#include "mothur.h"
#include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
class SensSpecCommand : public Command {
void help() { m->mothurOut(getHelpString()); }
private:
- void processPhylip();
- void processColumn();
+ int processPhylip();
+ int processColumn();
void setUpOutput();
void outputStatistics(string, string);
string outputDir;
string format;
vector<string> outputNames;
+ set<string> labels; //holds labels to be used
long int truePositives, falsePositives, trueNegatives, falseNegatives;
- bool abort;
+ bool abort, allLines;
bool hard;
- string lineLabel;
+ //string lineLabel;
double cutoff;
int precision;
+
+ int fillSeqMap(map<string, int>&, ListVector*&);
+ int fillSeqPairSet(set<string>&, ListVector*&);
+ int process(map<string, int>&, string, bool&, string&);
+ int process(set<string>&, string, bool&, string&, int);
+
};
#endif