ghmmwrapper.py

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

# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

import _ghmmwrapper

def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
    if (name == "this"):
        if isinstance(value, class_type):
            self.__dict__[name] = value.this
            if hasattr(value,"thisown"): self.__dict__["thisown"] = value.thisown
            del value.thisown
            return
    method = class_type.__swig_setmethods__.get(name,None)
    if method: return method(self,value)
    if (not static) or hasattr(self,name) or (name == "thisown"):
        self.__dict__[name] = value
    else:
        raise AttributeError("You cannot add attributes to %s" % self)

def _swig_setattr(self,class_type,name,value):
    return _swig_setattr_nondynamic(self,class_type,name,value,0)

def _swig_getattr(self,class_type,name):
    method = class_type.__swig_getmethods__.get(name,None)
    if method: return method(self)
    raise AttributeError,name

import types
try:
    _object = types.ObjectType
    _newclass = 1
except AttributeError:
    class _object : pass
    _newclass = 0
del types



gsl_rng_init = _ghmmwrapper.gsl_rng_init

gsl_rng_timeseed = _ghmmwrapper.gsl_rng_timeseed

time_seed = _ghmmwrapper.time_seed

matrix_d_alloc = _ghmmwrapper.matrix_d_alloc

matrix_d_alloc_copy = _ghmmwrapper.matrix_d_alloc_copy

matrix_d_free = _ghmmwrapper.matrix_d_free

matrix_i_alloc = _ghmmwrapper.matrix_i_alloc

matrix_i_free = _ghmmwrapper.matrix_i_free

matrix_d_print = _ghmmwrapper.matrix_d_print
class sequence_t(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, sequence_t, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, sequence_t, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C sequence_t instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["seq"] = _ghmmwrapper.sequence_t_seq_set
    __swig_getmethods__["seq"] = _ghmmwrapper.sequence_t_seq_get
    if _newclass:seq = property(_ghmmwrapper.sequence_t_seq_get, _ghmmwrapper.sequence_t_seq_set)
    __swig_setmethods__["states"] = _ghmmwrapper.sequence_t_states_set
    __swig_getmethods__["states"] = _ghmmwrapper.sequence_t_states_get
    if _newclass:states = property(_ghmmwrapper.sequence_t_states_get, _ghmmwrapper.sequence_t_states_set)
    __swig_setmethods__["seq_len"] = _ghmmwrapper.sequence_t_seq_len_set
    __swig_getmethods__["seq_len"] = _ghmmwrapper.sequence_t_seq_len_get
    if _newclass:seq_len = property(_ghmmwrapper.sequence_t_seq_len_get, _ghmmwrapper.sequence_t_seq_len_set)
    __swig_setmethods__["seq_label"] = _ghmmwrapper.sequence_t_seq_label_set
    __swig_getmethods__["seq_label"] = _ghmmwrapper.sequence_t_seq_label_get
    if _newclass:seq_label = property(_ghmmwrapper.sequence_t_seq_label_get, _ghmmwrapper.sequence_t_seq_label_set)
    __swig_setmethods__["seq_id"] = _ghmmwrapper.sequence_t_seq_id_set
    __swig_getmethods__["seq_id"] = _ghmmwrapper.sequence_t_seq_id_get
    if _newclass:seq_id = property(_ghmmwrapper.sequence_t_seq_id_get, _ghmmwrapper.sequence_t_seq_id_set)
    __swig_setmethods__["seq_w"] = _ghmmwrapper.sequence_t_seq_w_set
    __swig_getmethods__["seq_w"] = _ghmmwrapper.sequence_t_seq_w_get
    if _newclass:seq_w = property(_ghmmwrapper.sequence_t_seq_w_get, _ghmmwrapper.sequence_t_seq_w_set)
    __swig_setmethods__["seq_number"] = _ghmmwrapper.sequence_t_seq_number_set
    __swig_getmethods__["seq_number"] = _ghmmwrapper.sequence_t_seq_number_get
    if _newclass:seq_number = property(_ghmmwrapper.sequence_t_seq_number_get, _ghmmwrapper.sequence_t_seq_number_set)
    __swig_setmethods__["total_w"] = _ghmmwrapper.sequence_t_total_w_set
    __swig_getmethods__["total_w"] = _ghmmwrapper.sequence_t_total_w_get
    if _newclass:total_w = property(_ghmmwrapper.sequence_t_total_w_get, _ghmmwrapper.sequence_t_total_w_set)
    __swig_setmethods__["state_labels"] = _ghmmwrapper.sequence_t_state_labels_set
    __swig_getmethods__["state_labels"] = _ghmmwrapper.sequence_t_state_labels_get
    if _newclass:state_labels = property(_ghmmwrapper.sequence_t_state_labels_get, _ghmmwrapper.sequence_t_state_labels_set)
    __swig_setmethods__["state_labels_len"] = _ghmmwrapper.sequence_t_state_labels_len_set
    __swig_getmethods__["state_labels_len"] = _ghmmwrapper.sequence_t_state_labels_len_get
    if _newclass:state_labels_len = property(_ghmmwrapper.sequence_t_state_labels_len_get, _ghmmwrapper.sequence_t_state_labels_len_set)

class sequence_tPtr(sequence_t):
    def __init__(self, this):
        _swig_setattr(self, sequence_t, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, sequence_t, 'thisown', 0)
        _swig_setattr(self, sequence_t,self.__class__,sequence_t)
_ghmmwrapper.sequence_t_swigregister(sequence_tPtr)
cvar = _ghmmwrapper.cvar


new_sequence_setPtr = _ghmmwrapper.new_sequence_setPtr

copy_sequence_setPtr = _ghmmwrapper.copy_sequence_setPtr

delete_sequence_setPtr = _ghmmwrapper.delete_sequence_setPtr

sequence_setPtr_assign = _ghmmwrapper.sequence_setPtr_assign

sequence_setPtr_value = _ghmmwrapper.sequence_setPtr_value
class sequence_d_t(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, sequence_d_t, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, sequence_d_t, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C sequence_d_t instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["seq"] = _ghmmwrapper.sequence_d_t_seq_set
    __swig_getmethods__["seq"] = _ghmmwrapper.sequence_d_t_seq_get
    if _newclass:seq = property(_ghmmwrapper.sequence_d_t_seq_get, _ghmmwrapper.sequence_d_t_seq_set)
    __swig_setmethods__["seq_len"] = _ghmmwrapper.sequence_d_t_seq_len_set
    __swig_getmethods__["seq_len"] = _ghmmwrapper.sequence_d_t_seq_len_get
    if _newclass:seq_len = property(_ghmmwrapper.sequence_d_t_seq_len_get, _ghmmwrapper.sequence_d_t_seq_len_set)
    __swig_setmethods__["seq_label"] = _ghmmwrapper.sequence_d_t_seq_label_set
    __swig_getmethods__["seq_label"] = _ghmmwrapper.sequence_d_t_seq_label_get
    if _newclass:seq_label = property(_ghmmwrapper.sequence_d_t_seq_label_get, _ghmmwrapper.sequence_d_t_seq_label_set)
    __swig_setmethods__["seq_id"] = _ghmmwrapper.sequence_d_t_seq_id_set
    __swig_getmethods__["seq_id"] = _ghmmwrapper.sequence_d_t_seq_id_get
    if _newclass:seq_id = property(_ghmmwrapper.sequence_d_t_seq_id_get, _ghmmwrapper.sequence_d_t_seq_id_set)
    __swig_setmethods__["seq_w"] = _ghmmwrapper.sequence_d_t_seq_w_set
    __swig_getmethods__["seq_w"] = _ghmmwrapper.sequence_d_t_seq_w_get
    if _newclass:seq_w = property(_ghmmwrapper.sequence_d_t_seq_w_get, _ghmmwrapper.sequence_d_t_seq_w_set)
    __swig_setmethods__["seq_number"] = _ghmmwrapper.sequence_d_t_seq_number_set
    __swig_getmethods__["seq_number"] = _ghmmwrapper.sequence_d_t_seq_number_get
    if _newclass:seq_number = property(_ghmmwrapper.sequence_d_t_seq_number_get, _ghmmwrapper.sequence_d_t_seq_number_set)
    __swig_setmethods__["total_w"] = _ghmmwrapper.sequence_d_t_total_w_set
    __swig_getmethods__["total_w"] = _ghmmwrapper.sequence_d_t_total_w_get
    if _newclass:total_w = property(_ghmmwrapper.sequence_d_t_total_w_get, _ghmmwrapper.sequence_d_t_total_w_set)

class sequence_d_tPtr(sequence_d_t):
    def __init__(self, this):
        _swig_setattr(self, sequence_d_t, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, sequence_d_t, 'thisown', 0)
        _swig_setattr(self, sequence_d_t,self.__class__,sequence_d_t)
_ghmmwrapper.sequence_d_t_swigregister(sequence_d_tPtr)


new_sequence_d_setPtr = _ghmmwrapper.new_sequence_d_setPtr

copy_sequence_d_setPtr = _ghmmwrapper.copy_sequence_d_setPtr

delete_sequence_d_setPtr = _ghmmwrapper.delete_sequence_d_setPtr

sequence_d_setPtr_assign = _ghmmwrapper.sequence_d_setPtr_assign

sequence_d_setPtr_value = _ghmmwrapper.sequence_d_setPtr_value

sequence_calloc = _ghmmwrapper.sequence_calloc

sequence_d_calloc = _ghmmwrapper.sequence_d_calloc

sequence_clean = _ghmmwrapper.sequence_clean

sequence_d_clean = _ghmmwrapper.sequence_d_clean

sequence_print = _ghmmwrapper.sequence_print

sequence_copy = _ghmmwrapper.sequence_copy

sequence_d_read = _ghmmwrapper.sequence_d_read

sequence_add = _ghmmwrapper.sequence_add

sequence_d_add = _ghmmwrapper.sequence_d_add

sequence_free = _ghmmwrapper.sequence_free

sequence_d_free = _ghmmwrapper.sequence_d_free

sequence_d_print = _ghmmwrapper.sequence_d_print

get_onesequence = _ghmmwrapper.get_onesequence

seq_read = _ghmmwrapper.seq_read

get_seq_ptr = _ghmmwrapper.get_seq_ptr

sequence_d_t_array = _ghmmwrapper.sequence_d_t_array

get_seq_d_ptr = _ghmmwrapper.get_seq_d_ptr

set_seq_d_array = _ghmmwrapper.set_seq_d_array

set_sequence_d_label = _ghmmwrapper.set_sequence_d_label

get_sequence_d_label = _ghmmwrapper.get_sequence_d_label

seq_d_read = _ghmmwrapper.seq_d_read

call_sequence_print = _ghmmwrapper.call_sequence_print

call_sequence_d_print = _ghmmwrapper.call_sequence_d_print
class background_distributions(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, background_distributions, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, background_distributions, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C background_distributions instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["n"] = _ghmmwrapper.background_distributions_n_set
    __swig_getmethods__["n"] = _ghmmwrapper.background_distributions_n_get
    if _newclass:n = property(_ghmmwrapper.background_distributions_n_get, _ghmmwrapper.background_distributions_n_set)
    __swig_setmethods__["m"] = _ghmmwrapper.background_distributions_m_set
    __swig_getmethods__["m"] = _ghmmwrapper.background_distributions_m_get
    if _newclass:m = property(_ghmmwrapper.background_distributions_m_get, _ghmmwrapper.background_distributions_m_set)
    __swig_setmethods__["order"] = _ghmmwrapper.background_distributions_order_set
    __swig_getmethods__["order"] = _ghmmwrapper.background_distributions_order_get
    if _newclass:order = property(_ghmmwrapper.background_distributions_order_get, _ghmmwrapper.background_distributions_order_set)
    __swig_setmethods__["b"] = _ghmmwrapper.background_distributions_b_set
    __swig_getmethods__["b"] = _ghmmwrapper.background_distributions_b_get
    if _newclass:b = property(_ghmmwrapper.background_distributions_b_get, _ghmmwrapper.background_distributions_b_set)

class background_distributionsPtr(background_distributions):
    def __init__(self, this):
        _swig_setattr(self, background_distributions, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, background_distributions, 'thisown', 0)
        _swig_setattr(self, background_distributions,self.__class__,background_distributions)
_ghmmwrapper.background_distributions_swigregister(background_distributionsPtr)

class state(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, state, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, state, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C state instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
    __swig_setmethods__["pi"] = _ghmmwrapper.state_pi_set
    __swig_getmethods__["pi"] = _ghmmwrapper.state_pi_get
    if _newclass:pi = property(_ghmmwrapper.state_pi_get, _ghmmwrapper.state_pi_set)
    __swig_setmethods__["b"] = _ghmmwrapper.state_b_set
    __swig_getmethods__["b"] = _ghmmwrapper.state_b_get
    if _newclass:b = property(_ghmmwrapper.state_b_get, _ghmmwrapper.state_b_set)
    __swig_setmethods__["order"] = _ghmmwrapper.state_order_set
    __swig_getmethods__["order"] = _ghmmwrapper.state_order_get
    if _newclass:order = property(_ghmmwrapper.state_order_get, _ghmmwrapper.state_order_set)
    __swig_setmethods__["out_id"] = _ghmmwrapper.state_out_id_set
    __swig_getmethods__["out_id"] = _ghmmwrapper.state_out_id_get
    if _newclass:out_id = property(_ghmmwrapper.state_out_id_get, _ghmmwrapper.state_out_id_set)
    __swig_setmethods__["in_id"] = _ghmmwrapper.state_in_id_set
    __swig_getmethods__["in_id"] = _ghmmwrapper.state_in_id_get
    if _newclass:in_id = property(_ghmmwrapper.state_in_id_get, _ghmmwrapper.state_in_id_set)
    __swig_setmethods__["out_a"] = _ghmmwrapper.state_out_a_set
    __swig_getmethods__["out_a"] = _ghmmwrapper.state_out_a_get
    if _newclass:out_a = property(_ghmmwrapper.state_out_a_get, _ghmmwrapper.state_out_a_set)
    __swig_setmethods__["in_a"] = _ghmmwrapper.state_in_a_set
    __swig_getmethods__["in_a"] = _ghmmwrapper.state_in_a_get
    if _newclass:in_a = property(_ghmmwrapper.state_in_a_get, _ghmmwrapper.state_in_a_set)
    __swig_setmethods__["out_states"] = _ghmmwrapper.state_out_states_set
    __swig_getmethods__["out_states"] = _ghmmwrapper.state_out_states_get
    if _newclass:out_states = property(_ghmmwrapper.state_out_states_get, _ghmmwrapper.state_out_states_set)
    __swig_setmethods__["in_states"] = _ghmmwrapper.state_in_states_set
    __swig_getmethods__["in_states"] = _ghmmwrapper.state_in_states_get
    if _newclass:in_states = property(_ghmmwrapper.state_in_states_get, _ghmmwrapper.state_in_states_set)
    __swig_setmethods__["fix"] = _ghmmwrapper.state_fix_set
    __swig_getmethods__["fix"] = _ghmmwrapper.state_fix_get
    if _newclass:fix = property(_ghmmwrapper.state_fix_get, _ghmmwrapper.state_fix_set)
    __swig_setmethods__["label"] = _ghmmwrapper.state_label_set
    __swig_getmethods__["label"] = _ghmmwrapper.state_label_get
    if _newclass:label = property(_ghmmwrapper.state_label_get, _ghmmwrapper.state_label_set)

class statePtr(state):
    def __init__(self, this):
        _swig_setattr(self, state, 'this', this)
        if not hasattr(self,"thisown"): _swig_setattr(self, state, 'thisown', 0)
        _swig_setattr(self, state,self.__class__,state)
_ghmmwrapper.state_swigregister(statePtr)

class model(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, model, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, model, name)
    def __init__(self): raise RuntimeError, "No constructor defined"
    def __repr__(self):
        return "<%s.%s; proxy of C model instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)