X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.h;h=c2645562f1111c4a03be95c4e27c143745311ed5;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=196d245002498043dd8a32d11de45c5e1eb7c0cb;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/getlistcountcommand.h b/getlistcountcommand.h
index 196d245..c264556 100644
--- a/getlistcountcommand.h
+++ b/getlistcountcommand.h
@@ -12,32 +12,40 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
-
-class GlobalData;
 
 /**********************************************************/
 
 class GetListCountCommand : public Command {
 	
 public:
-	GetListCountCommand(string);	
-	~GetListCountCommand();
-	int execute();
-	void help();	
+	GetListCountCommand(string);
+	GetListCountCommand();	
+	~GetListCountCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.otulist";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
+	string getDescription()		{ return "lists each OTU number and the sequence contained in that OTU"; }
+
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	ListVector* list;
-	ReadOTUFile* read;
 	InputData* input;
 	
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string label, listfile, outputDir;
+	string label, listfile, outputDir, sort;
 	ofstream out;
 	vector<string> outputNames;
-	
+		
 	void process(ListVector*);
 };
 /**********************************************************/