src/clustal/symmatrix.c File Reference

#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <assert.h>
#include "symmatrix.h"

Include dependency graph for symmatrix.c:

Defines
#define	MAX_BUF_SIZE   65536
Functions
int	NewSymMatrix (symmatrix_t **symmat, int nrows, int ncols)
	Allocates symmat and its members and initialises them. Data will be calloced, i.e. initialised with zeros.
void	SymMatrixSetValue (symmatrix_t *symmat, const int i, const int j, const double value)
	Sets symmat data of given index to given value.
double	SymMatrixGetValue (symmatrix_t *symmat, const int i, const int j)
	Returns element of symmat corresponding to given indices.
void	SymMatrixGetValueP (double **val, symmatrix_t *symmat, const int i, const int j)
	Returns a pointer to an element of symmat corresponding to given indices.
void	FreeSymMatrix (symmatrix_t **symmat)
	Frees memory allocated by data members of symmat and symmat itself.
void	SymMatrixPrint (symmatrix_t *symmat, char **labels, const char *path)
	Print out a symmat in phylip style. Distances are printed on one line per sequence/object. Since we also support matrices with rows<cols, the first line can also be nrows by ncolumns instead of just nrows.
int	SymMatrixRead (char *pcFileIn, symmatrix_t **prSymMat_p)
	Read a distance matrix in phylip format.

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Define Documentation

#define MAX_BUF_SIZE   65536

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Function Documentation

void FreeSymMatrix

(

symmatrix_t **

symmat

)

Frees memory allocated by data members of symmat and symmat itself.

Parameters:

[in]

symmat

symmatrix_t to be freed

Note:

Use in conjunction with NewSymMatrix()

See also:

NewSymMatrix()

int NewSymMatrix	(	symmatrix_t **	symmat,
		int	nrows,
		int	ncols
	)

Allocates symmat and its members and initialises them. Data will be calloced, i.e. initialised with zeros.

Parameters:

[out]	symmat	newly allocated and initialised symmatrix instance
[in]	nrows	number of rows
[in]	ncols	number of columns

Returns:

: non-zero on error

See also:

FreeSymMatrix()

Note:

: symmat data will be of fake shape nrows x ncols

double SymMatrixGetValue	(	symmatrix_t *	symmat,
		const int	i,
		const int	j
	)

Returns element of symmat corresponding to given indices.

Parameters:

[in]	symmat	symmatrix_t of question
[in]	i	index i
[in]	j	index j

Returns:

requested value

See also:

SymMatrixSetValue()

Note:

This is a convenience function that checks index order.

void SymMatrixGetValueP	(	double **	val,
		symmatrix_t *	symmat,
		const int	i,
		const int	j
	)

Returns a pointer to an element of symmat corresponding to given indices.

Parameters:

[out]	val	Value to be set
[in]	symmat	symmatrix_t of question
[in]	i	index i
[in]	j	index j

Returns:

pointer to value

See also:

SymMatrixGetValue()

Note:

This is a convenience function that checks index order.

void SymMatrixPrint	(	symmatrix_t *	symmat,
		char **	labels,
		const char *	path
	)

Print out a symmat in phylip style. Distances are printed on one line per sequence/object. Since we also support matrices with rows<cols, the first line can also be nrows by ncolumns instead of just nrows.

Parameters:

[in]	symmat	the symmatrix_t to print
[in]	labels	sequence/objects labels/names. must be at least of length symmat nrows
[in]	path	filename or NULL. If NULL stdout will be used.

int SymMatrixRead	(	char *	pcFileIn,
		symmatrix_t **	prSymMat_p
	)

Read a distance matrix in phylip format.

Parameters:

[in]	pcFileIn	distance matrix filename
[out]	prSymMat_p	the symmatrix_t. will be allocated here.

Returns:

: non-zero on error

Note:

: FIXME untested code

void SymMatrixSetValue	(	symmatrix_t *	symmat,
		const int	i,
		const int	j,
		const double	value
	)

Sets symmat data of given index to given value.

Parameters:

[in]	symmat	symmatrix_t whose data is to be set
[in]	i	first index
[in]	j	second index
[in]	value	value used to set data point

See also:

SymMatrixGetValue()

Note:

This is a convenience function that checks index order.