X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=b4dd1f66ddb0472f9eed4f09d03da4ea77760de3;hb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;hp=8f104c5fed6cf5ed7bd46cd76cde182a03f4feb6;hpb=91416b3038a6f3fc655791512770da07cb6cb251;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 8f104c5..b4dd1f6 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -30,13 +30,19 @@ 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.services.das.registry.DasRegistryAxisClient;
-import org.biojava.services.das.registry.DasSource;
+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 jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
+import javax.swing.*;
 
 /**
  * DOCUMENT ME!
@@ -46,22 +52,92 @@ import jalview.bin.Cache;
  */
 public class DasSequenceFeatureFetcher implements Runnable
 {
-  final AlignmentI dataset;
-  final AlignmentPanel ap;
+  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, AlignmentPanel ap)
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
+                                   final AlignFrame af,
+                                   Vector selectedSources)
   {
-    this.dataset = align.getDataset();
-    this.ap = ap;
+    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++)
+      {
+        System.out.println(coords[c].getName());
+        if (coords[c].getName().indexOf("UniProt")>-1)
+        {
+          uniprotCount++;
+          break;
+        }
+      }
+    }
+
+    int refCount = 0;
+    for(int i=0; i<sequences.length; i++)
+    {
+      Vector dbref = sequences[i].getDBRef();
+      if(dbref!=null)
+      {
+        for(int j=0; j<dbref.size(); j++)
+        {
+          DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);
+          System.out.println(entry.getSource()
+                             +" "+jalview.datamodel.DBRefSource.UNIPROT);
+          if(entry.getSource()
+             .equals(jalview.datamodel.DBRefSource.UNIPROT))
+          {
+            System.out.println("got a match");
+            refCount++;
+            break;
+          }
+        }
+      }
+    }
+
+   System.out.println(refCount+" "+uniprotCount+" "+sequences.length);
+    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)
+     {
+       new DBRefFetcher(
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);
+
+     }
+    }
+
+   System.out.println("User selection is "
+                      +
+                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
+                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");
+
 
     Thread thread = new Thread(this);
     thread.start();
@@ -134,10 +210,11 @@ 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();
@@ -147,15 +224,33 @@ public class DasSequenceFeatureFetcher implements Runnable
 
           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
                           sourceUrl);
+
           if (id != null && id.length() > 0)
           {
-            FeatureThread fetcher = new FeatureThread(id + ":" + seq.getStart() + "," +seq.getEnd()
-                , source);
+            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.");
@@ -163,6 +258,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 
               public void newFeatures(FeatureEvent e)
               {
+                setThreadsRunning(-1);
                 Das1Source ds = e.getDasSource();
 
                 Map[] features = e.getFeatures();
@@ -170,88 +266,85 @@ public class DasSequenceFeatureFetcher implements Runnable
                 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],
+                      SequenceFeature f = newSequenceFeature(features[i],
                         source.getNickname());
 
-                    if (seq.sequenceFeatures != null)
-                    {
-                      for (int j = 0; (f != null) && j < seq.sequenceFeatures.length;
-                           j++)
-                      {
-                        if (seq.sequenceFeatures[j].equals(f))
-                        {
-                          f = null;
-                        }
-                      }
-                    }
-                    if (f != null)
-                    {
                       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(ap);
+            fetcher.addFeatureListener(af);
 
             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()
   {
+    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;
+          }
         }
       }
     }
- // DasSource test = new DasSource();
- // test.setUrl("http://localhost:8080/das/gffdb/");
-  //test.setNickname("Trixkid");
- // selectedSources.addElement(test);
-
 
     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;
-      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(),
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
               new String[]  {
               jalview.datamodel.DBRefSource.PDB,
               jalview.datamodel.DBRefSource.UNIPROT});
@@ -263,17 +356,21 @@ 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, k = uprefs.size(); j < k; j++)
+              for (int j = 0;  j < uprefs.size(); 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.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
-                for (int l=0; l<cs.length; l++) {
+                org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                for (int l=0; l<cs.length; l++)
+                {
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
                       uprefs.get(j)))
                   {
                     Cache.log.debug("Launched fetcher for coordinate system " +
                                     cs[l].getName());
-                    createFeatureFetcher(sequence,
+
+
+                    createFeatureFetcher(sequences[seqIndex],
                                          dasSource.getUrl(),
                                          ( (DBRefEntry) uprefs.get(j)).
                                          getAccessionId(),
@@ -286,19 +383,19 @@ 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());
@@ -316,30 +413,49 @@ public class DasSequenceFeatureFetcher implements Runnable
   }
 
 
- public static DasSource[] getDASSources()
+  public static DasSource[] getDASSources()
   {
-    try
-    {
-      String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-          "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");
+    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);
 
-      DasRegistryAxisClient client = new DasRegistryAxisClient(url);
+      DasSource[] sources = reader.readDasSource(url);
 
-      DasSource[] services = client.listServices();
+      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 services;
+      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
+      return null;
     }
-    return null;
 
   }
-
 }