
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 nthlast 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
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