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A very basic obicount

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This commit is contained in:
Celine Mercier
2015-05-22 17:54:34 +02:00
parent 2073f9f307
commit 0b031da28c
7 changed files with 264 additions and 128 deletions
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47
src/obicolumn.h
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/****************************************************************************
* OBIColumn header file *
****************************************************************************/
/**
* @file obicolumn.h
* @author Celine Mercier
* @date 12 May 2015
* @brief Header file for the shared elements of all the OBIColumn structures.
*/
#ifndef OBICOLUMN_H_
#define OBICOLUMN_H_
#include <stdio.h>
/**
* @brief enum OBIDataType for the data type of the OBIColumns.
*/
typedef enum OBIDataType {
OBI_VOID = 0, /**< data type not specified */
OBI_INT32, /**< type int32_t */
OBI_INT64, /**< type int64_t */
OBI_UINT32, /**< type uint32_t */
OBI_UNIT64, /**< type uint64_t */
OBI_STRING /**< type char* */
} OBIDataType_t, *OBIDataType_p;
/**
* @brief OBIColumnHeader structure.
*/
typedef struct OBIColumnHeader {
bool endyan_byte_order; /**< endyan byte order */
int header_size_value; /**< size of the header: a multiple of PAGESIZE */
int line_count; /**< number of lines of data */
OBIDataType_t data_type; /**< type of the data */
char* creation_date; /**< date of creation of the file */
int version; /**< version of the OBIColumn */
char* comments; /**< comments */>
} OBIIntColumn_t, *OBIIntColumn_p;
#endif /* OBICOLUMN_H_ */

18
src/obicount/Makefile Normal file
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CC = gcc
CFLAGS = -c -Wall
LDFLAGS =
SOURCES = obicount.c ../obidmscolumn.c
OBJECTS = $(SOURCES:.c=.o)
EXECUTABLE = obicount
all: $(SOURCES) $(EXECUTABLE)
$(EXECUTABLE): $(OBJECTS)
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
.c.o:
$(CC) $(CFLAGS) $< -o $@
clean:
rm *o
rm $(EXECUTABLE)

87
src/obicount/obicount.c Normal file
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#include <stdio.h>
#include <stdlib.h>
#include <sys/mman.h> /* mmap() is defined in this header */
#include <stdint.h>
#include <fcntl.h>
#include <sys/stat.h>
#include "../obitypes.h"
#include "../obidmscolumn.h"
/**
* @brief Computes the size to map.
*
* * @param OBIDMSColumn_file The file to map.
* @return The size to map.
*/
int get_size_to_map(int OBIDMSColumn_file)
// compute size to map : file size minus size of the header
{
int size;
struct stat s;
fstat(OBIDMSColumn_file, &s);
size = (s.st_size) - HEADER_SIZE;
return(size);
}
/**
* @brief Computes and prints the total number of sequences by summing their counts.
*
* * @param The count file.
*/
int main(int argc, char const *argv[])
{
char* map;
int size;
int OBIDMSColumn_file;
int count;
char c;
char num_str[10] = "";
int num_int;
int i,j;
// initialize variables
OBIDMSColumn_file = open(argv[1], O_RDONLY); //read only
count = 0;
j = 0;
// compute size to map
size = get_size_to_map(OBIDMSColumn_file);
// map the data
map = obi_map_read_only(OBIDMSColumn_file, HEADER_SIZE, size);
// sum the counts
for (i=0; i<size; i++)
{
c = map[i];
if (c != SEPARATOR) // reading lines
{
num_str[j] = c;
j++;
}
else if (c == SEPARATOR) // end of a line
{
num_int = atoi(num_str); // turn number from character string to int
count = count + num_int; // add the number to the sum
j = 0;
num_str[j] = '\0';
}
}
// print the final count of sequences
fprintf(stderr, "Sequence count = %d\n", count);
// unmap
obi_unmap(size);
// close file
close(OBIDMSColumn_file);
return(0);
}

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src/obidmscolumn.c Normal file
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/****************************************************************************
* OBIDMSColumn functions *
****************************************************************************/
/**
* @file obidmscolumn.h
* @author Celine Mercier
* @date 22 May 2015
* @brief Functions for the shared elements of all the OBIColumn structures.
*/
#include <stdio.h>
#include <stdlib.h>
#include <sys/mman.h> /* mmap() is defined in this header */
/**
* @brief Reads a memory block from a file.
*
* * @param file The file that should be mapped.
* * @param size The number of bytes that should be mapped.
* * @param start The position at which the mapping should start.
* @return A pointer on the first element of the block.
*/
char* obi_map_read_only(int file, int start, int size)
{
char* map;
map = (char*) mmap(0, size, PROT_READ, MAP_PRIVATE, file, start);
if (map == MAP_FAILED)
{
fprintf(stderr, "\nmmap read-only error\n");
exit(1);
}
return(map);
}
/**
* @brief Unmaps a memory block.
*
* * @param size The size of the block that should be unmapped.
*/
void obi_unmap(int size)
{
munmap(0, size);
}

63
src/obidmscolumn.h Normal file
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/****************************************************************************
* OBIDMSColumn header file *
****************************************************************************/
/**
* @file obidmscolumn.h
* @author Celine Mercier
* @date 12 May 2015
* @brief Header file for the shared elements of all the OBIColumn structures.
*/
#ifndef OBIDMSCOLUMN_H_
#define OBIDMSCOLUMN_H_
#include <stdio.h>
#include <sys/types.h>
#include <unistd.h>
#include <stdbool.h>
#include "obitypes.h"
/**
* @brief Value separator in OBIDMSColumn files.
*/
static const char SEPARATOR = '\n';
/**
* @brief Header size in OBIDMSColumn files.
*/
static const int HEADER_SIZE = 4096;
/**
* @brief Number of bytes to map
*/
static const int BUFFER_SIZE = 4;
/**
* @brief OBIColumnHeader structure.
*/
typedef struct OBIDMSColumnHeader {
bool endyan_byte_order; /**< endyan byte order */
int header_size_value; /**< size of the header: a multiple of PAGESIZE */
bool file_status; /**< file status : 0 is Open and 1 is Closed */
pid_t PID; /**< PID of the process that created the file and is
the only one allowed to modify it if it is open */
int line_count; /**< number of lines of data */
OBIType_t data_type; /**< type of the data */
char* creation_date; /**< date of creation of the file */
int version; /**< version of the OBIColumn */
char* comments; /**< comments */
} OBIDMSColumnHeader_t, *OBIDMSColumnHeader_p;
char* obi_map_read_only(int file, int start, int size);
void obi_unmap(int size);
#endif /* OBIDMSCOLUMN_H_ */

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src/obiintcolumn.h
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/****************************************************************************
* OBIIntColumn header file *
****************************************************************************/
/**
* @file obiintcolumn.h
* @author Celine Mercier
* @date 11 May 2015
* @brief Header file for the OBIIntColumn structure.
*/
#ifndef OBIINTCOLUMN_H_
#define OBIINTCOLUMN_H_
#include <stdio.h>
#include <stdlib.h>
#include "obicolumn.h"
/**
* @brief OBIIntColumn stucture.
*/
typedef struct OBIIntcolumn {
} OBIIntColumn_t, *OBIIntColumn_p;
/**
* @brief Reads a memory block from an OBIIntColumn file.
*
* @param OBIIntColumn The OBIColumn that should be read.
* @return A pointer on the first element of the block.
*/
int* readMemoryBlock(int* OBIIntcolumn, int startingPosition, int memoryBlockSize);
/**
* @brief Writes a memory block line by line at the end of a file.
*/
void writeMemoryBlock(int* OBIIntcolumn, int memoryBlockSize, char* fileName);
/**
* @brief Returns one line of an OBIColumn.
*/
int readLine(int line);
/**
* @brief Creates a new file for a new version of the OBIColumn.
*/
void newColumn(OBIIntcolumn* column);
/**
* @brief malloc for OBIIntColumn.
*/
int* OBIIntMalloc();
/**
* @brief realloc for OBIIntColumn.
*/
int* OBIIntRealloc();
/**
* @brief free for OBIIntColumn.
*/
void OBIIntFree();
#endif /* OBIINTCOLUMN_H_ */

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src/obitypes.h Normal file
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/****************************************************************************
* OBITypes header file *
****************************************************************************/
/**
* @file obitypes.h
* @author Celine Mercier
* @date 18 May 2015
* @brief Header file for the OBITypes.
*/
#ifndef OBITYPES_H_
#define OBITYPES_H_
#include <stdio.h>
#define OBIInt_NA (INT32_MIN)
#define OBIFloat_NA (NAN)
#define OBIIdx_NA (SIZE_MAX)
/**
* @brief enum for the boolean OBIType.
*/
typedef enum {
FALSE = 0,
TRUE = 1,
OBIBool_NA = 2
} OBIBool_t, *OBIBool_p; /**< a boolean true/false value */
/**
* @brief enum OBITypes for the data type of the OBIColumns.
*/
typedef enum OBIType {
OBI_VOID = 0, /**< data type not specified */
OBIInt_t, /**< a signed integer value (C type : int32_t) */
OBIFloat_t, /**< a floating value (C type : double) */
OBIChar_t, /**< a character (C type : char) */
OBIIdx_t /**< an index in a data structure (C type : size_t) */
} OBIType_t, *OBIType_p;
typedef int32_t obiint_t;
typedef double obifloat_t;
typedef char obichar_t;
typedef size_t obiidx_t;
#endif /* OBITYPES_H_ */