public:
SensSpecCommand(string);
- ~SensSpecCommand();
- int execute();
- void help();
+ SensSpecCommand();
+ ~SensSpecCommand(){}
+
+ 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 getDescription() { return "sens.spec"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
void processPhylip();
-/// void processColumn(map<string, int>);
+ void processColumn();
+ void setUpOutput();
+ void outputStatistics(string, string);
- string listFile, distFile, nameFile, outputDir;
+ string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
+ string outputDir;
string format;
-// int numSeqs, numDists;
- int truePositives, falsePositives, trueNegatives, falseNegatives;
+ vector<string> outputNames;
+
+ long int truePositives, falsePositives, trueNegatives, falseNegatives;
bool abort;
bool hard;
string lineLabel;
double cutoff;
+ int precision;
};
-#endif
\ No newline at end of file
+#endif
+
+
+