X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getrabundcommand.h;h=fd7a6b07fecf135262e310598a3936221cb98826;hp=4b2c37f11340e8dfc940f549b2c97a7c8c339b38;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 4b2c37f..fd7a6b0 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,35 +13,41 @@
 
 #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 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, countfile;
 	ofstream out;
-	ReadOTUFile* read;
-	InputData* input;
-	ListVector* list;
-	RAbundVector* rabund;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	vector<string> outputNames;
+
+	bool abort, allLines, sorted;
 	set<string> labels; //holds labels to be used
-	string line, label;
+	string label;
 
-	
+	int processList(ofstream& out);
+    int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
 };
 
 #endif