X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=415279c9b2adad30f95a11eeef309d9d3fd3b802;hb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;hp=e026bc222a3005332e2e509da060d9de6fc11539;hpb=fc7cf3aac8fd6106fd725b43baa8ab5ca6f836f8;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e026bc2..415279c 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,47 +13,59 @@
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
-
-using namespace std;
-
-class GlobalData;
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; }
-		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"; }
+	
+		int execute();
+		void help() { m->mothurOut(getHelpString()); }
+	
 	
 	private:
-		GlobalData* globaldata;
+		ReadTree* read;
+		SharedUtil* util;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
-		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Unweighted* unweighted;
-		string sumFile, unweightedFile;
+		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp;
+		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.
 		vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
-		vector< map<float, float> > validScores;  //map contains scores from both user and random
+		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> > uscoreFreq;  //map <unweighted score, number of user 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.
-		vector< map<float, float> > uCumul;  //map <unweighted score, cumulative percentage of number of user trees with that score or higher.> -vector entry for each combination.		map<float, float>::iterator it;
-		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();
+		void printUWSummaryFile(int);
 		void printUnweightedFile();
-		void setGroups();   
+		void createPhylipFile(int);
+		int readNamesFile();
+		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif