saves and loads annotations with seqrefs

[jalview.git] / src / jalview / gui / Jalview2XML.java

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