libuproc  1.2.0
Data Structures | Enumerations | Functions

DNA/RNA sequence classifier. More...

Data Structures

struct  uproc_dnaclass
 DNA/RNA sequence classifier. More...
 

Enumerations

enum  uproc_dnaclass_mode {
  UPROC_DNACLASS_ALL,
  UPROC_DNACLASS_MAX
}
 Classification mode. More...
 

Functions

uproc_dnaclassuproc_dnaclass_create (enum uproc_dnaclass_mode mode, const uproc_protclass *pc, const uproc_matrix *codon_scores, uproc_orffilter *orf_filter, void *orf_filter_arg)
 Create new DNA classifier. More...
 
void uproc_dnaclass_destroy (uproc_dnaclass *dc)
 Destroy DNA classifier. More...
 
int uproc_dnaclass_classify (const uproc_dnaclass *dc, const char *seq, uproc_list **results)
 Classify DNA sequence. More...
 

Detailed Description

DNA/RNA sequence classifier.

An object of this type is used to classify DNA/RNA sequences. The result is a List of uproc_dnaresult objects. It does so in the following way:

Enumeration Type Documentation

Classification mode.

Determines which results uproc_dnaclass_classify produces.

Enumerator
UPROC_DNACLASS_ALL 

Only the result with the maximum score.

UPROC_DNACLASS_MAX 

All results (unordered)

Function Documentation

uproc_dnaclass* uproc_dnaclass_create ( enum uproc_dnaclass_mode  mode,
const uproc_protclass pc,
const uproc_matrix codon_scores,
uproc_orffilter orf_filter,
void *  orf_filter_arg 
)

Create new DNA classifier.

Parameters
modeWhich results to produce
pcuproc_protclass to use for classifying ORFs
codon_scoresCodon scoring matrix (or NULL)
orf_filterORF filtering function
orf_filter_argAdditional argument to orf_filter
void uproc_dnaclass_destroy ( uproc_dnaclass dc)

Destroy DNA classifier.

int uproc_dnaclass_classify ( const uproc_dnaclass dc,
const char *  seq,
uproc_list **  results 
)

Classify DNA sequence.

results should be a pointer to a (uproc_list *) that is either NULL (in which case a new list is created) or which has which has already been used with this function. The list will contain items of type struct uproc_dnaresult. If *results is not NULL, all its elements will be passed to uproc_dnaresult_free at the beginning.

Parameters
dcDNA classifier
seqsequence to classify
resultsOUT: classification results