31 import java.util.ArrayList;
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32 import java.util.Arrays;
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33 import java.util.Enumeration;
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34 import java.util.HashMap;
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35 import java.util.HashSet;
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36 import java.util.Iterator;
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37 import java.util.List;
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38 import java.util.Map;
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39 import java.util.Set;
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40 import java.util.StringTokenizer;
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41 import java.util.Vector;
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43 import javax.swing.JOptionPane;
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45 import org.biodas.jdas.client.FeaturesClient;
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46 import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
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47 import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
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48 import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;
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49 import org.biodas.jdas.schema.features.ERRORSEGMENT;
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50 import org.biodas.jdas.schema.features.FEATURE;
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51 import org.biodas.jdas.schema.features.LINK;
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52 import org.biodas.jdas.schema.features.SEGMENT;
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53 import org.biodas.jdas.schema.features.TYPE;
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54 import org.biodas.jdas.schema.features.UNKNOWNFEATURE;
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55 import org.biodas.jdas.schema.features.UNKNOWNSEGMENT;
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56 import org.biodas.jdas.schema.sources.COORDINATES;
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62 * @version $Revision$
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64 public class DasSequenceFeatureFetcher
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66 SequenceI[] sequences;
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70 FeatureSettings fsettings;
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72 StringBuffer sbuffer = new StringBuffer();
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74 List<jalviewSourceI> selectedSources;
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76 boolean cancelled = false;
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78 private void debug(String mesg)
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83 private void debug(String mesg, Exception e)
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85 if (Cache.log != null)
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87 Cache.log.debug(mesg, e);
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91 System.err.println(mesg);
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94 e.printStackTrace();
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101 private DasSourceRegistryI sourceRegistry;
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102 private boolean useJDASMultiThread=true;
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104 * Creates a new SequenceFeatureFetcher object. Uses default
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111 public DasSequenceFeatureFetcher(SequenceI[] sequences,
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112 FeatureSettings fsettings, Vector selectedSources)
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114 this(sequences, fsettings, selectedSources, true, true, true);
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117 public DasSequenceFeatureFetcher(SequenceI[] oursequences,
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118 FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
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119 boolean checkDbrefs, boolean promptFetchDbrefs)
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121 this(oursequences,fsettings,selectedSources2,checkDbrefs,promptFetchDbrefs,true);
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123 public DasSequenceFeatureFetcher(SequenceI[] oursequences,
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124 FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
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125 boolean checkDbrefs, boolean promptFetchDbrefs, boolean useJDasMultiThread)
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127 this.useJDASMultiThread=useJDasMultiThread;
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128 this.selectedSources = new ArrayList<jalviewSourceI>();
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129 // filter both sequences and sources to eliminate duplicates
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130 for (jalviewSourceI src : selectedSources2)
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132 if (!selectedSources.contains(src))
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134 selectedSources.add(src);
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138 Vector sqs = new Vector();
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139 for (int i = 0; i < oursequences.length; i++)
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141 if (!sqs.contains(oursequences[i]))
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143 sqs.addElement(oursequences[i]);
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146 sequences = new SequenceI[sqs.size()];
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147 for (int i = 0; i < sequences.length; i++)
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149 sequences[i] = (SequenceI) sqs.elementAt(i);
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151 if (fsettings != null)
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153 this.fsettings = fsettings;
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154 this.af = fsettings.af;
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155 af.setShowSeqFeatures(true);
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157 int uniprotCount = 0;
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158 for (jalviewSourceI source : selectedSources)
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160 for (COORDINATES coords : source.getVersion().getCOORDINATES())
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162 // TODO: match UniProt coord system canonically (?) - does
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163 // UniProt==uniprot==UNIPROT ?
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164 if (coords.getAuthority().toLowerCase().equals("uniprot"))
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173 for (int i = 0; i < sequences.length; i++)
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175 DBRefEntry[] dbref = sequences[i].getDBRef();
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178 for (int j = 0; j < dbref.length; j++)
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180 if (dbref[j].getSource().equals(
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181 jalview.datamodel.DBRefSource.UNIPROT))
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190 if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
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193 int reply = JOptionPane.YES_OPTION;
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194 if (promptFetchDbrefs)
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196 reply = JOptionPane
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197 .showInternalConfirmDialog(
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199 "Do you want Jalview to find\n"
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200 + "Uniprot Accession ids for given sequence names?",
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201 "Find Uniprot Accession Ids",
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202 JOptionPane.YES_NO_OPTION,
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203 JOptionPane.QUESTION_MESSAGE);
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206 if (reply == JOptionPane.YES_OPTION)
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208 Thread thread = new Thread(new FetchDBRefs());
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222 private void _startFetching()
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225 new Thread(new FetchSeqFeatures()).start();
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227 class FetchSeqFeatures implements Runnable
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232 setGuiFetchComplete();
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235 class FetchDBRefs implements Runnable
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240 new DBRefFetcher(sequences, af).fetchDBRefs(true);
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242 setGuiFetchComplete();
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247 * Spawns Fetcher threads to add features to sequences in the dataset
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249 void startFetching()
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253 startTime = System.currentTimeMillis();
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256 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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258 if (sourceRegistry == null)
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260 sourceRegistry = Cache.getDasSourceRegistry();
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262 if (selectedSources == null || selectedSources.size() == 0)
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266 jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
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267 new jalviewSourceI[0]);
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268 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
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270 StringTokenizer st = new StringTokenizer(active, "\t");
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271 selectedSources = new Vector();
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273 while (st.hasMoreTokens())
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275 token = st.nextToken();
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276 for (int i = 0; i < sources.length; i++)
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278 if (sources[i].getTitle().equals(token))
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280 selectedSources.add(sources[i]);
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285 } catch (Exception ex)
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287 debug("Exception whilst setting default feature sources from registry and local preferences.",
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292 if (selectedSources == null || selectedSources.size() == 0)
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294 System.out.println("No DAS Sources active");
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296 setGuiNoDassourceActive();
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300 sourcesRemaining = selectedSources.size();
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301 FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();
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302 fc.setConnProps(sourceRegistry.getSessionHandler());
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303 // Now sending requests one at a time to each server
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304 ArrayList<jalviewSourceI> srcobj = new ArrayList<jalviewSourceI>();
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305 ArrayList<String> src = new ArrayList<String>();
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306 List<List<String>> ids = new ArrayList<List<String>>();
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307 List<List<DBRefEntry>> idobj = new ArrayList<List<DBRefEntry>>();
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308 List<Map<String, SequenceI>> sqset = new ArrayList<Map<String, SequenceI>>();
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309 for (jalviewSourceI _sr : selectedSources)
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312 Map<String, SequenceI> slist = new HashMap<String, SequenceI>();
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313 List<DBRefEntry> idob = new ArrayList<DBRefEntry>();
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314 List<String> qset = new ArrayList<String>();
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316 for (SequenceI seq : sequences)
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318 Object[] idset = nextSequence(_sr, seq);
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321 List<DBRefEntry> _idob = (List<DBRefEntry>) idset[0];
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322 List<String> _qset = (List<String>) idset[1];
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323 if (_idob.size() > 0)
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325 // add sequence's ref for each id derived from it
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326 // (space inefficient, but most unambiguous)
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327 // could replace with hash with _qset values as keys.
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328 Iterator<DBRefEntry> dbobj = _idob.iterator();
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329 for (String q : _qset)
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331 SequenceI osq = slist.get(q);
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332 DBRefEntry dr = dbobj.next();
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333 if (osq != null && osq != seq)
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335 // skip - non-canonical query
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347 if (idob.size() > 0)
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350 src.add(_sr.getSourceURL());
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356 Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
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357 Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();
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358 if (!useJDASMultiThread)
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360 Iterator<String> sources=src.iterator();
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361 // iterate over each query for each source and do each one individually
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362 for (List<String> idl:ids)
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364 String source=sources.next();
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365 FeaturesClient featuresc=new FeaturesClient(sourceRegistry.getSessionHandler().getConnectionPropertyProviderFor(source));
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366 for (String id:idl)
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368 List<String> qid=Arrays.asList(new String[] { id});
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370 DasGFFAdapter dga=featuresc.fetchData(source, qid);
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371 Map<List<String>,DasGFFAdapter> ers=results.get(source);
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374 results.put(source, ers=new HashMap<List<String>,DasGFFAdapter>());
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377 } catch (Exception ex)
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379 Map<List<String>,Exception> ers=errors.get(source);
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382 errors.put(source, ers=new HashMap<List<String>,Exception>());
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389 // pass them all at once
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390 fc.fetchData(src, ids, false, results, errors);
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392 while (!fc.isTerminated())
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397 } catch (InterruptedException x)
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403 Iterator<List<String>> idset = ids.iterator();
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404 Iterator<List<DBRefEntry>> idobjset = idobj.iterator();
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405 Iterator<Map<String, SequenceI>> seqset = sqset.iterator();
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406 for (jalviewSourceI source : srcobj)
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408 processResponse(seqset.next(), source, idset.next(), idobjset.next(),
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409 results.get(source.getSourceURL()),
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410 errors.get(source.getSourceURL()));
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414 private void processResponse(Map<String, SequenceI> sequencemap,
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415 jalviewSourceI jvsource, List<String> ids,
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416 List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,
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417 Map<List<String>, Exception> errors)
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419 Set<SequenceI> sequences = new HashSet<SequenceI>();
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420 String source = jvsource.getSourceURL();
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421 // process features
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422 DasGFFAdapter result = (results == null) ? null : results.get(ids);
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423 Exception error = (errors == null) ? null : errors.get(ids);
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424 if (result == null)
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426 debug("das source " + source + " could not be contacted. "
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427 + (error == null ? "" : error.toString()));
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432 GFFAdapter gff = result.getGFF();
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433 List<SEGMENT> segments = gff.getSegments();
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434 List<ERRORSEGMENT> errorsegs = gff.getErrorSegments();
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435 List<UNKNOWNFEATURE> unkfeats = gff.getUnknownFeatures();
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436 List<UNKNOWNSEGMENT> unksegs = gff.getUnknownSegments();
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437 debug("das source " + source + " returned " + gff.getTotal()
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438 + " responses. " + (errorsegs != null ? errorsegs.size() : 0)
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439 + " were incorrect segment queries, "
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440 + (unkfeats != null ? unkfeats.size() : 0)
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441 + " were unknown features "
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442 + (unksegs != null ? unksegs.size() : 0)
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443 + " were unknown segments and "
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444 + (segments != null ? segments.size() : 0)
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445 + " were segment responses.");
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446 Iterator<DBRefEntry> dbr = idobj.iterator();
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447 if (segments != null)
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449 for (SEGMENT seg : segments)
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451 String id = seg.getId();
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452 if (ids.indexOf(id)==-1)
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454 id=id.toUpperCase();
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456 DBRefEntry dbref = idobj.get(ids.indexOf(id));
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457 SequenceI sequence = sequencemap.get(id);
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458 boolean added = false;
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459 sequences.add(sequence);
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461 for (FEATURE feat : seg.getFEATURE())
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463 // standard DAS feature-> jalview sequence feature transformation
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464 SequenceFeature f = newSequenceFeature(feat, jvsource.getTitle());
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465 if (!parseSeqFeature(sequence, f, feat, jvsource))
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467 if (dbref.getMap() != null && f.getBegin() > 0
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470 debug("mapping from " + f.getBegin() + " - " + f.getEnd());
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471 SequenceFeature vf[] = null;
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475 vf = dbref.getMap().locateFeature(f);
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476 } catch (Exception ex)
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479 .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
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480 Cache.log.info("Mapping feature from " + f.getBegin()
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481 + " to " + f.getEnd() + " in dbref "
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482 + dbref.getAccessionId() + " in "
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483 + dbref.getSource());
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484 Cache.log.info("using das Source " + source);
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485 Cache.log.info("Exception", ex);
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490 for (int v = 0; v < vf.length; v++)
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492 debug("mapping to " + v + ": " + vf[v].getBegin()
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493 + " - " + vf[v].getEnd());
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494 sequence.addSequenceFeature(vf[v]);
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500 sequence.addSequenceFeature(f);
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505 featuresAdded(sequences);
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509 // System.out.println("No features found for " + seq.getName()
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510 // + " from: " + e.getDasSource().getNickname());
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515 private void setGuiNoDassourceActive()
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520 af.setProgressBar("No DAS Sources Active", startTime);
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522 if (getFeatSettings() != null)
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524 fsettings.noDasSourceActive();
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529 * Update our fsettings dialog reference if we didn't have one when we were
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530 * first initialised.
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532 * @return fsettings
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534 private FeatureSettings getFeatSettings()
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536 if (fsettings == null)
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540 fsettings = af.featureSettings;
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546 public void cancel()
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550 af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
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555 int sourcesRemaining = 0;
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556 private boolean running=false;
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557 private void setGuiFetchComplete()
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560 if (!cancelled && af != null)
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562 // only update the progress bar if we've completed the fetch normally
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563 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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566 if (af != null && af.featureSettings != null)
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568 af.featureSettings.setTableData();
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571 if (getFeatSettings() != null)
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573 fsettings.complete();
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577 void featuresAdded(Set<SequenceI> seqs)
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581 // no gui to update with features.
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584 af.getFeatureRenderer().featuresAdded();
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586 int start = af.getViewport().getStartSeq();
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587 int end = af.getViewport().getEndSeq();
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589 for (index = start; index < end; index++)
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591 for (SequenceI seq : seqs)
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593 if (seq == af.getViewport().getAlignment().getSequenceAt(index)
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594 .getDatasetSequence())
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596 af.alignPanel.paintAlignment(true);
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604 Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)
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608 DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
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609 seq.getDBRef(), new String[]
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611 // jalview.datamodel.DBRefSource.PDB,
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612 jalview.datamodel.DBRefSource.UNIPROT,
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613 // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
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616 // TODO: minimal list of DAS queries to make by querying with untyped ID if
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617 // distinct from any typed IDs
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619 List<DBRefEntry> ids = new ArrayList<DBRefEntry>();
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620 List<String> qstring = new ArrayList<String>();
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621 boolean dasCoordSysFound = false;
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623 if (uprefs != null)
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625 // do any of these ids match the source's coordinate system ?
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626 for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
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629 for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
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631 if (jalview.util.DBRefUtils.isDasCoordinateSystem(
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632 csys.getAuthority(), uprefs[j]))
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634 debug("Launched fetcher for coordinate system "
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635 + csys.getAuthority());
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636 // Will have to pass any mapping information to the fetcher
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637 // - the start/end for the DBRefEntry may not be the same as the
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638 // sequence's start/end
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640 System.out.println(seq.getName() + " "
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641 + (seq.getDatasetSequence() == null) + " "
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644 dasCoordSysFound = true; // break's out of the loop
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645 ids.add(uprefs[j]);
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646 qstring.add(uprefs[j].getAccessionId());
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649 System.out.println("IGNORE " + csys.getAuthority());
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654 if (!dasCoordSysFound)
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657 // try and use the name as the sequence id
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658 if (seq.getName().indexOf("|") > -1)
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660 id = seq.getName().substring(seq.getName().lastIndexOf("|") + 1);
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661 if (id.trim().length() < 4)
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663 // hack - we regard a significant ID as being at least 4
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664 // non-whitespace characters
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665 id = seq.getName().substring(0, seq.getName().lastIndexOf("|"));
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666 if (id.indexOf("|") > -1)
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668 id = id.substring(id.lastIndexOf("|") + 1);
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674 id = seq.getName();
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678 DBRefEntry dbre = new DBRefEntry();
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679 dbre.setAccessionId(id);
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680 // Should try to call a general feature fetcher that
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681 // queries many sources with name to discover applicable ID references
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683 qstring.add(dbre.getAccessionId());
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687 return new Object[]
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692 * examine the given sequence feature to determine if it should actually be
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693 * turned into sequence annotation or database cross references rather than a
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694 * simple sequence feature.
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697 * the sequence to annotate
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699 * the jalview sequence feature generated from the DAS feature
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701 * the sequence feature attributes
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703 * the source that emitted the feature
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704 * @return true if feature was consumed as another kind of annotation.
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706 protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,
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707 FEATURE feature, jalviewSourceI source)
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709 SequenceI mseq = seq;
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710 while (seq.getDatasetSequence() != null)
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712 seq = seq.getDatasetSequence();
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714 if (f.getType() != null)
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716 String type = f.getType();
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717 if (type.equalsIgnoreCase("protein_name"))
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719 // parse name onto the alignment sequence or the dataset sequence.
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720 if (seq.getDescription() == null
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721 || seq.getDescription().trim().length() == 0)
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723 // could look at the note series to pick out the first long name, for
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724 // the moment just use the whole description string
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725 seq.setDescription(f.getDescription());
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727 if (mseq.getDescription() == null
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728 || mseq.getDescription().trim().length() == 0)
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730 // could look at the note series to pick out the first long name, for
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731 // the moment just use the whole description string
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732 mseq.setDescription(f.getDescription());
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736 // check if source has biosapiens or other sequence ontology label
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737 if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))
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739 // try to parse the accession out
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741 DBRefEntry dbr = new DBRefEntry();
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742 dbr.setVersion(source.getTitle());
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743 StringTokenizer st = new StringTokenizer(f.getDescription(), ":");
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744 if (st.hasMoreTokens())
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746 dbr.setSource(st.nextToken());
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748 if (st.hasMoreTokens())
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750 dbr.setAccessionId(st.nextToken());
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754 if (f.links != null && f.links.size() > 0)
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756 // feature is also appended to enable links to be seen.
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757 // TODO: consider extending dbrefs to have their own links ?
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758 // TODO: new feature: extract dbref links from DAS servers and add the
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759 // URL pattern to the list of DB name associated links in the user's
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761 // for the moment - just fix up the existing feature so it displays
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763 // f.setType(dbr.getSource());
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764 // f.setDescription();
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765 f.setValue("linkonly", Boolean.TRUE);
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766 // f.setDescription("");
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767 Vector newlinks = new Vector();
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768 Enumeration it = f.links.elements();
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769 while (it.hasMoreElements())
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772 UrlLink urllink = new UrlLink(elm = (String) it.nextElement());
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773 if (urllink.isValid())
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775 urllink.setLabel(f.getDescription());
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776 newlinks.addElement(urllink.toString());
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780 // couldn't parse the link properly. Keep it anyway - just in
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782 debug("couldn't parse link string - " + elm);
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783 newlinks.addElement(elm);
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786 f.links = newlinks;
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787 seq.addSequenceFeature(f);
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796 * creates a jalview sequence feature from a das feature document
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799 * @return sequence feature object created using dasfeature information
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801 SequenceFeature newSequenceFeature(FEATURE feat, String nickname)
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810 * Different qNames for a DAS Feature - are string keys to the HashMaps in
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811 * features "METHOD") || qName.equals("TYPE") || qName.equals("START") ||
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812 * qName.equals("END") || qName.equals("NOTE") || qName.equals("LINK") ||
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813 * qName.equals("SCORE")
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815 String desc = new String();
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816 if (feat.getNOTE() != null)
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818 for (String note : feat.getNOTE())
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820 desc += (String) note;
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824 int start = 0, end = 0;
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829 start = Integer.parseInt(feat.getSTART().toString());
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830 } catch (Exception ex)
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835 end = Integer.parseInt(feat.getEND().toString());
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836 } catch (Exception ex)
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841 Object scr = feat.getSCORE();
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844 score = (float) Double.parseDouble(scr.toString());
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847 } catch (Exception ex)
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851 SequenceFeature f = new SequenceFeature(
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852 getTypeString(feat.getTYPE()), desc, start, end, score,
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855 if (feat.getLINK() != null)
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857 for (LINK link : feat.getLINK())
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859 // Do not put feature extent in link text for non-positional features
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860 if (f.begin == 0 && f.end == 0)
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862 f.addLink(f.getType() + " " + link.getContent() + "|"
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867 f.addLink(f.getType() + " " + f.begin + "_" + f.end + " "
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868 + link.getContent() + "|" + link.getHref());
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874 } catch (Exception e)
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876 System.out.println("ERRR " + e);
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877 e.printStackTrace();
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878 System.out.println("############");
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879 debug("Failed to parse " + feat.toString(), e);
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884 private String getTypeString(TYPE type)
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886 return type.getContent();
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889 public boolean isRunning()
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