X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=unifracunweightedcommand.h;h=3961e53cb68c96e70dd5bcd55449ed5d72346cd9;hp=c6fc46ac0bce0437b2d04315442fcf33e045b4d3;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index c6fc46a..3961e53 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -12,50 +12,58 @@
 
 #include "command.hpp"
 #include "unweighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-class GlobalData;
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
 		UnifracUnweightedCommand(string);	
-		~UnifracUnweightedCommand() { delete unweighted; delete util; }
+		UnifracUnweightedCommand();
+		~UnifracUnweightedCommand() {}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "unifrac.unweighted";		}
+		string getCommandCategory()		{ return "Hypothesis Testing";		}
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
+		string getDescription()		{ return "generic tests that describes whether two or more communities have the same structure"; }
+
 		int execute();
-		void help();	
+		void help() { m->mothurOut(getHelpString()); }
+	
 	
 	private:
-		GlobalData* globaldata;
-		SharedUtil* util;
 		FileOutput* output;
 		vector<Tree*> T;	   //user trees
-		TreeMap* tmap;
-		Unweighted* unweighted;
+		CountTable* ct;
 		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
+		int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
 		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.
 		
-		bool abort, phylip, random;
-		string groups, itersString, outputDir;
+		bool abort, phylip, random, includeRoot, consensus, subsample;
+		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
 		vector<string> Groups, outputNames; //holds groups to be used
 
 		ofstream outSum, out;
 		ifstream inFile;
 		
+        int runRandomCalcs(Tree*, vector<double>);
 		void printUWSummaryFile(int);
 		void printUnweightedFile();
 		void createPhylipFile(int);
-		 
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
 		
 };