iPE::Sequence::Region(3)

NAME
iPE::Sequence::Region - A region of any sequence.

DESCRIPTION
Generically defines a region of a sequence either in the forward or reverse strand of the sequence. This is intended for passing a region to a model where observations will be counted.

All regions are initially defined by a series of positions within a feature where the counting gets the same weight. These are further broken down into subregions where models are. Due to the fact that the boundaries of the original regions may not fall on the same boundaries as the boundaries of the model, a "context" member variable is provided for information about where in the model to begin counting. For example, if a model is a 10 base position specific model, and the model starts at 5, then The region looks like this:

         0123456789
Model:   |--------|
Region:       |---|
Context: |---|

The context would be 5, and you would count the 5 last bases with the provided weight.

FUNCTIONS

new (memberHash)
    Construct a new region. This is generally done internally in iPE and passed up to the models. The following keys must be defined in order to construct a new region:

    start, end
        The beginning and end of the region.

    parentStart, parentEnd
        The beginning and end of the parent region of this region. The parent region is the region of immediate relevance to the region. Regions are either the same size of the parent region or smaller. If they are smaller, it is because of a layering difference in the middle of the region. If this is not supplied, it is assumed that the parent region is (start, end).

    feature
        The associated feature of the region.

    seq The sequence object to be used.

    weight
        The weight to give each count. If no weight is supplied, this is set to 1.

clone ()
    Create a copy of the region object.

subregion(parentStart, parentEnd)
    Create a subregion of the current region with new parent coordinates (parentStart, parentEnd). The new (start, end) coordinates will be the intersection of the current (start, end) coordinates and (parentStart, parentEnd). If the intersection is the empty set, undef is returned.

strRef ()
    The string object to count parameters with. This is usually a reference to a Perl string, but in the case of multiple alignment sequences is different.

parentStart (), parentEnd ()
    The start and end of the parent region in the string.

start (), end ()
    The start and end region in the string.

context ()
    The distance between the beginning of the parent region and the beginning of this region.

feature ()
    The assocated feature of this region.

seq ()
    The actual iPE::Sequence that the parameters are being estimated on.

weight ()
    The weight to give each count.

SEE ALSO
iPE::Sequence

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