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sequence.h File Reference

#include "numberingsystem.h"
#include "seqdata.h"
#include "seqannotation.h"
#include "object.h"
#include "xmlcpg.h"

Go to the source code of this file.

Typedefs

typedef rnamlSEQUENCE rnamlSequence
 Rnaml structure containing the sequence informations.


Functions

rnamlSequencernamlnewSequence ()
 Creates a new rnamlSequence structure.

rnamlSequencernamlcloneSequence (const rnamlSequence *sequence)
 Clones a rnamlSequence struture.

void rnamldeleteSequence (rnamlSequence *sequence)
 Frees the rnamlSequence structure.

int rnamlisSequence (const rnamlObject *obj)
 Tells wheter the object is a rnamlSequence.

int rnamlequalsSequence (const rnamlSequence *left, const rnamlSequence *right)
 Tells if left and right are equals.

const char * rnamlgetSequenceStrand (const rnamlSequence *sequence)
 Gets the sequence strand.

void rnamlsetSequenceStrand (rnamlSequence *sequence, const char *strand)
 Sets the sequence strand.

int rnamlgetSequenceLength (const rnamlSequence *sequence)
 Gets the sequence length.

void rnamlsetSequenceLength (rnamlSequence *sequence, int length)
 Sets the sequence length.

int rnamlgetSequenceCircular (const rnamlSequence *sequence)
 Gets the sequence circularflag.

void rnamlsetSequenceCircular (rnamlSequence *sequence, int circular)
 Sets the sequence circular flag.

void rnamladdSequenceNumberingSystem (rnamlSequence *sequence, rnamlNumberingSystem *numberingSystem)
 Adds a numberingSystem into a sequence.

xmlcpgListrnamlgetSequenceNumberingSystems (rnamlSequence *sequence)
 Gets the sequence's numberingSystem list.

rnamlSeqDatarnamlgetSequenceSeqData (rnamlSequence *sequence)
 Gets the seqData from the sequence.

void rnamlsetSequenceSeqData (rnamlSequence *sequence, rnamlSeqData *seqData)
 Sets the sequence seqData.

rnamlSeqAnnotationrnamlgetSequenceSeqAnnotation (rnamlSequence *sequence)
 Gets the seqAnnotation from the sequence.

void rnamlsetSequenceSeqAnnotation (rnamlSequence *sequence, rnamlSeqAnnotation *seqAnnotation)
 Sets the sequence seqAnnotation.

xmlcpgObjectrnamltoXMLSequence (const rnamlSequence *sequence)
 Translates the rnamlSequence structure into a xmlcpgElement conforming to the RNAML standard.


Typedef Documentation

typedef struct rnamlSEQUENCE rnamlSequence
 

Rnaml structure containing the sequence informations.


Function Documentation

void rnamladdSequenceNumberingSystem rnamlSequence   sequence,
rnamlNumberingSystem   numberingSystem
 

Adds a numberingSystem into a sequence.

Parameters:
sequence  the rnamlSequence structure.
numberingSystem  the rnamlNumberingSystem structure.

rnamlSequence* rnamlcloneSequence const rnamlSequence   sequence
 

Clones a rnamlSequence struture.

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

void rnamldeleteSequence rnamlSequence   sequence
 

Frees the rnamlSequence structure.

Parameters:
sequence  the rnamlSequence structure to free.

int rnamlequalsSequence const rnamlSequence   left,
const rnamlSequence   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.

int rnamlgetSequenceCircular const rnamlSequence   sequence
 

Gets the sequence circularflag.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence circular flag or 0 if sequence is NULL or not a rnamlSequence.

int rnamlgetSequenceLength const rnamlSequence   sequence
 

Gets the sequence length.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence length or 0 if sequence is NULL or not an rnamlSequence.

xmlcpgList* rnamlgetSequenceNumberingSystems rnamlSequence   sequence
 

Gets the sequence's numberingSystem list.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence's numberingSystem xmlcpgList or NULL if something goes wrong.

rnamlSeqAnnotation* rnamlgetSequenceSeqAnnotation rnamlSequence   sequence
 

Gets the seqAnnotation from the sequence.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence seqAnnotation is NULL or if sequence is NULL or not an rnamlSequence.

rnamlSeqData* rnamlgetSequenceSeqData rnamlSequence   sequence
 

Gets the seqData from the sequence.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence seqData is NULL or if sequence is NULL or not an rnamlSequence.

const char* rnamlgetSequenceStrand const rnamlSequence   sequence
 

Gets the sequence strand.

Parameters:
sequence  the rnamlSequence structure.
Returns:
the sequence strand string or NULL if sequence is NULL or not an rnamlSequence.

int rnamlisSequence const rnamlObject   obj
 

Tells wheter the object is a rnamlSequence.

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

rnamlSequence* rnamlnewSequence  
 

Creates a new rnamlSequence structure.

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

void rnamlsetSequenceCircular rnamlSequence   sequence,
int    circular
 

Sets the sequence circular flag.

Any non zero value will be recorded as 1.

Parameters:
sequence  the rnamlSequence structure.
circular  the sequence circular flag.

void rnamlsetSequenceLength rnamlSequence   sequence,
int    length
 

Sets the sequence length.

Parameters:
sequence  the rnamlSequence structure.
length  the sequence length.

void rnamlsetSequenceSeqAnnotation rnamlSequence   sequence,
rnamlSeqAnnotation   seqAnnotation
 

Sets the sequence seqAnnotation.

The previous seqAnnotation info is freed

Parameters:
sequence  the rnamlSequence structure.
sequence  the sequence seqAnnotation.

void rnamlsetSequenceSeqData rnamlSequence   sequence,
rnamlSeqData   seqData
 

Sets the sequence seqData.

The previous seqData info is freed

Parameters:
sequence  the rnamlSequence structure.
sequence  the sequence seqData.

void rnamlsetSequenceStrand rnamlSequence   sequence,
const char *    strand
 

Sets the sequence strand.

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

Parameters:
sequence  the rnamlSequence structure.
strand  the sequence strand.

xmlcpgObject* rnamltoXMLSequence const rnamlSequence   sequence
 

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

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


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