X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.h;h=868cd473b29cb97ba5ee38f847aab8343e06c3ac;hp=e8b7b96a608453f5c5c7c6e510cd9b96bacd661b;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=f37a59b81c339f574d97042ff6e364146feb457a

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index e8b7b96..868cd47 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -12,45 +12,44 @@
 
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "sharedutilities.h"
 
-class GlobalData;
 
 class CollectSharedCommand : public Command {
 	
 public:
 	CollectSharedCommand(string);	
+	CollectSharedCommand();	
 	~CollectSharedCommand();
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "collect.shared";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
+	string getDescription()		{ return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	SharedUtil* util;
-	GroupMap* groupmap;
-	SharedListVector* SharedList;
-	ReadOTUFile* read;
 	SharedOrderVector* order;
 	InputData* input;
-	ValidCalculators* validCalculator;
 	Collect* cCurve;
 	vector<Display*> cDisplays;
-	int freq;
-	string format;
+	float freq;
 
-	bool abort, allLines;
+	bool abort, allLines, all;
 	set<string> labels; //holds labels to be used
-	string label, calc, groups;
-	vector<string>  Estimators, Groups;
-
-
+	string label, calc, groups, outputDir, sharedfile;
+	vector<string>  Estimators, Groups, outputNames;
 };
 
 #endif