iPE::Annotation::SegmentedAnnotation(3)

NAME
iPE::Annotation::SegmentedAnnotation - A multilayered gene annotation segmented on boundaries where the layers are exactly the same.

DESCRIPTION
A SegmentedAnnotation is a data structure which represents a gene annotation of one or more splices of the gene in a single structure.

The data structure contains 2 major components: transcripts and segments. The transcripts array identifies the transcript for each layer on each segment. The segments array contains all of the segments (see iPE::Annotation::Segment). These contain information about the states in a region for all transcripts.

FUNCTIONS

new(memberHash)
    Create a new iPE::Annotation::SegmentedAnnotation. Segments all transcripts into iPE::Annotation::Segments. It is assumed that the transcripts all overlap. To use this function, pass an reference to an array of transcripts to the transcripts key of the memberHash.

transcripts ()
    Return the transcripts in this segmented annotation.

segments ()
    Return the segments in this segmented annotation.

min ()
    Return the minimum coordinate of the overlapping transcripts

max ()
    Return the maximum coordinate of the overlapping transcripts

numTranscriptsAt(x)
    Returns how many transcripts exist at the point x.

numTranscriptsInRange(start, end)
    Returns the number of transcripts that overlap the range [start, end].

format ()
    Format the segmented annotation for output.

SEE ALSO
iPE::Annotation::Segment, iPE::Annotation

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