unifrac.unweighted command changes

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e026bc222a3005332e2e509da060d9de6fc11539..b572e4679845e63674bcecfb23710876504af90b 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -28,29 +28,31 @@ class UnifracUnweightedCommand : public Command {
        private:
                GlobalData* globaldata;
                vector<Tree*> T;           //user trees
-               Tree* randT;  //random tree
                TreeMap* tmap;
                Unweighted* unweighted;
-               string sumFile, unweightedFile;
+               string sumFile, unweightedFile, unweightedFileout;
                vector<string> groupComb; // AB. AC, BC...
-               int iters, numGroups, numComp;
+               int iters, numGroups, numComp, counter;
                EstOutput userData;                     //unweighted score info for user tree
                EstOutput randomData;           //unweighted score info for random trees
                vector< vector<float> > utreeScores; //scores for users trees for each comb.
                vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
                vector< map<float, float> > validScores;  //map contains scores from both user and 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> > uscoreFreq;  //map <unweighted score, number of user 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> > uCumul;  //map <unweighted score, cumulative percentage of number of user trees with that score or higher.> -vector entry for each combination.             map<float, float>::iterator it;
                map<float, float>::iterator it2;
                map<float, float>::iterator it;
                
                ofstream outSum, out;
+               ifstream inFile;
                
                void printUWSummaryFile();
                void printUnweightedFile();
-               void setGroups();   
+               void setGroups();  
+               void initFile(string);
+               void output(vector<double>);
+               void resetFile();
+ 
                
 };