/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch){ // This assumes that the template database is in fasta format, may
+AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may
try { // need to alter this in the future?
longest = 0;