Each Motif
contains a reference to an Alphabet
, which
defines what bases can be used. Three different Alphabets
are
defined: Alphabet.PRIMARY
, Alphabet.FULL
, and
Alphabet.ACGTRY
. Currently Alphabet.FULL
is used so that
Motifs
can represent consensus sequences. New Alphabets
can be added if needed. See {@link edu.dartmouth.bglab.motif.Alphabet Alphabet}
for details.
MotifLists
allow sets of related Motifs
to be grouped
together so that they can be evaluated as a set or combined into a single motif.
MotifUtils
adds peripheral functionality to the Motif
and
MotifList
classes.
The distinction between what functionality is contained in Motif
and
MotifUtils
is fuzzy, so check both classes before
implementing new methods.
The remaining classes are Comparators
for comparing motifs.