X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;fp=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=f78f943bbac8e4526331d4f01b108af58cb7bc12;hb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;hp=0000000000000000000000000000000000000000;hpb=072fc418c393cbd2a40dfa1d3e46f90178b79572;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
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+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import java.util.*;
+
+import java.net.URL;
+
+import org.biojava.dasobert.das.FeatureThread;
+import org.biojava.dasobert.eventmodel.FeatureEvent;
+import org.biojava.dasobert.eventmodel.FeatureListener;
+import org.biojava.dasobert.dasregistry.DasSource;
+
+import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.DasSourceConverter;
+
+
+import jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class DasSequenceFeatureFetcher implements Runnable
+{
+  SequenceI [] sequences;
+  AlignFrame af;
+  StringBuffer sbuffer = new StringBuffer();
+  Vector selectedSources;
+
+  long startTime;
+  int threadsRunning = 0;
+
+
+  /**
+   * Creates a new SequenceFeatureFetcher object.
+   * Uses default
+   *
+   * @param align DOCUMENT ME!
+   * @param ap DOCUMENT ME!
+   */
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
+                                   final AlignFrame af,
+                                   Vector selectedSources)
+  {
+    this.selectedSources = selectedSources;
+    this.sequences = sequences;
+    this.af = af;
+
+    int uniprotCount = 0;
+    for (int i = 0; i < selectedSources.size(); i++)
+    {
+      DasSource source = (DasSource) selectedSources.elementAt(i);
+      DasCoordinateSystem[] coords = source.getCoordinateSystem();
+      for (int c = 0; c < coords.length; c++)
+      {
+        if (coords[c].getName().indexOf("UniProt")>-1)
+        {
+          uniprotCount++;
+          break;
+        }
+      }
+    }
+
+    int refCount = 0;
+    for(int i=0; i<sequences.length; i++)
+    {
+      DBRefEntry [] dbref = sequences[i].getDBRef();
+      if(dbref!=null)
+      {
+        for(int j=0; j<dbref.length; j++)
+        {
+          if(dbref[j].getSource()
+             .equals(jalview.datamodel.DBRefSource.UNIPROT))
+          {
+            refCount++;
+            break;
+          }
+        }
+      }
+    }
+
+    if(refCount<sequences.length && uniprotCount>0)
+    {
+
+     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "Do you want Jalview to find\n"
+         +"Uniprot Accession ids for given sequence names?",
+         "Find Uniprot Accession Ids",
+         JOptionPane.YES_NO_OPTION,
+         JOptionPane.QUESTION_MESSAGE);
+
+     if(reply == JOptionPane.YES_OPTION)
+     {
+       Thread thread = new Thread(new FetchDBRefs());
+       thread.start();
+     }
+     else
+      startFetching();
+    }
+    else
+      startFetching();
+
+  /* System.out.println("User selection is "   +
+                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
+                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");
+*/
+  }
+
+  void startFetching()
+  {
+    Thread thread = new Thread(this);
+    thread.start();
+  }
+
+  class FetchDBRefs implements Runnable
+  {
+    public void run()
+    {
+      new DBRefFetcher(
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);
+      startFetching();
+    }
+  }
+
+
+  /**
+   * creates a jalview sequence feature from a das feature document
+   * @param dasfeature
+   * @return sequence feature object created using dasfeature information
+   */
+  SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
+  {
+	  try {
+		/**
+	   * Different qNames for a DAS Feature - are string keys to the HashMaps in features
+	   * "METHOD") ||
+	   qName.equals("TYPE") ||
+	   qName.equals("START") ||
+	   qName.equals("END") ||
+	   qName.equals("NOTE") ||
+	   qName.equals("LINK") ||
+	   qName.equals("SCORE")
+	   */
+		  String desc = new String();
+		  if (dasfeature.containsKey("NOTE"))
+				desc+=(String) dasfeature.get("NOTE");
+
+
+                  int start = 0, end = 0;
+                  float score = 0f;
+
+                  try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
+                  catch( Exception ex){}
+                  try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
+                  catch (Exception ex){}
+                  try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
+                  catch (Exception ex){}
+
+
+		  SequenceFeature f = new SequenceFeature(
+				  (String) dasfeature.get("TYPE"),
+				  desc,
+				  start,
+				  end,
+                                  score,
+				  nickname);
+
+                  if (dasfeature.containsKey("LINK"))
+                 {
+                      f.addLink(f.getType()+" "+f.begin+"_"+f.end
+                                +"|"+ dasfeature.get("LINK"));
+		  }
+                  // (String) dasfeature.get("ID"),
+                  ////  (String) dasfeature.get("METHOD"),
+				//  (String) dasfeature.get("SCORE"),
+				//  null
+		  	// );
+
+	  return f;
+	  }
+	  catch (Exception e) {
+            e.printStackTrace();
+		  Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
+		  return null;
+	  }
+  }
+  /**
+   * fetch and add das features to a sequence using the given source URL and Id to create a feature request
+   * @param seq
+   * @param SourceUrl
+   * @param id
+   */
+  protected void createFeatureFetcher(final SequenceI seq,
+                                      final String sourceUrl,
+                                      String id,
+                                      String nickname)
+  {
+	  //////////////
+	  /// fetch DAS features
+          final Das1Source source = new Das1Source();
+          source.setUrl(sourceUrl);
+          source.setNickname(nickname);
+
+
+          Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
+                          sourceUrl);
+
+          if (id != null && id.length() > 0)
+          {
+            setThreadsRunning(+1);
+
+          //  int start=seq.getStart(), end = seq.getEnd();
+          /*  if(af.getViewport().getSelectionGroup()!=null)
+            {
+              SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
+              start = tmp.findPosition(
+              af.getViewport().getSelectionGroup().getStartRes()
+                  );
+
+              end = tmp.findPosition(
+                 af.getViewport().getSelectionGroup().getEndRes()
+                 );
+            }*/
+
+            FeatureThread fetcher = new FeatureThread(id
+                                                   //  +  ":" + start + "," + end,
+                                                      , source);
+
+
+            fetcher.addFeatureListener(new FeatureListener()
+            {
+              public void comeBackLater(FeatureEvent e)
+              {
+                setThreadsRunning(-1);
+                Cache.log.debug("das source " + e.getDasSource().getNickname() +
+                                " asked us to come back in " + e.getComeBackLater() +
+                                " secs.");
+              }
+
+              public void newFeatures(FeatureEvent e)
+              {
+                setThreadsRunning(-1);
+                Das1Source ds = e.getDasSource();
+
+                Map[] features = e.getFeatures();
+                // add features to sequence
+                Cache.log.debug("das source " + ds.getUrl() + " returned " +
+                                features.length + " features");
+
+                if (features.length > 0)
+                {
+                  for (int i = 0; i < features.length; i++)
+                  {
+                      SequenceFeature f = newSequenceFeature(features[i],
+                        source.getNickname());
+
+                      seq.addSequenceFeature(f);
+                  }
+                }
+                else
+                {
+                  System.out.println("No features found for sequence " +seq.getName()
+                                     +" from: "+ e.getDasSource().getNickname());
+                }
+
+              }
+            }
+
+            );
+
+            //NOTE alignPanel listener will be called after the previous
+            //anonymous listener!!!
+            fetcher.addFeatureListener(af);
+
+            fetcher.start();
+	  }
+  }
+
+  synchronized void setThreadsRunning(int i)
+  {
+    threadsRunning += i;
+    if(threadsRunning<1)
+    {
+      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+
+      if(af.featureSettings!=null)
+        af.featureSettings.setTableData();
+    }
+  }
+
+  /**
+   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
+   */
+  public void run()
+  {
+    startTime = System.currentTimeMillis();
+    af.setProgressBar("Fetching DAS Sequence Features", startTime);
+
+    DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
+
+    if(selectedSources==null || selectedSources.size()==0)
+    {
+      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+      StringTokenizer st = new StringTokenizer(active, "\t");
+      Vector selectedSources = new Vector();
+      String token;
+      while (st.hasMoreTokens())
+      {
+        token = st.nextToken();
+        for (int i = 0; i < sources.length; i++)
+        {
+          if (sources[i].getNickname().equals(token))
+          {
+            selectedSources.addElement(sources[i]);
+            break;
+          }
+        }
+      }
+    }
+
+    if(selectedSources == null || selectedSources.size()==0)
+    {
+      System.out.println("No DAS Sources active");
+      af.setProgressBar("No DAS Sources Active", startTime);
+      return;
+    }
+
+    try
+    {
+      int seqIndex = 0;
+      while (seqIndex < sequences.length)
+      {
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
+              new String[]  {
+              jalview.datamodel.DBRefSource.PDB,
+              jalview.datamodel.DBRefSource.UNIPROT});
+
+          for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
+          {
+            DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
+
+            if (uprefs != null)
+            {
+              // we know the id for this entry, so don't note its ID in the unknownSequences list
+              for (int j = 0;  j < uprefs.length; j++)
+              {
+
+                // 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
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                for (int l=0; l<cs.length; l++)
+                {
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
+                  {
+                    Cache.log.debug("Launched fetcher for coordinate system " +
+                                    cs[l].getName());
+
+
+                    createFeatureFetcher(sequences[seqIndex],
+                                         dasSource.getUrl(),
+                                          uprefs[j].getAccessionId(),
+                                         dasSource.getNickname());
+                  }
+                }
+              }
+            }
+            else
+            {
+              String id = null;
+              // try and use the name as the sequence id
+              if (sequences[seqIndex].getName().indexOf("|") > -1)
+              {
+                id = sequences[seqIndex].getName().substring(
+                    sequences[seqIndex].getName().lastIndexOf("|") + 1);
+              }
+              else
+              {
+                id = sequences[seqIndex].getName();
+              }
+              if (id != null)
+              {
+                // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
+                createFeatureFetcher(sequences[seqIndex],
+                                     dasSource.getUrl(),
+                                     id,
+                                     dasSource.getNickname());
+              }
+            }
+          }
+
+          seqIndex++;
+    }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+
+  public static DasSource[] getDASSources()
+  {
+    DasSourceReaderImpl reader = new DasSourceReaderImpl();
+
+    String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+        "http://das.sanger.ac.uk/registry/das1/sources/"
+      );
+
+    try
+    {
+      URL url = new URL(registryURL);
+
+      DasSource[] sources = reader.readDasSource(url);
+
+      List das1sources = new ArrayList();
+      for (int i = 0; i < sources.length; i++)
+      {
+        DasSource ds = sources[i];
+        if (ds instanceof Das2Source)
+        {
+          Das2Source d2s = (Das2Source) ds;
+          if (d2s.hasDas1Capabilities())
+          {
+            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
+            das1sources.add(d1s);
+          }
+
+        }
+        else if (ds instanceof Das1Source)
+        {
+          das1sources.add( (Das1Source) ds);
+        }
+      }
+
+      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      return null;
+    }
+
+  }
+}
+
+