/*\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
public class Comparison\r
{\r
/** DOCUMENT ME!! */\r
- public static String GapChars = " .-";\r
+ public static final String GapChars = " .-";\r
\r
/**\r
* DOCUMENT ME!\r
*\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
*/\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
*\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