X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=21b877d4083609affa599393782ab5f92ad741a6;hb=e33b171845992fd21094ba754498f9ab3d29f110;hp=22929f59bc6f97bda4da4bb9750e2a8976184674;hpb=8a92c2fed93b2adfac07a8bc29d3556ee7b1be62;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 22929f5..21b877d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -571,13 +577,9 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   * 
-   * @param pos
-   *          lying from start to end
-   * 
-   * @return aligned position of residue pos
+  
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
   {
@@ -895,8 +897,10 @@ 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 +1176,17 @@ 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; }
 }