iPE::gHMM(3)

NAME
iPE::gHMM - The generalized Hidden Markov Model structure for iParameterEstimation.

DESCRIPTION
A main container class for all models in iParameterEstimation. Handles all types of input for the gHMM, and outputs via the models it contains.

FUNCTIONS

new(filename)
    Creates a new gHMM object based on the file passed. If the file ends in .xml, the file is interpreted as an xml parameter template. Some initial checking of the file is performed for validity, and then each of the objects described in the parameter template file are constructed. Some additional checking is done there as well.

author
    Return the author of the parameter template.

date
    Return the date of creation indicated in the parameter template.

comments
    Return the Comments object contained in the gHMM.

initISOs, transISOs
    Return the iPE::Model::ISO levels object which contains the ISO levels of the initial and transition probabilities.

nullDefinitions ()
    Returns a reference to an array of all the NullDefinition objects created in the gHMM.

states ()
    Return the state hash, keyed by the name of the state.

altspliceStates ()
    Return the altsplice state hash, keyed by the name of the altsplice state.

state (name)
    Return the state with the passed name, if none exists, undef is returned.

conversion ()
    Return the gtf conversion for zoe.

getEmissions (type)
    Return the array reference to the emissions type that is passed.

dnaEmissions (), consEmissions (), estEmissions (), malignEmissions (), etc.
    Accessor functions for the array of dna and conservation sequence emission models.

countNullRegion (region)
    The gHMM, being the holder of all references to models, is responsible for counting the null region, to ensure that each model gets counted only once.

finalizeCounts ()
    Takes all of the models and requests that they take all the observed ambiguity codes and include them in the counts for the finalized counts.

smooth ()
    Smooths all the distributions in the gHMM.

normalize ()
    Normalizes all models after they have been counted.

score ()
    Scores all models after having been normalized.

optimize ()
    Optimize the tuple counts against the global N-SCAN BNTree. Note that this is fairly monolithic since the author did not reimpliment the EM optimization algorithm.

outputPrepare(out, mode)
    Prepare all the states and models contained in the gHMM for outputting. out is an iPE::Util::Output object and mode is one of "count", "prob", or "score", indicating what kind of parameters will be output.

outputZoe(out, mode)
    Output the gHMM, estimated or not, to the iPE::Util::Output object passed to the function. The mode is one of "count", "prob", or "score" depending on the mode of output. This is outputted in Zoe format.

SEE ALSO
iPE

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