Only set the sequence oncecvs diff datamodel/Alignment.java

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d35d84c..50472a5 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -30,7 +30,7 @@ import jalview.datamodel.*;
 public class Comparison\r
 {\r
   /** DOCUMENT ME!! */\r
-  public static String GapChars = " .-";\r
+  public static final String GapChars = " .-";\r
 \r
   /**\r
    * DOCUMENT ME!\r
@@ -40,7 +40,7 @@ public class Comparison
    *\r
    * @return DOCUMENT ME!\r
    */\r
-  public static float compare(SequenceI ii, SequenceI jj)\r
+  public static final float compare(SequenceI ii, SequenceI jj)\r
   {\r
     return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
   }\r
@@ -55,8 +55,8 @@ public class Comparison
    */\r
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
   {\r
-    String si = ii.getSequence();\r
-    String sj = jj.getSequence();\r
+    String si = ii.getSequenceAsString();\r
+    String sj = jj.getSequenceAsString();\r
 \r
     int ilen = si.length() - 1;\r
     int jlen = sj.length() - 1;\r
@@ -184,12 +184,12 @@ public class Comparison
    *\r
    * @return DOCUMENT ME!\r
    */\r
-  public static boolean isGap(char c)\r
+  public static final boolean isGap(char c)\r
   {\r
     return (c == '-' || c == '.' || c == ' ') ? true : false;\r
   }\r
 \r
-  public static boolean isNucleotide(SequenceI [] seqs)\r
+  public static final boolean isNucleotide(SequenceI [] seqs)\r
   {\r
     int i = 0, iSize = seqs.length, j, jSize;\r
     float nt = 0, aa = 0;\r