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"
14 #include "counttable.h"
15 #include "sharedutilities.h"
18 class PhyloDiversityCommand : public Command {
21 PhyloDiversityCommand(string);
22 PhyloDiversityCommand();
23 ~PhyloDiversityCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "phylo.diversity"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 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"; }
32 string getDescription() { return "phylo.diversity"; }
35 void help() { m->mothurOut(getHelpString()); }
39 int iters, processors, numUniquesInName;
40 bool abort, rarefy, summary, collect, scale;
41 string groups, outputDir, treefile, groupfile, namefile, countfile;
42 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
44 map<string, int> getRootForGroups(Tree* t);
46 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
47 void printSumData(map< string, vector<float> >&, ofstream&, int);
48 vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
49 int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
50 int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);