#include "command.hpp"
#include "treemap.h"
-#include "globaldata.hpp"
+#include "readtree.h"
+#include "sharedutilities.h"
+
class PhyloDiversityCommand : public Command {
public:
PhyloDiversityCommand(string);
PhyloDiversityCommand();
- ~PhyloDiversityCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~PhyloDiversityCommand(){}
- private:
- GlobalData* globaldata;
-
+ vector<string> setParameters();
+ string getCommandName() { return "phylo.diversity"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+private:
+ ReadTree* read;
+ TreeMap* tmap;
float freq;
- int iters, processors;
+ 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
- map<string, vector<string> > outputTypes;
+ map<string, string> nameMap;
+ 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> >&);