X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=5f1833168071d763100697fb4b50f3dd9456390b;hb=9829b31986b83957217a6b9086665ef7be9b1c8c;hp=7a78d8d6b9f001d4e75ee880b2d93037f8ed27e3;hpb=e04c42710f41ec0e1d12161a6379de280407c081;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 7a78d8d..5f18331 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -25,8 +25,10 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SequenceClient;
 import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
+import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
 import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
 import org.biodas.jdas.schema.sequence.SEQUENCE;
 import org.biodas.jdas.schema.sources.COORDINATES;
@@ -65,7 +67,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected String dbname = "DASCS";
 
   protected String dbrefname = "das:source";
-
+  protected MultipleConnectionPropertyProviderI connprops=null;
   /**
    * create a new DbSource proxy for a DAS 1 source
    * 
@@ -82,9 +84,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
    *           if source is not capable of the 'sequence' command
    */
   public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
-          VERSION version, COORDINATES coordsys) throws Exception
+          VERSION version, COORDINATES coordsys, MultipleConnectionPropertyProviderI connprops) throws Exception
   {
-    if (!(jsrc = new JalviewSource(source, false)).isSequenceSource())
+    if (!(jsrc = new JalviewSource(source, connprops, false)).isSequenceSource())
     {
       throw new Exception("Source " + source.getTitle()
               + " does not support the sequence command.");
@@ -93,6 +95,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     this.dbname = dbname;
     this.dbrefname = dbrefname;
     this.coordsys = coordsys;
+    this.connprops=connprops;
   }
 
   public String getAccessionSeparator()
@@ -149,8 +152,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
           System.err
                   .println("Retrieving IDs individually from das source: "
                           + sr);
-          // todo : get conn property provider
-          org.biodas.jdas.client.SequenceClient sq = new SequenceClient();
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
           {
             List<String> qset = Arrays.asList(new String[]
@@ -273,6 +275,16 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         {
           jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
                   false, multiple);
+          while (dssf.isRunning())
+          {
+            try {
+              Thread.sleep(200);
+            } catch (InterruptedException x)
+            {
+              
+            }
+          }
+          
         } catch (Exception x)
         {
           Cache.log