io.c File Reference

Input, output, error and memory allocation functions More...

#include <mxml.h>
#include "shiba.h"

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Functions
void	readXML ()
	Open file and parse XML.
void	printIndata ()
	Output matrices for checking by user.
void	error (char *error_msg)
	Basic error output and exit function.
double *	mem1d_d (int dimx)
	Dimensions an initialized 1-D array of doubles.
int *	mem1d_i (int dimx)
	Dimensions an initialized 1-D array of int.
int **	mem2d1_i (int dimx)
	Dimensions a initialized 1-D array of int pointers, ready to be allocated using mem1d_i() .
void	free2d1_i (int **ptr, int dimx)
	Frees the ragged array allocated by mem2d1_i().
char **	mem2d1_c (int dimx)
	Dimensions a initialized 1-D array of character pointers, ready to be allocated using asprintf.
void	free2d1_c (char **ptr, int dimx)
	Frees the ragged array allocated by mem2d1_c().
int **	mem2d_i (int dimx, int dimy)
	Dimensions an initialized 2-D array of int.
void	free2d_i (int **ptr, int dimx)
double **	mem2d_d (int dimx, int dimy)
	Dimensions an initialized 2-D array of doubles.
void	free2d_d (double **ptr, int dimx)
double ***	mem3d_d (int dimx, int dimy, int dimz)
	Dimensions an initialized 3-D array of doubles.
void	free3d_d (double ***ptr, int dimx, int dimy)
int ***	mem3d_i (int dimx, int dimy, int dimz)
	Dimensions an initialized 3-D array of int.
void	free3d_i (int ***ptr, int dimx, int dimy)
void	help ()
	Default help output.

Detailed Description

Input, output, error and memory allocation functions

Definition in file io.c.

Function Documentation

void error

(

char *

error_msg

)

Basic error output and exit function.

Note that no freeing is done, possibly leading to memory leaks.

Parameters

error_msg

the error message

Definition at line 612 of file io.c.

Referenced by main(), mem1d_d(), mem1d_i(), mem2d1_c(), mem2d1_i(), mem2d_d(), mem2d_i(), mem3d_d(), mem3d_i(), parseNewick(), phyloToLineage(), readArgs(), and readXML().

void free2d1_c	(	char **	ptr,
		int	dimx
	)

Frees the ragged array allocated by mem2d1_c().

Parameters

dimx	The dimensions of the vector

Definition at line 700 of file io.c.

Referenced by main(), and readXML().

void free2d1_i	(	int **	ptr,
		int	dimx
	)

Frees the ragged array allocated by mem2d1_i().

Parameters

dimx	The dimensions of the vector

Definition at line 670 of file io.c.

Referenced by main().

double* mem1d_d

(

int

dimx

)

Dimensions an initialized 1-D array of doubles.

To free, just use free().

Parameters

dimx	The dimensions of the vector

Returns

A pointer to an array of doubles

Definition at line 628 of file io.c.

References error().

Referenced by parseNewick(), and readXML().

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int* mem1d_i

(

int

dimx

)

Dimensions an initialized 1-D array of int.

To free, just use free().

Parameters

dimx	The dimensions of the vector

Returns

A pointer to an array of ints

Definition at line 643 of file io.c.

References error().

Referenced by parseNewick(), phyloToLineage(), and readXML().

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char** mem2d1_c

(

int

dimx

)

Dimensions a initialized 1-D array of character pointers, ready to be allocated using asprintf.

The result will be a `ragged' matrix. To free, use free2d1_c() .

Parameters

dimx	The dimensions of the vector

Returns

A pointer to an array of character pointers

Definition at line 685 of file io.c.

References error().

Referenced by parseNewick(), and readXML().

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int** mem2d1_i

(

int

dimx

)

Dimensions a initialized 1-D array of int pointers, ready to be allocated using mem1d_i() .

The result will be a `ragged' matrix. To free, use free2d1_i() .

Parameters

dimx	The dimensions of the vector

Returns

A pointer to an array of int pointers

Definition at line 658 of file io.c.

References error().

Referenced by phyloToLineage().

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double** mem2d_d	(	int	dimx,
		int	dimy
	)

Dimensions an initialized 2-D array of doubles.

Free with free2d_d()

Definition at line 736 of file io.c.

References error().

Referenced by readXML().

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int** mem2d_i	(	int	dimx,
		int	dimy
	)

Dimensions an initialized 2-D array of int.

Free with free2d_i()

Definition at line 712 of file io.c.

References error().

Referenced by phyloToLineage().

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double*** mem3d_d	(	int	dimx,
		int	dimy,
		int	dimz
	)

Dimensions an initialized 3-D array of doubles.

Free with free3d_d()

Definition at line 760 of file io.c.

References error().

Referenced by readXML().

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int*** mem3d_i	(	int	dimx,
		int	dimy,
		int	dimz
	)

Dimensions an initialized 3-D array of int.

Free with free3d_i()

Definition at line 793 of file io.c.

References error().

Referenced by phyloToLineage(), and readXML().

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void readXML

(

)

Open file and parse XML.

Derived from mini-xml website examples.

Todo:

Remove the constraint of having to have the ages included in the XML file in decreasing order. Will need a sorting stage

Definition at line 13 of file io.c.

References Area, Cfg, DataFile, Dist, error(), Extant, free2d1_c(), mem1d_d(), mem1d_i(), mem2d1_c(), mem2d_d(), mem3d_d(), mem3d_i(), Phylo, Phylos, RealTime, RUN_BATCH, Sasprintf, SpaceName, Spaces, config::startSpace, Taxa, Taxon, and Times.

Referenced by main().

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