/* Generated by Cython 0.16 on Wed Apr 25 13:44:32 2012 */

#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 <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
#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 <math.h>
#define __PYX_HAVE__obitools__align___codonnws
#define __PYX_HAVE_API__obitools__align___codonnws
#include "stdlib.h"
#include "string.h"
#ifdef _OPENMP
#include <omp.h>
#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[] = {
  "_codonnws.pyx",
  "_dynamic.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming;
struct __pyx_obj_8obitools_5align_4_nws_NWS;
struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS;
struct __pyx_t_8obitools_5align_8_dynamic_AlignCell;
struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix;
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateMatrix;
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence;
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath;
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath;

/* "_dynamic.pxd":11
 *     void memcpy(void* s1, void* s2, int n)
 * 
 * cdef struct AlignCell :             # <<<<<<<<<<<<<<
 *     double score
 *     int   path
 */
struct __pyx_t_8obitools_5align_8_dynamic_AlignCell {
  double score;
  int path;
};

/* "_dynamic.pxd":15
 *     int   path
 * 
 * cdef struct AlignMatrix :             # <<<<<<<<<<<<<<
 *     AlignCell*  matrix
 *     int*        bestVJump
 */
struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix {
  struct __pyx_t_8obitools_5align_8_dynamic_AlignCell *matrix;
  int *bestVJump;
  int *bestHJump;
  int msize;
  int vsize;
  int hsize;
};

/* "_dynamic.pxd":25
 * 
 * 
 * cdef AlignMatrix* allocateMatrix(int hsize, int vsize,AlignMatrix *matrix=?)             # <<<<<<<<<<<<<<
 * 
 * cdef void freeMatrix(AlignMatrix* matrix)
 */
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateMatrix {
  int __pyx_n;
  struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *matrix;
};

/* "_dynamic.pxd":32
 * 
 * 
 * cdef struct alignSequence:             # <<<<<<<<<<<<<<
 *     long    length
 *     long    buffsize
 */
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence {
  long length;
  long buffsize;
  int hasQuality;
  char *sequence;
  double *quality;
};

/* "_dynamic.pxd":39
 *     double* quality
 * 
 * cdef alignSequence* allocateSequence(object bioseq, alignSequence* seq=?) except *             # <<<<<<<<<<<<<<
 * 
 * cdef void freeSequence(alignSequence* seq)
 */
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence {
  int __pyx_n;
  struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *seq;
};

/* "_dynamic.pxd":43
 * cdef void freeSequence(alignSequence* seq)
 * 
 * cdef struct alignPath:             # <<<<<<<<<<<<<<
 *     long length
 *     long buffsize
 */
struct __pyx_t_8obitools_5align_8_dynamic_alignPath {
  long length;
  long buffsize;
  long vStart;
  long hStart;
  long *path;
};

/* "_dynamic.pxd":50
 *     long *path
 * 
 * cdef alignPath* allocatePath(long l1,long l2,alignPath* path=?)             # <<<<<<<<<<<<<<
 * 
 * cdef void reversePath(alignPath* path)
 */
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath {
  int __pyx_n;
  struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
};

/* "_dynamic.pxd":63
 * cpdef unsigned char encodeBase(unsigned char lettre)
 * 
 * cdef class DynamicProgramming:             # <<<<<<<<<<<<<<
 *     cdef AlignMatrix* matrix
 * 
 */
struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming {
  PyObject_HEAD
  struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming *__pyx_vtab;
  struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *matrix;
  PyObject *horizontalSeq;
  PyObject *verticalSeq;
  struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *hSeq;
  struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *vSeq;
  struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
  double _opengap;
  double _extgap;
  PyObject *alignment;
  int sequenceChanged;
  int scoreChanged;
};


/* "_nws.pxd":3
 * from _dynamic cimport *
 * 
 * cdef class NWS(DynamicProgramming):             # <<<<<<<<<<<<<<
 *     cdef double _match
 *     cdef double _mismatch
 */
struct __pyx_obj_8obitools_5align_4_nws_NWS {
  struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming __pyx_base;
  double _match;
  double _mismatch;
};

struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS {
  struct __pyx_obj_8obitools_5align_4_nws_NWS __pyx_base;
  int _phasedA;
  int _phasedB;
};



/* "_dynamic.pxd":63
 * cpdef unsigned char encodeBase(unsigned char lettre)
 * 
 * cdef class DynamicProgramming:             # <<<<<<<<<<<<<<
 *     cdef AlignMatrix* matrix
 * 
 */

struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming {
  int (*_vlen)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  int (*_hlen)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  int (*allocate)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  double (*doAlignment)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  void (*reset)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  int (*index)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int);
  int (*_needToCompute)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  void (*backtrack)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
  void (*clean)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
};
static struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming *__pyx_vtabptr_8obitools_5align_8_dynamic_DynamicProgramming;


/* "_nws.pxd":3
 * from _dynamic cimport *
 * 
 * cdef class NWS(DynamicProgramming):             # <<<<<<<<<<<<<<
 *     cdef double _match
 *     cdef double _mismatch
 */

struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS {
  struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming __pyx_base;
  double (*matchScore)(struct __pyx_obj_8obitools_5align_4_nws_NWS *, int, int);
};
static struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *__pyx_vtabptr_8obitools_5align_4_nws_NWS;


/* "obitools/align/_codonnws.pyx":1372
 * 
 * 
 * cdef class CodonNWS(NWS):             # <<<<<<<<<<<<<<
 * 
 *     def __init__(self,match=2,mismatch=-3,opengap=-4,extgap=-1, phasedA = -1, phasedB = -1):#, AAmatrix=_blosum62, translationtable=None):
 */

struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS {
  struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS __pyx_base;
  double (*matchCodon)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int, int);
  int (*colindex)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int);
  int (*rowindex)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int);
};
static struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *__pyx_vtabptr_8obitools_5align_9_codonnws_CodonNWS;
static int __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_colindex(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int);
static int __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_rowindex(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int);
#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 PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*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 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 CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */

static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */

#define UNARY_NEG_WOULD_OVERFLOW(x)            (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x)))

static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/
#if PY_MAJOR_VERSION >= 3
static PyObject* __pyx_print = 0;
static PyObject* __pyx_print_kwargs = 0;
#endif

static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*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 CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/

static void __Pyx_WriteUnraisable(const char *name, int clineno,
                                  int lineno, const char *filename); /*proto*/

static int __Pyx_check_binary_version(void);

#if !defined(__Pyx_PyIdentifier_FromString)
#if PY_MAJOR_VERSION < 3
  #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
#else
  #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
#endif
#endif

static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);  /*proto*/

static PyObject *__Pyx_ImportModule(const char *name); /*proto*/

static void* __Pyx_GetVtable(PyObject *dict); /*proto*/

static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/

static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); /*proto*/

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 'obitools.align._dynamic' */
static PyTypeObject *__pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming = 0;
static struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(*__pyx_f_8obitools_5align_8_dynamic_allocatePath)(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args); /*proto*/
static double (*__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch)(unsigned char, unsigned char, int __pyx_skip_dispatch); /*proto*/

/* Module declarations from 'obitools.align._nws' */
static PyTypeObject *__pyx_ptype_8obitools_5align_4_nws_NWS = 0;

/* Module declarations from 'obitools.align._codonnws' */
static PyTypeObject *__pyx_ptype_8obitools_5align_9_codonnws_CodonNWS = 0;
static char __pyx_f_8obitools_5align_9_codonnws__translate(char, char, char); /*proto*/
static double __pyx_f_8obitools_5align_9_codonnws__blosum62(char, char, char, char, char, char); /*proto*/
#define __Pyx_MODULE_NAME "obitools.align._codonnws"
int __pyx_module_is_main_obitools__align___codonnws = 0;

/* Implementation of 'obitools.align._codonnws' */
static PyObject *__pyx_builtin_range;
static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS___init__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_match, PyObject *__pyx_v_mismatch, PyObject *__pyx_v_opengap, PyObject *__pyx_v_extgap, PyObject *__pyx_v_phasedA, PyObject *__pyx_v_phasedB); /* proto */
static PyObject *__pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match___get__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self); /* proto */
static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match_2__set__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_match); /* proto */
static PyObject *__pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch___get__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self); /* proto */
static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_2__set__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_mismatch); /* proto */
static char __pyx_k_2[] = "badaboum !";
static char __pyx_k_3[] = "\nCreated on 6 Nov. 2009\n\n@author: coissac\n";
static char __pyx_k__match[] = "match";
static char __pyx_k__range[] = "range";
static char __pyx_k__extgap[] = "extgap";
static char __pyx_k__opengap[] = "opengap";
static char __pyx_k__phasedA[] = "phasedA";
static char __pyx_k__phasedB[] = "phasedB";
static char __pyx_k____init__[] = "__init__";
static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__mismatch[] = "mismatch";
static char __pyx_k__needToCompute[] = "needToCompute";
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_n_s____init__;
static PyObject *__pyx_n_s____main__;
static PyObject *__pyx_n_s____test__;
static PyObject *__pyx_n_s__extgap;
static PyObject *__pyx_n_s__match;
static PyObject *__pyx_n_s__mismatch;
static PyObject *__pyx_n_s__needToCompute;
static PyObject *__pyx_n_s__opengap;
static PyObject *__pyx_n_s__phasedA;
static PyObject *__pyx_n_s__phasedB;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_2;
static PyObject *__pyx_int_3;
static PyObject *__pyx_int_neg_1;
static PyObject *__pyx_int_neg_3;
static PyObject *__pyx_int_neg_4;
static PyObject *__pyx_k_tuple_1;

/* "obitools/align/_codonnws.pyx":26
 * 
 * #TODO : fonction completement cablee en dure a changer vite !
 * cdef char _translate(char c1, char c2, char c3):             # <<<<<<<<<<<<<<
 *     if c1=='a':
 *         if c2=='a':
 */

static char __pyx_f_8obitools_5align_9_codonnws__translate(char __pyx_v_c1, char __pyx_v_c2, char __pyx_v_c3) {
  char __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("_translate", 0);

  /* "obitools/align/_codonnws.pyx":27
 * #TODO : fonction completement cablee en dure a changer vite !
 * cdef char _translate(char c1, char c2, char c3):
 *     if c1=='a':             # <<<<<<<<<<<<<<
 *         if c2=='a':
 *             if c3=='a':
 */
  __pyx_t_1 = (__pyx_v_c1 == 'a');
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":28
 * cdef char _translate(char c1, char c2, char c3):
 *     if c1=='a':
 *         if c2=='a':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'k'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'a');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":29
 *     if c1=='a':
 *         if c2=='a':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'k'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":30
 *         if c2=='a':
 *             if c3=='a':
 *                 return 'k'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'n'
 */
        __pyx_r = 'k';
        goto __pyx_L0;
        goto __pyx_L5;
      }

      /* "obitools/align/_codonnws.pyx":31
 *             if c3=='a':
 *                 return 'k'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'n'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":32
 *                 return 'k'
 *             elif c3=='c':
 *                 return 'n'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'k'
 */
        __pyx_r = 'n';
        goto __pyx_L0;
        goto __pyx_L5;
      }

      /* "obitools/align/_codonnws.pyx":33
 *             elif c3=='c':
 *                 return 'n'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'k'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":34
 *                 return 'n'
 *             elif c3=='g':
 *                 return 'k'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'n'
 */
        __pyx_r = 'k';
        goto __pyx_L0;
        goto __pyx_L5;
      }

      /* "obitools/align/_codonnws.pyx":35
 *             elif c3=='g':
 *                 return 'k'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'n'
 *         elif c2=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":36
 *                 return 'k'
 *             elif c3=='t':
 *                 return 'n'             # <<<<<<<<<<<<<<
 *         elif c2=='c':
 *             if c3=='a':
 */
        __pyx_r = 'n';
        goto __pyx_L0;
        goto __pyx_L5;
      }
      __pyx_L5:;
      goto __pyx_L4;
    }

    /* "obitools/align/_codonnws.pyx":37
 *             elif c3=='t':
 *                 return 'n'
 *         elif c2=='c':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 't'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'c');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":38
 *                 return 'n'
 *         elif c2=='c':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 't'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":39
 *         elif c2=='c':
 *             if c3=='a':
 *                 return 't'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 't'
 */
        __pyx_r = 't';
        goto __pyx_L0;
        goto __pyx_L6;
      }

      /* "obitools/align/_codonnws.pyx":40
 *             if c3=='a':
 *                 return 't'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 't'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":41
 *                 return 't'
 *             elif c3=='c':
 *                 return 't'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 't'
 */
        __pyx_r = 't';
        goto __pyx_L0;
        goto __pyx_L6;
      }

      /* "obitools/align/_codonnws.pyx":42
 *             elif c3=='c':
 *                 return 't'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 't'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":43
 *                 return 't'
 *             elif c3=='g':
 *                 return 't'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 't'
 */
        __pyx_r = 't';
        goto __pyx_L0;
        goto __pyx_L6;
      }

      /* "obitools/align/_codonnws.pyx":44
 *             elif c3=='g':
 *                 return 't'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 't'
 *         elif c2=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":45
 *                 return 't'
 *             elif c3=='t':
 *                 return 't'             # <<<<<<<<<<<<<<
 *         elif c2=='g':
 *             if c3=='a':
 */
        __pyx_r = 't';
        goto __pyx_L0;
        goto __pyx_L6;
      }
      __pyx_L6:;
      goto __pyx_L4;
    }

    /* "obitools/align/_codonnws.pyx":46
 *             elif c3=='t':
 *                 return 't'
 *         elif c2=='g':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'r'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'g');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":47
 *                 return 't'
 *         elif c2=='g':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":48
 *         elif c2=='g':
 *             if c3=='a':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 's'
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L7;
      }

      /* "obitools/align/_codonnws.pyx":49
 *             if c3=='a':
 *                 return 'r'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 's'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":50
 *                 return 'r'
 *             elif c3=='c':
 *                 return 's'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'r'
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L7;
      }

      /* "obitools/align/_codonnws.pyx":51
 *             elif c3=='c':
 *                 return 's'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":52
 *                 return 's'
 *             elif c3=='g':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 's'
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L7;
      }

      /* "obitools/align/_codonnws.pyx":53
 *             elif c3=='g':
 *                 return 'r'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 's'
 *         elif c2=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":54
 *                 return 'r'
 *             elif c3=='t':
 *                 return 's'             # <<<<<<<<<<<<<<
 *         elif c2=='t':
 *             if c3=='a':
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L7;
      }
      __pyx_L7:;
      goto __pyx_L4;
    }

    /* "obitools/align/_codonnws.pyx":55
 *             elif c3=='t':
 *                 return 's'
 *         elif c2=='t':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'i'
 */
    __pyx_t_1 = (__pyx_v_c2 == 't');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":56
 *                 return 's'
 *         elif c2=='t':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'i'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":57
 *         elif c2=='t':
 *             if c3=='a':
 *                 return 'i'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'i'
 */
        __pyx_r = 'i';
        goto __pyx_L0;
        goto __pyx_L8;
      }

      /* "obitools/align/_codonnws.pyx":58
 *             if c3=='a':
 *                 return 'i'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'i'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":59
 *                 return 'i'
 *             elif c3=='c':
 *                 return 'i'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'm'
 */
        __pyx_r = 'i';
        goto __pyx_L0;
        goto __pyx_L8;
      }

      /* "obitools/align/_codonnws.pyx":60
 *             elif c3=='c':
 *                 return 'i'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'm'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":61
 *                 return 'i'
 *             elif c3=='g':
 *                 return 'm'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'i'
 */
        __pyx_r = 'm';
        goto __pyx_L0;
        goto __pyx_L8;
      }

      /* "obitools/align/_codonnws.pyx":62
 *             elif c3=='g':
 *                 return 'm'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'i'
 *     elif c1=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":63
 *                 return 'm'
 *             elif c3=='t':
 *                 return 'i'             # <<<<<<<<<<<<<<
 *     elif c1=='c':
 *         if c2=='a':
 */
        __pyx_r = 'i';
        goto __pyx_L0;
        goto __pyx_L8;
      }
      __pyx_L8:;
      goto __pyx_L4;
    }
    __pyx_L4:;
    goto __pyx_L3;
  }

  /* "obitools/align/_codonnws.pyx":64
 *             elif c3=='t':
 *                 return 'i'
 *     elif c1=='c':             # <<<<<<<<<<<<<<
 *         if c2=='a':
 *             if c3=='a':
 */
  __pyx_t_1 = (__pyx_v_c1 == 'c');
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":65
 *                 return 'i'
 *     elif c1=='c':
 *         if c2=='a':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'q'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'a');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":66
 *     elif c1=='c':
 *         if c2=='a':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'q'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":67
 *         if c2=='a':
 *             if c3=='a':
 *                 return 'q'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'h'
 */
        __pyx_r = 'q';
        goto __pyx_L0;
        goto __pyx_L10;
      }

      /* "obitools/align/_codonnws.pyx":68
 *             if c3=='a':
 *                 return 'q'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'h'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":69
 *                 return 'q'
 *             elif c3=='c':
 *                 return 'h'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'q'
 */
        __pyx_r = 'h';
        goto __pyx_L0;
        goto __pyx_L10;
      }

      /* "obitools/align/_codonnws.pyx":70
 *             elif c3=='c':
 *                 return 'h'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'q'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":71
 *                 return 'h'
 *             elif c3=='g':
 *                 return 'q'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'h'
 */
        __pyx_r = 'q';
        goto __pyx_L0;
        goto __pyx_L10;
      }

      /* "obitools/align/_codonnws.pyx":72
 *             elif c3=='g':
 *                 return 'q'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'h'
 *         elif c2=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":73
 *                 return 'q'
 *             elif c3=='t':
 *                 return 'h'             # <<<<<<<<<<<<<<
 *         elif c2=='c':
 *             if c3=='a':
 */
        __pyx_r = 'h';
        goto __pyx_L0;
        goto __pyx_L10;
      }
      __pyx_L10:;
      goto __pyx_L9;
    }

    /* "obitools/align/_codonnws.pyx":74
 *             elif c3=='t':
 *                 return 'h'
 *         elif c2=='c':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'p'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'c');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":75
 *                 return 'h'
 *         elif c2=='c':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'p'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":76
 *         elif c2=='c':
 *             if c3=='a':
 *                 return 'p'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'p'
 */
        __pyx_r = 'p';
        goto __pyx_L0;
        goto __pyx_L11;
      }

      /* "obitools/align/_codonnws.pyx":77
 *             if c3=='a':
 *                 return 'p'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'p'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":78
 *                 return 'p'
 *             elif c3=='c':
 *                 return 'p'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'p'
 */
        __pyx_r = 'p';
        goto __pyx_L0;
        goto __pyx_L11;
      }

      /* "obitools/align/_codonnws.pyx":79
 *             elif c3=='c':
 *                 return 'p'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'p'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":80
 *                 return 'p'
 *             elif c3=='g':
 *                 return 'p'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'p'
 */
        __pyx_r = 'p';
        goto __pyx_L0;
        goto __pyx_L11;
      }

      /* "obitools/align/_codonnws.pyx":81
 *             elif c3=='g':
 *                 return 'p'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'p'
 *         elif c2=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":82
 *                 return 'p'
 *             elif c3=='t':
 *                 return 'p'             # <<<<<<<<<<<<<<
 *         elif c2=='g':
 *             if c3=='a':
 */
        __pyx_r = 'p';
        goto __pyx_L0;
        goto __pyx_L11;
      }
      __pyx_L11:;
      goto __pyx_L9;
    }

    /* "obitools/align/_codonnws.pyx":83
 *             elif c3=='t':
 *                 return 'p'
 *         elif c2=='g':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'r'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'g');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":84
 *                 return 'p'
 *         elif c2=='g':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":85
 *         elif c2=='g':
 *             if c3=='a':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'r'
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L12;
      }

      /* "obitools/align/_codonnws.pyx":86
 *             if c3=='a':
 *                 return 'r'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":87
 *                 return 'r'
 *             elif c3=='c':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'r'
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L12;
      }

      /* "obitools/align/_codonnws.pyx":88
 *             elif c3=='c':
 *                 return 'r'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":89
 *                 return 'r'
 *             elif c3=='g':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'r'
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L12;
      }

      /* "obitools/align/_codonnws.pyx":90
 *             elif c3=='g':
 *                 return 'r'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'r'
 *         elif c2=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":91
 *                 return 'r'
 *             elif c3=='t':
 *                 return 'r'             # <<<<<<<<<<<<<<
 *         elif c2=='g':
 *             if c3=='a':
 */
        __pyx_r = 'r';
        goto __pyx_L0;
        goto __pyx_L12;
      }
      __pyx_L12:;
      goto __pyx_L9;
    }

    /* "obitools/align/_codonnws.pyx":92
 *             elif c3=='t':
 *                 return 'r'
 *         elif c2=='g':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'l'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'g');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":93
 *                 return 'r'
 *         elif c2=='g':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":94
 *         elif c2=='g':
 *             if c3=='a':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'l'
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L13;
      }

      /* "obitools/align/_codonnws.pyx":95
 *             if c3=='a':
 *                 return 'l'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":96
 *                 return 'l'
 *             elif c3=='c':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'l'
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L13;
      }

      /* "obitools/align/_codonnws.pyx":97
 *             elif c3=='c':
 *                 return 'l'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":98
 *                 return 'l'
 *             elif c3=='g':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'l'
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L13;
      }

      /* "obitools/align/_codonnws.pyx":99
 *             elif c3=='g':
 *                 return 'l'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *     elif c1=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":100
 *                 return 'l'
 *             elif c3=='t':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *     elif c1=='g':
 *         if c2=='a':
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L13;
      }
      __pyx_L13:;
      goto __pyx_L9;
    }
    __pyx_L9:;
    goto __pyx_L3;
  }

  /* "obitools/align/_codonnws.pyx":101
 *             elif c3=='t':
 *                 return 'l'
 *     elif c1=='g':             # <<<<<<<<<<<<<<
 *         if c2=='a':
 *             if c3=='a':
 */
  __pyx_t_1 = (__pyx_v_c1 == 'g');
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":102
 *                 return 'l'
 *     elif c1=='g':
 *         if c2=='a':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'e'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'a');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":103
 *     elif c1=='g':
 *         if c2=='a':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'e'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":104
 *         if c2=='a':
 *             if c3=='a':
 *                 return 'e'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'd'
 */
        __pyx_r = 'e';
        goto __pyx_L0;
        goto __pyx_L15;
      }

      /* "obitools/align/_codonnws.pyx":105
 *             if c3=='a':
 *                 return 'e'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'd'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":106
 *                 return 'e'
 *             elif c3=='c':
 *                 return 'd'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'e'
 */
        __pyx_r = 'd';
        goto __pyx_L0;
        goto __pyx_L15;
      }

      /* "obitools/align/_codonnws.pyx":107
 *             elif c3=='c':
 *                 return 'd'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'e'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":108
 *                 return 'd'
 *             elif c3=='g':
 *                 return 'e'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'd'
 */
        __pyx_r = 'e';
        goto __pyx_L0;
        goto __pyx_L15;
      }

      /* "obitools/align/_codonnws.pyx":109
 *             elif c3=='g':
 *                 return 'e'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'd'
 *         elif c2=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":110
 *                 return 'e'
 *             elif c3=='t':
 *                 return 'd'             # <<<<<<<<<<<<<<
 *         elif c2=='c':
 *             if c3=='a':
 */
        __pyx_r = 'd';
        goto __pyx_L0;
        goto __pyx_L15;
      }
      __pyx_L15:;
      goto __pyx_L14;
    }

    /* "obitools/align/_codonnws.pyx":111
 *             elif c3=='t':
 *                 return 'd'
 *         elif c2=='c':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'a'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'c');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":112
 *                 return 'd'
 *         elif c2=='c':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'a'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":113
 *         elif c2=='c':
 *             if c3=='a':
 *                 return 'a'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'a'
 */
        __pyx_r = 'a';
        goto __pyx_L0;
        goto __pyx_L16;
      }

      /* "obitools/align/_codonnws.pyx":114
 *             if c3=='a':
 *                 return 'a'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'a'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":115
 *                 return 'a'
 *             elif c3=='c':
 *                 return 'a'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'a'
 */
        __pyx_r = 'a';
        goto __pyx_L0;
        goto __pyx_L16;
      }

      /* "obitools/align/_codonnws.pyx":116
 *             elif c3=='c':
 *                 return 'a'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'a'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":117
 *                 return 'a'
 *             elif c3=='g':
 *                 return 'a'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'a'
 */
        __pyx_r = 'a';
        goto __pyx_L0;
        goto __pyx_L16;
      }

      /* "obitools/align/_codonnws.pyx":118
 *             elif c3=='g':
 *                 return 'a'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'a'
 *         elif c2=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":119
 *                 return 'a'
 *             elif c3=='t':
 *                 return 'a'             # <<<<<<<<<<<<<<
 *         elif c2=='g':
 *             if c3=='a':
 */
        __pyx_r = 'a';
        goto __pyx_L0;
        goto __pyx_L16;
      }
      __pyx_L16:;
      goto __pyx_L14;
    }

    /* "obitools/align/_codonnws.pyx":120
 *             elif c3=='t':
 *                 return 'a'
 *         elif c2=='g':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'g'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'g');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":121
 *                 return 'a'
 *         elif c2=='g':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'g'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":122
 *         elif c2=='g':
 *             if c3=='a':
 *                 return 'g'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'g'
 */
        __pyx_r = 'g';
        goto __pyx_L0;
        goto __pyx_L17;
      }

      /* "obitools/align/_codonnws.pyx":123
 *             if c3=='a':
 *                 return 'g'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'g'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":124
 *                 return 'g'
 *             elif c3=='c':
 *                 return 'g'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'g'
 */
        __pyx_r = 'g';
        goto __pyx_L0;
        goto __pyx_L17;
      }

      /* "obitools/align/_codonnws.pyx":125
 *             elif c3=='c':
 *                 return 'g'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'g'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":126
 *                 return 'g'
 *             elif c3=='g':
 *                 return 'g'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'g'
 */
        __pyx_r = 'g';
        goto __pyx_L0;
        goto __pyx_L17;
      }

      /* "obitools/align/_codonnws.pyx":127
 *             elif c3=='g':
 *                 return 'g'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'g'
 *         elif c2=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":128
 *                 return 'g'
 *             elif c3=='t':
 *                 return 'g'             # <<<<<<<<<<<<<<
 *         elif c2=='t':
 *             if c3=='a':
 */
        __pyx_r = 'g';
        goto __pyx_L0;
        goto __pyx_L17;
      }
      __pyx_L17:;
      goto __pyx_L14;
    }

    /* "obitools/align/_codonnws.pyx":129
 *             elif c3=='t':
 *                 return 'g'
 *         elif c2=='t':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'v'
 */
    __pyx_t_1 = (__pyx_v_c2 == 't');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":130
 *                 return 'g'
 *         elif c2=='t':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'v'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":131
 *         elif c2=='t':
 *             if c3=='a':
 *                 return 'v'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'v'
 */
        __pyx_r = 'v';
        goto __pyx_L0;
        goto __pyx_L18;
      }

      /* "obitools/align/_codonnws.pyx":132
 *             if c3=='a':
 *                 return 'v'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'v'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":133
 *                 return 'v'
 *             elif c3=='c':
 *                 return 'v'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'v'
 */
        __pyx_r = 'v';
        goto __pyx_L0;
        goto __pyx_L18;
      }

      /* "obitools/align/_codonnws.pyx":134
 *             elif c3=='c':
 *                 return 'v'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'v'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":135
 *                 return 'v'
 *             elif c3=='g':
 *                 return 'v'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'v'
 */
        __pyx_r = 'v';
        goto __pyx_L0;
        goto __pyx_L18;
      }

      /* "obitools/align/_codonnws.pyx":136
 *             elif c3=='g':
 *                 return 'v'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'v'
 *     elif c1=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":137
 *                 return 'v'
 *             elif c3=='t':
 *                 return 'v'             # <<<<<<<<<<<<<<
 *     elif c1=='t':
 *         if c2=='a':
 */
        __pyx_r = 'v';
        goto __pyx_L0;
        goto __pyx_L18;
      }
      __pyx_L18:;
      goto __pyx_L14;
    }
    __pyx_L14:;
    goto __pyx_L3;
  }

  /* "obitools/align/_codonnws.pyx":138
 *             elif c3=='t':
 *                 return 'v'
 *     elif c1=='t':             # <<<<<<<<<<<<<<
 *         if c2=='a':
 *             if c3=='a':
 */
  __pyx_t_1 = (__pyx_v_c1 == 't');
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":139
 *                 return 'v'
 *     elif c1=='t':
 *         if c2=='a':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return '*'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'a');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":140
 *     elif c1=='t':
 *         if c2=='a':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return '*'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":141
 *         if c2=='a':
 *             if c3=='a':
 *                 return '*'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'y'
 */
        __pyx_r = '*';
        goto __pyx_L0;
        goto __pyx_L20;
      }

      /* "obitools/align/_codonnws.pyx":142
 *             if c3=='a':
 *                 return '*'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'y'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":143
 *                 return '*'
 *             elif c3=='c':
 *                 return 'y'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return '*'
 */
        __pyx_r = 'y';
        goto __pyx_L0;
        goto __pyx_L20;
      }

      /* "obitools/align/_codonnws.pyx":144
 *             elif c3=='c':
 *                 return 'y'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return '*'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":145
 *                 return 'y'
 *             elif c3=='g':
 *                 return '*'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'y'
 */
        __pyx_r = '*';
        goto __pyx_L0;
        goto __pyx_L20;
      }

      /* "obitools/align/_codonnws.pyx":146
 *             elif c3=='g':
 *                 return '*'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'y'
 *         elif c2=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":147
 *                 return '*'
 *             elif c3=='t':
 *                 return 'y'             # <<<<<<<<<<<<<<
 *         elif c2=='c':
 *             if c3=='a':
 */
        __pyx_r = 'y';
        goto __pyx_L0;
        goto __pyx_L20;
      }
      __pyx_L20:;
      goto __pyx_L19;
    }

    /* "obitools/align/_codonnws.pyx":148
 *             elif c3=='t':
 *                 return 'y'
 *         elif c2=='c':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 's'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'c');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":149
 *                 return 'y'
 *         elif c2=='c':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 's'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":150
 *         elif c2=='c':
 *             if c3=='a':
 *                 return 's'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 's'
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L21;
      }

      /* "obitools/align/_codonnws.pyx":151
 *             if c3=='a':
 *                 return 's'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 's'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":152
 *                 return 's'
 *             elif c3=='c':
 *                 return 's'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 's'
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L21;
      }

      /* "obitools/align/_codonnws.pyx":153
 *             elif c3=='c':
 *                 return 's'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 's'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":154
 *                 return 's'
 *             elif c3=='g':
 *                 return 's'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 's'
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L21;
      }

      /* "obitools/align/_codonnws.pyx":155
 *             elif c3=='g':
 *                 return 's'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 's'
 *         elif c2=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":156
 *                 return 's'
 *             elif c3=='t':
 *                 return 's'             # <<<<<<<<<<<<<<
 *         elif c2=='g':
 *             if c3=='a':
 */
        __pyx_r = 's';
        goto __pyx_L0;
        goto __pyx_L21;
      }
      __pyx_L21:;
      goto __pyx_L19;
    }

    /* "obitools/align/_codonnws.pyx":157
 *             elif c3=='t':
 *                 return 's'
 *         elif c2=='g':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return '*'
 */
    __pyx_t_1 = (__pyx_v_c2 == 'g');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":158
 *                 return 's'
 *         elif c2=='g':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return '*'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":159
 *         elif c2=='g':
 *             if c3=='a':
 *                 return '*'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'c'
 */
        __pyx_r = '*';
        goto __pyx_L0;
        goto __pyx_L22;
      }

      /* "obitools/align/_codonnws.pyx":160
 *             if c3=='a':
 *                 return '*'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'c'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":161
 *                 return '*'
 *             elif c3=='c':
 *                 return 'c'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'w'
 */
        __pyx_r = 'c';
        goto __pyx_L0;
        goto __pyx_L22;
      }

      /* "obitools/align/_codonnws.pyx":162
 *             elif c3=='c':
 *                 return 'c'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'w'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":163
 *                 return 'c'
 *             elif c3=='g':
 *                 return 'w'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'c'
 */
        __pyx_r = 'w';
        goto __pyx_L0;
        goto __pyx_L22;
      }

      /* "obitools/align/_codonnws.pyx":164
 *             elif c3=='g':
 *                 return 'w'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'c'
 *         elif c2=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":165
 *                 return 'w'
 *             elif c3=='t':
 *                 return 'c'             # <<<<<<<<<<<<<<
 *         elif c2=='t':
 *             if c3=='a':
 */
        __pyx_r = 'c';
        goto __pyx_L0;
        goto __pyx_L22;
      }
      __pyx_L22:;
      goto __pyx_L19;
    }

    /* "obitools/align/_codonnws.pyx":166
 *             elif c3=='t':
 *                 return 'c'
 *         elif c2=='t':             # <<<<<<<<<<<<<<
 *             if c3=='a':
 *                 return 'l'
 */
    __pyx_t_1 = (__pyx_v_c2 == 't');
    if (__pyx_t_1) {

      /* "obitools/align/_codonnws.pyx":167
 *                 return 'c'
 *         elif c2=='t':
 *             if c3=='a':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *             elif c3=='c':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'a');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":168
 *         elif c2=='t':
 *             if c3=='a':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *             elif c3=='c':
 *                 return 'f'
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L23;
      }

      /* "obitools/align/_codonnws.pyx":169
 *             if c3=='a':
 *                 return 'l'
 *             elif c3=='c':             # <<<<<<<<<<<<<<
 *                 return 'f'
 *             elif c3=='g':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'c');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":170
 *                 return 'l'
 *             elif c3=='c':
 *                 return 'f'             # <<<<<<<<<<<<<<
 *             elif c3=='g':
 *                 return 'l'
 */
        __pyx_r = 'f';
        goto __pyx_L0;
        goto __pyx_L23;
      }

      /* "obitools/align/_codonnws.pyx":171
 *             elif c3=='c':
 *                 return 'f'
 *             elif c3=='g':             # <<<<<<<<<<<<<<
 *                 return 'l'
 *             elif c3=='t':
 */
      __pyx_t_1 = (__pyx_v_c3 == 'g');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":172
 *                 return 'f'
 *             elif c3=='g':
 *                 return 'l'             # <<<<<<<<<<<<<<
 *             elif c3=='t':
 *                 return 'f'
 */
        __pyx_r = 'l';
        goto __pyx_L0;
        goto __pyx_L23;
      }

      /* "obitools/align/_codonnws.pyx":173
 *             elif c3=='g':
 *                 return 'l'
 *             elif c3=='t':             # <<<<<<<<<<<<<<
 *                 return 'f'
 * 
 */
      __pyx_t_1 = (__pyx_v_c3 == 't');
      if (__pyx_t_1) {

        /* "obitools/align/_codonnws.pyx":174
 *                 return 'l'
 *             elif c3=='t':
 *                 return 'f'             # <<<<<<<<<<<<<<
 * 
 *     return '*'
 */
        __pyx_r = 'f';
        goto __pyx_L0;
        goto __pyx_L23;
      }
      __pyx_L23:;
      goto __pyx_L19;
    }
    __pyx_L19:;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "obitools/align/_codonnws.pyx":176
 *                 return 'f'
 * 
 *     return '*'             # <<<<<<<<<<<<<<
 * 
 * #http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
 */
  __pyx_r = '*';
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":213
 * #
 * 
 * cdef double _blosum62(char c1_1, char c1_2, char c1_3, char c2_1, char c2_2, char c2_3):             # <<<<<<<<<<<<<<
 * 
 *     cdef char aa1 = _translate(c1_1, c1_2, c1_3)
 */

static double __pyx_f_8obitools_5align_9_codonnws__blosum62(char __pyx_v_c1_1, char __pyx_v_c1_2, char __pyx_v_c1_3, char __pyx_v_c2_1, char __pyx_v_c2_2, char __pyx_v_c2_3) {
  char __pyx_v_aa1;
  char __pyx_v_aa2;
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  __Pyx_RefNannySetupContext("_blosum62", 0);

  /* "obitools/align/_codonnws.pyx":215
 * cdef double _blosum62(char c1_1, char c1_2, char c1_3, char c2_1, char c2_2, char c2_3):
 * 
 *     cdef char aa1 = _translate(c1_1, c1_2, c1_3)             # <<<<<<<<<<<<<<
 *     cdef char aa2 = _translate(c2_1, c2_2, c2_3)
 * 
 */
  __pyx_v_aa1 = __pyx_f_8obitools_5align_9_codonnws__translate(__pyx_v_c1_1, __pyx_v_c1_2, __pyx_v_c1_3);

  /* "obitools/align/_codonnws.pyx":216
 * 
 *     cdef char aa1 = _translate(c1_1, c1_2, c1_3)
 *     cdef char aa2 = _translate(c2_1, c2_2, c2_3)             # <<<<<<<<<<<<<<
 * 
 *     if aa1=="a" and aa2=="a":
 */
  __pyx_v_aa2 = __pyx_f_8obitools_5align_9_codonnws__translate(__pyx_v_c2_1, __pyx_v_c2_2, __pyx_v_c2_3);

  /* "obitools/align/_codonnws.pyx":218
 *     cdef char aa2 = _translate(c2_1, c2_2, c2_3)
 * 
 *     if aa1=="a" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="a" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":219
 * 
 *     if aa1=="a" and aa2=="a":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="r":
 *         return -1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "obitools/align/_codonnws.pyx":220
 *     if aa1=="a" and aa2=="a":
 *         return 4
 *     if aa1=="a" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":221
 *         return 4
 *     if aa1=="a" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="n":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "obitools/align/_codonnws.pyx":222
 *     if aa1=="a" and aa2=="r":
 *         return -1
 *     if aa1=="a" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":223
 *         return -1
 *     if aa1=="a" and aa2=="n":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="d":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L5;
  }
  __pyx_L5:;

  /* "obitools/align/_codonnws.pyx":224
 *     if aa1=="a" and aa2=="n":
 *         return -2
 *     if aa1=="a" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":225
 *         return -2
 *     if aa1=="a" and aa2=="d":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="c":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L6;
  }
  __pyx_L6:;

  /* "obitools/align/_codonnws.pyx":226
 *     if aa1=="a" and aa2=="d":
 *         return -2
 *     if aa1=="a" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="a" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":227
 *         return -2
 *     if aa1=="a" and aa2=="c":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="q":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L7;
  }
  __pyx_L7:;

  /* "obitools/align/_codonnws.pyx":228
 *     if aa1=="a" and aa2=="c":
 *         return 0
 *     if aa1=="a" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":229
 *         return 0
 *     if aa1=="a" and aa2=="q":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="e":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L8;
  }
  __pyx_L8:;

  /* "obitools/align/_codonnws.pyx":230
 *     if aa1=="a" and aa2=="q":
 *         return -1
 *     if aa1=="a" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":231
 *         return -1
 *     if aa1=="a" and aa2=="e":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="g":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L9;
  }
  __pyx_L9:;

  /* "obitools/align/_codonnws.pyx":232
 *     if aa1=="a" and aa2=="e":
 *         return -1
 *     if aa1=="a" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="a" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":233
 *         return -1
 *     if aa1=="a" and aa2=="g":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="h":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L10;
  }
  __pyx_L10:;

  /* "obitools/align/_codonnws.pyx":234
 *     if aa1=="a" and aa2=="g":
 *         return 0
 *     if aa1=="a" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":235
 *         return 0
 *     if aa1=="a" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="i":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L11;
  }
  __pyx_L11:;

  /* "obitools/align/_codonnws.pyx":236
 *     if aa1=="a" and aa2=="h":
 *         return -2
 *     if aa1=="a" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":237
 *         return -2
 *     if aa1=="a" and aa2=="i":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="l":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L12;
  }
  __pyx_L12:;

  /* "obitools/align/_codonnws.pyx":238
 *     if aa1=="a" and aa2=="i":
 *         return -1
 *     if aa1=="a" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":239
 *         return -1
 *     if aa1=="a" and aa2=="l":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="k":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L13;
  }
  __pyx_L13:;

  /* "obitools/align/_codonnws.pyx":240
 *     if aa1=="a" and aa2=="l":
 *         return -1
 *     if aa1=="a" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":241
 *         return -1
 *     if aa1=="a" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="m":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L14;
  }
  __pyx_L14:;

  /* "obitools/align/_codonnws.pyx":242
 *     if aa1=="a" and aa2=="k":
 *         return -1
 *     if aa1=="a" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":243
 *         return -1
 *     if aa1=="a" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="f":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L15;
  }
  __pyx_L15:;

  /* "obitools/align/_codonnws.pyx":244
 *     if aa1=="a" and aa2=="m":
 *         return -1
 *     if aa1=="a" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":245
 *         return -1
 *     if aa1=="a" and aa2=="f":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="p":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L16;
  }
  __pyx_L16:;

  /* "obitools/align/_codonnws.pyx":246
 *     if aa1=="a" and aa2=="f":
 *         return -2
 *     if aa1=="a" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":247
 *         return -2
 *     if aa1=="a" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="s":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L17;
  }
  __pyx_L17:;

  /* "obitools/align/_codonnws.pyx":248
 *     if aa1=="a" and aa2=="p":
 *         return -1
 *     if aa1=="a" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="a" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":249
 *         return -1
 *     if aa1=="a" and aa2=="s":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="t":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L18;
  }
  __pyx_L18:;

  /* "obitools/align/_codonnws.pyx":250
 *     if aa1=="a" and aa2=="s":
 *         return 1
 *     if aa1=="a" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="a" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":251
 *         return 1
 *     if aa1=="a" and aa2=="t":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="w":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L19;
  }
  __pyx_L19:;

  /* "obitools/align/_codonnws.pyx":252
 *     if aa1=="a" and aa2=="t":
 *         return 0
 *     if aa1=="a" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="a" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":253
 *         return 0
 *     if aa1=="a" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L20;
  }
  __pyx_L20:;

  /* "obitools/align/_codonnws.pyx":254
 *     if aa1=="a" and aa2=="w":
 *         return -3
 *     if aa1=="a" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":255
 *         return -3
 *     if aa1=="a" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="v":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L21;
  }
  __pyx_L21:;

  /* "obitools/align/_codonnws.pyx":256
 *     if aa1=="a" and aa2=="y":
 *         return -2
 *     if aa1=="a" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="a" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":257
 *         return -2
 *     if aa1=="a" and aa2=="v":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="b":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L22;
  }
  __pyx_L22:;

  /* "obitools/align/_codonnws.pyx":258
 *     if aa1=="a" and aa2=="v":
 *         return 0
 *     if aa1=="a" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="a" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":259
 *         return 0
 *     if aa1=="a" and aa2=="b":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="z":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L23;
  }
  __pyx_L23:;

  /* "obitools/align/_codonnws.pyx":260
 *     if aa1=="a" and aa2=="b":
 *         return -2
 *     if aa1=="a" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="a" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":261
 *         return -2
 *     if aa1=="a" and aa2=="z":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="x":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L24;
  }
  __pyx_L24:;

  /* "obitools/align/_codonnws.pyx":262
 *     if aa1=="a" and aa2=="z":
 *         return -1
 *     if aa1=="a" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="a" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":263
 *         return -1
 *     if aa1=="a" and aa2=="x":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="a" and aa2=="*":
 *         return -4
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L25;
  }
  __pyx_L25:;

  /* "obitools/align/_codonnws.pyx":264
 *     if aa1=="a" and aa2=="x":
 *         return 0
 *     if aa1=="a" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="r" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'a');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":265
 *         return 0
 *     if aa1=="a" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L26;
  }
  __pyx_L26:;

  /* "obitools/align/_codonnws.pyx":266
 *     if aa1=="a" and aa2=="*":
 *         return -4
 *     if aa1=="r" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":267
 *         return -4
 *     if aa1=="r" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="r":
 *         return 5
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L27;
  }
  __pyx_L27:;

  /* "obitools/align/_codonnws.pyx":268
 *     if aa1=="r" and aa2=="a":
 *         return -1
 *     if aa1=="r" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="r" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":269
 *         return -1
 *     if aa1=="r" and aa2=="r":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="n":
 *         return 0
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L28;
  }
  __pyx_L28:;

  /* "obitools/align/_codonnws.pyx":270
 *     if aa1=="r" and aa2=="r":
 *         return 5
 *     if aa1=="r" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="r" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":271
 *         return 5
 *     if aa1=="r" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="d":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L29;
  }
  __pyx_L29:;

  /* "obitools/align/_codonnws.pyx":272
 *     if aa1=="r" and aa2=="n":
 *         return 0
 *     if aa1=="r" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="r" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":273
 *         return 0
 *     if aa1=="r" and aa2=="d":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="c":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L30;
  }
  __pyx_L30:;

  /* "obitools/align/_codonnws.pyx":274
 *     if aa1=="r" and aa2=="d":
 *         return -2
 *     if aa1=="r" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="r" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":275
 *         return -2
 *     if aa1=="r" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="q":
 *         return 1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L31;
  }
  __pyx_L31:;

  /* "obitools/align/_codonnws.pyx":276
 *     if aa1=="r" and aa2=="c":
 *         return -3
 *     if aa1=="r" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="r" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":277
 *         return -3
 *     if aa1=="r" and aa2=="q":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="e":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L32;
  }
  __pyx_L32:;

  /* "obitools/align/_codonnws.pyx":278
 *     if aa1=="r" and aa2=="q":
 *         return 1
 *     if aa1=="r" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="r" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":279
 *         return 1
 *     if aa1=="r" and aa2=="e":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="g":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L33;
  }
  __pyx_L33:;

  /* "obitools/align/_codonnws.pyx":280
 *     if aa1=="r" and aa2=="e":
 *         return 0
 *     if aa1=="r" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="r" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":281
 *         return 0
 *     if aa1=="r" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="h":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L34;
  }
  __pyx_L34:;

  /* "obitools/align/_codonnws.pyx":282
 *     if aa1=="r" and aa2=="g":
 *         return -2
 *     if aa1=="r" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="r" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":283
 *         return -2
 *     if aa1=="r" and aa2=="h":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="i":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L35;
  }
  __pyx_L35:;

  /* "obitools/align/_codonnws.pyx":284
 *     if aa1=="r" and aa2=="h":
 *         return 0
 *     if aa1=="r" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="r" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":285
 *         return 0
 *     if aa1=="r" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="l":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L36;
  }
  __pyx_L36:;

  /* "obitools/align/_codonnws.pyx":286
 *     if aa1=="r" and aa2=="i":
 *         return -3
 *     if aa1=="r" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="r" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":287
 *         return -3
 *     if aa1=="r" and aa2=="l":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="k":
 *         return 2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L37;
  }
  __pyx_L37:;

  /* "obitools/align/_codonnws.pyx":288
 *     if aa1=="r" and aa2=="l":
 *         return -2
 *     if aa1=="r" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="r" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":289
 *         return -2
 *     if aa1=="r" and aa2=="k":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="m":
 *         return -1
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L38;
  }
  __pyx_L38:;

  /* "obitools/align/_codonnws.pyx":290
 *     if aa1=="r" and aa2=="k":
 *         return 2
 *     if aa1=="r" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":291
 *         return 2
 *     if aa1=="r" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="f":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L39;
  }
  __pyx_L39:;

  /* "obitools/align/_codonnws.pyx":292
 *     if aa1=="r" and aa2=="m":
 *         return -1
 *     if aa1=="r" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="r" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":293
 *         return -1
 *     if aa1=="r" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="p":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L40;
  }
  __pyx_L40:;

  /* "obitools/align/_codonnws.pyx":294
 *     if aa1=="r" and aa2=="f":
 *         return -3
 *     if aa1=="r" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="r" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":295
 *         return -3
 *     if aa1=="r" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="s":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L41;
  }
  __pyx_L41:;

  /* "obitools/align/_codonnws.pyx":296
 *     if aa1=="r" and aa2=="p":
 *         return -2
 *     if aa1=="r" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":297
 *         return -2
 *     if aa1=="r" and aa2=="s":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="t":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L42;
  }
  __pyx_L42:;

  /* "obitools/align/_codonnws.pyx":298
 *     if aa1=="r" and aa2=="s":
 *         return -1
 *     if aa1=="r" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":299
 *         return -1
 *     if aa1=="r" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="w":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L43;
  }
  __pyx_L43:;

  /* "obitools/align/_codonnws.pyx":300
 *     if aa1=="r" and aa2=="t":
 *         return -1
 *     if aa1=="r" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="r" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":301
 *         return -1
 *     if aa1=="r" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L44;
  }
  __pyx_L44:;

  /* "obitools/align/_codonnws.pyx":302
 *     if aa1=="r" and aa2=="w":
 *         return -3
 *     if aa1=="r" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="r" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":303
 *         return -3
 *     if aa1=="r" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="v":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L45;
  }
  __pyx_L45:;

  /* "obitools/align/_codonnws.pyx":304
 *     if aa1=="r" and aa2=="y":
 *         return -2
 *     if aa1=="r" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="r" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":305
 *         return -2
 *     if aa1=="r" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="b":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L46;
  }
  __pyx_L46:;

  /* "obitools/align/_codonnws.pyx":306
 *     if aa1=="r" and aa2=="v":
 *         return -3
 *     if aa1=="r" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":307
 *         return -3
 *     if aa1=="r" and aa2=="b":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="z":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L47;
  }
  __pyx_L47:;

  /* "obitools/align/_codonnws.pyx":308
 *     if aa1=="r" and aa2=="b":
 *         return -1
 *     if aa1=="r" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="r" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":309
 *         return -1
 *     if aa1=="r" and aa2=="z":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="x":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L48;
  }
  __pyx_L48:;

  /* "obitools/align/_codonnws.pyx":310
 *     if aa1=="r" and aa2=="z":
 *         return 0
 *     if aa1=="r" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="r" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":311
 *         return 0
 *     if aa1=="r" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="r" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L49;
  }
  __pyx_L49:;

  /* "obitools/align/_codonnws.pyx":312
 *     if aa1=="r" and aa2=="x":
 *         return -1
 *     if aa1=="r" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="n" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'r');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":313
 *         return -1
 *     if aa1=="r" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L50;
  }
  __pyx_L50:;

  /* "obitools/align/_codonnws.pyx":314
 *     if aa1=="r" and aa2=="*":
 *         return -4
 *     if aa1=="n" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="n" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":315
 *         return -4
 *     if aa1=="n" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="r":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L51;
  }
  __pyx_L51:;

  /* "obitools/align/_codonnws.pyx":316
 *     if aa1=="n" and aa2=="a":
 *         return -2
 *     if aa1=="n" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":317
 *         return -2
 *     if aa1=="n" and aa2=="r":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="n":
 *         return 6
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L52;
  }
  __pyx_L52:;

  /* "obitools/align/_codonnws.pyx":318
 *     if aa1=="n" and aa2=="r":
 *         return 0
 *     if aa1=="n" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 6
 *     if aa1=="n" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":319
 *         return 0
 *     if aa1=="n" and aa2=="n":
 *         return 6             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="d":
 *         return 1
 */
    __pyx_r = 6.0;
    goto __pyx_L0;
    goto __pyx_L53;
  }
  __pyx_L53:;

  /* "obitools/align/_codonnws.pyx":320
 *     if aa1=="n" and aa2=="n":
 *         return 6
 *     if aa1=="n" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="n" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":321
 *         return 6
 *     if aa1=="n" and aa2=="d":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="c":
 *         return -3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L54;
  }
  __pyx_L54:;

  /* "obitools/align/_codonnws.pyx":322
 *     if aa1=="n" and aa2=="d":
 *         return 1
 *     if aa1=="n" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="n" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":323
 *         return 1
 *     if aa1=="n" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="q":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L55;
  }
  __pyx_L55:;

  /* "obitools/align/_codonnws.pyx":324
 *     if aa1=="n" and aa2=="c":
 *         return -3
 *     if aa1=="n" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":325
 *         return -3
 *     if aa1=="n" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="e":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L56;
  }
  __pyx_L56:;

  /* "obitools/align/_codonnws.pyx":326
 *     if aa1=="n" and aa2=="q":
 *         return 0
 *     if aa1=="n" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":327
 *         return 0
 *     if aa1=="n" and aa2=="e":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="g":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L57;
  }
  __pyx_L57:;

  /* "obitools/align/_codonnws.pyx":328
 *     if aa1=="n" and aa2=="e":
 *         return 0
 *     if aa1=="n" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":329
 *         return 0
 *     if aa1=="n" and aa2=="g":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="h":
 *         return 1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L58;
  }
  __pyx_L58:;

  /* "obitools/align/_codonnws.pyx":330
 *     if aa1=="n" and aa2=="g":
 *         return 0
 *     if aa1=="n" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="n" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":331
 *         return 0
 *     if aa1=="n" and aa2=="h":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="i":
 *         return -3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L59;
  }
  __pyx_L59:;

  /* "obitools/align/_codonnws.pyx":332
 *     if aa1=="n" and aa2=="h":
 *         return 1
 *     if aa1=="n" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="n" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":333
 *         return 1
 *     if aa1=="n" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="l":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L60;
  }
  __pyx_L60:;

  /* "obitools/align/_codonnws.pyx":334
 *     if aa1=="n" and aa2=="i":
 *         return -3
 *     if aa1=="n" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="n" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":335
 *         return -3
 *     if aa1=="n" and aa2=="l":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="k":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L61;
  }
  __pyx_L61:;

  /* "obitools/align/_codonnws.pyx":336
 *     if aa1=="n" and aa2=="l":
 *         return -3
 *     if aa1=="n" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":337
 *         return -3
 *     if aa1=="n" and aa2=="k":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="m":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L62;
  }
  __pyx_L62:;

  /* "obitools/align/_codonnws.pyx":338
 *     if aa1=="n" and aa2=="k":
 *         return 0
 *     if aa1=="n" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="n" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":339
 *         return 0
 *     if aa1=="n" and aa2=="m":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="f":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L63;
  }
  __pyx_L63:;

  /* "obitools/align/_codonnws.pyx":340
 *     if aa1=="n" and aa2=="m":
 *         return -2
 *     if aa1=="n" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="n" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":341
 *         return -2
 *     if aa1=="n" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="p":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L64;
  }
  __pyx_L64:;

  /* "obitools/align/_codonnws.pyx":342
 *     if aa1=="n" and aa2=="f":
 *         return -3
 *     if aa1=="n" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="n" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":343
 *         return -3
 *     if aa1=="n" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="s":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L65;
  }
  __pyx_L65:;

  /* "obitools/align/_codonnws.pyx":344
 *     if aa1=="n" and aa2=="p":
 *         return -2
 *     if aa1=="n" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="n" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":345
 *         return -2
 *     if aa1=="n" and aa2=="s":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="t":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L66;
  }
  __pyx_L66:;

  /* "obitools/align/_codonnws.pyx":346
 *     if aa1=="n" and aa2=="s":
 *         return 1
 *     if aa1=="n" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":347
 *         return 1
 *     if aa1=="n" and aa2=="t":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="w":
 *         return -4
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L67;
  }
  __pyx_L67:;

  /* "obitools/align/_codonnws.pyx":348
 *     if aa1=="n" and aa2=="t":
 *         return 0
 *     if aa1=="n" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="n" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":349
 *         return 0
 *     if aa1=="n" and aa2=="w":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="y":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L68;
  }
  __pyx_L68:;

  /* "obitools/align/_codonnws.pyx":350
 *     if aa1=="n" and aa2=="w":
 *         return -4
 *     if aa1=="n" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="n" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":351
 *         return -4
 *     if aa1=="n" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="v":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L69;
  }
  __pyx_L69:;

  /* "obitools/align/_codonnws.pyx":352
 *     if aa1=="n" and aa2=="y":
 *         return -2
 *     if aa1=="n" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="n" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":353
 *         return -2
 *     if aa1=="n" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="b":
 *         return 3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L70;
  }
  __pyx_L70:;

  /* "obitools/align/_codonnws.pyx":354
 *     if aa1=="n" and aa2=="v":
 *         return -3
 *     if aa1=="n" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="n" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":355
 *         return -3
 *     if aa1=="n" and aa2=="b":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="z":
 *         return 0
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L71;
  }
  __pyx_L71:;

  /* "obitools/align/_codonnws.pyx":356
 *     if aa1=="n" and aa2=="b":
 *         return 3
 *     if aa1=="n" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="n" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":357
 *         return 3
 *     if aa1=="n" and aa2=="z":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="x":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L72;
  }
  __pyx_L72:;

  /* "obitools/align/_codonnws.pyx":358
 *     if aa1=="n" and aa2=="z":
 *         return 0
 *     if aa1=="n" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="n" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":359
 *         return 0
 *     if aa1=="n" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="n" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L73;
  }
  __pyx_L73:;

  /* "obitools/align/_codonnws.pyx":360
 *     if aa1=="n" and aa2=="x":
 *         return -1
 *     if aa1=="n" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="d" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'n');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":361
 *         return -1
 *     if aa1=="n" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L74;
  }
  __pyx_L74:;

  /* "obitools/align/_codonnws.pyx":362
 *     if aa1=="n" and aa2=="*":
 *         return -4
 *     if aa1=="d" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="d" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":363
 *         return -4
 *     if aa1=="d" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="r":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L75;
  }
  __pyx_L75:;

  /* "obitools/align/_codonnws.pyx":364
 *     if aa1=="d" and aa2=="a":
 *         return -2
 *     if aa1=="d" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="d" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":365
 *         return -2
 *     if aa1=="d" and aa2=="r":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="n":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L76;
  }
  __pyx_L76:;

  /* "obitools/align/_codonnws.pyx":366
 *     if aa1=="d" and aa2=="r":
 *         return -2
 *     if aa1=="d" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="d" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":367
 *         return -2
 *     if aa1=="d" and aa2=="n":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="d":
 *         return 6
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L77;
  }
  __pyx_L77:;

  /* "obitools/align/_codonnws.pyx":368
 *     if aa1=="d" and aa2=="n":
 *         return 1
 *     if aa1=="d" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 6
 *     if aa1=="d" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":369
 *         return 1
 *     if aa1=="d" and aa2=="d":
 *         return 6             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="c":
 *         return -3
 */
    __pyx_r = 6.0;
    goto __pyx_L0;
    goto __pyx_L78;
  }
  __pyx_L78:;

  /* "obitools/align/_codonnws.pyx":370
 *     if aa1=="d" and aa2=="d":
 *         return 6
 *     if aa1=="d" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":371
 *         return 6
 *     if aa1=="d" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="q":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L79;
  }
  __pyx_L79:;

  /* "obitools/align/_codonnws.pyx":372
 *     if aa1=="d" and aa2=="c":
 *         return -3
 *     if aa1=="d" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="d" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":373
 *         return -3
 *     if aa1=="d" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="e":
 *         return 2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L80;
  }
  __pyx_L80:;

  /* "obitools/align/_codonnws.pyx":374
 *     if aa1=="d" and aa2=="q":
 *         return 0
 *     if aa1=="d" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="d" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":375
 *         return 0
 *     if aa1=="d" and aa2=="e":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="g":
 *         return -1
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L81;
  }
  __pyx_L81:;

  /* "obitools/align/_codonnws.pyx":376
 *     if aa1=="d" and aa2=="e":
 *         return 2
 *     if aa1=="d" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":377
 *         return 2
 *     if aa1=="d" and aa2=="g":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="h":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L82;
  }
  __pyx_L82:;

  /* "obitools/align/_codonnws.pyx":378
 *     if aa1=="d" and aa2=="g":
 *         return -1
 *     if aa1=="d" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":379
 *         return -1
 *     if aa1=="d" and aa2=="h":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="i":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L83;
  }
  __pyx_L83:;

  /* "obitools/align/_codonnws.pyx":380
 *     if aa1=="d" and aa2=="h":
 *         return -1
 *     if aa1=="d" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":381
 *         return -1
 *     if aa1=="d" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="l":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L84;
  }
  __pyx_L84:;

  /* "obitools/align/_codonnws.pyx":382
 *     if aa1=="d" and aa2=="i":
 *         return -3
 *     if aa1=="d" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="d" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":383
 *         return -3
 *     if aa1=="d" and aa2=="l":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="k":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L85;
  }
  __pyx_L85:;

  /* "obitools/align/_codonnws.pyx":384
 *     if aa1=="d" and aa2=="l":
 *         return -4
 *     if aa1=="d" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":385
 *         return -4
 *     if aa1=="d" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="m":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L86;
  }
  __pyx_L86:;

  /* "obitools/align/_codonnws.pyx":386
 *     if aa1=="d" and aa2=="k":
 *         return -1
 *     if aa1=="d" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":387
 *         return -1
 *     if aa1=="d" and aa2=="m":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="f":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L87;
  }
  __pyx_L87:;

  /* "obitools/align/_codonnws.pyx":388
 *     if aa1=="d" and aa2=="m":
 *         return -3
 *     if aa1=="d" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":389
 *         return -3
 *     if aa1=="d" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="p":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L88;
  }
  __pyx_L88:;

  /* "obitools/align/_codonnws.pyx":390
 *     if aa1=="d" and aa2=="f":
 *         return -3
 *     if aa1=="d" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":391
 *         return -3
 *     if aa1=="d" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="s":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L89;
  }
  __pyx_L89:;

  /* "obitools/align/_codonnws.pyx":392
 *     if aa1=="d" and aa2=="p":
 *         return -1
 *     if aa1=="d" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="d" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":393
 *         return -1
 *     if aa1=="d" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L90;
  }
  __pyx_L90:;

  /* "obitools/align/_codonnws.pyx":394
 *     if aa1=="d" and aa2=="s":
 *         return 0
 *     if aa1=="d" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":395
 *         return 0
 *     if aa1=="d" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="w":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L91;
  }
  __pyx_L91:;

  /* "obitools/align/_codonnws.pyx":396
 *     if aa1=="d" and aa2=="t":
 *         return -1
 *     if aa1=="d" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="d" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":397
 *         return -1
 *     if aa1=="d" and aa2=="w":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="y":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L92;
  }
  __pyx_L92:;

  /* "obitools/align/_codonnws.pyx":398
 *     if aa1=="d" and aa2=="w":
 *         return -4
 *     if aa1=="d" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":399
 *         return -4
 *     if aa1=="d" and aa2=="y":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="v":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L93;
  }
  __pyx_L93:;

  /* "obitools/align/_codonnws.pyx":400
 *     if aa1=="d" and aa2=="y":
 *         return -3
 *     if aa1=="d" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="d" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":401
 *         return -3
 *     if aa1=="d" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="b":
 *         return 4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L94;
  }
  __pyx_L94:;

  /* "obitools/align/_codonnws.pyx":402
 *     if aa1=="d" and aa2=="v":
 *         return -3
 *     if aa1=="d" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="d" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":403
 *         return -3
 *     if aa1=="d" and aa2=="b":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="z":
 *         return 1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L95;
  }
  __pyx_L95:;

  /* "obitools/align/_codonnws.pyx":404
 *     if aa1=="d" and aa2=="b":
 *         return 4
 *     if aa1=="d" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="d" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":405
 *         return 4
 *     if aa1=="d" and aa2=="z":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="x":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L96;
  }
  __pyx_L96:;

  /* "obitools/align/_codonnws.pyx":406
 *     if aa1=="d" and aa2=="z":
 *         return 1
 *     if aa1=="d" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="d" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":407
 *         return 1
 *     if aa1=="d" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="d" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L97;
  }
  __pyx_L97:;

  /* "obitools/align/_codonnws.pyx":408
 *     if aa1=="d" and aa2=="x":
 *         return -1
 *     if aa1=="d" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="c" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'd');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":409
 *         return -1
 *     if aa1=="d" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="a":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L98;
  }
  __pyx_L98:;

  /* "obitools/align/_codonnws.pyx":410
 *     if aa1=="d" and aa2=="*":
 *         return -4
 *     if aa1=="c" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="c" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":411
 *         return -4
 *     if aa1=="c" and aa2=="a":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="r":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L99;
  }
  __pyx_L99:;

  /* "obitools/align/_codonnws.pyx":412
 *     if aa1=="c" and aa2=="a":
 *         return 0
 *     if aa1=="c" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":413
 *         return 0
 *     if aa1=="c" and aa2=="r":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="n":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L100;
  }
  __pyx_L100:;

  /* "obitools/align/_codonnws.pyx":414
 *     if aa1=="c" and aa2=="r":
 *         return -3
 *     if aa1=="c" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":415
 *         return -3
 *     if aa1=="c" and aa2=="n":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="d":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L101;
  }
  __pyx_L101:;

  /* "obitools/align/_codonnws.pyx":416
 *     if aa1=="c" and aa2=="n":
 *         return -3
 *     if aa1=="c" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":417
 *         return -3
 *     if aa1=="c" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="c":
 *         return 9
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L102;
  }
  __pyx_L102:;

  /* "obitools/align/_codonnws.pyx":418
 *     if aa1=="c" and aa2=="d":
 *         return -3
 *     if aa1=="c" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return 9
 *     if aa1=="c" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":419
 *         return -3
 *     if aa1=="c" and aa2=="c":
 *         return 9             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="q":
 *         return -3
 */
    __pyx_r = 9.0;
    goto __pyx_L0;
    goto __pyx_L103;
  }
  __pyx_L103:;

  /* "obitools/align/_codonnws.pyx":420
 *     if aa1=="c" and aa2=="c":
 *         return 9
 *     if aa1=="c" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":421
 *         return 9
 *     if aa1=="c" and aa2=="q":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="e":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L104;
  }
  __pyx_L104:;

  /* "obitools/align/_codonnws.pyx":422
 *     if aa1=="c" and aa2=="q":
 *         return -3
 *     if aa1=="c" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="c" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":423
 *         return -3
 *     if aa1=="c" and aa2=="e":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="g":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L105;
  }
  __pyx_L105:;

  /* "obitools/align/_codonnws.pyx":424
 *     if aa1=="c" and aa2=="e":
 *         return -4
 *     if aa1=="c" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":425
 *         return -4
 *     if aa1=="c" and aa2=="g":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="h":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L106;
  }
  __pyx_L106:;

  /* "obitools/align/_codonnws.pyx":426
 *     if aa1=="c" and aa2=="g":
 *         return -3
 *     if aa1=="c" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":427
 *         return -3
 *     if aa1=="c" and aa2=="h":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="i":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L107;
  }
  __pyx_L107:;

  /* "obitools/align/_codonnws.pyx":428
 *     if aa1=="c" and aa2=="h":
 *         return -3
 *     if aa1=="c" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":429
 *         return -3
 *     if aa1=="c" and aa2=="i":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="l":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L108;
  }
  __pyx_L108:;

  /* "obitools/align/_codonnws.pyx":430
 *     if aa1=="c" and aa2=="i":
 *         return -1
 *     if aa1=="c" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":431
 *         return -1
 *     if aa1=="c" and aa2=="l":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="k":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L109;
  }
  __pyx_L109:;

  /* "obitools/align/_codonnws.pyx":432
 *     if aa1=="c" and aa2=="l":
 *         return -1
 *     if aa1=="c" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":433
 *         return -1
 *     if aa1=="c" and aa2=="k":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="m":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L110;
  }
  __pyx_L110:;

  /* "obitools/align/_codonnws.pyx":434
 *     if aa1=="c" and aa2=="k":
 *         return -3
 *     if aa1=="c" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":435
 *         return -3
 *     if aa1=="c" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="f":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L111;
  }
  __pyx_L111:;

  /* "obitools/align/_codonnws.pyx":436
 *     if aa1=="c" and aa2=="m":
 *         return -1
 *     if aa1=="c" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="c" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":437
 *         return -1
 *     if aa1=="c" and aa2=="f":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="p":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L112;
  }
  __pyx_L112:;

  /* "obitools/align/_codonnws.pyx":438
 *     if aa1=="c" and aa2=="f":
 *         return -2
 *     if aa1=="c" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":439
 *         return -2
 *     if aa1=="c" and aa2=="p":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="s":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L113;
  }
  __pyx_L113:;

  /* "obitools/align/_codonnws.pyx":440
 *     if aa1=="c" and aa2=="p":
 *         return -3
 *     if aa1=="c" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":441
 *         return -3
 *     if aa1=="c" and aa2=="s":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="t":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L114;
  }
  __pyx_L114:;

  /* "obitools/align/_codonnws.pyx":442
 *     if aa1=="c" and aa2=="s":
 *         return -1
 *     if aa1=="c" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":443
 *         return -1
 *     if aa1=="c" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="w":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L115;
  }
  __pyx_L115:;

  /* "obitools/align/_codonnws.pyx":444
 *     if aa1=="c" and aa2=="t":
 *         return -1
 *     if aa1=="c" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="c" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":445
 *         return -1
 *     if aa1=="c" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="y":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L116;
  }
  __pyx_L116:;

  /* "obitools/align/_codonnws.pyx":446
 *     if aa1=="c" and aa2=="w":
 *         return -2
 *     if aa1=="c" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="c" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":447
 *         return -2
 *     if aa1=="c" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="v":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L117;
  }
  __pyx_L117:;

  /* "obitools/align/_codonnws.pyx":448
 *     if aa1=="c" and aa2=="y":
 *         return -2
 *     if aa1=="c" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="c" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":449
 *         return -2
 *     if aa1=="c" and aa2=="v":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="b":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L118;
  }
  __pyx_L118:;

  /* "obitools/align/_codonnws.pyx":450
 *     if aa1=="c" and aa2=="v":
 *         return -1
 *     if aa1=="c" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":451
 *         return -1
 *     if aa1=="c" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="z":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L119;
  }
  __pyx_L119:;

  /* "obitools/align/_codonnws.pyx":452
 *     if aa1=="c" and aa2=="b":
 *         return -3
 *     if aa1=="c" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="c" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":453
 *         return -3
 *     if aa1=="c" and aa2=="z":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="x":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L120;
  }
  __pyx_L120:;

  /* "obitools/align/_codonnws.pyx":454
 *     if aa1=="c" and aa2=="z":
 *         return -3
 *     if aa1=="c" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="c" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":455
 *         return -3
 *     if aa1=="c" and aa2=="x":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="c" and aa2=="*":
 *         return -4
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L121;
  }
  __pyx_L121:;

  /* "obitools/align/_codonnws.pyx":456
 *     if aa1=="c" and aa2=="x":
 *         return -2
 *     if aa1=="c" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="q" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'c');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":457
 *         return -2
 *     if aa1=="c" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L122;
  }
  __pyx_L122:;

  /* "obitools/align/_codonnws.pyx":458
 *     if aa1=="c" and aa2=="*":
 *         return -4
 *     if aa1=="q" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="q" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":459
 *         return -4
 *     if aa1=="q" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="r":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L123;
  }
  __pyx_L123:;

  /* "obitools/align/_codonnws.pyx":460
 *     if aa1=="q" and aa2=="a":
 *         return -1
 *     if aa1=="q" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="q" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":461
 *         return -1
 *     if aa1=="q" and aa2=="r":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="n":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L124;
  }
  __pyx_L124:;

  /* "obitools/align/_codonnws.pyx":462
 *     if aa1=="q" and aa2=="r":
 *         return 1
 *     if aa1=="q" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":463
 *         return 1
 *     if aa1=="q" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="d":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L125;
  }
  __pyx_L125:;

  /* "obitools/align/_codonnws.pyx":464
 *     if aa1=="q" and aa2=="n":
 *         return 0
 *     if aa1=="q" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":465
 *         return 0
 *     if aa1=="q" and aa2=="d":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="c":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L126;
  }
  __pyx_L126:;

  /* "obitools/align/_codonnws.pyx":466
 *     if aa1=="q" and aa2=="d":
 *         return 0
 *     if aa1=="q" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="q" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":467
 *         return 0
 *     if aa1=="q" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="q":
 *         return 5
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L127;
  }
  __pyx_L127:;

  /* "obitools/align/_codonnws.pyx":468
 *     if aa1=="q" and aa2=="c":
 *         return -3
 *     if aa1=="q" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="q" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":469
 *         return -3
 *     if aa1=="q" and aa2=="q":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="e":
 *         return 2
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L128;
  }
  __pyx_L128:;

  /* "obitools/align/_codonnws.pyx":470
 *     if aa1=="q" and aa2=="q":
 *         return 5
 *     if aa1=="q" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="q" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":471
 *         return 5
 *     if aa1=="q" and aa2=="e":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="g":
 *         return -2
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L129;
  }
  __pyx_L129:;

  /* "obitools/align/_codonnws.pyx":472
 *     if aa1=="q" and aa2=="e":
 *         return 2
 *     if aa1=="q" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="q" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":473
 *         return 2
 *     if aa1=="q" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="h":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L130;
  }
  __pyx_L130:;

  /* "obitools/align/_codonnws.pyx":474
 *     if aa1=="q" and aa2=="g":
 *         return -2
 *     if aa1=="q" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":475
 *         return -2
 *     if aa1=="q" and aa2=="h":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="i":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L131;
  }
  __pyx_L131:;

  /* "obitools/align/_codonnws.pyx":476
 *     if aa1=="q" and aa2=="h":
 *         return 0
 *     if aa1=="q" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="q" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":477
 *         return 0
 *     if aa1=="q" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="l":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L132;
  }
  __pyx_L132:;

  /* "obitools/align/_codonnws.pyx":478
 *     if aa1=="q" and aa2=="i":
 *         return -3
 *     if aa1=="q" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="q" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":479
 *         return -3
 *     if aa1=="q" and aa2=="l":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="k":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L133;
  }
  __pyx_L133:;

  /* "obitools/align/_codonnws.pyx":480
 *     if aa1=="q" and aa2=="l":
 *         return -2
 *     if aa1=="q" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="q" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":481
 *         return -2
 *     if aa1=="q" and aa2=="k":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="m":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L134;
  }
  __pyx_L134:;

  /* "obitools/align/_codonnws.pyx":482
 *     if aa1=="q" and aa2=="k":
 *         return 1
 *     if aa1=="q" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":483
 *         return 1
 *     if aa1=="q" and aa2=="m":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="f":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L135;
  }
  __pyx_L135:;

  /* "obitools/align/_codonnws.pyx":484
 *     if aa1=="q" and aa2=="m":
 *         return 0
 *     if aa1=="q" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="q" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":485
 *         return 0
 *     if aa1=="q" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="p":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L136;
  }
  __pyx_L136:;

  /* "obitools/align/_codonnws.pyx":486
 *     if aa1=="q" and aa2=="f":
 *         return -3
 *     if aa1=="q" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="q" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":487
 *         return -3
 *     if aa1=="q" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="s":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L137;
  }
  __pyx_L137:;

  /* "obitools/align/_codonnws.pyx":488
 *     if aa1=="q" and aa2=="p":
 *         return -1
 *     if aa1=="q" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":489
 *         return -1
 *     if aa1=="q" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L138;
  }
  __pyx_L138:;

  /* "obitools/align/_codonnws.pyx":490
 *     if aa1=="q" and aa2=="s":
 *         return 0
 *     if aa1=="q" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="q" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":491
 *         return 0
 *     if aa1=="q" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="w":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L139;
  }
  __pyx_L139:;

  /* "obitools/align/_codonnws.pyx":492
 *     if aa1=="q" and aa2=="t":
 *         return -1
 *     if aa1=="q" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="q" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":493
 *         return -1
 *     if aa1=="q" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="y":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L140;
  }
  __pyx_L140:;

  /* "obitools/align/_codonnws.pyx":494
 *     if aa1=="q" and aa2=="w":
 *         return -2
 *     if aa1=="q" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="q" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":495
 *         return -2
 *     if aa1=="q" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="v":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L141;
  }
  __pyx_L141:;

  /* "obitools/align/_codonnws.pyx":496
 *     if aa1=="q" and aa2=="y":
 *         return -1
 *     if aa1=="q" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="q" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":497
 *         return -1
 *     if aa1=="q" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="b":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L142;
  }
  __pyx_L142:;

  /* "obitools/align/_codonnws.pyx":498
 *     if aa1=="q" and aa2=="v":
 *         return -2
 *     if aa1=="q" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="q" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":499
 *         return -2
 *     if aa1=="q" and aa2=="b":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="z":
 *         return 3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L143;
  }
  __pyx_L143:;

  /* "obitools/align/_codonnws.pyx":500
 *     if aa1=="q" and aa2=="b":
 *         return 0
 *     if aa1=="q" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="q" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":501
 *         return 0
 *     if aa1=="q" and aa2=="z":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="x":
 *         return -1
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L144;
  }
  __pyx_L144:;

  /* "obitools/align/_codonnws.pyx":502
 *     if aa1=="q" and aa2=="z":
 *         return 3
 *     if aa1=="q" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="q" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":503
 *         return 3
 *     if aa1=="q" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="q" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L145;
  }
  __pyx_L145:;

  /* "obitools/align/_codonnws.pyx":504
 *     if aa1=="q" and aa2=="x":
 *         return -1
 *     if aa1=="q" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="e" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'q');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":505
 *         return -1
 *     if aa1=="q" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L146;
  }
  __pyx_L146:;

  /* "obitools/align/_codonnws.pyx":506
 *     if aa1=="q" and aa2=="*":
 *         return -4
 *     if aa1=="e" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="e" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":507
 *         return -4
 *     if aa1=="e" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="r":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L147;
  }
  __pyx_L147:;

  /* "obitools/align/_codonnws.pyx":508
 *     if aa1=="e" and aa2=="a":
 *         return -1
 *     if aa1=="e" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="e" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":509
 *         return -1
 *     if aa1=="e" and aa2=="r":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="n":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L148;
  }
  __pyx_L148:;

  /* "obitools/align/_codonnws.pyx":510
 *     if aa1=="e" and aa2=="r":
 *         return 0
 *     if aa1=="e" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="e" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":511
 *         return 0
 *     if aa1=="e" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="d":
 *         return 2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L149;
  }
  __pyx_L149:;

  /* "obitools/align/_codonnws.pyx":512
 *     if aa1=="e" and aa2=="n":
 *         return 0
 *     if aa1=="e" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="e" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":513
 *         return 0
 *     if aa1=="e" and aa2=="d":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="c":
 *         return -4
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L150;
  }
  __pyx_L150:;

  /* "obitools/align/_codonnws.pyx":514
 *     if aa1=="e" and aa2=="d":
 *         return 2
 *     if aa1=="e" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="e" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":515
 *         return 2
 *     if aa1=="e" and aa2=="c":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="q":
 *         return 2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L151;
  }
  __pyx_L151:;

  /* "obitools/align/_codonnws.pyx":516
 *     if aa1=="e" and aa2=="c":
 *         return -4
 *     if aa1=="e" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="e" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":517
 *         return -4
 *     if aa1=="e" and aa2=="q":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="e":
 *         return 5
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L152;
  }
  __pyx_L152:;

  /* "obitools/align/_codonnws.pyx":518
 *     if aa1=="e" and aa2=="q":
 *         return 2
 *     if aa1=="e" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="e" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":519
 *         return 2
 *     if aa1=="e" and aa2=="e":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="g":
 *         return -2
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L153;
  }
  __pyx_L153:;

  /* "obitools/align/_codonnws.pyx":520
 *     if aa1=="e" and aa2=="e":
 *         return 5
 *     if aa1=="e" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="e" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":521
 *         return 5
 *     if aa1=="e" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="h":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L154;
  }
  __pyx_L154:;

  /* "obitools/align/_codonnws.pyx":522
 *     if aa1=="e" and aa2=="g":
 *         return -2
 *     if aa1=="e" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="e" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":523
 *         return -2
 *     if aa1=="e" and aa2=="h":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="i":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L155;
  }
  __pyx_L155:;

  /* "obitools/align/_codonnws.pyx":524
 *     if aa1=="e" and aa2=="h":
 *         return 0
 *     if aa1=="e" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="e" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":525
 *         return 0
 *     if aa1=="e" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="l":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L156;
  }
  __pyx_L156:;

  /* "obitools/align/_codonnws.pyx":526
 *     if aa1=="e" and aa2=="i":
 *         return -3
 *     if aa1=="e" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="e" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":527
 *         return -3
 *     if aa1=="e" and aa2=="l":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="k":
 *         return 1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L157;
  }
  __pyx_L157:;

  /* "obitools/align/_codonnws.pyx":528
 *     if aa1=="e" and aa2=="l":
 *         return -3
 *     if aa1=="e" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="e" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":529
 *         return -3
 *     if aa1=="e" and aa2=="k":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="m":
 *         return -2
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L158;
  }
  __pyx_L158:;

  /* "obitools/align/_codonnws.pyx":530
 *     if aa1=="e" and aa2=="k":
 *         return 1
 *     if aa1=="e" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="e" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":531
 *         return 1
 *     if aa1=="e" and aa2=="m":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="f":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L159;
  }
  __pyx_L159:;

  /* "obitools/align/_codonnws.pyx":532
 *     if aa1=="e" and aa2=="m":
 *         return -2
 *     if aa1=="e" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="e" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":533
 *         return -2
 *     if aa1=="e" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="p":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L160;
  }
  __pyx_L160:;

  /* "obitools/align/_codonnws.pyx":534
 *     if aa1=="e" and aa2=="f":
 *         return -3
 *     if aa1=="e" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="e" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":535
 *         return -3
 *     if aa1=="e" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="s":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L161;
  }
  __pyx_L161:;

  /* "obitools/align/_codonnws.pyx":536
 *     if aa1=="e" and aa2=="p":
 *         return -1
 *     if aa1=="e" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="e" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":537
 *         return -1
 *     if aa1=="e" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L162;
  }
  __pyx_L162:;

  /* "obitools/align/_codonnws.pyx":538
 *     if aa1=="e" and aa2=="s":
 *         return 0
 *     if aa1=="e" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="e" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":539
 *         return 0
 *     if aa1=="e" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="w":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L163;
  }
  __pyx_L163:;

  /* "obitools/align/_codonnws.pyx":540
 *     if aa1=="e" and aa2=="t":
 *         return -1
 *     if aa1=="e" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="e" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":541
 *         return -1
 *     if aa1=="e" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L164;
  }
  __pyx_L164:;

  /* "obitools/align/_codonnws.pyx":542
 *     if aa1=="e" and aa2=="w":
 *         return -3
 *     if aa1=="e" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="e" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":543
 *         return -3
 *     if aa1=="e" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="v":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L165;
  }
  __pyx_L165:;

  /* "obitools/align/_codonnws.pyx":544
 *     if aa1=="e" and aa2=="y":
 *         return -2
 *     if aa1=="e" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="e" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":545
 *         return -2
 *     if aa1=="e" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="b":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L166;
  }
  __pyx_L166:;

  /* "obitools/align/_codonnws.pyx":546
 *     if aa1=="e" and aa2=="v":
 *         return -2
 *     if aa1=="e" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="e" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":547
 *         return -2
 *     if aa1=="e" and aa2=="b":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="z":
 *         return 4
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L167;
  }
  __pyx_L167:;

  /* "obitools/align/_codonnws.pyx":548
 *     if aa1=="e" and aa2=="b":
 *         return 1
 *     if aa1=="e" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="e" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":549
 *         return 1
 *     if aa1=="e" and aa2=="z":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="x":
 *         return -1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L168;
  }
  __pyx_L168:;

  /* "obitools/align/_codonnws.pyx":550
 *     if aa1=="e" and aa2=="z":
 *         return 4
 *     if aa1=="e" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="e" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":551
 *         return 4
 *     if aa1=="e" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="e" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L169;
  }
  __pyx_L169:;

  /* "obitools/align/_codonnws.pyx":552
 *     if aa1=="e" and aa2=="x":
 *         return -1
 *     if aa1=="e" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="g" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'e');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":553
 *         return -1
 *     if aa1=="e" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="a":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L170;
  }
  __pyx_L170:;

  /* "obitools/align/_codonnws.pyx":554
 *     if aa1=="e" and aa2=="*":
 *         return -4
 *     if aa1=="g" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="g" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":555
 *         return -4
 *     if aa1=="g" and aa2=="a":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="r":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L171;
  }
  __pyx_L171:;

  /* "obitools/align/_codonnws.pyx":556
 *     if aa1=="g" and aa2=="a":
 *         return 0
 *     if aa1=="g" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":557
 *         return 0
 *     if aa1=="g" and aa2=="r":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="n":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L172;
  }
  __pyx_L172:;

  /* "obitools/align/_codonnws.pyx":558
 *     if aa1=="g" and aa2=="r":
 *         return -2
 *     if aa1=="g" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="g" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":559
 *         return -2
 *     if aa1=="g" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="d":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L173;
  }
  __pyx_L173:;

  /* "obitools/align/_codonnws.pyx":560
 *     if aa1=="g" and aa2=="n":
 *         return 0
 *     if aa1=="g" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="g" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":561
 *         return 0
 *     if aa1=="g" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="c":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L174;
  }
  __pyx_L174:;

  /* "obitools/align/_codonnws.pyx":562
 *     if aa1=="g" and aa2=="d":
 *         return -1
 *     if aa1=="g" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="g" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":563
 *         return -1
 *     if aa1=="g" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="q":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L175;
  }
  __pyx_L175:;

  /* "obitools/align/_codonnws.pyx":564
 *     if aa1=="g" and aa2=="c":
 *         return -3
 *     if aa1=="g" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":565
 *         return -3
 *     if aa1=="g" and aa2=="q":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="e":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L176;
  }
  __pyx_L176:;

  /* "obitools/align/_codonnws.pyx":566
 *     if aa1=="g" and aa2=="q":
 *         return -2
 *     if aa1=="g" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":567
 *         return -2
 *     if aa1=="g" and aa2=="e":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="g":
 *         return 6
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L177;
  }
  __pyx_L177:;

  /* "obitools/align/_codonnws.pyx":568
 *     if aa1=="g" and aa2=="e":
 *         return -2
 *     if aa1=="g" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return 6
 *     if aa1=="g" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":569
 *         return -2
 *     if aa1=="g" and aa2=="g":
 *         return 6             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="h":
 *         return -2
 */
    __pyx_r = 6.0;
    goto __pyx_L0;
    goto __pyx_L178;
  }
  __pyx_L178:;

  /* "obitools/align/_codonnws.pyx":570
 *     if aa1=="g" and aa2=="g":
 *         return 6
 *     if aa1=="g" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":571
 *         return 6
 *     if aa1=="g" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="i":
 *         return -4
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L179;
  }
  __pyx_L179:;

  /* "obitools/align/_codonnws.pyx":572
 *     if aa1=="g" and aa2=="h":
 *         return -2
 *     if aa1=="g" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="g" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":573
 *         return -2
 *     if aa1=="g" and aa2=="i":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="l":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L180;
  }
  __pyx_L180:;

  /* "obitools/align/_codonnws.pyx":574
 *     if aa1=="g" and aa2=="i":
 *         return -4
 *     if aa1=="g" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="g" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":575
 *         return -4
 *     if aa1=="g" and aa2=="l":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="k":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L181;
  }
  __pyx_L181:;

  /* "obitools/align/_codonnws.pyx":576
 *     if aa1=="g" and aa2=="l":
 *         return -4
 *     if aa1=="g" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":577
 *         return -4
 *     if aa1=="g" and aa2=="k":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="m":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L182;
  }
  __pyx_L182:;

  /* "obitools/align/_codonnws.pyx":578
 *     if aa1=="g" and aa2=="k":
 *         return -2
 *     if aa1=="g" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="g" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":579
 *         return -2
 *     if aa1=="g" and aa2=="m":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="f":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L183;
  }
  __pyx_L183:;

  /* "obitools/align/_codonnws.pyx":580
 *     if aa1=="g" and aa2=="m":
 *         return -3
 *     if aa1=="g" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="g" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":581
 *         return -3
 *     if aa1=="g" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="p":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L184;
  }
  __pyx_L184:;

  /* "obitools/align/_codonnws.pyx":582
 *     if aa1=="g" and aa2=="f":
 *         return -3
 *     if aa1=="g" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":583
 *         return -3
 *     if aa1=="g" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="s":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L185;
  }
  __pyx_L185:;

  /* "obitools/align/_codonnws.pyx":584
 *     if aa1=="g" and aa2=="p":
 *         return -2
 *     if aa1=="g" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="g" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":585
 *         return -2
 *     if aa1=="g" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="t":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L186;
  }
  __pyx_L186:;

  /* "obitools/align/_codonnws.pyx":586
 *     if aa1=="g" and aa2=="s":
 *         return 0
 *     if aa1=="g" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":587
 *         return 0
 *     if aa1=="g" and aa2=="t":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="w":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L187;
  }
  __pyx_L187:;

  /* "obitools/align/_codonnws.pyx":588
 *     if aa1=="g" and aa2=="t":
 *         return -2
 *     if aa1=="g" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":589
 *         return -2
 *     if aa1=="g" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="y":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L188;
  }
  __pyx_L188:;

  /* "obitools/align/_codonnws.pyx":590
 *     if aa1=="g" and aa2=="w":
 *         return -2
 *     if aa1=="g" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="g" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":591
 *         return -2
 *     if aa1=="g" and aa2=="y":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="v":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L189;
  }
  __pyx_L189:;

  /* "obitools/align/_codonnws.pyx":592
 *     if aa1=="g" and aa2=="y":
 *         return -3
 *     if aa1=="g" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="g" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":593
 *         return -3
 *     if aa1=="g" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="b":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L190;
  }
  __pyx_L190:;

  /* "obitools/align/_codonnws.pyx":594
 *     if aa1=="g" and aa2=="v":
 *         return -3
 *     if aa1=="g" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="g" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":595
 *         return -3
 *     if aa1=="g" and aa2=="b":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="z":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L191;
  }
  __pyx_L191:;

  /* "obitools/align/_codonnws.pyx":596
 *     if aa1=="g" and aa2=="b":
 *         return -1
 *     if aa1=="g" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="g" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":597
 *         return -1
 *     if aa1=="g" and aa2=="z":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="x":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L192;
  }
  __pyx_L192:;

  /* "obitools/align/_codonnws.pyx":598
 *     if aa1=="g" and aa2=="z":
 *         return -2
 *     if aa1=="g" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="g" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":599
 *         return -2
 *     if aa1=="g" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="g" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L193;
  }
  __pyx_L193:;

  /* "obitools/align/_codonnws.pyx":600
 *     if aa1=="g" and aa2=="x":
 *         return -1
 *     if aa1=="g" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="h" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'g');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":601
 *         return -1
 *     if aa1=="g" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L194;
  }
  __pyx_L194:;

  /* "obitools/align/_codonnws.pyx":602
 *     if aa1=="g" and aa2=="*":
 *         return -4
 *     if aa1=="h" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":603
 *         return -4
 *     if aa1=="h" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="r":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L195;
  }
  __pyx_L195:;

  /* "obitools/align/_codonnws.pyx":604
 *     if aa1=="h" and aa2=="a":
 *         return -2
 *     if aa1=="h" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="h" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":605
 *         return -2
 *     if aa1=="h" and aa2=="r":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="n":
 *         return 1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L196;
  }
  __pyx_L196:;

  /* "obitools/align/_codonnws.pyx":606
 *     if aa1=="h" and aa2=="r":
 *         return 0
 *     if aa1=="h" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="h" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":607
 *         return 0
 *     if aa1=="h" and aa2=="n":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="d":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L197;
  }
  __pyx_L197:;

  /* "obitools/align/_codonnws.pyx":608
 *     if aa1=="h" and aa2=="n":
 *         return 1
 *     if aa1=="h" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="h" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":609
 *         return 1
 *     if aa1=="h" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="c":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L198;
  }
  __pyx_L198:;

  /* "obitools/align/_codonnws.pyx":610
 *     if aa1=="h" and aa2=="d":
 *         return -1
 *     if aa1=="h" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="h" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":611
 *         return -1
 *     if aa1=="h" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="q":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L199;
  }
  __pyx_L199:;

  /* "obitools/align/_codonnws.pyx":612
 *     if aa1=="h" and aa2=="c":
 *         return -3
 *     if aa1=="h" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="h" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":613
 *         return -3
 *     if aa1=="h" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="e":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L200;
  }
  __pyx_L200:;

  /* "obitools/align/_codonnws.pyx":614
 *     if aa1=="h" and aa2=="q":
 *         return 0
 *     if aa1=="h" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="h" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":615
 *         return 0
 *     if aa1=="h" and aa2=="e":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="g":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L201;
  }
  __pyx_L201:;

  /* "obitools/align/_codonnws.pyx":616
 *     if aa1=="h" and aa2=="e":
 *         return 0
 *     if aa1=="h" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":617
 *         return 0
 *     if aa1=="h" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="h":
 *         return 8
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L202;
  }
  __pyx_L202:;

  /* "obitools/align/_codonnws.pyx":618
 *     if aa1=="h" and aa2=="g":
 *         return -2
 *     if aa1=="h" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 8
 *     if aa1=="h" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":619
 *         return -2
 *     if aa1=="h" and aa2=="h":
 *         return 8             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="i":
 *         return -3
 */
    __pyx_r = 8.0;
    goto __pyx_L0;
    goto __pyx_L203;
  }
  __pyx_L203:;

  /* "obitools/align/_codonnws.pyx":620
 *     if aa1=="h" and aa2=="h":
 *         return 8
 *     if aa1=="h" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="h" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":621
 *         return 8
 *     if aa1=="h" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="l":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L204;
  }
  __pyx_L204:;

  /* "obitools/align/_codonnws.pyx":622
 *     if aa1=="h" and aa2=="i":
 *         return -3
 *     if aa1=="h" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="h" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":623
 *         return -3
 *     if aa1=="h" and aa2=="l":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="k":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L205;
  }
  __pyx_L205:;

  /* "obitools/align/_codonnws.pyx":624
 *     if aa1=="h" and aa2=="l":
 *         return -3
 *     if aa1=="h" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="h" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":625
 *         return -3
 *     if aa1=="h" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="m":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L206;
  }
  __pyx_L206:;

  /* "obitools/align/_codonnws.pyx":626
 *     if aa1=="h" and aa2=="k":
 *         return -1
 *     if aa1=="h" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":627
 *         return -1
 *     if aa1=="h" and aa2=="m":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="f":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L207;
  }
  __pyx_L207:;

  /* "obitools/align/_codonnws.pyx":628
 *     if aa1=="h" and aa2=="m":
 *         return -2
 *     if aa1=="h" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="h" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":629
 *         return -2
 *     if aa1=="h" and aa2=="f":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="p":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L208;
  }
  __pyx_L208:;

  /* "obitools/align/_codonnws.pyx":630
 *     if aa1=="h" and aa2=="f":
 *         return -1
 *     if aa1=="h" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":631
 *         return -1
 *     if aa1=="h" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="s":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L209;
  }
  __pyx_L209:;

  /* "obitools/align/_codonnws.pyx":632
 *     if aa1=="h" and aa2=="p":
 *         return -2
 *     if aa1=="h" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="h" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":633
 *         return -2
 *     if aa1=="h" and aa2=="s":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="t":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L210;
  }
  __pyx_L210:;

  /* "obitools/align/_codonnws.pyx":634
 *     if aa1=="h" and aa2=="s":
 *         return -1
 *     if aa1=="h" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":635
 *         return -1
 *     if aa1=="h" and aa2=="t":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="w":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L211;
  }
  __pyx_L211:;

  /* "obitools/align/_codonnws.pyx":636
 *     if aa1=="h" and aa2=="t":
 *         return -2
 *     if aa1=="h" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="h" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":637
 *         return -2
 *     if aa1=="h" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="y":
 *         return 2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L212;
  }
  __pyx_L212:;

  /* "obitools/align/_codonnws.pyx":638
 *     if aa1=="h" and aa2=="w":
 *         return -2
 *     if aa1=="h" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="h" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":639
 *         return -2
 *     if aa1=="h" and aa2=="y":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="v":
 *         return -3
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L213;
  }
  __pyx_L213:;

  /* "obitools/align/_codonnws.pyx":640
 *     if aa1=="h" and aa2=="y":
 *         return 2
 *     if aa1=="h" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="h" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":641
 *         return 2
 *     if aa1=="h" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="b":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L214;
  }
  __pyx_L214:;

  /* "obitools/align/_codonnws.pyx":642
 *     if aa1=="h" and aa2=="v":
 *         return -3
 *     if aa1=="h" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="h" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":643
 *         return -3
 *     if aa1=="h" and aa2=="b":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="z":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L215;
  }
  __pyx_L215:;

  /* "obitools/align/_codonnws.pyx":644
 *     if aa1=="h" and aa2=="b":
 *         return 0
 *     if aa1=="h" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="h" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":645
 *         return 0
 *     if aa1=="h" and aa2=="z":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="x":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L216;
  }
  __pyx_L216:;

  /* "obitools/align/_codonnws.pyx":646
 *     if aa1=="h" and aa2=="z":
 *         return 0
 *     if aa1=="h" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="h" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":647
 *         return 0
 *     if aa1=="h" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="h" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L217;
  }
  __pyx_L217:;

  /* "obitools/align/_codonnws.pyx":648
 *     if aa1=="h" and aa2=="x":
 *         return -1
 *     if aa1=="h" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="i" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'h');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":649
 *         return -1
 *     if aa1=="h" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L218;
  }
  __pyx_L218:;

  /* "obitools/align/_codonnws.pyx":650
 *     if aa1=="h" and aa2=="*":
 *         return -4
 *     if aa1=="i" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="i" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":651
 *         return -4
 *     if aa1=="i" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="r":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L219;
  }
  __pyx_L219:;

  /* "obitools/align/_codonnws.pyx":652
 *     if aa1=="i" and aa2=="a":
 *         return -1
 *     if aa1=="i" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":653
 *         return -1
 *     if aa1=="i" and aa2=="r":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="n":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L220;
  }
  __pyx_L220:;

  /* "obitools/align/_codonnws.pyx":654
 *     if aa1=="i" and aa2=="r":
 *         return -3
 *     if aa1=="i" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":655
 *         return -3
 *     if aa1=="i" and aa2=="n":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="d":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L221;
  }
  __pyx_L221:;

  /* "obitools/align/_codonnws.pyx":656
 *     if aa1=="i" and aa2=="n":
 *         return -3
 *     if aa1=="i" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":657
 *         return -3
 *     if aa1=="i" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="c":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L222;
  }
  __pyx_L222:;

  /* "obitools/align/_codonnws.pyx":658
 *     if aa1=="i" and aa2=="d":
 *         return -3
 *     if aa1=="i" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="i" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":659
 *         return -3
 *     if aa1=="i" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="q":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L223;
  }
  __pyx_L223:;

  /* "obitools/align/_codonnws.pyx":660
 *     if aa1=="i" and aa2=="c":
 *         return -1
 *     if aa1=="i" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":661
 *         return -1
 *     if aa1=="i" and aa2=="q":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="e":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L224;
  }
  __pyx_L224:;

  /* "obitools/align/_codonnws.pyx":662
 *     if aa1=="i" and aa2=="q":
 *         return -3
 *     if aa1=="i" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":663
 *         return -3
 *     if aa1=="i" and aa2=="e":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="g":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L225;
  }
  __pyx_L225:;

  /* "obitools/align/_codonnws.pyx":664
 *     if aa1=="i" and aa2=="e":
 *         return -3
 *     if aa1=="i" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="i" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":665
 *         return -3
 *     if aa1=="i" and aa2=="g":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="h":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L226;
  }
  __pyx_L226:;

  /* "obitools/align/_codonnws.pyx":666
 *     if aa1=="i" and aa2=="g":
 *         return -4
 *     if aa1=="i" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":667
 *         return -4
 *     if aa1=="i" and aa2=="h":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="i":
 *         return 4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L227;
  }
  __pyx_L227:;

  /* "obitools/align/_codonnws.pyx":668
 *     if aa1=="i" and aa2=="h":
 *         return -3
 *     if aa1=="i" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="i" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":669
 *         return -3
 *     if aa1=="i" and aa2=="i":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="l":
 *         return 2
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L228;
  }
  __pyx_L228:;

  /* "obitools/align/_codonnws.pyx":670
 *     if aa1=="i" and aa2=="i":
 *         return 4
 *     if aa1=="i" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="i" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":671
 *         return 4
 *     if aa1=="i" and aa2=="l":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="k":
 *         return -3
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L229;
  }
  __pyx_L229:;

  /* "obitools/align/_codonnws.pyx":672
 *     if aa1=="i" and aa2=="l":
 *         return 2
 *     if aa1=="i" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":673
 *         return 2
 *     if aa1=="i" and aa2=="k":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="m":
 *         return 1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L230;
  }
  __pyx_L230:;

  /* "obitools/align/_codonnws.pyx":674
 *     if aa1=="i" and aa2=="k":
 *         return -3
 *     if aa1=="i" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="i" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":675
 *         return -3
 *     if aa1=="i" and aa2=="m":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="f":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L231;
  }
  __pyx_L231:;

  /* "obitools/align/_codonnws.pyx":676
 *     if aa1=="i" and aa2=="m":
 *         return 1
 *     if aa1=="i" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="i" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":677
 *         return 1
 *     if aa1=="i" and aa2=="f":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="p":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L232;
  }
  __pyx_L232:;

  /* "obitools/align/_codonnws.pyx":678
 *     if aa1=="i" and aa2=="f":
 *         return 0
 *     if aa1=="i" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":679
 *         return 0
 *     if aa1=="i" and aa2=="p":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="s":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L233;
  }
  __pyx_L233:;

  /* "obitools/align/_codonnws.pyx":680
 *     if aa1=="i" and aa2=="p":
 *         return -3
 *     if aa1=="i" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="i" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":681
 *         return -3
 *     if aa1=="i" and aa2=="s":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="t":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L234;
  }
  __pyx_L234:;

  /* "obitools/align/_codonnws.pyx":682
 *     if aa1=="i" and aa2=="s":
 *         return -2
 *     if aa1=="i" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="i" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":683
 *         return -2
 *     if aa1=="i" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="w":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L235;
  }
  __pyx_L235:;

  /* "obitools/align/_codonnws.pyx":684
 *     if aa1=="i" and aa2=="t":
 *         return -1
 *     if aa1=="i" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":685
 *         return -1
 *     if aa1=="i" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="y":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L236;
  }
  __pyx_L236:;

  /* "obitools/align/_codonnws.pyx":686
 *     if aa1=="i" and aa2=="w":
 *         return -3
 *     if aa1=="i" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="i" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":687
 *         return -3
 *     if aa1=="i" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="v":
 *         return 3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L237;
  }
  __pyx_L237:;

  /* "obitools/align/_codonnws.pyx":688
 *     if aa1=="i" and aa2=="y":
 *         return -1
 *     if aa1=="i" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="i" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":689
 *         return -1
 *     if aa1=="i" and aa2=="v":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="b":
 *         return -3
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L238;
  }
  __pyx_L238:;

  /* "obitools/align/_codonnws.pyx":690
 *     if aa1=="i" and aa2=="v":
 *         return 3
 *     if aa1=="i" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":691
 *         return 3
 *     if aa1=="i" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="z":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L239;
  }
  __pyx_L239:;

  /* "obitools/align/_codonnws.pyx":692
 *     if aa1=="i" and aa2=="b":
 *         return -3
 *     if aa1=="i" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="i" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":693
 *         return -3
 *     if aa1=="i" and aa2=="z":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="x":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L240;
  }
  __pyx_L240:;

  /* "obitools/align/_codonnws.pyx":694
 *     if aa1=="i" and aa2=="z":
 *         return -3
 *     if aa1=="i" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="i" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":695
 *         return -3
 *     if aa1=="i" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="i" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L241;
  }
  __pyx_L241:;

  /* "obitools/align/_codonnws.pyx":696
 *     if aa1=="i" and aa2=="x":
 *         return -1
 *     if aa1=="i" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="l" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'i');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":697
 *         return -1
 *     if aa1=="i" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L242;
  }
  __pyx_L242:;

  /* "obitools/align/_codonnws.pyx":698
 *     if aa1=="i" and aa2=="*":
 *         return -4
 *     if aa1=="l" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="l" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":699
 *         return -4
 *     if aa1=="l" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="r":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L243;
  }
  __pyx_L243:;

  /* "obitools/align/_codonnws.pyx":700
 *     if aa1=="l" and aa2=="a":
 *         return -1
 *     if aa1=="l" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="l" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":701
 *         return -1
 *     if aa1=="l" and aa2=="r":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="n":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L244;
  }
  __pyx_L244:;

  /* "obitools/align/_codonnws.pyx":702
 *     if aa1=="l" and aa2=="r":
 *         return -2
 *     if aa1=="l" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="l" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":703
 *         return -2
 *     if aa1=="l" and aa2=="n":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="d":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L245;
  }
  __pyx_L245:;

  /* "obitools/align/_codonnws.pyx":704
 *     if aa1=="l" and aa2=="n":
 *         return -3
 *     if aa1=="l" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="l" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":705
 *         return -3
 *     if aa1=="l" and aa2=="d":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="c":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L246;
  }
  __pyx_L246:;

  /* "obitools/align/_codonnws.pyx":706
 *     if aa1=="l" and aa2=="d":
 *         return -4
 *     if aa1=="l" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="l" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":707
 *         return -4
 *     if aa1=="l" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="q":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L247;
  }
  __pyx_L247:;

  /* "obitools/align/_codonnws.pyx":708
 *     if aa1=="l" and aa2=="c":
 *         return -1
 *     if aa1=="l" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="l" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":709
 *         return -1
 *     if aa1=="l" and aa2=="q":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="e":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L248;
  }
  __pyx_L248:;

  /* "obitools/align/_codonnws.pyx":710
 *     if aa1=="l" and aa2=="q":
 *         return -2
 *     if aa1=="l" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="l" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":711
 *         return -2
 *     if aa1=="l" and aa2=="e":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="g":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L249;
  }
  __pyx_L249:;

  /* "obitools/align/_codonnws.pyx":712
 *     if aa1=="l" and aa2=="e":
 *         return -3
 *     if aa1=="l" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="l" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":713
 *         return -3
 *     if aa1=="l" and aa2=="g":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="h":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L250;
  }
  __pyx_L250:;

  /* "obitools/align/_codonnws.pyx":714
 *     if aa1=="l" and aa2=="g":
 *         return -4
 *     if aa1=="l" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="l" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":715
 *         return -4
 *     if aa1=="l" and aa2=="h":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="i":
 *         return 2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L251;
  }
  __pyx_L251:;

  /* "obitools/align/_codonnws.pyx":716
 *     if aa1=="l" and aa2=="h":
 *         return -3
 *     if aa1=="l" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="l" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":717
 *         return -3
 *     if aa1=="l" and aa2=="i":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="l":
 *         return 4
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L252;
  }
  __pyx_L252:;

  /* "obitools/align/_codonnws.pyx":718
 *     if aa1=="l" and aa2=="i":
 *         return 2
 *     if aa1=="l" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="l" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":719
 *         return 2
 *     if aa1=="l" and aa2=="l":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="k":
 *         return -2
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L253;
  }
  __pyx_L253:;

  /* "obitools/align/_codonnws.pyx":720
 *     if aa1=="l" and aa2=="l":
 *         return 4
 *     if aa1=="l" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="l" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":721
 *         return 4
 *     if aa1=="l" and aa2=="k":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="m":
 *         return 2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L254;
  }
  __pyx_L254:;

  /* "obitools/align/_codonnws.pyx":722
 *     if aa1=="l" and aa2=="k":
 *         return -2
 *     if aa1=="l" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="l" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":723
 *         return -2
 *     if aa1=="l" and aa2=="m":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="f":
 *         return 0
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L255;
  }
  __pyx_L255:;

  /* "obitools/align/_codonnws.pyx":724
 *     if aa1=="l" and aa2=="m":
 *         return 2
 *     if aa1=="l" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="l" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":725
 *         return 2
 *     if aa1=="l" and aa2=="f":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="p":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L256;
  }
  __pyx_L256:;

  /* "obitools/align/_codonnws.pyx":726
 *     if aa1=="l" and aa2=="f":
 *         return 0
 *     if aa1=="l" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="l" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":727
 *         return 0
 *     if aa1=="l" and aa2=="p":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="s":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L257;
  }
  __pyx_L257:;

  /* "obitools/align/_codonnws.pyx":728
 *     if aa1=="l" and aa2=="p":
 *         return -3
 *     if aa1=="l" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="l" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":729
 *         return -3
 *     if aa1=="l" and aa2=="s":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="t":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L258;
  }
  __pyx_L258:;

  /* "obitools/align/_codonnws.pyx":730
 *     if aa1=="l" and aa2=="s":
 *         return -2
 *     if aa1=="l" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="l" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":731
 *         return -2
 *     if aa1=="l" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="w":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L259;
  }
  __pyx_L259:;

  /* "obitools/align/_codonnws.pyx":732
 *     if aa1=="l" and aa2=="t":
 *         return -1
 *     if aa1=="l" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="l" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":733
 *         return -1
 *     if aa1=="l" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="y":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L260;
  }
  __pyx_L260:;

  /* "obitools/align/_codonnws.pyx":734
 *     if aa1=="l" and aa2=="w":
 *         return -2
 *     if aa1=="l" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="l" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":735
 *         return -2
 *     if aa1=="l" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="v":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L261;
  }
  __pyx_L261:;

  /* "obitools/align/_codonnws.pyx":736
 *     if aa1=="l" and aa2=="y":
 *         return -1
 *     if aa1=="l" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="l" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":737
 *         return -1
 *     if aa1=="l" and aa2=="v":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="b":
 *         return -4
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L262;
  }
  __pyx_L262:;

  /* "obitools/align/_codonnws.pyx":738
 *     if aa1=="l" and aa2=="v":
 *         return 1
 *     if aa1=="l" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="l" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":739
 *         return 1
 *     if aa1=="l" and aa2=="b":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="z":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L263;
  }
  __pyx_L263:;

  /* "obitools/align/_codonnws.pyx":740
 *     if aa1=="l" and aa2=="b":
 *         return -4
 *     if aa1=="l" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="l" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":741
 *         return -4
 *     if aa1=="l" and aa2=="z":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="x":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L264;
  }
  __pyx_L264:;

  /* "obitools/align/_codonnws.pyx":742
 *     if aa1=="l" and aa2=="z":
 *         return -3
 *     if aa1=="l" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="l" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":743
 *         return -3
 *     if aa1=="l" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="l" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L265;
  }
  __pyx_L265:;

  /* "obitools/align/_codonnws.pyx":744
 *     if aa1=="l" and aa2=="x":
 *         return -1
 *     if aa1=="l" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="k" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'l');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":745
 *         return -1
 *     if aa1=="l" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L266;
  }
  __pyx_L266:;

  /* "obitools/align/_codonnws.pyx":746
 *     if aa1=="l" and aa2=="*":
 *         return -4
 *     if aa1=="k" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":747
 *         return -4
 *     if aa1=="k" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="r":
 *         return 2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L267;
  }
  __pyx_L267:;

  /* "obitools/align/_codonnws.pyx":748
 *     if aa1=="k" and aa2=="a":
 *         return -1
 *     if aa1=="k" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="k" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":749
 *         return -1
 *     if aa1=="k" and aa2=="r":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="n":
 *         return 0
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L268;
  }
  __pyx_L268:;

  /* "obitools/align/_codonnws.pyx":750
 *     if aa1=="k" and aa2=="r":
 *         return 2
 *     if aa1=="k" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="k" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":751
 *         return 2
 *     if aa1=="k" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="d":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L269;
  }
  __pyx_L269:;

  /* "obitools/align/_codonnws.pyx":752
 *     if aa1=="k" and aa2=="n":
 *         return 0
 *     if aa1=="k" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":753
 *         return 0
 *     if aa1=="k" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="c":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L270;
  }
  __pyx_L270:;

  /* "obitools/align/_codonnws.pyx":754
 *     if aa1=="k" and aa2=="d":
 *         return -1
 *     if aa1=="k" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="k" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":755
 *         return -1
 *     if aa1=="k" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="q":
 *         return 1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L271;
  }
  __pyx_L271:;

  /* "obitools/align/_codonnws.pyx":756
 *     if aa1=="k" and aa2=="c":
 *         return -3
 *     if aa1=="k" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="k" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":757
 *         return -3
 *     if aa1=="k" and aa2=="q":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="e":
 *         return 1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L272;
  }
  __pyx_L272:;

  /* "obitools/align/_codonnws.pyx":758
 *     if aa1=="k" and aa2=="q":
 *         return 1
 *     if aa1=="k" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="k" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":759
 *         return 1
 *     if aa1=="k" and aa2=="e":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="g":
 *         return -2
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L273;
  }
  __pyx_L273:;

  /* "obitools/align/_codonnws.pyx":760
 *     if aa1=="k" and aa2=="e":
 *         return 1
 *     if aa1=="k" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="k" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":761
 *         return 1
 *     if aa1=="k" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="h":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L274;
  }
  __pyx_L274:;

  /* "obitools/align/_codonnws.pyx":762
 *     if aa1=="k" and aa2=="g":
 *         return -2
 *     if aa1=="k" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":763
 *         return -2
 *     if aa1=="k" and aa2=="h":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="i":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L275;
  }
  __pyx_L275:;

  /* "obitools/align/_codonnws.pyx":764
 *     if aa1=="k" and aa2=="h":
 *         return -1
 *     if aa1=="k" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="k" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":765
 *         return -1
 *     if aa1=="k" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="l":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L276;
  }
  __pyx_L276:;

  /* "obitools/align/_codonnws.pyx":766
 *     if aa1=="k" and aa2=="i":
 *         return -3
 *     if aa1=="k" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="k" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":767
 *         return -3
 *     if aa1=="k" and aa2=="l":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="k":
 *         return 5
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L277;
  }
  __pyx_L277:;

  /* "obitools/align/_codonnws.pyx":768
 *     if aa1=="k" and aa2=="l":
 *         return -2
 *     if aa1=="k" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="k" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":769
 *         return -2
 *     if aa1=="k" and aa2=="k":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="m":
 *         return -1
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L278;
  }
  __pyx_L278:;

  /* "obitools/align/_codonnws.pyx":770
 *     if aa1=="k" and aa2=="k":
 *         return 5
 *     if aa1=="k" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":771
 *         return 5
 *     if aa1=="k" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="f":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L279;
  }
  __pyx_L279:;

  /* "obitools/align/_codonnws.pyx":772
 *     if aa1=="k" and aa2=="m":
 *         return -1
 *     if aa1=="k" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="k" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":773
 *         return -1
 *     if aa1=="k" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="p":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L280;
  }
  __pyx_L280:;

  /* "obitools/align/_codonnws.pyx":774
 *     if aa1=="k" and aa2=="f":
 *         return -3
 *     if aa1=="k" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":775
 *         return -3
 *     if aa1=="k" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="s":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L281;
  }
  __pyx_L281:;

  /* "obitools/align/_codonnws.pyx":776
 *     if aa1=="k" and aa2=="p":
 *         return -1
 *     if aa1=="k" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="k" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":777
 *         return -1
 *     if aa1=="k" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L282;
  }
  __pyx_L282:;

  /* "obitools/align/_codonnws.pyx":778
 *     if aa1=="k" and aa2=="s":
 *         return 0
 *     if aa1=="k" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":779
 *         return 0
 *     if aa1=="k" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="w":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L283;
  }
  __pyx_L283:;

  /* "obitools/align/_codonnws.pyx":780
 *     if aa1=="k" and aa2=="t":
 *         return -1
 *     if aa1=="k" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="k" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":781
 *         return -1
 *     if aa1=="k" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L284;
  }
  __pyx_L284:;

  /* "obitools/align/_codonnws.pyx":782
 *     if aa1=="k" and aa2=="w":
 *         return -3
 *     if aa1=="k" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="k" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":783
 *         return -3
 *     if aa1=="k" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="v":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L285;
  }
  __pyx_L285:;

  /* "obitools/align/_codonnws.pyx":784
 *     if aa1=="k" and aa2=="y":
 *         return -2
 *     if aa1=="k" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="k" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":785
 *         return -2
 *     if aa1=="k" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="b":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L286;
  }
  __pyx_L286:;

  /* "obitools/align/_codonnws.pyx":786
 *     if aa1=="k" and aa2=="v":
 *         return -2
 *     if aa1=="k" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="k" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":787
 *         return -2
 *     if aa1=="k" and aa2=="b":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="z":
 *         return 1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L287;
  }
  __pyx_L287:;

  /* "obitools/align/_codonnws.pyx":788
 *     if aa1=="k" and aa2=="b":
 *         return 0
 *     if aa1=="k" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="k" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":789
 *         return 0
 *     if aa1=="k" and aa2=="z":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="x":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L288;
  }
  __pyx_L288:;

  /* "obitools/align/_codonnws.pyx":790
 *     if aa1=="k" and aa2=="z":
 *         return 1
 *     if aa1=="k" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="k" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":791
 *         return 1
 *     if aa1=="k" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="k" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L289;
  }
  __pyx_L289:;

  /* "obitools/align/_codonnws.pyx":792
 *     if aa1=="k" and aa2=="x":
 *         return -1
 *     if aa1=="k" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="m" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'k');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":793
 *         return -1
 *     if aa1=="k" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L290;
  }
  __pyx_L290:;

  /* "obitools/align/_codonnws.pyx":794
 *     if aa1=="k" and aa2=="*":
 *         return -4
 *     if aa1=="m" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":795
 *         return -4
 *     if aa1=="m" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="r":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L291;
  }
  __pyx_L291:;

  /* "obitools/align/_codonnws.pyx":796
 *     if aa1=="m" and aa2=="a":
 *         return -1
 *     if aa1=="m" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":797
 *         return -1
 *     if aa1=="m" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="n":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L292;
  }
  __pyx_L292:;

  /* "obitools/align/_codonnws.pyx":798
 *     if aa1=="m" and aa2=="r":
 *         return -1
 *     if aa1=="m" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="m" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":799
 *         return -1
 *     if aa1=="m" and aa2=="n":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="d":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L293;
  }
  __pyx_L293:;

  /* "obitools/align/_codonnws.pyx":800
 *     if aa1=="m" and aa2=="n":
 *         return -2
 *     if aa1=="m" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="m" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":801
 *         return -2
 *     if aa1=="m" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="c":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L294;
  }
  __pyx_L294:;

  /* "obitools/align/_codonnws.pyx":802
 *     if aa1=="m" and aa2=="d":
 *         return -3
 *     if aa1=="m" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":803
 *         return -3
 *     if aa1=="m" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="q":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L295;
  }
  __pyx_L295:;

  /* "obitools/align/_codonnws.pyx":804
 *     if aa1=="m" and aa2=="c":
 *         return -1
 *     if aa1=="m" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="m" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":805
 *         return -1
 *     if aa1=="m" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="e":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L296;
  }
  __pyx_L296:;

  /* "obitools/align/_codonnws.pyx":806
 *     if aa1=="m" and aa2=="q":
 *         return 0
 *     if aa1=="m" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="m" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":807
 *         return 0
 *     if aa1=="m" and aa2=="e":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="g":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L297;
  }
  __pyx_L297:;

  /* "obitools/align/_codonnws.pyx":808
 *     if aa1=="m" and aa2=="e":
 *         return -2
 *     if aa1=="m" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="m" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":809
 *         return -2
 *     if aa1=="m" and aa2=="g":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="h":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L298;
  }
  __pyx_L298:;

  /* "obitools/align/_codonnws.pyx":810
 *     if aa1=="m" and aa2=="g":
 *         return -3
 *     if aa1=="m" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="m" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":811
 *         return -3
 *     if aa1=="m" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="i":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L299;
  }
  __pyx_L299:;

  /* "obitools/align/_codonnws.pyx":812
 *     if aa1=="m" and aa2=="h":
 *         return -2
 *     if aa1=="m" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="m" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":813
 *         return -2
 *     if aa1=="m" and aa2=="i":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="l":
 *         return 2
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L300;
  }
  __pyx_L300:;

  /* "obitools/align/_codonnws.pyx":814
 *     if aa1=="m" and aa2=="i":
 *         return 1
 *     if aa1=="m" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="m" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":815
 *         return 1
 *     if aa1=="m" and aa2=="l":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="k":
 *         return -1
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L301;
  }
  __pyx_L301:;

  /* "obitools/align/_codonnws.pyx":816
 *     if aa1=="m" and aa2=="l":
 *         return 2
 *     if aa1=="m" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":817
 *         return 2
 *     if aa1=="m" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="m":
 *         return 5
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L302;
  }
  __pyx_L302:;

  /* "obitools/align/_codonnws.pyx":818
 *     if aa1=="m" and aa2=="k":
 *         return -1
 *     if aa1=="m" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="m" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":819
 *         return -1
 *     if aa1=="m" and aa2=="m":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="f":
 *         return 0
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L303;
  }
  __pyx_L303:;

  /* "obitools/align/_codonnws.pyx":820
 *     if aa1=="m" and aa2=="m":
 *         return 5
 *     if aa1=="m" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="m" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":821
 *         return 5
 *     if aa1=="m" and aa2=="f":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="p":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L304;
  }
  __pyx_L304:;

  /* "obitools/align/_codonnws.pyx":822
 *     if aa1=="m" and aa2=="f":
 *         return 0
 *     if aa1=="m" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="m" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":823
 *         return 0
 *     if aa1=="m" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="s":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L305;
  }
  __pyx_L305:;

  /* "obitools/align/_codonnws.pyx":824
 *     if aa1=="m" and aa2=="p":
 *         return -2
 *     if aa1=="m" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":825
 *         return -2
 *     if aa1=="m" and aa2=="s":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="t":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L306;
  }
  __pyx_L306:;

  /* "obitools/align/_codonnws.pyx":826
 *     if aa1=="m" and aa2=="s":
 *         return -1
 *     if aa1=="m" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":827
 *         return -1
 *     if aa1=="m" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="w":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L307;
  }
  __pyx_L307:;

  /* "obitools/align/_codonnws.pyx":828
 *     if aa1=="m" and aa2=="t":
 *         return -1
 *     if aa1=="m" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":829
 *         return -1
 *     if aa1=="m" and aa2=="w":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="y":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L308;
  }
  __pyx_L308:;

  /* "obitools/align/_codonnws.pyx":830
 *     if aa1=="m" and aa2=="w":
 *         return -1
 *     if aa1=="m" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":831
 *         return -1
 *     if aa1=="m" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="v":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L309;
  }
  __pyx_L309:;

  /* "obitools/align/_codonnws.pyx":832
 *     if aa1=="m" and aa2=="y":
 *         return -1
 *     if aa1=="m" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="m" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":833
 *         return -1
 *     if aa1=="m" and aa2=="v":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="b":
 *         return -3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L310;
  }
  __pyx_L310:;

  /* "obitools/align/_codonnws.pyx":834
 *     if aa1=="m" and aa2=="v":
 *         return 1
 *     if aa1=="m" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="m" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":835
 *         return 1
 *     if aa1=="m" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="z":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L311;
  }
  __pyx_L311:;

  /* "obitools/align/_codonnws.pyx":836
 *     if aa1=="m" and aa2=="b":
 *         return -3
 *     if aa1=="m" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":837
 *         return -3
 *     if aa1=="m" and aa2=="z":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="x":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L312;
  }
  __pyx_L312:;

  /* "obitools/align/_codonnws.pyx":838
 *     if aa1=="m" and aa2=="z":
 *         return -1
 *     if aa1=="m" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="m" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":839
 *         return -1
 *     if aa1=="m" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="m" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L313;
  }
  __pyx_L313:;

  /* "obitools/align/_codonnws.pyx":840
 *     if aa1=="m" and aa2=="x":
 *         return -1
 *     if aa1=="m" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="f" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'm');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":841
 *         return -1
 *     if aa1=="m" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L314;
  }
  __pyx_L314:;

  /* "obitools/align/_codonnws.pyx":842
 *     if aa1=="m" and aa2=="*":
 *         return -4
 *     if aa1=="f" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="f" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":843
 *         return -4
 *     if aa1=="f" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="r":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L315;
  }
  __pyx_L315:;

  /* "obitools/align/_codonnws.pyx":844
 *     if aa1=="f" and aa2=="a":
 *         return -2
 *     if aa1=="f" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":845
 *         return -2
 *     if aa1=="f" and aa2=="r":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="n":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L316;
  }
  __pyx_L316:;

  /* "obitools/align/_codonnws.pyx":846
 *     if aa1=="f" and aa2=="r":
 *         return -3
 *     if aa1=="f" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":847
 *         return -3
 *     if aa1=="f" and aa2=="n":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="d":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L317;
  }
  __pyx_L317:;

  /* "obitools/align/_codonnws.pyx":848
 *     if aa1=="f" and aa2=="n":
 *         return -3
 *     if aa1=="f" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":849
 *         return -3
 *     if aa1=="f" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="c":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L318;
  }
  __pyx_L318:;

  /* "obitools/align/_codonnws.pyx":850
 *     if aa1=="f" and aa2=="d":
 *         return -3
 *     if aa1=="f" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="f" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":851
 *         return -3
 *     if aa1=="f" and aa2=="c":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="q":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L319;
  }
  __pyx_L319:;

  /* "obitools/align/_codonnws.pyx":852
 *     if aa1=="f" and aa2=="c":
 *         return -2
 *     if aa1=="f" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":853
 *         return -2
 *     if aa1=="f" and aa2=="q":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="e":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L320;
  }
  __pyx_L320:;

  /* "obitools/align/_codonnws.pyx":854
 *     if aa1=="f" and aa2=="q":
 *         return -3
 *     if aa1=="f" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":855
 *         return -3
 *     if aa1=="f" and aa2=="e":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="g":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L321;
  }
  __pyx_L321:;

  /* "obitools/align/_codonnws.pyx":856
 *     if aa1=="f" and aa2=="e":
 *         return -3
 *     if aa1=="f" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":857
 *         return -3
 *     if aa1=="f" and aa2=="g":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="h":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L322;
  }
  __pyx_L322:;

  /* "obitools/align/_codonnws.pyx":858
 *     if aa1=="f" and aa2=="g":
 *         return -3
 *     if aa1=="f" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="f" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":859
 *         return -3
 *     if aa1=="f" and aa2=="h":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="i":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L323;
  }
  __pyx_L323:;

  /* "obitools/align/_codonnws.pyx":860
 *     if aa1=="f" and aa2=="h":
 *         return -1
 *     if aa1=="f" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="f" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":861
 *         return -1
 *     if aa1=="f" and aa2=="i":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="l":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L324;
  }
  __pyx_L324:;

  /* "obitools/align/_codonnws.pyx":862
 *     if aa1=="f" and aa2=="i":
 *         return 0
 *     if aa1=="f" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="f" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":863
 *         return 0
 *     if aa1=="f" and aa2=="l":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="k":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L325;
  }
  __pyx_L325:;

  /* "obitools/align/_codonnws.pyx":864
 *     if aa1=="f" and aa2=="l":
 *         return 0
 *     if aa1=="f" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":865
 *         return 0
 *     if aa1=="f" and aa2=="k":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="m":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L326;
  }
  __pyx_L326:;

  /* "obitools/align/_codonnws.pyx":866
 *     if aa1=="f" and aa2=="k":
 *         return -3
 *     if aa1=="f" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="f" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":867
 *         return -3
 *     if aa1=="f" and aa2=="m":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="f":
 *         return 6
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L327;
  }
  __pyx_L327:;

  /* "obitools/align/_codonnws.pyx":868
 *     if aa1=="f" and aa2=="m":
 *         return 0
 *     if aa1=="f" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 6
 *     if aa1=="f" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":869
 *         return 0
 *     if aa1=="f" and aa2=="f":
 *         return 6             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="p":
 *         return -4
 */
    __pyx_r = 6.0;
    goto __pyx_L0;
    goto __pyx_L328;
  }
  __pyx_L328:;

  /* "obitools/align/_codonnws.pyx":870
 *     if aa1=="f" and aa2=="f":
 *         return 6
 *     if aa1=="f" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="f" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":871
 *         return 6
 *     if aa1=="f" and aa2=="p":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="s":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L329;
  }
  __pyx_L329:;

  /* "obitools/align/_codonnws.pyx":872
 *     if aa1=="f" and aa2=="p":
 *         return -4
 *     if aa1=="f" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="f" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":873
 *         return -4
 *     if aa1=="f" and aa2=="s":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="t":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L330;
  }
  __pyx_L330:;

  /* "obitools/align/_codonnws.pyx":874
 *     if aa1=="f" and aa2=="s":
 *         return -2
 *     if aa1=="f" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="f" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":875
 *         return -2
 *     if aa1=="f" and aa2=="t":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="w":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L331;
  }
  __pyx_L331:;

  /* "obitools/align/_codonnws.pyx":876
 *     if aa1=="f" and aa2=="t":
 *         return -2
 *     if aa1=="f" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="f" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":877
 *         return -2
 *     if aa1=="f" and aa2=="w":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="y":
 *         return 3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L332;
  }
  __pyx_L332:;

  /* "obitools/align/_codonnws.pyx":878
 *     if aa1=="f" and aa2=="w":
 *         return 1
 *     if aa1=="f" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="f" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":879
 *         return 1
 *     if aa1=="f" and aa2=="y":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="v":
 *         return -1
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L333;
  }
  __pyx_L333:;

  /* "obitools/align/_codonnws.pyx":880
 *     if aa1=="f" and aa2=="y":
 *         return 3
 *     if aa1=="f" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="f" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":881
 *         return 3
 *     if aa1=="f" and aa2=="v":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="b":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L334;
  }
  __pyx_L334:;

  /* "obitools/align/_codonnws.pyx":882
 *     if aa1=="f" and aa2=="v":
 *         return -1
 *     if aa1=="f" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":883
 *         return -1
 *     if aa1=="f" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="z":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L335;
  }
  __pyx_L335:;

  /* "obitools/align/_codonnws.pyx":884
 *     if aa1=="f" and aa2=="b":
 *         return -3
 *     if aa1=="f" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="f" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":885
 *         return -3
 *     if aa1=="f" and aa2=="z":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="x":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L336;
  }
  __pyx_L336:;

  /* "obitools/align/_codonnws.pyx":886
 *     if aa1=="f" and aa2=="z":
 *         return -3
 *     if aa1=="f" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="f" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":887
 *         return -3
 *     if aa1=="f" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="f" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L337;
  }
  __pyx_L337:;

  /* "obitools/align/_codonnws.pyx":888
 *     if aa1=="f" and aa2=="x":
 *         return -1
 *     if aa1=="f" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="p" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'f');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":889
 *         return -1
 *     if aa1=="f" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L338;
  }
  __pyx_L338:;

  /* "obitools/align/_codonnws.pyx":890
 *     if aa1=="f" and aa2=="*":
 *         return -4
 *     if aa1=="p" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":891
 *         return -4
 *     if aa1=="p" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="r":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L339;
  }
  __pyx_L339:;

  /* "obitools/align/_codonnws.pyx":892
 *     if aa1=="p" and aa2=="a":
 *         return -1
 *     if aa1=="p" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":893
 *         return -1
 *     if aa1=="p" and aa2=="r":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="n":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L340;
  }
  __pyx_L340:;

  /* "obitools/align/_codonnws.pyx":894
 *     if aa1=="p" and aa2=="r":
 *         return -2
 *     if aa1=="p" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":895
 *         return -2
 *     if aa1=="p" and aa2=="n":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="d":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L341;
  }
  __pyx_L341:;

  /* "obitools/align/_codonnws.pyx":896
 *     if aa1=="p" and aa2=="n":
 *         return -2
 *     if aa1=="p" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":897
 *         return -2
 *     if aa1=="p" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="c":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L342;
  }
  __pyx_L342:;

  /* "obitools/align/_codonnws.pyx":898
 *     if aa1=="p" and aa2=="d":
 *         return -1
 *     if aa1=="p" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="p" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":899
 *         return -1
 *     if aa1=="p" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="q":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L343;
  }
  __pyx_L343:;

  /* "obitools/align/_codonnws.pyx":900
 *     if aa1=="p" and aa2=="c":
 *         return -3
 *     if aa1=="p" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":901
 *         return -3
 *     if aa1=="p" and aa2=="q":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="e":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L344;
  }
  __pyx_L344:;

  /* "obitools/align/_codonnws.pyx":902
 *     if aa1=="p" and aa2=="q":
 *         return -1
 *     if aa1=="p" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":903
 *         return -1
 *     if aa1=="p" and aa2=="e":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="g":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L345;
  }
  __pyx_L345:;

  /* "obitools/align/_codonnws.pyx":904
 *     if aa1=="p" and aa2=="e":
 *         return -1
 *     if aa1=="p" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":905
 *         return -1
 *     if aa1=="p" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="h":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L346;
  }
  __pyx_L346:;

  /* "obitools/align/_codonnws.pyx":906
 *     if aa1=="p" and aa2=="g":
 *         return -2
 *     if aa1=="p" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":907
 *         return -2
 *     if aa1=="p" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="i":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L347;
  }
  __pyx_L347:;

  /* "obitools/align/_codonnws.pyx":908
 *     if aa1=="p" and aa2=="h":
 *         return -2
 *     if aa1=="p" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="p" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":909
 *         return -2
 *     if aa1=="p" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="l":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L348;
  }
  __pyx_L348:;

  /* "obitools/align/_codonnws.pyx":910
 *     if aa1=="p" and aa2=="i":
 *         return -3
 *     if aa1=="p" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="p" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":911
 *         return -3
 *     if aa1=="p" and aa2=="l":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="k":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L349;
  }
  __pyx_L349:;

  /* "obitools/align/_codonnws.pyx":912
 *     if aa1=="p" and aa2=="l":
 *         return -3
 *     if aa1=="p" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":913
 *         return -3
 *     if aa1=="p" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="m":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L350;
  }
  __pyx_L350:;

  /* "obitools/align/_codonnws.pyx":914
 *     if aa1=="p" and aa2=="k":
 *         return -1
 *     if aa1=="p" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":915
 *         return -1
 *     if aa1=="p" and aa2=="m":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="f":
 *         return -4
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L351;
  }
  __pyx_L351:;

  /* "obitools/align/_codonnws.pyx":916
 *     if aa1=="p" and aa2=="m":
 *         return -2
 *     if aa1=="p" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="p" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":917
 *         return -2
 *     if aa1=="p" and aa2=="f":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="p":
 *         return 7
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L352;
  }
  __pyx_L352:;

  /* "obitools/align/_codonnws.pyx":918
 *     if aa1=="p" and aa2=="f":
 *         return -4
 *     if aa1=="p" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return 7
 *     if aa1=="p" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":919
 *         return -4
 *     if aa1=="p" and aa2=="p":
 *         return 7             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="s":
 *         return -1
 */
    __pyx_r = 7.0;
    goto __pyx_L0;
    goto __pyx_L353;
  }
  __pyx_L353:;

  /* "obitools/align/_codonnws.pyx":920
 *     if aa1=="p" and aa2=="p":
 *         return 7
 *     if aa1=="p" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":921
 *         return 7
 *     if aa1=="p" and aa2=="s":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="t":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L354;
  }
  __pyx_L354:;

  /* "obitools/align/_codonnws.pyx":922
 *     if aa1=="p" and aa2=="s":
 *         return -1
 *     if aa1=="p" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":923
 *         return -1
 *     if aa1=="p" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="w":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L355;
  }
  __pyx_L355:;

  /* "obitools/align/_codonnws.pyx":924
 *     if aa1=="p" and aa2=="t":
 *         return -1
 *     if aa1=="p" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="p" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":925
 *         return -1
 *     if aa1=="p" and aa2=="w":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="y":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L356;
  }
  __pyx_L356:;

  /* "obitools/align/_codonnws.pyx":926
 *     if aa1=="p" and aa2=="w":
 *         return -4
 *     if aa1=="p" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="p" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":927
 *         return -4
 *     if aa1=="p" and aa2=="y":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="v":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L357;
  }
  __pyx_L357:;

  /* "obitools/align/_codonnws.pyx":928
 *     if aa1=="p" and aa2=="y":
 *         return -3
 *     if aa1=="p" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":929
 *         return -3
 *     if aa1=="p" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="b":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L358;
  }
  __pyx_L358:;

  /* "obitools/align/_codonnws.pyx":930
 *     if aa1=="p" and aa2=="v":
 *         return -2
 *     if aa1=="p" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":931
 *         return -2
 *     if aa1=="p" and aa2=="b":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="z":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L359;
  }
  __pyx_L359:;

  /* "obitools/align/_codonnws.pyx":932
 *     if aa1=="p" and aa2=="b":
 *         return -2
 *     if aa1=="p" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="p" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":933
 *         return -2
 *     if aa1=="p" and aa2=="z":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="x":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L360;
  }
  __pyx_L360:;

  /* "obitools/align/_codonnws.pyx":934
 *     if aa1=="p" and aa2=="z":
 *         return -1
 *     if aa1=="p" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="p" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":935
 *         return -1
 *     if aa1=="p" and aa2=="x":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="p" and aa2=="*":
 *         return -4
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L361;
  }
  __pyx_L361:;

  /* "obitools/align/_codonnws.pyx":936
 *     if aa1=="p" and aa2=="x":
 *         return -2
 *     if aa1=="p" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="s" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'p');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":937
 *         return -2
 *     if aa1=="p" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="a":
 *         return 1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L362;
  }
  __pyx_L362:;

  /* "obitools/align/_codonnws.pyx":938
 *     if aa1=="p" and aa2=="*":
 *         return -4
 *     if aa1=="s" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="s" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":939
 *         return -4
 *     if aa1=="s" and aa2=="a":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="r":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L363;
  }
  __pyx_L363:;

  /* "obitools/align/_codonnws.pyx":940
 *     if aa1=="s" and aa2=="a":
 *         return 1
 *     if aa1=="s" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="s" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":941
 *         return 1
 *     if aa1=="s" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="n":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L364;
  }
  __pyx_L364:;

  /* "obitools/align/_codonnws.pyx":942
 *     if aa1=="s" and aa2=="r":
 *         return -1
 *     if aa1=="s" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="s" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":943
 *         return -1
 *     if aa1=="s" and aa2=="n":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="d":
 *         return 0
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L365;
  }
  __pyx_L365:;

  /* "obitools/align/_codonnws.pyx":944
 *     if aa1=="s" and aa2=="n":
 *         return 1
 *     if aa1=="s" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":945
 *         return 1
 *     if aa1=="s" and aa2=="d":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="c":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L366;
  }
  __pyx_L366:;

  /* "obitools/align/_codonnws.pyx":946
 *     if aa1=="s" and aa2=="d":
 *         return 0
 *     if aa1=="s" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="s" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":947
 *         return 0
 *     if aa1=="s" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="q":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L367;
  }
  __pyx_L367:;

  /* "obitools/align/_codonnws.pyx":948
 *     if aa1=="s" and aa2=="c":
 *         return -1
 *     if aa1=="s" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":949
 *         return -1
 *     if aa1=="s" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="e":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L368;
  }
  __pyx_L368:;

  /* "obitools/align/_codonnws.pyx":950
 *     if aa1=="s" and aa2=="q":
 *         return 0
 *     if aa1=="s" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":951
 *         return 0
 *     if aa1=="s" and aa2=="e":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="g":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L369;
  }
  __pyx_L369:;

  /* "obitools/align/_codonnws.pyx":952
 *     if aa1=="s" and aa2=="e":
 *         return 0
 *     if aa1=="s" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":953
 *         return 0
 *     if aa1=="s" and aa2=="g":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="h":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L370;
  }
  __pyx_L370:;

  /* "obitools/align/_codonnws.pyx":954
 *     if aa1=="s" and aa2=="g":
 *         return 0
 *     if aa1=="s" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="s" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":955
 *         return 0
 *     if aa1=="s" and aa2=="h":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="i":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L371;
  }
  __pyx_L371:;

  /* "obitools/align/_codonnws.pyx":956
 *     if aa1=="s" and aa2=="h":
 *         return -1
 *     if aa1=="s" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="s" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":957
 *         return -1
 *     if aa1=="s" and aa2=="i":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="l":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L372;
  }
  __pyx_L372:;

  /* "obitools/align/_codonnws.pyx":958
 *     if aa1=="s" and aa2=="i":
 *         return -2
 *     if aa1=="s" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="s" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":959
 *         return -2
 *     if aa1=="s" and aa2=="l":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="k":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L373;
  }
  __pyx_L373:;

  /* "obitools/align/_codonnws.pyx":960
 *     if aa1=="s" and aa2=="l":
 *         return -2
 *     if aa1=="s" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":961
 *         return -2
 *     if aa1=="s" and aa2=="k":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="m":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L374;
  }
  __pyx_L374:;

  /* "obitools/align/_codonnws.pyx":962
 *     if aa1=="s" and aa2=="k":
 *         return 0
 *     if aa1=="s" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="s" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":963
 *         return 0
 *     if aa1=="s" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="f":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L375;
  }
  __pyx_L375:;

  /* "obitools/align/_codonnws.pyx":964
 *     if aa1=="s" and aa2=="m":
 *         return -1
 *     if aa1=="s" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="s" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":965
 *         return -1
 *     if aa1=="s" and aa2=="f":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="p":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L376;
  }
  __pyx_L376:;

  /* "obitools/align/_codonnws.pyx":966
 *     if aa1=="s" and aa2=="f":
 *         return -2
 *     if aa1=="s" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="s" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":967
 *         return -2
 *     if aa1=="s" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="s":
 *         return 4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L377;
  }
  __pyx_L377:;

  /* "obitools/align/_codonnws.pyx":968
 *     if aa1=="s" and aa2=="p":
 *         return -1
 *     if aa1=="s" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="s" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":969
 *         return -1
 *     if aa1=="s" and aa2=="s":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="t":
 *         return 1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L378;
  }
  __pyx_L378:;

  /* "obitools/align/_codonnws.pyx":970
 *     if aa1=="s" and aa2=="s":
 *         return 4
 *     if aa1=="s" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="s" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":971
 *         return 4
 *     if aa1=="s" and aa2=="t":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="w":
 *         return -3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L379;
  }
  __pyx_L379:;

  /* "obitools/align/_codonnws.pyx":972
 *     if aa1=="s" and aa2=="t":
 *         return 1
 *     if aa1=="s" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="s" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":973
 *         return 1
 *     if aa1=="s" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L380;
  }
  __pyx_L380:;

  /* "obitools/align/_codonnws.pyx":974
 *     if aa1=="s" and aa2=="w":
 *         return -3
 *     if aa1=="s" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="s" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":975
 *         return -3
 *     if aa1=="s" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="v":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L381;
  }
  __pyx_L381:;

  /* "obitools/align/_codonnws.pyx":976
 *     if aa1=="s" and aa2=="y":
 *         return -2
 *     if aa1=="s" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="s" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":977
 *         return -2
 *     if aa1=="s" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="b":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L382;
  }
  __pyx_L382:;

  /* "obitools/align/_codonnws.pyx":978
 *     if aa1=="s" and aa2=="v":
 *         return -2
 *     if aa1=="s" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":979
 *         return -2
 *     if aa1=="s" and aa2=="b":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="z":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L383;
  }
  __pyx_L383:;

  /* "obitools/align/_codonnws.pyx":980
 *     if aa1=="s" and aa2=="b":
 *         return 0
 *     if aa1=="s" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 's');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":981
 *         return 0
 *     if aa1=="s" and aa2=="z":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="x":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L384;
  }
  __pyx_L384:;

  /* "obitools/align/_codonnws.pyx":982
 *     if aa1=="s" and aa2=="z":
 *         return 0
 *     if aa1=="s" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="s" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 's');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":983
 *         return 0
 *     if aa1=="s" and aa2=="x":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="s" and aa2=="*":
 *         return -4
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L385;
  }
  __pyx_L385:;

  /* "obitools/align/_codonnws.pyx":984
 *     if aa1=="s" and aa2=="x":
 *         return 0
 *     if aa1=="s" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="t" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 's');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":985
 *         return 0
 *     if aa1=="s" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="a":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L386;
  }
  __pyx_L386:;

  /* "obitools/align/_codonnws.pyx":986
 *     if aa1=="s" and aa2=="*":
 *         return -4
 *     if aa1=="t" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="t" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":987
 *         return -4
 *     if aa1=="t" and aa2=="a":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="r":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L387;
  }
  __pyx_L387:;

  /* "obitools/align/_codonnws.pyx":988
 *     if aa1=="t" and aa2=="a":
 *         return 0
 *     if aa1=="t" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":989
 *         return 0
 *     if aa1=="t" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="n":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L388;
  }
  __pyx_L388:;

  /* "obitools/align/_codonnws.pyx":990
 *     if aa1=="t" and aa2=="r":
 *         return -1
 *     if aa1=="t" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="t" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":991
 *         return -1
 *     if aa1=="t" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="d":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L389;
  }
  __pyx_L389:;

  /* "obitools/align/_codonnws.pyx":992
 *     if aa1=="t" and aa2=="n":
 *         return 0
 *     if aa1=="t" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":993
 *         return 0
 *     if aa1=="t" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="c":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L390;
  }
  __pyx_L390:;

  /* "obitools/align/_codonnws.pyx":994
 *     if aa1=="t" and aa2=="d":
 *         return -1
 *     if aa1=="t" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":995
 *         return -1
 *     if aa1=="t" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="q":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L391;
  }
  __pyx_L391:;

  /* "obitools/align/_codonnws.pyx":996
 *     if aa1=="t" and aa2=="c":
 *         return -1
 *     if aa1=="t" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":997
 *         return -1
 *     if aa1=="t" and aa2=="q":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="e":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L392;
  }
  __pyx_L392:;

  /* "obitools/align/_codonnws.pyx":998
 *     if aa1=="t" and aa2=="q":
 *         return -1
 *     if aa1=="t" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":999
 *         return -1
 *     if aa1=="t" and aa2=="e":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="g":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L393;
  }
  __pyx_L393:;

  /* "obitools/align/_codonnws.pyx":1000
 *     if aa1=="t" and aa2=="e":
 *         return -1
 *     if aa1=="t" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="t" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1001
 *         return -1
 *     if aa1=="t" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="h":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L394;
  }
  __pyx_L394:;

  /* "obitools/align/_codonnws.pyx":1002
 *     if aa1=="t" and aa2=="g":
 *         return -2
 *     if aa1=="t" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="t" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1003
 *         return -2
 *     if aa1=="t" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="i":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L395;
  }
  __pyx_L395:;

  /* "obitools/align/_codonnws.pyx":1004
 *     if aa1=="t" and aa2=="h":
 *         return -2
 *     if aa1=="t" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1005
 *         return -2
 *     if aa1=="t" and aa2=="i":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="l":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L396;
  }
  __pyx_L396:;

  /* "obitools/align/_codonnws.pyx":1006
 *     if aa1=="t" and aa2=="i":
 *         return -1
 *     if aa1=="t" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1007
 *         return -1
 *     if aa1=="t" and aa2=="l":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="k":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L397;
  }
  __pyx_L397:;

  /* "obitools/align/_codonnws.pyx":1008
 *     if aa1=="t" and aa2=="l":
 *         return -1
 *     if aa1=="t" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1009
 *         return -1
 *     if aa1=="t" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="m":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L398;
  }
  __pyx_L398:;

  /* "obitools/align/_codonnws.pyx":1010
 *     if aa1=="t" and aa2=="k":
 *         return -1
 *     if aa1=="t" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1011
 *         return -1
 *     if aa1=="t" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="f":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L399;
  }
  __pyx_L399:;

  /* "obitools/align/_codonnws.pyx":1012
 *     if aa1=="t" and aa2=="m":
 *         return -1
 *     if aa1=="t" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="t" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1013
 *         return -1
 *     if aa1=="t" and aa2=="f":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="p":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L400;
  }
  __pyx_L400:;

  /* "obitools/align/_codonnws.pyx":1014
 *     if aa1=="t" and aa2=="f":
 *         return -2
 *     if aa1=="t" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1015
 *         return -2
 *     if aa1=="t" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="s":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L401;
  }
  __pyx_L401:;

  /* "obitools/align/_codonnws.pyx":1016
 *     if aa1=="t" and aa2=="p":
 *         return -1
 *     if aa1=="t" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="t" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1017
 *         return -1
 *     if aa1=="t" and aa2=="s":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="t":
 *         return 5
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L402;
  }
  __pyx_L402:;

  /* "obitools/align/_codonnws.pyx":1018
 *     if aa1=="t" and aa2=="s":
 *         return 1
 *     if aa1=="t" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 5
 *     if aa1=="t" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1019
 *         return 1
 *     if aa1=="t" and aa2=="t":
 *         return 5             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="w":
 *         return -2
 */
    __pyx_r = 5.0;
    goto __pyx_L0;
    goto __pyx_L403;
  }
  __pyx_L403:;

  /* "obitools/align/_codonnws.pyx":1020
 *     if aa1=="t" and aa2=="t":
 *         return 5
 *     if aa1=="t" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="t" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1021
 *         return 5
 *     if aa1=="t" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="y":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L404;
  }
  __pyx_L404:;

  /* "obitools/align/_codonnws.pyx":1022
 *     if aa1=="t" and aa2=="w":
 *         return -2
 *     if aa1=="t" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="t" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1023
 *         return -2
 *     if aa1=="t" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="v":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L405;
  }
  __pyx_L405:;

  /* "obitools/align/_codonnws.pyx":1024
 *     if aa1=="t" and aa2=="y":
 *         return -2
 *     if aa1=="t" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="t" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1025
 *         return -2
 *     if aa1=="t" and aa2=="v":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="b":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L406;
  }
  __pyx_L406:;

  /* "obitools/align/_codonnws.pyx":1026
 *     if aa1=="t" and aa2=="v":
 *         return 0
 *     if aa1=="t" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1027
 *         return 0
 *     if aa1=="t" and aa2=="b":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="z":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L407;
  }
  __pyx_L407:;

  /* "obitools/align/_codonnws.pyx":1028
 *     if aa1=="t" and aa2=="b":
 *         return -1
 *     if aa1=="t" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="t" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 't');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1029
 *         return -1
 *     if aa1=="t" and aa2=="z":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="x":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L408;
  }
  __pyx_L408:;

  /* "obitools/align/_codonnws.pyx":1030
 *     if aa1=="t" and aa2=="z":
 *         return -1
 *     if aa1=="t" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="t" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 't');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1031
 *         return -1
 *     if aa1=="t" and aa2=="x":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="t" and aa2=="*":
 *         return -4
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L409;
  }
  __pyx_L409:;

  /* "obitools/align/_codonnws.pyx":1032
 *     if aa1=="t" and aa2=="x":
 *         return 0
 *     if aa1=="t" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="w" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 't');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1033
 *         return 0
 *     if aa1=="t" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="a":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L410;
  }
  __pyx_L410:;

  /* "obitools/align/_codonnws.pyx":1034
 *     if aa1=="t" and aa2=="*":
 *         return -4
 *     if aa1=="w" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1035
 *         return -4
 *     if aa1=="w" and aa2=="a":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="r":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L411;
  }
  __pyx_L411:;

  /* "obitools/align/_codonnws.pyx":1036
 *     if aa1=="w" and aa2=="a":
 *         return -3
 *     if aa1=="w" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1037
 *         return -3
 *     if aa1=="w" and aa2=="r":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="n":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L412;
  }
  __pyx_L412:;

  /* "obitools/align/_codonnws.pyx":1038
 *     if aa1=="w" and aa2=="r":
 *         return -3
 *     if aa1=="w" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="w" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1039
 *         return -3
 *     if aa1=="w" and aa2=="n":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="d":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L413;
  }
  __pyx_L413:;

  /* "obitools/align/_codonnws.pyx":1040
 *     if aa1=="w" and aa2=="n":
 *         return -4
 *     if aa1=="w" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="w" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1041
 *         return -4
 *     if aa1=="w" and aa2=="d":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="c":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L414;
  }
  __pyx_L414:;

  /* "obitools/align/_codonnws.pyx":1042
 *     if aa1=="w" and aa2=="d":
 *         return -4
 *     if aa1=="w" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1043
 *         return -4
 *     if aa1=="w" and aa2=="c":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="q":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L415;
  }
  __pyx_L415:;

  /* "obitools/align/_codonnws.pyx":1044
 *     if aa1=="w" and aa2=="c":
 *         return -2
 *     if aa1=="w" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1045
 *         return -2
 *     if aa1=="w" and aa2=="q":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="e":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L416;
  }
  __pyx_L416:;

  /* "obitools/align/_codonnws.pyx":1046
 *     if aa1=="w" and aa2=="q":
 *         return -2
 *     if aa1=="w" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1047
 *         return -2
 *     if aa1=="w" and aa2=="e":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="g":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L417;
  }
  __pyx_L417:;

  /* "obitools/align/_codonnws.pyx":1048
 *     if aa1=="w" and aa2=="e":
 *         return -3
 *     if aa1=="w" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1049
 *         return -3
 *     if aa1=="w" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="h":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L418;
  }
  __pyx_L418:;

  /* "obitools/align/_codonnws.pyx":1050
 *     if aa1=="w" and aa2=="g":
 *         return -2
 *     if aa1=="w" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1051
 *         return -2
 *     if aa1=="w" and aa2=="h":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="i":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L419;
  }
  __pyx_L419:;

  /* "obitools/align/_codonnws.pyx":1052
 *     if aa1=="w" and aa2=="h":
 *         return -2
 *     if aa1=="w" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1053
 *         return -2
 *     if aa1=="w" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="l":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L420;
  }
  __pyx_L420:;

  /* "obitools/align/_codonnws.pyx":1054
 *     if aa1=="w" and aa2=="i":
 *         return -3
 *     if aa1=="w" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1055
 *         return -3
 *     if aa1=="w" and aa2=="l":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="k":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L421;
  }
  __pyx_L421:;

  /* "obitools/align/_codonnws.pyx":1056
 *     if aa1=="w" and aa2=="l":
 *         return -2
 *     if aa1=="w" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1057
 *         return -2
 *     if aa1=="w" and aa2=="k":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="m":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L422;
  }
  __pyx_L422:;

  /* "obitools/align/_codonnws.pyx":1058
 *     if aa1=="w" and aa2=="k":
 *         return -3
 *     if aa1=="w" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="w" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1059
 *         return -3
 *     if aa1=="w" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="f":
 *         return 1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L423;
  }
  __pyx_L423:;

  /* "obitools/align/_codonnws.pyx":1060
 *     if aa1=="w" and aa2=="m":
 *         return -1
 *     if aa1=="w" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="w" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1061
 *         return -1
 *     if aa1=="w" and aa2=="f":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="p":
 *         return -4
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L424;
  }
  __pyx_L424:;

  /* "obitools/align/_codonnws.pyx":1062
 *     if aa1=="w" and aa2=="f":
 *         return 1
 *     if aa1=="w" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="w" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1063
 *         return 1
 *     if aa1=="w" and aa2=="p":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="s":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L425;
  }
  __pyx_L425:;

  /* "obitools/align/_codonnws.pyx":1064
 *     if aa1=="w" and aa2=="p":
 *         return -4
 *     if aa1=="w" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1065
 *         return -4
 *     if aa1=="w" and aa2=="s":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="t":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L426;
  }
  __pyx_L426:;

  /* "obitools/align/_codonnws.pyx":1066
 *     if aa1=="w" and aa2=="s":
 *         return -3
 *     if aa1=="w" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1067
 *         return -3
 *     if aa1=="w" and aa2=="t":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="w":
 *         return 11
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L427;
  }
  __pyx_L427:;

  /* "obitools/align/_codonnws.pyx":1068
 *     if aa1=="w" and aa2=="t":
 *         return -2
 *     if aa1=="w" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return 11
 *     if aa1=="w" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1069
 *         return -2
 *     if aa1=="w" and aa2=="w":
 *         return 11             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="y":
 *         return 2
 */
    __pyx_r = 11.0;
    goto __pyx_L0;
    goto __pyx_L428;
  }
  __pyx_L428:;

  /* "obitools/align/_codonnws.pyx":1070
 *     if aa1=="w" and aa2=="w":
 *         return 11
 *     if aa1=="w" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="w" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1071
 *         return 11
 *     if aa1=="w" and aa2=="y":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="v":
 *         return -3
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L429;
  }
  __pyx_L429:;

  /* "obitools/align/_codonnws.pyx":1072
 *     if aa1=="w" and aa2=="y":
 *         return 2
 *     if aa1=="w" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1073
 *         return 2
 *     if aa1=="w" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="b":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L430;
  }
  __pyx_L430:;

  /* "obitools/align/_codonnws.pyx":1074
 *     if aa1=="w" and aa2=="v":
 *         return -3
 *     if aa1=="w" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="w" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1075
 *         return -3
 *     if aa1=="w" and aa2=="b":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="z":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L431;
  }
  __pyx_L431:;

  /* "obitools/align/_codonnws.pyx":1076
 *     if aa1=="w" and aa2=="b":
 *         return -4
 *     if aa1=="w" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="w" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1077
 *         return -4
 *     if aa1=="w" and aa2=="z":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="x":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L432;
  }
  __pyx_L432:;

  /* "obitools/align/_codonnws.pyx":1078
 *     if aa1=="w" and aa2=="z":
 *         return -3
 *     if aa1=="w" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="w" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1079
 *         return -3
 *     if aa1=="w" and aa2=="x":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="w" and aa2=="*":
 *         return -4
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L433;
  }
  __pyx_L433:;

  /* "obitools/align/_codonnws.pyx":1080
 *     if aa1=="w" and aa2=="x":
 *         return -2
 *     if aa1=="w" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="y" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'w');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1081
 *         return -2
 *     if aa1=="w" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L434;
  }
  __pyx_L434:;

  /* "obitools/align/_codonnws.pyx":1082
 *     if aa1=="w" and aa2=="*":
 *         return -4
 *     if aa1=="y" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1083
 *         return -4
 *     if aa1=="y" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="r":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L435;
  }
  __pyx_L435:;

  /* "obitools/align/_codonnws.pyx":1084
 *     if aa1=="y" and aa2=="a":
 *         return -2
 *     if aa1=="y" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1085
 *         return -2
 *     if aa1=="y" and aa2=="r":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="n":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L436;
  }
  __pyx_L436:;

  /* "obitools/align/_codonnws.pyx":1086
 *     if aa1=="y" and aa2=="r":
 *         return -2
 *     if aa1=="y" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1087
 *         return -2
 *     if aa1=="y" and aa2=="n":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="d":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L437;
  }
  __pyx_L437:;

  /* "obitools/align/_codonnws.pyx":1088
 *     if aa1=="y" and aa2=="n":
 *         return -2
 *     if aa1=="y" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="y" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1089
 *         return -2
 *     if aa1=="y" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="c":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L438;
  }
  __pyx_L438:;

  /* "obitools/align/_codonnws.pyx":1090
 *     if aa1=="y" and aa2=="d":
 *         return -3
 *     if aa1=="y" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1091
 *         return -3
 *     if aa1=="y" and aa2=="c":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="q":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L439;
  }
  __pyx_L439:;

  /* "obitools/align/_codonnws.pyx":1092
 *     if aa1=="y" and aa2=="c":
 *         return -2
 *     if aa1=="y" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1093
 *         return -2
 *     if aa1=="y" and aa2=="q":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="e":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L440;
  }
  __pyx_L440:;

  /* "obitools/align/_codonnws.pyx":1094
 *     if aa1=="y" and aa2=="q":
 *         return -1
 *     if aa1=="y" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1095
 *         return -1
 *     if aa1=="y" and aa2=="e":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="g":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L441;
  }
  __pyx_L441:;

  /* "obitools/align/_codonnws.pyx":1096
 *     if aa1=="y" and aa2=="e":
 *         return -2
 *     if aa1=="y" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="y" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1097
 *         return -2
 *     if aa1=="y" and aa2=="g":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="h":
 *         return 2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L442;
  }
  __pyx_L442:;

  /* "obitools/align/_codonnws.pyx":1098
 *     if aa1=="y" and aa2=="g":
 *         return -3
 *     if aa1=="y" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="y" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1099
 *         return -3
 *     if aa1=="y" and aa2=="h":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="i":
 *         return -1
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L443;
  }
  __pyx_L443:;

  /* "obitools/align/_codonnws.pyx":1100
 *     if aa1=="y" and aa2=="h":
 *         return 2
 *     if aa1=="y" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1101
 *         return 2
 *     if aa1=="y" and aa2=="i":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="l":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L444;
  }
  __pyx_L444:;

  /* "obitools/align/_codonnws.pyx":1102
 *     if aa1=="y" and aa2=="i":
 *         return -1
 *     if aa1=="y" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1103
 *         return -1
 *     if aa1=="y" and aa2=="l":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="k":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L445;
  }
  __pyx_L445:;

  /* "obitools/align/_codonnws.pyx":1104
 *     if aa1=="y" and aa2=="l":
 *         return -1
 *     if aa1=="y" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1105
 *         return -1
 *     if aa1=="y" and aa2=="k":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="m":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L446;
  }
  __pyx_L446:;

  /* "obitools/align/_codonnws.pyx":1106
 *     if aa1=="y" and aa2=="k":
 *         return -2
 *     if aa1=="y" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1107
 *         return -2
 *     if aa1=="y" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="f":
 *         return 3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L447;
  }
  __pyx_L447:;

  /* "obitools/align/_codonnws.pyx":1108
 *     if aa1=="y" and aa2=="m":
 *         return -1
 *     if aa1=="y" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="y" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1109
 *         return -1
 *     if aa1=="y" and aa2=="f":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="p":
 *         return -3
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L448;
  }
  __pyx_L448:;

  /* "obitools/align/_codonnws.pyx":1110
 *     if aa1=="y" and aa2=="f":
 *         return 3
 *     if aa1=="y" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="y" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1111
 *         return 3
 *     if aa1=="y" and aa2=="p":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="s":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L449;
  }
  __pyx_L449:;

  /* "obitools/align/_codonnws.pyx":1112
 *     if aa1=="y" and aa2=="p":
 *         return -3
 *     if aa1=="y" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1113
 *         return -3
 *     if aa1=="y" and aa2=="s":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="t":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L450;
  }
  __pyx_L450:;

  /* "obitools/align/_codonnws.pyx":1114
 *     if aa1=="y" and aa2=="s":
 *         return -2
 *     if aa1=="y" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1115
 *         return -2
 *     if aa1=="y" and aa2=="t":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="w":
 *         return 2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L451;
  }
  __pyx_L451:;

  /* "obitools/align/_codonnws.pyx":1116
 *     if aa1=="y" and aa2=="t":
 *         return -2
 *     if aa1=="y" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return 2
 *     if aa1=="y" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1117
 *         return -2
 *     if aa1=="y" and aa2=="w":
 *         return 2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="y":
 *         return 7
 */
    __pyx_r = 2.0;
    goto __pyx_L0;
    goto __pyx_L452;
  }
  __pyx_L452:;

  /* "obitools/align/_codonnws.pyx":1118
 *     if aa1=="y" and aa2=="w":
 *         return 2
 *     if aa1=="y" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return 7
 *     if aa1=="y" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1119
 *         return 2
 *     if aa1=="y" and aa2=="y":
 *         return 7             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="v":
 *         return -1
 */
    __pyx_r = 7.0;
    goto __pyx_L0;
    goto __pyx_L453;
  }
  __pyx_L453:;

  /* "obitools/align/_codonnws.pyx":1120
 *     if aa1=="y" and aa2=="y":
 *         return 7
 *     if aa1=="y" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1121
 *         return 7
 *     if aa1=="y" and aa2=="v":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="b":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L454;
  }
  __pyx_L454:;

  /* "obitools/align/_codonnws.pyx":1122
 *     if aa1=="y" and aa2=="v":
 *         return -1
 *     if aa1=="y" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="y" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1123
 *         return -1
 *     if aa1=="y" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="z":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L455;
  }
  __pyx_L455:;

  /* "obitools/align/_codonnws.pyx":1124
 *     if aa1=="y" and aa2=="b":
 *         return -3
 *     if aa1=="y" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="y" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1125
 *         return -3
 *     if aa1=="y" and aa2=="z":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="x":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L456;
  }
  __pyx_L456:;

  /* "obitools/align/_codonnws.pyx":1126
 *     if aa1=="y" and aa2=="z":
 *         return -2
 *     if aa1=="y" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="y" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1127
 *         return -2
 *     if aa1=="y" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="y" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L457;
  }
  __pyx_L457:;

  /* "obitools/align/_codonnws.pyx":1128
 *     if aa1=="y" and aa2=="x":
 *         return -1
 *     if aa1=="y" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="v" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'y');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1129
 *         return -1
 *     if aa1=="y" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="a":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L458;
  }
  __pyx_L458:;

  /* "obitools/align/_codonnws.pyx":1130
 *     if aa1=="y" and aa2=="*":
 *         return -4
 *     if aa1=="v" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="v" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1131
 *         return -4
 *     if aa1=="v" and aa2=="a":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="r":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L459;
  }
  __pyx_L459:;

  /* "obitools/align/_codonnws.pyx":1132
 *     if aa1=="v" and aa2=="a":
 *         return 0
 *     if aa1=="v" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1133
 *         return 0
 *     if aa1=="v" and aa2=="r":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="n":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L460;
  }
  __pyx_L460:;

  /* "obitools/align/_codonnws.pyx":1134
 *     if aa1=="v" and aa2=="r":
 *         return -3
 *     if aa1=="v" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1135
 *         return -3
 *     if aa1=="v" and aa2=="n":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="d":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L461;
  }
  __pyx_L461:;

  /* "obitools/align/_codonnws.pyx":1136
 *     if aa1=="v" and aa2=="n":
 *         return -3
 *     if aa1=="v" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1137
 *         return -3
 *     if aa1=="v" and aa2=="d":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="c":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L462;
  }
  __pyx_L462:;

  /* "obitools/align/_codonnws.pyx":1138
 *     if aa1=="v" and aa2=="d":
 *         return -3
 *     if aa1=="v" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="v" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1139
 *         return -3
 *     if aa1=="v" and aa2=="c":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="q":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L463;
  }
  __pyx_L463:;

  /* "obitools/align/_codonnws.pyx":1140
 *     if aa1=="v" and aa2=="c":
 *         return -1
 *     if aa1=="v" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1141
 *         return -1
 *     if aa1=="v" and aa2=="q":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="e":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L464;
  }
  __pyx_L464:;

  /* "obitools/align/_codonnws.pyx":1142
 *     if aa1=="v" and aa2=="q":
 *         return -2
 *     if aa1=="v" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1143
 *         return -2
 *     if aa1=="v" and aa2=="e":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="g":
 *         return -3
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L465;
  }
  __pyx_L465:;

  /* "obitools/align/_codonnws.pyx":1144
 *     if aa1=="v" and aa2=="e":
 *         return -2
 *     if aa1=="v" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1145
 *         return -2
 *     if aa1=="v" and aa2=="g":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="h":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L466;
  }
  __pyx_L466:;

  /* "obitools/align/_codonnws.pyx":1146
 *     if aa1=="v" and aa2=="g":
 *         return -3
 *     if aa1=="v" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1147
 *         return -3
 *     if aa1=="v" and aa2=="h":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="i":
 *         return 3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L467;
  }
  __pyx_L467:;

  /* "obitools/align/_codonnws.pyx":1148
 *     if aa1=="v" and aa2=="h":
 *         return -3
 *     if aa1=="v" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="v" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1149
 *         return -3
 *     if aa1=="v" and aa2=="i":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="l":
 *         return 1
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L468;
  }
  __pyx_L468:;

  /* "obitools/align/_codonnws.pyx":1150
 *     if aa1=="v" and aa2=="i":
 *         return 3
 *     if aa1=="v" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="v" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1151
 *         return 3
 *     if aa1=="v" and aa2=="l":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="k":
 *         return -2
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L469;
  }
  __pyx_L469:;

  /* "obitools/align/_codonnws.pyx":1152
 *     if aa1=="v" and aa2=="l":
 *         return 1
 *     if aa1=="v" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1153
 *         return 1
 *     if aa1=="v" and aa2=="k":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="m":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L470;
  }
  __pyx_L470:;

  /* "obitools/align/_codonnws.pyx":1154
 *     if aa1=="v" and aa2=="k":
 *         return -2
 *     if aa1=="v" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="v" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1155
 *         return -2
 *     if aa1=="v" and aa2=="m":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="f":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L471;
  }
  __pyx_L471:;

  /* "obitools/align/_codonnws.pyx":1156
 *     if aa1=="v" and aa2=="m":
 *         return 1
 *     if aa1=="v" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="v" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1157
 *         return 1
 *     if aa1=="v" and aa2=="f":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="p":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L472;
  }
  __pyx_L472:;

  /* "obitools/align/_codonnws.pyx":1158
 *     if aa1=="v" and aa2=="f":
 *         return -1
 *     if aa1=="v" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1159
 *         return -1
 *     if aa1=="v" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="s":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L473;
  }
  __pyx_L473:;

  /* "obitools/align/_codonnws.pyx":1160
 *     if aa1=="v" and aa2=="p":
 *         return -2
 *     if aa1=="v" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1161
 *         return -2
 *     if aa1=="v" and aa2=="s":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="t":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L474;
  }
  __pyx_L474:;

  /* "obitools/align/_codonnws.pyx":1162
 *     if aa1=="v" and aa2=="s":
 *         return -2
 *     if aa1=="v" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="v" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1163
 *         return -2
 *     if aa1=="v" and aa2=="t":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="w":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L475;
  }
  __pyx_L475:;

  /* "obitools/align/_codonnws.pyx":1164
 *     if aa1=="v" and aa2=="t":
 *         return 0
 *     if aa1=="v" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1165
 *         return 0
 *     if aa1=="v" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="y":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L476;
  }
  __pyx_L476:;

  /* "obitools/align/_codonnws.pyx":1166
 *     if aa1=="v" and aa2=="w":
 *         return -3
 *     if aa1=="v" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="v" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1167
 *         return -3
 *     if aa1=="v" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="v":
 *         return 4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L477;
  }
  __pyx_L477:;

  /* "obitools/align/_codonnws.pyx":1168
 *     if aa1=="v" and aa2=="y":
 *         return -1
 *     if aa1=="v" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="v" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1169
 *         return -1
 *     if aa1=="v" and aa2=="v":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="b":
 *         return -3
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L478;
  }
  __pyx_L478:;

  /* "obitools/align/_codonnws.pyx":1170
 *     if aa1=="v" and aa2=="v":
 *         return 4
 *     if aa1=="v" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="v" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1171
 *         return 4
 *     if aa1=="v" and aa2=="b":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="z":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L479;
  }
  __pyx_L479:;

  /* "obitools/align/_codonnws.pyx":1172
 *     if aa1=="v" and aa2=="b":
 *         return -3
 *     if aa1=="v" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="v" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1173
 *         return -3
 *     if aa1=="v" and aa2=="z":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="x":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L480;
  }
  __pyx_L480:;

  /* "obitools/align/_codonnws.pyx":1174
 *     if aa1=="v" and aa2=="z":
 *         return -2
 *     if aa1=="v" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="v" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1175
 *         return -2
 *     if aa1=="v" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="v" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L481;
  }
  __pyx_L481:;

  /* "obitools/align/_codonnws.pyx":1176
 *     if aa1=="v" and aa2=="x":
 *         return -1
 *     if aa1=="v" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="b" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'v');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1177
 *         return -1
 *     if aa1=="v" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="a":
 *         return -2
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L482;
  }
  __pyx_L482:;

  /* "obitools/align/_codonnws.pyx":1178
 *     if aa1=="v" and aa2=="*":
 *         return -4
 *     if aa1=="b" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="b" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1179
 *         return -4
 *     if aa1=="b" and aa2=="a":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="r":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L483;
  }
  __pyx_L483:;

  /* "obitools/align/_codonnws.pyx":1180
 *     if aa1=="b" and aa2=="a":
 *         return -2
 *     if aa1=="b" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="b" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1181
 *         return -2
 *     if aa1=="b" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="n":
 *         return 3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L484;
  }
  __pyx_L484:;

  /* "obitools/align/_codonnws.pyx":1182
 *     if aa1=="b" and aa2=="r":
 *         return -1
 *     if aa1=="b" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="b" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1183
 *         return -1
 *     if aa1=="b" and aa2=="n":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="d":
 *         return 4
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L485;
  }
  __pyx_L485:;

  /* "obitools/align/_codonnws.pyx":1184
 *     if aa1=="b" and aa2=="n":
 *         return 3
 *     if aa1=="b" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="b" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1185
 *         return 3
 *     if aa1=="b" and aa2=="d":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="c":
 *         return -3
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L486;
  }
  __pyx_L486:;

  /* "obitools/align/_codonnws.pyx":1186
 *     if aa1=="b" and aa2=="d":
 *         return 4
 *     if aa1=="b" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1187
 *         return 4
 *     if aa1=="b" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="q":
 *         return 0
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L487;
  }
  __pyx_L487:;

  /* "obitools/align/_codonnws.pyx":1188
 *     if aa1=="b" and aa2=="c":
 *         return -3
 *     if aa1=="b" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="b" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1189
 *         return -3
 *     if aa1=="b" and aa2=="q":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="e":
 *         return 1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L488;
  }
  __pyx_L488:;

  /* "obitools/align/_codonnws.pyx":1190
 *     if aa1=="b" and aa2=="q":
 *         return 0
 *     if aa1=="b" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="b" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1191
 *         return 0
 *     if aa1=="b" and aa2=="e":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="g":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L489;
  }
  __pyx_L489:;

  /* "obitools/align/_codonnws.pyx":1192
 *     if aa1=="b" and aa2=="e":
 *         return 1
 *     if aa1=="b" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="b" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1193
 *         return 1
 *     if aa1=="b" and aa2=="g":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="h":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L490;
  }
  __pyx_L490:;

  /* "obitools/align/_codonnws.pyx":1194
 *     if aa1=="b" and aa2=="g":
 *         return -1
 *     if aa1=="b" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="b" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1195
 *         return -1
 *     if aa1=="b" and aa2=="h":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="i":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L491;
  }
  __pyx_L491:;

  /* "obitools/align/_codonnws.pyx":1196
 *     if aa1=="b" and aa2=="h":
 *         return 0
 *     if aa1=="b" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1197
 *         return 0
 *     if aa1=="b" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="l":
 *         return -4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L492;
  }
  __pyx_L492:;

  /* "obitools/align/_codonnws.pyx":1198
 *     if aa1=="b" and aa2=="i":
 *         return -3
 *     if aa1=="b" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="b" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1199
 *         return -3
 *     if aa1=="b" and aa2=="l":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="k":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L493;
  }
  __pyx_L493:;

  /* "obitools/align/_codonnws.pyx":1200
 *     if aa1=="b" and aa2=="l":
 *         return -4
 *     if aa1=="b" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="b" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1201
 *         return -4
 *     if aa1=="b" and aa2=="k":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="m":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L494;
  }
  __pyx_L494:;

  /* "obitools/align/_codonnws.pyx":1202
 *     if aa1=="b" and aa2=="k":
 *         return 0
 *     if aa1=="b" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1203
 *         return 0
 *     if aa1=="b" and aa2=="m":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="f":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L495;
  }
  __pyx_L495:;

  /* "obitools/align/_codonnws.pyx":1204
 *     if aa1=="b" and aa2=="m":
 *         return -3
 *     if aa1=="b" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1205
 *         return -3
 *     if aa1=="b" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="p":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L496;
  }
  __pyx_L496:;

  /* "obitools/align/_codonnws.pyx":1206
 *     if aa1=="b" and aa2=="f":
 *         return -3
 *     if aa1=="b" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="b" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1207
 *         return -3
 *     if aa1=="b" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="s":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L497;
  }
  __pyx_L497:;

  /* "obitools/align/_codonnws.pyx":1208
 *     if aa1=="b" and aa2=="p":
 *         return -2
 *     if aa1=="b" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="b" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1209
 *         return -2
 *     if aa1=="b" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L498;
  }
  __pyx_L498:;

  /* "obitools/align/_codonnws.pyx":1210
 *     if aa1=="b" and aa2=="s":
 *         return 0
 *     if aa1=="b" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="b" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1211
 *         return 0
 *     if aa1=="b" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="w":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L499;
  }
  __pyx_L499:;

  /* "obitools/align/_codonnws.pyx":1212
 *     if aa1=="b" and aa2=="t":
 *         return -1
 *     if aa1=="b" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="b" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1213
 *         return -1
 *     if aa1=="b" and aa2=="w":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="y":
 *         return -3
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L500;
  }
  __pyx_L500:;

  /* "obitools/align/_codonnws.pyx":1214
 *     if aa1=="b" and aa2=="w":
 *         return -4
 *     if aa1=="b" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1215
 *         return -4
 *     if aa1=="b" and aa2=="y":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="v":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L501;
  }
  __pyx_L501:;

  /* "obitools/align/_codonnws.pyx":1216
 *     if aa1=="b" and aa2=="y":
 *         return -3
 *     if aa1=="b" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="b" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1217
 *         return -3
 *     if aa1=="b" and aa2=="v":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="b":
 *         return 4
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L502;
  }
  __pyx_L502:;

  /* "obitools/align/_codonnws.pyx":1218
 *     if aa1=="b" and aa2=="v":
 *         return -3
 *     if aa1=="b" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="b" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1219
 *         return -3
 *     if aa1=="b" and aa2=="b":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="z":
 *         return 1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L503;
  }
  __pyx_L503:;

  /* "obitools/align/_codonnws.pyx":1220
 *     if aa1=="b" and aa2=="b":
 *         return 4
 *     if aa1=="b" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="b" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1221
 *         return 4
 *     if aa1=="b" and aa2=="z":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="x":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L504;
  }
  __pyx_L504:;

  /* "obitools/align/_codonnws.pyx":1222
 *     if aa1=="b" and aa2=="z":
 *         return 1
 *     if aa1=="b" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="b" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1223
 *         return 1
 *     if aa1=="b" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="b" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L505;
  }
  __pyx_L505:;

  /* "obitools/align/_codonnws.pyx":1224
 *     if aa1=="b" and aa2=="x":
 *         return -1
 *     if aa1=="b" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="z" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'b');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1225
 *         return -1
 *     if aa1=="b" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="a":
 *         return -1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L506;
  }
  __pyx_L506:;

  /* "obitools/align/_codonnws.pyx":1226
 *     if aa1=="b" and aa2=="*":
 *         return -4
 *     if aa1=="z" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="z" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1227
 *         return -4
 *     if aa1=="z" and aa2=="a":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="r":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L507;
  }
  __pyx_L507:;

  /* "obitools/align/_codonnws.pyx":1228
 *     if aa1=="z" and aa2=="a":
 *         return -1
 *     if aa1=="z" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="z" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1229
 *         return -1
 *     if aa1=="z" and aa2=="r":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="n":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L508;
  }
  __pyx_L508:;

  /* "obitools/align/_codonnws.pyx":1230
 *     if aa1=="z" and aa2=="r":
 *         return 0
 *     if aa1=="z" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="z" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1231
 *         return 0
 *     if aa1=="z" and aa2=="n":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="d":
 *         return 1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L509;
  }
  __pyx_L509:;

  /* "obitools/align/_codonnws.pyx":1232
 *     if aa1=="z" and aa2=="n":
 *         return 0
 *     if aa1=="z" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="z" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1233
 *         return 0
 *     if aa1=="z" and aa2=="d":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="c":
 *         return -3
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L510;
  }
  __pyx_L510:;

  /* "obitools/align/_codonnws.pyx":1234
 *     if aa1=="z" and aa2=="d":
 *         return 1
 *     if aa1=="z" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="z" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1235
 *         return 1
 *     if aa1=="z" and aa2=="c":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="q":
 *         return 3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L511;
  }
  __pyx_L511:;

  /* "obitools/align/_codonnws.pyx":1236
 *     if aa1=="z" and aa2=="c":
 *         return -3
 *     if aa1=="z" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return 3
 *     if aa1=="z" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1237
 *         return -3
 *     if aa1=="z" and aa2=="q":
 *         return 3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="e":
 *         return 4
 */
    __pyx_r = 3.0;
    goto __pyx_L0;
    goto __pyx_L512;
  }
  __pyx_L512:;

  /* "obitools/align/_codonnws.pyx":1238
 *     if aa1=="z" and aa2=="q":
 *         return 3
 *     if aa1=="z" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="z" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1239
 *         return 3
 *     if aa1=="z" and aa2=="e":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="g":
 *         return -2
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L513;
  }
  __pyx_L513:;

  /* "obitools/align/_codonnws.pyx":1240
 *     if aa1=="z" and aa2=="e":
 *         return 4
 *     if aa1=="z" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="z" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1241
 *         return 4
 *     if aa1=="z" and aa2=="g":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="h":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L514;
  }
  __pyx_L514:;

  /* "obitools/align/_codonnws.pyx":1242
 *     if aa1=="z" and aa2=="g":
 *         return -2
 *     if aa1=="z" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="z" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1243
 *         return -2
 *     if aa1=="z" and aa2=="h":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="i":
 *         return -3
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L515;
  }
  __pyx_L515:;

  /* "obitools/align/_codonnws.pyx":1244
 *     if aa1=="z" and aa2=="h":
 *         return 0
 *     if aa1=="z" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="z" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1245
 *         return 0
 *     if aa1=="z" and aa2=="i":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="l":
 *         return -3
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L516;
  }
  __pyx_L516:;

  /* "obitools/align/_codonnws.pyx":1246
 *     if aa1=="z" and aa2=="i":
 *         return -3
 *     if aa1=="z" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="z" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1247
 *         return -3
 *     if aa1=="z" and aa2=="l":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="k":
 *         return 1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L517;
  }
  __pyx_L517:;

  /* "obitools/align/_codonnws.pyx":1248
 *     if aa1=="z" and aa2=="l":
 *         return -3
 *     if aa1=="z" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="z" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1249
 *         return -3
 *     if aa1=="z" and aa2=="k":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="m":
 *         return -1
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L518;
  }
  __pyx_L518:;

  /* "obitools/align/_codonnws.pyx":1250
 *     if aa1=="z" and aa2=="k":
 *         return 1
 *     if aa1=="z" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="z" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1251
 *         return 1
 *     if aa1=="z" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="f":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L519;
  }
  __pyx_L519:;

  /* "obitools/align/_codonnws.pyx":1252
 *     if aa1=="z" and aa2=="m":
 *         return -1
 *     if aa1=="z" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="z" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1253
 *         return -1
 *     if aa1=="z" and aa2=="f":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="p":
 *         return -1
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L520;
  }
  __pyx_L520:;

  /* "obitools/align/_codonnws.pyx":1254
 *     if aa1=="z" and aa2=="f":
 *         return -3
 *     if aa1=="z" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="z" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1255
 *         return -3
 *     if aa1=="z" and aa2=="p":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="s":
 *         return 0
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L521;
  }
  __pyx_L521:;

  /* "obitools/align/_codonnws.pyx":1256
 *     if aa1=="z" and aa2=="p":
 *         return -1
 *     if aa1=="z" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="z" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1257
 *         return -1
 *     if aa1=="z" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="t":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L522;
  }
  __pyx_L522:;

  /* "obitools/align/_codonnws.pyx":1258
 *     if aa1=="z" and aa2=="s":
 *         return 0
 *     if aa1=="z" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="z" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1259
 *         return 0
 *     if aa1=="z" and aa2=="t":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="w":
 *         return -3
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L523;
  }
  __pyx_L523:;

  /* "obitools/align/_codonnws.pyx":1260
 *     if aa1=="z" and aa2=="t":
 *         return -1
 *     if aa1=="z" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -3
 *     if aa1=="z" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1261
 *         return -1
 *     if aa1=="z" and aa2=="w":
 *         return -3             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="y":
 *         return -2
 */
    __pyx_r = -3.0;
    goto __pyx_L0;
    goto __pyx_L524;
  }
  __pyx_L524:;

  /* "obitools/align/_codonnws.pyx":1262
 *     if aa1=="z" and aa2=="w":
 *         return -3
 *     if aa1=="z" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="z" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1263
 *         return -3
 *     if aa1=="z" and aa2=="y":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="v":
 *         return -2
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L525;
  }
  __pyx_L525:;

  /* "obitools/align/_codonnws.pyx":1264
 *     if aa1=="z" and aa2=="y":
 *         return -2
 *     if aa1=="z" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="z" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1265
 *         return -2
 *     if aa1=="z" and aa2=="v":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="b":
 *         return 1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L526;
  }
  __pyx_L526:;

  /* "obitools/align/_codonnws.pyx":1266
 *     if aa1=="z" and aa2=="v":
 *         return -2
 *     if aa1=="z" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return 1
 *     if aa1=="z" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1267
 *         return -2
 *     if aa1=="z" and aa2=="b":
 *         return 1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="z":
 *         return 4
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L527;
  }
  __pyx_L527:;

  /* "obitools/align/_codonnws.pyx":1268
 *     if aa1=="z" and aa2=="b":
 *         return 1
 *     if aa1=="z" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return 4
 *     if aa1=="z" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1269
 *         return 1
 *     if aa1=="z" and aa2=="z":
 *         return 4             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="x":
 *         return -1
 */
    __pyx_r = 4.0;
    goto __pyx_L0;
    goto __pyx_L528;
  }
  __pyx_L528:;

  /* "obitools/align/_codonnws.pyx":1270
 *     if aa1=="z" and aa2=="z":
 *         return 4
 *     if aa1=="z" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="z" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1271
 *         return 4
 *     if aa1=="z" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="z" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L529;
  }
  __pyx_L529:;

  /* "obitools/align/_codonnws.pyx":1272
 *     if aa1=="z" and aa2=="x":
 *         return -1
 *     if aa1=="z" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="x" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'z');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1273
 *         return -1
 *     if aa1=="z" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="a":
 *         return 0
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L530;
  }
  __pyx_L530:;

  /* "obitools/align/_codonnws.pyx":1274
 *     if aa1=="z" and aa2=="*":
 *         return -4
 *     if aa1=="x" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="x" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1275
 *         return -4
 *     if aa1=="x" and aa2=="a":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="r":
 *         return -1
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L531;
  }
  __pyx_L531:;

  /* "obitools/align/_codonnws.pyx":1276
 *     if aa1=="x" and aa2=="a":
 *         return 0
 *     if aa1=="x" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1277
 *         return 0
 *     if aa1=="x" and aa2=="r":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="n":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L532;
  }
  __pyx_L532:;

  /* "obitools/align/_codonnws.pyx":1278
 *     if aa1=="x" and aa2=="r":
 *         return -1
 *     if aa1=="x" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1279
 *         return -1
 *     if aa1=="x" and aa2=="n":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="d":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L533;
  }
  __pyx_L533:;

  /* "obitools/align/_codonnws.pyx":1280
 *     if aa1=="x" and aa2=="n":
 *         return -1
 *     if aa1=="x" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1281
 *         return -1
 *     if aa1=="x" and aa2=="d":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="c":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L534;
  }
  __pyx_L534:;

  /* "obitools/align/_codonnws.pyx":1282
 *     if aa1=="x" and aa2=="d":
 *         return -1
 *     if aa1=="x" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="x" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1283
 *         return -1
 *     if aa1=="x" and aa2=="c":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="q":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L535;
  }
  __pyx_L535:;

  /* "obitools/align/_codonnws.pyx":1284
 *     if aa1=="x" and aa2=="c":
 *         return -2
 *     if aa1=="x" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1285
 *         return -2
 *     if aa1=="x" and aa2=="q":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="e":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L536;
  }
  __pyx_L536:;

  /* "obitools/align/_codonnws.pyx":1286
 *     if aa1=="x" and aa2=="q":
 *         return -1
 *     if aa1=="x" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1287
 *         return -1
 *     if aa1=="x" and aa2=="e":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="g":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L537;
  }
  __pyx_L537:;

  /* "obitools/align/_codonnws.pyx":1288
 *     if aa1=="x" and aa2=="e":
 *         return -1
 *     if aa1=="x" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1289
 *         return -1
 *     if aa1=="x" and aa2=="g":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="h":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L538;
  }
  __pyx_L538:;

  /* "obitools/align/_codonnws.pyx":1290
 *     if aa1=="x" and aa2=="g":
 *         return -1
 *     if aa1=="x" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1291
 *         return -1
 *     if aa1=="x" and aa2=="h":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="i":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L539;
  }
  __pyx_L539:;

  /* "obitools/align/_codonnws.pyx":1292
 *     if aa1=="x" and aa2=="h":
 *         return -1
 *     if aa1=="x" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1293
 *         return -1
 *     if aa1=="x" and aa2=="i":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="l":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L540;
  }
  __pyx_L540:;

  /* "obitools/align/_codonnws.pyx":1294
 *     if aa1=="x" and aa2=="i":
 *         return -1
 *     if aa1=="x" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1295
 *         return -1
 *     if aa1=="x" and aa2=="l":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="k":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L541;
  }
  __pyx_L541:;

  /* "obitools/align/_codonnws.pyx":1296
 *     if aa1=="x" and aa2=="l":
 *         return -1
 *     if aa1=="x" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1297
 *         return -1
 *     if aa1=="x" and aa2=="k":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="m":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L542;
  }
  __pyx_L542:;

  /* "obitools/align/_codonnws.pyx":1298
 *     if aa1=="x" and aa2=="k":
 *         return -1
 *     if aa1=="x" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1299
 *         return -1
 *     if aa1=="x" and aa2=="m":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="f":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L543;
  }
  __pyx_L543:;

  /* "obitools/align/_codonnws.pyx":1300
 *     if aa1=="x" and aa2=="m":
 *         return -1
 *     if aa1=="x" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1301
 *         return -1
 *     if aa1=="x" and aa2=="f":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="p":
 *         return -2
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L544;
  }
  __pyx_L544:;

  /* "obitools/align/_codonnws.pyx":1302
 *     if aa1=="x" and aa2=="f":
 *         return -1
 *     if aa1=="x" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="x" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1303
 *         return -1
 *     if aa1=="x" and aa2=="p":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="s":
 *         return 0
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L545;
  }
  __pyx_L545:;

  /* "obitools/align/_codonnws.pyx":1304
 *     if aa1=="x" and aa2=="p":
 *         return -2
 *     if aa1=="x" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="x" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1305
 *         return -2
 *     if aa1=="x" and aa2=="s":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="t":
 *         return 0
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L546;
  }
  __pyx_L546:;

  /* "obitools/align/_codonnws.pyx":1306
 *     if aa1=="x" and aa2=="s":
 *         return 0
 *     if aa1=="x" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return 0
 *     if aa1=="x" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1307
 *         return 0
 *     if aa1=="x" and aa2=="t":
 *         return 0             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="w":
 *         return -2
 */
    __pyx_r = 0.0;
    goto __pyx_L0;
    goto __pyx_L547;
  }
  __pyx_L547:;

  /* "obitools/align/_codonnws.pyx":1308
 *     if aa1=="x" and aa2=="t":
 *         return 0
 *     if aa1=="x" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -2
 *     if aa1=="x" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1309
 *         return 0
 *     if aa1=="x" and aa2=="w":
 *         return -2             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="y":
 *         return -1
 */
    __pyx_r = -2.0;
    goto __pyx_L0;
    goto __pyx_L548;
  }
  __pyx_L548:;

  /* "obitools/align/_codonnws.pyx":1310
 *     if aa1=="x" and aa2=="w":
 *         return -2
 *     if aa1=="x" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1311
 *         return -2
 *     if aa1=="x" and aa2=="y":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="v":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L549;
  }
  __pyx_L549:;

  /* "obitools/align/_codonnws.pyx":1312
 *     if aa1=="x" and aa2=="y":
 *         return -1
 *     if aa1=="x" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1313
 *         return -1
 *     if aa1=="x" and aa2=="v":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="b":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L550;
  }
  __pyx_L550:;

  /* "obitools/align/_codonnws.pyx":1314
 *     if aa1=="x" and aa2=="v":
 *         return -1
 *     if aa1=="x" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1315
 *         return -1
 *     if aa1=="x" and aa2=="b":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="z":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L551;
  }
  __pyx_L551:;

  /* "obitools/align/_codonnws.pyx":1316
 *     if aa1=="x" and aa2=="b":
 *         return -1
 *     if aa1=="x" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1317
 *         return -1
 *     if aa1=="x" and aa2=="z":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="x":
 *         return -1
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L552;
  }
  __pyx_L552:;

  /* "obitools/align/_codonnws.pyx":1318
 *     if aa1=="x" and aa2=="z":
 *         return -1
 *     if aa1=="x" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -1
 *     if aa1=="x" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1319
 *         return -1
 *     if aa1=="x" and aa2=="x":
 *         return -1             # <<<<<<<<<<<<<<
 *     if aa1=="x" and aa2=="*":
 *         return -4
 */
    __pyx_r = -1.0;
    goto __pyx_L0;
    goto __pyx_L553;
  }
  __pyx_L553:;

  /* "obitools/align/_codonnws.pyx":1320
 *     if aa1=="x" and aa2=="x":
 *         return -1
 *     if aa1=="x" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="a":
 */
  __pyx_t_2 = (__pyx_v_aa1 == 'x');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1321
 *         return -1
 *     if aa1=="x" and aa2=="*":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="a":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L554;
  }
  __pyx_L554:;

  /* "obitools/align/_codonnws.pyx":1322
 *     if aa1=="x" and aa2=="*":
 *         return -4
 *     if aa1=="*" and aa2=="a":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="r":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'a');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1323
 *         return -4
 *     if aa1=="*" and aa2=="a":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="r":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L555;
  }
  __pyx_L555:;

  /* "obitools/align/_codonnws.pyx":1324
 *     if aa1=="*" and aa2=="a":
 *         return -4
 *     if aa1=="*" and aa2=="r":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="n":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'r');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1325
 *         return -4
 *     if aa1=="*" and aa2=="r":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="n":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L556;
  }
  __pyx_L556:;

  /* "obitools/align/_codonnws.pyx":1326
 *     if aa1=="*" and aa2=="r":
 *         return -4
 *     if aa1=="*" and aa2=="n":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="d":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'n');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1327
 *         return -4
 *     if aa1=="*" and aa2=="n":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="d":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L557;
  }
  __pyx_L557:;

  /* "obitools/align/_codonnws.pyx":1328
 *     if aa1=="*" and aa2=="n":
 *         return -4
 *     if aa1=="*" and aa2=="d":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="c":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'd');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1329
 *         return -4
 *     if aa1=="*" and aa2=="d":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="c":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L558;
  }
  __pyx_L558:;

  /* "obitools/align/_codonnws.pyx":1330
 *     if aa1=="*" and aa2=="d":
 *         return -4
 *     if aa1=="*" and aa2=="c":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="q":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'c');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1331
 *         return -4
 *     if aa1=="*" and aa2=="c":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="q":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L559;
  }
  __pyx_L559:;

  /* "obitools/align/_codonnws.pyx":1332
 *     if aa1=="*" and aa2=="c":
 *         return -4
 *     if aa1=="*" and aa2=="q":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="e":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'q');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1333
 *         return -4
 *     if aa1=="*" and aa2=="q":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="e":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L560;
  }
  __pyx_L560:;

  /* "obitools/align/_codonnws.pyx":1334
 *     if aa1=="*" and aa2=="q":
 *         return -4
 *     if aa1=="*" and aa2=="e":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="g":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'e');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1335
 *         return -4
 *     if aa1=="*" and aa2=="e":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="g":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L561;
  }
  __pyx_L561:;

  /* "obitools/align/_codonnws.pyx":1336
 *     if aa1=="*" and aa2=="e":
 *         return -4
 *     if aa1=="*" and aa2=="g":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="h":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'g');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1337
 *         return -4
 *     if aa1=="*" and aa2=="g":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="h":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L562;
  }
  __pyx_L562:;

  /* "obitools/align/_codonnws.pyx":1338
 *     if aa1=="*" and aa2=="g":
 *         return -4
 *     if aa1=="*" and aa2=="h":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="i":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'h');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1339
 *         return -4
 *     if aa1=="*" and aa2=="h":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="i":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L563;
  }
  __pyx_L563:;

  /* "obitools/align/_codonnws.pyx":1340
 *     if aa1=="*" and aa2=="h":
 *         return -4
 *     if aa1=="*" and aa2=="i":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="l":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'i');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1341
 *         return -4
 *     if aa1=="*" and aa2=="i":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="l":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L564;
  }
  __pyx_L564:;

  /* "obitools/align/_codonnws.pyx":1342
 *     if aa1=="*" and aa2=="i":
 *         return -4
 *     if aa1=="*" and aa2=="l":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="k":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'l');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1343
 *         return -4
 *     if aa1=="*" and aa2=="l":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="k":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L565;
  }
  __pyx_L565:;

  /* "obitools/align/_codonnws.pyx":1344
 *     if aa1=="*" and aa2=="l":
 *         return -4
 *     if aa1=="*" and aa2=="k":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="m":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'k');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1345
 *         return -4
 *     if aa1=="*" and aa2=="k":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="m":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L566;
  }
  __pyx_L566:;

  /* "obitools/align/_codonnws.pyx":1346
 *     if aa1=="*" and aa2=="k":
 *         return -4
 *     if aa1=="*" and aa2=="m":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="f":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'm');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1347
 *         return -4
 *     if aa1=="*" and aa2=="m":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="f":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L567;
  }
  __pyx_L567:;

  /* "obitools/align/_codonnws.pyx":1348
 *     if aa1=="*" and aa2=="m":
 *         return -4
 *     if aa1=="*" and aa2=="f":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="p":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'f');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1349
 *         return -4
 *     if aa1=="*" and aa2=="f":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="p":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L568;
  }
  __pyx_L568:;

  /* "obitools/align/_codonnws.pyx":1350
 *     if aa1=="*" and aa2=="f":
 *         return -4
 *     if aa1=="*" and aa2=="p":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="s":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'p');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1351
 *         return -4
 *     if aa1=="*" and aa2=="p":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="s":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L569;
  }
  __pyx_L569:;

  /* "obitools/align/_codonnws.pyx":1352
 *     if aa1=="*" and aa2=="p":
 *         return -4
 *     if aa1=="*" and aa2=="s":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="t":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 's');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1353
 *         return -4
 *     if aa1=="*" and aa2=="s":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="t":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L570;
  }
  __pyx_L570:;

  /* "obitools/align/_codonnws.pyx":1354
 *     if aa1=="*" and aa2=="s":
 *         return -4
 *     if aa1=="*" and aa2=="t":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="w":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 't');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1355
 *         return -4
 *     if aa1=="*" and aa2=="t":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="w":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L571;
  }
  __pyx_L571:;

  /* "obitools/align/_codonnws.pyx":1356
 *     if aa1=="*" and aa2=="t":
 *         return -4
 *     if aa1=="*" and aa2=="w":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="y":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'w');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1357
 *         return -4
 *     if aa1=="*" and aa2=="w":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="y":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L572;
  }
  __pyx_L572:;

  /* "obitools/align/_codonnws.pyx":1358
 *     if aa1=="*" and aa2=="w":
 *         return -4
 *     if aa1=="*" and aa2=="y":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="v":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'y');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1359
 *         return -4
 *     if aa1=="*" and aa2=="y":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="v":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L573;
  }
  __pyx_L573:;

  /* "obitools/align/_codonnws.pyx":1360
 *     if aa1=="*" and aa2=="y":
 *         return -4
 *     if aa1=="*" and aa2=="v":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="b":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'v');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1361
 *         return -4
 *     if aa1=="*" and aa2=="v":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="b":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L574;
  }
  __pyx_L574:;

  /* "obitools/align/_codonnws.pyx":1362
 *     if aa1=="*" and aa2=="v":
 *         return -4
 *     if aa1=="*" and aa2=="b":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="z":
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == 'b');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1363
 *         return -4
 *     if aa1=="*" and aa2=="b":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="z":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L575;
  }
  __pyx_L575:;

  /* "obitools/align/_codonnws.pyx":1364
 *     if aa1=="*" and aa2=="b":
 *         return -4
 *     if aa1=="*" and aa2=="z":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="x":
 */
  __pyx_t_1 = (__pyx_v_aa1 == '*');
  if (__pyx_t_1) {
    __pyx_t_2 = (__pyx_v_aa2 == 'z');
    __pyx_t_3 = __pyx_t_2;
  } else {
    __pyx_t_3 = __pyx_t_1;
  }
  if (__pyx_t_3) {

    /* "obitools/align/_codonnws.pyx":1365
 *         return -4
 *     if aa1=="*" and aa2=="z":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="x":
 *         return -4
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L576;
  }
  __pyx_L576:;

  /* "obitools/align/_codonnws.pyx":1366
 *     if aa1=="*" and aa2=="z":
 *         return -4
 *     if aa1=="*" and aa2=="x":             # <<<<<<<<<<<<<<
 *         return -4
 *     if aa1=="*" and aa2=="*":
 */
  __pyx_t_3 = (__pyx_v_aa1 == '*');
  if (__pyx_t_3) {
    __pyx_t_1 = (__pyx_v_aa2 == 'x');
    __pyx_t_2 = __pyx_t_1;
  } else {
    __pyx_t_2 = __pyx_t_3;
  }
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1367
 *         return -4
 *     if aa1=="*" and aa2=="x":
 *         return -4             # <<<<<<<<<<<<<<
 *     if aa1=="*" and aa2=="*":
 *         return 1
 */
    __pyx_r = -4.0;
    goto __pyx_L0;
    goto __pyx_L577;
  }
  __pyx_L577:;

  /* "obitools/align/_codonnws.pyx":1368
 *     if aa1=="*" and aa2=="x":
 *         return -4
 *     if aa1=="*" and aa2=="*":             # <<<<<<<<<<<<<<
 *         return 1
 * 
 */
  __pyx_t_2 = (__pyx_v_aa1 == '*');
  if (__pyx_t_2) {
    __pyx_t_3 = (__pyx_v_aa2 == '*');
    __pyx_t_1 = __pyx_t_3;
  } else {
    __pyx_t_1 = __pyx_t_2;
  }
  if (__pyx_t_1) {

    /* "obitools/align/_codonnws.pyx":1369
 *         return -4
 *     if aa1=="*" and aa2=="*":
 *         return 1             # <<<<<<<<<<<<<<
 * 
 * 
 */
    __pyx_r = 1.0;
    goto __pyx_L0;
    goto __pyx_L578;
  }
  __pyx_L578:;

  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_match = 0;
  PyObject *__pyx_v_mismatch = 0;
  PyObject *__pyx_v_opengap = 0;
  PyObject *__pyx_v_extgap = 0;
  PyObject *__pyx_v_phasedA = 0;
  PyObject *__pyx_v_phasedB = 0;
  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__match,&__pyx_n_s__mismatch,&__pyx_n_s__opengap,&__pyx_n_s__extgap,&__pyx_n_s__phasedA,&__pyx_n_s__phasedB,0};
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
  {
    PyObject* values[6] = {0,0,0,0,0,0};
    values[0] = ((PyObject *)__pyx_int_2);
    values[1] = ((PyObject *)__pyx_int_neg_3);
    values[2] = ((PyObject *)__pyx_int_neg_4);
    values[3] = ((PyObject *)__pyx_int_neg_1);
    values[4] = ((PyObject *)__pyx_int_neg_1);
    values[5] = ((PyObject *)__pyx_int_neg_1);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        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:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__match);
          if (value) { values[0] = value; kw_args--; }
        }
        case  1:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__mismatch);
          if (value) { values[1] = value; kw_args--; }
        }
        case  2:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__opengap);
          if (value) { values[2] = value; kw_args--; }
        }
        case  3:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__extgap);
          if (value) { values[3] = value; kw_args--; }
        }
        case  4:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__phasedA);
          if (value) { values[4] = value; kw_args--; }
        }
        case  5:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__phasedB);
          if (value) { values[5] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1374; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        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;
      }
    }
    __pyx_v_match = values[0];
    __pyx_v_mismatch = values[1];
    __pyx_v_opengap = values[2];
    __pyx_v_extgap = values[3];
    __pyx_v_phasedA = values[4];
    __pyx_v_phasedB = values[5];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1374; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS___init__(((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self), __pyx_v_match, __pyx_v_mismatch, __pyx_v_opengap, __pyx_v_extgap, __pyx_v_phasedA, __pyx_v_phasedB);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1374
 * cdef class CodonNWS(NWS):
 * 
 *     def __init__(self,match=2,mismatch=-3,opengap=-4,extgap=-1, phasedA = -1, phasedB = -1):#, AAmatrix=_blosum62, translationtable=None):             # <<<<<<<<<<<<<<
 *         NWS.__init__(self,match, mismatch, opengap, extgap)
 *         self._phasedA = -1 if phasedA == -1 else phasedA%3
 */

static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS___init__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_match, PyObject *__pyx_v_mismatch, PyObject *__pyx_v_opengap, PyObject *__pyx_v_extgap, PyObject *__pyx_v_phasedA, PyObject *__pyx_v_phasedB) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__init__", 0);

  /* "obitools/align/_codonnws.pyx":1375
 * 
 *     def __init__(self,match=2,mismatch=-3,opengap=-4,extgap=-1, phasedA = -1, phasedB = -1):#, AAmatrix=_blosum62, translationtable=None):
 *         NWS.__init__(self,match, mismatch, opengap, extgap)             # <<<<<<<<<<<<<<
 *         self._phasedA = -1 if phasedA == -1 else phasedA%3
 *         self._phasedB = -1 if phasedB == -1 else phasedB%3
 */
  __pyx_t_1 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_8obitools_5align_4_nws_NWS)), __pyx_n_s____init__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = PyTuple_New(5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_INCREF(((PyObject *)__pyx_v_self));
  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
  __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
  __Pyx_INCREF(__pyx_v_match);
  PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_match);
  __Pyx_GIVEREF(__pyx_v_match);
  __Pyx_INCREF(__pyx_v_mismatch);
  PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_mismatch);
  __Pyx_GIVEREF(__pyx_v_mismatch);
  __Pyx_INCREF(__pyx_v_opengap);
  PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_opengap);
  __Pyx_GIVEREF(__pyx_v_opengap);
  __Pyx_INCREF(__pyx_v_extgap);
  PyTuple_SET_ITEM(__pyx_t_2, 4, __pyx_v_extgap);
  __Pyx_GIVEREF(__pyx_v_extgap);
  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

  /* "obitools/align/_codonnws.pyx":1376
 *     def __init__(self,match=2,mismatch=-3,opengap=-4,extgap=-1, phasedA = -1, phasedB = -1):#, AAmatrix=_blosum62, translationtable=None):
 *         NWS.__init__(self,match, mismatch, opengap, extgap)
 *         self._phasedA = -1 if phasedA == -1 else phasedA%3             # <<<<<<<<<<<<<<
 *         self._phasedB = -1 if phasedB == -1 else phasedB%3
 * 
 */
  __pyx_t_2 = PyObject_RichCompare(__pyx_v_phasedA, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (__pyx_t_4) {
    __Pyx_INCREF(__pyx_int_neg_1);
    __pyx_t_3 = __pyx_int_neg_1;
  } else {
    __pyx_t_2 = PyNumber_Remainder(__pyx_v_phasedA, __pyx_int_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = __pyx_t_2;
    __pyx_t_2 = 0;
  }
  __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_v_self->_phasedA = __pyx_t_5;

  /* "obitools/align/_codonnws.pyx":1377
 *         NWS.__init__(self,match, mismatch, opengap, extgap)
 *         self._phasedA = -1 if phasedA == -1 else phasedA%3
 *         self._phasedB = -1 if phasedB == -1 else phasedB%3             # <<<<<<<<<<<<<<
 * 
 *     cdef double matchCodon(self, int h, int v):
 */
  __pyx_t_2 = PyObject_RichCompare(__pyx_v_phasedB, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (__pyx_t_4) {
    __Pyx_INCREF(__pyx_int_neg_1);
    __pyx_t_3 = __pyx_int_neg_1;
  } else {
    __pyx_t_2 = PyNumber_Remainder(__pyx_v_phasedB, __pyx_int_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = __pyx_t_2;
    __pyx_t_2 = 0;
  }
  __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_v_self->_phasedB = __pyx_t_5;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1379
 *         self._phasedB = -1 if phasedB == -1 else phasedB%3
 * 
 *     cdef double matchCodon(self, int h, int v):             # <<<<<<<<<<<<<<
 *         cdef double score
 *         cdef double match
 */

static double __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_matchCodon(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, int __pyx_v_h, int __pyx_v_v) {
  double __pyx_v_score;
  double __pyx_v_match;
  PyObject *__pyx_v_i = NULL;
  double __pyx_v_bl;
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  PyObject *(*__pyx_t_4)(PyObject *);
  PyObject *__pyx_t_5 = NULL;
  Py_ssize_t __pyx_t_6;
  Py_ssize_t __pyx_t_7;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("matchCodon", 0);

  /* "obitools/align/_codonnws.pyx":1382
 *         cdef double score
 *         cdef double match
 *         score = 0             # <<<<<<<<<<<<<<
 * 
 *         for i in range(3):
 */
  __pyx_v_score = 0.0;

  /* "obitools/align/_codonnws.pyx":1384
 *         score = 0
 * 
 *         for i in range(3):             # <<<<<<<<<<<<<<
 *             match = iupacPartialMatch(self.hSeq.sequence[h-i-1],self.vSeq.sequence[v-i-1])
 *             score += match * self._match + (1-match) * self._mismatch
 */
  __pyx_t_1 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_k_tuple_1), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
    __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
  } else {
    __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  for (;;) {
    if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
      if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
      __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
    } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
      if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
      __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
    } else {
      __pyx_t_1 = __pyx_t_4(__pyx_t_2);
      if (unlikely(!__pyx_t_1)) {
        if (PyErr_Occurred()) {
          if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_1);
    }
    __Pyx_XDECREF(__pyx_v_i);
    __pyx_v_i = __pyx_t_1;
    __pyx_t_1 = 0;

    /* "obitools/align/_codonnws.pyx":1385
 * 
 *         for i in range(3):
 *             match = iupacPartialMatch(self.hSeq.sequence[h-i-1],self.vSeq.sequence[v-i-1])             # <<<<<<<<<<<<<<
 *             score += match * self._match + (1-match) * self._mismatch
 *         bl = _blosum62(self.hSeq.sequence[h-1], self.hSeq.sequence[h-2], self.hSeq.sequence[h-3], self.vSeq.sequence[v-1], self.vSeq.sequence[v-2], self.vSeq.sequence[v-3])
 */
    __pyx_t_1 = PyInt_FromLong(__pyx_v_h); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_v_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = PyNumber_Subtract(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_6 = __Pyx_PyIndex_AsSsize_t(__pyx_t_1); if (unlikely((__pyx_t_6 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = PyInt_FromLong(__pyx_v_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_v_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = PyNumber_Subtract(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_7 = __Pyx_PyIndex_AsSsize_t(__pyx_t_1); if (unlikely((__pyx_t_7 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_v_match = __pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch((__pyx_v_self->__pyx_base.__pyx_base.hSeq->sequence[__pyx_t_6]), (__pyx_v_self->__pyx_base.__pyx_base.vSeq->sequence[__pyx_t_7]), 0);

    /* "obitools/align/_codonnws.pyx":1386
 *         for i in range(3):
 *             match = iupacPartialMatch(self.hSeq.sequence[h-i-1],self.vSeq.sequence[v-i-1])
 *             score += match * self._match + (1-match) * self._mismatch             # <<<<<<<<<<<<<<
 *         bl = _blosum62(self.hSeq.sequence[h-1], self.hSeq.sequence[h-2], self.hSeq.sequence[h-3], self.vSeq.sequence[v-1], self.vSeq.sequence[v-2], self.vSeq.sequence[v-3])
 *         #print "MatchCodon","h=",h,"v=",v, "   ",\
 */
    __pyx_v_score = (__pyx_v_score + ((__pyx_v_match * __pyx_v_self->__pyx_base._match) + ((1.0 - __pyx_v_match) * __pyx_v_self->__pyx_base._mismatch)));
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "obitools/align/_codonnws.pyx":1387
 *             match = iupacPartialMatch(self.hSeq.sequence[h-i-1],self.vSeq.sequence[v-i-1])
 *             score += match * self._match + (1-match) * self._mismatch
 *         bl = _blosum62(self.hSeq.sequence[h-1], self.hSeq.sequence[h-2], self.hSeq.sequence[h-3], self.vSeq.sequence[v-1], self.vSeq.sequence[v-2], self.vSeq.sequence[v-3])             # <<<<<<<<<<<<<<
 *         #print "MatchCodon","h=",h,"v=",v, "   ",\
 *         #                   ''.join(['%c'%(self.hSeq.sequence[h-3],),\
 */
  __pyx_v_bl = __pyx_f_8obitools_5align_9_codonnws__blosum62((__pyx_v_self->__pyx_base.__pyx_base.hSeq->sequence[(__pyx_v_h - 1)]), (__pyx_v_self->__pyx_base.__pyx_base.hSeq->sequence[(__pyx_v_h - 2)]), (__pyx_v_self->__pyx_base.__pyx_base.hSeq->sequence[(__pyx_v_h - 3)]), (__pyx_v_self->__pyx_base.__pyx_base.vSeq->sequence[(__pyx_v_v - 1)]), (__pyx_v_self->__pyx_base.__pyx_base.vSeq->sequence[(__pyx_v_v - 2)]), (__pyx_v_self->__pyx_base.__pyx_base.vSeq->sequence[(__pyx_v_v - 3)]));

  /* "obitools/align/_codonnws.pyx":1398
 *         #print '--> score = %d + %d'%(score,bl)
 * 
 *         score += bl             # <<<<<<<<<<<<<<
 *         return score
 * 
 */
  __pyx_v_score = (__pyx_v_score + __pyx_v_bl);

  /* "obitools/align/_codonnws.pyx":1399
 * 
 *         score += bl
 *         return score             # <<<<<<<<<<<<<<
 * 
 *     cdef inline int colindex(self, int idx):
 */
  __pyx_r = __pyx_v_score;
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_WriteUnraisable("obitools.align._codonnws.CodonNWS.matchCodon", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_i);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1401
 *         return score
 * 
 *     cdef inline int colindex(self, int idx):             # <<<<<<<<<<<<<<
 *         return idx%(self._hlen()+1)
 * 
 */

static CYTHON_INLINE int __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_colindex(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, int __pyx_v_idx) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  long __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("colindex", 0);

  /* "obitools/align/_codonnws.pyx":1402
 * 
 *     cdef inline int colindex(self, int idx):
 *         return idx%(self._hlen()+1)             # <<<<<<<<<<<<<<
 * 
 *     cdef inline int rowindex(self, int idx):
 */
  __pyx_t_1 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
  if (unlikely(__pyx_t_1 == 0)) {
    PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_r = __Pyx_mod_long(__pyx_v_idx, __pyx_t_1);
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("obitools.align._codonnws.CodonNWS.colindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1404
 *         return idx%(self._hlen()+1)
 * 
 *     cdef inline int rowindex(self, int idx):             # <<<<<<<<<<<<<<
 *         return idx/(self._hlen()+1)
 * 
 */

static CYTHON_INLINE int __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_rowindex(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, int __pyx_v_idx) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  long __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("rowindex", 0);

  /* "obitools/align/_codonnws.pyx":1405
 * 
 *     cdef inline int rowindex(self, int idx):
 *         return idx/(self._hlen()+1)             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_t_1 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
  if (unlikely(__pyx_t_1 == 0)) {
    PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  else if (sizeof(long) == sizeof(long) && unlikely(__pyx_t_1 == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_idx))) {
    PyErr_Format(PyExc_OverflowError, "value too large to perform division");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_r = __Pyx_div_long(__pyx_v_idx, __pyx_t_1);
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("obitools.align._codonnws.CodonNWS.rowindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1411
 *     #on met l'indice de la cellule d'origine
 * 
 *     cdef double doAlignment(self) except? 0:             # <<<<<<<<<<<<<<
 *         cdef int i  # vertical index
 *         cdef int j  # horizontal index
 */

static double __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_doAlignment(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self) {
  int __pyx_v_i;
  int __pyx_v_j;
  int __pyx_v_idx;
  int __pyx_v_jump;
  int __pyx_v_delta;
  double __pyx_v_score;
  double __pyx_v_scoremax;
  int __pyx_v_path;
  double __pyx_v_contrib;
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_t_2;
  int __pyx_t_3;
  long __pyx_t_4;
  long __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  int __pyx_t_8;
  int __pyx_t_9;
  int __pyx_t_10;
  int __pyx_t_11;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("doAlignment", 0);

  /* "obitools/align/_codonnws.pyx":1422
 * 
 * 
 *         if self.needToCompute:             # <<<<<<<<<<<<<<
 *             self.allocate()
 *             self.reset()
 */
  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__needToCompute); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (__pyx_t_2) {

    /* "obitools/align/_codonnws.pyx":1423
 * 
 *         if self.needToCompute:
 *             self.allocate()             # <<<<<<<<<<<<<<
 *             self.reset()
 * 
 */
    __pyx_t_3 = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.allocate(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

    /* "obitools/align/_codonnws.pyx":1424
 *         if self.needToCompute:
 *             self.allocate()
 *             self.reset()             # <<<<<<<<<<<<<<
 * 
 *             for j in range(1,self._hlen()+1):
 */
    ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.reset(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self));

    /* "obitools/align/_codonnws.pyx":1426
 *             self.reset()
 * 
 *             for j in range(1,self._hlen()+1):             # <<<<<<<<<<<<<<
 *                 idx = self.index(j,0)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
 */
    __pyx_t_4 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
    for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_4; __pyx_t_3+=1) {
      __pyx_v_j = __pyx_t_3;

      /* "obitools/align/_codonnws.pyx":1427
 * 
 *             for j in range(1,self._hlen()+1):
 *                 idx = self.index(j,0)             # <<<<<<<<<<<<<<
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
 *                 self.matrix.matrix[idx].path  = 0
 */
      __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, 0);

      /* "obitools/align/_codonnws.pyx":1428
 *             for j in range(1,self._hlen()+1):
 *                 idx = self.index(j,0)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))             # <<<<<<<<<<<<<<
 *                 self.matrix.matrix[idx].path  = 0
 * 
 */
      (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score = (__pyx_v_self->__pyx_base.__pyx_base._opengap + (__pyx_v_self->__pyx_base.__pyx_base._extgap * (__pyx_v_j - 1)));

      /* "obitools/align/_codonnws.pyx":1429
 *                 idx = self.index(j,0)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
 *                 self.matrix.matrix[idx].path  = 0             # <<<<<<<<<<<<<<
 * 
 *             for i in range(1,self._vlen()+1):
 */
      (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).path = 0;
    }

    /* "obitools/align/_codonnws.pyx":1431
 *                 self.matrix.matrix[idx].path  = 0
 * 
 *             for i in range(1,self._vlen()+1):             # <<<<<<<<<<<<<<
 *                 idx = self.index(0,i)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
 */
    __pyx_t_4 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._vlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
    for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_4; __pyx_t_3+=1) {
      __pyx_v_i = __pyx_t_3;

      /* "obitools/align/_codonnws.pyx":1432
 * 
 *             for i in range(1,self._vlen()+1):
 *                 idx = self.index(0,i)             # <<<<<<<<<<<<<<
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
 *                 self.matrix.matrix[idx].path  = 0
 */
      __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), 0, __pyx_v_i);

      /* "obitools/align/_codonnws.pyx":1433
 *             for i in range(1,self._vlen()+1):
 *                 idx = self.index(0,i)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))             # <<<<<<<<<<<<<<
 *                 self.matrix.matrix[idx].path  = 0
 * 
 */
      (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score = (__pyx_v_self->__pyx_base.__pyx_base._opengap + (__pyx_v_self->__pyx_base.__pyx_base._extgap * (__pyx_v_i - 1)));

      /* "obitools/align/_codonnws.pyx":1434
 *                 idx = self.index(0,i)
 *                 self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
 *                 self.matrix.matrix[idx].path  = 0             # <<<<<<<<<<<<<<
 * 
 *             for i in range(1,self._vlen()+1):
 */
      (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).path = 0;
    }

    /* "obitools/align/_codonnws.pyx":1436
 *                 self.matrix.matrix[idx].path  = 0
 * 
 *             for i in range(1,self._vlen()+1):             # <<<<<<<<<<<<<<
 *                 for j in range(1,self._hlen()+1):
 * 
 */
    __pyx_t_4 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._vlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
    for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_4; __pyx_t_3+=1) {
      __pyx_v_i = __pyx_t_3;

      /* "obitools/align/_codonnws.pyx":1437
 * 
 *             for i in range(1,self._vlen()+1):
 *                 for j in range(1,self._hlen()+1):             # <<<<<<<<<<<<<<
 * 
 *                     # 1 - came from diagonal
 */
      __pyx_t_5 = (((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)) + 1);
      for (__pyx_t_6 = 1; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
        __pyx_v_j = __pyx_t_6;

        /* "obitools/align/_codonnws.pyx":1440
 * 
 *                     # 1 - came from diagonal
 *                     idx = self.index(j-1,i-1)             # <<<<<<<<<<<<<<
 *                     # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
 *                     scoremax = self.matrix.matrix[idx].score + \
 */
        __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), (__pyx_v_i - 1));

        /* "obitools/align/_codonnws.pyx":1443
 *                     # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
 *                     scoremax = self.matrix.matrix[idx].score + \
 *                                self.matchScore(j,i)             # <<<<<<<<<<<<<<
 *                     path = idx
 * 
 */
        __pyx_v_scoremax = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.matchScore(((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self), __pyx_v_j, __pyx_v_i));

        /* "obitools/align/_codonnws.pyx":1444
 *                     scoremax = self.matrix.matrix[idx].score + \
 *                                self.matchScore(j,i)
 *                     path = idx             # <<<<<<<<<<<<<<
 * 
 *                     # print "so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),
 */
        __pyx_v_path = __pyx_v_idx;

        /* "obitools/align/_codonnws.pyx":1450
 *                     # 1.1 - came from diagonal by aligning a codon with a codon
 *                     #print i, i%3, self._phasedB, i%3==self._phasedB
 *                     if (j-3)>=0 and (i-3)>=0 and (self._phasedB==-1 or (i%3)==self._phasedB) and (self._phasedA==-1 or (j%3)==self._phasedA):             # <<<<<<<<<<<<<<
 *                         idx = self.index(j-3,i-3)
 *                         contrib = self.matchCodon(j,i)
 */
        __pyx_t_2 = ((__pyx_v_j - 3) >= 0);
        if (__pyx_t_2) {
          __pyx_t_7 = ((__pyx_v_i - 3) >= 0);
          if (__pyx_t_7) {
            __pyx_t_8 = (__pyx_v_self->_phasedB == -1);
            if (!__pyx_t_8) {
              __pyx_t_9 = (__Pyx_mod_long(__pyx_v_i, 3) == __pyx_v_self->_phasedB);
              __pyx_t_10 = __pyx_t_9;
            } else {
              __pyx_t_10 = __pyx_t_8;
            }
            if (__pyx_t_10) {
              __pyx_t_8 = (__pyx_v_self->_phasedA == -1);
              if (!__pyx_t_8) {
                __pyx_t_9 = (__Pyx_mod_long(__pyx_v_j, 3) == __pyx_v_self->_phasedA);
                __pyx_t_11 = __pyx_t_9;
              } else {
                __pyx_t_11 = __pyx_t_8;
              }
              __pyx_t_8 = __pyx_t_11;
            } else {
              __pyx_t_8 = __pyx_t_10;
            }
            __pyx_t_10 = __pyx_t_8;
          } else {
            __pyx_t_10 = __pyx_t_7;
          }
          __pyx_t_7 = __pyx_t_10;
        } else {
          __pyx_t_7 = __pyx_t_2;
        }
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1451
 *                     #print i, i%3, self._phasedB, i%3==self._phasedB
 *                     if (j-3)>=0 and (i-3)>=0 and (self._phasedB==-1 or (i%3)==self._phasedB) and (self._phasedA==-1 or (j%3)==self._phasedA):
 *                         idx = self.index(j-3,i-3)             # <<<<<<<<<<<<<<
 *                         contrib = self.matchCodon(j,i)
 *                         score = self.matrix.matrix[idx].score + \
 */
          __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 3), (__pyx_v_i - 3));

          /* "obitools/align/_codonnws.pyx":1452
 *                     if (j-3)>=0 and (i-3)>=0 and (self._phasedB==-1 or (i%3)==self._phasedB) and (self._phasedA==-1 or (j%3)==self._phasedA):
 *                         idx = self.index(j-3,i-3)
 *                         contrib = self.matchCodon(j,i)             # <<<<<<<<<<<<<<
 *                         score = self.matrix.matrix[idx].score + \
 *                                 contrib
 */
          __pyx_v_contrib = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->matchCodon(__pyx_v_self, __pyx_v_j, __pyx_v_i);

          /* "obitools/align/_codonnws.pyx":1454
 *                         contrib = self.matchCodon(j,i)
 *                         score = self.matrix.matrix[idx].score + \
 *                                 contrib             # <<<<<<<<<<<<<<
 * 
 *                         #print "so=%f sd=%f score=%f sm=%f" % (self.matrix.matrix[idx].score,contrib,score, scoremax)
 */
          __pyx_v_score = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + __pyx_v_contrib);

          /* "obitools/align/_codonnws.pyx":1458
 *                         #print "so=%f sd=%f score=%f sm=%f" % (self.matrix.matrix[idx].score,contrib,score, scoremax)
 * 
 *                         if score > scoremax :             # <<<<<<<<<<<<<<
 *                             #print "putain trop bien !"
 *                             scoremax = score
 */
          __pyx_t_7 = (__pyx_v_score > __pyx_v_scoremax);
          if (__pyx_t_7) {

            /* "obitools/align/_codonnws.pyx":1460
 *                         if score > scoremax :
 *                             #print "putain trop bien !"
 *                             scoremax = score             # <<<<<<<<<<<<<<
 *                             path = idx
 * 
 */
            __pyx_v_scoremax = __pyx_v_score;

            /* "obitools/align/_codonnws.pyx":1461
 *                             #print "putain trop bien !"
 *                             scoremax = score
 *                             path = idx             # <<<<<<<<<<<<<<
 * 
 * 
 */
            __pyx_v_path = __pyx_v_idx;
            goto __pyx_L13;
          }
          __pyx_L13:;
          goto __pyx_L12;
        }
        __pyx_L12:;

        /* "obitools/align/_codonnws.pyx":1465
 * 
 *                     # 2 - open horizontal gap
 *                     idx = self.index(j-1,i)             # <<<<<<<<<<<<<<
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap
 */
        __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), __pyx_v_i);

        /* "obitools/align/_codonnws.pyx":1467
 *                     idx = self.index(j-1,i)
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap             # <<<<<<<<<<<<<<
 *                     if score > scoremax :
 *                         scoremax = score
 */
        __pyx_v_score = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + __pyx_v_self->__pyx_base.__pyx_base._opengap);

        /* "obitools/align/_codonnws.pyx":1468
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap
 *                     if score > scoremax :             # <<<<<<<<<<<<<<
 *                         scoremax = score
 *                         path = idx
 */
        __pyx_t_7 = (__pyx_v_score > __pyx_v_scoremax);
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1469
 *                             self._opengap
 *                     if score > scoremax :
 *                         scoremax = score             # <<<<<<<<<<<<<<
 *                         path = idx
 * 
 */
          __pyx_v_scoremax = __pyx_v_score;

          /* "obitools/align/_codonnws.pyx":1470
 *                     if score > scoremax :
 *                         scoremax = score
 *                         path = idx             # <<<<<<<<<<<<<<
 * 
 *                     # 3 - open vertical gap
 */
          __pyx_v_path = __pyx_v_idx;
          goto __pyx_L14;
        }
        __pyx_L14:;

        /* "obitools/align/_codonnws.pyx":1473
 * 
 *                     # 3 - open vertical gap
 *                     idx = self.index(j,i-1)             # <<<<<<<<<<<<<<
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap
 */
        __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, (__pyx_v_i - 1));

        /* "obitools/align/_codonnws.pyx":1475
 *                     idx = self.index(j,i-1)
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap             # <<<<<<<<<<<<<<
 *                     if score > scoremax :
 *                         scoremax = score
 */
        __pyx_v_score = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + __pyx_v_self->__pyx_base.__pyx_base._opengap);

        /* "obitools/align/_codonnws.pyx":1476
 *                     score = self.matrix.matrix[idx].score + \
 *                             self._opengap
 *                     if score > scoremax :             # <<<<<<<<<<<<<<
 *                         scoremax = score
 *                         path = idx
 */
        __pyx_t_7 = (__pyx_v_score > __pyx_v_scoremax);
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1477
 *                             self._opengap
 *                     if score > scoremax :
 *                         scoremax = score             # <<<<<<<<<<<<<<
 *                         path = idx
 * 
 */
          __pyx_v_scoremax = __pyx_v_score;

          /* "obitools/align/_codonnws.pyx":1478
 *                     if score > scoremax :
 *                         scoremax = score
 *                         path = idx             # <<<<<<<<<<<<<<
 * 
 *                     # 4 - extend horizontal gap
 */
          __pyx_v_path = __pyx_v_idx;
          goto __pyx_L15;
        }
        __pyx_L15:;

        /* "obitools/align/_codonnws.pyx":1481
 * 
 *                     # 4 - extend horizontal gap
 *                     jump = self.matrix.bestHJump[i]             # <<<<<<<<<<<<<<
 *                     if jump >= 0:
 *                         idx = self.index(jump,i)
 */
        __pyx_v_jump = (__pyx_v_self->__pyx_base.__pyx_base.matrix->bestHJump[__pyx_v_i]);

        /* "obitools/align/_codonnws.pyx":1482
 *                     # 4 - extend horizontal gap
 *                     jump = self.matrix.bestHJump[i]
 *                     if jump >= 0:             # <<<<<<<<<<<<<<
 *                         idx = self.index(jump,i)
 *                         delta = j-jump
 */
        __pyx_t_7 = (__pyx_v_jump >= 0);
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1483
 *                     jump = self.matrix.bestHJump[i]
 *                     if jump >= 0:
 *                         idx = self.index(jump,i)             # <<<<<<<<<<<<<<
 *                         delta = j-jump
 *                         score = self.matrix.matrix[idx].score + \
 */
          __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_jump, __pyx_v_i);

          /* "obitools/align/_codonnws.pyx":1484
 *                     if jump >= 0:
 *                         idx = self.index(jump,i)
 *                         delta = j-jump             # <<<<<<<<<<<<<<
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta
 */
          __pyx_v_delta = (__pyx_v_j - __pyx_v_jump);

          /* "obitools/align/_codonnws.pyx":1486
 *                         delta = j-jump
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta             # <<<<<<<<<<<<<<
 *                         if score > scoremax :
 *                             scoremax = score
 */
          __pyx_v_score = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + (__pyx_v_self->__pyx_base.__pyx_base._extgap * __pyx_v_delta));

          /* "obitools/align/_codonnws.pyx":1487
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta
 *                         if score > scoremax :             # <<<<<<<<<<<<<<
 *                             scoremax = score
 *                             path = idx
 */
          __pyx_t_7 = (__pyx_v_score > __pyx_v_scoremax);
          if (__pyx_t_7) {

            /* "obitools/align/_codonnws.pyx":1488
 *                                 self._extgap * delta
 *                         if score > scoremax :
 *                             scoremax = score             # <<<<<<<<<<<<<<
 *                             path = idx
 * 
 */
            __pyx_v_scoremax = __pyx_v_score;

            /* "obitools/align/_codonnws.pyx":1489
 *                         if score > scoremax :
 *                             scoremax = score
 *                             path = idx             # <<<<<<<<<<<<<<
 * 
 *                     # 5 - extend vertical gap
 */
            __pyx_v_path = __pyx_v_idx;
            goto __pyx_L17;
          }
          __pyx_L17:;
          goto __pyx_L16;
        }
        __pyx_L16:;

        /* "obitools/align/_codonnws.pyx":1492
 * 
 *                     # 5 - extend vertical gap
 *                     jump = self.matrix.bestVJump[j]             # <<<<<<<<<<<<<<
 *                     if jump >= 0:
 *                         idx = self.index(j,jump)
 */
        __pyx_v_jump = (__pyx_v_self->__pyx_base.__pyx_base.matrix->bestVJump[__pyx_v_j]);

        /* "obitools/align/_codonnws.pyx":1493
 *                     # 5 - extend vertical gap
 *                     jump = self.matrix.bestVJump[j]
 *                     if jump >= 0:             # <<<<<<<<<<<<<<
 *                         idx = self.index(j,jump)
 *                         delta = i-jump
 */
        __pyx_t_7 = (__pyx_v_jump >= 0);
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1494
 *                     jump = self.matrix.bestVJump[j]
 *                     if jump >= 0:
 *                         idx = self.index(j,jump)             # <<<<<<<<<<<<<<
 *                         delta = i-jump
 *                         score = self.matrix.matrix[idx].score + \
 */
          __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, __pyx_v_jump);

          /* "obitools/align/_codonnws.pyx":1495
 *                     if jump >= 0:
 *                         idx = self.index(j,jump)
 *                         delta = i-jump             # <<<<<<<<<<<<<<
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta
 */
          __pyx_v_delta = (__pyx_v_i - __pyx_v_jump);

          /* "obitools/align/_codonnws.pyx":1497
 *                         delta = i-jump
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta             # <<<<<<<<<<<<<<
 *                         if score > scoremax :
 *                             scoremax = score
 */
          __pyx_v_score = ((__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score + (__pyx_v_self->__pyx_base.__pyx_base._extgap * __pyx_v_delta));

          /* "obitools/align/_codonnws.pyx":1498
 *                         score = self.matrix.matrix[idx].score + \
 *                                 self._extgap * delta
 *                         if score > scoremax :             # <<<<<<<<<<<<<<
 *                             scoremax = score
 *                             path = idx
 */
          __pyx_t_7 = (__pyx_v_score > __pyx_v_scoremax);
          if (__pyx_t_7) {

            /* "obitools/align/_codonnws.pyx":1499
 *                                 self._extgap * delta
 *                         if score > scoremax :
 *                             scoremax = score             # <<<<<<<<<<<<<<
 *                             path = idx
 * 
 */
            __pyx_v_scoremax = __pyx_v_score;

            /* "obitools/align/_codonnws.pyx":1500
 *                         if score > scoremax :
 *                             scoremax = score
 *                             path = idx             # <<<<<<<<<<<<<<
 * 
 *                     idx = self.index(j,i)
 */
            __pyx_v_path = __pyx_v_idx;
            goto __pyx_L19;
          }
          __pyx_L19:;
          goto __pyx_L18;
        }
        __pyx_L18:;

        /* "obitools/align/_codonnws.pyx":1502
 *                             path = idx
 * 
 *                     idx = self.index(j,i)             # <<<<<<<<<<<<<<
 *                     self.matrix.matrix[idx].score = scoremax
 *                     self.matrix.matrix[idx].path  = path
 */
        __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, __pyx_v_i);

        /* "obitools/align/_codonnws.pyx":1503
 * 
 *                     idx = self.index(j,i)
 *                     self.matrix.matrix[idx].score = scoremax             # <<<<<<<<<<<<<<
 *                     self.matrix.matrix[idx].path  = path
 * 
 */
        (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score = __pyx_v_scoremax;

        /* "obitools/align/_codonnws.pyx":1504
 *                     idx = self.index(j,i)
 *                     self.matrix.matrix[idx].score = scoremax
 *                     self.matrix.matrix[idx].path  = path             # <<<<<<<<<<<<<<
 * 
 *                     #si on a choisi l'ouverture de gap
 */
        (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).path = __pyx_v_path;

        /* "obitools/align/_codonnws.pyx":1507
 * 
 *                     #si on a choisi l'ouverture de gap
 *                     if path == self.index(j,i-1):             # <<<<<<<<<<<<<<
 *                         self.matrix.bestVJump[j]=i
 *                     elif path == self.index(j-1,i):
 */
        __pyx_t_7 = (__pyx_v_path == ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, (__pyx_v_i - 1)));
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1508
 *                     #si on a choisi l'ouverture de gap
 *                     if path == self.index(j,i-1):
 *                         self.matrix.bestVJump[j]=i             # <<<<<<<<<<<<<<
 *                     elif path == self.index(j-1,i):
 *                         self.matrix.bestHJump[i]=j
 */
          (__pyx_v_self->__pyx_base.__pyx_base.matrix->bestVJump[__pyx_v_j]) = __pyx_v_i;
          goto __pyx_L20;
        }

        /* "obitools/align/_codonnws.pyx":1509
 *                     if path == self.index(j,i-1):
 *                         self.matrix.bestVJump[j]=i
 *                     elif path == self.index(j-1,i):             # <<<<<<<<<<<<<<
 *                         self.matrix.bestHJump[i]=j
 * 
 */
        __pyx_t_7 = (__pyx_v_path == ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), __pyx_v_i));
        if (__pyx_t_7) {

          /* "obitools/align/_codonnws.pyx":1510
 *                         self.matrix.bestVJump[j]=i
 *                     elif path == self.index(j-1,i):
 *                         self.matrix.bestHJump[i]=j             # <<<<<<<<<<<<<<
 * 
 *         self.sequenceChanged=False
 */
          (__pyx_v_self->__pyx_base.__pyx_base.matrix->bestHJump[__pyx_v_i]) = __pyx_v_j;
          goto __pyx_L20;
        }
        __pyx_L20:;
      }
    }
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "obitools/align/_codonnws.pyx":1512
 *                         self.matrix.bestHJump[i]=j
 * 
 *         self.sequenceChanged=False             # <<<<<<<<<<<<<<
 *         self.scoreChanged=False
 * 
 */
  __pyx_v_self->__pyx_base.__pyx_base.sequenceChanged = 0;

  /* "obitools/align/_codonnws.pyx":1513
 * 
 *         self.sequenceChanged=False
 *         self.scoreChanged=False             # <<<<<<<<<<<<<<
 * 
 *         idx = self.index(self._hlen(),self._vlen())
 */
  __pyx_v_self->__pyx_base.__pyx_base.scoreChanged = 0;

  /* "obitools/align/_codonnws.pyx":1515
 *         self.scoreChanged=False
 * 
 *         idx = self.index(self._hlen(),self._vlen())             # <<<<<<<<<<<<<<
 *         return self.matrix.matrix[idx].score
 * 
 */
  __pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)), ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._vlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)));

  /* "obitools/align/_codonnws.pyx":1516
 * 
 *         idx = self.index(self._hlen(),self._vlen())
 *         return self.matrix.matrix[idx].score             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_r = (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[__pyx_v_idx]).score;
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.doAlignment", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0.0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1519
 * 
 * 
 *     cdef void backtrack(self):             # <<<<<<<<<<<<<<
 *         #cdef list path=[]
 *         cdef int i
 */

static void __pyx_f_8obitools_5align_9_codonnws_8CodonNWS_backtrack(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self) {
  int __pyx_v_i;
  int __pyx_v_j;
  int __pyx_v_p;
  int __pyx_v_idx;
  PyObject *__pyx_v_ori_j = NULL;
  PyObject *__pyx_v_ori_i = NULL;
  __Pyx_RefNannyDeclarations
  double __pyx_t_1;
  struct __pyx_t_8obitools_5align_8_dynamic_alignPath *__pyx_t_2;
  struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath __pyx_t_3;
  int __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  int __pyx_t_8;
  int __pyx_t_9;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("backtrack", 0);

  /* "obitools/align/_codonnws.pyx":1525
 *         cdef int p
 * 
 *         self.doAlignment()             # <<<<<<<<<<<<<<
 *         i=self._vlen()
 *         j=self._hlen()
 */
  __pyx_t_1 = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.doAlignment(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)); if (unlikely(__pyx_t_1 == 0.0 && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "obitools/align/_codonnws.pyx":1526
 * 
 *         self.doAlignment()
 *         i=self._vlen()             # <<<<<<<<<<<<<<
 *         j=self._hlen()
 *         self.path=allocatePath(i,j,self.path)
 */
  __pyx_v_i = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._vlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self));

  /* "obitools/align/_codonnws.pyx":1527
 *         self.doAlignment()
 *         i=self._vlen()
 *         j=self._hlen()             # <<<<<<<<<<<<<<
 *         self.path=allocatePath(i,j,self.path)
 * 
 */
  __pyx_v_j = ((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base._hlen(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self));

  /* "obitools/align/_codonnws.pyx":1528
 *         i=self._vlen()
 *         j=self._hlen()
 *         self.path=allocatePath(i,j,self.path)             # <<<<<<<<<<<<<<
 * 
 *         while (i or j):
 */
  __pyx_t_3.__pyx_n = 1;
  __pyx_t_3.path = __pyx_v_self->__pyx_base.__pyx_base.path;
  __pyx_t_2 = __pyx_f_8obitools_5align_8_dynamic_allocatePath(__pyx_v_i, __pyx_v_j, &__pyx_t_3); 
  __pyx_v_self->__pyx_base.__pyx_base.path = __pyx_t_2;

  /* "obitools/align/_codonnws.pyx":1530
 *         self.path=allocatePath(i,j,self.path)
 * 
 *         while (i or j):             # <<<<<<<<<<<<<<
 *             idx=self.matrix.matrix[self.index(j,i)].path
 *             ori_j = self.colindex(idx)
 */
  while (1) {
    if (!__pyx_v_i) {
      __pyx_t_4 = __pyx_v_j;
    } else {
      __pyx_t_4 = __pyx_v_i;
    }
    if (!__pyx_t_4) break;

    /* "obitools/align/_codonnws.pyx":1531
 * 
 *         while (i or j):
 *             idx=self.matrix.matrix[self.index(j,i)].path             # <<<<<<<<<<<<<<
 *             ori_j = self.colindex(idx)
 *             ori_i = self.rowindex(idx)
 */
    __pyx_v_idx = (__pyx_v_self->__pyx_base.__pyx_base.matrix->matrix[((struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, __pyx_v_i)]).path;

    /* "obitools/align/_codonnws.pyx":1532
 *         while (i or j):
 *             idx=self.matrix.matrix[self.index(j,i)].path
 *             ori_j = self.colindex(idx)             # <<<<<<<<<<<<<<
 *             ori_i = self.rowindex(idx)
 * 
 */
    __pyx_t_5 = PyInt_FromLong(__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_colindex(__pyx_v_self, __pyx_v_idx)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_XDECREF(__pyx_v_ori_j);
    __pyx_v_ori_j = __pyx_t_5;
    __pyx_t_5 = 0;

    /* "obitools/align/_codonnws.pyx":1533
 *             idx=self.matrix.matrix[self.index(j,i)].path
 *             ori_j = self.colindex(idx)
 *             ori_i = self.rowindex(idx)             # <<<<<<<<<<<<<<
 * 
 *             #print i,j
 */
    __pyx_t_5 = PyInt_FromLong(__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_rowindex(__pyx_v_self, __pyx_v_idx)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_XDECREF(__pyx_v_ori_i);
    __pyx_v_ori_i = __pyx_t_5;
    __pyx_t_5 = 0;

    /* "obitools/align/_codonnws.pyx":1537
 *             #print i,j
 * 
 *             if i-ori_i == 3 and j-ori_j == 3:             # <<<<<<<<<<<<<<
 *                 #print 'on passe par un codon'
 *                 p = 0
 */
    __pyx_t_5 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (__pyx_t_4) {
      __pyx_t_5 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_j); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_8 = __pyx_t_7;
    } else {
      __pyx_t_8 = __pyx_t_4;
    }
    if (__pyx_t_8) {

      /* "obitools/align/_codonnws.pyx":1539
 *             if i-ori_i == 3 and j-ori_j == 3:
 *                 #print 'on passe par un codon'
 *                 p = 0             # <<<<<<<<<<<<<<
 * 
 *                 self.path.path[self.path.length]=p
 */
      __pyx_v_p = 0;

      /* "obitools/align/_codonnws.pyx":1541
 *                 p = 0
 * 
 *                 self.path.path[self.path.length]=p             # <<<<<<<<<<<<<<
 *                 self.path.length+=1
 * 
 */
      (__pyx_v_self->__pyx_base.__pyx_base.path->path[__pyx_v_self->__pyx_base.__pyx_base.path->length]) = __pyx_v_p;

      /* "obitools/align/_codonnws.pyx":1542
 * 
 *                 self.path.path[self.path.length]=p
 *                 self.path.length+=1             # <<<<<<<<<<<<<<
 * 
 *                 self.path.path[self.path.length]=p
 */
      __pyx_v_self->__pyx_base.__pyx_base.path->length = (__pyx_v_self->__pyx_base.__pyx_base.path->length + 1);

      /* "obitools/align/_codonnws.pyx":1544
 *                 self.path.length+=1
 * 
 *                 self.path.path[self.path.length]=p             # <<<<<<<<<<<<<<
 *                 self.path.length+=1
 * 
 */
      (__pyx_v_self->__pyx_base.__pyx_base.path->path[__pyx_v_self->__pyx_base.__pyx_base.path->length]) = __pyx_v_p;

      /* "obitools/align/_codonnws.pyx":1545
 * 
 *                 self.path.path[self.path.length]=p
 *                 self.path.length+=1             # <<<<<<<<<<<<<<
 * 
 *             elif i-ori_i == 1 and j-ori_j == 1:
 */
      __pyx_v_self->__pyx_base.__pyx_base.path->length = (__pyx_v_self->__pyx_base.__pyx_base.path->length + 1);
      goto __pyx_L5;
    }

    /* "obitools/align/_codonnws.pyx":1547
 *                 self.path.length+=1
 * 
 *             elif i-ori_i == 1 and j-ori_j == 1:             # <<<<<<<<<<<<<<
 *                 #print 'on passe par un match'
 *                 p = 0
 */
    __pyx_t_5 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (__pyx_t_8) {
      __pyx_t_5 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_j); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_7 = __pyx_t_4;
    } else {
      __pyx_t_7 = __pyx_t_8;
    }
    if (__pyx_t_7) {

      /* "obitools/align/_codonnws.pyx":1549
 *             elif i-ori_i == 1 and j-ori_j == 1:
 *                 #print 'on passe par un match'
 *                 p = 0             # <<<<<<<<<<<<<<
 *             elif i-ori_i == 0:
 *                 #print 'on passe par un gap'
 */
      __pyx_v_p = 0;
      goto __pyx_L5;
    }

    /* "obitools/align/_codonnws.pyx":1550
 *                 #print 'on passe par un match'
 *                 p = 0
 *             elif i-ori_i == 0:             # <<<<<<<<<<<<<<
 *                 #print 'on passe par un gap'
 *                 p = (j-ori_j)
 */
    __pyx_t_5 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (__pyx_t_7) {

      /* "obitools/align/_codonnws.pyx":1552
 *             elif i-ori_i == 0:
 *                 #print 'on passe par un gap'
 *                 p = (j-ori_j)             # <<<<<<<<<<<<<<
 *             elif j-ori_j == 0:
 *                 #print 'on passe par un gap'
 */
      __pyx_t_5 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_ori_j); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_v_p = __pyx_t_9;
      goto __pyx_L5;
    }

    /* "obitools/align/_codonnws.pyx":1553
 *                 #print 'on passe par un gap'
 *                 p = (j-ori_j)
 *             elif j-ori_j == 0:             # <<<<<<<<<<<<<<
 *                 #print 'on passe par un gap'
 *                 p = -(i-ori_i)
 */
    __pyx_t_6 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_5 = PyNumber_Subtract(__pyx_t_6, __pyx_v_ori_j); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    if (__pyx_t_7) {

      /* "obitools/align/_codonnws.pyx":1555
 *             elif j-ori_j == 0:
 *                 #print 'on passe par un gap'
 *                 p = -(i-ori_i)             # <<<<<<<<<<<<<<
 *             else:
 *                 print "badaboum !"
 */
      __pyx_t_6 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_5 = PyNumber_Subtract(__pyx_t_6, __pyx_v_ori_i); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_6 = PyNumber_Negative(__pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_v_p = __pyx_t_9;
      goto __pyx_L5;
    }
    /*else*/ {

      /* "obitools/align/_codonnws.pyx":1557
 *                 p = -(i-ori_i)
 *             else:
 *                 print "badaboum !"             # <<<<<<<<<<<<<<
 * 
 *             i = ori_i
 */
      if (__Pyx_PrintOne(0, ((PyObject *)__pyx_kp_s_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    __pyx_L5:;

    /* "obitools/align/_codonnws.pyx":1559
 *                 print "badaboum !"
 * 
 *             i = ori_i             # <<<<<<<<<<<<<<
 *             j = ori_j
 * 
 */
    __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_v_ori_i); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_v_i = __pyx_t_9;

    /* "obitools/align/_codonnws.pyx":1560
 * 
 *             i = ori_i
 *             j = ori_j             # <<<<<<<<<<<<<<
 * 
 *             #print '->', i, j
 */
    __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_v_ori_j); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_v_j = __pyx_t_9;

    /* "obitools/align/_codonnws.pyx":1564
 *             #print '->', i, j
 * 
 *             self.path.path[self.path.length]=p             # <<<<<<<<<<<<<<
 *             self.path.length+=1
 * 
 */
    (__pyx_v_self->__pyx_base.__pyx_base.path->path[__pyx_v_self->__pyx_base.__pyx_base.path->length]) = __pyx_v_p;

    /* "obitools/align/_codonnws.pyx":1565
 * 
 *             self.path.path[self.path.length]=p
 *             self.path.length+=1             # <<<<<<<<<<<<<<
 * 
 *         self.path.hStart=0
 */
    __pyx_v_self->__pyx_base.__pyx_base.path->length = (__pyx_v_self->__pyx_base.__pyx_base.path->length + 1);
  }

  /* "obitools/align/_codonnws.pyx":1567
 *             self.path.length+=1
 * 
 *         self.path.hStart=0             # <<<<<<<<<<<<<<
 *         self.path.vStart=0
 * 
 */
  __pyx_v_self->__pyx_base.__pyx_base.path->hStart = 0;

  /* "obitools/align/_codonnws.pyx":1568
 * 
 *         self.path.hStart=0
 *         self.path.vStart=0             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_v_self->__pyx_base.__pyx_base.path->vStart = 0;

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_WriteUnraisable("obitools.align._codonnws.CodonNWS.backtrack", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_ori_j);
  __Pyx_XDECREF(__pyx_v_ori_i);
  __Pyx_RefNannyFinishContext();
}

/* Python wrapper */
static PyObject *__pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match___get__(((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1572
 * 
 *     property match:
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             return self._match
 * 
 */

static PyObject *__pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match___get__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "obitools/align/_codonnws.pyx":1573
 *     property match:
 *         def __get__(self):
 *             return self._match             # <<<<<<<<<<<<<<
 * 
 *         def __set__(self,match):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->__pyx_base._match); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.match.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_match); /*proto*/
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_match) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match_2__set__(((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self), ((PyObject *)__pyx_v_match));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1575
 *             return self._match
 * 
 *         def __set__(self,match):             # <<<<<<<<<<<<<<
 *             self._match=match
 *             self.scoreChanged=True
 */

static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_5match_2__set__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_match) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  double __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__set__", 0);

  /* "obitools/align/_codonnws.pyx":1576
 * 
 *         def __set__(self,match):
 *             self._match=match             # <<<<<<<<<<<<<<
 *             self.scoreChanged=True
 * 
 */
  __pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_match); if (unlikely((__pyx_t_1 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_v_self->__pyx_base._match = __pyx_t_1;

  /* "obitools/align/_codonnws.pyx":1577
 *         def __set__(self,match):
 *             self._match=match
 *             self.scoreChanged=True             # <<<<<<<<<<<<<<
 * 
 *     property mismatch:
 */
  __pyx_v_self->__pyx_base.__pyx_base.scoreChanged = 1;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.match.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch___get__(((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1580
 * 
 *     property mismatch:
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             return self._mismatch
 * 
 */

static PyObject *__pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch___get__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "obitools/align/_codonnws.pyx":1581
 *     property mismatch:
 *         def __get__(self):
 *             return self._mismatch             # <<<<<<<<<<<<<<
 * 
 *         def __set__(self,mismatch):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->__pyx_base._mismatch); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.mismatch.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mismatch); /*proto*/
static int __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mismatch) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_2__set__(((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)__pyx_v_self), ((PyObject *)__pyx_v_mismatch));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "obitools/align/_codonnws.pyx":1583
 *             return self._mismatch
 * 
 *         def __set__(self,mismatch):             # <<<<<<<<<<<<<<
 *             self._mismatch=mismatch
 *             self.scoreChanged=True
 */

static int __pyx_pf_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_2__set__(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *__pyx_v_self, PyObject *__pyx_v_mismatch) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  double __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__set__", 0);

  /* "obitools/align/_codonnws.pyx":1584
 * 
 *         def __set__(self,mismatch):
 *             self._mismatch=mismatch             # <<<<<<<<<<<<<<
 *             self.scoreChanged=True
 * 
 */
  __pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_mismatch); if (unlikely((__pyx_t_1 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_v_self->__pyx_base._mismatch = __pyx_t_1;

  /* "obitools/align/_codonnws.pyx":1585
 *         def __set__(self,mismatch):
 *             self._mismatch=mismatch
 *             self.scoreChanged=True             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_v_self->__pyx_base.__pyx_base.scoreChanged = 1;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("obitools.align._codonnws.CodonNWS.mismatch.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}
static struct __pyx_vtabstruct_8obitools_5align_9_codonnws_CodonNWS __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS;

static PyObject *__pyx_tp_new_8obitools_5align_9_codonnws_CodonNWS(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *p;
  PyObject *o = __pyx_ptype_8obitools_5align_4_nws_NWS->tp_new(t, a, k);
  if (!o) return 0;
  p = ((struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *)o);
  p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming*)__pyx_vtabptr_8obitools_5align_9_codonnws_CodonNWS;
  return o;
}

static void __pyx_tp_dealloc_8obitools_5align_9_codonnws_CodonNWS(PyObject *o) {
  __pyx_ptype_8obitools_5align_4_nws_NWS->tp_dealloc(o);
}

static int __pyx_tp_traverse_8obitools_5align_9_codonnws_CodonNWS(PyObject *o, visitproc v, void *a) {
  int e;
  if (__pyx_ptype_8obitools_5align_4_nws_NWS->tp_traverse) {
    e = __pyx_ptype_8obitools_5align_4_nws_NWS->tp_traverse(o, v, a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_8obitools_5align_9_codonnws_CodonNWS(PyObject *o) {
  if (__pyx_ptype_8obitools_5align_4_nws_NWS->tp_clear) {
    __pyx_ptype_8obitools_5align_4_nws_NWS->tp_clear(o);
  }
  return 0;
}

static PyObject *__pyx_getprop_8obitools_5align_9_codonnws_8CodonNWS_match(PyObject *o, void *x) {
  return __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_1__get__(o);
}

static int __pyx_setprop_8obitools_5align_9_codonnws_8CodonNWS_match(PyObject *o, PyObject *v, void *x) {
  if (v) {
    return __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_5match_3__set__(o, v);
  }
  else {
    PyErr_SetString(PyExc_NotImplementedError, "__del__");
    return -1;
  }
}

static PyObject *__pyx_getprop_8obitools_5align_9_codonnws_8CodonNWS_mismatch(PyObject *o, void *x) {
  return __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_1__get__(o);
}

static int __pyx_setprop_8obitools_5align_9_codonnws_8CodonNWS_mismatch(PyObject *o, PyObject *v, void *x) {
  if (v) {
    return __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_8mismatch_3__set__(o, v);
  }
  else {
    PyErr_SetString(PyExc_NotImplementedError, "__del__");
    return -1;
  }
}

static PyMethodDef __pyx_methods_8obitools_5align_9_codonnws_CodonNWS[] = {
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_8obitools_5align_9_codonnws_CodonNWS[] = {
  {(char *)"match", __pyx_getprop_8obitools_5align_9_codonnws_8CodonNWS_match, __pyx_setprop_8obitools_5align_9_codonnws_8CodonNWS_match, 0, 0},
  {(char *)"mismatch", __pyx_getprop_8obitools_5align_9_codonnws_8CodonNWS_mismatch, __pyx_setprop_8obitools_5align_9_codonnws_8CodonNWS_mismatch, 0, 0},
  {0, 0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_CodonNWS = {
  0, /*nb_add*/
  0, /*nb_subtract*/
  0, /*nb_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
  #endif
  0, /*nb_remainder*/
  0, /*nb_divmod*/
  0, /*nb_power*/
  0, /*nb_negative*/
  0, /*nb_positive*/
  0, /*nb_absolute*/
  0, /*nb_nonzero*/
  0, /*nb_invert*/
  0, /*nb_lshift*/
  0, /*nb_rshift*/
  0, /*nb_and*/
  0, /*nb_xor*/
  0, /*nb_or*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_coerce*/
  #endif
  0, /*nb_int*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_long*/
  #else
  0, /*reserved*/
  #endif
  0, /*nb_float*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_oct*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*nb_hex*/
  #endif
  0, /*nb_inplace_add*/
  0, /*nb_inplace_subtract*/
  0, /*nb_inplace_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_inplace_divide*/
  #endif
  0, /*nb_inplace_remainder*/
  0, /*nb_inplace_power*/
  0, /*nb_inplace_lshift*/
  0, /*nb_inplace_rshift*/
  0, /*nb_inplace_and*/
  0, /*nb_inplace_xor*/
  0, /*nb_inplace_or*/
  0, /*nb_floor_divide*/
  0, /*nb_true_divide*/
  0, /*nb_inplace_floor_divide*/
  0, /*nb_inplace_true_divide*/
  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
  #endif
};

static PySequenceMethods __pyx_tp_as_sequence_CodonNWS = {
  0, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_CodonNWS = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_CodonNWS = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

static PyTypeObject __pyx_type_8obitools_5align_9_codonnws_CodonNWS = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("obitools.align._codonnws.CodonNWS"), /*tp_name*/
  sizeof(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8obitools_5align_9_codonnws_CodonNWS, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  &__pyx_tp_as_number_CodonNWS, /*tp_as_number*/
  &__pyx_tp_as_sequence_CodonNWS, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_CodonNWS, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_CodonNWS, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8obitools_5align_9_codonnws_CodonNWS, /*tp_traverse*/
  __pyx_tp_clear_8obitools_5align_9_codonnws_CodonNWS, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8obitools_5align_9_codonnws_CodonNWS, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_8obitools_5align_9_codonnws_CodonNWS, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  __pyx_pw_8obitools_5align_9_codonnws_8CodonNWS_1__init__, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8obitools_5align_9_codonnws_CodonNWS, /*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*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};

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

#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
    PyModuleDef_HEAD_INIT,
    __Pyx_NAMESTR("_codonnws"),
    __Pyx_DOCSTR(__pyx_k_3), /* 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_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
  {&__pyx_n_s____init__, __pyx_k____init__, sizeof(__pyx_k____init__), 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__extgap, __pyx_k__extgap, sizeof(__pyx_k__extgap), 0, 0, 1, 1},
  {&__pyx_n_s__match, __pyx_k__match, sizeof(__pyx_k__match), 0, 0, 1, 1},
  {&__pyx_n_s__mismatch, __pyx_k__mismatch, sizeof(__pyx_k__mismatch), 0, 0, 1, 1},
  {&__pyx_n_s__needToCompute, __pyx_k__needToCompute, sizeof(__pyx_k__needToCompute), 0, 0, 1, 1},
  {&__pyx_n_s__opengap, __pyx_k__opengap, sizeof(__pyx_k__opengap), 0, 0, 1, 1},
  {&__pyx_n_s__phasedA, __pyx_k__phasedA, sizeof(__pyx_k__phasedA), 0, 0, 1, 1},
  {&__pyx_n_s__phasedB, __pyx_k__phasedB, sizeof(__pyx_k__phasedB), 0, 0, 1, 1},
  {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  return 0;
  __pyx_L1_error:;
  return -1;
}

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

  /* "obitools/align/_codonnws.pyx":1384
 *         score = 0
 * 
 *         for i in range(3):             # <<<<<<<<<<<<<<
 *             match = iupacPartialMatch(self.hSeq.sequence[h-i-1],self.vSeq.sequence[v-i-1])
 *             score += match * self._match + (1-match) * self._mismatch
 */
  __pyx_k_tuple_1 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_1);
  __Pyx_INCREF(__pyx_int_3);
  PyTuple_SET_ITEM(__pyx_k_tuple_1, 0, __pyx_int_3);
  __Pyx_GIVEREF(__pyx_int_3);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_1));
  __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;};
  __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_neg_3 = PyInt_FromLong(-3); if (unlikely(!__pyx_int_neg_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_neg_4 = PyInt_FromLong(-4); if (unlikely(!__pyx_int_neg_4)) {__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 init_codonnws(void); /*proto*/
PyMODINIT_FUNC init_codonnws(void)
#else
PyMODINIT_FUNC PyInit__codonnws(void); /*proto*/
PyMODINIT_FUNC PyInit__codonnws(void)
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = 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__codonnws(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("_codonnws"), __pyx_methods, __Pyx_DOCSTR(__pyx_k_3), 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_obitools__align___codonnws) {
    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 ---*/
  __pyx_ptype_8obitools_5align_4_nws_NWS = __Pyx_ImportType("obitools.align._nws", "NWS", sizeof(struct __pyx_obj_8obitools_5align_4_nws_NWS), 1); if (unlikely(!__pyx_ptype_8obitools_5align_4_nws_NWS)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_vtabptr_8obitools_5align_4_nws_NWS = (struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS*)__Pyx_GetVtable(__pyx_ptype_8obitools_5align_4_nws_NWS->tp_dict); if (unlikely(!__pyx_vtabptr_8obitools_5align_4_nws_NWS)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_vtabptr_8obitools_5align_9_codonnws_CodonNWS = &__pyx_vtable_8obitools_5align_9_codonnws_CodonNWS;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.__pyx_base = *__pyx_vtabptr_8obitools_5align_4_nws_NWS;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.__pyx_base.__pyx_base.doAlignment = (double (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_doAlignment;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.__pyx_base.__pyx_base.backtrack = (void (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_backtrack;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.matchCodon = (double (*)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int, int))__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_matchCodon;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.colindex = (int (*)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int))__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_colindex;
  __pyx_vtable_8obitools_5align_9_codonnws_CodonNWS.rowindex = (int (*)(struct __pyx_obj_8obitools_5align_9_codonnws_CodonNWS *, int))__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_rowindex;
  __pyx_type_8obitools_5align_9_codonnws_CodonNWS.tp_base = __pyx_ptype_8obitools_5align_4_nws_NWS;
  if (PyType_Ready(&__pyx_type_8obitools_5align_9_codonnws_CodonNWS) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetVtable(__pyx_type_8obitools_5align_9_codonnws_CodonNWS.tp_dict, __pyx_vtabptr_8obitools_5align_9_codonnws_CodonNWS) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetAttrString(__pyx_m, "CodonNWS", (PyObject *)&__pyx_type_8obitools_5align_9_codonnws_CodonNWS) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_8obitools_5align_9_codonnws_CodonNWS = &__pyx_type_8obitools_5align_9_codonnws_CodonNWS;
  /*--- Type import code ---*/
  __pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming = __Pyx_ImportType("obitools.align._dynamic", "DynamicProgramming", sizeof(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming), 1); if (unlikely(!__pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_vtabptr_8obitools_5align_8_dynamic_DynamicProgramming = (struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming*)__Pyx_GetVtable(__pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming->tp_dict); if (unlikely(!__pyx_vtabptr_8obitools_5align_8_dynamic_DynamicProgramming)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Variable import code ---*/
  /*--- Function import code ---*/
  __pyx_t_1 = __Pyx_ImportModule("obitools.align._dynamic"); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ImportFunction(__pyx_t_1, "allocatePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_allocatePath, "struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ImportFunction(__pyx_t_1, "iupacPartialMatch", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch, "double (unsigned char, unsigned char, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  /*--- Execution code ---*/

  /* "obitools/align/_codonnws.pyx":1
 * '''             # <<<<<<<<<<<<<<
 * Created on 6 Nov. 2009
 * 
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  if (__pyx_m) {
    __Pyx_AddTraceback("init obitools.align._codonnws", __pyx_clineno, __pyx_lineno, __pyx_filename);
    Py_DECREF(__pyx_m); __pyx_m = 0;
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init obitools.align._codonnws");
  }
  __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 PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
    PyObject *result;
    result = PyObject_GetAttr(dict, name);
    if (!result) {
        if (dict != __pyx_b) {
            PyErr_Clear();
            result = PyObject_GetAttr(__pyx_b, name);
        }
        if (!result) {
            PyErr_SetObject(PyExc_NameError, name);
        }
    }
    return result;
}

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 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 CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
    long r = a % b;
    r += ((r != 0) & ((r ^ b) < 0)) * b;
    return r;
}

static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
    long q = a / b;
    long r = a - q*b;
    q -= ((r != 0) & ((r ^ b) < 0));
    return q;
}

#if PY_MAJOR_VERSION < 3
static PyObject *__Pyx_GetStdout(void) {
    PyObject *f = PySys_GetObject((char *)"stdout");
    if (!f) {
        PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
    }
    return f;
}
static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
    PyObject* v;
    int i;
    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
        if (PyFile_SoftSpace(f, 1)) {
            if (PyFile_WriteString(" ", f) < 0)
                return -1;
        }
        v = PyTuple_GET_ITEM(arg_tuple, i);
        if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
            return -1;
        if (PyString_Check(v)) {
            char *s = PyString_AsString(v);
            Py_ssize_t len = PyString_Size(v);
            if (len > 0 &&
                isspace(Py_CHARMASK(s[len-1])) &&
                s[len-1] != ' ')
                    PyFile_SoftSpace(f, 0);
        }
    }
    if (newline) {
        if (PyFile_WriteString("\n", f) < 0)
            return -1;
        PyFile_SoftSpace(f, 0);
    }
    return 0;
}
#else /* Python 3 has a print function */
static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
    PyObject* kwargs = 0;
    PyObject* result = 0;
    PyObject* end_string;
    if (unlikely(!__pyx_print)) {
        __pyx_print = __Pyx_GetAttrString(__pyx_b, "print");
        if (!__pyx_print)
            return -1;
    }
    if (stream) {
        kwargs = PyDict_New();
        if (unlikely(!kwargs))
            return -1;
        if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0))
            goto bad;
        if (!newline) {
            end_string = PyUnicode_FromStringAndSize(" ", 1);
            if (unlikely(!end_string))
                goto bad;
            if (PyDict_SetItemString(kwargs, "end", end_string) < 0) {
                Py_DECREF(end_string);
                goto bad;
            }
            Py_DECREF(end_string);
        }
    } else if (!newline) {
        if (unlikely(!__pyx_print_kwargs)) {
            __pyx_print_kwargs = PyDict_New();
            if (unlikely(!__pyx_print_kwargs))
                return -1;
            end_string = PyUnicode_FromStringAndSize(" ", 1);
            if (unlikely(!end_string))
                return -1;
            if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
                Py_DECREF(end_string);
                return -1;
            }
            Py_DECREF(end_string);
        }
        kwargs = __pyx_print_kwargs;
    }
    result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
    if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
        Py_DECREF(kwargs);
    if (!result)
        return -1;
    Py_DECREF(result);
    return 0;
bad:
    if (kwargs != __pyx_print_kwargs)
        Py_XDECREF(kwargs);
    return -1;
}
#endif

#if PY_MAJOR_VERSION < 3
static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    if (PyFile_SoftSpace(f, 0)) {
        if (PyFile_WriteString(" ", f) < 0)
            return -1;
    }
    if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
        return -1;
    if (PyFile_WriteString("\n", f) < 0)
        return -1;
    return 0;
    /* the line below is just to avoid compiler
     * compiler warnings about unused functions */
    return __Pyx_Print(f, NULL, 0);
}
#else /* Python 3 has a print function */
static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
    int res;
    PyObject* arg_tuple = PyTuple_New(1);
    if (unlikely(!arg_tuple))
        return -1;
    Py_INCREF(o);
    PyTuple_SET_ITEM(arg_tuple, 0, o);
    res = __Pyx_Print(stream, arg_tuple, 1);
    Py_DECREF(arg_tuple);
    return res;
}
#endif

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 CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyThreadState *tstate = PyThreadState_GET();
    tmp_type = tstate->curexc_type;
    tmp_value = tstate->curexc_value;
    tmp_tb = tstate->curexc_traceback;
    tstate->curexc_type = type;
    tstate->curexc_value = value;
    tstate->curexc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
#else
    PyErr_Restore(type, value, tb);
#endif
}
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyThreadState *tstate = PyThreadState_GET();
    *type = tstate->curexc_type;
    *value = tstate->curexc_value;
    *tb = tstate->curexc_traceback;
    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
#else
    PyErr_Fetch(type, value, tb);
#endif
}

static void __Pyx_WriteUnraisable(const char *name, int clineno,
                                  int lineno, const char *filename) {
    PyObject *old_exc, *old_val, *old_tb;
    PyObject *ctx;
    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
    #if PY_MAJOR_VERSION < 3
    ctx = PyString_FromString(name);
    #else
    ctx = PyUnicode_FromString(name);
    #endif
    __Pyx_ErrRestore(old_exc, old_val, old_tb);
    if (!ctx) {
        PyErr_WriteUnraisable(Py_None);
    } else {
        PyErr_WriteUnraisable(ctx);
        Py_DECREF(ctx);
    }
}

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;
}

#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
    size_t size, int strict)
{
    PyObject *py_module = 0;
    PyObject *result = 0;
    PyObject *py_name = 0;
    char warning[200];
    py_module = __Pyx_ImportModule(module_name);
    if (!py_module)
        goto bad;
    py_name = __Pyx_PyIdentifier_FromString(class_name);
    if (!py_name)
        goto bad;
    result = PyObject_GetAttr(py_module, py_name);
    Py_DECREF(py_name);
    py_name = 0;
    Py_DECREF(py_module);
    py_module = 0;
    if (!result)
        goto bad;
    if (!PyType_Check(result)) {
        PyErr_Format(PyExc_TypeError,
            "%s.%s is not a type object",
            module_name, class_name);
        goto bad;
    }
    if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
        PyOS_snprintf(warning, sizeof(warning),
            "%s.%s size changed, may indicate binary incompatibility",
            module_name, class_name);
        #if PY_VERSION_HEX < 0x02050000
        if (PyErr_Warn(NULL, warning) < 0) goto bad;
        #else
        if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
        #endif
    }
    else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
        PyErr_Format(PyExc_ValueError,
            "%s.%s has the wrong size, try recompiling",
            module_name, class_name);
        goto bad;
    }
    return (PyTypeObject *)result;
bad:
    Py_XDECREF(py_module);
    Py_XDECREF(result);
    return NULL;
}
#endif

#ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
    PyObject *py_name = 0;
    PyObject *py_module = 0;
    py_name = __Pyx_PyIdentifier_FromString(name);
    if (!py_name)
        goto bad;
    py_module = PyImport_Import(py_name);
    Py_DECREF(py_name);
    return py_module;
bad:
    Py_XDECREF(py_name);
    return 0;
}
#endif

static void* __Pyx_GetVtable(PyObject *dict) {
    void* ptr;
    PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
    if (!ob)
        goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    ptr = PyCapsule_GetPointer(ob, 0);
#else
    ptr = PyCObject_AsVoidPtr(ob);
#endif
    if (!ptr && !PyErr_Occurred())
        PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
    Py_DECREF(ob);
    return ptr;
bad:
    Py_XDECREF(ob);
    return NULL;
}

static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    PyObject *ob = PyCapsule_New(vtable, 0, 0);
#else
    PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
#endif
    if (!ob)
        goto bad;
    if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
        goto bad;
    Py_DECREF(ob);
    return 0;
bad:
    Py_XDECREF(ob);
    return -1;
}

#ifndef __PYX_HAVE_RT_ImportFunction
#define __PYX_HAVE_RT_ImportFunction
static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    union {
        void (*fp)(void);
        void *p;
    } tmp;
    d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
    if (!d)
        goto bad;
    cobj = PyDict_GetItemString(d, funcname);
    if (!cobj) {
        PyErr_Format(PyExc_ImportError,
            "%s does not export expected C function %s",
                PyModule_GetName(module), funcname);
        goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    if (!PyCapsule_IsValid(cobj, sig)) {
        PyErr_Format(PyExc_TypeError,
            "C function %s.%s has wrong signature (expected %s, got %s)",
             PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
        goto bad;
    }
    tmp.p = PyCapsule_GetPointer(cobj, sig);
#else
    {const char *desc, *s1, *s2;
    desc = (const char *)PyCObject_GetDesc(cobj);
    if (!desc)
        goto bad;
    s1 = desc; s2 = sig;
    while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
    if (*s1 != *s2) {
        PyErr_Format(PyExc_TypeError,
            "C function %s.%s has wrong signature (expected %s, got %s)",
             PyModule_GetName(module), funcname, sig, desc);
        goto bad;
    }
    tmp.p = PyCObject_AsVoidPtr(cobj);}
#endif
    *f = tmp.fp;
    if (!(*f))
        goto bad;
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(d);
    return -1;
}
#endif

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 */
