1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#ifndef DEGAPSEQSCOMMAND_H
#define DEGAPSEQSCOMMAND_H
/*
* degapseqscommand.h
* Mothur
*
* Created by westcott on 6/21/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
#include "writer.h"
class DegapSeqsCommand : public Command {
public:
DegapSeqsCommand(string);
~DegapSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "degap.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
string getDescription() { return "removes gap characters from sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int processors;
bool abort;
string fastafile;
vector<string> outputNames;
long long createProcesses(string, string);
};
#endif
|
