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alignment.h File Reference

#include "alisequence.h"
#include "object.h"
#include "xmlcpg.h"

Go to the source code of this file.

Typedefs

typedef rnamlALIGNMENT rnamlAlignment
 Rnaml structure containing the alignment informations.


Functions

rnamlAlignmentrnamlnewAlignment ()
 Creates a new rnamlAlignment structure.

rnamlAlignmentrnamlcloneAlignment (const rnamlAlignment *alignment)
 Clones a rnamlAlignment struture.

void rnamldeleteAlignment (rnamlAlignment *alignment)
 Frees the rnamlAlignment structure.

int rnamlisAlignment (const rnamlObject *obj)
 Tells wheter the object is a rnamlAlignment.

int rnamlequalsAlignment (const rnamlAlignment *left, const rnamlAlignment *right)
 Tells if left and right are equals.

const char * rnamlgetAlignmentId (const rnamlAlignment *alignment)
 Gets the alignment id.

void rnamlsetAlignmentId (rnamlAlignment *alignment, const char *id)
 Sets the alignment id.

void rnamladdAlignmentAliSequence (rnamlAlignment *alignment, rnamlAliSequence *aliSequence)
 Adds a aliSequence into a alignment.

xmlcpgListrnamlgetAlignmentAliSequences (rnamlAlignment *alignment)
 Gets the alignment's aliSequence list.

xmlcpgObjectrnamltoXMLAlignment (const rnamlAlignment *alignment)
 Translates the rnamlAlignment structure into a xmlcpgElement conforming to the RNAML standard.


Typedef Documentation

typedef struct rnamlALIGNMENT rnamlAlignment
 

Rnaml structure containing the alignment informations.


Function Documentation

void rnamladdAlignmentAliSequence rnamlAlignment   alignment,
rnamlAliSequence   aliSequence
 

Adds a aliSequence into a alignment.

Parameters:
alignment  the rnamlAlignment structure.
aliSequence  the rnamlAliSequence structure.

rnamlAlignment* rnamlcloneAlignment const rnamlAlignment   alignment
 

Clones a rnamlAlignment struture.

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

void rnamldeleteAlignment rnamlAlignment   alignment
 

Frees the rnamlAlignment structure.

Parameters:
alignment  the rnamlAlignment structure to free.

int rnamlequalsAlignment const rnamlAlignment   left,
const rnamlAlignment   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.

xmlcpgList* rnamlgetAlignmentAliSequences rnamlAlignment   alignment
 

Gets the alignment's aliSequence list.

Parameters:
alignment  the rnamlAlignment structure.
Returns:
the alignment's aliSequence xmlcpgList or NULL if something goes wrong.

const char* rnamlgetAlignmentId const rnamlAlignment   alignment
 

Gets the alignment id.

Parameters:
alignment  the rnamlAlignment structure.
Returns:
the alignment id string or NULL if alignment is NULL or not an rnamlAlignment.

int rnamlisAlignment const rnamlObject   obj
 

Tells wheter the object is a rnamlAlignment.

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

rnamlAlignment* rnamlnewAlignment  
 

Creates a new rnamlAlignment structure.

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

void rnamlsetAlignmentId rnamlAlignment   alignment,
const char *    id
 

Sets the alignment id.

The previous alignment id is freed and a copy of id is generated.

Parameters:
alignment  the rnamlAlignment structure.
id  the alignment id.

xmlcpgObject* rnamltoXMLAlignment const rnamlAlignment   alignment
 

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

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


Generated on Tue Nov 11 14:59:41 2003 for xmlcpg by doxygen1.2.18