X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=c98abc48d748be4dcbb8928283d808b118db29b8;hb=315e38cf393c82be238da5b32574f225a020d25c;hp=ecf78f58a981e1f95602ed4e10973bcf7695cf14;hpb=fb5a52d8d7896ba00c9ccc6add22ed89c5fb2ad7;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index ecf78f5..c98abc4 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -10,55 +10,53 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; }
-		int execute();	
+		UnifracUnweightedCommand(string);	
+		~UnifracUnweightedCommand() { delete unweighted; delete util; }
+		int execute();
+		void help();	
 	
 	private:
 		GlobalData* globaldata;
+		SharedUtil* util;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
-		vector<float> utreeScores;  //user tree unweighted scores
-		vector<float> UWScoreSig;  //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
-		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Unweighted* unweighted;
-		string sumFile, distFile, unweightedFile;
-		int iters;
+		string sumFile, allGroups;
+		vector<string> groupComb; // AB. AC, BC...
+		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//unweighted score info for user tree
 		EstOutput randomData;		//unweighted score info for random trees
-		map<float, float> validScores;  //contains scores from both user and random
-		map<float, float> rscoreFreq;  //unweighted score, number of random trees with that score.
-		map<float, float> uscoreFreq;  //unweighted, number of user trees with that score.
-		map<float, float> totalrscoreFreq;  //unweighted score, number of random trees with that score.
-		map<float, float> rCumul;		//unweighted score, cumulative percentage of number of random trees with that score or higher.
-		map<float, float> uCumul;  //unweighted, cumulative percentage of number of user trees with that score or higher .
-		map<float, float>::iterator it;
-		map<float, float>::iterator it2;
+		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.
+		map<float, float>  validScores;  //map contains scores from 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> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
 		
-		ofstream outSum, outDist, out;
+		bool abort, phylip, random;
+		string groups, itersString, outputDir;
+		vector<string> Groups; //holds groups to be used
+
+		ofstream outSum, out;
+		ifstream inFile;
 		
-		void printUWSummaryFile();
+		void printUWSummaryFile(int);
 		void printUnweightedFile();
-		void saveRandomScores();    
+		void createPhylipFile(int);
+		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif