X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=5cd93a94c0dcf96547ee409d4ca641092309d2bc;hb=edec660ee2be477ac1539109d949a60cb7e16243;hp=4d8f6624dae66605a2169f2d081d49e94b918272;hpb=5318771152ee5b1a280b3dc50aedd887dd1da8a8;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 4d8f662..5cd93a9 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -13,6 +13,9 @@
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 using namespace std;
 
@@ -22,11 +25,13 @@ class UnifracWeightedCommand : public Command {
 	
 	public:
 		UnifracWeightedCommand();	
-		~UnifracWeightedCommand() { delete weighted; }
+		~UnifracWeightedCommand() { delete weighted; delete util; }
 		int execute();	
 	
 	private:
 		GlobalData* globaldata;
+		SharedUtil* util;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
 		vector<double> utreeScores;  //user tree unweighted scores
 		vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
@@ -34,21 +39,27 @@ class UnifracWeightedCommand : public Command {
 		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
-		string weightedFile, sumFile;
-		int iters, numGroups, numComp;
+		string 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();
+		
 };