X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=293528d13c186a1ef6db43720f0e8b615e0d4be1;hb=3ccc8045265bf23335df3c4b7448e0d91cb7c4df;hp=b0969b5cdf686aa08a809435e17a65707d2a1bd9;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b0969b5..293528d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -17,9 +17,10 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
 
-import jalview.analysis.*;
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
  * 
@@ -53,6 +54,11 @@ public class Sequence implements SequenceI
    * to the residues of this sequence
    */
   Vector annotation;
+  
+  /**
+   * The index of the sequence in a MSA 
+   */
+  int index = -1;
 
   /** array of seuqence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
@@ -895,8 +901,10 @@ public class Sequence implements SequenceI
     {
       this.annotation = new Vector();
     }
-
-    this.annotation.addElement(annotation);
+    if (!this.annotation.contains(annotation))
+    {
+      this.annotation.addElement(annotation);
+    }
     annotation.setSequenceRef(this);
   }
 
@@ -1172,4 +1180,17 @@ public class Sequence implements SequenceI
     }
   }
 
+  /**
+   * @return The index (zero-based) on this sequence in the MSA. 
+   * It returns {@code -1} if this information is not available.
+   */
+  public int getIndex() { return index; }
+  
+  /**
+   * Defines the position of this sequence in the MSA. 
+   * Use the value {@code -1} if this information is undefined.
+   * 
+   * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+   */
+  public void setIndex(int value) { index = value; }
 }