X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.h;h=4c967b5e9f3455c3a7ceea5fd3dac67a99f9695b;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=27d25c2f2c3d2739bb6cfecd85f7b059b4867442;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2..4c967b5 100644
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -13,26 +13,36 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
-class GlobalData;
-
 class GetSAbundCommand : public Command {
 public:
+	GetSAbundCommand(string);
 	GetSAbundCommand();
-	~GetSAbundCommand();
-	int execute();
+	~GetSAbundCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.sabund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
+	string getDescription()		{ return "creates a sabund file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
-	string filename, format;
+	string filename, format, inputfile, listfile, rabundfile, outputDir;
 	ofstream out;
-	ReadOTUFile* read;
-	OrderVector* order;
-	OrderVector* lastOrder;
 	InputData* input;
 	SAbundVector* sabund;
+	vector<string> outputNames;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string label;
+
 };
 
 #endif