Sequence is char []

[jalview.git] / src / jalview / ws / MsaWSThread.java

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 3fd5fbc..cd14a24 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -127,20 +127,20 @@ class MsaWSThread
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
           seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequence()
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
                                : AlignSeq.extractGaps(
                                    jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequence()));
+                                   .getSequenceAsString()));
         }
         else
         {
           String empty = null;
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
-            empty = (submitGaps) ? seqs[i].getSequence()
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
                 : AlignSeq.extractGaps(
                     jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequence());
+                    .getSequenceAsString());
           }
           emptySeqs.add(new String[]
                         {newname, empty});