X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=6384125d719f0d9e10c06bd1abd8974bdd2c1393;hb=8df07ef03d3eee2dd34b597548be1fe56922c773;hp=d652da2a5aec05c6abeda173a8c290f6019d2211;hpb=129fc8c4f960f978baef88779939592e7b4227d2;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d652da2..6384125 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -316,6 +316,12 @@ public class Jalview2XML
 
                 Annotation an = new Annotation();
                 an.setDescription(aa[i].description);
+
+                if(aa[i].sequenceRef!=null)
+                 {
+                   an.setSequenceRef(aa[i].sequenceRef.getName());
+                 }
+
                 if(aa[i].graph>0)
                 {
                   an.setGraph(true);
@@ -816,6 +822,14 @@ public class Jalview2XML
                             an[i].getDescription(), anot);
                 }
 
+                if(an[i].getSequenceRef()!=null)
+                {
+                  jaa.createSequenceMapping(
+                      al.findName(an[i].getSequenceRef()), 1
+                      );
+                  al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+                }
+
                 al.addAnnotation(jaa);
             }
         }