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();
22 ~PhyloDiversityCommand();
23 vector<string> getRequiredParameters();
24 vector<string> getValidParameters();
25 vector<string> getRequiredFiles();
26 map<string, vector<string> > getOutputFiles() { return outputTypes; }
31 GlobalData* globaldata;
34 int iters, processors;
35 bool abort, rarefy, summary, collect, scale;
36 string groups, outputDir;
37 vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
38 map<string, vector<string> > outputTypes;
40 void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
41 void printSumData(map< string, vector<float> >&, ofstream&, int);
42 vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
43 int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
44 int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);