X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d35a05bb7cc6df87e94c5f7e949e11c7e6e71357;hb=9480f18113c0d16dfb157eb3fff60a1e29c33d39;hp=65537ae5b79cb5a7f4204e48c0cb4397b13afbe0;hpb=8e73c98073451713e9094a80feafd9b9e8bfd917;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 65537ae..d35a05b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -42,6 +42,9 @@ public class Sequence implements SequenceI
     String vamsasId;
     Vector dbrefs;
 
+    /** This annotation is displayed below the alignment but the
+     * positions are tied to the residues of this sequence */
+    Vector annotation;
 
     /** DOCUMENT ME!! */
     public Vector sequenceFeatures;
@@ -574,4 +577,24 @@ public class Sequence implements SequenceI
       return datasetSequence;
     }
 
+    public AlignmentAnnotation [] getAnnotation()
+    {
+      if(annotation==null)
+        return null;
+
+      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
+      for(int r = 0; r<ret.length; r++)
+        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+
+      return ret;
+    }
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    {
+      if(this.annotation==null)
+        this.annotation = new Vector();
+
+      this.annotation.addElement( annotation );
+    }
+
 }