X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.h;h=df925f34cc70bc405ac35e2302ecc49a8fd97872;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=fb8838063e408223df815f80844e51c04569c16a;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/splitabundcommand.h b/splitabundcommand.h
index fb88380..df925f3 100644
--- a/splitabundcommand.h
+++ b/splitabundcommand.h
@@ -21,6 +21,7 @@ also allow an option where a user can give a group file with the list or names f
 #include "groupmap.h"
 #include "inputdata.h"
 #include "listvector.hpp"
+#include "sequence.hpp"
 
 /***************************************************************************************/
 
@@ -28,16 +29,24 @@ class SplitAbundCommand : public Command {
 	
 public:
 	SplitAbundCommand(string);	
+	SplitAbundCommand();
 	~SplitAbundCommand();
-	int execute();	
-	void help();
-
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "split.abund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Split.abund"; }
+	string getDescription()		{ return "split a list, name, group or fasta file based on abundance"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	int splitList(ListVector*);
 	int splitNames(); //namefile
 	int writeNames(); 
-	int writeList(ListVector*); 
+	int writeList(ListVector*, string); 
 	int writeAccnos(string); 
 	int parseGroup(string); 
 	int parseFasta(string); 
@@ -54,7 +63,7 @@ private:
 	vector<string> Groups;
 	bool abort, allLines, accnos;
 	int cutoff;
-	map<string, bool> wroteListFile;
+	//map<string, bool> wroteListFile;
 	map<string, string> nameMap;