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                 ~PhyloDiversityCommand();
  23                 vector<string> getRequiredParameters();
  24                 vector<string> getValidParameters();
  25                 vector<string> getRequiredFiles();
  26                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27                 int execute();
  28                 void help();
  29
  30         private:
  31                 GlobalData* globaldata;
  32
  33                 float freq;
  34                 int iters, processors;
  35                 bool abort, rarefy, summary, collect, scale;
  36                 string groups, outputDir;
  37                 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
  38                 map<string, vector<string> > outputTypes;
  39
  40                 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
  41                 void printSumData(map< string, vector<float> >&, ofstream&, int);
  42                 float calcBranchLength(Tree*, int, map< string, set<int> >&);
  43                 int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
  44                 int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);
  45
  46 };
  47
  48 #endif
  49