struct model

o N
Number of states
o M
Number of outputs
o s
Vector of the states
o prior
The a priori probability for the model.
o model_type
Contains bit flags for varios model extensions such as kSilentStates, kTiedEmissions (see ghmmh for a complete list)
o silent
Flag variables for each state indicating whether it is emitting or not.
o maxorder
Int variable for the maximum level of higher order emissions
o emission_history
saves the history of emissions as int, the nth-last emission is (emission_history * |alphabet|^n+1) % |alphabet| see
o tied_to
Flag variables for each state indicating whether the states emissions are tied to another state.
o Note: State store order information of the emissions.
o topo_order
(WR) added these variables for topological ordering of silent states Condition: topo_order != NULL iff (model_type & kSilentStates) == 1
o EXTENSIONS for Pair HMMs *
o size_of_alphabet
list of sizes of the alphabets *
o number_of_d_seqs
number of double sequences to modify the transition classes
o max_offset_x
maximal offset in sequence X (for the viterbi lookback matrix) *
o 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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