X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=a210574002969c411be4d9e9c705af9d88c980f0;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=ee16221903ce2ee738cd7b941ca90c5b57e05c04;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index ee16221..a210574 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -13,42 +13,41 @@
 #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();
-	~RareFactSharedCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~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;
+     map<int, string> file2Group; //index in outputNames[i] -> group
+	bool abort, allLines, jumble, groupMode;
 	set<string> labels; //holds labels to be used
-	string label, calc, groups, outputDir;
-	vector<string>  Estimators, Groups, outputNames;
-	map<string, vector<string> > outputTypes;
-
+	string label, calc, groups, outputDir, sharedfile, designfile;
+	vector<string>  Estimators, Groups, outputNames, Sets;
+    
+    int process(GroupMap&, string);
+    vector<string> createGroupFile(vector<string>&);
 
 };