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1 #ifndef PARSELISTCOMMAND_H
2 #define PARSELISTCOMMAND_H
3 /*
4  *  parselistcommand.h
5  *  Mothur
6  *
7  *  Created by westcott on 2/24/10.
8  *  Copyright 2010 Schloss Lab. All rights reserved.
9  *
10  */
11
12 #include "command.hpp"
13 #include "groupmap.h"
14 #include "inputdata.h"
15 #include "listvector.hpp"
16
17 /***************************************************************************************/
18
19 class ParseListCommand : public Command {
20         
21 public:
22         ParseListCommand(string);
23         ParseListCommand();     
24         ~ParseListCommand() {}
25         
26         vector<string> setParameters();
27         string getCommandName()                 { return "parse.list";                          }
28         string getCommandCategory()             { return "OTU-Based Approaches";        }
29         string getHelpString(); 
30         string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
31         string getDescription()         { return "parses a list file by group"; }
32         
33         int execute(); 
34         void help() { m->mothurOut(getHelpString()); }  
35         
36 private:
37         int parse(ListVector*);
38                 
39         ListVector* list;
40         GroupMap* groupMap;
41         InputData* input;
42         
43         ofstream out;
44         string outputDir, listfile, groupfile, label;
45         set<string> labels;
46         bool abort, allLines;
47         vector<string> outputNames;
48         
49         map<string, ofstream*> filehandles;
50         map<string, ofstream*>::iterator it3;
51
52 };
53
54 /***************************************************************************************/
55
56 #endif
57