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"
15 #include "globaldata.hpp"
17 class PhyloDiversityCommand : public Command {
20 PhyloDiversityCommand(string);
21 ~PhyloDiversityCommand();
26 GlobalData* globaldata;
29 int iters, processors;
30 bool abort, rarefy, summary, collect, scale;
31 string groups, outputDir;
32 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
34 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
35 void printSumData(map< string, vector<float> >&, ofstream&, int);
36 float calcBranchLength(Tree*, int, map< string, set<int> >&);
37 int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
38 int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);