ghmmwrapper_wrap.c

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

  
  void double_2d_print(double **ary, int row, int col){
	int i,j;
	printf("(%dx%d) Matrix", row, col);
	for(i =0;i<row;i++){		  
      printf("\n");
      for(j =0;j<col;j++){		  		 
        printf("%f ",ary[i][j]);
	  }
	}
	printf("\n");  	
  }

  double** cast_ptr_d(double* array){
     double ** res = (double **) malloc(sizeof(double*));
	 res[0] = array;
	 return res;
  }	  
  
  void free_2darrayd(double **pt,int row) { matrix_d_free(&pt,row); }
   
  /************  Create and access int[size1][size2] arrays ************/
  
   int **int_2d_array_nocols(int rows){
	return (int **) malloc(rows*sizeof(int*));
  }	  
  
  void set_2d_arrayint_col(int **ary, int index, int *col){
	  ary[index] = col;
  }	  
  
  int *get_col_pointer_int(int **ary, int index) {
	  return ary[index];
  }
  
  
  void set_2d_arrayint(int **ary, int index1,int index2, int value) {
    ary[index1][index2] = value;
  }
  
  /* Get two dimensional array entry */
  int  get_2d_arrayint (int **ary, int index1, int index2) {return ary[index1][index2]; }
   
   int** cast_ptr_int(int* array){

	 int ** res = (int **) malloc(sizeof(int*));
	 res[0] = array;
	 return res; 
  }	 
  
  void free_2darrayint(int **pt, int rows,int cols) {  matrix_i_free(&pt, rows); }


  /**************** generalized deallocation *******************/  
  void freearray(void *pt)  { m_free(pt); }
   

#ifdef __cplusplus
extern "C" {
#endif
static int _wrap_RNG_set(PyObject *_val) {
    {
        void *temp;
        if ((SWIG_ConvertPtr(_val, &temp, SWIGTYPE_p_gsl_rng, SWIG_POINTER_EXCEPTION | SWIG_POINTER_DISOWN)) == -1) {
            SWIG_append_errmsg("C/C++ variable 'RNG'");
            return 1;
        }
        RNG = (gsl_rng *) temp;
    }
    return 0;
}


static PyObject *_wrap_RNG_get(void) {
    PyObject *pyobj;
    
    pyobj = SWIG_NewPointerObj((void *)(RNG), SWIGTYPE_p_gsl_rng, 0);
    return pyobj;
}


static PyObject *_wrap_gsl_rng_init(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    
    if(!PyArg_ParseTuple(args,(char *)":gsl_rng_init")) goto fail;
    gsl_rng_init();
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_gsl_rng_timeseed(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    gsl_rng *arg1 = (gsl_rng *) 0 ;
    PyObject * obj0 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"O:gsl_rng_timeseed",&obj0)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_gsl_rng, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    gsl_rng_timeseed(arg1);
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_time_seed(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    
    if(!PyArg_ParseTuple(args,(char *)":time_seed")) goto fail;
    time_seed();
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_d_alloc(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    int arg1 ;
    int arg2 ;
    double **result;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:matrix_d_alloc",&obj0,&obj1)) goto fail;
    {
        arg1 = (int)(SWIG_As_int(obj0)); 
        if (SWIG_arg_fail(1)) SWIG_fail;
    }
    {
        arg2 = (int)(SWIG_As_int(obj1)); 
        if (SWIG_arg_fail(2)) SWIG_fail;
    }
    result = (double **)matrix_d_alloc(arg1,arg2);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_p_double, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_d_alloc_copy(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    int arg1 ;
    int arg2 ;
    double **arg3 = (double **) 0 ;
    double **result;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    PyObject * obj2 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OOO:matrix_d_alloc_copy",&obj0,&obj1,&obj2)) goto fail;
    {
        arg1 = (int)(SWIG_As_int(obj0)); 
        if (SWIG_arg_fail(1)) SWIG_fail;
    }
    {
        arg2 = (int)(SWIG_As_int(obj1)); 
        if (SWIG_arg_fail(2)) SWIG_fail;
    }
    SWIG_Python_ConvertPtr(obj2, (void **)&arg3, SWIGTYPE_p_p_double, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(3)) SWIG_fail;
    result = (double **)matrix_d_alloc_copy(arg1,arg2,arg3);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_p_double, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_d_free(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    double ***arg1 = (double ***) 0 ;
    int arg2 ;
    int result;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:matrix_d_free",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_p_p_double, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    {
        arg2 = (int)(SWIG_As_int(obj1)); 
        if (SWIG_arg_fail(2)) SWIG_fail;
    }
    result = (int)matrix_d_free(arg1,arg2);
    
    {
        resultobj = SWIG_From_int((int)(result)); 
    }
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_i_alloc(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    int arg1 ;
    int arg2 ;
    int **result;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:matrix_i_alloc",&obj0,&obj1)) goto fail;
    {
        arg1 = (int)(SWIG_As_int(obj0)); 
        if (SWIG_arg_fail(1)) SWIG_fail;
    }
    {
        arg2 = (int)(SWIG_As_int(obj1)); 
        if (SWIG_arg_fail(2)) SWIG_fail;
    }
    result = (int **)matrix_i_alloc(arg1,arg2);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_p_int, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_i_free(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    int ***arg1 = (int ***) 0 ;
    long arg2 ;
    int result;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:matrix_i_free",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_p_p_int, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    {
        arg2 = (long)(SWIG_As_long(obj1)); 
        if (SWIG_arg_fail(2)) SWIG_fail;
    }
    result = (int)matrix_i_free(arg1,arg2);
    
    {
        resultobj = SWIG_From_int((int)(result)); 
    }
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_matrix_d_print(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    FILE *arg1 = (FILE *) 0 ;
    double **arg2 = (double **) 0 ;
    int arg3 ;
    int arg4 ;
    char *arg5 = (char *) 0 ;
    char *arg6 = (char *) 0 ;
    char *arg7 = (char *) 0 ;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    PyObject * obj2 = 0 ;
    PyObject * obj3 = 0 ;
    PyObject * obj4 = 0 ;
    PyObject * obj5 = 0 ;
    PyObject * obj6 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OOOOOOO:matrix_d_print",&obj0,&obj1,&obj2,&obj3,&obj4,&obj5,&obj6)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_FILE, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    SWIG_Python_ConvertPtr(obj1, (void **)&arg2, SWIGTYPE_p_p_double, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(2)) SWIG_fail;
    {
        arg3 = (int)(SWIG_As_int(obj2)); 
        if (SWIG_arg_fail(3)) SWIG_fail;
    }
    {
        arg4 = (int)(SWIG_As_int(obj3)); 
        if (SWIG_arg_fail(4)) SWIG_fail;
    }
    if (!SWIG_AsCharPtr(obj4, (char**)&arg5)) {
        SWIG_arg_fail(5);SWIG_fail;
    }
    if (!SWIG_AsCharPtr(obj5, (char**)&arg6)) {
        SWIG_arg_fail(6);SWIG_fail;
    }
    if (!SWIG_AsCharPtr(obj6, (char**)&arg7)) {
        SWIG_arg_fail(7);SWIG_fail;
    }
    matrix_d_print(arg1,arg2,arg3,arg4,arg5,arg6,arg7);
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_set(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int **arg2 = (int **) 0 ;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:sequence_t_seq_set",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    SWIG_Python_ConvertPtr(obj1, (void **)&arg2, SWIGTYPE_p_p_int, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(2)) SWIG_fail;
    if (arg1) (arg1)->seq = arg2;
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_get(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int **result;
    PyObject * obj0 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"O:sequence_t_seq_get",&obj0)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    result = (int **) ((arg1)->seq);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_p_int, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_states_set(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int **arg2 = (int **) 0 ;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:sequence_t_states_set",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    SWIG_Python_ConvertPtr(obj1, (void **)&arg2, SWIGTYPE_p_p_int, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(2)) SWIG_fail;
    if (arg1) (arg1)->states = arg2;
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_states_get(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int **result;
    PyObject * obj0 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"O:sequence_t_states_get",&obj0)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    result = (int **) ((arg1)->states);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_p_int, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_len_set(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int *arg2 = (int *) 0 ;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:sequence_t_seq_len_set",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    SWIG_Python_ConvertPtr(obj1, (void **)&arg2, SWIGTYPE_p_int, SWIG_POINTER_EXCEPTION | SWIG_POINTER_DISOWN);
    if (SWIG_arg_fail(2)) SWIG_fail;
    if (arg1) (arg1)->seq_len = arg2;
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_len_get(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    int *result;
    PyObject * obj0 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"O:sequence_t_seq_len_get",&obj0)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    result = (int *) ((arg1)->seq_len);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_int, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_label_set(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    long *arg2 = (long *) 0 ;
    PyObject * obj0 = 0 ;
    PyObject * obj1 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"OO:sequence_t_seq_label_set",&obj0,&obj1)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    SWIG_Python_ConvertPtr(obj1, (void **)&arg2, SWIGTYPE_p_long, SWIG_POINTER_EXCEPTION | SWIG_POINTER_DISOWN);
    if (SWIG_arg_fail(2)) SWIG_fail;
    if (arg1) (arg1)->seq_label = arg2;
    
    Py_INCREF(Py_None); resultobj = Py_None;
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_label_get(PyObject *self, PyObject *args) {
    PyObject *resultobj;
    struct sequence_t *arg1 = (struct sequence_t *) 0 ;
    long *result;
    PyObject * obj0 = 0 ;
    
    if(!PyArg_ParseTuple(args,(char *)"O:sequence_t_seq_label_get",&obj0)) goto fail;
    SWIG_Python_ConvertPtr(obj0, (void **)&arg1, SWIGTYPE_p_sequence_t, SWIG_POINTER_EXCEPTION | 0);
    if (SWIG_arg_fail(1)) SWIG_fail;
    result = (long *) ((arg1)->seq_label);
    
    resultobj = SWIG_NewPointerObj((void*)(result), SWIGTYPE_p_long, 0);
    return resultobj;
    fail:
    return NULL;
}


static PyObject *_wrap_sequence_t_seq_id_set(PyObject *self, PyObject *args) {
    PyObject *resultobj