X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=cd8d51dcad76a44dbc0ca064bd79a5ef3e0fbe80;hb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;hp=e900af4f8b0cc434bf16fae2f15535779032f901;hpb=9653c9f8c1b63ecb1a63b45e781c303713d5b5df;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e900af4..cd8d51d 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -15,21 +15,28 @@
 #include "treemap.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-using namespace std;
-
-class GlobalData;
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; delete util; }
-		int execute();	
+		UnifracUnweightedCommand(string);	
+		UnifracUnweightedCommand();
+		~UnifracUnweightedCommand() {}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "unifrac.unweighted";		}
+		string getCommandCategory()		{ return "Hypothesis Testing";		}
+		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"; }
+
+		int execute();
+		void help() { m->mothurOut(getHelpString()); }
+	
 	
 	private:
-		GlobalData* globaldata;
+		ReadTree* read;
 		SharedUtil* util;
 		FileOutput* output;
 		vector<Tree*> T;	   //user trees
@@ -37,7 +44,7 @@ class UnifracUnweightedCommand : public Command {
 		Unweighted* unweighted;
 		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp, counter;
+		int iters, numGroups, numComp, counter, processors, numUniquesInName;
 		EstOutput userData;			//unweighted score info for user tree
 		EstOutput randomData;		//unweighted score info for random trees
 		vector< vector<float> > utreeScores; //scores for users trees for each comb.
@@ -45,18 +52,21 @@ 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, includeRoot;
+		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;
 		
 		void printUWSummaryFile(int);
 		void printUnweightedFile();
+		void createPhylipFile(int);
+		int readNamesFile();
 		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif