iPE::Annotation::Segment(3)

NAME
iPE::Annotation::Segment - Defines a contiguous segment of a layered annotation where all layers are consistent.

DESCRIPTION
This is the smallest unit of the final annotation. Each annotation file is grouped into annotations of locuses which overlap. These are divided into segments which have the consistent state annotations in all layers of the annotation.

A segment contains information on each layer of the annotation including the state that the gHMM is in for the entirety of the segment, as well as an iPE::Annnotation::Transcript object describing the entire isoform.

FUNCTIONS

new (memberHash)
    Creates a new annotation Segment with the keys of the member hash. Required keys are:

    start
        The beginning coordinate of the segment.

    end The ending coordinate of the segment.

    features
        Array reference to references to features in each layer.

    transcripts
        Array reference to references to the transcripts in each layer.

start (), end ()
    The start and end coordinates of the segment, respectively.

features ()
    The feature layers of the segment. For each layer there is either a defined feature or undef.

transcripts ()
    The transcripts of the segment. As with features, these are either defined as a locus or undef. These layers give you an overall picture of the coordinates of the locus, which features are where and a transcript ID if provided. See iPE::Annotation::Transcript for more details.

layers ()
    The total number of layers in this segment.

validLayers ()
    The number of valid layers in this segment. There may be more layers that are empty, but they are not counted in this function.

SEE ALSO
iPE::Annotation::SegmentedAnnotation, iPE::Annotation

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