iPE::Annotation(3)

NAME
iPE::Annotation - object which contains the state annotation of a sequence and corresponding conservation sequence.

DESCRIPTION
An annotation is a collection of iPE::Annoation::SegmentedAnnotations. Several intermediate steps are taken to achieve this, first via the iPE::AnnotationPlugin, which creates iPE::Annotation::Transcripts, which are finally layered into iPE::Annotation::SegmentedAnnotations.

Each SegmentedAnnotation represents a region in which one or more Transcripts occur, flanked by intergenic/unannotated regions. Note that there is no relationship between a locus and a SegmentedAnnotation. All locuses will be contained in a single SegmentedAnnotation, but some transcripts which are not in the same locus may be included.

FUNCTIONS

new (memberHash)
    Create a new iPE::Annotation. The memberHash hash reference is expected to have the following keys defined:

    filename
        The name of the file which contains the annotation

    featureMaps
        A reference to an array of feature maps which relate specific features in an annotation format to a feature in the gHMM.

    nullDefinitions
        Definitions of null regions relative to features in transcripts. This is of the iPE::NullDefinition class.

    seqLength
        The length of the underlying sequence. This is used to remove any transcripts which step over the end.

    levels
        Optional. Pass to set each feature with a gc level. This is of the iPE::GCLevels class. DEPRECATED.

format ()
    Format the annotation for output.

SEE ALSO
iPE::Annotation::SegmentedAnnotation, iPE::Annotation::Transcript, iPE::Annotation::Feature, iPE::FeatureMap, iPE::AnnotationPlugin

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

POD ERRORS
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Around line 13:
    You forgot a '=back' before '=head1'

Around line 26:
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