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 "counttable.h"
  15 #include "sharedutilities.h"
  16 #include "tree.h"
  17
  18 class PhyloDiversityCommand : public Command {
  19
  20         public:
  21                 PhyloDiversityCommand(string);
  22                 PhyloDiversityCommand();
  23                 ~PhyloDiversityCommand(){}
  24
  25                 vector<string> setParameters();
  26                 string getCommandName()                 { return "phylo.diversity";                     }
  27                 string getCommandCategory()             { return "Hypothesis Testing";          }
  28                 string getOutputFileNameTag(string, string);
  29         string getHelpString();
  30                 string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
  31                 string getDescription()         { return "phylo.diversity"; }
  32
  33                 int execute();
  34                 void help() { m->mothurOut(getHelpString()); }
  35 private:
  36                 CountTable* ct;
  37                 float freq;
  38                 int iters, processors, numUniquesInName;
  39                 bool abort, rarefy, summary, collect, scale;
  40                 string groups, outputDir, treefile, groupfile, namefile, countfile;
  41                 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
  42
  43         map<string, int> getRootForGroups(Tree* t);
  44                 int readNamesFile();
  45                 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
  46                 void printSumData(map< string, vector<float> >&, ofstream&, int);
  47         vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
  48                 int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
  49                 int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);
  50
  51 };
  52
  53 #endif
  54