/* Generated by Cython 0.25.2 */

#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
    #error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
    #error Cython requires Python 2.6+ or Python 3.2+.
#else
#define CYTHON_ABI "0_25_2"
#include <stddef.h>
#ifndef offsetof
  #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
#if !defined(WIN32) && !defined(MS_WINDOWS)
  #ifndef __stdcall
    #define __stdcall
  #endif
  #ifndef __cdecl
    #define __cdecl
  #endif
  #ifndef __fastcall
    #define __fastcall
  #endif
#endif
#ifndef DL_IMPORT
  #define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
  #define DL_EXPORT(t) t
#endif
#ifndef HAVE_LONG_LONG
  #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000)
    #define HAVE_LONG_LONG
  #endif
#endif
#ifndef PY_LONG_LONG
  #define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
  #define Py_HUGE_VAL HUGE_VAL
#endif
#ifdef PYPY_VERSION
  #define CYTHON_COMPILING_IN_PYPY 1
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #undef CYTHON_USE_TYPE_SLOTS
  #define CYTHON_USE_TYPE_SLOTS 0
  #undef CYTHON_USE_ASYNC_SLOTS
  #define CYTHON_USE_ASYNC_SLOTS 0
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #undef CYTHON_USE_UNICODE_INTERNALS
  #define CYTHON_USE_UNICODE_INTERNALS 0
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #undef CYTHON_AVOID_BORROWED_REFS
  #define CYTHON_AVOID_BORROWED_REFS 1
  #undef CYTHON_ASSUME_SAFE_MACROS
  #define CYTHON_ASSUME_SAFE_MACROS 0
  #undef CYTHON_UNPACK_METHODS
  #define CYTHON_UNPACK_METHODS 0
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
#elif defined(PYSTON_VERSION)
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 1
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #undef CYTHON_USE_ASYNC_SLOTS
  #define CYTHON_USE_ASYNC_SLOTS 0
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
#else
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 1
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #if PY_MAJOR_VERSION < 3
    #undef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 0
  #elif !defined(CYTHON_USE_ASYNC_SLOTS)
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #if PY_VERSION_HEX < 0x02070000
    #undef CYTHON_USE_PYLONG_INTERNALS
    #define CYTHON_USE_PYLONG_INTERNALS 0
  #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
    #define CYTHON_USE_PYLONG_INTERNALS 1
  #endif
  #ifndef CYTHON_USE_PYLIST_INTERNALS
    #define CYTHON_USE_PYLIST_INTERNALS 1
  #endif
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #if PY_VERSION_HEX < 0x030300F0
    #undef CYTHON_USE_UNICODE_WRITER
    #define CYTHON_USE_UNICODE_WRITER 0
  #elif !defined(CYTHON_USE_UNICODE_WRITER)
    #define CYTHON_USE_UNICODE_WRITER 1
  #endif
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #ifndef CYTHON_FAST_THREAD_STATE
    #define CYTHON_FAST_THREAD_STATE 1
  #endif
  #ifndef CYTHON_FAST_PYCALL
    #define CYTHON_FAST_PYCALL 1
  #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
  #include "longintrepr.h"
  #undef SHIFT
  #undef BASE
  #undef MASK
#endif
#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
  #define Py_OptimizeFlag 0
#endif
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyClass_Type
#else
  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyType_Type
#endif
#ifndef Py_TPFLAGS_CHECKTYPES
  #define Py_TPFLAGS_CHECKTYPES 0
#endif
#ifndef Py_TPFLAGS_HAVE_INDEX
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#ifndef Py_TPFLAGS_HAVE_NEWBUFFER
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#ifndef Py_TPFLAGS_HAVE_FINALIZE
  #define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
#ifndef METH_FASTCALL
  #define METH_FASTCALL 0x80
  typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args,
                                              Py_ssize_t nargs, PyObject *kwnames);
#else
  #define __Pyx_PyCFunctionFast _PyCFunctionFast
#endif
#if CYTHON_FAST_PYCCALL
#define __Pyx_PyFastCFunction_Check(func)\
    ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)))))
#else
#define __Pyx_PyFastCFunction_Check(func) 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
  #define CYTHON_PEP393_ENABLED 1
  #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ?\
                                              0 : _PyUnicode_Ready((PyObject *)(op)))
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   PyUnicode_MAX_CHAR_VALUE(u)
  #define __Pyx_PyUnicode_KIND(u)         PyUnicode_KIND(u)
  #define __Pyx_PyUnicode_DATA(u)         PyUnicode_DATA(u)
  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  PyUnicode_WRITE(k, d, i, ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#else
  #define CYTHON_PEP393_ENABLED 0
  #define PyUnicode_1BYTE_KIND  1
  #define PyUnicode_2BYTE_KIND  2
  #define PyUnicode_4BYTE_KIND  4
  #define __Pyx_PyUnicode_READY(op)       (0)
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
  #define __Pyx_PyUnicode_KIND(u)         (sizeof(Py_UNICODE))
  #define __Pyx_PyUnicode_DATA(u)         ((void*)PyUnicode_AS_UNICODE(u))
  #define __Pyx_PyUnicode_READ(k, d, i)   ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
  #define __Pyx_PyUnicode_Concat(a, b)      PyNumber_Add(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  PyNumber_Add(a, b)
#else
  #define __Pyx_PyUnicode_Concat(a, b)      PyUnicode_Concat(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
      PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
  #define PyUnicode_Contains(u, s)  PySequence_Contains(u, s)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
  #define PyByteArray_Check(obj)  PyObject_TypeCheck(obj, &PyByteArray_Type)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
  #define PyObject_Format(obj, fmt)  PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
  #define PyObject_Malloc(s)   PyMem_Malloc(s)
  #define PyObject_Free(p)     PyMem_Free(p)
  #define PyObject_Realloc(p)  PyMem_Realloc(p)
#endif
#if CYTHON_COMPILING_IN_PYSTON
  #define __Pyx_PyCode_HasFreeVars(co)  PyCode_HasFreeVars(co)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
#else
  #define __Pyx_PyCode_HasFreeVars(co)  (PyCode_GetNumFree(co) > 0)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
#endif
#define __Pyx_PyString_FormatSafe(a, b)   ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b)  ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyString_Format(a, b)  PyUnicode_Format(a, b)
#else
  #define __Pyx_PyString_Format(a, b)  PyString_Format(a, b)
#endif
#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
  #define PyObject_ASCII(o)            PyObject_Repr(o)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBaseString_Type            PyUnicode_Type
  #define PyStringObject               PyUnicodeObject
  #define PyString_Type                PyUnicode_Type
  #define PyString_Check               PyUnicode_Check
  #define PyString_CheckExact          PyUnicode_CheckExact
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
  #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
#else
  #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
  #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
#endif
#ifndef PySet_CheckExact
  #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
#if PY_MAJOR_VERSION >= 3
  #define PyIntObject                  PyLongObject
  #define PyInt_Type                   PyLong_Type
  #define PyInt_Check(op)              PyLong_Check(op)
  #define PyInt_CheckExact(op)         PyLong_CheckExact(op)
  #define PyInt_FromString             PyLong_FromString
  #define PyInt_FromUnicode            PyLong_FromUnicode
  #define PyInt_FromLong               PyLong_FromLong
  #define PyInt_FromSize_t             PyLong_FromSize_t
  #define PyInt_FromSsize_t            PyLong_FromSsize_t
  #define PyInt_AsLong                 PyLong_AsLong
  #define PyInt_AS_LONG                PyLong_AS_LONG
  #define PyInt_AsSsize_t              PyLong_AsSsize_t
  #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
  #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
  #define PyNumber_Int                 PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBoolObject                 PyLongObject
#endif
#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
  #ifndef PyUnicode_InternFromString
    #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
  #endif
#endif
#if PY_VERSION_HEX < 0x030200A4
  typedef long Py_hash_t;
  #define __Pyx_PyInt_FromHash_t PyInt_FromLong
  #define __Pyx_PyInt_AsHash_t   PyInt_AsLong
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#else
  #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
#if CYTHON_USE_ASYNC_SLOTS
  #if PY_VERSION_HEX >= 0x030500B1
    #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
    #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
  #else
    typedef struct {
        unaryfunc am_await;
        unaryfunc am_aiter;
        unaryfunc am_anext;
    } __Pyx_PyAsyncMethodsStruct;
    #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
  #endif
#else
  #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef CYTHON_RESTRICT
  #if defined(__GNUC__)
    #define CYTHON_RESTRICT __restrict__
  #elif defined(_MSC_VER) && _MSC_VER >= 1400
    #define CYTHON_RESTRICT __restrict
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_RESTRICT restrict
  #else
    #define CYTHON_RESTRICT
  #endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
#   if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
#     define CYTHON_UNUSED __attribute__ ((__unused__))
#   else
#     define CYTHON_UNUSED
#   endif
# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
#   define CYTHON_UNUSED __attribute__ ((__unused__))
# else
#   define CYTHON_UNUSED
# endif
#endif
#ifndef CYTHON_MAYBE_UNUSED_VAR
#  if defined(__cplusplus)
     template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
#  else
#    define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
#  endif
#endif
#ifndef CYTHON_NCP_UNUSED
# if CYTHON_COMPILING_IN_CPYTHON
#  define CYTHON_NCP_UNUSED
# else
#  define CYTHON_NCP_UNUSED CYTHON_UNUSED
# endif
#endif
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)

#ifndef __cplusplus
  #error "Cython files generated with the C++ option must be compiled with a C++ compiler."
#endif
#ifndef CYTHON_INLINE
  #if defined(__clang__)
    #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
  #else
    #define CYTHON_INLINE inline
  #endif
#endif
template<typename T>
void __Pyx_call_destructor(T& x) {
    x.~T();
}
template<typename T>
class __Pyx_FakeReference {
  public:
    __Pyx_FakeReference() : ptr(NULL) { }
    __Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { }
    T *operator->() { return ptr; }
    T *operator&() { return ptr; }
    operator T&() { return *ptr; }
    template<typename U> bool operator ==(U other) { return *ptr == other; }
    template<typename U> bool operator !=(U other) { return *ptr != other; }
  private:
    T *ptr;
};

#if defined(WIN32) || defined(MS_WINDOWS)
  #define _USE_MATH_DEFINES
#endif
#include <math.h>
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
  float value;
  memset(&value, 0xFF, sizeof(value));
  return value;
}
#endif
#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
#define __Pyx_truncl trunc
#else
#define __Pyx_truncl truncl
#endif


#define __PYX_ERR(f_index, lineno, Ln_error) \
{ \
  __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \
}

#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
#else
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_Divide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(x,y)
#endif

#ifndef __PYX_EXTERN_C
  #ifdef __cplusplus
    #define __PYX_EXTERN_C extern "C"
  #else
    #define __PYX_EXTERN_C extern
  #endif
#endif

#define __PYX_HAVE__CGAT__Components
#define __PYX_HAVE_API__CGAT__Components
#include "connected_components.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */

#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
#endif

typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;

#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#define __Pyx_uchar_cast(c) ((unsigned char)c)
#define __Pyx_long_cast(x) ((long)x)
#define __Pyx_fits_Py_ssize_t(v, type, is_signed)  (\
    (sizeof(type) < sizeof(Py_ssize_t))  ||\
    (sizeof(type) > sizeof(Py_ssize_t) &&\
          likely(v < (type)PY_SSIZE_T_MAX ||\
                 v == (type)PY_SSIZE_T_MAX)  &&\
          (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
                                v == (type)PY_SSIZE_T_MIN)))  ||\
    (sizeof(type) == sizeof(Py_ssize_t) &&\
          (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
                               v == (type)PY_SSIZE_T_MAX)))  )
#if defined (__cplusplus) && __cplusplus >= 201103L
    #include <cstdlib>
    #define __Pyx_sst_abs(value) std::abs(value)
#elif SIZEOF_INT >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) abs(value)
#elif SIZEOF_LONG >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) labs(value)
#elif defined (_MSC_VER) && defined (_M_X64)
    #define __Pyx_sst_abs(value) _abs64(value)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define __Pyx_sst_abs(value) llabs(value)
#elif defined (__GNUC__)
    #define __Pyx_sst_abs(value) __builtin_llabs(value)
#else
    #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
#endif
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
#define __Pyx_PyBytes_FromString        PyBytes_FromString
#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
#if PY_MAJOR_VERSION < 3
    #define __Pyx_PyStr_FromString        __Pyx_PyBytes_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#else
    #define __Pyx_PyStr_FromString        __Pyx_PyUnicode_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
#endif
#define __Pyx_PyObject_AsSString(s)    ((signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsUString(s)    ((unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_FromCString(s)  __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromCString(s)   __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
#if PY_MAJOR_VERSION < 3
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
{
    const Py_UNICODE *u_end = u;
    while (*u_end++) ;
    return (size_t)(u_end - u - 1);
}
#else
#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
#endif
#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
#else
#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
#endif
#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    const char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    if (strcmp(default_encoding_c, "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        char ascii_chars[128];
        int c;
        for (c = 0; c < 128; c++) {
            ascii_chars[c] = c;
        }
        __Pyx_sys_getdefaultencoding_not_ascii = 1;
        ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
        if (!ascii_chars_u) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
            PyErr_Format(
                PyExc_ValueError,
                "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
        Py_DECREF(ascii_chars_u);
        Py_DECREF(ascii_chars_b);
    }
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return -1;
}
#endif
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
#else
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
    if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
    strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    return -1;
}
#endif
#endif


/* Test for GCC > 2.95 */
#if defined(__GNUC__)     && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
  #define likely(x)   __builtin_expect(!!(x), 1)
  #define unlikely(x) __builtin_expect(!!(x), 0)
#else /* !__GNUC__ or GCC < 2.95 */
  #define likely(x)   (x)
  #define unlikely(x) (x)
#endif /* __GNUC__ */

static PyObject *__pyx_m;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
static PyObject *__pyx_empty_unicode;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;


static const char *__pyx_f[] = {
  "CGAT/Components/Components.pyx",
};

/*--- Type declarations ---*/
struct __pyx_obj_4CGAT_10Components_SComponents;
struct __pyx_obj_4CGAT_10Components_IComponents;

/* "CGAT/Components/Components.pyx":52
 *     void del_IComponents "delete" (cIComponents * c)
 * 
 * cdef class SComponents:             # <<<<<<<<<<<<<<
 *     """Components for a graph with string indices."""
 *     cdef cSComponents *thisptr      # hold a C++ instance which we're wrapping
 */
struct __pyx_obj_4CGAT_10Components_SComponents {
  PyObject_HEAD
  CharComponents *thisptr;
};


/* "CGAT/Components/Components.pyx":104
 *         self.thisptr.reset()
 * 
 * cdef class IComponents:             # <<<<<<<<<<<<<<
 *     """Components for a graph with numeric indices."""
 *     cdef cIComponents *thisptr      # hold a C++ instance which we're wrapping
 */
struct __pyx_obj_4CGAT_10Components_IComponents {
  PyObject_HEAD
  IntComponents *thisptr;
};


/* --- Runtime support code (head) --- */
/* Refnanny.proto */
#ifndef CYTHON_REFNANNY
  #define CYTHON_REFNANNY 0
#endif
#if CYTHON_REFNANNY
  typedef struct {
    void (*INCREF)(void*, PyObject*, int);
    void (*DECREF)(void*, PyObject*, int);
    void (*GOTREF)(void*, PyObject*, int);
    void (*GIVEREF)(void*, PyObject*, int);
    void* (*SetupContext)(const char*, int, const char*);
    void (*FinishContext)(void**);
  } __Pyx_RefNannyAPIStruct;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
  #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
  #define __Pyx_RefNannySetupContext(name, acquire_gil)\
          if (acquire_gil) {\
              PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
              PyGILState_Release(__pyx_gilstate_save);\
          } else {\
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
          }
#else
  #define __Pyx_RefNannySetupContext(name, acquire_gil)\
          __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
#endif
  #define __Pyx_RefNannyFinishContext()\
          __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
  #define __Pyx_INCREF(r)  __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_DECREF(r)  __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GOTREF(r)  __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_XINCREF(r)  do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
  #define __Pyx_XDECREF(r)  do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
  #define __Pyx_XGOTREF(r)  do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
  #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
  #define __Pyx_RefNannyDeclarations
  #define __Pyx_RefNannySetupContext(name, acquire_gil)
  #define __Pyx_RefNannyFinishContext()
  #define __Pyx_INCREF(r) Py_INCREF(r)
  #define __Pyx_DECREF(r) Py_DECREF(r)
  #define __Pyx_GOTREF(r)
  #define __Pyx_GIVEREF(r)
  #define __Pyx_XINCREF(r) Py_XINCREF(r)
  #define __Pyx_XDECREF(r) Py_XDECREF(r)
  #define __Pyx_XGOTREF(r)
  #define __Pyx_XGIVEREF(r)
#endif
#define __Pyx_XDECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_XDECREF(tmp);\
    } while (0)
#define __Pyx_DECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_DECREF(tmp);\
    } while (0)
#define __Pyx_CLEAR(r)    do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r)   do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)

/* PyObjectGetAttrStr.proto */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
    PyTypeObject* tp = Py_TYPE(obj);
    if (likely(tp->tp_getattro))
        return tp->tp_getattro(obj, attr_name);
#if PY_MAJOR_VERSION < 3
    if (likely(tp->tp_getattr))
        return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
#endif
    return PyObject_GetAttr(obj, attr_name);
}
#else
#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
#endif

/* GetBuiltinName.proto */
static PyObject *__Pyx_GetBuiltinName(PyObject *name);

/* RaiseArgTupleInvalid.proto */
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
    Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);

/* KeywordStringCheck.proto */
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed);

/* RaiseDoubleKeywords.proto */
static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);

/* ParseKeywords.proto */
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
    PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
    const char* function_name);

/* PyDictContains.proto */
static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) {
    int result = PyDict_Contains(dict, item);
    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}

/* ListAppend.proto */
#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
    PyListObject* L = (PyListObject*) list;
    Py_ssize_t len = Py_SIZE(list);
    if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
        Py_INCREF(x);
        PyList_SET_ITEM(list, len, x);
        Py_SIZE(list) = len+1;
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif

/* PyCFunctionFastCall.proto */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
#else
#define __Pyx_PyCFunction_FastCall(func, args, nargs)  (assert(0), NULL)
#endif

/* PyFunctionFastCall.proto */
#if CYTHON_FAST_PYCALL
#define __Pyx_PyFunction_FastCall(func, args, nargs)\
    __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs);
#else
#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
#endif
#endif

/* PyObjectCall.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
#else
#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
#endif

/* PyObjectCallMethO.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
#endif

/* PyObjectCallOneArg.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);

/* PyObjectCallMethod1.proto */
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);

/* append.proto */
static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x);

/* DictGetItem.proto */
#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
    PyObject *value;
    value = PyDict_GetItemWithError(d, key);
    if (unlikely(!value)) {
        if (!PyErr_Occurred()) {
            PyObject* args = PyTuple_Pack(1, key);
            if (likely(args))
                PyErr_SetObject(PyExc_KeyError, args);
            Py_XDECREF(args);
        }
        return NULL;
    }
    Py_INCREF(value);
    return value;
}
#else
    #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif

/* py_dict_values.proto */
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d);

/* UnpackUnboundCMethod.proto */
typedef struct {
    PyObject *type;
    PyObject **method_name;
    PyCFunction func;
    PyObject *method;
    int flag;
} __Pyx_CachedCFunction;

/* CallUnboundCMethod0.proto */
static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self);
#if CYTHON_COMPILING_IN_CPYTHON
#define __Pyx_CallUnboundCMethod0(cfunc, self)\
    ((likely((cfunc)->func)) ?\
        (likely((cfunc)->flag == METH_NOARGS) ?  (*((cfunc)->func))(self, NULL) :\
         (likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ?  ((*(PyCFunctionWithKeywords)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\
             ((cfunc)->flag == METH_VARARGS ?  (*((cfunc)->func))(self, __pyx_empty_tuple) :\
              (PY_VERSION_HEX >= 0x030600B1 && (cfunc)->flag == METH_FASTCALL ?  (*(__Pyx_PyCFunctionFast)(cfunc)->func)(self, &PyTuple_GET_ITEM(__pyx_empty_tuple, 0), 0, NULL) :\
                __Pyx__CallUnboundCMethod0(cfunc, self))))) :\
        __Pyx__CallUnboundCMethod0(cfunc, self))
#else
#define __Pyx_CallUnboundCMethod0(cfunc, self)  __Pyx__CallUnboundCMethod0(cfunc, self)
#endif

/* CodeObjectCache.proto */
typedef struct {
    PyCodeObject* code_object;
    int code_line;
} __Pyx_CodeObjectCacheEntry;
struct __Pyx_CodeObjectCache {
    int count;
    int max_count;
    __Pyx_CodeObjectCacheEntry* entries;
};
static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
static PyCodeObject *__pyx_find_code_object(int code_line);
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);

/* AddTraceback.proto */
static void __Pyx_AddTraceback(const char *funcname, int c_line,
                               int py_line, const char *filename);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);

/* CIntFromPy.proto */
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);

/* CIntFromPy.proto */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);

/* CheckBinaryVersion.proto */
static int __Pyx_check_binary_version(void);

/* InitStrings.proto */
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);


/* Module declarations from 'CGAT.Components' */
static PyTypeObject *__pyx_ptype_4CGAT_10Components_SComponents = 0;
static PyTypeObject *__pyx_ptype_4CGAT_10Components_IComponents = 0;
#define __Pyx_MODULE_NAME "CGAT.Components"
int __pyx_module_is_main_CGAT__Components = 0;

/* Implementation of 'CGAT.Components' */
static PyObject *__pyx_builtin_range;
static const char __pyx_k_a[] = "a";
static const char __pyx_k_b[] = "b";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_append[] = "append";
static const char __pyx_k_values[] = "values";
static const char __pyx_k_Class_to_compute_connected_compo[] = "Class to compute connected components\n\nConnected components list all nodes in a graph that\nare connected either directly or via intermediate egdes.\n\nThe module computes connected components using the\nalgorithm listed by Sedgwick: Algorithms in C, p507.\nComponents are computed in an on-line fashion, so that\nthe whole graph is not kept in memory.\n\nUSAGE:\n\n# create object for string identifiers\n>>> x = SComponents()\n\n# add edges\n>>> x.add( \"1\", \"2\" )\n>>> x.add( \"1\", \"3\" )\n>>> x.add( \"4\", \"5\" )\n\n# retrieve components\n>>> print x.getComponents()\n\nThis is a cython extension class.";
static PyObject *__pyx_n_s_a;
static PyObject *__pyx_n_s_append;
static PyObject *__pyx_n_s_b;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_values;
static int __pyx_pf_4CGAT_10Components_11SComponents___cinit__(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self); /* proto */
static void __pyx_pf_4CGAT_10Components_11SComponents_2__dealloc__(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_4add(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_6getNumNodes(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_8getComponent(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_10getToken(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_12getIndex(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_token); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_14get(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_v); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_16getComponents(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_18reset(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self); /* proto */
static int __pyx_pf_4CGAT_10Components_11IComponents___cinit__(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self); /* proto */
static void __pyx_pf_4CGAT_10Components_11IComponents_2__dealloc__(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_4add(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_6getNumNodes(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_8getComponent(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_10getToken(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_12getIndex(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_token); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_14get(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_v); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_16getComponents(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_18reset(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self); /* proto */
static PyObject *__pyx_tp_new_4CGAT_10Components_SComponents(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_4CGAT_10Components_IComponents(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_values = {0, &__pyx_n_s_values, 0, 0, 0};

/* "CGAT/Components/Components.pyx":55
 *     """Components for a graph with string indices."""
 *     cdef cSComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):             # <<<<<<<<<<<<<<
 *         self.thisptr = new_SComponents()
 *     def __dealloc__(self):
 */

/* Python wrapper */
static int __pyx_pw_4CGAT_10Components_11SComponents_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_4CGAT_10Components_11SComponents_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
    __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
  if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents___cinit__(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_4CGAT_10Components_11SComponents___cinit__(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "CGAT/Components/Components.pyx":56
 *     cdef cSComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):
 *         self.thisptr = new_SComponents()             # <<<<<<<<<<<<<<
 *     def __dealloc__(self):
 *         del_SComponents(self.thisptr)
 */
  __pyx_v_self->thisptr = new CharComponents();

  /* "CGAT/Components/Components.pyx":55
 *     """Components for a graph with string indices."""
 *     cdef cSComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):             # <<<<<<<<<<<<<<
 *         self.thisptr = new_SComponents()
 *     def __dealloc__(self):
 */

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":57
 *     def __cinit__(self ):
 *         self.thisptr = new_SComponents()
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         del_SComponents(self.thisptr)
 *     def add(self, a, b):
 */

/* Python wrapper */
static void __pyx_pw_4CGAT_10Components_11SComponents_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_4CGAT_10Components_11SComponents_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_4CGAT_10Components_11SComponents_2__dealloc__(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_4CGAT_10Components_11SComponents_2__dealloc__(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "CGAT/Components/Components.pyx":58
 *         self.thisptr = new_SComponents()
 *     def __dealloc__(self):
 *         del_SComponents(self.thisptr)             # <<<<<<<<<<<<<<
 *     def add(self, a, b):
 *         """add an edge between nodes a and b
 */
  delete(__pyx_v_self->thisptr);

  /* "CGAT/Components/Components.pyx":57
 *     def __cinit__(self ):
 *         self.thisptr = new_SComponents()
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         del_SComponents(self.thisptr)
 *     def add(self, a, b):
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "CGAT/Components/Components.pyx":59
 *     def __dealloc__(self):
 *         del_SComponents(self.thisptr)
 *     def add(self, a, b):             # <<<<<<<<<<<<<<
 *         """add an edge between nodes a and b
 *         return True, if the link joins two previously disconnected componenents.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_5add(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_4add[] = "add an edge between nodes a and b\n        return True, if the link joins two previously disconnected componenents.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_5add(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_a = 0;
  PyObject *__pyx_v_b = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_a,&__pyx_n_s_b,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_a)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_b)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add", 1, 2, 2, 1); __PYX_ERR(0, 59, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add") < 0)) __PYX_ERR(0, 59, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_a = values[0];
    __pyx_v_b = values[1];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("add", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 59, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("CGAT.Components.SComponents.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_4add(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self), __pyx_v_a, __pyx_v_b);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_4add(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  char *__pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  __Pyx_RefNannySetupContext("add", 0);

  /* "CGAT/Components/Components.pyx":63
 *         return True, if the link joins two previously disconnected componenents.
 *         """
 *         return self.thisptr.add(a, b) > 0             # <<<<<<<<<<<<<<
 *     def getNumNodes(self):
 *         """return the number of nodes in the graph."""
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_a); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 63, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyObject_AsString(__pyx_v_b); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) __PYX_ERR(0, 63, __pyx_L1_error)
  __pyx_t_3 = __Pyx_PyBool_FromLong((__pyx_v_self->thisptr->add(__pyx_t_1, __pyx_t_2) > 0)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 63, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_r = __pyx_t_3;
  __pyx_t_3 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":59
 *     def __dealloc__(self):
 *         del_SComponents(self.thisptr)
 *     def add(self, a, b):             # <<<<<<<<<<<<<<
 *         """add an edge between nodes a and b
 *         return True, if the link joins two previously disconnected componenents.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("CGAT.Components.SComponents.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":64
 *         """
 *         return self.thisptr.add(a, b) > 0
 *     def getNumNodes(self):             # <<<<<<<<<<<<<<
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_7getNumNodes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_6getNumNodes[] = "return the number of nodes in the graph.";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_7getNumNodes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getNumNodes (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_6getNumNodes(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_6getNumNodes(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("getNumNodes", 0);

  /* "CGAT/Components/Components.pyx":66
 *     def getNumNodes(self):
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()             # <<<<<<<<<<<<<<
 *     def getComponent(self, id):
 *         """return component an id belongs to.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getNumNodes()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 66, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":64
 *         """
 *         return self.thisptr.add(a, b) > 0
 *     def getNumNodes(self):             # <<<<<<<<<<<<<<
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("CGAT.Components.SComponents.getNumNodes", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":67
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 *     def getComponent(self, id):             # <<<<<<<<<<<<<<
 *         """return component an id belongs to.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_9getComponent(PyObject *__pyx_v_self, PyObject *__pyx_v_id); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_8getComponent[] = "return component an id belongs to.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_9getComponent(PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getComponent (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_8getComponent(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self), ((PyObject *)__pyx_v_id));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_8getComponent(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getComponent", 0);

  /* "CGAT/Components/Components.pyx":71
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.getComponent(id)             # <<<<<<<<<<<<<<
 *     def getToken(self, id):
 *         """return token for an id.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_id); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 71, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getComponent(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 71, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":67
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 *     def getComponent(self, id):             # <<<<<<<<<<<<<<
 *         """return component an id belongs to.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.SComponents.getComponent", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":72
 *         """
 *         return self.thisptr.getComponent(id)
 *     def getToken(self, id):             # <<<<<<<<<<<<<<
 *         """return token for an id.
 *         """
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_11getToken(PyObject *__pyx_v_self, PyObject *__pyx_v_id); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_10getToken[] = "return token for an id.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_11getToken(PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getToken (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_10getToken(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self), ((PyObject *)__pyx_v_id));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_10getToken(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getToken", 0);

  /* "CGAT/Components/Components.pyx":75
 *         """return token for an id.
 *         """
 *         return self.thisptr.getToken(id)             # <<<<<<<<<<<<<<
 *     def getIndex(self, token):
 *         """return id for a token.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_id); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 75, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_self->thisptr->getToken(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 75, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":72
 *         """
 *         return self.thisptr.getComponent(id)
 *     def getToken(self, id):             # <<<<<<<<<<<<<<
 *         """return token for an id.
 *         """
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.SComponents.getToken", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":76
 *         """
 *         return self.thisptr.getToken(id)
 *     def getIndex(self, token):             # <<<<<<<<<<<<<<
 *         """return id for a token.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_13getIndex(PyObject *__pyx_v_self, PyObject *__pyx_v_token); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_12getIndex[] = "return id for a token.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_13getIndex(PyObject *__pyx_v_self, PyObject *__pyx_v_token) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getIndex (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_12getIndex(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self), ((PyObject *)__pyx_v_token));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_12getIndex(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_token) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getIndex", 0);

  /* "CGAT/Components/Components.pyx":80
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.getIndex(token)             # <<<<<<<<<<<<<<
 *     def get(self, v):
 *         """return component for a token.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_token); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 80, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getIndex(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 80, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":76
 *         """
 *         return self.thisptr.getToken(id)
 *     def getIndex(self, token):             # <<<<<<<<<<<<<<
 *         """return id for a token.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.SComponents.getIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":81
 *         """
 *         return self.thisptr.getIndex(token)
 *     def get(self, v):             # <<<<<<<<<<<<<<
 *         """return component for a token.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_15get(PyObject *__pyx_v_self, PyObject *__pyx_v_v); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_14get[] = "return component for a token.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_15get(PyObject *__pyx_v_self, PyObject *__pyx_v_v) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_14get(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self), ((PyObject *)__pyx_v_v));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_14get(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self, PyObject *__pyx_v_v) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("get", 0);

  /* "CGAT/Components/Components.pyx":85
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.get(v)             # <<<<<<<<<<<<<<
 * 
 *     def getComponents(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_v); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 85, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->get(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 85, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":81
 *         """
 *         return self.thisptr.getIndex(token)
 *     def get(self, v):             # <<<<<<<<<<<<<<
 *         """return component for a token.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.SComponents.get", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":87
 *         return self.thisptr.get(v)
 * 
 *     def getComponents(self):             # <<<<<<<<<<<<<<
 *         """return all connected components as a list of lists."""
 *         components = {}
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_17getComponents(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_16getComponents[] = "return all connected components as a list of lists.";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_17getComponents(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getComponents (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_16getComponents(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_16getComponents(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self) {
  PyObject *__pyx_v_components = NULL;
  long __pyx_v_x;
  int __pyx_v_c;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  long __pyx_t_2;
  long __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  __Pyx_RefNannySetupContext("getComponents", 0);

  /* "CGAT/Components/Components.pyx":89
 *     def getComponents(self):
 *         """return all connected components as a list of lists."""
 *         components = {}             # <<<<<<<<<<<<<<
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 89, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_components = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "CGAT/Components/Components.pyx":91
 *         components = {}
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):             # <<<<<<<<<<<<<<
 *             c = self.thisptr.getComponent(x)
 *             if c not in components:
 */
  __pyx_t_2 = (__pyx_v_self->thisptr->getNumNodes() + 1);
  for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_x = __pyx_t_3;

    /* "CGAT/Components/Components.pyx":92
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 *             c = self.thisptr.getComponent(x)             # <<<<<<<<<<<<<<
 *             if c not in components:
 *                 components[c] = []
 */
    __pyx_v_c = __pyx_v_self->thisptr->getComponent(__pyx_v_x);

    /* "CGAT/Components/Components.pyx":93
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 *             c = self.thisptr.getComponent(x)
 *             if c not in components:             # <<<<<<<<<<<<<<
 *                 components[c] = []
 *             components[c].append(self.thisptr.getToken(x))
 */
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 93, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_4 = (__Pyx_PyDict_ContainsTF(__pyx_t_1, __pyx_v_components, Py_NE)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 93, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_5 = (__pyx_t_4 != 0);
    if (__pyx_t_5) {

      /* "CGAT/Components/Components.pyx":94
 *             c = self.thisptr.getComponent(x)
 *             if c not in components:
 *                 components[c] = []             # <<<<<<<<<<<<<<
 *             components[c].append(self.thisptr.getToken(x))
 * 
 */
      __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 94, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 94, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      if (unlikely(PyDict_SetItem(__pyx_v_components, __pyx_t_6, __pyx_t_1) < 0)) __PYX_ERR(0, 94, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

      /* "CGAT/Components/Components.pyx":93
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 *             c = self.thisptr.getComponent(x)
 *             if c not in components:             # <<<<<<<<<<<<<<
 *                 components[c] = []
 *             components[c].append(self.thisptr.getToken(x))
 */
    }

    /* "CGAT/Components/Components.pyx":95
 *             if c not in components:
 *                 components[c] = []
 *             components[c].append(self.thisptr.getToken(x))             # <<<<<<<<<<<<<<
 * 
 *         return components.values()
 */
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 95, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_components, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 95, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_self->thisptr->getToken(__pyx_v_x)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 95, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_7 = __Pyx_PyObject_Append(__pyx_t_6, __pyx_t_1); if (unlikely(__pyx_t_7 == -1)) __PYX_ERR(0, 95, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "CGAT/Components/Components.pyx":97
 *             components[c].append(self.thisptr.getToken(x))
 * 
 *         return components.values()             # <<<<<<<<<<<<<<
 * 
 *     def reset(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_components); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 97, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":87
 *         return self.thisptr.get(v)
 * 
 *     def getComponents(self):             # <<<<<<<<<<<<<<
 *         """return all connected components as a list of lists."""
 *         components = {}
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("CGAT.Components.SComponents.getComponents", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_components);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":99
 *         return components.values()
 * 
 *     def reset(self):             # <<<<<<<<<<<<<<
 *         """clear graph.
 *         """
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_19reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11SComponents_18reset[] = "clear graph.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11SComponents_19reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("reset (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11SComponents_18reset(((struct __pyx_obj_4CGAT_10Components_SComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11SComponents_18reset(struct __pyx_obj_4CGAT_10Components_SComponents *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("reset", 0);

  /* "CGAT/Components/Components.pyx":102
 *         """clear graph.
 *         """
 *         self.thisptr.reset()             # <<<<<<<<<<<<<<
 * 
 * cdef class IComponents:
 */
  __pyx_v_self->thisptr->reset();

  /* "CGAT/Components/Components.pyx":99
 *         return components.values()
 * 
 *     def reset(self):             # <<<<<<<<<<<<<<
 *         """clear graph.
 *         """
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":107
 *     """Components for a graph with numeric indices."""
 *     cdef cIComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):             # <<<<<<<<<<<<<<
 *         self.thisptr = new_IComponents()
 *     def __dealloc__(self):
 */

/* Python wrapper */
static int __pyx_pw_4CGAT_10Components_11IComponents_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_4CGAT_10Components_11IComponents_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
    __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
  if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents___cinit__(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_4CGAT_10Components_11IComponents___cinit__(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "CGAT/Components/Components.pyx":108
 *     cdef cIComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):
 *         self.thisptr = new_IComponents()             # <<<<<<<<<<<<<<
 *     def __dealloc__(self):
 *         del_IComponents(self.thisptr)
 */
  __pyx_v_self->thisptr = new IntComponents();

  /* "CGAT/Components/Components.pyx":107
 *     """Components for a graph with numeric indices."""
 *     cdef cIComponents *thisptr      # hold a C++ instance which we're wrapping
 *     def __cinit__(self ):             # <<<<<<<<<<<<<<
 *         self.thisptr = new_IComponents()
 *     def __dealloc__(self):
 */

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":109
 *     def __cinit__(self ):
 *         self.thisptr = new_IComponents()
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         del_IComponents(self.thisptr)
 *     def add(self, a,b):
 */

/* Python wrapper */
static void __pyx_pw_4CGAT_10Components_11IComponents_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_4CGAT_10Components_11IComponents_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_4CGAT_10Components_11IComponents_2__dealloc__(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_4CGAT_10Components_11IComponents_2__dealloc__(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "CGAT/Components/Components.pyx":110
 *         self.thisptr = new_IComponents()
 *     def __dealloc__(self):
 *         del_IComponents(self.thisptr)             # <<<<<<<<<<<<<<
 *     def add(self, a,b):
 *         """add an edge between nodes a and b
 */
  delete(__pyx_v_self->thisptr);

  /* "CGAT/Components/Components.pyx":109
 *     def __cinit__(self ):
 *         self.thisptr = new_IComponents()
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         del_IComponents(self.thisptr)
 *     def add(self, a,b):
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "CGAT/Components/Components.pyx":111
 *     def __dealloc__(self):
 *         del_IComponents(self.thisptr)
 *     def add(self, a,b):             # <<<<<<<<<<<<<<
 *         """add an edge between nodes a and b
 *         return True, if the link joins two previously disconnected componenents.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_5add(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_4add[] = "add an edge between nodes a and b\n        return True, if the link joins two previously disconnected componenents.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_5add(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_a = 0;
  PyObject *__pyx_v_b = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_a,&__pyx_n_s_b,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_a)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_b)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add", 1, 2, 2, 1); __PYX_ERR(0, 111, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add") < 0)) __PYX_ERR(0, 111, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_a = values[0];
    __pyx_v_b = values[1];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("add", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 111, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("CGAT.Components.IComponents.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_4add(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self), __pyx_v_a, __pyx_v_b);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_4add(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  __Pyx_RefNannySetupContext("add", 0);

  /* "CGAT/Components/Components.pyx":115
 *         return True, if the link joins two previously disconnected componenents.
 *         """
 *         return self.thisptr.add( a, b ) > 0             # <<<<<<<<<<<<<<
 *     def getNumNodes(self):
 *         """return the number of nodes in the graph."""
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_a); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 115, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_v_b); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 115, __pyx_L1_error)
  __pyx_t_3 = __Pyx_PyBool_FromLong((__pyx_v_self->thisptr->add(__pyx_t_1, __pyx_t_2) > 0)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 115, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_r = __pyx_t_3;
  __pyx_t_3 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":111
 *     def __dealloc__(self):
 *         del_IComponents(self.thisptr)
 *     def add(self, a,b):             # <<<<<<<<<<<<<<
 *         """add an edge between nodes a and b
 *         return True, if the link joins two previously disconnected componenents.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("CGAT.Components.IComponents.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":116
 *         """
 *         return self.thisptr.add( a, b ) > 0
 *     def getNumNodes(self):             # <<<<<<<<<<<<<<
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_7getNumNodes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_6getNumNodes[] = "return the number of nodes in the graph.";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_7getNumNodes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getNumNodes (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_6getNumNodes(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_6getNumNodes(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("getNumNodes", 0);

  /* "CGAT/Components/Components.pyx":118
 *     def getNumNodes(self):
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()             # <<<<<<<<<<<<<<
 *     def getComponent(self, id):
 *         """return component an id belongs to.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getNumNodes()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 118, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":116
 *         """
 *         return self.thisptr.add( a, b ) > 0
 *     def getNumNodes(self):             # <<<<<<<<<<<<<<
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("CGAT.Components.IComponents.getNumNodes", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":119
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 *     def getComponent(self, id):             # <<<<<<<<<<<<<<
 *         """return component an id belongs to.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_9getComponent(PyObject *__pyx_v_self, PyObject *__pyx_v_id); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_8getComponent[] = "return component an id belongs to.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_9getComponent(PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getComponent (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_8getComponent(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self), ((PyObject *)__pyx_v_id));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_8getComponent(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getComponent", 0);

  /* "CGAT/Components/Components.pyx":123
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.getComponent(id)             # <<<<<<<<<<<<<<
 *     def getToken(self, id):
 *         """return token for an id.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_id); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 123, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getComponent(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 123, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":119
 *         """return the number of nodes in the graph."""
 *         return self.thisptr.getNumNodes()
 *     def getComponent(self, id):             # <<<<<<<<<<<<<<
 *         """return component an id belongs to.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.IComponents.getComponent", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":124
 *         """
 *         return self.thisptr.getComponent(id)
 *     def getToken(self, id):             # <<<<<<<<<<<<<<
 *         """return token for an id.
 *         """
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_11getToken(PyObject *__pyx_v_self, PyObject *__pyx_v_id); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_10getToken[] = "return token for an id.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_11getToken(PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getToken (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_10getToken(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self), ((PyObject *)__pyx_v_id));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_10getToken(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_id) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getToken", 0);

  /* "CGAT/Components/Components.pyx":127
 *         """return token for an id.
 *         """
 *         return self.thisptr.getToken(id)             # <<<<<<<<<<<<<<
 *     def getIndex(self, token):
 *         """return id for a token.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_id); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 127, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getToken(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 127, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":124
 *         """
 *         return self.thisptr.getComponent(id)
 *     def getToken(self, id):             # <<<<<<<<<<<<<<
 *         """return token for an id.
 *         """
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.IComponents.getToken", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":128
 *         """
 *         return self.thisptr.getToken(id)
 *     def getIndex(self, token):             # <<<<<<<<<<<<<<
 *         """return id for a token.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_13getIndex(PyObject *__pyx_v_self, PyObject *__pyx_v_token); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_12getIndex[] = "return id for a token.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_13getIndex(PyObject *__pyx_v_self, PyObject *__pyx_v_token) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getIndex (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_12getIndex(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self), ((PyObject *)__pyx_v_token));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_12getIndex(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_token) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("getIndex", 0);

  /* "CGAT/Components/Components.pyx":132
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.getIndex(token)             # <<<<<<<<<<<<<<
 *     def get(self, v):
 *         """return component for a token.
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_token); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 132, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getIndex(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 132, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":128
 *         """
 *         return self.thisptr.getToken(id)
 *     def getIndex(self, token):             # <<<<<<<<<<<<<<
 *         """return id for a token.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.IComponents.getIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":133
 *         """
 *         return self.thisptr.getIndex(token)
 *     def get(self, v):             # <<<<<<<<<<<<<<
 *         """return component for a token.
 *         If the token is unknown, return 0.
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_15get(PyObject *__pyx_v_self, PyObject *__pyx_v_v); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_14get[] = "return component for a token.\n        If the token is unknown, return 0.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_15get(PyObject *__pyx_v_self, PyObject *__pyx_v_v) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_14get(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self), ((PyObject *)__pyx_v_v));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_14get(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self, PyObject *__pyx_v_v) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("get", 0);

  /* "CGAT/Components/Components.pyx":137
 *         If the token is unknown, return 0.
 *         """
 *         return self.thisptr.get(v)             # <<<<<<<<<<<<<<
 * 
 *     def getComponents(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_v); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 137, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->get(__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 137, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":133
 *         """
 *         return self.thisptr.getIndex(token)
 *     def get(self, v):             # <<<<<<<<<<<<<<
 *         """return component for a token.
 *         If the token is unknown, return 0.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("CGAT.Components.IComponents.get", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":139
 *         return self.thisptr.get(v)
 * 
 *     def getComponents(self):             # <<<<<<<<<<<<<<
 *         """return all connected components as a list of lists."""
 *         components = {}
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_17getComponents(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_16getComponents[] = "return all connected components as a list of lists.";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_17getComponents(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("getComponents (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_16getComponents(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_16getComponents(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self) {
  PyObject *__pyx_v_components = NULL;
  long __pyx_v_x;
  int __pyx_v_c;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  long __pyx_t_2;
  long __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  __Pyx_RefNannySetupContext("getComponents", 0);

  /* "CGAT/Components/Components.pyx":141
 *     def getComponents(self):
 *         """return all connected components as a list of lists."""
 *         components = {}             # <<<<<<<<<<<<<<
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 141, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_components = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "CGAT/Components/Components.pyx":143
 *         components = {}
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):             # <<<<<<<<<<<<<<
 *             c = self.thisptr.getComponent(x)
 *             if c not in components: components[c] = []
 */
  __pyx_t_2 = (__pyx_v_self->thisptr->getNumNodes() + 1);
  for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_x = __pyx_t_3;

    /* "CGAT/Components/Components.pyx":144
 * 
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 *             c = self.thisptr.getComponent(x)             # <<<<<<<<<<<<<<
 *             if c not in components: components[c] = []
 *             components[ c  ].append( self.thisptr.getToken( x ) )
 */
    __pyx_v_c = __pyx_v_self->thisptr->getComponent(__pyx_v_x);

    /* "CGAT/Components/Components.pyx":145
 *         for x in range(1, self.thisptr.getNumNodes() + 1):
 *             c = self.thisptr.getComponent(x)
 *             if c not in components: components[c] = []             # <<<<<<<<<<<<<<
 *             components[ c  ].append( self.thisptr.getToken( x ) )
 * 
 */
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 145, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_4 = (__Pyx_PyDict_ContainsTF(__pyx_t_1, __pyx_v_components, Py_NE)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 145, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_5 = (__pyx_t_4 != 0);
    if (__pyx_t_5) {
      __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 145, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 145, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      if (unlikely(PyDict_SetItem(__pyx_v_components, __pyx_t_6, __pyx_t_1) < 0)) __PYX_ERR(0, 145, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    }

    /* "CGAT/Components/Components.pyx":146
 *             c = self.thisptr.getComponent(x)
 *             if c not in components: components[c] = []
 *             components[ c  ].append( self.thisptr.getToken( x ) )             # <<<<<<<<<<<<<<
 * 
 *         return components.values()
 */
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_c); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 146, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_components, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 146, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->getToken(__pyx_v_x)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 146, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_7 = __Pyx_PyObject_Append(__pyx_t_6, __pyx_t_1); if (unlikely(__pyx_t_7 == -1)) __PYX_ERR(0, 146, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "CGAT/Components/Components.pyx":148
 *             components[ c  ].append( self.thisptr.getToken( x ) )
 * 
 *         return components.values()             # <<<<<<<<<<<<<<
 * 
 *     def reset(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_components); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "CGAT/Components/Components.pyx":139
 *         return self.thisptr.get(v)
 * 
 *     def getComponents(self):             # <<<<<<<<<<<<<<
 *         """return all connected components as a list of lists."""
 *         components = {}
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("CGAT.Components.IComponents.getComponents", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_components);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "CGAT/Components/Components.pyx":150
 *         return components.values()
 * 
 *     def reset(self):             # <<<<<<<<<<<<<<
 *         """clear graph.
 *         """
 */

/* Python wrapper */
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_19reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_4CGAT_10Components_11IComponents_18reset[] = "clear graph.\n        ";
static PyObject *__pyx_pw_4CGAT_10Components_11IComponents_19reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("reset (wrapper)", 0);
  __pyx_r = __pyx_pf_4CGAT_10Components_11IComponents_18reset(((struct __pyx_obj_4CGAT_10Components_IComponents *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_4CGAT_10Components_11IComponents_18reset(struct __pyx_obj_4CGAT_10Components_IComponents *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("reset", 0);

  /* "CGAT/Components/Components.pyx":153
 *         """clear graph.
 *         """
 *         self.thisptr.reset()             # <<<<<<<<<<<<<<
 */
  __pyx_v_self->thisptr->reset();

  /* "CGAT/Components/Components.pyx":150
 *         return components.values()
 * 
 *     def reset(self):             # <<<<<<<<<<<<<<
 *         """clear graph.
 *         """
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_tp_new_4CGAT_10Components_SComponents(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_4CGAT_10Components_11SComponents_1__cinit__(o, __pyx_empty_tuple, NULL) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_4CGAT_10Components_SComponents(PyObject *o) {
  #if PY_VERSION_HEX >= 0x030400a1
  if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_4CGAT_10Components_11SComponents_3__dealloc__(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_4CGAT_10Components_SComponents[] = {
  {"add", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_5add, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4CGAT_10Components_11SComponents_4add},
  {"getNumNodes", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_7getNumNodes, METH_NOARGS, __pyx_doc_4CGAT_10Components_11SComponents_6getNumNodes},
  {"getComponent", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_9getComponent, METH_O, __pyx_doc_4CGAT_10Components_11SComponents_8getComponent},
  {"getToken", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_11getToken, METH_O, __pyx_doc_4CGAT_10Components_11SComponents_10getToken},
  {"getIndex", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_13getIndex, METH_O, __pyx_doc_4CGAT_10Components_11SComponents_12getIndex},
  {"get", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_15get, METH_O, __pyx_doc_4CGAT_10Components_11SComponents_14get},
  {"getComponents", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_17getComponents, METH_NOARGS, __pyx_doc_4CGAT_10Components_11SComponents_16getComponents},
  {"reset", (PyCFunction)__pyx_pw_4CGAT_10Components_11SComponents_19reset, METH_NOARGS, __pyx_doc_4CGAT_10Components_11SComponents_18reset},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_4CGAT_10Components_SComponents = {
  PyVarObject_HEAD_INIT(0, 0)
  "CGAT.Components.SComponents", /*tp_name*/
  sizeof(struct __pyx_obj_4CGAT_10Components_SComponents), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_4CGAT_10Components_SComponents, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  "Components for a graph with string indices.", /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_4CGAT_10Components_SComponents, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_4CGAT_10Components_SComponents, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
};

static PyObject *__pyx_tp_new_4CGAT_10Components_IComponents(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_4CGAT_10Components_11IComponents_1__cinit__(o, __pyx_empty_tuple, NULL) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_4CGAT_10Components_IComponents(PyObject *o) {
  #if PY_VERSION_HEX >= 0x030400a1
  if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_4CGAT_10Components_11IComponents_3__dealloc__(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_4CGAT_10Components_IComponents[] = {
  {"add", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_5add, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4CGAT_10Components_11IComponents_4add},
  {"getNumNodes", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_7getNumNodes, METH_NOARGS, __pyx_doc_4CGAT_10Components_11IComponents_6getNumNodes},
  {"getComponent", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_9getComponent, METH_O, __pyx_doc_4CGAT_10Components_11IComponents_8getComponent},
  {"getToken", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_11getToken, METH_O, __pyx_doc_4CGAT_10Components_11IComponents_10getToken},
  {"getIndex", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_13getIndex, METH_O, __pyx_doc_4CGAT_10Components_11IComponents_12getIndex},
  {"get", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_15get, METH_O, __pyx_doc_4CGAT_10Components_11IComponents_14get},
  {"getComponents", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_17getComponents, METH_NOARGS, __pyx_doc_4CGAT_10Components_11IComponents_16getComponents},
  {"reset", (PyCFunction)__pyx_pw_4CGAT_10Components_11IComponents_19reset, METH_NOARGS, __pyx_doc_4CGAT_10Components_11IComponents_18reset},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_4CGAT_10Components_IComponents = {
  PyVarObject_HEAD_INIT(0, 0)
  "CGAT.Components.IComponents", /*tp_name*/
  sizeof(struct __pyx_obj_4CGAT_10Components_IComponents), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_4CGAT_10Components_IComponents, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  "Components for a graph with numeric indices.", /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_4CGAT_10Components_IComponents, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_4CGAT_10Components_IComponents, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
};

static PyMethodDef __pyx_methods[] = {
  {0, 0, 0, 0}
};

#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
  #if PY_VERSION_HEX < 0x03020000
    { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
  #else
    PyModuleDef_HEAD_INIT,
  #endif
    "Components",
    __pyx_k_Class_to_compute_connected_compo, /* m_doc */
    -1, /* m_size */
    __pyx_methods /* m_methods */,
    NULL, /* m_reload */
    NULL, /* m_traverse */
    NULL, /* m_clear */
    NULL /* m_free */
};
#endif

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1},
  {&__pyx_n_s_append, __pyx_k_append, sizeof(__pyx_k_append), 0, 0, 1, 1},
  {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1},
  {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
  {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_values, __pyx_k_values, sizeof(__pyx_k_values), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 91, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

static int __Pyx_InitCachedConstants(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_InitGlobals(void) {
  __pyx_umethod_PyDict_Type_values.type = (PyObject*)&PyDict_Type;
  if (__Pyx_InitStrings(__pyx_string_tab) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  return 0;
  __pyx_L1_error:;
  return -1;
}

#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC initComponents(void); /*proto*/
PyMODINIT_FUNC initComponents(void)
#else
PyMODINIT_FUNC PyInit_Components(void); /*proto*/
PyMODINIT_FUNC PyInit_Components(void)
#endif
{
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannyDeclarations
  #if CYTHON_REFNANNY
  __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
  if (!__Pyx_RefNanny) {
      PyErr_Clear();
      __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
      if (!__Pyx_RefNanny)
          Py_FatalError("failed to import 'refnanny' module");
  }
  #endif
  __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_Components(void)", 0);
  if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
  #ifdef __Pyx_CyFunction_USED
  if (__pyx_CyFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Coroutine_USED
  if (__pyx_Coroutine_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_StopAsyncIteration_USED
  if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  #ifdef WITH_THREAD /* Python build with threading support? */
  PyEval_InitThreads();
  #endif
  #endif
  /*--- Module creation code ---*/
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4("Components", __pyx_methods, __pyx_k_Class_to_compute_connected_compo, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  /*--- Initialize various global constants etc. ---*/
  if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
  if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  if (__pyx_module_is_main_CGAT__Components) {
    if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
    if (!PyDict_GetItemString(modules, "CGAT.Components")) {
      if (unlikely(PyDict_SetItemString(modules, "CGAT.Components", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Constants init code ---*/
  if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Global init code ---*/
  /*--- Variable export code ---*/
  /*--- Function export code ---*/
  /*--- Type init code ---*/
  if (PyType_Ready(&__pyx_type_4CGAT_10Components_SComponents) < 0) __PYX_ERR(0, 52, __pyx_L1_error)
  __pyx_type_4CGAT_10Components_SComponents.tp_print = 0;
  if (PyObject_SetAttrString(__pyx_m, "SComponents", (PyObject *)&__pyx_type_4CGAT_10Components_SComponents) < 0) __PYX_ERR(0, 52, __pyx_L1_error)
  __pyx_ptype_4CGAT_10Components_SComponents = &__pyx_type_4CGAT_10Components_SComponents;
  if (PyType_Ready(&__pyx_type_4CGAT_10Components_IComponents) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
  __pyx_type_4CGAT_10Components_IComponents.tp_print = 0;
  if (PyObject_SetAttrString(__pyx_m, "IComponents", (PyObject *)&__pyx_type_4CGAT_10Components_IComponents) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
  __pyx_ptype_4CGAT_10Components_IComponents = &__pyx_type_4CGAT_10Components_IComponents;
  /*--- Type import code ---*/
  /*--- Variable import code ---*/
  /*--- Function import code ---*/
  /*--- Execution code ---*/
  #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
  if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif

  /* "CGAT/Components/Components.pyx":1
 * """Class to compute connected components             # <<<<<<<<<<<<<<
 * 
 * Connected components list all nodes in a graph that
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /*--- Wrapped vars code ---*/

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init CGAT.Components", __pyx_clineno, __pyx_lineno, __pyx_filename);
    }
    Py_DECREF(__pyx_m); __pyx_m = 0;
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init CGAT.Components");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if PY_MAJOR_VERSION < 3
  return;
  #else
  return __pyx_m;
  #endif
}

/* --- Runtime support code --- */
/* Refnanny */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
    PyObject *m = NULL, *p = NULL;
    void *r = NULL;
    m = PyImport_ImportModule((char *)modname);
    if (!m) goto end;
    p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
    if (!p) goto end;
    r = PyLong_AsVoidPtr(p);
end:
    Py_XDECREF(p);
    Py_XDECREF(m);
    return (__Pyx_RefNannyAPIStruct *)r;
}
#endif

/* GetBuiltinName */
static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
    PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
    if (unlikely(!result)) {
        PyErr_Format(PyExc_NameError,
#if PY_MAJOR_VERSION >= 3
            "name '%U' is not defined", name);
#else
            "name '%.200s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

/* RaiseArgTupleInvalid */
static void __Pyx_RaiseArgtupleInvalid(
    const char* func_name,
    int exact,
    Py_ssize_t num_min,
    Py_ssize_t num_max,
    Py_ssize_t num_found)
{
    Py_ssize_t num_expected;
    const char *more_or_less;
    if (num_found < num_min) {
        num_expected = num_min;
        more_or_less = "at least";
    } else {
        num_expected = num_max;
        more_or_less = "at most";
    }
    if (exact) {
        more_or_less = "exactly";
    }
    PyErr_Format(PyExc_TypeError,
                 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                 func_name, more_or_less, num_expected,
                 (num_expected == 1) ? "" : "s", num_found);
}

/* KeywordStringCheck */
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
    PyObject *kwdict,
    const char* function_name,
    int kw_allowed)
{
    PyObject* key = 0;
    Py_ssize_t pos = 0;
#if CYTHON_COMPILING_IN_PYPY
    if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
        goto invalid_keyword;
    return 1;
#else
    while (PyDict_Next(kwdict, &pos, &key, 0)) {
        #if PY_MAJOR_VERSION < 3
        if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
        #endif
            if (unlikely(!PyUnicode_Check(key)))
                goto invalid_keyword_type;
    }
    if ((!kw_allowed) && unlikely(key))
        goto invalid_keyword;
    return 1;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%.200s() keywords must be strings", function_name);
    return 0;
#endif
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
    return 0;
}

/* RaiseDoubleKeywords */
static void __Pyx_RaiseDoubleKeywordsError(
    const char* func_name,
    PyObject* kw_name)
{
    PyErr_Format(PyExc_TypeError,
        #if PY_MAJOR_VERSION >= 3
        "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
        #else
        "%s() got multiple values for keyword argument '%s'", func_name,
        PyString_AsString(kw_name));
        #endif
}

/* ParseKeywords */
static int __Pyx_ParseOptionalKeywords(
    PyObject *kwds,
    PyObject **argnames[],
    PyObject *kwds2,
    PyObject *values[],
    Py_ssize_t num_pos_args,
    const char* function_name)
{
    PyObject *key = 0, *value = 0;
    Py_ssize_t pos = 0;
    PyObject*** name;
    PyObject*** first_kw_arg = argnames + num_pos_args;
    while (PyDict_Next(kwds, &pos, &key, &value)) {
        name = first_kw_arg;
        while (*name && (**name != key)) name++;
        if (*name) {
            values[name-argnames] = value;
            continue;
        }
        name = first_kw_arg;
        #if PY_MAJOR_VERSION < 3
        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
            while (*name) {
                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
                        && _PyString_Eq(**name, key)) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    if ((**argname == key) || (
                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
                             && _PyString_Eq(**argname, key))) {
                        goto arg_passed_twice;
                    }
                    argname++;
                }
            }
        } else
        #endif
        if (likely(PyUnicode_Check(key))) {
            while (*name) {
                int cmp = (**name == key) ? 0 :
                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                #endif
                    PyUnicode_Compare(**name, key);
                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                if (cmp == 0) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    int cmp = (**argname == key) ? 0 :
                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                    #endif
                        PyUnicode_Compare(**argname, key);
                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                    if (cmp == 0) goto arg_passed_twice;
                    argname++;
                }
            }
        } else
            goto invalid_keyword_type;
        if (kwds2) {
            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
        } else {
            goto invalid_keyword;
        }
    }
    return 0;
arg_passed_twice:
    __Pyx_RaiseDoubleKeywordsError(function_name, key);
    goto bad;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%.200s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

/* PyCFunctionFastCall */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) {
    PyCFunctionObject *func = (PyCFunctionObject*)func_obj;
    PyCFunction meth = PyCFunction_GET_FUNCTION(func);
    PyObject *self = PyCFunction_GET_SELF(func);
    assert(PyCFunction_Check(func));
    assert(METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)));
    assert(nargs >= 0);
    assert(nargs == 0 || args != NULL);
    /* _PyCFunction_FastCallDict() must not be called with an exception set,
       because it may clear it (directly or indirectly) and so the
       caller loses its exception */
    assert(!PyErr_Occurred());
    return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
}
#endif  // CYTHON_FAST_PYCCALL

/* PyFunctionFastCall */
#if CYTHON_FAST_PYCALL
#include "frameobject.h"
static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
                                               PyObject *globals) {
    PyFrameObject *f;
    PyThreadState *tstate = PyThreadState_GET();
    PyObject **fastlocals;
    Py_ssize_t i;
    PyObject *result;
    assert(globals != NULL);
    /* XXX Perhaps we should create a specialized
       PyFrame_New() that doesn't take locals, but does
       take builtins without sanity checking them.
       */
    assert(tstate != NULL);
    f = PyFrame_New(tstate, co, globals, NULL);
    if (f == NULL) {
        return NULL;
    }
    fastlocals = f->f_localsplus;
    for (i = 0; i < na; i++) {
        Py_INCREF(*args);
        fastlocals[i] = *args++;
    }
    result = PyEval_EvalFrameEx(f,0);
    ++tstate->recursion_depth;
    Py_DECREF(f);
    --tstate->recursion_depth;
    return result;
}
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) {
    PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
    PyObject *globals = PyFunction_GET_GLOBALS(func);
    PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
    PyObject *closure;
#if PY_MAJOR_VERSION >= 3
    PyObject *kwdefs;
#endif
    PyObject *kwtuple, **k;
    PyObject **d;
    Py_ssize_t nd;
    Py_ssize_t nk;
    PyObject *result;
    assert(kwargs == NULL || PyDict_Check(kwargs));
    nk = kwargs ? PyDict_Size(kwargs) : 0;
    if (Py_EnterRecursiveCall((char*)" while calling a Python object")) {
        return NULL;
    }
    if (
#if PY_MAJOR_VERSION >= 3
            co->co_kwonlyargcount == 0 &&
#endif
            likely(kwargs == NULL || nk == 0) &&
            co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
        if (argdefs == NULL && co->co_argcount == nargs) {
            result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
            goto done;
        }
        else if (nargs == 0 && argdefs != NULL
                 && co->co_argcount == Py_SIZE(argdefs)) {
            /* function called with no arguments, but all parameters have
               a default value: use default values as arguments .*/
            args = &PyTuple_GET_ITEM(argdefs, 0);
            result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
            goto done;
        }
    }
    if (kwargs != NULL) {
        Py_ssize_t pos, i;
        kwtuple = PyTuple_New(2 * nk);
        if (kwtuple == NULL) {
            result = NULL;
            goto done;
        }
        k = &PyTuple_GET_ITEM(kwtuple, 0);
        pos = i = 0;
        while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
            Py_INCREF(k[i]);
            Py_INCREF(k[i+1]);
            i += 2;
        }
        nk = i / 2;
    }
    else {
        kwtuple = NULL;
        k = NULL;
    }
    closure = PyFunction_GET_CLOSURE(func);
#if PY_MAJOR_VERSION >= 3
    kwdefs = PyFunction_GET_KW_DEFAULTS(func);
#endif
    if (argdefs != NULL) {
        d = &PyTuple_GET_ITEM(argdefs, 0);
        nd = Py_SIZE(argdefs);
    }
    else {
        d = NULL;
        nd = 0;
    }
#if PY_MAJOR_VERSION >= 3
    result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
                               args, nargs,
                               k, (int)nk,
                               d, (int)nd, kwdefs, closure);
#else
    result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
                               args, nargs,
                               k, (int)nk,
                               d, (int)nd, closure);
#endif
    Py_XDECREF(kwtuple);
done:
    Py_LeaveRecursiveCall();
    return result;
}
#endif  // CPython < 3.6
#endif  // CYTHON_FAST_PYCALL

/* PyObjectCall */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
    PyObject *result;
    ternaryfunc call = func->ob_type->tp_call;
    if (unlikely(!call))
        return PyObject_Call(func, arg, kw);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = (*call)(func, arg, kw);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCallMethO */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
    PyObject *self, *result;
    PyCFunction cfunc;
    cfunc = PyCFunction_GET_FUNCTION(func);
    self = PyCFunction_GET_SELF(func);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = cfunc(self, arg);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCallOneArg */
#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_New(1);
    if (unlikely(!args)) return NULL;
    Py_INCREF(arg);
    PyTuple_SET_ITEM(args, 0, arg);
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
#if CYTHON_FAST_PYCALL
    if (PyFunction_Check(func)) {
        return __Pyx_PyFunction_FastCall(func, &arg, 1);
    }
#endif
#ifdef __Pyx_CyFunction_USED
    if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
    if (likely(PyCFunction_Check(func))) {
#endif
        if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
            return __Pyx_PyObject_CallMethO(func, arg);
#if CYTHON_FAST_PYCCALL
        } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) {
            return __Pyx_PyCFunction_FastCall(func, &arg, 1);
#endif
        }
    }
    return __Pyx__PyObject_CallOneArg(func, arg);
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_Pack(1, arg);
    if (unlikely(!args)) return NULL;
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
#endif

/* PyObjectCallMethod1 */
  static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
    PyObject *method, *result = NULL;
    method = __Pyx_PyObject_GetAttrStr(obj, method_name);
    if (unlikely(!method)) goto done;
#if CYTHON_UNPACK_METHODS
    if (likely(PyMethod_Check(method))) {
        PyObject *self = PyMethod_GET_SELF(method);
        if (likely(self)) {
            PyObject *args;
            PyObject *function = PyMethod_GET_FUNCTION(method);
            #if CYTHON_FAST_PYCALL
            if (PyFunction_Check(function)) {
                PyObject *args[2] = {self, arg};
                result = __Pyx_PyFunction_FastCall(function, args, 2);
                goto done;
            }
            #endif
            #if CYTHON_FAST_PYCCALL
            if (__Pyx_PyFastCFunction_Check(function)) {
                PyObject *args[2] = {self, arg};
                result = __Pyx_PyCFunction_FastCall(function, args, 2);
                goto done;
            }
            #endif
            args = PyTuple_New(2);
            if (unlikely(!args)) goto done;
            Py_INCREF(self);
            PyTuple_SET_ITEM(args, 0, self);
            Py_INCREF(arg);
            PyTuple_SET_ITEM(args, 1, arg);
            Py_INCREF(function);
            Py_DECREF(method); method = NULL;
            result = __Pyx_PyObject_Call(function, args, NULL);
            Py_DECREF(args);
            Py_DECREF(function);
            return result;
        }
    }
#endif
    result = __Pyx_PyObject_CallOneArg(method, arg);
done:
    Py_XDECREF(method);
    return result;
}

/* append */
  static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
    if (likely(PyList_CheckExact(L))) {
        if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
    } else {
        PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
        if (unlikely(!retval))
            return -1;
        Py_DECREF(retval);
    }
    return 0;
}

/* UnpackUnboundCMethod */
  static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) {
    PyObject *method;
    method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name);
    if (unlikely(!method))
        return -1;
    target->method = method;
#if CYTHON_COMPILING_IN_CPYTHON
    #if PY_MAJOR_VERSION >= 3
    if (likely(PyObject_TypeCheck(method, &PyMethodDescr_Type)))
    #endif
    {
        PyMethodDescrObject *descr = (PyMethodDescrObject*) method;
        target->func = descr->d_method->ml_meth;
        target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST);
    }
#endif
    return 0;
}

/* CallUnboundCMethod0 */
  static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) {
    PyObject *args, *result = NULL;
    if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL;
#if CYTHON_ASSUME_SAFE_MACROS
    args = PyTuple_New(1);
    if (unlikely(!args)) goto bad;
    Py_INCREF(self);
    PyTuple_SET_ITEM(args, 0, self);
#else
    args = PyTuple_Pack(1, self);
    if (unlikely(!args)) goto bad;
#endif
    result = __Pyx_PyObject_Call(cfunc->method, args, NULL);
    Py_DECREF(args);
bad:
    return result;
}

/* py_dict_values */
  static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d) {
    if (PY_MAJOR_VERSION >= 3)
        return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_values, d);
    else
        return PyDict_Values(d);
}

/* CodeObjectCache */
  static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
    int start = 0, mid = 0, end = count - 1;
    if (end >= 0 && code_line > entries[end].code_line) {
        return count;
    }
    while (start < end) {
        mid = start + (end - start) / 2;
        if (code_line < entries[mid].code_line) {
            end = mid;
        } else if (code_line > entries[mid].code_line) {
             start = mid + 1;
        } else {
            return mid;
        }
    }
    if (code_line <= entries[mid].code_line) {
        return mid;
    } else {
        return mid + 1;
    }
}
static PyCodeObject *__pyx_find_code_object(int code_line) {
    PyCodeObject* code_object;
    int pos;
    if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
        return NULL;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
        return NULL;
    }
    code_object = __pyx_code_cache.entries[pos].code_object;
    Py_INCREF(code_object);
    return code_object;
}
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
    int pos, i;
    __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
    if (unlikely(!code_line)) {
        return;
    }
    if (unlikely(!entries)) {
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
        if (likely(entries)) {
            __pyx_code_cache.entries = entries;
            __pyx_code_cache.max_count = 64;
            __pyx_code_cache.count = 1;
            entries[0].code_line = code_line;
            entries[0].code_object = code_object;
            Py_INCREF(code_object);
        }
        return;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
        PyCodeObject* tmp = entries[pos].code_object;
        entries[pos].code_object = code_object;
        Py_DECREF(tmp);
        return;
    }
    if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
        int new_max = __pyx_code_cache.max_count + 64;
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
            __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
        if (unlikely(!entries)) {
            return;
        }
        __pyx_code_cache.entries = entries;
        __pyx_code_cache.max_count = new_max;
    }
    for (i=__pyx_code_cache.count; i>pos; i--) {
        entries[i] = entries[i-1];
    }
    entries[pos].code_line = code_line;
    entries[pos].code_object = code_object;
    __pyx_code_cache.count++;
    Py_INCREF(code_object);
}

/* AddTraceback */
  #include "compile.h"
#include "frameobject.h"
#include "traceback.h"
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
            const char *funcname, int c_line,
            int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyObject *py_srcfile = 0;
    PyObject *py_funcname = 0;
    #if PY_MAJOR_VERSION < 3
    py_srcfile = PyString_FromString(filename);
    #else
    py_srcfile = PyUnicode_FromString(filename);
    #endif
    if (!py_srcfile) goto bad;
    if (c_line) {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #else
        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #endif
    }
    else {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromString(funcname);
        #else
        py_funcname = PyUnicode_FromString(funcname);
        #endif
    }
    if (!py_funcname) goto bad;
    py_code = __Pyx_PyCode_New(
        0,
        0,
        0,
        0,
        0,
        __pyx_empty_bytes, /*PyObject *code,*/
        __pyx_empty_tuple, /*PyObject *consts,*/
        __pyx_empty_tuple, /*PyObject *names,*/
        __pyx_empty_tuple, /*PyObject *varnames,*/
        __pyx_empty_tuple, /*PyObject *freevars,*/
        __pyx_empty_tuple, /*PyObject *cellvars,*/
        py_srcfile,   /*PyObject *filename,*/
        py_funcname,  /*PyObject *name,*/
        py_line,
        __pyx_empty_bytes  /*PyObject *lnotab*/
    );
    Py_DECREF(py_srcfile);
    Py_DECREF(py_funcname);
    return py_code;
bad:
    Py_XDECREF(py_srcfile);
    Py_XDECREF(py_funcname);
    return NULL;
}
static void __Pyx_AddTraceback(const char *funcname, int c_line,
                               int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyFrameObject *py_frame = 0;
    py_code = __pyx_find_code_object(c_line ? c_line : py_line);
    if (!py_code) {
        py_code = __Pyx_CreateCodeObjectForTraceback(
            funcname, c_line, py_line, filename);
        if (!py_code) goto bad;
        __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
    }
    py_frame = PyFrame_New(
        PyThreadState_GET(), /*PyThreadState *tstate,*/
        py_code,             /*PyCodeObject *code,*/
        __pyx_d,      /*PyObject *globals,*/
        0                    /*PyObject *locals*/
    );
    if (!py_frame) goto bad;
    __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
    PyTraceBack_Here(py_frame);
bad:
    Py_XDECREF(py_code);
    Py_XDECREF(py_frame);
}

/* CIntToPy */
  static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
    const int neg_one = (int) -1, const_zero = (int) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(int) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(int) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(int) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(int),
                                     little, !is_unsigned);
    }
}

/* CIntFromPyVerify */
  #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
    {\
        func_type value = func_value;\
        if (sizeof(target_type) < sizeof(func_type)) {\
            if (unlikely(value != (func_type) (target_type) value)) {\
                func_type zero = 0;\
                if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
                    return (target_type) -1;\
                if (is_unsigned && unlikely(value < zero))\
                    goto raise_neg_overflow;\
                else\
                    goto raise_overflow;\
            }\
        }\
        return (target_type) value;\
    }

/* CIntToPy */
  static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
    const long neg_one = (long) -1, const_zero = (long) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(long) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(long) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(long) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(long),
                                     little, !is_unsigned);
    }
}

/* CIntFromPy */
  static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
    const int neg_one = (int) -1, const_zero = (int) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(int) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (int) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case  1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0])
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) {
                            return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) {
                            return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) {
                            return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (int) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(int) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(int,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(int) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            int val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (int) -1;
        }
    } else {
        int val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (int) -1;
        val = __Pyx_PyInt_As_int(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to int");
    return (int) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to int");
    return (int) -1;
}

/* CIntFromPy */
  static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
    const long neg_one = (long) -1, const_zero = (long) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(long) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (long) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case  1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0])
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) {
                            return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) {
                            return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) {
                            return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (long) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(long) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(long,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(long) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            long val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (long) -1;
        }
    } else {
        long val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (long) -1;
        val = __Pyx_PyInt_As_long(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to long");
    return (long) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to long");
    return (long) -1;
}

/* CheckBinaryVersion */
  static int __Pyx_check_binary_version(void) {
    char ctversion[4], rtversion[4];
    PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
    PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
    if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
        char message[200];
        PyOS_snprintf(message, sizeof(message),
                      "compiletime version %s of module '%.100s' "
                      "does not match runtime version %s",
                      ctversion, __Pyx_MODULE_NAME, rtversion);
        return PyErr_WarnEx(NULL, message, 1);
    }
    return 0;
}

/* InitStrings */
  static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
    while (t->p) {
        #if PY_MAJOR_VERSION < 3
        if (t->is_unicode) {
            *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
        } else if (t->intern) {
            *t->p = PyString_InternFromString(t->s);
        } else {
            *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
        }
        #else
        if (t->is_unicode | t->is_str) {
            if (t->intern) {
                *t->p = PyUnicode_InternFromString(t->s);
            } else if (t->encoding) {
                *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
            } else {
                *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
            }
        } else {
            *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
        }
        #endif
        if (!*t->p)
            return -1;
        ++t;
    }
    return 0;
}

static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
}
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
    Py_ssize_t ignore;
    return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
    if (
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
            __Pyx_sys_getdefaultencoding_not_ascii &&
#endif
            PyUnicode_Check(o)) {
#if PY_VERSION_HEX < 0x03030000
        char* defenc_c;
        PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
        if (!defenc) return NULL;
        defenc_c = PyBytes_AS_STRING(defenc);
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
        {
            char* end = defenc_c + PyBytes_GET_SIZE(defenc);
            char* c;
            for (c = defenc_c; c < end; c++) {
                if ((unsigned char) (*c) >= 128) {
                    PyUnicode_AsASCIIString(o);
                    return NULL;
                }
            }
        }
#endif
        *length = PyBytes_GET_SIZE(defenc);
        return defenc_c;
#else
        if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
        if (PyUnicode_IS_ASCII(o)) {
            *length = PyUnicode_GET_LENGTH(o);
            return PyUnicode_AsUTF8(o);
        } else {
            PyUnicode_AsASCIIString(o);
            return NULL;
        }
#else
        return PyUnicode_AsUTF8AndSize(o, length);
#endif
#endif
    } else
#endif
#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
    if (PyByteArray_Check(o)) {
        *length = PyByteArray_GET_SIZE(o);
        return PyByteArray_AS_STRING(o);
    } else
#endif
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (unlikely(r < 0)) {
            return NULL;
        } else {
            return result;
        }
    }
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
#if CYTHON_USE_TYPE_SLOTS
  PyNumberMethods *m;
#endif
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
  if (PyInt_Check(x) || PyLong_Check(x))
#else
  if (PyLong_Check(x))
#endif
    return __Pyx_NewRef(x);
#if CYTHON_USE_TYPE_SLOTS
  m = Py_TYPE(x)->tp_as_number;
  #if PY_MAJOR_VERSION < 3
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = PyNumber_Long(x);
  }
  #else
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Long(x);
  }
  #endif
#else
  res = PyNumber_Int(x);
#endif
  if (res) {
#if PY_MAJOR_VERSION < 3
    if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
    if (!PyLong_Check(res)) {
#endif
      PyErr_Format(PyExc_TypeError,
                   "__%.4s__ returned non-%.4s (type %.200s)",
                   name, name, Py_TYPE(res)->tp_name);
      Py_DECREF(res);
      return NULL;
    }
  }
  else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_TypeError,
                    "an integer is required");
  }
  return res;
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
  Py_ssize_t ival;
  PyObject *x;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_CheckExact(b))) {
    if (sizeof(Py_ssize_t) >= sizeof(long))
        return PyInt_AS_LONG(b);
    else
        return PyInt_AsSsize_t(x);
  }
#endif
  if (likely(PyLong_CheckExact(b))) {
    #if CYTHON_USE_PYLONG_INTERNALS
    const digit* digits = ((PyLongObject*)b)->ob_digit;
    const Py_ssize_t size = Py_SIZE(b);
    if (likely(__Pyx_sst_abs(size) <= 1)) {
        ival = likely(size) ? digits[0] : 0;
        if (size == -1) ival = -ival;
        return ival;
    } else {
      switch (size) {
         case 2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
      }
    }
    #endif
    return PyLong_AsSsize_t(b);
  }
  x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
    return PyInt_FromSize_t(ival);
}


#endif /* Py_PYTHON_H */
