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"
16 #include "listvector.hpp"
17 #include "inputdata.h"
19 class SensSpecCommand : public Command {
22 SensSpecCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "sens.spec"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 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 string getDescription() { return "sens.spec"; }
34 void help() { m->mothurOut(getHelpString()); }
40 void outputStatistics(string, string);
42 string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
45 vector<string> outputNames;
46 set<string> labels; //holds labels to be used
48 long int truePositives, falsePositives, trueNegatives, falseNegatives;
55 int fillSeqMap(map<string, int>&, ListVector*&);
56 int fillSeqPairSet(set<string>&, ListVector*&);
57 int process(map<string, int>&, string, bool&, string&);
58 int process(set<string>&, string, bool&, string&, int);