sensspeccommand.h

   1 #ifndef SENSSPECCOMMAND_H
   2 #define SENSSPECCOMMAND_H
   3
   4
   5 /*
   6  *  sensspeccommand.h
   7  *  Mothur
   8  *
   9  *  Created by Pat Schloss on 7/6/10.
  10  *  Copyright 2010 Schloss Lab. All rights reserved.
  11  *
  12  */
  13
  14 #include "mothur.h"
  15 #include "command.hpp"
  16
  17 class SensSpecCommand : public Command {
  18
  19 public:
  20         SensSpecCommand(string);
  21         SensSpecCommand();
  22         ~SensSpecCommand(){}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "sens.spec";                           }
  26         string getCommandCategory()             { return "OTU-Based Approaches";        }
  27         string getHelpString();
  28
  29         int execute();
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33         void processPhylip();
  34         void processColumn();
  35         void setUpOutput();
  36         void outputStatistics(string, string);
  37
  38         string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
  39         string outputDir;
  40         string format;
  41         vector<string> outputNames;
  42
  43         long int truePositives, falsePositives, trueNegatives, falseNegatives;
  44         bool abort;
  45         bool hard;
  46         string lineLabel;
  47         double cutoff;
  48         int precision;
  49 };
  50
  51 #endif
  52
  53
  54