Use AAFrequency final keys

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6c9fa2a..8291026 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
- * 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
@@ -151,18 +151,18 @@ public interface SequenceI
     public int findIndex(int pos);
 
     /**
-     * DOCUMENT ME!
+     * Returns the sequence position for an alignment position
      *
-     * @param i DOCUMENT ME!
+     * @param i column index in alignment (from 1)
      *
-     * @return DOCUMENT ME!
+     * @return residue number for residue (left of and) nearest ith column
      */
     public int findPosition(int i);
 
     /**
-     * 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();
 
@@ -277,7 +277,7 @@ public interface SequenceI
   public int removeGaps();
   /**
    * remove all gaps from start to end columns in sequence
-   * @param start 
+   * @param start
    * @param end
    * @return number of gaps removed
    */