X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=b4dd1f66ddb0472f9eed4f09d03da4ea77760de3;hb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;hp=dc516174859bd2b7f1e249a8c8e3ba7f8a476323;hpb=062dc2bf3f9a188f2797c4133da4474f79704185;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index dc51617..b4dd1f6 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -40,7 +40,9 @@ import org.biojava.dasobert.das2.DasSourceConverter;
 
 
 import jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
+import javax.swing.*;
 
 /**
  * DOCUMENT ME!
@@ -50,8 +52,8 @@ 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;
 
@@ -66,14 +68,77 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
-  public DasSequenceFeatureFetcher(AlignmentI align,
-                                   AlignFrame af,
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
+                                   final AlignFrame af,
                                    Vector selectedSources)
   {
     this.selectedSources = selectedSources;
-    this.dataset = align.getDataset();
+    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();
   }
@@ -145,10 +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();
@@ -158,13 +224,27 @@ 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()
             {
@@ -262,11 +342,9 @@ 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(),
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
               new String[]  {
               jalview.datamodel.DBRefSource.PDB,
               jalview.datamodel.DBRefSource.UNIPROT});
@@ -292,7 +370,7 @@ public class DasSequenceFeatureFetcher implements Runnable
                                     cs[l].getName());
 
 
-                    createFeatureFetcher(sequence,
+                    createFeatureFetcher(sequences[seqIndex],
                                          dasSource.getUrl(),
                                          ( (DBRefEntry) uprefs.get(j)).
                                          getAccessionId(),
@@ -305,19 +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());
@@ -340,7 +418,7 @@ 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