X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.h;h=232c36ba36763dcdb325fb9f8404d537e92450a6;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=02d61f3dc3b7f343a9e0d9a73bb71e84fcdacbbd;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 02d61f3..232c36b 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"
 
 /***************************************************************************************/
 
@@ -30,19 +31,23 @@ public:
 	SplitAbundCommand(string);	
 	SplitAbundCommand();
 	~SplitAbundCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
-
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "split.abund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
+	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); 
@@ -50,7 +55,6 @@ private:
 	int createNameMap(ListVector*);
 	
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	ListVector* list;
 	GroupMap* groupMap;
 	InputData* input;