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1 #ifndef GETLISTCOUNTCOMMAND_H
2 #define GETLISTCOUNTCOMMAND_H
3 /*
4  *  getlistcountcommand.h
5  *  Mothur
6  *
7  *  Created by westcott on 10/12/09.
8  *  Copyright 2009 Schloss Lab. All rights reserved.
9  *
10  */
11
12 #include "command.hpp"
13 #include "inputdata.h"
14 #include "listvector.hpp"
15
16 /**********************************************************/
17
18 class GetListCountCommand : public Command {
19         
20 public:
21         GetListCountCommand(string);
22         GetListCountCommand();  
23         ~GetListCountCommand(){}
24         
25         vector<string> setParameters();
26         string getCommandName()                 { return "get.otulist";                         }
27         string getCommandCategory()             { return "OTU-Based Approaches";        }
28         string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
29         string getDescription()         { return "lists each OTU number and the sequence contained in that OTU"; }
30
31         string getHelpString(); 
32         
33         int execute(); 
34         void help() { m->mothurOut(getHelpString()); }  
35         
36         
37 private:
38         ListVector* list;
39         InputData* input;
40         
41         bool abort, allLines;
42         set<string> labels; //holds labels to be used
43         string label, listfile, outputDir, sort;
44         ofstream out;
45         vector<string> outputNames;
46                 
47         void process(ListVector*);
48 };
49 /**********************************************************/
50
51 #endif