X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDBRefFetcher.java;h=01e67cfc7bf4227b1ee10c67008ab88c1707410a;hb=0d6e36143a2d7471edb7ef386d0b79095e0cd63e;hp=6e4491059267415a949777d7c87eec82235ab77d;hpb=56e5bdc625697d50d7d3f422616f0f1b40ca2828;p=jalview.git

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 6e44910..01e67cf 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -48,6 +48,7 @@ public class DBRefFetcher implements Runnable
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
   boolean uniprotFlag = false;
+  boolean running = false;
 
   public DBRefFetcher()
   {}
@@ -91,9 +92,25 @@ public class DBRefFetcher implements Runnable
     unknownSequences = new ArrayList();
     this.align = align;
     this.dataset = align.getDataset();
+  }
 
+  public boolean fetchDBRefs(boolean waitTillFinished)
+  {
     Thread thread = new Thread(this);
     thread.start();
+    running = true;
+
+    if(waitTillFinished)
+    {
+      while(running)
+      {
+        try{
+          Thread.sleep(500);
+        }catch(Exception ex){}
+      }
+    }
+
+    return true;
   }
 
   /**
@@ -103,6 +120,7 @@ public class DBRefFetcher implements Runnable
   {
     long startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching db refs", startTime);
+    running = true;
 
     try
     {
@@ -117,13 +135,13 @@ public class DBRefFetcher implements Runnable
              seqIndex++, i++)
         {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
               jalview.datamodel.DBRefSource.UNIPROT});
           if (uprefs!=null)
           {
             // we know the id for this entry, so don't note its ID in the unknownSequences list
-            for (int j=0,k=uprefs.size(); j<k; j++)
-              ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());
+            for (int j=0,k=uprefs.length; j<k; j++)
+              ids.add(uprefs[j].getAccessionId());
             unknownSequences.add(sequence);
           } else {
             if (!ids.contains(sequence.getName()))
@@ -147,8 +165,12 @@ public class DBRefFetcher implements Runnable
                    ids.get(i).toString().lastIndexOf("|") + 1));
                uniprotFlag = true;
              }
-             remainingIds.append(ids.get(i) + ";");
+             else
+               remainingIds.append(ids.get(i));
+
+             remainingIds.append(";");
            }
+
           EBIFetchClient ebi = new EBIFetchClient();
           File file = ebi.fetchDataAsFile(remainingIds.toString(),
                                           "xml", "raw");
@@ -183,6 +205,8 @@ public class DBRefFetcher implements Runnable
     af.setProgressBar("DBRef search completed", startTime);
    // promptBeforeBlast();
 
+   running = false;
+
   }
 
 
@@ -244,7 +268,11 @@ public class DBRefFetcher implements Runnable
 
       else  if (sequence == null && uniprotFlag)
       {
-          sequence = dataset.findName("UniProt/Swiss-Prot|"+entry.getAccession().elementAt(0)+"|"+idmatch);
+          StringBuffer upid = new StringBuffer("UniProt/Swiss-Prot|");
+          for(int u=0; u<entry.getAccession().size(); u++)
+            upid.append(entry.getAccession().elementAt(u)+"|");
+
+          sequence = dataset.findName(upid+idmatch);
           ids.remove(idmatch);
       }