X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.h;h=c2645562f1111c4a03be95c4e27c143745311ed5;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=60d28cc6a351011fdc34af98189025af5d26f487;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getlistcountcommand.h b/getlistcountcommand.h
index 60d28cc..c264556 100644
--- a/getlistcountcommand.h
+++ b/getlistcountcommand.h
@@ -12,9 +12,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
-
-class GlobalData;
 
 /**********************************************************/
 
@@ -23,18 +20,24 @@ class GetListCountCommand : public Command {
 public:
 	GetListCountCommand(string);
 	GetListCountCommand();	
-	~GetListCountCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	~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;
@@ -42,8 +45,7 @@ private:
 	string label, listfile, outputDir, sort;
 	ofstream out;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
-	
+		
 	void process(ListVector*);
 };
 /**********************************************************/