1 #ifndef PHYLODIVERSITYCOMMAND_H
2 #define PHYLODIVERSITYCOMMAND_H
5 * phylodiversitycommand.h
8 * Created by westcott on 4/30/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
16 #include "sharedutilities.h"
19 class PhyloDiversityCommand : public Command {
22 PhyloDiversityCommand(string);
23 PhyloDiversityCommand();
24 ~PhyloDiversityCommand(){}
26 vector<string> setParameters();
27 string getCommandName() { return "phylo.diversity"; }
28 string getCommandCategory() { return "Hypothesis Testing"; }
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"; }
33 void help() { m->mothurOut(getHelpString()); }
38 int iters, processors, numUniquesInName;
39 bool abort, rarefy, summary, collect, scale;
40 string groups, outputDir, treefile, groupfile, namefile;
41 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
42 map<string, string> nameMap;
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, map< string, set<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&);