set<string> labels; //holds labels to be used
long int truePositives, falsePositives, trueNegatives, falseNegatives;
- bool abort, allLines;
+ bool abort, allLines, square;
bool hard;
//string lineLabel;
double cutoff;
int fillSeqPairSet(set<string>&, ListVector*&);
int process(map<string, int>&, string, bool&, string&);
int process(set<string>&, string, bool&, string&, int);
+ string preProcessList();
+ bool testFile();
};