X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.h;h=868cd473b29cb97ba5ee38f847aab8343e06c3ac;hp=327ce5d28832dbe7f25d69f6c0755f6e931c747d;hb=615301e57c25e241356a9c2380648d117709458d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 327ce5d..868cd47 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -12,16 +12,12 @@
 
 #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 {
 	
@@ -29,34 +25,31 @@ public:
 	CollectSharedCommand(string);	
 	CollectSharedCommand();	
 	~CollectSharedCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	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;
 	float freq;
-	string format;
 
 	bool abort, allLines, all;
 	set<string> labels; //holds labels to be used
-	string label, calc, groups, outputDir;
+	string label, calc, groups, outputDir, sharedfile;
 	vector<string>  Estimators, Groups, outputNames;
-	map<string, vector<string> > outputTypes;
-
-
 };
 
 #endif