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
|
/* This file is part of TransTerm v2.0 BETA and is covered by the GNU GPL
* License version 2.0. See file LICENSE.txt for more details. */
#ifndef GENE_READER_H
#define GENE_READER_H
#include <iostream>
#include <fstream>
#include <string>
#include "seq.h"
using namespace std;
// abstract base class of all classes that can read annotation files
class GeneReader
{
public:
virtual bool read_genes(Genome &) = 0;
virtual ~GeneReader() {};
virtual bool good() = 0;
};
// read a .coords file from TIGR CMR
class CoordsReader : public GeneReader
{
public:
CoordsReader(const string &);
virtual ~CoordsReader() {}
bool read_genes(Genome &);
bool good() { return _in.good(); }
private:
ifstream _in;
};
// read a .ptt file from GenBank
class PTTReader : public GeneReader
{
public:
PTTReader(const string &);
virtual ~PTTReader() {}
bool read_genes(Genome &);
bool good() { return _in.good(); }
private:
ifstream _in;
string _id;
};
// return the correct reader class given a filename
GeneReader * gene_reader_factory(const string &);
#endif
|
