Package | Description |
---|---|
edu.dartmouth.bglab |
Provides a class to hold global constants.
|
edu.dartmouth.bglab.beam |
Provides the top level of the algorithms for BEAM, PRISM, and SPACER, along with the
command-line version of SCOPE.
|
edu.dartmouth.bglab.beam.web |
Provides
WebDriver and its associated classes as a simple API to a
multi-process version of SCOPE designed for use by a web
front end. |
edu.dartmouth.bglab.dataImportPreparation | |
edu.dartmouth.bglab.io |
Provides static classes for reading and writing common objects to and from file,
along with a main class for loading new organisms into SCOPE.
|
edu.dartmouth.bglab.model |
Provides implementations of several different models for representing cis-regulatory
elements, along with command-line programs for testing the accuracy of these models.
|
edu.dartmouth.bglab.motif |
Provides classes for representing, manipulating, and comparing motifs.
|
edu.dartmouth.bglab.score |
Provides objective functions for scoring motifs.
|
edu.dartmouth.bglab.search |
Provides classes for finding the occurrences of motifs in biological
sequences.
|
edu.dartmouth.bglab.test |
Provides test code for the other packages, and a few other odds and
ends.
|
edu.dartmouth.bglab.util |
Provides an assortment of data structures and other utilities classes;
the classes in this package perform general functions which are not
directly related to biology, whereas all other packages are
motif-centric.
|