/*\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
* @param s2 SequenceI\r
* @return float\r
*/\r
- public static float PID(SequenceI s1, SequenceI s2)\r
+ public final static float PID(String seq1, String seq2)\r
{\r
- int len;\r
-\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
-\r
- int bad = 0;\r
-\r
- for (int i = 0; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (! (jalview.util.Comparison.isGap(chr1)) &&\r
- ! (jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
- }\r
-\r
- return ( (float) 100 * (len - bad)) / len;\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 static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+ public final static float PID(String seq1, String seq2, int start, int end)\r
{\r
- int len;\r
\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
+ int s1len = seq1.length();\r
+ int s2len = seq2.length();\r
+\r
+ int len = Math.min(s1len, s2len);\r
\r
if (end < len)\r
{\r
start = len - 1; // we just use a single residue for the difference\r
}\r
\r
+\r
int bad = 0;\r
+ char chr1;\r
+ char chr2;\r
+\r
\r
for (int i = start; i < len; i++)\r
{\r
- char chr1;\r
- char chr2;\r
+ chr1 = seq1.charAt(i) ;\r
\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
+ chr2 = seq2.charAt(i) ;\r
\r
- if (i < s2.getSequence().length())\r
+ if ('a' <= chr1 && chr1 <= 'z')\r
{\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ chr1 -= caseShift;\r
}\r
- else\r
+ if ('a' <= chr2 && chr2 <= 'z')\r
{\r
- chr2 = '.';\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ chr2 -= caseShift;\r
}\r
\r
- if (! (jalview.util.Comparison.isGap(chr1)) &&\r
- ! (jalview.util.Comparison.isGap(chr2)))\r
+\r
+ if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )\r
{\r
- if (chr1 != chr2)\r
- {\r
bad++;\r
- }\r
}\r
}\r
\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