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[mothur.git] / deuniqueseqscommand.h
1 #ifndef DEUNIQUESEQSCOMMAND_H
2 #define DEUNIQUESEQSCOMMAND_H
3 /*
4  *  deuniqueseqscommand.h
5  *  Mothur
6  *
7  *  Created by westcott on 10/19/10.
8  *  Copyright 2010 Schloss Lab. All rights reserved.
9  *
10  */
11
12 #include "command.hpp"
13
14 /* This command is the reverse of unique.seqs */ 
15
16 class DeUniqueSeqsCommand : public Command {
17
18 public:
19         DeUniqueSeqsCommand(string);
20         DeUniqueSeqsCommand();
21         ~DeUniqueSeqsCommand() {}
22         
23         vector<string> setParameters();
24         string getCommandName()                 { return "deunique.seqs";               }
25         string getCommandCategory()             { return "Sequence Processing";         }
26         string getHelpString(); 
27         string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
28         string getDescription()         { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
29
30         
31         int execute(); 
32         void help() { m->mothurOut(getHelpString()); }  
33         
34         
35 private:
36
37         string fastaFile, nameFile, outputDir;
38         vector<string> outputNames;
39         bool abort;
40         
41         map<string, string> nameMap;
42         
43         int readNamesFile();
44         
45 };
46
47 #endif
48