changing command name classify.shared to classifyrf.shared

[mothur.git] / splitabundcommand.h

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 2e409b2aedd7606b6c689f48cb9e0e58f7a0bcfe..9929b7967050308c2563561896fa615a6f371d12 100644 (file)
--- a/splitabundcommand.h
+++ b/splitabundcommand.h
@@ -21,6 +21,8 @@ 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"
+#include "counttable.h"
 
 /***************************************************************************************/
 
@@ -30,37 +32,41 @@ 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(); 
+    string getOutputPattern(string);   
+       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*, string); 
+       int writeList(ListVector*, string, int); 
        int writeAccnos(string); 
        int parseGroup(string); 
        int parseFasta(string); 
+    int parseCount(string);
+    int splitCount();
        int readNamesFile(); //namefile
        int createNameMap(ListVector*);
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-       ListVector* list;
-       GroupMap* groupMap;
-       InputData* input;
+    GroupMap groupMap;
+    CountTable ct;
        
-       string outputDir, listfile, namefile, groupfile, label, groups, fastafile, inputFile;
+       string outputDir, listfile, namefile, groupfile, countfile, label, groups, fastafile, inputFile;
        set<string> labels, rareNames, abundNames;
        vector<string> Groups;
        bool abort, allLines, accnos;
        int cutoff;
-       //map<string, bool> wroteListFile;
        map<string, string> nameMap;