- Tree* randT; //random tree
- TreeMap* tmap;
- Weighted* weighted;
- string weightedFile, sumFile;
- int iters, numGroups, numComp;
- EstOutput userData; //weighted score info for user tree
- EstOutput randomData; //weighted score info for random trees
- vector< vector<float> > validScores; //vector<contains scores from both user and random> each group comb has an entry
- vector< vector<float> > rScores; //vector<weighted scores for random trees.> each group comb has an entry
- vector< vector<float> > uScores; //vector<weighted scores for user trees.> each group comb has an entry
-
- ofstream outSum, out;
+ string sumFile, outputDir;
+ int iters, numGroups, numComp, counter;
+ 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, includeRoot, subsample, consensus;
+ string groups, itersString, outputForm, treefile, groupfile, namefile, countfile;
+ vector<string> Groups, outputNames; //holds groups to be used
+ int processors, subsampleSize, subsampleIters;
+ ofstream outSum;
+ map<string, string> nameMap;