X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=15c3b9684b01fa58403276b80864684f99e8d189;hb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;hp=cd8d51dcad76a44dbc0ca064bd79a5ef3e0fbe80;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index cd8d51d..15c3b96 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -27,7 +27,8 @@ class UnifracUnweightedCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "unifrac.unweighted";		}
 		string getCommandCategory()		{ return "Hypothesis Testing";		}
-		string getHelpString();	
+		string getOutputFileNameTag(string, string);
+	string getHelpString();	
 		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"; }
 
@@ -36,36 +37,32 @@ class UnifracUnweightedCommand : public Command {
 	
 	
 	private:
-		ReadTree* read;
-		SharedUtil* util;
 		FileOutput* output;
 		vector<Tree*> T;	   //user trees
 		TreeMap* tmap;
-		Unweighted* unweighted;
 		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp, counter, processors, numUniquesInName;
-		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, includeRoot;
+		bool abort, phylip, random, includeRoot, consensus, subsample;
 		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
 		vector<string> Groups, outputNames; //holds groups to be used
 
 		ofstream outSum, out;
 		ifstream inFile;
-		map<string, string> nameMap;
 		
+        int runRandomCalcs(Tree*, vector<double>);
 		void printUWSummaryFile(int);
 		void printUnweightedFile();
 		void createPhylipFile(int);
-		int readNamesFile();
-		 
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
 		
 };