X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactsharedcommand.h;h=4f08d00d7332ae32824464b809744042bd997d7f;hp=d81ff6dc2d1c6588d86f9cccbb0251778bd85011;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index d81ff6d..4f08d00 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -13,50 +13,44 @@
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#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 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, 
-	 sharedrarefaction=yourEstimators).  Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, 
-	 sharedrarefaction =sharedobserved).  The default values for 
-	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(string);	
-	~RareFactSharedCommand();
-	int execute();	
-	void help();
+	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;
-	ReadOTUFile* read;
+	
 	vector<SharedRAbundVector*> lookup;
-	InputData* input;
-	ValidCalculators* validCalculator;
-	Rarefact* rCurve;
-	vector<Display*> rDisplays;
-	int freq, nIters;
+	int nIters, subsampleSize, iters;
 	string format;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	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 line, label, calc, groups;
-	vector<string>  Estimators, Groups;
-
+	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);
 
 };