X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws2%2Foperations%2FAlignmentOperation.java;h=b70678a1b06dab9e756fa2f18a6df7bdb1864225;hb=a0477223e2f54d4c8f011da77ffcb3c879960a43;hp=f836c91a2600054bd1d11814ccb3a121276e23a2;hpb=4cfc4dee569d96ac8ce3c1c394318a460a1d0a87;p=jalview.git

diff --git a/src/jalview/ws2/operations/AlignmentOperation.java b/src/jalview/ws2/operations/AlignmentOperation.java
index f836c91..b70678a 100644
--- a/src/jalview/ws2/operations/AlignmentOperation.java
+++ b/src/jalview/ws2/operations/AlignmentOperation.java
@@ -302,6 +302,8 @@ public class AlignmentOperation implements Operation
 
     private final AlignmentI dataset;
 
+    private final AlignViewport viewport;
+
     private final List<AlignedCodonFrame> codonFrame = new ArrayList<>();
 
     private List<ArgumentI> args = Collections.emptyList();
@@ -337,6 +339,7 @@ public class AlignmentOperation implements Operation
       this.alnTitle = alnTitle;
       this.submitGaps = submitGaps;
       this.preserveOrder = preserveOrder;
+      this.viewport = viewport;
       this.gapCharacter = viewport.getGapCharacter();
 
       String panelInfo = String.format("%s using service hosted at %s%n%s",
@@ -528,7 +531,7 @@ public class AlignmentOperation implements Operation
           continue;
         try
         {
-          AlignmentI alignment = supplier.getResult(job);
+          AlignmentI alignment = supplier.getResult(job, dataset.getSequences(), viewport);
           if (alignment != null)
           {
             results.put(job.getUid(), alignment);