iPE::Annotation::NullDefinition(3)

NAME
iPE::Annotation::NullDefinition - defines a region in a transcript where the null models are counted.

DESCRIPTION
A NullDefinition defines an area in the transcript where all null models are counted. A NullDefinition is defined by a state name, a range of bases in the particular feature in the transcript, and the ordinality.

FUNCTIONS

new (tag, members)
    This object is automatically constructed by the containing Estimator object from the data in the XML file.

stateNames ()
    Returns the state names in which the NullDefinition resides

regionInterval ()
    Returns the boundaries of the region in the form of an iPE::Util::Interval object.

featureInterval ()
    Returns the first and last feature in which this region may happen in the form of an iPE::Util::Interval object.

seqtype ()
    Returns the type of sequence that the null definition pertains to. These will be used when estimating the null model.

samplingRate ()
    Returns the frequency with which a null region should be counted.

matchesState ()
    Returns 1 if the state is in the list of states to be included in the null region, 0 otherwise.

addToTranscript (transcript)
    Adds null regions to all eligible features in the transcript passed in. The transcript is required to be finalized.

SEE ALSO
iPE::Transcript, iPE::Feature, iPE::Util::Interval

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu)