X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=2577a8b866abbbbe7dc7233c92538168b12b7058;hb=3f8dab9bfe7202a4a83a86052bcfe18f12f138a2;hp=7dbb18390a500a668dda2b53db420c28355efd38;hpb=bf2bf43c980b18a26b724d2a2d51dddc1a79a185;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 7dbb183..2577a8b 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -27,7 +27,6 @@ import java.util.*;
 import java.net.URL;
 
 import org.biojava.dasobert.das.FeatureThread;
-import org.biojava.dasobert.dasregistry.Das1Source;
 import org.biojava.dasobert.eventmodel.FeatureEvent;
 import org.biojava.dasobert.eventmodel.FeatureListener;
 import org.biojava.dasobert.dasregistry.DasSource;
@@ -40,7 +39,9 @@ import org.biojava.dasobert.das2.DasSourceConverter;
 
 
 import jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
+import javax.swing.*;
 
 /**
  * DOCUMENT ME!
@@ -50,27 +51,107 @@ import jalview.bin.Cache;
  */
 public class DasSequenceFeatureFetcher implements Runnable
 {
-  final AlignmentI dataset;
-  final AlignFrame af;
+  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(AlignmentI align,
-                                   AlignFrame af)
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
+                                   final AlignFrame af,
+                                   Vector selectedSources)
   {
-    this.dataset = align.getDataset();
+    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
@@ -139,10 +220,11 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param SourceUrl
    * @param id
    */
-  protected void createFeatureFetcher(final Sequence seq,
+  protected void createFeatureFetcher(final SequenceI seq,
                                       final String sourceUrl,
                                       String id,
-                                      String nickname)  {
+                                      String nickname)
+  {
 	  //////////////
 	  /// fetch DAS features
           final Das1Source source = new Das1Source();
@@ -152,16 +234,35 @@ public class DasSequenceFeatureFetcher implements Runnable
 
           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
-               +  ":" + seq.getStart() + "," +seq.getEnd()
-                 , source);
+                                                   //  +  ":" + 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.");
@@ -169,6 +270,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 
               public void newFeatures(FeatureEvent e)
               {
+                setThreadsRunning(-1);
                 Das1Source ds = e.getDasSource();
 
                 Map[] features = e.getFeatures();
@@ -204,34 +306,44 @@ public class DasSequenceFeatureFetcher implements Runnable
             fetcher.start();
 	  }
   }
+
+  synchronized void setThreadsRunning(int i)
+  {
+    threadsRunning += i;
+    if(threadsRunning<1)
+      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+  }
+
   /**
    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
    */
   public void run()
   {
-    long startTime = System.currentTimeMillis();
+    startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching DAS Sequence Features", startTime);
 
     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
 
-    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())
+    if(selectedSources==null || selectedSources.size()==0)
     {
-      token = st.nextToken();
-      for(int i=0; i<sources.length; i++)
+      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())
       {
-        if(sources[i].getNickname().equals(token))
+        token = st.nextToken();
+        for (int i = 0; i < sources.length; i++)
         {
-          selectedSources.addElement(sources[i]);
-          break;
+          if (sources[i].getNickname().equals(token))
+          {
+            selectedSources.addElement(sources[i]);
+            break;
+          }
         }
       }
     }
 
-
     if(selectedSources == null || selectedSources.size()==0)
     {
       System.out.println("No DAS Sources active");
@@ -242,11 +354,9 @@ public class DasSequenceFeatureFetcher implements Runnable
     try
     {
       int seqIndex = 0;
-      Vector sequences = dataset.getSequences();
-      while (seqIndex < sequences.size())
+      while (seqIndex < sequences.length)
       {
-          Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
               new String[]  {
               jalview.datamodel.DBRefSource.PDB,
               jalview.datamodel.DBRefSource.UNIPROT});
@@ -258,24 +368,22 @@ public class DasSequenceFeatureFetcher implements Runnable
             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.size(); j++)
+              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
-                org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
                 for (int l=0; l<cs.length; l++)
                 {
-                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
-                      uprefs.get(j)))
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
                   {
                     Cache.log.debug("Launched fetcher for coordinate system " +
                                     cs[l].getName());
 
 
-                    createFeatureFetcher(sequence,
+                    createFeatureFetcher(sequences[seqIndex],
                                          dasSource.getUrl(),
-                                         ( (DBRefEntry) uprefs.get(j)).
-                                         getAccessionId(),
+                                          uprefs[j].getAccessionId(),
                                          dasSource.getNickname());
                   }
                 }
@@ -285,19 +393,19 @@ public class DasSequenceFeatureFetcher implements Runnable
             {
               String id = null;
               // try and use the name as the sequence id
-              if (sequence.getName().indexOf("|") > -1)
+              if (sequences[seqIndex].getName().indexOf("|") > -1)
               {
-                id = sequence.getName().substring(
-                    sequence.getName().lastIndexOf("|") + 1);
+                id = sequences[seqIndex].getName().substring(
+                    sequences[seqIndex].getName().lastIndexOf("|") + 1);
               }
               else
               {
-                id = sequence.getName();
+                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(sequence,
+                createFeatureFetcher(sequences[seqIndex],
                                      dasSource.getUrl(),
                                      id,
                                      dasSource.getNickname());
@@ -312,8 +420,6 @@ public class DasSequenceFeatureFetcher implements Runnable
     {
       ex.printStackTrace();
     }
-
-    af.setProgressBar("DAS Feature Fetching Complete", startTime);
   }
 
 
@@ -322,7 +428,7 @@ public class DasSequenceFeatureFetcher implements Runnable
     DasSourceReaderImpl reader = new DasSourceReaderImpl();
 
     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://www.spice-3d.org/dasregistry/das1/sources"
+        "http://das.sanger.ac.uk/registry/das1/sources/"
       );
 
     try