X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=f6f867877620e7e6e69e4e446bdbe8da3815861a;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=351e05212437174a9efeb09ecbecc9a7da53f449;hpb=813502505663a3d00555bf7633163432b643dd68;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 351e052..f6f8678 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,24 +13,28 @@
 #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() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
+		int execute();
+		void help();	
 	
 	private:
 		GlobalData* globaldata;
+		SharedUtil* util;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
 		TreeMap* tmap;
 		Unweighted* unweighted;
-		string sumFile, unweightedFile, unweightedFileout;
+		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
 		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//unweighted score info for user tree
@@ -40,22 +44,19 @@ class UnifracUnweightedCommand : public Command {
 		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.
-		map<float, float>::iterator it2;
-		map<float, float>::iterator it;
 		
+		bool abort, phylip, random;
+		string groups, itersString, outputDir;
+		vector<string> Groups, outputNames; //holds groups to be used
+
 		ofstream outSum, out;
 		ifstream inFile;
 		
-		void printUWSummaryFile();
+		void printUWSummaryFile(int);
 		void printUnweightedFile();
-		void setGroups();  
-		void initFile(string);
-		void output(vector<double>);
-		void resetFile();
- 
+		void createPhylipFile(int);
+		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif