#include "mothur.h"
#include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
class SensSpecCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "sens.spec"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+
string getHelpString();
- string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Sens.spec"; }
+ string getOutputPattern(string);
+ string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Sens.spec"; }
string getDescription() { return "sens.spec"; }
int execute();
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, square;
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);
+ string preProcessList();
+ bool testFile();
+
};
#endif