lowlevel.c File Reference

Lowest level basic functions, that should be available to all other modules. More...

#include "lowlevel.h"

Include dependency graph for lowlevel.c:

Macros
#define	MIN_CHUNK   128

Functions
void	hungarian_solve_integer (hungarian p, int this_size)
void	hungarian_solve_double (hungarian p, int this_size)
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)
void	hungarian_reset (hungarian p)
hungarian	new_hungarian (int size, bool is_double)
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 basic functions, that should be available to all other modules.

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.