1 #ifndef DECONVOLUTECOMMAND_H
2 #define DECONVOLUTECOMMAND_H
3 /*
4  *  deconvolute.h
5  *  Mothur
6  *
7  *  Created by Sarah Westcott on 1/21/09.
8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
9  *
10  */
11 
12 #include "command.hpp"
13 #include "fastamap.h"
14 #include "counttable.h"
15 
16 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
17 	containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */
18 
19 
20 class DeconvoluteCommand : public Command {
21 
22 public:
23 	DeconvoluteCommand(string);
~DeconvoluteCommand()24 	~DeconvoluteCommand() {}
25 
26 	vector<string> setParameters();
getCommandName()27 	string getCommandName()			{ return "unique.seqs";		}
getCommandCategory()28 	string getCommandCategory()		{ return "Sequence Processing";		}
29 
30 	string getHelpString();
31     string getOutputPattern(string);
getCitation()32 	string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
getDescription()33 	string getDescription()		{ return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
34 
35 
36 	int execute();
help()37 	void help() { m->mothurOut(getHelpString()); }
38 
39 
40 private:
41 	string fastafile, namefile,  countfile, format;
42 	vector<string> outputNames;
43 
44 	bool abort;
45 };
46 
47 #endif
48