X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.h;h=dcf8c686dbd2bf75847ef500bf7fea0fbd087cb5;hb=eb71e28b7b7afd82540f4a8f0bac9429c5b9d713;hp=e853ac5f913a1d758e7a633510478ad30449feec;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getrabundcommand.h b/getrabundcommand.h
index e853ac5..dcf8c68 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,33 +13,36 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
 	GetRAbundCommand(string);
 	GetRAbundCommand();
-	~GetRAbundCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~GetRAbundCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.rabund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+	string getDescription()		{ return "creates a rabund file"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	string filename;
+	
+	string filename, listfile, sabundfile, inputfile, format, outputDir;
 	ofstream out;
-	ReadOTUFile* read;
 	InputData* input;
-	ListVector* list;
 	RAbundVector* rabund;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 
 	bool abort, allLines, sorted;
 	set<string> labels; //holds labels to be used