JAL-1087 skip processing any of the other command line arguments if no alignment...

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index d1e3853..33045d0 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,7 +17,7 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -348,5 +348,15 @@ public interface SequenceI
    *          null or mapping from entry's numbering to local start/end
    */
   public void transferAnnotation(SequenceI entry, Mapping mp);
+  
+  /**
+   * @param index The sequence index in the MSA 
+   */
+  public void setIndex(int index);
+  
+  /**
+   * @return The index of the sequence in the alignment
+   */
+  public int getIndex();
 
 }