convert(globaldata->getMismatch(), misMatch);
convert(globaldata->getGapopen(), gapOpen);
convert(globaldata->getGapextend(), gapExtend);
convert(globaldata->getMismatch(), misMatch);
convert(globaldata->getGapopen(), gapOpen);
convert(globaldata->getGapextend(), gapExtend);
if(globaldata->getSearch() == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
else if(globaldata->getSearch() == "suffix") { templateDB = new SuffixDB(templateFileName); }
else if(globaldata->getSearch() == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
if(globaldata->getSearch() == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
else if(globaldata->getSearch() == "suffix") { templateDB = new SuffixDB(templateFileName); }
else if(globaldata->getSearch() == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
else { cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl;
templateDB = new SuffixDB(templateFileName); }
else { cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl;
templateDB = new SuffixDB(templateFileName); }