phylodiversitycommand.h

   1 #ifndef PHYLODIVERSITYCOMMAND_H
   2 #define PHYLODIVERSITYCOMMAND_H
   3
   4 /*
   5  *  phylodiversitycommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 4/30/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "treemap.h"
  15 #include "globaldata.hpp"
  16
  17 class PhyloDiversityCommand : public Command {
  18
  19         public:
  20                 PhyloDiversityCommand(string);
  21                 ~PhyloDiversityCommand();
  22                 int execute();
  23                 void help();
  24
  25         private:
  26                 GlobalData* globaldata;
  27
  28                 float freq;
  29                 int iters;
  30                 bool abort, rarefy, summary, collect, scale;
  31                 string groups, outputDir;
  32                 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
  33
  34                 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
  35                 void printSumData(map< string, vector<float> >&, ofstream&, int);
  36                 float calcBranchLength(Tree*, int);
  37 };
  38
  39 #endif
  40