Use AAFrequency final keys

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index dd2517c..fc52190 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -455,13 +455,12 @@ public class Sequence implements SequenceI
     }
 
     /**
-     * DOCUMENT ME!
+     * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
      *
-     * @return DOCUMENT ME!
+     * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
      */
     public int[] gapMap()
     {
-        // Returns an int array giving the position of each residue in the sequence in the alignment
         String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
         int[] map = new int[seq.length()];
         int j = 0;