1.18.1

[mothur.git] / splitabundcommand.h

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 02d61f3dc3b7f343a9e0d9a73bb71e84fcdacbbd..c883a690d9846febec2059b4d88ea1393ea2f52c 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"
 
 /***************************************************************************************/
 
@@ -30,19 +31,20 @@ 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 getHelpString(); 
+       
+       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 +52,6 @@ private:
        int createNameMap(ListVector*);
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        ListVector* list;
        GroupMap* groupMap;
        InputData* input;