libuproc  1.2.0
Data Structures | Functions

Iterates over a DNA/RNA sequence and yield all possible ORFs. More...

Data Structures

struct  uproc_orfiter
 Iterates over a DNA/RNA sequence and yield all possible ORFs. More...
 

Functions

uproc_orfiteruproc_orfiter_create (const char *seq, const double *codon_scores, uproc_orffilter *filter, void *filter_arg)
 Create orfiter object. More...
 
void uproc_orfiter_destroy (uproc_orfiter *iter)
 Destroy orfiter object. More...
 
int uproc_orfiter_next (uproc_orfiter *iter, struct uproc_orf *next)
 Obtain the next ORF. More...
 

Detailed Description

Iterates over a DNA/RNA sequence and yield all possible ORFs.

Function Documentation

uproc_orfiter* uproc_orfiter_create ( const char *  seq,
const double *  codon_scores,
uproc_orffilter filter,
void *  filter_arg 
)

Create orfiter object.

Parameters
seqsequence to iterate over
codon_scorescodon scores, must be a pointer to the first element of an array of size UPROC_BINARY_CODON_COUNT (see also uproc_orf_codonscores())
filterfilter function
filter_argadditional argument to filter
void uproc_orfiter_destroy ( uproc_orfiter iter)

Destroy orfiter object.

int uproc_orfiter_next ( uproc_orfiter iter,
struct uproc_orf next 
)

Obtain the next ORF.

A shallow copy of the next ORF will be stored in *orf, if you need to store a copy, use uproc_orf_copy().

Parameters
iterorfiter instance
nextOUT: read ORF