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

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 9e0aef6..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
@@ -116,21 +116,19 @@ public class Comparison
    * @param s2 SequenceI\r
    * @return float\r
    */\r
-  public final static float PID(SequenceI seq1, SequenceI seq2)\r
+  public final static float PID(String seq1, String seq2)\r
   {\r
-    return PID(seq1, seq2, 0, seq1.getLength());\r
+    return PID(seq1, seq2, 0, seq1.length());\r
   }\r
 \r
   static final int caseShift = 'a' - 'A';\r
 \r
   // Another pid with region specification\r
-  public final static  float PID(SequenceI seq1, SequenceI seq2, int start, int end)\r
+  public final static  float PID(String seq1, String seq2, int start, int end)\r
   {\r
-    String s1 = seq1.getSequence();//.toUpperCase();\r
-    String s2 = seq2.getSequence();//.toUpperCase();\r
-    int s1len = s1.length();\r
-    int s2len = s2.length();\r
 \r
+    int s1len = seq1.length();\r
+    int s2len = seq2.length();\r
 \r
     int len = Math.min(s1len, s2len);\r
 \r
@@ -152,9 +150,9 @@ public class Comparison
 \r
     for (int i = start; i < len; i++)\r
     {\r
-      chr1 =  s1.charAt(i) ;\r
+      chr1 =  seq1.charAt(i) ;\r
 \r
-      chr2 =  s2.charAt(i) ;\r
+      chr2 =  seq2.charAt(i) ;\r
 \r
       if ('a' <= chr1 && chr1 <= 'z')\r
       {\r
@@ -186,12 +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