@@ -45,19+45,18 @@ class UnifracUnweightedCommand : public Command {
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.
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.
- bool abort;
- string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ bool abort, phylip, random;
+ string groups, itersString, outputDir;
+ vector<string> Groups, outputNames; //holds groups to be used