From 68b63b7225615d09b8b870681fd59f11a0167fe7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:40:49 +0000
Subject: [PATCH] has ref to annotation

---
 src/jalview/datamodel/Sequence.java  |   23 +++++++++++++++++++++++
 src/jalview/datamodel/SequenceI.java |    5 +++++
 2 files changed, 28 insertions(+)

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 );
+    }
+
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 82d38b4..21f7cc4 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -251,4 +251,9 @@ public interface SequenceI
     public void setDatasetSequence(SequenceI seq);
 
     public SequenceI getDatasetSequence();
+
+    public AlignmentAnnotation [] getAnnotation();
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
 }
-- 
1.7.10.2