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#ifndef PHYLODIVERSITYCOMMAND_H
#define PHYLODIVERSITYCOMMAND_H
/*
* phylodiversitycommand.h
* Mothur
*
* Created by westcott on 4/30/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "counttable.h"
#include "tree.h"
class PhyloDiversityCommand : public Command {
public:
PhyloDiversityCommand(string);
~PhyloDiversityCommand(){}
vector<string> setParameters();
string getCommandName() { return "phylo.diversity"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
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"; }
string getDescription() { return "phylo.diversity"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
float freq;
int iters, processors, numUniquesInName, subsampleSize;
bool abort, rarefy, summary, collect, scale, subsample;
string groups, treefile, groupfile, namefile, countfile;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
//map<string, int> getRootForGroups(Tree* t);
//void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
//void printSumData(map< string, vector<float> >&, ofstream&, int);
//vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
//int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
int createProcesses(Tree*, CountTable*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, string, string);
};
/**************************************************************************************************/
#endif
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