X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactsharedcommand.h;h=4f08d00d7332ae32824464b809744042bd997d7f;hp=ab870242000bb0b07f3e28078feba84bcce1de4c;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index ab87024..4f08d00 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,47 +9,48 @@
  *
  */
 
-#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"
-
-/* 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;
+#include "validcalculator.h"
 
 class RareFactSharedCommand : public Command {
 	
 public:
-	RareFactSharedCommand();	
-	~RareFactSharedCommand();
-	int execute();	
+	RareFactSharedCommand(string);
+	RareFactSharedCommand();
+	~RareFactSharedCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "rarefaction.shared";		}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
-	SharedListVector* SharedList;
-	ReadMatrix* read;
-	SharedOrderVector* order;
-	InputData* input;
-	Rarefact* rCurve;
-	vector<Display*> rDisplays;
-	int freq, nIters;
+	
+	vector<SharedRAbundVector*> lookup;
+	int nIters, subsampleSize, iters;
+	string format;
+	float freq;
+	
+     map<int, string> file2Group; //index in outputNames[i] -> group
+	bool abort, allLines, jumble, groupMode, subsample;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups, outputDir, sharedfile, designfile;
+	vector<string>  Estimators, Groups, outputNames, Sets;
+    
+    int process(GroupMap&, string);
+    vector<string> createGroupFile(vector<string>&);
+    int subsampleLookup(vector<SharedRAbundVector*>&, string);
 
 };