X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDBRefFetcher.java;h=6d589f9df4c3c75d54639e91f0db56375ca41544;hb=4dd44779e0d1ffa07b52b67bd8178ad45801bb4f;hp=445c90acdb01c2469e03a7d79be358f45a3db590;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 445c90a..6d589f9 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -36,7 +36,7 @@ import jalview.gui.*;
 public class DBRefFetcher
     implements Runnable
 {
-  AlignmentI dataset;
+  SequenceI [] dataset;
   AlignFrame af;
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
@@ -55,7 +55,7 @@ public class DBRefFetcher
     try
     {
       // 1. Load the mapping information from the file
-      Mapping map = new Mapping(uni.getClass().getClassLoader());
+      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
       java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
       map.loadMapping(url);
 
@@ -80,10 +80,18 @@ public class DBRefFetcher
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
-  public DBRefFetcher(AlignmentI align, AlignFrame af)
+  public DBRefFetcher(SequenceI [] seqs, AlignFrame af)
   {
     this.af = af;
-    this.dataset = align.getDataset();
+    SequenceI [] ds = new SequenceI[seqs.length];
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if(seqs[i].getDatasetSequence()!=null)
+        ds[i] = seqs[i].getDatasetSequence();
+      else
+        ds[i] = seqs[i];
+    }
+    this.dataset = ds;
   }
 
   public boolean fetchDBRefs(boolean waitTillFinished)
@@ -157,16 +165,15 @@ public class DBRefFetcher
     try
     {
       int seqIndex = 0;
-      Vector sequences = dataset.getSequences();
 
-      while (seqIndex < sequences.size())
+      while (seqIndex < dataset.length)
       {
         StringBuffer queryString = new StringBuffer("uniprot:");
 
-        for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
+        for (int i = 0; (seqIndex < dataset.length) && (i < 50);
              seqIndex++, i++)
         {
-          Sequence sequence = (Sequence) sequences.get(seqIndex);
+          SequenceI sequence = dataset[seqIndex];
           DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.
               getDBRef(), new String[]
               {