+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ c -= ('a' - 'A');\r
+ s = String.valueOf(c);\r
+ }\r
+\r
+ if (consensus == null || consensus[j] == null)\r
+ return false;\r
+\r
+ if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&\r
+ consensus[j].contains(s))\r
+ {\r
+ if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
+ {\r
+ return true;\r
+ }\r