struct model

N

Number of states

M

Number of outputs

s

Vector of the states

prior

The a priori probability for the model.

model_type

Contains bit flags for varios model extensions such as kSilentStates, kTiedEmissions (see ghmmh for a complete list)

silent

Flag variables for each state indicating whether it is emitting or not.

maxorder

Int variable for the maximum level of higher order emissions

emission_history

saves the history of emissions as int, the nth-last emission is (emission_history * |alphabet|^n+1) % |alphabet| see

tied_to

Flag variables for each state indicating whether the states emissions are tied to another state.

Note: State store order information of the emissions.

topo_order

(WR) added these variables for topological ordering of silent states Condition: topo_order != NULL iff (model_type & kSilentStates) == 1

EXTENSIONS for Pair HMMs *

size_of_alphabet

list of sizes of the alphabets *

number_of_d_seqs

number of double sequences to modify the transition classes

max_offset_x

maximal offset in sequence X (for the viterbi lookback matrix) *

max_offset_y

maximal offset in sequence Y (for the viterbi lookback matrix) *

The complete HMM. Contains all parameters, that define a HMM.

Alphabetic index