+ for (int i = start; i < len; i++)\r
+ {\r
+ chr1 = seq1.charAt(i);\r
+\r
+ chr2 = seq2.charAt(i);\r
+\r
+ if ('a' <= chr1 && chr1 <= 'z')\r
+ {\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ chr1 -= caseShift;\r
+ }\r
+ if ('a' <= chr2 && chr2 <= 'z')\r
+ {\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ chr2 -= caseShift;\r
+ }\r
+\r
+ if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))\r
+ {\r
+ bad++;\r
+ }\r
+ }\r
+\r
+ return ( (float) 100 * (len - bad)) / len;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static final boolean isGap(char c)\r
+ {\r
+ return (c == '-' || c == '.' || c == ' ') ? true : false;\r
+ }\r
+\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
+ char c;\r
+ while (i < iSize)\r
+ {\r
+ jSize = seqs[i].getLength();\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ c = seqs[i].getCharAt(j);\r
+ if ('a' <= c && c <= 'z')\r