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
|
/*==============================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*/
#include <string>
#include <vector>
#include <iostream>
/*
* Fasta files:
* Fasta file consists of one of more sequences. A sequence in a fasta file
* consists of a seqid line followed by lines containing the bases of the
* sequence. A seqid line starts with '>' and the next word (whitespace
* delimited) is the seqid.
*/
class FastaFile {
FastaFile() : data(NULL) {}
FastaFile(std::istream &is);
void *data;
public:
struct Sequence {
std::string SEQID;
std::string SEQID_LINE;
char const *data;
unsigned length;
bool hadErrors; // erroneous base values are replaced with N
};
std::vector<Sequence const> sequences;
~FastaFile() {
free(data);
data = nullptr;
}
static FastaFile load(std::istream &is) {
return FastaFile(is);
}
static FastaFile load(std::string const filename);
};
|
