X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=50472a53ac0851542b951933e39c1927807f3eb5;hb=1d6bdfa4ce1d88c055a257e542de6b8542144d91;hp=d35d84cf53eff789efa86f539b8b82480bf12bf4;hpb=666701168bbf6308964633ade95bfa3a84903ad7;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d35d84c..50472a5 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.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
@@ -30,7 +30,7 @@ import jalview.datamodel.*;
 public class Comparison
 {
   /** DOCUMENT ME!! */
-  public static String GapChars = " .-";
+  public static final String GapChars = " .-";
 
   /**
    * DOCUMENT ME!
@@ -40,7 +40,7 @@ public class Comparison
    *
    * @return DOCUMENT ME!
    */
-  public static float compare(SequenceI ii, SequenceI jj)
+  public static final float compare(SequenceI ii, SequenceI jj)
   {
     return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
   }
@@ -55,8 +55,8 @@ public class Comparison
    */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)
   {
-    String si = ii.getSequence();
-    String sj = jj.getSequence();
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
 
     int ilen = si.length() - 1;
     int jlen = sj.length() - 1;
@@ -184,12 +184,12 @@ public class Comparison
    *
    * @return DOCUMENT ME!
    */
-  public static boolean isGap(char c)
+  public static final boolean isGap(char c)
   {
     return (c == '-' || c == '.' || c == ' ') ? true : false;
   }
 
-  public static boolean isNucleotide(SequenceI [] seqs)
+  public static final boolean isNucleotide(SequenceI [] seqs)
   {
     int i = 0, iSize = seqs.length, j, jSize;
     float nt = 0, aa = 0;