JAL-1065 - Visualize T-Coffee quality scores for an alignment

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 52d9a72..cc541be 100755 (executable)
--- 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;
@@ -1172,4 +1178,17 @@ 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; }
 }