X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=7a001a94212283507ad9391d1011df1e8a5eb6b2;hb=89a0b775abfaa90242a171ca8133784a424a3d7b;hp=1e07c49193355b20a102badef959c46eddff0497;hpb=91c5d2144a780716e755e99882acffe46b40f18f;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 1e07c49..7a001a9 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;
@@ -83,7 +82,6 @@ public class DasSequenceFeatureFetcher implements Runnable
       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++;
@@ -100,12 +98,9 @@ public class DasSequenceFeatureFetcher implements Runnable
       {
         for(int j=0; j<dbref.length; j++)
         {
-          System.out.println(dbref[j].getSource()
-                             +" "+jalview.datamodel.DBRefSource.UNIPROT);
           if(dbref[j].getSource()
              .equals(jalview.datamodel.DBRefSource.UNIPROT))
           {
-            System.out.println("got a match");
             refCount++;
             break;
           }
@@ -113,7 +108,6 @@ public class DasSequenceFeatureFetcher implements Runnable
       }
     }
 
-   System.out.println(refCount+" "+uniprotCount+" "+sequences.length);
     if(refCount<sequences.length && uniprotCount>0)
     {
 
@@ -126,21 +120,38 @@ public class DasSequenceFeatureFetcher implements Runnable
 
      if(reply == JOptionPane.YES_OPTION)
      {
-       new DBRefFetcher(
-             af.getViewport().getAlignment(), af).fetchDBRefs(true);
-
+       Thread thread = new Thread(new FetchDBRefs());
+       thread.start();
      }
+     else
+      startFetching();
     }
+    else
+      startFetching();
 
-   System.out.println("User selection is "
-                      +
+  /* 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
@@ -194,7 +205,6 @@ public class DasSequenceFeatureFetcher implements Runnable
 				//  null
 		  	// );
 
-                     // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);
 	  return f;
 	  }
 	  catch (Exception e) {
@@ -228,9 +238,8 @@ public class DasSequenceFeatureFetcher implements Runnable
           {
             setThreadsRunning(+1);
 
-            int start=seq.getStart(), end = seq.getEnd();
-
-            if(af.getViewport().getSelectionGroup()!=null)
+          //  int start=seq.getStart(), end = seq.getEnd();
+          /*  if(af.getViewport().getSelectionGroup()!=null)
             {
               SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
               start = tmp.findPosition(
@@ -240,7 +249,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               end = tmp.findPosition(
                  af.getViewport().getSelectionGroup().getEndRes()
                  );
-            }
+            }*/
 
             FeatureThread fetcher = new FeatureThread(id
                                                    //  +  ":" + start + "," + end,
@@ -300,7 +309,12 @@ public class DasSequenceFeatureFetcher implements Runnable
   {
     threadsRunning += i;
     if(threadsRunning<1)
+    {
       af.setProgressBar("DAS Feature Fetching Complete", startTime);
+
+      if(af.featureSettings!=null)
+        af.featureSettings.setTableData();
+    }
   }
 
   /**
@@ -361,7 +375,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               {
 
                 // 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(), uprefs[j]))