See: Description
Interface | Description |
---|---|
FindResults |
Class | Description |
---|---|
AggregatedFindResults | |
ComparatorMotifFinder |
Uses a
SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a
given motif and the indices of these occurrences in the sequence. |
CompositeMotifFinder |
Uses a
SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a
given motif and the indices of these occurrences in the sequence. |
CompositeMotifFinder.CompositeFindResults | |
MarkovModel |
A MarkovModel implementation of MotifFinder.
|
MarkovModel.KeyComparator |
Implements an ordering on markov keys.
|
MotifFinder |
A motif finder contains an internal representation of a biological sequence and allows access to the number of occurrences of a given
motif and the indices of these occurrences in the sequence.
|
MotifFinder.EmptyFindResults | |
MotifFinder.FindResultsSoftValueHashMap | |
MotifFinder.GenomeSoftValueHashMap | |
MotifFinder.UncompressedFindResults | |
MotifFinderFactory |
Contains static methods to create motif finders and aid in the creation of motif finders, along with a
main
method that saves a motif finder and its bipartite caches to file. |
SearchUtils |
A general class that provides static helper methods for extracting motifs from MotifFinders; This includes methods for randomly sampling
motifs from a motif finder or from a gene that is shared with a give motif, and methods for finding the instantiations of a degenerate
motif that actually occur in the motif finder.
|
SuffixArrayMotifFinder |
Uses a
SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a
given motif and the indices of these occurrences in the sequence. |
SuffixArrayMotifFinder.SuffixArrayFindResults |
Exception | Description |
---|---|
UnsearchableMotifException |
A runtime exception used by MotifFinder when it cannot find a motif due to the degree and distribution of ambiguity.
|
MotifFinder
is an abstract class that defines most
of the functionality needed by motif finders. Subclasses need only
define how to search a string for specific substrings. This is currently
done by SuffixArrayMotifFinder
using an edu.dartmouth.bglab.util.SuffixArray
to quickly look up substrings.
Motif finders can be created dynamically using reflection by
using the MotifFinderFactory
class.
In order for a new motif finder to work with this factory, it must
implement the constructors:
<ClassName>(String, int) <ClassName>(String, String, int)This can usually be done with simple calls to
super
.
GroupScorers maintain a notion of group and genome, or
background. At the top level, the only difference is in the constructor,
which takes two Motif Finders, one for the group and one for the genome.
Several of the utility methods are overridden by GroupScorer
to use the group-based Motif Finder. For example, the phi score methods
use the group Motif Finder to compute the phi score, and getMotifFinder()
and setMotifFinder()
work with the group Motif Finder. To
compensate for this, methods exist to get and set the genomic Motif
Finder.
Finally, SearchUtils
provides
additional search functionality, MarkovModel
provides a Markov model version
of a motif finder.