X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=479f22f1e1454d0a41b724e72a30189e0e17afd6;hb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;hp=6d46e4b145b2c24cc66eb929b4c2a0501a5b231c;hpb=87fc98c92b4d1083db30212139b1137b508a0c86;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 6d46e4b..479f22f 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -57,7 +57,7 @@ public class MsaWSClient
    */
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder)
+                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
 
     if (!sh.getAbstractName().equals("MsaWS"))
@@ -81,13 +81,13 @@ public class MsaWSClient
 
        return;
      }
-    startMsaWSClient(altitle, msa, submitGaps, preserveOrder);
+    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
   }
 
 
   private void startMsaWSClient(String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder)
+                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
     if (!locateWebService())
     {
@@ -99,7 +99,7 @@ public class MsaWSClient
 
     MsaWSThread musclethread = new MsaWSThread(WebServiceName +
                                                " alignment of " + altitle, msa,
-                                               submitGaps, preserveOrder);
+                                               submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(musclethread);
     musclethread.start();
   }
@@ -145,20 +145,22 @@ public class MsaWSClient
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
         SequenceSet();
     Hashtable SeqNames = null;
-    boolean submitGaps = false; // and always store and recover sequence order
+    boolean submitGaps = false; // pass sequences including gaps to alignment service
     boolean preserveOrder = true; // and always store and recover sequence order
     String jobId;
     String alTitle; // name which will be used to form new alignment window.
     int allowedServerExceptions = 3; // thread dies if too many exceptions.
     boolean jobComplete = false;
 
+    Alignment dataset; // dataset to which the new alignment will be associated.
+
     MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
-                boolean presorder)
+                boolean presorder, Alignment seqset)
     {
       alTitle = title;
       submitGaps = subgaps;
       preserveOrder = presorder;
-
+      dataset = seqset;
       OutputHeader = wsInfo.getProgressText();
       SeqNames = new Hashtable();
 
@@ -467,7 +469,9 @@ public class MsaWSClient
           jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
 
           Alignment al = new Alignment(seqs);
-
+          if (dataset!=null) {
+            al.setDataset(dataset);
+          }
           // TODO: JBPNote Should also rename the query sequence sometime...
           AlignFrame af = new AlignFrame(al);
           af.addSortByOrderMenuItem(ServiceName + " Ordering",