X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=e10aa44e8462d4690e095e4ab1ef37ea8542e9cd;hb=1c2f1171eee8879de9dbe03a8a9d9093fc6a1f95;hp=4d8f6624dae66605a2169f2d081d49e94b918272;hpb=5318771152ee5b1a280b3dc50aedd887dd1da8a8;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 4d8f662..e10aa44 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -34,21 +34,31 @@ class UnifracWeightedCommand : public Command {
 		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
-		string weightedFile, sumFile;
-		int iters, numGroups, numComp;
+		string weightedFile, weightedFileout, sumFile;
+		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//weighted score info for user tree
 		EstOutput randomData;		//weighted score info for random trees
-		vector< vector<double> > validScores;  //vector<contains scores from both user and random> each group comb has an entry
 		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
+		map<float, float>::iterator it2;
+		map<float, float>::iterator it;
+		
 		ofstream outSum, out;
+		ifstream inFile;
 		
 		void printWSummaryFile();
-	//	void printWeightedFile();  
-		void removeValidScoresDuplicates();
+		void printWeightedFile();  
+		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void setGroups(); 
+		void calculateFreqsCumuls();
+		void initFile(string);
+		void output(vector<double>);
+		void resetFile();
+
 };