iPE::State::AltSplice(3)

NAME
iPE::State::AltSplice - Defines a special kind of state called an altsplice state.

DESCRIPTION
The alt splice state distinguishes itself from states in that since ASEs are generally not explicitly annotataed, they have to be inferred by the occurrence of overlapping transcripts. This is done in the detect () function. This is a base class; the subclass is determined by the altsplice_type tag in the XML input file.

FUNCTIONS

new (attributes)
    Creates a new AltSplice state.

getClassname(altspliceType)
    This function gets the classname for a altsplice type after checking if it exists. If the class does not exist, it dies. This is not an object method.

inTransition (), altspliceType (), originState (), alternateStates ()
    These are all defined in the originating xml document that described the altsplice state. The altspliceType implies which class will be used to define the altsplice feature object, the inTransition is the expected transition preceding the altsplice state, and the originState is the state which will be examined for potential altsplicing, and thus altered. (If found, the incoming transition will be altered to have the state of the type in the in transition field as well.)

    The list of alternateStates contains states which may be considered candidate states for the alternate isoforms, whereas the origin state usually implies the core constituent state. For example, with MultiSite altsplice states, the frame of the innermost feature is the frame of the origin state. However when a frameshifting alternate site is found, different states must be considered for the other splice sites.

validAlternateState (state)
    Returns 1 if the state is in the list of valid alternate states for this AltSplice state, 0 otherwise.

validState (state)
    Returns 1 if the state passed is the origin state or is in the list of alternate states, 0 otherwise.

STUB FUNCTIONS

detect (transcripts, seqLength)
    This function must be defined in all altsplice states. It takes in a group of overlapping transcripts and finds all altsplice cases of its kind in the annotation and alters the annotation as necessary.

SEE ALSO
iPE::gHMM iPE::State

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