added count parameter to chimera.slayer command

[mothur.git] / splitabundcommand.h

diff --git a/splitabundcommand.h b/splitabundcommand.h
index df5bd55305a502803a8c1bfe36f24d60474061bb..232c36ba36763dcdb325fb9f8404d537e92450a6 100644 (file)
--- 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 +29,25 @@ 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 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);