X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=aded6e8faae93b48031aa0c6fcd7d903fdd17186;hb=e1476d3c4ebb1c8f6b3ec7d46bb824b23987960e;hp=3d91004dc1ee11c4e9be61bfa13e1ad07e99c298;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 3d91004..aded6e8 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -17,7 +17,7 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -164,12 +164,18 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * DOCUMENT ME!
+   * Return the alignment column for a sequence position * Return the alignment
+   * position for a sequence position
    * 
    * @param pos
-   *          DOCUMENT ME!
+   *          lying from start to end
+   * 
+   * @return aligned column for residue (0 if residue is upstream from
+   *         alignment, -1 if residue is downstream from alignment) note.
+   *         Sequence object returns sequence.getEnd() for positions upstream
+   *         currently. TODO: change sequence for
+   *         assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
    * 
-   * @return DOCUMENT ME!
    */
   public int findIndex(int pos);
 
@@ -349,4 +355,15 @@ public interface SequenceI
    */
   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();
+
 }