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BgzfFileTypeRecovery.h
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __BGZFFILETYPERECOVERY_H__
#define __BGZFFILETYPERECOVERY_H__
#ifdef __ZLIB_AVAILABLE__
#include "FileType.h"
#include <stdio.h> // for NULL
class BGZFReader;
class BgzfFileTypeRecovery : public FileType
{
public:
BgzfFileTypeRecovery()
{
bgzfReader = NULL;
}
~BgzfFileTypeRecovery()
{
close();
}
BgzfFileTypeRecovery(const char * filename, const char * mode);
// these methods should not be used. They are
// misleading because the rhs could be anything,
// (specifically not a BgzfFileTypeRecover object).
bool operator == (void * rhs);
bool operator != (void * rhs);
// Close the file.
int close();
// Reset to the beginning of the file.
inline void rewind()
{
// Just call rewind to move to the beginning of the file.
seek(0LL, SEEK_SET);
}
// Check to see if we have reached the EOF.
int eof();
// Check to see if the file is open.
bool isOpen()
{
return (bgzfReader != NULL);
}
// Write to the file
unsigned int write(const void * buffer, unsigned int size);
// Read into a buffer from the file. Since the buffer is passed in and
// this would bypass the fileBuffer used by this class, this method must
// be protected.
int read(void * buffer, unsigned int size);
// Get current position in the file.
// -1 return value indicates an error.
int64_t tell();
// Seek to the specified offset from the origin.
// origin can be any of the following:
// Note: not all are valid for all filetypes.
// SEEK_SET - Beginning of file
// SEEK_CUR - Current position of the file pointer
// SEEK_END - End of file
// Returns true on successful seek and false on a failed seek.
bool seek(int64_t offset, int origin);
bool attemptRecoverySync(bool (*checkSignature)(void *data) , int length);
protected:
// Read via BGZFReader
BGZFReader* bgzfReader;
};
#endif
#endif
FileType
Definition FileType.h:24