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"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 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"; }
33 string getDescription() { return "sens.spec"; }
36 void help() { m->mothurOut(getHelpString()); }
42 void outputStatistics(string, string);
44 string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
47 vector<string> outputNames;
48 set<string> labels; //holds labels to be used
50 long int truePositives, falsePositives, trueNegatives, falseNegatives;
57 int fillSeqMap(map<string, int>&, ListVector*&);
58 int fillSeqPairSet(set<string>&, ListVector*&);
59 int process(map<string, int>&, string, bool&, string&);
60 int process(set<string>&, string, bool&, string&, int);
61 string preProcessList();