X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=2f94d64bf721402d910b9ff9744d8ee3e4ab5b2c;hb=4741fc6fc72b7c5ffd75af5b1bc17070fef448f9;hp=33791ad773008352344294067f74eeb425336896;hpb=ac5f3842d7230ae9761f2330b86e515efab29ee5;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 33791ad..2f94d64 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -130,8 +130,7 @@ public class DasSequenceFeatureFetcher
   {
     public void run()
     {
-      new DBRefFetcher(
-          af.getViewport().getAlignment(), af).fetchDBRefs(true);
+      new DBRefFetcher(sequences, af).fetchDBRefs(true);
       startFetching();
     }
   }
@@ -173,6 +172,8 @@ public class DasSequenceFeatureFetcher
      {
        System.out.println("No DAS Sources active");
        af.setProgressBar("No DAS Sources Active", startTime);
+       cancelled = true;
+       fsettings.noDasSourceActive();
        return;
      }
 
@@ -250,7 +251,9 @@ public class DasSequenceFeatureFetcher
 
   void nextSequence(DasSource dasSource, SequenceI seq)
   {
-      DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+    if (cancelled)
+      return;
+    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
           new String[]
           {
         //  jalview.datamodel.DBRefSource.PDB,
@@ -264,11 +267,11 @@ public class DasSequenceFeatureFetcher
       if (uprefs != null)
         {
           // do any of these ids match the source's coordinate system ?
-          for (int j = 0; j < uprefs.length; j++)
+          for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
           {
             DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
 
-            for(int csIndex=0; csIndex<cs.length; csIndex++)
+            for(int csIndex=0; csIndex<cs.length && !dasCoordSysFound; csIndex++)
             {
               if (cs.length > 0 && jalview.util.DBRefUtils
                   .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))
@@ -281,11 +284,10 @@ public class DasSequenceFeatureFetcher
                 System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)
                                    + " " + dasSource.getUrl());
 
-                dasCoordSysFound = false;
+                dasCoordSysFound = true; // break's out of the loop
                 createFeatureFetcher(seq,
                                      dasSource,
                                      uprefs[j]);
-                break; // only do this for one reference - assume same source will send same features for all IDs
               }
               else
                 System.out.println("IGNORE " + cs[csIndex].getName());
@@ -372,7 +374,19 @@ public class DasSequenceFeatureFetcher
                   source.getNickname());
               if (dbref.getMap()!=null && f.getBegin()>0 && f.getEnd()>0) {
                 Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());
-                SequenceFeature vf[] = dbref.getMap().locateFeature(f);
+                SequenceFeature vf[]=null;
+                
+                try {
+                  vf = dbref.getMap().locateFeature(f);
+                }
+                catch (Exception ex)
+                {
+                  Cache.log.info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");
+                  Cache.log.info("Mapping feature from "+f.getBegin()+" to "+f.getEnd()+" in dbref "+dbref.getAccessionId()+" in "+dbref.getSource());
+                  Cache.log.info("using das Source "+ds.getUrl());
+                  Cache.log.info(ex);
+                }
+                
                 if (vf!=null) {
                   for (int v=0;v<vf.length;v++)
                   {
@@ -475,6 +489,10 @@ public class DasSequenceFeatureFetcher
    */
   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
   {
+    if (dasfeature==null)
+    {
+      return null;
+    }
     try
     {
       /**