X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getsabundcommand.h;h=7242342cdcdf455d2861f230fc65c039fd00bd6c;hp=b5363e1bce548af4af74408593d855cac4da973c;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/getsabundcommand.h b/getsabundcommand.h
index b5363e1..7242342 100644
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -13,37 +13,37 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
-class GlobalData;
-
 class GetSAbundCommand : public Command {
 public:
 	GetSAbundCommand(string);
 	GetSAbundCommand();
-	~GetSAbundCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~GetSAbundCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.sabund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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, countfile;
 	ofstream out;
-	ReadOTUFile* read;
-	OrderVector* order;
-	InputData* input;
-	SAbundVector* sabund;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string label;
+    
+    int processList(ofstream& out);
+    int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
 
 };