- 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