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createMapping alreadyMapped
[jalview.git] / src / jalview / gui / Jalview2XML.java
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8cf676d..e65f37d 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1089,7 +1089,7 @@ public class Jalview2XML
                 if(an[i].getSequenceRef()!=null)
                 {
                   jaa.createSequenceMapping(
-                      al.findName(an[i].getSequenceRef()), 1
+                      al.findName(an[i].getSequenceRef()), 1, true
                       );
                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
                 }