X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.h;h=81a5d910b53c84db70c560255ce2b508c4361f33;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=66a3211296edc7f2105af0ba2bfc10f85b7ae109;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 66a3211..81a5d91 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,25 +13,38 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
+	GetRAbundCommand(string);
 	GetRAbundCommand();
-	~GetRAbundCommand();
-	int execute();
+	~GetRAbundCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.rabund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+	
+	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;
+
+	bool abort, allLines, sorted;
+	set<string> labels; //holds labels to be used
+	string label;
+
+	
 };
 
 #endif