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
|
#ifndef ALIGNCOMMAND_H
#define ALIGNCOMMAND_H
/*
* aligncommand.h
* Mothur
*
* Created by Sarah Westcott on 5/15/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "searchdatabase.hpp"
#include "alignment.hpp"
#include "alignmentdb.h"
#include "sequence.hpp"
#include "gotohoverlap.hpp"
#include "needlemanoverlap.hpp"
#include "noalign.hpp"
#include "nast.hpp"
#include "alignreport.hpp"
//test
class AlignCommand : public Command {
#ifdef UNIT_TEST
friend class TestAlignSeqsIntegration;
#endif
public:
AlignCommand(string);
~AlignCommand();
vector<string> setParameters();
string getCommandName() { return "align.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
string getDescription() { return "align sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
protected:
long long createProcesses(string, string, string, string, vector<long long>&);
void appendReportFiles(string, string);
string fastafile, templateFileName, distanceFileName, search, align;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> outputNames;
bool abort, flip, calledHelp, save;
AlignmentDB* templateDB;
};
#endif
|
