#include "command.hpp"
#include "treemap.h"
-#include "globaldata.hpp"
+#include "sharedutilities.h"
+#include "tree.h"
class PhyloDiversityCommand : public Command {
public:
PhyloDiversityCommand(string);
- ~PhyloDiversityCommand();
- int execute();
- void help();
+ PhyloDiversityCommand();
+ ~PhyloDiversityCommand(){}
- private:
- GlobalData* globaldata;
-
+ vector<string> setParameters();
+ string getCommandName() { return "phylo.diversity"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ 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:
+ TreeMap* tmap;
float freq;
- int iters;
+ int iters, processors, numUniquesInName;
bool abort, rarefy, summary, collect, scale;
- string groups, outputDir;
+ string groups, outputDir, treefile, groupfile, namefile;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
+ int readNamesFile();
void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
void printSumData(map< string, vector<float> >&, ofstream&, int);
- float calcBranchLength(Tree*, int, map< string, set<int> >&);
+ vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
+ int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
+ int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);
+
};
#endif