X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=49c879b4d1d7748e515ee4b498cd4f0b8e79eb5d;hb=b19a9184ad28b62d2d4f199e23823cd2f8e59f89;hp=999fc96406fa3f2a3c648d76d3b7cd9b23d1e2d1;hpb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 999fc96..49c879b 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -58,7 +58,7 @@ public class MsaWSClient
    */
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
-                     SequenceI[] msa,
+                     jalview.datamodel.AlignmentView msa,
                      boolean submitGaps, boolean preserveOrder,
                      Alignment seqdataset,
                      AlignFrame _alignFrame)
@@ -91,7 +91,7 @@ public class MsaWSClient
   }
 
 
-  private void startMsaWSClient(String altitle, SequenceI[] msa,
+  private void startMsaWSClient(String altitle, AlignmentView msa,
                      boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
     if (!locateWebService())
@@ -141,6 +141,16 @@ public class MsaWSClient
     return true;
   }
 
+  protected String getServiceActionKey()
+  {
+    return "MsaWS";
+  }
+
+  protected String getServiceActionDescription()
+  {
+    return "Multiple Sequence Alignment";
+  }
+
   protected class MsaWSThread
       extends Thread implements WSClientI
   {
@@ -159,33 +169,34 @@ public class MsaWSClient
 
     Alignment dataset; // dataset to which the new alignment will be associated.
 
-    MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
+    MsaWSThread(String title, AlignmentView _msa, boolean subgaps,
                 boolean presorder, Alignment seqset)
     {
+      // jbpnote - transformation should be above here - this is per sequence set contig, not for many contigs.
       alTitle = title;
       submitGaps = subgaps;
       preserveOrder = presorder;
       dataset = seqset;
       OutputHeader = wsInfo.getProgressText();
       SeqNames = new Hashtable();
-
+      SeqCigar[] msa = _msa.getSequences();
       vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
           Sequence[msa.length];
 
-      for (int i = 0; i < msa.length; i++)
+      for (int i = 0,n=0; i < msa.length; i++)
       {
         String newname = jalview.analysis.SeqsetUtils.unique_name(i);
-
+        SequenceI mseq = msa[i].getSeq('-');
         // uniquify as we go
         // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
         SeqNames.put(newname,
-                     jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
+                     jalview.analysis.SeqsetUtils.SeqCharacterHash(mseq));
         seqarray[i] = new vamsas.objects.simple.Sequence();
         seqarray[i].setId(newname);
-        seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()
+        seqarray[i].setSeq( (submitGaps) ? mseq.getSequence()
                            : AlignSeq.extractGaps(
                                jalview.util.Comparison.GapChars,
-                               msa[i].getSequence()));
+                               mseq.getSequence()));
       }
 
       this.seqs = new vamsas.objects.simple.SequenceSet();