X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactcommand.h;h=02fe6e3aa4355a107e76f06d8f8f9a7f0df19118;hp=0da5f0c20548196ed65d6e200620a8b0d9009d39;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 0da5f0c..02fe6e3 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -9,48 +9,51 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
-
-
-/*The rarefaction() command:
-	The rarefaction command generates a rarefaction curve from a given file.  
-	The rarefaction command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
-	The rarefaction command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster. 
-	The rarefaction command outputs a file for each estimator you choose to use.  It is recommended to only use rarefaction estimator.  
-	The rarefaction command parameters are label, line, iters, freq, rarefaction.  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(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators). 
-	Example rarefaction(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson). 
-	The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness. 
-	The valid rarefaction estimators are: rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson.  
-	Rarefaction is the only recommended estimator.  The label and line parameters are used to analyze specific lines in your input. */
-	
-
-class GlobalData;
+#include "validcalculator.h"
 
 class RareFactCommand : public Command {
 	
 public:
+	RareFactCommand(string);
 	RareFactCommand();	
-	~RareFactCommand();
-	int execute();	
+	~RareFactCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "rarefaction.single";		}
+	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.single"; }
+	string getDescription()		{ return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
+	
 	vector<Display*> rDisplays;
-	ReadMatrix* read;
 	OrderVector* order;
 	InputData* input;
 	Rarefact* rCurve;
-	int freq, nIters;
+	int nIters, abund, processors;
+	float freq;
+	
+	bool abort, allLines, groupMode;
+	set<string> labels; //holds labels to be used
+	string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+	vector<string>  Estimators;
+	vector<string> inputFileNames, outputNames;
+	vector<string> groups;
+	string outputDir;
+	
+	vector<string> parseSharedFile(string, map<string, set<int> >&);
+	vector<string> createGroupFile(vector<string>&, map<int, string>);
 };
 
 #endif