NAME
Bio::Polloc::Typing::bandingPattern - banding-pattern-based methods for typing assessment
DESCRIPTION
Category 1 of genotyping methods in:
Li, W., Raoult, D., & Fournier, P.-E. (2009).
Bacterial strain typing in the genomic era.
FEMS Microbiology Reviews, 33(5), 892-916.AUTHOR - Luis M. Rodriguez-R
Email lmrodriguezr at gmail dot com
APPENDIX
Methods provided by the package
new
Generic initialization method
METHODS FROM Bio::Polloc::TypingI
scan
See Bio::Polloc::TypingI->scan.
fragments must be implemented by the Bio::Polloc::Typing::bandingPattern::* object.
cluster
typing_value
See Bio::Polloc::TypingI->typing_value.
Returns the size of the loci between the minimum (min_size) and the maximum (max_size) size.
Returns
A reference to an array of integers.
graph_content
Generates the expected gel. See Bio::Polloc::TypingI->graph.
SPECIFIC METHODS
fragments
Generates fragments.
Arguments
Returns
A Bio::Polloc::LociGrop, where each locus is a fragment.
Throws
A Bio::Polloc::Polloc::NotImplementedException unless implemented by the specific Bio::Polloc::Typing::bandingPattern::* object.
max_size
Gets/sets the maximum locus size. No limit (inf) by default.
min_size
Gets/sets the minimum locus size. 1 by default.
INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*