A B C D E F G H I J K L M N O P R S T U V W Y

B

b - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The high order b={g,c,t} symbol

b() - Method in class jbil.sequence.ExtendedDNAAlphabet

BACKGROUND_ORDER - Static variable in class jbil.sequence.GibbsMotifSiteSampler

BadInputException - Exception in jbil.common

Run-time exception used by algorithms to signalise that the some of the inputs are missing or invalid.

BadInputException(String) - Constructor for exception jbil.common.BadInputException

Creates an exception associated to an error message.

BooleanArrayUtilities - Class in jbil.util

Assorted boolean utility functions.

BooleanArrayUtilities() - Constructor for class jbil.util.BooleanArrayUtilities

BURN_IN - Static variable in class jbil.sequence.GibbsMotifSiteSampler

ByteArraySequence - Class in jbil.sequence

Implementation of Sequence in which the sequence of symbols is translated into an array of bytes s.t.

ByteArraySequence(Alphabet) - Constructor for class jbil.sequence.ByteArraySequence

Creates an empty sequence over a given alphabet.

ByteArraySequence(Alphabet, int) - Constructor for class jbil.sequence.ByteArraySequence

Creates an empty sequence with a given initial capacity over a given alphabet.