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[mothur.git] / chimerabellerophoncommand.h
1 #ifndef CHIMERABELLEROPHONCOMMAND_H
2 #define CHIMERABELLEROPHONCOMMAND_H
3
4 /*
5  *  chimerabellerophoncommand.h
6  *  Mothur
7  *
8  *  Created by westcott on 4/1/10.
9  *  Copyright 2010 Schloss Lab. All rights reserved.
10  *
11  */
12
13 #include "mothur.h"
14 #include "command.hpp"
15 #include "chimera.h"
16
17
18 /***********************************************************/
19
20 class ChimeraBellerophonCommand : public Command {
21 public:
22         ChimeraBellerophonCommand(string);
23         ChimeraBellerophonCommand();
24         ~ChimeraBellerophonCommand(){}
25         
26         vector<string> setParameters();
27         string getCommandName()                 { return "chimera.bellerophon"; }
28         string getCommandCategory()             { return "Sequence Processing"; }
29         
30         string getHelpString(); 
31     string getOutputPattern(string);    
32         string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
33         string getDescription()         { return "detect chimeric sequences"; }
34         
35         int execute(); 
36         void help() { m->mothurOut(getHelpString()); }  
37         
38                 
39 private:
40
41         bool abort, filter, correction;
42         string fastafile, outputDir;
43         int processors, window, increment, numSeqs;
44         Chimera* chimera;
45         vector<string> outputNames;
46         vector<string> fastaFileNames;
47 };
48
49 /***********************************************************/
50
51 #endif
52
53