X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=ee16221903ce2ee738cd7b941ca90c5b57e05c04;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=a0afb9607184e4d6e522fe92003047616e07c968;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index a0afb96..ee16221 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,50 +9,46 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
-/* The rarefaction.shared() command:
-	The rarefaction command generates a rarefaction curve from a given file representing several groups.  
-	The rarefaction.shared command can only be executed after a successful read.shared command. It outputs a file for each estimator you choose to use.  
-	The rarefaction.shared command parameters are label, line, iters, jumble and sharedrarefaction.  
-	No parameters are required, but you may not use both the line and label  parameters at the same time.  
-	The rarefaction command should be in the following format: rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, 
-	jumble= yourJumble, sharedrarefaction=yourEstimators).  Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, 
-	jumble=1, sharedrarefaction =sharedobserved).  The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
-	iters is 1000 and sharedrarefaction is sharedobserved which calculates the shared rarefaction curve for the observed richness. 
-	 The valid sharedrarefaction estimator is sharedobserved. The label and line parameters are used to analyze specific lines in your input. */
-
-
 class GlobalData;
 
 class RareFactSharedCommand : public Command {
 	
 public:
-	RareFactSharedCommand();	
+	RareFactSharedCommand(string);
+	RareFactSharedCommand();
 	~RareFactSharedCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	SharedListVector* SharedList;
-	ReadMatrix* read;
-	SharedOrderVector* order;
+	ReadOTUFile* read;
+	vector<SharedRAbundVector*> lookup;
 	InputData* input;
 	ValidCalculators* validCalculator;
 	Rarefact* rCurve;
 	vector<Display*> rDisplays;
-	int freq, nIters;
+	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;
+	map<string, vector<string> > outputTypes;
+
 
 };