base.h File Reference

#include "defines.h"

Include dependency graph for base.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Macros
#define	BASETYPES   4
#define	BASECHARS   (BASETYPES+1)
#define	BASEQUAD   (BASETYPES*BASETYPES)
#define	MAXBASECHAR   ((int)'t')
#define	PROB_NOT_DEF   (-1.0)
#define	isDeleted(b)   (charIsDelete[(int)(b)])
#define	isHelical(b)   (charIsHelical[(int)(b)])
#define	isPairing(b1, b2)   (basesArePairing[(int)(b1)][(int)(b2)])
#define	char2BaseType(c)   ((enum BaseType)baseCharType[(int)c])

Enumerations
enum	BaseType {   BASE_A, BASE_C, BASE_G, BASE_T,   BASE_DEL }

Functions
void	initBaseLookups ()

Variables
char	helixBaseChar [BASECHARS]
char	loopBaseChar [BASECHARS]
int	basesArePairing [BASECHARS][BASECHARS]
int	baseCharType []
int	charIsDelete []
int	charIsHelical []

Macro Definition Documentation

#define BASETYPES   4

Definition at line 17 of file base.h.

Referenced by calcMutationMatrix(), createOriginRNS(), dumpRNS(), and mutateRNS().

#define BASECHARS   (BASETYPES+1)

Definition at line 18 of file base.h.

Referenced by initBaseLookups().

#define BASEQUAD   (BASETYPES*BASETYPES)

Definition at line 19 of file base.h.

Referenced by createOriginRNS().

#define MAXBASECHAR   ((int)'t')

Definition at line 21 of file base.h.

Referenced by initBaseLookups().

#define PROB_NOT_DEF   (-1.0)

Definition at line 22 of file base.h.

#define isDeleted

(

b

)

(charIsDelete[(int)(b)])

Definition at line 24 of file base.h.

Referenced by mutateRNS().

#define isHelical

(

b

)

(charIsHelical[(int)(b)])

Definition at line 25 of file base.h.

Referenced by dumpRNS(), and mutateRNS().

#define isPairing	(		b1,
			b2
	)		(basesArePairing[(int)(b1)][(int)(b2)])

Definition at line 26 of file base.h.

Referenced by createOriginRNS(), and mutateRNS().

#define char2BaseType

(

c

)

((enum BaseType)baseCharType[(int)c])

Definition at line 35 of file base.h.

Referenced by dumpRNS(), and mutateRNS().

Enumeration Type Documentation

enum BaseType

Enumerator
BASE_A
BASE_C
BASE_G
BASE_T
BASE_DEL

Definition at line 8 of file base.h.

Function Documentation

void initBaseLookups

(

)

Definition at line 20 of file base.c.

References assert, BASECHARS, loopBaseChar, and MAXBASECHAR.

Referenced by ARB_main().

Variable Documentation

char helixBaseChar[BASECHARS]

Definition at line 4 of file base.c.

Referenced by createOriginRNS(), and mutateRNS().

char loopBaseChar[BASECHARS]

Definition at line 5 of file base.c.

Referenced by createOriginRNS(), initBaseLookups(), and mutateRNS().

int basesArePairing[BASECHARS][BASECHARS]

Definition at line 7 of file base.c.

int baseCharType[]

Definition at line 16 of file base.c.

int charIsDelete[]

Definition at line 16 of file base.c.

int charIsHelical[]

Definition at line 16 of file base.c.