See: Description
Class | Description |
---|---|
Alphabet |
Represents the set of bases that can be present in motifs.
|
EquivalenceComparator |
A comparator for assessing motif equivalence.
|
Motif |
Represents a biological motif as a consensus sequence and a sig score.
|
Motif.LastExpansion | |
Motif.ScoreData | |
MotifComparator |
A general contract for comparing motifs.
|
MotifInstance |
Used to represent the location on a gene of a particular instance of a motif.
|
MotifList |
A motif list consists of a list of motifs and a sig score.
|
MotifUtils |
Contains static methods for creating sets of motifs and performing various other motif-related tasks.
|
OverlapComparator |
A comparator for assessing partial motif equivalence.
|
ReverseScoreComparator |
A comparator for sorting motifs in ascending order of score.
|
ScoreComparator |
This mirrors the normal behavious of motifs for both compare() and equals(), therefore these two methods are not consistent.
|
SequenceComparator |
A comparator for sorting motifs alphabetically according to their sequences.
|
Exception | Description |
---|---|
UnknownBaseException |
A runtime exception used to notify a caller that a gene name couldn't be found.
|
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 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.