libuproc
1.2.0
|
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_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. 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... | |
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:
enum uproc_dnaclass_mode |
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) |
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.
mode | Which results to produce |
pc | uproc_protclass to use for classifying ORFs |
codon_scores | Codon scoring matrix (or NULL) |
orf_filter | ORF filtering function |
orf_filter_arg | Additional 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.
dc | DNA classifier |
seq | sequence to classify |
results | OUT: classification results |