moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / splitabundcommand.h

diff --git a/splitabundcommand.h b/splitabundcommand.h
deleted file mode 100644 (file)
index df925f3..0000000
--- a/splitabundcommand.h
+++ /dev/null
@@ -1,77 +0,0 @@
-#ifndef SPLITABUNDCOMMAND_H
-#define SPLITABUNDCOMMAND_H
-
-/*
- *  splitabundcommand.h
- *  Mothur
- *
- *  Created by westcott on 5/17/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-/* split.abund - given a list or name file and a number (cutoff), make two files - *rare* and *abund* 
-- where rare has data for otus that have fewer sequences than the cutoff and abund has data for otus 
-that have as many or more sequences as the cutoff. 
-also allow an option where a user can give a group file with the list or names file and split the group file into rare and abund. */
-
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "inputdata.h"
-#include "listvector.hpp"
-#include "sequence.hpp"
-
-/***************************************************************************************/
-
-class SplitAbundCommand : public Command {
-       
-public:
-       SplitAbundCommand(string);      
-       SplitAbundCommand();
-       ~SplitAbundCommand();
-       
-       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*, string); 
-       int writeAccnos(string); 
-       int parseGroup(string); 
-       int parseFasta(string); 
-       int readNamesFile(); //namefile
-       int createNameMap(ListVector*);
-       
-       vector<string> outputNames;
-       ListVector* list;
-       GroupMap* groupMap;
-       InputData* input;
-       
-       string outputDir, listfile, namefile, groupfile, 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;
-       
-       
-
-};
-
-/***************************************************************************************/
-
-#endif
-
-