See: Description
Class | Description |
---|---|
Ambiguizer |
A general utilities class for ambiguizing motifs.
|
AssessmentDriver |
This driver is a simple wrapper around the basic BeamDriver; it outputs a file in the format required for the Tompa assessment.
|
BackgroundDriver | |
BayesDeltaSig | |
Beam |
Contains the beam and bipartite beam search method.
|
BeamDriver |
Beam drivers are threads that can run beam, the ambiguizer, bipartite beam, and filters for a group of genes.
|
BeamDriverFactory |
This class builds BeamDrivers.
|
BiologicalBeamDriver |
Use this driver when you are running a biological test set and you know the motifs.
|
CGIDriver | |
CGIDriver.MotifGeneSummary | |
CGIScope | |
CorruptionDriver | |
FASTAdriver |
This is a simple BeamDriver that will generate FASTA files of the group genes, where the geneIDs are the unique integer IDs.
|
LinearityTesterDriver |
This is a general utility driver for testing things involved in the Linearity proof paper.
|
MLDriver |
This is an exploratory class; parts of this class will move to other classes when we figure out what we're really doing.
|
PhiScoreDriver |
This driver facilitates computing the phi scores for entire directories of files.
|
PRISM |
This is a simple commandline driver for PRISM.
|
RankedMotifPair |
A simple class used in comparing a set of identified motifs against a set of known motifs.
|
RankedMotifPair.FoundMotifComparator |
Compares two RankedMotifPairPair objects solely by the natural ordering of the motif instance variables.
|
ResultsEvaluator |
A hodgepodge of methods for evaluating results.
|
Scope |
The command-line driver for BEAM, PRISM, and SPACER.
|
ScoreDriver |
This is a simple driver that will score the known motifs of everything in the group.
|
ScoreKnownsDriver |
This is a simple driver that will score the known motifs of everything in the group.
|
WebScope |
The four most important classes in this package are:
Beam
: Provides the Beam algorithm and the BipartiteBeam algorithm. These are standalone
algorithms wrapped up in static methods. They take an UberProperties
and a
Scorer
.
Ambiguizer
: Provides all of the algorithms we have developed for ambiguizing motifs.
These are standalone algorithms wrapped up in static methods. They take an UberProperties
and a
Scorer
.
BeamDriver
: The top level driver for running SCOPE. (It is named BeamDriver
because SCOPE
originally consisted of only the Beam algorithm. Many other drivers extend this class
to provide the functionality of hooking up SCOPE as they see fit. Each subclass specifies the order in which the SCOPE programs are executed,
and constructs the appropriate Scorer
based on the properties that it is given. If you are looking
at adding functionality, you will most likely want to extend BeamDriver
to encapsulate the functionality you want. Current
subclasses in this package include drivers that run SCOPE then score Phis against known hits (BiologicalBeamDriver
),
generate corrupt data sets (CorruptionDriver
), score Phis from a file against known hits
(PhiScoreDriver
), and generate FASTA sequences for the driver's regulon
(FASTAdriver
). BeamDriver
does all of its file output through
protected methods that can be overridden to stop these files from being written. This functionality is used in
the edu.dartmouth.bglab.beam.web
package to restrict file output in the web front end to SCOPE.
Scope
: The SCOPE command-line program. Deals with parsing command-line flags and loading in
all of the necessary drivers. Scope
is set up to easily add and remove flags. Each flag is associated with a parameter
in the default params file. In general, there will be one driver per regulon.