NAME
Bio::Polloc::Locus::extend - A feature based on another one
DESCRIPTION
A feature of a sequence, inferred by similarity or surrounding regions similar to those of a known feature. Implements Bio::Polloc::LocusI.
AUTHOR - Luis M. Rodriguez-R
Email lmrodriguezr at gmail dot com
APPENDIX
Methods provided by the package
new
Creates a Bio::Polloc::Locus::repeat object.
Arguments
- -basefeature Bio::Polloc::LocusI object
-
The reference feature or part of the reference collection.
- -score float
-
The score of extension (bit-score on BLAST or score on HMMer, for example).
basefeature
Gets/sets the reference feature of the extension. Be careful, this can also refer to one feature in a collection of reference. Avoid using specific data from this feature.
Arguments
The reference feature (Bio::Polloc::LocusI object, optional).
Returns
The reference feature (Bio::Polloc::LocusI object or undef).
score
Gets/sets the score.
Arguments
The score (float, optional).
Returns
The score (float or undef).
distance
Tries to calculate the distance using the base-feature's distance() method. See Bio::Polloc::LocusI-distance()>.
Throws
INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*