Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 12]

StochHMM::alignment
StochHMM::alt_simple_stochTable
StochHMM::ambigCharacter	Define the ambiguous characters symbol and index number for digitizing ambiguous characters in the sequence For example in DNA N = [ACGT] = [0,1,2,3]
StochHMM::dynamic_bitset::bit_ref
StochHMM::cell
StochHMM::Counter
StochHMM::dynamic_bitset
StochHMM::emissionFuncParam
StochHMM::emm
StochHMM::ExDef
StochHMM::weightDef
StochHMM::ExDefSequence
StochHMM::gff_feature
StochHMM::Index
StochHMM::lexicalTable	Lexical table stores the log2 probabilities for both emissions and lexical transitions
StochHMM::matrixPosition
StochHMM::model
StochHMM::models
StochHMM::multiTraceback
StochHMM::nthScore
StochHMM::nthTrace
StochHMM::opt_data	Store the actual command line options data for each option defined by user
StochHMM::opt_parameters
StochHMM::options	Parse, Store, and access commandline options data
StochHMM::ppTrack
StochHMM::PWM
StochHMM::seqJob
StochHMM::seqTracks
SeqTracks	SeqTracks are used to integrate the information provided by the model with the sequences that are being imported
StochHMM::sequence
StochHMM::sequenceStream
StochHMM::sequences
StochHMM::simpleTable< T >
StochHMM::sparseArray< T >
StochHMM::state
StochHMM::StateFuncs	(**Adding in log space)
StochHMM::stateInfo	Contains state information for quick reference between states information
stateInfo
StochHMM::stencil	Class stencil: contains individial model template and keeps track of coordinates for replacement
StochHMM::alt_simple_stochTable::stoch_val
StochHMM::stochTable::stoch_value
StochHMM::stochTable
StochHMM::stringList	Stringlist is an list of strings that contains parsed comments and can be used to split string or remove whitespace from a string
StochHMM::templates	Class templates: contains a map of all templates
StochHMM::traceback_path
StochHMM::track
StochHMM::TrackFuncs	Stores pointer to user functions used to create Real Number Tracks
StochHMM::tracks
trainingEmission
trainingSeq
trainingSeqs
StochHMM::transition	Transition information for each state
StochHMM::transitionFuncParam
StochHMM::trellis
Trellis	Implements the HMM scoring trellis and algorithms
StochHMM::weight	Weight class contains scaling factors for external scores
StochHMM::weights