https://github.com/PublicHealthDynamicsLab/FRED
Revision a45e04ad99c865724a3c2b1a2d3fd979b3c6be88 authored by John Grefenstette on 07 January 2016, 16:32:02 UTC, committed by John Grefenstette on 07 January 2016, 16:32:02 UTC
1 parent 9bc2dce
Tip revision: a45e04ad99c865724a3c2b1a2d3fd979b3c6be88 authored by John Grefenstette on 07 January 2016, 16:32:02 UTC
working markov epidemic model
working markov epidemic model
Tip revision: a45e04a
Compression.h
/*
This file is part of the FRED system.
Copyright (c) 2010-2015, University of Pittsburgh, John Grefenstette,
Shawn Brown, Roni Rosenfield, Alona Fyshe, David Galloway, Nathan
Stone, Jay DePasse, Anuroop Sriram, and Donald Burke.
Licensed under the BSD 3-Clause license. See the file "LICENSE" for
more information.
*/
//
//
// File: Compression.h
//
// This file added to FRED by J. DePasse (jvd10@pitt.edu) in July 2012
//
//
#ifndef _FRED_COMPRESSION_H
#define _FRED_COMPRESSION_H
#include <cstring>
#include <string>
#include <iostream>
#include <sstream>
#include <fstream>
#include <stdio.h>
#include <stdlib.h>
#include <sys/mman.h>
#include <sys/types.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <errno.h>
#include <inttypes.h>
#include <vector>
#include <snappy.h>
#include "Global.h"
#define FSZ_WARNING(format, ...){ \
printf( "WARNING: <%s, LINE:%d> " format, __FILE__, __LINE__, ## __VA_ARGS__ ); \
}
#define FSZ_ABORT(format, ...){ \
printf( "WARNING: <%s, LINE:%d> " format, __FILE__, __LINE__, ## __VA_ARGS__ ); \
exit( 1 ); \
}
#define FSZ_STATUS(verbosity, format, ...){ \
printf( "STATUS: <%s, LINE:%d> " format, __FILE__, __LINE__, ## __VA_ARGS__ ); \
}
class SnappyFileCompression {
// try to include as close to default_block_size bytes (uncompressed)
// in each compressed block
static const size_t default_block_size = 1ul << 25;
static const char* FSZ_MAGIC() {
return "FSZ 20100404 v01";
}
static const int FSZ_MAGIC_LEN() {
return std::strlen( FSZ_MAGIC() );
}
char * infile_name;
char * begin;
char * end;
uint64_t total_uncompressed_bytes;
uint64_t total_compressed_bytes;
uint64_t total_header_bytes;
fred::Mutex mutex;
public:
SnappyFileCompression( char * _infile_name ) {
infile_name = new char[ std::strlen( _infile_name ) ];
std::strcpy( infile_name, _infile_name );
}
/*
* Compresses file supplied to constructor to stdout
*/
void compress_file_to_stdout();
/*
* Uncompresses file supplied to constructor to stdout
*/
void uncompress_file_to_stdout();
void init_compressed_block_reader();
bool check_magic_bytes();
bool load_next_block_stream( std::stringstream & stream );
};
#endif
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