X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=b1db317de0add4b28352315e20dc282110fad789;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=7317c8a43092a5712a06dda00589d1eb4528c649;hpb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 7317c8a..b1db317 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -16,17 +16,24 @@
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-class GlobalData;
+#include "readtree.h"
 
 class UnifracWeightedCommand : public Command {
 	
 	public:
 		UnifracWeightedCommand(string);
-		~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
-		int execute();	
-		void help();
+		UnifracWeightedCommand();
+		~UnifracWeightedCommand() {}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "unifrac.weighted";		}
+		string getCommandCategory()		{ return "Hypothesis Testing";		}
+		string getHelpString();	
+		string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
+		string getDescription()		{ return "generic tests that describes whether two or more communities have the same structure"; }
+
+		int execute();
+		void help() { m->mothurOut(getHelpString()); }
 	
 	private:
 		struct linePair {
@@ -36,7 +43,7 @@ class UnifracWeightedCommand : public Command {
 		};
 		vector<linePair> lines;
 		
-		GlobalData* globaldata;
+		ReadTree* read;
 		SharedUtil* util;
 		FileOutput* output;
 		vector<Tree*> T;	   //user trees
@@ -55,13 +62,12 @@ class UnifracWeightedCommand : public Command {
 		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
 		
-		bool abort, phylip, random;
-		string groups, itersString;
+		bool abort, phylip, random, includeRoot;
+		string groups, itersString, outputForm, treefile, groupfile, namefile;
 		vector<string> Groups, outputNames; //holds groups to be used
-		int processors;
-
-		
+		int processors, numUniquesInName;
 		ofstream outSum;
+		map<string, string> nameMap;
 		
 		void printWSummaryFile();
 		void printWeightedFile();  
@@ -69,8 +75,9 @@ class UnifracWeightedCommand : public Command {
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();
-		int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-		int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+		int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+		int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
+		int readNamesFile();
 		
 };