X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=e8daaefccbead969b54f2996f83ae378fc407a1c;hb=b2c44d69197045c26c1f4e62d248ab882c79a393;hp=45d3c7cec25d4d80448d32beeaa212a92295d366;hpb=fb5a52d8d7896ba00c9ccc6add22ed89c5fb2ad7;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 45d3c7c..e8daaef 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -10,11 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
@@ -39,24 +34,21 @@ class UnifracWeightedCommand : public Command {
 		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
-		string weightedFile, sumFile, distFile;
+		string weightedFile, sumFile;
 		int iters, numGroups, numComp;
 		EstOutput userData;			//weighted score info for user tree
 		EstOutput randomData;		//weighted score info for random trees
-		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 or higher.> each group comb has an entry
-		vector< map<float, float> > uCumul;  //vector<weighted, cumulative percentage of number of user trees with that score or higher.> each group comb has an entry
-		map<float, float>::iterator it;
-		map<float, float>::iterator it2;
-		
-		ofstream outSum, outDist, out;
+		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;
 		
 		void printWSummaryFile();
-		void printWeightedFile();  
-		void saveRandomScores(); 
+	//	void printWeightedFile();  
+		void removeValidScoresDuplicates();
+		int findIndex(float, int);
+		void setGroups(); 
 };