- vector< map<float, float> > validScores; //vector<contains scores from both user and random> each group comb has an entry
- vector< map<float, float> > rscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
- vector< map<float, float> > uscoreFreq; //vector<weighted, number of user trees with that score.> each group comb has an entry
- vector< map<float, float> > totalrscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
- vector< map<float, float> > rCumul; //vector<weighted score, number of random trees with that score.> each group comb has an entry
- vector< map<float, float> > uCumul; //vector<weighted, cumulative percentage of number of user trees with that score or lower.> each group comb has an entry
- map<float, float>::iterator it;
- map<float, float>::iterator it2;
+ vector< vector<double> > rScores; //vector<weighted scores for random trees.> each group comb has an entry
+ vector< vector<double> > uScores; //vector<weighted scores for user trees.> each group comb has an entry
+ vector< map<float, float> > rScoreFreq; //map <weighted score, number of random trees with that score.> -vector entry for each combination.
+ vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
+ map<float, float> validScores; //map contains scores from random
+
+ bool abort, phylip, random;
+ string groups, itersString, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
+ int processors;
+