Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123]

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