2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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21 import jalview.datamodel.*;
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23 import jalview.gui.*;
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27 import java.net.URL;
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29 import org.biojava.dasobert.das.FeatureThread;
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30 import org.biojava.dasobert.eventmodel.FeatureEvent;
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31 import org.biojava.dasobert.eventmodel.FeatureListener;
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32 import org.biojava.dasobert.dasregistry.DasSource;
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34 import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
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35 import org.biojava.dasobert.dasregistry.Das1Source;
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36 import org.biojava.dasobert.dasregistry.DasSource;
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37 import org.biojava.dasobert.das2.Das2Source;
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38 import org.biojava.dasobert.das2.DasSourceConverter;
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41 import jalview.bin.Cache;
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42 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
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44 import javax.swing.*;
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50 * @version $Revision$
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52 public class DasSequenceFeatureFetcher implements Runnable
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54 SequenceI [] sequences;
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56 StringBuffer sbuffer = new StringBuffer();
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57 Vector selectedSources;
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60 int threadsRunning = 0;
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61 boolean allBatchesComplete = false;
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65 * Creates a new SequenceFeatureFetcher object.
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68 * @param align DOCUMENT ME!
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69 * @param ap DOCUMENT ME!
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71 public DasSequenceFeatureFetcher(SequenceI [] sequences,
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72 final AlignFrame af,
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73 Vector selectedSources)
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75 this.selectedSources = selectedSources;
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76 this.sequences = sequences;
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79 int uniprotCount = 0;
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80 for (int i = 0; i < selectedSources.size(); i++)
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82 DasSource source = (DasSource) selectedSources.elementAt(i);
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83 DasCoordinateSystem[] coords = source.getCoordinateSystem();
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84 for (int c = 0; c < coords.length; c++)
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86 if (coords[c].getName().indexOf("UniProt")>-1)
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95 for(int i=0; i<sequences.length; i++)
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97 DBRefEntry [] dbref = sequences[i].getDBRef();
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100 for(int j=0; j<dbref.length; j++)
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102 if(dbref[j].getSource()
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103 .equals(jalview.datamodel.DBRefSource.UNIPROT))
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112 if(refCount<sequences.length && uniprotCount>0)
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115 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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116 "Do you want Jalview to find\n"
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117 +"Uniprot Accession ids for given sequence names?",
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118 "Find Uniprot Accession Ids",
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119 JOptionPane.YES_NO_OPTION,
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120 JOptionPane.QUESTION_MESSAGE);
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122 if(reply == JOptionPane.YES_OPTION)
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124 Thread thread = new Thread(new FetchDBRefs());
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133 /* System.out.println("User selection is " +
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134 ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
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135 + " % Uniprot, and "+refCount+" / " +sequences.length+" have uniprot accession");
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139 void startFetching()
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141 Thread thread = new Thread(this);
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145 class FetchDBRefs implements Runnable
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150 af.getViewport().getAlignment(), af).fetchDBRefs(true);
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157 * creates a jalview sequence feature from a das feature document
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158 * @param dasfeature
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159 * @return sequence feature object created using dasfeature information
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161 SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
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165 * Different qNames for a DAS Feature - are string keys to the HashMaps in features
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167 qName.equals("TYPE") ||
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168 qName.equals("START") ||
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169 qName.equals("END") ||
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170 qName.equals("NOTE") ||
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171 qName.equals("LINK") ||
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172 qName.equals("SCORE")
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174 String desc = new String();
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175 if (dasfeature.containsKey("NOTE"))
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176 desc+=(String) dasfeature.get("NOTE");
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179 int start = 0, end = 0;
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182 try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
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183 catch( Exception ex){}
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184 try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
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185 catch (Exception ex){}
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186 try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
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187 catch (Exception ex){}
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190 SequenceFeature f = new SequenceFeature(
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191 (String) dasfeature.get("TYPE"),
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198 if (dasfeature.containsKey("LINK"))
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200 f.addLink(f.getType()+" "+f.begin+"_"+f.end
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201 +"|"+ dasfeature.get("LINK"));
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203 // (String) dasfeature.get("ID"),
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204 //// (String) dasfeature.get("METHOD"),
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205 // (String) dasfeature.get("SCORE"),
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211 catch (Exception e) {
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212 System.out.println("ERRR "+e);
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213 e.printStackTrace();
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214 System.out.println("############");
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215 Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
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220 * fetch and add das features to a sequence using the given source URL and Id to create a feature request
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225 protected void createFeatureFetcher(final SequenceI seq,
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226 final String sourceUrl,
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231 /// fetch DAS features
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232 final Das1Source source = new Das1Source();
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233 source.setUrl(sourceUrl);
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234 source.setNickname(nickname);
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237 Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
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240 if (id != null && id.length() > 0)
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242 setThreadsRunning(+1);
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244 // int start=seq.getStart(), end = seq.getEnd();
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245 /* if(af.getViewport().getSelectionGroup()!=null)
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247 SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
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248 start = tmp.findPosition(
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249 af.getViewport().getSelectionGroup().getStartRes()
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252 end = tmp.findPosition(
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253 af.getViewport().getSelectionGroup().getEndRes()
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257 FeatureThread fetcher = new FeatureThread(id
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258 // + ":" + start + "," + end,
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262 fetcher.addFeatureListener(new FeatureListener()
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264 public void comeBackLater(FeatureEvent e)
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266 setThreadsRunning(-1);
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267 Cache.log.debug("das source " + e.getDasSource().getNickname() +
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268 " asked us to come back in " + e.getComeBackLater() +
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272 public void newFeatures(FeatureEvent e)
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274 setThreadsRunning(-1);
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275 Das1Source ds = e.getDasSource();
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277 Map[] features = e.getFeatures();
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278 // add features to sequence
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279 Cache.log.debug("das source " + ds.getUrl() + " returned " +
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280 features.length + " features");
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282 if (features.length > 0)
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284 for (int i = 0; i < features.length; i++)
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286 SequenceFeature f = newSequenceFeature(features[i],
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287 source.getNickname());
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289 seq.addSequenceFeature(f);
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294 System.out.println("No features found for sequence " +seq.getName()
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295 +" from: "+ e.getDasSource().getNickname());
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303 //NOTE alignPanel listener will be called after the previous
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304 //anonymous listener!!!
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305 fetcher.addFeatureListener(af);
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311 synchronized void setThreadsRunning(int i)
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313 threadsRunning += i;
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314 if(threadsRunning<1 && allBatchesComplete)
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316 af.setProgressBar("DAS Feature Fetching Complete", startTime);
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318 if(af.featureSettings!=null)
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319 af.featureSettings.setTableData();
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324 * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
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328 startTime = System.currentTimeMillis();
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329 af.setProgressBar("Fetching DAS Sequence Features", startTime);
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331 DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
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333 if(selectedSources==null || selectedSources.size()==0)
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335 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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336 StringTokenizer st = new StringTokenizer(active, "\t");
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337 Vector selectedSources = new Vector();
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339 while (st.hasMoreTokens())
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341 token = st.nextToken();
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342 for (int i = 0; i < sources.length; i++)
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344 if (sources[i].getNickname().equals(token))
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346 selectedSources.addElement(sources[i]);
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353 if(selectedSources == null || selectedSources.size()==0)
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355 System.out.println("No DAS Sources active");
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356 af.setProgressBar("No DAS Sources Active", startTime);
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362 //We must limit the feature fetching to 20 to prevent
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363 //Servers being overloaded with too many requests
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364 int batchCount = 0;
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365 int batchMaxSize = 10;
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367 while (seqIndex < sequences.length)
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370 if(batchCount>=batchMaxSize)
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372 waitTillBatchComplete();
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376 DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
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378 jalview.datamodel.DBRefSource.PDB,
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379 jalview.datamodel.DBRefSource.UNIPROT});
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381 for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
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383 DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
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385 if (uprefs != null)
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387 // we know the id for this entry, so don't note its ID in the unknownSequences list
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388 for (int j = 0; j < uprefs.length; j++)
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391 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
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392 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
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393 for (int l=0; l<cs.length; l++)
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395 if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
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397 Cache.log.debug("Launched fetcher for coordinate system " +
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401 createFeatureFetcher(sequences[seqIndex],
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402 dasSource.getUrl(),
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403 uprefs[j].getAccessionId(),
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404 dasSource.getNickname());
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412 // try and use the name as the sequence id
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413 if (sequences[seqIndex].getName().indexOf("|") > -1)
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415 id = sequences[seqIndex].getName().substring(
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416 sequences[seqIndex].getName().lastIndexOf("|") + 1);
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420 id = sequences[seqIndex].getName();
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424 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
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425 createFeatureFetcher(sequences[seqIndex],
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426 dasSource.getUrl(),
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428 dasSource.getNickname());
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436 catch (Exception ex)
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438 ex.printStackTrace();
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440 allBatchesComplete = true;
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443 void waitTillBatchComplete()
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445 while( threadsRunning > 0 )
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450 }catch(Exception ex)
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452 ex.printStackTrace();
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459 public static DasSource[] getDASSources()
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461 DasSourceReaderImpl reader = new DasSourceReaderImpl();
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463 String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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464 "http://das.sanger.ac.uk/registry/das1/sources/"
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469 URL url = new URL(registryURL);
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471 DasSource[] sources = reader.readDasSource(url);
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473 List das1sources = new ArrayList();
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474 for (int i = 0; i < sources.length; i++)
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476 DasSource ds = sources[i];
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477 if (ds instanceof Das2Source)
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479 Das2Source d2s = (Das2Source) ds;
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480 if (d2s.hasDas1Capabilities())
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482 Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
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483 das1sources.add(d1s);
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487 else if (ds instanceof Das1Source)
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489 das1sources.add( (Das1Source) ds);
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493 return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
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495 catch (Exception ex)
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497 ex.printStackTrace();
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