X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=77dd10d3490999def3789b91d405ac76e470f360;hb=afed323beddfc099c365104b9071600aea9731bd;hp=491d3846f65ae135d458c947b3f4a7539a5acde8;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 491d384..77dd10d 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -23,9 +23,10 @@ class GlobalData;
 class UnifracWeightedCommand : public Command {
 	
 	public:
-		UnifracWeightedCommand();	
-		~UnifracWeightedCommand() { delete weighted; delete util; }
+		UnifracWeightedCommand(string);
+		~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
 		int execute();	
+		void help();
 	
 	private:
 		GlobalData* globaldata;
@@ -38,7 +39,7 @@ class UnifracWeightedCommand : public Command {
 		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
-		string sumFile;
+		string sumFile, outputDir;
 		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//weighted score info for user tree
 		EstOutput randomData;		//weighted score info for random trees
@@ -47,14 +48,17 @@ class UnifracWeightedCommand : public Command {
 		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;
+		bool abort, phylip, random;
+		string groups, itersString;
+		vector<string> Groups, outputNames; //holds groups to be used
+
+		
+		ofstream outSum;
 		
 		void printWSummaryFile();
 		void printWeightedFile();  
+		void createPhylipFile();
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();