Mask

Provides the mask alphabet and functionality for creating masked composites. More...

Collaboration diagram for Mask:

Classes
class	bio::alphabet::mask
	Implementation of a masked semialphabet to be used for tuple composites.. More...
class	bio::alphabet::masked< sequence_alphabet_t >
	A template for composite alphabets that differentiate between upper and lower case characters.. More...

Detailed Description

Provides the mask alphabet and functionality for creating masked composites.

Introduction

Masks are useful as tuple composites when one wants to create a masked alphabet with don't care positions, but does not want to use the bio::alphabet::dna15 N or bio::alphabet::aa27 X because of loss of information. It will instead mark the specified characters as masked, and display them as lowercase representations when printed.
There are two types of masking: "hard-masking" which converts to the UNKNOWN character and "soft-masking", which is visualised by using lower-case instead of upper-case. However because regular nucleotide and aminoacid alphabets discard case on assignment, one needs to create additional alphabets to preserve this information (if desired).
This alphabet in itself is not useful to users directly, but instead the composite bio::alphabet::masked may be used to transform another alphabet into a new alphabet that can represent the original alphabet plus masking information.