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base.h File Reference

#include "atom.h"
#include "object.h"
#include "xmlcpg.h"

Go to the source code of this file.

Typedefs

typedef rnamlBASE rnamlBase
 Rnaml structure containing the base informations.


Functions

rnamlBasernamlnewBase ()
 Creates a new rnamlBase structure.

rnamlBasernamlcloneBase (const rnamlBase *base)
 Clones a rnamlBase struture.

void rnamldeleteBase (rnamlBase *base)
 Frees the rnamlBase structure.

int rnamlisBase (const rnamlObject *obj)
 Tells wheter the object is a rnamlBase.

int rnamlequalsBase (const rnamlBase *left, const rnamlBase *right)
 Tells if left and right are equals.

const char * rnamlgetBaseStrand (const rnamlBase *base)
 Gets the strand from the base.

void rnamlsetBaseStrand (rnamlBase *base, const char *strand)
 Sets the base strand.

int rnamlgetBasePosition (const rnamlBase *base)
 Gets the base position.

void rnamlsetBasePosition (rnamlBase *base, int position)
 Sets the base position.

const char * rnamlgetBaseBaseType (const rnamlBase *base)
 Gets the baseType from the base.

void rnamlsetBaseBaseType (rnamlBase *base, const char *baseType)
 Sets the base baseType.

char rnamlgetBaseAltLoc (const rnamlBase *base)
 Gets the base altLoc.

void rnamlsetBaseAltLoc (rnamlBase *base, char altLoc)
 Sets the base altLoc.

char rnamlgetBaseInsertion (const rnamlBase *base)
 Gets the base insertion.

void rnamlsetBaseInsertion (rnamlBase *base, char insertion)
 Sets the base insertion.

void rnamladdBaseAtom (rnamlBase *base, rnamlAtom *atom)
 Adds a atom into a base.

xmlcpgListrnamlgetBaseAtoms (rnamlBase *base)
 Gets the base's atom list.

xmlcpgObjectrnamltoXMLBase (const rnamlBase *base)
 Translates the rnamlBase structure into a xmlcpgElement conforming to the RNAML standard.


Typedef Documentation

typedef struct rnamlBASE rnamlBase
 

Rnaml structure containing the base informations.


Function Documentation

void rnamladdBaseAtom rnamlBase   base,
rnamlAtom   atom
 

Adds a atom into a base.

Parameters:
base  the rnamlBase structure.
atom  the rnamlAtom structure.

rnamlBase* rnamlcloneBase const rnamlBase   base
 

Clones a rnamlBase struture.

Parameters:
base  the structure to clone.
Returns:
the new allocated structure or NULL if something goes wrong.

void rnamldeleteBase rnamlBase   base
 

Frees the rnamlBase structure.

Parameters:
base  the rnamlBase structure to free.

int rnamlequalsBase const rnamlBase   left,
const rnamlBase   right
 

Tells if left and right are equals.

Parameters:
left  the left object to compare.
right  the right object to compare.
Returns:
1 if the objects are equals or 0 otherwise.

char rnamlgetBaseAltLoc const rnamlBase   base
 

Gets the base altLoc.

Parameters:
base  the rnamlBase structure.
Returns:
the base altLoc or EOF if base is NULL or not an rnamlBase.

xmlcpgList* rnamlgetBaseAtoms rnamlBase   base
 

Gets the base's atom list.

Parameters:
base  the rnamlBase structure.
Returns:
the base's atom xmlcpgList or NULL if something goes wrong.

const char* rnamlgetBaseBaseType const rnamlBase   base
 

Gets the baseType from the base.

Parameters:
base  the rnamlBase structure.
Returns:
the base baseType string or NULL if base is NULL or not an rnamlBase.

char rnamlgetBaseInsertion const rnamlBase   base
 

Gets the base insertion.

Parameters:
base  the rnamlBase structure.
Returns:
the base insertion or EOF if base is NULL or not an rnamlBase.

int rnamlgetBasePosition const rnamlBase   base
 

Gets the base position.

Parameters:
base  the rnamlBase structure.
Returns:
the base position or -1 if base is NULL or not an rnamlBase.

const char* rnamlgetBaseStrand const rnamlBase   base
 

Gets the strand from the base.

Parameters:
base  the rnamlBase structure.
Returns:
the base strand string or NULL if base is NULL or not an rnamlBase.

int rnamlisBase const rnamlObject   obj
 

Tells wheter the object is a rnamlBase.

Parameters:
obj  the rnamlObject to test.
Returns:
1 if the object is a rnamlBase, 0 otherwise.

rnamlBase* rnamlnewBase  
 

Creates a new rnamlBase structure.

Returns:
the new allocated structure or NULL if something goes wrong.

void rnamlsetBaseAltLoc rnamlBase   base,
char    altLoc
 

Sets the base altLoc.

Parameters:
base  the rnamlBase structure.
altLoc  the base altLoc.

void rnamlsetBaseBaseType rnamlBase   base,
const char *    baseType
 

Sets the base baseType.

The previous base baseType is freed and a copy of baseType is generated.

Parameters:
base  the rnamlBase structure.
baseType  the base baseType.

void rnamlsetBaseInsertion rnamlBase   base,
char    insertion
 

Sets the base insertion.

Parameters:
base  the rnamlBase structure.
insertion  the base insertion.

void rnamlsetBasePosition rnamlBase   base,
int    position
 

Sets the base position.

Parameters:
base  the rnamlBase structure.
position  the base position.

void rnamlsetBaseStrand rnamlBase   base,
const char *    strand
 

Sets the base strand.

The previous base strand is freed and a copy of strand is generated.

Parameters:
base  the rnamlBase structure.
strand  the base strand.

xmlcpgObject* rnamltoXMLBase const rnamlBase   base
 

Translates the rnamlBase structure into a xmlcpgElement conforming to the RNAML standard.

Parameters:
molecule  the rnamlBase structure to translate.
Returns:
the xmlcpgObject or NULL if something goes wrong.


Generated on Tue Nov 11 14:59:42 2003 for xmlcpg by doxygen1.2.18