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_ssw_wrapper.c
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_ssw_wrapper.c
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/* Generated by Cython 0.20.2 on Thu Sep 4 14:19:20 2014 */
#define PY_SSIZE_T_CLEAN
#ifndef CYTHON_USE_PYLONG_INTERNALS
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 0
#else
#include "pyconfig.h"
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 1
#else
#define CYTHON_USE_PYLONG_INTERNALS 0
#endif
#endif
#endif
#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 < 0x02040000
#error Cython requires Python 2.4+.
#else
#define CYTHON_ABI "0_20_2"
#include <stddef.h> /* For offsetof */
#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 PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
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#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
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#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
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#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600
#define Py_OptimizeFlag 0
#endif
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
#define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_As_int(o)
#define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
(PyErr_Format(PyExc_TypeError, \
"expected index value, got %.200s", Py_TYPE(o)->tp_name), \
(PyObject*)0))
#define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
!PyComplex_Check(o))
#define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#define __Pyx_PyIndex_Check PyIndex_Check
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#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
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PyObject_HEAD_INIT(type) size,
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typedef struct {
void *buf;
PyObject *obj;
Py_ssize_t len;
Py_ssize_t itemsize;
int readonly;
int ndim;
char *format;
Py_ssize_t *shape;
Py_ssize_t *strides;
Py_ssize_t *suboffsets;
void *internal;
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#define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
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#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
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#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)
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#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
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#define CYTHON_PEP393_ENABLED 1
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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_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)
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#define CYTHON_PEP393_ENABLED 0
#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_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]))
#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
#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
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyString_Type PyUnicode_Type
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
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#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
#define PyBytes_Check PyString_Check
#define PyBytes_CheckExact PyString_CheckExact
#define PyBytes_FromString PyString_FromString
#define PyBytes_FromStringAndSize PyString_FromStringAndSize
#define PyBytes_FromFormat PyString_FromFormat
#define PyBytes_DecodeEscape PyString_DecodeEscape
#define PyBytes_AsString PyString_AsString
#define PyBytes_AsStringAndSize PyString_AsStringAndSize
#define PyBytes_Size PyString_Size
#define PyBytes_AS_STRING PyString_AS_STRING
#define PyBytes_GET_SIZE PyString_GET_SIZE
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#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_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
PyString_Check(obj) || PyUnicode_Check(obj))
#define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
#endif
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#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_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) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
#define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
#define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
#define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
#define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
#else
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
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#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
#else
#define __Pyx_NAMESTR(n) (n)
#define __Pyx_DOCSTR(n) (n)
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#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
#elif defined(_MSC_VER)
#define CYTHON_INLINE __inline
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
#define CYTHON_INLINE
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#ifndef CYTHON_RESTRICT
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#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
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
/* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
a quiet NaN. */
float value;
memset(&value, 0xFF, sizeof(value));
return value;
}
#endif
#ifdef __cplusplus
template<typename T>
void __Pyx_call_destructor(T* x) {
x->~T();
}
#endif
#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
#if defined(WIN32) || defined(MS_WINDOWS)
#define _USE_MATH_DEFINES
#endif
#include <math.h>
#define __PYX_HAVE__skbio__alignment___ssw_wrapper
#define __PYX_HAVE_API__skbio__alignment___ssw_wrapper
#include "string.h"
#include "stdio.h"
#include "pythread.h"
#include "stdlib.h"
#include "numpy/arrayobject.h"
#include "numpy/ufuncobject.h"
#include "_lib/ssw.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */
#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
#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
typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
#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_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))) )
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_FromUString(s) __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromUString(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_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(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_COMPILING_IN_CPYTHON
#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 && __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*) (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;
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 int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
#if !defined(CYTHON_CCOMPLEX)
#if defined(__cplusplus)
#define CYTHON_CCOMPLEX 1
#elif defined(_Complex_I)
#define CYTHON_CCOMPLEX 1
#else
#define CYTHON_CCOMPLEX 0
#endif
#endif
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#include <complex>
#else
#include <complex.h>
#endif
#endif
#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
#undef _Complex_I
#define _Complex_I 1.0fj
#endif
static const char *__pyx_f[] = {
"_ssw_wrapper.pyx",
"__init__.pxd",
"type.pxd",
"bool.pxd",
"complex.pxd",
};
#define IS_UNSIGNED(type) (((type) -1) > 0)
struct __Pyx_StructField_;
#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
typedef struct {
const char* name; /* for error messages only */
struct __Pyx_StructField_* fields;
size_t size; /* sizeof(type) */
size_t arraysize[8]; /* length of array in each dimension */
int ndim;
char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
char is_unsigned;
int flags;
} __Pyx_TypeInfo;
typedef struct __Pyx_StructField_ {
__Pyx_TypeInfo* type;
const char* name;
size_t offset;
} __Pyx_StructField;
typedef struct {
__Pyx_StructField* field;
size_t parent_offset;
} __Pyx_BufFmt_StackElem;
typedef struct {
__Pyx_StructField root;
__Pyx_BufFmt_StackElem* head;
size_t fmt_offset;
size_t new_count, enc_count;
size_t struct_alignment;
int is_complex;
char enc_type;
char new_packmode;
char enc_packmode;
char is_valid_array;
} __Pyx_BufFmt_Context;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
* ctypedef npy_int64 int64_t
* #ctypedef npy_int96 int96_t
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
* #ctypedef npy_int96 int96_t
* #ctypedef npy_int128 int128_t
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
* ctypedef npy_uint64 uint64_t
* #ctypedef npy_uint96 uint96_t
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
* #ctypedef npy_uint96 uint96_t
* #ctypedef npy_uint128 uint128_t
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
* ctypedef npy_float64 float64_t
* #ctypedef npy_float80 float80_t
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
* #ctypedef npy_float80 float80_t
* #ctypedef npy_float128 float128_t
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t
*/
typedef npy_long __pyx_t_5numpy_int_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
* ctypedef npy_longlong longlong_t
*
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
*
* ctypedef npy_ulong uint_t
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
* ctypedef npy_ulonglong ulonglong_t
*
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
*
* ctypedef npy_intp intp_t
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
* ctypedef npy_uintp uintp_t
*
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
*
* ctypedef npy_double float_t
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t
*/
typedef npy_double __pyx_t_5numpy_float_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
* ctypedef npy_longdouble longdouble_t
*
*/
typedef npy_double __pyx_t_5numpy_double_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
*
* ctypedef npy_cfloat cfloat_t
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< float > __pyx_t_float_complex;
#else
typedef float _Complex __pyx_t_float_complex;
#endif
#else
typedef struct { float real, imag; } __pyx_t_float_complex;
#endif
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< double > __pyx_t_double_complex;
#else
typedef double _Complex __pyx_t_double_complex;
#endif
#else
typedef struct { double real, imag; } __pyx_t_double_complex;
#endif
/*--- Type declarations ---*/
struct __pyx_obj_5skbio_9alignment_12_ssw_wrapper_AlignmentStructure;
struct __pyx_obj_5skbio_9alignment_12_ssw_wrapper_StripedSmithWaterman;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
* ctypedef npy_clongdouble clongdouble_t
*
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
*
* ctypedef npy_cdouble complex_t
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
/* "/Users/jairideout/.virtualenvs/scikit-bio/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
*
* cdef inline object PyArray_MultiIterNew1(a):
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
/* "skbio/alignment/_ssw_wrapper.pyx":74
*
*
* cdef class AlignmentStructure: # <<<<<<<<<<<<<<
* """Wraps the result of an alignment c struct so it is accessible to Python
*
*/
struct __pyx_obj_5skbio_9alignment_12_ssw_wrapper_AlignmentStructure {
PyObject_HEAD
struct __pyx_vtabstruct_5skbio_9alignment_12_ssw_wrapper_AlignmentStructure *__pyx_vtab;
s_align *p;
PyObject *read_sequence;
PyObject *reference_sequence;
int index_starts_at;
PyObject *_cigar_string;
};
/* "skbio/alignment/_ssw_wrapper.pyx":416
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PyArrayObject *__pyx___KEEP_IT_IN_SCOPE_read;
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/* "skbio/alignment/_ssw_wrapper.pyx":74
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/* "skbio/alignment/_ssw_wrapper.pyx":416
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*
* cdef class StripedSmithWaterman: # <<<<<<<<<<<<<<
* """Performs a striped (banded) Smith Waterman Alignment.
*
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