iPE::Annotation::Feature(3)

NAME
iPE::Annotation::Feature - A feature component of a transcript

DESCRIPTION
A feature is defined as a state in a specified region of an annotation. For the transcript that owns it, it is the only state the gHMM is in for those positions of the annotation.

A feature includes an iPE::State object as well as a start and end point of the region.

FUNCTIONS

new (memberHash)
    This creates a new Feature. All information about the feature is given on instantiation. The the passed hash reference is expected to have the following keys:

    state
        The state of this feature. Should be an iPE::State object.

    start
        The begin coordinate of the feature, in a 0-based index

    end The end coordinate of the feature, in a 0-based index

    startFrame, endFrame
        The start and end frame of the feature. The start frame is the number of bases overhanging the lowest coordinate of the feature, and the end frame is the number of bases overhanging the highest coordinate of the feature.

    transcript
        The iPE::Transcript that contains this feature; required.

    id  An optional field specifying the transcript id associated with this feature.

clone
    Create a copy of an object instance.

state ()
    Returns the state of the feature.

start ()
    Returns the start coordinate of the feature.

end ()
    Returns the end coordinate of the feature.

transcript ()
    Returns the transcript containing the feature object.

length ()
    Returns the length of the feature.

strand ()
    Returns the strand of the feature.

startFrame (), endFrame ()
    Returns the starting and ending frame of the feature.

nullRegions ()
    Returns a reference to the (possibly empty) array of nullRegions for this feature.

gcLevel ()
    Returns the GC content of the DNA sequence at this feature, if it exists. If no GC content was passed in, this will return undef.

id ()
    Returns the transcript ID associated with the feature. If none is specified, the empty string is returned.

addNullRegion (nullRegion)
    Add a null region (defined by an iPE::Annotation::NullRegion object) to this feature. This blindly adds it to the feature, no bounds are checked. The iPE::Annotation::NullDefinition object checks this.

clearNullRegions ()
    Clear the null regions from the transcript. This would be useful if the feature is modified, and may no longer have any null regions. (For example, changing a state to an altsplice state after annotation.)

setID (id)
    Set the transcript id associated with this feature.

setLevel (levels)
    Set the level of the feature according to the iPE::GCContent object passed in.

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

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