class RefChimeraTest {
public:
- RefChimeraTest(vector<Sequence>&, string);
- int analyzeQuery(string, string);
+ RefChimeraTest(vector<Sequence>&);
+ int printHeader(ofstream&);
+ int analyzeQuery(string, string, ofstream&);
int getClosestRefIndex();
private:
int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
int numRefSeqs;
int alignLength;
int bestMatch;
- ofstream chimeraReportFile;
+ //ofstream chimeraReportFile;
MothurOut* m;
};