#include "fileoutput.h"
-using namespace std;
-
class GlobalData;
class UnifracUnweightedCommand : public Command {
public:
- UnifracUnweightedCommand();
+ UnifracUnweightedCommand(string);
~UnifracUnweightedCommand() { delete unweighted; delete util; }
- int execute();
+ int execute();
+ void help();
private:
GlobalData* globaldata;
map<float, float> validScores; //map contains scores from random
vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
- map<float, float>::iterator it2;
- map<float, float>::iterator it;
+ bool abort;
+ string groups, itersString;
+ vector<string> Groups; //holds groups to be used
+
ofstream outSum, out;
ifstream inFile;