iPE::FeatureMapping(3)

NAME
iPE::FeatureMapping - a mapping of a feature name in an annotation to a state in an HMM.

DESCRIPTION
Data structure for mapping a state to a relative position in a format-specific feature. The indexing here goes by 0-index, and all things passed to and retrieved from this packages should be 0-based.

FUNCTIONS

new (tag, members)
    This object is automatically constructed by the containing FeatureMap object directly from the XML file.

addToTranscript(transcript, featureName, featureStart, featureEnd, featureStartFrame, featureEndFrame, featureNo, nInTranscript, length)
    This function evaluates the feture against the calling featureMapping object and decides whether the feature is relevant to this feature mapping. If it is, it adds a state region to the passed Transcript. If it is not, it does nothing.

    Arguments:

    transcript
        The Transcript that will be added to if this FeatureMapping qualifies.

    featureName
        The name of the feature as it is defined in format (for example, a GTF feature name would be "CDS").

    featureStart, featureStop
        The start and stop position in the annotation of the feature.

    featureStartFrame, featureEndFrame
        Pass either the starting frame or the ending frame in here to determine if it matches with the state. Whichever one you do not pass in as a valid frame you may pass in as -1.

    featureNo
        Which feature of its time it is in the transcript, e.g. if it is the first CDS feature, the second, and so on. (Note that this is not which feature of all the features, it is which feature of this specific type of feature.)

    nInTranscript
        The total number of this type of feature in the transcript, e.g. how many total CDS features there are in the transcript, if this feature is a CDS feature.

    length
        The total length of the underlying sequence. This is used to check to see if the feature will step out of bounds and cause a problem with counting.

SEE ALSO
iPE::FeatureMap, iPE::AnnotationPlugin

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

POD ERRORS
Hey! The above document had some coding errors, which are explained below:

Around line 211:
    You forgot a '=back' before '=head1'