X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=1d63e5b1f72a06f6d6916481f758536c31ea17c5;hb=ef6291f17491f1c426e2cad44021c31f609e2808;hp=b4dd1f66ddb0472f9eed4f09d03da4ea77760de3;hpb=21b2c08c209b0c4eb1111dab1d81e8408c245ddd;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index b4dd1f6..1d63e5b 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -95,15 +95,14 @@ public class DasSequenceFeatureFetcher implements Runnable
     int refCount = 0;
     for(int i=0; i<sequences.length; i++)
     {
-      Vector dbref = sequences[i].getDBRef();
+      DBRefEntry [] dbref = sequences[i].getDBRef();
       if(dbref!=null)
       {
-        for(int j=0; j<dbref.size(); j++)
+        for(int j=0; j<dbref.length; j++)
         {
-          DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);
-          System.out.println(entry.getSource()
+          System.out.println(dbref[j].getSource()
                              +" "+jalview.datamodel.DBRefSource.UNIPROT);
-          if(entry.getSource()
+          if(dbref[j].getSource()
              .equals(jalview.datamodel.DBRefSource.UNIPROT))
           {
             System.out.println("got a match");
@@ -344,7 +343,7 @@ public class DasSequenceFeatureFetcher implements Runnable
       int seqIndex = 0;
       while (seqIndex < sequences.length)
       {
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
               new String[]  {
               jalview.datamodel.DBRefSource.PDB,
               jalview.datamodel.DBRefSource.UNIPROT});
@@ -356,15 +355,14 @@ 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();
                 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());
@@ -372,8 +370,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 
                     createFeatureFetcher(sequences[seqIndex],
                                          dasSource.getUrl(),
-                                         ( (DBRefEntry) uprefs.get(j)).
-                                         getAccessionId(),
+                                          uprefs[j].getAccessionId(),
                                          dasSource.getNickname());
                   }
                 }