X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=rarefactsharedcommand.h;h=1a2d944894feabe26b4103e5431c0da08c6574b4;hb=a5d3e10e24e503483d8e85b54f0fd34b9308d31b;hp=1bcddb5257f56967a63b66f0740e648811509204;hpb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 1bcddb5..1a2d944 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -13,36 +13,39 @@
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class RareFactSharedCommand : public Command {
 	
 public:
 	RareFactSharedCommand(string);
-	~RareFactSharedCommand();
-	int execute();	
-	void help();
+	RareFactSharedCommand();
+	~RareFactSharedCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "rarefaction.shared";		}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
+	string getDescription()		{ return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
+	
 	vector<SharedRAbundVector*> lookup;
-	InputData* input;
-	ValidCalculators* validCalculator;
-	Rarefact* rCurve;
-	vector<Display*> rDisplays;
 	int nIters;
 	string format;
 	float freq;
 	
 	bool abort, allLines, jumble;
 	set<string> labels; //holds labels to be used
-	string label, calc, groups, outputDir;
-	vector<string>  Estimators, Groups, outputNames;
-
+	string label, calc, groups, outputDir, sharedfile, designfile;
+	vector<string>  Estimators, Groups, outputNames, Sets;
+    
+    int process(GroupMap&, string);
 
 };