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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
#ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
#define SECONDARYSTRUCTURECHECKERCOMMAND_H
/*
* aligncheckcommand.h
* Mothur
*
* Created by westcott on 9/18/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
/**************************************************************************************************/
struct statData {
int pound;
int tilde;
int dash;
int plus;
int equal;
int loop;
int total;
statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};
};
/**************************************************************************************************/
class AlignCheckCommand : public Command {
public:
AlignCheckCommand(string);
~AlignCheckCommand(){}
vector<string> setParameters();
string getCommandName() { return "align.check"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<int> structMap;
string mapfile, fastafile, namefile, countfile;
bool abort;
int seqLength, haderror;
vector<string> outputNames;
map<string, int> nameMap;
void readMap();
statData getStats(string sequence);
};
/**************************************************************************************************/
#endif
|
