1 #ifndef SENSSPECCOMMAND_H
2 #define SENSSPECCOMMAND_H
9 * Created by Pat Schloss on 7/6/10.
10 * Copyright 2010 Schloss Lab. All rights reserved.
15 #include "command.hpp"
17 class SensSpecCommand : public Command {
20 SensSpecCommand(string);
24 vector<string> setParameters();
25 string getCommandName() { return "sens.spec"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
27 string getHelpString();
28 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"; }
31 void help() { m->mothurOut(getHelpString()); }
37 void outputStatistics(string, string);
39 string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
42 vector<string> outputNames;
44 long int truePositives, falsePositives, trueNegatives, falseNegatives;