ghmmwrapper.py

General Hidden Markov Model Library 一个通用的隐马尔科夫模型的C代码库

    __swig_setmethods__["N"] = _ghmmwrapper.model_N_set
    __swig_getmethods__["N"] = _ghmmwrapper.model_N_get
    if _newclass:N = property(_ghmmwrapper.model_N_get, _ghmmwrapper.model_N_set)
    __swig_setmethods__["M"] = _ghmmwrapper.model_M_set
    __swig_getmethods__["M"] = _ghmmwrapper.model_M_get
    if _newclass:M = property(_ghmmwrapper.model_M_get, _ghmmwrapper.model_M_set)
    __swig_setmethods__["s"] = _ghmmwrapper.model_s_set
    __swig_getmethods__["s"] = _ghmmwrapper.model_s_get
    if _newclass:s = property(_ghmmwrapper.model_s_get, _ghmmwrapper.model_s_set)
    __swig_setmethods__["prior"] = _ghmmwrapper.model_prior_set
    __swig_getmethods__["prior"] = _ghmmwrapper.model_prior_get
    if _newclass:prior = property(_ghmmwrapper.model_prior_get, _ghmmwrapper.model_prior_set)
    __swig_setmethods__["name"] = _ghmmwrapper.model_name_set
    __swig_getmethods__["name"] = _ghmmwrapper.model_name_get
    if _newclass:name = property(_ghmmwrapper.model_name_get, _ghmmwrapper.model_name_set)
    __swig_setmethods__["model_type"] = _ghmmwrapper.model_model_type_set
    __swig_getmethods__["model_type"] = _ghmmwrapper.model_model_type_get
    if _newclass:model_type = property(_ghmmwrapper.model_model_type_get, _ghmmwrapper.model_model_type_set)
    __swig_setmethods__["silent"] = _ghmmwrapper.model_silent_set
    __swig_getmethods__["silent"] = _ghmmwrapper.model_silent_get
    if _newclass:silent = property(_ghmmwrapper.model_silent_get, _ghmmwrapper.model_silent_set)
    __swig_setmethods__["maxorder"] = _ghmmwrapper.model_maxorder_set
    __swig_getmethods__["maxorder"] = _ghmmwrapper.model_maxorder_get
    if _newclass:maxorder = property(_ghmmwrapper.model_maxorder_get, _ghmmwrapper.model_maxorder_set)
    __swig_setmethods__["emission_history"] = _ghmmwrapper.model_emission_history_set
    __swig_getmethods__["emission_history"] = _ghmmwrapper.model_emission_history_get
    if _newclass:emission_history = property(_ghmmwrapper.model_emission_history_get, _ghmmwrapper.model_emission_history_set)
    __swig_setmethods__["tied_to"] = _ghmmwrapper.model_tied_to_set
    __swig_getmethods__["tied_to"] = _ghmmwrapper.model_tied_to_get
    if _newclass:tied_to = property(_ghmmwrapper.model_tied_to_get, _ghmmwrapper.model_tied_to_set)
    __swig_setmethods__["background_id"] = _ghmmwrapper.model_background_id_set
    __swig_getmethods__["background_id"] = _ghmmwrapper.model_background_id_get
    if _newclass:background_id = property(_ghmmwrapper.model_background_id_get, _ghmmwrapper.model_background_id_set)
    __swig_setmethods__["bp"] = _ghmmwrapper.model_bp_set
    __swig_getmethods__["bp"] = _ghmmwrapper.model_bp_get
    if _newclass:bp = property(_ghmmwrapper.model_bp_get, _ghmmwrapper.model_bp_set)
    __swig_setmethods__["topo_order"] = _ghmmwrapper.model_topo_order_set
    __swig_getmethods__["topo_order"] = _ghmmwrapper.model_topo_order_get
    if _newclass:topo_order = property(_ghmmwrapper.model_topo_order_get, _ghmmwrapper.model_topo_order_set)
    __swig_setmethods__["topo_order_length"] = _ghmmwrapper.model_topo_order_length_set
    __swig_getmethods__["topo_order_length"] = _ghmmwrapper.model_topo_order_length_get
    if _newclass:topo_order_length = property(_ghmmwrapper.model_topo_order_length_get, _ghmmwrapper.model_topo_order_length_set)

class modelPtr(model):
    def __init__(self, this):
        _swig_setattr(self, model, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, model, 'thisown', 0)
        _swig_setattr(self, model,self.__class__,model)
_ghmmwrapper.model_swigregister(modelPtr)


model_free = _ghmmwrapper.model_free

model_read = _ghmmwrapper.model_read

model_print = _ghmmwrapper.model_print

model_from_sequence_ascii = _ghmmwrapper.model_from_sequence_ascii

model_from_sequence = _ghmmwrapper.model_from_sequence

model_copy = _ghmmwrapper.model_copy

model_check = _ghmmwrapper.model_check

model_check_compatibility = _ghmmwrapper.model_check_compatibility

model_generate_from_sequence = _ghmmwrapper.model_generate_from_sequence

model_generate_sequences = _ghmmwrapper.model_generate_sequences

model_likelihood = _ghmmwrapper.model_likelihood

model_prob_distance = _ghmmwrapper.model_prob_distance

reestimate_baum_welch = _ghmmwrapper.reestimate_baum_welch

reestimate_baum_welch_nstep = _ghmmwrapper.reestimate_baum_welch_nstep

reestimate_update_tie_groups = _ghmmwrapper.reestimate_update_tie_groups

reestimate_baum_welch_label = _ghmmwrapper.reestimate_baum_welch_label

reestimate_baum_welch_nstep_label = _ghmmwrapper.reestimate_baum_welch_nstep_label

gradient_descent = _ghmmwrapper.gradient_descent

kbest = _ghmmwrapper.kbest

viterbi = _ghmmwrapper.viterbi

viterbi_logp = _ghmmwrapper.viterbi_logp

discriminative = _ghmmwrapper.discriminative

discrime_compute_performance = _ghmmwrapper.discrime_compute_performance

discrime_modelarray_alloc = _ghmmwrapper.discrime_modelarray_alloc

discrime_modelarray_dealloc = _ghmmwrapper.discrime_modelarray_dealloc

discrime_modelarray_setptr = _ghmmwrapper.discrime_modelarray_setptr

discrime_modelarray_getptr = _ghmmwrapper.discrime_modelarray_getptr

discrime_seqarray_alloc = _ghmmwrapper.discrime_seqarray_alloc

discrime_seqarray_dealloc = _ghmmwrapper.discrime_seqarray_dealloc

discrime_seqarray_setptr = _ghmmwrapper.discrime_seqarray_setptr

discrime_seqarray_getptr = _ghmmwrapper.discrime_seqarray_getptr

foba_forward = _ghmmwrapper.foba_forward

foba_backward = _ghmmwrapper.foba_backward

foba_logp = _ghmmwrapper.foba_logp

model_set_transition = _ghmmwrapper.model_set_transition

foba_forward_lean = _ghmmwrapper.foba_forward_lean

foba_label_forward = _ghmmwrapper.foba_label_forward

foba_label_logp = _ghmmwrapper.foba_label_logp

foba_label_backward = _ghmmwrapper.foba_label_backward

model_alloc_background_distributions = _ghmmwrapper.model_alloc_background_distributions

model_copy_background_distributions = _ghmmwrapper.model_copy_background_distributions

model_free_background_distributions = _ghmmwrapper.model_free_background_distributions

get_emission_index = _ghmmwrapper.get_emission_index

update_emission_history = _ghmmwrapper.update_emission_history

update_emission_history_front = _ghmmwrapper.update_emission_history_front

model_normalize = _ghmmwrapper.model_normalize

model_add_noise = _ghmmwrapper.model_add_noise

model_apply_background = _ghmmwrapper.model_apply_background

new_model = _ghmmwrapper.new_model

arraystate = _ghmmwrapper.arraystate

get_stateptr = _ghmmwrapper.get_stateptr

call_model_print = _ghmmwrapper.call_model_print

call_model_free = _ghmmwrapper.call_model_free

get_model_ptr = _ghmmwrapper.get_model_ptr

cast_model_ptr = _ghmmwrapper.cast_model_ptr

model_label_generate_sequences = _ghmmwrapper.model_label_generate_sequences
class sdstate(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, sdstate, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, sdstate, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C sdstate instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["pi"] = _ghmmwrapper.sdstate_pi_set
    __swig_getmethods__["pi"] = _ghmmwrapper.sdstate_pi_get
    if _newclass:pi = property(_ghmmwrapper.sdstate_pi_get, _ghmmwrapper.sdstate_pi_set)
    __swig_setmethods__["b"] = _ghmmwrapper.sdstate_b_set
    __swig_getmethods__["b"] = _ghmmwrapper.sdstate_b_get
    if _newclass:b = property(_ghmmwrapper.sdstate_b_get, _ghmmwrapper.sdstate_b_set)
    __swig_setmethods__["out_id"] = _ghmmwrapper.sdstate_out_id_set
    __swig_getmethods__["out_id"] = _ghmmwrapper.sdstate_out_id_get
    if _newclass:out_id = property(_ghmmwrapper.sdstate_out_id_get, _ghmmwrapper.sdstate_out_id_set)
    __swig_setmethods__["in_id"] = _ghmmwrapper.sdstate_in_id_set
    __swig_getmethods__["in_id"] = _ghmmwrapper.sdstate_in_id_get
    if _newclass:in_id = property(_ghmmwrapper.sdstate_in_id_get, _ghmmwrapper.sdstate_in_id_set)
    __swig_setmethods__["out_a"] = _ghmmwrapper.sdstate_out_a_set
    __swig_getmethods__["out_a"] = _ghmmwrapper.sdstate_out_a_get
    if _newclass:out_a = property(_ghmmwrapper.sdstate_out_a_get, _ghmmwrapper.sdstate_out_a_set)
    __swig_setmethods__["in_a"] = _ghmmwrapper.sdstate_in_a_set
    __swig_getmethods__["in_a"] = _ghmmwrapper.sdstate_in_a_get
    if _newclass:in_a = property(_ghmmwrapper.sdstate_in_a_get, _ghmmwrapper.sdstate_in_a_set)
    __swig_setmethods__["out_states"] = _ghmmwrapper.sdstate_out_states_set
    __swig_getmethods__["out_states"] = _ghmmwrapper.sdstate_out_states_get
    if _newclass:out_states = property(_ghmmwrapper.sdstate_out_states_get, _ghmmwrapper.sdstate_out_states_set)
    __swig_setmethods__["in_states"] = _ghmmwrapper.sdstate_in_states_set
    __swig_getmethods__["in_states"] = _ghmmwrapper.sdstate_in_states_get
    if _newclass:in_states = property(_ghmmwrapper.sdstate_in_states_get, _ghmmwrapper.sdstate_in_states_set)
    __swig_setmethods__["fix"] = _ghmmwrapper.sdstate_fix_set
    __swig_getmethods__["fix"] = _ghmmwrapper.sdstate_fix_get
    if _newclass:fix = property(_ghmmwrapper.sdstate_fix_get, _ghmmwrapper.sdstate_fix_set)

class sdstatePtr(sdstate):
    def __init__(self, this):
        _swig_setattr(self, sdstate, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, sdstate, 'thisown', 0)
        _swig_setattr(self, sdstate,self.__class__,sdstate)
_ghmmwrapper.sdstate_swigregister(sdstatePtr)

class sdmodel(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, sdmodel, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, sdmodel, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C sdmodel instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["N"] = _ghmmwrapper.sdmodel_N_set
    __swig_getmethods__["N"] = _ghmmwrapper.sdmodel_N_get
    if _newclass:N = property(_ghmmwrapper.sdmodel_N_get, _ghmmwrapper.sdmodel_N_set)
    __swig_setmethods__["M"] = _ghmmwrapper.sdmodel_M_set
    __swig_getmethods__["M"] = _ghmmwrapper.sdmodel_M_get
    if _newclass:M = property(_ghmmwrapper.sdmodel_M_get, _ghmmwrapper.sdmodel_M_set)
    __swig_setmethods__["cos"] = _ghmmwrapper.sdmodel_cos_set
    __swig_getmethods__["cos"] = _ghmmwrapper.sdmodel_cos_get
    if _newclass:cos = property(_ghmmwrapper.sdmodel_cos_get, _ghmmwrapper.sdmodel_cos_set)
    __swig_setmethods__["s"] = _ghmmwrapper.sdmodel_s_set
    __swig_getmethods__["s"] = _ghmmwrapper.sdmodel_s_get
    if _newclass:s = property(_ghmmwrapper.sdmodel_s_get, _ghmmwrapper.sdmodel_s_set)
    __swig_setmethods__["prior"] = _ghmmwrapper.sdmodel_prior_set
    __swig_getmethods__["prior"] = _ghmmwrapper.sdmodel_prior_get
    if _newclass:prior = property(_ghmmwrapper.sdmodel_prior_get, _ghmmwrapper.sdmodel_prior_set)
    __swig_setmethods__["get_class"] = _ghmmwrapper.sdmodel_get_class_set
    __swig_getmethods__["get_class"] = _ghmmwrapper.sdmodel_get_class_get
    if _newclass:get_class = property(_ghmmwrapper.sdmodel_get_class_get, _ghmmwrapper.sdmodel_get_class_set)
    __swig_setmethods__["model_type"] = _ghmmwrapper.sdmodel_model_type_set
    __swig_getmethods__["model_type"] = _ghmmwrapper.sdmodel_model_type_get
    if _newclass:model_type = property(_ghmmwrapper.sdmodel_model_type_get, _ghmmwrapper.sdmodel_model_type_set)
    __swig_setmethods__["silent"] = _ghmmwrapper.sdmodel_silent_set
    __swig_getmethods__["silent"] = _ghmmwrapper.sdmodel_silent_get
    if _newclass:silent = property(_ghmmwrapper.sdmodel_silent_get, _ghmmwrapper.sdmodel_silent_set)

class sdmodelPtr(sdmodel):
    def __init__(self, this):
        _swig_setattr(self, sdmodel, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, sdmodel, 'thisown', 0)
        _swig_setattr(self, sdmodel,self.__class__,sdmodel)
_ghmmwrapper.sdmodel_swigregister(sdmodelPtr)


sdmodel_free = _ghmmwrapper.sdmodel_free

sdmodel_generate_sequences = _ghmmwrapper.sdmodel_generate_sequences

sdmodel_likelihood = _ghmmwrapper.sdmodel_likelihood

smodel_individual_likelihoods = _ghmmwrapper.smodel_individual_likelihoods

sdviterbi = _ghmmwrapper.sdviterbi

sdfoba_forward = _ghmmwrapper.sdfoba_forward

cp_class_change = _ghmmwrapper.cp_class_change

setSwitchingFunction = _ghmmwrapper.setSwitchingFunction

call_sdmodel_free = _ghmmwrapper.call_sdmodel_free

arraysdstate = _ghmmwrapper.arraysdstate

get_sdstateptr = _ghmmwrapper.get_sdstateptr
normal = _ghmmwrapper.normal
normal_pos = _ghmmwrapper.normal_pos
normal_approx = _ghmmwrapper.normal_approx
density_number = _ghmmwrapper.density_number
class sstate(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, sstate, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, sstate, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C sstate instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["pi"] = _ghmmwrapper.sstate_pi_set
    __swig_getmethods__["pi"] = _ghmmwrapper.sstate_pi_get
    if _newclass:pi = property(_ghmmwrapper.sstate_pi_get, _ghmmwrapper.sstate_pi_set)
    __swig_setmethods__["out_id"] = _ghmmwrapper.sstate_out_id_set
    __swig_getmethods__["out_id"] = _ghmmwrapper.sstate_out_id_get
    if _newclass:out_id = property(_ghmmwrapper.sstate_out_id_get, _ghmmwrapper.sstate_out_id_set)
    __swig_setmethods__["in_id"] = _ghmmwrapper.sstate_in_id_set
    __swig_getmethods__["in_id"] = _ghmmwrapper.sstate_in_id_get
    if _newclass:in_id = property(_ghmmwrapper.sstate_in_id_get, _ghmmwrapper.sstate_in_id_set)
    __swig_setmethods__["out_a"] = _ghmmwrapper.sstate_out_a_set
    __swig_getmethods__["out_a"] = _ghmmwrapper.sstate_out_a_get
    if _newclass:out_a = property(_ghmmwrapper.sstate_out_a_get, _ghmmwrapper.sstate_out_a_set)