libStatGen Software 1
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BgzfFileTypeRecovery.h
1/*
2 * Copyright (C) 2010 Regents of the University of Michigan
3 *
4 * This program is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * This program is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */
17
18#ifndef __BGZFFILETYPERECOVERY_H__
19#define __BGZFFILETYPERECOVERY_H__
20
21#ifdef __ZLIB_AVAILABLE__
22
23#include "FileType.h"
24#include <stdio.h> // for NULL
25
26class BGZFReader;
27
28class BgzfFileTypeRecovery : public FileType
29{
30public:
31 BgzfFileTypeRecovery()
32 {
33 bgzfReader = NULL;
34 }
35
36 ~BgzfFileTypeRecovery()
37 {
38 close();
39 }
40
41 BgzfFileTypeRecovery(const char * filename, const char * mode);
42
43 // these methods should not be used. They are
44 // misleading because the rhs could be anything,
45 // (specifically not a BgzfFileTypeRecover object).
46 bool operator == (void * rhs);
47
48 bool operator != (void * rhs);
49
50 // Close the file.
51 int close();
52
53 // Reset to the beginning of the file.
54 inline void rewind()
55 {
56 // Just call rewind to move to the beginning of the file.
57 seek(0LL, SEEK_SET);
58 }
59
60 // Check to see if we have reached the EOF.
61 int eof();
62
63 // Check to see if the file is open.
64 bool isOpen()
65 {
66 return (bgzfReader != NULL);
67 }
68
69 // Write to the file
70 unsigned int write(const void * buffer, unsigned int size);
71
72 // Read into a buffer from the file. Since the buffer is passed in and
73 // this would bypass the fileBuffer used by this class, this method must
74 // be protected.
75 int read(void * buffer, unsigned int size);
76
77 // Get current position in the file.
78 // -1 return value indicates an error.
79 int64_t tell();
80
81 // Seek to the specified offset from the origin.
82 // origin can be any of the following:
83 // Note: not all are valid for all filetypes.
84 // SEEK_SET - Beginning of file
85 // SEEK_CUR - Current position of the file pointer
86 // SEEK_END - End of file
87 // Returns true on successful seek and false on a failed seek.
88 bool seek(int64_t offset, int origin);
89
90 bool attemptRecoverySync(bool (*checkSignature)(void *data) , int length);
91
92protected:
93 // Read via BGZFReader
94 BGZFReader* bgzfReader;
95
96};
97
98#endif
99#endif