-#ifndef SENSSPECCOMMAND_H
-#define SENSSPECCOMMAND_H
-
-
-/*
- * sensspeccommand.h
- * Mothur
- *
- * Created by Pat Schloss on 7/6/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "listvector.hpp"
-#include "inputdata.h"
-
-class SensSpecCommand : public Command {
-
-public:
- SensSpecCommand(string);
- 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:
- int processPhylip();
- int processColumn();
- void setUpOutput();
- void outputStatistics(string, string);
-
- string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
- string outputDir;
- string format;
- vector<string> outputNames;
- set<string> labels; //holds labels to be used
-
- long int truePositives, falsePositives, trueNegatives, falseNegatives;
- bool abort, allLines;
- bool hard;
- //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
-
-
-