Uses of Class
org.biojava.bio.symbol.SoftMaskedAlphabet

Packages that use SoftMaskedAlphabet

Package	Description
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Uses of SoftMaskedAlphabet in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that return SoftMaskedAlphabet

Modifier and Type	Method and Description
static SoftMaskedAlphabet	SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask) Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
static SoftMaskedAlphabet	SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask, SoftMaskedAlphabet.MaskingDetector maskingDetector) Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.