X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.h;h=88e32acc0426a15525b1278bd5fc6d9c4d6392fc;hb=8c8acb6218f58f662466e4111ab8aa4da0caf93c;hp=9c9f455b4e8b4f45d309e5453da5c41fbba813d7;hpb=d051154d778b77ba36dc603bbdb3c148a62a8e33;p=mothur.git

diff --git a/metastatscommand.h b/metastatscommand.h
index 9c9f455..88e32ac 100644
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -12,35 +12,47 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class MetaStatsCommand : public Command {
 
 public:
 	MetaStatsCommand(string);
-	~MetaStatsCommand();
-	int execute();
-	void help();
+	MetaStatsCommand();
+	~MetaStatsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "metastats";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
+	string getDescription()		{ return "detects differentially abundant features in clinical metagenomic samples"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
+	struct linePair {
+		int start;
+		int num;
+		linePair(int i, int j) : start(i), num(j) {}
+	};
+	vector<linePair> lines;
+	
 	GroupMap* designMap;
-	ReadOTUFile* read;
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
-	
+		
 	bool abort, allLines, pickedGroups;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, inputDir, designfile;
-	vector<string> Groups, outputNames;
-	int iters, g;
+	string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
+	vector<string> Groups, outputNames, Sets;
+	vector< vector<string> > namesOfGroupCombos;
+	int iters, processors;
 	float threshold;
 	
 	int process(vector<SharedRAbundVector*>&);
-	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int driver(int, int, vector<SharedRAbundVector*>&);
 };
 
 #endif