gclib/tophat_cpp/FastaTools.h

//
//  FastaTools.h
//  TopHat
//
//  Created by Harold Pimentel on 10/27/11.
//

#ifndef TopHat_FastaTools_h
#define TopHat_FastaTools_h

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <cassert>
#include <cstdlib>
#include <cstring>
#include <fstream>
// #include <ifstream>
#include <iostream>
#include <map>
#include <string>
#include <utility>
#include <vector>

#include "common.h"

#define LINE_BUF_SIZE 1024
#define ID_BUF_SIZE 1024
#define DESC_BUF_SIZE 1024

struct FastaRecord {
    // The identifier after ">"
    std::string id_;
    
    // The description after the identifier
    std::string desc_;

    // The sequence
    std::string seq_;

};

class FastaReader {
public:
    FastaReader();    
    FastaReader(std::string fname);
    ~FastaReader();
    void init(std::string fname);
    bool good() const;
    void next(FastaRecord* rec);    
private:
    std::string fname_;
    std::string prev_line_;
    
    std::ifstream ifstream_;
    
    // We assume the description is no longer than 2048 characters long
    // TODO: Think of a better way of doing this in the future.
    char line_buf_[LINE_BUF_SIZE];    
    
    char id_buf_[ID_BUF_SIZE];
    
    char desc_buf_[DESC_BUF_SIZE];
    
    // variable to check if stream is primed (has already been initialized)
    bool isPrimed_;
};

class FastaWriter {
public:
    FastaWriter();
    FastaWriter(std::string fname);
    ~FastaWriter();
    void init(std::string fname);
    void write(FastaRecord* rec, size_t column_size = 60);    
private:
    std::string fname_;
    
    std::ofstream ofstream_;
    
    bool isPrimed_;
};
#endif
Revision:	165
Committed:	Fri Feb 10 01:04:05 2012 UTC (12 years, 6 months ago) by gpertea
File size:	1632 byte(s)
Log Message:	sync back with Daehwan. Test bam_merge for memory leaks!
Line	File contents
1	//
2	// FastaTools.h
3	// TopHat
4	//
5	// Created by Harold Pimentel on 10/27/11.
6	//
7
8	#ifndef TopHat_FastaTools_h
9	#define TopHat_FastaTools_h
10
11	#ifdef HAVE_CONFIG_H
12	#include <config.h>
13	#endif
14
15	#include <cassert>
16	#include <cstdlib>
17	#include <cstring>
18	#include <fstream>
19	// #include <ifstream>
20	#include <iostream>
21	#include <map>
22	#include <string>
23	#include <utility>
24	#include <vector>
25
26	#include "common.h"
27
28	#define LINE_BUF_SIZE 1024
29	#define ID_BUF_SIZE 1024
30	#define DESC_BUF_SIZE 1024
31
32	struct FastaRecord {
33	// The identifier after ">"
34	std::string id_;
35
36	// The description after the identifier
37	std::string desc_;
38
39	// The sequence
40	std::string seq_;
41
42	};
43
44	class FastaReader {
45	public:
46	FastaReader();
47	FastaReader(std::string fname);
48	~FastaReader();
49	void init(std::string fname);
50	bool good() const;
51	void next(FastaRecord* rec);
52	private:
53	std::string fname_;
54	std::string prev_line_;
55
56	std::ifstream ifstream_;
57
58	// We assume the description is no longer than 2048 characters long
59	// TODO: Think of a better way of doing this in the future.
60	char line_buf_[LINE_BUF_SIZE];
61
62	char id_buf_[ID_BUF_SIZE];
63
64	char desc_buf_[DESC_BUF_SIZE];
65
66	// variable to check if stream is primed (has already been initialized)
67	bool isPrimed_;
68	};
69
70	class FastaWriter {
71	public:
72	FastaWriter();
73	FastaWriter(std::string fname);
74	~FastaWriter();
75	void init(std::string fname);
76	void write(FastaRecord* rec, size_t column_size = 60);
77	private:
78	std::string fname_;
79
80	std::ofstream ofstream_;
81
82	bool isPrimed_;
83	};
84	#endif