lowlevel.h File Reference

Lowest level header file. Header file for lowlevel.c. More...

#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <stdint.h>
#include <ctype.h>
#include <math.h>
#include <float.h>
#include <time.h>
#include <unistd.h>
#include <sys/time.h>
#include <sys/times.h>
#include <sys/types.h>
#include <assert.h>
#include <libgen.h>

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Data Structures
struct	hungarian_struct

Macros
#define	EXP_1   2.71828182845904523536028747135266 /* Euler's number */
#define	true   1U
#define	false   0U
#define	attribute_FALLTHROUGH   ((void)0);
#define	MIN(x, y)   (((x)<(y)) ? (x) : (y))
#define	MAX(x, y)   (((x)>(y)) ? (x) : (y))
#define	MOD(a)   (((a)>0) ? (a) :(-a))

Typedefs
typedef unsigned char	bool
	Mnemonic for boolean (char is smaller than int)
typedef struct hungarian_struct *	hungarian

Functions
void *	biomcmc_malloc (size_t size)
	Memory-safe malloc() function. More...
void *	biomcmc_realloc (void *ptr, size_t size)
	Memory-safe realloc() function. More...
FILE *	biomcmc_fopen (const char *path, const char *mode)
	Memory-safe fopen() function. More...
void	biomcmc_error (const char *template,...)
	Prints error message and quits program. More...
int	compare_int_increasing (const void *a, const void *b)
	Comparison between integers, doubles, etc. used by qsort()
int	compare_int_decreasing (const void *a, const void *b)
int	compare_uint64_increasing (const void *a, const void *b)
int	compare_uint64_decreasing (const void *a, const void *b)
int	compare_double_increasing (const void *a, const void *b)
int	compare_double_decreasing (const void *a, const void *b)
int	biomcmc_getline (char **lineptr, size_t *n, FILE *stream)
	read file line-by-line (like homonymous function from GNU C library) More...
uint32_t	biomcmc_levenshtein_distance (const char *s1, uint32_t n1, const char *s2, uint32_t n2, uint32_t cost_sub, uint32_t cost_indel, bool skip_borders)
	edit distance between two sequences (slow), with option to allow one of sequences to terminate soon (o.w. global cost from end to end)
hungarian	new_hungarian (int size, bool is_double)
void	hungarian_reset (hungarian p)
void	hungarian_update_cost (hungarian p, int row, int col, void *cost)
void	del_hungarian (hungarian p)
void	hungarian_solve (hungarian p, int this_size)

Detailed Description

Lowest level header file. Header file for lowlevel.c.

Macro Definition Documentation

true

#define true   1U

Boolean TRUE

false

#define false   0U

Boolean FALSE

Function Documentation

biomcmc_malloc()

void* biomcmc_malloc

(

size_t

size

)

Memory-safe malloc() function.

Allocates size bytes and returns a pointer to the allocated memory. An error message is thrown in case of failure.

Parameters

[in]

size

allocated size, in bytes

Returns

pointer to newly allocated memory

biomcmc_realloc()

void* biomcmc_realloc	(	void *	ptr,
		size_t	size
	)

Memory-safe realloc() function.

Changes the size of the memory block pointed to by ptr to size bytes. An error message is thrown in case of failure.

Parameters

[in]	size	allocated size, in bytes
[in,out]	ptr	pointer to previously allocated memory

Returns

pointer to newly allocated memory

biomcmc_fopen()

FILE* biomcmc_fopen	(	const char *	path,
		const char *	mode
	)

Memory-safe fopen() function.

Opens the file whose name is the string pointed to by path and associates a stream with it. An error message is thrown in case of failure.

Parameters

[in]	path	file name
[in]	mode	opening mode ("r" for reading, "w" for writing, etc)

Returns

pointer to file stream

biomcmc_error()

void biomcmc_error	(	const char *	template,
			...
	)

Prints error message and quits program.

similar to fprintf (stderr, ...), but exits after printing the message

Parameters

[in]

template

va_list following same format as printf()

Returns

exits program

biomcmc_getline()

int biomcmc_getline	(	char **	lineptr,
		size_t *	n,
		FILE *	stream
	)

read file line-by-line (like homonymous function from GNU C library)

This implementation is originally from the CvsGui project (http://www.wincvs.org/). The explanation from the original file adapted to our system follows:

Read up to (and including) a newline ("\n") from STREAM into *LINEPTR and null-terminate it. *LINEPTR is a pointer 
returned from malloc (or NULL), pointing to *N characters of space.  It is realloc'd as necessary.  Return the 
number of characters read (not including the null terminator), or -1 on error or EOF.