From: jprocter <Jim Procter>
Date: Tue, 1 Nov 2005 16:02:04 +0000 (+0000)
Subject: dataset reference propagated to new MsaWS alignment.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7aacb54f3c93587417dbf4dc2279049db9f22b7;p=jalview.git

dataset reference propagated to new MsaWS alignment.
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 77396c9..89aadac 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2372,7 +2372,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true);
+                  false, true, viewport.getAlignment().getDataset());
 
             }
 
@@ -2389,7 +2389,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true);
+                    true, true, viewport.getAlignment().getDataset());
 
               }
 
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",