#include "command.hpp"
#include "treemap.h"
-#include "readtree.h"
#include "sharedutilities.h"
-
+#include "tree.h"
class PhyloDiversityCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "phylo.diversity"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Phylo.diversity"; }
-
+ string getOutputFileNameTag(string, string);
+ 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:
- ReadTree* read;
TreeMap* tmap;
float freq;
int iters, processors, numUniquesInName;
bool abort, rarefy, summary, collect, scale;
string groups, outputDir, treefile, groupfile, namefile;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
- map<string, string> nameMap;
+ map<string, int> getRootForGroups(Tree* t);
int readNamesFile();
void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
void printSumData(map< string, vector<float> >&, ofstream&, int);
- vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
+ vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, 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&);