/* Generated by Cython 0.16 on Mon Jun 3 13:26:28 2013 */ #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 < 0x02040000 #error Cython requires Python 2.4+. #else #include /* 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 #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyCFunction_Call PyObject_Call #else #define __Pyx_PyCFunction_Call PyCFunction_Call #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 PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #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" #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) 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; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #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 *); #endif #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, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #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) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #else #define CYTHON_PEP393_ENABLED 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])) #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_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_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 #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 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)) #endif #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) #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 #define __PYX_HAVE__pyDNase__footprinting__fastbinom #define __PYX_HAVE_API__pyDNase__footprinting__fastbinom #include "fastbinom.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif /* inline attribute */ #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 #endif #endif /* unused attribute */ #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 long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ /* Type Conversion Predeclarations */ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #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); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; 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; static const char *__pyx_f[] = { "fastbinom.pyx", }; /*--- Type declarations ---*/ #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); /*proto*/ #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 /* CYTHON_REFNANNY */ #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) 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); /*proto*/ static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ const char* function_name); /*proto*/ static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static int __Pyx_check_binary_version(void); typedef struct { int code_line; PyCodeObject* code_object; } __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); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'pyDNase.footprinting.fastbinom' */ #define __Pyx_MODULE_NAME "pyDNase.footprinting.fastbinom" int __pyx_module_is_main_pyDNase__footprinting__fastbinom = 0; /* Implementation of 'pyDNase.footprinting.fastbinom' */ static PyObject *__pyx_pf_7pyDNase_12footprinting_9fastbinom_logsf(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c); /* proto */ static PyObject *__pyx_pf_7pyDNase_12footprinting_9fastbinom_2logcdf(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c); /* proto */ static char __pyx_k_3[] = "/Users/jasonlozier/Dropbox/PhD/wellington/pyDNase/footprinting/fastbinom.pyx"; static char __pyx_k_4[] = "pyDNase.footprinting.fastbinom"; static char __pyx_k__a[] = "a"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__logsf[] = "logsf"; static char __pyx_k__logcdf[] = "logcdf"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static PyObject *__pyx_kp_s_3; static PyObject *__pyx_n_s_4; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s__a; static PyObject *__pyx_n_s__b; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__logcdf; static PyObject *__pyx_n_s__logsf; static PyObject *__pyx_k_tuple_1; static PyObject *__pyx_k_tuple_5; static PyObject *__pyx_k_codeobj_2; static PyObject *__pyx_k_codeobj_6; /* Python wrapper */ static PyObject *__pyx_pw_7pyDNase_12footprinting_9fastbinom_1logsf(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyMethodDef __pyx_mdef_7pyDNase_12footprinting_9fastbinom_1logsf = {__Pyx_NAMESTR("logsf"), (PyCFunction)__pyx_pw_7pyDNase_12footprinting_9fastbinom_1logsf, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; static PyObject *__pyx_pw_7pyDNase_12footprinting_9fastbinom_1logsf(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_a = 0; PyObject *__pyx_v_b = 0; PyObject *__pyx_v_c = 0; static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__a,&__pyx_n_s__b,&__pyx_n_s__c,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("logsf (wrapper)", 0); __pyx_self = __pyx_self; { PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); 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: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__a); if (likely(values[0])) kw_args--; else goto __pyx_L5_argtuple_error; case 1: values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__b); if (likely(values[1])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("logsf", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__c); if (likely(values[2])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("logsf", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "logsf") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } __pyx_v_a = values[0]; __pyx_v_b = values[1]; __pyx_v_c = values[2]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("logsf", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("pyDNase.footprinting.fastbinom.logsf", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_7pyDNase_12footprinting_9fastbinom_logsf(__pyx_self, __pyx_v_a, __pyx_v_b, __pyx_v_c); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "pyDNase/footprinting/fastbinom.pyx":5 * double bdtr(int, int, float) * * def logsf(a,b,c): # <<<<<<<<<<<<<< * return bdtrc(a, b, c) * def logcdf(a,b,c): */ static PyObject *__pyx_pf_7pyDNase_12footprinting_9fastbinom_logsf(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; float __pyx_t_3; PyObject *__pyx_t_4 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("logsf", 0); /* "pyDNase/footprinting/fastbinom.pyx":6 * * def logsf(a,b,c): * return bdtrc(a, b, c) # <<<<<<<<<<<<<< * def logcdf(a,b,c): * return bdtr(a,b,c) */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_a); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_v_b); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __pyx_PyFloat_AsFloat(__pyx_v_c); if (unlikely((__pyx_t_3 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = PyFloat_FromDouble(bdtrc(__pyx_t_1, __pyx_t_2, __pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_r = __pyx_t_4; __pyx_t_4 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_4); __Pyx_AddTraceback("pyDNase.footprinting.fastbinom.logsf", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_7pyDNase_12footprinting_9fastbinom_3logcdf(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyMethodDef __pyx_mdef_7pyDNase_12footprinting_9fastbinom_3logcdf = {__Pyx_NAMESTR("logcdf"), (PyCFunction)__pyx_pw_7pyDNase_12footprinting_9fastbinom_3logcdf, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; static PyObject *__pyx_pw_7pyDNase_12footprinting_9fastbinom_3logcdf(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_a = 0; PyObject *__pyx_v_b = 0; PyObject *__pyx_v_c = 0; static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__a,&__pyx_n_s__b,&__pyx_n_s__c,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("logcdf (wrapper)", 0); __pyx_self = __pyx_self; { PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); 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: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__a); if (likely(values[0])) kw_args--; else goto __pyx_L5_argtuple_error; case 1: values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__b); if (likely(values[1])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("logcdf", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__c); if (likely(values[2])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("logcdf", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "logcdf") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } __pyx_v_a = values[0]; __pyx_v_b = values[1]; __pyx_v_c = values[2]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("logcdf", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("pyDNase.footprinting.fastbinom.logcdf", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_7pyDNase_12footprinting_9fastbinom_2logcdf(__pyx_self, __pyx_v_a, __pyx_v_b, __pyx_v_c); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "pyDNase/footprinting/fastbinom.pyx":7 * def logsf(a,b,c): * return bdtrc(a, b, c) * def logcdf(a,b,c): # <<<<<<<<<<<<<< * return bdtr(a,b,c) */ static PyObject *__pyx_pf_7pyDNase_12footprinting_9fastbinom_2logcdf(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; float __pyx_t_3; PyObject *__pyx_t_4 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("logcdf", 0); /* "pyDNase/footprinting/fastbinom.pyx":8 * return bdtrc(a, b, c) * def logcdf(a,b,c): * return bdtr(a,b,c) # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_a); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_v_b); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __pyx_PyFloat_AsFloat(__pyx_v_c); if (unlikely((__pyx_t_3 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = PyFloat_FromDouble(bdtr(__pyx_t_1, __pyx_t_2, __pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_r = __pyx_t_4; __pyx_t_4 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_4); __Pyx_AddTraceback("pyDNase.footprinting.fastbinom.logcdf", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } static PyMethodDef __pyx_methods[] = { {0, 0, 0, 0} }; #if PY_MAJOR_VERSION >= 3 static struct PyModuleDef __pyx_moduledef = { PyModuleDef_HEAD_INIT, __Pyx_NAMESTR("fastbinom"), 0, /* 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_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0}, {&__pyx_n_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 1}, {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1}, {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1}, {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1}, {&__pyx_n_s__b, __pyx_k__b, sizeof(__pyx_k__b), 0, 0, 1, 1}, {&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1}, {&__pyx_n_s__logcdf, __pyx_k__logcdf, sizeof(__pyx_k__logcdf), 0, 0, 1, 1}, {&__pyx_n_s__logsf, __pyx_k__logsf, sizeof(__pyx_k__logsf), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { return 0; } static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); /* "pyDNase/footprinting/fastbinom.pyx":5 * double bdtr(int, int, float) * * def logsf(a,b,c): # <<<<<<<<<<<<<< * return bdtrc(a, b, c) * def logcdf(a,b,c): */ __pyx_k_tuple_1 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_1); __Pyx_INCREF(((PyObject *)__pyx_n_s__a)); PyTuple_SET_ITEM(__pyx_k_tuple_1, 0, ((PyObject *)__pyx_n_s__a)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a)); __Pyx_INCREF(((PyObject *)__pyx_n_s__b)); PyTuple_SET_ITEM(__pyx_k_tuple_1, 1, ((PyObject *)__pyx_n_s__b)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__b)); __Pyx_INCREF(((PyObject *)__pyx_n_s__c)); PyTuple_SET_ITEM(__pyx_k_tuple_1, 2, ((PyObject *)__pyx_n_s__c)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__c)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_1)); __pyx_k_codeobj_2 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_1, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_3, __pyx_n_s__logsf, 5, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pyDNase/footprinting/fastbinom.pyx":7 * def logsf(a,b,c): * return bdtrc(a, b, c) * def logcdf(a,b,c): # <<<<<<<<<<<<<< * return bdtr(a,b,c) */ __pyx_k_tuple_5 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_5); __Pyx_INCREF(((PyObject *)__pyx_n_s__a)); PyTuple_SET_ITEM(__pyx_k_tuple_5, 0, ((PyObject *)__pyx_n_s__a)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a)); __Pyx_INCREF(((PyObject *)__pyx_n_s__b)); PyTuple_SET_ITEM(__pyx_k_tuple_5, 1, ((PyObject *)__pyx_n_s__b)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__b)); __Pyx_INCREF(((PyObject *)__pyx_n_s__c)); PyTuple_SET_ITEM(__pyx_k_tuple_5, 2, ((PyObject *)__pyx_n_s__c)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__c)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5)); __pyx_k_codeobj_6 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_5, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_3, __pyx_n_s__logcdf, 7, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; __Pyx_RefNannyFinishContext(); return -1; } static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; return 0; __pyx_L1_error:; return -1; } #if PY_MAJOR_VERSION < 3 PyMODINIT_FUNC initfastbinom(void); /*proto*/ PyMODINIT_FUNC initfastbinom(void) #else PyMODINIT_FUNC PyInit_fastbinom(void); /*proto*/ PyMODINIT_FUNC PyInit_fastbinom(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_fastbinom(void)", 0); if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #ifdef __Pyx_CyFunction_USED if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif #ifdef __Pyx_FusedFunction_USED if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif #ifdef __Pyx_Generator_USED if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __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(__Pyx_NAMESTR("fastbinom"), __pyx_methods, 0, 0, PYTHON_API_VERSION); #else __pyx_m = PyModule_Create(&__pyx_moduledef); #endif if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; #if PY_MAJOR_VERSION < 3 Py_INCREF(__pyx_m); #endif __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; /*--- Initialize various global constants etc. ---*/ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_module_is_main_pyDNase__footprinting__fastbinom) { if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } /*--- Builtin init code ---*/ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Constants init code ---*/ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ /*--- Type import code ---*/ /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ /* "pyDNase/footprinting/fastbinom.pyx":5 * double bdtr(int, int, float) * * def logsf(a,b,c): # <<<<<<<<<<<<<< * return bdtrc(a, b, c) * def logcdf(a,b,c): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7pyDNase_12footprinting_9fastbinom_1logsf, NULL, __pyx_n_s_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__logsf, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "pyDNase/footprinting/fastbinom.pyx":7 * def logsf(a,b,c): * return bdtrc(a, b, c) * def logcdf(a,b,c): # <<<<<<<<<<<<<< * return bdtr(a,b,c) */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7pyDNase_12footprinting_9fastbinom_3logcdf, NULL, __pyx_n_s_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__logcdf, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "pyDNase/footprinting/fastbinom.pyx":1 * cdef extern from "fastbinom.h": # <<<<<<<<<<<<<< * double bdtrc(int, int, float) * double bdtr(int, int, float) */ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); if (__pyx_m) { __Pyx_AddTraceback("init pyDNase.footprinting.fastbinom", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init pyDNase.footprinting.fastbinom"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); #if PY_MAJOR_VERSION < 3 return; #else return __pyx_m; #endif } /* Runtime support code */ #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 /* CYTHON_REFNANNY */ 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, "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } 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_AS_STRING(kw_name)); #endif } 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; } else { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { #else if (unlikely(!PyUnicode_Check(key))) { #endif goto invalid_keyword_type; } else { for (name = first_kw_arg; *name; name++) { #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) break; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) break; #endif } if (*name) { values[name-argnames] = value; } else { for (name=argnames; name != first_kw_arg; name++) { if (**name == key) goto arg_passed_twice; #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) goto arg_passed_twice; #endif } if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } } } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, **name); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } 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); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } 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) / 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, 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); } #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, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __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, /*int firstlineno,*/ __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; PyObject *py_globals = 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_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } 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 /* Python 3+ has unicode identifiers */ 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; } /* Type Conversion Functions */ 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_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 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 if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (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 = 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) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */