/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 3.0.12
 *
 * This file is not intended to be easily readable and contains a number of
 * coding conventions designed to improve portability and efficiency. Do not make
 * changes to this file unless you know what you are doing--modify the SWIG
 * interface file instead.
 * ----------------------------------------------------------------------------- */


#ifndef SWIGPERL
#define SWIGPERL
#endif

#define SWIG_CASTRANK_MODE


#ifdef __cplusplus
/* SwigValueWrapper is described in swig.swg */
template<typename T> class SwigValueWrapper {
  struct SwigMovePointer {
    T *ptr;
    SwigMovePointer(T *p) : ptr(p) { }
    ~SwigMovePointer() { delete ptr; }
    SwigMovePointer& operator=(SwigMovePointer& rhs) { T* oldptr = ptr; ptr = 0; delete oldptr; ptr = rhs.ptr; rhs.ptr = 0; return *this; }
  } pointer;
  SwigValueWrapper& operator=(const SwigValueWrapper<T>& rhs);
  SwigValueWrapper(const SwigValueWrapper<T>& rhs);
public:
  SwigValueWrapper() : pointer(0) { }
  SwigValueWrapper& operator=(const T& t) { SwigMovePointer tmp(new T(t)); pointer = tmp; return *this; }
  operator T&() const { return *pointer.ptr; }
  T *operator&() { return pointer.ptr; }
};

template <typename T> T SwigValueInit() {
  return T();
}
#endif

/* -----------------------------------------------------------------------------
 *  This section contains generic SWIG labels for method/variable
 *  declarations/attributes, and other compiler dependent labels.
 * ----------------------------------------------------------------------------- */

/* template workaround for compilers that cannot correctly implement the C++ standard */
#ifndef SWIGTEMPLATEDISAMBIGUATOR
# if defined(__SUNPRO_CC) && (__SUNPRO_CC <= 0x560)
#  define SWIGTEMPLATEDISAMBIGUATOR template
# elif defined(__HP_aCC)
/* Needed even with `aCC -AA' when `aCC -V' reports HP ANSI C++ B3910B A.03.55 */
/* If we find a maximum version that requires this, the test would be __HP_aCC <= 35500 for A.03.55 */
#  define SWIGTEMPLATEDISAMBIGUATOR template
# else
#  define SWIGTEMPLATEDISAMBIGUATOR
# endif
#endif

/* inline attribute */
#ifndef SWIGINLINE
# if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__))
#   define SWIGINLINE inline
# else
#   define SWIGINLINE
# endif
#endif

/* attribute recognised by some compilers to avoid 'unused' warnings */
#ifndef SWIGUNUSED
# if defined(__GNUC__)
#   if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
#     define SWIGUNUSED __attribute__ ((__unused__))
#   else
#     define SWIGUNUSED
#   endif
# elif defined(__ICC)
#   define SWIGUNUSED __attribute__ ((__unused__))
# else
#   define SWIGUNUSED
# endif
#endif

#ifndef SWIG_MSC_UNSUPPRESS_4505
# if defined(_MSC_VER)
#   pragma warning(disable : 4505) /* unreferenced local function has been removed */
# endif
#endif

#ifndef SWIGUNUSEDPARM
# ifdef __cplusplus
#   define SWIGUNUSEDPARM(p)
# else
#   define SWIGUNUSEDPARM(p) p SWIGUNUSED
# endif
#endif

/* internal SWIG method */
#ifndef SWIGINTERN
# define SWIGINTERN static SWIGUNUSED
#endif

/* internal inline SWIG method */
#ifndef SWIGINTERNINLINE
# define SWIGINTERNINLINE SWIGINTERN SWIGINLINE
#endif

/* exporting methods */
#if defined(__GNUC__)
#  if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
#    ifndef GCC_HASCLASSVISIBILITY
#      define GCC_HASCLASSVISIBILITY
#    endif
#  endif
#endif

#ifndef SWIGEXPORT
# if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
#   if defined(STATIC_LINKED)
#     define SWIGEXPORT
#   else
#     define SWIGEXPORT __declspec(dllexport)
#   endif
# else
#   if defined(__GNUC__) && defined(GCC_HASCLASSVISIBILITY)
#     define SWIGEXPORT __attribute__ ((visibility("default")))
#   else
#     define SWIGEXPORT
#   endif
# endif
#endif

/* calling conventions for Windows */
#ifndef SWIGSTDCALL
# if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
#   define SWIGSTDCALL __stdcall
# else
#   define SWIGSTDCALL
# endif
#endif

/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE)
# define _CRT_SECURE_NO_DEPRECATE
#endif

/* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */
#if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE)
# define _SCL_SECURE_NO_DEPRECATE
#endif

/* Deal with Apple's deprecated 'AssertMacros.h' from Carbon-framework */
#if defined(__APPLE__) && !defined(__ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES)
# define __ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES 0
#endif

/* Intel's compiler complains if a variable which was never initialised is
 * cast to void, which is a common idiom which we use to indicate that we
 * are aware a variable isn't used.  So we just silence that warning.
 * See: https://github.com/swig/swig/issues/192 for more discussion.
 */
#ifdef __INTEL_COMPILER
# pragma warning disable 592
#endif

/* -----------------------------------------------------------------------------
 * swigrun.swg
 *
 * This file contains generic C API SWIG runtime support for pointer
 * type checking.
 * ----------------------------------------------------------------------------- */

/* This should only be incremented when either the layout of swig_type_info changes,
   or for whatever reason, the runtime changes incompatibly */
#define SWIG_RUNTIME_VERSION "4"

/* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */
#ifdef SWIG_TYPE_TABLE
# define SWIG_QUOTE_STRING(x) #x
# define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x)
# define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE)
#else
# define SWIG_TYPE_TABLE_NAME
#endif

/*
  You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for
  creating a static or dynamic library from the SWIG runtime code.
  In 99.9% of the cases, SWIG just needs to declare them as 'static'.

  But only do this if strictly necessary, ie, if you have problems
  with your compiler or suchlike.
*/

#ifndef SWIGRUNTIME
# define SWIGRUNTIME SWIGINTERN
#endif

#ifndef SWIGRUNTIMEINLINE
# define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE
#endif

/*  Generic buffer size */
#ifndef SWIG_BUFFER_SIZE
# define SWIG_BUFFER_SIZE 1024
#endif

/* Flags for pointer conversions */
#define SWIG_POINTER_DISOWN        0x1
#define SWIG_CAST_NEW_MEMORY       0x2

/* Flags for new pointer objects */
#define SWIG_POINTER_OWN           0x1


/*
   Flags/methods for returning states.

   The SWIG conversion methods, as ConvertPtr, return an integer
   that tells if the conversion was successful or not. And if not,
   an error code can be returned (see swigerrors.swg for the codes).

   Use the following macros/flags to set or process the returning
   states.

   In old versions of SWIG, code such as the following was usually written:

     if (SWIG_ConvertPtr(obj,vptr,ty.flags) != -1) {
       // success code
     } else {
       //fail code
     }

   Now you can be more explicit:

    int res = SWIG_ConvertPtr(obj,vptr,ty.flags);
    if (SWIG_IsOK(res)) {
      // success code
    } else {
      // fail code
    }

   which is the same really, but now you can also do

    Type *ptr;
    int res = SWIG_ConvertPtr(obj,(void **)(&ptr),ty.flags);
    if (SWIG_IsOK(res)) {
      // success code
      if (SWIG_IsNewObj(res) {
        ...
	delete *ptr;
      } else {
        ...
      }
    } else {
      // fail code
    }

   I.e., now SWIG_ConvertPtr can return new objects and you can
   identify the case and take care of the deallocation. Of course that
   also requires SWIG_ConvertPtr to return new result values, such as

      int SWIG_ConvertPtr(obj, ptr,...) {
        if (<obj is ok>) {
          if (<need new object>) {
            *ptr = <ptr to new allocated object>;
            return SWIG_NEWOBJ;
          } else {
            *ptr = <ptr to old object>;
            return SWIG_OLDOBJ;
          }
        } else {
          return SWIG_BADOBJ;
        }
      }

   Of course, returning the plain '0(success)/-1(fail)' still works, but you can be
   more explicit by returning SWIG_BADOBJ, SWIG_ERROR or any of the
   SWIG errors code.

   Finally, if the SWIG_CASTRANK_MODE is enabled, the result code
   allows to return the 'cast rank', for example, if you have this

       int food(double)
       int fooi(int);

   and you call

      food(1)   // cast rank '1'  (1 -> 1.0)
      fooi(1)   // cast rank '0'

   just use the SWIG_AddCast()/SWIG_CheckState()
*/

#define SWIG_OK                    (0)
#define SWIG_ERROR                 (-1)
#define SWIG_IsOK(r)               (r >= 0)
#define SWIG_ArgError(r)           ((r != SWIG_ERROR) ? r : SWIG_TypeError)

/* The CastRankLimit says how many bits are used for the cast rank */
#define SWIG_CASTRANKLIMIT         (1 << 8)
/* The NewMask denotes the object was created (using new/malloc) */
#define SWIG_NEWOBJMASK            (SWIG_CASTRANKLIMIT  << 1)
/* The TmpMask is for in/out typemaps that use temporal objects */
#define SWIG_TMPOBJMASK            (SWIG_NEWOBJMASK << 1)
/* Simple returning values */
#define SWIG_BADOBJ                (SWIG_ERROR)
#define SWIG_OLDOBJ                (SWIG_OK)
#define SWIG_NEWOBJ                (SWIG_OK | SWIG_NEWOBJMASK)
#define SWIG_TMPOBJ                (SWIG_OK | SWIG_TMPOBJMASK)
/* Check, add and del mask methods */
#define SWIG_AddNewMask(r)         (SWIG_IsOK(r) ? (r | SWIG_NEWOBJMASK) : r)
#define SWIG_DelNewMask(r)         (SWIG_IsOK(r) ? (r & ~SWIG_NEWOBJMASK) : r)
#define SWIG_IsNewObj(r)           (SWIG_IsOK(r) && (r & SWIG_NEWOBJMASK))
#define SWIG_AddTmpMask(r)         (SWIG_IsOK(r) ? (r | SWIG_TMPOBJMASK) : r)
#define SWIG_DelTmpMask(r)         (SWIG_IsOK(r) ? (r & ~SWIG_TMPOBJMASK) : r)
#define SWIG_IsTmpObj(r)           (SWIG_IsOK(r) && (r & SWIG_TMPOBJMASK))

/* Cast-Rank Mode */
#if defined(SWIG_CASTRANK_MODE)
#  ifndef SWIG_TypeRank
#    define SWIG_TypeRank             unsigned long
#  endif
#  ifndef SWIG_MAXCASTRANK            /* Default cast allowed */
#    define SWIG_MAXCASTRANK          (2)
#  endif
#  define SWIG_CASTRANKMASK          ((SWIG_CASTRANKLIMIT) -1)
#  define SWIG_CastRank(r)           (r & SWIG_CASTRANKMASK)
SWIGINTERNINLINE int SWIG_AddCast(int r) {
  return SWIG_IsOK(r) ? ((SWIG_CastRank(r) < SWIG_MAXCASTRANK) ? (r + 1) : SWIG_ERROR) : r;
}
SWIGINTERNINLINE int SWIG_CheckState(int r) {
  return SWIG_IsOK(r) ? SWIG_CastRank(r) + 1 : 0;
}
#else /* no cast-rank mode */
#  define SWIG_AddCast(r) (r)
#  define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0)
#endif


#include <string.h>

#ifdef __cplusplus
extern "C" {
#endif

typedef void *(*swig_converter_func)(void *, int *);
typedef struct swig_type_info *(*swig_dycast_func)(void **);

/* Structure to store information on one type */
typedef struct swig_type_info {
  const char             *name;			/* mangled name of this type */
  const char             *str;			/* human readable name of this type */
  swig_dycast_func        dcast;		/* dynamic cast function down a hierarchy */
  struct swig_cast_info  *cast;			/* linked list of types that can cast into this type */
  void                   *clientdata;		/* language specific type data */
  int                    owndata;		/* flag if the structure owns the clientdata */
} swig_type_info;

/* Structure to store a type and conversion function used for casting */
typedef struct swig_cast_info {
  swig_type_info         *type;			/* pointer to type that is equivalent to this type */
  swig_converter_func     converter;		/* function to cast the void pointers */
  struct swig_cast_info  *next;			/* pointer to next cast in linked list */
  struct swig_cast_info  *prev;			/* pointer to the previous cast */
} swig_cast_info;

/* Structure used to store module information
 * Each module generates one structure like this, and the runtime collects
 * all of these structures and stores them in a circularly linked list.*/
typedef struct swig_module_info {
  swig_type_info         **types;		/* Array of pointers to swig_type_info structures that are in this module */
  size_t                 size;		        /* Number of types in this module */
  struct swig_module_info *next;		/* Pointer to next element in circularly linked list */
  swig_type_info         **type_initial;	/* Array of initially generated type structures */
  swig_cast_info         **cast_initial;	/* Array of initially generated casting structures */
  void                    *clientdata;		/* Language specific module data */
} swig_module_info;

/*
  Compare two type names skipping the space characters, therefore
  "char*" == "char *" and "Class<int>" == "Class<int >", etc.

  Return 0 when the two name types are equivalent, as in
  strncmp, but skipping ' '.
*/
SWIGRUNTIME int
SWIG_TypeNameComp(const char *f1, const char *l1,
		  const char *f2, const char *l2) {
  for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) {
    while ((*f1 == ' ') && (f1 != l1)) ++f1;
    while ((*f2 == ' ') && (f2 != l2)) ++f2;
    if (*f1 != *f2) return (*f1 > *f2) ? 1 : -1;
  }
  return (int)((l1 - f1) - (l2 - f2));
}

/*
  Check type equivalence in a name list like <name1>|<name2>|...
  Return 0 if equal, -1 if nb < tb, 1 if nb > tb
*/
SWIGRUNTIME int
SWIG_TypeCmp(const char *nb, const char *tb) {
  int equiv = 1;
  const char* te = tb + strlen(tb);
  const char* ne = nb;
  while (equiv != 0 && *ne) {
    for (nb = ne; *ne; ++ne) {
      if (*ne == '|') break;
    }
    equiv = SWIG_TypeNameComp(nb, ne, tb, te);
    if (*ne) ++ne;
  }
  return equiv;
}

/*
  Check type equivalence in a name list like <name1>|<name2>|...
  Return 0 if not equal, 1 if equal
*/
SWIGRUNTIME int
SWIG_TypeEquiv(const char *nb, const char *tb) {
  return SWIG_TypeCmp(nb, tb) == 0 ? 1 : 0;
}

/*
  Check the typename
*/
SWIGRUNTIME swig_cast_info *
SWIG_TypeCheck(const char *c, swig_type_info *ty) {
  if (ty) {
    swig_cast_info *iter = ty->cast;
    while (iter) {
      if (strcmp(iter->type->name, c) == 0) {
        if (iter == ty->cast)
          return iter;
        /* Move iter to the top of the linked list */
        iter->prev->next = iter->next;
        if (iter->next)
          iter->next->prev = iter->prev;
        iter->next = ty->cast;
        iter->prev = 0;
        if (ty->cast) ty->cast->prev = iter;
        ty->cast = iter;
        return iter;
      }
      iter = iter->next;
    }
  }
  return 0;
}

/*
  Identical to SWIG_TypeCheck, except strcmp is replaced with a pointer comparison
*/
SWIGRUNTIME swig_cast_info *
SWIG_TypeCheckStruct(swig_type_info *from, swig_type_info *ty) {
  if (ty) {
    swig_cast_info *iter = ty->cast;
    while (iter) {
      if (iter->type == from) {
        if (iter == ty->cast)
          return iter;
        /* Move iter to the top of the linked list */
        iter->prev->next = iter->next;
        if (iter->next)
          iter->next->prev = iter->prev;
        iter->next = ty->cast;
        iter->prev = 0;
        if (ty->cast) ty->cast->prev = iter;
        ty->cast = iter;
        return iter;
      }
      iter = iter->next;
    }
  }
  return 0;
}

/*
  Cast a pointer up an inheritance hierarchy
*/
SWIGRUNTIMEINLINE void *
SWIG_TypeCast(swig_cast_info *ty, void *ptr, int *newmemory) {
  return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr, newmemory);
}

/*
   Dynamic pointer casting. Down an inheritance hierarchy
*/
SWIGRUNTIME swig_type_info *
SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) {
  swig_type_info *lastty = ty;
  if (!ty || !ty->dcast) return ty;
  while (ty && (ty->dcast)) {
    ty = (*ty->dcast)(ptr);
    if (ty) lastty = ty;
  }
  return lastty;
}

/*
  Return the name associated with this type
*/
SWIGRUNTIMEINLINE const char *
SWIG_TypeName(const swig_type_info *ty) {
  return ty->name;
}

/*
  Return the pretty name associated with this type,
  that is an unmangled type name in a form presentable to the user.
*/
SWIGRUNTIME const char *
SWIG_TypePrettyName(const swig_type_info *type) {
  /* The "str" field contains the equivalent pretty names of the
     type, separated by vertical-bar characters.  We choose
     to print the last name, as it is often (?) the most
     specific. */
  if (!type) return NULL;
  if (type->str != NULL) {
    const char *last_name = type->str;
    const char *s;
    for (s = type->str; *s; s++)
      if (*s == '|') last_name = s+1;
    return last_name;
  }
  else
    return type->name;
}

/*
   Set the clientdata field for a type
*/
SWIGRUNTIME void
SWIG_TypeClientData(swig_type_info *ti, void *clientdata) {
  swig_cast_info *cast = ti->cast;
  /* if (ti->clientdata == clientdata) return; */
  ti->clientdata = clientdata;

  while (cast) {
    if (!cast->converter) {
      swig_type_info *tc = cast->type;
      if (!tc->clientdata) {
	SWIG_TypeClientData(tc, clientdata);
      }
    }
    cast = cast->next;
  }
}
SWIGRUNTIME void
SWIG_TypeNewClientData(swig_type_info *ti, void *clientdata) {
  SWIG_TypeClientData(ti, clientdata);
  ti->owndata = 1;
}

/*
  Search for a swig_type_info structure only by mangled name
  Search is a O(log #types)

  We start searching at module start, and finish searching when start == end.
  Note: if start == end at the beginning of the function, we go all the way around
  the circular list.
*/
SWIGRUNTIME swig_type_info *
SWIG_MangledTypeQueryModule(swig_module_info *start,
                            swig_module_info *end,
		            const char *name) {
  swig_module_info *iter = start;
  do {
    if (iter->size) {
      size_t l = 0;
      size_t r = iter->size - 1;
      do {
	/* since l+r >= 0, we can (>> 1) instead (/ 2) */
	size_t i = (l + r) >> 1;
	const char *iname = iter->types[i]->name;
	if (iname) {
	  int compare = strcmp(name, iname);
	  if (compare == 0) {
	    return iter->types[i];
	  } else if (compare < 0) {
	    if (i) {
	      r = i - 1;
	    } else {
	      break;
	    }
	  } else if (compare > 0) {
	    l = i + 1;
	  }
	} else {
	  break; /* should never happen */
	}
      } while (l <= r);
    }
    iter = iter->next;
  } while (iter != end);
  return 0;
}

/*
  Search for a swig_type_info structure for either a mangled name or a human readable name.
  It first searches the mangled names of the types, which is a O(log #types)
  If a type is not found it then searches the human readable names, which is O(#types).

  We start searching at module start, and finish searching when start == end.
  Note: if start == end at the beginning of the function, we go all the way around
  the circular list.
*/
SWIGRUNTIME swig_type_info *
SWIG_TypeQueryModule(swig_module_info *start,
                     swig_module_info *end,
		     const char *name) {
  /* STEP 1: Search the name field using binary search */
  swig_type_info *ret = SWIG_MangledTypeQueryModule(start, end, name);
  if (ret) {
    return ret;
  } else {
    /* STEP 2: If the type hasn't been found, do a complete search
       of the str field (the human readable name) */
    swig_module_info *iter = start;
    do {
      size_t i = 0;
      for (; i < iter->size; ++i) {
	if (iter->types[i]->str && (SWIG_TypeEquiv(iter->types[i]->str, name)))
	  return iter->types[i];
      }
      iter = iter->next;
    } while (iter != end);
  }

  /* neither found a match */
  return 0;
}

/*
   Pack binary data into a string
*/
SWIGRUNTIME char *
SWIG_PackData(char *c, void *ptr, size_t sz) {
  static const char hex[17] = "0123456789abcdef";
  const unsigned char *u = (unsigned char *) ptr;
  const unsigned char *eu =  u + sz;
  for (; u != eu; ++u) {
    unsigned char uu = *u;
    *(c++) = hex[(uu & 0xf0) >> 4];
    *(c++) = hex[uu & 0xf];
  }
  return c;
}

/*
   Unpack binary data from a string
*/
SWIGRUNTIME const char *
SWIG_UnpackData(const char *c, void *ptr, size_t sz) {
  unsigned char *u = (unsigned char *) ptr;
  const unsigned char *eu = u + sz;
  for (; u != eu; ++u) {
    char d = *(c++);
    unsigned char uu;
    if ((d >= '0') && (d <= '9'))
      uu = (unsigned char)((d - '0') << 4);
    else if ((d >= 'a') && (d <= 'f'))
      uu = (unsigned char)((d - ('a'-10)) << 4);
    else
      return (char *) 0;
    d = *(c++);
    if ((d >= '0') && (d <= '9'))
      uu |= (unsigned char)(d - '0');
    else if ((d >= 'a') && (d <= 'f'))
      uu |= (unsigned char)(d - ('a'-10));
    else
      return (char *) 0;
    *u = uu;
  }
  return c;
}

/*
   Pack 'void *' into a string buffer.
*/
SWIGRUNTIME char *
SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) {
  char *r = buff;
  if ((2*sizeof(void *) + 2) > bsz) return 0;
  *(r++) = '_';
  r = SWIG_PackData(r,&ptr,sizeof(void *));
  if (strlen(name) + 1 > (bsz - (r - buff))) return 0;
  strcpy(r,name);
  return buff;
}

SWIGRUNTIME const char *
SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) {
  if (*c != '_') {
    if (strcmp(c,"NULL") == 0) {
      *ptr = (void *) 0;
      return name;
    } else {
      return 0;
    }
  }
  return SWIG_UnpackData(++c,ptr,sizeof(void *));
}

SWIGRUNTIME char *
SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) {
  char *r = buff;
  size_t lname = (name ? strlen(name) : 0);
  if ((2*sz + 2 + lname) > bsz) return 0;
  *(r++) = '_';
  r = SWIG_PackData(r,ptr,sz);
  if (lname) {
    strncpy(r,name,lname+1);
  } else {
    *r = 0;
  }
  return buff;
}

SWIGRUNTIME const char *
SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) {
  if (*c != '_') {
    if (strcmp(c,"NULL") == 0) {
      memset(ptr,0,sz);
      return name;
    } else {
      return 0;
    }
  }
  return SWIG_UnpackData(++c,ptr,sz);
}

#ifdef __cplusplus
}
#endif

/*  Errors in SWIG */
#define  SWIG_UnknownError    	   -1
#define  SWIG_IOError        	   -2
#define  SWIG_RuntimeError   	   -3
#define  SWIG_IndexError     	   -4
#define  SWIG_TypeError      	   -5
#define  SWIG_DivisionByZero 	   -6
#define  SWIG_OverflowError  	   -7
#define  SWIG_SyntaxError    	   -8
#define  SWIG_ValueError     	   -9
#define  SWIG_SystemError    	   -10
#define  SWIG_AttributeError 	   -11
#define  SWIG_MemoryError    	   -12
#define  SWIG_NullReferenceError   -13



#ifdef __cplusplus
/* Needed on some windows machines---since MS plays funny games with the header files under C++ */
#include <math.h>
#include <stdlib.h>
extern "C" {
#endif
#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

/* Add in functionality missing in older versions of Perl. Much of this is based on Devel-PPPort on cpan. */

/* Add PERL_REVISION, PERL_VERSION, PERL_SUBVERSION if missing */
#ifndef PERL_REVISION
#  if !defined(__PATCHLEVEL_H_INCLUDED__) && !(defined(PATCHLEVEL) && defined(SUBVERSION))
#    define PERL_PATCHLEVEL_H_IMPLICIT
#    include <patchlevel.h>
#  endif
#  if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL)))
#    include <could_not_find_Perl_patchlevel.h>
#  endif
#  ifndef PERL_REVISION
#    define PERL_REVISION       (5)
#    define PERL_VERSION        PATCHLEVEL
#    define PERL_SUBVERSION     SUBVERSION
#  endif
#endif

#if defined(WIN32) && defined(PERL_OBJECT) && !defined(PerlIO_exportFILE)
#define PerlIO_exportFILE(fh,fl) (FILE*)(fh)
#endif

#ifndef SvIOK_UV
# define SvIOK_UV(sv)       (SvIOK(sv) && (SvUVX(sv) == SvIVX(sv)))
#endif

#ifndef SvUOK
# define SvUOK(sv)           SvIOK_UV(sv)
#endif

#if ((PERL_VERSION < 4) || ((PERL_VERSION == 4) && (PERL_SUBVERSION <= 5)))
#  define PL_sv_undef               sv_undef
#  define PL_na	                    na
#  define PL_errgv                  errgv
#  define PL_sv_no                  sv_no
#  define PL_sv_yes                 sv_yes
#  define PL_markstack_ptr          markstack_ptr
#endif

#ifndef IVSIZE
#  ifdef LONGSIZE
#    define IVSIZE LONGSIZE
#  else
#    define IVSIZE 4 /* A bold guess, but the best we can make. */
#  endif
#endif

#ifndef INT2PTR
#  if (IVSIZE == PTRSIZE) && (UVSIZE == PTRSIZE)
#    define PTRV                  UV
#    define INT2PTR(any,d)        (any)(d)
#  else
#    if PTRSIZE == LONGSIZE
#      define PTRV                unsigned long
#    else
#      define PTRV                unsigned
#    endif
#    define INT2PTR(any,d)        (any)(PTRV)(d)
#  endif

#  define NUM2PTR(any,d)  (any)(PTRV)(d)
#  define PTR2IV(p)       INT2PTR(IV,p)
#  define PTR2UV(p)       INT2PTR(UV,p)
#  define PTR2NV(p)       NUM2PTR(NV,p)

#  if PTRSIZE == LONGSIZE
#    define PTR2ul(p)     (unsigned long)(p)
#  else
#    define PTR2ul(p)     INT2PTR(unsigned long,p)
#  endif
#endif /* !INT2PTR */

#ifndef SvPV_nolen
# define SvPV_nolen(x) SvPV(x,PL_na)
#endif

#ifndef get_sv
#  define get_sv perl_get_sv
#endif

#ifndef ERRSV
#  define ERRSV get_sv("@",FALSE)
#endif

#ifndef pTHX_
#define pTHX_
#endif   

#include <string.h>
#ifdef __cplusplus
}
#endif

/* -----------------------------------------------------------------------------
 * error manipulation
 * ----------------------------------------------------------------------------- */

SWIGINTERN const char*
SWIG_Perl_ErrorType(int code) {
  switch(code) {
  case SWIG_MemoryError:
    return "MemoryError";
  case SWIG_IOError:
    return "IOError";
  case SWIG_RuntimeError:
    return "RuntimeError";
  case SWIG_IndexError:
    return "IndexError";
  case SWIG_TypeError:
    return "TypeError";
  case SWIG_DivisionByZero:
    return "ZeroDivisionError";
  case SWIG_OverflowError:
    return "OverflowError";
  case SWIG_SyntaxError:
    return "SyntaxError";
  case SWIG_ValueError:
    return "ValueError";
  case SWIG_SystemError:
    return "SystemError";
  case SWIG_AttributeError:
    return "AttributeError";
  default:
    return "RuntimeError";
  }
}


/* -----------------------------------------------------------------------------
 * perlrun.swg
 *
 * This file contains the runtime support for Perl modules
 * and includes code for managing global variables and pointer
 * type checking.
 * ----------------------------------------------------------------------------- */

#ifdef PERL_OBJECT
#define SWIG_PERL_OBJECT_DECL CPerlObj *SWIGUNUSEDPARM(pPerl),
#define SWIG_PERL_OBJECT_CALL pPerl,
#else
#define SWIG_PERL_OBJECT_DECL
#define SWIG_PERL_OBJECT_CALL
#endif

/* Common SWIG API */

/* for raw pointers */
#define SWIG_ConvertPtr(obj, pp, type, flags)           SWIG_Perl_ConvertPtr(SWIG_PERL_OBJECT_CALL obj, pp, type, flags)
#define SWIG_ConvertPtrAndOwn(obj, pp, type, flags,own) SWIG_Perl_ConvertPtrAndOwn(SWIG_PERL_OBJECT_CALL obj, pp, type, flags, own)
#define SWIG_NewPointerObj(p, type, flags)              SWIG_Perl_NewPointerObj(SWIG_PERL_OBJECT_CALL p, type, flags)
#define swig_owntype                                    int

/* for raw packed data */
#define SWIG_ConvertPacked(obj, p, s, type)             SWIG_Perl_ConvertPacked(SWIG_PERL_OBJECT_CALL obj, p, s, type)
#define SWIG_NewPackedObj(p, s, type)	                SWIG_Perl_NewPackedObj(SWIG_PERL_OBJECT_CALL p, s, type)

/* for class or struct pointers */
#define SWIG_ConvertInstance(obj, pptr, type, flags)    SWIG_ConvertPtr(obj, pptr, type, flags)
#define SWIG_NewInstanceObj(ptr, type, flags)           SWIG_NewPointerObj(ptr, type, flags)

/* for C or C++ function pointers */
#define SWIG_ConvertFunctionPtr(obj, pptr, type)        SWIG_ConvertPtr(obj, pptr, type, 0)
#define SWIG_NewFunctionPtrObj(ptr, type)               SWIG_NewPointerObj(ptr, type, 0)

/* for C++ member pointers, ie, member methods */
#define SWIG_ConvertMember(obj, ptr, sz, ty)            SWIG_ConvertPacked(obj, ptr, sz, ty)
#define SWIG_NewMemberObj(ptr, sz, type)                SWIG_NewPackedObj(ptr, sz, type)


/* Runtime API */

#define SWIG_GetModule(clientdata)                      SWIG_Perl_GetModule(clientdata)
#define SWIG_SetModule(clientdata, pointer)             SWIG_Perl_SetModule(pointer)


/* Error manipulation */

#define SWIG_ErrorType(code)                            SWIG_Perl_ErrorType(code)               
#define SWIG_Error(code, msg)            		sv_setpvf(get_sv("@", GV_ADD), "%s %s", SWIG_ErrorType(code), msg)
#define SWIG_fail                        		goto fail						    

/* Perl-specific SWIG API */

#define SWIG_MakePtr(sv, ptr, type, flags)              SWIG_Perl_MakePtr(SWIG_PERL_OBJECT_CALL sv, ptr, type, flags)
#define SWIG_MakePackedObj(sv, p, s, type)	        SWIG_Perl_MakePackedObj(SWIG_PERL_OBJECT_CALL sv, p, s, type)
#define SWIG_SetError(str)                              SWIG_Error(SWIG_RuntimeError, str)


#define SWIG_PERL_DECL_ARGS_1(arg1)                     (SWIG_PERL_OBJECT_DECL arg1)
#define SWIG_PERL_CALL_ARGS_1(arg1)                     (SWIG_PERL_OBJECT_CALL arg1)
#define SWIG_PERL_DECL_ARGS_2(arg1, arg2)               (SWIG_PERL_OBJECT_DECL arg1, arg2)
#define SWIG_PERL_CALL_ARGS_2(arg1, arg2)               (SWIG_PERL_OBJECT_CALL arg1, arg2)

/* -----------------------------------------------------------------------------
 * pointers/data manipulation
 * ----------------------------------------------------------------------------- */

/* For backward compatibility only */
#define SWIG_POINTER_EXCEPTION  0

#ifdef __cplusplus
extern "C" {
#endif

#define SWIG_OWNER   SWIG_POINTER_OWN
#define SWIG_SHADOW  SWIG_OWNER << 1

#define SWIG_MAYBE_PERL_OBJECT SWIG_PERL_OBJECT_DECL

/* SWIG Perl macros */

/* Macro to declare an XS function */
#ifndef XSPROTO
#   define XSPROTO(name) void name(pTHX_ CV* cv)
#endif

/* Macro to call an XS function */
#ifdef PERL_OBJECT 
#  define SWIG_CALLXS(_name) _name(cv,pPerl) 
#else 
#  ifndef MULTIPLICITY 
#    define SWIG_CALLXS(_name) _name(cv) 
#  else 
#    define SWIG_CALLXS(_name) _name(PERL_GET_THX, cv) 
#  endif 
#endif 

#ifdef PERL_OBJECT
#define MAGIC_PPERL  CPerlObj *pPerl = (CPerlObj *) this;

#ifdef __cplusplus
extern "C" {
#endif
typedef int (CPerlObj::*SwigMagicFunc)(SV *, MAGIC *);
#ifdef __cplusplus
}
#endif

#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b)
#define SWIGCLASS_STATIC

#else /* PERL_OBJECT */

#define MAGIC_PPERL
#define SWIGCLASS_STATIC static SWIGUNUSED

#ifndef MULTIPLICITY
#define SWIG_MAGIC(a,b) (SV *a, MAGIC *b)

#ifdef __cplusplus
extern "C" {
#endif
typedef int (*SwigMagicFunc)(SV *, MAGIC *);
#ifdef __cplusplus
}
#endif

#else /* MULTIPLICITY */

#define SWIG_MAGIC(a,b) (struct interpreter *interp, SV *a, MAGIC *b)

#ifdef __cplusplus
extern "C" {
#endif
typedef int (*SwigMagicFunc)(struct interpreter *, SV *, MAGIC *);
#ifdef __cplusplus
}
#endif

#endif /* MULTIPLICITY */
#endif /* PERL_OBJECT */

#  ifdef PERL_OBJECT
#    define SWIG_croak_null() SWIG_Perl_croak_null(pPerl)
static void SWIGUNUSED SWIG_Perl_croak_null(CPerlObj *pPerl)
#  else
static void SWIGUNUSED SWIG_croak_null()
#  endif
{
  SV *err = get_sv("@", GV_ADD);
#  if (PERL_VERSION < 6)
  croak("%_", err);
#  else
  if (sv_isobject(err))
    croak(0);
  else
    croak("%s", SvPV_nolen(err));
#  endif
}


/* 
   Define how strict is the cast between strings and integers/doubles
   when overloading between these types occurs.
   
   The default is making it as strict as possible by using SWIG_AddCast
   when needed.
   
   You can use -DSWIG_PERL_NO_STRICT_STR2NUM at compilation time to
   disable the SWIG_AddCast, making the casting between string and
   numbers less strict.

   In the end, we try to solve the overloading between strings and
   numerical types in the more natural way, but if you can avoid it,
   well, avoid it using %rename, for example.
*/
#ifndef SWIG_PERL_NO_STRICT_STR2NUM
# ifndef SWIG_PERL_STRICT_STR2NUM
#  define SWIG_PERL_STRICT_STR2NUM
# endif
#endif
#ifdef SWIG_PERL_STRICT_STR2NUM
/* string takes precedence */
#define SWIG_Str2NumCast(x) SWIG_AddCast(x)  
#else
/* number takes precedence */
#define SWIG_Str2NumCast(x) x
#endif



#include <stdlib.h>

SWIGRUNTIME const char *
SWIG_Perl_TypeProxyName(const swig_type_info *type) {
  if (!type) return NULL;
  if (type->clientdata != NULL) {
    return (const char*) type->clientdata;
  } 
  else {
    return type->name;
  }
}

/* Identical to SWIG_TypeCheck, except for strcmp comparison */
SWIGRUNTIME swig_cast_info *
SWIG_TypeProxyCheck(const char *c, swig_type_info *ty) {
  if (ty) {
    swig_cast_info *iter = ty->cast;
    while (iter) {
      if (strcmp(SWIG_Perl_TypeProxyName(iter->type), c) == 0) {
        if (iter == ty->cast)
          return iter;
        /* Move iter to the top of the linked list */
        iter->prev->next = iter->next;
        if (iter->next)
          iter->next->prev = iter->prev;
        iter->next = ty->cast;
        iter->prev = 0;
        if (ty->cast) ty->cast->prev = iter;
        ty->cast = iter;
        return iter;
      }
      iter = iter->next;
    }
  }
  return 0;
}

/* Function for getting a pointer value */

SWIGRUNTIME int
SWIG_Perl_ConvertPtrAndOwn(SWIG_MAYBE_PERL_OBJECT SV *sv, void **ptr, swig_type_info *_t, int flags, int *own) {
  swig_cast_info *tc;
  void *voidptr = (void *)0;
  SV *tsv = 0;

  if (own)
    *own = 0;

  /* If magical, apply more magic */
  if (SvGMAGICAL(sv))
    mg_get(sv);

  /* Check to see if this is an object */
  if (sv_isobject(sv)) {
    IV tmp = 0;
    tsv = (SV*) SvRV(sv);
    if ((SvTYPE(tsv) == SVt_PVHV)) {
      MAGIC *mg;
      if (SvMAGICAL(tsv)) {
        mg = mg_find(tsv,'P');
        if (mg) {
          sv = mg->mg_obj;
          if (sv_isobject(sv)) {
	    tsv = (SV*)SvRV(sv);
            tmp = SvIV(tsv);
          }
        }
      } else {
        return SWIG_ERROR;
      }
    } else {
      tmp = SvIV(tsv);
    }
    voidptr = INT2PTR(void *,tmp);
  } else if (! SvOK(sv)) {            /* Check for undef */
    *(ptr) = (void *) 0;
    return SWIG_OK;
  } else if (SvTYPE(sv) == SVt_RV) {  /* Check for NULL pointer */
    if (!SvROK(sv)) {
      /* In Perl 5.12 and later, SVt_RV == SVt_IV, so sv could be a valid integer value.  */
      if (SvIOK(sv)) {
        return SWIG_ERROR;
      } else {
        /* NULL pointer (reference to undef). */
        *(ptr) = (void *) 0;
        return SWIG_OK;
      }
    } else {
      return SWIG_ERROR;
    }
  } else {                            /* Don't know what it is */
    return SWIG_ERROR;
  }
  if (_t) {
    /* Now see if the types match */
    char *_c = HvNAME(SvSTASH(SvRV(sv)));
    tc = SWIG_TypeProxyCheck(_c,_t);
#ifdef SWIG_DIRECTORS
    if (!tc && !sv_derived_from(sv,SWIG_Perl_TypeProxyName(_t))) {
#else
    if (!tc) {
#endif
      return SWIG_ERROR;
    }
    {
      int newmemory = 0;
      *ptr = SWIG_TypeCast(tc,voidptr,&newmemory);
      if (newmemory == SWIG_CAST_NEW_MEMORY) {
        assert(own); /* badly formed typemap which will lead to a memory leak - it must set and use own to delete *ptr */
        if (own)
          *own = *own | SWIG_CAST_NEW_MEMORY;
      }
    }
  } else {
    *ptr = voidptr;
  }

  /* 
   *  DISOWN implementation: we need a perl guru to check this one.
   */
  if (tsv && (flags & SWIG_POINTER_DISOWN)) {
    /* 
     *  almost copy paste code from below SWIG_POINTER_OWN setting
     */
    SV *obj = sv;
    HV *stash = SvSTASH(SvRV(obj));
    GV *gv = *(GV**)hv_fetch(stash, "OWNER", 5, TRUE);
    if (isGV(gv)) {
      HV *hv = GvHVn(gv);
      /*
       * To set ownership (see below), a newSViv(1) entry is added. 
       * Hence, to remove ownership, we delete the entry.
       */
      if (hv_exists_ent(hv, obj, 0)) {
	hv_delete_ent(hv, obj, 0, 0);
      }
    }
  }
  return SWIG_OK;
}

SWIGRUNTIME int
SWIG_Perl_ConvertPtr(SWIG_MAYBE_PERL_OBJECT SV *sv, void **ptr, swig_type_info *_t, int flags) {
  return SWIG_Perl_ConvertPtrAndOwn(sv, ptr, _t, flags, 0);
}

SWIGRUNTIME void
SWIG_Perl_MakePtr(SWIG_MAYBE_PERL_OBJECT SV *sv, void *ptr, swig_type_info *t, int flags) {
  if (ptr && (flags & (SWIG_SHADOW | SWIG_POINTER_OWN))) {
    SV *self;
    SV *obj=newSV(0);
    HV *hash=newHV();
    HV *stash;
    sv_setref_pv(obj, SWIG_Perl_TypeProxyName(t), ptr);
    stash=SvSTASH(SvRV(obj));
    if (flags & SWIG_POINTER_OWN) {
      HV *hv;
      GV *gv = *(GV**)hv_fetch(stash, "OWNER", 5, TRUE);
      if (!isGV(gv))
        gv_init(gv, stash, "OWNER", 5, FALSE);
      hv=GvHVn(gv);
      hv_store_ent(hv, obj, newSViv(1), 0);
    }
    sv_magic((SV *)hash, (SV *)obj, 'P', Nullch, 0);
    SvREFCNT_dec(obj);
    self=newRV_noinc((SV *)hash);
    sv_setsv(sv, self);
    SvREFCNT_dec((SV *)self);
    sv_bless(sv, stash);
  }
  else {
    sv_setref_pv(sv, SWIG_Perl_TypeProxyName(t), ptr);
  }
}

SWIGRUNTIMEINLINE SV *
SWIG_Perl_NewPointerObj(SWIG_MAYBE_PERL_OBJECT void *ptr, swig_type_info *t, int flags) {
  SV *result = sv_newmortal();
  SWIG_MakePtr(result, ptr, t, flags);
  return result;
}

SWIGRUNTIME void
SWIG_Perl_MakePackedObj(SWIG_MAYBE_PERL_OBJECT SV *sv, void *ptr, int sz, swig_type_info *type) {
  char result[1024];
  char *r = result;
  if ((2*sz + 1 + strlen(SWIG_Perl_TypeProxyName(type))) > 1000) return;
  *(r++) = '_';
  r = SWIG_PackData(r,ptr,sz);
  strcpy(r,SWIG_Perl_TypeProxyName(type));
  sv_setpv(sv, result);
}

SWIGRUNTIME SV *
SWIG_Perl_NewPackedObj(SWIG_MAYBE_PERL_OBJECT void *ptr, int sz, swig_type_info *type) {
  SV *result = sv_newmortal();
  SWIG_Perl_MakePackedObj(result, ptr, sz, type);
  return result;
}

/* Convert a packed value value */
SWIGRUNTIME int
SWIG_Perl_ConvertPacked(SWIG_MAYBE_PERL_OBJECT SV *obj, void *ptr, int sz, swig_type_info *ty) {
  swig_cast_info *tc;
  const char  *c = 0;

  if ((!obj) || (!SvOK(obj))) return SWIG_ERROR;
  c = SvPV_nolen(obj);
  /* Pointer values must start with leading underscore */
  if (*c != '_') return SWIG_ERROR;
  c++;
  c = SWIG_UnpackData(c,ptr,sz);
  if (ty) {
    tc = SWIG_TypeCheck(c,ty);
    if (!tc) return SWIG_ERROR;
  }
  return SWIG_OK;
}


/* Macros for low-level exception handling */
#define SWIG_croak(x)    { SWIG_Error(SWIG_RuntimeError, x); SWIG_fail; }


typedef XSPROTO(SwigPerlWrapper);
typedef SwigPerlWrapper *SwigPerlWrapperPtr;

/* Structure for command table */
typedef struct {
  const char         *name;
  SwigPerlWrapperPtr  wrapper;
} swig_command_info;

/* Information for constant table */

#define SWIG_INT     1
#define SWIG_FLOAT   2
#define SWIG_STRING  3
#define SWIG_POINTER 4
#define SWIG_BINARY  5

/* Constant information structure */
typedef struct swig_constant_info {
    int              type;
    const char      *name;
    long             lvalue;
    double           dvalue;
    void            *pvalue;
    swig_type_info **ptype;
} swig_constant_info;


/* Structure for variable table */
typedef struct {
  const char   *name;
  SwigMagicFunc   set;
  SwigMagicFunc   get;
  swig_type_info  **type;
} swig_variable_info;

/* Magic variable code */
#ifndef PERL_OBJECT
# ifdef __cplusplus
#  define swig_create_magic(s,a,b,c) _swig_create_magic(s,const_cast<char*>(a),b,c)
# else
#  define swig_create_magic(s,a,b,c) _swig_create_magic(s,(char*)(a),b,c)
# endif
# ifndef MULTIPLICITY
SWIGRUNTIME void _swig_create_magic(SV *sv, char *name, int (*set)(SV *, MAGIC *), int (*get)(SV *,MAGIC *)) 
# else
SWIGRUNTIME void _swig_create_magic(SV *sv, char *name, int (*set)(struct interpreter*, SV *, MAGIC *), int (*get)(struct interpreter*, SV *,MAGIC *)) 
# endif
#else
#  define swig_create_magic(s,a,b,c) _swig_create_magic(pPerl,s,a,b,c)
SWIGRUNTIME void _swig_create_magic(CPerlObj *pPerl, SV *sv, const char *name, int (CPerlObj::*set)(SV *, MAGIC *), int (CPerlObj::*get)(SV *, MAGIC *)) 
#endif
{
  MAGIC *mg;
  sv_magic(sv,sv,'U',name,strlen(name));
  mg = mg_find(sv,'U');
  mg->mg_virtual = (MGVTBL *) malloc(sizeof(MGVTBL));
  mg->mg_virtual->svt_get = (SwigMagicFunc) get;
  mg->mg_virtual->svt_set = (SwigMagicFunc) set;
  mg->mg_virtual->svt_len = 0;
  mg->mg_virtual->svt_clear = 0;
  mg->mg_virtual->svt_free = 0;
}


SWIGRUNTIME swig_module_info *
SWIG_Perl_GetModule(void *SWIGUNUSEDPARM(clientdata)) {
  static void *type_pointer = (void *)0;
  SV *pointer;

  /* first check if pointer already created */
  if (!type_pointer) {
    pointer = get_sv("swig_runtime_data::type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME, FALSE | GV_ADDMULTI);
    if (pointer && SvOK(pointer)) {
      type_pointer = INT2PTR(swig_type_info **, SvIV(pointer));
    }
  }

  return (swig_module_info *) type_pointer;
}

SWIGRUNTIME void
SWIG_Perl_SetModule(swig_module_info *module) {
  SV *pointer;

  /* create a new pointer */
  pointer = get_sv("swig_runtime_data::type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME, TRUE | GV_ADDMULTI);
  sv_setiv(pointer, PTR2IV(module));
}

#ifdef __cplusplus
}
#endif

/* Workaround perl5 global namespace pollution. Note that undefining library
 * functions like fopen will not solve the problem on all platforms as fopen
 * might be a macro on Windows but not necessarily on other operating systems. */
#ifdef do_open
  #undef do_open
#endif
#ifdef do_close
  #undef do_close
#endif
#ifdef do_exec
  #undef do_exec
#endif
#ifdef scalar
  #undef scalar
#endif
#ifdef list
  #undef list
#endif
#ifdef apply
  #undef apply
#endif
#ifdef convert
  #undef convert
#endif
#ifdef Error
  #undef Error
#endif
#ifdef form
  #undef form
#endif
#ifdef vform
  #undef vform
#endif
#ifdef LABEL
  #undef LABEL
#endif
#ifdef METHOD
  #undef METHOD
#endif
#ifdef Move
  #undef Move
#endif
#ifdef yylex
  #undef yylex
#endif
#ifdef yyparse
  #undef yyparse
#endif
#ifdef yyerror
  #undef yyerror
#endif
#ifdef invert
  #undef invert
#endif
#ifdef ref
  #undef ref
#endif
#ifdef read
  #undef read
#endif
#ifdef write
  #undef write
#endif
#ifdef eof
  #undef eof
#endif
#ifdef close
  #undef close
#endif
#ifdef rewind
  #undef rewind
#endif
#ifdef free
  #undef free
#endif
#ifdef malloc
  #undef malloc
#endif
#ifdef calloc
  #undef calloc
#endif
#ifdef Stat
  #undef Stat
#endif
#ifdef check
  #undef check
#endif
#ifdef seekdir
  #undef seekdir
#endif
#ifdef open
  #undef open
#endif
#ifdef readdir
  #undef readdir
#endif
#ifdef bind
  #undef bind
#endif
#ifdef access
  #undef access
#endif
#ifdef stat
  #undef stat
#endif
#ifdef seed
  #undef seed
#endif

#ifdef bool
  /* Leave if macro is from C99 stdbool.h */
  #ifndef __bool_true_false_are_defined
    #undef bool
  #endif
#endif




#define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0) 

#define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else 



  #define SWIG_exception(code, msg) do { SWIG_Error(code, msg); SWIG_fail;; } while(0) 


/* -------- TYPES TABLE (BEGIN) -------- */

#define SWIGTYPE_p_char swig_types[0]
#define SWIGTYPE_p_mummer__nucmer__Options swig_types[1]
#define SWIGTYPE_p_mummer__postnuc__Alignment swig_types[2]
#define SWIGTYPE_p_size_type swig_types[3]
#define SWIGTYPE_p_std__vectorT_long_t swig_types[4]
#define SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t swig_types[5]
#define SWIGTYPE_p_value_type swig_types[6]
static swig_type_info *swig_types[8];
static swig_module_info swig_module = {swig_types, 7, 0, 0, 0, 0};
#define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name)
#define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name)

/* -------- TYPES TABLE (END) -------- */

#define SWIG_init    boot_mummer

#define SWIG_name   "mummerc::boot_mummer"
#define SWIG_prefix "mummerc::"

#define SWIGVERSION 0x030012 
#define SWIG_VERSION SWIGVERSION


#define SWIG_as_voidptr(a) const_cast< void * >(static_cast< const void * >(a)) 
#define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),reinterpret_cast< void** >(a)) 


#include <stdexcept>


#ifdef __cplusplus
extern "C"
#endif
#ifndef PERL_OBJECT
#ifndef MULTIPLICITY
SWIGEXPORT void SWIG_init (CV* cv);
#else
SWIGEXPORT void SWIG_init (pTHXo_ CV* cv);
#endif
#else
SWIGEXPORT void SWIG_init (CV *cv, CPerlObj *);
#endif


#ifdef SWIGPERL
#undef seed
#endif

#include <mummer/nucmer.hpp>


#include <string>


#include <typeinfo>
#include <stdexcept>


SWIGINTERN
double SwigSvToNumber(SV* sv) {
    return SvIOK(sv) ? double(SvIVX(sv)) : SvNVX(sv);
}
SWIGINTERN
std::string SwigSvToString(SV* sv) {
    STRLEN len;
    char *ptr = SvPV(sv, len);
    return std::string(ptr, len);
}
SWIGINTERN
void SwigSvFromString(SV* sv, const std::string& s) {
    sv_setpvn(sv,s.data(),s.size());
}


#include <vector>


#include <algorithm>


#include <sstream>


#include <limits.h>
#if !defined(SWIG_NO_LLONG_MAX)
# if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__)
#   define LLONG_MAX __LONG_LONG_MAX__
#   define LLONG_MIN (-LLONG_MAX - 1LL)
#   define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL)
# endif
#endif


#include <stdlib.h>
#ifdef _MSC_VER
# ifndef strtoull
#  define strtoull _strtoui64
# endif
# ifndef strtoll
#  define strtoll _strtoi64
# endif
#endif


SWIGINTERN int
SWIG_AsVal_double SWIG_PERL_DECL_ARGS_2(SV *obj, double *val)
{
  if (SvNIOK(obj)) {
    if (val) *val = SvNV(obj);
    return SWIG_OK;
  } else if (SvIOK(obj)) {
    if (val) *val = (double) SvIV(obj);
    return SWIG_AddCast(SWIG_OK);
  } else {
    const char *nptr = SvPV_nolen(obj);
    if (nptr) {
      char *endptr;
      double v;
      errno = 0;
      v = strtod(nptr, &endptr);
      if (errno == ERANGE) {
	errno = 0;
	return SWIG_OverflowError;
      } else {
	if (*endptr == '\0') {
	  if (val) *val = v;
	  return SWIG_Str2NumCast(SWIG_OK);
	}
      }
    }
  }
  return SWIG_TypeError;
}


#include <float.h>


#include <math.h>


SWIGINTERNINLINE int
SWIG_CanCastAsInteger(double *d, double min, double max) {
  double x = *d;
  if ((min <= x && x <= max)) {
   double fx = floor(x);
   double cx = ceil(x);
   double rd =  ((x - fx) < 0.5) ? fx : cx; /* simple rint */
   if ((errno == EDOM) || (errno == ERANGE)) {
     errno = 0;
   } else {
     double summ, reps, diff;
     if (rd < x) {
       diff = x - rd;
     } else if (rd > x) {
       diff = rd - x;
     } else {
       return 1;
     }
     summ = rd + x;
     reps = diff/summ;
     if (reps < 8*DBL_EPSILON) {
       *d = rd;
       return 1;
     }
   }
  }
  return 0;
}


SWIGINTERN int
SWIG_AsVal_unsigned_SS_long SWIG_PERL_DECL_ARGS_2(SV *obj, unsigned long *val) 
{
  if (SvUOK(obj)) {
    UV v = SvUV(obj);
    if (UVSIZE <= sizeof(*val) || v <= ULONG_MAX) {
      if (val) *val = v;
      return SWIG_OK;
    }
    return SWIG_OverflowError;
  } else if (SvIOK(obj)) {
    IV v = SvIV(obj);
    if (v >= 0 && (IVSIZE <= sizeof(*val) || v <= ULONG_MAX)) {
      if (val) *val = v;
      return SWIG_OK;
    }
    return SWIG_OverflowError;
  } else {
    int dispatch = 0;
    const char *nptr = SvPV_nolen(obj);
    if (nptr) {
      char *endptr;
      unsigned long v;
      errno = 0;
      v = strtoul(nptr, &endptr,0);
      if (errno == ERANGE) {
	errno = 0;
	return SWIG_OverflowError;
      } else {
	if (*endptr == '\0') {
	  if (val) *val = v;
	  return SWIG_Str2NumCast(SWIG_OK);
	}
      }
    }
    if (!dispatch) {
      double d;
      int res = SWIG_AddCast(SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(obj,&d));
      if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, 0, ULONG_MAX)) {
	if (val) *val = (unsigned long)(d);
	return res;
      }
    }
  }
  return SWIG_TypeError;
}


SWIGINTERN int
SWIG_AsVal_unsigned_SS_int SWIG_PERL_DECL_ARGS_2(SV * obj, unsigned int *val)
{
  unsigned long v;
  int res = SWIG_AsVal_unsigned_SS_long SWIG_PERL_CALL_ARGS_2(obj, &v);
  if (SWIG_IsOK(res)) {
    if ((v > UINT_MAX)) {
      return SWIG_OverflowError;
    } else {
      if (val) *val = static_cast< unsigned int >(v);
    }
  }  
  return res;
}


SWIGINTERN int
SWIG_AsVal_long SWIG_PERL_DECL_ARGS_2(SV *obj, long* val)
{
  if (SvUOK(obj)) {
    UV v = SvUV(obj);
    if (UVSIZE < sizeof(*val) || v <= LONG_MAX) {
      if (val) *val = v;
      return SWIG_OK;
    }
    return SWIG_OverflowError;
  } else if (SvIOK(obj)) {
    IV v = SvIV(obj);
    if (IVSIZE <= sizeof(*val) || (v >= LONG_MIN && v <= LONG_MAX)) {
      if(val) *val = v;
      return SWIG_OK;
    }
    return SWIG_OverflowError;
  } else {
    int dispatch = 0;
    const char *nptr = SvPV_nolen(obj);
    if (nptr) {
      char *endptr;
      long v;
      errno = 0;
      v = strtol(nptr, &endptr,0);
      if (errno == ERANGE) {
	errno = 0;
	return SWIG_OverflowError;
      } else {
	if (*endptr == '\0') {
	  if (val) *val = v;
	  return SWIG_Str2NumCast(SWIG_OK);
	}
      }
    }
    if (!dispatch) {
      double d;
      int res = SWIG_AddCast(SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(obj,&d));
      if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, LONG_MIN, LONG_MAX)) {
	if (val) *val = (long)(d);
	return res;
      }
    }
  }
  return SWIG_TypeError;
}


SWIGINTERNINLINE SV *
SWIG_From_unsigned_SS_long  SWIG_PERL_DECL_ARGS_1(unsigned long value)
{
  SV *sv;
  if (UVSIZE >= sizeof(value) || value <= UV_MAX)
    sv = newSVuv(value);
  else
    sv = newSVpvf("%lu", value);
  return sv_2mortal(sv);
}


SWIGINTERNINLINE SV *
SWIG_From_unsigned_SS_int  SWIG_PERL_DECL_ARGS_1(unsigned int value)
{    
  return SWIG_From_unsigned_SS_long  SWIG_PERL_CALL_ARGS_1(value);
}


SWIGINTERNINLINE SV *
SWIG_From_bool  SWIG_PERL_DECL_ARGS_1(bool value)
{
  return boolSV(value);
}

SWIGINTERN long std_vector_Sl_long_Sg__pop(std::vector< long > *self){
                if (self->size() == 0)
                    throw std::out_of_range("pop from empty vector");
                long x = self->back();
                self->pop_back();
                return x;
            }

SWIGINTERNINLINE SV *
SWIG_From_long  SWIG_PERL_DECL_ARGS_1(long value)
{
  SV *sv;
  if (IVSIZE >= sizeof(value) || (value >= IV_MIN && value <= IV_MAX))
    sv = newSViv(value);
  else
    sv = newSVpvf("%ld", value);
  return sv_2mortal(sv);
}


SWIGINTERN int
SWIG_AsVal_int SWIG_PERL_DECL_ARGS_2(SV * obj, int *val)
{
  long v;
  int res = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(obj, &v);
  if (SWIG_IsOK(res)) {
    if ((v < INT_MIN || v > INT_MAX)) {
      return SWIG_OverflowError;
    } else {
      if (val) *val = static_cast< int >(v);
    }
  }  
  return res;
}

SWIGINTERN long std_vector_Sl_long_Sg__get(std::vector< long > *self,int i){
                int size = int(self->size());
                if (i>=0 && i<size)
                    return (*self)[i];
                else
                    throw std::out_of_range("vector index out of range");
            }
SWIGINTERN void std_vector_Sl_long_Sg__set(std::vector< long > *self,int i,long x){
                int size = int(self->size());
                if (i>=0 && i<size)
                    (*self)[i] = x;
                else
                    throw std::out_of_range("vector index out of range");
            }

SWIGINTERNINLINE SV *
SWIG_From_int  SWIG_PERL_DECL_ARGS_1(int value)
{    
  return SWIG_From_long  SWIG_PERL_CALL_ARGS_1(value);
}


SWIGINTERN int
SWIG_AsVal_signed_SS_char SWIG_PERL_DECL_ARGS_2(SV * obj, signed char *val)
{
  long v;
  int res = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(obj, &v);
  if (SWIG_IsOK(res)) {
    if ((v < SCHAR_MIN || v > SCHAR_MAX)) {
      return SWIG_OverflowError;
    } else {
      if (val) *val = static_cast< signed char >(v);
    }
  }  
  return res;
}


SWIGINTERNINLINE SV *
SWIG_From_signed_SS_char  SWIG_PERL_DECL_ARGS_1(signed char value)
{    
  return SWIG_From_long  SWIG_PERL_CALL_ARGS_1(value);
}


SWIGINTERNINLINE SV *
SWIG_From_double  SWIG_PERL_DECL_ARGS_1(double value)
{
  return sv_2mortal(newSVnv(value));
}

SWIGINTERN std::string mummer_postnuc_Alignment___str__(mummer::postnuc::Alignment *self){
      std::ostringstream os;
      os << *self;
      return os.str();
    }

SWIGINTERNINLINE SV *
SWIG_FromCharPtrAndSize(const char* carray, size_t size)
{
  SV *obj = sv_newmortal();
  if (carray) {
    sv_setpvn(obj, carray, size);
  } else {
    sv_setsv(obj, &PL_sv_undef);
  }
  return obj;
}


SWIGINTERNINLINE SV *
SWIG_From_std_string  SWIG_PERL_DECL_ARGS_1(const std::string& s)
{
  return SWIG_FromCharPtrAndSize(s.data(), s.size());
}

SWIGINTERN mummer::postnuc::Alignment std_vector_Sl_mummer_postnuc_Alignment_Sg__pop(std::vector< mummer::postnuc::Alignment > *self){
                if (self->size() == 0)
                    throw std::out_of_range("pop from empty vector");
                mummer::postnuc::Alignment x = self->back();
                self->pop_back();
                return x;
            }
SWIGINTERN mummer::postnuc::Alignment &std_vector_Sl_mummer_postnuc_Alignment_Sg__get(std::vector< mummer::postnuc::Alignment > *self,int i){
                int size = int(self->size());
                if (i>=0 && i<size)
                    return (*self)[i];
                else
                    throw std::out_of_range("vector index out of range");
            }
SWIGINTERN void std_vector_Sl_mummer_postnuc_Alignment_Sg__set(std::vector< mummer::postnuc::Alignment > *self,int i,mummer::postnuc::Alignment const &x){
                int size = int(self->size());
                if (i>=0 && i<size)
                    (*self)[i] = x;
                else
                    throw std::out_of_range("vector index out of range");
            }

SWIGINTERN int
SWIG_AsVal_bool SWIG_PERL_DECL_ARGS_2(SV *obj, bool* val)
{
  if (obj == &PL_sv_yes) {
    if (val) *val = true;
    return SWIG_OK;
  } else if (obj == &PL_sv_no) { 
    if (val) *val = false;
    return SWIG_OK;
  } else {
    if (val) *val = SvTRUE(obj) ? true : false;
    return SWIG_AddCast(SWIG_OK);    
  }
}


SWIGINTERN swig_type_info*
SWIG_pchar_descriptor(void)
{
  static int init = 0;
  static swig_type_info* info = 0;
  if (!init) {
    info = SWIG_TypeQuery("_p_char");
    init = 1;
  }
  return info;
}


SWIGINTERN int
SWIG_AsCharPtrAndSize(SV *obj, char** cptr, size_t* psize, int *alloc)
{
  if (SvMAGICAL(obj)) {
     SV *tmp = sv_newmortal();
     SvSetSV(tmp, obj);
     obj = tmp;
  }
  if (SvPOK(obj)) {
    STRLEN len = 0;
    char *cstr = SvPV(obj, len); 
    size_t size = len + 1;
    if (cptr)  {
      if (alloc) {
	if (*alloc == SWIG_NEWOBJ) {
	  *cptr = reinterpret_cast< char* >(memcpy(new char[size], cstr, sizeof(char)*(size)));
	} else {
	  *cptr = cstr;
	  *alloc = SWIG_OLDOBJ;
	}
      }
    }
    if (psize) *psize = size;
    return SWIG_OK;
  } else {
    swig_type_info* pchar_descriptor = SWIG_pchar_descriptor();
    if (pchar_descriptor) {
      char* vptr = 0; 
      if (SWIG_ConvertPtr(obj, (void**)&vptr, pchar_descriptor, 0) == SWIG_OK) {
	if (cptr) *cptr = vptr;
	if (psize) *psize = vptr ? (strlen(vptr) + 1) : 0;
	if (alloc) *alloc = SWIG_OLDOBJ;
	return SWIG_OK;
      }
    }
  }
  return SWIG_TypeError;
}





#if defined(LLONG_MAX) && !defined(SWIG_LONG_LONG_AVAILABLE)
#  define SWIG_LONG_LONG_AVAILABLE
#endif


#ifdef SWIG_LONG_LONG_AVAILABLE
SWIGINTERN int
SWIG_AsVal_unsigned_SS_long_SS_long SWIG_PERL_DECL_ARGS_2(SV *obj, unsigned long long *val)
{
  if (SvUOK(obj)) {
    /* pretty sure this should be conditional on
     * (UVSIZE <= sizeof(*val) || v <= ULLONG_MAX) */
    if (val) *val = SvUV(obj);
    return SWIG_OK;
  } else  if (SvIOK(obj)) {
    IV v = SvIV(obj);
    if (v >= 0 && (IVSIZE <= sizeof(*val) || v <= ULLONG_MAX)) {
      if (val) *val = v;
      return SWIG_OK;
    } else {
      return SWIG_OverflowError;
    }
  } else {
    int dispatch = 0;
    const char *nptr = SvPV_nolen(obj);
    if (nptr) {
      char *endptr;
      unsigned long long v;
      errno = 0;
      v = strtoull(nptr, &endptr,0);
      if (errno == ERANGE) {
	errno = 0;
	return SWIG_OverflowError;
      } else {
	if (*endptr == '\0') {
	  if (val) *val = v;
	  return SWIG_Str2NumCast(SWIG_OK);
	}
      }
    }
    if (!dispatch) {
      const double mant_max = 1LL << DBL_MANT_DIG;
      double d;
      int res = SWIG_AddCast(SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(obj,&d));
      if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, 0, mant_max)) {
	if (val) *val = (unsigned long long)(d);
	return res;
      }
    }
  }
  return SWIG_TypeError;
}
#endif


SWIGINTERNINLINE int
SWIG_AsVal_size_t SWIG_PERL_DECL_ARGS_2(SV * obj, size_t *val)
{
  int res = SWIG_TypeError;
#ifdef SWIG_LONG_LONG_AVAILABLE
  if (sizeof(size_t) <= sizeof(unsigned long)) {
#endif
    unsigned long v;
    res = SWIG_AsVal_unsigned_SS_long SWIG_PERL_CALL_ARGS_2(obj, val ? &v : 0);
    if (SWIG_IsOK(res) && val) *val = static_cast< size_t >(v);
#ifdef SWIG_LONG_LONG_AVAILABLE
  } else if (sizeof(size_t) <= sizeof(unsigned long long)) {
    unsigned long long v;
    res = SWIG_AsVal_unsigned_SS_long_SS_long SWIG_PERL_CALL_ARGS_2(obj, val ? &v : 0);
    if (SWIG_IsOK(res) && val) *val = static_cast< size_t >(v);
  }
#endif
  return res;
}

#ifdef __cplusplus
extern "C" {
#endif

#ifdef PERL_OBJECT
#define MAGIC_CLASS _wrap_mummer_var::
class _wrap_mummer_var : public CPerlObj {
public:
#else
#define MAGIC_CLASS
#endif
SWIGCLASS_STATIC int swig_magic_readonly(pTHX_ SV *SWIGUNUSEDPARM(sv), MAGIC *SWIGUNUSEDPARM(mg)) {
    MAGIC_PPERL
    croak("Value is read-only.");
    return 0;
}


#ifdef PERL_OBJECT
};
#endif

#ifdef __cplusplus
}
#endif

#ifdef __cplusplus
extern "C" {
#endif
XS(_wrap_new_LongVector__SWIG_0) {
  {
    unsigned int arg1 ;
    unsigned int val1 ;
    int ecode1 = 0 ;
    int argvi = 0;
    std::vector< long > *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: new_LongVector(size);");
    }
    ecode1 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1);
    if (!SWIG_IsOK(ecode1)) {
      SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_LongVector" "', argument " "1"" of type '" "unsigned int""'");
    } 
    arg1 = static_cast< unsigned int >(val1);
    result = (std::vector< long > *)new std::vector< long >(arg1);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_long_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_LongVector__SWIG_1) {
  {
    int argvi = 0;
    std::vector< long > *result = 0 ;
    dXSARGS;
    
    if ((items < 0) || (items > 0)) {
      SWIG_croak("Usage: new_LongVector();");
    }
    result = (std::vector< long > *)new std::vector< long >();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_long_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    XSRETURN(argvi);
  fail:
    SWIG_croak_null();
  }
}


XS(_wrap_new_LongVector__SWIG_2) {
  {
    unsigned int arg1 ;
    long arg2 ;
    unsigned int val1 ;
    int ecode1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    std::vector< long > *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: new_LongVector(size,value);");
    }
    ecode1 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1);
    if (!SWIG_IsOK(ecode1)) {
      SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_LongVector" "', argument " "1"" of type '" "unsigned int""'");
    } 
    arg1 = static_cast< unsigned int >(val1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "new_LongVector" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (std::vector< long > *)new std::vector< long >(arg1,arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_long_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_LongVector__SWIG_3) {
  {
    std::vector< long > *arg1 = 0 ;
    std::vector< long > temp1 ;
    std::vector< long > *v1 ;
    int argvi = 0;
    std::vector< long > *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: new_LongVector(std::vector< long > const &);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_long_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of new_LongVector. "
          "Expected an array of ""long");
        SV **tv;
        I32 len = av_len(av) + 1;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SvIOK(*tv)) {
            temp1.push_back((long)SvIVX(*tv));
          } else {
            SWIG_croak("Type error in argument 1 of "
              "new_LongVector. "
              "Expected an array of ""long");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of new_LongVector. "
          "Expected an array of ""long");
      }
    }
    result = (std::vector< long > *)new std::vector< long >((std::vector< long > const &)*arg1);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_long_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_LongVector) {
  dXSARGS;
  
  {
    unsigned long _index = 0;
    SWIG_TypeRank _rank = 0; 
    if (items == 0) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 1;
        if (_rank == _rankm) goto dispatch;
      }
    }
    if (items == 1) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), NULL);
          _v = SWIG_CheckState(res);
        }
      }
      if (!_v) goto check_2;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 2;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_2:
    
    if (items == 1) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          {
            /* wrapped vector? */
            std::vector< long >* v;
            if (SWIG_ConvertPtr(ST(0),(void **) &v, 
                SWIGTYPE_p_std__vectorT_long_t,0) != -1) {
              _v = 1;
            } else if (SvROK(ST(0))) {
              /* native sequence? */
              AV *av = (AV *)SvRV(ST(0));
              if (SvTYPE(av) == SVt_PVAV) {
                I32 len = av_len(av) + 1;
                if (len == 0) {
                  /* an empty sequence can be of any type */
                  _v = 1;
                } else {
                  /* check the first element only */
                  SV **tv = av_fetch(av, 0, 0);
                  if (SvIOK(*tv))
                  _v = 1;
                  else
                  _v = 0;
                }
              }
            } else {
              _v = 0;
            }
          }
        }
      }
      if (!_v) goto check_3;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 3;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_3:
    
    if (items == 2) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), NULL);
          _v = SWIG_CheckState(res);
        }
      }
      if (!_v) goto check_4;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      {
        {
          int res = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), NULL);
          _v = SWIG_CheckState(res);
        }
      }
      if (!_v) goto check_4;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 4;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_4:
    
  dispatch:
    switch(_index) {
    case 1:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_LongVector__SWIG_1); return;
    case 2:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_LongVector__SWIG_0); return;
    case 3:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_LongVector__SWIG_3); return;
    case 4:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_LongVector__SWIG_2); return;
    }
  }
  
  croak("No matching function for overloaded 'new_LongVector'");
  XSRETURN(0);
}


XS(_wrap_LongVector_size) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    std::vector< long > temp1 ;
    std::vector< long > *v1 ;
    int argvi = 0;
    unsigned int result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: LongVector_size(self);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_long_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of LongVector_size. "
          "Expected an array of ""long");
        SV **tv;
        I32 len = av_len(av) + 1;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SvIOK(*tv)) {
            temp1.push_back((long)SvIVX(*tv));
          } else {
            SWIG_croak("Type error in argument 1 of "
              "LongVector_size. "
              "Expected an array of ""long");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of LongVector_size. "
          "Expected an array of ""long");
      }
    }
    result = (unsigned int)((std::vector< long > const *)arg1)->size();
    ST(argvi) = SWIG_From_unsigned_SS_int  SWIG_PERL_CALL_ARGS_1(static_cast< unsigned int >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_empty) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    std::vector< long > temp1 ;
    std::vector< long > *v1 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: LongVector_empty(self);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_long_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of LongVector_empty. "
          "Expected an array of ""long");
        SV **tv;
        I32 len = av_len(av) + 1;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SvIOK(*tv)) {
            temp1.push_back((long)SvIVX(*tv));
          } else {
            SWIG_croak("Type error in argument 1 of "
              "LongVector_empty. "
              "Expected an array of ""long");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of LongVector_empty. "
          "Expected an array of ""long");
      }
    }
    result = (bool)((std::vector< long > const *)arg1)->empty();
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_clear) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: LongVector_clear(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "LongVector_clear" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    (arg1)->clear();
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_push) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: LongVector_push(self,x);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "LongVector_push" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "LongVector_push" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    (arg1)->push_back(arg2);
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_pop) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: LongVector_pop(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "LongVector_pop" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    try {
      result = (long)std_vector_Sl_long_Sg__pop(arg1);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_get) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    int arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: LongVector_get(self,i);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "LongVector_get" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "LongVector_get" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    try {
      result = (long)std_vector_Sl_long_Sg__get(arg1,arg2);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_LongVector_set) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    int arg2 ;
    long arg3 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    long val3 ;
    int ecode3 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 3) || (items > 3)) {
      SWIG_croak("Usage: LongVector_set(self,i,x);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "LongVector_set" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "LongVector_set" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    ecode3 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(2), &val3);
    if (!SWIG_IsOK(ecode3)) {
      SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "LongVector_set" "', argument " "3"" of type '" "long""'");
    } 
    arg3 = static_cast< long >(val3);
    try {
      std_vector_Sl_long_Sg__set(arg1,arg2,arg3);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = sv_newmortal();
    
    
    
    XSRETURN(argvi);
  fail:
    
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_delete_LongVector) {
  {
    std::vector< long > *arg1 = (std::vector< long > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: delete_LongVector(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_long_t, SWIG_POINTER_DISOWN |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_LongVector" "', argument " "1"" of type '" "std::vector< long > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< long > * >(argp1);
    delete arg1;
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_set_num_threads) {
  {
    int arg1 ;
    int val1 ;
    int ecode1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: set_num_threads(nb);");
    }
    ecode1 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1);
    if (!SWIG_IsOK(ecode1)) {
      SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "set_num_threads" "', argument " "1"" of type '" "int""'");
    } 
    arg1 = static_cast< int >(val1);
    mummer::set_num_threads(arg1);
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_get_num_threads) {
  {
    int argvi = 0;
    int result;
    dXSARGS;
    
    if ((items < 0) || (items > 0)) {
      SWIG_croak("Usage: get_num_threads();");
    }
    result = (int)mummer::get_num_threads();
    ST(argvi) = SWIG_From_int  SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ;
    XSRETURN(argvi);
  fail:
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_dirB_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    signed char arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    signed char val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_dirB_set(self,dirB);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_dirB_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_signed_SS_char SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_dirB_set" "', argument " "2"" of type '" "signed char""'");
    } 
    arg2 = static_cast< signed char >(val2);
    if (arg1) (arg1)->dirB = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_dirB_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    signed char result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_dirB_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_dirB_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (signed char) ((arg1)->dirB);
    ST(argvi) = SWIG_From_signed_SS_char  SWIG_PERL_CALL_ARGS_1(static_cast< signed char >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_sA_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_sA_set(self,sA);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_sA_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_sA_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->sA = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_sA_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_sA_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_sA_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->sA);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_sB_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_sB_set(self,sB);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_sB_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_sB_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->sB = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_sB_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_sB_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_sB_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->sB);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_eA_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_eA_set(self,eA);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_eA_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_eA_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->eA = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_eA_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_eA_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_eA_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->eA);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_eB_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_eB_set(self,eB);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_eB_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_eB_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->eB = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_eB_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_eB_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_eB_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->eB);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_delta_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    ::std::vector< long > *arg2 = 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    std::vector< long > temp2 ;
    std::vector< long > *v2 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_delta_set(self,delta);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_delta_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    {
      if (SWIG_ConvertPtr(ST(1),(void **) &v2, 
          SWIGTYPE_p_std__vectorT_long_t,1) != -1) {
        arg2 = v2;
      } else if (SvROK(ST(1))) {
        AV *av = (AV *)SvRV(ST(1));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 2 of Alignment_delta_set. "
          "Expected an array of ""long");
        SV **tv;
        I32 len = av_len(av) + 1;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SvIOK(*tv)) {
            temp2.push_back((long)SvIVX(*tv));
          } else {
            SWIG_croak("Type error in argument 2 of "
              "Alignment_delta_set. "
              "Expected an array of ""long");
          }
        }
        arg2 = &temp2;
      } else {
        SWIG_croak("Type error in argument 2 of Alignment_delta_set. "
          "Expected an array of ""long");
      }
    }
    if (arg1) (arg1)->delta = *arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_delta_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    ::std::vector< long > *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_delta_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_delta_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (::std::vector< long > *) & ((arg1)->delta);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_long_t, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_deltaApos_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_deltaApos_set(self,deltaApos);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_deltaApos_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_deltaApos_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->deltaApos = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_deltaApos_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_deltaApos_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_deltaApos_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->deltaApos);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_Errors_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_Errors_set(self,Errors);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_Errors_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_Errors_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->Errors = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_Errors_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_Errors_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_Errors_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->Errors);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_SimErrors_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_SimErrors_set(self,SimErrors);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_SimErrors_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_SimErrors_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->SimErrors = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_SimErrors_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_SimErrors_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_SimErrors_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->SimErrors);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_NonAlphas_set) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Alignment_NonAlphas_set(self,NonAlphas);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_NonAlphas_set" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Alignment_NonAlphas_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->NonAlphas = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_NonAlphas_get) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_NonAlphas_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_NonAlphas_get" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (long) ((arg1)->NonAlphas);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_identity) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    double result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_identity(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_identity" "', argument " "1"" of type '" "mummer::postnuc::Alignment const *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (double)((mummer::postnuc::Alignment const *)arg1)->identity();
    ST(argvi) = SWIG_From_double  SWIG_PERL_CALL_ARGS_1(static_cast< double >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_similarity) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    double result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_similarity(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_similarity" "', argument " "1"" of type '" "mummer::postnuc::Alignment const *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (double)((mummer::postnuc::Alignment const *)arg1)->similarity();
    ST(argvi) = SWIG_From_double  SWIG_PERL_CALL_ARGS_1(static_cast< double >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment_stopity) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    double result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment_stopity(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment_stopity" "', argument " "1"" of type '" "mummer::postnuc::Alignment const *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = (double)((mummer::postnuc::Alignment const *)arg1)->stopity();
    ST(argvi) = SWIG_From_double  SWIG_PERL_CALL_ARGS_1(static_cast< double >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Alignment___str__) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    std::string result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Alignment___str__(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Alignment___str__" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    result = mummer_postnuc_Alignment___str__(arg1);
    ST(argvi) = SWIG_From_std_string  SWIG_PERL_CALL_ARGS_1(static_cast< std::string >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_Alignment) {
  {
    int argvi = 0;
    mummer::postnuc::Alignment *result = 0 ;
    dXSARGS;
    
    if ((items < 0) || (items > 0)) {
      SWIG_croak("Usage: new_Alignment();");
    }
    result = (mummer::postnuc::Alignment *)new mummer::postnuc::Alignment();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__postnuc__Alignment, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    XSRETURN(argvi);
  fail:
    SWIG_croak_null();
  }
}


XS(_wrap_delete_Alignment) {
  {
    mummer::postnuc::Alignment *arg1 = (mummer::postnuc::Alignment *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: delete_Alignment(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__postnuc__Alignment, SWIG_POINTER_DISOWN |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_Alignment" "', argument " "1"" of type '" "mummer::postnuc::Alignment *""'"); 
    }
    arg1 = reinterpret_cast< mummer::postnuc::Alignment * >(argp1);
    delete arg1;
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_AlignmentVector__SWIG_0) {
  {
    unsigned int arg1 ;
    unsigned int val1 ;
    int ecode1 = 0 ;
    int argvi = 0;
    std::vector< mummer::postnuc::Alignment > *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: new_AlignmentVector(size);");
    }
    ecode1 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1);
    if (!SWIG_IsOK(ecode1)) {
      SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_AlignmentVector" "', argument " "1"" of type '" "unsigned int""'");
    } 
    arg1 = static_cast< unsigned int >(val1);
    result = (std::vector< mummer::postnuc::Alignment > *)new std::vector< mummer::postnuc::Alignment >(arg1);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_AlignmentVector__SWIG_1) {
  {
    int argvi = 0;
    std::vector< mummer::postnuc::Alignment > *result = 0 ;
    dXSARGS;
    
    if ((items < 0) || (items > 0)) {
      SWIG_croak("Usage: new_AlignmentVector();");
    }
    result = (std::vector< mummer::postnuc::Alignment > *)new std::vector< mummer::postnuc::Alignment >();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    XSRETURN(argvi);
  fail:
    SWIG_croak_null();
  }
}


XS(_wrap_new_AlignmentVector__SWIG_2) {
  {
    unsigned int arg1 ;
    mummer::postnuc::Alignment *arg2 = 0 ;
    unsigned int val1 ;
    int ecode1 = 0 ;
    void *argp2 ;
    int res2 = 0 ;
    int argvi = 0;
    std::vector< mummer::postnuc::Alignment > *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: new_AlignmentVector(size,value);");
    }
    ecode1 = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), &val1);
    if (!SWIG_IsOK(ecode1)) {
      SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_AlignmentVector" "', argument " "1"" of type '" "unsigned int""'");
    } 
    arg1 = static_cast< unsigned int >(val1);
    res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_mummer__postnuc__Alignment,  0 );
    if (!SWIG_IsOK(res2)) {
      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "new_AlignmentVector" "', argument " "2"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    if (!argp2) {
      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_AlignmentVector" "', argument " "2"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    arg2 = reinterpret_cast< mummer::postnuc::Alignment * >(argp2);
    result = (std::vector< mummer::postnuc::Alignment > *)new std::vector< mummer::postnuc::Alignment >(arg1,(mummer::postnuc::Alignment const &)*arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_AlignmentVector__SWIG_3) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = 0 ;
    std::vector< mummer::postnuc::Alignment > temp1 ;
    std::vector< mummer::postnuc::Alignment > *v1 ;
    int argvi = 0;
    std::vector< mummer::postnuc::Alignment > *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: new_AlignmentVector(std::vector< mummer::postnuc::Alignment > const &);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of new_AlignmentVector. "
          "Expected an array of " "mummer::postnuc::Alignment");
        SV **tv;
        I32 len = av_len(av) + 1;
        mummer::postnuc::Alignment* obj;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SWIG_ConvertPtr(*tv, (void **)&obj, 
              SWIGTYPE_p_mummer__postnuc__Alignment,0) != -1) {
            temp1.push_back(*obj);
          } else {
            SWIG_croak("Type error in argument 1 of "
              "new_AlignmentVector. "
              "Expected an array of " "mummer::postnuc::Alignment");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of new_AlignmentVector. "
          "Expected an array of " "mummer::postnuc::Alignment");
      }
    }
    result = (std::vector< mummer::postnuc::Alignment > *)new std::vector< mummer::postnuc::Alignment >((std::vector< mummer::postnuc::Alignment > const &)*arg1);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_AlignmentVector) {
  dXSARGS;
  
  {
    unsigned long _index = 0;
    SWIG_TypeRank _rank = 0; 
    if (items == 0) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 1;
        if (_rank == _rankm) goto dispatch;
      }
    }
    if (items == 1) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), NULL);
          _v = SWIG_CheckState(res);
        }
      }
      if (!_v) goto check_2;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 2;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_2:
    
    if (items == 1) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          {
            /* wrapped vector? */
            std::vector< mummer::postnuc::Alignment >* v;
            if (SWIG_ConvertPtr(ST(0),(void **) &v, 
                SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t,0) != -1) {
              _v = 1;
            } else if (SvROK(ST(0))) {
              /* native sequence? */
              AV *av = (AV *)SvRV(ST(0));
              if (SvTYPE(av) == SVt_PVAV) {
                I32 len = av_len(av) + 1;
                if (len == 0) {
                  /* an empty sequence can be of any type */
                  _v = 1;
                } else {
                  /* check the first element only */
                  mummer::postnuc::Alignment* obj;
                  SV **tv = av_fetch(av, 0, 0);
                  if (SWIG_ConvertPtr(*tv, (void **)&obj, 
                      SWIGTYPE_p_mummer__postnuc__Alignment,0) != -1)
                  _v = 1;
                  else
                  _v = 0;
                }
              }
            } else {
              _v = 0;
            }
          }
        }
      }
      if (!_v) goto check_3;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 3;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_3:
    
    if (items == 2) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        {
          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(0), NULL);
          _v = SWIG_CheckState(res);
        }
      }
      if (!_v) goto check_4;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      {
        void *vptr = 0;
        int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_mummer__postnuc__Alignment, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_4;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 4;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_4:
    
  dispatch:
    switch(_index) {
    case 1:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_AlignmentVector__SWIG_1); return;
    case 2:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_AlignmentVector__SWIG_0); return;
    case 3:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_AlignmentVector__SWIG_3); return;
    case 4:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_new_AlignmentVector__SWIG_2); return;
    }
  }
  
  croak("No matching function for overloaded 'new_AlignmentVector'");
  XSRETURN(0);
}


XS(_wrap_AlignmentVector_size) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    std::vector< mummer::postnuc::Alignment > temp1 ;
    std::vector< mummer::postnuc::Alignment > *v1 ;
    int argvi = 0;
    unsigned int result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: AlignmentVector_size(self);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of AlignmentVector_size. "
          "Expected an array of " "mummer::postnuc::Alignment");
        SV **tv;
        I32 len = av_len(av) + 1;
        mummer::postnuc::Alignment* obj;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SWIG_ConvertPtr(*tv, (void **)&obj, 
              SWIGTYPE_p_mummer__postnuc__Alignment,0) != -1) {
            temp1.push_back(*obj);
          } else {
            SWIG_croak("Type error in argument 1 of "
              "AlignmentVector_size. "
              "Expected an array of " "mummer::postnuc::Alignment");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of AlignmentVector_size. "
          "Expected an array of " "mummer::postnuc::Alignment");
      }
    }
    result = (unsigned int)((std::vector< mummer::postnuc::Alignment > const *)arg1)->size();
    ST(argvi) = SWIG_From_unsigned_SS_int  SWIG_PERL_CALL_ARGS_1(static_cast< unsigned int >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_empty) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    std::vector< mummer::postnuc::Alignment > temp1 ;
    std::vector< mummer::postnuc::Alignment > *v1 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: AlignmentVector_empty(self);");
    }
    {
      if (SWIG_ConvertPtr(ST(0),(void **) &v1, 
          SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t,1) != -1) {
        arg1 = v1;
      } else if (SvROK(ST(0))) {
        AV *av = (AV *)SvRV(ST(0));
        if (SvTYPE(av) != SVt_PVAV)
        SWIG_croak("Type error in argument 1 of AlignmentVector_empty. "
          "Expected an array of " "mummer::postnuc::Alignment");
        SV **tv;
        I32 len = av_len(av) + 1;
        mummer::postnuc::Alignment* obj;
        for (int i=0; i<len; i++) {
          tv = av_fetch(av, i, 0);
          if (SWIG_ConvertPtr(*tv, (void **)&obj, 
              SWIGTYPE_p_mummer__postnuc__Alignment,0) != -1) {
            temp1.push_back(*obj);
          } else {
            SWIG_croak("Type error in argument 1 of "
              "AlignmentVector_empty. "
              "Expected an array of " "mummer::postnuc::Alignment");
          }
        }
        arg1 = &temp1;
      } else {
        SWIG_croak("Type error in argument 1 of AlignmentVector_empty. "
          "Expected an array of " "mummer::postnuc::Alignment");
      }
    }
    result = (bool)((std::vector< mummer::postnuc::Alignment > const *)arg1)->empty();
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_clear) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: AlignmentVector_clear(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "AlignmentVector_clear" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    (arg1)->clear();
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_push) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    mummer::postnuc::Alignment *arg2 = 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    void *argp2 ;
    int res2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: AlignmentVector_push(self,x);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "AlignmentVector_push" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_mummer__postnuc__Alignment,  0 );
    if (!SWIG_IsOK(res2)) {
      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "AlignmentVector_push" "', argument " "2"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    if (!argp2) {
      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "AlignmentVector_push" "', argument " "2"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    arg2 = reinterpret_cast< mummer::postnuc::Alignment * >(argp2);
    (arg1)->push_back((mummer::postnuc::Alignment const &)*arg2);
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_pop) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::postnuc::Alignment result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: AlignmentVector_pop(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "AlignmentVector_pop" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    try {
      result = std_vector_Sl_mummer_postnuc_Alignment_Sg__pop(arg1);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = SWIG_NewPointerObj((new mummer::postnuc::Alignment(static_cast< const mummer::postnuc::Alignment& >(result))), SWIGTYPE_p_mummer__postnuc__Alignment, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_get) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    int arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::postnuc::Alignment *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: AlignmentVector_get(self,i);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "AlignmentVector_get" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "AlignmentVector_get" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    try {
      result = (mummer::postnuc::Alignment *) &std_vector_Sl_mummer_postnuc_Alignment_Sg__get(arg1,arg2);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__postnuc__Alignment, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_AlignmentVector_set) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    int arg2 ;
    mummer::postnuc::Alignment *arg3 = 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    void *argp3 ;
    int res3 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 3) || (items > 3)) {
      SWIG_croak("Usage: AlignmentVector_set(self,i,x);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "AlignmentVector_set" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "AlignmentVector_set" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    res3 = SWIG_ConvertPtr(ST(2), &argp3, SWIGTYPE_p_mummer__postnuc__Alignment,  0 );
    if (!SWIG_IsOK(res3)) {
      SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "AlignmentVector_set" "', argument " "3"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    if (!argp3) {
      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "AlignmentVector_set" "', argument " "3"" of type '" "mummer::postnuc::Alignment const &""'"); 
    }
    arg3 = reinterpret_cast< mummer::postnuc::Alignment * >(argp3);
    try {
      std_vector_Sl_mummer_postnuc_Alignment_Sg__set(arg1,arg2,(mummer::postnuc::Alignment const &)*arg3);
    }
    catch(std::out_of_range &_e) {
      SWIG_exception_fail(SWIG_IndexError, (&_e)->what());
    }
    
    ST(argvi) = sv_newmortal();
    
    
    
    XSRETURN(argvi);
  fail:
    
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_delete_AlignmentVector) {
  {
    std::vector< mummer::postnuc::Alignment > *arg1 = (std::vector< mummer::postnuc::Alignment > *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: delete_AlignmentVector(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, SWIG_POINTER_DISOWN |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_AlignmentVector" "', argument " "1"" of type '" "std::vector< mummer::postnuc::Alignment > *""'"); 
    }
    arg1 = reinterpret_cast< std::vector< mummer::postnuc::Alignment > * >(argp1);
    delete arg1;
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_mum) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_mum(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_mum" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->mum();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_mumcand) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_mumcand(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_mumcand" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->mumcand();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_mumreference) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_mumreference(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_mumreference" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->mumreference();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_maxmatch) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_maxmatch(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_maxmatch" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->maxmatch();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_breaklen) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_breaklen(self,l);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_breaklen" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_breaklen" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->breaklen(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_banded) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_banded(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_banded" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->banded();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_nobanded) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_nobanded(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_nobanded" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->nobanded();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_mincluster) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_mincluster(self,m);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_mincluster" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_mincluster" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->mincluster(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_diagdiff) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_diagdiff(self,d);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_diagdiff" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_diagdiff" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->diagdiff(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_diagfactor) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    double arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    double val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_diagfactor(self,f);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_diagfactor" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_diagfactor" "', argument " "2"" of type '" "double""'");
    } 
    arg2 = static_cast< double >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->diagfactor(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_extend) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_extend(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_extend" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->extend();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_noextend) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_noextend(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_noextend" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->noextend();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_forward) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_forward(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_forward" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->forward();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_maxgap) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_maxgap(self,m);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_maxgap" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_maxgap" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->maxgap(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_minmatch) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_minmatch(self,m);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_minmatch" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_minmatch" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    result = (mummer::nucmer::Options *) &(arg1)->minmatch(arg2);
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_optimize) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_optimize(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_optimize" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->optimize();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_nooptimize) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_nooptimize(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_nooptimize" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->nooptimize();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_reverse) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_reverse(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_reverse" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->reverse();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_simplify) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_simplify(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_simplify" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->simplify();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_nosimplify) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_nosimplify(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_nosimplify" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (mummer::nucmer::Options *) &(arg1)->nosimplify();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, 0 | SWIG_SHADOW); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_min_len_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    int arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_min_len_set(self,min_len);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_min_len_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_min_len_set" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    if (arg1) (arg1)->min_len = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_min_len_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    int result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_min_len_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_min_len_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (int) ((arg1)->min_len);
    ST(argvi) = SWIG_From_int  SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_fixed_separation_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_fixed_separation_set(self,fixed_separation);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_fixed_separation_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_fixed_separation_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->fixed_separation = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_fixed_separation_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_fixed_separation_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_fixed_separation_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (long) ((arg1)->fixed_separation);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_max_separation_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_max_separation_set(self,max_separation);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_max_separation_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_max_separation_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->max_separation = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_max_separation_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_max_separation_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_max_separation_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (long) ((arg1)->max_separation);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_min_output_score_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    long arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    long val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_min_output_score_set(self,min_output_score);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_min_output_score_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_long SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_min_output_score_set" "', argument " "2"" of type '" "long""'");
    } 
    arg2 = static_cast< long >(val2);
    if (arg1) (arg1)->min_output_score = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_min_output_score_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    long result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_min_output_score_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_min_output_score_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (long) ((arg1)->min_output_score);
    ST(argvi) = SWIG_From_long  SWIG_PERL_CALL_ARGS_1(static_cast< long >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_separation_factor_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    double arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    double val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_separation_factor_set(self,separation_factor);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_separation_factor_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_double SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_separation_factor_set" "', argument " "2"" of type '" "double""'");
    } 
    arg2 = static_cast< double >(val2);
    if (arg1) (arg1)->separation_factor = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_separation_factor_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    double result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_separation_factor_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_separation_factor_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (double) ((arg1)->separation_factor);
    ST(argvi) = SWIG_From_double  SWIG_PERL_CALL_ARGS_1(static_cast< double >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_use_extent_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    bool arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    bool val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_use_extent_set(self,use_extent);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_use_extent_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_bool SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_use_extent_set" "', argument " "2"" of type '" "bool""'");
    } 
    arg2 = static_cast< bool >(val2);
    if (arg1) (arg1)->use_extent = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_use_extent_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_use_extent_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_use_extent_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (bool) ((arg1)->use_extent);
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_delta_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    bool arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    bool val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_do_delta_set(self,do_delta);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_delta_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_bool SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_do_delta_set" "', argument " "2"" of type '" "bool""'");
    } 
    arg2 = static_cast< bool >(val2);
    if (arg1) (arg1)->do_delta = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_delta_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_do_delta_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_delta_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (bool) ((arg1)->do_delta);
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_extend_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    bool arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    bool val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_do_extend_set(self,do_extend);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_extend_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_bool SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_do_extend_set" "', argument " "2"" of type '" "bool""'");
    } 
    arg2 = static_cast< bool >(val2);
    if (arg1) (arg1)->do_extend = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_extend_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_do_extend_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_extend_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (bool) ((arg1)->do_extend);
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_to_seqend_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    bool arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    bool val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_to_seqend_set(self,to_seqend);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_to_seqend_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_bool SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_to_seqend_set" "', argument " "2"" of type '" "bool""'");
    } 
    arg2 = static_cast< bool >(val2);
    if (arg1) (arg1)->to_seqend = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_to_seqend_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_to_seqend_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_to_seqend_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (bool) ((arg1)->to_seqend);
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_shadows_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    bool arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    bool val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_do_shadows_set(self,do_shadows);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_shadows_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_bool SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_do_shadows_set" "', argument " "2"" of type '" "bool""'");
    } 
    arg2 = static_cast< bool >(val2);
    if (arg1) (arg1)->do_shadows = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_do_shadows_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    bool result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_do_shadows_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_do_shadows_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (bool) ((arg1)->do_shadows);
    ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_break_len_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    int arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_break_len_set(self,break_len);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_break_len_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_break_len_set" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    if (arg1) (arg1)->break_len = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_break_len_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    int result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_break_len_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_break_len_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (int) ((arg1)->break_len);
    ST(argvi) = SWIG_From_int  SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_banding_set) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    int arg2 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int val2 ;
    int ecode2 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: Options_banding_set(self,banding);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_banding_set" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2);
    if (!SWIG_IsOK(ecode2)) {
      SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "Options_banding_set" "', argument " "2"" of type '" "int""'");
    } 
    arg2 = static_cast< int >(val2);
    if (arg1) (arg1)->banding = arg2;
    ST(argvi) = sv_newmortal();
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_Options_banding_get) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    int result;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: Options_banding_get(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, 0 |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Options_banding_get" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    result = (int) ((arg1)->banding);
    ST(argvi) = SWIG_From_int  SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ;
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_new_Options) {
  {
    int argvi = 0;
    mummer::nucmer::Options *result = 0 ;
    dXSARGS;
    
    if ((items < 0) || (items > 0)) {
      SWIG_croak("Usage: new_Options();");
    }
    result = (mummer::nucmer::Options *)new mummer::nucmer::Options();
    ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_mummer__nucmer__Options, SWIG_OWNER | SWIG_SHADOW); argvi++ ;
    XSRETURN(argvi);
  fail:
    SWIG_croak_null();
  }
}


XS(_wrap_delete_Options) {
  {
    mummer::nucmer::Options *arg1 = (mummer::nucmer::Options *) 0 ;
    void *argp1 = 0 ;
    int res1 = 0 ;
    int argvi = 0;
    dXSARGS;
    
    if ((items < 1) || (items > 1)) {
      SWIG_croak("Usage: delete_Options(self);");
    }
    res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_mummer__nucmer__Options, SWIG_POINTER_DISOWN |  0 );
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_Options" "', argument " "1"" of type '" "mummer::nucmer::Options *""'"); 
    }
    arg1 = reinterpret_cast< mummer::nucmer::Options * >(argp1);
    delete arg1;
    ST(argvi) = sv_newmortal();
    
    XSRETURN(argvi);
  fail:
    
    SWIG_croak_null();
  }
}


XS(_wrap_align_sequences__SWIG_0) {
  {
    char *arg1 = (char *) 0 ;
    size_t arg2 ;
    char *arg3 = (char *) 0 ;
    size_t arg4 ;
    mummer::nucmer::Options arg5 ;
    int res1 ;
    char *buf1 = 0 ;
    size_t size1 = 0 ;
    int alloc1 = 0 ;
    int res3 ;
    char *buf3 = 0 ;
    size_t size3 = 0 ;
    int alloc3 = 0 ;
    void *argp5 ;
    int res5 = 0 ;
    int argvi = 0;
    ::std::vector< mummer::postnuc::Alignment > result;
    dXSARGS;
    
    if ((items < 3) || (items > 3)) {
      SWIG_croak("Usage: align_sequences(reference,reference_len,query,query_len,opts);");
    }
    res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, &size1, &alloc1);
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "align_sequences" "', argument " "1"" of type '" "char const *""'");
    }  
    arg1 = reinterpret_cast< char * >(buf1);
    arg2 = static_cast< size_t >(size1 - 1);
    res3 = SWIG_AsCharPtrAndSize(ST(1), &buf3, &size3, &alloc3);
    if (!SWIG_IsOK(res3)) {
      SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "align_sequences" "', argument " "3"" of type '" "char const *""'");
    }  
    arg3 = reinterpret_cast< char * >(buf3);
    arg4 = static_cast< size_t >(size3 - 1);
    {
      res5 = SWIG_ConvertPtr(ST(2), &argp5, SWIGTYPE_p_mummer__nucmer__Options,  0 );
      if (!SWIG_IsOK(res5)) {
        SWIG_exception_fail(SWIG_ArgError(res5), "in method '" "align_sequences" "', argument " "5"" of type '" "mummer::nucmer::Options""'"); 
      }  
      if (!argp5) {
        SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "align_sequences" "', argument " "5"" of type '" "mummer::nucmer::Options""'");
      } else {
        arg5 = *(reinterpret_cast< mummer::nucmer::Options * >(argp5));
      }
    }
    result = mummer::nucmer::align_sequences((char const *)arg1,arg2,(char const *)arg3,arg4,arg5);
    {
      size_t len = (&result)->size();
      SV **svs = new SV*[len];
      for (size_t i=0; i<len; i++) {
        mummer::postnuc::Alignment* ptr = new mummer::postnuc::Alignment(result[i]);
        svs[i] = sv_newmortal();
        SWIG_MakePtr(svs[i], (void*) ptr, 
          SWIGTYPE_p_mummer__postnuc__Alignment, SWIG_SHADOW|0);
      }
      AV *myav = av_make(len, svs);
      delete[] svs;
      ST(argvi) = newRV_noinc((SV*) myav);
      sv_2mortal(ST(argvi));
      argvi++;
    }
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_align_sequences__SWIG_1) {
  {
    char *arg1 = (char *) 0 ;
    size_t arg2 ;
    char *arg3 = (char *) 0 ;
    size_t arg4 ;
    int res1 ;
    char *buf1 = 0 ;
    size_t size1 = 0 ;
    int alloc1 = 0 ;
    int res3 ;
    char *buf3 = 0 ;
    size_t size3 = 0 ;
    int alloc3 = 0 ;
    int argvi = 0;
    ::std::vector< mummer::postnuc::Alignment > result;
    dXSARGS;
    
    if ((items < 2) || (items > 2)) {
      SWIG_croak("Usage: align_sequences(reference,reference_len,query,query_len);");
    }
    res1 = SWIG_AsCharPtrAndSize(ST(0), &buf1, &size1, &alloc1);
    if (!SWIG_IsOK(res1)) {
      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "align_sequences" "', argument " "1"" of type '" "char const *""'");
    }  
    arg1 = reinterpret_cast< char * >(buf1);
    arg2 = static_cast< size_t >(size1 - 1);
    res3 = SWIG_AsCharPtrAndSize(ST(1), &buf3, &size3, &alloc3);
    if (!SWIG_IsOK(res3)) {
      SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "align_sequences" "', argument " "3"" of type '" "char const *""'");
    }  
    arg3 = reinterpret_cast< char * >(buf3);
    arg4 = static_cast< size_t >(size3 - 1);
    result = mummer::nucmer::align_sequences((char const *)arg1,arg2,(char const *)arg3,arg4);
    {
      size_t len = (&result)->size();
      SV **svs = new SV*[len];
      for (size_t i=0; i<len; i++) {
        mummer::postnuc::Alignment* ptr = new mummer::postnuc::Alignment(result[i]);
        svs[i] = sv_newmortal();
        SWIG_MakePtr(svs[i], (void*) ptr, 
          SWIGTYPE_p_mummer__postnuc__Alignment, SWIG_SHADOW|0);
      }
      AV *myav = av_make(len, svs);
      delete[] svs;
      ST(argvi) = newRV_noinc((SV*) myav);
      sv_2mortal(ST(argvi));
      argvi++;
    }
    
    
    XSRETURN(argvi);
  fail:
    
    
    SWIG_croak_null();
  }
}


XS(_wrap_align_sequences) {
  dXSARGS;
  
  {
    unsigned long _index = 0;
    SWIG_TypeRank _rank = 0; 
    if (items == 2) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        int res = SWIG_AsCharPtrAndSize(ST(0), 0, NULL, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_1;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      {
        int res = SWIG_AsCharPtrAndSize(ST(1), 0, NULL, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_1;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (items > 2) {
        {
          {
            int res = SWIG_AsVal_size_t SWIG_PERL_CALL_ARGS_2(ST(2), NULL);
            _v = SWIG_CheckState(res);
          }
        }
        if (!_v) goto check_1;
        _ranki += _v*_pi;
        _rankm += _pi;
        _pi *= SWIG_MAXCASTRANK;
      }
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 1;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_1:
    
    if (items == 3) {
      SWIG_TypeRank _ranki = 0;
      SWIG_TypeRank _rankm = 0;
      SWIG_TypeRank _pi = 1;
      int _v = 0;
      {
        int res = SWIG_AsCharPtrAndSize(ST(0), 0, NULL, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_2;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      {
        int res = SWIG_AsCharPtrAndSize(ST(1), 0, NULL, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_2;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      {
        void *vptr = 0;
        int res = SWIG_ConvertPtr(ST(2), &vptr, SWIGTYPE_p_mummer__nucmer__Options, 0);
        _v = SWIG_CheckState(res);
      }
      if (!_v) goto check_2;
      _ranki += _v*_pi;
      _rankm += _pi;
      _pi *= SWIG_MAXCASTRANK;
      if (!_index || (_ranki < _rank)) {
        _rank = _ranki; _index = 2;
        if (_rank == _rankm) goto dispatch;
      }
    }
  check_2:
    
  dispatch:
    switch(_index) {
    case 1:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_align_sequences__SWIG_1); return;
    case 2:
      PUSHMARK(MARK); SWIG_CALLXS(_wrap_align_sequences__SWIG_0); return;
    }
  }
  
  croak("No matching function for overloaded 'align_sequences'");
  XSRETURN(0);
}



/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */

static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0};
static swig_type_info _swigt__p_mummer__nucmer__Options = {"_p_mummer__nucmer__Options", "mummer::nucmer::Options *", 0, 0, (void*)"mummer::Options", 0};
static swig_type_info _swigt__p_mummer__postnuc__Alignment = {"_p_mummer__postnuc__Alignment", "mummer::postnuc::Alignment *", 0, 0, (void*)"mummer::Alignment", 0};
static swig_type_info _swigt__p_size_type = {"_p_size_type", "size_type *", 0, 0, (void*)0, 0};
static swig_type_info _swigt__p_std__vectorT_long_t = {"_p_std__vectorT_long_t", "std::vector< long > *|::std::vector< long > *", 0, 0, (void*)"mummer::LongVector", 0};
static swig_type_info _swigt__p_std__vectorT_mummer__postnuc__Alignment_t = {"_p_std__vectorT_mummer__postnuc__Alignment_t", "std::vector< mummer::postnuc::Alignment > *", 0, 0, (void*)"mummer::AlignmentVector", 0};
static swig_type_info _swigt__p_value_type = {"_p_value_type", "value_type *", 0, 0, (void*)0, 0};

static swig_type_info *swig_type_initial[] = {
  &_swigt__p_char,
  &_swigt__p_mummer__nucmer__Options,
  &_swigt__p_mummer__postnuc__Alignment,
  &_swigt__p_size_type,
  &_swigt__p_std__vectorT_long_t,
  &_swigt__p_std__vectorT_mummer__postnuc__Alignment_t,
  &_swigt__p_value_type,
};

static swig_cast_info _swigc__p_char[] = {  {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_mummer__nucmer__Options[] = {  {&_swigt__p_mummer__nucmer__Options, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_mummer__postnuc__Alignment[] = {  {&_swigt__p_mummer__postnuc__Alignment, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_size_type[] = {  {&_swigt__p_size_type, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_std__vectorT_long_t[] = {  {&_swigt__p_std__vectorT_long_t, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_std__vectorT_mummer__postnuc__Alignment_t[] = {  {&_swigt__p_std__vectorT_mummer__postnuc__Alignment_t, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_value_type[] = {  {&_swigt__p_value_type, 0, 0, 0},{0, 0, 0, 0}};

static swig_cast_info *swig_cast_initial[] = {
  _swigc__p_char,
  _swigc__p_mummer__nucmer__Options,
  _swigc__p_mummer__postnuc__Alignment,
  _swigc__p_size_type,
  _swigc__p_std__vectorT_long_t,
  _swigc__p_std__vectorT_mummer__postnuc__Alignment_t,
  _swigc__p_value_type,
};


/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */

static swig_constant_info swig_constants[] = {
{0,0,0,0,0,0}
};
#ifdef __cplusplus
}
#endif
static swig_variable_info swig_variables[] = {
{0,0,0,0}
};
static swig_command_info swig_commands[] = {
{"mummerc::new_LongVector", _wrap_new_LongVector},
{"mummerc::LongVector_size", _wrap_LongVector_size},
{"mummerc::LongVector_empty", _wrap_LongVector_empty},
{"mummerc::LongVector_clear", _wrap_LongVector_clear},
{"mummerc::LongVector_push", _wrap_LongVector_push},
{"mummerc::LongVector_pop", _wrap_LongVector_pop},
{"mummerc::LongVector_get", _wrap_LongVector_get},
{"mummerc::LongVector_set", _wrap_LongVector_set},
{"mummerc::delete_LongVector", _wrap_delete_LongVector},
{"mummerc::set_num_threads", _wrap_set_num_threads},
{"mummerc::get_num_threads", _wrap_get_num_threads},
{"mummerc::Alignment_dirB_set", _wrap_Alignment_dirB_set},
{"mummerc::Alignment_dirB_get", _wrap_Alignment_dirB_get},
{"mummerc::Alignment_sA_set", _wrap_Alignment_sA_set},
{"mummerc::Alignment_sA_get", _wrap_Alignment_sA_get},
{"mummerc::Alignment_sB_set", _wrap_Alignment_sB_set},
{"mummerc::Alignment_sB_get", _wrap_Alignment_sB_get},
{"mummerc::Alignment_eA_set", _wrap_Alignment_eA_set},
{"mummerc::Alignment_eA_get", _wrap_Alignment_eA_get},
{"mummerc::Alignment_eB_set", _wrap_Alignment_eB_set},
{"mummerc::Alignment_eB_get", _wrap_Alignment_eB_get},
{"mummerc::Alignment_delta_set", _wrap_Alignment_delta_set},
{"mummerc::Alignment_delta_get", _wrap_Alignment_delta_get},
{"mummerc::Alignment_deltaApos_set", _wrap_Alignment_deltaApos_set},
{"mummerc::Alignment_deltaApos_get", _wrap_Alignment_deltaApos_get},
{"mummerc::Alignment_Errors_set", _wrap_Alignment_Errors_set},
{"mummerc::Alignment_Errors_get", _wrap_Alignment_Errors_get},
{"mummerc::Alignment_SimErrors_set", _wrap_Alignment_SimErrors_set},
{"mummerc::Alignment_SimErrors_get", _wrap_Alignment_SimErrors_get},
{"mummerc::Alignment_NonAlphas_set", _wrap_Alignment_NonAlphas_set},
{"mummerc::Alignment_NonAlphas_get", _wrap_Alignment_NonAlphas_get},
{"mummerc::Alignment_identity", _wrap_Alignment_identity},
{"mummerc::Alignment_similarity", _wrap_Alignment_similarity},
{"mummerc::Alignment_stopity", _wrap_Alignment_stopity},
{"mummerc::Alignment___str__", _wrap_Alignment___str__},
{"mummerc::new_Alignment", _wrap_new_Alignment},
{"mummerc::delete_Alignment", _wrap_delete_Alignment},
{"mummerc::new_AlignmentVector", _wrap_new_AlignmentVector},
{"mummerc::AlignmentVector_size", _wrap_AlignmentVector_size},
{"mummerc::AlignmentVector_empty", _wrap_AlignmentVector_empty},
{"mummerc::AlignmentVector_clear", _wrap_AlignmentVector_clear},
{"mummerc::AlignmentVector_push", _wrap_AlignmentVector_push},
{"mummerc::AlignmentVector_pop", _wrap_AlignmentVector_pop},
{"mummerc::AlignmentVector_get", _wrap_AlignmentVector_get},
{"mummerc::AlignmentVector_set", _wrap_AlignmentVector_set},
{"mummerc::delete_AlignmentVector", _wrap_delete_AlignmentVector},
{"mummerc::Options_mum", _wrap_Options_mum},
{"mummerc::Options_mumcand", _wrap_Options_mumcand},
{"mummerc::Options_mumreference", _wrap_Options_mumreference},
{"mummerc::Options_maxmatch", _wrap_Options_maxmatch},
{"mummerc::Options_breaklen", _wrap_Options_breaklen},
{"mummerc::Options_banded", _wrap_Options_banded},
{"mummerc::Options_nobanded", _wrap_Options_nobanded},
{"mummerc::Options_mincluster", _wrap_Options_mincluster},
{"mummerc::Options_diagdiff", _wrap_Options_diagdiff},
{"mummerc::Options_diagfactor", _wrap_Options_diagfactor},
{"mummerc::Options_extend", _wrap_Options_extend},
{"mummerc::Options_noextend", _wrap_Options_noextend},
{"mummerc::Options_forward", _wrap_Options_forward},
{"mummerc::Options_maxgap", _wrap_Options_maxgap},
{"mummerc::Options_minmatch", _wrap_Options_minmatch},
{"mummerc::Options_optimize", _wrap_Options_optimize},
{"mummerc::Options_nooptimize", _wrap_Options_nooptimize},
{"mummerc::Options_reverse", _wrap_Options_reverse},
{"mummerc::Options_simplify", _wrap_Options_simplify},
{"mummerc::Options_nosimplify", _wrap_Options_nosimplify},
{"mummerc::Options_min_len_set", _wrap_Options_min_len_set},
{"mummerc::Options_min_len_get", _wrap_Options_min_len_get},
{"mummerc::Options_fixed_separation_set", _wrap_Options_fixed_separation_set},
{"mummerc::Options_fixed_separation_get", _wrap_Options_fixed_separation_get},
{"mummerc::Options_max_separation_set", _wrap_Options_max_separation_set},
{"mummerc::Options_max_separation_get", _wrap_Options_max_separation_get},
{"mummerc::Options_min_output_score_set", _wrap_Options_min_output_score_set},
{"mummerc::Options_min_output_score_get", _wrap_Options_min_output_score_get},
{"mummerc::Options_separation_factor_set", _wrap_Options_separation_factor_set},
{"mummerc::Options_separation_factor_get", _wrap_Options_separation_factor_get},
{"mummerc::Options_use_extent_set", _wrap_Options_use_extent_set},
{"mummerc::Options_use_extent_get", _wrap_Options_use_extent_get},
{"mummerc::Options_do_delta_set", _wrap_Options_do_delta_set},
{"mummerc::Options_do_delta_get", _wrap_Options_do_delta_get},
{"mummerc::Options_do_extend_set", _wrap_Options_do_extend_set},
{"mummerc::Options_do_extend_get", _wrap_Options_do_extend_get},
{"mummerc::Options_to_seqend_set", _wrap_Options_to_seqend_set},
{"mummerc::Options_to_seqend_get", _wrap_Options_to_seqend_get},
{"mummerc::Options_do_shadows_set", _wrap_Options_do_shadows_set},
{"mummerc::Options_do_shadows_get", _wrap_Options_do_shadows_get},
{"mummerc::Options_break_len_set", _wrap_Options_break_len_set},
{"mummerc::Options_break_len_get", _wrap_Options_break_len_get},
{"mummerc::Options_banding_set", _wrap_Options_banding_set},
{"mummerc::Options_banding_get", _wrap_Options_banding_get},
{"mummerc::new_Options", _wrap_new_Options},
{"mummerc::delete_Options", _wrap_delete_Options},
{"mummerc::align_sequences", _wrap_align_sequences},
{0,0}
};
/* -----------------------------------------------------------------------------
 * Type initialization:
 * This problem is tough by the requirement that no dynamic
 * memory is used. Also, since swig_type_info structures store pointers to
 * swig_cast_info structures and swig_cast_info structures store pointers back
 * to swig_type_info structures, we need some lookup code at initialization.
 * The idea is that swig generates all the structures that are needed.
 * The runtime then collects these partially filled structures.
 * The SWIG_InitializeModule function takes these initial arrays out of
 * swig_module, and does all the lookup, filling in the swig_module.types
 * array with the correct data and linking the correct swig_cast_info
 * structures together.
 *
 * The generated swig_type_info structures are assigned statically to an initial
 * array. We just loop through that array, and handle each type individually.
 * First we lookup if this type has been already loaded, and if so, use the
 * loaded structure instead of the generated one. Then we have to fill in the
 * cast linked list. The cast data is initially stored in something like a
 * two-dimensional array. Each row corresponds to a type (there are the same
 * number of rows as there are in the swig_type_initial array). Each entry in
 * a column is one of the swig_cast_info structures for that type.
 * The cast_initial array is actually an array of arrays, because each row has
 * a variable number of columns. So to actually build the cast linked list,
 * we find the array of casts associated with the type, and loop through it
 * adding the casts to the list. The one last trick we need to do is making
 * sure the type pointer in the swig_cast_info struct is correct.
 *
 * First off, we lookup the cast->type name to see if it is already loaded.
 * There are three cases to handle:
 *  1) If the cast->type has already been loaded AND the type we are adding
 *     casting info to has not been loaded (it is in this module), THEN we
 *     replace the cast->type pointer with the type pointer that has already
 *     been loaded.
 *  2) If BOTH types (the one we are adding casting info to, and the
 *     cast->type) are loaded, THEN the cast info has already been loaded by
 *     the previous module so we just ignore it.
 *  3) Finally, if cast->type has not already been loaded, then we add that
 *     swig_cast_info to the linked list (because the cast->type) pointer will
 *     be correct.
 * ----------------------------------------------------------------------------- */

#ifdef __cplusplus
extern "C" {
#if 0
} /* c-mode */
#endif
#endif

#if 0
#define SWIGRUNTIME_DEBUG
#endif


SWIGRUNTIME void
SWIG_InitializeModule(void *clientdata) {
  size_t i;
  swig_module_info *module_head, *iter;
  int init;
  
  /* check to see if the circular list has been setup, if not, set it up */
  if (swig_module.next==0) {
    /* Initialize the swig_module */
    swig_module.type_initial = swig_type_initial;
    swig_module.cast_initial = swig_cast_initial;
    swig_module.next = &swig_module;
    init = 1;
  } else {
    init = 0;
  }
  
  /* Try and load any already created modules */
  module_head = SWIG_GetModule(clientdata);
  if (!module_head) {
    /* This is the first module loaded for this interpreter */
    /* so set the swig module into the interpreter */
    SWIG_SetModule(clientdata, &swig_module);
  } else {
    /* the interpreter has loaded a SWIG module, but has it loaded this one? */
    iter=module_head;
    do {
      if (iter==&swig_module) {
        /* Our module is already in the list, so there's nothing more to do. */
        return;
      }
      iter=iter->next;
    } while (iter!= module_head);
    
    /* otherwise we must add our module into the list */
    swig_module.next = module_head->next;
    module_head->next = &swig_module;
  }
  
  /* When multiple interpreters are used, a module could have already been initialized in
       a different interpreter, but not yet have a pointer in this interpreter.
       In this case, we do not want to continue adding types... everything should be
       set up already */
  if (init == 0) return;
  
  /* Now work on filling in swig_module.types */
#ifdef SWIGRUNTIME_DEBUG
  printf("SWIG_InitializeModule: size %d\n", swig_module.size);
#endif
  for (i = 0; i < swig_module.size; ++i) {
    swig_type_info *type = 0;
    swig_type_info *ret;
    swig_cast_info *cast;
    
#ifdef SWIGRUNTIME_DEBUG
    printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name);
#endif
    
    /* if there is another module already loaded */
    if (swig_module.next != &swig_module) {
      type = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, swig_module.type_initial[i]->name);
    }
    if (type) {
      /* Overwrite clientdata field */
#ifdef SWIGRUNTIME_DEBUG
      printf("SWIG_InitializeModule: found type %s\n", type->name);
#endif
      if (swig_module.type_initial[i]->clientdata) {
        type->clientdata = swig_module.type_initial[i]->clientdata;
#ifdef SWIGRUNTIME_DEBUG
        printf("SWIG_InitializeModule: found and overwrite type %s \n", type->name);
#endif
      }
    } else {
      type = swig_module.type_initial[i];
    }
    
    /* Insert casting types */
    cast = swig_module.cast_initial[i];
    while (cast->type) {
      /* Don't need to add information already in the list */
      ret = 0;
#ifdef SWIGRUNTIME_DEBUG
      printf("SWIG_InitializeModule: look cast %s\n", cast->type->name);
#endif
      if (swig_module.next != &swig_module) {
        ret = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, cast->type->name);
#ifdef SWIGRUNTIME_DEBUG
        if (ret) printf("SWIG_InitializeModule: found cast %s\n", ret->name);
#endif
      }
      if (ret) {
        if (type == swig_module.type_initial[i]) {
#ifdef SWIGRUNTIME_DEBUG
          printf("SWIG_InitializeModule: skip old type %s\n", ret->name);
#endif
          cast->type = ret;
          ret = 0;
        } else {
          /* Check for casting already in the list */
          swig_cast_info *ocast = SWIG_TypeCheck(ret->name, type);
#ifdef SWIGRUNTIME_DEBUG
          if (ocast) printf("SWIG_InitializeModule: skip old cast %s\n", ret->name);
#endif
          if (!ocast) ret = 0;
        }
      }
      
      if (!ret) {
#ifdef SWIGRUNTIME_DEBUG
        printf("SWIG_InitializeModule: adding cast %s\n", cast->type->name);
#endif
        if (type->cast) {
          type->cast->prev = cast;
          cast->next = type->cast;
        }
        type->cast = cast;
      }
      cast++;
    }
    /* Set entry in modules->types array equal to the type */
    swig_module.types[i] = type;
  }
  swig_module.types[i] = 0;
  
#ifdef SWIGRUNTIME_DEBUG
  printf("**** SWIG_InitializeModule: Cast List ******\n");
  for (i = 0; i < swig_module.size; ++i) {
    int j = 0;
    swig_cast_info *cast = swig_module.cast_initial[i];
    printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name);
    while (cast->type) {
      printf("SWIG_InitializeModule: cast type %s\n", cast->type->name);
      cast++;
      ++j;
    }
    printf("---- Total casts: %d\n",j);
  }
  printf("**** SWIG_InitializeModule: Cast List ******\n");
#endif
}

/* This function will propagate the clientdata field of type to
* any new swig_type_info structures that have been added into the list
* of equivalent types.  It is like calling
* SWIG_TypeClientData(type, clientdata) a second time.
*/
SWIGRUNTIME void
SWIG_PropagateClientData(void) {
  size_t i;
  swig_cast_info *equiv;
  static int init_run = 0;
  
  if (init_run) return;
  init_run = 1;
  
  for (i = 0; i < swig_module.size; i++) {
    if (swig_module.types[i]->clientdata) {
      equiv = swig_module.types[i]->cast;
      while (equiv) {
        if (!equiv->converter) {
          if (equiv->type && !equiv->type->clientdata)
          SWIG_TypeClientData(equiv->type, swig_module.types[i]->clientdata);
        }
        equiv = equiv->next;
      }
    }
  }
}

#ifdef __cplusplus
#if 0
{
  /* c-mode */
#endif
}
#endif



#if defined(__cplusplus) && ! defined(XSPROTO)
extern "C"
#endif

XS(SWIG_init) {
  dXSARGS;
  int i;
  (void)items;
  
  SWIG_InitializeModule(0);
  
  /* Install commands */
  for (i = 0; swig_commands[i].name; i++) {
    /* Casts only needed for Perl < 5.10. */
#ifdef __cplusplus
    newXS(const_cast<char*>(swig_commands[i].name), swig_commands[i].wrapper, const_cast<char*>(__FILE__));
#else
    newXS((char*)swig_commands[i].name, swig_commands[i].wrapper, (char*)__FILE__);
#endif
  }
  
  /* Install variables */
  for (i = 0; swig_variables[i].name; i++) {
    SV *sv;
    sv = get_sv(swig_variables[i].name, TRUE | 0x2 | GV_ADDMULTI);
    if (swig_variables[i].type) {
      SWIG_MakePtr(sv,(void *)1, *swig_variables[i].type,0);
    } else {
      sv_setiv(sv,(IV) 0);
    }
    swig_create_magic(sv, swig_variables[i].name, swig_variables[i].set, swig_variables[i].get); 
  }
  
  /* Install constant */
  for (i = 0; swig_constants[i].type; i++) {
    SV *sv;
    sv = get_sv(swig_constants[i].name, TRUE | 0x2 | GV_ADDMULTI);
    switch(swig_constants[i].type) {
    case SWIG_INT:
      sv_setiv(sv, (IV) swig_constants[i].lvalue);
      break;
    case SWIG_FLOAT:
      sv_setnv(sv, (double) swig_constants[i].dvalue);
      break;
    case SWIG_STRING:
      sv_setpv(sv, (const char *) swig_constants[i].pvalue);
      break;
    case SWIG_POINTER:
      SWIG_MakePtr(sv, swig_constants[i].pvalue, *(swig_constants[i].ptype),0);
      break;
    case SWIG_BINARY:
      SWIG_MakePackedObj(sv, swig_constants[i].pvalue, swig_constants[i].lvalue, *(swig_constants[i].ptype));
      break;
    default:
      break;
    }
    SvREADONLY_on(sv);
  }
  
  SWIG_TypeClientData(SWIGTYPE_p_std__vectorT_long_t, (void*) "mummer::LongVector");
  SWIG_TypeClientData(SWIGTYPE_p_mummer__postnuc__Alignment, (void*) "mummer::Alignment");
  SWIG_TypeClientData(SWIGTYPE_p_std__vectorT_mummer__postnuc__Alignment_t, (void*) "mummer::AlignmentVector");
  SWIG_TypeClientData(SWIGTYPE_p_mummer__nucmer__Options, (void*) "mummer::Options");
  ST(0) = &PL_sv_yes;
  XSRETURN(1);
}

