X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.h;h=7e9363080e7bf7b794b3797c37df9527d8f84764;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=38b5ec7643fdd4e79e4d70408c59ba9fe3210be0;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 38b5ec7..7e93630 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,31 +13,39 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
 	GetRAbundCommand(string);
-	~GetRAbundCommand();
-	int execute();
-	void help();
+	GetRAbundCommand();
+	~GetRAbundCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.rabund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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;
 
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	bool abort, allLines, sorted;
 	set<string> labels; //holds labels to be used
-	string line, label;
+	string label;
 
 	
 };